Java Experiment.getArrayDesigns方法代码示例

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
/**
 * @return true if this experiment's design provider is not Affy (not beed to do more validations).
 */
private boolean checkArrayDesigns(List<String> errors, Experiment experiment) {
    if (experiment.getArrayDesigns().isEmpty()) {
        errors.add("No (" + AFFYMETRIX_PROVIDER + ") array design specified");
        return true;
    }
    for (final ArrayDesign ad : experiment.getArrayDesigns()) {
        // * The array provider should be Affymetrix.
        if (!AFFYMETRIX_PROVIDER.equals(ad.getProvider().getName())) {
            errors.add(AFFYMETRIX_PROVIDER + " is not the provider for array design " + ad.getName());
        }
        if (!errors.isEmpty()) {
            return true;
        }
        // * All array designs associated with the experiment must be ones for which the System has the GEO
        // accession.
        if (StringUtils.isBlank(ad.getGeoAccession())) {
            errors.add("Array design " + ad.getName() + " has no GEO accession");
        }
    }
    return false;
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private void lookupExperiments(CaArraySearchService service, DataRetrievalRequest request, String expId) {
      ArrayDesign ad = null;

// Locate each experiment, and add its hybridizations to the request.
Experiment exampleExperiment = new Experiment();

exampleExperiment.setPublicIdentifier(expId);
List<Experiment> experimentList = service.search(exampleExperiment);

Experiment exp = experimentList.iterator().next();

// TODO: For now assume it's just one experiment
experiment = exp;
Set<ArrayDesign> arrDesigns = exp.getArrayDesigns();
ad = arrDesigns.iterator().next();
Set<Hybridization> allHybs = getAllHybridizations(experimentList);
request.getHybridizations().addAll(allHybs);

arrayDesignName = ad.getName();
System.out.println("****Array desing name = " + ad.getName());
  }
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private ArrayDesign findArrayDesignFromExperiment(Experiment experiment) {
    final Set<ArrayDesign> experimentDesigns = experiment.getArrayDesigns();
    if (experimentDesigns.size() == 1) {
        return experimentDesigns.iterator().next();
    }
    return null;
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
/**
	 * Retrieve list of experiments with samples. No need to show experiments with no samples
	 * since they do not have data.
	 * 
	 * @param service
	 * @return
	 * @throws Exception
	 */
	public Collection<Experiment> getExperimentsWithSamples() throws Exception{
      
        Experiment exampleExperiment = new Experiment();
        searchService = server.getSearchService();
        List<Experiment> experimentList = searchService.search(exampleExperiment);
        List<Experiment> expListWithSamples = new ArrayList<Experiment>(); 
        
        // remove experiments that do not have samples
        for (Experiment e : experimentList){
        	int sampleCnt = e.getSampleCount();
        	
            
        	if (sampleCnt > 0){
        		// check if experiment array design is the one we support
        		Set<ArrayDesign> arrDesigns = e.getArrayDesigns();
        		if (arrDesigns.isEmpty() || arrDesigns == null)
        			continue;
        		ArrayDesign ad = arrDesigns.iterator().next();
        		
        		if (SupportedArrayDesigns.isSupported(ad.getName()))
        			expListWithSamples.add(e);
        	}	
        }
                            
        return expListWithSamples;
    
}