/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import java.util.Enumeration;
-import java.util.Hashtable;
+import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import java.util.Vector;
/**
String[] selectedChars, List<SequenceGroup> list)
{
// TODO: determine how to get/recover input data for group generation
- Hashtable gps = new Hashtable();
+ Map<String, List<SequenceI>> gps = new HashMap<String, List<SequenceI>>();
int width = 0, i;
- Hashtable pgroup = new Hashtable();
+ Map<String, SequenceGroup> pgroup = new HashMap<String, SequenceGroup>();
if (list != null)
{
- for (SequenceGroup sg:list)
+ for (SequenceGroup sg : list)
{
- for (SequenceI sq :sg.getSequences(null))
+ for (SequenceI sq : sg.getSequences(null))
{
pgroup.put(sq.toString(), sg);
}
for (i = 0; i < sequences.length; i++)
{
String schar = selectedChars[i];
- SequenceGroup pgp = (SequenceGroup) pgroup
- .get(((Object) sequences[i]).toString());
+ SequenceGroup pgp = pgroup.get(((Object) sequences[i]).toString());
if (pgp != null)
{
schar = pgp.getName() + ":" + schar;
}
- Vector svec = (Vector) gps.get(schar);
+ List<SequenceI> svec = gps.get(schar);
if (svec == null)
{
- svec = new Vector();
+ svec = new ArrayList<SequenceI>();
gps.put(schar, svec);
}
if (width < sequences[i].getLength())
{
width = sequences[i].getLength();
}
- svec.addElement(sequences[i]);
+ svec.add(sequences[i]);
+ }
+ // make some groups
+ SequenceGroup[] groups = new SequenceGroup[gps.size()];
+ i = 0;
+ for (String key : gps.keySet())
+ {
+ SequenceGroup group = new SequenceGroup(gps.get(key),
+ "Subseq: " + key, null, true, true, false, 0, width - 1);
+
+ groups[i++] = group;
+ }
+ gps.clear();
+ pgroup.clear();
+ return groups;
+ }
+
+ /**
+ * Divide the given sequences based on the equivalence of characters at
+ * selected columns If exgroups is provided, existing groups will be
+ * subdivided.
+ *
+ * @param sequences
+ * @param columnSelection
+ * @param list
+ * @param hiddenColumns
+ * @return
+ */
+ public static SequenceGroup[] makeGroupsFromCols(SequenceI[] sequences,
+ ColumnSelection cs, List<SequenceGroup> list,
+ HiddenColumns hiddenColumns)
+ {
+ // TODO: determine how to get/recover input data for group generation
+ Map<String, List<SequenceI>> gps = new HashMap<String, List<SequenceI>>();
+ Map<String, SequenceGroup> pgroup = new HashMap<String, SequenceGroup>();
+ if (list != null)
+ {
+ for (SequenceGroup sg : list)
+ {
+ for (SequenceI sq : sg.getSequences(null))
+ {
+ pgroup.put(sq.toString(), sg);
+ }
+ }
+ }
+
+ /*
+ * get selected columns (in the order they were selected);
+ * note this could include right-to-left ranges
+ */
+ int[] spos = new int[cs.getSelected().size()];
+ int width = -1;
+ int i = 0;
+ for (Integer pos : cs.getSelected())
+ {
+ if (hiddenColumns == null || hiddenColumns.isVisible(pos.intValue()))
+ {
+ spos[i++] = pos.intValue();
+ }
+ }
+ if (i < spos.length)
+ {
+ // mark end of visible column position
+ spos[i] = -1;
+ }
+ // actual number of visible columns
+ for (i = 0; i < sequences.length; i++)
+ {
+ int slen = sequences[i].getLength();
+ if (width < slen)
+ {
+ width = slen;
+ }
+
+ SequenceGroup pgp = pgroup.get(((Object) sequences[i]).toString());
+ StringBuilder schar = new StringBuilder();
+ if (pgp != null)
+ {
+ schar.append(pgp.getName() + ":");
+ }
+ for (int p : spos)
+ {
+ if (p < 0)
+ {
+ break;
+ }
+ if (p >= slen)
+ {
+ schar.append("~");
+ }
+ else
+ {
+ schar.append(sequences[i].getCharAt(p));
+ }
+ }
+ List<SequenceI> svec = gps.get(schar.toString());
+ if (svec == null)
+ {
+ svec = new ArrayList<SequenceI>();
+ gps.put(schar.toString(), svec);
+ }
+ svec.add(sequences[i]);
}
// make some groups
- java.util.Enumeration sge = gps.keys();
SequenceGroup[] groups = new SequenceGroup[gps.size()];
i = 0;
- while (sge.hasMoreElements())
+ for (String key : gps.keySet())
{
- String key = (String) sge.nextElement();
- SequenceGroup group = new SequenceGroup((Vector) gps.get(key),
+ SequenceGroup group = new SequenceGroup(gps.get(key),
"Subseq: " + key, null, true, true, false, 0, width - 1);
groups[i++] = group;
git://source.jalview.org / jalview.git / blobdiff