List of usage examples for java.awt.geom Path2D append
public abstract void append(PathIterator pi, boolean connect);
From source file:org.jfree.graphics2d.demo.ImageTest.java
private static void drawArcTest(Graphics2D g2) { g2.setPaint(Color.GREEN);/*from w w w . j a va2 s . c o m*/ g2.drawRect(0, 20, 70, 50); g2.setPaint(Color.RED); Path2D path1 = new Path2D.Double(); double[] pts = calculateReferenceArc(90); path1.moveTo(pts[0], pts[1]); path1.curveTo(pts[2], pts[3], pts[4], pts[5], pts[6], pts[7]); AffineTransform t = new AffineTransform(); t.translate(35, 45); t.scale(35, 25); t.rotate(Math.PI / 4); path1.transform(t); g2.draw(path1); Path2D path2 = new Path2D.Double(); path2.moveTo(pts[0], pts[1]); path2.curveTo(pts[2], pts[3], pts[4], pts[5], pts[6], pts[7]); AffineTransform t2 = new AffineTransform(); t2.rotate(3 * Math.PI / 4); t2.scale(35, 25); t2.translate(35, 35); path2.transform(t2); //g2.draw(path2); Path2D arc = new Path2D.Double(); arc.append(path1, false); arc.append(path2, false); //g2.draw(arc); //g2.draw(path1); //g2.transform(t); g2.setPaint(Color.BLUE); g2.drawArc(0, 20, 70, 50, 0, -270); //Arc2D arc2d = new Arc2D.Double(0d, 20d, 70d, 50d, 0d, 90, Arc2D.OPEN); //g2.draw(arc2d); }
From source file:Main.java
public Main() { this.setUndecorated(true); this.setDefaultCloseOperation(EXIT_ON_CLOSE); this.setSize(200, 200); Ellipse2D.Double ellipse = new Ellipse2D.Double(0, 0, 200, 100); Rectangle2D.Double rect = new Rectangle2D.Double(0, 100, 200, 200); Path2D path = new Path2D.Double(); path.append(rect, true); path.append(ellipse, true);/*from w ww. j a va 2 s. c o m*/ this.setShape(path); JButton closeButton = new JButton("Close"); this.add(closeButton, BorderLayout.SOUTH); closeButton.addActionListener(e -> System.exit(0)); }
From source file:org.earthtime.UPb_Redux.dateInterpretation.WeightedMeanGraphPanel.java
/** * * @param g2d/*from ww w. ja v a 2s .co m*/ */ public void paint(Graphics2D g2d) { // setup painting parameters String fractionSortOrder = "name"; //random, weight, date if (getWeightedMeanOptions().containsKey("fractionSortOrder")) { fractionSortOrder = getWeightedMeanOptions().get("fractionSortOrder"); } double rangeX = (getMaxX_Display() - getMinX_Display()); double rangeY = (getMaxY_Display() - getMinY_Display()); g2d.setClip(getLeftMargin(), getTopMargin(), getGraphWidth(), getGraphHeight()); RenderingHints rh = g2d.getRenderingHints(); rh.put(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); rh.put(RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY); g2d.setRenderingHints(rh); // walk the sampleDateInterpretations and produce graphs g2d.setPaint(Color.BLACK); g2d.setStroke(new BasicStroke(2.0f)); g2d.setFont(new Font("SansSerif", Font.BOLD, 10)); double barWidth = 15.0; double barGap = 10.0; double startSamX = 10.0; double saveStartSamX = 0.0; double samSpace = 3.0; for (int i = 0; i < selectedSampleDateModels.length; i++) { for (int j = 1; j < 9; j++) { if (selectedSampleDateModels[i][j] instanceof SampleDateModel) { final SampleDateModel SAM = ((SampleDateModel) selectedSampleDateModels[i][j]); double wMean = SAM.getValue().movePointLeft(6).doubleValue(); double wMeanOneSigma = SAM.getOneSigmaAbs().movePointLeft(6).doubleValue(); Path2D mean = new Path2D.Double(Path2D.WIND_NON_ZERO); // july 2008 // modified to show de-selected fractions as gray // this means a new special list of fractionIDs is created fromall non-rejected fractions // and each instance is tested for being included // should eventually refactor Vector<String> allFIDs = new Vector<String>(); for (String f : ((UPbReduxAliquot) SAM.getAliquot()).getAliquotFractionIDs()) { // test added for Sample-based wm if (SAM.fractionDateIsPositive(// ((UPbReduxAliquot) SAM.getAliquot()).getAliquotFractionByName(f))) { allFIDs.add(f); } } final int iFinal = i; if (fractionSortOrder.equalsIgnoreCase("weight")) { Collections.sort(allFIDs, new Comparator<String>() { public int compare(String fID1, String fID2) { double invertOneSigmaF1 = // 1.0 // / ((UPbReduxAliquot) selectedSampleDateModels[iFinal][0])// .getAliquotFractionByName(fID1)// .getRadiogenicIsotopeDateByName(SAM.getDateName())// .getOneSigmaAbs().movePointLeft(6).doubleValue(); double invertOneSigmaF2 = // 1.0 // / ((UPbReduxAliquot) selectedSampleDateModels[iFinal][0])// .getAliquotFractionByName(fID2)// .getRadiogenicIsotopeDateByName(SAM.getDateName())// .getOneSigmaAbs().movePointLeft(6).doubleValue(); return Double.compare(invertOneSigmaF2, invertOneSigmaF1); } }); } else if (fractionSortOrder.equalsIgnoreCase("date")) { Collections.sort(allFIDs, new Comparator<String>() { public int compare(String fID1, String fID2) { double dateF1 = // ((UPbReduxAliquot) selectedSampleDateModels[iFinal][0])// .getAliquotFractionByName(fID1)// .getRadiogenicIsotopeDateByName(SAM.getDateName())// .getValue().doubleValue(); double dateF2 = // ((UPbReduxAliquot) selectedSampleDateModels[iFinal][0])// .getAliquotFractionByName(fID2)// .getRadiogenicIsotopeDateByName(SAM.getDateName())// .getValue().doubleValue(); return Double.compare(dateF1, dateF2); } }); } else if ( /* ! isInRandomMode() &&*/fractionSortOrder.equalsIgnoreCase("random")) { Collections.shuffle(allFIDs, new Random()); } else if (fractionSortOrder.equalsIgnoreCase("name")) { // default to alphabetic by name //Collections.sort(allFIDs); // april 2010 give same lexigraphic ordering that UPbFractions get Collections.sort(allFIDs, new IntuitiveStringComparator<String>()); } else { // do nothing } double actualWidthX = (allFIDs.size()) * (barWidth + barGap);//; + barGap; // plot 2-sigma of mean mean.moveTo((float) mapX(startSamX, getMinX_Display(), rangeX, graphWidth), (float) mapY(wMean + 2.0 * wMeanOneSigma, getMaxY_Display(), rangeY, graphHeight)); mean.lineTo((float) mapX(startSamX + actualWidthX, getMinX_Display(), rangeX, graphWidth), (float) mapY(wMean + 2.0 * wMeanOneSigma, getMaxY_Display(), rangeY, graphHeight)); mean.lineTo((float) mapX(startSamX + actualWidthX, getMinX_Display(), rangeX, graphWidth), (float) mapY(wMean - 2.0 * wMeanOneSigma, getMaxY_Display(), rangeY, graphHeight)); mean.lineTo((float) mapX(startSamX, getMinX_Display(), rangeX, graphWidth), (float) mapY(wMean - 2.0 * wMeanOneSigma, getMaxY_Display(), rangeY, graphHeight)); mean.closePath(); g2d.setColor(ReduxConstants.mySampleYellowColor); g2d.fill(mean); g2d.setPaint(Color.BLACK); // plot 1-sigma of mean mean.reset(); mean.moveTo((float) mapX(startSamX, getMinX_Display(), rangeX, graphWidth), (float) mapY(wMean + wMeanOneSigma, getMaxY_Display(), rangeY, graphHeight)); mean.lineTo((float) mapX(startSamX + actualWidthX, getMinX_Display(), rangeX, graphWidth), (float) mapY(wMean + wMeanOneSigma, getMaxY_Display(), rangeY, graphHeight)); mean.lineTo((float) mapX(startSamX + actualWidthX, getMinX_Display(), rangeX, graphWidth), (float) mapY(wMean - wMeanOneSigma, getMaxY_Display(), rangeY, graphHeight)); mean.lineTo((float) mapX(startSamX, getMinX_Display(), rangeX, graphWidth), (float) mapY(wMean - wMeanOneSigma, getMaxY_Display(), rangeY, graphHeight)); mean.closePath(); g2d.setColor(ReduxConstants.ColorOfRedux); g2d.fill(mean); g2d.setPaint(Color.BLACK); // plot mean mean.reset(); mean.moveTo((float) mapX(startSamX, getMinX_Display(), rangeX, graphWidth), (float) mapY(wMean, getMaxY_Display(), rangeY, graphHeight)); mean.lineTo((float) mapX(startSamX + actualWidthX, getMinX_Display(), rangeX, graphWidth), (float) mapY(wMean, getMaxY_Display(), rangeY, graphHeight)); g2d.setStroke(new BasicStroke(1.0f)); g2d.draw(mean); g2d.setStroke(new BasicStroke(2.0f)); saveStartSamX = startSamX; // plot fraction bars double minPoint = 5000.0; double maxWeight = 0.0; double totalWeight = 0.0; int barNum = 0; for (String fID : allFIDs) { // the dateModel has an associated aliquot, but in sample mode, it is a // standin aliquot for the sample. to get the aliquot number for // use in coloring fractions, we need to query the fraction itself String aliquotName = sample.getAliquotNameByFractionID(fID); Color includedFillColor = new Color(0, 0, 0); if (sample.getSampleDateInterpretationGUISettings().getAliquotOptions().get(aliquotName) .containsKey("includedFillColor")) { String[] temp = // sample.getSampleDateInterpretationGUISettings().getAliquotOptions() .get(aliquotName).get("includedFillColor").split(","); includedFillColor = buildRGBColor(temp); } Fraction f = ((UPbReduxAliquot) selectedSampleDateModels[i][0]) .getAliquotFractionByName(fID); double date = f.//((UPbReduxAliquot) selectedSampleDateModels[i][0]).getAliquotFractionByName(fID).// getRadiogenicIsotopeDateByName(SAM.getDateName()).getValue().movePointLeft(6) .doubleValue(); double twoSigma = f.//((UPbReduxAliquot) selectedSampleDateModels[i][0]).getAliquotFractionByName(fID).// getRadiogenicIsotopeDateByName(SAM.getDateName()).getTwoSigmaAbs().movePointLeft(6) .doubleValue(); if ((date - twoSigma) < minPoint) { minPoint = (date - twoSigma); } double invertedOneSigma = // 1.0 // / f.//((UPbReduxAliquot) selectedSampleDateModels[i][0]).getAliquotFractionByName(fID).// getRadiogenicIsotopeDateByName(SAM.getDateName()).getOneSigmaAbs() .movePointLeft(6).doubleValue(); if (invertedOneSigma > maxWeight) { maxWeight = invertedOneSigma; } Path2D bar = new Path2D.Double(Path2D.WIND_NON_ZERO); bar.moveTo( (float) mapX(saveStartSamX + ((barGap / 2.0) + barNum * (barWidth + barGap)), getMinX_Display(), rangeX, graphWidth), (float) mapY(date + twoSigma, getMaxY_Display(), rangeY, graphHeight)); bar.lineTo( (float) mapX( saveStartSamX + ((barGap / 2.0) + barNum * (barWidth + barGap)) + barWidth, getMinX_Display(), rangeX, graphWidth), (float) mapY(date + twoSigma, getMaxY_Display(), rangeY, graphHeight)); bar.lineTo( (float) mapX( saveStartSamX + ((barGap / 2.0) + barNum * (barWidth + barGap)) + barWidth, getMinX_Display(), rangeX, graphWidth), (float) mapY(date - twoSigma, getMaxY_Display(), rangeY, graphHeight)); bar.lineTo( (float) mapX(saveStartSamX + ((barGap / 2.0) + barNum * (barWidth + barGap)), getMinX_Display(), rangeX, graphWidth), (float) mapY(date - twoSigma, getMaxY_Display(), rangeY, graphHeight)); bar.closePath(); Composite originalComposite = g2d.getComposite(); if (SAM.getIncludedFractionIDsVector().contains(fID)) { g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.8f)); totalWeight += Math.pow(invertedOneSigma, 2.0); // april 2014 experiment if (f.getRgbColor() != 0) { includedFillColor = new Color(f.getRgbColor()); } } else { g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.2f)); } g2d.setPaint(includedFillColor); g2d.draw(bar); //restore composite g2d.setComposite(originalComposite); g2d.setColor(Color.black); // label fraction at top g2d.rotate(-Math.PI / 4.0, (float) mapX(saveStartSamX + ((barGap / 2.0) + barNum * (barWidth + barGap)), getMinX_Display(), rangeX, graphWidth), (float) mapY(date + twoSigma, getMaxY_Display(), rangeY, graphHeight)); g2d.drawString( ((UPbReduxAliquot) selectedSampleDateModels[i][0]).getAliquotFractionByName(fID) .getFractionID(), (float) mapX(saveStartSamX + ((barGap / 2.0) + barNum * (barWidth + barGap)), getMinX_Display(), rangeX, graphWidth) + 15, (float) mapY(date + twoSigma, getMaxY_Display(), rangeY, graphHeight)); g2d.rotate(Math.PI / 4.0, (float) mapX(saveStartSamX + ((barGap / 2.0) + barNum * (barWidth + barGap)), getMinX_Display(), rangeX, graphWidth), (float) mapY(date + twoSigma, getMaxY_Display(), rangeY, graphHeight)); barNum++; // startSamX += 2 * barWidth; startSamX += barWidth + barGap; } // display three info boxes below weighted means // each tic is the height of one calculated y-axis tic // determine the y axis tic double minYtic = Math.ceil(getMinY_Display() * 100) / 100; double maxYtic = Math.floor(getMaxY_Display() * 100) / 100; double deltay = Math.rint((maxYtic - minYtic) * 10 + 0.5); double yTic = deltay / 100; double yTopSummary = minPoint - yTic / 2.0;// wMeanOneSigma; //double specialYTic = yTic; double yTopWeights = yTopSummary - yTic * 1.1; double yTopMSWD_PDF = yTopWeights - yTic * 1.1; // summary box Path2D box = new Path2D.Double(Path2D.WIND_NON_ZERO); box.moveTo((float) mapX(saveStartSamX, getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopSummary, getMaxY_Display(), rangeY, graphHeight)); box.lineTo((float) mapX(saveStartSamX + actualWidthX, getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopSummary, getMaxY_Display(), rangeY, graphHeight)); box.lineTo((float) mapX(saveStartSamX + actualWidthX, getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopSummary - yTic, getMaxY_Display(), rangeY, graphHeight)); box.lineTo((float) mapX(saveStartSamX, getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopSummary - yTic, getMaxY_Display(), rangeY, graphHeight)); box.closePath(); g2d.setStroke(new BasicStroke(1.5f)); g2d.draw(box); // Info Box g2d.drawString(// SAM.getAliquot().getAliquotName(), (float) mapX(saveStartSamX, getMinX_Display(), rangeX, graphWidth) + 4f, (float) mapY(yTopSummary, getMaxY_Display(), rangeY, graphHeight) + 13f); g2d.drawString(// SAM.getName(), (float) mapX(saveStartSamX, getMinX_Display(), rangeX, graphWidth) + 4f, (float) mapY(yTopSummary, getMaxY_Display(), rangeY, graphHeight) + 25f); g2d.drawString(// SAM.FormatValueAndTwoSigmaABSThreeWaysForPublication(6, 2), (float) mapX(saveStartSamX, getMinX_Display(), rangeX, graphWidth) + 4f, (float) mapY(yTopSummary, getMaxY_Display(), rangeY, graphHeight) + 36f); g2d.drawString(// SAM.ShowCustomMSWDwithN(), (float) mapX(saveStartSamX, getMinX_Display(), rangeX, graphWidth) + 4f, (float) mapY(yTopSummary, getMaxY_Display(), rangeY, graphHeight) + 48f); // weights box box.reset(); box.moveTo((float) mapX(saveStartSamX, getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopWeights, getMaxY_Display(), rangeY, graphHeight)); box.lineTo((float) mapX(saveStartSamX + actualWidthX, getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopWeights, getMaxY_Display(), rangeY, graphHeight)); box.lineTo((float) mapX(saveStartSamX + actualWidthX, getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopWeights - yTic, getMaxY_Display(), rangeY, graphHeight)); box.lineTo((float) mapX(saveStartSamX, getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopWeights - yTic, getMaxY_Display(), rangeY, graphHeight)); box.closePath(); g2d.setStroke(new BasicStroke(1.5f)); g2d.draw(box); // plot fraction weights double artificialXRange = allFIDs.size(); double count = 0; //double weightWidth = Math.min(3.0 * barWidth, (yTic / rangeY * graphHeight)) - 15;//yTic;//barWidth * 2.0; double weightWidth = (barWidth + barGap) * 0.9; for (String fID : allFIDs) { // the dateModel has an associated aliquot, but in sample mode, it is a // standin aliquot for the sample. to get the aliquot number for // use in coloring fractions, we need to query the fraction itself String aliquotName = sample.getAliquotNameByFractionID(fID); Fraction f = ((UPbReduxAliquot) selectedSampleDateModels[i][0]) .getAliquotFractionByName(fID); Color includedFillColor = new Color(0, 0, 0); if (sample.getSampleDateInterpretationGUISettings().getAliquotOptions().get(aliquotName) .containsKey("includedFillColor")) { String[] temp = // sample.getSampleDateInterpretationGUISettings().getAliquotOptions() .get(aliquotName).get("includedFillColor").split(","); includedFillColor = buildRGBColor(temp); } double invertOneSigma = // 1.0 // / ((UPbReduxAliquot) selectedSampleDateModels[i][0]) .getAliquotFractionByName(fID)// .getRadiogenicIsotopeDateByName(SAM.getDateName()).getOneSigmaAbs() .movePointLeft(6).doubleValue(); Path2D weight = new Path2D.Double(Path2D.WIND_NON_ZERO); weight.moveTo( (float) mapX(saveStartSamX + (count + 0.5) / artificialXRange * actualWidthX, getMinX_Display(), rangeX, graphWidth) // - (float) (invertOneSigma / maxWeight / 2.0 * weightWidth), (float) mapY(yTopWeights - (yTic / 2.0), getMaxY_Display(), rangeY, graphHeight) // + (float) (invertOneSigma / maxWeight / 2.0 * weightWidth) - 5f); weight.lineTo( (float) mapX(saveStartSamX + (count + 0.5) / artificialXRange * actualWidthX, getMinX_Display(), rangeX, graphWidth) // + (float) (invertOneSigma / maxWeight / 2.0 * weightWidth), (float) mapY(yTopWeights - (yTic / 2.0), getMaxY_Display(), rangeY, graphHeight) // + (float) (invertOneSigma / maxWeight / 2.0 * weightWidth) - 5f); weight.lineTo( (float) mapX(saveStartSamX + (count + 0.5) / artificialXRange * actualWidthX, getMinX_Display(), rangeX, graphWidth) // + (float) (invertOneSigma / maxWeight / 2.0 * weightWidth), (float) mapY(yTopWeights - (yTic / 2.0), getMaxY_Display(), rangeY, graphHeight) // - (float) (invertOneSigma / maxWeight / 2.0 * weightWidth) - 5f); weight.lineTo( (float) mapX(saveStartSamX + (count + 0.5) / artificialXRange * actualWidthX, getMinX_Display(), rangeX, graphWidth) // - (float) (invertOneSigma / maxWeight / 2.0 * weightWidth), (float) mapY(yTopWeights - (yTic / 2.0), getMaxY_Display(), rangeY, graphHeight) // - (float) (invertOneSigma / maxWeight / 2.0 * weightWidth) - 5f); weight.closePath(); g2d.setStroke(new BasicStroke(2.5f)); // test for included or not == black or gray String weightPerCent = " 0";//0.0%"; // g2d.setPaint(includedFillColor); Composite originalComposite = g2d.getComposite(); if (SAM.getIncludedFractionIDsVector().contains(fID)) { g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.8f)); weightPerCent = formatter1DecPlace .format(Math.pow(invertOneSigma, 2.0) / totalWeight * 100.0);// + "%"; // april 2014 experiment if (f.getRgbColor() != 0) { includedFillColor = new Color(f.getRgbColor()); } } else { g2d.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, 0.2f)); } g2d.setPaint(includedFillColor); g2d.fill(weight); //restore composite g2d.setComposite(originalComposite); // write percent of total weight g2d.drawString(weightPerCent, (float) mapX(saveStartSamX + (count + 0.5) / artificialXRange * actualWidthX, getMinX_Display(), rangeX, graphWidth) // - (float) (invertOneSigma / maxWeight / 2.0 * weightWidth), (float) mapY(yTopWeights - yTic, getMaxY_Display(), rangeY, graphHeight) - 5f); g2d.setColor(Color.black); count += 1.0; } // double box height for graph yTic *= 2.0; // plot MSWD_PDF // store function x,y values Vector<Double> xVals = new Vector<Double>(); Vector<Double> yVals = new Vector<Double>(); double f = SAM.getIncludedFractionIDsVector().size() - 1; if (f > 1.0) { g2d.setStroke(new BasicStroke(1.0f)); double yRange = MSWDCoordinates.valuesByPointCount[(int) f][5] * 1.03; // alitle air at the top of curve double xStart = MSWDCoordinates.valuesByPointCount[(int) f][1]; double xRange = MSWDCoordinates.valuesByPointCount[(int) f][4] - xStart; double xStep = 0.005; Path2D MSWD_PDF = new Path2D.Double(Path2D.WIND_NON_ZERO); Path2D MSWD_right = new Path2D.Double(Path2D.WIND_NON_ZERO); // start at lower left corner of box (may or may not be 0,0 ) MSWD_PDF.moveTo(// (float) mapX((double) saveStartSamX, getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopMSWD_PDF - yTic, getMaxY_Display(), rangeY, graphHeight)); // setup MSWD to paint last Path2D MSWD = null; // calculate function values for (double x = xStart; x < xRange; x += xStep) { xVals.add((((x - xStart) / xRange) * actualWidthX) + (double) saveStartSamX); double y = // Math.pow(2, -1.0 * f / 2.0)// * Math.exp(-1.0 * f * x / 2.0)// * Math.pow(f, f / 2.0)// * Math.pow(x, (-1.0 + f / 2.0))// / Math.exp(Gamma.logGamma(f / 2.0)); yVals.add(((y / yRange) * yTic) + yTopMSWD_PDF - yTic); MSWD_PDF.lineTo(// (float) mapX(xVals.lastElement(), getMinX_Display(), rangeX, graphWidth), (float) mapY(yVals.lastElement(), getMaxY_Display(), rangeY, graphHeight)); // test for location of left RED zone if ((MSWDCoordinates.valuesByPointCount[(int) f][2] >= x) && (MSWDCoordinates.valuesByPointCount[(int) f][2] < (x + xStep))) { double leftX = MSWDCoordinates.valuesByPointCount[(int) f][2]; xVals.add((((leftX - xStart) / xRange) * actualWidthX) + (double) saveStartSamX); double leftY = // Math.pow(2, -1.0 * f / 2.0)// * Math.exp(-1.0 * f * leftX / 2.0)// * Math.pow(f, f / 2.0)// * Math.pow(leftX, (-1.0 + f / 2.0))// / Math.exp(Gamma.logGamma(f / 2.0)); yVals.add(((leftY / yRange) * yTic) + yTopMSWD_PDF - yTic); MSWD_PDF.lineTo(// (float) mapX(xVals.lastElement(), getMinX_Display(), rangeX, graphWidth), (float) mapY(yVals.lastElement(), getMaxY_Display(), rangeY, graphHeight)); Path2D ciLower = new Path2D.Double(Path2D.WIND_NON_ZERO); ciLower.append(MSWD_PDF.getPathIterator(new AffineTransform()), true); ciLower.lineTo(// (float) mapX(xVals.lastElement(), getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopMSWD_PDF - yTic, getMaxY_Display(), rangeY, graphHeight)); ciLower.closePath(); g2d.setColor(Color.RED); g2d.fill(ciLower); // draw right hand border line to compensate for a bug in the filler Line2D right = new Line2D.Double(// mapX(xVals.lastElement(), getMinX_Display(), rangeX, graphWidth), mapY(yVals.lastElement(), getMaxY_Display(), rangeY, graphHeight), mapX(xVals.lastElement(), getMinX_Display(), rangeX, graphWidth), mapY(yTopMSWD_PDF - yTic, getMaxY_Display(), rangeY, graphHeight)); g2d.setStroke(new BasicStroke(0.5f)); g2d.draw(right); g2d.setStroke(new BasicStroke(1.0f)); g2d.setColor(Color.BLACK); System.out.println("Left Red = (" + leftX + ", " + leftY + ")"); } // test for location of right RED zone if ((MSWDCoordinates.valuesByPointCount[(int) f][3] >= x) && (MSWDCoordinates.valuesByPointCount[(int) f][3] < (x + xStep))) { double rightX = MSWDCoordinates.valuesByPointCount[(int) f][3]; xVals.add((((rightX - xStart) / xRange) * actualWidthX) + (double) saveStartSamX); double rightY = // Math.pow(2, -1.0 * f / 2.0)// * Math.exp(-1.0 * f * rightX / 2.0)// * Math.pow(f, f / 2.0)// * Math.pow(rightX, (-1.0 + f / 2.0))// / Math.exp(Gamma.logGamma(f / 2.0)); yVals.add(((rightY / yRange) * yTic) + yTopMSWD_PDF - yTic); MSWD_PDF.lineTo(// (float) mapX(xVals.lastElement(), getMinX_Display(), rangeX, graphWidth), (float) mapY(yVals.lastElement(), getMaxY_Display(), rangeY, graphHeight)); // here the strategy is to draw the curve and then reset it to record the remainder g2d.setStroke(new BasicStroke(1.0f)); g2d.draw(MSWD_PDF); MSWD_PDF = new Path2D.Double(Path2D.WIND_NON_ZERO); MSWD_PDF.moveTo(// (float) mapX(xVals.lastElement(), getMinX_Display(), rangeX, graphWidth), (float) mapY(yVals.lastElement(), getMaxY_Display(), rangeY, graphHeight)); MSWD_right.moveTo(// (float) mapX(xVals.lastElement(), getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopMSWD_PDF - yTic, getMaxY_Display(), rangeY, graphHeight)); MSWD_right.lineTo(// (float) mapX(xVals.lastElement(), getMinX_Display(), rangeX, graphWidth), (float) mapY(yVals.lastElement(), getMaxY_Display(), rangeY, graphHeight)); System.out.println("Right Red = (" + rightX + ", " + rightY + ")"); } // test for location of MSWD AND paint last if ((SAM.getMeanSquaredWeightedDeviation().doubleValue() >= x) && (SAM.getMeanSquaredWeightedDeviation().doubleValue() < (x + xStep))) { MSWD = new Path2D.Double(Path2D.WIND_NON_ZERO); MSWD.moveTo(// (float) mapX(xVals.lastElement(), getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopMSWD_PDF - yTic, getMaxY_Display(), rangeY, graphHeight)); MSWD.lineTo(// (float) mapX(xVals.lastElement(), getMinX_Display(), rangeX, graphWidth), (float) mapY(yVals.lastElement(), getMaxY_Display(), rangeY, graphHeight)); } } g2d.setStroke(new BasicStroke(1.0f)); // merge with border of right RED and fill MSWD_right.append(MSWD_PDF.getPathIterator(new AffineTransform()), true); g2d.setColor(Color.RED); g2d.fill(MSWD_right); g2d.setColor(Color.BLACK); // draw the remaining curves g2d.draw(MSWD_PDF); // MSWD may be off the graph and hence not exist try { g2d.draw(MSWD); } catch (Exception e) { } // label 95% conf interval and MSWD g2d.drawString(// "95% CI: (" + formatter2DecPlaces.format(MSWDCoordinates.valuesByPointCount[(int) f][2]) + ", " + formatter2DecPlaces.format(MSWDCoordinates.valuesByPointCount[(int) f][3]) + ")", (float) mapX(saveStartSamX + (actualWidthX / 2.0), getMinX_Display(), rangeX, graphWidth) - 30f, (float) mapY(yTopMSWD_PDF, getMaxY_Display(), rangeY, graphHeight) + 15f); // determine if MSWD is out of range String mswdAlert = ""; if (SAM.getMeanSquaredWeightedDeviation() .doubleValue() > MSWDCoordinates.valuesByPointCount[(int) f][4]) { mswdAlert = "\n !Out of Range!"; } g2d.drawString(// "MSWD = " + formatter2DecPlaces .format(SAM.getMeanSquaredWeightedDeviation().doubleValue()) + ", n = " + (int) (f + 1) + mswdAlert, (float) mapX(saveStartSamX + (actualWidthX / 2.0), getMinX_Display(), rangeX, graphWidth) - 15f, (float) mapY(yTopMSWD_PDF, getMaxY_Display(), rangeY, graphHeight) + 30f); } else { g2d.drawString("need more data...", (float) mapX((double) saveStartSamX, getMinX_Display(), rangeX, graphWidth) + 4f, (float) mapY(yTopMSWD_PDF - yTic, getMaxY_Display(), rangeY, graphHeight) - 10f); } // MSWD_PDF box box.reset(); box.moveTo((float) mapX(saveStartSamX, getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopMSWD_PDF, getMaxY_Display(), rangeY, graphHeight)); box.lineTo((float) mapX(saveStartSamX + actualWidthX, getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopMSWD_PDF, getMaxY_Display(), rangeY, graphHeight)); box.lineTo((float) mapX(saveStartSamX + actualWidthX, getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopMSWD_PDF - yTic, getMaxY_Display(), rangeY, graphHeight)); box.lineTo((float) mapX(saveStartSamX, getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopMSWD_PDF - yTic, getMaxY_Display(), rangeY, graphHeight)); box.closePath(); g2d.setStroke(new BasicStroke(1.5f)); g2d.draw(box); // MSWD_PDF x-axis tics if (f > 1.0) { g2d.setStroke(new BasicStroke(1.0f)); double xStart = (MSWDCoordinates.valuesByPointCount[(int) f][1] <= 0.5) ? 0.5 : 1.0; double xRange = MSWDCoordinates.valuesByPointCount[(int) f][4] - MSWDCoordinates.valuesByPointCount[(int) f][1]; double xStep = 0.5; for (double x = xStart; x < xRange; x += xStep) { double xPlot = (((x - MSWDCoordinates.valuesByPointCount[(int) f][1]) / xRange) * actualWidthX) + (double) saveStartSamX; Line2D line = new Line2D.Double(mapX(xPlot, getMinX_Display(), rangeX, graphWidth), mapY(yTopMSWD_PDF - yTic, getMaxY_Display(), rangeY, graphHeight), mapX(xPlot, getMinX_Display(), rangeX, graphWidth), mapY(yTopMSWD_PDF - yTic, getMaxY_Display(), rangeY, graphHeight) + 7); g2d.draw(line); g2d.rotate(-Math.PI / 2.0, (float) mapX(xPlot, getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopMSWD_PDF - yTic, getMaxY_Display(), rangeY, graphHeight)); g2d.drawString(formatter1DecPlace.format(x), (float) mapX(xPlot, getMinX_Display(), rangeX, graphWidth) - 30f, (float) mapY(yTopMSWD_PDF - yTic, getMaxY_Display(), rangeY, graphHeight) + 5f); g2d.rotate(Math.PI / 2.0, (float) mapX(xPlot, getMinX_Display(), rangeX, graphWidth), (float) mapY(yTopMSWD_PDF - yTic, getMaxY_Display(), rangeY, graphHeight)); } } // set counters barNum += samSpace; startSamX += 2 * samSpace * barWidth; } } } // // prevents re-randomization // setInRandomMode( true ); drawAxesAndTicks(g2d, rangeX, rangeY); // draw zoom box if in use if ((Math.abs(zoomMaxX - zoomMinX) * Math.abs(zoomMinY - zoomMaxY)) > 0.0) { g2d.setStroke(new BasicStroke(2.0f)); g2d.setColor(Color.red); g2d.drawRect(// Math.min(zoomMinX, zoomMaxX), Math.min(zoomMaxY, zoomMinY), Math.abs(zoomMaxX - zoomMinX), Math.abs(zoomMinY - zoomMaxY)); } }
From source file:savant.view.tracks.BAMTrackRenderer.java
private void renderArcPairedMode(Graphics2D g2, GraphPaneAdapter gp) { g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); LOG.debug("YMAX for ARC mode: " + ((AxisRange) instructions.get(DrawingInstruction.AXIS_RANGE)).getYMax()); AxisRange axisRange = (AxisRange) instructions.get(DrawingInstruction.AXIS_RANGE); ColourScheme cs = (ColourScheme) instructions.get(DrawingInstruction.COLOUR_SCHEME); int discordantMin = (Integer) instructions.get(DrawingInstruction.DISCORDANT_MIN); int discordantMax = (Integer) instructions.get(DrawingInstruction.DISCORDANT_MAX); //LOG.info("discordantMin=" + discordantMin + " discordantMax=" + discordantMax); // set up colors Color normalArcColor = makeTransparent(cs.getColor(ColourKey.CONCORDANT_LENGTH)); Color invertedReadColor = makeTransparent(cs.getColor(ColourKey.ONE_READ_INVERTED)); Color evertedPairColor = makeTransparent(cs.getColor(ColourKey.EVERTED_PAIR)); Color discordantLengthColor = makeTransparent(cs.getColor(ColourKey.DISCORDANT_LENGTH)); Color unmappedMateColor = makeTransparent(cs.getColor(ColourKey.UNMAPPED_MATE)); // set graph pane's range parameters gp.setXRange(axisRange.getXRange()); gp.setYRange(axisRange.getYRange()); // iterate through the data and draw LOG.debug("BAMTrackRenderer.renderArcMatePairMode: " + data.size() + " records."); for (Record record : data) { BAMIntervalRecord bamRecord = (BAMIntervalRecord) record; SAMRecord samRecord = bamRecord.getSAMRecord(); SAMReadUtils.PairedSequencingProtocol prot = (SAMReadUtils.PairedSequencingProtocol) instructions .get(DrawingInstruction.PAIRED_PROTOCOL); SAMReadUtils.PairMappingType type = SAMReadUtils.getPairType(samRecord, prot); if (samRecord.getReadPairedFlag() && type != null) { if (samRecord.getMateUnmappedFlag()) { // Read with unmapped mate. int alignmentStart = samRecord.getAlignmentStart(); double x = gp.transformXPos(alignmentStart); double radius = 4.0; double top = gp.transformYPos(axisRange.getYRange().getTo() * 0.25) + radius; g2.setColor(unmappedMateColor); g2.setStroke(ONE_STROKE); Path2D flower = new Path2D.Double(); flower.moveTo(x, gp.transformYPos(0.0)); flower.lineTo(x, top);//from ww w. j a v a2 s . c o m flower.moveTo(x - radius, top - radius); flower.lineTo(x + radius, top + radius); flower.moveTo(x - radius, top + radius); flower.lineTo(x + radius, top - radius); //flower.append(new Ellipse2D.Double(x - radius, top - radius, radius * 2.0, radius * 2.0), false); g2.draw(flower); recordToShapeMap.put(record, flower); // mates map to different chrs } else if (!samRecord.getMateReferenceName().equals(samRecord.getReferenceName())) { int alignmentStart = samRecord.getAlignmentStart(); double x = gp.transformXPos(alignmentStart); double arrowWidth = 10; double arrowHeight = 15; double top = gp.transformYPos(axisRange.getYRange().getTo() * 0.9); g2.setColor(invertedReadColor); g2.setStroke(TWO_STROKE); Path2D stem = new Path2D.Double(); stem.moveTo(x, gp.transformYPos(0.0)); stem.lineTo(x, top + arrowHeight); g2.draw(stem); Path2D pointer = new Path2D.Double(); pointer.moveTo(x, top); pointer.lineTo(x - arrowWidth / 2, top + arrowHeight); pointer.lineTo(x + arrowWidth / 2, top + arrowHeight); pointer.lineTo(x, top); g2.fill(pointer); pointer.append(stem, false); //flower.append(new Ellipse2D.Double(x - radius, top - radius, radius * 2.0, radius * 2.0), false); //g2.draw(pointer); recordToShapeMap.put(record, pointer); // mates map to the same chr } else { // Paired read with normal mate. int arcLength = Math.abs(samRecord.getInferredInsertSize()); // skip reads with a zero insert length--probably mapping errors if (arcLength == 0) { continue; } int alignmentStart; int mateAlignmentStart = samRecord.getMateAlignmentStart(); if (samRecord.getAlignmentStart() > mateAlignmentStart) { if (!(mateAlignmentStart < LocationController.getInstance().getRangeStart())) { // this is the second in the pair, and it doesn't span the beginning of the range, so don't draw anything continue; } else { // switch the mate start/end for the read start/end to deal with reversed position alignmentStart = mateAlignmentStart; } } else { alignmentStart = samRecord.getAlignmentStart(); } // at this point alignmentStart/End refers the the start end of the first occurrence in the pair int intervalStart; switch (type) { case INVERTED_READ: case INVERTED_MATE: intervalStart = alignmentStart; g2.setColor(invertedReadColor); g2.setStroke(TWO_STROKE); break; case EVERTED: intervalStart = alignmentStart; g2.setColor(evertedPairColor); g2.setStroke(TWO_STROKE); break; default: // make sure arclength is over our threshold /*if (threshold != 0.0d && threshold < 1.0d && arcLength < axisRange.getXRange().getLength()*threshold) { continue; } else if (threshold > 1.0d && arcLength < threshold) { continue; }*/ intervalStart = alignmentStart; if (arcLength > discordantMax || arcLength < discordantMin) { g2.setColor(discordantLengthColor); g2.setStroke(TWO_STROKE); } else { g2.setColor(normalArcColor); g2.setStroke(ONE_STROKE); } break; } int arcHeight = arcLength; double rectWidth = arcLength * gp.getUnitWidth(); double rectHeight = arcHeight * 2 * gp.getUnitHeight(); double xOrigin = gp.transformXPos(intervalStart); double yOrigin = gp.transformYPos(arcHeight); Arc2D arc = new Arc2D.Double(xOrigin, yOrigin, rectWidth, rectHeight, -180, -180, Arc2D.OPEN); g2.draw(arc); recordToShapeMap.put(record, arc); } } } }