X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=ab5fb17bdb6ac808581b722f15788bac4ed33ef1;hb=48555d99e5255063a40ed1818a9090dd88f9a665;hp=a977623a7becdaff27bc068a4582ebbe911d524e;hpb=edd50f0798768bc48fc0ae7be6401db6c925d06a;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a977623..ab5fb17 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -70,7 +70,7 @@ public class AlignFrame extends GAlignFrame
 
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
-    HTMLOutput htmlOutput = new HTMLOutput(viewport.getAlignment(), alignPanel.seqPanel.getColourScheme());
+    HTMLOutput htmlOutput = new HTMLOutput(viewport);
     htmlOutput = null;
   }
 
@@ -407,7 +407,8 @@ public class AlignFrame extends GAlignFrame
 
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
-      updateResidueView();
+      viewport.setColourText( colourTextMenuItem.isSelected() );
+      alignPanel.RefreshPanels();
   }
 
   void SetFont()
@@ -427,18 +428,21 @@ public class AlignFrame extends GAlignFrame
 
   protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
-     updateResidueView();
+    viewport.setWrapAlignment( wrapMenuItem.isSelected() );
+    alignPanel.RefreshPanels();
   }
 
 
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
-     updateResidueView();
+    viewport.setShowBoxes( viewBoxesMenuItem.isSelected() );
+    alignPanel.RefreshPanels();
   }
 
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
-     updateResidueView();
+    viewport.setShowText( viewTextMenuItem.isSelected() );
+    alignPanel.RefreshPanels();
   }
 
 
@@ -449,43 +453,6 @@ public class AlignFrame extends GAlignFrame
   }
 
 
-  void updateResidueView()
-  {
-    if (viewport.getSelection().size() == 0)
-     {
-       for (int i = 0; i < viewport.alignment.getGroups().size(); i++)
-       {
-         SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);
-         sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );
-         sg.setDisplayText( viewTextMenuItem.isSelected() );
-         sg.setColourText( colourTextMenuItem.isSelected() );
-       }
-     }
-     else
-     {
-       SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));
-       if (alignPanel.seqPanel.isNewSelection(sg))
-       {
-         sg = viewport.getAlignment().addGroup();
-         for (int i = 0; i < viewport.getSelection().size(); i++)
-         {
-           viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (
-               Sequence) viewport.sel.sequenceAt(i)),
-                                              (Sequence) viewport.sel.sequenceAt(
-               i));
-           viewport.alignment.addToGroup(sg,
-                                         (Sequence) viewport.sel.sequenceAt(i));
-         }
-       }
-
-       sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());
-       sg.setDisplayText(viewTextMenuItem.isSelected());
-       sg.setColourText(colourTextMenuItem.isSelected());
-     }
-    alignPanel.RefreshPanels();
-  }
-
-
   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
   {
     alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );
@@ -522,7 +489,8 @@ public class AlignFrame extends GAlignFrame
 
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme(null, false);
+    viewport.setGlobalColourScheme( null );
+    alignPanel.setColourScheme();
   }
 
 
@@ -533,52 +501,58 @@ public class AlignFrame extends GAlignFrame
 
   public void zappoColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new ZappoColourScheme(), conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme(new ZappoColourScheme() );
+    alignPanel.setColourScheme(  );
   }
 
   public void taylorColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new TaylorColourScheme(),conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme(new TaylorColourScheme() );
+    alignPanel.setColourScheme(  );
   }
 
 
   public void hydrophobicityColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new HydrophobicColourScheme(),conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme( new HydrophobicColourScheme() );
+    alignPanel.setColourScheme( );
   }
 
   public void helixColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new HelixColourScheme(),conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme( new HelixColourScheme()  );
+    alignPanel.setColourScheme();
   }
 
 
   public void strandColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new StrandColourScheme() ,conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme(new StrandColourScheme() );
+    alignPanel.setColourScheme(  );
   }
 
 
   public void turnColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new TurnColourScheme() ,conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme(new TurnColourScheme() );
+    alignPanel.setColourScheme(  );
   }
 
 
   public void buriedColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new BuriedColourScheme() ,conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme( new BuriedColourScheme() );
+    alignPanel.setColourScheme( );
   }
 
 
   protected  void conservationMenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme ( alignPanel.seqPanel.getColourScheme(),conservationMenuItem.isSelected() );
+    viewport.setConservationSelected(conservationMenuItem.isSelected());
     conservationColourIncMenuItem.setEnabled( conservationMenuItem.isSelected() );
+    alignPanel.setColourScheme();
   }
 
-
-
   public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
  {
    ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
@@ -591,14 +565,15 @@ public class AlignFrame extends GAlignFrame
 
   public void abovePIDColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new PIDColourScheme() ,conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme(new PIDColourScheme());
+    alignPanel.setColourScheme( );
   }
 
 
   public void userDefinedColour_actionPerformed(ActionEvent e)
   {
     JInternalFrame frame = new JInternalFrame();
-    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel.seqPanel );
+    UserDefinedColours chooser = new UserDefinedColours( frame, viewport );
     frame.setContentPane(chooser);
     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
     frame.setResizable(false);
@@ -608,20 +583,22 @@ public class AlignFrame extends GAlignFrame
 
   public void PIDColour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new PIDColourScheme(),conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme(new PIDColourScheme() );
+    alignPanel.setColourScheme( );
   }
 
 
   public void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme( new Blosum62ColourScheme(viewport) ,conservationMenuItem.isSelected() );
+    viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport)  );
+    alignPanel.setColourScheme();
   }
 
 
 
   protected void schemeKeyMenuItem_actionPerformed(ActionEvent e)
   {
-    ColourKey colourKey = new ColourKey( alignPanel.seqPanel.getColourScheme() );
+    ColourKey colourKey = new ColourKey( viewport.getGlobalColourScheme() );
     Desktop.addInternalFrame(colourKey, "Colour scheme key", 400, 320);
   }