phylo-1.0.6/0000755000175000017500000000000011434510123007644 500000000000000phylo-1.0.6/INSTALL0000644000175000017500000002243211434510050010617 00000000000000Installation Instructions ************************* Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005 Free Software Foundation, Inc. This file is free documentation; the Free Software Foundation gives unlimited permission to copy, distribute and modify it. Basic Installation ================== These are generic installation instructions. The `configure' shell script attempts to guess correct values for various system-dependent variables used during compilation. It uses those values to create a `Makefile' in each directory of the package. It may also create one or more `.h' files containing system-dependent definitions. 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FILE defaults to `/dev/null' to disable caching. `--config-cache' `-C' Alias for `--cache-file=config.cache'. `--quiet' `--silent' `-q' Do not print messages saying which checks are being made. To suppress all normal output, redirect it to `/dev/null' (any error messages will still be shown). `--srcdir=DIR' Look for the package's source code in directory DIR. Usually `configure' can determine that directory automatically. `configure' also accepts some other, not widely useful, options. Run `configure --help' for more details. phylo-1.0.6/AUTHORS0000644000175000017500000000005011434510050010626 00000000000000Martin Bader martin.bader@uni-ulm.de phylo-1.0.6/NEWS0000644000175000017500000000000011434510050010250 00000000000000phylo-1.0.6/README0000644000175000017500000001702311434510050010446 00000000000000phylo - phylogenetic reconstruction based on the weighted reversal and transposition distance. Installation ============ The standard way to install is to call the following three commands. It will install the program in /usr/local ./configure make make install If you want to install it in some other directory (e.g. because you do not have writing permissions in /usr/local), install with the commands ./configure --prefix=/path/to/install make make install For additional options, see the INSTALL file. If the standard installation should fail, try first to call reconf and then do the standard installation steps ./configure make make install After the installation, you will find the executable programs phylo, SwRT, revDist, and median under /bin. The main program phylo depends on the libraries minswrt, revDist, and median, weightedbb, and these libraries have all their own tiny frontend. phylo ===== phylo contains of two parts: 1. the program itself, which is compiled into a library. 2. a tiny frontend that calls the library. The frontend: Call the program with the following parameters. phylo [OPTIONS] available options: -h Just print some help information (ignore all other options) -w wr wt Set weights to wr (for reversals) and wt (for transpositions). If you use reversal only distance, call -w wr inf. (default: -w 1 inf). Note that the weights must be integer. -v x Set the output (verbosity) level to x. -v 0 produces the most output, while -v 3 only reports serious errors. (default: -v 1) -t If this parameter is set, the input file is a tree instead of a set of permutations, so only the improvement steps will be performed. -f name Load the file with the given name. This option is required. -s x If this parameter is set, the tree is only created from starting node x. -i [n|t|m|tm] Set he improvement technique to use. t means topology improvement, m means median improvement, tm means first using t then m, n means no improvement. (default: -i tm) -o name If this parameter is set, the best found tree will be written to a file with the given name. The input file consists of the specifications of several genomes (as signed permutations). Each genome consists of a line > genome name and a line containing a signed permutation. Lines beginning with # are comments. As an example, you can call phylo -w 1 2 -f ../share/phylo/campanulaceae The library: The functions provided by the library are documented in minswrt.h in the include directory. As example of how to use the library, you can have a look at minswrt/start.cpp. The interesting part is in the main function. minswrt ======= minswrt (minimal sorting by weighted reversals and transpositions) contains of two parts: 1. the program itself, which is compiled into a library. 2. a tiny frontend that calls the library. The frontend: Call the program with the following parameters: ./minswrt file wr wt - file is the file containing the permutation. The file consists of a line containing the number of elements in the permutation. The next two lines contain the source and the target permutation. An example can be found in share/minswrt/test.in - wr is the weight of reversals - wt is the weight of transpositions and inverted transpositions The library: The functions provided by the library are documented in minswrt.h in the include directory. As example of how to use the library, you can have a look at minswrt/start.cpp. The interesting part is in the main function. weightedbb ========== wightedbb is an exact branch and bound algorithm to calculate the weighted reversal and transposition distance between two genomes. It contains of two parts: 1. the program itself, which is compiled into a library. 2. a tiny frontend that calls the library. The frontend: Call the program with the following parameters: ./weightedbb file wr wt distmode - file is the file containing the permutation. The file consists of a line containing the number of elements in the permutation. The next two lines contain the source and the target permutation. An example can be found in share/weightedbb/test.in - wr is the weight of reversals - wt is the weight of transpositions and inverted transpositions - distmode determines the distance measure. 0 means transposition distance, and 1 means weighted reversal and transposition distance The library: The functions provided by the library are documented in weightedbb.h in the include directory. As example of how to use the library, you can have a look at weightedbb/start.cpp. The interesting part is in the main function. revDist ======= revDist is a small program to calculate the reversal distance between two cyclic signed permutations. It contains of two parts: 1. the program itself, which is compiled into a library. 2. a tiny frontend that calls the library. The frontend: Call the program with revDist infile where infile contains a line containing the permutation size, followed by two lines with the signed permutations. Lines beginning with # are comments. As an example, see the file revDist/test.in The library: The functions provided by the library are documented in revDist.h in the include directory. As example of how to use the library, you can have a look at share/revDist/start.cpp. The interesting part is in the main function. median ====== median is an extension of Caprara's median solver that can calculate a median of three cyclic signed permutations either under the reversal distance or under the weighte reversal and transposition distance. It contains of two parts: 1. the program itself, which is compiled into a library. 2. a tiny frontend that calls the library. The frontend: Call the program with median infile wr wt distMode exact all where infile contains the three genomes (signed permutations). Each genome consists of a line > genome name and a line containing the signed permuation. wr and wt are the weights for reversals and transpositions. Both must be integer. distMode defines the used distance measure, where 0 is the reversal distance, 1 is the transposition distance, and 2 is the weighted reversal and transposition distance. If exact is set to 1, the pairwise distances will be calculated by an exact branch and bound algorithm (this will guarantee the medians to be true medians, not only approximations), otherwise a faster approximation algorithm is used. If all is set to 1, all medians will be returned, otherwise only one median will be returned. As the algorithm is a branch and bound algorithm that works on a heap, the algorithm will prune the heap when it runs out of memory. Note that there is a risk that an optimal solution gets lost. In this case, a warning message will be displayed. As example, you can call median ../share/median/test.in 1 2 2 0 0 In the momentary form, the program calculates just one median. If one is interested in all medians, this can easily be achieved by editing the main function in median/start.cpp (for details, see there). The library: The functions provided by the library are documented in median.h in the include directory. As example of how to use the library, you can have a look at median/start.cpp. The interesting part is in the main function. Copyright: ========== Copyright (C) 2007-2010 Martin Bader This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions. 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" >&6; } if test "${lt_cv_prog_gnu_ld+set}" = set; then : $as_echo_n "(cached) " >&6 else # I'd rather use --version here, but apparently some GNU lds only accept -v. case `$LD -v 2>&1 &5 $as_echo "$lt_cv_prog_gnu_ld" >&6; } with_gnu_ld=$lt_cv_prog_gnu_ld { $as_echo "$as_me:${as_lineno-$LINENO}: checking for BSD- or MS-compatible name lister (nm)" >&5 $as_echo_n "checking for BSD- or MS-compatible name lister (nm)... 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" >&6; } if test "${ac_cv_prog_DUMPBIN+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$DUMPBIN"; then ac_cv_prog_DUMPBIN="$DUMPBIN" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_DUMPBIN="$ac_tool_prefix$ac_prog" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi DUMPBIN=$ac_cv_prog_DUMPBIN if test -n "$DUMPBIN"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DUMPBIN" >&5 $as_echo "$DUMPBIN" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi test -n "$DUMPBIN" && break done fi if test -z "$DUMPBIN"; then ac_ct_DUMPBIN=$DUMPBIN for ac_prog in "dumpbin -symbols" "link -dump -symbols" do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... 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" >&6; } if test "${lt_cv_nm_interface+set}" = set; then : $as_echo_n "(cached) " >&6 else lt_cv_nm_interface="BSD nm" echo "int some_variable = 0;" > conftest.$ac_ext (eval echo "\"\$as_me:4501: $ac_compile\"" >&5) (eval "$ac_compile" 2>conftest.err) cat conftest.err >&5 (eval echo "\"\$as_me:4504: $NM \\\"conftest.$ac_objext\\\"\"" >&5) (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out) cat conftest.err >&5 (eval echo "\"\$as_me:4507: output\"" >&5) cat conftest.out >&5 if $GREP 'External.*some_variable' conftest.out > /dev/null; then lt_cv_nm_interface="MS dumpbin" fi rm -f conftest* fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_nm_interface" >&5 $as_echo "$lt_cv_nm_interface" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ln -s works" >&5 $as_echo_n "checking whether ln -s works... 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Even if it were fixed, the result of this # check would be larger than it should be. lt_cv_sys_max_cmd_len=12288; # 12K is about right ;; gnu*) # Under GNU Hurd, this test is not required because there is # no limit to the length of command line arguments. # Libtool will interpret -1 as no limit whatsoever lt_cv_sys_max_cmd_len=-1; ;; cygwin* | mingw* | cegcc*) # On Win9x/ME, this test blows up -- it succeeds, but takes # about 5 minutes as the teststring grows exponentially. # Worse, since 9x/ME are not pre-emptively multitasking, # you end up with a "frozen" computer, even though with patience # the test eventually succeeds (with a max line length of 256k). # Instead, let's just punt: use the minimum linelength reported by # all of the supported platforms: 8192 (on NT/2K/XP). lt_cv_sys_max_cmd_len=8192; ;; amigaos*) # On AmigaOS with pdksh, this test takes hours, literally. # So we just punt and use a minimum line length of 8192. lt_cv_sys_max_cmd_len=8192; ;; netbsd* | freebsd* | openbsd* | darwin* | dragonfly*) # This has been around since 386BSD, at least. Likely further. if test -x /sbin/sysctl; then lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax` elif test -x /usr/sbin/sysctl; then lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax` else lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs fi # And add a safety zone lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` ;; interix*) # We know the value 262144 and hardcode it with a safety zone (like BSD) lt_cv_sys_max_cmd_len=196608 ;; osf*) # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not # nice to cause kernel panics so lets avoid the loop below. # First set a reasonable default. lt_cv_sys_max_cmd_len=16384 # if test -x /sbin/sysconfig; then case `/sbin/sysconfig -q proc exec_disable_arg_limit` in *1*) lt_cv_sys_max_cmd_len=-1 ;; esac fi ;; sco3.2v5*) lt_cv_sys_max_cmd_len=102400 ;; sysv5* | sco5v6* | sysv4.2uw2*) kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null` if test -n "$kargmax"; then lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[ ]//'` else lt_cv_sys_max_cmd_len=32768 fi ;; *) lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null` if test -n "$lt_cv_sys_max_cmd_len"; then lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` else # Make teststring a little bigger before we do anything with it. # a 1K string should be a reasonable start. for i in 1 2 3 4 5 6 7 8 ; do teststring=$teststring$teststring done SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}} # If test is not a shell built-in, we'll probably end up computing a # maximum length that is only half of the actual maximum length, but # we can't tell. while { test "X"`$SHELL $0 --fallback-echo "X$teststring$teststring" 2>/dev/null` \ = "XX$teststring$teststring"; } >/dev/null 2>&1 && test $i != 17 # 1/2 MB should be enough do i=`expr $i + 1` teststring=$teststring$teststring done # Only check the string length outside the loop. lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1` teststring= # Add a significant safety factor because C++ compilers can tack on # massive amounts of additional arguments before passing them to the # linker. It appears as though 1/2 is a usable value. lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2` fi ;; esac fi if test -n $lt_cv_sys_max_cmd_len ; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_sys_max_cmd_len" >&5 $as_echo "$lt_cv_sys_max_cmd_len" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: none" >&5 $as_echo "none" >&6; } fi max_cmd_len=$lt_cv_sys_max_cmd_len : ${CP="cp -f"} : ${MV="mv -f"} : ${RM="rm -f"} { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the shell understands some XSI constructs" >&5 $as_echo_n "checking whether the shell understands some XSI constructs... 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" >&6; } if test "${ac_cv_prog_ac_ct_OBJDUMP+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OBJDUMP"; then ac_cv_prog_ac_ct_OBJDUMP="$ac_ct_OBJDUMP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_OBJDUMP="objdump" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OBJDUMP=$ac_cv_prog_ac_ct_OBJDUMP if test -n "$ac_ct_OBJDUMP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OBJDUMP" >&5 $as_echo "$ac_ct_OBJDUMP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OBJDUMP" = x; then OBJDUMP="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OBJDUMP=$ac_ct_OBJDUMP fi else OBJDUMP="$ac_cv_prog_OBJDUMP" fi test -z "$OBJDUMP" && OBJDUMP=objdump { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to recognize dependent libraries" >&5 $as_echo_n "checking how to recognize dependent libraries... " >&6; } if test "${lt_cv_deplibs_check_method+set}" = set; then : $as_echo_n "(cached) " >&6 else lt_cv_file_magic_cmd='$MAGIC_CMD' lt_cv_file_magic_test_file= lt_cv_deplibs_check_method='unknown' # Need to set the preceding variable on all platforms that support # interlibrary dependencies. # 'none' -- dependencies not supported. # `unknown' -- same as none, but documents that we really don't know. # 'pass_all' -- all dependencies passed with no checks. # 'test_compile' -- check by making test program. # 'file_magic [[regex]]' -- check by looking for files in library path # which responds to the $file_magic_cmd with a given extended regex. # If you have `file' or equivalent on your system and you're not sure # whether `pass_all' will *always* work, you probably want this one. case $host_os in aix[4-9]*) lt_cv_deplibs_check_method=pass_all ;; beos*) lt_cv_deplibs_check_method=pass_all ;; bsdi[45]*) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib)' lt_cv_file_magic_cmd='/usr/bin/file -L' lt_cv_file_magic_test_file=/shlib/libc.so ;; cygwin*) # func_win32_libid is a shell function defined in ltmain.sh lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd='func_win32_libid' ;; mingw* | pw32*) # Base MSYS/MinGW do not provide the 'file' command needed by # func_win32_libid shell function, so use a weaker test based on 'objdump', # unless we find 'file', for example because we are cross-compiling. if ( file / ) >/dev/null 2>&1; then lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd='func_win32_libid' else lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?' lt_cv_file_magic_cmd='$OBJDUMP -f' fi ;; cegcc) # use the weaker test based on 'objdump'. See mingw*. lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?' lt_cv_file_magic_cmd='$OBJDUMP -f' ;; darwin* | rhapsody*) lt_cv_deplibs_check_method=pass_all ;; freebsd* | dragonfly*) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then case $host_cpu in i*86 ) # Not sure whether the presence of OpenBSD here was a mistake. # Let's accept both of them until this is cleared up. lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[3-9]86 (compact )?demand paged shared library' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*` ;; esac else lt_cv_deplibs_check_method=pass_all fi ;; gnu*) lt_cv_deplibs_check_method=pass_all ;; hpux10.20* | hpux11*) lt_cv_file_magic_cmd=/usr/bin/file case $host_cpu in ia64*) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - IA64' lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so ;; hppa*64*) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]' lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl ;; *) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|PA-RISC[0-9].[0-9]) shared library' lt_cv_file_magic_test_file=/usr/lib/libc.sl ;; esac ;; interix[3-9]*) # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|\.a)$' ;; irix5* | irix6* | nonstopux*) case $LD in *-32|*"-32 ") libmagic=32-bit;; *-n32|*"-n32 ") libmagic=N32;; *-64|*"-64 ") libmagic=64-bit;; *) libmagic=never-match;; esac lt_cv_deplibs_check_method=pass_all ;; # This must be Linux ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) lt_cv_deplibs_check_method=pass_all ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|_pic\.a)$' fi ;; newos6*) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (executable|dynamic lib)' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=/usr/lib/libnls.so ;; *nto* | *qnx*) lt_cv_deplibs_check_method=pass_all ;; openbsd*) if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|\.so|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' fi ;; osf3* | osf4* | osf5*) lt_cv_deplibs_check_method=pass_all ;; rdos*) lt_cv_deplibs_check_method=pass_all ;; solaris*) lt_cv_deplibs_check_method=pass_all ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) lt_cv_deplibs_check_method=pass_all ;; sysv4 | sysv4.3*) case $host_vendor in motorola) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib) M[0-9][0-9]* Version [0-9]' lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*` ;; ncr) lt_cv_deplibs_check_method=pass_all ;; sequent) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )' ;; sni) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method="file_magic ELF [0-9][0-9]*-bit [LM]SB dynamic lib" lt_cv_file_magic_test_file=/lib/libc.so ;; siemens) lt_cv_deplibs_check_method=pass_all ;; pc) lt_cv_deplibs_check_method=pass_all ;; esac ;; tpf*) lt_cv_deplibs_check_method=pass_all ;; esac fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_deplibs_check_method" >&5 $as_echo "$lt_cv_deplibs_check_method" >&6; } file_magic_cmd=$lt_cv_file_magic_cmd deplibs_check_method=$lt_cv_deplibs_check_method test -z "$deplibs_check_method" && deplibs_check_method=unknown if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}ar", so it can be a program name with args. set dummy ${ac_tool_prefix}ar; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_AR+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$AR"; then ac_cv_prog_AR="$AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_AR="${ac_tool_prefix}ar" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi AR=$ac_cv_prog_AR if test -n "$AR"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AR" >&5 $as_echo "$AR" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_AR"; then ac_ct_AR=$AR # Extract the first word of "ar", so it can be a program name with args. set dummy ar; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_AR+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_AR"; then ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_AR="ar" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_AR=$ac_cv_prog_ac_ct_AR if test -n "$ac_ct_AR"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_AR" >&5 $as_echo "$ac_ct_AR" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_AR" = x; then AR="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac AR=$ac_ct_AR fi else AR="$ac_cv_prog_AR" fi test -z "$AR" && AR=ar test -z "$AR_FLAGS" && AR_FLAGS=cru if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. set dummy ${ac_tool_prefix}strip; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_STRIP+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$STRIP"; then ac_cv_prog_STRIP="$STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_STRIP="${ac_tool_prefix}strip" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi STRIP=$ac_cv_prog_STRIP if test -n "$STRIP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5 $as_echo "$STRIP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_STRIP"; then ac_ct_STRIP=$STRIP # Extract the first word of "strip", so it can be a program name with args. set dummy strip; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_STRIP"; then ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_STRIP="strip" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP if test -n "$ac_ct_STRIP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5 $as_echo "$ac_ct_STRIP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_STRIP" = x; then STRIP=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac STRIP=$ac_ct_STRIP fi else STRIP="$ac_cv_prog_STRIP" fi test -z "$STRIP" && STRIP=: if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. set dummy ${ac_tool_prefix}ranlib; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_RANLIB+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$RANLIB"; then ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi RANLIB=$ac_cv_prog_RANLIB if test -n "$RANLIB"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $RANLIB" >&5 $as_echo "$RANLIB" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_RANLIB"; then ac_ct_RANLIB=$RANLIB # Extract the first word of "ranlib", so it can be a program name with args. set dummy ranlib; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_RANLIB"; then ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_RANLIB="ranlib" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB if test -n "$ac_ct_RANLIB"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_RANLIB" >&5 $as_echo "$ac_ct_RANLIB" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_RANLIB" = x; then RANLIB=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac RANLIB=$ac_ct_RANLIB fi else RANLIB="$ac_cv_prog_RANLIB" fi test -z "$RANLIB" && RANLIB=: # Determine commands to create old-style static archives. old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs' old_postinstall_cmds='chmod 644 $oldlib' old_postuninstall_cmds= if test -n "$RANLIB"; then case $host_os in openbsd*) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib" ;; *) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib" ;; esac old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib" fi # If no C compiler was specified, use CC. LTCC=${LTCC-"$CC"} # If no C compiler flags were specified, use CFLAGS. LTCFLAGS=${LTCFLAGS-"$CFLAGS"} # Allow CC to be a program name with arguments. compiler=$CC # Check for command to grab the raw symbol name followed by C symbol from nm. { $as_echo "$as_me:${as_lineno-$LINENO}: checking command to parse $NM output from $compiler object" >&5 $as_echo_n "checking command to parse $NM output from $compiler object... " >&6; } if test "${lt_cv_sys_global_symbol_pipe+set}" = set; then : $as_echo_n "(cached) " >&6 else # These are sane defaults that work on at least a few old systems. # [They come from Ultrix. What could be older than Ultrix?!! ;)] # Character class describing NM global symbol codes. symcode='[BCDEGRST]' # Regexp to match symbols that can be accessed directly from C. sympat='\([_A-Za-z][_A-Za-z0-9]*\)' # Define system-specific variables. case $host_os in aix*) symcode='[BCDT]' ;; cygwin* | mingw* | pw32* | cegcc*) symcode='[ABCDGISTW]' ;; hpux*) if test "$host_cpu" = ia64; then symcode='[ABCDEGRST]' fi ;; irix* | nonstopux*) symcode='[BCDEGRST]' ;; osf*) symcode='[BCDEGQRST]' ;; solaris*) symcode='[BDRT]' ;; sco3.2v5*) symcode='[DT]' ;; sysv4.2uw2*) symcode='[DT]' ;; sysv5* | sco5v6* | unixware* | OpenUNIX*) symcode='[ABDT]' ;; sysv4) symcode='[DFNSTU]' ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[ABCDGIRSTW]' ;; esac # Transform an extracted symbol line into a proper C declaration. # Some systems (esp. on ia64) link data and code symbols differently, # so use this general approach. lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" # Transform an extracted symbol line into symbol name and symbol address lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (void *) \&\2},/p'" lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \(lib[^ ]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"lib\2\", (void *) \&\2},/p'" # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # Try without a prefix underscore, then with it. for ac_symprfx in "" "_"; do # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. symxfrm="\\1 $ac_symprfx\\2 \\2" # Write the raw and C identifiers. if test "$lt_cv_nm_interface" = "MS dumpbin"; then # Fake it for dumpbin and say T for any non-static function # and D for any global variable. # Also find C++ and __fastcall symbols from MSVC++, # which start with @ or ?. lt_cv_sys_global_symbol_pipe="$AWK '"\ " {last_section=section; section=\$ 3};"\ " /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ " \$ 0!~/External *\|/{next};"\ " / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ " {if(hide[section]) next};"\ " {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ " {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ " s[1]~/^[@?]/{print s[1], s[1]; next};"\ " s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ " ' prfx=^$ac_symprfx" else lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ ]\($symcode$symcode*\)[ ][ ]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" fi # Check to see that the pipe works correctly. pipe_works=no rm -f conftest* cat > conftest.$ac_ext <<_LT_EOF #ifdef __cplusplus extern "C" { #endif char nm_test_var; void nm_test_func(void); void nm_test_func(void){} #ifdef __cplusplus } #endif int main(){nm_test_var='a';nm_test_func();return(0);} _LT_EOF if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then # Now try to grab the symbols. nlist=conftest.nm if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist\""; } >&5 (eval $NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && test -s "$nlist"; then # Try sorting and uniquifying the output. if sort "$nlist" | uniq > "$nlist"T; then mv -f "$nlist"T "$nlist" else rm -f "$nlist"T fi # Make sure that we snagged all the symbols we need. if $GREP ' nm_test_var$' "$nlist" >/dev/null; then if $GREP ' nm_test_func$' "$nlist" >/dev/null; then cat <<_LT_EOF > conftest.$ac_ext #ifdef __cplusplus extern "C" { #endif _LT_EOF # Now generate the symbol file. eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' cat <<_LT_EOF >> conftest.$ac_ext /* The mapping between symbol names and symbols. */ const struct { const char *name; void *address; } lt__PROGRAM__LTX_preloaded_symbols[] = { { "@PROGRAM@", (void *) 0 }, _LT_EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext cat <<\_LT_EOF >> conftest.$ac_ext {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt__PROGRAM__LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif _LT_EOF # Now try linking the two files. mv conftest.$ac_objext conftstm.$ac_objext lt_save_LIBS="$LIBS" lt_save_CFLAGS="$CFLAGS" LIBS="conftstm.$ac_objext" CFLAGS="$CFLAGS$lt_prog_compiler_no_builtin_flag" if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5 (eval $ac_link) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && test -s conftest${ac_exeext}; then pipe_works=yes fi LIBS="$lt_save_LIBS" CFLAGS="$lt_save_CFLAGS" else echo "cannot find nm_test_func in $nlist" >&5 fi else echo "cannot find nm_test_var in $nlist" >&5 fi else echo "cannot run $lt_cv_sys_global_symbol_pipe" >&5 fi else echo "$progname: failed program was:" >&5 cat conftest.$ac_ext >&5 fi rm -rf conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$pipe_works" = yes; then break else lt_cv_sys_global_symbol_pipe= fi done fi if test -z "$lt_cv_sys_global_symbol_pipe"; then lt_cv_sys_global_symbol_to_cdecl= fi if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: failed" >&5 $as_echo "failed" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: ok" >&5 $as_echo "ok" >&6; } fi # Check whether --enable-libtool-lock was given. if test "${enable_libtool_lock+set}" = set; then : enableval=$enable_libtool_lock; fi test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes # Some flags need to be propagated to the compiler or linker for good # libtool support. case $host in ia64-*-hpux*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.$ac_objext` in *ELF-32*) HPUX_IA64_MODE="32" ;; *ELF-64*) HPUX_IA64_MODE="64" ;; esac fi rm -rf conftest* ;; *-*-irix6*) # Find out which ABI we are using. echo '#line 5713 "configure"' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then if test "$lt_cv_prog_gnu_ld" = yes; then case `/usr/bin/file conftest.$ac_objext` in *32-bit*) LD="${LD-ld} -melf32bsmip" ;; *N32*) LD="${LD-ld} -melf32bmipn32" ;; *64-bit*) LD="${LD-ld} -melf64bmip" ;; esac else case `/usr/bin/file conftest.$ac_objext` in *32-bit*) LD="${LD-ld} -32" ;; *N32*) LD="${LD-ld} -n32" ;; *64-bit*) LD="${LD-ld} -64" ;; esac fi fi rm -rf conftest* ;; x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \ s390*-*linux*|s390*-*tpf*|sparc*-*linux*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.o` in *32-bit*) case $host in x86_64-*kfreebsd*-gnu) LD="${LD-ld} -m elf_i386_fbsd" ;; x86_64-*linux*) LD="${LD-ld} -m elf_i386" ;; ppc64-*linux*|powerpc64-*linux*) LD="${LD-ld} -m elf32ppclinux" ;; s390x-*linux*) LD="${LD-ld} -m elf_s390" ;; sparc64-*linux*) LD="${LD-ld} -m elf32_sparc" ;; esac ;; *64-bit*) case $host in x86_64-*kfreebsd*-gnu) LD="${LD-ld} -m elf_x86_64_fbsd" ;; x86_64-*linux*) LD="${LD-ld} -m elf_x86_64" ;; ppc*-*linux*|powerpc*-*linux*) LD="${LD-ld} -m elf64ppc" ;; s390*-*linux*|s390*-*tpf*) LD="${LD-ld} -m elf64_s390" ;; sparc*-*linux*) LD="${LD-ld} -m elf64_sparc" ;; esac ;; esac fi rm -rf conftest* ;; *-*-sco3.2v5*) # On SCO OpenServer 5, we need -belf to get full-featured binaries. SAVE_CFLAGS="$CFLAGS" CFLAGS="$CFLAGS -belf" { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler needs -belf" >&5 $as_echo_n "checking whether the C compiler needs -belf... " >&6; } if test "${lt_cv_cc_needs_belf+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_cv_cc_needs_belf=yes else lt_cv_cc_needs_belf=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_cc_needs_belf" >&5 $as_echo "$lt_cv_cc_needs_belf" >&6; } if test x"$lt_cv_cc_needs_belf" != x"yes"; then # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf CFLAGS="$SAVE_CFLAGS" fi ;; sparc*-*solaris*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.o` in *64-bit*) case $lt_cv_prog_gnu_ld in yes*) LD="${LD-ld} -m elf64_sparc" ;; *) if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then LD="${LD-ld} -64" fi ;; esac ;; esac fi rm -rf conftest* ;; esac need_locks="$enable_libtool_lock" case $host_os in rhapsody* | darwin*) if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}dsymutil", so it can be a program name with args. set dummy ${ac_tool_prefix}dsymutil; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_DSYMUTIL+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$DSYMUTIL"; then ac_cv_prog_DSYMUTIL="$DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_DSYMUTIL="${ac_tool_prefix}dsymutil" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi DSYMUTIL=$ac_cv_prog_DSYMUTIL if test -n "$DSYMUTIL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DSYMUTIL" >&5 $as_echo "$DSYMUTIL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_DSYMUTIL"; then ac_ct_DSYMUTIL=$DSYMUTIL # Extract the first word of "dsymutil", so it can be a program name with args. set dummy dsymutil; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_DSYMUTIL+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_DSYMUTIL"; then ac_cv_prog_ac_ct_DSYMUTIL="$ac_ct_DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_DSYMUTIL="dsymutil" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_DSYMUTIL=$ac_cv_prog_ac_ct_DSYMUTIL if test -n "$ac_ct_DSYMUTIL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DSYMUTIL" >&5 $as_echo "$ac_ct_DSYMUTIL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_DSYMUTIL" = x; then DSYMUTIL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac DSYMUTIL=$ac_ct_DSYMUTIL fi else DSYMUTIL="$ac_cv_prog_DSYMUTIL" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}nmedit", so it can be a program name with args. set dummy ${ac_tool_prefix}nmedit; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_NMEDIT+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$NMEDIT"; then ac_cv_prog_NMEDIT="$NMEDIT" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_NMEDIT="${ac_tool_prefix}nmedit" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi NMEDIT=$ac_cv_prog_NMEDIT if test -n "$NMEDIT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $NMEDIT" >&5 $as_echo "$NMEDIT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_NMEDIT"; then ac_ct_NMEDIT=$NMEDIT # Extract the first word of "nmedit", so it can be a program name with args. set dummy nmedit; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_NMEDIT+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_NMEDIT"; then ac_cv_prog_ac_ct_NMEDIT="$ac_ct_NMEDIT" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_NMEDIT="nmedit" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_NMEDIT=$ac_cv_prog_ac_ct_NMEDIT if test -n "$ac_ct_NMEDIT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_NMEDIT" >&5 $as_echo "$ac_ct_NMEDIT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_NMEDIT" = x; then NMEDIT=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac NMEDIT=$ac_ct_NMEDIT fi else NMEDIT="$ac_cv_prog_NMEDIT" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}lipo", so it can be a program name with args. set dummy ${ac_tool_prefix}lipo; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_LIPO+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$LIPO"; then ac_cv_prog_LIPO="$LIPO" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_LIPO="${ac_tool_prefix}lipo" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi LIPO=$ac_cv_prog_LIPO if test -n "$LIPO"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LIPO" >&5 $as_echo "$LIPO" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_LIPO"; then ac_ct_LIPO=$LIPO # Extract the first word of "lipo", so it can be a program name with args. set dummy lipo; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_LIPO+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_LIPO"; then ac_cv_prog_ac_ct_LIPO="$ac_ct_LIPO" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_LIPO="lipo" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_LIPO=$ac_cv_prog_ac_ct_LIPO if test -n "$ac_ct_LIPO"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_LIPO" >&5 $as_echo "$ac_ct_LIPO" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_LIPO" = x; then LIPO=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac LIPO=$ac_ct_LIPO fi else LIPO="$ac_cv_prog_LIPO" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}otool", so it can be a program name with args. set dummy ${ac_tool_prefix}otool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_OTOOL+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$OTOOL"; then ac_cv_prog_OTOOL="$OTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_OTOOL="${ac_tool_prefix}otool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OTOOL=$ac_cv_prog_OTOOL if test -n "$OTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL" >&5 $as_echo "$OTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OTOOL"; then ac_ct_OTOOL=$OTOOL # Extract the first word of "otool", so it can be a program name with args. set dummy otool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... 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" >&6; } if test "${lt_cv_apple_cc_single_mod+set}" = set; then : $as_echo_n "(cached) " >&6 else lt_cv_apple_cc_single_mod=no if test -z "${LT_MULTI_MODULE}"; then # By default we will add the -single_module flag. You can override # by either setting the environment variable LT_MULTI_MODULE # non-empty at configure time, or by adding -multi_module to the # link flags. rm -rf libconftest.dylib* echo "int foo(void){return 1;}" > conftest.c echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ -dynamiclib -Wl,-single_module conftest.c" >&5 $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ -dynamiclib -Wl,-single_module conftest.c 2>conftest.err _lt_result=$? if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then lt_cv_apple_cc_single_mod=yes else cat conftest.err >&5 fi rm -rf libconftest.dylib* rm -f conftest.* fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_apple_cc_single_mod" >&5 $as_echo "$lt_cv_apple_cc_single_mod" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -exported_symbols_list linker flag" >&5 $as_echo_n "checking for -exported_symbols_list linker flag... 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Now check whether nonexistent headers # can be detected and how. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include _ACEOF if ac_fn_c_try_cpp "$LINENO"; then : # Broken: success on invalid input. continue else # Passes both tests. ac_preproc_ok=: break fi rm -f conftest.err conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. rm -f conftest.err conftest.$ac_ext if $ac_preproc_ok; then : break fi done ac_cv_prog_CPP=$CPP fi CPP=$ac_cv_prog_CPP else ac_cv_prog_CPP=$CPP fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPP" >&5 $as_echo "$CPP" >&6; } ac_preproc_ok=false for ac_c_preproc_warn_flag in '' yes do # Use a header file that comes with gcc, so configuring glibc # with a fresh cross-compiler works. # Prefer to if __STDC__ is defined, since # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #ifdef __STDC__ # include #else # include #endif Syntax error _ACEOF if ac_fn_c_try_cpp "$LINENO"; then : else # Broken: fails on valid input. continue fi rm -f conftest.err conftest.$ac_ext # OK, works on sane cases. 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"$LINENO" 5; } fi ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5 $as_echo_n "checking for ANSI C header files... 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((c) | 0x40) : (c)) #endif #define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) int main () { int i; for (i = 0; i < 256; i++) if (XOR (islower (i), ISLOWER (i)) || toupper (i) != TOUPPER (i)) return 2; return 0; } _ACEOF if ac_fn_c_try_run "$LINENO"; then : else ac_cv_header_stdc=no fi rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ conftest.$ac_objext conftest.beam conftest.$ac_ext fi fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5 $as_echo "$ac_cv_header_stdc" >&6; } if test $ac_cv_header_stdc = yes; then $as_echo "#define STDC_HEADERS 1" >>confdefs.h fi # On IRIX 5.3, sys/types and inttypes.h are conflicting. for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ inttypes.h stdint.h unistd.h do : as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default " eval as_val=\$$as_ac_Header if test "x$as_val" = x""yes; then : cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF fi done for ac_header in dlfcn.h do : ac_fn_c_check_header_compile "$LINENO" "dlfcn.h" "ac_cv_header_dlfcn_h" "$ac_includes_default " if test "x$ac_cv_header_dlfcn_h" = x""yes; then : cat >>confdefs.h <<_ACEOF #define HAVE_DLFCN_H 1 _ACEOF fi done # Set options enable_dlopen=no enable_win32_dll=no # Check whether --enable-shared was given. if test "${enable_shared+set}" = set; then : enableval=$enable_shared; p=${PACKAGE-default} case $enableval in yes) enable_shared=yes ;; no) enable_shared=no ;; *) enable_shared=no # Look at the argument we got. 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The following line is correct: shared_flag='-G' else if test "$aix_use_runtimelinking" = yes; then shared_flag='${wl}-G' else shared_flag='${wl}-bM:SRE' fi fi fi export_dynamic_flag_spec='${wl}-bexpall' # It seems that -bexpall does not export symbols beginning with # underscore (_), so it is better to generate a list of symbols to export. always_export_symbols=yes if test "$aix_use_runtimelinking" = yes; then # Warning - without using the other runtime loading flags (-brtl), # -berok will link without error, but may produce a broken library. allow_undefined_flag='-berok' # Determine the default libpath from the value encoded in an # empty executable. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_aix_libpath_sed=' /Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/ p } }' aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` # Check for a 64-bit object if we didn't find anything. if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath" archive_expsym_cmds='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag" else if test "$host_cpu" = ia64; then hardcode_libdir_flag_spec='${wl}-R $libdir:/usr/lib:/lib' allow_undefined_flag="-z nodefs" archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols" else # Determine the default libpath from the value encoded in an # empty executable. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_aix_libpath_sed=' /Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/ p } }' aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` # Check for a 64-bit object if we didn't find anything. if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath" # Warning - without using the other run time loading flags, # -berok will link without error, but may produce a broken library. no_undefined_flag=' ${wl}-bernotok' allow_undefined_flag=' ${wl}-berok' # Exported symbols can be pulled into shared objects from archives whole_archive_flag_spec='$convenience' archive_cmds_need_lc=yes # This is similar to how AIX traditionally builds its shared libraries. archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' fi fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='' ;; m68k) archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes ;; esac ;; bsdi[45]*) export_dynamic_flag_spec=-rdynamic ;; cygwin* | mingw* | pw32* | cegcc*) # When not using gcc, we currently assume that we are using # Microsoft Visual C++. # hardcode_libdir_flag_spec is actually meaningless, as there is # no search path for DLLs. hardcode_libdir_flag_spec=' ' allow_undefined_flag=unsupported # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. archive_cmds='$CC -o $lib $libobjs $compiler_flags `$ECHO "X$deplibs" | $Xsed -e '\''s/ -lc$//'\''` -link -dll~linknames=' # The linker will automatically build a .lib file if we build a DLL. old_archive_from_new_cmds='true' # FIXME: Should let the user specify the lib program. old_archive_cmds='lib -OUT:$oldlib$oldobjs$old_deplibs' fix_srcfile_path='`cygpath -w "$srcfile"`' enable_shared_with_static_runtimes=yes ;; darwin* | rhapsody*) archive_cmds_need_lc=no hardcode_direct=no hardcode_automatic=yes hardcode_shlibpath_var=unsupported whole_archive_flag_spec='' link_all_deplibs=yes allow_undefined_flag="$_lt_dar_allow_undefined" case $cc_basename in ifort*) _lt_dar_can_shared=yes ;; *) _lt_dar_can_shared=$GCC ;; esac if test "$_lt_dar_can_shared" = "yes"; then output_verbose_link_cmd=echo archive_cmds="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}" module_cmds="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}" archive_expsym_cmds="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}" module_expsym_cmds="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}" else ld_shlibs=no fi ;; dgux*) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec='-L$libdir' hardcode_shlibpath_var=no ;; freebsd1*) ld_shlibs=no ;; # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor # support. Future versions do this automatically, but an explicit c++rt0.o # does not break anything, and helps significantly (at the cost of a little # extra space). freebsd2.2*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o' hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; # Unfortunately, older versions of FreeBSD 2 do not have this feature. freebsd2*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes hardcode_minus_L=yes hardcode_shlibpath_var=no ;; # FreeBSD 3 and greater uses gcc -shared to do shared libraries. freebsd* | dragonfly*) archive_cmds='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; hpux9*) if test "$GCC" = yes; then archive_cmds='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' else archive_cmds='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' fi hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: hardcode_direct=yes # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes export_dynamic_flag_spec='${wl}-E' ;; hpux10*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_flag_spec_ld='+b $libdir' hardcode_libdir_separator=: hardcode_direct=yes hardcode_direct_absolute=yes export_dynamic_flag_spec='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes fi ;; hpux11*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then case $host_cpu in hppa*64*) archive_cmds='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac else case $host_cpu in hppa*64*) archive_cmds='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: case $host_cpu in hppa*64*|ia64*) hardcode_direct=no hardcode_shlibpath_var=no ;; *) hardcode_direct=yes hardcode_direct_absolute=yes export_dynamic_flag_spec='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes ;; esac fi ;; irix5* | irix6* | nonstopux*) if test "$GCC" = yes; then archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' # Try to use the -exported_symbol ld option, if it does not # work, assume that -exports_file does not work either and # implicitly export all symbols. save_LDFLAGS="$LDFLAGS" LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int foo(void) {} _ACEOF if ac_fn_c_try_link "$LINENO"; then : archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib' fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LDFLAGS="$save_LDFLAGS" else archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib' fi archive_cmds_need_lc='no' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: inherit_rpath=yes link_all_deplibs=yes ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out else archive_cmds='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF fi hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; newsos6) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: hardcode_shlibpath_var=no ;; *nto* | *qnx*) ;; openbsd*) if test -f /usr/libexec/ld.so; then hardcode_direct=yes hardcode_shlibpath_var=no hardcode_direct_absolute=yes if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' hardcode_libdir_flag_spec='${wl}-rpath,$libdir' export_dynamic_flag_spec='${wl}-E' else case $host_os in openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec='-R$libdir' ;; *) archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='${wl}-rpath,$libdir' ;; esac fi else ld_shlibs=no fi ;; os2*) hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes allow_undefined_flag=unsupported archive_cmds='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' old_archive_from_new_cmds='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; osf3*) if test "$GCC" = yes; then allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else allow_undefined_flag=' -expect_unresolved \*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' fi archive_cmds_need_lc='no' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: ;; osf4* | osf5*) # as osf3* with the addition of -msym flag if test "$GCC" = yes; then allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' else allow_undefined_flag=' -expect_unresolved \*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp' # Both c and cxx compiler support -rpath directly hardcode_libdir_flag_spec='-rpath $libdir' fi archive_cmds_need_lc='no' hardcode_libdir_separator=: ;; solaris*) no_undefined_flag=' -z defs' if test "$GCC" = yes; then wlarc='${wl}' archive_cmds='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' else case `$CC -V 2>&1` in *"Compilers 5.0"*) wlarc='' archive_cmds='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp' ;; *) wlarc='${wl}' archive_cmds='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' ;; esac fi hardcode_libdir_flag_spec='-R$libdir' hardcode_shlibpath_var=no case $host_os in solaris2.[0-5] | solaris2.[0-5].*) ;; *) # The compiler driver will combine and reorder linker options, # but understands `-z linker_flag'. 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# No shared lib support for Linux oldld, aout, or coff. linux*oldld* | linux*aout* | linux*coff*) dynamic_linker=no ;; # This must be Linux ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no # Some binutils ld are patched to set DT_RUNPATH save_LDFLAGS=$LDFLAGS save_libdir=$libdir eval "libdir=/foo; wl=\"$lt_prog_compiler_wl\"; \ LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec\"" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then : shlibpath_overrides_runpath=yes fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LDFLAGS=$save_LDFLAGS libdir=$save_libdir # This implies no fast_install, which is unacceptable. # Some rework will be needed to allow for fast_install # before this can be enabled. hardcode_into_libs=yes # Append ld.so.conf contents to the search path if test -f /etc/ld.so.conf; then lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '` sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra" fi # We used to test for /lib/ld.so.1 and disable shared libraries on # powerpc, because MkLinux only supported shared libraries with the # GNU dynamic linker. Since this was broken with cross compilers, # most powerpc-linux boxes support dynamic linking these days and # people can always --disable-shared, the test was removed, and we # assume the GNU/Linux dynamic linker is in use. dynamic_linker='GNU/Linux ld.so' ;; netbsdelf*-gnu) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes dynamic_linker='NetBSD ld.elf_so' ;; netbsd*) version_type=sunos need_lib_prefix=no need_version=no if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' dynamic_linker='NetBSD (a.out) ld.so' else library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' dynamic_linker='NetBSD ld.elf_so' fi shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes ;; newsos6) version_type=linux library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes ;; *nto* | *qnx*) version_type=qnx need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes dynamic_linker='ldqnx.so' ;; openbsd*) version_type=sunos sys_lib_dlsearch_path_spec="/usr/lib" need_lib_prefix=no # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs. case $host_os in openbsd3.3 | openbsd3.3.*) need_version=yes ;; *) need_version=no ;; esac library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' shlibpath_var=LD_LIBRARY_PATH if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then case $host_os in openbsd2.[89] | openbsd2.[89].*) shlibpath_overrides_runpath=no ;; *) shlibpath_overrides_runpath=yes ;; esac else shlibpath_overrides_runpath=yes fi ;; os2*) libname_spec='$name' shrext_cmds=".dll" need_lib_prefix=no library_names_spec='$libname${shared_ext} $libname.a' dynamic_linker='OS/2 ld.exe' shlibpath_var=LIBPATH ;; osf3* | osf4* | osf5*) version_type=osf need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib" sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec" ;; rdos*) dynamic_linker=no ;; solaris*) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes # ldd complains unless libraries are executable postinstall_cmds='chmod +x $lib' ;; sunos4*) version_type=sunos library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes if test "$with_gnu_ld" = yes; then need_lib_prefix=no fi need_version=yes ;; sysv4 | sysv4.3*) version_type=linux library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH case $host_vendor in sni) shlibpath_overrides_runpath=no need_lib_prefix=no runpath_var=LD_RUN_PATH ;; siemens) need_lib_prefix=no ;; motorola) need_lib_prefix=no need_version=no shlibpath_overrides_runpath=no sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib' ;; esac ;; sysv4*MP*) if test -d /usr/nec ;then version_type=linux library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}' soname_spec='$libname${shared_ext}.$major' shlibpath_var=LD_LIBRARY_PATH fi ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) version_type=freebsd-elf need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes if test "$with_gnu_ld" = yes; then sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib' else sys_lib_search_path_spec='/usr/ccs/lib /usr/lib' case $host_os in sco3.2v5*) sys_lib_search_path_spec="$sys_lib_search_path_spec /lib" ;; esac fi sys_lib_dlsearch_path_spec='/usr/lib' ;; tpf*) # TPF is a cross-target only. Preferred cross-host = GNU/Linux. version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes ;; uts4*) version_type=linux library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH ;; *) dynamic_linker=no ;; esac { $as_echo "$as_me:${as_lineno-$LINENO}: result: $dynamic_linker" >&5 $as_echo "$dynamic_linker" >&6; } test "$dynamic_linker" = no && can_build_shared=no variables_saved_for_relink="PATH $shlibpath_var $runpath_var" if test "$GCC" = yes; then variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH" fi if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec" fi if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec" fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to hardcode library paths into programs" >&5 $as_echo_n "checking how to hardcode library paths into programs... " >&6; } hardcode_action= if test -n "$hardcode_libdir_flag_spec" || test -n "$runpath_var" || test "X$hardcode_automatic" = "Xyes" ; then # We can hardcode non-existent directories. if test "$hardcode_direct" != no && # If the only mechanism to avoid hardcoding is shlibpath_var, we # have to relink, otherwise we might link with an installed library # when we should be linking with a yet-to-be-installed one ## test "$_LT_TAGVAR(hardcode_shlibpath_var, )" != no && test "$hardcode_minus_L" != no; then # Linking always hardcodes the temporary library directory. hardcode_action=relink else # We can link without hardcoding, and we can hardcode nonexisting dirs. hardcode_action=immediate fi else # We cannot hardcode anything, or else we can only hardcode existing # directories. hardcode_action=unsupported fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $hardcode_action" >&5 $as_echo "$hardcode_action" >&6; } if test "$hardcode_action" = relink || test "$inherit_rpath" = yes; then # Fast installation is not supported enable_fast_install=no elif test "$shlibpath_overrides_runpath" = yes || test "$enable_shared" = no; then # Fast installation is not necessary enable_fast_install=needless fi if test "x$enable_dlopen" != xyes; then enable_dlopen=unknown enable_dlopen_self=unknown enable_dlopen_self_static=unknown else lt_cv_dlopen=no lt_cv_dlopen_libs= case $host_os in beos*) lt_cv_dlopen="load_add_on" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes ;; mingw* | pw32* | cegcc*) lt_cv_dlopen="LoadLibrary" lt_cv_dlopen_libs= ;; cygwin*) lt_cv_dlopen="dlopen" lt_cv_dlopen_libs= ;; darwin*) # if libdl is installed we need to link against it { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -ldl" >&5 $as_echo_n "checking for dlopen in -ldl... " >&6; } if test "${ac_cv_lib_dl_dlopen+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldl $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dlopen (); int main () { return dlopen (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dl_dlopen=yes else ac_cv_lib_dl_dlopen=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dl_dlopen" >&5 $as_echo "$ac_cv_lib_dl_dlopen" >&6; } if test "x$ac_cv_lib_dl_dlopen" = x""yes; then : lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl" else lt_cv_dlopen="dyld" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes fi ;; *) ac_fn_c_check_func "$LINENO" "shl_load" "ac_cv_func_shl_load" if test "x$ac_cv_func_shl_load" = x""yes; then : lt_cv_dlopen="shl_load" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for shl_load in -ldld" >&5 $as_echo_n "checking for shl_load in -ldld... " >&6; } if test "${ac_cv_lib_dld_shl_load+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldld $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char shl_load (); int main () { return shl_load (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dld_shl_load=yes else ac_cv_lib_dld_shl_load=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dld_shl_load" >&5 $as_echo "$ac_cv_lib_dld_shl_load" >&6; } if test "x$ac_cv_lib_dld_shl_load" = x""yes; then : lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld" else ac_fn_c_check_func "$LINENO" "dlopen" "ac_cv_func_dlopen" if test "x$ac_cv_func_dlopen" = x""yes; then : lt_cv_dlopen="dlopen" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -ldl" >&5 $as_echo_n "checking for dlopen in -ldl... " >&6; } if test "${ac_cv_lib_dl_dlopen+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldl $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dlopen (); int main () { return dlopen (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dl_dlopen=yes else ac_cv_lib_dl_dlopen=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dl_dlopen" >&5 $as_echo "$ac_cv_lib_dl_dlopen" >&6; } if test "x$ac_cv_lib_dl_dlopen" = x""yes; then : lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dlopen in -lsvld" >&5 $as_echo_n "checking for dlopen in -lsvld... " >&6; } if test "${ac_cv_lib_svld_dlopen+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lsvld $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dlopen (); int main () { return dlopen (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_svld_dlopen=yes else ac_cv_lib_svld_dlopen=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_svld_dlopen" >&5 $as_echo "$ac_cv_lib_svld_dlopen" >&6; } if test "x$ac_cv_lib_svld_dlopen" = x""yes; then : lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld" else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dld_link in -ldld" >&5 $as_echo_n "checking for dld_link in -ldld... " >&6; } if test "${ac_cv_lib_dld_dld_link+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldld $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dld_link (); int main () { return dld_link (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_dld_dld_link=yes else ac_cv_lib_dld_dld_link=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_dld_dld_link" >&5 $as_echo "$ac_cv_lib_dld_dld_link" >&6; } if test "x$ac_cv_lib_dld_dld_link" = x""yes; then : lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-ldld" fi fi fi fi fi fi ;; esac if test "x$lt_cv_dlopen" != xno; then enable_dlopen=yes else enable_dlopen=no fi case $lt_cv_dlopen in dlopen) save_CPPFLAGS="$CPPFLAGS" test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H" save_LDFLAGS="$LDFLAGS" wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\" save_LIBS="$LIBS" LIBS="$lt_cv_dlopen_libs $LIBS" { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether a program can dlopen itself" >&5 $as_echo_n "checking whether a program can dlopen itself... " >&6; } if test "${lt_cv_dlopen_self+set}" = set; then : $as_echo_n "(cached) " >&6 else if test "$cross_compiling" = yes; then : lt_cv_dlopen_self=cross else lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2 lt_status=$lt_dlunknown cat > conftest.$ac_ext <<_LT_EOF #line 10122 "configure" #include "confdefs.h" #if HAVE_DLFCN_H #include #endif #include #ifdef RTLD_GLOBAL # define LT_DLGLOBAL RTLD_GLOBAL #else # ifdef DL_GLOBAL # define LT_DLGLOBAL DL_GLOBAL # else # define LT_DLGLOBAL 0 # endif #endif /* We may have to define LT_DLLAZY_OR_NOW in the command line if we find out it does not work in some platform. */ #ifndef LT_DLLAZY_OR_NOW # ifdef RTLD_LAZY # define LT_DLLAZY_OR_NOW RTLD_LAZY # else # ifdef DL_LAZY # define LT_DLLAZY_OR_NOW DL_LAZY # else # ifdef RTLD_NOW # define LT_DLLAZY_OR_NOW RTLD_NOW # else # ifdef DL_NOW # define LT_DLLAZY_OR_NOW DL_NOW # else # define LT_DLLAZY_OR_NOW 0 # endif # endif # endif # endif #endif void fnord() { int i=42;} int main () { void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW); int status = $lt_dlunknown; if (self) { if (dlsym (self,"fnord")) status = $lt_dlno_uscore; else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore; /* dlclose (self); */ } else puts (dlerror ()); return status; } _LT_EOF if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5 (eval $ac_link) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && test -s conftest${ac_exeext} 2>/dev/null; then (./conftest; exit; ) >&5 2>/dev/null lt_status=$? case x$lt_status in x$lt_dlno_uscore) lt_cv_dlopen_self=yes ;; x$lt_dlneed_uscore) lt_cv_dlopen_self=yes ;; x$lt_dlunknown|x*) lt_cv_dlopen_self=no ;; esac else : # compilation failed lt_cv_dlopen_self=no fi fi rm -fr conftest* fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_dlopen_self" >&5 $as_echo "$lt_cv_dlopen_self" >&6; } if test "x$lt_cv_dlopen_self" = xyes; then wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\" { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether a statically linked program can dlopen itself" >&5 $as_echo_n "checking whether a statically linked program can dlopen itself... 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See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "weightedbb.h" #include #include "globals.h" #include "permutation.h" namespace weightedbb { /*************************************************************************** * public methods ***************************************************************************/ WeightedBB::WeightedBB() { // init the class m_permSize = 0; m_source = NULL; m_target = NULL; m_wr = 1; m_wt = 1; m_distMode = 1; m_mapping = NULL; m_queue = NULL; m_candidates = new vector[HASHSIZE]; m_lowerBound = 0; m_upperBound = -1; m_distance = -1; m_minswrt.setGreedy(1); m_heapSize = 0; m_heapMax = 0; m_heapLimit = INT_MAX; } WeightedBB::~WeightedBB() { clear(); delete[] m_candidates; m_candidates = NULL; } void WeightedBB::setPermutation(int f_size, const int* f_source) { clear(); gIntArray0 = new int[f_size+1]; gIntArray1 = new int[f_size+1]; gIntArray2 = new int[f_size+1]; gIntArray3 = new int[f_size+1]; gIntArray4 = new int[f_size+1]; gIntArray5 = new int[f_size+1]; gIntArray6 = new int[f_size+1]; gBoolArray0 = new bool[f_size+1]; m_permSize = f_size; m_source = new int[f_size]; m_target = new int[f_size]; m_mapping = new int[f_size+1]; for (int i = 0; i < f_size; i++) m_source[i] = f_source[i]; for (int i = 0; i < f_size; i++) m_target[i] = i+1; for (int i = 1; i <= f_size; i++) m_mapping[i] = i; m_minswrt.setPermutations(m_permSize, m_source, m_target); } void WeightedBB::setPermutations(int f_size, const int* f_source, const int* f_target) { clear(); gIntArray0 = new int[f_size+1]; gIntArray1 = new int[f_size+1]; gIntArray2 = new int[f_size+1]; gIntArray3 = new int[f_size+1]; gIntArray4 = new int[f_size+1]; gIntArray5 = new int[f_size+1]; gIntArray6 = new int[f_size+1]; gBoolArray0 = new bool[f_size+1]; m_permSize = f_size; m_source = new int[f_size]; m_target = new int[f_size]; m_mapping = new int[f_size+1]; for (int i = 0; i < f_size; i++) f_target[i] > 0? m_mapping[f_target[i]] = i+1 : m_mapping[-f_target[i]] = -(i+1); for (int i = 0; i < f_size; i++) m_source[i] = (f_source[i] > 0? m_mapping[f_source[i]] : -m_mapping[-f_source[i]]); for (int i = 0; i < f_size; i++) m_target[i] = i+1; m_minswrt.setPermutations(m_permSize, m_source, m_target); } void WeightedBB::setWeights(int f_wr, int f_wt, int f_distMode) { m_wr = f_wr; m_wt = f_wt; m_distMode = f_distMode; if (m_distMode == 0) // transposition distance { m_wr = f_wt; m_wt = f_wt; m_minswrt.setWeights(m_wt, m_wt); } else { m_wr = f_wr; m_wt = f_wt; m_minswrt.setWeights(m_wr, m_wt); } } void WeightedBB::sort(int f_maxDist) { const vector* approx; // sorting sequence of the approximation algorithm Permutation* perm; // the initial permutation Candidate* cand; // + additional information // check if the permutations are set - otherwise return if (m_source == NULL) { cout << "permutations not set - cannot sort\n"; return; } // if we have to clear the old queues, do so if (m_queue != NULL) { for (int i = 0; i <= m_upperBound - m_lowerBound; i++) { for (unsigned int j = 0; j < m_queue[i].size(); j++) deleteAncestors(m_queue[i][j]); m_queue[i].clear(); } delete[] m_queue; for (int i = 0; i < HASHSIZE; i++) m_candidates[i].clear(); } // create the initial permutation perm = new Permutation(m_permSize, m_source); m_lowerBound = perm->getLowerBound(m_wr, m_wt); cand = new Candidate; cand->m_lbRem = m_lowerBound; cand->m_lbWhole = m_lowerBound; cand->m_perm = perm; cand->m_positionC = 0; cand->m_positionQ = 0; cand->m_numChildren = 0; cand->m_parent = NULL; cand->m_op = NULL; // calculate the bounds and init the queues m_minswrt.sort(); approx = m_minswrt.getResult(); m_upperBound = 0; for (unsigned int i = 0; i < approx->size(); i++) m_upperBound += ((*approx)[i].m_type == minswrt::Operation::OPERATION_REVERSAL? m_wr : m_wt); if (f_maxDist < m_upperBound) m_upperBound = f_maxDist; if (m_upperBound < m_lowerBound) // there can be no solution { cerr << "upperBound < lowerBound " << m_upperBound << " < " << m_lowerBound << endl; m_distance = -1; return; } m_queue = new vector[m_upperBound - m_lowerBound + 1]; m_queue[0].push_back(cand); m_candidates[perm->m_hash].push_back(cand); m_heapSize = 1; m_heapMax = 1; // expand for (int x = 0; x <= m_upperBound - m_lowerBound; x++) // position in queue array { while (!m_queue[x].empty()) { cand = m_queue[x][m_queue[x].size()-1]; if (cand->m_lbRem == 0) // solution found { m_distance = x + m_lowerBound; m_terminal = cand; return; } if (m_heapMax > m_heapLimit) // more elements on the heap than allowed -> abort { m_distance = -2; return; } m_queue[x].pop_back(); m_candidates[cand->m_perm->m_hash][cand->m_positionC] = m_candidates[cand->m_perm->m_hash][m_candidates[cand->m_perm->m_hash].size()-1]; m_candidates[cand->m_perm->m_hash][cand->m_positionC]->m_positionC = cand->m_positionC; m_candidates[cand->m_perm->m_hash].pop_back(); expand(cand); if (cand->m_numChildren == 0) deleteAncestors(cand); } } m_distance = -1; } int WeightedBB::getLowerBound() const { Permutation* perm; // the initial permutation int result; // this will be returned // check if the permutations are set - otherwise return if (m_source == NULL) { cout << "permutations not set - cannot calculate a lower bound\n"; return -1; } // create the initial permutation perm = new Permutation(m_permSize, m_source); result = perm->getLowerBound(m_wr, m_wt); delete perm; return result; } bool WeightedBB::getNumCycles(int& f_odd, int& f_even, int& f_blocks) { Permutation* perm; // the initial permutation // check if the permutations are set - otherwise return if (m_source == NULL) { cout << "permutations not set - cannot calculate a lower bound\n"; return false; } // create the initial permutation perm = new Permutation(m_permSize, m_source); f_odd = perm->m_codd; f_even = perm->m_ceven; f_blocks = perm->m_size; delete perm; return true; } int WeightedBB::getDistance() { return m_distance; } bool WeightedBB::getSortingSequence(unsigned int& f_numOps, Operation*& f_ops, int**& f_perms) const { unsigned int opCounter = 0; // counts the written operations stack seq; // sequence of candidates Candidate* cand; // A candidate of the sequence Permutation* perm = NULL; // its permutation int size; // its size ElementList* blocks; // the mapping from internal elements to real elements int value; // an elements value bool found = false; // used for searching, indicates that we have found an element int firstblock = -1; // id of the real first block int offset = 0; // position of the real first element in its block bool firstori = true; // true if it has positive orientation bool ori = true; // orientation to use for the current perm int counter; // counts printed elements int it; // loop iterator int swap; // swap two variables int b0, b1, b2, b3, b4, b5; // border elements of an operation int m[3]; // merge points (smaller elements) int shift; // shift of the start point bool invert; // true if we must invert the new start point int tmp; if (m_distance < 0) // not successfully sorted return false; // fill the stack cand = m_terminal; f_numOps = 0; while (cand != NULL) { seq.push(cand); cand = cand->m_parent; f_numOps++; } f_numOps--; // init the result f_ops = new Operation[f_numOps]; f_perms = new int*[f_numOps + 1]; // invert m_mapping for (int i = 1; i <= m_permSize; i++) { if (m_mapping[i] > 0) gIntArray1[m_mapping[i]] = i; else gIntArray1[-m_mapping[i]] = -i; } // create the initial mapping.... size = m_permSize; value = 1; // mark values to delete for (int i = 1; i <= size; i++) gIntArray0[i] = 0; for (int i = 1; i < m_permSize; i++) { if ((m_source[i-1] + 1 == m_source[i]) || ((m_source[i-1] == m_permSize) && (m_source[i] == 1)) || ((m_source[i-1] == -1) && (m_source[i] == -m_permSize))) { gIntArray0[abs(m_source[i])] = -1; // mark value to delete size--; } } if ((m_source[m_permSize-1] + 1 == m_source[0]) || ((m_source[m_permSize-1] == m_permSize) && (m_source[0] == 1)) || ((m_source[m_permSize-1] == -1) && (m_source[0] == -m_permSize))) { gIntArray0[abs(m_source[0])] = -1; // mark value to delete size--; } if (size == 0) // already sorted { blocks = new ElementList[2]; blocks[1].m_size = m_permSize; for (int i = 1; i <= m_permSize; i++) blocks[1].m_elements.push_back(gIntArray1[i]); firstblock = 1; offset = 0; firstori = true; } else { // create mapping for (int i = 1; i <= m_permSize; i++) { if (gIntArray0[i] != -1) gIntArray0[i] = value++; } for (int i = 0; i < m_permSize; i++) // indicate orientation of elements { if (m_source[i] > 0) gBoolArray0[m_source[i]] = true; else gBoolArray0[-m_source[i]] = false; } blocks = new ElementList[size+1]; for (int i = 0; i < m_permSize; i++) { if (gIntArray0[abs(m_source[i])] != -1) { if (m_source[i] > 0) { blocks[gIntArray0[m_source[i]]].m_elements.push_back(gIntArray1[m_source[i]]); blocks[gIntArray0[m_source[i]]].m_size = 1; for (int j = (m_source[i]==m_permSize?1:m_source[i]+1); (gIntArray0[j] == -1) && gBoolArray0[j]; (j==m_permSize? j=1 : j++)) { blocks[gIntArray0[m_source[i]]].m_elements.push_back(gIntArray1[j]); blocks[gIntArray0[m_source[i]]].m_size++; } } else { blocks[gIntArray0[-m_source[i]]].m_elements.push_front(gIntArray1[-m_source[i]]); blocks[gIntArray0[-m_source[i]]].m_size = 1; for (int j = (m_source[i]==-1?m_permSize:-m_source[i]-1); (gIntArray0[j] == -1) && !gBoolArray0[j]; (j==1? j=m_permSize : j--)) { blocks[gIntArray0[-m_source[i]]].m_elements.push_front(gIntArray1[j]); blocks[gIntArray0[-m_source[i]]].m_size++; } } } } // check for permutation start for (int i = 1; (i <= size) && !found; i++) { offset = 0; for (list::iterator j = blocks[i].m_elements.begin(); j != blocks[i].m_elements.end(); j++, offset++) { if (*j == m_source[0]) { firstblock = i; firstori = true; found = true; break; } else if (*j == -m_source[0]) { firstblock = i; firstori = false; found = true; break; } } } } // go down the stack while (!seq.empty()) { cand = seq.top(); if (cand->m_op != NULL) { // translate the operation f_ops[opCounter].m_type = cand->m_op->m_type; f_ops[opCounter].m_edges[0] = 0; f_ops[opCounter].m_edges[1] = 0; f_ops[opCounter].m_edges[2] = 0; for (int i = 0; i < cand->m_op->m_edges[0]; i++) f_ops[opCounter].m_edges[0] += blocks[abs(perm->m_perm[i])].m_size; for (int i = 0; i < cand->m_op->m_edges[1]; i++) f_ops[opCounter].m_edges[1] += blocks[abs(perm->m_perm[i])].m_size; if (f_ops[opCounter].m_type != Operation::REVERSAL) { for (int i = 0; i < cand->m_op->m_edges[2]; i++) f_ops[opCounter].m_edges[2] += blocks[abs(perm->m_perm[i])].m_size; } // count shift counter = 0; for (it = 0; abs(perm->m_perm[it]) != firstblock; it++) counter += blocks[abs(perm->m_perm[it])].m_size; if (perm->m_perm[it] > 0) counter += offset; else counter += (blocks[firstblock].m_size - offset - 1); if (firstori == (perm->m_perm[it] > 0)) { f_ops[opCounter].m_edges[0] -= (counter - 1); f_ops[opCounter].m_edges[1] -= (counter - 1); f_ops[opCounter].m_edges[2] -= (counter - 1); } else { f_ops[opCounter].m_edges[0] = counter - f_ops[opCounter].m_edges[0] + 2; f_ops[opCounter].m_edges[1] = counter - f_ops[opCounter].m_edges[1] + 2; f_ops[opCounter].m_edges[2] = counter - f_ops[opCounter].m_edges[2] + 2; } if (f_ops[opCounter].m_edges[0] <= 0) f_ops[opCounter].m_edges[0] += m_permSize; else if (f_ops[opCounter].m_edges[0] > m_permSize) f_ops[opCounter].m_edges[0] -= m_permSize; if (f_ops[opCounter].m_edges[1] <= 0) f_ops[opCounter].m_edges[1] += m_permSize; else if (f_ops[opCounter].m_edges[1] > m_permSize) f_ops[opCounter].m_edges[1] -= m_permSize; if (f_ops[opCounter].m_edges[2] <= 0) f_ops[opCounter].m_edges[2] += m_permSize; else if (f_ops[opCounter].m_edges[2] > m_permSize) f_ops[opCounter].m_edges[2] -= m_permSize; if ((f_ops[opCounter].m_type == Operation::REVERSAL) && (f_ops[opCounter].m_edges[0] > f_ops[opCounter].m_edges[1])) { swap = f_ops[opCounter].m_edges[0]; f_ops[opCounter].m_edges[0] = f_ops[opCounter].m_edges[1]; f_ops[opCounter].m_edges[1] = swap; } if (f_ops[opCounter].m_type == Operation::TRANSPOSITION) { if (firstori != (perm->m_perm[it] > 0)) { swap = f_ops[opCounter].m_edges[0]; f_ops[opCounter].m_edges[0] = f_ops[opCounter].m_edges[1]; f_ops[opCounter].m_edges[1] = swap; } if ((f_ops[opCounter].m_edges[0] > f_ops[opCounter].m_edges[1]) || (f_ops[opCounter].m_edges[1] > f_ops[opCounter].m_edges[2])) { swap = f_ops[opCounter].m_edges[0]; f_ops[opCounter].m_edges[0] = f_ops[opCounter].m_edges[2]; f_ops[opCounter].m_edges[2] = f_ops[opCounter].m_edges[1]; f_ops[opCounter].m_edges[1] = swap; } if ((f_ops[opCounter].m_edges[0] > f_ops[opCounter].m_edges[1]) || (f_ops[opCounter].m_edges[1] > f_ops[opCounter].m_edges[2])) { swap = f_ops[opCounter].m_edges[0]; f_ops[opCounter].m_edges[0] = f_ops[opCounter].m_edges[2]; f_ops[opCounter].m_edges[2] = f_ops[opCounter].m_edges[1]; f_ops[opCounter].m_edges[1] = swap; } } if (f_ops[opCounter].m_type == Operation::TRANSREVA) { if (firstori != (perm->m_perm[it] > 0)) { swap = f_ops[opCounter].m_edges[0]; f_ops[opCounter].m_edges[0] = f_ops[opCounter].m_edges[1]; f_ops[opCounter].m_edges[1] = swap; } } if (f_ops[opCounter].m_type == Operation::TRANSREVB) { if (firstori == (perm->m_perm[it] > 0)) { swap = f_ops[opCounter].m_edges[0]; f_ops[opCounter].m_edges[0] = f_ops[opCounter].m_edges[1]; f_ops[opCounter].m_edges[1] = f_ops[opCounter].m_edges[2]; f_ops[opCounter].m_edges[2] = swap; } else { swap = f_ops[opCounter].m_edges[0]; f_ops[opCounter].m_edges[0] = f_ops[opCounter].m_edges[2]; f_ops[opCounter].m_edges[2] = swap; } } if (f_ops[opCounter].m_type == Operation::REVREV) { if (firstori == (perm->m_perm[it] > 0)) { swap = f_ops[opCounter].m_edges[0]; f_ops[opCounter].m_edges[0] = f_ops[opCounter].m_edges[2]; f_ops[opCounter].m_edges[2] = f_ops[opCounter].m_edges[1]; f_ops[opCounter].m_edges[1] = swap; } else { swap = f_ops[opCounter].m_edges[1]; f_ops[opCounter].m_edges[1] = f_ops[opCounter].m_edges[2]; f_ops[opCounter].m_edges[2] = swap; } } if ((f_ops[opCounter].m_type == Operation::TRANSREVA) || (f_ops[opCounter].m_type == Operation::TRANSREVB) || (f_ops[opCounter].m_type == Operation::REVREV)) f_ops[opCounter].m_type = Operation::INVTRANS; // calculate the effects of the operation: does the startpoint change? shift = 0; if (f_ops[opCounter].m_type == Operation::REVERSAL) { if (f_ops[opCounter].m_edges[0] == 1) { shift = f_ops[opCounter].m_edges[1] - 2; invert = true; } else invert = false; } else if (f_ops[opCounter].m_type == Operation::TRANSPOSITION) { if (f_ops[opCounter].m_edges[0] == 1) shift = f_ops[opCounter].m_edges[1] - 1; invert = false; } else // any kind of inverted transposition { if ((f_ops[opCounter].m_edges[0] == 1) || ((f_ops[opCounter].m_edges[1] != 1) && (f_ops[opCounter].m_edges[0] > f_ops[opCounter].m_edges[1]))) // first point in inverted segment { if ((m_permSize + 1 - f_ops[opCounter].m_edges[0]) % m_permSize < (m_permSize + f_ops[opCounter].m_edges[2] - f_ops[opCounter].m_edges[1]) % m_permSize) { shift = f_ops[opCounter].m_edges[1] - f_ops[opCounter].m_edges[0]; invert = false; } else { shift = f_ops[opCounter].m_edges[2] + f_ops[opCounter].m_edges[0] - 3; invert = true; } } else if ((f_ops[opCounter].m_edges[1] == 1) || ((f_ops[opCounter].m_edges[2] != 1) && (f_ops[opCounter].m_edges[1] > f_ops[opCounter].m_edges[2]))) // first point in moved segment { if ((1 - f_ops[opCounter].m_edges[0] + m_permSize) % m_permSize < (f_ops[opCounter].m_edges[2] - f_ops[opCounter].m_edges[1] + m_permSize) % m_permSize) { shift = f_ops[opCounter].m_edges[1] - f_ops[opCounter].m_edges[0]; invert = false; } else { shift = f_ops[opCounter].m_edges[0] + f_ops[opCounter].m_edges[2] - 3; invert = true; } } else invert = false; if (shift < 0) shift += m_permSize; else if (shift >= m_permSize) shift -= m_permSize; } tmp = 0; while (abs(perm->m_perm[tmp]) != firstblock) tmp++; ori = ((perm->m_perm[tmp] > 0) == firstori); while (shift > 0) { if (ori == (perm->m_perm[tmp] > 0)) { if (offset + shift >= blocks[abs(perm->m_perm[tmp])].m_size) { shift -= (blocks[abs(perm->m_perm[tmp])].m_size - offset); if (ori) tmp = (tmp + 1) % size; else tmp = (tmp - 1 + size) % size; if (ori == (perm->m_perm[tmp] > 0)) offset = 0; else offset = blocks[abs(perm->m_perm[tmp])].m_size - 1; } else { offset += shift; shift = 0; } } else { if (offset < shift) { shift -= (offset + 1); if (ori) tmp = (tmp + 1) % size; else tmp = (tmp - 1 + size) % size; if (ori == (perm->m_perm[tmp] > 0)) offset = 0; else offset = blocks[abs(perm->m_perm[tmp])].m_size - 1; } else { offset -= shift; shift = 0; } } } firstblock = abs(perm->m_perm[tmp]); firstori = (ori == (perm->m_perm[tmp] > 0)) ^ invert; // calculate the effects of the operation: merging of blocks m[0] = -1; m[1] = -1; m[2] = -1; b0 = (cand->m_op->m_edges[0] == 0? perm->m_perm[perm->m_size-1] : perm->m_perm[cand->m_op->m_edges[0]-1]); b1 = perm->m_perm[cand->m_op->m_edges[0] % size]; b2 = (cand->m_op->m_edges[1] == 0? perm->m_perm[perm->m_size-1] : perm->m_perm[cand->m_op->m_edges[1]-1]); b3 = perm->m_perm[cand->m_op->m_edges[1] % size]; if (cand->m_op->m_type != Operation::REVERSAL) { b4 = (cand->m_op->m_edges[2] == 0? perm->m_perm[perm->m_size-1] : perm->m_perm[cand->m_op->m_edges[2]-1]); b5 = perm->m_perm[cand->m_op->m_edges[2] % size]; } if (cand->m_op->m_type == Operation::REVERSAL) { if (b0 > 0) { if ((b0 % perm->m_size) + 1 == -b2) m[0] = b0; } else if (b2 > 0) { if ((b2 % perm->m_size) + 1 == -b0) m[0] = b2; } if (b1 < 0) { if ((-b1 % perm->m_size) + 1 == b3) m[1] = -b1; } else if (b3 < 0) { if ((-b3 % perm->m_size) + 1 == b1) m[1] = -b3; } } else if (cand->m_op->m_type == Operation::TRANSPOSITION) { if (b0 > 0) { if ((b0 % perm->m_size) + 1 == b3) m[0] = b0; } else if (b3 < 0) { if ((-b3 % perm->m_size) + 1 == -b0) m[0] = -b3; } if (b2 > 0) { if ((b2 % perm->m_size) + 1 == b5) m[1] = b2; } else if (b5 < 0) { if ((-b5 % perm->m_size) + 1 == -b2) m[1] = -b5; } if (b4 > 0) { if ((b4 % perm->m_size) + 1 == b1) m[2] = b4; } else if (b1 < 0) { if ((-b1 % perm->m_size) + 1 == -b4) m[2] = -b1; } } else if (cand->m_op->m_type == Operation::TRANSREVA) { if (b0 > 0) { if ((b0 % perm->m_size) + 1 == b3) m[0] = b0; } else if (b3 < 0) { if ((-b3 % perm->m_size) + 1 == -b0) m[0] = -b3; } if (b4 > 0) { if ((b4 % perm->m_size) + 1 == -b2) m[1] = b4; } else if (b2 > 0) { if ((b2 % perm->m_size) + 1 == -b4) m[1] = b2; } if (b1 < 0) { if ((-b1 % perm->m_size) + 1 == b5) m[2] = -b1; } else if (b5 < 0) { if ((-b5 % perm->m_size) + 1 == b1) m[2] = -b5; } } else if (cand->m_op->m_type == Operation::TRANSREVB) { if (b0 > 0) { if ((b0 % perm->m_size) + 1 == -b4) m[0] = b0; } else if (b4 > 0) { if ((b4 % perm->m_size) + 1 == -b0) m[0] = b4; } if (b3 < 0) { if ((-b3 % perm->m_size) + 1 == b1) m[1] = -b3; } else if (b1 < 0) { if ((-b1 % perm->m_size) + 1 == b3) m[1] = -b1; } if (b2 > 0) { if ((b2 % perm->m_size) + 1 == b5) m[2] = b2; } else if (b5 < 0) { if ((-b5 % perm->m_size) + 1 == -b2) m[2] = -b5; } } else if (cand->m_op->m_type == Operation::REVREV) { if (b0 > 0) { if ((b0 % perm->m_size) + 1 == -b2) m[0] = b0; } else if (b2 > 0) { if ((b2 % perm->m_size) + 1 == -b0) m[0] = b2; } if (b1 < 0) { if ((-b1 % perm->m_size) + 1 == -b4) m[1] = -b1; } else if (b4 > 0) { if ((b4 % perm->m_size) + 1 == b1) m[1] = b4; } if (b3 < 0) { if ((-b3 % perm->m_size) + 1 == b5) m[2] = -b3; } else if (b5 < 0) { if ((-b5 % perm->m_size) + 1 == b3) m[2] = -b5; } } // merge for (int i = 0; i < 3; i++) { if (m[i] < 0) continue; if (size == 1) // never merge all break; tmp = (m[i] == size? 1 : m[i] + 1); if (tmp == 1) { if (firstblock == m[i]) firstblock = 1; else if (firstblock == 1) offset += blocks[m[i]].m_size; blocks[1].m_elements.splice(blocks[1].m_elements.begin(), blocks[m[i]].m_elements); blocks[1].m_size += blocks[m[i]].m_size; } else { if (firstblock == tmp) { firstblock = m[i]; offset += blocks[m[i]].m_size; } else if (firstblock > tmp) firstblock--; blocks[m[i]].m_elements.splice(blocks[m[i]].m_elements.end(), blocks[tmp].m_elements); blocks[m[i]].m_size += blocks[tmp].m_size; for (int j = i+1; j < 3; j++) { if (m[j] >= tmp) m[j]--; } for (int j = tmp; j < size; j++) { blocks[j].m_elements = blocks[j+1].m_elements; blocks[j].m_size = blocks[j+1].m_size; } } size--; } opCounter++; } size = cand->m_perm->m_size; perm = cand->m_perm; if (size == 0) { value = 0; ori = firstori; size = 1; } else { for (int i = 0; i < size; i++) { if (perm->m_perm[i] == firstblock) { value = i; ori = firstori; break; } else if (perm->m_perm[i] == -firstblock) { value = i; ori = !firstori; break; } } } counter = (firstori? -offset : -blocks[firstblock].m_size + offset + 1); f_perms[opCounter] = new int[m_permSize]; while (counter < m_permSize) // print exactly this amount of elements { if (ori == (perm->m_perm[value] > 0)) // run through this block in positive direction { for (list::iterator i = blocks[abs(perm->m_perm[value])].m_elements.begin(); (i != blocks[abs(perm->m_perm[value])].m_elements.end()) && (counter < m_permSize); i++, counter++) { if (counter >= 0) f_perms[opCounter][counter] = *i; } } else // run through this block in negative direction { for (list::reverse_iterator i = blocks[abs(perm->m_perm[value])].m_elements.rbegin(); (i != blocks[abs(perm->m_perm[value])].m_elements.rend()) && (counter < m_permSize); i++, counter++) { if (counter >= 0) f_perms[opCounter][counter] = -(*i); } } if (ori) value = (value+1)%size; else value = (value+size-1)%size; } seq.pop(); } delete[] blocks; return true; } void WeightedBB::printResult(int f_printLevel) { stack seq; // sequence of candidates Candidate* cand; // A candidate of the sequence Permutation* perm = NULL; // its permutation int size; // its size ElementList* blocks; // the mapping from internal elements to real elements int value; // an elements value bool found = false; // used for searching, indicates that we have found an element int firstblock = -1; // id of the real first block int offset = 0; // position of the real first element in its block bool firstori = true; // true if it has positive orientation bool ori = true; // orientation to use for the current perm int counter; // counts printed elements Operation op; // the current operation int it; // loop iterator int swap; // swap two variables int b0, b1, b2, b3, b4, b5; // border elements of an operation int m[3]; // merge points (smaller elements) int shift; // shift of the start point bool invert; // true if we must invert the new start point int tmp; /** * Prints the result to stdout. sort must have been called before this. * f_printLevel determins how much information will be written. * f_printLevel: * 0: only write overall weight * 1: write operations * 2: write operations + overall weight * 3: write operations + permutations * 4: write operations + permutations + overall weight * @param f_printLevel the print level */ cout << CONSOLE_BOLD; if (m_distance == -1) { cout << "no solution within upper bound found\n"; cout << CONSOLE_RESET; return; } else if (m_distance == -2) { cout << "calculation required too much resources -> aborted\n"; cout << CONSOLE_RESET; return; } if (f_printLevel > 0) { // fill the stack cand = m_terminal; while (cand != NULL) { seq.push(cand); cand = cand->m_parent; } // invert m_mapping for (int i = 1; i <= m_permSize; i++) { if (m_mapping[i] > 0) gIntArray1[m_mapping[i]] = i; else gIntArray1[-m_mapping[i]] = -i; } // create the initial mapping.... size = m_permSize; value = 1; // mark values to delete for (int i = 1; i <= size; i++) gIntArray0[i] = 0; for (int i = 1; i < m_permSize; i++) { if ((m_source[i-1] + 1 == m_source[i]) || ((m_source[i-1] == m_permSize) && (m_source[i] == 1)) || ((m_source[i-1] == -1) && (m_source[i] == -m_permSize))) { gIntArray0[abs(m_source[i])] = -1; // mark value to delete size--; } } if ((m_source[m_permSize-1] + 1 == m_source[0]) || ((m_source[m_permSize-1] == m_permSize) && (m_source[0] == 1)) || ((m_source[m_permSize-1] == -1) && (m_source[0] == -m_permSize))) { gIntArray0[abs(m_source[0])] = -1; // mark value to delete size--; } if (size == 0) // already sorted { blocks = new ElementList[2]; blocks[1].m_size = m_permSize; for (int i = 1; i <= m_permSize; i++) blocks[1].m_elements.push_back(gIntArray1[i]); firstblock = 1; offset = 0; firstori = true; } else { // create mapping for (int i = 1; i <= m_permSize; i++) { if (gIntArray0[i] != -1) gIntArray0[i] = value++; } for (int i = 0; i < m_permSize; i++) // indicate orientation of elements { if (m_source[i] > 0) gBoolArray0[m_source[i]] = true; else gBoolArray0[-m_source[i]] = false; } blocks = new ElementList[size+1]; for (int i = 0; i < m_permSize; i++) { if (gIntArray0[abs(m_source[i])] != -1) { if (m_source[i] > 0) { blocks[gIntArray0[m_source[i]]].m_elements.push_back(gIntArray1[m_source[i]]); blocks[gIntArray0[m_source[i]]].m_size = 1; for (int j = (m_source[i]==m_permSize?1:m_source[i]+1); (gIntArray0[j] == -1) && gBoolArray0[j]; (j==m_permSize? j=1 : j++)) { blocks[gIntArray0[m_source[i]]].m_elements.push_back(gIntArray1[j]); blocks[gIntArray0[m_source[i]]].m_size++; } } else { blocks[gIntArray0[-m_source[i]]].m_elements.push_front(gIntArray1[-m_source[i]]); blocks[gIntArray0[-m_source[i]]].m_size = 1; for (int j = (m_source[i]==-1?m_permSize:-m_source[i]-1); (gIntArray0[j] == -1) && !gBoolArray0[j]; (j==1? j=m_permSize : j--)) { blocks[gIntArray0[-m_source[i]]].m_elements.push_front(gIntArray1[j]); blocks[gIntArray0[-m_source[i]]].m_size++; } } } } // check for permutation start for (int i = 1; (i <= size) && !found; i++) { offset = 0; for (list::iterator j = blocks[i].m_elements.begin(); j != blocks[i].m_elements.end(); j++, offset++) { if (*j == m_source[0]) { firstblock = i; firstori = true; found = true; break; } else if (*j == -m_source[0]) { firstblock = i; firstori = false; found = true; break; } } } } // go down the stack while (!seq.empty()) { cand = seq.top(); if (cand->m_op != NULL) { // translate the operation op.m_type = cand->m_op->m_type; op.m_edges[0] = 0; op.m_edges[1] = 0; op.m_edges[2] = 0; for (int i = 0; i < cand->m_op->m_edges[0]; i++) op.m_edges[0] += blocks[abs(perm->m_perm[i])].m_size; for (int i = 0; i < cand->m_op->m_edges[1]; i++) op.m_edges[1] += blocks[abs(perm->m_perm[i])].m_size; if (op.m_type != Operation::REVERSAL) { for (int i = 0; i < cand->m_op->m_edges[2]; i++) op.m_edges[2] += blocks[abs(perm->m_perm[i])].m_size; } // count shift counter = 0; for (it = 0; abs(perm->m_perm[it]) != firstblock; it++) counter += blocks[abs(perm->m_perm[it])].m_size; if (perm->m_perm[it] > 0) counter += offset; else counter += (blocks[firstblock].m_size - offset - 1); if (firstori == (perm->m_perm[it] > 0)) { op.m_edges[0] -= (counter - 1); op.m_edges[1] -= (counter - 1); op.m_edges[2] -= (counter - 1); } else { op.m_edges[0] = counter - op.m_edges[0] + 2; op.m_edges[1] = counter - op.m_edges[1] + 2; op.m_edges[2] = counter - op.m_edges[2] + 2; } if (op.m_edges[0] <= 0) op.m_edges[0] += m_permSize; else if (op.m_edges[0] > m_permSize) op.m_edges[0] -= m_permSize; if (op.m_edges[1] <= 0) op.m_edges[1] += m_permSize; else if (op.m_edges[1] > m_permSize) op.m_edges[1] -= m_permSize; if (op.m_edges[2] <= 0) op.m_edges[2] += m_permSize; else if (op.m_edges[2] > m_permSize) op.m_edges[2] -= m_permSize; if ((op.m_type == Operation::REVERSAL) && (op.m_edges[0] > op.m_edges[1])) { swap = op.m_edges[0]; op.m_edges[0] = op.m_edges[1]; op.m_edges[1] = swap; } if (op.m_type == Operation::TRANSPOSITION) { if (firstori != (perm->m_perm[it] > 0)) { swap = op.m_edges[0]; op.m_edges[0] = op.m_edges[1]; op.m_edges[1] = swap; } if ((op.m_edges[0] > op.m_edges[1]) || (op.m_edges[1] > op.m_edges[2])) { swap = op.m_edges[0]; op.m_edges[0] = op.m_edges[2]; op.m_edges[2] = op.m_edges[1]; op.m_edges[1] = swap; } if ((op.m_edges[0] > op.m_edges[1]) || (op.m_edges[1] > op.m_edges[2])) { swap = op.m_edges[0]; op.m_edges[0] = op.m_edges[2]; op.m_edges[2] = op.m_edges[1]; op.m_edges[1] = swap; } } if (op.m_type == Operation::TRANSREVA) { if (firstori != (perm->m_perm[it] > 0)) { swap = op.m_edges[0]; op.m_edges[0] = op.m_edges[1]; op.m_edges[1] = swap; } } if (op.m_type == Operation::TRANSREVB) { if (firstori == (perm->m_perm[it] > 0)) { swap = op.m_edges[0]; op.m_edges[0] = op.m_edges[1]; op.m_edges[1] = op.m_edges[2]; op.m_edges[2] = swap; } else { swap = op.m_edges[0]; op.m_edges[0] = op.m_edges[2]; op.m_edges[2] = swap; } } if (op.m_type == Operation::REVREV) { if (firstori == (perm->m_perm[it] > 0)) { swap = op.m_edges[0]; op.m_edges[0] = op.m_edges[2]; op.m_edges[2] = op.m_edges[1]; op.m_edges[1] = swap; } else { swap = op.m_edges[1]; op.m_edges[1] = op.m_edges[2]; op.m_edges[2] = swap; } } if ((op.m_type == Operation::TRANSREVA) || (op.m_type == Operation::TRANSREVB) || (op.m_type == Operation::REVREV)) op.m_type = Operation::INVTRANS; cout << CONSOLE_COLOR_WHITE; printOperation(&op); // delayed print of the permutation if (f_printLevel > 2) { if (((op.m_type == Operation::REVERSAL) || (op.m_type == Operation::INVTRANS)) && ((op.m_edges[0] == 1) || ((op.m_edges[1] != 1) && (op.m_edges[0] > op.m_edges[1])))) cout << CONSOLE_COLOR_RED; else if ((op.m_type == Operation::TRANSPOSITION) && ((op.m_edges[0] == 1) || ((op.m_edges[1] != 1) && (op.m_edges[0] > op.m_edges[1])))) cout << CONSOLE_COLOR_CYAN; else if (((op.m_type == Operation::TRANSPOSITION) || (op.m_type == Operation::INVTRANS)) && ((op.m_edges[1] == 1) || ((op.m_edges[2] != 1) && (op.m_edges[1] > op.m_edges[2])))) cout << CONSOLE_COLOR_GREEN; else cout << CONSOLE_COLOR_WHITE; for (int i = 0; i < m_permSize; i++) { if (i + 1 == op.m_edges[0]) { if ((op.m_type == Operation::REVERSAL) || (op.m_type == Operation::INVTRANS)) cout << CONSOLE_COLOR_RED; else cout << CONSOLE_COLOR_CYAN; } else if (i + 1 == op.m_edges[1]) { if ((op.m_type == Operation::TRANSPOSITION) || (op.m_type == Operation::INVTRANS)) cout << CONSOLE_COLOR_GREEN; else cout << CONSOLE_COLOR_WHITE; } else if ((i + 1 == op.m_edges[2]) && (op.m_type != Operation::REVERSAL)) cout << CONSOLE_COLOR_WHITE; cout << gIntArray2[i] << " "; } } cout << endl; // calculate the effects of the operation: does the startpoint change? shift = 0; if (op.m_type == Operation::REVERSAL) { if (op.m_edges[0] == 1) { shift = op.m_edges[1] - 2; invert = true; } else invert = false; } else if (op.m_type == Operation::TRANSPOSITION) { if (op.m_edges[0] == 1) shift = op.m_edges[1] - 1; invert = false; } else // any kind of inverted transposition { if ((op.m_edges[0] == 1) || ((op.m_edges[1] != 1) && (op.m_edges[0] > op.m_edges[1]))) // first point in inverted segment { if ((m_permSize + 1 - op.m_edges[0]) % m_permSize < (m_permSize + op.m_edges[2] - op.m_edges[1]) % m_permSize) { shift = op.m_edges[1] - op.m_edges[0]; invert = false; } else { shift = op.m_edges[2] + op.m_edges[0] - 3; invert = true; } } else if ((op.m_edges[1] == 1) || ((op.m_edges[2] != 1) && (op.m_edges[1] > op.m_edges[2]))) // first point in moved segment { if ((1 - op.m_edges[0] + m_permSize) % m_permSize < (op.m_edges[2] - op.m_edges[1] + m_permSize) % m_permSize) { shift = op.m_edges[1] - op.m_edges[0]; invert = false; } else { shift = op.m_edges[0] + op.m_edges[2] - 3; invert = true; } } else invert = false; if (shift < 0) shift += m_permSize; else if (shift >= m_permSize) shift -= m_permSize; } tmp = 0; while (abs(perm->m_perm[tmp]) != firstblock) tmp++; ori = ((perm->m_perm[tmp] > 0) == firstori); while (shift > 0) { if (ori == (perm->m_perm[tmp] > 0)) { if (offset + shift >= blocks[abs(perm->m_perm[tmp])].m_size) { shift -= (blocks[abs(perm->m_perm[tmp])].m_size - offset); if (ori) tmp = (tmp + 1) % size; else tmp = (tmp - 1 + size) % size; if (ori == (perm->m_perm[tmp] > 0)) offset = 0; else offset = blocks[abs(perm->m_perm[tmp])].m_size - 1; } else { offset += shift; shift = 0; } } else { if (offset < shift) { shift -= (offset + 1); if (ori) tmp = (tmp + 1) % size; else tmp = (tmp - 1 + size) % size; if (ori == (perm->m_perm[tmp] > 0)) offset = 0; else offset = blocks[abs(perm->m_perm[tmp])].m_size - 1; } else { offset -= shift; shift = 0; } } } firstblock = abs(perm->m_perm[tmp]); firstori = (ori == (perm->m_perm[tmp] > 0)) ^ invert; // calculate the effects of the operation: merging of blocks m[0] = -1; m[1] = -1; m[2] = -1; b0 = (cand->m_op->m_edges[0] == 0? perm->m_perm[perm->m_size-1] : perm->m_perm[cand->m_op->m_edges[0]-1]); b1 = perm->m_perm[cand->m_op->m_edges[0] % size]; b2 = (cand->m_op->m_edges[1] == 0? perm->m_perm[perm->m_size-1] : perm->m_perm[cand->m_op->m_edges[1]-1]); b3 = perm->m_perm[cand->m_op->m_edges[1] % size]; if (cand->m_op->m_type != Operation::REVERSAL) { b4 = (cand->m_op->m_edges[2] == 0? perm->m_perm[perm->m_size-1] : perm->m_perm[cand->m_op->m_edges[2]-1]); b5 = perm->m_perm[cand->m_op->m_edges[2] % size]; } if (cand->m_op->m_type == Operation::REVERSAL) { if (b0 > 0) { if ((b0 % perm->m_size) + 1 == -b2) m[0] = b0; } else if (b2 > 0) { if ((b2 % perm->m_size) + 1 == -b0) m[0] = b2; } if (b1 < 0) { if ((-b1 % perm->m_size) + 1 == b3) m[1] = -b1; } else if (b3 < 0) { if ((-b3 % perm->m_size) + 1 == b1) m[1] = -b3; } } else if (cand->m_op->m_type == Operation::TRANSPOSITION) { if (b0 > 0) { if ((b0 % perm->m_size) + 1 == b3) m[0] = b0; } else if (b3 < 0) { if ((-b3 % perm->m_size) + 1 == -b0) m[0] = -b3; } if (b2 > 0) { if ((b2 % perm->m_size) + 1 == b5) m[1] = b2; } else if (b5 < 0) { if ((-b5 % perm->m_size) + 1 == -b2) m[1] = -b5; } if (b4 > 0) { if ((b4 % perm->m_size) + 1 == b1) m[2] = b4; } else if (b1 < 0) { if ((-b1 % perm->m_size) + 1 == -b4) m[2] = -b1; } } else if (cand->m_op->m_type == Operation::TRANSREVA) { if (b0 > 0) { if ((b0 % perm->m_size) + 1 == b3) m[0] = b0; } else if (b3 < 0) { if ((-b3 % perm->m_size) + 1 == -b0) m[0] = -b3; } if (b4 > 0) { if ((b4 % perm->m_size) + 1 == -b2) m[1] = b4; } else if (b2 > 0) { if ((b2 % perm->m_size) + 1 == -b4) m[1] = b2; } if (b1 < 0) { if ((-b1 % perm->m_size) + 1 == b5) m[2] = -b1; } else if (b5 < 0) { if ((-b5 % perm->m_size) + 1 == b1) m[2] = -b5; } } else if (cand->m_op->m_type == Operation::TRANSREVB) { if (b0 > 0) { if ((b0 % perm->m_size) + 1 == -b4) m[0] = b0; } else if (b4 > 0) { if ((b4 % perm->m_size) + 1 == -b0) m[0] = b4; } if (b3 < 0) { if ((-b3 % perm->m_size) + 1 == b1) m[1] = -b3; } else if (b1 < 0) { if ((-b1 % perm->m_size) + 1 == b3) m[1] = -b1; } if (b2 > 0) { if ((b2 % perm->m_size) + 1 == b5) m[2] = b2; } else if (b5 < 0) { if ((-b5 % perm->m_size) + 1 == -b2) m[2] = -b5; } } else if (cand->m_op->m_type == Operation::REVREV) { if (b0 > 0) { if ((b0 % perm->m_size) + 1 == -b2) m[0] = b0; } else if (b2 > 0) { if ((b2 % perm->m_size) + 1 == -b0) m[0] = b2; } if (b1 < 0) { if ((-b1 % perm->m_size) + 1 == -b4) m[1] = -b1; } else if (b4 > 0) { if ((b4 % perm->m_size) + 1 == b1) m[1] = b4; } if (b3 < 0) { if ((-b3 % perm->m_size) + 1 == b5) m[2] = -b3; } else if (b5 < 0) { if ((-b5 % perm->m_size) + 1 == b3) m[2] = -b5; } } // merge for (int i = 0; i < 3; i++) { if (m[i] < 0) continue; if (size == 1) // never merge all break; tmp = (m[i] == size? 1 : m[i] + 1); if (tmp == 1) { if (firstblock == m[i]) firstblock = 1; else if (firstblock == 1) offset += blocks[m[i]].m_size; blocks[1].m_elements.splice(blocks[1].m_elements.begin(), blocks[m[i]].m_elements); blocks[1].m_size += blocks[m[i]].m_size; } else { if (firstblock == tmp) { firstblock = m[i]; offset += blocks[m[i]].m_size; } else if (firstblock > tmp) firstblock--; blocks[m[i]].m_elements.splice(blocks[m[i]].m_elements.end(), blocks[tmp].m_elements); blocks[m[i]].m_size += blocks[tmp].m_size; for (int j = i+1; j < 3; j++) { if (m[j] >= tmp) m[j]--; } for (int j = tmp; j < size; j++) { blocks[j].m_elements = blocks[j+1].m_elements; blocks[j].m_size = blocks[j+1].m_size; } } size--; } } size = cand->m_perm->m_size; perm = cand->m_perm; if (f_printLevel > 2) { if (size == 0) { value = 0; ori = firstori; size = 1; } else { for (int i = 0; i < size; i++) { if (perm->m_perm[i] == firstblock) { value = i; ori = firstori; break; } else if (perm->m_perm[i] == -firstblock) { value = i; ori = !firstori; break; } } } counter = (firstori? -offset : -blocks[firstblock].m_size + offset + 1); while (counter < m_permSize) // print exactly this amount of elements { if (ori == (perm->m_perm[value] > 0)) // run through this block in positive direction { for (list::iterator i = blocks[abs(perm->m_perm[value])].m_elements.begin(); (i != blocks[abs(perm->m_perm[value])].m_elements.end()) && (counter < m_permSize); i++, counter++) { if (counter >= 0) gIntArray2[counter] = *i; // delay the output } } else // run through this block in negative direction { for (list::reverse_iterator i = blocks[abs(perm->m_perm[value])].m_elements.rbegin(); (i != blocks[abs(perm->m_perm[value])].m_elements.rend()) && (counter < m_permSize); i++, counter++) { if (counter >= 0) gIntArray2[counter] = -(*i); // delay the output } } if (ori) value = (value+1)%size; else value = (value+size-1)%size; } } seq.pop(); } // delayed print of the permutation if (f_printLevel > 2) { cout << CONSOLE_COLOR_WHITE; cout << " "; for (int i = 0; i < m_permSize; i++) cout << gIntArray2[i] << " "; cout << endl; } delete[] blocks; } if (!(f_printLevel & 1)) cout << "overall weight: " << m_distance << endl; cout << CONSOLE_RESET; } /*************************************************************************** * private methods ***************************************************************************/ void WeightedBB::expand(Candidate* f_cand) { Permutation* perm = f_cand->m_perm; // permutation to expand Operation op; // operation to perform int weight = f_cand->m_lbWhole - f_cand->m_lbRem; // so far performed weight if (m_distMode == 1) { // for all reversals op.m_type = Operation::REVERSAL; for (int i = 1; i < perm->m_size; i++) { op.m_edges[0] = i; for (int j = i+1; j <= perm->m_size; j++) { op.m_edges[1] = j; applyOperation(f_cand, &op, weight); } } } // for all (inverted) transpositions for (int i = 1; i < perm->m_size - 1; i++) { op.m_edges[0] = i; for (int j = i+1; j < perm->m_size; j++) { op.m_edges[1] = j; for (int k = j+1; k <= perm->m_size; k++) { op.m_edges[2] = k; op.m_type = Operation::TRANSPOSITION; applyOperation(f_cand, &op, weight); if (m_distMode == 1) { op.m_type = Operation::TRANSREVA; applyOperation(f_cand, &op, weight); op.m_type = Operation::TRANSREVB; applyOperation(f_cand, &op, weight); op.m_type = Operation::REVREV; applyOperation(f_cand, &op, weight); } } } } } void WeightedBB::applyOperation(Candidate* f_cand, const Operation* f_op, int f_weight) { Permutation* succ = f_cand->m_perm->performOperation(*f_op); // successor permutation int lbRem; // lower bound of the remaining distance int lbWhole; // lower bound for the whole sequence Candidate* cand; // a candidate // calc bounds lbRem = succ->getLowerBound(m_wr, m_wt); lbWhole = f_weight + lbRem + (f_op->m_type == Operation::REVERSAL? m_wr : m_wt); if (lbWhole > m_upperBound) // not good enough { delete succ; return; } // search if duplicated for (unsigned int i = 0; i < m_candidates[succ->m_hash].size(); i++) { if (*succ == *(m_candidates[succ->m_hash][i]->m_perm)) { cand = m_candidates[succ->m_hash][i]; // use cand as duplicate of succ // check which one to take if (lbWhole < cand->m_lbWhole) { // move to better position in m_queue m_queue[cand->m_lbWhole - m_lowerBound][cand->m_positionQ] = m_queue[cand->m_lbWhole - m_lowerBound][m_queue[cand->m_lbWhole - m_lowerBound].size() - 1]; m_queue[cand->m_lbWhole - m_lowerBound][cand->m_positionQ]->m_positionQ = cand->m_positionQ; m_queue[cand->m_lbWhole - m_lowerBound].pop_back(); cand->m_lbWhole = lbWhole; cand->m_positionQ = m_queue[lbWhole - m_lowerBound].size(); cand->m_parent->m_numChildren--; if (cand->m_parent->m_numChildren == 0) deleteAncestors(cand->m_parent); cand->m_parent = f_cand; cand->m_op->m_type = f_op->m_type; cand->m_op->m_edges[0] = f_op->m_edges[0]; cand->m_op->m_edges[1] = f_op->m_edges[1]; cand->m_op->m_edges[2] = f_op->m_edges[2]; f_cand->m_numChildren++; m_queue[lbWhole - m_lowerBound].push_back(cand); delete succ; return; } else // duplicate is better { delete succ; return; } } } // new candidate, add cand = new Candidate; cand->m_perm = succ; cand->m_lbWhole = lbWhole; cand->m_lbRem = lbRem; cand->m_positionC = m_candidates[succ->m_hash].size(); cand->m_positionQ = m_queue[lbWhole - m_lowerBound].size(); cand->m_numChildren = 0; cand->m_parent = f_cand; cand->m_op = new Operation; cand->m_op->m_type = f_op->m_type; cand->m_op->m_edges[0] = f_op->m_edges[0]; cand->m_op->m_edges[1] = f_op->m_edges[1]; cand->m_op->m_edges[2] = f_op->m_edges[2]; f_cand->m_numChildren++; m_candidates[succ->m_hash].push_back(cand); m_queue[lbWhole - m_lowerBound].push_back(cand); m_heapSize++; if (m_heapSize > m_heapMax) m_heapMax = m_heapSize; } void WeightedBB::deleteAncestors(Candidate* f_cand) { Candidate* cand = f_cand; Candidate* parent; do { parent = cand->m_parent; delete cand->m_perm; cand->m_perm = NULL; delete cand->m_op; cand->m_op = NULL; delete cand; cand = NULL; m_heapSize--; cand = parent; if (cand == NULL) return; } while (cand->m_numChildren == 1); cand->m_numChildren--; } void WeightedBB::clear() { if (m_queue != NULL) { for (int i = 0; i <= m_upperBound - m_lowerBound; i++) { for (unsigned int j = 0; j < m_queue[i].size(); j++) deleteAncestors(m_queue[i][j]); m_queue[i].clear(); } delete[] m_queue; m_queue = NULL; } for (int i = 0; i < HASHSIZE; i++) m_candidates[i].clear(); delete[] m_source; m_source = NULL; delete[] m_target; m_target = NULL; delete[] m_mapping; m_mapping = NULL; delete[] gIntArray0; gIntArray0 = NULL; delete[] gIntArray1; gIntArray1 = NULL; delete[] gIntArray2; gIntArray2 = NULL; delete[] gIntArray3; gIntArray3 = NULL; delete[] gIntArray4; gIntArray4 = NULL; delete[] gIntArray5; gIntArray5 = NULL; delete[] gIntArray6; gIntArray6 = NULL; delete[] gBoolArray0; gBoolArray0 = NULL; m_lowerBound = 0; m_upperBound = -1; m_distance = -1; } /*************************************************************************** * debugging methods ***************************************************************************/ #if DEBUG_WEIGHTEDBB void WeightedBB::debug() { } #endif } // end namespace weightedbb phylo-1.0.6/weightedbb/permutation.h0000644000175000017500000001055311434510050014413 00000000000000/** * filename: permutation.h * author: Martin Bader * begin: 11.08.2008 * last change: 19.11.2008 * * The representation of a permutation. * * Copyright (C) 2008 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef WBB_PERMUTATION_H_ #define WBB_PERMUTATION_H_ namespace weightedbb { /** * The different operation types. */ struct Operation { /** Type of the operation */ enum { REVERSAL, // A B A -> A -B A TRANSPOSITION, // A B C A -> A C B A TRANSREVA, // A B C A -> A C -B A TRANSREVB, // A B C A -> A -C B A REVREV, // A B C A -> A -B -C A INVTRANS // general case of inverted transposition (use for human readable output only) } m_type; /** The edges of the operation */ int m_edges[3]; }; /** * This class represents a permutation, with all necessary additional * information. */ class Permutation { /*********************************************************************** * member variables ***********************************************************************/ public: /** Size of the permutation */ int m_size; /** Permutation data */ int* m_perm; /** Inverse permutation - indices of elements */ int* m_index; /** Hash value of the permutation */ long m_hash; /** Number of odd cycles */ int m_codd; /** Number of even cycles */ int m_ceven; /*********************************************************************** * methods ***********************************************************************/ public: /** * Constructor. */ Permutation(); /** * This constructor also computes all memebers. The input data will be * transformed such that it does not contain any breakpoints, and the first * element is +1. * @param f_size size of the data array * @param f_data the input data array */ Permutation(int f_size, int* f_data); /** * The destructor. */ ~Permutation(); /** * Performs an operation. * @param f_op the operation to perform * @return the resulting permutation */ Permutation* performOperation(const Operation& f_op) const; /** * Calculates the lower bound. * @param f_wr weight of reversals * @param f_wt weight of (inverted) transpositions and revrevs * @return the lower bound */ int getLowerBound(int f_wr, int f_wt); /** * Checks if two permutations are equal (that means the elements are equal). * @return true if they are equal */ bool operator==(Permutation& f_perm) const; /** * Direct access to an element. * @param f_pos position of the element * @return the element as reference */ inline int& operator[](int f_pos) { return m_perm[f_pos]; } private: /** * Calcualtes the hash value of the permutation and writes it to m_hash. */ void calcHash(); /** * Calculates the number of even and odd cycles and writes them to ceven, codd. */ void calcCycles(); /*********************************************************************** * debugging methods ***********************************************************************/ public: /** * Dumps the permutation to stdout */ void dump(); }; /** * Prints a permutation (int array) * @param f_size size of the array * @param f_perm data array */ void printPermutation(int f_size, int* f_perm); /** * Prints an operation. * @param f_op the oepration to print */ void printOperation(Operation* f_op); } // end namespace weightedbb #endif phylo-1.0.6/weightedbb/weightedbb.h0000644000175000017500000002363511434510050014155 00000000000000/** * filename: weightedbb.h * author: Martin Bader * begin: 11.08.2008 * last change: 31.03.2010 * * Main file of the branch n bound algorithm for weighted Sorting by * reversals, transpositions, and transreversals. * * Copyright (C) 2008-2010 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef WEIGHTEDBB_H_ #define WEIGHTEDBB_H_ #include #include #include #include "minswrt.h" #define DEBUG_WEIGHTEDBB 0 namespace weightedbb { // forward declarations struct Operation; class Permutation; /** * A candidate for expansion - consists of the perm and the position where to * find in the different queues. */ struct Candidate { /** The permutation object */ Permutation* m_perm; /** The lower bound for the whole sequence */ int m_lbWhole; /** The lower bound for the remaining sequence */ int m_lbRem; /** Vector position in WeightedBB::m_candidates */ int m_positionC; /** Vector position in WeightedBB::m_queue */ int m_positionQ; /** The number of children that are still valid */ int m_numChildren; /** The parent candidate */ Candidate* m_parent; /** The Operation that led to this candidate */ Operation* m_op; }; /** * Struct that maps elements in the internal representation to lists of * elements corresponding to the real permutation */ struct ElementList { /** List size */ int m_size; /** List of elements */ std::list m_elements; }; /** * The main class, contains the branch n bound algorithm. */ class WeightedBB { /*********************************************************************** * member variables ***********************************************************************/ protected: /** Size of permutation to sort */ int m_permSize; /** Copy of the source permutation */ int* m_source; /** Copy of the target permutation */ int* m_target; /** The weight for reversals */ int m_wr; /** The weight for transpositions and transreversals */ int m_wt; /** Distance mode: 0: transposition distance; 1: weighted reversal and transposition distance */ int m_distMode; /** Mapping target -> id */ int* m_mapping; /** The queue of permutations to expand */ std::vector* m_queue; /** All candidate permutations, sorted by the lower bound */ std::vector* m_candidates; /** The lower bound for the distance */ int m_lowerBound; /** The upper bound for the distance */ int m_upperBound; /** The calculated distance */ int m_distance; /** Elements currently on the heap */ int m_heapSize; /** Maximal number of elements on the heap */ int m_heapMax; /** Maximal allowed number of elements on the heap */ int m_heapLimit; /** The last candidate of the sorting sequence */ Candidate* m_terminal; /** Tool for calculating the upper bound. */ minswrt::MinSWRT m_minswrt; /*********************************************************************** * methods ***********************************************************************/ public: /** * Constructor. */ WeightedBB(); /** * Destructor. */ ~WeightedBB(); /** * Sets the heap limit (maximum number of elements allowed on the heap). * As the limit is not checked in each step, it is possible that this limit is * exceeded by a small number. * @param f_limit the new heap limit */ inline void setHeapLimit(int f_limit) { m_heapLimit = f_limit; } /** * Sets the permutation to sort. Clears the memory of old data. * f_size is the permutation size, and f_source is a int[f_size] array * that contains the signed elements. Elements go from 1 to f_size. * The algorithm assumes that the target permutation is the ID. * @param f_size size of the permutation * @param f_source permutation data */ void setPermutation(int f_size, const int* f_source); /** * Sets two permutations. Clears the memory of old data. * f_size is the permutation size, f_source and f_target * are two int[f_size} arrays that contain the signed elements. Elements * go from 1 to f_size. * @param f_size size of the permutation * @param f_source source permutation * @param f_target target permutation */ void setPermutations(int f_size, const int* f_source, const int* f_target); /** * Sets the weights for reversals and transpositions + transreversals. * @param f_wr weight for reversals * @param f_wt weight for transpositions and transreversals * @param f_distMode 0 transposition distance, 1 weighted rev/t distance */ void setWeights(int f_wr, int f_wt, int f_distMode = 1); /** * Starts the sorting algorithm. Only searches for solutions <= f_maxDist. * @param f_maxDist maximum distance to search */ void sort(int f_maxDist = INT_MAX); /** * Returns the lower bound between the input permutations. * If the input permutations are not set, -1 will be returned. * @return the lower bound */ int getLowerBound() const; /** * Returns the number of odd and even cycles between the input permutations. * The results will be written to f_odd and f_even, which are references * of integers. As adjacency cycles are eliminated, it also returns the number * of blocks (= number of breakpoints), which will be written to f_blocks. * The return value is true on success, and false if no * permutations are set. * @param f_odd the number of odd cylces (return value) * @param f_even the number of even cycles (return value) * @return true if successfull, false otherwise */ bool getNumCycles(int& f_odd, int& f_even, int& f_blocks); /** * Returns the weighted distance of the input permutation. This can only * be called aftzer a call of sort. * @return the weighted distance */ int getDistance(); /** * Returns the calculated sorting sequence. The result will be written to * the parameters f_numOps, f_ops, and f_perms (all data in these parameters * will be lost). f_numOps is the number of performed operations, f_ops are * the operations, and f_perms are the permutations on the sorting scenario * (all from source to target). I.e. f_perms are f_ops + 1 permutations, * f_perms[0] is the source permutation, f_perms[f_ops] is the target * permutation. f_op[i] is the operation from permutation f_perm[i] to * f_perm[i+1]. All returned values are copies, so make sure to delete them * in your program when no longer needed. * The return value indicates whether we could return a sorting sequence * or not. You must have performed a successfull call of sort(), or false * will be returned and none of the parameters will be written. * @param f_numOps the number of operations (result will be written here) * @param f_ops the operations (result will be written here) * @param f_perms the permutations on the sorting sequence (result will be written here) * @return true if successfull, false otherwise */ bool getSortingSequence(unsigned int& f_numOps, Operation*& f_ops, int**& f_perms) const; /** * Prints the result to stdout. sort must have been called before this. * f_printLevel determins how much information will be written. * f_printLevel: * 0: only write overall weight * 1: write operations * 2: write operations + overall weight * 3: write operations + permutations * 4: write operations + permutations + overall weight * @param f_printLevel the print level */ void printResult(int f_printLevel); /** * Returns the maximum heap size during the last calculation. * @return maximum heap size */ inline int getHeapMax() { return m_heapMax; } private: /** * Expands a candidate * @param f_cand the candidate */ void expand(Candidate* f_cand); /** * Applys the operation f_op to the permutation f_perm. The resulting permutation * will be added at the correct position in the queues. This also contains a * check against the upper bound and duplicate elimination. * @param f_perm source permutation * @param f_op the operation to apply * @param f_weight weight of sequence m_source -> f_perm */ void applyOperation(Candidate* f_perm, const Operation* f_op, int weight); /** * Deletes the candidate plus all its ancestors (frees memory). * @param f_can the candidate to delete */ void deleteAncestors(Candidate* f_cand); /** * Clears all current data. */ void clear(); /*********************************************************************** * debuging methods ***********************************************************************/ #if DEBUG_WEIGHTEDBB public: /** * Debugging method, functionality can change. */ void debug(); #endif }; } // end namespace weightedbb #endif /*WEIGHTEDBB_H_*/ phylo-1.0.6/weightedbb/README0000644000175000017500000001702311434510050012552 00000000000000phylo - phylogenetic reconstruction based on the weighted reversal and transposition distance. Installation ============ The standard way to install is to call the following three commands. It will install the program in /usr/local ./configure make make install If you want to install it in some other directory (e.g. because you do not have writing permissions in /usr/local), install with the commands ./configure --prefix=/path/to/install make make install For additional options, see the INSTALL file. If the standard installation should fail, try first to call reconf and then do the standard installation steps ./configure make make install After the installation, you will find the executable programs phylo, SwRT, revDist, and median under /bin. The main program phylo depends on the libraries minswrt, revDist, and median, weightedbb, and these libraries have all their own tiny frontend. phylo ===== phylo contains of two parts: 1. the program itself, which is compiled into a library. 2. a tiny frontend that calls the library. The frontend: Call the program with the following parameters. phylo [OPTIONS] available options: -h Just print some help information (ignore all other options) -w wr wt Set weights to wr (for reversals) and wt (for transpositions). If you use reversal only distance, call -w wr inf. (default: -w 1 inf). Note that the weights must be integer. -v x Set the output (verbosity) level to x. -v 0 produces the most output, while -v 3 only reports serious errors. (default: -v 1) -t If this parameter is set, the input file is a tree instead of a set of permutations, so only the improvement steps will be performed. -f name Load the file with the given name. This option is required. -s x If this parameter is set, the tree is only created from starting node x. -i [n|t|m|tm] Set he improvement technique to use. t means topology improvement, m means median improvement, tm means first using t then m, n means no improvement. (default: -i tm) -o name If this parameter is set, the best found tree will be written to a file with the given name. The input file consists of the specifications of several genomes (as signed permutations). Each genome consists of a line > genome name and a line containing a signed permutation. Lines beginning with # are comments. As an example, you can call phylo -w 1 2 -f ../share/phylo/campanulaceae The library: The functions provided by the library are documented in minswrt.h in the include directory. As example of how to use the library, you can have a look at minswrt/start.cpp. The interesting part is in the main function. minswrt ======= minswrt (minimal sorting by weighted reversals and transpositions) contains of two parts: 1. the program itself, which is compiled into a library. 2. a tiny frontend that calls the library. The frontend: Call the program with the following parameters: ./minswrt file wr wt - file is the file containing the permutation. The file consists of a line containing the number of elements in the permutation. The next two lines contain the source and the target permutation. An example can be found in share/minswrt/test.in - wr is the weight of reversals - wt is the weight of transpositions and inverted transpositions The library: The functions provided by the library are documented in minswrt.h in the include directory. As example of how to use the library, you can have a look at minswrt/start.cpp. The interesting part is in the main function. weightedbb ========== wightedbb is an exact branch and bound algorithm to calculate the weighted reversal and transposition distance between two genomes. It contains of two parts: 1. the program itself, which is compiled into a library. 2. a tiny frontend that calls the library. The frontend: Call the program with the following parameters: ./weightedbb file wr wt distmode - file is the file containing the permutation. The file consists of a line containing the number of elements in the permutation. The next two lines contain the source and the target permutation. An example can be found in share/weightedbb/test.in - wr is the weight of reversals - wt is the weight of transpositions and inverted transpositions - distmode determines the distance measure. 0 means transposition distance, and 1 means weighted reversal and transposition distance The library: The functions provided by the library are documented in weightedbb.h in the include directory. As example of how to use the library, you can have a look at weightedbb/start.cpp. The interesting part is in the main function. revDist ======= revDist is a small program to calculate the reversal distance between two cyclic signed permutations. It contains of two parts: 1. the program itself, which is compiled into a library. 2. a tiny frontend that calls the library. The frontend: Call the program with revDist infile where infile contains a line containing the permutation size, followed by two lines with the signed permutations. Lines beginning with # are comments. As an example, see the file revDist/test.in The library: The functions provided by the library are documented in revDist.h in the include directory. As example of how to use the library, you can have a look at share/revDist/start.cpp. The interesting part is in the main function. median ====== median is an extension of Caprara's median solver that can calculate a median of three cyclic signed permutations either under the reversal distance or under the weighte reversal and transposition distance. It contains of two parts: 1. the program itself, which is compiled into a library. 2. a tiny frontend that calls the library. The frontend: Call the program with median infile wr wt distMode exact all where infile contains the three genomes (signed permutations). Each genome consists of a line > genome name and a line containing the signed permuation. wr and wt are the weights for reversals and transpositions. Both must be integer. distMode defines the used distance measure, where 0 is the reversal distance, 1 is the transposition distance, and 2 is the weighted reversal and transposition distance. If exact is set to 1, the pairwise distances will be calculated by an exact branch and bound algorithm (this will guarantee the medians to be true medians, not only approximations), otherwise a faster approximation algorithm is used. If all is set to 1, all medians will be returned, otherwise only one median will be returned. As the algorithm is a branch and bound algorithm that works on a heap, the algorithm will prune the heap when it runs out of memory. Note that there is a risk that an optimal solution gets lost. In this case, a warning message will be displayed. As example, you can call median ../share/median/test.in 1 2 2 0 0 In the momentary form, the program calculates just one median. If one is interested in all medians, this can easily be achieved by editing the main function in median/start.cpp (for details, see there). The library: The functions provided by the library are documented in median.h in the include directory. As example of how to use the library, you can have a look at median/start.cpp. The interesting part is in the main function. Copyright: ========== Copyright (C) 2007/2008 Martin Bader This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions. For details about the licence, read the file COPYING phylo-1.0.6/weightedbb/permutation.cpp0000644000175000017500000006700311434510050014750 00000000000000/** * filename: permutation.cpp * author: Martin Bader * begin: 11.08.2008 * last change: 19.11.2008 * * Implementation of permutation.h * * Copyright (C) 2008 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "permutation.h" #include #include #include "globals.h" using namespace std; namespace weightedbb { /*************************************************************************** * public methods ***************************************************************************/ Permutation::Permutation() { m_size = 0; m_perm = NULL; m_index = NULL; m_hash = 0; m_codd = 0; m_ceven = 0; } Permutation::Permutation(int f_size, int* f_data) { int value = 1; // value of an element int posData = 0; // position in f_data int posPerm = 0; // position in m_perm bool inv; // true if we must invert f_data m_size = f_size; // mark values to delete for (int i = 1; i <= f_size; i++) gIntArray0[i] = 0; for (int i = 1; i < f_size; i++) { if ((f_data[i-1] + 1 == f_data[i]) || ((f_data[i-1] == f_size) && (f_data[i] == 1)) || ((f_data[i-1] == -1) && (f_data[i] == -f_size))) { gIntArray0[abs(f_data[i])] = -1; // mark value to delete m_size--; } } if ((f_data[f_size-1] + 1 == f_data[0]) || ((f_data[f_size-1] == f_size) && (f_data[0] == 1)) || ((f_data[f_size-1] == -1) && (f_data[0] == -f_size))) { gIntArray0[abs(f_data[0])] = -1; // mark value to delete m_size--; } // check if we already have the id if (m_size == 0) { m_size = 1; m_perm = new int[1]; m_perm[0] = 1; m_index = new int[2]; m_index[1] = 0; calcHash(); calcCycles(); return; } // create mapping for (int i = 1; i <= f_size; i++) { if (gIntArray0[i] != -1) gIntArray0[i] = value++; } // search starting point for (; posData < f_size; posData++) { if (gIntArray0[abs(f_data[posData])] == 1) break; } inv = (f_data[posData] < 0); // create the permutation m_perm = new int[m_size]; m_index = new int[m_size+1]; for (int i = 0; i < f_size; i++) { if (f_data[posData] > 0) { if (gIntArray0[f_data[posData]] != -1) { m_perm[posPerm] = (inv? -gIntArray0[f_data[posData]] : gIntArray0[f_data[posData]]); m_index[abs(m_perm[posPerm])] = (m_perm[posPerm] > 0? posPerm : -posPerm); posPerm++; } inv? (posData == 0? posData = f_size - 1 : posData--) : (posData == f_size - 1? posData = 0: posData++); } else { if (gIntArray0[-f_data[posData]] != -1) { m_perm[posPerm] = (inv? gIntArray0[-f_data[posData]] : -gIntArray0[-f_data[posData]]); m_index[abs(m_perm[posPerm])] = (m_perm[posPerm] > 0? posPerm : -posPerm); posPerm++; } inv? (posData == 0? posData = f_size - 1 : posData--) : (posData == f_size - 1? posData = 0: posData++); } } calcHash(); calcCycles(); } Permutation::~Permutation() { delete[] m_perm; delete[] m_index; } Permutation* Permutation::performOperation(const Operation& f_op) const { Permutation* result = new Permutation(); // the resulting permutation int adj0, adj1, adj2; // 1 if the edges become adjacencies, 0 otherwise int pos; // position for writing // init, create mappings result->m_size = m_size; adj0 = 0; adj1 = 0; adj2 = 0; for (int i = 1; i <= m_size; i++) // gIntArray0 for positiv vars gIntArray0[i] = i; for (int i = 1; i <= m_size; i++) // gIntArray1 for negativ vars gIntArray1[i] = -i; // check optype if (f_op.m_type == Operation::REVERSAL) // A B A -> A -B A { // check for adjacencies if (m_perm[f_op.m_edges[0]-1] + 1 == -m_perm[f_op.m_edges[1] - 1]) { adj0 = 1; for (int i = (m_perm[f_op.m_edges[0]-1] > 0? m_perm[f_op.m_edges[0]-1] + 1 : -m_perm[f_op.m_edges[0]-1]); i <= m_size; i++) { gIntArray0[i]--; gIntArray1[i]++; } result->m_size--; } if (f_op.m_edges[1] == m_size) { if (m_perm[f_op.m_edges[0]] == -m_size) { adj1 = 1; gIntArray0[m_size]--; gIntArray1[m_size]++; result->m_size--; } } else { if (-m_perm[f_op.m_edges[0]] + 1 == m_perm[f_op.m_edges[1]]) { adj1 = 1; for (int i = (m_perm[f_op.m_edges[0]] > 0? m_perm[f_op.m_edges[0]] : m_perm[f_op.m_edges[1]]); i <= m_size; i++) { gIntArray0[i]--; gIntArray1[i]++; } result->m_size--; } } // init arrays if (result->m_size == 0) { result->m_size = 1; result->m_perm = new int[1]; result->m_index = new int[2]; result->m_perm[0] = 1; result->m_index[1] = 0; result->calcHash(); result->calcCycles(); return result; } result->m_perm = new int[result->m_size]; result->m_index = new int[result->m_size + 1]; // write first block for (int i = 0; i < f_op.m_edges[0] - adj0; i++) { if (m_perm[i] > 0) { result->m_perm[i] = gIntArray0[m_perm[i]]; result->m_index[result->m_perm[i]] = i; } else { result->m_perm[i] = gIntArray1[-m_perm[i]]; result->m_index[-result->m_perm[i]] = -i; } } // write second block pos = f_op.m_edges[0] - adj0; for (int i = f_op.m_edges[1] - 1; i >= f_op.m_edges[0] + adj1; i--, pos++) { if (m_perm[i] > 0) { result->m_perm[pos] = gIntArray1[m_perm[i]]; result->m_index[-result->m_perm[pos]] = -pos; } else { result->m_perm[pos] = gIntArray0[-m_perm[i]]; result->m_index[result->m_perm[pos]] = pos; } } // write last block for (int i = f_op.m_edges[1]; i < m_size; i++, pos++) { if (m_perm[i] > 0) { result->m_perm[pos] = gIntArray0[m_perm[i]]; result->m_index[result->m_perm[pos]] = pos; } else { result->m_perm[pos] = gIntArray1[-m_perm[i]]; result->m_index[-result->m_perm[pos]] = -pos; } } } else if (f_op.m_type == Operation::TRANSPOSITION) // A B C A -> A C B A { // check for adjacencies if (m_perm[f_op.m_edges[0]-1] + 1 == m_perm[f_op.m_edges[1]]) { adj0 = 1; for (int i = (m_perm[f_op.m_edges[1]] > 0? m_perm[f_op.m_edges[1]] : -m_perm[f_op.m_edges[0]-1]); i <= m_size; i++) { gIntArray0[i]--; gIntArray1[i]++; } result->m_size--; } if (m_perm[f_op.m_edges[2]-1] + 1 == m_perm[f_op.m_edges[0]]) { adj1 = 1; for (int i = (m_perm[f_op.m_edges[0]] > 0? m_perm[f_op.m_edges[0]] : -m_perm[f_op.m_edges[2]-1]); i <= m_size; i++) { gIntArray0[i]--; gIntArray1[i]++; } result->m_size--; } if (f_op.m_edges[2] == m_size) { if (m_perm[f_op.m_edges[1] - 1] == m_size) { adj2 = 1; gIntArray0[m_size]--; gIntArray1[m_size]++; result->m_size--; } } else { if (m_perm[f_op.m_edges[1]-1] + 1 == m_perm[f_op.m_edges[2]]) { adj2 = 1; for (int i = (m_perm[f_op.m_edges[2]] > 0? m_perm[f_op.m_edges[2]] : -m_perm[f_op.m_edges[1]-1]); i <= m_size; i++) { gIntArray0[i]--; gIntArray1[i]++; } result->m_size--; } } // init arrays if (result->m_size == 0) { result->m_size = 1; result->m_perm = new int[1]; result->m_index = new int[2]; result->m_perm[0] = 1; result->m_index[1] = 0; result->calcHash(); result->calcCycles(); return result; } result->m_perm = new int[result->m_size]; result->m_index = new int[result->m_size + 1]; // write first block for (int i = 0; i < f_op.m_edges[0] - adj0; i++) { if (m_perm[i] > 0) { result->m_perm[i] = gIntArray0[m_perm[i]]; result->m_index[result->m_perm[i]] = i; } else { result->m_perm[i] = gIntArray1[-m_perm[i]]; result->m_index[-result->m_perm[i]] = -i; } } // write second block pos = f_op.m_edges[0] - adj0; for (int i = f_op.m_edges[1]; i < f_op.m_edges[2] - adj1; i++, pos++) { if (m_perm[i] > 0) { result->m_perm[pos] = gIntArray0[m_perm[i]]; result->m_index[result->m_perm[pos]] = pos; } else { result->m_perm[pos] = gIntArray1[-m_perm[i]]; result->m_index[-result->m_perm[pos]] = -pos; } } // write third block for (int i = f_op.m_edges[0]; i < f_op.m_edges[1] - adj2; i++, pos++) { if (m_perm[i] > 0) { result->m_perm[pos] = gIntArray0[m_perm[i]]; result->m_index[result->m_perm[pos]] = pos; } else { result->m_perm[pos] = gIntArray1[-m_perm[i]]; result->m_index[-result->m_perm[pos]] = -pos; } } // write last block for (int i = f_op.m_edges[2]; i < m_size; i++, pos++) { if (m_perm[i] > 0) { result->m_perm[pos] = gIntArray0[m_perm[i]]; result->m_index[result->m_perm[pos]] = pos; } else { result->m_perm[pos] = gIntArray1[-m_perm[i]]; result->m_index[-result->m_perm[pos]] = -pos; } } } else if (f_op.m_type == Operation::TRANSREVA) // A B C A -> A C -B A { // check for adjacencies if (m_perm[f_op.m_edges[0]-1] + 1 == m_perm[f_op.m_edges[1]]) { adj0 = 1; for (int i = (m_perm[f_op.m_edges[1]] > 0? m_perm[f_op.m_edges[1]] : -m_perm[f_op.m_edges[0]-1]); i <= m_size; i++) { gIntArray0[i]--; gIntArray1[i]++; } result->m_size--; } if (m_perm[f_op.m_edges[2]-1] + 1 == -m_perm[f_op.m_edges[1]-1]) { adj1 = 1; for (int i = (m_perm[f_op.m_edges[2]-1] > 0? -m_perm[f_op.m_edges[1]-1] : -m_perm[f_op.m_edges[2]-1]); i <= m_size; i++) { gIntArray0[i]--; gIntArray1[i]++; } result->m_size--; } if (f_op.m_edges[2] == m_size) { if (m_perm[f_op.m_edges[0]] == -m_size) { adj2 = 1; gIntArray0[m_size]--; gIntArray1[m_size]++; result->m_size--; } } else { if (-m_perm[f_op.m_edges[0]] + 1 == m_perm[f_op.m_edges[2]]) { adj2 = 1; for (int i = (m_perm[f_op.m_edges[2]] > 0? m_perm[f_op.m_edges[2]] : m_perm[f_op.m_edges[0]]); i <= m_size; i++) { gIntArray0[i]--; gIntArray1[i]++; } result->m_size--; } } // init arrays if (result->m_size == 0) { result->m_size = 1; result->m_perm = new int[1]; result->m_index = new int[2]; result->m_perm[0] = 1; result->m_index[1] = 0; result->calcHash(); result->calcCycles(); return result; } result->m_perm = new int[result->m_size]; result->m_index = new int[result->m_size + 1]; // write first block for (int i = 0; i < f_op.m_edges[0] - adj0; i++) { if (m_perm[i] > 0) { result->m_perm[i] = gIntArray0[m_perm[i]]; result->m_index[result->m_perm[i]] = i; } else { result->m_perm[i] = gIntArray1[-m_perm[i]]; result->m_index[-result->m_perm[i]] = -i; } } // write second block pos = f_op.m_edges[0] - adj0; for (int i = f_op.m_edges[1]; i < f_op.m_edges[2] - adj1; i++, pos++) { if (m_perm[i] > 0) { result->m_perm[pos] = gIntArray0[m_perm[i]]; result->m_index[result->m_perm[pos]] = pos; } else { result->m_perm[pos] = gIntArray1[-m_perm[i]]; result->m_index[-result->m_perm[pos]] = -pos; } } // write third block for (int i = f_op.m_edges[1]-1; i >= f_op.m_edges[0] + adj2; i--, pos++) { if (m_perm[i] > 0) { result->m_perm[pos] = gIntArray1[m_perm[i]]; result->m_index[-result->m_perm[pos]] = -pos; } else { result->m_perm[pos] = gIntArray0[-m_perm[i]]; result->m_index[result->m_perm[pos]] = pos; } } // write last block for (int i = f_op.m_edges[2]; i < m_size; i++, pos++) { if (m_perm[i] > 0) { result->m_perm[pos] = gIntArray0[m_perm[i]]; result->m_index[result->m_perm[pos]] = pos; } else { result->m_perm[pos] = gIntArray1[-m_perm[i]]; result->m_index[-result->m_perm[pos]] = -pos; } } } else if (f_op.m_type == Operation::TRANSREVB) // A B C A -> A -C B A { // check for adjacencies if (m_perm[f_op.m_edges[0]-1] + 1 == -m_perm[f_op.m_edges[2]-1]) { adj0 = 1; for (int i = (m_perm[f_op.m_edges[0]-1] > 0? -m_perm[f_op.m_edges[2]-1] : -m_perm[f_op.m_edges[0]-1]); i <= m_size; i++) { gIntArray0[i]--; gIntArray1[i]++; } result->m_size--; } if (-m_perm[f_op.m_edges[1]] + 1 == m_perm[f_op.m_edges[0]]) { adj1 = 1; for (int i = (m_perm[f_op.m_edges[0]] > 0? m_perm[f_op.m_edges[0]] : m_perm[f_op.m_edges[1]]); i <= m_size; i++) { gIntArray0[i]--; gIntArray1[i]++; } result->m_size--; } if (f_op.m_edges[2] == m_size) { if (m_perm[f_op.m_edges[1] - 1] == m_size) { adj2 = 1; gIntArray0[m_size]--; gIntArray1[m_size]++; result->m_size--; } } else { if (m_perm[f_op.m_edges[1]-1] + 1 == m_perm[f_op.m_edges[2]]) { adj2 = 1; for (int i = (m_perm[f_op.m_edges[2]] > 0? m_perm[f_op.m_edges[2]] : -m_perm[f_op.m_edges[1]-1]); i <= m_size; i++) { gIntArray0[i]--; gIntArray1[i]++; } result->m_size--; } } // init arrays if (result->m_size == 0) { result->m_size = 1; result->m_perm = new int[1]; result->m_index = new int[2]; result->m_perm[0] = 1; result->m_index[1] = 0; result->calcHash(); result->calcCycles(); return result; } result->m_perm = new int[result->m_size]; result->m_index = new int[result->m_size + 1]; // write first block for (int i = 0; i < f_op.m_edges[0] - adj0; i++) { if (m_perm[i] > 0) { result->m_perm[i] = gIntArray0[m_perm[i]]; result->m_index[result->m_perm[i]] = i; } else { result->m_perm[i] = gIntArray1[-m_perm[i]]; result->m_index[-result->m_perm[i]] = -i; } } // write second block pos = f_op.m_edges[0] - adj0; for (int i = f_op.m_edges[2]-1; i >= f_op.m_edges[1] + adj1; i--, pos++) { if (m_perm[i] > 0) { result->m_perm[pos] = gIntArray1[m_perm[i]]; result->m_index[-result->m_perm[pos]] = -pos; } else { result->m_perm[pos] = gIntArray0[-m_perm[i]]; result->m_index[result->m_perm[pos]] = pos; } } // write third block for (int i = f_op.m_edges[0]; i < f_op.m_edges[1] - adj2; i++, pos++) { if (m_perm[i] > 0) { result->m_perm[pos] = gIntArray0[m_perm[i]]; result->m_index[result->m_perm[pos]] = pos; } else { result->m_perm[pos] = gIntArray1[-m_perm[i]]; result->m_index[-result->m_perm[pos]] = -pos; } } // write last block for (int i = f_op.m_edges[2]; i < m_size; i++, pos++) { if (m_perm[i] > 0) { result->m_perm[pos] = gIntArray0[m_perm[i]]; result->m_index[result->m_perm[pos]] = pos; } else { result->m_perm[pos] = gIntArray1[-m_perm[i]]; result->m_index[-result->m_perm[pos]] = -pos; } } } else if (f_op.m_type == Operation::REVREV) // A B C A -> A -B -C A { // check for adjacencies if (m_perm[f_op.m_edges[0]-1] + 1 == -m_perm[f_op.m_edges[1]-1]) { adj0 = 1; for (int i = (m_perm[f_op.m_edges[0]-1] > 0? -m_perm[f_op.m_edges[1]-1] : -m_perm[f_op.m_edges[0]-1]); i <= m_size; i++) { gIntArray0[i]--; gIntArray1[i]++; } result->m_size--; } if (m_perm[f_op.m_edges[0]] - 1 == m_perm[f_op.m_edges[2]-1]) { adj1 = 1; for (int i = (m_perm[f_op.m_edges[0]] > 0? m_perm[f_op.m_edges[0]] : -m_perm[f_op.m_edges[2]-1]); i <= m_size; i++) { gIntArray0[i]--; gIntArray1[i]++; } result->m_size--; } if (f_op.m_edges[2] == m_size) { if (m_perm[f_op.m_edges[1]] == -m_size) { adj2 = 1; gIntArray0[m_size]--; gIntArray1[m_size]++; result->m_size--; } } else { if (-m_perm[f_op.m_edges[1]] + 1 == m_perm[f_op.m_edges[2]]) { adj2 = 1; for (int i = (m_perm[f_op.m_edges[2]] > 0? m_perm[f_op.m_edges[2]] : m_perm[f_op.m_edges[1]]); i <= m_size; i++) { gIntArray0[i]--; gIntArray1[i]++; } result->m_size--; } } // init arrays if (result->m_size == 0) { result->m_size = 1; result->m_perm = new int[1]; result->m_index = new int[2]; result->m_perm[0] = 1; result->m_index[1] = 0; result->calcHash(); result->calcCycles(); return result; } result->m_perm = new int[result->m_size]; result->m_index = new int[result->m_size + 1]; // write first block for (int i = 0; i < f_op.m_edges[0] - adj0; i++) { if (m_perm[i] > 0) { result->m_perm[i] = gIntArray0[m_perm[i]]; result->m_index[result->m_perm[i]] = i; } else { result->m_perm[i] = gIntArray1[-m_perm[i]]; result->m_index[-result->m_perm[i]] = -i; } } // write second block pos = f_op.m_edges[0] - adj0; for (int i = f_op.m_edges[1]-1; i >= f_op.m_edges[0] + adj1; i--, pos++) { if (m_perm[i] > 0) { result->m_perm[pos] = gIntArray1[m_perm[i]]; result->m_index[-result->m_perm[pos]] = -pos; } else { result->m_perm[pos] = gIntArray0[-m_perm[i]]; result->m_index[result->m_perm[pos]] = pos; } } // write third block for (int i = f_op.m_edges[2]-1; i >= f_op.m_edges[1] + adj2; i--, pos++) { if (m_perm[i] > 0) { result->m_perm[pos] = gIntArray1[m_perm[i]]; result->m_index[-result->m_perm[pos]] = -pos; } else { result->m_perm[pos] = gIntArray0[-m_perm[i]]; result->m_index[result->m_perm[pos]] = pos; } } // write last block for (int i = f_op.m_edges[2]; i < m_size; i++, pos++) { if (m_perm[i] > 0) { result->m_perm[pos] = gIntArray0[m_perm[i]]; result->m_index[result->m_perm[pos]] = pos; } else { result->m_perm[pos] = gIntArray1[-m_perm[i]]; result->m_index[-result->m_perm[pos]] = -pos; } } } result->calcHash(); result->calcCycles(); return result; } int Permutation::getLowerBound(int f_wr, int f_wt) { return m_ceven * f_wr + ((m_size - m_codd) / 2 - m_ceven) * f_wt; } bool Permutation::operator==(Permutation& f_perm) const { if ((m_hash != f_perm.m_hash) || (m_size != f_perm.m_size)) return false; for (int i = 0; i < m_size; i++) { if (m_perm[i] != f_perm.m_perm[i]) return false; } return true; } /*************************************************************************** * private methods ***************************************************************************/ void Permutation::calcHash() { m_hash = 0; for (int i = 1; i < m_size; i++) { m_hash += m_perm[i]; m_hash *= (m_perm[i] - m_perm[i-1]); } m_hash = abs(m_hash); m_hash %= HASHSIZE; } void Permutation::calcCycles() { int length; // length of the current cycle bool left; // true if we are at the left point of an element int pos; // current position int element; // current element m_codd = 0; m_ceven = 0; for (int i = 0; i < m_size; i++) // use as visited array gIntArray0[i] = 0; for (int i = 0; i < m_size; i++) { if (gIntArray0[i] == 1) // already visited continue; length = 0; left = false; pos = i; while (gIntArray0[pos] == 0) { length++; gIntArray0[pos] = 1; // current element - negativ if we are at its lower point if (left) element = -m_perm[pos]; else element = (pos == 0? m_perm[m_size - 1] : m_perm[pos-1]); // target element - negativ if we want to its lower point element = -element - 1; if (element == 0) element = m_size; else if (element == -(m_size + 1)) element = -1; pos = abs(m_index[abs(element)]); if ((element > 0) ^ (m_perm[pos] > 0)) left = false; else { (pos == m_size - 1? pos = 0 : pos++); left = true; } } if (length & 1) m_codd++; else m_ceven++; } } /*************************************************************************** * static (non-class) methods ***************************************************************************/ void printPermutation(int f_size, int* f_perm) { for (int i = 0; i < f_size; i++) cout << f_perm[i] << " "; cout << endl; } void printOperation(Operation* f_op) { switch (f_op->m_type) { case Operation::REVERSAL: cout << " rev(" << f_op->m_edges[0] << ", " << f_op->m_edges[1] << ") "; break; case Operation::TRANSPOSITION: cout << " t(" << f_op->m_edges[0] << ", " << f_op->m_edges[1] << ", " << f_op->m_edges[2]<< ") "; break; case Operation::TRANSREVA: cout << "tra(" << f_op->m_edges[0] << ", " << f_op->m_edges[1] << ", " << f_op->m_edges[2]<< ") "; break; case Operation::TRANSREVB: cout << "trb(" << f_op->m_edges[0] << ", " << f_op->m_edges[1] << ", " << f_op->m_edges[2]<< ") "; break; case Operation::REVREV: cout << "rr(" << f_op->m_edges[0] << ", " << f_op->m_edges[1] << ", " << f_op->m_edges[2]<< ") "; break; case Operation::INVTRANS: cout << "inv t(" << f_op->m_edges[0] << ", " << f_op->m_edges[1] << ", " << f_op->m_edges[2]<< ") "; break; } } /*************************************************************************** * debugging methods ***************************************************************************/ void Permutation::dump() { cout << "*** dumping Permutation " << this << " ***\n"; cout << "size: " << m_size << endl; cout << "perm:\n"; for (int i = 0; i < m_size; i++) cout << m_perm[i] << " "; cout << "\nm_index:\n"; for (int i = 1; i <= m_size; i++) cout << m_index[i] << " "; cout << "\nhash: " << m_hash << endl; cout << "codd / ceven: " << m_codd << " / " << m_ceven << endl; cout << "***************\n"; } } // end namespace weightedbb phylo-1.0.6/weightedbb/COPYING0000644000175000017500000010451311434510050012726 00000000000000 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef WBB_GLOBALS_H_ #define WBB_GLOBALS_H_ #include namespace weightedbb { #define HASHSIZE 32768 // define console commandos #define CONSOLE_RESET "\033[0m" #define CONSOLE_BOLD "\033[1m" #define CONSOLE_HALFBRIGHT "\033[2m" #define CONSOLE_UNDERSCORE "\033[4m" #define CONSOLE_BLINK "\033[5m" #define CONSOLE_REVERSE "\033[7m" #define CONSOLE_NORMALBRIGHT "\033[22m" #define CONSOLE_UNDERSCROE_OFF "\033[24m" #define CONSOLE_BLINK_OFF "\033[25m" #define CONSOLE_REVERSE_OFF "\033[27m" #define CONSOLE_COLOR_BLACK "\033[30m" #define CONSOLE_COLOR_RED "\033[31m" #define CONSOLE_COLOR_GREEN "\033[32m" #define CONSOLE_COLOR_BROWN "\033[33m" #define CONSOLE_COLOR_BLUE "\033[34m" #define CONSOLE_COLOR_MAGENTA "\033[35m" #define CONSOLE_COLOR_CYAN "\033[36m" #define CONSOLE_COLOR_WHITE "\033[37m" #define CONSOLE_UNDERSCORE_CDEFAULT "\033[38m" #define CONSOLE_UNDERSCORE_OFF_CDEFAULT "\033[39m" #define CONSOLE_BACKGROUND_BLACK "\033[40m" #define CONSOLE_BACKGROUND_RED "\033[41m" #define CONSOLE_BACKGROUND_GREEN "\033[42m" #define CONSOLE_BACKGROUND_BROWN "\033[43m" #define CONSOLE_BACKGROUND_BLUE "\033[44m" #define CONSOLE_BACKGROUND_MAGENTA "\033[45m" #define CONSOLE_BACKGROUND_CYAN "\033[46m" #define CONSOLE_BACKGROUND_WHITE "\033[47m" #define CONSOLE_BACKGROUND_DEFAULT "\033[49m" /** An int array of suifficient size */ extern int* gIntArray0; extern int* gIntArray1; extern int* gIntArray2; extern int* gIntArray3; extern int* gIntArray4; extern int* gIntArray5; extern int* gIntArray6; /** A bool array of suifficient size */ extern bool* gBoolArray0; } // end namespace weightedbb #endif phylo-1.0.6/weightedbb/Makefile.am0000644000175000017500000000111411434510050013720 00000000000000lib_LTLIBRARIES = libweightedbb.la libweightedbb_ladir = $(includedir) libweightedbb_la_SOURCES = globals.cpp permutation.cpp weightedbb.cpp libweightedbb_la_HEADERS = $(libweightedbb_la_SOURCES:%.cpp=%.h) libweightedbb_la_LIBADD = -L../minswrt -lminswrt INCLUDES = -I$(includedir) -I../minswrt libweightedbb_la_LDFLAGS = -version-info 1:1:1 bin_PROGRAMS = weightedbb weightedbb_SOURCES = start.cpp weightedbb_LDADD = libweightedbb.la EXTRA_DIST = $(libweightedbb_la_HEADERS) test.in COPYING README weightedbbextradir = $(datadir)/weightedbb weightedbbextra_DATA = test.in COPYING README phylo-1.0.6/weightedbb/start.cpp0000644000175000017500000000732111434510050013533 00000000000000/** * filename: start.cpp * author: Martin Bader * begin: 11.08.2008 * last change: 23.08.2010 * * Start file for weightedbb. * * Copyright (C) 2008-2010 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include #include #include #include "weightedbb.h" using namespace std; using namespace weightedbb; /** * Reads a permutation from an input file. The array will be written to * f_origin and f_target (which are references of a pointer), and the * permutation size will be returned. * @param f_filename the name of the file * @param f_origin reference of the origin data pointer * @param f_target reference of the target data pointer * @return permutation size */ int readFile(char* f_filename, int*& f_origin, int*& f_target) { ifstream input; // file input stream int size; // permutation size input.open(f_filename); if (!input.is_open()) { cerr << "error while opening the file " << f_filename << endl; return -1; } while (input.peek() == '#') // line is a comment input.ignore(999, '\n'); input >> size; input.ignore(999, '\n'); f_origin = new int[size]; f_target = new int[size]; while (input.peek() == '#') // line is a comment input.ignore(999, '\n'); for (int i = 0; i < size; i++) input >> f_origin[i]; input.ignore(999, '\n'); while (input.peek() == '#') // line is a comment input.ignore(999, '\n'); for (int i = 0; i < size; i++) input >> f_target[i]; input.close(); return size; } /** * The main file. At the moment, only for debugging and testing. * parameter is name of the test file * @param f_argc number of arguments * @param f_argv the arguments * @return the exit code */ int main(int f_argc, char** f_argv) { WeightedBB weightedbb; // this class contains the algorithm int size; int* origin; int* target; cout << "*****************************************************************\n"; cout << "weightedbb v1.1.1 Copyright (C) 2008-2010 Martin Bader\n"; cout << "This program comes with ABSOLUTELY NO WARRANTY.\n"; cout << "This is free software, and you are welcome to redistribute it\n"; cout << "under certain conditions.\n"; cout << "For details about the licence, read the file gpl.txt\n"; cout << "*****************************************************************\n"; if (f_argc != 5) { cout << "usage: weightedbb testfile wr wt distmode" << endl; cout << " where distmode=0 means transposition distance, distmode=1 means weighted reversal and transposition distance\n"; return 0; } size = readFile(f_argv[1], origin, target); weightedbb.setHeapLimit(250000000 / size); weightedbb.setWeights(atoi(f_argv[2]), atoi(f_argv[3]), atoi(f_argv[4])); weightedbb.setPermutations(size, origin, target); weightedbb.sort(); weightedbb.printResult(4); cout << "maximum heap size: " << weightedbb.getHeapMax() << endl; delete[] origin; delete[] target; return 0; } phylo-1.0.6/weightedbb/test.in0000644000175000017500000000017211434510050013176 0000000000000020 -12 -7 16 -10 17 2 13 5 19 18 15 8 -9 11 -14 -20 -4 3 -6 -1 17 2 9 -10 7 -16 -6 8 11 4 20 5 14 -18 13 -15 -12 3 1 19 phylo-1.0.6/weightedbb/globals.cpp0000644000175000017500000000217311434510050014021 00000000000000/** * filename: globals.cpp * author: Martin Bader * begin: 11.08.2008 * last change: 12.08.2008 * * Implementation of globals.h * * Copyright (C) 2008 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "globals.h" namespace weightedbb { int* gIntArray0 = NULL; int* gIntArray1 = NULL; int* gIntArray2 = NULL; int* gIntArray3 = NULL; int* gIntArray4 = NULL; int* gIntArray5 = NULL; int* gIntArray6 = NULL; bool* gBoolArray0 = NULL; } // end namespace weightedbb phylo-1.0.6/reconf0000744000175000017500000000024611434510050010765 00000000000000#run this script whenever configure.in changed libtoolize &&\ aclocal &&\ autoconf &&\ #autoheader &&\ automake -a echo "now say ./configure && make && make install" phylo-1.0.6/config.guess0000755000175000017500000012763711344453613012136 00000000000000#! /bin/sh # Attempt to guess a canonical system name. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, # 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 # Free Software Foundation, Inc. timestamp='2009-12-30' # This file is free software; you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 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I hope that # covers most systems running today. This code pipes the CPU # types through head -n 1, so we only detect the type of CPU 0. 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Ake) contributed MIS and NILE. if test "`(/bin/universe) 2>/dev/null`" = att ; then echo pyramid-pyramid-sysv3 else echo pyramid-pyramid-bsd fi exit ;; NILE*:*:*:dcosx) echo pyramid-pyramid-svr4 exit ;; DRS?6000:unix:4.0:6*) echo sparc-icl-nx6 exit ;; DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*) case `/usr/bin/uname -p` in sparc) echo sparc-icl-nx7; exit ;; esac ;; s390x:SunOS:*:*) echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4H:SunOS:5.*:*) echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*) echo i386-pc-auroraux${UNAME_RELEASE} exit ;; i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*) eval $set_cc_for_build SUN_ARCH="i386" # If there is a compiler, see if it is configured for 64-bit objects. # Note that the Sun cc does not turn __LP64__ into 1 like gcc does. # This test works for both compilers. if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \ (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ grep IS_64BIT_ARCH >/dev/null then SUN_ARCH="x86_64" fi fi echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:6*:*) # According to config.sub, this is the proper way to canonicalize # SunOS6. Hard to guess exactly what SunOS6 will be like, but # it's likely to be more like Solaris than SunOS4. echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:*:*) case "`/usr/bin/arch -k`" in Series*|S4*) UNAME_RELEASE=`uname -v` ;; esac # Japanese Language versions have a version number like `4.1.3-JL'. echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'` exit ;; sun3*:SunOS:*:*) echo m68k-sun-sunos${UNAME_RELEASE} exit ;; sun*:*:4.2BSD:*) UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null` test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3 case "`/bin/arch`" in sun3) echo m68k-sun-sunos${UNAME_RELEASE} ;; sun4) echo sparc-sun-sunos${UNAME_RELEASE} ;; esac exit ;; aushp:SunOS:*:*) echo sparc-auspex-sunos${UNAME_RELEASE} exit ;; # The situation for MiNT is a little confusing. The machine name # can be virtually everything (everything which is not # "atarist" or "atariste" at least should have a processor # > m68000). The system name ranges from "MiNT" over "FreeMiNT" # to the lowercase version "mint" (or "freemint"). Finally # the system name "TOS" denotes a system which is actually not # MiNT. But MiNT is downward compatible to TOS, so this should # be no problem. atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) echo m68k-milan-mint${UNAME_RELEASE} exit ;; hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) echo m68k-hades-mint${UNAME_RELEASE} exit ;; *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) echo m68k-unknown-mint${UNAME_RELEASE} exit ;; m68k:machten:*:*) echo m68k-apple-machten${UNAME_RELEASE} exit ;; powerpc:machten:*:*) echo powerpc-apple-machten${UNAME_RELEASE} exit ;; RISC*:Mach:*:*) echo mips-dec-mach_bsd4.3 exit ;; RISC*:ULTRIX:*:*) echo mips-dec-ultrix${UNAME_RELEASE} exit ;; VAX*:ULTRIX*:*:*) echo vax-dec-ultrix${UNAME_RELEASE} exit ;; 2020:CLIX:*:* | 2430:CLIX:*:*) echo clipper-intergraph-clix${UNAME_RELEASE} exit ;; mips:*:*:UMIPS | mips:*:*:RISCos) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #ifdef __cplusplus #include /* for printf() prototype */ int main (int argc, char *argv[]) { #else int main (argc, argv) int argc; char *argv[]; { #endif #if defined (host_mips) && defined (MIPSEB) #if defined (SYSTYPE_SYSV) printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_SVR4) printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0); #endif #endif exit (-1); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` && SYSTEM_NAME=`$dummy $dummyarg` && { echo "$SYSTEM_NAME"; exit; } echo mips-mips-riscos${UNAME_RELEASE} exit ;; Motorola:PowerMAX_OS:*:*) echo powerpc-motorola-powermax exit ;; Motorola:*:4.3:PL8-*) echo powerpc-harris-powermax exit ;; Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) echo powerpc-harris-powermax exit ;; Night_Hawk:Power_UNIX:*:*) echo powerpc-harris-powerunix exit ;; m88k:CX/UX:7*:*) echo m88k-harris-cxux7 exit ;; m88k:*:4*:R4*) echo m88k-motorola-sysv4 exit ;; m88k:*:3*:R3*) echo m88k-motorola-sysv3 exit ;; AViiON:dgux:*:*) # DG/UX returns AViiON for all architectures UNAME_PROCESSOR=`/usr/bin/uname -p` if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ] then if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \ [ ${TARGET_BINARY_INTERFACE}x = x ] then echo m88k-dg-dgux${UNAME_RELEASE} else echo m88k-dg-dguxbcs${UNAME_RELEASE} fi else echo i586-dg-dgux${UNAME_RELEASE} fi exit ;; M88*:DolphinOS:*:*) # DolphinOS (SVR3) echo m88k-dolphin-sysv3 exit ;; M88*:*:R3*:*) # Delta 88k system running SVR3 echo m88k-motorola-sysv3 exit ;; XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) echo m88k-tektronix-sysv3 exit ;; Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) echo m68k-tektronix-bsd exit ;; *:IRIX*:*:*) echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'` exit ;; ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id exit ;; # Note that: echo "'`uname -s`'" gives 'AIX ' i*86:AIX:*:*) echo i386-ibm-aix exit ;; ia64:AIX:*:*) if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${UNAME_MACHINE}-ibm-aix${IBM_REV} exit ;; *:AIX:2:3) if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include main() { if (!__power_pc()) exit(1); puts("powerpc-ibm-aix3.2.5"); exit(0); } EOF if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` then echo "$SYSTEM_NAME" else echo rs6000-ibm-aix3.2.5 fi elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then echo rs6000-ibm-aix3.2.4 else echo rs6000-ibm-aix3.2 fi exit ;; *:AIX:*:[456]) IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'` if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then IBM_ARCH=rs6000 else IBM_ARCH=powerpc fi if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${IBM_ARCH}-ibm-aix${IBM_REV} exit ;; *:AIX:*:*) echo rs6000-ibm-aix exit ;; ibmrt:4.4BSD:*|romp-ibm:BSD:*) echo romp-ibm-bsd4.4 exit ;; ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to exit ;; # report: romp-ibm BSD 4.3 *:BOSX:*:*) echo rs6000-bull-bosx exit ;; DPX/2?00:B.O.S.:*:*) echo m68k-bull-sysv3 exit ;; 9000/[34]??:4.3bsd:1.*:*) echo m68k-hp-bsd exit ;; hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) echo m68k-hp-bsd4.4 exit ;; 9000/[34678]??:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` case "${UNAME_MACHINE}" in 9000/31? ) HP_ARCH=m68000 ;; 9000/[34]?? ) HP_ARCH=m68k ;; 9000/[678][0-9][0-9]) if [ -x /usr/bin/getconf ]; then sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` case "${sc_cpu_version}" in 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 532) # CPU_PA_RISC2_0 case "${sc_kernel_bits}" in 32) HP_ARCH="hppa2.0n" ;; 64) HP_ARCH="hppa2.0w" ;; '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20 esac ;; esac fi if [ "${HP_ARCH}" = "" ]; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #define _HPUX_SOURCE #include #include int main () { #if defined(_SC_KERNEL_BITS) long bits = sysconf(_SC_KERNEL_BITS); #endif long cpu = sysconf (_SC_CPU_VERSION); switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0"); break; case CPU_PA_RISC1_1: puts ("hppa1.1"); break; case CPU_PA_RISC2_0: #if defined(_SC_KERNEL_BITS) switch (bits) { case 64: puts ("hppa2.0w"); break; case 32: puts ("hppa2.0n"); break; default: puts ("hppa2.0"); break; } break; #else /* !defined(_SC_KERNEL_BITS) */ puts ("hppa2.0"); break; #endif default: puts ("hppa1.0"); break; } exit (0); } EOF (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy` test -z "$HP_ARCH" && HP_ARCH=hppa fi ;; esac if [ ${HP_ARCH} = "hppa2.0w" ] then eval $set_cc_for_build # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler # generating 64-bit code. GNU and HP use different nomenclature: # # $ CC_FOR_BUILD=cc ./config.guess # => hppa2.0w-hp-hpux11.23 # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess # => hppa64-hp-hpux11.23 if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | grep -q __LP64__ then HP_ARCH="hppa2.0w" else HP_ARCH="hppa64" fi fi echo ${HP_ARCH}-hp-hpux${HPUX_REV} exit ;; ia64:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` echo ia64-hp-hpux${HPUX_REV} exit ;; 3050*:HI-UX:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include int main () { long cpu = sysconf (_SC_CPU_VERSION); /* The order matters, because CPU_IS_HP_MC68K erroneously returns true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct results, however. */ if (CPU_IS_PA_RISC (cpu)) { switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; default: puts ("hppa-hitachi-hiuxwe2"); break; } } else if (CPU_IS_HP_MC68K (cpu)) puts ("m68k-hitachi-hiuxwe2"); else puts ("unknown-hitachi-hiuxwe2"); exit (0); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` && { echo "$SYSTEM_NAME"; exit; } echo unknown-hitachi-hiuxwe2 exit ;; 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* ) echo hppa1.1-hp-bsd exit ;; 9000/8??:4.3bsd:*:*) echo hppa1.0-hp-bsd exit ;; *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) echo hppa1.0-hp-mpeix exit ;; hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* ) echo hppa1.1-hp-osf exit ;; hp8??:OSF1:*:*) echo hppa1.0-hp-osf exit ;; i*86:OSF1:*:*) if [ -x /usr/sbin/sysversion ] ; then echo ${UNAME_MACHINE}-unknown-osf1mk else echo ${UNAME_MACHINE}-unknown-osf1 fi exit ;; parisc*:Lites*:*:*) echo hppa1.1-hp-lites exit ;; C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) echo c1-convex-bsd exit ;; C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit ;; C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) echo c34-convex-bsd exit ;; C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) echo c38-convex-bsd exit ;; C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) echo c4-convex-bsd exit ;; CRAY*Y-MP:*:*:*) echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*[A-Z]90:*:*:*) echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ -e 's/\.[^.]*$/.X/' exit ;; CRAY*TS:*:*:*) echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*T3E:*:*:*) echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*SV1:*:*:*) echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; *:UNICOS/mp:*:*) echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; 5000:UNIX_System_V:4.*:*) FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'` echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} exit ;; sparc*:BSD/OS:*:*) echo sparc-unknown-bsdi${UNAME_RELEASE} exit ;; *:BSD/OS:*:*) echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} exit ;; *:FreeBSD:*:*) case ${UNAME_MACHINE} in pc98) echo i386-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; amd64) echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; *) echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; esac exit ;; i*:CYGWIN*:*) echo ${UNAME_MACHINE}-pc-cygwin exit ;; *:MINGW*:*) echo ${UNAME_MACHINE}-pc-mingw32 exit ;; i*:windows32*:*) # uname -m includes "-pc" on this system. echo ${UNAME_MACHINE}-mingw32 exit ;; i*:PW*:*) echo ${UNAME_MACHINE}-pc-pw32 exit ;; *:Interix*:*) case ${UNAME_MACHINE} in x86) echo i586-pc-interix${UNAME_RELEASE} exit ;; authenticamd | genuineintel | EM64T) echo x86_64-unknown-interix${UNAME_RELEASE} exit ;; IA64) echo ia64-unknown-interix${UNAME_RELEASE} exit ;; esac ;; [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) echo i${UNAME_MACHINE}-pc-mks exit ;; 8664:Windows_NT:*) echo x86_64-pc-mks exit ;; i*:Windows_NT*:* | Pentium*:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we # UNAME_MACHINE based on the output of uname instead of i386? echo i586-pc-interix exit ;; i*:UWIN*:*) echo ${UNAME_MACHINE}-pc-uwin exit ;; amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*) echo x86_64-unknown-cygwin exit ;; p*:CYGWIN*:*) echo powerpcle-unknown-cygwin exit ;; prep*:SunOS:5.*:*) echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; *:GNU:*:*) # the GNU system echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'` exit ;; *:GNU/*:*:*) # other systems with GNU libc and userland echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu exit ;; i*86:Minix:*:*) echo ${UNAME_MACHINE}-pc-minix exit ;; alpha:Linux:*:*) case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in EV5) UNAME_MACHINE=alphaev5 ;; EV56) UNAME_MACHINE=alphaev56 ;; PCA56) UNAME_MACHINE=alphapca56 ;; PCA57) UNAME_MACHINE=alphapca56 ;; EV6) UNAME_MACHINE=alphaev6 ;; EV67) UNAME_MACHINE=alphaev67 ;; EV68*) UNAME_MACHINE=alphaev68 ;; esac objdump --private-headers /bin/sh | grep -q ld.so.1 if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} exit ;; arm*:Linux:*:*) eval $set_cc_for_build if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ARM_EABI__ then echo ${UNAME_MACHINE}-unknown-linux-gnu else echo ${UNAME_MACHINE}-unknown-linux-gnueabi fi exit ;; avr32*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; cris:Linux:*:*) echo cris-axis-linux-gnu exit ;; crisv32:Linux:*:*) echo crisv32-axis-linux-gnu exit ;; frv:Linux:*:*) echo frv-unknown-linux-gnu exit ;; i*86:Linux:*:*) LIBC=gnu eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #ifdef __dietlibc__ LIBC=dietlibc #endif EOF eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'` echo "${UNAME_MACHINE}-pc-linux-${LIBC}" exit ;; ia64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; m32r*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; 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*:SINIX-*:*:*) if uname -p 2>/dev/null >/dev/null ; then UNAME_MACHINE=`(uname -p) 2>/dev/null` echo ${UNAME_MACHINE}-sni-sysv4 else echo ns32k-sni-sysv fi exit ;; PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort # says echo i586-unisys-sysv4 exit ;; *:UNIX_System_V:4*:FTX*) # From Gerald Hewes . # How about differentiating between stratus architectures? -djm echo hppa1.1-stratus-sysv4 exit ;; *:*:*:FTX*) # From seanf@swdc.stratus.com. echo i860-stratus-sysv4 exit ;; i*86:VOS:*:*) # From Paul.Green@stratus.com. echo ${UNAME_MACHINE}-stratus-vos exit ;; *:VOS:*:*) # From Paul.Green@stratus.com. echo hppa1.1-stratus-vos exit ;; mc68*:A/UX:*:*) echo m68k-apple-aux${UNAME_RELEASE} exit ;; news*:NEWS-OS:6*:*) echo mips-sony-newsos6 exit ;; R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) if [ -d /usr/nec ]; then echo mips-nec-sysv${UNAME_RELEASE} else echo mips-unknown-sysv${UNAME_RELEASE} fi exit ;; BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. echo powerpc-be-beos exit ;; 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then wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\" AC_CACHE_CHECK([whether a statically linked program can dlopen itself], lt_cv_dlopen_self_static, [dnl _LT_TRY_DLOPEN_SELF( lt_cv_dlopen_self_static=yes, lt_cv_dlopen_self_static=yes, lt_cv_dlopen_self_static=no, lt_cv_dlopen_self_static=cross) ]) fi CPPFLAGS="$save_CPPFLAGS" LDFLAGS="$save_LDFLAGS" LIBS="$save_LIBS" ;; esac case $lt_cv_dlopen_self in yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;; *) enable_dlopen_self=unknown ;; esac case $lt_cv_dlopen_self_static in yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;; *) enable_dlopen_self_static=unknown ;; esac fi _LT_DECL([dlopen_support], [enable_dlopen], [0], [Whether dlopen is supported]) _LT_DECL([dlopen_self], [enable_dlopen_self], [0], [Whether dlopen of programs is supported]) _LT_DECL([dlopen_self_static], [enable_dlopen_self_static], [0], [Whether dlopen of statically linked programs is supported]) ])# LT_SYS_DLOPEN_SELF # Old name: AU_ALIAS([AC_LIBTOOL_DLOPEN_SELF], [LT_SYS_DLOPEN_SELF]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_LIBTOOL_DLOPEN_SELF], []) # _LT_COMPILER_C_O([TAGNAME]) # --------------------------- # Check to see if options -c and -o are simultaneously supported by compiler. # This macro does not hard code the compiler like AC_PROG_CC_C_O. m4_defun([_LT_COMPILER_C_O], [m4_require([_LT_DECL_SED])dnl m4_require([_LT_FILEUTILS_DEFAULTS])dnl m4_require([_LT_TAG_COMPILER])dnl AC_CACHE_CHECK([if $compiler supports -c -o file.$ac_objext], [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)], [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=no $RM -r conftest 2>/dev/null mkdir conftest cd conftest mkdir out echo "$lt_simple_compile_test_code" > conftest.$ac_ext lt_compiler_flag="-o out/conftest2.$ac_objext" # Insert the option either (1) after the last *FLAGS variable, or # (2) before a word containing "conftest.", or (3) at the end. # Note that $ac_compile itself does not contain backslashes and begins # with a dollar sign (not a hyphen), so the echo should work correctly. lt_compile=`echo "$ac_compile" | $SED \ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; 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then lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '` sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra" fi # We used to test for /lib/ld.so.1 and disable shared libraries on # powerpc, because MkLinux only supported shared libraries with the # GNU dynamic linker. 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newsos6) version_type=linux library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes ;; *nto* | *qnx*) version_type=qnx need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes dynamic_linker='ldqnx.so' ;; openbsd*) version_type=sunos sys_lib_dlsearch_path_spec="/usr/lib" need_lib_prefix=no # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs. case $host_os in openbsd3.3 | openbsd3.3.*) need_version=yes ;; *) need_version=no ;; esac library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir' shlibpath_var=LD_LIBRARY_PATH if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then case $host_os in openbsd2.[[89]] | openbsd2.[[89]].*) shlibpath_overrides_runpath=no ;; *) shlibpath_overrides_runpath=yes ;; esac else shlibpath_overrides_runpath=yes fi ;; os2*) libname_spec='$name' shrext_cmds=".dll" need_lib_prefix=no library_names_spec='$libname${shared_ext} $libname.a' dynamic_linker='OS/2 ld.exe' shlibpath_var=LIBPATH ;; osf3* | osf4* | osf5*) version_type=osf need_lib_prefix=no need_version=no soname_spec='${libname}${release}${shared_ext}$major' library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib" sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec" ;; rdos*) dynamic_linker=no ;; solaris*) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes # ldd complains unless libraries are executable postinstall_cmds='chmod +x $lib' ;; sunos4*) version_type=sunos library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix' finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes if test "$with_gnu_ld" = yes; then need_lib_prefix=no fi need_version=yes ;; sysv4 | sysv4.3*) version_type=linux library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH case $host_vendor in sni) shlibpath_overrides_runpath=no need_lib_prefix=no runpath_var=LD_RUN_PATH ;; siemens) need_lib_prefix=no ;; motorola) need_lib_prefix=no need_version=no shlibpath_overrides_runpath=no sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib' ;; esac ;; sysv4*MP*) if test -d /usr/nec ;then version_type=linux library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}' soname_spec='$libname${shared_ext}.$major' shlibpath_var=LD_LIBRARY_PATH fi ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) version_type=freebsd-elf need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes hardcode_into_libs=yes if test "$with_gnu_ld" = yes; then sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib' else sys_lib_search_path_spec='/usr/ccs/lib /usr/lib' case $host_os in sco3.2v5*) sys_lib_search_path_spec="$sys_lib_search_path_spec /lib" ;; esac fi sys_lib_dlsearch_path_spec='/usr/lib' ;; tpf*) # TPF is a cross-target only. Preferred cross-host = GNU/Linux. version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no hardcode_into_libs=yes ;; uts4*) version_type=linux library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' shlibpath_var=LD_LIBRARY_PATH ;; *) dynamic_linker=no ;; esac AC_MSG_RESULT([$dynamic_linker]) test "$dynamic_linker" = no && can_build_shared=no variables_saved_for_relink="PATH $shlibpath_var $runpath_var" if test "$GCC" = yes; then variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH" fi if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec" fi if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec" fi _LT_DECL([], [variables_saved_for_relink], [1], [Variables whose values should be saved in libtool wrapper scripts and restored at link time]) _LT_DECL([], [need_lib_prefix], [0], [Do we need the "lib" prefix for modules?]) _LT_DECL([], [need_version], [0], [Do we need a version for libraries?]) _LT_DECL([], [version_type], [0], [Library versioning type]) _LT_DECL([], [runpath_var], [0], [Shared library runtime path variable]) _LT_DECL([], [shlibpath_var], [0],[Shared library path variable]) _LT_DECL([], [shlibpath_overrides_runpath], [0], [Is shlibpath searched before the hard-coded library search path?]) _LT_DECL([], [libname_spec], [1], [Format of library name prefix]) _LT_DECL([], [library_names_spec], [1], [[List of archive names. First name is the real one, the rest are links. The last name is the one that the linker finds with -lNAME]]) _LT_DECL([], [soname_spec], [1], [[The coded name of the library, if different from the real name]]) _LT_DECL([], [postinstall_cmds], [2], [Command to use after installation of a shared archive]) _LT_DECL([], [postuninstall_cmds], [2], [Command to use after uninstallation of a shared archive]) _LT_DECL([], [finish_cmds], [2], [Commands used to finish a libtool library installation in a directory]) _LT_DECL([], [finish_eval], [1], [[As "finish_cmds", except a single script fragment to be evaled but not shown]]) _LT_DECL([], [hardcode_into_libs], [0], [Whether we should hardcode library paths into libraries]) _LT_DECL([], [sys_lib_search_path_spec], [2], [Compile-time system search path for libraries]) _LT_DECL([], [sys_lib_dlsearch_path_spec], [2], [Run-time system search path for libraries]) ])# _LT_SYS_DYNAMIC_LINKER # _LT_PATH_TOOL_PREFIX(TOOL) # -------------------------- # find a file program which can recognize shared library AC_DEFUN([_LT_PATH_TOOL_PREFIX], [m4_require([_LT_DECL_EGREP])dnl AC_MSG_CHECKING([for $1]) AC_CACHE_VAL(lt_cv_path_MAGIC_CMD, [case $MAGIC_CMD in [[\\/*] | ?:[\\/]*]) lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path. ;; *) lt_save_MAGIC_CMD="$MAGIC_CMD" lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR dnl $ac_dummy forces splitting on constant user-supplied paths. dnl POSIX.2 word splitting is done only on the output of word expansions, dnl not every word. This closes a longstanding sh security hole. ac_dummy="m4_if([$2], , $PATH, [$2])" for ac_dir in $ac_dummy; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. if test -f $ac_dir/$1; then lt_cv_path_MAGIC_CMD="$ac_dir/$1" if test -n "$file_magic_test_file"; then case $deplibs_check_method in "file_magic "*) file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"` MAGIC_CMD="$lt_cv_path_MAGIC_CMD" if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null | $EGREP "$file_magic_regex" > /dev/null; then : else cat <<_LT_EOF 1>&2 *** Warning: the command libtool uses to detect shared libraries, *** $file_magic_cmd, produces output that libtool cannot recognize. *** The result is that libtool may fail to recognize shared libraries *** as such. This will affect the creation of libtool libraries that *** depend on shared libraries, but programs linked with such libtool *** libraries will work regardless of this problem. Nevertheless, you *** may want to report the problem to your system manager and/or to *** bug-libtool@gnu.org _LT_EOF fi ;; esac fi break fi done IFS="$lt_save_ifs" MAGIC_CMD="$lt_save_MAGIC_CMD" ;; esac]) MAGIC_CMD="$lt_cv_path_MAGIC_CMD" if test -n "$MAGIC_CMD"; then AC_MSG_RESULT($MAGIC_CMD) else AC_MSG_RESULT(no) fi _LT_DECL([], [MAGIC_CMD], [0], [Used to examine libraries when file_magic_cmd begins with "file"])dnl ])# _LT_PATH_TOOL_PREFIX # Old name: AU_ALIAS([AC_PATH_TOOL_PREFIX], [_LT_PATH_TOOL_PREFIX]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_PATH_TOOL_PREFIX], []) # _LT_PATH_MAGIC # -------------- # find a file program which can recognize a shared library m4_defun([_LT_PATH_MAGIC], [_LT_PATH_TOOL_PREFIX(${ac_tool_prefix}file, /usr/bin$PATH_SEPARATOR$PATH) if test -z "$lt_cv_path_MAGIC_CMD"; then if test -n "$ac_tool_prefix"; then _LT_PATH_TOOL_PREFIX(file, /usr/bin$PATH_SEPARATOR$PATH) else MAGIC_CMD=: fi fi ])# _LT_PATH_MAGIC # LT_PATH_LD # ---------- # find the pathname to the GNU or non-GNU linker AC_DEFUN([LT_PATH_LD], [AC_REQUIRE([AC_PROG_CC])dnl AC_REQUIRE([AC_CANONICAL_HOST])dnl AC_REQUIRE([AC_CANONICAL_BUILD])dnl m4_require([_LT_DECL_SED])dnl m4_require([_LT_DECL_EGREP])dnl AC_ARG_WITH([gnu-ld], [AS_HELP_STRING([--with-gnu-ld], [assume the C compiler uses GNU ld @<:@default=no@:>@])], [test "$withval" = no || with_gnu_ld=yes], [with_gnu_ld=no])dnl ac_prog=ld if test "$GCC" = yes; then # Check if gcc -print-prog-name=ld gives a path. AC_MSG_CHECKING([for ld used by $CC]) case $host in *-*-mingw*) # gcc leaves a trailing carriage return which upsets mingw ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;; *) ac_prog=`($CC -print-prog-name=ld) 2>&5` ;; esac case $ac_prog in # Accept absolute paths. [[\\/]]* | ?:[[\\/]]*) re_direlt='/[[^/]][[^/]]*/\.\./' # Canonicalize the pathname of ld ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'` while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"` done test -z "$LD" && LD="$ac_prog" ;; "") # If it fails, then pretend we aren't using GCC. ac_prog=ld ;; *) # If it is relative, then search for the first ld in PATH. with_gnu_ld=unknown ;; esac elif test "$with_gnu_ld" = yes; then AC_MSG_CHECKING([for GNU ld]) else AC_MSG_CHECKING([for non-GNU ld]) fi AC_CACHE_VAL(lt_cv_path_LD, [if test -z "$LD"; then lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR for ac_dir in $PATH; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then lt_cv_path_LD="$ac_dir/$ac_prog" # Check to see if the program is GNU ld. 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See mingw*. lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?' lt_cv_file_magic_cmd='$OBJDUMP -f' ;; darwin* | rhapsody*) lt_cv_deplibs_check_method=pass_all ;; freebsd* | dragonfly*) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then case $host_cpu in i*86 ) # Not sure whether the presence of OpenBSD here was a mistake. # Let's accept both of them until this is cleared up. lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[[3-9]]86 (compact )?demand paged shared library' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*` ;; esac else lt_cv_deplibs_check_method=pass_all fi ;; gnu*) lt_cv_deplibs_check_method=pass_all ;; hpux10.20* | hpux11*) lt_cv_file_magic_cmd=/usr/bin/file case $host_cpu in ia64*) lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|ELF-[[0-9]][[0-9]]) shared object file - IA64' lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so ;; hppa*64*) [lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]'] lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl ;; *) lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|PA-RISC[[0-9]].[[0-9]]) shared library' lt_cv_file_magic_test_file=/usr/lib/libc.sl ;; esac ;; interix[[3-9]]*) # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|\.a)$' ;; irix5* | irix6* | nonstopux*) case $LD in *-32|*"-32 ") libmagic=32-bit;; *-n32|*"-n32 ") libmagic=N32;; *-64|*"-64 ") libmagic=64-bit;; *) libmagic=never-match;; esac lt_cv_deplibs_check_method=pass_all ;; # This must be Linux ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) lt_cv_deplibs_check_method=pass_all ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|_pic\.a)$' fi ;; newos6*) lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (executable|dynamic lib)' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=/usr/lib/libnls.so ;; *nto* | *qnx*) lt_cv_deplibs_check_method=pass_all ;; openbsd*) if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|\.so|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$' fi ;; osf3* | osf4* | osf5*) lt_cv_deplibs_check_method=pass_all ;; rdos*) lt_cv_deplibs_check_method=pass_all ;; solaris*) lt_cv_deplibs_check_method=pass_all ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) lt_cv_deplibs_check_method=pass_all ;; sysv4 | sysv4.3*) case $host_vendor in motorola) lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (shared object|dynamic lib) M[[0-9]][[0-9]]* Version [[0-9]]' lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*` ;; ncr) lt_cv_deplibs_check_method=pass_all ;; sequent) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB (shared object|dynamic lib )' ;; sni) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method="file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB dynamic lib" lt_cv_file_magic_test_file=/lib/libc.so ;; siemens) lt_cv_deplibs_check_method=pass_all ;; pc) lt_cv_deplibs_check_method=pass_all ;; esac ;; tpf*) lt_cv_deplibs_check_method=pass_all ;; esac ]) file_magic_cmd=$lt_cv_file_magic_cmd deplibs_check_method=$lt_cv_deplibs_check_method test -z "$deplibs_check_method" && deplibs_check_method=unknown _LT_DECL([], [deplibs_check_method], [1], [Method to check whether dependent libraries are shared objects]) _LT_DECL([], [file_magic_cmd], [1], [Command to use when deplibs_check_method == "file_magic"]) ])# _LT_CHECK_MAGIC_METHOD # LT_PATH_NM # ---------- # find the pathname to a BSD- or MS-compatible name lister AC_DEFUN([LT_PATH_NM], [AC_REQUIRE([AC_PROG_CC])dnl AC_CACHE_CHECK([for BSD- or MS-compatible name lister (nm)], lt_cv_path_NM, [if test -n "$NM"; then # Let the user override the test. lt_cv_path_NM="$NM" else lt_nm_to_check="${ac_tool_prefix}nm" if test -n "$ac_tool_prefix" && test "$build" = "$host"; then lt_nm_to_check="$lt_nm_to_check nm" fi for lt_tmp_nm in $lt_nm_to_check; do lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. tmp_nm="$ac_dir/$lt_tmp_nm" if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then # Check to see if the nm accepts a BSD-compat flag. # Adding the `sed 1q' prevents false positives on HP-UX, which says: # nm: unknown option "B" ignored # Tru64's nm complains that /dev/null is an invalid object file case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in */dev/null* | *'Invalid file or object type'*) lt_cv_path_NM="$tmp_nm -B" break ;; *) case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in */dev/null*) lt_cv_path_NM="$tmp_nm -p" break ;; *) lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but continue # so that we can try to find one that supports BSD flags ;; esac ;; esac fi done IFS="$lt_save_ifs" done : ${lt_cv_path_NM=no} fi]) if test "$lt_cv_path_NM" != "no"; then NM="$lt_cv_path_NM" else # Didn't find any BSD compatible name lister, look for dumpbin. AC_CHECK_TOOLS(DUMPBIN, ["dumpbin -symbols" "link -dump -symbols"], :) AC_SUBST([DUMPBIN]) if test "$DUMPBIN" != ":"; then NM="$DUMPBIN" fi fi test -z "$NM" && NM=nm AC_SUBST([NM]) _LT_DECL([], [NM], [1], [A BSD- or MS-compatible name lister])dnl AC_CACHE_CHECK([the name lister ($NM) interface], [lt_cv_nm_interface], [lt_cv_nm_interface="BSD nm" echo "int some_variable = 0;" > conftest.$ac_ext (eval echo "\"\$as_me:__oline__: $ac_compile\"" >&AS_MESSAGE_LOG_FD) (eval "$ac_compile" 2>conftest.err) cat conftest.err >&AS_MESSAGE_LOG_FD (eval echo "\"\$as_me:__oline__: $NM \\\"conftest.$ac_objext\\\"\"" >&AS_MESSAGE_LOG_FD) (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out) cat conftest.err >&AS_MESSAGE_LOG_FD (eval echo "\"\$as_me:__oline__: output\"" >&AS_MESSAGE_LOG_FD) cat conftest.out >&AS_MESSAGE_LOG_FD if $GREP 'External.*some_variable' conftest.out > /dev/null; then lt_cv_nm_interface="MS dumpbin" fi rm -f conftest*]) ])# LT_PATH_NM # Old names: AU_ALIAS([AM_PROG_NM], [LT_PATH_NM]) AU_ALIAS([AC_PROG_NM], [LT_PATH_NM]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AM_PROG_NM], []) dnl AC_DEFUN([AC_PROG_NM], []) # LT_LIB_M # -------- # check for math library AC_DEFUN([LT_LIB_M], [AC_REQUIRE([AC_CANONICAL_HOST])dnl LIBM= case $host in *-*-beos* | *-*-cygwin* | *-*-pw32* | *-*-darwin*) # These system don't have libm, or don't need it ;; *-ncr-sysv4.3*) AC_CHECK_LIB(mw, _mwvalidcheckl, LIBM="-lmw") AC_CHECK_LIB(m, cos, LIBM="$LIBM -lm") ;; *) AC_CHECK_LIB(m, cos, LIBM="-lm") ;; esac AC_SUBST([LIBM]) ])# LT_LIB_M # Old name: AU_ALIAS([AC_CHECK_LIBM], [LT_LIB_M]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_CHECK_LIBM], []) # _LT_COMPILER_NO_RTTI([TAGNAME]) # ------------------------------- m4_defun([_LT_COMPILER_NO_RTTI], [m4_require([_LT_TAG_COMPILER])dnl _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)= if test "$GCC" = yes; then _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin' _LT_COMPILER_OPTION([if $compiler supports -fno-rtti -fno-exceptions], lt_cv_prog_compiler_rtti_exceptions, [-fno-rtti -fno-exceptions], [], [_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)="$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1) -fno-rtti -fno-exceptions"]) fi _LT_TAGDECL([no_builtin_flag], [lt_prog_compiler_no_builtin_flag], [1], [Compiler flag to turn off builtin functions]) ])# _LT_COMPILER_NO_RTTI # _LT_CMD_GLOBAL_SYMBOLS # ---------------------- m4_defun([_LT_CMD_GLOBAL_SYMBOLS], [AC_REQUIRE([AC_CANONICAL_HOST])dnl AC_REQUIRE([AC_PROG_CC])dnl AC_REQUIRE([LT_PATH_NM])dnl AC_REQUIRE([LT_PATH_LD])dnl m4_require([_LT_DECL_SED])dnl m4_require([_LT_DECL_EGREP])dnl m4_require([_LT_TAG_COMPILER])dnl # Check for command to grab the raw symbol name followed by C symbol from nm. AC_MSG_CHECKING([command to parse $NM output from $compiler object]) AC_CACHE_VAL([lt_cv_sys_global_symbol_pipe], [ # These are sane defaults that work on at least a few old systems. # [They come from Ultrix. What could be older than Ultrix?!! ;)] # Character class describing NM global symbol codes. symcode='[[BCDEGRST]]' # Regexp to match symbols that can be accessed directly from C. sympat='\([[_A-Za-z]][[_A-Za-z0-9]]*\)' # Define system-specific variables. case $host_os in aix*) symcode='[[BCDT]]' ;; cygwin* | mingw* | pw32* | cegcc*) symcode='[[ABCDGISTW]]' ;; hpux*) if test "$host_cpu" = ia64; then symcode='[[ABCDEGRST]]' fi ;; irix* | nonstopux*) symcode='[[BCDEGRST]]' ;; osf*) symcode='[[BCDEGQRST]]' ;; solaris*) symcode='[[BDRT]]' ;; sco3.2v5*) symcode='[[DT]]' ;; sysv4.2uw2*) symcode='[[DT]]' ;; sysv5* | sco5v6* | unixware* | OpenUNIX*) symcode='[[ABDT]]' ;; sysv4) symcode='[[DFNSTU]]' ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[[ABCDGIRSTW]]' ;; esac # Transform an extracted symbol line into a proper C declaration. # Some systems (esp. on ia64) link data and code symbols differently, # so use this general approach. lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" # Transform an extracted symbol line into symbol name and symbol address lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p'" lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \(lib[[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"lib\2\", (void *) \&\2},/p'" # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # Try without a prefix underscore, then with it. for ac_symprfx in "" "_"; do # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. symxfrm="\\1 $ac_symprfx\\2 \\2" # Write the raw and C identifiers. if test "$lt_cv_nm_interface" = "MS dumpbin"; then # Fake it for dumpbin and say T for any non-static function # and D for any global variable. # Also find C++ and __fastcall symbols from MSVC++, # which start with @ or ?. lt_cv_sys_global_symbol_pipe="$AWK ['"\ " {last_section=section; section=\$ 3};"\ " /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ " \$ 0!~/External *\|/{next};"\ " / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ " {if(hide[section]) next};"\ " {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ " {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ " s[1]~/^[@?]/{print s[1], s[1]; next};"\ " s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ " ' prfx=^$ac_symprfx]" else lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[[ ]]\($symcode$symcode*\)[[ ]][[ ]]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" fi # Check to see that the pipe works correctly. pipe_works=no rm -f conftest* cat > conftest.$ac_ext <<_LT_EOF #ifdef __cplusplus extern "C" { #endif char nm_test_var; void nm_test_func(void); void nm_test_func(void){} #ifdef __cplusplus } #endif int main(){nm_test_var='a';nm_test_func();return(0);} _LT_EOF if AC_TRY_EVAL(ac_compile); then # Now try to grab the symbols. nlist=conftest.nm if AC_TRY_EVAL(NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) && test -s "$nlist"; then # Try sorting and uniquifying the output. if sort "$nlist" | uniq > "$nlist"T; then mv -f "$nlist"T "$nlist" else rm -f "$nlist"T fi # Make sure that we snagged all the symbols we need. if $GREP ' nm_test_var$' "$nlist" >/dev/null; then if $GREP ' nm_test_func$' "$nlist" >/dev/null; then cat <<_LT_EOF > conftest.$ac_ext #ifdef __cplusplus extern "C" { #endif _LT_EOF # Now generate the symbol file. eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' cat <<_LT_EOF >> conftest.$ac_ext /* The mapping between symbol names and symbols. */ const struct { const char *name; void *address; } lt__PROGRAM__LTX_preloaded_symbols[[]] = { { "@PROGRAM@", (void *) 0 }, _LT_EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext cat <<\_LT_EOF >> conftest.$ac_ext {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt__PROGRAM__LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif _LT_EOF # Now try linking the two files. mv conftest.$ac_objext conftstm.$ac_objext lt_save_LIBS="$LIBS" lt_save_CFLAGS="$CFLAGS" LIBS="conftstm.$ac_objext" CFLAGS="$CFLAGS$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)" if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext}; then pipe_works=yes fi LIBS="$lt_save_LIBS" CFLAGS="$lt_save_CFLAGS" else echo "cannot find nm_test_func in $nlist" >&AS_MESSAGE_LOG_FD fi else echo "cannot find nm_test_var in $nlist" >&AS_MESSAGE_LOG_FD fi else echo "cannot run $lt_cv_sys_global_symbol_pipe" >&AS_MESSAGE_LOG_FD fi else echo "$progname: failed program was:" >&AS_MESSAGE_LOG_FD cat conftest.$ac_ext >&5 fi rm -rf conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$pipe_works" = yes; then break else lt_cv_sys_global_symbol_pipe= fi done ]) if test -z "$lt_cv_sys_global_symbol_pipe"; then lt_cv_sys_global_symbol_to_cdecl= fi if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then AC_MSG_RESULT(failed) else AC_MSG_RESULT(ok) fi _LT_DECL([global_symbol_pipe], [lt_cv_sys_global_symbol_pipe], [1], [Take the output of nm and produce a listing of raw symbols and C names]) _LT_DECL([global_symbol_to_cdecl], [lt_cv_sys_global_symbol_to_cdecl], [1], [Transform the output of nm in a proper C declaration]) _LT_DECL([global_symbol_to_c_name_address], [lt_cv_sys_global_symbol_to_c_name_address], [1], [Transform the output of nm in a C name address pair]) _LT_DECL([global_symbol_to_c_name_address_lib_prefix], [lt_cv_sys_global_symbol_to_c_name_address_lib_prefix], [1], [Transform the output of nm in a C name address pair when lib prefix is needed]) ]) # _LT_CMD_GLOBAL_SYMBOLS # _LT_COMPILER_PIC([TAGNAME]) # --------------------------- m4_defun([_LT_COMPILER_PIC], [m4_require([_LT_TAG_COMPILER])dnl _LT_TAGVAR(lt_prog_compiler_wl, $1)= _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)= AC_MSG_CHECKING([for $compiler option to produce PIC]) m4_if([$1], [CXX], [ # C++ specific cases for pic, static, wl, etc. if test "$GXX" = yes; then _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' case $host_os in aix*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; m68k) # FIXME: we need at least 68020 code to build shared libraries, but # adding the `-m68020' flag to GCC prevents building anything better, # like `-m68040'. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' ;; esac ;; beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) # PIC is the default for these OSes. ;; mingw* | cygwin* | os2* | pw32* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). # Although the cygwin gcc ignores -fPIC, still need this for old-style # (--disable-auto-import) libraries m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; darwin* | rhapsody*) # PIC is the default on this platform # Common symbols not allowed in MH_DYLIB files _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common' ;; *djgpp*) # DJGPP does not support shared libraries at all _LT_TAGVAR(lt_prog_compiler_pic, $1)= ;; interix[[3-9]]*) # Interix 3.x gcc -fpic/-fPIC options generate broken code. # Instead, we relocate shared libraries at runtime. ;; sysv4*MP*) if test -d /usr/nec; then _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic fi ;; hpux*) # PIC is the default for 64-bit PA HP-UX, but not for 32-bit # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag # sets the default TLS model and affects inlining. case $host_cpu in hppa*64*) ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac ;; *qnx* | *nto*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac else case $host_os in aix[[4-9]]*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' else _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' fi ;; chorus*) case $cc_basename in cxch68*) # Green Hills C++ Compiler # _LT_TAGVAR(lt_prog_compiler_static, $1)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a" ;; esac ;; dgux*) case $cc_basename in ec++*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' ;; ghcx*) # Green Hills C++ Compiler _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; *) ;; esac ;; freebsd* | dragonfly*) # FreeBSD uses GNU C++ ;; hpux9* | hpux10* | hpux11*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' if test "$host_cpu" != ia64; then _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' fi ;; aCC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' case $host_cpu in hppa*64*|ia64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' ;; esac ;; *) ;; esac ;; interix*) # This is c89, which is MS Visual C++ (no shared libs) # Anyone wants to do a port? ;; irix5* | irix6* | nonstopux*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' # CC pic flag -KPIC is the default. ;; *) ;; esac ;; linux* | k*bsd*-gnu | kopensolaris*-gnu) case $cc_basename in KCC*) # KAI C++ Compiler _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; ecpc* ) # old Intel C++ for x86_64 which still supported -KPIC. _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; icpc* ) # Intel C++, used to be incompatible with GCC. # ICC 10 doesn't accept -KPIC any more. _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; pgCC* | pgcpp*) # Portland Group C++ compiler _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; cxx*) # Compaq C++ # Make sure the PIC flag is empty. It appears that all Alpha # Linux and Compaq Tru64 Unix objects are PIC. _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; xlc* | xlC*) # IBM XL 8.0 on PPC _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink' ;; *) case `$CC -V 2>&1 | sed 5q` in *Sun\ C*) # Sun C++ 5.9 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' ;; esac ;; esac ;; lynxos*) ;; m88k*) ;; mvs*) case $cc_basename in cxx*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-W c,exportall' ;; *) ;; esac ;; netbsd* | netbsdelf*-gnu) ;; *qnx* | *nto*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; osf3* | osf4* | osf5*) case $cc_basename in KCC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' ;; RCC*) # Rational C++ 2.4.1 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; cxx*) # Digital/Compaq C++ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # Make sure the PIC flag is empty. It appears that all Alpha # Linux and Compaq Tru64 Unix objects are PIC. _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; *) ;; esac ;; psos*) ;; solaris*) case $cc_basename in CC*) # Sun C++ 4.2, 5.x and Centerline C++ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' ;; gcx*) # Green Hills C++ Compiler _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC' ;; *) ;; esac ;; sunos4*) case $cc_basename in CC*) # Sun C++ 4.x _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; lcc*) # Lucid _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; *) ;; esac ;; sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; esac ;; tandem*) case $cc_basename in NCC*) # NonStop-UX NCC 3.20 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' ;; *) ;; esac ;; vxworks*) ;; *) _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no ;; esac fi ], [ if test "$GCC" = yes; then _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' case $host_os in aix*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; m68k) # FIXME: we need at least 68020 code to build shared libraries, but # adding the `-m68020' flag to GCC prevents building anything better, # like `-m68040'. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' ;; esac ;; beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) # PIC is the default for these OSes. ;; mingw* | cygwin* | pw32* | os2* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). # Although the cygwin gcc ignores -fPIC, still need this for old-style # (--disable-auto-import) libraries m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; darwin* | rhapsody*) # PIC is the default on this platform # Common symbols not allowed in MH_DYLIB files _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common' ;; hpux*) # PIC is the default for 64-bit PA HP-UX, but not for 32-bit # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag # sets the default TLS model and affects inlining. case $host_cpu in hppa*64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac ;; interix[[3-9]]*) # Interix 3.x gcc -fpic/-fPIC options generate broken code. # Instead, we relocate shared libraries at runtime. ;; msdosdjgpp*) # Just because we use GCC doesn't mean we suddenly get shared libraries # on systems that don't support them. _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no enable_shared=no ;; *nto* | *qnx*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; sysv4*MP*) if test -d /usr/nec; then _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic fi ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac else # PORTME Check for flag to pass linker flags through the system compiler. case $host_os in aix*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' else _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' fi ;; mingw* | cygwin* | pw32* | os2* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; hpux9* | hpux10* | hpux11*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but # not for PA HP-UX. case $host_cpu in hppa*64*|ia64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' ;; esac # Is there a better lt_prog_compiler_static that works with the bundled CC? _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' ;; irix5* | irix6* | nonstopux*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # PIC (with -KPIC) is the default. _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; linux* | k*bsd*-gnu | kopensolaris*-gnu) case $cc_basename in # old Intel for x86_64 which still supported -KPIC. ecc*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; 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netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out else _LT_TAGVAR(archive_cmds, $1)='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF fi _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; newsos6) _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' _LT_TAGVAR(hardcode_libdir_separator, $1)=: _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; *nto* | *qnx*) ;; openbsd*) if test -f /usr/libexec/ld.so; then _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_shlibpath_var, $1)=no _LT_TAGVAR(hardcode_direct_absolute, $1)=yes if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' else case $host_os in openbsd[[01]].* | openbsd2.[[0-7]] | openbsd2.[[0-7]].*) _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' ;; *) _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' ;; esac fi else _LT_TAGVAR(ld_shlibs, $1)=no fi ;; os2*) _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' _LT_TAGVAR(hardcode_minus_L, $1)=yes _LT_TAGVAR(allow_undefined_flag, $1)=unsupported _LT_TAGVAR(archive_cmds, $1)='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' _LT_TAGVAR(old_archive_from_new_cmds, $1)='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; 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do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp' # Both c and cxx compiler support -rpath directly _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir' fi _LT_TAGVAR(archive_cmds_need_lc, $1)='no' _LT_TAGVAR(hardcode_libdir_separator, $1)=: ;; solaris*) _LT_TAGVAR(no_undefined_flag, $1)=' -z defs' if test "$GCC" = yes; then wlarc='${wl}' _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' else case `$CC -V 2>&1` in *"Compilers 5.0"*) wlarc='' _LT_TAGVAR(archive_cmds, $1)='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; 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AC_MSG_CHECKING([whether -lc should be explicitly linked in]) $RM conftest* echo "$lt_simple_compile_test_code" > conftest.$ac_ext if AC_TRY_EVAL(ac_compile) 2>conftest.err; then soname=conftest lib=conftest libobjs=conftest.$ac_objext deplibs= wl=$_LT_TAGVAR(lt_prog_compiler_wl, $1) pic_flag=$_LT_TAGVAR(lt_prog_compiler_pic, $1) compiler_flags=-v linker_flags=-v verstring= output_objdir=. libname=conftest lt_save_allow_undefined_flag=$_LT_TAGVAR(allow_undefined_flag, $1) _LT_TAGVAR(allow_undefined_flag, $1)= if AC_TRY_EVAL(_LT_TAGVAR(archive_cmds, $1) 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1) then _LT_TAGVAR(archive_cmds_need_lc, $1)=no else _LT_TAGVAR(archive_cmds_need_lc, $1)=yes fi _LT_TAGVAR(allow_undefined_flag, $1)=$lt_save_allow_undefined_flag else cat conftest.err 1>&5 fi $RM conftest* AC_MSG_RESULT([$_LT_TAGVAR(archive_cmds_need_lc, $1)]) ;; esac fi ;; esac _LT_TAGDECL([build_libtool_need_lc], [archive_cmds_need_lc], [0], [Whether or not to add -lc for building shared libraries]) _LT_TAGDECL([allow_libtool_libs_with_static_runtimes], [enable_shared_with_static_runtimes], [0], [Whether or not to disallow shared libs when runtime libs are static]) _LT_TAGDECL([], [export_dynamic_flag_spec], [1], [Compiler flag to allow reflexive dlopens]) _LT_TAGDECL([], [whole_archive_flag_spec], [1], [Compiler flag to generate shared objects directly from archives]) _LT_TAGDECL([], [compiler_needs_object], [1], [Whether the compiler copes with passing no objects directly]) _LT_TAGDECL([], [old_archive_from_new_cmds], [2], [Create an old-style archive from a shared archive]) _LT_TAGDECL([], [old_archive_from_expsyms_cmds], [2], [Create a temporary old-style archive to link instead of a shared archive]) _LT_TAGDECL([], [archive_cmds], [2], [Commands used to build a shared archive]) _LT_TAGDECL([], [archive_expsym_cmds], [2]) _LT_TAGDECL([], [module_cmds], [2], [Commands used to build a loadable module if different from building a shared archive.]) _LT_TAGDECL([], [module_expsym_cmds], [2]) _LT_TAGDECL([], [with_gnu_ld], [1], [Whether we are building with GNU ld or not]) _LT_TAGDECL([], [allow_undefined_flag], [1], [Flag that allows shared libraries with undefined symbols to be built]) _LT_TAGDECL([], [no_undefined_flag], [1], [Flag that enforces no undefined symbols]) _LT_TAGDECL([], [hardcode_libdir_flag_spec], [1], [Flag to hardcode $libdir into a binary during linking. 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We just wanted to have am__tar # and am__untar set. test -n "${am_cv_prog_tar_$1}" && break # tar/untar a dummy directory, and stop if the command works rm -rf conftest.dir mkdir conftest.dir echo GrepMe > conftest.dir/file AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar]) rm -rf conftest.dir if test -s conftest.tar; then AM_RUN_LOG([$am__untar /dev/null 2>&1 && break fi done rm -rf conftest.dir AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool]) AC_MSG_RESULT([$am_cv_prog_tar_$1])]) AC_SUBST([am__tar]) AC_SUBST([am__untar]) ]) # _AM_PROG_TAR phylo-1.0.6/median/0000755000175000017500000000000011434510124011102 500000000000000phylo-1.0.6/median/README0000644000175000017500000000415511434510050011705 00000000000000median ====== median is an extension of Caprara's median solver that can calculate a median of three cyclic signed permutations either under the reversal distance or under the weighte reversal and transposition distance. It contains of two parts: 1. the program itself, which is compiled into a library. 2. a tiny frontend that calls the library. The frontend: Call the program with median infile wr wt distMode exact all where infile contains the three genomes (signed permutations). Each genome consists of a line > genome name and a line containing the signed permuation. wr and wt are the weights for reversals and transpositions. Both must be integer. distMode defines the used distance measure, where 0 is the reversal distance, 1 is the transposition distance, and 2 is the weighted reversal and transposition distance. If exact is set to 1, the pairwise distances will be calculated by an exact branch and bound algorithm (this will guarantee the medians to be true medians, not only approximations), otherwise a faster approximation algorithm is used. If all is set to 1, all medians will be returned, otherwise only one median will be returned. As the algorithm is a branch and bound algorithm that works on a heap, the algorithm will prune the heap when it runs out of memory. Note that there is a risk that an optimal solution gets lost. In this case, a warning message will be displayed. As example, you can call ../../bin/median test.in 1 2 2 0 0 In the momentary form, the program calculates just one median. If one is interested in all medians, this can easily be achieved by editing the main function in median/start.cpp (for details, see there). The library: The functions provided by the library are documented in median.h in the include directory. As example of how to use the library, you can have a look at median/start.cpp. The interesting part is in the main function. Copyright: ========== Copyright (C) 2007/2008 Martin Bader This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions. For details about the licence, read the file COPYING phylo-1.0.6/median/medianPools.cpp0000644000175000017500000000370211434510050014000 00000000000000/** * filename: medianPools.cpp * author: Martin Bader * begin: 25.06.2007 * last change: 01.10.2008 * * Implementation of medianPools.h * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "medianPools.h" #include "solution.h" namespace median { using namespace std; /*************************************************************************** * public methods ***************************************************************************/ SolutionPool::SolutionPool() { m_size = 0; m_solutions.reserve(1024); } SolutionPool::~SolutionPool() { for (unsigned int i = 0; i < m_solutions.size(); i++) delete m_solutions[i]; } void SolutionPool::init(int f_size, bool f_even) { // delete old Solution (if there are any) for (unsigned int i = 0; i < m_solutions.size(); i++) delete m_solutions[i]; m_solutions.clear(); // set the new size m_size = 2 * f_size; m_even = f_even; } Solution* SolutionPool::getSolution() { Solution* result; if (m_solutions.size() > 0) { result = m_solutions[m_solutions.size()-1]; m_solutions.pop_back(); } else result = new Solution(m_size, m_even); return result; } /***************************************************************************/ } // end namespace median phylo-1.0.6/median/median.cpp0000644000175000017500000023161611434510050012772 00000000000000/** * filename: median.cpp * author: Martin Bader * begin: 25.06.2007 * last change: 20.08.2010 * * Implementation of median.h * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "median.h" #include #include #include #include "medianPools.h" #include "minswrt.h" #include "solution.h" namespace median { using namespace std; /*************************************************************************** * public methods ***************************************************************************/ Median::Median() { m_size = 0; m_input = new const int*[3]; m_wr = 1; m_wt = 2; m_distMode = 2; m_upperBound = INT_MAX; m_solutionPool = NULL; m_heap.reserve(4096); m_heapPeak = 0; m_heapMax = 2000000; m_overlooked = INT_MAX - 3; m_boolArray2 = NULL; m_cycle12 = NULL; m_cycle13 = NULL; m_cycle23 = NULL; m_perm = NULL; m_d1 = -1; m_d2 = -1; m_d3 = -1; m_nodeOrder = NULL; m_minswrt.setGreedy(1); #if DEBUG_MEDIAN // init debug vars m_perm1 = NULL; m_perm2 = NULL; m_perm3 = NULL; #endif } Median::~Median() { delete[] m_input; delete m_solutionPool; delete[] m_boolArray2; delete[] m_cycle12; delete[] m_cycle13; delete[] m_cycle23; delete[] m_perm; delete[] m_nodeOrder; #if DEBUG_MEDIAN delete[] m_perm1; delete[] m_perm2; delete[] m_perm3; #endif } void Median::init(int f_size, int f_wr, int f_wt, int f_distMode, bool f_exact, unsigned int f_heapMax, int f_pairwiseHeapMax) { // if there is any old data, clear it if (m_solutionPool != NULL) delete m_solutionPool; if (m_boolArray2 != NULL) delete[] m_boolArray2; if (m_cycle12 != NULL) delete[] m_cycle12; if (m_cycle13 != NULL) delete[] m_cycle13; if (m_cycle23 != NULL) delete[] m_cycle23; if (m_perm != NULL) delete[] m_perm; if (m_nodeOrder != NULL) delete[] m_nodeOrder; m_size = f_size; m_wr = f_wr; m_wt = f_wt; m_distMode = f_distMode; m_exact = f_exact; m_solutionPool = new SolutionPool(); m_solutionPool->init(f_size, (f_distMode > 0)); m_boolArray2 = new bool[f_size * 2]; m_cycle12 = new int[f_size * 2]; m_cycle13 = new int[f_size * 2]; m_cycle23 = new int[f_size * 2]; m_perm = new int[f_size]; m_d1 = -1; m_d2 = -1; m_d3 = -1; m_nodeOrder = new int[f_size * 2]; if (m_distMode == 0) // reversals only { m_revdist.init(f_size); } else if (m_distMode == 1) // transpositions only { m_minswrt.setWeights(f_wt, f_wt); m_minswrt.setPermutationSize(f_size); if (m_exact) { m_weightedbb.setWeights(f_wr, f_wt, 0); m_weightedbb.setHeapLimit(f_pairwiseHeapMax); } } else // weighted r/t distance { m_minswrt.setWeights(f_wr, f_wt); m_minswrt.setPermutationSize(f_size); if (m_exact) m_weightedbb.setWeights(f_wr, f_wt, 1); } m_heapMax = f_heapMax; } int Median::solve(const int* f_perm1, const int* f_perm2, const int* f_perm3, int* f_result, int f_upperBound) { int weight; #if DEBUG_MEDIAN m_numExpansions = 0; #endif weight = solveWithoutClean(f_perm1, f_perm2, f_perm3, f_result, f_upperBound); cleanHeap(); #if DEBUG_MEDIAN cout << m_numExpansions << " expansions calculated\n"; #endif return weight; } int Median::getFirstSolution(const int* f_perm1, const int* f_perm2, const int* f_perm3, int* f_result, int f_upperBound) { return solveWithoutClean(f_perm1, f_perm2, f_perm3, f_result, f_upperBound); } int Median::getNextSolution(int* f_result) { Solution* sol = m_solutionPool->getSolution(); // the actual partial solution int node; // a node in a MBG int resultweight; // weight of the median int bestweight; // best possible weight if (m_heap.size() == 0) // heap empty! should never happen with proper use... { m_d1 = -1; m_d2 = -1; m_d3 = -1; return -1; } bestweight = m_heap[0]->m_lb; // remove heap top element (we already used this solution), heapify m_solutionPool->freeSolution(m_heap[0]); m_heap[0] = m_heap[m_heap.size()-1]; m_heap.pop_back(); heapifyDown(); if ((m_heap.size() == 0) || (m_heap[0]->m_lb > bestweight)) // no more optimal medians { m_d1 = -1; m_d2 = -1; m_d3 = -1; return -1; } // find next solution while (m_heap.size() > 0) { if (m_heap[0]->m_steps == m_size) { if (verifyWeight()) break; } else { if (m_distMode == 0) expandRev(); // includes heapify else expand(); // includes heapify } } if ((m_heap.size() == 0) || (m_heap[0]->m_lb > bestweight)) // no solution within upper bound { m_d1 = -1; m_d2 = -1; m_d3 = -1; return -1; } // the optimal complete solution is now the heap top element // build resulting permutation by following hamiltonian cycle sol = m_heap[0]; f_result[0] = 1; node = 1; for (int i = 1; i < m_size; i++) { node = sol->m_median[node]; if (node & 1) // connected to right point { f_result[i] = -((node + 1) / 2); node--; } else // connected to left point { f_result[i] = (node + 2) / 2; node++; } } if (m_distMode == 0) resultweight = m_wr * sol->m_lb / 2; else resultweight = sol->m_lb / 4; return resultweight; } void Median::getMedianDist(int& f_d1, int& f_d2, int& f_d3) { f_d1 = m_d1; f_d2 = m_d2; f_d3 = m_d3; } void Median::cleanHeap() { // clean up the heap for (unsigned int i = 0; i < m_heap.size(); i++) m_solutionPool->freeSolution(m_heap[i]); m_heap.clear(); } int Median::getLeastCutoff() { if (m_distMode == 0) return (m_overlooked + 1) / 2; else return (m_overlooked + 3) / 4; } int Median::pairDist(const int* f_perm0, const int* f_perm1, int f_mode) { int lb; int dist0 = 0; // forward distance int dist1 = 0; // reverse distance const vector* sorting; // sorting sequence if (m_distMode == 0) return m_revdist.getDistance(f_perm0, f_perm1); else { m_minswrt.setTarget(f_perm1); m_minswrt.setOrigin(f_perm0); lb = (int)(m_minswrt.getLowerBound() + 0.01f); if (f_mode == 1) return lb; m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int i = 0; i < sorting->size(); i++) dist0 += ((*sorting)[i].m_type == minswrt::Operation::OPERATION_REVERSAL? m_wr : m_wt); if (dist0 > lb) { m_minswrt.setTarget(f_perm0); m_minswrt.setOrigin(f_perm1); m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int i = 0; i < sorting->size(); i++) dist1 += ((*sorting)[i].m_type == minswrt::Operation::OPERATION_REVERSAL? m_wr : m_wt); if (dist1 < dist0) dist0 = dist1; } if ((dist0 > lb) && m_exact && (f_mode == 0)) { m_weightedbb.setPermutations(m_size, f_perm0, f_perm1); m_weightedbb.sort(dist0); dist1 = m_weightedbb.getDistance(); if (dist1 < dist0) dist0 = dist1; } return dist0; } } /*************************************************************************** * private methods ***************************************************************************/ int Median::solveWithoutClean(const int* f_perm1, const int* f_perm2, const int* f_perm3, int* f_result, int f_upperBound) { Solution* sol = m_solutionPool->getSolution(); // the actual partial solution int node1, node2; // two nodes in a MBG int resultweight; // weight of the median int d12, d13, d23; // pairwise distances for upper bound int lb; // lower bound for weighted distance const vector* sorting; // sorting sequence // init some members m_input[0] = f_perm1; m_input[1] = f_perm2; m_input[2] = f_perm3; // set the upper bound m_upperBound = f_upperBound; if (m_distMode == 0) { d12 = m_revdist.getDistance(f_perm1, f_perm2); d13 = m_revdist.getDistance(f_perm1, f_perm3); d23 = m_revdist.getDistance(f_perm2, f_perm3); if (d12 + d13 < m_upperBound) m_upperBound = d12 + d13; if (d12 + d23 < m_upperBound) m_upperBound = d12 + d23; if (d13 + d23 < m_upperBound) m_upperBound = d13 + d23; m_upperBound *= 2; } else { m_minswrt.setTarget(f_perm2); m_minswrt.setOrigin(f_perm1); lb = (int)(m_minswrt.getLowerBound() + 0.01f); d12 = 0; m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int i = 0; i < sorting->size(); i++) d12 += ((*sorting)[i].m_type == minswrt::Operation::OPERATION_REVERSAL? m_wr : m_wt); if (d12 > lb) { m_minswrt.setTarget(f_perm1); m_minswrt.setOrigin(f_perm2); lb = 0; m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int i = 0; i < sorting->size(); i++) lb += ((*sorting)[i].m_type == minswrt::Operation::OPERATION_REVERSAL? m_wr : m_wt); if (lb < d12) d12 = lb; } m_minswrt.setTarget(f_perm3); m_minswrt.setOrigin(f_perm1); lb = (int)(m_minswrt.getLowerBound() + 0.01f); d13 = 0; m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int i = 0; i < sorting->size(); i++) d13 += ((*sorting)[i].m_type == minswrt::Operation::OPERATION_REVERSAL? m_wr : m_wt); if (d13 > lb) { m_minswrt.setTarget(f_perm1); m_minswrt.setOrigin(f_perm3); lb = 0; m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int i = 0; i < sorting->size(); i++) lb += ((*sorting)[i].m_type == minswrt::Operation::OPERATION_REVERSAL? m_wr : m_wt); if (lb < d13) d13 = lb; } m_minswrt.setTarget(f_perm3); m_minswrt.setOrigin(f_perm2); lb = (int)(m_minswrt.getLowerBound() + 0.01f); d23 = 0; m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int i = 0; i < sorting->size(); i++) d23 += ((*sorting)[i].m_type == minswrt::Operation::OPERATION_REVERSAL? m_wr : m_wt); if (d23 > lb) { m_minswrt.setTarget(f_perm2); m_minswrt.setOrigin(f_perm3); lb = 0; m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int i = 0; i < sorting->size(); i++) lb += ((*sorting)[i].m_type == minswrt::Operation::OPERATION_REVERSAL? m_wr : m_wt); if (lb < d23) d23 = lb; } if (d12 + d13 < m_upperBound) m_upperBound = d12 + d13; if (d12 + d23 < m_upperBound) m_upperBound = d12 + d23; if (d13 + d23 < m_upperBound) m_upperBound = d13 + d23; m_upperBound *= 4; } // create initial partial solution for (int i = 1; i < m_size; i++) { node1 = (f_perm1[i-1] > 0? 2 * f_perm1[i-1] - 1 : -2 * f_perm1[i-1] - 2); node2 = (f_perm1[i] > 0? 2 * f_perm1[i] - 2 : -2 * f_perm1[i] - 1); sol->m_edges1[node1] = node2; sol->m_edges1[node2] = node1; } node1 = (f_perm1[m_size-1] > 0? 2 * f_perm1[m_size-1] - 1 : -2 * f_perm1[m_size-1] - 2); node2 = (f_perm1[0] > 0? 2 * f_perm1[0] - 2 : -2 * f_perm1[0] - 1); sol->m_edges1[node1] = node2; sol->m_edges1[node2] = node1; for (int i = 1; i < m_size; i++) { node1 = (f_perm2[i-1] > 0? 2 * f_perm2[i-1] - 1 : -2 * f_perm2[i-1] - 2); node2 = (f_perm2[i] > 0? 2 * f_perm2[i] - 2 : -2 * f_perm2[i] - 1); sol->m_edges2[node1] = node2; sol->m_edges2[node2] = node1; } node1 = (f_perm2[m_size-1] > 0? 2 * f_perm2[m_size-1] - 1 : -2 * f_perm2[m_size-1] - 2); node2 = (f_perm2[0] > 0? 2 * f_perm2[0] - 2 : -2 * f_perm2[0] - 1); sol->m_edges2[node1] = node2; sol->m_edges2[node2] = node1; for (int i = 1; i < m_size; i++) { node1 = (f_perm3[i-1] > 0? 2 * f_perm3[i-1] - 1 : -2 * f_perm3[i-1] - 2); node2 = (f_perm3[i] > 0? 2 * f_perm3[i] - 2 : -2 * f_perm3[i] - 1); sol->m_edges3[node1] = node2; sol->m_edges3[node2] = node1; } node1 = (f_perm3[m_size-1] > 0? 2 * f_perm3[m_size-1] - 1 : -2 * f_perm3[m_size-1] - 2); node2 = (f_perm3[0] > 0? 2 * f_perm3[0] - 2 : -2 * f_perm3[0] - 1); sol->m_edges3[node1] = node2; sol->m_edges3[node2] = node1; for (int i = 0; i < 2 * m_size; i++) sol->m_median[i] = -1; // node not yet connected if (m_distMode == 0) { sol->m_steps = 0; calcLowerBoundRev(sol); } else { for (int i = 0; i < 2 * m_size; i++) sol->m_even1[i] = true; for (int i = 0; i < 2 * m_size; i++) sol->m_even2[i] = true; for (int i = 0; i < 2 * m_size; i++) sol->m_even3[i] = true; sol->m_steps = 0; calcLowerBound(sol); } if (m_distMode == 0) createNodeOrderRev(sol); else createNodeOrder(sol); #if DEBUG_MEDIAN m_perm1 = new int[2 * m_size]; for (int i = 0; i < 2 * m_size; i++) m_perm1[i] = sol->m_edges1[i]; m_perm2 = new int[2 * m_size]; for (int i = 0; i < 2 * m_size; i++) m_perm2[i] = sol->m_edges2[i]; m_perm3 = new int[2 * m_size]; for (int i = 0; i < 2 * m_size; i++) m_perm3[i] = sol->m_edges3[i]; #endif m_heap.push_back(sol); m_heapPeak = 1; m_overlooked = INT_MAX - 3; while (m_heap.size() > 0) { if (m_heap[0]->m_steps == m_size) { if (verifyWeight()) break; } else if (m_distMode == 0) expandRev(); else expand(); // includes heapify } if (m_heap.size() == 0) // no solution within upper bound { m_d1 = -1; m_d2 = -1; m_d3 = -1; return -1; } // the optimal complete solution is now the heap top element // build resulting permutation by following hamiltonian cycle sol = m_heap[0]; f_result[0] = 1; node1 = 1; for (int i = 1; i < m_size; i++) { node1 = sol->m_median[node1]; if (node1 & 1) // connected to right point { f_result[i] = -((node1 + 1) / 2); node1--; } else // connected to left point { f_result[i] = (node1 + 2) / 2; node1++; } } if (m_distMode == 0) resultweight = m_wr * sol->m_lb / 2; else resultweight = sol->m_lb / 4; return resultweight; } void Median::calcLowerBound(Solution* f_sol) { unsigned int even = 0; // number of even cycles unsigned int odd = 0; // number of odd cycles int pos; // the actual position bool length; // length of the actual cycle (0: odd, 1: even) // perm1 vs perm2 for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (m_boolArray2[i]) // already visited continue; pos = i; length = true; do { m_boolArray2[pos] = true; pos = f_sol->m_edges1[pos]; m_boolArray2[pos] = true; pos = f_sol->m_edges2[pos]; length = !length; } while (pos != i); length? even++ : odd++; } // perm1 vs perm3 for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (m_boolArray2[i]) // already visited continue; pos = i; length = true; do { m_boolArray2[pos] = true; pos = f_sol->m_edges1[pos]; m_boolArray2[pos] = true; pos = f_sol->m_edges3[pos]; length = !length; } while (pos != i); length? even++ : odd++; } // perm2 vs perm3 for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (m_boolArray2[i]) // already visited continue; pos = i; length = true; do { m_boolArray2[pos] = true; pos = f_sol->m_edges2[pos]; m_boolArray2[pos] = true; pos = f_sol->m_edges3[pos]; length = !length; } while (pos != i); length? even++ : odd++; } f_sol->m_lb = (3 * m_size - odd) * m_wt - (m_wt - m_wr) * 2 * even; } void Median::calcLowerBoundRev(Solution* f_sol) { unsigned int cycles = 0; // number of cycles int pos; // the actual position // perm1 vs perm2 for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (m_boolArray2[i]) // already visited continue; pos = i; do { m_boolArray2[pos] = true; pos = f_sol->m_edges1[pos]; m_boolArray2[pos] = true; pos = f_sol->m_edges2[pos]; } while (pos != i); cycles++; } // perm1 vs perm3 for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (m_boolArray2[i]) // already visited continue; pos = i; do { m_boolArray2[pos] = true; pos = f_sol->m_edges1[pos]; m_boolArray2[pos] = true; pos = f_sol->m_edges3[pos]; } while (pos != i); cycles++; } // perm2 vs perm3 for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (m_boolArray2[i]) // already visited continue; pos = i; do { m_boolArray2[pos] = true; pos = f_sol->m_edges2[pos]; m_boolArray2[pos] = true; pos = f_sol->m_edges3[pos]; } while (pos != i); cycles++; } f_sol->m_lb = 3 * m_size - cycles; } void Median::createNodeOrder(Solution* f_sol) { pair* scores = new pair[2 * m_size]; // array which // contains for each node its score (first) and its index (second) int node1; // first node of a cycle int pos; // a position in a cycle int deltaLb; // change of the lower bound due to an extension (+ fixed bias) int* node2Cycle12 = new int[2 * m_size]; // maps each node to a cycle index between perm1 and perm2 int* node2Cycle13 = new int[2 * m_size]; // maps each node to a cycle index between perm1 and perm3 int* node2Cycle23 = new int[2 * m_size]; // maps each node to a cycle index between perm2 and perm3 int* cyclelength12 = new int[m_size]; // the length of the cycles between perm1 and perm2 int* cyclelength13 = new int[m_size]; // the length of the cycles between perm1 and perm3 int* cyclelength23 = new int[m_size]; // the length of the cycles between perm2 and perm3 // init some data for (int i = 0; i < 2 * m_size; ++i) { scores[i].first = 0; scores[i].second = i; m_cycle12[i] = 0; m_cycle13[i] = 0; m_cycle23[i] = 0; } // precalculate cycle information // find cycles between perm1 and perm2 node1 = 0; for (int i = 0; true; ++i) { while ((node1 < 2 * m_size) && (m_cycle12[node1] != 0)) node1++; if (node1 == 2 * m_size) break; pos = node1; do { m_cycle12[f_sol->m_edges1[pos]] = m_cycle12[pos] + 1; pos = f_sol->m_edges1[pos]; node2Cycle12[pos] = i; m_cycle12[f_sol->m_edges2[pos]] = m_cycle12[pos] + 1; pos = f_sol->m_edges2[pos]; node2Cycle12[pos] = i; } while (pos != node1); cyclelength12[i] = m_cycle12[pos]; } // find cycles between perm1 and perm3 node1 = 0; for (int i = 0; true; ++i) { while ((node1 < 2 * m_size) && (m_cycle13[node1] != 0)) node1++; if (node1 == 2 * m_size) break; pos = node1; do { m_cycle13[f_sol->m_edges1[pos]] = m_cycle13[pos] + 1; pos = f_sol->m_edges1[pos]; node2Cycle13[pos] = i; m_cycle13[f_sol->m_edges3[pos]] = m_cycle13[pos] + 1; pos = f_sol->m_edges3[pos]; node2Cycle13[pos] = i; } while (pos != node1); cyclelength13[i] = m_cycle13[pos]; } // find cycles between perm2 and perm3 node1 = 0; for (int i = 0; true; ++i) { while ((node1 < 2 * m_size) && (m_cycle23[node1] != 0)) node1++; if (node1 == 2 * m_size) break; pos = node1; do { m_cycle23[f_sol->m_edges2[pos]] = m_cycle23[pos] + 1; pos = f_sol->m_edges2[pos]; node2Cycle23[pos] = i; m_cycle23[f_sol->m_edges3[pos]] = m_cycle23[pos] + 1; pos = f_sol->m_edges3[pos]; node2Cycle23[pos] = i; } while (pos != node1); cyclelength23[i] = m_cycle23[pos]; } // calculate the scores; the score of a node is the sum of the lower bounds of its extensions // -> calculate the score of all extensions for (node1 = 0; node1 < 2 * m_size; ++node1) { // check scores for expansion node1 - i for (int i = node1 + 1; i < m_size * 2; (m_distMode == 1? i += 2 : i++)) { if ((node1 ^ i) == 1) // short cycle -> not a permutation matching continue; deltaLb = 0; // do not add the basic change for step +=1, node -= 1, as its always the same // edges parallel to contracted edge if (f_sol->m_edges1[node1] == i) deltaLb -= 2 * m_wt; if (f_sol->m_edges2[node1] == i) deltaLb -= 2 * m_wt; if (f_sol->m_edges3[node1] == i) deltaLb -= 2 * m_wt; // pairwise distances: perm1 vs perm2 if ((f_sol->m_edges1[node1] == i) && (f_sol->m_edges2[node1] == i)) // both edges parallel to m deltaLb += m_wt; else if (f_sol->m_edges1[node1] == i) // one edge (1) parallel to m { if (!f_sol->m_even1[node1]) // else no change in lb deltaLb += (cyclelength12[node2Cycle12[node1]] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); } else if (f_sol->m_edges2[node1] == i) // one edge (2) parallel to m { if (!f_sol->m_even2[node1]) // else no change in lb deltaLb += (cyclelength12[node2Cycle12[node1]] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); } else if (node2Cycle12[i] != node2Cycle12[node1]) // merge cycles { if (cyclelength12[node2Cycle12[node1]] & 2) deltaLb += m_wt; else if (cyclelength12[node2Cycle12[i]] & 2) deltaLb += m_wt; else deltaLb += 3 * m_wt - 4 * m_wr; } else if ((m_cycle12[node1] - m_cycle12[i]) % 2 == 0) // cycle changes sign deltaLb += (cyclelength12[node2Cycle12[node1]] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); else if (!(cyclelength12[node2Cycle12[node1]] & 2) || (!(abs(m_cycle12[i] - m_cycle12[node1]) & 2))) deltaLb -= m_wt; // split in two cycles else deltaLb += 4 * m_wr - 3 * m_wt; // split in two cycles // pairwise distances: perm1 vs perm3 if ((f_sol->m_edges1[node1] == i) && (f_sol->m_edges3[node1] == i)) // both edges parallel to m deltaLb += m_wt; else if (f_sol->m_edges1[node1] == i) // one edge (1) parallel to m { if (!f_sol->m_even1[node1]) // else no change in lb deltaLb += (cyclelength13[node2Cycle13[node1]] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); } else if (f_sol->m_edges3[node1] == i) // one edge (3) parallel to m { if (!f_sol->m_even3[node1]) // else no change in lb deltaLb += (cyclelength13[node2Cycle13[node1]] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); } else if (node2Cycle13[i] != node2Cycle13[node1]) // merge cycles { if (cyclelength13[node2Cycle13[node1]] & 2) deltaLb += m_wt; else if (cyclelength13[node2Cycle13[i]] & 2) deltaLb += m_wt; else deltaLb += 3 * m_wt - 4 * m_wr; } else if ((m_cycle13[node1] - m_cycle13[i]) % 2 == 0) // cycle changes sign deltaLb += (cyclelength13[node2Cycle13[node1]] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); else if (!(cyclelength13[node2Cycle13[node1]] & 2) || (!(abs(m_cycle13[i] - m_cycle13[node1]) & 2))) deltaLb -= m_wt; // split in two cycles else deltaLb += 4 * m_wr - 3 * m_wt; // split in two cycles // pairwise distances: perm2 vs perm3 if ((f_sol->m_edges2[node1] == i) && (f_sol->m_edges3[node1] == i)) // both edges parallel to m deltaLb += m_wt; else if (f_sol->m_edges2[node1] == i) // one edge (2) parallel to m { if (!f_sol->m_even2[node1]) // else no change in lb deltaLb += (cyclelength23[node2Cycle23[node1]] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); } else if (f_sol->m_edges3[node1] == i) // one edge (3) parallel to m { if (!f_sol->m_even3[node1]) // else no change in lb deltaLb += (cyclelength23[node2Cycle23[node1]] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); } else if (node2Cycle23[i] != node2Cycle23[node1]) // merge cycles { if (cyclelength23[node2Cycle23[node1]] & 2) deltaLb += m_wt; else if (cyclelength23[node2Cycle23[i]] & 2) deltaLb += m_wt; else deltaLb += 3 * m_wt - 4 * m_wr; } else if ((m_cycle23[node1] - m_cycle23[i]) % 2 == 0) // cycle changes sign deltaLb += (cyclelength23[node2Cycle23[node1]] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); else if (!(cyclelength23[node2Cycle23[node1]] & 2) || (!(abs(m_cycle23[i] - m_cycle23[node1]) & 2))) deltaLb -= m_wt; // split in two cycles else deltaLb += 4 * m_wr - 3 * m_wt; // split in two cycles // add to the two score entries scores[node1].first += deltaLb; scores[i].first += deltaLb; } } // sort the scores sort(scores, &(scores[2 * m_size])); // inverse copy the result for (int i = 0; i < 2 * m_size; ++i) m_nodeOrder[i] = scores[2 * m_size - 1 - i].second; // clean up delete[] scores; delete[] node2Cycle12; delete[] node2Cycle13; delete[] node2Cycle23; delete[] cyclelength12; delete[] cyclelength13; delete[] cyclelength23; } void Median::createNodeOrderRev(Solution* f_sol) { pair* scores = new pair[2 * m_size]; // array which // contains for each node its score (first) and its index (second) int node1; // first node of a cycle int pos; // a position in a cycle int deltaLb; // change of the lower bound due to an extension (+ fixed bias) int* node2Cycle12 = new int[2 * m_size]; // maps each node to a cycle index between perm1 and perm2 int* node2Cycle13 = new int[2 * m_size]; // maps each node to a cycle index between perm1 and perm3 int* node2Cycle23 = new int[2 * m_size]; // maps each node to a cycle index between perm2 and perm3 // init some data for (int i = 0; i < 2 * m_size; ++i) { scores[i].first = 0; scores[i].second = i; m_cycle12[i] = 0; m_cycle13[i] = 0; m_cycle23[i] = 0; } // precalculate cycle information // find cycles between perm1 and perm2 node1 = 0; for (int i = 0; true; ++i) { while ((node1 < 2 * m_size) && (m_cycle12[node1] != 0)) node1++; if (node1 == 2 * m_size) break; pos = node1; do { m_cycle12[f_sol->m_edges1[pos]] = m_cycle12[pos] + 1; pos = f_sol->m_edges1[pos]; node2Cycle12[pos] = i; m_cycle12[f_sol->m_edges2[pos]] = m_cycle12[pos] + 1; pos = f_sol->m_edges2[pos]; node2Cycle12[pos] = i; } while (pos != node1); } // find cycles between perm1 and perm3 node1 = 0; for (int i = 0; true; ++i) { while ((node1 < 2 * m_size) && (m_cycle13[node1] != 0)) node1++; if (node1 == 2 * m_size) break; pos = node1; do { m_cycle13[f_sol->m_edges1[pos]] = m_cycle13[pos] + 1; pos = f_sol->m_edges1[pos]; node2Cycle13[pos] = i; m_cycle13[f_sol->m_edges3[pos]] = m_cycle13[pos] + 1; pos = f_sol->m_edges3[pos]; node2Cycle13[pos] = i; } while (pos != node1); } // find cycles between perm2 and perm3 node1 = 0; for (int i = 0; true; ++i) { while ((node1 < 2 * m_size) && (m_cycle23[node1] != 0)) node1++; if (node1 == 2 * m_size) break; pos = node1; do { m_cycle23[f_sol->m_edges2[pos]] = m_cycle23[pos] + 1; pos = f_sol->m_edges2[pos]; node2Cycle23[pos] = i; m_cycle23[f_sol->m_edges3[pos]] = m_cycle23[pos] + 1; pos = f_sol->m_edges3[pos]; node2Cycle23[pos] = i; } while (pos != node1); } // calculate the scores; the score of a node is the sum of the lower bounds of its extensions // -> calculate the score of all extensions for (node1 = 0; node1 < 2 * m_size; ++node1) { // check scores for expansion node1 - i for (int i = node1 + 1; i < m_size * 2; (m_distMode == 1? i += 2 : i++)) { if ((node1 ^ i) == 1) // short cycle -> not a permutation matching continue; deltaLb = 0; // do not add the basic change for step +=1, node -= 1, as its always the same // edges parallel to contracted edge if (f_sol->m_edges1[node1] == i) deltaLb -= 2; if (f_sol->m_edges2[node1] == i) deltaLb -= 2; if (f_sol->m_edges3[node1] == i) deltaLb -= 2; // pairwise distances: perm1 vs perm2 if ((f_sol->m_edges1[node1] == i) && (f_sol->m_edges2[node1] == i)) // both edges parallel to m deltaLb += 1; else if ((f_sol->m_edges1[node1] == i) || (f_sol->m_edges2[node1] == i)); // one edge parallel to m -> no change in score else if (node2Cycle12[i] != node2Cycle12[node1]) // merge cycles deltaLb += 1; else if ((m_cycle12[node1] - m_cycle12[i]) % 2 != 0) // split in two cycles deltaLb -= 1; // pairwise distances: perm1 vs perm3 if ((f_sol->m_edges1[node1] == i) && (f_sol->m_edges3[node1] == i)) // both edges parallel to m deltaLb += 1; else if ((f_sol->m_edges1[node1] == i) || (f_sol->m_edges3[node1] == i)); // one edge parallel to m -> no change in score else if (node2Cycle13[i] != node2Cycle13[node1]) // merge cycles deltaLb += 1; else if ((m_cycle13[node1] - m_cycle13[i]) % 2 != 0) // split in two cycles deltaLb -= 1; // pairwise distances: perm2 vs perm3 if ((f_sol->m_edges2[node1] == i) && (f_sol->m_edges3[node1] == i)) // both edges parallel to m deltaLb += 1; else if ((f_sol->m_edges1[node1] == i) || (f_sol->m_edges2[node1] == i)); // one edge parallel to m -> no change in score else if (node2Cycle23[i] != node2Cycle23[node1]) // merge cycles deltaLb += 1; else if ((m_cycle23[node1] - m_cycle23[i]) % 2 != 0) // split in two cycles deltaLb -= 1; // add to the two score entries scores[node1].first += deltaLb; scores[i].first += deltaLb; } } // sort the scores sort(scores, &(scores[2 * m_size])); // inverse copy the result for (int i = 0; i < 2 * m_size; ++i) m_nodeOrder[i] = scores[2 * m_size - 1 - i].second; // clean up delete[] scores; delete[] node2Cycle12; delete[] node2Cycle13; delete[] node2Cycle23; } void Median::expand() { Solution* exp = m_heap[0]; // solution to expand int node1; // node to expand int nodeA, nodeB; // neighbors of contracted edge Solution* sol; // a new solution int pos; // position in the cycle bool length; // length of a cycle (0: odd, 1: even) bool down = true; // use a heapify downwards for the first expansion #if DEBUG_MEDIAN m_numExpansions++; #endif // find node for expanding node1 = exp->m_steps; // previous nodes are always expanded while (exp->m_median[m_nodeOrder[node1]] != -1) node1++; node1 = m_nodeOrder[node1]; // for the score calculation, we need the cycles of the pairwise comparison // that include node1. Nodes set to 0 are not in the cycle pos = node1; // genome 1 vs genome 2 for (int i = 0; i < m_size * 2; i++) m_cycle12[i] = 0; do { m_cycle12[exp->m_edges1[pos]]= (exp->m_even1[pos]? m_cycle12[pos] + 1 : m_cycle12[pos] + 3); pos = exp->m_edges1[pos]; m_cycle12[exp->m_edges2[pos]]= (exp->m_even2[pos]? m_cycle12[pos] + 1 : m_cycle12[pos] + 3); pos = exp->m_edges2[pos]; } while (pos != node1); // genome 1 vs genome 3 for (int i = 0; i < m_size * 2; i++) m_cycle13[i] = 0; do { m_cycle13[exp->m_edges1[pos]]= (exp->m_even1[pos]? m_cycle13[pos] + 1 : m_cycle13[pos] + 3); pos = exp->m_edges1[pos]; m_cycle13[exp->m_edges3[pos]]= (exp->m_even3[pos]? m_cycle13[pos] + 1 : m_cycle13[pos] + 3); pos = exp->m_edges3[pos]; } while (pos != node1); // genome 2 vs genome 3 for (int i = 0; i < m_size * 2; i++) m_cycle23[i] = 0; do { m_cycle23[exp->m_edges2[pos]]= (exp->m_even2[pos]? m_cycle23[pos] + 1 : m_cycle23[pos] + 3); pos = exp->m_edges2[pos]; m_cycle23[exp->m_edges3[pos]]= (exp->m_even3[pos]? m_cycle23[pos] + 1 : m_cycle23[pos] + 3); pos = exp->m_edges3[pos]; } while (pos != node1); // try all possible expansions for (int i = (m_distMode == 1? 1 - (node1 & 1) : 0); i < 2 * m_size; (m_distMode == 1? i += 2 : ++i)) { if (i == node1) continue; if (exp->m_median[i] != -1) // node already used continue; if (shortCycle(exp->m_median, node1, i)) // not a permutation matching continue; // create new partial solution sol = m_solutionPool->getSolution(); for (int j = 0; j < 2 * m_size; j++) sol->m_edges1[j] = exp->m_edges1[j]; for (int j = 0; j < 2 * m_size; j++) sol->m_edges2[j] = exp->m_edges2[j]; for (int j = 0; j < 2 * m_size; j++) sol->m_edges3[j] = exp->m_edges3[j]; for (int j = 0; j < 2 * m_size; j++) sol->m_median[j] = exp->m_median[j]; for (int j = 0; j < 2 * m_size; j++) sol->m_even1[j] = exp->m_even1[j]; for (int j = 0; j < 2 * m_size; j++) sol->m_even2[j] = exp->m_even2[j]; for (int j = 0; j < 2 * m_size; j++) sol->m_even3[j] = exp->m_even3[j]; // contract edge sol->m_median[node1] = i; sol->m_median[i] = node1; nodeA = sol->m_edges1[node1]; nodeB = sol->m_edges1[i]; sol->m_edges1[nodeA] = nodeB; sol->m_edges1[nodeB] = nodeA; sol->m_even1[nodeA] ^= sol->m_even1[nodeB]; sol->m_even1[nodeB] = sol->m_even1[nodeA]; nodeA = sol->m_edges2[node1]; nodeB = sol->m_edges2[i]; sol->m_edges2[nodeA] = nodeB; sol->m_edges2[nodeB] = nodeA; sol->m_even2[nodeA] ^= sol->m_even2[nodeB]; sol->m_even2[nodeB] = sol->m_even2[nodeA]; nodeA = sol->m_edges3[node1]; nodeB = sol->m_edges3[i]; sol->m_edges3[nodeA] = nodeB; sol->m_edges3[nodeB] = nodeA; sol->m_even3[nodeA] ^= sol->m_even3[nodeB]; sol->m_even3[nodeB] = sol->m_even3[nodeA]; sol->m_steps = exp->m_steps + 1; // update the score: // step += 1, n -= 1 sol->m_lb = exp->m_lb + 3 * m_wt; // edges parallel to contracted edge if (exp->m_edges1[node1] == i) sol->m_lb -= (exp->m_even1[node1]? 2 * m_wt : 4 * (m_wt - m_wr)); if (exp->m_edges2[node1] == i) sol->m_lb -= (exp->m_even2[node1]? 2 * m_wt : 4 * (m_wt - m_wr)); if (exp->m_edges3[node1] == i) sol->m_lb -= (exp->m_even3[node1]? 2 * m_wt : 4 * (m_wt - m_wr)); // pairwise distances: perm1 vs perm2 if ((exp->m_edges1[node1] == i) && (exp->m_edges2[node1] == i)) // both edges parallel to m sol->m_lb += (exp->m_even1[node1] == exp->m_even2[node1]? m_wt : 2 * (m_wt - m_wr)); else if (exp->m_edges1[node1] == i) // one edge (1) parallel to m { if (!exp->m_even1[node1]) // else no change in lb sol->m_lb += (m_cycle12[node1] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); } else if (exp->m_edges2[node1] == i) // one edge (2) parallel to m { if (!exp->m_even2[node1]) // else no change in lb sol->m_lb += (m_cycle12[node1] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); } else if (m_cycle12[i] == 0) // merge cycles { if (m_cycle12[node1] & 2) sol->m_lb += m_wt; else // get length of second cycle { length = true; pos = i; do { if (!exp->m_even1[pos]) length = !length; pos = exp->m_edges1[pos]; if (exp->m_even2[pos]) length = !length; pos = exp->m_edges2[pos]; } while (pos != i); sol->m_lb += (length? 3 * m_wt - 4 * m_wr : m_wt); } } else if (m_cycle12[exp->m_edges2[i]] < m_cycle12[exp->m_edges1[i]]) // cycle changes sign sol->m_lb += (m_cycle12[node1] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); else if ((!(m_cycle12[node1] & 2)) || (!(m_cycle12[i] & 2))) // split in two cycles sol->m_lb -= m_wt; else sol->m_lb += 4 * m_wr - 3 * m_wt; // split in two cycles // pairwise distances: perm1 vs perm3 if ((exp->m_edges1[node1] == i) && (exp->m_edges3[node1] == i)) // both edges parallel to m sol->m_lb += (exp->m_even1[node1] == exp->m_even3[node1]? m_wt : 2 * (m_wt - m_wr)); else if (exp->m_edges1[node1] == i) // one edge (1) parallel to m { if (!exp->m_even1[node1]) // else no change in lb sol->m_lb += (m_cycle13[node1] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); } else if (exp->m_edges3[node1] == i) // one edge (3) parallel to m { if (!exp->m_even3[node1]) // else no change in lb sol->m_lb += (m_cycle13[node1] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); } else if (m_cycle13[i] == 0) // merge cycles { if (m_cycle13[node1] & 2) sol->m_lb += m_wt; else // get length of second cycle { length = true; pos = i; do { if (!exp->m_even1[pos]) length = !length; pos = exp->m_edges1[pos]; if (exp->m_even3[pos]) length = !length; pos = exp->m_edges3[pos]; } while (pos != i); sol->m_lb += (length? 3 * m_wt - 4 * m_wr : m_wt); } } else if (m_cycle13[exp->m_edges3[i]] < m_cycle13[exp->m_edges1[i]]) // cycle changes sign sol->m_lb += (m_cycle13[node1] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); else if ((!(m_cycle13[node1] & 2)) || (!(m_cycle13[i] & 2))) // split in two cycles sol->m_lb -= m_wt; else sol->m_lb += 4 * m_wr - 3 * m_wt; // split in two cycles // pairwise distances: perm2 vs perm3 if ((exp->m_edges2[node1] == i) && (exp->m_edges3[node1] == i)) // both edges parallel to m sol->m_lb += (exp->m_even2[node1] == exp->m_even3[node1]? m_wt : 2 * (m_wt - m_wr)); else if (exp->m_edges2[node1] == i) // one edge (2) parallel to m { if (!exp->m_even2[node1]) // else no change in lb sol->m_lb += (m_cycle23[node1] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); } else if (exp->m_edges3[node1] == i) // one edge (3) parallel to m { if (!exp->m_even3[node1]) // else no change in lb sol->m_lb += (m_cycle23[node1] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); } else if (m_cycle23[i] == 0) // merge cycles { if (m_cycle23[node1] & 2) sol->m_lb += m_wt; else // get length of second cycle { length = true; pos = i; do { if (!exp->m_even2[pos]) length = !length; pos = exp->m_edges2[pos]; if (exp->m_even3[pos]) length = !length; pos = exp->m_edges3[pos]; } while (pos != i); sol->m_lb += (length? 3 * m_wt - 4 * m_wr : m_wt); } } else if (m_cycle23[exp->m_edges3[i]] < m_cycle23[exp->m_edges2[i]]) // cycle changes sign sol->m_lb += (m_cycle23[node1] & 2? 2 * m_wr - m_wt : m_wt - 2 * m_wr); else if ((!(m_cycle23[node1] & 2)) || (!(m_cycle23[i] & 2))) // split in two cycles sol->m_lb -= m_wt; else sol->m_lb += 4 * m_wr - 3 * m_wt; // split in two cycles #if DEBUG_MEDIAN // !!DEBUG int tmp = calcLowerBoundFromScratch(sol); if (sol->m_lb != tmp) { cout << "ERROR!! lower bound mismatch! (" << sol->m_lb << " vs. " << tmp << ")\n"; sol->dump(2 * m_size); } if (sol->m_lb < exp->m_lb) cout << "ERROR!! exp -> sol " << exp->m_lb << " -> " << sol->m_lb << endl; #endif // add new solution to heap if (sol->m_lb <= m_upperBound) { if (down) { m_heap[0] = sol; heapifyDown(); down = false; } else { m_heap.push_back(sol); heapifyUp(); if (m_heap.size() > m_heapPeak) m_heapPeak++; } if (m_heap.size() > m_heapMax) { if (m_heap[m_heap.size()-1]->m_lb < m_overlooked) m_overlooked = m_heap[m_heap.size()-1]->m_lb; m_solutionPool->freeSolution(m_heap[m_heap.size() - 1]); m_heap.pop_back(); } #if DEBUG_MEDIAN // if (!isHeap()) // cout << "ERROR!! heap condition violated!\n"; #endif } else m_solutionPool->freeSolution(sol); } // remove old solution m_solutionPool->freeSolution(exp); // if all expansions are below the upper bound, we must fill the heap top if (down) { m_heap[0] = m_heap[m_heap.size()-1]; m_heap.pop_back(); heapifyDown(); #if DEBUG_MEDIAN // if (!isHeap()) // cout << "ERROR!! heap condition violated!\n"; #endif } } void Median::expandRev() { Solution* exp = m_heap[0]; // solution to expand int node1; // node to expand int nodeA, nodeB; // neighbors of contracted edge Solution* sol; // a new solution int pos; // position in the cycle bool down = true; // use a heapify downwards for the first expansion // find node for expanding node1 = exp->m_steps; // previous nodes are always expanded while (exp->m_median[m_nodeOrder[node1]] != -1) node1++; node1 = m_nodeOrder[node1]; // for the score calculation, we need the cycles of the pairwise comparison // that include node1. Nodes set to 0 are not in the cycle pos = node1; // genome 1 vs genome 2 for (int i = 0; i < m_size * 2; i++) m_cycle12[i] = 0; do { m_cycle12[exp->m_edges1[pos]] = m_cycle12[pos] + 1; pos = exp->m_edges1[pos]; m_cycle12[exp->m_edges2[pos]] = m_cycle12[pos] + 1; pos = exp->m_edges2[pos]; } while (pos != node1); // genome 1 vs genome 3 for (int i = 0; i < m_size * 2; i++) m_cycle13[i] = 0; do { m_cycle13[exp->m_edges1[pos]] = m_cycle13[pos] + 1; pos = exp->m_edges1[pos]; m_cycle13[exp->m_edges3[pos]] = m_cycle13[pos] + 1; pos = exp->m_edges3[pos]; } while (pos != node1); // genome 2 vs genome 3 for (int i = 0; i < m_size * 2; i++) m_cycle23[i] = 0; do { m_cycle23[exp->m_edges2[pos]] = m_cycle23[pos] + 1; pos = exp->m_edges2[pos]; m_cycle23[exp->m_edges3[pos]] = m_cycle23[pos] + 1; pos = exp->m_edges3[pos]; } while (pos != node1); // try all possible expansions for (int i = 0; i < m_size * 2; i++) { if (i == node1) continue; if (exp->m_median[i] != -1) // node already used continue; if (shortCycle(exp->m_median, node1, i)) // not a permutation matching continue; // create new partial solution sol = m_solutionPool->getSolution(); for (int j = 0; j < 2 * m_size; j++) sol->m_edges1[j] = exp->m_edges1[j]; for (int j = 0; j < 2 * m_size; j++) sol->m_edges2[j] = exp->m_edges2[j]; for (int j = 0; j < 2 * m_size; j++) sol->m_edges3[j] = exp->m_edges3[j]; for (int j = 0; j < 2 * m_size; j++) sol->m_median[j] = exp->m_median[j]; // contract edge sol->m_median[node1] = i; sol->m_median[i] = node1; nodeA = sol->m_edges1[node1]; nodeB = sol->m_edges1[i]; sol->m_edges1[nodeA] = nodeB; sol->m_edges1[nodeB] = nodeA; nodeA = sol->m_edges2[node1]; nodeB = sol->m_edges2[i]; sol->m_edges2[nodeA] = nodeB; sol->m_edges2[nodeB] = nodeA; nodeA = sol->m_edges3[node1]; nodeB = sol->m_edges3[i]; sol->m_edges3[nodeA] = nodeB; sol->m_edges3[nodeB] = nodeA; sol->m_steps = exp->m_steps + 1; // update the score: // step += 1, n -= 1 sol->m_lb = exp->m_lb + 3; // edges parallel to contracted edge if (exp->m_edges1[node1] == i) sol->m_lb -= 2; if (exp->m_edges2[node1] == i) sol->m_lb -= 2; if (exp->m_edges3[node1] == i) sol->m_lb -= 2; // pairwise distances: perm1 vs perm2 if ((exp->m_edges1[node1] == i) && (exp->m_edges2[node1] == i)) // both edges parallel to m sol->m_lb += 1; else if ((exp->m_edges1[node1] == i) || (exp->m_edges2[node1] == i)); // one edge parallel to m -> no change in score else if (m_cycle12[i] == 0) // merge cycles sol->m_lb += 1; else if (m_cycle12[exp->m_edges2[i]] > m_cycle12[exp->m_edges1[i]]) // split in two cycles sol->m_lb -= 1; // pairwise distances: perm1 vs perm3 if ((exp->m_edges1[node1] == i) && (exp->m_edges3[node1] == i)) // both edges parallel to m sol->m_lb += 1; else if ((exp->m_edges1[node1] == i) || (exp->m_edges3[node1] == i)); // one edge parallel to m -> no change in score else if (m_cycle13[i] == 0) // merge cycles sol->m_lb += 1; else if (m_cycle13[exp->m_edges3[i]] > m_cycle13[exp->m_edges1[i]]) // split in two cycles sol->m_lb -= 1; // pairwise distances: perm2 vs perm3 if ((exp->m_edges2[node1] == i) && (exp->m_edges3[node1] == i)) // both edges parallel to m sol->m_lb += 1; else if ((exp->m_edges2[node1] == i) || (exp->m_edges3[node1] == i)); // one edge parallel to m -> no change in score else if (m_cycle23[i] == 0) // merge cycles sol->m_lb += 1; else if (m_cycle23[exp->m_edges3[i]] > m_cycle23[exp->m_edges2[i]]) // split in two cycles sol->m_lb -= 1; #if DEBUG_MEDIAN // !!DEBUG int tmp = calcLowerBoundFromScratchRev(sol); if (sol->m_lb != tmp) { cout << "ERROR!! lower bound mismatch! (" << sol->m_lb << " vs. " << tmp << ")\n"; sol->dump(2 * m_size); } if (sol->m_lb < exp->m_lb) cout << "ERROR!! exp -> sol " << exp->m_lb << " -> " << sol->m_lb << endl; #endif // add new solution to heap if (sol->m_lb <= m_upperBound) { if (down) { m_heap[0] = sol; heapifyDown(); down = false; } else { m_heap.push_back(sol); heapifyUp(); if (m_heap.size() > m_heapPeak) m_heapPeak++; } if (m_heap.size() > m_heapMax) { if (m_heap[m_heap.size()-1]->m_lb < m_overlooked) m_overlooked = m_heap[m_heap.size()-1]->m_lb; m_solutionPool->freeSolution(m_heap[m_heap.size() - 1]); m_heap.pop_back(); } #if DEBUG_MEDIAN // if (!isHeap()) // cout << "ERROR!! heap condition violated!\n"; #endif } else m_solutionPool->freeSolution(sol); } // remove old solution m_solutionPool->freeSolution(exp); // if all expansions are below the upper bound, we must fill the heap top if (down) { m_heap[0] = m_heap[m_heap.size()-1]; m_heap.pop_back(); heapifyDown(); #if DEBUG_MEDIAN // if (!isHeap()) // cout << "ERROR!! heap condition violated!\n"; #endif } } bool Median::shortCycle(const int* f_edges, int f_node1, int f_node2) { int pos = f_node1; // position in the graph // follow H pos & 1? pos-- : pos++; if ((pos == f_node2) && (m_size > 1)) // short cycle return true; for (int i = 2; i < m_size; i++) { if (f_edges[pos] == -1) // we are on a path, not a cycle return false; // follow f_edges pos = f_edges[pos]; // follow H pos & 1? pos-- : pos++; if (pos == f_node2) // short cycle return true; } return false; } void Median::heapifyDown() { Solution* swap; // solution for swapping unsigned int pos = 0; // actual position in the heap unsigned int child = 1; // child of actual element while (child < m_heap.size()) { // get smaller child if ((child + 1 < m_heap.size()) && ((m_heap[child+1]->m_lb < m_heap[child]->m_lb) || ((m_heap[child+1]->m_lb == m_heap[child]->m_lb) && (m_heap[child+1]->m_steps > m_heap[child]->m_steps)))) child++; // compare with child if ((m_heap[child]->m_lb < m_heap[pos]->m_lb) || (((m_heap[child]->m_lb == m_heap[pos]->m_lb)) && (m_heap[child]->m_steps > m_heap[pos]->m_steps))) { // swap swap = m_heap[pos]; m_heap[pos] = m_heap[child]; m_heap[child] = swap; pos = child; child = 2 * pos + 1; } else // heap condition fulfilled return; } } void Median::heapifyUp() { Solution* swap; // solution for swapping unsigned int pos = m_heap.size() - 1; // actual position in the heap unsigned int parent; // parent of pos while (pos != 0) { parent = (pos - 1) / 2; // compare with parent if ((m_heap[pos]->m_lb < m_heap[parent]->m_lb) || (((m_heap[pos]->m_lb == m_heap[parent]->m_lb)) && (m_heap[pos]->m_steps > m_heap[parent]->m_steps))) { // swap swap = m_heap[pos]; m_heap[pos] = m_heap[parent]; m_heap[parent] = swap; pos = parent; } else // heap condition fulfilled return; } } bool Median::verifyWeight() { Solution* sol = m_heap[0]; // solution to verifiy int pos; // position in the cycle int lb1, lb2, lb3; // lower bound for exact comparisons int d1, d2, d3; // distances for exact comparison int dtmp; // temporary distance for exact comparison const vector* sorting; // sorting sequence int diff; // remaining difference to predicted bound // create the median m_perm[0] = 1; pos = 1; for (int i = 1; i < m_size; i++) { pos = sol->m_median[pos]; if (pos & 1) // connected to right point { m_perm[i] = -((pos + 1) / 2); pos--; } else // connected to left point { m_perm[i] = (pos + 2) / 2; pos++; } } // calculate the distances if (m_distMode == 0) { d1 = m_revdist.getDistance(m_input[0], m_perm); d2 = m_revdist.getDistance(m_input[1], m_perm); d3 = m_revdist.getDistance(m_input[2], m_perm); if (sol->m_lb / 2 < d1 + d2 + d3) { sol->m_lb = 2 * (d1 + d2 + d3); heapifyDown(); return false; } else { sol->m_lb = 2 * (d1 + d2 + d3); m_d1 = d1; m_d2 = d2; m_d3 = d3; return true; } } else { m_minswrt.setTarget(m_perm); m_minswrt.setOrigin(m_input[0]); lb1 = (int)(m_minswrt.getLowerBound() + 0.01f); d1 = 0; m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int j = 0; j < sorting->size(); j++) d1 += ((*sorting)[j].m_type == minswrt::Operation::OPERATION_REVERSAL? m_wr : m_wt); m_minswrt.setOrigin(m_input[1]); lb2 = (int)(m_minswrt.getLowerBound() + 0.01f); d2 = 0; m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int j = 0; j < sorting->size(); j++) d2 += ((*sorting)[j].m_type == minswrt::Operation::OPERATION_REVERSAL? m_wr : m_wt); m_minswrt.setOrigin(m_input[2]); lb3 = (int)(m_minswrt.getLowerBound() + 0.01f); d3 = 0; m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int j = 0; j < sorting->size(); j++) d3 += ((*sorting)[j].m_type == minswrt::Operation::OPERATION_REVERSAL? m_wr : m_wt); m_minswrt.setOrigin(m_perm); if (d1 != lb1) // try to optimize { m_minswrt.setTarget(m_input[0]); dtmp = 0; m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int j = 0; j < sorting->size(); j++) dtmp += ((*sorting)[j].m_type == minswrt::Operation::OPERATION_REVERSAL? m_wr : m_wt); if (dtmp < d1) d1 = dtmp; } if (d2 != lb2) // try to optimize { m_minswrt.setTarget(m_input[1]); dtmp = 0; m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int j = 0; j < sorting->size(); j++) dtmp += ((*sorting)[j].m_type == minswrt::Operation::OPERATION_REVERSAL? m_wr : m_wt); if (dtmp < d2) d2 = dtmp; } if (d3 != lb3) // try to optimize { m_minswrt.setTarget(m_input[2]); dtmp = 0; m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int j = 0; j < sorting->size(); j++) dtmp += ((*sorting)[j].m_type == minswrt::Operation::OPERATION_REVERSAL? m_wr : m_wt); if (dtmp < d3) d3 = dtmp; } diff = sol->m_lb / 4 - (lb1 + lb2 + lb3); if (!m_exact) { if (sol->m_lb / 4 < d1 + d2 + d3) { sol->m_lb = 4 * (d1 + d2 + d3); heapifyDown(); return false; } else { sol->m_lb = 4 * (d1 + d2 + d3); m_d1 = d1; m_d2 = d2; m_d3 = d3; return true; } } if (d1 != lb1) // further optimize { m_weightedbb.setPermutations(m_size, m_perm, m_input[0]); m_weightedbb.sort(lb1 + diff); d1 = m_weightedbb.getDistance(); if (d1 == -1) // no solution found { sol->m_lb += 4; heapifyDown(); return false; } else if (d1 != -2) diff -= (d1 - lb1); } if (d2 != lb2) // further optimize { m_weightedbb.setPermutations(m_size, m_perm, m_input[1]); m_weightedbb.sort(lb2 + diff); d2 = m_weightedbb.getDistance(); if (d2 == -1) // no solution found { sol->m_lb += 4; heapifyDown(); return false; } else if (d2 != -2) diff -= (d2 - lb2); } if (d3 != lb3) // further optimize { m_weightedbb.setPermutations(m_size, m_perm, m_input[2]); m_weightedbb.sort(lb3 + diff); d3 = m_weightedbb.getDistance(); if (d3 == -1) // no solution found { sol->m_lb += 4; heapifyDown(); return false; } else if (d3 != -2) diff -= (d3 - lb3); } if ((d1 == -2) || (d2 == -2) || (d3 == -2)) // cannot calc this solution exactly -> remove { if (sol->m_lb < m_overlooked) m_overlooked = sol->m_lb; m_solutionPool->freeSolution(sol); m_heap[0] = m_heap[m_heap.size()-1]; heapifyDown(); return false; } sol->m_lb = 4 * (d1 + d2 + d3); m_d1 = d1; m_d2 = d2; m_d3 = d3; return true; } } /*************************************************************************** * debugging methods ***************************************************************************/ #if DEBUG_MEDIAN int Median::calcLowerBoundFromScratch(Solution* f_sol) { int score; // the resulting score int pos; // position in the cycle int length; // basic value: 3 n wt + 6 step wt = (size + steps) * 3 wt score = (m_size + f_sol->m_steps) * 3 * m_wt; // cycles of perm1 and median for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (f_sol->m_median[i] == -1) // not in a cycle continue; if (m_boolArray2[i]) // already visited continue; // follow the path length = 0; pos = i; do { if (m_boolArray2[pos]) // not a cycle but a path { length = -1; break; } m_boolArray2[pos] = true; pos = f_sol->m_median[pos]; m_boolArray2[pos] = true; pos = m_perm1[pos]; if (f_sol->m_median[pos] == -1) // not a cycle but a path { length = -1; break; } else length++; } while (pos != i); if (length > 0) { if (length & 1) // odd cycle score -= 2 * m_wt; else // even cycle score -= 4 * (m_wt - m_wr); } } // cycles of perm2 and median for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (f_sol->m_median[i] == -1) // not in a cycle continue; if (m_boolArray2[i]) // already visited continue; // follow the path length = 0; pos = i; do { if (m_boolArray2[pos]) // not a cycle but a path { length = -1; break; } m_boolArray2[pos] = true; pos = f_sol->m_median[pos]; m_boolArray2[pos] = true; pos = m_perm2[pos]; if (f_sol->m_median[pos] == -1) // not a cycle but a path { length = -1; break; } else length++; } while (pos != i); if (length > 0) { if (length & 1) // odd cycle score -= 2 * m_wt; else // even cycle score -= 4 * (m_wt - m_wr); } } // cycles of perm3 and median for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (f_sol->m_median[i] == -1) // not in a cycle continue; if (m_boolArray2[i]) // already visited continue; // follow the path length = 0; pos = i; do { if (m_boolArray2[pos]) // not a cycle but a path { length = -1; break; } m_boolArray2[pos] = true; pos = f_sol->m_median[pos]; m_boolArray2[pos] = true; pos = m_perm3[pos]; if (f_sol->m_median[pos] == -1) // not a cycle but a path { length = -1; break; } else length++; } while (pos != i); if (length > 0) { if (length & 1) // odd cycle score -= 2 * m_wt; else // even cycle score -= 4 * (m_wt - m_wr); } } // cycles between perm1 and perm2 for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (m_boolArray2[i]) continue; // already visited if (f_sol->m_median[i] != -1) // edge contracted continue; // follow the cycle length = 0; pos = i; do { m_boolArray2[pos] = true; if (f_sol->m_even1[pos]) length += 1; else length += 3; pos = f_sol->m_edges1[pos]; m_boolArray2[pos] = true; if (f_sol->m_even2[pos]) length += 1; else length += 3; pos = f_sol->m_edges2[pos]; } while (pos != i); if ((length / 2) & 1) // odd cycle score -= m_wt; else score -= 2 * (m_wt - m_wr); } // cout << score << " "; // cycles between perm1 and perm3 for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (m_boolArray2[i]) continue; // already visited if (f_sol->m_median[i] != -1) // edge contracted continue; // follow the cycle length = 0; pos = i; do { m_boolArray2[pos] = true; if (f_sol->m_even1[pos]) length += 1; else length += 3; pos = f_sol->m_edges1[pos]; m_boolArray2[pos] = true; if (f_sol->m_even3[pos]) length += 1; else length += 3; pos = f_sol->m_edges3[pos]; } while (pos != i); if ((length / 2) & 1) // odd cycle score -= m_wt; else score -= 2 * (m_wt - m_wr); } // cycles between perm2 and perm3 for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (m_boolArray2[i]) continue; // already visited if (f_sol->m_median[i] != -1) // edge contracted continue; // follow the cycle length = 0; pos = i; do { m_boolArray2[pos] = true; if (f_sol->m_even2[pos]) length += 1; else length += 3; pos = f_sol->m_edges2[pos]; m_boolArray2[pos] = true; if (f_sol->m_even3[pos]) length += 1; else length += 3; pos = f_sol->m_edges3[pos]; } while (pos != i); if ((length / 2) & 1) // odd cycle score -= m_wt; else score -= 2 * (m_wt - m_wr); } return score; } int Median::calcLowerBoundFromScratchRev(Solution* f_sol) { int score; // the resulting score int pos; // position in the cycle bool isCycle; // true if we are on a cycle // basic value: 3 n + 6 step = (size + steps) * 3 score = (m_size + f_sol->m_steps) * 3; // cycles of perm1 and median for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (f_sol->m_median[i] == -1) // not in a cycle continue; if (m_boolArray2[i]) // already visited continue; // follow the path isCycle = true; pos = i; do { if (m_boolArray2[pos]) // not a cycle but a path { isCycle = false; break; } m_boolArray2[pos] = true; pos = f_sol->m_median[pos]; m_boolArray2[pos] = true; pos = m_perm1[pos]; if (f_sol->m_median[pos] == -1) // not a cycle but a path { isCycle = false; break; } } while (pos != i); if (isCycle) score -= 2; } // cout << score << " "; // cycles of perm2 and median for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (f_sol->m_median[i] == -1) // not in a cycle continue; if (m_boolArray2[i]) // already visited continue; // follow the path isCycle = true; pos = i; do { if (m_boolArray2[pos]) // not a cycle but a path { isCycle = false; break; } m_boolArray2[pos] = true; pos = f_sol->m_median[pos]; m_boolArray2[pos] = true; pos = m_perm2[pos]; if (f_sol->m_median[pos] == -1) // not a cycle but a path { isCycle = false; break; } } while (pos != i); if (isCycle) score -= 2; } // cycles of perm3 and median for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (f_sol->m_median[i] == -1) // not in a cycle continue; if (m_boolArray2[i]) // already visited continue; // follow the path isCycle = true; pos = i; do { if (m_boolArray2[pos]) // not a cycle but a path { isCycle = false; break; } m_boolArray2[pos] = true; pos = f_sol->m_median[pos]; m_boolArray2[pos] = true; pos = m_perm3[pos]; if (f_sol->m_median[pos] == -1) // not a cycle but a path { isCycle = false; break; } } while (pos != i); if (isCycle) score -= 2; } // cout << score << " "; // cycles between perm1 and perm2 for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (m_boolArray2[i]) continue; // already visited if (f_sol->m_median[i] != -1) // edge contracted continue; // follow the cycle pos = i; do { m_boolArray2[pos] = true; pos = f_sol->m_edges1[pos]; m_boolArray2[pos] = true; pos = f_sol->m_edges2[pos]; } while (pos != i); score -= 1; } // cycles between perm1 and perm3 for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (m_boolArray2[i]) continue; // already visited if (f_sol->m_median[i] != -1) // edge contracted continue; // follow the cycle pos = i; do { m_boolArray2[pos] = true; pos = f_sol->m_edges1[pos]; m_boolArray2[pos] = true; pos = f_sol->m_edges3[pos]; } while (pos != i); score -= 1; } // cout << score << " "; // cycles between perm2 and perm3 for (int i = 0; i < 2 * m_size; i++) m_boolArray2[i] = false; // use as visited array for (int i = 0; i < 2 * m_size; i++) { if (m_boolArray2[i]) continue; // already visited if (f_sol->m_median[i] != -1) // edge contracted continue; // follow the cycle pos = i; do { m_boolArray2[pos] = true; pos = f_sol->m_edges2[pos]; m_boolArray2[pos] = true; pos = f_sol->m_edges3[pos]; } while (pos != i); score -= 1; } return score; } bool Median::isHeap() { for (unsigned int i = 0; 2 * i + 1 < m_heap.size(); i++) { if ((m_heap[i]->m_lb > m_heap[2*i+1]->m_lb) || ((m_heap[i]->m_lb == m_heap[2*i+1]->m_lb) && (m_heap[i]->m_steps < m_heap[2*i+1]->m_steps))) return false; if (2 * i + 2 < m_heap.size()) { if ((m_heap[i]->m_lb > m_heap[2*i+2]->m_lb) || ((m_heap[i]->m_lb == m_heap[2*i+2]->m_lb) && (m_heap[i]->m_steps < m_heap[2*i+2]->m_steps))) return false; } } return true; } bool Median::debug(Solution* f_sol) { return true; } #endif /***************************************************************************/ } // end namespace median phylo-1.0.6/median/COPYING0000644000175000017500000010451311434510050012057 00000000000000 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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uninstall-libLTLIBRARIES \ uninstall-libmedian_laHEADERS uninstall-medianextraDATA # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: phylo-1.0.6/median/medianPools.h0000644000175000017500000000523711434510050013452 00000000000000/** * filename: medianPools.h * author: Martin Bader * begin: 25.06.2006 * last change: 01.10.2008 * * Pools of several data structures, to avoid frequent allocation / freeing * of memory. * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef MEDIANPOOLS_H_ #define MEDIANPOOLS_H_ #include namespace median { // class forward declarations class Solution; /** * Pool for solutions */ class SolutionPool { /*********************************************************************** * member variables ***********************************************************************/ protected: /** size of the solutions; this is the number of nodes, which is twice * the number of elements in the permutations. */ int m_size; /** If this variable is set to true, the solutons will have the even * arrays (needed for weighted distance). */ bool m_even; /** the solutions */ std::vector m_solutions; /*********************************************************************** * methods ***********************************************************************/ public: /** * Constructor. */ SolutionPool(); /** * Destructor. */ ~SolutionPool(); /** * Initializes the pool with a given permutation size. * Set if the solutions shall have the even arrays * @param f_size the permutation size * @param f_even if true, the solutions will have the even array */ void init(int f_size, bool f_even); /** * Returns a Solution * @return pointer to a Solution */ Solution* getSolution(); /** * Return the Solution back to the pool. * @param f_solution the Solution to give back */ inline void freeSolution(Solution* f_solution) { m_solutions.push_back(f_solution); } }; /***************************************************************************/ } // end namespace median #endif /*MEDIANPOOLS_H_*/ phylo-1.0.6/median/Makefile.am0000644000175000017500000000113611434510050013055 00000000000000lib_LTLIBRARIES = libmedian.la libmedian_ladir = $(includedir) libmedian_la_SOURCES = median.cpp medianPools.cpp solution.cpp libmedian_la_HEADERS = $(libmedian_la_SOURCES:%.cpp=%.h) libmedian_la_LIBADD = -L../revDist -L../minswrt -L../weightedbb -lrevDist -lminswrt -lweightedbb INCLUDES = -I$(includedir) -I../revDist -I../minswrt -I../weightedbb libmedian_la_LDFLAGS = -version-info 3:1:3 bin_PROGRAMS = median median_SOURCES = start.cpp median_LDADD = libmedian.la EXTRA_DIST = $(libmedian_la_HEADERS) test.in COPYING README medianextradir = $(datadir)/median medianextra_DATA = test.in COPYING README phylo-1.0.6/median/start.cpp0000644000175000017500000001776111434510050012675 00000000000000/** * filename: start.cpp * author: Martin Bader * begin: 25.06.2007 * last change: 23.08.2010 * * Start file. This is a small user interface. * * Copyright (C) 2007-2010 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "median.h" #include #include #include #include #include using namespace std; using namespace median; /** * Reads permutations from a file. The permutations will be written to * f_perm1, f_perm2, f_perm3, which are passed uninitialized. The genome * names are written to f_name1, f_name2, f_name3, which are also passed * uninitialized. The permutation size will be returned (on error -1) * So far, only minor error handling implemented * @param f_filename name of the file * @param f_perm1 first permutation will be written here * @param f_perm2 second permutation will be written here * @param f_perm3 third permutation will be written here * @param f_name1 name of the first genome * @param f_name2 name of the second genome * @param f_name3 name of the third genome * @return the permutation size */ int readFile(const char* f_filename, int* &f_perm1, int* &f_perm2, int* &f_perm3, char* &f_name1, char* &f_name2, char* &f_name3) { ifstream input; char buffer[256]; vector tmpPerm; int stringsize; int permsize; input.open(f_filename); while (input.peek() == '#') // line is a comment input.ignore(1024, '\n'); if (input.peek() != '>') // wrong format { input.close(); return -1; } input.ignore(1, ' '); input.getline(buffer, 256); stringsize = input.gcount(); f_name1 = new char[stringsize]; strncpy(f_name1, buffer, stringsize); while (input.peek() == '#') // line is a comment input.ignore(1024, '\n'); permsize = 0; while (input.peek() == ' ') input.ignore(1); do { tmpPerm.push_back(0); // increment vector size for (stringsize = 0; (input.peek() != ' ') && (input.peek() != '\n'); stringsize++) input >> buffer[stringsize]; buffer[stringsize] = 0; tmpPerm[permsize++] = atoi(buffer); while (input.peek() == ' ') input.ignore(1); } while (input.peek() != '\n'); input.ignore(1); f_perm1 = new int[permsize]; for (int i = 0; i < permsize; i++) f_perm1[i] = tmpPerm[i]; while (input.peek() == '#') // line is a comment input.ignore(1024, '\n'); if (input.peek() != '>') // wrong format { input.close(); delete[] f_perm1; f_perm1 = NULL; delete[] f_name1; f_name1 = NULL; return -1; } input.ignore(1, ' '); input.getline(buffer, 256); stringsize = input.gcount(); f_name2 = new char[stringsize]; strncpy(f_name2, buffer, stringsize); while (input.peek() == '#') // line is a comment input.ignore(1024, '\n'); f_perm2 = new int[permsize]; for (int i = 0; i < permsize; i++) input >> f_perm2[i]; input.ignore(256, '\n'); while (input.peek() == '#') // line is a comment input.ignore(1024, '\n'); if (input.peek() != '>') // wrong format { input.close(); delete[] f_perm1; f_perm1 = NULL; delete[] f_name1; f_name1 = NULL; delete[] f_perm2; f_perm2 = NULL; delete[] f_name2; f_name2 = NULL; return -1; } input.ignore(1, ' '); input.getline(buffer, 256); stringsize = input.gcount(); f_name3 = new char[stringsize]; strncpy(f_name3, buffer, stringsize); while (input.peek() == '#') // line is a comment input.ignore(1024, '\n'); f_perm3 = new int[permsize]; for (int i = 0; i < permsize; i++) input >> f_perm3[i]; input.close(); return permsize; } int main(int f_argc, char** f_argv) { int* perm1 = NULL; int* perm2 = NULL; int* perm3 = NULL; int* result = NULL; char* name1 = NULL; char* name2 = NULL; char* name3 = NULL; int size; Median* solver = new Median(); // the median solver int resultweight; int bestweight; // store resultweight for comparing with cutoff value cout << "*****************************************************************\n"; cout << "median v2.3.0 Copyright (C) 2007-2010 Martin Bader\n"; cout << "This program comes with ABSOLUTELY NO WARRANTY.\n"; cout << "This is free software, and you are welcome to redistribute it\n"; cout << "under certain conditions.\n"; cout << "For details about the licence, read the file gpl.txt\n"; cout << "*****************************************************************\n"; if (f_argc != 7) { cout << "Usage: median infile wr wt distMode exact all\n"; cout << " wr, wt: integer weights for reversals and (inverted) transpositions,\n"; cout << " distmode: 0: reversals only; 1: transpositions only; 2: weighted reversal and transposition distance\n"; cout << " exact: 0 if pairwise distances are evaluated approximately, 1 otherwise\n"; cout << " all: 0 gives only one optimal solution, 1 gives all optimal solutions\n"; return 0; } cout << "reading file...\n"; size = readFile(f_argv[1], perm1, perm2, perm3, name1, name2, name3); cout << "done\n"; result = new int[size]; if ((f_argv[4][0] != '0') && (f_argv[5][0] == '1')) // weighted branch and bound needed solver->init(size, atoi(f_argv[2]), atoi(f_argv[3]), atoi(f_argv[4]), (f_argv[5][0] == '1'), 60000000 / size, 15000000 / size); else solver->init(size, atoi(f_argv[2]), atoi(f_argv[3]), atoi(f_argv[4]), (f_argv[5][0] == '1'), 75000000 / size); if (f_argv[6][0] == '0') // only one solution seeked { // use this for only one median resultweight = solver->solve(perm1, perm2, perm3, result); cout << "resulting permutation:\n"; for (int i = 0; i < size; i++) cout << result[i] << " "; cout << endl; cout << "weight: " << resultweight << endl; cout << "heap peak: " << solver->getHeapPeak() << endl; if (solver->getLeastCutoff() < resultweight) cout << "A solution of weight " << solver->getLeastCutoff() << " might have been overlooked\n"; } else // all optimal solutions seeked { resultweight = solver->getFirstSolution(perm1, perm2, perm3, result); bestweight = resultweight; while (resultweight >= 0) { cout << "resulting permutation:\n"; for (int i = 0; i < size; i++) cout << result[i] << " "; cout << endl; cout << "weight: " << resultweight << endl; cout << "heap peak: " << solver->getHeapPeak() << endl; resultweight = solver->getNextSolution(result); } if (solver->getLeastCutoff() <= bestweight) cout << "Some solutions of weight " << solver->getLeastCutoff() << " might have been overlooked\n"; } delete[] perm1; delete[] perm2; delete[] perm3; if (name1 != NULL) delete[] name1; if (name2 != NULL) delete[] name2; if (name3 != NULL) delete[] name3; delete[] result; delete solver; return 0; } phylo-1.0.6/median/solution.h0000644000175000017500000000614411434510050013052 00000000000000/** * filename: solution.h * author: Martin Bader * begin: 25.06.2007 * last change: 23.08.2007 * * (Partially) solution of the median problem. * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef SOLUTION_H_ #define SOLUTION_H_ namespace median { /** * (Partially) solution of the median problem. */ class Solution { /*********************************************************************** * member variables ***********************************************************************/ public: /** Edges of first genome */ int* m_edges1; /** Edges of second genome */ int* m_edges2; /** Edges of third genome */ int* m_edges3; /** Current edges of the median */ int* m_median; /** Marks edges of the first genome with even length (after length / 2) */ bool* m_even1; /** Marks edges of the second genome with even length (after length / 2) */ bool* m_even2; /** Marks edges of the third genome with even length (after length / 2) */ bool* m_even3; /** already performed steps for this solution */ int m_steps; /** lower bound for the solutions weight (including some multipliers) */ int m_lb; /*********************************************************************** * methods ***********************************************************************/ public: /** * Standard Constructor. All arrays are set to NULL. */ Solution(); /** * This Constructor sets the size of the graphs and reserves memory for * the arrays. Size is the number of nodes, which is twice the number * of elements in the permutations. * You can also set if you are interested in the even arrays. Else they * won't be initialized. * @param f_size permutation size * @param f_even if true the even arrays are initialized */ Solution(int f_size, bool f_even); /** * Destructor. */ ~Solution(); /*********************************************************************** * debug methods ***********************************************************************/ public: /** * Dumps the solution to stderr. * @param f_size solution size (number of nodes). */ void dump(int f_size); }; /***************************************************************************/ } // end namespace median #endif /*SOLUTION_H_*/ phylo-1.0.6/median/test.in0000644000175000017500000000061011434510050012324 00000000000000>Human 1 -32 17 2 23 12 3 20 6 30 7 8 21 31 24 9 -10 -18 11 33 -28 19 14 34 13 25 4 22 -29 26 5 35 -15 -27 -16 -36 >Drosophila yakuba 1 25 2 23 17 12 3 20 6 15 30 27 31 18 -19 -9 -21 -8 -7 33 -28 10 11 32 -4 -24 -13 -34 -14 22 -29 26 5 35 -16 -36 >Katharina tunicata 1 17 2 12 -19 -9 -21 -8 -7 33 -32 -11 -10 28 -4 -25 -24 -13 -34 -14 -26 -16 -36 -35 -29 -20 -18 3 23 15 30 27 22 6 31 5 phylo-1.0.6/median/median.h0000644000175000017500000003351711434510050012437 00000000000000/** * filename: median.h * author: Martin Bader * begin: 25.06.2007 * last change: 20.08.2010 * * Calculates the median between three genomes. * Either uses the reversal distance or the weighted reversal/transposition * distance. This is a pimped version of Capraras algorithm. * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef MEDIAN_H_ #define MEDIAN_H_ #include #include "minswrt.h" #include "revDist.h" #include "weightedbb.h" #include namespace median { #define DEBUG_MEDIAN 0 // class forward declarations class Solution; class SolutionPool; /** * The main class. */ class Median { /*********************************************************************** * member variables ***********************************************************************/ private: /** Permutation size */ int m_size; /** Pointer to the input genomes */ int const ** m_input; /** Distance mode: 0: reversal only, 1: transposition only, 2: weighted reversal/ * transposition distance */ int m_distMode; /** TRUE if we are solving the problem exactly, i.e. pairwise distances are calculated * by an exact solver. */ bool m_exact; /** Weight of a reversal */ int m_wr; /** Weight of an (inverted) transposition */ int m_wt; /** An upper bound for the median weight */ int m_upperBound; /** Pool for partial solutions */ SolutionPool* m_solutionPool; /** The heap of partial solutions */ std::vector m_heap; /** The maximum allowed heap size */ unsigned int m_heapMax; /** For statistical purposes: maximum number of solutions on the heap. */ unsigned int m_heapPeak; /** By pruning the tree or aborting exact calculations, some solutions * can get lost. This value indicates the weight of the possible best * lost solution. */ int m_overlooked; /** A boolean array of size 2 * permSize for multiple purposes; member * variable to prevent frequent allocation. */ bool* m_boolArray2; /** For score update: a cycle between perm1 and perm2 */ int* m_cycle12; /** For score update: a cycle between perm1 and perm3 */ int* m_cycle13; /** For score update: a cycle between perm2 and perm3 */ int* m_cycle23; /** A permutation (needed for exact distance calculation */ int* m_perm; /** Distance last calculated median - perm1 */ int m_d1; /** Distance last calculated median - perm2 */ int m_d2; /** Distance last calculated median - perm3 */ int m_d3; /** Order in which the nodes should be expanded */ int* m_nodeOrder; /** Solver for pairwise distances (weighted reversal/transposition * distance), approximation algorithm */ minswrt::MinSWRT m_minswrt; /** Solver for pairwise distances (weighted reversal/transposition * distance), branch n bound algorithm */ weightedbb::WeightedBB m_weightedbb; /** Solver for pairwise distances (weighted reversal/transposition * distance) */ revDist::RevDist m_revdist; // !!DEBUG /** Original edges of perm1, 2, 3 */ #if DEBUG_MEDIAN int* m_perm1; int* m_perm2; int* m_perm3; int m_numExpansions; #endif /*********************************************************************** * methods ***********************************************************************/ public: /** * Constructor. Please call init() after the call of the constructor. */ Median(); /** * Destructor. */ ~Median(); /** * Initializes the median solver. * @param f_size the permutation size * @param f_wr weight of a reversal * @param f_wt weight of an (inverted) transposition * @param f_distMode distance mode (0: reversals only; 1: transpositions only; 2: weighted reversal and transposition distance) * @param f_exact TRUE if we want exact solutions (branch and bound for pairwise comparison) * @param f_heapMax maximum allowed number of elements on the heap * @param f_pairwiseHeapMax maximum allowes number of elements on the heap for exact pairwise comparison */ void init(int f_size, int f_wr, int f_wt, int f_mode = 2, bool f_exact = false, unsigned int f_heapMax = 2000000, int f_pairwiseHeapMax = 2000000); /** * Solves the median problem. The solver must be initialized. f_result * must be initialized with the correct size. The return value is the * weight of the median. * If any upper bound for the median weight is known, you can set it with * the parameter f_upperBound. This will speed up the calculation. If there * is no median within the upper bound, -1 will be returned. * @param f_perm1 first permutation * @param f_perm2 second permutation * @param f_perm3 third permutation * @param f_result the result will be written to here * @param f_upperBound we search only for medians with weight <= this bound * @return the weight of the median */ int solve(const int* f_perm1, const int* f_perm2, const int* f_perm3, int* f_result, int f_upperBound = INT_MAX); /** * Same as solve, but without clearing the heap in the end. Use this if * you need all medians: first call getFirstSolution, then iterate over * getNextSolution until -1 is returned. Then call cleanHeap. * @param f_perm1 first permutation * @param f_perm2 second permutation * @param f_perm3 third permutation * @param f_result the result will be written to here * @param f_upperBound we search only for medians with weight <= this bound * @return the weight of the median */ int getFirstSolution(const int* f_perm1, const int* f_perm2, const int* f_perm3, int* f_result, int f_upperBound = INT_MAX); /** * Calculates another median with the same weight if there is any, * otherwise returns -1. The new median will be written to f_result which * must be initialized. * @param f_result the result will be written to here * @return the weight of the median */ int getNextSolution(int* f_result); /** * Get the distances from the input permutations to the last created median. * Only call this if you have called solve, getFirstSolution, or getNextSolution. * The results will be written to f_d1, f_d2, f_d3, which are integer * references. * @param f_d1 distance median - perm1 * @param f_d2 distance median - perm2 * @param f_d3 distance median - perm3 */ void getMedianDist(int& f_d1, int& f_d2, int& f_d3); /** * Cleans up the heap. Call this after getting several medians with * getFirstResult / getNextResult. */ void cleanHeap(); /** * Returns the maximum number of elements in the heap during the last * solving. * @return the heap peak */ inline int getHeapPeak() { return m_heapPeak; } /** * Returns the least weight of a solution that might have been lost by some * pruning techniques. * @return weight of best possible lost solution */ int getLeastCutoff(); /** * Returns the pairwise distance between two genomes. f_mode determines * what is calculated: 0 is exact (works only if m_exact is true, otherwise * returns an upper bound), 1 is lower bound, 2 is an upper bound. * @param f_perm0 first permutation * @param f_perm1 second permutation * @param f_mode determines if solved exactly(0), as lower bound(1), or as upper bound(2) * @return pairwise genome distance */ int pairDist(const int* f_perm0, const int* f_perm1, int f_mode = 1); protected: /** * Finds a first solution and does not clean the heap. This is the main * part of solve / getFirstSolution. For a more detailed description, * look at the comment of solve. * @param f_perm1 first permutation * @param f_perm2 second permutation * @param f_perm3 third permutation * @param f_result the result will be written to here * @param f_upperBound we search only for medians with weight <= this bound * @return the weight of the median */ int solveWithoutClean(const int* f_perm1, const int* f_perm2, const int* f_perm3, int* f_result, int f_upperBound = INT_MAX); /** Calculates the lower bound of a partial solution (from scratch). * It is assumed that all edges are of length 1 and the median contains * no edges so far. * This is the version for weighted reversal/transposition distance. * The result will be written to f_sol->m_lb. * @param f_sol the solution to handle */ void calcLowerBound(Solution* f_sol); /** * Calculates the lower bound of a partial solution (from scratch). * It is assumed that all edges are of length 1 and the median contains * no edges so far. * This is the version for the reversal only distance. * The result will be written to f_sol->m_lb. * @param f_sol the solution to handle */ void calcLowerBoundRev(Solution* f_sol); /** * Calculates in which order the nodes should be expanded. Nodes that * increase the lower bound for many extensions should be preferred. This * ordering is calculated w.r.t. a given partial solution. This must be * the initial empty solution! * @param f_sol the partial solution used for calculating the ordering */ void createNodeOrder(Solution* f_sol); /** * Calculates in which order the nodes should be expanded. Nodes that * increase the lower bound for many extensions should be preferred. This * ordering is calculated w.r.t. a given partial solution. This must be * the initial empty solution! * This is the version for the reversal distance * @param f_sol the partial solution used for calculating the ordering */ void createNodeOrderRev(Solution* f_sol); /** * Expands the heap top element. This includes preserving the heap * condition. If an optimal solution is found during the expand process, * it will be put on the top of the heap and the function will be aborted * (in this case the heap condition might be broken). */ void expand(); /** * Expands the heap top element. This includes preserving the heap * condition. If an optimal solution is found during the expand process, * it will be put on the top of the heap and the function will be aborted * (in this case the heap condition might be broken). * This version is taken for the reversal only distance. */ void expandRev(); /** * Tests if by adding an edge from f_node1 to f_node2, the union of * H and f_edges will have a short cycle. In this case, the result * cannot be a permutaton matching. * @param f_edges the edges to test * @param f_node1 start node of new edge * @param f_node2 end node of new edge * @return true if there is a short cycle and we cannot expand the * solution to a permutation matching. */ bool shortCycle(const int* f_edges, int f_node1, int f_node2); /** * Recreates the heap condition after changing the top element. */ void heapifyDown(); /** * Recreates the heap conditon after adding an element at the bottom. */ void heapifyUp(); /** * Verifies the weight of a solution by an exact branch and bound algorithm. * If the weight could not be verified, it is actualized and the heap * condition will be repaired. The solution to check is the heap peak * element. * @return true if the weight is correct */ bool verifyWeight(); /*********************************************************************** * debugging methods ***********************************************************************/ #if DEBUG_MEDIAN /** * Calculates the lower bound from scratch, i.e. without using previous * informations. The calculated lower bound will be returned. * @param f_sol solution of which we shall calculate the lower bound * @return the lower bound */ int calcLowerBoundFromScratch(Solution* f_sol); /** * Calculates the lower bound from scratch, i.e. without using previous * informations. The calculated lower bound will be returned. * This version is for the reversal only distance. * @param f_sol solution of which we shall calculate the lower bound * @return the lower bound */ int calcLowerBoundFromScratchRev(Solution* f_sol); /** * Checks if the current heap fulfills the heap condition. * @return true if the heap condition is fulfilled */ bool isHeap(); /** * Debugging method, functionality may change. */ bool debug(Solution* f_sol); #endif }; /***************************************************************************/ } // end namespace median #endif /*MEDIAN_H_*/ phylo-1.0.6/median/solution.cpp0000644000175000017500000000661111434510050013404 00000000000000/** * filename: solution.cpp * author: Martin Bader * begin: 25.06.2007 * last change: 01.10.2008 * * Implementation of solution.h * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "solution.h" #include #include "medianPools.h" #include namespace median { using namespace std; /*************************************************************************** * public methods ***************************************************************************/ Solution::Solution() { m_edges1 = NULL; m_edges2 = NULL; m_edges3 = NULL; m_median = NULL; m_even1 = NULL; m_even2 = NULL; m_even3 = NULL; m_steps = 0; m_lb = 0; } Solution::Solution(int f_size, bool f_even) { m_edges1 = new int[f_size]; m_edges2 = new int[f_size]; m_edges3 = new int[f_size]; m_median = new int[f_size]; if (f_even) { m_even1 = new bool[f_size]; m_even2 = new bool[f_size]; m_even3 = new bool[f_size]; } else { m_even1 = NULL; m_even2 = NULL; m_even3 = NULL; } m_steps = 0; m_lb = 0; } Solution::~Solution() { delete[] m_edges1; delete[] m_edges2; delete[] m_edges3; delete[] m_median; if (m_even1 != NULL) { delete[] m_even1; delete[] m_even2; delete[] m_even3; } } /*************************************************************************** * debug methods ***************************************************************************/ void Solution::dump(int f_size) { cout << "***** dumping solution " << (long)this << " ******\n"; cout << "steps: " << m_steps << " lb: " << m_lb << endl; cout << "m_edges1\n"; for (int i = 0; i < f_size; i++) cout << m_edges1[i] << " "; cout << endl; cout << "m_edges2\n"; for (int i = 0; i < f_size; i++) cout << m_edges2[i] << " "; cout << endl; cout << "m_edges3\n"; for (int i = 0; i < f_size; i++) cout << m_edges3[i] << " "; cout << endl; cout << "m_median\n"; for (int i = 0; i < f_size; i++) cout << m_median[i] << " "; cout << endl; if (m_even1 != NULL) { cout << "m_even1\n"; for (int i = 0; i < f_size; i++) cout << (m_even1[i]? "e " : "o "); cout << endl; cout << "m_even2\n"; for (int i = 0; i < f_size; i++) cout << (m_even2[i]? "e " : "o "); cout << endl; cout << "m_even3\n"; for (int i = 0; i < f_size; i++) cout << (m_even3[i]? "e " : "o "); cout << endl; } cout << "***********************\n"; } /***************************************************************************/ } // end namespace median phylo-1.0.6/COPYING0000644000175000017500000010451311434510050010622 00000000000000 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The GNU General Public License is a free, copyleft license for software and other kinds of works. The licenses for most software and other practical works are designed to take away your freedom to share and change the works. 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But first, please read . phylo-1.0.6/revDist/0000755000175000017500000000000011434510123011264 500000000000000phylo-1.0.6/revDist/README0000644000175000017500000000172211434510050012065 00000000000000revDist ======= revDist is a small program to calculate the reversal distance between two cyclic signed permutations. It contains of two parts: 1. the program itself, which is compiled into a library. 2. a tiny frontend that calls the library. The frontend: Call the program with revDist infile where infile contains a line containing the permutation size, followed by two lines with the signed permutations. Lines beginning with # are comments. As an example, see the file test.in The library: The functions provided by the library are documented in revDist.h in the include directory. As example of how to use the library, you can have a look at share/revDist/start.cpp. The interesting part is in the main function. Copyright: ========== Copyright (C) 2007-2010 Martin Bader This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions. For details about the licence, read the file COPYING phylo-1.0.6/revDist/revDist.cpp0000644000175000017500000003241111434510050013330 00000000000000/** * filename: revDist.cpp * author: Martin Bader * begin: 17.01.2007 * last change: 17.08.2009 * * Implementation of revDist.h * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "revDist.h" #include #include namespace revDist { using namespace std; /*************************************************************************** * public methods ***************************************************************************/ RevDist::RevDist() { m_state = 0; m_permSize = 0; m_mapped = NULL; m_element2Index = NULL; m_numCycles = 0; m_perm2Cycle = NULL; m_components = NULL;; m_compStarts = NULL; m_compEnds = NULL; m_compStack = NULL; m_chainStack = NULL; m_orientedStack = NULL; } RevDist::~RevDist() { delete[] m_mapped; delete[] m_element2Index; delete[] m_perm2Cycle; delete[] m_components; delete[] m_compStarts; delete[] m_compEnds; delete[] m_compStack; delete[] m_chainStack; delete[] m_orientedStack; } void RevDist::init(int f_size) { m_permSize = f_size; m_state = 1; m_mapped = new int[f_size]; m_element2Index = new int[f_size + 1]; m_numCycles = 0; m_perm2Cycle = new int[f_size]; m_components = new IntPair[f_size]; m_compStarts = new bool[f_size]; m_compEnds = new bool[f_size]; m_compStack = new int[f_size]; m_chainStack = new int[f_size]; m_orientedStack = new bool[f_size]; } int RevDist::getDistance(const int* f_perm1, const int* f_perm2) { if (m_state != 1) { cerr << "RevDist not initialized! Aborting getDistance\n"; return -1; } if (m_permSize == 1) // for this case, some arrays are to small -> handle it as trivial case return 0; mapPermutations(f_perm1, f_perm2); markCycles(); findComponents(); return m_permSize - m_numCycles + calcHurdles(); // calcHurdles also calculates the fortress indicator } /*************************************************************************** * public methods ***************************************************************************/ void RevDist::mapPermutations(const int* f_perm1, const int* f_perm2) { // use element2Index as mapping for (int i = 0; i < m_permSize; i++) { if (f_perm2[i] > 0) m_element2Index[f_perm2[i]] = i+1; else m_element2Index[-f_perm2[i]] = -(i+1); } // map perm1 for (int i = 0; i < m_permSize; i++) { if (f_perm1[i] > 0) m_mapped[i] = m_element2Index[f_perm1[i]]; else m_mapped[i] = -m_element2Index[-f_perm1[i]]; } // set element2Index according to the mapping for (int i = 0; i < m_permSize; i++) m_element2Index[abs(m_mapped[i])] = i; /* cerr << "mapped: "; for (int i = 0; i < m_permSize; i++) cerr << m_mapped[i] << " "; cerr << endl << "element2Index: "; for (int i = 0; i <= m_permSize; i++) cerr << m_element2Index[i] << " "; cerr << endl;*/ } void RevDist::markCycles() { int edge; // the actual RE where we are int element; // next element to find bool positiv; // true if we walk in positiv direction /** * Gives each cycle a label, and marks for each RE the cycle it belongs * to. Stores to each cycle begin- and endpoint. This sets the initial * values of m_numCycles, m_perm2Cycle, and m_components. */ m_numCycles = 0; for (int i = 0; i < m_permSize; i++) // mark all RE as not yet visited m_perm2Cycle[i] = -1; for (int i = 0; i < m_permSize; i++) // start with each RE { if (m_perm2Cycle[i] != -1) // RE already visited continue; edge = i; positiv = true; m_components[m_numCycles].first = i; m_components[m_numCycles].second = i; while (m_perm2Cycle[edge] == -1) // walk through cycle { m_perm2Cycle[edge] = m_numCycles; if (edge > m_components[m_numCycles].second) m_components[m_numCycles].second = edge; // search next element if (positiv) { element = m_mapped[edge]; if (element < 0) { element = (element == -m_permSize? 1 : -element + 1); positiv = false; } else { element = (element == 1? m_permSize : element - 1); positiv = true; } } else { element = (edge == 0? m_mapped[m_permSize - 1] : m_mapped[edge - 1]); if (element < 0) { element = (element == -1? m_permSize : -element - 1); positiv = true; } else { element = (element == m_permSize? 1 : element + 1); positiv = false; } } edge = m_element2Index[element]; if (positiv ^ (m_mapped[edge] > 0)) // correct edge positiv = false; else // walk one edge to the right { edge = (edge == m_permSize - 1? 0 : edge + 1); positiv = true; } } /* cerr << " (" << m_components[m_numCycles].first << " - " << m_components[m_numCycles].second << endl;*/ m_numCycles++; } // cout << "#cycles: " << m_numCycles << endl; } void RevDist::findComponents() { int stacksize = 0; // size of the stack int extent; // max edge index in component // init some vars for (int i = 0; i < m_permSize; i++) m_compStarts[i] = false; for (int i = 0; i < m_permSize; i++) m_compEnds[i] = false; // get for each RE the component for (int i = 0; i < m_permSize; i++) { if (i == m_components[m_perm2Cycle[i]].first) // start of a cycle m_compStack[stacksize++] = m_perm2Cycle[i]; // push cycle extent = m_components[m_perm2Cycle[i]].second; while (m_components[m_compStack[stacksize-1]].first > m_components[m_perm2Cycle[i]].first) { if (m_components[m_compStack[stacksize-1]].second > extent) extent = m_components[m_compStack[stacksize-1]].second; stacksize--; } if (m_components[m_compStack[stacksize-1]].second < extent) m_components[m_compStack[stacksize-1]].second = extent; if (i == m_components[m_compStack[stacksize-1]].second) // component found { m_compStarts[m_components[m_compStack[stacksize-1]].first] = true; m_compEnds[i] = true; stacksize--; } } } int RevDist::calcHurdles() { int shortpaths = 0; // number of short paths int longpaths = 0; // number of long paths int highestbranch = m_permSize+1; // height of the highest branching node bool hbiscomp = false; // true if the highest branch is a component int highestunor = m_permSize+1; // height of the highest unoriented component int secondunor = m_permSize+1; // height of the second highest unoriented component int numunor = 0; // number of unoriented components int depth = 0; // the current depth int state; // state of a component m_chainStack[0] = 0; // the parent chain for (int i = 0; i < m_permSize; i++) { if (m_compStarts[i]) // start of a new component { depth++; m_compStack[depth] = 0; m_chainStack[depth] = 0; m_orientedStack[depth] = false; } if (m_mapped[(i+m_permSize-1)%m_permSize] * m_mapped[i] < 0) // component is oriented m_orientedStack[depth] = true; if (m_compEnds[i]) // end of a component { // don't count adjacencies as unoriented components if (m_compStarts[i]) m_orientedStack[depth] = true; if (!m_orientedStack[depth]) { numunor++; if (depth < highestunor) { secondunor = highestunor; highestunor = depth; } else if (depth < secondunor) secondunor = depth; } // also end child chain if (m_compStack[depth] == 0) m_compStack[depth] = m_chainStack[depth]; else if (m_chainStack[depth] != 0) { // node becomes branching - report child paths if (m_chainStack[depth] == 1) shortpaths++; else if (m_chainStack[depth] == 2) longpaths++; if (m_compStack[depth] == 1) shortpaths++; else if (m_compStack[depth] == 2) longpaths++; m_compStack[depth] = 4; if (depth <= highestbranch) { highestbranch = depth; hbiscomp = true; } } // get the state of this component if (!m_orientedStack[depth] && (m_compStack[depth] <= 1)) state = m_compStack[depth] + 1; else state = m_compStack[depth]; // report to parent chain depth--; if (m_chainStack[depth] == 0) { if (state == 4) m_chainStack[depth] = 3; else m_chainStack[depth] = state; } else if (state != 0) { // chain becomes branching - report child paths if (state == 1) shortpaths++; else if (state == 2) longpaths++; if (m_chainStack[depth] == 1) shortpaths++; else if (m_chainStack[depth] == 2) longpaths++; m_chainStack[depth] = 4; if (depth < highestbranch) { highestbranch = depth; hbiscomp = false; } } if ((i != m_permSize - 1) && !m_compStarts[i+1]) // also end the parent chain { if (m_compStack[depth] == 0) m_compStack[depth] = m_chainStack[depth]; else if (m_chainStack[depth] != 0) { // node becomes branching - report child paths if (m_chainStack[depth] == 1) shortpaths++; else if (m_chainStack[depth] == 2) longpaths++; if (m_compStack[depth] == 1) shortpaths++; else if (m_compStack[depth] == 2) longpaths++; m_compStack[depth] = 4; if (depth <= highestbranch) { highestbranch = depth; hbiscomp = true; } } // create new parent chain m_chainStack[depth] = 0; } if (i == m_permSize - 1) // end last chain { if (m_chainStack[depth] == 1) shortpaths++; else if (m_chainStack[depth] == 2) longpaths++; else if (m_chainStack[depth] == 4) { highestbranch = depth; hbiscomp = false; } } } } // check root path if (highestbranch != m_permSize+1) { if (!hbiscomp) highestbranch++; if (highestunor < highestbranch) { if (secondunor < highestbranch) longpaths++; else shortpaths++; } } /* cerr << "#unor: " << numunor << endl; cerr << "long: " << longpaths << endl; cerr << "short: " << shortpaths << endl; */ if (((longpaths & 1) == 1) && (shortpaths == 0)) return longpaths + 1; else return longpaths + shortpaths; } /***************************************************************************/ } // end namespace revDist phylo-1.0.6/revDist/COPYING0000644000175000017500000010451311434510050012242 00000000000000 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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For a particular product received by a particular user, "normally used" refers to a typical or common use of that class of product, regardless of the status of the particular user or of the way in which the particular user actually uses, or expects or is expected to use, the product. A product is a consumer product regardless of whether the product has substantial commercial, industrial or non-consumer uses, unless such uses represent the only significant mode of use of the product. "Installation Information" for a User Product means any methods, procedures, authorization keys, or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source. The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made. If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information. But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for example, the work has been installed in ROM). The requirement to provide Installation Information does not include a requirement to continue to provide support service, warranty, or updates for a work that has been modified or installed by the recipient, or for the User Product in which it has been modified or installed. Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network. Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form), and must require no special password or key for unpacking, reading or copying. 7. Additional Terms. "Additional permissions" are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions. When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission. Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms: a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it; or c) Prohibiting misrepresentation of the origin of that material, or requiring that modified versions of such material be marked in reasonable ways as different from the original version; or d) Limiting the use for publicity purposes of names of licensors or authors of the material; or e) Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability to the recipient, for any liability that these contractual assumptions directly impose on those licensors and authors. All other non-permissive additional terms are considered "further restrictions" within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying. If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement of the additional terms that apply to those files, or a notice indicating where to find the applicable terms. Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way. 8. Termination. You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11). However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation. Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice. Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10. 9. Acceptance Not Required for Having Copies. You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so. 10. Automatic Licensing of Downstream Recipients. Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License. An "entity transaction" is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party's predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts. You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it. 11. Patents. A "contributor" is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor's "contributor version". A contributor's "essential patent claims" are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, "control" includes the right to grant patent sublicenses in a manner consistent with the requirements of this License. Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor's essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version. In the following three paragraphs, a "patent license" is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To "grant" such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party. If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent license to downstream recipients. "Knowingly relying" means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient's use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid. If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it. A patent license is "discriminatory" if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007. Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law. 12. No Surrender of Others' Freedom. If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program. 13. Use with the GNU Affero General Public License. Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such. 14. Revised Versions of this License. The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation. If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program. Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version. 15. Disclaimer of Warranty. THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 16. Limitation of Liability. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 17. Interpretation of Sections 15 and 16. If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. 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phylo-1.0.6/revDist/revDist.h0000644000175000017500000000771311434510050013004 00000000000000/** * filename: revDist.h * author: Martin Bader * begin: 17.01.2007 * last change: 23.08.2007 * * Calculates the reversal distance between two genomes. * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef REVDIST_H_ #define REVDIST_H_ namespace revDist { /** * Pair of integers. */ struct IntPair { int first; int second; }; /** * The main class. */ class RevDist { /*********************************************************************** * member variables ***********************************************************************/ public: private: /** state of the program; 0: not yet initialized; 1: initialized */ int m_state; /** size of the permutations */ int m_permSize; /** the mapped permutation 1 (perm 2 is mapped to id) */ int* m_mapped; /** indicates the index for each element */ int* m_element2Index; /** the number of cycles */ int m_numCycles; /** maps each RE to a cylce */ int* m_perm2Cycle; /** stores for each component start- and endpoint */ IntPair* m_components; /** Indicates for each RE in the permutation wether it is a start point of * a component. */ bool* m_compStarts; /** Indicates for each RE in the permutation wether it is a end point of * a component. */ bool* m_compEnds; /** stack of component indices */ int* m_compStack; /** stack of chains */ int* m_chainStack; /** stack indicates which components are oriented */ bool* m_orientedStack; /*********************************************************************** * methods ***********************************************************************/ public: /** * Constructor. */ RevDist(); /** * Destructor. */ ~RevDist(); /** * Initializes the member variables. Call this after the constructor. * @param f_size permutation size */ void init(int f_size); /** * Calculates the distance between f_perm1 and f_perm2. Both permutations * must be of the size determined by calling init(). * @param f_perm1 the source permutation * @param f_perm2 the target permutation * @return the reversal distance */ int getDistance(const int* f_perm1, const int* f_perm2); private: /** * Maps the permutations such that f_perm2 is the id. The mapping of * f_pem1 will be written to m_mapping. This also initializes * m_element2Index */ void mapPermutations(const int* f_perm1, const int* f_perm2); /** * Gives each cycle a label, and marks for each RE the cycle it belongs * to. Stores to each cycle begin- and endpoint. This sets the initial * values of m_numCycles, m_perm2Cycle, and m_components. */ void markCycles(); /** * Finds all components, and fills their start/endpoints in m_compStarts * and m_compEnds. */ void findComponents(); /** * Calculates the number of hurdles (h) + the fortress indicator (f). * Returns h + f. * @return h + f */ int calcHurdles(); }; /***************************************************************************/ } // end namespace revDist #endif /*REVDIST_H_*/ phylo-1.0.6/revDist/Makefile.am0000644000175000017500000000065311434510050013243 00000000000000lib_LTLIBRARIES = librevDist.la librevDist_ladir = $(includedir) librevDist_la_SOURCES = revDist.cpp librevDist_la_HEADERS = $(librevDist_la_SOURCES:%.cpp=%.h) librevDist_la_LDFLAGS = -version-info 0:2:0 bin_PROGRAMS = revDist revDist_SOURCES = start.cpp revDist_LDADD = librevDist.la EXTRA_DIST = $(librevDist_la_HEADERS) test.in COPYING README revDistextradir = $(datadir)/revDist revDistextra_DATA = test.in COPYING README phylo-1.0.6/revDist/start.cpp0000644000175000017500000000606411434510050013052 00000000000000/** * filename: start.cpp * author: Martin Bader * begin: 17.01.2007 * last change: 23.08.2010 * * Start file. Small UI. * * Copyright (C) 2007-2010 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "revDist.h" #include #include using namespace std; /** * Reads a permutation from an input file. The array will be written to * f_origin and f_target (which are references of a pointer), and the * permutation size will be returned. * @param f_filename the name of the file * @param f_origin reference of the origin data pointer * @param f_target reference of the target data pointer * @return permutation size */ int readFile(const char* f_filename, int*& f_origin, int*& f_target) { ifstream input; // file input stream int size; // permutation size input.open(f_filename); if (!input.is_open()) { cerr << "error while opening the file " << f_filename << endl; return -1; } while (input.peek() == '#') // line is a comment input.ignore(999, '\n'); input >> size; input.ignore(999, '\n'); f_origin = new int[size]; f_target = new int[size]; while (input.peek() == '#') // line is a comment input.ignore(999, '\n'); for (int i = 0; i < size; i++) input >> f_origin[i]; input.ignore(999, '\n'); while (input.peek() == '#') // line is a comment input.ignore(999, '\n'); for (int i = 0; i < size; i++) input >> f_target[i]; input.close(); return size; } int main(int f_argc, char** f_argv) { revDist::RevDist rd; int size = 0; int* perm1, *perm2; int dist; cout << "*****************************************************************\n"; cout << "revDist v1.0.2 Copyright (C) 2007-2010 Martin Bader\n"; cout << "This program comes with ABSOLUTELY NO WARRANTY.\n"; cout << "This is free software, and you are welcome to redistribute it\n"; cout << "under certain conditions.\n"; cout << "For details about the licence, read the file gpl.txt\n"; cout << "*****************************************************************\n"; if (f_argc != 2) { cout << "Usage: revDist infile\n"; return 0; } cout << "reading file\n"; size = readFile(f_argv[1], perm1, perm2); rd.init(size); dist = rd.getDistance(perm1, perm2); cout << "dist: " << dist << endl; return 0; } phylo-1.0.6/revDist/test.in0000644000175000017500000000056511434510050012520 00000000000000# example file 36 1 -32 17 2 23 12 3 20 6 30 7 8 21 31 24 9 -10 -18 11 33 -28 19 14 34 13 25 4 22 -29 26 5 35 -15 -27 -16 -36 1 35 10 30 29 11 24 3 23 15 25 27 26 7 14 36 4 19 12 22 20 2 21 13 6 16 32 28 17 34 9 18 31 5 33 8 phylo-1.0.6/Makefile.in0000644000175000017500000005246511434510065011652 00000000000000# Makefile.in generated by automake 1.11.1 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, # Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; without # even the implied warranty of MERCHANTABILITY or FITNESS FOR A # PARTICULAR PURPOSE. @SET_MAKE@ VPATH = @srcdir@ pkgdatadir = $(datadir)/@PACKAGE@ pkgincludedir = $(includedir)/@PACKAGE@ pkglibdir = $(libdir)/@PACKAGE@ pkglibexecdir = $(libexecdir)/@PACKAGE@ am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd install_sh_DATA = $(install_sh) -c -m 644 install_sh_PROGRAM = $(install_sh) -c install_sh_SCRIPT = $(install_sh) -c INSTALL_HEADER = $(INSTALL_DATA) transform = $(program_transform_name) NORMAL_INSTALL = : PRE_INSTALL = : POST_INSTALL = : NORMAL_UNINSTALL = : PRE_UNINSTALL = : POST_UNINSTALL = : build_triplet = @build@ host_triplet = @host@ subdir = . 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see the source for copying conditions. There is NO # warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. # GNU Libtool is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # As a special exception to the GNU General Public License, # if you distribute this file as part of a program or library that # is built using GNU Libtool, you may include this file under the # same distribution terms that you use for the rest of that program. # # GNU Libtool is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with GNU Libtool; see the file COPYING. If not, a copy # can be downloaded from http://www.gnu.org/licenses/gpl.html, # or obtained by writing to the Free Software Foundation, Inc., # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. # Usage: $progname [OPTION]... [MODE-ARG]... # # Provide generalized library-building support services. # # --config show all configuration variables # --debug enable verbose shell tracing # -n, --dry-run display commands without modifying any files # --features display basic configuration information and exit # --mode=MODE use operation mode MODE # --preserve-dup-deps don't remove duplicate dependency libraries # --quiet, --silent don't print informational messages # --tag=TAG use configuration variables from tag TAG # -v, --verbose print informational messages (default) # --version print version information # -h, --help print short or long help message # # MODE must be one of the following: # # clean remove files from the build directory # compile compile a source file into a libtool object # execute automatically set library path, then run a program # finish complete the installation of libtool libraries # install install libraries or executables # link create a library or an executable # uninstall remove libraries from an installed directory # # MODE-ARGS vary depending on the MODE. # Try `$progname --help --mode=MODE' for a more detailed description of MODE. # # When reporting a bug, please describe a test case to reproduce it and # include the following information: # # host-triplet: $host # shell: $SHELL # compiler: $LTCC # compiler flags: $LTCFLAGS # linker: $LD (gnu? $with_gnu_ld) # $progname: (GNU libtool) 2.2.6b Debian-2.2.6b-2 # automake: $automake_version # autoconf: $autoconf_version # # Report bugs to . 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This is $PACKAGE $VERSION, but the $progname: definition of this LT_INIT comes from an older release. $progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION $progname: and run autoconf again. _LT_EOF else cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, but the $progname: definition of this LT_INIT comes from $PACKAGE $macro_version. $progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION $progname: and run autoconf again. _LT_EOF fi else cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, revision $package_revision, $progname: but the definition of this LT_INIT comes from revision $macro_revision. $progname: You should recreate aclocal.m4 with macros from revision $package_revision $progname: of $PACKAGE $VERSION and run autoconf again. _LT_EOF fi exit $EXIT_MISMATCH fi } ## ----------- ## ## Main. ## ## ----------- ## $opt_help || { # Sanity checks first: func_check_version_match if test "$build_libtool_libs" != yes && test "$build_old_libs" != yes; then func_fatal_configuration "not configured to build any kind of library" fi test -z "$mode" && func_fatal_error "error: you must specify a MODE." # Darwin sucks eval std_shrext=\"$shrext_cmds\" # Only execute mode is allowed to have -dlopen flags. if test -n "$execute_dlfiles" && test "$mode" != execute; then func_error "unrecognized option \`-dlopen'" $ECHO "$help" 1>&2 exit $EXIT_FAILURE fi # Change the help message to a mode-specific one. generic_help="$help" help="Try \`$progname --help --mode=$mode' for more information." } # func_lalib_p file # True iff FILE is a libtool `.la' library or `.lo' object file. # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_lalib_p () { test -f "$1" && $SED -e 4q "$1" 2>/dev/null \ | $GREP "^# Generated by .*$PACKAGE" > /dev/null 2>&1 } # func_lalib_unsafe_p file # True iff FILE is a libtool `.la' library or `.lo' object file. # This function implements the same check as func_lalib_p without # resorting to external programs. To this end, it redirects stdin and # closes it afterwards, without saving the original file descriptor. # As a safety measure, use it only where a negative result would be # fatal anyway. Works if `file' does not exist. func_lalib_unsafe_p () { lalib_p=no if test -f "$1" && test -r "$1" && exec 5<&0 <"$1"; then for lalib_p_l in 1 2 3 4 do read lalib_p_line case "$lalib_p_line" in \#\ Generated\ by\ *$PACKAGE* ) lalib_p=yes; break;; esac done exec 0<&5 5<&- fi test "$lalib_p" = yes } # func_ltwrapper_script_p file # True iff FILE is a libtool wrapper script # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_script_p () { func_lalib_p "$1" } # func_ltwrapper_executable_p file # True iff FILE is a libtool wrapper executable # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_executable_p () { func_ltwrapper_exec_suffix= case $1 in *.exe) ;; *) func_ltwrapper_exec_suffix=.exe ;; esac $GREP "$magic_exe" "$1$func_ltwrapper_exec_suffix" >/dev/null 2>&1 } # func_ltwrapper_scriptname file # Assumes file is an ltwrapper_executable # uses $file to determine the appropriate filename for a # temporary ltwrapper_script. func_ltwrapper_scriptname () { func_ltwrapper_scriptname_result="" if func_ltwrapper_executable_p "$1"; then func_dirname_and_basename "$1" "" "." func_stripname '' '.exe' "$func_basename_result" func_ltwrapper_scriptname_result="$func_dirname_result/$objdir/${func_stripname_result}_ltshwrapper" fi } # func_ltwrapper_p file # True iff FILE is a libtool wrapper script or wrapper executable # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_p () { func_ltwrapper_script_p "$1" || func_ltwrapper_executable_p "$1" } # func_execute_cmds commands fail_cmd # Execute tilde-delimited COMMANDS. # If FAIL_CMD is given, eval that upon failure. # FAIL_CMD may read-access the current command in variable CMD! func_execute_cmds () { $opt_debug save_ifs=$IFS; IFS='~' for cmd in $1; do IFS=$save_ifs eval cmd=\"$cmd\" func_show_eval "$cmd" "${2-:}" done IFS=$save_ifs } # func_source file # Source FILE, adding directory component if necessary. # Note that it is not necessary on cygwin/mingw to append a dot to # FILE even if both FILE and FILE.exe exist: automatic-append-.exe # behavior happens only for exec(3), not for open(2)! Also, sourcing # `FILE.' does not work on cygwin managed mounts. func_source () { $opt_debug case $1 in */* | *\\*) . "$1" ;; *) . "./$1" ;; esac } # func_infer_tag arg # Infer tagged configuration to use if any are available and # if one wasn't chosen via the "--tag" command line option. # Only attempt this if the compiler in the base compile # command doesn't match the default compiler. # arg is usually of the form 'gcc ...' func_infer_tag () { $opt_debug if test -n "$available_tags" && test -z "$tagname"; then CC_quoted= for arg in $CC; do func_quote_for_eval "$arg" CC_quoted="$CC_quoted $func_quote_for_eval_result" done case $@ in # Blanks in the command may have been stripped by the calling shell, # but not from the CC environment variable when configure was run. " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) ;; # Blanks at the start of $base_compile will cause this to fail # if we don't check for them as well. *) for z in $available_tags; do if $GREP "^# ### BEGIN LIBTOOL TAG CONFIG: $z$" < "$progpath" > /dev/null; then # Evaluate the configuration. eval "`${SED} -n -e '/^# ### BEGIN LIBTOOL TAG CONFIG: '$z'$/,/^# ### END LIBTOOL TAG CONFIG: '$z'$/p' < $progpath`" CC_quoted= for arg in $CC; do # Double-quote args containing other shell metacharacters. func_quote_for_eval "$arg" CC_quoted="$CC_quoted $func_quote_for_eval_result" done case "$@ " in " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) # The compiler in the base compile command matches # the one in the tagged configuration. # Assume this is the tagged configuration we want. tagname=$z break ;; esac fi done # If $tagname still isn't set, then no tagged configuration # was found and let the user know that the "--tag" command # line option must be used. if test -z "$tagname"; then func_echo "unable to infer tagged configuration" func_fatal_error "specify a tag with \`--tag'" # else # func_verbose "using $tagname tagged configuration" fi ;; esac fi } # func_write_libtool_object output_name pic_name nonpic_name # Create a libtool object file (analogous to a ".la" file), # but don't create it if we're doing a dry run. func_write_libtool_object () { write_libobj=${1} if test "$build_libtool_libs" = yes; then write_lobj=\'${2}\' else write_lobj=none fi if test "$build_old_libs" = yes; then write_oldobj=\'${3}\' else write_oldobj=none fi $opt_dry_run || { cat >${write_libobj}T <?"'"'"' &()|`$[]' \ && func_warning "libobj name \`$libobj' may not contain shell special characters." func_dirname_and_basename "$obj" "/" "" objname="$func_basename_result" xdir="$func_dirname_result" lobj=${xdir}$objdir/$objname test -z "$base_compile" && \ func_fatal_help "you must specify a compilation command" # Delete any leftover library objects. if test "$build_old_libs" = yes; then removelist="$obj $lobj $libobj ${libobj}T" else removelist="$lobj $libobj ${libobj}T" fi # On Cygwin there's no "real" PIC flag so we must build both object types case $host_os in cygwin* | mingw* | pw32* | os2* | cegcc*) pic_mode=default ;; esac if test "$pic_mode" = no && test "$deplibs_check_method" != pass_all; then # non-PIC code in shared libraries is not supported pic_mode=default fi # Calculate the filename of the output object if compiler does # not support -o with -c if test "$compiler_c_o" = no; then output_obj=`$ECHO "X$srcfile" | $Xsed -e 's%^.*/%%' -e 's%\.[^.]*$%%'`.${objext} lockfile="$output_obj.lock" else output_obj= need_locks=no lockfile= fi # Lock this critical section if it is needed # We use this script file to make the link, it avoids creating a new file if test "$need_locks" = yes; then until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do func_echo "Waiting for $lockfile to be removed" sleep 2 done elif test "$need_locks" = warn; then if test -f "$lockfile"; then $ECHO "\ *** ERROR, $lockfile exists and contains: `cat $lockfile 2>/dev/null` This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi removelist="$removelist $output_obj" $ECHO "$srcfile" > "$lockfile" fi $opt_dry_run || $RM $removelist removelist="$removelist $lockfile" trap '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' 1 2 15 if test -n "$fix_srcfile_path"; then eval srcfile=\"$fix_srcfile_path\" fi func_quote_for_eval "$srcfile" qsrcfile=$func_quote_for_eval_result # Only build a PIC object if we are building libtool libraries. if test "$build_libtool_libs" = yes; then # Without this assignment, base_compile gets emptied. fbsd_hideous_sh_bug=$base_compile if test "$pic_mode" != no; then command="$base_compile $qsrcfile $pic_flag" else # Don't build PIC code command="$base_compile $qsrcfile" fi func_mkdir_p "$xdir$objdir" if test -z "$output_obj"; then # Place PIC objects in $objdir command="$command -o $lobj" fi func_show_eval_locale "$command" \ 'test -n "$output_obj" && $RM $removelist; exit $EXIT_FAILURE' if test "$need_locks" = warn && test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then $ECHO "\ *** ERROR, $lockfile contains: `cat $lockfile 2>/dev/null` but it should contain: $srcfile This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi # Just move the object if needed, then go on to compile the next one if test -n "$output_obj" && test "X$output_obj" != "X$lobj"; then func_show_eval '$MV "$output_obj" "$lobj"' \ 'error=$?; $opt_dry_run || $RM $removelist; exit $error' fi # Allow error messages only from the first compilation. if test "$suppress_opt" = yes; then suppress_output=' >/dev/null 2>&1' fi fi # Only build a position-dependent object if we build old libraries. if test "$build_old_libs" = yes; then if test "$pic_mode" != yes; then # Don't build PIC code command="$base_compile $qsrcfile$pie_flag" else command="$base_compile $qsrcfile $pic_flag" fi if test "$compiler_c_o" = yes; then command="$command -o $obj" fi # Suppress compiler output if we already did a PIC compilation. command="$command$suppress_output" func_show_eval_locale "$command" \ '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' if test "$need_locks" = warn && test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then $ECHO "\ *** ERROR, $lockfile contains: `cat $lockfile 2>/dev/null` but it should contain: $srcfile This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi # Just move the object if needed if test -n "$output_obj" && test "X$output_obj" != "X$obj"; then func_show_eval '$MV "$output_obj" "$obj"' \ 'error=$?; $opt_dry_run || $RM $removelist; exit $error' fi fi $opt_dry_run || { func_write_libtool_object "$libobj" "$objdir/$objname" "$objname" # Unlock the critical section if it was locked if test "$need_locks" != no; then removelist=$lockfile $RM "$lockfile" fi } exit $EXIT_SUCCESS } $opt_help || { test "$mode" = compile && func_mode_compile ${1+"$@"} } func_mode_help () { # We need to display help for each of the modes. case $mode in "") # Generic help is extracted from the usage comments # at the start of this file. func_help ;; clean) $ECHO \ "Usage: $progname [OPTION]... --mode=clean RM [RM-OPTION]... FILE... Remove files from the build directory. RM is the name of the program to use to delete files associated with each FILE (typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed to RM. If FILE is a libtool library, object or program, all the files associated with it are deleted. Otherwise, only FILE itself is deleted using RM." ;; compile) $ECHO \ "Usage: $progname [OPTION]... --mode=compile COMPILE-COMMAND... SOURCEFILE Compile a source file into a libtool library object. This mode accepts the following additional options: -o OUTPUT-FILE set the output file name to OUTPUT-FILE -no-suppress do not suppress compiler output for multiple passes -prefer-pic try to building PIC objects only -prefer-non-pic try to building non-PIC objects only -shared do not build a \`.o' file suitable for static linking -static only build a \`.o' file suitable for static linking COMPILE-COMMAND is a command to be used in creating a \`standard' object file from the given SOURCEFILE. The output file name is determined by removing the directory component from SOURCEFILE, then substituting the C source code suffix \`.c' with the library object suffix, \`.lo'." ;; execute) $ECHO \ "Usage: $progname [OPTION]... --mode=execute COMMAND [ARGS]... Automatically set library path, then run a program. This mode accepts the following additional options: -dlopen FILE add the directory containing FILE to the library path This mode sets the library path environment variable according to \`-dlopen' flags. If any of the ARGS are libtool executable wrappers, then they are translated into their corresponding uninstalled binary, and any of their required library directories are added to the library path. Then, COMMAND is executed, with ARGS as arguments." ;; finish) $ECHO \ "Usage: $progname [OPTION]... --mode=finish [LIBDIR]... Complete the installation of libtool libraries. Each LIBDIR is a directory that contains libtool libraries. The commands that this mode executes may require superuser privileges. Use the \`--dry-run' option if you just want to see what would be executed." ;; install) $ECHO \ "Usage: $progname [OPTION]... --mode=install INSTALL-COMMAND... Install executables or libraries. INSTALL-COMMAND is the installation command. The first component should be either the \`install' or \`cp' program. The following components of INSTALL-COMMAND are treated specially: -inst-prefix PREFIX-DIR Use PREFIX-DIR as a staging area for installation The rest of the components are interpreted as arguments to that command (only BSD-compatible install options are recognized)." ;; link) $ECHO \ "Usage: $progname [OPTION]... --mode=link LINK-COMMAND... Link object files or libraries together to form another library, or to create an executable program. LINK-COMMAND is a command using the C compiler that you would use to create a program from several object files. The following components of LINK-COMMAND are treated specially: -all-static do not do any dynamic linking at all -avoid-version do not add a version suffix if possible -dlopen FILE \`-dlpreopen' FILE if it cannot be dlopened at runtime -dlpreopen FILE link in FILE and add its symbols to lt_preloaded_symbols -export-dynamic allow symbols from OUTPUT-FILE to be resolved with dlsym(3) -export-symbols SYMFILE try to export only the symbols listed in SYMFILE -export-symbols-regex REGEX try to export only the symbols matching REGEX -LLIBDIR search LIBDIR for required installed libraries -lNAME OUTPUT-FILE requires the installed library libNAME -module build a library that can dlopened -no-fast-install disable the fast-install mode -no-install link a not-installable executable -no-undefined declare that a library does not refer to external symbols -o OUTPUT-FILE create OUTPUT-FILE from the specified objects -objectlist FILE Use a list of object files found in FILE to specify objects -precious-files-regex REGEX don't remove output files matching REGEX -release RELEASE specify package release information -rpath LIBDIR the created library will eventually be installed in LIBDIR -R[ ]LIBDIR add LIBDIR to the runtime path of programs and libraries -shared only do dynamic linking of libtool libraries -shrext SUFFIX override the standard shared library file extension -static do not do any dynamic linking of uninstalled libtool libraries -static-libtool-libs do not do any dynamic linking of libtool libraries -version-info CURRENT[:REVISION[:AGE]] specify library version info [each variable defaults to 0] -weak LIBNAME declare that the target provides the LIBNAME interface All other options (arguments beginning with \`-') are ignored. Every other argument is treated as a filename. Files ending in \`.la' are treated as uninstalled libtool libraries, other files are standard or library object files. If the OUTPUT-FILE ends in \`.la', then a libtool library is created, only library objects (\`.lo' files) may be specified, and \`-rpath' is required, except when creating a convenience library. If OUTPUT-FILE ends in \`.a' or \`.lib', then a standard library is created using \`ar' and \`ranlib', or on Windows using \`lib'. If OUTPUT-FILE ends in \`.lo' or \`.${objext}', then a reloadable object file is created, otherwise an executable program is created." ;; uninstall) $ECHO \ "Usage: $progname [OPTION]... --mode=uninstall RM [RM-OPTION]... FILE... Remove libraries from an installation directory. RM is the name of the program to use to delete files associated with each FILE (typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed to RM. If FILE is a libtool library, all the files associated with it are deleted. Otherwise, only FILE itself is deleted using RM." ;; *) func_fatal_help "invalid operation mode \`$mode'" ;; esac $ECHO $ECHO "Try \`$progname --help' for more information about other modes." exit $? } # Now that we've collected a possible --mode arg, show help if necessary $opt_help && func_mode_help # func_mode_execute arg... func_mode_execute () { $opt_debug # The first argument is the command name. cmd="$nonopt" test -z "$cmd" && \ func_fatal_help "you must specify a COMMAND" # Handle -dlopen flags immediately. for file in $execute_dlfiles; do test -f "$file" \ || func_fatal_help "\`$file' is not a file" dir= case $file in *.la) # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$file" \ || func_fatal_help "\`$lib' is not a valid libtool archive" # Read the libtool library. dlname= library_names= func_source "$file" # Skip this library if it cannot be dlopened. if test -z "$dlname"; then # Warn if it was a shared library. test -n "$library_names" && \ func_warning "\`$file' was not linked with \`-export-dynamic'" continue fi func_dirname "$file" "" "." dir="$func_dirname_result" if test -f "$dir/$objdir/$dlname"; then dir="$dir/$objdir" else if test ! -f "$dir/$dlname"; then func_fatal_error "cannot find \`$dlname' in \`$dir' or \`$dir/$objdir'" fi fi ;; *.lo) # Just add the directory containing the .lo file. func_dirname "$file" "" "." dir="$func_dirname_result" ;; *) func_warning "\`-dlopen' is ignored for non-libtool libraries and objects" continue ;; esac # Get the absolute pathname. absdir=`cd "$dir" && pwd` test -n "$absdir" && dir="$absdir" # Now add the directory to shlibpath_var. if eval "test -z \"\$$shlibpath_var\""; then eval "$shlibpath_var=\"\$dir\"" else eval "$shlibpath_var=\"\$dir:\$$shlibpath_var\"" fi done # This variable tells wrapper scripts just to set shlibpath_var # rather than running their programs. libtool_execute_magic="$magic" # Check if any of the arguments is a wrapper script. args= for file do case $file in -*) ;; *) # Do a test to see if this is really a libtool program. if func_ltwrapper_script_p "$file"; then func_source "$file" # Transform arg to wrapped name. file="$progdir/$program" elif func_ltwrapper_executable_p "$file"; then func_ltwrapper_scriptname "$file" func_source "$func_ltwrapper_scriptname_result" # Transform arg to wrapped name. file="$progdir/$program" fi ;; esac # Quote arguments (to preserve shell metacharacters). func_quote_for_eval "$file" args="$args $func_quote_for_eval_result" done if test "X$opt_dry_run" = Xfalse; then if test -n "$shlibpath_var"; then # Export the shlibpath_var. eval "export $shlibpath_var" fi # Restore saved environment variables for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES do eval "if test \"\${save_$lt_var+set}\" = set; then $lt_var=\$save_$lt_var; export $lt_var else $lt_unset $lt_var fi" done # Now prepare to actually exec the command. exec_cmd="\$cmd$args" else # Display what would be done. if test -n "$shlibpath_var"; then eval "\$ECHO \"\$shlibpath_var=\$$shlibpath_var\"" $ECHO "export $shlibpath_var" fi $ECHO "$cmd$args" exit $EXIT_SUCCESS fi } test "$mode" = execute && func_mode_execute ${1+"$@"} # func_mode_finish arg... func_mode_finish () { $opt_debug libdirs="$nonopt" admincmds= if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then for dir do libdirs="$libdirs $dir" done for libdir in $libdirs; do if test -n "$finish_cmds"; then # Do each command in the finish commands. func_execute_cmds "$finish_cmds" 'admincmds="$admincmds '"$cmd"'"' fi if test -n "$finish_eval"; then # Do the single finish_eval. eval cmds=\"$finish_eval\" $opt_dry_run || eval "$cmds" || admincmds="$admincmds $cmds" fi done fi # Exit here if they wanted silent mode. $opt_silent && exit $EXIT_SUCCESS $ECHO "X----------------------------------------------------------------------" | $Xsed $ECHO "Libraries have been installed in:" for libdir in $libdirs; do $ECHO " $libdir" done $ECHO $ECHO "If you ever happen to want to link against installed libraries" $ECHO "in a given directory, LIBDIR, you must either use libtool, and" $ECHO "specify the full pathname of the library, or use the \`-LLIBDIR'" $ECHO "flag during linking and do at least one of the following:" if test -n "$shlibpath_var"; then $ECHO " - add LIBDIR to the \`$shlibpath_var' environment variable" $ECHO " during execution" fi if test -n "$runpath_var"; then $ECHO " - add LIBDIR to the \`$runpath_var' environment variable" $ECHO " during linking" fi if test -n "$hardcode_libdir_flag_spec"; then libdir=LIBDIR eval flag=\"$hardcode_libdir_flag_spec\" $ECHO " - use the \`$flag' linker flag" fi if test -n "$admincmds"; then $ECHO " - have your system administrator run these commands:$admincmds" fi if test -f /etc/ld.so.conf; then $ECHO " - have your system administrator add LIBDIR to \`/etc/ld.so.conf'" fi $ECHO $ECHO "See any operating system documentation about shared libraries for" case $host in solaris2.[6789]|solaris2.1[0-9]) $ECHO "more information, such as the ld(1), crle(1) and ld.so(8) manual" $ECHO "pages." ;; *) $ECHO "more information, such as the ld(1) and ld.so(8) manual pages." ;; esac $ECHO "X----------------------------------------------------------------------" | $Xsed exit $EXIT_SUCCESS } test "$mode" = finish && func_mode_finish ${1+"$@"} # func_mode_install arg... func_mode_install () { $opt_debug # There may be an optional sh(1) argument at the beginning of # install_prog (especially on Windows NT). if test "$nonopt" = "$SHELL" || test "$nonopt" = /bin/sh || # Allow the use of GNU shtool's install command. $ECHO "X$nonopt" | $GREP shtool >/dev/null; then # Aesthetically quote it. func_quote_for_eval "$nonopt" install_prog="$func_quote_for_eval_result " arg=$1 shift else install_prog= arg=$nonopt fi # The real first argument should be the name of the installation program. # Aesthetically quote it. func_quote_for_eval "$arg" install_prog="$install_prog$func_quote_for_eval_result" # We need to accept at least all the BSD install flags. dest= files= opts= prev= install_type= isdir=no stripme= for arg do if test -n "$dest"; then files="$files $dest" dest=$arg continue fi case $arg in -d) isdir=yes ;; -f) case " $install_prog " in *[\\\ /]cp\ *) ;; *) prev=$arg ;; esac ;; -g | -m | -o) prev=$arg ;; -s) stripme=" -s" continue ;; -*) ;; *) # If the previous option needed an argument, then skip it. if test -n "$prev"; then prev= else dest=$arg continue fi ;; esac # Aesthetically quote the argument. func_quote_for_eval "$arg" install_prog="$install_prog $func_quote_for_eval_result" done test -z "$install_prog" && \ func_fatal_help "you must specify an install program" test -n "$prev" && \ func_fatal_help "the \`$prev' option requires an argument" if test -z "$files"; then if test -z "$dest"; then func_fatal_help "no file or destination specified" else func_fatal_help "you must specify a destination" fi fi # Strip any trailing slash from the destination. func_stripname '' '/' "$dest" dest=$func_stripname_result # Check to see that the destination is a directory. test -d "$dest" && isdir=yes if test "$isdir" = yes; then destdir="$dest" destname= else func_dirname_and_basename "$dest" "" "." destdir="$func_dirname_result" destname="$func_basename_result" # Not a directory, so check to see that there is only one file specified. set dummy $files; shift test "$#" -gt 1 && \ func_fatal_help "\`$dest' is not a directory" fi case $destdir in [\\/]* | [A-Za-z]:[\\/]*) ;; *) for file in $files; do case $file in *.lo) ;; *) func_fatal_help "\`$destdir' must be an absolute directory name" ;; esac done ;; esac # This variable tells wrapper scripts just to set variables rather # than running their programs. libtool_install_magic="$magic" staticlibs= future_libdirs= current_libdirs= for file in $files; do # Do each installation. case $file in *.$libext) # Do the static libraries later. staticlibs="$staticlibs $file" ;; *.la) # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$file" \ || func_fatal_help "\`$file' is not a valid libtool archive" library_names= old_library= relink_command= func_source "$file" # Add the libdir to current_libdirs if it is the destination. if test "X$destdir" = "X$libdir"; then case "$current_libdirs " in *" $libdir "*) ;; *) current_libdirs="$current_libdirs $libdir" ;; esac else # Note the libdir as a future libdir. case "$future_libdirs " in *" $libdir "*) ;; *) future_libdirs="$future_libdirs $libdir" ;; esac fi func_dirname "$file" "/" "" dir="$func_dirname_result" dir="$dir$objdir" if test -n "$relink_command"; then # Determine the prefix the user has applied to our future dir. inst_prefix_dir=`$ECHO "X$destdir" | $Xsed -e "s%$libdir\$%%"` # Don't allow the user to place us outside of our expected # location b/c this prevents finding dependent libraries that # are installed to the same prefix. # At present, this check doesn't affect windows .dll's that # are installed into $libdir/../bin (currently, that works fine) # but it's something to keep an eye on. test "$inst_prefix_dir" = "$destdir" && \ func_fatal_error "error: cannot install \`$file' to a directory not ending in $libdir" if test -n "$inst_prefix_dir"; then # Stick the inst_prefix_dir data into the link command. relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"` else relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%%"` fi func_warning "relinking \`$file'" func_show_eval "$relink_command" \ 'func_fatal_error "error: relink \`$file'\'' with the above command before installing it"' fi # See the names of the shared library. set dummy $library_names; shift if test -n "$1"; then realname="$1" shift srcname="$realname" test -n "$relink_command" && srcname="$realname"T # Install the shared library and build the symlinks. func_show_eval "$install_prog $dir/$srcname $destdir/$realname" \ 'exit $?' tstripme="$stripme" case $host_os in cygwin* | mingw* | pw32* | cegcc*) case $realname in *.dll.a) tstripme="" ;; esac ;; esac if test -n "$tstripme" && test -n "$striplib"; then func_show_eval "$striplib $destdir/$realname" 'exit $?' fi if test "$#" -gt 0; then # Delete the old symlinks, and create new ones. # Try `ln -sf' first, because the `ln' binary might depend on # the symlink we replace! Solaris /bin/ln does not understand -f, # so we also need to try rm && ln -s. for linkname do test "$linkname" != "$realname" \ && func_show_eval "(cd $destdir && { $LN_S -f $realname $linkname || { $RM $linkname && $LN_S $realname $linkname; }; })" done fi # Do each command in the postinstall commands. lib="$destdir/$realname" func_execute_cmds "$postinstall_cmds" 'exit $?' fi # Install the pseudo-library for information purposes. func_basename "$file" name="$func_basename_result" instname="$dir/$name"i func_show_eval "$install_prog $instname $destdir/$name" 'exit $?' # Maybe install the static library, too. test -n "$old_library" && staticlibs="$staticlibs $dir/$old_library" ;; *.lo) # Install (i.e. copy) a libtool object. # Figure out destination file name, if it wasn't already specified. if test -n "$destname"; then destfile="$destdir/$destname" else func_basename "$file" destfile="$func_basename_result" destfile="$destdir/$destfile" fi # Deduce the name of the destination old-style object file. case $destfile in *.lo) func_lo2o "$destfile" staticdest=$func_lo2o_result ;; *.$objext) staticdest="$destfile" destfile= ;; *) func_fatal_help "cannot copy a libtool object to \`$destfile'" ;; esac # Install the libtool object if requested. test -n "$destfile" && \ func_show_eval "$install_prog $file $destfile" 'exit $?' # Install the old object if enabled. if test "$build_old_libs" = yes; then # Deduce the name of the old-style object file. func_lo2o "$file" staticobj=$func_lo2o_result func_show_eval "$install_prog \$staticobj \$staticdest" 'exit $?' fi exit $EXIT_SUCCESS ;; *) # Figure out destination file name, if it wasn't already specified. if test -n "$destname"; then destfile="$destdir/$destname" else func_basename "$file" destfile="$func_basename_result" destfile="$destdir/$destfile" fi # If the file is missing, and there is a .exe on the end, strip it # because it is most likely a libtool script we actually want to # install stripped_ext="" case $file in *.exe) if test ! -f "$file"; then func_stripname '' '.exe' "$file" file=$func_stripname_result stripped_ext=".exe" fi ;; esac # Do a test to see if this is really a libtool program. case $host in *cygwin* | *mingw*) if func_ltwrapper_executable_p "$file"; then func_ltwrapper_scriptname "$file" wrapper=$func_ltwrapper_scriptname_result else func_stripname '' '.exe' "$file" wrapper=$func_stripname_result fi ;; *) wrapper=$file ;; esac if func_ltwrapper_script_p "$wrapper"; then notinst_deplibs= relink_command= func_source "$wrapper" # Check the variables that should have been set. test -z "$generated_by_libtool_version" && \ func_fatal_error "invalid libtool wrapper script \`$wrapper'" finalize=yes for lib in $notinst_deplibs; do # Check to see that each library is installed. libdir= if test -f "$lib"; then func_source "$lib" fi libfile="$libdir/"`$ECHO "X$lib" | $Xsed -e 's%^.*/%%g'` ### testsuite: skip nested quoting test if test -n "$libdir" && test ! -f "$libfile"; then func_warning "\`$lib' has not been installed in \`$libdir'" finalize=no fi done relink_command= func_source "$wrapper" outputname= if test "$fast_install" = no && test -n "$relink_command"; then $opt_dry_run || { if test "$finalize" = yes; then tmpdir=`func_mktempdir` func_basename "$file$stripped_ext" file="$func_basename_result" outputname="$tmpdir/$file" # Replace the output file specification. relink_command=`$ECHO "X$relink_command" | $Xsed -e 's%@OUTPUT@%'"$outputname"'%g'` $opt_silent || { func_quote_for_expand "$relink_command" eval "func_echo $func_quote_for_expand_result" } if eval "$relink_command"; then : else func_error "error: relink \`$file' with the above command before installing it" $opt_dry_run || ${RM}r "$tmpdir" continue fi file="$outputname" else func_warning "cannot relink \`$file'" fi } else # Install the binary that we compiled earlier. file=`$ECHO "X$file$stripped_ext" | $Xsed -e "s%\([^/]*\)$%$objdir/\1%"` fi fi # remove .exe since cygwin /usr/bin/install will append another # one anyway case $install_prog,$host in */usr/bin/install*,*cygwin*) case $file:$destfile in *.exe:*.exe) # this is ok ;; *.exe:*) destfile=$destfile.exe ;; *:*.exe) func_stripname '' '.exe' "$destfile" destfile=$func_stripname_result ;; esac ;; esac func_show_eval "$install_prog\$stripme \$file \$destfile" 'exit $?' $opt_dry_run || if test -n "$outputname"; then ${RM}r "$tmpdir" fi ;; esac done for file in $staticlibs; do func_basename "$file" name="$func_basename_result" # Set up the ranlib parameters. oldlib="$destdir/$name" func_show_eval "$install_prog \$file \$oldlib" 'exit $?' if test -n "$stripme" && test -n "$old_striplib"; then func_show_eval "$old_striplib $oldlib" 'exit $?' fi # Do each command in the postinstall commands. func_execute_cmds "$old_postinstall_cmds" 'exit $?' done test -n "$future_libdirs" && \ func_warning "remember to run \`$progname --finish$future_libdirs'" if test -n "$current_libdirs"; then # Maybe just do a dry run. $opt_dry_run && current_libdirs=" -n$current_libdirs" exec_cmd='$SHELL $progpath $preserve_args --finish$current_libdirs' else exit $EXIT_SUCCESS fi } test "$mode" = install && func_mode_install ${1+"$@"} # func_generate_dlsyms outputname originator pic_p # Extract symbols from dlprefiles and create ${outputname}S.o with # a dlpreopen symbol table. func_generate_dlsyms () { $opt_debug my_outputname="$1" my_originator="$2" my_pic_p="${3-no}" my_prefix=`$ECHO "$my_originator" | sed 's%[^a-zA-Z0-9]%_%g'` my_dlsyms= if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then if test -n "$NM" && test -n "$global_symbol_pipe"; then my_dlsyms="${my_outputname}S.c" else func_error "not configured to extract global symbols from dlpreopened files" fi fi if test -n "$my_dlsyms"; then case $my_dlsyms in "") ;; *.c) # Discover the nlist of each of the dlfiles. nlist="$output_objdir/${my_outputname}.nm" func_show_eval "$RM $nlist ${nlist}S ${nlist}T" # Parse the name list into a source file. func_verbose "creating $output_objdir/$my_dlsyms" $opt_dry_run || $ECHO > "$output_objdir/$my_dlsyms" "\ /* $my_dlsyms - symbol resolution table for \`$my_outputname' dlsym emulation. */ /* Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION */ #ifdef __cplusplus extern \"C\" { #endif /* External symbol declarations for the compiler. */\ " if test "$dlself" = yes; then func_verbose "generating symbol list for \`$output'" $opt_dry_run || echo ': @PROGRAM@ ' > "$nlist" # Add our own program objects to the symbol list. progfiles=`$ECHO "X$objs$old_deplibs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` for progfile in $progfiles; do func_verbose "extracting global C symbols from \`$progfile'" $opt_dry_run || eval "$NM $progfile | $global_symbol_pipe >> '$nlist'" done if test -n "$exclude_expsyms"; then $opt_dry_run || { eval '$EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' } fi if test -n "$export_symbols_regex"; then $opt_dry_run || { eval '$EGREP -e "$export_symbols_regex" "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' } fi # Prepare the list of exported symbols if test -z "$export_symbols"; then export_symbols="$output_objdir/$outputname.exp" $opt_dry_run || { $RM $export_symbols eval "${SED} -n -e '/^: @PROGRAM@ $/d' -e 's/^.* \(.*\)$/\1/p' "'< "$nlist" > "$export_symbols"' case $host in *cygwin* | *mingw* | *cegcc* ) eval "echo EXPORTS "'> "$output_objdir/$outputname.def"' eval 'cat "$export_symbols" >> "$output_objdir/$outputname.def"' ;; esac } else $opt_dry_run || { eval "${SED} -e 's/\([].[*^$]\)/\\\\\1/g' -e 's/^/ /' -e 's/$/$/'"' < "$export_symbols" > "$output_objdir/$outputname.exp"' eval '$GREP -f "$output_objdir/$outputname.exp" < "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' case $host in *cygwin | *mingw* | *cegcc* ) eval "echo EXPORTS "'> "$output_objdir/$outputname.def"' eval 'cat "$nlist" >> "$output_objdir/$outputname.def"' ;; esac } fi fi for dlprefile in $dlprefiles; do func_verbose "extracting global C symbols from \`$dlprefile'" func_basename "$dlprefile" name="$func_basename_result" $opt_dry_run || { eval '$ECHO ": $name " >> "$nlist"' eval "$NM $dlprefile 2>/dev/null | $global_symbol_pipe >> '$nlist'" } done $opt_dry_run || { # Make sure we have at least an empty file. test -f "$nlist" || : > "$nlist" if test -n "$exclude_expsyms"; then $EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T $MV "$nlist"T "$nlist" fi # Try sorting and uniquifying the output. if $GREP -v "^: " < "$nlist" | if sort -k 3 /dev/null 2>&1; then sort -k 3 else sort +2 fi | uniq > "$nlist"S; then : else $GREP -v "^: " < "$nlist" > "$nlist"S fi if test -f "$nlist"S; then eval "$global_symbol_to_cdecl"' < "$nlist"S >> "$output_objdir/$my_dlsyms"' else $ECHO '/* NONE */' >> "$output_objdir/$my_dlsyms" fi $ECHO >> "$output_objdir/$my_dlsyms" "\ /* The mapping between symbol names and symbols. */ typedef struct { const char *name; void *address; } lt_dlsymlist; " case $host in *cygwin* | *mingw* | *cegcc* ) $ECHO >> "$output_objdir/$my_dlsyms" "\ /* DATA imports from DLLs on WIN32 con't be const, because runtime relocations are performed -- see ld's documentation on pseudo-relocs. */" lt_dlsym_const= ;; *osf5*) echo >> "$output_objdir/$my_dlsyms" "\ /* This system does not cope well with relocations in const data */" lt_dlsym_const= ;; *) lt_dlsym_const=const ;; esac $ECHO >> "$output_objdir/$my_dlsyms" "\ extern $lt_dlsym_const lt_dlsymlist lt_${my_prefix}_LTX_preloaded_symbols[]; $lt_dlsym_const lt_dlsymlist lt_${my_prefix}_LTX_preloaded_symbols[] = {\ { \"$my_originator\", (void *) 0 }," case $need_lib_prefix in no) eval "$global_symbol_to_c_name_address" < "$nlist" >> "$output_objdir/$my_dlsyms" ;; *) eval "$global_symbol_to_c_name_address_lib_prefix" < "$nlist" >> "$output_objdir/$my_dlsyms" ;; esac $ECHO >> "$output_objdir/$my_dlsyms" "\ {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt_${my_prefix}_LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif\ " } # !$opt_dry_run pic_flag_for_symtable= case "$compile_command " in *" -static "*) ;; *) case $host in # compiling the symbol table file with pic_flag works around # a FreeBSD bug that causes programs to crash when -lm is # linked before any other PIC object. But we must not use # pic_flag when linking with -static. The problem exists in # FreeBSD 2.2.6 and is fixed in FreeBSD 3.1. *-*-freebsd2*|*-*-freebsd3.0*|*-*-freebsdelf3.0*) pic_flag_for_symtable=" $pic_flag -DFREEBSD_WORKAROUND" ;; *-*-hpux*) pic_flag_for_symtable=" $pic_flag" ;; *) if test "X$my_pic_p" != Xno; then pic_flag_for_symtable=" $pic_flag" fi ;; esac ;; esac symtab_cflags= for arg in $LTCFLAGS; do case $arg in -pie | -fpie | -fPIE) ;; *) symtab_cflags="$symtab_cflags $arg" ;; esac done # Now compile the dynamic symbol file. func_show_eval '(cd $output_objdir && $LTCC$symtab_cflags -c$no_builtin_flag$pic_flag_for_symtable "$my_dlsyms")' 'exit $?' # Clean up the generated files. func_show_eval '$RM "$output_objdir/$my_dlsyms" "$nlist" "${nlist}S" "${nlist}T"' # Transform the symbol file into the correct name. symfileobj="$output_objdir/${my_outputname}S.$objext" case $host in *cygwin* | *mingw* | *cegcc* ) if test -f "$output_objdir/$my_outputname.def"; then compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` else compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` fi ;; *) compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` ;; esac ;; *) func_fatal_error "unknown suffix for \`$my_dlsyms'" ;; esac else # We keep going just in case the user didn't refer to # lt_preloaded_symbols. The linker will fail if global_symbol_pipe # really was required. # Nullify the symbol file. compile_command=`$ECHO "X$compile_command" | $Xsed -e "s% @SYMFILE@%%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s% @SYMFILE@%%"` fi } # func_win32_libid arg # return the library type of file 'arg' # # Need a lot of goo to handle *both* DLLs and import libs # Has to be a shell function in order to 'eat' the argument # that is supplied when $file_magic_command is called. func_win32_libid () { $opt_debug win32_libid_type="unknown" win32_fileres=`file -L $1 2>/dev/null` case $win32_fileres in *ar\ archive\ import\ library*) # definitely import win32_libid_type="x86 archive import" ;; *ar\ archive*) # could be an import, or static if eval $OBJDUMP -f $1 | $SED -e '10q' 2>/dev/null | $EGREP 'file format pe-i386(.*architecture: i386)?' >/dev/null ; then win32_nmres=`eval $NM -f posix -A $1 | $SED -n -e ' 1,100{ / I /{ s,.*,import, p q } }'` case $win32_nmres in import*) win32_libid_type="x86 archive import";; *) win32_libid_type="x86 archive static";; esac fi ;; *DLL*) win32_libid_type="x86 DLL" ;; *executable*) # but shell scripts are "executable" too... case $win32_fileres in *MS\ Windows\ PE\ Intel*) win32_libid_type="x86 DLL" ;; esac ;; esac $ECHO "$win32_libid_type" } # func_extract_an_archive dir oldlib func_extract_an_archive () { $opt_debug f_ex_an_ar_dir="$1"; shift f_ex_an_ar_oldlib="$1" func_show_eval "(cd \$f_ex_an_ar_dir && $AR x \"\$f_ex_an_ar_oldlib\")" 'exit $?' if ($AR t "$f_ex_an_ar_oldlib" | sort | sort -uc >/dev/null 2>&1); then : else func_fatal_error "object name conflicts in archive: $f_ex_an_ar_dir/$f_ex_an_ar_oldlib" fi } # func_extract_archives gentop oldlib ... func_extract_archives () { $opt_debug my_gentop="$1"; shift my_oldlibs=${1+"$@"} my_oldobjs="" my_xlib="" my_xabs="" my_xdir="" for my_xlib in $my_oldlibs; do # Extract the objects. case $my_xlib in [\\/]* | [A-Za-z]:[\\/]*) my_xabs="$my_xlib" ;; *) my_xabs=`pwd`"/$my_xlib" ;; esac func_basename "$my_xlib" my_xlib="$func_basename_result" my_xlib_u=$my_xlib while :; do case " $extracted_archives " in *" $my_xlib_u "*) func_arith $extracted_serial + 1 extracted_serial=$func_arith_result my_xlib_u=lt$extracted_serial-$my_xlib ;; *) break ;; esac done extracted_archives="$extracted_archives $my_xlib_u" my_xdir="$my_gentop/$my_xlib_u" func_mkdir_p "$my_xdir" case $host in *-darwin*) func_verbose "Extracting $my_xabs" # Do not bother doing anything if just a dry run $opt_dry_run || { darwin_orig_dir=`pwd` cd $my_xdir || exit $? darwin_archive=$my_xabs darwin_curdir=`pwd` darwin_base_archive=`basename "$darwin_archive"` darwin_arches=`$LIPO -info "$darwin_archive" 2>/dev/null | $GREP Architectures 2>/dev/null || true` if test -n "$darwin_arches"; then darwin_arches=`$ECHO "$darwin_arches" | $SED -e 's/.*are://'` darwin_arch= func_verbose "$darwin_base_archive has multiple architectures $darwin_arches" for darwin_arch in $darwin_arches ; do func_mkdir_p "unfat-$$/${darwin_base_archive}-${darwin_arch}" $LIPO -thin $darwin_arch -output "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" "${darwin_archive}" cd "unfat-$$/${darwin_base_archive}-${darwin_arch}" func_extract_an_archive "`pwd`" "${darwin_base_archive}" cd "$darwin_curdir" $RM "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" done # $darwin_arches ## Okay now we've a bunch of thin objects, gotta fatten them up :) darwin_filelist=`find unfat-$$ -type f -name \*.o -print -o -name \*.lo -print | $SED -e "$basename" | sort -u` darwin_file= darwin_files= for darwin_file in $darwin_filelist; do darwin_files=`find unfat-$$ -name $darwin_file -print | $NL2SP` $LIPO -create -output "$darwin_file" $darwin_files done # $darwin_filelist $RM -rf unfat-$$ cd "$darwin_orig_dir" else cd $darwin_orig_dir func_extract_an_archive "$my_xdir" "$my_xabs" fi # $darwin_arches } # !$opt_dry_run ;; *) func_extract_an_archive "$my_xdir" "$my_xabs" ;; esac my_oldobjs="$my_oldobjs "`find $my_xdir -name \*.$objext -print -o -name \*.lo -print | $NL2SP` done func_extract_archives_result="$my_oldobjs" } # func_emit_wrapper_part1 [arg=no] # # Emit the first part of a libtool wrapper script on stdout. # For more information, see the description associated with # func_emit_wrapper(), below. func_emit_wrapper_part1 () { func_emit_wrapper_part1_arg1=no if test -n "$1" ; then func_emit_wrapper_part1_arg1=$1 fi $ECHO "\ #! $SHELL # $output - temporary wrapper script for $objdir/$outputname # Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION # # The $output program cannot be directly executed until all the libtool # libraries that it depends on are installed. # # This wrapper script should never be moved out of the build directory. # If it is, it will not operate correctly. # Sed substitution that helps us do robust quoting. It backslashifies # metacharacters that are still active within double-quoted strings. Xsed='${SED} -e 1s/^X//' sed_quote_subst='$sed_quote_subst' # Be Bourne compatible if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: # Zsh 3.x and 4.x performs word splitting on \${1+\"\$@\"}, which # is contrary to our usage. Disable this feature. alias -g '\${1+\"\$@\"}'='\"\$@\"' setopt NO_GLOB_SUBST else case \`(set -o) 2>/dev/null\` in *posix*) set -o posix;; esac fi BIN_SH=xpg4; export BIN_SH # for Tru64 DUALCASE=1; export DUALCASE # for MKS sh # The HP-UX ksh and POSIX shell print the target directory to stdout # if CDPATH is set. (unset CDPATH) >/dev/null 2>&1 && unset CDPATH relink_command=\"$relink_command\" # This environment variable determines our operation mode. if test \"\$libtool_install_magic\" = \"$magic\"; then # install mode needs the following variables: generated_by_libtool_version='$macro_version' notinst_deplibs='$notinst_deplibs' else # When we are sourced in execute mode, \$file and \$ECHO are already set. if test \"\$libtool_execute_magic\" != \"$magic\"; then ECHO=\"$qecho\" file=\"\$0\" # Make sure echo works. if test \"X\$1\" = X--no-reexec; then # Discard the --no-reexec flag, and continue. shift elif test \"X\`{ \$ECHO '\t'; } 2>/dev/null\`\" = 'X\t'; then # Yippee, \$ECHO works! : else # Restart under the correct shell, and then maybe \$ECHO will work. exec $SHELL \"\$0\" --no-reexec \${1+\"\$@\"} fi fi\ " $ECHO "\ # Find the directory that this script lives in. thisdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*$%%'\` test \"x\$thisdir\" = \"x\$file\" && thisdir=. # Follow symbolic links until we get to the real thisdir. file=\`ls -ld \"\$file\" | ${SED} -n 's/.*-> //p'\` while test -n \"\$file\"; do destdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*\$%%'\` # If there was a directory component, then change thisdir. if test \"x\$destdir\" != \"x\$file\"; then case \"\$destdir\" in [\\\\/]* | [A-Za-z]:[\\\\/]*) thisdir=\"\$destdir\" ;; *) thisdir=\"\$thisdir/\$destdir\" ;; esac fi file=\`\$ECHO \"X\$file\" | \$Xsed -e 's%^.*/%%'\` file=\`ls -ld \"\$thisdir/\$file\" | ${SED} -n 's/.*-> //p'\` done " } # end: func_emit_wrapper_part1 # func_emit_wrapper_part2 [arg=no] # # Emit the second part of a libtool wrapper script on stdout. # For more information, see the description associated with # func_emit_wrapper(), below. func_emit_wrapper_part2 () { func_emit_wrapper_part2_arg1=no if test -n "$1" ; then func_emit_wrapper_part2_arg1=$1 fi $ECHO "\ # Usually 'no', except on cygwin/mingw when embedded into # the cwrapper. WRAPPER_SCRIPT_BELONGS_IN_OBJDIR=$func_emit_wrapper_part2_arg1 if test \"\$WRAPPER_SCRIPT_BELONGS_IN_OBJDIR\" = \"yes\"; then # special case for '.' if test \"\$thisdir\" = \".\"; then thisdir=\`pwd\` fi # remove .libs from thisdir case \"\$thisdir\" in *[\\\\/]$objdir ) thisdir=\`\$ECHO \"X\$thisdir\" | \$Xsed -e 's%[\\\\/][^\\\\/]*$%%'\` ;; $objdir ) thisdir=. ;; esac fi # Try to get the absolute directory name. absdir=\`cd \"\$thisdir\" && pwd\` test -n \"\$absdir\" && thisdir=\"\$absdir\" " if test "$fast_install" = yes; then $ECHO "\ program=lt-'$outputname'$exeext progdir=\"\$thisdir/$objdir\" if test ! -f \"\$progdir/\$program\" || { file=\`ls -1dt \"\$progdir/\$program\" \"\$progdir/../\$program\" 2>/dev/null | ${SED} 1q\`; \\ test \"X\$file\" != \"X\$progdir/\$program\"; }; then file=\"\$\$-\$program\" if test ! -d \"\$progdir\"; then $MKDIR \"\$progdir\" else $RM \"\$progdir/\$file\" fi" $ECHO "\ # relink executable if necessary if test -n \"\$relink_command\"; then if relink_command_output=\`eval \$relink_command 2>&1\`; then : else $ECHO \"\$relink_command_output\" >&2 $RM \"\$progdir/\$file\" exit 1 fi fi $MV \"\$progdir/\$file\" \"\$progdir/\$program\" 2>/dev/null || { $RM \"\$progdir/\$program\"; $MV \"\$progdir/\$file\" \"\$progdir/\$program\"; } $RM \"\$progdir/\$file\" fi" else $ECHO "\ program='$outputname' progdir=\"\$thisdir/$objdir\" " fi $ECHO "\ if test -f \"\$progdir/\$program\"; then" # Export our shlibpath_var if we have one. if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then $ECHO "\ # Add our own library path to $shlibpath_var $shlibpath_var=\"$temp_rpath\$$shlibpath_var\" # Some systems cannot cope with colon-terminated $shlibpath_var # The second colon is a workaround for a bug in BeOS R4 sed $shlibpath_var=\`\$ECHO \"X\$$shlibpath_var\" | \$Xsed -e 's/::*\$//'\` export $shlibpath_var " fi # fixup the dll searchpath if we need to. if test -n "$dllsearchpath"; then $ECHO "\ # Add the dll search path components to the executable PATH PATH=$dllsearchpath:\$PATH " fi $ECHO "\ if test \"\$libtool_execute_magic\" != \"$magic\"; then # Run the actual program with our arguments. " case $host in # Backslashes separate directories on plain windows *-*-mingw | *-*-os2* | *-cegcc*) $ECHO "\ exec \"\$progdir\\\\\$program\" \${1+\"\$@\"} " ;; *) $ECHO "\ exec \"\$progdir/\$program\" \${1+\"\$@\"} " ;; esac $ECHO "\ \$ECHO \"\$0: cannot exec \$program \$*\" 1>&2 exit 1 fi else # The program doesn't exist. \$ECHO \"\$0: error: \\\`\$progdir/\$program' does not exist\" 1>&2 \$ECHO \"This script is just a wrapper for \$program.\" 1>&2 $ECHO \"See the $PACKAGE documentation for more information.\" 1>&2 exit 1 fi fi\ " } # end: func_emit_wrapper_part2 # func_emit_wrapper [arg=no] # # Emit a libtool wrapper script on stdout. # Don't directly open a file because we may want to # incorporate the script contents within a cygwin/mingw # wrapper executable. Must ONLY be called from within # func_mode_link because it depends on a number of variables # set therein. # # ARG is the value that the WRAPPER_SCRIPT_BELONGS_IN_OBJDIR # variable will take. If 'yes', then the emitted script # will assume that the directory in which it is stored is # the $objdir directory. This is a cygwin/mingw-specific # behavior. func_emit_wrapper () { func_emit_wrapper_arg1=no if test -n "$1" ; then func_emit_wrapper_arg1=$1 fi # split this up so that func_emit_cwrapperexe_src # can call each part independently. func_emit_wrapper_part1 "${func_emit_wrapper_arg1}" func_emit_wrapper_part2 "${func_emit_wrapper_arg1}" } # func_to_host_path arg # # Convert paths to host format when used with build tools. # Intended for use with "native" mingw (where libtool itself # is running under the msys shell), or in the following cross- # build environments: # $build $host # mingw (msys) mingw [e.g. native] # cygwin mingw # *nix + wine mingw # where wine is equipped with the `winepath' executable. # In the native mingw case, the (msys) shell automatically # converts paths for any non-msys applications it launches, # but that facility isn't available from inside the cwrapper. # Similar accommodations are necessary for $host mingw and # $build cygwin. Calling this function does no harm for other # $host/$build combinations not listed above. # # ARG is the path (on $build) that should be converted to # the proper representation for $host. The result is stored # in $func_to_host_path_result. func_to_host_path () { func_to_host_path_result="$1" if test -n "$1" ; then case $host in *mingw* ) lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g' case $build in *mingw* ) # actually, msys # awkward: cmd appends spaces to result lt_sed_strip_trailing_spaces="s/[ ]*\$//" func_to_host_path_tmp1=`( cmd //c echo "$1" |\ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""` func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ $SED -e "$lt_sed_naive_backslashify"` ;; *cygwin* ) func_to_host_path_tmp1=`cygpath -w "$1"` func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ $SED -e "$lt_sed_naive_backslashify"` ;; * ) # Unfortunately, winepath does not exit with a non-zero # error code, so we are forced to check the contents of # stdout. On the other hand, if the command is not # found, the shell will set an exit code of 127 and print # *an error message* to stdout. So we must check for both # error code of zero AND non-empty stdout, which explains # the odd construction: func_to_host_path_tmp1=`winepath -w "$1" 2>/dev/null` if test "$?" -eq 0 && test -n "${func_to_host_path_tmp1}"; then func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ $SED -e "$lt_sed_naive_backslashify"` else # Allow warning below. func_to_host_path_result="" fi ;; esac if test -z "$func_to_host_path_result" ; then func_error "Could not determine host path corresponding to" func_error " '$1'" func_error "Continuing, but uninstalled executables may not work." # Fallback: func_to_host_path_result="$1" fi ;; esac fi } # end: func_to_host_path # func_to_host_pathlist arg # # Convert pathlists to host format when used with build tools. # See func_to_host_path(), above. This function supports the # following $build/$host combinations (but does no harm for # combinations not listed here): # $build $host # mingw (msys) mingw [e.g. native] # cygwin mingw # *nix + wine mingw # # Path separators are also converted from $build format to # $host format. If ARG begins or ends with a path separator # character, it is preserved (but converted to $host format) # on output. # # ARG is a pathlist (on $build) that should be converted to # the proper representation on $host. The result is stored # in $func_to_host_pathlist_result. func_to_host_pathlist () { func_to_host_pathlist_result="$1" if test -n "$1" ; then case $host in *mingw* ) lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g' # Remove leading and trailing path separator characters from # ARG. msys behavior is inconsistent here, cygpath turns them # into '.;' and ';.', and winepath ignores them completely. func_to_host_pathlist_tmp2="$1" # Once set for this call, this variable should not be # reassigned. It is used in tha fallback case. func_to_host_pathlist_tmp1=`echo "$func_to_host_pathlist_tmp2" |\ $SED -e 's|^:*||' -e 's|:*$||'` case $build in *mingw* ) # Actually, msys. # Awkward: cmd appends spaces to result. lt_sed_strip_trailing_spaces="s/[ ]*\$//" func_to_host_pathlist_tmp2=`( cmd //c echo "$func_to_host_pathlist_tmp1" |\ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""` func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\ $SED -e "$lt_sed_naive_backslashify"` ;; *cygwin* ) func_to_host_pathlist_tmp2=`cygpath -w -p "$func_to_host_pathlist_tmp1"` func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\ $SED -e "$lt_sed_naive_backslashify"` ;; * ) # unfortunately, winepath doesn't convert pathlists func_to_host_pathlist_result="" func_to_host_pathlist_oldIFS=$IFS IFS=: for func_to_host_pathlist_f in $func_to_host_pathlist_tmp1 ; do IFS=$func_to_host_pathlist_oldIFS if test -n "$func_to_host_pathlist_f" ; then func_to_host_path "$func_to_host_pathlist_f" if test -n "$func_to_host_path_result" ; then if test -z "$func_to_host_pathlist_result" ; then func_to_host_pathlist_result="$func_to_host_path_result" else func_to_host_pathlist_result="$func_to_host_pathlist_result;$func_to_host_path_result" fi fi fi IFS=: done IFS=$func_to_host_pathlist_oldIFS ;; esac if test -z "$func_to_host_pathlist_result" ; then func_error "Could not determine the host path(s) corresponding to" func_error " '$1'" func_error "Continuing, but uninstalled executables may not work." # Fallback. This may break if $1 contains DOS-style drive # specifications. The fix is not to complicate the expression # below, but for the user to provide a working wine installation # with winepath so that path translation in the cross-to-mingw # case works properly. lt_replace_pathsep_nix_to_dos="s|:|;|g" func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp1" |\ $SED -e "$lt_replace_pathsep_nix_to_dos"` fi # Now, add the leading and trailing path separators back case "$1" in :* ) func_to_host_pathlist_result=";$func_to_host_pathlist_result" ;; esac case "$1" in *: ) func_to_host_pathlist_result="$func_to_host_pathlist_result;" ;; esac ;; esac fi } # end: func_to_host_pathlist # func_emit_cwrapperexe_src # emit the source code for a wrapper executable on stdout # Must ONLY be called from within func_mode_link because # it depends on a number of variable set therein. func_emit_cwrapperexe_src () { cat < #include #ifdef _MSC_VER # include # include # include # define setmode _setmode #else # include # include # ifdef __CYGWIN__ # include # define HAVE_SETENV # ifdef __STRICT_ANSI__ char *realpath (const char *, char *); int putenv (char *); int setenv (const char *, const char *, int); # endif # endif #endif #include #include #include #include #include #include #include #include #if defined(PATH_MAX) # define LT_PATHMAX PATH_MAX #elif defined(MAXPATHLEN) # define LT_PATHMAX MAXPATHLEN #else # define LT_PATHMAX 1024 #endif #ifndef S_IXOTH # define S_IXOTH 0 #endif #ifndef S_IXGRP # define S_IXGRP 0 #endif #ifdef _MSC_VER # define S_IXUSR _S_IEXEC # define stat _stat # ifndef _INTPTR_T_DEFINED # define intptr_t int # endif #endif #ifndef DIR_SEPARATOR # define DIR_SEPARATOR '/' # define PATH_SEPARATOR ':' #endif #if defined (_WIN32) || defined (__MSDOS__) || defined (__DJGPP__) || \ defined (__OS2__) # define HAVE_DOS_BASED_FILE_SYSTEM # define FOPEN_WB "wb" # ifndef DIR_SEPARATOR_2 # define DIR_SEPARATOR_2 '\\' # endif # ifndef PATH_SEPARATOR_2 # define PATH_SEPARATOR_2 ';' # endif #endif #ifndef DIR_SEPARATOR_2 # define IS_DIR_SEPARATOR(ch) ((ch) == DIR_SEPARATOR) #else /* DIR_SEPARATOR_2 */ # define IS_DIR_SEPARATOR(ch) \ (((ch) == DIR_SEPARATOR) || ((ch) == DIR_SEPARATOR_2)) #endif /* DIR_SEPARATOR_2 */ #ifndef PATH_SEPARATOR_2 # define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR) #else /* PATH_SEPARATOR_2 */ # define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR_2) #endif /* PATH_SEPARATOR_2 */ #ifdef __CYGWIN__ # define FOPEN_WB "wb" #endif #ifndef FOPEN_WB # define FOPEN_WB "w" #endif #ifndef _O_BINARY # define _O_BINARY 0 #endif #define XMALLOC(type, num) ((type *) xmalloc ((num) * sizeof(type))) #define XFREE(stale) do { \ if (stale) { free ((void *) stale); stale = 0; } \ } while (0) #undef LTWRAPPER_DEBUGPRINTF #if defined DEBUGWRAPPER # define LTWRAPPER_DEBUGPRINTF(args) ltwrapper_debugprintf args static void ltwrapper_debugprintf (const char *fmt, ...) { va_list args; va_start (args, fmt); (void) vfprintf (stderr, fmt, args); va_end (args); } #else # define LTWRAPPER_DEBUGPRINTF(args) #endif const char *program_name = NULL; void *xmalloc (size_t num); char *xstrdup (const char *string); const char *base_name (const char *name); char *find_executable (const char *wrapper); char *chase_symlinks (const char *pathspec); int make_executable (const char *path); int check_executable (const char *path); char *strendzap (char *str, const char *pat); void lt_fatal (const char *message, ...); void lt_setenv (const char *name, const char *value); char *lt_extend_str (const char *orig_value, const char *add, int to_end); void lt_opt_process_env_set (const char *arg); void lt_opt_process_env_prepend (const char *arg); void lt_opt_process_env_append (const char *arg); int lt_split_name_value (const char *arg, char** name, char** value); void lt_update_exe_path (const char *name, const char *value); void lt_update_lib_path (const char *name, const char *value); static const char *script_text_part1 = EOF func_emit_wrapper_part1 yes | $SED -e 's/\([\\"]\)/\\\1/g' \ -e 's/^/ "/' -e 's/$/\\n"/' echo ";" cat <"))); for (i = 0; i < newargc; i++) { LTWRAPPER_DEBUGPRINTF (("(main) newargz[%d] : %s\n", i, (newargz[i] ? newargz[i] : ""))); } EOF case $host_os in mingw*) cat <<"EOF" /* execv doesn't actually work on mingw as expected on unix */ rval = _spawnv (_P_WAIT, lt_argv_zero, (const char * const *) newargz); if (rval == -1) { /* failed to start process */ LTWRAPPER_DEBUGPRINTF (("(main) failed to launch target \"%s\": errno = %d\n", lt_argv_zero, errno)); return 127; } return rval; EOF ;; *) cat <<"EOF" execv (lt_argv_zero, newargz); return rval; /* =127, but avoids unused variable warning */ EOF ;; esac cat <<"EOF" } void * xmalloc (size_t num) { void *p = (void *) malloc (num); if (!p) lt_fatal ("Memory exhausted"); return p; } char * xstrdup (const char *string) { return string ? strcpy ((char *) xmalloc (strlen (string) + 1), string) : NULL; } const char * base_name (const char *name) { const char *base; #if defined (HAVE_DOS_BASED_FILE_SYSTEM) /* Skip over the disk name in MSDOS pathnames. */ if (isalpha ((unsigned char) name[0]) && name[1] == ':') name += 2; #endif for (base = name; *name; name++) if (IS_DIR_SEPARATOR (*name)) base = name + 1; return base; } int check_executable (const char *path) { struct stat st; LTWRAPPER_DEBUGPRINTF (("(check_executable) : %s\n", path ? (*path ? path : "EMPTY!") : "NULL!")); if ((!path) || (!*path)) return 0; if ((stat (path, &st) >= 0) && (st.st_mode & (S_IXUSR | S_IXGRP | S_IXOTH))) return 1; else return 0; } int make_executable (const char *path) { int rval = 0; struct stat st; LTWRAPPER_DEBUGPRINTF (("(make_executable) : %s\n", path ? (*path ? path : "EMPTY!") : "NULL!")); if ((!path) || (!*path)) return 0; if (stat (path, &st) >= 0) { rval = chmod (path, st.st_mode | S_IXOTH | S_IXGRP | S_IXUSR); } return rval; } /* Searches for the full path of the wrapper. Returns newly allocated full path name if found, NULL otherwise Does not chase symlinks, even on platforms that support them. */ char * find_executable (const char *wrapper) { int has_slash = 0; const char *p; const char *p_next; /* static buffer for getcwd */ char tmp[LT_PATHMAX + 1]; int tmp_len; char *concat_name; LTWRAPPER_DEBUGPRINTF (("(find_executable) : %s\n", wrapper ? (*wrapper ? wrapper : "EMPTY!") : "NULL!")); if ((wrapper == NULL) || (*wrapper == '\0')) return NULL; /* Absolute path? */ #if defined (HAVE_DOS_BASED_FILE_SYSTEM) if (isalpha ((unsigned char) wrapper[0]) && wrapper[1] == ':') { concat_name = xstrdup (wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } else { #endif if (IS_DIR_SEPARATOR (wrapper[0])) { concat_name = xstrdup (wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } #if defined (HAVE_DOS_BASED_FILE_SYSTEM) } #endif for (p = wrapper; *p; p++) if (*p == '/') { has_slash = 1; break; } if (!has_slash) { /* no slashes; search PATH */ const char *path = getenv ("PATH"); if (path != NULL) { for (p = path; *p; p = p_next) { const char *q; size_t p_len; for (q = p; *q; q++) if (IS_PATH_SEPARATOR (*q)) break; p_len = q - p; p_next = (*q == '\0' ? q : q + 1); if (p_len == 0) { /* empty path: current directory */ if (getcwd (tmp, LT_PATHMAX) == NULL) lt_fatal ("getcwd failed"); tmp_len = strlen (tmp); concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, tmp, tmp_len); concat_name[tmp_len] = '/'; strcpy (concat_name + tmp_len + 1, wrapper); } else { concat_name = XMALLOC (char, p_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, p, p_len); concat_name[p_len] = '/'; strcpy (concat_name + p_len + 1, wrapper); } if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } } /* not found in PATH; assume curdir */ } /* Relative path | not found in path: prepend cwd */ if (getcwd (tmp, LT_PATHMAX) == NULL) lt_fatal ("getcwd failed"); tmp_len = strlen (tmp); concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, tmp, tmp_len); concat_name[tmp_len] = '/'; strcpy (concat_name + tmp_len + 1, wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); return NULL; } char * chase_symlinks (const char *pathspec) { #ifndef S_ISLNK return xstrdup (pathspec); #else char buf[LT_PATHMAX]; struct stat s; char *tmp_pathspec = xstrdup (pathspec); char *p; int has_symlinks = 0; while (strlen (tmp_pathspec) && !has_symlinks) { LTWRAPPER_DEBUGPRINTF (("checking path component for symlinks: %s\n", tmp_pathspec)); if (lstat (tmp_pathspec, &s) == 0) { if (S_ISLNK (s.st_mode) != 0) { has_symlinks = 1; break; } /* search backwards for last DIR_SEPARATOR */ p = tmp_pathspec + strlen (tmp_pathspec) - 1; while ((p > tmp_pathspec) && (!IS_DIR_SEPARATOR (*p))) p--; if ((p == tmp_pathspec) && (!IS_DIR_SEPARATOR (*p))) { /* no more DIR_SEPARATORS left */ break; } *p = '\0'; } else { char *errstr = strerror (errno); lt_fatal ("Error accessing file %s (%s)", tmp_pathspec, errstr); } } XFREE (tmp_pathspec); if (!has_symlinks) { return xstrdup (pathspec); } tmp_pathspec = realpath (pathspec, buf); if (tmp_pathspec == 0) { lt_fatal ("Could not follow symlinks for %s", pathspec); } return xstrdup (tmp_pathspec); #endif } char * strendzap (char *str, const char *pat) { size_t len, patlen; assert (str != NULL); assert (pat != NULL); len = strlen (str); patlen = strlen (pat); if (patlen <= len) { str += len - patlen; if (strcmp (str, pat) == 0) *str = '\0'; } return str; } static void lt_error_core (int exit_status, const char *mode, const char *message, va_list ap) { fprintf (stderr, "%s: %s: ", program_name, mode); vfprintf (stderr, message, ap); fprintf (stderr, ".\n"); if (exit_status >= 0) exit (exit_status); } void lt_fatal (const char *message, ...) { va_list ap; va_start (ap, message); lt_error_core (EXIT_FAILURE, "FATAL", message, ap); va_end (ap); } void lt_setenv (const char *name, const char *value) { LTWRAPPER_DEBUGPRINTF (("(lt_setenv) setting '%s' to '%s'\n", (name ? name : ""), (value ? value : ""))); { #ifdef HAVE_SETENV /* always make a copy, for consistency with !HAVE_SETENV */ char *str = xstrdup (value); setenv (name, str, 1); #else int len = strlen (name) + 1 + strlen (value) + 1; char *str = XMALLOC (char, len); sprintf (str, "%s=%s", name, value); if (putenv (str) != EXIT_SUCCESS) { XFREE (str); } #endif } } char * lt_extend_str (const char *orig_value, const char *add, int to_end) { char *new_value; if (orig_value && *orig_value) { int orig_value_len = strlen (orig_value); int add_len = strlen (add); new_value = XMALLOC (char, add_len + orig_value_len + 1); if (to_end) { strcpy (new_value, orig_value); strcpy (new_value + orig_value_len, add); } else { strcpy (new_value, add); strcpy (new_value + add_len, orig_value); } } else { new_value = xstrdup (add); } return new_value; } int lt_split_name_value (const char *arg, char** name, char** value) { const char *p; int len; if (!arg || !*arg) return 1; p = strchr (arg, (int)'='); if (!p) return 1; *value = xstrdup (++p); len = strlen (arg) - strlen (*value); *name = XMALLOC (char, len); strncpy (*name, arg, len-1); (*name)[len - 1] = '\0'; return 0; } void lt_opt_process_env_set (const char *arg) { char *name = NULL; char *value = NULL; if (lt_split_name_value (arg, &name, &value) != 0) { XFREE (name); XFREE (value); lt_fatal ("bad argument for %s: '%s'", env_set_opt, arg); } lt_setenv (name, value); XFREE (name); XFREE (value); } void lt_opt_process_env_prepend (const char *arg) { char *name = NULL; char *value = NULL; char *new_value = NULL; if (lt_split_name_value (arg, &name, &value) != 0) { XFREE (name); XFREE (value); lt_fatal ("bad argument for %s: '%s'", env_prepend_opt, arg); } new_value = lt_extend_str (getenv (name), value, 0); lt_setenv (name, new_value); XFREE (new_value); XFREE (name); XFREE (value); } void lt_opt_process_env_append (const char *arg) { char *name = NULL; char *value = NULL; char *new_value = NULL; if (lt_split_name_value (arg, &name, &value) != 0) { XFREE (name); XFREE (value); lt_fatal ("bad argument for %s: '%s'", env_append_opt, arg); } new_value = lt_extend_str (getenv (name), value, 1); lt_setenv (name, new_value); XFREE (new_value); XFREE (name); XFREE (value); } void lt_update_exe_path (const char *name, const char *value) { LTWRAPPER_DEBUGPRINTF (("(lt_update_exe_path) modifying '%s' by prepending '%s'\n", (name ? name : ""), (value ? value : ""))); if (name && *name && value && *value) { char *new_value = lt_extend_str (getenv (name), value, 0); /* some systems can't cope with a ':'-terminated path #' */ int len = strlen (new_value); while (((len = strlen (new_value)) > 0) && IS_PATH_SEPARATOR (new_value[len-1])) { new_value[len-1] = '\0'; } lt_setenv (name, new_value); XFREE (new_value); } } void lt_update_lib_path (const char *name, const char *value) { LTWRAPPER_DEBUGPRINTF (("(lt_update_lib_path) modifying '%s' by prepending '%s'\n", (name ? name : ""), (value ? value : ""))); if (name && *name && value && *value) { char *new_value = lt_extend_str (getenv (name), value, 0); lt_setenv (name, new_value); XFREE (new_value); } } EOF } # end: func_emit_cwrapperexe_src # func_mode_link arg... func_mode_link () { $opt_debug case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) # It is impossible to link a dll without this setting, and # we shouldn't force the makefile maintainer to figure out # which system we are compiling for in order to pass an extra # flag for every libtool invocation. # allow_undefined=no # FIXME: Unfortunately, there are problems with the above when trying # to make a dll which has undefined symbols, in which case not # even a static library is built. For now, we need to specify # -no-undefined on the libtool link line when we can be certain # that all symbols are satisfied, otherwise we get a static library. allow_undefined=yes ;; *) allow_undefined=yes ;; esac libtool_args=$nonopt base_compile="$nonopt $@" compile_command=$nonopt finalize_command=$nonopt compile_rpath= finalize_rpath= compile_shlibpath= finalize_shlibpath= convenience= old_convenience= deplibs= old_deplibs= compiler_flags= linker_flags= dllsearchpath= lib_search_path=`pwd` inst_prefix_dir= new_inherited_linker_flags= avoid_version=no dlfiles= dlprefiles= dlself=no export_dynamic=no export_symbols= export_symbols_regex= generated= libobjs= ltlibs= module=no no_install=no objs= non_pic_objects= precious_files_regex= prefer_static_libs=no preload=no prev= prevarg= release= rpath= xrpath= perm_rpath= temp_rpath= thread_safe=no vinfo= vinfo_number=no weak_libs= single_module="${wl}-single_module" func_infer_tag $base_compile # We need to know -static, to get the right output filenames. for arg do case $arg in -shared) test "$build_libtool_libs" != yes && \ func_fatal_configuration "can not build a shared library" build_old_libs=no break ;; -all-static | -static | -static-libtool-libs) case $arg in -all-static) if test "$build_libtool_libs" = yes && test -z "$link_static_flag"; then func_warning "complete static linking is impossible in this configuration" fi if test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=yes ;; -static) if test -z "$pic_flag" && test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=built ;; -static-libtool-libs) if test -z "$pic_flag" && test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=yes ;; esac build_libtool_libs=no build_old_libs=yes break ;; esac done # See if our shared archives depend on static archives. test -n "$old_archive_from_new_cmds" && build_old_libs=yes # Go through the arguments, transforming them on the way. while test "$#" -gt 0; do arg="$1" shift func_quote_for_eval "$arg" qarg=$func_quote_for_eval_unquoted_result func_append libtool_args " $func_quote_for_eval_result" # If the previous option needs an argument, assign it. if test -n "$prev"; then case $prev in output) func_append compile_command " @OUTPUT@" func_append finalize_command " @OUTPUT@" ;; esac case $prev in dlfiles|dlprefiles) if test "$preload" = no; then # Add the symbol object into the linking commands. func_append compile_command " @SYMFILE@" func_append finalize_command " @SYMFILE@" preload=yes fi case $arg in *.la | *.lo) ;; # We handle these cases below. force) if test "$dlself" = no; then dlself=needless export_dynamic=yes fi prev= continue ;; self) if test "$prev" = dlprefiles; then dlself=yes elif test "$prev" = dlfiles && test "$dlopen_self" != yes; then dlself=yes else dlself=needless export_dynamic=yes fi prev= continue ;; *) if test "$prev" = dlfiles; then dlfiles="$dlfiles $arg" else dlprefiles="$dlprefiles $arg" fi prev= continue ;; esac ;; expsyms) export_symbols="$arg" test -f "$arg" \ || func_fatal_error "symbol file \`$arg' does not exist" prev= continue ;; expsyms_regex) export_symbols_regex="$arg" prev= continue ;; framework) case $host in *-*-darwin*) case "$deplibs " in *" $qarg.ltframework "*) ;; *) deplibs="$deplibs $qarg.ltframework" # this is fixed later ;; esac ;; esac prev= continue ;; inst_prefix) inst_prefix_dir="$arg" prev= continue ;; objectlist) if test -f "$arg"; then save_arg=$arg moreargs= for fil in `cat "$save_arg"` do # moreargs="$moreargs $fil" arg=$fil # A libtool-controlled object. # Check to see that this really is a libtool object. if func_lalib_unsafe_p "$arg"; then pic_object= non_pic_object= # Read the .lo file func_source "$arg" if test -z "$pic_object" || test -z "$non_pic_object" || test "$pic_object" = none && test "$non_pic_object" = none; then func_fatal_error "cannot find name of object for \`$arg'" fi # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" if test "$pic_object" != none; then # Prepend the subdirectory the object is found in. pic_object="$xdir$pic_object" if test "$prev" = dlfiles; then if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then dlfiles="$dlfiles $pic_object" prev= continue else # If libtool objects are unsupported, then we need to preload. prev=dlprefiles fi fi # CHECK ME: I think I busted this. -Ossama if test "$prev" = dlprefiles; then # Preload the old-style object. dlprefiles="$dlprefiles $pic_object" prev= fi # A PIC object. func_append libobjs " $pic_object" arg="$pic_object" fi # Non-PIC object. if test "$non_pic_object" != none; then # Prepend the subdirectory the object is found in. non_pic_object="$xdir$non_pic_object" # A standard non-PIC object func_append non_pic_objects " $non_pic_object" if test -z "$pic_object" || test "$pic_object" = none ; then arg="$non_pic_object" fi else # If the PIC object exists, use it instead. # $xdir was prepended to $pic_object above. non_pic_object="$pic_object" func_append non_pic_objects " $non_pic_object" fi else # Only an error if not doing a dry-run. if $opt_dry_run; then # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" func_lo2o "$arg" pic_object=$xdir$objdir/$func_lo2o_result non_pic_object=$xdir$func_lo2o_result func_append libobjs " $pic_object" func_append non_pic_objects " $non_pic_object" else func_fatal_error "\`$arg' is not a valid libtool object" fi fi done else func_fatal_error "link input file \`$arg' does not exist" fi arg=$save_arg prev= continue ;; precious_regex) precious_files_regex="$arg" prev= continue ;; release) release="-$arg" prev= continue ;; rpath | xrpath) # We need an absolute path. case $arg in [\\/]* | [A-Za-z]:[\\/]*) ;; *) func_fatal_error "only absolute run-paths are allowed" ;; esac if test "$prev" = rpath; then case "$rpath " in *" $arg "*) ;; *) rpath="$rpath $arg" ;; esac else case "$xrpath " in *" $arg "*) ;; *) xrpath="$xrpath $arg" ;; esac fi prev= continue ;; shrext) shrext_cmds="$arg" prev= continue ;; weak) weak_libs="$weak_libs $arg" prev= continue ;; xcclinker) linker_flags="$linker_flags $qarg" compiler_flags="$compiler_flags $qarg" prev= func_append compile_command " $qarg" func_append finalize_command " $qarg" continue ;; xcompiler) compiler_flags="$compiler_flags $qarg" prev= func_append compile_command " $qarg" func_append finalize_command " $qarg" continue ;; xlinker) linker_flags="$linker_flags $qarg" compiler_flags="$compiler_flags $wl$qarg" prev= func_append compile_command " $wl$qarg" func_append finalize_command " $wl$qarg" continue ;; *) eval "$prev=\"\$arg\"" prev= continue ;; esac fi # test -n "$prev" prevarg="$arg" case $arg in -all-static) if test -n "$link_static_flag"; then # See comment for -static flag below, for more details. func_append compile_command " $link_static_flag" func_append finalize_command " $link_static_flag" fi continue ;; -allow-undefined) # FIXME: remove this flag sometime in the future. func_fatal_error "\`-allow-undefined' must not be used because it is the default" ;; -avoid-version) avoid_version=yes continue ;; -dlopen) prev=dlfiles continue ;; -dlpreopen) prev=dlprefiles continue ;; -export-dynamic) export_dynamic=yes continue ;; -export-symbols | -export-symbols-regex) if test -n "$export_symbols" || test -n "$export_symbols_regex"; then func_fatal_error "more than one -exported-symbols argument is not allowed" fi if test "X$arg" = "X-export-symbols"; then prev=expsyms else prev=expsyms_regex fi continue ;; -framework) prev=framework continue ;; -inst-prefix-dir) prev=inst_prefix continue ;; # The native IRIX linker understands -LANG:*, -LIST:* and -LNO:* # so, if we see these flags be careful not to treat them like -L -L[A-Z][A-Z]*:*) case $with_gcc/$host in no/*-*-irix* | /*-*-irix*) func_append compile_command " $arg" func_append finalize_command " $arg" ;; esac continue ;; -L*) func_stripname '-L' '' "$arg" dir=$func_stripname_result if test -z "$dir"; then if test "$#" -gt 0; then func_fatal_error "require no space between \`-L' and \`$1'" else func_fatal_error "need path for \`-L' option" fi fi # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) ;; *) absdir=`cd "$dir" && pwd` test -z "$absdir" && \ func_fatal_error "cannot determine absolute directory name of \`$dir'" dir="$absdir" ;; esac case "$deplibs " in *" -L$dir "*) ;; *) deplibs="$deplibs -L$dir" lib_search_path="$lib_search_path $dir" ;; esac case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) testbindir=`$ECHO "X$dir" | $Xsed -e 's*/lib$*/bin*'` case :$dllsearchpath: in *":$dir:"*) ;; ::) dllsearchpath=$dir;; *) dllsearchpath="$dllsearchpath:$dir";; esac case :$dllsearchpath: in *":$testbindir:"*) ;; ::) dllsearchpath=$testbindir;; *) dllsearchpath="$dllsearchpath:$testbindir";; esac ;; esac continue ;; -l*) if test "X$arg" = "X-lc" || test "X$arg" = "X-lm"; then case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-beos* | *-cegcc*) # These systems don't actually have a C or math library (as such) continue ;; *-*-os2*) # These systems don't actually have a C library (as such) test "X$arg" = "X-lc" && continue ;; *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc due to us having libc/libc_r. test "X$arg" = "X-lc" && continue ;; *-*-rhapsody* | *-*-darwin1.[012]) # Rhapsody C and math libraries are in the System framework deplibs="$deplibs System.ltframework" continue ;; *-*-sco3.2v5* | *-*-sco5v6*) # Causes problems with __ctype test "X$arg" = "X-lc" && continue ;; *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*) # Compiler inserts libc in the correct place for threads to work test "X$arg" = "X-lc" && continue ;; esac elif test "X$arg" = "X-lc_r"; then case $host in *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc_r directly, use -pthread flag. continue ;; esac fi deplibs="$deplibs $arg" continue ;; -module) module=yes continue ;; # Tru64 UNIX uses -model [arg] to determine the layout of C++ # classes, name mangling, and exception handling. # Darwin uses the -arch flag to determine output architecture. -model|-arch|-isysroot) compiler_flags="$compiler_flags $arg" func_append compile_command " $arg" func_append finalize_command " $arg" prev=xcompiler continue ;; -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads) compiler_flags="$compiler_flags $arg" func_append compile_command " $arg" func_append finalize_command " $arg" case "$new_inherited_linker_flags " in *" $arg "*) ;; * ) new_inherited_linker_flags="$new_inherited_linker_flags $arg" ;; esac continue ;; -multi_module) single_module="${wl}-multi_module" continue ;; -no-fast-install) fast_install=no continue ;; -no-install) case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-darwin* | *-cegcc*) # The PATH hackery in wrapper scripts is required on Windows # and Darwin in order for the loader to find any dlls it needs. func_warning "\`-no-install' is ignored for $host" func_warning "assuming \`-no-fast-install' instead" fast_install=no ;; *) no_install=yes ;; esac continue ;; -no-undefined) allow_undefined=no continue ;; -objectlist) prev=objectlist continue ;; -o) prev=output ;; -precious-files-regex) prev=precious_regex continue ;; -release) prev=release continue ;; -rpath) prev=rpath continue ;; -R) prev=xrpath continue ;; -R*) func_stripname '-R' '' "$arg" dir=$func_stripname_result # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) ;; *) func_fatal_error "only absolute run-paths are allowed" ;; esac case "$xrpath " in *" $dir "*) ;; *) xrpath="$xrpath $dir" ;; esac continue ;; -shared) # The effects of -shared are defined in a previous loop. continue ;; -shrext) prev=shrext continue ;; -static | -static-libtool-libs) # The effects of -static are defined in a previous loop. # We used to do the same as -all-static on platforms that # didn't have a PIC flag, but the assumption that the effects # would be equivalent was wrong. It would break on at least # Digital Unix and AIX. continue ;; -thread-safe) thread_safe=yes continue ;; -version-info) prev=vinfo continue ;; -version-number) prev=vinfo vinfo_number=yes continue ;; -weak) prev=weak continue ;; -Wc,*) func_stripname '-Wc,' '' "$arg" args=$func_stripname_result arg= save_ifs="$IFS"; IFS=',' for flag in $args; do IFS="$save_ifs" func_quote_for_eval "$flag" arg="$arg $wl$func_quote_for_eval_result" compiler_flags="$compiler_flags $func_quote_for_eval_result" done IFS="$save_ifs" func_stripname ' ' '' "$arg" arg=$func_stripname_result ;; -Wl,*) func_stripname '-Wl,' '' "$arg" args=$func_stripname_result arg= save_ifs="$IFS"; IFS=',' for flag in $args; do IFS="$save_ifs" func_quote_for_eval "$flag" arg="$arg $wl$func_quote_for_eval_result" compiler_flags="$compiler_flags $wl$func_quote_for_eval_result" linker_flags="$linker_flags $func_quote_for_eval_result" done IFS="$save_ifs" func_stripname ' ' '' "$arg" arg=$func_stripname_result ;; -Xcompiler) prev=xcompiler continue ;; -Xlinker) prev=xlinker continue ;; -XCClinker) prev=xcclinker continue ;; # -msg_* for osf cc -msg_*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; # -64, -mips[0-9] enable 64-bit mode on the SGI compiler # -r[0-9][0-9]* specifies the processor on the SGI compiler # -xarch=*, -xtarget=* enable 64-bit mode on the Sun compiler # +DA*, +DD* enable 64-bit mode on the HP compiler # -q* pass through compiler args for the IBM compiler # -m*, -t[45]*, -txscale* pass through architecture-specific # compiler args for GCC # -F/path gives path to uninstalled frameworks, gcc on darwin # -p, -pg, --coverage, -fprofile-* pass through profiling flag for GCC # @file GCC response files -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \ -t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" func_append compile_command " $arg" func_append finalize_command " $arg" compiler_flags="$compiler_flags $arg" continue ;; # Some other compiler flag. -* | +*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; *.$objext) # A standard object. objs="$objs $arg" ;; *.lo) # A libtool-controlled object. # Check to see that this really is a libtool object. if func_lalib_unsafe_p "$arg"; then pic_object= non_pic_object= # Read the .lo file func_source "$arg" if test -z "$pic_object" || test -z "$non_pic_object" || test "$pic_object" = none && test "$non_pic_object" = none; then func_fatal_error "cannot find name of object for \`$arg'" fi # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" if test "$pic_object" != none; then # Prepend the subdirectory the object is found in. pic_object="$xdir$pic_object" if test "$prev" = dlfiles; then if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then dlfiles="$dlfiles $pic_object" prev= continue else # If libtool objects are unsupported, then we need to preload. prev=dlprefiles fi fi # CHECK ME: I think I busted this. -Ossama if test "$prev" = dlprefiles; then # Preload the old-style object. dlprefiles="$dlprefiles $pic_object" prev= fi # A PIC object. func_append libobjs " $pic_object" arg="$pic_object" fi # Non-PIC object. if test "$non_pic_object" != none; then # Prepend the subdirectory the object is found in. non_pic_object="$xdir$non_pic_object" # A standard non-PIC object func_append non_pic_objects " $non_pic_object" if test -z "$pic_object" || test "$pic_object" = none ; then arg="$non_pic_object" fi else # If the PIC object exists, use it instead. # $xdir was prepended to $pic_object above. non_pic_object="$pic_object" func_append non_pic_objects " $non_pic_object" fi else # Only an error if not doing a dry-run. if $opt_dry_run; then # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" func_lo2o "$arg" pic_object=$xdir$objdir/$func_lo2o_result non_pic_object=$xdir$func_lo2o_result func_append libobjs " $pic_object" func_append non_pic_objects " $non_pic_object" else func_fatal_error "\`$arg' is not a valid libtool object" fi fi ;; *.$libext) # An archive. deplibs="$deplibs $arg" old_deplibs="$old_deplibs $arg" continue ;; *.la) # A libtool-controlled library. if test "$prev" = dlfiles; then # This library was specified with -dlopen. dlfiles="$dlfiles $arg" prev= elif test "$prev" = dlprefiles; then # The library was specified with -dlpreopen. dlprefiles="$dlprefiles $arg" prev= else deplibs="$deplibs $arg" fi continue ;; # Some other compiler argument. *) # Unknown arguments in both finalize_command and compile_command need # to be aesthetically quoted because they are evaled later. func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; esac # arg # Now actually substitute the argument into the commands. if test -n "$arg"; then func_append compile_command " $arg" func_append finalize_command " $arg" fi done # argument parsing loop test -n "$prev" && \ func_fatal_help "the \`$prevarg' option requires an argument" if test "$export_dynamic" = yes && test -n "$export_dynamic_flag_spec"; then eval arg=\"$export_dynamic_flag_spec\" func_append compile_command " $arg" func_append finalize_command " $arg" fi oldlibs= # calculate the name of the file, without its directory func_basename "$output" outputname="$func_basename_result" libobjs_save="$libobjs" if test -n "$shlibpath_var"; then # get the directories listed in $shlibpath_var eval shlib_search_path=\`\$ECHO \"X\${$shlibpath_var}\" \| \$Xsed -e \'s/:/ /g\'\` else shlib_search_path= fi eval sys_lib_search_path=\"$sys_lib_search_path_spec\" eval sys_lib_dlsearch_path=\"$sys_lib_dlsearch_path_spec\" func_dirname "$output" "/" "" output_objdir="$func_dirname_result$objdir" # Create the object directory. func_mkdir_p "$output_objdir" # Determine the type of output case $output in "") func_fatal_help "you must specify an output file" ;; *.$libext) linkmode=oldlib ;; *.lo | *.$objext) linkmode=obj ;; *.la) linkmode=lib ;; *) linkmode=prog ;; # Anything else should be a program. esac specialdeplibs= libs= # Find all interdependent deplibs by searching for libraries # that are linked more than once (e.g. -la -lb -la) for deplib in $deplibs; do if $opt_duplicate_deps ; then case "$libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi libs="$libs $deplib" done if test "$linkmode" = lib; then libs="$predeps $libs $compiler_lib_search_path $postdeps" # Compute libraries that are listed more than once in $predeps # $postdeps and mark them as special (i.e., whose duplicates are # not to be eliminated). pre_post_deps= if $opt_duplicate_compiler_generated_deps; then for pre_post_dep in $predeps $postdeps; do case "$pre_post_deps " in *" $pre_post_dep "*) specialdeplibs="$specialdeplibs $pre_post_deps" ;; esac pre_post_deps="$pre_post_deps $pre_post_dep" done fi pre_post_deps= fi deplibs= newdependency_libs= newlib_search_path= need_relink=no # whether we're linking any uninstalled libtool libraries notinst_deplibs= # not-installed libtool libraries notinst_path= # paths that contain not-installed libtool libraries case $linkmode in lib) passes="conv dlpreopen link" for file in $dlfiles $dlprefiles; do case $file in *.la) ;; *) func_fatal_help "libraries can \`-dlopen' only libtool libraries: $file" ;; esac done ;; prog) compile_deplibs= finalize_deplibs= alldeplibs=no newdlfiles= newdlprefiles= passes="conv scan dlopen dlpreopen link" ;; *) passes="conv" ;; esac for pass in $passes; do # The preopen pass in lib mode reverses $deplibs; put it back here # so that -L comes before libs that need it for instance... if test "$linkmode,$pass" = "lib,link"; then ## FIXME: Find the place where the list is rebuilt in the wrong ## order, and fix it there properly tmp_deplibs= for deplib in $deplibs; do tmp_deplibs="$deplib $tmp_deplibs" done deplibs="$tmp_deplibs" fi if test "$linkmode,$pass" = "lib,link" || test "$linkmode,$pass" = "prog,scan"; then libs="$deplibs" deplibs= fi if test "$linkmode" = prog; then case $pass in dlopen) libs="$dlfiles" ;; dlpreopen) libs="$dlprefiles" ;; link) libs="$deplibs %DEPLIBS%" test "X$link_all_deplibs" != Xno && libs="$libs $dependency_libs" ;; esac fi if test "$linkmode,$pass" = "lib,dlpreopen"; then # Collect and forward deplibs of preopened libtool libs for lib in $dlprefiles; do # Ignore non-libtool-libs dependency_libs= case $lib in *.la) func_source "$lib" ;; esac # Collect preopened libtool deplibs, except any this library # has declared as weak libs for deplib in $dependency_libs; do deplib_base=`$ECHO "X$deplib" | $Xsed -e "$basename"` case " $weak_libs " in *" $deplib_base "*) ;; *) deplibs="$deplibs $deplib" ;; esac done done libs="$dlprefiles" fi if test "$pass" = dlopen; then # Collect dlpreopened libraries save_deplibs="$deplibs" deplibs= fi for deplib in $libs; do lib= found=no case $deplib in -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads) if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else compiler_flags="$compiler_flags $deplib" if test "$linkmode" = lib ; then case "$new_inherited_linker_flags " in *" $deplib "*) ;; * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;; esac fi fi continue ;; -l*) if test "$linkmode" != lib && test "$linkmode" != prog; then func_warning "\`-l' is ignored for archives/objects" continue fi func_stripname '-l' '' "$deplib" name=$func_stripname_result if test "$linkmode" = lib; then searchdirs="$newlib_search_path $lib_search_path $compiler_lib_search_dirs $sys_lib_search_path $shlib_search_path" else searchdirs="$newlib_search_path $lib_search_path $sys_lib_search_path $shlib_search_path" fi for searchdir in $searchdirs; do for search_ext in .la $std_shrext .so .a; do # Search the libtool library lib="$searchdir/lib${name}${search_ext}" if test -f "$lib"; then if test "$search_ext" = ".la"; then found=yes else found=no fi break 2 fi done done if test "$found" != yes; then # deplib doesn't seem to be a libtool library if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs" fi continue else # deplib is a libtool library # If $allow_libtool_libs_with_static_runtimes && $deplib is a stdlib, # We need to do some special things here, and not later. if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then case " $predeps $postdeps " in *" $deplib "*) if func_lalib_p "$lib"; then library_names= old_library= func_source "$lib" for l in $old_library $library_names; do ll="$l" done if test "X$ll" = "X$old_library" ; then # only static version available found=no func_dirname "$lib" "" "." ladir="$func_dirname_result" lib=$ladir/$old_library if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs" fi continue fi fi ;; *) ;; esac fi fi ;; # -l *.ltframework) if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" if test "$linkmode" = lib ; then case "$new_inherited_linker_flags " in *" $deplib "*) ;; * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;; esac fi fi continue ;; -L*) case $linkmode in lib) deplibs="$deplib $deplibs" test "$pass" = conv && continue newdependency_libs="$deplib $newdependency_libs" func_stripname '-L' '' "$deplib" newlib_search_path="$newlib_search_path $func_stripname_result" ;; prog) if test "$pass" = conv; then deplibs="$deplib $deplibs" continue fi if test "$pass" = scan; then deplibs="$deplib $deplibs" else compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" fi func_stripname '-L' '' "$deplib" newlib_search_path="$newlib_search_path $func_stripname_result" ;; *) func_warning "\`-L' is ignored for archives/objects" ;; esac # linkmode continue ;; # -L -R*) if test "$pass" = link; then func_stripname '-R' '' "$deplib" dir=$func_stripname_result # Make sure the xrpath contains only unique directories. case "$xrpath " in *" $dir "*) ;; *) xrpath="$xrpath $dir" ;; esac fi deplibs="$deplib $deplibs" continue ;; *.la) lib="$deplib" ;; *.$libext) if test "$pass" = conv; then deplibs="$deplib $deplibs" continue fi case $linkmode in lib) # Linking convenience modules into shared libraries is allowed, # but linking other static libraries is non-portable. case " $dlpreconveniencelibs " in *" $deplib "*) ;; *) valid_a_lib=no case $deplibs_check_method in match_pattern*) set dummy $deplibs_check_method; shift match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"` if eval "\$ECHO \"X$deplib\"" 2>/dev/null | $Xsed -e 10q \ | $EGREP "$match_pattern_regex" > /dev/null; then valid_a_lib=yes fi ;; pass_all) valid_a_lib=yes ;; esac if test "$valid_a_lib" != yes; then $ECHO $ECHO "*** Warning: Trying to link with static lib archive $deplib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have" $ECHO "*** because the file extensions .$libext of this argument makes me believe" $ECHO "*** that it is just a static archive that I should not use here." else $ECHO $ECHO "*** Warning: Linking the shared library $output against the" $ECHO "*** static library $deplib is not portable!" deplibs="$deplib $deplibs" fi ;; esac continue ;; prog) if test "$pass" != link; then deplibs="$deplib $deplibs" else compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" fi continue ;; esac # linkmode ;; # *.$libext *.lo | *.$objext) if test "$pass" = conv; then deplibs="$deplib $deplibs" elif test "$linkmode" = prog; then if test "$pass" = dlpreopen || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then # If there is no dlopen support or we're linking statically, # we need to preload. newdlprefiles="$newdlprefiles $deplib" compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else newdlfiles="$newdlfiles $deplib" fi fi continue ;; %DEPLIBS%) alldeplibs=yes continue ;; esac # case $deplib if test "$found" = yes || test -f "$lib"; then : else func_fatal_error "cannot find the library \`$lib' or unhandled argument \`$deplib'" fi # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$lib" \ || func_fatal_error "\`$lib' is not a valid libtool archive" func_dirname "$lib" "" "." ladir="$func_dirname_result" dlname= dlopen= dlpreopen= libdir= library_names= old_library= inherited_linker_flags= # If the library was installed with an old release of libtool, # it will not redefine variables installed, or shouldnotlink installed=yes shouldnotlink=no avoidtemprpath= # Read the .la file func_source "$lib" # Convert "-framework foo" to "foo.ltframework" if test -n "$inherited_linker_flags"; then tmp_inherited_linker_flags=`$ECHO "X$inherited_linker_flags" | $Xsed -e 's/-framework \([^ $]*\)/\1.ltframework/g'` for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do case " $new_inherited_linker_flags " in *" $tmp_inherited_linker_flag "*) ;; *) new_inherited_linker_flags="$new_inherited_linker_flags $tmp_inherited_linker_flag";; esac done fi dependency_libs=`$ECHO "X $dependency_libs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` if test "$linkmode,$pass" = "lib,link" || test "$linkmode,$pass" = "prog,scan" || { test "$linkmode" != prog && test "$linkmode" != lib; }; then test -n "$dlopen" && dlfiles="$dlfiles $dlopen" test -n "$dlpreopen" && dlprefiles="$dlprefiles $dlpreopen" fi if test "$pass" = conv; then # Only check for convenience libraries deplibs="$lib $deplibs" if test -z "$libdir"; then if test -z "$old_library"; then func_fatal_error "cannot find name of link library for \`$lib'" fi # It is a libtool convenience library, so add in its objects. convenience="$convenience $ladir/$objdir/$old_library" old_convenience="$old_convenience $ladir/$objdir/$old_library" tmp_libs= for deplib in $dependency_libs; do deplibs="$deplib $deplibs" if $opt_duplicate_deps ; then case "$tmp_libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi tmp_libs="$tmp_libs $deplib" done elif test "$linkmode" != prog && test "$linkmode" != lib; then func_fatal_error "\`$lib' is not a convenience library" fi continue fi # $pass = conv # Get the name of the library we link against. linklib= for l in $old_library $library_names; do linklib="$l" done if test -z "$linklib"; then func_fatal_error "cannot find name of link library for \`$lib'" fi # This library was specified with -dlopen. if test "$pass" = dlopen; then if test -z "$libdir"; then func_fatal_error "cannot -dlopen a convenience library: \`$lib'" fi if test -z "$dlname" || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then # If there is no dlname, no dlopen support or we're linking # statically, we need to preload. We also need to preload any # dependent libraries so libltdl's deplib preloader doesn't # bomb out in the load deplibs phase. dlprefiles="$dlprefiles $lib $dependency_libs" else newdlfiles="$newdlfiles $lib" fi continue fi # $pass = dlopen # We need an absolute path. case $ladir in [\\/]* | [A-Za-z]:[\\/]*) abs_ladir="$ladir" ;; *) abs_ladir=`cd "$ladir" && pwd` if test -z "$abs_ladir"; then func_warning "cannot determine absolute directory name of \`$ladir'" func_warning "passing it literally to the linker, although it might fail" abs_ladir="$ladir" fi ;; esac func_basename "$lib" laname="$func_basename_result" # Find the relevant object directory and library name. if test "X$installed" = Xyes; then if test ! -f "$libdir/$linklib" && test -f "$abs_ladir/$linklib"; then func_warning "library \`$lib' was moved." dir="$ladir" absdir="$abs_ladir" libdir="$abs_ladir" else dir="$libdir" absdir="$libdir" fi test "X$hardcode_automatic" = Xyes && avoidtemprpath=yes else if test ! -f "$ladir/$objdir/$linklib" && test -f "$abs_ladir/$linklib"; then dir="$ladir" absdir="$abs_ladir" # Remove this search path later notinst_path="$notinst_path $abs_ladir" else dir="$ladir/$objdir" absdir="$abs_ladir/$objdir" # Remove this search path later notinst_path="$notinst_path $abs_ladir" fi fi # $installed = yes func_stripname 'lib' '.la' "$laname" name=$func_stripname_result # This library was specified with -dlpreopen. if test "$pass" = dlpreopen; then if test -z "$libdir" && test "$linkmode" = prog; then func_fatal_error "only libraries may -dlpreopen a convenience library: \`$lib'" fi # Prefer using a static library (so that no silly _DYNAMIC symbols # are required to link). if test -n "$old_library"; then newdlprefiles="$newdlprefiles $dir/$old_library" # Keep a list of preopened convenience libraries to check # that they are being used correctly in the link pass. test -z "$libdir" && \ dlpreconveniencelibs="$dlpreconveniencelibs $dir/$old_library" # Otherwise, use the dlname, so that lt_dlopen finds it. elif test -n "$dlname"; then newdlprefiles="$newdlprefiles $dir/$dlname" else newdlprefiles="$newdlprefiles $dir/$linklib" fi fi # $pass = dlpreopen if test -z "$libdir"; then # Link the convenience library if test "$linkmode" = lib; then deplibs="$dir/$old_library $deplibs" elif test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$dir/$old_library $compile_deplibs" finalize_deplibs="$dir/$old_library $finalize_deplibs" else deplibs="$lib $deplibs" # used for prog,scan pass fi continue fi if test "$linkmode" = prog && test "$pass" != link; then newlib_search_path="$newlib_search_path $ladir" deplibs="$lib $deplibs" linkalldeplibs=no if test "$link_all_deplibs" != no || test -z "$library_names" || test "$build_libtool_libs" = no; then linkalldeplibs=yes fi tmp_libs= for deplib in $dependency_libs; do case $deplib in -L*) func_stripname '-L' '' "$deplib" newlib_search_path="$newlib_search_path $func_stripname_result" ;; esac # Need to link against all dependency_libs? if test "$linkalldeplibs" = yes; then deplibs="$deplib $deplibs" else # Need to hardcode shared library paths # or/and link against static libraries newdependency_libs="$deplib $newdependency_libs" fi if $opt_duplicate_deps ; then case "$tmp_libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi tmp_libs="$tmp_libs $deplib" done # for deplib continue fi # $linkmode = prog... if test "$linkmode,$pass" = "prog,link"; then if test -n "$library_names" && { { test "$prefer_static_libs" = no || test "$prefer_static_libs,$installed" = "built,yes"; } || test -z "$old_library"; }; then # We need to hardcode the library path if test -n "$shlibpath_var" && test -z "$avoidtemprpath" ; then # Make sure the rpath contains only unique directories. case "$temp_rpath:" in *"$absdir:"*) ;; *) temp_rpath="$temp_rpath$absdir:" ;; esac fi # Hardcode the library path. # Skip directories that are in the system default run-time # search path. case " $sys_lib_dlsearch_path " in *" $absdir "*) ;; *) case "$compile_rpath " in *" $absdir "*) ;; *) compile_rpath="$compile_rpath $absdir" esac ;; esac case " $sys_lib_dlsearch_path " in *" $libdir "*) ;; *) case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" esac ;; esac fi # $linkmode,$pass = prog,link... if test "$alldeplibs" = yes && { test "$deplibs_check_method" = pass_all || { test "$build_libtool_libs" = yes && test -n "$library_names"; }; }; then # We only need to search for static libraries continue fi fi link_static=no # Whether the deplib will be linked statically use_static_libs=$prefer_static_libs if test "$use_static_libs" = built && test "$installed" = yes; then use_static_libs=no fi if test -n "$library_names" && { test "$use_static_libs" = no || test -z "$old_library"; }; then case $host in *cygwin* | *mingw* | *cegcc*) # No point in relinking DLLs because paths are not encoded notinst_deplibs="$notinst_deplibs $lib" need_relink=no ;; *) if test "$installed" = no; then notinst_deplibs="$notinst_deplibs $lib" need_relink=yes fi ;; esac # This is a shared library # Warn about portability, can't link against -module's on some # systems (darwin). Don't bleat about dlopened modules though! dlopenmodule="" for dlpremoduletest in $dlprefiles; do if test "X$dlpremoduletest" = "X$lib"; then dlopenmodule="$dlpremoduletest" break fi done if test -z "$dlopenmodule" && test "$shouldnotlink" = yes && test "$pass" = link; then $ECHO if test "$linkmode" = prog; then $ECHO "*** Warning: Linking the executable $output against the loadable module" else $ECHO "*** Warning: Linking the shared library $output against the loadable module" fi $ECHO "*** $linklib is not portable!" fi if test "$linkmode" = lib && test "$hardcode_into_libs" = yes; then # Hardcode the library path. # Skip directories that are in the system default run-time # search path. case " $sys_lib_dlsearch_path " in *" $absdir "*) ;; *) case "$compile_rpath " in *" $absdir "*) ;; *) compile_rpath="$compile_rpath $absdir" esac ;; esac case " $sys_lib_dlsearch_path " in *" $libdir "*) ;; *) case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" esac ;; esac fi if test -n "$old_archive_from_expsyms_cmds"; then # figure out the soname set dummy $library_names shift realname="$1" shift libname=`eval "\\$ECHO \"$libname_spec\""` # use dlname if we got it. it's perfectly good, no? if test -n "$dlname"; then soname="$dlname" elif test -n "$soname_spec"; then # bleh windows case $host in *cygwin* | mingw* | *cegcc*) func_arith $current - $age major=$func_arith_result versuffix="-$major" ;; esac eval soname=\"$soname_spec\" else soname="$realname" fi # Make a new name for the extract_expsyms_cmds to use soroot="$soname" func_basename "$soroot" soname="$func_basename_result" func_stripname 'lib' '.dll' "$soname" newlib=libimp-$func_stripname_result.a # If the library has no export list, then create one now if test -f "$output_objdir/$soname-def"; then : else func_verbose "extracting exported symbol list from \`$soname'" func_execute_cmds "$extract_expsyms_cmds" 'exit $?' fi # Create $newlib if test -f "$output_objdir/$newlib"; then :; else func_verbose "generating import library for \`$soname'" func_execute_cmds "$old_archive_from_expsyms_cmds" 'exit $?' fi # make sure the library variables are pointing to the new library dir=$output_objdir linklib=$newlib fi # test -n "$old_archive_from_expsyms_cmds" if test "$linkmode" = prog || test "$mode" != relink; then add_shlibpath= add_dir= add= lib_linked=yes case $hardcode_action in immediate | unsupported) if test "$hardcode_direct" = no; then add="$dir/$linklib" case $host in *-*-sco3.2v5.0.[024]*) add_dir="-L$dir" ;; *-*-sysv4*uw2*) add_dir="-L$dir" ;; *-*-sysv5OpenUNIX* | *-*-sysv5UnixWare7.[01].[10]* | \ *-*-unixware7*) add_dir="-L$dir" ;; *-*-darwin* ) # if the lib is a (non-dlopened) module then we can not # link against it, someone is ignoring the earlier warnings if /usr/bin/file -L $add 2> /dev/null | $GREP ": [^:]* bundle" >/dev/null ; then if test "X$dlopenmodule" != "X$lib"; then $ECHO "*** Warning: lib $linklib is a module, not a shared library" if test -z "$old_library" ; then $ECHO $ECHO "*** And there doesn't seem to be a static archive available" $ECHO "*** The link will probably fail, sorry" else add="$dir/$old_library" fi elif test -n "$old_library"; then add="$dir/$old_library" fi fi esac elif test "$hardcode_minus_L" = no; then case $host in *-*-sunos*) add_shlibpath="$dir" ;; esac add_dir="-L$dir" add="-l$name" elif test "$hardcode_shlibpath_var" = no; then add_shlibpath="$dir" add="-l$name" else lib_linked=no fi ;; relink) if test "$hardcode_direct" = yes && test "$hardcode_direct_absolute" = no; then add="$dir/$linklib" elif test "$hardcode_minus_L" = yes; then add_dir="-L$dir" # Try looking first in the location we're being installed to. if test -n "$inst_prefix_dir"; then case $libdir in [\\/]*) add_dir="$add_dir -L$inst_prefix_dir$libdir" ;; esac fi add="-l$name" elif test "$hardcode_shlibpath_var" = yes; then add_shlibpath="$dir" add="-l$name" else lib_linked=no fi ;; *) lib_linked=no ;; esac if test "$lib_linked" != yes; then func_fatal_configuration "unsupported hardcode properties" fi if test -n "$add_shlibpath"; then case :$compile_shlibpath: in *":$add_shlibpath:"*) ;; *) compile_shlibpath="$compile_shlibpath$add_shlibpath:" ;; esac fi if test "$linkmode" = prog; then test -n "$add_dir" && compile_deplibs="$add_dir $compile_deplibs" test -n "$add" && compile_deplibs="$add $compile_deplibs" else test -n "$add_dir" && deplibs="$add_dir $deplibs" test -n "$add" && deplibs="$add $deplibs" if test "$hardcode_direct" != yes && test "$hardcode_minus_L" != yes && test "$hardcode_shlibpath_var" = yes; then case :$finalize_shlibpath: in *":$libdir:"*) ;; *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;; esac fi fi fi if test "$linkmode" = prog || test "$mode" = relink; then add_shlibpath= add_dir= add= # Finalize command for both is simple: just hardcode it. if test "$hardcode_direct" = yes && test "$hardcode_direct_absolute" = no; then add="$libdir/$linklib" elif test "$hardcode_minus_L" = yes; then add_dir="-L$libdir" add="-l$name" elif test "$hardcode_shlibpath_var" = yes; then case :$finalize_shlibpath: in *":$libdir:"*) ;; *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;; esac add="-l$name" elif test "$hardcode_automatic" = yes; then if test -n "$inst_prefix_dir" && test -f "$inst_prefix_dir$libdir/$linklib" ; then add="$inst_prefix_dir$libdir/$linklib" else add="$libdir/$linklib" fi else # We cannot seem to hardcode it, guess we'll fake it. add_dir="-L$libdir" # Try looking first in the location we're being installed to. if test -n "$inst_prefix_dir"; then case $libdir in [\\/]*) add_dir="$add_dir -L$inst_prefix_dir$libdir" ;; esac fi add="-l$name" fi if test "$linkmode" = prog; then test -n "$add_dir" && finalize_deplibs="$add_dir $finalize_deplibs" test -n "$add" && finalize_deplibs="$add $finalize_deplibs" else test -n "$add_dir" && deplibs="$add_dir $deplibs" test -n "$add" && deplibs="$add $deplibs" fi fi elif test "$linkmode" = prog; then # Here we assume that one of hardcode_direct or hardcode_minus_L # is not unsupported. This is valid on all known static and # shared platforms. if test "$hardcode_direct" != unsupported; then test -n "$old_library" && linklib="$old_library" compile_deplibs="$dir/$linklib $compile_deplibs" finalize_deplibs="$dir/$linklib $finalize_deplibs" else compile_deplibs="-l$name -L$dir $compile_deplibs" finalize_deplibs="-l$name -L$dir $finalize_deplibs" fi elif test "$build_libtool_libs" = yes; then # Not a shared library if test "$deplibs_check_method" != pass_all; then # We're trying link a shared library against a static one # but the system doesn't support it. # Just print a warning and add the library to dependency_libs so # that the program can be linked against the static library. $ECHO $ECHO "*** Warning: This system can not link to static lib archive $lib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have." if test "$module" = yes; then $ECHO "*** But as you try to build a module library, libtool will still create " $ECHO "*** a static module, that should work as long as the dlopening application" $ECHO "*** is linked with the -dlopen flag to resolve symbols at runtime." if test -z "$global_symbol_pipe"; then $ECHO $ECHO "*** However, this would only work if libtool was able to extract symbol" $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could" $ECHO "*** not find such a program. So, this module is probably useless." $ECHO "*** \`nm' from GNU binutils and a full rebuild may help." fi if test "$build_old_libs" = no; then build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi fi else deplibs="$dir/$old_library $deplibs" link_static=yes fi fi # link shared/static library? if test "$linkmode" = lib; then if test -n "$dependency_libs" && { test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes || test "$link_static" = yes; }; then # Extract -R from dependency_libs temp_deplibs= for libdir in $dependency_libs; do case $libdir in -R*) func_stripname '-R' '' "$libdir" temp_xrpath=$func_stripname_result case " $xrpath " in *" $temp_xrpath "*) ;; *) xrpath="$xrpath $temp_xrpath";; esac;; *) temp_deplibs="$temp_deplibs $libdir";; esac done dependency_libs="$temp_deplibs" fi newlib_search_path="$newlib_search_path $absdir" # Link against this library test "$link_static" = no && newdependency_libs="$abs_ladir/$laname $newdependency_libs" # ... and its dependency_libs tmp_libs= for deplib in $dependency_libs; do newdependency_libs="$deplib $newdependency_libs" if $opt_duplicate_deps ; then case "$tmp_libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi tmp_libs="$tmp_libs $deplib" done if test "$link_all_deplibs" != no; then # Add the search paths of all dependency libraries for deplib in $dependency_libs; do path= case $deplib in -L*) path="$deplib" ;; *.la) func_dirname "$deplib" "" "." dir="$func_dirname_result" # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) absdir="$dir" ;; *) absdir=`cd "$dir" && pwd` if test -z "$absdir"; then func_warning "cannot determine absolute directory name of \`$dir'" absdir="$dir" fi ;; esac if $GREP "^installed=no" $deplib > /dev/null; then case $host in *-*-darwin*) depdepl= eval deplibrary_names=`${SED} -n -e 's/^library_names=\(.*\)$/\1/p' $deplib` if test -n "$deplibrary_names" ; then for tmp in $deplibrary_names ; do depdepl=$tmp done if test -f "$absdir/$objdir/$depdepl" ; then depdepl="$absdir/$objdir/$depdepl" darwin_install_name=`${OTOOL} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'` if test -z "$darwin_install_name"; then darwin_install_name=`${OTOOL64} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'` fi compiler_flags="$compiler_flags ${wl}-dylib_file ${wl}${darwin_install_name}:${depdepl}" linker_flags="$linker_flags -dylib_file ${darwin_install_name}:${depdepl}" path= fi fi ;; *) path="-L$absdir/$objdir" ;; esac else eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib` test -z "$libdir" && \ func_fatal_error "\`$deplib' is not a valid libtool archive" test "$absdir" != "$libdir" && \ func_warning "\`$deplib' seems to be moved" path="-L$absdir" fi ;; esac case " $deplibs " in *" $path "*) ;; *) deplibs="$path $deplibs" ;; esac done fi # link_all_deplibs != no fi # linkmode = lib done # for deplib in $libs if test "$pass" = link; then if test "$linkmode" = "prog"; then compile_deplibs="$new_inherited_linker_flags $compile_deplibs" finalize_deplibs="$new_inherited_linker_flags $finalize_deplibs" else compiler_flags="$compiler_flags "`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` fi fi dependency_libs="$newdependency_libs" if test "$pass" = dlpreopen; then # Link the dlpreopened libraries before other libraries for deplib in $save_deplibs; do deplibs="$deplib $deplibs" done fi if test "$pass" != dlopen; then if test "$pass" != conv; then # Make sure lib_search_path contains only unique directories. lib_search_path= for dir in $newlib_search_path; do case "$lib_search_path " in *" $dir "*) ;; *) lib_search_path="$lib_search_path $dir" ;; esac done newlib_search_path= fi if test "$linkmode,$pass" != "prog,link"; then vars="deplibs" else vars="compile_deplibs finalize_deplibs" fi for var in $vars dependency_libs; do # Add libraries to $var in reverse order eval tmp_libs=\"\$$var\" new_libs= for deplib in $tmp_libs; do # FIXME: Pedantically, this is the right thing to do, so # that some nasty dependency loop isn't accidentally # broken: #new_libs="$deplib $new_libs" # Pragmatically, this seems to cause very few problems in # practice: case $deplib in -L*) new_libs="$deplib $new_libs" ;; -R*) ;; *) # And here is the reason: when a library appears more # than once as an explicit dependence of a library, or # is implicitly linked in more than once by the # compiler, it is considered special, and multiple # occurrences thereof are not removed. Compare this # with having the same library being listed as a # dependency of multiple other libraries: in this case, # we know (pedantically, we assume) the library does not # need to be listed more than once, so we keep only the # last copy. This is not always right, but it is rare # enough that we require users that really mean to play # such unportable linking tricks to link the library # using -Wl,-lname, so that libtool does not consider it # for duplicate removal. case " $specialdeplibs " in *" $deplib "*) new_libs="$deplib $new_libs" ;; *) case " $new_libs " in *" $deplib "*) ;; *) new_libs="$deplib $new_libs" ;; esac ;; esac ;; esac done tmp_libs= for deplib in $new_libs; do case $deplib in -L*) case " $tmp_libs " in *" $deplib "*) ;; *) tmp_libs="$tmp_libs $deplib" ;; esac ;; *) tmp_libs="$tmp_libs $deplib" ;; esac done eval $var=\"$tmp_libs\" done # for var fi # Last step: remove runtime libs from dependency_libs # (they stay in deplibs) tmp_libs= for i in $dependency_libs ; do case " $predeps $postdeps $compiler_lib_search_path " in *" $i "*) i="" ;; esac if test -n "$i" ; then tmp_libs="$tmp_libs $i" fi done dependency_libs=$tmp_libs done # for pass if test "$linkmode" = prog; then dlfiles="$newdlfiles" fi if test "$linkmode" = prog || test "$linkmode" = lib; then dlprefiles="$newdlprefiles" fi case $linkmode in oldlib) if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then func_warning "\`-dlopen' is ignored for archives" fi case " $deplibs" in *\ -l* | *\ -L*) func_warning "\`-l' and \`-L' are ignored for archives" ;; esac test -n "$rpath" && \ func_warning "\`-rpath' is ignored for archives" test -n "$xrpath" && \ func_warning "\`-R' is ignored for archives" test -n "$vinfo" && \ func_warning "\`-version-info/-version-number' is ignored for archives" test -n "$release" && \ func_warning "\`-release' is ignored for archives" test -n "$export_symbols$export_symbols_regex" && \ func_warning "\`-export-symbols' is ignored for archives" # Now set the variables for building old libraries. build_libtool_libs=no oldlibs="$output" objs="$objs$old_deplibs" ;; lib) # Make sure we only generate libraries of the form `libNAME.la'. case $outputname in lib*) func_stripname 'lib' '.la' "$outputname" name=$func_stripname_result eval shared_ext=\"$shrext_cmds\" eval libname=\"$libname_spec\" ;; *) test "$module" = no && \ func_fatal_help "libtool library \`$output' must begin with \`lib'" if test "$need_lib_prefix" != no; then # Add the "lib" prefix for modules if required func_stripname '' '.la' "$outputname" name=$func_stripname_result eval shared_ext=\"$shrext_cmds\" eval libname=\"$libname_spec\" else func_stripname '' '.la' "$outputname" libname=$func_stripname_result fi ;; esac if test -n "$objs"; then if test "$deplibs_check_method" != pass_all; then func_fatal_error "cannot build libtool library \`$output' from non-libtool objects on this host:$objs" else $ECHO $ECHO "*** Warning: Linking the shared library $output against the non-libtool" $ECHO "*** objects $objs is not portable!" libobjs="$libobjs $objs" fi fi test "$dlself" != no && \ func_warning "\`-dlopen self' is ignored for libtool libraries" set dummy $rpath shift test "$#" -gt 1 && \ func_warning "ignoring multiple \`-rpath's for a libtool library" install_libdir="$1" oldlibs= if test -z "$rpath"; then if test "$build_libtool_libs" = yes; then # Building a libtool convenience library. # Some compilers have problems with a `.al' extension so # convenience libraries should have the same extension an # archive normally would. oldlibs="$output_objdir/$libname.$libext $oldlibs" build_libtool_libs=convenience build_old_libs=yes fi test -n "$vinfo" && \ func_warning "\`-version-info/-version-number' is ignored for convenience libraries" test -n "$release" && \ func_warning "\`-release' is ignored for convenience libraries" else # Parse the version information argument. save_ifs="$IFS"; IFS=':' set dummy $vinfo 0 0 0 shift IFS="$save_ifs" test -n "$7" && \ func_fatal_help "too many parameters to \`-version-info'" # convert absolute version numbers to libtool ages # this retains compatibility with .la files and attempts # to make the code below a bit more comprehensible case $vinfo_number in yes) number_major="$1" number_minor="$2" number_revision="$3" # # There are really only two kinds -- those that # use the current revision as the major version # and those that subtract age and use age as # a minor version. But, then there is irix # which has an extra 1 added just for fun # case $version_type in darwin|linux|osf|windows|none) func_arith $number_major + $number_minor current=$func_arith_result age="$number_minor" revision="$number_revision" ;; freebsd-aout|freebsd-elf|sunos) current="$number_major" revision="$number_minor" age="0" ;; irix|nonstopux) func_arith $number_major + $number_minor current=$func_arith_result age="$number_minor" revision="$number_minor" lt_irix_increment=no ;; *) func_fatal_configuration "$modename: unknown library version type \`$version_type'" ;; esac ;; no) current="$1" revision="$2" age="$3" ;; esac # Check that each of the things are valid numbers. case $current in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "CURRENT \`$current' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac case $revision in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "REVISION \`$revision' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac case $age in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "AGE \`$age' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac if test "$age" -gt "$current"; then func_error "AGE \`$age' is greater than the current interface number \`$current'" func_fatal_error "\`$vinfo' is not valid version information" fi # Calculate the version variables. major= versuffix= verstring= case $version_type in none) ;; darwin) # Like Linux, but with the current version available in # verstring for coding it into the library header func_arith $current - $age major=.$func_arith_result versuffix="$major.$age.$revision" # Darwin ld doesn't like 0 for these options... func_arith $current + 1 minor_current=$func_arith_result xlcverstring="${wl}-compatibility_version ${wl}$minor_current ${wl}-current_version ${wl}$minor_current.$revision" verstring="-compatibility_version $minor_current -current_version $minor_current.$revision" ;; freebsd-aout) major=".$current" versuffix=".$current.$revision"; ;; freebsd-elf) major=".$current" versuffix=".$current" ;; irix | nonstopux) if test "X$lt_irix_increment" = "Xno"; then func_arith $current - $age else func_arith $current - $age + 1 fi major=$func_arith_result case $version_type in nonstopux) verstring_prefix=nonstopux ;; *) verstring_prefix=sgi ;; esac verstring="$verstring_prefix$major.$revision" # Add in all the interfaces that we are compatible with. loop=$revision while test "$loop" -ne 0; do func_arith $revision - $loop iface=$func_arith_result func_arith $loop - 1 loop=$func_arith_result verstring="$verstring_prefix$major.$iface:$verstring" done # Before this point, $major must not contain `.'. major=.$major versuffix="$major.$revision" ;; linux) func_arith $current - $age major=.$func_arith_result versuffix="$major.$age.$revision" ;; osf) func_arith $current - $age major=.$func_arith_result versuffix=".$current.$age.$revision" verstring="$current.$age.$revision" # Add in all the interfaces that we are compatible with. loop=$age while test "$loop" -ne 0; do func_arith $current - $loop iface=$func_arith_result func_arith $loop - 1 loop=$func_arith_result verstring="$verstring:${iface}.0" done # Make executables depend on our current version. verstring="$verstring:${current}.0" ;; qnx) major=".$current" versuffix=".$current" ;; sunos) major=".$current" versuffix=".$current.$revision" ;; windows) # Use '-' rather than '.', since we only want one # extension on DOS 8.3 filesystems. func_arith $current - $age major=$func_arith_result versuffix="-$major" ;; *) func_fatal_configuration "unknown library version type \`$version_type'" ;; esac # Clear the version info if we defaulted, and they specified a release. if test -z "$vinfo" && test -n "$release"; then major= case $version_type in darwin) # we can't check for "0.0" in archive_cmds due to quoting # problems, so we reset it completely verstring= ;; *) verstring="0.0" ;; esac if test "$need_version" = no; then versuffix= else versuffix=".0.0" fi fi # Remove version info from name if versioning should be avoided if test "$avoid_version" = yes && test "$need_version" = no; then major= versuffix= verstring="" fi # Check to see if the archive will have undefined symbols. if test "$allow_undefined" = yes; then if test "$allow_undefined_flag" = unsupported; then func_warning "undefined symbols not allowed in $host shared libraries" build_libtool_libs=no build_old_libs=yes fi else # Don't allow undefined symbols. allow_undefined_flag="$no_undefined_flag" fi fi func_generate_dlsyms "$libname" "$libname" "yes" libobjs="$libobjs $symfileobj" test "X$libobjs" = "X " && libobjs= if test "$mode" != relink; then # Remove our outputs, but don't remove object files since they # may have been created when compiling PIC objects. removelist= tempremovelist=`$ECHO "$output_objdir/*"` for p in $tempremovelist; do case $p in *.$objext | *.gcno) ;; $output_objdir/$outputname | $output_objdir/$libname.* | $output_objdir/${libname}${release}.*) if test "X$precious_files_regex" != "X"; then if $ECHO "$p" | $EGREP -e "$precious_files_regex" >/dev/null 2>&1 then continue fi fi removelist="$removelist $p" ;; *) ;; esac done test -n "$removelist" && \ func_show_eval "${RM}r \$removelist" fi # Now set the variables for building old libraries. if test "$build_old_libs" = yes && test "$build_libtool_libs" != convenience ; then oldlibs="$oldlibs $output_objdir/$libname.$libext" # Transform .lo files to .o files. oldobjs="$objs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}'$/d' -e "$lo2o" | $NL2SP` fi # Eliminate all temporary directories. #for path in $notinst_path; do # lib_search_path=`$ECHO "X$lib_search_path " | $Xsed -e "s% $path % %g"` # deplibs=`$ECHO "X$deplibs " | $Xsed -e "s% -L$path % %g"` # dependency_libs=`$ECHO "X$dependency_libs " | $Xsed -e "s% -L$path % %g"` #done if test -n "$xrpath"; then # If the user specified any rpath flags, then add them. temp_xrpath= for libdir in $xrpath; do temp_xrpath="$temp_xrpath -R$libdir" case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" ;; esac done if test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes; then dependency_libs="$temp_xrpath $dependency_libs" fi fi # Make sure dlfiles contains only unique files that won't be dlpreopened old_dlfiles="$dlfiles" dlfiles= for lib in $old_dlfiles; do case " $dlprefiles $dlfiles " in *" $lib "*) ;; *) dlfiles="$dlfiles $lib" ;; esac done # Make sure dlprefiles contains only unique files old_dlprefiles="$dlprefiles" dlprefiles= for lib in $old_dlprefiles; do case "$dlprefiles " in *" $lib "*) ;; *) dlprefiles="$dlprefiles $lib" ;; esac done if test "$build_libtool_libs" = yes; then if test -n "$rpath"; then case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos* | *-cegcc*) # these systems don't actually have a c library (as such)! ;; *-*-rhapsody* | *-*-darwin1.[012]) # Rhapsody C library is in the System framework deplibs="$deplibs System.ltframework" ;; *-*-netbsd*) # Don't link with libc until the a.out ld.so is fixed. ;; *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc due to us having libc/libc_r. ;; *-*-sco3.2v5* | *-*-sco5v6*) # Causes problems with __ctype ;; *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*) # Compiler inserts libc in the correct place for threads to work ;; *) # Add libc to deplibs on all other systems if necessary. if test "$build_libtool_need_lc" = "yes"; then deplibs="$deplibs -lc" fi ;; esac fi # Transform deplibs into only deplibs that can be linked in shared. name_save=$name libname_save=$libname release_save=$release versuffix_save=$versuffix major_save=$major # I'm not sure if I'm treating the release correctly. I think # release should show up in the -l (ie -lgmp5) so we don't want to # add it in twice. Is that correct? release="" versuffix="" major="" newdeplibs= droppeddeps=no case $deplibs_check_method in pass_all) # Don't check for shared/static. Everything works. # This might be a little naive. We might want to check # whether the library exists or not. But this is on # osf3 & osf4 and I'm not really sure... Just # implementing what was already the behavior. newdeplibs=$deplibs ;; test_compile) # This code stresses the "libraries are programs" paradigm to its # limits. Maybe even breaks it. We compile a program, linking it # against the deplibs as a proxy for the library. Then we can check # whether they linked in statically or dynamically with ldd. $opt_dry_run || $RM conftest.c cat > conftest.c </dev/null` for potent_lib in $potential_libs; do # Follow soft links. if ls -lLd "$potent_lib" 2>/dev/null | $GREP " -> " >/dev/null; then continue fi # The statement above tries to avoid entering an # endless loop below, in case of cyclic links. # We might still enter an endless loop, since a link # loop can be closed while we follow links, # but so what? potlib="$potent_lib" while test -h "$potlib" 2>/dev/null; do potliblink=`ls -ld $potlib | ${SED} 's/.* -> //'` case $potliblink in [\\/]* | [A-Za-z]:[\\/]*) potlib="$potliblink";; *) potlib=`$ECHO "X$potlib" | $Xsed -e 's,[^/]*$,,'`"$potliblink";; esac done if eval $file_magic_cmd \"\$potlib\" 2>/dev/null | $SED -e 10q | $EGREP "$file_magic_regex" > /dev/null; then newdeplibs="$newdeplibs $a_deplib" a_deplib="" break 2 fi done done fi if test -n "$a_deplib" ; then droppeddeps=yes $ECHO $ECHO "*** Warning: linker path does not have real file for library $a_deplib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have" $ECHO "*** because I did check the linker path looking for a file starting" if test -z "$potlib" ; then $ECHO "*** with $libname but no candidates were found. (...for file magic test)" else $ECHO "*** with $libname and none of the candidates passed a file format test" $ECHO "*** using a file magic. Last file checked: $potlib" fi fi ;; *) # Add a -L argument. newdeplibs="$newdeplibs $a_deplib" ;; esac done # Gone through all deplibs. ;; match_pattern*) set dummy $deplibs_check_method; shift match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"` for a_deplib in $deplibs; do case $a_deplib in -l*) func_stripname -l '' "$a_deplib" name=$func_stripname_result if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then case " $predeps $postdeps " in *" $a_deplib "*) newdeplibs="$newdeplibs $a_deplib" a_deplib="" ;; esac fi if test -n "$a_deplib" ; then libname=`eval "\\$ECHO \"$libname_spec\""` for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do potential_libs=`ls $i/$libname[.-]* 2>/dev/null` for potent_lib in $potential_libs; do potlib="$potent_lib" # see symlink-check above in file_magic test if eval "\$ECHO \"X$potent_lib\"" 2>/dev/null | $Xsed -e 10q | \ $EGREP "$match_pattern_regex" > /dev/null; then newdeplibs="$newdeplibs $a_deplib" a_deplib="" break 2 fi done done fi if test -n "$a_deplib" ; then droppeddeps=yes $ECHO $ECHO "*** Warning: linker path does not have real file for library $a_deplib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have" $ECHO "*** because I did check the linker path looking for a file starting" if test -z "$potlib" ; then $ECHO "*** with $libname but no candidates were found. (...for regex pattern test)" else $ECHO "*** with $libname and none of the candidates passed a file format test" $ECHO "*** using a regex pattern. Last file checked: $potlib" fi fi ;; *) # Add a -L argument. newdeplibs="$newdeplibs $a_deplib" ;; esac done # Gone through all deplibs. ;; none | unknown | *) newdeplibs="" tmp_deplibs=`$ECHO "X $deplibs" | $Xsed \ -e 's/ -lc$//' -e 's/ -[LR][^ ]*//g'` if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then for i in $predeps $postdeps ; do # can't use Xsed below, because $i might contain '/' tmp_deplibs=`$ECHO "X $tmp_deplibs" | $Xsed -e "s,$i,,"` done fi if $ECHO "X $tmp_deplibs" | $Xsed -e 's/[ ]//g' | $GREP . >/dev/null; then $ECHO if test "X$deplibs_check_method" = "Xnone"; then $ECHO "*** Warning: inter-library dependencies are not supported in this platform." else $ECHO "*** Warning: inter-library dependencies are not known to be supported." fi $ECHO "*** All declared inter-library dependencies are being dropped." droppeddeps=yes fi ;; esac versuffix=$versuffix_save major=$major_save release=$release_save libname=$libname_save name=$name_save case $host in *-*-rhapsody* | *-*-darwin1.[012]) # On Rhapsody replace the C library with the System framework newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's/ -lc / System.ltframework /'` ;; esac if test "$droppeddeps" = yes; then if test "$module" = yes; then $ECHO $ECHO "*** Warning: libtool could not satisfy all declared inter-library" $ECHO "*** dependencies of module $libname. Therefore, libtool will create" $ECHO "*** a static module, that should work as long as the dlopening" $ECHO "*** application is linked with the -dlopen flag." if test -z "$global_symbol_pipe"; then $ECHO $ECHO "*** However, this would only work if libtool was able to extract symbol" $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could" $ECHO "*** not find such a program. So, this module is probably useless." $ECHO "*** \`nm' from GNU binutils and a full rebuild may help." fi if test "$build_old_libs" = no; then oldlibs="$output_objdir/$libname.$libext" build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi else $ECHO "*** The inter-library dependencies that have been dropped here will be" $ECHO "*** automatically added whenever a program is linked with this library" $ECHO "*** or is declared to -dlopen it." if test "$allow_undefined" = no; then $ECHO $ECHO "*** Since this library must not contain undefined symbols," $ECHO "*** because either the platform does not support them or" $ECHO "*** it was explicitly requested with -no-undefined," $ECHO "*** libtool will only create a static version of it." if test "$build_old_libs" = no; then oldlibs="$output_objdir/$libname.$libext" build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi fi fi fi # Done checking deplibs! deplibs=$newdeplibs fi # Time to change all our "foo.ltframework" stuff back to "-framework foo" case $host in *-*-darwin*) newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` new_inherited_linker_flags=`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` deplibs=`$ECHO "X $deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` ;; esac # move library search paths that coincide with paths to not yet # installed libraries to the beginning of the library search list new_libs= for path in $notinst_path; do case " $new_libs " in *" -L$path/$objdir "*) ;; *) case " $deplibs " in *" -L$path/$objdir "*) new_libs="$new_libs -L$path/$objdir" ;; esac ;; esac done for deplib in $deplibs; do case $deplib in -L*) case " $new_libs " in *" $deplib "*) ;; *) new_libs="$new_libs $deplib" ;; esac ;; *) new_libs="$new_libs $deplib" ;; esac done deplibs="$new_libs" # All the library-specific variables (install_libdir is set above). library_names= old_library= dlname= # Test again, we may have decided not to build it any more if test "$build_libtool_libs" = yes; then if test "$hardcode_into_libs" = yes; then # Hardcode the library paths hardcode_libdirs= dep_rpath= rpath="$finalize_rpath" test "$mode" != relink && rpath="$compile_rpath$rpath" for libdir in $rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" dep_rpath="$dep_rpath $flag" fi elif test -n "$runpath_var"; then case "$perm_rpath " in *" $libdir "*) ;; *) perm_rpath="$perm_rpath $libdir" ;; esac fi done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" if test -n "$hardcode_libdir_flag_spec_ld"; then eval dep_rpath=\"$hardcode_libdir_flag_spec_ld\" else eval dep_rpath=\"$hardcode_libdir_flag_spec\" fi fi if test -n "$runpath_var" && test -n "$perm_rpath"; then # We should set the runpath_var. rpath= for dir in $perm_rpath; do rpath="$rpath$dir:" done eval "$runpath_var='$rpath\$$runpath_var'; export $runpath_var" fi test -n "$dep_rpath" && deplibs="$dep_rpath $deplibs" fi shlibpath="$finalize_shlibpath" test "$mode" != relink && shlibpath="$compile_shlibpath$shlibpath" if test -n "$shlibpath"; then eval "$shlibpath_var='$shlibpath\$$shlibpath_var'; export $shlibpath_var" fi # Get the real and link names of the library. eval shared_ext=\"$shrext_cmds\" eval library_names=\"$library_names_spec\" set dummy $library_names shift realname="$1" shift if test -n "$soname_spec"; then eval soname=\"$soname_spec\" else soname="$realname" fi if test -z "$dlname"; then dlname=$soname fi lib="$output_objdir/$realname" linknames= for link do linknames="$linknames $link" done # Use standard objects if they are pic test -z "$pic_flag" && libobjs=`$ECHO "X$libobjs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` test "X$libobjs" = "X " && libobjs= delfiles= if test -n "$export_symbols" && test -n "$include_expsyms"; then $opt_dry_run || cp "$export_symbols" "$output_objdir/$libname.uexp" export_symbols="$output_objdir/$libname.uexp" delfiles="$delfiles $export_symbols" fi orig_export_symbols= case $host_os in cygwin* | mingw* | cegcc*) if test -n "$export_symbols" && test -z "$export_symbols_regex"; then # exporting using user supplied symfile if test "x`$SED 1q $export_symbols`" != xEXPORTS; then # and it's NOT already a .def file. Must figure out # which of the given symbols are data symbols and tag # them as such. So, trigger use of export_symbols_cmds. # export_symbols gets reassigned inside the "prepare # the list of exported symbols" if statement, so the # include_expsyms logic still works. orig_export_symbols="$export_symbols" export_symbols= always_export_symbols=yes fi fi ;; esac # Prepare the list of exported symbols if test -z "$export_symbols"; then if test "$always_export_symbols" = yes || test -n "$export_symbols_regex"; then func_verbose "generating symbol list for \`$libname.la'" export_symbols="$output_objdir/$libname.exp" $opt_dry_run || $RM $export_symbols cmds=$export_symbols_cmds save_ifs="$IFS"; IFS='~' for cmd in $cmds; do IFS="$save_ifs" eval cmd=\"$cmd\" func_len " $cmd" len=$func_len_result if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then func_show_eval "$cmd" 'exit $?' skipped_export=false else # The command line is too long to execute in one step. func_verbose "using reloadable object file for export list..." skipped_export=: # Break out early, otherwise skipped_export may be # set to false by a later but shorter cmd. break fi done IFS="$save_ifs" if test -n "$export_symbols_regex" && test "X$skipped_export" != "X:"; then func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"' func_show_eval '$MV "${export_symbols}T" "$export_symbols"' fi fi fi if test -n "$export_symbols" && test -n "$include_expsyms"; then tmp_export_symbols="$export_symbols" test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"' fi if test "X$skipped_export" != "X:" && test -n "$orig_export_symbols"; then # The given exports_symbols file has to be filtered, so filter it. func_verbose "filter symbol list for \`$libname.la' to tag DATA exports" # FIXME: $output_objdir/$libname.filter potentially contains lots of # 's' commands which not all seds can handle. GNU sed should be fine # though. Also, the filter scales superlinearly with the number of # global variables. join(1) would be nice here, but unfortunately # isn't a blessed tool. $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter delfiles="$delfiles $export_symbols $output_objdir/$libname.filter" export_symbols=$output_objdir/$libname.def $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols fi tmp_deplibs= for test_deplib in $deplibs; do case " $convenience " in *" $test_deplib "*) ;; *) tmp_deplibs="$tmp_deplibs $test_deplib" ;; esac done deplibs="$tmp_deplibs" if test -n "$convenience"; then if test -n "$whole_archive_flag_spec" && test "$compiler_needs_object" = yes && test -z "$libobjs"; then # extract the archives, so we have objects to list. # TODO: could optimize this to just extract one archive. whole_archive_flag_spec= fi if test -n "$whole_archive_flag_spec"; then save_libobjs=$libobjs eval libobjs=\"\$libobjs $whole_archive_flag_spec\" test "X$libobjs" = "X " && libobjs= else gentop="$output_objdir/${outputname}x" generated="$generated $gentop" func_extract_archives $gentop $convenience libobjs="$libobjs $func_extract_archives_result" test "X$libobjs" = "X " && libobjs= fi fi if test "$thread_safe" = yes && test -n "$thread_safe_flag_spec"; then eval flag=\"$thread_safe_flag_spec\" linker_flags="$linker_flags $flag" fi # Make a backup of the uninstalled library when relinking if test "$mode" = relink; then $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}U && $MV $realname ${realname}U)' || exit $? fi # Do each of the archive commands. if test "$module" = yes && test -n "$module_cmds" ; then if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then eval test_cmds=\"$module_expsym_cmds\" cmds=$module_expsym_cmds else eval test_cmds=\"$module_cmds\" cmds=$module_cmds fi else if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then eval test_cmds=\"$archive_expsym_cmds\" cmds=$archive_expsym_cmds else eval test_cmds=\"$archive_cmds\" cmds=$archive_cmds fi fi if test "X$skipped_export" != "X:" && func_len " $test_cmds" && len=$func_len_result && test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then : else # The command line is too long to link in one step, link piecewise # or, if using GNU ld and skipped_export is not :, use a linker # script. # Save the value of $output and $libobjs because we want to # use them later. If we have whole_archive_flag_spec, we # want to use save_libobjs as it was before # whole_archive_flag_spec was expanded, because we can't # assume the linker understands whole_archive_flag_spec. # This may have to be revisited, in case too many # convenience libraries get linked in and end up exceeding # the spec. if test -z "$convenience" || test -z "$whole_archive_flag_spec"; then save_libobjs=$libobjs fi save_output=$output output_la=`$ECHO "X$output" | $Xsed -e "$basename"` # Clear the reloadable object creation command queue and # initialize k to one. test_cmds= concat_cmds= objlist= last_robj= k=1 if test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "$with_gnu_ld" = yes; then output=${output_objdir}/${output_la}.lnkscript func_verbose "creating GNU ld script: $output" $ECHO 'INPUT (' > $output for obj in $save_libobjs do $ECHO "$obj" >> $output done $ECHO ')' >> $output delfiles="$delfiles $output" elif test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "X$file_list_spec" != X; then output=${output_objdir}/${output_la}.lnk func_verbose "creating linker input file list: $output" : > $output set x $save_libobjs shift firstobj= if test "$compiler_needs_object" = yes; then firstobj="$1 " shift fi for obj do $ECHO "$obj" >> $output done delfiles="$delfiles $output" output=$firstobj\"$file_list_spec$output\" else if test -n "$save_libobjs"; then func_verbose "creating reloadable object files..." output=$output_objdir/$output_la-${k}.$objext eval test_cmds=\"$reload_cmds\" func_len " $test_cmds" len0=$func_len_result len=$len0 # Loop over the list of objects to be linked. for obj in $save_libobjs do func_len " $obj" func_arith $len + $func_len_result len=$func_arith_result if test "X$objlist" = X || test "$len" -lt "$max_cmd_len"; then func_append objlist " $obj" else # The command $test_cmds is almost too long, add a # command to the queue. if test "$k" -eq 1 ; then # The first file doesn't have a previous command to add. eval concat_cmds=\"$reload_cmds $objlist $last_robj\" else # All subsequent reloadable object files will link in # the last one created. eval concat_cmds=\"\$concat_cmds~$reload_cmds $objlist $last_robj~\$RM $last_robj\" fi last_robj=$output_objdir/$output_la-${k}.$objext func_arith $k + 1 k=$func_arith_result output=$output_objdir/$output_la-${k}.$objext objlist=$obj func_len " $last_robj" func_arith $len0 + $func_len_result len=$func_arith_result fi done # Handle the remaining objects by creating one last # reloadable object file. All subsequent reloadable object # files will link in the last one created. test -z "$concat_cmds" || concat_cmds=$concat_cmds~ eval concat_cmds=\"\${concat_cmds}$reload_cmds $objlist $last_robj\" if test -n "$last_robj"; then eval concat_cmds=\"\${concat_cmds}~\$RM $last_robj\" fi delfiles="$delfiles $output" else output= fi if ${skipped_export-false}; then func_verbose "generating symbol list for \`$libname.la'" export_symbols="$output_objdir/$libname.exp" $opt_dry_run || $RM $export_symbols libobjs=$output # Append the command to create the export file. test -z "$concat_cmds" || concat_cmds=$concat_cmds~ eval concat_cmds=\"\$concat_cmds$export_symbols_cmds\" if test -n "$last_robj"; then eval concat_cmds=\"\$concat_cmds~\$RM $last_robj\" fi fi test -n "$save_libobjs" && func_verbose "creating a temporary reloadable object file: $output" # Loop through the commands generated above and execute them. save_ifs="$IFS"; IFS='~' for cmd in $concat_cmds; do IFS="$save_ifs" $opt_silent || { func_quote_for_expand "$cmd" eval "func_echo $func_quote_for_expand_result" } $opt_dry_run || eval "$cmd" || { lt_exit=$? # Restore the uninstalled library and exit if test "$mode" = relink; then ( cd "$output_objdir" && \ $RM "${realname}T" && \ $MV "${realname}U" "$realname" ) fi exit $lt_exit } done IFS="$save_ifs" if test -n "$export_symbols_regex" && ${skipped_export-false}; then func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"' func_show_eval '$MV "${export_symbols}T" "$export_symbols"' fi fi if ${skipped_export-false}; then if test -n "$export_symbols" && test -n "$include_expsyms"; then tmp_export_symbols="$export_symbols" test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"' fi if test -n "$orig_export_symbols"; then # The given exports_symbols file has to be filtered, so filter it. func_verbose "filter symbol list for \`$libname.la' to tag DATA exports" # FIXME: $output_objdir/$libname.filter potentially contains lots of # 's' commands which not all seds can handle. GNU sed should be fine # though. Also, the filter scales superlinearly with the number of # global variables. join(1) would be nice here, but unfortunately # isn't a blessed tool. $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter delfiles="$delfiles $export_symbols $output_objdir/$libname.filter" export_symbols=$output_objdir/$libname.def $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols fi fi libobjs=$output # Restore the value of output. output=$save_output if test -n "$convenience" && test -n "$whole_archive_flag_spec"; then eval libobjs=\"\$libobjs $whole_archive_flag_spec\" test "X$libobjs" = "X " && libobjs= fi # Expand the library linking commands again to reset the # value of $libobjs for piecewise linking. # Do each of the archive commands. if test "$module" = yes && test -n "$module_cmds" ; then if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then cmds=$module_expsym_cmds else cmds=$module_cmds fi else if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then cmds=$archive_expsym_cmds else cmds=$archive_cmds fi fi fi if test -n "$delfiles"; then # Append the command to remove temporary files to $cmds. eval cmds=\"\$cmds~\$RM $delfiles\" fi # Add any objects from preloaded convenience libraries if test -n "$dlprefiles"; then gentop="$output_objdir/${outputname}x" generated="$generated $gentop" func_extract_archives $gentop $dlprefiles libobjs="$libobjs $func_extract_archives_result" test "X$libobjs" = "X " && libobjs= fi save_ifs="$IFS"; IFS='~' for cmd in $cmds; do IFS="$save_ifs" eval cmd=\"$cmd\" $opt_silent || { func_quote_for_expand "$cmd" eval "func_echo $func_quote_for_expand_result" } $opt_dry_run || eval "$cmd" || { lt_exit=$? # Restore the uninstalled library and exit if test "$mode" = relink; then ( cd "$output_objdir" && \ $RM "${realname}T" && \ $MV "${realname}U" "$realname" ) fi exit $lt_exit } done IFS="$save_ifs" # Restore the uninstalled library and exit if test "$mode" = relink; then $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}T && $MV $realname ${realname}T && $MV ${realname}U $realname)' || exit $? if test -n "$convenience"; then if test -z "$whole_archive_flag_spec"; then func_show_eval '${RM}r "$gentop"' fi fi exit $EXIT_SUCCESS fi # Create links to the real library. for linkname in $linknames; do if test "$realname" != "$linkname"; then func_show_eval '(cd "$output_objdir" && $RM "$linkname" && $LN_S "$realname" "$linkname")' 'exit $?' fi done # If -module or -export-dynamic was specified, set the dlname. if test "$module" = yes || test "$export_dynamic" = yes; then # On all known operating systems, these are identical. dlname="$soname" fi fi ;; obj) if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then func_warning "\`-dlopen' is ignored for objects" fi case " $deplibs" in *\ -l* | *\ -L*) func_warning "\`-l' and \`-L' are ignored for objects" ;; esac test -n "$rpath" && \ func_warning "\`-rpath' is ignored for objects" test -n "$xrpath" && \ func_warning "\`-R' is ignored for objects" test -n "$vinfo" && \ func_warning "\`-version-info' is ignored for objects" test -n "$release" && \ func_warning "\`-release' is ignored for objects" case $output in *.lo) test -n "$objs$old_deplibs" && \ func_fatal_error "cannot build library object \`$output' from non-libtool objects" libobj=$output func_lo2o "$libobj" obj=$func_lo2o_result ;; *) libobj= obj="$output" ;; esac # Delete the old objects. $opt_dry_run || $RM $obj $libobj # Objects from convenience libraries. This assumes # single-version convenience libraries. Whenever we create # different ones for PIC/non-PIC, this we'll have to duplicate # the extraction. reload_conv_objs= gentop= # reload_cmds runs $LD directly, so let us get rid of # -Wl from whole_archive_flag_spec and hope we can get by with # turning comma into space.. wl= if test -n "$convenience"; then if test -n "$whole_archive_flag_spec"; then eval tmp_whole_archive_flags=\"$whole_archive_flag_spec\" reload_conv_objs=$reload_objs\ `$ECHO "X$tmp_whole_archive_flags" | $Xsed -e 's|,| |g'` else gentop="$output_objdir/${obj}x" generated="$generated $gentop" func_extract_archives $gentop $convenience reload_conv_objs="$reload_objs $func_extract_archives_result" fi fi # Create the old-style object. reload_objs="$objs$old_deplibs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}$'/d' -e '/\.lib$/d' -e "$lo2o" | $NL2SP`" $reload_conv_objs" ### testsuite: skip nested quoting test output="$obj" func_execute_cmds "$reload_cmds" 'exit $?' # Exit if we aren't doing a library object file. if test -z "$libobj"; then if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi exit $EXIT_SUCCESS fi if test "$build_libtool_libs" != yes; then if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi # Create an invalid libtool object if no PIC, so that we don't # accidentally link it into a program. # $show "echo timestamp > $libobj" # $opt_dry_run || eval "echo timestamp > $libobj" || exit $? exit $EXIT_SUCCESS fi if test -n "$pic_flag" || test "$pic_mode" != default; then # Only do commands if we really have different PIC objects. reload_objs="$libobjs $reload_conv_objs" output="$libobj" func_execute_cmds "$reload_cmds" 'exit $?' fi if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi exit $EXIT_SUCCESS ;; prog) case $host in *cygwin*) func_stripname '' '.exe' "$output" output=$func_stripname_result.exe;; esac test -n "$vinfo" && \ func_warning "\`-version-info' is ignored for programs" test -n "$release" && \ func_warning "\`-release' is ignored for programs" test "$preload" = yes \ && test "$dlopen_support" = unknown \ && test "$dlopen_self" = unknown \ && test "$dlopen_self_static" = unknown && \ func_warning "\`LT_INIT([dlopen])' not used. Assuming no dlopen support." case $host in *-*-rhapsody* | *-*-darwin1.[012]) # On Rhapsody replace the C library is the System framework compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'` finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'` ;; esac case $host in *-*-darwin*) # Don't allow lazy linking, it breaks C++ global constructors # But is supposedly fixed on 10.4 or later (yay!). if test "$tagname" = CXX ; then case ${MACOSX_DEPLOYMENT_TARGET-10.0} in 10.[0123]) compile_command="$compile_command ${wl}-bind_at_load" finalize_command="$finalize_command ${wl}-bind_at_load" ;; esac fi # Time to change all our "foo.ltframework" stuff back to "-framework foo" compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` ;; esac # move library search paths that coincide with paths to not yet # installed libraries to the beginning of the library search list new_libs= for path in $notinst_path; do case " $new_libs " in *" -L$path/$objdir "*) ;; *) case " $compile_deplibs " in *" -L$path/$objdir "*) new_libs="$new_libs -L$path/$objdir" ;; esac ;; esac done for deplib in $compile_deplibs; do case $deplib in -L*) case " $new_libs " in *" $deplib "*) ;; *) new_libs="$new_libs $deplib" ;; esac ;; *) new_libs="$new_libs $deplib" ;; esac done compile_deplibs="$new_libs" compile_command="$compile_command $compile_deplibs" finalize_command="$finalize_command $finalize_deplibs" if test -n "$rpath$xrpath"; then # If the user specified any rpath flags, then add them. for libdir in $rpath $xrpath; do # This is the magic to use -rpath. case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" ;; esac done fi # Now hardcode the library paths rpath= hardcode_libdirs= for libdir in $compile_rpath $finalize_rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" rpath="$rpath $flag" fi elif test -n "$runpath_var"; then case "$perm_rpath " in *" $libdir "*) ;; *) perm_rpath="$perm_rpath $libdir" ;; esac fi case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) testbindir=`${ECHO} "$libdir" | ${SED} -e 's*/lib$*/bin*'` case :$dllsearchpath: in *":$libdir:"*) ;; ::) dllsearchpath=$libdir;; *) dllsearchpath="$dllsearchpath:$libdir";; esac case :$dllsearchpath: in *":$testbindir:"*) ;; ::) dllsearchpath=$testbindir;; *) dllsearchpath="$dllsearchpath:$testbindir";; esac ;; esac done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" eval rpath=\" $hardcode_libdir_flag_spec\" fi compile_rpath="$rpath" rpath= hardcode_libdirs= for libdir in $finalize_rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" rpath="$rpath $flag" fi elif test -n "$runpath_var"; then case "$finalize_perm_rpath " in *" $libdir "*) ;; *) finalize_perm_rpath="$finalize_perm_rpath $libdir" ;; esac fi done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" eval rpath=\" $hardcode_libdir_flag_spec\" fi finalize_rpath="$rpath" if test -n "$libobjs" && test "$build_old_libs" = yes; then # Transform all the library objects into standard objects. compile_command=`$ECHO "X$compile_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` finalize_command=`$ECHO "X$finalize_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` fi func_generate_dlsyms "$outputname" "@PROGRAM@" "no" # template prelinking step if test -n "$prelink_cmds"; 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then finalize_command="$shlibpath_var=\"$finalize_shlibpath\$$shlibpath_var\" $finalize_command" fi compile_var= finalize_var= if test -n "$runpath_var"; then if test -n "$perm_rpath"; then # We should set the runpath_var. rpath= for dir in $perm_rpath; do rpath="$rpath$dir:" done compile_var="$runpath_var=\"$rpath\$$runpath_var\" " fi if test -n "$finalize_perm_rpath"; then # We should set the runpath_var. rpath= for dir in $finalize_perm_rpath; do rpath="$rpath$dir:" done finalize_var="$runpath_var=\"$rpath\$$runpath_var\" " fi fi if test "$no_install" = yes; then # We don't need to create a wrapper script. link_command="$compile_var$compile_command$compile_rpath" # Replace the output file specification. link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'` # Delete the old output file. $opt_dry_run || $RM $output # Link the executable and exit func_show_eval "$link_command" 'exit $?' exit $EXIT_SUCCESS fi if test "$hardcode_action" = relink; then # Fast installation is not supported link_command="$compile_var$compile_command$compile_rpath" relink_command="$finalize_var$finalize_command$finalize_rpath" func_warning "this platform does not like uninstalled shared libraries" func_warning "\`$output' will be relinked during installation" else if test "$fast_install" != no; then link_command="$finalize_var$compile_command$finalize_rpath" if test "$fast_install" = yes; then relink_command=`$ECHO "X$compile_var$compile_command$compile_rpath" | $Xsed -e 's%@OUTPUT@%\$progdir/\$file%g'` else # fast_install is set to needless relink_command= fi else link_command="$compile_var$compile_command$compile_rpath" relink_command="$finalize_var$finalize_command$finalize_rpath" fi fi # Replace the output file specification. link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output_objdir/$outputname"'%g'` # Delete the old output files. $opt_dry_run || $RM $output $output_objdir/$outputname $output_objdir/lt-$outputname func_show_eval "$link_command" 'exit $?' # Now create the wrapper script. func_verbose "creating $output" # Quote the relink command for shipping. if test -n "$relink_command"; then # Preserve any variables that may affect compiler behavior for var in $variables_saved_for_relink; do if eval test -z \"\${$var+set}\"; then relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command" elif eval var_value=\$$var; test -z "$var_value"; then relink_command="$var=; export $var; $relink_command" else func_quote_for_eval "$var_value" relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command" fi done relink_command="(cd `pwd`; $relink_command)" relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"` fi # Quote $ECHO for shipping. if test "X$ECHO" = "X$SHELL $progpath --fallback-echo"; then case $progpath in [\\/]* | [A-Za-z]:[\\/]*) qecho="$SHELL $progpath --fallback-echo";; *) qecho="$SHELL `pwd`/$progpath --fallback-echo";; esac qecho=`$ECHO "X$qecho" | $Xsed -e "$sed_quote_subst"` else qecho=`$ECHO "X$ECHO" | $Xsed -e "$sed_quote_subst"` fi # Only actually do things if not in dry run mode. $opt_dry_run || { # win32 will think the script is a binary if it has # a .exe suffix, so we strip it off here. case $output in *.exe) func_stripname '' '.exe' "$output" output=$func_stripname_result ;; esac # test for cygwin because mv fails w/o .exe extensions case $host in *cygwin*) exeext=.exe func_stripname '' '.exe' "$outputname" outputname=$func_stripname_result ;; 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fi ;; esac done func_show_eval "ln $obj $gentop/$newobj || cp $obj $gentop/$newobj" oldobjs="$oldobjs $gentop/$newobj" ;; *) oldobjs="$oldobjs $obj" ;; esac done fi eval cmds=\"$old_archive_cmds\" func_len " $cmds" len=$func_len_result if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then cmds=$old_archive_cmds else # the command line is too long to link in one step, link in parts func_verbose "using piecewise archive linking..." save_RANLIB=$RANLIB RANLIB=: objlist= concat_cmds= save_oldobjs=$oldobjs oldobjs= # Is there a better way of finding the last object in the list? for obj in $save_oldobjs do last_oldobj=$obj done eval test_cmds=\"$old_archive_cmds\" func_len " $test_cmds" len0=$func_len_result len=$len0 for obj in $save_oldobjs do func_len " $obj" func_arith $len + $func_len_result len=$func_arith_result func_append objlist " $obj" if test "$len" -lt "$max_cmd_len"; then : else # the above command should be used before it gets too long oldobjs=$objlist if test "$obj" = "$last_oldobj" ; then RANLIB=$save_RANLIB fi test -z "$concat_cmds" || concat_cmds=$concat_cmds~ eval concat_cmds=\"\${concat_cmds}$old_archive_cmds\" objlist= len=$len0 fi done RANLIB=$save_RANLIB oldobjs=$objlist if test "X$oldobjs" = "X" ; then eval cmds=\"\$concat_cmds\" else eval cmds=\"\$concat_cmds~\$old_archive_cmds\" fi fi fi func_execute_cmds "$cmds" 'exit $?' done test -n "$generated" && \ func_show_eval "${RM}r$generated" # Now create the libtool archive. case $output in *.la) old_library= test "$build_old_libs" = yes && old_library="$libname.$libext" func_verbose "creating $output" # Preserve any variables that may affect compiler behavior for var in $variables_saved_for_relink; do if eval test -z \"\${$var+set}\"; then relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command" elif eval var_value=\$$var; test -z "$var_value"; then relink_command="$var=; export $var; $relink_command" else func_quote_for_eval "$var_value" relink_command="$var=$func_quote_for_eval_result; 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then $ECHO >> $output "\ relink_command=\"$relink_command\"" fi done } # Do a symbolic link so that the libtool archive can be found in # LD_LIBRARY_PATH before the program is installed. func_show_eval '( cd "$output_objdir" && $RM "$outputname" && $LN_S "../$outputname" "$outputname" )' 'exit $?' ;; esac exit $EXIT_SUCCESS } { test "$mode" = link || test "$mode" = relink; } && func_mode_link ${1+"$@"} # func_mode_uninstall arg... func_mode_uninstall () { $opt_debug RM="$nonopt" files= rmforce= exit_status=0 # This variable tells wrapper scripts just to set variables rather # than running their programs. libtool_install_magic="$magic" for arg do case $arg in -f) RM="$RM $arg"; rmforce=yes ;; -*) RM="$RM $arg" ;; *) files="$files $arg" ;; esac done test -z "$RM" && \ func_fatal_help "you must specify an RM program" rmdirs= origobjdir="$objdir" for file in $files; do func_dirname "$file" "" "." dir="$func_dirname_result" if test "X$dir" = X.; then objdir="$origobjdir" else objdir="$dir/$origobjdir" fi func_basename "$file" name="$func_basename_result" test "$mode" = uninstall && objdir="$dir" # Remember objdir for removal later, being careful to avoid duplicates if test "$mode" = clean; then case " $rmdirs " in *" $objdir "*) ;; *) rmdirs="$rmdirs $objdir" ;; esac fi # Don't error if the file doesn't exist and rm -f was used. if { test -L "$file"; } >/dev/null 2>&1 || { test -h "$file"; } >/dev/null 2>&1 || test -f "$file"; then : elif test -d "$file"; then exit_status=1 continue elif test "$rmforce" = yes; then continue fi rmfiles="$file" case $name in *.la) # Possibly a libtool archive, so verify it. if func_lalib_p "$file"; then func_source $dir/$name # Delete the libtool libraries and symlinks. for n in $library_names; do rmfiles="$rmfiles $objdir/$n" done test -n "$old_library" && rmfiles="$rmfiles $objdir/$old_library" case "$mode" in clean) case " $library_names " in # " " in the beginning catches empty $dlname *" $dlname "*) ;; *) rmfiles="$rmfiles $objdir/$dlname" ;; esac test -n "$libdir" && rmfiles="$rmfiles $objdir/$name $objdir/${name}i" ;; uninstall) if test -n "$library_names"; then # Do each command in the postuninstall commands. func_execute_cmds "$postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1' fi if test -n "$old_library"; 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then eval exec "$exec_cmd" exit $EXIT_FAILURE fi exit $exit_status # The TAGs below are defined such that we never get into a situation # in which we disable both kinds of libraries. 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See the # GNU General Public License for more details. # You should have received a copy of the GNU General Public License # along with this program. If not, see . # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Originally written by Alexandre Oliva . case $1 in '') echo "$0: No command. Try \`$0 --help' for more information." 1>&2 exit 1; ;; -h | --h*) cat <<\EOF Usage: depcomp [--help] [--version] PROGRAM [ARGS] Run PROGRAMS ARGS to compile a file, generating dependencies as side-effects. Environment variables: depmode Dependency tracking mode. source Source file read by `PROGRAMS ARGS'. object Object file output by `PROGRAMS ARGS'. DEPDIR directory where to store dependencies. depfile Dependency file to output. tmpdepfile Temporary file to use when outputing dependencies. libtool Whether libtool is used (yes/no). Report bugs to . EOF exit $? ;; -v | --v*) echo "depcomp $scriptversion" exit $? ;; esac if test -z "$depmode" || test -z "$source" || test -z "$object"; then echo "depcomp: Variables source, object and depmode must be set" 1>&2 exit 1 fi # Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po. depfile=${depfile-`echo "$object" | sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`} tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`} rm -f "$tmpdepfile" # Some modes work just like other modes, but use different flags. We # parameterize here, but still list the modes in the big case below, # to make depend.m4 easier to write. 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It does not imply ALL GNU software can. # # This file is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA # 02110-1301, USA. # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Please send patches to . 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The user should be able to distinguish # a failure to support a valid configuration from a meaningless # configuration. # The goal of this file is to map all the various variations of a given # machine specification into a single specification in the form: # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM # or in some cases, the newer four-part form: # CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM # It is wrong to echo any other type of specification. me=`echo "$0" | sed -e 's,.*/,,'` usage="\ Usage: $0 [OPTION] CPU-MFR-OPSYS $0 [OPTION] ALIAS Canonicalize a configuration name. Operation modes: -h, --help print this help, then exit -t, --time-stamp print date of last modification, then exit -v, --version print version number, then exit Report bugs and patches to ." version="\ GNU config.sub ($timestamp) Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software Foundation, Inc. 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There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." help=" Try \`$me --help' for more information." # Parse command line while test $# -gt 0 ; do case $1 in --time-stamp | --time* | -t ) echo "$timestamp" ; exit ;; --version | -v ) echo "$version" ; exit ;; --help | --h* | -h ) echo "$usage"; exit ;; -- ) # Stop option processing shift; break ;; - ) # Use stdin as input. break ;; -* ) echo "$me: invalid option $1$help" exit 1 ;; *local*) # First pass through any local machine types. echo $1 exit ;; * ) break ;; esac done case $# in 0) echo "$me: missing argument$help" >&2 exit 1;; 1) ;; *) echo "$me: too many arguments$help" >&2 exit 1;; esac # Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any). # Here we must recognize all the valid KERNEL-OS combinations. maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` case $maybe_os in nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \ uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \ kopensolaris*-gnu* | \ storm-chaos* | os2-emx* | rtmk-nova*) os=-$maybe_os basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` ;; *) basic_machine=`echo $1 | sed 's/-[^-]*$//'` if [ $basic_machine != $1 ] then os=`echo $1 | sed 's/.*-/-/'` else os=; fi ;; esac ### Let's recognize common machines as not being operating systems so ### that things like config.sub decstation-3100 work. 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esac # Decode aliases for certain CPU-COMPANY combinations. case $basic_machine in # Recognize the basic CPU types without company name. # Some are omitted here because they have special meanings below. 1750a | 580 \ | a29k \ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \ | am33_2.0 \ | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \ | bfin \ | c4x | clipper \ | d10v | d30v | dlx | dsp16xx \ | fido | fr30 | frv \ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ | i370 | i860 | i960 | ia64 \ | ip2k | iq2000 \ | lm32 \ | m32c | m32r | m32rle | m68000 | m68k | m88k \ | maxq | mb | microblaze | mcore | mep | metag \ | mips | mipsbe | mipseb | mipsel | mipsle \ | mips16 \ | mips64 | mips64el \ | mips64octeon | mips64octeonel \ | mips64orion | mips64orionel \ | mips64r5900 | mips64r5900el \ | mips64vr | mips64vrel \ | mips64vr4100 | mips64vr4100el \ | mips64vr4300 | mips64vr4300el \ | mips64vr5000 | mips64vr5000el \ | mips64vr5900 | mips64vr5900el \ | mipsisa32 | mipsisa32el \ | mipsisa32r2 | mipsisa32r2el \ | mipsisa64 | mipsisa64el \ | mipsisa64r2 | mipsisa64r2el \ | mipsisa64sb1 | mipsisa64sb1el \ | mipsisa64sr71k | mipsisa64sr71kel \ | mipstx39 | mipstx39el \ | mn10200 | mn10300 \ | moxie \ | mt \ | msp430 \ | nios | nios2 \ | ns16k | ns32k \ | or32 \ | pdp10 | pdp11 | pj | pjl \ | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \ | pyramid \ | rx \ | score \ | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ | sh64 | sh64le \ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \ | spu | strongarm \ | tahoe | thumb | tic4x | tic80 | tron \ | ubicom32 \ | v850 | v850e \ | we32k \ | x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \ | z8k | z80) basic_machine=$basic_machine-unknown ;; m6811 | m68hc11 | m6812 | m68hc12 | picochip) # Motorola 68HC11/12. basic_machine=$basic_machine-unknown os=-none ;; m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k) ;; ms1) basic_machine=mt-unknown ;; # We use `pc' rather than `unknown' # because (1) that's what they normally are, and # (2) the word "unknown" tends to confuse beginning users. i*86 | x86_64) basic_machine=$basic_machine-pc ;; # Object if more than one company name word. *-*-*) echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 exit 1 ;; # Recognize the basic CPU types with company name. 580-* \ | a29k-* \ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \ | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \ | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \ | arm-* | armbe-* | armle-* | armeb-* | armv*-* \ | avr-* | avr32-* \ | bfin-* | bs2000-* \ | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \ | clipper-* | craynv-* | cydra-* \ | d10v-* | d30v-* | dlx-* \ | elxsi-* \ | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \ | h8300-* | h8500-* \ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ | i*86-* | i860-* | i960-* | ia64-* \ | ip2k-* | iq2000-* \ | lm32-* \ | m32c-* | m32r-* | m32rle-* \ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ | m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ | mips16-* \ | mips64-* | mips64el-* \ | mips64octeon-* | mips64octeonel-* \ | mips64orion-* | mips64orionel-* \ | mips64r5900-* | mips64r5900el-* \ | mips64vr-* | mips64vrel-* \ | mips64vr4100-* | mips64vr4100el-* \ | mips64vr4300-* | mips64vr4300el-* \ | mips64vr5000-* | mips64vr5000el-* \ | mips64vr5900-* | mips64vr5900el-* \ | mipsisa32-* | mipsisa32el-* \ | mipsisa32r2-* | mipsisa32r2el-* \ | mipsisa64-* | mipsisa64el-* \ | mipsisa64r2-* | mipsisa64r2el-* \ | mipsisa64sb1-* | mipsisa64sb1el-* \ | mipsisa64sr71k-* | mipsisa64sr71kel-* \ | mipstx39-* | mipstx39el-* \ | mmix-* \ | mt-* \ | msp430-* \ | nios-* | nios2-* \ | none-* | np1-* | ns16k-* | ns32k-* \ | orion-* \ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ | pyramid-* \ | romp-* | rs6000-* | rx-* \ | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \ | sparclite-* \ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \ | tahoe-* | thumb-* \ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \ | tile-* | tilegx-* \ | tron-* \ | ubicom32-* \ | v850-* | v850e-* | vax-* \ | we32k-* \ | x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \ | xstormy16-* | xtensa*-* \ | ymp-* \ | z8k-* | z80-*) ;; # Recognize the basic CPU types without company name, with glob match. xtensa*) basic_machine=$basic_machine-unknown ;; # Recognize the various machine names and aliases which stand # for a CPU type and a company and sometimes even an OS. 386bsd) basic_machine=i386-unknown os=-bsd ;; 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) basic_machine=m68000-att ;; 3b*) basic_machine=we32k-att ;; a29khif) basic_machine=a29k-amd os=-udi ;; abacus) basic_machine=abacus-unknown ;; adobe68k) basic_machine=m68010-adobe os=-scout ;; alliant | fx80) basic_machine=fx80-alliant ;; altos | altos3068) basic_machine=m68k-altos ;; am29k) basic_machine=a29k-none os=-bsd ;; amd64) basic_machine=x86_64-pc ;; amd64-*) basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'` ;; amdahl) basic_machine=580-amdahl os=-sysv ;; amiga | amiga-*) basic_machine=m68k-unknown ;; amigaos | amigados) basic_machine=m68k-unknown os=-amigaos ;; amigaunix | amix) basic_machine=m68k-unknown os=-sysv4 ;; apollo68) basic_machine=m68k-apollo os=-sysv ;; apollo68bsd) basic_machine=m68k-apollo os=-bsd ;; aros) basic_machine=i386-pc os=-aros ;; aux) basic_machine=m68k-apple os=-aux ;; balance) basic_machine=ns32k-sequent os=-dynix ;; blackfin) basic_machine=bfin-unknown os=-linux ;; blackfin-*) basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; bluegene*) basic_machine=powerpc-ibm os=-cnk ;; c90) basic_machine=c90-cray os=-unicos ;; cegcc) basic_machine=arm-unknown os=-cegcc ;; convex-c1) basic_machine=c1-convex os=-bsd ;; convex-c2) basic_machine=c2-convex os=-bsd ;; convex-c32) basic_machine=c32-convex os=-bsd ;; convex-c34) basic_machine=c34-convex os=-bsd ;; convex-c38) basic_machine=c38-convex os=-bsd ;; cray | j90) basic_machine=j90-cray os=-unicos ;; craynv) basic_machine=craynv-cray os=-unicosmp ;; cr16) basic_machine=cr16-unknown os=-elf ;; crds | unos) basic_machine=m68k-crds ;; crisv32 | crisv32-* | etraxfs*) basic_machine=crisv32-axis ;; cris | cris-* | etrax*) basic_machine=cris-axis ;; crx) basic_machine=crx-unknown os=-elf ;; da30 | da30-*) basic_machine=m68k-da30 ;; decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn) basic_machine=mips-dec ;; decsystem10* | dec10*) basic_machine=pdp10-dec os=-tops10 ;; decsystem20* | dec20*) basic_machine=pdp10-dec os=-tops20 ;; delta | 3300 | motorola-3300 | motorola-delta \ | 3300-motorola | delta-motorola) basic_machine=m68k-motorola ;; delta88) basic_machine=m88k-motorola os=-sysv3 ;; dicos) basic_machine=i686-pc os=-dicos ;; djgpp) basic_machine=i586-pc os=-msdosdjgpp ;; dpx20 | dpx20-*) basic_machine=rs6000-bull os=-bosx ;; dpx2* | dpx2*-bull) basic_machine=m68k-bull os=-sysv3 ;; ebmon29k) basic_machine=a29k-amd os=-ebmon ;; elxsi) basic_machine=elxsi-elxsi os=-bsd ;; encore | umax | mmax) basic_machine=ns32k-encore ;; es1800 | OSE68k | ose68k | ose | OSE) basic_machine=m68k-ericsson os=-ose ;; fx2800) basic_machine=i860-alliant ;; genix) basic_machine=ns32k-ns ;; gmicro) basic_machine=tron-gmicro os=-sysv ;; go32) basic_machine=i386-pc os=-go32 ;; h3050r* | hiux*) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; h8300hms) basic_machine=h8300-hitachi os=-hms ;; h8300xray) basic_machine=h8300-hitachi os=-xray ;; h8500hms) basic_machine=h8500-hitachi os=-hms ;; harris) basic_machine=m88k-harris os=-sysv3 ;; hp300-*) basic_machine=m68k-hp ;; hp300bsd) basic_machine=m68k-hp os=-bsd ;; hp300hpux) basic_machine=m68k-hp os=-hpux ;; hp3k9[0-9][0-9] | hp9[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k2[0-9][0-9] | hp9k31[0-9]) basic_machine=m68000-hp ;; hp9k3[2-9][0-9]) basic_machine=m68k-hp ;; hp9k6[0-9][0-9] | hp6[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k7[0-79][0-9] | hp7[0-79][0-9]) basic_machine=hppa1.1-hp ;; hp9k78[0-9] | hp78[0-9]) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[0-9][13679] | hp8[0-9][13679]) basic_machine=hppa1.1-hp ;; hp9k8[0-9][0-9] | hp8[0-9][0-9]) basic_machine=hppa1.0-hp ;; hppa-next) os=-nextstep3 ;; hppaosf) basic_machine=hppa1.1-hp os=-osf ;; hppro) basic_machine=hppa1.1-hp os=-proelf ;; i370-ibm* | ibm*) basic_machine=i370-ibm ;; # I'm not sure what "Sysv32" means. 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nh[45]000) basic_machine=m88k-harris os=-cxux ;; nindy960) basic_machine=i960-intel os=-nindy ;; mon960) basic_machine=i960-intel os=-mon960 ;; nonstopux) basic_machine=mips-compaq os=-nonstopux ;; np1) basic_machine=np1-gould ;; nsr-tandem) basic_machine=nsr-tandem ;; op50n-* | op60c-*) basic_machine=hppa1.1-oki os=-proelf ;; openrisc | openrisc-*) basic_machine=or32-unknown ;; os400) basic_machine=powerpc-ibm os=-os400 ;; OSE68000 | ose68000) basic_machine=m68000-ericsson os=-ose ;; os68k) basic_machine=m68k-none os=-os68k ;; pa-hitachi) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; paragon) basic_machine=i860-intel os=-osf ;; parisc) basic_machine=hppa-unknown os=-linux ;; parisc-*) basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; pbd) basic_machine=sparc-tti ;; pbb) basic_machine=m68k-tti ;; pc532 | pc532-*) basic_machine=ns32k-pc532 ;; pc98) basic_machine=i386-pc ;; pc98-*) basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentium | p5 | k5 | k6 | nexgen | viac3) basic_machine=i586-pc ;; pentiumpro | p6 | 6x86 | athlon | athlon_*) basic_machine=i686-pc ;; pentiumii | pentium2 | pentiumiii | pentium3) basic_machine=i686-pc ;; pentium4) basic_machine=i786-pc ;; pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*) basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentiumpro-* | p6-* | 6x86-* | athlon-*) basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*) basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentium4-*) basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pn) basic_machine=pn-gould ;; power) basic_machine=power-ibm ;; ppc) basic_machine=powerpc-unknown ;; ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppcle | powerpclittle | ppc-le | powerpc-little) basic_machine=powerpcle-unknown ;; ppcle-* | powerpclittle-*) basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppc64) basic_machine=powerpc64-unknown ;; ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppc64le | powerpc64little | ppc64-le | powerpc64-little) basic_machine=powerpc64le-unknown ;; ppc64le-* | powerpc64little-*) basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ps2) basic_machine=i386-ibm ;; pw32) basic_machine=i586-unknown os=-pw32 ;; rdos) basic_machine=i386-pc os=-rdos ;; rom68k) basic_machine=m68k-rom68k os=-coff ;; rm[46]00) basic_machine=mips-siemens ;; rtpc | rtpc-*) basic_machine=romp-ibm ;; s390 | s390-*) basic_machine=s390-ibm ;; s390x | s390x-*) basic_machine=s390x-ibm ;; sa29200) basic_machine=a29k-amd os=-udi ;; sb1) basic_machine=mipsisa64sb1-unknown ;; sb1el) basic_machine=mipsisa64sb1el-unknown ;; sde) basic_machine=mipsisa32-sde os=-elf ;; sei) basic_machine=mips-sei os=-seiux ;; sequent) basic_machine=i386-sequent ;; sh) basic_machine=sh-hitachi os=-hms ;; sh5el) basic_machine=sh5le-unknown ;; sh64) basic_machine=sh64-unknown ;; sparclite-wrs | simso-wrs) basic_machine=sparclite-wrs os=-vxworks ;; sps7) basic_machine=m68k-bull os=-sysv2 ;; spur) basic_machine=spur-unknown ;; st2000) basic_machine=m68k-tandem ;; stratus) basic_machine=i860-stratus os=-sysv4 ;; sun2) basic_machine=m68000-sun ;; sun2os3) basic_machine=m68000-sun os=-sunos3 ;; sun2os4) basic_machine=m68000-sun os=-sunos4 ;; sun3os3) basic_machine=m68k-sun os=-sunos3 ;; sun3os4) basic_machine=m68k-sun os=-sunos4 ;; sun4os3) basic_machine=sparc-sun os=-sunos3 ;; sun4os4) basic_machine=sparc-sun os=-sunos4 ;; sun4sol2) basic_machine=sparc-sun os=-solaris2 ;; sun3 | sun3-*) basic_machine=m68k-sun ;; sun4) basic_machine=sparc-sun ;; sun386 | sun386i | roadrunner) basic_machine=i386-sun ;; sv1) basic_machine=sv1-cray os=-unicos ;; symmetry) basic_machine=i386-sequent os=-dynix ;; t3e) basic_machine=alphaev5-cray os=-unicos ;; t90) basic_machine=t90-cray os=-unicos ;; tic54x | c54x*) basic_machine=tic54x-unknown os=-coff ;; tic55x | c55x*) basic_machine=tic55x-unknown os=-coff ;; tic6x | c6x*) basic_machine=tic6x-unknown os=-coff ;; # This must be matched before tile*. tilegx*) basic_machine=tilegx-unknown os=-linux-gnu ;; tile*) basic_machine=tile-unknown os=-linux-gnu ;; tx39) basic_machine=mipstx39-unknown ;; tx39el) basic_machine=mipstx39el-unknown ;; toad1) basic_machine=pdp10-xkl os=-tops20 ;; tower | tower-32) basic_machine=m68k-ncr ;; tpf) basic_machine=s390x-ibm os=-tpf ;; udi29k) basic_machine=a29k-amd os=-udi ;; ultra3) basic_machine=a29k-nyu os=-sym1 ;; v810 | necv810) basic_machine=v810-nec os=-none ;; vaxv) basic_machine=vax-dec os=-sysv ;; vms) basic_machine=vax-dec os=-vms ;; vpp*|vx|vx-*) basic_machine=f301-fujitsu ;; vxworks960) basic_machine=i960-wrs os=-vxworks ;; vxworks68) basic_machine=m68k-wrs os=-vxworks ;; vxworks29k) basic_machine=a29k-wrs os=-vxworks ;; w65*) basic_machine=w65-wdc os=-none ;; w89k-*) basic_machine=hppa1.1-winbond os=-proelf ;; xbox) basic_machine=i686-pc os=-mingw32 ;; xps | xps100) basic_machine=xps100-honeywell ;; ymp) basic_machine=ymp-cray os=-unicos ;; z8k-*-coff) basic_machine=z8k-unknown os=-sim ;; z80-*-coff) basic_machine=z80-unknown os=-sim ;; none) basic_machine=none-none os=-none ;; # Here we handle the default manufacturer of certain CPU types. It is in # some cases the only manufacturer, in others, it is the most popular. w89k) basic_machine=hppa1.1-winbond ;; op50n) basic_machine=hppa1.1-oki ;; op60c) basic_machine=hppa1.1-oki ;; romp) basic_machine=romp-ibm ;; mmix) basic_machine=mmix-knuth ;; rs6000) basic_machine=rs6000-ibm ;; vax) basic_machine=vax-dec ;; pdp10) # there are many clones, so DEC is not a safe bet basic_machine=pdp10-unknown ;; pdp11) basic_machine=pdp11-dec ;; we32k) basic_machine=we32k-att ;; sh[1234] | sh[24]a | sh[24]aeb | sh[34]eb | sh[1234]le | sh[23]ele) basic_machine=sh-unknown ;; sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v) basic_machine=sparc-sun ;; cydra) basic_machine=cydra-cydrome ;; orion) basic_machine=orion-highlevel ;; orion105) basic_machine=clipper-highlevel ;; mac | mpw | mac-mpw) basic_machine=m68k-apple ;; pmac | pmac-mpw) basic_machine=powerpc-apple ;; *-unknown) # Make sure to match an already-canonicalized machine name. ;; *) echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 exit 1 ;; esac # Here we canonicalize certain aliases for manufacturers. case $basic_machine in *-digital*) basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'` ;; *-commodore*) basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'` ;; *) ;; esac # Decode manufacturer-specific aliases for certain operating systems. if [ x"$os" != x"" ] then case $os in # First match some system type aliases # that might get confused with valid system types. # -solaris* is a basic system type, with this one exception. -auroraux) os=-auroraux ;; -solaris1 | -solaris1.*) os=`echo $os | sed -e 's|solaris1|sunos4|'` ;; -solaris) os=-solaris2 ;; -svr4*) os=-sysv4 ;; -unixware*) os=-sysv4.2uw ;; -gnu/linux*) os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'` ;; # First accept the basic system types. # The portable systems comes first. # Each alternative MUST END IN A *, to match a version number. # -sysv* is not here because it comes later, after sysvr4. -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \ | -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\ | -hpux* | -unos* | -osf* | -luna* | -dgux* | -auroraux* | -solaris* \ | -sym* | -kopensolaris* \ | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \ | -aos* | -aros* \ | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \ | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \ | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \ | -openbsd* | -solidbsd* \ | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \ | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \ | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \ | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \ | -chorusos* | -chorusrdb* | -cegcc* \ | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \ | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \ | -uxpv* | -beos* | -mpeix* | -udk* \ | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \ | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \ | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \ | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \ | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \ | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \ | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es*) # Remember, each alternative MUST END IN *, to match a version number. ;; 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IN NO EVENT SHALL THE # X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN # AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC- # TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # # Except as contained in this notice, the name of the X Consortium shall not # be used in advertising or otherwise to promote the sale, use or other deal- # ings in this Software without prior written authorization from the X Consor- # tium. # # # FSF changes to this file are in the public domain. # # Calling this script install-sh is preferred over install.sh, to prevent # `make' implicit rules from creating a file called install from it # when there is no Makefile. # # This script is compatible with the BSD install script, but was written # from scratch. nl=' ' IFS=" "" $nl" # set DOITPROG to echo to test this script # Don't use :- since 4.3BSD and earlier shells don't like it. doit=${DOITPROG-} if test -z "$doit"; then doit_exec=exec else doit_exec=$doit fi # Put in absolute file names if you don't have them in your path; # or use environment vars. chgrpprog=${CHGRPPROG-chgrp} chmodprog=${CHMODPROG-chmod} chownprog=${CHOWNPROG-chown} cmpprog=${CMPPROG-cmp} cpprog=${CPPROG-cp} mkdirprog=${MKDIRPROG-mkdir} mvprog=${MVPROG-mv} rmprog=${RMPROG-rm} stripprog=${STRIPPROG-strip} posix_glob='?' initialize_posix_glob=' test "$posix_glob" != "?" || { if (set -f) 2>/dev/null; then posix_glob= else posix_glob=: fi } ' posix_mkdir= # Desired mode of installed file. mode=0755 chgrpcmd= chmodcmd=$chmodprog chowncmd= mvcmd=$mvprog rmcmd="$rmprog -f" stripcmd= src= dst= dir_arg= dst_arg= copy_on_change=false no_target_directory= usage="\ Usage: $0 [OPTION]... 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This bugfix included a small change of the interface. v1.0.4 - Fixed an issue where -w 1 inf and -w 2 inf could result in different trees. Thanks to Megan Cevasco for the bug report. - Fixed a compability issue with gcc 4.4.3 v1.0.3 - Fixed a serious bug where the combination of both improvement strategies could lead to a memory bug and wrong results. Thanks to Megan Cevasco for the bug report. v1.0.2 - Fixed some memory bugs and leaks - Fixed an issue where different runs of minswrt lead to different results. This could lead to an infinite loop in improveTreeMedian. Thanks to Megan Cevasco for the bug report. - Fixed an initialization bug of the median solver. Thanks to Megan Cevasco for the bug report. v1.0.1 - Updates for compatibility with median v2.0.0 v1.0.0 - First release minswrt ======= v1.1.1 - Speed improvement by changing compiler flags v1.1.0 - If all elements in the input file have positive orientation and wr=wt, the algorithm will return a sequence that consists solely of transpositions v1.0.0 - First release weightedbb ========== v1.1.1 - Speed improvement by changing compiler flags v1.1.0 - Extended interface - Fixed a memory leak v1.0.1 - Bugfix: In previous versions, the lower bound for the transposition distance was dependant of w_r. This could lead to wrong results and even crashes when w_r != w_t. Thanks to Matthias Bernt for the bug report. v1.0.0 - First release revDist ======= v1.0.2 - Passing no arguments no longer gives a segfault - Speed improvement by changing compiler flags v1.0.1 - Removed compiler warnings v1.0.0 - First release median ====== v2.3.0 - Serious speed improvement by improved branching strategy - Speed improvement by changing compiler flags - Fixed some memory leaks in the interface v2.2.0 - Added function that returns the distances to the calculated median v2.1.0 - Added wrapper function to get pairwise distance v2.0.0 - Added possibility to use exact branch and bound algorithm for pairwise distances (weightedbb) instead of approximation algorithm (minswrt) - Change in the frontend, now the user can choose if he wants just one median or all medians - Running out of memory during the algorithm will now set an error flag. The cutoff value (least lower bound that had to be discarded due to heap pruning) can be get by calling getLeastCutoff(); v1.0.0 - First release phylo-1.0.6/phylo/0000755000175000017500000000000011434510124011000 500000000000000phylo-1.0.6/phylo/phylo.cpp0000644000175000017500000037751411434510050012576 00000000000000/** * filename: phylo.cpp * author: Martin Bader * begin: 12.12.2006 * last change: 23.04.2010 * * The main class of the program. Contains the tree + functionality. * * Copyright (C) 2007-2009 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "phylo.h" #include #include #include #include #include #include #include #include "edge.h" #include "node.h" #include "phyloTools.h" #include "pools.h" #include "tree.h" namespace phylo { using namespace std; using namespace minswrt; extern Logger g_logger; extern PermPool* g_permPool; /*************************************************************************** * public methods ***************************************************************************/ Phylo::Phylo() { m_state = 0; m_numInputGenomes = 0; m_permSize = 0; m_inputGenomes = NULL; m_genomeNames = NULL; m_actTree = NULL; m_bestTree = NULL; m_wr = 1; m_wt = 2; m_revOnly = false; m_minswrt.setGreedy(1); m_element2Index = NULL; m_mapping = NULL; m_cycle = NULL; m_inCycle = NULL; g_permPool = new PermPool(); } Phylo::~Phylo() { if (m_bestTree != NULL) delete m_bestTree; if (m_genomeNames != NULL) { for (int i = 0; i < m_numInputGenomes; i++) delete[] m_genomeNames[i]; delete[] m_genomeNames; } if (m_element2Index != NULL) delete[] m_element2Index; if (m_mapping != NULL) delete[] m_mapping; if (m_inCycle != NULL) delete[] m_inCycle; if (m_cycle != NULL) delete[] m_cycle; delete g_permPool; } bool Phylo::setGenomes(int f_numGenomes, int f_genomeSize, int** f_genomes, bool f_check) { // if there is old data to clear, do it switch (m_state) { case 0: case 1: break; // nothing to do case 2: case 3: delete m_bestTree; m_bestTree = NULL; delete[] m_element2Index; m_element2Index = NULL; delete[] m_mapping; m_mapping = NULL; delete[] m_inCycle; m_inCycle = NULL; delete[] m_cycle; m_cycle = NULL; break; default: break; } // init members m_numInputGenomes = f_numGenomes; m_permSize = f_genomeSize; m_inputGenomes = f_genomes; m_element2Index = new int[f_genomeSize + 1]; m_mapping = new int[f_genomeSize + 1]; m_inCycle = new bool[f_genomeSize]; m_cycle = new int[f_genomeSize]; // init the permutation array g_permPool->init(m_permSize); // init minswrt + revdist + medianSolver m_minswrt.setPermutationSize(m_permSize); m_revdist.init(m_permSize); if (m_revOnly) m_medianSolver.init(m_permSize, m_wr, m_wt, 0, 1, 50000000 / m_permSize); else m_medianSolver.init(m_permSize, m_wr, m_wt, 2, 0, 50000000 / m_permSize); if (!f_check || checkInputGenomes()) { m_state = 1; return true; } else { m_state = 0; g_logger.log(PHYLO_WARNING, "WARNING: Phylo::setGenomes: input data corrupted\n"); return false; } } void Phylo::setGenomeNames(char** f_names) { m_genomeNames = f_names; } bool Phylo::readGenomesFromFile(const char* f_filename, int &f_numPerms, int &f_permSize, int** &f_perms, char** &f_names) { ifstream input; // file input stream char buffer[256]; // buffer for reading char* name; // the name of a genome int* perm; // the actual permutation vector tmpPerm; // temporary permutation (as perm size is not yet known) vector tmpArray; // temporary array with all permutations (as they are not yet known) vector tmpNames; // array with the genome names int stringsize; // size of a string int permsize; // number of elements in the actual permutation g_logger.log(PHYLO_INFO, "reading file %s\n", f_filename); f_numPerms = 0; input.open(f_filename); if (!input.is_open()) { g_logger.log(PHYLO_WARNING, "WARNING: could not open %s\n"); f_numPerms = -1; f_permSize = -1; f_perms = NULL; f_names = NULL; return false; } while (input.peek() >= 0) { while ((input.peek() >= 0) && (input.peek() != '>') && (input.peek() != '+') && (input.peek() != '-') && ((input.peek() < '0') || (input.peek() > '9'))) // line is a comment input.ignore(1024, '\n'); if (input.peek() != '>') // wrong format { g_logger.log(PHYLO_WARNING, "WARNING: Phylo::readGenomesFromFile: %s has an invalid file format\n", f_filename); input.close(); for (unsigned int i = 0; i < tmpArray.size(); i++) delete[] tmpArray[i]; for (unsigned int i = 0; i < tmpNames.size(); i++) delete[] tmpNames[i]; f_numPerms = -1; f_permSize = -1; f_perms = NULL; f_names = NULL; return false; } input.ignore(1, ' '); input.getline(buffer, 256); stringsize = input.gcount(); name = new char[stringsize]; strncpy(name, buffer, stringsize); tmpNames.push_back(name); while ((input.peek() >= 0) && (input.peek() != '>') && (input.peek() != '+') && (input.peek() != '-') && ((input.peek() < '0') || (input.peek() > '9'))) // line is a comment input.ignore(1024, '\n'); permsize = 0; while (input.peek() == ' ') input.ignore(1); do { tmpPerm.push_back(0); // increment vector size for (stringsize = 0; (input.peek() != ' ') && (input.peek() != '\n'); stringsize++) input >> buffer[stringsize]; buffer[stringsize] = 0; tmpPerm[permsize++] = atoi(buffer); while (input.peek() == ' ') input.ignore(1); } while (input.peek() != '\n'); input.ignore(1); if (f_numPerms == 0) f_permSize = permsize; else if (f_permSize != permsize) { g_logger.log(PHYLO_WARNING, "WARNING: Phylo::readGenomesFromFile: input genomes have different sizes -> abort reading the file\n"); input.close(); // delete old data for (unsigned int i = 0; i < tmpArray.size(); i++) delete[] tmpArray[i]; for (unsigned int i = 0; i < tmpNames.size(); i++) delete[] tmpNames[i]; f_numPerms = -1; f_permSize = -1; f_perms = NULL; f_names = NULL; return false; } perm = new int[permsize]; for (int i = 0; i < permsize; i++) perm[i] = tmpPerm[i]; tmpArray.push_back(perm); f_numPerms++; } input.close(); // copy the data f_perms = new int*[f_numPerms]; for (int i = 0; i < f_numPerms; i++) f_perms[i] = tmpArray[i]; f_names = new char*[f_numPerms]; for (int i = 0; i < f_numPerms; i++) f_names[i] = tmpNames[i]; g_logger.log(PHYLO_INFO, "done\n"); return true; } bool Phylo::readTreeFromFile(const char* f_filename, int& f_numPerms, int& f_permSize, int**& f_inputGenomes) { ifstream input; // file input stream char buffer[256]; // char buffer for reading file input char buffer2[256]; // secondary buffer char nextchar; // the next character in the file bool firstline = true; // true if we are reading the first line of the file (excluding comments) Node* node = NULL; // a node in the tree int index; // index of the node int inputGenome; // -1: not set; 0: false; 1: true; char* name = NULL; // genome name int stringlength; // length of a string int numInputGenomes = 0; // number of found input genomes Edge* edge = NULL; // an edge int pos; // position in the tree bool weightsSet = false; // true if we have set the weights g_logger.log(PHYLO_INFO, "reading tree from file %s\n", f_filename); // delete old data, init some members switch (m_state) { case 0: case 1: break; // nothing to do case 2: case 3: delete m_bestTree; m_bestTree = NULL; delete[] m_element2Index; m_element2Index = NULL; delete[] m_mapping; m_mapping = NULL; delete[] m_inCycle; m_inCycle = NULL; delete[] m_cycle; m_cycle = NULL; break; default: break; } m_state = 0; m_numInputGenomes = -1; m_permSize = -1; m_inputGenomes = NULL; m_genomeNames = NULL; m_bestTree = new Tree(); m_bestTree->m_permSize = -1; m_bestTree->m_numNodes = -1; m_bestTree->m_weight = -1; input.open(f_filename); if (!input.is_open()) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: could not open %s\n", f_filename); return false; } while (input.peek() >= 0) { nextchar = input.peek(); if (nextchar == '#') // line is a comment { input.ignore(1024, '\n'); continue; } if (firstline && (nextchar == 'N')) // could be NULL line { input.getline(buffer, 256); if (strcmp(buffer, "NULL") == 0) { input.close(); return false; } } firstline = false; if (nextchar == '<') // subfield start { input.getline(buffer, 256); if (strcmp(buffer, "") == 0) // node subfield { // check preconditions if (m_numInputGenomes == -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: number of input genomes not set before first node in file %s", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } if (m_bestTree->m_numNodes == -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: number of permutations not set before first node in file %s", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } if (m_permSize == -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: permutation size not set before first node in file %s", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } node = new Node(); index = -1; inputGenome = -1; node->m_father = -2; while (true) { nextchar = input.peek(); if (nextchar == '#') // line is a comment { input.ignore(1024, '\n'); continue; } if (nextchar == '<') // subfield tag { input.getline(buffer, 256); if (strcmp(buffer, "") == 0) { if (node->m_edge != NULL) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: node %s has two edges in file %s", index, f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } edge = new Edge(); edge->m_weight = -1; edge->m_cloudSize = -1; while (true) { nextchar = input.peek(); if (nextchar == '#') // line is a comment { input.ignore(1024, '\n'); continue; } if (nextchar == '<') // subfield tag { input.getline(buffer, 256); if (strcmp(buffer, "") == 0) break; else // unknown subfield { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: unknown subfield %s in file %s", buffer, f_filename); do { if (input.peek() < 0) // EOF { cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input.getline(buffer2, 256); } while (strcmp(buffer + 1, buffer2 + 2) != 0); } continue; } input.getline(buffer, 256, ':'); if (strcmp(buffer, "weight") == 0) { if (edge->m_weight != -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: edge of node %d has two weights in file %s", index, f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input >> edge->m_weight; input.ignore(256, '\n'); } else if (strcmp(buffer, "cloud size") == 0) { if (edge->m_cloudSize != -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: edge of node %d has two cloud sizes in file %s", index, f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input >> edge->m_cloudSize; input.ignore(256, '\n'); edge->m_cloud = new int*[edge->m_cloudSize]; for (int i = 0; i < edge->m_cloudSize; i++) edge->m_cloud[i] = NULL; edge->m_distSource = new int[edge->m_cloudSize]; for (int i = 0; i < edge->m_cloudSize; i++) edge->m_distSource[i] = -1; edge->m_distTarget = new int[edge->m_cloudSize]; for (int i = 0; i < edge->m_cloudSize; i++) edge->m_distTarget[i] = -1; } else if (strcmp(buffer, "cloud") == 0) { if ((edge->m_cloudSize > 0) && (edge->m_cloud[0] != NULL)) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: edge of node %d has two clouds in file %s", index, f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input.ignore(256, '\n'); for (int i = 0; i < edge->m_cloudSize; i++) { edge->m_cloud[i] = g_permPool->getPerm(); for (int j = 0; j < m_permSize; j++) input >> edge->m_cloud[i][j]; input.ignore(256, '\n'); } } else if (strcmp(buffer, "dist source") == 0) { if ((edge->m_cloudSize > 0) && (edge->m_distSource[0] != -1)) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: edge of node %d has two source distance arrays in file %s", index, f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input.ignore(256, '\n'); for (int i = 0; i < edge->m_cloudSize; i++) { input >> edge->m_distSource[i]; input.ignore(256, '\n'); } } else if (strcmp(buffer, "dist target") == 0) { if ((edge->m_cloudSize > 0) && (edge->m_distTarget[0] != -1)) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: edge of node %d has two target distance arrays in file %s", index, f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input.ignore(256, '\n'); for (int i = 0; i < edge->m_cloudSize; i++) { input >> edge->m_distTarget[i]; input.ignore(256, '\n'); } } else // unknown tag { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: unknown tag %s in file %s\n", buffer, f_filename); input.ignore(256, '\n'); } } // end while // consistency checks of the edge if ((edge->m_cloudSize > 0) && (edge->m_cloud[0] == NULL)) // cloud not set! { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: cloud of a node not set in file %s\n", f_filename); delete[] edge->m_cloud; edge->m_cloud = NULL; delete[] edge->m_distSource; edge->m_distSource = NULL; delete[] edge->m_distTarget; edge->m_distTarget = NULL; } node->m_edge = edge; } else if (strcmp(buffer, "") == 0) break; else // unknown subfield { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: unknown subfield %s in file %s", buffer, f_filename); do { if (input.peek() < 0) // EOF { cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input.getline(buffer2, 256); } while (strcmp(buffer + 1, buffer2 + 2) != 0); } continue; } input.getline(buffer, 256, ':'); if (strcmp(buffer, "index") == 0) { if (index != -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: node has two indices in file %s", index, f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input >> index; input.ignore(256, '\n'); } else if (strcmp(buffer, "input genome") == 0) { if (inputGenome != -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: node %d has two input genome entries in file %s", index, f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input.getline(buffer, 256); if (strcmp(buffer, " true") == 0) inputGenome = 1; else if (strcmp(buffer, " false") == 0) inputGenome = 0; else { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: wrong entry in input genome field in file %s\n", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } } else if (strcmp(buffer, "name") == 0) { if (name != NULL) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: node %d has two names in file %s", index, f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input.getline(buffer, 256); stringlength = 0; while ((stringlength < 255) && (buffer[stringlength] != 0)) stringlength++; name = new char[stringlength + 1]; for (int i = 0; i < stringlength; i++) name[i] = buffer[i]; name[stringlength] = 0; } else if (strcmp(buffer, "perm") == 0) { if (node->m_perm != NULL) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: node %d has two permutations in file %s", index, f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input.ignore(256, '\n'); node->m_perm = g_permPool->getPerm(); for (int i = 0; i < m_permSize; i++) input >> node->m_perm[i]; input.ignore(256, '\n'); } else if (strcmp(buffer, "connected to") == 0) { if (node->m_father != -2) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: node %d has two connected to entries in file %s", index, f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input >> node->m_father; input.ignore(256, '\n'); } else // unknown tag { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: unknown tag %s in file %s\n", buffer, f_filename); input.ignore(256, '\n'); } } // end while // check if we have all required input if (index == -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: node has no index in file %s\n", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } if (inputGenome == -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: input genome tag of a node not set in file %s\n", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } if (node->m_perm == NULL) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: permutation of a node not set in file %s\n", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } if (node->m_father == -2) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: father of a node not set in file %s\n", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } // consistency checks if ((index < 0) || (index >= m_bestTree->m_numNodes)) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: wrong node index in file %s\n", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } if ((inputGenome == 1) && (numInputGenomes >= m_numInputGenomes)) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: too much input genomes in file %s\n", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } if (m_bestTree->m_nodes[index] != NULL) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: two nodes with same index in file %s\n", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } // write the data m_bestTree->m_nodes[index] = node; if (inputGenome == 1) { node->m_protectPerm = true; m_inputGenomes[numInputGenomes] = node->m_perm; m_genomeNames[numInputGenomes++] = name; name = NULL; } else if (name != NULL) { delete[] name; name = NULL; } } else // unknown subfield { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: unknown subfield %s in file %s", buffer, f_filename); do { if (input.peek() < 0) // EOF { cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input.getline(buffer2, 256); } while (strcmp(buffer + 1, buffer2 + 2) != 0); } continue; } input.getline(buffer, 256, ':'); if (strcmp(buffer, "num perms") == 0) { if (m_bestTree->m_numNodes != -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: two different numbers of permutations in file %s", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input >> m_bestTree->m_numNodes; input.ignore(256, '\n'); m_bestTree->m_nodes.resize(m_bestTree->m_numNodes, NULL); m_bestTree->m_node2input.resize(m_bestTree->m_numNodes, -1); } else if (strcmp(buffer, "num input genomes") == 0) { if (m_numInputGenomes != -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: two different numbers of input genomes in file %s", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input >> m_numInputGenomes; input.ignore(256, '\n'); m_inputGenomes = new int*[m_numInputGenomes]; for (int i = 0; i < m_numInputGenomes; i++) m_inputGenomes[i] = NULL; m_genomeNames = new char*[m_numInputGenomes]; for (int i = 0; i < m_numInputGenomes; i++) m_genomeNames[i] = NULL; } else if (strcmp(buffer, "perm size") == 0) { if (m_permSize != -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: two different permutation sizes in file %s", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input >> m_permSize; input.ignore(256, '\n'); m_bestTree->m_permSize = m_permSize; g_permPool->init(m_permSize); } else if (strcmp(buffer, "wr wt") == 0) { if (weightsSet) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: weights set two times in file %s", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input >> m_wr; input.getline(buffer2, 256); if (strcmp(buffer2, " inf") == 0) m_revOnly = true; else { m_wt = atoi(buffer2 + 1); m_revOnly = false; } weightsSet = true; } else if (strcmp(buffer, "weight") == 0) { if (m_bestTree->m_weight != -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: tree weight set two times in file %s", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } input >> m_bestTree->m_weight; input.ignore(256, '\n'); } else // unknown tag { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: unknown tag %s in file %s\n", buffer, f_filename); input.ignore(256, '\n'); } } // check tree consistency and fill missing data if (m_bestTree->m_numNodes == -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: number of nodes not set in file %s\n", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } if (m_numInputGenomes == -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: number of input genomes not set in file %s\n", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } if (m_permSize == -1) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: permutation size not set in file %s\n", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } if (m_bestTree->m_nodes.size() == 0) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: nodes not set in file %s\n", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } if (m_numInputGenomes > numInputGenomes) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: not enough nodes tagged as input genomes in file %s\n", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } for (int i = 0; i < m_bestTree->m_numNodes; i++) { if (m_bestTree->m_nodes[i] == NULL) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: not all nodes set in file %s\n", f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } } m_minswrt.setPermutationSize(m_permSize); m_minswrt.setWeights(m_wr, m_wt); m_revdist.init(m_permSize); if (m_revOnly) m_medianSolver.init(m_permSize, m_wr, m_wt, 0, 1, 50000000 / m_permSize); else m_medianSolver.init(m_permSize, m_wr, m_wt, 2, 0, 50000000 / m_permSize); for (int i = 0; i < m_bestTree->m_numNodes; i++) { if (!checkPerm(m_bestTree->m_nodes[i]->m_perm)) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: invalid permutation in node %d in file %s\n", i, f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } if ((m_bestTree->m_nodes[i]->m_father < -1) || (m_bestTree->m_nodes[i]->m_father >= m_bestTree->m_numNodes)) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: edge of node %d has an invalid target in file %s\n", i, f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } if (m_bestTree->m_nodes[i]->m_father != -1) { if (m_bestTree->m_nodes[i]->m_edge != NULL) { for (int j = 0; j < m_bestTree->m_nodes[i]->m_edge->m_cloudSize; j++) { if (!checkPerm(m_bestTree->m_nodes[i]->m_edge->m_cloud[j])) { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: invalid permutation in node %d cloud[%d] in file %s\n", i, j, f_filename); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } } for (int j = 0; j < m_bestTree->m_nodes[i]->m_edge->m_cloudSize; j++) { if (m_bestTree->m_nodes[i]->m_edge->m_distSource[j] < 0) m_bestTree->m_nodes[i]->m_edge->m_distSource[j] = getDistance(m_bestTree->m_nodes[i]->m_edge->m_cloud[j], m_bestTree->m_nodes[i]->m_perm); if (m_bestTree->m_nodes[i]->m_edge->m_distSource[j] < 0) m_bestTree->m_nodes[i]->m_edge->m_distSource[j] = getDistance(m_bestTree->m_nodes[i]->m_edge->m_cloud[j], m_bestTree->m_nodes[m_bestTree->m_nodes[i]->m_father]->m_perm); } if (m_bestTree->m_nodes[i]->m_edge->m_weight < 0) { m_bestTree->m_nodes[i]->m_edge->m_weight = getDistance(m_bestTree->m_nodes[i]->m_perm, m_bestTree->m_nodes[m_bestTree->m_nodes[i]->m_father]->m_perm); for (int j = 0; j < m_bestTree->m_nodes[i]->m_edge->m_cloudSize; j++) { if (m_bestTree->m_nodes[i]->m_edge->m_distSource[j] + m_bestTree->m_nodes[i]->m_edge->m_distTarget[j] < m_bestTree->m_nodes[i]->m_edge->m_weight) m_bestTree->m_nodes[i]->m_edge->m_weight = m_bestTree->m_nodes[i]->m_edge->m_distSource[j] + m_bestTree->m_nodes[i]->m_edge->m_distTarget[j]; } } } } } if (m_bestTree->m_weight < 0) { m_bestTree->m_weight = 0; for (int i = 0; i < m_bestTree->m_numNodes; i++) { if (m_bestTree->m_nodes[i]->m_edge != NULL) m_bestTree->m_weight += m_bestTree->m_nodes[i]->m_edge->m_weight; else if (m_bestTree->m_nodes[i]->m_father != -1) m_bestTree->m_weight += getDistance(m_bestTree->m_nodes[i]->m_perm, m_bestTree->m_nodes[m_bestTree->m_nodes[i]->m_father]->m_perm); } } // check if we really have a tree for (int i = 0; i < m_bestTree->m_numNodes; i++) { pos = i; for (int j = 0; (j < m_bestTree->m_numNodes) && (m_bestTree->m_nodes[pos]->m_father != -1); j++) pos = m_bestTree->m_nodes[pos]->m_father; if (m_bestTree->m_nodes[pos]->m_father != -1) // cycle { g_logger.log(PHYLO_WARNING, "WARNING: readTreeFromFile: the graph is not a tree\n"); cleanTreeLoadErrors(node, name, edge, input); f_inputGenomes = NULL; return false; } } // everthing is ok - init members input.close(); m_element2Index = new int[m_permSize + 1]; m_mapping = new int[m_permSize + 1]; m_inCycle = new bool[m_permSize]; m_cycle = new int[m_permSize]; m_state = 3; f_inputGenomes = m_inputGenomes; m_actTree = NULL; // init return values f_numPerms = m_numInputGenomes; f_permSize = m_permSize; g_logger.log(PHYLO_INFO, "done\n"); return true; } void Phylo::setWeights(int f_wt, int f_wr, double f_revOnly) { m_wt = f_wt; m_wr = f_wr; m_revOnly = f_revOnly; m_minswrt.setWeights(f_wr, f_wt); if (m_revOnly) { m_wt = m_wr; m_medianSolver.init(m_permSize, m_wr, m_wt, 0, 1, 50000000 / m_permSize); } else m_medianSolver.init(m_permSize, m_wr, m_wt, 2, 0, 50000000 / m_permSize); if (m_state == 3) m_state = 2; } void Phylo::createTree(int f_improve) { Tree** trees; int bestWeight = INT_MAX; /* if (!m_revOnly && (f_improve != 0)) // use speed hack function { createTreeSpeedHack(f_improve); return; }*/ trees = new Tree*[m_numInputGenomes]; if (m_state == 0) { g_logger.log(PHYLO_WARNING, "Phylo::createTree: input genomes not initialized -> aborting\n"); return; } if (m_state > 1) // delete old trees { delete m_bestTree; m_bestTree = NULL; } // phase 1: creating the trees initCTVars(); for (int i = 0; i < m_numInputGenomes; i++) { createTreeFromNode(i); trees[i] = m_actTree; if (m_actTree->m_weight < bestWeight) bestWeight = m_actTree->m_weight; m_actTree = NULL; } freeCTVars(); // phase 2: improving the trees g_logger.log(PHYLO_INFO, "Starting improvement phase\n"); for (int i = 0; i < m_numInputGenomes; i++) { if ((trees[i]->m_weight < bestWeight + 5) || (trees[i]->m_weight < (int)(1.1 * bestWeight))) { g_logger.log(PHYLO_INFO, "Improving tree %d (weight %d)\n", i, trees[i]->m_weight); m_actTree = trees[i]; if (f_improve == 1) improveTreePerturb(); else if (f_improve == 2) improveTreeMedian(); else if (f_improve == 3) improveTree(); } if (m_bestTree == NULL) { g_logger.log(PHYLO_INFO, "Accepting tree %d (weight %d)\n\n", i, trees[i]->m_weight); if (trees[i]->m_weight < bestWeight ) bestWeight = trees[i]->m_weight; m_bestTree = trees[i]; } else if (trees[i]->m_weight <= bestWeight) { g_logger.log(PHYLO_INFO, "Accepting tree %d (weight %d)\n\n", i, trees[i]->m_weight); bestWeight = trees[i]->m_weight; delete m_bestTree; m_bestTree = trees[i]; } else { g_logger.log(PHYLO_INFO, "Rejecting tree %d (weight %d)\n\n", i, trees[i]->m_weight); delete trees[i]; } } delete[] trees; m_state = 3; } void Phylo::createTree(int f_startGenome, int f_improve) { /* if (!m_revOnly && (f_improve != 0)) // use speed hack function { createTreeSpeedHack(f_startGenome, f_improve); return; }*/ if (m_state == 0) { g_logger.log(PHYLO_WARNING, "Phylo::createTree: input genomes not initialized -> aborting\n"); return; } if (m_state > 1) // delete old trees { delete m_bestTree; m_bestTree = NULL; } initCTVars(); createTreeFromNode(f_startGenome); m_bestTree = m_actTree; freeCTVars(); if (f_improve != 0) g_logger.log(PHYLO_INFO, "Starting improvement phase\n"); if (f_improve == 1) improveTreePerturb(); else if (f_improve == 2) improveTreeMedian(); else if (f_improve == 3) improveTree(); m_actTree = NULL; m_state = 3; } void Phylo::improveTree() { g_logger.log(PHYLO_DEBUG, "improveTree called\n"); bool ibt = false; // true if we improve m_bestTree if (m_actTree == NULL) // improve m_bestTree { m_actTree = m_bestTree; ibt = true; } #if 0 // alternately call the two improve functions repairClouds(); improveTreePerturb(); while (true) { weight = m_actTree->m_weight; improveTreeMedian(); if (m_actTree->m_weight >= weight) // no improvement break; repairClouds(); weight = m_actTree->m_weight; improveTreePerturb(); if (m_actTree->m_weight >= weight) // no improvement break; } #endif // first p then m repairClouds(); improveTreePerturb(); improveTreeMedian(); // clean up if (ibt) m_actTree = NULL; } void Phylo::improveTreePerturb() { bool improve; // true if we could find an improvement int target1, target2; // target of two edges int d1, d2, d3, d4, dei, dej; // some distances int splitedge = -1; // split this edge when improving int edge1 = -1; // insert new edge between this edge and edge2 int edge2 = -1; // insert new edge between this edge and edge1 Edge* edgeold; Edge* edgenew; int size; int fact; bool ibt = false; // true if we improve m_bestTree g_logger.log(PHYLO_INFO, "Trying to perturb the tree\n"); if (m_actTree == NULL) // improve m_bestTree { m_actTree = m_bestTree; ibt = true; } if (m_revOnly) m_branchparam = 5; else m_branchparam = 2; // reduce edge size for (int i = 1; i < m_actTree->m_numNodes; i++) { edgeold = m_actTree->m_nodes[i]->m_edge; if (m_revOnly && (edgeold->m_weight / m_wr > 1000)) size = (int)(edgeold->m_weight / m_wr - 500) * 500; else if (!m_revOnly && (edgeold->m_weight / m_wr > 400)) size = (int)(edgeold->m_weight / m_wr - 20) * 20; else size = (int)((edgeold->m_weight * edgeold->m_weight * m_branchparam) / (4.0 * m_wr)); if (size == 0) fact = 1; else fact = edgeold->m_cloudSize / size; if (fact == 0) fact = 1; if (edgeold->m_cloudSize % fact == 0) size = edgeold->m_cloudSize / fact; else size = edgeold->m_cloudSize / fact + 1; if (size > edgeold->m_cloudSize) size = edgeold->m_cloudSize; edgenew = new Edge(); edgenew->init(size); edgenew->m_weight = edgeold->m_weight; for (int j = 0; j < edgeold->m_cloudSize; j++) { if (j % fact == 0) // copy the perm { edgenew->m_cloud[j/fact] = edgeold->m_cloud[j]; edgenew->m_distSource[j/fact] = edgeold->m_distSource[j]; edgenew->m_distTarget[j/fact] = edgeold->m_distTarget[j]; } else g_permPool->freePerm(edgeold->m_cloud[j]); } delete[] edgeold->m_cloud; edgeold->m_cloud = NULL; delete[] edgeold->m_distSource; delete[] edgeold->m_distTarget; delete edgeold; m_actTree->m_nodes[i]->m_edge = edgenew; } // init some variables // array of input genomes already in the tree - needed for the secondary score m_visited = new bool[m_numInputGenomes]; for (int i = 0; i < m_numInputGenomes; i++) m_visited[i] = true; m_ITNodeDist.reserve(5 * m_actTree->m_numNodes * m_actTree->m_numNodes); // init pairwise node distances m_ITNodeDist.resize(getITIndex(m_actTree->m_numNodes - 1, m_actTree->m_numNodes - 1) + 1); for (int i = 0; i < m_actTree->m_numNodes; i++) { for (int j = i; j < m_actTree->m_numNodes; j++) m_ITNodeDist[getITIndex(i, j)] = getLowerBound(m_actTree->m_nodes[i]->m_perm, m_actTree->m_nodes[j]->m_perm); } m_ITLowerBound.reserve(35 * m_actTree->m_numNodes * m_actTree->m_numNodes); // init the lower bounds m_ITLowerBound.resize(getITIndex(m_actTree->m_numNodes - 1, m_actTree->m_numNodes - 1) + 1); for (int i = 0; i < m_actTree->m_numNodes; i++) { target1 = (m_actTree->m_nodes[i]->m_father == -1? i : m_actTree->m_nodes[i]->m_father); dei = (m_actTree->m_nodes[i]->m_father == -1? 0 : m_actTree->m_nodes[i]->m_edge->m_weight); for (int j = i; j < m_actTree->m_numNodes; j++) { target2 = (m_actTree->m_nodes[j]->m_father == -1? j : m_actTree->m_nodes[j]->m_father); dej = (m_actTree->m_nodes[j]->m_father == -1? 0 : m_actTree->m_nodes[j]->m_edge->m_weight); d1 = m_ITNodeDist[getITIndex(i, j)]; d2 = m_ITNodeDist[getITIndex(i, target2)]; d3 = m_ITNodeDist[getITIndex(target1, j)]; d4 = m_ITNodeDist[getITIndex(target1, target2)]; if (d1 + d4 > d2 + d3) m_ITLowerBound[getITIndex(i, j)] = (d1 + d4 - dei - dej) / 2; else m_ITLowerBound[getITIndex(i, j)] = (d2 + d3 - dei - dej) / 2; } } m_ITBestDist.reserve(35 * m_actTree->m_numNodes * m_actTree->m_numNodes); // init the bestDist array m_ITBestDist.resize(getITIndex(m_actTree->m_numNodes - 1, m_actTree->m_numNodes - 1) + 1); for (int i = 0; i < getITIndex(m_actTree->m_numNodes - 1, m_actTree->m_numNodes - 1) + 1; i++) m_ITBestDist[i] = -1; m_ITBestCloudNodes.reserve(35 * m_actTree->m_numNodes * m_actTree->m_numNodes); // init the bestCloudNodes array m_ITBestCloudNodes.resize(getITIndex(m_actTree->m_numNodes - 1, m_actTree->m_numNodes - 1) + 1); m_ITEdge2Node.reserve(6 * m_actTree->m_numNodes * m_actTree->m_numNodes); // init edge2node m_ITEdge2Node.resize(m_actTree->m_numNodes); for (int i = 0; i < m_actTree->m_numNodes; i++) m_ITEdge2Node[i] = i; m_ITNode2Edge.reserve(6 * m_actTree->m_numNodes * m_actTree->m_numNodes); // init node2edge m_ITNode2Edge.resize(m_actTree->m_numNodes); for (int i = 0; i < m_actTree->m_numNodes; i++) m_ITNode2Edge[i] = i; m_ITPartitioning.reserve(3 * m_actTree->m_numNodes); // init tree partitioning m_ITPartitioning.resize(m_actTree->m_numNodes); m_maxEdge = m_actTree->m_numNodes - 1; // search for improvements, and perform them do { improve = findImprovement(splitedge, edge1, edge2); if (improve) performImprovement(splitedge, edge1, edge2); } while (improve); // clear the variables m_ITNodeDist.clear(); m_ITLowerBound.clear(); m_ITBestDist.clear(); m_ITBestCloudNodes.clear(); m_ITEdge2Node.clear(); m_ITEdge2Node.clear(); delete[] m_visited; m_visited = NULL; if (ibt) m_actTree = NULL; } void Phylo::improveTreeMedian() { int* neighbors; // neighbors of a node int* numNeighbors; // number of neighbors (to determine leaves); int* distances; // distances to the neighbors bool* isMedian; // true if a node is the calculated median of its neighbors bool improving = true; // true if the tree is still improving int* median; // a fresh calculated median int medianWeightOld; // old weight of the median int medianWeightNew; // new weight of the median bool ibt = false; // true if we improve m_bestTree g_logger.log(PHYLO_INFO, "Trying to improve the medians\n"); if (m_actTree == NULL) // improve m_bestTree { m_actTree = m_bestTree; ibt = true; } // make all inner nodes of degree 3 relaxTree(); // calculate the neighbors of each node numNeighbors = new int[m_actTree->m_numNodes]; neighbors = new int[3 * m_actTree->m_numNodes]; distances = new int[3 * m_actTree->m_numNodes]; for (int i = 0; i < m_actTree->m_numNodes; i++) numNeighbors[i] = 0; for (int i = 0; i < 3 * m_actTree->m_numNodes; i++) neighbors[i] = -1; isMedian = new bool[m_actTree->m_numNodes]; for (int i = 0; i < m_actTree->m_numNodes; i++) isMedian[i] = false; for (int i = 0; i < m_actTree->m_numNodes; i++) { if (m_actTree->m_nodes[i]->m_father != -1) { neighbors[3*i + numNeighbors[i]] = m_actTree->m_nodes[i]->m_father; neighbors[3*m_actTree->m_nodes[i]->m_father + numNeighbors[m_actTree->m_nodes[i]->m_father]] = i; if (m_actTree->m_nodes[i]->m_edge == NULL) distances[3*i + numNeighbors[i]] = getDistance(m_actTree->m_nodes[i]->m_perm, m_actTree->m_nodes[m_actTree->m_nodes[i]->m_father]->m_perm); else distances[3*i + numNeighbors[i]] = m_actTree->m_nodes[i]->m_edge->m_weight; distances[3*m_actTree->m_nodes[i]->m_father + numNeighbors[m_actTree->m_nodes[i]->m_father]] = distances[3*i + numNeighbors[i]]; numNeighbors[i]++; numNeighbors[m_actTree->m_nodes[i]->m_father]++; } } while (improving) { improving = false; for (int i = 0; i < m_actTree->m_numNodes; i++) { if ((numNeighbors[i] == 1) || isMedian[i]) continue; medianWeightOld = distances[3*i] + distances[3*i+1] + distances[3*i+2]; median = g_permPool->getPerm(); medianWeightNew = m_medianSolver.solve(m_actTree->m_nodes[neighbors[3*i]]->m_perm, m_actTree->m_nodes[neighbors[3*i+1]]->m_perm, m_actTree->m_nodes[neighbors[3*i+2]]->m_perm, median, medianWeightOld); if ((medianWeightNew >= 0) && (medianWeightNew < medianWeightOld)) // improvement { g_logger.log(PHYLO_INFO, "Improvement step decreased tree weight by %d\n", medianWeightOld - medianWeightNew); improving = true; // delete edges if (m_actTree->m_nodes[i]->m_edge != NULL) { delete m_actTree->m_nodes[i]->m_edge; m_actTree->m_nodes[i]->m_edge = NULL; } if ((m_actTree->m_nodes[neighbors[3*i]]->m_father == i) && (m_actTree->m_nodes[neighbors[3*i]]->m_edge != NULL)) { delete m_actTree->m_nodes[neighbors[3*i]]->m_edge; m_actTree->m_nodes[neighbors[3*i]]->m_edge = NULL; } if ((m_actTree->m_nodes[neighbors[3*i+1]]->m_father == i) && (m_actTree->m_nodes[neighbors[3*i+1]]->m_edge != NULL)) { delete m_actTree->m_nodes[neighbors[3*i+1]]->m_edge; m_actTree->m_nodes[neighbors[3*i+1]]->m_edge = NULL; } if ((m_actTree->m_nodes[neighbors[3*i+2]]->m_father == i) && (m_actTree->m_nodes[neighbors[3*i+2]]->m_edge != NULL)) { delete m_actTree->m_nodes[neighbors[3*i+2]]->m_edge; m_actTree->m_nodes[neighbors[3*i+2]]->m_edge = NULL; } // replace node + recalculate the distances g_permPool->freePerm(m_actTree->m_nodes[i]->m_perm); m_actTree->m_nodes[i]->m_perm = median; m_medianSolver.getMedianDist(distances[3*i], distances[3*i+1], distances[3*i+2]); for (int j = 0; j < 3; j++) { if (neighbors[3*neighbors[3*i]+j] == i) distances[3*neighbors[3*i]+j] = distances[3*i]; if (neighbors[3*neighbors[3*i+1]+j] == i) distances[3*neighbors[3*i+1]+j] = distances[3*i+1]; if (neighbors[3*neighbors[3*i+2]+j] == i) distances[3*neighbors[3*i+2]+j] = distances[3*i+2]; } m_actTree->m_weight = m_actTree->m_weight + medianWeightNew - medianWeightOld; } else g_permPool->freePerm(median); } } delete[] numNeighbors; delete[] neighbors; delete[] isMedian; delete[] distances; if (ibt) m_actTree = NULL; } int Phylo::getTreeWeight() const { return m_bestTree->m_weight; } Tree* Phylo::getTree() const { return m_bestTree; } void Phylo::printTree(std::ostream& f_outstream) { if (m_bestTree == NULL) { f_outstream << "Tree is NULL!\n"; return; } for (int i = 0; i < m_bestTree->m_numNodes; i++) { f_outstream << "Node " << i << ": "; if ((m_bestTree->m_node2input[i] != -1) && (m_genomeNames != NULL) && (m_genomeNames[m_bestTree->m_node2input[i]] != NULL)) f_outstream << m_genomeNames[m_bestTree->m_node2input[i]]; f_outstream << endl; for (int j = 0; j < m_permSize; j++) f_outstream << m_bestTree->m_nodes[i]->m_perm[j] << " "; f_outstream << "\n"; if (m_bestTree->m_nodes[i]->m_father == -1) f_outstream << "root node\n"; else { f_outstream << "connected to node " << m_bestTree->m_nodes[i]->m_father << endl; if (m_bestTree->m_nodes[i]->m_edge != NULL) f_outstream << " (dist = " << m_bestTree->m_nodes[i]->m_edge->m_weight << ")\n"; else f_outstream << " (dist = " << getDistance(m_bestTree->m_nodes[i]->m_perm, m_bestTree->m_nodes[m_bestTree->m_nodes[i]->m_father]->m_perm) << ")\n"; } f_outstream << "\n"; } f_outstream << "overall tree weight: " << m_bestTree->m_weight << endl; } bool Phylo::writeTreeToFile(const char* f_filename) const { ofstream output; // file output stream g_logger.log(PHYLO_INFO, "writing tree to file %s\n", f_filename); output.open(f_filename); if (m_bestTree == NULL) { output << "NULL:\n"; output.close(); return true; } output << "num perms: "<< m_bestTree->m_numNodes << endl; output << "num input genomes: " << m_numInputGenomes << endl; output << "perm size: " << m_bestTree->m_permSize << endl; output << "wr wt: " << m_wr << " "; if (m_revOnly) output << "inf\n"; else output << m_wt << endl; output << "weight: " << m_bestTree->m_weight << endl; for (int i = 0; i < m_bestTree->m_numNodes; i++) { output << "\n"; output << "index: " << i << endl; output << "input genome: " << (m_bestTree->m_node2input[i] != -1? "true":"false") << endl; if ((m_bestTree->m_node2input[i] != -1) && (m_genomeNames != NULL) && (m_genomeNames[m_bestTree->m_node2input[i]] != NULL)) output << "name: " << m_genomeNames[m_bestTree->m_node2input[i]] << endl; output << "perm:\n"; for (int j = 0; j < m_permSize; j++) output << m_bestTree->m_nodes[i]->m_perm[j] << " "; output << endl; output << "connected to: " << m_bestTree->m_nodes[i]->m_father << endl; if (m_bestTree->m_nodes[i]->m_edge != NULL) { output << "\n"; output << "weight: " << m_bestTree->m_nodes[i]->m_edge->m_weight << endl; output << "cloud size: " << m_bestTree->m_nodes[i]->m_edge->m_cloudSize << endl; output << "cloud:\n"; for (int k = 0; k < m_bestTree->m_nodes[i]->m_edge->m_cloudSize; k++) { for (int j = 0; j < m_permSize; j++) output << m_bestTree->m_nodes[i]->m_edge->m_cloud[k][j] << " "; output << endl; } output << "dist source:\n"; for (int k = 0; k < m_bestTree->m_nodes[i]->m_edge->m_cloudSize; k++) output << m_bestTree->m_nodes[i]->m_edge->m_distSource[k] << endl; output << "dist target:\n"; for (int k = 0; k < m_bestTree->m_nodes[i]->m_edge->m_cloudSize; k++) output << m_bestTree->m_nodes[i]->m_edge->m_distTarget[k] << endl; output << "\n"; } output << "\n"; } output.close(); g_logger.log(PHYLO_INFO, "done\n"); return true; } /*************************************************************************** * protected methods ***************************************************************************/ bool Phylo::checkInputGenomes() { bool* visited = new bool[m_permSize]; // these elements were found int absval; // absolute value of an element for (int i = 0; i < m_numInputGenomes; i++) { for (int j = 0; j < m_permSize; j++) visited[j] = false; for (int j = 0; j < m_permSize; j++) { absval = abs(m_inputGenomes[i][j]); if ((absval == 0) || (absval > m_permSize) || visited[absval-1]) { delete[] visited; // test failed return false; } visited[absval-1] = true; } } delete[] visited; return true; } void Phylo::cleanTreeLoadErrors(Node* f_node, char* f_char, Edge* f_edge, ifstream &f_input) { // delete temporaray vars delete f_node; delete[] f_char; delete f_edge; f_input.close(); // delete the tree delete m_bestTree; m_bestTree = NULL; // reset members of phylo m_state = 0; m_permSize = 0; if (m_genomeNames != NULL) { for (int i = 0; i < m_numInputGenomes; i++) { if (m_genomeNames[i] != NULL) delete[] m_genomeNames[i]; } delete[] m_genomeNames; m_genomeNames = NULL; } m_inputGenomes = NULL; m_numInputGenomes = 0; delete[] m_element2Index; m_element2Index = NULL; } void Phylo::initCTVars() { // create table with distances input genomes -> nodes m_nodeDist = new int*[m_numInputGenomes]; for (int i = 0; i < m_numInputGenomes; i++) m_nodeDist[i] = new int[3 * m_numInputGenomes - 5]; // create mapping input node -> best found edge m_bestEdge = new int[m_numInputGenomes]; // create mapping edge -> source node; max edge index is 3 * #inputs - 5 m_edge2Node = new int[3 * m_numInputGenomes - 5]; // for each input node, create an array storing the best found steiner nodes on each edge m_steinerDist = new SteinerDist*[m_numInputGenomes]; for (int i = 0; i < m_numInputGenomes; i++) m_steinerDist[i] = new SteinerDist[3 * m_numInputGenomes - 5]; } void Phylo::freeCTVars() { for (int i = 0; i < m_numInputGenomes; i++) delete[] m_nodeDist[i]; delete[] m_nodeDist; m_nodeDist = NULL; delete[] m_bestEdge; m_bestEdge = NULL; delete[] m_edge2Node; m_edge2Node = NULL; for (int i = 0; i < m_numInputGenomes; i++) delete[] m_steinerDist[i]; delete[] m_steinerDist; m_steinerDist = NULL; } void Phylo::createTreeSpeedHack(int f_improve) { #if 0 Tree** trees = new Tree*[m_numInputGenomes]; int bestWeight = INT_MAX; int* source; int* target; // use revOnly dist for better performance setWeights(m_wt, m_wr, true); if (m_state == 0) { g_logger.log(PHYLO_WARNING, "Phylo::createTree: input genomes not initialized -> aborting\n"); return; } if (m_state > 1) // delete old trees { delete m_bestTree; m_bestTree = NULL; } // phase 1: creating the trees initCTVars(); for (int i = 0; i < m_numInputGenomes; i++) { createTreeFromNode(i); trees[i] = m_actTree; m_actTree = NULL; } freeCTVars(); // phase 2: recalculate the tree weights g_logger.log(PHYLO_INFO, "recalculating the distances\n"); setWeights(m_wt, m_wr, false); for (int i = 0; i < m_numInputGenomes; i++) { trees[i]->m_weight = 0; for (int j = 0; j < trees[i]->m_numNodes; j++) { if (trees[i]->m_nodes[j]->m_edge == NULL) continue; source = trees[i]->m_nodes[j]->m_perm; target = trees[i]->m_nodes[trees[i]->m_nodes[j]->m_father]->m_perm; trees[i]->m_nodes[j]->m_edge->m_weight = getDistance(source, target); for (int k = 0; k < trees[i]->m_nodes[j]->m_edge->m_cloudSize; k++) { trees[i]->m_nodes[j]->m_edge->m_distSource[k] = getDistance(trees[i]->m_nodes[j]->m_edge->m_cloud[k], source); trees[i]->m_nodes[j]->m_edge->m_distTarget[k] = getDistance(trees[i]->m_nodes[j]->m_edge->m_cloud[k], target); if (trees[i]->m_nodes[j]->m_edge->m_distSource[k] + trees[i]->m_nodes[j]->m_edge->m_distTarget[k] < trees[i]->m_nodes[j]->m_edge->m_weight) trees[i]->m_nodes[j]->m_edge->m_weight = trees[i]->m_nodes[j]->m_edge->m_distSource[k] + trees[i]->m_nodes[j]->m_edge->m_distTarget[k]; } trees[i]->m_weight += trees[i]->m_nodes[j]->m_edge->m_weight; } if (trees[i]->m_weight < bestWeight) bestWeight = trees[i]->m_weight; } // phase 3: improve the tree g_logger.log(PHYLO_INFO, "Starting improvement phase\n"); for (int i = 0; i < m_numInputGenomes; i++) { // if ((trees[i]->m_weight < bestWeight + 5) || (trees[i]->m_weight < (int)(1.1 * bestWeight))) // { g_logger.log(PHYLO_INFO, "Improving tree %d (weight %d)\n", i, trees[i]->m_weight); m_actTree = trees[i]; if (f_improve == 1) improveTreePerturb(); else if (f_improve == 2) improveTreeMedian(); else if (f_improve == 3) improveTree(); // } if (m_bestTree == NULL) { g_logger.log(PHYLO_INFO, "Accepting tree %d (weight %d)\n\n", i, trees[i]->m_weight); if (trees[i]->m_weight < bestWeight ) bestWeight = trees[i]->m_weight; m_bestTree = trees[i]; } else if (trees[i]->m_weight <= bestWeight) { g_logger.log(PHYLO_INFO, "Accepting tree %d (weight %d)\n\n", i, trees[i]->m_weight); bestWeight = trees[i]->m_weight; delete m_bestTree; m_bestTree = trees[i]; } else { g_logger.log(PHYLO_INFO, "Rejecting tree %d (weight %d)\n\n", i, trees[i]->m_weight); delete trees[i]; } } delete[] trees; m_state = 3; #endif int* source; int* target; if (m_state == 0) { g_logger.log(PHYLO_WARNING, "Phylo::createTree: input genomes not initialized -> aborting\n"); return; } if (m_state > 1) // delete old trees { delete m_bestTree; m_bestTree = NULL; } initCTVars(); // prepare for creating the trees for (int i = 0; i < m_numInputGenomes; i++) // for each starting genome { setWeights(m_wt, m_wr, true); // use revOnly dist for better performance createTreeFromNode(i); // recalculate the distances g_logger.log(PHYLO_INFO, "recalculating the distances\n"); setWeights(m_wt, m_wr, false); m_actTree->m_weight = 0; for (int j = 0; j < m_actTree->m_numNodes; j++) { if (m_actTree->m_nodes[j]->m_edge == NULL) continue; source = m_actTree->m_nodes[j]->m_perm; target = m_actTree->m_nodes[m_actTree->m_nodes[j]->m_father]->m_perm; m_actTree->m_nodes[j]->m_edge->m_weight = getDistance(source, target); for (int k = 0; k < m_actTree->m_nodes[j]->m_edge->m_cloudSize; k++) { m_actTree->m_nodes[j]->m_edge->m_distSource[k] = getDistance(m_actTree->m_nodes[j]->m_edge->m_cloud[k], source); m_actTree->m_nodes[j]->m_edge->m_distTarget[k] = getDistance(m_actTree->m_nodes[j]->m_edge->m_cloud[k], target); if (m_actTree->m_nodes[j]->m_edge->m_distSource[k] + m_actTree->m_nodes[j]->m_edge->m_distTarget[k] < m_actTree->m_nodes[j]->m_edge->m_weight) m_actTree->m_nodes[j]->m_edge->m_weight = m_actTree->m_nodes[j]->m_edge->m_distSource[k] + m_actTree->m_nodes[j]->m_edge->m_distTarget[k]; } m_actTree->m_weight += m_actTree->m_nodes[j]->m_edge->m_weight; } // improve the tree delete m_visited; m_visited = NULL; // improveTree needs the array for its own purposes g_logger.log(PHYLO_INFO, "Improving tree %d (weight %d)\n", i, m_actTree->m_weight); if (f_improve == 1) improveTreePerturb(); else if (f_improve == 2) improveTreeMedian(); else if (f_improve == 3) improveTree(); m_visited = new bool[m_numInputGenomes]; // realloc memory // check if new best tree and store if (m_bestTree == NULL) { g_logger.log(PHYLO_INFO, "Accepting tree %d (weight %d)\n\n", i, m_actTree->m_weight); m_bestTree = m_actTree; m_actTree = NULL; } else if (m_actTree->m_weight <= m_bestTree->m_weight) { g_logger.log(PHYLO_INFO, "Accepting tree %d (weight %d)\n\n", i, m_actTree->m_weight); delete m_bestTree; m_bestTree = m_actTree; m_actTree = NULL; } else { g_logger.log(PHYLO_INFO, "Rejecting tree %d (weight %d)\n\n", i, m_actTree->m_weight); delete m_actTree; } } freeCTVars(); m_state = 3; } void Phylo::createTreeSpeedHack(int f_startGenome, int f_improve) { int* source; int* target; // use revOnly dist for better performance setWeights(m_wt, m_wr, true); if (m_state == 0) { g_logger.log(PHYLO_WARNING, "Phylo::createTree: input genomes not initialized -> aborting\n"); return; } if (m_state > 1) // delete old trees { delete m_bestTree; m_bestTree = NULL; } // phase 1: create the tree initCTVars(); createTreeFromNode(f_startGenome); freeCTVars(); // phase 2: recaluclate the distances g_logger.log(PHYLO_INFO, "recalculating the distances\n"); setWeights(m_wt, m_wr, false); m_actTree->m_weight = 0; for (int j = 0; j < m_actTree->m_numNodes; j++) { if (m_actTree->m_nodes[j]->m_edge == NULL) continue; source = m_actTree->m_nodes[j]->m_perm; target = m_actTree->m_nodes[m_actTree->m_nodes[j]->m_father]->m_perm; m_actTree->m_nodes[j]->m_edge->m_weight = getDistance(source, target); for (int k = 0; k < m_actTree->m_nodes[j]->m_edge->m_cloudSize; k++) { m_actTree->m_nodes[j]->m_edge->m_distSource[k] = getDistance(m_actTree->m_nodes[j]->m_edge->m_cloud[k], source); m_actTree->m_nodes[j]->m_edge->m_distTarget[k] = getDistance(m_actTree->m_nodes[j]->m_edge->m_cloud[k], target); if (m_actTree->m_nodes[j]->m_edge->m_distSource[k] + m_actTree->m_nodes[j]->m_edge->m_distTarget[k] < m_actTree->m_nodes[j]->m_edge->m_weight) m_actTree->m_nodes[j]->m_edge->m_weight = m_actTree->m_nodes[j]->m_edge->m_distSource[k] + m_actTree->m_nodes[j]->m_edge->m_distTarget[k]; } m_actTree->m_weight += m_actTree->m_nodes[j]->m_edge->m_weight; } // phase 3: improving the tree g_logger.log(PHYLO_INFO, "Tree weight: %d\n", m_actTree->m_weight); g_logger.log(PHYLO_INFO, "Starting improvement phase\n"); if (f_improve == 1) improveTreePerturb(); else if (f_improve == 2) improveTreeMedian(); else if (f_improve == 3) improveTree(); m_bestTree = m_actTree; m_actTree = NULL; m_state = 3; } void Phylo::createTreeFromNode(int f_startGenome) { Node* node; // new node to add int oldMaxEdge = 0; // value of max edge before performSplit if (m_revOnly) m_branchparam = 20; else m_branchparam = 4; g_logger.log(PHYLO_INFO, "creating tree from node %d\n", f_startGenome); // setting up the ct member variables m_visited = new bool[m_numInputGenomes]; for (int i = 0; i < m_numInputGenomes; i++) m_visited[i] = false; for (int i = 0; i < m_numInputGenomes; i++) m_bestEdge[i] = 0; m_edge2Node[0] = 0; for (int i = 1; i < 3 * m_numInputGenomes - 5; i++) m_edge2Node[i] = -1; for (int i = 0; i < m_numInputGenomes; i++) { if (i == f_startGenome) continue; m_nodeDist[i][0] = getDistance(m_inputGenomes[i], m_inputGenomes[f_startGenome]); m_steinerDist[i][0].m_node = -1; m_steinerDist[i][0].m_dist = m_nodeDist[i][0]; for (int j = 1; j < 3 * m_numInputGenomes - 5; j++) m_steinerDist[i][j].m_dist = -1; } m_maxEdge = 0; // add start genome as first node m_actTree = new Tree(m_permSize); for (int i = 0; i < m_numInputGenomes; i++) m_visited[i] = false; node = new Node(); node->m_perm = m_inputGenomes[f_startGenome]; node->m_protectPerm = true; m_visited[f_startGenome] = true; m_actTree->m_nodes.push_back(node); m_actTree->m_node2input.push_back(f_startGenome); m_actTree->m_numNodes = 1; // add the other input genomes for (int i = 1; i < m_numInputGenomes; i++) { selectSplit(oldMaxEdge); oldMaxEdge = m_maxEdge; performSplit(); } delete[] m_visited; m_visited = NULL; g_logger.log(PHYLO_INFO, "found tree with weight %3d\n\n", m_actTree->m_weight); } void Phylo::selectSplit(int f_oldMaxEdge) { int bestDist = INT_MAX; // overall best dist (also use as bound) int bestNodeDist; // best distance of a node; int dist; // a distance (wherever needed) Edge* edge; // the current edge int source; // source of an edge int target; // target of an edge m_bestInput = -1; // not really necessary // create a fast bound for (int i = 0; i < m_numInputGenomes; i++) { if (m_visited[i]) continue; for (int j = 0; j < m_actTree->m_numNodes; j++) { if (m_nodeDist[i][j] < bestDist) bestDist = m_nodeDist[i][j]; } } // force to set best split once bestDist++; // search for best split for (int i = 0; i < m_numInputGenomes; i++) // test each possible input genome { if (m_visited[i]) // already in the tree continue; if (m_edge2Node[m_bestEdge[i]] != -1) { bestNodeDist = m_steinerDist[i][m_bestEdge[i]].m_dist; if (bestNodeDist < bestDist) // tighten the bound { bestDist = bestNodeDist; m_bestInput = i; } } else bestNodeDist = INT_MAX; for (int j = 0; j <= m_maxEdge; j++) { source = m_edge2Node[j]; if (source == -1) // edge invalid continue; if (m_steinerDist[i][j].m_dist < 0) // not yet calculated { target = m_actTree->m_nodes[source]->m_father; // check if triangle unequation is fulfilled; if not, add shortcut in distance list if (m_nodeDist[i][source] > m_nodeDist[i][target] + m_actTree->m_nodes[source]->m_edge->m_weight) m_nodeDist[i][source] = m_nodeDist[i][target] + m_actTree->m_nodes[source]->m_edge->m_weight; if (m_nodeDist[i][target] > m_nodeDist[i][source] + m_actTree->m_nodes[source]->m_edge->m_weight) m_nodeDist[i][target] = m_nodeDist[i][source] + m_actTree->m_nodes[source]->m_edge->m_weight; // check if within bound if (m_nodeDist[i][source] + m_nodeDist[i][target] - m_actTree->m_nodes[source]->m_edge->m_weight <= 2 * bestDist) { m_steinerDist[i][j].m_node = -1; // begin with source node m_steinerDist[i][j].m_dist = m_nodeDist[i][source]; // search through cloud for best split point for (int k = 0; k < m_actTree->m_nodes[source]->m_edge->m_cloudSize; k++) { edge = m_actTree->m_nodes[source]->m_edge; dist = edge->m_distSource[k] + edge->m_distTarget[k] - edge->m_weight + getLowerBound(m_inputGenomes[i], edge->m_cloud[k]); if (dist < m_steinerDist[i][j].m_dist) dist = edge->m_distSource[k] + edge->m_distTarget[k] - edge->m_weight + getDistance(m_inputGenomes[i], edge->m_cloud[k]); if (dist < m_steinerDist[i][j].m_dist) { m_steinerDist[i][j].m_node = k; m_steinerDist[i][j].m_dist = dist; } } } } if (m_steinerDist[i][j].m_dist < 0) // all values beyond the bound continue; if (m_steinerDist[i][j].m_dist < bestNodeDist) { m_bestEdge[i] = j; bestNodeDist = m_steinerDist[i][j].m_dist; if (bestNodeDist < bestDist) // tighten the bound { bestDist = bestNodeDist; m_bestInput = i; } } } } } void Phylo::performSplit() { Node* node; // a node to add bool steiner = (m_steinerDist[m_bestInput][m_bestEdge[m_bestInput]].m_node != -1); // add steiner node? int source = m_edge2Node[m_bestEdge[m_bestInput]]; // index of source node of split edge int cloudnode = m_steinerDist[m_bestInput][m_bestEdge[m_bestInput]].m_node; // index of // the steiner node in the cloud int delta = 0; // weight increment m_visited[m_bestInput] = true; g_logger.log(PHYLO_DEBUG, "performSplit: input %d to edge %d cloud %d (dist = %d)\n", m_bestInput, m_bestEdge[m_bestInput], cloudnode, m_steinerDist[m_bestInput][m_bestEdge[m_bestInput]].m_dist); // if connected to a cloud node, add it to the tree if (steiner) { node = new Node(); node->m_perm = m_actTree->m_nodes[source]->m_edge->m_cloud[cloudnode]; node->m_father = m_actTree->m_nodes[source]->m_father; m_actTree->m_nodes.push_back(node); m_actTree->m_node2input.push_back(-1); // create edge for the steiner node createEdge(m_actTree->m_numNodes); delta += m_actTree->m_nodes[m_actTree->m_numNodes]->m_edge->m_weight; m_edge2Node[++m_maxEdge] = m_actTree->m_numNodes; m_actTree->m_numNodes++; // create new edge for the source node delta -= m_actTree->m_nodes[source]->m_edge->m_weight; m_actTree->m_nodes[source]->m_edge->m_protected = cloudnode; delete m_actTree->m_nodes[source]->m_edge; m_edge2Node[m_bestEdge[m_bestInput]] = -1; // edge no longer valid m_actTree->m_nodes[source]->m_father = m_actTree->m_numNodes - 1; createEdge(source); delta += m_actTree->m_nodes[source]->m_edge->m_weight; m_edge2Node[++m_maxEdge] = source; } // add the input node node = new Node(); node->m_perm = m_inputGenomes[m_bestInput]; node->m_protectPerm = true; if (steiner) node->m_father = m_actTree->m_numNodes - 1; else node->m_father = source; m_actTree->m_nodes.push_back(node); m_actTree->m_node2input.push_back(m_bestInput); // create edge for the input node createEdge(m_actTree->m_numNodes); delta += m_actTree->m_nodes[m_actTree->m_numNodes]->m_edge->m_weight; m_edge2Node[++m_maxEdge] = m_actTree->m_numNodes; // update the distance table for (int i = 0; i < m_numInputGenomes; i++) { if (m_visited[i]) continue; if (steiner) // also update dist ot steiner node m_nodeDist[i][m_actTree->m_numNodes - 1] = getDistance(m_inputGenomes[i], m_actTree->m_nodes[m_actTree->m_numNodes - 1]->m_perm); m_nodeDist[i][m_actTree->m_numNodes] = getDistance(m_inputGenomes[i], m_actTree->m_nodes[m_actTree->m_numNodes]->m_perm); } // update some variables m_actTree->m_numNodes++; m_actTree->m_weight += delta; } void Phylo::createEdge(int f_node) { createEdgeCuttedPaths(f_node); } void Phylo::createEdgeEmpty(int f_node) { Edge* edge = new Edge(); // the new edge int target = m_actTree->m_nodes[f_node]->m_father; edge->m_weight = getDistance(m_actTree->m_nodes[f_node]->m_perm, m_actTree->m_nodes[target]->m_perm); m_actTree->m_nodes[f_node]->m_edge = edge; } void Phylo::createEdgeCuttedPaths(int f_node) { Edge* edge = new Edge(); // the new edge unsigned int act; // actual permutation to expand (index in vector) unsigned int last; // index after the last permutation to expand int dist; // distance source->target int counter = 0; // counts depth of the search m_actTree->m_nodes[f_node]->m_edge = edge; // assign edge to the tree m_targetPerm = m_actTree->m_nodes[m_actTree->m_nodes[f_node]->m_father]->m_perm; dist = getDistance(m_actTree->m_nodes[f_node]->m_perm, m_targetPerm); m_branchfactor = (int)(dist * m_branchparam / m_wr) + 1; if (m_revOnly && (m_branchfactor > 500)) m_branchfactor = 500; if (!m_revOnly && (m_branchfactor > 20)) m_branchfactor = 20; g_logger.log(PHYLO_DEBUG, "branchfactor: %d\n", m_branchfactor); // create the mapping for (int i = 0; i < m_permSize; i++) m_mapping[abs(m_targetPerm[i])] = m_targetPerm[i] > 0 ? i+1 : -(i+1); // push the source permutation into the vector m_vecPerms.push_back(m_actTree->m_nodes[f_node]->m_perm); m_vecDistSource.push_back(0); m_vecDistTarget.push_back(dist); m_vecScore.push_back(0); // never touch the first block -> set the best possible score m_vecScore2.push_back(0); m_vecHash.push_back(getHash(m_permSize, m_actTree->m_nodes[f_node]->m_perm)); act = 0; last = 1; // build cloud as long as not finished while ((act < last) && (counter < dist / m_wr)) { counter += 1; // expand the actual permutations while (act < last) { expand(act); act++; } // build a heap of the new candidates buildHeap(last); // select the best candidates last += select(last, m_branchfactor); // erase unused perms for (unsigned int i = last; i < m_vecPerms.size(); i++) g_permPool->freePerm(m_vecPerms[i]); m_vecPerms.resize(last); m_vecDistSource.resize(last); m_vecDistTarget.resize(last); m_vecScore.resize(last); m_vecScore2.resize(last); } // copy the result edge->init(m_vecPerms.size() - 1); edge->m_weight = m_vecDistTarget[0]; for (unsigned int i = 1; i < last; i++) { edge->m_cloud[i-1] = m_vecPerms[i]; edge->m_distSource[i-1] = m_vecDistSource[i]; edge->m_distTarget[i-1] = m_vecDistTarget[i]; if (m_vecDistSource[i] + m_vecDistTarget[i] < edge->m_weight) edge->m_weight = m_vecDistSource[i] + m_vecDistTarget[i]; } // clean up m_vecPerms.clear(); m_vecDistSource.clear(); m_vecDistTarget.clear(); m_vecScore.clear(); m_vecScore2.clear(); m_vecHash.clear(); g_logger.log(PHYLO_DEBUG, "created edge has weight %d\n", edge->m_weight); } void Phylo::expand(int f_index) { int* mapped; // the mapped source permutation vector moves; // operations with a high score bool close = (m_vecDistTarget[f_index] <= m_wt); // true if we are real close to the target int* source = m_vecPerms[f_index]; // source permutation int* perm; // successor permutation int distSource; // distance to source permutation int distTarget; // distance to target permutation int score; // score of the operation int* id; // only expand if next move does not reach the target permutation if (m_vecDistTarget[f_index] <= m_wr) return; // map the source permutation mapped = g_permPool->getPerm(); for (int i = 0; i < m_permSize; i++) mapped[i] = source[i] > 0? m_mapping[abs(source[i])] : -m_mapping[abs(source[i])]; // create id id = g_permPool->getPerm(); for (int i = 0; i < m_permSize; i++) id[i] = i+1; // set up m_element2Index for (int i = 0; i < m_permSize; i++) m_element2Index[abs(mapped[i])] = i; // search for good moves getGoodMoves(mapped, moves); // if there are no good moves, invert an elementary interval if (moves.size() == 0) get0rMoves(mapped, moves); // apply the moves perm = g_permPool->getPerm(); for (unsigned int i = 0; i < moves.size(); i++) { // if we can reach the target with one step, abort if (close && (moves[i].m_type != Operation::OPERATION_REVERSAL)) // -> must be t or tr { g_permPool->freePerm(perm); g_permPool->freePerm(mapped); g_permPool->freePerm(id); return; } performOperation(m_permSize, moves[i], source, perm); distSource = (moves[i].m_type == Operation::OPERATION_REVERSAL? m_vecDistSource[f_index] + m_wr : m_vecDistSource[f_index] + m_wt); distTarget = getDistance(perm, m_targetPerm); score = distSource + distTarget; m_vecScore.push_back(score); m_vecScore2.push_back(calcSecondaryScore(perm)); m_vecPerms.push_back(perm); m_vecDistSource.push_back(distSource); m_vecDistTarget.push_back(distTarget); perm = g_permPool->getPerm(); } g_permPool->freePerm(perm); g_permPool->freePerm(mapped); g_permPool->freePerm(id); } int Phylo::select(unsigned int f_first, unsigned int f_amount) { int top = m_vecPerms.size() - 1; // heap top element int element; // element in the heap int child; // child of element int minparent; // smallest element that is a parent int heapleft = f_first; // leftmost heap index unsigned int hash; // hash of the choosen permutation bool found; // did we find a certain perm? int selected = 0; // number of selected elements int* swapPerm; // swapping permutations int swapInt; // swapping ints while (f_amount > 0) { if (heapleft > top) // out of elements return selected; // check if we already have the top permutation hash = getHash(m_permSize, m_vecPerms[top]); found = false; for (unsigned int i = 0; i < f_first; i++) { if ((m_vecHash[i] == hash) && equalPerms(m_permSize, m_vecPerms[i], m_vecPerms[top])) { found = true; break; } } if (found) // reject the perm (swap to discarded) { swapPerm = m_vecPerms[top]; m_vecPerms[top] = m_vecPerms[heapleft]; m_vecPerms[heapleft] = swapPerm; swapInt = m_vecDistSource[top]; m_vecDistSource[top] = m_vecDistSource[heapleft]; m_vecDistSource[heapleft] = swapInt; swapInt = m_vecDistTarget[top]; m_vecDistTarget[top] = m_vecDistTarget[heapleft]; m_vecDistTarget[heapleft] = swapInt; swapInt = m_vecScore[top]; m_vecScore[top] = m_vecScore[heapleft]; m_vecScore[heapleft] = swapInt; swapInt = m_vecScore2[top]; m_vecScore2[top] = m_vecScore2[heapleft]; m_vecScore2[heapleft] = swapInt; heapleft++; } else // accept the perm (swap to accepted) { swapPerm = m_vecPerms[top]; m_vecPerms[top] = m_vecPerms[heapleft]; m_vecPerms[heapleft] = m_vecPerms[f_first]; m_vecPerms[f_first] = swapPerm; swapInt = m_vecDistSource[top]; m_vecDistSource[top] = m_vecDistSource[heapleft]; m_vecDistSource[heapleft] = m_vecDistSource[f_first]; m_vecDistSource[f_first] = swapInt; swapInt = m_vecDistTarget[top]; m_vecDistTarget[top] = m_vecDistTarget[heapleft]; m_vecDistTarget[heapleft] = m_vecDistTarget[f_first]; m_vecDistTarget[f_first] = swapInt; swapInt = m_vecScore[top]; m_vecScore[top] = m_vecScore[heapleft]; m_vecScore[heapleft] = m_vecScore[f_first]; m_vecScore[f_first] = swapInt; swapInt = m_vecScore2[top]; m_vecScore2[top] = m_vecScore2[heapleft]; m_vecScore2[heapleft] = m_vecScore2[f_first]; m_vecScore2[f_first] = swapInt; m_vecHash.push_back(hash); heapleft++; f_first++; selected++; f_amount--; } // heapify minparent = (heapleft + top + 2) / 2; element = top; while (element >= minparent) { child = 2 * element - top - 1; if (child > heapleft) // node has two children { if ((m_vecScore[child+1] < m_vecScore[child]) // second child has better score || ((m_vecScore[child+1] == m_vecScore[child]) && (m_vecScore2[child+1] < m_vecScore2[child]))) child--; } if ((m_vecScore[element] < m_vecScore[child]) // heap condition fulfilled || ((m_vecScore[element] == m_vecScore[child]) && (m_vecScore2[element] < m_vecScore2[child]))) break; // swap element and child swapPerm = m_vecPerms[element]; m_vecPerms[element] = m_vecPerms[child]; m_vecPerms[child] = swapPerm; swapInt = m_vecDistSource[element]; m_vecDistSource[element] = m_vecDistSource[child]; m_vecDistSource[child] = swapInt; swapInt = m_vecDistTarget[element]; m_vecDistTarget[element] = m_vecDistTarget[child]; m_vecDistTarget[child] = swapInt; swapInt = m_vecScore[element]; m_vecScore[element] = m_vecScore[child]; m_vecScore[child] = swapInt; swapInt = m_vecScore2[element]; m_vecScore2[element] = m_vecScore2[child]; m_vecScore2[child] = swapInt; // continue heapify on child element = child; } } return selected; } void Phylo::buildHeap(int f_left) { int top = m_vecPerms.size() - 1; // index of the top element int minparent = (f_left + top + 2) / 2; // smallest element that is a parent int element; // index of an element int child; // index of the child // swap variables int swapInt; int* swapPerm; for (int i = minparent; i <= top; i++) //shift heap boundary towards heap top { // heapify element = i; while (element >= minparent) // not at bottom level { child = 2 * element - top - 1; if (child > f_left) // node has two children { if ((m_vecScore[child+1] < m_vecScore[child]) // second child has better score || ((m_vecScore[child+1] == m_vecScore[child]) && (m_vecScore2[child+1] < m_vecScore2[child]))) child--; } if ((m_vecScore[element] < m_vecScore[child]) // heap condition fulfilled || ((m_vecScore[element] == m_vecScore[child]) && (m_vecScore2[element] < m_vecScore2[child]))) break; // swap element and child swapPerm = m_vecPerms[element]; m_vecPerms[element] = m_vecPerms[child]; m_vecPerms[child] = swapPerm; swapInt = m_vecDistSource[element]; m_vecDistSource[element] = m_vecDistSource[child]; m_vecDistSource[child] = swapInt; swapInt = m_vecDistTarget[element]; m_vecDistTarget[element] = m_vecDistTarget[child]; m_vecDistTarget[child] = swapInt; swapInt = m_vecScore[element]; m_vecScore[element] = m_vecScore[child]; m_vecScore[child] = swapInt; swapInt = m_vecScore2[element]; m_vecScore2[element] = m_vecScore2[child]; m_vecScore2[child] = swapInt; // continue heapify on child element = child; } } } int Phylo::calcSecondaryScore(const int* f_perm) { // secondary score: average dist of nearest nodes not yet in tree int* dbest = new int[m_numInputGenomes]; int num = 0; int dist; int index; int score = 0; for (int i = 0; i < m_numInputGenomes; i++) dbest[i] = INT_MAX; for (int i = 0; i < m_numInputGenomes; i++) { if (m_visited[i]) continue; num++; dist = getDistance(f_perm, m_inputGenomes[i]); index = 0; while (dist > dbest[index]) index++; for (int j = m_numInputGenomes - 1; j > index; j--) dbest[j] = dbest[j-1]; dbest[index] = dist; } for (int i = 0; i < 3; i++) { if (i+1 == num) break; score += dbest[i]; } delete[] dbest; return score / m_wr; } void Phylo::getGoodMoves(int* f_perm, vector& f_moves) { int cyclelength; // length of the actual cycle int pos; // actual position in the cycle bool ori; // true if we go from left to right through reality edge int element; // value of the next element Operation op; // an operation we found // init some vars for (int i = 0; i < m_permSize; i++) m_inCycle[i] = false; for (int i = 0; i < m_permSize; i++) // use each potential cycle start { if (m_inCycle[i]) // we already visited this cycle continue; // create the cycle cyclelength = 0; pos = i; ori = true; while (!m_inCycle[pos]) { m_inCycle[pos] = true; m_cycle[cyclelength] = (ori? pos : -pos); // leaving the edge at this element element = (ori? f_perm[pos] : (pos == 0? f_perm[m_permSize - 1] : f_perm[pos - 1])); if (element > 0) element = (ori? (element == 1? m_permSize : element - 1) : (element == m_permSize? 1 : element + 1)); else { element = (ori? (element == -m_permSize? 1 : -element + 1) : (element == -1? m_permSize : -element - 1)); ori ^= 1; } // element is now the absolute value of the target element // ori indicates if we need the upper point (true) or the lower point (false) pos = m_element2Index[element]; if ((f_perm[pos] > 0) ^ ori) ori = false; else { pos = (pos == m_permSize - 1? 0 : pos + 1); ori = true; } cyclelength++; } // search in the cycle for good moves for (int i = 0; i < cyclelength - 1; i++) { for (int j = i+1; j < cyclelength; j++) { if (m_cycle[i] * m_cycle[j] < 0) // divergent edges -> 1_r-move { op.m_type = Operation::OPERATION_REVERSAL; op.m_edges[0] = abs(m_cycle[i]) + 1; op.m_edges[1] = abs(m_cycle[j]) + 1; f_moves.push_back(op); } if (m_revOnly) continue; for (int k = j+1; k < cyclelength; k++) { if (!cyclicSorted(abs(m_cycle[i]), abs(m_cycle[j]), abs(m_cycle[k]))) { // a 2-move is possible // search edges with same orientation if (m_cycle[i] * m_cycle[j] > 0) // same orientation { op.m_edges[0] = abs(m_cycle[j]) + 1; op.m_edges[1] = abs(m_cycle[i]) + 1; op.m_edges[2] = abs(m_cycle[k]) + 1; op.m_type = (m_cycle[i] * m_cycle[k] > 0? Operation::OPERATION_TRANSPOSITION : Operation::OPERATION_TRANSREVERSAL); } else { op.m_type = Operation::OPERATION_TRANSREVERSAL; if (m_cycle[i] * m_cycle[k] > 0) { op.m_edges[0] = abs(m_cycle[i]) + 1; op.m_edges[1] = abs(m_cycle[k]) + 1; op.m_edges[2] = abs(m_cycle[j]) + 1; } else { op.m_edges[0] = abs(m_cycle[k]) + 1; op.m_edges[1] = abs(m_cycle[j]) + 1; op.m_edges[2] = abs(m_cycle[i]) + 1; } } f_moves.push_back(op); } } } } } } void Phylo::get0rMoves(int* f_perm, vector& f_moves) { Operation op; // the actual operation op.m_type = Operation::OPERATION_REVERSAL; // we're only interested in reversals for (int i = 1; i < m_permSize; i++) { op.m_edges[0] = m_element2Index[i] + 1; if (f_perm[m_element2Index[i]] > 0) op.m_edges[0] == m_permSize? op.m_edges[0] = 1 : op.m_edges[0]++; op.m_edges[1] = m_element2Index[i+1] + 1; if (f_perm[m_element2Index[i+1]] < 0) op.m_edges[1] == m_permSize? op.m_edges[1] = 1 : op.m_edges[1]++; if (op.m_edges[0] != op.m_edges[1]) // else adjacency { if (op.m_edges[0] > m_permSize) op.m_edges[0] = 1; if (op.m_edges[1] > m_permSize) op.m_edges[1] = 1; f_moves.push_back(op); } } // handle last elementary interval separately because of cyclic index op.m_edges[0] = m_element2Index[m_permSize] + 1; if (f_perm[m_element2Index[m_permSize]] > 0) op.m_edges[0] == m_permSize? op.m_edges[0] = 1 : op.m_edges[0]++; op.m_edges[1] = m_element2Index[1] + 1; if (f_perm[m_element2Index[1]] < 0) op.m_edges[1] == m_permSize? op.m_edges[1] = 1 : op.m_edges[1]++; if (op.m_edges[0] != op.m_edges[1]) // else adjacency { if (op.m_edges[0] > m_permSize) op.m_edges[0] = 1; if (op.m_edges[1] > m_permSize) op.m_edges[1] = 1; f_moves.push_back(op); } } bool Phylo::findImprovement(int& f_splitedge, int& f_edge1, int& f_edge2) { int node; // node index vector nodestack; // stack with nodes on one side of the partitioning edge int side; // side of the partitioning (0: root side; 1 split node side) int edgeweight; // weight of the split edge int index; // translate edgepair to index Node* node1, *node2; // starting nodes of the edges where we want to build a new one int dist; // a calculated distance // check all possible split edges; edge 0 is always root edge, so don't split this for (int i = 1; i <= m_maxEdge; i++) { if (m_ITEdge2Node[i] == -1) // invalid edge continue; edgeweight = m_actTree->m_nodes[m_ITEdge2Node[i]]->m_edge->m_weight; // split the tree in two parts for (int j = 0; j < m_actTree->m_numNodes; j++) m_ITPartitioning[j] = -1; m_ITPartitioning[0] = 0; m_ITPartitioning[m_ITEdge2Node[i]] = 1; for (int j = 1; j < m_actTree->m_numNodes; j++) { if (m_ITPartitioning[j] != -1) continue; node = j; while (m_ITPartitioning[node] == -1) { nodestack.push_back(node); node = m_actTree->m_nodes[node]->m_father; } side = m_ITPartitioning[node]; for (unsigned int k = 0; k < nodestack.size(); k++) m_ITPartitioning[nodestack[k]] = side; nodestack.clear(); } // search for edge pairs that allow an improvement for (int j = 0; j <= m_maxEdge; j++) { if (m_ITEdge2Node[j] == -1) // invalid edge continue; if (m_ITPartitioning[m_ITEdge2Node[j]] != 0) continue; for (int k = 0; k < m_actTree->m_numNodes; k++) { if (k == i) // never use the nodes of the edge we erase continue; if (m_ITEdge2Node[k] == -1) // invalid edge continue; if (m_ITPartitioning[m_ITEdge2Node[k]] != 1) continue; index = getITIndex(j, k); if (m_ITLowerBound[index] >= edgeweight) // edges too far from each other continue; if (m_ITBestDist[index] < 0) // calculate the best distance { node1 = m_actTree->m_nodes[m_ITEdge2Node[j]]; node2 = m_actTree->m_nodes[m_ITEdge2Node[k]]; // distance between start nodes m_ITBestDist[index] = getDistance(node1->m_perm, node2->m_perm); m_ITBestCloudNodes[index].first = -1; m_ITBestCloudNodes[index].second = -1; // start node j vs cloud nodes k (k has always an edge) for (int l = 0; l < node2->m_edge->m_cloudSize; l++) { dist = getLowerBound(node1->m_perm, node2->m_edge->m_cloud[l]) + node2->m_edge->m_distSource[l] + node2->m_edge->m_distTarget[l] - node2->m_edge->m_weight; if (dist < m_ITBestDist[index]) dist = getDistance(node1->m_perm, node2->m_edge->m_cloud[l]) + node2->m_edge->m_distSource[l] + node2->m_edge->m_distTarget[l] - node2->m_edge->m_weight; if (dist < m_ITBestDist[index]) { m_ITBestDist[index] = dist; if (j < k) { // m_ITBestCloudNodes[index].first = -1; // this var is already set correctly m_ITBestCloudNodes[index].second = l; } else { m_ITBestCloudNodes[index].first = l; //m_ITBestCloudNodes[index].second = -1; // this var is already set correctly } } } // cloud nodes j vs start node k if (j != 0) // j has an edge { for (int l = 0; l < node1->m_edge->m_cloudSize; l++) { dist = getLowerBound(node1->m_edge->m_cloud[l], node2->m_perm) + node1->m_edge->m_distSource[l] + node1->m_edge->m_distTarget[l] - node1->m_edge->m_weight; if (dist < m_ITBestDist[index]) dist = getDistance(node1->m_edge->m_cloud[l], node2->m_perm) + node1->m_edge->m_distSource[l] + node1->m_edge->m_distTarget[l] - node1->m_edge->m_weight; if (dist < m_ITBestDist[index]) { m_ITBestDist[index] = dist; if (j < k) { m_ITBestCloudNodes[index].first = l; m_ITBestCloudNodes[index].second = -1; } else { m_ITBestCloudNodes[index].first = -1; m_ITBestCloudNodes[index].second = l; } } } } // cloud nodes j vs cloud nodes k if (j != 0) // both nodes have an edge { for (int l = 0; l < node1->m_edge->m_cloudSize; l++) { for (int m = 0; m < node2->m_edge->m_cloudSize; m++) { dist = getDistance(node1->m_edge->m_cloud[l], node2->m_edge->m_cloud[m]) + node1->m_edge->m_distSource[l] + node1->m_edge->m_distTarget[l] - node1->m_edge->m_weight + node2->m_edge->m_distSource[m] + node2->m_edge->m_distTarget[m] - node2->m_edge->m_weight; if (dist < m_ITBestDist[index]) dist = getDistance(node1->m_edge->m_cloud[l], node2->m_edge->m_cloud[m]) + node1->m_edge->m_distSource[l] + node1->m_edge->m_distTarget[l] - node1->m_edge->m_weight + node2->m_edge->m_distSource[m] + node2->m_edge->m_distTarget[m] - node2->m_edge->m_weight; if (dist < m_ITBestDist[index]) { m_ITBestDist[index] = dist; if (j < k) { m_ITBestCloudNodes[index].first = l; m_ITBestCloudNodes[index].second = m; } else { m_ITBestCloudNodes[index].first = m; m_ITBestCloudNodes[index].second = l; } } } } } } if (m_ITBestDist[index] < edgeweight) // we found an improvement { f_splitedge = i; f_edge1 = j; f_edge2 = k; return true; } } } } return false; } void Phylo::performImprovement(int f_splitedge, int f_edge1, int f_edge2) { int index = getITIndex(f_edge1, f_edge2); // index of the exact data int n1s = m_ITEdge2Node[f_edge1]; // start node of edge 1 (index) int n2s = m_ITEdge2Node[f_edge2]; // start node of edge 2 (index) int n1t = m_actTree->m_nodes[n1s]->m_father; // target node of edge 1 (index) int n2t = m_actTree->m_nodes[n2s]->m_father; // target node of edge 2 (index) int cloudindex1, cloudindex2; // indices of the cloud nodes of edge 1 and edge 2 int nsplit = m_ITEdge2Node[f_splitedge]; // index of start node of the split edge Node* node; // new node in the tree int delta = 0; // weight difference by the improvement step int oldMaxEdge = m_maxEdge; // old value for m_maxEdge int source, target; // source and target node of the new edge int t1, t2; // target of two edges int d1, d2, d3, d4, dei, dej; // some distances g_logger.log(PHYLO_DEBUG, "perform improvement:\n"); if (f_edge1 < f_edge2) g_logger.log(PHYLO_DEBUG, "remove edge %d, insert between edge %d.%d and edge %d.%d\n", f_splitedge, f_edge1, m_ITBestCloudNodes[index].first, f_edge2, m_ITBestCloudNodes[index].second); else g_logger.log(PHYLO_DEBUG, "remove edge %d, insert between edge %d.%d and edge %d.%d\n", f_splitedge, f_edge1, m_ITBestCloudNodes[index].second, f_edge2, m_ITBestCloudNodes[index].first); if (f_edge1 < f_edge2) { cloudindex1 = m_ITBestCloudNodes[index].first; cloudindex2 = m_ITBestCloudNodes[index].second; } else { cloudindex1 = m_ITBestCloudNodes[index].second; cloudindex2 = m_ITBestCloudNodes[index].first; } // if we must split edge1 or edge2, do it if (cloudindex1 != -1) // split edge 1 { // create the new node, insert into the tree node = new Node(); node->m_perm = m_actTree->m_nodes[n1s]->m_edge->m_cloud[cloudindex1]; node->m_father = n1t; m_actTree->m_nodes.push_back(node); m_actTree->m_node2input.push_back(-1); // delete the old edge, set new node as father delta -= m_actTree->m_nodes[n1s]->m_edge->m_weight; m_actTree->m_nodes[n1s]->m_edge->m_protected = cloudindex1; delete m_actTree->m_nodes[n1s]->m_edge; m_actTree->m_nodes[n1s]->m_father = m_actTree->m_numNodes; // create the edges createEdge(n1s); createEdge(m_actTree->m_numNodes); delta += m_actTree->m_nodes[n1s]->m_edge->m_weight; delta += m_actTree->m_nodes[m_actTree->m_numNodes]->m_edge->m_weight; // actualize some member variables target = m_actTree->m_numNodes; m_ITEdge2Node[f_edge1] = -1; m_ITEdge2Node.push_back(n1s); m_ITEdge2Node.push_back(m_actTree->m_numNodes); m_ITNode2Edge[n1s] = m_maxEdge + 1; m_ITNode2Edge.push_back(m_maxEdge + 2); m_maxEdge += 2; m_ITNodeDist.resize(getITIndex(m_actTree->m_numNodes, m_actTree->m_numNodes) + 1); for (int i = 0; i < m_actTree->m_numNodes; i++) m_ITNodeDist[getITIndex(i, m_actTree->m_numNodes)] = getLowerBound(m_actTree->m_nodes[i]->m_perm, node->m_perm); m_actTree->m_numNodes++; } else target = n1s; if (cloudindex2 != -1) // split edge 2 { // create the new node, insert into the tree node = new Node(); node->m_perm = m_actTree->m_nodes[n2s]->m_edge->m_cloud[cloudindex2]; node->m_father = n2t; m_actTree->m_nodes.push_back(node); m_actTree->m_node2input.push_back(-1); // delete the old edge, set new node as father delta -= m_actTree->m_nodes[n2s]->m_edge->m_weight; m_actTree->m_nodes[n2s]->m_edge->m_protected = cloudindex2; delete m_actTree->m_nodes[n2s]->m_edge; m_actTree->m_nodes[n2s]->m_father = m_actTree->m_numNodes; // create the edges createEdge(n2s); createEdge(m_actTree->m_numNodes); delta += m_actTree->m_nodes[n2s]->m_edge->m_weight; delta += m_actTree->m_nodes[m_actTree->m_numNodes]->m_edge->m_weight; // actualize some member variables source = m_actTree->m_numNodes; m_ITEdge2Node[f_edge2] = -1; m_ITEdge2Node.push_back(n2s); m_ITEdge2Node.push_back(m_actTree->m_numNodes); m_ITNode2Edge[n2s] = m_maxEdge + 1; m_ITNode2Edge.push_back(m_maxEdge + 2); m_maxEdge += 2; m_ITNodeDist.resize(getITIndex(m_actTree->m_numNodes, m_actTree->m_numNodes) + 1); for (int i = 0; i < m_actTree->m_numNodes; i++) m_ITNodeDist[getITIndex(i, m_actTree->m_numNodes)] = getLowerBound(m_actTree->m_nodes[i]->m_perm, node->m_perm); m_actTree->m_numNodes++; } else source = n2s; // delete the split edge delta -= m_actTree->m_nodes[nsplit]->m_edge->m_weight; delete m_actTree->m_nodes[nsplit]->m_edge; m_ITEdge2Node[f_splitedge] = -1; // invert the path (this also sets father and edge of nsplit correctly) invertPath(source, nsplit); // create the new edge m_actTree->m_nodes[source]->m_father = target; createEdge(source); m_ITEdge2Node.push_back(source); m_ITNode2Edge[source] = ++m_maxEdge; delta += m_actTree->m_nodes[source]->m_edge->m_weight; m_actTree->m_weight += delta; // update the lower bounds for the node pairs m_ITLowerBound.resize(getITIndex(m_maxEdge + 1, m_maxEdge + 1) + 1); m_ITBestDist.resize(getITIndex(m_maxEdge + 1, m_maxEdge + 1) + 1); for (int i = oldMaxEdge + 1; i <= m_maxEdge; i++) // for all new edges { t1 = (m_actTree->m_nodes[m_ITEdge2Node[i]]->m_father == -1? i : m_actTree->m_nodes[m_ITEdge2Node[i]]->m_father); dei = (m_actTree->m_nodes[m_ITEdge2Node[i]]->m_father == -1? 0 : m_actTree->m_nodes[m_ITEdge2Node[i]]->m_edge->m_weight); for (int j = 0; j <= i; j++) // for all other edges { if (m_ITEdge2Node[j] == -1) // invalid edge continue; index = getITIndex(i, j); t2 = (m_actTree->m_nodes[m_ITEdge2Node[j]]->m_father == -1? j : m_actTree->m_nodes[m_ITEdge2Node[j]]->m_father); dej = (m_actTree->m_nodes[m_ITEdge2Node[j]]->m_father == -1? 0 : m_actTree->m_nodes[m_ITEdge2Node[j]]->m_edge->m_weight); d1 = m_ITNodeDist[getITIndex(m_ITEdge2Node[i], m_ITEdge2Node[j])]; d2 = m_ITNodeDist[getITIndex(m_ITEdge2Node[i], t2)]; d3 = m_ITNodeDist[getITIndex(t1, m_ITEdge2Node[j])]; d4 = m_ITNodeDist[getITIndex(t1, t2)]; if (d1 + d4 > d2 + d3) m_ITLowerBound[getITIndex(i, j)] = (d1 + d4 - dei - dej) / 2; else m_ITLowerBound[getITIndex(i, j)] = (d2 + d3 - dei - dej) / 2; m_ITBestDist[index] = -1; } } g_logger.log(PHYLO_INFO, "Improvement step decreased tree weight by %d\n", -delta); } void Phylo::invertPath(int f_source, int f_target) { stack nodestack; // nodes on the path int node = f_source; // the actual node int predecessor; // predecessor of node in the path Edge* edge; // edge to invert int* swapInt; // needed to swap double-arrays // push path on stack while (node != f_target) { nodestack.push(node); node = m_actTree->m_nodes[node]->m_father; } // invert the path while (!nodestack.empty()) { predecessor = nodestack.top(); nodestack.pop(); edge = m_actTree->m_nodes[predecessor]->m_edge; // invert the edge swapInt = edge->m_distSource; edge->m_distSource = edge->m_distTarget; edge->m_distTarget = swapInt; // assign edge to the new node m_actTree->m_nodes[node]->m_father = predecessor; m_actTree->m_nodes[node]->m_edge = edge; m_ITEdge2Node[m_ITNode2Edge[predecessor]] = node; m_ITNode2Edge[node] = m_ITNode2Edge[predecessor]; node = predecessor; } } void Phylo::repairClouds() { g_logger.log(PHYLO_DEBUG, "repairClouds called\n"); // init some variables m_visited = new bool[m_numInputGenomes]; for (int i = 0; i < m_numInputGenomes; i++) m_visited[i] = true; if (m_revOnly) m_branchparam = 5; else m_branchparam = 2; // repair the clouds for (int i = 0; i < m_actTree->m_numNodes; i++) { if ((m_actTree->m_nodes[i]->m_father != -1) && (m_actTree->m_nodes[i]->m_edge == NULL)) createEdge(i); } // clean up delete[] m_visited; m_visited = NULL; } void Phylo::relaxTree() { g_logger.log(PHYLO_DEBUG, "relaxTree called\n"); int degree; // degree of a node bool root; // true if the actual node is the root node int* neighbors = new int[m_actTree->m_numNodes + 2 * m_numInputGenomes]; // neigbors of the actual node int* perm; // a permutation Node* node; // a node for (int i = 0; i < m_actTree->m_numNodes; i++) { // calculate the degree degree = 0; if (m_actTree->m_nodes[i]->m_father == -1) root = true; else { neighbors[0] = m_actTree->m_nodes[i]->m_father; degree++; root = false; } for (int j = 0; j < m_actTree->m_numNodes; j++) { if (m_actTree->m_nodes[j]->m_father == i) neighbors[degree++] = j; } if ((m_actTree->m_node2input[i] != -1) && (degree > 1)) // make it a leaf { // create a copy of the taxon perm = g_permPool->getPerm(); for (int j = 0; j < m_permSize; j++) perm[j] = m_actTree->m_nodes[i]->m_perm[j]; node = new Node(); node->m_perm = perm; if (root) { node->m_father = i; for (int j = 0; j < degree; j++) m_actTree->m_nodes[neighbors[j]]->m_father = m_actTree->m_numNodes; } else { node->m_father = neighbors[0]; node->m_edge = m_actTree->m_nodes[i]->m_edge; m_actTree->m_nodes[i]->m_edge = NULL; m_actTree->m_nodes[i]->m_father = m_actTree->m_numNodes; for (int j = 1; j < degree; j++) m_actTree->m_nodes[neighbors[j]]->m_father = m_actTree->m_numNodes; } m_actTree->m_nodes.push_back(node); m_actTree->m_node2input.push_back(-1); m_actTree->m_numNodes++; } else if (degree == 2) { if (root) // create new root { m_actTree->m_nodes[neighbors[0]]->m_father = -1; delete m_actTree->m_nodes[neighbors[0]]->m_edge; m_actTree->m_nodes[neighbors[0]]->m_edge = NULL; } else { delete m_actTree->m_nodes[i]->m_edge; m_actTree->m_nodes[i]->m_edge = NULL; } m_actTree->m_nodes[neighbors[1]]->m_father = neighbors[0]; delete m_actTree->m_nodes[neighbors[1]]->m_edge; m_actTree->m_nodes[neighbors[1]]->m_edge = NULL; // move last node to the front for (int j = 0; j < m_actTree->m_numNodes; j++) { if (m_actTree->m_nodes[j]->m_father == m_actTree->m_numNodes - 1) m_actTree->m_nodes[j]->m_father = i; } delete m_actTree->m_nodes[i]; m_actTree->m_nodes[i] = m_actTree->m_nodes[m_actTree->m_numNodes-1]; m_actTree->m_node2input[i] = m_actTree->m_node2input[m_actTree->m_numNodes-1]; m_actTree->m_nodes.pop_back(); m_actTree->m_node2input.pop_back(); m_actTree->m_numNodes--; i--; // continue with the replacement node } else if (degree > 3) // split node { // create a copy of the node perm = g_permPool->getPerm(); for (int j = 0; j < m_permSize; j++) perm[j] = m_actTree->m_nodes[i]->m_perm[j]; node = new Node(); node->m_perm = perm; node->m_father = i; for (int j = 2; j < degree; j++) m_actTree->m_nodes[neighbors[j]]->m_father = m_actTree->m_numNodes; m_actTree->m_nodes.push_back(node); m_actTree->m_node2input.push_back(-1); m_actTree->m_numNodes++; } } delete[] neighbors; } int Phylo::getDistance(const int* f_perm1, const int* f_perm2) { double lb; // lower bound for the distance int result1 = 0; // distance measured from source to target int result2 = 0; // distance measured from target to source const vector* sorting; // a sorting sequence if (m_revOnly) return m_revdist.getDistance(f_perm1, f_perm2) * m_wr; else { m_minswrt.setOrigin(f_perm1); m_minswrt.setTarget(f_perm2); lb = m_minswrt.getLowerBound(); m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int i = 0; i < sorting->size(); i++) { if ((*sorting)[i].m_type == Operation::OPERATION_REVERSAL) result1 += m_wr; else result1 += m_wt; } if (result1 <= (int)(lb + PHYLO_EPS)) return result1; m_minswrt.setOrigin(f_perm2); m_minswrt.setTarget(f_perm1); m_minswrt.sort(); sorting = m_minswrt.getResult(); for (unsigned int i = 0; i < sorting->size(); i++) { if ((*sorting)[i].m_type == Operation::OPERATION_REVERSAL) result2 += m_wr; else result2 += m_wt; } return (result1 < result2? result1 : result2); } } int Phylo::getLowerBound(const int* f_perm1, const int* f_perm2) { if (m_revOnly) // we have an exact algorithm here :-) return getDistance(f_perm1, f_perm2); else { m_minswrt.setOrigin(f_perm1); m_minswrt.setTarget(f_perm2); return (int)(m_minswrt.getLowerBound() + PHYLO_EPS); } } /*************************************************************************** * debugging methods ***************************************************************************/ void Phylo::debugCTVars() { g_logger.log(PHYLO_DEBUG, "---- debugCTVars ----\n\n"); g_logger.log(PHYLO_DEBUG, "max edge: %d\n\n", m_maxEdge); g_logger.log(PHYLO_DEBUG, "nodeDist\n"); for (int i = 0; i < m_numInputGenomes; i++) { for (int j = 0; j < m_actTree->m_numNodes; j++) g_logger.log(PHYLO_DEBUG, "%2.2f ", m_nodeDist[i][j]); g_logger.log(PHYLO_DEBUG, "\n"); } g_logger.log(PHYLO_DEBUG, "\n"); g_logger.log(PHYLO_DEBUG, "edge->node:\n"); for (int i = 0; i < 3 * m_numInputGenomes - 5; i++) { if (i < 10) g_logger.log(PHYLO_DEBUG, " "); g_logger.log(PHYLO_DEBUG, "%d ", i); } g_logger.log(PHYLO_DEBUG, "\n"); for (int i = 0; i < 3 * m_numInputGenomes - 5; i++) { if ((m_edge2Node[i] < 10) && (m_edge2Node[i] >= 0)) g_logger.log(PHYLO_DEBUG, " "); g_logger.log(PHYLO_DEBUG, "%d ", m_edge2Node[i]); } g_logger.log(PHYLO_DEBUG, "\n\n"); for (int i = 0; i < m_numInputGenomes; i++) { g_logger.log(PHYLO_DEBUG, "input genome %d (visited = %d): bestEdge = %d\n", i, m_visited[i], m_bestEdge[i]); if (m_visited[i]) { g_logger.log(PHYLO_DEBUG, "\n"); continue; } g_logger.log(PHYLO_DEBUG, "steiner dist:\n"); for (int j = 0; j <= m_maxEdge; j++) { if (j < 10) g_logger.log(PHYLO_DEBUG, " "); g_logger.log(PHYLO_DEBUG, " %d ", j); } g_logger.log(PHYLO_DEBUG, "\n"); for (int j = 0; j <= m_maxEdge; j++) { if (m_steinerDist[i][j].m_dist < 10.0) g_logger.log(PHYLO_DEBUG, " "); g_logger.log(PHYLO_DEBUG, " %2.2f (", m_steinerDist[i][j].m_dist); if ((m_steinerDist[i][j].m_node < 10) && (m_steinerDist[i][j].m_node >= 0)) g_logger.log(PHYLO_DEBUG, " "); g_logger.log(PHYLO_DEBUG, "%d) ", m_steinerDist[i][j].m_node); } g_logger.log(PHYLO_DEBUG, "\n\n"); } g_logger.log(PHYLO_DEBUG, "\n---------------------\n"); } bool Phylo::checkPerm(const int* f_perm) const { bool* visited = new bool[m_permSize+1]; for (int i = 0; i <= m_permSize; i++) visited[i] = false; for (int i = 0; i < m_permSize; i++) { if ((abs(f_perm[i]) == 0) || (abs(f_perm[i]) > m_permSize) || (visited[abs(f_perm[i])])) { delete[] visited; return false; } visited[abs(f_perm[i])] = true; } delete[] visited; return true; } bool Phylo::checkPerm(int f_size, const int* f_perm) const { bool* visited = new bool[f_size+1]; for (int i = 0; i <= f_size; i++) visited[i] = false; for (int i = 0; i < f_size; i++) { if ((abs(f_perm[i]) == 0) || (abs(f_perm[i]) > f_size) || (visited[abs(f_perm[i])])) { delete[] visited; return false; } visited[abs(f_perm[i])] = true; } delete[] visited; return true; } bool Phylo::checkVecPerms() { for (unsigned int i = 0; i < m_vecPerms.size() ; i++) { for (unsigned int j = i+1; j < m_vecPerms.size(); j++) { if (m_vecPerms[i] == m_vecPerms[j]) { g_logger.log(PHYLO_DEBUG, "found permutation %X twice\n", m_vecPerms[i]); return false; } } } return true; } void Phylo::debug() { m_actTree = m_bestTree; cerr << "**** Phylo::debug() called\n"; cerr << "Tree:\n"; cerr << "permSize = " << m_actTree->m_permSize << ", numNodes = " << m_actTree->m_numNodes << ", weight = " << m_actTree->m_weight << endl; for (int i = 0; i < m_actTree->m_numNodes; i++) { cerr << "Node " << i << ":\n"; cerr << "node2input = " << m_actTree->m_node2input[i] << endl; if (m_actTree->m_nodes[i] == NULL) cerr << "NULL\n"; else { cerr << "perm = "; for (int j = 0; j < m_actTree->m_permSize; j++) cerr << m_actTree->m_nodes[i]->m_perm[j] << " "; cerr << endl; cerr << "father = " << m_actTree->m_nodes[i]->m_father << endl; if (m_actTree->m_nodes[i]->m_edge == NULL) cerr << "edge = NULL\n"; else cerr << "edge != NULL\n"; cerr << "protectPerm = " << m_actTree->m_nodes[i]->m_protectPerm << endl; } } cerr << "numInputGenome = " << m_numInputGenomes << endl; cerr << "****\n"; } /***************************************************************************/ } // end namespace phylo phylo-1.0.6/phylo/tree.cpp0000644000175000017500000000274711434510050012373 00000000000000/** * filename: tree.cpp * author: Martin Bader * begin: 13.12.2006 * last change: 23.08.2007 * * Implementation of tree.h * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "tree.h" #include #include "node.h" namespace phylo { using namespace std; /*************************************************************************** * public methods ***************************************************************************/ Tree::Tree() { m_permSize = 0; m_numNodes = 0; m_weight = 0; } Tree::Tree(int f_permSize) { m_permSize = f_permSize; m_numNodes = 0; m_weight = 0; } Tree::~Tree() { for (unsigned int i = 0; i < m_nodes.size(); i++) delete m_nodes[i]; } /***************************************************************************/ } // end namespace phylo phylo-1.0.6/phylo/logger.cpp0000644000175000017500000000367711434510050012716 00000000000000/** * filename: logger.cpp * author: Martin Bader * begin: 13.12.2006 * last change: 08.03.2010 * * Implementation of logger.h * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "logger.h" #include #include #include namespace phylo { using namespace std; Logger g_logger; /*************************************************************************** * public methods ***************************************************************************/ Logger::Logger() { m_minLevel = PHYLO_INFO; m_outstreams = new FILE*[PHYLO_ERROR+1]; for (int i = 0; i <= PHYLO_ERROR; i++) m_outstreams[i] = stdout; } Logger::~Logger() { delete[] m_outstreams; } void Logger::setOutstream(Loglevel f_level, FILE* f_stream) { m_outstreams[f_level] = f_stream; } void Logger::setMinLoglevel(Loglevel f_level) { m_minLevel = f_level; } void Logger::log(Loglevel f_level, const char* f_message, ...) { va_list argpointer; // pointer to the arguments if (f_level >= m_minLevel) { va_start(argpointer, f_message); // set the pointer vfprintf(m_outstreams[f_level], f_message, argpointer); va_end(argpointer); } } /***************************************************************************/ } // end namespace phylo phylo-1.0.6/phylo/README0000644000175000017500000000431411434510050011600 00000000000000phylo ===== phylo - phylogenetic reconstruction based on the weighted reversal and transposition distance. phylo contains of two parts: 1. the program itself, which is compiled into a library. 2. a tiny frontend that calls the library. The frontend: Call the program with the following parameters. phylo [OPTIONS] available options: -h Just print some help information (ignore all other options) -w wr wt Set weights to wr (for reversals) and wt (for transpositions). If you use reversal only distance, call -w wr inf. (default: -w 1 inf). Note that the weights must be integer. -v x Set the output (verbosity) level to x. -v 0 produces the most output, while -v 3 only reports serious errors. (default: -v 1) -t If this parameter is set, the input file is a tree instead of a set of permutations, so only the improvement steps will be performed. -f name Load the file with the given name. This option is required. -s x If this parameter is set, the tree is only created from starting node x. -i [n|t|m|tm] Set he improvement technique to use. t means topology improvement, m means median improvement, tm means first using t then m, n means no improvement. (default: -i tm) -o name If this parameter is set, the best found tree will be written to a file with the given name. The input file consists of the specifications of several genomes (as signed permutations). Each genome consists of a line > genome name and a line containing a signed permutation. Lines beginning with # are comments. As an example, you can call ../../bin/phylo -w 1 2 -f campanulaceae The library: The functions provided by the library are documented in minswrt.h in the include directory. As example of how to use the library, you can have a look at minswrt/start.cpp. The interesting part is in the main function. Copyright: ========== Copyright (C) 2007-2010 Martin Bader This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions. For details about the licence, read the file COPYING phylo-1.0.6/phylo/node.cpp0000644000175000017500000000275611434510050012361 00000000000000/** * filename: node.cpp * author: Martin Bader * begin: 13.12.2006 * last change: 01.07.2009 * * Implementation of tree.h * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "node.h" #include #include "edge.h" #include "pools.h" namespace phylo { using namespace std; extern PermPool* g_permPool; /*************************************************************************** * public methods ***************************************************************************/ Node::Node() { m_perm = NULL; m_father = -1; m_edge = NULL; m_protectPerm = false; } Node::~Node() { if (!m_protectPerm) { g_permPool->freePerm(m_perm); } if (m_edge != NULL) delete m_edge; } /***************************************************************************/ } // end namespace phylo phylo-1.0.6/phylo/campanulaceae0000644000175000017500000001146211434510050013424 00000000000000>trachelium 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -53 -52 -51 -50 -49 37 38 39 40 -35 -34 -33 -32 -31 -30 -29 -28 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 -55 -54 -105 -104 -103 -102 -101 -100 -99 -98 -97 >campanula 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -53 -52 -51 -50 -49 -39 -38 -37 40 -35 -34 -33 -32 -31 -30 -29 -28 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 -55 -54 -105 -104 -103 -102 -101 -100 -99 -98 -97 >adenophora 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -53 -52 -51 -50 -49 -39 -38 -37 28 29 30 31 32 33 34 35 40 26 27 -44 -43 -42 -41 45 46 47 48 -36 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 -55 -54 -105 -104 -103 -102 -101 -100 -99 -98 -97 >symphyandra 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -39 -38 -37 49 50 51 52 53 40 -35 -34 -33 -32 -31 -30 -29 -28 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 -55 -54 -105 -104 -103 -102 -101 -100 -99 -98 -97 >legousia 1 2 3 4 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -35 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 5 6 7 8 -55 -54 -53 -105 -104 -103 -102 -101 -100 -99 -98 28 29 30 31 32 33 34 -40 -39 -38 -37 49 50 51 52 -97 >asyneuma 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -56 -55 -54 -53 -60 -59 -58 -57 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -35 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 90 91 92 93 94 95 96 -105 -104 -103 -102 -101 -100 -99 -98 28 29 30 31 32 33 34 -40 -39 -38 -37 49 50 51 52 -97 >triodanus 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -60 -59 -58 -57 -56 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 -35 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 90 91 92 93 94 95 96 -55 -54 -53 -105 -104 -103 -102 -101 -100 -99 -98 28 29 30 31 32 33 34 -40 -39 -38 -37 49 50 51 52 -97 >wahlenbergia 1 2 3 4 5 6 7 8 9 10 11 -60 -59 -58 -57 -56 -53 -52 -51 -50 -49 37 38 39 40 -35 -34 -33 -32 -31 -30 -29 -28 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 54 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 -84 77 78 79 80 81 82 83 91 92 93 94 95 96 -55 -105 -104 -103 -102 -101 -100 -99 -98 -97 >merciera 1 2 3 4 5 6 7 8 9 10 49 50 51 52 53 28 29 30 31 32 33 34 35 -40 -39 -38 -37 -60 -59 -58 -57 -56 11 12 13 14 15 -76 -75 -74 -73 -72 -71 -70 -69 -68 -67 -66 -65 -64 -63 -62 -61 -27 -26 -44 -43 -42 -41 45 46 47 48 -36 54 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -90 -89 -88 -87 -86 -85 77 78 79 80 81 82 83 84 91 92 93 94 95 96 -55 -105 -104 -103 -102 -101 -100 -99 -98 -97 >codonopsis 1 2 3 4 5 6 7 8 -36 -35 -34 -33 -32 -31 -30 -29 -28 -27 -26 -25 -24 -23 -22 -21 -20 -19 -18 -15 -14 -13 -12 -11 -10 -9 40 56 57 58 59 60 37 38 39 -44 -43 -42 -41 45 46 47 48 49 50 51 52 53 16 17 54 55 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 -96 -95 -94 -93 -92 -91 -90 -89 -88 -87 -86 -85 -84 -83 -82 -81 -80 -79 -78 -77 -105 -104 -103 -102 -101 -100 -99 -98 -97 >cyananthus 1 2 3 4 5 6 7 8 28 -36 -35 -34 -33 -32 -31 -30 -29 -27 -26 40 56 57 58 59 60 37 38 39 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -15 -14 -13 -12 -11 -10 -9 -44 -43 -42 -41 45 46 47 48 -55 -54 -53 -52 -51 -50 -49 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 -105 -104 -103 -102 -101 -100 -99 -98 -97 >platycodon 1 8 2 3 4 5 29 30 31 32 33 34 35 36 -56 -55 -54 -53 -52 -51 -50 -28 -27 -26 9 -49 -48 -47 -46 -45 41 42 43 44 37 38 39 40 16 17 18 19 20 21 22 23 24 25 10 11 12 13 14 15 57 58 59 6 7 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 -105 -104 -103 -102 -101 -100 -99 -98 -97 >tobacco 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 phylo-1.0.6/phylo/node.h0000644000175000017500000000370211434510050012016 00000000000000/** * filename: node.h * author: Martin Bader * begin: 13.12.2006 * last change: 01.07.2009 * * This class represents a node in the phylogenetic tree. * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef NODE_H_ #define NODE_H_ namespace phylo { // forward declarations class Edge; /** * Data of a single node in the tree. */ class Node { /*********************************************************************** * member variables ***********************************************************************/ public: /** the permutation */ int* m_perm; /** index of the father node (-1 for root node) */ int m_father; /** the edge to the father node */ Edge* m_edge; /** Indicates whether m_perm must be preserved when deleting the node */ bool m_protectPerm; /*********************************************************************** * methods ***********************************************************************/ public: /** * Constructor. */ Node(); /** * Destructor. Note that the permutation contained in the node will not be * deleted. */ ~Node(); }; /***************************************************************************/ } // end namespace phylo #endif /*NODE_H_*/ phylo-1.0.6/phylo/tree.h0000644000175000017500000000441011434510050012025 00000000000000/** * filename: tree.h * author: Martin Bader * begin: 13.12.2006 * last change: 23.08.2007 * * This class represents a phylogenetic tree, plus some functionality. * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef TREE_H_ #define TREE_H_ #include namespace phylo { // forward declarations class Node; /** * Contains the tree data, and all functions for handling the tree. */ class Tree { /*********************************************************************** * member variables ***********************************************************************/ public: /** the size of a permutation */ int m_permSize; /** the number of nodes in the tree */ int m_numNodes; /** the nodes in the tree */ std::vector m_nodes; /** mapping treenodes -> input genomes; -1 means steiner node */ std::vector m_node2input; /** the weight of the tree */ int m_weight; /*********************************************************************** * methods ***********************************************************************/ public: /** * Constructor. */ Tree(); /** * Constructor setting the permutation size * @param f_permSize the permutation size */ Tree(int f_permSize); /** * Destructor. Deletes the tree data and all internal (Steiner) nodes. * Permutations from the input genomes will not be deleted. */ ~Tree(); }; /***************************************************************************/ } // end namespace phylo #endif /*TREE_H_*/ phylo-1.0.6/phylo/pools.cpp0000644000175000017500000000351411434510050012561 00000000000000/** * filename: pools.cpp * author: Martin Bader * begin: 13.12.2006 * last change: 01.07.2009 * * Implementation of pools.h * * Copyright (C) 2007-2009 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "pools.h" #include namespace phylo { using namespace std; PermPool* g_permPool; /*************************************************************************** * public methods ***************************************************************************/ PermPool::PermPool() { m_permSize = 0; m_perms.reserve(1024); } PermPool::~PermPool() { for (unsigned int i = 0; i < m_perms.size(); i++) delete[] m_perms[i]; } void PermPool::init(int f_size) { // delete old perms (if there are any) for (unsigned int i = 0; i < m_perms.size(); i++) delete[] m_perms[i]; m_perms.clear(); // set the new size m_permSize = f_size; } int* PermPool::getPerm() { int* result; if (m_perms.size() > 0) { result = m_perms[m_perms.size()-1]; m_perms.pop_back(); } else result = new int[m_permSize]; return result; } /***************************************************************************/ } // end namespace phylo phylo-1.0.6/phylo/COPYING0000644000175000017500000010451311434510050011755 00000000000000 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice. Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10. 9. Acceptance Not Required for Having Copies. You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so. 10. Automatic Licensing of Downstream Recipients. Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License. An "entity transaction" is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party's predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts. You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it. 11. Patents. A "contributor" is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor's "contributor version". A contributor's "essential patent claims" are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, "control" includes the right to grant patent sublicenses in a manner consistent with the requirements of this License. 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You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007. Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law. 12. No Surrender of Others' Freedom. If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program. 13. Use with the GNU Affero General Public License. Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such. 14. Revised Versions of this License. The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation. If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program. Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version. 15. Disclaimer of Warranty. THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 16. Limitation of Liability. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 17. Interpretation of Sections 15 and 16. If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read . phylo-1.0.6/phylo/Makefile.in0000644000175000017500000005276011434510065013003 00000000000000# Makefile.in generated by automake 1.11.1 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, # Inc. # This Makefile.in is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; without # even the implied warranty of MERCHANTABILITY or FITNESS FOR A # PARTICULAR PURPOSE. @SET_MAKE@ VPATH = @srcdir@ pkgdatadir = $(datadir)/@PACKAGE@ pkgincludedir = $(includedir)/@PACKAGE@ pkglibdir = $(libdir)/@PACKAGE@ pkglibexecdir = $(libexecdir)/@PACKAGE@ am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd 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Contains the tree + functionality. * * Copyright (C) 2007-2008 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef PHYLO_H_ #define PHYLO_H_ #include #include #include #include namespace phylo { // forward declarations class Edge; class Node; class Tree; /** * This struct stores the index of a steiner node and the increment of * distance if we use this steiner node with a given input node. */ struct SteinerDist { int m_node; // index of the cloud node int m_dist; // increment of the distance }; /** * The main class. Contains the data, and all functions for constructing and * handling the tree. */ class Phylo { /*********************************************************************** * member variables ***********************************************************************/ protected: /** the different states of the program: * 0: nothing initialized * 1: input perms set, pools initialized * 2: tree constructed, result available in m_bestTree (weights can be * corrupted) * 3: tree constructed, results available in m_bestTree */ int m_state; /** the number of input genomes */ int m_numInputGenomes; /** the size of a permutation */ int m_permSize; /** the input permutation array */ int** m_inputGenomes; /** the genome names */ char** m_genomeNames; /** the actual tree we're working on */ Tree* m_actTree; /** the best tree we found so far */ Tree* m_bestTree; /** the weight of a reversal */ int m_wr; /** the weight of an (inverted) transposition */ int m_wt; /** if true, reversals are the only allowed operation */ bool m_revOnly; /** Needed to calculate distances */ minswrt::MinSWRT m_minswrt; /** Calculates reversal only distances */ revDist::RevDist m_revdist; /** sometimes we need the mapping element->index for a permutaion. Use * this variable to store it to avoid frewuent memory reallocation. */ int* m_element2Index; /** Median solver */ median::Median m_medianSolver; // the following variables are needed to store information while creating // the tree; initializing and freeing memory is done in the createTree // methods /** input genomes already in the tree (also used in improveTree because * needed for secondary score) */ bool* m_visited; /** distances from input nodes to tree nodes */ int** m_nodeDist; /** the best input node to add to the tree */ int m_bestInput; /** store for each input node the so far found best edge */ int* m_bestEdge; /** mapping from edge indices to source node indices (if -1, edge invalid) */ int* m_edge2Node; /** store for each node and each edge the increment of distance and the * optimal steiner node */ SteinerDist** m_steinerDist; /** the current max edge index */ int m_maxEdge; // the following variables are needed in generateEdgeCuttedPaths and // the related subroutines. Initializing and freeing the memory is done // in createEdgeCuttedPaths /** number of parallel paths */ unsigned int m_branchfactor; /** parameter to control the branchfactor */ unsigned int m_branchparam; /** the target of the edge */ int* m_targetPerm; /** mapping target permutation -> id */ int* m_mapping; /** all permutation candidates */ vector m_vecPerms; /** distances to source permutation */ vector m_vecDistSource; /** distances to target permutation */ vector m_vecDistTarget; /** scores of the different blocks of permutations, * or of the different perms (new strategy) */ vector m_vecScore; /** part two of the score */ vector m_vecScore2; /** hash values of the accepted permutations; the hash function is * invariant to cyclic shifts and the reflection */ vector m_vecHash; /** Indicates if an edge is already in a cycle */ bool* m_inCycle; /** the edges of a cycle */ int* m_cycle; // The following variables are needed for improveTree() and subroutines. // They are initialized and cleared there. /** pairwise node distances; positions are coded with a diagonalization, * distance between nodes i and j can be found at position * (max(f_i, f_j)^2 + max(f_i, f_j)) / 2 + min(f_i, f_j) . This formula is provided * in the function getITIndex. */ vector m_ITNodeDist; /** lower bounds for edge pairs; access see m_ITNodeDist */ vector m_ITLowerBound; /** best distances for edge pairs; access see m_ITNodeDist */ vector m_ITBestDist; /** the clouds that induced the best distances for each edge pair; * access see m_ITNodeDist; the first cloud node is always the one of the * edge with the lower index */ vector > m_ITBestCloudNodes; /** indicates for each edge a parent node */ vector m_ITEdge2Node; /** inverse to m_ITEdge2Node */ vector m_ITNode2Edge; /** partitioning of the tree */ vector m_ITPartitioning; /*********************************************************************** * methods ***********************************************************************/ public: /** * Constructor. */ Phylo(); /** * Destructor. */ ~Phylo(); /** * Sets the input genomes. This automatically deletes old results. Note * that old genomes will NOT be deleted. * The first two parameters are the number of input genomes and the size * (number of elements) of each genome. The third parameter is an array * of size f_numGenomes, containing the genomes as permutations. Each * permutation is an int-array of size m_genomeSize, containing all * integers from 1 to m_genomeSize plus additional sign. * You can check if the input genomes contain correct data. For doing so, * set f_check to true, and the function will return true if the data is * correct. If f_check is false, the function will always return true. * @param f_numGenomes number of genomes * @param f_genomeSize size of a single genome * @param f_genomes the genomes (as array of permutations) * @param f_check if true, do a data check * @return result of the data check */ bool setGenomes(int f_numGenomes, int f_genomeSize, int** f_genomes, bool f_check = false); /** * Sets the genome names. This is not necessary, but it might make the * output more readable. The names are in a char-array that must have the * correct size. Any previously set name arrays will be overwritten but not * deleted. * @param f_names the array with the genome names */ void setGenomeNames(char** f_names); /** * Reads a file with genome information. The number of permutations will * be written to f_numPerms, the permutation size to f_permSize, the * permutations to f_perms, and the permutation names to f_names. The return * value is true if the file could be read successfully, false otherwise. * If false will be returned, f_numPerms and f_permSize will be set to -1, * while f_perms and f_names will be set to NULL. * This function contains no integrity check for the permutations. * @param f_filename name of the file to open * @param f_numPerms number of permutations will be written to here * @param f_permSize permutation size will be written to here * @param f_perms permutations will be written to here * @param f_names permutation names will be written to here * @return true if reading of the file was successful */ static bool readGenomesFromFile(const char* f_filename, int &f_numPerms, int &f_permSize, int** &f_perms, char** &f_names); /** * Reads in a tree from a file. This automatically deletes old results * and overwrites old parameters. Note that old genomes will NOT be * deleted. * This function contains error checking for the input file, in case of * failure false will be returned. If the function is successfull, * the permutation size will be written to f_permSize and the number of * original input permutations (i.e. the given taxa of the tree * reconstruction) will be written to f_numPerms. * As this program never deletes input genomes, a pointer to the input * permutation array will be written to f_inputGenomes * * The file format: * Lines beginning with # are comments * If the tree is NULL, the first line that is not a comment must be NULL * The file contains general information about the tree, and information * about its nodes. General information lines look like this: * tag_of_field: data * The following lines can occur: * num perms: x // number of permutations in the tree, required * num input genomes: x // number of input genomes, required * perm size: x // number of elements in a permutation, required * wr wt: x y // weight of a reversal and an (inverted) transposition, * set y=inf if reversal only distance measure * weight: x // weight of the tree * Each node is between lines and . Before setting the first node, * num perms, num input genomes, and perm size must be set. A node contains * information about its data and can contain an edge field where the edge * data of the node is stored. The following lines can occur: * index: x // index of the node, required * input genome: true|false // true if the node is an input genome, required * name: sss // name of the genome (if it is an input genome) * perm: * pi_1 pi_2 ... pi_n // the signed permutation, required * connected to: x // the father node of this node, set to -1 if this is * // the root node, required * The edge of a node is between the lines and and can contain * the following lines: * weight: x // weight of the edge * cloud size: x // number of nodes in the cloud * cloud: * pi1_1 pi1_2 ... pi1_n * ... * pim_1 pim_2 ... pim_n // the permutations of the cloud * dist source: * x1 * ... * xm // distances of the cloud permutations to the source permutation * dist target: * x1 * ... * xm // distances of the cloud permutations to the target permutation * * @param f_filename name of the input file * @param f_numPerms the number of input permutations of the tree reconstruction * @param f_permSize the size of the permutations * @return true if reading the file was successful */ bool readTreeFromFile(const char* f_filename, int& f_numPerms, int& f_permSize, int**& f_inputGenomes); /** * Sets the weights for (inverted) transpositions and reversals. If * f_revOnly is set to true, (inverted) transpositions will be omitted * in the following process, and the first parameter will be ignored. * @param f_wt weight of an (inverted) transposition * @param f_wr weight of a reversal * @param f_revOnly if true we consider only reversals */ void setWeights(int f_wt, int f_wr = 1, double f_revOnly = false); /** * Creates the tree by using any possible input genome as start node. * The best tree will be stored, all others will be discarded. * The parameter f_improve sets the used improvement strategy: * 0: no improvement, 1: perturb; 2: median; 3: alternate perturb/median * @param f_improve the improvement strategy */ void createTree(int f_improve); /** * Creates the tree by starting with a specific input genome. The genome * index must be smaller as the number of input genomes. * The parameter f_improve sets the used improvement strategy: * 0: no improvement, 1: perturb; 2: median; 3: alternate perturb/median * @param f_startGenome index of first genome to add */ void createTree(int f_startGenome, int f_improve); /** * Improves the tree by alternatingly calling improveTreePerturb and * improveTreeMedian. */ void improveTree(); /** * Improves the tree by using a perturbation algorithm. */ void improveTreePerturb(); /** * Improves the tree by using a median heuristic. */ void improveTreeMedian(); /** * Returns the weight of the tree. * @return the tree weight */ int getTreeWeight() const; /** * Returns a pointer to the tree. * Handle this with care, changes in the tree can violate the program. * @return a pointer to the tree */ Tree* getTree() const; /** * Prints the tree to a stream (by default, stdout). * @param outstream the output stream */ void printTree(std::ostream& f_outstream ); // const; can only be const if no call of getDistance is used /** * Writes the tree to a file. * If successful, true will be returned. * @param f_filename name of the output file * @return true if tree successfully written to the file */ bool writeTreeToFile(const char* f_filename) const; protected: /** * Checks if the input permutation array is valid. */ bool checkInputGenomes(); /** * Cleans up all data if something goes wrong with readTreeFromFile * @param f_node node pointer to delete * @param f_char char pointer to delete * @param f_edge edge pointer to delete * @param f_input ifstream to close */ void cleanTreeLoadErrors(Node* f_node, char* f_char, Edge* f_edge, ifstream &f_input); /** * Initializes the variables needed for creating the tree. */ void initCTVars(); /** * Frees the variables needed to create the tree. */ void freeCTVars(); /** * Speed hack for creating + improving the tree if we use the weighted * distance: First creates the tree using reversal only distance, than * recalculates the weights and improves the tree. * Improvement strategies: 1: perturb; 2: median; 3: alternate * This is the function for starting from all starting nodes. * @param f_improve improvement strategy */ void createTreeSpeedHack(int f_improve); /** * Speed hack for creating + improving the tree if we use the weighted * distance: First creates the tree using reversal only distance, than * recalculates the weights and improves the tree. * Improvement strategies: 1: perturb; 2: median; 3: alternate * This is the function for starting from all starting nodes. * @param f_improve improvement strategy */ void createTreeSpeedHack(int f_startGenome, int f_improve); /** * Creates the tree by starting with a specific input genome. The genome * index must be smaller as the number of input genomes. The resulting tree * is stored in m_actTree. * @param f_startGenome index of first genome to add */ void createTreeFromNode(int f_startGenome); /** * Selects the next input genome to add, and where to add it in the tree. * As input parameter, this method needs to know the maximum edge index * before the last performSplit(), to know which variables must be updated. * @param f_oldMaxEdge old value of m_maxEdge */ void selectSplit(int f_oldMaxEdge); /** * Performs the split by splitting the splitedge at the steiner node * and adding an edge from the steiner node to the inputnode. */ void performSplit(); /** * Creates an edge from m_actTree->m_nodes[f_node] to its father node * Wrapper function for the different implementations. * @param f_node index of the source node */ void createEdge(int f_node); /** * Implementation of createEdge, building a cloud with no nodes. * @param f_node node index to build the edge */ void createEdgeEmpty(int f_node); /** * Implentation of createEdge, building a cloud by branching paths and * cut them to keep the cloud size at a low level. * @param f_node node index to build the edge */ void createEdgeCuttedPaths(int f_node); /** * Subroutine of createEdgeCuttedPaths. Expands a node by searching * promising successors, and stores them (ordered by score) in the * m_vecPerms vector. * @param f_index index of permutation to expand */ void expand(int f_index); /** * Selects from the actual permutations f_amount with the best possible * score. As it is possible that f_amount is more than the maximum * possible number of selectable permutations, the amount of selected * permutations will be returned. * @param f_first first possible index to select * @param f_amount amount to select * @return number of selected perms */ int select(unsigned int f_first, unsigned int f_amount); /** * Builds the heap select2 works on. Note that the top element will be * the rightmost element of the heap. * @param f_left leftmost element of the heap */ void buildHeap(int f_left); /** * Calculates the secondary score of a perm. Check inside details for * chosen strategy. * @param f_perm the permutation to score * @return the secondary score */ int calcSecondaryScore(const int* f_perm); /** * Gets all possible good moves. That are: * - (inverted) transpositions that split one cycle into three * - reversals that split one cycle into two * Relative moves are always seen w.r.t. the identity permutation, so the * permutation in the arguments should be a mapped permutation. * @param f_perm the permutation * @param f_moves resulting moves will be added to this vector */ void getGoodMoves(int* f_perm, vector& f_moves); /** * Gets all reversals that invert an elementary interval. * Relative moves are always seen w.r.t. the identity permutation, so the * permutation in the arguments should be a mapped permutation. * @param f_perm the permutation * @param f_moves resulting moves will be added to this vector */ void get0rMoves(int* f_perm, vector& f_moves); /** * Translates a pair of indices into the index in the IT vectors, * using the followiung formula: * index = (max(f_i, f_j)^2 + max(f_i, f_j)) / 2 + min(f_i, f_j) * @param f_i first input index * @param f_j second input index * @return resulting index in the IT vectors */ inline int getITIndex(int f_i, int f_j) const { return (f_i > f_j? ((f_i * f_i + f_i) / 2 + f_j) : ((f_j * f_j + f_j) / 2 + f_i)); } /** * Searches for an improvement step. If there is a possible improvement * step, true will be returned, otherwise false. * The parameters of the split will be written to the three arguments, * where f_splitedge is the edge we have to remove, and the new edge * will be inserted between the edges f_edge1 and f_edge2 (vars are * passed as reference). * @param f_splitedge the edge to delete * @param f_edge1 new edge between this edge and f_edge2 * @param f_edge2 new edge between this edge and f_edge1 * @return true if we found an improvement step */ bool findImprovement(int& f_splitedge, int& f_edge1, int& f_edge2); /** * Performs an improvement step. The edge to remove is f_splitedge, * and a new edge will be inserted between f_edge1 and f_edge2; more * accurate positions of where to insert the edge can be found in the * member variables. * @param f_splitedge remove this edge * @param f_edge1 insert new edge between this edge and f_edge2 * @param f_edge2 insert new edge between this edge and f_edge1 */ void performImprovement(int f_splitedge, int f_edge1, int f_edge2); /** * Inverts the path between node f_source and node f_target (arguments * are the node indices). This must be a valid directed path! * @param f_source source of the path * @param f_target target of the path */ void invertPath(int f_source, int f_target); /** * Repairs the clouds. */ void repairClouds(); /** * Relaxes the tree such that every internal node has a degree of 3. */ void relaxTree(); /** * Calculates the distance between two permutations. * @param f_perm1 first permutation * @param f_perm2 second permutation * @return an upper bound for the real distance */ int getDistance(const int* f_perm1, const int* f_perm2); /** * Calculates the lower bound of the distance between two permutations. * The formula for the lower bound is: * lb = c_even w_r + ((n - c_odd) / 2 - c_even) w_t * Note that for the real distance d, d <= 1.5 lb. * @param f_perm1 first permutation * @param f_perm2 second permutation * @return a lower bound for the real distance */ int getLowerBound(const int* f_perm1, const int* f_perm2); /*********************************************************************** * debugging methods ***********************************************************************/ public: /** * Debugging output of the create tree variables. */ void debugCTVars(); /** * Checks if a permutation is valid. It is assumed that the permutation * size is m_permSize * @param f_perm the permutation * @return true iff the permutation is valid */ bool checkPerm(const int* f_perm) const; /** * Checks if a permutation is valid. The permutation must have the size * f_size. * @param f_size permutation size * @param f_perm the permutation * @return true iff the permutation is valid */ bool checkPerm(int f_size, const int* f_perm) const; /** * Checks if the permutations in m_vecPerms are unique. Returns true if * yes, false otherwise. * @return true if the permutations are unique */ bool checkVecPerms(); /** * Debugging function. Functionality may change. */ void debug(); }; /***************************************************************************/ } // end namespace phylo #endif /*PHYLO_H_*/ phylo-1.0.6/phylo/phyloTools.cpp0000644000175000017500000001313611434510050013602 00000000000000/** * filename: phyloTools.cpp * author: Martin Bader * begin: 13.12.2006 * last change: 20.11.2008 * * Implementation of phyloTools.h * * Copyright (C) 2007-2008 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "phyloTools.h" #include #include #include "logger.h" namespace phylo { using namespace minswrt; extern Logger g_logger; void performOperation(int f_size, const Operation& f_op, const int* f_source, int* f_target) { int pos; // target position of an element if (f_op.m_type == Operation::OPERATION_REVERSAL) { // invert first segment pos = f_op.m_edges[1] == 1? f_size - 1 : f_op.m_edges[1] - 2; for (int i = f_op.m_edges[0] - 1; i != f_op.m_edges[1] - 1; i == f_size - 1? i = 0 : i++) { f_target[pos] = -f_source[i]; pos == 0? pos = f_size - 1 : pos--; } // copy the rest for (int i = f_op.m_edges[1] - 1; i != f_op.m_edges[0] - 1; i == f_size - 1? i = 0 : i++) f_target[i] = f_source[i]; return; } if (f_op.m_type == Operation::OPERATION_TRANSPOSITION) { // move second segment to the front pos = f_op.m_edges[0] - 1; for (int i = f_op.m_edges[1] - 1; i != f_op.m_edges[2] - 1; i == f_size - 1? i = 0 : i++) { f_target[pos] = f_source[i]; pos == f_size - 1? pos = 0 : pos++; } // move first segment to the back // pos = (f_op.m_edges[0] + f_op.m_edges[2] - f_op.m_edges[1] - 1 + f_size) % f_size; for (int i = f_op.m_edges[0] - 1; i != f_op.m_edges[1] - 1; i == f_size - 1? i = 0 : i++) { f_target[pos] = f_source[i]; pos == f_size - 1? pos = 0 : pos++; } // copy the rest for (int i = f_op.m_edges[2] - 1; i != f_op.m_edges[0] - 1; i == f_size - 1? i = 0 : i++) f_target[i] = f_source[i]; return; } if (f_op.m_type == Operation::OPERATION_TRANSREVERSAL) { // move second segment to the front pos = f_op.m_edges[0] - 1; for (int i = f_op.m_edges[1] - 1; i != f_op.m_edges[2] - 1; i == f_size - 1? i = 0 : i++) { f_target[pos] = f_source[i]; pos == f_size - 1? pos = 0 : pos++; } // move first segment to the back, invert pos = f_op.m_edges[2] == 1? f_size - 1 : f_op.m_edges[2] - 2; for (int i = f_op.m_edges[0] - 1; i != f_op.m_edges[1] - 1; i == f_size - 1? i = 0 : i++) { f_target[pos] = -f_source[i]; pos == 0? pos = f_size - 1 : pos--; } // copy the rest for (int i = f_op.m_edges[2] - 1; i != f_op.m_edges[0] - 1; i == f_size - 1? i = 0 : i++) f_target[i] = f_source[i]; return; } } unsigned int getHash(int f_size, const int* f_perm) { unsigned int x = 1; for (int i = 1; i < f_size; i++) x *= abs(f_perm[i-1] - f_perm[i]); x *= abs(f_perm[f_size-1] - f_perm[0]); return x; } bool equalPerms(int f_size, const int* f_perm1, const int* f_perm2) { int pos = 0; // position in perm2 bool reflection = false; // check if perm2 is the reflecion of perm1 // search f_perm1[0] in second permutation for (int i = 0; i < f_size; i++) { if (f_perm2[i] == f_perm1[0]) { pos = i; break; } else if (f_perm2[i] == -f_perm1[0]) { pos = i; reflection = true; break; } } // cycle through permutation if (reflection) { for (int i = 1; i < f_size; i++) { pos == 0? pos = f_size - 1 : pos--; if (f_perm1[i] != -f_perm2[pos]) return false; } } else { for (int i = 1; i < f_size; i++) { pos == f_size - 1? pos = 0 : pos++; if (f_perm1[i] != f_perm2[pos]) return false; } } return true; } void printPerm(int f_size, const int* f_perm, Loglevel f_loglevel) { for (int i = 0; i < f_size; i++) g_logger.log(f_loglevel, "%d ", f_perm[i]); g_logger.log(f_loglevel, "\n"); } void printOperation(const Operation& f_op, Loglevel f_loglevel) { switch (f_op.m_type) { case Operation::OPERATION_REVERSAL: g_logger.log(f_loglevel, " r("); break; case Operation::OPERATION_TRANSPOSITION: g_logger.log(f_loglevel, " t("); break; case Operation::OPERATION_TRANSREVERSAL: g_logger.log(f_loglevel, "tr("); break; default: g_logger.log(f_loglevel, "INVALID OPERATION!\n"); return; } g_logger.log(f_loglevel, "%d, %d", f_op.m_edges[0], f_op.m_edges[1]); if (f_op.m_type == Operation::OPERATION_REVERSAL) g_logger.log(f_loglevel, ")\n"); else g_logger.log(f_loglevel, ", %d)\n", f_op.m_edges[2]); } /***************************************************************************/ } // end namespace phylo phylo-1.0.6/phylo/edge.h0000644000175000017500000000421211434510050011772 00000000000000/** * filename: edge.h * author: Martin Bader * begin: 13.12.2006 * last change: 23.08.2007 * * An edge of the phylogenetic tree. * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef EDGE_H_ #define EDGE_H_ namespace phylo { /** * Contains the edge data. */ class Edge { /*********************************************************************** * member variables ***********************************************************************/ public: /** the weight of the edge */ int m_weight; /** number of nodes in the cloud */ int m_cloudSize; /** the permutation cloud */ int** m_cloud; /** distances to source node */ int* m_distSource; /** distances to target node */ int* m_distTarget; /** this cloud node (determined by index) will not be deleted in the * destructor */ int m_protected; /*********************************************************************** * methods ***********************************************************************/ public: /** * Constructor. */ Edge(); /** * Destructor. Deletes all internal (steiner) nodes. */ ~Edge(); /** * Initializes the member variables (reserves memory). * @param f_cloudSize number of cloud nodes */ void init(int f_cloudSize); }; /***************************************************************************/ } // end namespace phylo #endif /*EDGE_H_*/ phylo-1.0.6/phylo/Makefile.am0000644000175000017500000000123511434510050012753 00000000000000lib_LTLIBRARIES = libphylo.la libphylo_ladir = $(includedir) libphylo_la_SOURCES = edge.cpp logger.cpp node.cpp phylo.cpp phyloTools.cpp pools.cpp tree.cpp libphylo_la_HEADERS = $(libphylo_la_SOURCES:%.cpp=%.h) libphylo_la_LIBADD = -L../revDist -L../minswrt -L../median -L../weightedbb -lrevDist -lminswrt -lmedian -lweightedbb INCLUDES = -I$(includedir) -I../revDist -I../minswrt -I../median -I../weightedbb libphylo_la_LDFLAGS = -version-info 2:1:0 bin_PROGRAMS = phylo phylo_SOURCES = start.cpp phylo_LDADD = libphylo.la EXTRA_DIST = $(libphylo_la_HEADERS) campanulaceae COPYING README phyloextradir = $(datadir)/phylo phyloextra_DATA = campanulaceae COPYING README phylo-1.0.6/phylo/start.cpp0000644000175000017500000002405511434510050012565 00000000000000/** * filename: start.cpp * author: Martin Bader * begin: 12.12.2006 * last change: 23.08.2010 * * Start file. This is a small interface for using the library. * For usage, see details of the main function. * * Copyright (C) 2007-2010 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include #include #include "phylo.h" #include "logger.h" namespace phylo { using namespace std; extern Logger g_logger; /** * Wrapper for the main function to get it inside the namespace. * @param f_argc the number of arguments * @param f_argv the arguments * @return the program exit code */ int phylomain(int f_argc, char** f_argv) { phylo::Phylo phylo; // the main class // program parameters bool help = false; // true if we just print the help int wr = 1; // weight for reversals int wt = 2; // weight for (inverted) transpositions bool revOnly = true; // true if we use reversal only distance int verbosity = 1; // the verbosity level bool loadTreeFile = false; // true if we load a tree file bool infileSet = false; // true if we have set the name of the infile char* infile = NULL; // name of the file to load int startnode = -1; // startnode to create the tree int improve = 3; // improvement technique (0: n; 1: p; 2: m; 3: pm) bool saveTreeFile = false; // true if we shall save the tree char* outfile = NULL; // filename of the output file // further vars int numPerms; // number of input permutations int permSize; // size of a permutation int** perms = NULL; // the input permutations char** genomeNames = NULL; // names of the input genomes cout << "*****************************************************************\n"; cout << "phylo v1.0.6 Copyright (C) 2008-2010 Martin Bader\n"; cout << "This program comes with ABSOLUTELY NO WARRANTY.\n"; cout << "This is free software, and you are welcome to redistribute it\n"; cout << "under certain conditions.\n"; cout << "For details about the licence, read the file gpl.txt\n"; cout << "*****************************************************************\n"; // read the parameters for (int i = 1; i < f_argc;) { if (strcmp(f_argv[i], "-h") == 0) { help = true; i++; } else if (strcmp(f_argv[i], "-w") == 0) { if (i + 2 >= f_argc) { cout << "Invalid use of parameter -w; Use -w wr wt for weighted distance, or -w wr inf for reversal only distance\n"; return 0; } wr = atoi(f_argv[i+1]); if (strcmp(f_argv[i+2], "inf") == 0) revOnly = true; else { revOnly = false; wt = atoi(f_argv[i+2]); } i += 3; } else if (strcmp(f_argv[i], "-v") == 0) { if (i + 1 >= f_argc) { cout << "Invalid use of parameter -v; Use -v x where x is the verbosity level\n"; return 0; } verbosity = atoi(f_argv[i+1]); i += 2; } else if (strcmp(f_argv[i], "-t") == 0) { loadTreeFile = true; i++; } else if (strcmp(f_argv[i], "-f") == 0) { if (i + 1 >= f_argc) { cout << "Invalid use of parameter -f; Use -v filename\n"; return 0; } infile = f_argv[i+1]; infileSet = true; i += 2; } else if (strcmp(f_argv[i], "-s") == 0) { if (i + 1 >= f_argc) { cout << "Invalid use of parameter -s; Use -v x where x is the index of the starting node\n"; return 0; } startnode = atoi(f_argv[i+1]); i += 2; } else if (strcmp(f_argv[i], "-i") == 0) { if (i + 1 >= f_argc) { cout << "Invalid use of parameter -i; Use -i [t|m|tm|n]\n"; return 0; } if (strcmp(f_argv[i+1], "n") == 0) improve = 0; else if (strcmp(f_argv[i+1], "t") == 0) improve = 1; else if (strcmp(f_argv[i+1], "m") == 0) improve = 2; else if (strcmp(f_argv[i+1], "tm") == 0) improve = 3; else { cout << "Invalid use of parameter -i; Use -i [t|m|tm|n]\n"; return 0; } i += 2; } else if (strcmp(f_argv[i], "-o") == 0) { if (i + 1 >= f_argc) { cout << "Invalid use of parameter -o; Use -o filename\n"; return 0; } saveTreeFile = true; outfile = f_argv[i+1]; i += 2; } } if (help) { cout << "Phylo version 1.0.4\n"; cout << "Usage: phylo [OPTIONS]\n"; cout << "available options:\n"; cout << "-h Just print some help information (ignore all other options)\n"; cout << "-w wr wt Set weights to wr (for reversals) and wt (for transpositions).\n"; cout << " If you use reversal only distance, call -w wr inf.\n"; cout << " (default: -w 1 inf) Note that the weights must be integer.\n"; cout << "-v x Set the output (verbosity) level to x. -v 0 produces the most\n"; cout << " output, while -v 3 only reports serious errors. (default: -v 1)\n"; cout << "-t If this parameter is set, the input file is a tree instead of a\n"; cout << " set of permutations, so only the improvement steps will be\n"; cout << " performed.\n"; cout << "-f name Load the file with the given name. This option is required.\n"; cout << "-s x If this parameter is set, the tree is only created from starting\n"; cout << " node x.\n"; cout << "-i [n|t|m|tm] Set he improvement technique to use. t means topology improvement, \n"; cout << " m means median improvement, tm means first using t then m,\n"; cout << " n means no improvement. (default: -i tm)\n"; cout << "-o name If this parameter is set, the best found tree will be written to\n"; cout << " a file with the given name.\n"; return 0; } if (!infileSet) { cout << "No input file set\n"; cout << "For detailed instructions, call phylo -h\n"; return 0; } // set logger params g_logger.setMinLoglevel((phylo::Loglevel)verbosity); g_logger.setOutstream(phylo::PHYLO_ERROR, stderr); if (loadTreeFile) { if (!phylo.readTreeFromFile(infile, numPerms, permSize, perms)) return 0; phylo.setWeights(wt, wr, revOnly); if (improve == 1) phylo.improveTreePerturb(); else if (improve == 2) phylo.improveTreeMedian(); else if (improve == 3) phylo.improveTree(); } else { if (!phylo.readGenomesFromFile(infile, numPerms, permSize, perms, genomeNames)) return 0; phylo.setGenomes(numPerms, permSize, perms); phylo.setGenomeNames(genomeNames); phylo.setWeights(wt, wr, revOnly); if (startnode == -1) phylo.createTree(improve); else if (startnode >= numPerms) cout << "Startnode has invalid index!\n"; else phylo.createTree(startnode, improve); } phylo.printTree(cout); if (saveTreeFile) phylo.writeTreeToFile(outfile); // clean up for (int i = 0; i < numPerms; i++) delete[] perms[i]; delete[] perms; return 0; } } // end namespace phylo /** * The main function. * Usage of the program: phylo parameters * Parameters are: * -h just print some help information (ignore all other parameters) * -w wr wt set weights to wr (for reversals) and wt (for transpositions). * If you use reversal only distance, call -w wr inf. The default parameter * is - w 1 inf. * -v x the output (verbosity) level. -v 0 produces the most output, while -v 3 * only reports serious errors. Default is -v 1. * -t If this parameter is set, the input file is a tree instead of a set * of permutations, so only the improvement steps will be performed. * -f filename The name of the file that contains the input data. This parameter * is required. * -s x If this parameter is set, the tree is only created from starting node x. * -i [p|m|pm] the improvement technique to use. p means tree perturbation, * m means median improvement, pm means alternating both techniques until the * result does not improve any further, n means no improvement. Default is -i m * -o filename If this parameter is set, the best found tree will be written to * a file with the given filename. * * @param f_argc the number of arguments * @param f_argv the arguments * @return the program exit code */ int main(int f_argc, char** f_argv) { return phylo::phylomain(f_argc, f_argv); } phylo-1.0.6/phylo/pools.h0000644000175000017500000000433411434510050012227 00000000000000/** * filename: pools.h * author: Martin Bader * begin: 13.12.2006 * last change: 01.07.2009 * * Pools of several data structures, to avoid frequent allocation / freeing * of memory. * * Copyright (C) 2007-2009 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef POOLS_H_ #define POOLS_H_ #include namespace phylo { /** * Pool for permutations. */ class PermPool { /*********************************************************************** * member variables ***********************************************************************/ protected: /** size of the permutations */ int m_permSize; /** the permutations */ std::vector m_perms; /*********************************************************************** * methods ***********************************************************************/ public: /** * Constructor. */ PermPool(); /** * Destructor. */ ~PermPool(); /** * Initializes the pool with a given permutation size. * @param f_size the permutation size */ void init(int f_size); /** * Returns a permutation (int[m_permSize]-array). * @return pointer to a permutation */ int* getPerm(); /** * Return the permutation back to the pool. * @param f_perm the permutation to give back */ inline void freePerm(int* f_perm) { m_perms.push_back(f_perm); } }; /***************************************************************************/ } // end namespace phylo #endif /*POOLS_H_*/ phylo-1.0.6/phylo/edge.cpp0000644000175000017500000000357011434510050012333 00000000000000/** * filename: edge.cpp * author: Martin Bader * begin: 13.12.2006 * last change: 01.07.2009 * * Implementation of edge.h * * Copyright (C) 2007-2009 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "edge.h" #include #include "pools.h" namespace phylo { using namespace std; extern PermPool* g_permPool; /*************************************************************************** * public methods ***************************************************************************/ Edge::Edge() { m_weight = 0; m_cloudSize = 0; m_cloud = NULL; m_distSource = NULL; m_distTarget = NULL; m_protected = -1; } Edge::~Edge() { if (m_cloud == NULL) return; // delete the cloud for (int i = 0; i < m_cloudSize; i++) { if (i == m_protected) continue; g_permPool->freePerm(m_cloud[i]); } delete[] m_cloud; delete[] m_distSource; delete[] m_distTarget; } void Edge::init(int f_cloudSize) { m_cloud = new int*[f_cloudSize]; m_distSource = new int[f_cloudSize]; m_distTarget = new int[f_cloudSize]; m_cloudSize = f_cloudSize; } /***************************************************************************/ } // end namespace phylo phylo-1.0.6/phylo/phyloTools.h0000644000175000017500000000563711434510050013256 00000000000000/** * filename: phyloTools.h * author: Martin Bader * begin: 13.12.2006 * last change: 20.11.2008 * * Some useful tools needed by the program * * Copyright (C) 2007-2008 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef PHYLOTOOLS_H_ #define PHYLOTOOLS_H_ #include #include #include "logger.h" namespace phylo { #define PHYLO_EPS 0.001 // epsilon for floating point comparison /** * Performs an operation; the result will be written to f_target, which must * be initialized and of the correct size. * @param f_size permutation size * @param f_op the operation to perform * @param f_source the source permutation * @param f_target the target permutation (result will be written to here) */ void performOperation(int f_size, const minswrt::Operation& f_op, const int* f_source, int* f_target); /** * Calculates a hash value for a permutation. The hash value is invariant to * cyclic shifts and the reflection. * @param f_size permutation size * @param f_perm permutation to check * @return the hash value */ unsigned int getHash(int f_size, const int* f_perm); /** * Compares if two permutations are equal. This is invariant to rotation and * reflection. * @return true if the permutations are considered to be equal. */ bool equalPerms(int f_size, const int* f_perm1, const int* f_perm2); /** * Checks if three integers are cyclic sorted, i.e. f_x < f_y < f_z in a cyclic group. * @param f_x first integer * @param f_y second integer * @param f_z third integer * @return true if they are cyclic sorted */ inline bool cyclicSorted(int f_x, int f_y, int f_z) { return !((f_x < f_y) ^ (f_y < f_z) ^ (f_z < f_x)); } /** * Prints a permutation via the logger. * f_perm must be an array of size f_size. * @param f_size size of the permutation * @param f_perm the permutation to print * @param f_loglevel the output loglevel */ void printPerm(int f_size, const int* f_perm, Loglevel f_loglevel = PHYLO_INFO); /** * Prints an operation via the logger. * @param f_op the operation to print * @param f_loglevel the output loglevel */ void printOperation(const minswrt::Operation& f_op, Loglevel f_loglevel = PHYLO_INFO); /***************************************************************************/ } // end namespace phylo #endif /*PHYLOTOOLS_H_*/ phylo-1.0.6/phylo/logger.h0000644000175000017500000000513511434510050012352 00000000000000/** * filename: logger.h * author: Martin Bader * begin: 13.12.2006 * last change: 20.11.2008 * * Class to handle log messages. Supports different log levels and different * output streams of logging messages with different level. * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef LOGGER_H_ #define LOGGER_H_ #include namespace phylo { enum Loglevel { PHYLO_DEBUG, PHYLO_INFO, PHYLO_WARNING, PHYLO_ERROR }; /** * The Logger. */ class Logger { /*********************************************************************** * member variables ***********************************************************************/ protected: /** the minimum loglevel to use (default: INFO) */ Loglevel m_minLevel; /** the different output streams for the loglevels (default: all are * stdout)*/ FILE** m_outstreams; /*********************************************************************** * methods ***********************************************************************/ public: /** * Constructor. */ Logger(); /** * Destructor. */ ~Logger(); /** * Sets the output stream for a loglevel. * @param f_level the loglevel * @param f_stream the output stream */ void setOutstream(Loglevel f_level, FILE* f_stream); /** * Sets the minimum loglevel. All messages below this level will be * suppressed. * @param m_level the minimum log level */ void setMinLoglevel(Loglevel f_level); /** * Logs a message with loglevel f_level. The format of the message is the * same ase you use with printf. * @param f_level the loglevel * @param f_message the message to log */ void log(Loglevel f_level, const char* f_message, ...); }; /***************************************************************************/ } // end namespace phylo #endif /*LOGGER_H_*/ phylo-1.0.6/minswrt/0000755000175000017500000000000011434510123011347 500000000000000phylo-1.0.6/minswrt/config.h0000644000175000017500000000167211434510050012712 00000000000000/** * filename: config.h * author: Martin Bader * begin: 22.07.2005 * last change: 03.09.2008 * * Some configurations for MinSWRT (namespaces, ...). * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef CONFIG_H_ #define CONFIG_H_ #include using namespace std; #define DEBUG 0 #endif phylo-1.0.6/minswrt/permutation.h0000644000175000017500000001746111434510050014017 00000000000000/** * filename: permutation.h * author: Martin Bader * begin: 22.07.2005 * last change: 11.08.2008 * * The representation of a permutation. * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef PERMUTATION_H_ #define PERMUTATION_H_ #include "config.h" namespace minswrt { /** * This struct represents a cycle. As we only work on simple permutations, * we can only represent short cycles (max length = 3). The position of the * reality-edges must be a cyclic increasing sequence. If the cycle is a * 1-twisted 3-cycle, the twisted edge is the last edge. If the cycle is * a 2-twisted 3-cycle, the untwisted edge is the last edge. */ struct Cycle { /** Type of the cycle. */ enum { CYCLE_INVALID, // invalid cycle CYCLE_ADJACENCY, // adjacency CYCLE_2UNORIENTED, // r-unoriented 2-cycle CYCLE_2ORIENTED, // r-oriented 2-cycle CYCLE_0TWISTED, // nontwisted 3-cycle CYCLE_1TWISTED, // 1-twisted 3-cycle CYCLE_2TWISTED, // 2-twisted 3-cycle CYCLE_3TWISTED, // 3-twisted 3-cycle CYCLE_LONGCYCLE // cycle length > 3 (->WARNING! edge data corrupted) } m_type; /** The positions of the reality-edges; this is always a cyclic * increasing sequence. If the cycle is a 1-twisted 3-cycle, the twisted * edge is the last edge. If the cycle is a 2-twisted 3-cycle, the * untwisted edge is the last edge. */ int m_edges[3]; }; /** * This struct represents an operation on the permutation. */ struct Operation { /** type of the operation */ enum { OPERATION_REVERSAL, OPERATION_TRANSPOSITION, OPERATION_TRANSREVERSAL, OPERATION_INVALID } m_type; /** involved reality-edges; for reversals and transreversals, the segment * between m_edges[0] and m_edges[1] will be inverted. f_edges must be a * cyclic increasing sequence. */ int m_edges[3]; }; /** * A sequence of operations, including delta sigma, w, delta sigma / w */ struct Sequence { /** the number of operations */ int m_numOperations; /** the Operations (maximum 4) */ Operation m_operations[4]; /** delta sigma of the sequence */ float m_dsigma; /** weight of the sequence */ float m_weight; /** ratio delta sigma / weight */ float m_ratio; }; /** * This class represents a permutation, with all necessary additional * information. */ class Permutation { /*********************************************************************** * member variables ***********************************************************************/ public: /** The data elements. Elements go from 1 to m_size, plus additional * sign. */ int* m_data; /** Index of the elements. m_index[i] returns the index in the data array * of the unsigned element i. m_index[0] = 0 by definition. */ int* m_index; protected: /** Size of the permutation. */ int m_size; private: /** temporary data array for performing operation; avoids frequent * memory allocation */ int* m_tempData; /*********************************************************************** * methods ***********************************************************************/ public: /** * The constructor. After calling the constructor, don't forget to call * init(int f_size). */ Permutation(); /** * The destructor. */ ~Permutation(); /** * Initialises the permutation. f_size is the permutation size. Deletes * any old data, doesn't set new data. * @param f_size the size of the permutation */ void init(int f_size); /** * Initialises the permutation. f_size is the permutation size. Deletes * any old data, and sets the new data. Size of the new data array must * be f_size. * @param f_size the size of the permutation * @param f_data the elements */ void init(int f_size, const int* f_data); /** * Sets the data of the permutation, and actualises the index array. * f_data must have the size of the permutation. */ void setData(const int* f_data); /** * Returns the permutation size. * @return the permutation size */ inline int size() const { return m_size; } /** * Searches for a cycle in the permutation that is not an adjacency. The * cycle will be written to f_result. If there are only adjacencies, the * result will have the type CYCLE_INVALID. Use this only for simple * permutations, because the cycle data for long cycles will be * corrupted. * Additional, it is possible to search for cycles that intersect a given * interval. For this, f_intersect must be set. If it is set to 1, the * algorithm searches for a cycle intersecting with the interval * (f_a1, f_a2). If it is set to 2, the algorithm searches for a cycle * intersecting with the union (f_a1, f_a2) || (f_b1, f_b2). The intervals * must be non-intersecting. * Intersecting cycles must have one edge inside the interval, and the other * outside the interval, excluding the interval bounds. * @param f_result the result will be written here * @param f_intersect choose intersection level * @param f_a1 start of first interval * @param f_a2 end of first interval * @param f_b1 start of second interval * @param f_b2 end of second interval */ void getCycle(Cycle* f_result, int f_intersect = 0, int f_a1 = -1, int f_a2 = -1, int f_b1 = -1, int f_b2 = -1) const; /** * Searches for a cycle with a given reality-edge. The result will be * written to f_cycle, which must be initialized. * @param f_edge index of the reality-edge * @param f_cycle the resulting cycle */ void getCycleOfEdge(int f_edge, Cycle* f_result); /** * Performs an operation on the permutation. * @param f_operation the operation to perform */ void performOperation(const Operation& f_operation); /** * Prints the permutation on the console. */ void print() const; /*********************************************************************** * debugging methods ***********************************************************************/ /** * Prints all info about the permutation to stderr. */ void debugPrint(); /** * Checks if the permutation contains a long cycle. * @return true if it has a long cycle */ bool hasLongCycle(); /** * Checks if the permutation is sorted. * @return true if the permutation is sorted */ bool isSorted(); }; /*************************************************************************** * debugging non-class functions ***************************************************************************/ /** * Prints a cycle to stderr. * @param f_cycle the cycle to print */ void printCycle(const Cycle& f_cycle); } // end namespace minswrt #endif phylo-1.0.6/minswrt/README0000644000175000017500000000211611434510050012146 00000000000000minswrt ======= minswrt (minimal sorting by weighted reversals and transpositions) contains of two parts: 1. the program itself, which is compiled into a library. 2. a tiny frontend that calls the library. The frontend: Call the program with the following parameters: ./minswrt file wr wt - file is the file containing the permutation. The file consists of a line containing the number of elements in the permutation. The next two lines contain the source and the target permutation. An example can be found in test.in - wr is the weight of reversals - wt is the weight of transpositions and inverted transpositions The library: The functions provided by the library are documented in minswrt.h in the include directory. As example of how to use the library, you can have a look at minswrt/start.cpp. The interesting part is in the main function. Copyright: ========== Copyright (C) 2007/2008 Martin Bader This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions. For details about the licence, read the file COPYING phylo-1.0.6/minswrt/permutation.cpp0000644000175000017500000005133611434510050014351 00000000000000/** * filename: permutation.cpp * author: Martin Bader * begin: 22.07.2005 * last change: 15.08.2008 * * The representation of a permutation. * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "permutation.h" #include #include "tools.h" namespace minswrt { using namespace std; /*************************************************************************** * public methods ***************************************************************************/ Permutation::Permutation() { m_size = 0; m_data = NULL; m_index = NULL; m_tempData = NULL; } Permutation::~Permutation() { delete[] m_data; m_data = NULL; delete[] m_index; m_index = NULL; delete[] m_tempData; m_tempData = NULL; } void Permutation::init(int f_size) { m_size = f_size; delete[] m_data; delete[] m_index; delete[] m_tempData; m_data = new int[f_size]; m_index = new int[f_size+1]; m_index[0] = 0; m_tempData = new int[f_size]; } void Permutation::init(int f_size, const int* f_data) { m_size = f_size; delete[] m_data; delete[] m_index; delete[] m_tempData; m_data = new int[f_size]; m_index = new int[f_size+1]; m_index[0] = 0; m_tempData = new int[f_size]; for (int i = 0; i < f_size; i++) { m_data[i] = f_data[i]; m_index[abs(f_data[i])] = i; } } void Permutation::setData(const int* f_data) { for (int i = 0; i < m_size; i++) { m_data[i] = f_data[i]; m_index[abs(f_data[i])] = i; } } void Permutation::getCycle(Cycle* f_result, int f_intersect, int f_a1, int f_a2, int f_b1, int f_b2) const { bool left[4]; // did we leave the last RE to the left? int element; // the next element int order1[3]; // needed to check if intersecton is ok int order2[3]; // needed to check if intersecton is ok // adjust bounds if (f_intersect == 0) { f_b2 = m_size; } else if (f_intersect == 1) { f_b2 = f_a2; } if (f_b2 == 0) f_b2 = m_size; // search cycle for (int i = f_a1 + 1; i != f_b2; i++) { if (i == m_size) i = 0; if (i == f_a2) { i = (f_b1 + 1) % m_size; if (i == f_b2) break; } f_result->m_edges[0] = i; left[0] = true; for (int j = 0; j < 2;) // increment in loop { if (left[j]) element = m_data[f_result->m_edges[j]]; else element = m_data[(f_result->m_edges[j]+1) % m_size]; if (left[j] ^ (element > 0)) // go to element - 1, upper point { j++; // increment j left[j] = false; // left now indicates point of target element = abs(element) - 1; if (element == 0) element = m_size; } else // go to element + 1, lower point { j++; // increment j left[j] = true; // left now indicates point of target element = abs(element) + 1; if (element > m_size) element = 1; } f_result->m_edges[j] = m_index[element]; if (!(left[j] ^ (m_data[f_result->m_edges[j]] > 0))) { f_result->m_edges[j] = (f_result->m_edges[j] + m_size - 1) % m_size; left[j] = true; } else left[j] = false; } #if 0 cerr << "cycle found\n"; cerr << "edges: " << f_result->m_edges[0] << " " << f_result->m_edges[1] << " " << f_result->m_edges[2] << endl; #endif // check intersection; first edge is always in interval if (f_intersect == 1) { order1[0] = f_a1; order1[1] = f_result->m_edges[1]; order1[2] = f_a2; if (cyclicSorted(order1)) // second element in interval { order1[1] = f_result->m_edges[2]; if (cyclicSorted(order1)) // third element in interval continue; } } else if (f_intersect == 2) { order1[0] = f_a1; order1[1] = f_result->m_edges[1]; order1[2] = f_a2; order2[0] = f_b1; order2[1] = f_result->m_edges[1]; order2[2] = f_b2; if (cyclicSorted(order1) || cyclicSorted(order2)) // second in interval { order1[1] = f_result->m_edges[2]; order2[1] = f_result->m_edges[2]; if (cyclicSorted(order1) || cyclicSorted(order2)) // third in interval continue; } } // check cycle type if (f_result->m_edges[0] == f_result->m_edges[1]) f_result->m_type = Cycle::CYCLE_ADJACENCY; else if (f_result->m_edges[0] == f_result->m_edges[2]) { if (left[0] == left[1]) f_result->m_type = Cycle::CYCLE_2UNORIENTED; else f_result->m_type = Cycle::CYCLE_2ORIENTED; } else { // check if long cycle if (left[2]) element = m_data[f_result->m_edges[2]]; else element = m_data[(f_result->m_edges[2]+1) % m_size]; if (left[2] ^ (element > 0)) // go to element - 1, upper point { left[3] = false; // left now indicates point of target element = abs(element) - 1; if (element == 0) element = m_size; } else // go to element + 1, lower point { left[3] = true; // left now indicates point of target element = abs(element) + 1; if (element > m_size) element = 1; } element = m_index[element]; // use element as edge index (save memory) if (!(left[3] ^ (m_data[element] > 0))) element = (element + m_size - 1) % m_size; if (element == f_result->m_edges[0]) // 3-cycle { if (left[1] && left[2]) // all RE have same orientation { if (cyclicSorted(f_result->m_edges)) f_result->m_type = Cycle::CYCLE_3TWISTED; else { f_result->m_type = Cycle::CYCLE_0TWISTED; element = f_result->m_edges[1]; // switch order f_result->m_edges[1] = f_result->m_edges[2]; f_result->m_edges[2] = element; } } else // RE with different orientations { // move special edge at correct position - use element as // temporary variable if (!left[1] && !left[2]) // first edge is special edge { element = f_result->m_edges[0]; f_result->m_edges[0] = f_result->m_edges[1]; f_result->m_edges[1] = f_result->m_edges[2]; f_result->m_edges[2] = element; } else if (left[2]) // second edge is special edge { // also invert order element = f_result->m_edges[1]; f_result->m_edges[1] = f_result->m_edges[2]; f_result->m_edges[2] = element; } else // third edge is special edge { // invert order element = f_result->m_edges[0]; f_result->m_edges[0] = f_result->m_edges[1]; f_result->m_edges[1] = element; } if (cyclicSorted(f_result->m_edges)) f_result->m_type = Cycle::CYCLE_1TWISTED; else { f_result->m_type = Cycle::CYCLE_2TWISTED; element = f_result->m_edges[0]; // invert order f_result->m_edges[0] = f_result->m_edges[1]; f_result->m_edges[1] = element; } } } // end 3-cycle else f_result->m_type = Cycle::CYCLE_LONGCYCLE; } // end > 2-cycle if (f_result->m_type != Cycle::CYCLE_ADJACENCY) return; } // end for f_result->m_type = Cycle::CYCLE_INVALID; // no cycle found } void Permutation::getCycleOfEdge(int f_edge, Cycle* f_result) { bool left[4]; // did we leave the last RE to the left? int element; // the next element f_result->m_edges[0] = f_edge; left[0] = true; for (int j = 0; j < 2;) // increment in loop { if (left[j]) element = m_data[f_result->m_edges[j]]; else element = m_data[(f_result->m_edges[j]+1) % m_size]; if (left[j] ^ (element > 0)) // go to element - 1, upper point { j++; // increment j left[j] = false; // left now indicates point of target element = abs(element) - 1; if (element == 0) element = m_size; } else // go to element + 1, lower point { j++; // increment j left[j] = true; // left now indicates point of target element = abs(element) + 1; if (element > m_size) element = 1; } f_result->m_edges[j] = m_index[element]; if (!(left[j] ^ (m_data[f_result->m_edges[j]] > 0))) { f_result->m_edges[j] = (f_result->m_edges[j] + m_size - 1) % m_size; left[j] = true; } else left[j] = false; } #if 0 cerr << "cycle found\n"; cerr << "edges: " << f_result->m_edges[0] << " " << f_result->m_edges[1] << " " << f_result->m_edges[2] << endl; #endif // check cycle type if (f_result->m_edges[0] == f_result->m_edges[1]) f_result->m_type = Cycle::CYCLE_ADJACENCY; else if (f_result->m_edges[0] == f_result->m_edges[2]) { if (left[0] == left[1]) f_result->m_type = Cycle::CYCLE_2UNORIENTED; else f_result->m_type = Cycle::CYCLE_2ORIENTED; } else { // check if long cycle if (left[2]) element = m_data[f_result->m_edges[2]]; else element = m_data[(f_result->m_edges[2]+1) % m_size]; if (left[2] ^ (element > 0)) // go to element - 1, upper point { left[3] = false; // left now indicates point of target element = abs(element) - 1; if (element == 0) element = m_size; } else // go to element + 1, lower point { left[3] = true; // left now indicates point of target element = abs(element) + 1; if (element > m_size) element = 1; } element = m_index[element]; // use element as edge index (save memory) if (!(left[3] ^ (m_data[element] > 0))) element = (element + m_size - 1) % m_size; if (element == f_result->m_edges[0]) // 3-cycle { if (left[1] && left[2]) // all RE have same orientation { if (cyclicSorted(f_result->m_edges)) f_result->m_type = Cycle::CYCLE_3TWISTED; else { f_result->m_type = Cycle::CYCLE_0TWISTED; element = f_result->m_edges[1]; // switch order f_result->m_edges[1] = f_result->m_edges[2]; f_result->m_edges[2] = element; } } else // RE with different orientations { // move special edge at correct position - use element as // temporary variable if (!left[1] && !left[2]) // first edge is special edge { element = f_result->m_edges[0]; f_result->m_edges[0] = f_result->m_edges[1]; f_result->m_edges[1] = f_result->m_edges[2]; f_result->m_edges[2] = element; } else if (left[2]) // second edge is special edge { // also invert order element = f_result->m_edges[1]; f_result->m_edges[1] = f_result->m_edges[2]; f_result->m_edges[2] = element; } else // third edge is special edge { // invert order element = f_result->m_edges[0]; f_result->m_edges[0] = f_result->m_edges[1]; f_result->m_edges[1] = element; } if (cyclicSorted(f_result->m_edges)) f_result->m_type = Cycle::CYCLE_1TWISTED; else { f_result->m_type = Cycle::CYCLE_2TWISTED; element = f_result->m_edges[0]; // invert order f_result->m_edges[0] = f_result->m_edges[1]; f_result->m_edges[1] = element; } } } // end 3-cycle else f_result->m_type = Cycle::CYCLE_LONGCYCLE; } // end > 2-cycle } void Permutation::performOperation(const Operation& f_operation) { int pos; // actual position int range; // length of a segment if ((f_operation.m_type == Operation::OPERATION_REVERSAL) || (f_operation.m_type == Operation::OPERATION_TRANSREVERSAL)) { for (int i = f_operation.m_edges[1]; i != f_operation.m_edges[0]; (i == 0? i = m_size - 1:i--)) m_tempData[i] = m_data[i]; for (int i = 1; i <= (f_operation.m_edges[1] - f_operation.m_edges[0] + m_size) % m_size; i++) { pos = (f_operation.m_edges[0] + i) % m_size; m_data[pos] = -m_tempData[(f_operation.m_edges[1] + m_size + 1 - i) % m_size]; m_index[abs(m_data[pos])] = pos; } } if ((f_operation.m_type == Operation::OPERATION_TRANSPOSITION) || (f_operation.m_type == Operation::OPERATION_TRANSREVERSAL)) { // store length of first segment to change range = (f_operation.m_edges[2] - f_operation.m_edges[1] + m_size) % m_size; for (int i = 1; i <= range; i++) // store segment m_tempData[i] = m_data[(f_operation.m_edges[1] + i) % m_size]; pos = f_operation.m_edges[1]; for (int i = 0; i < (f_operation.m_edges[0] - f_operation.m_edges[2] + m_size) % m_size; i++) { pos == m_size - 1?pos = 0 : pos++; m_data[pos] = m_data[(pos + range) % m_size]; m_index[abs(m_data[pos])] = pos; } for (int i = 1; i <= range; i++) { pos == m_size - 1?pos = 0 : pos++; m_data[pos] = m_tempData[i]; m_index[abs(m_data[pos])] = pos; } } } void Permutation::print() const { for (int i = 0; i < m_size; i++) cout << m_data[i] << " "; cout << endl; } /*************************************************************************** * debugging methods ***************************************************************************/ void Permutation::debugPrint() { cerr << "m_size: " << m_size << endl; cerr << "m_data: " << endl; for (int i = 0; i < m_size; i++) cerr << m_data[i] << " "; cerr << endl << "m_index: " << endl; for (int i = 1; i <= m_size; i++) cerr << m_index[i] << " "; cerr << endl; } bool Permutation::hasLongCycle() { bool* visited = new bool[m_size]; // visited edges int cyclelength; // length of the current cycle bool left; // true if we leave the RE at the left point int element; // the next element (unsigned) int pos; // position in permutation for (int i = 0; i < m_size; i++) visited[i] = false; for (int i = 0; i < m_size; i++) { if (!visited[i]) // new cycle { cyclelength = 0; pos = i; left = true; do { visited[pos] = true; cyclelength++; if (left) element = m_data[pos]; else element = m_data[(pos+1) % m_size]; if (left ^ (element > 0)) // go to element - 1, upper point { left = false; // left now indicates point of target element = abs(element) - 1; if (element == 0) element = m_size; } else // go to element + 1, lower point { left = true; // left now indicates point of target element = abs(element) + 1; if (element > m_size) element = 1; } pos = m_index[element]; if (!(left ^ (m_data[pos] > 0))) { pos = (pos + m_size - 1) % m_size; left = true; } else left = false; } while (!visited[pos]); if (cyclelength > 3) { delete[] visited; return true; } } } delete[] visited; return false; } bool Permutation::isSorted() { int lowest = 0; // lowest element of the permutation for (int i = 0; i < m_size; i++) { if ((m_data[i] == 1) || (m_data[i] == -m_size)) { lowest = i; break; } } for (int i = 1; i < m_size; i++) { if (m_data[(lowest + i) % m_size] != m_data[(lowest + i - 1) % m_size] + 1) return false; } return true; } /*************************************************************************** * debugging non-class functions ***************************************************************************/ void printCycle(const Cycle& f_cycle) { switch (f_cycle.m_type) { case Cycle::CYCLE_ADJACENCY: cerr << "adjacency\n"; break; case Cycle::CYCLE_2ORIENTED: cerr << "oriented 2-cycle\n"; break; case Cycle::CYCLE_2UNORIENTED: cerr << "unoriented 2-cycle\n"; break; case Cycle::CYCLE_0TWISTED: cerr << "nontwisted\n"; break; case Cycle::CYCLE_1TWISTED: cerr << "1-twisted\n"; break; case Cycle::CYCLE_2TWISTED: cerr << "2-twisted\n"; break; case Cycle::CYCLE_3TWISTED: cerr << "3-twisted\n"; break; case Cycle::CYCLE_LONGCYCLE: cerr << "long cycle\n"; break; case Cycle::CYCLE_INVALID: cerr << "invalid\n"; break; } cerr << "edges: " << f_cycle.m_edges[0] << " " << f_cycle.m_edges[1] << " " << f_cycle.m_edges[2] << endl; } } // end namespace minswrt phylo-1.0.6/minswrt/COPYING0000644000175000017500000010451311434510050012325 00000000000000 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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For a particular product received by a particular user, "normally used" refers to a typical or common use of that class of product, regardless of the status of the particular user or of the way in which the particular user actually uses, or expects or is expected to use, the product. A product is a consumer product regardless of whether the product has substantial commercial, industrial or non-consumer uses, unless such uses represent the only significant mode of use of the product. "Installation Information" for a User Product means any methods, procedures, authorization keys, or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source. The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made. If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information. But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for example, the work has been installed in ROM). The requirement to provide Installation Information does not include a requirement to continue to provide support service, warranty, or updates for a work that has been modified or installed by the recipient, or for the User Product in which it has been modified or installed. Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network. Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form), and must require no special password or key for unpacking, reading or copying. 7. Additional Terms. "Additional permissions" are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions. When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission. Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms: a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it; or c) Prohibiting misrepresentation of the origin of that material, or requiring that modified versions of such material be marked in reasonable ways as different from the original version; or d) Limiting the use for publicity purposes of names of licensors or authors of the material; or e) Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability to the recipient, for any liability that these contractual assumptions directly impose on those licensors and authors. All other non-permissive additional terms are considered "further restrictions" within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying. If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement of the additional terms that apply to those files, or a notice indicating where to find the applicable terms. Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way. 8. Termination. You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11). However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation. Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice. Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10. 9. Acceptance Not Required for Having Copies. You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so. 10. Automatic Licensing of Downstream Recipients. Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License. An "entity transaction" is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party's predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts. You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it. 11. Patents. A "contributor" is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor's "contributor version". A contributor's "essential patent claims" are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, "control" includes the right to grant patent sublicenses in a manner consistent with the requirements of this License. Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor's essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version. In the following three paragraphs, a "patent license" is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To "grant" such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party. If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent license to downstream recipients. "Knowingly relying" means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient's use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid. If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it. A patent license is "discriminatory" if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007. Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law. 12. No Surrender of Others' Freedom. If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program. 13. Use with the GNU Affero General Public License. Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such. 14. Revised Versions of this License. The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation. If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program. Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version. 15. Disclaimer of Warranty. THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 16. Limitation of Liability. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 17. Interpretation of Sections 15 and 16. If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. 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mostlyclean-libtool pdf pdf-am ps ps-am tags uninstall \ uninstall-am uninstall-binPROGRAMS uninstall-libLTLIBRARIES \ uninstall-libminswrt_laHEADERS uninstall-minswrtextraDATA # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: phylo-1.0.6/minswrt/config.cpp0000644000175000017500000000137311434510050013243 00000000000000/** * This file is only needed by the Makefile. It contains no data. * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ phylo-1.0.6/minswrt/tools.h0000644000175000017500000000523511434510050012604 00000000000000/** * filename: tools.h * author: Martin Bader * begin: 25.07.2005 * last change: 11.08.2008 * * Useful functions for MinSWRT. * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef TOOLS_H_ #define TOOLS_H_ #include "config.h" #include "permutation.h" namespace minswrt { // define console commandos #define CONSOLE_RESET "\033[0m" #define CONSOLE_BOLD "\033[1m" #define CONSOLE_HALFBRIGHT "\033[2m" #define CONSOLE_UNDERSCORE "\033[4m" #define CONSOLE_BLINK "\033[5m" #define CONSOLE_REVERSE "\033[7m" #define CONSOLE_NORMALBRIGHT "\033[22m" #define CONSOLE_UNDERSCROE_OFF "\033[24m" #define CONSOLE_BLINK_OFF "\033[25m" #define CONSOLE_REVERSE_OFF "\033[27m" #define CONSOLE_COLOR_BLACK "\033[30m" #define CONSOLE_COLOR_RED "\033[31m" #define CONSOLE_COLOR_GREEN "\033[32m" #define CONSOLE_COLOR_BROWN "\033[33m" #define CONSOLE_COLOR_BLUE "\033[34m" #define CONSOLE_COLOR_MAGENTA "\033[35m" #define CONSOLE_COLOR_CYAN "\033[36m" #define CONSOLE_COLOR_WHITE "\033[37m" #define CONSOLE_UNDERSCORE_CDEFAULT "\033[38m" #define CONSOLE_UNDERSCORE_OFF_CDEFAULT "\033[39m" #define CONSOLE_BACKGROUND_BLACK "\033[40m" #define CONSOLE_BACKGROUND_RED "\033[41m" #define CONSOLE_BACKGROUND_GREEN "\033[42m" #define CONSOLE_BACKGROUND_BROWN "\033[43m" #define CONSOLE_BACKGROUND_BLUE "\033[44m" #define CONSOLE_BACKGROUND_MAGENTA "\033[45m" #define CONSOLE_BACKGROUND_CYAN "\033[46m" #define CONSOLE_BACKGROUND_WHITE "\033[47m" #define CONSOLE_BACKGROUND_DEFAULT "\033[49m" /** * Checks if an array of size 3 is cyclic sorted. If two elements are equal, * it will return true. If all elements are equal, it will return false. * @param f_array the array * @return true if the array is cyclic sorted */ inline bool cyclicSorted(int f_array[3]) { return (f_array[0] > f_array[1]) ^ (f_array[1] > f_array[2]) ^ (f_array[2] > f_array[0]); } /** * Checks if two 3-cycles are interleaving. * @param f_c first cycle * @param f_d second cycle */ bool interleaving(const Cycle& f_c, const Cycle& f_d); } // end namespace minswrt #endif phylo-1.0.6/minswrt/Makefile.am0000644000175000017500000000071711434510050013327 00000000000000lib_LTLIBRARIES = libminswrt.la libminswrt_ladir = $(includedir) libminswrt_la_SOURCES = config.cpp minswrt.cpp permutation.cpp tools.cpp libminswrt_la_HEADERS = $(libminswrt_la_SOURCES:%.cpp=%.h) libminswrt_la_LDFLAGS = -version-info 0:2:0 bin_PROGRAMS = minswrt minswrt_SOURCES = start.cpp minswrt_LDADD = libminswrt.la EXTRA_DIST = $(libminswrt_la_HEADERS) test.in COPYING README minswrtextradir = $(datadir)/minswrt minswrtextra_DATA = test.in COPYING README phylo-1.0.6/minswrt/start.cpp0000644000175000017500000000715511434510050013137 00000000000000/** * filename: start.cpp * author: Martin Bader * begin: 21.07.2005 * last change: 23.08.2010 * * Start file for minswrt. Contains a small UI. * * Copyright (C) 2005-2010 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include #include #include #include #include "minswrt.h" #include "permutation.h" using namespace std; using namespace minswrt; /** * Reads a permutation from an input file. The array will be written to * f_origin and f_target (which are references of a pointer), and the * permutation size will be returned. * @param f_filename the name of the file * @param f_origin reference of the origin data pointer * @param f_target reference of the target data pointer * @return permutation size */ int readFile(char* f_filename, int*& f_origin, int*& f_target) { ifstream input; // file input stream int size; // permutation size input.open(f_filename); if (!input.is_open()) { cerr << "error while opening the file " << f_filename << endl; return -1; } while (input.peek() == '#') // line is a comment input.ignore(999, '\n'); input >> size; input.ignore(999, '\n'); f_origin = new int[size]; f_target = new int[size]; while (input.peek() == '#') // line is a comment input.ignore(999, '\n'); for (int i = 0; i < size; i++) input >> f_origin[i]; input.ignore(999, '\n'); while (input.peek() == '#') // line is a comment input.ignore(999, '\n'); for (int i = 0; i < size; i++) input >> f_target[i]; input.close(); return size; } /** * The main file. * Usage: minswrt testfile wr wt * @param f_argc number of arguments * @param f_argv the arguments * @return the exit code */ int main(int f_argc, char** f_argv) { MinSWRT minswrt; int size; int* origin; int* target; int branch[4]; cout << "*****************************************************************\n"; cout << "minswrt v1.1.1 Copyright (C) 2005-2010 Martin Bader\n"; cout << "This program comes with ABSOLUTELY NO WARRANTY.\n"; cout << "This is free software, and you are welcome to redistribute it\n"; cout << "under certain conditions.\n"; cout << "For details about the licence, read the file gpl.txt\n"; cout << "*****************************************************************\n"; if (f_argc != 4) { cerr << "usage: minswrt testfile wr wt" << endl; return 0; } size = readFile(f_argv[1], origin, target); minswrt.setWeights(atof(f_argv[2]), atof(f_argv[3])); minswrt.setGreedy(0); branch[0] = 30; branch[1] = 30; branch[2] = 30; branch[3] = 30; minswrt.setPermutationSize(size); minswrt.setOrigin(origin); minswrt.setTarget(target); cout << "minDistance: " << minswrt.getLowerBound() << endl; minswrt.sort(); minswrt.printResult(4); delete[] origin; delete[] target; return 0; } phylo-1.0.6/minswrt/test.in0000644000175000017500000000133611434510050012600 00000000000000105 1 2 3 4 5 6 7 8 -40 -39 -38 -37 -60 -59 -58 -57 -56 -36 -35 -34 -33 -32 -31 -30 -29 -28 -27 -26 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -15 -14 -13 -12 -11 -10 -9 -44 -43 -42 -41 45 46 47 48 -55 -54 -53 -52 -51 -50 -49 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 -105 -104 -103 -102 -101 -100 -99 -98 -97 1 2 3 4 5 6 7 8 28 -36 -35 -34 -33 -32 -31 -30 -29 -27 -26 40 56 57 58 59 60 37 38 39 -25 -24 -23 -22 -21 -20 -19 -18 -17 -16 -15 -14 -13 -12 -11 -10 -9 -44 -43 -42 -41 45 46 47 48 -55 -54 -53 -52 -51 -50 -49 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 -105 -104 -103 -102 -101 -100 -99 -98 -97 phylo-1.0.6/minswrt/minswrt.h0000644000175000017500000006215211434510050013150 00000000000000/** * filename: minswrt.h * author: Martin Bader * begin: 22.07.2005 * last change: 11.08.2008 * * The main class of Sorting by Weighted Reversals and Transpositions. * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #ifndef MINSWRT_H_ #define MINSWRT_H_ #include "config.h" #include #include "permutation.h" namespace minswrt { // forward declarations class Permutation; /** * The main class, contains the whole functionality. */ class MinSWRT { /*********************************************************************** * member variables ***********************************************************************/ protected: /** Searching strategy: 0 without greedy (default, O(n^2) ); 1 greedy * ( O(n^3) ); 2 greedy with lookahead */ int m_greedy; /** The depth of the lookahead (if used) */ int m_lookaheadDepth; /** The lookahead branching parameters (i.th value: branch a[i] best * sequences */ int m_lookaheadBranch[64]; /** Weight of reversals */ float m_wr; /** Weight of transpositions and transreversals */ float m_wt; /** Size of the permutations (origin and target) */ int m_size; /** The origin permutation */ const int* m_origin; /** The target permutation. */ const int* m_target; /** The permutation to sort (mapped origin permutation). */ Permutation* m_perm; /** The equivalent simple permutation. */ Permutation* m_simplePerm; /** Position of the elements of m_perm in m_simplePerm. */ int* m_simplePosition; /** Dirty-flag for the mapping of origin/target to m_perm/id */ bool m_dirtyMapping; /** The actual starting sequence (nodes write directly in this) */ Sequence* m_sequence; /** A vector of operations that sorts the permutation */ vector m_sorting; /** While mimicking the sorting, there occurs a cyclic shift of the * permutation. This variable is the actual shift of m_perm. */ int m_shift; private: /** Avoids frequent memory allocation */ int* m_tempData; // !!DEBUG int twomoves; int othermoves; /*********************************************************************** * methods ***********************************************************************/ public: /** * The constructor. */ MinSWRT(); /** * The destructor. */ ~MinSWRT(); /** * Sets the searching strategy of the algorithm: 0: no greedy; 1 greedy * without lookahead; 2 greedy with lookahead. * The Greedy-algorithm has a running-time of O(n^3), but is * expected to return better sequences than without greedy (non-Greedy * has running time of O(n^2). Use of lookahead increases the running * time to !!TODO but should return even better results. * @param f_greedy searching strategy */ void setGreedy(int f_greedy) { m_greedy = f_greedy; } /** * Sets the lookahead depth and branching parameters. Automatically sets * the mode to lookahead. f_depth is the lookahead depth, and must be * >= 0 (0 means a pseudo-lookahead for moves with delta codd = 2). * f_branch is an array with the branching degree for the different * depths (so f_depth[i] = k means that the k best sequences will be * expanded in the i.th recursive step). The array must have a size * >= f_depth. * Additional to the lookahead depth, one pseudo-lookahead step * (calculating the change of t/tr-oriented 3-cycles and r-oriented * 2-cycles) will be performed when using lookahead. * @param f_depth the depth of the lookahead * @param f_branch array with branching degrees */ void setLookaheadParams(int f_depth, const int* f_branch); /** * Sets the weights w_r (for reversals) and w_t (for transpositions and * transreversals). The algorithm provides a 1.5-approximation for * w_r <= w_t <= 2 w_r. * @param f_wr weight of reversals * @param f_wt weight of transpositions and transreversals */ void setWeights(float f_wr, float f_wt); /** * Sets the size of the permutations. You must call this function before * calling setOrigin or setTarget. * @param f_size permutation size */ void setPermutationSize(int f_size); /** * Sets the origin permutation. The size of the permutation must be set * with setPermutationSize; the data must be a permutation of the * integers 1 .. f_size, plus additional sign. */ void setOrigin(const int* f_data); /** * Sets the target permutation. The size of the permutation must be set * with setPermutationSize; the data must be a permutation of the * integers 1 .. f_size, plus additional sign. */ void setTarget(const int* f_data); /** * Sets both the origin and the target permutation. Both must have the * size f_size. f_origin and f_target contain the permutation data. The * data must be a permutation of the integers 1 .. f_size, plus * additional signs. * @param f_size the permutation size * @param f_data the elements */ void setPermutations(int f_size, const int* f_origin, const int* f_target); /** * Returns a lower bound for the weighted distance. * @return a lower bound for the weighted distance */ float getLowerBound(); /** * Performs the sorting algorithm, including all preparing steps * (permutation mapping, generating simple permutation. ...). */ void sort(); /** * Initializes the starting sequences functionality. * Call this before the first call of getStartingSequences. */ void initStartingSequences(); /** * Creates a vector of possible starting sequences. The result * will be written to f_result, which must be initialized with * the size of the simple permutation. The number of valid sequences * in the result will be the returned value. * @param f_result the resulting sequences will be written to here * @return the number of found sequences */ int getStartingSequences(Sequence* f_result); /** * Performs a sequence on the simple permutation. * @param f_seq the sequence to perform * */ void performStartingSequence(Sequence* f_seq); /** * Prints the result to stdout. sort must have been called before this. * f_printLevel determins how much information will be written. * f_printLevel: * 0: only write overall weight * 1: write operations * 2: write operations + overall weight * 3: write operations + permutations * 4: write operations + permutations + overall weight * @param f_printLevel the print level */ void printResult(int f_printLevel); /** * Returns a pointer to the result vector. * @return the result vector */ const vector* getResult(); protected: /** * Maps the permutation from origin/target to m_perm/id. After this, * m_perm is correctly initialized. */ void mapPermutations(); /** * Generates the simple permutation. The permutation must be set. */ void generateSimplePermutation(); /** * Performs a sequence of operations. * @param f_seq the sequence to perform */ void performSequence(Sequence* f_seq); /** * Mimicks an operation on the original permutation. This just changes * the array m_simplePosition and writes the the operation to the result * vector. * @param f_operation the operation to mimick */ void mimickOperation(Operation& f_operation); /** * Root node of the sorting algorithm; as long as the simple permutation * is not yet sorted, a cycle will be choosen, a known case in the tree * will be searched for, and a sequence to solve the case will be * performed. */ void nodeRoot(); /** * Greedy version of the root node; always searches for the best sequence * (but this is not an exhaustive search). */ void nodeRootGreedy(); /** * Lookahead version of the root node; always searches for the best * sequence, use a lookahead of 1 (but this is not an exhaustive search). */ void nodeRootLookahead(); /** * Performs the lookahead for the Sequence f_seq. The return value is the * best ratio delta sigma / w that the lookahead can find if we begin * with the given sequence. f_depth is the used lookahead depth (so if it * is 1 only the next sequences will be considered). Note that this is * not an exhaustive search. * The sequence not passed by a reference but by a copy because we have * to perform some changes on it and don't want to have side effects. * @param f_seq the first sequence to perform * @param f_depth depth of the lookahead * @return delta sigma / w for the best concatenation of sequences */ float doLookahead(Sequence f_seq, int f_depth); /** * Node 000: c is an r-oriented 2-cycle. * @param f_c cycle c */ void node000(Cycle& f_c); /** * Node 001: c is a 3-twisted 3-cycle. * @param f_c cycle c */ void node001(Cycle& f_c); /** * Node 002: c is a 2-twisted 3-cycle. * @param f_c cycle c */ void node002(Cycle& f_c); /** * Node 003: c is an r-unoriented 2-cycle. * @param f_c cycle c */ void node003(Cycle& f_c); /** * Node 004: c is a nontwisted 3-cycle. * @param f_c cycle c */ void node004(Cycle& f_c); /** * Node 005: c is a 1-twisted 3-cycle. * @param f_c cycle c */ void node005(Cycle& f_c); /** * Node 006: c,d are intersecting r-unoriented 2-cycles. * @param f_c cycle c * @param f_d cycle d */ void node006(Cycle& f_c, Cycle& f_d); /** * Node 007: c is an r-unoriented 2-cycle, d is a 1-twisted 3-cycle. c * intersects the nontwisted chord of d. The edge of c that lies between * the nontwisted edges of d is m_edge[0]. * @param f_c cycle c * @param f_d cycle d */ void node007(Cycle& f_c, Cycle& f_d); /** * Node 008: c is an r-unoriented 2-cycle, d is a nontwisted 3-cycle. c * and d are intersecting. The chord of d not intersected by c is between * the reality-edges m_edges[1] and m_edges[2]. m_edges[0] of c lies * between m_edges[0] and m_edges[1] of d. * @param f_c cycle c * @param f_d cycle d */ void node008(Cycle& f_c, Cycle& f_d); /** * Node 009: c and e are r-unoriented 2-cycles, d is a nontwisted 3-cycle. * c.m_edges[0] lies between the reality-edges m_edges[0] and m_edges[1] * of d, e.m_edges[0] lies between m_edges[1] and m_edges[2] of d. * c.m_edges[1] lies between m_edges[0] and m_edges[2] of d. The position * of e.m_edges[1] is arbitrary. * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node009(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 010: c is an r-unoriented 2-cycle, d and e are nontwisted 3-cycles. * c intersects d (m_edges[0] of c between m_edges[0] and m_edges[1] of * d, m_edges[1] of c between m_edges[2] and m_edges[0] of d). e * intersects d (m_edges[0] of e between m_edges[1] and m_edges[2] * of d, no edge of d between m_edges[1] and m_edges[2] of e). * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node010(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 011: c is r-unoriented 2-cycle, d and e are nontwisted 3-cycles. * The configuration looks like this: * * c0 * e2 e1 * * d1 d0 * * e0 c1 * d2 * * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node011(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 012: c and e are r-unoriented 2-cycles, d is a nontwisted * 3-cycle. c.m_edges[0] lies between the reality-edges m_edges[0] and * m_edges[1] of d, c.m_edges[1] lies between the reality-edges * m_edges[2] and m_edges[0] of d, e.m_edges[0] lies between m_edges[1] * and m_edges[2] of d. The two 2-cycles are not intersecting. * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node012(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 013: c is r-unoriented 2-cycle, d and e are nontwisted 3-cycles. * The configuration looks like this: * * c0 * d1 d0 * * e0 e2 * * d2 c1 * e1 * * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node013(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 014: c is an r-unoriented 2-cycle, d and e are nontwisted 3-cycles. * c intersects d (m_edges[0] of c between m_edges[0] and m_edges[1] of * d, m_edges[1] of c between m_edges[2] and m_edges[0] of d). e * intersects d (at least one edge of e between m_edges[1] and m_edges[2] * of d). The chord between m_edges[1] and m_edges[2] of e is neither * intersected by c nor by d. * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node014(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 015: c and f are an r-unoriented 2-cycle, d and e are nontwisted * 3-cycles. c intersects d (m_edges[0] of c between m_edges[0] and * m_edges[1] of d, m_edges[1] of c between m_edges[2] and m_edges[0] of * d). e intersects d (at least one edge of e between m_edges[1] and * m_edges[2] of d). The chord between m_edges[1] and m_edges[2] of e is * neither intersected by c nor by d, but intersected by f (f.m_edges[0] * between the reality-edges). c and f are not intersecting; if d and f * are intersecting, no reality-edge of f is between d.m_edges[1] and * d.m_edges[2]. * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e * @param f_f cycle f */ void node015(Cycle& f_c, Cycle& f_d, Cycle& f_e, Cycle& f_f); /** * Node 016: c and d are two interleaving nontwisted 3-cycles. * @param f_c cycle c * @param f_d cycle d */ void node016(Cycle& f_c, Cycle& f_d); /** * Node 017: c and d are two intersecting, non-interleaving nontwisted * 3-cycles. For both cycles, the non-intersected chord is between the * reality-edges m_edges[1] and m_edges[2]. * and d are intersecting * @param f_c cycle c * @param f_d cycle d */ void node017(Cycle& f_c, Cycle& f_d); /** * Node 018: c, d and e are nontwisted 3-cycles. c intersects d * (d.m_edges[0] between c.m_edges[0] and c.m_edges[1], others outside), * e intersects d (e.m_edges[0] between d.m_edges[1] and d.m_edges[2]). * There is no pair of interleaving cycles. * @param f_c cycle c * @param f_d cycle d * @param f_d cycle e */ void node018(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 019: c and d are nontwisted 3-cycles, e is a 1-twisted 3-cycle. * There is no pair of interleaving cycles. c intersects with d (with * the chords between reality-edges 0,1 and 2, 0 of both cycles). e * intersects with d (at least one reality-edge of e between * reality-edges 1 and 2 of d). * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node019(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 020: c, d and e are nontwisted 3-cycles. c intersects d * (d.m_edges[0] between c.m_edges[0] and c.m_edges[1], others outside), * e intersects d (e.m_edges[0] between d.m_edges[1] and d.m_edges[2]). * There is no pair of interleaving cycles. c and e are not intersecting. * @param f_c cycle c * @param f_d cycle d * @param f_d cycle e */ void node020(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 021: c, d and e are nontwisted 3-cycles. c intersects d * (d.m_edges[0] between c.m_edges[0] and c.m_edges[1], others outside), * e intersects d (e.m_edges[0] between d.m_edges[1] and d.m_edges[2]). * There is no pair of interleaving cycles. c and e are intersecting (so * the cycles are mutually intersecting). * @param f_c cycle c * @param f_d cycle d * @param f_d cycle e */ void node021(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 022: c and d are nontwisted 3-cycles, e is a 1-twisted 3-cycle. * There is no pair of interleaving cycles. c intersects with d (with * the chords between reality-edges 0,1 and 2, 0 of both cycles). e * intersects with d (at least one reality-edge of e between * reality-edges 1 and 2 of d). c and e are not intersecting. * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node022(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 023: c and d are nontwisted 3-cycles, e is a 1-twisted 3-cycle. * There is no pair of interleaving cycles. c intersects with d (with * the chords between reality-edges 0,1 and 2, 0 of both cycles). e * intersects with d (at least one reality-edge of e between * reality-edges 1 and 2 of d). c and e are intersecting (so the cycles * are mutually intersecting). * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node023(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 024: c and d are two interleaving 1-twisted 3-cycles. * @param f_c cycle c * @param f_d cycle d */ void node024(Cycle& f_c, Cycle& f_d); /** * Node 025: c and d are non-interleaving 1-twisted 3-cycles. d * intersects the nontwisted chord of c. * @param f_c cycle c * @param f_d cycle d */ void node025(Cycle& f_c, Cycle& f_d); /** * Node 026: c is a 1-twisted 3-cycle, d is a nontwisted 3-cycle. d * intersects the nontwisted chord of c. The chord of d that is not * intersected by c lies between the reality edges m_edges[1] and * m_edges[2]. * and d are intersecting * @param f_c cycle c * @param f_d cycle d */ void node026(Cycle& f_c, Cycle& f_d); /** * Node 027: c and d are two 1-twisted 3-cycles that form a 1-twisted * pair. The twist of c is left (counterclockwise after) the twist of d. * @param f_c cycle c * @param f_d cycle d */ void node027(Cycle& f_c, Cycle& f_d); /** * Node 028: c, d are intersecting, non-interleaving 1-twisted 3-cycles. * Both cycles intersect the nontwisted chord of the other cycle. * Reality-edge m_edges[0] of cycle d lies between reality-edges * m_edges[0] and m_edges[1] of cycle c. * @param f_c cycle c * @param f_d cycle d */ void node028(Cycle& f_c, Cycle& f_d); /** * Node 029: c, d are intersecting, non-interleaving 1-twisted 3-cycles. * d intersects the nontwisted chord of c, but c doesn't intersect the * nontwisted chord of d * @param f_c cycle c * @param f_d cycle d */ void node029(Cycle& f_c, Cycle& f_d); /** * Node 030: c is 1-twisted 3-cycle, d is nontwisted 3-cycle, e is * r-unoriented 2-cycle. d intersects the nontwisted chord of c, c does * not intersect the chord between m_edges[1] and m_edges[2] of d. This * chord is intersected by e (with m_edges[0] between the reality-edges. * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node030(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 031: c, e are 1-twisted 3-cycles, d is nontwisted 3-cycle. d * intersects the nontwisted chord of c, c does not intersect the chord * between m_edges[1] and m_edges[2] of d. This chord is intersected by * e. There is no pair of interleaving cycles. * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node031(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 032: c is 1-twisted 3-cycle, d is nontwisted 3-cycle, e is * r-unoriented 2-cycle. d intersects the nontwisted chord of c. * d.m_edges[1] and d.m_edges[2] lie between c.m_edges[0] and * c.m_edges[1]. e intersects d (e.m_edges[0] between d.m_edges[1] and * d.m_edges[2]), but does not intersect c. * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node032(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 033: c is 1-twisted 3-cycle, d is nontwisted 3-cycle, e is * r-unoriented 2-cycle. d intersects the nontwisted chord of c. * d.m_edges[1] and d.m_edges[2] are outside of arc c.m_edges[0], * c.m_edges[1]. e intersects d (e.m_edges[0] between d.m_edges[1] and * d.m_edges[2]), but does not intersect c. * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node033(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 034: c, e are 1-twisted 3-cycles, d is nontwisted 3-cycle. d * intersects the nontwisted chord of c, c does not intersect the chord * between m_edges[1] and m_edges[2] of d. This chord is intersected by * e. c and e are not intersecting. * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node034(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 035: c, e are 1-twisted 3-cycles, d is nontwisted 3-cycle. d * intersects the nontwisted chord of c, c does not intersect the chord * between m_edges[1] and m_edges[2] of d. This chord is intersected by * e. There is no pair of interleaving cycles. c and e are intersecting. * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node035(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node036: c and d are two interleaving 1-twisted 3-cycles that do not * form a 1-twisted pair. * @param f_c cycle c * @param f_d cycle d */ void node036(Cycle& f_c, Cycle& f_d); /** * Node 037: c, e are 1-twisted 3-cycles, d is nontwisted 3-cycle. d * intersects the nontwisted chord of c, c does not intersect the chord * between m_edges[1] and m_edges[2] of d. This chord is intersected by * a nontwisted chord of e. c and e are not intersecting. * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node037(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 038: c, e are 1-twisted 3-cycles, d is nontwisted 3-cycle. d * intersects the nontwisted chord of c, c does not intersect the chord * between m_edges[1] and m_edges[2] of d. This chord is intersected by * the two twisted chords of e. c and e are not intersecting. * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node038(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 039: c, e are 1-twisted 3-cycles, d is nontwisted 3-cycle. d * intersects the nontwisted chord of c, c does not intersect the chord * between m_edges[1] and m_edges[2] of d. This chord is intersected by * e. There is no pair of interleaving cycles. c and e are intersecting * with their twisted chords. * @param f_c cycle c * @param f_d cycle d * @param f_e cycle e */ void node039(Cycle& f_c, Cycle& f_d, Cycle& f_e); /** * Node 040: c is a nontwisted 3-cycle, d is a 1-twisted 3-cycle. c and d * are interleaving. The twisted edge of d lies between m_edges[1] and * m_edges[2] of cycle c. * @param f_c cycle c * @param f_d cycle d */ void node040(Cycle& f_c, Cycle& f_d); /*********************************************************************** * debugging methods ***********************************************************************/ public: /** * Debugging stuff; changes permanently. */ void debug(); }; } // end namespace minswrt #endif phylo-1.0.6/minswrt/minswrt.cpp0000644000175000017500000071565611434510050013521 00000000000000/** * filename: minswrt.cpp * author: Martin Bader * begin: 22.07.2005 * last change: 15.08.2008 * * The main class of Sorting by Weighted Reversals and Transpositions. * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "minswrt.h" #include #include #include "permutation.h" #include "tools.h" namespace minswrt { using namespace std; /*************************************************************************** * public methods ***************************************************************************/ MinSWRT::MinSWRT() { m_greedy = false; m_lookaheadDepth = 2; m_lookaheadBranch[0] = 5; m_lookaheadBranch[1] = 5; m_wr = 2.0f / 3.0f; m_wt = 1.0f; m_origin = NULL; m_target = NULL; m_perm = new Permutation(); m_simplePerm = NULL; m_simplePosition = NULL; m_dirtyMapping = true; m_sequence = new Sequence(); m_sequence->m_numOperations = 0; m_shift = 0; m_tempData = NULL; } MinSWRT::~MinSWRT() { delete m_perm; m_perm = NULL; delete m_simplePerm; m_simplePerm = NULL; delete[] m_simplePosition; m_simplePosition = NULL; delete m_sequence; m_sequence = NULL; delete[] m_tempData; m_tempData = NULL; } void MinSWRT::setLookaheadParams(int f_depth, const int* f_branch) { m_greedy = 2; m_lookaheadDepth = f_depth; for (int i = 0; i < m_lookaheadDepth; i++) m_lookaheadBranch[i] = f_branch[i]; } void MinSWRT::setWeights(float f_wr, float f_wt) { m_wr = f_wr; m_wt = f_wt; } void MinSWRT::setPermutationSize(int f_size) { m_size = f_size; delete[] m_tempData; m_tempData = new int[f_size]; } void MinSWRT::setOrigin(const int* f_data) { m_origin = f_data; m_dirtyMapping = true; } void MinSWRT::setTarget(const int* f_data) { m_target = f_data; m_dirtyMapping = true; } void MinSWRT::setPermutations(int f_size, const int* f_origin, const int* f_target) { m_size = f_size; m_origin = f_origin; m_target = f_target; m_dirtyMapping = true; delete[] m_tempData; m_tempData = new int[f_size]; } float MinSWRT::getLowerBound() { bool* visited = new bool[m_size]; // visited reality-edges int cyclelength; // length of the current cycle int pos; // position of current reality-edge bool left; // true if we leave the RE at the left point int element; // the next element (unsigned) int ceven = 0; // number of even cycles int codd = 0; // number of odd cycles if (m_dirtyMapping) { mapPermutations(); delete[] m_simplePosition; m_simplePosition = new int[m_size]; } for (int i = 0; i < m_size; i++) visited[i] = false; for (int i = 0; i < m_size; i++) { if (!visited[i]) // new cycle { cyclelength = 0; pos = i; left = true; do { visited[pos] = true; cyclelength++; if (left) element = m_perm->m_data[pos]; else element = m_perm->m_data[(pos+1) % m_size]; if (left ^ (element > 0)) // go to element - 1, upper point { left = false; // left now indicates point of target element = abs(element) - 1; if (element == 0) element = m_size; } else // go to element + 1, lower point { left = true; // left now indicates point of target element = abs(element) + 1; if (element > m_size) element = 1; } pos = m_perm->m_index[element]; if (!(left ^ (m_perm->m_data[pos] > 0))) { pos = (pos + m_size - 1) % m_size; left = true; } else left = false; } while (!visited[pos]); if (cyclelength & 1) codd++; else ceven++; } } delete[] visited; return ceven * m_wr + ((m_size - codd) / 2 - ceven) * m_wt; } void MinSWRT::sort() { if (m_dirtyMapping) { mapPermutations(); delete[] m_simplePosition; m_simplePosition = new int[m_size]; } generateSimplePermutation(); m_sorting.erase(m_sorting.begin(), m_sorting.end()); m_shift = 0; if (m_greedy == 0) nodeRoot(); else if (m_greedy == 1) nodeRootGreedy(); else if (m_greedy == 2) { if (m_lookaheadDepth == 0) // only do pseudo lookahead nodeRootGreedy(); else nodeRootLookahead(); } else cerr << "minSWRT::sort: invalid parameter for greedy strategy\n"; } void MinSWRT::initStartingSequences() { if (m_dirtyMapping) { mapPermutations(); delete[] m_simplePosition; m_simplePosition = new int[m_size]; } generateSimplePermutation(); } int MinSWRT::getStartingSequences(Sequence* f_result) { Cycle cycle; int counter = 0; for (int i = 0; i < m_simplePerm->size(); i++) // for all possible cycles { m_simplePerm->getCycleOfEdge(i, &cycle); // choose node switch (cycle.m_type) { case Cycle::CYCLE_ADJACENCY: continue; case Cycle::CYCLE_2ORIENTED: node000(cycle); break; case Cycle::CYCLE_2UNORIENTED: node003(cycle); break; case Cycle::CYCLE_0TWISTED: node004(cycle); break; case Cycle::CYCLE_1TWISTED: node005(cycle); break; case Cycle::CYCLE_2TWISTED: node002(cycle); break; case Cycle::CYCLE_3TWISTED: node001(cycle); break; default: cerr << "error in MinSWRT::nodeRootGreedy: Algo found unexpected cycle type\n"; printCycle(cycle); return counter; } // copy to result vector f_result[counter].m_numOperations = m_sequence->m_numOperations; for (int j = 0; j < m_sequence->m_numOperations; j++) f_result[counter].m_operations[j] = m_sequence->m_operations[j]; f_result[counter].m_ratio = m_sequence->m_ratio; f_result[counter].m_dsigma = m_sequence->m_dsigma; f_result[counter].m_weight = m_sequence->m_weight; counter++; } return counter; } void MinSWRT::performStartingSequence(Sequence* f_seq) { int order1[3]; // needed to check is something is cyclic sorted int order2[3]; // needed to check is something is cyclic sorted int delta1, delta2; // distance to move int size = m_simplePerm->size(); // permutation size for (int i = 0; i < f_seq->m_numOperations; i++) { m_simplePerm->performOperation(f_seq->m_operations[i]); // update operations if ((f_seq->m_operations[i].m_type == Operation::OPERATION_REVERSAL) || (f_seq->m_operations[i].m_type == Operation::OPERATION_TRANSREVERSAL)) { order1[0] = f_seq->m_operations[i].m_edges[0]; order1[1] = f_seq->m_operations[i].m_edges[1]; for (int j = i+1; j < f_seq->m_numOperations; j++) { for (int k = 0; k < 3; k++) { order1[2] = f_seq->m_operations[j].m_edges[k]; if (!cyclicSorted(order1)) // move the edge f_seq->m_operations[j].m_edges[k] = (f_seq->m_operations[i].m_edges[0] + f_seq->m_operations[i].m_edges[1] - f_seq->m_operations[j].m_edges[k] + size) % size; } } } if ((f_seq->m_operations[i].m_type == Operation::OPERATION_TRANSPOSITION) || (f_seq->m_operations[i].m_type == Operation::OPERATION_TRANSREVERSAL)) { order1[0] = f_seq->m_operations[i].m_edges[1]; order1[1] = f_seq->m_operations[i].m_edges[2]; order2[0] = f_seq->m_operations[i].m_edges[2]; order2[1] = f_seq->m_operations[i].m_edges[0]; delta1 = f_seq->m_operations[i].m_edges[0] - f_seq->m_operations[i].m_edges[2]; delta2 = f_seq->m_operations[i].m_edges[2] - f_seq->m_operations[i].m_edges[1]; for (int j = i+1; j < f_seq->m_numOperations; j++) { for (int k = 0; k < 3; k++) { if (f_seq->m_operations[j].m_edges[k] == f_seq->m_operations[i].m_edges[2]) f_seq->m_operations[j].m_edges[k] = (f_seq->m_operations[j].m_edges[k] + delta1 - delta2 + size) % size; else { order1[2] = f_seq->m_operations[j].m_edges[k]; // move first segment to the back if (!cyclicSorted(order1)) // move the edge f_seq->m_operations[j].m_edges[k] = (f_seq->m_operations[j].m_edges[k] + delta1 + size) % size; else { // move second segment to the front order2[2] = f_seq->m_operations[j].m_edges[k]; if (!cyclicSorted(order2)) // move the edge { f_seq->m_operations[j].m_edges[k] = (f_seq->m_operations[j].m_edges[k] - delta2 + size) % size; } } } } } } } } void MinSWRT::printResult(int f_printLevel) { float weight = 0.0f; // overall weight int* perm; // copy of the permutation int blanks; // blanks to print before an element int p[3]; // the three splitpoints of the operation int range1; // length of firt segment int range2; // length of second segment cout << CONSOLE_BACKGROUND_BLACK << CONSOLE_COLOR_WHITE << CONSOLE_BOLD << endl << endl; if ((f_printLevel == 1) || (f_printLevel == 2)) { for (unsigned int i = 0; i < m_sorting.size(); i++) { switch (m_sorting[i].m_type) { case Operation::OPERATION_REVERSAL: cout << " r("; break; case Operation::OPERATION_TRANSPOSITION: cout << " t("; break; case Operation::OPERATION_TRANSREVERSAL: cout << "tr("; break; default: cerr << "WARNING! MinSWRT::printResult found unexpected operation type!"; break; } cout << m_sorting[i].m_edges[0]; cout << ", " << m_sorting[i].m_edges[1]; if (m_sorting[i].m_type != Operation::OPERATION_REVERSAL) cout << ", " << m_sorting[i].m_edges[2]; cout << ")\n"; } } else if ((f_printLevel == 3) || (f_printLevel == 4)) { // copy permutation perm = new int[m_size]; for (int i = 0; i < m_size; i++) perm[i] = m_origin[i]; // print operation for (unsigned int i = 0; i < m_sorting.size(); i++) { p[0] = m_sorting[i].m_edges[0] - 1; p[1] = m_sorting[i].m_edges[1] - 1; p[2] = m_sorting[i].m_edges[2] - 1; switch (m_sorting[i].m_type) { case Operation::OPERATION_REVERSAL: cout << " r("; break; case Operation::OPERATION_TRANSPOSITION: cout << " t("; break; case Operation::OPERATION_TRANSREVERSAL: cout << "tr("; break; default: cout << "WARNING! Unexpected operation in MinSWRT::printResult\n"; } cout << (m_sorting[i].m_edges[0] < 10?" ":"") << m_sorting[i].m_edges[0] << (m_sorting[i].m_edges[1] < 10?", ":", ") << m_sorting[i].m_edges[1]; if (m_sorting[i].m_type != Operation::OPERATION_REVERSAL) cout << (m_sorting[i].m_edges[2] < 10?", ":", ") << m_sorting[i].m_edges[2]; cout << ")("; // print current permutation if (p[0] > p[1]) // we are in the first segment cout << CONSOLE_COLOR_RED << CONSOLE_BOLD; else if ((p[1] > p[2]) && (m_sorting[i].m_type != Operation::OPERATION_REVERSAL)) // we are in the second segment cout << CONSOLE_COLOR_GREEN << CONSOLE_BOLD; for (int j = 0; j < m_size; j++) { if (j == p[0]) // begin of first segment cout << CONSOLE_COLOR_RED << CONSOLE_BOLD; else if ((j == p[1]) && (m_sorting[i].m_type != Operation::OPERATION_REVERSAL)) // begin of second segment cout << CONSOLE_COLOR_GREEN << CONSOLE_BOLD; else if (((j == p[1]) && (m_sorting[i].m_type == Operation::OPERATION_REVERSAL)) || ((j == p[2]) && (m_sorting[i].m_type != Operation::OPERATION_REVERSAL))) cout << CONSOLE_COLOR_WHITE;// << CONSOLE_NORMALBRIGHT; blanks = (j == 0? 0:1); if (perm[j] > 0) blanks++; if (abs(perm[j]) < 10) blanks++; for (int k = 0; k < blanks; k++) cout << " "; cout << perm[j]; } cout << CONSOLE_COLOR_WHITE << ")\n"; // << CONSOLE_NORMALBRIGHT << ")\n"; // perform the operation if ((m_sorting[i].m_type == Operation::OPERATION_REVERSAL) || (m_sorting[i].m_type == Operation::OPERATION_TRANSREVERSAL)) { for (int j = p[0]; j != p[1]; (j == m_size - 1? j = 0 : j++)) m_tempData[j] = perm[j]; for (int j = p[0]; j != p[1]; (j == m_size - 1? j = 0 : j++)) perm[j] = -m_tempData[(p[0] + p[1] - 1 - j + m_size) % m_size]; } if ((m_sorting[i].m_type == Operation::OPERATION_TRANSPOSITION) || (m_sorting[i].m_type == Operation::OPERATION_TRANSREVERSAL)) { range1 = (p[1] - p[0] + m_size) % m_size; range2 = (p[2] - p[1] + m_size) % m_size; for (int j = 0; j < range1; j++) // store first segment m_tempData[j] = perm[(p[0] + j) % m_size]; for (int j = 0; j < range2; j++) // move second segment to front perm[(p[0] + j) % m_size] = perm[(p[1] + j) % m_size]; for (int j = 0; j < range1; j++) // move first segment to back perm[(p[0] + range2 + j) % m_size] = m_tempData[j]; } } // print current permutation cout << " ("; for (int j = 0; j < m_size; j++) { blanks = (j == 0? 0:1); if (perm[j] > 0) blanks++; if (abs(perm[j]) < 10) blanks++; for (int k = 0; k < blanks; k++) cout << " "; cout << perm[j]; } cout << ")\n"; delete[] perm; } if (!(f_printLevel & 1)) { for (unsigned int i = 0; i < m_sorting.size(); i++) { if (m_sorting[i].m_type == Operation::OPERATION_REVERSAL) weight += m_wr; else weight += m_wt; } cout << "weight: " << weight << endl; } cout << CONSOLE_RESET << endl; } /** * Returns a pointer to the result vector. */ const vector* MinSWRT::getResult() { return &m_sorting; } /*************************************************************************** * protected methods ***************************************************************************/ void MinSWRT::mapPermutations() { int* index = new int[m_size+1]; // stores index of elements of origin for (int i = 0; i < m_size; i++) // initialize index index[abs(m_origin[i])] = i; m_perm->init(m_size); for (int i = 0; i < m_size; i++) // map target to id { if ((m_target[i] > 0) == (m_origin[index[abs(m_target[i])]] > 0)) m_perm->m_data[index[abs(m_target[i])]] = i+1; else m_perm->m_data[index[abs(m_target[i])]] = -(i+1); m_perm->m_index[i+1] = index[abs(m_target[i])]; } m_dirtyMapping = false; delete[] index; } void MinSWRT::generateSimplePermutation() { int size = m_size; // size of the current permutation int simplesize = size; // size of the simple permutation bool* visited = new bool[3 * m_size / 2]; // visited reality-edges // size also ok for simple perm int cyclelength; // length of the current cycle int pos; // position of current reality-edge bool left; // true if we leave the RE at the left point int element; // the next element (unsigned) int splitelement; // the new inserted element int lastpos; // last visited reality-edge int lastleft; // last value for left for (int i = 0; i < size; i++) { visited[i] = false; m_simplePosition[i] = i; } for (int i = 0; i < size; i++) { if (!visited[i]) // new cycle { cyclelength = 0; pos = i; left = true; do { visited[pos] = true; cyclelength++; if (left) element = m_perm->m_data[pos]; else element = m_perm->m_data[(pos+1) % size]; if (left ^ (element > 0)) // go to element - 1, upper point { left = false; // left now indicates point of target element = abs(element) - 1; if (element == 0) element = size; } else // go to element + 1, lower point { left = true; // left now indicates point of target element = abs(element) + 1; if (element > size) element = 1; } pos = m_perm->m_index[element]; if (!(left ^ (m_perm->m_data[pos] > 0))) { pos = (pos + size - 1) % size; left = true; } else left = false; } while (!visited[pos]); if (cyclelength > 3) simplesize += (cyclelength / 2 - 1); } } #if DEBUG cerr << "simplesize: " << simplesize << endl; #endif // create simple permutation delete m_simplePerm; m_simplePerm = new Permutation(); m_simplePerm->init(simplesize); for (int i = 0; i < size; i++) // copy data from original permutation { m_simplePerm->m_data[i] = m_perm->m_data[i]; m_simplePerm->m_index[i+1] = m_perm->m_index[i+1]; } if (size == simplesize) // no splits to perform { delete[] visited; return; } // expand cycles for (int i = 0; i < simplesize; i++) visited[i] = false; for (int i = 0; i < simplesize; i++) // search all reality-edges for long cycles { if (!visited[i]) // new cycle { cyclelength = 0; pos = i; left = false; if (m_simplePerm->m_data[i] > 0) // precalculate the splitelement splitelement = m_simplePerm->m_data[i] + 1; else splitelement = m_simplePerm->m_data[i]; do { visited[pos] = true; lastpos = pos; lastleft = left; cyclelength++; if (left) element = m_simplePerm->m_data[pos]; else element = m_simplePerm->m_data[(pos+1) % size]; if (left ^ (element > 0)) // go to element - 1, upper point { left = false; // left now indicates point of target element = abs(element) - 1; if (element == 0) element = size; } else // go to element + 1, lower point { left = true; // left now indicates point of target element = abs(element) + 1; if (element > size) element = 1; } pos = m_simplePerm->m_index[element]; if (!(left ^ (m_simplePerm->m_data[pos] > 0))) { pos = (pos + size - 1) % size; left = true; } else left = false; } while (!visited[pos] && (cyclelength < 3)); if ((cyclelength == 3) && !visited[pos]) // split this cycle { // increment all values >= splitelement, adjust m_index for (int j = size; j >= abs(splitelement); j--) { if (m_simplePerm->m_data[m_simplePerm->m_index[j]] > 0) m_simplePerm->m_data[m_simplePerm->m_index[j]]++; else m_simplePerm->m_data[m_simplePerm->m_index[j]]--; m_simplePerm->m_index[j+1] = m_simplePerm->m_index[j]; } // move all to the right for (int j = size - 1; j > lastpos; j--) { m_simplePerm->m_data[j+1] = m_simplePerm->m_data[j]; m_simplePerm->m_index[abs(m_simplePerm->m_data[j])]++; visited[j+1] = visited[j]; } // fill in splitelement if (lastleft) { visited[lastpos] = false; visited[lastpos + 1] = true; splitelement *= -1; } else visited[lastpos+1] = false; lastpos++; m_simplePerm->m_data[lastpos] = splitelement; m_simplePerm->m_index[abs(splitelement)] = lastpos; size++; for (int j = 0; j < m_size; j++) // update m_simplePosition { if (m_simplePosition[j] >= lastpos) m_simplePosition[j]++; } if (size == simplesize) { delete[] visited; return; } } } // end if(!visited[i]) } delete[] visited; } void MinSWRT::performSequence(Sequence* f_seq) { int order1[3]; // needed to check is something is cyclic sorted int order2[3]; // needed to check is something is cyclic sorted int delta1, delta2; // distance to move int size = m_simplePerm->size(); // permutation size for (int i = 0; i m_numOperations; i++) { m_simplePerm->performOperation(f_seq->m_operations[i]); // update operations if ((f_seq->m_operations[i].m_type == Operation::OPERATION_REVERSAL) || (f_seq->m_operations[i].m_type == Operation::OPERATION_TRANSREVERSAL)) { order1[0] = f_seq->m_operations[i].m_edges[0]; order1[1] = f_seq->m_operations[i].m_edges[1]; for (int j = i+1; j < f_seq->m_numOperations; j++) { for (int k = 0; k < 3; k++) { order1[2] = f_seq->m_operations[j].m_edges[k]; if (!cyclicSorted(order1)) // move the edge f_seq->m_operations[j].m_edges[k] = (f_seq->m_operations[i].m_edges[0] + f_seq->m_operations[i].m_edges[1] - f_seq->m_operations[j].m_edges[k] + size) % size; } } } if ((f_seq->m_operations[i].m_type == Operation::OPERATION_TRANSPOSITION) || (f_seq->m_operations[i].m_type == Operation::OPERATION_TRANSREVERSAL)) { order1[0] = f_seq->m_operations[i].m_edges[1]; order1[1] = f_seq->m_operations[i].m_edges[2]; order2[0] = f_seq->m_operations[i].m_edges[2]; order2[1] = f_seq->m_operations[i].m_edges[0]; delta1 = f_seq->m_operations[i].m_edges[0] - f_seq->m_operations[i].m_edges[2]; delta2 = f_seq->m_operations[i].m_edges[2] - f_seq->m_operations[i].m_edges[1]; for (int j = i+1; j < f_seq->m_numOperations; j++) { for (int k = 0; k < 3; k++) { if (f_seq->m_operations[j].m_edges[k] == f_seq->m_operations[i].m_edges[2]) f_seq->m_operations[j].m_edges[k] = (f_seq->m_operations[j].m_edges[k] + delta1 - delta2 + size) % size; else { order1[2] = f_seq->m_operations[j].m_edges[k]; // move first segment to the back if (!cyclicSorted(order1)) // move the edge f_seq->m_operations[j].m_edges[k] = (f_seq->m_operations[j].m_edges[k] + delta1 + size) % size; else { // move second segment to the front order2[2] = f_seq->m_operations[j].m_edges[k]; if (!cyclicSorted(order2)) // move the edge { f_seq->m_operations[j].m_edges[k] = (f_seq->m_operations[j].m_edges[k] - delta2 + size) % size; } } } } } } mimickOperation(f_seq->m_operations[i]); } } void MinSWRT::mimickOperation(Operation& f_operation) { int p[3]; // the splitpoints in m_perm int range; // length of a segment int range2; // length of a segment int simplerange; // length of a segment in m_simplePerm int position; // position in m_simplePerm #if 0 // !!DEBUG for (int i = 0; i < m_size; i++) cerr << m_simplePosition[i] << " "; cerr << endl; switch (f_operation.m_type) { case Operation::OPERATION_REVERSAL: cerr << " r "; break; case Operation::OPERATION_TRANSPOSITION: cerr << " t "; break; case Operation::OPERATION_TRANSREVERSAL: cerr << "tr "; break; default: break; } cerr << f_operation.m_edges[0] << " " << f_operation.m_edges[1] << " " << f_operation.m_edges[2] << endl; #endif p[0] = -1; p[1] = -1; p[2] = -1; // find splitpoints for (int j = 0; j < 3; j++) { for (int i = m_size - 1; i >= 0; i--) { if (m_simplePosition[i] > f_operation.m_edges[j]) p[j] = i-1; } if (p[j] == -1) p[j] = m_size - 1; } // update m_simplePos if ((f_operation.m_type == Operation::OPERATION_REVERSAL) || (f_operation.m_type == Operation::OPERATION_TRANSREVERSAL)) { range = (p[1] - p[0] + m_size) % m_size; for (int i = p[1]; i != p[0]; i == 0? i = m_size - 1 : i--) m_tempData[i] = m_simplePosition[i]; for (int i = 0; i < range; i++) { position = m_tempData[(p[1]-i+m_size) % m_size]; position = (f_operation.m_edges[0] + f_operation.m_edges[1] + 1 - position + m_simplePerm->size()) % m_simplePerm->size(); m_simplePosition[(p[0]+i+1) % m_size] = position; } } if ((f_operation.m_type == Operation::OPERATION_TRANSPOSITION) || (f_operation.m_type == Operation::OPERATION_TRANSREVERSAL)) { range = (p[2] - p[1] + m_size) % m_size; range2 = (p[0] - p[2] + m_size) % m_size; simplerange = (f_operation.m_edges[2] - f_operation.m_edges[1] + m_simplePerm->size()) % m_simplePerm->size(); for (int i = 0; i < range; i++) m_tempData[i] = m_simplePosition[(p[1] + i + 1) % m_size]; for (int i = 1; i <= range2; i++) { position = (m_simplePosition[(p[2] + i) % m_size] - simplerange + m_simplePerm->size()) % m_simplePerm->size(); m_simplePosition[(p[2] + i - range + m_size) % m_size] = position; } simplerange = (f_operation.m_edges[0] - f_operation.m_edges[2] + m_simplePerm->size()) % m_simplePerm->size(); for (int i = 0; i < range; i++) m_simplePosition[(p[1] + 1 + range2 + i) % m_size] = (m_tempData[i] + simplerange) % m_simplePerm->size(); } // if the number of dummy elements in the tail segment changes, // m_simplePosition becomes shifted; remove this shift range = 0; // reuse range for (int i = 1; i < m_size; i++) { if (m_simplePosition[i] < m_simplePosition[i-1]) { range = i; break; } } for (int i = 0; i < m_size; i++) m_tempData[i] = m_simplePosition[(i + range) % m_size]; for (int i = 0; i < m_size; i++) m_simplePosition[i] = m_tempData[i]; // write the operation if (p[0] == p[1]) f_operation.m_type = Operation::OPERATION_INVALID; if (p[2] == p[0]) // avoid shifting - shift only when segment1 does not exist p[2] = p[1]; else if ((f_operation.m_type == Operation::OPERATION_TRANSPOSITION) && ((p[0] == p[2]) || (p[1] == p[2]))) f_operation.m_type = Operation::OPERATION_INVALID; else if ((f_operation.m_type == Operation::OPERATION_TRANSREVERSAL) && ((p[0] == p[2]) || (p[1] == p[2]))) f_operation.m_type = Operation::OPERATION_REVERSAL; if (f_operation.m_type == Operation::OPERATION_REVERSAL) // avoid shifting p[2] = p[1]; if (f_operation.m_type != Operation::OPERATION_INVALID) { f_operation.m_edges[0] = (p[0] + 1 + m_shift) % m_size + 1; f_operation.m_edges[1] = (p[1] + 1 + m_shift) % m_size + 1; f_operation.m_edges[2] = (p[2] + 1 + m_shift) % m_size + 1; m_sorting.push_back(f_operation); } // adjust the offset m_shift = (m_shift + p[2] - p[1] + range + m_size) % m_size; } void MinSWRT::nodeRoot() { Cycle cycle; m_simplePerm->getCycle(&cycle); while (cycle.m_type != Cycle::CYCLE_INVALID) { // choose node switch (cycle.m_type) { case Cycle::CYCLE_2ORIENTED: node000(cycle); break; case Cycle::CYCLE_2UNORIENTED: node003(cycle); break; case Cycle::CYCLE_0TWISTED: node004(cycle); break; case Cycle::CYCLE_1TWISTED: node005(cycle); break; case Cycle::CYCLE_2TWISTED: node002(cycle); break; case Cycle::CYCLE_3TWISTED: node001(cycle); break; default: cerr << "error in MinSWRT::nodeRoot: Algo found unexpected cycle type\n"; printCycle(cycle); return; } performSequence(m_sequence); m_simplePerm->getCycle(&cycle); // !!DEBUG: avoid infinite loop if (m_sequence->m_numOperations == 0) { cycle.m_type = Cycle::CYCLE_INVALID; cout << endl << "unexpected behaviour in MinSWRT::nodeRoot\n"; } m_sequence->m_numOperations = 0; } } void MinSWRT::nodeRootGreedy() { Cycle cycle; Sequence gcSeq; // golden cage sequence while (true) { gcSeq.m_ratio = 0.0f; gcSeq.m_numOperations = 0; for (int i = 0; i < m_simplePerm->size(); i++) // for all possible cycles { m_simplePerm->getCycleOfEdge(i, &cycle); // choose node switch (cycle.m_type) { case Cycle::CYCLE_ADJACENCY: continue; case Cycle::CYCLE_2ORIENTED: node000(cycle); break; case Cycle::CYCLE_2UNORIENTED: node003(cycle); break; case Cycle::CYCLE_0TWISTED: node004(cycle); break; case Cycle::CYCLE_1TWISTED: node005(cycle); break; case Cycle::CYCLE_2TWISTED: node002(cycle); break; case Cycle::CYCLE_3TWISTED: node001(cycle); break; default: cerr << "error in MinSWRT::nodeRootGreedy: Algo found unexpected cycle type\n"; printCycle(cycle); return; } if (m_sequence->m_ratio > gcSeq.m_ratio) // copy to golden cage { gcSeq.m_numOperations = m_sequence->m_numOperations; for (int j = 0; j < m_sequence->m_numOperations; j++) gcSeq.m_operations[j] = m_sequence->m_operations[j]; gcSeq.m_ratio = m_sequence->m_ratio; // dsigma and weight are not of interest, so don't copy them } } if (gcSeq.m_numOperations == 0) // permutation sorted return; // perform golden cage sequence performSequence(&gcSeq); } } void MinSWRT::nodeRootLookahead() { Cycle cycle; // cycle in the RDD Sequence* gcSeq = NULL; // sequence in the golden cage list seqList; // list with all actual sequences, sorted by ratio list::iterator it; // list iterator int rank; // current rank in the sequence list float ratio; // overall ratio of the sequence (including LAH) while (true) { for (int i = 0; i < m_simplePerm->size(); i++) // for all possible cycles { m_simplePerm->getCycleOfEdge(i, &cycle); // choose node switch (cycle.m_type) { case Cycle::CYCLE_ADJACENCY: continue; case Cycle::CYCLE_2ORIENTED: node000(cycle); break; case Cycle::CYCLE_2UNORIENTED: node003(cycle); break; case Cycle::CYCLE_0TWISTED: node004(cycle); break; case Cycle::CYCLE_1TWISTED: node005(cycle); break; case Cycle::CYCLE_2TWISTED: node002(cycle); break; case Cycle::CYCLE_3TWISTED: node001(cycle); break; default: cerr << "error in MinSWRT::nodeRootLookahead: Algo found unexpected cycle type\n"; printCycle(cycle); return; } // store sequence it = seqList.begin(); rank = 1; while ((it != seqList.end()) && (rank < m_lookaheadBranch[0]) && ((*it)->m_ratio > m_sequence->m_ratio)) { rank++; it++; } if (rank <= m_lookaheadBranch[0]) { seqList.insert(it, m_sequence); m_sequence = new Sequence(); } } // do lookahead for the best sequences of the list it = seqList.begin(); for (int i = 0; (it != seqList.end()) && (i < m_lookaheadBranch[0]); i++, it++) { ratio = doLookahead(**it, m_lookaheadDepth); if ((gcSeq == NULL) || (ratio > gcSeq->m_ratio)) { gcSeq = *it; gcSeq->m_ratio = ratio; } } if (gcSeq == NULL) // permutation sorted return; // perform golden cage sequence performSequence(gcSeq); // cleaning up for (it = seqList.begin(); it != seqList.end(); it++) delete *it; gcSeq = NULL; seqList.clear(); } } float MinSWRT::doLookahead(Sequence f_seq, int f_depth) { // cerr << "\n entering doLookahead\n"; // cerr << "ratio: " << f_seq.m_ratio << " dsigma: " << f_seq.m_dsigma << " weight: " << f_seq.m_weight << endl; int size = m_simplePerm->size(); // permutation size Permutation* tmp; // used for swapping permutations int order1[3]; // needed to check is something is cyclic sorted int order2[3]; // needed to check is something is cyclic sorted int delta1, delta2; // distance to move Cycle cycle; // a cycle in the RDD (starting cycle of case analysis) list seqList; // list with all actual sequences, sorted by ratio list::iterator it; // list iterator int rank; // current rank in the sequence list int branch = 0; // branching degree in this recursion depth float ratio; // ratio returned from a recursive call float result = 0.0f; // best possible ratio over all sequences if (f_depth > 1) // else not needed branch = m_lookaheadBranch[m_lookaheadDepth - f_depth + 1]; // store old permutation tmp = m_simplePerm; m_simplePerm = new Permutation(); m_simplePerm->init(size, tmp->m_data); // perform sequence for (int i = 0; i < f_seq.m_numOperations; i++) { m_simplePerm->performOperation(f_seq.m_operations[i]); // update operations if ((f_seq.m_operations[i].m_type == Operation::OPERATION_REVERSAL) || (f_seq.m_operations[i].m_type == Operation::OPERATION_TRANSREVERSAL)) { order1[0] = f_seq.m_operations[i].m_edges[0]; order1[1] = f_seq.m_operations[i].m_edges[1]; for (int j = i+1; j < f_seq.m_numOperations; j++) { for (int k = 0; k < 3; k++) { order1[2] = f_seq.m_operations[j].m_edges[k]; if (!cyclicSorted(order1)) // move the edge f_seq.m_operations[j].m_edges[k] = (f_seq.m_operations[i].m_edges[0] + f_seq.m_operations[i].m_edges[1] - f_seq.m_operations[j].m_edges[k] + size) % size; } } } if ((f_seq.m_operations[i].m_type == Operation::OPERATION_TRANSPOSITION) || (f_seq.m_operations[i].m_type == Operation::OPERATION_TRANSREVERSAL)) { order1[0] = f_seq.m_operations[i].m_edges[1]; order1[1] = f_seq.m_operations[i].m_edges[2]; order2[0] = f_seq.m_operations[i].m_edges[2]; order2[1] = f_seq.m_operations[i].m_edges[0]; delta1 = f_seq.m_operations[i].m_edges[0] - f_seq.m_operations[i].m_edges[2]; delta2 = f_seq.m_operations[i].m_edges[2] - f_seq.m_operations[i].m_edges[1]; for (int j = i+1; j < f_seq.m_numOperations; j++) { for (int k = 0; k < 3; k++) { if (f_seq.m_operations[j].m_edges[k] == f_seq.m_operations[i].m_edges[2]) f_seq.m_operations[j].m_edges[k] = (f_seq.m_operations[j].m_edges[k] + delta1 - delta2 + size) % size; else { order1[2] = f_seq.m_operations[j].m_edges[k]; // move first segment to the back if (!cyclicSorted(order1)) // move the edge f_seq.m_operations[j].m_edges[k] = (f_seq.m_operations[j].m_edges[k] + delta1 + size) % size; else { // move second segment to the front order2[2] = f_seq.m_operations[j].m_edges[k]; if (!cyclicSorted(order2)) // move the edge { f_seq.m_operations[j].m_edges[k] = (f_seq.m_operations[j].m_edges[k] - delta2 + size) % size; } } } } } } } // lookahead for (int i = 0; i < m_simplePerm->size(); i++) // for all possible cycles { m_simplePerm->getCycleOfEdge(i, &cycle); // choose node switch (cycle.m_type) { case Cycle::CYCLE_ADJACENCY: continue; case Cycle::CYCLE_2ORIENTED: node000(cycle); break; case Cycle::CYCLE_2UNORIENTED: node003(cycle); break; case Cycle::CYCLE_0TWISTED: node004(cycle); break; case Cycle::CYCLE_1TWISTED: node005(cycle); break; case Cycle::CYCLE_2TWISTED: node002(cycle); break; case Cycle::CYCLE_3TWISTED: node001(cycle); break; default: cerr << "error in MinSWRT::doLookahead: Algo found unexpected cycle type\n"; printCycle(cycle); continue; } m_sequence->m_weight += f_seq.m_weight; // dsigma, w, ratio shall be m_sequence->m_dsigma += f_seq.m_dsigma; // calculated over the whole sequence m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; if (f_depth > 1) { // store sequence it = seqList.begin(); rank = 1; while ((it != seqList.end()) && (rank < branch) && ((*it)->m_ratio > m_sequence->m_ratio)) { rank++; it++; } if (rank <= branch) { seqList.insert(it, m_sequence); m_sequence = new Sequence(); } } else if (m_sequence->m_ratio > result) result = m_sequence->m_ratio; } if (f_depth == 1) // abort recursion { // clean up memory delete m_simplePerm; // unswap permutations m_simplePerm = tmp; // return the result if (result < 0.01f) // sequence sorted return f_seq.m_ratio; else return result; } // do lookahead for the best sequences of the list it = seqList.begin(); for (int i = 0; (it != seqList.end()) && (i < branch); i++, it++) { ratio = doLookahead(**it, f_depth - 1); if (ratio > result) result = ratio; } // clean up memory delete m_simplePerm; for (it = seqList.begin(); it != seqList.end(); it++) delete *it; // unswap permutations m_simplePerm = tmp; // return the result if (result < 0.01f) // sequence sorted return f_seq.m_weight; else return result; } void MinSWRT::node000(Cycle& f_c) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node000" << endl; cerr << "cycle c:" << endl; printCycle(f_c); #endif int create = 0; // new created followup-2moves int destroy = 0; // destroyed followup-2moves int size = m_simplePerm->size(); Cycle d; int order1[3]; int order2[3]; /* c: r-oriented 2-cycle */ m_sequence->m_numOperations = 1; m_sequence->m_operations[0].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[1]; m_sequence->m_dsigma = 2.0f * m_wr / m_wt; m_sequence->m_weight = m_wr; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; // small lookahead: check for destroyed / new-created followups if (m_greedy < 2) return; order1[0] = f_c.m_edges[0]; order1[2] = f_c.m_edges[1]; order2[0] = f_c.m_edges[0]; order2[2] = f_c.m_edges[1]; for (int i = (f_c.m_edges[0] + 1) % size; i != f_c.m_edges[1]; (i+1 == size? i = 0 : i++)) { m_simplePerm->getCycleOfEdge(i, &d); switch (d.m_type) { case Cycle::CYCLE_2UNORIENTED: order1[1] = d.m_edges[1]; if (!cyclicSorted(order1)) // intersecting create++; break; case Cycle::CYCLE_2ORIENTED: order1[1] = d.m_edges[1]; if (!cyclicSorted(order1)) // intersecting destroy++; break; case Cycle::CYCLE_1TWISTED: order1[1] = d.m_edges[0]; order2[1] = d.m_edges[1]; if (cyclicSorted(order1) ^ cyclicSorted(order2)) create++; break; case Cycle::CYCLE_2TWISTED: order1[1] = d.m_edges[0]; order2[1] = d.m_edges[1]; if (cyclicSorted(order1) ^ cyclicSorted(order2)) destroy++; break; default: break; } } m_sequence->m_ratio += (float)(create - destroy) * 0.01f / (float)size; } void MinSWRT::node001(Cycle& f_c) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node001" << endl; cerr << "cycle c:" << endl; printCycle(f_c); #endif int create = 0; // new created followup-2moves int destroy = 0; // destroyed followup-2moves int size = m_simplePerm->size(); Cycle d; /* c: 3-twisted 3-cycle */ m_sequence->m_numOperations = 1; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[2]; m_sequence->m_dsigma = 2.0f; m_sequence->m_weight = m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; // small lookahead: check for destroyed / new-created followups if (m_greedy < 2) return; for (int i = (f_c.m_edges[0] + 1) % size; i != f_c.m_edges[1]; (i+1 == size? i = 0 : i++)) { m_simplePerm->getCycleOfEdge(i, &d); switch (d.m_type) { case Cycle::CYCLE_0TWISTED: case Cycle::CYCLE_1TWISTED: if (interleaving(f_c, d)) create++; break; case Cycle::CYCLE_2TWISTED: case Cycle::CYCLE_3TWISTED: if (interleaving(f_c, d)) destroy++; break; default: break; } } m_sequence->m_ratio += (float)(create - destroy) * 0.01f / (float)size; } void MinSWRT::node002(Cycle& f_c) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node002" << endl; cerr << "cycle c:" << endl; printCycle(f_c); #endif int create = 0; // new created followup-2moves int destroy = 0; // destroyed followup-2moves int size = m_simplePerm->size(); Cycle d; int order1[3]; int order2[3]; /* c: 2-twisted 3-cycle */ m_sequence->m_numOperations = 1; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[2]; m_sequence->m_dsigma = 2.0f; m_sequence->m_weight = m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; // small lookahead: check for destroyed / new-created followups if (m_greedy < 2) return; order1[0] = f_c.m_edges[0]; order1[2] = f_c.m_edges[1]; order2[0] = f_c.m_edges[0]; order2[2] = f_c.m_edges[1]; for (int i = (f_c.m_edges[0] + 1) % size; i != f_c.m_edges[1]; (i+1 == size? i = 0 : i++)) { m_simplePerm->getCycleOfEdge(i, &d); switch (d.m_type) { case Cycle::CYCLE_2UNORIENTED: order1[1] = d.m_edges[1]; if (cyclicSorted(order1)) create++; break; case Cycle::CYCLE_2ORIENTED: order1[1] = d.m_edges[1]; if (cyclicSorted(order1)) destroy++; break; case Cycle::CYCLE_0TWISTED: if (interleaving(f_c, d)) create++; break; case Cycle::CYCLE_1TWISTED: if (interleaving(f_c, d)) create++; else { order1[1] = d.m_edges[0]; order2[1] = d.m_edges[1]; if (cyclicSorted(order1) ^ cyclicSorted(order2)) create++; } break; case Cycle::CYCLE_2TWISTED: if (interleaving(f_c, d)) destroy++; else { order1[1] = d.m_edges[0]; order2[1] = d.m_edges[1]; if (cyclicSorted(order1) ^ cyclicSorted(order2)) destroy++; } break; case Cycle::CYCLE_3TWISTED: if (interleaving(f_c, d)) destroy++; break; default: break; } } m_sequence->m_ratio += (float)(create - destroy) * 0.01f / (float)size; } void MinSWRT::node003(Cycle& f_c) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node003" << endl; cerr << "cycle c:" << endl; printCycle(f_c); #endif /* c is r-unoriented 2-cycle -> search intersecting cycle d */ Cycle d; // d intersects c int order[3]; // needed to check cyclic sorting of three edges m_simplePerm->getCycle(&d, 1, f_c.m_edges[0], f_c.m_edges[1]); switch (d.m_type) { case Cycle::CYCLE_2ORIENTED: node000(d); break; case Cycle::CYCLE_2UNORIENTED: node006(f_c, d); break; case Cycle::CYCLE_0TWISTED: // search for the chord of d not intersected by c order[0] = f_c.m_edges[0]; order[2] = f_c.m_edges[1]; order[1] = d.m_edges[1]; if (cyclicSorted(order)) // chord between RE 0 and 1 is not { // intersected d.m_edges[1] = d.m_edges[0]; d.m_edges[0] = d.m_edges[2]; d.m_edges[2] = order[1]; } else { order[1] = d.m_edges[2]; if (cyclicSorted(order)) // chord between RE 0 and 1 is not { // intersected d.m_edges[2] = d.m_edges[0]; d.m_edges[0] = d.m_edges[1]; d.m_edges[1] = order[1]; } else // switch RE of c { f_c.m_edges[0] = f_c.m_edges[1]; f_c.m_edges[1] = order[0]; } } node008(f_c, d); break; case Cycle::CYCLE_1TWISTED: order[0] = d.m_edges[0]; order[2] = d.m_edges[1]; order[1] = f_c.m_edges[0]; if (cyclicSorted(order)) // c intersect nontwisted chord { node007(f_c, d); break; } order[1] = f_c.m_edges[1]; if (cyclicSorted(order)) // c intersect nontwisted chord { // switch edges of c f_c.m_edges[2] = f_c.m_edges[1]; f_c.m_edges[1] = f_c.m_edges[0]; f_c.m_edges[0] = f_c.m_edges[2]; node007(f_c, d); break; } node005(d); break; case Cycle::CYCLE_2TWISTED: node002(d); break; case Cycle::CYCLE_3TWISTED: node001(d); break; default: cerr << "error in MinSWRT::node003: Algo found unexpected cycle type\n"; return; } } void MinSWRT::node004(Cycle& f_c) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node004" << endl; cerr << "cycle c:" << endl; printCycle(f_c); #endif /* c is a nontwisted 3-cycle -> search intersecting cycle d */ Cycle d; // d intersects c int order[3]; // needed to check cyclic sorting of three edges m_simplePerm->getCycle(&d, 1, f_c.m_edges[0], f_c.m_edges[1]); switch (d.m_type) { case Cycle::CYCLE_2ORIENTED: node000(d); break; case Cycle::CYCLE_2UNORIENTED: // search for the non-intersected chord of c order[0] = f_c.m_edges[1]; order[2] = f_c.m_edges[2]; order[1] = d.m_edges[1]; if (cyclicSorted(order)) // non-intersected chord between { // RE 2 and 0 f_c.m_edges[2] = f_c.m_edges[0]; f_c.m_edges[0] = f_c.m_edges[1]; f_c.m_edges[1] = order[2]; d.m_edges[1] = d.m_edges[0]; d.m_edges[0] = order[1]; } // else no shift necessary node008(d, f_c); break; case Cycle::CYCLE_0TWISTED: if (interleaving(f_c, d)) // check if interleaving { node016(f_c, d); break; } // search non-intersected chord of d order[0] = f_c.m_edges[0]; order[2] = f_c.m_edges[1]; order[1] = d.m_edges[1]; if (cyclicSorted(order)) // non-intersected chord between { // RE 0 and 1 d.m_edges[1] = d.m_edges[0]; d.m_edges[0] = d.m_edges[2]; d.m_edges[2] = order[1]; order[1] = d.m_edges[0]; // store edge that is not between RE 0 and 1 of c } else { order[1] = d.m_edges[2]; if (cyclicSorted(order)) // non-intersected chord between { // RE 2 and 0 d.m_edges[2] = d.m_edges[0]; d.m_edges[0] = d.m_edges[1]; d.m_edges[1] = order[1]; order[1] = d.m_edges[0];// store edge that is not between RE 0 and 1 of c } } // else no shift necessary // search non-intersected edge of c order[2] = f_c.m_edges[2]; if (cyclicSorted(order)) // intersection between RE 1 and 2 of c { f_c.m_edges[2] = f_c.m_edges[0]; f_c.m_edges[0] = f_c.m_edges[1]; f_c.m_edges[1] = order[2]; } node017(f_c, d); break; case Cycle::CYCLE_1TWISTED: if (interleaving(f_c, d)) // check if interleaving { // search position of twisted edge order[0] = f_c.m_edges[0]; order[2] = f_c.m_edges[1]; order[1] = d.m_edges[0]; if (cyclicSorted(order)) { f_c.m_edges[0] = f_c.m_edges[1]; f_c.m_edges[1] = f_c.m_edges[2]; f_c.m_edges[2] = order[0]; } else { order[1] = d.m_edges[1]; if (!cyclicSorted(order)) { f_c.m_edges[0] = f_c.m_edges[2]; f_c.m_edges[2] = f_c.m_edges[1]; f_c.m_edges[1] = order[0]; } } node040(f_c, d); break; } order[0] = d.m_edges[0]; order[2] = d.m_edges[1]; order[1] = f_c.m_edges[0]; if (cyclicSorted(order)) // c intersect nontwisted chord { order[1] = f_c.m_edges[2]; if (cyclicSorted(order)) // no intersection between c2, c0 { // -> shift c f_c.m_edges[2] = f_c.m_edges[0]; f_c.m_edges[0] = f_c.m_edges[1]; f_c.m_edges[1] = order[1]; } node026(d, f_c); break; } order[1] = f_c.m_edges[1]; if (cyclicSorted(order)) // c intersect nontwisted chord { order[1] = f_c.m_edges[2]; if (!cyclicSorted(order)) // no intersection between c2, c0 { // -> shift c f_c.m_edges[2] = f_c.m_edges[0]; f_c.m_edges[0] = f_c.m_edges[1]; f_c.m_edges[1] = order[1]; } node026(d, f_c); break; } /* order[1] = f_c.m_edges[2]; if (cyclicSorted(order)) // c intersect nontwisted chord { node026(d, f_c); break; } */ node005(d); // discard c break; case Cycle::CYCLE_2TWISTED: node002(d); break; case Cycle::CYCLE_3TWISTED: node001(d); break; default: cerr << "error in MinSWRT::node004: Algo found unexpected cycle type\n"; return; } } void MinSWRT::node005(Cycle& f_c) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node005" << endl; cerr << "cycle c:" << endl; printCycle(f_c); #endif /* Node 005: c is a 1-twisted 3-cycle -> intersecting cycle d */ Cycle d; // d intersects c int order[3]; // needed to check cyclic sorting of three edges m_simplePerm->getCycle(&d, 1, f_c.m_edges[0], f_c.m_edges[1]); switch (d.m_type) { case Cycle::CYCLE_2ORIENTED: node000(d); break; case Cycle::CYCLE_2UNORIENTED: node007(d, f_c); break; case Cycle::CYCLE_0TWISTED: if (interleaving(f_c, d)) { node040(d, f_c); break; } order[0] = f_c.m_edges[0]; order[2] = f_c.m_edges[1]; order[1] = d.m_edges[1]; if (cyclicSorted(order)) // non-intersected chord between { // RE 0 and 1 d.m_edges[1] = d.m_edges[0]; d.m_edges[0] = d.m_edges[2]; d.m_edges[2] = order[1]; } else { order[1] = d.m_edges[2]; if (cyclicSorted(order)) // non-intersected chord between { // RE 2 and 0 d.m_edges[2] = d.m_edges[0]; d.m_edges[0] = d.m_edges[1]; d.m_edges[1] = order[1]; } } // else no shift necessary node026(f_c, d); break; case Cycle::CYCLE_1TWISTED: if (interleaving(f_c, d)) { node024(f_c, d); break; } node025(f_c, d); break; case Cycle::CYCLE_2TWISTED: node002(d); break; case Cycle::CYCLE_3TWISTED: node001(d); break; default: cerr << "error in MinSWRT::node005: Algo found unexpected cycle type\n"; return; } } void MinSWRT::node006(Cycle& f_c, Cycle& f_d) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node006" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); #endif /* c,d are intersecting r-unoriented 2-cycles.*/ int order[3]; // needed to check cyclic sorting of three edges if (3 * m_wr < 2 * m_wt) { m_sequence->m_numOperations = 3; m_sequence->m_operations[0].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[1]; m_sequence->m_dsigma = 4.0f * m_wr / m_wt; m_sequence->m_weight = 3.0f * m_wr; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } else { // edges should be sorted c0 d0 c1 d1 order[0] = f_c.m_edges[0]; order[1] = f_d.m_edges[0]; order[2] = f_c.m_edges[1]; if (!cyclicSorted(order)) { f_d.m_edges[2] = f_d.m_edges[0]; f_d.m_edges[0] = f_d.m_edges[1]; f_d.m_edges[1] = f_d.m_edges[2]; } m_sequence->m_numOperations = 2; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_d.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[2] = f_c.m_edges[1]; m_sequence->m_dsigma = 4.0f * m_wr / m_wt; m_sequence->m_weight = 2.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } } void MinSWRT::node007(Cycle& f_c, Cycle& f_d) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node007" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); #endif /* c is an r-unoriented 2-cycle, d is a 1-twisted 3-cycle. c intersects * the nontwisted chord of d. The edge of c that lies between the * nontwisted edges of d is m_edge[0].*/ int order[3]; // needed to check cyclic sorting of three edges m_sequence->m_numOperations = 3; order[0] = f_d.m_edges[1]; order[1] = f_c.m_edges[1]; order[2] = f_d.m_edges[2]; if (cyclicSorted(order)) // edge sequence d2 d0 c0 d1 c1 { m_sequence->m_operations[0].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[0].m_edges[0] = f_d.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_d.m_edges[2]; } else // edge sequence d2 c1 d0 c0 d1 { m_sequence->m_operations[0].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[0].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_d.m_edges[0]; } m_sequence->m_operations[1].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[1].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[2].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_d.m_edges[1]; m_sequence->m_dsigma = 2.0f + 2.0f * m_wr / m_wt; m_sequence->m_weight = 3.0f * m_wr; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } void MinSWRT::node008(Cycle& f_c, Cycle& f_d) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node008" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); #endif /* c is an r-unoriented 2-cycle, d is a nontwisted 3-cycle. c and d are * intersecting. The chord of d not intersected by c is between the * reality-edges m_edges[1] and m_edges[2]. m_edges[0] of c lies between * m_edges[0] and m_edges[1] of d. */ Cycle e; // intersects open chord of d int order[3]; // needed to check cyclic sorting int twisted; // position of twisted edge m_simplePerm->getCycle(&e,1, f_d.m_edges[1], f_d.m_edges[2]); switch (e.m_type) { case Cycle::CYCLE_2ORIENTED: node000(e); break; case Cycle::CYCLE_2UNORIENTED: node009(f_c, f_d, e); break; case Cycle::CYCLE_0TWISTED: if (interleaving(f_d, e)) { node016(f_d, e); break; } order[0] = f_d.m_edges[1]; order[2] = f_d.m_edges[2]; order[1] = e.m_edges[1]; if (cyclicSorted(order)) // no intersection between RE 0 and 1 { e.m_edges[1] = e.m_edges[0]; e.m_edges[0] = e.m_edges[2]; e.m_edges[2] = order[1]; } else { order[1] = e.m_edges[2]; if (cyclicSorted(order)) // no intersection between RE 2 and 0 { e.m_edges[2] = e.m_edges[0]; e.m_edges[0] = e.m_edges[1]; e.m_edges[1] = order[1]; } } // else no shift necessary node010(f_c, f_d, e); break; case Cycle::CYCLE_1TWISTED: order[0] = f_d.m_edges[0]; // search position of twisted edge order[2] = f_d.m_edges[1]; order[1] = e.m_edges[2]; if (cyclicSorted(order)) twisted = 0; else { order[0] = f_d.m_edges[1]; order[2] = f_d.m_edges[2]; if (cyclicSorted(order)) twisted = 1; else twisted = 2; } if (interleaving(f_d, e)) { if (twisted == 0) { f_d.m_edges[0] = f_d.m_edges[2]; f_d.m_edges[2] = f_d.m_edges[1]; f_d.m_edges[1] = order[0]; } else if (twisted == 2) { f_d.m_edges[2] = f_d.m_edges[0]; f_d.m_edges[0] = f_d.m_edges[1]; f_d.m_edges[1] = order[2]; } node040(f_d, e); break; } node005(e); break; case Cycle::CYCLE_2TWISTED: node002(e); break; case Cycle::CYCLE_3TWISTED: node001(e); break; default: cerr << "error in MinSWRT::node008: Algo found unexpected cycle type\n"; return; } } void MinSWRT::node009(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node009" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* c and e are r-unoriented 2-cycles, d is a nontwisted 3-cycle. * c.m_edges[0] lies between the reality-edges m_edges[0] and m_edges[1] * of d, e.m_edges[0] lies between m_edges[1] and m_edges[2] of d. * c.m_edges[1] lies between m_edges[0] and m_edges[2] of d. The position * of e.m_edges[1] is arbitrary.*/ int order1[3]; // needed to check cyclic sorting of three edges int order2[3]; // needed to check cyclic sorting of three edges order1[0] = f_c.m_edges[0]; order1[2] = f_c.m_edges[1]; order1[1] = f_e.m_edges[0]; order2[0] = f_c.m_edges[0]; order2[2] = f_c.m_edges[1]; order2[1] = f_e.m_edges[1]; if (cyclicSorted(order1) ^ cyclicSorted(order2)) node006(f_c, f_e); else node012(f_c, f_d, f_e); } void MinSWRT::node010(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node010" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* c is an r-unoriented 2-cycle, d and e are nontwisted 3-cycles. * c intersects d (m_edges[0] of c between m_edges[0] and m_edges[1] of * d, m_edges[1] of c between m_edges[2] and m_edges[0] of d). e * intersects d (at least one edge of e between m_edges[1] and m_edges[2] * of d, no edge of d between m_edges[1] and m_edges[2] of e). */ int order[3]; // needed to check cyclic sorting of three edges order[0] = f_e.m_edges[1]; order[2] = f_e.m_edges[2]; order[1] = f_c.m_edges[0]; if (cyclicSorted(order)) { node011(f_c, f_d, f_e); return; } order[1] = f_c.m_edges[1]; if (cyclicSorted(order)) { node013(f_c, f_d, f_e); return; } node014(f_c, f_d, f_e); } void MinSWRT::node011(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node011" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* Node 011: c is r-unoriented 2-cycle, d and e are nontwisted 3-cycles. * The configuration looks like this: * * c0 * e2 e1 * * d1 d0 * * e0 c1 * d2 */ if (m_wr < m_wt) { m_sequence->m_numOperations = 3; m_sequence->m_operations[0].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[0].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[1].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; m_sequence->m_dsigma = 2.0f + 2.0f * m_wr / m_wt; m_sequence->m_weight = 2.0f * m_wr + m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } else { m_sequence->m_numOperations = 3; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } } void MinSWRT::node012(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node012" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* Node 012: c and e are r-unoriented 2-cycles, d is a nontwisted * 3-cycle. c.m_edges[0] lies between the reality-edges m_edges[0] and * m_edges[1] of d, c.m_edges[1] lies between the reality-edges * m_edges[2] and m_edges[0] of d, e.m_edges[0] lies between m_edges[1] * and m_edges[2] of d. The two 2-cycles are not intersecting. */ m_sequence->m_numOperations = 3; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; m_sequence->m_dsigma = 2.0f + 4.0f * m_wr / m_wt; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } void MinSWRT::node013(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node013" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* Node 013: c is r-unoriented 2-cycle, d and e are nontwisted 3-cycles. * The configuration looks like this: * * c0 * d1 d0 * * e0 e2 * * d2 c1 * e1 */ if (m_wr < m_wt) { m_sequence->m_numOperations = 3; m_sequence->m_operations[0].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[1].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[1].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_d.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_d.m_edges[0]; m_sequence->m_dsigma = 2.0f + 2.0f * m_wr / m_wt; m_sequence->m_weight = 2.0f * m_wr + m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } else { m_sequence->m_numOperations = 3; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_e.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_d.m_edges[0]; m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } } void MinSWRT::node014(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node014" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* Node 014: c is an r-unoriented 2-cycle, d and e are nontwisted 3-cycles. * c intersects d (m_edges[0] of c between m_edges[0] and m_edges[1] of * d, m_edges[1] of c between m_edges[2] and m_edges[0] of d). e * intersects d (at least one edge of e between m_edges[1] and m_edges[2] * of d). The chord between m_edges[1] and m_edges[2] of e is neither * intersected by c nor by d. */ Cycle f; // intersects chord between RE 1 and 2 of e int order[3]; // needed to check cyclic sorting of three edges int cs1, cs2; // result of a call of cyclicSorted m_simplePerm->getCycle(&f, 1, f_e.m_edges[1], f_e.m_edges[2]); switch (f.m_type) { case Cycle::CYCLE_2ORIENTED: node000(f); break; case Cycle::CYCLE_2UNORIENTED: // check if c, f are intersecting order[0] = f_c.m_edges[1]; order[2] = f_c.m_edges[0]; order[1] = f.m_edges[0]; cs1 = cyclicSorted(order); order[1] = f.m_edges[1]; cs2 = cyclicSorted(order); if (cs1 ^ cs2) // c, f intersecting { node006(f_c, f); break; } if (cs1) // -> e must intersect c -> node012 { f_c.m_edges[0] = f_c.m_edges[1]; // switch c f_c.m_edges[1] = order[2]; node012(f_c, f_e, f); break; } // check if d, f are intersecting order[0] = f_d.m_edges[0]; order[2] = f_d.m_edges[1]; cs2 = cyclicSorted(order); order[1] = f.m_edges[0]; cs1 = cyclicSorted(order); if (cs1 ^ cs2) // f intersects d between RE0 and RE1 { // search position of second edge of f if (cs1) order[1] = f.m_edges[1]; order[0] = f_d.m_edges[1]; order[2] = f_d.m_edges[2]; if (cyclicSorted(order)) { if (cs1) { f.m_edges[1] = f.m_edges[0]; f.m_edges[0] = order[1]; } node012(f_c, f_d, f); } else if (cs1) node011(f, f_d, f_e); else { f.m_edges[0] = f.m_edges[1]; f.m_edges[1] = order[1]; node013(f, f_d, f_e); } break; } order[0] = f_d.m_edges[1]; order[2] = f_d.m_edges[2]; cs1 = cyclicSorted(order); order[1] = f.m_edges[1]; cs2 = cyclicSorted(order); if (cs1 ^ cs2) // f intersects d between RE1 and RE2 { // other RE of f between d.RE2 and d.RE0 if (cs2) { f.m_edges[1] = f.m_edges[0]; f.m_edges[0] = order[1]; } node012(f_c, f_d, f); break; } node015(f_c, f_d, f_e, f); break; case Cycle::CYCLE_0TWISTED: if (interleaving(f_d, f)) node016(f_d, f); else if (interleaving(f_e, f)) node016(f_e, f); else { // search position of d.m_edges[0] order[0] = f_d.m_edges[1]; order[2] = f_d.m_edges[2]; order[1] = f_e.m_edges[0]; if (cyclicSorted(order)) // shift d { f_d.m_edges[1] = f_d.m_edges[2]; f_d.m_edges[2] = f_d.m_edges[0]; f_d.m_edges[0] = order[0]; } else { order[0] = f_d.m_edges[2]; order[2] = f_d.m_edges[0]; if (cyclicSorted(order)) // shift d { f_d.m_edges[2] = f_d.m_edges[1]; f_d.m_edges[1] = f_d.m_edges[0]; f_d.m_edges[0] = order[0]; } } // else no shift necessary node018(f_d, f_e, f); } break; case Cycle::CYCLE_1TWISTED: if (interleaving(f_d, f)) { order[0] = f_d.m_edges[1]; order[2] = f_d.m_edges[2]; order[1] = f.m_edges[0]; if (cyclicSorted(order)) // shift d { f_d.m_edges[2] = f_d.m_edges[0]; f_d.m_edges[0] = f_d.m_edges[1]; f_d.m_edges[1] = order[2]; } else { order[1] = f.m_edges[1]; if (cyclicSorted(order)) // shift d { f_d.m_edges[2] = f_d.m_edges[1]; f_d.m_edges[1] = f_d.m_edges[0]; f_d.m_edges[0] = order[2]; } } // else no shift necessary node040(f_d, f); break; } if (interleaving(f_e, f)) { order[0] = f_e.m_edges[1]; order[2] = f_e.m_edges[2]; order[1] = f.m_edges[0]; if (cyclicSorted(order)) // shift e { f_e.m_edges[2] = f_e.m_edges[0]; f_e.m_edges[0] = f_e.m_edges[1]; f_e.m_edges[1] = order[2]; } else { order[1] = f.m_edges[1]; if (cyclicSorted(order)) // shift d { f_e.m_edges[2] = f_e.m_edges[1]; f_e.m_edges[1] = f_e.m_edges[0]; f_e.m_edges[0] = order[2]; } } // else no shift necessary node040(f_e, f); break; } // search separated edge of d order[0] = f_d.m_edges[1]; order[2] = f_d.m_edges[2]; order[1] = f_e.m_edges[0]; if (cyclicSorted(order)) { order[2] = f_d.m_edges[0]; order[1] = f_e.m_edges[1]; if (cyclicSorted(order)) // separated edge: d.2 { f_d.m_edges[0] = f_d.m_edges[2]; f_d.m_edges[2] = f_d.m_edges[1]; f_d.m_edges[1] = order[2]; } else // separated edge: d.1 { f_d.m_edges[0] = f_d.m_edges[1]; f_d.m_edges[1] = f_d.m_edges[2]; f_d.m_edges[2] = order[2]; } } else { order[2] = f_d.m_edges[0]; if (cyclicSorted(order)) // separated edge: d.2 { f_d.m_edges[0] = f_d.m_edges[2]; f_d.m_edges[2] = f_d.m_edges[1]; f_d.m_edges[1] = order[2]; } else // separated edge: d.1 { f_d.m_edges[0] = f_d.m_edges[1]; f_d.m_edges[1] = f_d.m_edges[2]; f_d.m_edges[2] = order[2]; } } node019(f_d, f_e, f); break; case Cycle::CYCLE_2TWISTED: node002(f); break; case Cycle::CYCLE_3TWISTED: node001(f); break; default: cerr << "error in MinSWRT::node014: Algo found unexpected cycle type\n"; printCycle(f); return; } } void MinSWRT::node015(Cycle& f_c, Cycle& f_d, Cycle& f_e, Cycle& f_f) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node015" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); cerr << "cycle f:" << endl; printCycle(f_f); #endif /* c and f are an r-unoriented 2-cycle, d and e are nontwisted * 3-cycles. c intersects d (m_edges[0] of c between m_edges[0] and * m_edges[1] of d, m_edges[1] of c between m_edges[2] and m_edges[0] of * d). e intersects d (at least one edge of e between m_edges[1] and * m_edges[2] of d). The chord between m_edges[1] and m_edges[2] of e is * neither intersected by c nor by d, but intersected by f (f.m_edges[0] * between the reality-edges). c and f are not intersecting; if d and f * are intersecting, no reality-edge of f is between d.m_edges[1] and * d.m_edges[2]. */ int order[3]; // needed to check cyclic sorting of three edges // search position of f.RE0 order[0] = f_c.m_edges[0]; order[2] = f_d.m_edges[1]; order[1] = f_f.m_edges[0]; if (cyclicSorted(order)) // f.RE0 between c.RE0 and d.RE1 { // search position of f.RE1 order[1] = f_f.m_edges[1]; if (!cyclicSorted(order)) // edge sequence d0 c0 e1 f0 e2 d1 e0 d2 f1 c1 { #if DEBUG cerr << "node015.1\n"; #endif m_sequence->m_numOperations = 3; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_f.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_f.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_f.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[0]; m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; return; } order[2] = f_e.m_edges[1]; if (cyclicSorted(order)) // edge sequence d0 c0 f1 e1 f0 e2 d1 e0 d2 c1 { #if DEBUG cerr << "node015.2\n"; #endif m_sequence->m_numOperations = 3; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[2]; m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; return; } #if DEBUG cerr << "node015.3\n"; #endif m_sequence->m_numOperations = 4; // edge sequence d0 c0 e1 f0 e2 f1 d1 e0 d2 c1 m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_f.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_f.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_e.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[3].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[3].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[3].m_edges[1] = f_f.m_edges[1]; m_sequence->m_operations[3].m_edges[2] = f_f.m_edges[0]; m_sequence->m_dsigma = 4.0f + 4.0f * m_wr / m_wt; m_sequence->m_weight = 4.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; return; } order[0] = f_d.m_edges[2]; order[2] = f_c.m_edges[1]; if (cyclicSorted(order)) // f.RE0 between d.RE2 and c.RE1 { // search position of f.RE1 order[1] = f_f.m_edges[1]; if (!cyclicSorted(order)) // edge sequence d0 c0 f1 d1 e0 d2 e1 f0 e2 c1 { #if DEBUG cerr << "node015.4\n"; #endif m_sequence->m_numOperations = 3; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_f.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_f.m_edges[0]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_f.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[2]; m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; return; } order[0] = f_e.m_edges[2]; if (cyclicSorted(order)) // edge sequence d0 c0 d1 e0 d2 e1 f0 e2 f1 c1 { #if DEBUG cerr << "node015.5\n"; #endif m_sequence->m_numOperations = 3; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[2]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[2]; m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; return; } #if DEBUG cerr << "node015.6\n"; #endif m_sequence->m_numOperations = 4; // edge sequence d0 c0 d1 e0 d2 f1 e1 f0 e2 c1 m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_f.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_f.m_edges[0]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_e.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[3].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[3].m_edges[0] = f_f.m_edges[0]; m_sequence->m_operations[3].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[3].m_edges[2] = f_c.m_edges[0]; m_sequence->m_dsigma = 4.0f + 4.0f * m_wr / m_wt; m_sequence->m_weight = 4.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; return; } // f.RE0 between d.RE1 and d.RE2 // search e.RE0 order[1] = f_e.m_edges[0]; if (cyclicSorted(order)) // e.RE0 between d.RE2 and c.RE1 { // position of f.RE1 doesn't matter, same operations // edge sequence d0 c0 d1 e1 f0 e2 f1 d2 e0 c1 // or d0 c0 d1 f1 e1 f0 e2 d2 e0 c1 #if DEBUG cerr << "node015.7\n"; #endif m_sequence->m_numOperations = 4; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_f.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; m_sequence->m_operations[3].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[3].m_edges[0] = f_f.m_edges[0]; m_sequence->m_operations[3].m_edges[1] = f_f.m_edges[1]; m_sequence->m_operations[3].m_edges[2] = f_c.m_edges[1]; m_sequence->m_dsigma = 4.0f + 4.0f * m_wr / m_wt; m_sequence->m_weight = 4.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; return; } // e.RE0 between c.RE0 and d.RE1 // position of f.RE1 doesn't really matter - operations are the same // edge sequence d0 c0 e0 d1 e1 f0 e2 f1 d2 c1 // or d0 c0 e0 d1 f1 e1 f0 e2 d2 c1 #if DEBUG cerr << "node015.8\n"; #endif m_sequence->m_numOperations = 4; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_f.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; m_sequence->m_operations[3].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[3].m_edges[0] = f_f.m_edges[0]; m_sequence->m_operations[3].m_edges[1] = f_f.m_edges[1]; m_sequence->m_operations[3].m_edges[2] = f_c.m_edges[1]; m_sequence->m_dsigma = 4.0f + 4.0f * m_wr / m_wt; m_sequence->m_weight = 4.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } void MinSWRT::node016(Cycle& f_c, Cycle& f_d) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node016" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); #endif /* c and d are two interleaving nontwisted 3-cycles */ m_sequence->m_numOperations = 3; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[2]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } void MinSWRT::node017(Cycle& f_c, Cycle& f_d) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node017" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); #endif /* c and d are two intersecting, non-interleaving nontwisted 3-cycles. * For both cycles, the non-intersected chord is between the * reality-edges m_edges[1] and m_edges[2]. */ Cycle e; // intersects open arc of d int order[3]; // needed to check cyclic sorting of three edges m_simplePerm->getCycle(&e, 1, f_d.m_edges[1], f_d.m_edges[2]) ; switch (e.m_type) { case Cycle::CYCLE_2ORIENTED: node000(e); break; case Cycle::CYCLE_2UNORIENTED: order[0] = f_c.m_edges[1]; order[2] = f_c.m_edges[2]; order[1] = e.m_edges[1]; if (cyclicSorted(order)) { order[1] = f_d.m_edges[0]; order[2] = e.m_edges[0]; if (cyclicSorted(order)) { f_c.m_edges[1] = f_c.m_edges[2]; f_c.m_edges[2] = f_c.m_edges[0]; f_c.m_edges[0] = order[0]; e.m_edges[0] = e.m_edges[1]; e.m_edges[1] = order[2]; node013(e, f_c, f_d); } else { f_c.m_edges[1] = f_c.m_edges[0]; f_c.m_edges[0] = f_c.m_edges[2]; f_c.m_edges[2] = order[0]; node011(e, f_c, f_d); } break; } // find second chord of d intersected by e order[0] = f_d.m_edges[0]; order[2] = f_d.m_edges[1]; if (cyclicSorted(order)) { f_d.m_edges[0] = f_d.m_edges[1]; f_d.m_edges[1] = f_d.m_edges[2]; f_d.m_edges[2] = order[0]; } else { f_d.m_edges[0] = f_d.m_edges[2]; f_d.m_edges[2] = f_d.m_edges[1]; f_d.m_edges[1] = order[0]; e.m_edges[1] = e.m_edges[0]; e.m_edges[0] = order[1]; } node014(e, f_d, f_c); break; case Cycle::CYCLE_0TWISTED: if (interleaving(f_c, e)) { node016(f_c, e); break; } if (interleaving(f_d, e)) { node016(f_d, e); break; } // find position of d.m_edges[0] in cycle c order[0] = f_c.m_edges[0]; order[2] = f_c.m_edges[1]; order[1] = f_d.m_edges[0]; if (!cyclicSorted(order)) // d.RE0 between c.RE2 and c.RE0 { // -> shift c f_c.m_edges[0] = f_c.m_edges[2]; f_c.m_edges[2] = f_c.m_edges[1]; f_c.m_edges[1] = order[0]; } node018(f_c, f_d, e); break; case Cycle::CYCLE_1TWISTED: if (interleaving(f_c, e)) { // search position of the twisted edge order[0] = f_c.m_edges[0]; order[2] = f_c.m_edges[1]; order[1] = e.m_edges[2]; if (cyclicSorted(order)) // shift c { f_c.m_edges[0] = f_c.m_edges[2]; f_c.m_edges[2] = f_c.m_edges[1]; f_c.m_edges[1] = order[0]; } else { order[0] = f_c.m_edges[2]; if (cyclicSorted(order)) // shift c { f_c.m_edges[2] = f_c.m_edges[0]; f_c.m_edges[0] = f_c.m_edges[1]; f_c.m_edges[1] = order[0]; } } node040(f_c, e); break; } if (interleaving(f_d, e)) { // search position of the twisted edge order[0] = f_d.m_edges[0]; order[2] = f_d.m_edges[1]; order[1] = e.m_edges[2]; if (cyclicSorted(order)) // shift c { f_d.m_edges[0] = f_d.m_edges[2]; f_d.m_edges[2] = f_d.m_edges[1]; f_d.m_edges[1] = order[0]; } else { order[0] = f_d.m_edges[2]; if (cyclicSorted(order)) // shift c { f_d.m_edges[2] = f_d.m_edges[0]; f_d.m_edges[0] = f_d.m_edges[1]; f_d.m_edges[1] = order[0]; } } node040(f_d, e); break; } node019(f_c, f_d, e); break; case Cycle::CYCLE_2TWISTED: node002(e); break; case Cycle::CYCLE_3TWISTED: node001(e); break; default: cerr << "error in MinSWRT::node017: Algo found unexpected cycle type\n"; printCycle(e); return; } } void MinSWRT::node018(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node018" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* c, d and e are nontwisted 3-cycles. c intersects d (d.m_edges[0] * between c.m_edges[0] and c.m_edges[1], others outside), e intersects d * (e.m_edges[0] between d.m_edges[1] and d.m_edges[2]). * There is no pair of interleaving cycles. */ int order[3]; // needed to check cyclic sorting of three edges // get position of RE 0 of e relativ to c order[0] = f_c.m_edges[0]; order[2] = f_c.m_edges[1]; order[1] = f_e.m_edges[0]; if (cyclicSorted(order)) { order[1] = f_e.m_edges[1]; if (!cyclicSorted(order)) // mutually intersecting { node021(f_c, f_d, f_e); return; } order[1] = f_e.m_edges[2]; if (!cyclicSorted(order)) // mutually intersecting { node021(f_c, f_d, f_e); return; } node020(f_c, f_d, f_e); return;; } order[0] = f_c.m_edges[1]; order[2] = f_c.m_edges[2]; if (cyclicSorted(order)) { order[1] = f_e.m_edges[1]; if (!cyclicSorted(order)) // mutually intersecting { node021(f_c, f_d, f_e); return;; } order[1] = f_e.m_edges[2]; if (!cyclicSorted(order)) // mutually intersecting { node021(f_c, f_d, f_e); return;; } node020(f_c, f_d, f_e); return; } order[0] = f_c.m_edges[2]; order[2] = f_c.m_edges[0]; order[1] = f_e.m_edges[1]; if (!cyclicSorted(order)) // mutually intersecting { node021(f_c, f_d, f_e); return; } order[1] = f_e.m_edges[2]; if (!cyclicSorted(order)) // mutually intersecting { node021(f_c, f_d, f_e); return; } node020(f_c, f_d, f_e); } void MinSWRT::node019(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node019" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* c and d are nontwisted 3-cycles, e is a 1-twisted 3-cycle. There is no * pair of interleaving cycles. c intersects with d (with the chords * between reality-edges 0,1 and 2, 0 of both cycles). e intersects with * d (at least one reality-edge of e between reality-edges 1 and 2 of d).*/ int order[3]; // needed to check cyclic sorting of three edges order[0] = f_c.m_edges[0]; order[2] = f_c.m_edges[1]; order[1] = f_d.m_edges[0]; if (cyclicSorted(order)) // at least one edge of e between c.2 and c.0 { order[2] = f_c.m_edges[2]; order[1] = f_e.m_edges[0]; if (cyclicSorted(order)) // mutually intersecting { node023(f_c, f_d, f_e); return; } order[1] = f_e.m_edges[1]; if (cyclicSorted(order)) // mutually intersecting { node023(f_c, f_d, f_e); return; } order[1] = f_e.m_edges[2]; if (cyclicSorted(order)) // mutually intersecting { node023(f_c, f_d, f_e); return; } node022(f_c, f_d, f_e); } else // at least one edge of e between c.0 and c.1 { order[1] = f_c.m_edges[0]; order[0] = f_e.m_edges[0]; if (cyclicSorted(order)) // mutually intersecting { node023(f_c, f_d, f_e); return; } order[0] = f_e.m_edges[1]; if (cyclicSorted(order)) // mutually intersecting { node023(f_c, f_d, f_e); return; } order[0] = f_e.m_edges[2]; if (cyclicSorted(order)) // mutually intersecting { node023(f_c, f_d, f_e); return; } node022(f_c, f_d, f_e); } } void MinSWRT::node020(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node020" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* c, d and e are nontwisted 3-cycles. c intersects d * (d.m_edges[0] between c.m_edges[0] and c.m_edges[1], others outside), * e intersects d (e.m_edges[0] between d.m_edges[1] and d.m_edges[2]). * There is no pair of interleaving cycles. c and e are * not intersecting. */ int order[3]; // needed to check cyclic sorting of three edges bool leftarc; // true if e0 in arc between c.1 and c.2 m_sequence->m_numOperations = 3; // for all sequences m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; // get position of e.0 relativ to c order[0] = f_c.m_edges[1]; order[2] = f_c.m_edges[2]; order[1] = f_e.m_edges[0]; leftarc = cyclicSorted(order); // get position of e.1 and e.2 relativ to d order[2] = f_e.m_edges[1]; order[0] = f_d.m_edges[2]; if (cyclicSorted(order)) // e0, e1 between d.1 and d.2 { order[1] = f_e.m_edges[2]; order[2] = f_d.m_edges[0]; if (cyclicSorted(order)) { if (leftarc) // edge sequence c0 d0 c1 d1 e0 e1 d2 e2 c2 { #if DEBUG cerr << "node020.1\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; return; } else // edge sequence c0 d0 c1 c2 d1 e0 e1 d2 e2 { #if DEBUG cerr << "node020.2\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[0]; return; } } else if (leftarc) // edge sequence c0 d0 c1 e2 d1 e0 e1 d2 c2 { #if DEBUG cerr << "node020.3\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; return; } else // edge sequence c0 d0 c1 c2 e2 d1 e0 e1 d2 { #if DEBUG cerr << "node020.4\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[0]; return; } } order[0] = f_d.m_edges[0]; if (cyclicSorted(order)) // e1 between d2 and d0 { order[1] = f_e.m_edges[2]; if (cyclicSorted(order)) { if (leftarc) // edge sequence c0 d0 c1 d1 e2 e0 d2 e1 c2 { #if DEBUG cerr << "node020.5\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; return; } else // edge sequence c0 d0 c1 c2 d1 e2 e0 d2 e1 { #if DEBUG cerr << "node020.6\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[0]; return; } } else if (leftarc) // edge sequence c0 d0 c1 d1 e0 d2 e1 e2 c2 { #if DEBUG cerr << "node020.7\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[2]; return; } else // edge sequence c0 d0 c1 c2 d1 e0 d2 e1 e2 { #if DEBUG cerr << "node020.8\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; return; } } // e1 between d0 and d1 order[0] = f_e.m_edges[2]; order[1] = f_d.m_edges[1]; if (cyclicSorted(order)) { if (leftarc) // edge sequence c0 d0 c1 e1 e2 d1 e0 d2 c2 { #if DEBUG cerr << "node020.9\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; return; } else // edge sequence c0 d0 c1 c2 e1 e2 d1 e0 d2 { #if DEBUG cerr << "node020.10\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; return; } } else if (leftarc) // edge sequence c0 d0 c1 e1 d1 e2 e0 d2 c2 { #if DEBUG cerr << "node020.11\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; return; } else // edge sequence c0 d0 c1 c2 e1 d1 e2 e0 d2 { #if DEBUG cerr << "node020.12\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[0]; return; } } void MinSWRT::node021(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node021" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* c, d and e are nontwisted 3-cycles. c intersects d * (d.m_edges[0] between c.m_edges[0] and c.m_edges[1], others outside), * e intersects d (e.m_edges[0] between d.m_edges[1] and d.m_edges[2]). * There is no pair of interleaving cycles. c and e are intersecting * (so the cycles are mutually intersecting). */ int order[3]; // needed to check cyclic sorting of three edges m_sequence->m_numOperations = 3; // for all sequences m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; // get position of d1 relativ to c order[0] = f_c.m_edges[1]; order[2] = f_c.m_edges[2]; order[1] = f_d.m_edges[1]; if (cyclicSorted(order)) // d1, d2 between c1, c2 { // for all possibilities m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[1]; // get position of e1 order[2] = f_e.m_edges[1]; order[0] = f_c.m_edges[2]; if (cyclicSorted(order)) // e1 somewhere between e0 and c2 { #if DEBUG cerr << "node021.1\n"; #endif // for all possible edge sequences m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; return; } order[0] = f_c.m_edges[0]; if (cyclicSorted(order)) // e1 between c2 and c0 { // get position of e2 order[2] = f_e.m_edges[2]; if (cyclicSorted(order)) // edge sequence c0 d0 c1 d1 e0 d2 c2 e1 e2 { #if DEBUG cerr << "node021.2\n"; #endif m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; return; } else // edge sequence c0 d0 c1 d1 e2 e0 d2 c2 e1 { #if DEBUG cerr << "node021.3\n"; #endif m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; return; } } // e1 between somewhere between c0 and c1 // for all edge sequences #if DEBUG cerr << "node021.4\n"; #endif m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[0]; return; } else // d1, d2 between c2, c0 { // for all sequences m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[2]; // get position of e1 order[2] = f_e.m_edges[1]; order[0] = f_c.m_edges[0]; if (cyclicSorted(order)) // e1 somewhere between e0 and c0 { #if DEBUG cerr << "node021.5\n"; #endif // for all sequences m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; return; } order[0] = f_d.m_edges[0]; if (cyclicSorted(order)) // e1 between c0 and d0 { // get position of e2 order[2] = f_e.m_edges[2]; if (cyclicSorted(order)) // edge sequence c0 e1 e2 d0 c1 c2 d1 e0 d2 { #if DEBUG cerr << "node021.6\n"; #endif m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[2]; return; } else // edge sequence c0 e1 d0 c1 c2 d1 e2 e0 d2 { #if DEBUG cerr << "node021.7\n"; #endif m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; return; } } order[0] = f_c.m_edges[1]; if (cyclicSorted(order)) // e1 between d0 and c1 { // get position of e2 order[2] = f_e.m_edges[2]; if (cyclicSorted(order)) // edge sequence c0 d0 e1 e2 c1 c2 d1 e0 d2 { #if DEBUG cerr << "node021.8\n"; #endif m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[2]; return; } else { #if DEBUG cerr << "node021.9\n"; #endif // for both sequences m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; return; } } else // e1 between c1 and c2 { #if DEBUG cerr << "node021.10\n"; #endif // for all cases m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[0]; return; } } } void MinSWRT::node022(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node022" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* c and d are nontwisted 3-cycles, e is a 1-twisted 3-cycle. * There is no pair of interleaving cycles. c intersects with d (with * the chords between reality-edges 0,1 and 2, 0 of both cycles). e * intersects with d (at least one reality-edge of e between * reality-edges 1 and 2 of d). c and e are not intersecting. */ int order[3]; // needed to check cyclic sorting of three edges bool alphac1; // true if first transposition does not act on c1 int isolated; // isolated edge of e int ex; // edge of e where the first transposition acts on m_sequence->m_numOperations = 3; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; // search the two edges of c close to e order[0] = f_c.m_edges[0]; order[1] = f_d.m_edges[0]; order[2] = f_c.m_edges[1]; if (cyclicSorted(order)) { m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[2]; alphac1 = true; } else { m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[0]; alphac1 = false; } // search edge of e between d1 and d2 + isolated edge of e order[0] = f_d.m_edges[1]; order[2] = f_d.m_edges[2]; order[1] = f_e.m_edges[0]; if (cyclicSorted(order)) { ex = 0; order[1] = f_e.m_edges[1]; if (cyclicSorted(order)) isolated = 2; else { order[1] = f_e.m_edges[2]; if (cyclicSorted(order)) isolated = 1; else isolated = 0; } } else { order[1] = f_e.m_edges[1]; if (cyclicSorted(order)) { ex = 1; order[1] = f_e.m_edges[2]; if (cyclicSorted(order)) isolated = 0; else isolated = 1; } else { ex = 2; isolated = 2; } } m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[ex]; // second operation: eliminate d m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; // search third operation if (isolated == ex) { if (ex == 2) // isolated edge == twisted edge { if (alphac1) { m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[0]; } else { m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; } } else { if (alphac1) { m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[(ex + 2) % 3]; if (m_sequence->m_operations[2].m_edges[2] != f_e.m_edges[2]) m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; else m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; } else { m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[ex + 1]; // ex < 2 if (m_sequence->m_operations[2].m_edges[2] != f_e.m_edges[2]) m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; else m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; } } } else { m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[2]; if (ex == 0) { m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[1]; if (isolated == 1) { if (alphac1) m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; else m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[0]; } else // isolated == 2 { if (alphac1) m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[0]; else m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[1]; } } else // ex == 1 { m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[0]; if (isolated == 0) { if (alphac1) m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; else m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[1]; } else // isolated == 2 { if (alphac1) m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[2]; else m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; } } } m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } void MinSWRT::node023(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node023" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* Node 023: c and d are nontwisted 3-cycles, e is a 1-twisted 3-cycle. * There is no pair of interleaving cycles. c intersects with d (with * the chords between reality-edges 0,1 and 2, 0 of both cycles). e * intersects with d (at least one reality-edge of e between * reality-edges 1 and 2 of d). c and e are intersecting (so the cycles * are mutually intersecting). */ int order[3]; // needed to check cyclic sorting of three edges bool mirror = false; // true if we work with mirrored configuration bool alphac1; // true if first transposition does not act on c1 int ex; // edge of e where the first transposition acts on bool beta, gamma; // position of the other two edges of e; true if // between ca, cb // search chord through center of the configuration order[0] = f_c.m_edges[0]; order[1] = f_d.m_edges[0]; order[2] = f_c.m_edges[2]; alphac1 = cyclicSorted(order); // search third edge of first transposition order[0] = f_d.m_edges[1]; order[2] = f_d.m_edges[2]; order[1] = f_e.m_edges[0]; if (cyclicSorted(order)) ex = 0; else { order[1] = f_e.m_edges[1]; if (cyclicSorted(order)) ex = 1; else ex = 2; } // check if we need to mirror the configuration order[1] = f_d.m_edges[0]; order[0] = f_e.m_edges[(ex + 1) % 3]; if (cyclicSorted(order)) mirror = true; else { order[0] = f_e.m_edges[(ex + 2) % 3]; mirror = cyclicSorted(order); } if (mirror) { // mirror configuration order[0] = f_c.m_edges[1]; // use as temporary variable f_c.m_edges[0] = m_simplePerm->size() - f_c.m_edges[0]; f_c.m_edges[1] = m_simplePerm->size() - f_c.m_edges[2]; f_c.m_edges[2] = m_simplePerm->size() - order[0]; order[0] = f_d.m_edges[1]; // use as temporary variable f_d.m_edges[0] = m_simplePerm->size() - f_d.m_edges[0]; f_d.m_edges[1] = m_simplePerm->size() - f_d.m_edges[2]; f_d.m_edges[2] = m_simplePerm->size() - order[0]; order[0] = f_e.m_edges[0]; // use as temporary variable f_e.m_edges[0] = m_simplePerm->size() - f_e.m_edges[1]; f_e.m_edges[1] = m_simplePerm->size() - order[0]; f_e.m_edges[2] = m_simplePerm->size() - f_e.m_edges[2]; // solve mirrored configuration node023(f_c, f_d, f_e); // re-mirror operations order[0] = m_sequence->m_operations[0].m_edges[0]; // use as temporary variable m_sequence->m_operations[0].m_edges[0] = m_simplePerm->size() - m_sequence->m_operations[0].m_edges[1]; m_sequence->m_operations[0].m_edges[1] = m_simplePerm->size() - order[0]; m_sequence->m_operations[0].m_edges[2] = m_simplePerm->size() - m_sequence->m_operations[0].m_edges[2]; order[0] = m_sequence->m_operations[1].m_edges[0]; // use as temporary variable m_sequence->m_operations[1].m_edges[0] = m_simplePerm->size() - m_sequence->m_operations[1].m_edges[1]; m_sequence->m_operations[1].m_edges[1] = m_simplePerm->size() - order[0]; m_sequence->m_operations[1].m_edges[2] = m_simplePerm->size() - m_sequence->m_operations[1].m_edges[2]; order[0] = m_sequence->m_operations[2].m_edges[0]; // use as temporary variable m_sequence->m_operations[2].m_edges[0] = m_simplePerm->size() - m_sequence->m_operations[2].m_edges[1]; m_sequence->m_operations[2].m_edges[1] = m_simplePerm->size() - order[0]; m_sequence->m_operations[2].m_edges[2] = m_simplePerm->size() - m_sequence->m_operations[2].m_edges[2]; return; } // write first operation m_sequence->m_numOperations = 3; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; if (alphac1) { m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[2]; } else { m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[0]; } m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[ex]; // second operation: eliminate d m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; // check position of other edges of e order[0] = m_sequence->m_operations[0].m_edges[0]; order[2] = m_sequence->m_operations[0].m_edges[1]; order[1] = f_e.m_edges[(ex + 2) % 3]; beta = cyclicSorted(order); order[1] = f_e.m_edges[(ex + 1) % 3]; gamma = cyclicSorted(order); if (beta && gamma) { // check if before alpha if (alphac1) order[2] = f_c.m_edges[1]; else order[2] = f_c.m_edges[2]; if (cyclicSorted(order)) // both before alpha { m_sequence->m_operations[2].m_edges[0] = order[2]; // alpha m_sequence->m_operations[2].m_edges[1] = m_sequence->m_operations[0].m_edges[0]; // ca if (ex == 2) m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[0]; // gamma else m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[(ex+2) % 3];// beta } else // both after alpha { m_sequence->m_operations[2].m_edges[0] = m_sequence->m_operations[0].m_edges[1]; // cb m_sequence->m_operations[2].m_edges[1] = order[2]; // alpha if (ex == 2) m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; // beta else m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[ex+1]; // gamma } if ((ex == 2) || (m_sequence->m_operations[2].m_edges[2] == f_e.m_edges[2])) m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; else m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; } else if (beta) // beta, !gamma { m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; if (ex == 0) { m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[1]; // gamma m_sequence->m_operations[2].m_edges[1] = m_sequence->m_operations[0].m_edges[0]; // ca m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[2]; // beta } else if (ex == 1) { m_sequence->m_operations[2].m_edges[0] = m_sequence->m_operations[0].m_edges[0]; // ca m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[0]; // beta m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[2]; // gamma } else // ex == 2 { m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[1]; // beta m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[0]; // gamma m_sequence->m_operations[2].m_edges[2] = m_sequence->m_operations[0].m_edges[0]; // ca } } else // gamma, !beta { m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; if (ex == 0) { m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[1]; // gamma m_sequence->m_operations[2].m_edges[1] = m_sequence->m_operations[0].m_edges[1]; // cb m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[2]; // beta } else if (ex == 1) { m_sequence->m_operations[2].m_edges[0] = m_sequence->m_operations[0].m_edges[1]; // cb m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[0]; // beta m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[2]; // gamma } else // ex == 2 { m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[1]; // beta m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[0]; // gamma m_sequence->m_operations[2].m_edges[2] = m_sequence->m_operations[0].m_edges[1]; // cb } } m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } void MinSWRT::node024(Cycle& f_c, Cycle& f_d) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node024" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); #endif /* c and d are two interleaving 1-twisted 3-cycles. */ int order[3]; // needed to check cyclic sorting of three edges bool arc1, arc2; // true if an edge is in the arc order[0] = f_c.m_edges[2]; order[2] = f_d.m_edges[2]; order[1] = f_c.m_edges[0]; arc1 = cyclicSorted(order); order[1] = f_d.m_edges[0]; arc2 = !cyclicSorted(order); if (arc1 && arc2) { node036(f_c, f_d); return; } if (arc1) node027(f_c, f_d); else node027(f_d, f_c); } void MinSWRT::node025(Cycle& f_c, Cycle& f_d) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node025" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); #endif /* c and d are non-interleaving 1-twisted 3-cycles. d intersects * the nontwisted chord of c. */ int order[3]; // needed to check cyclic sorting of three edges bool ord0, ord1; // true if d0, d1 between c0, c1 order[0] = f_c.m_edges[0]; order[2] = f_c.m_edges[1]; order[1] = f_d.m_edges[0]; ord0 = cyclicSorted(order); order[1] = f_d.m_edges[1]; ord1 = cyclicSorted(order); if (ord0 && !ord1) // nontwisted chord of d intersected by c node028(f_c, f_d); else if (!ord0 && ord1) // nontwisted chord of d intersected by c node028(f_d, f_c); else node029(f_c, f_d); } void MinSWRT::node026(Cycle& f_c, Cycle& f_d) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node026" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); #endif /* c is a 1-twisted 3-cycle, d is a nontwisted 3-cycle. d intersects the * nontwisted chord of c. The chord of d that is not intersected by c * lies between the reality edges m_edges[1] and m_edges[2]. */ Cycle e; // intersects open arc of d int order[3]; // needed to check cyclic sorting of three edges m_simplePerm->getCycle(&e, 1, f_d.m_edges[1], f_d.m_edges[2]); switch (e.m_type) { case Cycle::CYCLE_2ORIENTED: node000(e); break; case Cycle::CYCLE_2UNORIENTED: node030(f_c, f_d, e); break; case Cycle::CYCLE_0TWISTED: if (interleaving(f_d, e)) { node016(f_d, e); break; } if (interleaving(f_c, e)) { order[0] = e.m_edges[1]; order[2] = e.m_edges[2]; order[1] = f_c.m_edges[0]; if (cyclicSorted(order)) { e.m_edges[2] = e.m_edges[1]; e.m_edges[1] = e.m_edges[0]; e.m_edges[0] = order[2]; } else { order[1] = f_c.m_edges[1]; if (cyclicSorted(order)) { e.m_edges[2] = e.m_edges[0]; e.m_edges[0] = e.m_edges[1]; e.m_edges[1] = order[2]; } } // else no shift necessary node040(e, f_c); break; } // shift e order[0] = f_d.m_edges[1]; order[2] = f_d.m_edges[2]; order[1] = e.m_edges[1]; if (cyclicSorted(order)) // isolated edge: e2 { e.m_edges[1] = e.m_edges[0]; e.m_edges[0] = e.m_edges[2]; e.m_edges[2] = order[1]; order[1] = e.m_edges[0]; // store edge outside d1-d2 } else { order[1] = e.m_edges[2]; if (cyclicSorted(order)) // isolated edge: e1 { e.m_edges[2] = e.m_edges[0]; e.m_edges[0] = e.m_edges[1]; e.m_edges[1] = order[1]; order[1] = e.m_edges[0]; // store edge outside d1-d2 } // else: isolated edge: e0; no shift necessary else order[1] = e.m_edges[1]; // store edge outside d1-d2 } // shift d order[2] = f_d.m_edges[0]; if (cyclicSorted(order)) // edge 0-1 of d not intersected by e { f_d.m_edges[0] = f_d.m_edges[2]; f_d.m_edges[2] = f_d.m_edges[1]; f_d.m_edges[1] = order[2]; } else // edge 2-0 of d not intersected by e { f_d.m_edges[0] = f_d.m_edges[1]; f_d.m_edges[1] = f_d.m_edges[2]; f_d.m_edges[2] = order[2]; } node019(e, f_d, f_c); break; case Cycle::CYCLE_1TWISTED: if (interleaving(f_d, e)) { order[0] = f_d.m_edges[1]; order[2] = f_d.m_edges[2]; order[1] = e.m_edges[0]; if (cyclicSorted(order)) { f_d.m_edges[2] = f_d.m_edges[1]; f_d.m_edges[1] = f_d.m_edges[0]; f_d.m_edges[0] = order[2]; } else { order[1] = e.m_edges[1]; if (cyclicSorted(order)) { f_d.m_edges[2] = f_d.m_edges[0]; f_d.m_edges[0] = f_d.m_edges[1]; f_d.m_edges[1] = order[2]; } } // else no shift necessary node040(f_d, e); break; } if (interleaving(f_c, e)) { node024(f_c, e); break; } node031(f_c, f_d, e); break; case Cycle::CYCLE_2TWISTED: node002(e); break; case Cycle::CYCLE_3TWISTED: node001(e); break; default: cerr << "error in MinSWRT::node026: Algo found unexpected cycle type\n"; printCycle(e); return; } } void MinSWRT::node027(Cycle& f_c, Cycle& f_d) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node027" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); #endif /* c and d are two 1-twisted 3-cycles that form a 1-twisted pair. The * twist of c is left (counterclockwise after) the twist of d. */ Cycle e; // intersects the adjacent arcs int order1[3]; // search edges in left arc int order2[3]; // search edges in right arc int order3[3]; // search edges outside the arcs int a1 = -1, a2 = -1, a3 = -1, a4 = -1; // edge index of e in // arc 1(left), 2(right), 3(down), 4(up); no edge -> -1 m_simplePerm->getCycle(&e, 2, f_c.m_edges[2], f_d.m_edges[0], f_c.m_edges[1], f_d.m_edges[2]); // check trivial cases switch (e.m_type) { case Cycle::CYCLE_2ORIENTED: node000(e); return; case Cycle::CYCLE_2TWISTED: node002(e); return; case Cycle::CYCLE_3TWISTED: node001(e); return; default: // no trivial case break; } m_sequence->m_numOperations = 3; // for all cases // check edge positions of cycle e order1[0] = f_c.m_edges[2]; order1[2] = f_d.m_edges[0]; order2[0] = f_c.m_edges[1]; order2[2] = f_d.m_edges[2]; order3[0] = f_d.m_edges[0]; order3[2] = f_c.m_edges[1]; for (int i = 0; (e.m_type == Cycle::CYCLE_2UNORIENTED? (i < 2) : (i < 3)); i++) { order1[1] = e.m_edges[i]; if (cyclicSorted(order1)) a1 = i; else { order2[1] = e.m_edges[i]; if (cyclicSorted(order2)) a2 = i; else { order3[1] = e.m_edges[i]; if (cyclicSorted(order3)) a3 = i; else a4 = i; } } } // check case: intersection with nontwisted edge if (a3 != -1) { m_sequence->m_operations[0].m_type = Operation::OPERATION_REVERSAL; if (a1 != -1) { m_sequence->m_operations[0].m_edges[0] = e.m_edges[a1]; m_sequence->m_operations[0].m_edges[1] = e.m_edges[a3]; // search exact position of intersecting edge order3[1] = e.m_edges[a3]; order3[2] = f_c.m_edges[0]; if (cyclicSorted(order3)) // edge before c0 { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; } else // edge after c0 { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[1].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_d.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_d.m_edges[1]; } } else { m_sequence->m_operations[0].m_edges[0] = e.m_edges[a3]; m_sequence->m_operations[0].m_edges[1] = e.m_edges[a2]; // search exact position of intersecting edge order3[1] = e.m_edges[a3]; order3[0] = f_d.m_edges[1]; if (cyclicSorted(order3)) // edge after d1 { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[1].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_c.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_d.m_edges[1]; } else // edge before d1 { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[0]; } } // calculate ratio: if reversal splits 1-twisted 3-cycle, ratio is better if ((e.m_type == Cycle::CYCLE_1TWISTED) && ((e.m_edges[2] == m_sequence->m_operations[0].m_edges[0]) || (e.m_edges[2] == m_sequence->m_operations[0].m_edges[1]))) m_sequence->m_dsigma = 6.0f - 2.0f * m_wr / m_wt; else m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = m_wr + 2.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; return; } // check case: e is 2-cycle, intersecting with a twisted edge if (e.m_type == Cycle::CYCLE_2UNORIENTED) { if (a1 != -1) { m_sequence->m_operations[0].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[0].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[1].m_edges[2] = f_c.m_edges[1]; } else { m_sequence->m_operations[0].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[0]; } m_sequence->m_operations[2].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[2].m_edges[0] = e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = e.m_edges[1]; m_sequence->m_dsigma = 2.0f + 2.0f * m_wr / m_wt; m_sequence->m_weight = 2.0f * m_wr + m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; return; } // e is t-unoriented 3-cycle if (e.m_type == Cycle::CYCLE_0TWISTED) { m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; if ((a1 != -1) && (a2 != -1)) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = e.m_edges[a2]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[0]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = e.m_edges[a4]; return; } if (a1 == 0) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_d.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = e.m_edges[2]; return; } if (a1 == 2) // shift e { order1[0] = e.m_edges[0]; e.m_edges[0] = e.m_edges[2]; e.m_edges[2] = e.m_edges[1]; e.m_edges[1] = order1[0]; a1 = 1; } if (a1 == 1) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = e.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = e.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = e.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_d.m_edges[1]; return; } if (a2 == 0) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = e.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[0]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = e.m_edges[1]; return; } if (a2 == 2) // shift e { order1[0] = e.m_edges[0]; e.m_edges[0] = e.m_edges[2]; e.m_edges[2] = e.m_edges[1]; e.m_edges[1] = order1[0]; a2 = 1; } // a2 now == 1 m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = e.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[0]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = e.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[0]; return; } if (e.m_type == Cycle::CYCLE_1TWISTED) { // check if nontwisted chord of e is intersected order1[0] = e.m_edges[0]; order1[2] = e.m_edges[1]; order1[1] = f_c.m_edges[2]; order2[0] = e.m_edges[0]; order2[2] = e.m_edges[1]; order2[1] = f_c.m_edges[0]; if (cyclicSorted(order1) ^ cyclicSorted(order2)) { node029(e, f_c); return; } order1[1] = f_d.m_edges[2]; order2[1] = f_d.m_edges[0]; if (cyclicSorted(order1) ^ cyclicSorted(order2)) { node029(e, f_d); return; } // four possible configurations m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; if (a1 == 1) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = e.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = e.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_d.m_edges[0]; return; } if (a1 == 2) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = e.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_d.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = e.m_edges[0]; return; } if (a2 == 1) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = e.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[0]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; return; } // a2 == 2 m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = e.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[0]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = e.m_edges[1]; return; } cerr << "error in MinSWRT::node027: Algo found unexpected cycle type\n"; printCycle(e); } void MinSWRT::node028(Cycle& f_c, Cycle& f_d) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node028" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); #endif /* c, d are intersecting, non-interleaving 1-twisted 3-cycles. * Both cycles intersect the nontwisted chord of the other cycle. * Reality-edge m_edges[0] of cycle d lies between reality-edges * m_edges[0] and m_edges[1] of cycle c. */ int order[3]; // needed to check cyclic sorting of three edges // for all configurations m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 2.0f * m_wr + m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; m_sequence->m_numOperations = 3; m_sequence->m_operations[2].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[2].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_d.m_edges[1]; // find configurations order[0] = f_c.m_edges[0]; order[1] = f_d.m_edges[2]; order[2] = f_c.m_edges[1]; if (cyclicSorted(order)) // d2 between c0, c1 { m_sequence->m_operations[0].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[0].m_edges[0] = f_d.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_d.m_edges[2]; order[0] = f_d.m_edges[1]; order[2] = f_c.m_edges[2]; if (cyclicSorted(order)) // edge sequence c0 d2 d0 c1 c2 d1 { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[1].m_edges[2] = f_c.m_edges[1]; return; } else // edge sequence c0 d2 d0 c1 d1 c2 { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[1].m_edges[2] = f_c.m_edges[0]; return; } } else { m_sequence->m_operations[0].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[0].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_d.m_edges[0]; order[0] = f_d.m_edges[0]; order[2] = f_c.m_edges[2]; if (cyclicSorted(order)) // edge sequence c0 d0 c1 d1 d2 c2 { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[1].m_edges[2] = f_c.m_edges[0]; return; } else // edge sequence c0 d0 c1 c2 d1 d2 { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[1].m_edges[2] = f_c.m_edges[1]; return; } } } void MinSWRT::node029(Cycle& f_c, Cycle& f_d) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node029" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); #endif /* c, d are intersecting, non-interleaving 1-twisted 3-cycles. * d intersects the nontwisted chord of c, but c doesn't intersect the * nontwisted chord of d. */ Cycle e; // intersects open arc of d int order[3]; // needed to check cyclic sorting of three edges m_simplePerm->getCycle(&e, 1, f_d.m_edges[0], f_d.m_edges[1]); // check trivial cases switch (e.m_type) { case Cycle::CYCLE_2ORIENTED: node000(e); return; case Cycle::CYCLE_2UNORIENTED: node007(e, f_d); return; case Cycle::CYCLE_2TWISTED: node002(e); return; case Cycle::CYCLE_3TWISTED: node001(e); return; default: break; } m_sequence->m_numOperations = 3; // search edges intersecting with open chord -> first operation m_sequence->m_operations[0].m_type = Operation::OPERATION_REVERSAL; order[0] = f_d.m_edges[0]; order[2] = f_d.m_edges[1]; for (int i = 0; i < 3; i++) // e is 3-cycle { order[1] = e.m_edges[i]; if (cyclicSorted(order)) m_sequence->m_operations[0].m_edges[0] = e.m_edges[i]; else m_sequence->m_operations[0].m_edges[1] = e.m_edges[i]; } // is d2 in first reversal? order[0] = m_sequence->m_operations[0].m_edges[0]; order[1] = f_d.m_edges[2]; order[2] = m_sequence->m_operations[0].m_edges[1]; if (cyclicSorted(order)) { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; } else { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[0]; } order[0] = f_c.m_edges[0]; order[2] = f_c.m_edges[1]; order[1] = f_d.m_edges[2]; if (cyclicSorted(order)) // twisted edge of d between nontwisted of c { // are c1, c2 adjacent on the circle? order[0] = f_c.m_edges[1]; order[1] = f_d.m_edges[0]; order[2] = f_c.m_edges[2]; if (cyclicSorted(order)) // no, d0, d1 between c1, c2 { m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[0]; } else // yes, c1, c2 adjacent { m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; } } else // twisted edge of d not between nontwisted of c { // are c1, c2 adjacent on the circle? order[0] = f_c.m_edges[1]; order[2] = f_c.m_edges[2]; if (cyclicSorted(order)) // no, d2 between c1, c2 { m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[0]; } else // yes, c1, c2 adjacent { m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; } } // check ratio - if first reversal splits a cycle, ratio is higher if ((e.m_type == Cycle::CYCLE_1TWISTED) && ((e.m_edges[2] == m_sequence->m_operations[0].m_edges[0]) || (e.m_edges[2] == m_sequence->m_operations[0].m_edges[1]))) m_sequence->m_dsigma = 6.0f - 2.0f * m_wr / m_wt; else m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = m_wr + 2.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } void MinSWRT::node030(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node030" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* Node 030: c is 1-twisted 3-cycle, d is nontwisted 3-cycle, e is * r-unoriented 2-cycle. d intersects the nontwisted chord of c, c does * not intersect the chord between m_edges[1] and m_edges[2] of d. This * chord is intersected by e (with m_edges[0] between the reality-edges. */ int order[3]; // needed to check cyclic sorting of three edges bool e0, e1; // true if e0, e1 is between c0, c1 order[0] = f_c.m_edges[0]; order[2] = f_c.m_edges[1]; order[1] = f_e.m_edges[0]; e0 = cyclicSorted(order); order[1] = f_e.m_edges[1]; e1 = cyclicSorted(order); if (e0 && !e1) { node007(f_e, f_c); return; } if (!e0 && e1) { f_e.m_edges[1] = f_e.m_edges[0]; f_e.m_edges[0] = order[1]; node007(f_e, f_c); return; } if (e0 && e1) node032(f_c, f_d, f_e); else node033(f_c, f_d, f_e); } void MinSWRT::node031(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node031" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* Node 031: c, e are 1-twisted 3-cycles, d is nontwisted 3-cycle. d * intersects the nontwisted chord of c, c does not intersect the chord * between m_edges[1] and m_edges[2] of d. This chord is intersected by * e. There is no pair of interleaving cycles. */ int order[3]; // needed to check cyclic order of three edges bool e0, e1, e2; // true if e0, e1, e2 is in a given interval // check intersection between c, e order[0] = f_c.m_edges[0]; order[2] = f_c.m_edges[1]; order[1] = f_e.m_edges[0]; e0 = cyclicSorted(order); order[1] = f_e.m_edges[1]; e1 = cyclicSorted(order); if (e0 != e1) // c and e are intersecting { node035(f_c, f_d, f_e); return; } order[1] = f_e.m_edges[2]; e2 = cyclicSorted(order); if (e0 != e2) // c and e are intersecting { node035(f_c, f_d, f_e); return; } order[0] = f_c.m_edges[1]; order[2] = f_c.m_edges[2]; e2 = cyclicSorted(order); order[1] = f_e.m_edges[0]; e0 = cyclicSorted(order); if (e0 != e2) // c and e are intersecting { node035(f_c, f_d, f_e); return; } order[1] = f_e.m_edges[1]; e1 = cyclicSorted(order); if (e0 != e1) // c and e are intersecting { node035(f_c, f_d, f_e); return; } // c and e are not intersecting node034(f_c, f_d, f_e); } void MinSWRT::node032(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node032" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* c is 1-twisted 3-cycle, d is nontwisted 3-cycle, e is r-unoriented * 2-cycle. d intersects the nontwisted chord of c. d.m_edges[1] and * d.m_edges[2] lie between c.m_edges[0] and c.m_edges[1]. e intersects d * (e.m_edges[0] between d.m_edges[1] and d.m_edges[2]), but does not * intersect c. */ int order[3]; // needed to check cyclic order of three edges // for all configurations m_sequence->m_numOperations = 4; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; // check position of d0 order[0] = f_c.m_edges[1]; order[1] = f_d.m_edges[0]; order[2] = f_c.m_edges[2]; if (cyclicSorted(order)) // d0 between c1, c2 { // check position of e1 order[0] = f_d.m_edges[1]; order[1] = f_e.m_edges[1]; if (cyclicSorted(order)) // edge sequence d0 c0 c0 d1 e0 d2 d1 c1 { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[2]; m_sequence->m_operations[3].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[3].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[3].m_edges[1] = f_e.m_edges[0]; } else // edge sequence d0 c2 c0 e1 d1 e0 d2 c1 { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[2]; m_sequence->m_operations[3].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[3].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[3].m_edges[1] = f_e.m_edges[0]; } } else // d0 between c2, c0 { // check position of e1 order[0] = f_d.m_edges[1]; order[1] = f_e.m_edges[1]; if (cyclicSorted(order)) // edge sequence d0 c0 d1 e0 d2 e1 c1 c2 { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[2]; m_sequence->m_operations[3].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[3].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[3].m_edges[1] = f_e.m_edges[0]; } else // edge sequence d0 c0 e1 d1 e0 d2 c1 c2 { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[2]; m_sequence->m_operations[3].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[3].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[3].m_edges[1] = f_e.m_edges[0]; } } m_sequence->m_dsigma = 4.0f + 2.0f * m_wr / m_wt; m_sequence->m_weight = m_wr + 3 * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } void MinSWRT::node033(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node033" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* c is 1-twisted 3-cycle, d is nontwisted 3-cycle, e is r-unoriented * 2-cycle. d intersects the nontwisted chord of c. d.m_edges[1] and * d.m_edges[2] are outside of arc c.m_edges[0], c.m_edges[1]. e * intersects d (e.m_edges[0] between d.m_edges[1] and d.m_edges[2]), but * does not intersect c. */ int order[3]; // needed to check cyclic order of three edges // for all configurations m_sequence->m_numOperations = 4; // check position of d1, dd2 order[0] = f_c.m_edges[1]; order[1] = f_d.m_edges[1]; order[2] = f_c.m_edges[2]; if (cyclicSorted(order)) // d1, d2, between c1, c2 { // check position of e1 order[1] = f_e.m_edges[1]; order[2] = f_d.m_edges[1]; if (cyclicSorted(order)) // edge sequence d0 c1 e1 d1 e0 d2 c2 c0 { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[0]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[2]; m_sequence->m_operations[3].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[3].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[3].m_edges[1] = f_e.m_edges[1]; m_sequence->m_dsigma = 4.0f + 2.0f * m_wr / m_wt; m_sequence->m_weight = m_wr + 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; return; } order[2] = f_c.m_edges[2]; if (cyclicSorted(order)) // edge sequence d0 c1 d1 e0 d2 e1 c2 c0 { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[2]; m_sequence->m_operations[3].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[3].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[3].m_edges[1] = f_e.m_edges[1]; m_sequence->m_dsigma = 4.0f + 2.0f * m_wr / m_wt; m_sequence->m_weight = m_wr + 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; return; } else // edge sequence d0 c1 d1 e0 d2 c2 e1 c0 { m_sequence->m_operations[0].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[1].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[1].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_d.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_d.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_d.m_edges[2]; m_sequence->m_operations[3].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[3].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[3].m_edges[1] = f_c.m_edges[1]; m_sequence->m_dsigma = 4.0f + 2.0f * m_wr / m_wt; m_sequence->m_weight = 3.0f * m_wr + m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; return; } } else // d1, d2 between c2, c0 { // check position of e1 order[1] = f_e.m_edges[1]; order[2] = f_c.m_edges[2]; if (cyclicSorted(order)) // edge sequence d0 c1 e1 c2 d1 e0 d2 c0 { m_sequence->m_operations[0].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[1].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[1].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[1].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[3].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[3].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[3].m_edges[1] = f_c.m_edges[1]; m_sequence->m_dsigma = 4.0f + 2.0f * m_wr / m_wt; m_sequence->m_weight = 3.0f * m_wr + m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; return; } order[2] = f_d.m_edges[1]; if (cyclicSorted(order)) // edge sequence d0 c1 c2 e1 d1 e0 d2 c0 { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[0]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[2]; m_sequence->m_operations[3].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[3].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[3].m_edges[1] = f_e.m_edges[1]; m_sequence->m_dsigma = 4.0f + 2.0f * m_wr / m_wt; m_sequence->m_weight = m_wr + 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; return; } else // edge sequence d0 c1 c2 e1 d1 e0 d2 c0 { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[2]; m_sequence->m_operations[3].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[3].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[3].m_edges[1] = f_e.m_edges[1]; m_sequence->m_dsigma = 4.0f + 2.0f * m_wr / m_wt; m_sequence->m_weight = m_wr + 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; return; } } } void MinSWRT::node034(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node034" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* c, e are 1-twisted 3-cycles, d is nontwisted 3-cycle. d intersects the * nontwisted chord of c, c does not intersect the chord between * m_edges[1] and m_edges[2] of d. This chord is intersected by e. c and * e are not intersecting. */ int order[3]; // needed to check cyclic order of three edges // check if d intersects the nontwisted chord of e order[0] = f_e.m_edges[0]; order[2] = f_e.m_edges[1]; order[1] = f_d.m_edges[1]; if (cyclicSorted(order)) // d intersects nontwisted chord of e { node037(f_c, f_d, f_e); return; } order[1] = f_d.m_edges[2]; if (cyclicSorted(order)) // d intersects nontwisted chord of e { node037(f_c, f_d, f_e); return; } node038(f_c, f_d, f_e); } void MinSWRT::node035(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node035" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* c, e are 1-twisted 3-cycles, d is nontwisted 3-cycle. d intersects the * nontwisted chord of c, c does not intersect the chord between * m_edges[1] and m_edges[2] of d. This chord is intersected by e. There * is no pair of interleaving cycles. c and e are intersecting. */ int order[3]; // needed to check cyclic order of three edges // intersects e the nontwisted chord of c? order[0] = f_c.m_edges[0]; order[2] = f_c.m_edges[1]; order[1] = f_e.m_edges[0]; if (cyclicSorted(order)) // e intersects nontwisted chord of c { node025(f_c, f_e); return; } order[1] = f_e.m_edges[1]; if (cyclicSorted(order)) // e intersects nontwisted chord of c { node025(f_c, f_e); return; } order[1] = f_e.m_edges[2]; if (cyclicSorted(order)) // e intersects nontwisted chord of c { node025(f_c, f_e); return; } // intersects c the nontwisted chord of e? order[0] = f_e.m_edges[0]; order[2] = f_e.m_edges[1]; order[1] = f_c.m_edges[0]; if (cyclicSorted(order)) // c intersects nontwisted chord of e, { // but not vice versa node029(f_e, f_c); return; } order[1] = f_c.m_edges[1]; if (cyclicSorted(order)) // e intersects nontwisted chord of c { // but not vice versa node029(f_e, f_c); return; } order[1] = f_c.m_edges[2]; if (cyclicSorted(order)) // e intersects nontwisted chord of c { // but not vice versa node029(f_e, f_c); return; } node039(f_c, f_d, f_e); } void MinSWRT::node036(Cycle& f_c, Cycle& f_d) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node036" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); #endif /* c and d are two interleaving 1-twisted 3-cycles that do not form a * 1-twisted pair. */ m_sequence->m_numOperations = 3; m_sequence->m_operations[0].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_REVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[1]; m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 2.0f * m_wr + m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } void MinSWRT::node037(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node037" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* c, e are 1-twisted 3-cycles, d is nontwisted 3-cycle. d intersects the * nontwisted chord of c, c does not intersect the chord between * m_edges[1] and m_edges[2] of d. This chord is intersected by a * nontwisted chord of e. c and e are not intersecting. */ int order[3]; // needed to check cyclic order of three edges int separatedc; // edge of c separated from the others int separatede; // edge of e separated from the others bool reverted; // true if twisted edge is reverted m_sequence->m_numOperations = 4; // find arc with edges from c and e order[0] = f_d.m_edges[2]; order[2] = f_d.m_edges[0]; order[1] = f_e.m_edges[0]; if (cyclicSorted(order)) // arc between d2, d0 { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_d.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_d.m_edges[1]; // search separated edge order[1] = f_e.m_edges[2]; if (cyclicSorted(order)) separatede = 1; else separatede = 0; } else { order[1] = f_e.m_edges[1]; if (cyclicSorted(order)) // arc between d2, d0 { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_d.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_d.m_edges[1]; // search separated edge order[1] = f_e.m_edges[2]; if (cyclicSorted(order)) separatede = 0; else separatede = 1; } else // arc between d0, d1 { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_d.m_edges[2]; // search separated edge order[0] = f_e.m_edges[1]; order[2] = f_e.m_edges[2]; order[1] = f_d.m_edges[0]; if (cyclicSorted(order)) separatede = 1; else { order[1] = f_d.m_edges[1]; if (cyclicSorted(order)) separatede = 1; else separatede = 0; } } } // check if e2 is reverted in the first move order[0] = m_sequence->m_operations[0].m_edges[0]; order[2] = m_sequence->m_operations[0].m_edges[1]; order[1] = f_e.m_edges[2]; reverted = cyclicSorted(order); // second move if (separatede == 0) { if (reverted) { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_e.m_edges[1]; } else { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[1].m_edges[2] = f_e.m_edges[1]; } } else { if (reverted) { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[1].m_edges[2] = f_e.m_edges[0]; } else { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[1].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_e.m_edges[0]; } } // find separated edge of c order[0] = f_c.m_edges[1]; order[2] = f_c.m_edges[2]; order[1] = f_d.m_edges[0]; if (cyclicSorted(order)) separatedc = 1; else { order[1] = f_d.m_edges[1]; if (cyclicSorted(order)) separatedc = 1; else separatedc = 0; } // check if c2 is reverted in the first move order[0] = m_sequence->m_operations[0].m_edges[0]; order[2] = m_sequence->m_operations[0].m_edges[1]; order[1] = f_c.m_edges[2]; reverted = cyclicSorted(order); // third move if (separatedc == 0) { if (reverted ^ (m_sequence->m_operations[0].m_edges[2] == f_d.m_edges[1]) ^ (separatede == 0)) { m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; } else { m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; } } else { if (reverted ^ (m_sequence->m_operations[0].m_edges[2] == f_d.m_edges[1]) ^ (separatede == 0)) { m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[0]; } else { m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[0]; } } // last move if (separatedc == separatede) { m_sequence->m_operations[3].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[3].m_edges[0] = m_sequence->m_operations[0].m_edges[1]; m_sequence->m_operations[3].m_edges[1] = m_sequence->m_operations[0].m_edges[0]; m_sequence->m_operations[3].m_edges[2] = m_sequence->m_operations[0].m_edges[2]; } else { m_sequence->m_operations[3].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[3].m_edges[0] = m_sequence->m_operations[0].m_edges[0]; m_sequence->m_operations[3].m_edges[1] = m_sequence->m_operations[0].m_edges[1]; m_sequence->m_operations[3].m_edges[2] = m_sequence->m_operations[0].m_edges[2]; } m_sequence->m_dsigma = 6.0f; m_sequence->m_weight = 4.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } void MinSWRT::node038(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node038" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* c, e are 1-twisted 3-cycles, d is nontwisted 3-cycle. d intersects the * nontwisted chord of c, c does not intersect the chord between * m_edges[1] and m_edges[2] of d. This chord is intersected by the two * twisted chords of e. c and e are not intersecting. */ int order[3]; // needed to check cyclic order of three edges int confdc; // configuration of cycles c and d; 0: d0 c2 c0 d1 d2 c1 // 1: d0 c1 c2 d1 d2 c0; 2: d0 c0 d1 d2 c1 c2 // 3: d0 c1 d1 d2 c2 c0 int confde; // configuration of cycles d and e; 0: d0 d1 e0 e1 d2 e2 // 1: d0 d1 e2 d2 e0 e1; 2: d0 e2 d1 e0 e1 d2 // 3: d0 e0 e1 d1 e1 d2 // configuration of c and d order[0] = f_d.m_edges[0]; order[2] = f_d.m_edges[2]; order[1] = f_c.m_edges[2]; if (cyclicSorted(order)) { order[1] = f_c.m_edges[0]; if (cyclicSorted(order)) // edge sequence d0 c2 c0 d1 d2 c1 confdc = 0; else // edge sequence d0 c1 c2 d1 d2 c0 confdc = 1; } else { order[1] = f_c.m_edges[0]; if (cyclicSorted(order)) // edge sequence d0 c0 d1 d2 c1 c2 confdc = 2; else // edge sequence d0 c1 d1 d2 c2 c0 confdc = 3; } // configuration of d and e order[0] = f_d.m_edges[1]; order[2] = f_d.m_edges[2]; order[1] = f_e.m_edges[2]; if (cyclicSorted(order)) { order[2] = f_d.m_edges[0]; order[1] = f_e.m_edges[0]; if (cyclicSorted(order)) // edge sequence d0 d1 e2 d2 e0 e1 confde = 1; else // edge sequence d0 e0 e1 d1 e2 d2 confde = 3; } else { order[2] = f_d.m_edges[0]; if (cyclicSorted(order)) // edge sequence d0 d1 e0 e1 d2 e2 confde = 0; else // edge sequence d0 e2 d1 e0 e1 d2 confde = 2; } m_sequence->m_numOperations = 3; if (confdc == 0) { if (confde == 0) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; } else if (confde == 1) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[2]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[2]; } else if (confde == 2) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[2]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[0]; } else // confde == 3 { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[0]; } } else if (confdc == 1) { if (confde == 0) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; } else if (confde == 1) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[2]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[0]; } else if (confde == 2) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[2]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; } else // confde == 3 { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[1]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; } } else if (confdc == 2) { if (confde == 0) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[2]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; } else if (confde == 1) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[0]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[0]; } else if (confde == 2) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[0]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[0]; } else // confde == 3 { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[2]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[2]; } } else // confdc == 3 { if (confde == 0) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[2]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; } else if (confde == 1) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[0]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[0]; } else if (confde == 2) { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[0]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[0]; } else // confde == 3 { m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[2]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[2]; } } m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } void MinSWRT::node039(Cycle& f_c, Cycle& f_d, Cycle& f_e) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node039" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); cerr << "cycle e:" << endl; printCycle(f_e); #endif /* c, e are 1-twisted 3-cycles, d is nontwisted 3-cycle. d intersects the * nontwisted chord of c, c does not intersect the chord between * m_edges[1] and m_edges[2] of d. This chord is intersected by e. There * is no pair of interleaving cycles. c and e are intersecting with their * twisted chords. */ int order[3]; // needed to check cyclic order of three edges int edgeseq; // there are 6 possible edge sequences // getting edge sequence order[0] = f_d.m_edges[1]; order[2] = f_d.m_edges[2]; order[1] = f_e.m_edges[2]; if (cyclicSorted(order)) // e2 between d1, d2 { order[1] = f_e.m_edges[0]; order[2] = f_d.m_edges[0]; if (cyclicSorted(order)) edgeseq = 0; // edge sequence d0 c1 d1 e2 d2 c2 e0 e1 c0 else edgeseq = 1; // edge sequence d0 c1 e0 e1 c2 d1 e2 d2 c0 } else { order[2] = f_d.m_edges[0]; if (cyclicSorted(order)) // e2 between c2, c0 { order[1] = f_e.m_edges[1]; order[2] = f_d.m_edges[2]; if (cyclicSorted(order)) edgeseq = 2; // edge sequence d0 c1 d1 e0 e1 d2 c2 e2 c0 else edgeseq = 3; // edge sequence d0 c1 d1 e0 d2 e1 c2 e2 c0 } else // e2 between c1, c2 { order[1] = f_e.m_edges[0]; order[2] = f_d.m_edges[2]; if (cyclicSorted(order)) edgeseq = 4; // edge sequence d0 c1 e2 c2 d1 e0 e1 d2 c0 else edgeseq = 5; // edge sequence d0 c1 e2 c2 e0 d1 e1 d2 c0 } } m_sequence->m_numOperations = 3; switch (edgeseq) { case 0: #if DEBUG cerr << "node039.0\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[1]; break; case 1: #if DEBUG cerr << "node039.1\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[0]; break; case 2: #if DEBUG cerr << "node039.2\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[1]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[2]; break; case 3: #if DEBUG cerr << "node039.3\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_e.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[2]; break; case 4: #if DEBUG cerr << "node039.4\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_e.m_edges[2]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[0]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[2]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[2]; break; case 5: #if DEBUG cerr << "node039.5\n"; #endif m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[0].m_edges[0] = f_e.m_edges[1]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[2] = f_e.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_e.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[2].m_edges[2] = f_e.m_edges[2]; break; } // second move is for four sequences identical if (edgeseq == 3) { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[1]; } else if (edgeseq == 5) { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[2]; } else { m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[2]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[0]; } m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } void MinSWRT::node040(Cycle& f_c, Cycle& f_d) { #if DEBUG // !!DEBUG: cycle info cerr << "entering node040" << endl; cerr << "cycle c:" << endl; printCycle(f_c); cerr << "cycle d:" << endl; printCycle(f_d); #endif /* c is a nontwisted 3-cycle, d is a 1-twisted 3-cycle. c and d are * interleaving. The twisted edge of d lies between m_edges[1] and * m_edges[2] of cycle c. */ m_sequence->m_numOperations = 3; m_sequence->m_operations[0].m_type = Operation::OPERATION_TRANSPOSITION; m_sequence->m_operations[0].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[0].m_edges[1] = f_c.m_edges[1]; m_sequence->m_operations[0].m_edges[2] = f_c.m_edges[2]; m_sequence->m_operations[1].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[1].m_edges[0] = f_d.m_edges[1]; m_sequence->m_operations[1].m_edges[1] = f_d.m_edges[0]; m_sequence->m_operations[1].m_edges[2] = f_d.m_edges[2]; m_sequence->m_operations[2].m_type = Operation::OPERATION_TRANSREVERSAL; m_sequence->m_operations[2].m_edges[0] = f_c.m_edges[0]; m_sequence->m_operations[2].m_edges[1] = f_c.m_edges[2]; m_sequence->m_operations[2].m_edges[2] = f_c.m_edges[1]; m_sequence->m_dsigma = 4.0f; m_sequence->m_weight = 3.0f * m_wt; m_sequence->m_ratio = m_sequence->m_dsigma / m_sequence->m_weight; } /*************************************************************************** * debugging methods ***************************************************************************/ void MinSWRT::debug() { cerr << "simple perm is " << (m_simplePerm->isSorted()?"":"not ") << "sorted\n"; cerr << "n = " << m_size << endl; /* cerr << "target:\n"; for (int i = 0; i < m_size; i++) cerr << m_target[i] << " "; cerr << endl; */ // printResult(4); } } // end namespace minswrt phylo-1.0.6/minswrt/tools.cpp0000644000175000017500000000427511434510050013142 00000000000000/** * filename: tools.cpp * author: Martin Bader * begin: 25.07.2005 * last change: 11.08.2008 * * Useful functions for MinSWRT. * * Copyright (C) 2007 Martin Bader * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see . */ #include "tools.h" #include "permutation.h" namespace minswrt { /*************************************************************************** * debugging non-class functions ***************************************************************************/ bool interleaving(const Cycle& f_c, const Cycle& f_d) { int i1, i2; // edge indexes // search minimum edges if (f_c.m_edges[0] < f_c.m_edges[1]) { if (f_c.m_edges[0] < f_c.m_edges[2]) i1 = 0; else i1 = 2; } else if (f_c.m_edges[1] < f_c.m_edges[2]) i1 = 1; else i1 = 2; if (f_d.m_edges[0] < f_d.m_edges[1]) { if (f_d.m_edges[0] < f_d.m_edges[2]) i2 = 0; else i2 = 2; } else if (f_d.m_edges[1] < f_d.m_edges[2]) i2 = 1; else i2 = 2; // check if interleaving if (f_c.m_edges[i1] > f_d.m_edges[i2]) i2 == 2? i2 = 0 : i2++; else if (f_c.m_edges[(i1 + 2) % 3] > f_d.m_edges[(i2 + 2) % 3]) return false; for (int i = 0; i < 2; i++) { if (f_c.m_edges[i1] > f_d.m_edges[i2]) return false; i1 == 2? i1 = 0 : i1++; if (f_d.m_edges[i2] > f_c.m_edges[i1]) return false; i2 == 2? i2 = 0 : i2++; } return true; } } // end namespace minswrt