sigma-1.1.3/0000777000175000017500000000000011157376463007636 500000000000000sigma-1.1.3/Background/0000777000175000017500000000000011157376463011715 500000000000000sigma-1.1.3/Background/README0000644000175000017500000000166610604173575012515 00000000000000The "background probabilities" (by default, dinucleotide probabilities) that Sigma uses are, if no other options exist, extracted from the input sequence itself. This is generally not advisable: it is better to estimate them from larger quantities of similar sequence (eg, all intergenic sequence in the organism of interest). Sigma offers two options for this: with the -b option, one can supply an auxiliary file (in fasta format) containing such sequences, or with the -B option, one can supply a file containing just the single-nucleotide and di-nucleotide frequencies. An example is in this directory. Each line either begins with # (and is ignored), or contains a single nucleotide or di-nucleotide, whitespace, and the frequency. All possible single- and di-nucleotides should be present; tri-nucleotides and higher will be ignored. An example file is yeast_bg in this directory and corresponds to intergenic sequence in S. cerevisiae. sigma-1.1.3/Background/yeast_bg0000644000175000017500000000066510604172061013340 00000000000000#single site A 0.320215090662 C 0.185829015523 G 0.181955902657 T 0.311999991159 #dinucleotide AA 0.117425388423 AC 0.0537991899563 AG 0.0585365557146 AT 0.0900790233279 CA 0.0616164236784 CC 0.0360908471253 CG 0.0309185919641 CT 0.0572528859775 GA 0.0577549152311 GC 0.0383241451204 GG 0.0353995553297 GT 0.0504308693008 TA 0.0834183633294 TC 0.0576148333205 TG 0.0571011996482 TT 0.114237212552 sigma-1.1.3/README0000644000175000017500000000631711157375172010435 00000000000000Sigma: Simple greedy multiple alignment Version 1.1.3, (C) 2009, Rahul Siddharthan Portions written and (C) 2009, Gayathri Jayaraman This is a port to C of Sigma, which was originally (version 1.0) written in ocaml. A paper describing the algorithm was published in BMC Bioinformatics 7:143 (2006). A couple of important bugs have been fixed, and it is about 3 to 4 times faster than the ocaml version. It does everything that the ocaml version did, but more correctly (and faster). 1.1.1 is a minor update (see ChangeLog) with no new features. 1.1.2 gives a significant speed boost for larger input files but should not otherwise behave differently. 1.1.3 contains a new local alignment algorithm that is linear in memory usage, though still quadratic in time. A kludge that had been put in 1.1 (pre-fragmentation of sequences to avoid running out memory) has therefore been removed. Changes since version 1.0: 1. Mismatches in previously-aligned sequence fragments are treated more intelligently. Earlier, "N" was always used, which led to problems in aligning large numbers of sequences, where mismatches became more and more common. Now the majority base, if one exists, is used. There is scope for improvement, which will be dealt with in a future version, but the current treatment seems adequate for most common situations. 2. The dynamic programming algorithm for finding local alignments tended to become slow for large input sequences: it is O(NM), in time and memory usage, for sequence lengths N and M. The current version however needs only linear ie O(M+N) memory usage. Versions 1.1 through 1.1.2 included a workaround where sequences are pre-fragmented into pieces of average size smaller than L (4000 by default, changeable with the -l option, now removed). There is also an important bugfix in this function. (Optimisation and bugfix by Gayathri Jayaraman) As a result, this version of Sigma scales well to much larger datasets than earlier (eg, 10 seqs each 10000bp long), and performs much faster than many existing programs (including ClustalW and Dialign). Sigma 1.0 was almost unusable on such datasets. 3. Some bugs relating to the consistency condition enforcement have been fixed. These had the effect of occasionally disallowing legitimate alignments (but, I believe, did not cause incorrect alignments). For help on compiling, see the file COMPILING. For command-line options, see the file NOTES or simply run the program without options. A unix manual page, contributed by Charles Plessy, is in "sigma.1" and will be installed with "make install". The docbook source is in "sigma.1.xml". For discussion of background models and a sample file, see the Background directory. For a detailed description of the algorithm, see BMC Bioinformatics 7:143 (2006). The program is distributed under the GNU General Public License, version 2. For copyright and licensing information, see COPYING. The program's website is http://www.imsc.res.in/~rsidd/sigma/ and source code, as well as pre-compiled binaries for some platforms, are available there. 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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 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 '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$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$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS 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.exe 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 '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$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$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS 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=$CC for ac_prog in cl.exe do # Extract the first word of "$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; 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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 grep that handles long lines and -e" >&5 echo $ECHO_N "checking for grep that handles long lines and -e... $ECHO_C" >&6; } if test "${ac_cv_path_GREP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else # Extract the first word of "grep ggrep" to use in msg output if test -z "$GREP"; then set dummy grep ggrep; ac_prog_name=$2 if test "${ac_cv_path_GREP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_path_GREP_found=false # Loop through the user's path and test for each of PROGNAME-LIST as_save_IFS=$IFS; 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esac $ac_path_GREP_found && break 3 done done done IFS=$as_save_IFS fi GREP="$ac_cv_path_GREP" if test -z "$GREP"; then { { echo "$as_me:$LINENO: error: no acceptable $ac_prog_name could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5 echo "$as_me: error: no acceptable $ac_prog_name could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;} { (exit 1); exit 1; }; } fi else ac_cv_path_GREP=$GREP fi fi { echo "$as_me:$LINENO: result: $ac_cv_path_GREP" >&5 echo "${ECHO_T}$ac_cv_path_GREP" >&6; } GREP="$ac_cv_path_GREP" { echo "$as_me:$LINENO: checking for egrep" >&5 echo $ECHO_N "checking for egrep... $ECHO_C" >&6; } if test "${ac_cv_path_EGREP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else if echo a | $GREP -E '(a|b)' >/dev/null 2>&1 then ac_cv_path_EGREP="$GREP -E" else # Extract the first word of "egrep" to use in msg output if test -z "$EGREP"; then set dummy egrep; ac_prog_name=$2 if test "${ac_cv_path_EGREP+set}" = set; then echo $ECHO_N "(cached) $ECHO_C" >&6 else ac_path_EGREP_found=false # Loop through the user's path and test for each of PROGNAME-LIST as_save_IFS=$IFS; 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esac $ac_path_EGREP_found && break 3 done done done IFS=$as_save_IFS fi EGREP="$ac_cv_path_EGREP" if test -z "$EGREP"; then { { echo "$as_me:$LINENO: error: no acceptable $ac_prog_name could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5 echo "$as_me: error: no acceptable $ac_prog_name could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;} { (exit 1); exit 1; }; } fi else ac_cv_path_EGREP=$EGREP fi fi fi { echo "$as_me:$LINENO: result: $ac_cv_path_EGREP" >&5 echo "${ECHO_T}$ac_cv_path_EGREP" >&6; } EGREP="$ac_cv_path_EGREP" { 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.$ac_objext if { (ac_try="$ac_compile" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5 (eval "$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 $ac_status); } && { test -z "$ac_c_werror_flag" || test ! -s conftest.err } && test -s conftest.$ac_objext; then ac_cv_header_stdc=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_cv_header_stdc=no fi rm -f core conftest.err conftest.$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.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include #if ((' ' & 0x0FF) == 0x020) # define ISLOWER(c) ('a' <= (c) && (c) <= 'z') # define TOUPPER(c) (ISLOWER(c) ? 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{ echo "$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.$ac_objext if { (ac_try="$ac_compile" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5 (eval "$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 $ac_status); } && { test -z "$ac_c_werror_flag" || test ! -s conftest.err } && test -s conftest.$ac_objext; then ac_header_compiler=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_header_compiler=no fi rm -f core conftest.err conftest.$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 <$ac_header> _ACEOF if { (ac_try="$ac_cpp conftest.$ac_ext" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5 (eval "$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 $ac_status); } >/dev/null && { test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || test ! -s conftest.err }; then ac_header_preproc=yes else echo "$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? What about this header? case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in yes:no: ) { echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5 echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;} { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5 echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;} ac_header_preproc=yes ;; no:yes:* ) { echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5 echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;} { echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5 echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;} { echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5 echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;} { echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5 echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;} { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5 echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;} { echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5 echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;} ;; esac { echo "$as_me:$LINENO: checking for $ac_header" >&5 echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6; } if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then echo $ECHO_N "(cached) $ECHO_C" >&6 else eval "$as_ac_Header=\$ac_header_preproc" fi ac_res=`eval echo '${'$as_ac_Header'}'` { echo "$as_me:$LINENO: result: $ac_res" >&5 echo "${ECHO_T}$ac_res" >&6; } fi if test `eval echo '${'$as_ac_Header'}'` = yes; then cat >>confdefs.h <<_ACEOF #define `echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF else echo " ** Couldn't find necessary system header **" exit -1 fi done old_CFLAGS="$CFLAGS" old_CPPFLAGS="$CPPFLAGS" #CPPFLAGS=`pkg-config --cflags glib-2.0` CFLAGS="$DEPS_CFLAGS" CPPFLAGS="$DEPS_CFLAGS" for ac_header in glib.h do as_ac_Header=`echo "ac_cv_header_$ac_header" | $as_tr_sh` if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then { echo "$as_me:$LINENO: checking for $ac_header" >&5 echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6; } if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then echo $ECHO_N "(cached) $ECHO_C" >&6 fi ac_res=`eval echo '${'$as_ac_Header'}'` { echo "$as_me:$LINENO: result: $ac_res" >&5 echo "${ECHO_T}$ac_res" >&6; } else # Is the header compilable? { echo "$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.$ac_objext if { (ac_try="$ac_compile" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5 (eval "$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 $ac_status); } && { test -z "$ac_c_werror_flag" || test ! -s conftest.err } && test -s conftest.$ac_objext; then ac_header_compiler=yes else echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 ac_header_compiler=no fi rm -f core conftest.err conftest.$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 <$ac_header> _ACEOF if { (ac_try="$ac_cpp conftest.$ac_ext" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5 (eval "$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 $ac_status); } >/dev/null && { test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || test ! -s conftest.err }; then ac_header_preproc=yes else echo "$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? What about this header? case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in yes:no: ) { echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5 echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;} { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5 echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;} ac_header_preproc=yes ;; no:yes:* ) { echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5 echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;} { echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5 echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;} { echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5 echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;} { echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5 echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;} { echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5 echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;} { echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5 echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;} ;; esac { echo "$as_me:$LINENO: checking for $ac_header" >&5 echo $ECHO_N "checking for $ac_header... $ECHO_C" >&6; } if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then echo $ECHO_N "(cached) $ECHO_C" >&6 else eval "$as_ac_Header=\$ac_header_preproc" fi ac_res=`eval echo '${'$as_ac_Header'}'` { echo "$as_me:$LINENO: result: $ac_res" >&5 echo "${ECHO_T}$ac_res" >&6; } fi if test `eval echo '${'$as_ac_Header'}'` = yes; then cat >>confdefs.h <<_ACEOF #define `echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF else echo " ** Couldn't find necessary header glib.h **" echo " ** Make sure the glib library and headers are installed **" echo " ** If they are in a non-standard location, set the **" echo " ** environment variables CPPFLAGS and LDFLAGS appropriately **" exit -1 fi done CFLAGS=$old_CFLAGS CPPFLAGS=$old_CPPFLAGS # Checks for typedefs, structures, and compiler characteristics. { echo "$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 cs; /* SunOS 4.1.1 cc rejects this. */ char const *const *pcpcc; char **ppc; /* 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. 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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 sigma-1.1.3/AUTHORS0000644000175000017500000000014610604240252010601 00000000000000Rahul Siddharthan The Institute of Mathematical Sciences, Chennai 600 113, India sigma-1.1.3/COPYING0000644000175000017500000004402310631766617010610 00000000000000Sigma: simple greedy multiple alignment Program for multiple alignment of non-coding DNA sequence This version (C) 2007, Rahul Siddharthan The files getopt.h and getopt_long.c in the src/ subdirectory are copyright (C) 2000 The NetBSD Foundation and subject to the BSD license: see the files for licensing information. 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(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. sigma-1.1.3/ChangeLog0000644000175000017500000000174711157374454011333 00000000000000Version 1.1.3: * Make local gapless alignment function linear in memory consumption (Gayathri Jayaraman); related to this, remove "maxfraglen" and the "-l" option, since these are no longer needed. The function continues to be quadratic in time. * Bugfix in gapless alignment function (off-by-one error) (Gayathri Jayaraman) * Another small improvement to best_match() * Fix string-bounds bug relating to pre-fragmentation of sequences Version 1.1.2: * a trivial change to best_match() that increases the speed by over 30% with larger input files * include NetBSD->FreeBSD version of getopt_long(), for compatibility on platforms that lack it Version 1.1.1: * fix compilation error on powerpc (and maybe other platforms) * include manpage contributed by Charles Plessy * document -l option in NOTES and printhelp.c Version 1.1: rewrite in C, a few bugfixes and improvements described in README Version 1.0: first release, in Objective Caml sigma-1.1.3/INSTALL0000644000175000017500000002231210604240413010560 00000000000000The following is generic information. See README and COMPILING for information specific to this program. ---------------------------------------------------------------------- Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002 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=PATH'. You can specify separate installation prefixes for architecture-specific files and architecture-independent files. If you give `configure' the option `--exec-prefix=PATH', the package will use PATH 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=PATH' 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. Run `configure --help' for more details. sigma-1.1.3/NEWS0000644000175000017500000000006110604240445010230 00000000000000Version 1.1 released April 3, 2007: rewrite in C sigma-1.1.3/TODO0000644000175000017500000000000010604240027010206 00000000000000sigma-1.1.3/config.guess0000755000175000017500000012475310427646672012107 00000000000000#! /bin/sh # Attempt to guess a canonical system name. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, # 2000, 2001, 2002, 2003, 2004, 2005 Free Software Foundation, Inc. timestamp='2005-08-03' # This file is free software; you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA # 02110-1301, USA. # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # 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 ($timestamp) Originally written by Per Bothner. Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." help=" Try \`$me --help' for more information." # Parse command line while test $# -gt 0 ; do case $1 in --time-stamp | --time* | -t ) echo "$timestamp" ; exit ;; --version | -v ) echo "$version" ; exit ;; --help | --h* | -h ) echo "$usage"; exit ;; -- ) # Stop option processing shift; break ;; - ) # Use stdin as input. break ;; -* ) echo "$me: invalid option $1$help" >&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'. We still # use `HOST_CC' if defined, but it is deprecated. # Portable tmp directory creation inspired by the Autoconf team. set_cc_for_build=' trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ; trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ; : ${TMPDIR=/tmp} ; { tmp=`(umask 077 && mktemp -d -q "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } || { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } || { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } || { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ; dummy=$tmp/dummy ; tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ; case $CC_FOR_BUILD,$HOST_CC,$CC in ,,) echo "int x;" > $dummy.c ; for c in cc gcc c89 c99 ; do if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then CC_FOR_BUILD="$c"; break ; fi ; done ; if test x"$CC_FOR_BUILD" = x ; then CC_FOR_BUILD=no_compiler_found ; fi ;; ,,*) CC_FOR_BUILD=$CC ;; ,*,*) CC_FOR_BUILD=$HOST_CC ;; esac ; set_cc_for_build= ;' # This is needed to find uname on a Pyramid OSx when run in the BSD universe. # (ghazi@noc.rutgers.edu 1994-08-24) if (test -f /.attbin/uname) >/dev/null 2>&1 ; then PATH=$PATH:/.attbin ; export PATH fi UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown # Note: order is significant - the case branches are not exclusive. case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in *:NetBSD:*:*) # NetBSD (nbsd) targets should (where applicable) match one or # more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*, # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently # switched to ELF, *-*-netbsd* would select the old # object file format. This provides both forward # compatibility and a consistent mechanism for selecting the # object file format. # # Note: NetBSD doesn't particularly care about the vendor # portion of the name. We always set it to "unknown". sysctl="sysctl -n hw.machine_arch" UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \ /usr/sbin/$sysctl 2>/dev/null || echo unknown)` case "${UNAME_MACHINE_ARCH}" in armeb) machine=armeb-unknown ;; arm*) machine=arm-unknown ;; sh3el) machine=shl-unknown ;; sh3eb) machine=sh-unknown ;; *) machine=${UNAME_MACHINE_ARCH}-unknown ;; esac # The Operating System including object format, if it has switched # to ELF recently, or will in the future. case "${UNAME_MACHINE_ARCH}" in arm*|i386|m68k|ns32k|sh3*|sparc|vax) eval $set_cc_for_build if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \ | grep __ELF__ >/dev/null then # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout). # Return netbsd for either. FIX? os=netbsd else os=netbsdelf fi ;; *) os=netbsd ;; esac # The OS release # Debian GNU/NetBSD machines have a different userland, and # thus, need a distinct triplet. However, they do not need # kernel version information, so it can be replaced with a # suitable tag, in the style of linux-gnu. case "${UNAME_VERSION}" in Debian*) release='-gnu' ;; *) release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'` ;; esac # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM: # contains redundant information, the shorter form: # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used. echo "${machine}-${os}${release}" exit ;; *:OpenBSD:*:*) UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'` echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE} exit ;; *:ekkoBSD:*:*) echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE} exit ;; macppc:MirBSD:*:*) echo powerppc-unknown-mirbsd${UNAME_RELEASE} exit ;; *:MirBSD:*:*) echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE} exit ;; alpha:OSF1:*:*) case $UNAME_RELEASE in *4.0) UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'` ;; *5.*) UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'` ;; esac # According to Compaq, /usr/sbin/psrinfo has been available on # OSF/1 and Tru64 systems produced since 1995. 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 Pn.n version is a patched version. # 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/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` exit ;; 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 ;; 21064:Windows_NT:50:3) echo alpha-dec-winnt3.5 exit ;; Amiga*:UNIX_System_V:4.0:*) echo m68k-unknown-sysv4 exit ;; *:[Aa]miga[Oo][Ss]:*:*) echo ${UNAME_MACHINE}-unknown-amigaos exit ;; *:[Mm]orph[Oo][Ss]:*:*) echo ${UNAME_MACHINE}-unknown-morphos exit ;; *:OS/390:*:*) echo i370-ibm-openedition exit ;; *:z/VM:*:*) echo s390-ibm-zvmoe exit ;; *:OS400:*:*) echo powerpc-ibm-os400 exit ;; arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*) echo arm-acorn-riscix${UNAME_RELEASE} exit ;; arm:riscos:*:*|arm:RISCOS:*:*) echo arm-unknown-riscos exit ;; SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*) echo hppa1.1-hitachi-hiuxmpp exit ;; 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 ;; NILE*:*:*:dcosx) echo pyramid-pyramid-svr4 exit ;; DRS?6000:unix:4.0:6*) echo sparc-icl-nx6 exit ;; DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*) case `/usr/bin/uname -p` in sparc) echo sparc-icl-nx7; exit ;; esac ;; sun4H:SunOS:5.*:*) echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; i86pc:SunOS:5.*:*) echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:6*:*) # According to config.sub, this is the proper way to canonicalize # SunOS6. Hard to guess exactly what SunOS6 will be like, but # it's likely to be more like Solaris than SunOS4. echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:*:*) case "`/usr/bin/arch -k`" in Series*|S4*) UNAME_RELEASE=`uname -v` ;; esac # Japanese Language versions have a version number like `4.1.3-JL'. echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'` exit ;; sun3*:SunOS:*:*) echo m68k-sun-sunos${UNAME_RELEASE} exit ;; sun*:*:4.2BSD:*) UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null` test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3 case "`/bin/arch`" in sun3) echo m68k-sun-sunos${UNAME_RELEASE} ;; sun4) echo sparc-sun-sunos${UNAME_RELEASE} ;; esac exit ;; aushp:SunOS:*:*) echo sparc-auspex-sunos${UNAME_RELEASE} exit ;; # The situation for MiNT is a little confusing. The machine name # can be virtually everything (everything which is not # "atarist" or "atariste" at least should have a processor # > m68000). The system name ranges from "MiNT" over "FreeMiNT" # to the lowercase version "mint" (or "freemint"). Finally # the system name "TOS" denotes a system which is actually not # MiNT. But MiNT is downward compatible to TOS, so this should # be no problem. atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) echo m68k-milan-mint${UNAME_RELEASE} exit ;; hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) echo m68k-hades-mint${UNAME_RELEASE} exit ;; *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) echo m68k-unknown-mint${UNAME_RELEASE} exit ;; m68k:machten:*:*) echo m68k-apple-machten${UNAME_RELEASE} exit ;; powerpc:machten:*:*) echo powerpc-apple-machten${UNAME_RELEASE} exit ;; RISC*:Mach:*:*) echo mips-dec-mach_bsd4.3 exit ;; RISC*:ULTRIX:*:*) echo mips-dec-ultrix${UNAME_RELEASE} exit ;; VAX*:ULTRIX*:*:*) echo vax-dec-ultrix${UNAME_RELEASE} exit ;; 2020:CLIX:*:* | 2430:CLIX:*:*) echo clipper-intergraph-clix${UNAME_RELEASE} exit ;; mips:*:*:UMIPS | mips:*:*:RISCos) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #ifdef __cplusplus #include /* for printf() prototype */ int main (int argc, char *argv[]) { #else int main (argc, argv) int argc; char *argv[]; { #endif #if defined (host_mips) && defined (MIPSEB) #if defined (SYSTYPE_SYSV) printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_SVR4) printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0); #endif #endif exit (-1); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` && SYSTEM_NAME=`$dummy $dummyarg` && { echo "$SYSTEM_NAME"; exit; } echo mips-mips-riscos${UNAME_RELEASE} exit ;; Motorola:PowerMAX_OS:*:*) echo powerpc-motorola-powermax exit ;; Motorola:*:4.3:PL8-*) echo powerpc-harris-powermax exit ;; Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) echo powerpc-harris-powermax exit ;; Night_Hawk:Power_UNIX:*:*) echo powerpc-harris-powerunix exit ;; m88k:CX/UX:7*:*) echo m88k-harris-cxux7 exit ;; m88k:*:4*:R4*) echo m88k-motorola-sysv4 exit ;; m88k:*:3*:R3*) echo m88k-motorola-sysv3 exit ;; AViiON:dgux:*:*) # DG/UX returns AViiON for all architectures UNAME_PROCESSOR=`/usr/bin/uname -p` if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ] then if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \ [ ${TARGET_BINARY_INTERFACE}x = x ] then echo m88k-dg-dgux${UNAME_RELEASE} else echo m88k-dg-dguxbcs${UNAME_RELEASE} fi else echo i586-dg-dgux${UNAME_RELEASE} fi exit ;; M88*:DolphinOS:*:*) # DolphinOS (SVR3) echo m88k-dolphin-sysv3 exit ;; M88*:*:R3*:*) # Delta 88k system running SVR3 echo m88k-motorola-sysv3 exit ;; XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) echo m88k-tektronix-sysv3 exit ;; Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) echo m68k-tektronix-bsd exit ;; *:IRIX*:*:*) echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'` exit ;; ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id exit ;; # Note that: echo "'`uname -s`'" gives 'AIX ' i*86:AIX:*:*) echo i386-ibm-aix exit ;; ia64:AIX:*:*) if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${UNAME_MACHINE}-ibm-aix${IBM_REV} exit ;; *:AIX:2:3) if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include main() { if (!__power_pc()) exit(1); puts("powerpc-ibm-aix3.2.5"); exit(0); } EOF if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` then echo "$SYSTEM_NAME" else echo rs6000-ibm-aix3.2.5 fi elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then echo rs6000-ibm-aix3.2.4 else echo rs6000-ibm-aix3.2 fi exit ;; *:AIX:*:[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 ;; *:AIX:*:*) echo rs6000-ibm-aix exit ;; ibmrt:4.4BSD:*|romp-ibm:BSD:*) echo romp-ibm-bsd4.4 exit ;; ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to exit ;; # report: romp-ibm BSD 4.3 *:BOSX:*:*) echo rs6000-bull-bosx exit ;; DPX/2?00:B.O.S.:*:*) echo m68k-bull-sysv3 exit ;; 9000/[34]??:4.3bsd:1.*:*) echo m68k-hp-bsd exit ;; hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) echo m68k-hp-bsd4.4 exit ;; 9000/[34678]??:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` case "${UNAME_MACHINE}" in 9000/31? ) HP_ARCH=m68000 ;; 9000/[34]?? ) HP_ARCH=m68k ;; 9000/[678][0-9][0-9]) if [ -x /usr/bin/getconf ]; then sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` case "${sc_cpu_version}" in 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 532) # CPU_PA_RISC2_0 case "${sc_kernel_bits}" in 32) HP_ARCH="hppa2.0n" ;; 64) HP_ARCH="hppa2.0w" ;; '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20 esac ;; esac fi if [ "${HP_ARCH}" = "" ]; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #define _HPUX_SOURCE #include #include int main () { #if defined(_SC_KERNEL_BITS) long bits = sysconf(_SC_KERNEL_BITS); #endif long cpu = sysconf (_SC_CPU_VERSION); switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0"); break; case CPU_PA_RISC1_1: puts ("hppa1.1"); break; case CPU_PA_RISC2_0: #if defined(_SC_KERNEL_BITS) switch (bits) { case 64: puts ("hppa2.0w"); break; case 32: puts ("hppa2.0n"); break; default: puts ("hppa2.0"); break; } break; #else /* !defined(_SC_KERNEL_BITS) */ puts ("hppa2.0"); break; #endif default: puts ("hppa1.0"); break; } exit (0); } EOF (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy` test -z "$HP_ARCH" && HP_ARCH=hppa fi ;; esac if [ ${HP_ARCH} = "hppa2.0w" ] then eval $set_cc_for_build # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler # generating 64-bit code. GNU and HP use different nomenclature: # # $ CC_FOR_BUILD=cc ./config.guess # => hppa2.0w-hp-hpux11.23 # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess # => hppa64-hp-hpux11.23 if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | grep __LP64__ >/dev/null then HP_ARCH="hppa2.0w" else HP_ARCH="hppa64" fi fi echo ${HP_ARCH}-hp-hpux${HPUX_REV} exit ;; ia64:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` echo ia64-hp-hpux${HPUX_REV} exit ;; 3050*:HI-UX:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include int main () { long cpu = sysconf (_SC_CPU_VERSION); /* The order matters, because CPU_IS_HP_MC68K erroneously returns true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct results, however. */ if (CPU_IS_PA_RISC (cpu)) { switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; default: puts ("hppa-hitachi-hiuxwe2"); break; } } else if (CPU_IS_HP_MC68K (cpu)) puts ("m68k-hitachi-hiuxwe2"); else puts ("unknown-hitachi-hiuxwe2"); exit (0); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` && { echo "$SYSTEM_NAME"; exit; } echo unknown-hitachi-hiuxwe2 exit ;; 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* ) echo hppa1.1-hp-bsd exit ;; 9000/8??:4.3bsd:*:*) echo hppa1.0-hp-bsd exit ;; *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) echo hppa1.0-hp-mpeix exit ;; hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* ) echo hppa1.1-hp-osf exit ;; hp8??:OSF1:*:*) echo hppa1.0-hp-osf exit ;; i*86:OSF1:*:*) if [ -x /usr/sbin/sysversion ] ; then echo ${UNAME_MACHINE}-unknown-osf1mk else echo ${UNAME_MACHINE}-unknown-osf1 fi exit ;; parisc*:Lites*:*:*) echo hppa1.1-hp-lites exit ;; C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) echo c1-convex-bsd exit ;; C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit ;; C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) echo c34-convex-bsd exit ;; C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) echo c38-convex-bsd exit ;; C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) echo c4-convex-bsd exit ;; CRAY*Y-MP:*:*:*) echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*[A-Z]90:*:*:*) echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ -e 's/\.[^.]*$/.X/' exit ;; CRAY*TS:*:*:*) echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*T3E:*:*:*) echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*SV1:*:*:*) echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; *:UNICOS/mp:*:*) echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; 5000:UNIX_System_V:4.*:*) FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'` echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} exit ;; sparc*:BSD/OS:*:*) echo sparc-unknown-bsdi${UNAME_RELEASE} exit ;; *:BSD/OS:*:*) echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} exit ;; *:FreeBSD:*:*) echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` exit ;; i*:CYGWIN*:*) echo ${UNAME_MACHINE}-pc-cygwin exit ;; i*:MINGW*:*) echo ${UNAME_MACHINE}-pc-mingw32 exit ;; i*:windows32*:*) # uname -m includes "-pc" on this system. echo ${UNAME_MACHINE}-mingw32 exit ;; i*:PW*:*) echo ${UNAME_MACHINE}-pc-pw32 exit ;; x86:Interix*:[34]*) echo i586-pc-interix${UNAME_RELEASE}|sed -e 's/\..*//' exit ;; [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) echo i${UNAME_MACHINE}-pc-mks exit ;; i*:Windows_NT*:* | Pentium*:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we # UNAME_MACHINE based on the output of uname instead of i386? echo i586-pc-interix exit ;; i*:UWIN*:*) echo ${UNAME_MACHINE}-pc-uwin exit ;; amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*) echo x86_64-unknown-cygwin exit ;; p*:CYGWIN*:*) echo powerpcle-unknown-cygwin exit ;; prep*:SunOS:5.*:*) echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; *:GNU:*:*) # the GNU system echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'` exit ;; *:GNU/*:*:*) # other systems with GNU libc and userland echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu exit ;; i*86:Minix:*:*) echo ${UNAME_MACHINE}-pc-minix exit ;; arm*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; cris:Linux:*:*) echo cris-axis-linux-gnu exit ;; crisv32:Linux:*:*) echo crisv32-axis-linux-gnu exit ;; frv:Linux:*:*) echo frv-unknown-linux-gnu exit ;; ia64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; m32r*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; m68*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; 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; } ;; 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; } ;; or32:Linux:*:*) echo or32-unknown-linux-gnu exit ;; ppc:Linux:*:*) echo powerpc-unknown-linux-gnu exit ;; ppc64:Linux:*:*) echo powerpc64-unknown-linux-gnu exit ;; alpha:Linux:*:*) case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in EV5) UNAME_MACHINE=alphaev5 ;; EV56) UNAME_MACHINE=alphaev56 ;; PCA56) UNAME_MACHINE=alphapca56 ;; PCA57) UNAME_MACHINE=alphapca56 ;; EV6) UNAME_MACHINE=alphaev6 ;; EV67) UNAME_MACHINE=alphaev67 ;; EV68*) UNAME_MACHINE=alphaev68 ;; esac objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} exit ;; 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 ;; parisc64:Linux:*:* | hppa64:Linux:*:*) echo hppa64-unknown-linux-gnu exit ;; s390:Linux:*:* | s390x:Linux:*:*) echo ${UNAME_MACHINE}-ibm-linux exit ;; sh64*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; sh*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; sparc:Linux:*:* | sparc64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; x86_64:Linux:*:*) echo x86_64-unknown-linux-gnu exit ;; i*86:Linux:*:*) # The BFD linker knows what the default object file format is, so # first see if it will tell us. cd to the root directory to prevent # problems with other programs or directories called `ld' in the path. # Set LC_ALL=C to ensure ld outputs messages in English. ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \ | sed -ne '/supported targets:/!d s/[ ][ ]*/ /g s/.*supported targets: *// s/ .*// p'` case "$ld_supported_targets" in elf32-i386) TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu" ;; a.out-i386-linux) echo "${UNAME_MACHINE}-pc-linux-gnuaout" exit ;; coff-i386) echo "${UNAME_MACHINE}-pc-linux-gnucoff" exit ;; "") # Either a pre-BFD a.out linker (linux-gnuoldld) or # one that does not give us useful --help. echo "${UNAME_MACHINE}-pc-linux-gnuoldld" exit ;; 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TSUNAMI:LynxOS:2.*:*) echo sparc-unknown-lynxos${UNAME_RELEASE} exit ;; rs6000:LynxOS:2.*:*) echo rs6000-unknown-lynxos${UNAME_RELEASE} exit ;; PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*) echo powerpc-unknown-lynxos${UNAME_RELEASE} exit ;; SM[BE]S:UNIX_SV:*:*) echo mips-dde-sysv${UNAME_RELEASE} exit ;; RM*:ReliantUNIX-*:*:*) echo mips-sni-sysv4 exit ;; RM*:SINIX-*:*:*) echo mips-sni-sysv4 exit ;; *:SINIX-*:*:*) if uname -p 2>/dev/null >/dev/null ; then UNAME_MACHINE=`(uname -p) 2>/dev/null` echo ${UNAME_MACHINE}-sni-sysv4 else echo ns32k-sni-sysv fi exit ;; PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort # says echo i586-unisys-sysv4 exit ;; *:UNIX_System_V:4*:FTX*) # From Gerald Hewes . # How about differentiating between stratus architectures? -djm echo hppa1.1-stratus-sysv4 exit ;; *:*:*:FTX*) # From seanf@swdc.stratus.com. echo i860-stratus-sysv4 exit ;; i*86:VOS:*:*) # From Paul.Green@stratus.com. echo ${UNAME_MACHINE}-stratus-vos exit ;; *:VOS:*:*) # From Paul.Green@stratus.com. echo hppa1.1-stratus-vos exit ;; mc68*:A/UX:*:*) echo m68k-apple-aux${UNAME_RELEASE} exit ;; news*:NEWS-OS:6*:*) echo mips-sony-newsos6 exit ;; R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) if [ -d /usr/nec ]; then echo mips-nec-sysv${UNAME_RELEASE} else echo mips-unknown-sysv${UNAME_RELEASE} fi exit ;; BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. echo powerpc-be-beos exit ;; BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. echo powerpc-apple-beos exit ;; BePC:BeOS:*:*) # BeOS running on Intel PC compatible. echo i586-pc-beos exit ;; SX-4:SUPER-UX:*:*) echo sx4-nec-superux${UNAME_RELEASE} exit ;; SX-5:SUPER-UX:*:*) echo sx5-nec-superux${UNAME_RELEASE} exit ;; SX-6:SUPER-UX:*:*) echo sx6-nec-superux${UNAME_RELEASE} exit ;; Power*:Rhapsody:*:*) echo powerpc-apple-rhapsody${UNAME_RELEASE} exit ;; *:Rhapsody:*:*) echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE} exit ;; *:Darwin:*:*) UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown case $UNAME_PROCESSOR in *86) UNAME_PROCESSOR=i686 ;; unknown) UNAME_PROCESSOR=powerpc ;; esac echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE} exit ;; *: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${UNAME_RELEASE} exit ;; *:QNX:*:4*) echo i386-pc-qnx exit ;; NSE-?:NONSTOP_KERNEL:*:*) echo nse-tandem-nsk${UNAME_RELEASE} exit ;; NSR-?:NONSTOP_KERNEL:*:*) echo nsr-tandem-nsk${UNAME_RELEASE} exit ;; *:NonStop-UX:*:*) echo mips-compaq-nonstopux exit ;; BS2000:POSIX*:*:*) echo bs2000-siemens-sysv exit ;; DS/*:UNIX_System_V:*:*) echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE} exit ;; *: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 ${UNAME_MACHINE}-unknown-plan9 exit ;; *:TOPS-10:*:*) echo pdp10-unknown-tops10 exit ;; *:TENEX:*:*) echo pdp10-unknown-tenex exit ;; KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) echo pdp10-dec-tops20 exit ;; XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) echo pdp10-xkl-tops20 exit ;; *:TOPS-20:*:*) echo pdp10-unknown-tops20 exit ;; *:ITS:*:*) echo pdp10-unknown-its exit ;; SEI:*:*:SEIUX) echo mips-sei-seiux${UNAME_RELEASE} exit ;; *:DragonFly:*:*) echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` exit ;; *:*VMS:*:*) UNAME_MACHINE=`(uname -p) 2>/dev/null` case "${UNAME_MACHINE}" in A*) echo alpha-dec-vms ; exit ;; I*) echo ia64-dec-vms ; exit ;; V*) echo vax-dec-vms ; exit ;; esac ;; *:XENIX:*:SysV) echo i386-pc-xenix exit ;; i*86:skyos:*:*) echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//' exit ;; 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". Perhaps BFD should be changed, I don't know.... */ printf ("mips-sony-bsd\n"); exit (0); #else #include printf ("m68k-sony-newsos%s\n", #ifdef NEWSOS4 "4" #else "" #endif ); exit (0); #endif #endif #if defined (__arm) && defined (__acorn) && defined (__unix) printf ("arm-acorn-riscix\n"); exit (0); #endif #if defined (hp300) && !defined (hpux) printf ("m68k-hp-bsd\n"); exit (0); #endif #if defined (NeXT) #if !defined (__ARCHITECTURE__) #define __ARCHITECTURE__ "m68k" #endif int version; version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`; if (version < 4) printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); else printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); exit (0); #endif #if defined (MULTIMAX) || defined (n16) #if defined (UMAXV) printf ("ns32k-encore-sysv\n"); exit (0); #else #if defined (CMU) printf ("ns32k-encore-mach\n"); exit (0); #else printf ("ns32k-encore-bsd\n"); exit (0); #endif #endif #endif #if defined (__386BSD__) printf ("i386-pc-bsd\n"); exit (0); #endif #if defined (sequent) #if defined (i386) printf ("i386-sequent-dynix\n"); exit (0); #endif #if defined (ns32000) printf ("ns32k-sequent-dynix\n"); exit (0); #endif #endif #if defined (_SEQUENT_) struct utsname un; uname(&un); if (strncmp(un.version, "V2", 2) == 0) { printf ("i386-sequent-ptx2\n"); exit (0); } if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ printf ("i386-sequent-ptx1\n"); exit (0); } printf ("i386-sequent-ptx\n"); exit (0); #endif #if defined (vax) # if !defined (ultrix) # include # if defined (BSD) # if BSD == 43 printf ("vax-dec-bsd4.3\n"); exit (0); # else # if BSD == 199006 printf ("vax-dec-bsd4.3reno\n"); exit (0); # else printf ("vax-dec-bsd\n"); exit (0); # endif # endif # else printf ("vax-dec-bsd\n"); exit (0); # endif # else printf ("vax-dec-ultrix\n"); exit (0); # endif #endif #if defined (alliant) && defined (i860) printf ("i860-alliant-bsd\n"); exit (0); #endif exit (1); } EOF $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` && { echo "$SYSTEM_NAME"; exit; } # Apollos put the system type in the environment. test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; } # Convex versions that predate uname can use getsysinfo(1) if [ -x /usr/convex/getsysinfo ] then case `getsysinfo -f cpu_type` in c1*) echo c1-convex-bsd exit ;; c2*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit ;; c34*) echo c34-convex-bsd exit ;; c38*) echo c38-convex-bsd exit ;; c4*) echo c4-convex-bsd exit ;; esac fi cat >&2 < in order to provide the needed information to handle your system. config.guess timestamp = $timestamp uname -m = `(uname -m) 2>/dev/null || echo unknown` uname -r = `(uname -r) 2>/dev/null || echo unknown` uname -s = `(uname -s) 2>/dev/null || echo unknown` uname -v = `(uname -v) 2>/dev/null || echo unknown` /usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null` /bin/uname -X = `(/bin/uname -X) 2>/dev/null` hostinfo = `(hostinfo) 2>/dev/null` /bin/universe = `(/bin/universe) 2>/dev/null` /usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null` /bin/arch = `(/bin/arch) 2>/dev/null` /usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null` /usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null` UNAME_MACHINE = ${UNAME_MACHINE} UNAME_RELEASE = ${UNAME_RELEASE} UNAME_SYSTEM = ${UNAME_SYSTEM} UNAME_VERSION = ${UNAME_VERSION} EOF exit 1 # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "timestamp='" # time-stamp-format: "%:y-%02m-%02d" # time-stamp-end: "'" # End: sigma-1.1.3/config.sub0000755000175000017500000007577710427646672011565 00000000000000#! /bin/sh # Configuration validation subroutine script. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, # 2000, 2001, 2002, 2003, 2004, 2005 Free Software Foundation, Inc. timestamp='2005-07-08' # 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., 51 Franklin Street - Fifth Floor, Boston, MA # 02110-1301, USA. # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Please send patches to . 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, 2002, 2003, 2004, 2005 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 ;; --version | -v ) echo "$version" ; exit ;; --help | --h* | -h ) echo "$usage"; exit ;; -- ) # Stop option processing shift; break ;; - ) # Use stdin as input. break ;; -* ) echo "$me: invalid option $1$help" exit 1 ;; *local*) # First pass through any local machine types. echo $1 exit ;; * ) break ;; esac done case $# in 0) echo "$me: missing argument$help" >&2 exit 1;; 1) ;; *) echo "$me: too many arguments$help" >&2 exit 1;; esac # Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any). # Here we must recognize all the valid KERNEL-OS combinations. maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` case $maybe_os in nto-qnx* | linux-gnu* | linux-dietlibc | linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | \ kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | storm-chaos* | os2-emx* | rtmk-nova*) os=-$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 | -knuth | -cray) 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 $basic_machine in # Recognize the basic CPU types without company name. # Some are omitted here because they have special meanings below. 1750a | 580 \ | a29k \ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \ | am33_2.0 \ | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr \ | bfin \ | c4x | clipper \ | d10v | d30v | dlx | dsp16xx \ | fr30 | frv \ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ | i370 | i860 | i960 | ia64 \ | ip2k | iq2000 \ | m32r | m32rle | m68000 | m68k | m88k | maxq | mcore \ | mips | mipsbe | mipseb | mipsel | mipsle \ | mips16 \ | mips64 | mips64el \ | mips64vr | mips64vrel \ | mips64orion | mips64orionel \ | mips64vr4100 | mips64vr4100el \ | mips64vr4300 | mips64vr4300el \ | mips64vr5000 | mips64vr5000el \ | mips64vr5900 | mips64vr5900el \ | mipsisa32 | mipsisa32el \ | mipsisa32r2 | mipsisa32r2el \ | mipsisa64 | mipsisa64el \ | mipsisa64r2 | mipsisa64r2el \ | mipsisa64sb1 | mipsisa64sb1el \ | mipsisa64sr71k | mipsisa64sr71kel \ | mipstx39 | mipstx39el \ | mn10200 | mn10300 \ | ms1 \ | msp430 \ | ns16k | ns32k \ | or32 \ | pdp10 | pdp11 | pj | pjl \ | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \ | pyramid \ | sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | shbe | shle | sh[1234]le | sh3ele \ | sh64 | sh64le \ | sparc | sparc64 | sparc64b | sparc86x | sparclet | sparclite \ | sparcv8 | sparcv9 | sparcv9b \ | strongarm \ | tahoe | thumb | tic4x | tic80 | tron \ | v850 | v850e \ | we32k \ | x86 | xscale | xscalee[bl] | xstormy16 | xtensa \ | z8k) basic_machine=$basic_machine-unknown ;; m32c) 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-* \ | bfin-* | bs2000-* \ | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \ | clipper-* | craynv-* | 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-* | iq2000-* \ | m32r-* | m32rle-* \ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ | m88110-* | m88k-* | maxq-* | mcore-* \ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ | mips16-* \ | mips64-* | mips64el-* \ | mips64vr-* | mips64vrel-* \ | mips64orion-* | mips64orionel-* \ | mips64vr4100-* | mips64vr4100el-* \ | mips64vr4300-* | mips64vr4300el-* \ | mips64vr5000-* | mips64vr5000el-* \ | mips64vr5900-* | mips64vr5900el-* \ | mipsisa32-* | mipsisa32el-* \ | mipsisa32r2-* | mipsisa32r2el-* \ | mipsisa64-* | mipsisa64el-* \ | mipsisa64r2-* | mipsisa64r2el-* \ | mipsisa64sb1-* | mipsisa64sb1el-* \ | mipsisa64sr71k-* | mipsisa64sr71kel-* \ | mipstx39-* | mipstx39el-* \ | mmix-* \ | ms1-* \ | msp430-* \ | none-* | np1-* | ns16k-* | ns32k-* \ | orion-* \ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ | pyramid-* \ | romp-* | rs6000-* \ | sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | shbe-* \ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ | sparc-* | sparc64-* | sparc64b-* | sparc86x-* | sparclet-* \ | sparclite-* \ | sparcv8-* | sparcv9-* | sparcv9b-* | strongarm-* | sv1-* | sx?-* \ | tahoe-* | thumb-* \ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \ | tron-* \ | v850-* | v850e-* | vax-* \ | we32k-* \ | x86-* | x86_64-* | xps100-* | xscale-* | xscalee[bl]-* \ | xstormy16-* | xtensa-* \ | ymp-* \ | z8k-*) ;; m32c-*) ;; # Recognize the various machine names and aliases which stand # for a CPU type and a company and sometimes even an OS. 386bsd) basic_machine=i386-unknown os=-bsd ;; 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) basic_machine=m68000-att ;; 3b*) basic_machine=we32k-att ;; a29khif) basic_machine=a29k-amd os=-udi ;; abacus) basic_machine=abacus-unknown ;; adobe68k) basic_machine=m68010-adobe os=-scout ;; alliant | fx80) basic_machine=fx80-alliant ;; altos | altos3068) basic_machine=m68k-altos ;; am29k) basic_machine=a29k-none os=-bsd ;; amd64) basic_machine=x86_64-pc ;; amd64-*) basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'` ;; amdahl) basic_machine=580-amdahl os=-sysv ;; amiga | amiga-*) basic_machine=m68k-unknown ;; amigaos | amigados) basic_machine=m68k-unknown os=-amigaos ;; amigaunix | amix) basic_machine=m68k-unknown os=-sysv4 ;; apollo68) basic_machine=m68k-apollo os=-sysv ;; apollo68bsd) basic_machine=m68k-apollo os=-bsd ;; 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 ;; craynv) basic_machine=craynv-cray os=-unicosmp ;; cr16c) basic_machine=cr16c-unknown os=-elf ;; crds | unos) basic_machine=m68k-crds ;; crisv32 | crisv32-* | etraxfs*) basic_machine=crisv32-axis ;; cris | cris-* | etrax*) basic_machine=cris-axis ;; crx) basic_machine=crx-unknown os=-elf ;; da30 | da30-*) basic_machine=m68k-da30 ;; decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn) basic_machine=mips-dec ;; decsystem10* | dec10*) basic_machine=pdp10-dec os=-tops10 ;; decsystem20* | dec20*) basic_machine=pdp10-dec os=-tops20 ;; delta | 3300 | motorola-3300 | motorola-delta \ | 3300-motorola | delta-motorola) basic_machine=m68k-motorola ;; delta88) basic_machine=m88k-motorola os=-sysv3 ;; djgpp) basic_machine=i586-pc os=-msdosdjgpp ;; dpx20 | dpx20-*) basic_machine=rs6000-bull os=-bosx ;; dpx2* | dpx2*-bull) basic_machine=m68k-bull os=-sysv3 ;; ebmon29k) basic_machine=a29k-amd os=-ebmon ;; elxsi) basic_machine=elxsi-elxsi os=-bsd ;; encore | umax | mmax) basic_machine=ns32k-encore ;; es1800 | OSE68k | ose68k | ose | OSE) basic_machine=m68k-ericsson os=-ose ;; fx2800) basic_machine=i860-alliant ;; genix) basic_machine=ns32k-ns ;; gmicro) basic_machine=tron-gmicro os=-sysv ;; go32) basic_machine=i386-pc os=-go32 ;; h3050r* | hiux*) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; h8300hms) basic_machine=h8300-hitachi os=-hms ;; h8300xray) basic_machine=h8300-hitachi os=-xray ;; h8500hms) basic_machine=h8500-hitachi os=-hms ;; harris) basic_machine=m88k-harris os=-sysv3 ;; hp300-*) basic_machine=m68k-hp ;; hp300bsd) basic_machine=m68k-hp os=-bsd ;; hp300hpux) basic_machine=m68k-hp os=-hpux ;; hp3k9[0-9][0-9] | hp9[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k2[0-9][0-9] | hp9k31[0-9]) basic_machine=m68000-hp ;; hp9k3[2-9][0-9]) basic_machine=m68k-hp ;; hp9k6[0-9][0-9] | hp6[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k7[0-79][0-9] | hp7[0-79][0-9]) basic_machine=hppa1.1-hp ;; hp9k78[0-9] | hp78[0-9]) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[0-9][13679] | hp8[0-9][13679]) basic_machine=hppa1.1-hp ;; hp9k8[0-9][0-9] | hp8[0-9][0-9]) basic_machine=hppa1.0-hp ;; hppa-next) os=-nextstep3 ;; hppaosf) basic_machine=hppa1.1-hp os=-osf ;; hppro) basic_machine=hppa1.1-hp os=-proelf ;; i370-ibm* | ibm*) basic_machine=i370-ibm ;; # I'm not sure what "Sysv32" means. Should this be sysv3.2? i*86v32) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv32 ;; i*86v4*) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv4 ;; i*86v) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv ;; i*86sol2) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-solaris2 ;; i386mach) basic_machine=i386-mach os=-mach ;; i386-vsta | vsta) basic_machine=i386-unknown os=-vsta ;; iris | iris4d) basic_machine=mips-sgi case $os in -irix*) ;; *) os=-irix4 ;; esac ;; isi68 | isi) basic_machine=m68k-isi os=-sysv ;; m88k-omron*) basic_machine=m88k-omron ;; magnum | m3230) basic_machine=mips-mips os=-sysv ;; merlin) basic_machine=ns32k-utek os=-sysv ;; mingw32) basic_machine=i386-pc os=-mingw32 ;; miniframe) basic_machine=m68000-convergent ;; *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*) basic_machine=m68k-atari os=-mint ;; mips3*-*) basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'` ;; mips3*) basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown ;; monitor) basic_machine=m68k-rom68k os=-coff ;; morphos) basic_machine=powerpc-unknown os=-morphos ;; msdos) basic_machine=i386-pc os=-msdos ;; mvs) basic_machine=i370-ibm os=-mvs ;; ncr3000) basic_machine=i486-ncr os=-sysv4 ;; netbsd386) basic_machine=i386-unknown os=-netbsd ;; netwinder) basic_machine=armv4l-rebel os=-linux ;; news | news700 | news800 | news900) basic_machine=m68k-sony os=-newsos ;; news1000) basic_machine=m68030-sony os=-newsos ;; news-3600 | risc-news) basic_machine=mips-sony os=-newsos ;; necv70) basic_machine=v70-nec os=-sysv ;; next | m*-next ) basic_machine=m68k-next case $os in -nextstep* ) ;; -ns2*) os=-nextstep2 ;; *) os=-nextstep3 ;; esac ;; nh3000) basic_machine=m68k-harris os=-cxux ;; nh[45]000) basic_machine=m88k-harris os=-cxux ;; nindy960) basic_machine=i960-intel os=-nindy ;; mon960) basic_machine=i960-intel os=-mon960 ;; nonstopux) basic_machine=mips-compaq os=-nonstopux ;; np1) basic_machine=np1-gould ;; nsr-tandem) basic_machine=nsr-tandem ;; op50n-* | op60c-*) basic_machine=hppa1.1-oki os=-proelf ;; openrisc | openrisc-*) basic_machine=or32-unknown ;; os400) basic_machine=powerpc-ibm os=-os400 ;; OSE68000 | ose68000) basic_machine=m68000-ericsson os=-ose ;; os68k) basic_machine=m68k-none os=-os68k ;; pa-hitachi) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; paragon) basic_machine=i860-intel os=-osf ;; pbd) basic_machine=sparc-tti ;; pbb) basic_machine=m68k-tti ;; pc532 | pc532-*) basic_machine=ns32k-pc532 ;; pentium | p5 | k5 | k6 | nexgen | viac3) basic_machine=i586-pc ;; pentiumpro | p6 | 6x86 | athlon | athlon_*) basic_machine=i686-pc ;; pentiumii | pentium2 | pentiumiii | pentium3) basic_machine=i686-pc ;; pentium4) basic_machine=i786-pc ;; pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*) basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentiumpro-* | p6-* | 6x86-* | athlon-*) basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*) basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentium4-*) basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pn) basic_machine=pn-gould ;; power) basic_machine=power-ibm ;; ppc) basic_machine=powerpc-unknown ;; ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppcle | powerpclittle | ppc-le | powerpc-little) basic_machine=powerpcle-unknown ;; ppcle-* | powerpclittle-*) basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppc64) basic_machine=powerpc64-unknown ;; ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppc64le | powerpc64little | ppc64-le | powerpc64-little) basic_machine=powerpc64le-unknown ;; ppc64le-* | powerpc64little-*) basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ps2) basic_machine=i386-ibm ;; pw32) basic_machine=i586-unknown os=-pw32 ;; rom68k) basic_machine=m68k-rom68k os=-coff ;; rm[46]00) basic_machine=mips-siemens ;; rtpc | rtpc-*) basic_machine=romp-ibm ;; s390 | s390-*) basic_machine=s390-ibm ;; s390x | s390x-*) basic_machine=s390x-ibm ;; sa29200) basic_machine=a29k-amd os=-udi ;; sb1) basic_machine=mipsisa64sb1-unknown ;; sb1el) basic_machine=mipsisa64sb1el-unknown ;; sei) basic_machine=mips-sei os=-seiux ;; sequent) basic_machine=i386-sequent ;; sh) basic_machine=sh-hitachi os=-hms ;; sh64) basic_machine=sh64-unknown ;; sparclite-wrs | simso-wrs) basic_machine=sparclite-wrs os=-vxworks ;; sps7) basic_machine=m68k-bull os=-sysv2 ;; spur) basic_machine=spur-unknown ;; st2000) basic_machine=m68k-tandem ;; stratus) basic_machine=i860-stratus os=-sysv4 ;; sun2) basic_machine=m68000-sun ;; sun2os3) basic_machine=m68000-sun os=-sunos3 ;; sun2os4) basic_machine=m68000-sun os=-sunos4 ;; sun3os3) basic_machine=m68k-sun os=-sunos3 ;; sun3os4) basic_machine=m68k-sun os=-sunos4 ;; sun4os3) basic_machine=sparc-sun os=-sunos3 ;; sun4os4) basic_machine=sparc-sun os=-sunos4 ;; sun4sol2) basic_machine=sparc-sun os=-solaris2 ;; sun3 | sun3-*) basic_machine=m68k-sun ;; sun4) basic_machine=sparc-sun ;; sun386 | sun386i | roadrunner) basic_machine=i386-sun ;; sv1) basic_machine=sv1-cray os=-unicos ;; symmetry) basic_machine=i386-sequent os=-dynix ;; t3e) basic_machine=alphaev5-cray os=-unicos ;; t90) basic_machine=t90-cray os=-unicos ;; tic54x | c54x*) basic_machine=tic54x-unknown os=-coff ;; tic55x | c55x*) basic_machine=tic55x-unknown os=-coff ;; tic6x | c6x*) basic_machine=tic6x-unknown os=-coff ;; tx39) basic_machine=mipstx39-unknown ;; tx39el) basic_machine=mipstx39el-unknown ;; toad1) basic_machine=pdp10-xkl os=-tops20 ;; tower | tower-32) basic_machine=m68k-ncr ;; tpf) basic_machine=s390x-ibm os=-tpf ;; udi29k) basic_machine=a29k-amd os=-udi ;; ultra3) basic_machine=a29k-nyu os=-sym1 ;; v810 | necv810) basic_machine=v810-nec os=-none ;; vaxv) basic_machine=vax-dec os=-sysv ;; vms) basic_machine=vax-dec os=-vms ;; vpp*|vx|vx-*) basic_machine=f301-fujitsu ;; vxworks960) basic_machine=i960-wrs os=-vxworks ;; vxworks68) basic_machine=m68k-wrs os=-vxworks ;; vxworks29k) basic_machine=a29k-wrs os=-vxworks ;; w65*) basic_machine=w65-wdc os=-none ;; w89k-*) basic_machine=hppa1.1-winbond os=-proelf ;; xbox) basic_machine=i686-pc os=-mingw32 ;; xps | xps100) basic_machine=xps100-honeywell ;; ymp) basic_machine=ymp-cray os=-unicos ;; z8k-*-coff) basic_machine=z8k-unknown os=-sim ;; none) basic_machine=none-none os=-none ;; # Here we handle the default manufacturer of certain CPU types. It is in # some cases the only manufacturer, in others, it is the most popular. w89k) basic_machine=hppa1.1-winbond ;; op50n) basic_machine=hppa1.1-oki ;; op60c) basic_machine=hppa1.1-oki ;; romp) basic_machine=romp-ibm ;; mmix) basic_machine=mmix-knuth ;; rs6000) basic_machine=rs6000-ibm ;; vax) basic_machine=vax-dec ;; pdp10) # there are many clones, so DEC is not a safe bet basic_machine=pdp10-unknown ;; pdp11) basic_machine=pdp11-dec ;; we32k) basic_machine=we32k-att ;; sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele) basic_machine=sh-unknown ;; sparc | sparcv8 | sparcv9 | sparcv9b) basic_machine=sparc-sun ;; cydra) basic_machine=cydra-cydrome ;; orion) basic_machine=orion-highlevel ;; orion105) basic_machine=clipper-highlevel ;; mac | mpw | mac-mpw) basic_machine=m68k-apple ;; pmac | pmac-mpw) basic_machine=powerpc-apple ;; *-unknown) # Make sure to match an already-canonicalized machine name. ;; *) echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 exit 1 ;; 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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. # Originally written by Alexandre Oliva . if test -z "$depmode" || test -z "$source" || test -z "$object"; then echo "depcomp: Variables source, object and depmode must be set" 1>&2 exit 1 fi # `libtool' can also be set to `yes' or `no'. if test -z "$depfile"; then base=`echo "$object" | sed -e 's,^.*/,,' -e 's,\.\([^.]*\)$,.P\1,'` dir=`echo "$object" | sed 's,/.*$,/,'` if test "$dir" = "$object"; then dir= fi # FIXME: should be _deps on DOS. depfile="$dir.deps/$base" fi tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`} rm -f "$tmpdepfile" # Some modes work just like other modes, but use different flags. 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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 sigma-1.1.3/mkinstalldirs0000755000175000017500000000370410426532102012342 00000000000000#! /bin/sh # mkinstalldirs --- make directory hierarchy # Author: Noah Friedman # Created: 1993-05-16 # Public domain errstatus=0 dirmode="" usage="\ Usage: mkinstalldirs [-h] [--help] [-m mode] dir ..." # process command line arguments while test $# -gt 0 ; do case $1 in -h | --help | --h*) # -h for help echo "$usage" 1>&2 exit 0 ;; -m) # -m PERM arg shift test $# -eq 0 && { echo "$usage" 1>&2; exit 1; } dirmode=$1 shift ;; --) # stop option processing shift break ;; -*) # unknown option echo "$usage" 1>&2 exit 1 ;; *) # first non-opt arg break ;; esac done for file do if test -d "$file"; then shift else break fi done case $# in 0) exit 0 ;; esac case $dirmode in '') if mkdir -p -- . 2>/dev/null; then echo "mkdir -p -- $*" exec mkdir -p -- "$@" fi ;; *) if mkdir -m "$dirmode" -p -- . 2>/dev/null; then echo "mkdir -m $dirmode -p -- $*" exec mkdir -m "$dirmode" -p -- "$@" fi ;; esac for file do set fnord `echo ":$file" | sed -ne 's/^:\//#/;s/^://;s/\// /g;s/^#/\//;p'` shift pathcomp= for d do pathcomp="$pathcomp$d" case $pathcomp in -*) pathcomp=./$pathcomp ;; esac if test ! -d "$pathcomp"; then echo "mkdir $pathcomp" mkdir "$pathcomp" || lasterr=$? if test ! -d "$pathcomp"; then errstatus=$lasterr else if test ! -z "$dirmode"; then echo "chmod $dirmode $pathcomp" lasterr="" chmod "$dirmode" "$pathcomp" || lasterr=$? if test ! -z "$lasterr"; then errstatus=$lasterr fi fi fi fi pathcomp="$pathcomp/" done done exit $errstatus # Local Variables: # mode: shell-script # sh-indentation: 2 # End: # mkinstalldirs ends here sigma-1.1.3/sigma.10000644000175000017500000001235211157376441010733 00000000000000.\" Title: SIGMA .\" Author: Rahul Siddharthan .\" Generator: DocBook XSL Stylesheets v1.71.0 .\" Date: 2007.04.07 .\" Manual: Manual of Sigma .\" Source: sigma 1.1 .\" .TH "SIGMA" "1" "2007\-04\-07" "sigma 1.1" "Manual of Sigma" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" sigma \- Simple greedy multiple alignment of non\-coding DNA sequences .SH "SYNOPSIS" .HP 6 \fBsigma\fR [options] [\fIinputfile.fasta\fR] [\fIinputfile2.fasta\ ...\fR] .PP Each fasta file may contain a single sequence or multiple sequences; all sequences will be aligned together. .SH "DESCRIPTION" .PP \fBSigma\fR ("Simple greedy multiple alignment") is an alignment program with a new algorithm and scoring scheme designed specifically for non\-coding DNA sequence. It uses a strategy of seeking the best possible gapless local alignments, at each step making the best possible alignment consistent with existing alignments, and scores the significance of the alignment based on the lengths of the aligned fragments and a background model which may be supplied or estimated from an auxiliary file of intergenic DNA. With real data, while "correctness" can't be directly quantified for the alignment, running the PhyloGibbs motif finder on pre\-aligned sequence suggests that Sigma's alignments are superior. .SH "OPTIONS" .PP \fB\-A\fR \fB\-\-aligned_output\fR .RS 3n Aligned, pretty\-printed output (compare with \fB\-F\fR option) (default: only this). See also \fB\-C\fR. .RE .PP \fB\-b\fR \fB\-\-bgprobfile\fR \fIfilename\fR .RS 3n Auxiliary file (in fasta format) from which to read background sequences (overridden by \fB\-B\fR). Typically this is a file containing large quantities of similar non\-coding sequence, from which background probabilities of single\- and di\-nucleotides may be estimated. .RE .PP \fB\-B\fR \fB\-\-bgseqfile\fR \fIfilename\fR .RS 3n File containing background probabilities. The format is described further below. .RE .PP \fB\-C\fR \fB\-\-caps_only\fR .RS 3n Use only upper\-case letters in output sequence, for compatibility with output of some other programs like ClustalW and MLagan. By default, output is mixed\-case (as in Dialign), and lower\-case bases are treated as not aligned. .RE .PP \fB\-F\fR \fB\-\-fasta_output\fR .RS 3n Multi\-fasta output (can use both \fB\-A\fR and \fB\-F\fR in either order). See also \fB\-C\fR. .RE .PP \fB\-n\fR \fB\-\-ncorrel\fR \fInumber\fR .RS 3n Background correlation (default \fI2\fR=dinucleotide; \fI1\fR=single\-site basecounts, \fI0\fR=0.25 per base). .RE .PP \fB\-x\fR, \fB\-\-significance\fR \fInumber\fR .RS 3n Set limit for how probable the match is by chance (default 0.002, smaller=more stringent). .RE .PP \fB\-h\fR, \fB\-\-help\fR .RS 3n Displays this list of options. .RE .SH "MORE HELP" .PP The "significance" parameter (\fB\-x\fR) determines whether local alignments are accepted or rejected. The default at present is 0.002. Experiments on synthetic data (described in the paper) suggest that 0.002 is about the threshold where sigma fails to align phylogenetically\-unrelated data that has moderate (yeast\-like) dinucleotide correlation. .PP Using a \(lqbackground model\(rq appropriate to the sequences being aligned greatly reduces spurious alignments on synthetic data (and, one hopes, on real data too). The simplest way to ensure this is to supply, via the \fB\-b\fR parameter, a FASTA\-format file containing large quantities of similar sequence data (eg, if one is aligning yeast sequences, supply a file containing all intergenic yeast sequence). .PP Instead of this, if the single\-site and dinucleotide frequencies are known already, they may be supplied in a file via the \fB\-B\fR option. The file format should be: one entry per line, with the mononucleotide or dinucleotide (case\-insensitive) followed by the frequency. (eg, "A 0.3", "AT 0.16", etc on successive lines.) A sample file is in the "Background" subdirectory of the source distribution (on Debian systems, this file can be found in the \fI/usr/share/doc/sigma\-align/Background\fR directory). A file like "yeast.nc.3.freq" in the "tests" subdirectory of the MEME source distribution works fine (trinucleotide counts are ignored). .SH "REFERENCE" .PP Please cite Sigma: Rahul Siddharthan (2006) Multiple alignment of weakly\-conserved non\-coding DNA sequence BMC Bioinformatics 2006, 7:143 doi:10.1186/1471\-2105\-7\-143 Published 16 March 2006, available online at http://www.biomedcentral.com/1471\-2105/7/143/ .SH "AUTHORS" .PP \fBRahul Siddharthan\fR <\&rsidd@imsc.res.in\&> .sp -1n .IP "" 3n Wrote sigma. If you're using Sigma for actual research, please let the author know so that he can alert you of bugfixes or new releases. .PP \fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy.org\&> .sp -1n .IP "" 3n Wrote the manpage in DocBook XML for the Debian distribution. .SH "COPYRIGHT" Copyright \(co 2006\-2007 Rahul Siddharthan .br Copyright \(co 2006\-2007 Charles Plessy .br .PP Sigma 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. .PP On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common\-licenses/GPL. .br sigma-1.1.3/COMPILING0000644000175000017500000000275210604174305011007 00000000000000Before compiling, make sure that the following library and headers are installed: the Glib library version 2, part of the GTK toolkit (http://www.gtk.org) (standard on most systems; version 1 should also work if you manually create the Makefile) If using debian or RPM packages, make sure to install the header package (glib2-devel). The library should also be compilable from source on most unix systems. ---------------------------------------------------------------------- AUTOMATIC COMPILING If the libraries are installed in standard places, the following should be sufficient to compile and install Sigma: ./configure make make install This installs the sigma binary into /usr/local/bin. Since, at the moment, nothing else is installed (a manual page may appear in a later release), you can omit "make install" and manually copy the binary from "src" to your desired destination. If the GSL and Glib libraries and headers are in nonstandard places, set appropriate CPPFLAGS and LDFLAGS variables: eg, export CPPFLAGS="-I/opt/include" (csh: setenv CPPFLAGS "-I/opt/include") export LDFLAGS="-L/opt/lib" (csh: setenv LDFLAGS "-L/opt/lib") before running the configure script. -------------------------------------------------------------------- MANUAL COMPILING If the above fails, or if you don't like GNU Autoconf, a manual makefile will be supplied at a later date; or you can try one of the pre-compiled binaries from the website, http://www.imsc.res.in/~rsidd/sigma/ sigma-1.1.3/NOTES0000644000175000017500000000313211157375507010362 00000000000000Sigma, version 1.1.3: simple greedy multiple alignment Copyright (C) 2006-2009 Rahul Siddharthan Licensed under the GNU General Public License, version 2 Usage: sigma [options] inputfile.fasta [inputfile2.fasta ...] Each fasta file may contain a single sequence or multiple sequences; all sequences will be aligned together. Options: -A, --aligned_output (aligned output; this is the default. Compare the -F option. -A and -F may both be specified, in either order.) -B, --bgprobfile filename (name of file containing background probabilities; each line should contain either a single nucleotide or a dinucleotide followed by a space and a count. Counts will automatically be normalised. Trinucleotides and higher will be ignored.) -b, --bgseqfile filename (name of auxiliary file from which to read background sequences; overridden by -B) -C, --caps_only (output sequence in uppercase only, as in output of some other programs like ClustalW and MLagan. Default is mixed-case, where uppercase indicates aligned sequence, as in Dialign.) -F, --fasta_output (multi-fasta output; compare -A option. Default is mixed-case; for upper-case only, specify -C) -n, --ncorrel (background correlation order; 2=dinucleotide is the default, 1=single-site basecounts, 0=0.25 per base. Higher than 2 not implemented at present.) -x, --significance (set limit for how probable the match is by chance: the default is 0.002, smaller=more stringent) -h, --help (display this help summary) sigma-1.1.3/sigma.1.xml0000644000175000017500000002173611157376461011542 00000000000000 ]> &dhtitle; &dhpackage; &dhrelease; &dhdate; Rahul Siddharthan Wrote sigma. If you're using Sigma for actual research, please let the author know so that he can alert you of bugfixes or new releases.
The Institute of Mathematical Sciences
Chennai India
rsidd@imsc.res.in
&dhfirstname; &dhsurname; Wrote the manpage in DocBook XML for the Debian distribution.
&dhemail;
2006 2007 Rahul Siddharthan 2006 2007 &dhusername; Sigma 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. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. &dhucpackage; &dhsection; &dhpackage; Simple greedy multiple alignment of non-coding DNA sequences &dhpackage; options inputfile.fasta inputfile2.fasta ... Each fasta file may contain a single sequence or multiple sequences; all sequences will be aligned together. DESCRIPTION Sigma ("Simple greedy multiple alignment") is an alignment program with a new algorithm and scoring scheme designed specifically for non-coding DNA sequence. It uses a strategy of seeking the best possible gapless local alignments, at each step making the best possible alignment consistent with existing alignments, and scores the significance of the alignment based on the lengths of the aligned fragments and a background model which may be supplied or estimated from an auxiliary file of intergenic DNA. With real data, while "correctness" can't be directly quantified for the alignment, running the PhyloGibbs motif finder on pre-aligned sequence suggests that Sigma's alignments are superior. OPTIONS Aligned, pretty-printed output (compare with option) (default: only this). See also . filename Auxiliary file (in fasta format) from which to read background sequences (overridden by ). Typically this is a file containing large quantities of similar non-coding sequence, from which background probabilities of single- and di-nucleotides may be estimated. filename File containing background probabilities. The format is described further below. Use only upper-case letters in output sequence, for compatibility with output of some other programs like ClustalW and MLagan. By default, output is mixed-case (as in Dialign), and lower-case bases are treated as not aligned. Multi-fasta output (can use both and in either order). See also . number Background correlation (default 2=dinucleotide; 1=single-site basecounts, 0=0.25 per base). , number Set limit for how probable the match is by chance (default 0.002, smaller=more stringent). , Displays this list of options. MORE HELP The "significance" parameter () determines whether local alignments are accepted or rejected. The default at present is 0.002. Experiments on synthetic data (described in the paper) suggest that 0.002 is about the threshold where sigma fails to align phylogenetically-unrelated data that has moderate (yeast-like) dinucleotide correlation. Using a background model appropriate to the sequences being aligned greatly reduces spurious alignments on synthetic data (and, one hopes, on real data too). The simplest way to ensure this is to supply, via the parameter, a FASTA-format file containing large quantities of similar sequence data (eg, if one is aligning yeast sequences, supply a file containing all intergenic yeast sequence). Instead of this, if the single-site and dinucleotide frequencies are known already, they may be supplied in a file via the option. The file format should be: one entry per line, with the mononucleotide or dinucleotide (case-insensitive) followed by the frequency. (eg, "A 0.3", "AT 0.16", etc on successive lines.) A sample file is in the "Background" subdirectory of the source distribution (on Debian systems, this file can be found in the /usr/share/doc/sigma-align/Background directory). A file like "yeast.nc.3.freq" in the "tests" subdirectory of the MEME source distribution works fine (trinucleotide counts are ignored). REFERENCE Please cite Sigma: Rahul Siddharthan (2006) Multiple alignment of weakly-conserved non-coding DNA sequence BMC Bioinformatics 2006, 7:143 doi:10.1186/1471-2105-7-143 Published 16 March 2006, available online at http://www.biomedcentral.com/1471-2105/7/143/ sigma-1.1.3/src/0000777000175000017500000000000011157376464010426 500000000000000sigma-1.1.3/src/Makefile.am0000644000175000017500000000111510631766306012366 00000000000000bin_PROGRAMS = sigma sigma_SOURCES = fasta.h main.c parseopts.c parseopts.h readfasta.c \ readfasta.h sigma.h getbgprobs.c getbgprobs.h setbgprobs.c \ setbgprobs.h initseqfrags.c initseqfrags.h commonroutines.c \ commonroutines.h setbgw.c setbgw.h printhelp.c printhelp.h \ blockseq.c blockseq.h assemble_frags_to_seqs.c \ assemble_frags_to_seqs.h print_routines.c print_routines.h \ getopt_long.c getopt.h sigma_LDADD = $(DEPS_LIBS) AM_CPPFLAGS = $(DEPS_CPPFLAGS) #AM_CFLAGS = $(DEPS_CFLAGS) -DDEBUG -O2 -g -Wall -Werror AM_CFLAGS = $(DEPS_CFLAGS) -DDEBUG -O2 -g sigma-1.1.3/src/Makefile.in0000644000175000017500000003353110752301442012374 00000000000000# Makefile.in generated by automake 1.9.6 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005 Free Software Foundation, Inc. # This Makefile.in is free software; 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Siggia at The Rockefeller University, New York, USA * * and at The Institute of Mathematical Sciences, Chennai, India * * * * This code copyright (C) 2004-2006 Rahul Siddharthan * * Licensed under the GNU General Public License (see COPYING) * * For support and contact information, see the webpage: * * http://www.imsc.res.in/~rsidd/phylogibbs/ */ /* * $Id: fasta.h,v 1.3 2006/03/27 18:44:20 rsidd Exp $ */ typedef struct { GString *header; GString *seq; } fastaseq; sigma-1.1.3/src/main.c0000644000175000017500000000561111157373201011417 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ #include #include #include #include "sigma.h" #include "fasta.h" #include "readfasta.h" #include "printhelp.h" #include "parseopts.h" #include "getbgprobs.h" #include "setbgprobs.h" #include "initseqfrags.h" #include "blockseq.h" #include "assemble_frags_to_seqs.h" #include "print_routines.h" int main(int argc, char *argv[]) { int n; params v; GArray *seqs, *bgseqs; GPtrArray *outarray; seqs=NULL; bgseqs=NULL; v.filenamelist=NULL; v.outtype[0]='\0'; v.auxfilename[0]='\0'; v.bgfilename[0]='\0'; v.correlbg=2; v.pmatch=0.002; v.printhelp=0; v.caps_only=0; v.seqfraglist=NULL; v.seqheadlist=NULL; if (parseopts(argc,argv,&v)) exit(1); if (v.printhelp) { printhelp(); exit(0); } if (v.filenamelist->len==0) { fprintf(stderr,"Error: must specify files to be aligned, in fasta format\n\n"); fflush(NULL); printhelp(); exit(1); } if (strlen(v.outtype)==0) { v.outtype[0]='A'; v.outtype[1]='\0'; } for (n=0; nlen; n++) { if (readfasta((char*)g_ptr_array_index(v.filenamelist,n),&seqs)) fprintf(stderr,"Error reading from file %s\n",(char *)g_ptr_array_index(v.filenamelist,n)); } if (seqs->len ==0 ) { fprintf(stderr,"Error: no sequences read (check filename and file format): exiting\n"); exit(1); } if (seqs->len == 1 ) { fprintf(stderr,"Error: only one sequence read successfully, nothing to be done\n"); exit(1); } v.nseqs=seqs->len; if (strlen(v.auxfilename)>0) { if (readfasta(v.auxfilename,&bgseqs)) { fprintf(stderr,"Error reading background sequence file: %d sequences read\n",bgseqs->len); if (bgseqs->len==0) { g_array_free(bgseqs,TRUE); bgseqs=NULL; } } } if (((bgseqs==NULL)||(bgseqs->len==0)) && (strlen(v.bgfilename)>0)) { if (getbgprobs(&v)) { fprintf(stderr, "Error reading bgcounts from file %s; using input sequence\n",v.bgfilename); setbgprobs(&v,seqs); } } else if ((bgseqs!=NULL)&&(bgseqs->len>0)) setbgprobs(&v,bgseqs); else setbgprobs(&v,seqs); initseqfrags(&v,seqs); init_sw_matrix(&v,seqs); /* if we have got here, we must be all set to do the alignment */ blockseq(&v); assemble_frags_to_seqs(&v,&outarray); // print_raw(&v,seqs); for (n=0; n #include #include #include #include "sigma.h" int parseopts(int argc, char *argv[], params *v) { char Nstr[256],*seqname; int n,ch; if (argc==0) { v->printhelp=1; return 0; } static struct option longopts[] = { {"aligned_output", no_argument, 0, 'A'}, {"bgseqfile", required_argument, 0, 'b'}, {"bgprobfile",required_argument, 0, 'B'}, {"caps_only",no_argument, 0, 'C'}, {"fasta_output", no_argument, 0, 'F'}, {"help", no_argument, 0, 'h'}, {"ncorrel", required_argument, 0, 'n'}, { "significance", required_argument, 0, 'x' }, {0, 0, 0, 0} }; while ((ch = getopt_long(argc,argv,"Ab:B:CFhn:x:", longopts, NULL)) != -1) { switch ((char) ch) { case 'A': n = strlen(v->outtype); if (n < 255){ v->outtype[n]='A'; v->outtype[n+1]='\0'; } break; case 'B': /* name of background prob file name */ strncpy(v->bgfilename,optarg,255); break; case 'C': v->caps_only=1; break; case 'F': n = strlen(v->outtype); if (n < 255){ v->outtype[n]='F'; v->outtype[n+1]='\0'; } break; case 'b': /* name of bg file */ strncpy(v->auxfilename,optarg,255); break; case 'n': /* correlated background */ strncpy(Nstr,optarg,255); v->correlbg = atoi(Nstr); if (v->correlbg >2) { fprintf(stderr,"Warning: correlation > 2 (dinucleotide) not implemented, using 2\n"); v->correlbg=2; } if (v->correlbg < 0) { fprintf(stderr,"Error: correlation must be zero or positive\n"); return 1; } break; case 'x': /* value of significance threshold */ strncpy(Nstr,optarg,255); v->pmatch=atof(Nstr); if (v->pmatch < -0.000000000001) { /* disallow negative values */ fprintf(stderr,"Error: negative values not allowed for pmatch (-x)\n"); return 1; } if (v->pmatch > 0.999999999999) { fprintf(stderr,"Error: pmatch (-x) must be substantially less than 1\n"); return 1; } if (v->pmatch < 0.0) v->pmatch = 0.0; break; default: v->printhelp=1; break; } } v->filenamelist = g_ptr_array_new(); while (optindfilenamelist,seqname); optind++; } return 0; } sigma-1.1.3/src/parseopts.h0000644000175000017500000000035710604245467012532 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ int parseopts(int argc, char *argv[], params *v); sigma-1.1.3/src/readfasta.c0000644000175000017500000000505710604245752012436 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ /* This routine was originally written for PhyloGibbs */ /* Copyright (C) 2004-2006 Rahul Siddharthan */ #include #include #include #include #include #include "fasta.h" void chomp(char *s) { if (s[strlen(s)-1]=='\n') s[strlen(s)-1]='\0'; if (s[strlen(s)-1]=='\r') s[strlen(s)-1]='\0'; } int readfasta(const char *filename, GArray **fastaseqs) { FILE *seqfile; fastaseq oneseq; int headernext; char s[131072]; headernext=1; if (*fastaseqs == NULL) *fastaseqs =g_array_new(TRUE,TRUE,sizeof(fastaseq)); oneseq.seq=g_string_new(""); seqfile=fopen(filename,"rt"); if (seqfile==NULL) return 1; while (fgets(s,131072,seqfile)) { while ((isspace(s[0]))||(s[0]==';')||(s[0]=='#')) { if (!fgets(s,131072,seqfile)) { if (!headernext) { if (oneseq.seq->len==0) { fclose(seqfile); return 1; } else { g_array_append_val((*fastaseqs),oneseq); fclose(seqfile); return 0; } } else { fclose(seqfile); return 0; } } if (oneseq.seq->len > 0) { g_array_append_val((*fastaseqs),oneseq); oneseq.seq=g_string_new(""); headernext=1; } } if ((s[0]!='>')&&headernext) { fclose(seqfile); return 1; } if (headernext) { chomp(s); oneseq.header=g_string_new(s+1); headernext=0; } else { chomp(s); if (s[0]=='>') { if (oneseq.seq->len==0){ g_string_free(oneseq.header, TRUE); oneseq.header=g_string_new(s+1); } else { g_array_append_val((*fastaseqs),oneseq); oneseq.header=g_string_new(s+1); oneseq.seq=g_string_new(""); } } else oneseq.seq=g_string_append(oneseq.seq, s); } } if (!headernext) g_array_append_val((*fastaseqs),oneseq); fclose(seqfile); return 0; } sigma-1.1.3/src/readfasta.h0000644000175000017500000000036610604245533012436 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ int readfasta(const char *filename, GArray **fastaseqs); sigma-1.1.3/src/sigma.h0000644000175000017500000000206011157373160011577 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ #include typedef struct { GPtrArray *filenamelist; char outtype[255]; char auxfilename[255]; char bgfilename[255]; int correlbg; double pmatch; int nseqs; double singlesite[4]; double dinucleotide[16]; int printhelp; int caps_only; GPtrArray *seqfraglist; GPtrArray *seqheadlist; } params; typedef struct _seq_frag seq_frag; struct _seq_frag { int seqlen; int nseqs; int swept; int *seqindex; char **seq; char *aseq; double *abgw; char **seqlabel; seq_frag **neighbours_l, **neighbours_r; char **limits_l, **limits_r; }; struct swmatrix /* allocated once and then retained, to save cycles */ { double *fmat; int *lmat, *mmat; int m,n; /* dimensions of matrix */ } swmat; typedef struct { seq_frag *frag1, *frag2; int n1, n2, l; double p; } match; sigma-1.1.3/src/getbgprobs.c0000644000175000017500000000550510604245467012643 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ #include #include #include #include #include "sigma.h" #include "commonroutines.h" int get_count_from_str(char *s, int *nuc1, int *nuc2, double *count) { /* return code 1 = acceptable error (continue), 2 = unacceptable error */ int m=0; if (strlen(s)==0) return 1; if (s[0]=='#') return 1; if (strlen(s) < 3) return 2; m=0; while ((mbgfilename,"rt"); if (probfile==NULL) return 1; for (m=0; m<4; m++) { v->singlesite[m] = -1.0; for (n=0; n<4; n++) v->dinucleotide[m*4+n] = -1.0; } while (fgets(s,255,probfile)) { status = get_count_from_str(s,&nuc1,&nuc2,&count); if (status == 1) continue; if (status) return 1; if (count <= 0.0) return 1; if (nuc2 < 0) v->singlesite[nuc1] = count; else { dinuc_counted = 1; v->dinucleotide[nuc1*4+nuc2] = count; } } stot=0.0; for (m=0; m<4; m++) { if (v->singlesite[m]<0.0) return 2; stot += v->singlesite[m]; if (dinuc_counted) { dtot=0.0; if (v->dinucleotide[m*4+n] < 0.0) return 2; for (n=0; n<4; n++) dtot += v->dinucleotide[m*4+n]; for (n=0; n<4; n++) v->dinucleotide[m*4+n] /= dtot; } else if (v->correlbg == 2) { fprintf(stderr,"Warning: dinucleotide counts asked for, but file %s\n only contains single-nucleotide counts; using uncorrelated background\n\n",v->bgfilename); v->correlbg = 1; } } for (m=0; m<4; m++) v->singlesite[m] /= stot; return 0; } sigma-1.1.3/src/getbgprobs.h0000644000175000017500000000033010604245467012637 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ int getbgprobs(params *v); sigma-1.1.3/src/setbgprobs.c0000644000175000017500000000243010604245467012651 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ #include "sigma.h" #include "fasta.h" #include "commonroutines.h" int setbgprobs(params *v, GArray *bgseqs) { int i,p,m,n; fastaseq *fseq; double stot,dtot; for (m=0; m<4; m++) { v->singlesite[m]=0.0; for (n=0; n<4; n++) v->dinucleotide[m*4+n]=0.0; } for (i=0; ilen; i++) { fseq = &g_array_index(bgseqs,fastaseq,i); for (p=0; pseq->len-1; p++) { if (base2num(fseq->seq->str[p])<0) continue; v->singlesite[base2num(fseq->seq->str[p])] += 1.0; if (base2num(fseq->seq->str[p+1])<0) continue; v->dinucleotide[base2num(fseq->seq->str[p])*4 + base2num(fseq->seq->str[p+1])] += 1.0; } } stot=0.0; for (m=0; m<4; m++) { stot += v->singlesite[m]; dtot=0.0; for (n=0; n<4; n++) dtot += v->dinucleotide[m*4+n]; for (n=0; n<4; n++) v->dinucleotide[m*4+n] /= dtot; } for (m=0; m<4; m++) v->singlesite[m] /= stot; return 0; } sigma-1.1.3/src/setbgprobs.h0000644000175000017500000000034710604245467012663 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ void setbgprobs(params *v, GArray *seqs); sigma-1.1.3/src/initseqfrags.c0000644000175000017500000000257511157374057013212 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ #include #include #include "sigma.h" #include "fasta.h" #include "setbgw.h" #include "commonroutines.h" void initseqfrags(params *v, GArray *seqs) { int n,len,len1; fastaseq *oneseq; seq_frag *onefrag; v->seqfraglist = g_ptr_array_new(); v->seqheadlist = g_ptr_array_new(); for (n=0; nlen; n++) { oneseq= &g_array_index(seqs,fastaseq,n); len = (oneseq->seq->len); onefrag = new_seqfrag(v); onefrag->seqlen = len; onefrag->nseqs=1; onefrag->seqindex[0] = n; onefrag->seq[n] = (oneseq->seq->str); onefrag->aseq = malloc(sizeof(char)*(onefrag->seqlen + 1)); strncpy(onefrag->aseq,onefrag->seq[n],onefrag->seqlen); setbgw(v,onefrag); onefrag->seqlabel[n] = malloc((4)*sizeof(char)); onefrag->seqlabel[n][0] = '0'; onefrag->seqlabel[n][1] = '.'; onefrag->seqlabel[n][2] = '1'; onefrag->seqlabel[n][3] = '\0'; onefrag->neighbours_l[n] = NULL; onefrag->neighbours_r[n] = NULL; g_ptr_array_add((v->seqfraglist),onefrag); g_ptr_array_add((v->seqheadlist),onefrag); } } sigma-1.1.3/src/initseqfrags.h0000644000175000017500000000035110604245467013203 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ void initseqfrags(params *v, GArray *seqs); sigma-1.1.3/src/commonroutines.c0000644000175000017500000000247110604245467013565 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ #include #include "sigma.h" int base2num(char b) { switch(b) { case 'A': case 'a': return 0; break; case 'C': case 'c': return 1; break; case 'G': case 'g': return 2; break; case 'T': case 't': return 3; break; default: return -1; } } seq_frag* new_seqfrag(params *v) { int n; seq_frag *frag; frag=malloc(sizeof(seq_frag)); frag->seqindex = malloc(v->nseqs * sizeof(int)); frag->seq = calloc(v->nseqs, sizeof(char*)); frag->aseq = NULL; frag->abgw = NULL; frag->seqlabel = calloc(v->nseqs, sizeof(char*)); frag->neighbours_l = calloc(v->nseqs, sizeof(seq_frag*)); frag->neighbours_r = calloc(v->nseqs, sizeof(seq_frag*)); frag->limits_l = malloc(v->nseqs * sizeof(char*)); frag->limits_r = malloc(v->nseqs * sizeof(char*)); for (n=0; n < v->nseqs; n++) { frag->limits_l[n] = malloc(2*sizeof(char)); frag->limits_r[n] = malloc(2*sizeof(char)); frag->limits_l[n][0] = '0'; frag->limits_l[n][1] = '\0'; frag->limits_r[n][0] = '3'; frag->limits_r[n][1] = '\0'; } return frag; } sigma-1.1.3/src/commonroutines.h0000644000175000017500000000036510604245467013572 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ int base2num(char b); seq_frag* new_seqfrag(params *v); sigma-1.1.3/src/setbgw.c0000644000175000017500000000210410604245467011770 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ #include #include "sigma.h" #include "commonroutines.h" void setbgw(params *v, seq_frag *onefrag) { int n,bn,bn1; /* if a base is not ACGT, set bgw as 0.25 */ onefrag->abgw = malloc(onefrag->seqlen * sizeof(double)); if (v->correlbg==0) { for (n=0; nseqlen; n++) onefrag->abgw[n]=0.25; return; } bn=base2num(onefrag->aseq[0]); if (bn>=0) onefrag->abgw[0] = v->singlesite[bn]; else onefrag->abgw[0] = 0.25; for (n=1; nseqlen; n++) { bn=base2num(onefrag->aseq[n]); if (bn<0) onefrag->abgw[n]=0.25; else { if ((v->correlbg==1) || ((bn1=base2num(onefrag->aseq[n-1]))<0)) { onefrag->abgw[n]=v->singlesite[bn]; } else onefrag->abgw[n] = v->dinucleotide[bn1*4+bn]; } } } sigma-1.1.3/src/setbgw.h0000644000175000017500000000035010604245467011776 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ void setbgw(params *v, seq_frag *onefrag); sigma-1.1.3/src/printhelp.c0000644000175000017500000000436711157375643012523 00000000000000#include void printhelp() { printf("Sigma, version 1.1.3: simple greedy multiple alignment\n"); printf("Copyright (C) 2006-2009 Rahul Siddharthan \n"); printf("Licensed under the GNU General Public License, version 2\n"); printf("\n"); printf("Usage: sigma [options] inputfile.fasta [inputfile2.fasta ...]\n"); printf("\n"); printf("Each fasta file may contain a single sequence or multiple sequences;\n"); printf("all sequences will be aligned together.\n"); printf("\n"); printf("Options:\n"); printf(" -A, --aligned_output \n"); printf(" (aligned output; this is the default. Compare the -F option.\n"); printf(" -A and -F may both be specified, in either order.)\n"); printf(" -B, --bgprobfile filename \n"); printf(" (name of file containing background probabilities; each line\n"); printf(" should contain either a single nucleotide or a dinucleotide\n"); printf(" followed by a space and a count. Counts will automatically be\n"); printf(" normalised. Trinucleotides and higher will be ignored.)\n"); printf(" -b, --bgseqfile filename\n"); printf(" (name of auxiliary file from which to read background sequences; \n"); printf(" overridden by -B)\n"); printf(" -C, --caps_only\n"); printf(" (output sequence in uppercase only, as in output of some other\n"); printf(" programs like ClustalW and MLagan. Default is mixed-case,\n"); printf(" where uppercase indicates aligned sequence, as in Dialign.)\n"); printf(" -F, --fasta_output \n"); printf(" (multi-fasta output; compare -A option. Default is mixed-case;\n"); printf(" for upper-case only, specify -C)\n"); printf(" -n, --ncorrel \n"); printf(" (background correlation order; 2=dinucleotide is the default,\n"); printf(" 1=single-site basecounts, 0=0.25 per base. Higher than 2 not\n"); printf(" implemented at present.)\n"); printf(" -x, --significance \n"); printf(" (set limit for how probable the match is by chance: the default \n"); printf(" is 0.002, smaller=more stringent)\n"); printf(" -h, --help\n"); printf(" (display this help summary)\n"); } sigma-1.1.3/src/printhelp.h0000644000175000017500000000031710604245467012513 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ void printhelp(); sigma-1.1.3/src/blockseq.c0000644000175000017500000004724311157374137012316 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ /* This is the working folder for sigma - Gayathri */ #include #include #include #include #include #include "sigma.h" #include "fasta.h" #include "commonroutines.h" double *bmfmat; int *bmlmat,*bmmmat; void printn(char *s, int n) { int m; for (m=0; mnseqs; n++) { printf("\nSequence number %d\n",n); frag = g_ptr_array_index(v->seqheadlist,n); while (frag) { printf(" consensus "); printn(frag->aseq,frag->seqlen); printf("\n"); for (p=0; pnseqs; p++) { printed=0; for (m=0; mnseqs; m++) if (frag->seqindex[m]==p) { printf(" seq %d ",p); printn(frag->seq[p],frag->seqlen); printf(" %s seq %d\n", frag->seqlabel[p],p); printed=1; break; } if (printed==0) printf(" pairseq %d limit_l %s limit_r %s\n", p, frag->limits_l[p],frag->limits_r[p]); } frag = frag->neighbours_r[n]; } printf("\n\n"); } } void init_sw_matrix(params *v, GArray *seqs) { int n,i,maxlen=0; fastaseq *seq; int j=0; for (n=0; nlen; n++) { seq= &g_array_index(seqs,fastaseq,n); if (seq->seq->len > maxlen) maxlen=seq->seq->len; } swmat.fmat = malloc((maxlen+1)*sizeof(double)); swmat.lmat = malloc((maxlen+1)*sizeof(int)); swmat.mmat = malloc((maxlen+1)*sizeof(int)); for (i=0; i<=maxlen; i++) { swmat.fmat[i]=1.0; swmat.lmat[i]=0; swmat.mmat[i]=0; } swmat.m = maxlen+1; swmat.n = maxlen+1; bmfmat =calloc (sizeof(double),maxlen+1); bmlmat = calloc(sizeof(int), maxlen+1); bmmmat = calloc(sizeof(int), maxlen+1); for (j = 0;jseqlen; sl2 = frag2->seqlen; for (i=0; i<=sl2; i++) { swmat.fmat[i]=1.0; swmat.lmat[i]=0; swmat.mmat[i]=0; } for (j = 0;jaseq[m-1]; b1 = frag2->aseq[n-1]; f_old = swmat.fmat[n-1]; m_old = swmat.mmat[n-1]; l_new = swmat.lmat[n-1] + 1; if ((a1==b1)&&(a1 != 'N')) { m_new = m_old; f_new = f_old * sqrt(frag1->abgw[m-1]*frag2->abgw[n-1]) * (float) (l_new) / ((float)(l_new - m_old)); } else { m_new = m_old + 1; f_new = f_old * l_new/(m_old + 1.0); } if (f_new >= 1.0) { f_new = 1.0; l_new = 0; m_new = 0; } bmfmat[n] = f_new; bmlmat[n] = l_new; bmmmat[n] = m_new; if (f_new < best) { best = f_new; bestm = m; bestn = n; } } /* end of n loop */ memcpy(swmat.fmat,bmfmat,sizeof(double)* (sl2+1)); memcpy(swmat.lmat,bmlmat,sizeof(int)*(sl2+1)); memcpy(swmat.mmat,bmmmat,sizeof(int)*sl2); } /*end of m loop */ i = bestm; j=bestn; if (i>j) { i=i-j; j=0; } else if (j>i) { j=j-i; i= 0; } else i=j=0; f_old = 1.0; l_new = 1; m_old = 0; while ((i< bestm) && (jaseq[i]; b1 = frag2->aseq[j]; if ((a1==b1)&&(a1 != 'N')) { f_new = f_old * sqrt(frag1->abgw[i]*frag2->abgw[j]) * (float) (l_new) / ((float)(l_new - m_old)); } else { f_new = f_old * l_new/(m_old + 1.0); m_old ++; } if (f_new < 1.0) { lbest++; } else { lbest = 0; l_new =0; f_new = 1.0; m_old = 0; } i++; j++;f_old = f_new; l_new++; } best = best * (sl1-lbest+1) * (sl2-lbest+1); if (best < v->pmatch) { *n1 = bestm-lbest; *n2 = bestn-lbest; *lbestout = lbest; *bestout = best; } else { *n1 = 0; *n2 = 0; *lbestout = 0; *bestout = 1.0; } } void replace_string(char **s1, char **s2, char c) { int n; if (*s1) free(*s1); n=strlen(*s2); if (c=='\0') *s1 = calloc(n+1,sizeof(char)); else *s1 = calloc(n+2,sizeof(char)); strncpy(*s1, *s2, n+1); if (c=='\0') (*s1)[n]='\0'; else { (*s1)[n]=c; (*s1)[n+1]='\0'; } } void reset_swept(params *v) /* avoid sweeping twice from same frag */ { seq_frag *frag; int n; for (n=0; n < v->seqfraglist->len; n++) { frag = g_ptr_array_index(v->seqfraglist,n); frag->swept = 0; } } void sweep_limits(char **lim, seq_frag *frag, int ns, int dir) { int n; if ((frag==NULL)||(frag->swept)) return; frag->swept = 1; if (dir) { /* left sweep, right lims */ if (strcmp(frag->limits_r[ns],*lim) > 0) { replace_string(&(frag->limits_r[ns]),lim,'\0'); } for (n=0; nnseqs; n++) sweep_limits(lim,frag->neighbours_l[frag->seqindex[n]],ns,dir); } else { /* right sweep, left lims */ if (strcmp(frag->limits_l[ns],*lim) < 0) { replace_string(&(frag->limits_l[ns]),lim,'\0'); } for (n=0; nnseqs; n++) sweep_limits(lim,frag->neighbours_r[frag->seqindex[n]],ns,dir); } } void update_limits(params *v, seq_frag *frag) { int m,ns,ns2,is_diag; seq_frag *fragn; for (ns=0; ns nseqs; ns++) { is_diag = 0; for (m=0; m < frag->nseqs; m++) if (frag->seqindex[m]==ns) { is_diag = 1; break; } if (is_diag) { /* diagonal limits */ replace_string(&((frag->limits_l)[ns]),&((frag->seqlabel)[ns]),'\0'); replace_string(&((frag->limits_r)[ns]),&((frag->seqlabel)[ns]),'\0'); } else /* off-diag */ /* replace limit for ns with most stringent limit of a neighbouring fragment */ for (m=0; m < frag->nseqs; m++) { ns2 = frag->seqindex[m]; fragn = frag->neighbours_l[ns2]; if (fragn) { if (strcmp(fragn->limits_l[ns],frag->limits_l[ns])>0) replace_string(&(frag->limits_l[ns]),&(fragn->limits_l[ns]),'\0'); } fragn = frag->neighbours_r[ns2]; if (fragn) { if (strcmp(fragn->limits_r[ns],frag->limits_r[ns])<0) replace_string(&(frag->limits_r[ns]),&(fragn->limits_r[ns]),'\0'); } } } for (ns = 0; ns < v->nseqs; ns++) { reset_swept(v); sweep_limits(&(frag->limits_l[ns]),frag,ns,0); reset_swept(v); sweep_limits(&(frag->limits_r[ns]),frag,ns,1); } } int inconsistent_frags(seq_frag *frag1, seq_frag *frag2) { int n1, n2, s1, s2; char *label, *lim_l, *lim_r; for (n1=0; n1< frag1->nseqs; n1++) { s1 = frag1->seqindex[n1]; for (n2=0; n2 < frag2->nseqs; n2++) { s2 = frag2->seqindex[n2]; if (s2 == s1) return 1; else { label = frag2->seqlabel[s2]; lim_l = frag1->limits_l[s2]; lim_r = frag1->limits_r[s2]; if ((strcmp(label,lim_l)<=0)||(strcmp(label,lim_r)>=0)) return 1; label = frag1->seqlabel[s1]; lim_l = frag2->limits_l[s1]; lim_r = frag2->limits_r[s1]; if ((strcmp(label,lim_l)<=0)||(strcmp(label,lim_r)>=0)) return 1; } } } return 0; } gint compare_matches(gconstpointer *a, gconstpointer *b) { match *m1, *m2; m1 = (match*)(*a); m2 = (match*)(*b); if (m1->p < m2->p) return -1; else if (m1->p> m2->p) return 1; else return 0; } void make_match_list(params *v, GPtrArray **matchlist) { int n1, n2; seq_frag *frag1, *frag2; match *onematch; if (*matchlist) { for (n1=0; n1<(*matchlist)->len; n1++) { onematch = g_ptr_array_index(*matchlist,n1); free(onematch); } g_ptr_array_free(*matchlist, TRUE); } *matchlist = g_ptr_array_new(); onematch = malloc(sizeof(match)); for (n1=0; n1seqfraglist->len - 1; n1++) { frag1 = g_ptr_array_index(v->seqfraglist,n1); for (n2 = n1+1; n2 < v->seqfraglist->len; n2++) { frag2 = g_ptr_array_index(v->seqfraglist,n2); if (inconsistent_frags(frag1,frag2)) continue; best_match(v,frag1,frag2,&(onematch->n1),&(onematch->n2), &(onematch->l),&(onematch->p)); //printf("\n n1 = %d, n2 = %d, l= %d, p=%f\n", onematch->n1, onematch->n2, onematch->l, onematch->p); if (onematch->l > 0) { onematch->frag1 = frag1; onematch->frag2 = frag2; g_ptr_array_add(*matchlist,onematch); onematch = malloc(sizeof(match)); } } } free(onematch); g_ptr_array_sort((*matchlist), (GCompareFunc) compare_matches); } char consensus(seq_frag *frag, int n) { int n1,nseq,n2; double counts[4]; counts[0] = 0.0; counts[1] = 0.0; counts[2] = 0.0; counts[3] = 0.0; for (n1=0; n1nseqs; n1++) { nseq=frag->seqindex[n1]; switch(frag->seq[nseq][n]) { case 'A': case 'a': counts[0] += 1.0; break; case 'C': case 'c': counts[1] += 1.0; break; case 'G': case 'g': counts[2] += 1.0; break; case 'T': case 't': counts[3] += 1.0; break; default: for (n2=0; n2<4; n2++) counts[n2] += 0.25; break; } } if (counts[0] > (frag->nseqs * 0.5)) return 'A'; else if (counts[1] > (frag->nseqs * 0.5)) return 'C'; else if (counts[2] > (frag->nseqs * 0.5)) return 'G'; else if (counts[3] > (frag->nseqs * 0.5)) return 'T'; else return 'N'; } void fuse_one_match(params *v, match *onematch) { int n,ns; seq_frag *f1, *f2, *f3, *f4, *f5; f1 = onematch->frag1; f2 = onematch->frag2; if (inconsistent_frags(f1,f2)) return; f3 = new_seqfrag(v); f4 = new_seqfrag(v); f5 = new_seqfrag(v); /* set seqs of various frags */ f3->nseqs = f1->nseqs + f2->nseqs; f4->nseqs = f1->nseqs; f5->nseqs = f2->nseqs; f3->seqlen = onematch->l; f4->seqlen = f1->seqlen - onematch->n1 - onematch->l; f5->seqlen = f2->seqlen - onematch->n2 - onematch->l; f1->seqlen = onematch->n1; f2->seqlen = onematch->n2; for (n=0; nnseqs; n++) { ns = f1->seqindex[n]; f3->seqindex[n] = ns; f4->seqindex[n] = ns; (f3->seq)[ns] = (char*)((f1->seq)[ns] + onematch->n1); (f4->seq)[ns] = (char*)((f1->seq)[ns] + onematch->n1 + onematch->l); /* relabel */ replace_string(&(f3->seqlabel[ns]),&(f1->seqlabel[ns]),'1'); replace_string(&(f4->seqlabel[ns]),&(f1->seqlabel[ns]),'2'); /* trickery to relabel first frag */ replace_string(&(f1->seqlabel[ns]),&(f4->seqlabel[ns]),'\0'); f1->seqlabel[ns][strlen(f1->seqlabel[ns])-1] = '0'; /* neighbours */ f4->neighbours_r[ns] = f1->neighbours_r[ns]; f1->neighbours_r[ns] = f3; f3->neighbours_l[ns] = f1; f3->neighbours_r[ns] = f4; f4->neighbours_l[ns] = f3; } for (n=0; nnseqs;n++) { ns = f2->seqindex[n]; f3->seqindex[n+f1->nseqs] = ns; f5->seqindex[n] = ns; (f3->seq)[ns] = (char*)((f2->seq)[ns] + onematch->n2); (f5->seq)[ns] = (char*)((f2->seq)[ns] + onematch->n2 + onematch->l); /* relabel */ replace_string(&(f3->seqlabel[ns]),&(f2->seqlabel[ns]),'1'); replace_string(&(f5->seqlabel[ns]),&(f2->seqlabel[ns]),'2'); /* trickery */ replace_string(&(f2->seqlabel[ns]),&(f5->seqlabel[ns]),'\0'); f2->seqlabel[ns][strlen(f2->seqlabel[ns])-1] = '0'; /* neighbours */ f5->neighbours_r[ns] = f2->neighbours_r[ns]; f2->neighbours_r[ns] = f3; f3->neighbours_l[ns] = f2; f3->neighbours_r[ns] = f5; f5->neighbours_l[ns] = f3; } /* limits */ for (n=0; nnseqs; n++) { replace_string(&(f4->limits_l[n]),&(f1->limits_l[n]),'\0'); replace_string(&(f5->limits_l[n]),&(f2->limits_l[n]),'\0'); replace_string(&(f4->limits_r[n]),&(f1->limits_r[n]),'\0'); replace_string(&(f5->limits_r[n]),&(f2->limits_r[n]),'\0'); } /* aseq, abgw */ f4->aseq = (char *)(f1->aseq + onematch->n1 + onematch->l); f4->abgw = (double *)(f1->abgw + onematch->n1 + onematch->l); f5->aseq = (char *)(f2->aseq + onematch->n2 + onematch->l); f5->abgw = (double *)(f2->abgw + onematch->n2 + onematch->l); f3->aseq = calloc(f3->seqlen + 1, sizeof(char)); f3->abgw = calloc(f3->seqlen + 1, sizeof(double)); for (n=0; nseqlen; n++) { f3->aseq[n] = consensus(f3,n); if (f1->abgw[n+onematch->n1] == f2->abgw[n+onematch->n2]) f3->abgw[n] = f1->abgw[n+onematch->n1]; else f3->abgw[n] = sqrt((f1->abgw[n+onematch->n1]) * (f2->abgw[n+onematch->n2])); } g_ptr_array_add(v->seqfraglist,f3); g_ptr_array_add(v->seqfraglist,f4); g_ptr_array_add(v->seqfraglist,f5); update_limits(v,f3); // printf("\n--------------------------------------\n"); // printfrags(v); // fflush(NULL); } int seqindices_match(seq_frag *frag1, seq_frag *frag2) { int n1,n2, is_in; if (frag1->nseqs != frag2->nseqs) return 0; for (n1=0; n1nseqs; n1++) { is_in = 0; for (n2=0; n2nseqs; n2++) if (frag1->seqindex[n1]==frag2->seqindex[n2]) { is_in=1; break; } if (is_in==0) return 0; } return 1; } void expand_match(match *onematch, GPtrArray **outmatches) { /* In case of earlier fusions, a match may now be split over multiple fragments; recover from this situation */ match *tmpmatch, *nextmatch; seq_frag *nextfrag1, *nextfrag2; int s1,s2, n1, n2; *outmatches = g_ptr_array_new(); tmpmatch=malloc(sizeof(match)); tmpmatch->frag1 = onematch->frag1; tmpmatch->frag2 = onematch->frag2; tmpmatch->n1 = onematch->n1; tmpmatch->n2 = onematch->n2; tmpmatch->l = onematch->l; tmpmatch->p = onematch->p; s1 = tmpmatch->frag1->seqindex[0]; s2 = tmpmatch->frag2->seqindex[0]; while ((tmpmatch->n1 + tmpmatch->l > tmpmatch->frag1->seqlen)|| (tmpmatch->n2 + tmpmatch->l > tmpmatch->frag2->seqlen)) { n1=0; while ((tmpmatch->frag1->seqindex[n1] != s1) && (n1 < tmpmatch->frag1->nseqs)) n1++; assert(n1frag1->nseqs); nextfrag1 = tmpmatch->frag1->neighbours_r[s1]; n2=0; while ((tmpmatch->frag2->seqindex[n2] != s2) && (n2 < tmpmatch->frag2->nseqs)) n2++; assert(n2 < tmpmatch->frag2->nseqs); nextfrag2 = tmpmatch->frag2->neighbours_r[s2]; if ((tmpmatch->frag1->seqlen <= tmpmatch->n1) &&(tmpmatch->frag2->seqlen <= tmpmatch->n2)) { /* match lies outside both current frags */ assert(nextfrag1 != NULL); assert(nextfrag2 != NULL); tmpmatch->n1 -= tmpmatch->frag1->seqlen; tmpmatch->n2 -= tmpmatch->frag2->seqlen; tmpmatch->frag1 = nextfrag1; tmpmatch->frag2 = nextfrag2; } else if (tmpmatch->frag1->seqlen <= tmpmatch->n1) { /* only frag1 is outside bounds */ assert(nextfrag1 != NULL); tmpmatch->n1 -= tmpmatch->frag1->seqlen; tmpmatch->frag1 = nextfrag1; } else if (tmpmatch->frag2->seqlen <= tmpmatch->n2) { assert(nextfrag2!=NULL); tmpmatch->n2 -= tmpmatch->frag2->seqlen; tmpmatch->frag2 = nextfrag2; } else { /* Both frags contain some alignable sequence; we align what exists and continue */ nextmatch = malloc(sizeof(match)); nextmatch->frag1 = tmpmatch->frag1; nextmatch->frag2 = tmpmatch->frag2; nextmatch->p = tmpmatch->p; if ((tmpmatch->frag1->seqlen - tmpmatch->n1) < (tmpmatch->frag2->seqlen - tmpmatch->n2)) { /* frag1 contains less alignable sequence than frag2 */ nextmatch->frag1 = nextfrag1; nextmatch->n1 = 0; nextmatch->l = tmpmatch->n1 + tmpmatch->l - tmpmatch->frag1->seqlen; nextmatch->n2 = tmpmatch->n2 + tmpmatch->l - nextmatch->l; tmpmatch->l = tmpmatch->frag1->seqlen - tmpmatch->n1; } else { /* frag2 contains less alignable seq than frag1 */ nextmatch->frag2 = nextfrag2; nextmatch->n2 = 0; nextmatch->l = tmpmatch->n2 + tmpmatch->l - tmpmatch->frag2->seqlen; nextmatch->n1 = tmpmatch->n1 + tmpmatch->l - nextmatch->l; tmpmatch->l = tmpmatch->frag2->seqlen - tmpmatch->n2; } g_ptr_array_add(*outmatches,tmpmatch); tmpmatch=nextmatch; } } g_ptr_array_add(*outmatches,tmpmatch); return; } int fuse_match_list(params *v, GPtrArray *matchlist) { int m,n,aligned=0; match *onematch, *tmpmatch; GPtrArray *outmatches; /* assume matchlist is sorted, carry out fusions */ for (m=0; mlen; m++) { onematch = g_ptr_array_index(matchlist,m); expand_match(onematch, &outmatches); if (outmatches) { for (n=0; nlen; n++) { tmpmatch=g_ptr_array_index(outmatches,n); if (inconsistent_frags(tmpmatch->frag1,tmpmatch->frag2)) break; fuse_one_match(v,tmpmatch); aligned=1; } for (n=0; nlen; n++) { tmpmatch = g_ptr_array_index(outmatches,n); free(tmpmatch); } g_ptr_array_free(outmatches,TRUE); } } return aligned; } void blockseq(params *v) { int aligned; GPtrArray *matchlist; matchlist = NULL; do { aligned=0; make_match_list(v,&matchlist); if (matchlist->len > 0) { aligned=fuse_match_list(v,matchlist); } } while (aligned); } sigma-1.1.3/src/blockseq.h0000644000175000017500000000040610604245467012310 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ void init_sw_matrix(params *v, GArray *seqs); void blockseq(params *v); sigma-1.1.3/src/assemble_frags_to_seqs.c0000644000175000017500000000755610604245467015227 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ #include #include #include #include #include "sigma.h" int is_complete(seq_frag **frag, GPtrArray **nexthead) /* if frag is multi-sequence, then all copies are at head of seqlist */ { int n,ncount=0; if ((*frag)==NULL) return 0; for (n=0; n<(*nexthead)->len; n++) if (g_ptr_array_index((*nexthead),n)== *frag) ncount++; assert(ncount <= (*frag)->nseqs); if (ncount==(*frag)->nseqs) return 1; else return 0; } int is_in_frag(int nseq, seq_frag *frag) { int n; for (n=0; nnseqs; n++) if (frag->seqindex[n]==nseq) return 1; return 0; } void add_frag(seq_frag *frag, GPtrArray **nexthead, GPtrArray **outarray, int caps_only) { GString *outseq; int lseq = frag->seqlen, pad_needed,n,n1,nseq, npad; outseq = g_ptr_array_index((*outarray),frag->seqindex[0]); if ((frag->nseqs == 1)&&(caps_only==0)) { nseq = frag->seqindex[0]; for (n=0; nseq[nseq][n])); g_ptr_array_index((*nexthead),nseq) = frag->neighbours_r[nseq]; return; } /* multi-seq frag or caps-only, otherwise we'd have exited */ npad = outseq->len - 1; do { pad_needed=0; npad++; for (nseq=0; nseq<(*outarray)->len; nseq++) { outseq = g_ptr_array_index((*outarray),nseq); if (is_in_frag(nseq,frag)) { if (npadlen) { pad_needed = 1; break; } } else for (n=0; nlen) &&(isupper(outseq->str[npad+n]))) { pad_needed = 1; break; } } if (pad_needed) break; } } while (pad_needed); for (n=0; nnseqs; n++) { nseq = frag->seqindex[n]; outseq = g_ptr_array_index((*outarray),nseq); while (outseq->len < npad) g_string_append_c(outseq,'-'); for (n1=0; n1seq[nseq][n1])); g_ptr_array_index((*nexthead),nseq) = frag->neighbours_r[nseq]; } } int remains(GPtrArray **nexthead) { int n; for (n=0; n<(*nexthead)->len; n++) if (g_ptr_array_index((*nexthead),n)!=NULL) return 1; return 0; } void assemble_frags_to_seqs(params *v, GPtrArray **outarray) { GPtrArray *nexthead; GString *onestring; seq_frag *frag; int n,maxlen; *outarray = g_ptr_array_new(); nexthead = g_ptr_array_new(); for (n=0; nnseqs; n++) { onestring = g_string_new(""); g_ptr_array_add(*outarray,onestring); frag = g_ptr_array_index(v->seqheadlist,n); g_ptr_array_add(nexthead,frag); } n = 0; while (remains(&nexthead)) { frag = g_ptr_array_index(nexthead,n); if (is_complete(&frag,&nexthead)) add_frag(frag,&nexthead,outarray,v->caps_only); else { n++; if (n == v->nseqs) n=0; continue; } } maxlen=0; for (n=0; n<(*outarray)->len; n++) { onestring = g_ptr_array_index((*outarray),n); if ((onestring->len) > maxlen) maxlen = onestring->len; } for (n=0; n<(*outarray)->len; n++) { onestring = g_ptr_array_index((*outarray),n); while ((onestring->len) < maxlen) g_string_append_c(onestring,'-'); } } sigma-1.1.3/src/assemble_frags_to_seqs.h0000644000175000017500000000037310604245467015222 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ void assemble_frags_to_seqs(params *v, GPtrArray **outarray); sigma-1.1.3/src/print_routines.c0000644000175000017500000000525410604245467013572 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ #include #include #include "sigma.h" #include "fasta.h" void print_fasta(GArray *seqs, GPtrArray *outarray) { GString *onestring; fastaseq *oneseq; int n; for (n=0; nlen; n++) { oneseq = &g_array_index(seqs,fastaseq,n); onestring = g_ptr_array_index(outarray,n); printf(">%s\n",oneseq->header->str); printf("%s\n",onestring->str); } printf("\n"); } void print_raw(params *v, GArray *seqs) { fastaseq *oneseq; seq_frag *onefrag; int n,m,k; for (n=0; nnseqs; n++) { oneseq = &g_array_index(seqs,fastaseq,n); printf(">%s\n",oneseq->header->str); onefrag=g_ptr_array_index(v->seqheadlist,n); while (onefrag != NULL) { m=0; while ((onefrag->seqindex[m])!=n) m++; for (k=0; kseqlen; k++) printf("%c",onefrag->seq[m][k]); onefrag = onefrag->neighbours_r[m]; } printf("\n"); } } void print_aligned(GArray *seqs, GPtrArray *outarray) { GString *onestring; fastaseq *oneseq; int n,m,ctr,maxlen,*currlens; char **outheads; onestring = g_ptr_array_index(outarray,0); maxlen = onestring->len; currlens = calloc(sizeof(int),outarray->len); outheads = calloc(sizeof(char*),seqs->len); for (n=0; nlen; n++) { outheads[n] = calloc(sizeof(char),18); oneseq = &g_array_index(seqs,fastaseq,n); m=0; while ((m < 15)&&(mheader->len)) { outheads[n][m] = oneseq->header->str[m]; m++; } while (m<17) { outheads[n][m] = ' '; m++; } outheads[n][17]='\0'; } ctr = 0; while (ctr < maxlen) { for (n=0; nlen; n++) { onestring = g_ptr_array_index(outarray,n); printf("%17s ",outheads[n]); for (m=0; m<50; m++) { if (ctr+mlen){ printf("%c",onestring->str[m+ctr]); if (onestring->str[m+ctr]!='-') currlens[n]++; } else printf(" "); if ((m+1)%10 == 0) printf(" "); } printf(" %5d\n",currlens[n]); } printf("\n"); ctr += 50; } printf("\n"); free(currlens); for (n=0; nlen; n++) free(outheads[n]); free(outheads); } sigma-1.1.3/src/print_routines.h0000644000175000017500000000052210604245467013570 00000000000000/* Sigma - Simple greedy multiple alignment */ /* Copyright (C) 2007 Rahul Siddharthan */ /* Licensed under the GNU GPL, version 2 */ /* See file COPYING in source distribution */ void print_fasta(GArray *seqs, GPtrArray *outarray); void print_aligned(GArray *seqs, GPtrArray *outarray); void print_raw(params *v, GArray *seqs); sigma-1.1.3/src/getopt_long.c0000644000175000017500000003350510631765636013034 00000000000000/* $NetBSD: getopt_long.c,v 1.15 2002/01/31 22:43:40 tv Exp $ */ /* $FreeBSD: src/lib/libc/stdlib/getopt_long.c,v 1.2 2002/10/16 22:18:42 alfred Exp $ */ /*- * Copyright (c) 2000 The NetBSD Foundation, Inc. * All rights reserved. * * This code is derived from software contributed to The NetBSD Foundation * by Dieter Baron and Thomas Klausner. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * 3. All advertising materials mentioning features or use of this software * must display the following acknowledgement: * This product includes software developed by the NetBSD * Foundation, Inc. and its contributors. * 4. Neither the name of The NetBSD Foundation nor the names of its * contributors may be used to endorse or promote products derived * from this software without specific prior written permission. * * THIS SOFTWARE IS PROVIDED BY THE NETBSD FOUNDATION, INC. AND CONTRIBUTORS * ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE FOUNDATION OR CONTRIBUTORS * BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE * POSSIBILITY OF SUCH DAMAGE. */ #include #include #include #ifdef _WIN32 /* Windows needs warnx(). We change the definition though: * 1. (another) global is defined, opterrmsg, which holds the error message * 2. errors are always printed out on stderr w/o the program name * Note that opterrmsg always gets set no matter what opterr is set to. The * error message will not be printed if opterr is 0 as usual. */ #include #include GETOPT_API extern char opterrmsg[128]; char opterrmsg[128]; /* last error message is stored here */ static void warnx(int print_error, const char *fmt, ...) { va_list ap; va_start(ap, fmt); if (fmt != NULL) _vsnprintf(opterrmsg, 128, fmt, ap); else opterrmsg[0]='\0'; va_end(ap); if (print_error) { fprintf(stderr, opterrmsg); fprintf(stderr, "\n"); } } #endif /*_WIN32*/ /* not part of the original file */ #ifndef _DIAGASSERT #define _DIAGASSERT(X) #endif #define REPLACE_GETOPT #ifdef REPLACE_GETOPT #ifdef __weak_alias __weak_alias(getopt,_getopt) #endif int opterr = 1; /* if error message should be printed */ int optind = 1; /* index into parent argv vector */ int optopt = '?'; /* character checked for validity */ int optreset; /* reset getopt */ char *optarg; /* argument associated with option */ #elif HAVE_CONFIG_H && !HAVE_DECL_OPTRESET static int optreset; #endif #ifdef __weak_alias __weak_alias(getopt_long,_getopt_long) #endif #if !HAVE_GETOPT_LONG #define IGNORE_FIRST (*options == '-' || *options == '+') #define PRINT_ERROR ((opterr) && ((*options != ':') \ || (IGNORE_FIRST && options[1] != ':'))) #define IS_POSIXLY_CORRECT (getenv("POSIXLY_CORRECT") != NULL) #define PERMUTE (!IS_POSIXLY_CORRECT && !IGNORE_FIRST) /* XXX: GNU ignores PC if *options == '-' */ #define IN_ORDER (!IS_POSIXLY_CORRECT && *options == '-') /* return values */ #define BADCH (int)'?' #define BADARG ((IGNORE_FIRST && options[1] == ':') \ || (*options == ':') ? (int)':' : (int)'?') #define INORDER (int)1 #define EMSG "" static int getopt_internal(int, char * const *, const char *); static int gcd(int, int); static void permute_args(int, int, int, char * const *); static char *place = EMSG; /* option letter processing */ /* XXX: set optreset to 1 rather than these two */ static int nonopt_start = -1; /* first non option argument (for permute) */ static int nonopt_end = -1; /* first option after non options (for permute) */ /* Error messages */ static const char recargchar[] = "option requires an argument -- %c"; static const char recargstring[] = "option requires an argument -- %s"; static const char ambig[] = "ambiguous option -- %.*s"; static const char noarg[] = "option doesn't take an argument -- %.*s"; static const char illoptchar[] = "unknown option -- %c"; static const char illoptstring[] = "unknown option -- %s"; /* * Compute the greatest common divisor of a and b. */ static int gcd(a, b) int a; int b; { int c; c = a % b; while (c != 0) { a = b; b = c; c = a % b; } return b; } /* * Exchange the block from nonopt_start to nonopt_end with the block * from nonopt_end to opt_end (keeping the same order of arguments * in each block). */ static void permute_args(panonopt_start, panonopt_end, opt_end, nargv) int panonopt_start; int panonopt_end; int opt_end; char * const *nargv; { int cstart, cyclelen, i, j, ncycle, nnonopts, nopts, pos; char *swap; _DIAGASSERT(nargv != NULL); /* * compute lengths of blocks and number and size of cycles */ nnonopts = panonopt_end - panonopt_start; nopts = opt_end - panonopt_end; ncycle = gcd(nnonopts, nopts); cyclelen = (opt_end - panonopt_start) / ncycle; for (i = 0; i < ncycle; i++) { cstart = panonopt_end+i; pos = cstart; for (j = 0; j < cyclelen; j++) { if (pos >= panonopt_end) pos -= nnonopts; else pos += nopts; swap = nargv[pos]; /* LINTED const cast */ ((char **) nargv)[pos] = nargv[cstart]; /* LINTED const cast */ ((char **)nargv)[cstart] = swap; } } } /* * getopt_internal -- * Parse argc/argv argument vector. Called by user level routines. * Returns -2 if -- is found (can be long option or end of options marker). */ static int getopt_internal(nargc, nargv, options) int nargc; char * const *nargv; const char *options; { char *oli; /* option letter list index */ int optchar; _DIAGASSERT(nargv != NULL); _DIAGASSERT(options != NULL); optarg = NULL; /* * XXX Some programs (like rsyncd) expect to be able to * XXX re-initialize optind to 0 and have getopt_long(3) * XXX properly function again. Work around this braindamage. */ if (optind == 0) optind = 1; if (optreset) nonopt_start = nonopt_end = -1; start: if (optreset || !*place) { /* update scanning pointer */ optreset = 0; if (optind >= nargc) { /* end of argument vector */ place = EMSG; if (nonopt_end != -1) { /* do permutation, if we have to */ permute_args(nonopt_start, nonopt_end, optind, nargv); optind -= nonopt_end - nonopt_start; } else if (nonopt_start != -1) { /* * If we skipped non-options, set optind * to the first of them. */ optind = nonopt_start; } nonopt_start = nonopt_end = -1; return -1; } if ((*(place = nargv[optind]) != '-') || (place[1] == '\0')) { /* found non-option */ place = EMSG; if (IN_ORDER) { /* * GNU extension: * return non-option as argument to option 1 */ optarg = nargv[optind++]; return INORDER; } if (!PERMUTE) { /* * if no permutation wanted, stop parsing * at first non-option */ return -1; } /* do permutation */ if (nonopt_start == -1) nonopt_start = optind; else if (nonopt_end != -1) { permute_args(nonopt_start, nonopt_end, optind, nargv); nonopt_start = optind - (nonopt_end - nonopt_start); nonopt_end = -1; } optind++; /* process next argument */ goto start; } if (nonopt_start != -1 && nonopt_end == -1) nonopt_end = optind; if (place[1] && *++place == '-') { /* found "--" */ place++; return -2; } } if ((optchar = (int)*place++) == (int)':' || (oli = strchr(options + (IGNORE_FIRST ? 1 : 0), optchar)) == NULL) { /* option letter unknown or ':' */ if (!*place) ++optind; #ifndef _WIN32 if (PRINT_ERROR) warnx(illoptchar, optchar); #else warnx(PRINT_ERROR, illoptchar, optchar); #endif optopt = optchar; return BADCH; } if (optchar == 'W' && oli[1] == ';') { /* -W long-option */ /* XXX: what if no long options provided (called by getopt)? */ if (*place) return -2; if (++optind >= nargc) { /* no arg */ place = EMSG; #ifndef _WIN32 if (PRINT_ERROR) warnx(recargchar, optchar); #else warnx(PRINT_ERROR, recargchar, optchar); #endif optopt = optchar; return BADARG; } else /* white space */ place = nargv[optind]; /* * Handle -W arg the same as --arg (which causes getopt to * stop parsing). */ return -2; } if (*++oli != ':') { /* doesn't take argument */ if (!*place) ++optind; } else { /* takes (optional) argument */ optarg = NULL; if (*place) /* no white space */ optarg = place; /* XXX: disable test for :: if PC? (GNU doesn't) */ else if (oli[1] != ':') { /* arg not optional */ if (++optind >= nargc) { /* no arg */ place = EMSG; #ifndef _WIN32 if (PRINT_ERROR) warnx(recargchar, optchar); #else warnx(PRINT_ERROR, recargchar, optchar); #endif optopt = optchar; return BADARG; } else optarg = nargv[optind]; } place = EMSG; ++optind; } /* dump back option letter */ return optchar; } #ifdef REPLACE_GETOPT /* * getopt -- * Parse argc/argv argument vector. * * [eventually this will replace the real getopt] */ int getopt(nargc, nargv, options) int nargc; char * const *nargv; const char *options; { int retval; _DIAGASSERT(nargv != NULL); _DIAGASSERT(options != NULL); if ((retval = getopt_internal(nargc, nargv, options)) == -2) { ++optind; /* * We found an option (--), so if we skipped non-options, * we have to permute. */ if (nonopt_end != -1) { permute_args(nonopt_start, nonopt_end, optind, nargv); optind -= nonopt_end - nonopt_start; } nonopt_start = nonopt_end = -1; retval = -1; } return retval; } #endif /* * getopt_long -- * Parse argc/argv argument vector. */ int getopt_long(nargc, nargv, options, long_options, idx) int nargc; char * const *nargv; const char *options; const struct option *long_options; int *idx; { int retval; _DIAGASSERT(nargv != NULL); _DIAGASSERT(options != NULL); _DIAGASSERT(long_options != NULL); /* idx may be NULL */ if ((retval = getopt_internal(nargc, nargv, options)) == -2) { char *current_argv, *has_equal; size_t current_argv_len; int i, match; current_argv = place; match = -1; optind++; place = EMSG; if (*current_argv == '\0') { /* found "--" */ /* * We found an option (--), so if we skipped * non-options, we have to permute. */ if (nonopt_end != -1) { permute_args(nonopt_start, nonopt_end, optind, nargv); optind -= nonopt_end - nonopt_start; } nonopt_start = nonopt_end = -1; return -1; } if ((has_equal = strchr(current_argv, '=')) != NULL) { /* argument found (--option=arg) */ current_argv_len = has_equal - current_argv; has_equal++; } else current_argv_len = strlen(current_argv); for (i = 0; long_options[i].name; i++) { /* find matching long option */ if (strncmp(current_argv, long_options[i].name, current_argv_len)) continue; if (strlen(long_options[i].name) == (unsigned)current_argv_len) { /* exact match */ match = i; break; } if (match == -1) /* partial match */ match = i; else { /* ambiguous abbreviation */ #ifndef _WIN32 if (PRINT_ERROR) warnx(ambig, (int)current_argv_len, current_argv); #else warnx(PRINT_ERROR, ambig, (int)current_argv_len, current_argv); #endif optopt = 0; return BADCH; } } if (match != -1) { /* option found */ if (long_options[match].has_arg == no_argument && has_equal) { #ifndef _WIN32 if (PRINT_ERROR) warnx(noarg, (int)current_argv_len, current_argv); #else warnx(PRINT_ERROR, noarg, (int)current_argv_len, current_argv); #endif /* * XXX: GNU sets optopt to val regardless of * flag */ if (long_options[match].flag == NULL) optopt = long_options[match].val; else optopt = 0; return BADARG; } if (long_options[match].has_arg == required_argument || long_options[match].has_arg == optional_argument) { if (has_equal) optarg = has_equal; else if (long_options[match].has_arg == required_argument) { /* * optional argument doesn't use * next nargv */ optarg = nargv[optind++]; } } if ((long_options[match].has_arg == required_argument) && (optarg == NULL)) { /* * Missing argument; leading ':' * indicates no error should be generated */ #ifndef _WIN32 if (PRINT_ERROR) warnx(recargstring, current_argv); #else warnx(PRINT_ERROR, recargstring, current_argv); #endif /* * XXX: GNU sets optopt to val regardless * of flag */ if (long_options[match].flag == NULL) optopt = long_options[match].val; else optopt = 0; --optind; return BADARG; } } else { /* unknown option */ #ifndef _WIN32 if (PRINT_ERROR) warnx(illoptstring, current_argv); #else warnx(PRINT_ERROR, illoptstring, current_argv); #endif optopt = 0; return BADCH; } if (long_options[match].flag) { *long_options[match].flag = long_options[match].val; retval = 0; } else retval = long_options[match].val; if (idx) *idx = match; } return retval; } #endif /* !GETOPT_LONG */ sigma-1.1.3/src/getopt.h0000644000175000017500000000630510631764506012013 00000000000000/* $NetBSD: getopt.h,v 1.4 2000/07/07 10:43:54 ad Exp $ */ /* $FreeBSD: /repoman/r/ncvs/src/include/getopt.h,v 1.6 2004/02/24 08:09:20 ache Exp $ */ /*- * Copyright (c) 2000 The NetBSD Foundation, Inc. * All rights reserved. * * This code is derived from software contributed to The NetBSD Foundation * by Dieter Baron and Thomas Klausner. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions * are met: * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * 3. All advertising materials mentioning features or use of this software * must display the following acknowledgement: * This product includes software developed by the NetBSD * Foundation, Inc. and its contributors. * 4. Neither the name of The NetBSD Foundation nor the names of its * contributors may be used to endorse or promote products derived * from this software without specific prior written permission. * * THIS SOFTWARE IS PROVIDED BY THE NETBSD FOUNDATION, INC. AND CONTRIBUTORS * ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE FOUNDATION OR CONTRIBUTORS * BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE * POSSIBILITY OF SUCH DAMAGE. */ #ifndef _GETOPT_H_ #define _GETOPT_H_ #include /* * GNU-like getopt_long()/getopt_long_only() with 4.4BSD optreset extension. * getopt() is declared here too for GNU programs. */ #define no_argument 0 #define required_argument 1 #define optional_argument 2 struct option { /* name of long option */ const char *name; /* * one of no_argument, required_argument, and optional_argument: * whether option takes an argument */ int has_arg; /* if not NULL, set *flag to val when option found */ int *flag; /* if flag not NULL, value to set *flag to; else return value */ int val; }; __BEGIN_DECLS int getopt_long(int, char * const *, const char *, const struct option *, int *); int getopt_long_only(int, char * const *, const char *, const struct option *, int *); #ifndef _GETOPT_DECLARED #define _GETOPT_DECLARED int getopt(int, char * const [], const char *); extern char *optarg; /* getopt(3) external variables */ extern int optind, opterr, optopt; #endif #ifndef _OPTRESET_DECLARED #define _OPTRESET_DECLARED extern int optreset; /* getopt(3) external variable */ #endif __END_DECLS #endif /* !_GETOPT_H_ */