X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=c464af2db4fa8d181219e7455c4ad5bf56f6ac82;hb=be762d8d9c71a7aa3121e845c45911c7192b7827;hp=6bbd56614559c0bea3381156f7dba04888cf7316;hpb=e327ac5df98f528afeb347ac9a79085ad0d0975b;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 6bbd566..c464af2 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -96,14 +96,13 @@ public class AlignmentAnnotation
    * Updates the _rnasecstr field Determines the positions that base pair and
    * the positions of helices based on secondary structure from a Stockholm file
    * 
-   * @param RNAannot
+   * @param rnaAnnotation
    */
-  private void _updateRnaSecStr(CharSequence RNAannot)
+  private void _updateRnaSecStr(CharSequence rnaAnnotation)
   {
     try
     {
-      bps = Rna.getModeleBP(RNAannot);
-      _rnasecstr = Rna.getBasePairs(bps);
+      _rnasecstr = Rna.getHelixMap(rnaAnnotation);
       invalidrnastruc = -1;
     } catch (WUSSParseException px)
     {
@@ -114,8 +113,6 @@ public class AlignmentAnnotation
     {
       return;
     }
-    Rna.HelixMap(_rnasecstr);
-    // setRNAStruc(RNAannot);
 
     if (_rnasecstr != null && _rnasecstr.length > 0)
     {
@@ -273,12 +270,6 @@ public class AlignmentAnnotation
     }
   }
 
-  // JBPNote: what does this do ?
-  public void ConcenStru(CharSequence RNAannot) throws WUSSParseException
-  {
-    bps = Rna.getModeleBP(RNAannot);
-  }
-
   /**
    * Creates a new AlignmentAnnotation object.
    *