RubyGems - complearn - Versions diffs - 0.6.2 - Mend

complearn 0.6.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (104) hide show

data/AUTHORS +13 -0
data/COPYING +340 -0
data/ChangeLog +0 -0
data/INSTALL +231 -0
data/Makefile +352 -0
data/Makefile.am +76 -0
data/Makefile.in +352 -0
data/NEWS +7 -0
data/README +0 -0
data/aclocal.m4 +104 -0
data/bin/Makefile +209 -0
data/bin/Makefile.am +8 -0
data/bin/Makefile.in +209 -0
data/bin/labeltree +68 -0
data/bin/labeltree.in +68 -0
data/bin/makesvm +70 -0
data/bin/makesvm.in +70 -0
data/bin/maketree +98 -0
data/bin/maketree.in +98 -0
data/bin/ncd +43 -0
data/bin/ncd.in +43 -0
data/bin/ncdmatrix +54 -0
data/bin/ncdmatrix.in +54 -0
data/bin/ncdvector +50 -0
data/bin/ncdvector.in +50 -0
data/complearn-0.6.2.gem +0 -0
data/complearn.gemspec +57 -0
data/config.log +597 -0
data/config.status +1082 -0
data/configure +4922 -0
data/configure.ac +91 -0
data/confstat5FpLBf/config.h +65 -0
data/confstat5FpLBf/subs-1.sed +50 -0
data/confstat5FpLBf/subs-2.sed +13 -0
data/confstat5FpLBf/subs.frag +0 -0
data/confstat5FpLBf/subs.sed +59 -0
data/confstat5FpLBf/undefs.sed +24 -0
data/doc/FAQ.txt +67 -0
data/doc/Makefile +286 -0
data/doc/Makefile.am +11 -0
data/doc/Makefile.in +286 -0
data/doc/devguide.txt +15 -0
data/doc/example.complearnrc +14 -0
data/doc/examples.txt +35 -0
data/doc/man/Makefile +255 -0
data/doc/man/Makefile.am +11 -0
data/doc/man/Makefile.in +255 -0
data/doc/man/complearn.5 +91 -0
data/doc/man/labeltree.1 +35 -0
data/doc/man/makesvm.1 +60 -0
data/doc/man/maketree.1 +58 -0
data/doc/man/ncd.1 +51 -0
data/doc/man/ncdmatrix.1 +40 -0
data/doc/man/ncdvector.1 +42 -0
data/doc/readme.txt +101 -0
data/doc/userguide.txt +46 -0
data/examples/genes/blueWhale.txt +1 -0
data/examples/genes/cat.txt +1 -0
data/examples/genes/chimpanzee.txt +1 -0
data/examples/genes/finWhale.txt +1 -0
data/examples/genes/graySeal.txt +1 -0
data/examples/genes/harborSeal.txt +1 -0
data/examples/genes/horse.txt +1 -0
data/examples/genes/human.txt +1 -0
data/examples/genes/mouse.txt +1 -0
data/examples/genes/rat.txt +1 -0
data/ext/Makefile +167 -0
data/ext/Quartet.c +399 -0
data/ext/Quartet.h +62 -0
data/ext/TreeScore.c +244 -0
data/ext/TreeScore.h +3 -0
data/ext/config.h +65 -0
data/ext/config.h.in +64 -0
data/ext/extconf.rb +3 -0
data/ext/lib/CompLearnLib/CLConfig.rb +241 -0
data/ext/lib/CompLearnLib/CompressionObject.rb +59 -0
data/ext/lib/CompLearnLib/CompressionTask.rb +99 -0
data/ext/lib/CompLearnLib/DistMatrix.rb +18 -0
data/ext/lib/CompLearnLib/FoundComp.rb +10 -0
data/ext/lib/CompLearnLib/FoundComp.rb.in +10 -0
data/ext/lib/CompLearnLib/Ncd.rb +248 -0
data/ext/lib/CompLearnLib/RunEnv.rb +150 -0
data/ext/lib/CompLearnLib/Task.rb +39 -0
data/ext/lib/CompLearnLib/TaskMaster.rb +13 -0
data/ext/lib/CompLearnLib/TaskMasterMPI.rb +112 -0
data/ext/lib/CompLearnLib/TaskMasterSingle.rb +39 -0
data/ext/lib/CompLearnLib/Tree.rb +300 -0
data/install-sh +294 -0
data/missing +336 -0
data/mkinstalldirs +111 -0
data/o +24 -0
data/scripts/CompLearn.iss +89 -0
data/scripts/CompLearn.iss.in +89 -0
data/scripts/debian/changelog +6 -0
data/scripts/debian/control +14 -0
data/scripts/makeSetup.sh +23 -0
data/scripts/makeSetup.sh.in +23 -0
data/scripts/makedeb.zsh +46 -0
data/scripts/makedeb.zsh.in +46 -0
data/tests/alltests.rb +2 -0
data/tests/bz2test.rb +516 -0
data/tests/sshagent-test.rb +48 -0
data/tests/tests.rb +275 -0
metadata +164 -0

data/Makefile ADDED

@@ -0,0 +1,352 @@
+# Makefile.in generated automatically by automake 1.4-p4 from Makefile.am
+# Copyright (C) 1994, 1995-8, 1999 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+SHELL = /bin/sh
+srcdir = .
+top_srcdir = .
+prefix = /usr/local
+exec_prefix = ${prefix}
+bindir = ${exec_prefix}/bin
+sbindir = ${exec_prefix}/sbin
+libexecdir = ${exec_prefix}/libexec
+datadir = ${prefix}/share
+sysconfdir = ${prefix}/etc
+sharedstatedir = ${prefix}/com
+localstatedir = ${prefix}/var
+libdir = ${exec_prefix}/lib
+infodir = ${prefix}/info
+mandir = ${prefix}/man
+includedir = ${prefix}/include
+oldincludedir = /usr/include
+DESTDIR =
+pkgdatadir = $(datadir)/complearn
+pkglibdir = $(libdir)/complearn
+pkgincludedir = $(includedir)/complearn
+top_builddir = .
+ACLOCAL = aclocal
+AUTOCONF = autoconf
+AUTOMAKE = automake
+AUTOHEADER = autoheader
+INSTALL = /usr/bin/install -c
+INSTALL_PROGRAM = ${INSTALL} $(AM_INSTALL_PROGRAM_FLAGS)
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_SCRIPT = ${INSTALL}
+transform = s,x,x,
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+CC = gcc
+FOUNDBZIP2 = true
+FOUNDGZIP = true
+MAKEINFO = makeinfo
+PACKAGE = complearn
+RANLIB = ranlib
+RUBYBIN = /usr/bin/ruby1.8
+SET_MAKE =
+TOPDIR = /home/cilibrar/src/complearngem/complearn-0.6.2
+VERSION = 0.6.2
+WINBUILDDIR = c:\build
+SUBDIRS = doc bin ext
+EXTRA_DIST =  $(libsrc) $(scriptsrc) $(extsrc) $(examples) $(miscdoc)
+miscdoc =  doc/examples.txt doc/devguide.txt doc/FAQ.txt doc/readme.txt doc/userguide.txt doc/example.complearnrc
+extsrc =  ext/extconf.rb ext/Quartet.c ext/Quartet.h ext/TreeScore.c ext/TreeScore.h ext/config.h.in
+complearndir = complearn
+scriptsrc =  bin/labeltree.in bin/makesvm.in bin/maketree.in bin/ncd.in bin/ncdmatrix.in bin/ncdvector.in scripts/CompLearn.iss.in scripts/makeSetup.sh.in
+libsrc =  ext/lib/CompLearnLib/CompressionObject.rb ext/lib/CompLearnLib/CompressionTask.rb ext/lib/CompLearnLib/CLConfig.rb ext/lib/CompLearnLib/DistMatrix.rb ext/lib/CompLearnLib/Ncd.rb ext/lib/CompLearnLib/RunEnv.rb ext/lib/CompLearnLib/TaskMasterMPI.rb ext/lib/CompLearnLib/TaskMaster.rb ext/lib/CompLearnLib/TaskMasterSingle.rb ext/lib/CompLearnLib/Task.rb ext/lib/CompLearnLib/Tree.rb ext/lib/CompLearnLib/FoundComp.rb.in ext/config.h.in tests/alltests.rb tests/bz2test.rb tests/sshagent-test.rb tests/tests.rb scripts/makedeb.zsh.in scripts/debian/control scripts/debian/changelog
+examples =  examples/genes/blueWhale.txt examples/genes/cat.txt examples/genes/chimpanzee.txt examples/genes/finWhale.txt examples/genes/graySeal.txt examples/genes/harborSeal.txt examples/genes/horse.txt examples/genes/human.txt examples/genes/mouse.txt examples/genes/rat.txt
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_CLEAN_FILES =
+DIST_COMMON =  README AUTHORS COPYING ChangeLog INSTALL Makefile.am \
+Makefile.in NEWS aclocal.m4 configure configure.ac install-sh missing \
+mkinstalldirs
+DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
+TAR = tar
+GZIP_ENV = --best
+all: all-redirect
+.SUFFIXES:
+$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.ac $(ACLOCAL_M4)
+	cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps Makefile
+Makefile: $(srcdir)/Makefile.in  $(top_builddir)/config.status
+	cd $(top_builddir) \
+	  && CONFIG_FILES=$@ CONFIG_HEADERS= $(SHELL) ./config.status
+$(ACLOCAL_M4):  configure.ac
+	cd $(srcdir) && $(ACLOCAL)
+config.status: $(srcdir)/configure.ac $(CONFIG_STATUS_DEPENDENCIES)
+	$(SHELL) ./config.status --recheck
+$(srcdir)/configure: $(srcdir)/configure.ac $(ACLOCAL_M4) $(CONFIGURE_DEPENDENCIES)
+	cd $(srcdir) && $(AUTOCONF)
+# This directory's subdirectories are mostly independent; you can cd
+# into them and run `make' without going through this Makefile.
+# To change the values of `make' variables: instead of editing Makefiles,
+# (1) if the variable is set in `config.status', edit `config.status'
+#     (which will cause the Makefiles to be regenerated when you run `make');
+# (2) otherwise, pass the desired values on the `make' command line.
+all-recursive install-data-recursive install-exec-recursive \
+installdirs-recursive install-recursive uninstall-recursive  \
+check-recursive installcheck-recursive info-recursive dvi-recursive:
+	@set fnord $(MAKEFLAGS); amf=$$2; \
+	dot_seen=no; \
+	target=`echo $@ | sed s/-recursive//`; \
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  echo "Making $$target in $$subdir"; \
+	  if test "$$subdir" = "."; then \
+	    dot_seen=yes; \
+	    local_target="$$target-am"; \
+	  else \
+	    local_target="$$target"; \
+	  fi; \
+	  (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	   || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
+	done; \
+	if test "$$dot_seen" = "no"; then \
+	  $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
+	fi; test -z "$$fail"
+mostlyclean-recursive clean-recursive distclean-recursive \
+maintainer-clean-recursive:
+	@set fnord $(MAKEFLAGS); amf=$$2; \
+	dot_seen=no; \
+	rev=''; list='$(SUBDIRS)'; for subdir in $$list; do \
+	  rev="$$subdir $$rev"; \
+	  test "$$subdir" = "." && dot_seen=yes; \
+	done; \
+	test "$$dot_seen" = "no" && rev=". $$rev"; \
+	target=`echo $@ | sed s/-recursive//`; \
+	for subdir in $$rev; do \
+	  echo "Making $$target in $$subdir"; \
+	  if test "$$subdir" = "."; then \
+	    local_target="$$target-am"; \
+	  else \
+	    local_target="$$target"; \
+	  fi; \
+	  (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	   || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
+	done && test -z "$$fail"
+tags-recursive:
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
+	done
+tags: TAGS
+ID: $(HEADERS) $(SOURCES) $(LISP)
+	list='$(SOURCES) $(HEADERS)'; \
+	unique=`for i in $$list; do echo $$i; done | \
+	  awk '    { files[$$0] = 1; } \
+	       END { for (i in files) print i; }'`; \
+	here=`pwd` && cd $(srcdir) \
+	  && mkid -f$$here/ID $$unique $(LISP)
+TAGS: tags-recursive $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) $(LISP)
+	tags=; \
+	here=`pwd`; \
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+   if test "$$subdir" = .; then :; else \
+	    test -f $$subdir/TAGS && tags="$$tags -i $$here/$$subdir/TAGS"; \
+   fi; \
+	done; \
+	list='$(SOURCES) $(HEADERS)'; \
+	unique=`for i in $$list; do echo $$i; done | \
+	  awk '    { files[$$0] = 1; } \
+	       END { for (i in files) print i; }'`; \
+	test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
+	  || (cd $(srcdir) && etags $(ETAGS_ARGS) $$tags  $$unique $(LISP) -o $$here/TAGS)
+mostlyclean-tags:
+clean-tags:
+distclean-tags:
+	-rm -f TAGS ID
+maintainer-clean-tags:
+distdir = $(PACKAGE)-$(VERSION)
+top_distdir = $(distdir)
+# This target untars the dist file and tries a VPATH configuration.  Then
+# it guarantees that the distribution is self-contained by making another
+# tarfile.
+distcheck: dist
+	-rm -rf $(distdir)
+	GZIP=$(GZIP_ENV) $(TAR) zxf $(distdir).tar.gz
+	mkdir $(distdir)/=build
+	mkdir $(distdir)/=inst
+	dc_install_base=`cd $(distdir)/=inst && pwd`; \
+	cd $(distdir)/=build \
+	  && ../configure --srcdir=.. --prefix=$$dc_install_base \
+	  && $(MAKE) $(AM_MAKEFLAGS) \
+	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
+	  && $(MAKE) $(AM_MAKEFLAGS) check \
+	  && $(MAKE) $(AM_MAKEFLAGS) install \
+	  && $(MAKE) $(AM_MAKEFLAGS) installcheck \
+	  && $(MAKE) $(AM_MAKEFLAGS) dist
+	-rm -rf $(distdir)
+	@banner="$(distdir).tar.gz is ready for distribution"; \
+	dashes=`echo "$$banner" | sed s/./=/g`; \
+	echo "$$dashes"; \
+	echo "$$banner"; \
+	echo "$$dashes"
+dist: distdir
+	-chmod -R a+r $(distdir)
+	GZIP=$(GZIP_ENV) $(TAR) chozf $(distdir).tar.gz $(distdir)
+	-rm -rf $(distdir)
+dist-all: distdir
+	-chmod -R a+r $(distdir)
+	GZIP=$(GZIP_ENV) $(TAR) chozf $(distdir).tar.gz $(distdir)
+	-rm -rf $(distdir)
+distdir: $(DISTFILES)
+	-rm -rf $(distdir)
+	mkdir $(distdir)
+	-chmod 777 $(distdir)
+	$(mkinstalldirs) $(distdir)/bin $(distdir)/doc $(distdir)/examples/genes \
+	   $(distdir)/ext $(distdir)/ext/lib/CompLearnLib \
+	   $(distdir)/scripts $(distdir)/scripts/debian \
+	   $(distdir)/tests
+	@for file in $(DISTFILES); do \
+	  d=$(srcdir); \
+	  if test -d $$d/$$file; then \
+	    cp -pr $$d/$$file $(distdir)/$$file; \
+	  else \
+	    test -f $(distdir)/$$file \
+	    || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
+	    || cp -p $$d/$$file $(distdir)/$$file || :; \
+	  fi; \
+	done
+	for subdir in $(SUBDIRS); do \
+	  if test "$$subdir" = .; then :; else \
+	    test -d $(distdir)/$$subdir \
+	    || mkdir $(distdir)/$$subdir \
+	    || exit 1; \
+	    chmod 777 $(distdir)/$$subdir; \
+	    (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir=../$(distdir) distdir=../$(distdir)/$$subdir distdir) \
+	      || exit 1; \
+	  fi; \
+	done
+info-am:
+info: info-recursive
+dvi-am:
+dvi: dvi-recursive
+check-am: all-am
+check: check-recursive
+installcheck-am:
+installcheck: installcheck-recursive
+install-exec-am:
+install-exec: install-exec-recursive
+install-data-am:
+install-data: install-data-recursive
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+install: install-recursive
+uninstall-am:
+uninstall: uninstall-recursive
+all-am: Makefile
+all-redirect: all-recursive
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
+installdirs: installdirs-recursive
+installdirs-am:
+mostlyclean-generic:
+clean-generic:
+distclean-generic:
+	-rm -f Makefile $(CONFIG_CLEAN_FILES)
+	-rm -f config.cache config.log stamp-h stamp-h[0-9]*
+maintainer-clean-generic:
+mostlyclean-am:  mostlyclean-tags mostlyclean-generic
+mostlyclean: mostlyclean-recursive
+clean-am:  clean-tags clean-generic mostlyclean-am
+clean: clean-recursive
+distclean-am:  distclean-tags distclean-generic clean-am
+distclean: distclean-recursive
+	-rm -f config.status
+maintainer-clean-am:  maintainer-clean-tags maintainer-clean-generic \
+		distclean-am
+	@echo "This command is intended for maintainers to use;"
+	@echo "it deletes files that may require special tools to rebuild."
+maintainer-clean: maintainer-clean-recursive
+	-rm -f config.status
+.PHONY: install-data-recursive uninstall-data-recursive \
+install-exec-recursive uninstall-exec-recursive installdirs-recursive \
+uninstalldirs-recursive all-recursive check-recursive \
+installcheck-recursive info-recursive dvi-recursive \
+mostlyclean-recursive distclean-recursive clean-recursive \
+maintainer-clean-recursive tags tags-recursive mostlyclean-tags \
+distclean-tags clean-tags maintainer-clean-tags distdir info-am info \
+dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
+install-exec install-data-am install-data install-am install \
+uninstall-am uninstall all-redirect all-am all installdirs-am \
+installdirs mostlyclean-generic distclean-generic clean-generic \
+maintainer-clean-generic clean mostlyclean distclean maintainer-clean
+clean:
+	rm -rf confstat*
+deb:
+	./scripts/makedeb.zsh
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:

data/Makefile.am ADDED

@@ -0,0 +1,76 @@
+SUBDIRS = doc bin ext
+EXTRA_DIST = \
+$(libsrc) \
+$(scriptsrc) \
+$(extsrc) \
+$(examples) \
+$(miscdoc)
+miscdoc = \
+doc/examples.txt \
+doc/devguide.txt \
+doc/FAQ.txt \
+doc/readme.txt \
+doc/userguide.txt \
+doc/example.complearnrc
+extsrc = \
+ext/extconf.rb \
+ext/Quartet.c \
+ext/Quartet.h \
+ext/TreeScore.c \
+ext/TreeScore.h \
+ext/config.h.in
+complearndir = complearn
+scriptsrc = \
+bin/labeltree.in \
+bin/makesvm.in \
+bin/maketree.in \
+bin/ncd.in \
+bin/ncdmatrix.in \
+bin/ncdvector.in \
+scripts/CompLearn.iss.in \
+scripts/makeSetup.sh.in
+libsrc = \
+ext/lib/CompLearnLib/CompressionObject.rb \
+ext/lib/CompLearnLib/CompressionTask.rb \
+ext/lib/CompLearnLib/CLConfig.rb \
+ext/lib/CompLearnLib/DistMatrix.rb \
+ext/lib/CompLearnLib/Ncd.rb \
+ext/lib/CompLearnLib/RunEnv.rb \
+ext/lib/CompLearnLib/TaskMasterMPI.rb \
+ext/lib/CompLearnLib/TaskMaster.rb \
+ext/lib/CompLearnLib/TaskMasterSingle.rb \
+ext/lib/CompLearnLib/Task.rb \
+ext/lib/CompLearnLib/Tree.rb \
+ext/lib/CompLearnLib/FoundComp.rb.in \
+ext/config.h.in \
+tests/alltests.rb \
+tests/bz2test.rb \
+tests/sshagent-test.rb \
+tests/tests.rb \
+scripts/makedeb.zsh.in \
+scripts/debian/control \
+scripts/debian/changelog
+examples = \
+examples/genes/blueWhale.txt \
+examples/genes/cat.txt \
+examples/genes/chimpanzee.txt \
+examples/genes/finWhale.txt \
+examples/genes/graySeal.txt \
+examples/genes/harborSeal.txt \
+examples/genes/horse.txt \
+examples/genes/human.txt \
+examples/genes/mouse.txt \
+examples/genes/rat.txt
+clean:
+	rm -rf confstat*
+deb:
+	./scripts/makedeb.zsh

data/Makefile.in ADDED

@@ -0,0 +1,352 @@
+# Makefile.in generated automatically by automake 1.4-p4 from Makefile.am
+# Copyright (C) 1994, 1995-8, 1999 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+SHELL = @SHELL@
+srcdir = @srcdir@
+top_srcdir = @top_srcdir@
+VPATH = @srcdir@
+prefix = @prefix@
+exec_prefix = @exec_prefix@
+bindir = @bindir@
+sbindir = @sbindir@
+libexecdir = @libexecdir@
+datadir = @datadir@
+sysconfdir = @sysconfdir@
+sharedstatedir = @sharedstatedir@
+localstatedir = @localstatedir@
+libdir = @libdir@
+infodir = @infodir@
+mandir = @mandir@
+includedir = @includedir@
+oldincludedir = /usr/include
+DESTDIR =
+pkgdatadir = $(datadir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+top_builddir = .
+ACLOCAL = @ACLOCAL@
+AUTOCONF = @AUTOCONF@
+AUTOMAKE = @AUTOMAKE@
+AUTOHEADER = @AUTOHEADER@
+INSTALL = @INSTALL@
+INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(AM_INSTALL_PROGRAM_FLAGS)
+INSTALL_DATA = @INSTALL_DATA@
+INSTALL_SCRIPT = @INSTALL_SCRIPT@
+transform = @program_transform_name@
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+CC = @CC@
+FOUNDBZIP2 = @FOUNDBZIP2@
+FOUNDGZIP = @FOUNDGZIP@
+MAKEINFO = @MAKEINFO@
+PACKAGE = @PACKAGE@
+RANLIB = @RANLIB@
+RUBYBIN = @RUBYBIN@
+SET_MAKE = @SET_MAKE@
+TOPDIR = @TOPDIR@
+VERSION = @VERSION@
+WINBUILDDIR = @WINBUILDDIR@
+SUBDIRS = doc bin ext
+EXTRA_DIST =  $(libsrc) $(scriptsrc) $(extsrc) $(examples) $(miscdoc)
+miscdoc =  doc/examples.txt doc/devguide.txt doc/FAQ.txt doc/readme.txt doc/userguide.txt doc/example.complearnrc
+extsrc =  ext/extconf.rb ext/Quartet.c ext/Quartet.h ext/TreeScore.c ext/TreeScore.h ext/config.h.in
+complearndir = complearn
+scriptsrc =  bin/labeltree.in bin/makesvm.in bin/maketree.in bin/ncd.in bin/ncdmatrix.in bin/ncdvector.in scripts/CompLearn.iss.in scripts/makeSetup.sh.in
+libsrc =  ext/lib/CompLearnLib/CompressionObject.rb ext/lib/CompLearnLib/CompressionTask.rb ext/lib/CompLearnLib/CLConfig.rb ext/lib/CompLearnLib/DistMatrix.rb ext/lib/CompLearnLib/Ncd.rb ext/lib/CompLearnLib/RunEnv.rb ext/lib/CompLearnLib/TaskMasterMPI.rb ext/lib/CompLearnLib/TaskMaster.rb ext/lib/CompLearnLib/TaskMasterSingle.rb ext/lib/CompLearnLib/Task.rb ext/lib/CompLearnLib/Tree.rb ext/lib/CompLearnLib/FoundComp.rb.in ext/config.h.in tests/alltests.rb tests/bz2test.rb tests/sshagent-test.rb tests/tests.rb scripts/makedeb.zsh.in scripts/debian/control scripts/debian/changelog
+examples =  examples/genes/blueWhale.txt examples/genes/cat.txt examples/genes/chimpanzee.txt examples/genes/finWhale.txt examples/genes/graySeal.txt examples/genes/harborSeal.txt examples/genes/horse.txt examples/genes/human.txt examples/genes/mouse.txt examples/genes/rat.txt
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_CLEAN_FILES =
+DIST_COMMON =  README AUTHORS COPYING ChangeLog INSTALL Makefile.am \
+Makefile.in NEWS aclocal.m4 configure configure.ac install-sh missing \
+mkinstalldirs
+DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)
+TAR = tar
+GZIP_ENV = --best
+all: all-redirect
+.SUFFIXES:
+$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.ac $(ACLOCAL_M4)
+	cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps Makefile
+Makefile: $(srcdir)/Makefile.in  $(top_builddir)/config.status
+	cd $(top_builddir) \
+	  && CONFIG_FILES=$@ CONFIG_HEADERS= $(SHELL) ./config.status
+$(ACLOCAL_M4):  configure.ac
+	cd $(srcdir) && $(ACLOCAL)
+config.status: $(srcdir)/configure.ac $(CONFIG_STATUS_DEPENDENCIES)
+	$(SHELL) ./config.status --recheck
+$(srcdir)/configure: $(srcdir)/configure.ac $(ACLOCAL_M4) $(CONFIGURE_DEPENDENCIES)
+	cd $(srcdir) && $(AUTOCONF)
+# This directory's subdirectories are mostly independent; you can cd
+# into them and run `make' without going through this Makefile.
+# To change the values of `make' variables: instead of editing Makefiles,
+# (1) if the variable is set in `config.status', edit `config.status'
+#     (which will cause the Makefiles to be regenerated when you run `make');
+# (2) otherwise, pass the desired values on the `make' command line.
+@SET_MAKE@
+all-recursive install-data-recursive install-exec-recursive \
+installdirs-recursive install-recursive uninstall-recursive  \
+check-recursive installcheck-recursive info-recursive dvi-recursive:
+	@set fnord $(MAKEFLAGS); amf=$$2; \
+	dot_seen=no; \
+	target=`echo $@ | sed s/-recursive//`; \
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  echo "Making $$target in $$subdir"; \
+	  if test "$$subdir" = "."; then \
+	    dot_seen=yes; \
+	    local_target="$$target-am"; \
+	  else \
+	    local_target="$$target"; \
+	  fi; \
+	  (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	   || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
+	done; \
+	if test "$$dot_seen" = "no"; then \
+	  $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
+	fi; test -z "$$fail"
+mostlyclean-recursive clean-recursive distclean-recursive \
+maintainer-clean-recursive:
+	@set fnord $(MAKEFLAGS); amf=$$2; \
+	dot_seen=no; \
+	rev=''; list='$(SUBDIRS)'; for subdir in $$list; do \
+	  rev="$$subdir $$rev"; \
+	  test "$$subdir" = "." && dot_seen=yes; \
+	done; \
+	test "$$dot_seen" = "no" && rev=". $$rev"; \
+	target=`echo $@ | sed s/-recursive//`; \
+	for subdir in $$rev; do \
+	  echo "Making $$target in $$subdir"; \
+	  if test "$$subdir" = "."; then \
+	    local_target="$$target-am"; \
+	  else \
+	    local_target="$$target"; \
+	  fi; \
+	  (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	   || case "$$amf" in *=*) exit 1;; *k*) fail=yes;; *) exit 1;; esac; \
+	done && test -z "$$fail"
+tags-recursive:
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  test "$$subdir" = . || (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) tags); \
+	done
+tags: TAGS
+ID: $(HEADERS) $(SOURCES) $(LISP)
+	list='$(SOURCES) $(HEADERS)'; \
+	unique=`for i in $$list; do echo $$i; done | \
+	  awk '    { files[$$0] = 1; } \
+	       END { for (i in files) print i; }'`; \
+	here=`pwd` && cd $(srcdir) \
+	  && mkid -f$$here/ID $$unique $(LISP)
+TAGS: tags-recursive $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) $(LISP)
+	tags=; \
+	here=`pwd`; \
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+   if test "$$subdir" = .; then :; else \
+	    test -f $$subdir/TAGS && tags="$$tags -i $$here/$$subdir/TAGS"; \
+   fi; \
+	done; \
+	list='$(SOURCES) $(HEADERS)'; \
+	unique=`for i in $$list; do echo $$i; done | \
+	  awk '    { files[$$0] = 1; } \
+	       END { for (i in files) print i; }'`; \
+	test -z "$(ETAGS_ARGS)$$unique$(LISP)$$tags" \
+	  || (cd $(srcdir) && etags $(ETAGS_ARGS) $$tags  $$unique $(LISP) -o $$here/TAGS)
+mostlyclean-tags:
+clean-tags:
+distclean-tags:
+	-rm -f TAGS ID
+maintainer-clean-tags:
+distdir = $(PACKAGE)-$(VERSION)
+top_distdir = $(distdir)
+# This target untars the dist file and tries a VPATH configuration.  Then
+# it guarantees that the distribution is self-contained by making another
+# tarfile.
+distcheck: dist
+	-rm -rf $(distdir)
+	GZIP=$(GZIP_ENV) $(TAR) zxf $(distdir).tar.gz
+	mkdir $(distdir)/=build
+	mkdir $(distdir)/=inst
+	dc_install_base=`cd $(distdir)/=inst && pwd`; \
+	cd $(distdir)/=build \
+	  && ../configure --srcdir=.. --prefix=$$dc_install_base \
+	  && $(MAKE) $(AM_MAKEFLAGS) \
+	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
+	  && $(MAKE) $(AM_MAKEFLAGS) check \
+	  && $(MAKE) $(AM_MAKEFLAGS) install \
+	  && $(MAKE) $(AM_MAKEFLAGS) installcheck \
+	  && $(MAKE) $(AM_MAKEFLAGS) dist
+	-rm -rf $(distdir)
+	@banner="$(distdir).tar.gz is ready for distribution"; \
+	dashes=`echo "$$banner" | sed s/./=/g`; \
+	echo "$$dashes"; \
+	echo "$$banner"; \
+	echo "$$dashes"
+dist: distdir
+	-chmod -R a+r $(distdir)
+	GZIP=$(GZIP_ENV) $(TAR) chozf $(distdir).tar.gz $(distdir)
+	-rm -rf $(distdir)
+dist-all: distdir
+	-chmod -R a+r $(distdir)
+	GZIP=$(GZIP_ENV) $(TAR) chozf $(distdir).tar.gz $(distdir)
+	-rm -rf $(distdir)
+distdir: $(DISTFILES)
+	-rm -rf $(distdir)
+	mkdir $(distdir)
+	-chmod 777 $(distdir)
+	$(mkinstalldirs) $(distdir)/bin $(distdir)/doc $(distdir)/examples/genes \
+	   $(distdir)/ext $(distdir)/ext/lib/CompLearnLib \
+	   $(distdir)/scripts $(distdir)/scripts/debian \
+	   $(distdir)/tests
+	@for file in $(DISTFILES); do \
+	  d=$(srcdir); \
+	  if test -d $$d/$$file; then \
+	    cp -pr $$d/$$file $(distdir)/$$file; \
+	  else \
+	    test -f $(distdir)/$$file \
+	    || ln $$d/$$file $(distdir)/$$file 2> /dev/null \
+	    || cp -p $$d/$$file $(distdir)/$$file || :; \
+	  fi; \
+	done
+	for subdir in $(SUBDIRS); do \
+	  if test "$$subdir" = .; then :; else \
+	    test -d $(distdir)/$$subdir \
+	    || mkdir $(distdir)/$$subdir \
+	    || exit 1; \
+	    chmod 777 $(distdir)/$$subdir; \
+	    (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir=../$(distdir) distdir=../$(distdir)/$$subdir distdir) \
+	      || exit 1; \
+	  fi; \
+	done
+info-am:
+info: info-recursive
+dvi-am:
+dvi: dvi-recursive
+check-am: all-am
+check: check-recursive
+installcheck-am:
+installcheck: installcheck-recursive
+install-exec-am:
+install-exec: install-exec-recursive
+install-data-am:
+install-data: install-data-recursive
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+install: install-recursive
+uninstall-am:
+uninstall: uninstall-recursive
+all-am: Makefile
+all-redirect: all-recursive
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
+installdirs: installdirs-recursive
+installdirs-am:
+mostlyclean-generic:
+clean-generic:
+distclean-generic:
+	-rm -f Makefile $(CONFIG_CLEAN_FILES)
+	-rm -f config.cache config.log stamp-h stamp-h[0-9]*
+maintainer-clean-generic:
+mostlyclean-am:  mostlyclean-tags mostlyclean-generic
+mostlyclean: mostlyclean-recursive
+clean-am:  clean-tags clean-generic mostlyclean-am
+clean: clean-recursive
+distclean-am:  distclean-tags distclean-generic clean-am
+distclean: distclean-recursive
+	-rm -f config.status
+maintainer-clean-am:  maintainer-clean-tags maintainer-clean-generic \
+		distclean-am
+	@echo "This command is intended for maintainers to use;"
+	@echo "it deletes files that may require special tools to rebuild."
+maintainer-clean: maintainer-clean-recursive
+	-rm -f config.status
+.PHONY: install-data-recursive uninstall-data-recursive \
+install-exec-recursive uninstall-exec-recursive installdirs-recursive \
+uninstalldirs-recursive all-recursive check-recursive \
+installcheck-recursive info-recursive dvi-recursive \
+mostlyclean-recursive distclean-recursive clean-recursive \
+maintainer-clean-recursive tags tags-recursive mostlyclean-tags \
+distclean-tags clean-tags maintainer-clean-tags distdir info-am info \
+dvi-am dvi check check-am installcheck-am installcheck install-exec-am \
+install-exec install-data-am install-data install-am install \
+uninstall-am uninstall all-redirect all-am all installdirs-am \
+installdirs mostlyclean-generic distclean-generic clean-generic \
+maintainer-clean-generic clean mostlyclean distclean maintainer-clean
+clean:
+	rm -rf confstat*
+deb:
+	./scripts/makedeb.zsh
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT: