complearn 0.6.2

data/Makefile

@@ -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

@@ -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

@@ -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: