X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FPurinePyrimidineColourScheme.java;h=a8270cca72d66580841a102170a6a82a734d460b;hb=e1aa3fdd1ca82abf5acc0cd3c2b86a5ca1083941;hp=9c43ed1eb7a4b89939cdc32c5aa0bc4bceccb94c;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/schemes/PurinePyrimidineColourScheme.java b/src/jalview/schemes/PurinePyrimidineColourScheme.java
index 9c43ed1..a8270cc 100644
--- a/src/jalview/schemes/PurinePyrimidineColourScheme.java
+++ b/src/jalview/schemes/PurinePyrimidineColourScheme.java
@@ -20,7 +20,8 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
+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();
   }
 }