Java tutorial
/* * Copyright (C) 2014 Kai Bernd Stadermann <kstaderm at cebitec.uni-bielefeld.de> * * 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/>. */ package de.cebitec.readXplorer.differentialExpression.plot; import de.cebitec.readXplorer.differentialExpression.DeAnalysisHandler; import de.cebitec.readXplorer.differentialExpression.DeSeqAnalysisHandler; import de.cebitec.readXplorer.differentialExpression.GnuR; import de.cebitec.readXplorer.differentialExpression.ResultDeAnalysis; import de.cebitec.readXplorer.plotting.ChartExporter; import static de.cebitec.readXplorer.plotting.ChartExporter.ChartExportStatus.FAILED; import static de.cebitec.readXplorer.plotting.ChartExporter.ChartExportStatus.FINISHED; import static de.cebitec.readXplorer.plotting.ChartExporter.ChartExportStatus.RUNNING; import de.cebitec.readXplorer.plotting.CreatePlots; import de.cebitec.readXplorer.util.Observer; import de.cebitec.readXplorer.util.fileChooser.ReadXplorerFileChooser; import de.cebitec.readXplorer.view.TopComponentExtended; import java.awt.BorderLayout; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.io.File; import java.io.IOException; import java.lang.reflect.InvocationTargetException; import java.nio.file.FileSystems; import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.StandardCopyOption; import java.sql.Timestamp; import java.util.Calendar; import java.util.Date; import java.util.logging.Level; import java.util.logging.Logger; import javax.swing.ComboBoxModel; import javax.swing.DefaultComboBoxModel; import javax.swing.JOptionPane; import javax.swing.SwingUtilities; import org.apache.batik.swing.JSVGCanvas; import org.apache.batik.swing.svg.SVGDocumentLoaderEvent; import org.apache.batik.swing.svg.SVGDocumentLoaderListener; import org.jfree.chart.ChartPanel; import org.netbeans.api.progress.ProgressHandle; import org.netbeans.api.progress.ProgressHandleFactory; import org.netbeans.api.settings.ConvertAsProperties; import org.openide.awt.ActionID; import org.openide.awt.ActionReference; import org.openide.util.NbBundle.Messages; import org.openide.windows.TopComponent; /** * TopComponent, which displays all graphics available for a DESeq analysis. */ @ConvertAsProperties(dtd = "-//de.cebitec.readXplorer.differentialExpression//DeSeqGraphics//EN", autostore = false) @TopComponent.Description(preferredID = "DeSeqGraphicsTopComponent", //iconBase="SET/PATH/TO/ICON/HERE", persistenceType = TopComponent.PERSISTENCE_NEVER) @TopComponent.Registration(mode = "bottomSlidingSide", openAtStartup = false) @ActionID(category = "Window", id = "de.cebitec.readXplorer.differentialExpression.DeSeqGraphicsTopComponent") @ActionReference(path = "Menu/Window" /*, position = 333 */) @TopComponent.OpenActionRegistration(displayName = "#CTL_DeSeqGraphicsAction", preferredID = "DeSeqGraphicsTopComponent") @Messages({ "CTL_DeSeqGraphicsAction=DeSeqGraphics", "CTL_DeSeqGraphicsTopComponent=DESeq Graphics", "HINT_DeSeqGraphicsTopComponent=This is a DESeq graphics window" }) public final class DeSeqGraphicsTopComponent extends TopComponentExtended implements Observer, ItemListener { private static final long serialVersionUID = 1L; private DeAnalysisHandler analysisHandler; private JSVGCanvas svgCanvas; private ChartPanel chartPanel; private ComboBoxModel cbm; private File currentlyDisplayed; private ResultDeAnalysis result; private boolean SVGCanvasActive; private ProgressHandle progressHandle = ProgressHandleFactory.createHandle("Creating plot"); private ProgressHandle svgExportProgressHandle; /** * TopComponent, which displays all graphics available for a DESeq analysis. */ public DeSeqGraphicsTopComponent() { } /** * TopComponent, which displays all graphics available for a DESeq analysis. * @param analysisHandler The analysis handler containing the results * @param usedTool The tool used for the analysis (has to be DESeq in this * case) */ public DeSeqGraphicsTopComponent(DeAnalysisHandler handler, boolean moreThanTwoConditions) { analysisHandler = handler; this.result = handler.getResults().get(0); cbm = new DefaultComboBoxModel(DeSeqAnalysisHandler.Plot.getValues(moreThanTwoConditions)); initComponents(); setupGraphics(); iSymbol.setVisible(false); iSymbol.setToolTipText(org.openide.util.NbBundle.getMessage(DeSeqGraphicsTopComponent.class, "GraphicsTopComponent.iSymbol.toolTipText")); } /** * This method is called from within the constructor to initialize the form. * WARNING: Do NOT modify this code. The content of this method is always * regenerated by the Form Editor. */ // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents private void initComponents() { jSplitPane1 = new javax.swing.JSplitPane(); optionsPanel = new javax.swing.JPanel(); iSymbol = new javax.swing.JLabel(); jScrollPane1 = new javax.swing.JScrollPane(); messages = new javax.swing.JTextArea(); saveButton = new javax.swing.JButton(); plotButton = new javax.swing.JButton(); plotType = new javax.swing.JComboBox(); jLabel1 = new javax.swing.JLabel(); plotPanel = new javax.swing.JPanel(); jScrollPane2 = new javax.swing.JScrollPane(); plotDescriptionArea = new javax.swing.JTextArea(); iSymbol.setHorizontalAlignment(javax.swing.SwingConstants.CENTER); iSymbol.setIcon(new javax.swing.ImageIcon( getClass().getResource("/de/cebitec/readXplorer/differentialExpression/plot/i.png"))); // NOI18N org.openide.awt.Mnemonics.setLocalizedText(iSymbol, org.openide.util.NbBundle .getMessage(DeSeqGraphicsTopComponent.class, "DeSeqGraphicsTopComponent.iSymbol.text_1")); // NOI18N jScrollPane1.setBorder(null); messages.setEditable(false); messages.setBackground(new java.awt.Color(240, 240, 240)); messages.setColumns(20); messages.setLineWrap(true); messages.setRows(5); messages.setWrapStyleWord(true); messages.setBorder(null); jScrollPane1.setViewportView(messages); org.openide.awt.Mnemonics.setLocalizedText(saveButton, org.openide.util.NbBundle .getMessage(DeSeqGraphicsTopComponent.class, "DeSeqGraphicsTopComponent.saveButton.text_1")); // NOI18N saveButton.setEnabled(false); saveButton.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { saveButtonActionPerformed(evt); } }); org.openide.awt.Mnemonics.setLocalizedText(plotButton, org.openide.util.NbBundle .getMessage(DeSeqGraphicsTopComponent.class, "DeSeqGraphicsTopComponent.plotButton.text_1")); // NOI18N plotButton.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { plotButtonActionPerformed(evt); } }); plotType.setModel(cbm); plotType.addItemListener(this); org.openide.awt.Mnemonics.setLocalizedText(jLabel1, org.openide.util.NbBundle .getMessage(DeSeqGraphicsTopComponent.class, "DeSeqGraphicsTopComponent.jLabel1.text_1")); // NOI18N javax.swing.GroupLayout optionsPanelLayout = new javax.swing.GroupLayout(optionsPanel); optionsPanel.setLayout(optionsPanelLayout); optionsPanelLayout.setHorizontalGroup(optionsPanelLayout .createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addGroup(optionsPanelLayout.createSequentialGroup().addContainerGap() .addGroup(optionsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addGroup(optionsPanelLayout.createSequentialGroup().addComponent(jLabel1) .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)) .addComponent(plotType, 0, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE) .addComponent(plotButton, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE) .addComponent(saveButton, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE) .addComponent(jScrollPane1, javax.swing.GroupLayout.PREFERRED_SIZE, 0, Short.MAX_VALUE))) .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, optionsPanelLayout.createSequentialGroup() .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE) .addComponent(iSymbol).addContainerGap())); optionsPanelLayout.setVerticalGroup(optionsPanelLayout .createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addGroup(optionsPanelLayout.createSequentialGroup().addContainerGap().addComponent(jLabel1) .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED) .addComponent(plotType, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE) .addGap(18, 18, 18).addComponent(plotButton) .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED) .addComponent(saveButton).addGap(18, 18, 18) .addComponent(jScrollPane1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE) .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 261, Short.MAX_VALUE) .addComponent(iSymbol).addContainerGap())); jSplitPane1.setLeftComponent(optionsPanel); plotPanel.setBorder(javax.swing.BorderFactory.createLineBorder(new java.awt.Color(0, 0, 0))); plotPanel.setLayout(new java.awt.BorderLayout()); plotDescriptionArea.setEditable(false); plotDescriptionArea.setBackground(new java.awt.Color(240, 240, 240)); plotDescriptionArea.setColumns(3); plotDescriptionArea.setFont(new java.awt.Font("Tahoma", 0, 11)); // NOI18N plotDescriptionArea.setLineWrap(true); plotDescriptionArea.setRows(3); plotDescriptionArea.setWrapStyleWord(true); plotDescriptionArea.setMaximumSize(new java.awt.Dimension(2147483647, 42)); plotDescriptionArea.setMinimumSize(new java.awt.Dimension(164, 42)); plotDescriptionArea.setPreferredSize(new java.awt.Dimension(164, 42)); jScrollPane2.setViewportView(plotDescriptionArea); plotPanel.add(jScrollPane2, java.awt.BorderLayout.PAGE_END); jSplitPane1.setRightComponent(plotPanel); javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this); this.setLayout(layout); layout.setHorizontalGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addComponent(jSplitPane1, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, 653, Short.MAX_VALUE)); layout.setVerticalGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addComponent(jSplitPane1, javax.swing.GroupLayout.Alignment.TRAILING)); }// </editor-fold>//GEN-END:initComponents private void plotButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_plotButtonActionPerformed try { messages.setText(""); plotButton.setEnabled(false); saveButton.setEnabled(false); DeSeqAnalysisHandler.Plot selectedPlot = (DeSeqAnalysisHandler.Plot) plotType.getSelectedItem(); if (selectedPlot == DeSeqAnalysisHandler.Plot.MAplot) { progressHandle.start(); progressHandle.switchToIndeterminate(); chartPanel = CreatePlots.createInfPlot( ConvertData.createMAvalues(result, DeAnalysisHandler.Tool.DeSeq, null, null), "A ((log(baseMeanA)/log(2)) + (log(baseMeanB)/log(2)))/2", "M (log(baseMeanA)/log(2)) - (log(baseMeanB)/log(2))", new ToolTip()); if (SVGCanvasActive) { plotPanel.remove(svgCanvas); SVGCanvasActive = false; } // plotDescriptionArea.setText("A (normalized mean expression (0.5 * log2 (baseMeanA * baseMeanB))) against M (log2 fold change)"); plotDescriptionArea.setVisible(false); plotPanel.add(chartPanel, BorderLayout.CENTER); plotPanel.repaint(); plotPanel.updateUI(); plotButton.setEnabled(true); saveButton.setEnabled(true); progressHandle.switchToDeterminate(100); progressHandle.finish(); } else { plotDescriptionArea.setVisible(true); if (!SVGCanvasActive) { plotPanel.remove(chartPanel); plotPanel.add(svgCanvas, BorderLayout.CENTER); plotPanel.updateUI(); SVGCanvasActive = true; } currentlyDisplayed = ((DeSeqAnalysisHandler) analysisHandler).plot(selectedPlot); svgCanvas.setURI(currentlyDisplayed.toURI().toString()); svgCanvas.setVisible(true); svgCanvas.repaint(); } plotDescriptionArea.repaint(); } catch (IOException ex) { Date currentTimestamp = new Timestamp(Calendar.getInstance().getTime().getTime()); Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, "{0}: " + ex.getMessage(), currentTimestamp); JOptionPane.showMessageDialog(null, "Can't create the temporary svg file!", "Gnu R Error", JOptionPane.WARNING_MESSAGE); } catch (GnuR.PackageNotLoadableException ex) { Date currentTimestamp = new Timestamp(Calendar.getInstance().getTime().getTime()); Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, "{0}: " + ex.getMessage(), currentTimestamp); JOptionPane.showMessageDialog(null, ex.getMessage(), "Gnu R Error", JOptionPane.WARNING_MESSAGE); } }//GEN-LAST:event_plotButtonActionPerformed private void saveButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_saveButtonActionPerformed ReadXplorerFileChooser fc = new ReadXplorerFileChooser(new String[] { "svg" }, "svg") { private static final long serialVersionUID = 1L; @Override public void save(String fileLocation) { ProgressHandle progressHandle = ProgressHandleFactory .createHandle("Save plot to svg file: " + fileLocation); Path to = FileSystems.getDefault().getPath(fileLocation, ""); DeSeqAnalysisHandler.Plot selectedPlot = (DeSeqAnalysisHandler.Plot) plotType.getSelectedItem(); if (selectedPlot == DeSeqAnalysisHandler.Plot.MAplot) { saveToSVG(fileLocation); } else { Path from = currentlyDisplayed.toPath(); try { Path outputFile = Files.copy(from, to, StandardCopyOption.REPLACE_EXISTING); messages.setText("SVG image saved to " + outputFile.toString()); } catch (IOException ex) { Date currentTimestamp = new Timestamp(Calendar.getInstance().getTime().getTime()); Logger.getLogger(this.getClass().getName()).log(Level.SEVERE, "{0}: " + ex.getMessage(), currentTimestamp); JOptionPane.showMessageDialog(null, ex.getMessage(), "Could not write to file.", JOptionPane.WARNING_MESSAGE); } finally { progressHandle.switchToDeterminate(100); progressHandle.finish(); } } } @Override public void open(String fileLocation) { } }; fc.openFileChooser(ReadXplorerFileChooser.SAVE_DIALOG); }//GEN-LAST:event_saveButtonActionPerformed // Variables declaration - do not modify//GEN-BEGIN:variables private javax.swing.JLabel iSymbol; private javax.swing.JLabel jLabel1; private javax.swing.JScrollPane jScrollPane1; private javax.swing.JScrollPane jScrollPane2; private javax.swing.JSplitPane jSplitPane1; private javax.swing.JTextArea messages; private javax.swing.JPanel optionsPanel; private javax.swing.JButton plotButton; private javax.swing.JTextArea plotDescriptionArea; private javax.swing.JPanel plotPanel; private javax.swing.JComboBox plotType; private javax.swing.JButton saveButton; // End of variables declaration//GEN-END:variables @Override public void componentOpened() { // TODO add custom code on component opening } @Override public void componentClosed() { analysisHandler.removeObserver(this); } void writeProperties(java.util.Properties p) { // better to version settings since initial version as advocated at // http://wiki.apidesign.org/wiki/PropertyFiles p.setProperty("version", "1.0"); // TODO store your settings } void readProperties(java.util.Properties p) { String version = p.getProperty("version"); // TODO read your settings according to their version } private void setupGraphics() { setName(Bundle.CTL_DeSeqGraphicsTopComponent()); setToolTipText(Bundle.HINT_DeSeqGraphicsTopComponent()); svgCanvas = new JSVGCanvas(); plotPanel.add(svgCanvas, BorderLayout.CENTER); SVGCanvasActive = true; svgCanvas.addSVGDocumentLoaderListener(new SVGDocumentLoaderListener() { @Override public void documentLoadingStarted(SVGDocumentLoaderEvent e) { progressHandle.start(); progressHandle.switchToIndeterminate(); } @Override public void documentLoadingCompleted(SVGDocumentLoaderEvent e) { progressHandle.switchToDeterminate(100); progressHandle.finish(); saveButton.setEnabled(true); plotButton.setEnabled(true); // DispEsts("Per gene estimates against normalized mean expression"), // DE("Log2 fold change against base means"), // HIST("Histogram of p values"), String description = ""; switch ((DeSeqAnalysisHandler.Plot) plotType.getSelectedItem()) { case DispEsts: description = "DESeq's dispersion estimates plot: Empirical (black dots) per gene and fitted (red line) dispersion values (Y) plotted against mean expression strength (X) (doubly logarithmic)"; break; case DE: description = "Normalized mean expression (A) against log2 fold change (M) = MA plot"; break; case HIST: description = "p-value histogram: Probability of genes not to be differentially expressed against its frequency in the experiment"; break; default: description = ""; } plotDescriptionArea.setText(description); plotDescriptionArea.repaint(); } @Override public void documentLoadingCancelled(SVGDocumentLoaderEvent e) { } @Override public void documentLoadingFailed(SVGDocumentLoaderEvent e) { messages.setText("Could not load SVG file. Please try again."); } }); } private void saveToSVG(String fileLocation) { svgExportProgressHandle = ProgressHandleFactory.createHandle("Save plot to svg file: " + fileLocation); Path to = FileSystems.getDefault().getPath(fileLocation, ""); ChartExporter exporter = new ChartExporter(to, chartPanel.getChart()); exporter.registerObserver(this); new Thread(exporter).start(); } @Override public void update(Object args) { if (args instanceof ChartExporter.ChartExportStatus) { final ChartExporter.ChartExportStatus status = (ChartExporter.ChartExportStatus) args; try { SwingUtilities.invokeAndWait(new Runnable() { @Override public void run() { switch (status) { case RUNNING: saveButton.setEnabled(false); svgExportProgressHandle.start(); svgExportProgressHandle.switchToIndeterminate(); break; case FAILED: messages.setText("The export of the plot failed."); case FINISHED: messages.setText("SVG image saved."); svgExportProgressHandle.switchToDeterminate(100); svgExportProgressHandle.finish(); break; } } }); } catch (InterruptedException | InvocationTargetException ex) { Date currentTimestamp = new Timestamp(Calendar.getInstance().getTime().getTime()); Logger.getLogger(this.getClass().getName()).log(Level.WARNING, ex.getMessage(), currentTimestamp); } } } @Override public void itemStateChanged(ItemEvent e) { DeSeqAnalysisHandler.Plot plotType = (DeSeqAnalysisHandler.Plot) e.getItem(); if (plotType == DeSeqAnalysisHandler.Plot.MAplot) { iSymbol.setVisible(true); } else { iSymbol.setVisible(false); } } }