X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=28f0474ed408d90f4aad0d3ed70c308cc5bd10c3;hb=c865a01627208f07db46ae7d28c06f39d83924ee;hp=0c181b00acbd77a799daf83089fa6762c0318bfd;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 0c181b0..28f0474 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -1,6 +1,7 @@
 package jalview.gui;
 
 import jalview.jbgui.GUserDefinedColours;
+import jalview.datamodel.*;
 import javax.swing.*;
 import java.awt.*;
 import java.awt.event.*;
@@ -13,20 +14,19 @@ import java.util.*;
 public class UserDefinedColours extends GUserDefinedColours implements ChangeListener
 {
 
-  SeqPanel seqPanel;
-  ColourSchemeI colourScheme;
+  AlignmentPanel ap;
+  SequenceGroup seqGroup;
   JButton selectedButton;
   Vector oldColours = new Vector();
   JInternalFrame frame;
 
-  public UserDefinedColours(JInternalFrame f, SeqPanel sp)
+  public UserDefinedColours(JInternalFrame f, AlignmentPanel ap, SequenceGroup sg)
   {
     super();
     colorChooser.getSelectionModel().addChangeListener(this);
-    seqPanel = sp;
+    this.ap = ap;
     frame = f;
-    colourScheme = seqPanel.getColourScheme();
-   // colourScheme.
+   seqGroup = sg;
 
     for(int i=0; i<20; i++)
       makeButton(ResidueProperties.aa2Triplet.get( ResidueProperties.aa[i] )+"", ResidueProperties.aa[i]);
@@ -53,8 +53,18 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
   void makeButton(String label, String aa)
   {
     final JButton button = new JButton();
-    button.setBackground( colourScheme.findColour(null,aa,-1,null) );
-    oldColours.addElement( colourScheme.findColour(null,aa,-1,null) );
+    Color col = Color.white;
+    ColourSchemeI cs = null;
+    if(seqGroup!=null)
+      cs = seqGroup.cs;
+    else
+      cs = ap.av.getGlobalColourScheme();
+
+    if(cs!=null)
+      col = cs.findColour( aa, -1, null);
+
+    button.setBackground(  col );
+    oldColours.addElement( col );
     button.setText( label );
     button.setFont(new java.awt.Font("Verdana", 1, 10));
     button.addMouseListener(new java.awt.event.MouseAdapter()
@@ -89,7 +99,13 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
 
     ucs.setThreshold(0);
     ucs.setColourScheme( newColours );
-    seqPanel.setColourScheme( ucs );
+
+    if(seqGroup!=null)
+      seqGroup.cs = ucs;
+    else
+      ap.av.setGlobalColourScheme(ucs);
+
+    ap.RefreshPanels();
   }
 
   protected void loadbutton_actionPerformed(ActionEvent e)
@@ -157,7 +173,12 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
     }
 
     ucs.setColourScheme( newColours );
-    seqPanel.setColourScheme( ucs );
+    if (seqGroup != null)
+      seqGroup.cs = ucs;
+    else
+      ap.av.setGlobalColourScheme(ucs);
+
+    ap.RefreshPanels();
 
   }