Java tutorial
/** * This file is part of Genevar (GENe Expression VARiation) * Copyright (C) 2013 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.mqtl.snp; import java.awt.BorderLayout; import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.util.ArrayList; import java.util.List; import java.util.Vector; import javax.swing.JButton; import javax.swing.JComboBox; import javax.swing.JLabel; import javax.swing.JOptionPane; import javax.swing.JScrollPane; import javax.swing.JTextArea; import javax.swing.SwingWorker; import org.jfree.chart.ChartPanel; import sanger.team16.common.business.dao.MatchedFeature; import sanger.team16.common.business.dao.Statistic; import sanger.team16.common.hbm.Algorithm; import sanger.team16.common.hbm.ModificationMapping; import sanger.team16.common.hbm.Study; import sanger.team16.common.hbm.Variation; import sanger.team16.common.hbm.Reference; import sanger.team16.common.xqtl.QTL; import sanger.team16.gui.genevar.Message; import sanger.team16.gui.genevar.SelectedIndex; import sanger.team16.gui.genevar.UI; import sanger.team16.gui.genevar.mqtl.MQTLAnalysisPane; import sanger.team16.gui.genevar.mqtl.MatchedFeatureTableModel; import sanger.team16.gui.jface.BaseJLabel; import sanger.team16.gui.jface.BaseJPane; import sanger.team16.gui.jface.BaseJTextField; 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/resources/software/genevar/ */ @SuppressWarnings("serial") public class CisMQTLSNPPane extends MQTLAnalysisPane implements ActionListener { private Study study; //TODO only in cis-SNP private JComboBox cbStudy, cbReference, cbDistance, cbPValue; private JTextArea taSNP; private JButton bSNPFile; private BaseJTextField tfSNPFile; private MatchedFeatureTableModel matchedFeatureTableModel; private BaseJTable matchedFeatureTable; private Vector<Algorithm> algorithms; private boolean isDefault = true; public CisMQTLSNPPane(UI ui) { super(ui); this.refresh(new SelectedIndex()); } public void refresh(SelectedIndex selectedIndex) { this.removeAll(); this.repaint(); this.setSubmitSNPPanel(selectedIndex); this.setBlankPanel(); this.setParameterPanel(selectedIndex, "2. Distance to SNP: "); this.setBlankPanel(); this.setResetSubmitPanel(this, " Run "); bReset.setVisible(true); // MUST HAVE!!! Together with CommonPane.setResetButton() } public void setSubmitSNPPanel(SelectedIndex selectedIndex) { BaseJPane panel = new BaseJPane("Query SNPs"); // ------------------ Panel p0 (start) ------------------ // BaseJPane p0 = new BaseJPane(); p0.add(new JLabel("1. Select a study: ")); cbStudy = new JComboBox(this.ui.getStudies("M")); cbStudy.setSelectedIndex(selectedIndex.studyIndex); cbStudy.addActionListener(this); p0.add(cbStudy); 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. Choose a reference: ")); this.study = (Study) cbStudy.getSelectedItem(); cbReference = new JComboBox( this.ui.getReferences(study.getGenotypeAssemblyId(), study.getMethylationPlatformId())); cbReference.setSelectedIndex(selectedIndex.referencesIndex); cbReference.addActionListener(this); p1.add(cbReference); p1.add(new JLabel(" ")); p1.setBaseSpringBoxTrailing(); panel.add(p1); // ------------------ Panel p1 (end) ------------------ // panel.add(new JLabel("")); /* ----------------- Panel p3 (start) ----------------- */ BaseJPane p3 = new BaseJPane(); p3.add(new JLabel("3. Enter rs ID(s): ")); taSNP = new JTextArea(selectedIndex.textArea1, 6, 1); p3.add(new JScrollPane(taSNP)); p3.add(new JLabel(" ")); p3.setBaseSpringBoxTrailing(); panel.add(p3); /* ----------------- Panel p3 (end) ----------------- */ // /* ----------------- Panel p4 (start) ----------------- */ BaseJPane p4 = new BaseJPane(); p4.add(new JLabel(" or read from a text file with list of SNPs: ")); tfSNPFile = new BaseJTextField(5, true, true); tfSNPFile.setText(""); p4.add(tfSNPFile); bSNPFile = new JButton("Browse..."); bSNPFile.addActionListener(this); p4.add(bSNPFile); p4.add(new JLabel(" ")); p4.setBaseSpringBoxTrailing(); panel.add(p4); /* ----------------- Panel p4 (end) ----------------- */ panel.add(new JLabel("")); panel.add(new JLabel("")); panel.add(this.setMatchedFeaturePanel()); panel.setBaseSpringGrid(1); this.add(panel); } private BaseJPane setMatchedFeaturePanel() { BaseJPane panel = new BaseJPane("Genotype-Methylation Pairs"); //Study study = (Study) cbStudy.getSelectedItem(); // ------------------ Panel p0 (start) ------------------ // BaseJPane p0 = new BaseJPane(); p0.add(new JLabel("Study: ")); p0.add(this.getJLabeledSelectedItem(cbStudy)); p0.setBaseSpringBoxTrailing(); panel.add(p0); // ------------------ Panel p0 (end) ------------------ // // ------------------ Panel p1 (start) ------------------ // List<MatchedFeature> matchedFeatures = this.getMatchedFeaturesGxM(study.getId()); this.matchedFeatureTableModel = new MatchedFeatureTableModel(matchedFeatures); this.matchedFeatureTable = matchedFeatureTableModel.getTable(); //TODO BaseJPane p1 = new BaseJPane(); p1.setLayout(new BorderLayout()); p1.add(matchedFeatureTable.getTableHeader(), BorderLayout.PAGE_START); p1.add(matchedFeatureTable, BorderLayout.CENTER); //p0.setBaseSpringGrid(1, 1); panel.add(p1); // ------------------ Panel p1 (end) ------------------ // panel.setBaseSpringGrid(1); return panel; } public void setParameterPanel(SelectedIndex selectedIndex, String distanceTo) { BaseJPane panel = new BaseJPane("Analysis Parameters"); // ------------------ Panel p0 (start) ------------------ // BaseJPane p0 = new BaseJPane(); algorithms = this.getQTLAlgorithms(study.getId(), "M"); p0.add(new JLabel("1. Correlation and regression: ")); cbStatistic = new JComboBox(Message.getStatistics(this.ui.getAddress())); if (isDefault) if (algorithms.size() != 0 && selectedIndex.studyIndex != 0) { this.setAlgorithms(algorithms); isDefault = false; } else { this.setNullAlgorithms(selectedIndex.statisticIndex); cbStatistic.removeItemAt(cbStatistic.getComponentCount()); //ADD 02/12/10 } else if (selectedIndex.statisticIndex == cbStatistic.getComponentCount()) this.setAlgorithms(algorithms); else this.setNullAlgorithms(selectedIndex.statisticIndex); 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(distanceTo)); cbDistance = new JComboBox(distances); //TODO cbDistance.setEditable(true); cbDistance.addActionListener(this); p1.add(cbDistance); p1.add(new BaseJLabel("(Editable, no greater than 100 kb)", Color.GREEN.darker())); p1.setBaseSpringBoxTrailing(); panel.add(p1); // ------------------ Panel p1 (end) ------------------ // panel.add(new JLabel("")); // ------------------ Panel p2 (start) ------------------ // BaseJPane p2 = new BaseJPane(); p2.add(new JLabel("3. P-value threshold: ")); cbPValue = new JComboBox(pValues); cbPValue.setSelectedIndex(2); cbPValue.setEditable(true); cbPValue.addActionListener(this); p2.add(cbPValue); p2.add(new BaseJLabel("(Editable)", Color.GREEN.darker())); p2.setBaseSpringBoxTrailing(); panel.add(p2); // ------------------ Panel p2 (end) ------------------ // panel.setBaseSpringGrid(1); this.add(panel); } public void actionPerformed(ActionEvent ae) { try { this.cisSNPPaneActionPerformed(ae); } catch (Exception e) { //ADD 19/11/10 this.showConnectionErrorMessage(e); } } private void cisSNPPaneActionPerformed(ActionEvent ae) { int studyIndex = cbStudy.getSelectedIndex(); int statisticIndex = cbStatistic.getSelectedIndex(); //SelectedIndex selectedIndex = new SelectedIndex(studyIndex, this.getStudyReferenceIndex(studyIndex), statisticIndex, taSNP.getText()); //CHANGE 07/12/11 dun know? only do it if ae.getSource() == cbStudy //int referenceIndex = cbReference.getSelectedIndex(); //TODO merge into SelectedIndex //int referenceId = ((Reference) cbReference.getSelectedItem()).getId(); //TODO if (ae.getSource() == cbStudy) { if (studyIndex == 0) this.refresh(new SelectedIndex()); else { //TODO //List<MatchedFeature> matchedFeatures = this.getMatchedFeatures(study.getId()); //this.matchedFeatureTable = new MatchedFeatureTableModel(matchedFeatures).getTable(); statisticIndex = 0; //ADD 02/12/10 this.refresh(new SelectedIndex(studyIndex, this.getStudyReferenceIndex(studyIndex), statisticIndex, taSNP.getText())); this.setSubmitButton(); } isDefault = true; //ADD 02/12/10 } else if (ae.getSource() == cbReference) { this.setSubmitButton(); // ADD 18/06/10 } else if (ae.getSource() == cbStatistic) { this.refresh(new SelectedIndex(studyIndex, this.getStudyReferenceIndex(studyIndex), statisticIndex, taSNP.getText())); this.setSubmitButton(); } else if (ae.getSource() == bReset) { this.refresh(new SelectedIndex()); } else if (ae.getSource() == bSNPFile) { this.ui.addChoosableFileFilter(Message.TXT); if (this.ui.showFileChooserOpenDialog(this.ui, null)) tfSNPFile.setText(this.ui.getFileChooserSelectedFile().getAbsolutePath()); } else if (ae.getSource() == bSubmit) { int distance = new Integer(((String) cbDistance.getSelectedItem()).replaceAll(",", "")); if (distance > 100000) JOptionPane.showMessageDialog(ui, "No greater than 100 kb", "Distance to SNP", JOptionPane.WARNING_MESSAGE); else new CisSNPPaneProgressBar().execute(); //bSubmit.setEnabled(false); } } private int getStudyReferenceIndex(int studyIndex) { //TODO Study study = (Study) cbStudy.getItemAt(studyIndex); String etal = ""; if (study.getName().contains("(")) etal = study.getName().split("\\(")[1].split("\\)")[0]; cbReference = new JComboBox( this.ui.getReferences(study.getGenotypeAssemblyId(), study.getMethylationPlatformId())); for (int i = 0; i < cbReference.getItemCount(); i++) if (((Reference) cbReference.getItemAt(i)).getName().contains(etal)) return i; return 0; } private void setSubmitButton() { //TODO if (matchedFeatureTable.getRowCount() == 0) this.bSubmit.setEnabled(false); else this.bSubmit.setEnabled(true); } /** * @author Tsun-Po Yang <tpy@sanger.ac.uk> * @link http://www.sanger.ac.uk/resources/software/genevar/ */ private class CisSNPPaneProgressBar extends SwingWorker<Object, Object> { private BaseProgressBar progressBar = new BaseProgressBar(ui); @Override protected Void doInBackground() { int assemblyId = ((Reference) cbReference.getSelectedItem()).getAssemblyId(); //TODO int referenceId = ((Reference) cbReference.getSelectedItem()).getId(); //TODO Statistic statistic = (Statistic) cbStatistic.getSelectedItem(); int statisticId = getStatisticId(statistic, cbAlgorithm); int distance = new Integer(((String) cbDistance.getSelectedItem()).replaceAll(",", "")); double threshold = getThreshold((String) cbPValue.getSelectedItem()); List<String> inputSNPs = getInputSNPs(taSNP.getText(), tfSNPFile.getText()); //!!!! try { for (int i = 0; i < inputSNPs.size(); i++) { String variationName = inputSNPs.get(i); Variation snp = getSNP(study.getId(), variationName); List<String> sigEQTLs = new ArrayList<String>(); //TODO globle? if (snp != null) { String chromosome = snp.getChromosome(); int position = snp.getPosition(); List<ModificationMapping> modificationMappings = getModificationMappingsWhereSNP( study.getMethylationPlatformId(), referenceId, snp, distance); RegionalLinePlot regionalLinePlot = createRegionalLinePlot(snp, modificationMappings, sigEQTLs, statisticId, threshold); ChartPanel reginalLinePanel = regionalLinePlot.getChartPanel(chromosome, position, distance, threshold); String treeNoteName = getTreeNoteName(snp.getName(), statistic, threshold, distance); ui.addToCurrentNode(treeNoteName, new CisMQTLSNPPane2(ui, snp, matchedFeatureTable, reginalLinePanel, modificationMappings, sigEQTLs, assemblyId, distance, statisticId, algorithms, treeNoteName)); } else ui.addToCurrentNode(variationName, new CisMQTLSNPPane2(ui, variationName)); } } catch (Exception e) { //ADD 19/11/10 showConnectionErrorMessage(e); } return null; } private RegionalLinePlot createRegionalLinePlot(Variation snp, List<ModificationMapping> modificationMappings, List<String> sigEQTLs, int statisticId, double threshold) { RegionalLinePlot regionalLinePlot = new RegionalLinePlot(); for (int i = 0; i < matchedFeatureTable.getRowCount(); i++) if (((Boolean) matchedFeatureTable.getValueAt(i, 0)).booleanValue()) { String populationName = (String) matchedFeatureTable.getValueAt(i, 1); MatchedFeature matchedFeature = (MatchedFeature) matchedFeatureTable.getValueAt(i, 4); //EQTLStats eqtlStats = new EQTLStats(ui.isServices(), ui.getAddress()); //int genotypeFeatureId = getGenotypeFeatureId(matchedFeature, snp); //ADD 08/12/11 List<QTL> eqtls = getMQTLsWhereSNP(matchedFeature, snp, modificationMappings, statisticId, threshold); if (eqtls != null && eqtls.size() != 0) { // BUG 20/10/10 sigEQTLs.addAll(this.getSigMQTLs(eqtls, threshold)); regionalLinePlot.addToDataset(populationName, eqtls); } } return regionalLinePlot; } @Override protected void done() { progressBar.dispose(ui); } private List<String> getSigMQTLs(List<QTL> mqtls, double threshold) { List<String> significants = new ArrayList<String>(); if (mqtls != null && mqtls.size() != 0) // BUG 20/10/10 for (int i = 0; i < mqtls.size(); i++) { QTL eqtl = mqtls.get(i); if (eqtl.nominalP <= threshold) significants.add(eqtl.modificationMapping.getProbeId()); } return significants; } } }