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CXX = g++
GCC = gcc
CXXFLAGS = -g -O3 -Wall -Wextra -Wno-char-subscripts -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -lpthread -lmstoolkitlite
EXECNAME = comet-ms
COMETSEARCH = Comet.o Threading.o CometInterfaces.o CometSearch.o CometPreprocess.o CometPostAnalysis.o CometMassSpecUtils.o CometWriteOut.o CometWriteSqt.o CometWritePepXML.o CometWritePercolator.o CometWriteTxt.o CometSearchManager.o
comet: $(COMETSEARCH)
${CXX} $(CXXFLAGS) $(COMETSEARCH) $(LIBPATHS) $(LIBS) -o ${EXECNAME}
Comet.o: Comet.cpp
${CXX} ${CXXFLAGS} Comet.cpp -c
Threading.o: Threading.cpp Threading.h
${CXX} ${CXXFLAGS} Threading.cpp -c
CometSearch.o: CometSearch.cpp Common.h CometData.h CometDataInternal.h CometSearch.h CometInterfaces.h ThreadPool.h
${CXX} ${CXXFLAGS} CometSearch.cpp -c
CometPreprocess.o: CometPreprocess.cpp Common.h CometData.h CometDataInternal.h CometPreprocess.h CometInterfaces.h
${CXX} ${CXXFLAGS} CometPreprocess.cpp -c
CometMassSpecUtils.o: CometMassSpecUtils.cpp Common.h CometData.h CometDataInternal.h CometMassSpecUtils.h CometInterfaces.h
${CXX} ${CXXFLAGS} CometMassSpecUtils.cpp -c
CometPostAnalysis.o: CometPostAnalysis.cpp Common.h CometData.h CometDataInternal.h ThreadPool.h CometPostAnalysis.h CometMassSpecUtils.h CometInterfaces.h CometDecoys.h
${CXX} ${CXXFLAGS} CometPostAnalysis.cpp -c
CometWriteOut.o: CometWriteOut.cpp Common.h CometData.h CometDataInternal.h CometMassSpecUtils.h CometWriteOut.h CometInterfaces.h
${CXX} ${CXXFLAGS} CometWriteOut.cpp -c
CometWriteSqt.o: CometWriteSqt.cpp Common.h CometData.h CometDataInternal.h CometMassSpecUtils.h CometWriteSqt.h CometInterfaces.h
${CXX} ${CXXFLAGS} CometWriteSqt.cpp -c
CometWritePepXML.o: CometWritePepXML.cpp Common.h CometData.h CometDataInternal.h CometMassSpecUtils.h CometWritePepXML.h CometInterfaces.h
${CXX} ${CXXFLAGS} CometWritePepXML.cpp -c
CometWritePercolator.o: CometWritePercolator.cpp Common.h CometData.h CometDataInternal.h CometMassSpecUtils.h CometWritePercolator.h CometInterfaces.h
${CXX} ${CXXFLAGS} CometWritePercolator.cpp -c
CometWriteTxt.o: CometWriteTxt.cpp Common.h CometData.h CometDataInternal.h CometMassSpecUtils.h CometWriteTxt.h CometInterfaces.h
${CXX} ${CXXFLAGS} CometWriteTxt.cpp -c
CometSearchManager.o: CometSearchManager.cpp Common.h CometData.h CometDataInternal.h CometMassSpecUtils.h CometSearch.h CometPostAnalysis.h CometWriteOut.h CometWriteSqt.h CometWriteTxt.h CometWritePepXML.h CometWritePercolator.h Threading.h ThreadPool.h CometSearchManager.h CometInterfaces.h
${CXX} ${CXXFLAGS} CometSearchManager.cpp -c
CometInterfaces.o: CometInterfaces.cpp Common.h CometData.h CometDataInternal.h CometMassSpecUtils.h CometSearch.h CometPostAnalysis.h CometWriteOut.h CometWriteSqt.h CometWriteTxt.h CometWritePepXML.h CometWritePercolator.h Threading.h ThreadPool.h CometSearchManager.h CometInterfaces.h
${CXX} ${CXXFLAGS} CometInterfaces.cpp -c
clean:
rm -f *.o
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