initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
seq.getEnd());
description = seq.getDescription();
+ sourceDBRef = seq.getSourceDBRef();
if (seq.getSequenceFeatures() != null)
{
SequenceFeature[] sf = seq.getSequenceFeatures();
}
}
setDatasetSequence(seq.getDatasetSequence());
- if (datasetSequence == null && seq.getDBRef() != null)
+ if (datasetSequence == null && seq.getDBRefs() != null)
{
// only copy DBRefs if we really are a dataset sequence
- DBRefEntry[] dbr = seq.getDBRef();
+ DBRefEntry[] dbr = seq.getDBRefs();
for (int i = 0; i < dbr.length; i++)
{
addDBRef(new DBRefEntry(dbr[i]));
}
if (seq.getAllPDBEntries() != null)
{
- Vector ids = seq.getAllPDBEntries();
- Enumeration e = ids.elements();
- while (e.hasMoreElements())
+ Vector<PDBEntry> ids = seq.getAllPDBEntries();
+ for (PDBEntry pdb : ids)
{
- this.addPDBId(new PDBEntry((PDBEntry) e.nextElement()));
+ this.addPDBId(new PDBEntry(pdb));
}
}
}
@Override
public synchronized void addSequenceFeature(SequenceFeature sf)
{
+ // TODO add to dataset sequence instead if there is one?
if (sequenceFeatures == null)
{
sequenceFeatures = new SequenceFeature[0];
}
@Override
- public void setDBRef(DBRefEntry[] dbref)
+ public void setDBRefs(DBRefEntry[] dbref)
{
dbrefs = dbref;
}
@Override
- public DBRefEntry[] getDBRef()
+ public DBRefEntry[] getDBRefs()
{
if (dbrefs == null && datasetSequence != null
&& this != datasetSequence)
{
- return datasetSequence.getDBRef();
+ return datasetSequence.getDBRefs();
}
return dbrefs;
}
@Override
public void addDBRef(DBRefEntry entry)
{
+ // TODO add to dataset sequence instead if there is one?
if (dbrefs == null)
{
dbrefs = new DBRefEntry[0];
@Override
public void setDatasetSequence(SequenceI seq)
{
+ // TODO check for circular reference before setting?
datasetSequence = seq;
}
datasetSequence.setDescription(getDescription());
setSequenceFeatures(null);
// move database references onto dataset sequence
- datasetSequence.setDBRef(getDBRef());
- setDBRef(null);
+ datasetSequence.setDBRefs(getDBRefs());
+ setDBRefs(null);
datasetSequence.setPDBId(getAllPDBEntries());
setPDBId(null);
datasetSequence.updatePDBIds();
}
}
// transfer database references
- DBRefEntry[] entryRefs = entry.getDBRef();
+ DBRefEntry[] entryRefs = entry.getDBRefs();
if (entryRefs != null)
{
for (int r = 0; r < entryRefs.length; r++)