public static Collection<String> extractReportersFromGene(
Collection<GeneIdentifierDE> geneDEs, ArrayPlatformDE platform)
throws OperationNotSupportedException {
Collection<String> reporters = new ArrayList<String>();
Resultant resultant;
GeneIDCriteria geneIDCrit = new GeneIDCriteria();
geneIDCrit.setGeneIdentifiers(geneDEs);
GeneExpressionQuery geneExpressionQuery =
(GeneExpressionQuery) QueryManager.createQuery(QueryType.GENE_EXPR_QUERY_TYPE);
geneExpressionQuery.setQueryName("EXTRACT REPORTERS");
geneExpressionQuery.setAssociatedView(ViewFactory.newView(ViewType.GENE_GROUP_SAMPLE_VIEW));
geneExpressionQuery.setGeneIDCrit(geneIDCrit);
ArrayPlatformCriteria arrayPlatformCriteria = new ArrayPlatformCriteria();
arrayPlatformCriteria.setPlatform(platform);
geneExpressionQuery.setArrayPlatformCrit(arrayPlatformCriteria);
try {
CompoundQuery compoundQuery = new CompoundQuery(geneExpressionQuery);
resultant = ResultsetManager.executeCompoundQuery(compoundQuery);
} catch (Exception e) {
throw new OperationNotSupportedException(
"We are not able to extract Reporters " + e.getMessage());
}
if (resultant != null) {
reporters = extractReporters(resultant.getResultsContainer());
}
return reporters;
}
/**
* Overrides the protected Object.clone() method exposing it as public. It performs a 2 tier copy,
* that is, it does a memcopy of the instance and then sets all the non-primitive data fields to
* clones of themselves.
*
* @return -A minimum 2 deep copy of this object.
*/
public Object clone() {
GeneExpressionQuery myClone = null;
myClone = (GeneExpressionQuery) super.clone();
if (allGenesCrit != null) {
myClone.allGenesCrit = (AllGenesCriteria) allGenesCrit.clone();
}
if (arrayPlatformCriteria != null) {
myClone.arrayPlatformCriteria = (ArrayPlatformCriteria) arrayPlatformCriteria.clone();
}
if (cloneOrProbeIDCriteria != null) {
myClone.cloneOrProbeIDCriteria = (CloneOrProbeIDCriteria) cloneOrProbeIDCriteria.clone();
}
if (foldChgCrit != null) {
myClone.foldChgCrit = (FoldChangeCriteria) foldChgCrit.clone();
}
if (geneIDCrit != null) {
myClone.geneIDCrit = (GeneIDCriteria) geneIDCrit.clone();
}
if (geneOntologyCriteria != null) {
myClone.geneOntologyCriteria = (GeneOntologyCriteria) geneOntologyCriteria.clone();
}
if (pathwayCriteria != null) {
myClone.pathwayCriteria = (PathwayCriteria) pathwayCriteria.clone();
}
if (regionCrit != null) {
myClone.regionCrit = (RegionCriteria) regionCrit.clone();
}
return myClone;
}