# -*- Makefile -*-

CXX = g++
#CXXFLAGS = -O2 -g -Icommon -Wall -Wextra -Winline
CXXFLAGS = -O2 -Icommon -Wall -Wextra
OUTDIR = build
COMMON_DIR = common
GENBANK_DIR = genbank-to-fasta
PDB_DIR = pdb-to-fasta
UNIPROT_DIR = uniprot-to-fasta

COMMON_OBJS = $(OUTDIR)/GzipReader.o \
              $(OUTDIR)/Parser.o \
              $(OUTDIR)/SystemError.o

GENBANK_OBJS = $(OUTDIR)/GenbankParser.o \
               $(OUTDIR)/GenbankToFasta.o

PDB_OBJS = $(OUTDIR)/PdbToFasta.o

UNIPROT_OBJS = $(OUTDIR)/UniprotParser.o \
               $(OUTDIR)/UniprotToFasta.o

all: genbank-to-fasta pdb-to-fasta uniprot-to-fasta

$(OUTDIR):
	mkdir -p $(OUTDIR)

$(OUTDIR)/%.o: $(COMMON_DIR)/%.cpp
	$(COMPILE.cpp) $(OUTPUT_OPTION) $<

$(OUTDIR)/%.o: $(GENBANK_DIR)/%.cpp
	$(COMPILE.cpp) $(OUTPUT_OPTION) $<

$(OUTDIR)/%.o: $(PDB_DIR)/%.cpp
	$(COMPILE.cpp) $(OUTPUT_OPTION) $<

$(OUTDIR)/%.o: $(UNIPROT_DIR)/%.cpp
	$(COMPILE.cpp) $(OUTPUT_OPTION) $<

genbank-to-fasta: $(OUTDIR) $(COMMON_OBJS) $(GENBANK_OBJS)
	$(LINK.cpp) -o $(OUTDIR)/genbank-to-fasta -lz $(COMMON_OBJS) $(GENBANK_OBJS)

pdb-to-fasta: $(OUTDIR) $(COMMON_OBJS) $(PDB_OBJS)
	$(LINK.cpp) -o $(OUTDIR)/pdb-to-fasta -lz $(COMMON_OBJS) $(PDB_OBJS)

uniprot-to-fasta: $(OUTDIR) $(COMMON_OBJS) $(UNIPROT_OBJS)
	$(LINK.cpp) -o $(OUTDIR)/uniprot-to-fasta -lz $(COMMON_OBJS) $(UNIPROT_OBJS)

clean:
	rm -rf $(OUTDIR)/*

clean-emacs:
	rm -f *~
	rm -f scripts/*~
	rm -f $(COMMON_DIR)/*~
	rm -f $(GENBANK_DIR)/*~
	rm -f $(PDB_DIR)/*~
	rm -f $(UNIPROT_DIR)/*~