X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FPurinePyrimidineColourScheme.java;h=a8270cca72d66580841a102170a6a82a734d460b;hb=4f1c8f3fdd352d5e6c3e6cfe1b729f9ef7d6e47f;hp=877afad179d622e5768be342e702bd542d4a6c06;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/src/jalview/schemes/PurinePyrimidineColourScheme.java b/src/jalview/schemes/PurinePyrimidineColourScheme.java
index 877afad..a8270cc 100644
--- a/src/jalview/schemes/PurinePyrimidineColourScheme.java
+++ b/src/jalview/schemes/PurinePyrimidineColourScheme.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,7 +20,8 @@
  */
 package jalview.schemes;
 
-import java.awt.Color;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
 
 /**
  * Class is based off of NucleotideColourScheme
@@ -35,56 +36,29 @@ public class PurinePyrimidineColourScheme extends ResidueColourScheme
   public PurinePyrimidineColourScheme()
   {
     super(ResidueProperties.purinepyrimidineIndex,
-            ResidueProperties.purinepyrimidine, 0);
+            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(AlignViewportI view,
+          AnnotatedCollectionI coll)
   {
-    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();
   }
 }