WSTester updated to work plus hopefully all the other changes that need to go into...
[jabaws.git] / binaries / src / ViennaRNA / Progs / Makefile.in
diff --git a/binaries/src/ViennaRNA/Progs/Makefile.in b/binaries/src/ViennaRNA/Progs/Makefile.in
new file mode 100644 (file)
index 0000000..1972855
--- /dev/null
@@ -0,0 +1,938 @@
+# Makefile.in generated by automake 1.11.6 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 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.
+
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+host_triplet = @host@
+bin_PROGRAMS = RNAfold$(EXEEXT) RNAeval$(EXEEXT) RNAheat$(EXEEXT) \
+       RNApdist$(EXEEXT) RNAdistance$(EXEEXT) RNAinverse$(EXEEXT) \
+       RNAplot$(EXEEXT) RNAsubopt$(EXEEXT) RNALfold$(EXEEXT) \
+       RNAcofold$(EXEEXT) RNApaln$(EXEEXT) RNAduplex$(EXEEXT) \
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+       RNAparconv$(EXEEXT) RNAPKplex$(EXEEXT) RNAplex$(EXEEXT) \
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+@WITH_LIBSVM_FALSE@                  $(AM_LDFLAGS) $(LDFLAGS) -o $@
+
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+GENGETOPT_CMDL = RNAfold_cmdl.c RNAfold_cmdl.h\
+              RNAalifold_cmdl.c RNAalifold_cmdl.h\
+              RNAcofold_cmdl.c  RNAcofold_cmdl.h\
+              RNAup_cmdl.c  RNAup_cmdl.h\
+              RNALfold_cmdl.c RNALfold_cmdl.h\
+              RNALalifold_cmdl.c RNALalifold_cmdl.h\
+              RNAplfold_cmdl.c RNAplfold_cmdl.h\
+              RNAduplex_cmdl.c RNAduplex_cmdl.h\
+              RNAaliduplex_cmdl.c RNAaliduplex_cmdl.h\
+              RNAeval_cmdl.c RNAeval_cmdl.h\
+              RNAheat_cmdl.c RNAheat_cmdl.h\
+              RNAsubopt_cmdl.c RNAsubopt_cmdl.h\
+              RNA2Dfold_cmdl.c RNA2Dfold_cmdl.h\
+              RNAparconv_cmdl.c RNAparconv_cmdl.h\
+              RNAinverse_cmdl.c RNAinverse_cmdl.h\
+              RNApaln_cmdl.c RNApaln_cmdl.h\
+              RNAplot_cmdl.c RNAplot_cmdl.h\
+              RNAPKplex_cmdl.c RNAPKplex_cmdl.h\
+              RNAplex_cmdl.c RNAplex_cmdl.h\
+              RNAsnoop_cmdl.c RNAsnoop_cmdl.h\
+              RNAdistance_cmdl.c RNAdistance_cmdl.h\
+              RNApdist_cmdl.c RNApdist_cmdl.h
+
+GENGETOPT_FILES = RNAfold.ggo RNAalifold.ggo RNAcofold.ggo\
+              RNAup.ggo RNALfold.ggo RNALalifold.ggo\
+              RNAplfold.ggo RNAduplex.ggo RNAaliduplex.ggo\
+              RNAeval.ggo RNAheat.ggo RNAsubopt.ggo RNA2Dfold.ggo\
+              RNAparconv.ggo RNAinverse.ggo RNApaln.ggo RNAplot.ggo\
+              RNAPKplex.ggo RNAplex.ggo RNAsnoop.ggo RNAdistance.ggo\
+              RNApdist.ggo
+
+EXTRA_DIST = ${GENGETOPT_FILES} ${GENGETOPT_CMDL}
+RNAfold_SOURCES = RNAfold_cmdl.c RNAfold.c
+RNAsubopt_SOURCES = RNAsubopt_cmdl.c RNAsubopt.c
+RNAalifold_SOURCES = RNAalifold_cmdl.c RNAalifold.c
+RNAcofold_SOURCES = RNAcofold_cmdl.c RNAcofold.c
+RNAup_SOURCES = RNAup_cmdl.c RNAup.c
+RNALfold_SOURCES = RNALfold_cmdl.c RNALfold.c
+RNALalifold_SOURCES = RNALalifold_cmdl.c RNALalifold.c
+RNAplfold_SOURCES = RNAplfold_cmdl.c RNAplfold.c
+RNAduplex_SOURCES = RNAduplex_cmdl.c RNAduplex.c
+RNAaliduplex_SOURCES = RNAaliduplex_cmdl.c RNAaliduplex.c
+RNAeval_SOURCES = RNAeval_cmdl.c RNAeval.c
+RNAheat_SOURCES = RNAheat_cmdl.c RNAheat.c
+RNA2Dfold_SOURCES = RNA2Dfold_cmdl.c RNA2Dfold.c
+RNAparconv_SOURCES = RNAparconv_cmdl.c RNAparconv.c
+RNAinverse_SOURCES = RNAinverse_cmdl.c RNAinverse.c
+RNApaln_SOURCES = RNApaln_cmdl.c RNApaln.c
+RNAplot_SOURCES = RNAplot_cmdl.c RNAplot.c
+RNAPKplex_SOURCES = RNAPKplex_cmdl.c RNAPKplex.c
+RNAplex_SOURCES = RNAplex_cmdl.c RNAplex.c
+RNAsnoop_SOURCES = RNAsnoop_cmdl.c RNAsnoop.c
+RNAdistance_SOURCES = RNAdistance_cmdl.c RNAdistance.c
+RNApdist_SOURCES = RNApdist_cmdl.c RNApdist.c
+all: all-am
+
+.SUFFIXES:
+.SUFFIXES: .c .o .obj
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
+       @for dep in $?; do \
+         case '$(am__configure_deps)' in \
+           *$$dep*) \
+             ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+               && { if test -f $@; then exit 0; else break; fi; }; \
+             exit 1;; \
+         esac; \
+       done; \
+       echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu Progs/Makefile'; \
+       $(am__cd) $(top_srcdir) && \
+         $(AUTOMAKE) --gnu Progs/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+       @case '$?' in \
+         *config.status*) \
+           cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
+         *) \
+           echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
+           cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe);; \
+       esac;
+
+$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
+       cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
+$(top_srcdir)/configure:  $(am__configure_deps)
+       cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
+       cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+$(am__aclocal_m4_deps):
+install-binPROGRAMS: $(bin_PROGRAMS)
+       @$(NORMAL_INSTALL)
+       @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+       if test -n "$$list"; then \
+         echo " $(MKDIR_P) '$(DESTDIR)$(bindir)'"; \
+         $(MKDIR_P) "$(DESTDIR)$(bindir)" || exit 1; \
+       fi; \
+       for p in $$list; do echo "$$p $$p"; done | \
+       sed 's/$(EXEEXT)$$//' | \
+       while read p p1; do if test -f $$p; \
+         then echo "$$p"; echo "$$p"; else :; fi; \
+       done | \
+       sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \
+           -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \
+       sed 'N;N;N;s,\n, ,g' | \
+       $(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \
+         { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \
+           if ($$2 == $$4) files[d] = files[d] " " $$1; \
+           else { print "f", $$3 "/" $$4, $$1; } } \
+         END { for (d in files) print "f", d, files[d] }' | \
+       while read type dir files; do \
+           if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \
+           test -z "$$files" || { \
+             echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \
+             $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \
+           } \
+       ; done
+
+uninstall-binPROGRAMS:
+       @$(NORMAL_UNINSTALL)
+       @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \
+       files=`for p in $$list; do echo "$$p"; done | \
+         sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \
+             -e 's/$$/$(EXEEXT)/' `; \
+       test -n "$$list" || exit 0; \
+       echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \
+       cd "$(DESTDIR)$(bindir)" && rm -f $$files
+
+clean-binPROGRAMS:
+       -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS)
+RNA2Dfold$(EXEEXT): $(RNA2Dfold_OBJECTS) $(RNA2Dfold_DEPENDENCIES) $(EXTRA_RNA2Dfold_DEPENDENCIES) 
+       @rm -f RNA2Dfold$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNA2Dfold_OBJECTS) $(RNA2Dfold_LDADD) $(LIBS)
+RNALalifold$(EXEEXT): $(RNALalifold_OBJECTS) $(RNALalifold_DEPENDENCIES) $(EXTRA_RNALalifold_DEPENDENCIES) 
+       @rm -f RNALalifold$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNALalifold_OBJECTS) $(RNALalifold_LDADD) $(LIBS)
+RNALfold$(EXEEXT): $(RNALfold_OBJECTS) $(RNALfold_DEPENDENCIES) $(EXTRA_RNALfold_DEPENDENCIES) 
+       @rm -f RNALfold$(EXEEXT)
+       $(AM_V_GEN)$(RNALfold_LINK) $(RNALfold_OBJECTS) $(RNALfold_LDADD) $(LIBS)
+RNAPKplex$(EXEEXT): $(RNAPKplex_OBJECTS) $(RNAPKplex_DEPENDENCIES) $(EXTRA_RNAPKplex_DEPENDENCIES) 
+       @rm -f RNAPKplex$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAPKplex_OBJECTS) $(RNAPKplex_LDADD) $(LIBS)
+RNAaliduplex$(EXEEXT): $(RNAaliduplex_OBJECTS) $(RNAaliduplex_DEPENDENCIES) $(EXTRA_RNAaliduplex_DEPENDENCIES) 
+       @rm -f RNAaliduplex$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAaliduplex_OBJECTS) $(RNAaliduplex_LDADD) $(LIBS)
+RNAalifold$(EXEEXT): $(RNAalifold_OBJECTS) $(RNAalifold_DEPENDENCIES) $(EXTRA_RNAalifold_DEPENDENCIES) 
+       @rm -f RNAalifold$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAalifold_OBJECTS) $(RNAalifold_LDADD) $(LIBS)
+RNAcofold$(EXEEXT): $(RNAcofold_OBJECTS) $(RNAcofold_DEPENDENCIES) $(EXTRA_RNAcofold_DEPENDENCIES) 
+       @rm -f RNAcofold$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAcofold_OBJECTS) $(RNAcofold_LDADD) $(LIBS)
+RNAdistance$(EXEEXT): $(RNAdistance_OBJECTS) $(RNAdistance_DEPENDENCIES) $(EXTRA_RNAdistance_DEPENDENCIES) 
+       @rm -f RNAdistance$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAdistance_OBJECTS) $(RNAdistance_LDADD) $(LIBS)
+RNAduplex$(EXEEXT): $(RNAduplex_OBJECTS) $(RNAduplex_DEPENDENCIES) $(EXTRA_RNAduplex_DEPENDENCIES) 
+       @rm -f RNAduplex$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAduplex_OBJECTS) $(RNAduplex_LDADD) $(LIBS)
+RNAeval$(EXEEXT): $(RNAeval_OBJECTS) $(RNAeval_DEPENDENCIES) $(EXTRA_RNAeval_DEPENDENCIES) 
+       @rm -f RNAeval$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAeval_OBJECTS) $(RNAeval_LDADD) $(LIBS)
+RNAfold$(EXEEXT): $(RNAfold_OBJECTS) $(RNAfold_DEPENDENCIES) $(EXTRA_RNAfold_DEPENDENCIES) 
+       @rm -f RNAfold$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAfold_OBJECTS) $(RNAfold_LDADD) $(LIBS)
+RNAheat$(EXEEXT): $(RNAheat_OBJECTS) $(RNAheat_DEPENDENCIES) $(EXTRA_RNAheat_DEPENDENCIES) 
+       @rm -f RNAheat$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAheat_OBJECTS) $(RNAheat_LDADD) $(LIBS)
+RNAinverse$(EXEEXT): $(RNAinverse_OBJECTS) $(RNAinverse_DEPENDENCIES) $(EXTRA_RNAinverse_DEPENDENCIES) 
+       @rm -f RNAinverse$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAinverse_OBJECTS) $(RNAinverse_LDADD) $(LIBS)
+RNApaln$(EXEEXT): $(RNApaln_OBJECTS) $(RNApaln_DEPENDENCIES) $(EXTRA_RNApaln_DEPENDENCIES) 
+       @rm -f RNApaln$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNApaln_OBJECTS) $(RNApaln_LDADD) $(LIBS)
+RNAparconv$(EXEEXT): $(RNAparconv_OBJECTS) $(RNAparconv_DEPENDENCIES) $(EXTRA_RNAparconv_DEPENDENCIES) 
+       @rm -f RNAparconv$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAparconv_OBJECTS) $(RNAparconv_LDADD) $(LIBS)
+RNApdist$(EXEEXT): $(RNApdist_OBJECTS) $(RNApdist_DEPENDENCIES) $(EXTRA_RNApdist_DEPENDENCIES) 
+       @rm -f RNApdist$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNApdist_OBJECTS) $(RNApdist_LDADD) $(LIBS)
+RNAplex$(EXEEXT): $(RNAplex_OBJECTS) $(RNAplex_DEPENDENCIES) $(EXTRA_RNAplex_DEPENDENCIES) 
+       @rm -f RNAplex$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAplex_OBJECTS) $(RNAplex_LDADD) $(LIBS)
+RNAplfold$(EXEEXT): $(RNAplfold_OBJECTS) $(RNAplfold_DEPENDENCIES) $(EXTRA_RNAplfold_DEPENDENCIES) 
+       @rm -f RNAplfold$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAplfold_OBJECTS) $(RNAplfold_LDADD) $(LIBS)
+RNAplot$(EXEEXT): $(RNAplot_OBJECTS) $(RNAplot_DEPENDENCIES) $(EXTRA_RNAplot_DEPENDENCIES) 
+       @rm -f RNAplot$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAplot_OBJECTS) $(RNAplot_LDADD) $(LIBS)
+RNAsnoop$(EXEEXT): $(RNAsnoop_OBJECTS) $(RNAsnoop_DEPENDENCIES) $(EXTRA_RNAsnoop_DEPENDENCIES) 
+       @rm -f RNAsnoop$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAsnoop_OBJECTS) $(RNAsnoop_LDADD) $(LIBS)
+RNAsubopt$(EXEEXT): $(RNAsubopt_OBJECTS) $(RNAsubopt_DEPENDENCIES) $(EXTRA_RNAsubopt_DEPENDENCIES) 
+       @rm -f RNAsubopt$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAsubopt_OBJECTS) $(RNAsubopt_LDADD) $(LIBS)
+RNAup$(EXEEXT): $(RNAup_OBJECTS) $(RNAup_DEPENDENCIES) $(EXTRA_RNAup_DEPENDENCIES) 
+       @rm -f RNAup$(EXEEXT)
+       $(AM_V_CCLD)$(LINK) $(RNAup_OBJECTS) $(RNAup_LDADD) $(LIBS)
+
+mostlyclean-compile:
+       -rm -f *.$(OBJEXT)
+
+distclean-compile:
+       -rm -f *.tab.c
+
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNA2Dfold.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNA2Dfold_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNALalifold.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNALalifold_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNALfold.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNALfold_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAPKplex.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAPKplex_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAaliduplex.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAaliduplex_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAalifold.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAalifold_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAcofold.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAcofold_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAdistance.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAdistance_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAduplex.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAduplex_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAeval.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAeval_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAfold.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAfold_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAheat.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAheat_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAinverse.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAinverse_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNApaln.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNApaln_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAparconv.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAparconv_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNApdist.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNApdist_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAplex.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAplex_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAplfold.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAplfold_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAplot.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAplot_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAsnoop.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAsnoop_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAsubopt.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAsubopt_cmdl.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAup.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/RNAup_cmdl.Po@am__quote@
+
+.c.o:
+@am__fastdepCC_TRUE@   $(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+@am__fastdepCC_TRUE@   $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+@AMDEP_TRUE@@am__fastdepCC_FALSE@      $(AM_V_CC)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCC_FALSE@      DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCC_FALSE@  $(AM_V_CC@am__nodep@)$(COMPILE) -c $<
+
+.c.obj:
+@am__fastdepCC_TRUE@   $(AM_V_CC)$(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
+@am__fastdepCC_TRUE@   $(AM_V_at)$(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+@AMDEP_TRUE@@am__fastdepCC_FALSE@      $(AM_V_CC)source='$<' object='$@' libtool=no @AMDEPBACKSLASH@
+@AMDEP_TRUE@@am__fastdepCC_FALSE@      DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+@am__fastdepCC_FALSE@  $(AM_V_CC@am__nodep@)$(COMPILE) -c `$(CYGPATH_W) '$<'`
+
+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; nonempty = 1; } \
+             END { if (nonempty) { for (i in files) print i; }; }'`; \
+       mkid -fID $$unique
+tags: TAGS
+
+TAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+               $(TAGS_FILES) $(LISP)
+       set x; \
+       here=`pwd`; \
+       list='$(SOURCES) $(HEADERS)  $(LISP) $(TAGS_FILES)'; \
+       unique=`for i in $$list; do \
+           if test -f "$$i"; then echo $$i; else echo $(srcdir)/$$i; fi; \
+         done | \
+         $(AWK) '{ files[$$0] = 1; nonempty = 1; } \
+             END { if (nonempty) { for (i in files) print i; }; }'`; \
+       shift; \
+       if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
+         test -n "$$unique" || unique=$$empty_fix; \
+         if test $$# -gt 0; then \
+           $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+             "$$@" $$unique; \
+         else \
+           $(ETAGS) $(ETAGSFLAGS) $(AM_ETAGSFLAGS) $(ETAGS_ARGS) \
+             $$unique; \
+         fi; \
+       fi
+ctags: CTAGS
+CTAGS:  $(HEADERS) $(SOURCES)  $(TAGS_DEPENDENCIES) \
+               $(TAGS_FILES) $(LISP)
+       list='$(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[$$0] = 1; nonempty = 1; } \
+             END { if (nonempty) { for (i in files) print i; }; }'`; \
+       test -z "$(CTAGS_ARGS)$$unique" \
+         || $(CTAGS) $(CTAGSFLAGS) $(AM_CTAGSFLAGS) $(CTAGS_ARGS) \
+            $$unique
+
+GTAGS:
+       here=`$(am__cd) $(top_builddir) && pwd` \
+         && $(am__cd) $(top_srcdir) \
+         && gtags -i $(GTAGS_ARGS) "$$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)'; \
+         dist_files=`for file in $$list; do echo $$file; done | \
+         sed -e "s|^$$srcdirstrip/||;t" \
+             -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
+       case $$dist_files in \
+         */*) $(MKDIR_P) `echo "$$dist_files" | \
+                          sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
+                          sort -u` ;; \
+       esac; \
+       for file in $$dist_files; do \
+         if test -f $$file || test -d $$file; then d=.; else d=$(srcdir); fi; \
+         if test -d $$d/$$file; then \
+           dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
+           if test -d "$(distdir)/$$file"; then \
+             find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+           fi; \
+           if test -d $(srcdir)/$$file && test $$d != $(srcdir); then \
+             cp -fpR $(srcdir)/$$file "$(distdir)$$dir" || exit 1; \
+             find "$(distdir)/$$file" -type d ! -perm -700 -exec chmod u+rwx {} \;; \
+           fi; \
+           cp -fpR $$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 $(PROGRAMS)
+installdirs:
+       for dir in "$(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) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-am
+install-strip:
+       if test -z '$(STRIP)'; then \
+         $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+           install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+             install; \
+       else \
+         $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+           install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+           "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
+       fi
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+       -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+       -test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+
+maintainer-clean-generic:
+       @echo "This command is intended for maintainers to use"
+       @echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
+
+distclean: distclean-am
+       -rm -rf ./$(DEPDIR)
+       -rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+       distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am: install-binPROGRAMS
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+       -rm -rf ./$(DEPDIR)
+       -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic \
+       maintainer-clean-local
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-binPROGRAMS
+
+.MAKE: install-am install-strip
+
+.PHONY: CTAGS GTAGS all all-am check check-am clean clean-binPROGRAMS \
+       clean-generic ctags distclean distclean-compile \
+       distclean-generic distclean-tags distdir dvi dvi-am html \
+       html-am info info-am install install-am install-binPROGRAMS \
+       install-data install-data-am install-dvi install-dvi-am \
+       install-exec install-exec-am install-html install-html-am \
+       install-info install-info-am install-man install-pdf \
+       install-pdf-am install-ps install-ps-am install-strip \
+       installcheck installcheck-am installdirs maintainer-clean \
+       maintainer-clean-generic maintainer-clean-local mostlyclean \
+       mostlyclean-compile mostlyclean-generic pdf pdf-am ps ps-am \
+       tags uninstall uninstall-am uninstall-binPROGRAMS
+
+
+# remove all generated man pages
+maintainer-clean-local:
+       rm -rf $(GENGETOPT_CMDL)
+
+RNAfold.c:    RNAfold_cmdl.h
+
+RNAfold_cmdl.h  RNAfold_cmdl.c: RNAfold.ggo
+       gengetopt -i RNAfold.ggo
+
+RNAsubopt.c:    RNAsubopt_cmdl.h
+
+RNAsubopt_cmdl.h  RNAsubopt_cmdl.c: RNAsubopt.ggo
+       gengetopt -i RNAsubopt.ggo
+
+RNAalifold.c:    RNAalifold_cmdl.h
+
+RNAalifold_cmdl.h  RNAalifold_cmdl.c: RNAalifold.ggo
+       gengetopt -i RNAalifold.ggo
+
+RNAcofold.c:    RNAcofold_cmdl.h
+
+RNAcofold_cmdl.h  RNAcofold_cmdl.c: RNAcofold.ggo
+       gengetopt -i RNAcofold.ggo
+
+RNAup.c:        RNAup_cmdl.h
+
+RNAup_cmdl.h  RNAup_cmdl.c: RNAup.ggo
+       gengetopt -i RNAup.ggo
+
+RNALfold.c:       RNALfold_cmdl.h
+
+RNALfold_cmdl.h  RNALfold_cmdl.c: RNALfold.ggo
+       gengetopt -i RNALfold.ggo
+
+RNALalifold.c:      RNALalifold_cmdl.h
+
+RNALalifold_cmdl.h  RNALalifold_cmdl.c: RNALalifold.ggo
+       gengetopt -i RNALalifold.ggo
+
+RNAplfold.c:      RNAplfold_cmdl.h
+
+RNAplfold_cmdl.h  RNAplfold_cmdl.c: RNAplfold.ggo
+       gengetopt -i RNAplfold.ggo
+
+RNAduplex.c:      RNAduplex_cmdl.h
+
+RNAduplex_cmdl.h  RNAduplex_cmdl.c: RNAduplex.ggo
+       gengetopt -i RNAduplex.ggo
+
+RNAaliduplex.c:   RNAaliduplex_cmdl.h
+
+RNAaliduplex_cmdl.h  RNAaliduplex_cmdl.c: RNAaliduplex.ggo
+       gengetopt -i RNAaliduplex.ggo
+
+RNAeval.c:   RNAeval_cmdl.h
+
+RNAeval_cmdl.h  RNAeval_cmdl.c: RNAeval.ggo
+       gengetopt -i RNAeval.ggo
+
+RNAheat.c:   RNAheat_cmdl.h
+
+RNAheat_cmdl.h  RNAheat_cmdl.c: RNAheat.ggo
+       gengetopt -i RNAheat.ggo
+
+RNA2Dfold.c:    RNA2Dfold_cmdl.h
+
+RNA2Dfold_cmdl.h  RNA2Dfold_cmdl.c: RNA2Dfold.ggo
+       gengetopt -i RNA2Dfold.ggo
+
+RNAparconv.c:    RNAparconv_cmdl.h
+
+RNAparconv_cmdl.h  RNAparconv_cmdl.c: RNAparconv.ggo
+       gengetopt -i RNAparconv.ggo
+
+RNAinverse.c:   RNAinverse_cmdl.h
+
+RNAinverse_cmdl.h  RNAinverse_cmdl.c: RNAinverse.ggo
+       gengetopt -i RNAinverse.ggo
+
+RNApaln.c:   RNApaln_cmdl.h
+
+RNApaln_cmdl.h  RNApaln_cmdl.c: RNApaln.ggo
+       gengetopt -i RNApaln.ggo
+
+RNAplot.c:   RNAplot_cmdl.h
+
+RNAplot_cmdl.h  RNAplot_cmdl.c: RNAplot.ggo
+       gengetopt -i RNAplot.ggo
+
+RNAPKplex.c:    RNAPKplex_cmdl.h
+
+RNAPKplex_cmdl.h  RNAPKplex_cmdl.c: RNAPKplex.ggo
+       gengetopt -i RNAPKplex.ggo
+
+RNAplex.c:    RNAplex_cmdl.h
+
+RNAplex_cmdl.h  RNAplex_cmdl.c: RNAplex.ggo
+       gengetopt -i RNAplex.ggo
+
+RNAsnoop.c:    RNAsnoop_cmdl.h
+
+RNAsnoop_cmdl.h  RNAsnoop_cmdl.c: RNAsnoop.ggo
+       gengetopt -i RNAsnoop.ggo
+
+RNAdistance.c:    RNAdistance_cmdl.h
+
+RNAdistance_cmdl.h  RNAdistance_cmdl.c: RNAdistance.ggo
+       gengetopt -i RNAdistance.ggo
+
+RNApdist.c:    RNApdist_cmdl.h
+
+RNApdist_cmdl.h  RNApdist_cmdl.c: RNApdist.ggo
+       gengetopt -i RNApdist.ggo
+
+# 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: