src/jalview/io/WSWUBlastClient.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2005 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 \r
  33 \r
  34 /**\r
  35  * DOCUMENT ME!\r
  36  *\r
  37  * @author $author$\r
  38  * @version $Revision$\r
  39  */\r
  40 public class WSWUBlastClient\r
  41 {\r
  42     AlignmentPanel ap;\r
  43     AlignmentI al;\r
  44     CutAndPasteTransfer output = new CutAndPasteTransfer();\r
  45     int jobsRunning = 0;\r
  46 \r
  47     Hashtable suggestedIds = new Hashtable();\r
  48     /**\r
  49      * Creates a new WSWUBlastClient object.\r
  50      *\r
  51      * @param al DOCUMENT ME!\r
  52      * @param ids DOCUMENT ME!\r
  53      */\r
  54     public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)\r
  55     {\r
  56         this.ap = ap;\r
  57         this.al = al;\r
  58         output.setText(\r
  59             "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered." +\r
  60             "\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");\r
  61         Desktop.addInternalFrame(output,\r
  62             "BLASTing for unidentified sequences ", 800, 300);\r
  63 \r
  64         for (int i = 0; i < ids.size(); i++)\r
  65         {\r
  66             SequenceI sequence = al.findName(ids.get(i).toString());\r
  67             System.out.println(ids.get(i).toString());\r
  68             StringBuffer nonGapped = new StringBuffer();\r
  69 \r
  70 \r
  71             for (int n = 0; n < sequence.getSequence().length(); n++)\r
  72             {\r
  73                 if (!jalview.util.Comparison.isGap(sequence.getCharAt(n)))\r
  74                 {\r
  75                     nonGapped.append(sequence.getCharAt(n));\r
  76                 }\r
  77             }\r
  78 \r
  79             BlastThread thread = new BlastThread(ids.get(i).toString(),\r
  80                     nonGapped.toString());\r
  81             thread.start();\r
  82             jobsRunning++;\r
  83         }\r
  84 \r
  85         ImageTwirler thread = new ImageTwirler();\r
  86         thread.start();\r
  87     }\r
  88 \r
  89 \r
  90     /**\r
  91      * DOCUMENT ME!\r
  92      *\r
  93      * @param id1 DOCUMENT ME!\r
  94      * @param res DOCUMENT ME!\r
  95      */\r
  96     void parseResult(String id1, String res)\r
  97     {\r
  98         StringTokenizer st = new StringTokenizer(res, "\n");\r
  99         String data;\r
 100         String id2;\r
 101         int maxFound = 90;\r
 102         StringBuffer buffer = new StringBuffer("\n\n" + id1 + " :");\r
 103 \r
 104         while (st.hasMoreTokens())\r
 105         {\r
 106             data = st.nextToken();\r
 107 \r
 108             if (data.indexOf(">UNIPROT") > -1)\r
 109             {\r
 110                 int index = data.indexOf(">UNIPROT") + 9;\r
 111                 id2 = data.substring(index, data.indexOf(" ", index));\r
 112 \r
 113                 boolean identitiesFound = false;\r
 114                 while (!identitiesFound)\r
 115                 {\r
 116                     data = st.nextToken();\r
 117 \r
 118                     if (data.indexOf("Identities") > -1)\r
 119                     {\r
 120                        identitiesFound = true;\r
 121 \r
 122                        int value = Integer.parseInt(data.substring(data.indexOf(\r
 123                            "(") + 1,\r
 124                                                                    data.indexOf("%")));\r
 125 \r
 126                         if (value >= maxFound)\r
 127                         {\r
 128                             maxFound = value;\r
 129                             buffer.append(" " + id2 + " " + value + "%; ");\r
 130                             if(!suggestedIds.containsKey(id1))\r
 131                              {\r
 132                                suggestedIds.put(id1, id2);\r
 133                              }\r
 134                         }\r
 135                     }\r
 136                 }\r
 137             }\r
 138         }\r
 139 \r
 140         output.appendText(buffer.toString());\r
 141     }\r
 142 \r
 143     void updateIds()\r
 144     {\r
 145         // This must be outside the run() body as java 1.5\r
 146      // will not return any value from the OptionPane to the expired thread.\r
 147       int reply = JOptionPane.showConfirmDialog(\r
 148           Desktop.desktop, "Automatically update suggested ids?",\r
 149           "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);\r
 150 \r
 151       if (reply == JOptionPane.YES_OPTION)\r
 152       {\r
 153         Enumeration keys = suggestedIds.keys();\r
 154         while(keys.hasMoreElements())\r
 155         {\r
 156           String oldid = keys.nextElement().toString();\r
 157           SequenceI sequence = al.findName(oldid);\r
 158           sequence.setName( suggestedIds.get(oldid).toString() );\r
 159 \r
 160           sequence = sequence.getDatasetSequence();\r
 161           if(sequence!=null)\r
 162           {\r
 163 \r
 164             sequence.setName(suggestedIds.get(oldid).toString());\r
 165 \r
 166             Vector entries = sequence.getDBRef();\r
 167             if(entries!=null)\r
 168             {\r
 169               DBRefEntry entry = (DBRefEntry) entries.elementAt(0);\r
 170               sequence.addDBRef(new jalview.datamodel.DBRefEntry("UNIPROT",\r
 171                   "0",\r
 172                   entry.getAccessionId()));\r
 173             }\r
 174           }\r
 175           System.out.println("replace "+oldid+" with "+suggestedIds.get(oldid));\r
 176         }\r
 177       }\r
 178       ap.repaint();\r
 179 \r
 180     }\r
 181 \r
 182     class ImageTwirler extends Thread\r
 183     {\r
 184         ImageIcon[] imageIcon;\r
 185         int imageIndex = 0;\r
 186 \r
 187         public ImageTwirler()\r
 188         {\r
 189             imageIcon = new ImageIcon[9];\r
 190 \r
 191             for (int i = 0; i < 9; i++)\r
 192             {\r
 193                 java.net.URL url = getClass().getResource("/images/dna" +\r
 194                         (i + 1) + ".gif");\r
 195 \r
 196                 if (url != null)\r
 197                 {\r
 198                     imageIcon[i] = new ImageIcon(url);\r
 199                 }\r
 200             }\r
 201         }\r
 202 \r
 203         public void run()\r
 204         {\r
 205             while (jobsRunning > 0)\r
 206             {\r
 207                 try\r
 208                 {\r
 209                     Thread.sleep(100);\r
 210                     imageIndex++;\r
 211                     imageIndex %= 9;\r
 212                     output.setFrameIcon(imageIcon[imageIndex]);\r
 213                     output.setTitle("BLASTing for unidentified sequences - " +\r
 214                         jobsRunning + " jobs running.");\r
 215                 }\r
 216                 catch (Exception ex)\r
 217                 {\r
 218                 }\r
 219             }\r
 220 \r
 221             if (jobsRunning == 0)\r
 222             {\r
 223               updateIds();\r
 224             }\r
 225         }\r
 226     }\r
 227 \r
 228     class BlastThread extends Thread\r
 229     {\r
 230         String sequence;\r
 231         String seqid;\r
 232         String jobid;\r
 233         boolean jobComplete = false;\r
 234 \r
 235         BlastThread(String id, String sequence)\r
 236         {\r
 237           System.out.println("blasting for: "+id);\r
 238             this.sequence = sequence;\r
 239             seqid = id;\r
 240         }\r
 241 \r
 242         public void run()\r
 243         {\r
 244             StartJob();\r
 245 \r
 246             while (!jobComplete)\r
 247             {\r
 248                 try\r
 249                 {\r
 250                     Call call = (Call) new Service().createCall();\r
 251                     call.setTargetEndpointAddress(new java.net.URL(\r
 252                             "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
 253                     call.setOperationName(new QName("WSWUBlast", "polljob"));\r
 254 \r
 255                     Object object = (String) call.invoke(new Object[]\r
 256                             {\r
 257                                 jobid, "xml"\r
 258                             });\r
 259 \r
 260                     if(object instanceof String)\r
 261                     {\r
 262                       parseResult(seqid, (String)object);\r
 263                       jobComplete = true;\r
 264                       jobsRunning--;\r
 265                     }\r
 266 \r
 267                     Thread.sleep(5000);\r
 268 \r
 269                     System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug\r
 270                 }\r
 271                 catch (Exception ex)\r
 272                 {\r
 273                 }\r
 274             }\r
 275         }\r
 276 \r
 277         void StartJob()\r
 278         {\r
 279             HashMap params = new HashMap();\r
 280             params.put("database", "uniprot");\r
 281             params.put("sensitivity", "low");\r
 282             params.put("sort", "totalscore");\r
 283             params.put("matrix", "pam10");\r
 284             params.put("program", "blastp");\r
 285             params.put("alignments", "5");\r
 286             params.put("type", "xml");\r
 287             params.put("async", "true");\r
 288 \r
 289             byte[] seqbytes = sequence.getBytes();\r
 290 \r
 291             try\r
 292             {\r
 293                 Call call = (Call) new Service().createCall();\r
 294                 call.setTargetEndpointAddress(new java.net.URL(\r
 295                         "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
 296                 call.setOperationName(new QName("WSWUBlast", "doWUBlast"));\r
 297 \r
 298                 Object object = call.invoke(new Object[]\r
 299                         {\r
 300                             params, seqbytes\r
 301                         });\r
 302 \r
 303                 if(object instanceof byte[])\r
 304                   jobid = new String( (byte[])object);\r
 305 \r
 306                 else\r
 307                 {\r
 308                   jobComplete = true;\r
 309                   jobsRunning--;\r
 310                   parseResult(seqid, (String)object);\r
 311                 }\r
 312 \r
 313             }\r
 314             catch (Exception exp)\r
 315             {\r
 316                 System.err.println("WSWUBlastClient error:\n" + exp.toString());\r
 317                 exp.printStackTrace();\r
 318             }\r
 319         }\r
 320     }\r
 321 }\r