Examples with XYTextAnnotation org.jfree.chart.annotations.XYTextAnnotation used on opensource projects

Example 1 with XYTextAnnotation

use of org.jfree.chart.annotations.XYTextAnnotation in project polyGembler by c-zhou.

the class JfreeChart method plotLineChart.

private void plotLineChart(String file_in, Dimension dim, Color color, String position, String title) {
    JPanel collinearChart = new JPanel();
    collinearChart.setSize(dim);
    collinearChart.setMinimumSize(dim);
    collinearChart.setPreferredSize(dim);
    collinearChart.setBackground(color);
    final XYSeriesCollection lineSeries = new XYSeriesCollection();
    int n1 = 0;
    double x_max = Double.NEGATIVE_INFINITY, y_max = Double.NEGATIVE_INFINITY;
    try {
        BufferedReader br = Utils.getBufferedReader(file_in);
        String line = br.readLine();
        String[] s;
        int series = 0;
        while ((line = br.readLine()) != null && line.length() > 0) {
            s = line.split("\\s+");
            series = Integer.parseInt(s[2]);
            if (lineSeries.getSeriesCount() < series) {
                lineSeries.addSeries(new XYSeries(series));
                n1 = 0;
            }
            double x = Double.parseDouble(s[1]) / 1000, y = Double.parseDouble(s[0]);
            lineSeries.getSeries(series - 1).add(x, y);
            if (x > x_max)
                x_max = x;
            if (y > y_max)
                y_max = y;
            n1++;
        }
        br.close();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    final int n = n1;
    final int m = lineSeries.getSeriesCount();
    // create error bars
    final XYSeriesCollection errorBarSeries2 = new XYSeriesCollection();
    for (int i = 0; i < n; i++) {
        double[] f = new double[m];
        for (int j = 0; j < m; j++) f[j] = lineSeries.getSeries(j).getY(i).doubleValue();
        double mean = StatUtils.mean(f), sd = Math.sqrt(StatUtils.variance(f));
        double x = lineSeries.getSeries(0).getX(i).doubleValue();
        errorBarSeries2.addSeries(new XYSeries(i));
        errorBarSeries2.getSeries(i).add(x, mean - sd);
        errorBarSeries2.getSeries(i).add(x, mean);
        errorBarSeries2.getSeries(i).add(x, mean + sd);
    }
    final XYSeriesCollection upperBoundSeries = new XYSeriesCollection();
    final XYSeriesCollection upperQ3Series = new XYSeriesCollection();
    final XYSeriesCollection boxSeriesE = new XYSeriesCollection();
    final XYSeriesCollection boxSeriesN = new XYSeriesCollection();
    final XYSeriesCollection boxSeriesW = new XYSeriesCollection();
    final XYSeriesCollection boxSeriesS = new XYSeriesCollection();
    final XYSeriesCollection q2Series = new XYSeriesCollection();
    final XYSeriesCollection lowerQ2Series = new XYSeriesCollection();
    final XYSeriesCollection lowerBoundSeries = new XYSeriesCollection();
    final XYSeriesCollection meanDotSeries = new XYSeriesCollection();
    final XYSeriesCollection fillingSeries = new XYSeriesCollection();
    for (int i = 0; i < n; i++) {
        double[] f = new double[m];
        for (int j = 0; j < m; j++) f[j] = lineSeries.getSeries(j).getY(i).doubleValue();
        double q1 = StatUtils.percentile(f, 25), q2 = StatUtils.percentile(f, 50), q3 = StatUtils.percentile(f, 75);
        double IQR = q3 - q1;
        double[] boundary = new double[] { q1 - 1.5 * IQR, q3 + 1.5 * IQR };
        final Set<Integer> outliers = new HashSet<Integer>();
        for (int k = 0; k < m; k++) if (f[k] < boundary[0] || f[k] > boundary[1])
            outliers.add(k);
        double lower_bound = Double.POSITIVE_INFINITY, upper_bound = Double.NEGATIVE_INFINITY;
        for (int k = 0; k < m; k++) {
            if (outliers.contains(k))
                continue;
            if (f[k] < lower_bound)
                lower_bound = f[k];
            if (f[k] > upper_bound)
                upper_bound = f[k];
        }
        double x = lineSeries.getSeries(0).getX(i).doubleValue();
        double mean = StatUtils.mean(f);
        if (mean >= thres) {
            int w = upperBoundSeries.getSeriesCount();
            upperBoundSeries.addSeries(new XYSeries(i));
            upperBoundSeries.getSeries(w).add(x - half_width, upper_bound);
            upperBoundSeries.getSeries(w).add(x + half_width, upper_bound);
            upperQ3Series.addSeries(new XYSeries(i));
            upperQ3Series.getSeries(w).add(x, upper_bound);
            upperQ3Series.getSeries(w).add(x, q3);
            boxSeriesE.addSeries(new XYSeries(i));
            boxSeriesE.getSeries(w).add(x + half_width, q1);
            boxSeriesE.getSeries(w).add(x + half_width, q3);
            boxSeriesN.addSeries(new XYSeries(i));
            boxSeriesN.getSeries(w).add(x + half_width, q3);
            boxSeriesN.getSeries(w).add(x - half_width, q3);
            boxSeriesW.addSeries(new XYSeries(i));
            boxSeriesW.getSeries(w).add(x - half_width, q3);
            boxSeriesW.getSeries(w).add(x - half_width, q1);
            boxSeriesS.addSeries(new XYSeries(i));
            boxSeriesS.getSeries(w).add(x - half_width, q1);
            boxSeriesS.getSeries(w).add(x + half_width, q1);
            q2Series.addSeries(new XYSeries(i));
            q2Series.getSeries(w).add(x - half_width, q2);
            q2Series.getSeries(w).add(x + half_width, q2);
            lowerQ2Series.addSeries(new XYSeries(i));
            lowerQ2Series.getSeries(w).add(x, q1);
            lowerQ2Series.getSeries(w).add(x, lower_bound);
            lowerBoundSeries.addSeries(new XYSeries(i));
            lowerBoundSeries.getSeries(w).add(x - half_width, lower_bound);
            lowerBoundSeries.getSeries(w).add(x + half_width, lower_bound);
            double x_inter = x - half_width, x_end = x + half_width;
            while (x_inter < x_end) {
                XYSeries tmp = new XYSeries("shading");
                tmp.add(x_inter, q1);
                tmp.add(x_inter, q3);
                fillingSeries.addSeries(tmp);
                x_inter += 0.01;
            }
        }
        meanDotSeries.addSeries(new XYSeries(i));
        meanDotSeries.getSeries(i).add(x, mean);
    }
    final JFreeChart chart = ChartFactory.createXYLineChart(null, // domain axis label
    null, // range axis label
    null, // data
    null, PlotOrientation.VERTICAL, // include legend
    false, // tooltips?
    true, // URL generator? Not required...
    false);
    final NumberAxis domainAxis = new NumberAxis("SNP Physical Position (Kb) [" + n + " SNPs]");
    final NumberAxis rangeAxis = new NumberAxis("Estimated RF");
    domainAxis.setTickUnit(new NumberTickUnit(50));
    domainAxis.setRange(-x_max / 20 / dim.getWidth() * dim.getHeight(), x_max * (1 + 0.1 / dim.getWidth() * dim.getHeight()));
    rangeAxis.setRange(-y_max / 20, y_max * 1.1);
    domainAxis.setLabelFont(font3);
    rangeAxis.setLabelFont(font3);
    domainAxis.setTickLabelFont(font4);
    rangeAxis.setTickLabelFont(font4);
    XYPlot plot = chart.getXYPlot();
    plot.setDomainAxis(domainAxis);
    plot.setRangeAxis(rangeAxis);
    for (int i = 0; i < meanDotSeries.getSeriesCount(); i++) {
        double mean = meanDotSeries.getSeries(i).getY(0).doubleValue();
        if (mean < thres)
            continue;
        double x = meanDotSeries.getSeries(i).getX(0).doubleValue();
        XYTextAnnotation anno = new XYTextAnnotation(String.format(formatStr2, mean) + "\u00B1" + String.format(formatStr2, mean - errorBarSeries2.getSeries(i).getY(0).doubleValue()), x > x_max / 2 ? x - 30 : x + 30, mean);
        anno.setFont(font3);
        plot.addAnnotation((XYAnnotation) anno);
    }
    final ChartPanel cp = new ChartPanel(chart, collinearChart.getWidth(), collinearChart.getHeight(), collinearChart.getWidth(), collinearChart.getHeight(), collinearChart.getWidth(), collinearChart.getHeight(), ChartPanel.DEFAULT_BUFFER_USED, true, true, true, true, true);
    plot.setDataset(0, meanDotSeries);
    plot.setRenderer(0, getRenderer1());
    plot.setDataset(1, upperQ3Series);
    plot.setRenderer(1, getRenderer3());
    plot.setDataset(2, lowerQ2Series);
    plot.setRenderer(2, getRenderer3());
    plot.setDataset(3, boxSeriesE);
    plot.setRenderer(3, getRenderer2());
    plot.setDataset(4, boxSeriesN);
    plot.setRenderer(4, getRenderer2());
    plot.setDataset(5, boxSeriesW);
    plot.setRenderer(5, getRenderer2());
    plot.setDataset(6, boxSeriesS);
    plot.setRenderer(6, getRenderer2());
    plot.setDataset(7, q2Series);
    plot.setRenderer(7, getRenderer2());
    plot.setDataset(8, upperBoundSeries);
    plot.setRenderer(8, getRenderer2());
    plot.setDataset(9, lowerBoundSeries);
    plot.setRenderer(9, getRenderer2());
    plot.setDataset(10, fillingSeries);
    plot.setRenderer(10, getRenderer4());
    plot.setDataset(99, lineSeries);
    plot.setRenderer(99, getRenderer0());
    /**
     *		XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer(){
     *			Stroke soild = new BasicStroke(2.0f);
     *			Stroke dashed =  new BasicStroke(1.0f,BasicStroke.CAP_BUTT, BasicStroke.JOIN_MITER, 10.0f, new float[] {10.0f}, 0.0f);
     *			@Override
     *			public Stroke getItemStroke(int row, int column) {
     *				if (row>=N[0]&&row<N[1]){
     *					return new BasicStroke(stroke*2);
     *				}  else if(row>=N[1]&&row<N[2]) {
     *					return new BasicStroke(stroke*2);
     *				} else {
     *					return new BasicStroke(stroke/2);
     *				}
     *			}
     *		};
     *
     *		//XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();
     *		for(int i=0; i<seriesCollection.getSeriesCount(); i++) {
     *			if(i>=N[3]) {
     *				renderer.setSeriesPaint(i, Color.gray);
     *			} else if(i>=N[2]) {
     *				renderer.setSeriesPaint(i, Color.decode(hex_str[0]));
     *			} else if(i>=N[1]) {
     *				renderer.setSeriesPaint(i, Color.decode(hex_str[0]));
     *			} else if(i>=N[0]) {
     *				renderer.setSeriesPaint(i, Color.black);
     *			} else {
     *				renderer.setSeriesPaint(i, Color.decode(hex_str[4]));
     *				renderer.setSeriesShapesVisible(i,true);
     *				renderer.setSeriesShapesFilled(i,true);
     *				renderer.setSeriesShape(i, shape);
     *			}
     *
     *		}
     */
    chart.setBackgroundPaint(Color.WHITE);
    chart.setBorderPaint(Color.WHITE);
    chart.setTitle(title);
    cp.setPreferredSize(dim);
    cp.setBorder(null);
    collinearChart.add(cp);
    jframe.add(collinearChart, position);
}

Example 2 with XYTextAnnotation

use of org.jfree.chart.annotations.XYTextAnnotation in project zaproxy by zaproxy.

the class ScanProgressDialog method updateProgress.

/**
 * Updates the scan progress shown by the dialogue (scanners' progress/state and chart).
 */
private void updateProgress() {
    // Start panel data settings
    HostProcess hp = getSelectedHostProcess();
    if (scan.getHostProcesses() != null && hp != null) {
        // Update the main table entries
        model.updateValues(scan, hp);
        if (scan.isStopped()) {
            this.stopThread = true;
        }
        if (chart != null) {
            ResponseCountSnapshot snapshot = scan.getRequestHistory();
            while (snapshot != null) {
                try {
                    Second second = new Second(snapshot.getDate());
                    this.seriesTotal.add(second, snapshot.getTotal());
                    this.series100.add(second, snapshot.getResp100());
                    this.series200.add(second, snapshot.getResp200());
                    this.series300.add(second, snapshot.getResp300());
                    this.series400.add(second, snapshot.getResp400());
                    this.series500.add(second, snapshot.getResp500());
                    snapshot = scan.getRequestHistory();
                    for (Plugin plugin : scan.getHostProcesses().get(0).getRunning()) {
                        if (!labelsAdded.contains(plugin.getName())) {
                            // Add a vertical line with the plugin name
                            ValueMarker vm = new ValueMarker(plugin.getTimeStarted().getTime());
                            double center = chart.getXYPlot().getRangeAxis().getRange().getCentralValue();
                            if (lastCentre != center) {
                                if (lastCentre != -1) {
                                    // Move the existing labels so they stay in the centre
                                    @SuppressWarnings("rawtypes") List annotations = chart.getXYPlot().getAnnotations();
                                    for (Object o : annotations) {
                                        if (o instanceof XYTextAnnotation) {
                                            XYTextAnnotation annotation = (XYTextAnnotation) o;
                                            annotation.setY(center);
                                        }
                                    }
                                }
                                lastCentre = center;
                            }
                            XYTextAnnotation updateLabel = new XYTextAnnotation(plugin.getName(), plugin.getTimeStarted().getTime(), center);
                            updateLabel.setFont(FontUtils.getFont("Sans Serif"));
                            updateLabel.setRotationAnchor(TextAnchor.BASELINE_CENTER);
                            updateLabel.setTextAnchor(TextAnchor.BASELINE_CENTER);
                            updateLabel.setRotationAngle(-3.14 / 2);
                            updateLabel.setPaint(Color.black);
                            chart.getXYPlot().addDomainMarker(vm, Layer.BACKGROUND);
                            chart.getXYPlot().addAnnotation(updateLabel);
                            labelsAdded.add(plugin.getName());
                        }
                    }
                } catch (Exception e) {
                    log.error(e.getMessage(), e);
                    snapshot = null;
                }
            }
        }
    }
}

Example 3 with XYTextAnnotation

use of org.jfree.chart.annotations.XYTextAnnotation in project SIMVA-SoS by SESoS.

the class CombinedDomainXYPlotTest method createPlot.

/**
 * Creates a sample plot.
 *
 * @return A sample plot.
 */
private CombinedDomainXYPlot createPlot() {
    // create subplot 1...
    XYDataset data1 = createDataset1();
    XYItemRenderer renderer1 = new StandardXYItemRenderer();
    NumberAxis rangeAxis1 = new NumberAxis("Range 1");
    XYPlot subplot1 = new XYPlot(data1, null, rangeAxis1, renderer1);
    subplot1.setRangeAxisLocation(AxisLocation.BOTTOM_OR_LEFT);
    XYTextAnnotation annotation = new XYTextAnnotation("Hello!", 50.0, 10000.0);
    annotation.setFont(new Font("SansSerif", Font.PLAIN, 9));
    annotation.setRotationAngle(Math.PI / 4.0);
    subplot1.addAnnotation(annotation);
    // create subplot 2...
    XYDataset data2 = createDataset2();
    XYItemRenderer renderer2 = new StandardXYItemRenderer();
    NumberAxis rangeAxis2 = new NumberAxis("Range 2");
    rangeAxis2.setAutoRangeIncludesZero(false);
    XYPlot subplot2 = new XYPlot(data2, null, rangeAxis2, renderer2);
    subplot2.setRangeAxisLocation(AxisLocation.TOP_OR_LEFT);
    // parent plot...
    CombinedDomainXYPlot plot = new CombinedDomainXYPlot(new NumberAxis("Domain"));
    plot.setGap(10.0);
    // add the subplots...
    plot.add(subplot1, 1);
    plot.add(subplot2, 1);
    plot.setOrientation(PlotOrientation.VERTICAL);
    return plot;
}

Example 4 with XYTextAnnotation

use of org.jfree.chart.annotations.XYTextAnnotation in project SIMVA-SoS by SESoS.

the class YIntervalRendererTest method testCloning.

/**
 * Confirm that cloning works.
 */
@Test
public void testCloning() throws CloneNotSupportedException {
    YIntervalRenderer r1 = new YIntervalRenderer();
    YIntervalRenderer r2 = (YIntervalRenderer) r1.clone();
    assertTrue(r1 != r2);
    assertTrue(r1.getClass() == r2.getClass());
    assertTrue(r1.equals(r2));
    // check independence
    r1.setSeriesItemLabelGenerator(0, new StandardXYItemLabelGenerator());
    assertFalse(r1.equals(r2));
    r2.setSeriesItemLabelGenerator(0, new StandardXYItemLabelGenerator());
    assertTrue(r1.equals(r2));
    r1.setSeriesToolTipGenerator(0, new StandardXYToolTipGenerator());
    assertFalse(r1.equals(r2));
    r2.setSeriesToolTipGenerator(0, new StandardXYToolTipGenerator());
    assertTrue(r1.equals(r2));
    r1.addAnnotation(new XYTextAnnotation("ABC", 1.0, 2.0), Layer.FOREGROUND);
    assertFalse(r1.equals(r2));
    r2.addAnnotation(new XYTextAnnotation("ABC", 1.0, 2.0), Layer.FOREGROUND);
    assertTrue(r1.equals(r2));
    r1.addAnnotation(new XYTextAnnotation("ABC", 1.0, 2.0), Layer.BACKGROUND);
    assertFalse(r1.equals(r2));
    r2.addAnnotation(new XYTextAnnotation("ABC", 1.0, 2.0), Layer.BACKGROUND);
    assertTrue(r1.equals(r2));
}

Example 5 with XYTextAnnotation

use of org.jfree.chart.annotations.XYTextAnnotation in project polyGembler by c-zhou.

the class HMMPanel method getChart.

public ChartPanel getChart() {
    Range range = this.updateRates();
    final JFreeChart chart = ChartFactory.createXYLineChart(null, // domain axis label
    null, // range axis label
    null, // data
    rates, PlotOrientation.VERTICAL, // include legend
    false, // tooltips?
    true, // URL generator? Not required...
    false);
    final NumberAxis domainAxis = new NumberAxis("SNP relative physical position");
    // final LogarithmicAxis rangeAxis = new LogarithmicAxis("Trans-out probability");
    final NumberAxis rangeAxis = new NumberAxis("Trans-out probability");
    AxisSpace space = new AxisSpace();
    // reserved space on the left side of the plot
    space.setRight(22);
    space.setLeft(67);
    chart.getXYPlot().setFixedRangeAxisSpace(space);
    // double fixedDemension = HMMPanel.this.getX(0, false)+shift;
    // rangeAxis.setFixedDimension(fixedDemension);
    domainAxis.setTickUnit(new NumberTickUnit(1));
    // rangeAxis.setLog10TickLabelsFlag(true);
    rangeAxis.setRange(range);
    domainAxis.setRange(new Range(1 - offset_yR, noSnps + offset_yR));
    chart.getXYPlot().setDomainAxis(domainAxis);
    chart.getXYPlot().setRangeAxis(rangeAxis);
    final XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();
    for (int i = 0; i < rates.getSeriesCount(); i++) {
        Color c;
        if (i == 0)
            c = ca.getColor(i);
        else
            c = Color.lightGray;
        renderer.setSeriesPaint(i, c);
        if (i == 0)
            renderer.setSeriesShapesVisible(i, true);
        else
            renderer.setSeriesShapesVisible(i, false);
    }
    /**
     *		XYPolygonAnnotation a = new XYPolygonAnnotation(new double[] {5.0,
     *				   0.0, 5.0, 0.5, 6.0, 0.5, 6.0, 0.0}, null, null,Color.black) {
     *            @Override
     *            public void draw(Graphics2D g2, XYPlot plot, Rectangle2D dataArea, ValueAxis domainAxis, ValueAxis rangeAxis, int rendererIndex, PlotRenderingInfo info) {
     *                Graphics2D g22 = (Graphics2D) g2.create();
     *                g22.setXORMode(new Color(0xff0000));
     *                super.draw(g22, plot, dataArea, domainAxis, rangeAxis, rendererIndex, info);
     *            }
     *        };
     *		renderer.addAnnotation(a, Layer.BACKGROUND);
     */
    chart.getXYPlot().setRenderer(renderer);
    double anno_offset_x = 0.5;
    XYSeries d = rates.getSeries(0);
    for (int i = 0; i < d.getItemCount(); i++) {
        double x = d.getX(i).doubleValue();
        double y = d.getY(i).doubleValue();
        if (y > 0.1)
            chart.getXYPlot().addAnnotation((XYAnnotation) new XYTextAnnotation(String.format(formatStr2, y), x > noSnps / 2 ? (x - anno_offset_x) : (x + anno_offset_x), y));
        else
            chart.getXYPlot().addAnnotation((XYAnnotation) new XYTextAnnotation(String.format(formatStr, y), x, y + .05));
    }
    // chart.getXYPlot().getRangeAxis().get
    // chart.getXYPlot().setRangeAxis(new LogarithmicAxis("rates"));
    final ChartPanel cp = new ChartPanel(chart, // width
    this.getWidth(), // height
    150, // mindrawWidth
    this.getWidth(), // mindrawHeight
    150, // maxDrawWith
    this.getWidth(), // maxDrawHeight
    150, ChartPanel.DEFAULT_BUFFER_USED, // properties
    true, // save
    true, // print
    true, // zoom
    true, // tooltips
    true);
    {
        Range r = chart.getXYPlot().getDomainAxis().getRange();
        chart.getXYPlot().getDomainAxis().setAutoRange(false);
        chart.getXYPlot().getDomainAxis().setRange(1, r.getUpperBound());
    }
    {
        Range r = chart.getXYPlot().getRangeAxis().getRange();
        if (r.getLowerBound() < range.getUpperBound()) {
            chart.getXYPlot().getRangeAxis().setAutoRange(false);
            chart.getXYPlot().getRangeAxis().setRange(r.getLowerBound(), range.getUpperBound());
        }
    }
    chart.setBackgroundPaint(Color.WHITE);
    chart.setBorderPaint(Color.WHITE);
    cp.setBorder(null);
    /**
     *		RectangleEdge edge = chart.getXYPlot().getDomainAxisEdge();
     *		Rectangle2D edge2 = cp.getScreenDataArea();
     *		double x = RectangleEdge.coordinate(edge2, edge);
     *		ValueAxis edge3 = chart.getXYPlot().getDomainAxisForDataset(0);
     *		double xx = domainAxis.valueToJava2D(3, edge2, edge);
     */
    return cp;
}