*/
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.List;
+import java.util.Vector;
public class SeqsetUtils
{
{
sqinfo.put("Description", seq.getDescription());
}
- Vector sfeat = new Vector();
- jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
- if (sfarray != null && sfarray.length > 0)
+
+ Vector<SequenceFeature> sfeat = new Vector<SequenceFeature>();
+ List<SequenceFeature> sfs = seq.getFeatures().getAllFeatures();
+ sfeat.addAll(sfs);
+
+ if (seq.getDatasetSequence() == null)
{
- for (int i = 0; i < sfarray.length; i++)
- {
- sfeat.addElement(sfarray[i]);
- }
+ 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", ""));
}
- 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", ""));
return sqinfo;
}
String oldname = (String) sqinfo.get("Name");
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<SequenceFeature> sfeatures = (Vector<SequenceFeature>) sqinfo
+ .get("SeqFeatures");
+ Vector<PDBEntry> pdbid = (Vector<PDBEntry>) sqinfo.get("PdbId");
String description = (String) sqinfo.get("Description");
Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
if (oldname == null)
sq.setEnd(end.intValue());
}
- if ((sfeatures != null) && (sfeatures.size() > 0))
+ if (sfeatures != null && !sfeatures.isEmpty())
{
- SequenceFeature[] sfarray = new SequenceFeature[sfeatures.size()];
- for (int is = 0, isize = sfeatures.size(); is < isize; is++)
- {
- sfarray[is] = (SequenceFeature) sfeatures.elementAt(is);
- }
- sq.setSequenceFeatures(sfarray);
+ sq.setSequenceFeatures(sfeatures);
}
if (description != 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()))
{
;
}