2 * BioJava development code
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,
9 * http://www.gnu.org/copyleft/lesser.html
11 * Copyright for this code is held jointly by the individual
12 * authors. These should be listed in @author doc comments.
14 * For more information on the BioJava project and its aims,
15 * or to join the biojava-l mailing list, visit the home page
18 * http://www.biojava.org/
20 * Created on Nov 20, 2005
23 package org.biojava.dasobert.das;
25 import java.io.InputStream;
26 import java.net.HttpURLConnection;
28 import java.util.Iterator;
29 import java.util.logging.Level;
30 import java.util.logging.Logger;
31 import javax.xml.parsers.ParserConfigurationException;
32 import javax.xml.parsers.SAXParser;
33 import javax.xml.parsers.SAXParserFactory;
35 import org.biojava.dasobert.dasregistry.Das1Source;
36 import org.biojava.dasobert.eventmodel.SequenceEvent;
37 import org.biojava.dasobert.eventmodel.SequenceListener;
38 import org.xml.sax.InputSource;
39 import org.xml.sax.SAXException;
40 import org.xml.sax.SAXNotRecognizedException;
41 import org.xml.sax.XMLReader;
45 * a thread that gets the sequence from a DAS server
47 * @author Andreas Prlic
50 public class SequenceThread extends Thread
53 Das1Source[] sequenceServers;
61 static Logger logger = Logger.getLogger("org.biojava.spice");
63 public SequenceThread(String sp_accession, Das1Source ds)
66 Das1Source[] dss = new Das1Source[1];
68 this.sp_accession = sp_accession;
69 this.sequenceServers = dss;
70 clearSequenceListeners();
74 public SequenceThread(String sp_accession, Das1Source[] ds)
78 this.sp_accession = sp_accession;
79 this.sequenceServers = ds;
80 clearSequenceListeners();
83 public void clearSequenceListeners()
85 seqListeners = new ArrayList();
88 public void addSequenceListener(SequenceListener lis)
90 seqListeners.add(lis);
98 public void getSequence()
101 boolean gotSequence = false;
103 for (int i = 0; i < sequenceServers.length; i++)
109 Das1Source ds = sequenceServers[i];
110 String url = ds.getUrl();
111 char lastChar = url.charAt(url.length() - 1);
112 if (!(lastChar == '/'))
114 String dascmd = url + "sequence?segment=";
115 String connstr = dascmd + sp_accession;
121 String sequence = retrieveSequence(connstr);
122 // TODO: discriminate exceptions caused by connection/server errors and ones caused by the sequence not being found in the reference source.
125 // bug in aristotle das source?
126 sequence.replaceAll(" ", "");
128 // set the sequence ...
130 triggerNewSequence(sp_accession, sequence, ds, version);
133 } catch (Exception ex)
135 ex.printStackTrace();
136 logger.warning(ex.getMessage());
138 // triggerException(ex);
146 "could not retreive UniProt sequence from any available DAS sequence server");
148 triggerNoSequence(sp_accession);
152 // private void triggerException(Exception e){
153 // Iterator iter = seqListeners.iterator();
154 // while (iter.hasNext()){
155 // SequenceListener li = (SequenceListener)iter.next();
156 // li.exceptionOccured(e);
160 private void triggerNewSequence(String sp_accession, String sequence,
161 Das1Source source, String version)
164 Iterator iter = seqListeners.iterator();
165 while (iter.hasNext())
167 SequenceListener li = (SequenceListener) iter.next();
168 // SequenceEvent event = new SequenceEvent(sequence);
169 SequenceEvent event = new SequenceEvent(sp_accession, sequence,
171 event.setSource(source);
172 li.newSequence(event);
176 private void triggerNoSequence(String ac)
179 Iterator iter = seqListeners.iterator();
180 while (iter.hasNext())
182 SequenceListener li = (SequenceListener) iter.next();
183 li.noObjectFound(ac);
189 * retrieve the Sequence from a DAS server.
192 * the DAS - request string. e.g.
193 * http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/sequence?segment=P00280
194 * @return the requested Sequence
197 public String retrieveSequence(String connstr) throws Exception
200 // logger.finest("trying: " + connstr) ;
201 URL dasUrl = new URL(connstr);
202 // DAS_httpConnector dhtp = new DAS_httpConnector() ;
203 logger.info("requesting sequence from " + connstr);
204 InputStream dasInStream = open(dasUrl);
206 SAXParserFactory spfactory = SAXParserFactory.newInstance();
209 // String vali = System.getProperty("XMLVALIDATION");
210 String vali = "false";
211 boolean validate = false;
212 if ((vali != null) && (vali.equals("true")))
214 spfactory.setValidating(validate);
216 SAXParser saxParser = null;
220 saxParser = spfactory.newSAXParser();
221 } catch (ParserConfigurationException e)
223 // e.printStackTrace();
224 logger.log(Level.FINER, "Uncaught exception", e);
227 XMLReader xmlreader = saxParser.getXMLReader();
231 xmlreader.setFeature("http://xml.org/sax/features/validation",
233 } catch (SAXException e)
235 logger.finer("Cannot set validation to " + validate);
236 logger.log(Level.FINER, "Uncaught exception", e);
243 "http://apache.org/xml/features/nonvalidating/load-external-dtd",
245 } catch (SAXNotRecognizedException e)
247 // e.printStackTrace();
248 logger.finer("Cannot set load-external-dtd to" + validate);
249 logger.log(Level.FINER, "Uncaught exception", e);
250 // System.err.println("Cannot set load-external-dtd to" + validate);
252 if (dasInStream==null)
256 // DAS_DNA_Handler cont_handle = new DAS_DNA_Handler() ;
257 DAS_Sequence_Handler cont_handle = new DAS_Sequence_Handler();
258 xmlreader.setContentHandler(cont_handle);
259 xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
260 InputSource insource = new InputSource();
261 insource.setByteStream(dasInStream);
263 xmlreader.parse(insource);
264 String sequence = cont_handle.get_sequence();
265 version = cont_handle.getVersion();
266 // logger.finest("Got sequence from DAS: " +sequence);
268 logger.exiting(this.getClass().getName(), "retreiveSequence", sequence);
272 private InputStream open(URL url)
276 InputStream inStream = null;
280 HttpURLConnection huc = null;
282 huc = DAS_FeatureRetrieve.openHttpURLConnection(url);
284 logger.finest(huc.getResponseMessage());
286 inStream = huc.getInputStream();
288 } catch (Exception ex)
290 ex.printStackTrace();
291 logger.log(Level.WARNING, "exception occured", ex);