X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=942e55b9854c8089b886db22db4d9d147173e500;hb=6de79bcd38555e77ca18e3a1dc99eefb4fef249b;hp=0cca608c6dca3563dcd6ebc0ee6e7d22cfc34953;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 0cca608..942e55b 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -21,25 +21,64 @@ package jalview.schemes;
 import java.awt.*;
 
 
-public class NucleotideColourScheme extends ResidueColourScheme {
-    public NucleotideColourScheme() {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class NucleotideColourScheme extends ResidueColourScheme
+{
+    /**
+     * Creates a new NucleotideColourScheme object.
+     */
+    public NucleotideColourScheme()
+    {
         super(ResidueProperties.nucleotide, 0);
     }
 
-    public Color findColour(String n) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String n)
+    {
         // System.out.println("called"); log.debug
         return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
     }
 
-    public Color findColour(String n, int j) {
-        if ((threshold == 0) || aboveThreshold(n, j)) {
-            try {
-                return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
-            } catch (Exception ex) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String n, int j)
+    {
+        if ((threshold == 0) || aboveThreshold(n, j))
+        {
+            try
+            {
+                currentColour = colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
+            }
+            catch (Exception ex)
+            {
                 return Color.white;
             }
-        } else {
+        }
+        else
+        {
             return Color.white;
         }
+
+        if(conservationColouring)
+         applyConservation(j);
+
+       return currentColour;
     }
 }