X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=4afb3219a95fa2a62c291434900790ef2f7952de;hb=d587f1aa61946dc14f6f089cf1dc2a3116cfb773;hp=9768d9a34f7421e62af65a93795869275e7ea49b;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 9768d9a..4afb321 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -47,7 +47,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
     public Color findColour(String n)
     {
         // System.out.println("called"); log.debug
-        return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
+        return colors[ResidueProperties.nucleotideIndex[n.charAt(0)]];
     }
 
     /**
@@ -60,11 +60,12 @@ public class NucleotideColourScheme extends ResidueColourScheme
      */
     public Color findColour(String n, int j)
     {
+        Color currentColour;
         if ((threshold == 0) || aboveThreshold(n, j))
         {
             try
             {
-                currentColour = colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
+                currentColour = colors[ ResidueProperties.nucleotideIndex[n.charAt(0)]];
             }
             catch (Exception ex)
             {
@@ -77,7 +78,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
         }
 
         if(conservationColouring)
-         applyConservation(j);
+         currentColour = applyConservation(currentColour, j);
 
        return currentColour;
     }