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             StringBuffer nonGapped = new StringBuffer();\r
  68 \r
  69 \r
  70             for (int n = 0; n < sequence.getSequence().length(); n++)\r
  71             {\r
  72                 if (!jalview.util.Comparison.isGap(sequence.getCharAt(n)))\r
  73                 {\r
  74                     nonGapped.append(sequence.getCharAt(n));\r
  75                 }\r
  76             }\r
  77 \r
  78             BlastThread thread = new BlastThread(ids.get(i).toString(),\r
  79                     nonGapped.toString());\r
  80             thread.start();\r
  81             jobsRunning++;\r
  82         }\r
  83 \r
  84         ImageTwirler thread = new ImageTwirler();\r
  85         thread.start();\r
  86     }\r
  87 \r
  88 \r
  89     /**\r
  90      * DOCUMENT ME!\r
  91      *\r
  92      * @param id1 DOCUMENT ME!\r
  93      * @param res DOCUMENT ME!\r
  94      */\r
  95     void parseResult(String id1, String res)\r
  96     {\r
  97         StringTokenizer st = new StringTokenizer(res, "\n");\r
  98         String data;\r
  99         String id2;\r
 100         int maxFound = 90;\r
 101         StringBuffer buffer = new StringBuffer("\n\n" + id1 + " :");\r
 102 \r
 103         while (st.hasMoreTokens())\r
 104         {\r
 105             data = st.nextToken();\r
 106 \r
 107             if (data.indexOf(">UNIPROT") > -1)\r
 108             {\r
 109                 int index = data.indexOf(">UNIPROT") + 9;\r
 110                 id2 = data.substring(index, data.indexOf(" ", index));\r
 111 \r
 112                 boolean identitiesFound = false;\r
 113                 while (!identitiesFound)\r
 114                 {\r
 115                     data = st.nextToken();\r
 116 \r
 117                     if (data.indexOf("Identities") > -1)\r
 118                     {\r
 119                        identitiesFound = true;\r
 120 \r
 121                        int value = Integer.parseInt(data.substring(data.indexOf(\r
 122                            "(") + 1,\r
 123                                                                    data.indexOf("%")));\r
 124 \r
 125                         if (value >= maxFound)\r
 126                         {\r
 127                             maxFound = value;\r
 128                             buffer.append(" " + id2 + " " + value + "%; ");\r
 129                             suggestedIds.put(id1, id2);\r
 130                         }\r
 131                     }\r
 132                 }\r
 133             }\r
 134         }\r
 135 \r
 136         output.appendText(buffer.toString());\r
 137     }\r
 138 \r
 139     void updateIds()\r
 140     {\r
 141 \r
 142     }\r
 143 \r
 144     class ImageTwirler extends Thread\r
 145     {\r
 146         ImageIcon[] imageIcon;\r
 147         int imageIndex = 0;\r
 148 \r
 149         public ImageTwirler()\r
 150         {\r
 151             imageIcon = new ImageIcon[9];\r
 152 \r
 153             for (int i = 0; i < 9; i++)\r
 154             {\r
 155                 java.net.URL url = getClass().getResource("/images/dna" +\r
 156                         (i + 1) + ".gif");\r
 157 \r
 158                 if (url != null)\r
 159                 {\r
 160                     imageIcon[i] = new ImageIcon(url);\r
 161                 }\r
 162             }\r
 163         }\r
 164 \r
 165         public void run()\r
 166         {\r
 167             while (jobsRunning > 0)\r
 168             {\r
 169                 try\r
 170                 {\r
 171                     Thread.sleep(100);\r
 172                     imageIndex++;\r
 173                     imageIndex %= 9;\r
 174                     output.setFrameIcon(imageIcon[imageIndex]);\r
 175                     output.setTitle("BLASTing for unidentified sequences - " +\r
 176                         jobsRunning + " jobs running.");\r
 177                 }\r
 178                 catch (Exception ex)\r
 179                 {\r
 180                 }\r
 181             }\r
 182 \r
 183             if (jobsRunning == 0)\r
 184             {\r
 185               int reply = JOptionPane.showConfirmDialog(\r
 186                   Desktop.desktop, "Automatically update suggested ids?",\r
 187                   "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);\r
 188 \r
 189               if (reply == JOptionPane.YES_OPTION)\r
 190               {\r
 191                 Enumeration keys = suggestedIds.keys();\r
 192                 while(keys.hasMoreElements())\r
 193                 {\r
 194                   String oldid = keys.nextElement().toString();\r
 195                   SequenceI sequence = al.findName(oldid);\r
 196                   sequence.setName( suggestedIds.get(oldid).toString() );\r
 197 \r
 198                   sequence = al.getDataset().findName(oldid);\r
 199                   Vector entries = sequence.getDBRef();\r
 200                   DBRefEntry entry = (DBRefEntry) entries.elementAt(0);\r
 201                   sequence.addDBRef(new jalview.datamodel.DBRefEntry("UNIPROT",\r
 202                       "0",\r
 203                       entry.getAccessionId()));\r
 204 \r
 205                   sequence.setName(suggestedIds.get(oldid).toString());\r
 206 \r
 207                   System.out.println("replace "+oldid+" with "+suggestedIds.get(oldid));\r
 208                 }\r
 209               }\r
 210               ap.repaint();\r
 211             }\r
 212         }\r
 213     }\r
 214 \r
 215     class BlastThread extends Thread\r
 216     {\r
 217         String sequence;\r
 218         String seqid;\r
 219         String jobid;\r
 220         boolean jobComplete = false;\r
 221 \r
 222         BlastThread(String id, String sequence)\r
 223         {\r
 224           System.out.println("blasting for: "+id);\r
 225             this.sequence = sequence;\r
 226             seqid = id;\r
 227         }\r
 228 \r
 229         public void run()\r
 230         {\r
 231             StartJob();\r
 232 \r
 233             while (!jobComplete)\r
 234             {\r
 235                 try\r
 236                 {\r
 237                     Call call = (Call) new Service().createCall();\r
 238                     call.setTargetEndpointAddress(new java.net.URL(\r
 239                             "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
 240                     call.setOperationName(new QName("WSWUBlast", "polljob"));\r
 241 \r
 242                     Object object = (String) call.invoke(new Object[]\r
 243                             {\r
 244                                 jobid, "xml"\r
 245                             });\r
 246 \r
 247                     if(object instanceof String)\r
 248                     {\r
 249                       parseResult(seqid, (String)object);\r
 250                       jobComplete = true;\r
 251                       jobsRunning--;\r
 252                     }\r
 253 \r
 254                     Thread.sleep(5000);\r
 255 \r
 256                     System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug\r
 257                 }\r
 258                 catch (Exception ex)\r
 259                 {\r
 260                 }\r
 261             }\r
 262         }\r
 263 \r
 264         void StartJob()\r
 265         {\r
 266             HashMap params = new HashMap();\r
 267             params.put("database", "uniprot");\r
 268             params.put("sensitivity", "low");\r
 269             params.put("sort", "totalscore");\r
 270             params.put("matrix", "pam10");\r
 271             params.put("program", "blastp");\r
 272             params.put("alignments", "5");\r
 273             params.put("type", "xml");\r
 274             params.put("async", "true");\r
 275 \r
 276             byte[] seqbytes = sequence.getBytes();\r
 277 \r
 278             try\r
 279             {\r
 280                 Call call = (Call) new Service().createCall();\r
 281                 call.setTargetEndpointAddress(new java.net.URL(\r
 282                         "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
 283                 call.setOperationName(new QName("WSWUBlast", "doWUBlast"));\r
 284 \r
 285                 Object object = call.invoke(new Object[]\r
 286                         {\r
 287                             params, seqbytes\r
 288                         });\r
 289 \r
 290                 if(object instanceof byte[])\r
 291                   jobid = new String( (byte[])object);\r
 292 \r
 293                 else\r
 294                 {\r
 295                   jobComplete = true;\r
 296                   jobsRunning--;\r
 297                   parseResult(seqid, (String)object);\r
 298                 }\r
 299 \r
 300             }\r
 301             catch (Exception exp)\r
 302             {\r
 303                 System.err.println("WSWUBlastClient error:\n" + exp.toString());\r
 304                 exp.printStackTrace();\r
 305             }\r
 306         }\r
 307     }\r
 308 }\r