X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=ae81a90cf28e631113a8c975324ccd5c5ff267dd;hb=b7620d52027f3bb6f8bc7673563ea30a6adacf22;hp=20a3633499bb6ad34b38881de60969c6162266c6;hpb=86bf99474fd78966716a9d82ff925e4ec7c0663b;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 20a3633..ae81a90 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -152,8 +152,10 @@ Loading...
       }
 
       if(annotations[i].displayCharacter==null)
+      {
+        padGaps = false;
         continue;
-
+      }
 
       if (annotations[i].displayCharacter.length() == 1
           && !annotations[i].displayCharacter.equals("H")
@@ -396,8 +398,7 @@ Loading...
   public boolean padAnnotation(int length) {
     if (annotations==null)
     {
-      annotations = new Annotation[length];
-      return true;
+      return true; // annotation row is correct - null == not visible and undefined length 
     }
     if (annotations.length<length)
     {
@@ -637,4 +638,15 @@ Loading...
   {
     return hasScore || !Double.isNaN(score);
   }
+  /**
+   * Score only annotation
+   * @param label
+   * @param description
+   * @param score
+   */
+  public AlignmentAnnotation(String label, String description, double score)
+  {
+    this(label, description, null);
+    setScore(score);
+  }
 }