{
char[] oseq = seq.getSequence();
initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
- seq.getStart(),
- seq.getEnd());
+ seq.getStart(), seq.getEnd());
}
description = seq.getDescription();
if (seq != datasetSequence)
}
}
-
@Override
public void setSequenceFeatures(SequenceFeature[] features)
{
}
@Override
- public synchronized void addSequenceFeature(SequenceFeature sf)
+ public synchronized boolean addSequenceFeature(SequenceFeature sf)
{
- if (sequenceFeatures==null && datasetSequence != null)
+ if (sequenceFeatures == null && datasetSequence != null)
{
- datasetSequence.addSequenceFeature(sf);
- return;
+ return datasetSequence.addSequenceFeature(sf);
}
if (sequenceFeatures == null)
{
{
if (sequenceFeatures[i].equals(sf))
{
- return;
+ return false;
}
}
temp[sequenceFeatures.length] = sf;
sequenceFeatures = temp;
+ return true;
}
@Override
{
if (sequenceFeatures == null)
{
- if (datasetSequence!=null) {
- datasetSequence.deleteFeature(sf);
+ if (datasetSequence != null)
+ {
+ datasetSequence.deleteFeature(sf);
}
return;
}
@Override
public SequenceI deriveSequence()
{
- Sequence seq=null;
+ Sequence seq = null;
if (datasetSequence == null)
{
if (isValidDatasetSequence())
else
{
// Create a new, valid dataset sequence
- createDatasetSequence();
+ createDatasetSequence();
}
}
return new Sequence(this);
dsseq.setDescription(description);
// move features and database references onto dataset sequence
dsseq.sequenceFeatures = sequenceFeatures;
- sequenceFeatures=null;
+ sequenceFeatures = null;
dsseq.dbrefs = dbrefs;
- dbrefs=null;
+ dbrefs = null;
// TODO: search and replace any references to this sequence with
// references to the dataset sequence in Mappings on dbref
dsseq.pdbIds = pdbIds;
return null;
}
-
@Override
public List<DBRefEntry> getPrimaryDBRefs()
{
- if (datasetSequence!=null)
+ if (datasetSequence != null)
{
return datasetSequence.getPrimaryDBRefs();
}
- if (dbrefs==null || dbrefs.length==0)
+ if (dbrefs == null || dbrefs.length == 0)
{
return Collections.emptyList();
}