X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;fp=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=d1e18ef8a52c42d070affa8610b7a06edcc9c29c;hb=8e1be43e250107a4d86898bd554cf03098fa5957;hp=3a7173261417c3d355b1d9d9b306b950c09812ed;hpb=8b55eedb9d76a8c65b80f756c4412bf029906bf7;p=jalview.git

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 3a71732..d1e18ef 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -40,8 +40,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
    */
   public NucleotideColourScheme()
   {
-    super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide,
-            0);
+    super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide);
   }
 
   /**
@@ -55,47 +54,9 @@ public class NucleotideColourScheme extends ResidueColourScheme
   @Override
   public Color findColour(char c)
   {
-    // System.out.println("called"); log.debug
     return colors[ResidueProperties.nucleotideIndex[c]];
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param n
-   *          DOCUMENT ME!
-   * @param j
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  @Override
-  public Color findColour(char c, int j, SequenceI seq)
-  {
-    Color currentColour;
-    if ((threshold == 0) || aboveThreshold(c, j))
-    {
-      try
-      {
-        currentColour = colors[ResidueProperties.nucleotideIndex[c]];
-      } catch (Exception ex)
-      {
-        return Color.white;
-      }
-    }
-    else
-    {
-      return Color.white;
-    }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
-    return currentColour;
-  }
-
   @Override
   public boolean isNucleotideSpecific()
   {