/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on Mar 19, 2014
 * Author: andreas
 *
 */

package demo;

import org.biojava.nbio.ontology.Ontology;
import org.biojava.nbio.ontology.Term;
import org.biojava.nbio.ontology.io.OboParser;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.net.URL;
import java.util.Iterator;
import java.util.Set;

public class ParseGO {

	private static final Logger logger = LoggerFactory.getLogger(ParseGO.class);

	/**
	 * Downloads Biosapiens OBO file from Sourceforge and prints out name/description pairs
	 * @param args
	 */
	public static void main(String[] args){


		try {

			OboParser parser = new OboParser();
			InputStream inStream = OboParser.class.getResourceAsStream("/ontology/biosapiens.obo");

			BufferedReader oboFile = new BufferedReader ( new InputStreamReader ( inStream ) );

			Ontology ontology = parser.parseOBO(oboFile, "BioSapiens", "the BioSapiens ontology");

			Set<Term> keys = ontology.getTerms();
			Iterator<Term> iter = keys.iterator();
			while (iter.hasNext()){
				Term t = iter.next();
				logger.info("{} [{}]", t.getName(), t.getDescription());
			}
		} catch (Exception e){
			logger.error("Exception: ", e);
		}
	}
}

@@ -1124,16 +1124,13 @@
 %09 * 
-Download
+Parse
 s Bi
@@ -1729,31 +1729,27 @@
 %09%09%09%09
-logger.info(%22%7B%7D %5B%7B%7D%5D%22, 
+System.out.println(
 t.ge
@@ -1755,17 +1755,25 @@
 etName()
-,
+ + %22 %22 + 
  t.getDe
@@ -1823,20 +1823,26 @@
 %0A%09%09%09
-logger.error
+System.err.println
 (%22Ex
@@ -1851,17 +1851,19 @@
 ption: %22
-,
+ + 
  e);%0A%09%09%7D

replace log with system out calls