#CC = gcc
CFLAGS = -DBSD -O
#CFLAGS = -DSYS5 -DSYSV -O
LIBS = -lm

OBJS1 = \
check_argc.o \
align.o readfile.o tool.o \
dp.o keep_memory.o \
keep_memory_b.o make_prof.o \
keep_memory_s.o \
generateD_b.o dist_b.o cost_b.o minimum_b.o \
generateD_s.o dist_s.o cost_s.o minimum_s.o \
make_alignment.o

OBJS2 = \
align_apdp_s.o readfile.o tool.o \
keep_memory_s.o \
generateD_s.o dist_s.o cost_s.o minimum_s.o

all: align_amino dist_amino align_dna dist_dna

align_amino: $(OBJS1) matrix_amino.o aligner.o
	cc -o align_amino $(OBJS1) matrix_amino.o aligner.o $(LIBS)

dist_amino: $(OBJS2) matrix_amino.o apdp_s.o
	cc -o dist_amino $(OBJS2) matrix_amino.o apdp_s.o $(LIBS)

align_dna: $(OBJS1) matrix_dna.o aligner.o
	cc -o align_dna $(OBJS1) matrix_dna.o aligner.o $(LIBS)

dist_dna: $(OBJS2) matrix_dna.o apdp_s.o
	cc -o dist_dna $(OBJS2) matrix_dna.o apdp_s.o $(LIBS)

clean:
	rm -f $(OBJS1) align_apdp_s.o \
	matrix_amino.o aligner.o \
	apdp_s.o matrix_dna.o
