Java tutorial
/** * This file is part of Genevar (GENe Expression VARiation) * Copyright (C) 2010 Genome Research Ltd. * * Genevar is free software: you can redistribute it and/or modify * it under the terms of the GNU Lesser 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 Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package sanger.team16.gui.genevar.eqtl.snp; import java.awt.BorderLayout; import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.BufferedWriter; import java.io.FileWriter; import java.io.IOException; import java.util.List; import java.util.Vector; import javax.swing.Box; import javax.swing.JButton; import javax.swing.JComboBox; import javax.swing.JLabel; import javax.swing.JTable; import javax.swing.SwingWorker; import org.jfree.chart.ChartPanel; import sanger.team16.common.business.dao.Statistic; import sanger.team16.common.hbm.Algorithm; import sanger.team16.common.hbm.TranscriptMapping; import sanger.team16.common.hbm.Variation; import sanger.team16.gui.genevar.Message; import sanger.team16.gui.genevar.UI; import sanger.team16.gui.genevar.eqtl.EQTLAnalysisPane; import sanger.team16.gui.genevar.eqtl.TranscriptTableModel; import sanger.team16.gui.genevar.eqtl.query.EQTLQueryPane3; import sanger.team16.gui.jface.BaseJPane; import sanger.team16.gui.jface.BaseProgressBar; import sanger.team16.gui.jface.table.BaseJTable; /** * @author Tsun-Po Yang <tpy@sanger.ac.uk> * @link http://www.sanger.ac.uk/Teams/Team16/ */ @SuppressWarnings("serial") public class CisEQTLSNPPane2 extends EQTLAnalysisPane implements ActionListener { private JComboBox cbPermutation; private Variation snp; private BaseJTable matchedFeatureTable; private JTable transcriptTable; private List<String> significants; private int assemblyId, distanceToSNP; private String fileName; public CisEQTLSNPPane2(UI ui, Variation snp, BaseJTable matchedFeatureTable, ChartPanel regionalLinePlot, List<TranscriptMapping> transcriptMappings, List<String> significants, int assemblyId, int distanceToSNP, int statisticId, Vector<Algorithm> algorithms, String fileName) { super(ui); this.assemblyId = assemblyId; this.snp = snp; this.matchedFeatureTable = matchedFeatureTable; this.transcriptTable = new TranscriptTableModel(false, transcriptMappings).getSortedTable(); //TODO this.significants = significants; this.distanceToSNP = distanceToSNP; this.fileName = fileName; this.setTranscriptPanel(snp.getName(), regionalLinePlot); this.setBlankPanel(); this.setParameterPanel(statisticId, algorithms); this.setBlankPanel(); this.setRemoveSubmitPanel(this, " SNP-Gene Association Plot "); //TODO if (Statistic.isExternalAlgorithm(statisticId)) { cbStatistic.setEnabled(false); //TODO cbAlgorithm.setEnabled(false); //TODO cbPermutation.setEnabled(false); //TODO bSubmit.setEnabled(false); //TODO } } public CisEQTLSNPPane2(UI ui, String variationName) { super(ui); this.setErrorPanel(variationName); this.setBlankPanel(); this.setRemovePanel(this); } private void setTranscriptPanel(String variationName, ChartPanel regionalLinePlot) throws ArrayIndexOutOfBoundsException { BaseJPane panel = new BaseJPane(variationName, 10, 20, 10, 20); // ------------------ Panel p0 (start) ------------------ // BaseJPane p0 = new BaseJPane(); p0.add(regionalLinePlot); //p0.setBaseSpringBoxTrailing(); panel.add(p0); // ------------------ Panel p0 (end) ------------------ // panel.add(new JLabel("")); panel.add(new JLabel("")); panel.add(new JLabel("")); // ------------------ Panel p1 (start) ------------------ // BaseJPane p1 = new BaseJPane(); JButton bSelectAll = new JButton(" Deselect All "); JButton bExport = new JButton(" Export List "); CisSNPPane2Listener cisSNP2Listener = new CisSNPPane2Listener(bSelectAll, bExport); //bSelectAll.setForeground(new Color(34,139,34)); bSelectAll.setForeground(Color.GREEN.darker()); bSelectAll.addActionListener(cisSNP2Listener); p1.add(bSelectAll); bExport.addActionListener(cisSNP2Listener); p1.add(bExport); p1.add(Box.createHorizontalGlue()); this.setLinkToPanel(p1, assemblyId, snp.getChromosome(), snp.getPosition(), distanceToSNP); p1.setBaseSpringBox(); panel.add(p1); // ------------------ Panel p1 (end) ------------------ // // ------------------ Panel p2 (start) ------------------ // //BaseJTable transcriptTable = this.transcriptTable.getSortedTable(); //TODO if (transcriptTable.isEnabled()) { bSelectAll.setEnabled(false); bExport.setEnabled(false); } this.setTranscriptTable(); BaseJPane p2 = new BaseJPane(); p2.setLayout(new BorderLayout()); p2.add(transcriptTable.getTableHeader(), BorderLayout.PAGE_START); p2.add(transcriptTable, BorderLayout.CENTER); //p0.setBaseSpringGrid(1, 1); panel.add(p2); // ------------------ Panel p2 (end) ------------------ // panel.add(new JLabel(" (Use CTRL+C to copy genes of interest)")); panel.setBaseSpringGrid(1); this.add(panel); } private void setTranscriptTable() { if (significants != null && significants.size() != 0) // BUG 20/10/10 for (int i = 0; i < significants.size(); i++) { int row = transcriptTable.getRowCount(); for (int j = 0; j < row; j++) if (((String) transcriptTable.getValueAt(j, 1)).equals(significants.get(i))) transcriptTable.setValueAt(true, j, 0); } } public void setParameterPanel(int statisticId, Vector<Algorithm> algorithms) { BaseJPane panel = new BaseJPane("Analysis Parameters", 10, 20, 10, 20); // ------------------ Panel p0 (start) ----------------- */ BaseJPane p0 = new BaseJPane(); p0.add(new JLabel("1. Correlation and regression: ")); cbStatistic = new JComboBox(Message.getStatistics(this.ui.getAddress())); if (!Statistic.isExternalAlgorithm(statisticId)) { this.setNullAlgorithms(Statistic.getStatisticIndex(statisticId)); cbStatistic.removeItemAt(2); } else this.setAlgorithms(algorithms); cbStatistic.addActionListener(this); p0.add(cbStatistic); p0.add(cbAlgorithm); p0.add(new JLabel(" ")); p0.setBaseSpringBoxTrailing(); panel.add(p0); // ------------------ Panel p0 (end) ----------------- */ panel.add(new JLabel("")); // ------------------ Panel p1 (start) ----------------- */ BaseJPane p1 = new BaseJPane(); p1.add(new JLabel("2. Number of permutations: ")); cbPermutation = new JComboBox(permutations); cbPermutation.setSelectedIndex(1); cbPermutation.addActionListener(this); p1.add(cbPermutation); p1.add(new JLabel(" ")); p1.setBaseSpringBoxTrailing(); panel.add(p1); // ------------------ Panel p1 (end) ----------------- */ panel.setBaseSpringGrid(1); this.add(panel); } public void actionPerformed(ActionEvent ae) { try { this.cisSNPPane2ActionPerformed(ae); } catch (Exception e) { //ADD 19/11/10 this.showConnectionErrorMessage(e); } } private void cisSNPPane2ActionPerformed(ActionEvent e) { if (e.getSource() == bRemove) this.ui.removeCurrentNode(); else if (e.getSource() == bSubmit) new CisSNPPane2ProgressBar().execute(); } /** * @author Tsun-Po Yang <tpy@sanger.ac.uk> * @link http://www.sanger.ac.uk/Teams/Team16/ */ private class CisSNPPane2Listener implements ActionListener { //private UI ui; //BUG 07/02/11 private JButton bSelectAll, bExport; private boolean isSelectAll = false; public CisSNPPane2Listener(JButton bSelectAll, JButton bExport) { //this.ui = ui; this.bSelectAll = bSelectAll; this.bExport = bExport; } public void actionPerformed(ActionEvent ae) { if (ae.getSource() == bSelectAll) { int row = transcriptTable.getRowCount(); for (int i = 0; i < row; i++) transcriptTable.setValueAt(this.isSelectAll, i, 0); if (this.isSelectAll) { this.bSelectAll.setText(" Deselect All "); this.isSelectAll = false; } else { this.bSelectAll.setText(" Select All "); this.isSelectAll = true; } } else if (ae.getSource() == bExport) { ui.showFileChooserSaveDialog(ui, fileName + ".txt"); int col = transcriptTable.getColumnCount(); int row = transcriptTable.getRowCount(); try { BufferedWriter out = new BufferedWriter(new FileWriter(ui.getFileChooserSelectedFile())); for (int i = 1; i < col - 1; i++) out.write((String) transcriptTable.getColumnName(i) + "\t"); out.write((String) transcriptTable.getColumnName(col - 1) + "\n"); for (int j = 0; j < row; j++) if ((Boolean) transcriptTable.getValueAt(j, 0)) { out.write(transcriptTable.getValueAt(j, 1) + "\t"); out.write(transcriptTable.getValueAt(j, 2) + "\t"); out.write(transcriptTable.getValueAt(j, 3) + "\t"); out.write(transcriptTable.getValueAt(j, 4) + "\t"); out.write(transcriptTable.getValueAt(j, 5) + "\t"); out.write(transcriptTable.getValueAt(j, 6) + "\t"); out.write(transcriptTable.getValueAt(j, 7) + "\t"); out.write(transcriptTable.getValueAt(j, 8) + "\n"); } out.close(); } catch (IOException ex) { } } } } /** * @author Tsun-Po Yang <tpy@sanger.ac.uk> * @link http://www.sanger.ac.uk/Teams/Team16/ */ private class CisSNPPane2ProgressBar extends SwingWorker<Object, Object> { private BaseProgressBar progressBar = new BaseProgressBar(ui); @Override protected Void doInBackground() { //int statistic = cbStatistic.getSelectedIndex(); //BUG FIED 016/06/10 Statistic statistic = (Statistic) cbStatistic.getSelectedItem(); int permutation = 0; if (cbPermutation.getSelectedIndex() != 0) permutation = new Integer(((String) cbPermutation.getSelectedItem()).replaceAll(",", "")); try { for (int i = 0; i < transcriptTable.getRowCount(); i++) if (((Boolean) transcriptTable.getValueAt(i, 0)).booleanValue()) { TranscriptMapping transcriptMapping = (TranscriptMapping) transcriptTable.getValueAt(i, 9); //TODO String probeId = transcriptMapping.getProbeId(); String ensemblGene = transcriptMapping.getEnsemblGene(); String geneSymbol = transcriptMapping.getGeneSymbol(); int transcriptId = transcriptMapping.getTranscriptId(); String title = snp.getName() + " / " + probeId + " / " + ensemblGene + " / " + geneSymbol; String description = probeId; description += " (" + statistic.abbreviation; //TODO if (permutation != 0) description += ", FDR"; description += ")"; ui.addToCurrentNode(description, new EQTLQueryPane3(ui, title, matchedFeatureTable, snp, transcriptId, statistic.getId(), permutation)); } } catch (Exception e) { //ADD 19/11/10 showConnectionErrorMessage(e); } return null; } @Override protected void done() { progressBar.dispose(ui); } } }