From 9530ba3cfa321c4fba591683320552cf4bb03779 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 28 Feb 2005 10:43:43 +0000
Subject: [PATCH] first stab at a JPredClient.

---
 src/jalview/io/JPredClient.java |  183 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 183 insertions(+)
 create mode 100755 src/jalview/io/JPredClient.java

diff --git a/src/jalview/io/JPredClient.java b/src/jalview/io/JPredClient.java
new file mode 100755
index 0000000..c3415ee
--- /dev/null
+++ b/src/jalview/io/JPredClient.java
@@ -0,0 +1,183 @@
+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 java.util.*;
+import java.awt.*;
+import jalview.analysis.AlignSeq;
+import ext.vamsas.*;
+
+public class JPredClient
+{
+
+  JInternalFrame outputFrame = new JInternalFrame();
+  CutAndPasteTransfer output = new CutAndPasteTransfer(false);
+  int jobsRunning = 0;
+  ext.vamsas.JpredSoapBindingStub server;
+
+  public JPredClient(SequenceI seq)
+  {
+    output.formatForOutput();
+    outputFrame.setContentPane(output);
+
+    output.setText("Job details for prediction on sequence :\nName : "
+                   + seq.getName() + "\nSequence : " + seq.getSequence() + "\n");
+    Desktop.addInternalFrame(outputFrame,
+                             "JNet secondary structure prediction job", 800,
+                             300);
+
+    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default
+    try {
+      this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties
+    }
+    catch (Exception ex) {
+      output.setText("Serious! JPred Service location failed\nfor URL :"
+                     +loc.getjpredAddress()+"\n"+ex.getMessage());
+    }
+
+    JPredThread jthread = new JPredThread(seq);
+    jthread.start();
+    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);
+      }
+    }
+
+    public void run()
+    {
+      while (jobsRunning > 0)
+      {
+        try
+        {
+          Thread.sleep(100);
+          imageIndex++;
+          imageIndex %= 9;
+          outputFrame.setFrameIcon(imageIcon[imageIndex]);
+          outputFrame.setTitle("JNet Secondary Structure Prediction : " +
+                               jobsRunning + " jobs running.");
+
+        }
+        catch (Exception ex)
+        {}
+
+      }
+    }
+  }
+
+  class JPredThread
+      extends Thread
+  {
+    String OutputHeader;
+    ext.vamsas.Secstructpred result;
+    ext.vamsas.Sequence sequence;
+    String jobId;
+    boolean jobComplete = false;
+    int allowedServerExceptions = 3; // thread dies if too many exceptions.
+    JPredThread(SequenceI seq)
+    {
+      OutputHeader = output.getText();
+      this.sequence = new ext.vamsas.Sequence();
+      this.sequence.setId(seq.getName());
+      this.sequence.setSeq(AlignSeq.extractGaps("-. ",seq.getSequence()));
+    }
+
+    public void run()
+    {
+
+      StartJob();
+
+      while (!jobComplete
+             && (allowedServerExceptions > 0))
+      {
+        try
+        {
+          result = server.getpredict(jobId);
+
+          if (result.getOutput().indexOf("Job") != 0)
+          {
+            parseResult();
+            jobComplete = true;
+            jobsRunning--;
+          }
+          else
+          {
+            output.setText(OutputHeader + "\n" + result.getOutput());
+          }
+          Thread.sleep(5000);
+          //      System.out.println("I'm alive "+seqid+" "+jobid);
+
+        }
+        catch (Exception ex)
+        {
+          allowedServerExceptions--;
+          String msg = output.getText();
+          output.setText(msg + "\nJPredWS Server exception!\n" + ex.getMessage());
+        }
+      }
+    }
+
+    void StartJob()
+    {
+      try
+      {
+        jobId = server.predict(sequence);
+        System.out.println(jobId);
+      }
+      catch (Exception e)
+      {
+        System.out.println("JPredWS Client: Failed to submit the prediction\n" +
+                           e.toString() + "\n");
+        e.printStackTrace();
+      }
+    }
+
+    void parseResult()
+    {
+      output.setText(OutputHeader + result.getOutput());
+      try {
+        JPredFile prediction=new JPredFile(result.getOutput(), "Paste");
+        SequenceI[] preds = prediction.getSeqsAsArray();
+        int i=0;
+        // Rename the query sequence
+        while (i<preds.length && !preds[i].getName().equals("QUERY")) {
+          i++;
+        }
+        if (i<preds.length) {
+          preds[i].setName(sequence.getId());
+        }
+        AlignFrame af = new AlignFrame(new Alignment(preds));
+        /*  JBPNote - need to set correct style of display for the secstrpred alignment object.
+            af.clustalColour.setSelected(true);
+            af.clustalColour_actionPerformed(null);
+         */
+        Desktop.addInternalFrame(af, "JNet Prediction for sequence "+sequence.getId(),
+                                 700, 500);
+      }
+      catch (Exception e) {
+        output.setText(output.getText()+"\nError! File did not parse correctly\n"+e.getMessage()+"\n");
+        e.printStackTrace();
+      }
+
+    }
+
+  }
+}
-- 
1.7.10.2