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AC_INIT(libGenome/gnDefs.h) dnl Get the target and build system types and add appropriate options AC_CANONICAL_TARGET dnl ----------------------------------------------- dnl Package name and version number (user defined) dnl ----------------------------------------------- GENERIC_LIBRARY_NAME=libGenome #release versioning GENERIC_MAJOR_VERSION=1 GENERIC_MINOR_VERSION=3 GENERIC_MICRO_VERSION=1 #API version (often = GENERIC_MAJOR_VERSION.GENERIC_MINOR_VERSION) GENERIC_API_VERSION=1.3 AC_SUBST(GENERIC_API_VERSION) GENERIC_API_UNDERSCORE_VERS=1_3 AC_SUBST(GENERIC_API_UNDERSCORE_VERS) #shared library versioning GENERIC_LIBRARY_VERSION=1:3:1 # | | | # +------+ | +---+ # | | | # current:revision:age # | | | # | | +- increment if interfaces have been added # | | | # | | +- increment if interfaces have been added # | | set to zero if interfaces have been removed # or changed # | +- increment if source code has changed # | set to zero if current is incremented # +- increment if interfaces have been added, removed or changed dnl -------------------------------- dnl Package name and version number dnl -------------------------------- AC_SUBST(GENERIC_LIBRARY_VERSION) PACKAGE=$GENERIC_LIBRARY_NAME AC_SUBST(GENERIC_LIBRARY_NAME) GENERIC_VERSION=$GENERIC_MAJOR_VERSION.$GENERIC_MINOR_VERSION.$GENERIC_MICRO_VERSION GENERIC_RELEASE=$GENERIC_MAJOR_VERSION.$GENERIC_MINOR_VERSION AC_SUBST(GENERIC_RELEASE) AC_SUBST(GENERIC_VERSION) VERSION=$GENERIC_VERSION AM_INIT_AUTOMAKE($PACKAGE, $VERSION, no-define) AC_PREFIX_DEFAULT(/usr/local) dnl Checks for programs. 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AC_PROG_GCC_TRADITIONAL dnl SAVE_LIBRARY_VERSION AC_SUBST(LIBTOOL_VERSION_INFO) AC_OUTPUT(Makefile libGenome/Makefile libGenome-1.3.pc ) libGenome-1.3.1/install-sh0000755002622200470610000002176610126442331012360 00000000000000#!/bin/sh # install - install a program, script, or datafile scriptversion=2004-09-10.20 # This originates from X11R5 (mit/util/scripts/install.sh), which was # later released in X11R6 (xc/config/util/install.sh) with the # following copyright and license. # # Copyright (C) 1994 X Consortium # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to # deal in the Software without restriction, including without limitation the # rights to use, copy, modify, merge, publish, distribute, sublicense, and/or # sell copies of the Software, and to permit persons to whom the Software is # furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in # all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 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. It can only install one file at a time, a restriction # shared with many OS's install programs. # set DOITPROG to echo to test this script # Don't use :- since 4.3BSD and earlier shells don't like it. doit="${DOITPROG-}" # put in absolute paths if you don't have them in your path; or use env. vars. mvprog="${MVPROG-mv}" cpprog="${CPPROG-cp}" chmodprog="${CHMODPROG-chmod}" chownprog="${CHOWNPROG-chown}" chgrpprog="${CHGRPPROG-chgrp}" stripprog="${STRIPPROG-strip}" rmprog="${RMPROG-rm}" mkdirprog="${MKDIRPROG-mkdir}" chmodcmd="$chmodprog 0755" chowncmd= chgrpcmd= stripcmd= rmcmd="$rmprog -f" mvcmd="$mvprog" src= dst= dir_arg= dstarg= no_target_directory= usage="Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE or: $0 [OPTION]... SRCFILES... DIRECTORY or: $0 [OPTION]... -t DIRECTORY SRCFILES... or: $0 [OPTION]... -d DIRECTORIES... In the 1st form, copy SRCFILE to DSTFILE. In the 2nd and 3rd, copy all SRCFILES to DIRECTORY. In the 4th, create DIRECTORIES. 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ECHO=$echo if test "X$ECHO" = "X$CONFIG_SHELL [$]0 --fallback-echo"; then ECHO="$CONFIG_SHELL \\\$\[$]0 --fallback-echo" fi AC_SUBST(ECHO) ])])# _LT_AC_PROG_ECHO_BACKSLASH # _LT_AC_LOCK # ----------- AC_DEFUN([_LT_AC_LOCK], [AC_ARG_ENABLE([libtool-lock], [AC_HELP_STRING([--disable-libtool-lock], [avoid locking (might break parallel builds)])]) test "x$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 AC_TRY_EVAL(ac_compile); then case `/usr/bin/file conftest.$ac_objext` in *ELF-32*) HPUX_IA64_MODE="32" ;; *ELF-64*) HPUX_IA64_MODE="64" ;; esac fi rm -rf conftest* ;; *-*-irix6*) # Find out which ABI we are using. echo '[#]line __oline__ "configure"' > conftest.$ac_ext if AC_TRY_EVAL(ac_compile); 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="${LD-ld} -64" ;; esac fi fi rm -rf conftest* ;; x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*|s390*-*linux*|sparc*-*linux*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if AC_TRY_EVAL(ac_compile); then case "`/usr/bin/file conftest.o`" in *32-bit*) case $host in x86_64-*linux*) LD="${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 $host in x86_64-*linux*) LD="${LD-ld} -m elf_x86_64" ;; ppc*-*linux*|powerpc*-*linux*) LD="${LD-ld} -m elf64ppc" ;; s390*-*linux*) LD="${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. 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EOF elif $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else _LT_AC_TAGVAR(ld_shlibs, $1)=no fi ;; sunos4*) _LT_AC_TAGVAR(archive_cmds, $1)='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags' wlarc= _LT_AC_TAGVAR(hardcode_direct, $1)=yes _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no ;; linux*) if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then tmp_archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' _LT_AC_TAGVAR(archive_cmds, $1)="$tmp_archive_cmds" supports_anon_versioning=no case `$LD -v 2>/dev/null` in *\ [01].* | *\ 2.[[0-9]].* | *\ 2.10.*) ;; # catch versions < 2.11 *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ... *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ... *\ 2.11.*) ;; # other 2.11 versions *) supports_anon_versioning=yes ;; esac if test $supports_anon_versioning = yes; then _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$echo "{ global:" > $output_objdir/$libname.ver~ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ $echo "local: *; };" >> $output_objdir/$libname.ver~ $CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib' else _LT_AC_TAGVAR(archive_expsym_cmds, $1)="$tmp_archive_cmds" fi else _LT_AC_TAGVAR(ld_shlibs, $1)=no fi ;; *) if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else _LT_AC_TAGVAR(ld_shlibs, $1)=no fi ;; esac if test "$_LT_AC_TAGVAR(ld_shlibs, $1)" = yes; then runpath_var=LD_RUN_PATH _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}--rpath ${wl}$libdir' _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic' # ancient GNU ld didn't support --whole-archive et. al. if $LD --help 2>&1 | grep 'no-whole-archive' > /dev/null; then _LT_AC_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive' else _LT_AC_TAGVAR(whole_archive_flag_spec, $1)= fi fi else # PORTME fill in a description of your system's linker (not GNU ld) case $host_os in aix3*) _LT_AC_TAGVAR(allow_undefined_flag, $1)=unsupported _LT_AC_TAGVAR(always_export_symbols, $1)=yes _LT_AC_TAGVAR(archive_expsym_cmds, $1)='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname' # Note: this linker hardcodes the directories in LIBPATH if there # are no directories specified by -L. _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes if test "$GCC" = yes && test -z "$link_static_flag"; then # Neither direct hardcoding nor static linking is supported with a # broken collect2. _LT_AC_TAGVAR(hardcode_direct, $1)=unsupported fi ;; aix4* | aix5*) if test "$host_cpu" = ia64; then # On IA64, the linker does run time linking by default, so we don't # have to do anything special. aix_use_runtimelinking=no exp_sym_flag='-Bexport' no_entry_flag="" else # If we're using GNU nm, then we don't want the "-C" option. # -C means demangle to AIX nm, but means don't demangle with GNU nm if $NM -V 2>&1 | grep 'GNU' > /dev/null; then _LT_AC_TAGVAR(export_symbols_cmds, $1)='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\[$]2 == "T") || (\[$]2 == "D") || (\[$]2 == "B")) && ([substr](\[$]3,1,1) != ".")) { print \[$]3 } }'\'' | sort -u > $export_symbols' else _LT_AC_TAGVAR(export_symbols_cmds, $1)='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\[$]2 == "T") || (\[$]2 == "D") || (\[$]2 == "B")) && ([substr](\[$]3,1,1) != ".")) { print \[$]3 } }'\'' | sort -u > $export_symbols' fi aix_use_runtimelinking=no # Test if we are trying to use run time linking or normal # AIX style linking. If -brtl is somewhere in LDFLAGS, we # need to do runtime linking. case $host_os in aix4.[[23]]|aix4.[[23]].*|aix5*) for ld_flag in $LDFLAGS; do if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then aix_use_runtimelinking=yes break fi done esac exp_sym_flag='-bexport' no_entry_flag='-bnoentry' fi # When large executables or shared objects are built, AIX ld can # have problems creating the table of contents. If linking a library # or program results in "error TOC overflow" add -mminimal-toc to # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS. _LT_AC_TAGVAR(archive_cmds, $1)='' _LT_AC_TAGVAR(hardcode_direct, $1)=yes _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=':' _LT_AC_TAGVAR(link_all_deplibs, $1)=yes if test "$GCC" = yes; then case $host_os in aix4.[012]|aix4.[012].*) # We only want to do this on AIX 4.2 and lower, the check # below for broken collect2 doesn't work under 4.3+ collect2name=`${CC} -print-prog-name=collect2` if test -f "$collect2name" && \ strings "$collect2name" | grep resolve_lib_name >/dev/null then # We have reworked collect2 _LT_AC_TAGVAR(hardcode_direct, $1)=yes else # We have old collect2 _LT_AC_TAGVAR(hardcode_direct, $1)=unsupported # It fails to find uninstalled libraries when the uninstalled # path is not listed in the libpath. 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The following line is correct: shared_flag='-G' else if test "$aix_use_runtimelinking" = yes; then shared_flag='${wl}-G' else shared_flag='${wl}-bM:SRE' fi fi fi # It seems that -bexpall does not export symbols beginning with # underscore (_), so it is better to generate a list of symbols to export. _LT_AC_TAGVAR(always_export_symbols, $1)=yes if test "$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. _LT_AC_TAGVAR(allow_undefined_flag, $1)='-berok' # Determine the default libpath from the value encoded in an empty executable. _LT_AC_SYS_LIBPATH_AIX _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath" _LT_AC_TAGVAR(archive_expsym_cmds, $1)="\$CC"' -o $output_objdir/$soname $libobjs $deplibs $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then echo "${wl}${allow_undefined_flag}"; else :; fi` '"\${wl}$no_entry_flag \${wl}$exp_sym_flag:\$export_symbols $shared_flag" else if test "$host_cpu" = ia64; then _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $libdir:/usr/lib:/lib' _LT_AC_TAGVAR(allow_undefined_flag, $1)="-z nodefs" _LT_AC_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$no_entry_flag \${wl}$exp_sym_flag:\$export_symbols" else # Determine the default libpath from the value encoded in an empty executable. _LT_AC_SYS_LIBPATH_AIX _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${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. _LT_AC_TAGVAR(no_undefined_flag, $1)=' ${wl}-bernotok' _LT_AC_TAGVAR(allow_undefined_flag, $1)=' ${wl}-berok' # -bexpall does not export symbols beginning with underscore (_) _LT_AC_TAGVAR(always_export_symbols, $1)=yes # Exported symbols can be pulled into shared objects from archives _LT_AC_TAGVAR(whole_archive_flag_spec, $1)=' ' _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=yes # This is similar to how AIX traditionally builds it's shared libraries. _LT_AC_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs $compiler_flags ${wl}-bE:$export_symbols ${wl}-bnoentry${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' fi fi ;; amigaos*) _LT_AC_TAGVAR(archive_cmds, $1)='$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)' _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes # see comment about different semantics on the GNU ld section _LT_AC_TAGVAR(ld_shlibs, $1)=no ;; bsdi4*) _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)=-rdynamic ;; cygwin* | mingw* | pw32*) # 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. _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)=' ' _LT_AC_TAGVAR(allow_undefined_flag, $1)=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. _LT_AC_TAGVAR(archive_cmds, $1)='$CC -o $lib $libobjs $compiler_flags `echo "$deplibs" | $SED -e '\''s/ -lc$//'\''` -link -dll~linknames=' # The linker will automatically build a .lib file if we build a DLL. _LT_AC_TAGVAR(old_archive_From_new_cmds, $1)='true' # FIXME: Should let the user specify the lib program. _LT_AC_TAGVAR(old_archive_cmds, $1)='lib /OUT:$oldlib$oldobjs$old_deplibs' fix_srcfile_path='`cygpath -w "$srcfile"`' _LT_AC_TAGVAR(enable_shared_with_static_runtimes, $1)=yes ;; darwin* | rhapsody*) if test "$GXX" = yes ; then _LT_AC_TAGVAR(archive_cmds_need_lc, $1)=no case "$host_os" in rhapsody* | darwin1.[[012]]) _LT_AC_TAGVAR(allow_undefined_flag, $1)='-undefined suppress' ;; *) # Darwin 1.3 on if test -z ${MACOSX_DEPLOYMENT_TARGET} ; then _LT_AC_TAGVAR(allow_undefined_flag, $1)='-flat_namespace -undefined suppress' else case ${MACOSX_DEPLOYMENT_TARGET} in 10.[[012]]) _LT_AC_TAGVAR(allow_undefined_flag, $1)='-flat_namespace -undefined suppress' ;; 10.*) _LT_AC_TAGVAR(allow_undefined_flag, $1)='-undefined dynamic_lookup' ;; esac fi ;; esac lt_int_apple_cc_single_mod=no output_verbose_link_cmd='echo' if $CC -dumpspecs 2>&1 | grep 'single_module' >/dev/null ; then lt_int_apple_cc_single_mod=yes fi if test "X$lt_int_apple_cc_single_mod" = Xyes ; then _LT_AC_TAGVAR(archive_cmds, $1)='$CC -dynamiclib -single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring' else _LT_AC_TAGVAR(archive_cmds, $1)='$CC -r ${wl}-bind_at_load -keep_private_externs -nostdlib -o ${lib}-master.o $libobjs~$CC -dynamiclib $allow_undefined_flag -o $lib ${lib}-master.o $deplibs $compiler_flags -install_name $rpath/$soname $verstring' fi _LT_AC_TAGVAR(module_cmds, $1)='$CC ${wl}-bind_at_load $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags' # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin ld's if test "X$lt_int_apple_cc_single_mod" = Xyes ; then _LT_AC_TAGVAR(archive_expsym_cmds, $1)='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -dynamiclib -single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' else _LT_AC_TAGVAR(archive_expsym_cmds, $1)='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -r ${wl}-bind_at_load -keep_private_externs -nostdlib -o ${lib}-master.o $libobjs~$CC -dynamiclib $allow_undefined_flag -o $lib ${lib}-master.o $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' fi _LT_AC_TAGVAR(module_expsym_cmds, $1)='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' _LT_AC_TAGVAR(hardcode_direct, $1)=no _LT_AC_TAGVAR(hardcode_automatic, $1)=yes _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=unsupported _LT_AC_TAGVAR(whole_archive_flag_spec, $1)='-all_load $convenience' _LT_AC_TAGVAR(link_all_deplibs, $1)=yes else _LT_AC_TAGVAR(ld_shlibs, $1)=no fi ;; dgux*) _LT_AC_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' _LT_AC_TAGVAR(hardcode_shlibpath_var, $1)=no ;; freebsd1*) _LT_AC_TAGVAR(ld_shlibs, $1)=no ;; # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor # support. 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hpux9*) if test "$GCC" = yes; then _LT_AC_TAGVAR(archive_cmds, $1)='$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 _LT_AC_TAGVAR(archive_cmds, $1)='$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 _LT_AC_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir' _LT_AC_TAGVAR(hardcode_libdir_separator, $1)=: _LT_AC_TAGVAR(hardcode_direct, $1)=yes # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. _LT_AC_TAGVAR(hardcode_minus_L, $1)=yes _LT_AC_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' ;; hpux10* | hpux11*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then case "$host_cpu" in hppa*64*|ia64*) _LT_AC_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; 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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, write to the Free Software # Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA # 02111-1307, USA. # serial 1 # _AM_PROG_TAR(FORMAT) # -------------------- # Check how to create a tarball in format FORMAT. # FORMAT should be one of `v7', `ustar', or `pax'. # # Substitute a variable $(am__tar) that is a command # writing to stdout a FORMAT-tarball containing the directory # $tardir. # tardir=directory && $(am__tar) > result.tar # # Substitute a variable $(am__untar) that extract such # a tarball read from stdin. # $(am__untar) < result.tar AC_DEFUN([_AM_PROG_TAR], [# Always define AMTAR for backward compatibility. 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We just wanted to have am__tar # and am__untar set. test -n "${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 m4_include([m4/ax_openmp.m4]) m4_include([m4/ax_prog_doxygen.m4]) libGenome-1.3.1/NEWS0000644002622200470610000000000010647575617011053 00000000000000libGenome-1.3.1/doxygen.am0000644002622200470610000000665210766630706012364 00000000000000## --------------------------------- ## ## Format-independent Doxygen rules. ## ## --------------------------------- ## if DX_COND_doc ## ------------------------------- ## ## Rules specific for HTML output. ## ## ------------------------------- ## if DX_COND_html DX_CLEAN_HTML = @DX_DOCDIR@/html endif DX_COND_html ## ------------------------------ ## ## Rules specific for CHM output. ## ## ------------------------------ ## if DX_COND_chm DX_CLEAN_CHM = @DX_DOCDIR@/chm if DX_COND_chi DX_CLEAN_CHI = @DX_DOCDIR@/@PACKAGE@.chi endif DX_COND_chi endif DX_COND_chm ## ------------------------------ ## ## Rules specific for MAN output. ## ## ------------------------------ ## if DX_COND_man DX_CLEAN_MAN = @DX_DOCDIR@/man endif DX_COND_man ## ------------------------------ ## ## Rules specific for RTF output. ## ## ------------------------------ ## if DX_COND_rtf DX_CLEAN_RTF = @DX_DOCDIR@/rtf endif DX_COND_rtf ## ------------------------------ ## ## Rules specific for XML output. ## ## ------------------------------ ## if DX_COND_xml DX_CLEAN_XML = @DX_DOCDIR@/xml endif DX_COND_xml ## ----------------------------- ## ## Rules specific for PS output. ## ## ----------------------------- ## if DX_COND_ps DX_CLEAN_PS = @DX_DOCDIR@/@PACKAGE@.ps DX_PS_GOAL = doxygen-ps doxygen-ps: @DX_DOCDIR@/@PACKAGE@.ps @DX_DOCDIR@/@PACKAGE@.ps: @DX_DOCDIR@/@PACKAGE@.tag cd @DX_DOCDIR@/latex; \ rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \ $(DX_LATEX) refman.tex; \ $(MAKEINDEX_PATH) refman.idx; \ $(DX_LATEX) refman.tex; \ countdown=5; \ while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \ refman.log > /dev/null 2>&1 \ && test $$countdown -gt 0; do \ $(DX_LATEX) refman.tex; \ countdown=`expr $$countdown - 1`; \ done; \ $(DX_DVIPS) -o ../@PACKAGE@.ps refman.dvi endif DX_COND_ps ## ------------------------------ ## ## Rules specific for PDF output. ## ## ------------------------------ ## if DX_COND_pdf DX_CLEAN_PDF = @DX_DOCDIR@/@PACKAGE@.pdf DX_PDF_GOAL = doxygen-pdf doxygen-pdf: @DX_DOCDIR@/@PACKAGE@.pdf @DX_DOCDIR@/@PACKAGE@.pdf: @DX_DOCDIR@/@PACKAGE@.tag cd @DX_DOCDIR@/latex; \ rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \ $(DX_PDFLATEX) refman.tex; \ $(DX_MAKEINDEX) refman.idx; \ $(DX_PDFLATEX) refman.tex; \ countdown=5; \ while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \ refman.log > /dev/null 2>&1 \ && test $$countdown -gt 0; do \ $(DX_PDFLATEX) refman.tex; \ countdown=`expr $$countdown - 1`; \ done; \ mv refman.pdf ../@PACKAGE@.pdf endif DX_COND_pdf ## ------------------------------------------------- ## ## Rules specific for LaTeX (shared for PS and PDF). ## ## ------------------------------------------------- ## if DX_COND_latex DX_CLEAN_LATEX = @DX_DOCDIR@/latex endif DX_COND_latex .PHONY: doxygen-run doxygen-doc $(DX_PS_GOAL) $(DX_PDF_GOAL) .INTERMEDIATE: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL) doxygen-run: @DX_DOCDIR@/@PACKAGE@.tag doxygen-doc: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL) @DX_DOCDIR@/@PACKAGE@.tag: $(DX_CONFIG) $(pkginclude_HEADERS) rm -rf @DX_DOCDIR@ $(DX_ENV) $(DX_DOXYGEN) $(srcdir)/$(DX_CONFIG) DX_CLEANFILES = \ @DX_DOCDIR@/@PACKAGE@.tag \ -r \ $(DX_CLEAN_HTML) \ $(DX_CLEAN_CHM) \ $(DX_CLEAN_CHI) \ $(DX_CLEAN_MAN) \ $(DX_CLEAN_RTF) \ $(DX_CLEAN_XML) \ $(DX_CLEAN_PS) \ $(DX_CLEAN_PDF) \ $(DX_CLEAN_LATEX) endif DX_COND_doc libGenome-1.3.1/m4/0000777002622200470610000000000011030171200010731 500000000000000libGenome-1.3.1/m4/ax_openmp.m40000644002622200470610000001022110742567101013113 00000000000000##### http://autoconf-archive.cryp.to/ax_openmp.html # # SYNOPSIS # # AX_OPENMP([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]]) # # DESCRIPTION # # This macro tries to find out how to compile programs that use # OpenMP a standard API and set of compiler directives for parallel # programming (see http://www-unix.mcs/) # # On success, it sets the # OPENMP_CFLAGS/OPENMP_CXXFLAGS/OPENMP_F77FLAGS output variable to # the flag (e.g. -omp) used both to compile *and* link OpenMP # programs in the current language. # # NOTE: You are assumed to not only compile your program with these # flags, but also link it with them as well. # # If you want to compile everything with OpenMP, you should set: # # CFLAGS="$CFLAGS $OPENMP_CFLAGS" # #OR# CXXFLAGS="$CXXFLAGS $OPENMP_CXXFLAGS" # #OR# FFLAGS="$FFLAGS $OPENMP_FFLAGS" # # (depending on the selected language). # # The user can override the default choice by setting the # corresponding environment variable (e.g. OPENMP_CFLAGS). # # ACTION-IF-FOUND is a list of shell commands to run if an OpenMP # flag is found, and ACTION-IF-NOT-FOUND is a list of commands to run # it if it is not found. If ACTION-IF-FOUND is not specified, the # default action will define HAVE_OPENMP. # # LAST MODIFICATION # # 2006-01-24 # # COPYLEFT # # Copyright (c) 2006 Steven G. Johnson # # 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 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., 59 Temple Place - Suite 330, Boston, MA # 02111-1307, USA. # # As a special exception, the respective Autoconf Macro's copyright # owner gives unlimited permission to copy, distribute and modify the # configure scripts that are the output of Autoconf when processing # the Macro. You need not follow the terms of the GNU General Public # License when using or distributing such scripts, even though # portions of the text of the Macro appear in them. The GNU General # Public License (GPL) does govern all other use of the material that # constitutes the Autoconf Macro. # # This special exception to the GPL applies to versions of the # Autoconf Macro released by the Autoconf Macro Archive. When you # make and distribute a modified version of the Autoconf Macro, you # may extend this special exception to the GPL to apply to your # modified version as well. AC_DEFUN([AX_OPENMP], [ AC_PREREQ(2.59) dnl for _AC_LANG_PREFIX AC_CACHE_CHECK([for OpenMP flag of _AC_LANG compiler], ax_cv_[]_AC_LANG_ABBREV[]_openmp, [save[]_AC_LANG_PREFIX[]FLAGS=$[]_AC_LANG_PREFIX[]FLAGS ax_cv_[]_AC_LANG_ABBREV[]_openmp=unknown # Flags to try: -fopenmp (gcc), -openmp (icc), -mp (SGI & PGI), # -xopenmp (Sun), -omp (Tru64), -qsmp=omp (AIX), none ax_openmp_flags="-fopenmp -openmp -mp -xopenmp -omp -qsmp=omp none" if test "x$OPENMP_[]_AC_LANG_PREFIX[]FLAGS" != x; then ax_openmp_flags="$OPENMP_[]_AC_LANG_PREFIX[]FLAGS $ax_openmp_flags" fi for ax_openmp_flag in $ax_openmp_flags; do case $ax_openmp_flag in none) []_AC_LANG_PREFIX[]FLAGS=$save[]_AC_LANG_PREFIX[] ;; *) []_AC_LANG_PREFIX[]FLAGS="$save[]_AC_LANG_PREFIX[]FLAGS $ax_openmp_flag" ;; esac AC_TRY_LINK_FUNC(omp_set_num_threads, [ax_cv_[]_AC_LANG_ABBREV[]_openmp=$ax_openmp_flag; break]) done []_AC_LANG_PREFIX[]FLAGS=$save[]_AC_LANG_PREFIX[]FLAGS ]) if test "x$ax_cv_[]_AC_LANG_ABBREV[]_openmp" = "xunknown"; then m4_default([$2],:) else if test "x$ax_cv_[]_AC_LANG_ABBREV[]_openmp" != "xnone"; then OPENMP_[]_AC_LANG_PREFIX[]FLAGS=$ax_cv_[]_AC_LANG_ABBREV[]_openmp fi m4_default([$1], [AC_DEFINE(HAVE_OPENMP,1,[Define if OpenMP is enabled])]) fi ])dnl AX_OPENMP libGenome-1.3.1/m4/ax_prog_doxygen.m40000644002622200470610000004220211026443220014314 00000000000000##### http://autoconf-archive.cryp.to/ax_prog_doxygen.html # # SYNOPSIS # # DX_INIT_DOXYGEN(PROJECT-NAME, DOXYFILE-PATH, [OUTPUT-DIR]) # DX_DOXYGEN_FEATURE(ON|OFF) # DX_DOT_FEATURE(ON|OFF) # DX_HTML_FEATURE(ON|OFF) # DX_CHM_FEATURE(ON|OFF) # DX_CHI_FEATURE(ON|OFF) # DX_MAN_FEATURE(ON|OFF) # DX_RTF_FEATURE(ON|OFF) # DX_XML_FEATURE(ON|OFF) # DX_PDF_FEATURE(ON|OFF) # DX_PS_FEATURE(ON|OFF) # # DESCRIPTION # # The DX_*_FEATURE macros control the default setting for the given # Doxygen feature. Supported features are 'DOXYGEN' itself, 'DOT' for # generating graphics, 'HTML' for plain HTML, 'CHM' for compressed # HTML help (for MS users), 'CHI' for generating a seperate .chi file # by the .chm file, and 'MAN', 'RTF', 'XML', 'PDF' and 'PS' for the # appropriate output formats. The environment variable # DOXYGEN_PAPER_SIZE may be specified to override the default # 'a4wide' paper size. # # By default, HTML, PDF and PS documentation is generated as this # seems to be the most popular and portable combination. MAN pages # created by Doxygen are usually problematic, though by picking an # appropriate subset and doing some massaging they might be better # than nothing. CHM and RTF are specific for MS (note that you can't # generate both HTML and CHM at the same time). The XML is rather # useless unless you apply specialized post-processing to it. # # The macros mainly control the default state of the feature. The use # can override the default by specifying --enable or --disable. The # macros ensure that contradictory flags are not given (e.g., # --enable-doxygen-html and --enable-doxygen-chm, # --enable-doxygen-anything with --disable-doxygen, etc.) Finally, # each feature will be automatically disabled (with a warning) if the # required programs are missing. # # Once all the feature defaults have been specified, call # DX_INIT_DOXYGEN with the following parameters: a one-word name for # the project for use as a filename base etc., an optional # configuration file name (the default is 'Doxyfile', the same as # Doxygen's default), and an optional output directory name (the # default is 'doxygen-doc'). # # Automake Support # # The following is a template aminclude.am file for use with # Automake. Make targets and variables values are controlled by the # various DX_COND_* conditionals set by autoconf. # # The provided targets are: # # doxygen-doc: Generate all doxygen documentation. # # doxygen-run: Run doxygen, which will generate some of the # documentation (HTML, CHM, CHI, MAN, RTF, XML) # but will not do the post processing required # for the rest of it (PS, PDF, and some MAN). # # doxygen-man: Rename some doxygen generated man pages. # # doxygen-ps: Generate doxygen PostScript documentation. # # doxygen-pdf: Generate doxygen PDF documentation. # # Note that by default these are not integrated into the automake # targets. If doxygen is used to generate man pages, you can achieve # this integration by setting man3_MANS to the list of man pages # generated and then adding the dependency: # # $(man3_MANS): doxygen-doc # # This will cause make to run doxygen and generate all the # documentation. # # The following variable is intended for use in Makefile.am: # # DX_CLEANFILES = everything to clean. # # Then add this variable to MOSTLYCLEANFILES. # # ----- begin aminclude.am ------------------------------------- # # ## --------------------------------- ## # ## Format-independent Doxygen rules. ## # ## --------------------------------- ## # # if DX_COND_doc # # ## ------------------------------- ## # ## Rules specific for HTML output. ## # ## ------------------------------- ## # # if DX_COND_html # # DX_CLEAN_HTML = @DX_DOCDIR@/html # # endif DX_COND_html # # ## ------------------------------ ## # ## Rules specific for CHM output. ## # ## ------------------------------ ## # # if DX_COND_chm # # DX_CLEAN_CHM = @DX_DOCDIR@/chm # # if DX_COND_chi # # DX_CLEAN_CHI = @DX_DOCDIR@/@PACKAGE@.chi # # endif DX_COND_chi # # endif DX_COND_chm # # ## ------------------------------ ## # ## Rules specific for MAN output. ## # ## ------------------------------ ## # # if DX_COND_man # # DX_CLEAN_MAN = @DX_DOCDIR@/man # # endif DX_COND_man # # ## ------------------------------ ## # ## Rules specific for RTF output. ## # ## ------------------------------ ## # # if DX_COND_rtf # # DX_CLEAN_RTF = @DX_DOCDIR@/rtf # # endif DX_COND_rtf # # ## ------------------------------ ## # ## Rules specific for XML output. ## # ## ------------------------------ ## # # if DX_COND_xml # # DX_CLEAN_XML = @DX_DOCDIR@/xml # # endif DX_COND_xml # # ## ----------------------------- ## # ## Rules specific for PS output. ## # ## ----------------------------- ## # # if DX_COND_ps # # DX_CLEAN_PS = @DX_DOCDIR@/@PACKAGE@.ps # # DX_PS_GOAL = doxygen-ps # # doxygen-ps: @DX_DOCDIR@/@PACKAGE@.ps # # @DX_DOCDIR@/@PACKAGE@.ps: @DX_DOCDIR@/@PACKAGE@.tag # cd @DX_DOCDIR@/latex; \ # rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \ # $(DX_LATEX) refman.tex; \ # $(MAKEINDEX_PATH) refman.idx; \ # $(DX_LATEX) refman.tex; \ # countdown=5; \ # while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \ # refman.log > /dev/null 2>&1 \ # && test $$countdown -gt 0; do \ # $(DX_LATEX) refman.tex; \ # countdown=`expr $$countdown - 1`; \ # done; \ # $(DX_DVIPS) -o ../@PACKAGE@.ps refman.dvi # # endif DX_COND_ps # # ## ------------------------------ ## # ## Rules specific for PDF output. ## # ## ------------------------------ ## # # if DX_COND_pdf # # DX_CLEAN_PDF = @DX_DOCDIR@/@PACKAGE@.pdf # # DX_PDF_GOAL = doxygen-pdf # # doxygen-pdf: @DX_DOCDIR@/@PACKAGE@.pdf # # @DX_DOCDIR@/@PACKAGE@.pdf: @DX_DOCDIR@/@PACKAGE@.tag # cd @DX_DOCDIR@/latex; \ # rm -f *.aux *.toc *.idx *.ind *.ilg *.log *.out; \ # $(DX_PDFLATEX) refman.tex; \ # $(DX_MAKEINDEX) refman.idx; \ # $(DX_PDFLATEX) refman.tex; \ # countdown=5; \ # while $(DX_EGREP) 'Rerun (LaTeX|to get cross-references right)' \ # refman.log > /dev/null 2>&1 \ # && test $$countdown -gt 0; do \ # $(DX_PDFLATEX) refman.tex; \ # countdown=`expr $$countdown - 1`; \ # done; \ # mv refman.pdf ../@PACKAGE@.pdf # # endif DX_COND_pdf # # ## ------------------------------------------------- ## # ## Rules specific for LaTeX (shared for PS and PDF). ## # ## ------------------------------------------------- ## # # if DX_COND_latex # # DX_CLEAN_LATEX = @DX_DOCDIR@/latex # # endif DX_COND_latex # # .PHONY: doxygen-run doxygen-doc $(DX_PS_GOAL) $(DX_PDF_GOAL) # # .INTERMEDIATE: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL) # # doxygen-run: @DX_DOCDIR@/@PACKAGE@.tag # # doxygen-doc: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL) # # @DX_DOCDIR@/@PACKAGE@.tag: $(DX_CONFIG) $(pkginclude_HEADERS) # rm -rf @DX_DOCDIR@ # $(DX_ENV) $(DX_DOXYGEN) $(srcdir)/$(DX_CONFIG) # # DX_CLEANFILES = \ # @DX_DOCDIR@/@PACKAGE@.tag \ # -r \ # $(DX_CLEAN_HTML) \ # $(DX_CLEAN_CHM) \ # $(DX_CLEAN_CHI) \ # $(DX_CLEAN_MAN) \ # $(DX_CLEAN_RTF) \ # $(DX_CLEAN_XML) \ # $(DX_CLEAN_PS) \ # $(DX_CLEAN_PDF) \ # $(DX_CLEAN_LATEX) # # endif DX_COND_doc # # ----- end aminclude.am --------------------------------------- # # LAST MODIFICATION # # 2007-08-04 # # COPYLEFT # # Copyright (c) 2007 Oren Ben-Kiki # # Copying and distribution of this file, with or without # modification, are permitted in any medium without royalty provided # the copyright notice and this notice are preserved. ## ----------## ## Defaults. ## ## ----------## DX_ENV="" AC_DEFUN([DX_FEATURE_doc], ON) AC_DEFUN([DX_FEATURE_dot], ON) AC_DEFUN([DX_FEATURE_man], OFF) AC_DEFUN([DX_FEATURE_html], ON) AC_DEFUN([DX_FEATURE_chm], OFF) AC_DEFUN([DX_FEATURE_chi], OFF) AC_DEFUN([DX_FEATURE_rtf], OFF) AC_DEFUN([DX_FEATURE_xml], OFF) AC_DEFUN([DX_FEATURE_pdf], ON) AC_DEFUN([DX_FEATURE_ps], ON) ## --------------- ## ## Private macros. ## ## --------------- ## # DX_ENV_APPEND(VARIABLE, VALUE) # ------------------------------ # Append VARIABLE="VALUE" to DX_ENV for invoking doxygen. AC_DEFUN([DX_ENV_APPEND], [AC_SUBST([DX_ENV], ["$DX_ENV $1='$2'"])]) # DX_DIRNAME_EXPR # --------------- # Expand into a shell expression prints the directory part of a path. AC_DEFUN([DX_DIRNAME_EXPR], [[expr ".$1" : '\(\.\)[^/]*$' \| "x$1" : 'x\(.*\)/[^/]*$']]) # DX_IF_FEATURE(FEATURE, IF-ON, IF-OFF) # ------------------------------------- # Expands according to the M4 (static) status of the feature. AC_DEFUN([DX_IF_FEATURE], [ifelse(DX_FEATURE_$1, ON, [$2], [$3])]) # DX_REQUIRE_PROG(VARIABLE, PROGRAM) # ---------------------------------- # Require the specified program to be found for the DX_CURRENT_FEATURE to work. AC_DEFUN([DX_REQUIRE_PROG], [ AC_PATH_TOOL([$1], [$2]) if test "$DX_FLAG_[]DX_CURRENT_FEATURE$$1" = 1; then AC_MSG_WARN([$2 not found - will not DX_CURRENT_DESCRIPTION]) AC_SUBST([DX_FLAG_]DX_CURRENT_FEATURE, 0) fi ]) # DX_TEST_FEATURE(FEATURE) # ------------------------ # Expand to a shell expression testing whether the feature is active. AC_DEFUN([DX_TEST_FEATURE], [test "$DX_FLAG_$1" = 1]) # DX_CHECK_DEPEND(REQUIRED_FEATURE, REQUIRED_STATE) # ------------------------------------------------- # Verify that a required features has the right state before trying to turn on # the DX_CURRENT_FEATURE. AC_DEFUN([DX_CHECK_DEPEND], [ test "$DX_FLAG_$1" = "$2" \ || AC_MSG_ERROR([doxygen-DX_CURRENT_FEATURE ifelse([$2], 1, requires, contradicts) doxygen-DX_CURRENT_FEATURE]) ]) # DX_CLEAR_DEPEND(FEATURE, REQUIRED_FEATURE, REQUIRED_STATE) # ---------------------------------------------------------- # Turn off the DX_CURRENT_FEATURE if the required feature is off. AC_DEFUN([DX_CLEAR_DEPEND], [ test "$DX_FLAG_$1" = "$2" || AC_SUBST([DX_FLAG_]DX_CURRENT_FEATURE, 0) ]) # DX_FEATURE_ARG(FEATURE, DESCRIPTION, # CHECK_DEPEND, CLEAR_DEPEND, # REQUIRE, DO-IF-ON, DO-IF-OFF) # -------------------------------------------- # Parse the command-line option controlling a feature. CHECK_DEPEND is called # if the user explicitly turns the feature on (and invokes DX_CHECK_DEPEND), # otherwise CLEAR_DEPEND is called to turn off the default state if a required # feature is disabled (using DX_CLEAR_DEPEND). REQUIRE performs additional # requirement tests (DX_REQUIRE_PROG). Finally, an automake flag is set and # DO-IF-ON or DO-IF-OFF are called according to the final state of the feature. AC_DEFUN([DX_ARG_ABLE], [ AC_DEFUN([DX_CURRENT_FEATURE], [$1]) AC_DEFUN([DX_CURRENT_DESCRIPTION], [$2]) AC_ARG_ENABLE(doxygen-$1, [AS_HELP_STRING(DX_IF_FEATURE([$1], [--disable-doxygen-$1], [--enable-doxygen-$1]), DX_IF_FEATURE([$1], [don't $2], [$2]))], [ case "$enableval" in #( y|Y|yes|Yes|YES) AC_SUBST([DX_FLAG_$1], 1) $3 ;; #( n|N|no|No|NO) AC_SUBST([DX_FLAG_$1], 0) ;; #( *) AC_MSG_ERROR([invalid value '$enableval' given to doxygen-$1]) ;; esac ], [ AC_SUBST([DX_FLAG_$1], [DX_IF_FEATURE([$1], 1, 0)]) $4 ]) if DX_TEST_FEATURE([$1]); then $5 : fi if DX_TEST_FEATURE([$1]); then AM_CONDITIONAL(DX_COND_$1, :) $6 : else AM_CONDITIONAL(DX_COND_$1, false) $7 : fi ]) ## -------------- ## ## Public macros. ## ## -------------- ## # DX_XXX_FEATURE(DEFAULT_STATE) # ----------------------------- AC_DEFUN([DX_DOXYGEN_FEATURE], [AC_DEFUN([DX_FEATURE_doc], [$1])]) AC_DEFUN([DX_MAN_FEATURE], [AC_DEFUN([DX_FEATURE_man], [$1])]) AC_DEFUN([DX_HTML_FEATURE], [AC_DEFUN([DX_FEATURE_html], [$1])]) AC_DEFUN([DX_CHM_FEATURE], [AC_DEFUN([DX_FEATURE_chm], [$1])]) AC_DEFUN([DX_CHI_FEATURE], [AC_DEFUN([DX_FEATURE_chi], [$1])]) AC_DEFUN([DX_RTF_FEATURE], [AC_DEFUN([DX_FEATURE_rtf], [$1])]) AC_DEFUN([DX_XML_FEATURE], [AC_DEFUN([DX_FEATURE_xml], [$1])]) AC_DEFUN([DX_XML_FEATURE], [AC_DEFUN([DX_FEATURE_xml], [$1])]) AC_DEFUN([DX_PDF_FEATURE], [AC_DEFUN([DX_FEATURE_pdf], [$1])]) AC_DEFUN([DX_PS_FEATURE], [AC_DEFUN([DX_FEATURE_ps], [$1])]) # DX_INIT_DOXYGEN(PROJECT, [CONFIG-FILE], [OUTPUT-DOC-DIR]) # --------------------------------------------------------- # PROJECT also serves as the base name for the documentation files. # The default CONFIG-FILE is "Doxyfile" and OUTPUT-DOC-DIR is "doxygen-doc". AC_DEFUN([DX_INIT_DOXYGEN], [ # Files: AC_SUBST([DX_PROJECT], [$1]) AC_SUBST([DX_CONFIG], [ifelse([$2], [], Doxyfile, [$2])]) AC_SUBST([DX_DOCDIR], [ifelse([$3], [], doxygen-doc, [$3])]) # Environment variables used inside doxygen.cfg: DX_ENV_APPEND(SRCDIR, $srcdir) DX_ENV_APPEND(PROJECT, $DX_PROJECT) DX_ENV_APPEND(DOCDIR, $DX_DOCDIR) DX_ENV_APPEND(VERSION, $PACKAGE_VERSION) # Doxygen itself: DX_ARG_ABLE(doc, [generate any doxygen documentation], [], [], [DX_REQUIRE_PROG([DX_DOXYGEN], doxygen) DX_REQUIRE_PROG([DX_PERL], perl)], [DX_ENV_APPEND(PERL_PATH, $DX_PERL)]) # Dot for graphics: DX_ARG_ABLE(dot, [generate graphics for doxygen documentation], [DX_CHECK_DEPEND(doc, 1)], [DX_CLEAR_DEPEND(doc, 1)], [DX_REQUIRE_PROG([DX_DOT], dot)], [DX_ENV_APPEND(HAVE_DOT, YES) DX_ENV_APPEND(DOT_PATH, [`DX_DIRNAME_EXPR($DX_DOT)`])], [DX_ENV_APPEND(HAVE_DOT, NO)]) # Man pages generation: DX_ARG_ABLE(man, [generate doxygen manual pages], [DX_CHECK_DEPEND(doc, 1)], [DX_CLEAR_DEPEND(doc, 1)], [], [DX_ENV_APPEND(GENERATE_MAN, YES)], [DX_ENV_APPEND(GENERATE_MAN, NO)]) # RTF file generation: DX_ARG_ABLE(rtf, [generate doxygen RTF documentation], [DX_CHECK_DEPEND(doc, 1)], [DX_CLEAR_DEPEND(doc, 1)], [], [DX_ENV_APPEND(GENERATE_RTF, YES)], [DX_ENV_APPEND(GENERATE_RTF, NO)]) # XML file generation: DX_ARG_ABLE(xml, [generate doxygen XML documentation], [DX_CHECK_DEPEND(doc, 1)], [DX_CLEAR_DEPEND(doc, 1)], [], [DX_ENV_APPEND(GENERATE_XML, YES)], [DX_ENV_APPEND(GENERATE_XML, NO)]) # (Compressed) HTML help generation: DX_ARG_ABLE(chm, [generate doxygen compressed HTML help documentation], [DX_CHECK_DEPEND(doc, 1)], [DX_CLEAR_DEPEND(doc, 1)], [DX_REQUIRE_PROG([DX_HHC], hhc)], [DX_ENV_APPEND(HHC_PATH, $DX_HHC) DX_ENV_APPEND(GENERATE_HTML, YES) DX_ENV_APPEND(GENERATE_HTMLHELP, YES)], [DX_ENV_APPEND(GENERATE_HTMLHELP, NO)]) # Seperate CHI file generation. DX_ARG_ABLE(chi, [generate doxygen seperate compressed HTML help index file], [DX_CHECK_DEPEND(chm, 1)], [DX_CLEAR_DEPEND(chm, 1)], [], [DX_ENV_APPEND(GENERATE_CHI, YES)], [DX_ENV_APPEND(GENERATE_CHI, NO)]) # Plain HTML pages generation: DX_ARG_ABLE(html, [generate doxygen plain HTML documentation], [DX_CHECK_DEPEND(doc, 1) DX_CHECK_DEPEND(chm, 0)], [DX_CLEAR_DEPEND(doc, 1) DX_CLEAR_DEPEND(chm, 0)], [], [DX_ENV_APPEND(GENERATE_HTML, YES)], [DX_TEST_FEATURE(chm) || DX_ENV_APPEND(GENERATE_HTML, NO)]) # PostScript file generation: DX_ARG_ABLE(ps, [generate doxygen PostScript documentation], [DX_CHECK_DEPEND(doc, 1)], [DX_CLEAR_DEPEND(doc, 1)], [DX_REQUIRE_PROG([DX_LATEX], latex) DX_REQUIRE_PROG([DX_MAKEINDEX], makeindex) DX_REQUIRE_PROG([DX_DVIPS], dvips) DX_REQUIRE_PROG([DX_EGREP], egrep)]) # PDF file generation: DX_ARG_ABLE(pdf, [generate doxygen PDF documentation], [DX_CHECK_DEPEND(doc, 1)], [DX_CLEAR_DEPEND(doc, 1)], [DX_REQUIRE_PROG([DX_PDFLATEX], pdflatex) DX_REQUIRE_PROG([DX_MAKEINDEX], makeindex) DX_REQUIRE_PROG([DX_EGREP], egrep)]) # LaTeX generation for PS and/or PDF: if DX_TEST_FEATURE(ps) || DX_TEST_FEATURE(pdf); then AM_CONDITIONAL(DX_COND_latex, :) DX_ENV_APPEND(GENERATE_LATEX, YES) else AM_CONDITIONAL(DX_COND_latex, false) DX_ENV_APPEND(GENERATE_LATEX, NO) fi # Paper size for PS and/or PDF: AC_ARG_VAR(DOXYGEN_PAPER_SIZE, [a4wide (default), a4, letter, legal or executive]) case "$DOXYGEN_PAPER_SIZE" in #( "") AC_SUBST(DOXYGEN_PAPER_SIZE, "") ;; #( a4wide|a4|letter|legal|executive) DX_ENV_APPEND(PAPER_SIZE, $DOXYGEN_PAPER_SIZE) ;; #( *) AC_MSG_ERROR([unknown DOXYGEN_PAPER_SIZE='$DOXYGEN_PAPER_SIZE']) ;; esac #For debugging: #echo DX_FLAG_doc=$DX_FLAG_doc #echo DX_FLAG_dot=$DX_FLAG_dot #echo DX_FLAG_man=$DX_FLAG_man #echo DX_FLAG_html=$DX_FLAG_html #echo DX_FLAG_chm=$DX_FLAG_chm #echo DX_FLAG_chi=$DX_FLAG_chi #echo DX_FLAG_rtf=$DX_FLAG_rtf #echo DX_FLAG_xml=$DX_FLAG_xml #echo DX_FLAG_pdf=$DX_FLAG_pdf #echo DX_FLAG_ps=$DX_FLAG_ps #echo DX_ENV=$DX_ENV ]) libGenome-1.3.1/AUTHORS0000644002622200470610000000030610647575617011435 00000000000000Lead Developer Aaron Darling -- darling@cs.wisc.edu Lead Tester Robert Mau -- mau@genome.wisc.edu Supported By Nicole T. Perna -- perna@ahabs.wisc.edu Frederick R. Blattner -- fred@genome.wisc.edulibGenome-1.3.1/COPYING0000644002622200470610000004311010126442331011372 00000000000000 GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), 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 distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the 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 a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, 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. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE 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. 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 convey 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 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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision 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, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This 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 Library General Public License instead of this License. libGenome-1.3.1/config.h.in0000644002622200470610000000363611030167143012373 00000000000000/* config.h.in. Generated from configure.ac by autoheader. */ /* Define to 1 if you have the header file. */ #undef HAVE_DLFCN_H /* Define to 1 if you have the header file. */ #undef HAVE_INTTYPES_H /* Define to 1 if you have the header file. */ #undef HAVE_MEMORY_H /* Define if OpenMP is enabled */ #undef HAVE_OPENMP /* Define to 1 if you have the header file. */ #undef HAVE_STDINT_H /* Define to 1 if you have the header file. */ #undef HAVE_STDLIB_H /* Define to 1 if you have the header file. */ #undef HAVE_STRINGS_H /* Define to 1 if you have the header file. */ #undef HAVE_STRING_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_STAT_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_TYPES_H /* Define to 1 if you have the header file. */ #undef HAVE_UNISTD_H /* Define to the address where bug reports for this package should be sent. */ #undef PACKAGE_BUGREPORT /* Define to the full name of this package. */ #undef PACKAGE_NAME /* Define to the full name and version of this package. */ #undef PACKAGE_STRING /* Define to the one symbol short name of this package. */ #undef PACKAGE_TARNAME /* Define to the version of this package. */ #undef PACKAGE_VERSION /* Define to 1 if you have the ANSI C header files. */ #undef STDC_HEADERS /* Define to 1 if you can safely include both and . */ #undef TIME_WITH_SYS_TIME /* Number of bits in a file offset, on hosts where this is settable. */ #undef _FILE_OFFSET_BITS /* Define for large files, on AIX-style hosts. */ #undef _LARGE_FILES /* Define to empty if `const' does not conform to ANSI C. */ #undef const /* Define to `__inline__' or `__inline' if that's what the C compiler calls it, or to nothing if 'inline' is not supported under any name. */ #ifndef __cplusplus #undef inline #endif libGenome-1.3.1/config.guess0000755002622200470610000012206510640457075012702 00000000000000#! /bin/sh # Attempt to guess a canonical system name. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, # 2000, 2001, 2002, 2003 Free Software Foundation, Inc. timestamp='2003-06-17' # 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, 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. # Originally written by Per Bothner . # Please send patches to . Submit a context # diff and a properly formatted ChangeLog entry. # # This script attempts to guess a canonical system name similar to # config.sub. If it succeeds, it prints the system name on stdout, and # exits with 0. Otherwise, it exits with 1. # # The plan is that this can be called by configure scripts if you # don't specify an explicit build system type. me=`echo "$0" | sed -e 's,.*/,,'` usage="\ Usage: $0 [OPTION] Output the configuration name of the system \`$me' is run on. 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.guess ($timestamp) Originally written by Per Bothner. Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." help=" Try \`$me --help' for more information." # Parse command line while test $# -gt 0 ; do case $1 in --time-stamp | --time* | -t ) echo "$timestamp" ; exit 0 ;; --version | -v ) echo "$version" ; exit 0 ;; --help | --h* | -h ) echo "$usage"; exit 0 ;; -- ) # Stop option processing shift; break ;; - ) # Use stdin as input. break ;; -* ) echo "$me: invalid option $1$help" >&2 exit 1 ;; * ) break ;; esac done if test $# != 0; then echo "$me: too many arguments$help" >&2 exit 1 fi trap 'exit 1' 1 2 15 # CC_FOR_BUILD -- compiler used by this script. Note that the use of a # compiler to aid in system detection is discouraged as it requires # temporary files to be created and, as you can see below, it is a # headache to deal with in a portable fashion. # Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. 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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. ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1` case "$ALPHA_CPU_TYPE" in "EV4 (21064)") UNAME_MACHINE="alpha" ;; "EV4.5 (21064)") UNAME_MACHINE="alpha" ;; "LCA4 (21066/21068)") UNAME_MACHINE="alpha" ;; "EV5 (21164)") UNAME_MACHINE="alphaev5" ;; "EV5.6 (21164A)") UNAME_MACHINE="alphaev56" ;; "EV5.6 (21164PC)") UNAME_MACHINE="alphapca56" ;; "EV5.7 (21164PC)") UNAME_MACHINE="alphapca57" ;; "EV6 (21264)") UNAME_MACHINE="alphaev6" ;; "EV6.7 (21264A)") UNAME_MACHINE="alphaev67" ;; "EV6.8CB (21264C)") UNAME_MACHINE="alphaev68" ;; "EV6.8AL (21264B)") UNAME_MACHINE="alphaev68" ;; "EV6.8CX (21264D)") UNAME_MACHINE="alphaev68" ;; "EV6.9A (21264/EV69A)") UNAME_MACHINE="alphaev69" ;; "EV7 (21364)") UNAME_MACHINE="alphaev7" ;; "EV7.9 (21364A)") UNAME_MACHINE="alphaev79" ;; esac # A Vn.n version is a released version. # A Tn.n version is a released field test version. # A Xn.n version is an unreleased experimental baselevel. # 1.2 uses "1.2" for uname -r. echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[VTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` exit 0 ;; Alpha*:OpenVMS:*:*) echo alpha-hp-vms exit 0 ;; Alpha\ *:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # Should we change UNAME_MACHINE based on the output of uname instead # of the specific Alpha model? echo alpha-pc-interix exit 0 ;; 21064:Windows_NT:50:3) echo alpha-dec-winnt3.5 exit 0 ;; Amiga*:UNIX_System_V:4.0:*) echo m68k-unknown-sysv4 exit 0;; *:[Aa]miga[Oo][Ss]:*:*) echo ${UNAME_MACHINE}-unknown-amigaos exit 0 ;; *:[Mm]orph[Oo][Ss]:*:*) echo ${UNAME_MACHINE}-unknown-morphos exit 0 ;; *:OS/390:*:*) echo i370-ibm-openedition exit 0 ;; arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*) echo arm-acorn-riscix${UNAME_RELEASE} exit 0;; SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*) echo hppa1.1-hitachi-hiuxmpp exit 0;; Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*) # akee@wpdis03.wpafb.af.mil (Earle F. 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 0 ;; NILE*:*:*:dcosx) echo pyramid-pyramid-svr4 exit 0 ;; DRS?6000:unix:4.0:6*) echo sparc-icl-nx6 exit 0 ;; DRS?6000:UNIX_SV:4.2*:7*) case `/usr/bin/uname -p` in sparc) echo sparc-icl-nx7 && exit 0 ;; esac ;; sun4H:SunOS:5.*:*) echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit 0 ;; sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit 0 ;; i86pc:SunOS:5.*:*) echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit 0 ;; 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 0 ;; 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 ${UNAME_RELEASE}|sed -e 's/-/_/'` exit 0 ;; sun3*:SunOS:*:*) echo m68k-sun-sunos${UNAME_RELEASE} exit 0 ;; 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 0 ;; aushp:SunOS:*:*) echo sparc-auspex-sunos${UNAME_RELEASE} exit 0 ;; # The situation for MiNT is a little confusing. The machine name # can be virtually everything (everything which is not # "atarist" or "atariste" at least should have a processor # > m68000). The system name ranges from "MiNT" over "FreeMiNT" # to the lowercase version "mint" (or "freemint"). Finally # the system name "TOS" denotes a system which is actually not # MiNT. But MiNT is downward compatible to TOS, so this should # be no problem. atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit 0 ;; atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit 0 ;; *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit 0 ;; milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) echo m68k-milan-mint${UNAME_RELEASE} exit 0 ;; hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) echo m68k-hades-mint${UNAME_RELEASE} exit 0 ;; *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) echo m68k-unknown-mint${UNAME_RELEASE} exit 0 ;; powerpc:machten:*:*) echo powerpc-apple-machten${UNAME_RELEASE} exit 0 ;; RISC*:Mach:*:*) echo mips-dec-mach_bsd4.3 exit 0 ;; RISC*:ULTRIX:*:*) echo mips-dec-ultrix${UNAME_RELEASE} exit 0 ;; VAX*:ULTRIX*:*:*) echo vax-dec-ultrix${UNAME_RELEASE} exit 0 ;; 2020:CLIX:*:* | 2430:CLIX:*:*) echo clipper-intergraph-clix${UNAME_RELEASE} exit 0 ;; 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 \ && $dummy `echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` \ && exit 0 echo mips-mips-riscos${UNAME_RELEASE} exit 0 ;; Motorola:PowerMAX_OS:*:*) echo powerpc-motorola-powermax exit 0 ;; Motorola:*:4.3:PL8-*) echo powerpc-harris-powermax exit 0 ;; Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) echo powerpc-harris-powermax exit 0 ;; Night_Hawk:Power_UNIX:*:*) echo powerpc-harris-powerunix exit 0 ;; m88k:CX/UX:7*:*) echo m88k-harris-cxux7 exit 0 ;; m88k:*:4*:R4*) echo m88k-motorola-sysv4 exit 0 ;; m88k:*:3*:R3*) echo m88k-motorola-sysv3 exit 0 ;; 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 0 ;; M88*:DolphinOS:*:*) # DolphinOS (SVR3) echo m88k-dolphin-sysv3 exit 0 ;; M88*:*:R3*:*) # Delta 88k system running SVR3 echo m88k-motorola-sysv3 exit 0 ;; XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) echo m88k-tektronix-sysv3 exit 0 ;; Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) echo m68k-tektronix-bsd exit 0 ;; *:IRIX*:*:*) echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'` exit 0 ;; ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id exit 0 ;; # Note that: echo "'`uname -s`'" gives 'AIX ' i*86:AIX:*:*) echo i386-ibm-aix exit 0 ;; ia64:AIX:*:*) if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${UNAME_MACHINE}-ibm-aix${IBM_REV} exit 0 ;; *: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 $CC_FOR_BUILD -o $dummy $dummy.c && $dummy && exit 0 echo rs6000-ibm-aix3.2.5 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 0 ;; *:AIX:*:[45]) 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 0 ;; *:AIX:*:*) echo rs6000-ibm-aix exit 0 ;; ibmrt:4.4BSD:*|romp-ibm:BSD:*) echo romp-ibm-bsd4.4 exit 0 ;; ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to exit 0 ;; # report: romp-ibm BSD 4.3 *:BOSX:*:*) echo rs6000-bull-bosx exit 0 ;; DPX/2?00:B.O.S.:*:*) echo m68k-bull-sysv3 exit 0 ;; 9000/[34]??:4.3bsd:1.*:*) echo m68k-hp-bsd exit 0 ;; hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) echo m68k-hp-bsd4.4 exit 0 ;; 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 # avoid double evaluation of $set_cc_for_build test -n "$CC_FOR_BUILD" || eval $set_cc_for_build if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E -) | grep __LP64__ >/dev/null then HP_ARCH="hppa2.0w" else HP_ARCH="hppa64" fi fi echo ${HP_ARCH}-hp-hpux${HPUX_REV} exit 0 ;; ia64:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` echo ia64-hp-hpux${HPUX_REV} exit 0 ;; 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 && $dummy && exit 0 echo unknown-hitachi-hiuxwe2 exit 0 ;; 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* ) echo hppa1.1-hp-bsd exit 0 ;; 9000/8??:4.3bsd:*:*) echo hppa1.0-hp-bsd exit 0 ;; *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) echo hppa1.0-hp-mpeix exit 0 ;; hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* ) echo hppa1.1-hp-osf exit 0 ;; hp8??:OSF1:*:*) echo hppa1.0-hp-osf exit 0 ;; i*86:OSF1:*:*) if [ -x /usr/sbin/sysversion ] ; then echo ${UNAME_MACHINE}-unknown-osf1mk else echo ${UNAME_MACHINE}-unknown-osf1 fi exit 0 ;; parisc*:Lites*:*:*) echo hppa1.1-hp-lites exit 0 ;; C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) echo c1-convex-bsd exit 0 ;; C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit 0 ;; C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) echo c34-convex-bsd exit 0 ;; C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) echo c38-convex-bsd exit 0 ;; C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) echo c4-convex-bsd exit 0 ;; CRAY*Y-MP:*:*:*) echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit 0 ;; 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/\.[^.]*$/.X/' exit 0 ;; CRAY*TS:*:*:*) echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit 0 ;; CRAY*T3E:*:*:*) echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit 0 ;; CRAY*SV1:*:*:*) echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit 0 ;; *:UNICOS/mp:*:*) echo nv1-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit 0 ;; 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 0 ;; i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} exit 0 ;; sparc*:BSD/OS:*:*) echo sparc-unknown-bsdi${UNAME_RELEASE} exit 0 ;; *:BSD/OS:*:*) echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} exit 0 ;; *:FreeBSD:*:*|*:GNU/FreeBSD:*:*) # Determine whether the default compiler uses glibc. eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include #if __GLIBC__ >= 2 LIBC=gnu #else LIBC= #endif EOF eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^LIBC=` echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`${LIBC:+-$LIBC} exit 0 ;; i*:CYGWIN*:*) echo ${UNAME_MACHINE}-pc-cygwin exit 0 ;; i*:MINGW*:*) echo ${UNAME_MACHINE}-pc-mingw32 exit 0 ;; i*:PW*:*) echo ${UNAME_MACHINE}-pc-pw32 exit 0 ;; x86:Interix*:[34]*) echo i586-pc-interix${UNAME_RELEASE}|sed -e 's/\..*//' exit 0 ;; [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) echo i${UNAME_MACHINE}-pc-mks exit 0 ;; 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 0 ;; i*:UWIN*:*) echo ${UNAME_MACHINE}-pc-uwin exit 0 ;; p*:CYGWIN*:*) echo powerpcle-unknown-cygwin exit 0 ;; prep*:SunOS:5.*:*) echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit 0 ;; *:GNU:*:*) echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'` exit 0 ;; i*86:Minix:*:*) echo ${UNAME_MACHINE}-pc-minix exit 0 ;; arm*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit 0 ;; cris:Linux:*:*) echo cris-axis-linux-gnu exit 0 ;; ia64:Linux:*:*) echo ${UNAME_MACHINE}-${VENDOR:-unknown}-linux-gnu exit 0 ;; m68*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit 0 ;; mips:Linux:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #undef CPU #undef mips #undef mipsel #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) CPU=mipsel #else #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) CPU=mips #else CPU= #endif #endif EOF eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^CPU=` test x"${CPU}" != x && echo "${CPU}-unknown-linux-gnu" && exit 0 ;; mips64:Linux:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #undef CPU #undef mips64 #undef mips64el #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) CPU=mips64el #else #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) CPU=mips64 #else CPU= #endif #endif EOF eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^CPU=` test x"${CPU}" != x && echo "${CPU}-unknown-linux-gnu" && exit 0 ;; ppc:Linux:*:*) echo powerpc-${VENDOR:-unknown}-linux-gnu exit 0 ;; ppc64:Linux:*:*) echo powerpc64-${VENDOR:-unknown}-linux-gnu exit 0 ;; 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 ld.so.1 >/dev/null if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} exit 0 ;; parisc:Linux:*:* | hppa:Linux:*:*) # Look for CPU level case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in PA7*) echo hppa1.1-unknown-linux-gnu ;; PA8*) echo hppa2.0-unknown-linux-gnu ;; *) echo hppa-unknown-linux-gnu ;; esac exit 0 ;; parisc64:Linux:*:* | hppa64:Linux:*:*) echo hppa64-unknown-linux-gnu exit 0 ;; s390:Linux:*:* | s390x:Linux:*:*) echo ${UNAME_MACHINE}-${VENDOR:-ibm}-linux-gnu exit 0 ;; sh64*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit 0 ;; sh*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit 0 ;; sparc:Linux:*:* | sparc64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit 0 ;; x86_64:Linux:*:*) echo x86_64-${VENDOR:-unknown}-linux-gnu exit 0 ;; i*86:Linux:*:*) # The BFD linker knows what the default object file format is, so # first see if it will tell us. cd to the root directory to prevent # problems with other programs or directories called `ld' in the path. # Set LC_ALL=C to ensure ld outputs messages in English. ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \ | sed -ne '/supported targets:/!d s/[ ][ ]*/ /g s/.*supported targets: *// s/ .*// p'` case "$ld_supported_targets" in elf32-i386) TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu" ;; a.out-i386-linux) echo "${UNAME_MACHINE}-pc-linux-gnuaout" exit 0 ;; coff-i386) echo "${UNAME_MACHINE}-pc-linux-gnucoff" exit 0 ;; "") # Either a pre-BFD a.out linker (linux-gnuoldld) or # one that does not give us useful --help. echo "${UNAME_MACHINE}-pc-linux-gnuoldld" exit 0 ;; esac # Determine whether the default compiler is a.out or elf eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include #ifdef __ELF__ # ifdef __GLIBC__ # if __GLIBC__ >= 2 LIBC=gnu # else LIBC=gnulibc1 # endif # else LIBC=gnulibc1 # endif #else #ifdef __INTEL_COMPILER LIBC=gnu #else LIBC=gnuaout #endif #endif EOF eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^LIBC=` test x"${LIBC}" != x && echo "${UNAME_MACHINE}-${VENDOR:-pc}-linux-${LIBC}" && exit 0 test x"${TENTATIVE}" != x && echo "${TENTATIVE}" && exit 0 ;; i*86:DYNIX/ptx:4*:*) # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. # earlier versions are messed up and put the nodename in both # sysname and nodename. echo i386-sequent-sysv4 exit 0 ;; i*86:UNIX_SV:4.2MP:2.*) # Unixware is an offshoot of SVR4, but it has its own version # number series starting with 2... # I am not positive that other SVR4 systems won't match this, # I just have to hope. -- rms. # Use sysv4.2uw... so that sysv4* matches it. echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION} exit 0 ;; i*86:OS/2:*:*) # If we were able to find `uname', then EMX Unix compatibility # is probably installed. echo ${UNAME_MACHINE}-pc-os2-emx exit 0 ;; i*86:XTS-300:*:STOP) echo ${UNAME_MACHINE}-unknown-stop exit 0 ;; i*86:atheos:*:*) echo ${UNAME_MACHINE}-unknown-atheos exit 0 ;; i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*) echo i386-unknown-lynxos${UNAME_RELEASE} exit 0 ;; i*86:*DOS:*:*) echo ${UNAME_MACHINE}-pc-msdosdjgpp exit 0 ;; i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*) UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'` if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL} else echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL} fi exit 0 ;; i*86:*:5:[78]*) case `/bin/uname -X | grep "^Machine"` in *486*) UNAME_MACHINE=i486 ;; *Pentium) UNAME_MACHINE=i586 ;; *Pent*|*Celeron) UNAME_MACHINE=i686 ;; esac echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} exit 0 ;; i*86:*:3.2:*) if test -f /usr/options/cb.name; then UNAME_REL=`sed -n 's/.*Version //p' /dev/null >/dev/null ; then UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')` (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486 (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \ && UNAME_MACHINE=i586 (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \ && UNAME_MACHINE=i686 (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \ && UNAME_MACHINE=i686 echo ${UNAME_MACHINE}-pc-sco$UNAME_REL else echo ${UNAME_MACHINE}-pc-sysv32 fi exit 0 ;; pc:*:*:*) # Left here for compatibility: # uname -m prints for DJGPP always 'pc', but it prints nothing about # the processor, so we play safe by assuming i386. echo i386-pc-msdosdjgpp exit 0 ;; Intel:Mach:3*:*) echo i386-pc-mach3 exit 0 ;; paragon:*:*:*) echo i860-intel-osf1 exit 0 ;; i860:*:4.*:*) # i860-SVR4 if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4 else # Add other i860-SVR4 vendors below as they are discovered. echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4 fi exit 0 ;; mini*:CTIX:SYS*5:*) # "miniframe" echo m68010-convergent-sysv exit 0 ;; mc68k:UNIX:SYSTEM5:3.51m) echo m68k-convergent-sysv exit 0 ;; M680?0:D-NIX:5.3:*) echo m68k-diab-dnix exit 0 ;; M68*:*:R3V[567]*:*) test -r /sysV68 && echo 'm68k-motorola-sysv' && exit 0 ;; 3[34]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0) OS_REL='' test -r /etc/.relid \ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && echo i486-ncr-sysv4.3${OS_REL} && exit 0 /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ && echo i586-ncr-sysv4.3${OS_REL} && exit 0 ;; 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && echo i486-ncr-sysv4 && exit 0 ;; m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) echo m68k-unknown-lynxos${UNAME_RELEASE} exit 0 ;; mc68030:UNIX_System_V:4.*:*) echo m68k-atari-sysv4 exit 0 ;; TSUNAMI:LynxOS:2.*:*) echo sparc-unknown-lynxos${UNAME_RELEASE} exit 0 ;; rs6000:LynxOS:2.*:*) echo rs6000-unknown-lynxos${UNAME_RELEASE} exit 0 ;; PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*) echo powerpc-unknown-lynxos${UNAME_RELEASE} exit 0 ;; SM[BE]S:UNIX_SV:*:*) echo mips-dde-sysv${UNAME_RELEASE} exit 0 ;; RM*:ReliantUNIX-*:*:*) echo mips-sni-sysv4 exit 0 ;; RM*:SINIX-*:*:*) echo mips-sni-sysv4 exit 0 ;; *:SINIX-*:*:*) if uname -p 2>/dev/null >/dev/null ; then UNAME_MACHINE=`(uname -p) 2>/dev/null` echo ${UNAME_MACHINE}-sni-sysv4 else echo ns32k-sni-sysv fi exit 0 ;; PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort # says echo i586-unisys-sysv4 exit 0 ;; *:UNIX_System_V:4*:FTX*) # From Gerald Hewes . # How about differentiating between stratus architectures? -djm echo hppa1.1-stratus-sysv4 exit 0 ;; *:*:*:FTX*) # From seanf@swdc.stratus.com. echo i860-stratus-sysv4 exit 0 ;; *:VOS:*:*) # From Paul.Green@stratus.com. echo hppa1.1-stratus-vos exit 0 ;; mc68*:A/UX:*:*) echo m68k-apple-aux${UNAME_RELEASE} exit 0 ;; news*:NEWS-OS:6*:*) echo mips-sony-newsos6 exit 0 ;; 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 0 ;; BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. echo powerpc-be-beos exit 0 ;; BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. echo powerpc-apple-beos exit 0 ;; BePC:BeOS:*:*) # BeOS running on Intel PC compatible. echo i586-pc-beos exit 0 ;; SX-4:SUPER-UX:*:*) echo sx4-nec-superux${UNAME_RELEASE} exit 0 ;; SX-5:SUPER-UX:*:*) echo sx5-nec-superux${UNAME_RELEASE} exit 0 ;; SX-6:SUPER-UX:*:*) echo sx6-nec-superux${UNAME_RELEASE} exit 0 ;; Power*:Rhapsody:*:*) echo powerpc-apple-rhapsody${UNAME_RELEASE} exit 0 ;; *:Rhapsody:*:*) echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE} exit 0 ;; *:Darwin:*:*) case `uname -p` in *86) UNAME_PROCESSOR=i686 ;; powerpc) UNAME_PROCESSOR=powerpc ;; esac echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE} exit 0 ;; *:procnto*:*:* | *:QNX:[0123456789]*:*) UNAME_PROCESSOR=`uname -p` if test "$UNAME_PROCESSOR" = "x86"; then UNAME_PROCESSOR=i386 UNAME_MACHINE=pc fi echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE} exit 0 ;; *:QNX:*:4*) echo i386-pc-qnx exit 0 ;; NSR-[DGKLNPTVW]:NONSTOP_KERNEL:*:*) echo nsr-tandem-nsk${UNAME_RELEASE} exit 0 ;; *:NonStop-UX:*:*) echo mips-compaq-nonstopux exit 0 ;; BS2000:POSIX*:*:*) echo bs2000-siemens-sysv exit 0 ;; DS/*:UNIX_System_V:*:*) echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE} exit 0 ;; *:Plan9:*:*) # "uname -m" is not consistent, so use $cputype instead. 386 # is converted to i386 for consistency with other x86 # operating systems. if test "$cputype" = "386"; then UNAME_MACHINE=i386 else UNAME_MACHINE="$cputype" fi echo ${UNAME_MACHINE}-unknown-plan9 exit 0 ;; *:TOPS-10:*:*) echo pdp10-unknown-tops10 exit 0 ;; *:TENEX:*:*) echo pdp10-unknown-tenex exit 0 ;; KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) echo pdp10-dec-tops20 exit 0 ;; XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) echo pdp10-xkl-tops20 exit 0 ;; *:TOPS-20:*:*) echo pdp10-unknown-tops20 exit 0 ;; *:ITS:*:*) echo pdp10-unknown-its exit 0 ;; SEI:*:*:SEIUX) echo mips-sei-seiux${UNAME_RELEASE} exit 0 ;; esac #echo '(No uname command or uname output not recognized.)' 1>&2 #echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2 eval $set_cc_for_build cat >$dummy.c < # include #endif main () { #if defined (sony) #if defined (MIPSEB) /* BFD wants "bsd" instead of "newsos". 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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, write to the Free Software # Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA # 02111-1307, 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. if test $# -eq 0; then echo 1>&2 "Try \`$0 --help' for more information" exit 1 fi run=: # In the cases where this matters, `missing' is being run in the # srcdir already. if test -f configure.ac; then configure_ac=configure.ac else configure_ac=configure.in fi msg="missing on your system" case "$1" in --run) # Try to run requested program, and just exit if it succeeds. run= shift "$@" && exit 0 # Exit code 63 means version mismatch. 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You can get \`Bison' from any GNU archive site." rm -f y.tab.c y.tab.h if [ $# -ne 1 ]; then eval LASTARG="\${$#}" case "$LASTARG" in *.y) SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'` if [ -f "$SRCFILE" ]; then cp "$SRCFILE" y.tab.c fi SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'` if [ -f "$SRCFILE" ]; then cp "$SRCFILE" y.tab.h fi ;; esac fi if [ ! -f y.tab.h ]; then echo >y.tab.h fi if [ ! -f y.tab.c ]; then echo 'main() { return 0; }' >y.tab.c fi ;; lex|flex) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified a \`.l' file. You may need the \`Flex' package in order for those modifications to take effect. You can get \`Flex' from any GNU archive site." rm -f lex.yy.c if [ $# -ne 1 ]; then eval LASTARG="\${$#}" case "$LASTARG" in *.l) SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'` if [ -f "$SRCFILE" ]; then cp "$SRCFILE" lex.yy.c fi ;; esac fi if [ ! -f lex.yy.c ]; then echo 'main() { return 0; }' >lex.yy.c fi ;; help2man) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified a dependency of a manual page. You may need the \`Help2man' package in order for those modifications to take effect. You can get \`Help2man' from any GNU archive site." file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'` if test -z "$file"; then file=`echo "$*" | sed -n 's/.*--output=\([^ ]*\).*/\1/p'` fi if [ -f "$file" ]; then touch $file else test -z "$file" || exec >$file echo ".ab help2man is required to generate this page" exit 1 fi ;; makeinfo) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified a \`.texi' or \`.texinfo' file, or any other file indirectly affecting the aspect of the manual. The spurious call might also be the consequence of using a buggy \`make' (AIX, DU, IRIX). You might want to install the \`Texinfo' package or the \`GNU make' package. Grab either from any GNU archive site." file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'` if test -z "$file"; then file=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'` file=`sed -n '/^@setfilename/ { s/.* \([^ ]*\) *$/\1/; p; q; }' $file` fi touch $file ;; tar) shift # We have already tried tar in the generic part. # Look for gnutar/gtar before invocation to avoid ugly error # messages. if (gnutar --version > /dev/null 2>&1); then gnutar "$@" && exit 0 fi if (gtar --version > /dev/null 2>&1); then gtar "$@" && exit 0 fi firstarg="$1" if shift; then case "$firstarg" in *o*) firstarg=`echo "$firstarg" | sed s/o//` tar "$firstarg" "$@" && exit 0 ;; esac case "$firstarg" in *h*) firstarg=`echo "$firstarg" | sed s/h//` tar "$firstarg" "$@" && exit 0 ;; esac fi echo 1>&2 "\ WARNING: I can't seem to be able to run \`tar' with the given arguments. You may want to install GNU tar or Free paxutils, or check the command line arguments." exit 1 ;; *) echo 1>&2 "\ WARNING: \`$1' is needed, and is $msg. You might have modified some files without having the proper tools for further handling them. Check the \`README' file, it often tells you about the needed prerequisites for installing this package. You may also peek at any GNU archive site, in case some other package would contain this missing \`$1' program." exit 1 ;; esac exit 0 # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-end: "$" # End: libGenome-1.3.1/projects/0000777002622200470610000000000011030171200012242 500000000000000libGenome-1.3.1/projects/libGenome.vcproj0000644002622200470610000004233610726437313015341 00000000000000 libGenome-1.3.1/projects/libGenome.nsi0000644002622200470610000004306010647575617014636 00000000000000;NSIS Script For libGenome ;Backgound Colors BGGradient 8080FF 0000A8 FFFFFF BrandingText " " ;Title Of Your Application Name "libGenome 0.5.2" ;Do A CRC Check CRCCheck On ;Output File Name OutFile "libGenome_installer.exe" ;License Page Introduction LicenseText "You must agree to this license before installing." ;License Data LicenseData "C:\Development\libGenome\COPYING" ComponentText "Select libGenome components to install" "All are recommended" CompletedText "Completed successfully. You may need to log out or restart the computer." ;The Default Installation Directory InstallDir "$DESKTOP\libGenome" ;The text to prompt the user to enter a directory DirText "Please select a libGenome development folder below" AllowRootDirInstall true SubSection "libGenome Development" Section "libGenomeBase" ;Install Files SetOutPath $INSTDIR SetCompress Auto SetOverwrite IfNewer ; Top level directory files File "C:\Development\libGenome\AUTHORS" File "C:\Development\libGenome\ChangeLog" File "C:\Development\libGenome\configure.in" File "C:\Development\libGenome\COPYING" File "C:\Development\libGenome\INSTALL" File "C:\Development\libGenome\Makefile.am" File "C:\Development\libGenome\NEWS" File "C:\Development\libGenome\README" SectionEnd Section "Header Files" ;Install Files SetOutPath $INSTDIR SetCompress Auto SetOverwrite IfNewer ; /include files SetOutPath "$INSTDIR\include" File "C:\Development\libGenome\libGenome\gn_cw.h" File "C:\Development\libGenome\libGenome\gn_cw.pch" File "C:\Development\libGenome\libGenome\gn_cw.pch++" File "C:\Development\libGenome\libGenome\gn_cw_d.h" File "C:\Development\libGenome\libGenome\gn_cw_d.pch" File "C:\Development\libGenome\libGenome\gn_cw_d.pch++" File "C:\Development\libGenome\libGenome\gn_cw_dll.h" File "C:\Development\libGenome\libGenome\gn_cw_dll.pch" File "C:\Development\libGenome\libGenome\gn_cw_dll.pch++" File "C:\Development\libGenome\libGenome\gn_cw_dlld.h" File "C:\Development\libGenome\libGenome\gn_cw_dlld.pch" File "C:\Development\libGenome\libGenome\gn_cw_dlld.pch++" File "C:\Development\libGenome\libGenome\Makefile.am" ; /include/gn files SetOutPath "$INSTDIR\include" File "C:\Development\libGenome\libGenome\gn\gnABISource.h" File "C:\Development\libGenome\libGenome\gn\gnBaseFeature.h" File "C:\Development\libGenome\libGenome\gn\gnBaseFilter.h" File "C:\Development\libGenome\libGenome\gn\gnBaseHeader.h" File "C:\Development\libGenome\libGenome\gn\gnBaseQualifier.h" File "C:\Development\libGenome\libGenome\gn\gnBaseSource.h" File "C:\Development\libGenome\libGenome\gn\gnBaseSpec.h" File "C:\Development\libGenome\libGenome\gn\gnClone.h" File "C:\Development\libGenome\libGenome\gn\gnCompare.h" File "C:\Development\libGenome\libGenome\gn\gnContigSpec.h" File "C:\Development\libGenome\libGenome\gn\gnDataBaseSource.h" File "C:\Development\libGenome\libGenome\gn\gnDebug.h" File "C:\Development\libGenome\libGenome\gn\gnDefs.h" File "C:\Development\libGenome\libGenome\gn\gnDNASequence.h" File "C:\Development\libGenome\libGenome\gn\gnDNXSource.h" File "C:\Development\libGenome\libGenome\gn\gnException.h" File "C:\Development\libGenome\libGenome\gn\gnExceptionCode.h" File "C:\Development\libGenome\libGenome\gn\gnFASSource.h" File "C:\Development\libGenome\libGenome\gn\gnFastTranslator.h" File "C:\Development\libGenome\libGenome\gn\gnFeature.h" File "C:\Development\libGenome\libGenome\gn\gnFileContig.h" File "C:\Development\libGenome\libGenome\gn\gnFileSource.h" File "C:\Development\libGenome\libGenome\gn\gnFilter.h" File "C:\Development\libGenome\libGenome\gn\gnFragmentSpec.h" File "C:\Development\libGenome\libGenome\gn\gnGBKSource.h" File "C:\Development\libGenome\libGenome\gn\gnGenomeSpec.h" File "C:\Development\libGenome\libGenome\gn\gnLocation.h" File "C:\Development\libGenome\libGenome\gn\gnMultiSpec.h" File "C:\Development\libGenome\libGenome\gn\gnPosSpecificTranslator.h" File "C:\Development\libGenome\libGenome\gn\GNPREC.H" File "C:\Development\libGenome\libGenome\gn\gnProteinSequence.h" File "C:\Development\libGenome\libGenome\gn\gnRAWSource.h" File "C:\Development\libGenome\libGenome\gn\gnRNASequence.h" File "C:\Development\libGenome\libGenome\gn\gnSEQSource.h" File "C:\Development\libGenome\libGenome\gn\gnSequence.h" File "C:\Development\libGenome\libGenome\gn\gnSetup.h" File "C:\Development\libGenome\libGenome\gn\gnSourceFactory.h" File "C:\Development\libGenome\libGenome\gn\gnSourceHeader.h" File "C:\Development\libGenome\libGenome\gn\gnSourceQualifier.h" File "C:\Development\libGenome\libGenome\gn\gnSourceSpec.h" File "C:\Development\libGenome\libGenome\gn\gnStringHeader.h" File "C:\Development\libGenome\libGenome\gn\gnStringQualifier.h" File "C:\Development\libGenome\libGenome\gn\gnStringSpec.h" File "C:\Development\libGenome\libGenome\gn\gnStringTools.h" File "C:\Development\libGenome\libGenome\gn\gnTranslator.h" File "C:\Development\libGenome\libGenome\gn\gnVersion.h" File "C:\Development\libGenome\libGenome\gn\Makefile.am" SectionEnd Section "Precompiled Libraries" ; lib/ files SetOutPath "$INSTDIR\lib" File "C:\Development\libGenome\lib\genome.dll" File "C:\Development\libGenome\lib\genome.lib" File "C:\Development\libGenome\lib\genomed.dll" File "C:\Development\libGenome\lib\genomed.lib" File "C:\Development\libGenome\lib\genomeddll.lib" File "C:\Development\libGenome\lib\genomedll.lib" SectionEnd Section "libGenome Project Files" ; projects/ files SetOutPath "$INSTDIR\projects" File "C:\Development\libGenome\projects\libGenome.mcp" File "C:\Development\libGenome\projects\libGenome.nsi" SectionEnd Section "Source Files" ; src/ files SetOutPath "$INSTDIR\src" File "C:\Development\libGenome\libGenome\gnABISource.cpp" File "C:\Development\libGenome\libGenome\gnBaseFeature.cpp" File "C:\Development\libGenome\libGenome\gnCompare.cpp" File "C:\Development\libGenome\libGenome\gnContigSpec.cpp" File "C:\Development\libGenome\libGenome\gnDNXSource.cpp" File "C:\Development\libGenome\libGenome\gnException.cpp" File "C:\Development\libGenome\libGenome\gnExceptionCode.cpp" File "C:\Development\libGenome\libGenome\gnFASSource.cpp" File "C:\Development\libGenome\libGenome\gnFastTranslator.cpp" File "C:\Development\libGenome\libGenome\gnFeature.cpp" File "C:\Development\libGenome\libGenome\gnFileContig.cpp" File "C:\Development\libGenome\libGenome\gnFileSource.cpp" File "C:\Development\libGenome\libGenome\gnFilter.cpp" File "C:\Development\libGenome\libGenome\gnFragmentSpec.cpp" File "C:\Development\libGenome\libGenome\gnGBKSource.cpp" File "C:\Development\libGenome\libGenome\gnGenomeSpec.cpp" File "C:\Development\libGenome\libGenome\gnLocation.cpp" File "C:\Development\libGenome\libGenome\gnMultiSpec.cpp" File "C:\Development\libGenome\libGenome\gnPosSpecificTranslator.cpp" File "C:\Development\libGenome\libGenome\gnRAWSource.cpp" File "C:\Development\libGenome\libGenome\gnSEQSource.cpp" File "C:\Development\libGenome\libGenome\gnSeqStringTest.cpp" File "C:\Development\libGenome\libGenome\gnSequence.cpp" File "C:\Development\libGenome\libGenome\gnSourceFactory.cpp" File "C:\Development\libGenome\libGenome\gnSourceHeader.cpp" File "C:\Development\libGenome\libGenome\gnSourceQualifier.cpp" File "C:\Development\libGenome\libGenome\gnSourceSpec.cpp" File "C:\Development\libGenome\libGenome\gnStringHeader.cpp" File "C:\Development\libGenome\libGenome\gnStringQualifier.cpp" File "C:\Development\libGenome\libGenome\gnStringSpec.cpp" File "C:\Development\libGenome\libGenome\gnStringTools.cpp" File "C:\Development\libGenome\libGenome\gnTranslator.cpp" File "C:\Development\libGenome\libGenome\Makefile.am" SectionEnd Section "libGenome Stationary" ; stationary/ files SetOutPath "$INSTDIR\stationary\libGenome_App" File "C:\Development\libGenome\stationary\libGenome_App\libGenome_App.mcp" SetOutPath "$INSTDIR\stationary\libGenome_App\src" File "C:\Development\libGenome\stationary\libGenome_App\src\genomeApp.cpp" push $0 push $1 push $2 push $3 push 0 pop $0 EnumRegKey $1 HKLM "SOFTWARE\Metrowerks\CodeWarrior\Product Versions" $0 ReadRegStr $2 HKLM "SOFTWARE\Metrowerks\CodeWarrior\Product Versions\$1" VERSION ReadRegStr $3 HKLM "SOFTWARE\Metrowerks\CodeWarrior\Product Versions\$1" PATH DetailPrint "Installing libGenome stationary for $1 version $2 in directory $3" SetOutPath "$3\Stationery\libGenome_App" File "C:\Development\libGenome\stationary\libGenome_App\libGenome_App.mcp" SetOutPath "$3\Stationery\libGenome_App\src" File "C:\Development\libGenome\stationary\libGenome_App\src\genomeApp.cpp" CreateDirectory "$3\Stationery\libGenome_App\include" CreateDirectory "$3\Stationery\libGenome_App\doc" CreateDirectory "$3\Stationery\libGenome_App\bin" pop $3 pop $2 pop $1 pop $0 ; Add a registry key for the GenomeDev source tree push $0 push $1 StrLen $0 $INSTDIR IntOp $0 $0 - 10 StrCpy $1 $INSTDIR $0 WriteRegStr HKLM "SOFTWARE\libGenome\" "GenomeDev" "$1" pop $1 pop $0 SectionEnd SubSectionEnd SubSection "Documentation" Section "HTML documentation" ; copy documentation directories SetOutPath "$INSTDIR\doc" File "C:\Development\libGenome\doc\Doxyfile.txt" File "C:\Development\libGenome\doc\Makefile.am" File /r "C:\Development\libGenome\doc\html" SectionEnd Section "UNIX man page documentation" SetOutPath "$INSTDIR\doc" File "C:\Development\libGenome\doc\Doxyfile.txt" File "C:\Development\libGenome\doc\Makefile.am" File /r "C:\Development\libGenome\doc\man" SectionEnd Section "Documentation Start Menu Shortcut" ;Add Shortcuts CreateShortCut "$SMPROGRAMS\libGenome Documentation.lnk" "$INSTDIR\doc\html\index.html" SectionEnd SubSectionEnd Section "Uninstaller" ; Write the uninstall keys for Windows WriteRegStr HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\libGenome" "DisplayName" "libGenome (remove only)" WriteRegStr HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\libGenome" "UninstallString" "$INSTDIR\Uninst.exe" WriteUninstaller "Uninst.exe" SectionEnd UninstallText "This will uninstall libGenome from your system" Section Uninstall ;Delete Files ; Top level directory files Delete /REBOOTOK "$INSTDIR\AUTHORS" Delete /REBOOTOK "$INSTDIR\ChangeLog" Delete /REBOOTOK "$INSTDIR\configure.in" Delete /REBOOTOK "$INSTDIR\COPYING" Delete /REBOOTOK "$INSTDIR\INSTALL" Delete /REBOOTOK "$INSTDIR\Makefile.am" Delete /REBOOTOK "$INSTDIR\NEWS" Delete /REBOOTOK "$INSTDIR\README" ; /include/gn files Delete /REBOOTOK "$INSTDIR\libGenome\gnABISource.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnBaseFeature.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnBaseFilter.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnBaseHeader.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnBaseQualifier.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnBaseSource.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnBaseSpec.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnClone.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnCompare.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnContigSpec.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnDataBaseSource.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnDebug.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnDefs.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnDNASequence.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnDNXSource.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnException.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnExceptionCode.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnFASSource.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnFastTranslator.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnFeature.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnFileContig.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnFileSource.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnFilter.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnFragmentSpec.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnGBKSource.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnGenomeSpec.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnLocation.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnMultiSpec.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnPosSpecificTranslator.h" Delete /REBOOTOK "$INSTDIR\libGenome\GNPREC.H" Delete /REBOOTOK "$INSTDIR\libGenome\gnProteinSequence.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnRAWSource.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnRNASequence.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnSEQSource.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnSequence.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnSetup.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnSourceFactory.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnSourceHeader.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnSourceQualifier.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnSourceSpec.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnStringHeader.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnStringQualifier.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnStringSpec.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnStringTools.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnTranslator.h" Delete /REBOOTOK "$INSTDIR\libGenome\gnVersion.h" Delete /REBOOTOK "$INSTDIR\libGenome\Makefile.am" RMDir "$INSTDIR\include" ; /include files Delete /REBOOTOK "$INSTDIR\libGenome\gn_cw.h" Delete /REBOOTOK "$INSTDIR\libGenome\gn_cw.pch" Delete /REBOOTOK "$INSTDIR\libGenome\gn_cw.pch++" Delete /REBOOTOK "$INSTDIR\libGenome\gn_cw_d.h" Delete /REBOOTOK "$INSTDIR\libGenome\gn_cw_d.pch" Delete /REBOOTOK "$INSTDIR\libGenome\gn_cw_d.pch++" Delete /REBOOTOK "$INSTDIR\libGenome\gn_cw_dll.h" Delete /REBOOTOK "$INSTDIR\libGenome\gn_cw_dll.pch" Delete /REBOOTOK "$INSTDIR\libGenome\gn_cw_dll.pch++" Delete /REBOOTOK "$INSTDIR\libGenome\gn_cw_dlld.h" Delete /REBOOTOK "$INSTDIR\libGenome\gn_cw_dlld.pch" Delete /REBOOTOK "$INSTDIR\libGenome\gn_cw_dlld.pch++" Delete /REBOOTOK "$INSTDIR\libGenome\Makefile.am" RMDir "$INSTDIR\include" ; lib/ files Delete /REBOOTOK "$INSTDIR\lib\genome.dll" Delete /REBOOTOK "$INSTDIR\lib\genome.lib" Delete /REBOOTOK "$INSTDIR\lib\genomed.dll" Delete /REBOOTOK "$INSTDIR\lib\genomed.lib" Delete /REBOOTOK "$INSTDIR\lib\genomeddll.lib" Delete /REBOOTOK "$INSTDIR\lib\genomedll.lib" RMDir "$INSTDIR\lib" ; projects/ files Delete /REBOOTOK "$INSTDIR\projects\libGenome.mcp" Delete /REBOOTOK "$INSTDIR\projects\libGenome.nsi" RMDir "$INSTDIR\projects" ; src/ files Delete /REBOOTOK "$INSTDIR\libGenome\gnABISource.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnBaseFeature.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnCompare.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnContigSpec.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnDNXSource.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnException.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnExceptionCode.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnFASSource.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnFastTranslator.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnFeature.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnFileContig.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnFileSource.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnFilter.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnFragmentSpec.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnGBKSource.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnGenomeSpec.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnLocation.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnMultiSpec.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnPosSpecificTranslator.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnRAWSource.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnSEQSource.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnSeqStringTest.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnSequence.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnSourceFactory.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnSourceHeader.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnSourceQualifier.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnSourceSpec.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnStringHeader.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnStringQualifier.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnStringSpec.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnStringTools.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\gnTranslator.cpp" Delete /REBOOTOK "$INSTDIR\libGenome\Makefile.am" RMDir "$INSTDIR\src" ; stationary/ files Delete /REBOOTOK "$INSTDIR\stationary\libGenome_App\src\genomeApp.cpp" RMDir "$INSTDIR\stationary\libGenome_App\src" Delete /REBOOTOK "$INSTDIR\stationary\libGenome_App\libGenome_App.mcp" RMDir "$INSTDIR\stationary\libGenome_App" RMDir "$INSTDIR\stationary\include" RMDir "$INSTDIR\stationary\doc" RMDir "$INSTDIR\stationary\bin" RMDir "$INSTDIR\stationary\" ; copy documentation directories RMDir /r "$INSTDIR\doc\html" RMDir /r "$INSTDIR\doc\man" RMDir /r "$INSTDIR\doc" ; Delete documentation shortcut Delete "$SMPROGRAMS\libGenome Documentation.lnk" ; Delete the stationery push $0 push $1 push $2 push $3 push 0 pop $0 EnumRegKey $1 HKLM "SOFTWARE\Metrowerks\CodeWarrior\Product Versions" $0 ReadRegStr $2 HKLM "SOFTWARE\Metrowerks\CodeWarrior\Product Versions\$1" VERSION ReadRegStr $3 HKLM "SOFTWARE\Metrowerks\CodeWarrior\Product Versions\$1" PATH DetailPrint "Removing libGenome stationary for $1 version $2 in directory $3" Delete /REBOOTOK "$3\Stationery\libGenome_App\libGenome_App.mcp" Delete /REBOOTOK "$3\Stationery\libGenome_App\src\genomeApp.cpp" RMDir "$3\Stationery\libGenome_App\src" RMDir "$3\Stationery\libGenome_App\include" RMDir "$3\Stationery\libGenome_App\doc" RMDir "$3\Stationery\libGenome_App\bin" RMDir "$3\Stationery\libGenome_App" pop $3 pop $2 pop $1 pop $0 ;Delete Uninstaller And Unistall Registry Entries Delete "$INSTDIR\Uninst.exe" DeleteRegKey HKEY_LOCAL_MACHINE "SOFTWARE\libGenome" DeleteRegKey HKEY_LOCAL_MACHINE "SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall\libGenome" RMDir "$INSTDIR" SectionEnd libGenome-1.3.1/projects/libGenome.doxygen0000644002622200470610000002012210766631206015501 00000000000000# Doxyfile 1.3.7 #--------------------------------------------------------------------------- # Project related configuration options #--------------------------------------------------------------------------- PROJECT_NAME = $(PROJECT)-$(VERSION) PROJECT_NUMBER = OUTPUT_DIRECTORY = $(DOCDIR) CREATE_SUBDIRS = NO OUTPUT_LANGUAGE = English USE_WINDOWS_ENCODING = NO BRIEF_MEMBER_DESC = YES REPEAT_BRIEF = YES ABBREVIATE_BRIEF = ALWAYS_DETAILED_SEC = NO INLINE_INHERITED_MEMB = NO STRIP_FROM_INC_PATH = $(SRCDIR) FULL_PATH_NAMES = YES STRIP_FROM_PATH = $(SRCDIR) SHORT_NAMES = NO JAVADOC_AUTOBRIEF = YES MULTILINE_CPP_IS_BRIEF = NO DETAILS_AT_TOP = YES INHERIT_DOCS = YES DISTRIBUTE_GROUP_DOC = NO TAB_SIZE = 8 ALIASES = OPTIMIZE_OUTPUT_FOR_C = YES OPTIMIZE_OUTPUT_JAVA = NO SUBGROUPING = YES #--------------------------------------------------------------------------- # Build related configuration options #--------------------------------------------------------------------------- EXTRACT_ALL = YES EXTRACT_PRIVATE = YES EXTRACT_STATIC = YES EXTRACT_LOCAL_CLASSES = YES EXTRACT_LOCAL_METHODS = NO HIDE_UNDOC_MEMBERS = NO HIDE_UNDOC_CLASSES = NO HIDE_FRIEND_COMPOUNDS = NO HIDE_IN_BODY_DOCS = NO INTERNAL_DOCS = NO CASE_SENSE_NAMES = NO HIDE_SCOPE_NAMES = NO SHOW_INCLUDE_FILES = YES INLINE_INFO = YES SORT_MEMBER_DOCS = YES SORT_BRIEF_DOCS = NO SORT_BY_SCOPE_NAME = NO GENERATE_TODOLIST = YES GENERATE_TESTLIST = YES GENERATE_BUGLIST = YES GENERATE_DEPRECATEDLIST= YES ENABLED_SECTIONS = MAX_INITIALIZER_LINES = 30 SHOW_USED_FILES = YES #--------------------------------------------------------------------------- # configuration options related to warning and progress messages #--------------------------------------------------------------------------- QUIET = YES WARNINGS = YES WARN_IF_UNDOCUMENTED = YES WARN_IF_DOC_ERROR = YES WARN_FORMAT = "$file:$line: $text" WARN_LOGFILE = #--------------------------------------------------------------------------- # configuration options related to the input files #--------------------------------------------------------------------------- INPUT = $(SRCDIR) FILE_PATTERNS = *.c *.h RECURSIVE = YES EXCLUDE = EXCLUDE_SYMLINKS = NO EXCLUDE_PATTERNS = EXAMPLE_PATH = $(SRCDIR) EXAMPLE_PATTERNS = EXAMPLE_RECURSIVE = NO IMAGE_PATH = INPUT_FILTER = FILTER_SOURCE_FILES = NO #--------------------------------------------------------------------------- # configuration options related to source browsing #--------------------------------------------------------------------------- SOURCE_BROWSER = NO INLINE_SOURCES = NO STRIP_CODE_COMMENTS = YES REFERENCED_BY_RELATION = YES REFERENCES_RELATION = YES VERBATIM_HEADERS = YES #--------------------------------------------------------------------------- # configuration options related to the alphabetical class index #--------------------------------------------------------------------------- ALPHABETICAL_INDEX = NO COLS_IN_ALPHA_INDEX = 5 IGNORE_PREFIX = #--------------------------------------------------------------------------- # configuration options related to the HTML output #--------------------------------------------------------------------------- GENERATE_HTML = $(GENERATE_HTML) HTML_OUTPUT = html HTML_FILE_EXTENSION = .html HTML_HEADER = HTML_FOOTER = HTML_STYLESHEET = HTML_ALIGN_MEMBERS = YES GENERATE_HTMLHELP = $(GENERATE_CHM) CHM_FILE = ../$(PROJECT).chm HHC_LOCATION = $(HHC_PATH) GENERATE_CHI = $(GENERATE_CHI) BINARY_TOC = NO TOC_EXPAND = NO DISABLE_INDEX = NO ENUM_VALUES_PER_LINE = 4 GENERATE_TREEVIEW = YES TREEVIEW_WIDTH = 250 #--------------------------------------------------------------------------- # configuration options related to the LaTeX output #--------------------------------------------------------------------------- GENERATE_LATEX = $(GENERATE_LATEX) LATEX_OUTPUT = latex LATEX_CMD_NAME = latex MAKEINDEX_CMD_NAME = makeindex COMPACT_LATEX = NO PAPER_TYPE = $(PAPER_SIZE) EXTRA_PACKAGES = LATEX_HEADER = PDF_HYPERLINKS = NO USE_PDFLATEX = NO LATEX_BATCHMODE = YES LATEX_HIDE_INDICES = NO #--------------------------------------------------------------------------- # configuration options related to the RTF output #--------------------------------------------------------------------------- GENERATE_RTF = $(GENERATE_RTF) RTF_OUTPUT = rtf COMPACT_RTF = NO RTF_HYPERLINKS = NO RTF_STYLESHEET_FILE = RTF_EXTENSIONS_FILE = #--------------------------------------------------------------------------- # configuration options related to the man page output #--------------------------------------------------------------------------- GENERATE_MAN = $(GENERATE_MAN) MAN_OUTPUT = man MAN_EXTENSION = .1 MAN_LINKS = NO #--------------------------------------------------------------------------- # configuration options related to the XML output #--------------------------------------------------------------------------- GENERATE_XML = $(GENERATE_XML) XML_OUTPUT = xml XML_SCHEMA = XML_DTD = XML_PROGRAMLISTING = YES #--------------------------------------------------------------------------- # configuration options for the AutoGen Definitions output #--------------------------------------------------------------------------- GENERATE_AUTOGEN_DEF = NO #--------------------------------------------------------------------------- # configuration options related to the Perl module output #--------------------------------------------------------------------------- GENERATE_PERLMOD = NO PERLMOD_LATEX = NO PERLMOD_PRETTY = YES PERLMOD_MAKEVAR_PREFIX = #--------------------------------------------------------------------------- # Configuration options related to the preprocessor #--------------------------------------------------------------------------- ENABLE_PREPROCESSING = YES MACRO_EXPANSION = NO EXPAND_ONLY_PREDEF = NO SEARCH_INCLUDES = YES INCLUDE_PATH = INCLUDE_FILE_PATTERNS = PREDEFINED = EXPAND_AS_DEFINED = SKIP_FUNCTION_MACROS = YES #--------------------------------------------------------------------------- # Configuration::additions related to external references #--------------------------------------------------------------------------- TAGFILES = GENERATE_TAGFILE = $(DOCDIR)/$(PROJECT).tag ALLEXTERNALS = NO EXTERNAL_GROUPS = YES PERL_PATH = $(PERL_PATH) #--------------------------------------------------------------------------- # Configuration options related to the dot tool #--------------------------------------------------------------------------- CLASS_DIAGRAMS = YES HIDE_UNDOC_RELATIONS = YES HAVE_DOT = $(HAVE_DOT) CLASS_GRAPH = YES COLLABORATION_GRAPH = YES UML_LOOK = NO TEMPLATE_RELATIONS = NO INCLUDE_GRAPH = YES INCLUDED_BY_GRAPH = YES CALL_GRAPH = NO GRAPHICAL_HIERARCHY = YES DOT_IMAGE_FORMAT = png DOT_PATH = $(DOT_PATH) DOTFILE_DIRS = MAX_DOT_GRAPH_WIDTH = 1024 MAX_DOT_GRAPH_HEIGHT = 1024 MAX_DOT_GRAPH_DEPTH = 0 GENERATE_LEGEND = YES DOT_CLEANUP = YES #--------------------------------------------------------------------------- # Configuration::additions related to the search engine #--------------------------------------------------------------------------- SEARCHENGINE = NO libGenome-1.3.1/projects/libGenome.sln0000644002622200470610000000156710647575617014647 00000000000000 Microsoft Visual Studio Solution File, Format Version 9.00 # Visual C++ Express 2005 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "libGenome", "libGenome.vcproj", "{5B7186E6-EBD1-40CD-9B95-9974937EB5C3}" EndProject Global GlobalSection(SolutionConfigurationPlatforms) = preSolution Debug|Win32 = Debug|Win32 Release|Win32 = Release|Win32 EndGlobalSection GlobalSection(ProjectConfigurationPlatforms) = postSolution {5B7186E6-EBD1-40CD-9B95-9974937EB5C3}.Debug|Win32.ActiveCfg = Debug|Win32 {5B7186E6-EBD1-40CD-9B95-9974937EB5C3}.Debug|Win32.Build.0 = Debug|Win32 {5B7186E6-EBD1-40CD-9B95-9974937EB5C3}.Release|Win32.ActiveCfg = Release|Win32 {5B7186E6-EBD1-40CD-9B95-9974937EB5C3}.Release|Win32.Build.0 = Release|Win32 EndGlobalSection GlobalSection(SolutionProperties) = preSolution HideSolutionNode = FALSE EndGlobalSection EndGlobal libGenome-1.3.1/configure0000755002622200470610000266750511030167133012273 00000000000000#! /bin/sh # Guess values for system-dependent variables and create Makefiles. # Generated by GNU Autoconf 2.59. # # Copyright (C) 2003 Free Software Foundation, Inc. # This configure script is free software; the Free Software Foundation # gives unlimited permission to copy, distribute and modify it. ## --------------------- ## ## M4sh Initialization. ## ## --------------------- ## # Be Bourne compatible if test -n "${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. 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PACKAGE=$PACKAGE VERSION=$VERSION # Some tools Automake needs. ACLOCAL=${ACLOCAL-"${am_missing_run}aclocal-${am__api_version}"} AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"} AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"} AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"} MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"} install_sh=${install_sh-"$am_aux_dir/install-sh"} # Installed binaries are usually stripped using `strip' when the user # run `make install-strip'. However `strip' might not be the right # tool to use in cross-compilation environments, therefore Automake # will honor the `STRIP' environment variable to overrule this program. if test "$cross_compiling" != no; then if test -n "$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=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_STRIP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_STRIP="${ac_tool_prefix}strip" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi STRIP=$ac_cv_prog_STRIP if test -n "$STRIP"; then echo "$as_me:$LINENO: result: $STRIP" >&5 echo "${ECHO_T}$STRIP" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}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=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_STRIP="strip" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done test -z "$ac_cv_prog_ac_ct_STRIP" && ac_cv_prog_ac_ct_STRIP=":" fi fi ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP if test -n "$ac_ct_STRIP"; then echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5 echo "${ECHO_T}$ac_ct_STRIP" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi STRIP=$ac_ct_STRIP else STRIP="$ac_cv_prog_STRIP" fi fi INSTALL_STRIP_PROGRAM="\${SHELL} \$(install_sh) -c -s" # We need awk for the "check" target. The system "awk" is bad on # some platforms. # Always define AMTAR for backward compatibility. AMTAR=${AMTAR-"${am_missing_run}tar"} am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -' ac_ext=c ac_cpp='$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 if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args. set dummy ${ac_tool_prefix}gcc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_CC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else as_save_IFS=$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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_CC="${ac_tool_prefix}gcc" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then echo "$as_me:$LINENO: result: $CC" >&5 echo "${ECHO_T}$CC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_prog_CC"; then ac_ct_CC=$CC # Extract the first word of "gcc", so it can be a program name with args. set dummy gcc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_ac_ct_CC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. else as_save_IFS=$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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_CC="gcc" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 echo "${ECHO_T}$ac_ct_CC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi CC=$ac_ct_CC else CC="$ac_cv_prog_CC" fi if test -z "$CC"; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args. set dummy ${ac_tool_prefix}cc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_CC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else as_save_IFS=$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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_CC="${ac_tool_prefix}cc" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then echo "$as_me:$LINENO: result: $CC" >&5 echo "${ECHO_T}$CC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_prog_CC"; then ac_ct_CC=$CC # Extract the first word of "cc", so it can be a program name with args. set dummy cc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_ac_ct_CC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. else as_save_IFS=$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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_CC="cc" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 echo "${ECHO_T}$ac_ct_CC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi CC=$ac_ct_CC else CC="$ac_cv_prog_CC" fi fi if test -z "$CC"; then # Extract the first word of "cc", so it can be a program name with args. set dummy cc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_CC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else ac_prog_rejected=no as_save_IFS=$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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then ac_prog_rejected=yes continue fi ac_cv_prog_CC="cc" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done if test $ac_prog_rejected = yes; then # We found a bogon in the path, so make sure we never use it. set dummy $ac_cv_prog_CC shift if test $# != 0; then # We chose a different compiler from the bogus one. # However, it has the same basename, so the bogon will be chosen # first if we set CC to just the basename; use the full file name. shift ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@" fi fi fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then echo "$as_me:$LINENO: result: $CC" >&5 echo "${ECHO_T}$CC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$CC"; then if test -n "$ac_tool_prefix"; then for ac_prog in cl do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_CC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$CC"; then ac_cv_prog_CC="$CC" # Let the user override the test. else as_save_IFS=$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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_CC="$ac_tool_prefix$ac_prog" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then echo "$as_me:$LINENO: result: $CC" >&5 echo "${ECHO_T}$CC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi test -n "$CC" && break done fi if test -z "$CC"; then ac_ct_CC=$CC for ac_prog in cl do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_ac_ct_CC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$ac_ct_CC"; then ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test. else as_save_IFS=$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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_CC="$ac_prog" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 echo "${ECHO_T}$ac_ct_CC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi test -n "$ac_ct_CC" && break done CC=$ac_ct_CC fi fi test -z "$CC" && { { echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH See \`config.log' for more details." >&5 echo "$as_me: error: no acceptable C compiler found in \$PATH See \`config.log' for more details." >&2;} { (exit 1); exit 1; }; } # Provide some information about the compiler. echo "$as_me:$LINENO:" \ "checking for C compiler version" >&5 ac_compiler=`set X $ac_compile; echo $2` { (eval echo "$as_me:$LINENO: \"$ac_compiler --version &5\"") >&5 (eval $ac_compiler --version &5) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } { (eval echo "$as_me:$LINENO: \"$ac_compiler -v &5\"") >&5 (eval $ac_compiler -v &5) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } { (eval echo "$as_me:$LINENO: \"$ac_compiler -V &5\"") >&5 (eval $ac_compiler -V &5) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int main () { ; return 0; } _ACEOF ac_clean_files_save=$ac_clean_files ac_clean_files="$ac_clean_files a.out a.exe b.out" # Try to create an executable without -o first, disregard a.out. # It will help us diagnose broken compilers, and finding out an intuition # of exeext. echo "$as_me:$LINENO: checking for C compiler default output file name" >&5 echo $ECHO_N "checking for C compiler default output file name... $ECHO_C" >&6 ac_link_default=`echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` if { (eval echo "$as_me:$LINENO: \"$ac_link_default\"") >&5 (eval $ac_link_default) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; then # Find the output, starting from the most likely. This scheme is # not robust to junk in `.', hence go to wildcards (a.*) only as a last # resort. # Be careful to initialize this variable, since it used to be cached. # Otherwise an old cache value of `no' led to `EXEEXT = no' in a Makefile. ac_cv_exeext= # b.out is created by i960 compilers. for ac_file in a_out.exe a.exe conftest.exe a.out conftest a.* conftest.* b.out do test -f "$ac_file" || continue case $ac_file in *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.o | *.obj ) ;; conftest.$ac_ext ) # This is the source file. ;; [ab].out ) # We found the default executable, but exeext='' is most # certainly right. break;; *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` # FIXME: I believe we export ac_cv_exeext for Libtool, # but it would be cool to find out if it's true. Does anybody # maintain Libtool? --akim. export ac_cv_exeext break;; * ) break;; esac done else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 { { echo "$as_me:$LINENO: error: C compiler cannot create executables See \`config.log' for more details." >&5 echo "$as_me: error: C compiler cannot create executables See \`config.log' for more details." >&2;} { (exit 77); exit 77; }; } fi ac_exeext=$ac_cv_exeext echo "$as_me:$LINENO: result: $ac_file" >&5 echo "${ECHO_T}$ac_file" >&6 # Check the compiler produces executables we can run. 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SAVE_CFLAGS="$CFLAGS" CFLAGS="$CFLAGS -belf" echo "$as_me:$LINENO: checking whether the C compiler needs -belf" >&5 echo $ECHO_N "checking whether the C compiler needs -belf... $ECHO_C" >&6 if test "${lt_cv_cc_needs_belf+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_ext=c ac_cpp='$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 >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then lt_cv_cc_needs_belf=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 lt_cv_cc_needs_belf=no fi rm -f conftest.err conftest.$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 echo "$as_me:$LINENO: result: $lt_cv_cc_needs_belf" >&5 echo "${ECHO_T}$lt_cv_cc_needs_belf" >&6 if test x"$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="$SAVE_CFLAGS" fi ;; esac need_locks="$enable_libtool_lock" 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 echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5 echo $ECHO_N "checking how to run the C preprocessor... $ECHO_C" >&6 # On Suns, sometimes $CPP names a directory. if test -n "$CPP" && test -d "$CPP"; then CPP= fi if test -z "$CPP"; then if test "${ac_cv_prog_CPP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else # Double quotes because CPP needs to be expanded for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp" do ac_preproc_ok=false for ac_c_preproc_warn_flag in '' yes do # Use a header file that comes with gcc, so configuring glibc # with a fresh cross-compiler works. # Prefer to if __STDC__ is defined, since # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #ifdef __STDC__ # include #else # include #endif Syntax error _ACEOF if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } >/dev/null; then if test -s conftest.err; then ac_cpp_err=$ac_c_preproc_warn_flag ac_cpp_err=$ac_cpp_err$ac_c_werror_flag else ac_cpp_err= fi else ac_cpp_err=yes fi if test -z "$ac_cpp_err"; then : else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 # Broken: fails on valid input. continue fi rm -f conftest.err conftest.$ac_ext # OK, works on sane cases. 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Now check whether non-existent headers # can be detected and how. cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } >/dev/null; then if test -s conftest.err; then ac_cpp_err=$ac_c_preproc_warn_flag ac_cpp_err=$ac_cpp_err$ac_c_werror_flag else ac_cpp_err= fi else ac_cpp_err=yes fi if test -z "$ac_cpp_err"; then # Broken: success on invalid input. continue else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 # Passes both tests. ac_preproc_ok=: break fi rm -f conftest.err conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. rm -f conftest.err conftest.$ac_ext if $ac_preproc_ok; then : else { { echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check See \`config.log' for more details." >&5 echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check See \`config.log' for more details." >&2;} { (exit 1); exit 1; }; } 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 echo "$as_me:$LINENO: checking for ANSI C header files" >&5 echo $ECHO_N "checking for ANSI C header files... $ECHO_C" >&6 if test "${ac_cv_header_stdc+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include #include #include int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest.$ac_objext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_header_stdc=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_header_stdc=no fi rm -f conftest.err conftest.$ac_objext conftest.$ac_ext if test $ac_cv_header_stdc = yes; then # SunOS 4.x string.h does not declare mem*, contrary to ANSI. cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | $EGREP "memchr" >/dev/null 2>&1; then : else ac_cv_header_stdc=no fi rm -f conftest* fi if test $ac_cv_header_stdc = yes; then # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | $EGREP "free" >/dev/null 2>&1; then : else ac_cv_header_stdc=no fi rm -f conftest* fi if test $ac_cv_header_stdc = yes; then # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. if test "$cross_compiling" = yes; then : else cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #if ((' ' & 0x0FF) == 0x020) # define ISLOWER(c) ('a' <= (c) && (c) <= 'z') # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c)) #else # define ISLOWER(c) \ (('a' <= (c) && (c) <= 'i') \ || ('j' <= (c) && (c) <= 'r') \ || ('s' <= (c) && (c) <= 'z')) # define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) #endif #define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) int main () { int i; for (i = 0; i < 256; i++) if (XOR (islower (i), ISLOWER (i)) || toupper (i) != TOUPPER (i)) exit(2); exit (0); } _ACEOF rm -f conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='./conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then : else echo "$as_me: program exited with status $ac_status" >&5 echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ( exit $ac_status ) ac_cv_header_stdc=no fi rm -f core *.core gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext fi fi fi echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5 echo "${ECHO_T}$ac_cv_header_stdc" >&6 if test $ac_cv_header_stdc = yes; then cat >>confdefs.h <<\_ACEOF #define STDC_HEADERS 1 _ACEOF fi # On IRIX 5.3, sys/types and inttypes.h are conflicting. for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ inttypes.h stdint.h unistd.h do as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` echo "$as_me:$LINENO: checking for $ac_header" >&5 echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 if eval "test \"\${$as_ac_Header+set}\" = set"; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ $ac_includes_default #include <$ac_header> _ACEOF rm -f conftest.$ac_objext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest.$ac_objext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then eval "$as_ac_Header=yes" else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 eval "$as_ac_Header=no" fi rm -f conftest.err conftest.$ac_objext conftest.$ac_ext fi echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 if test `eval echo '${'$as_ac_Header'}'` = yes; then cat >>confdefs.h <<_ACEOF #define `echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF fi done for ac_header in dlfcn.h do as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` if eval "test \"\${$as_ac_Header+set}\" = set"; then echo "$as_me:$LINENO: checking for $ac_header" >&5 echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6 if eval "test \"\${$as_ac_Header+set}\" = set"; then echo $ECHO_N "(cached) $ECHO_C" >&6 fi echo "$as_me:$LINENO: result: `eval echo '${'$as_ac_Header'}'`" >&5 echo "${ECHO_T}`eval echo '${'$as_ac_Header'}'`" >&6 else # Is the header compilable? echo "$as_me:$LINENO: checking $ac_header usability" >&5 echo $ECHO_N "checking $ac_header usability... $ECHO_C" >&6 cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ $ac_includes_default #include <$ac_header> _ACEOF rm -f conftest.$ac_objext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest.$ac_objext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_header_compiler=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_header_compiler=no fi rm -f conftest.err conftest.$ac_objext conftest.$ac_ext echo "$as_me:$LINENO: result: $ac_header_compiler" >&5 echo "${ECHO_T}$ac_header_compiler" >&6 # Is the header present? echo "$as_me:$LINENO: checking $ac_header presence" >&5 echo $ECHO_N "checking $ac_header presence... $ECHO_C" >&6 cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include <$ac_header> _ACEOF if { (eval echo "$as_me:$LINENO: \"$ac_cpp conftest.$ac_ext\"") >&5 (eval $ac_cpp conftest.$ac_ext) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } >/dev/null; then if test -s conftest.err; then ac_cpp_err=$ac_c_preproc_warn_flag ac_cpp_err=$ac_cpp_err$ac_c_werror_flag else ac_cpp_err= fi else ac_cpp_err=yes fi if test -z "$ac_cpp_err"; then ac_header_preproc=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_header_preproc=no fi rm -f conftest.err conftest.$ac_ext echo "$as_me:$LINENO: result: $ac_header_preproc" >&5 echo "${ECHO_T}$ac_header_preproc" >&6 # So? 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Even if it were fixed, the result of this # check would be larger than it should be. lt_cv_sys_max_cmd_len=12288; # 12K is about right ;; gnu*) # Under GNU Hurd, this test is not required because there is # no limit to the length of command line arguments. # Libtool will interpret -1 as no limit whatsoever lt_cv_sys_max_cmd_len=-1; ;; cygwin* | mingw*) # On Win9x/ME, this test blows up -- it succeeds, but takes # about 5 minutes as the teststring grows exponentially. # Worse, since 9x/ME are not pre-emptively multitasking, # you end up with a "frozen" computer, even though with patience # the test eventually succeeds (with a max line length of 256k). # Instead, let's just punt: use the minimum linelength reported by # all of the supported platforms: 8192 (on NT/2K/XP). lt_cv_sys_max_cmd_len=8192; ;; amigaos*) # On AmigaOS with pdksh, this test takes hours, literally. # So we just punt and use a minimum line length of 8192. lt_cv_sys_max_cmd_len=8192; ;; *) # If test is not a shell built-in, we'll probably end up computing a # maximum length that is only half of the actual maximum length, but # we can't tell. while (test "X"`$CONFIG_SHELL $0 --fallback-echo "X$teststring" 2>/dev/null` \ = "XX$teststring") >/dev/null 2>&1 && new_result=`expr "X$teststring" : ".*" 2>&1` && lt_cv_sys_max_cmd_len=$new_result && test $i != 17 # 1/2 MB should be enough do i=`expr $i + 1` teststring=$teststring$teststring done 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` ;; esac fi if test -n $lt_cv_sys_max_cmd_len ; then echo "$as_me:$LINENO: result: $lt_cv_sys_max_cmd_len" >&5 echo "${ECHO_T}$lt_cv_sys_max_cmd_len" >&6 else echo "$as_me:$LINENO: result: none" >&5 echo "${ECHO_T}none" >&6 fi # Check for command to grab the raw symbol name followed by C symbol from nm. echo "$as_me:$LINENO: checking command to parse $NM output from $compiler object" >&5 echo $ECHO_N "checking command to parse $NM output from $compiler object... $ECHO_C" >&6 if test "${lt_cv_sys_global_symbol_pipe+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&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='\([_A-Za-z][_A-Za-z0-9]*\)' # Transform the above into a raw symbol and a C symbol. symxfrm='\1 \2\3 \3' # Transform an extracted symbol line into a proper C declaration lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^. .* \(.*\)$/extern int \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/^: \([^ ]*\) $/ {\\\"\1\\\", (lt_ptr) 0},/p' -e 's/^$symcode \([^ ]*\) \([^ ]*\)$/ {\"\2\", (lt_ptr) \&\2},/p'" # Define system-specific variables. case $host_os in aix*) symcode='[BCDT]' ;; cygwin* | mingw* | pw32*) symcode='[ABCDGISTW]' ;; hpux*) # Its linker distinguishes data from code symbols if test "$host_cpu" = ia64; then symcode='[ABCDEGRST]' fi lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (lt_ptr) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (lt_ptr) \&\2},/p'" ;; irix* | nonstopux*) symcode='[BCDEGRST]' ;; osf*) symcode='[BCDEGQRST]' ;; solaris* | sysv5*) symcode='[BDRT]' ;; sysv4) symcode='[DFNSTU]' ;; esac # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`echo 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[ABCDGIRSTW]' ;; esac # Try without a prefix undercore, then with it. for ac_symprfx in "" "_"; do # Write the raw and C identifiers. lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ ]\($symcode$symcode*\)[ ][ ]*\($ac_symprfx\)$sympat$opt_cr$/$symxfrm/p'" # Check to see that the pipe works correctly. pipe_works=no rm -f conftest* cat > conftest.$ac_ext <&5 (eval $ac_compile) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; then # Now try to grab the symbols. nlist=conftest.nm if { (eval echo "$as_me:$LINENO: \"$NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist\"") >&5 (eval $NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && test -s "$nlist"; then # Try sorting and uniquifying the output. if sort "$nlist" | uniq > "$nlist"T; then mv -f "$nlist"T "$nlist" else rm -f "$nlist"T fi # Make sure that we snagged all the symbols we need. if grep ' nm_test_var$' "$nlist" >/dev/null; then if grep ' nm_test_func$' "$nlist" >/dev/null; then cat < conftest.$ac_ext #ifdef __cplusplus extern "C" { #endif EOF # Now generate the symbol file. eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | grep -v main >> conftest.$ac_ext' cat <> conftest.$ac_ext #if defined (__STDC__) && __STDC__ # define lt_ptr_t void * #else # define lt_ptr_t char * # define const #endif /* The mapping between symbol names and symbols. */ const struct { const char *name; lt_ptr_t address; } lt_preloaded_symbols[] = { EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (lt_ptr_t) \&\2},/" < "$nlist" | grep -v main >> conftest.$ac_ext cat <<\EOF >> conftest.$ac_ext {0, (lt_ptr_t) 0} }; #ifdef __cplusplus } #endif 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:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && test -s conftest${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.$ac_ext >&5 fi rm -f conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$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$lt_cv_sys_global_symbol_to_cdecl"; then echo "$as_me:$LINENO: result: failed" >&5 echo "${ECHO_T}failed" >&6 else echo "$as_me:$LINENO: result: ok" >&5 echo "${ECHO_T}ok" >&6 fi echo "$as_me:$LINENO: checking for objdir" >&5 echo $ECHO_N "checking for objdir... $ECHO_C" >&6 if test "${lt_cv_objdir+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else rm -f .libs 2>/dev/null mkdir .libs 2>/dev/null if test -d .libs; then lt_cv_objdir=.libs else # MS-DOS does not allow filenames that begin with a dot. lt_cv_objdir=_libs fi rmdir .libs 2>/dev/null fi echo "$as_me:$LINENO: result: $lt_cv_objdir" >&5 echo "${ECHO_T}$lt_cv_objdir" >&6 objdir=$lt_cv_objdir case $host_os in aix3*) # AIX sometimes has problems with the GCC collect2 program. For some # reason, if we set the COLLECT_NAMES environment variable, the problems # vanish in a puff of smoke. if test "X${COLLECT_NAMES+set}" != Xset; then COLLECT_NAMES= export COLLECT_NAMES fi ;; esac # Sed substitution that helps us do robust quoting. It backslashifies # metacharacters that are still active within double-quoted strings. Xsed='sed -e s/^X//' sed_quote_subst='s/\([\\"\\`$\\\\]\)/\\\1/g' # Same as above, but do not quote variable references. double_quote_subst='s/\([\\"\\`\\\\]\)/\\\1/g' # Sed substitution to delay expansion of an escaped shell variable in a # double_quote_subst'ed string. delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g' # Sed substitution to avoid accidental globbing in evaled expressions no_glob_subst='s/\*/\\\*/g' # Constants: rm="rm -f" # Global variables: default_ofile=libtool can_build_shared=yes # All known linkers require a `.a' archive for static linking (except M$VC, # which needs '.lib'). libext=a ltmain="$ac_aux_dir/ltmain.sh" ofile="$default_ofile" with_gnu_ld="$lt_cv_prog_gnu_ld" 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=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_AR+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_AR="${ac_tool_prefix}ar" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi AR=$ac_cv_prog_AR if test -n "$AR"; then echo "$as_me:$LINENO: result: $AR" >&5 echo "${ECHO_T}$AR" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}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=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_ac_ct_AR+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_AR="ar" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done test -z "$ac_cv_prog_ac_ct_AR" && ac_cv_prog_ac_ct_AR="false" fi fi ac_ct_AR=$ac_cv_prog_ac_ct_AR if test -n "$ac_ct_AR"; then echo "$as_me:$LINENO: result: $ac_ct_AR" >&5 echo "${ECHO_T}$ac_ct_AR" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi AR=$ac_ct_AR else AR="$ac_cv_prog_AR" fi 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=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_RANLIB+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi RANLIB=$ac_cv_prog_RANLIB if test -n "$RANLIB"; then echo "$as_me:$LINENO: result: $RANLIB" >&5 echo "${ECHO_T}$RANLIB" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}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=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_RANLIB="ranlib" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done test -z "$ac_cv_prog_ac_ct_RANLIB" && ac_cv_prog_ac_ct_RANLIB=":" fi fi ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB if test -n "$ac_ct_RANLIB"; then echo "$as_me:$LINENO: result: $ac_ct_RANLIB" >&5 echo "${ECHO_T}$ac_ct_RANLIB" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi RANLIB=$ac_ct_RANLIB else RANLIB="$ac_cv_prog_RANLIB" fi 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=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_STRIP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_STRIP="${ac_tool_prefix}strip" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done fi fi STRIP=$ac_cv_prog_STRIP if test -n "$STRIP"; then echo "$as_me:$LINENO: result: $STRIP" >&5 echo "${ECHO_T}$STRIP" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}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=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test -n "$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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_prog_ac_ct_STRIP="strip" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done test -z "$ac_cv_prog_ac_ct_STRIP" && ac_cv_prog_ac_ct_STRIP=":" fi fi ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP if test -n "$ac_ct_STRIP"; then echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5 echo "${ECHO_T}$ac_ct_STRIP" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi STRIP=$ac_ct_STRIP else STRIP="$ac_cv_prog_STRIP" fi old_CC="$CC" old_CFLAGS="$CFLAGS" # Set sane defaults for various variables test -z "$AR" && AR=ar test -z "$AR_FLAGS" && AR_FLAGS=cru test -z "$AS" && AS=as test -z "$CC" && CC=cc test -z "$LTCC" && LTCC=$CC test -z "$DLLTOOL" && DLLTOOL=dlltool test -z "$LD" && LD=ld test -z "$LN_S" && LN_S="ln -s" test -z "$MAGIC_CMD" && MAGIC_CMD=file test -z "$NM" && NM=nm test -z "$SED" && SED=sed test -z "$OBJDUMP" && OBJDUMP=objdump test -z "$RANLIB" && RANLIB=: test -z "$STRIP" && STRIP=: test -z "$ac_objext" && ac_objext=o # Determine commands to create old-style static archives. old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs$old_deplibs' old_postinstall_cmds='chmod 644 $oldlib' old_postuninstall_cmds= if test -n "$RANLIB"; then case $host_os in openbsd*) old_postinstall_cmds="\$RANLIB -t \$oldlib~$old_postinstall_cmds" ;; *) old_postinstall_cmds="\$RANLIB \$oldlib~$old_postinstall_cmds" ;; esac old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib" fi # Only perform the check for file, if the check method requires it case $deplibs_check_method in file_magic*) if test "$file_magic_cmd" = '$MAGIC_CMD'; then echo "$as_me:$LINENO: checking for ${ac_tool_prefix}file" >&5 echo $ECHO_N "checking for ${ac_tool_prefix}file... $ECHO_C" >&6 if test "${lt_cv_path_MAGIC_CMD+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else 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=$PATH_SEPARATOR ac_dummy="/usr/bin$PATH_SEPARATOR$PATH" for ac_dir in $ac_dummy; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. if test -f $ac_dir/${ac_tool_prefix}file; then lt_cv_path_MAGIC_CMD="$ac_dir/${ac_tool_prefix}file" 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 <&2 *** Warning: the command libtool uses to detect shared libraries, *** $file_magic_cmd, produces output that libtool cannot recognize. *** The result is that libtool may fail to recognize shared libraries *** as such. This will affect the creation of libtool libraries that *** depend on shared libraries, but programs linked with such libtool *** libraries will work regardless of this problem. Nevertheless, you *** may want to report the problem to your system manager and/or to *** bug-libtool@gnu.org EOF fi ;; esac fi break fi done IFS="$lt_save_ifs" MAGIC_CMD="$lt_save_MAGIC_CMD" ;; esac fi MAGIC_CMD="$lt_cv_path_MAGIC_CMD" if test -n "$MAGIC_CMD"; then echo "$as_me:$LINENO: result: $MAGIC_CMD" >&5 echo "${ECHO_T}$MAGIC_CMD" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi if test -z "$lt_cv_path_MAGIC_CMD"; then if test -n "$ac_tool_prefix"; then echo "$as_me:$LINENO: checking for file" >&5 echo $ECHO_N "checking for file... $ECHO_C" >&6 if test "${lt_cv_path_MAGIC_CMD+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else 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=$PATH_SEPARATOR ac_dummy="/usr/bin$PATH_SEPARATOR$PATH" for ac_dir in $ac_dummy; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. if test -f $ac_dir/file; then lt_cv_path_MAGIC_CMD="$ac_dir/file" 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 <&2 *** Warning: the command libtool uses to detect shared libraries, *** $file_magic_cmd, produces output that libtool cannot recognize. *** The result is that libtool may fail to recognize shared libraries *** as such. This will affect the creation of libtool libraries that *** depend on shared libraries, but programs linked with such libtool *** libraries will work regardless of this problem. 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Therefore, libtool *** is disabling shared libraries support. We urge you to upgrade GNU *** binutils to release 2.9.1 or newer. Another option is to modify *** your PATH or compiler configuration so that the native linker is *** used, and then restart. 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} && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/; p; } }'` # Check for a 64-bit object if we didn't find anything. if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/; p; } }'`; fi else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f conftest.err conftest.$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 $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then echo "${wl}${allow_undefined_flag}"; else :; fi` '"\${wl}$no_entry_flag \${wl}$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 $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$no_entry_flag \${wl}$exp_sym_flag:\$export_symbols" else # Determine the default libpath from the value encoded in an empty executable. cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/; p; } }'` # Check for a 64-bit object if we didn't find anything. if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/; p; } }'`; fi else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f conftest.err conftest.$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' # -bexpall does not export symbols beginning with underscore (_) always_export_symbols=yes # Exported symbols can be pulled into shared objects from archives whole_archive_flag_spec=' ' archive_cmds_need_lc=yes # This is similar to how AIX traditionally builds it's shared libraries. archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs $compiler_flags ${wl}-bE:$export_symbols ${wl}-bnoentry${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' fi fi ;; amigaos*) 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 # see comment about different semantics on the GNU ld section ld_shlibs=no ;; bsdi4*) export_dynamic_flag_spec=-rdynamic ;; cygwin* | mingw* | pw32*) # 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 $compiler_flags `echo "$deplibs" | $SED -e '\''s/ -lc$//'\''` -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*) if test "$GXX" = yes ; then archive_cmds_need_lc=no case "$host_os" in rhapsody* | darwin1.[012]) allow_undefined_flag='-undefined suppress' ;; *) # Darwin 1.3 on if test -z ${MACOSX_DEPLOYMENT_TARGET} ; then allow_undefined_flag='-flat_namespace -undefined suppress' else case ${MACOSX_DEPLOYMENT_TARGET} in 10.[012]) allow_undefined_flag='-flat_namespace -undefined suppress' ;; 10.*) allow_undefined_flag='-undefined dynamic_lookup' ;; esac fi ;; esac lt_int_apple_cc_single_mod=no output_verbose_link_cmd='echo' if $CC -dumpspecs 2>&1 | grep 'single_module' >/dev/null ; then lt_int_apple_cc_single_mod=yes fi if test "X$lt_int_apple_cc_single_mod" = Xyes ; then archive_cmds='$CC -dynamiclib -single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring' else archive_cmds='$CC -r ${wl}-bind_at_load -keep_private_externs -nostdlib -o ${lib}-master.o $libobjs~$CC -dynamiclib $allow_undefined_flag -o $lib ${lib}-master.o $deplibs $compiler_flags -install_name $rpath/$soname $verstring' fi module_cmds='$CC ${wl}-bind_at_load $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags' # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin ld's if test "X$lt_int_apple_cc_single_mod" = Xyes ; then archive_expsym_cmds='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -dynamiclib -single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' else archive_expsym_cmds='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -r ${wl}-bind_at_load -keep_private_externs -nostdlib -o ${lib}-master.o $libobjs~$CC -dynamiclib $allow_undefined_flag -o $lib ${lib}-master.o $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' fi module_expsym_cmds='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' hardcode_direct=no hardcode_automatic=yes hardcode_shlibpath_var=unsupported whole_archive_flag_spec='-all_load $convenience' link_all_deplibs=yes else ld_shlibs=no fi ;; dgux*) archive_cmds='$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. 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hpux10* | hpux11*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then case "$host_cpu" in hppa*64*|ia64*) archive_cmds='$CC -shared ${wl}+h ${wl}$soname -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*|ia64*) archive_cmds='$LD -b +h $soname -o $lib $libobjs $deplibs $linker_flags' ;; *) archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' ;; esac fi if test "$with_gnu_ld" = no; then case "$host_cpu" in hppa*64*) hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_flag_spec_ld='+b $libdir' hardcode_libdir_separator=: hardcode_direct=no hardcode_shlibpath_var=no ;; ia64*) hardcode_libdir_flag_spec='-L$libdir' hardcode_direct=no hardcode_shlibpath_var=no # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes ;; *) hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: hardcode_direct=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 ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else archive_cmds='$LD -shared $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec_ld='-rpath $libdir' fi hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: link_all_deplibs=yes ;; netbsd*) 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 ;; openbsd*) hardcode_direct=yes hardcode_shlibpath_var=no 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 $compiler_flags' hardcode_libdir_flag_spec='${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,$libdir' ;; esac fi ;; os2*) hardcode_libdir_flag_spec='-L$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' ;; 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hpux9* | hpux10* | hpux11*) # Give a soname corresponding to the major version so that dld.sl refuses to # link against other versions. version_type=sunos need_lib_prefix=no need_version=no case "$host_cpu" in ia64*) shrext_cmds='.so' hardcode_into_libs=yes dynamic_linker="$host_os dld.so" shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' if test "X$HPUX_IA64_MODE" = X32; then sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib" else sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64" fi sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec ;; hppa*64*) shrext_cmds='.sl' hardcode_into_libs=yes dynamic_linker="$host_os dld.sl" shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64" sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec ;; *) shrext_cmds='.sl' dynamic_linker="$host_os dld.sl" shlibpath_var=SHLIB_PATH shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' ;; esac # HP-UX runs *really* slowly unless shared libraries are mode 555. postinstall_cmds='chmod 555 $lib' ;; irix5* | irix6* | nonstopux*) case $host_os in nonstopux*) version_type=nonstopux ;; *) if test "$lt_cv_prog_gnu_ld" = yes; then version_type=linux else version_type=irix fi ;; esac 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 ${libname}${release}${shared_ext} $libname${shared_ext}' case $host_os in irix5* | nonstopux*) libsuff= shlibsuff= ;; *) case $LD in # libtool.m4 will add one of these switches to LD *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ") libsuff= shlibsuff= libmagic=32-bit;; 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uts4*) version_type=linux library_names_spec='${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 echo "$as_me:$LINENO: result: $dynamic_linker" >&5 echo "${ECHO_T}$dynamic_linker" >&6 test "$dynamic_linker" = no && can_build_shared=no echo "$as_me:$LINENO: checking how to hardcode library paths into programs" >&5 echo $ECHO_N "checking how to hardcode library paths into programs... $ECHO_C" >&6 hardcode_action= if test -n "$hardcode_libdir_flag_spec" || \ test -n "$runpath_var " || \ test "X$hardcode_automatic"="Xyes" ; then # We can hardcode non-existant 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_AC_TAGVAR(hardcode_shlibpath_var, )" != no && test "$hardcode_minus_L" != no; then # Linking always hardcodes the temporary library directory. hardcode_action=relink else # We can link without hardcoding, and we can hardcode nonexisting dirs. hardcode_action=immediate fi else # We cannot hardcode anything, or else we can only hardcode existing # directories. hardcode_action=unsupported fi echo "$as_me:$LINENO: result: $hardcode_action" >&5 echo "${ECHO_T}$hardcode_action" >&6 if test "$hardcode_action" = relink; 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 striplib= old_striplib= echo "$as_me:$LINENO: checking whether stripping libraries is possible" >&5 echo $ECHO_N "checking whether stripping libraries is possible... $ECHO_C" >&6 if test -n "$STRIP" && $STRIP -V 2>&1 | grep "GNU strip" >/dev/null; then test -z "$old_striplib" && old_striplib="$STRIP --strip-debug" test -z "$striplib" && striplib="$STRIP --strip-unneeded" echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 else # FIXME - insert some real tests, host_os isn't really good enough case $host_os in darwin*) if test -n "$STRIP" ; then striplib="$STRIP -x" echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi ;; *) echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 ;; esac 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 $host_os in beos*) lt_cv_dlopen="load_add_on" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes ;; mingw* | pw32*) lt_cv_dlopen="LoadLibrary" lt_cv_dlopen_libs= ;; cygwin*) lt_cv_dlopen="dlopen" lt_cv_dlopen_libs= ;; darwin*) # if libdl is installed we need to link against it echo "$as_me:$LINENO: checking for dlopen in -ldl" >&5 echo $ECHO_N "checking for dlopen in -ldl... $ECHO_C" >&6 if test "${ac_cv_lib_dl_dlopen+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldl $LIBS" cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char dlopen (); int main () { dlopen (); ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_lib_dl_dlopen=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_lib_dl_dlopen=no fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi echo "$as_me:$LINENO: result: $ac_cv_lib_dl_dlopen" >&5 echo "${ECHO_T}$ac_cv_lib_dl_dlopen" >&6 if test $ac_cv_lib_dl_dlopen = yes; then lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl" else lt_cv_dlopen="dyld" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes fi ;; *) echo "$as_me:$LINENO: checking for shl_load" >&5 echo $ECHO_N "checking for shl_load... $ECHO_C" >&6 if test "${ac_cv_func_shl_load+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Define shl_load to an innocuous variant, in case declares shl_load. For example, HP-UX 11i declares gettimeofday. */ #define shl_load innocuous_shl_load /* System header to define __stub macros and hopefully few prototypes, which can conflict with char shl_load (); below. Prefer to if __STDC__ is defined, since exists even on freestanding compilers. */ #ifdef __STDC__ # include #else # include #endif #undef shl_load /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char shl_load (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ #if defined (__stub_shl_load) || defined (__stub___shl_load) choke me #else char (*f) () = shl_load; #endif #ifdef __cplusplus } #endif int main () { return f != shl_load; ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_func_shl_load=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_func_shl_load=no fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext fi echo "$as_me:$LINENO: result: $ac_cv_func_shl_load" >&5 echo "${ECHO_T}$ac_cv_func_shl_load" >&6 if test $ac_cv_func_shl_load = yes; then lt_cv_dlopen="shl_load" else echo "$as_me:$LINENO: checking for shl_load in -ldld" >&5 echo $ECHO_N "checking for shl_load in -ldld... $ECHO_C" >&6 if test "${ac_cv_lib_dld_shl_load+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldld $LIBS" cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char shl_load (); int main () { shl_load (); ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_lib_dld_shl_load=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_lib_dld_shl_load=no fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi echo "$as_me:$LINENO: result: $ac_cv_lib_dld_shl_load" >&5 echo "${ECHO_T}$ac_cv_lib_dld_shl_load" >&6 if test $ac_cv_lib_dld_shl_load = yes; then lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-dld" else echo "$as_me:$LINENO: checking for dlopen" >&5 echo $ECHO_N "checking for dlopen... $ECHO_C" >&6 if test "${ac_cv_func_dlopen+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Define dlopen to an innocuous variant, in case declares dlopen. For example, HP-UX 11i declares gettimeofday. */ #define dlopen innocuous_dlopen /* System header to define __stub macros and hopefully few prototypes, which can conflict with char dlopen (); below. Prefer to if __STDC__ is defined, since exists even on freestanding compilers. */ #ifdef __STDC__ # include #else # include #endif #undef dlopen /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char dlopen (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ #if defined (__stub_dlopen) || defined (__stub___dlopen) choke me #else char (*f) () = dlopen; #endif #ifdef __cplusplus } #endif int main () { return f != dlopen; ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_func_dlopen=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_func_dlopen=no fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext fi echo "$as_me:$LINENO: result: $ac_cv_func_dlopen" >&5 echo "${ECHO_T}$ac_cv_func_dlopen" >&6 if test $ac_cv_func_dlopen = yes; then lt_cv_dlopen="dlopen" else echo "$as_me:$LINENO: checking for dlopen in -ldl" >&5 echo $ECHO_N "checking for dlopen in -ldl... $ECHO_C" >&6 if test "${ac_cv_lib_dl_dlopen+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldl $LIBS" cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char dlopen (); int main () { dlopen (); ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? 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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 | sysv4.2uw2* | sysv4.3* | sysv5*) 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 $host_vendor in sni) shlibpath_overrides_runpath=no need_lib_prefix=no export_dynamic_flag_spec='${wl}-Blargedynsym' 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}.$major' shlibpath_var=LD_LIBRARY_PATH fi ;; uts4*) version_type=linux library_names_spec='${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 echo "$as_me:$LINENO: result: $dynamic_linker" >&5 echo "${ECHO_T}$dynamic_linker" >&6 test "$dynamic_linker" = no && can_build_shared=no echo "$as_me:$LINENO: checking how to hardcode library paths into programs" >&5 echo $ECHO_N "checking how to hardcode library paths into programs... $ECHO_C" >&6 hardcode_action_CXX= if test -n "$hardcode_libdir_flag_spec_CXX" || \ test -n "$runpath_var CXX" || \ test "X$hardcode_automatic_CXX"="Xyes" ; then # We can hardcode non-existant directories. if test "$hardcode_direct_CXX" != no && # If the only mechanism to avoid hardcoding is shlibpath_var, we # have to relink, otherwise we might link with an installed library # when we should be linking with a yet-to-be-installed one ## test "$_LT_AC_TAGVAR(hardcode_shlibpath_var, CXX)" != no && test "$hardcode_minus_L_CXX" != no; then # Linking always hardcodes the temporary library directory. hardcode_action_CXX=relink else # We can link without hardcoding, and we can hardcode nonexisting dirs. hardcode_action_CXX=immediate fi else # We cannot hardcode anything, or else we can only hardcode existing # directories. hardcode_action_CXX=unsupported fi echo "$as_me:$LINENO: result: $hardcode_action_CXX" >&5 echo "${ECHO_T}$hardcode_action_CXX" >&6 if test "$hardcode_action_CXX" = relink; 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 striplib= old_striplib= echo "$as_me:$LINENO: checking whether stripping libraries is possible" >&5 echo $ECHO_N "checking whether stripping libraries is possible... $ECHO_C" >&6 if test -n "$STRIP" && $STRIP -V 2>&1 | grep "GNU strip" >/dev/null; then test -z "$old_striplib" && old_striplib="$STRIP --strip-debug" test -z "$striplib" && striplib="$STRIP --strip-unneeded" echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 else # FIXME - insert some real tests, host_os isn't really good enough case $host_os in darwin*) if test -n "$STRIP" ; then striplib="$STRIP -x" echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi ;; *) echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 ;; esac 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 $host_os in beos*) lt_cv_dlopen="load_add_on" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes ;; mingw* | pw32*) lt_cv_dlopen="LoadLibrary" lt_cv_dlopen_libs= ;; cygwin*) lt_cv_dlopen="dlopen" lt_cv_dlopen_libs= ;; darwin*) # if libdl is installed we need to link against it echo "$as_me:$LINENO: checking for dlopen in -ldl" >&5 echo $ECHO_N "checking for dlopen in -ldl... $ECHO_C" >&6 if test "${ac_cv_lib_dl_dlopen+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldl $LIBS" cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char dlopen (); int main () { dlopen (); ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_cxx_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_lib_dl_dlopen=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_lib_dl_dlopen=no fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi echo "$as_me:$LINENO: result: $ac_cv_lib_dl_dlopen" >&5 echo "${ECHO_T}$ac_cv_lib_dl_dlopen" >&6 if test $ac_cv_lib_dl_dlopen = yes; then lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl" else lt_cv_dlopen="dyld" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes fi ;; *) echo "$as_me:$LINENO: checking for shl_load" >&5 echo $ECHO_N "checking for shl_load... $ECHO_C" >&6 if test "${ac_cv_func_shl_load+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Define shl_load to an innocuous variant, in case declares shl_load. For example, HP-UX 11i declares gettimeofday. */ #define shl_load innocuous_shl_load /* System header to define __stub macros and hopefully few prototypes, which can conflict with char shl_load (); below. Prefer to if __STDC__ is defined, since exists even on freestanding compilers. */ #ifdef __STDC__ # include #else # include #endif #undef shl_load /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char shl_load (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ #if defined (__stub_shl_load) || defined (__stub___shl_load) choke me #else char (*f) () = shl_load; #endif #ifdef __cplusplus } #endif int main () { return f != shl_load; ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_cxx_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_func_shl_load=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_func_shl_load=no fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext fi echo "$as_me:$LINENO: result: $ac_cv_func_shl_load" >&5 echo "${ECHO_T}$ac_cv_func_shl_load" >&6 if test $ac_cv_func_shl_load = yes; then lt_cv_dlopen="shl_load" else echo "$as_me:$LINENO: checking for shl_load in -ldld" >&5 echo $ECHO_N "checking for shl_load in -ldld... $ECHO_C" >&6 if test "${ac_cv_lib_dld_shl_load+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldld $LIBS" cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char shl_load (); int main () { shl_load (); ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_cxx_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_lib_dld_shl_load=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_lib_dld_shl_load=no fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi echo "$as_me:$LINENO: result: $ac_cv_lib_dld_shl_load" >&5 echo "${ECHO_T}$ac_cv_lib_dld_shl_load" >&6 if test $ac_cv_lib_dld_shl_load = yes; then lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-dld" else echo "$as_me:$LINENO: checking for dlopen" >&5 echo $ECHO_N "checking for dlopen... $ECHO_C" >&6 if test "${ac_cv_func_dlopen+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Define dlopen to an innocuous variant, in case declares dlopen. For example, HP-UX 11i declares gettimeofday. */ #define dlopen innocuous_dlopen /* System header to define __stub macros and hopefully few prototypes, which can conflict with char dlopen (); below. Prefer to if __STDC__ is defined, since exists even on freestanding compilers. */ #ifdef __STDC__ # include #else # include #endif #undef dlopen /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char dlopen (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ #if defined (__stub_dlopen) || defined (__stub___dlopen) choke me #else char (*f) () = dlopen; #endif #ifdef __cplusplus } #endif int main () { return f != dlopen; ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_cxx_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_func_dlopen=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_func_dlopen=no fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext fi echo "$as_me:$LINENO: result: $ac_cv_func_dlopen" >&5 echo "${ECHO_T}$ac_cv_func_dlopen" >&6 if test $ac_cv_func_dlopen = yes; then lt_cv_dlopen="dlopen" else echo "$as_me:$LINENO: checking for dlopen in -ldl" >&5 echo $ECHO_N "checking for dlopen in -ldl... $ECHO_C" >&6 if test "${ac_cv_lib_dl_dlopen+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldl $LIBS" cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char dlopen (); int main () { dlopen (); ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? 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FIXME archive_cmds_F77='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' else ld_shlibs_F77=no fi ;; cygwin* | mingw* | pw32*) # _LT_AC_TAGVAR(hardcode_libdir_flag_spec, F77) is actually meaningless, # as there is no search path for DLLs. hardcode_libdir_flag_spec_F77='-L$libdir' allow_undefined_flag_F77=unsupported always_export_symbols_F77=no enable_shared_with_static_runtimes_F77=yes export_symbols_cmds_F77='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGS] /s/.* \([^ ]*\)/\1 DATA/'\'' | $SED -e '\''/^[AITW] /s/.* //'\'' | sort | uniq > $export_symbols' if $LD --help 2>&1 | grep 'auto-import' > /dev/null; then archive_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--image-base=0x10000000 ${wl}--out-implib,$lib' # If the export-symbols file already is a .def file (1st line # is EXPORTS), use it as is; otherwise, prepend... archive_expsym_cmds_F77='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then cp $export_symbols $output_objdir/$soname.def; else echo EXPORTS > $output_objdir/$soname.def; cat $export_symbols >> $output_objdir/$soname.def; fi~ $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--image-base=0x10000000 ${wl}--out-implib,$lib' else ld_shlibs=no fi ;; netbsd*) if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then archive_cmds_F77='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib' wlarc= else archive_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' fi ;; solaris* | sysv5*) if $LD -v 2>&1 | grep 'BFD 2\.8' > /dev/null; then ld_shlibs_F77=no cat <&2 *** Warning: The releases 2.8.* of the GNU linker cannot reliably *** create shared libraries on Solaris systems. Therefore, libtool *** is disabling shared libraries support. We urge you to upgrade GNU *** binutils to release 2.9.1 or newer. Another option is to modify *** your PATH or compiler configuration so that the native linker is *** used, and then restart. EOF elif $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then archive_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else ld_shlibs_F77=no fi ;; sunos4*) archive_cmds_F77='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags' wlarc= hardcode_direct_F77=yes hardcode_shlibpath_var_F77=no ;; linux*) if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then tmp_archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_cmds_F77="$tmp_archive_cmds" supports_anon_versioning=no case `$LD -v 2>/dev/null` in *\ 01.* | *\ 2.[0-9].* | *\ 2.10.*) ;; # catch versions < 2.11 *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ... *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ... *\ 2.11.*) ;; # other 2.11 versions *) supports_anon_versioning=yes ;; esac if test $supports_anon_versioning = yes; then archive_expsym_cmds_F77='$echo "{ global:" > $output_objdir/$libname.ver~ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ $echo "local: *; };" >> $output_objdir/$libname.ver~ $CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib' else archive_expsym_cmds_F77="$tmp_archive_cmds" fi else ld_shlibs_F77=no fi ;; *) if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then archive_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else ld_shlibs_F77=no fi ;; esac if test "$ld_shlibs_F77" = yes; then runpath_var=LD_RUN_PATH hardcode_libdir_flag_spec_F77='${wl}--rpath ${wl}$libdir' export_dynamic_flag_spec_F77='${wl}--export-dynamic' # ancient GNU ld didn't support --whole-archive et. al. if $LD --help 2>&1 | grep 'no-whole-archive' > /dev/null; then whole_archive_flag_spec_F77="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive' else whole_archive_flag_spec_F77= fi fi else # PORTME fill in a description of your system's linker (not GNU ld) case $host_os in aix3*) allow_undefined_flag_F77=unsupported always_export_symbols_F77=yes archive_expsym_cmds_F77='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname' # Note: this linker hardcodes the directories in LIBPATH if there # are no directories specified by -L. hardcode_minus_L_F77=yes if test "$GCC" = yes && test -z "$link_static_flag"; then # Neither direct hardcoding nor static linking is supported with a # broken collect2. hardcode_direct_F77=unsupported fi ;; aix4* | aix5*) if test "$host_cpu" = ia64; then # On IA64, the linker does run time linking by default, so we don't # have to do anything special. aix_use_runtimelinking=no exp_sym_flag='-Bexport' no_entry_flag="" else # If we're using GNU nm, then we don't want the "-C" option. # -C means demangle to AIX nm, but means don't demangle with GNU nm if $NM -V 2>&1 | grep 'GNU' > /dev/null; then export_symbols_cmds_F77='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$2 == "T") || (\$2 == "D") || (\$2 == "B")) && (substr(\$3,1,1) != ".")) { print \$3 } }'\'' | sort -u > $export_symbols' else export_symbols_cmds_F77='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$2 == "T") || (\$2 == "D") || (\$2 == "B")) && (substr(\$3,1,1) != ".")) { print \$3 } }'\'' | sort -u > $export_symbols' fi aix_use_runtimelinking=no # Test if we are trying to use run time linking or normal # AIX style linking. If -brtl is somewhere in LDFLAGS, we # need to do runtime linking. case $host_os in aix4.[23]|aix4.[23].*|aix5*) for ld_flag in $LDFLAGS; do if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then aix_use_runtimelinking=yes break fi done esac exp_sym_flag='-bexport' no_entry_flag='-bnoentry' fi # When large executables or shared objects are built, AIX ld can # have problems creating the table of contents. If linking a library # or program results in "error TOC overflow" add -mminimal-toc to # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS. archive_cmds_F77='' hardcode_direct_F77=yes hardcode_libdir_separator_F77=':' link_all_deplibs_F77=yes if test "$GCC" = yes; then case $host_os in aix4.012|aix4.012.*) # We only want to do this on AIX 4.2 and lower, the check # below for broken collect2 doesn't work under 4.3+ collect2name=`${CC} -print-prog-name=collect2` if test -f "$collect2name" && \ strings "$collect2name" | grep resolve_lib_name >/dev/null then # We have reworked collect2 hardcode_direct_F77=yes else # We have old collect2 hardcode_direct_F77=unsupported # It fails to find uninstalled libraries when the uninstalled # path is not listed in the libpath. Setting hardcode_minus_L # to unsupported forces relinking hardcode_minus_L_F77=yes hardcode_libdir_flag_spec_F77='-L$libdir' hardcode_libdir_separator_F77= fi esac shared_flag='-shared' else # not using gcc if test "$host_cpu" = ia64; then # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release # chokes on -Wl,-G. The following line is correct: shared_flag='-G' else if test "$aix_use_runtimelinking" = yes; then shared_flag='${wl}-G' else shared_flag='${wl}-bM:SRE' fi fi fi # It seems that -bexpall does not export symbols beginning with # underscore (_), so it is better to generate a list of symbols to export. always_export_symbols_F77=yes if test "$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_F77='-berok' # Determine the default libpath from the value encoded in an empty executable. cat >conftest.$ac_ext <<_ACEOF program main end _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_f77_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/; p; } }'` # Check for a 64-bit object if we didn't find anything. if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/; p; } }'`; fi else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi hardcode_libdir_flag_spec_F77='${wl}-blibpath:$libdir:'"$aix_libpath" archive_expsym_cmds_F77="\$CC"' -o $output_objdir/$soname $libobjs $deplibs $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then echo "${wl}${allow_undefined_flag}"; else :; fi` '"\${wl}$no_entry_flag \${wl}$exp_sym_flag:\$export_symbols $shared_flag" else if test "$host_cpu" = ia64; then hardcode_libdir_flag_spec_F77='${wl}-R $libdir:/usr/lib:/lib' allow_undefined_flag_F77="-z nodefs" archive_expsym_cmds_F77="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$no_entry_flag \${wl}$exp_sym_flag:\$export_symbols" else # Determine the default libpath from the value encoded in an empty executable. cat >conftest.$ac_ext <<_ACEOF program main end _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_f77_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/; p; } }'` # Check for a 64-bit object if we didn't find anything. if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/; p; } }'`; fi else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi hardcode_libdir_flag_spec_F77='${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_F77=' ${wl}-bernotok' allow_undefined_flag_F77=' ${wl}-berok' # -bexpall does not export symbols beginning with underscore (_) always_export_symbols_F77=yes # Exported symbols can be pulled into shared objects from archives whole_archive_flag_spec_F77=' ' archive_cmds_need_lc_F77=yes # This is similar to how AIX traditionally builds it's shared libraries. archive_expsym_cmds_F77="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs $compiler_flags ${wl}-bE:$export_symbols ${wl}-bnoentry${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' fi fi ;; amigaos*) archive_cmds_F77='$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 $output_objdir && a2ixlibrary -32)' hardcode_libdir_flag_spec_F77='-L$libdir' hardcode_minus_L_F77=yes # see comment about different semantics on the GNU ld section ld_shlibs_F77=no ;; bsdi4*) export_dynamic_flag_spec_F77=-rdynamic ;; cygwin* | mingw* | pw32*) # 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_F77=' ' allow_undefined_flag_F77=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_F77='$CC -o $lib $libobjs $compiler_flags `echo "$deplibs" | $SED -e '\''s/ -lc$//'\''` -link -dll~linknames=' # The linker will automatically build a .lib file if we build a DLL. old_archive_From_new_cmds_F77='true' # FIXME: Should let the user specify the lib program. old_archive_cmds_F77='lib /OUT:$oldlib$oldobjs$old_deplibs' fix_srcfile_path='`cygpath -w "$srcfile"`' enable_shared_with_static_runtimes_F77=yes ;; darwin* | rhapsody*) if test "$GXX" = yes ; then archive_cmds_need_lc_F77=no case "$host_os" in rhapsody* | darwin1.[012]) allow_undefined_flag_F77='-undefined suppress' ;; *) # Darwin 1.3 on if test -z ${MACOSX_DEPLOYMENT_TARGET} ; then allow_undefined_flag_F77='-flat_namespace -undefined suppress' else case ${MACOSX_DEPLOYMENT_TARGET} in 10.[012]) allow_undefined_flag_F77='-flat_namespace -undefined suppress' ;; 10.*) allow_undefined_flag_F77='-undefined dynamic_lookup' ;; esac fi ;; esac lt_int_apple_cc_single_mod=no output_verbose_link_cmd='echo' if $CC -dumpspecs 2>&1 | grep 'single_module' >/dev/null ; then lt_int_apple_cc_single_mod=yes fi if test "X$lt_int_apple_cc_single_mod" = Xyes ; then archive_cmds_F77='$CC -dynamiclib -single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring' else archive_cmds_F77='$CC -r ${wl}-bind_at_load -keep_private_externs -nostdlib -o ${lib}-master.o $libobjs~$CC -dynamiclib $allow_undefined_flag -o $lib ${lib}-master.o $deplibs $compiler_flags -install_name $rpath/$soname $verstring' fi module_cmds_F77='$CC ${wl}-bind_at_load $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags' # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin ld's if test "X$lt_int_apple_cc_single_mod" = Xyes ; then archive_expsym_cmds_F77='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -dynamiclib -single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' else archive_expsym_cmds_F77='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -r ${wl}-bind_at_load -keep_private_externs -nostdlib -o ${lib}-master.o $libobjs~$CC -dynamiclib $allow_undefined_flag -o $lib ${lib}-master.o $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' fi module_expsym_cmds_F77='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' hardcode_direct_F77=no hardcode_automatic_F77=yes hardcode_shlibpath_var_F77=unsupported whole_archive_flag_spec_F77='-all_load $convenience' link_all_deplibs_F77=yes else ld_shlibs_F77=no fi ;; dgux*) archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec_F77='-L$libdir' hardcode_shlibpath_var_F77=no ;; freebsd1*) ld_shlibs_F77=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_F77='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o' hardcode_libdir_flag_spec_F77='-R$libdir' hardcode_direct_F77=yes hardcode_shlibpath_var_F77=no ;; # Unfortunately, older versions of FreeBSD 2 do not have this feature. freebsd2*) archive_cmds_F77='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_F77=yes hardcode_minus_L_F77=yes hardcode_shlibpath_var_F77=no ;; # FreeBSD 3 and greater uses gcc -shared to do shared libraries. freebsd* | kfreebsd*-gnu) archive_cmds_F77='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec_F77='-R$libdir' hardcode_direct_F77=yes hardcode_shlibpath_var_F77=no ;; hpux9*) if test "$GCC" = yes; then archive_cmds_F77='$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 $lib' else archive_cmds_F77='$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 $lib' fi hardcode_libdir_flag_spec_F77='${wl}+b ${wl}$libdir' hardcode_libdir_separator_F77=: hardcode_direct_F77=yes # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L_F77=yes export_dynamic_flag_spec_F77='${wl}-E' ;; hpux10* | hpux11*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then case "$host_cpu" in hppa*64*|ia64*) archive_cmds_F77='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds_F77='$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*|ia64*) archive_cmds_F77='$LD -b +h $soname -o $lib $libobjs $deplibs $linker_flags' ;; *) archive_cmds_F77='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' ;; esac fi if test "$with_gnu_ld" = no; then case "$host_cpu" in hppa*64*) hardcode_libdir_flag_spec_F77='${wl}+b ${wl}$libdir' hardcode_libdir_flag_spec_ld_F77='+b $libdir' hardcode_libdir_separator_F77=: hardcode_direct_F77=no hardcode_shlibpath_var_F77=no ;; ia64*) hardcode_libdir_flag_spec_F77='-L$libdir' hardcode_direct_F77=no hardcode_shlibpath_var_F77=no # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L_F77=yes ;; *) hardcode_libdir_flag_spec_F77='${wl}+b ${wl}$libdir' hardcode_libdir_separator_F77=: hardcode_direct_F77=yes export_dynamic_flag_spec_F77='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L_F77=yes ;; esac fi ;; irix5* | irix6* | nonstopux*) if test "$GCC" = yes; then archive_cmds_F77='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else archive_cmds_F77='$LD -shared $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec_ld_F77='-rpath $libdir' fi hardcode_libdir_flag_spec_F77='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator_F77=: link_all_deplibs_F77=yes ;; netbsd*) if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then archive_cmds_F77='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out else archive_cmds_F77='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF fi hardcode_libdir_flag_spec_F77='-R$libdir' hardcode_direct_F77=yes hardcode_shlibpath_var_F77=no ;; newsos6) archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_F77=yes hardcode_libdir_flag_spec_F77='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator_F77=: hardcode_shlibpath_var_F77=no ;; openbsd*) hardcode_direct_F77=yes hardcode_shlibpath_var_F77=no if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then archive_cmds_F77='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec_F77='${wl}-rpath,$libdir' export_dynamic_flag_spec_F77='${wl}-E' else case $host_os in openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*) archive_cmds_F77='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec_F77='-R$libdir' ;; *) archive_cmds_F77='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec_F77='${wl}-rpath,$libdir' ;; esac fi ;; os2*) hardcode_libdir_flag_spec_F77='-L$libdir' hardcode_minus_L_F77=yes allow_undefined_flag_F77=unsupported archive_cmds_F77='$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_F77='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; osf3*) if test "$GCC" = yes; then allow_undefined_flag_F77=' ${wl}-expect_unresolved ${wl}\*' archive_cmds_F77='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else allow_undefined_flag_F77=' -expect_unresolved \*' archive_cmds_F77='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' fi hardcode_libdir_flag_spec_F77='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator_F77=: ;; osf4* | osf5*) # as osf3* with the addition of -msym flag if test "$GCC" = yes; then allow_undefined_flag_F77=' ${wl}-expect_unresolved ${wl}\*' archive_cmds_F77='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec_F77='${wl}-rpath ${wl}$libdir' else allow_undefined_flag_F77=' -expect_unresolved \*' archive_cmds_F77='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -msym -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds_F77='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; echo "-hidden">> $lib.exp~ $LD -shared${allow_undefined_flag} -input $lib.exp $linker_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${objdir}/so_locations -o $lib~$rm $lib.exp' # Both c and cxx compiler support -rpath directly hardcode_libdir_flag_spec_F77='-rpath $libdir' fi hardcode_libdir_separator_F77=: ;; sco3.2v5*) archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var_F77=no export_dynamic_flag_spec_F77='${wl}-Bexport' runpath_var=LD_RUN_PATH hardcode_runpath_var=yes ;; solaris*) no_undefined_flag_F77=' -z text' if test "$GCC" = yes; then archive_cmds_F77='$CC -shared ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds_F77='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~ $CC -shared ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$rm $lib.exp' else archive_cmds_F77='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' archive_expsym_cmds_F77='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; 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siemens) ## LD is ld it makes a PLAMLIB ## CC just makes a GrossModule. archive_cmds_F77='$LD -G -o $lib $libobjs $deplibs $linker_flags' reload_cmds_F77='$CC -r -o $output$reload_objs' hardcode_direct_F77=no ;; motorola) archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_F77=no #Motorola manual says yes, but my tests say they lie ;; esac runpath_var='LD_RUN_PATH' hardcode_shlibpath_var_F77=no ;; sysv4.3*) archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var_F77=no export_dynamic_flag_spec_F77='-Bexport' ;; sysv4*MP*) if test -d /usr/nec; then archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var_F77=no runpath_var=LD_RUN_PATH hardcode_runpath_var=yes ld_shlibs_F77=yes fi ;; sysv4.2uw2*) archive_cmds_F77='$LD -G -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_F77=yes hardcode_minus_L_F77=no hardcode_shlibpath_var_F77=no hardcode_runpath_var=yes runpath_var=LD_RUN_PATH ;; sysv5OpenUNIX8* | sysv5UnixWare7* | sysv5uw[78]* | unixware7*) no_undefined_flag_F77='${wl}-z ${wl}text' if test "$GCC" = yes; then archive_cmds_F77='$CC -shared ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds_F77='$CC -G ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' fi runpath_var='LD_RUN_PATH' hardcode_shlibpath_var_F77=no ;; sysv5*) no_undefined_flag_F77=' -z text' # $CC -shared without GNU ld will not create a library from C++ # object files and a static libstdc++, better avoid it by now archive_cmds_F77='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' archive_expsym_cmds_F77='$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 $lib.exp' hardcode_libdir_flag_spec_F77= hardcode_shlibpath_var_F77=no runpath_var='LD_RUN_PATH' ;; uts4*) archive_cmds_F77='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec_F77='-L$libdir' hardcode_shlibpath_var_F77=no ;; *) ld_shlibs_F77=no ;; esac fi echo "$as_me:$LINENO: result: $ld_shlibs_F77" >&5 echo "${ECHO_T}$ld_shlibs_F77" >&6 test "$ld_shlibs_F77" = no && can_build_shared=no variables_saved_for_relink="PATH $shlibpath_var $runpath_var" if test "$GCC" = yes; then variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH" fi # # Do we need to explicitly link libc? # case "x$archive_cmds_need_lc_F77" in x|xyes) # Assume -lc should be added archive_cmds_need_lc_F77=yes if test "$enable_shared" = yes && test "$GCC" = yes; then case $archive_cmds_F77 in *'~'*) # FIXME: we may have to deal with multi-command sequences. ;; '$CC '*) # Test whether the compiler implicitly links with -lc since on some # systems, -lgcc has to come before -lc. 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The import file would start with # the line `#! .'. This would cause the generated library to # depend on `.', always an invalid library. This was fixed in # development snapshots of GCC prior to 3.0. case $host_os in aix4 | aix4.[01] | aix4.[01].*) if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)' echo ' yes ' echo '#endif'; } | ${CC} -E - | grep yes > /dev/null; then : else can_build_shared=no fi ;; esac # AIX (on Power*) has no versioning support, so currently we can not hardcode correct # soname into executable. Probably we can add versioning support to # collect2, so additional links can be useful in future. if test "$aix_use_runtimelinking" = yes; then # If using run time linking (on AIX 4.2 or later) use lib.so # instead of lib.a to let people know that these are not # typical AIX shared libraries. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' else # We preserve .a as extension for shared libraries through AIX4.2 # and later when we are not doing run time linking. library_names_spec='${libname}${release}.a $libname.a' soname_spec='${libname}${release}${shared_ext}$major' fi shlibpath_var=LIBPATH fi ;; amigaos*) library_names_spec='$libname.ixlibrary $libname.a' # Create ${libname}_ixlibrary.a entries in /sys/libs. finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$echo "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $rm /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done' ;; beos*) library_names_spec='${libname}${shared_ext}' dynamic_linker="$host_os ld.so" shlibpath_var=LIBRARY_PATH ;; bsdi4*) version_type=linux 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 $libdir' shlibpath_var=LD_LIBRARY_PATH sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib" sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib" # the default ld.so.conf also contains /usr/contrib/lib and # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow # libtool to hard-code these into programs ;; cygwin* | mingw* | pw32*) version_type=windows shrext_cmds=".dll" need_version=no need_lib_prefix=no case $GCC,$host_os in yes,cygwin* | yes,mingw* | yes,pw32*) library_names_spec='$libname.dll.a' # DLL is installed to $(libdir)/../bin by postinstall_cmds postinstall_cmds='base_file=`basename \${file}`~ dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i;echo \$dlname'\''`~ dldir=$destdir/`dirname \$dlpath`~ test -d \$dldir || mkdir -p \$dldir~ $install_prog $dir/$dlname \$dldir/$dlname' postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~ dlpath=$dir/\$dldll~ $rm \$dlpath' shlibpath_overrides_runpath=yes case $host_os in cygwin*) # Cygwin DLLs use 'cyg' prefix rather than 'lib' soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}' sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib" ;; mingw*) # MinGW DLLs use traditional 'lib' prefix soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}' sys_lib_search_path_spec=`$CC -print-search-dirs | grep "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"` if echo "$sys_lib_search_path_spec" | grep ';[c-zC-Z]:/' >/dev/null; then # It is most probably a Windows format PATH printed by # mingw gcc, but we are running on Cygwin. Gcc prints its search # path with ; separators, and with drive letters. We can handle the # drive letters (cygwin fileutils understands them), so leave them, # especially as we might pass files found there to a mingw objdump, # which wouldn't understand a cygwinified path. Ahh. sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'` else sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"` fi ;; pw32*) # pw32 DLLs use 'pw' prefix rather than 'lib' library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/./-/g'`${versuffix}${shared_ext}' ;; esac ;; *) library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib' ;; esac dynamic_linker='Win32 ld.exe' # FIXME: first we should search . and the directory the executable is in shlibpath_var=PATH ;; darwin* | rhapsody*) dynamic_linker="$host_os dyld" version_type=darwin need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${versuffix}$shared_ext ${libname}${release}${major}$shared_ext ${libname}$shared_ext' soname_spec='${libname}${release}${major}$shared_ext' shlibpath_overrides_runpath=yes shlibpath_var=DYLD_LIBRARY_PATH shrext_cmds='$(test .$module = .yes && echo .so || echo .dylib)' # Apple's gcc prints 'gcc -print-search-dirs' doesn't operate the same. if test "$GCC" = yes; then sys_lib_search_path_spec=`$CC -print-search-dirs | tr "\n" "$PATH_SEPARATOR" | sed -e 's/libraries:/@libraries:/' | tr "@" "\n" | grep "^libraries:" | sed -e "s/^libraries://" -e "s,=/,/,g" -e "s,$PATH_SEPARATOR, ,g" -e "s,.*,& /lib /usr/lib /usr/local/lib,g"` else sys_lib_search_path_spec='/lib /usr/lib /usr/local/lib' fi sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib' ;; dgux*) 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 ;; freebsd1*) dynamic_linker=no ;; kfreebsd*-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='GNU ld.so' ;; 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*) shrext_cmds='.sl' dynamic_linker="$host_os dld.sl" shlibpath_var=SHLIB_PATH shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' ;; esac # HP-UX runs *really* slowly unless shared libraries are mode 555. postinstall_cmds='chmod 555 $lib' ;; irix5* | irix6* | nonstopux*) case $host_os in nonstopux*) version_type=nonstopux ;; *) if test "$lt_cv_prog_gnu_ld" = yes; then version_type=linux else version_type=irix fi ;; esac 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 ${libname}${release}${shared_ext} $libname${shared_ext}' case $host_os in irix5* | nonstopux*) libsuff= shlibsuff= ;; *) case $LD in # libtool.m4 will add one of these switches to LD *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ") libsuff= shlibsuff= libmagic=32-bit;; 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FIXME archive_cmds_GCJ='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' else ld_shlibs_GCJ=no fi ;; cygwin* | mingw* | pw32*) # _LT_AC_TAGVAR(hardcode_libdir_flag_spec, GCJ) is actually meaningless, # as there is no search path for DLLs. hardcode_libdir_flag_spec_GCJ='-L$libdir' allow_undefined_flag_GCJ=unsupported always_export_symbols_GCJ=no enable_shared_with_static_runtimes_GCJ=yes export_symbols_cmds_GCJ='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGS] /s/.* \([^ ]*\)/\1 DATA/'\'' | $SED -e '\''/^[AITW] /s/.* //'\'' | sort | uniq > $export_symbols' if $LD --help 2>&1 | grep 'auto-import' > /dev/null; then archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--image-base=0x10000000 ${wl}--out-implib,$lib' # If the export-symbols file already is a .def file (1st line # is EXPORTS), use it as is; otherwise, prepend... archive_expsym_cmds_GCJ='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then cp $export_symbols $output_objdir/$soname.def; else echo EXPORTS > $output_objdir/$soname.def; cat $export_symbols >> $output_objdir/$soname.def; fi~ $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--image-base=0x10000000 ${wl}--out-implib,$lib' else ld_shlibs=no fi ;; netbsd*) if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then archive_cmds_GCJ='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib' wlarc= else archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' fi ;; solaris* | sysv5*) if $LD -v 2>&1 | grep 'BFD 2\.8' > /dev/null; then ld_shlibs_GCJ=no cat <&2 *** Warning: The releases 2.8.* of the GNU linker cannot reliably *** create shared libraries on Solaris systems. Therefore, libtool *** is disabling shared libraries support. We urge you to upgrade GNU *** binutils to release 2.9.1 or newer. Another option is to modify *** your PATH or compiler configuration so that the native linker is *** used, and then restart. EOF elif $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else ld_shlibs_GCJ=no fi ;; sunos4*) archive_cmds_GCJ='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags' wlarc= hardcode_direct_GCJ=yes hardcode_shlibpath_var_GCJ=no ;; linux*) if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then tmp_archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_cmds_GCJ="$tmp_archive_cmds" supports_anon_versioning=no case `$LD -v 2>/dev/null` in *\ 01.* | *\ 2.[0-9].* | *\ 2.10.*) ;; # catch versions < 2.11 *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ... *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ... *\ 2.11.*) ;; # other 2.11 versions *) supports_anon_versioning=yes ;; esac if test $supports_anon_versioning = yes; then archive_expsym_cmds_GCJ='$echo "{ global:" > $output_objdir/$libname.ver~ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ $echo "local: *; };" >> $output_objdir/$libname.ver~ $CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib' else archive_expsym_cmds_GCJ="$tmp_archive_cmds" fi else ld_shlibs_GCJ=no fi ;; *) if $LD --help 2>&1 | grep ': supported targets:.* elf' > /dev/null; then archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else ld_shlibs_GCJ=no fi ;; esac if test "$ld_shlibs_GCJ" = yes; then runpath_var=LD_RUN_PATH hardcode_libdir_flag_spec_GCJ='${wl}--rpath ${wl}$libdir' export_dynamic_flag_spec_GCJ='${wl}--export-dynamic' # ancient GNU ld didn't support --whole-archive et. al. if $LD --help 2>&1 | grep 'no-whole-archive' > /dev/null; then whole_archive_flag_spec_GCJ="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive' else whole_archive_flag_spec_GCJ= fi fi else # PORTME fill in a description of your system's linker (not GNU ld) case $host_os in aix3*) allow_undefined_flag_GCJ=unsupported always_export_symbols_GCJ=yes archive_expsym_cmds_GCJ='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname' # Note: this linker hardcodes the directories in LIBPATH if there # are no directories specified by -L. hardcode_minus_L_GCJ=yes if test "$GCC" = yes && test -z "$link_static_flag"; then # Neither direct hardcoding nor static linking is supported with a # broken collect2. hardcode_direct_GCJ=unsupported fi ;; aix4* | aix5*) if test "$host_cpu" = ia64; then # On IA64, the linker does run time linking by default, so we don't # have to do anything special. aix_use_runtimelinking=no exp_sym_flag='-Bexport' no_entry_flag="" else # If we're using GNU nm, then we don't want the "-C" option. # -C means demangle to AIX nm, but means don't demangle with GNU nm if $NM -V 2>&1 | grep 'GNU' > /dev/null; then export_symbols_cmds_GCJ='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$2 == "T") || (\$2 == "D") || (\$2 == "B")) && (substr(\$3,1,1) != ".")) { print \$3 } }'\'' | sort -u > $export_symbols' else export_symbols_cmds_GCJ='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$2 == "T") || (\$2 == "D") || (\$2 == "B")) && (substr(\$3,1,1) != ".")) { print \$3 } }'\'' | sort -u > $export_symbols' fi aix_use_runtimelinking=no # Test if we are trying to use run time linking or normal # AIX style linking. If -brtl is somewhere in LDFLAGS, we # need to do runtime linking. case $host_os in aix4.[23]|aix4.[23].*|aix5*) for ld_flag in $LDFLAGS; do if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then aix_use_runtimelinking=yes break fi done esac exp_sym_flag='-bexport' no_entry_flag='-bnoentry' fi # When large executables or shared objects are built, AIX ld can # have problems creating the table of contents. If linking a library # or program results in "error TOC overflow" add -mminimal-toc to # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS. archive_cmds_GCJ='' hardcode_direct_GCJ=yes hardcode_libdir_separator_GCJ=':' link_all_deplibs_GCJ=yes if test "$GCC" = yes; then case $host_os in aix4.012|aix4.012.*) # We only want to do this on AIX 4.2 and lower, the check # below for broken collect2 doesn't work under 4.3+ collect2name=`${CC} -print-prog-name=collect2` if test -f "$collect2name" && \ strings "$collect2name" | grep resolve_lib_name >/dev/null then # We have reworked collect2 hardcode_direct_GCJ=yes else # We have old collect2 hardcode_direct_GCJ=unsupported # It fails to find uninstalled libraries when the uninstalled # path is not listed in the libpath. Setting hardcode_minus_L # to unsupported forces relinking hardcode_minus_L_GCJ=yes hardcode_libdir_flag_spec_GCJ='-L$libdir' hardcode_libdir_separator_GCJ= fi esac shared_flag='-shared' else # not using gcc if test "$host_cpu" = ia64; then # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release # chokes on -Wl,-G. The following line is correct: shared_flag='-G' else if test "$aix_use_runtimelinking" = yes; then shared_flag='${wl}-G' else shared_flag='${wl}-bM:SRE' fi fi fi # It seems that -bexpall does not export symbols beginning with # underscore (_), so it is better to generate a list of symbols to export. always_export_symbols_GCJ=yes if test "$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_GCJ='-berok' # Determine the default libpath from the value encoded in an empty executable. cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/; p; } }'` # Check for a 64-bit object if we didn't find anything. if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/; p; } }'`; fi else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi hardcode_libdir_flag_spec_GCJ='${wl}-blibpath:$libdir:'"$aix_libpath" archive_expsym_cmds_GCJ="\$CC"' -o $output_objdir/$soname $libobjs $deplibs $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then echo "${wl}${allow_undefined_flag}"; else :; fi` '"\${wl}$no_entry_flag \${wl}$exp_sym_flag:\$export_symbols $shared_flag" else if test "$host_cpu" = ia64; then hardcode_libdir_flag_spec_GCJ='${wl}-R $libdir:/usr/lib:/lib' allow_undefined_flag_GCJ="-z nodefs" archive_expsym_cmds_GCJ="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$no_entry_flag \${wl}$exp_sym_flag:\$export_symbols" else # Determine the default libpath from the value encoded in an empty executable. cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/; p; } }'` # Check for a 64-bit object if we didn't find anything. if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e '/Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/; p; } }'`; fi else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi hardcode_libdir_flag_spec_GCJ='${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_GCJ=' ${wl}-bernotok' allow_undefined_flag_GCJ=' ${wl}-berok' # -bexpall does not export symbols beginning with underscore (_) always_export_symbols_GCJ=yes # Exported symbols can be pulled into shared objects from archives whole_archive_flag_spec_GCJ=' ' archive_cmds_need_lc_GCJ=yes # This is similar to how AIX traditionally builds it's shared libraries. archive_expsym_cmds_GCJ="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs $compiler_flags ${wl}-bE:$export_symbols ${wl}-bnoentry${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' fi fi ;; amigaos*) archive_cmds_GCJ='$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 $output_objdir && a2ixlibrary -32)' hardcode_libdir_flag_spec_GCJ='-L$libdir' hardcode_minus_L_GCJ=yes # see comment about different semantics on the GNU ld section ld_shlibs_GCJ=no ;; bsdi4*) export_dynamic_flag_spec_GCJ=-rdynamic ;; cygwin* | mingw* | pw32*) # 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_GCJ=' ' allow_undefined_flag_GCJ=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_GCJ='$CC -o $lib $libobjs $compiler_flags `echo "$deplibs" | $SED -e '\''s/ -lc$//'\''` -link -dll~linknames=' # The linker will automatically build a .lib file if we build a DLL. old_archive_From_new_cmds_GCJ='true' # FIXME: Should let the user specify the lib program. old_archive_cmds_GCJ='lib /OUT:$oldlib$oldobjs$old_deplibs' fix_srcfile_path='`cygpath -w "$srcfile"`' enable_shared_with_static_runtimes_GCJ=yes ;; darwin* | rhapsody*) if test "$GXX" = yes ; then archive_cmds_need_lc_GCJ=no case "$host_os" in rhapsody* | darwin1.[012]) allow_undefined_flag_GCJ='-undefined suppress' ;; *) # Darwin 1.3 on if test -z ${MACOSX_DEPLOYMENT_TARGET} ; then allow_undefined_flag_GCJ='-flat_namespace -undefined suppress' else case ${MACOSX_DEPLOYMENT_TARGET} in 10.[012]) allow_undefined_flag_GCJ='-flat_namespace -undefined suppress' ;; 10.*) allow_undefined_flag_GCJ='-undefined dynamic_lookup' ;; esac fi ;; esac lt_int_apple_cc_single_mod=no output_verbose_link_cmd='echo' if $CC -dumpspecs 2>&1 | grep 'single_module' >/dev/null ; then lt_int_apple_cc_single_mod=yes fi if test "X$lt_int_apple_cc_single_mod" = Xyes ; then archive_cmds_GCJ='$CC -dynamiclib -single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring' else archive_cmds_GCJ='$CC -r ${wl}-bind_at_load -keep_private_externs -nostdlib -o ${lib}-master.o $libobjs~$CC -dynamiclib $allow_undefined_flag -o $lib ${lib}-master.o $deplibs $compiler_flags -install_name $rpath/$soname $verstring' fi module_cmds_GCJ='$CC ${wl}-bind_at_load $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags' # Don't fix this by using the ld -exported_symbols_list flag, it doesn't exist in older darwin ld's if test "X$lt_int_apple_cc_single_mod" = Xyes ; then archive_expsym_cmds_GCJ='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -dynamiclib -single_module $allow_undefined_flag -o $lib $libobjs $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' else archive_expsym_cmds_GCJ='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC -r ${wl}-bind_at_load -keep_private_externs -nostdlib -o ${lib}-master.o $libobjs~$CC -dynamiclib $allow_undefined_flag -o $lib ${lib}-master.o $deplibs $compiler_flags -install_name $rpath/$soname $verstring~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' fi module_expsym_cmds_GCJ='sed -e "s,#.*,," -e "s,^[ ]*,," -e "s,^\(..*\),_&," < $export_symbols > $output_objdir/${libname}-symbols.expsym~$CC $allow_undefined_flag -o $lib -bundle $libobjs $deplibs$compiler_flags~nmedit -s $output_objdir/${libname}-symbols.expsym ${lib}' hardcode_direct_GCJ=no hardcode_automatic_GCJ=yes hardcode_shlibpath_var_GCJ=unsupported whole_archive_flag_spec_GCJ='-all_load $convenience' link_all_deplibs_GCJ=yes else ld_shlibs_GCJ=no fi ;; dgux*) archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec_GCJ='-L$libdir' hardcode_shlibpath_var_GCJ=no ;; freebsd1*) ld_shlibs_GCJ=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_GCJ='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o' hardcode_libdir_flag_spec_GCJ='-R$libdir' hardcode_direct_GCJ=yes hardcode_shlibpath_var_GCJ=no ;; # Unfortunately, older versions of FreeBSD 2 do not have this feature. freebsd2*) archive_cmds_GCJ='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_GCJ=yes hardcode_minus_L_GCJ=yes hardcode_shlibpath_var_GCJ=no ;; # FreeBSD 3 and greater uses gcc -shared to do shared libraries. freebsd* | kfreebsd*-gnu) archive_cmds_GCJ='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec_GCJ='-R$libdir' hardcode_direct_GCJ=yes hardcode_shlibpath_var_GCJ=no ;; hpux9*) if test "$GCC" = yes; then archive_cmds_GCJ='$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 $lib' else archive_cmds_GCJ='$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 $lib' fi hardcode_libdir_flag_spec_GCJ='${wl}+b ${wl}$libdir' hardcode_libdir_separator_GCJ=: hardcode_direct_GCJ=yes # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L_GCJ=yes export_dynamic_flag_spec_GCJ='${wl}-E' ;; hpux10* | hpux11*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then case "$host_cpu" in hppa*64*|ia64*) archive_cmds_GCJ='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds_GCJ='$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*|ia64*) archive_cmds_GCJ='$LD -b +h $soname -o $lib $libobjs $deplibs $linker_flags' ;; *) archive_cmds_GCJ='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' ;; esac fi if test "$with_gnu_ld" = no; then case "$host_cpu" in hppa*64*) hardcode_libdir_flag_spec_GCJ='${wl}+b ${wl}$libdir' hardcode_libdir_flag_spec_ld_GCJ='+b $libdir' hardcode_libdir_separator_GCJ=: hardcode_direct_GCJ=no hardcode_shlibpath_var_GCJ=no ;; ia64*) hardcode_libdir_flag_spec_GCJ='-L$libdir' hardcode_direct_GCJ=no hardcode_shlibpath_var_GCJ=no # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L_GCJ=yes ;; *) hardcode_libdir_flag_spec_GCJ='${wl}+b ${wl}$libdir' hardcode_libdir_separator_GCJ=: hardcode_direct_GCJ=yes export_dynamic_flag_spec_GCJ='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L_GCJ=yes ;; esac fi ;; irix5* | irix6* | nonstopux*) if test "$GCC" = yes; then archive_cmds_GCJ='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else archive_cmds_GCJ='$LD -shared $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec_ld_GCJ='-rpath $libdir' fi hardcode_libdir_flag_spec_GCJ='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator_GCJ=: link_all_deplibs_GCJ=yes ;; netbsd*) if echo __ELF__ | $CC -E - | grep __ELF__ >/dev/null; then archive_cmds_GCJ='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out else archive_cmds_GCJ='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF fi hardcode_libdir_flag_spec_GCJ='-R$libdir' hardcode_direct_GCJ=yes hardcode_shlibpath_var_GCJ=no ;; newsos6) archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_GCJ=yes hardcode_libdir_flag_spec_GCJ='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator_GCJ=: hardcode_shlibpath_var_GCJ=no ;; openbsd*) hardcode_direct_GCJ=yes hardcode_shlibpath_var_GCJ=no if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then archive_cmds_GCJ='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec_GCJ='${wl}-rpath,$libdir' export_dynamic_flag_spec_GCJ='${wl}-E' else case $host_os in openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*) archive_cmds_GCJ='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec_GCJ='-R$libdir' ;; *) archive_cmds_GCJ='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec_GCJ='${wl}-rpath,$libdir' ;; esac fi ;; os2*) hardcode_libdir_flag_spec_GCJ='-L$libdir' hardcode_minus_L_GCJ=yes allow_undefined_flag_GCJ=unsupported archive_cmds_GCJ='$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_GCJ='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; osf3*) if test "$GCC" = yes; then allow_undefined_flag_GCJ=' ${wl}-expect_unresolved ${wl}\*' archive_cmds_GCJ='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else allow_undefined_flag_GCJ=' -expect_unresolved \*' archive_cmds_GCJ='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' fi hardcode_libdir_flag_spec_GCJ='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator_GCJ=: ;; osf4* | osf5*) # as osf3* with the addition of -msym flag if test "$GCC" = yes; then allow_undefined_flag_GCJ=' ${wl}-expect_unresolved ${wl}\*' archive_cmds_GCJ='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && echo ${wl}-set_version ${wl}$verstring` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec_GCJ='${wl}-rpath ${wl}$libdir' else allow_undefined_flag_GCJ=' -expect_unresolved \*' archive_cmds_GCJ='$LD -shared${allow_undefined_flag} $libobjs $deplibs $linker_flags -msym -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds_GCJ='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; echo "-hidden">> $lib.exp~ $LD -shared${allow_undefined_flag} -input $lib.exp $linker_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && echo -set_version $verstring` -update_registry ${objdir}/so_locations -o $lib~$rm $lib.exp' # Both c and cxx compiler support -rpath directly hardcode_libdir_flag_spec_GCJ='-rpath $libdir' fi hardcode_libdir_separator_GCJ=: ;; sco3.2v5*) archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var_GCJ=no export_dynamic_flag_spec_GCJ='${wl}-Bexport' runpath_var=LD_RUN_PATH hardcode_runpath_var=yes ;; solaris*) no_undefined_flag_GCJ=' -z text' if test "$GCC" = yes; then archive_cmds_GCJ='$CC -shared ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds_GCJ='$echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~$echo "local: *; };" >> $lib.exp~ $CC -shared ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$rm $lib.exp' else archive_cmds_GCJ='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' archive_expsym_cmds_GCJ='$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 $lib.exp' fi hardcode_libdir_flag_spec_GCJ='-R$libdir' hardcode_shlibpath_var_GCJ=no case $host_os in solaris2.[0-5] | solaris2.[0-5].*) ;; *) # Supported since Solaris 2.6 (maybe 2.5.1?) whole_archive_flag_spec_GCJ='-z allextract$convenience -z defaultextract' ;; esac link_all_deplibs_GCJ=yes ;; sunos4*) if test "x$host_vendor" = xsequent; then # Use $CC to link under sequent, because it throws in some extra .o # files that make .init and .fini sections work. archive_cmds_GCJ='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds_GCJ='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags' fi hardcode_libdir_flag_spec_GCJ='-L$libdir' hardcode_direct_GCJ=yes hardcode_minus_L_GCJ=yes hardcode_shlibpath_var_GCJ=no ;; sysv4) case $host_vendor in sni) archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_GCJ=yes # is this really true??? ;; siemens) ## LD is ld it makes a PLAMLIB ## CC just makes a GrossModule. archive_cmds_GCJ='$LD -G -o $lib $libobjs $deplibs $linker_flags' reload_cmds_GCJ='$CC -r -o $output$reload_objs' hardcode_direct_GCJ=no ;; motorola) archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_GCJ=no #Motorola manual says yes, but my tests say they lie ;; esac runpath_var='LD_RUN_PATH' hardcode_shlibpath_var_GCJ=no ;; sysv4.3*) archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var_GCJ=no export_dynamic_flag_spec_GCJ='-Bexport' ;; sysv4*MP*) if test -d /usr/nec; then archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var_GCJ=no runpath_var=LD_RUN_PATH hardcode_runpath_var=yes ld_shlibs_GCJ=yes fi ;; sysv4.2uw2*) archive_cmds_GCJ='$LD -G -o $lib $libobjs $deplibs $linker_flags' hardcode_direct_GCJ=yes hardcode_minus_L_GCJ=no hardcode_shlibpath_var_GCJ=no hardcode_runpath_var=yes runpath_var=LD_RUN_PATH ;; sysv5OpenUNIX8* | sysv5UnixWare7* | sysv5uw[78]* | unixware7*) no_undefined_flag_GCJ='${wl}-z ${wl}text' if test "$GCC" = yes; then archive_cmds_GCJ='$CC -shared ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds_GCJ='$CC -G ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' fi runpath_var='LD_RUN_PATH' hardcode_shlibpath_var_GCJ=no ;; sysv5*) no_undefined_flag_GCJ=' -z text' # $CC -shared without GNU ld will not create a library from C++ # object files and a static libstdc++, better avoid it by now archive_cmds_GCJ='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' archive_expsym_cmds_GCJ='$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 $lib.exp' hardcode_libdir_flag_spec_GCJ= hardcode_shlibpath_var_GCJ=no runpath_var='LD_RUN_PATH' ;; uts4*) archive_cmds_GCJ='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec_GCJ='-L$libdir' hardcode_shlibpath_var_GCJ=no ;; *) ld_shlibs_GCJ=no ;; esac fi echo "$as_me:$LINENO: result: $ld_shlibs_GCJ" >&5 echo "${ECHO_T}$ld_shlibs_GCJ" >&6 test "$ld_shlibs_GCJ" = no && can_build_shared=no variables_saved_for_relink="PATH $shlibpath_var $runpath_var" if test "$GCC" = yes; then variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH" fi # # Do we need to explicitly link libc? # case "x$archive_cmds_need_lc_GCJ" in x|xyes) # Assume -lc should be added archive_cmds_need_lc_GCJ=yes if test "$enable_shared" = yes && test "$GCC" = yes; then case $archive_cmds_GCJ in *'~'*) # FIXME: we may have to deal with multi-command sequences. ;; '$CC '*) # Test whether the compiler implicitly links with -lc since on some # systems, -lgcc has to come before -lc. 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The import file would start with # the line `#! .'. This would cause the generated library to # depend on `.', always an invalid library. This was fixed in # development snapshots of GCC prior to 3.0. case $host_os in aix4 | aix4.[01] | aix4.[01].*) if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)' echo ' yes ' echo '#endif'; } | ${CC} -E - | grep yes > /dev/null; then : else can_build_shared=no fi ;; esac # AIX (on Power*) has no versioning support, so currently we can not hardcode correct # soname into executable. Probably we can add versioning support to # collect2, so additional links can be useful in future. if test "$aix_use_runtimelinking" = yes; then # If using run time linking (on AIX 4.2 or later) use lib.so # instead of lib.a to let people know that these are not # typical AIX shared libraries. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' else # We preserve .a as extension for shared libraries through AIX4.2 # and later when we are not doing run time linking. library_names_spec='${libname}${release}.a $libname.a' soname_spec='${libname}${release}${shared_ext}$major' fi shlibpath_var=LIBPATH fi ;; amigaos*) library_names_spec='$libname.ixlibrary $libname.a' # Create ${libname}_ixlibrary.a entries in /sys/libs. finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$echo "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $rm /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done' ;; beos*) library_names_spec='${libname}${shared_ext}' dynamic_linker="$host_os ld.so" shlibpath_var=LIBRARY_PATH ;; bsdi4*) version_type=linux 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 $libdir' shlibpath_var=LD_LIBRARY_PATH sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib" sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib" # the default ld.so.conf also contains /usr/contrib/lib and # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow # libtool to hard-code these into programs ;; cygwin* | mingw* | pw32*) version_type=windows shrext_cmds=".dll" need_version=no need_lib_prefix=no case $GCC,$host_os in yes,cygwin* | yes,mingw* | yes,pw32*) library_names_spec='$libname.dll.a' # DLL is installed to $(libdir)/../bin by postinstall_cmds postinstall_cmds='base_file=`basename \${file}`~ dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i;echo \$dlname'\''`~ dldir=$destdir/`dirname \$dlpath`~ test -d \$dldir || mkdir -p \$dldir~ $install_prog $dir/$dlname \$dldir/$dlname' postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~ dlpath=$dir/\$dldll~ $rm \$dlpath' shlibpath_overrides_runpath=yes case $host_os in cygwin*) # Cygwin DLLs use 'cyg' prefix rather than 'lib' soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}' sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib" ;; mingw*) # MinGW DLLs use traditional 'lib' prefix soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}' sys_lib_search_path_spec=`$CC -print-search-dirs | grep "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"` if echo "$sys_lib_search_path_spec" | grep ';[c-zC-Z]:/' >/dev/null; then # It is most probably a Windows format PATH printed by # mingw gcc, but we are running on Cygwin. Gcc prints its search # path with ; separators, and with drive letters. We can handle the # drive letters (cygwin fileutils understands them), so leave them, # especially as we might pass files found there to a mingw objdump, # which wouldn't understand a cygwinified path. Ahh. sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'` else sys_lib_search_path_spec=`echo "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"` fi ;; pw32*) # pw32 DLLs use 'pw' prefix rather than 'lib' library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/./-/g'`${versuffix}${shared_ext}' ;; esac ;; *) library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib' ;; esac dynamic_linker='Win32 ld.exe' # FIXME: first we should search . and the directory the executable is in shlibpath_var=PATH ;; darwin* | rhapsody*) dynamic_linker="$host_os dyld" version_type=darwin need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${versuffix}$shared_ext ${libname}${release}${major}$shared_ext ${libname}$shared_ext' soname_spec='${libname}${release}${major}$shared_ext' shlibpath_overrides_runpath=yes shlibpath_var=DYLD_LIBRARY_PATH shrext_cmds='$(test .$module = .yes && echo .so || echo .dylib)' # Apple's gcc prints 'gcc -print-search-dirs' doesn't operate the same. if test "$GCC" = yes; then sys_lib_search_path_spec=`$CC -print-search-dirs | tr "\n" "$PATH_SEPARATOR" | sed -e 's/libraries:/@libraries:/' | tr "@" "\n" | grep "^libraries:" | sed -e "s/^libraries://" -e "s,=/,/,g" -e "s,$PATH_SEPARATOR, ,g" -e "s,.*,& /lib /usr/lib /usr/local/lib,g"` else sys_lib_search_path_spec='/lib /usr/lib /usr/local/lib' fi sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib' ;; dgux*) 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 ;; freebsd1*) dynamic_linker=no ;; kfreebsd*-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='GNU ld.so' ;; freebsd*) objformat=`test -x /usr/bin/objformat && /usr/bin/objformat || echo aout` version_type=freebsd-$objformat case $version_type in freebsd-elf*) library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}' need_version=no need_lib_prefix=no ;; freebsd-*) library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix' need_version=yes ;; esac shlibpath_var=LD_LIBRARY_PATH case $host_os in freebsd2*) shlibpath_overrides_runpath=yes ;; freebsd3.01* | freebsdelf3.01*) shlibpath_overrides_runpath=yes hardcode_into_libs=yes ;; *) # from 3.2 on shlibpath_overrides_runpath=no hardcode_into_libs=yes ;; esac ;; gnu*) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${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 hardcode_into_libs=yes ;; hpux9* | hpux10* | hpux11*) # Give a soname corresponding to the major version so that dld.sl refuses to # link against other versions. version_type=sunos need_lib_prefix=no need_version=no case "$host_cpu" in ia64*) shrext_cmds='.so' hardcode_into_libs=yes dynamic_linker="$host_os dld.so" shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' if test "X$HPUX_IA64_MODE" = X32; then sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib" else sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64" fi sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec ;; hppa*64*) shrext_cmds='.sl' hardcode_into_libs=yes dynamic_linker="$host_os dld.sl" shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH shlibpath_overrides_runpath=yes # Unless +noenvvar is specified. library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64" sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec ;; *) shrext_cmds='.sl' dynamic_linker="$host_os dld.sl" shlibpath_var=SHLIB_PATH shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' ;; esac # HP-UX runs *really* slowly unless shared libraries are mode 555. postinstall_cmds='chmod 555 $lib' ;; irix5* | irix6* | nonstopux*) case $host_os in nonstopux*) version_type=nonstopux ;; *) if test "$lt_cv_prog_gnu_ld" = yes; then version_type=linux else version_type=irix fi ;; esac 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 ${libname}${release}${shared_ext} $libname${shared_ext}' case $host_os in irix5* | nonstopux*) libsuff= shlibsuff= ;; *) case $LD in # libtool.m4 will add one of these switches to LD *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ") libsuff= shlibsuff= libmagic=32-bit;; *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ") libsuff=32 shlibsuff=N32 libmagic=N32;; *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ") libsuff=64 shlibsuff=64 libmagic=64-bit;; *) libsuff= shlibsuff= libmagic=never-match;; esac ;; esac shlibpath_var=LD_LIBRARY${shlibsuff}_PATH shlibpath_overrides_runpath=no sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}" sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}" hardcode_into_libs=yes ;; # No shared lib support for Linux oldld, aout, or coff. linux*oldld* | linux*aout* | linux*coff*) dynamic_linker=no ;; # This must be Linux ELF. linux*) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${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 $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no # This implies no fast_install, which is unacceptable. # Some rework will be needed to allow for fast_install # before this can be enabled. hardcode_into_libs=yes # find out which ABI we are using libsuff= case "$host_cpu" in x86_64*|s390x*|powerpc64*) echo '#line 17228 "configure"' > conftest.$ac_ext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); 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sunos4*) version_type=sunos library_names_spec='${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 | sysv4.2uw2* | sysv4.3* | sysv5*) 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 $host_vendor in sni) shlibpath_overrides_runpath=no need_lib_prefix=no export_dynamic_flag_spec='${wl}-Blargedynsym' 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}.$major' shlibpath_var=LD_LIBRARY_PATH fi ;; uts4*) version_type=linux library_names_spec='${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 echo "$as_me:$LINENO: result: $dynamic_linker" >&5 echo "${ECHO_T}$dynamic_linker" >&6 test "$dynamic_linker" = no && can_build_shared=no echo "$as_me:$LINENO: checking how to hardcode library paths into programs" >&5 echo $ECHO_N "checking how to hardcode library paths into programs... $ECHO_C" >&6 hardcode_action_GCJ= if test -n "$hardcode_libdir_flag_spec_GCJ" || \ test -n "$runpath_var GCJ" || \ test "X$hardcode_automatic_GCJ"="Xyes" ; then # We can hardcode non-existant directories. if test "$hardcode_direct_GCJ" != no && # If the only mechanism to avoid hardcoding is shlibpath_var, we # have to relink, otherwise we might link with an installed library # when we should be linking with a yet-to-be-installed one ## test "$_LT_AC_TAGVAR(hardcode_shlibpath_var, GCJ)" != no && test "$hardcode_minus_L_GCJ" != no; then # Linking always hardcodes the temporary library directory. hardcode_action_GCJ=relink else # We can link without hardcoding, and we can hardcode nonexisting dirs. hardcode_action_GCJ=immediate fi else # We cannot hardcode anything, or else we can only hardcode existing # directories. hardcode_action_GCJ=unsupported fi echo "$as_me:$LINENO: result: $hardcode_action_GCJ" >&5 echo "${ECHO_T}$hardcode_action_GCJ" >&6 if test "$hardcode_action_GCJ" = relink; 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 striplib= old_striplib= echo "$as_me:$LINENO: checking whether stripping libraries is possible" >&5 echo $ECHO_N "checking whether stripping libraries is possible... $ECHO_C" >&6 if test -n "$STRIP" && $STRIP -V 2>&1 | grep "GNU strip" >/dev/null; then test -z "$old_striplib" && old_striplib="$STRIP --strip-debug" test -z "$striplib" && striplib="$STRIP --strip-unneeded" echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 else # FIXME - insert some real tests, host_os isn't really good enough case $host_os in darwin*) if test -n "$STRIP" ; then striplib="$STRIP -x" echo "$as_me:$LINENO: result: yes" >&5 echo "${ECHO_T}yes" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi ;; *) echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 ;; esac 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 $host_os in beos*) lt_cv_dlopen="load_add_on" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes ;; mingw* | pw32*) lt_cv_dlopen="LoadLibrary" lt_cv_dlopen_libs= ;; cygwin*) lt_cv_dlopen="dlopen" lt_cv_dlopen_libs= ;; darwin*) # if libdl is installed we need to link against it echo "$as_me:$LINENO: checking for dlopen in -ldl" >&5 echo $ECHO_N "checking for dlopen in -ldl... $ECHO_C" >&6 if test "${ac_cv_lib_dl_dlopen+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldl $LIBS" cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char dlopen (); int main () { dlopen (); ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_lib_dl_dlopen=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_lib_dl_dlopen=no fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi echo "$as_me:$LINENO: result: $ac_cv_lib_dl_dlopen" >&5 echo "${ECHO_T}$ac_cv_lib_dl_dlopen" >&6 if test $ac_cv_lib_dl_dlopen = yes; then lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl" else lt_cv_dlopen="dyld" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes fi ;; *) echo "$as_me:$LINENO: checking for shl_load" >&5 echo $ECHO_N "checking for shl_load... $ECHO_C" >&6 if test "${ac_cv_func_shl_load+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Define shl_load to an innocuous variant, in case declares shl_load. For example, HP-UX 11i declares gettimeofday. */ #define shl_load innocuous_shl_load /* System header to define __stub macros and hopefully few prototypes, which can conflict with char shl_load (); below. Prefer to if __STDC__ is defined, since exists even on freestanding compilers. */ #ifdef __STDC__ # include #else # include #endif #undef shl_load /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char shl_load (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ #if defined (__stub_shl_load) || defined (__stub___shl_load) choke me #else char (*f) () = shl_load; #endif #ifdef __cplusplus } #endif int main () { return f != shl_load; ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_func_shl_load=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_func_shl_load=no fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext fi echo "$as_me:$LINENO: result: $ac_cv_func_shl_load" >&5 echo "${ECHO_T}$ac_cv_func_shl_load" >&6 if test $ac_cv_func_shl_load = yes; then lt_cv_dlopen="shl_load" else echo "$as_me:$LINENO: checking for shl_load in -ldld" >&5 echo $ECHO_N "checking for shl_load in -ldld... $ECHO_C" >&6 if test "${ac_cv_lib_dld_shl_load+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldld $LIBS" cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char shl_load (); int main () { shl_load (); ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_lib_dld_shl_load=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_lib_dld_shl_load=no fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi echo "$as_me:$LINENO: result: $ac_cv_lib_dld_shl_load" >&5 echo "${ECHO_T}$ac_cv_lib_dld_shl_load" >&6 if test $ac_cv_lib_dld_shl_load = yes; then lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-dld" else echo "$as_me:$LINENO: checking for dlopen" >&5 echo $ECHO_N "checking for dlopen... $ECHO_C" >&6 if test "${ac_cv_func_dlopen+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Define dlopen to an innocuous variant, in case declares dlopen. For example, HP-UX 11i declares gettimeofday. */ #define dlopen innocuous_dlopen /* System header to define __stub macros and hopefully few prototypes, which can conflict with char dlopen (); below. Prefer to if __STDC__ is defined, since exists even on freestanding compilers. */ #ifdef __STDC__ # include #else # include #endif #undef dlopen /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" { #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char dlopen (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ #if defined (__stub_dlopen) || defined (__stub___dlopen) choke me #else char (*f) () = dlopen; #endif #ifdef __cplusplus } #endif int main () { return f != dlopen; ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_func_dlopen=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_func_dlopen=no fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext fi echo "$as_me:$LINENO: result: $ac_cv_func_dlopen" >&5 echo "${ECHO_T}$ac_cv_func_dlopen" >&6 if test $ac_cv_func_dlopen = yes; then lt_cv_dlopen="dlopen" else echo "$as_me:$LINENO: checking for dlopen in -ldl" >&5 echo $ECHO_N "checking for dlopen in -ldl... $ECHO_C" >&6 if test "${ac_cv_lib_dl_dlopen+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldl $LIBS" cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char dlopen (); int main () { dlopen (); ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_lib_dl_dlopen=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_lib_dl_dlopen=no fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi echo "$as_me:$LINENO: result: $ac_cv_lib_dl_dlopen" >&5 echo "${ECHO_T}$ac_cv_lib_dl_dlopen" >&6 if test $ac_cv_lib_dl_dlopen = yes; then lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl" else echo "$as_me:$LINENO: checking for dlopen in -lsvld" >&5 echo $ECHO_N "checking for dlopen in -lsvld... $ECHO_C" >&6 if test "${ac_cv_lib_svld_dlopen+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lsvld $LIBS" cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char dlopen (); int main () { dlopen (); ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_lib_svld_dlopen=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_lib_svld_dlopen=no fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi echo "$as_me:$LINENO: result: $ac_cv_lib_svld_dlopen" >&5 echo "${ECHO_T}$ac_cv_lib_svld_dlopen" >&6 if test $ac_cv_lib_svld_dlopen = yes; then lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld" else echo "$as_me:$LINENO: checking for dld_link in -ldld" >&5 echo $ECHO_N "checking for dld_link in -ldld... $ECHO_C" >&6 if test "${ac_cv_lib_dld_dld_link+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-ldld $LIBS" cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char dld_link (); int main () { dld_link (); ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_lib_dld_dld_link=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_lib_dld_dld_link=no fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi echo "$as_me:$LINENO: result: $ac_cv_lib_dld_dld_link" >&5 echo "${ECHO_T}$ac_cv_lib_dld_dld_link" >&6 if test $ac_cv_lib_dld_dld_link = yes; then lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-dld" fi fi fi fi fi fi ;; esac if test "x$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" eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\" save_LIBS="$LIBS" LIBS="$lt_cv_dlopen_libs $LIBS" echo "$as_me:$LINENO: checking whether a program can dlopen itself" >&5 echo $ECHO_N "checking whether a program can dlopen itself... $ECHO_C" >&6 if test "${lt_cv_dlopen_self+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$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 < #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 #ifdef __cplusplus extern "C" void exit (int); #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 = $lt_dlneed_uscore; /* dlclose (self); */ } exit (status); } EOF if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && test -s conftest${ac_exeext} 2>/dev/null; then (./conftest; exit; ) 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$lt_unknown|x*) lt_cv_dlopen_self=no ;; esac else : # compilation failed lt_cv_dlopen_self=no fi fi rm -fr conftest* fi echo "$as_me:$LINENO: result: $lt_cv_dlopen_self" >&5 echo "${ECHO_T}$lt_cv_dlopen_self" >&6 if test "x$lt_cv_dlopen_self" = xyes; then LDFLAGS="$LDFLAGS $link_static_flag" echo "$as_me:$LINENO: checking whether a statically linked program can dlopen itself" >&5 echo $ECHO_N "checking whether a statically linked program can dlopen itself... $ECHO_C" >&6 if test "${lt_cv_dlopen_self_static+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if test "$cross_compiling" = yes; then : lt_cv_dlopen_self_static=cross else lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2 lt_status=$lt_dlunknown cat > conftest.$ac_ext < #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 #ifdef __cplusplus extern "C" void exit (int); #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 = $lt_dlneed_uscore; /* dlclose (self); */ } exit (status); } EOF if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && test -s conftest${ac_exeext} 2>/dev/null; then (./conftest; exit; ) 2>/dev/null lt_status=$? case x$lt_status in x$lt_dlno_uscore) lt_cv_dlopen_self_static=yes ;; x$lt_dlneed_uscore) lt_cv_dlopen_self_static=yes ;; x$lt_unknown|x*) lt_cv_dlopen_self_static=no ;; esac else : # compilation failed lt_cv_dlopen_self_static=no fi fi rm -fr conftest* fi echo "$as_me:$LINENO: result: $lt_cv_dlopen_self_static" >&5 echo "${ECHO_T}$lt_cv_dlopen_self_static" >&6 fi CPPFLAGS="$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 # The else clause should only fire when bootstrapping the # libtool distribution, otherwise you forgot to ship ltmain.sh # with your package, and you will get complaints that there are # no rules to generate ltmain.sh. if test -f "$ltmain"; then # See if we are running on zsh, and set the options which allow our commands through # without removal of \ escapes. if test -n "${ZSH_VERSION+set}" ; then setopt NO_GLOB_SUBST fi # Now quote all the things that may contain metacharacters while being # careful not to overquote the AC_SUBSTed values. 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We can't simply define LARGE_OFF_T to be 9223372036854775807, since some C++ compilers masquerading as C compilers incorrectly reject 9223372036854775807. */ #define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62)) int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721 && LARGE_OFF_T % 2147483647 == 1) ? 1 : -1]; int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest.$ac_objext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then break else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f conftest.err conftest.$ac_objext conftest.$ac_ext cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #define _FILE_OFFSET_BITS 64 #include /* Check that off_t can represent 2**63 - 1 correctly. We can't simply define LARGE_OFF_T to be 9223372036854775807, since some C++ compilers masquerading as C compilers incorrectly reject 9223372036854775807. */ #define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62)) int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721 && LARGE_OFF_T % 2147483647 == 1) ? 1 : -1]; int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest.$ac_objext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_sys_file_offset_bits=64; break else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f conftest.err conftest.$ac_objext conftest.$ac_ext break done fi echo "$as_me:$LINENO: result: $ac_cv_sys_file_offset_bits" >&5 echo "${ECHO_T}$ac_cv_sys_file_offset_bits" >&6 if test "$ac_cv_sys_file_offset_bits" != no; then cat >>confdefs.h <<_ACEOF #define _FILE_OFFSET_BITS $ac_cv_sys_file_offset_bits _ACEOF fi rm -f conftest* echo "$as_me:$LINENO: checking for _LARGE_FILES value needed for large files" >&5 echo $ECHO_N "checking for _LARGE_FILES value needed for large files... $ECHO_C" >&6 if test "${ac_cv_sys_large_files+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else while :; do ac_cv_sys_large_files=no cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include /* Check that off_t can represent 2**63 - 1 correctly. We can't simply define LARGE_OFF_T to be 9223372036854775807, since some C++ compilers masquerading as C compilers incorrectly reject 9223372036854775807. */ #define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62)) int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721 && LARGE_OFF_T % 2147483647 == 1) ? 1 : -1]; int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest.$ac_objext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then break else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f conftest.err conftest.$ac_objext conftest.$ac_ext cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #define _LARGE_FILES 1 #include /* Check that off_t can represent 2**63 - 1 correctly. We can't simply define LARGE_OFF_T to be 9223372036854775807, since some C++ compilers masquerading as C compilers incorrectly reject 9223372036854775807. */ #define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62)) int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721 && LARGE_OFF_T % 2147483647 == 1) ? 1 : -1]; int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest.$ac_objext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_sys_large_files=1; break else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f conftest.err conftest.$ac_objext conftest.$ac_ext break done fi echo "$as_me:$LINENO: result: $ac_cv_sys_large_files" >&5 echo "${ECHO_T}$ac_cv_sys_large_files" >&6 if test "$ac_cv_sys_large_files" != no; then cat >>confdefs.h <<_ACEOF #define _LARGE_FILES $ac_cv_sys_large_files _ACEOF fi rm -f conftest* fi echo "$as_me:$LINENO: checking for ANSI C header files" >&5 echo $ECHO_N "checking for ANSI C header files... $ECHO_C" >&6 if test "${ac_cv_header_stdc+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include #include #include int main () { ; return 0; } _ACEOF rm -f conftest.$ac_objext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest.$ac_objext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_header_stdc=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_header_stdc=no fi rm -f conftest.err conftest.$ac_objext conftest.$ac_ext if test $ac_cv_header_stdc = yes; then # SunOS 4.x string.h does not declare mem*, contrary to ANSI. cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | $EGREP "memchr" >/dev/null 2>&1; then : else ac_cv_header_stdc=no fi rm -f conftest* fi if test $ac_cv_header_stdc = yes; then # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | $EGREP "free" >/dev/null 2>&1; then : else ac_cv_header_stdc=no fi rm -f conftest* fi if test $ac_cv_header_stdc = yes; then # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. if test "$cross_compiling" = yes; then : else cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #if ((' ' & 0x0FF) == 0x020) # define ISLOWER(c) ('a' <= (c) && (c) <= 'z') # define TOUPPER(c) (ISLOWER(c) ? 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then ax_openmp_flags="$OPENMP_CFLAGS $ax_openmp_flags" fi for ax_openmp_flag in $ax_openmp_flags; do case $ax_openmp_flag in none) CFLAGS=$saveC ;; *) CFLAGS="$saveCFLAGS $ax_openmp_flag" ;; esac cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any gcc2 internal prototype to avoid an error. */ #ifdef __cplusplus extern "C" #endif /* We use char because int might match the return type of a gcc2 builtin and then its argument prototype would still apply. */ char omp_set_num_threads (); int main () { omp_set_num_threads (); ; return 0; } _ACEOF rm -f conftest.$ac_objext conftest$ac_exeext if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5 (eval $ac_link) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest$ac_exeext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ax_cv_c_openmp=$ax_openmp_flag; break else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext done CFLAGS=$saveCFLAGS fi echo "$as_me:$LINENO: result: $ax_cv_c_openmp" >&5 echo "${ECHO_T}$ax_cv_c_openmp" >&6 if test "x$ax_cv_c_openmp" = "xunknown"; then : else if test "x$ax_cv_c_openmp" != "xnone"; then OPENMP_CFLAGS=$ax_cv_c_openmp fi cat >>confdefs.h <<\_ACEOF #define HAVE_OPENMP 1 _ACEOF fi # Files: DX_PROJECT="libGenome" DX_CONFIG="projects/libGenome.doxygen" DX_DOCDIR="doc" # Environment variables used inside doxygen.cfg: DX_ENV="$DX_ENV SRCDIR='$srcdir'" DX_ENV="$DX_ENV PROJECT='$DX_PROJECT'" DX_ENV="$DX_ENV DOCDIR='$DX_DOCDIR'" DX_ENV="$DX_ENV VERSION='$PACKAGE_VERSION'" # Doxygen itself: # Check whether --enable-doxygen-doc or --disable-doxygen-doc was given. if test "${enable_doxygen_doc+set}" = set; then enableval="$enable_doxygen_doc" case "$enableval" in #( y|Y|yes|Yes|YES) DX_FLAG_doc=1 ;; #( n|N|no|No|NO) DX_FLAG_doc=0 ;; #( *) { { echo "$as_me:$LINENO: error: invalid value '$enableval' given to doxygen-doc" >&5 echo "$as_me: error: invalid value '$enableval' given to doxygen-doc" >&2;} { (exit 1); exit 1; }; } ;; esac else DX_FLAG_doc=1 fi; if test "$DX_FLAG_doc" = 1; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}doxygen", so it can be a program name with args. set dummy ${ac_tool_prefix}doxygen; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_DX_DOXYGEN+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $DX_DOXYGEN in [\\/]* | ?:[\\/]*) ac_cv_path_DX_DOXYGEN="$DX_DOXYGEN" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_DX_DOXYGEN="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi DX_DOXYGEN=$ac_cv_path_DX_DOXYGEN if test -n "$DX_DOXYGEN"; then echo "$as_me:$LINENO: result: $DX_DOXYGEN" >&5 echo "${ECHO_T}$DX_DOXYGEN" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_path_DX_DOXYGEN"; then ac_pt_DX_DOXYGEN=$DX_DOXYGEN # Extract the first word of "doxygen", so it can be a program name with args. set dummy doxygen; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_ac_pt_DX_DOXYGEN+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $ac_pt_DX_DOXYGEN in [\\/]* | ?:[\\/]*) ac_cv_path_ac_pt_DX_DOXYGEN="$ac_pt_DX_DOXYGEN" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_ac_pt_DX_DOXYGEN="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi ac_pt_DX_DOXYGEN=$ac_cv_path_ac_pt_DX_DOXYGEN if test -n "$ac_pt_DX_DOXYGEN"; then echo "$as_me:$LINENO: result: $ac_pt_DX_DOXYGEN" >&5 echo "${ECHO_T}$ac_pt_DX_DOXYGEN" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi DX_DOXYGEN=$ac_pt_DX_DOXYGEN else DX_DOXYGEN="$ac_cv_path_DX_DOXYGEN" fi if test "$DX_FLAG_doc$DX_DOXYGEN" = 1; then { echo "$as_me:$LINENO: WARNING: doxygen not found - will not generate any doxygen documentation" >&5 echo "$as_me: WARNING: doxygen not found - will not generate any doxygen documentation" >&2;} DX_FLAG_doc=0 fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}perl", so it can be a program name with args. set dummy ${ac_tool_prefix}perl; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_DX_PERL+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $DX_PERL in [\\/]* | ?:[\\/]*) ac_cv_path_DX_PERL="$DX_PERL" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_DX_PERL="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi DX_PERL=$ac_cv_path_DX_PERL if test -n "$DX_PERL"; then echo "$as_me:$LINENO: result: $DX_PERL" >&5 echo "${ECHO_T}$DX_PERL" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_path_DX_PERL"; then ac_pt_DX_PERL=$DX_PERL # Extract the first word of "perl", so it can be a program name with args. set dummy perl; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_ac_pt_DX_PERL+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $ac_pt_DX_PERL in [\\/]* | ?:[\\/]*) ac_cv_path_ac_pt_DX_PERL="$ac_pt_DX_PERL" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_ac_pt_DX_PERL="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi ac_pt_DX_PERL=$ac_cv_path_ac_pt_DX_PERL if test -n "$ac_pt_DX_PERL"; then echo "$as_me:$LINENO: result: $ac_pt_DX_PERL" >&5 echo "${ECHO_T}$ac_pt_DX_PERL" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi DX_PERL=$ac_pt_DX_PERL else DX_PERL="$ac_cv_path_DX_PERL" fi if test "$DX_FLAG_doc$DX_PERL" = 1; then { echo "$as_me:$LINENO: WARNING: perl not found - will not generate any doxygen documentation" >&5 echo "$as_me: WARNING: perl not found - will not generate any doxygen documentation" >&2;} DX_FLAG_doc=0 fi : fi if test "$DX_FLAG_doc" = 1; then if :; then DX_COND_doc_TRUE= DX_COND_doc_FALSE='#' else DX_COND_doc_TRUE='#' DX_COND_doc_FALSE= fi DX_ENV="$DX_ENV PERL_PATH='$DX_PERL'" : else if false; then DX_COND_doc_TRUE= DX_COND_doc_FALSE='#' else DX_COND_doc_TRUE='#' DX_COND_doc_FALSE= fi : fi # Dot for graphics: # Check whether --enable-doxygen-dot or --disable-doxygen-dot was given. if test "${enable_doxygen_dot+set}" = set; then enableval="$enable_doxygen_dot" case "$enableval" in #( y|Y|yes|Yes|YES) DX_FLAG_dot=1 test "$DX_FLAG_doc" = "1" \ || { { echo "$as_me:$LINENO: error: doxygen-dot requires doxygen-dot" >&5 echo "$as_me: error: doxygen-dot requires doxygen-dot" >&2;} { (exit 1); exit 1; }; } ;; #( n|N|no|No|NO) DX_FLAG_dot=0 ;; #( *) { { echo "$as_me:$LINENO: error: invalid value '$enableval' given to doxygen-dot" >&5 echo "$as_me: error: invalid value '$enableval' given to doxygen-dot" >&2;} { (exit 1); exit 1; }; } ;; esac else DX_FLAG_dot=1 test "$DX_FLAG_doc" = "1" || DX_FLAG_dot=0 fi; if test "$DX_FLAG_dot" = 1; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}dot", so it can be a program name with args. set dummy ${ac_tool_prefix}dot; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_DX_DOT+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $DX_DOT in [\\/]* | ?:[\\/]*) ac_cv_path_DX_DOT="$DX_DOT" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_DX_DOT="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi DX_DOT=$ac_cv_path_DX_DOT if test -n "$DX_DOT"; then echo "$as_me:$LINENO: result: $DX_DOT" >&5 echo "${ECHO_T}$DX_DOT" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_path_DX_DOT"; then ac_pt_DX_DOT=$DX_DOT # Extract the first word of "dot", so it can be a program name with args. set dummy dot; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_ac_pt_DX_DOT+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $ac_pt_DX_DOT in [\\/]* | ?:[\\/]*) ac_cv_path_ac_pt_DX_DOT="$ac_pt_DX_DOT" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_ac_pt_DX_DOT="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi ac_pt_DX_DOT=$ac_cv_path_ac_pt_DX_DOT if test -n "$ac_pt_DX_DOT"; then echo "$as_me:$LINENO: result: $ac_pt_DX_DOT" >&5 echo "${ECHO_T}$ac_pt_DX_DOT" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi DX_DOT=$ac_pt_DX_DOT else DX_DOT="$ac_cv_path_DX_DOT" fi if test "$DX_FLAG_dot$DX_DOT" = 1; then { echo "$as_me:$LINENO: WARNING: dot not found - will not generate graphics for doxygen documentation" >&5 echo "$as_me: WARNING: dot not found - will not generate graphics for doxygen documentation" >&2;} DX_FLAG_dot=0 fi : fi if test "$DX_FLAG_dot" = 1; then if :; then DX_COND_dot_TRUE= DX_COND_dot_FALSE='#' else DX_COND_dot_TRUE='#' DX_COND_dot_FALSE= fi DX_ENV="$DX_ENV HAVE_DOT='YES'" DX_ENV="$DX_ENV DOT_PATH='`expr ".$DX_DOT" : '\(\.\)[^/]*$' \| "x$DX_DOT" : 'x\(.*\)/[^/]*$'`'" : else if false; then DX_COND_dot_TRUE= DX_COND_dot_FALSE='#' else DX_COND_dot_TRUE='#' DX_COND_dot_FALSE= fi DX_ENV="$DX_ENV HAVE_DOT='NO'" : fi # Man pages generation: # Check whether --enable-doxygen-man or --disable-doxygen-man was given. if test "${enable_doxygen_man+set}" = set; then enableval="$enable_doxygen_man" case "$enableval" in #( y|Y|yes|Yes|YES) DX_FLAG_man=1 test "$DX_FLAG_doc" = "1" \ || { { echo "$as_me:$LINENO: error: doxygen-man requires doxygen-man" >&5 echo "$as_me: error: doxygen-man requires doxygen-man" >&2;} { (exit 1); exit 1; }; } ;; #( n|N|no|No|NO) DX_FLAG_man=0 ;; #( *) { { echo "$as_me:$LINENO: error: invalid value '$enableval' given to doxygen-man" >&5 echo "$as_me: error: invalid value '$enableval' given to doxygen-man" >&2;} { (exit 1); exit 1; }; } ;; esac else DX_FLAG_man=0 test "$DX_FLAG_doc" = "1" || DX_FLAG_man=0 fi; if test "$DX_FLAG_man" = 1; then : fi if test "$DX_FLAG_man" = 1; then if :; then DX_COND_man_TRUE= DX_COND_man_FALSE='#' else DX_COND_man_TRUE='#' DX_COND_man_FALSE= fi DX_ENV="$DX_ENV GENERATE_MAN='YES'" : else if false; then DX_COND_man_TRUE= DX_COND_man_FALSE='#' else DX_COND_man_TRUE='#' DX_COND_man_FALSE= fi DX_ENV="$DX_ENV GENERATE_MAN='NO'" : fi # RTF file generation: # Check whether --enable-doxygen-rtf or --disable-doxygen-rtf was given. if test "${enable_doxygen_rtf+set}" = set; then enableval="$enable_doxygen_rtf" case "$enableval" in #( y|Y|yes|Yes|YES) DX_FLAG_rtf=1 test "$DX_FLAG_doc" = "1" \ || { { echo "$as_me:$LINENO: error: doxygen-rtf requires doxygen-rtf" >&5 echo "$as_me: error: doxygen-rtf requires doxygen-rtf" >&2;} { (exit 1); exit 1; }; } ;; #( n|N|no|No|NO) DX_FLAG_rtf=0 ;; #( *) { { echo "$as_me:$LINENO: error: invalid value '$enableval' given to doxygen-rtf" >&5 echo "$as_me: error: invalid value '$enableval' given to doxygen-rtf" >&2;} { (exit 1); exit 1; }; } ;; esac else DX_FLAG_rtf=0 test "$DX_FLAG_doc" = "1" || DX_FLAG_rtf=0 fi; if test "$DX_FLAG_rtf" = 1; then : fi if test "$DX_FLAG_rtf" = 1; then if :; then DX_COND_rtf_TRUE= DX_COND_rtf_FALSE='#' else DX_COND_rtf_TRUE='#' DX_COND_rtf_FALSE= fi DX_ENV="$DX_ENV GENERATE_RTF='YES'" : else if false; then DX_COND_rtf_TRUE= DX_COND_rtf_FALSE='#' else DX_COND_rtf_TRUE='#' DX_COND_rtf_FALSE= fi DX_ENV="$DX_ENV GENERATE_RTF='NO'" : fi # XML file generation: # Check whether --enable-doxygen-xml or --disable-doxygen-xml was given. if test "${enable_doxygen_xml+set}" = set; then enableval="$enable_doxygen_xml" case "$enableval" in #( y|Y|yes|Yes|YES) DX_FLAG_xml=1 test "$DX_FLAG_doc" = "1" \ || { { echo "$as_me:$LINENO: error: doxygen-xml requires doxygen-xml" >&5 echo "$as_me: error: doxygen-xml requires doxygen-xml" >&2;} { (exit 1); exit 1; }; } ;; #( n|N|no|No|NO) DX_FLAG_xml=0 ;; #( *) { { echo "$as_me:$LINENO: error: invalid value '$enableval' given to doxygen-xml" >&5 echo "$as_me: error: invalid value '$enableval' given to doxygen-xml" >&2;} { (exit 1); exit 1; }; } ;; esac else DX_FLAG_xml=0 test "$DX_FLAG_doc" = "1" || DX_FLAG_xml=0 fi; if test "$DX_FLAG_xml" = 1; then : fi if test "$DX_FLAG_xml" = 1; then if :; then DX_COND_xml_TRUE= DX_COND_xml_FALSE='#' else DX_COND_xml_TRUE='#' DX_COND_xml_FALSE= fi DX_ENV="$DX_ENV GENERATE_XML='YES'" : else if false; then DX_COND_xml_TRUE= DX_COND_xml_FALSE='#' else DX_COND_xml_TRUE='#' DX_COND_xml_FALSE= fi DX_ENV="$DX_ENV GENERATE_XML='NO'" : fi # (Compressed) HTML help generation: # Check whether --enable-doxygen-chm or --disable-doxygen-chm was given. if test "${enable_doxygen_chm+set}" = set; then enableval="$enable_doxygen_chm" case "$enableval" in #( y|Y|yes|Yes|YES) DX_FLAG_chm=1 test "$DX_FLAG_doc" = "1" \ || { { echo "$as_me:$LINENO: error: doxygen-chm requires doxygen-chm" >&5 echo "$as_me: error: doxygen-chm requires doxygen-chm" >&2;} { (exit 1); exit 1; }; } ;; #( n|N|no|No|NO) DX_FLAG_chm=0 ;; #( *) { { echo "$as_me:$LINENO: error: invalid value '$enableval' given to doxygen-chm" >&5 echo "$as_me: error: invalid value '$enableval' given to doxygen-chm" >&2;} { (exit 1); exit 1; }; } ;; esac else DX_FLAG_chm=0 test "$DX_FLAG_doc" = "1" || DX_FLAG_chm=0 fi; if test "$DX_FLAG_chm" = 1; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}hhc", so it can be a program name with args. set dummy ${ac_tool_prefix}hhc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_DX_HHC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $DX_HHC in [\\/]* | ?:[\\/]*) ac_cv_path_DX_HHC="$DX_HHC" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_DX_HHC="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi DX_HHC=$ac_cv_path_DX_HHC if test -n "$DX_HHC"; then echo "$as_me:$LINENO: result: $DX_HHC" >&5 echo "${ECHO_T}$DX_HHC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_path_DX_HHC"; then ac_pt_DX_HHC=$DX_HHC # Extract the first word of "hhc", so it can be a program name with args. set dummy hhc; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_ac_pt_DX_HHC+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $ac_pt_DX_HHC in [\\/]* | ?:[\\/]*) ac_cv_path_ac_pt_DX_HHC="$ac_pt_DX_HHC" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_ac_pt_DX_HHC="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi ac_pt_DX_HHC=$ac_cv_path_ac_pt_DX_HHC if test -n "$ac_pt_DX_HHC"; then echo "$as_me:$LINENO: result: $ac_pt_DX_HHC" >&5 echo "${ECHO_T}$ac_pt_DX_HHC" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi DX_HHC=$ac_pt_DX_HHC else DX_HHC="$ac_cv_path_DX_HHC" fi if test "$DX_FLAG_chm$DX_HHC" = 1; then { echo "$as_me:$LINENO: WARNING: hhc not found - will not generate doxygen compressed HTML help documentation" >&5 echo "$as_me: WARNING: hhc not found - will not generate doxygen compressed HTML help documentation" >&2;} DX_FLAG_chm=0 fi : fi if test "$DX_FLAG_chm" = 1; then if :; then DX_COND_chm_TRUE= DX_COND_chm_FALSE='#' else DX_COND_chm_TRUE='#' DX_COND_chm_FALSE= fi DX_ENV="$DX_ENV HHC_PATH='$DX_HHC'" DX_ENV="$DX_ENV GENERATE_HTML='YES'" DX_ENV="$DX_ENV GENERATE_HTMLHELP='YES'" : else if false; then DX_COND_chm_TRUE= DX_COND_chm_FALSE='#' else DX_COND_chm_TRUE='#' DX_COND_chm_FALSE= fi DX_ENV="$DX_ENV GENERATE_HTMLHELP='NO'" : fi # Seperate CHI file generation. # Check whether --enable-doxygen-chi or --disable-doxygen-chi was given. if test "${enable_doxygen_chi+set}" = set; then enableval="$enable_doxygen_chi" case "$enableval" in #( y|Y|yes|Yes|YES) DX_FLAG_chi=1 test "$DX_FLAG_chm" = "1" \ || { { echo "$as_me:$LINENO: error: doxygen-chi requires doxygen-chi" >&5 echo "$as_me: error: doxygen-chi requires doxygen-chi" >&2;} { (exit 1); exit 1; }; } ;; #( n|N|no|No|NO) DX_FLAG_chi=0 ;; #( *) { { echo "$as_me:$LINENO: error: invalid value '$enableval' given to doxygen-chi" >&5 echo "$as_me: error: invalid value '$enableval' given to doxygen-chi" >&2;} { (exit 1); exit 1; }; } ;; esac else DX_FLAG_chi=0 test "$DX_FLAG_chm" = "1" || DX_FLAG_chi=0 fi; if test "$DX_FLAG_chi" = 1; then : fi if test "$DX_FLAG_chi" = 1; then if :; then DX_COND_chi_TRUE= DX_COND_chi_FALSE='#' else DX_COND_chi_TRUE='#' DX_COND_chi_FALSE= fi DX_ENV="$DX_ENV GENERATE_CHI='YES'" : else if false; then DX_COND_chi_TRUE= DX_COND_chi_FALSE='#' else DX_COND_chi_TRUE='#' DX_COND_chi_FALSE= fi DX_ENV="$DX_ENV GENERATE_CHI='NO'" : fi # Plain HTML pages generation: # Check whether --enable-doxygen-html or --disable-doxygen-html was given. if test "${enable_doxygen_html+set}" = set; then enableval="$enable_doxygen_html" case "$enableval" in #( y|Y|yes|Yes|YES) DX_FLAG_html=1 test "$DX_FLAG_doc" = "1" \ || { { echo "$as_me:$LINENO: error: doxygen-html requires doxygen-html" >&5 echo "$as_me: error: doxygen-html requires doxygen-html" >&2;} { (exit 1); exit 1; }; } test "$DX_FLAG_chm" = "0" \ || { { echo "$as_me:$LINENO: error: doxygen-html contradicts doxygen-html" >&5 echo "$as_me: error: doxygen-html contradicts doxygen-html" >&2;} { (exit 1); exit 1; }; } ;; #( n|N|no|No|NO) DX_FLAG_html=0 ;; #( *) { { echo "$as_me:$LINENO: error: invalid value '$enableval' given to doxygen-html" >&5 echo "$as_me: error: invalid value '$enableval' given to doxygen-html" >&2;} { (exit 1); exit 1; }; } ;; esac else DX_FLAG_html=1 test "$DX_FLAG_doc" = "1" || DX_FLAG_html=0 test "$DX_FLAG_chm" = "0" || DX_FLAG_html=0 fi; if test "$DX_FLAG_html" = 1; then : fi if test "$DX_FLAG_html" = 1; then if :; then DX_COND_html_TRUE= DX_COND_html_FALSE='#' else DX_COND_html_TRUE='#' DX_COND_html_FALSE= fi DX_ENV="$DX_ENV GENERATE_HTML='YES'" : else if false; then DX_COND_html_TRUE= DX_COND_html_FALSE='#' else DX_COND_html_TRUE='#' DX_COND_html_FALSE= fi test "$DX_FLAG_chm" = 1 || DX_ENV="$DX_ENV GENERATE_HTML='NO'" : fi # PostScript file generation: # Check whether --enable-doxygen-ps or --disable-doxygen-ps was given. if test "${enable_doxygen_ps+set}" = set; then enableval="$enable_doxygen_ps" case "$enableval" in #( y|Y|yes|Yes|YES) DX_FLAG_ps=1 test "$DX_FLAG_doc" = "1" \ || { { echo "$as_me:$LINENO: error: doxygen-ps requires doxygen-ps" >&5 echo "$as_me: error: doxygen-ps requires doxygen-ps" >&2;} { (exit 1); exit 1; }; } ;; #( n|N|no|No|NO) DX_FLAG_ps=0 ;; #( *) { { echo "$as_me:$LINENO: error: invalid value '$enableval' given to doxygen-ps" >&5 echo "$as_me: error: invalid value '$enableval' given to doxygen-ps" >&2;} { (exit 1); exit 1; }; } ;; esac else DX_FLAG_ps=1 test "$DX_FLAG_doc" = "1" || DX_FLAG_ps=0 fi; if test "$DX_FLAG_ps" = 1; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}latex", so it can be a program name with args. set dummy ${ac_tool_prefix}latex; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_DX_LATEX+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $DX_LATEX in [\\/]* | ?:[\\/]*) ac_cv_path_DX_LATEX="$DX_LATEX" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_DX_LATEX="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi DX_LATEX=$ac_cv_path_DX_LATEX if test -n "$DX_LATEX"; then echo "$as_me:$LINENO: result: $DX_LATEX" >&5 echo "${ECHO_T}$DX_LATEX" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_path_DX_LATEX"; then ac_pt_DX_LATEX=$DX_LATEX # Extract the first word of "latex", so it can be a program name with args. set dummy latex; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_ac_pt_DX_LATEX+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $ac_pt_DX_LATEX in [\\/]* | ?:[\\/]*) ac_cv_path_ac_pt_DX_LATEX="$ac_pt_DX_LATEX" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_ac_pt_DX_LATEX="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi ac_pt_DX_LATEX=$ac_cv_path_ac_pt_DX_LATEX if test -n "$ac_pt_DX_LATEX"; then echo "$as_me:$LINENO: result: $ac_pt_DX_LATEX" >&5 echo "${ECHO_T}$ac_pt_DX_LATEX" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi DX_LATEX=$ac_pt_DX_LATEX else DX_LATEX="$ac_cv_path_DX_LATEX" fi if test "$DX_FLAG_ps$DX_LATEX" = 1; then { echo "$as_me:$LINENO: WARNING: latex not found - will not generate doxygen PostScript documentation" >&5 echo "$as_me: WARNING: latex not found - will not generate doxygen PostScript documentation" >&2;} DX_FLAG_ps=0 fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}makeindex", so it can be a program name with args. set dummy ${ac_tool_prefix}makeindex; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_DX_MAKEINDEX+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $DX_MAKEINDEX in [\\/]* | ?:[\\/]*) ac_cv_path_DX_MAKEINDEX="$DX_MAKEINDEX" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_DX_MAKEINDEX="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi DX_MAKEINDEX=$ac_cv_path_DX_MAKEINDEX if test -n "$DX_MAKEINDEX"; then echo "$as_me:$LINENO: result: $DX_MAKEINDEX" >&5 echo "${ECHO_T}$DX_MAKEINDEX" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_path_DX_MAKEINDEX"; then ac_pt_DX_MAKEINDEX=$DX_MAKEINDEX # Extract the first word of "makeindex", so it can be a program name with args. set dummy makeindex; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_ac_pt_DX_MAKEINDEX+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $ac_pt_DX_MAKEINDEX in [\\/]* | ?:[\\/]*) ac_cv_path_ac_pt_DX_MAKEINDEX="$ac_pt_DX_MAKEINDEX" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_ac_pt_DX_MAKEINDEX="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi ac_pt_DX_MAKEINDEX=$ac_cv_path_ac_pt_DX_MAKEINDEX if test -n "$ac_pt_DX_MAKEINDEX"; then echo "$as_me:$LINENO: result: $ac_pt_DX_MAKEINDEX" >&5 echo "${ECHO_T}$ac_pt_DX_MAKEINDEX" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi DX_MAKEINDEX=$ac_pt_DX_MAKEINDEX else DX_MAKEINDEX="$ac_cv_path_DX_MAKEINDEX" fi if test "$DX_FLAG_ps$DX_MAKEINDEX" = 1; then { echo "$as_me:$LINENO: WARNING: makeindex not found - will not generate doxygen PostScript documentation" >&5 echo "$as_me: WARNING: makeindex not found - will not generate doxygen PostScript documentation" >&2;} DX_FLAG_ps=0 fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}dvips", so it can be a program name with args. set dummy ${ac_tool_prefix}dvips; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_DX_DVIPS+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $DX_DVIPS in [\\/]* | ?:[\\/]*) ac_cv_path_DX_DVIPS="$DX_DVIPS" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_DX_DVIPS="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi DX_DVIPS=$ac_cv_path_DX_DVIPS if test -n "$DX_DVIPS"; then echo "$as_me:$LINENO: result: $DX_DVIPS" >&5 echo "${ECHO_T}$DX_DVIPS" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_path_DX_DVIPS"; then ac_pt_DX_DVIPS=$DX_DVIPS # Extract the first word of "dvips", so it can be a program name with args. set dummy dvips; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_ac_pt_DX_DVIPS+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $ac_pt_DX_DVIPS in [\\/]* | ?:[\\/]*) ac_cv_path_ac_pt_DX_DVIPS="$ac_pt_DX_DVIPS" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_ac_pt_DX_DVIPS="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi ac_pt_DX_DVIPS=$ac_cv_path_ac_pt_DX_DVIPS if test -n "$ac_pt_DX_DVIPS"; then echo "$as_me:$LINENO: result: $ac_pt_DX_DVIPS" >&5 echo "${ECHO_T}$ac_pt_DX_DVIPS" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi DX_DVIPS=$ac_pt_DX_DVIPS else DX_DVIPS="$ac_cv_path_DX_DVIPS" fi if test "$DX_FLAG_ps$DX_DVIPS" = 1; then { echo "$as_me:$LINENO: WARNING: dvips not found - will not generate doxygen PostScript documentation" >&5 echo "$as_me: WARNING: dvips not found - will not generate doxygen PostScript documentation" >&2;} DX_FLAG_ps=0 fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}egrep", so it can be a program name with args. set dummy ${ac_tool_prefix}egrep; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_DX_EGREP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $DX_EGREP in [\\/]* | ?:[\\/]*) ac_cv_path_DX_EGREP="$DX_EGREP" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_DX_EGREP="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi DX_EGREP=$ac_cv_path_DX_EGREP if test -n "$DX_EGREP"; then echo "$as_me:$LINENO: result: $DX_EGREP" >&5 echo "${ECHO_T}$DX_EGREP" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_path_DX_EGREP"; then ac_pt_DX_EGREP=$DX_EGREP # Extract the first word of "egrep", so it can be a program name with args. set dummy egrep; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_ac_pt_DX_EGREP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $ac_pt_DX_EGREP in [\\/]* | ?:[\\/]*) ac_cv_path_ac_pt_DX_EGREP="$ac_pt_DX_EGREP" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_ac_pt_DX_EGREP="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi ac_pt_DX_EGREP=$ac_cv_path_ac_pt_DX_EGREP if test -n "$ac_pt_DX_EGREP"; then echo "$as_me:$LINENO: result: $ac_pt_DX_EGREP" >&5 echo "${ECHO_T}$ac_pt_DX_EGREP" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi DX_EGREP=$ac_pt_DX_EGREP else DX_EGREP="$ac_cv_path_DX_EGREP" fi if test "$DX_FLAG_ps$DX_EGREP" = 1; then { echo "$as_me:$LINENO: WARNING: egrep not found - will not generate doxygen PostScript documentation" >&5 echo "$as_me: WARNING: egrep not found - will not generate doxygen PostScript documentation" >&2;} DX_FLAG_ps=0 fi : fi if test "$DX_FLAG_ps" = 1; then if :; then DX_COND_ps_TRUE= DX_COND_ps_FALSE='#' else DX_COND_ps_TRUE='#' DX_COND_ps_FALSE= fi : else if false; then DX_COND_ps_TRUE= DX_COND_ps_FALSE='#' else DX_COND_ps_TRUE='#' DX_COND_ps_FALSE= fi : fi # PDF file generation: # Check whether --enable-doxygen-pdf or --disable-doxygen-pdf was given. if test "${enable_doxygen_pdf+set}" = set; then enableval="$enable_doxygen_pdf" case "$enableval" in #( y|Y|yes|Yes|YES) DX_FLAG_pdf=1 test "$DX_FLAG_doc" = "1" \ || { { echo "$as_me:$LINENO: error: doxygen-pdf requires doxygen-pdf" >&5 echo "$as_me: error: doxygen-pdf requires doxygen-pdf" >&2;} { (exit 1); exit 1; }; } ;; #( n|N|no|No|NO) DX_FLAG_pdf=0 ;; #( *) { { echo "$as_me:$LINENO: error: invalid value '$enableval' given to doxygen-pdf" >&5 echo "$as_me: error: invalid value '$enableval' given to doxygen-pdf" >&2;} { (exit 1); exit 1; }; } ;; esac else DX_FLAG_pdf=1 test "$DX_FLAG_doc" = "1" || DX_FLAG_pdf=0 fi; if test "$DX_FLAG_pdf" = 1; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}pdflatex", so it can be a program name with args. set dummy ${ac_tool_prefix}pdflatex; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_DX_PDFLATEX+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $DX_PDFLATEX in [\\/]* | ?:[\\/]*) ac_cv_path_DX_PDFLATEX="$DX_PDFLATEX" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_DX_PDFLATEX="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi DX_PDFLATEX=$ac_cv_path_DX_PDFLATEX if test -n "$DX_PDFLATEX"; then echo "$as_me:$LINENO: result: $DX_PDFLATEX" >&5 echo "${ECHO_T}$DX_PDFLATEX" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_path_DX_PDFLATEX"; then ac_pt_DX_PDFLATEX=$DX_PDFLATEX # Extract the first word of "pdflatex", so it can be a program name with args. set dummy pdflatex; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_ac_pt_DX_PDFLATEX+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $ac_pt_DX_PDFLATEX in [\\/]* | ?:[\\/]*) ac_cv_path_ac_pt_DX_PDFLATEX="$ac_pt_DX_PDFLATEX" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_ac_pt_DX_PDFLATEX="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi ac_pt_DX_PDFLATEX=$ac_cv_path_ac_pt_DX_PDFLATEX if test -n "$ac_pt_DX_PDFLATEX"; then echo "$as_me:$LINENO: result: $ac_pt_DX_PDFLATEX" >&5 echo "${ECHO_T}$ac_pt_DX_PDFLATEX" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi DX_PDFLATEX=$ac_pt_DX_PDFLATEX else DX_PDFLATEX="$ac_cv_path_DX_PDFLATEX" fi if test "$DX_FLAG_pdf$DX_PDFLATEX" = 1; then { echo "$as_me:$LINENO: WARNING: pdflatex not found - will not generate doxygen PDF documentation" >&5 echo "$as_me: WARNING: pdflatex not found - will not generate doxygen PDF documentation" >&2;} DX_FLAG_pdf=0 fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}makeindex", so it can be a program name with args. set dummy ${ac_tool_prefix}makeindex; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_DX_MAKEINDEX+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $DX_MAKEINDEX in [\\/]* | ?:[\\/]*) ac_cv_path_DX_MAKEINDEX="$DX_MAKEINDEX" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_DX_MAKEINDEX="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi DX_MAKEINDEX=$ac_cv_path_DX_MAKEINDEX if test -n "$DX_MAKEINDEX"; then echo "$as_me:$LINENO: result: $DX_MAKEINDEX" >&5 echo "${ECHO_T}$DX_MAKEINDEX" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_path_DX_MAKEINDEX"; then ac_pt_DX_MAKEINDEX=$DX_MAKEINDEX # Extract the first word of "makeindex", so it can be a program name with args. set dummy makeindex; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_ac_pt_DX_MAKEINDEX+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $ac_pt_DX_MAKEINDEX in [\\/]* | ?:[\\/]*) ac_cv_path_ac_pt_DX_MAKEINDEX="$ac_pt_DX_MAKEINDEX" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_ac_pt_DX_MAKEINDEX="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi ac_pt_DX_MAKEINDEX=$ac_cv_path_ac_pt_DX_MAKEINDEX if test -n "$ac_pt_DX_MAKEINDEX"; then echo "$as_me:$LINENO: result: $ac_pt_DX_MAKEINDEX" >&5 echo "${ECHO_T}$ac_pt_DX_MAKEINDEX" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi DX_MAKEINDEX=$ac_pt_DX_MAKEINDEX else DX_MAKEINDEX="$ac_cv_path_DX_MAKEINDEX" fi if test "$DX_FLAG_pdf$DX_MAKEINDEX" = 1; then { echo "$as_me:$LINENO: WARNING: makeindex not found - will not generate doxygen PDF documentation" >&5 echo "$as_me: WARNING: makeindex not found - will not generate doxygen PDF documentation" >&2;} DX_FLAG_pdf=0 fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}egrep", so it can be a program name with args. set dummy ${ac_tool_prefix}egrep; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_DX_EGREP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $DX_EGREP in [\\/]* | ?:[\\/]*) ac_cv_path_DX_EGREP="$DX_EGREP" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_DX_EGREP="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi DX_EGREP=$ac_cv_path_DX_EGREP if test -n "$DX_EGREP"; then echo "$as_me:$LINENO: result: $DX_EGREP" >&5 echo "${ECHO_T}$DX_EGREP" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi fi if test -z "$ac_cv_path_DX_EGREP"; then ac_pt_DX_EGREP=$DX_EGREP # Extract the first word of "egrep", so it can be a program name with args. set dummy egrep; ac_word=$2 echo "$as_me:$LINENO: checking for $ac_word" >&5 echo $ECHO_N "checking for $ac_word... $ECHO_C" >&6 if test "${ac_cv_path_ac_pt_DX_EGREP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else case $ac_pt_DX_EGREP in [\\/]* | ?:[\\/]*) ac_cv_path_ac_pt_DX_EGREP="$ac_pt_DX_EGREP" # Let the user override the test with a path. ;; *) 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 $as_executable_p "$as_dir/$ac_word$ac_exec_ext"; then ac_cv_path_ac_pt_DX_EGREP="$as_dir/$ac_word$ac_exec_ext" echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done ;; esac fi ac_pt_DX_EGREP=$ac_cv_path_ac_pt_DX_EGREP if test -n "$ac_pt_DX_EGREP"; then echo "$as_me:$LINENO: result: $ac_pt_DX_EGREP" >&5 echo "${ECHO_T}$ac_pt_DX_EGREP" >&6 else echo "$as_me:$LINENO: result: no" >&5 echo "${ECHO_T}no" >&6 fi DX_EGREP=$ac_pt_DX_EGREP else DX_EGREP="$ac_cv_path_DX_EGREP" fi if test "$DX_FLAG_pdf$DX_EGREP" = 1; then { echo "$as_me:$LINENO: WARNING: egrep not found - will not generate doxygen PDF documentation" >&5 echo "$as_me: WARNING: egrep not found - will not generate doxygen PDF documentation" >&2;} DX_FLAG_pdf=0 fi : fi if test "$DX_FLAG_pdf" = 1; then if :; then DX_COND_pdf_TRUE= DX_COND_pdf_FALSE='#' else DX_COND_pdf_TRUE='#' DX_COND_pdf_FALSE= fi : else if false; then DX_COND_pdf_TRUE= DX_COND_pdf_FALSE='#' else DX_COND_pdf_TRUE='#' DX_COND_pdf_FALSE= fi : fi # LaTeX generation for PS and/or PDF: if test "$DX_FLAG_ps" = 1 || test "$DX_FLAG_pdf" = 1; then if :; then DX_COND_latex_TRUE= DX_COND_latex_FALSE='#' else DX_COND_latex_TRUE='#' DX_COND_latex_FALSE= fi DX_ENV="$DX_ENV GENERATE_LATEX='YES'" else if false; then DX_COND_latex_TRUE= DX_COND_latex_FALSE='#' else DX_COND_latex_TRUE='#' DX_COND_latex_FALSE= fi DX_ENV="$DX_ENV GENERATE_LATEX='NO'" fi # Paper size for PS and/or PDF: case "$DOXYGEN_PAPER_SIZE" in #( "") DOXYGEN_PAPER_SIZE="" ;; #( a4wide|a4|letter|legal|executive) DX_ENV="$DX_ENV PAPER_SIZE='$DOXYGEN_PAPER_SIZE'" ;; #( *) { { echo "$as_me:$LINENO: error: unknown DOXYGEN_PAPER_SIZE='$DOXYGEN_PAPER_SIZE'" >&5 echo "$as_me: error: unknown DOXYGEN_PAPER_SIZE='$DOXYGEN_PAPER_SIZE'" >&2;} { (exit 1); exit 1; }; } ;; esac #For debugging: #echo DX_FLAG_doc=$DX_FLAG_doc #echo DX_FLAG_dot=$DX_FLAG_dot #echo DX_FLAG_man=$DX_FLAG_man #echo DX_FLAG_html=$DX_FLAG_html #echo DX_FLAG_chm=$DX_FLAG_chm #echo DX_FLAG_chi=$DX_FLAG_chi #echo DX_FLAG_rtf=$DX_FLAG_rtf #echo DX_FLAG_xml=$DX_FLAG_xml #echo DX_FLAG_pdf=$DX_FLAG_pdf #echo DX_FLAG_ps=$DX_FLAG_ps #echo DX_ENV=$DX_ENV echo "$as_me:$LINENO: checking for an ANSI C-conforming const" >&5 echo $ECHO_N "checking for an ANSI C-conforming const... $ECHO_C" >&6 if test "${ac_cv_c_const+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int main () { /* FIXME: Include the comments suggested by Paul. */ #ifndef __cplusplus /* Ultrix mips cc rejects this. */ typedef int charset[2]; const charset x; /* SunOS 4.1.1 cc rejects this. */ char const *const *ccp; char **p; /* NEC SVR4.0.2 mips cc rejects this. */ struct point {int x, y;}; static struct point const zero = {0,0}; /* AIX XL C 1.02.0.0 rejects this. It does not let you subtract one const X* pointer from another in an arm of an if-expression whose if-part is not a constant expression */ const char *g = "string"; ccp = &g + (g ? g-g : 0); /* HPUX 7.0 cc rejects these. */ ++ccp; p = (char**) ccp; ccp = (char const *const *) p; { /* SCO 3.2v4 cc rejects this. */ char *t; char const *s = 0 ? (char *) 0 : (char const *) 0; *t++ = 0; } { /* Someone thinks the Sun supposedly-ANSI compiler will reject this. */ int x[] = {25, 17}; const int *foo = &x[0]; ++foo; } { /* Sun SC1.0 ANSI compiler rejects this -- but not the above. */ typedef const int *iptr; iptr p = 0; ++p; } { /* AIX XL C 1.02.0.0 rejects this saying "k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */ struct s { int j; const int *ap[3]; }; struct s *b; b->j = 5; } { /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */ const int foo = 10; } #endif ; return 0; } _ACEOF rm -f conftest.$ac_objext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>conftest.er1 ac_status=$? grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? 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grep -v '^ *+' conftest.er1 >conftest.err rm -f conftest.er1 cat conftest.err >&5 echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); } && { ac_try='test -z "$ac_c_werror_flag" || test ! -s conftest.err' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; } && { ac_try='test -s conftest.$ac_objext' { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 (eval $ac_try) 2>&5 ac_status=$? echo "$as_me:$LINENO: \$? = $ac_status" >&5 (exit $ac_status); }; }; then ac_cv_c_inline=$ac_kw; break else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 fi rm -f conftest.err conftest.$ac_objext conftest.$ac_ext done fi echo "$as_me:$LINENO: result: $ac_cv_c_inline" >&5 echo "${ECHO_T}$ac_cv_c_inline" >&6 case $ac_cv_c_inline in inline | yes) ;; *) case $ac_cv_c_inline in no) ac_val=;; *) ac_val=$ac_cv_c_inline;; esac cat >>confdefs.h <<_ACEOF #ifndef __cplusplus #define inline $ac_val #endif _ACEOF ;; esac echo "$as_me:$LINENO: checking whether time.h and sys/time.h may both be included" >&5 echo $ECHO_N "checking whether time.h and sys/time.h may both be included... $ECHO_C" >&6 if test "${ac_cv_header_time+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else cat >conftest.$ac_ext <<_ACEOF /* confdefs.h. */ _ACEOF cat confdefs.h >>conftest.$ac_ext cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include #include int main () { if ((struct tm *) 0) return 0; ; return 0; } _ACEOF rm -f conftest.$ac_objext if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 (eval $ac_compile) 2>conftest.er1 ac_status=$? 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So we exec the FD to /dev/null, # effectively closing config.log, so it can be properly (re)opened and # appended to by config.status. When coming back to configure, we # need to make the FD available again. if test "$no_create" != yes; then ac_cs_success=: ac_config_status_args= test "$silent" = yes && ac_config_status_args="$ac_config_status_args --quiet" exec 5>/dev/null $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false exec 5>>config.log # Use ||, not &&, to avoid exiting from the if with $? = 1, which # would make configure fail if this is the last instruction. $ac_cs_success || { (exit 1); exit 1; } fi libGenome-1.3.1/Makefile.am0000644002622200470610000000047110766631525012415 00000000000000ACLOCAL_AMFLAGS = -I m4 include doxygen.am MOSTLYCLEANFILES = $(DX_CLEANFILES) EXTRA_DIST = \ projects/libGenome.sln \ projects/libGenome.vcproj \ projects/libGenome.nsi \ projects/libGenome.doxygen pkgconfigdir = $(libdir)/pkgconfig pkgconfig_DATA = libGenome-@GENERIC_API_VERSION@.pc SUBDIRS = libGenome libGenome-1.3.1/ChangeLog0000644002622200470610000000171010647575617012137 00000000000000Changes between 0.5.1 and 0.5.2 =============================== Fixed critical gnGBKSource bug with end-of-line characters Fixed numerous gnRAWSource bugs Changed default source format to fastA Made gnSeqI 64-bit unsigned Now using a registry key for CodeWarrior source trees instead of an environment variable Updated project to CodeWarrior 8.3 format Changes between 0.5.0 and 0.5.1 =============================== Now using the NSIS installer to install libGenome in Windows. The libGenome_App CodeWarrior project stationary now uses the GenomeDev environment variable to specify the location of the libGenome source tree. Updates for compilation using gcc 3.2. Numerous fixes to the API documentation Bug fix for reading subsequences from GenBank flat files. An incorrect subsequence could potentially be read prior to version 0.5.1. Bug fix in gnRAWSource, thanks to Jean-Marc Lasgouttes. Numerous other bug fixes for memory leaks and access violations. libGenome-1.3.1/README0000644002622200470610000000003710647575617011246 00000000000000This is not quite a readme ... libGenome-1.3.1/libGenome/0000777002622200470610000000000011030171200012312 500000000000000libGenome-1.3.1/libGenome/testgnSequence.cpp0000644002622200470610000000534710647575617016001 00000000000000#ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnSourceFactory.h" #include "libGenome/gnFASSource.h" #include "libGenome/gnSequence.h" #include #include "libGenome/gnFilter.h" #include "libGenome/gnStringTools.h" #include "libGenome/gnFastTranslator.h" int main( int32 argc, char* argv[]) { argc; argv; try{ string filename; cout << "Enter a filename to read bases from.\n"; cin >> filename; cout << "Opening " + filename + "\n"; gnSequence gpseq, gnsubseq; // string pathname = filename; // standarizePathString( pathname ); // pathname = getPathString( pathname ); // gnSourceFactory * msf = gnSourceFactory::GetSourceFactory(); // msf->AddPath( pathname ); gpseq.LoadSource(filename); cout << "Length " << gpseq.length() << " in " << gpseq.contigListSize() << " contigs\n"; string pretrans, posttrans, posttrans2; const gnTranslator* dna2pro_good = gnTranslator::DNAProteinTranslator(); const gnFastTranslator* dna2pro_fast = gnFastTranslator::DNAProteinTranslator(); pretrans = gpseq.ToString(); posttrans = pretrans; posttrans2 = pretrans; cout << "Doing correct translation:\n"; dna2pro_good->Filter(posttrans); cout << "done\n"; gnsubseq = posttrans; gnFASSource::Write(gnsubseq, "profile_good.fas"); // posttrans = pretrans; cout << "Doing fast translation:\n"; dna2pro_fast->Filter(posttrans2); cout << "done\n"; gnsubseq = posttrans2; gnFASSource::Write(gnsubseq, "profile_fast.fas"); cout << "base pairs 8 thru 68 are: \n"; cout << gpseq.subseq(8, 60) << "\n"; for(uint32 i=0; i < 15; i++){ try{ cout << "Contig " << i << " length " << gpseq.contig(i).length() << "\n"; }catch(gnException& gne){ cout << gne; } } cout << gpseq.subseq(1000000, 10); cin >> filename; gnSeqI midpoint = gpseq.length() / 2; gnSequence seqA = gpseq.subseq(1, midpoint); gnSequence seqB = gpseq.subseq(1 + midpoint, gpseq.length() - midpoint); cout << "Splitting " << gpseq.length() << " to " << seqA.length() << " and " << seqB.length() << "\n"; cin >> filename; gnsubseq = gpseq.subseq(5, 10); cout << "subseq len: " << gnsubseq.length() << "\n"; cout << "subseq: " << gnsubseq << "\n"; gnSeqC* buf = new gnSeqC[gpseq.length()]; gpseq.ToArray(buf, gpseq.length()); cout << "Give a file name to output data: "; string outfilename; cin >> outfilename; gnFASSource::Write(gpseq, outfilename); /* gnSequence new_seq = gpseq.contig(3); cout << new_seq; new_seq += gpseq.contig(3); new_seq += gpseq.contig(2); new_seq += gpseq.contig(1); cout << new_seq; gnFASSource::Write(new_seq, outfilename); */ cout << "All done. Contigs 3, 2, 1 are in " << outfilename << "\n"; char bubba[50]; cin >> bubba; }catch(gnException& gne){ cout << gne; string reality_bites; cin >> reality_bites; } } libGenome-1.3.1/libGenome/gnRNASequence.h0000644002622200470610000000760010647575617015101 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnRNASequence.h // Purpose: Sequence class // Description: Provides a high level sequence interface to all types of // sequence data. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnRNASequence_h_ #define _gnRNASequence_h_ #include "libGenome/gnDefs.h" #include #include #include "libGenome/gnSequence.h" #include "libGenome/gnFilter.h" namespace genome { /** * gnRNASequence is a special kind of gnSequence which can be used for RNA sequences * It sets the default filters and comparators to the RNA filters and comparators. */ class GNDLLEXPORT gnRNASequence : public gnSequence { public: /** * Empty Constructor, creates an empty gnRNASequence. */ gnRNASequence(); /** * Creates a gnRNASequence with a single contig containing the bases in "seq". * @param seq The null terminated array of base pairs to use. */ gnRNASequence( const gnSeqC* seq ); /** * Creates a gnRNASequence with a single contig containing the bases in "str". * @param str The base pairs to use. */ gnRNASequence( const std::string& str ); /** * Creates a gnRNASequence with the contigs stored in "gngs". * @param gngs the gnGenomeSpec to get contigs from. */ gnRNASequence( const gnGenomeSpec& gngs ); /** * Creates a gnRNASequence with the contigs stored in "gnfs". * @param gnfs the gnFragmentSpec to get contigs from. */ gnRNASequence( const gnFragmentSpec& gnfs ); /** * Creates a gnRNASequence with the contigs stored in "gncs". * @param gncs the gnContigSpec to get contigs from. */ gnRNASequence( const gnContigSpec& gncs ); /** * Creates a gnRNASequence with a single contig containing the bases in "bases". * @param bases The base pairs to use * @param length The length of the base pair array. */ gnRNASequence( gnSeqC *bases, const gnSeqI length); /** * Copies the gnRNASequence "seq". * @param seq The gnRNASequence to copy. */ gnRNASequence( const gnRNASequence& seq); private: gnGenomeSpec *spec; list filter_list; const gnCompare* comparator; }; // class gnRNASequence inline gnRNASequence::gnRNASequence() : gnSequence(){ filter_list.push_back(gnFilter::fullRNASeqFilter()); comparator = gnCompare::RNASeqCompare(); } inline gnRNASequence::gnRNASequence( const gnSeqC* seq ) : gnSequence(seq){ filter_list.push_back(gnFilter::fullRNASeqFilter()); comparator = gnCompare::RNASeqCompare(); } inline gnRNASequence::gnRNASequence( const std::string& str ) : gnSequence(str){ filter_list.push_back(gnFilter::fullRNASeqFilter()); comparator = gnCompare::RNASeqCompare(); } inline gnRNASequence::gnRNASequence( const gnGenomeSpec& gngs ) : gnSequence(gngs){ filter_list.push_back(gnFilter::fullRNASeqFilter()); comparator = gnCompare::RNASeqCompare(); } inline gnRNASequence::gnRNASequence( const gnFragmentSpec& gnfs ) : gnSequence(gnfs){ filter_list.push_back(gnFilter::fullRNASeqFilter()); comparator = gnCompare::RNASeqCompare(); } inline gnRNASequence::gnRNASequence( const gnContigSpec& gncs ) : gnSequence(gncs){ filter_list.push_back(gnFilter::fullRNASeqFilter()); comparator = gnCompare::RNASeqCompare(); } inline gnRNASequence::gnRNASequence( gnSeqC *bases, const gnSeqI length) : gnSequence(bases, length){ filter_list.push_back(gnFilter::fullRNASeqFilter()); comparator = gnCompare::RNASeqCompare(); } inline gnRNASequence::gnRNASequence( const gnRNASequence& seq) : gnSequence(seq){ filter_list.push_back(gnFilter::fullRNASeqFilter()); comparator = gnCompare::RNASeqCompare(); } } // end namespace genome #endif // _gnRNASequence_h_ libGenome-1.3.1/libGenome/gnBaseHeader.h0000644002622200470610000000362710647575617014760 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnBaseHeader.h // Purpose: abstract Header class // Description: Provides an interface for Headers in memory and on disk. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnBaseHeader_h_ #define _gnBaseHeader_h_ #include "libGenome/gnDefs.h" #include #include "libGenome/gnClone.h" #include "libGenome/gnLocation.h" namespace genome { /** * This class provides a general interface to sequence related headers. * Headers commonly precede sequence data in several file formats. In * FastA files, the header is on the > line before a contig. * In GenBank files, each contig has headers describing authors and other * information. In GenBank files, the header name corresponds to the * name of the header field. A few genBank header names are: DEFINITION * ACCESSION, VERSION, KEYWORDS, SEGMENT, SOURCE, REFERENCE, and COMMENT. * Eventually, individual classes may be implemented for each header type. */ class GNDLLEXPORT gnBaseHeader : public gnClone { public: gnBaseHeader(){} virtual ~gnBaseHeader(){} virtual gnBaseHeader* Clone() const = 0; /** * Get the header. * @return The header as a std::string. */ virtual std::string GetHeader() const = 0; /** * Get the header's name, if any. * @return The header name as a std::string. */ virtual std::string GetHeaderName() const = 0; /** * Get the header's length in bytes. * @return The length of the header. */ virtual uint32 GetLength() const = 0; private: }; //class gnBaseHeader } // end namespace genome #endif // _gnBaseHeader_h_ libGenome-1.3.1/libGenome/testTests.cpp0000644002622200470610000001541410647575617015002 00000000000000#ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnSequence.h" #include "libGenome/gnGBKSource.h" #include "libGenome/gnFASSource.h" #include static boolean LocationLessthan(const gnLocation& a, const gnLocation& b); static boolean LocationLessthan(const gnLocation& a, const gnLocation& b){ return a.GetStart() < b.GetStart(); } static boolean LocationEndLessthan(const gnLocation& a, const gnLocation& b); static boolean LocationEndLessthan(const gnLocation& a, const gnLocation& b){ return a.GetEnd() < b.GetStart(); } static boolean LocationSizeLessthan(const gnLocation& a, const gnLocation& b); static boolean LocationSizeLessthan(const gnLocation& a, const gnLocation& b){ return a.GetEnd() - a.GetStart() < b.GetEnd() - b.GetStart(); } // create a location list which contains every intervening region // in l_list void ComplementLocation(vector& l_list){ if(l_list.size() < 2) return; //need 2 or more locations to get the in between regions vector comp_list; sort(l_list.begin(), l_list.end(), &LocationLessthan); for(uint32 locationI = 1; locationI < l_list.size(); locationI++){ //if they don't intersect there is an intervening region if( !l_list[locationI].Intersects( l_list[locationI-1] ) ){ //create the region between locationI and locationI - 1 gnLocation between_loc; between_loc.SetStart(l_list[locationI-1].GetEnd()); between_loc.SetEnd(l_list[locationI].GetStart()); //add it to the complement list comp_list.push_back(between_loc); } } l_list = comp_list; } void DeleteRepeats(list& loc_list){ loc_list.sort(&LocationLessthan); list::iterator loc_iter = loc_list.begin(); list::iterator cur_loc; for(; loc_iter != loc_list.end(); loc_iter++){ cur_loc = loc_iter; cur_loc++; while(cur_loc != loc_list.end() && !LocationEndLessthan(*loc_iter, *cur_loc)){ if(loc_iter->Intersects(*cur_loc)){ *loc_iter = loc_iter->GetUnion(*cur_loc); list::iterator to_del = cur_loc; cur_loc--; loc_list.erase(to_del); } cur_loc++; } } } void WriteData(gnSequence& file_sequence, list& loc_list, string& filename){ gnSequence loc_seq; cout << "Gathering sequence data to write...\n"; list::iterator loc_iter = loc_list.begin(); uint32 loc_count = loc_list.size(); uint32 notice_interval = loc_count / 10; uint32 cur_locI = 0; for(;loc_iter != loc_list.end(); loc_iter++){ loc_seq += file_sequence.ToString( loc_iter->GetEnd() - loc_iter->GetStart(), loc_iter->GetStart()); if(cur_locI % notice_interval == 0){ cout << (cur_locI / loc_count) * 10 << "%.."; } cur_locI++; } cout << "\nWriting sequence data...\n"; gnFASSource::Write(loc_seq, filename); } void WriteList(list& loc_list, string& filename){ ofstream list_out(filename.c_str()); list::iterator loc_iter = loc_list.begin(); for(;loc_iter != loc_list.end(); loc_iter++){ list_out << loc_iter->GetStart() << '\t' << loc_iter->GetEnd() << '\n'; } list_out.close(); } void print_usage(char* pname){ cout << "Usage: " << pname << " \n"; } int main( int argc, char* argv[] ) { boolean run_interactive = false; string seq_filename; string exon_list_filename; string intron_list_filename; string exon_seq_filename; string intron_seq_filename; // define a gnSequence to store the sequence gnSequence file_sequence; if(!run_interactive){ // check for correct calling semantics if(argc != 6){ print_usage(argv[0]); return -1; } seq_filename = argv[1]; exon_list_filename = argv[2]; intron_list_filename = argv[3]; exon_seq_filename = argv[4]; intron_seq_filename = argv[5]; }else{ // Get the name of the sequence to load cout << "Enter the name of the sequence file to load:\n" ; cin >> seq_filename; } // Load the sequence and tell the user if it loaded successfully if(file_sequence.LoadSource(seq_filename)) { cout << seq_filename << " loaded successfully. " << file_sequence.length() << " base pairs.\n"; }else{ cout << "Error loading file.\n"; return -1; } uint32 feature_count = file_sequence.getFeatureListLength(); uint32 cds_count = 0; //define a sequence for each type of data gnSequence exon_seq; gnSequence intron_seq; list exon_list; list intron_list; cout << "There are " << feature_count << " known features.\n"; for(uint32 featureI = 0; featureI < feature_count; featureI++){ gnBaseFeature* cur_feat = file_sequence.getFeature(featureI); if(cur_feat == NULL){ cout << "cur_feat is NULL, trace me!\n"; cur_feat = file_sequence.getFeature(featureI); continue; } if(cur_feat->GetName() == "CDS"){ cds_count++; uint32 loc_count = cur_feat->GetLocationListLength(); vector cur_exon_list, cur_intron_list; for(uint32 locationI = 0; locationI < loc_count; locationI++){ cur_exon_list.push_back(cur_feat->GetLocation(locationI)); exon_list.push_back(cur_exon_list[locationI]); } if(loc_count >= 2){ cur_intron_list = cur_exon_list; ComplementLocation(cur_intron_list); for(uint32 locationI = 0; locationI < cur_intron_list.size(); locationI++) intron_list.push_back(cur_intron_list[locationI]); } /* Code for exon size tracking */ /* sort(cur_exon_list.begin(), cur_exon_list.end(), &LocationSizeLessthan); gnSeqI cur_size = cur_exon_list[loc_count - 1].GetEnd() - cur_exon_list[loc_count - 1].GetStart(); size_out << cur_size << '\n'; if(cur_size > 5000){ cout << "psycho bob is at it again\n"; cout << "Found " << cur_size << " length exon in feature: " << cur_feat->GetName() << "\n"; cout << "Feature Index: " << featureI << "\n"; for(uint32 i=0; i < cur_feat->GetQualifierListLength(); i++){ cout << cur_feat->GetQualifierName(i) << "\t" << cur_feat->GetQualifierValue(i) << "\n"; } cout << "\n"; } */ delete cur_feat; } } cout << "There are " << cds_count << " cds features.\n"; //now sort the lists and delete repeats and fix overlaps uint32 exon_count = exon_list.size(); cout << "Deleting exon repeats... "; DeleteRepeats(exon_list); cout << "Eliminated " << exon_count - exon_list.size() << " repeats for a total of "; cout << exon_list.size() << " repeats\n"; uint32 intron_count = intron_list.size(); cout << "Deleting intron repeats... "; DeleteRepeats(intron_list); cout << "Eliminated " << intron_count - intron_list.size() << " repeats for a total of "; cout << intron_list.size() << " repeats\n"; WriteList(exon_list, exon_list_filename); WriteList(intron_list, intron_list_filename); WriteData(file_sequence, exon_list, exon_seq_filename); WriteData(file_sequence, intron_list, intron_seq_filename); if(run_interactive) cin >> seq_filename; return 0; }; libGenome-1.3.1/libGenome/gnGBKSource.h0000644002622200470610000001053211026443220014522 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnGBKSource.h // Purpose: Implements gnBaseSource for GenBank files // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnGBKSource_h_ #define _gnGBKSource_h_ #include "libGenome/gnDefs.h" #include #include #include #include "libGenome/gnFileSource.h" #include "libGenome/gnFileContig.h" #include "libGenome/gnSourceSpec.h" #include "libGenome/gnSequence.h" namespace genome { const uint32 SEQ_COLUMN_WIDTH = 80; const uint32 SEQ_HEADER_NAME_LENGTH = 11; const uint32 SEQ_SUBTAG_COLUMN = 5; const uint32 SEQ_LOCUS_CIRCULAR_COLUMN = 43; const uint32 SEQ_LOCUS_NAME_COLUMN = 13; const uint32 SEQ_LOCUS_NAME_LENGTH = 10; const uint32 SEQ_LOCUS_SIZE_LENGTH = 10; const uint32 SEQ_LOCUS_DNATYPE_OFFSET = 33; const uint32 SEQ_LOCUS_DNATYPE_LENGTH = 7; const uint32 SEQ_LOCUS_DIVCODE_OFFSET = 52; const uint32 SEQ_LOCUS_DIVCODE_LENGTH = 3; const uint32 SEQ_LOCUS_DATE_OFFSET = 62; const uint32 SEQ_LOCUS_DATE_LENGTH = 11; const uint32 SEQ_FEATURE_LOC_OFFSET = 21; const uint32 SEQ_BASES_INDEX_END = 9; /** * gnGBKSource is a GenBank sequence file reader. * This class reads and writes the GenBank file format. * gnGBKSource is used by gnSourceFactory to read files and should only be used * directly when writing out files in GBK file format by calling * gnGBKSource::Write( mySpec, "C:\\mySeqFile.gbk"); */ class GNDLLEXPORT gnGBKSource : public gnFileSource { public: /** * Empty Constructor, does nothing. */ gnGBKSource(); /** * Clone Constructor copies the specified gnGBKSource. * @param s The gnGBKSource to copy. */ gnGBKSource( const gnGBKSource& s ); /** * Destructor, frees memory. */ ~gnGBKSource(); /** * Returns an exact copy of this class. */ gnGBKSource* Clone() const; // Contig Access methods uint32 GetContigListLength() const; boolean HasContig( const std::string& name ) const; uint32 GetContigID( const std::string& name ) const; std::string GetContigName( const uint32 i ) const; gnSeqI GetContigSeqLength( const uint32 i ) const; boolean SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI=ALL_CONTIGS ); /** * Writes the specified gnSequence to a .GBK file named "filename". * @param seq The gnSequence to write out. * @param filename The name of the file to write. * @return True if successful, false otherwise. */ static boolean Write(gnSequence& seq, const std::string& filename); /** * Writes the specified source to a .GBK file named "filename". * @param source The source to write out. * @param filename The name of the file to write. * @return True if successful, false otherwise. */ static boolean Write(gnBaseSource *source, const std::string& filename); gnGenomeSpec *GetSpec() const; gnFileContig* GetFileContig( const uint32 contigI ) const; private: boolean SeqReadImpl( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI=ALL_CONTIGS ); boolean SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes ); boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes ); boolean ParseStream( std::istream& fin ); static std::string& Filler(uint32 length); static void FormatString(std::string& data, uint32 offset, uint32 width); // gnSeqI m_seqLength; gnGenomeSpec *m_spec; std::vector< gnFileContig* > m_contigList; };// class gnGBKSource template< class SubSpec > void WriteHeader(gnMultiSpec< SubSpec >* spec, const std::string& hdr, std::ofstream& m_ofstream); // Clone inline gnGBKSource* gnGBKSource::Clone() const { return new gnGBKSource( *this ); } // Contig Access methods inline uint32 gnGBKSource::GetContigListLength() const { return m_contigList.size(); } inline boolean gnGBKSource::Write(gnBaseSource *source, const std::string& filename){ gnSequence gns(*source->GetSpec()); return Write(gns, filename); } inline gnGenomeSpec *gnGBKSource::GetSpec() const{ return m_spec->Clone(); } } // end namespace genome #endif // _gnGBKSource_h_ libGenome-1.3.1/libGenome/testSource.cpp0000644002622200470610000000302210647575617015130 00000000000000#ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnFASSource.h" #include #include "libGenome/gnFilter.h" int32 main( int32 argc, char* argv[]) { argc; argv; gnFASSource source; string sourceFile = "w:/developm/_data/cft073/v6/cft073v6.fas"; cout << "Enter Source: "; cin >> sourceFile; cout << "Opening " << sourceFile << endl; if( !source.Open( sourceFile ) ) { cout << "Failed to open " << sourceFile << endl; return 1; } cout << "Number of Contigs " << source.GetContigListLength() << endl; for( uint32 i=0; i < source.GetContigListLength(); ++i ) { gnFileContig* fg = source.GetContig(i); cout << "\t" << fg->GetName() << endl; cout << "\t\t" << fg->GetSeqLength() << " : {" << fg->GetFileStartEnd().first << ", " << fg->GetFileStartEnd().second << ": "; for( uint32 j=0; jGetSectStartEnd( (gnContigSection)j ).first << "," << fg->GetSectStartEnd( (gnContigSection)j ).second << ") "; cout << "}" << endl; cout << "\t\t" << (fg->HasRepeatSeqGap()?"TRUE":"FALSE") << " (" << fg->GetRepeatSeqGapSize().first << "," << fg->GetRepeatSeqGapSize().second << ")" << endl; } uint32 seqLen = 75; gnSeqC* seq = new gnSeqC[seqLen+1]; for( uint32 i=0; i < seqLen; ++i ) seq[i] = '@'; seq[seqLen] = 0; cout << "SeqRead(0, seq, " << seqLen << ", 0)" << endl; if( source.SeqRead( 158, seq, seqLen, 0 ) ) { seq[seqLen] = 0; cout << seqLen << "> " << seq << endl; } else cout << "Read failed " << endl; return 0; }libGenome-1.3.1/libGenome/gnSetup.h0000644002622200470610000000405610727100417014047 00000000000000///////////////////////////////////////////////////////////////////////////// // File: libGenome/gnSetup.h // Purpose: libGenome setup // Description: Defines os/compiler specific constants, etc. // Included in libGenome/gnDefs.h. // Rev: A // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnSetup_h_ #define _gnSetup_h_ #include #ifdef GNMAKINGDLL // build the libgenome dll #define GNDLLEXPORT __declspec(dllexport) #define GNDLLEXPORT_DATA(type) __declspec(dllexport) type #elif defined(GNUSINGDLL) // the project uses a libGenome as a dll #define GNDLLEXPORT __declspec(dllimport) #define GNDLLEXPORT_DATA(type) __declspec(dllimport) type #else // static linking #define GNDLLEXPORT #define GNDLLEXPORT_DATA #endif // attempt to auto-link the genome library on windows #if defined(WIN64)&&defined(NDEBUG)&&!defined(FASTDEBUG)&&defined(_OPENMP) #pragma comment(lib, "genome64omp.lib") #endif #if defined(WIN64)&&defined(FASTDEBUG)&&defined(_OPENMP) #pragma comment(lib, "genome64fdomp.lib") #endif #if defined(WIN32)&&!defined(WIN64)&&defined(NDEBUG)&&!defined(FASTDEBUG)&&defined(_OPENMP) #pragma comment(lib, "genomeomp.lib") #endif #if defined(WIN32)&&!defined(WIN64)&&defined(FASTDEBUG)&&defined(_OPENMP) #pragma comment(lib, "genomefdomp.lib") #endif #if defined(WIN64)&&defined(NDEBUG)&&!defined(FASTDEBUG)&&!defined(_OPENMP) #pragma comment(lib, "genome64.lib") #endif #if defined(WIN64)&&defined(FASTDEBUG)&&!defined(_OPENMP) #pragma comment(lib, "genome64fd.lib") #endif #if defined(WIN32)&&!defined(WIN64)&&defined(NDEBUG)&&!defined(FASTDEBUG)&&!defined(_OPENMP) #pragma comment(lib, "genome.lib") #endif #if defined(WIN32)&&!defined(WIN64)&&defined(FASTDEBUG)&&!defined(_OPENMP) #pragma comment(lib, "genomefd.lib") #endif #endif //_gnSetup_h_ libGenome-1.3.1/libGenome/gnPosSpecificTranslator.h0000644002622200470610000000445210647575617017253 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnPosSpecificTranslator.h // Purpose: Special case ORF translation // Description: Used to translate sequences differently based on the position of // input characters. Useful for tranlating genes because the first // codon is translated differently // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnPosSpecificTranslator_h_ #define _gnPosSpecificTranslator_h_ #include "libGenome/gnDefs.h" #include #include #include #include "libGenome/gnClone.h" #include "libGenome/gnBaseFilter.h" #include "libGenome/gnFastTranslator.h" namespace genome { /** * Used to translate sequences differently based on the position of * input characters. Useful for tranlating genes because the first * codon is translated differently. */ class GNDLLEXPORT gnPosSpecificTranslator : public gnBaseFilter { public: static const gnPosSpecificTranslator *ProteinDNATranslator(); static const gnPosSpecificTranslator *DNAProteinTranslator(); enum gnTranslatorType{ ProteinDNATranslatorType, DNAProteinTranslatorType, }; gnPosSpecificTranslator(); gnPosSpecificTranslator( gnTranslatorType t_type ); gnPosSpecificTranslator( const gnPosSpecificTranslator& sf ); gnPosSpecificTranslator& operator= (const gnPosSpecificTranslator& sf); gnPosSpecificTranslator* Clone() const; // gnSeqC virtual gnSeqC Filter( const gnSeqC ch ) const; virtual void Filter( gnSeqC** seq, gnSeqI& len ) const; // std::string virtual void Filter( std::string &seq ) const; private: gnTranslatorType m_type; // defines the type of translator this is const gnBaseFilter* filter; // this is the filter used to do the translation void CreateProteinDNATranslator(); void CreateDNAProteinTranslator(); };//class gnPosSpecificTranslator inline gnPosSpecificTranslator* gnPosSpecificTranslator::Clone() const { return new gnPosSpecificTranslator(*this); } } // end namespace genome #endif // _gnPosSpecificTranslator_h_ libGenome-1.3.1/libGenome/gnBaseFilter.h0000644002622200470610000000362310647575617015011 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnBaseFilter.h // Purpose: Generic filter interface // Description: Filters sequences, translates, reverse complement, converts // additions, etc. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnBaseFilter_h_ #define _gnBaseFilter_h_ #include "libGenome/gnDefs.h" #include #include "libGenome/gnClone.h" #include "libGenome/gnDefs.h" namespace genome { class GNDLLEXPORT gnBaseFilter : public gnClone { public: virtual gnBaseFilter* Clone() const = 0; /** * Gets the name of this filter * @return the filter name */ virtual std::string GetName() const; /** * Sets the name of this filter * @param name the new filter name */ virtual void SetName( std::string name ); /** * Filter the given character * @param ch The character to filter * @return The filtered character */ virtual gnSeqC Filter( const gnSeqC ch ) const = 0; /** * Filter the given character array * @param seq A pointer to the character array * @param len the length of the character array to filter * @return The filtered character */ virtual void Filter( gnSeqC** seq, gnSeqI& len ) const = 0; /** * Filters the given std::string * @param seq The std::string to filter */ virtual void Filter( std::string &seq ) const = 0; protected: std::string m_name; };//class gnBaseFilter inline std::string gnBaseFilter::GetName() const { return m_name; } inline void gnBaseFilter::SetName( std::string name ) { m_name = name; } } // end namespace genome #endif // _gnBaseFilter_h_ libGenome-1.3.1/libGenome/gnProteinSequence.h0000644002622200470610000001011010647575617016067 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnProteinSequence.h // Purpose: Sequence class // Description: Provides a high level sequence interface to all types of // sequence data. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnProteinSequence_h_ #define _gnProteinSequence_h_ #include "libGenome/gnDefs.h" #include #include #include "libGenome/gnSequence.h" #include "libGenome/gnFilter.h" namespace genome { /** * gnProteinSequence is a special kind of gnSequence which can be used for RNA sequences * It sets the default filters and comparators to the RNA filters and comparators. */ class GNDLLEXPORT gnProteinSequence : public gnSequence { public: /** * Empty Constructor, creates an empty gnProteinSequence. */ gnProteinSequence(); /** * Creates a gnProteinSequence with a single contig containing the bases in "seq". * @param seq The null terminated array of base pairs to use. */ gnProteinSequence( const gnSeqC* seq ); /** * Creates a gnProteinSequence with a single contig containing the bases in "str". * @param str The base pairs to use. */ gnProteinSequence( const std::string& str ); /** * Creates a gnProteinSequence with the contigs stored in "gngs". * @param gngs the gnGenomeSpec to get contigs from. */ gnProteinSequence( const gnGenomeSpec& gngs ); /** * Creates a gnProteinSequence with the contigs stored in "gnfs". * @param gnfs the gnFragmentSpec to get contigs from. */ gnProteinSequence( const gnFragmentSpec& gnfs ); /** * Creates a gnProteinSequence with the contigs stored in "gncs". * @param gncs the gnContigSpec to get contigs from. */ gnProteinSequence( const gnContigSpec& gncs ); /** * Creates a gnProteinSequence with a single contig containing the bases in "bases". * @param bases The base pairs to use * @param length The length of the base pair array. */ gnProteinSequence( gnSeqC *bases, const gnSeqI length); /** * Copies the gnProteinSequence "seq". * @param seq The gnProteinSequence to copy. */ gnProteinSequence( const gnProteinSequence& seq); private: gnGenomeSpec *spec; list filter_list; const gnCompare* comparator; }; // class gnProteinSequence inline gnProteinSequence::gnProteinSequence() : gnSequence(){ filter_list.push_back(gnFilter::proteinSeqFilter()); comparator = gnCompare::ProteinSeqCompare(); } inline gnProteinSequence::gnProteinSequence( const gnSeqC* seq ) : gnSequence(seq){ filter_list.push_back(gnFilter::proteinSeqFilter()); comparator = gnCompare::ProteinSeqCompare(); } inline gnProteinSequence::gnProteinSequence( const std::string& str ) : gnSequence(str){ filter_list.push_back(gnFilter::proteinSeqFilter()); comparator = gnCompare::ProteinSeqCompare(); } inline gnProteinSequence::gnProteinSequence( const gnGenomeSpec& gngs ) : gnSequence(gngs){ filter_list.push_back(gnFilter::proteinSeqFilter()); comparator = gnCompare::ProteinSeqCompare(); } inline gnProteinSequence::gnProteinSequence( const gnFragmentSpec& gnfs ) : gnSequence(gnfs){ filter_list.push_back(gnFilter::proteinSeqFilter()); comparator = gnCompare::ProteinSeqCompare(); } inline gnProteinSequence::gnProteinSequence( const gnContigSpec& gncs ) : gnSequence(gncs){ filter_list.push_back(gnFilter::proteinSeqFilter()); comparator = gnCompare::ProteinSeqCompare(); } inline gnProteinSequence::gnProteinSequence( gnSeqC *bases, const gnSeqI length) : gnSequence(bases, length){ filter_list.push_back(gnFilter::proteinSeqFilter()); comparator = gnCompare::ProteinSeqCompare(); } inline gnProteinSequence::gnProteinSequence( const gnProteinSequence& seq) : gnSequence(seq){ filter_list.push_back(gnFilter::proteinSeqFilter()); comparator = gnCompare::ProteinSeqCompare(); } } // end namespace genome #endif // _gnProteinSequence_h_ libGenome-1.3.1/libGenome/gnStringHeader.h0000644002622200470610000000531010647575617015343 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnStringHeader.h // Purpose: abstract Header class // Description: Provides an interface for Headers in memory. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnStringHeader_h_ #define _gnStringHeader_h_ #include "libGenome/gnDefs.h" #include #include "libGenome/gnClone.h" #include "libGenome/gnLocation.h" #include "libGenome/gnBaseHeader.h" namespace genome { /** * gnStringHeader stores sequence related header information in memory. * Use gnStringHeader for a general purpose headers. * @see gnBaseHeader */ class GNDLLEXPORT gnStringHeader : public gnBaseHeader { public: /** * Empty constructor. */ gnStringHeader(); /** * Create a gnStringHeader. * @param name The header name. * @param header The header. */ gnStringHeader(const std::string& name, const std::string& header); /** * Copy constructor. * @param s The gnStringHeader to copy. */ gnStringHeader(const gnStringHeader& s); /** * Destructor, frees memory. */ ~gnStringHeader() {}; gnStringHeader* Clone() const; std::string GetHeader() const; std::string GetHeaderName() const; /** * Set the header stored in this class. * @param header The header as a std::string. */ void SetHeader(const std::string& header); /** * Set the header's name stored in this class. * @param name The header name as a std::string. */ void SetHeaderName(const std::string& name); uint32 GetLength() const; private: std::string m_name; std::string m_header; }; //class gnStringHeader inline gnStringHeader::gnStringHeader(){ m_header = std::string(); } inline gnStringHeader::gnStringHeader(const std::string& name, const std::string& header){ m_name = name; m_header = header; } inline gnStringHeader::gnStringHeader(const gnStringHeader& s){ m_header = std::string(s.m_header); } inline gnStringHeader* gnStringHeader::Clone() const{ return new gnStringHeader(*this); } inline std::string gnStringHeader::GetHeader() const{ return m_header; } inline std::string gnStringHeader::GetHeaderName() const{ return m_name; } inline void gnStringHeader::SetHeader(const std::string& header){ m_header = header; } inline void gnStringHeader::SetHeaderName(const std::string& name){ m_name = name; } inline uint32 gnStringHeader::GetLength() const{ return m_header.length(); } } // end namespace genome #endif // _gnStringHeader_h_ libGenome-1.3.1/libGenome/gnFileContig.h0000644002622200470610000001226210647575617015013 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnFileContig.h // Purpose: File Position holder. // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnFileContig_h_ #define _gnFileContig_h_ #include "libGenome/gnDefs.h" #include #include "libGenome/gnClone.h" #include namespace genome { /** * gnFileContig is used by source classes to track the location of * sequence data on disk. gnFileContig stores the start and end byte * offset, and the size of a repeated gap in the sequence data. * Also stores whether the sequence data is in the expected format or * if it is corrupted. */ class GNDLLEXPORT gnFileContig : public gnClone { public: gnFileContig(); gnFileContig( std::string nameStr, const uint64 pos, const uint64 len ); gnFileContig( const gnFileContig& fc ); ~gnFileContig(); gnFileContig* Clone() const; void Clear(); std::string GetName() const; gnSeqI GetSeqLength() const; std::pair GetFileStartEnd() const; uint64 GetFileLength() const; std::pair GetSectStartEnd( const gnContigSection i ) const; uint64 GetSectLength( gnContigSection i ) const; boolean HasRepeatSeqGap() const; std::pair GetRepeatSeqGapSize() const; boolean SetName( std::string nameStr ); boolean SetSeqLength( const gnSeqI len ); boolean AddToSeqLength( const gnSeqI len ); boolean SetFileStart( const uint64 s ); boolean SetFileEnd( const uint64 e ); boolean SetFileStartEnd( const std::pair se ); boolean SetSectStart( const gnContigSection i, const uint64 s ); boolean SetSectEnd( const gnContigSection i, const uint64 e ); boolean SetSectStartEnd( const gnContigSection i, const std::pair se); boolean SetRepeatSeqGap( const boolean rsg ); boolean SetRepeatSeqGapSize( const std::pair rsgSize ); boolean SetRepeatSeqSize( const uint64 seqSize ); boolean SetRepeatGapSize( const uint64 gapSize ); private: std::string m_name; gnSeqI m_seqLength; std::pair m_fileStartEnd; std::pair m_startEndArray[CONTIG_SECTION_SIZE]; // sequence access boolean m_repeatSeqGap; // if true, use m_repeatSeqGapSize std::pair< uint64, uint64 > m_repeatSeqGapSize; };// class gnFileContig // Clone inline gnFileContig* gnFileContig::Clone() const { return new gnFileContig( *this ); } // GET inline std::string gnFileContig::GetName() const { return m_name; } inline gnSeqI gnFileContig::GetSeqLength() const { return m_seqLength; } inline std::pair gnFileContig::GetFileStartEnd() const { return m_fileStartEnd; } inline uint64 gnFileContig::GetFileLength() const { return m_fileStartEnd.second - m_fileStartEnd.first + 1; } inline std::pair gnFileContig::GetSectStartEnd( const gnContigSection i ) const { if( (uint32)i < CONTIG_SECTION_SIZE ) return m_startEndArray[(uint32)i]; return std::pair(0,0); } inline uint64 gnFileContig::GetSectLength( gnContigSection i ) const { if( (uint32)i < CONTIG_SECTION_SIZE ) return m_startEndArray[(uint32)i].second - m_startEndArray[(uint32)i].first + 1; return 0; } inline boolean gnFileContig::HasRepeatSeqGap() const { return m_repeatSeqGap; } inline std::pair gnFileContig::GetRepeatSeqGapSize() const { return m_repeatSeqGapSize; } // SET inline boolean gnFileContig::SetName( std::string nameStr ) { m_name = nameStr; return true; } inline boolean gnFileContig::SetSeqLength( const gnSeqI len ) { m_seqLength = len; return true; } inline boolean gnFileContig::AddToSeqLength( const gnSeqI len ) { m_seqLength += len; return true; } inline boolean gnFileContig::SetFileStart( const uint64 s ) { m_fileStartEnd.first = s; return true; } inline boolean gnFileContig::SetFileEnd( const uint64 e ) { m_fileStartEnd.second = e; return true; } inline boolean gnFileContig::SetFileStartEnd( const std::pair se ) { m_fileStartEnd = se; return true; } inline boolean gnFileContig::SetSectStart( const gnContigSection i, const uint64 s ) { if( (uint32)i < CONTIG_SECTION_SIZE ) { m_startEndArray[(uint32)i].first = s; return true; } return false; } inline boolean gnFileContig::SetSectEnd( const gnContigSection i, const uint64 e ) { if( (uint32)i < CONTIG_SECTION_SIZE ) { m_startEndArray[(uint32)i].second = e; return true; } return false; } inline boolean gnFileContig::SetSectStartEnd( const gnContigSection i, const std::pair se ) { if( (uint32)i < CONTIG_SECTION_SIZE ) { m_startEndArray[(uint32)i] = se; return true; } return false; } inline boolean gnFileContig::SetRepeatSeqGap( const boolean rsg ) { m_repeatSeqGap = rsg; return true; } inline boolean gnFileContig::SetRepeatSeqGapSize( const std::pair rsgSize ) { return SetRepeatSeqSize( rsgSize.first ) && SetRepeatGapSize( rsgSize.second ); } } // end namespace genome #endif // _gnFileContig_h_ libGenome-1.3.1/libGenome/gnException.cpp0000644002622200470610000000200010647575617015246 00000000000000#ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnException.h" #include using namespace std; namespace genome { void gnException::AddCaller(const char* const function) { string func(function); string pretty_func = func.substr(0, func.find('(')+1); pretty_func += func.substr(func.rfind(')'), func.length()); function_trace.push_back(pretty_func); } ostream& operator<<(ostream& os, const gnException& gne){ //write exception to stream. os << "Exception " << gne.m_code.GetName() << " thrown "; list::const_iterator func_iter = gne.function_trace.begin(); //print the original function if(func_iter != gne.function_trace.end()){ os << "from\n" << *func_iter << " in " << gne.m_file << " " << gne.m_line; func_iter++; } //print the call stack while(func_iter != gne.function_trace.end()){ os << "\nCalled by " << *func_iter; func_iter++; } if(gne.m_message.length() > 0) os <<"\n" << gne.m_message; os << "\n"; return os; } } // end namespace genome libGenome-1.3.1/libGenome/gnSEQSource.h0000644002622200470610000001003110647575617014571 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnSEQSource.h // Purpose: Implements gnBaseSource for .SEQ files // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnSEQSource_h_ #define _gnSEQSource_h_ #include "libGenome/gnDefs.h" #include #include #include #include "libGenome/gnFileSource.h" #include "libGenome/gnFileContig.h" #include "libGenome/gnSourceSpec.h" #include "libGenome/gnSequence.h" namespace genome { /** * gnSEQSource is a SEQ file reader. * This class reads and writes the DNAStar SEQ file format. * gnSEQSource is used by gnSourceFactory to read files and should only be used * directly.when writing out files in SEQ file format by calling * gnSEQSource::Write( mySpec, "C:\\mySeqFile.seq"); */ class GNDLLEXPORT gnSEQSource : public gnFileSource { public: /** * Empty Constructor, does nothing. */ gnSEQSource(); /** * Clone Constructor copies the specified gnSEQSource. * @param s The gnSEQSource to copy. */ gnSEQSource( const gnSEQSource& s ); /** * Destructor, frees memory. */ ~gnSEQSource(); /** * Returns an exact copy of this class. */ gnSEQSource* Clone() const; // Contig Access methods uint32 GetContigListLength() const; boolean HasContig( const std::string& name ) const; uint32 GetContigID( const std::string& name ) const; std::string GetContigName( const uint32 i ) const; gnSeqI GetContigSeqLength( const uint32 i ) const; boolean SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI=ALL_CONTIGS ); /** * Writes the specified gnSequence to a .SEQ file named "filename". * @param sequence The gnSequence to write out. * @param filename The name of the file to write. * @return True if successful, false otherwise. */ static boolean Write(gnSequence& sequence, const std::string& filename); /** * Writes the specified source to a .SEQ file named "filename". * @param source The source to write out. * @param filename The name of the file to write. * @return True if successful, false otherwise. */ static boolean Write(gnBaseSource *source, const std::string& filename); /** * Writes the given spec to a .SEQ file named "filename". * @param spec The spec to write out. * @param filename The name of the file to write. * @return True if successful, false otherwise. */ static boolean Write(gnGenomeSpec *spec, const std::string& filename); gnGenomeSpec *GetSpec() const; gnFileContig* GetFileContig( const uint32 contigI ) const; private: boolean SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes ); boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes ); boolean ParseStream( std::istream& fin ); static std::string& Filler(uint32 length); static void FormatString(std::string& data, uint32 offset, uint32 width); static void BaseCount(const std::string& bases, gnSeqI& a_count, gnSeqI& c_count, gnSeqI& g_count, gnSeqI& t_count, gnSeqI& other_count); // gnSeqI m_seqLength; gnGenomeSpec *m_spec; std::vector< gnFileContig* > m_contigList; };// class gnSEQSource // Clone inline gnSEQSource* gnSEQSource::Clone() const { return new gnSEQSource( *this ); } // Contig Access methods inline uint32 gnSEQSource::GetContigListLength() const { return m_contigList.size(); } inline boolean gnSEQSource::Write(gnSequence& sequence, const std::string& filename){ return Write(sequence.GetSpec(), filename); } inline boolean gnSEQSource::Write(gnBaseSource *source, const std::string& filename){ return Write(source->GetSpec(), filename); } inline gnGenomeSpec *gnSEQSource::GetSpec() const{ return m_spec->Clone(); } } // end namespace genome #endif // _gnSEQSource_h_ libGenome-1.3.1/libGenome/gnLocation.h0000644002622200470610000002606310647575617014544 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnLocation.h // Purpose: Standard Location for Feature // Description: Feature location // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnLocation_h_ #define _gnLocation_h_ #include "libGenome/gnDefs.h" #include #include #include "libGenome/gnClone.h" namespace genome { /** * This class is used to store sequence locations. gnBaseFeature uses it * to track feature locations. gnLocation is capable of representing any * GenBank style location qualifier. gnLocation stores the start coordinate * and a startLength value which represents the length of an undetermined * region of sequence prior to the starting coordinate. A startLength of * GNSEQI_END represents an unknown start, whereas a startLength of 0 * implies that the start coordinate is unambiguous. Any value other value * indicates a range of coordinates for the starting position. The range is * bounded by the given start coordinate and extends startLength characters * upstream. Likewise, an endLength of GNSEQI_END represents an unknown * ambiguous end coordinate, and an endLength of 0 implies that the end * coordinate is unambiguous. Any other value for endLength denotes a range * of ending coordinates starting at end and continuing for endLength characters. */ class GNDLLEXPORT gnLocation : public gnClone { public: enum intersectRestriction{ determinedRegions, undeterminedRegions, allRegions }; enum gnLocationType{ LT_Standard, //standard == join multiple locations. LT_BetweenBases, LT_Complement, LT_Order, LT_Group, LT_OneOf, LT_Nothing }; static const gnSeqI Defined = 0; static const gnSeqI Unknown = GNSEQI_END; public: /** * Empty constructor, does nothing. */ gnLocation(); /** * Copy constructor, copies a gnLocation. * @param s the location to copy. */ gnLocation( const gnLocation& s); /** * Constructor, creates a gnLocation. * @param start The start position within the sequence. * @param end The end position within the sequence. * @param type The type of the location, LT_Standard by default. * @param contigName The name of the contig associated with this location, empty by default. * @see gnLocationType */ gnLocation( const gnSeqI start, const gnSeqI end, const gnLocationType type = LT_Standard, std::string contigName = ""); /** * Constructor, creates a gnLocation. * @param start The start position within the sequence. * @param startLength GNSEQI_END if the starting location is unbounded to the left, 0 if defined, otherwise it specifies a range * @param end The end position within the sequence. * @param endLength 0 if defined, GNSEQI_END if unbounded to the right, otherwise specifies a range * @param type The type of the location, LT_Standard by default. * @param contigName The name of the contig associated with this location, empty by default. * @see gnLocationType */ gnLocation( const gnSeqI start, const gnSeqI startLength, const gnSeqI end, gnSeqI endLength, const gnLocationType type = LT_Standard, std::string contigName = ""); gnLocation* Clone() const; /** * Resets this location to default values */ void Clear(); /** * Crops this location to fit within the specified location boundaries. * @param l The location boundaries. * @return True if the location still exists, false if the crop amount is larger than the location. */ boolean CropTo( const gnLocation &l ); /** * Crops the start location by the specified amount. * @param start The amount to crop. * @return True if the location still exists, false if the crop amount is larger than the location. */ boolean CropStart( const gnSeqI start ); /** * Crops the end location by the specified amount. * @param end The amount to crop. * @return True if the location still exists, false if the crop amount is larger than the location. */ boolean CropEnd( const gnSeqI end ); /** * Returns true if the given location intersects this location in the region specified by the parameter "ir". * @param l The location to check for intersection. * @param ir The region to check for intersection. This can be either determinedRegions, undeterminedRegions, or allRegions * @see intersectRestriction * @return True if the location still exists, false if the crop amount is larger than the location. */ boolean Intersects( const gnLocation &l, const intersectRestriction ir = determinedRegions ) const; /** * Checks wether another gnLocation is contained by this one. * @param l The gnLocation to be checked. * @param cr A specification of the type of intersection to be checked. * @see intersectRestriction * @return True if the location still exists, false if the crop amount is larger than the location. */ boolean Contains( const gnLocation& l, const intersectRestriction cr = determinedRegions ) const; /** * Increases the location start and end. * @param diff The amount to increase the location start and end. */ boolean MovePositive( const gnSeqI diff ); /** * Decreases the location start and end. * @param diff The amount to decrease the location start and end. */ boolean MoveNegative( const gnSeqI diff ); /** * Moves the location start and end. * @param direction Negative integer will decrease start and end, positive will increase them. * @param diff The amount to move the location start and end. */ boolean MoveTo( const int direction, const gnSeqI diff ); /** * Gets the ending base pair. * @return The ending base pair. */ gnSeqI GetEnd() const; /** * Gets the ending base pair's definition value. * @return -1 if the ending location is unbounded to the left, 0 if defined, 1 if unbounded to the right */ gnSeqI GetEndLength() const; gnSeqI GetLast() const; /** * Gets the starting base pair. * @return The starting base pair. */ gnSeqI GetStart() const; /** * Gets the starting base pair's definition value. * @return -1 if the starting location is unbounded to the left, 0 if defined, 1 if unbounded to the right */ gnSeqI GetStartLength() const; gnSeqI GetFirst() const; /** * Gets the location type. * @return the location type. * @see gnLocationType */ gnLocationType GetType() const; /** * Gets the location's boundaries. * @param s The start index. * @param sl The start length. * @param e The end index. * @param el The end length. */ void GetBounds( gnSeqI &s, gnSeqI &sl, gnSeqI &e, gnSeqI &el ) const; /** * Returns true if the end is unbounded to the right. * @return True if the end is unbounded to the right. */ bool IsEndBoundLonger() const; /** * Returns true if the start is unbounded to the right. * @return True if the start is unbounded to the right. */ bool IsStartBoundLonger() const; /** * Returns true if the end is unbounded to the left. * @return True if the end is unbounded to the left. */ bool IsEndBoundShorter() const; /** * Returns true if the start is unbounded to the left. * @return True if the start is unbounded to the left. */ bool IsStartBoundShorter() const; /** * Sets the end location. * @param end The end location. */ void SetEnd( const gnSeqI end ); /** * Sets the end location and definition. * @param end The end location. * @param endLength -1 if the ending location is unbounded to the left, 0 if defined, 1 if unbounded to the right */ void SetEnd( const gnSeqI end, const gnSeqI endLength ); /** * Sets the end definition. * @param endLength -1 if the ending location is unbounded to the left, 0 if defined, 1 if unbounded to the right */ void SetEndLength( const gnSeqI endLength ); /** * Sets the start location/ * @param start The start location. */ void SetStart( const gnSeqI start ); /** * Sets the start location and definition. * @param start The end location. * @param startLength -1 if the ending location is unbounded to the left, 0 if defined, 1 if unbounded to the right */ void SetStart( const gnSeqI start, const gnSeqI startLength ); /** * Sets the start definition. * @param startLength -1 if the ending location is unbounded to the left, 0 if defined, 1 if unbounded to the right */ void SetStartLength( const gnSeqI startLength ); /** * Sets the location type. * @param lt The location type. */ void SetType( const gnLocationType lt ); /** * Sets the location's boundaries. * @param start The start index. * @param startLength -1 if the ending location is unbounded to the left, 0 if defined, 1 if unbounded to the right * @param end The end index. * @param endLength -1 if the ending location is unbounded to the left, 0 if defined, 1 if unbounded to the right */ void SetBounds( const gnSeqI start, const gnSeqI startLength, const gnSeqI end, const gnSeqI endLength); /** * Sets the location's boundaries. * @param start The start index. * @param end The end index. */ void SetBounds( const gnSeqI start, const gnSeqI end); gnLocation GetUnion( const gnLocation &l ) const; gnLocation GetIntersection( const gnLocation &l, const intersectRestriction ir ) const; private: std::string m_name; gnSeqI m_start; gnSeqI m_startLength; gnSeqI m_end; gnSeqI m_endLength; gnLocationType m_type; }; // class gnLocation // GET END inline gnSeqI gnLocation::GetEnd() const { return m_end; } inline gnSeqI gnLocation::GetEndLength() const { return m_endLength; } inline gnSeqI gnLocation::GetLast() const { return m_end + m_endLength; } // GET START inline gnSeqI gnLocation::GetStart() const { return m_start; } inline gnSeqI gnLocation::GetStartLength() const { return m_startLength; } inline gnSeqI gnLocation::GetFirst() const { return m_start > m_startLength ? m_start - m_startLength : 0; } inline gnLocation::gnLocationType gnLocation::GetType() const { return m_type; } inline bool gnLocation::IsEndBoundLonger() const { return m_endLength > 0; } inline bool gnLocation::IsStartBoundLonger() const { return m_startLength > 0; } inline bool gnLocation::IsEndBoundShorter() const { return m_endLength == GNSEQI_END; } inline bool gnLocation::IsStartBoundShorter() const { return m_startLength == GNSEQI_END; } inline void gnLocation::SetEnd( const gnSeqI end ) { m_end = end; } inline void gnLocation::SetEnd( const gnSeqI end, const gnSeqI endLength ) { m_end = end; m_endLength = endLength; } inline void gnLocation::SetEndLength( const gnSeqI endLength ) { m_endLength = endLength; } inline void gnLocation::SetStart( const gnSeqI start ) { m_start = start; } inline void gnLocation::SetStart( const gnSeqI start, const gnSeqI startLength ) { m_start = start; m_startLength = startLength; } inline void gnLocation::SetStartLength( const gnSeqI startLength ) { m_startLength = startLength; } inline void gnLocation::SetType( const gnLocationType lt ) { m_type = lt; } } // end namespace genome #endif // _gnLocation_h_ libGenome-1.3.1/libGenome/gnBaseFeature.h0000644002622200470610000002556410647575617015167 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnBaseFeature.h // Purpose: abstract Feature class // Description: Provides an interface for Features in memory and on disk. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnBaseFeature_h_ #define _gnBaseFeature_h_ #include "libGenome/gnDefs.h" #include #include #include "libGenome/gnClone.h" #include "libGenome/gnLocation.h" #include "libGenome/gnBaseQualifier.h" namespace genome { class gnFragmentSpec; /** * Features of DNA sequences can be accessed and manipulated using classes * derived from gnBaseFeature. gnBaseFeature outlines a basic interface * and gives functionality its derived sequence classes, such as * gnCDSFeature. */ class GNDLLEXPORT gnBaseFeature : public gnClone { public: gnBaseFeature(); gnBaseFeature( std::string& name, uint32 id = 0, gnFragmentSpec* spec = NULL, gnLocation::gnLocationType lt = gnLocation::LT_Nothing, boolean broken = false ); /** * Destructor, frees memory. */ ~gnBaseFeature(); virtual gnBaseFeature* Clone() const = 0; /** * Gets the feature name (e.g. CDS, trna...). * @return The feature name. */ virtual std::string GetName() const; /** * Sets the feature name. * @param name The feature name. */ virtual void SetName( const std::string& name ); /** * Gets this feature's ID. * @return The feature's ID. */ virtual uint32 GetID() const; /** * Sets this feature's ID. * @param id The feature's ID. */ virtual void SetID(uint32 id); /** * Gets the gnFragmentSpec to which this feature refers. * @return The feature's ID. * @see gnFragmentSpec */ virtual gnFragmentSpec* GetSpec() const; /** * Sets the gnFragmentSpec to which this feature refers. * @param spec A pointer to the fragment spec. */ virtual void SetSpec(gnFragmentSpec* spec); /** * Gets this feature's location type. * @return The feature's location type. * @see gnLocationType */ virtual gnLocation::gnLocationType GetLocationType() const; /** * Sets this feature's location type. * LT_BetweenBases is not a valid feature location type. * @param lType The feature's location type. * @see gnLocationType */ virtual void SetLocationType( gnLocation::gnLocationType lType ); /** * Returns the number of locations this feature describes. * @return The number of locations this feature describes. */ virtual uint32 GetLocationListLength() const; /** * Adds a new location before the location at listI. * @param l The gnLocation to add. * @param listI The index into the location list to insert before. * @return True if successful, false otherwise. * @see gnLocation */ virtual boolean AddLocation( const gnLocation& l, uint32 listI = 0); /** * Gets the location at listI. * @param listI The index into the location list to get. * @return The location. */ virtual gnLocation GetLocation( uint32 listI ) const; /** * Deletes the location at listI. * @param listI The index into the location list to delete. * @return True if successful, false otherwise. */ virtual boolean RemoveLocation( uint32 listI ); /** * Sets the location at listI to a new location. * @param l The new location * @param listI The index into the location list to set. * @return True if successful, false otherwise. */ virtual boolean SetLocation( const gnLocation& l, uint32 listI ); /** * Increases this feature's coordinates by a specific number of bases. * @param i The number of bases to increase by. * @return True if successful, false if the feature was broken by the change. */ virtual boolean MovePositive( const gnSeqI i ); /** * Decreases this feature's coordinates by a specific number of bases. * @param i The number of bases to decrease by. * @return True if successful, false if the feature was broken by the change. */ virtual boolean MoveNegative( const gnSeqI i ); /** * Crops the start locations of this feature by the specified amount. * @param i The amount to crop. * @return True if successful, false if the feature was broken by the change. */ virtual boolean CropStart( const gnSeqI i ); /** * Crops the end locations of this feature by the specified amount. * @param i The amount to crop. * @return True if successful, false if the feature was broken by the change. */ virtual boolean CropEnd( const gnSeqI i ); /** * Crops the locations of this feature to fit within the given location. * @param l The location to crop reduce to. * @return True if successful, false if the feature was broken by the change. */ virtual boolean Crop( const gnLocation& l ); /** * Returns true if the feature is broken * @return True if the feature is broken */ virtual boolean IsBroken() const; /** * Sets whether the feature is broken or not. * @param broke True if the feature should be broken, false otherwise */ virtual void SetBroken(boolean broke); /** * Checks if the given coordinate is contained by this feature * @param i The coordinate to check * @return True if "i" is contained by this feature. False otherwise */ virtual boolean Contains( gnSeqI i ) const; /** * Checks if the given location is contained by this feature * @param l The location to check * @return True if "l" is contained by this feature. False otherwise */ virtual boolean Contains( const gnLocation& l ) const; /** * Checks if the given feature is entirely contained by this feature * @param feature The feature to check * @return True if "feature" is contained by this feature. False otherwise */ virtual boolean Contains( gnBaseFeature* feature ) const; /** * Checks if this feature is entirely contained by the given location * @param l The location to check * @return True if "l" contains by this feature. False otherwise */ virtual boolean IsContainedBy( const gnLocation& l ) const; /** * Checks if the given location intersects this feature * @param l The location to check * @return True if "l" intersects this feature. False otherwise */ virtual boolean Intersects( const gnLocation& l ) const; /** * Checks if the given feature intersects this feature * @param feature The location to check * @return True if "feature" intersects this feature. False otherwise */ virtual boolean Intersects( gnBaseFeature* feature ) const; /** * Returns the number of qualifiers in this feature. * @return The number of qualifiers in this feature. */ virtual uint32 GetQualifierListLength() const; /** * Adds a new qualifier. * @param qualifier The qualifier to add. * @return True if successful, false otherwise. */ virtual boolean AddQualifier( gnBaseQualifier* qualifier ); /** * Looks for a qualifier by name. * @param name The name of the qualifier to look for. * @return True if a qualifier was found, false otherwise. */ virtual boolean HasQualifier( const std::string& name ) const; /** * Searches for a qualifier by name, starting at the index listI. * @param name The name of the qualifier to look for. * @param listI The index into the qualifier list to start the search at. * @return The index of the qualifier. */ virtual uint32 FirstIndexOfQualifier( const std::string& name, uint32 listI ) const; /** * Searches for a qualifier by name, ending at the index listI. * @param name The name of the qualifier to look for. * @param listI The index into the qualifier list to end the search at. * @return The index of the qualifier. */ virtual uint32 LastIndexOfQualifier( const std::string& name, uint32 listI ) const; /** * Gets the name of the qualifier at the list index listI. * @param listI The index into the qualifier list. * @return The name of the qualifier. */ virtual std::string GetQualifierName( uint32 listI ) const; /** * Gets the value of the qualifier at the list index listI. * @param listI The index into the qualifier list. * @return The value of the qualifier. */ virtual std::string GetQualifierValue( uint32 listI ) const; /** * Gets the qualifier at the list index listI. * @param listI The index into the qualifier list. * @return The qualifier. */ virtual gnBaseQualifier* GetQualifier( uint32 listI ); /** * Deletes the qualifier at the list index listI. * @param listI The index into the qualifier list. * @return True if successful, false otherwise. */ virtual boolean RemoveQualifier( uint32 listI ); /** * Set the name and value of the qualifier at the list index listI. * @param name The new name of the qualifier. * @param value The new value of the qualifier. * @param listI The index into the qualifier list. * @return True if successful, false otherwise. */ virtual boolean SetQualifier( std::string& name, std::string& value, uint32 listI ); /** * Set the name of the qualifier at the list index listI. * @param name The new name of the qualifier. * @param listI The index into the qualifier list. * @return True if successful, false otherwise. */ virtual boolean SetQualifierName( std::string& name, uint32 listI ); /** * Set the value of the qualifier at the list index listI. * @param value The new value of the qualifier. * @param listI The index into the qualifier list. * @return True if successful, false otherwise. */ virtual boolean SetQualifierValue( std::string& value, uint32 listI ); protected: uint32 m_id; std::string m_name; boolean m_broken; gnLocation::gnLocationType m_locationType; std::vector< gnLocation > m_locationList; std::vector< gnBaseQualifier* > m_qualifierList; gnFragmentSpec* m_spec; };// class gnBaseFeature inline std::string gnBaseFeature::GetName() const{ return m_name; } inline void gnBaseFeature::SetName( const std::string& name ){ m_name = name; } inline uint32 gnBaseFeature::GetID() const{ return m_id; } inline void gnBaseFeature::SetID(uint32 id){ m_id = id; } inline gnFragmentSpec* gnBaseFeature::GetSpec() const{ return m_spec; } inline void gnBaseFeature::SetSpec(gnFragmentSpec* spec){ m_spec = spec; } inline boolean gnBaseFeature::IsBroken() const{ return m_broken; } inline void gnBaseFeature::SetBroken(boolean broke){ m_broken = broke; } inline gnLocation::gnLocationType gnBaseFeature::GetLocationType() const{ return m_locationType; } inline void gnBaseFeature::SetLocationType( gnLocation::gnLocationType lType ){ m_locationType = lType; } inline uint32 gnBaseFeature::GetLocationListLength() const{ return m_locationList.size(); } inline boolean gnBaseFeature::Crop( const gnLocation& l ){ return CropStart(l.GetStart()) && CropEnd(l.GetEnd()); } inline uint32 gnBaseFeature::GetQualifierListLength() const{ return m_qualifierList.size(); } } // end namespace genome #endif // _gnBaseFeature_h_ libGenome-1.3.1/libGenome/gnSourceHeader.cpp0000644002622200470610000000261110647575617015671 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnSourceHeader.cpp // Purpose: Source Header class // Description: Provides an interface for Headers on disk. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include #include "libGenome/gnBaseSource.h" #include "libGenome/gnSourceHeader.h" using namespace std; namespace genome { gnSourceHeader::gnSourceHeader(){ m_source = NULL; m_start = 0; m_length = 0; } gnSourceHeader::gnSourceHeader( gnBaseSource* source, const string& name, const uint32 begin, const uint32 length ){ m_source = source; m_name = string(name); m_start = begin; m_length = length; } gnSourceHeader::gnSourceHeader(const gnSourceHeader& s){ m_source = s.m_source; m_start = s.m_start; m_length = s.m_length; m_name = string(s.m_name); } gnSourceHeader::~gnSourceHeader(){ }; string gnSourceHeader::GetHeader() const{ Array array_buf( m_length ); char* buf = array_buf.data; gnSeqI readBytes = m_length; m_source->Read(m_start, buf, readBytes); string rval(buf, readBytes); return rval; } } // end namespace genome libGenome-1.3.1/libGenome/gnClone.h0000644002622200470610000000150210647575617014023 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnClone.h // Purpose: Abstract Clone class // Description: Define the a Clonable interface for other objects // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnClone_h_ #define _gnClone_h_ #include "libGenome/gnDefs.h" namespace genome { class GNDLLEXPORT gnClone { public: virtual ~gnClone(){} virtual gnClone* Clone() const = 0; gnClone(){} private: };// class gnClone } // end namespace genome #endif // _gnClone_h_ libGenome-1.3.1/libGenome/gnLocation.cpp0000644002622200470610000001237610647575617015101 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnLocation.cpp // Purpose: Standard Location for Feature // Description: Feature location // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnLocation.h" #include "libGenome/gnDebug.h" using namespace std; namespace genome { gnLocation::gnLocation() { Clear(); } gnLocation::gnLocation( const gnLocation& s) { SetBounds( s.m_start, s.m_startLength, s.m_end, s.m_endLength ); m_type = s.m_type; } gnLocation::gnLocation( const gnSeqI start, const gnSeqI startLength, const gnSeqI end, const gnSeqI endLength, gnLocationType type, string contigName) { SetBounds( start, startLength, end, endLength ); m_type = type; m_name = contigName; } gnLocation::gnLocation( const gnSeqI start, const gnSeqI end, const gnLocationType type, string contigName ) { SetBounds( start, 0, end, 0 ); m_type = type; m_name = contigName; } gnLocation* gnLocation::Clone() const { return new gnLocation(*this); } void gnLocation::Clear() { m_start = 0; m_end = 0; m_startLength = 0; m_endLength = 0; m_type = LT_Nothing; } void gnLocation::GetBounds( gnSeqI &s, gnSeqI &sl, gnSeqI &e, gnSeqI &el ) const { s = m_start; sl = m_startLength; e = m_end; el = m_endLength; } void gnLocation::SetBounds( const gnSeqI start, const gnSeqI startLength, const gnSeqI end, const gnSeqI endLength) { SetStart(start, startLength); SetEnd(end, endLength); } void gnLocation::SetBounds( const gnSeqI start, const gnSeqI end) { m_start = start; m_end = end; } boolean gnLocation::CropTo( const gnLocation &l ) { gnSeqI tmp; gnSeqI start = l.GetStart(); gnSeqI end = l.GetEnd(); if(m_start < start){ tmp = start < m_end ? start : m_end; m_startLength += tmp - m_start; m_start = tmp; } if(m_end < end){ tmp = end > m_start ? end : m_start; m_endLength += m_end - tmp; m_end = tmp; } if( (l.GetFirst() > GetFirst()) ) { if( l.GetFirst() <= m_end ) m_startLength = m_start - l.GetFirst(); else if( l.GetFirst() <= GetLast() ) { m_end = l.GetFirst(); m_start = l.GetFirst() + 1; m_startLength = 0; } else Clear(); } if( l.GetLast() < GetLast() ) { if( l.GetLast() >= m_start ) m_endLength = l.GetLast() - m_end; else if( l.GetLast() >= GetFirst() ) { m_start = l.GetLast(); m_end = l.GetLast() - 1; m_endLength = 0; } else Clear(); } if(m_start == m_end) return false; return true; } boolean gnLocation::CropStart( const gnSeqI start ){ gnSeqI tmp; if(m_start < start){ tmp = start < m_end ? start : m_end; m_startLength += tmp - m_start; m_start = tmp; } if(m_start == m_end) return false; return true; } boolean gnLocation::CropEnd( const gnSeqI end ){ gnSeqI tmp; if(m_end > end){ tmp = end > m_start ? end : m_start; m_endLength += m_end - tmp; m_end = tmp; } if(m_start == m_end) return false; return true; } // Intersects boolean gnLocation::Intersects( const gnLocation &l, const intersectRestriction ir ) const{ if( ir == determinedRegions ) { if( (l.GetStart() <= m_end) && (l.GetEnd() >= m_start) ) return true; } else if( ir == undeterminedRegions ) { if( (l.GetFirst() <= m_start) && (l.GetLast() >= GetFirst()) ) return true; if( (l.GetFirst() <= GetLast()) && (l.GetLast() >= m_end) ) return true; } else if( ir == allRegions ) { if( (l.GetFirst() <= GetLast()) && (l.GetLast() >= GetFirst()) ) return true; } return false; } boolean gnLocation::Contains( const gnLocation &l, const intersectRestriction ir ) const{ if(ir == determinedRegions) return m_start <= l.GetStart() && l.GetEnd() <= m_end; else if(ir == undeterminedRegions) return (GetFirst() <= l.GetFirst() && l.GetLast() < m_start) || (m_end < l.GetFirst() && l.GetLast() <= GetLast()); return GetFirst() <= l.GetFirst() && l.GetLast() <= GetLast(); } // Move boolean gnLocation::MovePositive( const gnSeqI diff ) { if(m_start > GNSEQI_END - diff || m_end > GNSEQI_END - diff) return false; m_start += diff; m_end += diff; return true; } boolean gnLocation::MoveNegative( const gnSeqI diff ) { if(m_start < diff || m_end < diff) return false; m_start -= diff; m_end -= diff; return true; } boolean gnLocation::MoveTo( const int direction, const gnSeqI diff ) { if( direction > 0 ) return MovePositive( diff ); return MoveNegative( diff ); } gnLocation gnLocation::GetUnion( const gnLocation &l ) const { ErrorMsg("gnLocation::getUnion -- not implemented\n"); return l; } // Intersects gnLocation gnLocation::GetIntersection( const gnLocation &l, const intersectRestriction ir ) const{ gnLocation inter_loc; if( ir == determinedRegions ) { if( (l.GetStart() <= m_end) && (l.GetEnd() >= m_start) ){ inter_loc.m_start = l.m_start > m_start ? l.m_start : m_start; inter_loc.m_end = l.m_end < m_end ? l.m_end : m_end; } } else if( ir == undeterminedRegions ) { ErrorMsg("Not implemented!"); } else if( ir == allRegions ) { ErrorMsg("Not implemented!"); } return inter_loc; } } // end namespace genome libGenome-1.3.1/libGenome/gnDataBaseSource.h0000644002622200470610000000342710647575617015620 00000000000000///////////////////////////////////////////////////////////////////////////// // DataBase: gnDataBaseSource.h // Purpose: Implements gnBaseSource for .DataBase files // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnDataBaseSource_h_ #define _gnDataBaseSource_h_ #include "libGenome/gnDefs.h" #include #include "gnBaseSource.h" namespace genome { /** * Not yet implemented. */ class gnDataBaseSource : public gnBaseSource { public: virtual ~gnDataBaseSourcee(){} virtual gnDataBaseSource* Clone() const = 0; virtual gnBaseSource* Clone() const = 0; virtual boolean Open( std::string openString ) = 0; virtual boolean Open() = 0; virtual boolean Close() = 0; virtual std::string GetOpenString() const = 0; virtual uint32 GetContigListLength() const = 0; virtual boolean HasContig( const std::string& name ) const = 0; virtual uint32 GetContigID( const std::string& name ) const = 0; virtual std::string GetContigName( const uint32 i ) const = 0; virtual gnSeqI GetContigSeqLength( const uint32 i ) const = 0; virtual const gnFilter* GetFilter() const = 0; virtual boolean SetFilter( gnFilter* filter ) = 0; virtual boolean Read( const uint64 pos, char* buf, uint32& bufLen) = 0; virtual boolean SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI=ALL_CONTIGS ) = 0; virtual gnGenomeSpec *GetSpec() const = 0; private: gnDataBaseSource(){} };// class gnDataBaseSource } // end namespace genome #endif // _gnDataBaseSource_h_ libGenome-1.3.1/libGenome/coordMapper.cpp0000644002622200470610000002757110647575617015262 00000000000000#ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnSequence.h" #include #include #include struct ExMem{ gnSeqI length; int64 ex_start; int64 in_start; }; static boolean LocationLessthan(const gnLocation& a, const gnLocation& b); static boolean LocationLessthan(const gnLocation& a, const gnLocation& b){ return a.GetStart() < b.GetStart(); } static boolean LocationEndLessthan(const gnLocation& a, const gnLocation& b); static boolean LocationEndLessthan(const gnLocation& a, const gnLocation& b){ return a.GetEnd() < b.GetStart(); } static boolean LocationSizeLessthan(const gnLocation& a, const gnLocation& b); static boolean LocationSizeLessthan(const gnLocation& a, const gnLocation& b){ return a.GetEnd() - a.GetStart() < b.GetEnd() - b.GetStart(); } static boolean ExMemLessthan(const ExMem& a, const ExMem& b){ if(a.ex_start == b.ex_start){ if(a.in_start == b.in_start){ return a.length < b.length; } return a.in_start < b.in_start; } return a.ex_start < b.ex_start; } void print_usage(char* pname){ cout << "Usage: " << pname << " \n"; } void load_map_file(string& filename, vector& loc_list){ ifstream coord_file; coord_file.open(filename.c_str()); if(!coord_file.is_open()){ cout << "couldn't open file\n"; return; } //read all the exon coordinates while(coord_file.good()){ gnSeqI start_coord, end_coord; coord_file >> start_coord; coord_file >> end_coord; gnLocation new_location(start_coord, end_coord); loc_list.push_back(new_location); } } void map_coordinates(vector& loc_list, vector& map_list){ gnSeqI curStart = 1; for(uint32 locationI = 0; locationI < loc_list.size(); locationI++){ gnSeqI cur_len = loc_list[locationI].GetEnd() - loc_list[locationI].GetStart() + 1; gnLocation map_location(curStart, curStart+cur_len-1); map_list.push_back(map_location); curStart += cur_len; } } void map_list_coordinates(list& loc_list, list& map_list){ gnSeqI curStart = 1; list::iterator loc_iter = loc_list.begin(); for(; loc_iter != loc_list.end(); loc_iter++){ gnSeqI cur_len = loc_iter->GetEnd() - loc_iter->GetStart() + 1; gnLocation map_location(curStart, curStart+cur_len-1); map_list.push_back(map_location); curStart += cur_len; } } void print_feature(ostream& os, gnBaseFeature* cur_feat){ os << cur_feat->GetName() << ": \n"; for(uint32 i=0; i < cur_feat->GetQualifierListLength(); i++) os << cur_feat->GetQualifierName(i) << "\t" << cur_feat->GetQualifierValue(i) << "\n"; os << "\n"; } uint32 loc_binary_search(vector& loc_list, uint32 startI, uint32 endI, gnLocation& query_loc){ uint32 midI = ((endI - startI) / 2) + startI; if(startI == endI) return endI; if(loc_list[midI].Intersects(query_loc)){ return midI; }else if(loc_list[midI].GetStart() < query_loc.GetStart()) return loc_binary_search(loc_list, midI + 1, endI, query_loc); else return loc_binary_search(loc_list, startI, midI, query_loc); } int main(int argc, char* argv[]){ boolean run_interactive = false; string seq_filename; string exon_list_filename; string intron_list_filename; string mem_list_filename; string reg_net_filename; vector exon_list; vector intron_list; vector exon_map_list; vector intron_map_list; vector mem_list; uint32 minimum_match_size; // check for correct calling semantics if(argc != 7){ print_usage(argv[0]); return -1; } seq_filename = argv[1]; exon_list_filename = argv[2]; intron_list_filename = argv[3]; mem_list_filename = argv[4]; reg_net_filename = argv[5]; minimum_match_size = atoi(argv[6]); ifstream mem_file(mem_list_filename.c_str()); if(!mem_file.is_open()){ cout << "Error opening " << mem_list_filename << "\n"; return -1; } if(run_interactive){ cout << "Give the name of the exon list to search\n"; cin >> exon_list_filename; cout << "Give the name of the intron list to search\n"; cin >> intron_list_filename; cout << "Give the name of the regulatory network to output\n"; cin >> reg_net_filename; } ofstream net_file(reg_net_filename.c_str()); if(!net_file.is_open()){ cout << "Error opening regulatory network file: " << reg_net_filename << "\n"; return -2; } load_map_file(exon_list_filename, exon_list); load_map_file(intron_list_filename, intron_list); cout << exon_list.size() << " unique exons loaded from file\n"; cout << intron_list.size() << " unique introns loaded from file\n"; //now load the genbank file gnSequence seq_file; if(run_interactive){ cout << "Enter the name of the genbank sequence file you are using\n"; cin >> seq_filename; } if(!seq_file.LoadSource(seq_filename)){ cout << "Error loading file\n"; return -1; } cout << "Sequence loaded successfully, " << seq_file.length() << " base pairs.\n"; //construct a mapping between coordinates... map_coordinates(exon_list, exon_map_list); map_coordinates(intron_list, intron_map_list); //now read the mem file while(mem_file.good()){ ExMem m; mem_file >> m.length; mem_file >> m.ex_start; mem_file >> m.in_start; if(m.length >= minimum_match_size) mem_list.push_back(m); } cout << mem_list.size() << " matches loaded.\n"; //sort the mem list sort(mem_list.begin(), mem_list.end(), &ExMemLessthan); //now get the intersection for each mem in the list... uint32 exonmapI = 0; uint32 notify_percent = 10; uint32 notify_interval = mem_list.size() / notify_percent; uint32 percent_count = 0; cout << "Searching for complementary matches:\n"; for(uint32 memI = 0; memI < mem_list.size(); memI++){ if(memI % notify_interval == 0){ cout << percent_count << "%.. "; percent_count += notify_percent; } //simple linear search for intersecting exon mapping gnLocation ex_map_loc(mem_list[memI].ex_start, mem_list[memI].ex_start + mem_list[memI].length - 1); for(; exonmapI < exon_map_list.size(); exonmapI++){ if(exon_map_list[exonmapI].Intersects(ex_map_loc)) break; } //continue to search for any other mappings that intersect uint32 mapEnd = exonmapI; for(; mapEnd < exon_map_list.size(); mapEnd++){ if(!exon_map_list[exonmapI].Intersects(ex_map_loc)) break; } mapEnd--; uint32 intronmapI = 0; // intronmapI will contain the index of the first intersecting intron //do a binary search for intersecting intron mappings int64 cur_in_start = mem_list[memI].in_start; if(cur_in_start < 0) cur_in_start = -cur_in_start; gnLocation in_map_loc(cur_in_start, cur_in_start + mem_list[memI].length - 1); uint32 search_mapI = loc_binary_search(intron_map_list, 0, intron_map_list.size()-1, in_map_loc); intronmapI = search_mapI; //search backwards for previous intersections for(; intronmapI >= 0; intronmapI--){ if(!intron_map_list[intronmapI].Intersects(in_map_loc)){ intronmapI++; break; } if(intronmapI == 0) break; } //continue to search for any other mappings that intersect uint32 intron_mapEnd = search_mapI; for(; intron_mapEnd < intron_map_list.size(); intron_mapEnd++){ if(!intron_map_list[intronmapI].Intersects(in_map_loc)) break; } intron_mapEnd--; //we have the mappings, now map the coordinates vector ex_feat_index, in_feat_index; vector ex_feat_list; vector in_feat_list; gnSeqI cur_match_len = mem_list[memI].length; //find out how much of the first exon was matched //extra exon start has the number of unmatched bases at the beginning of the exon gnSeqI extra_exon_start = mem_list[memI].ex_start - exon_map_list[exonmapI].GetStart(); gnSeqI cur_exon_len = exon_map_list[exonmapI].GetEnd() - exon_map_list[exonmapI].GetStart() + 1; gnSeqI max_exon_chunk = cur_exon_len - extra_exon_start; gnSeqI cur_exon_chunk = max_exon_chunk < cur_match_len ? max_exon_chunk : cur_match_len; //find out how much of the first intron was matched gnSeqI extra_intron_start, cur_intron_len, max_intron_chunk, cur_intron_chunk; boolean complement = false; if(mem_list[memI].in_start > 0){ extra_intron_start = mem_list[memI].in_start - intron_map_list[intronmapI].GetStart(); cur_intron_len = intron_map_list[intronmapI].GetEnd() - intron_map_list[intronmapI].GetStart() + 1; max_intron_chunk = cur_intron_len - extra_intron_start; cur_intron_chunk = max_intron_chunk < mem_list[memI].length ? max_intron_chunk : mem_list[memI].length; }else{ //reverse complement, start at the end. if(cur_in_start >= intron_map_list[intron_mapEnd].GetStart()) cur_intron_chunk = cur_match_len; else cur_intron_chunk = cur_in_start + cur_match_len - intron_map_list[intron_mapEnd].GetStart(); complement = true; seq_file.getIntersectingFeatures(intron_list[intronmapI], in_feat_list, in_feat_index); } //the current chunk will be the smaller of the two mappings gnSeqI cur_chunk = cur_intron_chunk < cur_exon_chunk ? cur_intron_chunk : cur_exon_chunk; gnLocation cur_exon_loc(exon_list[exonmapI].GetStart() + extra_exon_start, exon_list[exonmapI].GetStart() + cur_chunk); seq_file.getIntersectingFeatures(cur_exon_loc, ex_feat_list, ex_feat_index); if(mem_list[memI].in_start > 0){ gnLocation cur_intron_loc(intron_list[intronmapI].GetStart() - 1, intron_list[intronmapI].GetEnd() + 1); seq_file.getIntersectingFeatures(cur_intron_loc, in_feat_list, in_feat_index); }else{ gnLocation cur_intron_loc(intron_list[intron_mapEnd].GetStart() - 1, intron_list[intron_mapEnd].GetEnd() + 1); seq_file.getIntersectingFeatures(cur_intron_loc, in_feat_list, in_feat_index); } vector ex_forward; vector ex_reverse; vector in_forward; vector in_reverse; for(uint32 featI = 0; featI < ex_feat_list.size(); featI++){ string featName = ex_feat_list[featI]->GetName(); if(featName == "mRNA" || featName == "CDS" || featName == "gene" ) if(ex_feat_list[featI]->GetLocationType() == gnLocation::LT_Complement) ex_reverse.push_back(ex_feat_list[featI]); else ex_forward.push_back(ex_feat_list[featI]); } for(uint32 featI = 0; featI < in_feat_list.size(); featI++){ string featName = in_feat_list[featI]->GetName(); if(featName == "mRNA" || featName == "CDS" || featName == "gene" ) if(in_feat_list[featI]->GetLocationType() == gnLocation::LT_Complement) in_reverse.push_back(in_feat_list[featI]); else in_forward.push_back(in_feat_list[featI]); } if(complement){ vector tmp_in = in_forward; in_forward = in_reverse; in_reverse = tmp_in; } //now print out all the complementary features if((ex_forward.size() > 0 && in_reverse.size() > 0) || (in_forward.size() > 0 && ex_reverse.size() > 0)){ net_file << "================================\n"; net_file << "Mem: " << mem_list[memI].length << "\n"; net_file << "This exon/intron matching size: " << cur_chunk << "\n"; } if(ex_forward.size() > 0 && in_reverse.size() > 0){ net_file << "Forward Exons:\n"; for(uint32 featI = 0; featI < ex_forward.size(); featI++) print_feature(net_file, ex_forward[featI]); net_file << "Matching introns:\n"; for(uint32 featI = 0; featI < in_reverse.size(); featI++) print_feature(net_file, in_reverse[featI]); } if(in_forward.size() > 0 && ex_reverse.size() > 0){ net_file << "Reverse Exons:\n"; for(uint32 featI = 0; featI < ex_reverse.size(); featI++) print_feature(net_file, ex_reverse[featI]); net_file << "Matching introns:\n"; for(uint32 featI = 0; featI < in_forward.size(); featI++) print_feature(net_file, in_forward[featI]); } //release memory for(uint32 featI = 0; featI < ex_feat_list.size(); featI++) delete ex_feat_list[featI]; for(uint32 featI = 0; featI < in_feat_list.size(); featI++) delete in_feat_list[featI]; //loop while there is stuff to match // while(cur_match_len > 0){ // } } } libGenome-1.3.1/libGenome/gnFileContig.cpp0000644002622200470610000000403710647575617015347 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnFileContig.h // Purpose: File Position holder. // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnFileContig.h" #include using namespace std; namespace genome { gnFileContig::gnFileContig() { Clear(); } gnFileContig::gnFileContig( string nameStr, const uint64 s, const uint64 e ) { Clear(); m_name = nameStr; m_fileStartEnd.first = s; m_fileStartEnd.second = e; } gnFileContig::gnFileContig( const gnFileContig& fc ) { m_name = fc.m_name; m_seqLength = fc.m_seqLength; m_fileStartEnd = fc.m_fileStartEnd; for( uint32 i=0; i < CONTIG_SECTION_SIZE; ++i ) m_startEndArray[i] = fc.m_startEndArray[i]; m_repeatSeqGap = fc.m_repeatSeqGap; m_repeatSeqGapSize = fc.m_repeatSeqGapSize; } gnFileContig::~gnFileContig() { } void gnFileContig::Clear() { m_name = ""; m_seqLength = 0; m_fileStartEnd = pair(0,0); for( uint32 i=0; i < CONTIG_SECTION_SIZE; ++i ) m_startEndArray[i] = pair(0,0); m_repeatSeqGap = false; m_repeatSeqGapSize = pair(0,0); } boolean gnFileContig::SetRepeatSeqSize( const uint64 seqSize ) { if( !m_repeatSeqGap ) return false; if( m_repeatSeqGapSize.first == seqSize ) return true; if( m_repeatSeqGapSize.first == 0 ) { m_repeatSeqGapSize.first = seqSize; return true; } m_repeatSeqGap = false; return false; } boolean gnFileContig::SetRepeatGapSize( const uint64 gapSize ) { if( !m_repeatSeqGap ) return false; if( m_repeatSeqGapSize.second == gapSize ) return true; if( m_repeatSeqGapSize.second == 0 ) { m_repeatSeqGapSize.second = gapSize; return true; } m_repeatSeqGap = false; return false; } } // end namespace genome libGenome-1.3.1/libGenome/gnFASSource.cpp0000644002622200470610000004274711026443220015100 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnFASSource.h // Purpose: Implements gnBaseSource for .FAS files // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnFASSource.h" #include "libGenome/gnBaseSpec.h" #include "libGenome/gnFilter.h" #include "libGenome/gnStringTools.h" #include "libGenome/gnSourceSpec.h" #include "libGenome/gnSourceHeader.h" #include "libGenome/gnDebug.h" using namespace std; namespace genome { gnFASSource::gnFASSource() { m_openString = ""; m_pFilter = gnFilter::fullDNASeqFilter(); if(m_pFilter == NULL){ DebugMsg("Error using static sequence filters."); } } gnFASSource::gnFASSource( const gnFASSource& s ) : gnFileSource(s) { vector< gnFileContig* >::const_iterator iter = s.m_contigList.begin(); for( ; iter != s.m_contigList.end(); ++iter ) { m_contigList.push_back( (*iter)->Clone() ); } } gnFASSource::~gnFASSource() { m_ifstream.close(); vector< gnFileContig* >::iterator iter = m_contigList.begin(); for( ; iter != m_contigList.end(); ++iter ) { gnFileContig* fg = *iter; *iter = 0; delete fg; } } boolean gnFASSource::HasContig( const string& nameStr ) const { for(uint32 i = 0 ; i <= m_contigList.size(); i++ ) { if( nameStr == m_contigList[i]->GetName() ) return true; } return false; } uint32 gnFASSource::GetContigID( const string& name ) const { for(uint32 i = 0 ; i <= m_contigList.size(); i++ ) { if( name == m_contigList[i]->GetName() ) return i; } return ALL_CONTIGS; } string gnFASSource::GetContigName( const uint32 i ) const { if( i < m_contigList.size() ){ return m_contigList[i]->GetName(); } return ""; } gnSeqI gnFASSource::GetContigSeqLength( const uint32 i ) const { if( i < m_contigList.size() ){ return m_contigList[i]->GetSeqLength(); }else if( i == ALL_CONTIGS){ gnSeqI seqlen = 0; for(uint32 j=0; j < m_contigList.size(); j++) seqlen += m_contigList[j]->GetSeqLength(); return seqlen; } return GNSEQI_ERROR; } gnFileContig* gnFASSource::GetContig( const uint32 i ) const { if( i < m_contigList.size() ){ return m_contigList[i]; } return 0; } boolean gnFASSource::SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI ) { boolean result = true; #pragma omp critical { result = SeqReadImpl( start, buf, bufLen, contigI ); } return result; } boolean gnFASSource::SeqReadImpl( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI ) { m_ifstream.clear(); uint32 contigIndex = contigI; uint64 startPos = 0; uint64 readableBytes = 0; if( !SeqSeek( start, contigIndex, startPos, readableBytes ) ){ bufLen = 0; return false; } if( contigI == ALL_CONTIGS ){ uint32 curLen = 0; uint64 bytesRead = 0; while (curLen < bufLen){ //SeqSeek to start, Figure out how much can be read before SeqSeeking again. if(readableBytes <= 0) //Look out for zero length contigs! IMPLEMENT ME if( !SeqSeek( start + curLen, contigIndex, startPos, readableBytes ) ){ bufLen = curLen; return true; } //readLen is the amount to read on this pass uint64 readLen = (bufLen - curLen) < readableBytes ? (bufLen - curLen) : readableBytes; Array array_buf( readLen ); gnSeqC* tmpBuf = array_buf.data; //read into tmpBuf, then filter tmpBuf into curBuf // read chars and filter m_ifstream.read(tmpBuf, readLen); uint64 gc = m_ifstream.gcount(); bytesRead += gc; readableBytes -= gc; // cout << "Read " << gc << " chars from " << m_openString << "\n"; // cout << "Checking character validity on: " << tmpBuf << "\n"; for(uint32 i=0; i < gc; i++){ if( m_pFilter->IsValid(tmpBuf[i]) ){ buf[curLen] = tmpBuf[i]; curLen++; } } if(m_ifstream.eof()){ //we hit the end of the file. bail out. m_ifstream.clear(); bufLen = curLen; return true; } } bufLen = curLen; } else if( contigI < m_contigList.size() ) { uint32 curLen = 0; //check to see if the buffer is bigger than the contig. if so truncate it. gnSeqI contigSize = m_contigList[contigI]->GetSeqLength(); bufLen = bufLen < contigSize ? bufLen : contigSize; while (curLen < bufLen) { uint64 readLen = bufLen - curLen; //the amount to read on this pass Array array_buf( readLen ); // use Array template to ensure proper deallocation gnSeqC* tmpBuf = array_buf.data; //read into tmpBuf, then filter tmpBuf into curBuf // read chars and filter m_ifstream.read(tmpBuf, readLen); uint64 gc = m_ifstream.gcount(); // cout << "Read " << gc << " chars from " << m_openString << "\n"; // cout << "Checking character validity on: " << tmpBuf << "\n"; for(uint32 i=0; i < gc; i++){ if( m_pFilter->IsValid(tmpBuf[i]) ){ buf[curLen] = tmpBuf[i]; curLen++; } } if(m_ifstream.eof()){ //we hit the end of the file. bail out. m_ifstream.clear(); bufLen = curLen; return true; } } bufLen = curLen; } return true; } // private: // figures out which contig the sequence starts at then calls SeqStartPos to get the offset within that contig // returns startPos, the file offset where the sequence starts // returns true if successful, false otherwise boolean gnFASSource::SeqSeek( const gnSeqI start, const uint32 contigI, uint64& startPos, uint64& readableBytes ) { if( contigI == ALL_CONTIGS ){ // find first contig gnSeqI curIndex = 0; vector< gnFileContig* >::iterator iter = m_contigList.begin(); for( ; iter != m_contigList.end(); ++iter ) { uint64 len = (*iter)->GetSeqLength(); if( (curIndex + len) > start ) break; curIndex += len; } if( iter == m_contigList.end() ) return false; // seek to start gnSeqI startIndex = start - curIndex; //startIndex is starting pos. within the contig return SeqStartPos( startIndex, *(*iter), startPos, readableBytes ); } else if( contigI < m_contigList.size() ) { return SeqStartPos( start, *(m_contigList[contigI]), startPos, readableBytes ); } return false; } //Returns startPos, the file offset where the sequence starts. boolean gnFASSource::SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes ){ readableBytes = 0; uint32 curLen = 0; //seek to the file offset where the contig starts startPos = contig.GetSectStartEnd(gnContigSequence).first; //set startPos to start where the contig starts if(contig.HasRepeatSeqGap()) if(contig.GetRepeatSeqGapSize().first > 0) if(contig.GetRepeatSeqGapSize().second > 0){ //check this startPos += start + (start/contig.GetRepeatSeqGapSize().first)*contig.GetRepeatSeqGapSize().second; readableBytes = contig.GetSectStartEnd(gnContigSequence).second - startPos; m_ifstream.seekg( startPos, ios::beg ); return true; } m_ifstream.seekg( startPos, ios::beg ); if( m_ifstream.eof() ){ ErrorMsg("ERROR in gnFASSource::Incorrect contig start position, End of file reached!\n"); return false; } while( true ){ // READ the rest of the contig skipping over invalid characters until we get to the starting base pair. // startPos will contain the file offset with the starting base pair uint32 tmpbufsize = contig.GetSectStartEnd(gnContigSequence).second - startPos; if(tmpbufsize == 0){ ErrorMsg("ERROR in gnFASSource: stored contig size is incorrect.\n"); return false; } tmpbufsize = tmpbufsize < BUFFER_SIZE ? tmpbufsize : BUFFER_SIZE; //read in the smaller of the two. Array array_buf( tmpbufsize ); // use Array template to ensure proper deallocation char *tmpbuf = array_buf.data; m_ifstream.read( tmpbuf, tmpbufsize ); if( m_ifstream.eof() ){ ErrorMsg("ERROR in gnFASSource::Read End of file reached!\n"); return false; } for( uint32 i=0; i < tmpbufsize; ++i ){ if( m_pFilter->IsValid(tmpbuf[i]) ){ if( curLen >= start ){ //stop when we reach the starting offset within this contig startPos += i; m_ifstream.seekg( startPos, ios::beg ); //seek to startPos readableBytes = contig.GetSectStartEnd(gnContigSequence).second - startPos; return true; } ++curLen; //each time we read a valid b.p., increment the sequence length } } startPos += tmpbufsize; } return true; } //write out the given source in this file format. boolean gnFASSource::Write(gnBaseSource *source, const string& filename){ ofstream m_ofstream(filename.c_str(), ios::out | ios::binary); if(!m_ofstream.is_open()) return false; uint32 contigCount = source->GetContigListLength(); for(uint32 contigI = 0; contigI < contigCount; contigI++){ string contigName = source->GetContigName(contigI); m_ofstream << ">" << contigName << ";\n"; gnSeqI seqLength = source->GetContigSeqLength(contigI); while(seqLength > 0){ gnSeqI writeLen = seqLength < BUFFER_SIZE ? seqLength : BUFFER_SIZE; Array array_buf( writeLen+1 ); // use Array template to ensure proper deallocation gnSeqC *bases = array_buf.data; boolean success = source->SeqRead(0, bases, writeLen, contigI); if(!success) return false; bases[writeLen] = 0; m_ofstream << bases << "\n"; seqLength -= writeLen; } } m_ofstream.close(); return true; } //write out the given sequence in this file format. void gnFASSource::Write(gnSequence& seq, const string& filename, boolean write_coords, boolean enforce_unique_names){ ofstream m_ofstream(filename.c_str(), ios::out | ios::binary); if(!m_ofstream.is_open()) Throw_gnEx(FileNotOpened()); Write(seq, m_ofstream, write_coords, enforce_unique_names); m_ofstream.close(); } void gnFASSource::Write(gnSequence& seq, ostream& m_ostream, boolean write_coords, boolean enforce_unique_names){ vector contigNameList; Array array_buf( BUFFER_SIZE ); // use Array template to ensure proper deallocation gnSeqC *bases = array_buf.data; gnGenomeSpec* spec = seq.GetSpec(); //set the newline type. string newline = "\r\n"; gnSeqI readOffset = 1; for(uint32 fragI = 0; fragI < seq.contigListLength(); fragI++){ //write out contig name and header string contigName = seq.contigName(fragI); if(enforce_unique_names){ uint32 name_count = 0; for(uint32 i=0; i < contigNameList.size(); i++) if(contigNameList[i] == contigName) name_count++; contigNameList.push_back(contigName); if(name_count > 0) contigName += "_" + uintToString(name_count); } gnFragmentSpec* subSpec = spec->GetSpec(fragI); gnBaseHeader *gpbh = subSpec->GetHeader(0); string header = ""; if(gpbh != NULL){ header = gpbh->GetHeader(); //delete everything after the first newline. string::size_type newlinepos = header.find_first_of('\n', 0); if(newlinepos != string::npos){ if(header[newlinepos-1] == '\r') newlinepos--; header = header.substr(0, newlinepos); } } //IMPLEMENT ME!! Does header line need to be < 80 chars? //write out the sequence gnSeqI readLength = seq.contigLength(fragI); m_ostream << ">" << contigName; if(write_coords) m_ostream << " " << "(" << readOffset << ", " << readOffset + readLength - 1 << ")"; m_ostream << "; " << header << endl; gnSeqI linePos = 0; while(readLength > 0){ //buffer the read/writes gnSeqI read_chunk_size = (BUFFER_SIZE / FAS_LINE_WIDTH) * FAS_LINE_WIDTH; gnSeqI writeLen = readLength < read_chunk_size ? readLength : read_chunk_size; if(!seq.ToArray(bases, writeLen, readOffset)) return; for(gnSeqI curbase = 0; curbase < writeLen; curbase += FAS_LINE_WIDTH){ gnSeqI writeout_size = writeLen - curbase < FAS_LINE_WIDTH ? writeLen - curbase : FAS_LINE_WIDTH; m_ostream << string(bases + curbase, writeout_size) << endl; } readLength -= writeLen; readOffset += writeLen; } if(linePos != 0) m_ostream << endl; } } gnGenomeSpec *gnFASSource::GetSpec() const{ gnGenomeSpec *spec = new gnGenomeSpec(); for(uint32 i=0; i < m_contigList.size(); i++){ //create specs for the fragment and contig levels gnFragmentSpec *fragmentSpec = new gnFragmentSpec(); gnSourceSpec *contigSpec = new gnSourceSpec((gnBaseSource*)this, i); //set up the spec tree structure spec->AddSpec(fragmentSpec, i); fragmentSpec->AddSpec(contigSpec); fragmentSpec->SetName(m_contigList[i]->GetName()); fragmentSpec->SetSourceName(m_openString); contigSpec->SetName(m_contigList[i]->GetName()); contigSpec->SetSourceName(m_openString); pair headsect = m_contigList[i]->GetSectStartEnd(gnContigHeader); if(headsect.first != headsect.second){ gnSourceHeader *gpsh = new gnSourceHeader((gnBaseSource *)this, string(""), headsect.first, headsect.second - headsect.first); fragmentSpec->AddHeader(gpsh, 0); } } return spec; } gnFileContig* gnFASSource::GetFileContig( const uint32 contigI ) const{ if(m_contigList.size() > contigI) return m_contigList[contigI]; return NULL; } boolean gnFASSource::ParseStream( istream& fin ) { // INIT temp varables uint32 readState = 0; gnFileContig* currentContig = 0; string nameFStr; uint64 seqLength = 0, gapLength = 0; // INIT buffer uint64 streamPos = 0; uint64 bufReadLen = 0; Array array_buf( BUFFER_SIZE ); // use Array template to ensure proper deallocation char* buf = array_buf.data; boolean paren_hit = false; uint32 repeatSeqSize = 0; boolean corrupt_msg = false; //decide what type of newlines we have DetermineNewlineType(); while( !fin.eof() ) { // read chars fin.read( buf, BUFFER_SIZE); streamPos += bufReadLen; bufReadLen = fin.gcount(); for( uint32 i=0 ; i < bufReadLen ; i++ ) { char ch = buf[i]; switch( readState ) { case 0: // CHECK file validity if( !((buf[0] == '>') || !m_pFilter->IsValid(buf[0])) ) { return false; // NOT a .fas file } readState = 1; case 1: // BRANCH if( ch == '>' ) { seqLength = 0; gapLength = 0; // reset count currentContig = new gnFileContig(); currentContig->SetFileStart( streamPos + i ); currentContig->SetRepeatSeqGap(true); currentContig->SetRepeatSeqSize( repeatSeqSize ); currentContig->SetRepeatGapSize( m_newlineSize ); readState = 2; paren_hit = false; nameFStr = ""; } else ++gapLength; break; case 2: // > CONTIG NAME if( isNewLine(ch) || ch == ';') { currentContig->SetName( nameFStr ); currentContig->SetSectStart( gnContigHeader, streamPos + i + 1 ); if( ch == ';' ) readState = 3; else{ readState = 4; if(ch == '\r') currentContig->SetSectStart( gnContigHeader, streamPos + i + 2 ); } } else if( ch == '(' ){ if(isSpace(buf[i-1])){ //delete the last char in nameFStr nameFStr = nameFStr.substr(0, nameFStr.length()-1); } paren_hit = true; }else if((!isSpace(ch) || nameFStr.length()) && !paren_hit ) nameFStr += ch; break; case 3: // >... ; REMARK if( isNewLine(ch) ) readState = 4; break; case 4: // >... ; /n NEWLINE BRANCH if( ch == '>' ) { readState = 3; } else if( m_pFilter->IsValid(ch) ) { currentContig->SetSectEnd( gnContigHeader, streamPos + i ); currentContig->SetSectStart( gnContigSequence, streamPos + i); seqLength = 1; gapLength = 0; readState = 5; } break; case 5: // SEQUENCE while(i < bufReadLen){ ch = buf[i]; if( m_pFilter->IsValid(ch) ){ if(gapLength > 0){ if(seqLength != repeatSeqSize){ if( !corrupt_msg ){ corrupt_msg = true; ErrorMsg( "Sequence file appears corrupt, proceeding with caution\n" ); } currentContig->SetRepeatSeqGap(false); }if(gapLength != m_newlineSize){ //file is corrupt, can't do jumps. if( !corrupt_msg ){ corrupt_msg = true; ErrorMsg( "Sequence file appears corrupt, proceeding with caution\n" ); } currentContig->SetRepeatSeqGap(false); } currentContig->AddToSeqLength( seqLength ); seqLength = 0; gapLength = 0; } seqLength++; }else if( ch == '>'){ currentContig->AddToSeqLength( seqLength ); currentContig->SetSectEnd( gnContigSequence, streamPos + i - 1); currentContig->SetFileEnd( streamPos + i - 1 ); m_contigList.push_back(currentContig); readState = 1; i--; break; } else if( isNewLine(ch) ){ if( repeatSeqSize == 0 ){ repeatSeqSize = seqLength; currentContig->SetRepeatSeqSize( repeatSeqSize ); } gapLength++; } else{ // Error cannot do nice jumps currentContig->SetRepeatSeqGap(false); if( !corrupt_msg ){ corrupt_msg = true; ErrorMsg( "Sequence file appears corrupt, proceeding with caution\n" ); } } i++; } break; default: ErrorMsg("ERROR"); return false; break; } }// for all buf }// while !eof // CLEAN UP if( currentContig != 0 ) { if( readState == 2 ) { currentContig->SetName( nameFStr ); } if( (readState >= 2) && (readState < 5) ) { currentContig->SetSectEnd( gnContigHeader, streamPos + bufReadLen ); } else if( readState == 5 ) { currentContig->AddToSeqLength( seqLength ); currentContig->SetSectEnd( gnContigSequence, streamPos + bufReadLen ); } currentContig->SetFileEnd( streamPos + bufReadLen ); m_contigList.push_back(currentContig); } m_ifstream.clear(); return true; } } // end namespace genome libGenome-1.3.1/libGenome/gnSourceSpec.cpp0000644002622200470610000000504210647575617015374 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnSourceSpec.cpp // Purpose: implements gnContigSpec for source specs // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnSourceSpec.h" using namespace std; namespace genome { gnSourceSpec::gnSourceSpec() { Clear(); } gnSourceSpec::gnSourceSpec( const gnSourceSpec& s ) { m_pSource = s.m_pSource; m_sourceName = string(s.m_sourceName); m_name = string(s.m_name); m_SourceContigIndex = s.m_SourceContigIndex; m_start = s.m_start; m_length = s.m_length; m_reverseComplement = s.m_reverseComplement; m_circular = s.m_circular; } gnSourceSpec::gnSourceSpec( gnBaseSource* source, const uint32 m_ContigIndex, const gnSeqI start, const gnSeqI endI, const boolean revComp) { m_pSource = source; m_SourceContigIndex = m_ContigIndex; m_name = ""; m_reverseComplement = revComp; m_circular = false; m_start = start; gnSeqI actual_len = source->GetContigSeqLength(m_ContigIndex); gnSeqI actual_end = endI; if(actual_len == 0) return; //this is a bogus gnSourceSpec //trim start and end down if they are too big. m_start = m_start < actual_len ? m_start : actual_len - 1; actual_end = actual_end < actual_len ? actual_end : actual_len - 1; //set the circularity and length if(revComp){ m_circular = m_start < actual_end ? true : false; m_length = ((m_start - actual_end + actual_len) % actual_len); }else{ m_circular = m_start > actual_end ? true : false; m_length = ((actual_end - m_start + actual_len) % actual_len); } if(actual_len != 0) m_length++; } gnSourceSpec::~gnSourceSpec() { } void gnSourceSpec::Clear() { gnContigSpec::Clear(); m_SourceContigIndex = 0; m_pSource = NULL; } gnSourceSpec* gnSourceSpec::CloneRange( const gnSeqI startI, const gnSeqI len ) const{ gnSourceSpec* destSpec = new gnSourceSpec(); destSpec->m_pSource = m_pSource; destSpec->m_sourceName = m_sourceName; destSpec->m_name = m_name; destSpec->m_SourceContigIndex = m_SourceContigIndex; destSpec->m_start = m_start + startI; destSpec->m_length = len < m_length - startI ? len : m_length - startI; destSpec->m_reverseComplement = m_reverseComplement; destSpec->m_circular = m_circular; return destSpec; } } // end namespace genome libGenome-1.3.1/libGenome/gnDefs.h0000644002622200470610000001402610647575617013651 00000000000000///////////////////////////////////////////////////////////////////////////// // File: libGenome/gnDefs.h // Purpose: Defines common constants in libGenome. // Description: Defines, consts, typedef etc for libGenome // Rev: A // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnDefs_h_ #define _gnDefs_h_ #ifdef __GNUG__ #pragma interface "libGenome/gnDefs.h" #endif #include #include #include "libGenome/gnSetup.h" // bool typedef unsigned char boolean; typedef unsigned char int1; // signed typedef signed char int8; typedef signed short int int16; typedef signed int int32; typedef signed long long int64; typedef signed char sint8; typedef signed short int sint16; typedef signed int sint32; typedef signed long int sint64; // unsigned typedef unsigned char uint8; typedef unsigned short int uint16; typedef unsigned int uint32; typedef unsigned long long uint64; typedef unsigned int uint; // float typedef float float32; typedef double float64; // defines #ifndef TRUE #define TRUE 1 #endif #ifndef FALSE #define FALSE 0 #endif #ifndef PI #define PI 3.1415926535897932384626433832795028 #endif #ifndef BOOLEAN_MIN #define BOOLEAN_MIN 0 #endif #ifndef BOOLEAN_MAX #define BOOLEAN_MAX 1 #endif #ifndef INT1_MIN #define INT1_MIN 0 #endif #ifndef INT1_MAX #define INT1_MAX 1 #endif #define INT8_BYTE_SIZE 1 #define INT16_BYTE_SIZE 2 #define INT32_BYTE_SIZE 4 #define INT64_BYTE_SIZE 8 #define INT8_BIT_SIZE 8 #define INT16_BIT_SIZE 16 #define INT32_BIT_SIZE 32 #define INT64_BIT_SIZE 64 #define UINT8_BYTE_SIZE 1 #define UINT16_BYTE_SIZE 2 #define UINT32_BYTE_SIZE 4 #define UINT64_BYTE_SIZE 8 #define UINT8_BIT_SIZE 8 #define UINT16_BIT_SIZE 16 #define UINT32_BIT_SIZE 32 #define UINT64_BIT_SIZE 64 // limits.h #ifndef INT8_MIN #define INT8_MIN SCHAR_MIN //0x00 #endif #ifndef INT8_MAX #define INT8_MAX SCHAR_MAX //0x7f #endif #ifndef INT16_MIN #define INT16_MIN SHRT_MIN //0x0000 #endif #ifndef INT16_MAX #define INT16_MAX SHRT_MAX //0x7fff #endif #ifndef INT32_MIN #define INT32_MIN INT_MIN //0x0000000 #endif #ifndef INT32_MAX #define INT32_MAX INT_MAX //0x7fffffff #endif #ifndef INT64_MIN #define INT64_MIN LONG_MIN //0x0000000000000000 #endif #ifndef INT64_MAX #define INT64_MAX LONG_MAX //0x7fffffffffffffff #endif #ifndef UINT8_MIN #define UINT8_MIN 0 //0x00 #endif #ifndef UINT8_MAX #define UINT8_MAX UCHAR_MAX //0xff #endif #ifndef UINT16_MIN #define UINT16_MIN 0 //0x0000 #endif #ifndef UINT16_MAX #define UINT16_MAX USHRT_MAX //0xffff #endif #ifndef UINT32_MIN #define UINT32_MIN 0 //0x00000000 #endif #ifndef UINT32_MAX #define UINT32_MAX UINT_MAX //0xffffffff #endif #ifndef UINT64_MIN #define UINT64_MIN 0 //0x0000000000000000 #endif #ifndef UINT64_MAX #define UINT64_MAX ULONG_MAX //0xffffffffffffffff #endif // float.h #define FLOAT32_MIN FLT_MIN #define FLOAT32_MAX FLT_MAX #define FLOAT32_MIN_EXP FLT_MIN_EXP #define FLOAT32_MAX_EXP FLT_MAX_EXP #define FLOAT32_MIN_10_EXP FLT_MIN_10_EXP #define FLOAT32_MAX_10_EXP FLT_MAX_10_EXP #define FLOAT32_DIGIT FLT_DIG #define FLOAT32_RADIX FLT_RADIX #define FLOAT32_MIN_FRACTION FLT_EPSILON #define FLOAT64_MIN DBL_MIN #define FLOAT64_MAX DBL_MAX #define FLOAT64_MIN_EXP DBL_MIN_EXP #define FLOAT64_MAX_EXP DBL_MAX_EXP #define FLOAT64_MIN_10_EXP DBL_MIN_10_EXP #define FLOAT64_MAX_10_EXP DBL_MAX_10_EXP #define FLOAT64_DIGIT DBL_DIG #define FLOAT64_RADIX DBL_RADIX #define FLOAT64_MIN_FRACTION DBL_EPSILON // Sequence Types typedef char gnSeqC; // Sequence Character typedef uint64 gnSeqI; // Sequence Index #define GNSEQI_ERROR UINT32_MAX // return value #define GNSEQI_END UINT32_MAX // argument value #define GNSEQI_BEGIN UINT64_MIN // argument value #define GNSEQC_NULL 0 #define GNSEQC_MIN INT8_MIN #define GNSEQC_MAX INT8_MAX #define CONTIG_SECTION_SIZE 3 // some compilers don't have abs() for 64 bit ints #if (defined(__GNUG__) && ( __GNUC__ <= 2 )) || defined(__INTEL_COMPILER) || (defined _MSC_VER && defined __cplusplus) int64 abs( int64 a ); #endif #ifdef __cplusplus namespace genome { #endif enum gnContigSection{ gnContigHeader = 0, gnContigAnnotation = 1, gnContigSequence = 2 }; enum gnNewlineType{ gnNewlineUnix = 0, gnNewlineWindows = 1, gnNewlineMac = 2 }; static const uint32 ALL_CONTIGS = UINT32_MAX; static const uint32 BUFFER_SIZE = 100000; #ifdef __cplusplus template< typename T > T absolut( const T& t ) { return t < 0 ? -t : t; }; /** * Class used to ensure correct deallocation of arrays. */ template class Array{ public: /** Allocate a new array of length "bufsize". The array can be * accessed through the data member */ Array( uint64 bufsize ){ data = new T[bufsize]; } ~Array() { if (data != NULL) delete[] data; } /** The actual array */ T* data; private: Array( const Array& a ); Array& operator=( const Array& a ); Array(){}; }; #endif //__cplusplus #ifndef __PRETTY_FUNCTION__ #define __PRETTY_FUNCTION__ "Unknown( ) " #endif #ifdef __cplusplus } // end namespace genome #endif #endif //_gnDefs_h_ libGenome-1.3.1/libGenome/gnSequence.h0000644002622200470610000006045011003030307014503 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnSequence.h // Purpose: Sequence class // Description: Provides a high level sequence interface to all types of // sequence data. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnSequence_h_ #define _gnSequence_h_ #include "libGenome/gnDefs.h" #include #include #include #include #include "libGenome/gnBaseSource.h" #include "libGenome/gnGenomeSpec.h" #include "libGenome/gnSourceSpec.h" #include "libGenome/gnStringSpec.h" #include "libGenome/gnBaseFilter.h" #include "libGenome/gnCompare.h" namespace genome { /** * gnSequence is the most commonly used class in libGenome. It provides a simple * and general way to manipulate genetic sequences, regardless of what kind of * database, web site, or file they are stored in. Sequence data can be * manipulated like a c++ std::string by using subseq() and erase(). gnSequence * updates annotated sequences with each change, breaking features if necessary. */ class GNDLLEXPORT gnSequence : public gnClone { public: /** * Empty Constructor, creates an empty gnSequence. */ gnSequence(); /** * Creates a gnSequence with a single fragment containing the bases in "seq". * @param seq The null terminated character array of base pairs to use. */ gnSequence( const gnSeqC* seq ); /** * Creates a gnSequence with a single fragment containing the bases in "str". * @param str The base pairs to use. */ gnSequence( const std::string& str ); /** * Creates a gnSequence with the genome stored in the gnGenomeSpec "gngs". * @param gngs the gnGenomeSpec to get contigs from. */ gnSequence( const gnGenomeSpec& gngs ); /** * Creates a gnSequence with the sequence fragment stored in the gnFragmentSpec "gnfs". * @param gnfs the gnFragmentSpec to get contigs from. */ gnSequence( const gnFragmentSpec& gnfs ); /** * Creates a gnSequence with the contig stored in the gnContigSpec "gncs". * Usually gncs will be a gnStringSpec or a gnSourceSpec. * @param gncs the gnContigSpec to get contigs from. */ gnSequence( const gnContigSpec& gncs ); /** * Creates a gnSequence with a single fragment containing the bases in "bases". * @param bases The base pairs to use * @param length The length of the base pair array. */ gnSequence( gnSeqC *bases, const gnSeqI length); /** * Copies the gnSequence "seq". * @param seq The gnSequence to copy. */ gnSequence( const gnSequence& seq); /** * Destructor, frees the memory used by this sequence. */ ~gnSequence(); /** * Copies the gnSequence. */ gnSequence& operator=( const gnSequence& seq); gnSequence* Clone() const; /** * Returns the number of sequence fragments in this sequence. * @return the number of sequence fragments in this sequence. */ gnSeqI contigListSize() const; /** * Returns the number of sequence fragments in this sequence. * @return the number of sequence fragments in this sequence. */ gnSeqI contigListLength() const; /** * Returns the index of the contig which contains the specified base. * @param baseI A base pair in the contig. * @throws SeqIndexOutOfBounds will be propagated if baseI is invalid * @return The contig index which contains the base. */ uint32 contigIndexByBase( const gnSeqI baseI) const; /** * Returns a gnSequence containing the specified fragment. * @param contigI The index of the fragment to get. * @throws FragmentIndexOutOfBounds will be propagated if contigI is invalid * @return A gnSequence containing only the fragment. */ gnSequence contig( const uint32 contigI) const; /** * Returns a gnSequence containing only the fragment which contains the specified base. * @param baseI A base pair index in the contig * @throws SeqIndexOutOfBounds will be propagated if baseI is invalid * @return A gnSequence containing only the contig. */ gnSequence contigByBase( const gnSeqI baseI) const; /** * Returns the index of the base pair where the specified contig starts in this sequence. * @param contigI The index of the contig. * @throws FragmentIndexOutOfBounds will be propagated if contigI is invalid * @return The starting base pair index. */ virtual gnSeqI contigStart( const uint32 contigI) const; /** * Returns the length in base pairs of the specified contig in this sequence. * @param contigI The index of the contig. * @throws FragmentIndexOutOfBounds will be propagated if contigI is invalid * @return The length of the contig. */ virtual gnSeqI contigLength( const uint32 contigI) const; /** * Returns the index of the contig with the given name. * If two contigs have the same name, contigIndexByName() will return the first. * @param contigName The name of the contig. * @throws FragmentIndexOutOfBounds will be propagated if contigName is not found * @return The index of the contig. */ virtual uint32 contigIndexByName( std::string& contigName) const; /** * Returns the name of the specified contig. * @param contigI The index of the contig. * @throws FragmentIndexOutOfBounds will be propagated if contigI is invalid * @return The name of the contig. */ virtual std::string contigName( const uint32 contigI) const; /** * Returns a gnSequence containing only the named contig. * If two contigs have the same name, contigByName() will return the first. * @param contigName The name of the contig. * @throws FragmentIndexOutOfBounds will be propagated if contigName is not found * @return A gnSequence containing the contig. */ virtual gnSequence contigByName( std::string& contigName) const; /** * Merges the bases starting at base index "startI" and ending at "endI" into one contig, splitting existing contigs. * @param startI The starting base pair of the new contig. * @param endI The ending base pair of the new contig. * @throws SeqIndexOutOfBounds exception is propagated if startI or endI are invalid */ virtual void merge(const gnSeqI startI, const gnSeqI endI); /** * Merges the contigs starting at the contig index "startC" and ending at "endC" into one contig. * @param startC The starting contig of the new contig. * @param endC The ending contig of the new contig. * @throws FragmentIndexOutOfBounds exception is propagated if startC or endC are invalid */ virtual void mergeContigs(const uint32 startC, const uint32 endC); /** * Splits the specified contig after splitI * @param splitI The base pair to split after. * @param contigI The index of the contig to split or ALL_CONTIGS by default. */ virtual void splitContig(const gnSeqI splitI, const uint32 contigI=ALL_CONTIGS); virtual void setContigName( const uint32 contigI, const std::string& contig_name); /** * Returns the size of the feature list for the specified contig. * @return The feature list size. */ virtual uint32 getFeatureListLength() const; /** * Returns the feature specified by featureI. * @param featureI The index of the feature to return. * @throws FeatureIndexOutOfBounds exception is thrown if featureI does not reference a valid feature * @return A copy of the feature allocated on the heap. You must delete the feature when finished with it. */ virtual gnBaseFeature* getFeature(const uint32 featureI) const; /** * Creates a list of all features which are contained by coordinates specified. * @param lt The coordinates containing the features to return. * @param feature_vector The std::vector to store features in. Each feature pointer points to a copy of the feature on the heap which must be deleted. * @param index_vector A std::vector of indices which correspond to the features. */ virtual void getContainedFeatures(const gnLocation& lt, std::vector& feature_vector, std::vector& index_vector) const; /** * Creates a list of all features which intersect the coordinates specified. * @param lt The coordinates intersecting the features to return. * @param feature_vector The std::vector to store features in. Each feature pointer points to a copy of the feature on the heap which must be deleted. * @param index_vector A std::vector of indices which correspond to the features. */ virtual void getIntersectingFeatures(const gnLocation& lt, std::vector& feature_vector, std::vector& index_vector) const; /** * Adds the specified feature to the feature list. * @param feature The feature to add. * @return The feature index. */ virtual uint32 addFeature(gnBaseFeature* feature); /** * Removes the specified feature. * @param featureI The index in the feature list of the feature to remove. * @throws FeatureIndexOutOfBounds exception is thrown if featureI does not reference a valid feature */ virtual void removeFeature(const uint32 featureI); /** * Creates a list of features which may have been broken by an edit. * @param lt The coordinates containing the features to return. * @param feature_vector The std::vector to store features in. Each feature pointer points to a copy of the feature on the heap which must be deleted. */ virtual void getBrokenFeatures(const gnLocation& lt, std::vector& feature_vector) const; /** * Returns the size of the header list for the specified contig. * @param contigI The index of the contig to use, or ALL_CONTIGS to add a general header. * @throws FragmentIndexOutOfBounds will be propagated if contigI is invalid * @return The header list size. */ virtual uint32 getHeaderListLength(const uint32 contigI) const; /** * Returns the feature specified by featureI. * @param contigI The index of the contig to use, or ALL_CONTIGS to get a general header. * @param headerI The index of the header to return. * @throws FragmentIndexOutOfBounds will be propagated if contigI is invalid * @throws HeaderIndexOutOfBounds will be propagated if headerI is invalid * @return The header, or NULL if headerI is out of range. */ virtual gnBaseHeader* getHeader(const uint32 contigI, const uint32 headerI) const; /** * Adds header information to a specified contig. * @param contigI The index of the contig to use, or ALL_CONTIGS to add a general header. * @param header The header to add. * @param headerI The index in the header list where this header should be inserted. * @throws FragmentIndexOutOfBounds will be propagated if contigI is invalid */ virtual void addHeader(const uint32 contigI, gnBaseHeader* header, const uint32 headerI); /** * Removes header information from a specified contig. * @param contigI The index of the contig to use, or ALL_CONTIGS to remove a general header. * @param headerI The index in the header list of the header to remove. * @throws FragmentIndexOutOfBounds will be propagated if contigI is invalid */ virtual void removeHeader(const uint32 contigI, const uint32 headerI); /** * Reverse complements a specified contig, or the entire sequence if ALL_CONTIGS is specified. * @param revComp True if the area should be reverse complement, false otherwise. * @param contigI The index of the contig to use, or ALL_CONTIGS. * @throws FragmentIndexOutOfBounds will be propagated if contigI is invalid */ virtual void setReverseComplement( const boolean revComp, const uint32 contigI=ALL_CONTIGS); /** * Returns true if a specified contig, or the entire sequence is reverse complement. * @param contigI The index of the contig to use, or ALL_CONTIGS for the whole sequence. * @throws FragmentIndexOutOfBounds will be propagated if contigI is invalid * @return True if the sequence is reverse complement, false otherwise. */ virtual boolean isReverseComplement( const uint32 contigI=ALL_CONTIGS ); /** * Returns true if this sequence is circular. * @return True if this sequence is circular. */ virtual boolean isCircular() const; /** * Sets whether this sequence should be read circular. * If circular is set, reads beyond the end of the sequence will pick up * at the beginning. * @param value True for circular, false otherwise. */ virtual void setCircular( const boolean value ); /** * Converts the global sequence coordinate baseI to a contig local coordinate. * @param contigI This is set to the index of the contig containing baseI * @param baseI This is the global coordinate to be converted to contig local. * @throws SeqIndexOutOfBounds will be thrown if baseI is out of range */ virtual void globalToLocal(uint32& contigI, gnSeqI& baseI) const; /** * Converts the local contig coordinate baseI to a global sequence coordinate. * @param contigI The index of the contig containing baseI. * @param baseI The local contig coordinate to be converted to global. * @throws SeqIndexOutOfBounds will be thrown if baseI is out of range * @throws FragmentIndexOutOfBounds will be propagated if contigI is invalid */ virtual void localToGlobal(const uint32 contigI, gnSeqI& baseI) const; /** * Converts the global sequence coordinate baseI to a local coordinate in the original * data source. globalToSource() will overwrite any values passed to it! * @param contigI This will be set to contig index in the original source. * @param baseI This will be set to the contig local base index in the original source. * @throws SeqIndexOutOfBounds will be thrown if baseI is out of range */ virtual void globalToSource(uint32& contigI, gnSeqI& baseI) const; /** * Converts the contig local sequence coordinate baseI in contig contigI to a * local coordinate in the original data source. localToSource() will overwrite any values * passed to it! * @param contigI This will be set to contig index in the original source. * @param baseI This will be set to the contig local base index in the original source. * @throws SeqIndexOutOfBounds will be thrown if baseI is out of range * @throws FragmentIndexOutOfBounds will be propagated if contigI is invalid */ virtual void localToSource(uint32& contigI, gnSeqI& baseI) const; /** * Loads the sequence located at the URL in "sourcename". * Possible URLs currently include only "file:///" URLs. * If no URL prefix is found then LoadSource assumes that "sourcename" * contains the name of a local file. * @param sourcename The location of the data to load. * @return True if successful. False otherwise. */ virtual bool LoadSource(const std::string sourcename); /** Assigns a filter which all sequence data must pass through when * read from the object. * @param filt The filter to use. */ virtual void setFilter(const gnBaseFilter* filt); /** Assigns a list of filters which all sequence data passes through * in order when read from the object. There may not be any NULL * pointers in the list. * @param filt_list The ordered list of filters to use. */ virtual void setFilterList(std::list& filt_list); /** Returns the list of filters currently being used * @return The list of filters in use. */ virtual std::list getFilterList() const; /** * Assigns the sequence "seq" to this sequence. * @param seq The seqence to assign to this sequence. */ virtual void assign(gnSequence& seq); // Comparison Operators /** * Assigns the sequence "seq" to this sequence. */ void operator=(gnSequence& seq); boolean operator==(const gnSequence& seq) const; boolean operator!=(const gnSequence& seq) const; boolean operator<(const gnSequence& seq) const; boolean operator<=(const gnSequence& seq) const; boolean operator>(const gnSequence& seq) const; boolean operator>=(const gnSequence& seq) const; /** * Appends the bases in "seq" to this sequence. */ gnSequence& operator+=(const gnSequence& seq); /** * Compares the bases in "seq" to this sequence. * @param seq The sequence to compare this sequence to. * @return Negative if this sequence is lesser, 0 if the two sequences are * equal, and positive if this sequence is greater. */ virtual int compare(const gnSequence& seq) const; virtual int compare(const std::string& str) const; // Append and Insert Operators /** * Appends the bases in "seq" to this sequence. * @param seq The sequence to append to this sequence. */ virtual void append( const gnSequence& seq); /** * Inserts the first "len" bases in "bases" into this sequence.at "offset". * insert() will update the locations of all affected features. * @param offset The base pair to insert before. * @param bases The character array of bases to insert. * @param length The length of the character array. */ virtual void insert( const gnSeqI offset, const gnSeqC *bases, const gnSeqI length); /** * Inserts the annotated sequence in "seq" into this sequence.at "offset". * insert() will update the locations of all affected features. * @param offset The base pair to insert before. * @param seq The sequence to insert. */ virtual void insert( const gnSeqI offset, const gnSequence& seq); /** * Inserts the annotated sequence in "gnbs" into this sequence.at "offset". * insert() will update the locations of all affected features. * @param offset The base pair to insert before. * @param gnbs The spec to insert. */ virtual void insert( const gnSeqI offset, const gnGenomeSpec& gnbs); // Concatenation Operators /** * Concatenates this sequence with the annotated sequence in "seq". */ gnSequence const operator+(const gnSequence& seq) const; // Substrings and base deletion /** * Creates a sequence containing the "length" bases starting at "offset". * @param offset The base pair index to start the subsequence. * @param length The length of the subsequence. * @return The subsequence. */ gnSequence subseq(const gnSeqI offset, const gnSeqI length) const; /** * Deletes the "len" bases starting at "offset". * @param offset The base pair index to start erasing. * @param length The length of the sequence to erase */ virtual void erase( const gnSeqI offset=0, const gnSeqI length=GNSEQI_END ); // IO operators /** * Reads bases from the specified input stream (e.g. cin). */ friend std::istream& operator>>(std::istream& is, gnSequence& gns); //read from source. /** * Writes the bases in this sequence to the specified output stream (e.g. cout). */ friend std::ostream& operator<<(std::ostream& os, const gnSequence& gns); //write to source. // Size functions /** * Returns the length of this sequence. * @return the length of this sequence. */ virtual gnSeqI length() const; /** * Returns the length of this sequence. * @return the length of this sequence. */ virtual gnSeqI size() const; // Raw Sequence Access /** * Returns the "length" bases starting at "offset" as a std::string. * @param length The length of the sequence to convert * @param offset The base pair index of the sequence to convert * @return The std::string of base pairs. */ virtual std::string ToString( const gnSeqI length=GNSEQI_END, const gnSeqI offset=1 ) const; /** * Converts the "length" bases starting at "offset" into the std::string "str". * @param str The std::string to store bases in. * @param length The length, in base pairs, to convert. * @param offset The base pair index to start converting. * @return True if successful, false otherwise. */ virtual boolean ToString( std::string& str, const gnSeqI length=GNSEQI_END, const gnSeqI offset=1 ) const; /** * Converts the "length" bases starting at "offset" into the character array "pSeqC".. * After converting, "length" will be set to the actual length of the sequence. * Be sure to null terminate the character array if you are going to print it! * @param pSeqC The character array of bases to store bases in. * @param length The length, in base pairs, to convert. * @param offset The base pair index to start converting. * @return True if successful, false otherwise. */ virtual boolean ToArray( gnSeqC* pSeqC, gnSeqI length, const gnSeqI offset=1 ) const; /** * Returns the base at "offset". * @param offset The index of the base to get. * @return The base. */ virtual gnSeqC GetSeqC( const gnSeqI offset ) const; // return gnSeqC illegal char. /** * Returns the base at the specified index. * @return The base at the specified index. */ gnSeqC operator[]( const gnSeqI offset ) const; /** * Get the spec (annotated sequence) which this sequence represents. * @return The spec represented by this gnSequence. */ virtual gnGenomeSpec* GetSpec() const; /** * Set the spec (annotated sequence) which this sequence represents. * @param s The new spec. */ virtual void SetSpec(gnGenomeSpec* s); /** * Find looks for the search sequence within this gnSequence and returns * the position of the first match if any exists. * @param search The gnSequence to be found * @param offset The position where searching will begin (default is 0) * @return The first position where the search std::string is found or * GNSEQI_ERROR if the search sequence is not found. */ virtual gnSeqI find(const gnSequence& search, const gnSeqI offset=0) const; private: gnGenomeSpec *spec; std::list filter_list; const gnCompare* comparator; }; // class gnSequence GNDLLEXPORT std::istream& operator>>(std::istream& is, gnSequence& gns); //read from source. GNDLLEXPORT std::ostream& operator<<(std::ostream& os, const gnSequence& gns); //write to source. // Assignment Operators inline void gnSequence::operator=(gnSequence& seq){ spec = seq.spec->Clone(); } inline void gnSequence::assign(gnSequence& seq){ spec = seq.spec->Clone(); } inline boolean gnSequence::operator==(const gnSequence& seq) const{ return (compare(seq)==0); } inline boolean gnSequence::operator!=(const gnSequence& seq) const{ return (compare(seq)!=0); } inline boolean gnSequence::operator<(const gnSequence& seq) const{ return (compare(seq)<0); } inline boolean gnSequence::operator<=(const gnSequence& seq) const{ return (compare(seq)<=0); } inline boolean gnSequence::operator>(const gnSequence& seq) const{ return (compare(seq)>0); } inline boolean gnSequence::operator>=(const gnSequence& seq) const{ return (compare(seq)>=0); } // Append and Insert Operators inline gnSequence& gnSequence::operator+=(const gnSequence& seq){ insert(GNSEQI_END, *seq.spec); return *this; } inline void gnSequence::append( const gnSequence& seq){ insert(GNSEQI_END, *seq.spec); } //Feature functions inline uint32 gnSequence::getFeatureListLength() const{ return spec->GetFeatureListLength(); } inline gnBaseFeature* gnSequence::getFeature(const uint32 featureI) const{ return spec->GetFeature(featureI); } inline uint32 gnSequence::addFeature(gnBaseFeature* feature){ return spec->AddFeature(feature); } inline void gnSequence::removeFeature(const uint32 featureI){ spec->RemoveFeature(featureI); } inline void gnSequence::getContainedFeatures(const gnLocation& lt, std::vector& feature_vector, std::vector& index_vector) const{ spec->GetContainedFeatures(lt, feature_vector, index_vector); } inline void gnSequence::getIntersectingFeatures(const gnLocation& lt, std::vector& feature_vector, std::vector& index_vector) const{ spec->GetIntersectingFeatures(lt, feature_vector, index_vector); } inline void gnSequence::getBrokenFeatures(const gnLocation& lt, std::vector& feature_vector) const{ spec->GetBrokenFeatures(lt, feature_vector); } inline boolean gnSequence::isCircular() const{ return spec->IsCircular(); } inline void gnSequence::setCircular( const boolean value ){ spec->SetCircular(value); } inline void gnSequence::insert( const gnSeqI offset, const gnSequence& seq){ insert(offset, *seq.spec); } // Size functions inline gnSeqI gnSequence::length() const{ return spec->GetLength(); } inline gnSeqI gnSequence::size() const{ return spec->GetLength(); } inline gnGenomeSpec* gnSequence::GetSpec() const{ return spec; } inline void gnSequence::SetSpec(gnGenomeSpec* s){ if(spec != NULL) delete spec; spec = s; } inline void gnSequence::setFilter(const gnBaseFilter* filt){ filter_list.clear(); if(filt != NULL) filter_list.push_back(filt); } inline void gnSequence::setFilterList(std::list& filt_list){ filter_list = filt_list; } inline std::list gnSequence::getFilterList() const{ return filter_list; } } // end namespace genome #endif // _gnSequence_h_ libGenome-1.3.1/libGenome/gnDNASequence.h0000644002622200470610000000757710647575617015100 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnDNASequence.h // Purpose: Sequence class // Description: Provides a high level sequence interface to all types of // sequence data. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnDNASequence_h_ #define _gnDNASequence_h_ #include "libGenome/gnDefs.h" #include #include #include "libGenome/gnSequence.h" #include "libGenome/gnFilter.h" namespace genome { /** * gnDNASequence is a special kind of gnSequence which can be used for DNA sequences * It sets the default filters and comparators to the DNA filters and comparators. */ class GNDLLEXPORT gnDNASequence : public gnSequence { public: /** * Empty Constructor, creates an empty gnDNASequence. */ gnDNASequence(); /** * Creates a gnDNASequence with a single contig containing the bases in "seq". * @param seq The null terminated array of base pairs to use. */ gnDNASequence( const gnSeqC* seq ); /** * Creates a gnDNASequence with a single contig containing the bases in "str". * @param str The base pairs to use. */ gnDNASequence( const std::string& str ); /** * Creates a gnDNASequence with the contigs stored in "gngs". * @param gngs the gnGenomeSpec to get contigs from. */ gnDNASequence( const gnGenomeSpec& gngs ); /** * Creates a gnDNASequence with the contigs stored in "gnfs". * @param gnfs the gnFragmentSpec to get contigs from. */ gnDNASequence( const gnFragmentSpec& gnfs ); /** * Creates a gnDNASequence with the contigs stored in "gncs". * @param gncs the gnContigSpec to get contigs from. */ gnDNASequence( const gnContigSpec& gncs ); /** * Creates a gnDNASequence with a single contig containing the bases in "bases". * @param bases The base pairs to use * @param length The length of the base pair array. */ gnDNASequence( gnSeqC *bases, const gnSeqI length); /** * Copies the gnDNASequence "seq". * @param seq The gnDNASequence to copy. */ gnDNASequence( const gnDNASequence& seq); private: gnGenomeSpec *spec; list filter_list; const gnCompare* comparator; }; // class gnDNASequence inline gnDNASequence::gnDNASequence() : gnSequence(){ filter_list.push_back(gnFilter::fullDNASeqFilter()); comparator = gnCompare::DNASeqCompare(); } inline gnDNASequence::gnDNASequence( const gnSeqC* seq ) : gnSequence(seq){ filter_list.push_back(gnFilter::fullDNASeqFilter()); comparator = gnCompare::DNASeqCompare(); } inline gnDNASequence::gnDNASequence( const std::string& str ) : gnSequence(str){ filter_list.push_back(gnFilter::fullDNASeqFilter()); comparator = gnCompare::DNASeqCompare(); } inline gnDNASequence::gnDNASequence( const gnGenomeSpec& gngs ) : gnSequence(gngs){ filter_list.push_back(gnFilter::fullDNASeqFilter()); comparator = gnCompare::DNASeqCompare(); } inline gnDNASequence::gnDNASequence( const gnFragmentSpec& gnfs ) : gnSequence(gnfs){ filter_list.push_back(gnFilter::fullDNASeqFilter()); comparator = gnCompare::DNASeqCompare(); } inline gnDNASequence::gnDNASequence( const gnContigSpec& gncs ) : gnSequence(gncs){ filter_list.push_back(gnFilter::fullDNASeqFilter()); comparator = gnCompare::DNASeqCompare(); } inline gnDNASequence::gnDNASequence( gnSeqC *bases, const gnSeqI length) : gnSequence(bases, length){ filter_list.push_back(gnFilter::fullDNASeqFilter()); comparator = gnCompare::DNASeqCompare(); } inline gnDNASequence::gnDNASequence( const gnDNASequence& seq) : gnSequence(seq){ filter_list.push_back(gnFilter::fullDNASeqFilter()); comparator = gnCompare::DNASeqCompare(); } } // end namespace genome #endif // _gnDNASequence_h_ libGenome-1.3.1/libGenome/gnFeature.cpp0000644002622200470610000000261510647575617014717 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnFeature.cpp // Purpose: implements the gnBaseFeature for generic features // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnFeature.h" #include "libGenome/gnLocation.h" #include "libGenome/gnStringQualifier.h" #include "libGenome/gnDebug.h" #include using namespace std; namespace genome { gnFeature::gnFeature() { /* m_id = 0; m_name = ""; m_locationType = gnLocation::LT_Nothing; m_broken = false; */} gnFeature::gnFeature( string& name, uint32 id, gnLocation::gnLocationType lt, boolean broken ) : gnBaseFeature(name, id, NULL, lt, broken) { } gnFeature::gnFeature( const gnFeature& s ) { uint32 i; m_id = s.m_id; m_name = s.m_name; m_locationType = s.m_locationType; m_broken = s.m_broken; m_spec = s.m_spec; for( i=0; i < s.m_locationList.size(); i++) m_locationList.push_back(s.m_locationList[i]); for( i=0; i < s.m_qualifierList.size(); i++) m_qualifierList.push_back(s.m_qualifierList[i]->Clone()); } gnFeature::~gnFeature() { } } // end namespace genome libGenome-1.3.1/libGenome/gnFASSource.h0000644002622200470610000001135711026443220014536 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnFASSource.h // Purpose: Implements gnBaseSource for .FAS files // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnFASSource_h_ #define _gnFASSource_h_ #include "libGenome/gnDefs.h" #include #include #include #include "libGenome/gnFileSource.h" #include "libGenome/gnSequence.h" namespace genome { #define FAS_LINE_WIDTH 80 /** * gnFASSource reads and writes FastA files. * gnFASSource is used by gnSourceFactory to read files. * Files can be written in the FastA file format by calling * gnFASSource::Write( mySpec, "C:\\myFasFile.fas"); */ class GNDLLEXPORT gnFASSource : public gnFileSource { public: /** * Empty Constructor, does nothing. */ gnFASSource(); /** * Clone Constructor copies the specified gnFASSource. * @param s The gnFASSource to copy. */ gnFASSource( const gnFASSource& s ); /** * Destructor, frees memory. */ ~gnFASSource(); /** * Returns an exact copy of this class. */ gnFASSource* Clone() const; uint32 GetContigListLength() const; boolean HasContig( const std::string& name ) const; uint32 GetContigID( const std::string& name ) const; std::string GetContigName( const uint32 i ) const; gnSeqI GetContigSeqLength( const uint32 i ) const; gnFileContig* GetContig( const uint32 i ) const; boolean SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI=ALL_CONTIGS ) ; /** * Write the given gnSequence to a FastA file. * @param sequence The gnSequence to write out. * @param filename The name of the file to write. * @param write_coords If true each entry's name will be followed by the coordinates of the entry * in the context of the entrire file. * @param enforce_unique_names If true each entry's name will be recorded as they are written. Each * successive duplicate name that is found will have an underscore and a * number appended to it, indicating the number of entries by the same * name which have already been written. * Turning this off will yield a slight performance improvement when writing * files with a large number of entries. (More than 1000) * @throws A FileNotOpened() exception may be thrown. */ static void Write(gnSequence& sequence, const std::string& filename, boolean write_coords = true, boolean enforce_unique_names = true); /** * Write the given gnSequence to an ostream. * @param sequence The gnSequence to write out. * @param m_ostream The output stream to write to. * @param write_coords If true each entry's name will be followed by the coordinates of the entry * in the context of the entrire file. * @param enforce_unique_names If true each entry's name will be recorded as they are written. Each * successive duplicate name that is found will have an underscore and a * number appended to it, indicating the number of entries by the same * name which have already been written. * Turning this off will yield a slight performance improvement when writing * files with a large number of entries. (More than 1000) */ static void Write(gnSequence& sequence, std::ostream& m_ostream, boolean write_coords = true, boolean enforce_unique_names = true); /** * Deprecated - do not use. * Write the given source to a FastA file. * @param source The spec to write out. * @param filename The name of the file to write. */ static boolean Write(gnBaseSource *source, const std::string& filename); gnGenomeSpec *GetSpec() const; gnFileContig* GetFileContig( const uint32 contigI ) const; private: boolean SeqReadImpl( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI=ALL_CONTIGS ) ; boolean SeqSeek( const gnSeqI start, const uint32 contigI, uint64& startPos, uint64& readableBytes ); boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes ); boolean ParseStream( std::istream& fin ); std::vector< gnFileContig* > m_contigList; };// class gnFASSource inline gnFASSource* gnFASSource::Clone() const { return new gnFASSource( *this ); } inline uint32 gnFASSource::GetContigListLength() const { return m_contigList.size(); } } // end namespace genome #endif // _gnFASSource_h_ libGenome-1.3.1/libGenome/gnTranslator.h0000644002622200470610000001247610647575617015130 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnTranslator.h // Purpose: Translator for all Sequences // Description: Translates DNA and protein sequences // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnTranslator_h_ #define _gnTranslator_h_ #include "libGenome/gnDefs.h" #include #include #include "libGenome/gnClone.h" #include "libGenome/gnBaseFilter.h" #include "libGenome/gnCompare.h" namespace genome { /** * The gnTranslator class facilitates the translation of ambiguous DNA and RNA * sequences to protein sequence. It can also perform reverse translation from * Protein to RNA or DNA though the utility of this functionality is somewhat * questionable since it does not assign nucleotides probabilistically. * Do not attempt to instantiate this class unless you are defining a new * translation type. Instead use the static member access functions ProteinDNATranslator(), * ProteinRNATranslator(), DNAProteinTranslator(), and RNAProteinTranslator() * In general, the gnFastTranslator class should be used instead of this one. * @see gnFastTranslator */ class GNDLLEXPORT gnTranslator : public gnBaseFilter { public: static const gnTranslator *ProteinDNATranslator(); static const gnTranslator *ProteinRNATranslator(); static const gnTranslator *DNAProteinTranslator(); static const gnTranslator *RNAProteinTranslator(); enum gnTranslatorType{ ProteinDNATranslatorType, ProteinRNATranslatorType, DNAProteinTranslatorType, RNAProteinTranslatorType, }; gnTranslator(); gnTranslator( gnTranslatorType t_type ); gnTranslator( const gnTranslator& sf ); gnTranslator* Clone() const; // gnSeqC virtual gnSeqC Filter( const gnSeqC ch ) const; virtual void Filter( gnSeqC** seq, gnSeqI& len ) const; // std::string virtual void Filter( std::string &seq ) const; // Default gnSeqC /** * Sets the default character to insert when no valid translation exists. * @param ch1 The default character */ void SetDefaultChar( const gnSeqC ch1 ); /** * Gets the default character which is inserted into the destination * sequence when no valid translation exists. * @return The default character */ gnSeqC GetDefaultChar() const; /** * Set whether the default character is inserted upon translation failure. * @param use True if the default character should be used. */ void UseDefaultChar( const boolean use = true); /** * Set the expected number of characters in each unit of translation. For DNA to * Protein, for instance, this is 3 because each codon is 3 characters of input. * @param defaultInputWidth The expected input width */ void SetDefaultInputWidth( const uint32 defaultInputWidth); /** * Get the expected number of characters in each unit of translation. For DNA to * Protein, for instance, this is 3 because each codon is 3 characters of input. * @return The expected input width */ uint32 GetDefaultInputWidth() const; // fill map /** * Set a translation mapping. The first value is the input, the second value is the * output. During translation, any occurrences of the first std::string will be transformed * to the second std::string. A gnCompare object is used to facilitate ambiguity matching. * @param input The input std::string * @param output The std::string to output every time the input std::string is encountered */ void SetPair( const std::string& input, const std::string& output ); /** * Removes a translation mapping. RemovePair removes the translation mapping * corresponding to the given input std::string. * @param input The input std::string to delete */ void RemovePair( const std::string& input ); /** * Set the comparator to use. Ambiguous base matching is facilitated using a gnCompare * object. This must be set to allow sequences to be compared. * @param comp A pointer to the gnCompare object to use. */ void SetCompare( const gnCompare* comp ); private: void CreateProteinDNATranslator(); void CreateProteinRNATranslator(); void CreateDNAProteinTranslator(); void CreateRNAProteinTranslator(); //for each entry in the input table there is a corresponding //entry in the output table. std::vector m_inputTable, m_outputTable; const gnCompare* compare; boolean use_default; gnSeqC m_defaultChar; uint32 m_defaultInputWidth; };//class gnTranslator inline gnTranslator* gnTranslator::Clone() const { return new gnTranslator(*this); } inline void gnTranslator::SetDefaultChar( const gnSeqC ch1 ) { m_defaultChar = ch1; use_default = true; } inline gnSeqC gnTranslator::GetDefaultChar() const { return m_defaultChar; } inline void gnTranslator::UseDefaultChar(const boolean use) { use_default = use; } inline void gnTranslator::SetDefaultInputWidth( const uint32 defaultInputWidth){ m_defaultInputWidth = defaultInputWidth; } inline uint32 gnTranslator::GetDefaultInputWidth() const{ return m_defaultInputWidth; } inline void gnTranslator::SetCompare( const gnCompare* comp ){ compare = comp; } } // end namespace genome #endif // _gnTranslator_h_ libGenome-1.3.1/libGenome/gnStringQualifier.h0000644002622200470610000000560110647575617016077 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnStringQualifier.h // Purpose: abstract Qualifier class // Description: Provides an interface for Qualifiers in memory and on disk. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnStringQualifier_h_ #define _gnStringQualifier_h_ #include "libGenome/gnDefs.h" #include #include "libGenome/gnClone.h" #include "libGenome/gnBaseQualifier.h" namespace genome { /** * gnStringQualifier stores a sequence qualifier in memory. * Use gnStringQualifier for a general purpose qualifier class. */ class GNDLLEXPORT gnStringQualifier : public gnBaseQualifier { public: /** * Empty constructor. */ gnStringQualifier(); /** * Create a gnStringQualifier. * @param name The qualifier name. * @param value The qualifier. */ gnStringQualifier(const std::string& name, const std::string& value); /** * Copy constructor. * @param s The gnStringQualifier to copy. */ gnStringQualifier(const gnStringQualifier& s); /** * Destructor, frees memory. */ ~gnStringQualifier(){} gnStringQualifier* Clone() const; std::string GetName() const; std::string GetValue() const; /** * Set the name of qualifier stored in this class. * @param name The qualifier name as a std::string. */ void SetName(const std::string& name); /** * Set the qualifier stored in this class. * @param value The header as a std::string. */ void SetValue(const std::string& value); uint32 GetNameLength() const; uint32 GetValueLength() const; private: std::string m_name; std::string m_value; }; //class gnStringQualifier inline gnStringQualifier::gnStringQualifier(){ m_name = ""; m_value = ""; } inline gnStringQualifier::gnStringQualifier(const std::string& name, const std::string& value){ m_name = name; m_value = value; } inline gnStringQualifier::gnStringQualifier(const gnStringQualifier& s){ m_name = std::string(s.m_name); m_value = std::string(s.m_value); } inline gnStringQualifier* gnStringQualifier::Clone() const{ return new gnStringQualifier(*this); } inline std::string gnStringQualifier::GetName() const{ return m_name; } inline std::string gnStringQualifier::GetValue() const{ return m_value; } inline void gnStringQualifier::SetName(const std::string& name){ m_name = name; } inline void gnStringQualifier::SetValue(const std::string& value){ m_value = value; } inline uint32 gnStringQualifier::GetNameLength() const{ return m_name.length(); } inline uint32 gnStringQualifier::GetValueLength() const{ return m_value.length(); } } // end namespace genome #endif // _gnStringQualifier_h_ libGenome-1.3.1/libGenome/gnGBKSource.cpp0000644002622200470610000007577711026443220015103 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnGBKSource.h // Purpose: Implements gnBaseSource for GenBank sequences // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnFilter.h" #include "libGenome/gnFeature.h" #include "libGenome/gnGBKSource.h" #include "libGenome/gnSourceSpec.h" #include "libGenome/gnSourceHeader.h" #include "libGenome/gnSourceQualifier.h" #include "libGenome/gnLocation.h" #include "libGenome/gnStringTools.h" #include "libGenome/gnDebug.h" #include "libGenome/gnStringQualifier.h" #include #include using namespace std; namespace genome { gnGBKSource::gnGBKSource() { m_openString = ""; m_pFilter = gnFilter::proteinSeqFilter(); if(m_pFilter == NULL){ DebugMsg("Error using static sequence filters."); } } gnGBKSource::gnGBKSource( const gnGBKSource& s ) : gnFileSource(s) { vector< gnFileContig* >::const_iterator iter = s.m_contigList.begin(); for( ; iter != s.m_contigList.end(); ++iter ) { m_contigList.push_back( (*iter)->Clone() ); } } gnGBKSource::~gnGBKSource() { m_ifstream.close(); vector< gnFileContig* >::iterator iter = m_contigList.begin(); for( ; iter != m_contigList.end(); ++iter ) { gnFileContig* fg = *iter; *iter = 0; delete fg; } } boolean gnGBKSource::HasContig( const string& name ) const { for(uint32 i = 0 ; i <= m_contigList.size(); i++ ) { if( name == m_contigList[i]->GetName() ) return true; } return false; } uint32 gnGBKSource::GetContigID( const string& name ) const { for(uint32 i = 0 ; i <= m_contigList.size(); i++ ) { if( name == m_contigList[i]->GetName() ) return i; } return ALL_CONTIGS; } string gnGBKSource::GetContigName( const uint32 i ) const { if( i < m_contigList.size() ) { return m_contigList[i]->GetName(); } return ""; } gnSeqI gnGBKSource::GetContigSeqLength( const uint32 i ) const { if( i == ALL_CONTIGS) return m_spec->GetLength(); if( i < m_contigList.size() ) { return m_contigList[i]->GetSeqLength(); } return GNSEQI_ERROR; } boolean gnGBKSource::SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI ) { boolean result = false; #pragma omp critical { result = SeqReadImpl( start, buf, bufLen, contigI ); } return result; } boolean gnGBKSource::SeqReadImpl( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI ){ uint64 startPos = 0; uint64 readableBytes = 0; if( !SeqSeek( start, contigI, startPos, readableBytes ) ) { bufLen = 0; return false; } if( contigI == ALL_CONTIGS ) { uint32 curLen = 0; uint64 bytesRead = 0; while (curLen < bufLen) { //SeqSeek to start, Figure out how much can be read before SeqSeeking again. if(readableBytes <= 0) //Look out for zero length contigs! IMPLEMENT ME if( !SeqSeek( start + curLen, contigI, startPos, readableBytes ) ){ bufLen = curLen; return true; } //readLen is the amount to read on this pass uint64 readLen = (bufLen - curLen) < readableBytes ? (bufLen - curLen) : readableBytes; Array array_buf( readLen ); gnSeqC* tmpBuf = array_buf.data; // read chars and filter m_ifstream.read(tmpBuf, readLen); uint64 gc = m_ifstream.gcount(); bytesRead += gc; readableBytes -= gc; for(uint32 i=0; i < gc; i++){ if( m_pFilter->IsValid(tmpBuf[i]) ){ buf[curLen] = tmpBuf[i]; curLen++; } } if(m_ifstream.eof()){ //we hit the end of the file. bail out. m_ifstream.clear(); bufLen = curLen; return true; } } bufLen = curLen; } else if( contigI < m_contigList.size() ) { uint32 curLen = 0; //check to see if the buffer is bigger than the contig. if so truncate it. gnSeqI contigSize = m_contigList[contigI]->GetSeqLength(); bufLen = bufLen < contigSize ? bufLen : contigSize; while (curLen < bufLen) { uint64 readLen = bufLen - curLen; //the amount to read on this pass Array array_buf( readLen ); gnSeqC* tmpBuf = array_buf.data; // read chars and filter m_ifstream.read(tmpBuf, readLen); uint64 gc = m_ifstream.gcount(); // cout << "Read " << gc << " chars from " << m_openString << "\n"; // cout << "Checking character validity on: " << tmpBuf << "\n"; for(uint32 i=0; i < gc; i++){ if( m_pFilter->IsValid(tmpBuf[i]) ){ buf[curLen] = tmpBuf[i]; curLen++; } } if(m_ifstream.eof()){ //we hit the end of the file. bail out. m_ifstream.clear(); bufLen = curLen; return true; } } bufLen = curLen; } return true; } // private: // figures out which contig the sequence starts at then calls SeqStartPos to get the offset within that contig // returns startPos, the file offset where the sequence starts // returns true if successful, false otherwise boolean gnGBKSource::SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes ) { if( contigI == ALL_CONTIGS ) { // find first contig gnSeqI curIndex = 0; vector< gnFileContig* >::iterator iter = m_contigList.begin(); for( ; iter != m_contigList.end(); ++iter ) { uint64 len = (*iter)->GetSeqLength(); if( (curIndex + len) > start ) break; curIndex += len; } if( iter == m_contigList.end() ) return false; // seek to start gnSeqI startIndex = start - curIndex; //startIndex is starting pos. within the contig return SeqStartPos( startIndex, *(*iter), startPos, readableBytes ); } else if( contigI < m_contigList.size() ) { return SeqStartPos( start, *(m_contigList[contigI]), startPos, readableBytes ); } return false; } //Returns startPos, the file offset where the sequence starts. boolean gnGBKSource::SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes ) { readableBytes = 0; uint32 curLen = 0; //seek to the file offset where the contig starts startPos = contig.GetSectStartEnd(gnContigSequence).first; //set startPos to start where the contig starts m_ifstream.seekg( startPos, ios::beg ); if( m_ifstream.eof() ){ ErrorMsg("ERROR in gnGBKSource::Incorrect contig start position, End of file reached!\n"); return false; } while( true ) { // READ the rest of the contig skipping over invalid characters until we get to the starting base pair. // startPos will contain the file offset with the starting base pair uint32 tmpbufsize = contig.GetSectStartEnd(gnContigSequence).second - startPos; if(tmpbufsize == 0){ ErrorMsg("ERROR in gnGBKSource: stored contig size is incorrect."); return false; } uint64 startOffset = start; if(contig.HasRepeatSeqGap()){ //check for sequence integrity startOffset += (9 + m_newlineSize) * (start / 60 + 1) + start / 10 + 1; if( m_newlineSize == 2 ) // test compensation for strange bug startOffset--; startPos+=startOffset; m_ifstream.seekg(startPos , ios::beg); readableBytes = contig.GetSectStartEnd(gnContigSequence).second - startPos; return true; } //sequence is corrupt. read in base by base tmpbufsize = tmpbufsize < BUFFER_SIZE ? tmpbufsize : BUFFER_SIZE; //read in the smaller of the two. Array array_buf( tmpbufsize ); char* tmpbuf = array_buf.data; m_ifstream.read( tmpbuf, tmpbufsize ); if( m_ifstream.eof() ){ ErrorMsg("ERROR in gnGBKSource::Read End of file reached!\n"); return false; } for( uint32 i=0; i < tmpbufsize; ++i ){ if( m_pFilter->IsValid(tmpbuf[i]) ){ if( curLen >= start ){ //stop when we reach the starting offset within this contig startPos += i; m_ifstream.seekg( startPos, ios::beg ); //seek to startPos readableBytes = contig.GetSectStartEnd(gnContigSequence).second - startPos; return true; } ++curLen; //each time we read a valid b.p., increment the sequence length } } startPos += tmpbufsize; } return true; } void gnGBKSource::FormatString(string& data, uint32 offset, uint32 width){ //first remove newlines and corresponding whitespace string::size_type newline_loc = data.find_first_of('\n', 0); while(newline_loc != string::npos){ if(data[newline_loc-1] == '\r') newline_loc--; string::size_type text_loc = newline_loc; while((data[text_loc] == ' ') ||(data[text_loc] == ' ')||(data[text_loc] == '\n')||(data[text_loc] == '\r')){ text_loc++; if(text_loc+1 == data.length()) break; } data = (data.substr(0, newline_loc) + " " + data.substr(text_loc)); newline_loc = data.find_first_of('\n', 0); } //now reformat with newlines and whitespace, observing word boundaries... string output_string = ""; for(uint32 charI = 0; charI < data.length();){ //get the substring to append and increment charI string::size_type base_loc = charI; string append_string; while(base_loc - charI <= width){ string::size_type space_loc = data.find_first_of(' ', base_loc+1); if(space_loc - charI < width) base_loc = space_loc; else if(base_loc == charI){ //word is too big for one line. split it. append_string = data.substr(charI, width); charI+=width; }else{ append_string = data.substr(charI, base_loc - charI); charI = base_loc; } } output_string += string(offset, ' ') + append_string; if(charI + width < data.length()) output_string += "\r\n"; } data = output_string; } template< class SubSpec > void WriteHeader(gnMultiSpec< SubSpec >* spec, const string& hdr, ofstream& m_ofstream) { gnBaseHeader* gpbh = NULL; uint32 header_index = 0; try{ do{ gpbh = spec->GetHeader(hdr, header_index); m_ofstream << gpbh->GetHeader(); header_index++; }while(gpbh != NULL); }catch(gnException& gne){} } boolean gnGBKSource::Write(gnSequence& seq, const string& filename){ ofstream m_ofstream(filename.c_str(), ios::out | ios::binary); if(!m_ofstream.is_open()) return false; string newline = "\r\n"; gnGenomeSpec* spec = seq.GetSpec(); // output general file header first if one exists. if(spec->GetHeaderListLength() == 1){ gnBaseHeader *gpbh = spec->GetHeader(0); string name = gpbh->GetHeaderName(); //IMPLEMENT ME! Is platform specific newline substitution necessary? if(string::npos != name.find(".SEQ")){ string header = gpbh->GetHeader(); m_ofstream << header; } } // TODO: Figure out where the buffer overflow is and reduce // this back to BUFFER_SIZE -- overflow appears not to corrupt // sequence data Array array_buf( 2 * BUFFER_SIZE ); gnSeqC *bases = array_buf.data; for(uint32 specI = 0; specI < spec->GetSpecListLength(); specI++){ gnFragmentSpec* subSpec = spec->GetSpec(specI); //write out contig headers. start with LOCUS... m_ofstream << "LOCUS "; //write Locus Name string contigName = subSpec->GetName(); if(contigName.length() > SEQ_LOCUS_NAME_LENGTH) contigName = contigName.substr(0, SEQ_LOCUS_NAME_LENGTH); uint32 filler_size = SEQ_LOCUS_NAME_LENGTH - contigName.length(); m_ofstream << contigName << string(filler_size, ' '); //write Locus Length string length_string = uintToString(subSpec->GetLength()); filler_size = SEQ_LOCUS_SIZE_LENGTH - length_string.size(); m_ofstream << string(filler_size, ' ') << length_string << " bp "; //write dnatype string dnatype = string(SEQ_LOCUS_DNATYPE_LENGTH, ' '); uint32 head_look_i = 0; gnBaseHeader* gpbh = NULL; try{ gpbh = subSpec->GetHeader("LOCUS", head_look_i); }catch(gnException& gne){} if( gpbh != NULL ) dnatype = gpbh->GetHeader().substr(SEQ_LOCUS_DNATYPE_OFFSET, SEQ_LOCUS_DNATYPE_LENGTH); m_ofstream << dnatype << string(2, ' '); //write circularity string circular = subSpec->IsCircular() ? string("circular ") : string(10, ' '); m_ofstream << circular; //write division code string division = string(SEQ_LOCUS_DIVCODE_LENGTH, ' '); if(gpbh != NULL) division = gpbh->GetHeader().substr(SEQ_LOCUS_DIVCODE_OFFSET, SEQ_LOCUS_DIVCODE_LENGTH); m_ofstream << division; //write date -- IMPLEMENT ME! format the real date to spec! dd-mmm-yyyy string date = string(SEQ_LOCUS_DATE_LENGTH, ' '); if(gpbh != NULL) date = gpbh->GetHeader().substr(SEQ_LOCUS_DATE_OFFSET, SEQ_LOCUS_DATE_LENGTH); m_ofstream << string(7, ' ') << date << "\r\n"; //write out the rest of the headers if they were supplied! WriteHeader(subSpec, "DEFINITION", m_ofstream); WriteHeader(subSpec, "ACCESSION", m_ofstream); WriteHeader(subSpec, "VERSION", m_ofstream); WriteHeader(subSpec, "KEYWORDS", m_ofstream); WriteHeader(subSpec, "SEGMENT", m_ofstream); WriteHeader(subSpec, "SOURCE", m_ofstream); WriteHeader(subSpec, "REFERENCE", m_ofstream); WriteHeader(subSpec, "COMMENT", m_ofstream); //write out feature table! m_ofstream << "FEATURES Location/Qualifiers" << "\r\n"; for(uint32 featureI = 0; featureI < subSpec->GetFeatureListLength(); featureI++){ //write a feature tag gnBaseFeature *gpmf = subSpec->GetFeature(featureI); string featureName = gpmf->GetName(); m_ofstream << string(SEQ_SUBTAG_COLUMN, ' ') << featureName; m_ofstream << string(SEQ_FEATURE_LOC_OFFSET - featureName.length() - SEQ_SUBTAG_COLUMN, ' '); //ready to output location b.s. uint32 location_count = gpmf->GetLocationListLength(); uint32 line_pos = SEQ_FEATURE_LOC_OFFSET; uint32 parenthesis_count = 0; if(location_count > 1){ m_ofstream << "join("; line_pos += 5; parenthesis_count++; } gnLocation::gnLocationType loc_type = gpmf->GetLocationType(); switch(loc_type){ case gnLocation::LT_Standard: break; case gnLocation::LT_Complement: m_ofstream << "complement("; line_pos += 11; parenthesis_count++; break; case gnLocation::LT_Order: m_ofstream << "order("; line_pos += 6; parenthesis_count++; break; case gnLocation::LT_Group: m_ofstream << "group("; parenthesis_count++; line_pos += 6; break; case gnLocation::LT_OneOf: m_ofstream << "one-of("; parenthesis_count++; line_pos += 7; break; default: break; } //create the location string, then see if it will fit on the line string location; for(uint32 locationI = 0; locationI < location_count; locationI++){ gnLocation gpl = gpmf->GetLocation(locationI); if(gpl.IsStartBoundLonger()) location += ">"; if(gpl.IsStartBoundShorter()) location += "<"; location += uintToString(gpl.GetStart()); gnSeqI end_loc = gpl.GetEnd(); if(end_loc != 0){ switch(gpl.GetType()){ case gnLocation::LT_BetweenBases: location += "^"; break; case gnLocation::LT_OneOf: location += "."; break; default: location += ".."; break; } if(gpl.IsEndBoundShorter()) location += "<"; if(gpl.IsEndBoundLonger()) location += ">"; location+= uintToString(end_loc); } if(locationI +1 < location_count) location += ","; else{ //append necessary parenthesis for(;parenthesis_count > 0; parenthesis_count--) location += ")"; } //put it on this line if it fits. otherwise make a new line. if(line_pos + location.length() < SEQ_COLUMN_WIDTH){ m_ofstream << location; line_pos += location.length(); }else{ m_ofstream << "\r\n" << string(SEQ_FEATURE_LOC_OFFSET, ' ') << location; line_pos = SEQ_FEATURE_LOC_OFFSET + location.length(); } location = ""; } m_ofstream << "\r\n"; //now output qualifiers! yaay! //god damn this is a big ugly piece of code. uint32 qualifier_count = gpmf->GetQualifierListLength(); for(uint32 qualifierI = 0; qualifierI < qualifier_count; qualifierI++){ m_ofstream << string(SEQ_FEATURE_LOC_OFFSET, ' '); gnBaseQualifier* qualifier = gpmf->GetQualifier(qualifierI); m_ofstream << "/" << qualifier->GetName() << "="; //IMPLEMENT ME! do a better word wrap on this bitch. string qually = string(qualifier->GetValue()); // FormatString(qually, SEQ_FEATURE_LOC_OFFSET, 80 - SEQ_FEATURE_LOC_OFFSET); // qually = qually.substr(SEQ_FEATURE_LOC_OFFSET); m_ofstream << qually << "\r\n"; } if(gpmf != NULL) delete gpmf; } //get information about the sequence we're writing out. gnSeqI readOffset = seq.contigStart(specI); gnSeqI readLength = seq.contigLength(specI); //finally - output base count and origin m_ofstream << "BASE COUNT "; gnSeqI a_count=0, c_count=0, g_count=0, t_count=0, other_count=0; gnSeqI countLen = readLength + readOffset; for(gnSeqI countI = readOffset; countI < countLen;){ gnSeqI writeLen = countLen - countI < BUFFER_SIZE ? countLen - countI : BUFFER_SIZE; if(!seq.ToArray(bases, writeLen, countI)) return false; gnSeqI a, c, g, t, other; BaseCount(string(bases, writeLen), a, c, g, t, other); a_count += a; c_count += c; g_count += g; t_count += t; other_count += other; countI += writeLen; } m_ofstream << uintToString(a_count) << " a "; m_ofstream << uintToString(c_count) << " c "; m_ofstream << uintToString(g_count) << " g "; m_ofstream << uintToString(t_count) << " t "; m_ofstream << uintToString(other_count) << " others" << "\r\n"; string origin = "ORIGIN\r\n"; head_look_i = 0; try{ gpbh = subSpec->GetHeader("ORIGIN", head_look_i); origin = gpbh->GetHeader(); m_ofstream << origin; }catch(gnException& gne){ m_ofstream << "ORIGIN" << endl; } //write out the sequence gnSeqI contig_bases = 0; while(readLength > 0){ //buffer the read/writes gnSeqI writeLen = readLength < BUFFER_SIZE + 20 ? readLength : BUFFER_SIZE + 20; boolean success = seq.ToArray(bases, writeLen, readOffset); if(!success) return false; //print each 60 on their own lines... for(gnSeqI curbaseI = 0; curbaseI < writeLen; curbaseI += 60){ string baseIndexStr = uintToString(contig_bases + curbaseI +1); m_ofstream << string(SEQ_BASES_INDEX_END - baseIndexStr.length(), ' '); m_ofstream << baseIndexStr; for(gnSeqI base_offset = 0; base_offset <= 50; base_offset+=10){ if(writeLen <= curbaseI + base_offset) break; int64 print_length = writeLen - (curbaseI + base_offset); print_length = print_length > 10 ? 10 : print_length; m_ofstream << ' ' << string(bases + curbaseI + base_offset, print_length); } m_ofstream << "\r\n"; } readLength -= writeLen; readOffset += writeLen; contig_bases += writeLen; } m_ofstream << "//\r\n"; } m_ofstream.close(); return true; } gnFileContig* gnGBKSource::GetFileContig( const uint32 contigI ) const{ if(m_contigList.size() > contigI) return m_contigList[contigI]; return NULL; } //File parsing access routine boolean gnGBKSource::ParseStream( istream& fin ) { // INIT temp varables uint32 readState = 0; uint32 lineStart = 0; // INIT buffer uint32 sectionStart = 0; uint64 streamPos = 0; uint64 bufReadLen = 0; uint64 remainingBuffer = 0; Array array_buf( BUFFER_SIZE ); char* buf = array_buf.data; gnFragmentSpec* curFrag = 0; gnSourceSpec* curSpec = 0; gnSourceHeader *curHeader; gnFeature* curFeature; gnFileContig* curContig = 0; gnLocation::gnLocationType curBaseLocationType; gnSeqI curLocationStart; int32 curStartLength = 0; int32 curEndLength = 0; string curLocContig = ""; string curQualifierName; uint64 curQualifierStart; string curContigName = ""; gnSeqI seqLength = 0; gnSeqI seqChunk, seqChunkCount, gapChunk; boolean corruptWarning = false; //decide what type of newlines we have DetermineNewlineType(); m_spec = new gnGenomeSpec(); while( !fin.eof() ) { size_t newstart = sectionStart < lineStart ? sectionStart : lineStart; if(sectionStart > 0){ if(readState == 14) sectionStart = lineStart; else if( sectionStart >= lineStart ) sectionStart -= lineStart; remainingBuffer = bufReadLen - newstart; memmove(buf, buf+newstart, remainingBuffer); } // read chars fin.read( buf + remainingBuffer, BUFFER_SIZE - remainingBuffer); streamPos -= remainingBuffer; lineStart -= newstart; bufReadLen = fin.gcount(); bufReadLen += remainingBuffer; for( uint32 i=remainingBuffer ; i < bufReadLen ; i++ ) { char ch = buf[i]; switch( readState ) { case 0: //Assume we are in header at the start of a new line. //Look for keywords starting in column 1 if((ch == '\n')&&(buf[lineStart] != ' ')&&(buf[lineStart] != '\t') && buf[lineStart] != '\r' && buf[lineStart] != '\n'){ //not equal to whitespace if(curSpec == NULL){ curSpec = new gnSourceSpec(this, m_spec->GetSpecListLength()); curFrag = new gnFragmentSpec(); curFrag->AddSpec(curSpec); curSpec->SetSourceName(m_openString); m_spec->AddSpec(curFrag); } if(lineStart != sectionStart){ //Add the previous header to our list uint32 j = SEQ_HEADER_NAME_LENGTH-1; for(; j > 0; j--) if((buf[sectionStart+j] != ' ')&&(buf[sectionStart+j] != ' ')) break; string header_name = string(buf+sectionStart, j+1); curHeader = new gnSourceHeader(this, header_name, sectionStart + streamPos, lineStart - sectionStart); //if this is header info _before_ a locus statement then its a general file header. if(strncmp(&buf[lineStart], "LOCUS", 5) == 0) m_spec->AddHeader(curHeader); else //otherwise its a fragment header. curFrag->AddHeader(curHeader); sectionStart = lineStart; } if(strncmp(&buf[lineStart], "FEATURES", 8) == 0){ sectionStart = i + 1; readState = 1; //read in features }else if(strncmp(&buf[lineStart], "ORIGIN", 6) == 0){ curHeader = new gnSourceHeader(this, string("ORIGIN"), sectionStart + streamPos, i - sectionStart + 1); curFrag->AddHeader(curHeader); curContig = new gnFileContig(); curContig->SetName(curContigName); curContigName = ""; readState = 13; //read in base pairs }else if(strncmp(&buf[lineStart], "LOCUS", 5) == 0){ if(strncmp(&buf[lineStart+SEQ_LOCUS_CIRCULAR_COLUMN-1], "circular", 8) == 0) curFrag->SetCircular(true); string locus_line = string(buf+lineStart, 80); if( locus_line.find(" DNA ") == string::npos && locus_line.find(" dna ") == string::npos ) m_pFilter = gnFilter::proteinSeqFilter(); else m_pFilter = gnFilter::fullDNASeqFilter(); uint32 j = SEQ_LOCUS_NAME_LENGTH+1; for(; j > 0; j--) if((buf[lineStart+SEQ_LOCUS_NAME_COLUMN+j-1] != ' ')&&(buf[sectionStart+SEQ_LOCUS_NAME_COLUMN+j-1] != ' ')) break; curContigName = string(buf+lineStart+SEQ_LOCUS_NAME_COLUMN-1, j+1); curFrag->SetName(curContigName); } } if(ch == '\n'){ lineStart = i + 1; } break; case 1: //look for feature tag in column six. ignore whitespace before feature. if((ch == ' ')||(ch == ' ')){ break; }else if(ch == '\n'){ lineStart = i + 1; sectionStart = i + 1; break; }else if(sectionStart == i){ //there was no whitespace, we hit a TAG instead i--; readState = 0; //Deal with a Header TAG sectionStart = i + 1; break; }else if((i - lineStart == SEQ_SUBTAG_COLUMN)||((buf[lineStart]==' ')&&(i==lineStart+1))){ sectionStart = i; readState = 2; } // case 2: //Get the feature name. stop on whitespace if((ch == ' ')||(ch == ' ')){ string featureName(buf+sectionStart, i - sectionStart); curFeature = new gnFeature(featureName); curFrag->AddFeature(curFeature); sectionStart = i + 1; readState = 3; } break; case 3: //Ignore whitespace before feature location if((ch == ' ')||(ch == ' ')){ break; }else if((ch == '\r')||(ch == '\n')){ lineStart = i+1; break; } sectionStart = i; readState = 4; // KNOWN BUG HERE! // if JOIN is outside a group of complemented coordinates the feature type // is incorrectly set to LT_COMPLEMENT. Instead each location's type should be set to LT_COMPLEMENT case 4: //Read a location start. stop on (<.:^ and whitespace if((ch == ' ')||(ch == ' ')||(ch == '(')||(ch == '.')||(ch=='^')||(ch==':')){ string starter(buf+sectionStart, i - sectionStart); if(ch == '('){ if(starter == "complement") curFeature->SetLocationType(gnLocation::LT_Complement); else if(starter == "order") curFeature->SetLocationType(gnLocation::LT_Order); else if(starter == "group") curFeature->SetLocationType(gnLocation::LT_Group); else if(starter == "one-of") curFeature->SetLocationType(gnLocation::LT_OneOf); sectionStart = i + 1; //ignore join since it is default. break; }else if(ch == ':'){ curLocContig = starter; sectionStart = i + 1; break; } curLocationStart = atoi(starter.c_str()); readState = 6; //read in end base by default. if(ch == '.'){ //go to special state to look for another one. readState = 5; sectionStart = i + 1; break; }else if(ch == '^'){ curBaseLocationType = gnLocation::LT_BetweenBases; }else if((ch == ' ')||(ch == ' ')){ //no end location go to qualifier gnLocation curLocation(curLocationStart, curLocationStart); curFeature->AddLocation(curLocation, curFeature->GetLocationListLength()); readState = 7; } sectionStart = i + 1; }else if(ch == '<'){ curStartLength = -1; sectionStart = i + 1; }else if(ch == '>'){ curStartLength = 1; sectionStart = i + 1; } break; case 5: //look for another period or location start. if(ch == '.'){ curBaseLocationType = gnLocation::LT_Standard; readState = 6; sectionStart = i + 1; break; } curBaseLocationType = gnLocation::LT_OneOf; case 6: //see if there's a second location value. stop on >, and whitespace if(ch == '>'){ curEndLength = 1; sectionStart = i + 1; }else if(ch == '<'){ curEndLength = -1; sectionStart = i + 1; }else if((ch == ' ')||(ch == ' ')||(ch == ',')||(ch == '\r')||(ch == '\n')){ //read end location string ender(buf+sectionStart, i - sectionStart); gnSeqI curLocationEnd = atoi(ender.c_str()); gnLocation curLocation(curLocationStart, curStartLength, curLocationEnd, curEndLength, curBaseLocationType); curEndLength = 0; curStartLength = 0; curFeature->AddLocation(curLocation, curFeature->GetLocationListLength()); readState = ch == ',' ? 3 : 7; //read another loc if we need to. sectionStart = i+1; if( ch == '\n' ) lineStart = i+1; } break; case 7: //skip to start of qualifier if((ch != ' ')&&(ch != ' ')&&(lineStart == i)){ sectionStart = i; // Hit a tag. go deal with it. readState = 0; i--; }else if((ch != ' ')&&(ch != ' ')&&((lineStart == i - SEQ_SUBTAG_COLUMN)||((buf[lineStart]==' ')&&(i==lineStart+1)))){ sectionStart = i; // Hit a feature. go deal with it. readState = 2; i--; }else if(ch == ','){ //oops! another location to read! sectionStart = i+1; readState = 3; }else if(ch == '/'){ //finally, a qualifier. sectionStart = i+1; readState = 8; }else if(ch == '\n') lineStart = i + 1; break; case 8: //get a qualifier, stop on = if(ch == '='){ curQualifierName = string(buf+sectionStart, i - sectionStart); readState = 9; sectionStart = i+1; }else if( ch == '\r' || ch == '\n' ){ // this is a value-less qualifier curQualifierName = string(buf+sectionStart, i - sectionStart); curFeature->AddQualifier( new gnStringQualifier( curQualifierName, "" )); readState = 7; sectionStart = i+1; if( ch == '\n' ) lineStart = i + 1; } break; case 9: //are we getting a string? look for " or [ if(ch == '"'){ readState = 10; sectionStart = i; curQualifierStart = i + streamPos; }else if(ch == '['){ readState = 12; sectionStart = i; }else if((ch == '\r')||(ch == '\n')){ curFeature->AddQualifier(new gnSourceQualifier(this, curQualifierName, sectionStart + streamPos, i - sectionStart)); sectionStart = i+1; readState = 7; //look for another qualifier if( ch == '\n' ) lineStart = i + 1; } break; case 10: //read until the end of the quotation. look out for escaped quotes if(ch == '"') readState = 11; if(ch == '\n'){ lineStart = i + 1; } break; case 11: if(ch != '"'){ gnSourceQualifier* gnsq = new gnSourceQualifier(this, curQualifierName, curQualifierStart, i - sectionStart); curFeature->AddQualifier(gnsq); sectionStart = i+1; readState = 7; //look for another qualifier. if(ch == '\n') lineStart = i + 1; }else readState = 10; //quote was escaped. look for another. break; case 12: if(ch == ']'){ curFeature->AddQualifier(new gnSourceQualifier(this, curQualifierName, sectionStart + streamPos, i - sectionStart)); sectionStart = i+1; readState = 7; //look for another qualifier. } break; case 13: //start the sequence read. curContig->SetSectStart(gnContigSequence, i - 1 + streamPos); curContig->SetRepeatSeqGap(true); seqChunk = 0; seqChunkCount = 0; gapChunk = m_newlineSize + 1; readState = 14; break; case 14: while(i < bufReadLen){ ch = buf[i]; if((ch == '/')&&(i==lineStart)){ readState = 15; //end of this sequence break; }else if(m_pFilter->IsValid(ch)){ if(gapChunk > 0){ if((gapChunk > 1 && seqChunkCount > 0) || (gapChunk != 10 + m_newlineSize && seqChunkCount == 0)){ if( !corruptWarning ){ ErrorMsg("File is corrupt. Proceed with caution."); corruptWarning = true; } curContig->SetRepeatSeqGap(false); } gapChunk = 0; } seqChunk++; seqLength++; }else{ gapChunk++; if(seqChunk == 10){ seqChunk = 0; seqChunkCount++; if(seqChunkCount == 6){ //got a complete line. start over seqChunkCount = 0; } } if(ch == '\n') lineStart = i + 1; } i++; } break; case 15: if((ch == '\n')&&(buf[lineStart+1] == '/')){ curContig->SetSectEnd(gnContigSequence, lineStart - m_newlineSize + streamPos); curContig->SetSeqLength(seqLength); m_contigList.push_back(curContig); curContig = 0; curSpec->SetLength(seqLength); curSpec = 0; seqLength = 0; lineStart = i + 1; sectionStart = i + 1; readState = 0; } break; } } streamPos += bufReadLen; } if(curContig != 0){ curContig->SetSectEnd(gnContigSequence, streamPos - 1); curContig->SetSeqLength(seqLength); m_contigList.push_back(curContig); curSpec->SetLength(seqLength); } if(curSpec != 0) if((curFrag->GetFeatureListLength() == 0) && (curFrag->GetHeaderListLength() == 0) &&(curSpec->GetLength() == 0)){ m_spec->RemoveSpec(m_spec->GetSpecListLength() - 1); delete curFrag; } m_ifstream.clear(); return true; } } // end namespace genome libGenome-1.3.1/libGenome/gnFragmentSpec.h0000644002622200470610000001113310647575617015342 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnFragmentSpec.h // Purpose: abstract Spec class // Description: Genome level spec class // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnFragmentSpec_h_ #define _gnFragmentSpec_h_ #include "libGenome/gnDefs.h" #include #include #include "libGenome/gnClone.h" #include "libGenome/gnBaseFeature.h" #include "libGenome/gnBaseHeader.h" #include "libGenome/gnContigSpec.h" #include "libGenome/gnMultiSpec.h" #include "libGenome/gnException.h" namespace genome { /** * gnFragmentSpec contains a list of specs which make up a sequence * fragment. It also contains a list of features which relate to * the sequence fragment. Finally it contains a list of sequence * related header data. This class is usually created and filled by * a file reader class like gnGBKSource. */ class GNDLLEXPORT gnFragmentSpec : public gnMultiSpec< gnContigSpec > { public: gnFragmentSpec(); /** * Destructor, frees memory. */ virtual ~gnFragmentSpec(); /** * Copy constructor. * @param s the gnGenomeSpec to copy. */ gnFragmentSpec( const gnFragmentSpec& s); virtual gnFragmentSpec* Clone() const; virtual void Clear(); // Base Spec stuff virtual void SetReverseComplement( const boolean value ); //Multispec stuff /* virtual uint32 GetSpecListLength() const; virtual gnContigSpec* GetSpec( const uint32 i ) const; virtual gnContigSpec* GetSpecByBase( const gnSeqI baseI ) const; virtual void AddSpec( gnBaseSpec* spec, const uint32 i = UINT32_MAX ); virtual void RemoveSpec( uint32 i ); */ virtual void CropStart( gnSeqI cropLen ); virtual void CropEnd( gnSeqI cropLen ); virtual uint32 AddFeature( gnBaseFeature* feat ); virtual uint32 GetFeatureListLength() const; virtual gnBaseFeature* GetFeature( const uint32 i ) const; virtual void GetContainedFeatures(const gnLocation& lt, std::vector& feature_vector, std::vector& index_vector) const; virtual void GetIntersectingFeatures(const gnLocation& lt, std::vector& feature_vector, std::vector& index_vector) const; virtual void GetBrokenFeatures(const gnLocation& lt, std::vector& feature_vector) const; virtual void RemoveFeature( const uint32 i ); /** * Copies a specified range of bases and returns a pointer to * the resulting gnFragmentSpec. You must delete the copy when you * are finished with it. * @param startI The first base pair to copy * @param len The length of the piece to copy * @return A copy of the gnFragmentSpec containing only the specified bases */ virtual gnFragmentSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const; protected: // std::vector m_SpecList; //Feature stuff... std::vector m_featureList; }; // class gnFragmentSpec inline gnFragmentSpec* gnFragmentSpec::Clone() const{ return new gnFragmentSpec(*this); } /* inline uint32 gnFragmentSpec::GetSpecListLength() const{ return m_SpecList.size(); } inline gnContigSpec *gnFragmentSpec::GetSpec( const uint32 i ) const{ if(i < m_SpecList.size()) return m_SpecList[i]; Throw_gnEx(ContigIndexOutOfBounds()); } inline gnContigSpec* gnFragmentSpec::GetSpecByBase( const gnSeqI baseI ) const{ return m_SpecList[GetSpecIndexByBase(baseI)]; } inline void gnFragmentSpec::AddSpec( gnBaseSpec* spec, const uint32 i ){ uint32 index = i == UINT32_MAX ? m_SpecList.size() : i; if(index <= m_SpecList.size()){ m_SpecList.insert(m_SpecList.begin() + index, (gnContigSpec*)spec); } } inline void gnFragmentSpec::RemoveSpec( uint32 i ){ if(i < GetSpecListLength()){ m_SpecList.erase(m_SpecList.begin() + i); }else Throw_gnEx(ContigIndexOutOfBounds()); } */ inline uint32 gnFragmentSpec::AddFeature( gnBaseFeature* feat ) { m_featureList.push_back(feat); feat->SetSpec(this); return m_featureList.size()-1; } inline uint32 gnFragmentSpec::GetFeatureListLength() const { return m_featureList.size(); } inline gnBaseFeature* gnFragmentSpec::GetFeature(const uint32 i) const { return m_featureList[i]->Clone(); } inline void gnFragmentSpec::RemoveFeature( const uint32 i) { if(i >= m_featureList.size()) Throw_gnEx(FeatureIndexOutOfBounds()); delete m_featureList[i]; m_featureList.erase(m_featureList.begin() + i); } } // end namespace genome #endif // _gnFragmentSpec_h_ libGenome-1.3.1/libGenome/gnStringTools.h0000644002622200470610000000415010647575617015254 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnStringTools.h // Purpose: Random std::string manipulation tools // Description: Random std::string manipulation tools // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnStringTools_h_ #define _gnStringTools_h_ #include #include #include #include #include #include "libGenome/gnDefs.h" namespace genome { unsigned int removeSpace(std::string &str); void removeEndSpace(std::string &str); bool isNewLine(char ch); bool isWhiteSpace(char ch); bool isSpace(char ch); std::string uintToString(unsigned int value); std::string ulongToString(unsigned long value); std::string charArrayToString( char *charArray, unsigned int length); bool isBase(char base); void BaseCount(const std::string& bases, gnSeqI& a_count, gnSeqI& c_count, gnSeqI& g_count, gnSeqI& t_count, gnSeqI& other_count); unsigned int parseValue(std::string &valueString); int parseUintValue(std::string &valueString); int parseIntValue(std::string &valueString); std::vector< std::string > tokenizeString( const std::string &str, char delimiter = '\t' ); std::vector< std::string > tokenizeString( const char* str, unsigned int len, char delimiter = '\t' ); // **** MAKE SURE YOU STANDARDIZE ALL PATHS **** void standardizePathString( std::string &oFileName ); // **** ONLY '/' IS USED for file seperation on all below functions **** // make more robust to handle dir and files std::string getPathString( std::string oFileName ); // look for '/' at end std::string getFileString( std::string oFileName ); // look for '/' before '.' std::string getExtString( std::string oFileName ); // look for '/' before '.' std::string getFileNoExtString( std::string oFileName ); } // end namespace genome #endif // _gnStringTools_h_ libGenome-1.3.1/libGenome/gnMultiSpec.h0000644002622200470610000003173310647575617014701 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnMultiSpec.h // Purpose: multiple spec template class // Description: Template for specs which can contain multiple data sources // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnMultiSpec_h_ #define _gnMultiSpec_h_ #include "libGenome/gnDefs.h" #include "libGenome/gnException.h" #include #include #include "libGenome/gnClone.h" #include "libGenome/gnBaseFeature.h" #include "libGenome/gnBaseHeader.h" #include "libGenome/gnBaseSpec.h" namespace genome { /** * This class defines an interface for specs which have multiple subspecs * containing sequence data. */ template< class SubSpec > class GNDLLEXPORT gnMultiSpec : public gnBaseSpec { public: gnMultiSpec(){} /** * Destructor, frees memory. */ virtual ~gnMultiSpec(){} virtual gnMultiSpec* Clone() const = 0; // Base Spec stuff virtual gnSeqI GetLength() const; virtual void CropStart( gnSeqI cropLen ); virtual void CropEnd( gnSeqI cropLen ); virtual std::string GetSourceName() const; virtual void SetSourceName(const std::string& sourceName); virtual void Clear(); virtual boolean SeqRead(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen, const uint32 contigI ) const; //Multispec stuff /** * Returns the number of subspecs this spec contains. * @return The number of subspecs this spec contains. */ virtual uint32 GetSpecListLength() const; /** * Get the spec at index i in the list of subspecs. * @param i The index of the spec * @return The spec. */ virtual SubSpec* GetSpec( const uint32 i ) const; /** * Get the spec from the list of subspecs which contains the specified base pair. * @param baseI The base pair index. * @return The spec. */ virtual SubSpec* GetSpecByBase( const gnSeqI baseI ) const; /** * Get the index of the subspec which contains the specified base pair. * @param baseI The base pair index. * @return The subspec index. */ virtual uint32 GetSpecIndexByBase( const gnSeqI baseI ) const; /** * Get the index of the spec which has the given name. * @param name The name of the spec to find. * @return The spec index. */ virtual uint32 GetSpecIndexByName( const std::string& name ) const; /** * Get the starting base pair, in this spec's sequence, of the given subspec. * @param specI The subspec index. * @return The subspec's starting base pair. */ virtual gnSeqI GetSpecStartBase( const uint32 specI ) const; /** * Get the ending base pair, in this spec's sequence, of the given subspec. * @param specI The subspec index. * @return The subspec's ending base pair. */ virtual gnSeqI GetSpecEndBase( const uint32 specI ) const; /** * Add a subspec to this spec. * Throws an exception if the insertion index i is out of range * @param spec The subspec to add. * @param i The subspec to insert before * @return True if successful */ virtual void AddSpec( SubSpec* spec, const uint32 i = UINT32_MAX ); /** * Remove a subspec from this spec. * @param i The index of the subspec to remove. */ virtual void RemoveSpec( uint32 i ); /** * Returns the number of headers this spec contains. * @return The number of headers this spec contains. */ virtual uint32 GetHeaderListLength() const; /** * Add a header to this spec, adds to the end of the header list by default. * @param head The header to add. * @param i The header to insert before. If i is larger than the size of the header list * the header will be added to the end of the list. */ virtual void AddHeader( gnBaseHeader *head, const uint32 i = UINT32_MAX); /** * Get the headers at index i in the list of headers. * Throws a HeaderIndexOutOfBounds exception if a nonexistant header is referenced * @param i The index of the header * @return The header. */ virtual gnBaseHeader* GetHeader( const uint32 i ) const; /** * Find the first header with the specified name, starting at index i. * @param name The name of the header to find. * @param i The index to start looking at. * @return The header or NULL if none was found. */ virtual gnBaseHeader* GetHeader( const std::string& name, uint32& i) const; /** * Remove a header from this spec. * Throws a HeaderIndexOutOfBounds exception if a nonexistant header is referenced * @param i The index of the header to remove. */ virtual void RemoveHeader( uint32 i ); /** * Add a feature to this spec. * @param feat The feature to add. * @return True if successful */ uint32 AddFeature( gnBaseFeature* feat ); /** * Returns the number of features this spec contains. * @return The number of features this spec contains. */ virtual uint32 GetFeatureListLength() const = 0; /** * Get the feature at index i in the list of features. * @param i The index of the feature * @return The feature. */ virtual gnBaseFeature* GetFeature( const uint32 i ) const = 0; /** * Creates a list of all features which are contained by coordinates specified. * @param lt The coordinates containing the features to return. * @param feature_vector The std::vector to store features in. * @param index_vector A std::vector of indices which correspond to the features. */ virtual void GetContainedFeatures(const gnLocation& lt, std::vector& feature_vector, std::vector& index_vector) const = 0; /** * Creates a list of all features which intersect the coordinates specified. * @param lt The coordinates intersecting the features to return. * @param feature_vector The std::vector to store features in. * @param index_vector A std::vector of indices which correspond to the features. */ virtual void GetIntersectingFeatures(const gnLocation& lt, std::vector& feature_vector, std::vector& index_vector) const = 0; /** * Creates a list of features which may have been broken by an edit. * @param lt The coordinates containing the features to return. * @param feature_vector The std::vector to store features in. */ virtual void GetBrokenFeatures(const gnLocation& lt, std::vector& feature_vector) const = 0; /** * Remove a feature from this spec. * @param i The index of the feature to remove. * @return True if successful */ virtual void RemoveFeature( const uint32 i ) = 0; protected: std::string m_sourceName; std::vector < SubSpec* > m_SpecList; std::vector < gnBaseHeader* > m_headerList; private: }; // class gnMultiSpec template< class SubSpec > inline uint32 gnMultiSpec< SubSpec >::GetHeaderListLength() const { return m_headerList.size(); } template< class SubSpec > inline gnBaseHeader* gnMultiSpec< SubSpec >::GetHeader(const uint32 i) const { if(i < m_headerList.size()){ return m_headerList[i]; } return 0; } template< class SubSpec > inline std::string gnMultiSpec< SubSpec >::GetSourceName() const{ return m_sourceName; } template< class SubSpec > inline void gnMultiSpec< SubSpec >::SetSourceName(const std::string& sourceName){ m_sourceName = sourceName; } template< class SubSpec > uint32 gnMultiSpec< SubSpec >::GetSpecListLength() const{ return m_SpecList.size(); } template< class SubSpec > SubSpec* gnMultiSpec< SubSpec >::GetSpec( const uint32 i ) const{ if(i < m_SpecList.size()) return m_SpecList[i]; Throw_gnEx(FragmentIndexOutOfBounds()); } template< class SubSpec > SubSpec* gnMultiSpec< SubSpec >::GetSpecByBase( const gnSeqI baseI ) const{ return m_SpecList[GetSpecIndexByBase(baseI)]; } template< class SubSpec > void gnMultiSpec< SubSpec >::AddSpec( SubSpec* spec, const uint32 i ){ uint32 index = i == UINT32_MAX ? m_SpecList.size() : i; if(index <= m_SpecList.size()){ m_SpecList.insert(m_SpecList.begin() + index, spec); } } template< class SubSpec > void gnMultiSpec< SubSpec >::RemoveSpec( uint32 i ){ if(i < GetSpecListLength()){ m_SpecList.erase(m_SpecList.begin() + i); } } template< class SubSpec > void gnMultiSpec< SubSpec >::Clear() { gnBaseSpec::Clear(); uint32 list_size = m_headerList.size(); for(uint32 i=0; i < list_size; i++) delete m_headerList[i]; m_headerList.clear(); } template< class SubSpec > gnSeqI gnMultiSpec< SubSpec >::GetLength() const { gnSeqI subLen = 0; //aggregate the lower levels. for(uint32 i=0; i < GetSpecListLength(); i++) subLen += GetSpec(i)->GetLength(); return subLen; } //Return the index of the subspec which contains the base in question template< class SubSpec > uint32 gnMultiSpec< SubSpec >::GetSpecIndexByBase( const gnSeqI baseI ) const{ gnSeqI cur_length = 0; for(uint32 i=0; i < GetSpecListLength(); i++){ cur_length += GetSpec(i)->GetLength(); if(baseI < cur_length) return i; } //if we made it here then the base was out of bounds Throw_gnEx(SeqIndexOutOfBounds()); } template< class SubSpec > uint32 gnMultiSpec< SubSpec >::GetSpecIndexByName( const std::string& name ) const{ for(uint32 i=0; i < GetSpecListLength(); i++){ if(name == GetSpec(i)->GetName()) return i; } Throw_gnEx(SpecIndexOutOfBounds()); } //returns the starting base pair index of the given subspec. template< class SubSpec > gnSeqI gnMultiSpec< SubSpec >::GetSpecStartBase( const uint32 specI ) const{ uint32 i; if(specI >= GetSpecListLength()) Throw_gnEx(SpecIndexOutOfBounds()); gnSeqI start_base = 0; for(i=0; i < specI; i++){ start_base += GetSpec(i)->GetLength(); } return start_base; } template< class SubSpec > gnSeqI gnMultiSpec< SubSpec >::GetSpecEndBase( const uint32 specI ) const{ uint32 i; if(specI >= GetSpecListLength()) Throw_gnEx(SpecIndexOutOfBounds()); gnSeqI end_base = 0; for(i=0; i <= specI; i++){ end_base += GetSpec(i)->GetLength(); } return end_base; } template< class SubSpec > void gnMultiSpec< SubSpec >::CropStart( gnSeqI cropLen ){ gnSeqI curbase = 0; for(uint32 specI = 0; specI < GetSpecListLength(); specI++){ curbase += GetSpec(specI)->GetLength(); if(curbase <= cropLen){ //delete the spec completely gnBaseSpec *tmp_spec = GetSpec(specI); RemoveSpec(specI); delete tmp_spec; specI--; }else{ //recurse and break gnSeqI sub_len = cropLen - (curbase - GetSpec(specI)->GetLength()); GetSpec(specI)->CropStart(sub_len); break; } } } template< class SubSpec > void gnMultiSpec< SubSpec >::CropEnd( gnSeqI cropLen ){ gnSeqI curbase = 0; gnSeqI cropbase = GetLength() - cropLen; //last base to keep boolean trash_the_rest = false; for(uint32 specI = 0; specI < GetSpecListLength(); specI++){ curbase += GetSpec(specI)->GetLength(); if(trash_the_rest){ //delete the spec entirely gnBaseSpec *tmp_spec = GetSpec(specI); RemoveSpec(specI); delete tmp_spec; specI--; continue; }else if(curbase > cropbase){ GetSpec(specI)->CropEnd(curbase - cropbase); trash_the_rest = true; }else if(curbase == cropbase) trash_the_rest = true; } } template< class SubSpec > void gnMultiSpec< SubSpec >::AddHeader( gnBaseHeader* head, const uint32 i) { uint32 index = i == UINT32_MAX ? m_headerList.size() : i; m_headerList.insert(m_headerList.begin() + index, head); } template< class SubSpec > gnBaseHeader* gnMultiSpec< SubSpec >::GetHeader( const std::string& name, uint32& i) const{ for(; i < m_headerList.size(); i++){ if( m_headerList[i]->GetHeaderName() == name) return m_headerList[i]; } Throw_gnEx(HeaderIndexOutOfBounds()); } template< class SubSpec > void gnMultiSpec< SubSpec >::RemoveHeader( uint32 i) { if(i <= m_headerList.size()){ m_headerList.erase(m_headerList.begin() + i); } Throw_gnEx(HeaderIndexOutOfBounds()); } template< class SubSpec > boolean gnMultiSpec< SubSpec >::SeqRead(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen, const uint32 contigI ) const{ if( bufLen == 0 ) return true; if(contigI == ALL_CONTIGS){ gnSeqI curpos = 0; gnSeqI readBytes = 0; gnSeqI remainingBytes = bufLen; uint32 curSpecI = 0; //seek to start spec. for(curSpecI=0; curSpecI < GetSpecListLength(); curSpecI++){ curpos += GetSpec(curSpecI)->GetLength(); if(curpos > start) break; } if(curpos <= start) Throw_gnEx(SeqIndexOutOfBounds()); //read until we're done; while((remainingBytes > 0) && (curSpecI < GetSpecListLength())) { gnSeqI readable = GetSpec(curSpecI)->GetLength(); //check for circular gnSeqI start_pos = readBytes == 0 ? start - (curpos - readable) : 0; gnSeqI to_read = readable - start_pos >= remainingBytes ? remainingBytes : readable - start_pos; boolean success = GetSpec(curSpecI)->SeqRead(start_pos, buf+readBytes, to_read, contigI); readBytes += to_read; remainingBytes -= to_read; if(!success) break; curSpecI++; } bufLen = readBytes; return true; }else{ //read from the specified contig. if(contigI < GetSpecListLength()) return GetSpec(contigI)->SeqRead(start, buf, bufLen, ALL_CONTIGS); else Throw_gnEx(SpecIndexOutOfBounds()); } return false; } } // end namespace genome #endif // _gnMultiSpec_h_ libGenome-1.3.1/libGenome/test-o-matic.cpp0000644002622200470610000000726710647575617015315 00000000000000#ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnFASSource.h" #include "libGenome/gnSequence.h" #include "libGenome/gnTranslator.h" #include "libGenome/gnStringSpec.h" #include int main( int argc, char* argv[] ) { gnSequence seq_a, seq_b; string seq_a_name="styphi.fas"; string seq_b_name="typhi.gbk"; try{ seq_a.LoadSource( seq_a_name ); cout << seq_a_name << '\t' << seq_a.length() << " bp\n"; seq_b.LoadSource( seq_b_name ); cout << seq_b_name << '\t' << seq_b.length() << " bp\n"; }catch(gnException& gne){ cout << gne << "\n"; } uint len = 50; uint increment = 1027; const gnCompare* dna_comp = gnCompare::DNASeqCompare(); for( uint seqI = 1; seqI <= 200000; seqI+= increment ){ string str_a, str_b; str_a = seq_a.ToString( len, seqI ); str_b = seq_b.ToString( len, seqI ); if( !dna_comp->Contains( str_a, str_b ) ){ cout << str_a << endl << str_b << endl; seqI -= increment; } } gnSequence seq_in; string seq_name = "sequin.gbk"; string out_seq = "seqout.gbk"; try{ seq_in.LoadSource( seq_name ); cout << seq_name << '\t' << seq_in.length() << " bp\n"; gnFASSource::Write( seq_in, out_seq ); }catch(gnException& gne){ cout << gne << "\n"; } /* gnSequence erwinia_junk; gnSequence pruned_bush; string sequence_name = "mouse_small.fas"; string output_sequence = "mouse_filt.fas"; // cout << "Enter the name of the sequence file you want contig info on.\n"; // cin >> sequence_name; try{ erwinia_junk.LoadSource( sequence_name ); for(uint32 contigI = 0; contigI < erwinia_junk.contigListSize(); contigI++){ cout << erwinia_junk.contigName( contigI ) << '\t' << erwinia_junk.contigLength( contigI ) << '\n'; if( erwinia_junk.contigLength( contigI ) > 1000 ) pruned_bush += erwinia_junk.contig( contigI ); } gnFASSource::Write(pruned_bush, output_sequence); }catch(gnException& gne){ cout << gne << "\n"; } */ /* ifstream gbk1("cpneuJ.gbk"); ifstream gbk2("test_rc.gbk"); uint32 badline = 0; char buf[30000]; char buf2[30000]; while(gbk1.good() && gbk2.good()){ gbk1.getline(buf, 30000); gbk2.getline(buf2, 30000); if(strcmp(buf, buf2)){ cout << "mismatched line: " << badline << "\n"; cout << buf << endl << buf2 << endl; cout << "Length 1: " << strlen(buf) << " Length 2: " << strlen(buf2) << endl; cin >> buf; } badline++; } */ /* gnStringSpec s(""); cout < \n"; gnSequence aSeq(nseq); cout< \n"; gnTranslator::ProteinDNAConverter->ToProtein(nseq); cout << nseq << '\n';; // prot_trans.append(nseq); // output the first ten bases of the sequence // cout << prot_trans.subseq(1,10); return 0; } /*#include "libGenome/gnSequence.h" #include #include #include "libGenome/gnTranslator.h" #include "libGenome/gnFASSource.h" int main(int argc, char* argv[]){ gnSequence gps; string seq_filename; string out_filename; /* Get the name of the dnx file to convert to FastA / cout << "Debug-o-matic!\n"; cout << "Please give the name of the fof to test: "; cin >> seq_filename; gps.LoadSource(seq_filename); cout << "Output filename: "; cin >> out_filename; gnFASSource::Write(gps, out_filename); return 0; }*/libGenome-1.3.1/libGenome/gnGenomeSpec.cpp0000644002622200470610000001655410647575617015360 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnGenomeSpec.cpp // Purpose: implements gnMultiSpec< gnFragmentSpec > for genomes // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnGenomeSpec.h" #include using namespace std; namespace genome { gnGenomeSpec::gnGenomeSpec() { gnBaseSpec::Clear(); } gnGenomeSpec::gnGenomeSpec( const gnGenomeSpec& s ) { m_sourceName = s.m_sourceName; m_name = s.m_name; m_reverseComplement = s.m_reverseComplement; m_circular = s.m_circular; //copy the header list. uint32 list_size = s.m_headerList.size(); m_headerList.reserve(list_size); for(uint32 i=0; i < list_size; i++) m_headerList.push_back(s.m_headerList[i]->Clone()); //copy the fragment list. list_size = s.m_SpecList.size(); m_SpecList.reserve(list_size); for(uint32 i=0; i < list_size; i++) m_SpecList.push_back(s.m_SpecList[i]->Clone()); } gnGenomeSpec::~gnGenomeSpec() { Clear(); } // Clone void gnGenomeSpec::Clear() { uint32 list_size = m_SpecList.size(); for(uint32 i=0; i < list_size; i++) delete m_SpecList[i]; m_SpecList.clear(); gnMultiSpec< gnFragmentSpec >::Clear(); } void gnGenomeSpec::SetReverseComplement( const boolean value ) { if(value == m_reverseComplement) return; //reverse the spec list entries vector tmp_spec_list; for(uint32 i=0; i < GetSpecListLength(); i++){ //transmit rev_comp down to each fragment spec GetSpec(i)->SetReverseComplement(!GetSpec(i)->IsReverseComplement()); tmp_spec_list.insert(tmp_spec_list.begin(), GetSpec(i)); } m_SpecList = tmp_spec_list; m_reverseComplement = value; } gnGenomeSpec* gnGenomeSpec::CloneRange( const gnSeqI startI, const gnSeqI len ) const{ if(len == 0) return new gnGenomeSpec(); //find the valid range of specs to copy uint32 firstSpec = GetSpecIndexByBase(startI); gnSeqI total_copylen = len; uint32 endSpec; if(len != GNSEQI_END){ endSpec = GetSpecIndexByBase(startI + len - 1); }else{ endSpec = GetSpecListLength() - 1; total_copylen = GetLength() - startI; } //find their starting and ending bases gnSeqI firstBase = startI - GetSpecStartBase(firstSpec); gnSeqI firstSpecLen = GetSpec(firstSpec)->GetLength(); boolean spans_specs = true; gnSeqI firstCopyLen = firstSpecLen - firstBase; if(firstCopyLen >= total_copylen){ spans_specs = false; firstCopyLen = total_copylen; } gnGenomeSpec* destSpec = new gnGenomeSpec(); gnFragmentSpec* newSpec = m_SpecList[firstSpec]->CloneRange(firstBase, firstCopyLen); destSpec->AddSpec( newSpec ); gnSeqI cur_copylen = firstCopyLen; //add all the completely covered specs in the middle for(uint32 specI = firstSpec + 2; specI <= endSpec; specI++){ destSpec->AddSpec(GetSpec(specI-1)->Clone()); cur_copylen += GetSpec(specI-1)->GetLength(); } //add the last spec if necessary if(spans_specs){ newSpec = m_SpecList[endSpec]->CloneRange( 0, total_copylen - cur_copylen); destSpec->AddSpec(newSpec); } return destSpec; } //IMPLEMENT ME: What to do with headers? void gnGenomeSpec::MergeFragments(const uint32 startF, const uint32 endF){ if(startF > m_SpecList.size() || endF > m_SpecList.size()) Throw_gnEx(FragmentIndexOutOfBounds()); if(startF > endF) Throw_gnEx(FragmentIndexOutOfBounds()); for(uint32 i = startF + 1; i < endF; i++){ gnFragmentSpec* delspec = m_SpecList[startF + 1]; m_SpecList.erase(m_SpecList.begin() + startF + 1); for(uint32 j = 0; j < delspec->GetSpecListLength(); j++) m_SpecList[startF]->AddSpec(delspec->GetSpec(j)); delete delspec; } } uint32 gnGenomeSpec::AddFeature( gnBaseFeature* feat ){ uint32 count = 0; uint32 len = 0; uint32 featureI = 0; uint32 specListLen = GetSpecListLength(); for(uint32 specI = 0; specI < specListLen; specI++){ len = GetSpec(specI)->GetLength(); gnLocation lt(count, count+len); if(feat->IsContainedBy(lt)){ return featureI + GetSpec(specI)->AddFeature(feat); } count += len; featureI += GetSpec(specI)->GetFeatureListLength(); } //if we get this far then the feature has invalid coordinates Throw_gnEx(SeqIndexOutOfBounds()); } uint32 gnGenomeSpec::GetFeatureListLength() const { uint32 len = 0; for(uint32 i=0; i < GetSpecListLength(); i++) len += GetSpec(i)->GetFeatureListLength(); return len; } gnBaseFeature* gnGenomeSpec::GetFeature(const uint32 i ) const { uint32 count = 0; uint32 len = 0; for(uint32 specI=0; specI < GetSpecListLength(); specI++){ len = GetSpec(specI)->GetFeatureListLength(); if(count <= i && i < count + len){ gnBaseFeature* feat = GetSpec(specI)->GetFeature(i - count); feat->MovePositive(GetSpecStartBase(specI)); return feat; } count += len; } Throw_gnEx(FeatureIndexOutOfBounds()); } void gnGenomeSpec::GetContainedFeatures(const gnLocation& lt, vector& feature_vector, vector& index_vector) const{ uint32 ss_size = GetSpecListLength(); uint32 fl_size = 0; gnSeqI start_base = 0; for(uint32 i=0; i < ss_size; i++){ gnLocation sub_lt = lt; gnSeqI sub_len = GetSpec(i)->GetLength(); sub_lt.MoveNegative(start_base); sub_lt.CropEnd(sub_len); GetSpec(i)->GetContainedFeatures(sub_lt, feature_vector, index_vector); uint32 fvs = feature_vector.size(); for(uint32 j = 0; j < fvs; j++){ feature_vector[j]->MovePositive(start_base); index_vector[j]+= fl_size; } if(fvs > 0) return; start_base += sub_len; fl_size += GetSpec(i)->GetFeatureListLength(); } } void gnGenomeSpec::GetIntersectingFeatures(const gnLocation& lt, vector& feature_vector, vector& index_vector) const{ uint32 ss_size = GetSpecListLength(); uint32 fl_size = 0; gnSeqI start_base = 0; for(uint32 i=0; i < ss_size; i++){ gnLocation sub_lt = lt; gnSeqI sub_len = GetSpec(i)->GetLength(); sub_lt.MoveNegative(start_base); sub_lt.CropEnd(sub_len); GetSpec(i)->GetIntersectingFeatures(sub_lt, feature_vector, index_vector); uint32 fvs = feature_vector.size(); for(uint32 j = 0; j < fvs; j++){ feature_vector[j]->MovePositive(start_base); index_vector[j]+= fl_size; } if(fvs > 0) return; start_base += sub_len; fl_size += GetSpec(i)->GetFeatureListLength(); } } void gnGenomeSpec::GetBrokenFeatures(const gnLocation& lt, vector& feature_vector) const{ uint32 ss_size = GetSpecListLength(); uint32 fl_size = 0; gnSeqI start_base = 0; for(uint32 i=0; i < ss_size; i++){ gnLocation sub_lt = lt; gnSeqI sub_len = GetSpec(i)->GetLength(); sub_lt.MoveNegative(start_base); sub_lt.CropEnd(sub_len); GetSpec(i)->GetBrokenFeatures(sub_lt, feature_vector); uint32 fvs = feature_vector.size(); for(uint32 j = 0; j < fvs; j++) feature_vector[j]->MovePositive(start_base); if(fvs > 0) return; start_base += sub_len; fl_size += GetSpec(i)->GetFeatureListLength(); } } void gnGenomeSpec::RemoveFeature( const uint32 i ){ uint32 count = 0; uint32 len = 0; uint32 specI=0; for(; specI < GetSpecListLength(); specI++){ len = GetSpec(specI)->GetFeatureListLength(); if(count <= i && i < count + len){ GetSpec(specI)->RemoveFeature( i - count); } count += len; } Throw_gnEx(FeatureIndexOutOfBounds()); } } // end namespace genome libGenome-1.3.1/libGenome/gnException.h0000644002622200470610000000323410647575617014725 00000000000000#ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnException_h_ #define _gnException_h_ #include "libGenome/gnClone.h" #include "libGenome/gnExceptionCode.h" #include #include namespace genome { class GNDLLEXPORT gnException { public: gnException( const char* const srcFile, const unsigned int srcLine, const char* const function, gnExceptionCode& code, const char* const message ); friend std::ostream& operator<<(std::ostream& os, const gnException& gne); //write to source. gnExceptionCode& GetCode(){return m_code;} std::string GetMessage(){return m_message;} void AddCaller( const char* const function ); protected: gnExceptionCode& m_code; std::string m_message; const char* const m_file; unsigned int m_line; std::list function_trace; }; inline gnException::gnException(const char* const srcFile, const unsigned int srcLine, const char* const function, gnExceptionCode& code, const char* const message ) : m_code(code), m_message(message), m_file(srcFile), m_line(srcLine){ AddCaller(function); } GNDLLEXPORT std::ostream& operator<<(std::ostream& os, const gnException& gne); //write to source. #ifdef __GNDEBUG__ #define STACK_TRACE_START try{ #define STACK_TRACE_END \ }catch(genome::gnException& e){\ e.AddCaller(__PRETTY_FUNCTION__);\ throw e;\ } #else #define STACK_TRACE_START #define STACK_TRACE_END #endif // ifdef __DEBUG__ #define Throw_gnEx(code) throw genome::gnException(__FILE__, __LINE__, __PRETTY_FUNCTION__, code, "") #define Throw_gnExMsg(code,msg) throw genome::gnException(__FILE__, __LINE__, __PRETTY_FUNCTION__, code, msg) } // end namespace genome #endif //_gnException_h_ libGenome-1.3.1/libGenome/gnSourceFactory.cpp0000644002622200470610000002036111026443220016062 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnSourceFactory.cpp // Purpose: Source Factory for all Sources // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnSourceFactory.h" #include "libGenome/gnBaseSource.h" #include "libGenome/gnStringTools.h" #include "libGenome/gnFASSource.h" #include "libGenome/gnGBKSource.h" #include "libGenome/gnSEQSource.h" #include "libGenome/gnRAWSource.h" #include "libGenome/gnException.h" #ifdef HAVE_UNISTD_H #include #endif using namespace std; namespace genome { gnSourceFactory::gnSourceFactory() { m_sourceClassList.insert( map< string, gnBaseSource* >::value_type(".fas", new gnFASSource())); m_sourceClassList.insert( map< string, gnBaseSource* >::value_type(".FAS", new gnFASSource())); m_sourceClassList.insert( map< string, gnBaseSource* >::value_type(".seq", new gnSEQSource())); m_sourceClassList.insert( map< string, gnBaseSource* >::value_type(".SEQ", new gnSEQSource())); m_sourceClassList.insert( map< string, gnBaseSource* >::value_type(".gbk", new gnGBKSource())); m_sourceClassList.insert( map< string, gnBaseSource* >::value_type(".GBK", new gnGBKSource())); m_sourceClassList.insert( map< string, gnBaseSource* >::value_type(".raw", new gnRAWSource())); m_sourceClassList.insert( map< string, gnBaseSource* >::value_type(".RAW", new gnRAWSource())); m_pDefaultSourceClass = new gnFASSource(); } gnSourceFactory::~gnSourceFactory() { vector< gnBaseSource* >::iterator iter = m_sourceList.begin(); for(; iter != m_sourceList.end(); ++iter ) { delete *iter; } map< string, gnBaseSource* >::iterator cIter = m_sourceClassList.begin(); for(; cIter != m_sourceClassList.end(); ++cIter ) { delete cIter->second; } } gnSourceFactory* gnSourceFactory::GetSourceFactory() { //use construct on first use method to avoid the static constructor //initialization fiasco... static gnSourceFactory* m_sSourceFactory = new gnSourceFactory(); return m_sSourceFactory; } boolean gnSourceFactory::DelSourceClass( const string& ext ){ map< string, gnBaseSource* >::iterator iter = m_sourceClassList.find( ext ); if( iter != m_sourceClassList.end() ){ m_sourceClassList.erase( iter ); return true; } return false; } gnBaseSource* gnSourceFactory::GetSourceClass( const string& ext ) const{ map< string, gnBaseSource* >::const_iterator iter = m_sourceClassList.find( ext ); if( iter != m_sourceClassList.end() ){ return iter->second; } return m_pDefaultSourceClass; } gnBaseSource* gnSourceFactory::MatchSourceClass( const string& sourceStr ) const{ string::size_type dot_loc = sourceStr.rfind('.'); if(dot_loc != string::npos){ string ext = sourceStr.substr(dot_loc, sourceStr.length() - dot_loc); return GetSourceClass(ext); } return m_pDefaultSourceClass; } boolean gnSourceFactory::HasSourceClass( const string& ext ) const{ if( m_sourceClassList.find(ext) != m_sourceClassList.end() ){ return true; } return false; } boolean gnSourceFactory::SetSourceClass( const string& ext, const gnBaseSource& source ){ map< string, gnBaseSource* >::iterator iter = m_sourceClassList.find( ext ); if( iter == m_sourceClassList.end() ){ m_sourceClassList.insert( map< string, gnBaseSource* >::value_type( ext, source.Clone() ) ); }else{ iter->second = source.Clone(); } return true; } boolean gnSourceFactory::AddPath( const string& path ){ if( PathExists( path ) && !HasPath(path) ) { m_pathList.push_back( path ); return true; } return false; } boolean gnSourceFactory::DelPath( uint32 i ){ if( i < m_pathList.size() ){ vector::iterator iter = m_pathList.begin() + i; m_pathList.erase( iter ); return true; } return false; } boolean gnSourceFactory::InsPath( const string& path, uint32 i ){ if( (i < m_pathList.size()) && PathExists( path ) ) { vector::iterator iter = m_pathList.begin() + i; m_pathList.insert( iter, path ); return true; } return false; } string gnSourceFactory::GetPath( uint32 i ) const{ if( i < m_pathList.size() ){ return m_pathList[i]; } return ""; } boolean gnSourceFactory::HasPath( string path ) const{ standardizePathString( path ); for( uint32 i = 0; i < m_pathList.size(); ++i ){ if( m_pathList[i] == path ) return true; } return false; } boolean gnSourceFactory::GetURL( const string& urlStr, string& localFile ){ return false; } // Sources gnBaseSource* gnSourceFactory::AddSource( const string& sourceStr, boolean searchPaths ) { string openStr = sourceStr; // Check if Exists gnBaseSource* source = HasSource( sourceStr, false ); if( source != 0 ) return source; // Check if File Present and valid gnBaseSource* newSource = MatchSourceClass( sourceStr )->Clone(); if(newSource == NULL) return NULL; // Check the URL to see if we need to cache the file locally if(sourceStr.substr(0, 7) == "http://"){ ErrorMsg("Sorry, no HTTP support.\n"); return NULL; }else if(sourceStr.substr(0, 6) == "ftp://"){ ErrorMsg("Sorry, no FTP support.\n"); return NULL; }else if(sourceStr.substr(0, 8) == "file:///") openStr = sourceStr.substr(8); // Now try to open the local file try{ newSource->Open( openStr ); m_sourceList.push_back( newSource ); return newSource; }catch(gnException& e){ if(e.GetCode() != FileNotOpened()){ delete newSource; e.AddCaller(__PRETTY_FUNCTION__); throw e; } } if( searchPaths ) { // Check other paths for Exists or Presents/valid string file = getFileString( openStr ); vector< string >::iterator iter = m_pathList.begin(); for( ; iter != m_pathList.end(); ++iter ) { string newSourceStr = *iter + file; // Check if Exists source = HasSource( newSourceStr, false ); if( source != 0 ) { delete newSource; return source; } // Check if File Present and valid try{ newSource->Open( newSourceStr ); m_sourceList.push_back( newSource ); return newSource; }catch(gnException& e){ if(e.GetCode() != FileNotOpened()){ delete newSource; e.AddCaller(__PRETTY_FUNCTION__); throw e; } } } } // Cannot find a valid source delete newSource; Throw_gnEx(FileNotOpened()); } gnBaseSource* gnSourceFactory::GetSource( uint32 i ) const{ if( i < m_sourceList.size() ){ return *(m_sourceList.begin() + i); } return 0; } void gnSourceFactory::DelSource( uint32 i ){ if( i >= m_sourceList.size() ) Throw_gnEx(IndexOutOfBounds()); vector< gnBaseSource* >::iterator iter = m_sourceList.begin() + i; gnBaseSource* source = *iter; try{ source->Close(); m_sourceList.erase(iter); delete source; }catch(gnException& e){ e.AddCaller(__PRETTY_FUNCTION__); throw e; } } boolean gnSourceFactory::DelSource( const gnBaseSource* source ){ vector< gnBaseSource* >::iterator iter = m_sourceList.begin(); for( ; iter != m_sourceList.end(); ++iter ){ if( *iter == source ){ gnBaseSource* source = *iter; try{ source->Close(); m_sourceList.erase(iter); delete source; return true; }catch(gnException& e){ e.AddCaller(__PRETTY_FUNCTION__); throw e; } } } return false; } gnBaseSource* gnSourceFactory::HasSource( string sourceStr, boolean searchPaths ) const{ standardizePathString( sourceStr ); vector< gnBaseSource* >::const_iterator iter1 = m_sourceList.begin(); for( ; iter1 != m_sourceList.end(); ++iter1 ) { if( (*iter1)->GetOpenString() == sourceStr ) return *iter1; } if( searchPaths ) { string file = getFileString( sourceStr ); vector< string >::const_iterator iter2 = m_pathList.begin(); for( ; iter2 != m_pathList.end(); ++iter2 ) { iter1 = m_sourceList.begin(); for( ; iter1 != m_sourceList.end(); ++iter1 ) { if( (*iter1)->GetOpenString() == (*iter2 + file) ) return *iter1; } } } return 0; } // private: boolean gnSourceFactory::PathExists( string path ) const{ #ifdef HAVE_UNISTD_H standardizePathString( path ); char folder[FILENAME_MAX]; getcwd( folder, FILENAME_MAX ); if( chdir( path.c_str() ) ){ return false; } chdir( folder ); #endif return true; } } // end namespace genome libGenome-1.3.1/libGenome/Makefile.am0000644002622200470610000000526711026443220014305 00000000000000 if DEBUG D_CXXFLAGS = -Wall -g -DCOMMAND_LINE -D__GNDEBUG__ endif AM_CXXFLAGS = $(D_CXXFLAGS) @OPENMP_CFLAGS@ LIBGENOME_H = \ gnABISource.h gnDataBaseSource.h gnLocation.h gnSetup.h \ gnBaseFeature.h gnDebug.h gnMultiSpec.h gnSourceFactory.h \ gnBaseFilter.h gnDefs.h gnSourceHeader.h gnPosSpecificTranslator.h \ gnBaseHeader.h gnFASSource.h gnSourceQualifier.h \ gnBaseQualifier.h gnSourceSpec.h gnStringQualifier.h\ gnBaseSource.h gnFeature.h gnProteinSequence.h gnStringHeader.h \ gnBaseSpec.h gnFileContig.h gnRAWSource.h \ gnClone.h gnFileSource.h gnRNASequence.h gnStringSpec.h \ gnCompare.h gnFilter.h gnSEQSource.h gnStringTools.h \ gnContigSpec.h gnFragmentSpec.h gnTranslator.h \ gnDNASequence.h gnGBKSource.h gnVersion.h gnFastTranslator.h \ gnGenomeSpec.h gnSequence.h gnException.h gnExceptionCode.h \ IntervalSequenceTree.h OmpGuard.h LIBGENOME_SRC = \ gnFilter.cpp gnCompare.cpp gnTranslator.cpp gnSourceFactory.cpp \ gnFeature.cpp gnSourceQualifier.cpp gnFileContig.cpp gnSourceSpec.cpp \ gnFileSource.cpp gnFASSource.cpp \ gnFragmentSpec.cpp gnStringSpec.cpp gnGBKSource.cpp gnStringTools.cpp \ gnGenomeSpec.cpp gnLocation.cpp \ gnRAWSource.cpp gnBaseFeature.cpp gnSEQSource.cpp gnSequence.cpp \ gnContigSpec.cpp gnSourceHeader.cpp gnException.cpp \ gnFastTranslator.cpp gnPosSpecificTranslator.cpp gnDefs.cpp library_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME) library_include_HEADERS = $(LIBGENOME_H) lib_LTLIBRARIES = libGenome-1.3.la libGenome_1_3_la_SOURCES = $(LIBGENOME_SRC) libGenome_1_3_la_LDFLAGS= -version-info $(GENERIC_LIBRARY_VERSION) INCLUDES = -I$(top_srcdir) check_PROGRAMS = TestRevComp TestRevComp_SOURCES = TestRevComp.cpp TestRevComp_LDADD = $(top_builddir)/src/libGenome.a EXTRA_PROGRAMS = test_o_matic testSource testSourceFactory testSourceSeq testTests testgnSequence coordMapper test_o_matic_SOURCES = test-o-matic.cpp test_o_matic_LDADD = $(top_builddir)/src/libGenome.a test_o_matic_LDFLAGS = @STATIC_FLAG@ testSource_SOURCES = testSource.cpp testSource_LDADD = $(top_builddir)/src/libGenome.a testSourceFactory_SOURCES = testSourceFactory.cpp testSourceFactory_LDADD = $(top_builddir)/src/libGenome.a testSourceSeq_SOURCES = testSourceSeq.cpp testSourceSeq_LDADD = $(top_builddir)/src/libGenome.a testTests_SOURCES = testTests.cpp testTests_LDADD = $(top_builddir)/src/libGenome.a testgnSequence_SOURCES = testgnSequence.cpp testgnSequence_LDADD = $(top_builddir)/src/libGenome.a coordMapper_SOURCES = coordMapper.cpp coordMapper_LDADD = $(top_builddir)/src/libGenome.a libGenome-1.3.1/libGenome/gnContigSpec.h0000644002622200470610000001070410647575617015025 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnContigSpec.h // Purpose: Abstract Contig Spec class // Description: Defines an interface for contig specs // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnContigSpec_h_ #define _gnContigSpec_h_ #include "libGenome/gnDefs.h" #include #include #include "libGenome/gnBaseSpec.h" #include "libGenome/gnBaseFeature.h" #include "libGenome/gnDebug.h" namespace genome { /** * gnContigSpec is an interface for classes which store contigs, or reads, * of DNA or protein sequence */ class GNDLLEXPORT gnContigSpec : public gnBaseSpec { public: gnContigSpec(){} /** * Destructor, frees memory. */ virtual ~gnContigSpec(){} virtual gnContigSpec* Clone() const = 0; virtual gnContigSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const = 0; /** * Get the name of the source associated with this spec. * @return The source name or an empty std::string if none exists. */ virtual std::string GetSourceName() const; /** * Get the base pair index where this contig starts inside of the sequence data. * @return The starting base pair. */ virtual gnSeqI GetStart() const; /** * Get the length of this contig inside of the sequence data. * @return This contigs length. */ virtual gnSeqI GetLength() const; /** * Get the length of the source for this spec. * @return The source length. */ virtual gnSeqI GetSourceLength() const = 0; /** * Returns this contig's index in its source sequence. * @return This contig's index in the source sequence. */ virtual uint32 GetSourceContigIndex() const; /** * Sets the name of the source associated with this contig. * @param sourceName The new name. * @return True if successful. */ virtual void SetSourceName( const std::string& sourceName ); /** * Sets the starting base pair to read from in the contig's sequence. * This does not affect the actual sequence data but only where to begin * using it in this contig. * @param start The new starting base pair. * @return True if successful. */ virtual void SetStart( const gnSeqI start ); /** * Sets the length of reads into this sequence. * This does not affect the actual sequence data but only how much of it * is used in this contig. * @param len The new sequence length. * @return True if successful. */ virtual void SetLength( const gnSeqI len ); /** * Sets this contig's index in its source sequence. * @param contigI This contig's index in the source sequence. */ virtual void SetSourceContigIndex( const uint32 contigI ); /** * Sets the reverse complement bit for this contig. * This routine will translate the start index to the reverse base pair. * @param value True for reverse complement, false otherwise. * @return True if successful. */ virtual void SetReverseComplement( const boolean value ); virtual void CropStart( gnSeqI cropLen ); virtual void CropEnd( gnSeqI cropLen ); virtual boolean SeqRead(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen, const uint32 contigI ) const; virtual void Clear(); protected: gnSeqI m_start; //start within the genome. gnSeqI m_length; uint32 m_SourceContigIndex; /** * all derived classes must implement this! * it simply reads the specified bases into buf, disregarding circularity and reverse complement. */ virtual boolean Read(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen ) const = 0; private: }; // class gnContigSpec inline std::string gnContigSpec::GetSourceName() const{ return m_sourceName; } inline void gnContigSpec::SetSourceName(const std::string& sourceName){ m_sourceName = sourceName; } inline gnSeqI gnContigSpec::GetStart() const { return m_start; } inline gnSeqI gnContigSpec::GetLength() const { return m_length; } // SET inline void gnContigSpec::SetStart( const gnSeqI start ) { m_start = start; } inline void gnContigSpec::SetLength( const gnSeqI len ) { m_length = len; } inline uint32 gnContigSpec::GetSourceContigIndex() const{ return m_SourceContigIndex; } inline void gnContigSpec::SetSourceContigIndex( const uint32 contigI ){ m_SourceContigIndex = contigI; } } // end namespace genome #endif // _gnContigSpec_h_ libGenome-1.3.1/libGenome/gnStringTools.cpp0000644002622200470610000001305410647575617015612 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnStringTools.cpp // Purpose: Random string manipulation tools // Description: Random string manipulation tools // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnStringTools.h" using namespace std; namespace genome { void BaseCount(const string& bases, gnSeqI& a_count, gnSeqI& c_count, gnSeqI& g_count, gnSeqI& t_count, gnSeqI& other_count){ a_count = 0; c_count = 0; g_count = 0; t_count = 0; other_count = 0; for(uint32 i=0; i < bases.length(); i++){ if((bases[i] == 'a')||(bases[i] == 'A')) a_count++; else if((bases[i] == 'c')||(bases[i] == 'C')) c_count++; else if((bases[i] == 'g')||(bases[i] == 'G')) g_count++; else if((bases[i] == 't')||(bases[i] == 'T')) t_count++; else other_count++; } } // removes white space, keeps only one return for multiple returns unsigned int removeSpace(string &str) { bool onSpace = true; unsigned int nbrSpace = 0; bool containsReturn = false; unsigned int i; for( i = str.length(); i > 0 ; i--) { if( isspace(str[i-1]) ) { nbrSpace++; if( (str[i-1] == '\n') || (str[i-1] == '\r') ) containsReturn = true; onSpace = true; } else { onSpace = false; if( nbrSpace > 0 ) { str.erase( i, nbrSpace-1); str[i] = (containsReturn?'\n':' '); } containsReturn = false; nbrSpace = 0; } } if( nbrSpace > 0 ) { str.erase( i, nbrSpace); } if( str.length() > 0 ) { if( isspace(str[str.length()-1]) ) str.erase(str.length()-1, 1); } return nbrSpace; } void removeEndSpace(string &str) { unsigned int nbrSpace = 0; unsigned int i; for( i = str.length()-1; i > 0 ; i--) { if( !isSpace(str[i]) ) break; nbrSpace++; } if( i != str.length() ) { str.erase(i+1, nbrSpace); } } bool isNewLine(char ch) { if( (ch == '\n') || (ch == '\r') ) { return true; } return false; } bool isWhiteSpace(char ch) { if( (ch == ' ') || (ch == '\t') ) { return true; } return false; } bool isSpace(char ch) { if( isWhiteSpace(ch) || isNewLine(ch) ) { return true; } return false; } string uintToString(unsigned int value) { string str = ""; char ch = '\0'; unsigned int b = 0; if( value == 0 ) str = "0"; while( value != 0 ) { b = value % 10; value /= 10; ch = b + 48; str = ch + str; } return str; } string ulongToString(unsigned long value) { string str = ""; char ch = '\0'; unsigned long b = 0; if( value == 0 ) str = "0"; while( value != 0 ) { b = value % 10; value /= 10; ch = b + 48; str = ch + str; } return str; } unsigned int parseValue(string &valueString) { unsigned int retValue = 0; unsigned int length = valueString.length(); for( unsigned int i=0; i < length; i++) { retValue = (retValue * 10) + (valueString[i] - '0'); } return retValue; } int parseUintValue(string &valueString) { int retValue = 0; unsigned int length = valueString.length(); for( unsigned int i=0; i < length; i++) { if( isdigit( valueString[i] ) ) { retValue = (retValue * 10) + (valueString[i] - '0'); } else break; } return retValue; } int parseIntValue(string &valueString) { int sign = 1; int retValue = 0; unsigned int length = valueString.length(); unsigned int i=0; for( ; i < length; i++) { if( valueString[i] == '-' ) { sign = -1; break; } else if( isdigit( valueString[i] ) ) { retValue = (retValue * 10) + sign * (valueString[i] - '0'); break; } } i++; for( ; i < length; i++) { if( isdigit( valueString[i] ) ) { retValue = (retValue * 10) + sign * (valueString[i] - '0'); } else break; } return retValue; } vector< string > tokenizeString( const string &str, char delimiter ) { return tokenizeString( str.c_str(), str.length(), delimiter ); } vector< string > tokenizeString( const char* str, unsigned int len, char delimiter ) { unsigned int lastIndex = 0 ; vector< string > tokenizeVector; unsigned int i=0; for( i = 0; i < len ; ++i ) { if( str[i] == delimiter ) { if( i > (lastIndex + 1) ) { tokenizeVector.push_back( string( str + lastIndex, i - lastIndex ) ); } lastIndex = i + 1; } } if( i > (lastIndex + 1) ) { tokenizeVector.push_back( string( str + lastIndex, i - lastIndex ) ); } return tokenizeVector; } void standardizePathString( string &oFileName ) { unsigned int len = oFileName.size(); for( unsigned int i=0; i < len ; ++i ) { if( oFileName[i] == '\\' ) oFileName[i] = '/'; } } string getPathString( string oFileName ) { string::size_type i = oFileName.rfind('/'); if( i != string::npos ) oFileName.erase(i+1, oFileName.length() - (i+1)); // else // oFileName.clear(); return oFileName; } string getFileString( string oFileName ) { string::size_type i = oFileName.rfind('/'); if( i != string::npos ) oFileName.erase(0, i + 1); return oFileName; } string getExtString( string oFileName ) { string::size_type i = oFileName.rfind('.'); if( i != string::npos ) oFileName.erase( 0, i+1); // else // oFileName.clear(); return oFileName; } string getFileNoExtString( string oFileName ) { string::size_type i = oFileName.rfind('/'); if( i != string::npos ) oFileName.erase(0, i + 1); i = oFileName.rfind('.'); if( i != string::npos ) oFileName.erase( i, string::npos); return oFileName; } } // end namespace genome libGenome-1.3.1/libGenome/gnSourceSpec.h0000644002622200470610000000567310647575617015053 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnSourceSpec.h // Purpose: implements gnBaseSpec for source specs // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnSourceSpec_h_ #define _gnSourceSpec_h_ #include "libGenome/gnDefs.h" #include #include "libGenome/gnContigSpec.h" #include "libGenome/gnBaseSource.h" namespace genome { /** * gnSourceSpec stores sequence and annotation data from another source. * @see gnContigSpec * @see gnBaseSpec */ class GNDLLEXPORT gnSourceSpec : public gnContigSpec { public: /** * Empty constructor. */ gnSourceSpec(); /** * Constructor, creates a gnSourceSpec using sequence data in the given source. * A circular spec will be created if the end index is greater than the start. * @param m_pSource The source to read base pairs from. * @param m_ContigIndex The index of the contig in the source, ALL_CONTIGS by default. * @param startI The index to start reading base pairs from the source. * @param endI The index to stop reading base pairs from the source. * @param revComp True if the sequence is read reverse complement. */ gnSourceSpec( gnBaseSource* m_pSource, const uint32 m_ContigIndex=ALL_CONTIGS, const gnSeqI startI=0, const gnSeqI endI=GNSEQI_END, const boolean revComp = false); /** * Copy constructor. * @param s the gnSourceSpec to copy. */ gnSourceSpec( const gnSourceSpec& s ); ~gnSourceSpec(); gnSourceSpec* Clone() const; // Source Spec Specific functions virtual void Clear(); virtual gnSeqI GetSourceLength() const; virtual gnBaseSource *GetSource() const; /** * Copies a specified range of bases and returns a pointer to * the resulting gnSourceSpec. You must delete the copy when you * are finished with it. * @param startI The first base pair to copy * @param len The length of the piece to copy * @return A copy of the gnSourceSpec containing only the specified bases */ virtual gnSourceSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const; protected: virtual boolean Read(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen ) const; gnBaseSource* m_pSource; }; // class gnSourceSpec inline gnSourceSpec* gnSourceSpec::Clone() const { return new gnSourceSpec( *this ); } inline gnSeqI gnSourceSpec::GetSourceLength() const{ return m_pSource->GetContigSeqLength(m_SourceContigIndex); } inline gnBaseSource* gnSourceSpec::GetSource() const { return m_pSource; } inline boolean gnSourceSpec::Read(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen) const{ return m_pSource->SeqRead(start, buf, bufLen, m_SourceContigIndex); } } // end namespace genome #endif // _gnSourceSpec_h_ libGenome-1.3.1/libGenome/gnFastTranslator.cpp0000644002622200470610000001121011003030307016223 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnFastTranslator.h // Purpose: Filter for all Sequences // Description: translates, converts sequence // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnFastTranslator.h" #include #include using namespace std; namespace genome { // static data access, avoids static initialization order fiasco const gnFastTranslator *gnFastTranslator::ProteinDNATranslator(){ const static gnFastTranslator* t_trans = new gnFastTranslator(ProteinDNATranslatorType); return t_trans; } const gnFastTranslator *gnFastTranslator::DNAProteinTranslator(){ const static gnFastTranslator* t_trans = new gnFastTranslator(DNAProteinTranslatorType); return t_trans; } // public: gnFastTranslator::gnFastTranslator() { use_default = false; m_defaultChar = 0; } gnFastTranslator::gnFastTranslator( const gnFastTranslator &sf ) { m_name = sf.m_name; use_default = sf.use_default; m_defaultChar = sf.m_defaultChar; m_transCache = sf.m_transCache; } gnFastTranslator::gnFastTranslator( gnTranslatorType t_type ) { use_default = false; m_defaultChar = 0; switch(t_type){ case ProteinDNATranslatorType: CacheTranslator(gnTranslator::ProteinDNATranslator(), "FLIMVPTAY.HQNKDECGSR", 1); break; case DNAProteinTranslatorType: CacheTranslator(gnTranslator::DNAProteinTranslator(), "ACGTRYKMBVDHSWNX", 3); break; } } // gnSeqC gnSeqC gnFastTranslator::Filter( const gnSeqC ch ) const{ /* for(uint32 i=0; i < m_inputTable.size(); i++){ if(m_inputTable[i].length() == 1) if(compare->Contains(m_inputTable[i][0], ch)) return m_outputTable[i][0]; } */ return m_defaultChar; } void gnFastTranslator::Filter( gnSeqC** seq, gnSeqI& len ) const{ /* uint32 curpos = 0; string output; while(curpos < len){ uint32 i=0; for(; i < m_inputTable.size(); i++){ //don't compare if there aren't enough chars uint32 curlen = m_inputTable[i].length(); if(len - curpos < curlen) continue; if(compare->Contains(m_inputTable[i].data(), *seq + curpos, curlen)){ output += m_outputTable[i]; curpos += curlen; break; } } if(i == m_inputTable.size()){ //no match was found. if(use_default) //fill with the default char? output += m_defaultChar; curpos++; } } if(output.length() > len){ delete[] *seq; *seq = new gnSeqC[output.length()]; } len = output.length(); memcpy(*seq, output.data(), len); */} // string void gnFastTranslator::Filter( string &seq ) const{ uint32 curpos = 0, outpos = 0; uint32 len = seq.length(); uint32 width = m_transCache.begin()->first.length(); uint32 out_width = m_transCache.begin()->second.length(); uint32 out_size = (seq.length() / width) * out_width + seq.length() % width + 1; gnSeqC* output_array = new gnSeqC[out_size]; output_array[out_size-1] = 0; string seq_upper; while(curpos < len){ //transform to upper case seq_upper = seq.substr(curpos, width); for(uint32 i=0; i < seq_upper.size(); i++) seq_upper[i] = toupper(seq_upper[i]); map::const_iterator iter = m_transCache.find(seq_upper); if(iter == m_transCache.end()){ //no match was found. if(use_default) //fill with the default char? output_array[curpos] = m_defaultChar; curpos++; }else{ strcpy( output_array + outpos, iter->second.c_str() ); curpos += width; outpos += out_width; } } seq = output_array; } void gnFastTranslator::CacheTranslator(const gnTranslator* tranny, string inputs, const gnSeqI input_width){ string cur_input; string cur_trans; vector index; gnSeqI cur_index = input_width; //fill the index array with input_width 0's for(gnSeqI curI = 0; curI < input_width; curI++) index.push_back(0); while(true){ //ensure the validity of our indices cur_index = input_width - 1; while(index[cur_index] == inputs.length()){ if(cur_index == 0){ return; } index[cur_index] = 0; cur_index--; index[cur_index]++; continue; } //create a sequence to cache. for(gnSeqI i = 0; i < input_width; i++){ cur_input += inputs[index[i]]; } cur_trans = cur_input; tranny->Filter(cur_trans); m_transCache[cur_input] = cur_trans; // m_transCache.insert(map::value_type(cur_input, cur_trans)); // prepare for next time thru the loop cur_input = ""; index[input_width - 1]++; } } } // end namespace genome libGenome-1.3.1/libGenome/gnCompare.h0000644002622200470610000001333311003030307014317 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnCompare.h // Purpose: Compares all sequences // Description: Compares sequences // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnCompare_h_ #define _gnCompare_h_ #include "libGenome/gnDefs.h" #include #include #include #include "libGenome/gnClone.h" namespace genome { class GNDLLEXPORT gnCompare : public gnClone { public: /** * Returns a pointer to a ready to use Protein comparison object * Do not delete the object when finished with it, it is a static object. */ static const gnCompare *ProteinSeqCompare(); /** * Returns a pointer to a ready to use DNA comparison object * This comparator can handle comparisons between ambiguous DNA sequences. * Do not delete the object when finished with it, it is a static object. */ static const gnCompare *DNASeqCompare(); /** * Returns a pointer to a ready to use RNA comparison object * This comparator can handle comparisons between ambiguous RNA sequences. * Do not delete the object when finished with it, it is a static object. */ static const gnCompare *RNASeqCompare(); enum gnCompareType{ ProteinSeqCompareType, DNASeqCompareType, RNASeqCompareType, }; gnCompare(); /** * Creates a gnCompare for a predefined compare type. * Used by the static compare constructors to avoid the "static initialization order fiasco" * For general use of a predefined comaprison type, you should use one of the static * member functions to get a pointer to that comparison object. * @param c_type The type of comparator to create. * @see gnCompareType */ gnCompare( const gnCompareType c_type ); ~gnCompare(); gnCompare* Clone() const; std::string GetName() const; void SetName( std::string name ); // Use less than comparisons since all other operators can be derived // gnSeqC less than operations boolean LessThan( gnSeqC ch, gnSeqC ch2, boolean case_sensitive = false) const; /** True if ch2 is equal to or contained within the scope of ch * */ boolean Contains( gnSeqC ch, gnSeqC ch2, boolean case_sensitive = false ) const; // True if ch2 is general enough to equal ch // gnSeqC[] less than operations boolean LessThan( const gnSeqC* seq, const gnSeqC* seq2, const uint32 len, boolean case_sensitive = false ) const; boolean Contains( const gnSeqC* seq, const gnSeqC* seq2, const uint32 len, boolean case_sensitive = false ) const; // std::string boolean LessThan( const std::string &seq, const std::string &seq2, boolean case_sensitive = false) const; boolean Contains( const std::string &seq, const std::string &seq2, boolean case_sensitive = false) const; // fill map //adds a character which is equivalent to itself void SetSingle( const gnSeqC ch ); //adds a pair of equivalent characters void SetPair( const gnSeqC ch, const gnSeqC ch2 ); //adds ch as being wholly contained by ch2 void SetContained( const gnSeqC ch, const gnSeqC ch2 ); void RemoveSingle( const gnSeqC ch ); void RemovePair( const gnSeqC ch, const gnSeqC ch2 ); void RemoveContained( const gnSeqC ch, const gnSeqC ch2 ); private: gnCompare( const gnCompare& sf ){}; void CreateProteinComparator(); void CreateDNAComparator(); void CreateRNAComparator(); void AddArrayEntry( gnSeqC *array[GNSEQC_MAX], const gnSeqC ch, const gnSeqC ch2); void DelArrayEntry( gnSeqC *array[GNSEQC_MAX], const gnSeqC ch, const gnSeqC ch2); std::string m_name; boolean m_ignoreCase; gnSeqC* m_pairArray[GNSEQC_MAX]; gnSeqC* m_containArray[GNSEQC_MAX]; };//class gnCompare inline gnCompare* gnCompare::Clone() const{ return new gnCompare(*this); } inline std::string gnCompare::GetName() const{ return m_name; } inline void gnCompare::SetName( std::string name ){ m_name = name; } // gnSeqC inline boolean gnCompare::LessThan( gnSeqC ch, gnSeqC ch2, boolean case_sensitive) const { if(!case_sensitive){ ch = toupper(ch); ch2 = toupper(ch2); } if(strchr(m_pairArray[ch], ch2) == 0) return ch < ch2 ? true : false; return false; } // gnSeqC[] inline boolean gnCompare::LessThan( const gnSeqC* seq, const gnSeqC* seq2, const uint32 len, boolean case_sensitive ) const{ for( uint32 i=0; i < len ; ++i ) if(LessThan(seq[i], seq2[i], case_sensitive)) return true; return false; } // std::string inline boolean gnCompare::LessThan( const std::string &seq, const std::string &seq2, boolean case_sensitive) const { gnSeqI shorter_len = seq.length() < seq2.length() ? seq.length() : seq2.length(); return LessThan( (gnSeqC*)seq.data(), (gnSeqC*)seq2.data(), shorter_len, case_sensitive ); } // fill map inline void gnCompare::SetSingle( const gnSeqC ch ){ AddArrayEntry(m_pairArray, ch, ch); AddArrayEntry(m_containArray, ch, ch); } inline void gnCompare::SetPair( const gnSeqC ch, const gnSeqC ch2 ){ AddArrayEntry(m_pairArray, ch, ch2); AddArrayEntry(m_pairArray, ch2, ch); } inline void gnCompare::SetContained( const gnSeqC ch, const gnSeqC ch2 ){ AddArrayEntry(m_containArray, ch2, ch); } inline void gnCompare::RemoveSingle( const gnSeqC ch ) { DelArrayEntry(m_pairArray, ch, ch); DelArrayEntry(m_containArray, ch, ch); } inline void gnCompare::RemovePair( const gnSeqC ch, const gnSeqC ch2 ) { DelArrayEntry(m_pairArray, ch, ch2); DelArrayEntry(m_pairArray, ch2, ch); } inline void gnCompare::RemoveContained( const gnSeqC ch, const gnSeqC ch2 ) { DelArrayEntry(m_containArray, ch2, ch); } } // end namespace genome #endif // _gnSeqCompare_h_ libGenome-1.3.1/libGenome/testSourceFactory.cpp0000644002622200470610000001631110647575617016465 00000000000000#ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnSourceFactory.h" #include "libGenome/gnFASSource.h" #include "libGenome/gnDNXSource.h" #include int32 main( int32 argc, char* argv[]) { argc; argv; gnSourceFactory* sf = gnSourceFactory::GetSourceFactory(); // ######################################################## // ## Path // ######################################################## cout << " ***** TEST Path methods ***** " << endl; // add string path = "c:/tmp"; cout << "AddPath( " << path << " )" << endl; if( !sf->AddPath( path ) ) cout << " bad Unable to add path: " << path << endl; else cout << " good Path List Size: " << sf->GetPathListSize() << endl; // insert path = "c:\\temp"; cout << "InsPath( " << path << ", 0 )"<< endl; if( !sf->InsPath( path, 0 ) ) cout << " bad Unable to Insert path at 0: " << path << endl; else cout << " good Path List Size: " << sf->GetPathListSize() << endl; // has path = "c:\\tmp"; cout << "HasPath( " << path << " )" << endl; if( sf->HasPath( path ) ) cout << " good Does have " << path << endl; else cout << " bad Does NOT have " << path << endl; path = "c:\\temp"; cout << "HasPath( " << path << " )" << endl; if( sf->HasPath( path ) ) cout << " bad Does have " << path << endl; else cout << " good Does NOT have " << path << endl; // get cout << "GetPath(0) = " << endl; if( !(sf->GetPath(0).empty()) ) cout << " good" << endl; else cout << " bad" << endl; cout << "GetPath(300)" << endl; if( sf->GetPath(300).empty() ) cout << " good" << endl; else cout << " bad" << endl; // del cout << "DelPath( 0 )" << endl; if( !sf->DelPath( 0 ) ) cout << " bad Unable to delete 0" << endl; else cout << " good Path List Size: " << sf->GetPathListSize() << endl; cout << "DelPath( 0 )" << endl; if( !sf->DelPath( 0 ) ) cout << " bad Unable to delete 0" << endl; else cout << " good Path List Size: " << sf->GetPathListSize() << endl; cout << "DelPath( 0 )" << endl; if( !sf->DelPath( 0 ) ) cout << " good Unable to delete 0" << endl; else cout << " bad Path List Size: " << sf->GetPathListSize() << endl; // ######################################################## // ## Source Class // ######################################################## cout << " ***** TEST Source Class methods ***** " << endl; string extStr = ".fas"; // Set cout << "SetSourceClass( " << extStr << " , gnFASSource )" << endl; gnFASSource fasSource; if( !sf->SetSourceClass( extStr, fasSource ) ) cout << " bad Unable to add " << extStr << " , gnFASSource" << endl; else cout << " good SourceClass List Size: " << sf->GetSourceClassListSize() << endl; // Has cout << "HasSourceClass( " << extStr << " )" << endl; if( sf->HasSourceClass( extStr ) ) cout << " good Does have " << extStr << endl; else cout << " bad Does NOT have " << extStr << endl; extStr = ".seq"; cout << "HasSourceClass( " << extStr << " )" << endl; if( sf->HasSourceClass( extStr ) ) cout << " bad Does have " << extStr << endl; else cout << " good Does NOT have " << extStr << endl; // default cout << "SetDefaultSourceClass( new gnFASSource() )" << endl; if( !sf->SetDefaultSourceClass( fasSource ) ) cout << " bad Cannot set Default Source Class" << endl; else cout << " good DEFAULT source class set" << endl; // Get extStr = ".fas"; cout << "GetSourceClass( " << extStr << " )" << endl; if( sf->GetSourceClass( extStr ) != 0 ) cout << " good Does have " << extStr << endl; else cout << " bad Does NOT have " << extStr << endl; extStr = ".seq"; cout << "GetSourceClass( " << extStr << " )" << endl; if( sf->GetSourceClass( extStr ) != 0 ) cout << " good Does have " << extStr << endl; else cout << " bad Does NOT have " << extStr << endl; // Match string sourceStr = "c:/tests.fas" ; cout << "MatchSourceClass( " << sourceStr << " )" << endl; if( sf->MatchSourceClass( sourceStr ) != 0 ) cout << " good Does match" << endl; else cout << " bad Does NOT match" << endl; sourceStr = "c:/tests.dnx"; cout << "MatchSourceClass( " << sourceStr << " )" << endl; if( sf->MatchSourceClass( sourceStr ) != sf->GetDefaultSourceClass() ) cout << " bad Does match" << endl; else cout << " good Does NOT match" << endl; // Del extStr = ".fas"; cout << "DelSourceClass( " << extStr << " )" << endl; if( !sf->DelSourceClass( extStr ) ) cout << " bad Cannot Delete " << extStr << endl; else cout << " good SourceClass List Size: " << sf->GetSourceClassListSize() << endl; extStr = ".fas"; cout << "DelSourceClass( " << extStr << " )" << endl; if( !sf->DelSourceClass( extStr ) ) cout << " good Cannot Delete " << extStr << endl; else cout << " bad SourceClass List Size: " << sf->GetSourceClassListSize() << endl; // ######################################################## // ## Source // ######################################################## extStr = ".fas"; // Set cout << "SetSourceClass( " << extStr << " , gnFASSource )" << endl; if( !sf->SetSourceClass( extStr, fasSource ) ) cout << " bad Unable to add " << extStr << " , gnFASSource" << endl; else cout << " good SourceClass List Size: " << sf->GetSourceClassListSize() << endl; extStr = ".dnx"; // Set gnDNXSource dnxSource; cout << "SetSourceClass( " << extStr << " , gnDNXSource )" << endl; if( !sf->SetSourceClass( extStr, dnxSource ) ) cout << " bad Unable to add " << extStr << " , gnDNXSource" << endl; else cout << " good SourceClass List Size: " << sf->GetSourceClassListSize() << endl; cout << " ***** TEST Source Class methods ***** " << endl; // add path = "W:\\Developm\\_Data\\_Testing_data\\fas\\"; cout << "AddPath( " << path << " )" << endl; if( !sf->AddPath( path ) ) cout << " bad Unable to add path: " << path << endl; else cout << " good Path List Size: " << sf->GetPathListSize() << endl; // Add sourceStr = "W:/Developm/_Data/_Testing_data/fas/test.fas"; cout << "AddSource( " << sourceStr << ", true )" << endl; if( !sf->AddSource( sourceStr ) ) cout << " Source " << sourceStr << " NOT added" << endl; else cout << " Source List Size: " << sf->GetSourceListSize() << endl; sourceStr = "test.abi"; cout << "AddSource( " << sourceStr << ", true )" << endl; if( !sf->AddSource( sourceStr ) ) cout << " Source " << sourceStr << " NOT added" << endl; else cout << " Source List Size: " << sf->GetSourceListSize() << endl; char bubba[50]; cout << "Opening W:/Developm/_Data/_Testing_data/fas/V13anooz.fas...\n"; gpSourceSeq *asplundh = new gpSourceSeq("W:/Developm/_Data/_Testing_data/fas/test.fas"); cout << "Reading some bases.\n"; string mystring = asplundh->ToString(130, 2480); cout << mystring << "\n"; cout << "If that worked then congratulations! You're one step closer than you realized.\n"; cin >> bubba; delete asplundh; // test out DNX cout << "Opening W:/Developm/_Data/_Testing_data/fas/deenex.dnx...\n"; asplundh = new gpSourceSeq("W:/Developm/_Data/_Testing_data/fas/deenex.dnx"); cout << "Reading some bases.\n"; mystring = asplundh->ToString(); cout << mystring << "\n"; cout << "If that worked then congratulations! You're one step closer than you realized.\n"; cin >> bubba; }libGenome-1.3.1/libGenome/gnFastTranslator.h0000644002622200470610000000610310647575617015734 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnFastTranslator.h // Purpose: Fast translator for all Sequences // Description: Caches translations of each possible sequence in a tree // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnFastTranslator_h_ #define _gnFastTranslator_h_ #include "libGenome/gnDefs.h" #include #include #include #include "libGenome/gnClone.h" #include "libGenome/gnBaseFilter.h" #include "libGenome/gnTranslator.h" namespace genome { class GNDLLEXPORT gnFastTranslator : public gnBaseFilter { public: static const gnFastTranslator *ProteinDNATranslator(); static const gnFastTranslator *DNAProteinTranslator(); enum gnTranslatorType{ ProteinDNATranslatorType, DNAProteinTranslatorType, }; gnFastTranslator(); gnFastTranslator( gnTranslatorType t_type ); gnFastTranslator( const gnFastTranslator& sf ); gnFastTranslator& operator= (const gnFastTranslator& sf); gnFastTranslator* Clone() const; /** * Queries the specified gnTranslator for every possible combination translation * of the characters specified in the inputs std::string. An input_width may be specified * so that every possible combination of "input_width" characters in "inputs" will be * cached. This is useful for DNA to protein translations, for example. * @param tranny The gnTranslator to cache. * @param inputs The characters to cache from tranny. * @param input_width The number of characters in each query to make to tranny. */ virtual void CacheTranslator(const gnTranslator* tranny, std::string inputs, const gnSeqI input_width); // gnSeqC virtual gnSeqC Filter( const gnSeqC ch ) const; virtual void Filter( gnSeqC** seq, gnSeqI& len ) const; // std::string virtual void Filter( std::string &seq ) const; // Default gnSeqC void SetDefaultChar( const gnSeqC ch1 ); gnSeqC GetDefaultChar() const; void UseDefaultChar( const boolean use = true); // fill map void SetPair( const std::string& ch1, const std::string& ch2 ); void RemovePair( const std::string& ch ); private: void CreateProteinDNATranslator(); void CreateDNAProteinTranslator(); //map an input std::string to an output std::string std::map m_transCache; const gnTranslator * m_translator; boolean use_default; gnSeqC m_defaultChar; };//class gnFastTranslator inline gnFastTranslator* gnFastTranslator::Clone() const { return new gnFastTranslator(*this); } inline void gnFastTranslator::SetDefaultChar( const gnSeqC ch1 ) { m_defaultChar = ch1; use_default = true; } inline gnSeqC gnFastTranslator::GetDefaultChar() const { return m_defaultChar; } inline void gnFastTranslator::UseDefaultChar(const boolean use) { use_default = use; } } // end namespace genome #endif // _gnFastTranslator_h_ libGenome-1.3.1/libGenome/gnContigSpec.cpp0000644002622200470610000000434510647575617015364 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnContigSpec.cpp // Purpose: Abstract Contig Spec class // Description: Defines an interface for contig specs // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnContigSpec.h" #include "libGenome/gnFilter.h" using namespace std; namespace genome { void gnContigSpec::CropStart( gnSeqI cropLen ){ m_start = m_reverseComplement ? (GetSourceLength() + m_start - cropLen) % GetSourceLength() : (m_start + cropLen) % GetSourceLength(); m_length -= cropLen; return; } void gnContigSpec::CropEnd( gnSeqI cropLen ){ m_length -= cropLen; } void gnContigSpec::SetReverseComplement( const boolean value ) { //translate coordinates if revComp has changed. if((m_reverseComplement != value) && (m_length > 0)) m_start = (m_start + m_length) % GetSourceLength(); m_reverseComplement = value; } boolean gnContigSpec::SeqRead(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen, const uint32 contigI ) const{ boolean success; bufLen = bufLen < m_length - start? bufLen : m_length - start; //trim the read down to size. gnSeqI readable = bufLen; gnSeqI read_start = start; // coordinate translation if(contigI == ALL_CONTIGS) read_start = m_reverseComplement ? (m_start - start - readable + GetSourceLength()) % GetSourceLength() : start + m_start; success = Read(read_start, buf, readable); if(m_circular){ gnSeqI beginread = bufLen - readable; //read whatever couldn't be read before read_start = m_reverseComplement ? (m_start - readable + GetSourceLength()) % GetSourceLength() : m_start; success = Read(read_start , buf + readable, beginread); readable += beginread; } bufLen = readable; if(m_reverseComplement) gnFilter::DNAComplementFilter()->ReverseFilter(&buf, bufLen); return success; } void gnContigSpec::Clear(){ gnBaseSpec::Clear(); m_start = 0; m_length = 0; m_SourceContigIndex = ALL_CONTIGS; } } // end namespace genome libGenome-1.3.1/libGenome/gnStringSpec.cpp0000644002622200470610000000475711003030307015357 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnStringSpec.cpp // Purpose: implements gnContigSpec for strings // Description: stores sequence in memory // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnStringSpec.h" #include #include using namespace std; namespace genome { gnStringSpec::gnStringSpec() { gnContigSpec::Clear(); } gnStringSpec::gnStringSpec( const string& m_string, gnSeqI start, gnSeqI endI, boolean revComp) { m_seqString = m_string; m_start = start; gnSeqI actual_len = m_seqString.length(); //reverse comp has the end b.p. first, then start. switch them. m_start = revComp ? endI : start; gnSeqI actual_end = revComp ? start : endI; //trim start and end down if they are too big. actual_end = actual_end < actual_len ? actual_end : actual_len -1; m_start = m_start < actual_len ? m_start : actual_len - 1; if(actual_len == 0) m_start = 0; //if start is after end, we're using a circular sequence. m_circular = m_start > actual_end ? true : false; //if circular, the length will be different. m_length = m_circular ? (actual_len - m_start) + actual_end : actual_end - m_start + 1; m_reverseComplement = revComp; m_SourceContigIndex = ALL_CONTIGS; } gnStringSpec::gnStringSpec( const gnStringSpec& s ) { m_seqString = s.m_seqString; m_sourceName = s.m_sourceName; m_name = s.m_name; m_start = s.m_start; m_length = s.m_length; m_reverseComplement = s.m_reverseComplement; m_circular = s.m_circular; m_SourceContigIndex = s.m_SourceContigIndex; } gnStringSpec::~gnStringSpec() { Clear(); } void gnStringSpec::Clear() { gnContigSpec::Clear(); m_seqString = ""; } gnStringSpec* gnStringSpec::CloneRange( const gnSeqI startI, const gnSeqI len ) const{ gnStringSpec* destSpec = new gnStringSpec(); destSpec->m_seqString = m_seqString.substr(m_start + startI, len); destSpec->m_sourceName = m_sourceName; destSpec->m_name = m_name; destSpec->m_start = 0; destSpec->m_length = destSpec->m_seqString.length(); destSpec->m_reverseComplement = m_reverseComplement; destSpec->m_circular = m_circular; destSpec->m_SourceContigIndex = m_SourceContigIndex; return destSpec; } } // end namespace genome libGenome-1.3.1/libGenome/testSourceSeq.cpp0000644002622200470610000000411110647575617015601 00000000000000#ifdef HAVE_CONFIG_H #include "config.h" #endif #include #include "libGenome/gnSequence.h" #include #include "libGenome/gnFilter.h" #include "libGenome/gnFASSource.h" int32 main( int32 argc, char* argv[]) { argc; argv; gnSequence gps; string filename; cout << "Enter a filename to compute a base composition.\n"; cin >> filename; cout << "Opening " + filename + "\n"; gps.LoadSource(filename); cout << "Genome Length: " << gps.length() << " in " << gps.contigListLength() << " contigs\n"; cout << "Give a file name to output composition data: "; string outfilename; cin >> outfilename; ofstream outfile(outfilename.c_str(), ios::out); outfile << "Contig_Name A_count C_count G_count T_count\n"; ofstream ambig("ambigs.txt", ios::out); gnSeqI a_total = 0, c_total = 0, g_total = 0, t_total = 0, ambiguities = 0; for(int contigI=0; contigI < gps.contigListLength(); contigI++){ gnSeqI seqLength = gps.contig(contigI).length(); gnSeqC *bases = new gnSeqC[seqLength]; gps.contig(contigI).ToArray(bases, seqLength); string contigName = gps.contigName(contigI); gnSeqI a = 0, c = 0, g = 0, t = 0; for(int i=0; i < seqLength; i++){ if((bases[i] == 'a')||(bases[i] == 'A')) a++; else if((bases[i] == 'c')||(bases[i] == 'C')) c++; else if((bases[i] == 'g')||(bases[i] == 'G')) g++; else if((bases[i] == 't')||(bases[i] == 'T')) t++; else{ ambiguities++; ambig << bases[i]; } } delete[] bases; outfile << contigName << " " << a << " " << c << " " << g << " " << t << "\n"; a_total += a; c_total += c; g_total += g; t_total += t; } outfile.close(); ambig.close(); cout << "Enter a file for me to write to: "; cin >> outfilename; gnFASSource::Write(gps, outfilename); cout << "A: " << a_total << "\nC: " << c_total << "\nG: " << g_total << "\nT: " << t_total << "\n"; cout << "Ambiguities: " << ambiguities << "\n"; cout << "For a total of: " << a_total + c_total + g_total + t_total + ambiguities << "\n"; cout << "Base comp. completed. Results are in " << outfilename << "\n"; char bubba[50]; cin >> bubba; }libGenome-1.3.1/libGenome/gnFilter.h0000644002622200470610000001313110647575617014211 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnFilter.h // Purpose: Filter for all Sequences // Description: Filters sequences, translates, reverse complement, converts // additions, etc. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnSeqFilter_h_ #define _gnSeqFilter_h_ #include #include "libGenome/gnClone.h" #include "libGenome/gnDefs.h" #include "libGenome/gnBaseFilter.h" namespace genome { const gnSeqC NO_REVCOMP_CHAR = 0; class GNDLLEXPORT gnFilter : public gnBaseFilter { public: static const gnFilter *alphabetCharacterFilter(); static const gnFilter *numberCharacterFilter(); static const gnFilter *proteinSeqFilter(); static const gnFilter *basicDNASeqFilter(); static const gnFilter *fullDNASeqFilter(); static const gnFilter *basicRNASeqFilter(); static const gnFilter *fullRNASeqFilter(); static const gnFilter *DNAtoRNAFilter(); static const gnFilter *RNAtoDNAFilter(); static const gnFilter *DNAComplementFilter(); static const gnFilter *RNAComplementFilter(); enum gnFilterType{ alphabetCharacterFilterType, numberCharacterFilterType, proteinSeqFilterType, basicDNASeqFilterType, fullDNASeqFilterType, basicRNASeqFilterType, fullRNASeqFilterType, DNAtoRNAFilterType, RNAtoDNAFilterType, DNAComplementFilterType, RNAComplementFilterType }; public: gnFilter(); /** * Creates a gnFilter for a predefined filter type. * Used by the static sequence constructors to avoid the "static initialization order fiasco" * @param f_type The type of filter to create. * @see gnFilterType */ gnFilter( const gnFilterType f_type ); gnFilter( const gnSeqC defaultChar, const gnSeqC rdefaultChar ); gnFilter( const gnFilter& sf ); ~gnFilter(); gnFilter* Clone() const; // gnSeqC boolean IsValid( const gnSeqC ch ) const; gnSeqC MakeValid( const gnSeqC ch ) const; gnSeqC Filter( const gnSeqC ch ) const; // gnSeqC[] /** IsValid() scans the supplied character array for invalid characters. * @param seq The sequence to scan. This is a generic character array. * @param len The length of the sequence to scan. * @return The index of the first invalid character, or len if none exists */ uint32 IsValid( const gnSeqC* seq, const uint32 len ) const; void MakeValid( gnSeqC* seq, const uint32 len ) const; void Filter( gnSeqC** seq, gnSeqI& len ) const; void ReverseFilter( gnSeqC** seq, gnSeqI& len ) const; // std::string uint32 IsValid( const std::string &seq ) const; void MakeValid( std::string &seq ) const; void Filter( std::string &seq ) const; void ReverseFilter( std::string &seq ) const; // Default gnSeqC void SetDefaultChar( const gnSeqC ch1, const gnSeqC ch2 ); gnSeqC GetDefaultChar() const; gnSeqC GetRDefaultChar() const; // fill map void SetSingle( const gnSeqC ch ); void SetPair( const gnSeqC ch1, const gnSeqC ch2 ); boolean RemovePair( const gnSeqC ch ); boolean RemoveSingle( const gnSeqC ch ); // standard filters private: void CreateAlphabetCharacterFilter(); void CreateNumberCharacterFilter(); void CreateProteinFilter(); void CreateBasicDNAFilter(); void CreateFullDNAFilter(); void CreateBasicRNAFilter(); void CreateFullRNAFilter(); void CreateDNAtoRNAFilter(); void CreateRNAtoDNAFilter(); void CreateDNAComplementFilter(); void CreateRNAComplementFilter(); gnSeqC m_pairArray[GNSEQC_MAX]; gnSeqC m_defaultChar; gnSeqC m_rDefaultChar; };//class gnFilter inline gnFilter* gnFilter::Clone() const { return new gnFilter(*this); } // gnSeqC inline boolean gnFilter::IsValid( const gnSeqC ch ) const { return m_pairArray[(uint)ch] != NO_REVCOMP_CHAR; } inline gnSeqC gnFilter::MakeValid( const gnSeqC ch ) const { return (m_pairArray[(uint)ch] != NO_REVCOMP_CHAR? ch: m_defaultChar); } inline gnSeqC gnFilter::Filter( const gnSeqC ch ) const { return m_pairArray[(uint)ch] != NO_REVCOMP_CHAR ? m_pairArray[(uint)ch] : m_defaultChar; } // gnSeqC[] inline uint32 gnFilter::IsValid( const gnSeqC* seq, const uint32 len ) const { for( uint32 i=0; i < len ; ++i ) { if( !IsValid( seq[i] ) ) return i; } return len; } inline void gnFilter::MakeValid( gnSeqC* seq, const uint32 len ) const { for( uint32 i=0; i < len ; ++i ) { seq[i] = MakeValid( seq[i] ); } } // std::string inline uint32 gnFilter::IsValid( const std::string &seq ) const { return IsValid( (gnSeqC*)seq.data(), seq.length() ); } inline void gnFilter::MakeValid( std::string &seq ) const { MakeValid( (gnSeqC*)seq.data(), seq.length() ); } // Default gnSeqC inline void gnFilter::SetDefaultChar( const gnSeqC ch1, const gnSeqC ch2 ) { m_defaultChar = ch1; m_rDefaultChar = ch2; } inline gnSeqC gnFilter::GetDefaultChar() const { return m_defaultChar; } inline gnSeqC gnFilter::GetRDefaultChar() const { return m_rDefaultChar; } // fill map inline void gnFilter::SetSingle( const gnSeqC ch ) { m_pairArray[(uint)ch] = ch; } inline void gnFilter::SetPair( const gnSeqC ch1, const gnSeqC ch2 ) { m_pairArray[(uint)ch1] = ch2; // m_pairArray[(uint)ch2] = ch1; } inline boolean gnFilter::RemovePair( const gnSeqC ch ) { m_pairArray[(uint)ch] = NO_REVCOMP_CHAR; // m_pairArray[(uint)tmp] = NO_REVCOMP_CHAR; return true; } inline boolean gnFilter::RemoveSingle( const gnSeqC ch ) { m_pairArray[(uint)ch] = NO_REVCOMP_CHAR; return true; } } // end namespace genome #endif // __blSeqFilter_h__ libGenome-1.3.1/libGenome/gnFileSource.h0000644002622200470610000000430611026443220015000 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnFileSource.h // Purpose: Implements gnBaseSource for .File files // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnFileSource_h_ #define _gnFileSource_h_ #include "libGenome/gnDefs.h" #include #include #include "libGenome/gnBaseSource.h" #include "libGenome/gnFileContig.h" #include "libGenome/gnException.h" namespace genome { /** * gnFileSource is a standard interface to all file based sources of genetic information. * All file source classes are derived from this class. */ class GNDLLEXPORT gnFileSource : public gnBaseSource { public: gnFileSource(); gnFileSource(const gnFileSource& gnfs); virtual ~gnFileSource(){} virtual gnFileSource* Clone() const = 0; // Open, Close virtual void Open( std::string openString ); virtual void Open(); virtual void Close(); virtual std::string GetOpenString() const ; // Filter virtual const gnFilter* GetFilter() const ; virtual void SetFilter( gnFilter* filter ); virtual boolean Read( const uint64 pos, char* buf, gnSeqI& bufLen ); /** * Returns a pointer to the file contig corresponding to contigI or * null if none exists. */ virtual gnFileContig* GetFileContig( const uint32 contigI ) const = 0; protected: void DetermineNewlineType(); std::string m_openString; std::ifstream m_ifstream; const gnFilter* m_pFilter; gnNewlineType m_newlineType; uint32 m_newlineSize; private: virtual boolean ParseStream( std::istream& fin ) = 0; };// class gnFileSource inline std::string gnFileSource::GetOpenString( ) const { return m_openString; } // Filter inline const gnFilter* gnFileSource::GetFilter() const { return m_pFilter; } inline void gnFileSource::SetFilter( gnFilter* filter ) { if(filter == NULL){ Throw_gnEx(NullPointer()); } m_pFilter = filter; } } // end namespace genome #endif // _gnFileSource_h_ libGenome-1.3.1/libGenome/gnBaseSource.h0000644002622200470610000001341210647575617015021 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnBaseSource.h // Purpose: Abstract source class // Description: Basic interface to all source objects // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnBaseSource_h_ #define _gnBaseSource_h_ #include "libGenome/gnDefs.h" #include #include "libGenome/gnClone.h" namespace genome { class gnGenomeSpec; class gnFilter; /** * gnBaseSource defines a standard interface for derived classes to * provide access to file, database, and network sources of genetic data. * First the data source is opened and parsed, using the open() function. * The source class then creates and a gnGenomeSpec containing references * to its sequence data. The gnGenomeSpec can then be used by gnSequence * to give programmer friendly access to the sequence data. */ class GNDLLEXPORT gnBaseSource : public gnClone { public: gnBaseSource(){} /** * Destructor, frees memory used by this source class. */ virtual ~gnBaseSource(){} virtual gnBaseSource* Clone() const = 0; /** * Opens the source given in "openString" for reading. * @param openString The name of the source (file, network URL, or * database) to open. * @throws Will throw a FileNotOpened exception if the file was not found * or was not accessible. Will propagate a FileUnreadable exception if the * file format was invalid. */ virtual void Open( std::string openString ) = 0; /** * Opens this source for reading. * @throws Will throw a FileNotOpened exception if the file was not found * or was not accessible. */ virtual void Open() = 0; /** * Closes the file or connection this source is reading from. * @throws IOStreamError if an error occurs closing the file. */ virtual void Close() = 0; /** * Get the location of the source that is being used. * @return The location std::string describing this source, usually a file * name. */ virtual std::string GetOpenString() const = 0; /** * Get the number of sequence contigs in this source. * @return The number of contigs in this source. */ virtual uint32 GetContigListLength() const = 0; /** * Looks for a contig by name. * Returns true if it finds the contig, otherwise false. * @param name The name of the contig to look for. * @return True if the named contig exists, false otherwise. */ virtual boolean HasContig( const std::string& name ) const = 0; /** * Get a contig index by name. * If the source does not contain a contig by the specified name * GetContigID returns UINT32_MAX. * @param name The name of the contig to look for. * @return The index of the named contig or UINT32_MAX. */ virtual uint32 GetContigID( const std::string& name ) const = 0; /** * Get the name of the specified contig. * Returns an empty std::string if the specified contig is out of range. * @param i The index of the contig or ALL_CONTIGS. * @return The name of the contig or an empty std::string. */ virtual std::string GetContigName( const uint32 i ) const = 0; /** * Get the total number of base pairs in the specified contig. * @param i The index of the contig or ALL_CONTIGS. * @return The length in base pairs of the specified contig. */ virtual gnSeqI GetContigSeqLength( const uint32 i ) const = 0; /** * Get the filter currently being used to filter unwanted characters out of read sequences. * @return A pointer to the gnFilter currently in use. */ virtual const gnFilter* GetFilter() const = 0; /** * Set the filter that will be used to filter unwanted characters out of the sequence data. * @param filter The filter to remove unwanted characters from the sequence. * @throws NullPointer is thrown if the specified filter pointer is null. */ virtual void SetFilter( gnFilter* filter ) = 0; /** * Gets raw input from this source. * Read will attempt to read "bufLen" bytes starting at "pos" directly from the source. * It stores the data in "buf", and returns the actual number of bytes read in bufLen. * Read will return false if a serious error occurs. * @param pos The position in the file to start reading. * @param buf The character array to store data into. * @param bufLen The number of bytes to read. * @return True if the operation was successful. */ virtual boolean Read( const uint64 pos, char* buf, gnSeqI& bufLen) = 0; /** * Gets sequence data from this source. * SeqRead will attempt to read "bufLen" base pairs starting at "start", an offset into the sequence. * Reading inside a specific contig can be accomplished by supplying the "contigI" parameter with * a valid contig index. * SeqRead stores the sequence data in "buf" and returns the actual number of bases read in "bufLen". * SeqRead will return false if a serious error occurs. * @param start The base pair to start reading at. * @param buf The character array to store base pairs into. * @param bufLen The number of base pairs to read. * @param contigI The index of the contig to read or ALL_CONTIGS by default. * @return True if the operation was successful. */ virtual boolean SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI=ALL_CONTIGS ) = 0; /** * Get the annotated sequence data as a gnGenomeSpec. * GetSpec returns a gnGenomeSpec which contains the sequence, header, * and feature data contained by this source. * @return The annotated sequence data. */ virtual gnGenomeSpec *GetSpec() const = 0; private: };// class gnBaseSource } // end namespace genome #endif // _gnBaseSource_h_ libGenome-1.3.1/libGenome/gnSourceHeader.h0000644002622200470610000000724010647575617015341 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnSourceHeader.h // Purpose: Source Header class // Description: Provides an interface for Headers on disk. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnSourceHeader_h_ #define _gnSourceHeader_h_ #include "libGenome/gnDefs.h" #include #include "libGenome/gnBaseHeader.h" #include "libGenome/gnBaseSource.h" #include namespace genome { /** * gnSourceHeader is used to store a sequence header which resides in another source. * gnSourceHeaders are created by gnSEQSource and other sources and placed into a spec. */ class GNDLLEXPORT gnSourceHeader : public gnBaseHeader { public: /** * Empty constructor. */ gnSourceHeader(); /** * Constructor, records the header's name and byte offset in the source. * @param source The source which contains the header. * @param name The name of the header. * @param begin The offset into the source where the header starts. * @param length The length of the header. */ gnSourceHeader( gnBaseSource* source, const std::string& name, const uint32 begin, const uint32 length ); /** * Copy constructor. * @param s The gnSourceHeader to copy. */ gnSourceHeader( const gnSourceHeader& s ); /** * Destructor, frees memory. */ ~gnSourceHeader(); gnSourceHeader* Clone() const; std::string GetHeader() const; std::string GetHeaderName() const; /// Not implemented, use gnStringHeader. // void SetHeader(const std::string& header){}; /// Not implemented, use gnStringHeader. // void SetHeaderName(const std::string& name){}; uint32 GetLength() const; /** * Get the header's start position within the source. * @return The byte offset of the header's start position. */ uint32 GetHeaderStart() const; /** * Get the header's start position and length within the source. * @return The header start position and length as a pair. */ std::pair GetHeaderLoc() const; /** * Set the header's start position within the source. * @param start The header start position. */ void SetHeaderStart(const uint32 start); /** * Get the header's length within the source. * @param length The header length. */ void SetHeaderLength(const uint32 length); /** * Set the header's start position and length within the source. * @param startLen The header start position and length as a pair. */ void SetHeaderLoc(const std::pair startLen); private: std::string m_name; uint32 m_start, m_length; gnBaseSource *m_source; }; //class gnSourceHeader inline gnSourceHeader* gnSourceHeader::Clone() const{ return new gnSourceHeader(*this); } inline std::string gnSourceHeader::GetHeaderName() const{ return m_name; } inline uint32 gnSourceHeader::GetHeaderStart() const{ return m_start; } inline uint32 gnSourceHeader::GetLength() const{ return m_length; } inline std::pair gnSourceHeader::GetHeaderLoc() const{ std::pair p; p.first = m_start; p.second = m_length; return p; } inline void gnSourceHeader::SetHeaderStart(const uint32 start){ m_start = start; } inline void gnSourceHeader::SetHeaderLength(const uint32 length){ m_length = length; } inline void gnSourceHeader::SetHeaderLoc(const std::pair startLen){ m_start = startLen.first; m_length = startLen.second; } } // end namespace genome #endif // _gnSourceHeader_h_ libGenome-1.3.1/libGenome/gnExceptionCode.h0000644002622200470610000000563110647575617015523 00000000000000#ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnExceptionCode_h_ #define _gnExceptionCode_h_ #include "libGenome/gnDefs.h" #include namespace genome { class GNDLLEXPORT gnExceptionCode{ public: gnExceptionCode(uint32 code, const char* name); boolean operator==(gnExceptionCode& gnec); boolean operator!=(gnExceptionCode& gnec); uint32 GetInt(){ return m_code; } std::string GetName(){ return m_name; } private: gnExceptionCode(); //prevent instances from being copied gnExceptionCode(const gnExceptionCode& gnec); gnExceptionCode& operator=(gnExceptionCode& gnec); uint32 m_code; std::string m_name; }; inline gnExceptionCode::gnExceptionCode(uint32 code, const char* name) : m_code(code), m_name(name) {} inline boolean gnExceptionCode::operator==(gnExceptionCode& gnec){ return m_code == gnec.m_code; } inline boolean gnExceptionCode::operator!=(gnExceptionCode& gnec){ return m_code != gnec.m_code; } GNDLLEXPORT uint32& GetNewExceptionCode(); inline uint32& GetNewExceptionCode(){ //static initializer is called only once static uint32 new_code = 0; //increment it each time the function is called new_code++; return new_code; }; //Creates an exception code with the given name //currently it chooses a unique id for each exception //this may have to be changed in the future if the integer //associated with each exception must be the same across compiles #define CREATE_EXCEPTION(E_NAME) \ inline \ static genome::gnExceptionCode& E_NAME(){ \ static genome::gnExceptionCode* m_excp = new genome::gnExceptionCode(genome::GetNewExceptionCode(), #E_NAME); \ return *m_excp; \ } //define a bunch of exception codes //this must be done in a header file to work correctly /** * Thrown when a generic array index is too large or otherwise invalid */ CREATE_EXCEPTION(IndexOutOfBounds) /** * Thrown when a sequence index references an invalid coordinate */ CREATE_EXCEPTION(SeqIndexOutOfBounds) /** * Thrown when a fragment index references an invalid fragment */ CREATE_EXCEPTION(FragmentIndexOutOfBounds) /** * Thrown when a contig index references an invalid contig */ CREATE_EXCEPTION(ContigIndexOutOfBounds) /** * Thrown when a header index references an invalid header */ CREATE_EXCEPTION(HeaderIndexOutOfBounds) /** * Thrown when a spec index references an invalid spec */ CREATE_EXCEPTION(SpecIndexOutOfBounds) /** * Thrown when a feature index references an invalid feature */ CREATE_EXCEPTION(FeatureIndexOutOfBounds) /** * Thrown when a file can't be opened */ CREATE_EXCEPTION(FileNotOpened) /** * Thrown when a URL can't be opened */ CREATE_EXCEPTION(URLNotFound) /** * Thrown when a file's data is corrupt or unreadable */ CREATE_EXCEPTION(FileUnreadable) /** * Thrown when an operation on a stream fails */ CREATE_EXCEPTION(IOStreamFailed) /** * Thrown when an invalid pointer is given */ CREATE_EXCEPTION(NullPointer) } // end namespace genome #endif //_gnExceptionCode_h_ libGenome-1.3.1/libGenome/gnSourceQualifier.cpp0000644002622200470610000000264610647575617016432 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnSourceQualifier.cpp // Purpose: Source Qualifier class // Description: Provides an interface for Qualifier on disk. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include #include "libGenome/gnBaseSource.h" #include "libGenome/gnSourceQualifier.h" using namespace std; namespace genome { gnSourceQualifier::gnSourceQualifier(){ m_source = NULL; m_name = ""; m_start = 0; m_length = 0; } gnSourceQualifier::gnSourceQualifier( gnBaseSource* source, string& name, uint32 begin, uint32 length ){ m_source = source; m_name = name; m_start = begin; m_length = length; } gnSourceQualifier::gnSourceQualifier(const gnSourceQualifier& s){ m_source = s.m_source; m_start = s.m_start; m_length = s.m_length; m_name = string(s.m_name); } gnSourceQualifier::~gnSourceQualifier(){ }; string gnSourceQualifier::GetValue() const{ Array array_buf( m_length ); char* buf = array_buf.data; gnSeqI readBytes = m_length; m_source->Read(m_start, buf, readBytes); string rval(buf, readBytes); return rval; } } // end namespace genome libGenome-1.3.1/libGenome/gnGenomeSpec.h0000644002622200470610000000752410647575617015022 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnGenomeSpec.h // Purpose: abstract Spec class // Description: Genome level spec class // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnGenomeSpec_h_ #define _gnGenomeSpec_h_ #include "libGenome/gnDefs.h" #include #include #include "libGenome/gnClone.h" #include "libGenome/gnBaseFeature.h" #include "libGenome/gnBaseHeader.h" #include "libGenome/gnMultiSpec.h" #include "libGenome/gnFragmentSpec.h" #include "libGenome/gnException.h" namespace genome { /** * This class contains references to the sequence data, annotation, * and other related header data for an organism's genome. The genome * is organized into a list of sequence fragments (specs), a list of * features, and a list of headers. */ class GNDLLEXPORT gnGenomeSpec : public gnMultiSpec< gnFragmentSpec > { public: gnGenomeSpec(); /** * Copy constructor. * @param s the gnGenomeSpec to copy. */ gnGenomeSpec( const gnGenomeSpec& s); /** * Destructor, frees memory. */ virtual ~gnGenomeSpec(); // Clone virtual gnGenomeSpec* Clone() const; virtual void Clear(); // Base Spec stuff virtual void SetReverseComplement( const boolean value ); //Multispec stuff /* virtual uint32 GetSpecListLength() const; virtual gnFragmentSpec* GetSpec( const uint32 i ) const; virtual gnFragmentSpec* GetSpecByBase( const gnSeqI baseI ) const; virtual void AddSpec( gnBaseSpec* spec, const uint32 i = UINT32_MAX ); virtual void RemoveSpec( uint32 i ); */ virtual void MergeFragments( const uint32 startC, const uint32 endC); virtual uint32 AddFeature( gnBaseFeature* feat ); virtual uint32 GetFeatureListLength() const; virtual gnBaseFeature* GetFeature( const uint32 i ) const; virtual void GetContainedFeatures(const gnLocation& lt, std::vector& feature_vector, std::vector& index_vector) const; virtual void GetIntersectingFeatures(const gnLocation& lt, std::vector& feature_vector, std::vector& index_vector) const; virtual void GetBrokenFeatures(const gnLocation& lt, std::vector& feature_vector) const; virtual void RemoveFeature( const uint32 i ); /** * Copies a specified range of bases and returns a pointer to * the resulting gnGenomeSpec. You must delete the copy when you * are finished with it. * @param startI The first base pair to copy * @param len The length of the piece to copy * @return A copy of the gnGenomeSpec containing only the specified bases */ virtual gnGenomeSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const; protected: // std::vector m_SpecList; }; // class gnGenomeSpec inline gnGenomeSpec* gnGenomeSpec::Clone() const{ return new gnGenomeSpec(*this); } /* inline uint32 gnGenomeSpec::GetSpecListLength() const{ return m_SpecList.size(); } inline gnFragmentSpec* gnGenomeSpec::GetSpec( const uint32 i ) const{ if(i < m_SpecList.size()) return m_SpecList[i]; Throw_gnEx(FragmentIndexOutOfBounds()); } inline gnFragmentSpec* gnGenomeSpec::GetSpecByBase( const gnSeqI baseI ) const{ return m_SpecList[GetSpecIndexByBase(baseI)]; } inline void gnGenomeSpec::AddSpec( gnBaseSpec* spec, const uint32 i ){ uint32 index = i == UINT32_MAX ? m_SpecList.size() : i; if(index <= m_SpecList.size()){ m_SpecList.insert(m_SpecList.begin() + index, (gnFragmentSpec*)spec); } } inline void gnGenomeSpec::RemoveSpec( uint32 i ){ if(i < GetSpecListLength()){ m_SpecList.erase(m_SpecList.begin() + i); } } */ } // end namespace genome #endif // _gnGenomeSpec_h_ libGenome-1.3.1/libGenome/gnCompare.cpp0000644002622200470610000004525711003030307014664 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnCompare.cpp // Purpose: Coparator for all Sequences // Description: Compares sequences // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnCompare.h" #include // public: using namespace std; namespace genome { const gnCompare *gnCompare::ProteinSeqCompare(){ const static gnCompare* t_comp = new gnCompare(ProteinSeqCompareType); return t_comp; } const gnCompare *gnCompare::DNASeqCompare(){ const static gnCompare* t_comp = new gnCompare(DNASeqCompareType); return t_comp; } const gnCompare *gnCompare::RNASeqCompare(){ const static gnCompare* t_comp = new gnCompare(RNASeqCompareType); return t_comp; } gnCompare::gnCompare( const gnCompareType c_type ){ for( gnSeqC i = 0; i < GNSEQC_MAX; ++i ){ m_pairArray[i] = new gnSeqC[1]; m_pairArray[i][0] = 0; m_containArray[i] = new gnSeqC[1]; m_containArray[i][0] = 0; } switch(c_type){ case ProteinSeqCompareType: CreateProteinComparator(); break; case DNASeqCompareType: CreateDNAComparator(); break; case RNASeqCompareType: CreateRNAComparator(); break; } } boolean gnCompare::Contains( gnSeqC ch, gnSeqC ch2, boolean case_sensitive) const { if(!case_sensitive){ ch = toupper(ch); ch2 = toupper(ch2); } if(strchr(m_containArray[ch], ch2) == 0) return false; return true; } boolean gnCompare::Contains( const gnSeqC* seq, const gnSeqC* seq2, const uint32 len, boolean case_sensitive ) const{ for( uint32 i=0; i < len ; ++i ) if(!Contains(seq[i], seq2[i], case_sensitive)) return false; return true; } boolean gnCompare::Contains( const string &seq, const string &seq2, boolean case_sensitive) const { gnSeqI shorter_len = seq.length() < seq2.length() ? seq.length() : seq2.length(); return Contains( (gnSeqC*)seq.data(), (gnSeqC*)seq2.data(), shorter_len, case_sensitive ); } // public: gnCompare::gnCompare() { for( gnSeqC i = 0; i < GNSEQC_MAX; ++i ){ m_pairArray[i] = new gnSeqC[1]; m_pairArray[i][0] = 0; m_containArray[i] = new gnSeqC[1]; m_containArray[i][0] = 0; } } /* gnCompare::gnCompare( const gnCompare &sf ) { m_name = sf.m_name; for( gnSeqC i = 0; i < GNSEQC_MAX; ++i ){ m_pairArray[i] = new gnSeqC[strlen(sf.m_pairArray[i])+1]; strcpy(m_pairArray[i], sf.m_pairArray[i]); m_containArray[i] = new gnSeqC[strlen(sf.m_containArray[i])+1]; strcpy(m_containArray[i], sf.m_containArray[i]); } } */ gnCompare::~gnCompare() { for( gnSeqC i = 0; i < GNSEQC_MAX; ++i ){ delete[] m_pairArray[i]; delete[] m_containArray[i]; } } void gnCompare::AddArrayEntry( gnSeqC *array[GNSEQC_MAX], const gnSeqC ch, const gnSeqC ch2){ uint32 curlen = strlen(array[ch]); gnSeqC* tmp = new gnSeqC[curlen + 2]; strcpy(tmp, array[ch]); tmp[curlen] = ch2; tmp[curlen+1] = 0; delete[] array[ch]; array[ch] = tmp; } void gnCompare::DelArrayEntry( gnSeqC *array[GNSEQC_MAX], const gnSeqC ch, const gnSeqC ch2){ //check that the pair exists gnSeqC* loc = strchr(m_containArray[ch], ch2); uint32 count = 0; while(loc != NULL){ count++; loc = strchr(loc+1, ch2); } if(count == 0) return; uint32 curlen = strlen(array[ch]); gnSeqC* tmp = new gnSeqC[curlen - count]; uint32 tmppos = 0; for(uint32 i=0; i < curlen; i++) if(m_containArray[ch][i] != ch2) tmp[tmppos++] = m_containArray[ch][i]; tmp[tmppos] = 0; delete[] array[ch]; array[ch] = tmp; } void gnCompare::CreateProteinComparator() { SetName( "Protein Comparator" ); SetSingle( 'A' ); SetSingle( 'R' ); SetSingle( 'N' ); SetSingle( 'D' ); SetSingle( 'C' ); SetSingle( 'Q' ); SetSingle( 'E' ); SetSingle( 'G' ); SetSingle( 'H' ); SetSingle( 'I' ); SetSingle( 'L' ); SetSingle( 'K' ); SetSingle( 'M' ); SetSingle( 'F' ); SetSingle( 'P' ); SetSingle( 'S' ); SetSingle( 'T' ); SetSingle( 'W' ); SetSingle( 'Y' ); SetSingle( 'V' ); SetSingle( '.' ); SetSingle( 'a' ); SetSingle( 'r' ); SetSingle( 'n' ); SetSingle( 'd' ); SetSingle( 'c' ); SetSingle( 'q' ); SetSingle( 'e' ); SetSingle( 'g' ); SetSingle( 'h' ); SetSingle( 'i' ); SetSingle( 'l' ); SetSingle( 'k' ); SetSingle( 'm' ); SetSingle( 'f' ); SetSingle( 'p' ); SetSingle( 's' ); SetSingle( 't' ); SetSingle( 'w' ); SetSingle( 'y' ); SetSingle( 'v' ); } void gnCompare::CreateDNAComparator() { SetName( "Full DNA Comparator" ); SetSingle( 'a' ); SetSingle( 'c' ); SetSingle( 'g' ); SetSingle( 't' ); SetSingle( 'r' ); SetSingle( 'k' ); SetSingle( 's' ); SetSingle( 'm' ); SetSingle( 'y' ); SetSingle( 'w' ); SetSingle( 'b' ); SetSingle( 'v' ); SetSingle( 'd' ); SetSingle( 'h' ); SetSingle( 'n' ); SetSingle( 'x' ); SetSingle( 'A' ); SetSingle( 'C' ); SetSingle( 'G' ); SetSingle( 'T' ); SetSingle( 'R' ); SetSingle( 'K' ); SetSingle( 'S' ); SetSingle( 'M' ); SetSingle( 'Y' ); SetSingle( 'W' ); SetSingle( 'B' ); SetSingle( 'V' ); SetSingle( 'D' ); SetSingle( 'H' ); SetSingle( 'N' ); SetSingle( 'X' ); SetPair( 'g', 'r' ); SetPair( 'g', 'k' ); SetPair( 'g', 's' ); SetPair( 'g', 'd' ); SetPair( 'g', 'v' ); SetPair( 'g', 'b' ); SetPair( 'g', 'x' ); SetPair( 'g', 'n' ); SetPair( 'G', 'R' ); SetPair( 'G', 'K' ); SetPair( 'G', 'S' ); SetPair( 'G', 'D' ); SetPair( 'G', 'V' ); SetPair( 'G', 'B' ); SetPair( 'G', 'X' ); SetPair( 'G', 'N' ); SetPair( 'a', 'r' ); SetPair( 'a', 'w' ); SetPair( 'a', 'm' ); SetPair( 'a', 'd' ); SetPair( 'a', 'v' ); SetPair( 'a', 'h' ); SetPair( 'a', 'x' ); SetPair( 'a', 'n' ); SetPair( 'A', 'R' ); SetPair( 'A', 'W' ); SetPair( 'A', 'M' ); SetPair( 'A', 'D' ); SetPair( 'A', 'V' ); SetPair( 'A', 'H' ); SetPair( 'A', 'B' ); SetPair( 'A', 'X' ); SetPair( 'A', 'N' ); SetPair( 'c', 's' ); SetPair( 'c', 'm' ); SetPair( 'c', 'y' ); SetPair( 'c', 'v' ); SetPair( 'c', 'b' ); SetPair( 'c', 'h' ); SetPair( 'c', 'x' ); SetPair( 'c', 'n' ); SetPair( 'C', 'S' ); SetPair( 'C', 'M' ); SetPair( 'C', 'Y' ); SetPair( 'C', 'V' ); SetPair( 'C', 'B' ); SetPair( 'C', 'H' ); SetPair( 'C', 'X' ); SetPair( 'C', 'N' ); SetPair( 't', 'k' ); SetPair( 't', 'w' ); SetPair( 't', 'y' ); SetPair( 't', 'd' ); SetPair( 't', 'b' ); SetPair( 't', 'h' ); SetPair( 't', 'x' ); SetPair( 't', 'n' ); SetPair( 'T', 'K' ); SetPair( 'T', 'W' ); SetPair( 'T', 'Y' ); SetPair( 'T', 'D' ); SetPair( 'T', 'B' ); SetPair( 'T', 'H' ); SetPair( 'T', 'X' ); SetPair( 'T', 'N' ); SetPair( 'r', 'x' ); SetPair( 'y', 'x' ); SetPair( 'w', 'x' ); SetPair( 's', 'x' ); SetPair( 'k', 'x' ); SetPair( 'm', 'x' ); SetPair( 'b', 'x' ); SetPair( 'd', 'x' ); SetPair( 'h', 'x' ); SetPair( 'v', 'x' ); SetPair( 'n', 'x' ); SetPair( 'R', 'X' ); SetPair( 'Y', 'X' ); SetPair( 'W', 'X' ); SetPair( 'S', 'X' ); SetPair( 'K', 'X' ); SetPair( 'M', 'X' ); SetPair( 'B', 'X' ); SetPair( 'D', 'X' ); SetPair( 'H', 'X' ); SetPair( 'V', 'X' ); SetPair( 'N', 'X' ); SetPair( 'r', 'n' ); SetPair( 'y', 'n' ); SetPair( 'w', 'n' ); SetPair( 's', 'n' ); SetPair( 'k', 'n' ); SetPair( 'm', 'n' ); SetPair( 'b', 'n' ); SetPair( 'd', 'n' ); SetPair( 'h', 'n' ); SetPair( 'v', 'n' ); SetPair( 'x', 'n' ); SetPair( 'R', 'N' ); SetPair( 'Y', 'N' ); SetPair( 'W', 'N' ); SetPair( 'S', 'N' ); SetPair( 'K', 'N' ); SetPair( 'M', 'N' ); SetPair( 'B', 'N' ); SetPair( 'D', 'N' ); SetPair( 'H', 'N' ); SetPair( 'V', 'N' ); SetPair( 'X', 'N' ); SetPair( 'k', 'd' ); SetPair( 'k', 'b' ); SetPair( 'r', 'd' ); SetPair( 'r', 'v' ); SetPair( 's', 'v' ); SetPair( 's', 'b' ); SetPair( 'm', 'v' ); SetPair( 'm', 'h' ); SetPair( 'w', 'd' ); SetPair( 'w', 'h' ); SetPair( 'y', 'b' ); SetPair( 'y', 'h' ); SetPair( 'K', 'D' ); SetPair( 'K', 'B' ); SetPair( 'R', 'D' ); SetPair( 'R', 'V' ); SetPair( 'S', 'V' ); SetPair( 'S', 'B' ); SetPair( 'M', 'V' ); SetPair( 'M', 'H' ); SetPair( 'W', 'D' ); SetPair( 'W', 'H' ); SetPair( 'Y', 'B' ); SetPair( 'Y', 'H' ); //set the containment properties SetContained( 'g', 'r' ); SetContained( 'g', 'k' ); SetContained( 'g', 's' ); SetContained( 'g', 'd' ); SetContained( 'g', 'v' ); SetContained( 'g', 'b' ); SetContained( 'g', 'x' ); SetContained( 'g', 'n' ); SetContained( 'G', 'R' ); SetContained( 'G', 'K' ); SetContained( 'G', 'S' ); SetContained( 'G', 'D' ); SetContained( 'G', 'V' ); SetContained( 'G', 'B' ); SetContained( 'G', 'X' ); SetContained( 'G', 'N' ); SetContained( 'a', 'r' ); SetContained( 'a', 'w' ); SetContained( 'a', 'm' ); SetContained( 'a', 'd' ); SetContained( 'a', 'v' ); SetContained( 'a', 'h' ); SetContained( 'a', 'x' ); SetContained( 'a', 'n' ); SetContained( 'A', 'R' ); SetContained( 'A', 'W' ); SetContained( 'A', 'M' ); SetContained( 'A', 'D' ); SetContained( 'A', 'V' ); SetContained( 'A', 'H' ); SetContained( 'A', 'B' ); SetContained( 'A', 'X' ); SetContained( 'A', 'N' ); SetContained( 'c', 's' ); SetContained( 'c', 'm' ); SetContained( 'c', 'y' ); SetContained( 'c', 'v' ); SetContained( 'c', 'b' ); SetContained( 'c', 'h' ); SetContained( 'c', 'x' ); SetContained( 'c', 'n' ); SetContained( 'C', 'S' ); SetContained( 'C', 'M' ); SetContained( 'C', 'Y' ); SetContained( 'C', 'V' ); SetContained( 'C', 'B' ); SetContained( 'C', 'H' ); SetContained( 'C', 'X' ); SetContained( 'C', 'N' ); SetContained( 't', 'k' ); SetContained( 't', 'w' ); SetContained( 't', 'y' ); SetContained( 't', 'd' ); SetContained( 't', 'b' ); SetContained( 't', 'h' ); SetContained( 't', 'x' ); SetContained( 't', 'n' ); SetContained( 'T', 'K' ); SetContained( 'T', 'W' ); SetContained( 'T', 'Y' ); SetContained( 'T', 'D' ); SetContained( 'T', 'B' ); SetContained( 'T', 'H' ); SetContained( 'T', 'X' ); SetContained( 'T', 'N' ); SetContained( 'r', 'x' ); SetContained( 'y', 'x' ); SetContained( 'w', 'x' ); SetContained( 's', 'x' ); SetContained( 'k', 'x' ); SetContained( 'm', 'x' ); SetContained( 'b', 'x' ); SetContained( 'd', 'x' ); SetContained( 'h', 'x' ); SetContained( 'v', 'x' ); SetContained( 'n', 'x' ); SetContained( 'R', 'X' ); SetContained( 'Y', 'X' ); SetContained( 'W', 'X' ); SetContained( 'S', 'X' ); SetContained( 'K', 'X' ); SetContained( 'M', 'X' ); SetContained( 'B', 'X' ); SetContained( 'D', 'X' ); SetContained( 'H', 'X' ); SetContained( 'V', 'X' ); SetContained( 'N', 'X' ); SetContained( 'r', 'n' ); SetContained( 'y', 'n' ); SetContained( 'w', 'n' ); SetContained( 's', 'n' ); SetContained( 'k', 'n' ); SetContained( 'm', 'n' ); SetContained( 'b', 'n' ); SetContained( 'd', 'n' ); SetContained( 'h', 'n' ); SetContained( 'v', 'n' ); SetContained( 'x', 'n' ); SetContained( 'R', 'N' ); SetContained( 'Y', 'N' ); SetContained( 'W', 'N' ); SetContained( 'S', 'N' ); SetContained( 'K', 'N' ); SetContained( 'M', 'N' ); SetContained( 'B', 'N' ); SetContained( 'D', 'N' ); SetContained( 'H', 'N' ); SetContained( 'V', 'N' ); SetContained( 'X', 'N' ); SetContained( 'k', 'd' ); SetContained( 'k', 'b' ); SetContained( 'r', 'd' ); SetContained( 'r', 'v' ); SetContained( 's', 'v' ); SetContained( 's', 'b' ); SetContained( 'm', 'v' ); SetContained( 'm', 'h' ); SetContained( 'w', 'd' ); SetContained( 'w', 'h' ); SetContained( 'y', 'b' ); SetContained( 'y', 'h' ); SetContained( 'K', 'D' ); SetContained( 'K', 'B' ); SetContained( 'R', 'D' ); SetContained( 'R', 'V' ); SetContained( 'S', 'V' ); SetContained( 'S', 'B' ); SetContained( 'M', 'V' ); SetContained( 'M', 'H' ); SetContained( 'W', 'D' ); SetContained( 'W', 'H' ); SetContained( 'Y', 'B' ); SetContained( 'Y', 'H' ); } void gnCompare::CreateRNAComparator() { SetName( "Full RNA Comparator" ); SetSingle( 'a' ); SetSingle( 'c' ); SetSingle( 'g' ); SetSingle( 'u' ); SetSingle( 'r' ); SetSingle( 'k' ); SetSingle( 's' ); SetSingle( 'm' ); SetSingle( 'y' ); SetSingle( 'w' ); SetSingle( 'b' ); SetSingle( 'v' ); SetSingle( 'd' ); SetSingle( 'h' ); SetSingle( 'n' ); SetSingle( 'x' ); SetSingle( 'A' ); SetSingle( 'C' ); SetSingle( 'G' ); SetSingle( 'U' ); SetSingle( 'R' ); SetSingle( 'K' ); SetSingle( 'S' ); SetSingle( 'M' ); SetSingle( 'Y' ); SetSingle( 'W' ); SetSingle( 'B' ); SetSingle( 'V' ); SetSingle( 'D' ); SetSingle( 'H' ); SetSingle( 'N' ); SetSingle( 'X' ); SetPair( 'g', 'r' ); SetPair( 'g', 'k' ); SetPair( 'g', 's' ); SetPair( 'g', 'd' ); SetPair( 'g', 'v' ); SetPair( 'g', 'b' ); SetPair( 'g', 'x' ); SetPair( 'g', 'n' ); SetPair( 'G', 'R' ); SetPair( 'G', 'K' ); SetPair( 'G', 'S' ); SetPair( 'G', 'D' ); SetPair( 'G', 'V' ); SetPair( 'G', 'B' ); SetPair( 'G', 'X' ); SetPair( 'G', 'N' ); SetPair( 'a', 'r' ); SetPair( 'a', 'w' ); SetPair( 'a', 'm' ); SetPair( 'a', 'd' ); SetPair( 'a', 'v' ); SetPair( 'a', 'h' ); SetPair( 'a', 'x' ); SetPair( 'a', 'n' ); SetPair( 'A', 'R' ); SetPair( 'A', 'W' ); SetPair( 'A', 'M' ); SetPair( 'A', 'D' ); SetPair( 'A', 'V' ); SetPair( 'A', 'H' ); SetPair( 'A', 'B' ); SetPair( 'A', 'X' ); SetPair( 'A', 'N' ); SetPair( 'c', 's' ); SetPair( 'c', 'm' ); SetPair( 'c', 'y' ); SetPair( 'c', 'v' ); SetPair( 'c', 'b' ); SetPair( 'c', 'h' ); SetPair( 'c', 'x' ); SetPair( 'c', 'n' ); SetPair( 'C', 'S' ); SetPair( 'C', 'M' ); SetPair( 'C', 'Y' ); SetPair( 'C', 'V' ); SetPair( 'C', 'B' ); SetPair( 'C', 'H' ); SetPair( 'C', 'X' ); SetPair( 'C', 'N' ); SetPair( 'u', 'k' ); SetPair( 'u', 'w' ); SetPair( 'u', 'y' ); SetPair( 'u', 'd' ); SetPair( 'u', 'b' ); SetPair( 'u', 'h' ); SetPair( 'u', 'x' ); SetPair( 'u', 'n' ); SetPair( 'U', 'K' ); SetPair( 'U', 'W' ); SetPair( 'U', 'Y' ); SetPair( 'U', 'D' ); SetPair( 'U', 'B' ); SetPair( 'U', 'H' ); SetPair( 'U', 'X' ); SetPair( 'U', 'N' ); SetPair( 'r', 'x' ); SetPair( 'y', 'x' ); SetPair( 'w', 'x' ); SetPair( 's', 'x' ); SetPair( 'k', 'x' ); SetPair( 'm', 'x' ); SetPair( 'b', 'x' ); SetPair( 'd', 'x' ); SetPair( 'h', 'x' ); SetPair( 'v', 'x' ); SetPair( 'n', 'x' ); SetPair( 'R', 'X' ); SetPair( 'Y', 'X' ); SetPair( 'W', 'X' ); SetPair( 'S', 'X' ); SetPair( 'K', 'X' ); SetPair( 'M', 'X' ); SetPair( 'B', 'X' ); SetPair( 'D', 'X' ); SetPair( 'H', 'X' ); SetPair( 'V', 'X' ); SetPair( 'N', 'X' ); SetPair( 'r', 'n' ); SetPair( 'y', 'n' ); SetPair( 'w', 'n' ); SetPair( 's', 'n' ); SetPair( 'k', 'n' ); SetPair( 'm', 'n' ); SetPair( 'b', 'n' ); SetPair( 'd', 'n' ); SetPair( 'h', 'n' ); SetPair( 'v', 'n' ); SetPair( 'x', 'n' ); SetPair( 'R', 'N' ); SetPair( 'Y', 'N' ); SetPair( 'W', 'N' ); SetPair( 'S', 'N' ); SetPair( 'K', 'N' ); SetPair( 'M', 'N' ); SetPair( 'B', 'N' ); SetPair( 'D', 'N' ); SetPair( 'H', 'N' ); SetPair( 'V', 'N' ); SetPair( 'X', 'N' ); SetPair( 'k', 'd' ); SetPair( 'k', 'b' ); SetPair( 'r', 'd' ); SetPair( 'r', 'v' ); SetPair( 's', 'v' ); SetPair( 's', 'b' ); SetPair( 'm', 'v' ); SetPair( 'm', 'h' ); SetPair( 'w', 'd' ); SetPair( 'w', 'h' ); SetPair( 'y', 'b' ); SetPair( 'y', 'h' ); SetPair( 'K', 'D' ); SetPair( 'K', 'B' ); SetPair( 'R', 'D' ); SetPair( 'R', 'V' ); SetPair( 'S', 'V' ); SetPair( 'S', 'B' ); SetPair( 'M', 'V' ); SetPair( 'M', 'H' ); SetPair( 'W', 'D' ); SetPair( 'W', 'H' ); SetPair( 'Y', 'B' ); SetPair( 'Y', 'H' ); //set the containment properties SetContained( 'g', 'r' ); SetContained( 'g', 'k' ); SetContained( 'g', 's' ); SetContained( 'g', 'd' ); SetContained( 'g', 'v' ); SetContained( 'g', 'b' ); SetContained( 'g', 'x' ); SetContained( 'g', 'n' ); SetContained( 'G', 'R' ); SetContained( 'G', 'K' ); SetContained( 'G', 'S' ); SetContained( 'G', 'D' ); SetContained( 'G', 'V' ); SetContained( 'G', 'B' ); SetContained( 'G', 'X' ); SetContained( 'G', 'N' ); SetContained( 'a', 'r' ); SetContained( 'a', 'w' ); SetContained( 'a', 'm' ); SetContained( 'a', 'd' ); SetContained( 'a', 'v' ); SetContained( 'a', 'h' ); SetContained( 'a', 'x' ); SetContained( 'a', 'n' ); SetContained( 'A', 'R' ); SetContained( 'A', 'W' ); SetContained( 'A', 'M' ); SetContained( 'A', 'D' ); SetContained( 'A', 'V' ); SetContained( 'A', 'H' ); SetContained( 'A', 'B' ); SetContained( 'A', 'X' ); SetContained( 'A', 'N' ); SetContained( 'c', 's' ); SetContained( 'c', 'm' ); SetContained( 'c', 'y' ); SetContained( 'c', 'v' ); SetContained( 'c', 'b' ); SetContained( 'c', 'h' ); SetContained( 'c', 'x' ); SetContained( 'c', 'n' ); SetContained( 'C', 'S' ); SetContained( 'C', 'M' ); SetContained( 'C', 'Y' ); SetContained( 'C', 'V' ); SetContained( 'C', 'B' ); SetContained( 'C', 'H' ); SetContained( 'C', 'X' ); SetContained( 'C', 'N' ); SetContained( 'u', 'k' ); SetContained( 'u', 'w' ); SetContained( 'u', 'y' ); SetContained( 'u', 'd' ); SetContained( 'u', 'b' ); SetContained( 'u', 'h' ); SetContained( 'u', 'x' ); SetContained( 'u', 'n' ); SetContained( 'U', 'K' ); SetContained( 'U', 'W' ); SetContained( 'U', 'Y' ); SetContained( 'U', 'D' ); SetContained( 'U', 'B' ); SetContained( 'U', 'H' ); SetContained( 'U', 'X' ); SetContained( 'U', 'N' ); SetContained( 'r', 'x' ); SetContained( 'y', 'x' ); SetContained( 'w', 'x' ); SetContained( 's', 'x' ); SetContained( 'k', 'x' ); SetContained( 'm', 'x' ); SetContained( 'b', 'x' ); SetContained( 'd', 'x' ); SetContained( 'h', 'x' ); SetContained( 'v', 'x' ); SetContained( 'n', 'x' ); SetContained( 'R', 'X' ); SetContained( 'Y', 'X' ); SetContained( 'W', 'X' ); SetContained( 'S', 'X' ); SetContained( 'K', 'X' ); SetContained( 'M', 'X' ); SetContained( 'B', 'X' ); SetContained( 'D', 'X' ); SetContained( 'H', 'X' ); SetContained( 'V', 'X' ); SetContained( 'N', 'X' ); SetContained( 'r', 'n' ); SetContained( 'y', 'n' ); SetContained( 'w', 'n' ); SetContained( 's', 'n' ); SetContained( 'k', 'n' ); SetContained( 'm', 'n' ); SetContained( 'b', 'n' ); SetContained( 'd', 'n' ); SetContained( 'h', 'n' ); SetContained( 'v', 'n' ); SetContained( 'x', 'n' ); SetContained( 'R', 'N' ); SetContained( 'Y', 'N' ); SetContained( 'W', 'N' ); SetContained( 'S', 'N' ); SetContained( 'K', 'N' ); SetContained( 'M', 'N' ); SetContained( 'B', 'N' ); SetContained( 'D', 'N' ); SetContained( 'H', 'N' ); SetContained( 'V', 'N' ); SetContained( 'X', 'N' ); SetContained( 'k', 'd' ); SetContained( 'k', 'b' ); SetContained( 'r', 'd' ); SetContained( 'r', 'v' ); SetContained( 's', 'v' ); SetContained( 's', 'b' ); SetContained( 'm', 'v' ); SetContained( 'm', 'h' ); SetContained( 'w', 'd' ); SetContained( 'w', 'h' ); SetContained( 'y', 'b' ); SetContained( 'y', 'h' ); SetContained( 'K', 'D' ); SetContained( 'K', 'B' ); SetContained( 'R', 'D' ); SetContained( 'R', 'V' ); SetContained( 'S', 'V' ); SetContained( 'S', 'B' ); SetContained( 'M', 'V' ); SetContained( 'M', 'H' ); SetContained( 'W', 'D' ); SetContained( 'W', 'H' ); SetContained( 'Y', 'B' ); SetContained( 'Y', 'H' ); } } // end namespace genome libGenome-1.3.1/libGenome/gnPosSpecificTranslator.cpp0000644002622200470610000000576010647575617017611 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnPosSpecificTranslator.cpp // Purpose: Special case ORF translation // Description: Used to translate sequences differently based on the position of // input characters. Useful for tranlating genes because the first // codon is translated differently // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnPosSpecificTranslator.h" using namespace std; namespace genome { // static data access, avoids static initialization order fiasco const gnPosSpecificTranslator *gnPosSpecificTranslator::ProteinDNATranslator(){ const static gnPosSpecificTranslator* t_trans = new gnPosSpecificTranslator(ProteinDNATranslatorType); return t_trans; } const gnPosSpecificTranslator *gnPosSpecificTranslator::DNAProteinTranslator(){ const static gnPosSpecificTranslator* t_trans = new gnPosSpecificTranslator(DNAProteinTranslatorType); return t_trans; } // public: gnPosSpecificTranslator::gnPosSpecificTranslator() { } gnPosSpecificTranslator::gnPosSpecificTranslator( const gnPosSpecificTranslator &sf ) { m_name = sf.m_name; } gnPosSpecificTranslator::gnPosSpecificTranslator( gnTranslatorType t_type ) { m_type = t_type; switch(t_type){ case ProteinDNATranslatorType: // not special done for this case filter = gnFastTranslator::ProteinDNATranslator(); break; case DNAProteinTranslatorType: filter = gnFastTranslator::DNAProteinTranslator(); break; } } // gnSeqC gnSeqC gnPosSpecificTranslator::Filter( const gnSeqC ch ) const{ return filter->Filter(ch); } void gnPosSpecificTranslator::Filter( gnSeqC** seq, gnSeqI& len ) const{ return filter->Filter(seq, len); } // string void gnPosSpecificTranslator::Filter( string &seq ) const{ switch(m_type){ case ProteinDNATranslatorType: filter->Filter( seq ); break; case DNAProteinTranslatorType: string first_codon = seq.substr(0,3); string original_sequence = seq; filter->Filter( seq ); for(int charI = 0; charI < first_codon.length(); charI++ ) first_codon[charI] = tolower(first_codon[charI]); if( first_codon == "ttg" || first_codon == "gtg" ) seq[0] = 'M'; // replace . with selenocysteine U where appropriate string::size_type dot_pos = seq.find( "." ); while( dot_pos != string::npos ){ if( dot_pos == seq.size() - 1 ) break; // dont convert the final residue! string dot_codon = original_sequence.substr( dot_pos * 3, 3 ); dot_codon[0] = tolower( dot_codon[0] ); dot_codon[1] = tolower( dot_codon[1] ); dot_codon[2] = tolower( dot_codon[2] ); if( dot_codon == "tga" ) seq[ dot_pos ] = 'U'; dot_pos = seq.find( ".", dot_pos + 1 ); } break; } } } // end namespace genome libGenome-1.3.1/libGenome/gnABISource.h0000644002622200470610000000507510647575617014550 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnABISource.h // Purpose: Implements gnBaseSource for ABI files // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnABISource_h_ #define _gnABISource_h_ #include "libGenome/gnDefs.h" #include #include "libGenome/gnSequence.h" #include "libGenome/gnFileSource.h" #include "libGenome/gnFileContig.h" #include "libGenome/gnSourceSpec.h" #include "libGenome/gnGenomeSpec.h" #include "libGenome/gnFilter.h" namespace genome { /** * gnABISource is not implemented. */ class GNDLLEXPORT gnABISource : public gnFileSource { public: gnABISource(); /** * Clone Constructor copies the specified gnSEQSource. * @param s The gnABISource to copy. */ gnABISource( const gnABISource& s ); ~gnABISource(); gnABISource* Clone() const; uint32 GetContigListLength() const; boolean HasContig( const std::string& name ) const; uint32 GetContigID( const std::string& name ) const; std::string GetContigName( const uint32 i ) const; gnSeqI GetContigSeqLength( const uint32 i ) const; gnFileContig* GetContig( const uint32 i ) const; boolean SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI=ALL_CONTIGS ); /** * Writes the specified gnSequence to an ABI file named "filename". * @param sequence The gnSequence to write out. * @param filename The name of the file to write. * @return True if successful, false otherwise. */ static boolean Write(gnSequence& sequence, const std::string& filename); gnGenomeSpec *GetSpec() const; gnFileContig* GetFileContig( const uint32 contigI ) const; private: boolean SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes ); boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes ); boolean ParseStream( std::istream& fin ); gnGenomeSpec *m_spec; std::vector< gnFileContig* > m_contigList; };// class gnABISource inline gnABISource* gnABISource::Clone() const { return new gnABISource( *this ); } inline uint32 gnABISource::GetContigListLength() const { return m_contigList.size(); } inline gnGenomeSpec *gnABISource::GetSpec() const { return m_spec->Clone(); } } // end namespace genome #endif // _gnABISource_h_ libGenome-1.3.1/libGenome/gnVersion.h0000644002622200470610000000205310647575617014412 00000000000000///////////////////////////////////////////////////////////////////////////// // File: libGenome/gnVersion.h // Purpose: Defines libGenome version info // Description: Defines Version info // Rev: A // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnVersion_h_ #define _gnVersion_h_ /* Increment with each new version */ /* Build number with each build, minor with minor changes, major with major API changes */ #define gnMAJOR_VERSION 0 #define gnMINOR_VERSION 5 #define gnBUILD_NUMBER 1 #define gnVERSION_STRING "libGenome 0.5.1" #define gnVERSION_NUMBER (gnMAJOR_VERSION * 1000) + (gnMINOR_VERSION * 100) + gnRELEASE_NUMBER #define gnBETA_NUMBER 1 #define gnVERSION_FLOAT gnMAJOR_VERSION + (gnMINOR_VERSION/10.0) + (gnRELEASE_NUMBER/100.0) + (gnBETA_NUMBER/10000.0) #endif //_gnVersion_h_ libGenome-1.3.1/libGenome/gnFeature.h0000644002622200470610000000344310647575617014364 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnFeature.h // Purpose: implements the gnBaseFeature for generic features // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnFeature_h_ #define _gnFeature_h_ #include "libGenome/gnDefs.h" #include #include #include "libGenome/gnBaseFeature.h" #include "libGenome/gnBaseQualifier.h" namespace genome { /** * gnFeature stores sequence features in memory. * It contains a list of locations and qualifiers which are used to describe this feature. * It can be referred to by ID. */ class GNDLLEXPORT gnFeature : public gnBaseFeature { public: /** * Empty constructor. */ gnFeature( ); /** * Creates a memory feature with the specified name. * @param name The name of the feature. * @param id The id number of the feature * @param lt The type of sequence location covered by this feature * @param broken True if the feature was broken by some sequence manipulation, false otherwise. */ gnFeature( std::string& name, uint32 id = 0, gnLocation::gnLocationType lt = gnLocation::LT_Nothing, boolean broken = false ); /** * Copy constructor. * @param s The gnFeature to copy. */ gnFeature( const gnFeature& s ); /** * Destructor, frees memory. */ ~gnFeature(); // Clone gnFeature* Clone() const; private: }; // class gnFeature inline gnFeature* gnFeature::Clone() const { return new gnFeature(*this); } } // end namespace genome #endif // _gnFeature_h_ libGenome-1.3.1/libGenome/gnStringSpec.h0000644002622200470610000000560511003030307015015 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnStringSpec.h // Purpose: implements gnContigSpec for strings // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnStringSpec_h_ #define _gnStringSpec_h_ #include "libGenome/gnDefs.h" #include #include #include #include "libGenome/gnContigSpec.h" #include "libGenome/gnBaseSource.h" namespace genome { /** * gnStringSpec stores a sequence and annotation data in memory. * For a more complete description see the gnBaseSpec documentation. */ class GNDLLEXPORT gnStringSpec : public gnContigSpec { public: /** * Empty constructor. */ gnStringSpec(); /** * Constructor, creates a gnStringSpec using sequence data in the given std::string. * A circular spec will be created if the end index is greater than the start. * @param m_string The std::string to read base pairs from. * @param startI The index to start reading base pairs from the std::string. * @param endI The index to stop reading base pairs from the std::string. * @param revComp True if the sequence is read reverse complement. */ gnStringSpec( const std::string& m_string, const gnSeqI startI=0, const gnSeqI endI=GNSEQI_END, const boolean revComp = false); /** * Copy constructor. * @param s the gnStringSpec to copy. */ gnStringSpec( const gnStringSpec& s ); ~gnStringSpec(); // Clone gnStringSpec* Clone() const; virtual void Clear(); // Value Access methods virtual gnSeqI GetSourceLength() const; // Source Spec Specific functions virtual gnBaseSource *GetSource() const; /** * Copies a specified range of bases and returns a pointer to * the resulting gnStringSpec. You must delete the copy when you * are finished with it. * @param startI The first base pair to copy * @param len The length of the piece to copy * @return A copy of the gnStringSpec containing only the specified bases */ virtual gnStringSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const; protected: virtual boolean Read(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen ) const; std::string m_seqString; }; // class gnStringSpec inline gnStringSpec* gnStringSpec::Clone() const { return new gnStringSpec( *this ); } inline gnSeqI gnStringSpec::GetSourceLength() const{ return m_seqString.length(); } inline gnBaseSource* gnStringSpec::GetSource() const { return NULL; } inline boolean gnStringSpec::Read(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen) const{ memcpy(buf, m_seqString.data() + start, bufLen); return true; } } // end namespace genome #endif // _gnStringSpec_h_ libGenome-1.3.1/libGenome/gnSequence.cpp0000644002622200470610000003663711003030307015050 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnSequence.h // Purpose: Source Seq, where sequence is stored in source file // Description: implements the baseSeq interface for dna source files. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnSequence.h" #include "libGenome/gnSourceFactory.h" #include "libGenome/gnBaseSource.h" #include "libGenome/gnGenomeSpec.h" #include "libGenome/gnFragmentSpec.h" #include "libGenome/gnSourceSpec.h" #include "libGenome/gnStringSpec.h" #include "libGenome/gnStringHeader.h" #include using namespace std; namespace genome { // Constructor gnSequence::gnSequence( ) { spec = new gnGenomeSpec(); comparator = gnCompare::DNASeqCompare(); } gnSequence::gnSequence( const gnSeqC* seq){ spec = new gnGenomeSpec(); if (seq[0] != 0){ gnFragmentSpec *fragSpec = new gnFragmentSpec(); spec->AddSpec(fragSpec); fragSpec->AddSpec(new gnStringSpec(seq)); } comparator = gnCompare::DNASeqCompare(); } gnSequence::gnSequence( const string& str){ spec = new gnGenomeSpec(); if (str.length() != 0){ gnFragmentSpec *fragSpec = new gnFragmentSpec(); spec->AddSpec(fragSpec); fragSpec->AddSpec(new gnStringSpec(str)); } comparator = gnCompare::DNASeqCompare(); } gnSequence::gnSequence( const gnGenomeSpec& gngs){ spec = gngs.Clone(); comparator = gnCompare::DNASeqCompare(); } gnSequence::gnSequence( const gnFragmentSpec& gnfs){ spec = new gnGenomeSpec(); spec->AddSpec(gnfs.Clone()); comparator = gnCompare::DNASeqCompare(); } gnSequence::gnSequence( const gnContigSpec& gcs){ spec = new gnGenomeSpec(); gnFragmentSpec *fragSpec = new gnFragmentSpec(); fragSpec->AddSpec(gcs.Clone()); comparator = gnCompare::DNASeqCompare(); } gnSequence::gnSequence( gnSeqC *bases, gnSeqI length){ spec = new gnGenomeSpec(); if (length > 0){ gnFragmentSpec *fragSpec = new gnFragmentSpec(); spec->AddSpec(fragSpec); fragSpec->AddSpec(new gnStringSpec(string(bases, length))); } comparator = gnCompare::DNASeqCompare(); } gnSequence::gnSequence( const gnSequence& seq ) { *this = seq; } // Destructor gnSequence::~gnSequence() { if (spec != NULL) delete spec; } gnSequence& gnSequence::operator=( const gnSequence& seq){ spec = seq.spec->Clone(); filter_list = seq.filter_list; comparator = seq.comparator; return *this; } // Clone gnSequence* gnSequence::Clone() const { return new gnSequence( *this ); } //IMPLEMENT ME!! Consider ambiguities! int gnSequence::compare(const string& str) const{ STACK_TRACE_START gnSeqI len = length(); gnSeqI seq_len = str.length(); gnSeqI comparelen = len < seq_len ? len : seq_len; gnSeqI compared = 0; while(comparelen > 0){ gnSeqI curlen = comparelen < BUFFER_SIZE ? comparelen : BUFFER_SIZE; string bases = ToString(compared, curlen); string seq_bases = str.substr(compared, curlen); if(comparator->LessThan(bases, seq_bases)) return -1; else if(comparator->LessThan(seq_bases, bases)) return 1; compared += curlen; comparelen -= curlen; } if(len < seq_len) return -1; else if(len > seq_len) return 1; return 0; STACK_TRACE_END } int gnSequence::compare(const gnSequence& seq) const{ STACK_TRACE_START gnSeqI len = length(); gnSeqI seq_len = seq.length(); gnSeqI comparelen = len < seq_len ? len : seq_len; gnSeqI compared = 0; while(comparelen > 0){ gnSeqI curlen = comparelen < BUFFER_SIZE ? comparelen : BUFFER_SIZE; string bases = ToString(curlen, compared+1); string seq_bases = seq.ToString(curlen, compared+1); if(comparator->LessThan(bases, seq_bases)) return -1; else if(comparator->LessThan(seq_bases, bases)) return 1; compared+= curlen; comparelen -= curlen; } if(len < seq_len) return -1; else if(len > seq_len) return 1; return 0; STACK_TRACE_END } void gnSequence::insert( const gnSeqI offset, const gnSeqC *bases, const gnSeqI len){ STACK_TRACE_START string str(bases, len); gnStringSpec gpbs(str); insert(offset, gpbs); STACK_TRACE_END } //Offset is the gene index, not a computer index, to insert before. //This is the default insert. It inserts entire contigs void gnSequence::insert( const gnSeqI offset, const gnGenomeSpec& gpbs){ STACK_TRACE_START if(offset == 0) Throw_gnEx(SeqIndexOutOfBounds()); if(offset == GNSEQI_END || spec->GetLength() < offset){ //simple append. for(uint32 i=0; i < gpbs.GetSpecListLength(); i++) spec->AddSpec(gpbs.GetSpec(i)->Clone()); return; } //clone this sequence gnGenomeSpec* tmpSpec = spec->Clone(); //crop off the end of this sequence past the insert point //crop off the beginning of the cloned sequence up to the insert gnSeqI real_offset = offset - 1; gnSeqI endCrop = spec->GetLength() - real_offset; spec->CropEnd(endCrop); tmpSpec->CropStart(real_offset); //append the inserted sequence and the end of this sequence. insert(GNSEQI_END, gpbs); insert(GNSEQI_END, *tmpSpec); delete tmpSpec; STACK_TRACE_END } // Concatenation operators gnSequence const gnSequence::operator+(const gnSequence& seq) const{ STACK_TRACE_START gnSequence rval(*this); rval.append(seq); return rval; STACK_TRACE_END } // Subsequences and base deletion gnSequence gnSequence::subseq(const gnSeqI offset, const gnSeqI length) const{ STACK_TRACE_START if(length == 0) return gnSequence(); if(offset == 0) Throw_gnEx(SeqIndexOutOfBounds()); gnSequence tmpSeq; delete tmpSeq.spec; tmpSeq.spec = spec->CloneRange(offset - 1, length); return tmpSeq; STACK_TRACE_END } void gnSequence::erase( const gnSeqI offset, const gnSeqI len ){ STACK_TRACE_START if(offset == 0) Throw_gnEx(SeqIndexOutOfBounds()); //range checking, etc. gnSeqI current_length = length(); if(offset > current_length) Throw_gnEx(SeqIndexOutOfBounds()); gnSeqI endBase = offset + len - 1 < current_length ? offset + len - 1 : current_length; gnSeqI startBase = offset - 1; gnGenomeSpec* tmpSpec = spec->CloneRange(endBase, GNSEQI_END); uint32 lennard = tmpSpec->GetLength(); spec->CropEnd(current_length - startBase); lennard = length(); insert(GNSEQI_END, *tmpSpec); delete tmpSpec; STACK_TRACE_END } void gnSequence::splitContig(const gnSeqI splitI, const uint32 contigI){ STACK_TRACE_START gnSeqI splitBase = splitI; gnSeqI current_length = length(); if(splitI == 0) Throw_gnEx(SeqIndexOutOfBounds()); if(contigI == ALL_CONTIGS && splitI > current_length) Throw_gnEx(SeqIndexOutOfBounds()); else localToGlobal(contigI, splitBase); gnGenomeSpec* tmpSpec = spec->Clone(); tmpSpec->CropStart(splitBase); spec->CropEnd(current_length - splitBase); insert(GNSEQI_END, *tmpSpec); delete tmpSpec; STACK_TRACE_END } // IO operators istream& operator>>(istream& is, gnSequence& gps){ //read from source. string bases; is >> bases; gps.append(bases); return is; } ostream& operator<<(ostream& os, const gnSequence& gps){ //write to source. os << gps.ToString(); return os; } string gnSequence::ToString( const gnSeqI len, const gnSeqI offset ) const { STACK_TRACE_START string str; ToString(str, len, offset); return str; STACK_TRACE_END } boolean gnSequence::ToString( string& str, const gnSeqI len, const gnSeqI offset ) const { STACK_TRACE_START gnSeqI real_offset = offset - 1; gnSeqI m_length = length(); gnSeqI readSize = len > m_length - real_offset ? m_length - real_offset : len; Array array_buf( readSize+1 ); char *buf = array_buf.data; boolean success = spec->SeqRead( real_offset, buf, readSize, ALL_CONTIGS); buf[readSize] = '\0'; str = buf; //now filter the string list::const_iterator iter = filter_list.begin(); for(; iter != filter_list.end(); iter++) (*iter)->Filter(str); if( success ) return true; return false; STACK_TRACE_END } boolean gnSequence::ToArray( gnSeqC* pSeqC, gnSeqI length, const gnSeqI offset ) const { STACK_TRACE_START gnSeqI real_offset = offset - 1; if(offset == GNSEQI_END) return false; gnSeqC* tmp = new gnSeqC[length]; boolean success = spec->SeqRead( real_offset, tmp, length, ALL_CONTIGS); //now filter the array list::const_iterator iter = filter_list.begin(); gnSeqC** tomp = &tmp; for(; iter != filter_list.end(); iter++) (*iter)->Filter(tomp, length); memcpy(pSeqC, *tomp, length); delete[] *tomp; if( success ) return true; return false; STACK_TRACE_END } gnSeqC gnSequence::GetSeqC( const gnSeqI offset ) const { STACK_TRACE_START char block; gnSeqI readLen = 1; gnSeqI real_offset = offset - 1; boolean success = spec->SeqRead( real_offset, &block, readLen, ALL_CONTIGS); //now filter the char list::const_iterator iter = filter_list.begin(); for(; iter != filter_list.end(); iter++) block = (*iter)->Filter(block); if( success ) return block; return GNSEQC_NULL; STACK_TRACE_END } gnSeqC gnSequence::operator[]( const gnSeqI offset ) const { STACK_TRACE_START return GetSeqC( offset ); STACK_TRACE_END } gnSeqI gnSequence::contigListSize() const{ STACK_TRACE_START return spec->GetSpecListLength(); STACK_TRACE_END } gnSeqI gnSequence::contigListLength() const{ STACK_TRACE_START return spec->GetSpecListLength(); STACK_TRACE_END } //find the contig associated with base uint32 gnSequence::contigIndexByBase( const gnSeqI baseI) const{ STACK_TRACE_START return spec->GetSpecIndexByBase(baseI-1); STACK_TRACE_END } gnSequence gnSequence::contig( const uint32 contigI) const{ STACK_TRACE_START if(contigI == ALL_CONTIGS) return *this; return gnSequence(*spec->GetSpec(contigI)); STACK_TRACE_END } //returns a gnSequence pointer containing the specified contig. gnSequence gnSequence::contigByBase( const gnSeqI baseI) const{ STACK_TRACE_START return gnSequence(*spec->GetSpecByBase(baseI-1)); STACK_TRACE_END } uint32 gnSequence::contigIndexByName( string& contigName) const{ STACK_TRACE_START return spec->GetSpecIndexByName(contigName); STACK_TRACE_END } gnSeqI gnSequence::contigStart( const uint32 contigI) const{ STACK_TRACE_START int64 leafI = contigI; // add one for the stupid geneticists whose indices start at 1 return spec->GetSpecStartBase( leafI ) + 1; STACK_TRACE_END } gnSeqI gnSequence::contigLength( const uint32 contigI) const{ STACK_TRACE_START return spec->GetSpec( contigI )->GetLength(); STACK_TRACE_END } string gnSequence::contigName( const uint32 contigI) const{ STACK_TRACE_START return spec->GetSpec(contigI)->GetName(); STACK_TRACE_END } void gnSequence::globalToLocal(uint32& contigI, gnSeqI& baseI) const{ STACK_TRACE_START contigI = contigIndexByBase(baseI); baseI -= (contigStart(contigI) - 1); STACK_TRACE_END } void gnSequence::localToGlobal(const uint32 contigI, gnSeqI& baseI) const{ STACK_TRACE_START if(baseI > contigLength(contigI)) Throw_gnEx(SeqIndexOutOfBounds()); baseI += contigStart(contigI) - 1; STACK_TRACE_END } void gnSequence::globalToSource(uint32& contigI, gnSeqI& baseI) const{ STACK_TRACE_START baseI--; //convert from geneticist coordinates gnSeqI seq_contig = spec->GetSpecIndexByBase(baseI); gnSeqI new_base = baseI - spec->GetSpecStartBase(seq_contig); gnFragmentSpec *fragment_spec = spec->GetSpec(seq_contig); seq_contig = fragment_spec->GetSpecIndexByBase(new_base); new_base = new_base - fragment_spec->GetSpecStartBase(seq_contig); gnContigSpec* contig_spec = fragment_spec->GetSpec(seq_contig); contigI = contig_spec->GetSourceContigIndex(); gnSeqI contig_start = contig_spec->GetStart(); if(contig_spec->IsReverseComplement()){ gnSeqI source_len = contig_spec->GetSourceLength(); //it may seem counter intuitive, but we can add the source_len and mod by source_len //to deal with circularity // contig_start = (contig_start - contig_spec->GetLength() + source_len) % source_len; //if we are reverse complement then the contig_start will be the ending base pair //we want to subtract new_base from it. and we can add/mod by source_len to deal //with circles. baseI = (contig_start - new_base - 1 + source_len) % source_len; }else baseI = contig_start + new_base + 1; STACK_TRACE_END } void gnSequence::localToSource(uint32& contigI, gnSeqI& baseI) const{ STACK_TRACE_START localToGlobal(contigI, baseI); globalToSource(contigI, baseI); STACK_TRACE_END } gnSequence gnSequence::contigByName( string& contigName) const{ STACK_TRACE_START uint32 contigIndex = spec->GetSpecIndexByName(contigName); return gnSequence(*spec->GetSpec(contigIndex)); STACK_TRACE_END } void gnSequence::setContigName( const uint32 contigI, const string& contig_name) { STACK_TRACE_START if(contigI == ALL_CONTIGS) spec->SetName(contig_name); else spec->GetSpec(contigI)->SetName(contig_name); STACK_TRACE_END } void gnSequence::setReverseComplement( const boolean revComp, const uint32 contigI){ STACK_TRACE_START if(contigI == ALL_CONTIGS) spec->SetReverseComplement(revComp); else{ gnFragmentSpec* contig = spec->GetSpec(contigI); contig->SetReverseComplement(revComp); } STACK_TRACE_END } boolean gnSequence::isReverseComplement( const uint32 contigI ){ STACK_TRACE_START if(contigI == ALL_CONTIGS) return spec->IsReverseComplement(); gnFragmentSpec* contig = spec->GetSpec(contigI); return contig->IsReverseComplement(); STACK_TRACE_END } uint32 gnSequence::getHeaderListLength(const uint32 contigI) const{ STACK_TRACE_START if(contigI == ALL_CONTIGS) return spec->GetHeaderListLength(); else{ return spec->GetSpec(contigI)->GetHeaderListLength(); } STACK_TRACE_END } gnBaseHeader* gnSequence::getHeader(const uint32 contigI, const uint32 headerI) const{ STACK_TRACE_START if(contigI == ALL_CONTIGS) return spec->GetHeader(headerI); else{ return spec->GetSpec(contigI)->GetHeader(headerI); } STACK_TRACE_END } void gnSequence::addHeader(const uint32 contigI, gnBaseHeader* header, const uint32 headerI){ STACK_TRACE_START if(contigI == ALL_CONTIGS) spec->AddHeader(header, headerI); else{ spec->GetSpec(contigI)->AddHeader(header, headerI); } STACK_TRACE_END } void gnSequence::removeHeader(const uint32 contigI, const uint32 headerI){ STACK_TRACE_START if(contigI == ALL_CONTIGS) spec->RemoveHeader(headerI); else spec->GetSpec(contigI)->RemoveHeader(headerI); STACK_TRACE_END } void gnSequence::merge(const gnSeqI startBase, const gnSeqI endBase){ STACK_TRACE_START STACK_TRACE_END } void gnSequence::mergeContigs(const uint32 startC, const uint32 endC){ STACK_TRACE_START spec->MergeFragments(startC, endC); STACK_TRACE_END } bool gnSequence::LoadSource(const string sourcename){ STACK_TRACE_START gnSourceFactory* m_sourceFactory = gnSourceFactory::GetSourceFactory(); gnBaseSource *m_pSource = m_sourceFactory->AddSource(sourcename, true); if (m_pSource!=NULL) { if(spec != NULL) delete spec; spec = m_pSource->GetSpec(); return true; } return false; STACK_TRACE_END } gnSeqI gnSequence::find(const gnSequence& search, const gnSeqI offset)const{ STACK_TRACE_START //this is really adHoc... should probably be switched string searchIn=ToString(); string find= search.ToString(); string::size_type pos = searchIn.find(find, offset); if (pos == string::npos) return GNSEQI_ERROR; else{ return pos++; } STACK_TRACE_END } } // end namespace genome libGenome-1.3.1/libGenome/gnDefs.cpp0000644002622200470610000000026410647575617014203 00000000000000#ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnDefs.h" // some compilers don't have abs() for 64 bit ints int64 abs( int64 a ){ return a < 0 ? -a : a; } libGenome-1.3.1/libGenome/gnFilter.cpp0000644002622200470610000003020711003030307014510 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnFilter.h // Purpose: Filter for all Sequences // Description: Filters sequences, translates, reverse complement, converts // additions, etc. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnFilter.h" #include "libGenome/gnDebug.h" #include using namespace std; namespace genome { // public: const gnFilter *gnFilter::alphabetCharacterFilter(){ const static gnFilter* t_filt = new gnFilter(alphabetCharacterFilterType); return t_filt; } const gnFilter *gnFilter::numberCharacterFilter(){ const static gnFilter* t_filt = new gnFilter(numberCharacterFilterType); return t_filt; } const gnFilter *gnFilter::proteinSeqFilter(){ const static gnFilter* t_filt = new gnFilter(proteinSeqFilterType); return t_filt; } const gnFilter *gnFilter::basicDNASeqFilter(){ const static gnFilter* t_filt = new gnFilter(basicDNASeqFilterType); return t_filt; } const gnFilter *gnFilter::fullDNASeqFilter(){ const static gnFilter* t_filt = new gnFilter(fullDNASeqFilterType); return t_filt; } const gnFilter *gnFilter::basicRNASeqFilter(){ const static gnFilter* t_filt = new gnFilter(basicRNASeqFilterType); return t_filt; } const gnFilter *gnFilter::fullRNASeqFilter(){ const static gnFilter* t_filt = new gnFilter(fullRNASeqFilterType); return t_filt; } const gnFilter *gnFilter::DNAtoRNAFilter(){ const static gnFilter* t_filt = new gnFilter(DNAtoRNAFilterType); return t_filt; } const gnFilter *gnFilter::RNAtoDNAFilter(){ const static gnFilter* t_filt = new gnFilter(RNAtoDNAFilterType); return t_filt; } const gnFilter *gnFilter::DNAComplementFilter(){ const static gnFilter* t_filt = new gnFilter(DNAComplementFilterType); return t_filt; } const gnFilter *gnFilter::RNAComplementFilter(){ const static gnFilter* t_filt = new gnFilter(RNAComplementFilterType); return t_filt; } // public: gnFilter::gnFilter() { m_defaultChar = 'n'; m_rDefaultChar = 'n'; for( gnSeqC i = 0; i < GNSEQC_MAX; ++i ) m_pairArray[i] = NO_REVCOMP_CHAR; } gnFilter::gnFilter( const gnSeqC defaultChar, const gnSeqC rdefaultChar ) { m_defaultChar = defaultChar; m_rDefaultChar = rdefaultChar; for( gnSeqC i = 0; i < GNSEQC_MAX; ++i ) m_pairArray[i] = NO_REVCOMP_CHAR; } gnFilter::gnFilter( const gnFilter &sf ) { m_name = sf.m_name; for( gnSeqC i = 0; i < GNSEQC_MAX; ++i ) m_pairArray[i] = sf.m_pairArray[i]; m_defaultChar = sf.m_defaultChar; m_rDefaultChar = sf.m_rDefaultChar; } gnFilter::gnFilter( const gnFilterType f_type ){ for( gnSeqC i = 0; i < GNSEQC_MAX; ++i ) m_pairArray[i] = NO_REVCOMP_CHAR; switch(f_type){ case alphabetCharacterFilterType: CreateAlphabetCharacterFilter(); break; case numberCharacterFilterType: CreateNumberCharacterFilter(); break; case proteinSeqFilterType: CreateProteinFilter(); break; case basicDNASeqFilterType: CreateBasicDNAFilter(); break; case fullDNASeqFilterType: CreateFullDNAFilter(); break; case basicRNASeqFilterType: CreateBasicRNAFilter(); break; case fullRNASeqFilterType: CreateFullRNAFilter(); break; case DNAtoRNAFilterType: CreateDNAtoRNAFilter(); break; case RNAtoDNAFilterType: CreateRNAtoDNAFilter(); break; case DNAComplementFilterType: CreateDNAComplementFilter(); break; case RNAComplementFilterType: CreateRNAComplementFilter(); break; } } gnFilter::~gnFilter() { } inline void gnFilter::Filter( gnSeqC** seq, gnSeqI& len ) const { Array array_buf( len ); gnSeqC* tmp = array_buf.data; gnSeqI c=0; for(uint32 i=0; i < len; i++) if(IsValid((*seq)[i])) tmp[c++] = m_pairArray[(*seq)[i]]; len = c; memcpy(*seq, tmp, len); } void gnFilter::ReverseFilter( gnSeqC** seq, gnSeqI& len ) const { gnSeqC tmp, dum; uint32 halfLen = len/2; uint32 end = len - 1; uint32 curB = 0; uint32 curE = end; for( uint32 i=0; i < halfLen ; ++i ) { tmp = m_pairArray[(*seq)[i]]; dum = m_pairArray[(*seq)[ end - i ]]; if(dum != NO_REVCOMP_CHAR) (*seq)[ curB++ ] = dum; if(tmp != NO_REVCOMP_CHAR) (*seq)[ curE-- ] = tmp; } if(len&0x1){ tmp = m_pairArray[(*seq)[halfLen]]; if(tmp != NO_REVCOMP_CHAR) (*seq)[curB++] = tmp; } // now for the memmove if(curE >= curB){ memmove(*seq+curB, *seq+curE+1, end - curE); len = end - curE + curB; } } void gnFilter::Filter( string &seq ) const { gnSeqI c=0; for(uint32 i=0; i < seq.length(); i++) if(IsValid(seq[i])) seq[c++] = m_pairArray[seq[i]]; } void gnFilter::ReverseFilter( string &seq ) const { gnSeqC tmp, dum; uint32 halfLen = seq.length()/2; uint32 end = seq.length() - 1; uint32 curB = 0; uint32 curE = end; for( uint32 i=0; i < halfLen ; ++i ) { tmp = m_pairArray[seq[i]]; dum = m_pairArray[seq[ end - i ]]; if(dum != NO_REVCOMP_CHAR) seq[ curB++ ] = dum; if(tmp != NO_REVCOMP_CHAR) seq[ curE-- ] = tmp; } if(seq.length()&0x1){ tmp = m_pairArray[seq[halfLen]]; if(tmp != NO_REVCOMP_CHAR) seq[curB++] = tmp; } // now for the memmove if(curE >= curB){ seq.erase(curB, curE-curB); } } // standard filters void gnFilter::CreateAlphabetCharacterFilter() { SetDefaultChar( 0, 0 ); SetName( "Alphabet Character Filter" ); SetPair( 'A', 'a' ); SetPair( 'B', 'b' ); SetPair( 'C', 'c' ); SetPair( 'D', 'd' ); SetPair( 'E', 'e' ); SetPair( 'F', 'f' ); SetPair( 'G', 'g' ); SetPair( 'H', 'h' ); SetPair( 'I', 'i' ); SetPair( 'J', 'j' ); SetPair( 'K', 'k' ); SetPair( 'L', 'l' ); SetPair( 'M', 'm' ); SetPair( 'N', 'n' ); SetPair( 'O', 'o' ); SetPair( 'P', 'p' ); SetPair( 'Q', 'q' ); SetPair( 'R', 'r' ); SetPair( 'S', 's' ); SetPair( 'T', 't' ); SetPair( 'U', 'u' ); SetPair( 'V', 'v' ); SetPair( 'W', 'w' ); SetPair( 'X', 'x' ); SetPair( 'Y', 'y' ); SetPair( 'Z', 'z' ); } void gnFilter::CreateNumberCharacterFilter() { SetDefaultChar( 0, 0 ); SetName( "Number Character Filter" ); SetSingle( '0' ); SetSingle( '1' ); SetSingle( '2' ); SetSingle( '3' ); SetSingle( '4' ); SetSingle( '5' ); SetSingle( '6' ); SetSingle( '7' ); SetSingle( '8' ); SetSingle( '9' ); } void gnFilter::CreateProteinFilter() { SetDefaultChar( 'u', 'u' ); SetName( "Protein Filter" ); SetSingle( 'A' ); SetSingle( 'R' ); SetSingle( 'N' ); SetSingle( 'D' ); SetSingle( 'C' ); SetSingle( 'Q' ); SetSingle( 'E' ); SetSingle( 'G' ); SetSingle( 'H' ); SetSingle( 'I' ); SetSingle( 'L' ); SetSingle( 'K' ); SetSingle( 'M' ); SetSingle( 'F' ); SetSingle( 'P' ); SetSingle( 'S' ); SetSingle( 'T' ); SetSingle( 'W' ); SetSingle( 'Y' ); SetSingle( 'V' ); SetSingle( 'a' ); SetSingle( 'r' ); SetSingle( 'n' ); SetSingle( 'd' ); SetSingle( 'c' ); SetSingle( 'q' ); SetSingle( 'e' ); SetSingle( 'g' ); SetSingle( 'h' ); SetSingle( 'i' ); SetSingle( 'l' ); SetSingle( 'k' ); SetSingle( 'm' ); SetSingle( 'f' ); SetSingle( 'p' ); SetSingle( 's' ); SetSingle( 't' ); SetSingle( 'w' ); SetSingle( 'y' ); SetSingle( 'v' ); } void gnFilter::CreateBasicDNAFilter() { SetDefaultChar( 'n', 'n' ); SetName( "Basic DNA Filter" ); SetSingle( 'a' ); SetSingle( 'c' ); SetSingle( 'g' ); SetSingle( 't' ); SetSingle( 'A' ); SetSingle( 'C' ); SetSingle( 'G' ); SetSingle( 'T' ); SetSingle( 'n' ); SetSingle( 'N' ); SetSingle( 'x' ); SetSingle( 'X' ); SetSingle( '-' ); } void gnFilter::CreateFullDNAFilter() { SetDefaultChar( 'n', 'n' ); SetName( "Full DNA Filter" ); SetSingle( 'a' ); SetSingle( 'c' ); SetSingle( 'g' ); SetSingle( 't' ); SetSingle( 'A' ); SetSingle( 'C' ); SetSingle( 'G' ); SetSingle( 'T' ); SetSingle( 'r' ); SetSingle( 'y' ); SetSingle( 'k' ); SetSingle( 'm' ); SetSingle( 'b' ); SetSingle( 'v' ); SetSingle( 'd' ); SetSingle( 'h' ); SetSingle( 'R' ); SetSingle( 'Y' ); SetSingle( 'K' ); SetSingle( 'M' ); SetSingle( 'B' ); SetSingle( 'V' ); SetSingle( 'D' ); SetSingle( 'H' ); SetSingle( 's' ); SetSingle( 'S' ); SetSingle( 'w' ); SetSingle( 'W' ); SetSingle( 'n' ); SetSingle( 'N' ); SetSingle( 'x' ); SetSingle( 'X' ); SetSingle( '-' ); } void gnFilter::CreateBasicRNAFilter() { SetDefaultChar( 'n', 'n' ); SetName( "Basic RNA Filter" ); SetSingle( 'a' ); SetSingle( 'c' ); SetSingle( 'g' ); SetSingle( 'u' ); SetSingle( 'A' ); SetSingle( 'C' ); SetSingle( 'G' ); SetSingle( 'U' ); SetSingle( 'n' ); SetSingle( 'N' ); SetSingle( '-' ); } void gnFilter::CreateFullRNAFilter() { SetDefaultChar( 'n', 'n' ); SetName( "Full RNA Filter" ); SetSingle( 'a' ); SetSingle( 'c' ); SetSingle( 'g' ); SetSingle( 'u' ); SetSingle( 'A' ); SetSingle( 'C' ); SetSingle( 'G' ); SetSingle( 'U' ); SetSingle( 'r' ); SetSingle( 'y' ); SetSingle( 'k' ); SetSingle( 'm' ); SetSingle( 'b' ); SetSingle( 'v' ); SetSingle( 'd' ); SetSingle( 'h' ); SetSingle( 'R' ); SetSingle( 'Y' ); SetSingle( 'K' ); SetSingle( 'M' ); SetSingle( 'B' ); SetSingle( 'V' ); SetSingle( 'D' ); SetSingle( 'H' ); SetSingle( 's' ); SetSingle( 'S' ); SetSingle( 'w' ); SetSingle( 'W' ); SetSingle( 'n' ); SetSingle( 'N' ); SetSingle( '-' ); } void gnFilter::CreateDNAtoRNAFilter(){ SetDefaultChar( 'n', 'n' ); SetName( "Full DNA to RNA Filter" ); SetSingle( 'a' ); SetSingle( 'c' ); SetSingle( 'g' ); SetPair( 't', 'u' ); SetSingle( 'A' ); SetSingle( 'C' ); SetSingle( 'G' ); SetPair( 'T', 'U' ); SetSingle( 'r' ); SetSingle( 'y' ); SetSingle( 'k' ); SetSingle( 'm' ); SetSingle( 'b' ); SetSingle( 'v' ); SetSingle( 'd' ); SetSingle( 'h' ); SetSingle( 'R' ); SetSingle( 'Y' ); SetSingle( 'K' ); SetSingle( 'M' ); SetSingle( 'B' ); SetSingle( 'V' ); SetSingle( 'D' ); SetSingle( 'H' ); SetSingle( 's' ); SetSingle( 'S' ); SetSingle( 'w' ); SetSingle( 'W' ); SetSingle( 'n' ); SetSingle( 'N' ); SetSingle( '-' ); } void gnFilter::CreateRNAtoDNAFilter(){ SetDefaultChar( 'n', 'n' ); SetName( "Full RNA to DNA Filter" ); SetSingle( 'a' ); SetSingle( 'c' ); SetSingle( 'g' ); SetPair( 'u', 't' ); SetSingle( 'A' ); SetSingle( 'C' ); SetSingle( 'G' ); SetPair( 'U', 'T' ); SetSingle( 'r' ); SetSingle( 'y' ); SetSingle( 'k' ); SetSingle( 'm' ); SetSingle( 'b' ); SetSingle( 'v' ); SetSingle( 'd' ); SetSingle( 'h' ); SetSingle( 'R' ); SetSingle( 'Y' ); SetSingle( 'K' ); SetSingle( 'M' ); SetSingle( 'B' ); SetSingle( 'V' ); SetSingle( 'D' ); SetSingle( 'H' ); SetSingle( 's' ); SetSingle( 'S' ); SetSingle( 'w' ); SetSingle( 'W' ); SetSingle( 'n' ); SetSingle( 'N' ); SetSingle( '-' ); } void gnFilter::CreateDNAComplementFilter(){ SetDefaultChar( 'n', 'n' ); SetName( "Full DNA Complement Filter" ); SetPair( 'a', 't' ); SetPair( 'A', 'T' ); SetPair( 't', 'a' ); SetPair( 'T', 'A' ); SetPair( 'c', 'g' ); SetPair( 'C', 'G' ); SetPair( 'g', 'c' ); SetPair( 'G', 'C' ); SetPair( 'r', 'y' ); SetPair( 'R', 'Y' ); SetPair( 'y', 'r' ); SetPair( 'Y', 'R' ); SetPair( 'k', 'm' ); SetPair( 'K', 'M' ); SetPair( 'm', 'k' ); SetPair( 'M', 'K' ); SetSingle( 's' ); SetSingle( 'S' ); SetSingle( 'w' ); SetSingle( 'W' ); SetPair( 'b', 'v' ); SetPair( 'B', 'V' ); SetPair( 'v', 'b' ); SetPair( 'V', 'B' ); SetPair( 'd', 'h' ); SetPair( 'D', 'H' ); SetPair( 'h', 'd' ); SetPair( 'H', 'D' ); SetSingle( 'n' ); SetSingle( 'N' ); SetSingle( 'x' ); SetSingle( 'X' ); SetSingle( '-' ); } void gnFilter::CreateRNAComplementFilter(){ SetDefaultChar( 'n', 'n' ); SetName( "Full RNA Complement Filter" ); SetPair( 'a', 'u' ); SetPair( 'A', 'U' ); SetPair( 'u', 'a' ); SetPair( 'U', 'A' ); SetPair( 'c', 'g' ); SetPair( 'C', 'G' ); SetPair( 'g', 'c' ); SetPair( 'G', 'C' ); SetPair( 'r', 'y' ); SetPair( 'R', 'Y' ); SetPair( 'y', 'r' ); SetPair( 'Y', 'R' ); SetPair( 'k', 'm' ); SetPair( 'K', 'M' ); SetPair( 'm', 'k' ); SetPair( 'M', 'K' ); SetSingle( 's' ); SetSingle( 'S' ); SetSingle( 'w' ); SetSingle( 'W' ); SetPair( 'b', 'v' ); SetPair( 'B', 'V' ); SetPair( 'v', 'b' ); SetPair( 'V', 'B' ); SetPair( 'd', 'h' ); SetPair( 'D', 'H' ); SetPair( 'h', 'd' ); SetPair( 'H', 'D' ); SetSingle( 'n' ); SetSingle( 'N' ); SetSingle( '-' ); } } // end namespace genome libGenome-1.3.1/libGenome/gnBaseQualifier.h0000644002622200470610000000340410647575617015502 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnBaseQualifier.h // Purpose: abstract Qualifier class // Description: Provides an interface for Qualifiers in memory and on disk. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnBaseQualifier_h_ #define _gnBaseQualifier_h_ #include "libGenome/gnDefs.h" #include #include "libGenome/gnClone.h" namespace genome { /** * gnBaseQualifier is a general interface to sequence qualifiers. * gnBaseFeature uses qualifiers to store annotated sequences. * Use gnStringQualifier for a general purpose qualifier class. */ class GNDLLEXPORT gnBaseQualifier : public gnClone { public: gnBaseQualifier(){} virtual ~gnBaseQualifier(){} virtual gnBaseQualifier* Clone() const = 0; /** * Get the name of qualifier stored in this class. * @return The qualifier name as a std::string. */ virtual std::string GetName() const = 0; /** * Get the qualifier stored in this class. * @return The qualifier as a std::string. */ virtual std::string GetValue() const = 0; /** * Get the length of the qualifier name stored in this class. * @return The length of the qualifier name. */ virtual uint32 GetNameLength() const = 0; /** * Get the length of the qualifier stored in this class. * @return The length of the qualifier. */ virtual uint32 GetValueLength() const = 0; private: }; //class gnBaseQualifier } // end namespace genome #endif // _gnBaseQualifier_h_ libGenome-1.3.1/libGenome/gnSourceQualifier.h0000644002622200470610000000726210647575617016076 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnSourceQualifier.h // Purpose: Source Qualifier class // Description: Provides an interface for gnBaseQualifier in files. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnSourceQualifier_h_ #define _gnSourceQualifier_h_ #include "libGenome/gnDefs.h" #include #include "libGenome/gnBaseQualifier.h" #include "libGenome/gnBaseSource.h" #include namespace genome { /** * gnSourceQualifier is used to store a sequence qualifier which resides * in another source. They are created by gnGBKSource and other sources * and placed into a gnFeature. */ class GNDLLEXPORT gnSourceQualifier : public gnBaseQualifier { public: /** * Empty constructor. */ gnSourceQualifier(); /** * Constructor, records the location and name of the qualifier in the source. * @param source The source which contains the qualifier. * @param name The name of the qualifier. * @param begin The offset into the source where the qualifier starts. * @param length The length of the qualifier. */ gnSourceQualifier( gnBaseSource* source, std::string& name, uint32 begin, uint32 length ); /** * Copy constructor. * @param s The gnSourceQualifier to copy. */ gnSourceQualifier( const gnSourceQualifier& s ); /** * Destructor, frees memory. */ ~gnSourceQualifier(); gnSourceQualifier* Clone() const; std::string GetName() const; std::string GetValue() const; uint32 GetNameLength() const; uint32 GetValueLength() const; /** * Get the qualifier's start position within the source. * @return The qualifier start position. */ uint32 GetValueStart() const; /** * Get the qualifier's start position and length within the source. * @return The qualifier start position and length as a pair. */ std::pair GetValueLoc() const; /** * Set the qualifier's start position within the source. * @param start The qualifier start position. */ void SetValueStart(const uint32 start); /** * Get the qualifier's length within the source. * @param length The qualifier length. */ void SetValueLength(const uint32 length); /** * Set the qualifier's start position and length within the source. * @param startLen The qualifier start position and length as a pair. */ void SetValueLoc(const std::pair startLen); private: std::string m_name; uint32 m_start, m_length; gnBaseSource *m_source; }; //class gnSourceQualifier inline gnSourceQualifier* gnSourceQualifier::Clone() const{ return new gnSourceQualifier(*this); } inline std::string gnSourceQualifier::GetName() const{ return m_name; } inline uint32 gnSourceQualifier::GetNameLength() const{ return m_name.length(); } inline uint32 gnSourceQualifier::GetValueStart() const{ return m_start; } inline uint32 gnSourceQualifier::GetValueLength() const{ return m_length; } inline std::pair gnSourceQualifier::GetValueLoc() const{ std::pair p; p.first = m_start; p.second = m_length; return p; } inline void gnSourceQualifier::SetValueStart(const uint32 start){ m_start = start; } inline void gnSourceQualifier::SetValueLength(const uint32 length){ m_length = length; } inline void gnSourceQualifier::SetValueLoc(const std::pair startLen){ m_start = startLen.first; m_length = startLen.second; } } // end namespace genome #endif // _gnSourceQualifier_h_ libGenome-1.3.1/libGenome/gnRAWSource.h0000644002622200470610000000720510647575617014603 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnRAWSource.h // Purpose: Implements gnBaseSource for raw data files // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnRAWSource_h_ #define _gnRAWSource_h_ #include "libGenome/gnDefs.h" #include #include #include #include "libGenome/gnFileSource.h" #include "libGenome/gnFileContig.h" #include "libGenome/gnSourceSpec.h" #include "libGenome/gnSequence.h" namespace genome { /** * gnRAWSource reads raw sequence data from a text file. * This class reads and writes raw sequence to and from files. * A raw sequence does not contain any newlines, fragment delimiters, or other * type of annotation. * gnRAWSource is used by gnSourceFactory to read files and should only be used * directly.when writing out raw files by calling gnRAWSource::Write( mySpec, "C:\\myFile.txt"); */ class GNDLLEXPORT gnRAWSource : public gnFileSource { public: /** * Empty Constructor, does nothing. */ gnRAWSource(); /** * Clone Constructor copies the specified gnRAWSource. * @param s The gnRAWSource to copy. */ gnRAWSource( const gnRAWSource& s ); /** * Destructor, frees memory. */ ~gnRAWSource(); /** * Returns an exact copy of this class. */ gnRAWSource* Clone() const; // Contig Access methods uint32 GetContigListLength() const; boolean HasContig( const std::string& name ) const; uint32 GetContigID( const std::string& name ) const; std::string GetContigName( const uint32 i ) const; gnSeqI GetContigSeqLength( const uint32 i ) const; boolean SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI=ALL_CONTIGS ); /** * Writes the specified gnSequence to a raw file named "filename". * @param sequence The gnSequence to write out. * @param filename The name of the file to write. * @return True if successful, false otherwise. */ static boolean Write(gnSequence& sequence, const std::string& filename); /** * Writes the specified source to a raw file named "filename". * @param source The source to write out. * @param filename The name of the file to write. * @return True if successful, false otherwise. */ static boolean Write(gnBaseSource *source, const std::string& filename); gnGenomeSpec *GetSpec() const; gnFileContig* GetFileContig( const uint32 contigI ) const; static boolean CheckRawData( boolean set = false, boolean check = false ); private: boolean SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes ); boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes ); boolean ParseStream( std::istream& fin ); gnFileContig* m_contig; gnGenomeSpec* m_spec; };// class gnRAWSource // Clone inline gnRAWSource* gnRAWSource::Clone() const { return new gnRAWSource( *this ); } // Contig Access methods inline uint32 gnRAWSource::GetContigListLength() const { return m_contig == NULL? 0 : 1; } inline boolean gnRAWSource::Write(gnBaseSource *source, const std::string& filename){ gnSequence gns(*source->GetSpec()); return Write(gns, filename); } inline boolean gnRAWSource::CheckRawData( boolean set, boolean check ){ static boolean check_raw_data = false; if( set ){ check_raw_data = check; } return check_raw_data; } } // end namespace genome #endif // _gnRAWSource_h_ libGenome-1.3.1/libGenome/IntervalSequenceTree.h0000644002622200470610000005314010647575617016540 00000000000000#ifndef __IntervalSequenceTree_h__ #define __IntervalSequenceTree_h__ #include /* class interval { gnSeqI length(); cropEnd(); cropStart(); } */ // select idea shamelessly ripped from Metrowerks template class type_select { public: typedef If type; }; template class type_select { public: typedef Then type; }; static const uint64 IST_END = ((0xFFFFFFFF << 31) << 1 ) + 0xFFFFFFFF; /** * class implementing an Interval Sequence Tree * this is a tree for storing a changing sequence of intervals * that was invented one rainy afternoon by Aaron Darling and * Michael Rusch. * Important features are that stabbing queries, * stabbing insertions, and stabbing deletions are O( log n ) * assuming a uniform distribution of stab sites. */ template< class Key, class Allocator = std::allocator > class IntervalSequenceTree { public: typedef Key value_type; // typedef unsigned long long size_type; typedef Allocator allocator_type; typedef typename Allocator::reference reference; typedef typename Allocator::const_reference const_reference; typedef typename Allocator::size_type size_type; typedef typename Allocator::difference_type difference_type; typedef typename Allocator::pointer pointer; typedef typename Allocator::const_pointer const_pointer; // node types and iterator definitions protected: /** * This class represents nodes of an Interval Sequence Tree. Internal * nodes define any of left, center, and right to be non-null and key to * be null. Leaf nodes define left, center, and right as null and key points * to an interval. The length field in an internal node is always the sum * of lengths of the leaf nodes in its subtree. The subtree_size field is * defined as the number of nodes (leaf and internal) below the node. */ class IstNode { public: IstNode* parent; IstNode* left; IstNode* right; size_type subtree_size; size_type length; Key* key; IstNode() : parent( NULL ), left( NULL ), right( NULL ), subtree_size( 0 ), length( 0 ), key( NULL ) {} }; typedef typename Allocator::template rebind::other node_allocator_type; typedef typename node_allocator_type::pointer node_pointer; typedef typename node_allocator_type::const_pointer const_node_pointer; // typedef typename IstNode* node_pointer; // typedef typename const IstNode* const_node_pointer; public: // generic bidirectional iterator interface ripped from MSL, thanks guys template class __generic_iterator { public: typedef typename IntervalSequenceTree::value_type value_type; // typedef typename IntervalSequenceTree::difference_type difference_type; typedef typename type_select::type pointer; typedef typename type_select::type reference; typedef std::bidirectional_iterator_tag iterator_category; __generic_iterator() {} __generic_iterator(const __generic_iterator& i) : ptr_(i.ptr_) {} reference operator * () const {return ptr_->data_;} pointer operator -> () const {return &ptr_->data_;} __generic_iterator& operator ++ () {increment((const IstNode*&)ptr_); return *this;} __generic_iterator operator ++ (int) {__generic_iterator tmp(*this); ++(*this); return tmp;} __generic_iterator& operator -- () {decrement((const IstNode*&)ptr_); return *this;} __generic_iterator operator -- (int) {__generic_iterator tmp(*this); --(*this); return tmp;} friend bool operator ==(const __generic_iterator& x, const __generic_iterator& y) {return x.ptr_ == y.ptr_;} friend bool operator !=(const __generic_iterator& x, const __generic_iterator& y) {return x.ptr_ != y.ptr_;} private: typedef typename type_select::type node_pointer; node_pointer ptr_; explicit __generic_iterator(node_pointer n) : ptr_(n) {} friend class __generic_iterator; friend class IntervalSequenceTree; }; friend class __generic_iterator; friend class __generic_iterator; typedef __generic_iterator iterator; typedef __generic_iterator const_iterator; typedef std::reverse_iterator< iterator > reverse_iterator; typedef std::reverse_iterator< const_iterator > const_reverse_iterator; // constructor related methods IntervalSequenceTree(); template< class InputIterator > IntervalSequenceTree( InputIterator first, InputIterator last ); IntervalSequenceTree( const IntervalSequenceTree& ist ); IntervalSequenceTree& operator=( const IntervalSequenceTree& ist ); ~IntervalSequenceTree(); // standard container methods iterator begin(); const_iterator begin() const; iterator end(); const_iterator end() const; reverse_iterator rbegin(); const_reverse_iterator rbegin() const; reverse_iterator rend(); const_reverse_iterator rend() const; size_type max_size() const; bool empty() const; // insertion and erasure iterator insert( const value_type& val, size_type point = IST_END ); template void insert(InputIterator first, InputIterator last, size_type point = IST_END ); size_type erase( size_type point, size_type length ); void erase( iterator first, iterator last ); // search iterator find( size_type point ); const_iterator find( size_type point ) const; // interval sequence specific: /** * Returns the total length of intervals contained in this interval sequence */ size_type length() const; size_type nodeCount() const; size_type countNodes( IstNode* x = NULL ) const; protected: IstNode *root; /**< Root of the tree */ IstNode *leftmost; /**< Left most tree node, for begin() method */ IstNode *rightmost; /**< Right most tree node, for end() method */ static void propogateChanges( IstNode* cur_node, int64 length_diff, int64 subtree_diff ); static IstNode* recursiveFind( size_type& point, IstNode* node ); static void increment( IstNode*& x); void decrement( IstNode*& x) const; static void deleteSubtree( IstNode*& istn ); static void checkTree( node_pointer cur_node ); }; //template< class Key, class Allocator > //IntervalSequenceTree< Key, Allocator >::IST_END = -1; template< class Key, class Allocator > inline IntervalSequenceTree< Key, Allocator >::IntervalSequenceTree(){ root = NULL; leftmost = NULL; rightmost = NULL; // IST_END = -1; // wraps to UINT64_MAX because IST_END is unsigned } template< class Key, class Allocator > template< class InputIterator > IntervalSequenceTree< Key, Allocator >::IntervalSequenceTree( InputIterator first, InputIterator last ){ insert( first, last ); } template< class Key, class Allocator > IntervalSequenceTree< Key, Allocator >::IntervalSequenceTree( const IntervalSequenceTree& ist ){ insert( ist.begin(), ist.end() ); } template< class Key, class Allocator > IntervalSequenceTree< Key, Allocator >& IntervalSequenceTree< Key, Allocator >::operator=( const IntervalSequenceTree& ist ){ insert( ist.begin(), ist.end() ); } template< class Key, class Allocator > IntervalSequenceTree< Key, Allocator >::~IntervalSequenceTree(){ deleteSubtree( root ); } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::iterator IntervalSequenceTree< Key, Allocator >::begin(){ return iterator( leftmost ); } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::const_iterator IntervalSequenceTree< Key, Allocator >::begin() const{ return const_iterator( leftmost ); } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::iterator IntervalSequenceTree< Key, Allocator >::end(){ return iterator( NULL ); } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::const_iterator IntervalSequenceTree< Key, Allocator >::end() const{ return const_iterator( NULL ); } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::reverse_iterator IntervalSequenceTree< Key, Allocator >::rbegin(){ return reverse_iterator( end() ); } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::const_reverse_iterator IntervalSequenceTree< Key, Allocator >::rbegin() const{ return const_reverse_iterator( end() ); } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::reverse_iterator IntervalSequenceTree< Key, Allocator >::rend(){ return reverse_iterator( begin() ); } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::const_reverse_iterator IntervalSequenceTree< Key, Allocator >::rend() const{ return const_reverse_iterator( begin() ); } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::size_type IntervalSequenceTree< Key, Allocator >::max_size() const{ return IST_END - 1; } template< class Key, class Allocator > bool IntervalSequenceTree< Key, Allocator >::empty() const{ return root == NULL ? true : false; } template< class Key, class Allocator > void IntervalSequenceTree< Key, Allocator >::checkTree( // IntervalSequenceTree< Key, Allocator >::IstNode* node_pointer cur_node ){ if( cur_node ){ if( cur_node->parent == cur_node ) std::cerr << "freakout\n"; checkTree( cur_node->left ); checkTree( cur_node->right ); } } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::iterator IntervalSequenceTree< Key, Allocator >::insert( const Key& val, typename IntervalSequenceTree< Key, Allocator >::size_type point ) { size_type iv_offset = point; IstNode* ins_node = recursiveFind( iv_offset, root ); IstNode* new_node = new IstNode(); new_node->key = new Key( val ); new_node->length = val.GetLength(); new_node->subtree_size = 0; if( ins_node == NULL ){ // end insert rightmost = new_node; if( root == NULL ){ root = new_node; leftmost = new_node; return iterator( new_node ); } // find the shallowest right insertion point ins_node = NULL; decrement( ins_node ); // make a new parent node IstNode* new_parent = new IstNode(); new_parent->left = ins_node; new_parent->right = new_node; new_parent->parent = ins_node->parent; if( new_parent->parent == NULL ) root = new_parent; else new_parent->parent->right = new_parent; ins_node->parent = new_parent; new_parent->length = ins_node->length; // update lengths and subtree_sizes along the path to the root // checkTree( root ); // propogateChanges( new_node, 0, 0 ); // propogateChanges( ins_node, 0, 0 ); propogateChanges( new_parent, new_node->length, 2 ); return iterator( new_node ); } // iv_offset is the distance into the node that the leaf should be split // 0 is a special case (left insert) if( iv_offset == 0 ){ IstNode* new_parent = new IstNode(); new_parent->left = new_node; new_parent->right = ins_node; new_parent->parent = ins_node->parent; if( new_parent->parent->right == ins_node ) new_parent->parent->right = new_parent; else new_parent->parent->left = new_parent; new_parent->length = ins_node->length; ins_node->parent = new_parent; new_node->parent = new_parent; if( point == 0 ) leftmost = new_node; // update lengths and subtree_sizes along the path to the root // checkTree( root ); // propogateChanges( new_node, 0, 0 ); // propogateChanges( ins_node, 0, 0 ); propogateChanges( new_parent, new_node->length, 2 ); }else{ // need to split a leaf node IstNode* new_gp = new IstNode(); IstNode* new_parent = new IstNode(); new_gp->parent = ins_node->parent; new_gp->right = new_parent; new_gp->left = new IstNode(); new_gp->left->key = new Key( *ins_node->key ); new_gp->left->key->CropEnd( ins_node->length - iv_offset ); new_gp->left->length = new_gp->left->key->GetLength(); new_gp->left->parent = new_gp; ins_node->key->CropStart( iv_offset ); ins_node->length = ins_node->key->GetLength(); ins_node->parent = new_parent; new_node->parent = new_parent; new_parent->left = new_node; new_parent->right = ins_node; new_parent->parent = new_gp; new_parent->length = new_node->length + ins_node->length; new_parent->subtree_size = 2; new_gp->length = ins_node->length + new_gp->left->length; new_gp->subtree_size = 1; if( new_gp->parent == NULL ){ root = new_gp; leftmost = new_gp->left; rightmost = ins_node; }else if( new_gp->parent->right == ins_node ) new_gp->parent->right = new_gp; else new_gp->parent->left = new_gp; // update lengths and subtree_sizes along the path to the root // checkTree( root ); // propogateChanges( new_node, 0, 0 ); // propogateChanges( ins_node, 0, 0 ); // propogateChanges( new_gp->left, 0, 0 ); // propogateChanges( new_parent, 0, 0 ); new_gp->subtree_size = -1; propogateChanges( new_gp, new_node->length, 4 ); } return iterator( new_node ); } template< class Key, class Allocator > template void IntervalSequenceTree< Key, Allocator >::insert( InputIterator first, InputIterator last, typename IntervalSequenceTree< Key, Allocator >::size_type point ) { } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::size_type IntervalSequenceTree< Key, Allocator >::erase( typename IntervalSequenceTree< Key, Allocator >::size_type point, typename IntervalSequenceTree< Key, Allocator >::size_type length ) { size_type iv_offset = point; IstNode* ins_node = recursiveFind( iv_offset, root ); // iv_offset is the distance into the node that the leaf should be split // 0 is a special case (left delete) size_type deleted_nodes = 0; while( length > 0 ){ if( ins_node == NULL ){ // end delete? that's illegal return deleted_nodes; } if( iv_offset == 0 ){ if( length >= ins_node->length ){ // delete the whole thing length -= ins_node->length; if( ins_node->parent == NULL ){ // deleting the root delete ins_node; root = NULL; leftmost = NULL; rightmost = NULL; return deleted_nodes + 1; } IstNode* other_child, *del_node; if( ins_node->parent->left == ins_node ){ other_child = ins_node->parent->right; }else if( ins_node->parent->right == ins_node ){ other_child = ins_node->parent->left; } del_node = ins_node; increment( ins_node ); // update tree structure IstNode* tmp_parent = other_child->parent; IstNode* tmp_gp = tmp_parent->parent; *tmp_parent = *other_child; tmp_parent->parent = tmp_gp; if( tmp_parent->left ) tmp_parent->left->parent = tmp_parent; if( tmp_parent->right ) tmp_parent->right->parent = tmp_parent; if( ins_node == other_child ) ins_node = tmp_parent; delete other_child; // propogate deletion length thru root tmp_parent = tmp_parent->parent; // checkTree( root ); propogateChanges( tmp_parent, -del_node->length, -2 ); // finally delete ins_node delete del_node; ++deleted_nodes; }else{ // crop from start ins_node->key->CropStart( length ); // checkTree( root ); propogateChanges( ins_node, -length, 0 ); return deleted_nodes; } }else if( length >= ins_node->length - iv_offset ){ // crop from end ins_node->key->CropEnd( ins_node->length - iv_offset ); length -= ins_node->length - iv_offset; // checkTree( root ); propogateChanges( ins_node, -(ins_node->length - iv_offset), 0 ); increment( ins_node ); iv_offset = 0; }else{ // delete from middle (nastee part) IstNode* new_parent = new IstNode(); new_parent->left = ins_node; new_parent->length = ins_node->length; new_parent->right = new IstNode(); new_parent->right->key = new Key( *ins_node->key ); new_parent->right->length = ins_node->length - length - iv_offset; new_parent->right->key->CropStart( length + iv_offset ); new_parent->left->key->CropEnd( ins_node->length - iv_offset ); new_parent->left->length = iv_offset; new_parent->parent = ins_node->parent; if( new_parent->parent == NULL ){ root = new_parent; rightmost = new_parent->right; }else if( new_parent->parent->left == ins_node ) new_parent->parent->left = new_parent; else if( new_parent->parent->right == ins_node ) new_parent->parent->right = new_parent; ins_node->parent = new_parent; new_parent->right->parent = new_parent; // checkTree( root ); // propogateChanges( ins_node, 0, 0 ); // propogateChanges( new_parent->right, 0, 0 ); propogateChanges( new_parent, -length, 2 ); return deleted_nodes; } } return deleted_nodes; } template< class Key, class Allocator > void IntervalSequenceTree< Key, Allocator >::propogateChanges( IstNode* cur_node, int64 length_diff, int64 subtree_diff ) { std::vector< IstNode* > node_stack; while( cur_node != NULL ){ if( cur_node->parent == cur_node ) std::cerr << "when I say oh, you say shit!"; cur_node->length += length_diff; cur_node->subtree_size += subtree_diff; node_stack.push_back( cur_node ); cur_node = cur_node->parent; } } template< class Key, class Allocator > void IntervalSequenceTree< Key, Allocator >::erase( typename IntervalSequenceTree< Key, Allocator >::iterator first, typename IntervalSequenceTree< Key, Allocator >::iterator last ) { } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::iterator IntervalSequenceTree< Key, Allocator >::find( typename IntervalSequenceTree< Key, Allocator >::size_type point ) { return iterator( IntervalSequenceTree< Key, Allocator >::recursiveFind( point, root ) ); } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::const_iterator IntervalSequenceTree< Key, Allocator >::find( typename IntervalSequenceTree< Key, Allocator >::size_type point ) const { return const_iterator( IntervalSequenceTree< Key, Allocator >::recursiveFind( point, root ) ); } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::IstNode* IntervalSequenceTree< Key, Allocator >::recursiveFind( typename IntervalSequenceTree< Key, Allocator >::size_type& point, IstNode* node ) { if( node == NULL ) return NULL; // return this node if it's a leaf if( node->key != NULL ) return node; // look for the next node to recurse to if( point < node->length ){ if( node->left ){ if( point < node->left->length ) return recursiveFind( point, node->left ); point -= node->left->length; } return recursiveFind( point, node->right ); } point -= node->length; // out of range return NULL; } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::size_type IntervalSequenceTree< Key, Allocator >::length() const{ return root == NULL ? 0 : root->length; } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::size_type IntervalSequenceTree< Key, Allocator >::nodeCount() const{ return root == NULL ? 0 : root->subtree_size + 1; } template< class Key, class Allocator > typename IntervalSequenceTree< Key, Allocator >::size_type IntervalSequenceTree< Key, Allocator >::countNodes( IstNode* x ) const{ if( x == NULL ) x = root; if( x->key == NULL ) return countNodes( x->left ) + countNodes( x->right ) + 1; return 1; } template< class Key, class Allocator > void IntervalSequenceTree< Key, Allocator >::increment( IstNode*& x) { // find the least-ancestor with another child // and set x to that child while( x->parent != NULL ){ if( x == x->parent->left && x->parent->right != NULL ){ x = x->parent->right; break; }else x = x->parent; } // if there were no other children to the right then we're at the end if( x->parent == NULL ){ x = NULL; return; } // find the left-most leaf node below x while( x->key == NULL ){ if( x->left != NULL ) x = x->left; else if( x->right != NULL ) x = x->right; } } template< class Key, class Allocator > void IntervalSequenceTree< Key, Allocator >::decrement( IstNode*& x) const{ if( x != NULL ){ // find the least-ancestor with another child to the left // and set x to that child while( x->parent != NULL ){ if( x == x->parent->right && x->parent->left != NULL){ x = x->parent->left; break; }else x = x->parent; } // if there was no other children to the left then we're at the end // raise hell! (cause an access violation) if( x->parent == NULL ) x = NULL; }else{ x = root; } // find the right-most leaf node below x while( x->key == NULL ){ if( x->right != NULL ) x = x->right; else if( x->left != NULL ) x = x->left; } } template< class Key, class Allocator > void IntervalSequenceTree< Key, Allocator >::deleteSubtree( IstNode*& istn ) { if( istn->left != NULL ) deleteSubtree( istn->left ); if( istn->right != NULL ) deleteSubtree( istn->right ); if( istn->key != NULL ) delete istn->key; delete istn; } #endif // __IntervalSequenceTree_h__ libGenome-1.3.1/libGenome/gnBaseSpec.h0000644002622200470610000001112510647575617014452 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnBaseSpec.h // Purpose: abstract Spec class // Description: Defines a basic interface for all specs // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnBaseSpec_h_ #define _gnBaseSpec_h_ #include "libGenome/gnDefs.h" #include #include #include "libGenome/gnClone.h" #include "libGenome/gnBaseFeature.h" #include "libGenome/gnBaseHeader.h" namespace genome { /** * gnBaseSpec is the class which stores genetic information and is best accessed using gnSequence. */ class GNDLLEXPORT gnBaseSpec : public gnClone { public: gnBaseSpec(){} /** * Destructor, frees memory. */ virtual ~gnBaseSpec(){} virtual gnBaseSpec* Clone() const = 0; virtual gnBaseSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const = 0; /** * Get the name of the contig associated with this spec. * @return The contig name or an empty std::string if none exists. */ virtual std::string GetName() const; /** * Sets the name for this contig * @param name The new name. * @return True if successful. Honestly, I don't know how this could be unsuccessful... */ virtual void SetName( const std::string& name ); /** * Get the length of all the sequence data covered by this spec. * @return This spec's length in base pairs. */ virtual gnSeqI GetLength() const = 0; /** * Returns true if this spec is read reverse complement. * @return True if this spec is read reverse complement. */ virtual boolean IsReverseComplement() const; /** * Returns true if this spec's sequence is circular. * @return True if this spec's sequence is circular. */ virtual boolean IsCircular() const; /** * Sets the reverse complement bit for this spec. * @param value True for reverse complement, false otherwise. */ virtual void SetReverseComplement( const boolean value ) = 0; /** * Sets whether this spec should be read circular. * If circular is set, reads beyond the end of this spec will pick up * at the beginning and read up to the start index. * @param value True for circular, false otherwise. */ virtual void SetCircular( const boolean value ); /** * Crop the first cropLen bases from the sequence. CropStart will * delete features and headers associated with the cropped bases. * @param cropLen The number of base pairs to delete from the beginning. */ virtual void CropStart( gnSeqI cropLen ) = 0; /** * Crop the last cropLen bases from the sequence. CropEnd will * delete features and headers associated with the cropped bases. * @param cropLen The number of base pairs to delete from the end. */ virtual void CropEnd( gnSeqI cropLen ) = 0; /** * Reads sequence data from this spec. * SeqRead will attempt to read "bufLen" base pairs starting at "start", an offset into the sequence. * Reading inside a specific contig can be accomplished by supplying the "contigI" parameter with * a valid contig index. * SeqRead stores the sequence data in "buf" and returns the actual number of bases read in "bufLen". * SeqRead will return false if a serious error occurs. * @param start The base pair to start reading at. * @param buf The character array to store base pairs into. * @param bufLen The number of base pairs to read. This will be modified to reflect the actual number of bases read. * @param contigI The index of the subspec to read or ALL_CONTIGS by default. * @return True if the operation was successful. */ virtual boolean SeqRead(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen, const uint32 contigI ) const = 0; /** * Clears all data from this spec. */ virtual void Clear(); protected: boolean m_reverseComplement; boolean m_circular; std::string m_name; std::string m_sourceName; }; // class gnBaseSpec inline std::string gnBaseSpec::GetName() const{ return m_name; } inline void gnBaseSpec::SetName( const std::string& name ){ m_name = name; } inline boolean gnBaseSpec::IsReverseComplement() const{ return m_reverseComplement; } inline boolean gnBaseSpec::IsCircular() const{ return m_circular; } inline void gnBaseSpec::SetCircular( const boolean value ){ m_circular = value; } inline void gnBaseSpec::Clear(){ m_sourceName = ""; m_name = ""; m_reverseComplement = false; m_circular = false; } } // end namespace genome #endif // _gnBaseSpec_h_ libGenome-1.3.1/libGenome/gnSEQSource.cpp0000644002622200470610000005432611003030307015104 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnSEQSource.h // Purpose: Implements gnBaseSource for .SEQ files // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnFilter.h" #include "libGenome/gnFeature.h" #include "libGenome/gnSEQSource.h" #include "libGenome/gnGBKSource.h" #include "libGenome/gnSourceSpec.h" #include "libGenome/gnSourceHeader.h" #include "libGenome/gnSourceQualifier.h" #include "libGenome/gnLocation.h" #include "libGenome/gnStringTools.h" #include "libGenome/gnDebug.h" #include using namespace std; namespace genome { gnSEQSource::gnSEQSource() { m_openString = ""; m_pFilter = gnFilter::fullDNASeqFilter(); if(m_pFilter == NULL){ DebugMsg("Error using static sequence filters.\n"); } } gnSEQSource::gnSEQSource( const gnSEQSource& s ) : gnFileSource(s) { vector< gnFileContig* >::const_iterator iter = s.m_contigList.begin(); for( ; iter != s.m_contigList.end(); ++iter ) { m_contigList.push_back( (*iter)->Clone() ); } } gnSEQSource::~gnSEQSource() { m_ifstream.close(); vector< gnFileContig* >::iterator iter = m_contigList.begin(); for( ; iter != m_contigList.end(); ++iter ) { gnFileContig* fg = *iter; *iter = 0; delete fg; } } boolean gnSEQSource::HasContig( const string& name ) const { for(uint32 i = 0 ; i <= m_contigList.size(); i++ ) { if( name == m_contigList[i]->GetName() ) return true; } return false; } uint32 gnSEQSource::GetContigID( const string& name ) const { for(uint32 i = 0 ; i <= m_contigList.size(); i++ ) { if( name == m_contigList[i]->GetName() ) return i; } return ALL_CONTIGS; } string gnSEQSource::GetContigName( const uint32 i ) const { if( i < m_contigList.size() ) { return m_contigList[i]->GetName(); } return ""; } gnSeqI gnSEQSource::GetContigSeqLength( const uint32 i ) const { if( i == ALL_CONTIGS) return m_spec->GetLength(); if( i < m_contigList.size() ) { return m_contigList[i]->GetSeqLength(); } return GNSEQI_ERROR; } boolean gnSEQSource::SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI ){ uint64 startPos = 0; uint64 readableBytes = 0; if( !SeqSeek( start, contigI, startPos, readableBytes ) ) { bufLen = 0; return false; } if( contigI == ALL_CONTIGS ) { uint32 curLen = 0; uint64 bytesRead = 0; while (curLen < bufLen) { //SeqSeek to start, Figure out how much can be read before SeqSeeking again. if(readableBytes <= 0) //Look out for zero length contigs! IMPLEMENT ME if( !SeqSeek( start + curLen, contigI, startPos, readableBytes ) ){ bufLen = curLen; return true; } //readLen is the amount to read on this pass uint64 readLen = (bufLen - curLen) < readableBytes ? (bufLen - curLen) : readableBytes; gnSeqC* tmpBuf = new gnSeqC[readLen]; //read into tmpBuf, then filter tmpBuf into curBuf // read chars and filter m_ifstream.read(tmpBuf, readLen); uint64 gc = m_ifstream.gcount(); bytesRead += gc; readableBytes -= gc; for(uint32 i=0; i < gc; i++){ if( m_pFilter->IsValid(tmpBuf[i]) ){ buf[curLen] = tmpBuf[i]; curLen++; } } delete[] tmpBuf; if(m_ifstream.eof()){ //we hit the end of the file. bail out. m_ifstream.clear(); bufLen = curLen; return true; } } bufLen = curLen; } else if( contigI < m_contigList.size() ) { uint32 curLen = 0; //check to see if the buffer is bigger than the contig. if so truncate it. gnSeqI contigSize = m_contigList[contigI]->GetSeqLength(); bufLen = bufLen < contigSize ? bufLen : contigSize; while (curLen < bufLen) { uint64 readLen = bufLen - curLen; //the amount to read on this pass gnSeqC* tmpBuf = new gnSeqC[readLen]; //read into tmpBuf, then filter tmpBuf into curBuf // read chars and filter m_ifstream.read(tmpBuf, readLen); uint64 gc = m_ifstream.gcount(); // cout << "Read " << gc << " chars from " << m_openString << "\n"; // cout << "Checking character validity on: " << tmpBuf << "\n"; for(uint32 i=0; i < gc; i++){ if( m_pFilter->IsValid(tmpBuf[i]) ){ buf[curLen] = tmpBuf[i]; curLen++; } } if(m_ifstream.eof()){ //we hit the end of the file. bail out. m_ifstream.clear(); bufLen = curLen; return true; } delete[] tmpBuf; } bufLen = curLen; } return true; } // private: // figures out which contig the sequence starts at then calls SeqStartPos to get the offset within that contig // returns startPos, the file offset where the sequence starts // returns true if successful, false otherwise boolean gnSEQSource::SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes ) { if( contigI == ALL_CONTIGS ) { // find first contig gnSeqI curIndex = 0; vector< gnFileContig* >::iterator iter = m_contigList.begin(); for( ; iter != m_contigList.end(); ++iter ) { uint64 len = (*iter)->GetSeqLength(); if( (curIndex + len) > start ) break; curIndex += len; } if( iter == m_contigList.end() ) return false; // seek to start gnSeqI startIndex = start - curIndex; //startIndex is starting pos. within the contig return SeqStartPos( startIndex, *(*iter), startPos, readableBytes ); } else if( contigI < m_contigList.size() ) { return SeqStartPos( start, *(m_contigList[contigI]), startPos, readableBytes ); } return false; } //Returns startPos, the file offset where the sequence starts. boolean gnSEQSource::SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes ) { readableBytes = 0; uint32 curLen = 0; //seek to the file offset where the contig starts startPos = contig.GetSectStartEnd(gnContigSequence).first; //set startPos to start where the contig starts m_ifstream.seekg( startPos, ios::beg ); if( m_ifstream.eof() ){ DebugMsg("ERROR in gnSEQSource::Incorrect contig start position, End of file reached!\n"); return false; } while( true ) { // READ the rest of the contig skipping over invalid characters until we get to the starting base pair. // startPos will contain the file offset with the starting base pair uint32 tmpbufsize = contig.GetSectStartEnd(gnContigSequence).second - startPos; if(tmpbufsize == 0){ DebugMsg("ERROR in gnSEQSource: stored contig size is incorrect."); return false; } uint64 startOffset = start; if(contig.HasRepeatSeqGap()){ if(contig.GetRepeatSeqGapSize().first > 0){ if(contig.GetRepeatSeqGapSize().second > 0){ startOffset += (start*contig.GetRepeatSeqGapSize().second)/contig.GetRepeatSeqGapSize().first; startPos+=startOffset; m_ifstream.seekg(startPos , ios::beg); readableBytes = contig.GetSectStartEnd(gnContigSequence).second - startPos; return true; } }else{ startPos+=start; m_ifstream.seekg(startPos , ios::beg); readableBytes = contig.GetSectStartEnd(gnContigSequence).second - startPos; return true; } } tmpbufsize = tmpbufsize < BUFFER_SIZE ? tmpbufsize : BUFFER_SIZE; //read in the smaller of the two. char *tmpbuf = new char[tmpbufsize]; m_ifstream.read( tmpbuf, tmpbufsize ); if( m_ifstream.eof() ){ ErrorMsg("ERROR in gnSEQSource::Read End of file reached!\n"); delete[] tmpbuf; return false; } for( uint32 i=0; i < tmpbufsize; ++i ){ if( m_pFilter->IsValid(tmpbuf[i]) ){ if( curLen >= start ){ //stop when we reach the starting offset within this contig startPos += i; m_ifstream.seekg( startPos, ios::beg ); //seek to startPos readableBytes = contig.GetSectStartEnd(gnContigSequence).second - startPos; delete[] tmpbuf; return true; } ++curLen; //each time we read a valid b.p., increment the sequence length } } startPos += tmpbufsize; delete[] tmpbuf; } return true; } //IMPLEMENT ME! move these static methods somewhere else! especially basecount! void gnSEQSource::BaseCount(const string& bases, gnSeqI& a_count, gnSeqI& c_count, gnSeqI& g_count, gnSeqI& t_count, gnSeqI& other_count){ a_count = 0; c_count = 0; g_count = 0; t_count = 0; other_count = 0; for(uint32 i=0; i < bases.length(); i++){ if((bases[i] == 'a')||(bases[i] == 'A')) a_count++; else if((bases[i] == 'c')||(bases[i] == 'C')) c_count++; else if((bases[i] == 'g')||(bases[i] == 'G')) g_count++; else if((bases[i] == 't')||(bases[i] == 'T')) t_count++; else other_count++; } } void gnSEQSource::FormatString(string& data, uint32 offset, uint32 width){ //first remove newlines and corresponding whitespace string::size_type newline_loc = data.find_first_of('\n', 0); while(newline_loc != string::npos){ if(data[newline_loc-1] == '\r') newline_loc--; string::size_type text_loc = newline_loc; while((data[text_loc] == ' ') ||(data[text_loc] == ' ')||(data[text_loc] == '\n')||(data[text_loc] == '\r')){ text_loc++; if(text_loc+1 == data.length()) break; } data = (data.substr(0, newline_loc) + " " + data.substr(text_loc)); newline_loc = data.find_first_of('\n', 0); } //now reformat with newlines and whitespace, observing word boundaries... string output_string = ""; for(uint32 charI = 0; charI < data.length();){ //get the substring to append and increment charI string::size_type base_loc = charI; string append_string; while(base_loc - charI <= width){ string::size_type space_loc = data.find_first_of(' ', base_loc+1); if(space_loc - charI < width) base_loc = space_loc; else if(base_loc == charI){ //word is too big for one line. split it. append_string = data.substr(charI, width); charI+=width; }else{ append_string = data.substr(charI, base_loc - charI); charI = base_loc; } } output_string += string(offset, ' ') + append_string; if(charI + width < data.length()) output_string += "\r\n"; } data = output_string; } boolean gnSEQSource::Write(gnGenomeSpec *spec, const string& filename){ ErrorMsg("Writing DNAStar SEQ files is not supported at this time. Try again next week.\n"); return false; } gnFileContig* gnSEQSource::GetFileContig( const uint32 contigI ) const{ if(m_contigList.size() > contigI) return m_contigList[contigI]; return NULL; } //File parsing access routine boolean gnSEQSource::ParseStream( istream& fin ) { // INIT temp varables uint32 readState = 0; uint32 lineStart = 0; int64 gapstart = -1; // INIT buffer uint32 sectionStart = 0; uint64 streamPos = 0; uint64 bufReadLen = 0; uint64 remainingBuffer = 0; char* buf = new char[BUFFER_SIZE]; gnFragmentSpec* curFrag = 0; gnSourceSpec* curSpec = 0; gnSourceHeader *curHeader; gnBaseFeature* curFeature; gnFileContig* curContig = 0; gnLocation::gnLocationType curBaseLocationType; gnSeqI curLocationStart; int32 curStartLength = 0; int32 curEndLength = 0; string curLocContig = ""; string curQualifierName; uint64 curQualifierStart; string curContigName = ""; gnSeqI seqLength = 0; gnSeqI lineSeqSize = 0; m_spec = new gnGenomeSpec(); while( !fin.eof() ) { if(sectionStart > 0){ if(readState == 15) sectionStart = bufReadLen; else if(readState == 16) sectionStart = lineStart; remainingBuffer = bufReadLen - sectionStart; memmove(buf, buf+sectionStart, remainingBuffer); } // read chars fin.read( buf + remainingBuffer, BUFFER_SIZE - remainingBuffer); streamPos -= remainingBuffer; lineStart -= sectionStart; if(gapstart > 0) gapstart -= sectionStart; sectionStart = 0; bufReadLen = fin.gcount(); bufReadLen += remainingBuffer; for( uint32 i=remainingBuffer ; i < bufReadLen ; i++ ) { char ch = buf[i]; switch( readState ) { case 0: //Assume we are in header at the start of a new line. //Look for keywords starting in column 1 if((ch == '\n')&&(buf[lineStart] != ' ')&&(buf[lineStart] != ' ')){ //not equal to space or tab if(curSpec == NULL){ curSpec = new gnSourceSpec(this, m_spec->GetSpecListLength()); curFrag = new gnFragmentSpec(); curFrag->AddSpec(curSpec); curSpec->SetSourceName(m_openString); m_spec->AddSpec(curFrag); } if(lineStart != sectionStart){ //Add the previous header to our list uint32 j = SEQ_HEADER_NAME_LENGTH-1; for(; j > 0; j--) if((buf[sectionStart+j] != ' ')&&(buf[sectionStart+j] != ' ')) break; string header_name = string(buf+sectionStart, j+1); curHeader = new gnSourceHeader(this, header_name, sectionStart + streamPos, lineStart - sectionStart); //if this is header info _before_ a locus statement then its a general file header. if(strncmp(&buf[lineStart], "LOCUS", 5) == 0) m_spec->AddHeader(curHeader); else //otherwise its a fragment header. curFrag->AddHeader(curHeader); sectionStart = lineStart; } if(strncmp(&buf[lineStart], "FEATURES", 8) == 0){ sectionStart = i + 1; readState = 1; //read in features }else if(strncmp(&buf[lineStart], "ORIGIN", 6) == 0){ curHeader = new gnSourceHeader(this, string("ORIGIN"), sectionStart + streamPos, i - sectionStart + 1); curFrag->AddHeader(curHeader); curContig = new gnFileContig(); curContig->SetName(curContigName); curContigName = ""; readState = 13; //read in base pairs }else if(strncmp(&buf[lineStart], "LOCUS", 5) == 0){ if(strncmp(&buf[lineStart+SEQ_LOCUS_CIRCULAR_COLUMN-1], "circular", 8) == 0) curFrag->SetCircular(true); uint32 j = SEQ_LOCUS_NAME_LENGTH + 1; for(; j > 0; j--) if((buf[lineStart+SEQ_LOCUS_NAME_COLUMN+j-1] != ' ')&&(buf[sectionStart+SEQ_LOCUS_NAME_COLUMN+j-1] != ' ')) break; curContigName = string(buf+lineStart+SEQ_LOCUS_NAME_COLUMN-1, j+1); curFrag->SetName(curContigName); }else if(strncmp(&buf[lineStart], "^^", 2) == 0){ //start the sequence. if(curContig == NULL){ curContig = new gnFileContig(); curContig->SetName(curContigName); curContigName = ""; } i--; readState = 14; break; } } if(ch == '\n') lineStart = i + 1; break; case 1: //look for feature tag in column six. ignore whitespace before feature. if((ch == ' ')||(ch == ' ')){ break; }else if(ch == '\n'){ lineStart = i + 1; sectionStart = i + 1; break; }else if(sectionStart == i){ //there was no whitespace, we hit a TAG instead i--; readState = 0; //Deal with a Header TAG sectionStart = i + 1; break; }else if((i - lineStart == SEQ_SUBTAG_COLUMN)||((buf[lineStart]==' ')&&(i==lineStart+1))){ sectionStart = i; readState = 2; } // case 2: //Get the feature name. stop on whitespace if((ch == ' ')||(ch == ' ')){ string featureName(buf+sectionStart, i - sectionStart); curFeature = new gnFeature(featureName); curFrag->AddFeature(curFeature); sectionStart = i + 1; readState = 3; } break; case 3: //Ignore whitespace before feature location if((ch == ' ')||(ch == ' ')){ break; }else if((ch == '\r')||(ch == '\n')){ lineStart = i+1; break; } sectionStart = i; readState = 4; case 4: //Read a location start. stop on (<.:^ and whitespace if((ch == ' ')||(ch == ' ')||(ch == '(')||(ch == '.')||(ch=='^')||(ch==':')){ string starter(buf+sectionStart, i - sectionStart); if(ch == '('){ if(starter == "complement") curFeature->SetLocationType(gnLocation::LT_Complement); else if(starter == "order") curFeature->SetLocationType(gnLocation::LT_Order); else if(starter == "group") curFeature->SetLocationType(gnLocation::LT_Group); else if(starter == "one-of") curFeature->SetLocationType(gnLocation::LT_OneOf); sectionStart = i + 1; //ignore join since it is default. break; }else if(ch == ':'){ curLocContig = starter; sectionStart = i + 1; break; } curLocationStart = atoi(starter.c_str()); readState = 6; //read in end base by default. if(ch == '.'){ //go to special state to look for another one. readState = 5; sectionStart = i + 1; break; }else if(ch == '^'){ curBaseLocationType = gnLocation::LT_BetweenBases; }else if((ch == ' ')||(ch == ' ')){ //no end location go to qualifier gnLocation curLocation(curLocationStart, curLocationStart); curFeature->AddLocation(curLocation, curFeature->GetLocationListLength()); readState = 7; } sectionStart = i + 1; }else if(ch == '<'){ curStartLength = -1; sectionStart = i + 1; }else if(ch == '>'){ curStartLength = 1; sectionStart = i + 1; } break; case 5: //look for another period or location start. if(ch == '.'){ curBaseLocationType = gnLocation::LT_Standard; readState = 6; sectionStart = i + 1; break; } curBaseLocationType = gnLocation::LT_OneOf; case 6: //see if there's a second location value. stop on >, and whitespace if(ch == '>'){ curEndLength = 1; sectionStart = i + 1; }else if(ch == '<'){ curEndLength = -1; sectionStart = i + 1; }else if((ch == ' ')||(ch == ' ')||(ch == ',')){ //read end location string ender(buf+sectionStart, i - sectionStart); gnSeqI curLocationEnd = atoi(ender.c_str()); gnLocation curLocation(curLocationStart, curStartLength, curLocationEnd, curEndLength, curBaseLocationType); curEndLength = 0; curStartLength = 0; curFeature->AddLocation(curLocation, curFeature->GetLocationListLength()); readState = ch == ',' ? 3 : 7; //read another loc if we need to. sectionStart = i+1; } break; case 7: //skip to start of qualifier if((ch != ' ')&&(ch != ' ')&&(lineStart == i)){ sectionStart = i; // Hit a tag. go deal with it. readState = 0; i--; }else if((ch != ' ')&&(ch != ' ')&&((lineStart == i - SEQ_SUBTAG_COLUMN)||((buf[lineStart]==' ')&&(i==lineStart+1)))){ sectionStart = i; // Hit a feature. go deal with it. readState = 2; i--; }else if(ch == ','){ //oops! another location to read! sectionStart = i+1; readState = 3; }else if(ch == '/'){ //finally, a qualifier. sectionStart = i+1; readState = 8; }else if(ch == '\n') lineStart = i + 1; break; case 8: //get a qualifier, stop on = if(ch == '='){ curQualifierName = string(buf+sectionStart, i - sectionStart); readState = 9; sectionStart = i+1; } break; case 9: //are we getting a string? look for " or [ if(ch == '"'){ readState = 10; sectionStart = i; curQualifierStart = i + streamPos; }else if(ch == '['){ readState = 11; sectionStart = i; }else if((ch == '\r')||(ch == '\n')){ curFeature->AddQualifier(new gnSourceQualifier(this, curQualifierName, sectionStart + streamPos, i - sectionStart)); sectionStart = i+1; readState = 7; //look for another qualifier } break; case 10: //read until the end of the quotation. look out for escaped quotes if(ch == '"') readState = 11; if(ch == '\n'){ lineStart = i + 1; } break; case 11: if(ch != '"'){ curFeature->AddQualifier(new gnSourceQualifier(this, curQualifierName, curQualifierStart, i - sectionStart)); sectionStart = i+1; readState = 7; //look for another qualifier. if(ch == '\n') lineStart = i + 1; }else readState = 10; //quote was escaped. look for another. break; case 12: if(ch == ']'){ curFeature->AddQualifier(new gnSourceQualifier(this, curQualifierName, sectionStart + streamPos, i - sectionStart)); sectionStart = i+1; readState = 7; //look for another qualifier. } break; case 13: //start the sequence read. if(ch == '^') //stupid blattlab file format. readState = 14; else{ curContig->SetSectStart(gnContigSequence, i + 1 + streamPos); readState = 16; } break; case 14: //wait for newline before sequence starts. if(ch == '\n'){ curContig->SetRepeatSeqGap(true); lineStart = i + 1; sectionStart = i + 1; curContig->SetSectStart(gnContigSequence, i + 1 + streamPos); readState = 15; } break; case 15: if(m_pFilter->IsValid(ch)) seqLength++; else curContig->SetRepeatSeqGap(false); break; case 16: if((ch == '/')&&(i==lineStart)){ readState = 17; }else if(m_pFilter->IsValid(ch)){ seqLength++; lineSeqSize++; if(gapstart >= 0){ curContig->SetRepeatGapSize(i - gapstart); gapstart = -1; } }else if(ch == '\n'){ //IMPLEMENT ME! Needs consistent gap size checking if(sectionStart == lineStart){ curContig->SetRepeatSeqGap(true); curContig->SetRepeatSeqSize(seqLength); gapstart = i; for(; gapstart >= lineStart; gapstart--) if(m_pFilter->IsValid(buf[gapstart])) break; gapstart++; }else if(lineSeqSize != curContig->GetRepeatSeqGapSize().first) curContig->SetRepeatSeqGap(false); lineSeqSize = 0; lineStart = i + 1; } break; case 17: if((ch == '\n')&&(buf[lineStart+1] == '/')){ curContig->SetSectEnd(gnContigSequence, lineStart - 2 + streamPos); curContig->SetSeqLength(seqLength); m_contigList.push_back(curContig); curContig = 0; curSpec->SetLength(seqLength); curSpec = 0; seqLength = 0; lineStart = i + 1; sectionStart = i + 1; readState = 0; } break; } } streamPos += bufReadLen; } if(curContig != 0){ curContig->SetSectEnd(gnContigSequence, streamPos - 1); curContig->SetSeqLength(seqLength); m_contigList.push_back(curContig); curSpec->SetLength(seqLength); } if(curSpec != NULL) if((curFrag->GetFeatureListLength() == 0) && (curFrag->GetHeaderListLength() == 0) &&(curSpec->GetLength() == 0)){ m_spec->RemoveSpec(m_spec->GetSpecListLength() - 1); delete curFrag; } m_ifstream.clear(); delete[] buf; return true; } } // end namespace genome libGenome-1.3.1/libGenome/gnBaseFeature.cpp0000644002622200470610000001644410647575617015517 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnBaseFeature.cpp // Purpose: implements the gnBaseFeature // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnBaseFeature.h" #include "libGenome/gnLocation.h" #include "libGenome/gnStringQualifier.h" #include "libGenome/gnDebug.h" #include using namespace std; namespace genome { gnBaseFeature::gnBaseFeature( ) { m_id = 0; m_name = ""; m_locationType = gnLocation::LT_Nothing; m_broken = false; m_spec = NULL; } gnBaseFeature::gnBaseFeature( string& name, uint32 id, gnFragmentSpec* spec, gnLocation::gnLocationType lt, boolean broken ) { m_id = id; m_name = name; m_locationType = lt; m_broken = broken; m_spec = NULL; } gnBaseFeature::~gnBaseFeature() { for( uint32 i=0; i < m_qualifierList.size(); i++) delete m_qualifierList[i]; } // Clone // Location Modification methods boolean gnBaseFeature::MovePositive( const gnSeqI i ) { boolean still_valid = true; for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ still_valid = still_valid && m_locationList[locationI].MovePositive(i); } return still_valid; } boolean gnBaseFeature::MoveNegative( const gnSeqI i ) { boolean still_valid = true; for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ still_valid = still_valid && m_locationList[locationI].MoveNegative(i); } return still_valid; } //delete everything bigger than i boolean gnBaseFeature::CropEnd( const gnSeqI i ) { boolean still_valid = true; for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ still_valid = still_valid && m_locationList[locationI].CropEnd(i); } return still_valid; } //delete everything less than i boolean gnBaseFeature::CropStart( const gnSeqI i ){ boolean still_valid = true; for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ still_valid = still_valid && m_locationList[locationI].CropStart(i); } return still_valid; } uint32 gnBaseFeature::FirstIndexOfQualifier( const string& name, uint32 listI ) const{ if(listI >= m_qualifierList.size()) return GNSEQI_END; uint32 i=listI; for(; i < m_qualifierList.size(); i++){ string qname = m_qualifierList[i]->GetName(); if(qname == name) break; } return i; } uint32 gnBaseFeature::LastIndexOfQualifier( const string& name, uint32 listI ) const{ if(listI >= m_qualifierList.size()) return GNSEQI_END; uint32 i=m_qualifierList.size()-1; for(; i >= listI; i--) if(m_qualifierList[i]->GetName() == name) break; return i; } boolean gnBaseFeature::RemoveQualifier( uint32 listI ){ if(listI < m_qualifierList.size()){ delete m_qualifierList[ listI ]; m_qualifierList.erase(m_qualifierList.begin() + listI); return true; } return false; } boolean gnBaseFeature::SetQualifier( string& name, string& value, uint32 listI ){ if(listI < m_qualifierList.size()){ delete m_qualifierList[ listI ]; m_qualifierList[listI] = new gnStringQualifier(name, value); return true; } return false; } boolean gnBaseFeature::SetQualifierName( string& name, uint32 listI ){ if(listI < m_qualifierList.size()){ gnStringQualifier* new_qual = new gnStringQualifier(name, m_qualifierList[listI]->GetValue()); delete m_qualifierList[listI]; m_qualifierList[listI] = new_qual; return true; } return false; } boolean gnBaseFeature::SetQualifierValue( string& value, uint32 listI ){ if(listI < m_qualifierList.size()){ gnStringQualifier* new_qual = new gnStringQualifier(m_qualifierList[listI]->GetName(), value); delete m_qualifierList[listI]; m_qualifierList[listI] = new_qual; return true; } return false; } // Compare methods boolean gnBaseFeature::Contains( gnSeqI i ) const{ for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ if((m_locationList[locationI].GetStart() <= i) && (m_locationList[locationI].GetEnd() >= i)) return true; } return false; } boolean gnBaseFeature::Contains( const gnLocation& l ) const{ for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ if(m_locationList[locationI].Contains(l)) return true; } return false; } boolean gnBaseFeature::Contains( gnBaseFeature* feature ) const{ for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ uint32 i=0; for(; i < feature->GetLocationListLength(); i++){ if(m_locationList[locationI].Contains(feature->GetLocation(i))) break; //it's contained so we'll break the loop early } if(i == feature->GetLocationListLength()) return false; //the loop went full cycle. we found an uncontained location } return true; } boolean gnBaseFeature::IsContainedBy( const gnLocation& l ) const{ for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ if(!l.Contains(m_locationList[locationI])) return false; } return true; } boolean gnBaseFeature::Intersects( const gnLocation& l ) const{ for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ if(!l.Intersects(m_locationList[locationI])) return false; } return true; } boolean gnBaseFeature::Intersects( gnBaseFeature* feature ) const{ for(uint32 locationI=0; locationI< m_locationList.size(); locationI++){ uint32 i=0; for(; i < feature->GetLocationListLength(); i++){ if(m_locationList[locationI].Intersects(feature->GetLocation(i))) break; //it's contained so we'll break the loop early } if(i == feature->GetLocationListLength()) return false; //the loop went full cycle. we found an uncontained location } return true; } inline boolean gnBaseFeature::AddLocation( const gnLocation& l, uint32 listI ){ if(listI <= m_locationList.size()){ m_locationList.insert(m_locationList.begin() + listI, l); return true; } return false; } gnLocation gnBaseFeature::GetLocation( uint32 listI ) const{ if(listI < m_locationList.size()) return m_locationList[listI]; return gnLocation(); } boolean gnBaseFeature::RemoveLocation( uint32 listI ){ if(listI < m_locationList.size()){ m_locationList.erase(m_locationList.begin() + listI); return true; } return false; } boolean gnBaseFeature::SetLocation( const gnLocation& l, uint32 listI ){ if(listI < m_locationList.size()){ m_locationList[listI] = l; return true; } return false; } boolean gnBaseFeature::AddQualifier( gnBaseQualifier* qualifier ){ if(qualifier != NULL){ m_qualifierList.push_back(qualifier); return true; } return false; } boolean gnBaseFeature::HasQualifier( const string& name ) const{ for(uint32 i=0; i < m_qualifierList.size(); i++) if(m_qualifierList[i]->GetName() == name) return true; return false; } string gnBaseFeature::GetQualifierName( uint32 listI ) const{ if(listI < m_qualifierList.size()) return m_qualifierList[listI]->GetName(); return string(); } string gnBaseFeature::GetQualifierValue( uint32 listI ) const{ if(listI < m_qualifierList.size()) return m_qualifierList[listI]->GetValue(); return string(); } gnBaseQualifier* gnBaseFeature::GetQualifier( uint32 listI ){ if(listI < m_qualifierList.size()) return m_qualifierList[listI]->Clone(); return NULL; } } // end namespace genome libGenome-1.3.1/libGenome/gnTranslator.cpp0000644002622200470610000002120410647575617015450 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnTranslator.h // Purpose: Filter for all Sequences // Description: translates, converts sequence // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnTranslator.h" #include "libGenome/gnCompare.h" #include using namespace std; using namespace std; namespace genome { // static data access, avoids static initialization order fiasco const gnTranslator *gnTranslator::ProteinDNATranslator(){ const static gnTranslator* t_trans = new gnTranslator(ProteinDNATranslatorType); return t_trans; } const gnTranslator *gnTranslator::ProteinRNATranslator(){ const static gnTranslator* t_trans = new gnTranslator(ProteinRNATranslatorType); return t_trans; } const gnTranslator *gnTranslator::DNAProteinTranslator(){ const static gnTranslator* t_trans = new gnTranslator(DNAProteinTranslatorType); return t_trans; } const gnTranslator *gnTranslator::RNAProteinTranslator(){ const static gnTranslator* t_trans = new gnTranslator(RNAProteinTranslatorType); return t_trans; } // public: gnTranslator::gnTranslator() { use_default = false; m_defaultChar = 0; m_defaultInputWidth = 1; } gnTranslator::gnTranslator( const gnTranslator &sf ) { m_name = sf.m_name; use_default = sf.use_default; m_defaultChar = sf.m_defaultChar; compare = sf.compare; m_inputTable = sf.m_inputTable; m_outputTable = sf.m_outputTable; m_defaultInputWidth = sf.m_defaultInputWidth; } gnTranslator::gnTranslator( gnTranslatorType t_type ) { use_default = false; m_defaultChar = 0; switch(t_type){ case ProteinDNATranslatorType: CreateProteinDNATranslator(); break; case ProteinRNATranslatorType: CreateProteinRNATranslator(); break; case DNAProteinTranslatorType: CreateDNAProteinTranslator(); break; case RNAProteinTranslatorType: CreateRNAProteinTranslator(); break; } } // gnSeqC gnSeqC gnTranslator::Filter( const gnSeqC ch ) const{ for(uint32 i=0; i < m_inputTable.size(); i++){ if(m_inputTable[i].length() == 1) if(compare->Contains(m_inputTable[i][0], ch)) return m_outputTable[i][0]; } return m_defaultChar; } void gnTranslator::Filter( gnSeqC** seq, gnSeqI& len ) const{ uint32 curpos = 0; string output; while(curpos < len){ uint32 i=0; for(; i < m_inputTable.size(); i++){ //don't compare if there aren't enough chars uint32 curlen = m_inputTable[i].length(); if(len - curpos < curlen) continue; if(compare->Contains(m_inputTable[i].data(), *seq + curpos, curlen)){ output += m_outputTable[i]; curpos += curlen; break; } } if(i == m_inputTable.size()){ //no match was found. if(use_default) //fill with the default char? output += m_defaultChar; curpos += m_defaultInputWidth; } } if(output.length() > len){ delete[] *seq; *seq = new gnSeqC[output.length()]; } len = output.length(); memcpy(*seq, output.data(), len); } // string void gnTranslator::Filter( string &seq ) const{ uint32 curpos = 0; uint32 len = seq.length(); string output; while(curpos < len){ uint32 i=0; for(; i < m_inputTable.size(); i++){ //don't compare if there aren't enough chars uint32 curlen = m_inputTable[i].length(); if(len - curpos < curlen) continue; if(compare->Contains(m_inputTable[i], seq.substr(curpos, curlen))){ output += m_outputTable[i]; curpos += curlen; break; } } if(i == m_inputTable.size()){ //no match was found. if(use_default) //fill with the default char? output += m_defaultChar; curpos += m_defaultInputWidth; } } seq = output; } // fill map void gnTranslator::SetPair( const string& ch1, const string& ch2 ) { if(ch1.length() == 0) return; //cant have an empty input, empty output is ok m_inputTable.push_back(ch1); m_outputTable.push_back(ch2); } void gnTranslator::RemovePair( const string& ch ) { for(uint32 i=0; i < m_inputTable.size(); i++){ if(m_inputTable[i] == ch){ m_inputTable.erase(m_inputTable.begin()+i); m_outputTable.erase(m_outputTable.begin()+i); } } } // standard comparators void gnTranslator::CreateProteinDNATranslator(){ SetName( "Protein to DNA Translator" ); SetDefaultChar('X'); SetCompare(gnCompare::ProteinSeqCompare()); m_defaultInputWidth = 1; SetPair( "F", "TTY" ); SetPair( "L", "YTX" ); //fix this somehow. how? SetPair( "I", "ATH" ); SetPair( "M", "ATG" ); SetPair( "V", "GTX" ); SetPair( "P", "CCX" ); SetPair( "T", "ACX" ); SetPair( "A", "GCX" ); SetPair( "Y", "TAY" ); SetPair( ".", "TRR" );//fix this somehow. how? SetPair( "H", "CAY" ); SetPair( "Q", "CAR" ); SetPair( "N", "AAY" ); SetPair( "K", "AAR" ); SetPair( "D", "GAY" ); SetPair( "E", "GAR" ); SetPair( "C", "TGY" ); SetPair( "W", "TGG" ); SetPair( "G", "GGX" ); SetPair( "S", "TCX" ); SetPair( "S", "AGY"); SetPair( "R", "CGX"); SetPair( "R", "AGR"); } void gnTranslator::CreateProteinRNATranslator(){ SetName( "Protein to RNA Translator" ); SetDefaultChar('X'); SetCompare(gnCompare::ProteinSeqCompare()); m_defaultInputWidth = 1; SetPair( "F", "UUY" ); SetPair( "L", "YUX" ); //fix this somehow. how? SetPair( "I", "AUH" ); SetPair( "M", "AUG" ); SetPair( "V", "GUX" ); SetPair( "P", "CCX" ); SetPair( "U", "ACX" ); SetPair( "A", "GCX" ); SetPair( "Y", "UAY" ); SetPair( ".", "URR" );//fix this somehow. how? SetPair( "H", "CAY" ); SetPair( "Q", "CAR" ); SetPair( "N", "AAY" ); SetPair( "K", "AAR" ); SetPair( "D", "GAY" ); SetPair( "E", "GAR" ); SetPair( "C", "UGY" ); SetPair( "W", "UGG" ); SetPair( "G", "GGX" ); SetPair( "S", "UCX" ); SetPair( "S", "AGY"); SetPair( "R", "CGX"); SetPair( "R", "AGR"); } void gnTranslator::CreateDNAProteinTranslator(){ SetName( "DNA to Protein Translator" ); SetDefaultChar('X'); SetCompare(gnCompare::DNASeqCompare()); m_defaultInputWidth = 3; use_default = true; SetPair( "TTY", "F" ); SetPair( "CTX", "L" ); SetPair( "TTR", "L" ); SetPair( "ATH", "I" ); SetPair( "ATG", "M" ); SetPair( "GTX", "V" ); SetPair( "CCX", "P" ); SetPair( "ACX", "T" ); SetPair( "GCX", "A" ); SetPair( "TAY", "Y" ); SetPair( "TGG", "W" ); SetPair( "TGA", "." ); SetPair( "TAR", "." ); SetPair( "CAY", "H" ); SetPair( "CAR", "Q" ); SetPair( "AAY", "N" ); SetPair( "AAR", "K" ); SetPair( "GAY", "D" ); SetPair( "GAR", "E" ); SetPair( "TGY", "C" ); SetPair( "GGX", "G" ); SetPair( "TCX", "S" ); SetPair( "AGY", "S" ); SetPair( "CGX", "R" ); SetPair( "AGR", "R" ); SetPair( "tty", "F" ); SetPair( "ctx", "L" ); SetPair( "ttr", "L" ); SetPair( "ath", "I" ); SetPair( "atg", "M" ); SetPair( "gtx", "V" ); SetPair( "ccx", "P" ); SetPair( "acx", "T" ); SetPair( "gcx", "A" ); SetPair( "tay", "Y" ); SetPair( "tgg", "W" ); SetPair( "tga", "." ); SetPair( "tar", "." ); SetPair( "cay", "H" ); SetPair( "car", "Q" ); SetPair( "aay", "N" ); SetPair( "aar", "K" ); SetPair( "gay", "D" ); SetPair( "gar", "E" ); SetPair( "tgy", "C" ); SetPair( "ggx", "G" ); SetPair( "tcx", "S" ); SetPair( "agy", "S" ); SetPair( "cgx", "R" ); SetPair( "agr", "R" ); } void gnTranslator::CreateRNAProteinTranslator(){ SetName( "RNA to Protein Translator" ); SetDefaultChar('X'); SetCompare(gnCompare::RNASeqCompare()); m_defaultInputWidth = 3; use_default = true; SetPair( "UUY", "F" ); SetPair( "CUX", "L" ); SetPair( "UUR", "L" ); SetPair( "AUH", "I" ); SetPair( "AUG", "M" ); SetPair( "GUX", "V" ); SetPair( "CCX", "P" ); SetPair( "ACX", "T" ); SetPair( "GCX", "A" ); SetPair( "UAY", "Y" ); SetPair( "UGG", "W" ); SetPair( "UGA", "." ); SetPair( "UAR", "." ); SetPair( "CAY", "H" ); SetPair( "CAR", "Q" ); SetPair( "AAY", "N" ); SetPair( "AAR", "K" ); SetPair( "GAY", "D" ); SetPair( "GAR", "E" ); SetPair( "UGY", "C" ); SetPair( "GGX", "G" ); SetPair( "UCX", "S" ); SetPair( "AGY", "S" ); SetPair( "CGX", "R" ); SetPair( "AGR", "R" ); SetPair( "uuy", "F" ); SetPair( "cux", "L" ); SetPair( "uur", "L" ); SetPair( "auh", "I" ); SetPair( "aug", "M" ); SetPair( "gux", "V" ); SetPair( "ccx", "P" ); SetPair( "acx", "T" ); SetPair( "gcx", "A" ); SetPair( "uay", "Y" ); SetPair( "ugg", "W" ); SetPair( "uga", "." ); SetPair( "uar", "." ); SetPair( "cay", "H" ); SetPair( "car", "Q" ); SetPair( "aay", "N" ); SetPair( "aar", "K" ); SetPair( "gay", "D" ); SetPair( "gar", "E" ); SetPair( "ugy", "C" ); SetPair( "ggx", "G" ); SetPair( "ucx", "S" ); SetPair( "agy", "S" ); SetPair( "cgx", "R" ); SetPair( "agr", "R" ); } } // end namespace genome libGenome-1.3.1/libGenome/gnSourceFactory.h0000644002622200470610000001666211026443220015540 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnSourceFactory.h // Purpose: Manage data sources // Description: Manages data sources by tracking open files/databases/URLs // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnSourceFactory_h_ #define _gnSourceFactory_h_ #include "libGenome/gnDefs.h" #include #include #include #include "libGenome/gnBaseSource.h" namespace genome { /** * gnSourceFactory is the middle man when acessing a sequence data source * It tracks all data sources currently in use, ensuring that a particular * data source is only opened and parsed once. When opening a data source * it first tries to interpret the source location as a URL, opening the * specified file, or downloading it if necessary. If that fails, it will * attempt to open the source as a file on the local disk. * gnSourceFactory uses the file extension to determine file format, so a * file which ends with .fas will be opened by gnFASSource. Finally, * gnSourceFactory can be given directory paths to search when opening a * file whose path is not specified. * IMPORTANT: Do not try to instantiate this class. * To use this class do the following: * gnSourceFactory* mySourceFactory = gnSourceFactory::GetSourceFactory(); */ class GNDLLEXPORT gnSourceFactory{ public: ~gnSourceFactory(); /** * Returns the current source factory. * @return The current source factory. */ static gnSourceFactory* GetSourceFactory(); // Plugin Sources /** * Returns the number of file extension to class mappings. * @return The list size. */ uint32 GetSourceClassListSize() const; /** * Deletes a file extension to class mapping. * @param ext The extension to delete. * @return True if successful. */ boolean DelSourceClass( const std::string& ext ); /** * Gets the source class which is mapped to the specified file extension. * @param ext The extension to delete. * @return The class associated with the extension. */ gnBaseSource* GetSourceClass( const std::string& ext ) const; /** * Gets the source class which would be mapped to the std::string. * @param sourceStr The std::string to check, usually a filename. * @return The class associated with the extension. */ gnBaseSource* MatchSourceClass( const std::string& sourceStr ) const; /** * Checks if the specified file extension is recognized. * @param ext The extension to check. * @return True if the extension has a class. */ boolean HasSourceClass( const std::string& ext ) const; /** * Maps the specified file extension to the given source class. * e.g. ".fas" to gnFASSource * @param ext The extension to map. * @param source The class to map * @return True if successful. */ boolean SetSourceClass( const std::string& ext, const gnBaseSource& source ); /** * Sets a source class to be the default class for unknown file extensions. * @param source The default class to map * @return True if successful. */ boolean SetDefaultSourceClass( const gnBaseSource* source ); /** * Gets the source class which is the default class for unknown file extensions. * @return The default class */ gnBaseSource* GetDefaultSourceClass() const; // Directory paths to search for sources /** * Returns the number of directory paths to search for files. * @return The list size. */ uint32 GetPathListSize() const; /** * Adds the directory to the search path. * @param path The path to add. * @return True if successful. */ boolean AddPath( const std::string& path ); /** * Deletes the directory path at index i from the search path list. * @param i The index of the path to delete. * @return True if successful, false if i is out of range. */ boolean DelPath( uint32 i ); /** * Inserts the directory path at index i in the search path list. * @param path The path to insert. * @param i The index of the path to insert before. * @return True if successful, false if i is out of range. */ boolean InsPath( const std::string& path, uint32 i ); /** * Gets the directory path at index i in the path list. * @param i The index of the path to get. * @return The path or an empty std::string if i is out of range. */ std::string GetPath( uint32 i ) const; /** * Checks the path list for the given path. * @param path The path to look for. * @return True if the path is in the path list. */ boolean HasPath( std::string path ) const; // Sources /** * Returns the number of open data sources. * @return The list size. */ uint32 GetSourceListSize() const; /** * Opens and returns a pointer to a source of genetic sequence data. * If the source has already been opened, AddSource() returns a copy of the existing source class. * @param sourceStr The file name or URL where the source is located. * @param searchPaths Should the path list be searched if the file can't be found. * @return A pointer to the source. */ gnBaseSource* AddSource( const std::string& sourceStr, boolean searchPaths = true ); /** * Gets the source at index i in the source list. * @param i The index of the source to get. * @return The source. */ gnBaseSource* GetSource( uint32 i ) const; /** * Deletes the source at index i in the source list. * This will close the associated file, network, or database connection. * @param i The index of the source to delete. * @throws IndexOutOfBounds if i is too large */ void DelSource( uint32 i ); /** * Deletes the given source from the source list. * This will close the associated file, network, or database connection. * @param source The source to close. * @return True if successful. */ boolean DelSource( const gnBaseSource* source ); /** * Gets the source if it has already been opened. * @param sourceStr The file name or URL where the source is located. * @param searchPaths Should the path list be searched if the file can't be found. * @return A pointer to the source. */ gnBaseSource* HasSource( std::string sourceStr, boolean searchPaths = true ) const; private: gnSourceFactory(); gnSourceFactory(gnSourceFactory& gnsf); gnSourceFactory& operator=(gnSourceFactory& gnsf); boolean PathExists( std::string path ) const; static boolean GetURL( const std::string& urlStr, std::string& localFile ); std::vector< std::string > m_pathList; std::vector< gnBaseSource* > m_sourceList; std::map< std::string, gnBaseSource* > m_sourceClassList; gnBaseSource* m_pDefaultSourceClass; };//class gnSourceFactory // Plugin Sources inline uint32 gnSourceFactory::GetSourceClassListSize() const { return m_sourceClassList.size(); } inline boolean gnSourceFactory::SetDefaultSourceClass( const gnBaseSource* source ) { if(m_pDefaultSourceClass != NULL){ delete m_pDefaultSourceClass; } m_pDefaultSourceClass = source->Clone(); return true; } inline gnBaseSource* gnSourceFactory::GetDefaultSourceClass() const { return m_pDefaultSourceClass; } // Directory paths to search for sources inline uint32 gnSourceFactory::GetPathListSize() const { return m_pathList.size(); } inline uint32 gnSourceFactory::GetSourceListSize() const { return m_sourceList.size(); } } // end namespace genome #endif // _gnSourceFactory_h_ libGenome-1.3.1/libGenome/gnDebug.h0000644002622200470610000000302710647575617014015 00000000000000///////////////////////////////////////////////////////////////////////////// // File: libGenome/gnDebug.h // Purpose: Debug header used for libGenome // Description: Debug defines all debuging tools used for libGenome // Rev: A // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifndef _gnDebug_h_ #define _gnDebug_h_ #include "libGenome/gnDefs.h" #include #include #if(defined(WIN32)) #include "intrin.h" #endif namespace genome { /** this little function traps into the MSVC debugger */ inline void breakHere() { #if(defined(WIN32)) __debugbreak(); #endif } #if defined(COMMAND_LINE) || defined(_CONSOLE) const boolean USE_COMMAND_LINE = true; const boolean USE_GUI = false; #elif defined(GN_GUI) const boolean USE_COMMAND_LINE = false; const boolean USE_GUI = true; #else const boolean USE_COMMAND_LINE = false; const boolean USE_GUI = false; #endif GNDLLEXPORT void DebugMsg(std::string a); inline void DebugMsg(std::string a){ if(USE_COMMAND_LINE){ std::cout << a; }else if(USE_GUI){ } } GNDLLEXPORT void ErrorMsg(std::string a); inline void ErrorMsg(std::string a){ if(USE_COMMAND_LINE){ std::cout << a; }else if(USE_GUI){ } } } // end namespace genome #endif //_gnDebug_h_ libGenome-1.3.1/libGenome/TestRevComp.cpp0000644002622200470610000000227210647575617015211 00000000000000#ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnSourceFactory.h" #include "libGenome/gnFASSource.h" #include "libGenome/gnDNXSource.h" #include "libGenome/gnSEQSource.h" #include "libGenome/gnSequence.h" #include #include #include "libGenome/gnFilter.h" int main( int32 argc, char* argv[]) { argc; argv; string filename; cout << "Enter a filename to read bases from.\n"; cin >> filename; cout << "Opening " + filename + "\n"; gnSequence gnseq, smallseq; if(gnseq.LoadSource(filename)) cout << "Sequence has " << gnseq.length() << " base pairs.\n"; smallseq = gnseq.subseq(3836480, 10); cout << smallseq; string dump; cin >> dump; cout << "Give a file name to output reverse complement data: "; string outfilename; cin >> outfilename; cout << "Bases are:\n"; // cout << gpseq; cout << "\nComplement Bases are:\n"; gnBaseSpec* gpbs = gnseq.GetSpec(); gpbs->SetReverseComplement(true); // cout << gpseq << "\n"; gnFASSource::Write(gnseq, outfilename); // gnGBKSource::Write(gpbs, "testfile.seq"); // gnDNXSource::Write(gpbs, "testfile.dnx"); cout << "All done. RevComp is in " << outfilename << "\n"; char bubba[50]; cin >> bubba; } libGenome-1.3.1/libGenome/gnFileSource.cpp0000644002622200470610000000540011026443220015327 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnFileSource.h // Purpose: Implements generic gnBaseSource methods // Description: Provides a general implementation for accessing DNA // sequence contig data files. // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnFileSource.h" #include #include "libGenome/gnFilter.h" using namespace std; namespace genome { gnFileSource::gnFileSource() : m_pFilter(gnFilter::fullDNASeqFilter()) {} //copy constructor gnFileSource::gnFileSource(const gnFileSource& gnfs){ m_openString = gnfs.m_openString; m_pFilter = gnfs.m_pFilter; m_newlineType = gnfs.m_newlineType; m_newlineSize = gnfs.m_newlineSize; #pragma omp critical { m_ifstream.open( m_openString.c_str(), ios::in | ios::binary ); if( !m_ifstream.is_open() ) m_ifstream.clear(); } } // Open, Close void gnFileSource::Open( string openString ) { boolean opened = true; #pragma omp critical { m_ifstream.open(openString.c_str(), ios::in | ios::binary ); if( m_ifstream.is_open() ) { m_openString = openString; if( ParseStream(m_ifstream) ) { ; } else{ m_ifstream.clear(); m_ifstream.close(); } }else{ m_ifstream.clear(); opened = false; } } if(!opened) Throw_gnEx(FileNotOpened()); } void gnFileSource::Open( ) { bool opened = true; #pragma omp critical { m_ifstream.open( m_openString.c_str(), ios::in | ios::binary ); if( !m_ifstream.is_open() ){ opened = false; m_ifstream.clear(); } } if(!opened) Throw_gnEx(FileNotOpened()); } void gnFileSource::Close() { #pragma omp critical m_ifstream.close(); } boolean gnFileSource::Read( const uint64 pos, char* buf, gnSeqI& bufLen) { bool failure = false; #pragma omp critical { m_ifstream.seekg(pos, ios::beg); m_ifstream.read(buf, bufLen); failure = m_ifstream.fail(); } if(failure){ #pragma omp critical m_ifstream.clear(); return false; } return true; } void gnFileSource::DetermineNewlineType() { // set default values m_newlineType = gnNewlineUnix; m_newlineSize = 1; //decide what type of newlines we have char buf[ BUFFER_SIZE ]; m_ifstream.getline( buf, BUFFER_SIZE); m_ifstream.seekg(-2, ios::cur); m_ifstream.read( buf, 2); m_ifstream.seekg(0); if(buf[1] == '\n'){ if(buf[0] == '\r'){ m_newlineType = gnNewlineWindows; m_newlineSize = 2; }else{ if(buf[1] == '\r') m_newlineType = gnNewlineMac; else m_newlineType = gnNewlineUnix; } } } } // end namespace genome libGenome-1.3.1/libGenome/gnFragmentSpec.cpp0000644002622200470610000001252310647575617015701 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnFragmentSpec.cpp // Purpose: implements gnMultiSpec< gnContigSpec > for sequence fragments // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnFragmentSpec.h" #include using namespace std; namespace genome { gnFragmentSpec::gnFragmentSpec() { gnBaseSpec::Clear(); } gnFragmentSpec::gnFragmentSpec( const gnFragmentSpec& s ) { m_sourceName = s.m_sourceName; m_name = s.m_name; m_reverseComplement = s.m_reverseComplement; m_circular = s.m_circular; //copy the header list. uint32 list_size = s.m_headerList.size(); m_headerList.reserve(list_size); for(uint32 i=0; i < list_size; i++) m_headerList.push_back(s.m_headerList[i]->Clone()); //copy the contig list. list_size = s.m_SpecList.size(); m_SpecList.reserve(list_size); uint32 i=0; for(; i < list_size; i++) m_SpecList.push_back(s.m_SpecList[i]->Clone()); //copy the feature list list_size = s.m_featureList.size(); m_featureList.reserve(list_size); for(i=0; i < list_size; i++) m_featureList.push_back(s.m_featureList[i]->Clone()); } gnFragmentSpec::~gnFragmentSpec() { Clear(); } // Clone void gnFragmentSpec::Clear() { uint32 list_size = m_SpecList.size(); for(uint32 i=0; i < list_size; i++) delete m_SpecList[i]; m_SpecList.clear(); list_size = m_featureList.size(); for(uint32 i=0; i < list_size; i++) delete m_featureList[i]; m_featureList.clear(); gnMultiSpec< gnContigSpec >::Clear(); } //Fragment void gnFragmentSpec::GetContainedFeatures(const gnLocation& lt, vector& feature_vector, vector& index_vector) const{ for(uint32 i=0; i < m_featureList.size(); i++){ if(m_featureList[i]->IsContainedBy(lt)){ feature_vector.push_back(m_featureList[i]->Clone()); index_vector.push_back(i); } } } void gnFragmentSpec::GetIntersectingFeatures(const gnLocation& lt, vector& feature_vector, vector& index_vector) const{ for(uint32 i=0; i < m_featureList.size(); i++){ if(m_featureList[i]->Intersects(lt)){ feature_vector.push_back(m_featureList[i]->Clone()); index_vector.push_back(i); } } } void gnFragmentSpec::GetBrokenFeatures(const gnLocation& lt, vector& feature_vector) const{ for(uint32 i=0; i < m_featureList.size(); i++) if(m_featureList[i]->IsBroken() && m_featureList[i]->IsContainedBy(lt)) feature_vector.push_back(m_featureList[i]->Clone()); } //do feature cropping... done void gnFragmentSpec::CropStart( gnSeqI cropLen ){ uint32 flen = m_featureList.size(); for(uint32 featureI = 0; featureI < flen; featureI++){ m_featureList[featureI]->CropStart(cropLen); } gnMultiSpec< gnContigSpec >::CropStart(cropLen); } void gnFragmentSpec::CropEnd( gnSeqI cropLen ){ uint32 flen = m_featureList.size(); for(uint32 featureI = 0; featureI < flen; featureI++){ m_featureList[featureI]->CropEnd(cropLen); } gnMultiSpec< gnContigSpec >::CropEnd(cropLen); } gnFragmentSpec* gnFragmentSpec::CloneRange( const gnSeqI startI, const gnSeqI len ) const{ if(len == 0) return new gnFragmentSpec(); //find the valid range of specs to copy uint32 firstSpec = GetSpecIndexByBase(startI); gnSeqI total_copylen = len; uint32 endSpec; if(len != GNSEQI_END){ endSpec = GetSpecIndexByBase(startI + len - 1); }else{ endSpec = GetSpecListLength() - 1; total_copylen = GetLength() - startI; } //find their starting and ending bases gnSeqI firstBase = startI - GetSpecStartBase(firstSpec); gnSeqI firstSpecLen = GetSpec(firstSpec)->GetLength(); boolean spans_specs = true; gnSeqI firstCopyLen = firstSpecLen - firstBase; if(firstCopyLen >= total_copylen){ spans_specs = false; firstCopyLen = total_copylen; } gnFragmentSpec* destSpec = new gnFragmentSpec(); gnContigSpec* newSpec = m_SpecList[firstSpec]->CloneRange(firstBase, firstCopyLen); destSpec->AddSpec( newSpec ); gnSeqI cur_copylen = firstCopyLen; //add all the completely covered specs in the middle for(uint32 specI = firstSpec + 2; specI <= endSpec; specI++){ destSpec->AddSpec(GetSpec(specI-1)->Clone()); cur_copylen += GetSpec(specI-1)->GetLength(); } //add the last spec if necessary if(spans_specs){ newSpec = m_SpecList[endSpec]->CloneRange( 0, total_copylen - cur_copylen); destSpec->AddSpec(newSpec); } //now clone all the appropriate features gnLocation lt; vector feature_vector; vector index_vector; lt.SetStart(startI); lt.SetEnd(startI + total_copylen); GetIntersectingFeatures(lt, destSpec->m_featureList, index_vector); return destSpec; } /*IMPLEMENT ME!! 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distclean-tags dvi: dvi-am dvi-am: html: html-am info: info-am info-am: install-data-am: install-library_includeHEADERS install-exec-am: install-libLTLIBRARIES install-info: install-info-am install-man: installcheck-am: maintainer-clean: maintainer-clean-am -rm -rf ./$(DEPDIR) -rm -f Makefile maintainer-clean-am: distclean-am maintainer-clean-generic mostlyclean: mostlyclean-am mostlyclean-am: mostlyclean-compile mostlyclean-generic \ mostlyclean-libtool pdf: pdf-am pdf-am: ps: ps-am ps-am: uninstall-am: uninstall-info-am uninstall-libLTLIBRARIES \ uninstall-library_includeHEADERS .PHONY: CTAGS GTAGS all all-am check check-am clean \ clean-checkPROGRAMS clean-generic clean-libLTLIBRARIES \ clean-libtool ctags distclean distclean-compile \ distclean-generic distclean-libtool distclean-tags distdir dvi \ dvi-am html html-am info info-am install install-am \ install-data install-data-am install-exec install-exec-am \ install-info install-info-am install-libLTLIBRARIES \ install-library_includeHEADERS install-man install-strip \ installcheck installcheck-am installdirs maintainer-clean \ maintainer-clean-generic mostlyclean mostlyclean-compile \ mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \ tags uninstall uninstall-am uninstall-info-am \ uninstall-libLTLIBRARIES uninstall-library_includeHEADERS # 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: libGenome-1.3.1/libGenome/gnRAWSource.cpp0000644002622200470610000000731510647575617015140 00000000000000///////////////////////////////////////////////////////////////////////////// // File: gnRAWSource.h // Purpose: Implements gnBaseSource for raw data files // Description: // Changes: // Version: libGenome 0.5.1 // Author: Aaron Darling // Modified by: // Copyright: (c) Aaron Darling // Licenses: See COPYING file for details ///////////////////////////////////////////////////////////////////////////// #ifdef HAVE_CONFIG_H #include "config.h" #endif #include "libGenome/gnFilter.h" #include "libGenome/gnRAWSource.h" #include "libGenome/gnGenomeSpec.h" #include "libGenome/gnFragmentSpec.h" #include "libGenome/gnSourceSpec.h" #include "libGenome/gnStringTools.h" #include "libGenome/gnDebug.h" using namespace std; namespace genome { gnRAWSource::gnRAWSource() { m_openString = ""; m_contig = NULL; m_pFilter = NULL; } gnRAWSource::gnRAWSource( const gnRAWSource& s ) : gnFileSource(s) { m_contig = NULL; if(s.m_contig != NULL) m_contig = s.m_contig->Clone(); } gnRAWSource::~gnRAWSource() { m_ifstream.close(); delete m_contig; } boolean gnRAWSource::HasContig( const string& name ) const { if( name.length() == 0 ) return true; return false; } uint32 gnRAWSource::GetContigID( const string& name ) const { return ALL_CONTIGS; } string gnRAWSource::GetContigName( const uint32 i ) const { return ""; } gnSeqI gnRAWSource::GetContigSeqLength( const uint32 i ) const { if( m_contig && (i == 0 || i == ALL_CONTIGS)) return m_contig->GetSeqLength(); return GNSEQI_ERROR; } boolean gnRAWSource::SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI ){ return Read( start, buf, bufLen ); } gnGenomeSpec *gnRAWSource::GetSpec() const{ return m_spec->Clone(); } boolean gnRAWSource::Write(gnSequence& seq, const string& filename){ ofstream m_ofstream(filename.c_str(), ios::out | ios::binary); if(!m_ofstream.is_open()) return false; gnSeqC buf[BUFFER_SIZE + 1]; buf[BUFFER_SIZE] = 0; gnSeqI readOffset = 0; gnSeqI readLength = seq.length(); while(readLength > 0){ //buffer the read/writes gnSeqI writeLen = readLength < BUFFER_SIZE ? readLength : BUFFER_SIZE; if(!seq.ToArray(buf, writeLen, readOffset + 1)) return false; m_ofstream.write( buf, writeLen ); readLength -= writeLen; readOffset += writeLen; } m_ofstream.flush(); m_ofstream.close(); return true; } gnFileContig* gnRAWSource::GetFileContig( const uint32 contigI ) const{ if(contigI > 0) return NULL; return m_contig; } //File parsing access routine boolean gnRAWSource::ParseStream( istream& fin ) { // init variables uint64 streamPos = 0; uint64 bufReadLen = 0; Array array_buf( BUFFER_SIZE ); char* buf = array_buf.data; gnSeqI seqLength = 0; if( m_contig == NULL ) m_contig = new gnFileContig(); m_contig->SetName( "Raw Data" ); m_contig->SetRepeatSeqGap(true); m_contig->SetSectStart(gnContigSequence, 0); uint64 offset = 0; if( !CheckRawData() ){ fin.seekg( 0, ios::end ); offset = fin.tellg(); } else { while( !fin.eof() ) { // read chars fin.read( buf , BUFFER_SIZE ); bufReadLen = fin.gcount(); for( uint32 i=0 ; i < bufReadLen ; i++ ) { if(m_pFilter == NULL || m_pFilter->IsValid(buf[i])) seqLength++; else{ m_contig->SetRepeatSeqGap(false); } } streamPos += bufReadLen; } } m_contig->SetSectEnd(gnContigSequence, streamPos + offset); m_contig->SetSeqLength(seqLength + offset ); m_spec = new gnGenomeSpec(); gnFragmentSpec* fragspec = new gnFragmentSpec(); gnSourceSpec* sspec = new gnSourceSpec(this); sspec->SetSourceName(m_openString); m_spec->AddSpec(fragspec); fragspec->AddSpec(sspec); m_ifstream.clear(); return true; } } // end namespace genome libGenome-1.3.1/libGenome/OmpGuard.h0000644002622200470610000000362310742567004014145 00000000000000/******************************************************************************* * $Id: OmpGuard.h,v 1.6 2004/02/27 23:08:55 darling Exp $ * This file is copyright 2002-2007 Aaron Darling and authors listed in the AUTHORS file. * This file is licensed under the GPL. * Please see the file called COPYING for licensing details. * ************** ******************************************************************************/ #ifndef _OmpGuard_h_ #define _OmpGuard_h_ #ifdef HAVE_CONFIG_H #include "config.h" #endif #ifdef _OPENMP #include #endif namespace genome { #ifdef _OPENMP /** This is a class for guard objects using OpenMP * It is adapted from the book * "Pattern-Oriented Software Architecture". */ class omp_guard { public: /** Acquire the lock and store a pointer to it */ omp_guard (omp_lock_t &lock){ lock_ = &lock; acquire (); } /** Set the lock explicitly */ void acquire (){ omp_set_lock (lock_); owner_ = true; } /** Release the lock explicitly (owner thread only!) */ void release (){ if (owner_) { owner_ = false; omp_unset_lock (lock_); }; } /** Destruct guard object */ ~omp_guard (){ release (); } private: omp_lock_t *lock_; // pointer to our lock bool owner_; // is this object the owner of the lock? // Disallow copies or assignment omp_guard (const omp_guard &); void operator= (const omp_guard &); }; #else // provide non-openmp stubs typedef int omp_lock_t; class omp_guard { public: omp_guard (omp_lock_t &lock){} void acquire (){} void release (){} private: // Disallow copies or assignment omp_guard (const omp_guard &); void operator= (const omp_guard &); }; inline void omp_init_lock( omp_lock_t* dummy_lock ){} inline void omp_destroy_lock( omp_lock_t* dummy_lock ){} #endif // ifdef _OPENMP } // namespace genome #endif // _OmpGuard_h_ libGenome-1.3.1/config.sub0000755002622200470610000007301510640457075012345 00000000000000#! /bin/sh # Configuration validation subroutine script. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, # 2000, 2001, 2002, 2003 Free Software Foundation, Inc. timestamp='2003-06-18' # This file is (in principle) common to ALL GNU software. # The presence of a machine in this file suggests that SOME GNU software # can handle that machine. 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., 59 Temple Place - Suite 330, # Boston, MA 02111-1307, 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 . Submit a context # diff and a properly formatted ChangeLog entry. # # Configuration subroutine to validate and canonicalize a configuration type. # Supply the specified configuration type as an argument. # If it is invalid, we print an error message on stderr and exit with code 1. # Otherwise, we print the canonical config type on stdout and succeed. # This file is supposed to be the same for all GNU packages # and recognize all the CPU types, system types and aliases # that are meaningful with *any* GNU software. # Each package is responsible for reporting which valid configurations # it does not support. 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 Free Software Foundation, Inc. This is free software; see the source for copying conditions. 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 0 ;; --version | -v ) echo "$version" ; exit 0 ;; --help | --h* | -h ) echo "$usage"; exit 0 ;; -- ) # 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 0;; * ) 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 $maybe_os in nto-qnx* | linux-gnu* | freebsd*-gnu* | netbsd*-gnu* | storm-chaos* | os2-emx* | rtmk-nova*) os=-$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. We also ### recognize some manufacturers as not being operating systems, so we ### can provide default operating systems below. case $os in -sun*os*) # Prevent following clause from handling this invalid input. ;; -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \ -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \ -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \ -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \ -apple | -axis) os= basic_machine=$1 ;; -sim | -cisco | -oki | -wec | -winbond) os= basic_machine=$1 ;; -scout) ;; -wrs) os=-vxworks basic_machine=$1 ;; -chorusos*) os=-chorusos basic_machine=$1 ;; -chorusrdb) os=-chorusrdb basic_machine=$1 ;; -hiux*) os=-hiuxwe2 ;; -sco5) os=-sco3.2v5 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco4) os=-sco3.2v4 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2.[4-9]*) os=`echo $os | sed -e 's/sco3.2./sco3.2v/'` basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2v[4-9]*) # Don't forget version if it is 3.2v4 or newer. basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco*) os=-sco3.2v2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -udk*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -isc) os=-isc2.2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -clix*) basic_machine=clipper-intergraph ;; -isc*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -lynx*) os=-lynxos ;; -ptx*) basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'` ;; -windowsnt*) os=`echo $os | sed -e 's/windowsnt/winnt/'` ;; -psos*) os=-psos ;; -mint | -mint[0-9]*) basic_machine=m68k-atari os=-mint ;; esac # Decode aliases for certain CPU-COMPANY combinations. case $basic_machine in # Recognize the basic CPU types without company name. # Some are omitted here because they have special meanings below. 1750a | 580 \ | a29k \ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \ | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr \ | c4x | clipper \ | d10v | d30v | dlx | dsp16xx \ | fr30 | frv \ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ | i370 | i860 | i960 | ia64 \ | ip2k \ | m32r | m68000 | m68k | m88k | mcore \ | mips | mipsbe | mipseb | mipsel | mipsle \ | mips16 \ | mips64 | mips64el \ | mips64vr | mips64vrel \ | mips64orion | mips64orionel \ | mips64vr4100 | mips64vr4100el \ | mips64vr4300 | mips64vr4300el \ | mips64vr5000 | mips64vr5000el \ | mipsisa32 | mipsisa32el \ | mipsisa32r2 | mipsisa32r2el \ | mipsisa64 | mipsisa64el \ | mipsisa64sb1 | mipsisa64sb1el \ | mipsisa64sr71k | mipsisa64sr71kel \ | mipstx39 | mipstx39el \ | mn10200 | mn10300 \ | msp430 \ | ns16k | ns32k \ | openrisc | or32 \ | pdp10 | pdp11 | pj | pjl \ | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \ | pyramid \ | s390 | s390x \ | sh | sh[1234] | sh[23]e | sh[34]eb | shbe | shle | sh[1234]le | sh3ele \ | sh64 | sh64le \ | sparc | sparc64 | sparc86x | sparclet | sparclite | sparcv9 | sparcv9b \ | strongarm \ | tahoe | thumb | tic4x | tic80 | tron \ | v850 | v850e \ | we32k \ | x86 | xscale | xstormy16 | xtensa \ | z8k) basic_machine=$basic_machine-unknown ;; m6811 | m68hc11 | m6812 | m68hc12) # Motorola 68HC11/12. basic_machine=$basic_machine-unknown os=-none ;; m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k) ;; # We use `pc' rather than `unknown' # because (1) that's what they normally are, and # (2) the word "unknown" tends to confuse beginning users. i*86 | x86_64) basic_machine=$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-* \ | bs2000-* \ | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \ | clipper-* | cydra-* \ | d10v-* | d30v-* | dlx-* \ | elxsi-* \ | f30[01]-* | f700-* | fr30-* | frv-* | fx80-* \ | h8300-* | h8500-* \ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ | i*86-* | i860-* | i960-* | ia64-* \ | ip2k-* \ | m32r-* \ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ | m88110-* | m88k-* | mcore-* \ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ | mips16-* \ | mips64-* | mips64el-* \ | mips64vr-* | mips64vrel-* \ | mips64orion-* | mips64orionel-* \ | mips64vr4100-* | mips64vr4100el-* \ | mips64vr4300-* | mips64vr4300el-* \ | mips64vr5000-* | mips64vr5000el-* \ | mipsisa32-* | mipsisa32el-* \ | mipsisa32r2-* | mipsisa32r2el-* \ | mipsisa64-* | mipsisa64el-* \ | mipsisa64sb1-* | mipsisa64sb1el-* \ | mipsisa64sr71k-* | mipsisa64sr71kel-* \ | mipstx39-* | mipstx39el-* \ | msp430-* \ | none-* | np1-* | nv1-* | ns16k-* | ns32k-* \ | orion-* \ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ | pyramid-* \ | romp-* | rs6000-* \ | s390-* | s390x-* \ | sh-* | sh[1234]-* | sh[23]e-* | sh[34]eb-* | shbe-* \ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ | sparc-* | sparc64-* | sparc86x-* | sparclet-* | sparclite-* \ | sparcv9-* | sparcv9b-* | strongarm-* | sv1-* | sx?-* \ | tahoe-* | thumb-* \ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \ | tron-* \ | v850-* | v850e-* | vax-* \ | we32k-* \ | x86-* | x86_64-* | xps100-* | xscale-* | xstormy16-* \ | xtensa-* \ | ymp-* \ | z8k-*) ;; # 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 ;; 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 ;; 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 ;; aux) basic_machine=m68k-apple os=-aux ;; balance) basic_machine=ns32k-sequent os=-dynix ;; c90) basic_machine=c90-cray os=-unicos ;; 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 ;; crds | unos) basic_machine=m68k-crds ;; cris | cris-* | etrax*) basic_machine=cris-axis ;; 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 ;; 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 ;; 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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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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 ${skipped_export-false}; then $show "generating symbol list for \`$libname.la'" export_symbols="$output_objdir/$libname.exp" $run $rm $export_symbols libobjs=$output # Append the command to create the export file. eval concat_cmds=\"\$concat_cmds~$export_symbols_cmds\" fi # Set up a command to remove the reloadale object files # after they are used. i=0 while test "$i" -lt "$k" do i=`expr $i + 1` delfiles="$delfiles $output_objdir/$save_output-${i}.$objext" done $echo "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" $show "$cmd" $run eval "$cmd" || exit $? done IFS="$save_ifs" 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\" 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 # Append the command to remove the reloadable object files # to the just-reset $cmds. eval cmds=\"\$cmds~\$rm $delfiles\" fi save_ifs="$IFS"; IFS='~' for cmd in $cmds; do IFS="$save_ifs" eval cmd=\"$cmd\" $show "$cmd" $run eval "$cmd" || exit $? done IFS="$save_ifs" # Restore the uninstalled library and exit if test "$mode" = relink; then $run eval '(cd $output_objdir && $rm ${realname}T && $mv $realname ${realname}T && $mv "$realname"U $realname)' || exit $? exit $EXIT_SUCCESS fi # Create links to the real library. for linkname in $linknames; do if test "$realname" != "$linkname"; then $show "(cd $output_objdir && $rm $linkname && $LN_S $realname $linkname)" $run 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 "$deplibs"; then $echo "$modename: warning: \`-l' and \`-L' are ignored for objects" 1>&2 fi if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then $echo "$modename: warning: \`-dlopen' is ignored for objects" 1>&2 fi if test -n "$rpath"; then $echo "$modename: warning: \`-rpath' is ignored for objects" 1>&2 fi if test -n "$xrpath"; then $echo "$modename: warning: \`-R' is ignored for objects" 1>&2 fi if test -n "$vinfo"; then $echo "$modename: warning: \`-version-info' is ignored for objects" 1>&2 fi if test -n "$release"; then $echo "$modename: warning: \`-release' is ignored for objects" 1>&2 fi case $output in *.lo) if test -n "$objs$old_deplibs"; then $echo "$modename: cannot build library object \`$output' from non-libtool objects" 1>&2 exit $EXIT_FAILURE fi libobj="$output" obj=`$echo "X$output" | $Xsed -e "$lo2o"` ;; *) libobj= obj="$output" ;; esac # Delete the old objects. $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 $LD directly, so let us get rid of # -Wl from whole_archive_flag_spec wl= if test -n "$convenience"; then if test -n "$whole_archive_flag_spec"; then eval reload_conv_objs=\"\$reload_objs $whole_archive_flag_spec\" else gentop="$output_objdir/${obj}x" $show "${rm}r $gentop" $run ${rm}r "$gentop" $show "$mkdir $gentop" $run $mkdir "$gentop" status=$? if test "$status" -ne 0 && test ! -d "$gentop"; then exit $status fi generated="$generated $gentop" for xlib in $convenience; do # Extract the objects. case $xlib in [\\/]* | [A-Za-z]:[\\/]*) xabs="$xlib" ;; *) xabs=`pwd`"/$xlib" ;; esac xlib=`$echo "X$xlib" | $Xsed -e 's%^.*/%%'` xdir="$gentop/$xlib" $show "${rm}r $xdir" $run ${rm}r "$xdir" $show "$mkdir $xdir" $run $mkdir "$xdir" status=$? if test "$status" -ne 0 && test ! -d "$xdir"; then exit $status fi # We will extract separately just the conflicting names and we will no # longer touch any unique names. It is faster to leave these extract # automatically by $AR in one run. $show "(cd $xdir && $AR x $xabs)" $run eval "(cd \$xdir && $AR x \$xabs)" || exit $? if ($AR t "$xabs" | sort | sort -uc >/dev/null 2>&1); then : else $echo "$modename: warning: object name conflicts; renaming object files" 1>&2 $echo "$modename: warning: to ensure that they will not overwrite" 1>&2 $AR t "$xabs" | sort | uniq -cd | while read -r count name do i=1 while test "$i" -le "$count" do # Put our $i before any first dot (extension) # Never overwrite any file name_to="$name" while test "X$name_to" = "X$name" || test -f "$xdir/$name_to" do name_to=`$echo "X$name_to" | $Xsed -e "s/\([^.]*\)/\1-$i/"` done $show "(cd $xdir && $AR xN $i $xabs '$name' && $mv '$name' '$name_to')" $run eval "(cd \$xdir && $AR xN $i \$xabs '$name' && $mv '$name' '$name_to')" || exit $? i=`expr $i + 1` done done fi reload_conv_objs="$reload_objs "`find $xdir -name \*.$objext -print -o -name \*.lo -print | $NL2SP` done fi fi # Create the old-style object. reload_objs="$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" cmds=$reload_cmds save_ifs="$IFS"; IFS='~' for cmd in $cmds; do IFS="$save_ifs" eval cmd=\"$cmd\" $show "$cmd" $run eval "$cmd" || exit $? done IFS="$save_ifs" # Exit if we aren't doing a library object file. if test -z "$libobj"; then if test -n "$gentop"; then $show "${rm}r $gentop" $run ${rm}r $gentop fi exit $EXIT_SUCCESS fi if test "$build_libtool_libs" != yes; then if test -n "$gentop"; then $show "${rm}r $gentop" $run ${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" # $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" cmds=$reload_cmds save_ifs="$IFS"; IFS='~' for cmd in $cmds; do IFS="$save_ifs" eval cmd=\"$cmd\" $show "$cmd" $run eval "$cmd" || exit $? done IFS="$save_ifs" fi if test -n "$gentop"; then $show "${rm}r $gentop" $run ${rm}r $gentop fi exit $EXIT_SUCCESS ;; prog) case $host in *cygwin*) output=`$echo $output | ${SED} -e 's,.exe$,,;s,$,.exe,'` ;; esac if test -n "$vinfo"; then $echo "$modename: warning: \`-version-info' is ignored for programs" 1>&2 fi if test -n "$release"; then $echo "$modename: warning: \`-release' is ignored for programs" 1>&2 fi if test "$preload" = yes; then if test "$dlopen_support" = unknown && test "$dlopen_self" = unknown && test "$dlopen_self_static" = unknown; then $echo "$modename: warning: \`AC_LIBTOOL_DLOPEN' not used. Assuming no dlopen support." fi fi case $host in *-*-rhapsody* | *-*-darwin1.[012]) # On Rhapsody replace the C library is the System framework compile_deplibs=`$echo "X $compile_deplibs" | $Xsed -e 's/ -lc / -framework System /'` finalize_deplibs=`$echo "X $finalize_deplibs" | $Xsed -e 's/ -lc / -framework System /'` ;; esac case $host in *darwin*) # Don't allow lazy linking, it breaks C++ global constructors if test "$tagname" = CXX ; then compile_command="$compile_command ${wl}-bind_at_load" finalize_command="$finalize_command ${wl}-bind_at_load" fi ;; esac compile_command="$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 $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2*) case :$dllsearchpath: in *":$libdir:"*) ;; *) dllsearchpath="$dllsearchpath:$libdir";; esac ;; esac done # Substitute the hardcoded libdirs into the rpath. if test -n "$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" | $NL2SP` fi dlsyms= if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then if test -n "$NM" && test -n "$global_symbol_pipe"; then dlsyms="${outputname}S.c" else $echo "$modename: not configured to extract global symbols from dlpreopened files" 1>&2 fi fi if test -n "$dlsyms"; then case $dlsyms in "") ;; *.c) # Discover the nlist of each of the dlfiles. nlist="$output_objdir/${outputname}.nm" $show "$rm $nlist ${nlist}S ${nlist}T" $run $rm "$nlist" "${nlist}S" "${nlist}T" # Parse the name list into a source file. $show "creating $output_objdir/$dlsyms" test -z "$run" && $echo > "$output_objdir/$dlsyms" "\ /* $dlsyms - symbol resolution table for \`$outputname' dlsym emulation. */ /* Generated by $PROGRAM - GNU $PACKAGE $VERSION$TIMESTAMP */ #ifdef __cplusplus extern \"C\" { #endif /* Prevent the only kind of declaration conflicts we can make. */ #define lt_preloaded_symbols some_other_symbol /* External symbol declarations for the compiler. */\ " if test "$dlself" = yes; then $show "generating symbol list for \`$output'" test -z "$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 arg in $progfiles; do $show "extracting global C symbols from \`$arg'" $run eval "$NM $arg | $global_symbol_pipe >> '$nlist'" done if test -n "$exclude_expsyms"; then $run eval '$EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T' $run eval '$mv "$nlist"T "$nlist"' fi if test -n "$export_symbols_regex"; then $run eval '$EGREP -e "$export_symbols_regex" "$nlist" > "$nlist"T' $run eval '$mv "$nlist"T "$nlist"' fi # Prepare the list of exported symbols if test -z "$export_symbols"; then export_symbols="$output_objdir/$output.exp" $run $rm $export_symbols $run eval "${SED} -n -e '/^: @PROGRAM@$/d' -e 's/^.* \(.*\)$/\1/p' "'< "$nlist" > "$export_symbols"' else $run eval "${SED} -e 's/\([][.*^$]\)/\\\1/g' -e 's/^/ /' -e 's/$/$/'"' < "$export_symbols" > "$output_objdir/$output.exp"' $run eval 'grep -f "$output_objdir/$output.exp" < "$nlist" > "$nlist"T' $run eval 'mv "$nlist"T "$nlist"' fi fi for arg in $dlprefiles; do $show "extracting global C symbols from \`$arg'" name=`$echo "$arg" | ${SED} -e 's%^.*/%%'` $run eval '$echo ": $name " >> "$nlist"' $run eval "$NM $arg | $global_symbol_pipe >> '$nlist'" done if test -z "$run"; then # Make sure we have at least an empty file. test -f "$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 >> "$output_objdir/$dlsyms"' else $echo '/* NONE */' >> "$output_objdir/$dlsyms" fi $echo >> "$output_objdir/$dlsyms" "\ #undef lt_preloaded_symbols #if defined (__STDC__) && __STDC__ # define lt_ptr void * #else # define lt_ptr char * # define const #endif /* The mapping between symbol names and symbols. */ const struct { const char *name; lt_ptr address; } lt_preloaded_symbols[] = {\ " eval "$global_symbol_to_c_name_address" < "$nlist" >> "$output_objdir/$dlsyms" $echo >> "$output_objdir/$dlsyms" "\ {0, (lt_ptr) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt_preloaded_symbols; } #endif #ifdef __cplusplus } #endif\ " fi pic_flag_for_symtable= case $host in # compiling the symbol table file with pic_flag works around # a FreeBSD bug that causes programs to crash when -lm is # linked before any other PIC object. But we must not use # pic_flag when linking with -static. The problem exists in # FreeBSD 2.2.6 and is fixed in FreeBSD 3.1. *-*-freebsd2*|*-*-freebsd3.0*|*-*-freebsdelf3.0*) case "$compile_command " in *" -static "*) ;; *) pic_flag_for_symtable=" $pic_flag -DFREEBSD_WORKAROUND";; esac;; *-*-hpux*) case "$compile_command " in *" -static "*) ;; *) pic_flag_for_symtable=" $pic_flag";; esac esac # Now compile the dynamic symbol file. $show "(cd $output_objdir && $LTCC -c$no_builtin_flag$pic_flag_for_symtable \"$dlsyms\")" $run eval '(cd $output_objdir && $LTCC -c$no_builtin_flag$pic_flag_for_symtable "$dlsyms")' || exit $? # Clean up the generated files. $show "$rm $output_objdir/$dlsyms $nlist ${nlist}S ${nlist}T" $run $rm "$output_objdir/$dlsyms" "$nlist" "${nlist}S" "${nlist}T" # Transform the symbol file into the correct name. compile_command=`$echo "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}S.${objext}%"` finalize_command=`$echo "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}S.${objext}%"` ;; *) $echo "$modename: unknown suffix for \`$dlsyms'" 1>&2 exit $EXIT_FAILURE ;; esac else # We keep going just in case the user didn't refer to # lt_preloaded_symbols. 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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 -static do not do any dynamic linking of libtool libraries -version-info CURRENT[:REVISION[:AGE]] specify library version info [each variable defaults to 0] All other options (arguments beginning with \`-') are ignored. 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If FILE is a libtool library, all the files associated with it are deleted. Otherwise, only FILE itself is deleted using RM." ;; *) $echo "$modename: invalid operation mode \`$mode'" 1>&2 $echo "$help" 1>&2 exit $EXIT_FAILURE ;; esac $echo $echo "Try \`$modename --help' for more information about other modes." exit $EXIT_SUCCESS # The TAGs below are defined such that we never get into a situation # in which we disable both kinds of libraries. Given conflicting # choices, we go for a static library, that is the most portable, # since we can't tell whether shared libraries were disabled because # the user asked for that or because the platform doesn't support # them. This is particularly important on AIX, because we don't # support having both static and shared libraries enabled at the same # time on that platform, so we default to a shared-only configuration. # If a disable-shared tag is given, we'll fallback to a static-only # configuration. But we'll never go from static-only to shared-only. # ### BEGIN LIBTOOL TAG CONFIG: disable-shared build_libtool_libs=no build_old_libs=yes # ### END LIBTOOL TAG CONFIG: disable-shared # ### BEGIN LIBTOOL TAG CONFIG: disable-static build_old_libs=`case $build_libtool_libs in yes) $echo no;; *) $echo yes;; esac` # ### END LIBTOOL TAG CONFIG: disable-static # Local Variables: # mode:shell-script # sh-indentation:2 # End: libGenome-1.3.1/libGenome-1.3.pc.in0000644002622200470610000000054010742567543013511 00000000000000prefix=@prefix@ exec_prefix=@exec_prefix@ libdir=@libdir@ includedir=@includedir@ Name: libGenome Description: c++ library supporting sequence I/O and manipulation Version: @VERSION@ Requires: Libs: @OPENMP_CXXFLAGS@ -L${libdir} -lGenome-@GENERIC_API_VERSION@ Cflags: @OPENMP_CXXFLAGS@ -I${includedir}/@GENERIC_LIBRARY_NAME@-@GENERIC_API_VERSION@ libGenome-1.3.1/INSTALL0000644002622200470610000002207110126442331011373 00000000000000Installation Instructions ************************* Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004 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. Finally, it creates a shell script `config.status' that you can run in the future to recreate the current configuration, and a file `config.log' containing compiler output (useful mainly for debugging `configure'). It can also use an optional file (typically called `config.cache' and enabled with `--cache-file=config.cache' or simply `-C') that saves the results of its tests to speed up reconfiguring. (Caching is disabled by default to prevent problems with accidental use of stale cache files.) If you need to do unusual things to compile the package, please try to figure out how `configure' could check whether to do them, and mail diffs or instructions to the address given in the `README' so they can be considered for the next release. If you are using the cache, and at some point `config.cache' contains results you don't want to keep, you may remove or edit it. The file `configure.ac' (or `configure.in') is used to create `configure' by a program called `autoconf'. You only need `configure.ac' if you want to change it or regenerate `configure' using a newer version of `autoconf'. The simplest way to compile this package is: 1. `cd' to the directory containing the package's source code and type `./configure' to configure the package for your system. If you're using `csh' on an old version of System V, you might need to type `sh ./configure' instead to prevent `csh' from trying to execute `configure' itself. Running `configure' takes awhile. While running, it prints some messages telling which features it is checking for. 2. Type `make' to compile the package. 3. Optionally, type `make check' to run any self-tests that come with the package. 4. Type `make install' to install the programs and any data files and documentation. 5. You can remove the program binaries and object files from the source code directory by typing `make clean'. To also remove the files that `configure' created (so you can compile the package for a different kind of computer), type `make distclean'. There is also a `make maintainer-clean' target, but that is intended mainly for the package's developers. If you use it, you may have to get all sorts of other programs in order to regenerate files that came with the distribution. Compilers and Options ===================== Some systems require unusual options for compilation or linking that the `configure' script does not know about. Run `./configure --help' for details on some of the pertinent environment variables. You can give `configure' initial values for configuration parameters by setting variables in the command line or in the environment. Here is an example: ./configure CC=c89 CFLAGS=-O2 LIBS=-lposix *Note Defining Variables::, for more details. Compiling For Multiple Architectures ==================================== You can compile the package for more than one kind of computer at the same time, by placing the object files for each architecture in their own directory. To do this, you must use a version of `make' that supports the `VPATH' variable, such as GNU `make'. `cd' to the directory where you want the object files and executables to go and run the `configure' script. `configure' automatically checks for the source code in the directory that `configure' is in and in `..'. If you have to use a `make' that does not support the `VPATH' variable, you have to compile the package for one architecture at a time in the source code directory. After you have installed the package for one architecture, use `make distclean' before reconfiguring for another architecture. Installation Names ================== By default, `make install' will install the package's files in `/usr/local/bin', `/usr/local/man', etc. You can specify an installation prefix other than `/usr/local' by giving `configure' the option `--prefix=PREFIX'. You can specify separate installation prefixes for architecture-specific files and architecture-independent files. If you give `configure' the option `--exec-prefix=PREFIX', the package will use PREFIX as the prefix for installing programs and libraries. Documentation and other data files will still use the regular prefix. In addition, if you use an unusual directory layout you can give options like `--bindir=DIR' to specify different values for particular kinds of files. Run `configure --help' for a list of the directories you can set and what kinds of files go in them. If the package supports it, you can cause programs to be installed with an extra prefix or suffix on their names by giving `configure' the option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'. Optional Features ================= Some packages pay attention to `--enable-FEATURE' options to `configure', where FEATURE indicates an optional part of the package. They may also pay attention to `--with-PACKAGE' options, where PACKAGE is something like `gnu-as' or `x' (for the X Window System). The `README' should mention any `--enable-' and `--with-' options that the package recognizes. For packages that use the X Window System, `configure' can usually find the X include and library files automatically, but if it doesn't, you can use the `configure' options `--x-includes=DIR' and `--x-libraries=DIR' to specify their locations. Specifying the System Type ========================== There may be some features `configure' cannot figure out automatically, but needs to determine by the type of machine the package will run on. Usually, assuming the package is built to be run on the _same_ architectures, `configure' can figure that out, but if it prints a message saying it cannot guess the machine type, give it the `--build=TYPE' option. TYPE can either be a short name for the system type, such as `sun4', or a canonical name which has the form: CPU-COMPANY-SYSTEM where SYSTEM can have one of these forms: OS KERNEL-OS See the file `config.sub' for the possible values of each field. If `config.sub' isn't included in this package, then this package doesn't need to know the machine type. If you are _building_ compiler tools for cross-compiling, you should use the `--target=TYPE' option to select the type of system they will produce code for. If you want to _use_ a cross compiler, that generates code for a platform different from the build platform, you should specify the "host" platform (i.e., that on which the generated programs will eventually be run) with `--host=TYPE'. Sharing Defaults ================ If you want to set default values for `configure' scripts to share, you can create a site shell script called `config.site' that gives default values for variables like `CC', `cache_file', and `prefix'. `configure' looks for `PREFIX/share/config.site' if it exists, then `PREFIX/etc/config.site' if it exists. Or, you can set the `CONFIG_SITE' environment variable to the location of the site script. A warning: not all `configure' scripts look for a site script. Defining Variables ================== Variables not defined in a site shell script can be set in the environment passed to `configure'. However, some packages may run configure again during the build, and the customized values of these variables may be lost. In order to avoid this problem, you should set them in the `configure' command line, using `VAR=value'. For example: ./configure CC=/usr/local2/bin/gcc will cause the specified gcc to be used as the C compiler (unless it is overridden in the site shell script). `configure' Invocation ====================== `configure' recognizes the following options to control how it operates. `--help' `-h' Print a summary of the options to `configure', and exit. `--version' `-V' Print the version of Autoconf used to generate the `configure' script, and exit. `--cache-file=FILE' Enable the cache: use and save the results of the tests in FILE, traditionally `config.cache'. 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. 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This case will never be run, # since it is checked for above. exit 1 ;; sgi) if test "$libtool" = yes; then "$@" "-Wp,-MDupdate,$tmpdepfile" else "$@" -MDupdate "$tmpdepfile" fi stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files echo "$object : \\" > "$depfile" # Clip off the initial element (the dependent). Don't try to be # clever and replace this with sed code, as IRIX sed won't handle # lines with more than a fixed number of characters (4096 in # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines; # the IRIX cc adds comments like `#:fec' to the end of the # dependency line. tr ' ' ' ' < "$tmpdepfile" \ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \ tr ' ' ' ' >> $depfile echo >> $depfile # The second pass generates a dummy entry for each header file. tr ' ' ' ' < "$tmpdepfile" \ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \ >> $depfile else # The sourcefile does not contain any dependencies, so just # store a dummy comment line, to avoid errors with the Makefile # "include basename.Plo" scheme. echo "#dummy" > "$depfile" fi rm -f "$tmpdepfile" ;; aix) # The C for AIX Compiler uses -M and outputs the dependencies # in a .u file. In older versions, this file always lives in the # current directory. 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However on # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c # ICC 7.0 will fill foo.d with something like # foo.o: sub/foo.c # foo.o: sub/foo.h # which is wrong. We want: # sub/foo.o: sub/foo.c # sub/foo.o: sub/foo.h # sub/foo.c: # sub/foo.h: # ICC 7.1 will output # foo.o: sub/foo.c sub/foo.h # and will wrap long lines using \ : # foo.o: sub/foo.c ... \ # sub/foo.h ... \ # ... "$@" -MD -MF "$tmpdepfile" stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" # Each line is of the form `foo.o: dependent.h', # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'. # Do two passes, one to just change these to # `$object: dependent.h' and one to simply `dependent.h:'. sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile" # Some versions of the HPUX 10.20 sed can't process this invocation # correctly. 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"$@" || exit $? # Remove the call to Libtool. if test "$libtool" = yes; then while test $1 != '--mode=compile'; do shift done shift fi # Remove `-o $object'. IFS=" " for arg do case $arg in -o) shift ;; $object) shift ;; *) set fnord "$@" "$arg" shift # fnord shift # $arg ;; esac done test -z "$dashmflag" && dashmflag=-M # Require at least two characters before searching for `:' # in the target name. This is to cope with DOS-style filenames: # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise. "$@" $dashmflag | sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile" rm -f "$depfile" cat < "$tmpdepfile" > "$depfile" tr ' ' ' ' < "$tmpdepfile" | \ ## Some versions of the HPUX 10.20 sed can't process this invocation ## correctly. Breaking it into two sed invocations is a workaround. sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; dashXmstdout) # This case only exists to satisfy depend.m4. 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Breaking it into two sed invocations is a workaround. sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" "$tmpdepfile".bak ;; cpp) # Important note: in order to support this mode, a compiler *must* # always write the preprocessed file to stdout. "$@" || exit $? # Remove the call to Libtool. if test "$libtool" = yes; then while test $1 != '--mode=compile'; do shift done shift fi # Remove `-o $object'. IFS=" " for arg do case $arg in -o) shift ;; $object) shift ;; *) set fnord "$@" "$arg" shift # fnord shift # $arg ;; esac done "$@" -E | sed -n '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' | sed '$ s: \\$::' > "$tmpdepfile" rm -f "$depfile" echo "$object : \\" > "$depfile" cat < "$tmpdepfile" >> "$depfile" sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; msvisualcpp) # Important note: in order to support this mode, a compiler *must* # always write the preprocessed file to stdout, regardless of -o, # because we must use -o when running libtool. "$@" || exit $? IFS=" " for arg do case "$arg" in "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI") set fnord "$@" shift shift ;; *) set fnord "$@" "$arg" shift shift ;; esac done "$@" -E | sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile" rm -f "$depfile" echo "$object : \\" > "$depfile" . 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