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<SequenceFeature>();
+ List<SequenceFeature> sfs = seq.getFeatures().getAllFeatures();
+ sfeat.addAll(sfs);
+
if (seq.getDatasetSequence() == null)
{
sqinfo.put("SeqFeatures", sfeat);
*/
public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
{
+ return SeqCharacterUnhash(sq, sqinfo, false, false);
+ }
+
+ /**
+ * restore some characteristics for a sequence from its hash
+ * @param sq
+ * @param sqinfo
+ * @param excludeLimits - when true, start/end is left unmodified
+ * @param excludeFeatures - when true, features are not restored from stashed vector
+ * @return true if sequence's name was modified
+ */
+
+ public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo, boolean excludeLimits,boolean excludeFeatures)
+ {
boolean namePresent = true;
if (sqinfo == null)
{
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");
sq.setPDBId(pdbid);
}
- if ((start != null) && (end != null))
+ if (!excludeLimits && (start != null) && (end != null))
{
sq.setStart(start.intValue());
sq.setEnd(end.intValue());
}
-
- if ((sfeatures != null) && (sfeatures.size() > 0))
+ // TODO: drop this completely since we should not manipulate sequenceFeatures as a vector any more
+ if (!excludeFeatures && 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)
{