Java tutorial
/* * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard. All Rights Reserved. * * This software is licensed under the terms of the GNU Lesser General Public License (LGPL), * Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php. * * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR * WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING, * WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR * PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER * OR NOT DISCOVERABLE. IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE * TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES * OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES, * ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER * THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT * SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING. */ /* * Created by JFormDesigner on Sat Dec 04 19:26:01 EST 2010 */ package org.broad.igv.util.stats; import java.awt.*; import java.awt.event.*; import java.util.*; import java.util.List; import javax.swing.*; import javax.swing.border.*; import org.broad.igv.track.AttributeManager; import org.broad.igv.track.Track; import org.jfree.chart.ChartFactory; import org.jfree.chart.ChartPanel; import org.jfree.chart.JFreeChart; import org.jfree.chart.plot.PlotOrientation; import org.jfree.chart.plot.XYPlot; import org.jfree.chart.renderer.xy.XYStepRenderer; import org.jfree.data.xy.XYDataset; import org.jfree.data.xy.XYSeries; import org.jfree.data.xy.XYSeriesCollection; /** * @author jrobinso */ public class KMPlotFrame extends JFrame { Collection<Track> tracks; private XYPlot plot; // TODO -- control to set this int maxTime = 60; public KMPlotFrame(Collection<Track> tracks) { //setLocationRelativeTo(owner); this.tracks = tracks; initComponents(); XYDataset dataset = updateDataset(); JFreeChart chart = ChartFactory.createXYLineChart("", "Time", "Survival", dataset, PlotOrientation.VERTICAL, true, true, false); XYStepRenderer renderer = new XYStepRenderer(); plot = chart.getXYPlot(); plot.setRenderer(renderer); ChartPanel plotPanel = new ChartPanel(chart); contentPanel.add(plotPanel, BorderLayout.CENTER); censurColumnControl.addItem(""); //sampleColumnControl.addItem(""); survivalColumnControl.addItem(""); groupByControl.addItem(""); final List<String> allAttributes = AttributeManager.getInstance().getAttributeNames(); final List<String> groupableAttributes = AttributeManager.getInstance().getGroupableAttributes(); // Populate pulldowns, and make guesses for column names. String survivalColumn = null; String censureColumn = null; String sampleColumn = null; for (String key : allAttributes) { censurColumnControl.addItem(key); //sampleColumnControl.addItem(key); survivalColumnControl.addItem(key); String tmp = key.toLowerCase(); if (tmp.contains("survival") || tmp.contains("daystodeath")) survivalColumn = key; if (tmp.contains("censure")) censureColumn = key; if (tmp.contains("sample")) sampleColumn = key; } for (String key : groupableAttributes) { groupByControl.addItem(key); } if (survivalColumn != null) { survivalColumnControl.setSelectedItem(survivalColumn); } if (censureColumn != null) { censurColumnControl.setSelectedItem(censureColumn); } if (sampleColumn != null) { //sampleColumnControl.setSelectedItem(sampleColumn); } } private void closeButtonActionPerformed(ActionEvent e) { setVisible(false); } public XYDataset updateDataset() { XYSeriesCollection dataset = new XYSeriesCollection(); final String survivalColumn = (String) survivalColumnControl.getSelectedItem(); final String censureColumn = (String) censurColumnControl.getSelectedItem(); final String groupByColumn = (String) groupByControl.getSelectedItem(); if (survivalColumn != null) { ArrayList<DataPoint> dataPoints = new ArrayList(tracks.size()); HashSet<String> participants = new HashSet(); for (Track t : tracks) { try { // Get the participant (sample) attribute value for this track //final Object selectedItem = sampleColumnControl.getSelectedItem(); //if (selectedItem != null) { String participant = t.getSample(); // t.getAttributeValue(selectedItem.toString()); if (!participants.contains(participant)) { // Don't add same participant twice. participants.add(participant); // Get the survival time. String survivalString = t.getAttributeValue(survivalColumn); int survivalDays = Integer.parseInt(survivalString); int survival = survivalDays; // Is the patient censured at the end of the survival period? String censureString = censureColumn == null ? null : t.getAttributeValue(censureColumn); boolean censured = censureString != null && censureString.equals("1"); String group = groupByColumn == null ? null : t.getAttributeValue(groupByColumn); if (group == null) group = "<No value>"; dataPoints.add(new DataPoint(participant, survival, censured, group)); } else { // TODO -- check consistency of participant data } // } } catch (NumberFormatException e) { // Just skip } } // Segregate by group Map<String, ArrayList<DataPoint>> map = new HashMap(); for (DataPoint dp : dataPoints) { String g = dp.getGroup(); ArrayList<DataPoint> pts = map.get(g); if (pts == null) { pts = new ArrayList(); map.put(g, pts); } pts.add(dp); } //XYSeries series1; for (Map.Entry<String, ArrayList<DataPoint>> entry : map.entrySet()) { java.util.List<DataPoint> pts = entry.getValue(); Collections.sort(pts); int[] time = new int[pts.size()]; boolean[] censured = new boolean[pts.size()]; for (int i = 0; i < pts.size(); i++) { //int months = Math.max(1, pts.get(i).time / 30); // <= TODO -- HARDCODED MONTH DATE time[i] = pts.get(i).time; censured[i] = pts.get(i).censured; } java.util.List<KaplanMeierEstimator.Interval> controlIntervals = KaplanMeierEstimator.compute(time, censured); XYSeries series1 = new XYSeries(entry.getKey()); for (KaplanMeierEstimator.Interval interval : controlIntervals) { series1.add(interval.getEnd(), interval.getCumulativeSurvival()); } dataset.addSeries(series1); } } return dataset; } private void survivalColumnControlActionPerformed(ActionEvent e) { XYDataset dataset = updateDataset(); plot.setDataset(dataset); repaint(); } public static class DataPoint implements Comparable<DataPoint> { String participant; int time; boolean censured; private String group; DataPoint(String participant, int time, boolean censured, String group) { this.censured = censured; this.participant = participant; this.group = group; this.time = time; } public int compareTo(DataPoint dataPoint) { return time - dataPoint.time; } public String getGroup() { return group; } } private void initComponents() { // JFormDesigner - Component initialization - DO NOT MODIFY //GEN-BEGIN:initComponents // Generated using JFormDesigner non-commercial license dialogPane = new JPanel(); contentPanel = new JPanel(); panel1 = new JPanel(); panel2 = new JPanel(); label2 = new JLabel(); survivalColumnControl = new JComboBox(); panel3 = new JPanel(); label3 = new JLabel(); censurColumnControl = new JComboBox(); panel4 = new JPanel(); label4 = new JLabel(); groupByControl = new JComboBox(); //======== this ======== setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE); setTitle("Kaplan-Meier Plot"); Container contentPane = getContentPane(); contentPane.setLayout(new BorderLayout()); //======== dialogPane ======== { dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12)); dialogPane.setLayout(new BorderLayout()); //======== contentPanel ======== { contentPanel.setLayout(new BorderLayout()); //======== panel1 ======== { panel1.setAlignmentX(0.0F); panel1.setLayout(new BoxLayout(panel1, BoxLayout.Y_AXIS)); //======== panel2 ======== { panel2.setAlignmentX(1.0F); panel2.setLayout(null); //---- label2 ---- label2.setText("Survival column"); panel2.add(label2); label2.setBounds(new Rectangle(new Point(5, 10), label2.getPreferredSize())); //---- survivalColumnControl ---- survivalColumnControl.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { survivalColumnControlActionPerformed(e); } }); panel2.add(survivalColumnControl); survivalColumnControl.setBounds(120, 5, 235, survivalColumnControl.getPreferredSize().height); { // compute preferred size Dimension preferredSize = new Dimension(); for (int i = 0; i < panel2.getComponentCount(); i++) { Rectangle bounds = panel2.getComponent(i).getBounds(); preferredSize.width = Math.max(bounds.x + bounds.width, preferredSize.width); preferredSize.height = Math.max(bounds.y + bounds.height, preferredSize.height); } Insets insets = panel2.getInsets(); preferredSize.width += insets.right; preferredSize.height += insets.bottom; panel2.setMinimumSize(preferredSize); panel2.setPreferredSize(preferredSize); } } panel1.add(panel2); //======== panel3 ======== { panel3.setAlignmentX(1.0F); panel3.setLayout(null); //---- label3 ---- label3.setText("Censure column"); panel3.add(label3); label3.setBounds(new Rectangle(new Point(5, 10), label3.getPreferredSize())); //---- censurColumnControl ---- censurColumnControl.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { survivalColumnControlActionPerformed(e); } }); panel3.add(censurColumnControl); censurColumnControl.setBounds(120, 5, 235, censurColumnControl.getPreferredSize().height); { // compute preferred size Dimension preferredSize = new Dimension(); for (int i = 0; i < panel3.getComponentCount(); i++) { Rectangle bounds = panel3.getComponent(i).getBounds(); preferredSize.width = Math.max(bounds.x + bounds.width, preferredSize.width); preferredSize.height = Math.max(bounds.y + bounds.height, preferredSize.height); } Insets insets = panel3.getInsets(); preferredSize.width += insets.right; preferredSize.height += insets.bottom; panel3.setMinimumSize(preferredSize); panel3.setPreferredSize(preferredSize); } } panel1.add(panel3); //======== panel4 ======== { panel4.setAlignmentX(1.0F); panel4.setLayout(null); //---- label4 ---- label4.setText("Group by"); panel4.add(label4); label4.setBounds(new Rectangle(new Point(5, 10), label4.getPreferredSize())); //---- groupByControl ---- groupByControl.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { survivalColumnControlActionPerformed(e); } }); panel4.add(groupByControl); groupByControl.setBounds(120, 5, 235, groupByControl.getPreferredSize().height); { // compute preferred size Dimension preferredSize = new Dimension(); for (int i = 0; i < panel4.getComponentCount(); i++) { Rectangle bounds = panel4.getComponent(i).getBounds(); preferredSize.width = Math.max(bounds.x + bounds.width, preferredSize.width); preferredSize.height = Math.max(bounds.y + bounds.height, preferredSize.height); } Insets insets = panel4.getInsets(); preferredSize.width += insets.right; preferredSize.height += insets.bottom; panel4.setMinimumSize(preferredSize); panel4.setPreferredSize(preferredSize); } } panel1.add(panel4); } contentPanel.add(panel1, BorderLayout.NORTH); } dialogPane.add(contentPanel, BorderLayout.CENTER); } contentPane.add(dialogPane, BorderLayout.CENTER); setSize(565, 510); setLocationRelativeTo(getOwner()); // JFormDesigner - End of component initialization //GEN-END:initComponents } // JFormDesigner - Variables declaration - DO NOT MODIFY //GEN-BEGIN:variables // Generated using JFormDesigner non-commercial license private JPanel dialogPane; private JPanel contentPanel; private JPanel panel1; private JPanel panel2; private JLabel label2; private JComboBox survivalColumnControl; private JPanel panel3; private JLabel label3; private JComboBox censurColumnControl; private JPanel panel4; private JLabel label4; private JComboBox groupByControl; // JFormDesigner - End of variables declaration //GEN-END:variables }