/**
* Constructor
*
* @param writer ItemWriter
* @param seqClsName The class of the coordinate system for this GFF3 file (generally Chromosome)
* @param orgTaxonId The taxon ID of the organism we are loading
* @param dataSourceName name for dataSource
* @param dataSetTitle title for dataSet
* @param tgtModel the model to create items in
* @param handler object to perform optional additional operations per GFF3 line
* @param sequenceHandler the GFF3SeqHandler use to create sequence Items
* @throws ObjectStoreException if something goes wrong
*/
public GFF3Converter(
ItemWriter writer,
String seqClsName,
String orgTaxonId,
String dataSourceName,
String dataSetTitle,
Model tgtModel,
GFF3RecordHandler handler,
GFF3SeqHandler sequenceHandler)
throws ObjectStoreException {
super(writer, tgtModel);
this.seqClsName = seqClsName;
this.orgTaxonId = orgTaxonId;
this.tgtModel = tgtModel;
this.handler = handler;
this.sequenceHandler = sequenceHandler;
organism = getOrganism();
dataSource = getDataSourceItem(dataSourceName);
dataSet = getDataSetItem(dataSetTitle, null, null, dataSource);
if (sequenceHandler == null) {
this.sequenceHandler = new GFF3SeqHandler();
}
setStoreHook(
new BioStoreHook(
tgtModel,
dataSet.getIdentifier(),
dataSource.getIdentifier(),
BioConverterUtil.getOntology(this)));
handler.setConverter(this);
handler.setIdentifierMap(identifierMap);
handler.setOrganism(organism);
readConfig();
}
