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

OBJS1 = \
check_argc_sds.o \
align_sds_stem1.o readfile_sds_stem1.o tool_sds_stem1.o \
dp_sds_stem1.o keep_memory_sds_stem1.o \
keep_memory_b.o make_prof_stem1.o \
keep_memory_s.o \
generateD_b.o dist_b_sds.o cost_b_stem1.o minimum_b.o \
generateD_s.o dist_s_sds.o cost_s_stem1.o minimum_s.o \
make_alignment_sds_stem1.o

OBJS2 = \
align_apdp_s_sds_stem1.o readfile_sds_stem1.o tool_sds_stem1.o \
keep_memory_s.o \
generateD_s.o dist_s_sds.o cost_s_stem1.o minimum_s.o

OBJ_D = matrix_dna.o 

all: astem dstem

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

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

clean:
	rm -f $(OBJS1) $(OBJS2) $(OBJ_D) aligner_sds.o apdp_s_sds.o
