CC=g++
CFLAGS=-O3 -Wall -c -fmessage-length=0
LDFLAGS=-static
LIB=-lPopPhyl_Commons -lbpp-seq -lbpp-core
BPP=/usr/
LIBPATH=-L../../lib/ -L$(BPP)/lib/
SRC=-I../PopPhyl_Commons/ -I$(BPP)include/
EXEC=sam2alr


all: $(EXEC)

sam2alr: main.o Alr.o Sam2alr.o
	$(CC) $(LIBPATH) -o $@ $^ $(LIB) $(LDFLAGS)

Alr.o: ./Alr.cpp
	$(CC) $(SRC) -o $@ "Alr.cpp" $(CFLAGS)

Sam2alr.o: ./Sam2alr.cpp
	$(CC) $(SRC) -o $@ "Sam2alr.cpp" $(CFLAGS)

main.o: ./main.cpp
	$(CC) $(SRC) -o $@ "main.cpp" $(CFLAGS)

