+++ /dev/null
-/*
- * 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 15, 2006
- *
- */
-package org.biojava.dasobert.das2.io;
-
-import java.util.*;
-
-import org.biojava.dasobert.das2.*;
-import org.biojava.dasobert.dasregistry.*;
-import org.xml.sax.*;
-import org.xml.sax.helpers.*;
-
-/**
- * a parser for the DAS2 sources response
- *
- * @author Andreas Prlic
- * @since 6:53:45 PM
- * @version %I% %G%
- */
-public class DAS2SourceHandler extends DefaultHandler
-{
-
- List sources;
-
- Das2Source currentSource;
-
- List coordinates;
-
- List capabilities;
-
- List labels;
-
- public static final String LABELPROPERTY = "label";
-
- public DAS2SourceHandler()
- {
- super();
-
- sources = new ArrayList();
- currentSource = new Das2SourceImpl();
- coordinates = new ArrayList();
- capabilities = new ArrayList();
- labels = new ArrayList();
- }
-
- private void startSource(String uri, String name, String qName,
- Attributes atts)
- {
-
- String id = atts.getValue("uri");
- String title = atts.getValue("title");
- String doc_ref = atts.getValue("doc_href");
- String description = atts.getValue("description");
-
- currentSource.setId(id);
- currentSource.setNickname(title);
- currentSource.setHelperurl(doc_ref);
- currentSource.setDescription(description);
-
- }
-
- private DasCoordinateSystem getCoordinateSystem(String uri, String name,
- String qname, Attributes atts)
- {
- // e.g. uri="http://das.sanger.ac.uk/dasregistry/coordsys/CS_LOCAL6"
- // source="Protein Sequence" authority="UniProt" test_range="P06213" />
- DasCoordinateSystem dcs = new DasCoordinateSystem();
- String id = atts.getValue("uri");
- dcs.setUniqueId(id);
-
- String source = atts.getValue("source");
- dcs.setCategory(source);
-
- String authority = atts.getValue("authority");
- dcs.setName(authority);
-
- String test_range = atts.getValue("test_range");
- dcs.setTestCode(test_range);
-
- try
- {
- String taxidstr = atts.getValue("taxid");
- int taxid = Integer.parseInt(taxidstr);
- dcs.setNCBITaxId(taxid);
- } catch (Exception e)
- {
- }
-
- String version = atts.getValue("version");
- if (version != null)
- {
- dcs.setVersion(version);
- }
-
- return dcs;
- }
-
- public void startElement(String uri, String name, String qName,
- Attributes atts)
- {
- // System.out.println("new element "+qName);
-
- if (qName.equals("SOURCE"))
- {
- // System.out.println("new Source " + atts.getValue(uri));
- currentSource = new Das2SourceImpl();
- coordinates = new ArrayList();
- capabilities = new ArrayList();
-
- startSource(uri, name, qName, atts);
-
- }
- else if (qName.equals("MAINTAINER"))
- {
- String email = atts.getValue("email");
- currentSource.setAdminemail(email);
- }
- else if (qName.equals("COORDINATES"))
- {
- DasCoordinateSystem dcs = getCoordinateSystem(uri, name, qName, atts);
- coordinates.add(dcs);
-
- }
- else if (qName.equals("CAPABILITY"))
- {
- Das2Capability cap = getCapability(uri, name, qName, atts);
- capabilities.add(cap);
- }
- else if (qName.equals("PROPERTY"))
- {
- addProperty(uri, name, qName, atts);
- }
- }
-
- private Das2Capability getCapability(String uri, String name,
- String qName, Attributes atts)
- {
- // e.g <CAPABILITY type="features"
- // query_id="http://das.biopackages.net/das/genome/yeast/S228C/feature" />
- Das2Capability cap = new Das2CapabilityImpl();
-
- String type = atts.getValue("type");
- cap.setCapability(type);
- String query_uri = atts.getValue("query_uri");
- cap.setQueryUri(query_uri);
- return cap;
-
- }
-
- private void addProperty(String uri, String name, String qName,
- Attributes atts)
- {
- String pname = atts.getValue("name");
- String label = atts.getValue("value");
- if (pname.equals(LABELPROPERTY))
- {
- labels.add(label);
- }
- }
-
- public void startDocument()
- {
- sources = new ArrayList();
- coordinates = new ArrayList();
- capabilities = new ArrayList();
- }
-
- public void endElement(String uri, String name, String qName)
- {
- if (qName.equals("SOURCE"))
- {
- currentSource.setDas2Capabilities((Das2Capability[]) capabilities
- .toArray(new Das2Capability[capabilities.size()]));
- // System.out.println("got coordinates " + coordinates.size());
- currentSource.setCoordinateSystem((DasCoordinateSystem[]) coordinates
- .toArray(new DasCoordinateSystem[coordinates.size()]));
-
- currentSource.setLabels((String[]) labels.toArray(new String[labels
- .size()]));
- labels.clear();
-
- // System.out.println("Das2SourceHandler endElement name " + name + " uri
- // " + uri + " qName " + qName);
- // System.out.println("Das2SourceHandler adding to source: " +
- // currentSource.getId());
- sources.add(currentSource);
- currentSource = new Das2SourceImpl();
- }
- }
-
- public DasSource[] getSources()
- {
- // System.out.println("Das2SourceHandler: source size: " + sources.size());
- return (DasSource[]) sources.toArray(new DasSource[sources.size()]);
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff