private Map<String, Hybridization> getIdToHybridizationMap() throws InvalidInputException {
if (idToHybridizationMap == null) {
idToHybridizationMap = new HashMap<String, Hybridization>();
for (Hybridization hybridization : getAllHybridizations()) {
idToHybridizationMap.put(hybridization.getId(), hybridization);
}
}
return idToHybridizationMap;
}
protected DataSetRequest createRequest() throws InvalidInputException {
DataSetRequest request = new DataSetRequest();
for (Hybridization hybridization : getAllHybridizations()) {
if (getGenomicSource().getPlatformName().equals(hybridization.getArrayDesign().getName())) {
request.getHybridizations().add(hybridization.getReference());
}
}
if (request.getHybridizations().isEmpty()) {
throw new InvalidInputException(
"No caArray data found with Array Design: " + getGenomicSource().getPlatformName());
}
request.getQuantitationTypes().add(getSignal(request).getReference());
return request;
}
protected Platform getPlatform(Hybridization hybridization) throws DataRetrievalException {
ArrayDesign arrayDesign = hybridization.getArrayDesign();
if (arrayDesign == null) {
throw new DataRetrievalException(
"There is no array design associated with the array for the hybridization "
+ hybridization.getName()
+ ", unable to load array data");
}
Platform platform = getDao().getPlatform(arrayDesign.getName());
if (platform == null) {
throw new DataRetrievalException(
"The platform named " + arrayDesign.getName() + " hasn't been loaded into the system");
}
return platform;
}
protected Sample getAssociatedSample(Hybridization hybridization) throws InvalidInputException {
return getHybridizationToSampleMap().get(getIdToHybridizationMap().get(hybridization.getId()));
}
