OverviewPanel added

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