From c4609f79463d463d471b207a092f4d5af807391d Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 15 May 2015 14:13:28 +0100
Subject: [PATCH] JAL-1737 ignore non-positional annotations for display

---
 src/jalview/analysis/AlignmentAnnotationUtils.java |   16 ++++++++++++----
 src/jalview/gui/AlignFrame.java                    |    7 +++++++
 2 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/src/jalview/analysis/AlignmentAnnotationUtils.java b/src/jalview/analysis/AlignmentAnnotationUtils.java
index 9bdbf73..e02aa9e 100644
--- a/src/jalview/analysis/AlignmentAnnotationUtils.java
+++ b/src/jalview/analysis/AlignmentAnnotationUtils.java
@@ -1,9 +1,5 @@
 package jalview.analysis;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.AnnotationRenderer;
-
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
@@ -12,6 +8,10 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.AnnotationRenderer;
+
 public class AlignmentAnnotationUtils
 {
 
@@ -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)))
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1b2410a..1cd2ea8 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -5961,6 +5961,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     for (AlignmentAnnotation aa : alignPanel.getAlignment()
             .getAlignmentAnnotation())
     {
+      /*
+       * don't display non-positional annotations on an alignment
+       */
+      if (aa.annotations == null)
+      {
+        continue;
+      }
       boolean apply = (aa.sequenceRef == null && forAlignment)
               || (aa.sequenceRef != null && forSequences);
       if (apply)
-- 
1.7.10.2