X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FRNAalifoldClient.java;h=c7d8efdc611dbd97a46ad3cf1865e96c17f2dc60;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=ec40552b38048fe6b6a390c2c816fd6121c4550e;hpb=54da3e753588d95f08dd66ca2d111f16475b061c;p=jalview.git

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);