From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 24 Nov 2014 16:01:33 +0000 (+0000)
Subject: JAL-1595 annotation score is total number of rna helices
X-Git-Tag: Jalview_2_9~147^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a79d9d9c5d2e79f5d86bb7fcabf897a34d48dd13;p=jalview.git

JAL-1595 annotation score is total number of rna helices
---

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index c77cbdb..e137225 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -119,6 +119,7 @@ public class AlignmentAnnotation
 
   private void _markRnaHelices()
   {
+    int mxval = 0;
     // Figure out number of helices
     // Length of rnasecstr is the number of pairs of positions that base pair
     // with each other in the secondary structure
@@ -134,6 +135,10 @@ public class AlignmentAnnotation
       try
       {
         val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
+        if (mxval < val)
+        {
+          mxval = val;
+        }
       } catch (NumberFormatException q)
       {
       }
@@ -145,6 +150,7 @@ public class AlignmentAnnotation
       // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
       // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
     }
+    setScore(mxval);
   }
   /**
    * map of positions in the associated annotation