}
/**
- * DOCUMENT ME!
+ * Answers the sequence name, with '/start-end' appended if jvsuffix is true
*
- * @return DOCUMENT ME!
+ * @return
*/
@Override
public String getDisplayId(boolean jvsuffix)
{
- StringBuffer result = new StringBuffer(name);
- if (jvsuffix)
+ if (!jvsuffix)
{
- result.append("/" + start + "-" + end);
+ return name;
}
+ StringBuilder result = new StringBuilder(name);
+ result.append("/").append(start).append("-").append(end);
return result.toString();
}
public void setStart(int start)
{
this.start = start;
+ sequenceChanged();
}
/**
public void setGeneLoci(String speciesId, String assemblyId,
String chromosomeId, MapList map)
{
- addDBRef(new DBRefEntry(speciesId, assemblyId,
- DBRefEntry.CHROMOSOME + ":" + chromosomeId, new Mapping(map)));
+ addDBRef(new GeneLocus(speciesId, assemblyId, chromosomeId,
+ new Mapping(map)));
}
/**
{
for (final DBRefEntry ref : refs)
{
- if (ref.isChromosome())
+ if (ref instanceof GeneLociI)
{
- return new GeneLociI()
- {
- @Override
- public String getSpeciesId()
- {
- return ref.getSource();
- }
-
- @Override
- public String getAssemblyId()
- {
- // DEV NOTE: DBRefEntry is reused here to hold chromosomal locus
- // of a gene sequence.
- // source=species, version=assemblyId, accession=chromosome, map =
- // positions.
-
- return ref.getVersion();
- }
-
- @Override
- public String getChromosomeId()
- {
- // strip off "chromosome:" prefix to chrId
- return ref.getAccessionId()
- .substring(DBRefEntry.CHROMOSOME.length() + 1);
- }
-
- @Override
- public MapList getMap()
- {
- return ref.getMap().getMap();
- }
- };
+ return (GeneLociI) ref;
}
}
}
_isNa = Comparison.isNucleotide(this);
}
return !_isNa;
- };
+ }
/*
* (non-Javadoc)
List<SequenceFeature> result = getFeatures().findFeatures(startPos,
endPos, types);
- if (datasetSequence != null)
- {
- result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
- types);
- }
- else
- {
- result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
- }
/*
* if end column is gapped, endPos may be to the right,