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; }