makefile

马尔科夫模型的java版本实现

COMPILER = gcc




O_FILE_OPTIONS = -w -c
EXEC_FILE_OPTIONS = -w -lm

IO_FUNCS_MULTIALPHA = savehmm_multialpha.o readhmm_multialpha.o readseqs_multialpha.o readhmm.o savehmm.o
COMP_FUNCS_MULTIALPHA = core_algorithms_multialpha.o training_algorithms_multialpha.o
GEN_FUNCS = std_funcs.o debug_funcs.o std_calculation_funcs.o
GENGETOPT_FUNCS_TRAIN = cmdline_hmmtrain.o
GENGETOPT_FUNCS_SEARCH = cmdline_hmmsearch.o
GENGETOPT_FUNCS_SEQALIGN = cmdline_modseqalign.o
GENGETOPT_FUNCS_ALPHA = cmdline_add_alphabet.o
HEADERS = structs.h funcs.h


BASIC_TRAINING_PROGS = modhmmt
BASIC_SEARCHING_PROGS = modhmms
BASIC_ALIGN_PROGS = modseqalign
EXTENSION_PROGS = add_alphabet


all: $(BASIC_TRAINING_PROGS) $(BASIC_SEARCHING_PROGS) $(BASIC_ALIGN_PROGS) $(EXTENSION_PROGS)



#gengetopt functions
cmdline_hmmtrain.o: cmdline_hmmtrain.c cmdline_hmmtrain.h
	$(COMPILER) $(O_FILE_OPTIONS) cmdline_hmmtrain.c
cmdline_hmmsearch.o: cmdline_hmmsearch.c cmdline_hmmsearch.h
	$(COMPILER) $(O_FILE_OPTIONS) cmdline_hmmsearch.c
cmdline_modseqalign.o: cmdline_modseqalign.c cmdline_modseqalign.h
	$(COMPILER) $(O_FILE_OPTIONS) cmdline_modseqalign.c
cmdline_add_alphabet.o: cmdline_add_alphabet.c cmdline_add_alphabet.h
	$(COMPILER) $(O_FILE_OPTIONS) cmdline_add_alphabet.c

#general functions
std_funcs.o: std_funcs.c structs.h funcs.h
	$(COMPILER) $(O_FILE_OPTIONS) std_funcs.c

std_calculation_funcs.o: std_calculation_funcs.c structs.h funcs.h
	$(COMPILER) $(O_FILE_OPTIONS) std_calculation_funcs.c

debug_funcs.o: debug_funcs.c $(HEADERS)
	$(COMPILER) $(O_FILE_OPTIONS) debug_funcs.c


#io functions
readhmm.o: readhmm.c $(HEADERS)
	$(COMPILER) $(O_FILE_OPTIONS) readhmm.c

readhmm_multialpha.o: readhmm_multialpha.c $(HEADERS)
	$(COMPILER) $(O_FILE_OPTIONS) readhmm_multialpha.c

savehmm_multialpha.o: savehmm_multialpha.c $(HEADERS)
	$(COMPILER) $(O_FILE_OPTIONS) savehmm_multialpha.c

savehmm.o: savehmm.c $(HEADERS)
	$(COMPILER) $(O_FILE_OPTIONS) savehmm.c

readseqs_multialpha.o: readseqs_multialpha.c $(HEADERS)
	$(COMPILER) $(O_FILE_OPTIONS) readseqs_multialpha.c



#computational functions
core_algorithms_multialpha.o: core_algorithms_multialpha.c $(HEADERS)
	$(COMPILER) $(O_FILE_OPTIONS) core_algorithms_multialpha.c

training_algorithms_multialpha.o: training_algorithms_multialpha.c $(HEADERS)
	$(COMPILER) $(O_FILE_OPTIONS) training_algorithms_multialpha.c



#executables
modhmms: hmmsearch.o $(IO_FUNCS_MULTIALPHA) $(COMP_FUNCS_MULTIALPHA) $(GEN_FUNCS) $(GENGETOPT_FUNCS_SEARCH)
	$(COMPILER) $(EXEC_FILE_OPTIONS)  hmmsearch.o $(IO_FUNCS_MULTIALPHA) $(COMP_FUNCS_MULTIALPHA) $(GEN_FUNCS) $(GENGETOPT_FUNCS_SEARCH) -o modhmms
hmmsearch.o: hmmsearch.c $(HEADERS)
	$(COMPILER) $(O_FILE_OPTIONS) hmmsearch.c


modhmmt: hmmtrain.o $(IO_FUNCS_MULTIALPHA) $(COMP_FUNCS_MULTIALPHA) $(GEN_FUNCS) $(GENGETOPT_FUNCS_TRAIN)
	$(COMPILER) $(EXEC_FILE_OPTIONS)  hmmtrain.o $(IO_FUNCS_MULTIALPHA) $(COMP_FUNCS_MULTIALPHA) $(GEN_FUNCS) $(GENGETOPT_FUNCS_TRAIN) -o modhmmt
hmmtrain.o: hmmtrain.c $(HEADERS)
	$(COMPILER) $(O_FILE_OPTIONS) hmmtrain.c

modseqalign: modseqalign.o $(IO_FUNCS_MULTIALPHA) $(COMP_FUNCS_MULTIALPHA) $(GEN_FUNCS) $(GENGETOPT_FUNCS_SEQALIGN)
	$(COMPILER) $(EXEC_FILE_OPTIONS)  modseqalign.o $(IO_FUNCS_MULTIALPHA) $(COMP_FUNCS_MULTIALPHA) $(GEN_FUNCS) $(GENGETOPT_FUNCS_SEQALIGN) -o modseqalign
modseqalign.o: modseqalign.c $(HEADERS)
	$(COMPILER) $(O_FILE_OPTIONS) modseqalign.c

add_alphabet: add_alphabet.o $(IO_FUNCS_MULTIALPHA) $(GEN_FUNCS) $(GENGETOPT_FUNCS_ALPHA) 
	$(COMPILER) $(EXEC_FILE_OPTIONS)  add_alphabet.o $(IO_FUNCS_MULTIALPHA) $(GEN_FUNCS) $(GENGETOPT_FUNCS_ALPHA) -o add_alphabet
add_alphabet.o: add_alphabet.c $(HEADERS)
	$(COMPILER) $(O_FILE_OPTIONS) add_alphabet.c