X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FWSWUBlastClient.java;h=0906d12fa49c8f16c401eacd374cce89a73c956f;hb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;hp=f8d74bf1ddccfc0ea1055904cad9536b2a5624bf;hpb=944a2ac14705ce27cc38efb03531141d6da7cd61;p=jalview.git

diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index f8d74bf..0906d12 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -1,188 +1,306 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
 package jalview.io;
 
-import org.apache.axis.client.*;
-import javax.xml.namespace.QName;
-import java.util.*;
 import jalview.datamodel.*;
+
 import jalview.gui.*;
-import javax.swing.*;
+
+import org.apache.axis.client.*;
+
 import java.util.*;
-import java.awt.*;
 
+import javax.swing.*;
+
+import javax.xml.namespace.QName;
+import jalview.analysis.AlignSeq;
+
+import uk.ac.ebi.www.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
 public class WSWUBlastClient
 {
-  CutAndPasteTransfer output = new CutAndPasteTransfer();
-  int jobsRunning = 0;
+    AlignmentPanel ap;
+    AlignmentI al;
+    CutAndPasteTransfer output = new CutAndPasteTransfer();
+    int jobsRunning = 0;
 
-  public WSWUBlastClient(AlignmentI al, ArrayList ids)
-  {
-    output.setText("To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."
-                +"\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");
-    Desktop.addInternalFrame(output, "BLASTing for unidentified sequences ", 800,300);
-
-    for(int i=0; i<ids.size(); i++)
+    Vector suggestedIds = new Vector();
+    /**
+     * Creates a new WSWUBlastClient object.
+     *
+     * @param al DOCUMENT ME!
+     * @param ids DOCUMENT ME!
+     */
+    public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)
     {
-     SequenceI sequence =  al.findName( ids.get(i).toString() );
-     StringBuffer nonGapped = new StringBuffer();
-      for (int n = 0; n < sequence.getSequence().length(); n++)
-      {
-        if (!jalview.util.Comparison.isGap(sequence.getCharAt(n)))
-          nonGapped.append(sequence.getCharAt(n));
-      }
+        this.ap = ap;
+        this.al = al;
+        output.setText(
+            "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."
+            +"\nIn order to display these features, try changing the names of your sequences to the ids suggested below."
+            +"\n\nRunning WSWUBlast at EBI."
+            +"\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."
+            +"\nSOAP-based services provided by the European Bioinformatics Institute."
+            +"\nNucleic Acids Res. 33(1):W25-W28 (2005));");
 
-     BlastThread thread = new BlastThread(ids.get(i).toString(),  nonGapped.toString());
-     thread.start();
-     jobsRunning ++;
-     }
-     ImageTwirler thread = new ImageTwirler();
-     thread.start();
-  }
-
-  class ImageTwirler extends Thread
-  {
-    ImageIcon [] imageIcon;
-    int imageIndex = 0;
-    public ImageTwirler()
-    {
-      imageIcon = new ImageIcon[9];
-      for(int i=0; i<9; i++)
-      {
-        java.net.URL url = getClass().getResource("/images/dna" + (i+1) + ".gif");
-        if (url != null)
-          imageIcon[i] = new ImageIcon(url);
-      }
+        Desktop.addInternalFrame(output,
+            "BLASTing for unidentified sequences ", 800, 300);
+
+        for (int i = 0; i < ids.size(); i++)
+        {
+            Sequence sequence = (Sequence)ids.get(i);
+            System.out.println(sequence.getName());
+
+            BlastThread thread = new BlastThread(sequence);
+            thread.start();
+            jobsRunning++;
+        }
+
+        ImageTwirler thread = new ImageTwirler();
+        thread.start();
     }
 
-    public void run()
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param id1 DOCUMENT ME!
+     * @param res DOCUMENT ME!
+     */
+    void parseResult(Sequence seq, String res)
     {
-      while(jobsRunning>0)
-      {
-        try{
-          Thread.sleep(100);
-          imageIndex++;
-          imageIndex %=9;
-          output.setFrameIcon( imageIcon[imageIndex]);
-          output.setTitle("BLASTing for unidentified sequences - "+jobsRunning+" jobs running.");
+        StringTokenizer st = new StringTokenizer(res, "\n");
+        String data;
+        String id2;
+        int maxFound = 90;
+        StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");
 
-        }catch(Exception ex){}
+        while (st.hasMoreTokens())
+        {
+            data = st.nextToken();
 
-      }
-    }
-  }
+            if (data.indexOf(">UNIPROT") > -1)
+            {
+                int index = data.indexOf(">UNIPROT") + 9;
+                id2 = data.substring(index, data.indexOf(" ", index));
 
+                boolean identitiesFound = false;
+                while (!identitiesFound)
+                {
+                    data = st.nextToken();
 
+                    if (data.indexOf("Identities") > -1)
+                    {
+                       identitiesFound = true;
 
+                       int value = Integer.parseInt(data.substring(data.indexOf(
+                           "(") + 1,
+                                                                   data.indexOf("%")));
 
-  class BlastThread extends Thread
-  {
-    String sequence;
-    String seqid;
-    String jobid;
-    boolean jobComplete = false;
+                        if (value >= maxFound)
+                        {
+                            maxFound = value;
+                            buffer.append(" " + id2 + " " + value + "%; ");
+                            suggestedIds.addElement( new Object[]{seq, id2});
+                        }
+                    }
+                }
+            }
+        }
 
-    BlastThread(String id, String sequence)
-    {
-      this.sequence = sequence;
-      seqid = id;
+        output.appendText(buffer.toString());
     }
 
-    public void run()
+    void updateIds()
     {
-      StartJob();
+        // This must be outside the run() body as java 1.5
+     // will not return any value from the OptionPane to the expired thread.
+      int reply = JOptionPane.showConfirmDialog(
+          Desktop.desktop, "Automatically update suggested ids?",
+          "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);
 
-      while (!jobComplete)
+      if (reply == JOptionPane.YES_OPTION)
       {
-        try
+        Enumeration keys = suggestedIds.elements();
+        while(keys.hasMoreElements())
         {
-          Call call = (Call)new Service().createCall();
-          call.setTargetEndpointAddress(new java.net.URL(
-              "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));
-          call.setOperationName(new QName("WSWUBlast", "polljob"));
-          String result = (String) call.invoke(new Object[]
-                                               {jobid, "xml"});
-          if(result.indexOf("JOB PENDING")==-1 && result.indexOf("JOB RUNNING")==-1)
+          Object [] object = (Object[])keys.nextElement();
+
+          Sequence oldseq = (Sequence)object[0];
+
+          oldseq.setName( object[1].toString() );
+
+          // Oldseq is actually in the dataset, we must find the
+          // Visible seq and change its name also.
+          for (int i = 0; i < al.getHeight(); i++)
+          {
+            if (al.getSequenceAt(i).getDatasetSequence() == oldseq)
+            {
+              al.getSequenceAt(i).setName(oldseq.getName());
+              break;
+            }
+          }
+
+          Vector entries = oldseq.getDBRef();
+          if (entries != null)
           {
-                parseResult(seqid, result);
-                jobComplete = true;
-                jobsRunning --;
+            DBRefEntry entry = (DBRefEntry) entries.elementAt(0);
+            oldseq.addDBRef(new jalview.datamodel.
+                                                 DBRefEntry("UNIPROT",
+                "0",
+                entry.getAccessionId()));
           }
-          Thread.sleep(5000);
-          // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug
         }
-        catch (Exception ex)
-        {}
       }
+      ap.repaint();
+
     }
 
-    void StartJob()
+    class ImageTwirler extends Thread
     {
-      HashMap params = new HashMap();
-      params.put("database", "uniprot");
-      params.put("sensitivity", "low");
-      params.put("sort", "totalscore");
-      params.put("matrix", "pam10");
-      params.put("program", "blastp");
-      params.put("alignments", "5");
-      params.put("outformat", "xml");
-      params.put("searchtype", "1");
-      byte[] seqbytes = sequence.getBytes();
-
-      try
-      {
-        Call call = (Call)new Service().createCall();
-        call.setTargetEndpointAddress(new java.net.URL(
-            "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));
-        call.setOperationName(new QName("WSWUBlast", "doWUBlast"));
-        String result = (String) call.invoke(new Object[]
-                                             {params, seqbytes});
-        jobid = result;
-        System.out.println("http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '"+jobid+"'");
+        ImageIcon[] imageIcon;
+        int imageIndex = 0;
 
-      }
-      catch (Exception exp)
-      {
-        System.err.println("WSWUBlastClient error:\n" + exp.toString());
-        exp.printStackTrace();
-      }
+        public ImageTwirler()
+        {
+            imageIcon = new ImageIcon[9];
+
+            for (int i = 0; i < 9; i++)
+            {
+                java.net.URL url = getClass().getResource("/images/dna" +
+                        (i + 1) + ".gif");
+
+                if (url != null)
+                {
+                    imageIcon[i] = new ImageIcon(url);
+                }
+            }
+        }
+
+        public void run()
+        {
+            while (jobsRunning > 0)
+            {
+                try
+                {
+                    Thread.sleep(100);
+                    imageIndex++;
+                    imageIndex %= 9;
+                    output.setFrameIcon(imageIcon[imageIndex]);
+                    output.setTitle("BLASTing for unidentified sequences - " +
+                        jobsRunning + " jobs running.");
+                }
+                catch (Exception ex)
+                {
+                }
+            }
+
+            if (jobsRunning == 0)
+            {
+              updateIds();
+            }
+        }
     }
-  }
 
-    void parseResult(String id1, String res)
+    class BlastThread extends Thread
     {
-      StringTokenizer st = new StringTokenizer(res, "\n");
-      String data;
-      String id2;
-      int maxFound = 90;
-      StringBuffer buffer = new StringBuffer("\n\n"+id1+" :");
+        Sequence sequence;
+        String jobid;
+        boolean jobComplete = false;
 
-      while( st.hasMoreTokens() )
-      {
-        data = st.nextToken();
+        BlastThread(Sequence sequence)
+        {
+          System.out.println("blasting for: "+sequence.getName());
+          this.sequence = sequence;
+        }
 
-        if(data.indexOf("database=\"uniprot\" id=")>-1)
+        public void run()
         {
-          int index =  data.indexOf("database=\"uniprot\" id=")+ 23;
-          id2 = data.substring( index, data.indexOf("\"", index) );
-          while( data.indexOf("</alignment>")==-1)
-          {
-            data = st.nextToken();
-            if(data.indexOf("<identity>")>-1)
+            StartJob();
+
+            while (!jobComplete)
             {
-              int value = Integer.parseInt( data.substring(data.indexOf("<identity>")+10, data.indexOf("</identity>")));
-              if(value>=maxFound)
-              {
-                maxFound = value;
-                buffer.append(" "+ id2 + " " + value+"%; ");
-              }
-            }
-          }
+                try
+                {
+                  WSWUBlastService service =  new WSWUBlastServiceLocator();
+                  WSWUBlast wublast = service.getWSWUBlast();
+                  WSFile[] results = wublast.getResults(jobid);
 
+                  if(results!=null)
+                  {
+                      String result = new String(wublast.poll(jobid, "tooloutput"));
+                      parseResult(sequence, result);
+                      jobComplete = true;
+                      jobsRunning--;
+                  }
+                  else
+                  {
+                    Thread.sleep(10000);
+                    System.out.println("WSWuBlastClient: I'm alive " +
+                                       sequence.getName() + " " + jobid); // log.debug
+                  }
+                }
+                catch (Exception ex)
+                {
+                }
+            }
         }
 
+        void StartJob()
+        {
+          InputParams params = new InputParams();
 
-      }
+          params.setProgram("blastp");
+          params.setDatabase("uniprot");
+          params.setMatrix("pam10");
 
-      output.setText(output.getText()+buffer.toString());
-    }
+          params.setNumal(5);
+          params.setSensitivity("low");
+          params.setSort("totalscore");
+          params.setOutformat("txt");
+          params.setAsync(true);
+
+            try
+            {
+              Data inputs[] = new Data[1];
+              Data input= new Data();
+              input.setType("sequence");
+              input.setContent(AlignSeq.extractGaps("-. ",sequence.getSequence()));
+              inputs[0]=input;
 
+              WSWUBlastService service = new WSWUBlastServiceLocator();
+              WSWUBlast wublast = service.getWSWUBlast();
+              jobid = wublast.runWUBlast(params, inputs);
+            }
+            catch (Exception exp)
+            {
+              jobComplete = true;
+              jobsRunning--;
+              System.err.println("WSWUBlastClient error:\n" + exp.toString());
+              exp.printStackTrace();
+            }
+        }
+    }
 }