CC = g++
CCOPT = -O3 -g
LIBS = -lm
INCDIRS = -I./
CFLAGS = ${CCOPT} ${INCDIRS}

#----------------all programs----------------------------
all: rapsearch prerapsearch

#-----------------Objects--------------------------------
FUN0 = File.o StringEx.o SuffixArray.o Larsson.o Kasai.o MaximalExactPair.o\
       BioSuffixArray.o BioFile.o FastaFile.o FastaLikeFile.o MultipleSequence.o SequenceFactory.o\
       Reverse.o Complement.o ReverseComplement.o Translation.o\
       EncodeProtein.o Seg.o BlastStat.o AlnParser.o DBInfo.o PreSearch.o

#---------------include dependencies--------------------

#---------------make programs----------------------------

.cpp.o:
	$(CC) $(CFLAGS) -c $<

OBJ_PRE = PreSwift.o ExpSearch.o $(FUN0)
prerapsearch : $(OBJ_PRE)
	$(CC) $(CCOPT) -o prerapsearch $(OBJ_PRE) $(LIBS)

OBJ_SWIFT = Swift.o ExpSearch.o $(FUN0)
rapsearch :   $(OBJ_SWIFT)
	$(CC) $(CCOPT) -o rapsearch $(OBJ_SWIFT) $(LIBS)

clean:
	rm -f *.o
	rm -f rapsearch prerapsearch
