X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=3a7173261417c3d355b1d9d9b306b950c09812ed;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=0e2ecffd172b6702a7ed3ecab3d534bf0b79e5a5;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 0e2ecff..3a71732 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -1,23 +1,31 @@
 /*
- * 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 java.awt.*;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.util.Map;
 
 /**
  * DOCUMENT ME!
@@ -32,7 +40,8 @@ public class NucleotideColourScheme extends ResidueColourScheme
    */
   public NucleotideColourScheme()
   {
-    super(ResidueProperties.nucleotide, 0);
+    super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide,
+            0);
   }
 
   /**
@@ -43,6 +52,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public Color findColour(char c)
   {
     // System.out.println("called"); log.debug
@@ -59,7 +69,8 @@ public class NucleotideColourScheme extends ResidueColourScheme
    * 
    * @return DOCUMENT ME!
    */
-  public Color findColour(char c, int j)
+  @Override
+  public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour;
     if ((threshold == 0) || aboveThreshold(c, j))
@@ -84,4 +95,27 @@ public class NucleotideColourScheme extends ResidueColourScheme
 
     return currentColour;
   }
+
+  @Override
+  public boolean isNucleotideSpecific()
+  {
+    return true;
+  }
+
+  @Override
+  public String getSchemeName()
+  {
+    return JalviewColourScheme.Nucleotide.toString();
+  }
+
+  /**
+   * Returns a new instance of this colour scheme with which the given data may
+   * be coloured
+   */
+  @Override
+  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+          Map<SequenceI, SequenceCollectionI> hrs)
+  {
+    return new NucleotideColourScheme();
+  }
 }