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Add support RNAML format
[jalview.git]
/
src
/
jalview
/
analysis
/
Grouping.java
diff --git
a/src/jalview/analysis/Grouping.java
b/src/jalview/analysis/Grouping.java
index
57f1dcf
..
91fef84
100644
(file)
--- a/
src/jalview/analysis/Grouping.java
+++ b/
src/jalview/analysis/Grouping.java
@@
-1,6
+1,6
@@
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-24,6
+24,7
@@
import jalview.datamodel.SequenceI;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
/**
import java.util.Vector;
/**
@@
-42,25
+43,24
@@
public class Grouping
*
* @param sequences
* @param selectedChars
*
* @param sequences
* @param selectedChars
- * @param exgroups
+ * @param list
* @return
*/
public static SequenceGroup[] makeGroupsFrom(SequenceI[] sequences,
* @return
*/
public static SequenceGroup[] makeGroupsFrom(SequenceI[] sequences,
- String[] selectedChars, Vector exgroups)
+ String[] selectedChars, List<SequenceGroup> list)
{
// TODO: determine how to get/recover input data for group generation
Hashtable gps = new Hashtable();
int width = 0, i;
Hashtable pgroup = new Hashtable();
{
// TODO: determine how to get/recover input data for group generation
Hashtable gps = new Hashtable();
int width = 0, i;
Hashtable pgroup = new Hashtable();
- if (exgroups != null)
+ if (list != null)
{
{
- SequenceGroup sg;
- for (Enumeration g = exgroups.elements(); g.hasMoreElements();)
+ for (SequenceGroup sg:list)
{
{
- sg = (SequenceGroup) g.nextElement();
- for (Enumeration sq = sg.getSequences(null).elements(); sq
- .hasMoreElements();)
- pgroup.put(sq.nextElement().toString(), sg);
+ for (SequenceI sq :sg.getSequences(null))
+ {
+ pgroup.put(sq.toString(), sg);
+ }
}
}
for (i = 0; i < sequences.length; i++)
}
}
for (i = 0; i < sequences.length; i++)