private void loadSampleToCaArraySampleMap() {
nameToCaArraySampleMap = new HashMap<String, Biomaterial>();
try {
List<Biomaterial> samples =
CaArrayUtils.getSamples(getGenomicSource().getExperimentIdentifier(), searchService);
for (Biomaterial biomaterial : samples) {
nameToCaArraySampleMap.put(biomaterial.getName(), biomaterial);
}
} catch (ExperimentNotFoundException e) {
throw new IllegalStateException("Couldn't retrieve valid experiment");
}
}
protected List<Hybridization> getHybridizations(Biomaterial caArraySample)
throws InvalidInputException {
HybridizationSearchCriteria criteria = new HybridizationSearchCriteria();
Set<CaArrayEntityReference> sourceSet = new HashSet<CaArrayEntityReference>();
sourceSet.add(caArraySample.getReference());
criteria.setBiomaterials(sourceSet);
return getSearchService().searchForHybridizations(criteria, null).getResults();
}
private void printBiomaterialDetails(Biomaterial biomaterial) {
// Print basic biomaterial attributes.
System.out.print(biomaterial.getName() + "\t");
System.out.print(biomaterial.getType() + "\t");
Term term = biomaterial.getTissueSite() == null ? null : biomaterial.getTissueSite().getTerm();
String termVal = term == null ? null : term.getValue();
System.out.print(termVal + "\t");
term = biomaterial.getDiseaseState() == null ? null : biomaterial.getDiseaseState().getTerm();
termVal = term == null ? null : term.getValue();
System.out.println(termVal);
}
