complearn 0.6.2

data/doc/Makefile.am

@@ -0,0 +1,11 @@
+SUBDIRS = man
+
+rdoc:
+	(cd .. ; rdoc --op doc/rdoc)
+
+www:
+	(cd .. ; rdoc --op www/rdoc)
+
+clean:
+	rm -rf rdoc
+

data/doc/Makefile.in

@@ -0,0 +1,286 @@
+# 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 = man
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_CLEAN_FILES = 
+DIST_COMMON =  Makefile.am Makefile.in
+
+
+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 doc/Makefile
+
+Makefile: $(srcdir)/Makefile.in  $(top_builddir)/config.status
+	cd $(top_builddir) \
+	  && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+
+
+# 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 = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
+
+subdir = doc
+
+distdir: $(DISTFILES)
+	@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 $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir=../$(top_distdir) distdir=../$(distdir)/$$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
+
+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
+
+.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
+
+
+rdoc:
+	(cd .. ; rdoc --op doc/rdoc)
+
+www:
+	(cd .. ; rdoc --op www/rdoc)
+
+clean:
+	rm -rf rdoc
+
+# 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/doc/devguide.txt

@@ -0,0 +1,15 @@
+For developers:
+
+This project requires automake at least version 1.7
+
+When adjusting Makefile.am's or configure.ac,
+make sure to use the following commands:
+aclocal
+autoconf
+automake
+./configure
+
+To make a new release package:
+
+make dist-gzip
+

data/doc/example.complearnrc

@@ -0,0 +1,14 @@
+--- 
+SingleProcess: true
+Symmetric: true
+UnpairedPenalty: 0.0
+MaxFailedTries: 10
+InputDir: in
+Hosts: 
+  - localhost
+OutputDir: out
+WorkDir: work
+InternalNodePrefix: n
+UseBestThirdOnly: false
+TreesPerTry: 1000
+Compressor: bzip2

data/doc/examples.txt

@@ -0,0 +1,35 @@
+In the examples/ directory, you will see a subdirectory called "genes".
+This contains the genetic sequences from the mitochondria of several well
+known animals.  To run these examples, first follow the instructions in
+readme.txt to compile and install this package. 
+
+Now, from the top-level directory execute the following command:
+
+ncdmatrix examples/genes > test.dm
+
+This command should create a distance matrix file called "test.dm"
+It contains a list of computed distances for each pair of animals
+represented.  Next, we must calculate a tree:
+
+maketree test.dm tree.dot
+
+This should take a moment to compute a best-fitting tree according to
+the distance matrix.  The tree is stored in a file called test.dot.
+(this is a graphviz-format file)
+
+Now, it's time to relabel the numbered external nodes according to the
+original species they represent.  This is most easily done using
+
+labeltree tree.dot examples/genes
+
+Finally, it's time to create a PostScript or PDF file to look at your
+tree results:
+
+neato tree.dot -Tps >tree.ps
+
+(this last step is optional)
+ps2pdf tree.ps tree.pdf
+
+Now, you should be able to view or print out these files, for example
+by using gv or xpdf.
+

data/doc/man/Makefile

@@ -0,0 +1,255 @@
+# 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
+
+man_MANS =  complearn.5 labeltree.1 makesvm.1 maketree.1 ncd.1 ncdmatrix.1 ncdvector.1
+
+
+EXTRA_DIST = $(man_MANS)
+mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+CONFIG_CLEAN_FILES = 
+man1dir = $(mandir)/man1
+man5dir = $(mandir)/man5
+MANS = $(man_MANS)
+
+NROFF = nroff
+DIST_COMMON =  Makefile.am Makefile.in
+
+
+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 doc/man/Makefile
+
+Makefile: $(srcdir)/Makefile.in  $(top_builddir)/config.status
+	cd $(top_builddir) \
+	  && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status
+
+
+install-man1:
+	$(mkinstalldirs) $(DESTDIR)$(man1dir)
+	@list='$(man1_MANS)'; \
+	l2='$(man_MANS)'; for i in $$l2; do \
+	  case "$$i" in \
+	    *.1*) list="$$list $$i" ;; \
+	  esac; \
+	done; \
+	for i in $$list; do \
+	  if test -f $(srcdir)/$$i; then file=$(srcdir)/$$i; \
+	  else file=$$i; fi; \
+	  ext=`echo $$i | sed -e 's/^.*\\.//'`; \
+	  inst=`echo $$i | sed -e 's/\\.[0-9a-z]*$$//'`; \
+	  inst=`echo $$inst | sed '$(transform)'`.$$ext; \
+	  echo " $(INSTALL_DATA) $$file $(DESTDIR)$(man1dir)/$$inst"; \
+	  $(INSTALL_DATA) $$file $(DESTDIR)$(man1dir)/$$inst; \
+	done
+
+uninstall-man1:
+	@list='$(man1_MANS)'; \
+	l2='$(man_MANS)'; for i in $$l2; do \
+	  case "$$i" in \
+	    *.1*) list="$$list $$i" ;; \
+	  esac; \
+	done; \
+	for i in $$list; do \
+	  ext=`echo $$i | sed -e 's/^.*\\.//'`; \
+	  inst=`echo $$i | sed -e 's/\\.[0-9a-z]*$$//'`; \
+	  inst=`echo $$inst | sed '$(transform)'`.$$ext; \
+	  echo " rm -f $(DESTDIR)$(man1dir)/$$inst"; \
+	  rm -f $(DESTDIR)$(man1dir)/$$inst; \
+	done
+
+install-man5:
+	$(mkinstalldirs) $(DESTDIR)$(man5dir)
+	@list='$(man5_MANS)'; \
+	l2='$(man_MANS)'; for i in $$l2; do \
+	  case "$$i" in \
+	    *.5*) list="$$list $$i" ;; \
+	  esac; \
+	done; \
+	for i in $$list; do \
+	  if test -f $(srcdir)/$$i; then file=$(srcdir)/$$i; \
+	  else file=$$i; fi; \
+	  ext=`echo $$i | sed -e 's/^.*\\.//'`; \
+	  inst=`echo $$i | sed -e 's/\\.[0-9a-z]*$$//'`; \
+	  inst=`echo $$inst | sed '$(transform)'`.$$ext; \
+	  echo " $(INSTALL_DATA) $$file $(DESTDIR)$(man5dir)/$$inst"; \
+	  $(INSTALL_DATA) $$file $(DESTDIR)$(man5dir)/$$inst; \
+	done
+
+uninstall-man5:
+	@list='$(man5_MANS)'; \
+	l2='$(man_MANS)'; for i in $$l2; do \
+	  case "$$i" in \
+	    *.5*) list="$$list $$i" ;; \
+	  esac; \
+	done; \
+	for i in $$list; do \
+	  ext=`echo $$i | sed -e 's/^.*\\.//'`; \
+	  inst=`echo $$i | sed -e 's/\\.[0-9a-z]*$$//'`; \
+	  inst=`echo $$inst | sed '$(transform)'`.$$ext; \
+	  echo " rm -f $(DESTDIR)$(man5dir)/$$inst"; \
+	  rm -f $(DESTDIR)$(man5dir)/$$inst; \
+	done
+install-man: $(MANS)
+	@$(NORMAL_INSTALL)
+	$(MAKE) $(AM_MAKEFLAGS) install-man1 install-man5
+uninstall-man:
+	@$(NORMAL_UNINSTALL)
+	$(MAKE) $(AM_MAKEFLAGS) uninstall-man1 uninstall-man5
+tags: TAGS
+TAGS:
+
+
+distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)
+
+subdir = doc/man
+
+distdir: $(DISTFILES)
+	@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
+info-am:
+info: info-am
+dvi-am:
+dvi: dvi-am
+check-am: all-am
+check: check-am
+installcheck-am:
+installcheck: installcheck-am
+install-exec-am:
+install-exec: install-exec-am
+
+install-data-am: install-man
+install-data: install-data-am
+
+install-am: all-am
+	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+install: install-am
+uninstall-am: uninstall-man
+uninstall: uninstall-am
+all-am: Makefile $(MANS)
+all-redirect: all-am
+install-strip:
+	$(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
+installdirs:
+	$(mkinstalldirs)  $(DESTDIR)$(mandir)/man1 $(DESTDIR)$(mandir)/man5
+
+
+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-generic
+
+mostlyclean: mostlyclean-am
+
+clean-am:  clean-generic mostlyclean-am
+
+clean: clean-am
+
+distclean-am:  distclean-generic clean-am
+
+distclean: distclean-am
+
+maintainer-clean-am:  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-am
+
+.PHONY: install-man1 uninstall-man1 install-man5 uninstall-man5 \
+install-man uninstall-man 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 mostlyclean-generic \
+distclean-generic clean-generic maintainer-clean-generic clean \
+mostlyclean distclean maintainer-clean
+
+
+# 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: