Dont colour gaps

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 3cb7e17..789667e 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -117,11 +117,13 @@ public class AnnotationColourGradient extends ResidueColourScheme
      */\r
     public Color findColour(String n, int j)\r
     {\r
+        currentColour = Color.white;\r
+\r
         if ((threshold == 0) || aboveThreshold(n, j))\r
         {\r
-          if( j+1>annotation.annotations.length || annotation.annotations[j]==null)\r
-            currentColour = Color.white;\r
-          else\r
+          if( j<annotation.annotations.length\r
+              && annotation.annotations[j]!=null\r
+              && !jalview.util.Comparison.isGap(n.charAt(0)))\r
           {\r
             if(  aboveAnnotationThreshold==NO_THRESHOLD\r
                || (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)\r
@@ -148,17 +150,9 @@ public class AnnotationColourGradient extends ResidueColourScheme
 \r
                 currentColour = new Color( (int) dr, (int) dg, (int) db);\r
               }\r
-              else\r
-                currentColour = Color.white;\r
             }\r
-            else\r
-              currentColour = Color.white;\r
           }\r
         }\r
-        else\r
-        {\r
-            return Color.white;\r
-        }\r
 \r
         if(conservationColouring)\r
          applyConservation(j);\r