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

Example 11 with EnrichmentMapParameters

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

the class FileReaderTest method testExpression1ReaderCommentLines.

@Test
public void testExpression1ReaderCommentLines(Provider<EnrichmentMapParameters> empFactory) throws Exception {
    //load the test expression file
    String testDataFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/Expressiontestfile_comments.gct";
    //create a new instance of the parameters
    EnrichmentMapParameters params = empFactory.get();
    //set gmt file name 
    params.getFiles().get(LegacySupport.DATASET1).setExpressionFileName(testDataFileName);
    //Create a new Enrichment map
    EnrichmentMap map = new EnrichmentMap(params.getCreationParameters(), serviceRegistrar);
    //get the default dataset
    Method method = EnrichmentMapParameters.stringToMethod(params.getMethod());
    DataSetFiles files = params.getFiles().get(LegacySupport.DATASET1);
    EMDataSet dataset = map.createDataSet(LegacySupport.DATASET1, method, files);
    //make sure that the genes are empty
    assertEquals(0, map.getNumberOfGenes());
    //add the gene to the master list of genes
    map.addGene("GLS");
    map.addGene("PSMA1");
    map.addGene("ZP1");
    map.addGene("ZYX");
    //make sure all four genes have been associated
    assertEquals(4, map.getNumberOfGenes());
    //load expression file
    ExpressionFileReaderTask task = new ExpressionFileReaderTask(dataset);
    task.run(taskMonitor);
    //There was one more gene in the expression file that wasn't in the set of genes
    //make sure it was was added
    assertEquals(4, map.getNumberOfGenes());
    assertEquals(5.131481026, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getMaxExpression(), 0.0);
    assertEquals(4, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getNumGenes());
    assertEquals(59, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getNumConditions());
    assertEquals(0.008720342, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getMinExpression(), 0.0);
}