From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 30 Jun 2017 10:44:27 +0000 (+0100)
Subject: JAL-2602 same fix for applet
X-Git-Tag: Release_2_10_3b1~181^2~3
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=4d68dde4cec0aec2293d99dc7d00a38755fb5c06

JAL-2602 same fix for applet
---

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 73cd9e9..a894d0b 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -26,6 +26,7 @@ import jalview.api.FeatureSettingsModelI;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResults;
@@ -248,15 +249,18 @@ public class AlignViewport extends AlignmentViewport implements
     StringBuilder seqs = new StringBuilder(consensus.annotations.length);
     for (int i = 0; i < consensus.annotations.length; i++)
     {
-      if (consensus.annotations[i] != null)
+      Annotation annotation = consensus.annotations[i];
+      if (annotation != null)
       {
-        if (consensus.annotations[i].description.charAt(0) == '[')
+        String description = annotation.description;
+        if (description != null && description.startsWith("["))
         {
-          seqs.append(consensus.annotations[i].description.charAt(1));
+          // consensus is a tie - just pick the first one
+          seqs.append(annotation.description.charAt(1));
         }
         else
         {
-          seqs.append(consensus.annotations[i].displayCharacter);
+          seqs.append(annotation.displayCharacter);
         }
       }
     }