Merge branch 'features/JAL-2360colourSchemeApplicability' into

[jalview.git] / src / jalview / appletgui / UserDefinedColours.java

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 106f289..aecc0c9 100644 (file)
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -22,6 +22,7 @@ package jalview.appletgui;
 
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceGroup;
+import jalview.schemes.CollectionColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.FeatureColour;
 import jalview.schemes.ResidueProperties;
@@ -93,7 +94,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
 
     if (seqGroup != null)
     {
-      oldColourScheme = seqGroup.cs;
+      oldColourScheme = seqGroup.getColourScheme();
     }
     else
     {
@@ -407,14 +408,9 @@ public class UserDefinedColours extends Panel implements ActionListener,
   {
     final Button button = new Button();
     Color col = Color.white;
-    if (oldColourScheme != null)
+    if (oldColourScheme != null && oldColourScheme.isSimple())
     {
-      try
-      {
-        col = oldColourScheme.findColour(aa.charAt(0), -1, null);
-      } catch (Exception ex)
-      {
-      }
+      col = oldColourScheme.findColour(aa.charAt(0), 0, null, null, 0f);
     }
     button.setBackground(col);
     oldColours.addElement(col);
@@ -501,20 +497,24 @@ public class UserDefinedColours extends Panel implements ActionListener,
     }
 
     UserColourScheme ucs = new UserColourScheme(newColours);
-    if (ap != null)
-    {
-      ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
-    }
+    // if (ap != null)
+    // {
+    // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+    // }
 
     if (ap != null)
     {
       if (seqGroup != null)
       {
-        seqGroup.cs = ucs;
+        seqGroup.cs = new CollectionColourScheme(ucs);
+        seqGroup.getGroupColourScheme().setThreshold(0,
+                ap.av.isIgnoreGapsConsensus());
       }
       else
       {
         ap.av.setGlobalColourScheme(ucs);
+        ap.av.getViewportColourScheme().setThreshold(0,
+                ap.av.isIgnoreGapsConsensus());
       }
       ap.seqPanel.seqCanvas.img = null;
       ap.paintAlignment(true);
@@ -592,7 +592,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
     {
       if (seqGroup != null)
       {
-        seqGroup.cs = ucs;
+        seqGroup.cs = new CollectionColourScheme(ucs);
       }
       else
       {