X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBlosum62ColourScheme.java;h=9d092599860175227545083e840dbf595350b41a;hb=d2164f857e0729b86b1e0ffa4c858487f0a3298f;hp=0f04168574b927a93093c03ea4408846f0cafdc0;hpb=a79f9e113c51c032070c670e45ce3eb464691166;p=jalview.git

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 0f04168..9d09259 100755
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,26 +1,33 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
 import jalview.analysis.AAFrequency;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
-import jalview.datamodel.SequenceI;
+import java.util.Map;
+
 public class Blosum62ColourScheme extends ResidueColourScheme
 {
   public Blosum62ColourScheme()
@@ -51,6 +58,7 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 
       if (max.indexOf(res) > -1)
       {
+        // TODO use a constant here?
         currentColour = new Color(154, 154, 255);
       }
       else
@@ -66,6 +74,7 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 
         if (c > 0)
         {
+          // TODO use a constant here?
           currentColour = new Color(204, 204, 255);
         }
         else
@@ -86,4 +95,12 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 
     return currentColour;
   }
+
+  @Override
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    ColourSchemeI newcs = super.applyTo(sg, hiddenRepSequences);
+    return newcs;
+  }
 }