# Makefile.in generated automatically by automake 1.4-p6 from Makefile.am

# Copyright (C) 1994, 1995-8, 1999, 2001 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 = :
host_alias = @host_alias@
host_triplet = @host@
CC = @CC@
GLIB_CONFIG = @GLIB_CONFIG@
HAVE_LIB = @HAVE_LIB@
LIB = @LIB@
LTLIB = @LTLIB@
MAKEINFO = @MAKEINFO@
PACKAGE = @PACKAGE@
PKG_CONFIG = @PKG_CONFIG@
VERSION = @VERSION@
codegen_extra_ldadd = @codegen_extra_ldadd@
codegen_extra_sources = @codegen_extra_sources@
custom_guint64_format = @custom_guint64_format@
datarootdir = @datarootdir@
glib_cflags = @glib_cflags@
glib_libs = @glib_libs@
host = @host@
installed_util_list = @installed_util_list@
source_root_dir = @source_root_dir@
use_pthreads = @use_pthreads@

TESTS = region.test c4.test alignment.test codegen.test optimal.test          layout.test viterbi.test opair.test subopt.test cgutil.test


noinst_PROGRAMS = $(TESTS)

INCLUDES = -I$(top_srcdir)/src/struct                           -I$(top_srcdir)/src/comparison                       -I$(top_srcdir)/src/sequence                         -I$(top_srcdir)/src/general                          -DSOURCE_ROOT_DIR="\"@source_root_dir@\""            -DGLIB_CFLAGS="\"@glib_cflags@\""                    -DHOSTTYPE="\"@host@\""


noinst_HEADERS = region.h c4.h alignment.h codegen.h optimal.h                   layout.h viterbi.h opair.h subopt.h                  cgutil.h


region_test_SOURCES = region.test.c region.c

c4_test_SOURCES = c4.test.c c4.c region.c
c4_test_LDADD = $(top_srcdir)/src/struct/matrix.o                      $(top_srcdir)/src/general/threadref.o


SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o                 $(top_srcdir)/src/struct/matrix.o                      $(top_srcdir)/src/sequence/sequence.o                  $(top_srcdir)/src/sequence/alphabet.o                  $(top_srcdir)/src/sequence/splice.o                    $(top_srcdir)/src/sequence/translate.o                 $(top_srcdir)/src/general/argument.o                   $(top_srcdir)/src/general/lineparse.o                  -lm


ALIGNMENT_OBJ = $(top_srcdir)/src/comparison/match.o                     $(top_srcdir)/src/sequence/codonsubmat.o                 $(top_srcdir)/src/sequence/submat.o                      $(top_srcdir)/src/general/threadref.o                    $(SEQUENCE_OBJ)

alignment_test_SOURCES = alignment.test.c alignment.c c4.c region.c
alignment_test_LDADD = $(ALIGNMENT_OBJ)

codegen_test_SOURCES = codegen.test.c codegen.c
codegen_test_LDADD = $(top_srcdir)/src/general/argument.o

cgutil_test_SOURCES = cgutil.test.c cgutil.c codegen.c c4.c region.c
cgutil_test_LDADD = $(top_srcdir)/src/general/argument.o                      $(top_srcdir)/src/struct/matrix.o                         $(top_srcdir)/src/general/threadref.o


viterbi_test_SOURCES = viterbi.test.c viterbi.c c4.c region.c                        alignment.c codegen.c layout.c subopt.c                        cgutil.c

viterbi_test_LDADD = $(top_srcdir)/src/struct/slist.o                           $(top_srcdir)/src/struct/recyclebin.o                      $(top_srcdir)/src/struct/rangetree.o                       $(ALIGNMENT_OBJ)


optimal_test_SOURCES = optimal.test.c optimal.c c4.c alignment.c                        codegen.c region.c layout.c viterbi.c                            subopt.c cgutil.c

optimal_test_LDADD = $(top_srcdir)/src/struct/slist.o                           $(top_srcdir)/src/struct/recyclebin.o                      $(top_srcdir)/src/struct/rangetree.o                       $(ALIGNMENT_OBJ)


layout_test_SOURCES = layout.test.c layout.c
layout_test_LDADD = $(top_srcdir)/src/struct/matrix.o

opair_test_SOURCES = opair.test.c opair.c optimal.c c4.c alignment.c                      codegen.c region.c layout.c viterbi.c subopt.c                       cgutil.c

opair_test_LDADD = $(top_srcdir)/src/struct/slist.o                         $(top_srcdir)/src/struct/recyclebin.o                    $(top_srcdir)/src/struct/rangetree.o                     $(ALIGNMENT_OBJ)


subopt_test_SOURCES = subopt.test.c subopt.c region.c
subopt_test_LDADD = $(top_srcdir)/src/struct/rangetree.o                     $(top_srcdir)/src/struct/recyclebin.o


# Files to clear away

MAINTAINERCLEANFILES = Makefile.in
mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
CONFIG_CLEAN_FILES = 
PROGRAMS =  $(noinst_PROGRAMS)


DEFS = @DEFS@ -I. -I$(srcdir) 
CPPFLAGS = @CPPFLAGS@
LDFLAGS = @LDFLAGS@
LIBS = @LIBS@
region_test_OBJECTS =  region.test.o region.o
region_test_LDADD = $(LDADD)
region_test_DEPENDENCIES = 
region_test_LDFLAGS = 
c4_test_OBJECTS =  c4.test.o c4.o region.o
c4_test_DEPENDENCIES =  $(top_srcdir)/src/struct/matrix.o \
$(top_srcdir)/src/general/threadref.o
c4_test_LDFLAGS = 
alignment_test_OBJECTS =  alignment.test.o alignment.o c4.o region.o
alignment_test_DEPENDENCIES =  $(top_srcdir)/src/comparison/match.o \
$(top_srcdir)/src/sequence/codonsubmat.o \
$(top_srcdir)/src/sequence/submat.o \
$(top_srcdir)/src/general/threadref.o \
$(top_srcdir)/src/struct/sparsecache.o \
$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
$(top_srcdir)/src/sequence/alphabet.o \
$(top_srcdir)/src/sequence/splice.o \
$(top_srcdir)/src/sequence/translate.o \
$(top_srcdir)/src/general/argument.o \
$(top_srcdir)/src/general/lineparse.o
alignment_test_LDFLAGS = 
codegen_test_OBJECTS =  codegen.test.o codegen.o
codegen_test_DEPENDENCIES =  $(top_srcdir)/src/general/argument.o
codegen_test_LDFLAGS = 
optimal_test_OBJECTS =  optimal.test.o optimal.o c4.o alignment.o \
codegen.o region.o layout.o viterbi.o subopt.o cgutil.o
optimal_test_DEPENDENCIES =  $(top_srcdir)/src/struct/slist.o \
$(top_srcdir)/src/struct/recyclebin.o \
$(top_srcdir)/src/struct/rangetree.o \
$(top_srcdir)/src/comparison/match.o \
$(top_srcdir)/src/sequence/codonsubmat.o \
$(top_srcdir)/src/sequence/submat.o \
$(top_srcdir)/src/general/threadref.o \
$(top_srcdir)/src/struct/sparsecache.o \
$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
$(top_srcdir)/src/sequence/alphabet.o \
$(top_srcdir)/src/sequence/splice.o \
$(top_srcdir)/src/sequence/translate.o \
$(top_srcdir)/src/general/argument.o \
$(top_srcdir)/src/general/lineparse.o
optimal_test_LDFLAGS = 
layout_test_OBJECTS =  layout.test.o layout.o
layout_test_DEPENDENCIES =  $(top_srcdir)/src/struct/matrix.o
layout_test_LDFLAGS = 
viterbi_test_OBJECTS =  viterbi.test.o viterbi.o c4.o region.o \
alignment.o codegen.o layout.o subopt.o cgutil.o
viterbi_test_DEPENDENCIES =  $(top_srcdir)/src/struct/slist.o \
$(top_srcdir)/src/struct/recyclebin.o \
$(top_srcdir)/src/struct/rangetree.o \
$(top_srcdir)/src/comparison/match.o \
$(top_srcdir)/src/sequence/codonsubmat.o \
$(top_srcdir)/src/sequence/submat.o \
$(top_srcdir)/src/general/threadref.o \
$(top_srcdir)/src/struct/sparsecache.o \
$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
$(top_srcdir)/src/sequence/alphabet.o \
$(top_srcdir)/src/sequence/splice.o \
$(top_srcdir)/src/sequence/translate.o \
$(top_srcdir)/src/general/argument.o \
$(top_srcdir)/src/general/lineparse.o
viterbi_test_LDFLAGS = 
opair_test_OBJECTS =  opair.test.o opair.o optimal.o c4.o alignment.o \
codegen.o region.o layout.o viterbi.o subopt.o cgutil.o
opair_test_DEPENDENCIES =  $(top_srcdir)/src/struct/slist.o \
$(top_srcdir)/src/struct/recyclebin.o \
$(top_srcdir)/src/struct/rangetree.o \
$(top_srcdir)/src/comparison/match.o \
$(top_srcdir)/src/sequence/codonsubmat.o \
$(top_srcdir)/src/sequence/submat.o \
$(top_srcdir)/src/general/threadref.o \
$(top_srcdir)/src/struct/sparsecache.o \
$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
$(top_srcdir)/src/sequence/alphabet.o \
$(top_srcdir)/src/sequence/splice.o \
$(top_srcdir)/src/sequence/translate.o \
$(top_srcdir)/src/general/argument.o \
$(top_srcdir)/src/general/lineparse.o
opair_test_LDFLAGS = 
subopt_test_OBJECTS =  subopt.test.o subopt.o region.o
subopt_test_DEPENDENCIES =  $(top_srcdir)/src/struct/rangetree.o \
$(top_srcdir)/src/struct/recyclebin.o
subopt_test_LDFLAGS = 
cgutil_test_OBJECTS =  cgutil.test.o cgutil.o codegen.o c4.o region.o
cgutil_test_DEPENDENCIES =  $(top_srcdir)/src/general/argument.o \
$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/general/threadref.o
cgutil_test_LDFLAGS = 
CFLAGS = @CFLAGS@
COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(LDFLAGS) -o $@
HEADERS =  $(noinst_HEADERS)

DIST_COMMON =  Makefile.am Makefile.in


DISTFILES = $(DIST_COMMON) $(SOURCES) $(HEADERS) $(TEXINFOS) $(EXTRA_DIST)

TAR = tar
GZIP_ENV = --best
SOURCES = $(region_test_SOURCES) $(c4_test_SOURCES) $(alignment_test_SOURCES) $(codegen_test_SOURCES) $(optimal_test_SOURCES) $(layout_test_SOURCES) $(viterbi_test_SOURCES) $(opair_test_SOURCES) $(subopt_test_SOURCES) $(cgutil_test_SOURCES)
OBJECTS = $(region_test_OBJECTS) $(c4_test_OBJECTS) $(alignment_test_OBJECTS) $(codegen_test_OBJECTS) $(optimal_test_OBJECTS) $(layout_test_OBJECTS) $(viterbi_test_OBJECTS) $(opair_test_OBJECTS) $(subopt_test_OBJECTS) $(cgutil_test_OBJECTS)

all: all-redirect
.SUFFIXES:
.SUFFIXES: .S .c .o .s
$(srcdir)/Makefile.in: Makefile.am $(top_srcdir)/configure.in $(ACLOCAL_M4) 
	cd $(top_srcdir) && $(AUTOMAKE) --gnu --include-deps src/c4/Makefile

Makefile: $(srcdir)/Makefile.in  $(top_builddir)/config.status
	cd $(top_builddir) \
	  && CONFIG_FILES=$(subdir)/$@ CONFIG_HEADERS= $(SHELL) ./config.status


mostlyclean-noinstPROGRAMS:

clean-noinstPROGRAMS:
	-test -z "$(noinst_PROGRAMS)" || rm -f $(noinst_PROGRAMS)

distclean-noinstPROGRAMS:

maintainer-clean-noinstPROGRAMS:

.c.o:
	$(COMPILE) -c $<

.s.o:
	$(COMPILE) -c $<

.S.o:
	$(COMPILE) -c $<

mostlyclean-compile:
	-rm -f *.o core *.core

clean-compile:

distclean-compile:
	-rm -f *.tab.c

maintainer-clean-compile:

region.test: $(region_test_OBJECTS) $(region_test_DEPENDENCIES)
	@rm -f region.test
	$(LINK) $(region_test_LDFLAGS) $(region_test_OBJECTS) $(region_test_LDADD) $(LIBS)

c4.test: $(c4_test_OBJECTS) $(c4_test_DEPENDENCIES)
	@rm -f c4.test
	$(LINK) $(c4_test_LDFLAGS) $(c4_test_OBJECTS) $(c4_test_LDADD) $(LIBS)

alignment.test: $(alignment_test_OBJECTS) $(alignment_test_DEPENDENCIES)
	@rm -f alignment.test
	$(LINK) $(alignment_test_LDFLAGS) $(alignment_test_OBJECTS) $(alignment_test_LDADD) $(LIBS)

codegen.test: $(codegen_test_OBJECTS) $(codegen_test_DEPENDENCIES)
	@rm -f codegen.test
	$(LINK) $(codegen_test_LDFLAGS) $(codegen_test_OBJECTS) $(codegen_test_LDADD) $(LIBS)

optimal.test: $(optimal_test_OBJECTS) $(optimal_test_DEPENDENCIES)
	@rm -f optimal.test
	$(LINK) $(optimal_test_LDFLAGS) $(optimal_test_OBJECTS) $(optimal_test_LDADD) $(LIBS)

layout.test: $(layout_test_OBJECTS) $(layout_test_DEPENDENCIES)
	@rm -f layout.test
	$(LINK) $(layout_test_LDFLAGS) $(layout_test_OBJECTS) $(layout_test_LDADD) $(LIBS)

viterbi.test: $(viterbi_test_OBJECTS) $(viterbi_test_DEPENDENCIES)
	@rm -f viterbi.test
	$(LINK) $(viterbi_test_LDFLAGS) $(viterbi_test_OBJECTS) $(viterbi_test_LDADD) $(LIBS)

opair.test: $(opair_test_OBJECTS) $(opair_test_DEPENDENCIES)
	@rm -f opair.test
	$(LINK) $(opair_test_LDFLAGS) $(opair_test_OBJECTS) $(opair_test_LDADD) $(LIBS)

subopt.test: $(subopt_test_OBJECTS) $(subopt_test_DEPENDENCIES)
	@rm -f subopt.test
	$(LINK) $(subopt_test_LDFLAGS) $(subopt_test_OBJECTS) $(subopt_test_LDADD) $(LIBS)

cgutil.test: $(cgutil_test_OBJECTS) $(cgutil_test_DEPENDENCIES)
	@rm -f cgutil.test
	$(LINK) $(cgutil_test_LDFLAGS) $(cgutil_test_OBJECTS) $(cgutil_test_LDADD) $(LIBS)

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:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) $(LISP)
	tags=; \
	here=`pwd`; \
	list='$(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)$$tags" \
	  || (cd $(srcdir) && etags -o $$here/TAGS $(ETAGS_ARGS) $$tags  $$unique $(LISP))

mostlyclean-tags:

clean-tags:

distclean-tags:
	-rm -f TAGS ID

maintainer-clean-tags:

distdir = $(top_builddir)/$(PACKAGE)-$(VERSION)/$(subdir)

subdir = src/c4

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
check-TESTS: $(TESTS)
	@failed=0; all=0; \
	srcdir=$(srcdir); export srcdir; \
	for tst in $(TESTS); do \
	  if test -f $$tst; then dir=.; \
	  else dir="$(srcdir)"; fi; \
	  if $(TESTS_ENVIRONMENT) $$dir/$$tst; then \
	    all=`expr $$all + 1`; \
	    echo "PASS: $$tst"; \
	  elif test $$? -ne 77; then \
	    all=`expr $$all + 1`; \
	    failed=`expr $$failed + 1`; \
	    echo "FAIL: $$tst"; \
	  fi; \
	done; \
	if test "$$failed" -eq 0; then \
	  banner="All $$all tests passed"; \
	else \
	  banner="$$failed of $$all tests failed"; \
	fi; \
	dashes=`echo "$$banner" | sed s/./=/g`; \
	echo "$$dashes"; \
	echo "$$banner"; \
	echo "$$dashes"; \
	test "$$failed" -eq 0
info-am:
info: info-am
dvi-am:
dvi: dvi-am
check-am: all-am
	$(MAKE) $(AM_MAKEFLAGS) check-TESTS
check: check-am
installcheck-am:
installcheck: installcheck-am
install-exec-am:
install-exec: install-exec-am

install-data-am:
install-data: install-data-am

install-am: all-am
	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
install: install-am
uninstall-am:
uninstall: uninstall-am
all-am: Makefile $(PROGRAMS) $(HEADERS)
all-redirect: all-am
install-strip:
	$(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install
installdirs:


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:
	-test -z "$(MAINTAINERCLEANFILES)" || rm -f $(MAINTAINERCLEANFILES)
mostlyclean-am:  mostlyclean-noinstPROGRAMS mostlyclean-compile \
		mostlyclean-tags mostlyclean-generic

mostlyclean: mostlyclean-am

clean-am:  clean-noinstPROGRAMS clean-compile clean-tags clean-generic \
		mostlyclean-am

clean: clean-am

distclean-am:  distclean-noinstPROGRAMS distclean-compile distclean-tags \
		distclean-generic clean-am

distclean: distclean-am

maintainer-clean-am:  maintainer-clean-noinstPROGRAMS \
		maintainer-clean-compile 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-am

.PHONY: mostlyclean-noinstPROGRAMS distclean-noinstPROGRAMS \
clean-noinstPROGRAMS maintainer-clean-noinstPROGRAMS \
mostlyclean-compile distclean-compile clean-compile \
maintainer-clean-compile tags mostlyclean-tags distclean-tags \
clean-tags maintainer-clean-tags distdir check-TESTS 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: