Examples with GMTFileReaderTask org.baderlab.csplugins.enrichmentmap.parsers.GMTFileReaderTask used on opensource projects

Example 6 with GMTFileReaderTask

use of org.baderlab.csplugins.enrichmentmap.parsers.GMTFileReaderTask in project EnrichmentMapApp by BaderLab.

the class GeneSetSimilarityTest method before.

@Before
public void before(Provider<EnrichmentMapParameters> empFactory) throws Exception {
    //load Genesets from the gmt file associated with this test
    String testDataFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/model/Genesetstestfile.gmt";
    //create a new instance of the parameters
    EnrichmentMapParameters params = empFactory.get();
    //set gmt file name 
    params.getFiles().get(LegacySupport.DATASET1).setGMTFileName(testDataFileName);
    //Create a new Enrichment map
    map = new EnrichmentMap(params.getCreationParameters(), serviceRegistrar);
    Method method = EnrichmentMapParameters.stringToMethod(params.getMethod());
    DataSetFiles files = params.getFiles().get(LegacySupport.DATASET1);
    dataset = map.createDataSet(LegacySupport.DATASET1, method, files);
    //set up task
    GMTFileReaderTask task = new GMTFileReaderTask(dataset);
    task.run(taskMonitor);
    this.dataset.setGeneSetsOfInterest(this.dataset.getSetOfGeneSets());
}

Example 7 with GMTFileReaderTask

use of org.baderlab.csplugins.enrichmentmap.parsers.GMTFileReaderTask in project EnrichmentMapApp by BaderLab.

the class LoadSignatureGMTFilesTask method createTaskIterator.

@Override
public TaskIterator createTaskIterator() {
    TaskIterator tasks = new TaskIterator();
    String name = file.getName();
    if (name.toLowerCase().endsWith(FILE_EXT))
        name = name.substring(0, name.length() - FILE_EXT.length()).trim();
    // this is an out-paramter for GMTFileReaderTask and an in-parameter for FilterSignatureGSTask
    // MKTODO: find a better way to pass data from one task to another
    // doesn't this need to be made available to paParams?
    SetOfGeneSets setOfGeneSets = new SetOfGeneSets(name);
    tasks.append(new GMTFileReaderTask(map, file.getAbsolutePath(), setOfGeneSets));
    tasks.append(new FilterSignatureGSTask(map, setOfGeneSets, filterMetric));
    return tasks;
}