X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=20b08857c757ec16f291d6962d625118173f2762;hb=30e5fae28c2ecfffb28d834a2428255ca1f81b94;hp=8367cadc36020b23d62e1f1e29dc38423d1641b6;hpb=3d941a02a998676a12f8ff43fa98d9e1f4c27142;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 8367cad..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)
     {
         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(currentColour, j);
+         currentColour = applyConservation(currentColour, j);
 
        return currentColour;
     }