gov.nih.nci.caintegrator.ui.graphing.test.KaplanMeierGraphTester.java Source code

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Here is the source code for gov.nih.nci.caintegrator.ui.graphing.test.KaplanMeierGraphTester.java

Source

/*L
 *  Copyright SAIC
 *
 *  Distributed under the OSI-approved BSD 3-Clause License.
 *  See http://ncip.github.com/stats-analysis/LICENSE.txt for details.
 */

package gov.nih.nci.caintegrator.ui.graphing.test;

import gov.nih.nci.caintegrator.ui.graphing.chart.plot.KaplanMeierPlot;
import gov.nih.nci.caintegrator.ui.graphing.data.kaplanmeier.KaplanMeierPlotPointSeries;
import gov.nih.nci.caintegrator.ui.graphing.data.kaplanmeier.KaplanMeierPlotPointSeriesSet;
import java.awt.Color;
import java.util.ArrayList;
import java.util.Collection;
import org.jfree.chart.ChartPanel;
import org.jfree.chart.JFreeChart;
import org.jfree.ui.ApplicationFrame;
import org.jfree.ui.RefineryUtilities;

/**
* 
* 
*/

public class KaplanMeierGraphTester extends ApplicationFrame {

    public KaplanMeierGraphTester(String title) {
        super(title);
        Collection<KaplanMeierPlotPointSeriesSet> sets = new ArrayList<KaplanMeierPlotPointSeriesSet>();
        KaplanMeierPlotPointSeriesSet set1 = createKMPlotPointSeriesSet("Up Regulated", 10, .15);
        set1.setColor(Color.BLUE);
        sets.add(set1);

        KaplanMeierPlotPointSeriesSet set2 = createKMPlotPointSeriesSet("Down Regulated", 15, .25);
        set2.setColor(Color.RED);
        sets.add(set2);

        KaplanMeierPlotPointSeriesSet set3 = createKMPlotPointSeriesSet("Intermediate", 18, .07);
        set3.setColor(Color.GREEN);
        sets.add(set3);

        KaplanMeierPlot kmPlot = new KaplanMeierPlot(sets);
        JFreeChart chart = kmPlot.getKmChart();
        ChartPanel chartPanel = new ChartPanel(chart);
        chartPanel.setPreferredSize(new java.awt.Dimension(800, 600));
        setContentPane(chartPanel);
    }

    /**
     * Main Testing method
     * @param args
     */
    public static void main(String[] args) {

        KaplanMeierGraphTester demo = new KaplanMeierGraphTester("KaplanMeierAlgorithms Graph Test");
        demo.pack();
        RefineryUtilities.centerFrameOnScreen(demo);
        demo.setVisible(true);
    }

    private static KaplanMeierPlotPointSeriesSet createKMPlotPointSeriesSet(String setName, double xInterval,
            double yInterval) {
        KaplanMeierPlotPointSeries probabalitySeries = new KaplanMeierPlotPointSeries(setName, true);
        KaplanMeierPlotPointSeries censorSeries = new KaplanMeierPlotPointSeries(setName, true);
        double x = 0;
        double y = 1.0;
        boolean census = false;
        while (true) {
            if (!census) {
                probabalitySeries.add(x, y);
                x = x + xInterval;
                census = true;
            } else {
                if (y >= 0.0) {
                    probabalitySeries.add(x, y);
                    censorSeries.add(x, y);
                    y = y - yInterval;
                }
                census = false;
            }
            if (y <= 0) {
                break;
            }
        }
        KaplanMeierPlotPointSeriesSet theSet = new KaplanMeierPlotPointSeriesSet();
        theSet.setCensorPlotPoints(censorSeries);
        theSet.setProbabilityPlotPoints(probabalitySeries);
        return theSet;
    }
    /*
       private void generateSVG(JFreeChart chart) {
          // THE FOLLOWING CODE BASED ON THE EXAMPLE IN THE BATIK DOCUMENTATION...
          // Get a DOMImplementation
          DOMImplementation domImpl = GenericDOMImplementation
        .getDOMImplementation();
          // Create an instance of org.w3c.dom.Document
          Document document = domImpl.createDocument(null, "svg", null);
          // Create an instance of the SVG Generator
          SVGGraphics2D svgGenerator = new SVGGraphics2D(document);
          // Ask the chart to render into the SVG Graphics2D implementation
          chart.draw(svgGenerator, new Rectangle2D.Double(0, 0, 800, 600), null);
          // Finally, stream out SVG to a file using UTF-8 character to
          // byte encoding
          boolean useCSS = true;
          Writer out = null;
          try {
     out = new OutputStreamWriter(new FileOutputStream(new File(
           "/test.svg")), "UTF-8");
          } catch (UnsupportedEncodingException e) {
     // TODO Auto-generated catch block
     e.printStackTrace();
          } catch (FileNotFoundException e) {
     // TODO Auto-generated catch block
     e.printStackTrace();
          }
          try {
     svgGenerator.stream(out, useCSS);
          } catch (SVGGraphics2DIOException e) {
     // TODO Auto-generated catch block
     e.printStackTrace();
          }
    */

}