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 */ 021 022package org.biojava.bio.seq.io.game; 023 024import org.biojava.utils.stax.DelegationManager; 025import org.biojava.utils.stax.StAXContentHandler; 026import org.biojava.utils.stax.StringElementHandlerBase; 027import org.xml.sax.Attributes; 028import org.xml.sax.SAXException; 029 030/** 031 * StAX handler for GAME <type> elements. 032 * derived from Thomas Down's PropDetailHandler 033 * 034 * @author David Huen 035 * @author Thomas Down 036 * @since 1.8 037 */ 038public class GAMETypePropHandler extends StringElementHandlerBase { 039 // The <type> handler is context sensitive as the meaning of type depends on 040 // the element in which it is nested. 041 public static final StAXHandlerFactory GAME_TYPE_PROP_HANDLER_FACTORY = new StAXHandlerFactory() { 042 public StAXContentHandler getHandler(StAXFeatureHandler staxenv) { 043 return new GAMETypePropHandler(staxenv); 044 } 045 } ; 046 047 private StAXFeatureHandler staxenv; 048 049 public GAMETypePropHandler(StAXFeatureHandler staxenv) { 050 super(); 051 this.staxenv = staxenv; 052 } 053 054 public void startElement(String nsURI, 055 String localName, 056 String qName, 057 Attributes attrs, 058 DelegationManager dm) 059 throws SAXException 060 { 061 062 super.startElement(nsURI, localName, qName, attrs, dm); 063 } 064 065 protected void setStringValue(String s) 066 throws SAXException 067 { 068 // if this is <feature_span, the string will decide the type of feature to create 069 String trimmed = s.trim(); 070 071 if (trimmed.equals("translate offset")) { 072 // create a start codon annotation 073// System.out.println("setting ATG"); 074 staxenv.featureTemplate.type = "ATG"; 075 } 076 else if (trimmed.equals("exon")) { 077 // feature is an exon 078// System.out.println("Setting exon"); 079 staxenv.featureTemplate.type = "exon"; 080 } 081 } 082}