From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 26 Oct 2006 10:19:14 +0000 (+0000)
Subject: Sequences may be hidden, not in this aligment
X-Git-Tag: Release_2_2~220
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=92b6aeab12b161463c0292c0c963c0c8b1680f62;p=jalview.git

Sequences may be hidden, not in this aligment
---

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 938aa6a..e63b6e5 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -114,9 +114,11 @@ public class AlignmentSorter
         // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
         Vector algn = align.getSequences();
 
+        int index = 0;
         for (int i = 0; i < seqs.length; i++)
         {
-            algn.setElementAt(seqs[i], i);
+          if(algn.contains(seqs[i]))
+            algn.setElementAt(seqs[i], index++);
         }
     }