From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 4 Nov 2004 17:55:13 +0000 (+0000)
Subject: OverviewPanel added
X-Git-Tag: Release_2_0~949
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a9770d55354408173fddcf91fb90059c73497448;p=jalview.git

OverviewPanel added
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index af8a6c0..8af52d0 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -294,6 +294,7 @@ public class AlignFrame extends GAlignFrame
                                            style,
                                            Integer.parseInt(fontSizeMenuItem.getText())));
       alignPanel.RefreshPanels();
+
   }
 
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
@@ -314,26 +315,54 @@ public class AlignFrame extends GAlignFrame
     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
   }
 
+  public void overviewMenuItem_actionPerformed(ActionEvent e)
+  {
+
+    JInternalFrame frame = new JInternalFrame();
+    OverviewPanel overview = alignPanel.getOverviewPanel();
+   try{
+     overview = new OverviewPanel(alignPanel, viewport);
+     frame.setContentPane(overview);
+    Desktop.addInternalFrame(frame, "Overview " + this.getTitle(),
+                             frame.getWidth(), frame.getHeight());
+    frame.pack();
+    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)
+      {
+            alignPanel.setOverviewPanel(null);
+      };
+    });
+    alignPanel.setOverviewPanel( overview );
+
+  }catch(java.lang.OutOfMemoryError ex)
+   {
+     JOptionPane.showMessageDialog(this, "Sequence alignment too large to\nproduce overview image!!",
+                                   "Out of memory", JOptionPane.WARNING_MESSAGE);
+   }
+
+
+  }
+
 
   public void clustalColour_actionPerformed(ActionEvent e)
   {
-   // alignPanel.seqPanel.setColourScheme( new ClustalxColourScheme() );
+   // alignPanel.setColourScheme( new ClustalxColourScheme() );
   }
 
   public void zappoColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.seqPanel.setColourScheme( new ZappoColourScheme() );
+    alignPanel.setColourScheme( new ZappoColourScheme() );
   }
 
   public void taylorColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.seqPanel.setColourScheme( new TaylorColourScheme() );
+    alignPanel.setColourScheme( new TaylorColourScheme() );
   }
 
 
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.seqPanel.setColourScheme( new HydrophobicColourScheme() );
+    alignPanel.setColourScheme( new HydrophobicColourScheme() );
   }
 
   public void helixColour_actionPerformed(ActionEvent e)
@@ -343,17 +372,17 @@ public class AlignFrame extends GAlignFrame
 
   public void strandColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.seqPanel.setColourScheme( new StrandColourScheme() );
+    alignPanel.setColourScheme( new StrandColourScheme() );
   }
 
   public void turnColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.seqPanel.setColourScheme( new TurnColourScheme() );
+    alignPanel.setColourScheme( new TurnColourScheme() );
   }
 
   public void buriedColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.seqPanel.setColourScheme( new BuriedColourScheme() );
+    alignPanel.setColourScheme( new BuriedColourScheme() );
   }
 
   public void conservationColour_actionPerformed(ActionEvent e)
@@ -369,7 +398,7 @@ public class AlignFrame extends GAlignFrame
 
   public void abovePIDColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.seqPanel.setColourScheme( new PIDColourScheme() );
+    alignPanel.setColourScheme( new PIDColourScheme() );
   }
 
 
@@ -386,12 +415,12 @@ public class AlignFrame extends GAlignFrame
 
   public void PIDColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.seqPanel.setColourScheme( new PIDColourScheme() );
+    alignPanel.setColourScheme( new PIDColourScheme() );
   }
 
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    alignPanel.seqPanel.setColourScheme( new Blosum62ColourScheme(viewport) );
+    alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) );
   }
 
 
@@ -449,6 +478,16 @@ public class AlignFrame extends GAlignFrame
 
   public void PCAMenuItem_actionPerformed(ActionEvent e)
   {
+    if( (viewport.getSelection().size()<4 && viewport.getSelection().size()>0)
+       || viewport.getAlignment().getHeight()<4)
+    {
+      JOptionPane.showMessageDialog(this, "Principal component analysis must take\n"
+                                    +"at least 4 input sequences.",
+                                    "Sequence selection insufficient",
+                                    JOptionPane.WARNING_MESSAGE);
+      return;
+    }
+
     PCAPanel pcaPanel = new PCAPanel(viewport, null);
     JInternalFrame frame = new JInternalFrame();
     frame.setContentPane(pcaPanel);