Conservation colour scheme is no more

[jalview.git] / src / jalview / schemes / NucleotideColourScheme.java

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 8785954..942e55b 100755 (executable)
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -64,7 +64,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
         {\r
             try\r
             {\r
-                return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
+                currentColour = colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];\r
             }\r
             catch (Exception ex)\r
             {\r
@@ -75,5 +75,10 @@ public class NucleotideColourScheme extends ResidueColourScheme
         {\r
             return Color.white;\r
         }\r
+\r
+        if(conservationColouring)\r
+         applyConservation(j);\r
+\r
+       return currentColour;\r
     }\r
 }\r