Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

[jalview.git] / src / jalview / datamodel / AlignmentAnnotation.java

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index b608139..4c5ea17 100755 (executable)
--- 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!
  * 
@@ -502,9 +502,13 @@ public class AlignmentAnnotation
     public char charAt(int index)
     {
       return ((index + offset < 0) || (index + offset) >= max
-              || annotations[index + offset] == null || (annotations[index
- + offset].secondaryStructure < ' ') ? ' '
-              : annotations[index + offset].secondaryStructure);
+              || annotations[index + offset] == null
+              || (annotations[index + offset].secondaryStructure <= ' ') ? ' '
+              : annotations[index + offset].displayCharacter == null
+                      || annotations[index + offset].displayCharacter
+                              .length() == 0 ? annotations[index + offset].secondaryStructure
+                      : annotations[index + offset].displayCharacter
+                              .charAt(0));
     }
 
     @Override
@@ -515,8 +519,10 @@ 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 == null
+                        || annotations[i].displayCharacter.length() == 0 ? annotations[i].secondaryStructure
+                        : annotations[i].displayCharacter.charAt(0));
       }
       return new String(string);
     }
@@ -644,7 +650,7 @@ public class AlignmentAnnotation
       {
         if (annotations[i] != null)
         {
-          annotations[i].displayCharacter = "X";
+          annotations[i].displayCharacter = "";
         }
       }
     }