install: convseq resbias bias2relacs coils2relacs comp_query query_seqerrs query2relacs chain_blocks chain_allblocks phylo_blocks query2first

clean:
	rm *.o

HEADERS = general.h leon.h

OBJECTS = init.o readseq.o readxml.o writeseq.o util.o readmat.o quicknj.o rascal_util.o

CC	= cc
CFLAGS  = -c -O 
LFLAGS  = -O -lm  -L$(EXPAT_LIB) -lexpat
EXPAT_LIB       = /home/julie/expat-1.95.6/lib
EXPAT_INC       = /home/julie/expat-1.95.6/lib


convseq : $(OBJECTS) convseq.o
	$(CC) -o $@ $(OBJECTS) convseq.o $(LFLAGS)

resbias : util.o readseq.o readxml.o resbias.o
	$(CC) -o $@ util.o readseq.o readxml.o resbias.o $(LFLAGS)

bias2relacs : $(OBJECTS) bias2relacs.o
	$(CC) -o $@ $(OBJECTS) bias2relacs.o $(LFLAGS)

coils2relacs : $(OBJECTS) coils2relacs.o
	$(CC) -o $@ $(OBJECTS) coils2relacs.o $(LFLAGS)

comp_query : $(OBJECTS) readtree.o seqweight.o comp_query.o
	$(CC) -o $@ $(OBJECTS) readtree.o seqweight.o comp_query.o $(LFLAGS)

query_seqerrs : $(OBJECTS) readtree.o seqweight.o query_seqerrs.o
	$(CC) -o $@ $(OBJECTS) readtree.o seqweight.o query_seqerrs.o $(LFLAGS)

query2relacs : $(OBJECTS) query2relacs.o
	$(CC) -o $@ $(OBJECTS) query2relacs.o $(LFLAGS)

query2first : $(OBJECTS) query2first.o
	$(CC) -o $@ $(OBJECTS) query2first.o $(LFLAGS)

chain_blocks : $(OBJECTS) chain_blocks.o
	$(CC) -o $@ $(OBJECTS) chain_blocks.o $(LFLAGS)

chain_allblocks : $(OBJECTS) chain_allblocks.o
	$(CC) -o $@ $(OBJECTS) chain_allblocks.o $(LFLAGS)

phylo_blocks : $(OBJECTS) phylo_blocks.o
	$(CC) -o $@ $(OBJECTS) phylo_blocks.o $(LFLAGS)

amenu.o : amenu.c $(HEADERS) param.h
	$(CC) $(CFLAGS) $*.c

readmat.o : readmat.c $(HEADERS) matrices.h
	$(CC) $(CFLAGS) $*.c

readxml.o : readxml.c $(HEADERS)
	$(CC) $(CFLAGS) -I$(EXPAT_INC) $*.c

.c.o :	$(HEADERS)
	$(CC) $(CFLAGS) $?

