X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FWSWUBlastClient.java;h=81b4e55adc45fda4d3b0b0f22ddcc05abdc7d1f4;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=ed29f89cb2404aaa98d04ebf037ab7060b4f67c8;hpb=42f46263655185b0a436356c37295ec82d091dce;p=jalview.git

diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index ed29f89..81b4e55 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -1,119 +1,305 @@
-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.*;
-
-public class WSWUBlastClient
-{
-  CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
-
-  public WSWUBlastClient(AlignmentI al, ArrayList ids)
-  {
-    JInternalFrame frame = new JInternalFrame();
-    cap.formatForOutput();
-    frame.setContentPane(cap);
-    cap.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(frame, "BLASTing for unidentified sequences ", 800,300);
-
-    for(int i=0; i<ids.size(); i++)
-    {
-     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));
-      }
-
-     BlastThread thread = new BlastThread(ids.get(i).toString(),  nonGapped.toString());
-     thread.start();
-     }
-
-  }
-
-  class BlastThread extends Thread
-  {
-    String sequence;
-    String id;
-    BlastThread(String id, String sequence)
-    {
-      this.sequence = sequence;
-      this.id = id;
-    }
-
-    public void run()
-    {
-      FindUniprotIDFromUnknownSequence(id, sequence);
-    }
-  }
-
-  public void FindUniprotIDFromUnknownSequence (String id, String s)
-  {
-        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");
-        byte[] sequence = s.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,sequence});
-            parseResult(id, result);
-            }
-        catch (Exception exp) {
-             System.err.println ("ERROR:\n" + exp.toString());
-            exp.printStackTrace();
-        }
-    }
-
-    void parseResult(String id1, String res)
-    {
-      StringTokenizer st = new StringTokenizer(res, "\n");
-      String data;
-      String id2;
-      int maxFound = 90;
-      StringBuffer buffer = new StringBuffer("\n\n"+id1+" :");
-
-      while( st.hasMoreTokens() )
-      {
-        data = st.nextToken();
-
-        if(data.indexOf("database=\"uniprot\" id=")>-1)
-        {
-          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)
-            {
-              int value = Integer.parseInt( data.substring(data.indexOf("<identity>")+10, data.indexOf("</identity>")));
-              if(value>=maxFound)
-              {
-                maxFound = value;
-                buffer.append(" "+ id2 + " " + value+"%; ");
-              }
-            }
-          }
-
-        }
-
-
-      }
-
-      cap.setText(cap.getText()+buffer.toString());
-    }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.io;
+
+import java.util.*;
+
+import javax.swing.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+import uk.ac.ebi.www.*;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class WSWUBlastClient
+{
+  AlignmentPanel ap;
+
+  AlignmentI al;
+
+  CutAndPasteTransfer output = new CutAndPasteTransfer();
+
+  int jobsRunning = 0;
+
+  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)
+  {
+    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));");
+
+    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();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param id1
+   *          DOCUMENT ME!
+   * @param res
+   *          DOCUMENT ME!
+   */
+  void parseResult(Sequence seq, String res)
+  {
+    StringTokenizer st = new StringTokenizer(res, "\n");
+    String data;
+    String id2;
+    int maxFound = 90;
+    StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");
+
+    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("%")));
+
+            if (value >= maxFound)
+            {
+              maxFound = value;
+              buffer.append(" " + id2 + " " + value + "%; ");
+              suggestedIds.addElement(new Object[]
+              { seq, id2 });
+            }
+          }
+        }
+      }
+    }
+
+    output.appendText(buffer.toString());
+  }
+
+  void updateIds()
+  {
+    // 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);
+
+    if (reply == JOptionPane.YES_OPTION)
+    {
+      Enumeration keys = suggestedIds.elements();
+      while (keys.hasMoreElements())
+      {
+        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;
+          }
+        }
+
+        DBRefEntry[] entries = oldseq.getDBRef();
+        if (entries != null)
+        {
+          oldseq.addDBRef(new jalview.datamodel.DBRefEntry(
+                  jalview.datamodel.DBRefSource.UNIPROT, "0", entries[0]
+                          .getAccessionId()));
+        }
+      }
+    }
+    ap.paintAlignment(true);
+
+  }
+
+  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);
+        }
+      }
+    }
+
+    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();
+      }
+    }
+  }
+
+  class BlastThread extends Thread
+  {
+    Sequence sequence;
+
+    String jobid;
+
+    boolean jobComplete = false;
+
+    BlastThread(Sequence sequence)
+    {
+      System.out.println("blasting for: " + sequence.getName());
+      this.sequence = sequence;
+    }
+
+    public void run()
+    {
+      StartJob();
+
+      while (!jobComplete)
+      {
+        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");
+
+      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
+                .getSequenceAsString()));
+        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();
+      }
+    }
+  }
+}