/*
* #%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.plugins.mutex.ui;
import org.apache.velocity.VelocityContext;
import org.gitools.analysis.groupcomparison.GroupComparisonAnalysis;
import org.gitools.api.ApplicationContext;
import org.gitools.api.analysis.IProgressMonitor;
import org.gitools.api.matrix.IMatrix;
import org.gitools.api.resource.IResourceLocator;
import org.gitools.heatmap.Heatmap;
import org.gitools.heatmap.HeatmapDimension;
import org.gitools.heatmap.header.HeatmapHeader;
import org.gitools.plugins.mutex.analysis.MutualExclusiveAnalysis;
import org.gitools.plugins.mutex.analysis.MutualExclusiveAnalysisFormat;
import org.gitools.ui.core.Application;
import org.gitools.ui.core.components.editor.AnalysisEditor;
import org.gitools.ui.core.components.editor.EditorsPanel;
import org.gitools.ui.platform.progress.JobRunnable;
import org.gitools.ui.platform.progress.JobThread;
import javax.enterprise.context.ApplicationScoped;
import javax.swing.*;
import java.util.List;
import java.util.Map;
@ApplicationScoped
public class MutualExclusiveAnalysisEditor extends AnalysisEditor<MutualExclusiveAnalysis> {
public MutualExclusiveAnalysisEditor(MutualExclusiveAnalysis analysis) {
super(analysis, "/vm/analysis_details.vm", MutualExclusiveAnalysisFormat.EXTENSION);
setName(analysis.getTitle());
}
@Override
protected void prepareContext(VelocityContext context) {
MutualExclusiveAnalysis analysis = getModel();
IResourceLocator fileRef = analysis.getData().getLocator();
context.put("dataFile", fileRef != null ? fileRef.getName() : "Not defined");
/*
if (analysis.getMtc().equals("bh")) {
context.put("mtc", "Benjamini Hochberg FDR");
} else if (analysis.getMtc().equals("bonferroni")) {
context.put("mtc", "Bonferroni");
}
*/
if (analysis.getProperties().size() > 0) {
context.put("analysis.attributes", analysis.getProperties());
}
fileRef = analysis.getResults().getLocator();
context.put("resultsFile", fileRef != null ? fileRef.getName() : "Not defined");
fileRef = analysis.getLocator();
context.put("analysisLocation", fileRef != null ? fileRef.getURL() : "Not defined");
if (fileRef == null || fileRef.isWritable()) {
setSaveAllowed(true);
}
}
@Override
protected void performUrlAction(String name, Map<String, String> params) {
if ("NewDataHeatmap".equals(name)) {
newDataHeatmap();
} else if ("NewResultsHeatmap".equals(name)) {
newResultsHeatmap();
}
}
private void newDataHeatmap() {
final MutualExclusiveAnalysis analysis = getModel();
if (analysis.getData() == null) {
Application.get().showNotificationPermanent("Analysis doesn't contain data.");
return;
}
JobThread.execute(Application.get(), new JobRunnable() {
@Override
public void run(IProgressMonitor monitor) {
monitor.begin("Creating new heatmap from data ...", 1);
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
ApplicationContext.getEditorManger().addEditor(analysis.getData().get());
Application.get().showNotification("Data heatmap created.");
}
});
}
});
}
private void newResultsHeatmap() {
final MutualExclusiveAnalysis analysis = getModel();
if (analysis.getResults() == null) {
Application.get().showNotificationPermanent("Analysis doesn't contain results.");
return;
}
final Heatmap analysisResult = getModel().getResults().get();
final EditorsPanel editorPanel = Application.get().getEditorsPanel();
JobThread.execute(Application.get(), new JobRunnable() {
@Override
public void run(IProgressMonitor monitor) {
monitor.begin("Obtaining heatmap from results ...", 1);
analysisResult.setMetadata(MutualExclusiveAnalysis.CACHE_KEY_MUTEX_ANALYSIS, analysis);
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
ApplicationContext.getEditorManger().addEditor(analysisResult);
Application.get().showNotification("Heatmap for group comparison results created.");
}
});
}
});
}
@Deprecated
public static Heatmap createDataHeatmap(GroupComparisonAnalysis analysis) {
IMatrix data = analysis.getData().get();
if (Heatmap.class.isAssignableFrom(data.getClass())) {
return (Heatmap) data;
}
Heatmap heatmap = new Heatmap(data);
return heatmap;
}
@Deprecated
private Heatmap createResultsHeatmap(GroupComparisonAnalysis analysis) {
IMatrix results = analysis.getResults().get();
if (Heatmap.class.isAssignableFrom(results.getClass())) {
return (Heatmap) results;
}
Heatmap heatmap = new Heatmap(results);
return heatmap;
}
private void copyHeaders(HeatmapDimension dim, List<HeatmapHeader> headers) {
for (HeatmapHeader hh : headers) {
dim.addHeader(hh);
}
}
}