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From source file:probe.com.view.body.quantdatasetsoverview.quantproteinstabsheet.studies.ProteinStudyComparisonScatterPlotLayout.java
/** * Creates a sample jFreeChart.//w ww . j a v a2s .c o m * * @param dataset the dataset. * * @return The jFreeChart. */ private void generateScatterplotchart(DiseaseGroupsComparisonsProteinLayout cp, int w, int h) { final XYSeriesCollection dataset = new XYSeriesCollection(); XYSeries downSer = new XYSeries(0); XYSeries stableSer = new XYSeries(1); XYSeries upSer = new XYSeries(2); XYSeries novalueProvidedSer = new XYSeries(3); XYSeries downSerII = new XYSeries(4); XYSeries stableSerII = new XYSeries(5); XYSeries upSerII = new XYSeries(6); XYSeries novalueProvidedSerII = new XYSeries(7); // XYSeries plusSeries = new XYSeries(6); double downCounter = 1; double stableCounter = 3; double upCounter = 5; double novalueProvidedCounter = 3; patientGroupsNumToDsIdMap.clear(); final Map<Integer, int[]> paTGrNumbtrendMap = new HashMap<Integer, int[]>(); double maxPatNumber = -1.0; for (String protTrend : cp.getPatientsNumToTrindMap().keySet()) { List<Integer> patNums = cp.getPatientsNumToTrindMap().get(protTrend); int coun = 0; for (int i : patNums) { if (i > maxPatNumber) { maxPatNumber = i; } if (!patientGroupsNumToDsIdMap.containsKey(i)) { ComparisonDetailsBean pGr = new ComparisonDetailsBean(); patientGroupsNumToDsIdMap.put(i, pGr); } if (!paTGrNumbtrendMap.containsKey(i)) { int[] values = new int[4]; paTGrNumbtrendMap.put(i, values); } int[] values = paTGrNumbtrendMap.get(i); ComparisonDetailsBean pGr = patientGroupsNumToDsIdMap.get(i); if (protTrend.equalsIgnoreCase("noValueProvided")) { values[3] = values[3] + 1; pGr.addNovalueProvided(cp.getDSID(3, coun)); } else if (protTrend.equalsIgnoreCase("up")) { values[2] = values[2] + 1; pGr.addUpRegulated(cp.getDSID(0, coun)); } else if (protTrend.equalsIgnoreCase("down")) { values[0] = values[0] + 1; pGr.addDownRegulated(cp.getDSID(2, coun)); } else { values[1] = values[1] + 1; pGr.addNotRegulated(cp.getDSID(1, coun)); } paTGrNumbtrendMap.put(i, values); patientGroupsNumToDsIdMap.put(i, pGr); coun++; } } for (int i : paTGrNumbtrendMap.keySet()) { int[] values = paTGrNumbtrendMap.get(i); if ((values[2] > 1)) { upSer.add(upCounter, i); upSerII.add(upCounter, i); } else if ((values[2] == 1)) { upSer.add(upCounter, i); } if ((values[1] == 1)) { stableSer.add(stableCounter, i); } else if ((values[1] > 1)) { stableSer.add(stableCounter, i); stableSerII.add(stableCounter, i); } if ((values[0] > 1)) { downSer.add(downCounter, i); downSerII.add(downCounter, i); } else if ((values[0] == 1)) { downSer.add(downCounter, i); } if ((values[3] == 1)) { novalueProvidedSer.add(novalueProvidedCounter, i); } else if ((values[3] > 1)) { novalueProvidedSer.add(stableCounter, i); novalueProvidedSerII.add(stableCounter, i); } } dataset.addSeries(downSer); dataset.addSeries(stableSer); dataset.addSeries(upSer); dataset.addSeries(novalueProvidedSer); dataset.addSeries(downSerII); dataset.addSeries(stableSerII); dataset.addSeries(upSerII); dataset.addSeries(novalueProvidedSerII); // if((downSerII.getItemCount()+stableSerII.getItemCount()+upSerII.getItemCount()+downSer.getItemCount()+stableSer.getItemCount()+upSer.getItemCount())==0) // return; // dataset.addSeries(plusSeries); final String[] labels = new String[] { " ", ("Decreased (" + cp.getSignificantDown() + ")"), " ", ("Equal (" + cp.getStable() + ")"), " ", ("Increased (" + cp.getSignificantUp() + ")"), "" }; final Color[] labelsColor = new Color[] { Color.LIGHT_GRAY, new Color(80, 183, 71), Color.LIGHT_GRAY, new Color(1, 141, 244), Color.LIGHT_GRAY, Color.RED, Color.LIGHT_GRAY }; final SymbolAxis domainAxis = new SymbolAxis("X", labels) { @Override protected void drawGridBandsVertical(Graphics2D g2, Rectangle2D drawArea, Rectangle2D plotArea, boolean firstGridBandIsDark, List ticks) { List udatedTicksList = new ArrayList(); for (Object tick : ticks) { if (tick.toString().equalsIgnoreCase(labels[custTrend + 1])) { udatedTicksList.add(tick); } } // System.out.println("at ticks is "+ticks); // System.out.println("at udatedTicksList is "+udatedTicksList); // int factor = (int) ((plotArea.getHeight() / 5) * 0.25); // // Rectangle2D up = new Rectangle((int) drawArea.getX(), (int) drawArea.getY() - factor, (int) drawArea.getWidth(), (int) drawArea.getHeight()); // Rectangle2D pa = new Rectangle((int) plotArea.getX(), (int) plotArea.getY() - factor, (int) plotArea.getWidth(), (int) plotArea.getHeight()); super.drawGridBandsVertical(g2, drawArea, plotArea, firstGridBandIsDark, udatedTicksList); //To change body of generated methods, choose Tools | Templates. } int x = 0; @Override public Paint getTickLabelPaint() { if (x >= labels.length) { x = 0; } return labelsColor[x++]; } }; domainAxis.setAutoRangeIncludesZero(false); Font f = new Font("Verdana", Font.PLAIN, 11); domainAxis.setTickLabelFont(f); domainAxis.setAutoRange(false); domainAxis.setLabel(null); // domainAxis.setGridBandsVisible(false); String xTile = "#Patients"; JFreeChart jFreeChart = ChartFactory.createScatterPlot(null, null, // domain axis label null, // range axis label dataset, // data PlotOrientation.HORIZONTAL, // orientation false, // include legend false, // tooltips? false // URLs? ); XYPlot plot1 = (XYPlot) jFreeChart.getPlot(); XYPlot xyplot = new XYPlot(dataset, plot1.getDomainAxis(), plot1.getRangeAxis(), plot1.getRenderer()) { @Override public void drawDomainTickBands(Graphics2D g2, Rectangle2D dataArea, List ticks) { if (custTrend == -1) { super.drawDomainTickBands(g2, dataArea, ticks); return; } List udatedTicksList = new ArrayList(); for (Object tick : ticks) { if (tick.toString().equalsIgnoreCase(labels[custTrend + 1])) { udatedTicksList.add(tick); } } Rectangle2D up; int factor = (int) ((dataArea.getHeight() / 5) * 0.5); if (custTrend == 4) { up = new Rectangle((int) dataArea.getX(), (int) dataArea.getY() + factor, (int) dataArea.getWidth(), (int) dataArea.getHeight()); } else if (custTrend == 2) { up = new Rectangle((int) dataArea.getX(), (int) dataArea.getY() - factor, (int) dataArea.getWidth(), (int) dataArea.getHeight()); } else { up = new Rectangle((int) dataArea.getX(), (int) dataArea.getY() - factor, (int) dataArea.getWidth(), (int) dataArea.getHeight()); } super.drawDomainTickBands(g2, up, udatedTicksList); //To change body of generated methods, choose Tools | Templates. } @Override protected void drawDomainGridlines(Graphics2D g2, Rectangle2D dataArea, List ticks) { super.drawDomainGridlines(g2, dataArea, ticks); //To change body of generated methods, choose Tools | Templates. } private int x = 0; @Override public Paint getDomainGridlinePaint() { if (x >= labels.length) { x = 0; } if (x == 1 || x == 3 || x == 5) { x++; return Color.WHITE; } else { x++; return super.getDomainGridlinePaint(); //To change body of generated methods, choose Tools | Templates. } } }; if (custTrend != -1) { domainAxis.setGridBandsVisible(true); if (custTrend == 4) { domainAxis.setGridBandPaint(Color.decode("#ffe5e5")); xyplot.setDomainTickBandPaint(Color.decode("#ffe5e5")); domainAxis.setGridBandAlternatePaint(Color.decode("#ffe5e5")); } else if (custTrend == 0) { domainAxis.setGridBandPaint(Color.decode("#e5ffe5")); xyplot.setDomainTickBandPaint(Color.white); } else if (custTrend == 2) { domainAxis.setGridBandPaint(Color.decode("#e6f4ff")); xyplot.setDomainTickBandPaint(Color.white); } } else { domainAxis.setGridBandsVisible(false); } xyplot.setOrientation(PlotOrientation.HORIZONTAL); JFreeChart tempScatterPlot = new JFreeChart(xyplot); tempScatterPlot.setBackgroundPaint(Color.WHITE); tempScatterPlot.getLegend().setVisible(false); Color c = new Color(242, 242, 242); xyplot.setDomainAxis(domainAxis); xyplot.setDomainGridlinePaint(Color.GRAY); xyplot.setDomainGridlinesVisible(true); xyplot.setRangeGridlinesVisible(true); xyplot.setRangeGridlinePaint(Color.GRAY); xyplot.setOutlinePaint(Color.GRAY); XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) xyplot.getRenderer(); ValueAxis va = xyplot.getDomainAxis(); va.setAutoRange(false); va.setMinorTickCount(0); va.setVisible(true); maxPatNumber = Math.ceil(maxPatNumber / 100.0) * 100; xyplot.getRangeAxis().setRange(0, maxPatNumber); NumberAxis rangeAxis = (NumberAxis) xyplot.getRangeAxis(); rangeAxis.setTickUnit(new NumberTickUnit(10)); rangeAxis.setLabel(xTile); rangeAxis.setLabelFont(f); rangeAxis.setLabelPaint(Color.GRAY); va.setRange(0, 6); xyplot.setBackgroundPaint(Color.WHITE); renderer.setUseOutlinePaint(true); Color c0 = new Color(80, 183, 71); renderer.setSeriesPaint(0, c0); renderer.setSeriesOutlinePaint(0, Color.WHITE); Color c1 = new Color(1, 141, 244); renderer.setSeriesPaint(1, c1); renderer.setSeriesOutlinePaint(1, Color.WHITE); Color c2 = new Color(204, 0, 0); renderer.setSeriesPaint(2, c2); renderer.setSeriesOutlinePaint(2, Color.WHITE); renderer.setSeriesPaint(3, Color.decode("#b5babb")); renderer.setSeriesOutlinePaint(3, Color.WHITE); renderer.setSeriesPaint(4, new Color(150, 212, 145)); renderer.setSeriesOutlinePaint(4, new Color(150, 212, 145)); renderer.setSeriesPaint(5, new Color(103, 187, 248)); renderer.setSeriesOutlinePaint(5, new Color(103, 187, 248)); renderer.setSeriesPaint(6, new Color(224, 102, 102)); renderer.setSeriesOutlinePaint(6, new Color(224, 102, 102)); renderer.setSeriesPaint(7, Color.decode("#b5babb")); renderer.setSeriesOutlinePaint(7, Color.GRAY); // renderer.setSeriesPaint(6, Color.BLACK); // renderer.setSeriesOutlinePaint(6, Color.BLACK); Shape downArr = ShapeUtilities.createDownTriangle(7f); Shape notRShape = ShapeUtilities.createDiamond(7f); Shape upArr = ShapeUtilities.createUpTriangle(7); Shape downArrII = ShapeUtilities.createTranslatedShape(ShapeUtilities.createDownTriangle(6f), 5, -5); Shape notRShapeII = ShapeUtilities.createTranslatedShape(ShapeUtilities.createDiamond(6f), 0, -7); Shape upArrII = ShapeUtilities.createTranslatedShape(ShapeUtilities.createUpTriangle(6f), 4, -4); // Shape plus = ShapeUtilities.createTranslatedShape(ShapeUtilities.createRegularCross(3f, 0.4f), 11, -7); renderer.setSeriesShape(0, downArr); renderer.setSeriesShape(1, notRShape); renderer.setSeriesShape(2, upArr); renderer.setSeriesShape(3, notRShape); renderer.setSeriesShape(4, downArrII); renderer.setSeriesShape(5, notRShapeII); renderer.setSeriesShape(6, upArrII); renderer.setSeriesShape(7, notRShapeII); // renderer.setSeriesShape(6, plus); renderer.setBaseItemLabelsVisible(true); renderer.setBaseItemLabelGenerator(new SymbolicXYItemLabelGenerator() { private final int[] indexer = new int[] { 0, 1, 2, 3, 0, 1, 2, 3 }; @Override public String generateLabel(XYDataset dataset, int series, int category) { if (series > 3) { int patNumber = (int) dataset.getYValue(series, category); // int trend = (int) dataset.getXValue(series, category); if (series == 7 || series == 5) { return "\t " + paTGrNumbtrendMap.get(patNumber)[indexer[series]]; } else { return "\t " + paTGrNumbtrendMap.get(patNumber)[indexer[series]]; } } return ""; //To change body of generated methods, choose Tools | Templates. } }); ItemLabelPosition position = new ItemLabelPosition(ItemLabelAnchor.OUTSIDE12, TextAnchor.BASELINE_LEFT, TextAnchor.TOP_LEFT, 0.0); renderer.setSeriesPositiveItemLabelPosition(4, position); renderer.setSeriesPositiveItemLabelPosition(5, position); renderer.setSeriesPositiveItemLabelPosition(6, position); renderer.setSeriesPositiveItemLabelPosition(7, position); renderer.setBaseItemLabelFont(f); tempScatterPlot.setBorderVisible(false); xyplot.setSeriesRenderingOrder(SeriesRenderingOrder.REVERSE); heighlightedScatterPlottImgUrl = saveToFile(tempScatterPlot, w, h, defaultScatterPlotRenderingInfo); xyplot.setBackgroundPaint(Color.WHITE); defaultScatterPlottImgUrl = saveToFile(tempScatterPlot, w, h, defaultScatterPlotRenderingInfo); // xyplot.setBackgroundPaint(c); if (custTrend != -1) { domainAxis.setGridBandsVisible(true); if (custTrend == 4) { domainAxis.setGridBandPaint(Color.decode("#ffe5e5")); xyplot.setDomainTickBandPaint(Color.decode("#ffe5e5")); domainAxis.setGridBandAlternatePaint(Color.decode("#ffe5e5")); } else if (custTrend == 0) { domainAxis.setGridBandPaint(Color.decode("#e5ffe5")); xyplot.setDomainTickBandPaint(c); } else if (custTrend == 2) { domainAxis.setGridBandPaint(Color.decode("#e6f4ff")); xyplot.setDomainTickBandPaint(c); } } String textTitle = comparisonTitle.getValue().split("bold;'>")[1].replace("</font>", ""); TextTitle title = new TextTitle(textTitle, f); scatterPlot = new JFreeChart(xyplot); scatterPlot.setTitle(title); scatterPlot.setBorderVisible(false); scatterPlot.setBackgroundPaint(Color.WHITE); scatterPlot.getLegend().setVisible(false); dsKeyDatasetMap.clear(); for (int i = 0; i < defaultScatterPlotRenderingInfo.getEntityCollection().getEntityCount(); i++) { final ChartEntity entity = defaultScatterPlotRenderingInfo.getEntityCollection().getEntity(i); if (entity instanceof XYItemEntity) { int x = ((XYItemEntity) entity).getSeriesIndex(); int y = ((XYItemEntity) entity).getItem(); if (((XYItemEntity) entity).getDataset().getYValue(x, y) > (int) ((XYItemEntity) entity).getDataset().getYValue(x, y)) { continue; } if (((XYItemEntity) entity).getSeriesIndex() > 3) { continue; } String[] arr = ((XYItemEntity) entity).getShapeCoords().split(","); int xSer = Integer.valueOf(arr[0]); int ySer = Integer.valueOf(arr[1]); int ySerEnd = Integer.valueOf(arr[3]); int patGrNumber = (int) ((XYItemEntity) entity).getDataset().getYValue(x, y); int trend = Integer.valueOf(((XYItemEntity) entity).getDataset() .getSeriesKey(((XYItemEntity) entity).getSeriesIndex()).toString()); ComparisonDetailsBean cpDetails = patientGroupsNumToDsIdMap.get(patGrNumber); List<Integer> dsList = cpDetails.getRegulatedList(trend); StringBuilder sb = new StringBuilder(); for (int dsId : dsList) { QuantDatasetObject ds; sb.append("<h4>").append((Quant_Central_Manager.getFullQuantDatasetMap().get(dsId)).getAuthor()) .append(" ") .append((Quant_Central_Manager.getFullQuantDatasetMap().get(dsId)).getYear()) .append("<h4/>"); sb.append("<p></p>"); ds = Quant_Central_Manager.getFullQuantDatasetMap().get(dsId); dsKeyDatasetMap.put("_-_" + dsId + "_-_" + comparisonProtein.getProteinAccssionNumber() + "_-_", ds); } String tooltip = sb.toString().substring(0, sb.toString().length() - 7); SquaredDot square = new SquaredDot("squared"); if (paTGrNumbtrendMap.get(patGrNumber)[trend] > 1) { square.setWidth(20 + "px"); square.setHeight(15 + "px"); } else { square.setWidth(10 + "px"); square.setHeight(10 + "px"); } square.setDescription(tooltip); square.setParam("trend", trend); square.setParam("pGrNumber", patGrNumber); int top = (ySer - 4); if (ySer > ySerEnd) { top = ySerEnd - 3; } defaultChartLayout.addComponent(square, "left: " + (xSer - 5) + "px; top: " + top + "px;"); } } }
From source file:com.diversityarrays.kdxplore.curate.SampleEntryPanel.java
private void updateSetValueAction() { boolean enableSet; SampleSource source = null;// w w w . java2 s . c o m if (sampleSourceControls.isVisible()) { source = getSelectedSampleSource(); } if (source != null) { enableSet = true; valueDescription.setText(null); // sampleValueTextField.setText(""); sampleValueTextField.setEnabled(false); } else { // Either "-- Please Select --" or nothing selected sampleValueTextField.setEnabled(true); String sampleValue = sampleValueTextField.getText().trim(); boolean statInField = false; StatType typeInField = null; if (kdsmartSampleStatistics != null) { for (StatType statType : statTypeByButton.values()) { String value = String.valueOf(statType.getStatValue(kdsmartSampleStatistics)); if (sampleValue.equals(value)) { statInField = true; typeInField = statType; break; } } } String validMsg = null; String valueDesc = sampleValue.isEmpty() ? null : EDITED_VALUE; if (sampleValue.isEmpty()) { enableSet = false; } else if (statInField) { valueDesc = typeInField.name(); enableSet = true; } else if (isMissingOrNA(sampleValue)) { enableSet = true; } else { ValidationRule valRule = getValidationRule(); if (NO_VALIDATION_RULE == valRule) { enableSet = true; } else if (valRule.evaluate(sampleValue)) { enableSet = true; } else { validMsg = valRule.getDescription(); enableSet = false; } } valueDescription.setText(valueDesc); if (Check.isEmpty(validMsg)) { validationMessage.setText("--"); validationMessage.setForeground(Color.GRAY); // validationMessage.setForeground(validationMessage.getBackground()); } else { validationMessage.setText(validMsg); validationMessage.setForeground(Color.RED); } showChangedValue.accept(Check.isEmpty(sampleValue) ? null : sampleValue, curationCellValues); } setValueAction.setEnabled(enableSet); }
From source file:gg.msn.ui.panel.MainPanel.java
@Override public void paint(Graphics g) { super.paint(g); try {// www . j a v a 2 s . co m Graphics2D g2 = (Graphics2D) g; g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g2.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_LCD_HRGB); g2.setRenderingHint(RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BILINEAR); //render per utenti Facebook if (ChatClientView.protocol.equals(ChatClientView.FACEBOOK_PROTOCOL)) { final FacebookUser user = (FacebookUser) value; int textY = (getHeight() / 2) + (g2.getFont().getSize() / 2); //name string g2.setFont(list.getFont()); g2.drawString(user.name, WHITE_SPACE + IMAGE_LATE + 3, textY); //status string // g2.setFont(list.getFont()); // g2.drawString(user.status, WHITE_SPACE + IMAGE_LATE + 3, textY); //icon ImageIcon icon = user.portrait; //log.debug("icon [" + icon + "]"); //ImageIcon scaledIcon = new ImageIcon(icon.getImage().getScaledInstance(24, 24, Image.SCALE_AREA_AVERAGING)); g2.drawImage(icon.getImage(), WHITE_SPACE, getHeight() / 2 - (IMAGE_LATE / 2), IMAGE_LATE, IMAGE_LATE, null); // g2.setColor(Color.WHITE); // g2.drawRoundRect(WHITE_SPACE, getHeight() / 2 - (IMAGE_LATE / 2), IMAGE_LATE, IMAGE_LATE, ARC_SIZE, ARC_SIZE); // g2.drawRoundRect(WHITE_SPACE, getHeight() / 2 - ((IMAGE_LATE+1) / 2), IMAGE_LATE+1, IMAGE_LATE+1, ARC_SIZE, ARC_SIZE); // g2.drawRoundRect(WHITE_SPACE, getHeight() / 2 - ((IMAGE_LATE+2) / 2), IMAGE_LATE+2, IMAGE_LATE+2, ARC_SIZE, ARC_SIZE); //render per utenti Client // log.debug("user status [" + user.status + "]"); // log.debug("user online status [" + user.onlineStatus + "]"); if (StringUtils.equals(user.status, FacebookUser.STATUS_ONLINE)) { g2.setColor(Color.GREEN); g2.fillOval(getWidth() - STATUS_ICON_OFFSET, (getHeight() / 2) - (STATUS_ICON_WIDTH / 2), STATUS_ICON_WIDTH, STATUS_ICON_WIDTH); } else { g2.setColor(Color.GRAY); g2.fillOval(getWidth() - STATUS_ICON_OFFSET, (getHeight() / 2) - (STATUS_ICON_WIDTH / 2), STATUS_ICON_WIDTH, STATUS_ICON_WIDTH); } } else { g2.setFont(list.getFont()); int textY = (getHeight() / 2) + (g2.getFont().getSize() / 2); Client client = (Client) value; // setText((client).getNick()); ImageIcon icon = null; try { new ImageIcon(client.getImage()); } catch (Exception e) { // log.debug("immgine non presente"); icon = ThemeManager.getTheme().get(ThemeManager.USER_ICON); } g2.drawString(client.getNick(), WHITE_SPACE + IMAGE_LATE + 3, textY); //log.debug("icon [" + icon + "]"); //ImageIcon scaledIcon = new ImageIcon(icon.getImage().getScaledInstance(24, 24, Image.SCALE_AREA_AVERAGING)); g2.drawImage(icon.getImage(), WHITE_SPACE, getHeight() / 2 - (IMAGE_LATE / 2), IMAGE_LATE, IMAGE_LATE, null); // setFont(list.getFont()); // setIcon(scaledIcon); } } catch (Exception e) { log.warn(e); } }
From source file:citation_prediction.CitationCore.java
/** * This function will take a list of WSB solutions and graph them. You can add solutions to the graph by saving * the return of the function the first time and passing it back in on the next call as the 'plot'. * //from w w w . j a v a 2s.c om * * @param data_in_days The citation data distributed mostly even in days (call fixdata function if data is in years). * @param m The average number of new references in each new paper for a journal. * @param plot The plot you would like the WSB solution plotted to. * @param graphTitle The title to display on the JPanel. * @param lineLegend The title of this curve. * @param wsbSolutions The list of WSB solutions to graph. * @param showGraph Display the graph to the user (generally called once all curves have been added.) * @param frame The frame to display the graph in. * @return A Panel containing the graph. */ public Plot2DPanel graphWSB(double[][] data_in_days, double m, Plot2DPanel plot, String graphTitle, String lineLegend, ArrayList<LinkedHashMap<String, Double>> wsbSolutions, boolean showGraph, JFrame frame) { //source of library: http://code.google.com/p/jmathplot/ int plotLength = data_in_days.length + (365 * 3); double[][] data_in_years = new double[plotLength][2]; //Translate the data into years instead of days for (int i = 0; i < data_in_days.length; i++) { data_in_years[i][0] = data_in_days[i][0] / 365; data_in_years[i][1] = data_in_days[i][1]; } for (int i = data_in_days.length; i < plotLength; i++) { data_in_years[i][0] = data_in_years[i - 1][0] + .025; data_in_years[i][1] = data_in_years[data_in_days.length - 1][1]; } if (plot == null) { plot = new Plot2DPanel(); plot.addScatterPlot("Actual Citations", data_in_years); //Plot the data } //Extract the timevalue column RealMatrix mdata = MatrixUtils.createRealMatrix(data_in_years); double[] tvalues = mdata.getColumn(0); double[] cvalues = new double[plotLength]; for (LinkedHashMap<String, Double> s : wsbSolutions) { //calculate their fitted y values for (int i = 0; i < plotLength; i++) { cvalues[i] = m * (Math.exp( s.get("lambda") * pnorm((Math.log(365 * tvalues[i]) - s.get("mu")) / s.get("sigma"))) - 1); } //Calculate the Ultimate Impact double c_impact = m * (Math.exp(s.get("lambda")) - 1); //plot the fit plot.addLinePlot("Ultimate Impact=" + c_impact + " :: " + lineLegend, tvalues, cvalues); } // put the PlotPanel in a JFrame, as a JPanel if (showGraph) { plot.setAxisLabel(0, "Time in Years"); plot.setAxisLabel(1, "Cumulative Citations"); //Uncomment these if you wish to have fixed axis. //plot.setFixedBounds(1, 0, 500); //plot.setFixedBounds(0, 0, 60); // Add the file Title BaseLabel filetitle = new BaseLabel(graphTitle, Color.GRAY, 0.5, 1.1); filetitle.setFont(new Font("Courier", Font.BOLD, 13)); plot.addPlotable(filetitle); plot.addLegend("SOUTH"); //JFrame frame = new JFrame(graphTitle); frame.setTitle(graphTitle); frame.setContentPane(plot); frame.setBounds(0, 0, 1000, 800); frame.setVisible(true); frame.repaint(); } return plot; }
From source file:com.att.aro.main.GraphPanel.java
/** * Initializes a new instance of the GraphPanel class. *///w w w .ja v a2 s . c o m public GraphPanel() { subplotMap.put(ChartPlotOptions.GPS, new GraphPanelPlotLabels(rb.getString("chart.gps"), createBarPlot(Color.gray), 1)); subplotMap.put(ChartPlotOptions.RADIO, new GraphPanelPlotLabels(rb.getString("chart.radio"), createRadioPlot(), 2)); subplotMap.put(ChartPlotOptions.BLUETOOTH, new GraphPanelPlotLabels(rb.getString("chart.bluetooth"), createBarPlot(Color.gray), 1)); subplotMap.put(ChartPlotOptions.CAMERA, new GraphPanelPlotLabels(rb.getString("chart.camera"), createBarPlot(Color.gray), 1)); subplotMap.put(ChartPlotOptions.SCREEN, new GraphPanelPlotLabels(rb.getString("chart.screen"), createBarPlot(new Color(34, 177, 76)), 1)); subplotMap.put(ChartPlotOptions.BATTERY, new GraphPanelPlotLabels(rb.getString("chart.battery"), createBatteryPlot(), 2)); subplotMap.put(ChartPlotOptions.WIFI, new GraphPanelPlotLabels(rb.getString("chart.wifi"), createBarPlot(Color.gray), 1)); subplotMap.put(ChartPlotOptions.NETWORK_TYPE, new GraphPanelPlotLabels(rb.getString("chart.networkType"), createBarPlot(Color.gray), 1)); subplotMap.put(ChartPlotOptions.THROUGHPUT, new GraphPanelPlotLabels(rb.getString("chart.throughput"), createThroughputPlot(), 2)); subplotMap.put(ChartPlotOptions.BURSTS, new GraphPanelPlotLabels(rb.getString("chart.bursts"), createBurstPlot(), 1)); subplotMap.put(ChartPlotOptions.USER_INPUT, new GraphPanelPlotLabels(rb.getString("chart.userInput"), createUserEventPlot(), 1)); subplotMap.put(ChartPlotOptions.RRC, new GraphPanelPlotLabels(rb.getString("chart.rrc"), createRrcPlot(), 1)); subplotMap.put(ChartPlotOptions.CPU, new GraphPanelPlotLabels(rb.getString("chart.cpu"), createCpuPlot(), 1)); this.pp = new PacketPlots(); subplotMap.put(ChartPlotOptions.UL_PACKETS, new GraphPanelPlotLabels(rb.getString("chart.ul"), pp.getUlPlot(), 1)); subplotMap.put(ChartPlotOptions.DL_PACKETS, new GraphPanelPlotLabels(rb.getString("chart.dl"), pp.getDlPlot(), 1)); this.axis = new NumberAxis(); this.axis.setStandardTickUnits(UNITS); this.axis.setRange(new Range(0, DEFAULT_TIMELINE)); this.axis.setLowerBound(0); this.axis.setAutoTickUnitSelection(true); this.axis.setTickMarkInsideLength(1); this.axis.setTickMarkOutsideLength(1); this.axis.setMinorTickMarksVisible(true); this.axis.setMinorTickMarkInsideLength(2f); this.axis.setMinorTickMarkOutsideLength(2f); this.axis.setTickMarkInsideLength(4f); this.axis.setTickMarkOutsideLength(4f); this.axisLabel = new JLabel(rb.getString("chart.timeline")); this.axisLabel.setHorizontalAlignment(SwingConstants.CENTER); this.setLayout(new BorderLayout()); this.setPreferredSize(new Dimension(200, 310)); this.add(getZoomSavePanel(), BorderLayout.EAST); this.add(getPane(), BorderLayout.CENTER); this.add(getLabelsPanel(), BorderLayout.WEST); setChartOptions(UserPreferences.getInstance().getChartPlotOptions()); }
From source file:cn.InstFS.wkr.NetworkMining.UIs.TimeSeriesChart1.java
public static Color getcolor(int i) { switch (i) {//from w w w . ja v a2 s . co m case 1: return Color.red; case 2: return Color.blue; case 3: return Color.cyan; case 4: return Color.gray; case 5: return Color.green; case 6: return Color.magenta; case 7: return Color.orange; case 8: return Color.yellow; case 9: return Color.white; case 0: return Color.pink; default: return Color.black; } }
From source file:net.java.sip.communicator.impl.gui.main.chat.ChatPanel.java
/** * Initializes the typing notification label. * @param typingLabelParent the parent container * of typing notification label. *///from w w w . j a v a 2 s. c o m private void initTypingNotificationLabel(JPanel typingLabelParent) { typingNotificationLabel = new JLabel(" ", SwingConstants.CENTER); typingNotificationLabel.setPreferredSize(new Dimension(500, 20)); typingNotificationLabel.setForeground(Color.GRAY); typingNotificationLabel.setFont(typingNotificationLabel.getFont().deriveFont(11f)); typingNotificationLabel.setVerticalTextPosition(JLabel.BOTTOM); typingNotificationLabel.setHorizontalTextPosition(JLabel.LEFT); typingNotificationLabel.setIconTextGap(0); typingLabelParent.add(typingNotificationLabel, BorderLayout.SOUTH); }
From source file:cool.pandora.modeller.ui.jpanel.base.BagView.java
/** * createBagButtonPanel.//from w w w.ja va 2s .c o m * * @return buttonPanel */ private JPanel createBagButtonPanel() { addDataHandler = new AddDataHandler(this); removeDataHandler = new RemoveDataHandler(this); final JPanel buttonPanel = new JPanel(); buttonPanel.setLayout(new FlowLayout(FlowLayout.RIGHT, 2, 2)); addDataToolBarAction = new JLabel(""); addDataToolBarAction.setEnabled(false); addDataToolBarAction.setHorizontalAlignment(SwingConstants.CENTER); addDataToolBarAction.setBorder(new LineBorder(addDataToolBarAction.getBackground(), 1)); addDataToolBarAction.setIcon(getPropertyImage("Bag_Content.add.icon")); addDataToolBarAction.setToolTipText(getMessage("bagView.payloadTree.addbutton.tooltip")); addDataToolBarAction.addMouseListener(new MouseAdapter() { @Override public void mousePressed(final MouseEvent e) { if (addDataToolBarAction.isEnabled()) { addDataHandler.actionPerformed(null); } } @Override public void mouseExited(final MouseEvent e) { addDataToolBarAction.setBorder(new LineBorder(addDataToolBarAction.getBackground(), 1)); } @Override public void mouseEntered(final MouseEvent e) { if (addDataToolBarAction.isEnabled()) { addDataToolBarAction.setBorder(new LineBorder(Color.GRAY, 1)); } } }); buttonPanel.add(addDataToolBarAction); removeDataToolBarAction = new JLabel(""); removeDataToolBarAction.setEnabled(false); removeDataToolBarAction.setHorizontalAlignment(SwingConstants.CENTER); removeDataToolBarAction.setBorder(new LineBorder(removeDataToolBarAction.getBackground(), 1)); removeDataToolBarAction.setIcon(getPropertyImage("Bag_Content.minus.icon")); removeDataToolBarAction.setToolTipText(getMessage("bagView.payloadTree.remove.tooltip")); buttonPanel.add(removeDataToolBarAction); removeDataToolBarAction.addMouseListener(new MouseAdapter() { @Override public void mousePressed(final MouseEvent e) { if (removeDataToolBarAction.isEnabled()) { removeDataHandler.actionPerformed(null); } } @Override public void mouseExited(final MouseEvent e) { removeDataToolBarAction.setBorder(new LineBorder(removeDataToolBarAction.getBackground(), 1)); } @Override public void mouseEntered(final MouseEvent e) { if (removeDataToolBarAction.isEnabled()) { removeDataToolBarAction.setBorder(new LineBorder(Color.GRAY, 1)); } } }); final JLabel spacerLabel = new JLabel(" "); buttonPanel.add(spacerLabel); addDataHandler = new AddDataHandler(this); removeDataHandler = new RemoveDataHandler(this); return buttonPanel; }
From source file:base.BasePlayer.ClusterTable.java
void drawScreen(Graphics g) { try {//from w w w . j av a2s . com buf.setColor(Color.black); buf.fillRect(0, 0, this.getWidth(), tablescroll.getViewport().getHeight()); genemutcount = 0; hoverVar = null; hoverSample = -1; headerHover = -1; geneHeaderHover = -1; if (!mouseDrag) { resizeColumn = -1; } if (Main.drawCanvas.clusterNodes != null) { firstrow = tablescroll.getVerticalScrollBar().getValue() / rowHeight - 1 - Main.drawCanvas.clusterNodes.size(); if (firstrow < 0) { firstrow = 0; } for (int i = 0; i < Main.drawCanvas.clusterNodes.size(); i++) { dot = false; if ((i + 1 + samplecount + Main.drawCanvas.clusterNodes.size()) * rowHeight < tablescroll .getVerticalScrollBar().getValue()) { continue; } if (i * rowHeight > tablescroll.getVerticalScrollBar().getValue() + tablescroll.getViewport().getHeight()) { break; } if (mouseY >= (rowHeight * (i + genemutcount + 1)) && mouseY < (rowHeight * (i + genemutcount + 2))) { hoverNode = Main.drawCanvas.clusterNodes.get(i); } try { buf.setColor(Color.darkGray); buf.drawLine(4, (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 3, this.getWidth(), (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 3); buf.setColor(linecolor); cluster = Main.drawCanvas.clusterNodes.get(i); if (cluster.varnodes.get(0).getTranscripts() != null) { if (!chrom.equals(cluster.varnodes.get(0).getTranscripts().get(0).getChrom())) { chrom = cluster.varnodes.get(0).getTranscripts().get(0).getChrom(); } } else { if (!chrom.equals(cluster.varnodes.get(0).getExons().get(0).transcript.getChrom())) { chrom = cluster.varnodes.get(0).getExons().get(0).transcript.getChrom(); } } for (int c = 0; c < header.size(); c++) { if (Main.drawCanvas.clusterNodes.get(i).equals(hoverNode) || Main.drawCanvas.clusterNodes.get(i).equals(selectedNode)) { buf.setColor(Color.yellow); } else { buf.setColor(Color.white); } if (c == 0) { buf.drawString("" + cluster.ID, (int) header.get(c)[1] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else if (c == 1) { buf.drawString("" + cluster.nodecount, (int) header.get(c)[1] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else if (c == 2) { buf.drawString("" + cluster.width, (int) header.get(c)[1] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else if (c == 3) { buf.drawString( chrom + ":" + MethodLibrary.formatNumber(cluster.varnodes.get(0).getPosition()), (int) header.get(c)[1] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else if (c == 4) { buf.drawString( "" + MethodLibrary.round((cluster.nodecount / (double) cluster.width), 4), (int) header.get(c)[1] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else if (c == 5) { if (cluster.varnodes.get(0).getExons() != null) { if (cluster.varnodes.get(0).coding) { buf.setColor(Color.red); buf.drawString( cluster.varnodes.get(0).getExons().get(0).getTranscript() .getGenename() + " (Coding)", (int) header.get(c)[1] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { buf.setColor(Color.lightGray); buf.drawString( cluster.varnodes.get(0).getExons().get(0).getTranscript() .getGenename() + " (UTR)", (int) header.get(c)[1] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } else if (cluster.varnodes.get(0).isInGene()) { buf.setColor(Color.lightGray); buf.drawString( cluster.varnodes.get(0).getTranscripts().get(0).getGenename() + " (Intronic)", (int) header.get(c)[1] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { buf.setColor(Color.gray); if (!cluster.varnodes.get(0).getTranscripts().get(0) .equals(cluster.varnodes.get(0).getTranscripts().get(1))) { buf.drawString( cluster.varnodes.get(0).getTranscripts().get(0).getGenename() + " ... " + cluster.varnodes .get(0).getTranscripts().get(1).getGenename(), (int) header.get(c)[1] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { if (cluster.varnodes.get(0).getTranscripts().get(0) .getEnd() > cluster.varnodes.get(0).getPosition()) { buf.drawString( " ... " + cluster.varnodes .get(0).getTranscripts().get(0).getGenename(), (int) header.get(c)[1] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { buf.drawString( cluster.varnodes.get(0).getTranscripts().get(0).getGenename() + " ... ", (int) header.get(c)[1] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } } } else if (c == 6) { if (cluster.varnodes.get(0).getBedHits() != null) { bedarray = MethodLibrary.makeTrackArray(cluster.varnodes.get(0), null); for (int b = 0; b < bedarray.length; b++) { buf.setColor(Color.black); if (b == bedarray.length - 1) { buf.fillRect((int) header.get(c + b)[1] + 1, (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth() - (int) header.get(c + b)[1], rowHeight - 1); } else { buf.fillRect((int) header.get(c + b)[1] + 1, (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 4, (int) header.get(c + b)[2], rowHeight - 1); } buf.setColor(Color.white); if (bedarray[b] != null) { buf.drawString(bedarray[b].toString(), (int) header.get(c + b)[1] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } } } if (c < header.size() - 1 - Main.bedCanvas.bedTrack.size()) { buf.setColor(Color.black); buf.fillRect((int) header.get(c + 1)[1] + 1, (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 4, (int) header.get(c + 1)[2], rowHeight - 1); } } buf.setColor(Color.darkGray); buf.drawLine(3, rowHeight + 3, 3, (rowHeight * (i + genemutcount + 2)) - tablescroll.getVerticalScrollBar().getValue() + 3); for (int r = 0; r < header.size(); r++) { buf.drawLine((int) header.get(r)[1], (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 4, (int) header.get(r)[1], (rowHeight * (i + genemutcount + 2)) - tablescroll.getVerticalScrollBar().getValue() + 3); } if (selectedNode != null && selectedNode.equals(cluster)) { hoverSample = -1; genemutcount = aminoarray.size() + 1; listAdd = 1; buf.drawLine(20, (rowHeight * (i + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 3, this.getWidth(), (rowHeight * (i + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 3); drawGeneheader((rowHeight * (i + listAdd + 1)) - tablescroll.getVerticalScrollBar().getValue() + 3); for (int s = 0; s < aminoarray.size(); s++) { buf.setColor(Color.darkGray); buf.drawLine(21, (rowHeight * (i + s + listAdd + 3)) - tablescroll.getVerticalScrollBar().getValue() + 3, this.getWidth(), (rowHeight * (i + s + listAdd + 3)) - tablescroll.getVerticalScrollBar().getValue() + 3); if (mouseY >= (rowHeight * (i + s + listAdd + 2)) && mouseY < (rowHeight * (i + s + listAdd + 3))) { hoverNode = null; hoverVar = aminoarray.get(s).getNode(); hoverString = aminoarray.get(s).getRow(); buf.setColor(Color.white); for (int v = 0; v < aminoarray.get(s).getNode().vars.size(); v++) { if (aminoarray.get(s).getNode().vars.get(v).getKey() .equals(aminoarray.get(s).getRow()[5])) { hoverSample = aminoarray.get(s).getNode().vars.get(v).getValue().get(0) .getSample().getIndex(); break; } } } else { if (MethodLibrary.aminoEffect(aminoarray.get(s).getRow()[3]) .equals("nonsense")) { buf.setColor(Color.red); } else if (MethodLibrary.aminoEffect(aminoarray.get(s).getRow()[3]) .equals("missense")) { buf.setColor(Color.yellow); } else if (MethodLibrary.aminoEffect(aminoarray.get(s).getRow()[3]) .equals("synonymous")) { buf.setColor(Color.green); } else if (MethodLibrary.aminoEffect(aminoarray.get(s).getRow()[3]) .equals("UTR")) { buf.setColor(Color.lightGray); } else { buf.setColor(Color.gray); } } if (!aminoarray.get(s).getRow()[1].equals("1")) { buf.drawString("Multiple", 24, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { for (int v = 0; v < aminoarray.get(s).getNode().vars.size(); v++) { if (aminoarray.get(s).getNode().vars.get(v).getKey() .equals(aminoarray.get(s).getRow()[5])) { buf.drawString( aminoarray.get(s).getNode().vars.get(v).getValue().get(0) .getSample().getName(), 24, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); break; } } } if (hoverVar != null && hoverString.equals(aminoarray.get(s).getRow())) { //TODO textcolor = Color.white; } else { if (MethodLibrary.aminoEffect(aminoarray.get(s).getRow()[3]) .equals("nonsense")) { textcolor = Color.red; } else if (MethodLibrary.aminoEffect(aminoarray.get(s).getRow()[3]) .equals("missense")) { textcolor = Color.yellow; } else if (MethodLibrary.aminoEffect(aminoarray.get(s).getRow()[3]) .equals("synonymous")) { textcolor = Color.green; } else if (aminoarray.get(s).getRow()[3].contains("UTR")) { textcolor = Color.lightGray; } else { textcolor = Color.gray; } } for (int h = 1; h < 4; h++) { buf.setColor(Color.black); buf.fillRect((int) geneheader.get(h)[1] + 10, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, (int) geneheader.get(h)[2], rowHeight - 1); buf.setColor(textcolor); buf.drawString(aminoarray.get(s).getRow()[h], (int) geneheader.get(h)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } if (aminoarray.get(s).getRow()[1].equals("1")) { buf.setColor(Color.black); buf.fillRect((int) geneheader.get(4)[1] + 10, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); for (int v = 0; v < aminoarray.get(s).getNode().vars.size(); v++) { if (aminoarray.get(s).getNode().vars.get(v).getKey() .equals(aminoarray.get(s).getRow()[5])) { if (aminoarray.get(s).getNode().vars.get(v).getValue().get(0) .isHomozygous()) { buf.drawString( "Hom (" + aminoarray.get(s).getNode().vars.get(v).getValue() .get(0).getCalls() + "/" + aminoarray.get(s).getNode().vars.get(v).getValue() .get(0).getCoverage() + ")", (int) geneheader.get(4)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); if (Control.controlData.controlsOn) { cases = 2; casefreq = 2 / (double) (Main.varsamples * 2); } } else { buf.drawString( "Het (" + aminoarray.get(s).getNode().vars.get(v).getValue() .get(0).getCalls() + "/" + aminoarray.get(s).getNode().vars.get(v).getValue() .get(0).getCoverage() + ")", (int) geneheader.get(4)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); if (Control.controlData.controlsOn) { cases = 1; casefreq = 1 / (double) (Main.varsamples * 2); } } buf.setColor(Color.black); buf.fillRect((int) geneheader.get(5)[1] + 1, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); buf.drawString( "" + aminoarray.get(s).getNode().vars .get(v).getValue().get(0).getQuality(), (int) geneheader.get(5)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } } if (Control.controlData.controlsOn) { cases = 0; for (int v = 0; v < aminoarray.get(s).getNode().vars.size(); v++) { if (aminoarray.get(s).getNode().vars.get(v).getKey() .equals(aminoarray.get(s).getRow()[5])) { if (aminoarray.get(s).getNode().vars.get(v).getValue().get(0) .isHomozygous()) { cases += Integer.parseInt(aminoarray.get(s).getRow()[1]) * 2; } else { cases += Integer.parseInt(aminoarray.get(s).getRow()[1]); } } } casefreq = cases / (double) (Main.varsamples * 2); } buf.setColor(textcolor); buf.drawString(aminoarray.get(s).getRow()[4], (int) geneheader.get(6)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); if (Control.controlData.controlsOn) { buf.setColor(textcolor); for (int v = 0; v < aminoarray.get(s).getNode().vars.size(); v++) { if (aminoarray.get(s).getNode().vars.get(v).getKey() .equals(aminoarray.get(s).getRow()[5])) { vararray = aminoarray.get(s).getNode().vars.get(v).getValue(); controlarray = new SampleNode[Control.controlData.fileArray.size()]; if (vararray.get(vararray.size() - 1).alleles != null) { for (int e = vararray.size() - 1; e > 0; e--) { if (vararray.get(e).alleles == null) { break; } controlarray[vararray.get(e).getControlSample() .getIndex()] = vararray.get(e); } } for (int e = 0; e < controlarray.length; e++) { if (Control.controlData.fileArray.get(e).controlOn) { if (controlarray[e] == null) { buf.setColor(Color.black); buf.fillRect( (int) geneheader .get(this.geneheaderlength + e * 2)[1] + 11, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); buf.drawString("0", (int) geneheader .get(this.geneheaderlength + e * 2)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + rowHeight); buf.setColor(Color.black); buf.fillRect( (int) geneheader .get(this.geneheaderlength + e * 2 + 1)[1] + 11, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); buf.drawString("-", (int) geneheader .get(this.geneheaderlength + e * 2 + 1)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + rowHeight); } else { buf.setColor(Color.black); buf.fillRect( (int) geneheader .get(this.geneheaderlength + e * 2)[1] + 11, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); buf.drawString( "" + MethodLibrary.round(controlarray[e].alleles / (double) controlarray[e].allelenumber, 2), (int) geneheader .get(this.geneheaderlength + e * 2)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + rowHeight); buf.setColor(Color.black); buf.fillRect( (int) geneheader .get(this.geneheaderlength + e * 2 + 1)[1] + 11, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); buf.drawString("" + MethodLibrary .round(casefreq / (controlarray[e].alleles / (double) controlarray[e].allelenumber), 2) + " (p=" + MethodLibrary.round( VariantHandler.table.fe.getRightTailedP( cases, Main.varsamples * 2 - cases, controlarray[e].alleles, controlarray[e].allelenumber - controlarray[e].alleles), 2) + ")", (int) geneheader .get(this.geneheaderlength + e * 2 + 1)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + rowHeight); } } else { buf.setColor(Color.black); buf.fillRect( (int) geneheader.get(this.geneheaderlength + e * 2)[1] + 11, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(Color.darkGray); buf.drawString("Apply controls", (int) geneheader.get(this.geneheaderlength + e * 2)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); buf.setColor(Color.black); buf.fillRect( (int) geneheader .get(this.geneheaderlength + e * 2 + 1)[1] + 11, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(Color.darkGray); buf.drawString("-", (int) geneheader .get(this.geneheaderlength + e * 2 + 1)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } } } } else { buf.setColor(Color.darkGray); for (int e = geneheaderlength; e < geneheader.size(); e++) { if (geneheader.get(e)[0] instanceof ControlFile) { buf.drawString("Apply controls", (int) geneheader.get(e)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } buf.setColor(Color.lightGray); } vararray = null; if (Main.bedCanvas.bedOn) { for (int a = 0; a < aminoarray.size(); a++) { bedarray = MethodLibrary.makeTrackArray(aminoarray.get(a).getNode(), aminoarray.get(a).getRow()[5]); if (bedarray != null) { for (int b = 0; b < bedarray.length; b++) { buf.setColor(Color.black); if (b == bedarray.length - 1) { buf.fillRect( (int) geneheader.get(geneheaderlength + Control.controlData.fileArray.size() * 2 + b)[1] + 12, (rowHeight * (i + a + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth() - (int) geneheader.get(geneheaderlength + Control.controlData.fileArray.size() * 2 + b)[1], rowHeight - 1); } else { buf.fillRect( (int) geneheader.get(geneheaderlength + Control.controlData.fileArray.size() * 2 + b)[1] + 12, (rowHeight * (i + a + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, (int) geneheader.get(geneheaderlength + Control.controlData.fileArray.size() * 2 + b)[2], rowHeight - 1); } buf.setColor(Color.white); if (bedarray[b] != null) { buf.drawString(bedarray[b].toString(), (int) geneheader.get(geneheaderlength + Control.controlData.fileArray.size() * 2 + b)[1] + 14, (rowHeight * (i + a + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } } } } buf.setColor(Color.darkGray); for (int j = 0; j < geneheader.size(); j++) { buf.drawLine((int) geneheader.get(j)[1] + 11, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, (int) geneheader.get(j)[1] + 11, (rowHeight * (i + s + listAdd + 3)) - tablescroll.getVerticalScrollBar().getValue() + 3); } if (selectedVar != null && selectedString.equals(aminoarray.get(s).getRow()) && Integer.parseInt(selectedString[1]) > 1) { //hoverSample = -1; pointer = 0; //TODO for (int v = 0; v < aminoarray.get(s).getNode().vars.size(); v++) { if (aminoarray.get(s).getNode().vars.get(v).getKey() .equals(selectedString[5])) { for (int l = 0; l < aminoarray.get(s).getNode().vars.get(v).getValue() .size(); l++) { if (aminoarray.get(s).getNode().vars.get(v).getValue() .get(l).alleles != null) { break; } if (mouseY > (rowHeight * (i + s + pointer + 4)) && mouseY < (rowHeight * (i + s + pointer + 5))) { textcolor = Color.white; hoverVar = aminoarray.get(s).getNode(); hoverString = aminoarray.get(s).getRow(); hoverSample = aminoarray.get(s).getNode().vars.get(v).getValue() .get(l).getSample().getIndex(); } else { textcolor = Color.lightGray; } // if(aminoarray.get(s).getNode().getSamples().get(l).getVariation().equals(selectedString[5])) { buf.setColor(textcolor); buf.drawString( aminoarray.get(s).getNode().vars.get(v).getValue().get(l) .getSample().getName(), 30, (rowHeight * (i + s + pointer + 4)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); pointer++; // } buf.setColor(Color.black); buf.fillRect((int) geneheader.get(4)[1] + 10, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); if (aminoarray.get(s).getNode().vars.get(v).getValue().get(l) .isHomozygous()) { buf.drawString( "Hom (" + aminoarray.get(s).getNode().vars.get(v) .getValue().get(l).getCalls() + "/" + aminoarray.get(s).getNode().vars.get(v) .getValue().get(l).getCoverage() + ")", (int) geneheader.get(4)[1] + 14, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { buf.drawString( "Het (" + aminoarray.get(s).getNode().vars.get(v) .getValue().get(l).getCalls() + "/" + aminoarray.get(s).getNode().vars.get(v) .getValue().get(l).getCoverage() + ")", (int) geneheader.get(4)[1] + 14, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } buf.setColor(Color.black); buf.fillRect((int) geneheader.get(5)[1] + 10, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); buf.drawString( "" + aminoarray.get(s).getNode().vars.get(v).getValue() .get(l).getQuality(), (int) geneheader.get(5)[1] + 14, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); buf.setColor(Color.darkGray); for (int j = 4; j < 7; j++) { buf.drawLine((int) geneheader.get(j)[1] + 11, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue(), (int) geneheader.get(j)[1] + 11, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight + 2); } } } } listAdd = Integer.parseInt(selectedString[1]) + 1; genemutcount = aminoarray.size() + listAdd; buf.setColor(Color.darkGray); buf.drawLine(21, (rowHeight * (i + s + listAdd + 3)) - tablescroll.getVerticalScrollBar().getValue() + 3, this.getWidth(), (rowHeight * (i + s + listAdd + 3)) - tablescroll.getVerticalScrollBar().getValue() + 3); } } } } catch (Exception e) { ErrorLog.addError(e.getStackTrace()); e.printStackTrace(); } } buf.setColor(Color.darkGray); buf.drawLine(4, (rowHeight * (Main.drawCanvas.clusterNodes.size() + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 3, this.getWidth(), (rowHeight * (Main.drawCanvas.clusterNodes.size() + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 3); } drawHeader(); if (headerHover == -1 && geneHeaderHover == -1) { setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } else { if (resizeColumn == -1) { setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR)); } else { setCursor(Cursor.getPredefinedCursor(Cursor.E_RESIZE_CURSOR)); } } g.drawImage(bufImage, 0, tablescroll.getVerticalScrollBar().getValue(), null); } catch (Exception e) { e.printStackTrace(); } }
From source file:bicat.gui.GraphicPane.java
/** * Creates a line chart with//from www . ja va 2s. c om * default settings. * * @param title the chart title (<code>null</code> permitted). * @param xAxisLabel a label for the X-axis (<code>null</code> permitted). * @param yAxisLabel a label for the Y-axis (<code>null</code> permitted). * @param dataset the dataset for the chart (<code>null</code> permitted). * @param orientation the plot orientation (horizontal or vertical) ( * <code>null</code> NOT permitted). * @param legend a flag specifying whether or not a legend is required. * @param tooltips configure chart to generate tool tips? * @param urls configure chart to generate URLs? * @return The chart. */ public static JFreeChart myCreateXYLineChart(String title, String xAxisLabel, String yAxisLabel, org.jfree.data.xy.XYDataset dataset, double marker, org.jfree.chart.plot.PlotOrientation orientation, boolean legend, boolean tooltips, boolean urls) { if (orientation == null) { throw new IllegalArgumentException("Null 'orientation' argument."); } NumberAxis xAxis = new NumberAxis(xAxisLabel); xAxis.setAutoRangeIncludesZero(false); NumberAxis yAxis = new NumberAxis(yAxisLabel); XYItemRenderer renderer = new StandardXYItemRenderer(StandardXYItemRenderer.LINES); XYPlot plot = new XYPlot(dataset, xAxis, yAxis, renderer); ValueMarker vm = new ValueMarker(marker); vm.setPaint(Color.GRAY); // plot.addRangeMarker(vm, Layer.FOREGROUND); //.setPaint(Color.PINK)); plot.addDomainMarker(vm, Layer.FOREGROUND); plot.setOrientation(orientation); if (tooltips) { renderer.setToolTipGenerator(new StandardXYToolTipGenerator()); } if (urls) { renderer.setURLGenerator(new StandardXYURLGenerator()); } return new JFreeChart(title, JFreeChart.DEFAULT_TITLE_FONT, plot, legend); }