Makefile

.PHONY:all test
URL=https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&retmode=xml
CC=g++
CFLAGS=-O3 -Wall

all: taxonomy2newick newick2json newick2dot newick2xml

newick2xml : newick2xml.y newick2xml.l
	bison -d newick2xml.y
	flex newick2xml.l
	$(CC) -o $@ $(CFLAGS) newick2xml.tab.c lex.yy.c

newick2json : newick2js.y newick2js.l
	bison -d newick2js.y
	flex newick2js.l
	$(CC) -o $@ $(CFLAGS) newick2js.tab.c lex.yy.c

newick2dot : newick2dot.y newick2dot.l
	bison -d newick2dot.y
	flex newick2dot.l
	$(CC) -o $@ $(CFLAGS) newick2dot.tab.c lex.yy.c	

taxonomy2newick : taxonomy2newick.cpp
	$(CC) -o $@ $(CFLAGS) $< `xml2-config --cflags --libs`

test: taxonomy2newick newick2json newick2dot
	curl -s '${URL}&id=9606' |./taxonomy2newick | ./newick2json
	curl -s '${URL}&id=9606,9605' |./taxonomy2newick | ./newick2json
	curl -s '${URL}&id=9606,10090,9031,7227,562' |./taxonomy2newick | ./newick2json
	curl -s '${URL}&id=9606,10090,9031,7227,562' |./taxonomy2newick | ./newick2xml
	curl -s '${URL}&id=9606,10090,9031,7227,562' |./taxonomy2newick | ./newick2xml | xsltproc xml2gexf.xslt -
	curl -s '${URL}&id=9606,10090,9031,7227,562' |./taxonomy2newick | ./newick2dot | dot -Tpng -otest01.png
	
	

clean:
	rm -f taxonomy2newick newick2dot newick2json lex.yy.c newick2js.tab.c newick2js.tab.h test01.png