X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FUserDefinedColours.java;h=845110e7d4464ed641fd163199f93ea1820fcd22;hb=1810df9d010000e434975a8a4e68dcbda238f7f1;hp=106f28959c7c7c180576ced12b0967c88613944f;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 106f289..845110e 100644
--- 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.
  * 
@@ -20,10 +20,14 @@
  */
 package jalview.appletgui;
 
+import jalview.analysis.AAFrequency;
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceGroup;
+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;
@@ -93,7 +97,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
 
     if (seqGroup != null)
     {
-      oldColourScheme = seqGroup.cs;
+      oldColourScheme = seqGroup.getColourScheme();
     }
     else
     {
@@ -407,14 +411,9 @@ 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 +500,24 @@ 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 ResidueShader(ucs);
+        seqGroup.getGroupColourScheme().setThreshold(0,
+                ap.av.isIgnoreGapsConsensus());
       }
       else
       {
         ap.av.setGlobalColourScheme(ucs);
+        ap.av.getResidueShading().setThreshold(0,
+                ap.av.isIgnoreGapsConsensus());
       }
       ap.seqPanel.seqCanvas.img = null;
       ap.paintAlignment(true);
@@ -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 = 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);
   }