/*
* #%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.overlapping.wizard;
import org.gitools.analysis.overlapping.OverlappingAnalysis;
import org.gitools.api.matrix.IMatrix;
import org.gitools.api.matrix.view.IMatrixView;
import org.gitools.api.resource.ResourceReference;
import org.gitools.ui.app.analysis.wizard.DataFilterPage;
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 org.gitools.utils.cutoffcmp.CutoffCmp;
public class OverlappingAnalysisWizard extends AnalysisWizard<OverlappingAnalysis> {
private DataFilterPage dataFilterPage;
private OverlappingAnalysisWizardPage overlappingPage;
private AnalysisDetailsPage analysisDetailsPage;
private IMatrixView data;
public OverlappingAnalysisWizard(IMatrixView data) {
super();
setTitle("Overlapping analysis");
setLogo(IconUtils.getImageIconResourceScaledByHeight(IconNames.LOGO_OVERLAPPING, 96));
setHelpContext("analysis_overlapping");
this.data = data;
}
@Override
public void addPages() {
// Data filters
dataFilterPage = new DataFilterPage();
dataFilterPage.setRowsFilterFileVisible(false);
dataFilterPage.setBinaryCutoffCmp(CutoffCmp.LT);
dataFilterPage.setBinaryCutoffValue(0.05);
dataFilterPage.setBinaryCutoffEnabled(true);
addPage(dataFilterPage);
// Overlapping parameters
overlappingPage = new OverlappingAnalysisWizardPage();
overlappingPage.setAttributes(data.getLayers());
addPage(overlappingPage);
// Analysis details
analysisDetailsPage = new AnalysisDetailsPage();
analysisDetailsPage.setAnalysisTitle("Overlapping");
addPage(analysisDetailsPage);
}
public OverlappingAnalysis createAnalysis() {
OverlappingAnalysis analysis = new OverlappingAnalysis();
analysis.setTitle(analysisDetailsPage.getAnalysisTitle());
analysis.setDescription(analysisDetailsPage.getAnalysisDescription());
analysis.setProperties(analysisDetailsPage.getAnalysisProperties());
analysis.setBinaryCutoffEnabled(dataFilterPage.isBinaryCutoffEnabled());
analysis.setBinaryCutoffCmp(dataFilterPage.getBinaryCutoffCmp());
analysis.setBinaryCutoffValue(dataFilterPage.getBinaryCutoffValue());
analysis.setAttributeName(overlappingPage.getAttributeName());
analysis.setReplaceNanValue(overlappingPage.isReplaceNanValuesEnabled() ? overlappingPage.getReplaceNanValue() : null);
analysis.setTransposeData(overlappingPage.isTransposeEnabled());
analysis.setSourceData(new ResourceReference<IMatrix>("source-data", data));
return analysis;
}
}