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