X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;fp=src%2Fjalview%2Fgui%2FJalview2XML.java;h=01e60d438081efc19751bb2014491d7e8bf4510e;hb=bad7a4b6634892d3174a940902e00704bf5007c1;hp=eeb42148b0505ee451294b789c2834927a6a9c92;hpb=048a384fa19ac37fbe2b63bbba139d5fa17107c5;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index eeb4214..01e60d4 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -680,9 +680,8 @@ public class Jalview2XML
     Set<String> calcIdSet = new HashSet<String>();
 
     // SAVE SEQUENCES
-    for (int i = 0; i < rjal.getHeight(); i++)
+    for (final SequenceI jds : rjal.getSequences())
     {
-      final SequenceI jds = rjal.getSequenceAt(i);
       final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
               : jds.getDatasetSequence();
       String id = seqHash(jds);
@@ -725,15 +724,15 @@ public class Jalview2XML
           jseq.setHidden(av.getAlignment().getHiddenSequences()
                   .isHidden(jds));
 
-          if (av.isHiddenRepSequence(rjal.getSequenceAt(i)))
+          if (av.isHiddenRepSequence(jds))
           {
             jalview.datamodel.SequenceI[] reps = av
-                    .getRepresentedSequences(rjal.getSequenceAt(i))
+                    .getRepresentedSequences(jds)
                     .getSequencesInOrder(rjal);
 
             for (int h = 0; h < reps.length; h++)
             {
-              if (reps[h] != rjal.getSequenceAt(i))
+              if (reps[h] != jds)
               {
                 jseq.addHiddenSequences(rjal.findIndex(reps[h]));
               }
@@ -743,7 +742,7 @@ public class Jalview2XML
         // mark sequence as reference - if it is the reference for this view
         if (jal.hasSeqrep())
         {
-          jseq.setViewreference(rjal.getSequenceAt(i) == jal.getSeqrep());
+          jseq.setViewreference(jds == jal.getSeqrep());
         }
       }