# Makefile.in generated by automake 1.10.2 from Makefile.am.
# src/Makefile.  Generated from Makefile.in by configure.

# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
# 2003, 2004, 2005, 2006, 2007, 2008  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.



# Andreas Wilm (UCD): 2007-12-10
# Generated using the following sites 
# http://www.openismus.com/documents/linux/automake/automake.shtml
# http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html


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# we do not use GNU-style files: NEWS README AUTHORS ChangeLog
AUTOMAKE_OPTIONS = foreign
SUBDIRS = 
clustalw2_SOURCES = ./pairwise/PairwiseAlignBase.h \
 ./pairwise/FastPairwiseAlign.h \
 ./pairwise/FullPairwiseAlign.cpp \
 ./pairwise/FullPairwiseAlign.h \
 ./pairwise/FastPairwiseAlign.cpp \
 ./fileInput/FileParser.h \
 ./fileInput/EMBLFileParser.h \
 ./fileInput/MSFFileParser.cpp \
 ./fileInput/FileReader.cpp \
 ./fileInput/PIRFileParser.cpp \
 ./fileInput/MSFFileParser.h \
 ./fileInput/FileReader.h \
 ./fileInput/RSFFileParser.cpp \
 ./fileInput/PIRFileParser.h \
 ./fileInput/GDEFileParser.cpp \
 ./fileInput/RSFFileParser.h \
 ./fileInput/GDEFileParser.h \
 ./fileInput/InFileStream.cpp \
 ./fileInput/ClustalFileParser.cpp \
 ./fileInput/PearsonFileParser.cpp \
 ./fileInput/InFileStream.h \
 ./fileInput/ClustalFileParser.h \
 ./fileInput/PearsonFileParser.h \
 ./fileInput/FileParser.cpp \
 ./fileInput/EMBLFileParser.cpp \
 ./tree/UPGMA/RootedClusterTree.cpp \
 ./tree/UPGMA/RootedGuideTree.h \
 ./tree/UPGMA/UPGMAAlgorithm.cpp \
 ./tree/UPGMA/RootedTreeOutput.h \
 ./tree/UPGMA/RootedClusterTree.h \
 ./tree/UPGMA/Node.cpp \
 ./tree/UPGMA/UPGMAAlgorithm.h \
 ./tree/UPGMA/upgmadata.h \
 ./tree/UPGMA/Node.h \
 ./tree/UPGMA/RootedGuideTree.cpp \
 ./tree/UPGMA/RootedTreeOutput.cpp \
 ./tree/Tree.cpp \
 ./tree/ClusterTree.cpp \
 ./tree/AlignmentSteps.h \
 ./tree/Tree.h \
 ./tree/ClusterTree.h \
 ./tree/ClusterTreeAlgorithm.h \
 ./tree/TreeInterface.cpp \
 ./tree/UnRootedClusterTree.cpp \
 ./tree/ClusterTreeOutput.cpp \
 ./tree/TreeInterface.h \
 ./tree/dayhoff.h \
 ./tree/UnRootedClusterTree.h \
 ./tree/RandomGenerator.cpp \
 ./tree/NJTree.cpp \
 ./tree/ClusterTreeOutput.h \
 ./tree/RandomGenerator.h \
 ./tree/NJTree.h \
 ./tree/AlignmentSteps.cpp \
 ./interface/InteractiveMenu.cpp \
 ./interface/CommandLineParser.cpp \
 ./interface/InteractiveMenu.h \
 ./interface/CommandLineParser.h \
 ./substitutionMatrix/SubMatrix.cpp \
 ./substitutionMatrix/SubMatrix.h \
 ./substitutionMatrix/globalmatrix.h \
 ./substitutionMatrix/matrices.h \
 ./multipleAlign/Iteration.cpp \
 ./multipleAlign/MSA.cpp \
 ./multipleAlign/MyersMillerProfileAlign.cpp \
 ./multipleAlign/ProfileBase.h \
 ./multipleAlign/ProfileStandard.cpp \
 ./multipleAlign/LowScoreSegProfile.h \
 ./multipleAlign/Iteration.h \
 ./multipleAlign/MSA.h \
 ./multipleAlign/MyersMillerProfileAlign.h \
 ./multipleAlign/ProfileStandard.h \
 ./multipleAlign/ProfileWithSub.cpp \
 ./multipleAlign/ProfileAlignAlgorithm.h \
 ./multipleAlign/ProfileBase.cpp \
 ./multipleAlign/ProfileWithSub.h \
 ./multipleAlign/LowScoreSegProfile.cpp \
 ./general/ClustalWResources.h \
 ./general/OutputFile.cpp \
 ./general/VectorOutOfRange.h \
 ./general/UserParameters.cpp \
 ./general/SymMatrix.h \
 ./general/Utility.cpp \
 ./general/clustalw.h \
 ./general/OutputFile.h \
 ./general/param.h \
 ./general/utils.h \
 ./general/UserParameters.h \
 ./general/SquareMat.h \
 ./general/Utility.h \
 ./general/SequenceNotFoundException.h \
 ./general/InvalidCombination.cpp \
 ./general/Array2D.h \
 ./general/RandomAccessLList.h \
 ./general/general.h \
 ./general/debuglogObject.h \
 ./general/statsObject.h \
 ./general/userparams.h \
 ./general/DebugLog.cpp \
 ./general/ClustalWResources.cpp \
 ./general/VectorUtility.h \
 ./general/VectorOutOfRange.cpp \
 ./general/SymMatrix.cpp \
 ./general/DebugLog.h \
 ./general/Stats.cpp \
 ./general/Stats.h \
 ./Help.cpp \
 ./Help.h \
 ./alignment/Alignment.cpp \
 ./alignment/AlignmentOutput.cpp \
 ./alignment/Alignment.h \
 ./alignment/AlignmentOutput.h \
 ./alignment/ObjectiveScore.cpp \
 ./alignment/Sequence.cpp \
 ./alignment/ObjectiveScore.h \
 ./alignment/Sequence.h \
 ./Clustal.cpp \
 ./Clustal.h \
 ./clustalw_version.h \
 ./main.cpp

all: config.h
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.SUFFIXES:
.SUFFIXES: .cpp .o .obj
$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
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	cd $(top_srcdir) && \
	  $(AUTOMAKE) --foreign  src/Makefile
.PRECIOUS: Makefile
Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
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$(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
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$(top_srcdir)/configure:  $(am__configure_deps)
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$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
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config.h: stamp-h1
	@if test ! -f $@; then \
	  rm -f stamp-h1; \
	  $(MAKE) $(AM_MAKEFLAGS) stamp-h1; \
	else :; fi

stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
	@rm -f stamp-h1
	cd $(top_builddir) && $(SHELL) ./config.status src/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
clustalw_version.h: $(top_builddir)/config.status $(srcdir)/clustalw_version.h.in
	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
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 $(bin_PROGRAMS)
clustalw2$(EXEEXT): $(clustalw2_OBJECTS) $(clustalw2_DEPENDENCIES) 
	@rm -f clustalw2$(EXEEXT)
	$(CXXLINK) $(clustalw2_OBJECTS) $(clustalw2_LDADD) $(LIBS)

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

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

include ./$(DEPDIR)/Alignment.Po
include ./$(DEPDIR)/AlignmentOutput.Po
include ./$(DEPDIR)/AlignmentSteps.Po
include ./$(DEPDIR)/Clustal.Po
include ./$(DEPDIR)/ClustalFileParser.Po
include ./$(DEPDIR)/ClustalWResources.Po
include ./$(DEPDIR)/ClusterTree.Po
include ./$(DEPDIR)/ClusterTreeOutput.Po
include ./$(DEPDIR)/CommandLineParser.Po
include ./$(DEPDIR)/DebugLog.Po
include ./$(DEPDIR)/EMBLFileParser.Po
include ./$(DEPDIR)/FastPairwiseAlign.Po
include ./$(DEPDIR)/FileParser.Po
include ./$(DEPDIR)/FileReader.Po
include ./$(DEPDIR)/FullPairwiseAlign.Po
include ./$(DEPDIR)/GDEFileParser.Po
include ./$(DEPDIR)/Help.Po
include ./$(DEPDIR)/InFileStream.Po
include ./$(DEPDIR)/InteractiveMenu.Po
include ./$(DEPDIR)/InvalidCombination.Po
include ./$(DEPDIR)/Iteration.Po
include ./$(DEPDIR)/LowScoreSegProfile.Po
include ./$(DEPDIR)/MSA.Po
include ./$(DEPDIR)/MSFFileParser.Po
include ./$(DEPDIR)/MyersMillerProfileAlign.Po
include ./$(DEPDIR)/NJTree.Po
include ./$(DEPDIR)/Node.Po
include ./$(DEPDIR)/ObjectiveScore.Po
include ./$(DEPDIR)/OutputFile.Po
include ./$(DEPDIR)/PIRFileParser.Po
include ./$(DEPDIR)/PearsonFileParser.Po
include ./$(DEPDIR)/ProfileBase.Po
include ./$(DEPDIR)/ProfileStandard.Po
include ./$(DEPDIR)/ProfileWithSub.Po
include ./$(DEPDIR)/RSFFileParser.Po
include ./$(DEPDIR)/RandomGenerator.Po
include ./$(DEPDIR)/RootedClusterTree.Po
include ./$(DEPDIR)/RootedGuideTree.Po
include ./$(DEPDIR)/RootedTreeOutput.Po
include ./$(DEPDIR)/Sequence.Po
include ./$(DEPDIR)/Stats.Po
include ./$(DEPDIR)/SubMatrix.Po
include ./$(DEPDIR)/SymMatrix.Po
include ./$(DEPDIR)/Tree.Po
include ./$(DEPDIR)/TreeInterface.Po
include ./$(DEPDIR)/UPGMAAlgorithm.Po
include ./$(DEPDIR)/UnRootedClusterTree.Po
include ./$(DEPDIR)/UserParameters.Po
include ./$(DEPDIR)/Utility.Po
include ./$(DEPDIR)/VectorOutOfRange.Po
include ./$(DEPDIR)/main.Po

.cpp.o:
	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
	mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
#	source='$<' object='$@' libtool=no \
#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
#	$(CXXCOMPILE) -c -o $@ $<

.cpp.obj:
	$(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'`
	mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
#	source='$<' object='$@' libtool=no \
#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
#	$(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'`

FullPairwiseAlign.o: ./pairwise/FullPairwiseAlign.cpp
	$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FullPairwiseAlign.o -MD -MP -MF $(DEPDIR)/FullPairwiseAlign.Tpo -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo '$(srcdir)/'`./pairwise/FullPairwiseAlign.cpp
	mv -f $(DEPDIR)/FullPairwiseAlign.Tpo $(DEPDIR)/FullPairwiseAlign.Po
#	source='./pairwise/FullPairwiseAlign.cpp' object='FullPairwiseAlign.o' libtool=no \
#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
#	$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo '$(srcdir)/'`./pairwise/FullPairwiseAlign.cpp

FullPairwiseAlign.obj: ./pairwise/FullPairwiseAlign.cpp
	$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FullPairwiseAlign.obj -MD -MP -MF $(DEPDIR)/FullPairwiseAlign.Tpo -c -o FullPairwiseAlign.obj `if test -f './pairwise/FullPairwiseAlign.cpp'; then $(CYGPATH_W) './pairwise/FullPairwiseAlign.cpp'; else $(CYGPATH_W) '$(srcdir)/./pairwise/FullPairwiseAlign.cpp'; fi`
	mv -f $(DEPDIR)/FullPairwiseAlign.Tpo $(DEPDIR)/FullPairwiseAlign.Po
#	source='./pairwise/FullPairwiseAlign.cpp' object='FullPairwiseAlign.obj' libtool=no \
#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
#	$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FullPairwiseAlign.obj `if test -f './pairwise/FullPairwiseAlign.cpp'; then $(CYGPATH_W) './pairwise/FullPairwiseAlign.cpp'; else $(CYGPATH_W) '$(srcdir)/./pairwise/FullPairwiseAlign.cpp'; fi`

FastPairwiseAlign.o: ./pairwise/FastPairwiseAlign.cpp
	$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT FastPairwiseAlign.o -MD -MP -MF $(DEPDIR)/FastPairwiseAlign.Tpo -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo '$(srcdir)/'`./pairwise/FastPairwiseAlign.cpp
	mv -f $(DEPDIR)/FastPairwiseAlign.Tpo $(DEPDIR)/FastPairwiseAlign.Po
#	source='./pairwise/FastPairwiseAlign.cpp' object='FastPairwiseAlign.o' libtool=no \
#	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \
#	$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo '$(srcdir)/'`./pairwise/FastPairwiseAlign.cpp

FastPairwiseAlign.obj: ./pairwise/FastPairwiseAlign.cpp
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MSFFileParser.o: ./fileInput/MSFFileParser.cpp
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MSFFileParser.obj: ./fileInput/MSFFileParser.cpp
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FileReader.o: ./fileInput/FileReader.cpp
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PIRFileParser.o: ./fileInput/PIRFileParser.cpp
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PIRFileParser.obj: ./fileInput/PIRFileParser.cpp
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RSFFileParser.o: ./fileInput/RSFFileParser.cpp
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RSFFileParser.obj: ./fileInput/RSFFileParser.cpp
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GDEFileParser.o: ./fileInput/GDEFileParser.cpp
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GDEFileParser.obj: ./fileInput/GDEFileParser.cpp
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InFileStream.o: ./fileInput/InFileStream.cpp
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InFileStream.obj: ./fileInput/InFileStream.cpp
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ClustalFileParser.o: ./fileInput/ClustalFileParser.cpp
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ClustalFileParser.obj: ./fileInput/ClustalFileParser.cpp
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PearsonFileParser.o: ./fileInput/PearsonFileParser.cpp
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PearsonFileParser.obj: ./fileInput/PearsonFileParser.cpp
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FileParser.o: ./fileInput/FileParser.cpp
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FileParser.obj: ./fileInput/FileParser.cpp
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EMBLFileParser.o: ./fileInput/EMBLFileParser.cpp
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EMBLFileParser.obj: ./fileInput/EMBLFileParser.cpp
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RootedClusterTree.o: ./tree/UPGMA/RootedClusterTree.cpp
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RootedClusterTree.obj: ./tree/UPGMA/RootedClusterTree.cpp
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UPGMAAlgorithm.o: ./tree/UPGMA/UPGMAAlgorithm.cpp
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UPGMAAlgorithm.obj: ./tree/UPGMA/UPGMAAlgorithm.cpp
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	    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)$$tags$$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:
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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|^$$srcdirstrip/||;t" \
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	case $$dist_files in \
	  */*) $(MKDIR_P) `echo "$$dist_files" | \
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			   sort -u` ;; \
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	    fi; \
	    cp -pR $$d/$$file $(distdir)$$dir || exit 1; \
	  else \
	    test -f $(distdir)/$$file \
	    || cp -p $$d/$$file $(distdir)/$$file \
	    || exit 1; \
	  fi; \
	done
	list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
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	    distdir=`$(am__cd) $(distdir) && pwd`; \
	    top_distdir=`$(am__cd) $(top_distdir) && pwd`; \
	    (cd $$subdir && \
	      $(MAKE) $(AM_MAKEFLAGS) \
	        top_distdir="$$top_distdir" \
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		am__remove_distdir=: \
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check: check-recursive
all-am: Makefile $(PROGRAMS) config.h
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installdirs-am:
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install-data: install-data-recursive
uninstall: uninstall-recursive

install-am: all-am
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installcheck: installcheck-recursive
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:
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maintainer-clean-generic:
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	@echo "it deletes files that may require special tools to rebuild."
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clean-am: clean-binPROGRAMS clean-generic mostlyclean-am

distclean: distclean-recursive
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	-rm -f Makefile
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dvi: dvi-recursive

dvi-am:

html: html-recursive

info: info-recursive

info-am:

install-data-am:

install-dvi: install-dvi-recursive

install-exec-am: install-binPROGRAMS

install-html: install-html-recursive

install-info: install-info-recursive

install-man:

install-pdf: install-pdf-recursive

install-ps: install-ps-recursive

installcheck-am:

maintainer-clean: maintainer-clean-recursive
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maintainer-clean-am: distclean-am maintainer-clean-generic

mostlyclean: mostlyclean-recursive

mostlyclean-am: mostlyclean-compile mostlyclean-generic

pdf: pdf-recursive

pdf-am:

ps: ps-recursive

ps-am:

uninstall-am: uninstall-binPROGRAMS

.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) install-am \
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.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
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	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 installdirs-am maintainer-clean \
	maintainer-clean-generic mostlyclean mostlyclean-compile \
	mostlyclean-generic pdf pdf-am ps ps-am tags tags-recursive \
	uninstall uninstall-am uninstall-binPROGRAMS

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# Otherwise a system limit (for SysV at least) may be exceeded.
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