001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 * Created on Jan 18, 2008 021 * 022 */ 023 024package org.biojava.nbio.ontology.io; 025 026import org.biojava.nbio.ontology.*; 027import org.biojava.nbio.ontology.obo.OboFileEventListener; 028import org.biojava.nbio.ontology.obo.OboFileHandler; 029import org.biojava.nbio.ontology.obo.OboFileParser; 030 031import java.io.BufferedReader; 032import java.io.IOException; 033import java.text.ParseException; 034 035 036 037 038/** Parses an OBO file. 039 * 040 * @author Andreas Prlic 041 * @since 1.7 042 * 043 * <h2>Example</h2> 044 * <pre> 045 * OboParser parser = new OboParser(); 046 InputStream inStream = this.getClass().getResourceAsStream("/files/ontology/biosapiens.obo"); 047 048 BufferedReader oboFile = new BufferedReader ( new InputStreamReader ( inStream ) ); 049 try { 050 Ontology ontology = parser.parseOBO(oboFile, "BioSapiens", "the BioSapiens ontology"); 051 052 Set keys = ontology.getTerms(); 053 Iterator iter = keys.iterator(); 054 while (iter.hasNext()){ 055 System.out.println(iter.next()); 056 } 057 058 } catch (Exception e){ 059 e.printStackTrace(); 060 } 061 * </pre> 062 * 063 */ 064public class OboParser { 065 066 /** Parse a OBO file and return its content as a BioJava Ontology object 067 * 068 * @param oboFile the file to be parsed 069 * @param ontoName 070 * @param ontoDescription 071 072 * @return the ontology represented as a BioJava ontology file 073 * @throws ParseException 074 * @throws IOException 075 */ 076 public Ontology parseOBO( 077 BufferedReader oboFile, 078 String ontoName, 079 String ontoDescription 080 ) 081 throws ParseException, IOException { 082 083 try { 084 OntologyFactory factory = OntoTools.getDefaultFactory(); 085 Ontology ontology = factory.createOntology(ontoName, ontoDescription); 086 087 OboFileParser parser = new OboFileParser(); 088 089 OboFileEventListener handler = new OboFileHandler(ontology); 090 091 parser.addOboFileEventListener(handler); 092 parser.parseOBO(oboFile); 093 094 return ontology; 095 096 097 } catch (AlreadyExistsException ex) { 098 throw new RuntimeException( "Duplication in ontology"); 099 } catch (OntologyException ex) { 100 throw new RuntimeException(ex); 101 } 102 103 } 104}