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

OBJS1 = \
check_argc_new.o \
align_new.o readfile.o tool_new.o \
dp_new.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_new.o readfile.o tool_new.o \
keep_memory_s.o \
generateD_s.o dist_s.o cost_s.o minimum_s.o

all: align_a dist_a align_d dist_d gtoa2 atog1

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

dist_a: $(OBJS2) matrix_amino.o apdp_s_amino.o
	cc -o dist_a $(OBJS2) matrix_amino.o apdp_s_amino.o $(LIBS)

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

dist_d: $(OBJS2) matrix_dna.o apdp_s_dna.o
	cc -o dist_d $(OBJS2) matrix_dna.o apdp_s_dna.o $(LIBS)

gtoa2: gtoa2.o
	cc -o gtoa2 gtoa2.o $(LIBS)

atog1: atog1.o
	cc -o atog1 atog1.o $(LIBS)

clean:
	rm -f $(OBJS1) $(OBJS2) \
	aligner.o apdp_s_amino.o \
	apdp_s_dna.o atog1.o \
	gtoa2.o matrix_amino.o \
	matrix_dna.o
