PREFIX			= /usr/local/bin
TEST				= test/
CC					= gcc  
CFLAGS			= -O9   -Wall 
DEBUGFLAGS		= -ggdb  -Wall -m32 

SOURCES			= main.c make_sets.c io.c best.c print_reliable_alignment.c
PROGS				= mumsa
DEBUGPROGS	= mumsa_debug
OBJECTS			= $(SOURCES:.c=.o)
DEBUGOBJECTS	= $(SOURCES:.c=_debug.o)


all: $(OBJECTS)
	$(CC) $(CFLAGS) $(OBJECTS) -o $(PROGS)

main.o: main.c cmsa.h
	$(CC) $(CFLAGS) -c main.c  

make_sets.o: make_sets.c cmsa.h
	$(CC) $(CFLAGS) -c make_sets.c  
	
io.o: io.c cmsa.h
	$(CC) $(CFLAGS) -c io.c  
	
best.o: best.c cmsa.h
	$(CC) $(CFLAGS) -c best.c  
	
print_reliable_alignment.o: print_reliable_alignment.c cmsa.h
	$(CC) $(CFLAGS) -c print_reliable_alignment.c  

	
debug: $(DEBUGOBJECTS)
	$(CC) $(DEBUGFLAGS) $(DEBUGOBJECTS) -o $(DEBUGPROGS)	
	
main_debug.o: main.c cmsa.h
	$(CC) $(DEBUGFLAGS) -c main.c -o main_debug.o

make_sets_debug.o: make_sets.c cmsa.h
	$(CC) $(DEBUGFLAGS) -c make_sets.c  -o make_sets_debug.o
	
io_debug.o: io.c cmsa.h
	$(CC) $(DEBUGFLAGS) -c io.c  -o io_debug.o

best_debug.o: best.c cmsa.h
	$(CC) $(DEBUGFLAGS) -c best.c  -o best_debug.o
	
print_reliable_alignment_debug.o: print_reliable_alignment.c cmsa.h
	$(CC) $(DEBUGFLAGS) -c print_reliable_alignment.c  -o print_reliable_alignment_debug.o

install : 
	mkdir -p $(PREFIX)
	cp $(PROGS)  $(PREFIX)
	chmod 755 $(PREFIX)/$(PROGS)



clean: 
	rm -f $(PROGS) $(OBJECTS)
	rm -f $(DEBUGPROGS) $(DEBUGOBJECTS)
	rm -f *~
	
