src/jalview/io/WSWUBlastClient.java

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