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From source file:sanger.team16.gui.genevar.mqtl.snp.CisMQTLSNPPane2.java
private void setMofidicationPanel(String variationName, ChartPanel regionalLinePlot) throws ArrayIndexOutOfBoundsException { BaseJPane panel = new BaseJPane(variationName, 10, 20, 10, 20); // ------------------ Panel p0 (start) ------------------ // BaseJPane p0 = new BaseJPane(); p0.add(regionalLinePlot);/*from ww w. j av a2 s .c om*/ //p0.setBaseSpringBoxTrailing(); panel.add(p0); // ------------------ Panel p0 (end) ------------------ // panel.add(new JLabel("")); panel.add(new JLabel("")); panel.add(new JLabel("")); // ------------------ Panel p1 (start) ------------------ // BaseJPane p1 = new BaseJPane(); JButton bSelectAll = new JButton(" Deselect All "); JButton bExport = new JButton(" Export List "); CisSNPPane2Listener cisSNP2Listener = new CisSNPPane2Listener(bSelectAll, bExport); //bSelectAll.setForeground(new Color(34,139,34)); bSelectAll.setForeground(Color.GREEN.darker()); bSelectAll.addActionListener(cisSNP2Listener); p1.add(bSelectAll); bExport.addActionListener(cisSNP2Listener); p1.add(bExport); p1.add(Box.createHorizontalGlue()); this.setLinkToPanel(p1, assemblyId, snp.getChromosome(), snp.getPosition(), distanceToSNP); p1.setBaseSpringBox(); panel.add(p1); // ------------------ Panel p1 (end) ------------------ // // ------------------ Panel p2 (start) ------------------ // //BaseJTable transcriptTable = this.transcriptTable.getSortedTable(); //TODO if (modificationTable.isEnabled()) { bSelectAll.setEnabled(false); bExport.setEnabled(false); } this.setTranscriptTable(); BaseJPane p2 = new BaseJPane(); p2.setLayout(new BorderLayout()); p2.add(modificationTable.getTableHeader(), BorderLayout.PAGE_START); p2.add(modificationTable, BorderLayout.CENTER); //p0.setBaseSpringGrid(1, 1); panel.add(p2); // ------------------ Panel p2 (end) ------------------ // panel.add(new JLabel(" (Use CTRL+C to copy CpG probes of interest)")); panel.setBaseSpringGrid(1); this.add(panel); }
From source file:guineu.modules.dataanalysis.correlations.CorrelationTask.java
@Override public void run() { setStatus(TaskStatus.PROCESSING);//w w w . j a v a 2 s . com try { Dataset data1 = dataset[0]; Dataset data2 = null; if (dataset.length == 1) { data2 = dataset[0]; } else if (dataset.length > 1) { data2 = dataset[1]; } Dataset newDataset = new SimpleBasicDataset("Correlation matrix"); newDataset.addColumnName("ID"); // Column names from the first dataset for (PeakListRow row : data1.getRows()) { String name = row.getID() + " - " + row.getName(); newDataset.addColumnName(name); if (this.showPvalue) { newDataset.addColumnName(name + " - pValue"); } } // Row names from the second dataset for (int i = 0; i < data2.getNumberRows(); i++) { PeakListRow row = data2.getRow(i); PeakListRow newRow = new SimplePeakListRowOther(); newRow.setPeak("ID", row.getID() + " - " + row.getName()); newDataset.addRow(newRow); } for (PeakListRow row : data1.getRows()) { String name = row.getID() + " - " + row.getName(); String pValueName = name + " - pValue"; for (int i = 0; i < data2.getNumberRows(); i++) { RealMatrix matrix = getCorrelation(row, data2.getRow(i), data1.getAllColumnNames()); PearsonsCorrelation correlation = null; if (this.correlationType.contains("Pearsons")) { correlation = new PearsonsCorrelation(matrix); } else if (this.correlationType.contains("Spearmans")) { SpearmansCorrelation scorrelation = new SpearmansCorrelation(matrix); correlation = scorrelation.getRankCorrelation(); } if (correlation != null) { double c = correlation.getCorrelationMatrix().getEntry(1, 0); double p = correlation.getCorrelationPValues().getEntry(1, 0); String cp = String.valueOf(c); Color cell = Color.WHITE; if (p < cutoff) { if (c < 0) { cell = Color.green; } else { cell = Color.red; } } int pColumnIndex = 0; if (this.showPvalue) { newDataset.getRow(i).setPeak(pValueName, String.valueOf(p)); pColumnIndex = newDataset.getAllColumnNames().indexOf(pValueName) + 2; newDataset.setCellColor(cell, i, pColumnIndex); } pColumnIndex = newDataset.getAllColumnNames().indexOf(name) + 2; newDataset.getRow(i).setPeak(name, cp); newDataset.setCellColor(cell, i, pColumnIndex); } if (this.correlationType.contains("Covariance")) { Covariance covariance = new Covariance(matrix); double c = covariance.getCovarianceMatrix().getEntry(1, 0); newDataset.getRow(i).setPeak(name, String.valueOf(c)); } } } GUIUtils.showNewTable(newDataset, true); setStatus(TaskStatus.FINISHED); } catch (Exception ex) { Logger.getLogger(CorrelationTask.class.getName()).log(Level.SEVERE, null, ex); setStatus(TaskStatus.ERROR); } }
From source file:com.joey.software.memoryToolkit.MemoryUsagePanel.java
/** * Creates a new application.//from w ww. j a v a 2 s .com * * @param historyCount * the history count (in milliseconds). */ public MemoryUsagePanel(int historyCount, int interval) { super(new BorderLayout()); // create two series that automatically discard data more than 30 // seconds old... this.total = new TimeSeries("Total Memory", Millisecond.class); this.total.setMaximumItemCount(historyCount); this.free = new TimeSeries("Free Memory", Millisecond.class); this.free.setMaximumItemCount(historyCount); this.used = new TimeSeries("Used Memory", Millisecond.class); this.used.setMaximumItemCount(historyCount); this.max = new TimeSeries("Used Memory", Millisecond.class); this.max.setMaximumItemCount(historyCount); TimeSeriesCollection dataset = new TimeSeriesCollection(); dataset.addSeries(this.total); dataset.addSeries(this.free); dataset.addSeries(this.used); dataset.addSeries(this.max); DateAxis domain = new DateAxis("Time"); NumberAxis range = new NumberAxis("Memory"); domain.setTickLabelFont(new Font("SansSerif", Font.PLAIN, 12)); range.setTickLabelFont(new Font("SansSerif", Font.PLAIN, 12)); domain.setLabelFont(new Font("SansSerif", Font.PLAIN, 14)); range.setLabelFont(new Font("SansSerif", Font.PLAIN, 14)); XYItemRenderer renderer = new XYLineAndShapeRenderer(true, false); renderer.setSeriesPaint(0, Color.red); renderer.setSeriesPaint(1, Color.green); renderer.setSeriesPaint(2, Color.black); renderer.setStroke(new BasicStroke(1f, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL)); XYPlot plot = new XYPlot(dataset, domain, range, renderer); plot.setBackgroundPaint(Color.lightGray); plot.setDomainGridlinePaint(Color.white); plot.setRangeGridlinePaint(Color.white); plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0)); domain.setAutoRange(true); domain.setLowerMargin(0.0); domain.setUpperMargin(0.0); domain.setTickLabelsVisible(true); range.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); JFreeChart chart = new JFreeChart("JVM Memory Usage", new Font("SansSerif", Font.BOLD, 24), plot, true); chart.setBackgroundPaint(Color.white); ChartPanel chartPanel = new ChartPanel(chart); chartPanel.setBorder(BorderFactory.createCompoundBorder(BorderFactory.createEmptyBorder(4, 4, 4, 4), BorderFactory.createLineBorder(Color.black))); add(chartPanel); gen = new DataGenerator(interval); }
From source file:edu.ucla.stat.SOCR.chart.demo.BarChartDemo4.java
/** * Creates a sample chart./* ww w . ja va 2s .com*/ * * @param dataset the dataset. * * @return The chart. */ protected JFreeChart createChart(CategoryDataset dataset) { // create the chart... JFreeChart chart = ChartFactory.createBarChart(chartTitle, // chart title domainLabel, // domain axis label rangeLabel, // range axis label dataset, // data PlotOrientation.VERTICAL, !legendPanelOn, // include legend true, // tooltips? false // URLs? ); // NOW DO SOME OPTIONAL CUSTOMISATION OF THE CHART... // set the background color for the chart... chart.setBackgroundPaint(new Color(0xBBBBDD)); // get a reference to the plot for further customisation... CategoryPlot plot = chart.getCategoryPlot(); // set the range axis to display integers only... NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis(); rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); // disable bar outlines... BarRenderer renderer = (BarRenderer) plot.getRenderer(); renderer.setDrawBarOutline(false); renderer.setMaximumBarWidth(0.10); // set up gradient paints for series... GradientPaint gp0 = new GradientPaint(0.0f, 0.0f, Color.blue, 0.0f, 0.0f, Color.lightGray); GradientPaint gp1 = new GradientPaint(0.0f, 0.0f, Color.green, 0.0f, 0.0f, Color.lightGray); renderer.setSeriesPaint(0, gp0); renderer.setSeriesPaint(1, gp1); // OPTIONAL CUSTOMISATION COMPLETED. renderer.setLegendItemLabelGenerator(new SOCRCategorySeriesLabelGenerator()); setCategorySummary(dataset); return chart; }
From source file:de.fub.maps.project.plugins.tasks.eval.OverviewChart.java
private void initRenderer(CategoryItemRenderer renderer) { Color[] colors = new Color[] { Color.red, Color.blue, Color.orange, Color.cyan, Color.yellow, Color.magenta, Color.green, Color.pink, Color.black, Color.gray }; if (!this.roadNetworkStatisticsList.isEmpty()) { for (int i = 0; i < this.roadNetworkStatisticsList.size(); i++) { renderer.setSeriesPaint(i, colors[i % colors.length]); }/*www . j av a 2s .c om*/ } }
From source file:eu.planets_project.tb.impl.chart.ExperimentExecutionCharts.java
public JFreeChart createXYChart(String expId) { ExperimentPersistencyRemote edao = ExperimentPersistencyImpl.getInstance(); long eid = Long.parseLong(expId); log.info("Building experiment chart for eid = " + eid); Experiment exp = edao.findExperiment(eid); final DefaultCategoryDataset dataset = new DefaultCategoryDataset(); final String expName = exp.getExperimentSetup().getBasicProperties().getExperimentName(); List<Boolean> success = new ArrayList<Boolean>(); for (BatchExecutionRecordImpl batch : exp.getExperimentExecutable().getBatchExecutionRecords()) { int i = 1; for (ExecutionRecordImpl exr : batch.getRuns()) { //log.info("Found Record... "+exr+" stages: "+exr.getStages()); if (exr != null && exr.getStages() != null) { // Look up the object, so we can get the name. DigitalObjectRefBean dh = new DataHandlerImpl().get(exr.getDigitalObjectReferenceCopy()); String dobName = "Object " + i; if (dh != null) dobName = dh.getName(); for (ExecutionStageRecordImpl exsr : exr.getStages()) { Double time = exsr.getDoubleMeasurement(TecRegMockup.PROP_SERVICE_TIME); // Look for timing: if (time != null) { dataset.addValue(time, expName, dobName); if (exsr.isMarkedAsSuccessful()) { success.add(Boolean.TRUE); } else { success.add(Boolean.FALSE); }// w w w .ja v a2 s . co m } } } // Increment, for the next run. i++; } } // Create the chart. JFreeChart chart = ChartFactory.createBarChart(null, "Digital Object", "Time [s]", dataset, PlotOrientation.VERTICAL, true, true, false); // set the background color for the chart... chart.setBackgroundPaint(Color.white); // get a reference to the plot for further customisation... final CategoryPlot plot = chart.getCategoryPlot(); plot.setBackgroundPaint(Color.lightGray); plot.setDomainGridlinePaint(Color.white); plot.setRangeGridlinePaint(Color.white); // set the range axis to display integers only... //final NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis(); //rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); Paint[] customColours = new Paint[success.size()]; for (int i = 0; i < success.size(); i++) { Boolean b = success.get(i); if (Boolean.TRUE.equals(b)) { customColours[i] = Color.GREEN; } else { customColours[i] = Color.RED; } } CategoryItemRenderer renderer = new CustomRenderer(customColours); // disable bar outlines... //final BarRenderer renderer = (BarRenderer) plot.getRenderer(); //renderer.setDrawBarOutline(false); plot.setRenderer(renderer); // set up gradient paints for series... final GradientPaint gp0 = new GradientPaint(0.0f, 0.0f, Color.blue, 0.0f, 0.0f, Color.blue); final GradientPaint gp1 = new GradientPaint(0.0f, 0.0f, Color.red, 0.0f, 0.0f, Color.pink); final GradientPaint gp2 = new GradientPaint(0.0f, 0.0f, Color.green, 0.0f, 0.0f, Color.lightGray); renderer.setSeriesPaint(0, gp0); renderer.setSeriesPaint(1, gp1); renderer.setSeriesPaint(2, gp2); // Set the tooltips... renderer.setBaseItemURLGenerator(new StandardCategoryURLGenerator("xy_chart.jsp", "series", "section")); renderer.setBaseToolTipGenerator(new StandardCategoryToolTipGenerator()); final CategoryAxis domainAxis = plot.getDomainAxis(); domainAxis.setCategoryLabelPositions(CategoryLabelPositions.createUpRotationLabelPositions(Math.PI / 4.0)); return chart; }
From source file:com.thalesgroup.hudson.plugins.cccc.CcccChartBuilder.java
protected JFreeChart createGraph() { JFreeChart chart = ChartFactory.createStackedAreaChart(null, null, "Number of modules", buildDataset(action), PlotOrientation.VERTICAL, true, false, true); chart.setBackgroundPaint(Color.white); CategoryPlot plot = chart.getCategoryPlot(); plot.setBackgroundPaint(Color.WHITE); plot.setOutlinePaint(null);/* ww w .ja va 2 s . co m*/ plot.setForegroundAlpha(0.8f); plot.setRangeGridlinesVisible(true); plot.setRangeGridlinePaint(Color.black); CategoryAxis domainAxis = new ShiftedCategoryAxis(null); plot.setDomainAxis(domainAxis); domainAxis.setCategoryLabelPositions(CategoryLabelPositions.UP_90); domainAxis.setLowerMargin(0.0); domainAxis.setUpperMargin(0.0); domainAxis.setCategoryMargin(0.0); NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis(); rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); // crop extra space around the graph plot.setInsets(new RectangleInsets(0, 0, 0, 5.0)); CategoryItemRenderer firstRender = new DefaultCategoryItemRenderer(); CcccAreaRenderer renderer = new CcccAreaRenderer(action.getUrlName()); plot.setRenderer(firstRender); //Second NumberAxis axis2 = new NumberAxis("Lines of Code"); axis2.setLabelPaint(Color.BLUE); axis2.setAxisLinePaint(Color.BLUE); axis2.setTickLabelPaint(Color.BLUE); CategoryPlot categoryPlot = chart.getCategoryPlot(); categoryPlot.setRangeAxis(1, axis2); //CategoryAxis categoryAxis = categoryPlot.getDomainAxis(); categoryPlot.setDataset(1, buildDataset2(action)); categoryPlot.mapDatasetToRangeAxis(1, 1); CategoryItemRenderer rendu = new DefaultCategoryItemRenderer(); rendu.setBasePaint(Color.BLUE); categoryPlot.setRenderer(1, rendu); //Third NumberAxis axis3 = new NumberAxis("McCabe's Cyclomatic Number"); axis3.setLabelPaint(Color.GREEN); axis3.setAxisLinePaint(Color.GREEN); axis3.setTickLabelPaint(Color.GREEN); CategoryPlot categoryPlot3 = chart.getCategoryPlot(); categoryPlot3.setRangeAxis(2, axis3); categoryPlot3.setDataset(2, buildDataset3(action)); categoryPlot3.mapDatasetToRangeAxis(2, 2); categoryPlot3.mapDatasetToDomainAxis(2, 0); CategoryItemRenderer rendu3 = new DefaultCategoryItemRenderer(); rendu3.setBasePaint(Color.GREEN); categoryPlot3.setRenderer(2, rendu3); return chart; }
From source file:com.twocents.report.charts.BarChartDemo1.java
/** * Creates a sample chart./*w w w. ja v a 2 s . c o m*/ * * @param dataset the dataset. * * @return The chart. */ private static JFreeChart createChart(CategoryDataset dataset) { // create the chart... JFreeChart chart = ChartFactory.createBarChart("Bar Chart Demo 1", // chart title "Category", // domain axis label "Value", // range axis label dataset, // data PlotOrientation.VERTICAL, // orientation true, // include legend true, // tooltips? false // URLs? ); // NOW DO SOME OPTIONAL CUSTOMISATION OF THE CHART... // set the background color for the chart... chart.setBackgroundPaint(Color.white); // get a reference to the plot for further customisation... CategoryPlot plot = (CategoryPlot) chart.getPlot(); // ****************************************************************** // More than 150 demo applications are included with the JFreeChart // Developer Guide...for more information, see: // // > http://www.object-refinery.com/jfreechart/guide.html // // ****************************************************************** // set the range axis to display integers only... NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis(); rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); // disable bar outlines... BarRenderer renderer = (BarRenderer) plot.getRenderer(); renderer.setDrawBarOutline(false); // set up gradient paints for series... GradientPaint gp0 = new GradientPaint(0.0f, 0.0f, Color.blue, 0.0f, 0.0f, new Color(0, 0, 64)); GradientPaint gp1 = new GradientPaint(0.0f, 0.0f, Color.green, 0.0f, 0.0f, new Color(0, 64, 0)); GradientPaint gp2 = new GradientPaint(0.0f, 0.0f, Color.red, 0.0f, 0.0f, new Color(64, 0, 0)); renderer.setSeriesPaint(0, gp0); renderer.setSeriesPaint(1, gp1); renderer.setSeriesPaint(2, gp2); CategoryAxis domainAxis = plot.getDomainAxis(); domainAxis.setCategoryLabelPositions(CategoryLabelPositions.createUpRotationLabelPositions(Math.PI / 6.0)); // OPTIONAL CUSTOMISATION COMPLETED. return chart; }
From source file:rod_design_compute.ShowPanel.java
private void paintSR(SR rodSR, Graphics g) { Graphics2D g2d = (Graphics2D) g; g2d.setStroke(new BasicStroke(2f)); if (rodSR.flag == true) { g2d.setColor(Color.red);/*from w ww . j a va 2 s . c o m*/ g.drawLine(toScreenX(rodSR.getPointA().X), toScreenY(rodSR.getPointA().Y), toScreenX(rodSR.getPointE().X), toScreenY(rodSR.getPointE().Y)); g.drawLine(toScreenX(rodSR.getPointB().X), toScreenY(rodSR.getPointB().Y), toScreenX(rodSR.getPointE().X), toScreenY(rodSR.getPointE().Y)); drawOtherPoint(rodSR.getPointE(), g); g2d.setColor(Color.black); } g2d.setColor(Color.green); g.drawLine(toScreenX(rodSR.getPointA().X), toScreenY(rodSR.getPointA().Y), toScreenX(rodSR.getPointB().X), toScreenY(rodSR.getPointB().Y)); g2d.setColor(Color.black); drawBasePoint(rodSR.getPointA(), g); drawJunctionPoint(rodSR.getPointB(), g); }
From source file:lab10part2.Chart.java
private JFreeChart createChart(final CategoryDataset dataset) { // create the chart... final JFreeChart chart = ChartFactory.createBarChart("Bar Chart Demo", // chart title "Category", // domain axis label "Value", // range axis label dataset, // data PlotOrientation.VERTICAL, // orientation true, // include legend true, // tooltips? false // URLs? );/*w w w. ja v a 2 s. com*/ // NOW DO SOME OPTIONAL CUSTOMISATION OF THE CHART... // set the background color for the chart... chart.setBackgroundPaint(Color.white); // get a reference to the plot for further customisation... final CategoryPlot plot = chart.getCategoryPlot(); plot.setBackgroundPaint(Color.lightGray); plot.setDomainGridlinePaint(Color.white); plot.setRangeGridlinePaint(Color.white); // set the range axis to display integers only... final NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis(); rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); // disable bar outlines... final BarRenderer renderer = (BarRenderer) plot.getRenderer(); renderer.setDrawBarOutline(false); // set up gradient paints for series... final GradientPaint gp0 = new GradientPaint(0.0f, 0.0f, Color.blue, 0.0f, 0.0f, Color.lightGray); final GradientPaint gp1 = new GradientPaint(0.0f, 0.0f, Color.green, 0.0f, 0.0f, Color.lightGray); final GradientPaint gp2 = new GradientPaint(0.0f, 0.0f, Color.red, 0.0f, 0.0f, Color.lightGray); renderer.setSeriesPaint(0, gp0); renderer.setSeriesPaint(1, gp1); renderer.setSeriesPaint(2, gp2); final CategoryAxis domainAxis = plot.getDomainAxis(); domainAxis.setCategoryLabelPositions(CategoryLabelPositions.createUpRotationLabelPositions(Math.PI / 6.0)); // OPTIONAL CUSTOMISATION COMPLETED. return chart; }