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