/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
/**
*
* @param sequences
* @param selectedChars
- * @param exgroups
+ * @param list
* @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();
- 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++)