X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentAnnotationUtils.java;h=a8e61e9cba53fe2561d026d2b8271664235a1f33;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=b5f77fd314c066e28f407097ead14535937a2c32;hpb=195c41c18f6a059b334d063312cd15de6a937ea5;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentAnnotationUtils.java b/src/jalview/analysis/AlignmentAnnotationUtils.java
index b5f77fd..a8e61e9 100644
--- a/src/jalview/analysis/AlignmentAnnotationUtils.java
+++ b/src/jalview/analysis/AlignmentAnnotationUtils.java
@@ -63,6 +63,14 @@ public class AlignmentAnnotationUtils
 
     for (AlignmentAnnotation aa : annotations)
     {
+      /*
+       * Ignore non-positional annotations, can't render these against an
+       * alignment
+       */
+      if (aa.annotations == null)
+      {
+        continue;
+      }
       if (forSequences != null
               && (aa.sequenceRef != null && forSequences
                       .contains(aa.sequenceRef)))
@@ -129,21 +137,28 @@ public class AlignmentAnnotationUtils
       }
     }
     /*
-     * finally add the 'composite group labels' to the appropriate lists,
-     * depending on whether the group is identified as visible or hidden
+     * Finally add the 'composite group labels' to the appropriate lists,
+     * depending on whether the group is identified as visible or hidden. Don't
+     * add the same label more than once (there may be many graph groups that
+     * generate it).
      */
     for (String calcId : groupLabels.keySet())
     {
       for (int group : groupLabels.get(calcId).keySet())
       {
         final List<String> groupLabel = groupLabels.get(calcId).get(group);
+        // don't want to duplicate 'same types in different order'
+        Collections.sort(groupLabel);
         if (visibleGraphGroups.get(group))
         {
           if (!shownTypes.containsKey(calcId))
           {
             shownTypes.put(calcId, new ArrayList<List<String>>());
           }
-          shownTypes.get(calcId).add(groupLabel);
+          if (!shownTypes.get(calcId).contains(groupLabel))
+          {
+            shownTypes.get(calcId).add(groupLabel);
+          }
         }
         else
         {
@@ -151,7 +166,10 @@ public class AlignmentAnnotationUtils
           {
             hiddenTypes.put(calcId, new ArrayList<List<String>>());
           }
-          hiddenTypes.get(calcId).add(groupLabel);
+          if (!hiddenTypes.get(calcId).contains(groupLabel))
+          {
+            hiddenTypes.get(calcId).add(groupLabel);
+          }
         }
       }
     }
@@ -196,8 +214,7 @@ public class AlignmentAnnotationUtils
    * @param anns
    * @return
    */
-  public static List<AlignmentAnnotation> asList(
-          AlignmentAnnotation[] anns)
+  public static List<AlignmentAnnotation> asList(AlignmentAnnotation[] anns)
   {
     // TODO use AlignmentAnnotationI instead when it exists
     return (anns == null ? Collections.<AlignmentAnnotation> emptyList()