From b920a3c8476e5f43399393d580d4e3d8b79c15b6 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 21 Feb 2014 16:27:50 +0000
Subject: [PATCH] patch for JAL-1449 - continuance of JAL-1364 - check bounds
 of gapMap - not the VIENNA results

---
 src/jalview/ws/jws2/RNAalifoldClient.java |    8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java
index ec40552..c7d8efd 100644
--- a/src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/src/jalview/ws/jws2/RNAalifoldClient.java
@@ -198,7 +198,7 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
   private AlignmentAnnotation constructAnnotationFromScoreHolder(
           AlignmentAnnotation annotation, String struct, TreeSet<Score> data)
   {
-    Annotation[] anns = new Annotation[struct.length()];
+    Annotation[] anns = new Annotation[gapMap!= null ? gapMap.length+1 : struct.length()];
 
     if (data != null
             && data.size() > 1
@@ -261,10 +261,14 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
         if (gapMap!=null)
         {
           // skip any gapped columns in the input data
-          while (!gapMap[ri])
+          while (!gapMap[ri] && ri<gapMap.length)
           {
             ri++;
           }
+          if (ri==gapMap.length)
+          {
+            break;
+          }
         }
         anns[ri] = new Annotation(struct.substring(i, i + 1), "",
                 isSS(struct.charAt(i)), Float.NaN);
-- 
1.7.10.2