| 1 | ################################################################################ |
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| 2 | # Makefile for probcons |
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| 3 | ################################################################################ |
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| 4 | |
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| 5 | ################################################################################ |
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| 6 | # 1) Choose C++ compiler. |
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| 7 | ################################################################################ |
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| 8 | |
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| 9 | CXX = g++ |
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| 10 | |
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| 11 | ################################################################################ |
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| 12 | # 2) Set C++ flags. |
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| 13 | # a) DEBUG mode -- no optimizations, enable SafeVector checking, no inlining |
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| 14 | # b) PROFILE mode -- for gprof |
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| 15 | # c) RELEASE mode |
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| 16 | ################################################################################ |
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| 17 | BIG_INLINE_LIMIT = 20000 |
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| 18 | |
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| 19 | PROBCONS = ./probconsRNA |
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| 20 | VIENNA = ./vienna |
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| 21 | |
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| 22 | # no -Wall option for warning |
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| 23 | #CXXFLAGS = -O3 -funroll-loops -finline-limit=$(BIG_INLINE_LIMIT) |
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| 24 | CXXFLAGS = -O3 # by katoh |
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| 25 | OFLAGS = -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" $(CXXFLAGS) $(CFLAGS1) |
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| 26 | LIBS = -L$(PROBCONS) -L./ |
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| 27 | INCL = -I$(PROBCONS) -I$(VIENNA) -I./ |
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| 28 | |
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| 29 | ################################################################################ |
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| 30 | # 3) Dependencies |
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| 31 | ################################################################################ |
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| 32 | |
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| 33 | TARGETS = mxscarna |
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| 34 | |
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| 35 | OBJS = Main.o McCaskill.o vienna/energy_param.o seq2scs.o Globaldp.o postProcessings.o AlifoldMEA.o |
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| 36 | |
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| 37 | .PHONY : all |
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| 38 | all : $(TARGETS) |
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| 39 | |
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| 40 | mxscarna : $(OBJS) |
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| 41 | $(CXX) $(LIBS) $(OFLAGS) -lm -o $@ $(OBJS) |
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| 42 | |
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| 43 | rfold: |
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| 44 | cd $(RFOLD); \ |
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| 45 | make; \ |
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| 46 | cd .. \ |
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| 47 | cd .. |
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| 48 | probcons: |
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| 49 | cd $(PROBCONS); \ |
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| 50 | make; \ |
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| 51 | cd .. |
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| 52 | |
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| 53 | #probcons : MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Main.cc |
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| 54 | # $(CXX) -lm -o probcons $(OBJS) |
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| 55 | #Main.cc |
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| 56 | |
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| 57 | Main.o : $(PROBCONS)/SafeVector.h $(PROBCONS)/FileBuffer.h $(PROBCONS)/Sequence.h $(PROBCONS)/MultiSequence.h $(PROBCONS)/EvolutionaryTree.h scarna.hpp BPPMatrix.hpp StemCandidate.hpp Globaldp.hpp AlifoldMEA.h Main.cc |
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| 58 | $(CXX) $(INCL) $(OFLAGS) -c Main.cc -o Main.o |
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| 59 | McCaskill.o: McCaskill.hpp $(VIENNA)/energy_param.hpp Util.hpp Beta.hpp ScoreType.hpp McCaskill.cpp |
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| 60 | $(CXX) $(INCL) $(OFLAGS) -c McCaskill.cpp -o McCaskill.o |
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| 61 | $(VIENNA)/energy_param.o: $(VIENNA)/energy_param.hpp $(VIENNA)/energy_param.cpp |
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| 62 | $(CXX) $(INCL) $(OFLAGS) -c $(VIENNA)/energy_param.cpp -o $(VIENNA)/energy_param.o |
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| 63 | seq2scs.o: $(PROBCONS)/SafeVector.h StemCandidate.hpp $(PROBCONS)/Sequence.h $(PROBCONS)/MultiSequence.h BPPMatrix.hpp nrutil.h seq2scs.cpp |
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| 64 | $(CXX) $(INCL) $(OFLAGS) -c seq2scs.cpp -o seq2scs.o |
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| 65 | Globaldp.o: Globaldp.hpp nrutil.h Util.hpp Beta.hpp scarna.hpp StemCandidate.hpp $(PROBCONS)/MultiSequence.h $(PROBCONS)/Sequence.h BPPMatrix.hpp |
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| 66 | $(CXX) $(INCL) $(OFLAGS) -c Globaldp.cpp -o Globaldp.o |
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| 67 | GlobalParameters.o: scarna.hpp |
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| 68 | $(CXX) $(INCL) $(OFLAGS) -c GlobalParameters.cpp -o GlobalParameters.o |
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| 69 | postProcessings.o: StemCandidate.hpp scarna.hpp |
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| 70 | $(CXX) $(INCL) $(OFLAGS) -c postProcessings.cpp -o postProcessings.o |
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| 71 | AlifoldMEA.o: nrutil.h Util.hpp Beta.hpp BPPMatrix.hpp $(PROBCONS)/MultiSequence.h $(PROBCONS)/Sequence.h $(PROBCONS)/SafeVector.h |
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| 72 | $(CXX) $(INCL) $(OFLAGS) -c AlifoldMEA.cpp -o AlifoldMEA.o |
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| 73 | |
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| 74 | .PHONY : clean |
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| 75 | clean: |
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| 76 | rm -f $(TARGETS) *.o *.h~ *.hpp~ *.cpp~ *.cc~ $(VIENNA)/*.o |
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| 77 | $(MAKE) -C $(PROBCONS) clean |
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