X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=20b08857c757ec16f291d6962d625118173f2762;hb=d70d7e5bc8da1189f44709b6ec59ea1e23f6f557;hp=c67eafc7738c0a63c6bccb21a214749f4ca1c196;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index c67eafc..20b0885 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -126,7 +126,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
      *
      * @return DOCUMENT ME!
      */
-    public Color findColour(String n)
+    public Color findColour(char c)
     {
         return Color.red;
     }
@@ -139,15 +139,15 @@ public class AnnotationColourGradient extends ResidueColourScheme
      *
      * @return DOCUMENT ME!
      */
-    public Color findColour(String n, int j)
+    public Color findColour(char c, int j)
     {
-        currentColour = Color.white;
+        Color currentColour = Color.white;
 
-        if ((threshold == 0) || aboveThreshold(n, j))
+        if ((threshold == 0) || aboveThreshold(c, j))
         {
           if( j<annotation.annotations.length
               && annotation.annotations[j]!=null
-              && !jalview.util.Comparison.isGap(n.charAt(0)))
+              && !jalview.util.Comparison.isGap(c))
           {
             if(  aboveAnnotationThreshold==NO_THRESHOLD
                || (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)
@@ -155,7 +155,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
             {
               if(colourScheme!=null)
               {
-                currentColour = colourScheme.findColour(n, j);
+                currentColour = colourScheme.findColour(c, j);
               }
               else if(range!=0)
               {
@@ -179,7 +179,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
         }
 
         if(conservationColouring)
-         applyConservation(j);
+         currentColour = applyConservation(currentColour, j);
 
        return currentColour;
     }