Makefile.in

PREFIX			= /usr/local/bin
TEST				= test/
CC					= gcc  
CFLAGS			= -O9  -Wall 
DEBUGFLAGS		= -ggdb -DDEBUG -DDEBUG_READ_SEQ -DDEBUG_MEM -DDEBUG_SS -DDEBUG_PS -DDEBUG_PROFILE -Wall 

SOURCES			= kalignP_distance_calculation.c kalignP_dp.c kalignP_input.c kalignP_main.c kalignP_mem.c kalignP_interface.c kalignP_misc.c kalignP_tree.c  kalignP_profile.c kalignP_alignment_types.c kalignP_feature.c kalignP_hirschberg.c  kalignP_advanced_gaps.c kalignP_hirschberg_dna.c  kalignP_output.c kalignP_string_matching.c kalignP_profile_alignment.c 
PROGS				= kalignP
DEBUGPROGS	= kalignP_debug


OBJECTS			= $(SOURCES:.c=.o)
DEBUGOBJECTS	= $(SOURCES:.c=_debug.o)


.PHONY: clean

all: $(OBJECTS)
	$(CC) $(CFLAGS) $(OBJECTS) -o $(PROGS)
	
%.o:	%.c
	$(CC) $(CFLAGS) -c $<
	
debug: $(DEBUGOBJECTS)
	$(CC) $(DEBUGFLAGS) $(DEBUGOBJECTS) -o $(DEBUGPROGS)	

%_debug.o:	%.c
	$(CC) $(DEBUGFLAGS) -c $< -o $@


install:
	cp $(PROGS) /usr/local/bin/
	
clean: 
	rm -f $(PROGS) $(OBJECTS)
	rm -f $(DEBUGPROGS) $(DEBUGOBJECTS)
	rm -f config.status config.log config.h Makefile
	rm -f test*
	rm -f *~