/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
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)