From 4f561ae47b0155fe5a76831f09c0812498f10ea3 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 9 Feb 2005 15:29:57 +0000
Subject: [PATCH] Blasts asynchronously

---
 src/jalview/io/WSWUBlastClient.java |  145 ++++++++++++++++++++++++++---------
 1 file changed, 109 insertions(+), 36 deletions(-)

diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index ed29f89..f2c2047 100755
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -6,19 +6,23 @@ import java.util.*;
 import jalview.datamodel.*;
 import jalview.gui.*;
 import javax.swing.*;
+import java.util.*;
+import java.awt.*;
 
 public class WSWUBlastClient
 {
-  CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+  JInternalFrame outputFrame = new JInternalFrame();
+  CutAndPasteTransfer output = new CutAndPasteTransfer(false);
+  int jobsRunning = 0;
 
   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."
+
+    output.formatForOutput();
+    outputFrame.setContentPane(output);
+    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(frame, "BLASTing for unidentified sequences ", 800,300);
+    Desktop.addInternalFrame(outputFrame, "BLASTing for unidentified sequences ", 800,300);
 
     for(int i=0; i<ids.size(); i++)
     {
@@ -31,52 +35,121 @@ public class WSWUBlastClient
       }
 
      BlastThread thread = new BlastThread(ids.get(i).toString(),  nonGapped.toString());
-     thread.start();
+  //   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("/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;
+          outputFrame.setFrameIcon( imageIcon[imageIndex]);
+          outputFrame.setTitle("BLASTing for unidentified sequences - "+jobsRunning+" jobs running.");
 
+        }catch(Exception ex){}
+
+      }
+    }
   }
 
+
+
+
   class BlastThread extends Thread
   {
     String sequence;
-    String id;
+    String seqid;
+    String jobid;
+    boolean jobComplete = false;
+
     BlastThread(String id, String sequence)
     {
       this.sequence = sequence;
-      this.id = id;
+      seqid = id;
     }
 
     public void run()
     {
-      FindUniprotIDFromUnknownSequence(id, sequence);
-    }
-  }
+      StartJob();
 
-  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();
+      while (!jobComplete)
+      {
+        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", "polljob"));
+          String result = (String) call.invoke(new Object[]
+                                               {jobid, "xml"});
+          if(result.indexOf("JOB PENDING")==-1 && result.indexOf("JOB RUNNING")==-1)
+          {
+                parseResult(seqid, result);
+                jobComplete = true;
+                jobsRunning --;
+          }
+          Thread.sleep(5000);
+          System.out.println("I'm alive "+seqid+" "+jobid);
         }
+        catch (Exception ex)
+        {}
+      }
+    }
+
+    void StartJob()
+    {
+      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(jobid);
+
+      }
+      catch (Exception exp)
+      {
+        System.err.println("ERROR:\n" + exp.toString());
+        exp.printStackTrace();
+      }
     }
+  }
 
     void parseResult(String id1, String res)
     {
@@ -113,7 +186,7 @@ public class WSWUBlastClient
 
       }
 
-      cap.setText(cap.getText()+buffer.toString());
+      output.setText(output.getText()+buffer.toString());
     }
 
 }
-- 
1.7.10.2