1. libsleipnir
  2. sleipnir

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chuttenh  committed 6e0c5c9

[svn r408] Update svm_light to svm_perf
Update all accompanying configure/Makefile/scripts/includes/etc.
Fix a Linux glitch or two in CStatistics and OntoShell
Update Linux cmdline.[ch] files

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  • Parent commits 1a27e9b
  • Branches sleipnir

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Files changed (20)

File Makefile.in

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  • Ignore whitespace
 CC = @CC@
 CXX = @CXX@
 DEPDIR = @DEPDIR@
+GENGETOPT_CFLAGS = @GENGETOPT_CFLAGS@
+GENGETOPT_LIBS = @GENGETOPT_LIBS@
+GENGETOPT_PREFIX = @GENGETOPT_PREFIX@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
 LOG4CPP_CFLAGS = @LOG4CPP_CFLAGS@
 LOG4CPP_LIBS = @LOG4CPP_LIBS@
 SMILE_LIBS = @SMILE_LIBS@
 SMILE_PREFIX = @SMILE_PREFIX@
 STRIP = @STRIP@
-SVM_LIGHT_CFLAGS = @SVM_LIGHT_CFLAGS@
-SVM_LIGHT_LIBS = @SVM_LIGHT_LIBS@
-SVM_LIGHT_PREFIX = @SVM_LIGHT_PREFIX@
+SVM_PERF_CFLAGS = @SVM_PERF_CFLAGS@
+SVM_PERF_LIBS = @SVM_PERF_LIBS@
+SVM_PERF_PREFIX = @SVM_PERF_PREFIX@
 VERSION = @VERSION@
 am__include = @am__include@
 am__quote = @am__quote@

File configure

View file
  • Ignore whitespace
 # include <unistd.h>
 #endif"
 
-ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA PACKAGE VERSION ACLOCAL AUTOCONF AUTOMAKE AUTOHEADER MAKEINFO AMTAR install_sh STRIP ac_ct_STRIP INSTALL_STRIP_PROGRAM AWK SET_MAKE CXX CXXFLAGS LDFLAGS CPPFLAGS ac_ct_CXX EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE AMDEPBACKSLASH CXXDEPMODE CC CFLAGS ac_ct_CC CCDEPMODE RANLIB ac_ct_RANLIB CXXCPP EGREP LIBOBJS POW_LIB prog_gengetopt prog_gengetopt_dir LOG4CPP_PREFIX LOG4CPP_CFLAGS LOG4CPP_LIBS SMILE_PREFIX SMILE_CFLAGS SMILE_LIBS SVM_LIGHT_PREFIX SVM_LIGHT_CFLAGS SVM_LIGHT_LIBS BOOST_CFLAGS BOOST_LIBS READLINE_PREFIX READLINE_CFLAGS READLINE_LIBS PTHREAD_PREFIX PTHREAD_CFLAGS PTHREAD_LIBS sleipnirdocdir SLEIPNIR_PREFIX SLEIPNIR_CFLAGS SLEIPNIR_LIBS WITH_TOOLS_TRUE WITH_TOOLS_FALSE WITH_SMILE_TOOLS_TRUE WITH_SMILE_TOOLS_FALSE WITH_SVM_TOOLS_TRUE WITH_SVM_TOOLS_FALSE WITH_READLINE_TOOLS_TRUE WITH_READLINE_TOOLS_FALSE WITH_BOOST_TOOLS_TRUE WITH_BOOST_TOOLS_FALSE WITH_GENGETOPT_TRUE WITH_GENGETOPT_FALSE LTLIBOBJS'
+ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA PACKAGE VERSION ACLOCAL AUTOCONF AUTOMAKE AUTOHEADER MAKEINFO AMTAR install_sh STRIP ac_ct_STRIP INSTALL_STRIP_PROGRAM AWK SET_MAKE CXX CXXFLAGS LDFLAGS CPPFLAGS ac_ct_CXX EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE AMDEPBACKSLASH CXXDEPMODE CC CFLAGS ac_ct_CC CCDEPMODE RANLIB ac_ct_RANLIB CXXCPP EGREP LIBOBJS POW_LIB prog_gengetopt prog_gengetopt_dir GENGETOPT_PREFIX GENGETOPT_CFLAGS GENGETOPT_LIBS LOG4CPP_PREFIX LOG4CPP_CFLAGS LOG4CPP_LIBS SMILE_PREFIX SMILE_CFLAGS SMILE_LIBS SVM_PERF_PREFIX SVM_PERF_CFLAGS SVM_PERF_LIBS BOOST_CFLAGS BOOST_LIBS READLINE_PREFIX READLINE_CFLAGS READLINE_LIBS PTHREAD_PREFIX PTHREAD_CFLAGS PTHREAD_LIBS sleipnirdocdir SLEIPNIR_PREFIX SLEIPNIR_CFLAGS SLEIPNIR_LIBS WITH_TOOLS_TRUE WITH_TOOLS_FALSE WITH_SMILE_TOOLS_TRUE WITH_SMILE_TOOLS_FALSE WITH_SVM_TOOLS_TRUE WITH_SVM_TOOLS_FALSE WITH_READLINE_TOOLS_TRUE WITH_READLINE_TOOLS_FALSE WITH_BOOST_TOOLS_TRUE WITH_BOOST_TOOLS_FALSE WITH_GENGETOPT_TRUE WITH_GENGETOPT_FALSE LTLIBOBJS'
 ac_subst_files=''
 
 # Initialize some variables set by options.
   --with-gengetopt=PATH   prefix of gengetopt installation
   --with-log4cpp=PATH     prefix of log4cpp installation or build directory
   --with-smile=PATH       prefix of SMILE installation
-  --with-svm-light=PATH   prefix of SVM Light installation
+  --with-svm-perf=PATH    prefix of SVM Perf installation
   --with-boost-includes=PATH
                           location of boost header files
   --with-boost-graph-lib=PATH
 
 
 ## LOCAL_CHECK_APPEND_PATHS(base path, paths to append, common path to look for, var to set,
-##   action if found in appended path, action if not found)
+##   action if not found)
 ## Look for the common path in one of the appendable paths under the base path.
 ## If found, set the variable to the concatenation of the prefix and the appended path,
 ## not including the common path. If not found use the base dir.
 # If the user specifies a path, use it.
 # If the user doesn't specify anything, check for it.
 # While checking, look for a source distribution in extlib/.
-# Gengetopt is required (for tools) only to rebuild cmdline.[ch] if ggo file is more recent.
-# No CFLAGS or LIBS needed.
+# Gengetopt is required (for tools).
+#! CFLAGS assumes headers in same directory as binaries for installed
 
 # Check whether --with-gengetopt or --without-gengetopt was given.
 if test "${with_gengetopt+set}" = set; then
 #  if echo with_gengetopt | $EGREP -q '^extlib/'; then extlib=true; else extlib=false; fi
   prog_gengetopt_info=$with_gengetopt
   prog_gengetopt_state=ok
-  qualify_path with_gengetopt    # need full path since we don't know where we will be
+  qualify_path with_gengetopt
   prog_gengetopt=$with_gengetopt
-
+  GENGETOPT_PREFIX=$prog_gengetopt_prefix
+         GENGETOPT_INCLUDES="-I${GENGETOPT_PREFIX}/include"
 
 else
   # Extract the first word of "gengetopt", so it can be a program name with args.
   else
     prog_gengetopt_info="found installed"
     prog_gengetopt_state=ok
-
+    GENGETOPT_PREFIX=$prog_gengetopt_prefix
+         GENGETOPT_INCLUDES="-I${GENGETOPT_PREFIX}/include"
 
   fi
 fi
   prog_gengetopt_prefix=$prog_gengetopt_dir/..     # assumes bin and include are at same level
 
 fi
-                                                    if test "x$prog_gengetopt" != "x"; then
-  # see if it the path is really to a source distribution
-
-result=$prog_gengetopt
-found=false
-for p in src; do
-  if test -e "$prog_gengetopt/$p/gengetopt"; then
-    result=$prog_gengetopt/$p
-    found=true
-    break
-  fi
-done
-prog_gengetopt_alt=$result
-if $found; then
-  true   # in case the following is empty
-  PROG_GENGETOPT_ALT=true
-else
-  if ! test -e $result/gengetopt; then
-    true   # in case the following is empty
-
-  fi
-fi
-
-  if test "x$PROG_GENGETOPT_ALT" != "x"; then
-    prog_gengetopt=$prog_gengetopt_alt/gengetopt
-    prog_gengetopt_info=$prog_gengetopt
-  fi
-fi
-
-
-#AC_SUBST(GENGETOPT_PREFIX)
-#AC_SUBST(GENGETOPT_CFLAGS)
-#AC_SUBST(GENGETOPT_LIBS)
+                                                    ## set CFLAGS and LIBS
+if test "x$GENGETOPT_PREFIX" != "x"; then
+  #! check (in LOCAL_PATH_PROG?)
+  GENGETOPT_CFLAGS=$GENGETOPT_INCLUDES
+  GENGETOPT_LIBS=
+fi
+
+
+
+
+
 
 
 ## LOG4CPP
   fi
 done
 LOG4CPP_INCLUDE_DIR=$result
-if $found; then
-  true   # in case the following is empty
-
-else
+if ! $found; then
   if ! test -e $result/log4cpp/Category.hh; then
     true   # in case the following is empty
     log4cpp_state=warn
   fi
 done
 LOG4CPP_LIB_DIR=$result
-if $found; then
-  true   # in case the following is empty
-
-else
+if ! $found; then
   if ! test -e $result/liblog4cpp.a; then
     true   # in case the following is empty
     log4cpp_state=warn
   fi
 done
 SMILE_INCLUDE_DIR=$result
-if $found; then
-  true   # in case the following is empty
-
-else
+if ! $found; then
   if ! test -e $result/smile.h; then
     true   # in case the following is empty
     smile_state=warn
   fi
 done
 SMILE_LIB_DIR=$result
-if $found; then
-  true   # in case the following is empty
-
-else
+if ! $found; then
   if ! test -e $result/libsmile.a; then
     true   # in case the following is empty
     smile_state=warn
 
 
 
-## SVM LIGHT
+## SVM PERF
 # If the user specifies a path, use it.
 # If the user says not to use it, then don't.
 # If the user doesn't specify anything, check for it.
 # While checking, look for a source distribution in extlib/.
-# If none, set NO_SVM_LIGHT=1.
-
-# Check whether --with-svm_light or --without-svm_light was given.
-if test "${with_svm_light+set}" = set; then
-  withval="$with_svm_light"
-
-else
-  with_svm_light=check
+# If none, set NO_SVM_PERF=1.
+
+# Check whether --with-svm_perf or --without-svm_perf was given.
+if test "${with_svm_perf+set}" = set; then
+  withval="$with_svm_perf"
+
+else
+  with_svm_perf=check
 fi;
 ac_ext=c
 ac_cpp='$CPP $CPPFLAGS'
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
 
-if test "x$with_svm_light" = "xno"; then
-  svm_light_info=NONE
-  svm_light_state=no
+if test "x$with_svm_perf" = "xno"; then
+  svm_perf_info=NONE
+  svm_perf_state=no
   true   # in case not defined or is empty
           cat >>confdefs.h <<\_ACEOF
-#define NO_SVM_LIGHT 1
-_ACEOF
-
-elif test "x$with_svm_light" != "xcheck"; then
+#define NO_SVM_PERF 1
+_ACEOF
+
+elif test "x$with_svm_perf" != "xcheck"; then
 # We rely on the AC_ARG_WITH call to set $with_(local name) to "check"
 # if the user does not specify it. That way it is never undefined.
 # That may not be necessary.
-#  if echo with_svm_light | $EGREP -q '^extlib/'; then extlib=true; else extlib=false; fi
-  svm_light_info=$with_svm_light
-  svm_light_state=ok
-  qualify_path with_svm_light
-
-          SVM_LIGHT_PREFIX=$with_svm_light
+#  if echo with_svm_perf | $EGREP -q '^extlib/'; then extlib=true; else extlib=false; fi
+  svm_perf_info=$with_svm_perf
+  svm_perf_state=ok
+  qualify_path with_svm_perf
+
+          SVM_PERF_PREFIX=$with_svm_perf
 else
   # In AC_LINK_IFELSE, the last argument is optional. If it is specified but is
   # empty, however, we get a syntax error. But, we have to be careful,
 cat >>conftest.$ac_ext <<_ACEOF
 /* end confdefs.h.  */
 	#include <sys/types.h>
-	 #include "svm_common.h"
-	 #include "svm_learn.h"
+	 #include "svm_struct_api.h"
+	 #include "svm_struct_api_types.h"
 int
 main ()
 {
   ac_status=$?
   echo "$as_me:$LINENO: \$? = $ac_status" >&5
   (exit $ac_status); }; }; then
-  svm_light_info="found installed"
-     svm_light_state=ok
+  svm_perf_info="found installed"
+     svm_perf_state=ok
 
 
 else
   if $flag; then
     # we also can't have an empty if block...
 #    true
-    svm_light_info="not found"
-    svm_light_state=no
+    svm_perf_info="not found"
+    svm_perf_state=no
     	cat >>confdefs.h <<\_ACEOF
-#define NO_SVM_LIGHT 1
+#define NO_SVM_PERF 1
 _ACEOF
 
   fi
 ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
 ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
 
-if test "x$svm_light_state" != "xno"; then
-  ## set SVM_LIGHT_CFLAGS and SVM_LIGHT_LIBS
-  if test "x$SVM_LIGHT_PREFIX" != "x"; then
-
-result=$SVM_LIGHT_PREFIX
+if test "x$svm_perf_state" != "xno"; then
+  ## set SVM_PERF_CFLAGS and SVM_PERF_LIBS
+  if test "x$SVM_PERF_PREFIX" != "x"; then
+
+result=$SVM_PERF_PREFIX
 found=false
 for p in include; do
-  if test -e "$SVM_LIGHT_PREFIX/$p/svm_common.h"; then
-    result=$SVM_LIGHT_PREFIX/$p
+  if test -e "$SVM_PERF_PREFIX/$p/svm_struct_api.h"; then
+    result=$SVM_PERF_PREFIX/$p
     found=true
     break
   fi
 done
-SVM_LIGHT_INCLUDE_DIR=$result
-if $found; then
-  true   # in case the following is empty
-
-else
-  if ! test -e $result/svm_common.h; then
+SVM_PERF_INCLUDE_DIR=$result
+if ! $found; then
+  if ! test -e $result/svm_struct_api.h; then
     true   # in case the following is empty
-    svm_light_state=warn
+    svm_perf_state=warn
   fi
 fi
 
 
-result=$SVM_LIGHT_PREFIX
+result=$SVM_PERF_PREFIX
 found=false
 for p in lib; do
-  if test -e "$SVM_LIGHT_PREFIX/$p/libsvmlight.a"; then
-    result=$SVM_LIGHT_PREFIX/$p
+  if test -e "$SVM_PERF_PREFIX/$p/libsvmperf.a"; then
+    result=$SVM_PERF_PREFIX/$p
     found=true
     break
   fi
 done
-SVM_LIGHT_LIB_DIR=$result
-if $found; then
-  true   # in case the following is empty
-
-else
-  if ! test -e $result/libsvmlight.a; then
+SVM_PERF_LIB_DIR=$result
+if ! $found; then
+  if ! test -e $result/libsvmperf.a; then
     true   # in case the following is empty
-    svm_light_state=warn
+    svm_perf_state=warn
   fi
 fi
 
-#    if ! test -f "$SVM_LIGHT_INCLUDE_DIR/svm_common.h"; then svm_light_state=warn; fi
-#    if ! test -f "$SVM_LIGHT_LIB_DIR/libsvmlight.a"; then svm_light_state=warn; fi
-    SVM_LIGHT_CFLAGS="-I$SVM_LIGHT_INCLUDE_DIR"
-    SVM_LIGHT_LIBS="-L$SVM_LIGHT_LIB_DIR"
+#    if ! test -f "$SVM_PERF_INCLUDE_DIR/svm_struct_api.h"; then svm_perf_state=warn; fi
+#    if ! test -f "$SVM_PERF_LIB_DIR/libsvmperf.a"; then svm_perf_state=warn; fi
+    SVM_PERF_CFLAGS="-I$SVM_PERF_INCLUDE_DIR"
+    SVM_PERF_LIBS="-L$SVM_PERF_LIB_DIR"
   fi
-  SVM_LIGHT_LIBS="$SVM_LIGHT_LIBS -lsvmlight"
+  SVM_PERF_LIBS="$SVM_PERF_LIBS -lsvmperf"
 fi
 
 
   fi
 done
 BOOST_INCLUDES_DIR=$result
-if $found; then
-  true   # in case the following is empty
-
-else
+if ! $found; then
   if ! test -e $result/boost/config.hpp; then
     true   # in case the following is empty
     boost_state=warn
   fi
 done
 READLINE_INCLUDE_DIR=$result
-if $found; then
-  true   # in case the following is empty
-
-else
+if ! $found; then
   if ! test -e $result/readline/readline.h; then
     true   # in case the following is empty
     readline_state=warn
   fi
 done
 READLINE_LIB_DIR=$result
-if $found; then
-  true   # in case the following is empty
-
-else
+if ! $found; then
   if ! test -e $result/libreadline.a; then
     true   # in case the following is empty
     readline_state=warn
   fi
 done
 PTHREAD_INCLUDE_DIR=$result
-if $found; then
-  true   # in case the following is empty
-
-else
+if ! $found; then
   if ! test -e $result/pthread.h; then
     true   # in case the following is empty
     pthread_state=warn
   fi
 done
 PTHREAD_LIB_DIR=$result
-if $found; then
-  true   # in case the following is empty
-
-else
+if ! $found; then
   if ! test -e $result/libpthread.a; then
     true   # in case the following is empty
     pthread_state=warn
 
 
 
-if test "x$svm_light_state" != "xno"; then
+if test "x$svm_perf_state" != "xno"; then
   WITH_SVM_TOOLS_TRUE=
   WITH_SVM_TOOLS_FALSE='#'
 else
 fi
 
 
-                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ac_config_files="$ac_config_files Makefile src/Makefile tools/Makefile tools/Answerer/Makefile tools/Cliquer/Makefile tools/Clusterer/Makefile tools/Clusters2Dab/Makefile tools/COALESCE/Makefile tools/Combiner/Makefile tools/DChecker/Makefile tools/Dat2Dab/Makefile tools/Dat2Graph/Makefile tools/Data2Bnt/Makefile tools/Data2Features/Makefile tools/Data2Sql/Makefile tools/DataDumper/Makefile tools/Distancer/Makefile tools/Explainer/Makefile tools/Funcaeologist/Makefile tools/Funcifier/Makefile tools/Funcographer/Makefile tools/Hubber/Makefile tools/KNNImputer/Makefile tools/Mat2Txt/Makefile tools/MCluster/Makefile tools/Matcher/Makefile tools/MIer/Makefile tools/Normalizer/Makefile tools/Orthologer/Makefile tools/Overlapper/Makefile tools/Randomizer/Makefile tools/Seqs2Ngrams/Makefile tools/Synthesizer/Makefile tools/Txt2Bin/Makefile tools/BNConverter/Makefile tools/BNCreator/Makefile tools/BNEvaluator/Makefile tools/BNFunc/Makefile tools/BNTester/Makefile tools/BNTruster/Makefile tools/BNs2Txt/Makefile tools/BNUnraveler/Makefile tools/BNWeaver/Makefile tools/Contexter/Makefile tools/Counter/Makefile tools/Data2DB/Makefile tools/DSLConverter/Makefile tools/Dab2Dad/Makefile tools/Edges2Posteriors/Makefile tools/MEFIT/Makefile tools/Data2Svm/Makefile tools/SVMer/Makefile tools/OntoShell/Makefile tools/BNServer/Makefile"
+                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      ac_config_files="$ac_config_files Makefile src/Makefile tools/Makefile tools/Answerer/Makefile tools/Cliquer/Makefile tools/Clusterer/Makefile tools/Clusters2Dab/Makefile tools/COALESCE/Makefile tools/Combiner/Makefile tools/DChecker/Makefile tools/Dat2Dab/Makefile tools/Dat2Graph/Makefile tools/Data2Bnt/Makefile tools/Data2Features/Makefile tools/Data2Sql/Makefile tools/DataDumper/Makefile tools/Distancer/Makefile tools/Explainer/Makefile tools/Funcaeologist/Makefile tools/Funcifier/Makefile tools/Funcographer/Makefile tools/Hubber/Makefile tools/KNNImputer/Makefile tools/Mat2Txt/Makefile tools/MCluster/Makefile tools/Matcher/Makefile tools/MIer/Makefile tools/Normalizer/Makefile tools/Orthologer/Makefile tools/Overlapper/Makefile tools/PCLPlotter/Makefile tools/Randomizer/Makefile tools/Seqs2Ngrams/Makefile tools/Synthesizer/Makefile tools/Txt2Bin/Makefile tools/BNConverter/Makefile tools/BNCreator/Makefile tools/BNEvaluator/Makefile tools/BNFunc/Makefile tools/BNTester/Makefile tools/BNTruster/Makefile tools/BNs2Txt/Makefile tools/BNUnraveler/Makefile tools/BNWeaver/Makefile tools/Contexter/Makefile tools/Counter/Makefile tools/Data2DB/Makefile tools/DSLConverter/Makefile tools/Dab2Dad/Makefile tools/Edges2Posteriors/Makefile tools/MEFIT/Makefile tools/Data2Svm/Makefile tools/SVMer/Makefile tools/OntoShell/Makefile tools/BNServer/Makefile"
 
 
 
   "tools/Normalizer/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/Normalizer/Makefile" ;;
   "tools/Orthologer/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/Orthologer/Makefile" ;;
   "tools/Overlapper/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/Overlapper/Makefile" ;;
+  "tools/PCLPlotter/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/PCLPlotter/Makefile" ;;
   "tools/Randomizer/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/Randomizer/Makefile" ;;
   "tools/Seqs2Ngrams/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/Seqs2Ngrams/Makefile" ;;
   "tools/Synthesizer/Makefile" ) CONFIG_FILES="$CONFIG_FILES tools/Synthesizer/Makefile" ;;
 s,@POW_LIB@,$POW_LIB,;t t
 s,@prog_gengetopt@,$prog_gengetopt,;t t
 s,@prog_gengetopt_dir@,$prog_gengetopt_dir,;t t
+s,@GENGETOPT_PREFIX@,$GENGETOPT_PREFIX,;t t
+s,@GENGETOPT_CFLAGS@,$GENGETOPT_CFLAGS,;t t
+s,@GENGETOPT_LIBS@,$GENGETOPT_LIBS,;t t
 s,@LOG4CPP_PREFIX@,$LOG4CPP_PREFIX,;t t
 s,@LOG4CPP_CFLAGS@,$LOG4CPP_CFLAGS,;t t
 s,@LOG4CPP_LIBS@,$LOG4CPP_LIBS,;t t
 s,@SMILE_PREFIX@,$SMILE_PREFIX,;t t
 s,@SMILE_CFLAGS@,$SMILE_CFLAGS,;t t
 s,@SMILE_LIBS@,$SMILE_LIBS,;t t
-s,@SVM_LIGHT_PREFIX@,$SVM_LIGHT_PREFIX,;t t
-s,@SVM_LIGHT_CFLAGS@,$SVM_LIGHT_CFLAGS,;t t
-s,@SVM_LIGHT_LIBS@,$SVM_LIGHT_LIBS,;t t
+s,@SVM_PERF_PREFIX@,$SVM_PERF_PREFIX,;t t
+s,@SVM_PERF_CFLAGS@,$SVM_PERF_CFLAGS,;t t
+s,@SVM_PERF_LIBS@,$SVM_PERF_LIBS,;t t
 s,@BOOST_CFLAGS@,$BOOST_CFLAGS,;t t
 s,@BOOST_LIBS@,$BOOST_LIBS,;t t
 s,@READLINE_PREFIX@,$READLINE_PREFIX,;t t
 fi
 echo "  log4cpp         = $log4cpp_info"
 echo "  SMILE           = $smile_info"
-echo "  SVM light       = $svm_light_info"
+echo "  SVM Perf        = $svm_perf_info"
 echo "  pthread         = $pthread_info"
 if $with_tools; then
 echo "Used for tools:"
 
 fi
 
-if test "x$svm_light_state" = "xno"; then
+if test "x$svm_perf_state" = "xno"; then
   cat << EOF
 
-** BUILDING WITHOUT SVM LIGHT
-SVM light is strongly recommended.
+** BUILDING WITHOUT SVM PERF
+SVM Perf is strongly recommended.
 It is available from http://svmlight.joachims.org/.
 EOF
 
-elif test "x$svm_light_state" = "xwarn"; then
+elif test "x$svm_perf_state" = "xwarn"; then
   cat << EOF
 
-** WARNING: The path to SVM light may be incorrect.
-I looked for svm_common.h and libsvmlight.a and did not
+** WARNING: The path to SVM Perf may be incorrect.
+I looked for svm_struct_api.h and libsvmperf.a and did not
 find both.
 EOF
 

File configure.ac

View file
  • Ignore whitespace
 
 #! TODO:
 #! b. Warn for pthread.
+#! d. Gengetopt checks.
 #! e. Improve boost logic?
 
 AC_PREREQ(2.59)
 #  if echo with_$2 | $EGREP -q '^extlib/'; then extlib=true; else extlib=false; fi
   prog_$2_info=$with_$2
   prog_$2_state=ok
-  qualify_path with_$2    # need full path since we don't know where we will be
+  qualify_path with_$2
   prog_$2=$with_$2
   $3
   $5
 
 
 ## LOCAL_CHECK_APPEND_PATHS(base path, paths to append, common path to look for, var to set,
-##   action if found in appended path, action if not found)
+##   action if not found)
 ## Look for the common path in one of the appendable paths under the base path.
 ## If found, set the variable to the concatenation of the prefix and the appended path,
 ## not including the common path. If not found use the base dir.
   fi
 done
 $4=$result
-if $found; then
-  true   # in case the following is empty
-  $5
-else
+if ! $found; then
   if ! test -e $result/$3; then
     true   # in case the following is empty
-    $6
+    $5
   fi
 fi
 ])
 # If the user specifies a path, use it.
 # If the user doesn't specify anything, check for it.
 # While checking, look for a source distribution in extlib/.
-# Gengetopt is required (for tools) only to rebuild cmdline.[ch] if ggo file is more recent.
-# No CFLAGS or LIBS needed.
+# Gengetopt is required (for tools).
+#! CFLAGS assumes headers in same directory as binaries for installed
 AC_ARG_WITH([gengetopt],
 	[AS_HELP_STRING([--with-gengetopt=PATH], [prefix of gengetopt installation])],
 	[],
 	[with_gengetopt=check])
 LOCAL_PATH_PROG([gengetopt], [gengetopt],
-        [],                                                    dnl found
+        [GENGETOPT_PREFIX=$prog_gengetopt_prefix
+         GENGETOPT_INCLUDES="-I${GENGETOPT_PREFIX}/include"],  dnl found
         [],                                                    dnl found installed
 	[],                                                    dnl found in with path
 	[],                                                    dnl not found
         [])                                                    dnl requested without
-if test "x$prog_gengetopt" != "x"; then
-  # see if it the path is really to a source distribution
-  LOCAL_CHECK_APPEND_PATHS([$prog_gengetopt], [src], [gengetopt], [prog_gengetopt_alt], [PROG_GENGETOPT_ALT=true], [])
-  if test "x$PROG_GENGETOPT_ALT" != "x"; then
-    prog_gengetopt=$prog_gengetopt_alt/gengetopt
-    prog_gengetopt_info=$prog_gengetopt
-  fi
+## set CFLAGS and LIBS
+if test "x$GENGETOPT_PREFIX" != "x"; then
+  #! check (in LOCAL_PATH_PROG?)
+  GENGETOPT_CFLAGS=$GENGETOPT_INCLUDES
+  GENGETOPT_LIBS=
 fi
 AC_SUBST(prog_gengetopt)
 AC_SUBST(prog_gengetopt_dir)
-#AC_SUBST(GENGETOPT_PREFIX)
-#AC_SUBST(GENGETOPT_CFLAGS)
-#AC_SUBST(GENGETOPT_LIBS)
+AC_SUBST(GENGETOPT_PREFIX)
+AC_SUBST(GENGETOPT_CFLAGS)
+AC_SUBST(GENGETOPT_LIBS)
 
 
 ## LOG4CPP
 if test "x$log4cpp_state" != "xstub"; then
   ## set LOG4CPP_CFLAGS and LOG4CPP_LIBS
   if test "x$LOG4CPP_PREFIX" != "x"; then
-    LOCAL_CHECK_APPEND_PATHS([$LOG4CPP_PREFIX], [include], [log4cpp/Category.hh], [LOG4CPP_INCLUDE_DIR], [], [log4cpp_state=warn])
-    LOCAL_CHECK_APPEND_PATHS([$LOG4CPP_PREFIX], [lib src/.libs], [liblog4cpp.a], [LOG4CPP_LIB_DIR], [], [log4cpp_state=warn])
+    LOCAL_CHECK_APPEND_PATHS([$LOG4CPP_PREFIX], [include], [log4cpp/Category.hh], [LOG4CPP_INCLUDE_DIR], [log4cpp_state=warn])
+    LOCAL_CHECK_APPEND_PATHS([$LOG4CPP_PREFIX], [lib src/.libs], [liblog4cpp.a], [LOG4CPP_LIB_DIR], [log4cpp_state=warn])
     LOG4CPP_CFLAGS="-I$LOG4CPP_INCLUDE_DIR"
     LOG4CPP_LIBS="-L$LOG4CPP_LIB_DIR"
 #    if ! test -f "$LOG4CPP_INCLUDE_DIR/log4cpp/Category.hh"; then log4cpp_state=warn; fi
 if test "x$smile_state" != "xno"; then
   ## set SMILE_CFLAGS and SMILE_LIBS
   if test "x$SMILE_PREFIX" != "x"; then
-    LOCAL_CHECK_APPEND_PATHS([$SMILE_PREFIX], [include], [smile.h], [SMILE_INCLUDE_DIR], [], [smile_state=warn])
-    LOCAL_CHECK_APPEND_PATHS([$SMILE_PREFIX], [lib], [libsmile.a], [SMILE_LIB_DIR], [], [smile_state=warn])
+    LOCAL_CHECK_APPEND_PATHS([$SMILE_PREFIX], [include], [smile.h], [SMILE_INCLUDE_DIR], [smile_state=warn])
+    LOCAL_CHECK_APPEND_PATHS([$SMILE_PREFIX], [lib], [libsmile.a], [SMILE_LIB_DIR], [smile_state=warn])
 #    if ! test -f "$SMILE_INCLUDE_DIR/smile.h"; then smile_state=warn; fi
 #    if ! test -f "$SMILE_LIB_DIR/libsmile.a"; then smile_state=warn; fi
     if test -f "$SMILE_LIB_DIR/libsmilexml.a"; then
 AC_SUBST(SMILE_LIBS)
 
 
-## SVM LIGHT
+## SVM PERF
 # If the user specifies a path, use it.
 # If the user says not to use it, then don't.
 # If the user doesn't specify anything, check for it.
 # While checking, look for a source distribution in extlib/.
-# If none, set NO_SVM_LIGHT=1.
-AC_ARG_WITH([svm_light],
-	[AS_HELP_STRING([--with-svm-light=PATH], [prefix of SVM Light installation])],
+# If none, set NO_SVM_PERF=1.
+AC_ARG_WITH([svm_perf],
+	[AS_HELP_STRING([--with-svm-perf=PATH], [prefix of SVM Perf installation])],
 	[],
-	[with_svm_light=check])
+	[with_svm_perf=check])
 AC_LANG_PUSH([C])
-LOCAL_CHECK_LIB([svmlight], [svm_light], [optimize_svm],
+LOCAL_CHECK_LIB([svmperf], [svm_perf], [optimize_svm],
         [],                                                        dnl found
         [],                                                        dnl and found installed
-        [SVM_LIGHT_PREFIX=$with_svm_light],                        dnl and found in specified path
-	[AC_DEFINE([NO_SVM_LIGHT], [1])],                          dnl not found
-        [AC_DEFINE([NO_SVM_LIGHT], [1])],                          dnl requested without
+        [SVM_PERF_PREFIX=$with_svm_perf],                        dnl and found in specified path
+	[AC_DEFINE([NO_SVM_PERF], [1])],                          dnl not found
+        [AC_DEFINE([NO_SVM_PERF], [1])],                          dnl requested without
 	[#include <sys/types.h>
-	 #include "svm_common.h"
-	 #include "svm_learn.h"])
+	 #include "svm_struct_api.h"
+	 #include "svm_struct_api_types.h"])
 AC_LANG_POP
-if test "x$svm_light_state" != "xno"; then
-  ## set SVM_LIGHT_CFLAGS and SVM_LIGHT_LIBS
-  if test "x$SVM_LIGHT_PREFIX" != "x"; then
-    LOCAL_CHECK_APPEND_PATHS([$SVM_LIGHT_PREFIX], [include], [svm_common.h], [SVM_LIGHT_INCLUDE_DIR], [], [svm_light_state=warn])
-    LOCAL_CHECK_APPEND_PATHS([$SVM_LIGHT_PREFIX], [lib], [libsvmlight.a], [SVM_LIGHT_LIB_DIR], [], [svm_light_state=warn])
-#    if ! test -f "$SVM_LIGHT_INCLUDE_DIR/svm_common.h"; then svm_light_state=warn; fi
-#    if ! test -f "$SVM_LIGHT_LIB_DIR/libsvmlight.a"; then svm_light_state=warn; fi
-    SVM_LIGHT_CFLAGS="-I$SVM_LIGHT_INCLUDE_DIR"
-    SVM_LIGHT_LIBS="-L$SVM_LIGHT_LIB_DIR"
+if test "x$svm_perf_state" != "xno"; then
+  ## set SVM_PERF_CFLAGS and SVM_PERF_LIBS
+  if test "x$SVM_PERF_PREFIX" != "x"; then
+    LOCAL_CHECK_APPEND_PATHS([$SVM_PERF_PREFIX], [include], [svm_struct_api.h], [SVM_PERF_INCLUDE_DIR], [svm_perf_state=warn])
+    LOCAL_CHECK_APPEND_PATHS([$SVM_PERF_PREFIX], [lib], [libsvmperf.a], [SVM_PERF_LIB_DIR], [svm_perf_state=warn])
+#    if ! test -f "$SVM_PERF_INCLUDE_DIR/svm_struct_api.h"; then svm_perf_state=warn; fi
+#    if ! test -f "$SVM_PERF_LIB_DIR/libsvmperf.a"; then svm_perf_state=warn; fi
+    SVM_PERF_CFLAGS="-I$SVM_PERF_INCLUDE_DIR"
+    SVM_PERF_LIBS="-L$SVM_PERF_LIB_DIR"
   fi
-  SVM_LIGHT_LIBS="$SVM_LIGHT_LIBS -lsvmlight"
+  SVM_PERF_LIBS="$SVM_PERF_LIBS -lsvmperf"
 fi
-AC_SUBST(SVM_LIGHT_PREFIX)
-AC_SUBST(SVM_LIGHT_CFLAGS)
-AC_SUBST(SVM_LIGHT_LIBS)
+AC_SUBST(SVM_PERF_PREFIX)
+AC_SUBST(SVM_PERF_CFLAGS)
+AC_SUBST(SVM_PERF_LIBS)
 
 
 ## BOOST
     # now look for the headers
     BOOST_LIBS=$BOOST_GRAPH_LIB
     qualify_path with_boost_includes
-    LOCAL_CHECK_APPEND_PATHS([$with_boost_includes], [..], [boost/config.hpp], [BOOST_INCLUDES_DIR], [], [boost_state=warn])
+    LOCAL_CHECK_APPEND_PATHS([$with_boost_includes], [..], [boost/config.hpp], [BOOST_INCLUDES_DIR], [boost_state=warn])
     if ! test -f $BOOST_GRAPH_LIB; then boost_state=warn; fi
     if ! echo $BOOST_GRAPH_LIB | $GREP -q "libboost_graph"; then boost_state=warn; fi
     BOOST_CFLAGS="-I$BOOST_INCLUDES_DIR"
 if test "x$readline_state" != "xno"; then
   ## set READLINE_CFLAGS and READLINE_LIBS
   if test "x$READLINE_PREFIX" != "x"; then
-    LOCAL_CHECK_APPEND_PATHS([$READLINE_PREFIX], [include], [readline/readline.h], [READLINE_INCLUDE_DIR], [], [readline_state=warn])
-    LOCAL_CHECK_APPEND_PATHS([$READLINE_PREFIX], [lib], [libreadline.a], [READLINE_LIB_DIR], [], [readline_state=warn])
+    LOCAL_CHECK_APPEND_PATHS([$READLINE_PREFIX], [include], [readline/readline.h], [READLINE_INCLUDE_DIR], [readline_state=warn])
+    LOCAL_CHECK_APPEND_PATHS([$READLINE_PREFIX], [lib], [libreadline.a], [READLINE_LIB_DIR], [readline_state=warn])
 #    if ! test -f "$READLINE_INCLUDE_DIR/readline/readline.h"; then readline_state=warn; fi
 #    if ! test -f "$READLINE_LIB_DIR/libreadline.a"; then readline_state=warn; fi
     READLINE_CFLAGS="-I$READLINE_INCLUDE_DIR"
 if test "x$pthread_state" != "xno"; then
   ## set PTHREAD_CFLAGS and PTHREAD_LIBS
   if test "x$PTHREAD_PREFIX" != "x"; then
-    LOCAL_CHECK_APPEND_PATHS([$PTHREAD_PREFIX], [include], [pthread.h], [PTHREAD_INCLUDE_DIR], [], [pthread_state=warn])
-    LOCAL_CHECK_APPEND_PATHS([$PTHREAD_PREFIX], [lib], [libpthread.a], [PTHREAD_LIB_DIR], [], [pthread_state=warn])
+    LOCAL_CHECK_APPEND_PATHS([$PTHREAD_PREFIX], [include], [pthread.h], [PTHREAD_INCLUDE_DIR], [pthread_state=warn])
+    LOCAL_CHECK_APPEND_PATHS([$PTHREAD_PREFIX], [lib], [libpthread.a], [PTHREAD_LIB_DIR], [pthread_state=warn])
     PTHREAD_CFLAGS="-I$PTHREAD_INCLUDE_DIR"
     PTHREAD_LIBS="-L$PTHREAD_LIB_DIR"
   fi
 
 AM_CONDITIONAL([WITH_TOOLS], [$with_tools])
 AM_CONDITIONAL([WITH_SMILE_TOOLS], [test "x$smile_state" != "xno"])
-AM_CONDITIONAL([WITH_SVM_TOOLS], [test "x$svm_light_state" != "xno"])
+AM_CONDITIONAL([WITH_SVM_TOOLS], [test "x$svm_perf_state" != "xno"])
 AM_CONDITIONAL([WITH_READLINE_TOOLS], [test "x$readline_state" != "xno"])
 AM_CONDITIONAL([WITH_BOOST_TOOLS], [test "x$boost_state" != "xno"])
 AM_CONDITIONAL([WITH_GENGETOPT], [test "x$prog_gengetopt_state" != "xno"])
 		 tools/Normalizer/Makefile \
 		 tools/Orthologer/Makefile \
 		 tools/Overlapper/Makefile \
+		 tools/PCLPlotter/Makefile \
 		 tools/Randomizer/Makefile \
 		 tools/Seqs2Ngrams/Makefile \
 		 tools/Synthesizer/Makefile \
 fi
 echo "  log4cpp         = $log4cpp_info"
 echo "  SMILE           = $smile_info"
-echo "  SVM light       = $svm_light_info"
+echo "  SVM Perf        = $svm_perf_info"
 echo "  pthread         = $pthread_info"
 if $with_tools; then
 echo "Used for tools:"
 
 fi
 
-if test "x$svm_light_state" = "xno"; then
+if test "x$svm_perf_state" = "xno"; then
   cat << EOF
 
-** BUILDING WITHOUT SVM LIGHT
-SVM light is strongly recommended.
+** BUILDING WITHOUT SVM PERF
+SVM Perf is strongly recommended.
 It is available from http://svmlight.joachims.org/.
 EOF
 
-elif test "x$svm_light_state" = "xwarn"; then
+elif test "x$svm_perf_state" = "xwarn"; then
   cat << EOF
 
-** WARNING: The path to SVM light may be incorrect.
-I looked for svm_common.h and libsvmlight.a and did not
+** WARNING: The path to SVM Perf may be incorrect.
+I looked for svm_struct_api.h and libsvmperf.a and did not
 find both.
 EOF
 

File gen_tools_am

View file
  • Ignore whitespace
 my $tools_common_libs1 = "\$(SLEIPNIR_LIBS)";
 my $tools_common_libs2 = " \$(LOG4CPP_LIBS) \$(PTHREAD_LIBS)";
 
-# packages are: SMILE, SVM_LIGHT, READLINE, PTHREADS, BOOST
+# packages are: SMILE, SVM_PERF, READLINE, PTHREADS, BOOST
 # ordering is important for linking
 my %tools_other_packages = (
 			    BNConverter => ['SMILE'],
 			    Data2DB  => ['SMILE'],
 			    Dab2Dad  => ['SMILE'],
 			    Dab2DB  => ['SMILE'],
-			    Data2Svm => ['SVM_LIGHT'],
+			    Data2Svm => ['SVM_PERF'],
 			    Edges2Posteriors => ['SMILE'],
 			    MEFIT  => ['SMILE'],
 			    OntoShell => ['READLINE'],
-			    SVMer => ['SVM_LIGHT'],
+			    SVMer => ['SVM_PERF'],
 			    );
 
 if (opendir(TOOLSDIR, "tools")) {
 		    }
 		    print AM_MAKEFILE "AM_CPPFLAGS = ".$tools_common_cflags1.$extra_cflags.$tools_common_cflags2."\n";
 		    print AM_MAKEFILE "LDADD = ".$tools_common_libs1.$extra_libs.$tools_common_libs2."\n";
-#		    print AM_MAKEFILE "AM_CPPFLAGS = \$(SLEIPNIR_CFLAGS) \$(SMILE_CFLAGS) \$(SVM_LIGHT_CFLAGS) \$(GENGETOPT_CFLAGS) \$(LOG4CPP_CFLAGS) \$(BOOST_CFLAGS) \$(READLINE_CFLAGS)\n";
-#		    print AM_MAKEFILE "LDADD = \$(SLEIPNIR_LIBS) \$(SMILE_LIBS) \$(SVM_LIGHT_LIBS) \$(GENGETOPT_LIBS) \$(LOG4CPP_LIBS) \$(BOOST_LIBS) \$(READLINE_LIBS)\n";
+#		    print AM_MAKEFILE "AM_CPPFLAGS = \$(SLEIPNIR_CFLAGS) \$(SMILE_CFLAGS) \$(SVM_PERF_CFLAGS) \$(GENGETOPT_CFLAGS) \$(LOG4CPP_CFLAGS) \$(BOOST_CFLAGS) \$(READLINE_CFLAGS)\n";
+#		    print AM_MAKEFILE "LDADD = \$(SLEIPNIR_LIBS) \$(SMILE_LIBS) \$(SVM_PERF_LIBS) \$(GENGETOPT_LIBS) \$(LOG4CPP_LIBS) \$(BOOST_LIBS) \$(READLINE_LIBS)\n";
 		    if ($ggo_file) {
 			print AM_MAKEFILE "\nif WITH_GENGETOPT\n";
 			print AM_MAKEFILE "gengetopt = \$(prog_gengetopt)\n";

File src/Makefile.am

View file
  • Ignore whitespace
 lib_LIBRARIES			= libSleipnir.a
 
-AM_CPPFLAGS = $(LOG4CPP_CFLAGS) $(SMILE_CFLAGS) $(SVM_LIGHT_CFLAGS) $(PTHREAD_CFLAGS)
+AM_CPPFLAGS = $(LOG4CPP_CFLAGS) $(SMILE_CFLAGS) $(SVM_PERF_CFLAGS) $(PTHREAD_CFLAGS)
 
-#LDADD = $(LOG4CPP_LIBS) $(SMILE_LIBS) $(SVM_LIGHT_LIBS) $(PTHREAD_LIBS)
+#LDADD = $(LOG4CPP_LIBS) $(SMILE_LIBS) $(SVM_PERF_LIBS) $(PTHREAD_LIBS)
 
 libSleipnir_a_SOURCES	=	\
 	annotation.cpp			\

File src/Makefile.in

View file
  • Ignore whitespace
 CC = @CC@
 CXX = @CXX@
 DEPDIR = @DEPDIR@
+GENGETOPT_CFLAGS = @GENGETOPT_CFLAGS@
+GENGETOPT_LIBS = @GENGETOPT_LIBS@
+GENGETOPT_PREFIX = @GENGETOPT_PREFIX@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
 LOG4CPP_CFLAGS = @LOG4CPP_CFLAGS@
 LOG4CPP_LIBS = @LOG4CPP_LIBS@
 SMILE_LIBS = @SMILE_LIBS@
 SMILE_PREFIX = @SMILE_PREFIX@
 STRIP = @STRIP@
-SVM_LIGHT_CFLAGS = @SVM_LIGHT_CFLAGS@
-SVM_LIGHT_LIBS = @SVM_LIGHT_LIBS@
-SVM_LIGHT_PREFIX = @SVM_LIGHT_PREFIX@
+SVM_PERF_CFLAGS = @SVM_PERF_CFLAGS@
+SVM_PERF_LIBS = @SVM_PERF_LIBS@
+SVM_PERF_PREFIX = @SVM_PERF_PREFIX@
 VERSION = @VERSION@
 am__include = @am__include@
 am__quote = @am__quote@
 sleipnirdocdir = @sleipnirdocdir@
 lib_LIBRARIES = libSleipnir.a
 
-AM_CPPFLAGS = $(LOG4CPP_CFLAGS) $(SMILE_CFLAGS) $(SVM_LIGHT_CFLAGS) $(PTHREAD_CFLAGS)
+AM_CPPFLAGS = $(LOG4CPP_CFLAGS) $(SMILE_CFLAGS) $(SVM_PERF_CFLAGS) $(PTHREAD_CFLAGS)
 
 
-#LDADD = $(LOG4CPP_LIBS) $(SMILE_LIBS) $(SVM_LIGHT_LIBS) $(PTHREAD_LIBS)
+#LDADD = $(LOG4CPP_LIBS) $(SMILE_LIBS) $(SVM_PERF_LIBS) $(PTHREAD_LIBS)
 libSleipnir_a_SOURCES = \
 	annotation.cpp			\
 	annotationgo.cpp		\

File src/statistics.h

View file
  • Ignore whitespace
 		size_t	iN;
 
 		Sums( Begin, End, NULL, &dRet, &iN );
-		return ( iN ? max( ( dRet / iN ) - ( dMean * dMean ), 0 ) : 0 ); }
+		return ( iN ? max( ( dRet / iN ) - ( dMean * dMean ), 0.0 ) : 0 ); }
 
 	/*!
 	 * \brief
 		if( !iN )
 			return 0;
 		dSum /= iN;
-		return max( ( dRet / iN ) - ( dSum * dSum ), 0 ); }
+		return max( ( dRet / iN ) - ( dSum * dSum ), 0.0 ); }
 
 	/*!
 	 * \brief

File src/stdafx.cpp

View file
  • Ignore whitespace
  *	Library at the University of Pittsburgh.  Sleipnir uses it to do most of its Bayesian analysis, so
  *	no Bayes nets will be available without it!  It is distributed by the DSL as binaries built for a wide
  *	variety of platforms; if you don't see yours listed, send them an email, and they can probably help.
- * - <a href="http://svmlight.joachims.org/">SVM Light</a> is a support vector machine library used for
+ * - <a href="http://svmlight.joachims.org/">SVM Perf</a> is a support vector machine library used for
  *	SVM learning and evaluation in Sleipnir.  No SVMs without it!  Easily built from source under just about
  *	any environment (it's plain old C).  Please note that you must use <a href="Makefile" class="crit">this
- *	Makefile</a> to build SVM Light as a library (rather than an executable) on Linux/Mac OS; in Visual
+ *	Makefile</a> to build SVM Perf as a library (rather than an executable) on Linux/Mac OS; in Visual
  *	Studio, set the project type to "Static Library".
  * 
  * \subsubsection sssec_building_prerequisites_suggestions Suggestions
  * <li>Obtain any \ref ssec_building_prerequisites you need/want.  These can often be installed using your
  *	favorite Linux package manager.  If you need to compile/install them to a nonstandard location by hand,
  *	please note the directory prefix where they are installed.
- *	<li>If you're using SVM Light, please use <a href="Makefile">this Makefile</a> to build it as a library
+ *	<li>If you're using SVM Perf, please use <a href="Makefile">this Makefile</a> to build it as a library
  *		rather than an executable.</li>
- *	<li>Note that SVM Light and SMILE are both nonstandard in that they expect header files and libraries to
- *		reside in the same directory (e.g. \c /usr/local/smile or \c /usr/local/svm_light).</li>
+ *	<li>Note that SVM Perf and SMILE are both nonstandard in that they expect header files and libraries to
+ *		reside in the same directory (e.g. \c /usr/local/smile or \c /usr/local/svm_perf).</li>
  * </li>
  * <li>\ref sec_download and unpack Sleipnir.</li>
  * <li>In the Sleipnir directory, run \c ./configure.  If you've installed prerequisite libraries that it
  *	doesn't find automatically, provide an appropriate \c --with switch for each one.  For example, to build
- *	Sleipnir with SMILE and SVM Light installed in custom directories under -c /usr/local/, type:</li>
+ *	Sleipnir with SMILE and SVM Perf installed in custom directories under -c /usr/local/, type:</li>
  * \code
- * ./configure --with-smile=/usr/local/smile/ --with-svm-light=/usr/local/svm_light/
+ * ./configure --with-smile=/usr/local/smile/ --with-svm-perf=/usr/local/svm_perf/
  * \endcode
  * <li>If you'd like to install Sleipnir itself to a custom location, include a
  *	<tt>--prefix=/custom/path/</tt> flag when you run \c configrue.</li>
  *	form compiled with that setting, it taints anything it interacts with; building without this flag and
  *	linking against Sleipnir in Release mode will result in weird memory corruption errors when dealing with
  *	STL objects.
- * - Don't forget to build <a href="http://svmlight.joachims.org/">SVM Light</a> as a library rather than an
+ * - Don't forget to build <a href="http://svmlight.joachims.org/">SVM Perf</a> as a library rather than an
  *	executable, using <a href="Makefile">this Makefile</a> on Linux/Mac OS or setting the project type to
  *	"Static Library" in Visual Studio.
  * - If you're building the \ref BNServer tool, you'll need the Boost graph library - but only the graph

File src/svm.cpp

View file
  • Ignore whitespace
 #include "meta.h"
 #include "genome.h"
 
-#ifndef NO_SVM_LIGHT
+#ifndef NO_SVM_PERF
 
 extern "C" {
 KERNEL_CACHE* kernel_cache_init( long, long );
 	uint32_t* piWords, uint32_t* piDocs ) {
 	char			szComment[ 1024 ];
 	FILE*			pfileDoc;
-	SVMLight::WORD*	aWords;
+	SVMPerf::WORD*	aWords;
 	uint32_t		i, iDoc, iWord;
 	float			d;
 	float*			ad;
 	(*papDocs) = (DOC**)my_malloc( sizeof(DOC*) * (*piDocs) );
 	(*padLabels) = (double*)my_malloc( sizeof(double) * (*piDocs) );
 	ad = (float*)my_malloc( sizeof(*ad) * (*piWords) );
-	aWords = (SVMLight::WORD*)my_malloc( sizeof(SVMLight::WORD) * ( (*piWords) + 1 ) );
+	aWords = (SVMPerf::WORD*)my_malloc( sizeof(SVMPerf::WORD) * ( (*piWords) + 1 ) );
 	for( iWord = 0; iWord < (*piWords); ++iWord )
 		aWords[ iWord ].wnum = iWord + 1;
 	aWords[ iWord ].wnum = 0;
 	return true;
 }
 
-SVMLight::WORD	CSVMImpl::s_asWords[ CSVMImpl::c_iWords ];
+SVMPerf::WORD	CSVMImpl::s_asWords[ CSVMImpl::c_iWords ];
 
 CSVMImpl::SLearn::SLearn( ) {
 
 	return -1; }
 
 DOC* CSVMImpl::CreateDoc( const SData& sData, size_t iOne, size_t iTwo, size_t iDoc ) const {
-	SVMLight::WORD*	asWords;
+	SVMPerf::WORD*	asWords;
 	size_t			i, j, iWord, iWords;
 	float			d;
 	DOC*			pRet;
 
 	iWords = GetWords( sData );
-	asWords = ( iWords >= c_iWords ) ? new SVMLight::WORD[ iWords + 1 ] : s_asWords;
+	asWords = ( iWords >= c_iWords ) ? new SVMPerf::WORD[ iWords + 1 ] : s_asWords;
 	for( i = 0; i < iWords; ++i )
 		asWords[ i ].wnum = i + 1;
 	asWords[ i ].wnum = 0;
 	return pRet; }
 
 DOC* CSVMImpl::CreateDoc( const SData& sData, size_t iGene ) const {
-	SVMLight::WORD*	asWords;
+	SVMPerf::WORD*	asWords;
 	size_t			i, iWords;
 	DOC*			pRet;
 	float			d;
 
 	iWords = GetWords( sData );
-	asWords = ( iWords >= c_iWords ) ? new SVMLight::WORD[ iWords + 1 ] : s_asWords;
+	asWords = ( iWords >= c_iWords ) ? new SVMPerf::WORD[ iWords + 1 ] : s_asWords;
 	for( i = 0; i < iWords; ++i )
 		asWords[ i ].wnum = i + 1;
 	asWords[ i ].wnum = 0;
 bool CSVMImpl::EvaluateFile( const char* szFile, CDat& DatOut ) const {
 	static const size_t	c_iSize	= 512;
 	char			szGene[ c_iSize ];
-	SVMLight::WORD*	asWords;
+	SVMPerf::WORD*	asWords;
 	char*			pc;
 	ifstream		ifsm;
 	vector<string>	vecstrGenes;
 		vecstrGenes[ i ] = szGene; }
 	DatOut.Open( vecstrGenes );
 
-	asWords = ( iWords >= c_iWords ) ? new SVMLight::WORD[ iWords + 1 ] : s_asWords;
+	asWords = ( iWords >= c_iWords ) ? new SVMPerf::WORD[ iWords + 1 ] : s_asWords;
 	for( i = 0; i < iWords; ++i )
 		asWords[ i ].wnum = i + 1;
 	asWords[ i ].wnum = 0;
 	static const size_t	c_iBuf	= 131072;
 	char			szBuf[ c_iBuf ];
 	vector<string>	vecstrLine, vecstrToken;
-	SVMLight::WORD*	asWords;
+	SVMPerf::WORD*	asWords;
 	size_t			i, j;
 
 	Reset( false, true, true );
 	m_pModel->index = NULL;
 	m_pModel->lin_weights = NULL;
 
-	asWords = new SVMLight::WORD[ m_pModel->totwords + 1 ];
+	asWords = new SVMPerf::WORD[ m_pModel->totwords + 1 ];
 	asWords[ m_pModel->totwords ].wnum = 0;
 	for( i = 1; i < (size_t)m_pModel->sv_num; ++i ) {
 		istm.getline( szBuf, c_iBuf - 1 );
 
 }
 
-#endif // NO_SVM_LIGHT
+#endif // NO_SVM_PERF

File src/svm.h

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  • Ignore whitespace
 #ifndef SVM_H
 #define SVM_H
 
-#ifndef NO_SVM_LIGHT
+#ifndef NO_SVM_PERF
 
 #include "svmi.h"
 
 
 /*!
  * \brief
- * Provides an interface for learning and evaluating support vector machines using svm_light.
+ * Provides an interface for learning and evaluating support vector machines using svm_perf.
  * 
  * The CSVM class provides a variety of methods for learning and evaluating SVMs based on biological
- * data types.  All SVM manipulation is done using the svm_light library (http://svmlight.joachims.org/),
- * but the interface between Sleipnir and svm_light has been optimized to pass appropriate data types
+ * data types.  All SVM manipulation is done using the svm_perf library (http://svmlight.joachims.org/),
+ * but the interface between Sleipnir and svm_perf has been optimized to pass appropriate data types
  * (datasets, PCLs, etc.) as efficiently as possible.  Note that SVM learning requires the entire
  * dataset to be in memory simultaneously, so subsampling large answer sets is often necessary for SVMs
  * when it would not be for Bayesian learning.  On the other hand, individual data points can be evaluated
 	 * genes and the gene pair indices labeling each example.
 	 * 
 	 * \remarks
-	 * Sorry the file format is so quirky; it was made to play nice with svm_light.  It's at least arranged
+	 * Sorry the file format is so quirky; it was made to play nice with svm_perf.  It's at least arranged
 	 * so that it can be marginally compatible with the equivalent Learn function.  Of course, feeding
 	 * either method bad input will cause who-knows-what horrific consequences.
 	 */
 
 	/*!
 	 * \brief
-	 * Set the verbosity parameter for svm_light.
+	 * Set the verbosity parameter for svm_perf.
 	 * 
 	 * \param iVerbosity
-	 * Verbosity of messages from svm_light.
+	 * Verbosity of messages from svm_perf.
 	 * 
 	 * \remarks
 	 * Equivalent to the -v parameter to svm_learn/svm_classify.
 
 }
 
-#endif // NO_SVM_LIGHT
+#endif // NO_SVM_PERF
 
 #endif // SVM_H

File src/svmi.h

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  • Ignore whitespace
 #ifndef SVMI_H
 #define SVMI_H
 
-namespace SVMLight {
+namespace SVMPerf {
 
 extern "C" {
-#include "svm_common.h"
+#include <svm_light/svm_common.h>
 }
 
 }
-using namespace SVMLight;
+using namespace SVMPerf;
 
 #include "typesi.h"
 
 		const CGenes*	m_pNegative;
 	};
 
-	static SVMLight::WORD	s_asWords[ c_iWords ];
+	static SVMPerf::WORD	s_asWords[ c_iWords ];
 
 	CSVMImpl( );
 	~CSVMImpl( );

File tools/COALESCE/cmdline.c

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  • Ignore whitespace
 /*
   File autogenerated by gengetopt version 2.22
   generated with the following command:
-  ../../extlib/gengetopt-2.22/src/gengetopt -i COALESCE.ggo --default-optional -u -N -e 
+  /r01/tergeo/chuttenh/sleipnir/trunk/../extlib/gengetopt-2.22/bin/gengetopt -iCOALESCE.ggo --default-optional -u -N -e 
 
   The developers of gengetopt consider the fixed text that goes in all
   gengetopt output files to be in the public domain:
   "  -T, --cutoff_trim=DOUBLE      Cocluster stdev cutoff for cluster trimming  \n                                  (default=`1')",
   "  -R, --remove_rcs              Convert RCs and RC-like PSTs to single strand  \n                                  (default=on)",
   "  -u, --min_info=DOUBLE         Uninformative motif threshhold (bits)  \n                                  (default=`0.3')",
-  "  -U, --min_zscore=DOUBLE       Minimum motif z-score magnitude  \n                                  (default=`0.25')",
+  "  -U, --min_zscore=DOUBLE       Minimum motif z-score magnitude  \n                                  (default=`0.2')",
   "  -x, --max_motifs=INT          Maximum motifs to merge exactly  \n                                  (default=`2500')",
   "\nMiscellaneous:",
   "  -e, --cache=filename          Cache file for sequence analysis",
   args_info->remove_rcs_flag = 1;
   args_info->min_info_arg = 0.3;
   args_info->min_info_orig = NULL;
-  args_info->min_zscore_arg = 0.25;
+  args_info->min_zscore_arg = 0.2;
   args_info->min_zscore_orig = NULL;
   args_info->max_motifs_arg = 2500;
   args_info->max_motifs_orig = NULL;
         
           if (update_arg( (void *)&(args_info->min_zscore_arg), 
                &(args_info->min_zscore_orig), &(args_info->min_zscore_given),
-              &(local_args_info.min_zscore_given), optarg, 0, "0.25", ARG_DOUBLE,
+              &(local_args_info.min_zscore_given), optarg, 0, "0.2", ARG_DOUBLE,
               check_ambiguity, override, 0, 0,
               "min_zscore", 'U',
               additional_error))

File tools/COALESCE/cmdline.h

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  • Ignore whitespace
   double min_info_arg;	/**< @brief Uninformative motif threshhold (bits) (default='0.3').  */
   char * min_info_orig;	/**< @brief Uninformative motif threshhold (bits) original value given at command line.  */
   const char *min_info_help; /**< @brief Uninformative motif threshhold (bits) help description.  */
-  double min_zscore_arg;	/**< @brief Minimum motif z-score magnitude (default='0.25').  */
+  double min_zscore_arg;	/**< @brief Minimum motif z-score magnitude (default='0.2').  */
   char * min_zscore_orig;	/**< @brief Minimum motif z-score magnitude original value given at command line.  */
   const char *min_zscore_help; /**< @brief Minimum motif z-score magnitude help description.  */
   int max_motifs_arg;	/**< @brief Maximum motifs to merge exactly (default='2500').  */

File tools/Clusters2Dab/cmdline.c

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  • Ignore whitespace
 /*
   File autogenerated by gengetopt version 2.22
   generated with the following command:
-  ../../extlib/gengetopt-2.22/src/gengetopt -i Clusters2Dab.ggo --default-optional -u -N -e 
+  /r01/tergeo/chuttenh/sleipnir/trunk/../extlib/gengetopt-2.22/bin/gengetopt -iClusters2Dab.ggo --default-optional -u -N -e 
 
   The developers of gengetopt consider the fixed text that goes in all
   gengetopt output files to be in the public domain:

File tools/Combiner/cmdline.c

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  • Ignore whitespace
   "  -V, --version              Print version and exit",
   "\nMain:",
   "  -t, --type=STRING          Output data file type  (possible values=\"pcl\", \n                               \"dat\", \"dab\", \"module\" default=`pcl')",
-  "  -m, --method=STRING        Combination method  (possible values=\"min\", \n                               \"max\", \"mean\", \"gmean\", \"hmean\" \n                               default=`mean')",
+  "  -m, --method=STRING        Combination method  (possible values=\"min\", \n                               \"max\", \"mean\", \"gmean\", \"hmean\", \"sum\" \n                               default=`mean')",
   "  -o, --output=filename      Output file",
   "\nModules:",
   "  -j, --jaccard=FLOAT        Minimum Jaccard index for module equivalence  \n                               (default=`0.5')",
 
 
 char *cmdline_parser_type_values[] = {"pcl", "dat", "dab", "module", 0} ;	/* Possible values for type.  */
-char *cmdline_parser_method_values[] = {"min", "max", "mean", "gmean", "hmean", 0} ;	/* Possible values for method.  */
+char *cmdline_parser_method_values[] = {"min", "max", "mean", "gmean", "hmean", "sum", 0} ;	/* Possible values for method.  */
 
 static char *
 gengetopt_strdup (const char *s);

File tools/Explainer/cmdline.c

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  • Ignore whitespace
 /*
   File autogenerated by gengetopt version 2.22
   generated with the following command:
-  /Genomics/Users/mark/projects/sleipnir/extlib/gengetopt-2.22/src/gengetopt -iExplainer.ggo --default-optional -C -N -e 
+  /r01/tergeo/chuttenh/sleipnir/trunk/../extlib/gengetopt-2.22/bin/gengetopt -iExplainer.ggo --default-optional -C -N -e 
 
   The developers of gengetopt consider the fixed text that goes in all
   gengetopt output files to be in the public domain:

File tools/Makefile.am

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  • Ignore whitespace
 	  Normalizer \
 	  Orthologer \
 	  Overlapper \
+	  PCLPlotter \
 	  Randomizer \
 	  Seqs2Ngrams \
 	  Synthesizer \

File tools/OntoShell/parserconsole.cpp

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  • Ignore whitespace
 		set<size_t>::const_iterator	iterParent;
 		vector<size_t>				veciIntersection;
 
+		if( vecfTerms[ i ] )
+			veciIntersection.push_back( i );
 		pOnto->GetParents( i, setiParents );
 		for( iterParent = setiParents.begin( ); iterParent != setiParents.end( ); ++iterParent )
 			if( vecfTerms[ *iterParent ] )

File tools/Synthesizer/cmdline.c

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  • Ignore whitespace
 /*
   File autogenerated by gengetopt version 2.22
   generated with the following command:
-  /r01/tergeo/chuttenh/sleipnir/trunk/../extlib/gengetopt-2.22/bin/gengetopt -iSynthesizer.ggo --default-optional -N -e 
+  /r01/tergeo/chuttenh/sleipnir/trunk/../extlib/gengetopt-2.22/bin/gengetopt -iSynthesizer.ggo --default-optional -u -N -e 
 
   The developers of gengetopt consider the fixed text that goes in all
   gengetopt output files to be in the public domain:
 
 const char *gengetopt_args_info_purpose = "Creates configurable synthetic microarray and sequence data.";
 
-const char *gengetopt_args_info_usage = "Usage: Synthesizer [OPTIONS]...";
+const char *gengetopt_args_info_usage = "Usage: Synthesizer [OPTIONS]... [FILES]...";
 
 const char *gengetopt_args_info_description = "";
 
   clear_given (args_info);
   clear_args (args_info);
   init_args_info (args_info);
+
+  args_info->inputs = NULL;
+  args_info->inputs_num = 0;
 }
 
 void
 static void
 cmdline_parser_release (struct gengetopt_args_info *args_info)
 {
-
+  unsigned int i;
   free_string_field (&(args_info->output_pcl_arg));
   free_string_field (&(args_info->output_pcl_orig));
   free_string_field (&(args_info->output_fasta_arg));
   free_string_field (&(args_info->verbosity_orig));
   
   
+  for (i = 0; i < args_info->inputs_num; ++i)
+    free (args_info->inputs [i]);
+
+  if (args_info->inputs_num)
+    free (args_info->inputs);
 
   clear_given (args_info);
 }
   if ( error )
     return (EXIT_FAILURE);
 
+  if (optind < argc)
+    {
+      int i = 0 ;
+      int found_prog_name = 0;
+      /* whether program name, i.e., argv[0], is in the remaining args
+         (this may happen with some implementations of getopt,
+          but surely not with the one included by gengetopt) */
+
+      i = optind;
+      while (i < argc)
+        if (argv[i++] == argv[0]) {
+          found_prog_name = 1;
+          break;
+        }
+      i = 0;
+
+      args_info->inputs_num = argc - optind - found_prog_name;
+      args_info->inputs =
+        (char **)(malloc ((args_info->inputs_num)*sizeof(char *))) ;
+      while (optind < argc)
+        if (argv[optind++] != argv[0])
+          args_info->inputs[ i++ ] = gengetopt_strdup (argv[optind-1]) ;
+    }
+
   return 0;
 
 failure:

File tools/Synthesizer/cmdline.h

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   unsigned int random_given ;	/**< @brief Whether random was given.  */
   unsigned int verbosity_given ;	/**< @brief Whether verbosity was given.  */
 
+  char **inputs ; /**< @brief unamed options (options without names) */
+  unsigned inputs_num ; /**< @brief unamed options number */
 } ;
 
 /** @brief The additional parameters to pass to parser functions */