/*
* #%L
* gitools-ui-app
* %%
* Copyright (C) 2013 Universitat Pompeu Fabra - Biomedical Genomics group
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
package org.gitools.ui.app.analysis.htest.wizard;
import org.gitools.analysis.htest.enrichment.EnrichmentAnalysis;
import org.gitools.api.matrix.IMatrix;
import org.gitools.api.matrix.view.IMatrixView;
import org.gitools.api.modulemap.IModuleMap;
import org.gitools.api.resource.IResourceFormat;
import org.gitools.api.resource.ResourceReference;
import org.gitools.matrix.geneset.GeneSetFormat;
import org.gitools.persistence.locators.UrlResourceLocator;
import org.gitools.ui.app.analysis.wizard.DataFilterPage;
import org.gitools.ui.app.analysis.wizard.ModulesPage;
import org.gitools.ui.core.components.wizard.AnalysisDetailsPage;
import org.gitools.ui.core.components.wizard.AnalysisWizard;
import org.gitools.ui.platform.IconUtils;
import org.gitools.ui.platform.icons.IconNames;
import java.io.File;
public class EnrichmentAnalysisWizard extends AnalysisWizard<EnrichmentAnalysis> {
private IMatrixView sourceData;
private DataFilterPage dataFilterPage;
private ModulesPage modulesPage;
private StatisticalTestPage statisticalTestPage;
private AnalysisDetailsPage analysisDetailsPage;
public EnrichmentAnalysisWizard(IMatrixView sourceData) {
super();
setTitle("Enrichment analysis");
setLogo(IconUtils.getImageIconResourceScaledByHeight(IconNames.LOGO_ENRICHMENT, 96));
setHelpContext("analysis_enrichment");
this.sourceData = sourceData;
}
@Override
public void addPages() {
// Modules
modulesPage = new ModulesPage();
addPage(modulesPage);
// Statistical test
statisticalTestPage = new StatisticalTestPage();
addPage(statisticalTestPage);
// Data filtering
dataFilterPage = new DataFilterPage();
dataFilterPage.setDiscardNonMappedRowsVisible(true);
addPage(dataFilterPage);
// Analysis details
analysisDetailsPage = new AnalysisDetailsPage();
analysisDetailsPage.setAnalysisTitle("Enrichment");
addPage(analysisDetailsPage);
}
@Override
public EnrichmentAnalysis createAnalysis() {
EnrichmentAnalysis analysis = new EnrichmentAnalysis();
// Details
analysis.setTitle(analysisDetailsPage.getAnalysisTitle());
analysis.setDescription(analysisDetailsPage.getAnalysisDescription());
analysis.setProperties(analysisDetailsPage.getAnalysisProperties());
// Source data
analysis.setLayer(sourceData.getLayers().getTopLayer().getId());
analysis.setData(new ResourceReference<IMatrix>("data", sourceData));
// Module map data
File file = modulesPage.getSelectedFile();
IResourceFormat<IModuleMap> format = modulesPage.getFileResourceFormat();
analysis.setModuleMap(new ResourceReference<>(new UrlResourceLocator(file), format));
// Test parameters
analysis.setTestConfig(statisticalTestPage.getTestConfig());
analysis.setBinaryCutoffEnabled(dataFilterPage.isBinaryCutoffEnabled());
if (dataFilterPage.isBinaryCutoffEnabled()) {
analysis.setBinaryCutoffCmp(dataFilterPage.getBinaryCutoffCmp());
analysis.setBinaryCutoffValue(dataFilterPage.getBinaryCutoffValue());
}
analysis.setDiscardNonMappedRows(dataFilterPage.isDiscardNonMappedRowsEnabled());
analysis.setMinModuleSize(modulesPage.getMinSize());
analysis.setMaxModuleSize(modulesPage.getMaxSize());
// Multiple test correction
analysis.setMtc(statisticalTestPage.getMtc());
// Population
File populationFile = dataFilterPage.getPopulationFile();
if (populationFile != null) {
analysis.setPopulation(new ResourceReference<>(new UrlResourceLocator(populationFile), new GeneSetFormat()));
analysis.setPopulationDefaultValue(dataFilterPage.getPopulationDefaultValue());
}
return analysis;
}
}