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hidden seqs and setOrder bug fixed
author
amwaterhouse
<Andrew Waterhouse>
Tue, 7 Nov 2006 11:51:49 +0000
(11:51 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Tue, 7 Nov 2006 11:51:49 +0000
(11:51 +0000)
src/jalview/analysis/AlignmentSorter.java
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diff --git
a/src/jalview/analysis/AlignmentSorter.java
b/src/jalview/analysis/AlignmentSorter.java
index
e63b6e5
..
c80c326
100755
(executable)
--- a/
src/jalview/analysis/AlignmentSorter.java
+++ b/
src/jalview/analysis/AlignmentSorter.java
@@
-113,13
+113,24
@@
public class AlignmentSorter
{
\r
// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
\r
Vector algn = align.getSequences();
\r
{
\r
// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
\r
Vector algn = align.getSequences();
\r
+ Vector tmp = new Vector();
\r
\r
\r
- int index = 0;
\r
for (int i = 0; i < seqs.length; i++)
\r
{
\r
if(algn.contains(seqs[i]))
\r
for (int i = 0; i < seqs.length; i++)
\r
{
\r
if(algn.contains(seqs[i]))
\r
- algn.setElementAt(seqs[i], index++);
\r
+ tmp.addElement(seqs[i]);
\r
+ }
\r
+
\r
+ algn.clear();
\r
+ //User may have hidden seqs, then clicked undo or redo
\r
+ for (int i = 0; i < tmp.size(); i++)
\r
+ {
\r
+ algn.addElement(tmp.elementAt(i));
\r
}
\r
}
\r
+
\r
+
\r
+
\r
+
\r
}
\r
\r
/**
\r
}
\r
\r
/**
\r