From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 21 Nov 2014 08:55:38 +0000 (+0000)
Subject: JAL-1489 change initial value to distinguish non-rna from valid and invalid RNA struc... 
X-Git-Tag: Jalview_2_9~148^2~15
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ae2aad01e22e7b6e300bbbd7c3a1ef15ec022b9f;p=jalview.git

JAL-1489 change initial value to distinguish non-rna from valid and invalid RNA structure with one call to .isValidStructure()
---

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 8a44535..c77cbdb 100755
--- 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;
     }
   }
   /**