src/org/biojava/dasobert/das/SequenceThread.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 Nov 20, 2005
  21  *
  22  */
  23 package org.biojava.dasobert.das;
  24
  25 import java.io.InputStream;
  26 import java.net.HttpURLConnection;
  27 import java.net.URL;
  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;
  34
  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;
  42 import java.util.*;
  43
  44 /** a thread that gets the sequence from a DAS server
  45  *
  46  * @author Andreas Prlic
  47  *
  48  */
  49 public class SequenceThread
  50 extends Thread {
  51
  52     Das1Source[] sequenceServers;
  53     String sp_accession;
  54     List seqListeners;
  55     String version ;
  56
  57     static Logger logger = Logger.getLogger("org.biojava.spice");
  58
  59      public SequenceThread(String sp_accession,Das1Source ds ) {
  60         super();
  61         Das1Source[] dss =new Das1Source[1];
  62         dss[0] = ds;
  63         this.sp_accession = sp_accession;
  64         this.sequenceServers =dss ;
  65         clearSequenceListeners();
  66         version = "";
  67     }
  68     public SequenceThread(String sp_accession,Das1Source[] ds ) {
  69         super();
  70
  71         this.sp_accession = sp_accession;
  72         this.sequenceServers =ds ;
  73         clearSequenceListeners();
  74     }
  75
  76     public void clearSequenceListeners(){
  77         seqListeners = new ArrayList();
  78     }
  79
  80     public void addSequenceListener(SequenceListener lis){
  81         seqListeners.add(lis);
  82     }
  83
  84     public void run() {
  85         getSequence();
  86     }
  87
  88     public void getSequence( ){
  89
  90         boolean gotSequence = false ;
  91
  92         for ( int i = 0 ; i< sequenceServers.length; i++){
  93
  94             if ( gotSequence ) break ;
  95
  96             Das1Source ds = sequenceServers[i];
  97             String url = ds.getUrl() ;
  98             char lastChar = url.charAt(url.length()-1);
  99             if ( ! (lastChar == '/') )
 100                 url +="/" ;
 101             String dascmd = url + "sequence?segment=";
 102             String connstr = dascmd + sp_accession ;
 103
 104             try {
 105                 version = "";
 106
 107                 String sequence = retrieveSequence(connstr);
 108                 // bug in aristotle das source?
 109                 sequence.replaceAll(" ","");
 110                 gotSequence = true ;
 111                 // set the sequence ...
 112
 113                 triggerNewSequence(sp_accession,sequence,ds,version);
 114
 115
 116                 return;
 117             }
 118             catch (Exception ex) {
 119                 ex.printStackTrace();
 120                 logger.warning(ex.getMessage());
 121
 122                 //triggerException(ex);
 123
 124             }
 125         }
 126
 127         logger.log(Level.WARNING,"could not retreive UniProt sequence from any available DAS sequence server");
 128
 129         triggerNoSequence(sp_accession);
 130
 131     }
 132
 133
 134
 135 //    private void triggerException(Exception e){
 136 //        Iterator iter = seqListeners.iterator();
 137 //        while (iter.hasNext()){
 138 //           SequenceListener li = (SequenceListener)iter.next();
 139 //           li.exceptionOccured(e);
 140 //        }
 141 //    }
 142
 143     private void triggerNewSequence(String sp_accession,String sequence,Das1Source source,String version){
 144
 145         Iterator iter = seqListeners.iterator();
 146         while (iter.hasNext()){
 147            SequenceListener li = (SequenceListener)iter.next();
 148             //SequenceEvent event = new SequenceEvent(sequence);
 149            SequenceEvent event = new SequenceEvent(sp_accession,sequence,version);
 150            event.setSource(source);
 151            li.newSequence(event);
 152         }
 153     }
 154
 155     private void triggerNoSequence(String ac){
 156
 157         Iterator iter = seqListeners.iterator();
 158         while (iter.hasNext()){
 159             SequenceListener li = (SequenceListener)iter.next();
 160             li.noObjectFound(ac);
 161         }
 162
 163     }
 164
 165     /** retrieve the Sequence from a DAS server.
 166      *
 167      * @param connstr - the DAS - request string. e.g. http://www.ebi.ac.uk/das-srv/uniprot/das/aristotle/sequence?segment=P00280
 168      * @return the requested Sequence
 169      * @throws Exception
 170      */
 171     public String retrieveSequence( String connstr)
 172     throws Exception
 173     {
 174
 175         //logger.finest("trying: " + connstr) ;
 176         URL dasUrl = new URL(connstr);
 177         //DAS_httpConnector dhtp = new DAS_httpConnector() ;
 178         logger.info("requesting sequence from " + connstr);
 179         InputStream dasInStream =open(dasUrl);
 180
 181
 182         SAXParserFactory spfactory =
 183             SAXParserFactory.newInstance();
 184
 185         // never do this
 186         //String vali = System.getProperty("XMLVALIDATION");
 187         String vali = "false";
 188         boolean validate = false ;
 189         if ((vali != null) && ( vali.equals("true")) )
 190             validate = true ;
 191         spfactory.setValidating(validate);
 192
 193         SAXParser saxParser = null ;
 194
 195         try{
 196             saxParser =
 197                 spfactory.newSAXParser();
 198         } catch (ParserConfigurationException e) {
 199             //e.printStackTrace();
 200             logger.log(Level.FINER,"Uncaught exception", e);
 201         }
 202
 203         XMLReader xmlreader = saxParser.getXMLReader();
 204
 205         try {
 206             xmlreader.setFeature("http://xml.org/sax/features/validation", validate);
 207         } catch (SAXException e) {
 208             logger.finer("Cannot set validation to " + validate);
 209             logger.log(Level.FINER,"Uncaught exception", e);
 210         }
 211
 212         try {
 213             xmlreader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",validate);
 214         } catch (SAXNotRecognizedException e){
 215             //e.printStackTrace();
 216             logger.finer("Cannot set load-external-dtd to" + validate);
 217             logger.log(Level.FINER,"Uncaught exception", e);
 218             //System.err.println("Cannot set load-external-dtd to" + validate);
 219         }
 220
 221
 222         //DAS_DNA_Handler cont_handle = new DAS_DNA_Handler() ;
 223         DAS_Sequence_Handler cont_handle = new DAS_Sequence_Handler() ;
 224         xmlreader.setContentHandler(cont_handle);
 225         xmlreader.setErrorHandler(new org.xml.sax.helpers.DefaultHandler());
 226         InputSource insource = new InputSource() ;
 227         insource.setByteStream(dasInStream);
 228
 229         xmlreader.parse(insource);
 230         String sequence = cont_handle.get_sequence();
 231         version = cont_handle.getVersion();
 232         //logger.finest("Got sequence from DAS: " +sequence);
 233
 234         logger.exiting(this.getClass().getName(), "retreiveSequence",  sequence);
 235         return sequence ;
 236     }
 237
 238     private InputStream open(URL url) {
 239         {
 240
 241             InputStream inStream = null;
 242             try{
 243
 244
 245
 246
 247                 HttpURLConnection huc = null;
 248
 249                 huc = DAS_FeatureRetrieve.openHttpURLConnection(url);
 250
 251
 252                 logger.finest(huc.getResponseMessage());
 253
 254                 inStream = huc.getInputStream();
 255
 256
 257             }
 258             catch ( Exception ex){
 259                 ex.printStackTrace();
 260                 logger.log(Level.WARNING,"exception occured", ex);
 261             }
 262
 263             return inStream;
 264         }
 265
 266     }
 267
 268 }