*/
package jalview.analysis;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.HiddenMarkovModel;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
public class SeqsetUtils
{
Hashtable sqinfo = new Hashtable();
sqinfo.put("Name", seq.getName());
- sqinfo.put("Start", new Integer(seq.getStart()));
- sqinfo.put("End", new Integer(seq.getEnd()));
+ sqinfo.put("Start", Integer.valueOf(seq.getStart()));
+ sqinfo.put("End", Integer.valueOf(seq.getEnd()));
if (seq.getDescription() != null)
{
sqinfo.put("Description", seq.getDescription());
}
- Vector sfeat = new Vector();
- jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
- if (sfarray != null && sfarray.length > 0)
- {
- for (int i = 0; i < sfarray.length; i++)
- {
- sfeat.addElement(sfarray[i]);
- }
- }
+
+ Vector<SequenceFeature> sfeat = new Vector<>();
+ List<SequenceFeature> sfs = seq.getFeatures().getAllFeatures();
+ sfeat.addAll(sfs);
+
if (seq.getDatasetSequence() == null)
{
sqinfo.put("SeqFeatures", sfeat);
(seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
: new Sequence("THISISAPLACEHOLDER", ""));
}
- if (seq.isHMMConsensusSequence())
+ if (seq.hasHMMProfile())
{
sqinfo.put("HMM", seq.getHMM());
}
+
+ if (seq.getAnnotation("Search Scores") != null)
+ {
+ sqinfo.put("Score", seq.getAnnotation("Search Scores"));
+ }
+
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<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");
HiddenMarkovModel hmm = (HiddenMarkovModel) sqinfo.get("HMM");
+ AlignmentAnnotation[] scores = (AlignmentAnnotation[]) sqinfo
+ .get("Score");
+
if (oldname == null)
{
namePresent = false;
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)
{
if (hmm != null)
{
- sq.setHMM(new HiddenMarkovModel(hmm));
- sq.setIsHMMConsensusSequence(true);
+ sq.setHMM(new HiddenMarkovModel(hmm, sq));
+ }
+
+ if (scores != null)
+ {
+ for (AlignmentAnnotation score : scores)
+ {
+ sq.addAlignmentAnnotation(score);
+ }
}
return namePresent;
}