From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 20 Nov 2014 14:54:01 +0000 (+0000)
Subject: JAL-1569 rna pair code in secondary structure character of annotation
X-Git-Tag: Jalview_2_9~148^2~17
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=59c8d9d6d8d42c579dc5ab6bfc37902ff4bd118f;p=jalview.git

JAL-1569 rna pair code in secondary structure character of annotation
---

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 0207575..8a44535 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -486,11 +486,10 @@ public class AlignmentAnnotation
     @Override
     public char charAt(int index)
     {
-      String dc;
       return ((index + offset < 0) || (index + offset) >= max
-              || annotations[index + offset] == null || (dc = annotations[index
-              + offset].displayCharacter.trim()).length() < 1) ? '.' : dc
-              .charAt(0);
+              || annotations[index + offset] == null || (annotations[index
+ + offset].secondaryStructure < ' ') ? ' '
+              : annotations[index + offset].secondaryStructure);
     }
 
     public String toString()
@@ -500,9 +499,8 @@ public class AlignmentAnnotation
 
       for (int i = offset; i < mx; i++)
       {
-        String dc;
-        string[i] = (annotations[i] == null || (dc = annotations[i].displayCharacter
-                .trim()).length() < 1) ? '.' : dc.charAt(0);
+        string[i] = (annotations[i] == null || (annotations[i].secondaryStructure < 32)) ? ' '
+                : annotations[i].secondaryStructure;
       }
       return new String(string);
     }