src/jalview/io/WSWUBlastClient.java

   1 /*
   2 * Jalview - A Sequence Alignment Editor and Viewer
   3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4 *
   5 * This program is free software; you can redistribute it and/or
   6 * modify it under the terms of the GNU General Public License
   7 * as published by the Free Software Foundation; either version 2
   8 * of the License, or (at your option) any later version.
   9 *
  10 * This program is distributed in the hope that it will be useful,
  11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13 * GNU General Public License for more details.
  14 *
  15 * You should have received a copy of the GNU General Public License
  16 * along with this program; if not, write to the Free Software
  17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18 */
  19 package jalview.io;
  20
  21 import jalview.datamodel.*;
  22
  23 import jalview.gui.*;
  24
  25 import org.apache.axis.client.*;
  26
  27 import java.util.*;
  28
  29 import javax.swing.*;
  30
  31 import javax.xml.namespace.QName;
  32 import jalview.analysis.AlignSeq;
  33
  34 import uk.ac.ebi.www.*;
  35
  36 /**
  37  * DOCUMENT ME!
  38  *
  39  * @author $author$
  40  * @version $Revision$
  41  */
  42 public class WSWUBlastClient
  43 {
  44     AlignmentPanel ap;
  45     AlignmentI al;
  46     CutAndPasteTransfer output = new CutAndPasteTransfer();
  47     int jobsRunning = 0;
  48
  49     Vector suggestedIds = new Vector();
  50     /**
  51      * Creates a new WSWUBlastClient object.
  52      *
  53      * @param al DOCUMENT ME!
  54      * @param ids DOCUMENT ME!
  55      */
  56     public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)
  57     {
  58         this.ap = ap;
  59         this.al = al;
  60         output.setText(
  61             "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."
  62             +"\nIn order to display these features, try changing the names of your sequences to the ids suggested below."
  63             +"\n\nRunning WSWUBlast at EBI."
  64             +"\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."
  65             +"\nSOAP-based services provided by the European Bioinformatics Institute."
  66             +"\nNucleic Acids Res. 33(1):W25-W28 (2005));");
  67
  68         Desktop.addInternalFrame(output,
  69             "BLASTing for unidentified sequences ", 800, 300);
  70
  71         for (int i = 0; i < ids.size(); i++)
  72         {
  73             Sequence sequence = (Sequence)ids.get(i);
  74             System.out.println(sequence.getName());
  75
  76             BlastThread thread = new BlastThread(sequence);
  77             thread.start();
  78             jobsRunning++;
  79         }
  80
  81         ImageTwirler thread = new ImageTwirler();
  82         thread.start();
  83     }
  84
  85
  86     /**
  87      * DOCUMENT ME!
  88      *
  89      * @param id1 DOCUMENT ME!
  90      * @param res DOCUMENT ME!
  91      */
  92     void parseResult(Sequence seq, String res)
  93     {
  94         StringTokenizer st = new StringTokenizer(res, "\n");
  95         String data;
  96         String id2;
  97         int maxFound = 90;
  98         StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");
  99
 100         while (st.hasMoreTokens())
 101         {
 102             data = st.nextToken();
 103
 104             if (data.indexOf(">UNIPROT") > -1)
 105             {
 106                 int index = data.indexOf(">UNIPROT") + 9;
 107                 id2 = data.substring(index, data.indexOf(" ", index));
 108
 109                 boolean identitiesFound = false;
 110                 while (!identitiesFound)
 111                 {
 112                     data = st.nextToken();
 113
 114                     if (data.indexOf("Identities") > -1)
 115                     {
 116                        identitiesFound = true;
 117
 118                        int value = Integer.parseInt(data.substring(data.indexOf(
 119                            "(") + 1,
 120                                                                    data.indexOf("%")));
 121
 122                         if (value >= maxFound)
 123                         {
 124                             maxFound = value;
 125                             buffer.append(" " + id2 + " " + value + "%; ");
 126                             suggestedIds.addElement( new Object[]{seq, id2});
 127                         }
 128                     }
 129                 }
 130             }
 131         }
 132
 133         output.appendText(buffer.toString());
 134     }
 135
 136     void updateIds()
 137     {
 138         // This must be outside the run() body as java 1.5
 139      // will not return any value from the OptionPane to the expired thread.
 140       int reply = JOptionPane.showConfirmDialog(
 141           Desktop.desktop, "Automatically update suggested ids?",
 142           "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);
 143
 144       if (reply == JOptionPane.YES_OPTION)
 145       {
 146         Enumeration keys = suggestedIds.elements();
 147         while(keys.hasMoreElements())
 148         {
 149           Object [] object = (Object[])keys.nextElement();
 150
 151           Sequence oldseq = (Sequence)object[0];
 152
 153           oldseq.setName( object[1].toString() );
 154
 155           // Oldseq is actually in the dataset, we must find the
 156           // Visible seq and change its name also.
 157           for (int i = 0; i < al.getHeight(); i++)
 158           {
 159             if (al.getSequenceAt(i).getDatasetSequence() == oldseq)
 160             {
 161               al.getSequenceAt(i).setName(oldseq.getName());
 162               break;
 163             }
 164           }
 165
 166           DBRefEntry [] entries = oldseq.getDBRef();
 167           if (entries != null)
 168           {
 169             oldseq.addDBRef(new jalview.datamodel.
 170                                                  DBRefEntry(jalview.datamodel.DBRefSource.UNIPROT,
 171                 "0",
 172                 entries[0].getAccessionId()));
 173           }
 174         }
 175       }
 176       ap.repaint();
 177
 178     }
 179
 180     class ImageTwirler extends Thread
 181     {
 182         ImageIcon[] imageIcon;
 183         int imageIndex = 0;
 184
 185         public ImageTwirler()
 186         {
 187             imageIcon = new ImageIcon[9];
 188
 189             for (int i = 0; i < 9; i++)
 190             {
 191                 java.net.URL url = getClass().getResource("/images/dna" +
 192                         (i + 1) + ".gif");
 193
 194                 if (url != null)
 195                 {
 196                     imageIcon[i] = new ImageIcon(url);
 197                 }
 198             }
 199         }
 200
 201         public void run()
 202         {
 203             while (jobsRunning > 0)
 204             {
 205                 try
 206                 {
 207                     Thread.sleep(100);
 208                     imageIndex++;
 209                     imageIndex %= 9;
 210                     output.setFrameIcon(imageIcon[imageIndex]);
 211                     output.setTitle("BLASTing for unidentified sequences - " +
 212                         jobsRunning + " jobs running.");
 213                 }
 214                 catch (Exception ex)
 215                 {
 216                 }
 217             }
 218
 219             if (jobsRunning == 0)
 220             {
 221               updateIds();
 222             }
 223         }
 224     }
 225
 226     class BlastThread extends Thread
 227     {
 228         Sequence sequence;
 229         String jobid;
 230         boolean jobComplete = false;
 231
 232         BlastThread(Sequence sequence)
 233         {
 234           System.out.println("blasting for: "+sequence.getName());
 235           this.sequence = sequence;
 236         }
 237
 238         public void run()
 239         {
 240             StartJob();
 241
 242             while (!jobComplete)
 243             {
 244                 try
 245                 {
 246                   WSWUBlastService service =  new WSWUBlastServiceLocator();
 247                   WSWUBlast wublast = service.getWSWUBlast();
 248                   WSFile[] results = wublast.getResults(jobid);
 249
 250                   if(results!=null)
 251                   {
 252                       String result = new String(wublast.poll(jobid, "tooloutput"));
 253                       parseResult(sequence, result);
 254                       jobComplete = true;
 255                       jobsRunning--;
 256                   }
 257                   else
 258                   {
 259                     Thread.sleep(10000);
 260                     System.out.println("WSWuBlastClient: I'm alive " +
 261                                        sequence.getName() + " " + jobid); // log.debug
 262                   }
 263                 }
 264                 catch (Exception ex)
 265                 {
 266                 }
 267             }
 268         }
 269
 270         void StartJob()
 271         {
 272           InputParams params = new InputParams();
 273
 274           params.setProgram("blastp");
 275           params.setDatabase("uniprot");
 276           params.setMatrix("pam10");
 277
 278           params.setNumal(5);
 279           params.setSensitivity("low");
 280           params.setSort("totalscore");
 281           params.setOutformat("txt");
 282           params.setAsync(true);
 283
 284             try
 285             {
 286               Data inputs[] = new Data[1];
 287               Data input= new Data();
 288               input.setType("sequence");
 289               input.setContent(AlignSeq.extractGaps("-. ",sequence.getSequence()));
 290               inputs[0]=input;
 291
 292               WSWUBlastService service = new WSWUBlastServiceLocator();
 293               WSWUBlast wublast = service.getWSWUBlast();
 294               jobid = wublast.runWUBlast(params, inputs);
 295             }
 296             catch (Exception exp)
 297             {
 298               jobComplete = true;
 299               jobsRunning--;
 300               System.err.println("WSWUBlastClient error:\n" + exp.toString());
 301               exp.printStackTrace();
 302             }
 303         }
 304     }
 305 }