src/jalview/io/WSWUBlastClient.java

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