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2.2 documentation
[jalview.git]
/
src
/
jalview
/
analysis
/
AlignmentSorter.java
diff --git
a/src/jalview/analysis/AlignmentSorter.java
b/src/jalview/analysis/AlignmentSorter.java
index
27d1e7b
..
bf18b70
100755
(executable)
--- a/
src/jalview/analysis/AlignmentSorter.java
+++ b/
src/jalview/analysis/AlignmentSorter.java
@@
-1,6
+1,6
@@
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer
\r
/*
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* Jalview - A Sequence Alignment Editor and Viewer
\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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*
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU General Public License
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*
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* This program is free software; you can redistribute it and/or
\r
* modify it under the terms of the GNU General Public License
\r
@@
-109,15
+109,28
@@
public class AlignmentSorter
* @param align DOCUMENT ME!
\r
* @param seqs sequences as an array
\r
*/
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* @param align DOCUMENT ME!
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* @param seqs sequences as an array
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*/
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- private static void setOrder(AlignmentI align, SequenceI[] seqs)
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+ public static void setOrder(AlignmentI align, SequenceI[] seqs)
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{
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// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
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Vector algn = align.getSequences();
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{
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// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
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Vector algn = align.getSequences();
\r
+ Vector tmp = new Vector();
\r
\r
for (int i = 0; i < seqs.length; i++)
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{
\r
\r
for (int i = 0; i < seqs.length; i++)
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{
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- algn.setElementAt(seqs[i], i);
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+ if(algn.contains(seqs[i]))
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+ tmp.addElement(seqs[i]);
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+ }
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+
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+ algn.removeAllElements();
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+ //User may have hidden seqs, then clicked undo or redo
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+ for (int i = 0; i < tmp.size(); i++)
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+ {
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+ algn.addElement(tmp.elementAt(i));
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}
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}
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+
\r
+
\r
+
\r
+
\r
}
\r
\r
/**
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}
\r
\r
/**
\r