JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / schemes / Blosum62ColourScheme.java

diff --git a/src/jalview/schemes/Blosum62ColourScheme.java b/src/jalview/schemes/Blosum62ColourScheme.java
index 0a943bd..9d09259 100755 (executable)
--- a/src/jalview/schemes/Blosum62ColourScheme.java
+++ b/src/jalview/schemes/Blosum62ColourScheme.java
@@ -1,25 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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 java.awt.*;
+import jalview.analysis.AAFrequency;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
 
-import jalview.analysis.*;
+import java.awt.Color;
+import java.util.Map;
 
 public class Blosum62ColourScheme extends ResidueColourScheme
 {
@@ -28,7 +35,8 @@ public class Blosum62ColourScheme extends ResidueColourScheme
     super();
   }
 
-  public Color findColour(char res, int j)
+  @Override
+  public Color findColour(char res, int j, SequenceI seq)
   {
     if ('a' <= res && res <= 'z')
     {
@@ -50,6 +58,7 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 
       if (max.indexOf(res) > -1)
       {
+        // TODO use a constant here?
         currentColour = new Color(154, 154, 255);
       }
       else
@@ -65,6 +74,7 @@ public class Blosum62ColourScheme extends ResidueColourScheme
 
         if (c > 0)
         {
+          // TODO use a constant here?
           currentColour = new Color(204, 204, 255);
         }
         else
@@ -85,4 +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;
+  }
 }