From 2bdd8fe3e044068769ca42c57bfa1ef5f52e2f2d Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Feb 2006 16:51:36 +0000
Subject: [PATCH] Dont colour gaps

---
 src/jalview/schemes/AnnotationColourGradient.java |   16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 3cb7e17..789667e 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -117,11 +117,13 @@ public class AnnotationColourGradient extends ResidueColourScheme
      */
     public Color findColour(String n, int j)
     {
+        currentColour = Color.white;
+
         if ((threshold == 0) || aboveThreshold(n, j))
         {
-          if( j+1>annotation.annotations.length || annotation.annotations[j]==null)
-            currentColour = Color.white;
-          else
+          if( j<annotation.annotations.length
+              && annotation.annotations[j]!=null
+              && !jalview.util.Comparison.isGap(n.charAt(0)))
           {
             if(  aboveAnnotationThreshold==NO_THRESHOLD
                || (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)
@@ -148,17 +150,9 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
                 currentColour = new Color( (int) dr, (int) dg, (int) db);
               }
-              else
-                currentColour = Color.white;
             }
-            else
-              currentColour = Color.white;
           }
         }
-        else
-        {
-            return Color.white;
-        }
 
         if(conservationColouring)
          applyConservation(j);
-- 
1.7.10.2