{
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());
*/
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)
{
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.isEmpty())
+ // TODO: drop this completely since we should not manipulate sequenceFeatures as a vector any more
+ if (!excludeFeatures && sfeatures != null && !sfeatures.isEmpty())
{
sq.setSequenceFeatures(sfeatures);
}