JAL-1319 (blacklist fix) check for presence of a score object before we start making...

[jalview.git] / src / jalview / schemes / AnnotationColourGradient.java

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 78e850b..218b5fa 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -108,13 +108,16 @@ public class AnnotationColourGradient extends ResidueColourScheme
   {
     // TODO Auto-generated method stub
     super.alignmentChanged(alignment, hiddenReps);
-    
+
     if (seqAssociated && annotation.getCalcId() != null)
     {
-      if (seqannot!=null) {
+      if (seqannot != null)
+      {
         seqannot.clear();
-      } else {
-        seqannot=new IdentityHashMap<SequenceI, AlignmentAnnotation>();
+      }
+      else
+      {
+        seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
       }
       for (AlignmentAnnotation alan : alignment.findAnnotation(annotation
               .getCalcId()))
@@ -193,8 +196,9 @@ public class AnnotationColourGradient extends ResidueColourScheme
   public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour = Color.white;
-    AlignmentAnnotation annotation=(seqAssociated ? seqannot.get(seq):this.annotation);
-    if (annotation==null)
+    AlignmentAnnotation annotation = (seqAssociated ? seqannot.get(seq)
+            : this.annotation);
+    if (annotation == null)
     {
       return currentColour;
     }