X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FBuriedColourScheme.java;h=a3b85b98130e7dd8f6c92bdfe92da930fe9381fb;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=476e9f7487663de05552941b5cd7c3015fa7dc03;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/schemes/BuriedColourScheme.java b/src/jalview/schemes/BuriedColourScheme.java
index 476e9f7..a3b85b9 100755
--- a/src/jalview/schemes/BuriedColourScheme.java
+++ b/src/jalview/schemes/BuriedColourScheme.java
@@ -1,24 +1,31 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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!
@@ -33,20 +40,44 @@ public class BuriedColourScheme extends ScoreColourScheme
    */
   public BuriedColourScheme()
   {
-    super(ResidueProperties.buried, ResidueProperties.buriedmin,
-            ResidueProperties.buriedmax);
+    super(ResidueProperties.aaIndex, ResidueProperties.buried,
+            ResidueProperties.buriedmin, ResidueProperties.buriedmax);
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param c
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public Color makeColour(float c)
   {
     return new Color(0, (float) (1.0 - c), c);
   }
+
+  @Override
+  public boolean isPeptideSpecific()
+  {
+    return true;
+  }
+
+  @Override
+  public String getSchemeName()
+  {
+    return JalviewColourScheme.Buried.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 BuriedColourScheme();
+  }
 }