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

OBJS1 = \
check_argc_sds.o \
align_sds.o readfile_sds.o tool_sds.o \
dp_sds.o keep_memory_sds.o \
keep_memory_b.o make_prof.o \
keep_memory_s.o \
generateD_b.o dist_b_sds.o cost_b.o minimum_b.o \
generateD_s.o dist_s_sds.o cost_s.o minimum_s.o \
make_alignment_sds.o

OBJS2 = \
align_apdp_s_sds.o readfile_sds.o tool_sds.o \
keep_memory_s.o \
generateD_s.o dist_s_sds.o cost_s.o minimum_s.o

OBJ_A = matrix_amino.o 

OBJ_D = matrix_dna.o 

all: ass_a dss_a ass_d dss_d

ass_a: $(OBJS1) $(OBJ_A) aligner_sds.o
	cc -o ass_a $(OBJS1) $(OBJ_A) aligner_sds.o $(LIBS)

dss_a: $(OBJS2) $(OBJ_A) apdp_s_sds.o
	cc -o dss_a $(OBJS2) $(OBJ_A) apdp_s_sds.o $(LIBS)

ass_d: $(OBJS1) $(OBJ_D) aligner_sds.o
	cc -o ass_d $(OBJS1) $(OBJ_D) aligner_sds.o $(LIBS)

dss_d: $(OBJS2) $(OBJ_D) apdp_s_sds.o
	cc -o dss_d $(OBJS2) $(OBJ_D) apdp_s_sds.o $(LIBS)

clean:
	rm -f $(OBJS1) $(OBJS2) \
	aligner_sds.o apdp_s_sds.o \
	matrix_amino.o 	matrix_dna.o
