Example usage for org.jfree.chart.renderer.category LineAndShapeRenderer setSeriesShapesVisible

List of usage examples for org.jfree.chart.renderer.category LineAndShapeRenderer setSeriesShapesVisible

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Introduction

In this page you can find the example usage for org.jfree.chart.renderer.category LineAndShapeRenderer setSeriesShapesVisible.

Prototype

public void setSeriesShapesVisible(int series, Boolean flag)

Source Link

Document

Sets the 'shapes visible' flag for a series and sends a RendererChangeEvent to all registered listeners.

Usage

From source file:mzmatch.ipeak.normalisation.VanDeSompele.java

public static void main(String args[]) {
    try {/*  w  ww. ja v  a 2  s  . c om*/
        Tool.init();

        // parse the commandline options
        Options options = new Options();
        CmdLineParser cmdline = new CmdLineParser(options);

        // check whether we need to show the help
        cmdline.parse(args);
        if (options.help) {
            Tool.printHeader(System.out, application, version);
            cmdline.printUsage(System.out, "");
            return;
        }

        if (options.verbose) {
            Tool.printHeader(System.out, application, version);
            cmdline.printOptions();
        }

        // check the command-line parameters
        {
            // if the output directories do not exist, create them
            if (options.output != null)
                Tool.createFilePath(options.output, true);
        }

        // load the data
        if (options.verbose)
            System.out.println("Loading data");
        ParseResult result = PeakMLParser.parse(new FileInputStream(options.input), true);

        Header header = result.header;
        IPeakSet<IPeakSet<? extends IPeak>> peaksets = (IPeakSet<IPeakSet<? extends IPeak>>) result.measurement;

        int nrmeasurements = header.getNrMeasurementInfos();

        // remove the stability factor annotation
        for (IPeak peak : peaksets)
            peak.removeAnnotation("stability factor");

        // load the database
        if (options.verbose)
            System.out.println("Loading the molecule database");
        HashMap<String, Molecule> database = MoleculeIO.parseXml(new FileInputStream(options.database));

        // filter the set to include only identifiable metabolites
        if (options.verbose)
            System.out.println("Creating selection");
        Vector<IPeakSet<? extends IPeak>> selection = new Vector<IPeakSet<? extends IPeak>>();
        for (Molecule molecule : database.values()) {
            double mass = molecule.getMass(Mass.MONOISOTOPIC);
            double delta = PeriodicTable.PPM(mass, options.ppm);

            // get the most intense peak containing all the measurements
            Vector<IPeakSet<? extends IPeak>> neighbourhoud = peaksets.getPeaksInMassRange(mass - delta,
                    mass + delta);
            Collections.sort(neighbourhoud, IPeak.sort_intensity_descending);
            for (IPeakSet<? extends IPeak> neighbour : neighbourhoud)
                if (count(neighbour) == nrmeasurements) {
                    selection.add(neighbour);
                    break;
                }
        }

        // calculate the stability factor for each peak in the selection
        if (options.verbose)
            System.out.println("Calculating stability factors");
        for (int peakid1 = 0; peakid1 < selection.size(); ++peakid1) {
            double stddeviations[] = new double[selection.size()];

            IPeakSet<? extends IPeak> peakset1 = selection.get(peakid1);
            for (int peakid2 = 0; peakid2 < selection.size(); ++peakid2) {
                IPeakSet<? extends IPeak> peakset2 = selection.get(peakid2);

                double values[] = new double[nrmeasurements];
                for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) {
                    int measurementid1 = peakset1.get(measurementid).getMeasurementID();
                    int setid1 = header.indexOfSetInfo(header.getSetInfoForMeasurementID(measurementid1));
                    int measurementid2 = peakset2.get(measurementid).getMeasurementID();
                    int setid2 = header.indexOfSetInfo(header.getSetInfoForMeasurementID(measurementid2));
                    if (setid1 != setid2 || measurementid1 != measurementid2)
                        System.err.println("[WARNING]: differing setid or spectrumid for comparison");

                    values[measurementid] = Math.log(peakset1.get(measurementid).getIntensity()
                            / peakset2.get(measurementid).getIntensity()) / Math.log(2);
                }
                stddeviations[peakid2] = Statistical.stddev(values);
            }

            peakset1.addAnnotation("stability factor", Statistical.mean(stddeviations));
        }

        // sort on the stability factor
        Collections.sort(selection, new IPeak.AnnotationAscending("stability factor"));

        // take the top 10% and calculate the geometric mean
        if (options.verbose)
            System.out.println("Calculating normalisation factors");
        int nrselected = (int) (0.1 * selection.size());
        if (nrselected < 10)
            nrselected = (10 < selection.size() ? 10 : selection.size());
        double normalization_factors[] = new double[nrmeasurements];
        for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) {
            double values[] = new double[nrselected];
            for (int i = 0; i < nrselected; ++i) {
                IPeak peak = selection.get(i).get(measurementid);
                values[i] = peak.getIntensity();
            }
            normalization_factors[measurementid] = Statistical.geomean(values);
        }

        // scale the found normalization factors
        double maxnf = Statistical.max(normalization_factors);
        for (int sampleid = 0; sampleid < nrmeasurements; ++sampleid)
            normalization_factors[sampleid] /= maxnf;

        // write the selection if needed
        if (options.selection != null) {
            if (options.verbose)
                System.out.println("Writing original selection data");

            PeakMLWriter.write(result.header, selection, null,
                    new GZIPOutputStream(new FileOutputStream(options.selection)), null);
        }

        // normalize all the peaks
        if (options.verbose)
            System.out.println("Normalizing all the entries");
        for (IPeakSet<? extends IPeak> peakset : peaksets) {
            for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) {
                // TODO why did I do this again ?
                int id = 0;
                int setid = 0;
                int spectrumid = 0;
                for (int i = 0; i < header.getNrSetInfos(); ++i) {
                    SetInfo set = header.getSetInfos().get(i);

                    if (id + set.getNrMeasurementIDs() > measurementid) {
                        setid = i;
                        spectrumid = measurementid - id;
                        break;
                    } else
                        id += set.getNrMeasurementIDs();
                }

                MassChromatogram<Peak> masschromatogram = null;
                for (IPeak p : peakset) {
                    int mymeasurementid = p.getMeasurementID();
                    int mysetid = header.indexOfSetInfo(header.getSetInfoForMeasurementID(mymeasurementid));
                    if (mysetid == setid && mymeasurementid == spectrumid) {
                        masschromatogram = (MassChromatogram<Peak>) p;
                        break;
                    }
                }
                if (masschromatogram == null)
                    continue;

                for (IPeak peak : masschromatogram.getPeaks())
                    peak.setIntensity(peak.getIntensity() / normalization_factors[measurementid]);
            }
        }

        // write the selection if needed
        if (options.selection_normalized != null) {
            if (options.verbose)
                System.out.println("Writing the normalized selection data");

            PeakMLWriter.write(result.header, selection, null,
                    new GZIPOutputStream(new FileOutputStream(options.selection_normalized)), null);
        }

        // write the factors if needed
        if (options.factors != null) {
            if (options.verbose)
                System.out.println("Writing the normalization factors");

            PrintStream out = new PrintStream(options.factors);
            for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid)
                out.println(header.getMeasurementInfo(measurementid).getLabel() + "\t"
                        + normalization_factors[measurementid]);
        }

        // write the plot if needed
        if (options.img != null) {
            if (options.verbose)
                System.out.println("Writing the graph");

            DefaultCategoryDataset dataset = new DefaultCategoryDataset();
            JFreeChart linechart = ChartFactory.createLineChart(null, "measurement", "normalization factor",
                    dataset, PlotOrientation.VERTICAL, false, // legend
                    false, // tooltips
                    false // urls
            );

            CategoryPlot plot = (CategoryPlot) linechart.getPlot();
            CategoryAxis axis = (CategoryAxis) plot.getDomainAxis();
            axis.setCategoryLabelPositions(CategoryLabelPositions.UP_45);
            LineAndShapeRenderer renderer = (LineAndShapeRenderer) plot.getRenderer();

            renderer.setSeriesShapesFilled(0, true);
            renderer.setSeriesShapesVisible(0, true);

            linechart.setBackgroundPaint(Color.WHITE);
            linechart.setBorderVisible(false);
            linechart.setAntiAlias(true);

            plot.setBackgroundPaint(Color.WHITE);
            plot.setDomainGridlinesVisible(true);
            plot.setRangeGridlinesVisible(true);

            // create the datasets
            for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid)
                dataset.addValue(normalization_factors[measurementid], "",
                        header.getMeasurementInfo(measurementid).getLabel());
            JFreeChartTools.writeAsPDF(new FileOutputStream(options.img), linechart, 800, 500);
        }

        // write the normalized values
        if (options.verbose)
            System.out.println("Writing the normalized data");
        PeakMLWriter.write(result.header, peaksets.getPeaks(), null,
                new GZIPOutputStream(new FileOutputStream(options.output)), null);
    } catch (Exception e) {
        Tool.unexpectedError(e, application);
    }
}

From source file:org.jfree.chart.demo.LineChartDemo7.java

private static JFreeChart createChart(CategoryDataset categorydataset) {
    JFreeChart jfreechart = ChartFactory.createLineChart("Line Chart Demo 7", "Category", "Count",
            categorydataset, PlotOrientation.VERTICAL, true, true, false);
    jfreechart.setBackgroundPaint(Color.white);
    CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot();
    categoryplot.setBackgroundPaint(Color.lightGray);
    categoryplot.setRangeGridlinePaint(Color.white);
    NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis();
    numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
    LineAndShapeRenderer lineandshaperenderer = (LineAndShapeRenderer) categoryplot.getRenderer();
    lineandshaperenderer.setSeriesShapesVisible(0, true);
    lineandshaperenderer.setSeriesShapesVisible(1, false);
    lineandshaperenderer.setSeriesShapesVisible(2, true);
    lineandshaperenderer.setSeriesLinesVisible(2, false);
    lineandshaperenderer.setSeriesShape(2, ShapeUtilities.createDiamond(4F));
    lineandshaperenderer.setDrawOutlines(true);
    lineandshaperenderer.setUseFillPaint(true);
    lineandshaperenderer.setBaseFillPaint(Color.white);
    return jfreechart;
}

From source file:org.jfree.chart.demo.LineChartDemo8.java

private static JFreeChart createChart(CategoryDataset categorydataset) {
    JFreeChart jfreechart = ChartFactory.createLineChart("Line Chart Demo 8", "Category", "Count",
            categorydataset, PlotOrientation.VERTICAL, true, true, false);
    jfreechart.setBackgroundPaint(Color.white);
    CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot();
    categoryplot.setBackgroundPaint(Color.lightGray);
    categoryplot.setRangeGridlinePaint(Color.white);
    SymbolAxis symbolaxis = new SymbolAxis("Group", new String[] { "A", "B", "C", "D", "E", "F" });
    categoryplot.setRangeAxis(symbolaxis);
    LineAndShapeRenderer lineandshaperenderer = (LineAndShapeRenderer) categoryplot.getRenderer();
    lineandshaperenderer.setSeriesShapesVisible(0, true);
    lineandshaperenderer.setSeriesShapesVisible(1, false);
    lineandshaperenderer.setSeriesShapesVisible(2, true);
    lineandshaperenderer.setSeriesLinesVisible(2, false);
    lineandshaperenderer.setSeriesShape(2, ShapeUtilities.createDiamond(4F));
    lineandshaperenderer.setDrawOutlines(true);
    lineandshaperenderer.setUseFillPaint(true);
    lineandshaperenderer.setBaseFillPaint(Color.white);
    return jfreechart;
}

From source file:org.jfree.chart.demo.CategoryMarkerDemo1.java

private static JFreeChart createChart(CategoryDataset categorydataset) {
    JFreeChart jfreechart = ChartFactory.createLineChart("Category Marker Demo 1", "Category", "Count",
            categorydataset, PlotOrientation.VERTICAL, true, true, false);
    jfreechart.setBackgroundPaint(Color.white);
    CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot();
    categoryplot.setBackgroundPaint(Color.lightGray);
    categoryplot.setRangeGridlinePaint(Color.white);
    NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis();
    numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
    LineAndShapeRenderer lineandshaperenderer = (LineAndShapeRenderer) categoryplot.getRenderer();
    lineandshaperenderer.setSeriesShapesVisible(0, true);
    lineandshaperenderer.setDrawOutlines(true);
    lineandshaperenderer.setUseFillPaint(true);
    lineandshaperenderer.setBaseFillPaint(Color.white);
    CategoryMarker categorymarker = new CategoryMarker("Category 4", Color.blue, new BasicStroke(1.0F));
    categorymarker.setDrawAsLine(true);//from ww  w.  ja  v  a 2  s . c o  m
    categorymarker.setLabel("Marker Label");
    categorymarker.setLabelFont(new Font("Dialog", 0, 11));
    categorymarker.setLabelTextAnchor(TextAnchor.TOP_RIGHT);
    categorymarker.setLabelOffset(new RectangleInsets(2D, 5D, 2D, 5D));
    categoryplot.addDomainMarker(categorymarker, Layer.BACKGROUND);
    return jfreechart;
}

From source file:org.jfree.chart.demo.CategoryMarkerDemo2.java

private static JFreeChart createChart(CategoryDataset categorydataset) {
    JFreeChart jfreechart = ChartFactory.createLineChart("Category Marker Demo 2", "Category", "Count",
            categorydataset, PlotOrientation.VERTICAL, true, true, false);
    jfreechart.setBackgroundPaint(Color.white);
    CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot();
    categoryplot.setBackgroundPaint(Color.lightGray);
    categoryplot.setRangeGridlinePaint(Color.white);
    NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis();
    numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits());
    LineAndShapeRenderer lineandshaperenderer = (LineAndShapeRenderer) categoryplot.getRenderer();
    lineandshaperenderer.setSeriesShapesVisible(0, true);
    lineandshaperenderer.setDrawOutlines(true);
    lineandshaperenderer.setUseFillPaint(true);
    lineandshaperenderer.setBaseFillPaint(Color.white);
    CategoryMarker categorymarker = new CategoryMarker("Category 4", new Color(0, 0, 255, 25),
            new BasicStroke(1.0F));
    categorymarker.setDrawAsLine(false);
    categorymarker.setAlpha(1.0F);// w ww  . j  av  a2s  .com
    categorymarker.setLabel("Marker Label");
    categorymarker.setLabelFont(new Font("Dialog", 0, 11));
    categorymarker.setLabelTextAnchor(TextAnchor.TOP_RIGHT);
    categorymarker.setLabelOffset(new RectangleInsets(2D, 5D, 2D, 5D));
    categoryplot.addDomainMarker(categorymarker, Layer.BACKGROUND);
    return jfreechart;
}

From source file:org.pentaho.chart.plugin.jfreechart.chart.line.JFreeLineChartGenerator.java

/**
 * @param categoryPlot//w  ww .  ja v  a  2s  . c o m
 * @param seriesElements
 * 
 * Set the line marker attributes
 */
private static void setSeriesMarkerStyles(CategoryPlot categoryPlot, ChartElement[] seriesElements) {
    final int length = seriesElements.length;
    final ShapeFactory shapeFacObj = ShapeFactory.getInstance();
    for (int i = 0; i < length; i++) {
        final ChartElement currElement = seriesElements[i];

        if (categoryPlot.getRenderer() instanceof LineAndShapeRenderer) {
            final LineAndShapeRenderer lineAndShapeRenderer = (LineAndShapeRenderer) categoryPlot.getRenderer();
            lineAndShapeRenderer.setSeriesShapesVisible(i, isMarkerVisible(currElement));
            lineAndShapeRenderer.setSeriesShape(i, shapeFacObj.getShape(currElement));
            lineAndShapeRenderer.setSeriesShapesFilled(i, isShapeFilled(currElement));
        }
    }
}

From source file:org.apache.qpid.disttest.charting.chartbuilder.CategoryStrokeAndPaintApplier.java

@Override
public void setSeriesShape(final int seriesIndex, final java.awt.Shape shape, final JFreeChart targetChart) {
    CategoryItemRenderer renderer = targetChart.getCategoryPlot().getRenderer();
    if (renderer instanceof LineAndShapeRenderer) {
        LineAndShapeRenderer lineAndShapeRenderer = (LineAndShapeRenderer) renderer;
        lineAndShapeRenderer.setSeriesShapesVisible(seriesIndex, true);
        lineAndShapeRenderer.setSeriesShape(seriesIndex, shape);
    }/*from w w w  .j  a v  a2  s .  co  m*/
}

From source file:guineu.modules.filter.report.RTShift.ReportTask.java

/**
 * Create the chart and save it into a png file.
 * @param dataset/*ww w . j  a  v a2 s . c om*/
 * @param lipidName
 */
private void createChart(CategoryDataset dataset, String lipidName) {
    try {

        JFreeChart chart = ChartFactory.createLineChart("RT shift", "Samples", "RT", dataset,
                PlotOrientation.VERTICAL, false, false, false);

        // Chart characteristics
        CategoryPlot plot = (CategoryPlot) chart.getPlot();
        final NumberAxis axis = (NumberAxis) plot.getRangeAxis();
        axis.setAutoRangeIncludesZero(false);
        axis.setAutoRangeMinimumSize(1.0);
        LineAndShapeRenderer categoryRenderer = new LineAndShapeRenderer();
        categoryRenderer.setSeriesLinesVisible(0, false);
        categoryRenderer.setSeriesShapesVisible(0, true);
        plot.setRenderer(categoryRenderer);

        // Save all the charts in the folder choosen by the user
        ChartUtilities.saveChartAsPNG(new File(this.reportFileName + "/RT Shift:" + lipidName + ".png"), chart,
                1000, (500));
    } catch (IOException ex) {
        Logger.getLogger(ReportTask.class.getName()).log(Level.SEVERE, null, ex);
    }

}

From source file:guineu.modules.filter.report.areaVSheight.ReportTask.java

/**
 * Create the chart and save it into a png file.
 * @param dataset/* w  w w  . j  a  va 2s.com*/
 * @param lipidName
 */
private void createChart(CategoryDataset dataset, String lipidName) {
    try {

        JFreeChart chart = ChartFactory.createLineChart("Height/Area", "Samples", "Height/Area", dataset,
                PlotOrientation.VERTICAL, false, false, false);

        // Chart characteristics
        CategoryPlot plot = (CategoryPlot) chart.getPlot();
        final NumberAxis axis = (NumberAxis) plot.getRangeAxis();
        axis.setAutoRangeIncludesZero(false);
        LineAndShapeRenderer categoryRenderer = new LineAndShapeRenderer();
        categoryRenderer.setSeriesLinesVisible(0, false);
        categoryRenderer.setSeriesShapesVisible(0, true);
        plot.setRenderer(categoryRenderer);

        // Save all the charts in the folder choosen by the user
        ChartUtilities.saveChartAsPNG(new File(this.reportFileName + "/HeightvsArea:" + lipidName + ".png"),
                chart, 1000, 500);
    } catch (IOException ex) {
        Logger.getLogger(ReportTask.class.getName()).log(Level.SEVERE, null, ex);
    }

}

From source file:guineu.modules.filter.report.intensitiesReport.ReportTask.java

/**
 * Create the chart and save it into a png file.
 * @param dataset//from  w  w w .  j ava2s  .c o m
 * @param lipidName
 */
private void createChart(CategoryDataset dataset, String lipidName) {
    try {
        String fieldY;
        if (this.useArea) {
            fieldY = "Area";
        } else {
            fieldY = "Heights";
        }

        JFreeChart chart = ChartFactory.createLineChart("Intensities", "Samples", fieldY, dataset,
                PlotOrientation.VERTICAL, false, false, false);

        // Chart characteristics
        CategoryPlot plot = (CategoryPlot) chart.getPlot();
        final NumberAxis axis = (NumberAxis) plot.getRangeAxis();
        axis.setAutoRangeIncludesZero(false);
        LineAndShapeRenderer categoryRenderer = new LineAndShapeRenderer();
        categoryRenderer.setSeriesLinesVisible(0, false);
        categoryRenderer.setSeriesShapesVisible(0, true);
        plot.setRenderer(categoryRenderer);

        // Save all the charts in the folder choosen by the user
        ChartUtilities.saveChartAsPNG(new File(this.reportFileName + "/" + fieldY + ":" + lipidName + ".png"),
                chart, 1000, 500);
    } catch (IOException ex) {
        Logger.getLogger(ReportTask.class.getName()).log(Level.SEVERE, null, ex);
    }

}