Userdefinedcolours works for groups as well

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9d0f60c..a50164a 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -543,7 +543,7 @@ public class AlignFrame extends GAlignFrame
   public void userDefinedColour_actionPerformed(ActionEvent e)\r
   {\r
     JInternalFrame frame = new JInternalFrame();\r
-    UserDefinedColours chooser = new UserDefinedColours( frame, viewport );\r
+    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
     frame.setContentPane(chooser);\r
     Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
     frame.setResizable(false);\r

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index a12672e..1fcc923 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -1,6 +1,7 @@
 package jalview.gui;\r
 \r
 import jalview.jbgui.GUserDefinedColours;\r
+import jalview.datamodel.*;\r
 import javax.swing.*;\r
 import java.awt.*;\r
 import java.awt.event.*;\r
@@ -13,19 +14,19 @@ import java.util.*;
 public class UserDefinedColours extends GUserDefinedColours implements ChangeListener\r
 {\r
 \r
-  AlignViewport av;\r
-  ColourSchemeI colourScheme;\r
+  AlignmentPanel ap;\r
+  SequenceGroup seqGroup;\r
   JButton selectedButton;\r
   Vector oldColours = new Vector();\r
   JInternalFrame frame;\r
 \r
-  public UserDefinedColours(JInternalFrame f, AlignViewport av)\r
+  public UserDefinedColours(JInternalFrame f, AlignmentPanel ap, SequenceGroup sg)\r
   {\r
     super();\r
     colorChooser.getSelectionModel().addChangeListener(this);\r
-    this.av = av;\r
+    this.ap = ap;\r
     frame = f;\r
-    colourScheme = av.getGlobalColourScheme();\r
+   seqGroup = sg;\r
 \r
     for(int i=0; i<20; i++)\r
       makeButton(ResidueProperties.aa2Triplet.get( ResidueProperties.aa[i] )+"", ResidueProperties.aa[i]);\r
@@ -52,8 +53,18 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
   void makeButton(String label, String aa)\r
   {\r
     final JButton button = new JButton();\r
-    button.setBackground( colourScheme.findColour(null,aa,-1,null) );\r
-    oldColours.addElement( colourScheme.findColour(null,aa,-1,null) );\r
+    Color col = Color.white;\r
+    ColourSchemeI cs = null;\r
+    if(seqGroup!=null)\r
+      cs = seqGroup.cs;\r
+    else\r
+      cs = ap.av.getGlobalColourScheme();\r
+\r
+    if(cs!=null)\r
+      col = cs.findColour(null, aa, -1, null);\r
+\r
+    button.setBackground(  col );\r
+    oldColours.addElement( col );\r
     button.setText( label );\r
     button.setFont(new java.awt.Font("Verdana", 1, 10));\r
     button.addMouseListener(new java.awt.event.MouseAdapter()\r
@@ -88,7 +99,13 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
 \r
     ucs.setThreshold(0);\r
     ucs.setColourScheme( newColours );\r
-    av.setGlobalColourScheme( ucs );\r
+\r
+    if(seqGroup!=null)\r
+      seqGroup.cs = ucs;\r
+    else\r
+      ap.av.setGlobalColourScheme(ucs);\r
+\r
+    ap.RefreshPanels();\r
   }\r
 \r
   protected void loadbutton_actionPerformed(ActionEvent e)\r
@@ -156,7 +173,12 @@ public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
     }\r
 \r
     ucs.setColourScheme( newColours );\r
-    av.setGlobalColourScheme( ucs );\r
+    if (seqGroup != null)\r
+      seqGroup.cs = ucs;\r
+    else\r
+      ap.av.setGlobalColourScheme(ucs);\r
+\r
+    ap.RefreshPanels();\r
 \r
   }\r
 \r