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if DEBUG
D_CXXFLAGS = -Wall -g -D__GNDEBUG__
endif
OPTIMIZATION = -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize
AM_CFLAGS = $(OPTIMIZATION) @DEPS_CFLAGS@ -DUSE_POSIX_AIO @OPENMP_CFLAGS@
AM_CXXFLAGS = $(OPTIMIZATION) @DEPS_CFLAGS@ @BOOST_CPPFLAGS@ $(D_CXXFLAGS) @EXTRA_CXX_FLAGS@ @OPENMP_CXXFLAGS@
AM_LDFLAGS = $(OPTIMIZATION)
LIBMEMS_H = \
RepeatHash.h MatchHashEntry.h \
DNAFileSML.h MemorySML.h MatchProjectionAdapter.h \
DNAMemorySML.h MatchFinder.h SortedMerList.h IntervalList.h \
FileSML.h gnAlignedSequences.h Interval.h \
MemHash.h AbstractMatch.h SlotAllocator.h \
Aligner.h Match.h MatchList.h Matrix.h NumericMatrix.h \
Islands.h MaskedMemHash.h SeedMasks.h GappedAlignment.h \
MuscleInterface.h GappedAligner.h PhyloTree.h SparseAbstractMatch.h \
DenseAbstractMatch.h RepeatMatch.h UngappedLocalAlignment.h \
AbstractGappedAlignment.h CompactGappedAlignment.h HybridAbstractMatch.h \
twister.h SubstitutionMatrix.h RepeatMatchList.h \
Backbone.h ProgressiveAligner.h PairwiseMatchAdapter.h PairwiseMatchFinder.h \
SeedOccurrenceList.h TreeUtilities.h SuperInterval.h GreedyBreakpointElimination.h \
LCB.h DistanceMatrix.h Scoring.h configuration.h Memory.h Files.h gnRAWSequence.h
HOMOLOGYHMM_H = HomologyHMM/homology.h HomologyHMM/dptables.h HomologyHMM/algebras.h HomologyHMM/parameters.h
DMSML_H = \
dmSML/asyncio.h dmSML/alinuxaio.h dmSML/aPOSIXaio.h \
dmSML/alibc.h dmSML/awin32aio.h dmSML/buffer.h \
dmSML/util.h dmSML/sorting.h dmSML/dmsort.h \
dmSML/timing.h dmSML/sml.h
LIBMEMS_SRC = \
RepeatHash.cpp \
DNAFileSML.cpp MatchFinder.cpp \
DNAMemorySML.cpp MemorySML.cpp SortedMerList.cpp \
FileSML.cpp MemHash.cpp MatchHashEntry.cpp \
Interval.cpp IntervalList.cpp twister.c \
gnAlignedSequences.cpp \
MatchList.cpp Aligner.cpp \
Islands.cpp MaskedMemHash.cpp GappedAlignment.cpp \
MuscleInterface.cpp PhyloTree.cpp \
RepeatMatchList.cpp RepeatMatch.cpp \
Backbone.cpp PairwiseMatchFinder.cpp ProgressiveAligner.cpp \
SuperInterval.cpp GreedyBreakpointElimination.cpp
HOMOLOGYHMM_SRC = \
HomologyHMM/algebras.cc HomologyHMM/homology.cc HomologyHMM/homologymain.cc
DMSML_SRC = \
dmSML/asyncio.c dmSML/alinuxaio.c dmSML/aPOSIXaio.c \
dmSML/alibc.c dmSML/awin32aio.c dmSML/buffer.c \
dmSML/util.c dmSML/sorting.c dmSML/dmsort.c \
dmSML/timing.c dmSML/sml.c
libmems_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)
libmems_include_HEADERS = $(LIBMEMS_H)
# build libraries with gcc (no suffix)
lib_LTLIBRARIES = libMems.la
libMems_la_SOURCES = $(LIBMEMS_SRC) $(HOMOLOGYHMM_SRC) $(DMSML_SRC)
libMems_la_LIBADD = @DEPS_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_IOSTREAMS_LIBS@ @BOOST_SYSTEM_LIBS@
libMems_la_LDFLAGS= -version-info $(GENERIC_LIBRARY_VERSION)
homologyhmm_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)/HomologyHMM
homologyhmm_include_HEADERS = $(HOMOLOGYHMM_H)
dmsml_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)/dmSML
dmsml_include_HEADERS = $(DMSML_H)
EXTRA_DIST = \
HomologyHMM/homology.xml
#EXTRA_PROGRAMS = TestSML TestSMLstatic
#TestSMLstatic_SOURCES = TestSML.cpp
#TestSMLstatic_INCLUDES = -I$(top_srcdir)/include/ `wx-config --cxxflags`
#TestSMLstatic_LDFLAGS = -static $(top_builddir)/libMems/libMems.a `wx-config --static --libs`
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