/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, 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 java.util.*;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
-import jalview.datamodel.*;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
public class SeqsetUtils
{
sqinfo.put("Description", seq.getDescription());
}
Vector sfeat = new Vector();
- jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
+ SequenceFeature[] sfarray = seq.getSequenceFeatures();
if (sfarray != null && sfarray.length > 0)
{
for (int i = 0; i < sfarray.length; i++)
}
sqinfo.put("SeqFeatures", sfeat);
sqinfo.put("PdbId", (seq.getPDBId() != null) ? seq.getPDBId()
- : new Vector());
+ : new Vector<PDBEntry>());
sqinfo.put("datasetSequence",
(seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
: new Sequence("THISISAPLACEHOLDER", ""));
Integer start = (Integer) sqinfo.get("Start");
Integer end = (Integer) sqinfo.get("End");
Vector sfeatures = (Vector) sqinfo.get("SeqFeatures");
- Vector pdbid = (Vector) sqinfo.get("PdbId");
+ Vector<PDBEntry> pdbid = (Vector<PDBEntry>) sqinfo.get("PdbId");
String description = (String) sqinfo.get("Description");
Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
if (oldname == null)
public static boolean deuniquify(Hashtable map, SequenceI[] sequences,
boolean quiet)
{
- jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
- sequences);
+ SequenceIdMatcher matcher = new SequenceIdMatcher(sequences);
SequenceI msq = null;
Enumeration keys = map.keys();
Vector unmatched = new Vector();
int msflen = 0;
for (int i = 0, j = sequences.length; i < j; i++)
{
- String tempseq = jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
+ String tempseq = AlignSeq.extractGaps(Comparison.GapChars,
sequences[i].getSequenceAsString());
if (tempseq.length() == 0)