X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPurinePyrimidineColourScheme.java;h=1b36f3040f5c6fd0d5c7b4f9bf4fbc11674d66ea;hb=c9f40e367fcb287b5b8a85ff63a37cdac3bcce4f;hp=7b0a6223dedea6aaee6e28295b3e1a2d301ee3f1;hpb=323a457c9d0643be2406b6661246e8e988c0d0f6;p=jalview.git

diff --git a/src/jalview/schemes/PurinePyrimidineColourScheme.java b/src/jalview/schemes/PurinePyrimidineColourScheme.java
index 7b0a622..1b36f30 100644
--- a/src/jalview/schemes/PurinePyrimidineColourScheme.java
+++ b/src/jalview/schemes/PurinePyrimidineColourScheme.java
@@ -1,23 +1,30 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * 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.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.util.Map;
 
 /**
  * Class is based off of NucleotideColourScheme
@@ -31,56 +38,30 @@ public class PurinePyrimidineColourScheme extends ResidueColourScheme
    */
   public PurinePyrimidineColourScheme()
   {
-    super(ResidueProperties.purinepyrimidine, 0);
+    super(ResidueProperties.purinepyrimidineIndex,
+            ResidueProperties.purinepyrimidine);
   }
 
-  /**
-   * Finds the corresponding color for the type of character inputed
-   * 
-   * @param c
-   *          Character in sequence
-   * 
-   * @return Color from purinepyrimidineIndex in
-   *         jalview.schemes.ResidueProperties
-   */
-  public Color findColour(char c)
+  @Override
+  public boolean isNucleotideSpecific()
   {
-    return colors[ResidueProperties.purinepyrimidineIndex[c]];
+    return true;
+  }
+
+  @Override
+  public String getSchemeName()
+  {
+    return JalviewColourScheme.PurinePyrimidine.toString();
   }
 
   /**
-   * Returns color based on conservation
-   * 
-   * @param c
-   *          Character in sequence
-   * @param j
-   *          Threshold
-   * 
-   * @return Color in RGB
+   * Returns a new instance of this colour scheme with which the given data may
+   * be coloured
    */
-  public Color findColour(char c, int j)
+  @Override
+  public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+          Map<SequenceI, SequenceCollectionI> hrs)
   {
-    Color currentColour;
-    if ((threshold == 0) || aboveThreshold(c, j))
-    {
-      try
-      {
-        currentColour = colors[ResidueProperties.purinepyrimidineIndex[c]];
-      } catch (Exception ex)
-      {
-        return Color.white;
-      }
-    }
-    else
-    {
-      return Color.white;
-    }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
+    return new PurinePyrimidineColourScheme();
   }
 }