X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=ac88d96b81898a2467db6bdfb7d6f6e22d73f62b;hb=e4dca3706ab423352c26ac100f3ca5a3e7c3d2c4;hp=3cb7e174ebdc895694bf5f9abef58a944e1cebf4;hpb=5963dedafa1af673a588f0d30710f7391eb822c4;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 3cb7e17..ac88d96 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -85,6 +85,30 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
     }
 
+
+    public String getAnnotation()
+    {
+      return annotation.label;
+    }
+
+    public int getAboveThreshold()
+    {
+      return aboveAnnotationThreshold;
+    }
+
+    public float getAnnotationThreshold()
+    {
+      if(annotationThreshold==null)
+        return 0;
+      else
+        return annotationThreshold.value;
+    }
+
+    public ColourSchemeI getBaseColour()
+    {
+      return colourScheme;
+    }
+
     public Color getMinColour()
     {
       return new Color( (int) r1, (int) g1, (int) b1);
@@ -117,11 +141,13 @@ 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 +174,9 @@ 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);