# Makefile.in generated by automake 1.9.6 from Makefile.am.
# PROGRAMS/Makefile.  Generated from Makefile.in by configure.

# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
# 2003, 2004, 2005  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.




srcdir = .
top_srcdir = ..

pkgdatadir = $(datadir)/FIRE
pkglibdir = $(libdir)/FIRE
pkgincludedir = $(includedir)/FIRE
top_builddir = ..
am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
INSTALL = /usr/bin/install -c
install_sh_DATA = $(install_sh) -c -m 644
install_sh_PROGRAM = $(install_sh) -c
install_sh_SCRIPT = $(install_sh) -c
INSTALL_HEADER = $(INSTALL_DATA)
transform = $(program_transform_name)
NORMAL_INSTALL = :
PRE_INSTALL = :
POST_INSTALL = :
NORMAL_UNINSTALL = :
PRE_UNINSTALL = :
POST_UNINSTALL = :
build_triplet = x86_64-unknown-linux-gnu
host_triplet = x86_64-unknown-linux-gnu
bin_PROGRAMS = genregexp$(EXEEXT) mi_find$(EXEEXT) \
	mi_optimize$(EXEEXT) mi_dist$(EXEEXT) mi_signif$(EXEEXT) \
	mi_optimize_1$(EXEEXT) mi_dist_mbins$(EXEEXT)  \
	mi_optimize_slow$(EXEEXT) binom_test_greater$(EXEEXT) \
	recompare$(EXEEXT) mi_combine$(EXEEXT) myhypergeom$(EXEEXT) \
	MyCompareAce$(EXEEXT) mi_motif_compare$(EXEEXT) \
	mi_optimize_motif_WM$(EXEEXT) mi_optimize_motif$(EXEEXT) \
	mi_optimize_X$(EXEEXT) mi_optimize_maxdeg_X$(EXEEXT) \
	mi_combine_mbins$(EXEEXT) mi_motif_compare_1$(EXEEXT) 
subdir = PROGRAMS
DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
	$(srcdir)/config.h.in
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/configure.ac
am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
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mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = config.h
CONFIG_CLEAN_FILES =
LIBRARIES = $(noinst_LIBRARIES)
AR = ar
ARFLAGS = cru
libfire_a_AR = $(AR) $(ARFLAGS)
libfire_a_LIBADD =
am_libfire_a_OBJECTS = statistics.$(OBJEXT) dataio.$(OBJEXT) \
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am__installdirs = "$(DESTDIR)$(bindir)"
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MyCompareAce_OBJECTS = $(am_MyCompareAce_OBJECTS)
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am_genregexp_OBJECTS = genregexp.$(OBJEXT)
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mi_combine_OBJECTS = $(am_mi_combine_OBJECTS)
mi_combine_LDADD = $(LDADD)
mi_combine_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
am_mi_dist_OBJECTS = mi_dist.$(OBJEXT)
mi_dist_OBJECTS = $(am_mi_dist_OBJECTS)
mi_dist_LDADD = $(LDADD)
mi_dist_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
am_mi_combine_mbins_OBJECTS = mi_combine_mbins.$(OBJEXT)
mi_combine_mbins_OBJECTS = $(am_mi_combine_mbins_OBJECTS)
mi_combine_mbins_LDADD = $(LDADD)
mi_combine_mbins_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
am_mi_dist_mbins_OBJECTS = mi_dist_mbins.$(OBJEXT)
mi_dist_mbins_OBJECTS = $(am_mi_dist_mbins_OBJECTS)
mi_dist_mbins_LDADD = $(LDADD)
mi_dist_mbins_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
am_mi_find_OBJECTS = mi_find.$(OBJEXT)
mi_find_OBJECTS = $(am_mi_find_OBJECTS)
mi_find_LDADD = $(LDADD)
mi_find_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
am_mi_motif_compare_OBJECTS = mi_motif_compare.$(OBJEXT)
mi_motif_compare_OBJECTS = $(am_mi_motif_compare_OBJECTS)
mi_motif_compare_LDADD = $(LDADD)
mi_motif_compare_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
am_mi_motif_compare_1_OBJECTS = mi_motif_compare_1.$(OBJEXT)
mi_motif_compare_1_OBJECTS = $(am_mi_motif_compare_1_OBJECTS)
mi_motif_compare_1_LDADD = $(LDADD)
mi_motif_compare_1_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
am_mi_optimize_1_OBJECTS = mi_optimize_1.$(OBJEXT)
mi_optimize_1_OBJECTS = $(am_mi_optimize_1_OBJECTS)
mi_optimize_1_LDADD = $(LDADD)
mi_optimize_1_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
am_mi_optimize_X_OBJECTS = mi_optimize_X.$(OBJEXT)
mi_optimize_X_OBJECTS = $(am_mi_optimize_X_OBJECTS)
mi_optimize_X_LDADD = $(LDADD)
mi_optimize_X_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
am_mi_optimize_maxdeg_X_OBJECTS = mi_optimize_maxdeg_X.$(OBJEXT)
mi_optimize_maxdeg_X_OBJECTS = $(am_mi_optimize_maxdeg_X_OBJECTS)
mi_optimize_maxdeg_X_LDADD = $(LDADD)
mi_optimize_maxdeg_X_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
am_mi_optimize_OBJECTS = mi_optimize.$(OBJEXT)
mi_optimize_OBJECTS = $(am_mi_optimize_OBJECTS)
mi_optimize_LDADD = $(LDADD)
mi_optimize_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
am_mi_optimize_motif_OBJECTS = mi_optimize_motif.$(OBJEXT)
mi_optimize_motif_OBJECTS = $(am_mi_optimize_motif_OBJECTS)
mi_optimize_motif_LDADD = $(LDADD)
mi_optimize_motif_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
am_mi_optimize_motif_WM_OBJECTS = mi_optimize_motif_WM.$(OBJEXT)
mi_optimize_motif_WM_OBJECTS = $(am_mi_optimize_motif_WM_OBJECTS)
mi_optimize_motif_WM_LDADD = $(LDADD)
mi_optimize_motif_WM_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
am_mi_optimize_slow_OBJECTS = mi_optimize_slow.$(OBJEXT)
mi_optimize_slow_OBJECTS = $(am_mi_optimize_slow_OBJECTS)
mi_optimize_slow_LDADD = $(LDADD)
mi_optimize_slow_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
am_mi_signif_OBJECTS = mi_signif.$(OBJEXT)
mi_signif_OBJECTS = $(am_mi_signif_OBJECTS)
mi_signif_LDADD = $(LDADD)
mi_signif_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
am_myhypergeom_OBJECTS = myhypergeom.$(OBJEXT)
myhypergeom_OBJECTS = $(am_myhypergeom_OBJECTS)
myhypergeom_DEPENDENCIES =
am_recompare_OBJECTS = recompare.$(OBJEXT)
recompare_OBJECTS = $(am_recompare_OBJECTS)
recompare_LDADD = $(LDADD)
recompare_DEPENDENCIES = libfire.a $(am__DEPENDENCIES_1)
DEFAULT_INCLUDES = -I. -I$(srcdir) -I.
depcomp = $(SHELL) $(top_srcdir)/depcomp
am__depfiles_maybe = depfiles
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
	$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
CCLD = $(CC)
LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@
SOURCES = $(libfire_a_SOURCES) $(MyCompareAce_SOURCES) \
	$(binom_test_greater_SOURCES) $(genregexp_SOURCES) \
	$(mi_combine_SOURCES) $(mi_dist_SOURCES) $(mi_find_SOURCES) \
	$(mi_combine_mbins_SOURCES) $(mi_dist_mbins_SOURCES) \
	$(mi_motif_compare_SOURCES) $(mi_optimize_SOURCES) \
	$(mi_motif_compare_1_SOURCES) $(mi_optimize_1_SOURCES) \
	$(mi_optimize_motif_SOURCES) $(mi_optimize_motif_WM_SOURCES) \
	$(mi_optimize_X_SOURCES) $(mi_optimize_maxdeg_X_SOURCES) \
	$(mi_optimize_slow_SOURCES) $(mi_signif_SOURCES) \
	$(myhypergeom_SOURCES) $(recompare_SOURCES)
DIST_SOURCES = $(libfire_a_SOURCES) $(MyCompareAce_SOURCES) \
	$(binom_test_greater_SOURCES) $(genregexp_SOURCES) \
	$(mi_combine_SOURCES) $(mi_dist_SOURCES) $(mi_find_SOURCES) \
	$(mi_combine_mbins_SOURCES) $(mi_dist_mbins_SOURCES) \
	$(mi_motif_compare_SOURCES) $(mi_optimize_SOURCES) \
	$(mi_motif_compare_1_SOURCES) $(mi_optimize_1_SOURCES) \
	$(mi_optimize_motif_SOURCES) $(mi_optimize_motif_WM_SOURCES) \
	$(mi_optimize_X_SOURCES) $(mi_optimize_maxdeg_X_SOURCES) \
	$(mi_optimize_slow_SOURCES) $(mi_signif_SOURCES) \
	$(myhypergeom_SOURCES) $(recompare_SOURCES)
ETAGS = etags
CTAGS = ctags
DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
ACLOCAL = ${SHELL} /media/data2/shares/FIRE-2.1/missing --run aclocal-1.9
AMDEP_FALSE = #
AMDEP_TRUE = 
AMTAR = ${SHELL} /media/data2/shares/FIRE-2.1/missing --run tar
AUTOCONF = ${SHELL} /media/data2/shares/FIRE-2.1/missing --run autoconf
AUTOHEADER = ${SHELL} /media/data2/shares/FIRE-2.1/missing --run autoheader
AUTOMAKE = ${SHELL} /media/data2/shares/FIRE-2.1/missing --run automake-1.9
AWK = mawk
CC = gcc
CCDEPMODE = depmode=gcc3
CFLAGS = -g -O2
CP = /bin/cp
CPP = gcc -E
CPPFLAGS = 
CYGPATH_W = echo
DEFS = -DHAVE_CONFIG_H
DEPDIR = .deps
ECHO_C = 
ECHO_N = -n
ECHO_T = 
EGREP = /bin/grep -E
EXEEXT = 
FIND = /usr/bin/find
HAVE_SUNMATH_FALSE = 
HAVE_SUNMATH_TRUE = #
INSTALL_DATA = ${INSTALL} -m 644
INSTALL_PROGRAM = ${INSTALL}
INSTALL_SCRIPT = ${INSTALL}
INSTALL_STRIP_PROGRAM = ${SHELL} $(install_sh) -c -s
LDFLAGS = 
LIBOBJS = 
LIBS = 
LTLIBOBJS = 
MAKEINFO = ${SHELL} /media/data2/shares/FIRE-2.1/missing --run makeinfo
OBJEXT = o
PACKAGE = FIRE
PACKAGE_BUGREPORT = elemento@princeton.edu
PACKAGE_NAME = FIRE
PACKAGE_STRING = FIRE 1.1
PACKAGE_TARNAME = FIRE
PACKAGE_VERSION = 1.1
PATH_SEPARATOR = :
PCRELIB = -lpcre
PCRELOCALLIB = yes
PERL = /usr/bin/perl
RANLIB = ranlib
SET_MAKE = 
SHELL = /bin/bash
STRIP = 
USE_MYHYPERGEOM_FALSE = 
USE_MYHYPERGEOM_TRUE = #
VERSION = 1.1
ac_ct_CC = gcc
ac_ct_RANLIB = @ac_ct_RANLIB@
ac_ct_STRIP = @ac_ct_STRIP@
am__fastdepCC_FALSE = #
am__fastdepCC_TRUE = 
am__include = include
am__leading_dot = .
am__quote = 
am__tar = ${AMTAR} chof - "$$tardir"
am__untar = ${AMTAR} xf -
bindir = ${exec_prefix}/bin
build = x86_64-unknown-linux-gnu
build_alias = 
build_cpu = x86_64
build_os = linux-gnu
build_vendor = unknown
datadir = ${prefix}/share
exec_prefix = ${prefix}
host = x86_64-unknown-linux-gnu
host_alias = 
host_cpu = x86_64
host_os = linux-gnu
host_vendor = unknown
includedir = ${prefix}/include
infodir = ${prefix}/share/info
install_sh = /media/data2/shares/FIRE-2.1/install-sh
libdir = ${exec_prefix}/lib
libexecdir = ${exec_prefix}/libexec
localstatedir = ${prefix}/var
mandir = ${prefix}/share/man
mkdir_p = mkdir -p --
oldincludedir = /usr/include
prefix = /usr/local
program_transform_name = s,x,x,
sbindir = ${exec_prefix}/sbin
sharedstatedir = ${prefix}/com
sysconfdir = ${prefix}/etc
target_alias = 

# includes and libraries for all
AM_CPPFLAGS = -I`pwd`/../modules/include -g
LDADD_SUNMATH = 
#LDADD_SUNMATH = -lsunmath
LDADD = libfire.a -L`pwd`/../modules/lib -lpcre -lm $(LDADD_SUNMATH)

# programs
mi_find_SOURCES = mi_find.c
mi_optimize_SOURCES = mi_optimize.c
mi_optimize_slow_SOURCES = mi_optimize_slow.c
mi_signif_SOURCES = mi_signif.c
mi_dist_SOURCES = mi_dist.c
mi_combine_SOURCES = mi_combine.c
mi_motif_compare_SOURCES = mi_motif_compare.c
mi_optimize_1_SOURCES = mi_optimize_1.c
mi_optimize_X_SOURCES = mi_optimize_X.c
mi_optimize_maxdeg_X_SOURCES = mi_optimize_maxdeg_X.c
mi_dist_mbins_SOURCES = mi_dist_mbins.c
mi_combine_mbins_SOURCES = mi_combine_mbins.c
mi_motif_compare_1_SOURCES = mi_motif_compare_1.c
mi_optimize_motif_WM_SOURCES = mi_optimize_motif_WM.c
mi_optimize_motif_SOURCES = mi_optimize_motif.c
binom_test_greater_SOURCES = binom_test_greater.c beta.c toms708.c d1mach.c i1mach.c rcode.h beta.h 
genregexp_SOURCES = genregexp.c
recompare_SOURCES = recompare.c
myhypergeom_SOURCES = myhypergeom.c
myhypergeom_LDADD = -lm
MyCompareAce_SOURCES = MyCompareAce.c
MyCompareAce_LDADD = -lm
noinst_LIBRARIES = libfire.a
libfire_a_SOURCES = statistics.h statistics.c dataio.h dataio.c prefix.c prefix.h information.c information.h mi_library.c mi_library.h sequences.c sequences.h regexp.c regexp.h

# to include in distribution
EXTRA_DIST = pcre-7.4
all: config.h
	$(MAKE) $(AM_MAKEFLAGS) all-am

.SUFFIXES:
.SUFFIXES: .c .o .obj
$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
	@for dep in $?; do \
	  case '$(am__configure_deps)' in \
	    *$$dep*) \
	      cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh \
		&& exit 0; \
	      exit 1;; \
	  esac; \
	done; \
	echo ' cd $(top_srcdir) && $(AUTOMAKE) --foreign  PROGRAMS/Makefile'; \
	cd $(top_srcdir) && \
	  $(AUTOMAKE) --foreign  PROGRAMS/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
	@case '$?' in \
	  *config.status*) \
	    cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
	  *) \
	    echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
	    cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
	esac;

$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh

$(top_srcdir)/configure:  $(am__configure_deps)
	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh

config.h: stamp-h1
	@if test ! -f $@; then \
	  rm -f stamp-h1; \
	  $(MAKE) stamp-h1; \
	else :; fi

stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
	@rm -f stamp-h1
	cd $(top_builddir) && $(SHELL) ./config.status PROGRAMS/config.h
$(srcdir)/config.h.in:  $(am__configure_deps) 
	cd $(top_srcdir) && $(AUTOHEADER)
	rm -f stamp-h1
	touch $@

distclean-hdr:
	-rm -f config.h stamp-h1

clean-noinstLIBRARIES:
	-test -z "$(noinst_LIBRARIES)" || rm -f $(noinst_LIBRARIES)
libfire.a: $(libfire_a_OBJECTS) $(libfire_a_DEPENDENCIES) 
	-rm -f libfire.a
	$(libfire_a_AR) libfire.a $(libfire_a_OBJECTS) $(libfire_a_LIBADD)
	$(RANLIB) libfire.a
install-binPROGRAMS: $(bin_PROGRAMS)
	@$(NORMAL_INSTALL)
	test -z "$(bindir)" || $(mkdir_p) "$(DESTDIR)$(bindir)"
	@list='$(bin_PROGRAMS)'; for p in $$list; do \
	  p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
	  if test -f $$p \
	  ; then \
	    f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \
	   echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) '$$p' '$(DESTDIR)$(bindir)/$$f'"; \
	   $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) "$$p" "$(DESTDIR)$(bindir)/$$f" || exit 1; \
	  else :; fi; \
	done

uninstall-binPROGRAMS:
	@$(NORMAL_UNINSTALL)
	@list='$(bin_PROGRAMS)'; for p in $$list; do \
	  f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \
	  echo " rm -f '$(DESTDIR)$(bindir)/$$f'"; \
	  rm -f "$(DESTDIR)$(bindir)/$$f"; \
	done

clean-binPROGRAMS:
	-test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
MyCompareAce$(EXEEXT): $(MyCompareAce_OBJECTS) $(MyCompareAce_DEPENDENCIES) 
	@rm -f MyCompareAce$(EXEEXT)
	$(LINK) $(MyCompareAce_LDFLAGS) $(MyCompareAce_OBJECTS) $(MyCompareAce_LDADD) $(LIBS)
binom_test_greater$(EXEEXT): $(binom_test_greater_OBJECTS) $(binom_test_greater_DEPENDENCIES) 
	@rm -f binom_test_greater$(EXEEXT)
	$(LINK) $(binom_test_greater_LDFLAGS) $(binom_test_greater_OBJECTS) $(binom_test_greater_LDADD) $(LIBS)
genregexp$(EXEEXT): $(genregexp_OBJECTS) $(genregexp_DEPENDENCIES) 
	@rm -f genregexp$(EXEEXT)
	$(LINK) $(genregexp_LDFLAGS) $(genregexp_OBJECTS) $(genregexp_LDADD) $(LIBS)
mi_combine$(EXEEXT): $(mi_combine_OBJECTS) $(mi_combine_DEPENDENCIES) 
	@rm -f mi_combine$(EXEEXT)
	$(LINK) $(mi_combine_LDFLAGS) $(mi_combine_OBJECTS) $(mi_combine_LDADD) $(LIBS)
mi_dist$(EXEEXT): $(mi_dist_OBJECTS) $(mi_dist_DEPENDENCIES) 
	@rm -f mi_dist$(EXEEXT)
	$(LINK) $(mi_dist_LDFLAGS) $(mi_dist_OBJECTS) $(mi_dist_LDADD) $(LIBS)
mi_combine_mbins$(EXEEXT): $(mi_combine_mbins_OBJECTS) $(mi_combine_mbins_DEPENDENCIES) 
	@rm -f mi_combine_mbins$(EXEEXT)
	$(LINK) $(mi_combine_mbins_LDFLAGS) $(mi_combine_mbins_OBJECTS) $(mi_combine_mbins_LDADD) $(LIBS)
mi_dist_mbins$(EXEEXT): $(mi_dist_mbins_OBJECTS) $(mi_dist_mbins_DEPENDENCIES) 
	@rm -f mi_dist_mbins$(EXEEXT)
	$(LINK) $(mi_dist_mbins_LDFLAGS) $(mi_dist_mbins_OBJECTS) $(mi_dist_mbins_LDADD) $(LIBS)
mi_find$(EXEEXT): $(mi_find_OBJECTS) $(mi_find_DEPENDENCIES) 
	@rm -f mi_find$(EXEEXT)
	$(LINK) $(mi_find_LDFLAGS) $(mi_find_OBJECTS) $(mi_find_LDADD) $(LIBS)
mi_motif_compare$(EXEEXT): $(mi_motif_compare_OBJECTS) $(mi_motif_compare_DEPENDENCIES) 
	@rm -f mi_motif_compare$(EXEEXT)
	$(LINK) $(mi_motif_compare_LDFLAGS) $(mi_motif_compare_OBJECTS) $(mi_motif_compare_LDADD) $(LIBS)
mi_motif_compare_1$(EXEEXT): $(mi_motif_compare_1_OBJECTS) $(mi_motif_compare_1_DEPENDENCIES) 
	@rm -f mi_motif_compare_1$(EXEEXT)
	$(LINK) $(mi_motif_compare_1_LDFLAGS) $(mi_motif_compare_1_OBJECTS) $(mi_motif_compare_1_LDADD) $(LIBS)
mi_optimize$(EXEEXT): $(mi_optimize_OBJECTS) $(mi_optimize_DEPENDENCIES) 
	@rm -f mi_optimize$(EXEEXT)
	$(LINK) $(mi_optimize_LDFLAGS) $(mi_optimize_OBJECTS) $(mi_optimize_LDADD) $(LIBS)
mi_optimize_1$(EXEEXT): $(mi_optimize_1_OBJECTS) $(mi_optimize_1_DEPENDENCIES) 
	@rm -f mi_optimize_1$(EXEEXT)
	$(LINK) $(mi_optimize_1_LDFLAGS) $(mi_optimize_1_OBJECTS) $(mi_optimize_1_LDADD) $(LIBS)
mi_optimize_X$(EXEEXT): $(mi_optimize_X_OBJECTS) $(mi_optimize_X_DEPENDENCIES) 
	@rm -f mi_optimize_X$(EXEEXT)
	$(LINK) $(mi_optimize_X_LDFLAGS) $(mi_optimize_X_OBJECTS) $(mi_optimize_X_LDADD) $(LIBS)
mi_optimize_maxdeg_X$(EXEEXT): $(mi_optimize_maxdeg_X_OBJECTS) $(mi_optimize_maxdeg_X_DEPENDENCIES) 
	@rm -f mi_optimize_maxdeg_X$(EXEEXT)
	$(LINK) $(mi_optimize_maxdegX_LDFLAGS) $(mi_optimize_maxdeg_X_OBJECTS) $(mi_optimize_maxdeg_X_LDADD) $(LIBS)
mi_optimize_motif$(EXEEXT): $(mi_optimize_motif_OBJECTS) $(mi_optimize_motif_DEPENDENCIES) 
	@rm -f mi_optimize_motif$(EXEEXT)
	$(LINK) $(mi_optimize_motif_LDFLAGS) $(mi_optimize_motif_OBJECTS) $(mi_optimize_motif_LDADD) $(LIBS)
mi_optimize_motif_WM$(EXEEXT): $(mi_optimize_motif_WM_OBJECTS) $(mi_optimize_motif_WM_DEPENDENCIES) 
	@rm -f mi_optimize_motif_WM$(EXEEXT)
	$(LINK) $(mi_optimize_motif_WM_LDFLAGS) $(mi_optimize_motif_WM_OBJECTS) $(mi_optimize_motif_WM_LDADD) $(LIBS)
mi_optimize_slow$(EXEEXT): $(mi_optimize_slow_OBJECTS) $(mi_optimize_slow_DEPENDENCIES) 
	@rm -f mi_optimize_slow$(EXEEXT)
	$(LINK) $(mi_optimize_slow_LDFLAGS) $(mi_optimize_slow_OBJECTS) $(mi_optimize_slow_LDADD) $(LIBS)
mi_signif$(EXEEXT): $(mi_signif_OBJECTS) $(mi_signif_DEPENDENCIES) 
	@rm -f mi_signif$(EXEEXT)
	$(LINK) $(mi_signif_LDFLAGS) $(mi_signif_OBJECTS) $(mi_signif_LDADD) $(LIBS)
myhypergeom$(EXEEXT): $(myhypergeom_OBJECTS) $(myhypergeom_DEPENDENCIES) 
	@rm -f myhypergeom$(EXEEXT)
	$(LINK) $(myhypergeom_LDFLAGS) $(myhypergeom_OBJECTS) $(myhypergeom_LDADD) $(LIBS)
recompare$(EXEEXT): $(recompare_OBJECTS) $(recompare_DEPENDENCIES) 
	@rm -f recompare$(EXEEXT)
	$(LINK) $(recompare_LDFLAGS) $(recompare_OBJECTS) $(recompare_LDADD) $(LIBS)

mostlyclean-compile:
	-rm -f *.$(OBJEXT)

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

include ./$(DEPDIR)/MyCompareAce.Po
include ./$(DEPDIR)/beta.Po
include ./$(DEPDIR)/binom_test_greater.Po
include ./$(DEPDIR)/d1mach.Po
include ./$(DEPDIR)/dataio.Po
include ./$(DEPDIR)/genregexp.Po
include ./$(DEPDIR)/i1mach.Po
include ./$(DEPDIR)/information.Po
include ./$(DEPDIR)/mi_combine.Po
include ./$(DEPDIR)/mi_dist.Po
include ./$(DEPDIR)/mi_combine_mbins.Po
include ./$(DEPDIR)/mi_dist_mbins.Po
include ./$(DEPDIR)/mi_find.Po
include ./$(DEPDIR)/mi_library.Po
include ./$(DEPDIR)/mi_motif_compare.Po
include ./$(DEPDIR)/mi_optimize.Po
include ./$(DEPDIR)/mi_motif_compare_1.Po
include ./$(DEPDIR)/mi_optimize_1.Po
include ./$(DEPDIR)/mi_optimize_X.Po
include ./$(DEPDIR)/mi_optimize_maxdeg_X.Po
include ./$(DEPDIR)/mi_optimize_motif.Po
include ./$(DEPDIR)/mi_optimize_motif_WM.Po
include ./$(DEPDIR)/mi_optimize_slow.Po
include ./$(DEPDIR)/mi_signif.Po
include ./$(DEPDIR)/myhypergeom.Po
include ./$(DEPDIR)/prefix.Po
include ./$(DEPDIR)/recompare.Po
include ./$(DEPDIR)/regexp.Po
include ./$(DEPDIR)/sequences.Po
include ./$(DEPDIR)/statistics.Po
include ./$(DEPDIR)/toms708.Po

.c.o:
	if $(COMPILE) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.Tpo" -c -o $@ $<; \
	then mv -f "$(DEPDIR)/$*.Tpo" "$(DEPDIR)/$*.Po"; else rm -f "$(DEPDIR)/$*.Tpo"; exit 1; fi
#	source='$<' object='$@' libtool=no \
#	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) \
#	$(COMPILE) -c $<

.c.obj:
	if $(COMPILE) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.Tpo" -c -o $@ `$(CYGPATH_W) '$<'`; \
	then mv -f "$(DEPDIR)/$*.Tpo" "$(DEPDIR)/$*.Po"; else rm -f "$(DEPDIR)/$*.Tpo"; exit 1; fi
#	source='$<' object='$@' libtool=no \
#	DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) \
#	$(COMPILE) -c `$(CYGPATH_W) '$<'`
uninstall-info-am:

ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES)
	list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \
	unique=`for i in $$list; do \
	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
	  done | \
	  $(AWK) '    { files[$$0] = 1; } \
	       END { for (i in files) print i; }'`; \
	mkid -fID $$unique
tags: TAGS

TAGS:  $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
		$(TAGS_FILES) $(LISP)
	tags=; \
	here=`pwd`; \
	list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \
	unique=`for i in $$list; do \
	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
	  done | \
	  $(AWK) '    { files[$$0] = 1; } \
	       END { for (i in files) print i; }'`; \
	if test -z "$(ETAGS_ARGS)$$tags$$unique"; then :; else \
	  test -n "$$unique" || unique=$$empty_fix; \
	  $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
	    $$tags $$unique; \
	fi
ctags: CTAGS
CTAGS:  $(HEADERS) $(SOURCES) config.h.in $(TAGS_DEPENDENCIES) \
		$(TAGS_FILES) $(LISP)
	tags=; \
	here=`pwd`; \
	list='$(SOURCES) $(HEADERS) config.h.in $(LISP) $(TAGS_FILES)'; \
	unique=`for i in $$list; do \
	    if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
	  done | \
	  $(AWK) '    { files[$$0] = 1; } \
	       END { for (i in files) print i; }'`; \
	test -z "$(CTAGS_ARGS)$$tags$$unique" \
	  || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
	     $$tags $$unique

GTAGS:
	here=`$(am__cd) $(top_builddir) && pwd` \
	  && cd $(top_srcdir) \
	  && gtags -i $(GTAGS_ARGS) $$here

distclean-tags:
	-rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags

distdir: $(DISTFILES)
	@srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; \
	topsrcdirstrip=`echo "$(top_srcdir)" | sed 's|.|.|g'`; \
	list='$(DISTFILES)'; for file in $$list; do \
	  case $$file in \
	    $(srcdir)/*) file=`echo "$$file" | sed "s|^$$srcdirstrip/||"`;; \
	    $(top_srcdir)/*) file=`echo "$$file" | sed "s|^$$topsrcdirstrip/|$(top_builddir)/|"`;; \
	  esac; \
	  if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
	  dir=`echo "$$file" | sed -e 's,/[^/]*$$,,'`; \
	  if test "$$dir" != "$$file" && test "$$dir" != "."; then \
	    dir="/$$dir"; \
	    $(mkdir_p) "$(distdir)$$dir"; \
	  else \
	    dir=''; \
	  fi; \
	  if test -d $$d/$$file; then \
	    if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
	      cp -pR $(srcdir)/$$file $(distdir)$$dir || exit 1; \
	    fi; \
	    cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
	  else \
	    test -f $(distdir)/$$file \
	    || cp -p $$d/$$file $(distdir)/$$file \
	    || exit 1; \
	  fi; \
	done
check-am: all-am
check: check-am
all-am: Makefile $(LIBRARIES) $(PROGRAMS) config.h
installdirs:
	for dir in "$(DESTDIR)$(bindir)"; do \
	  test -z "$$dir" || $(mkdir_p) "$$dir"; \
	done
install: install-am
install-exec: install-exec-am
install-data: install-data-am
uninstall: uninstall-am

install-am: all-am
	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am

installcheck: installcheck-am
install-strip:
	$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
	  install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
	  `test -z '$(STRIP)' || \
	    echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
mostlyclean-generic:

clean-generic:

distclean-generic:
	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)

maintainer-clean-generic:
	@echo "This command is intended for maintainers to use"
	@echo "it deletes files that may require special tools to rebuild."
clean: clean-am

clean-am: clean-binPROGRAMS clean-generic clean-noinstLIBRARIES \
	mostlyclean-am

distclean: distclean-am
	-rm -rf ./$(DEPDIR)
	-rm -f Makefile
distclean-am: clean-am distclean-compile distclean-generic \
	distclean-hdr distclean-tags

dvi: dvi-am

dvi-am:

html: html-am

info: info-am

info-am:

install-data-am:

install-exec-am: install-binPROGRAMS

install-info: install-info-am

install-man:

installcheck-am:

maintainer-clean: maintainer-clean-am
	-rm -rf ./$(DEPDIR)
	-rm -f Makefile
maintainer-clean-am: distclean-am maintainer-clean-generic

mostlyclean: mostlyclean-am

mostlyclean-am: mostlyclean-compile mostlyclean-generic

pdf: pdf-am

pdf-am:

ps: ps-am

ps-am:

uninstall-am: uninstall-binPROGRAMS uninstall-info-am

.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
	clean-generic clean-noinstLIBRARIES ctags distclean \
	distclean-compile distclean-generic distclean-hdr \
	distclean-tags distdir dvi dvi-am html html-am info info-am \
	install install-am install-binPROGRAMS install-data \
	install-data-am install-exec install-exec-am install-info \
	install-info-am install-man install-strip installcheck \
	installcheck-am installdirs maintainer-clean \
	maintainer-clean-generic mostlyclean mostlyclean-compile \
	mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \
	uninstall-am uninstall-binPROGRAMS uninstall-info-am

# 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:
