From 92b6aeab12b161463c0292c0c963c0c8b1680f62 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Thu, 26 Oct 2006 10:19:14 +0000 Subject: [PATCH] Sequences may be hidden, not in this aligment --- src/jalview/analysis/AlignmentSorter.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) 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++); } } -- 1.7.10.2