#Makefile for relateHMM 
#author thorfinn@binf.ku.dk


#program testet on gnu compilers
CC=g++
C=gcc



#this is the flags used for dev.
#flags=-ggdb -Wall -pedantic -ansi 

#flags= -O2 -pg

#this is the flag used for prod.
flags=-O3
fpic=-fPIC

 
all : relateHMM.o relateHMMRun HMMtest


bfgs.o : bfgs.c bfgs.h types.h
	$(C) -c $(fpic) -std=gnu99 -O2  bfgs.c 

alloc.o : alloc.h alloc.cpp types.h
	$(CC) -c $(fpic)   alloc.cpp ${flags}

ld.o : ld.cpp ld.h types.h
	$(CC)  -c $(fpic)  ld.cpp ${flags}

asort.o : asort.cpp asort.h types.h alloc.o
	$(CC) -c asort.cpp ${flags}

filereader_and_conversions.o : filereader_and_conversions.cpp filereader_and_conversions.h types.h
	$(CC) -c filereader_and_conversions.cpp ${flags}

extractors.o : extractors.cpp extractors.h types.h
	$(CC) -c extractors.cpp ${flags}

relateHMM.o:  relateHMM.cpp relateHMM.h ld.o alloc.o asort.o types.h filereader_and_conversions.o extractors.o
	$(CC) -c $(fpic)  relateHMM.cpp  ${flags}


relateHMMRun : relateHMM.o runRelate.cpp relateHMM.o bfgs.o alloc.o ld.o asort.o filereader_and_conversions.o types.h extractors.o
	$(CC) -o relateHMM runRelate.cpp asort.o relateHMM.o bfgs.o alloc.o ld.o filereader_and_conversions.o extractors.o ${flags}

HMMtest : HMMtest.cpp alloc.o types.h
	$(CC) -o HMMtest HMMtest.cpp alloc.o ${flags} 

makeR: HMMld.cpp relateHMM.o bfgs.o ld.o 
	R CMD SHLIB HMMld.cpp relateHMM.o bfgs.o alloc.o ld.o 

clean:
	rm  -f *.o  relateHMM Relate.so HMMtest