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.awt.*;\r
  28 \r
  29 import java.util.*;\r
  30 \r
  31 import javax.swing.*;\r
  32 \r
  33 import javax.xml.namespace.QName;\r
  34 \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     CutAndPasteTransfer output = new CutAndPasteTransfer();\r
  45     int jobsRunning = 0;\r
  46 \r
  47     /**\r
  48      * Creates a new WSWUBlastClient object.\r
  49      *\r
  50      * @param al DOCUMENT ME!\r
  51      * @param ids DOCUMENT ME!\r
  52      */\r
  53     public WSWUBlastClient(AlignmentI al, ArrayList ids)\r
  54     {\r
  55         output.setText(\r
  56             "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered." +\r
  57             "\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");\r
  58         Desktop.addInternalFrame(output,\r
  59             "BLASTing for unidentified sequences ", 800, 300);\r
  60 \r
  61         for (int i = 0; i < ids.size(); i++)\r
  62         {\r
  63             SequenceI sequence = al.findName(ids.get(i).toString());\r
  64             StringBuffer nonGapped = new StringBuffer();\r
  65 \r
  66             for (int n = 0; n < sequence.getSequence().length(); n++)\r
  67             {\r
  68                 if (!jalview.util.Comparison.isGap(sequence.getCharAt(n)))\r
  69                 {\r
  70                     nonGapped.append(sequence.getCharAt(n));\r
  71                 }\r
  72             }\r
  73 \r
  74             BlastThread thread = new BlastThread(ids.get(i).toString(),\r
  75                     nonGapped.toString());\r
  76             thread.start();\r
  77             jobsRunning++;\r
  78         }\r
  79 \r
  80         ImageTwirler thread = new ImageTwirler();\r
  81         thread.start();\r
  82     }\r
  83 \r
  84     /**\r
  85      * DOCUMENT ME!\r
  86      *\r
  87      * @param id1 DOCUMENT ME!\r
  88      * @param res DOCUMENT ME!\r
  89      */\r
  90     void parseResult(String id1, String res)\r
  91     {\r
  92         StringTokenizer st = new StringTokenizer(res, "\n");\r
  93         String data;\r
  94         String id2;\r
  95         int maxFound = 90;\r
  96         StringBuffer buffer = new StringBuffer("\n\n" + id1 + " :");\r
  97 \r
  98         while (st.hasMoreTokens())\r
  99         {\r
 100             data = st.nextToken();\r
 101 \r
 102             if (data.indexOf("database=\"uniprot\" id=") > -1)\r
 103             {\r
 104                 int index = data.indexOf("database=\"uniprot\" id=") + 23;\r
 105                 id2 = data.substring(index, data.indexOf("\"", index));\r
 106 \r
 107                 while (data.indexOf("</alignment>") == -1)\r
 108                 {\r
 109                     data = st.nextToken();\r
 110 \r
 111                     if (data.indexOf("<identity>") > -1)\r
 112                     {\r
 113                         int value = Integer.parseInt(data.substring(data.indexOf(\r
 114                                         "<identity>") + 10,\r
 115                                     data.indexOf("</identity>")));\r
 116 \r
 117                         if (value >= maxFound)\r
 118                         {\r
 119                             maxFound = value;\r
 120                             buffer.append(" " + id2 + " " + value + "%; ");\r
 121                         }\r
 122                     }\r
 123                 }\r
 124             }\r
 125         }\r
 126 \r
 127         output.setText(output.getText() + buffer.toString());\r
 128     }\r
 129 \r
 130     class ImageTwirler extends Thread\r
 131     {\r
 132         ImageIcon[] imageIcon;\r
 133         int imageIndex = 0;\r
 134 \r
 135         public ImageTwirler()\r
 136         {\r
 137             imageIcon = new ImageIcon[9];\r
 138 \r
 139             for (int i = 0; i < 9; i++)\r
 140             {\r
 141                 java.net.URL url = getClass().getResource("/images/dna" +\r
 142                         (i + 1) + ".gif");\r
 143 \r
 144                 if (url != null)\r
 145                 {\r
 146                     imageIcon[i] = new ImageIcon(url);\r
 147                 }\r
 148             }\r
 149         }\r
 150 \r
 151         public void run()\r
 152         {\r
 153             while (jobsRunning > 0)\r
 154             {\r
 155                 try\r
 156                 {\r
 157                     Thread.sleep(100);\r
 158                     imageIndex++;\r
 159                     imageIndex %= 9;\r
 160                     output.setFrameIcon(imageIcon[imageIndex]);\r
 161                     output.setTitle("BLASTing for unidentified sequences - " +\r
 162                         jobsRunning + " jobs running.");\r
 163                 }\r
 164                 catch (Exception ex)\r
 165                 {\r
 166                 }\r
 167             }\r
 168         }\r
 169     }\r
 170 \r
 171     class BlastThread extends Thread\r
 172     {\r
 173         String sequence;\r
 174         String seqid;\r
 175         String jobid;\r
 176         boolean jobComplete = false;\r
 177 \r
 178         BlastThread(String id, String sequence)\r
 179         {\r
 180             this.sequence = sequence;\r
 181             seqid = id;\r
 182         }\r
 183 \r
 184         public void run()\r
 185         {\r
 186             StartJob();\r
 187 \r
 188             while (!jobComplete)\r
 189             {\r
 190                 try\r
 191                 {\r
 192                     Call call = (Call) new Service().createCall();\r
 193                     call.setTargetEndpointAddress(new java.net.URL(\r
 194                             "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
 195                     call.setOperationName(new QName("WSWUBlast", "polljob"));\r
 196 \r
 197                     String result = (String) call.invoke(new Object[]\r
 198                             {\r
 199                                 jobid, "xml"\r
 200                             });\r
 201 \r
 202                     if ((result.indexOf("JOB PENDING") == -1) &&\r
 203                             (result.indexOf("JOB RUNNING") == -1))\r
 204                     {\r
 205                         parseResult(seqid, result);\r
 206                         jobComplete = true;\r
 207                         jobsRunning--;\r
 208                     }\r
 209 \r
 210                     Thread.sleep(5000);\r
 211 \r
 212                     // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug\r
 213                 }\r
 214                 catch (Exception ex)\r
 215                 {\r
 216                 }\r
 217             }\r
 218         }\r
 219 \r
 220         void StartJob()\r
 221         {\r
 222             HashMap params = new HashMap();\r
 223             params.put("database", "uniprot");\r
 224             params.put("sensitivity", "low");\r
 225             params.put("sort", "totalscore");\r
 226             params.put("matrix", "pam10");\r
 227             params.put("program", "blastp");\r
 228             params.put("alignments", "5");\r
 229             params.put("outformat", "xml");\r
 230             params.put("searchtype", "1");\r
 231 \r
 232             byte[] seqbytes = sequence.getBytes();\r
 233 \r
 234             try\r
 235             {\r
 236                 Call call = (Call) new Service().createCall();\r
 237                 call.setTargetEndpointAddress(new java.net.URL(\r
 238                         "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
 239                 call.setOperationName(new QName("WSWUBlast", "doWUBlast"));\r
 240 \r
 241                 String result = (String) call.invoke(new Object[]\r
 242                         {\r
 243                             params, seqbytes\r
 244                         });\r
 245                 jobid = result;\r
 246                 System.out.println(\r
 247                     "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '" +\r
 248                     jobid + "'");\r
 249             }\r
 250             catch (Exception exp)\r
 251             {\r
 252                 System.err.println("WSWUBlastClient error:\n" + exp.toString());\r
 253                 exp.printStackTrace();\r
 254             }\r
 255         }\r
 256     }\r
 257 }\r