src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java

   1 /*
   2  *                  BioJava development code
   3  *
   4  * This code may be freely distributed and modified under the
   5  * terms of the GNU Lesser General Public Licence.  This should
   6  * be distributed with the code.  If you do not have a copy,
   7  * see:
   8  *
   9  *      http://www.gnu.org/copyleft/lesser.html
  10  *
  11  * Copyright for this code is held jointly by the individual
  12  * authors.  These should be listed in @author doc comments.
  13  *
  14  * For more information on the BioJava project and its aims,
  15  * or to join the biojava-l mailing list, visit the home page
  16  * at:
  17  *
  18  *      http://www.biojava.org/
  19  *
  20  * Created on Mar 15, 2006
  21  *
  22  */
  23 package org.biojava.dasobert.das2.io;
  24
  25 import java.util.ArrayList;
  26 import java.util.List;
  27
  28 import org.biojava.dasobert.das2.Das2Capability;
  29 import org.biojava.dasobert.das2.Das2CapabilityImpl;
  30 import org.biojava.dasobert.das2.Das2Source;
  31 import org.biojava.dasobert.das2.Das2SourceImpl;
  32 import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
  33 import org.biojava.dasobert.dasregistry.DasSource;
  34 import org.xml.sax.Attributes;
  35 import org.xml.sax.helpers.DefaultHandler;
  36
  37 /** a parser for the DAS2 sources response
  38  *
  39  * @author Andreas Prlic
  40  * @since 6:53:45 PM
  41  * @version %I% %G%
  42  */
  43 public class DAS2SourceHandler extends DefaultHandler{
  44
  45     List sources;
  46     Das2Source currentSource;
  47     List coordinates;
  48     List capabilities;
  49
  50     public DAS2SourceHandler() {
  51         super();
  52
  53         sources = new ArrayList();
  54         currentSource = new Das2SourceImpl();
  55         coordinates = new ArrayList();
  56         capabilities = new ArrayList();
  57     }
  58
  59     private void startSource (String uri, String name, String qName, Attributes atts){
  60
  61         String id = atts.getValue("uri");
  62         String title = atts.getValue("title");
  63         String doc_ref = atts.getValue("doc_href");
  64         String description = atts.getValue("description");
  65
  66
  67         currentSource.setId(id);
  68         currentSource.setNickname(title);
  69         currentSource.setHelperurl(doc_ref);
  70         currentSource.setDescription(description);
  71
  72     }
  73
  74     private DasCoordinateSystem getCoordinateSystem(String uri, String name, String qname, Attributes atts){
  75         // e.g. uri="http://das.sanger.ac.uk/dasregistry/coordsys/CS_LOCAL6"
  76         // source="Protein Sequence" authority="UniProt" test_range="P06213" />
  77         DasCoordinateSystem dcs = new DasCoordinateSystem();
  78         String id = atts.getValue("uri");
  79         dcs.setUniqueId(id);
  80
  81         String source = atts.getValue("source");
  82         dcs.setCategory(source);
  83
  84         String authority = atts.getValue("authority");
  85         dcs.setName(authority);
  86
  87         String test_range = atts.getValue("test_range");
  88         dcs.setTestCode(test_range);
  89
  90         try {
  91             String taxidstr = atts.getValue("taxid");
  92             int taxid = Integer.parseInt(taxidstr);
  93             dcs.setNCBITaxId(taxid);
  94         } catch (Exception e){}
  95
  96         String version = atts.getValue("version");
  97         if ( version != null)
  98             dcs.setVersion(version);
  99
 100         return dcs;
 101     }
 102
 103     public void startElement (String uri, String name, String qName, Attributes atts){
 104         //System.out.println("new element "+qName);
 105
 106         if (qName.equals("SOURCE")) {
 107             //System.out.println("new Source " + atts.getValue(uri));
 108             currentSource = new Das2SourceImpl();
 109             coordinates = new ArrayList();
 110             capabilities = new ArrayList();
 111
 112             startSource(uri,name, qName, atts);
 113
 114         } else if ( qName.equals("MAINTAINER")){
 115             String email = atts.getValue("email");
 116             currentSource.setAdminemail(email);
 117         } else if ( qName.equals("COORDINATES")){
 118             DasCoordinateSystem dcs = getCoordinateSystem(uri,name,qName,atts);
 119             coordinates.add(dcs);
 120
 121         } else if ( qName.equals("CAPABILITY")){
 122             Das2Capability cap = getCapability(uri,name,qName,atts);
 123             capabilities.add(cap);
 124         }
 125
 126         //TODO: add support for "labels"
 127
 128     }
 129
 130     private Das2Capability getCapability(String uri, String name, String qName, Attributes atts){
 131         // e.g <CAPABILITY type="features" query_id="http://das.biopackages.net/das/genome/yeast/S228C/feature" />
 132         Das2Capability cap = new Das2CapabilityImpl();
 133
 134         String type = atts.getValue("type");
 135         cap.setCapability(type);
 136         String query_uri = atts.getValue("query_uri");
 137         cap.setQueryUri(query_uri);
 138         return cap;
 139
 140     }
 141
 142     public void startDocument(){
 143         sources = new ArrayList();
 144         coordinates = new ArrayList();
 145         capabilities = new ArrayList();
 146     }
 147
 148     public void endElement(String uri, String name, String qName) {
 149         if ( qName.equals("SOURCE")) {
 150             currentSource.setDas2Capabilities((Das2Capability[])capabilities.toArray(new Das2Capability[capabilities.size()]));
 151             //System.out.println("got coordinates " + coordinates.size());
 152             currentSource.setCoordinateSystem((DasCoordinateSystem[])coordinates.toArray(new DasCoordinateSystem[coordinates.size()]));
 153             //System.out.println("Das2SourceHandler endElement name " + name + " uri " + uri + " qName " + qName);
 154             //System.out.println("Das2SourceHandler adding to source: " + currentSource.getId());
 155             sources.add(currentSource);
 156             currentSource = new Das2SourceImpl();
 157         }
 158     }
 159
 160     public DasSource[] getSources(){
 161         //System.out.println("Das2SourceHandler: source size: " + sources.size());
 162         return (DasSource[])sources.toArray(new DasSource[sources.size()]);
 163     }
 164
 165
 166
 167 }