Examples with GenericResult org.baderlab.csplugins.enrichmentmap.model.GenericResult used on opensource projects

Example 6 with GenericResult

use of org.baderlab.csplugins.enrichmentmap.model.GenericResult in project EnrichmentMapApp by BaderLab.

the class CreateGMTEnrichmentMapTask method buildEnrichmentMap.

public void buildEnrichmentMap() {
    dataset.setMethod(Method.Generic);
    // in this case all the genesets are of interest
    dataset.setGeneSetsOfInterest(dataset.getSetOfGeneSets());
    Map<String, GeneSet> currentSets = dataset.getSetOfGeneSets().getGeneSets();
    // create an new Set of Enrichment Results                
    SetOfEnrichmentResults setOfEnrichments = new SetOfEnrichmentResults();
    Map<String, EnrichmentResult> currentEnrichments = setOfEnrichments.getEnrichments();
    // need also to put all genesets into enrichment results
    for (Iterator<String> i = currentSets.keySet().iterator(); i.hasNext(); ) {
        String geneset1Name = i.next();
        GeneSet gs = currentSets.get(geneset1Name);
        GenericResult tempResult = new GenericResult(gs.getName(), gs.getDescription(), 0.01, gs.getGenes().size());
        currentEnrichments.put(gs.getName(), tempResult);
    }
    dataset.setEnrichments(setOfEnrichments);
}