From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 10 Dec 2004 14:32:06 +0000 (+0000)
Subject: Colour etc is now globally set
X-Git-Tag: Release_2_0~854
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=48555d99e5255063a40ed1818a9090dd88f9a665;p=jalview.git

Colour etc is now globally set
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 67995b2..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;
   }
 
@@ -453,43 +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() );
@@ -526,7 +489,8 @@ public class AlignFrame extends GAlignFrame
 
   protected void noColourmenuItem_actionPerformed(ActionEvent e)
   {
-    alignPanel.setColourScheme(null, false);
+    viewport.setGlobalColourScheme( null );
+    alignPanel.setColourScheme();
   }
 
 
@@ -537,52 +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);
@@ -595,14 +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);
@@ -612,20 +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);
   }