+++ /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;
- 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();
- }
- 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 {
-
- String sequence = retrieveSequence(connstr);
- // bug in aristotle das source?
- sequence.replaceAll(" ","");
- gotSequence = true ;
- // set the sequence ...
-
- triggerNewSequence(sp_accession,sequence);
-
-
- 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){
-
- Iterator iter = seqListeners.iterator();
- while (iter.hasNext()){
- SequenceListener li = (SequenceListener)iter.next();
- //SequenceEvent event = new SequenceEvent(sequence);
- SequenceEvent event = new SequenceEvent(sp_accession,sequence);
- 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);
- }
-
-
- //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();
- //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