From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 21 Feb 2014 16:27:50 +0000 (+0000)
Subject: patch for JAL-1449 - continuance of JAL-1364 - check bounds of gapMap - not the VIENN... 
X-Git-Tag: Jalview_2_9~204^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b920a3c8476e5f43399393d580d4e3d8b79c15b6;p=jalview.git

patch for JAL-1449 - continuance of JAL-1364 - check bounds of gapMap - not the VIENNA results
---

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);