From 77dbfda22963c908129cae7947643ad5fce0caad Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 14 Apr 2005 15:04:13 +0000
Subject: [PATCH] use webservice info to display web service state

---
 src/jalview/gui/AlignFrame.java |  141 +++++++++++----------------------------
 1 file changed, 38 insertions(+), 103 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index c1a7105..9ec2f23 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -785,7 +785,6 @@ public class AlignFrame extends GAlignFrame
           c.calculate();
           c.verdict(false, viewport.ConsPercGaps);
           ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
-
           sg.cs = ccs;
         }
 
@@ -824,17 +823,13 @@ if ( viewport.getConservationSelected() )
    Conservation c = new Conservation("All",
                                      ResidueProperties.propHash, 3,
                                      al.getSequences(), 0,
-                                     al.getWidth());
+                                     al.getWidth()-1);
 
    c.calculate();
    c.verdict(false, viewport.ConsPercGaps);
 
    ccs = new ConservationColourScheme(c, cs);
 
- //  int threshold = Desktop.setConservationSliderSource(alignPanel, ccs,    "Background");
-
- //  ccs.inc = threshold;
-
    viewport.setGlobalColourScheme(ccs);
 
   }
@@ -846,11 +841,13 @@ if ( viewport.getConservationSelected() )
 
   protected void modifyPID_actionPerformed(ActionEvent e)
   {
+    if(viewport.getAbovePIDThreshold())
     Desktop.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background");
   }
 
   protected void modifyConservation_actionPerformed(ActionEvent e)
   {
+    if(viewport.getConservationSelected())
     Desktop.setConservationSliderSource(alignPanel, viewport.globalColourScheme,    "Background");
   }
 
@@ -1074,126 +1071,64 @@ if ( viewport.getConservationSelected() )
 
   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
   {
-    JInternalFrame frame = new JInternalFrame();
-    ClustalThread ct = new ClustalThread(frame);
-    Thread t = new Thread(ct);
-    t.start();
-    frame.setContentPane(ct);
-     Desktop.addInternalFrame(frame, title, 320, 90);
+     WebserviceInfo info = new WebserviceInfo("Clustal web service",
+     "\"Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"+
+     " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
+    +" Nucleic Acids Research, submitted, June 1994.",
+     450, 150);
 
+    ClustalThread thread = new ClustalThread(info);
+    thread.start();
   }
 
-  class ClustalThread extends JPanel implements Runnable
-  {
-    Image image;
-    int angle = 0;
-    boolean webServiceRunning = false;
-    JInternalFrame frame;
-    public ClustalThread(JInternalFrame frame)
+    class ClustalThread extends Thread
     {
-      this.frame = frame;
+      WebserviceInfo info;
+      public ClustalThread(WebserviceInfo info)
+      {this.info = info; }
 
-      java.net.URL url = getClass().getResource("/images/logo.gif");
-      if (url != null)
+      public void run()
       {
-        image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-        MediaTracker mt = new MediaTracker(this);
-        mt.addImage(image, 0);
-        try
+        info.setStatus(WebserviceInfo.STATE_RUNNING);
+        jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
+        Vector sv = viewport.getAlignment().getSequences();
+        SequenceI[] seqs = new SequenceI[sv.size()];
+
+        int i = 0;
+        do
         {
-          mt.waitForID(0);
+          seqs[i] = (SequenceI) sv.elementAt(i);
         }
-        catch (Exception ex)
-        {}
-      }
+        while (++i < sv.size());
 
-      ImageSpinner spinner = new ImageSpinner();
-      spinner.start();
-      webServiceRunning = true;
-    }
-
-    class ImageSpinner extends Thread
-    {
-      public void run()
-      {
-        while(webServiceRunning)
+        SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
+        if (alignment != null)
+        {
+          AlignFrame af = new AlignFrame(new Alignment(alignment));
+          Desktop.addInternalFrame(af, title.concat(" - ClustalW Alignment"),
+                                   NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
+          af.clustalColour_actionPerformed(null);
+          af.clustalColour.setSelected(true);
+          info.setStatus(WebserviceInfo.STATE_STOPPED_OK);
+        }
+        else
         {
-          try{
-            Thread.sleep(10);
-            angle+=1;
-            angle %=360;
-            repaint();
-          }
-          catch(Exception ex){}
+            info.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+            info.appendProgressText("Problem obtaining clustal alignment");
         }
       }
     }
 
-    // JBPNote
-    // Should check to see if the server settings are valid
-    // Need visual-delay indication here.
-    public void run()
-       {
-         jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
-         Vector sv = viewport.getAlignment().getSequences();
-         SequenceI[] seqs = new SequenceI[sv.size()];
-
-         int i = 0;
-         do
-         {
-           seqs[i] = (SequenceI) sv.elementAt(i);
-         }
-         while (++i < sv.size());
-
-         SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
-
-         if (alignment != null)
-         {
-           AlignFrame af = new AlignFrame(new Alignment(alignment));
-           Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT);
-           af.clustalColour_actionPerformed(null);
-           af.clustalColour.setSelected(true);
-         }
-         else
-           JOptionPane.showMessageDialog(Desktop.desktop, "Problem obtaining clustal alignment", "Web service error",
-                                         JOptionPane.WARNING_MESSAGE);
-
-         webServiceRunning = false;
-         try{
-           frame.setClosed(true);
-         }catch(Exception ex){}
-       }
-
-       public void paintComponent(Graphics g1)
-       {
-         Graphics2D g = (Graphics2D)g1;
-         g.setColor(Color.white);
-         g.fillRect(0,0,getWidth(), getHeight());
-         if(image!=null)
-         {
-
-           g.rotate (Math.toRadians(angle), 28, 28);
-
-           g.drawImage(image,10,10,this);
-           g.rotate (-Math.toRadians(angle), 28, 28 );
-         }
-         g.setFont(new Font("Arial", Font.BOLD, 12));
-         g.setColor(Color.black);
-         g.drawString("Clustal Alignment Web Service running", 60,30);
-       }
-  }
   protected void jpred_actionPerformed(ActionEvent e)
 {
 
-    JInternalFrame frame = new JInternalFrame();
     if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>0)
     {
       // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
       SequenceGroup seqs = viewport.getSelectionGroup();
       if (seqs.getSize() == 1 || !viewport.alignment.isAligned())
       {
-        JPredClient ct = new JPredClient( (SequenceI)
-                                         seqs.getSequenceAt(0));
+        JPredClient ct = new JPredClient( (SequenceI)seqs.getSequenceAt(0));
       }
       else
       {
-- 
1.7.10.2