LOCAL_POS = ../lib
#include "../lib/app.config"

XCOMM Program for overlap module
PROG1=jigsaw
XCOMM Build both automatically
PROGLIST=$(PROG1)

Annotation.o : RegionPrediction.hpp
AnnotationMatrix.o : RegionPrediction.hpp

LOCAL_LDFLAGS = 
CXXOPTIONS=-D__USE_ISOC9X -H -v
CXXOPTIONS=
BBLIBLOC=./$(BBLIB)
AALIBLOC=$(LOCAL_POS)/src/$(AALIB)
OBJS = InputData.o PrintVec.o Custom7.o LinComb.o LinComb2.o
LIBOBJ = \
CustomScore.o TerminalExon.o ScoreInterval.o \
MatrixIdx.o MatrixItemContents.o InternalExon.o \
IntronInterval.o IgrInterval.o TransProb.o InitialExon.o SingleExon.o AnsCheck.o \
RegionPrediction.o EvScores.o TraceBack.o Main.o \
AnnotationMatrix.o AnnotationItem.o Annotation.o Combine.o

XCOMM I want to keep these around to see if I can figure out a way to combine
XCOMM both my nonoverlapping scoring method with an overlaping interval scoring method
XCOMM CustomInterval.o RecordInterval.o PrintInterval.o

#define PassCDebugFlags 'CDEBUGFLAGS=$(CDEBUGFLAGS)'

MODULE_DIRS=../lib/src
SUBDIRS=$(MODULE_DIRS)

MakefileSubdirs($(SUBDIRS))
MakeSubdirs($(SUBDIRS))
CleanSubdirs($(SUBDIRS))
InstallSubdirs($(SUBDIRS))

DEPLIST = $(BBLIBLOC)
AllTarget( $(BBLIBLOC) $(PROGLIST))

LD_FLAGS=
SYSLIBS = -lm
LOCAL_LIBDIR=./lib
NormalLibraryTarget($(BB),$(LIBOBJ))
NormalCplusplusProgramTarget($(PROG1), comb1.o $(OBJS), $(DEPLIST) $(BBLIBLOC) $(AALIBLOC),, $(BBLIBLOC) $(AALIBLOC) $(SYSLIBS) $(CXXLIBS))
InstallProgram($(PROG1),../../bin/$(HOSTTYPE))
CleanTarget()
cl:
	rm -f *.o $(PROG1) *.a
