#  this looks better in -*- Makefile -*- mode
#	$Id: Makefile.generic 12479 2014-08-06 15:12:07Z haim $	

DEBUGEXEC = $(EXEC:=.debug)


#TEST_EXEC_SUB = 
TEST_EXEC = $(addprefix tests/,$(TEST_EXEC_SUB))

ifdef LIBNAME
  ifneq ($(LIBNAME),"")
	LIB = lib$(LIBNAME).a
  endif
endif
DEBUGLIB = $(LIB:.a=Debug.a)
DOUBLEREPLIB = $(LIB:.a=DoubleRep.a)

all: lib $(EXEC)

#CC=g++
CXX=g++
CC=$(CXX)

libDir=../../libs/phylogeny
binDir=../../bin

ifndef libEvol
  libEvol=$(libDir)/libEvolTree.a
  #libEvol=-lEvolTree
  libEvolDebug=$(libDir)/libEvolTreeDebug.a
  libEvolDoubleRep=$(libDir)/libEvolTreedoubleRep.a
endif

vpath % $(libDir)


#CPPFLAGS+= -I/usr/include/g++-v3

LDFLAGS += -L$(libDir)

#LDLIBS = -lEvolTree
#debug: LDLIBS = -lEvolTreeDebug
# LOADLIBES = $(LIB)

#LDFLAGS=  
#CPPFLAGS+= -DLOG -DLOGCLS -DMEMCHK


#GENGETOPT=/cs/++/phd/ninio/gengetopt-2.11/src/gengetopt
#GENGETOPT = /opt/local/bin/gengetopt
#GENGETOPT = ~privmane/code/gengetopt
GENGETOPT = gengetopt

.SECONDARY: $(addsuffix _cmdline.c,$(EXEC)) $(addsuffix _cmdline.h,$(EXEC)) $(addsuffix .ggo,$(EXEC))

CPPFLAGS=     -O3 -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG
CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -I$(libDir) -DLOG

LDFLAGSDEBUG := $(LDFLAGS) -g 
# sources
sources= $(Libsources) $(LibCsources) $(addsuffix .cpp,$(EXEC) $(TEST_EXEC))

.PHONY: tests lib test debug %.debug DOUBLEREP doubleRep

ifdef DOUBLEREP
CPPFLAGS+= -DDOUBLEREP
CPPFLAGSDEBUG += -DDOUBLEREP
LDFLAGSDEBUG +=  -DDOUBLEREP
endif

test: all tests
	+cd tests && make -k 

debug:  $(DEBUGLIB) $(DEBUGEXEC)

debug: CPPFLAGS = $(CPPFLAGSDEBUG)
#debug: LDLIBS = -lEvolTreeDebug
debug: LIB = $(DEBUGLIB)
# debug: CPPFLAGS = -g -Wall -Wno-sign-compare  -I. -I$(libDir) -DLOG
# debug: all




#$(libEvol) le:
#	+cd $(libDir);make -f Makefile all

#$(libEvolDebug):
#	+cd $(libDir);make -f Makefile debug

lib: $(LIB)

#lib$(LIBNAME).a: lib$(LIBNAME).a($(Libsources:.cpp=.o) $(LibCsources:.c=.o))
lib$(LIBNAME).a: $(Libsources:.cpp=.o) $(LibCsources:.c=.o)
	ar rv $@ $?
	ranlib $@

tags: *.cpp *.h
	etags --members --language=c++ $^ 
EVOLLIB=-lEvolTree
libEvolDebug=-lEvolTreeDebug
libEvolDoubleRep=-lEvolTreeDoubleRep

debug: EVOLLIB=$(libEvolDebug)

ifdef LIBNAME
#  LocalLib = -l$(LIBNAME)
  LocalLib = lib$(LIBNAME).a
endif

#$(EXEC): LDLIBS += $(EVOLLIB)
#$(EXEC) $(TEST_EXEC): $(LIB) #$(EVOLLIB)
#$(EXEC) $(TEST_EXEC): $(LIB) $(EVOLLIB)
$(EXEC) $(TEST_EXEC): $(LocalLib) $(libEvol)
$(DEBUGEXEC) $(TEST_EXEC): $(DEBUGLIB) $(libEvolDebug)

tests: $(TEST_EXEC) $(EXEC)

-include make.dep

install: $(addprefix $(binDir)/,$(EXEC))
$(binDir)/%: %
	cp $< $@



clean:
	-rm -f $(LIB) $(DEBUGLIB) $(DOUBLEREPLIB) $(EXEC) $(TEST_EXEC) $(DEBUGEXEC) $(DOUBLEREPEXEC) *.o


ifneq ($(wildcard make.dep), make.dep)
 make.dep: depend
endif


depend makedep: _make.dep
	@mv -f _make.dep make.dep 

_make.dep: $(sources)
	@echo making depend
#	$(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $^ | sed '\''s/\($*\)\.o[ :]*/\1.o $@ : /g'\'' > $@ ; [ -s $@ ] || rm -f $@' 
#	@$(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $^ > $@' 
	@$(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $^ | sed "s/\(^[^.]*\)\.o/\1.o \1.debug.o/g" > $@' 

_fast:
	+cd fast && make -k all

fast.% _fast.%:
	+cd fast && make -k $(*)

$(libEvol):
	+cd $(libDir)&&make -f Makefile all

$(libEvolDebug):
	+cd $(libDir)&&make -f Makefile debug

define ggo_template
ifeq ($(wildcard $(1).ggo), $(1).ggo)
   $(1): $(1)_cmdline.o
endif
endef

 $(foreach exec,$(EXEC),$(eval $(call ggo_template,$(exec))))

#$(EXEC): $(addsuffix _cmdline.o,$(EXEC))

define ggo_template_debug
   $(1).debug: $(1)_cmdline.debug.o
endef

$(foreach exec,$(EXEC),$(eval $(call ggo_template_debug,$(exec))))

define ggo_template_doublerep
ifeq ($(wildcard $(1).ggo), $(1).ggo)
   $(1).doubleRep: $(1)_cmdline.o
endif
endef

 $(foreach exec,$(EXEC),$(eval $(call ggo_template_doublerep,$(exec))))

#$(addsuffix .debug,$(EXEC)): $(addsuffix _cmdline.debug.o,$(EXEC))

%.ggo: %.args $(libDir)/evolObjs.args 
	cat $^ > $@


# commandline (gengetopts)
%_cmdline.h %_cmdline.c: %.ggo
	$(GENGETOPT)  -i$< -F$(*)_cmdline


debug: CPPFLAGS = $(CPPFLAGSDEBUG)
debug: $(addsuffix .debug,$(EXEC))
#$(addsuffix .debug,$(EXEC)): $(libEvolDebug)
pl:
	echo $(LIB)


%.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -I../.. -DLOG

%.debug: %.o 



#debug: LDLIBS = -lEvolTreeDebug
debug: LIB = $(DEBUGLIB)

%.debug: CPPFLAGS = $(CPPFLAGSDEBUG)
%.debug: LDFLAGS = $(LDFLAGSDEBUG)
#%.debug: %
#	@echo "made \""$(*)"\" in debug mode"


%.debug.o: %.c
	$(CC) -c $(CPPFLAGSDEBUG) $(CFLAGS) $< -o $@

%.debug.o: %.cpp
	$(CXX) -c $(CPPFLAGSDEBUG) $(CXXFLAGS) $< -o $@

#$(DEBUGLIB): $(Libsources:.cpp=.debug.o) $(LibCsources:.c=.debug.o)

lib$(LIBNAME)Debug.a: $(Libsources:.cpp=.debug.o) $(LibCsources:.c=.debug.o)
	ar rv $@ $?
	ranlib $@

DOUBLEREPEXEC = $(EXEC:=.doubleRep)

doubleRep: LOGREP=t
doubleRep: CPPFLAGS+= -DLOGREP
doubleRep: $(DOUBLEREPLIB) $(DOUBLEREPEXEC)
#	echo $@
$(DOUBLEREPEXEC): $(DOUBLEREPLIB) $(libEvolDoubleRep)

%.doubleRep.o: %.c
	$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@

%.doubleRep.o: %.cpp
	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@

$(DOUBLEREPLIB): $(Libsources:.cpp=.doubleRep.o) $(LibCsources:.c=.doubleRep.o)
	ar rv $@ $?
	ranlib $@

# DO NOT DELETE