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     List labels;
  50
  51     public static final String LABELPROPERTY = "label";
  52
  53     public DAS2SourceHandler() {
  54         super();
  55
  56         sources       = new ArrayList();
  57         currentSource = new Das2SourceImpl();
  58         coordinates   = new ArrayList();
  59         capabilities  = new ArrayList();
  60         labels        = new ArrayList();
  61     }
  62
  63     private void startSource (String uri, String name, String qName, Attributes atts){
  64
  65         String id = atts.getValue("uri");
  66         String title = atts.getValue("title");
  67         String doc_ref = atts.getValue("doc_href");
  68         String description = atts.getValue("description");
  69
  70
  71         currentSource.setId(id);
  72         currentSource.setNickname(title);
  73         currentSource.setHelperurl(doc_ref);
  74         currentSource.setDescription(description);
  75
  76     }
  77
  78     private DasCoordinateSystem getCoordinateSystem(String uri, String name, String qname, Attributes atts){
  79         // e.g. uri="http://das.sanger.ac.uk/dasregistry/coordsys/CS_LOCAL6"
  80         // source="Protein Sequence" authority="UniProt" test_range="P06213" />
  81         DasCoordinateSystem dcs = new DasCoordinateSystem();
  82         String id = atts.getValue("uri");
  83         dcs.setUniqueId(id);
  84
  85         String source = atts.getValue("source");
  86         dcs.setCategory(source);
  87
  88         String authority = atts.getValue("authority");
  89         dcs.setName(authority);
  90
  91         String test_range = atts.getValue("test_range");
  92         dcs.setTestCode(test_range);
  93
  94         try {
  95             String taxidstr = atts.getValue("taxid");
  96             int taxid = Integer.parseInt(taxidstr);
  97             dcs.setNCBITaxId(taxid);
  98         } catch (Exception e){}
  99
 100         String version = atts.getValue("version");
 101         if ( version != null)
 102             dcs.setVersion(version);
 103
 104         return dcs;
 105     }
 106
 107     public void startElement (String uri, String name, String qName, Attributes atts){
 108         //System.out.println("new element "+qName);
 109
 110         if (qName.equals("SOURCE")) {
 111             //System.out.println("new Source " + atts.getValue(uri));
 112             currentSource = new Das2SourceImpl();
 113             coordinates = new ArrayList();
 114             capabilities = new ArrayList();
 115
 116             startSource(uri,name, qName, atts);
 117
 118         } else if ( qName.equals("MAINTAINER")){
 119             String email = atts.getValue("email");
 120             currentSource.setAdminemail(email);
 121         } else if ( qName.equals("COORDINATES")){
 122             DasCoordinateSystem dcs = getCoordinateSystem(uri,name,qName,atts);
 123             coordinates.add(dcs);
 124
 125         } else if ( qName.equals("CAPABILITY")){
 126             Das2Capability cap = getCapability(uri,name,qName,atts);
 127             capabilities.add(cap);
 128         } else if (qName.equals("PROPERTY")) {
 129             addProperty(uri,name,qName,atts);
 130         }
 131     }
 132
 133     private Das2Capability getCapability(String uri, String name, String qName, Attributes atts){
 134         // e.g <CAPABILITY type="features" query_id="http://das.biopackages.net/das/genome/yeast/S228C/feature" />
 135         Das2Capability cap = new Das2CapabilityImpl();
 136
 137         String type = atts.getValue("type");
 138         cap.setCapability(type);
 139         String query_uri = atts.getValue("query_uri");
 140         cap.setQueryUri(query_uri);
 141         return cap;
 142
 143     }
 144
 145     private void addProperty(String uri, String name, String qName, Attributes atts){
 146         String pname = atts.getValue("name");
 147         String label = atts.getValue("value");
 148         if ( pname.equals(LABELPROPERTY) )
 149             labels.add(label);
 150     }
 151
 152     public void startDocument(){
 153         sources = new ArrayList();
 154         coordinates = new ArrayList();
 155         capabilities = new ArrayList();
 156     }
 157
 158     public void endElement(String uri, String name, String qName) {
 159         if ( qName.equals("SOURCE")) {
 160             currentSource.setDas2Capabilities((Das2Capability[])capabilities.toArray(new Das2Capability[capabilities.size()]));
 161             //System.out.println("got coordinates " + coordinates.size());
 162             currentSource.setCoordinateSystem((DasCoordinateSystem[])coordinates.toArray(new DasCoordinateSystem[coordinates.size()]));
 163
 164             currentSource.setLabels((String[])labels.toArray(new String[labels.size()]));
 165             labels.clear();
 166
 167             //System.out.println("Das2SourceHandler endElement name " + name + " uri " + uri + " qName " + qName);
 168             //System.out.println("Das2SourceHandler adding to source: " + currentSource.getId());
 169             sources.add(currentSource);
 170             currentSource = new Das2SourceImpl();
 171         }
 172     }
 173
 174     public DasSource[] getSources(){
 175         //System.out.println("Das2SourceHandler: source size: " + sources.size());
 176         return (DasSource[])sources.toArray(new DasSource[sources.size()]);
 177     }
 178
 179
 180
 181 }