From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 15 Jun 2015 15:08:47 +0000 (+0100)
Subject: fix for JAL-1775 (and reorganise imports)
X-Git-Tag: Release_2_10_0~606^2~2^2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=0cd071bd37b6833f59a0170ca0f9f8192905d404

fix for JAL-1775 (and reorganise imports)
---

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index b608139..a7e635f 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -20,6 +20,10 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
+
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -28,10 +32,6 @@ import java.util.Iterator;
 import java.util.Map;
 import java.util.Map.Entry;
 
-import jalview.analysis.Rna;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.analysis.WUSSParseException;
-
 /**
  * DOCUMENT ME!
  * 
@@ -503,8 +503,8 @@ public class AlignmentAnnotation
     {
       return ((index + offset < 0) || (index + offset) >= max
               || annotations[index + offset] == null || (annotations[index
- + offset].secondaryStructure < ' ') ? ' '
-              : annotations[index + offset].secondaryStructure);
+ + offset].secondaryStructure <= ' ') ? ' '
+              : annotations[index + offset].displayCharacter.charAt(0));
     }
 
     @Override
@@ -515,8 +515,8 @@ public class AlignmentAnnotation
 
       for (int i = offset; i < mx; i++)
       {
-        string[i] = (annotations[i] == null || (annotations[i].secondaryStructure < 32)) ? ' '
-                : annotations[i].secondaryStructure;
+        string[i] = (annotations[i] == null || (annotations[i].secondaryStructure <= 32)) ? ' '
+                : annotations[i].displayCharacter.charAt(0);
       }
       return new String(string);
     }