+++ /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 Nov 20, 2005
- *
- */
-package org.biojava.dasobert.das;
-
-import java.io.InputStream;
-import java.net.HttpURLConnection;
-import java.net.URL;
-import java.util.Iterator;
-import java.util.logging.Level;
-import java.util.logging.Logger;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.parsers.SAXParser;
-import javax.xml.parsers.SAXParserFactory;
-
-import org.biojava.dasobert.dasregistry.Das1Source;
-import org.biojava.dasobert.eventmodel.SequenceEvent;
-import org.biojava.dasobert.eventmodel.SequenceListener;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-import org.xml.sax.SAXNotRecognizedException;
-import org.xml.sax.XMLReader;
-import java.util.*;
-
-/**
- * a thread that gets the sequence from a DAS server
- *
- * @author Andreas Prlic
- *
- */
-public class SequenceThread extends Thread
-{
-
- Das1Source[] sequenceServers;
-
- String sp_accession;
-
- List seqListeners;
-
- String version;
-
- static Logger logger = Logger.getLogger("org.biojava.spice");
-
- public SequenceThread(String sp_accession, Das1Source ds)
- {
- super();
- Das1Source[] dss = new Das1Source[1];
- dss[0] = ds;
- this.sp_accession = sp_accession;
- this.sequenceServers = dss;
- clearSequenceListeners();
- version = "";
- }
-
- public SequenceThread(String sp_accession, Das1Source[] ds)
- {
- super();
-
- this.sp_accession = sp_accession;
- this.sequenceServers = ds;
- clearSequenceListeners();
- }
-
- public void clearSequenceListeners()
- {
- seqListeners = new ArrayList();
- }
-
- public void addSequenceListener(SequenceListener lis)
- {
- seqListeners.add(lis);
- }
-
- public void run()
- {
- getSequence();
- }
-
- public void getSequence()
- {
-
- boolean gotSequence = false;
-
- for (int i = 0; i < sequenceServers.length; i++)
- {
-
- if (gotSequence)
- break;
-
- Das1Source ds = sequenceServers[i];
- String url = ds.getUrl();
- char lastChar = url.charAt(url.length() - 1);
- if (!(lastChar == '/'))
- url += "/";
- String dascmd = url + "sequence?segment=";
- String connstr = dascmd + sp_accession;
-
- try
- {
- version = "";
-
- String sequence = retrieveSequence(connstr);
- // TODO: discriminate exceptions caused by connection/server errors and ones caused by the sequence not being found in the reference source.
- if (sequence!=null)
- {
- // bug in aristotle das source?
- sequence.replaceAll(" ", "");
- gotSequence = true;
- // set the sequence ...
-
- triggerNewSequence(sp_accession, sequence, ds, version);
- }
- return;
- } catch (Exception ex)
- {
- ex.printStackTrace();
- logger.warning(ex.getMessage());
-
- // triggerException(ex);
-
- }
- }
-
- logger
- .log(
- Level.WARNING,
- "could not retreive UniProt sequence from any available DAS sequence server");
-
- triggerNoSequence(sp_accession);
-
- }
-
- // private void triggerException(Exception e){
- // Iterator iter = seqListeners.iterator();
- // while (iter.hasNext()){
- // SequenceListener li = (SequenceListener)iter.next();
- // li.exceptionOccured(e);
- // }
- // }
-
- private void triggerNewSequence(String sp_accession, String sequence,
- Das1Source source, String version)
- {
-
- Iterator iter = seqListeners.iterator();
- while (iter.hasNext())
- {
- SequenceListener li = (SequenceListener) iter.next();
- // SequenceEvent event = new SequenceEvent(sequence);
- SequenceEvent event = new SequenceEvent(sp_accession, sequence,
- version);
- event.setSource(source);
- li.newSequence(event);
- }
- }
-
- private void triggerNoSequence(String ac)
- {
-
- Iterator iter = seqListeners.iterator();
- while (iter.hasNext())
- {
- SequenceListener li = (SequenceListener) iter.next();
- li.noObjectFound(ac);
- }
-
- }
-
- /**
- * retrieve the Sequence from a DAS server.
- *
- * @param connstr -
- * the DAS - request string. e.g.
- * http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/sequence?segment=P00280
- * @return the requested Sequence
- * @throws Exception
- */
- public String retrieveSequence(String connstr) throws Exception
- {
-
- // logger.finest("trying: " + connstr) ;
- URL dasUrl = new URL(connstr);
- // DAS_httpConnector dhtp = new DAS_httpConnector() ;
- logger.info("requesting sequence from " + connstr);
- InputStream dasInStream = open(dasUrl);
-
- SAXParserFactory spfactory = SAXParserFactory.newInstance();
-
- // never do this
- // String vali = System.getProperty("XMLVALIDATION");
- String vali = "false";
- boolean validate = false;
- if ((vali != null) && (vali.equals("true")))
- validate = true;
- spfactory.setValidating(validate);
-
- SAXParser saxParser = null;
-
- try
- {
- saxParser = spfactory.newSAXParser();
- } catch (ParserConfigurationException e)
- {
- // e.printStackTrace();
- logger.log(Level.FINER, "Uncaught exception", e);
- }
-
- XMLReader xmlreader = saxParser.getXMLReader();
-
- try
- {
- xmlreader.setFeature("http://xml.org/sax/features/validation",
- validate);
- } catch (SAXException e)
- {
- logger.finer("Cannot set validation to " + validate);
- logger.log(Level.FINER, "Uncaught exception", e);
- }
-
- try
- {
- xmlreader
- .setFeature(
- "http://apache.org/xml/features/nonvalidating/load-external-dtd",
- validate);
- } catch (SAXNotRecognizedException e)
- {
- // e.printStackTrace();
- logger.finer("Cannot set load-external-dtd to" + validate);
- logger.log(Level.FINER, "Uncaught exception", e);
- // System.err.println("Cannot set load-external-dtd to" + validate);
- }
- if (dasInStream==null)
- {
- return null;
- }
- // DAS_DNA_Handler cont_handle = new DAS_DNA_Handler() ;
- DAS_Sequence_Handler cont_handle = new DAS_Sequence_Handler();
- xmlreader.setContentHandler(cont_handle);
- xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
- InputSource insource = new InputSource();
- insource.setByteStream(dasInStream);
-
- xmlreader.parse(insource);
- String sequence = cont_handle.get_sequence();
- version = cont_handle.getVersion();
- // logger.finest("Got sequence from DAS: " +sequence);
-
- logger.exiting(this.getClass().getName(), "retreiveSequence", sequence);
- return sequence;
- }
-
- private InputStream open(URL url)
- {
- {
-
- InputStream inStream = null;
- try
- {
-
- HttpURLConnection huc = null;
-
- huc = DAS_FeatureRetrieve.openHttpURLConnection(url);
-
- logger.finest(huc.getResponseMessage());
-
- inStream = huc.getInputStream();
-
- } catch (Exception ex)
- {
- ex.printStackTrace();
- logger.log(Level.WARNING, "exception occured", ex);
- }
-
- return inStream;
- }
-
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff