/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 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.datamodel.*;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
-/**
- * <p>
- * Title:
- * </p>
- *
- * <p>
- * Description:
- * </p>
- *
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- *
- * <p>
- * Company: Dundee University
- * </p>
- *
- * @author not attributable
- * @version 1.0
- */
public class SeqsetUtils
{
sfeat.addElement(sfarray[i]);
}
}
- sqinfo.put("SeqFeatures", sfeat);
- sqinfo.put("PdbId", (seq.getPDBId() != null) ? seq.getPDBId()
- : new Vector());
- sqinfo.put("datasetSequence",
- (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
- : new Sequence("THISISAPLACEHOLDER", ""));
+ if (seq.getDatasetSequence() == null)
+ {
+ sqinfo.put("SeqFeatures", sfeat);
+ sqinfo.put("PdbId",
+ (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
+ : new Vector<PDBEntry>());
+ }
+ else
+ {
+ sqinfo.put("datasetSequence",
+ (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
+ : new Sequence("THISISAPLACEHOLDER", ""));
+ }
return sqinfo;
}
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)
{
sq.setDescription(description);
}
- if ((seqds != null)
- && !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds
- .getLength() == 0))
+ if ((seqds != null) && !(seqds.getName().equals("THISISAPLACEHOLDER")
+ && seqds.getLength() == 0))
{
+ if (sfeatures != null)
+ {
+ System.err.println(
+ "Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");
+ }
sq.setDatasetSequence(seqds);
}
if (unmatched.size() > 0 && !quiet)
{
System.err.println("Did not find matches for :");
- for (Enumeration i = unmatched.elements(); i.hasMoreElements(); System.out
- .println(((SequenceI) i.nextElement()).getName()))
+ for (Enumeration i = unmatched.elements(); i
+ .hasMoreElements(); System.out
+ .println(((SequenceI) i.nextElement()).getName()))
{
;
}