JAL-1489 change initial value to distinguish non-rna from valid and invalid RNA struc...

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 8a44535..c77cbdb 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -75,9 +75,10 @@ public class AlignmentAnnotation
   public SequenceFeature[] _rnasecstr = null;
 
   /**
-   * position of annotation resulting in invalid WUSS parsing or -1
+   * position of annotation resulting in invalid WUSS parsing or -1. -2 means
+   * there was no RNA structure in this annotation
    */
-  private long invalidrnastruc = -1;
+  private long invalidrnastruc = -2;
 
   /**
    * Updates the _rnasecstr field Determines the positions that base pair and
@@ -141,8 +142,8 @@ public class AlignmentAnnotation
       annotations[_rnasecstr[x].getBegin()].value = val;
       annotations[_rnasecstr[x].getEnd()].value = val;
 
-      annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
-      annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
+      // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
+      // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
     }
   }
   /**