X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=1d6cbf440f737c70e691168cdc20dd9b9431a305;hb=21e2a80f7db56c011481d65d5bcb458654226e20;hp=a41491a21137422ba57a353a07ac5400b4346bfc;hpb=6b792c2d7f4113eb52518b69dff3d6a59f003462;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a41491a..1d6cbf4 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -202,6 +202,13 @@ public class AlignFrame extends GAlignFrame
     frame.setResizable(false);
   }
 
+  protected void deleteGroups_actionPerformed(ActionEvent e)
+  {
+    viewport.alignment.deleteAllGroups();
+    alignPanel.RefreshPanels();
+  }
+
+
 
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
@@ -312,8 +319,9 @@ public class AlignFrame extends GAlignFrame
     JOptionPane op = new JOptionPane();
     JInternalFrame frame =  op.createInternalFrame(this, "Find");
     Finder finder = new Finder(viewport, alignPanel, frame);
+    frame.setClosable(true);
     frame.setContentPane(finder);
-    frame.setSize(300,110);
+    frame.setSize(340,110);
     frame.setVisible(true);
   }
 
@@ -518,6 +526,13 @@ public class AlignFrame extends GAlignFrame
     changeColour();
   }
 
+  public void nucleotideColour_actionPerformed(ActionEvent e)
+  {
+    viewport.setGlobalColourScheme( new NucleotideColourScheme() );
+    changeColour();
+  }
+
+
   void changeColour()
   {
     if(abovePIDThreshold.isSelected())
@@ -802,28 +817,107 @@ public class AlignFrame extends GAlignFrame
 
   public void clustalAlignMenuItem_actionPerformed(ActionEvent e)
   {
-    // JBPNote
-    // Should check to see if the server settings are valid
-    // Need visual-delay indication here.
-     jalview.ws.Jemboss jemboss = new jalview.ws.Jemboss();
+    JInternalFrame frame = new JInternalFrame();
+    ClustalThread ct = new ClustalThread(frame);
+    Thread t = new Thread(ct);
+    t.start();
+    frame.setContentPane(ct);
+     Desktop.addInternalFrame(frame, title, 300, 80);
 
-    Vector sv = viewport.getAlignment().getSequences();
-    SequenceI[] seqs = new SequenceI[sv.size()];
+  }
 
-    int i=0;
-    do
+  class ClustalThread extends JPanel implements Runnable
+  {
+    Image [] image;
+    int imageIndex = 0;
+    boolean webServiceRunning = false;
+    JInternalFrame frame;
+    public ClustalThread(JInternalFrame frame)
     {
-      seqs[i] = (SequenceI) sv.elementAt(i);
-    } while (++i<sv.size());
-
-    SequenceI[] alignment = jemboss.clustalW(seqs); // gaps removed within method
+      this.frame = frame;
+      image = new Image[9];
+      for(int i=0; i<9; i++)
+      {
+        java.net.URL url = getClass().getResource("/dna" + (i+1) + ".gif");
+        if (url != null)
+        {
+          image[i] = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+          MediaTracker mt = new MediaTracker(this);
+          mt.addImage(image[i], i);
+          try{mt.waitForID(i);}
+          catch(Exception ex){}
+        }
+      }
+      DNATwirler twirler = new DNATwirler();
+      twirler.start();
+      webServiceRunning = true;
+    }
 
-    if (alignment != null)
+    class DNATwirler extends Thread
     {
-      AlignFrame af = new AlignFrame(new Alignment(alignment));
-      Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
-                               700, 500); // JBPNote - is there a new window geom. property ?
+      public void run()
+      {
+        while(webServiceRunning)
+        {
+          try{
+            Thread.sleep(100);
+            imageIndex++;
+            imageIndex %=9;
+            repaint();
+          }
+          catch(Exception ex){}
+        }
+      }
     }
+
+    // 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"),
+                                    700, 500); // JBPNote - is there a new window geom. property ?
+         }
+         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 g)
+       {
+         g.setColor(Color.white);
+         g.fillRect(0,0,getWidth(), getHeight());
+         if(image!=null)
+         {
+           g.drawImage(image[imageIndex],10,10,this);
+         }
+         g.setFont(new Font("Arial", Font.BOLD, 12));
+         g.setColor(Color.black);
+         g.drawString("Clustal Alignment Web Service running", 30,30);
+       }
+
+
   }