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The purpose of this patch is to add a rule for the building of probcons-RNA.
--- probcons.orig/Makefile
+++ probcons/Makefile
@@ -16,6 +16,7 @@
################################################################################
OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.12"
+OTHERFLAGS-RNA = -DNumInsertStates=1 -DVERSION="1.12"
# debug mode
#CXXFLAGS = -g -W -Wall -pedantic -DENABLE_CHECKS -fno-inline $(OTHERFLAGS)
@@ -25,13 +26,16 @@
# release mode
#CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer
+
CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
+CXXFLAGS-RNA = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS-RNA) -funroll-loops
+
################################################################################
# 3) Dependencies
################################################################################
-TARGETS = probcons compare project makegnuplot
+TARGETS = probcons probcons-RNA compare project makegnuplot
.PHONY : all
all : $(TARGETS)
@@ -42,6 +46,9 @@
compare : MultiSequence.h Sequence.h FileBuffer.h SafeVector.h CompareToRef.cc
$(CXX) $(CXXFLAGS) -o compare CompareToRef.cc
+probcons-RNA : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults-RNA.h SafeVector.h Main-RNA.cc
+ $(CXX) $(CXXFLAGS-RNA) -lm -o probcons-RNA Main-RNA.cc
+
fixref : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h FixRef.cc
$(CXX) $(CXXFLAGS) -o fixref FixRef.cc
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