From 63d6bdbbe0626fa30497577faf6b3edc9d48abc6 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 7 Dec 2012 15:51:28 +0000
Subject: [PATCH] use new secstructure process algorithm

---
 src/jalview/datamodel/AlignmentAnnotation.java |   17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index ea13922..02446c4 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -18,6 +18,8 @@
 package jalview.datamodel;
 
 import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+
 import jalview.analysis.WUSSParseException;
 
 import java.util.ArrayList;
@@ -55,6 +57,7 @@ public class AlignmentAnnotation
   
   
 
+  public ArrayList<SimpleBP> bps=null;
   /**
    * RNA secondary structure contact positions
    */
@@ -73,13 +76,15 @@ public class AlignmentAnnotation
    */
   private void _updateRnaSecStr(CharSequence RNAannot)
   {
-    try
-    {
-      _rnasecstr = Rna.GetBasePairs(RNAannot);
-      invalidrnastruc = -1;
-    } catch (WUSSParseException px)
+    try {
+    _rnasecstr = Rna.GetBasePairs(RNAannot);
+    bps = Rna.GetModeleBP(RNAannot);
+    invalidrnastruc=-1;
+    }
+    catch (WUSSParseException px)
     {
-      invalidrnastruc = px.getProblemPos();
+      // DEBUG System.out.println(px);
+      invalidrnastruc=px.getProblemPos();
     }
     if (invalidrnastruc > -1)
     {
-- 
1.7.10.2