JAL-2483 JAL-2575 don't sort newly discovered features

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

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index aecc0c9..845110e 100644 (file)
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -20,11 +20,14 @@
  */
 package jalview.appletgui;
 
+import jalview.analysis.AAFrequency;
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceGroup;
-import jalview.schemes.CollectionColourScheme;
+import jalview.renderer.ResidueShader;
+import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.FeatureColour;
+import jalview.schemes.PIDColourScheme;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 import jalview.util.MessageManager;
@@ -506,14 +509,14 @@ public class UserDefinedColours extends Panel implements ActionListener,
     {
       if (seqGroup != null)
       {
-        seqGroup.cs = new CollectionColourScheme(ucs);
+        seqGroup.cs = new ResidueShader(ucs);
         seqGroup.getGroupColourScheme().setThreshold(0,
                 ap.av.isIgnoreGapsConsensus());
       }
       else
       {
         ap.av.setGlobalColourScheme(ucs);
-        ap.av.getViewportColourScheme().setThreshold(0,
+        ap.av.getResidueShading().setThreshold(0,
                 ap.av.isIgnoreGapsConsensus());
       }
       ap.seqPanel.seqCanvas.img = null;
@@ -579,35 +582,25 @@ public class UserDefinedColours extends Panel implements ActionListener,
       return;
     }
 
-    Color[] newColours = new Color[24];
-    for (int i = 0; i < 24; i++)
-    {
-      newColours[i] = oldColours.elementAt(i);
-      buttonPanel.getComponent(i).setBackground(newColours[i]);
-    }
-
-    UserColourScheme ucs = new UserColourScheme(newColours);
-
     if (ap != null)
     {
       if (seqGroup != null)
       {
-        seqGroup.cs = new CollectionColourScheme(ucs);
+        seqGroup.cs = new ResidueShader(oldColourScheme);
+        if (oldColourScheme instanceof PIDColourScheme
+                || oldColourScheme instanceof Blosum62ColourScheme)
+        {
+          seqGroup.cs.setConsensus(AAFrequency.calculate(
+                  seqGroup.getSequences(ap.av.getHiddenRepSequences()), 0,
+                  ap.av.getAlignment().getWidth()));
+        }
       }
       else
       {
-        ap.av.setGlobalColourScheme(ucs);
+        ap.av.setGlobalColourScheme(oldColourScheme);
       }
       ap.paintAlignment(true);
     }
-    else if (jmol != null)
-    {
-      jmol.setJalviewColourScheme(ucs);
-    }
-    else if (pdbcanvas != null)
-    {
-      pdbcanvas.pdb.setColours(ucs);
-    }
 
     frame.setVisible(false);
   }