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