
CC = g++
CPPFLAGS = -O3

XERCES_ROOT = /export/home/nbandeira/OpenMS_contrib-0.17

CPPLIB_OBJ = abruijn.o\
	alignment_scoring.o\
	aminoacid.o\
	base64.o\
	batch.o\
	db_fasta.o\
	graph.o\
	hash.o\
	inputParams.o\
	label.o\
	setmerger.o\
	spectral_alignment.o\
	spectral_pairs.o\
	spectrum.o\
	tags.o\
	utils.o

CPPLIB_SRC = abruijn.cpp abruijn.h\
	alignment_scoring.cpp alignment_scoring.h\
	aminoacid.cpp aminoacid.h\
	base64.c base64.h\
	batch.cpp batch.h\
	db_fasta.cpp db_fasta.h\
	graph.cpp graph.h\
	hash.cpp hash.h\
	inputParams.cpp inputParams.h\
	label.cpp label.h\
	setmerger.cpp setmerger.h\
	spectral_alignment.cpp spectral_alignment.h\
	spectral_pairs.cpp spectral_pairs.h\
	spectrum.cpp spectrum.h\
	tags.cpp tags.h\
	twovalues.h\
	utils.cpp utils.h 

all: $(CPPLIB_SRC) convert filterpairs specalign masab
	cd pepnovo ; make ; cp PepNovo_bin .. ; cd ..

clean:
	rm *.o convert filterpairs specalign filterstarpairs tagsearch pathproj PepNovo_bin; cd pepnovo; make clean; cd ..

.o.o: $(CPPLIB_SRC)
	$(CC) $(CPPFLAGS) $<

base64.o: base64.c base64.h
	$(CC) -c $(CPPFLAGS) base64.c

convert: convert.cpp mzxml.cpp $(CPPLIB_OBJ)
	$(CC) $(CPPFLAGS) -I$(XERCES_ROOT)/include -L$(XERCES_ROOT)/lib/ -lxerces-c $^ -o $@

filterpairs: filterpairs.cpp $(CPPLIB_OBJ)
	$(CC) $(CPPFLAGS) $^ -o $@

specalign: specalign.cpp $(CPPLIB_OBJ)
	$(CC) $(CPPFLAGS) $^ -o $@

masab: masab.cpp $(CPPLIB_OBJ)
	$(CC) $(CPPFLAGS) $^ -o $@
