prefix =   $(DESTDIR)/usr
bindir =   $(prefix)/bin
man1dir =  $(prefix)/share/man/man1
libdir =   $(prefix)/lib/strap-base
etcdir =   $(DESTDIR)/etc
jar=strap-protein-alignment-1.jar

all: $(jar) nativeTools_unix2

nativeTools_unix2: src/nativeTools_unix2.c
	cc -lm -lX11 -o nativeTools_unix2 src/nativeTools_unix2.c


$(jar):
	find src -name "*.java" | cut -c 5- > javaFiles.txt
	cd src; javac -cp @../classpath.txt  @../javaFiles.txt
	cd src; jar -cmf ../Manifest ../$(jar) *


clean:
	find . -name '*.class' -delete
	rm -f *.jar nativeTools_unix2

install: all
	mkdir -p $(libdir) $(man1dir) $(bindir) $(etcdir)/bash_completion.d
	install nativeTools_unix2 $(libdir)
	install -m 0644 $(jar) $(libdir)
	install -m 0644 man/*.1 $(man1dir)
	install -m 0644 strap_bash_completion.sh $(etcdir)/bash_completion.d/strap_base
	install sh/* $(bindir)


# (highlight-regexp "\t" 'hi-yellow)
