Java tutorial
/* * #%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.actions.data.analysis; import org.apache.commons.lang.StringUtils; import org.gitools.analysis.htest.enrichment.EnrichmentAnalysis; import org.gitools.api.analysis.IProgressMonitor; import org.gitools.api.matrix.IMatrix; import org.gitools.api.matrix.MatrixDimensionKey; import org.gitools.heatmap.Heatmap; import org.gitools.heatmap.HeatmapDimension; import org.gitools.heatmap.header.HeatmapColoredLabelsHeader; import org.gitools.ui.app.analysis.htest.editor.AbstractHtestAnalysisEditor; import org.gitools.ui.app.heatmap.editor.HeatmapEditor; import org.gitools.ui.core.Application; import org.gitools.ui.core.HeatmapPosition; import org.gitools.ui.core.actions.HeatmapAction; import org.gitools.ui.core.actions.dynamicactions.IHeatmapDimensionAction; import org.gitools.ui.core.components.editor.AbstractEditor; import org.gitools.ui.core.components.editor.EditorsPanel; import org.gitools.ui.platform.icons.IconNames; import org.gitools.ui.platform.progress.JobRunnable; import org.gitools.ui.platform.progress.JobThread; import java.awt.event.ActionEvent; import java.util.ArrayList; public class ViewEnrichmentModuleDataAction extends HeatmapAction implements IHeatmapDimensionAction { private String annotationValue; private HeatmapColoredLabelsHeader coloredHeader; private EnrichmentAnalysis analysis; private String moduleId; public ViewEnrichmentModuleDataAction() { super("<html><i>ViewEnrichmentModuleDataAction</i></html>"); setSmallIconFromResource(IconNames.view16); } @Override public void actionPerformed(ActionEvent e) { if (moduleId == null) { return; } JobThread.execute(Application.get(), new JobRunnable() { @Override public void run(IProgressMonitor monitor) throws Exception { IMatrix data = analysis.getData().get(); if (data instanceof Heatmap) { data = ((Heatmap) data).getContents(); } EditorsPanel epanel = Application.get().getEditorsPanel(); ArrayList moduleItems = new ArrayList(); moduleItems.addAll(analysis.getModuleMap().get().getMappingItems(moduleId)); HeatmapEditor heatmapEditor = getOpenInEditor(data); if (heatmapEditor != null) { epanel.setSelectedEditor(heatmapEditor); } else { monitor.begin("Creating new heatmap from data ...", 1); heatmapEditor = new HeatmapEditor(AbstractHtestAnalysisEditor.newDataHeatmap(analysis)); epanel.addEditor(heatmapEditor); heatmapEditor.setName(analysis.getTitle() + "-data"); } Heatmap dataHeatmap = heatmapEditor.getModel(); dataHeatmap.getRows().show(moduleItems); Application.get().showNotificationPermanent("Module '" + moduleId + "' shown."); } }); } public HeatmapEditor getOpenInEditor(IMatrix data) { EditorsPanel epanel = Application.get().getEditorsPanel(); for (AbstractEditor e : epanel.getEditors()) { if (e instanceof HeatmapEditor) { if (((Heatmap) e.getModel()).getContents() == data) { return (HeatmapEditor) e; } } } return null; } @Override public void onConfigure(HeatmapDimension dimension, HeatmapPosition position) { boolean enable = getHeatmap().getMetadata(EnrichmentAnalysis.CACHE_KEY_ENHRICHMENT) != null && dimension.getId().equals(MatrixDimensionKey.ROWS); setEnabled(enable); if (enable) { this.analysis = getHeatmap().getMetadata(EnrichmentAnalysis.CACHE_KEY_ENHRICHMENT); this.moduleId = dimension.getLabel(position.getRow()); } this.setName("<html><i>View</i> data for '" + StringUtils.abbreviate(moduleId, 25) + "' module</html>"); } }