List of usage examples for java.awt.geom Rectangle2D getMaxY
public double getMaxY()
From source file:com.rapidminer.gui.new_plotter.engine.jfreechart.link_and_brush.LinkAndBrushChartPanel.java
@Override public void mouseDragged(MouseEvent e) { // when not allowed to zoom / select, return if (blockSelectionOrZoom) { return;//from www .j a va 2s . c o m } // if the popup menu has already been triggered, then ignore dragging... if (getChartFieldValueByName("popup") != null && ((JPopupMenu) getChartFieldValueByName("popup")).isShowing()) { return; } // handle panning if we have a start point if (getChartFieldValueByName("panLast") != null) { double dx = e.getX() - ((Point) getChartFieldValueByName("panLast")).getX(); double dy = e.getY() - ((Point) getChartFieldValueByName("panLast")).getY(); if (dx == 0.0 && dy == 0.0) { return; } double wPercent = -dx / ((Double) getChartFieldValueByName("panW")); double hPercent = dy / ((Double) getChartFieldValueByName("panH")); boolean old = getChart().getPlot().isNotify(); getChart().getPlot().setNotify(false); Pannable p = (Pannable) getChart().getPlot(); if (p.getOrientation() == PlotOrientation.VERTICAL) { p.panDomainAxes(wPercent, getChartRenderingInfo().getPlotInfo(), (Point) getChartFieldValueByName("panLast")); p.panRangeAxes(hPercent, getChartRenderingInfo().getPlotInfo(), (Point) getChartFieldValueByName("panLast")); } else { p.panDomainAxes(hPercent, getChartRenderingInfo().getPlotInfo(), (Point) getChartFieldValueByName("panLast")); p.panRangeAxes(wPercent, getChartRenderingInfo().getPlotInfo(), (Point) getChartFieldValueByName("panLast")); } setChartFieldValue((getChartFieldByName("panLast")), e.getPoint()); getChart().getPlot().setNotify(old); return; } // if no initial zoom point was set, ignore dragging... if (getChartFieldValueByName("zoomPoint") == null) { return; } Graphics2D g2 = (Graphics2D) getGraphics(); // erase the previous zoom rectangle (if any). We only need to do // this is we are using XOR mode, which we do when we're not using // the buffer (if there is a buffer, then at the end of this method we // just trigger a repaint) if (!(Boolean) getChartFieldValueByName("useBuffer")) { drawZoomRectangle(g2, true); } boolean hZoom = false; boolean vZoom = false; if ((PlotOrientation) getChartFieldValueByName("orientation") == PlotOrientation.HORIZONTAL) { hZoom = (Boolean) getChartFieldValueByName("rangeZoomable"); vZoom = (Boolean) getChartFieldValueByName("domainZoomable"); } else { hZoom = (Boolean) getChartFieldValueByName("domainZoomable"); vZoom = (Boolean) getChartFieldValueByName("rangeZoomable"); } Point2D zoomPoint = (Point2D) getChartFieldValueByName("zoomPoint"); Rectangle2D scaledDataArea = getScreenDataArea((int) zoomPoint.getX(), (int) zoomPoint.getY()); if (hZoom && vZoom) { // selected rectangle shouldn't extend outside the data area... double xmax = Math.min(e.getX(), scaledDataArea.getMaxX()); double ymax = Math.min(e.getY(), scaledDataArea.getMaxY()); setChartFieldValue(getChartFieldByName("zoomRectangle"), new Rectangle2D.Double(zoomPoint.getX(), zoomPoint.getY(), xmax - zoomPoint.getX(), ymax - zoomPoint.getY())); } else if (hZoom) { double xmax = Math.min(e.getX(), scaledDataArea.getMaxX()); setChartFieldValue(getChartFieldByName("zoomRectangle"), new Rectangle2D.Double(zoomPoint.getX(), scaledDataArea.getMinY(), xmax - zoomPoint.getX(), scaledDataArea.getHeight())); } else if (vZoom) { double ymax = Math.min(e.getY(), scaledDataArea.getMaxY()); setChartFieldValue(getChartFieldByName("zoomRectangle"), new Rectangle2D.Double(scaledDataArea.getMinX(), zoomPoint.getY(), scaledDataArea.getWidth(), ymax - zoomPoint.getY())); } // Draw the new zoom rectangle... if ((Boolean) getChartFieldValueByName("useBuffer")) { repaint(); } else { // with no buffer, we use XOR to draw the rectangle "over" the // chart... drawZoomRectangle(g2, true); } g2.dispose(); }
From source file:org.esa.beam.visat.toolviews.stat.ScatterPlotPanel.java
private ChartPanel createChartPanel(final JFreeChart chart) { scatterPlotDisplay = new ChartPanel(chart) { @Override/*from www. j av a 2 s.co m*/ public void restoreAutoBounds() { // here we tweak the notify flag on the plot so that only // one notification happens even though we update multiple // axes... final XYPlot plot = chart.getXYPlot(); boolean savedNotify = plot.isNotify(); plot.setNotify(false); xAxisRangeControl.adjustAxis(plot.getDomainAxis(), 3); yAxisRangeControl.adjustAxis(plot.getRangeAxis(), 3); plot.setNotify(savedNotify); } }; MaskSelectionToolSupport maskSelectionToolSupport = new MaskSelectionToolSupport(this, scatterPlotDisplay, "correlative_plot_area", "Mask generated from selected correlative plot area", Color.RED, PlotAreaSelectionTool.AreaType.Y_RANGE) { @Override protected String createMaskExpression(PlotAreaSelectionTool.AreaType areaType, Shape shape) { Rectangle2D bounds = shape.getBounds2D(); return createMaskExpression(bounds.getMinY(), bounds.getMaxY()); } protected String createMaskExpression(double x1, double x2) { String bandName = BandArithmetic.createExternalName(getRaster().getName()); return String.format("%s >= %s && %s <= %s", bandName, x1, bandName, x2); } }; scatterPlotDisplay.getPopupMenu().addSeparator(); scatterPlotDisplay.getPopupMenu().add(maskSelectionToolSupport.createMaskSelectionModeMenuItem()); scatterPlotDisplay.getPopupMenu().add(maskSelectionToolSupport.createDeleteMaskMenuItem()); scatterPlotDisplay.getPopupMenu().addSeparator(); scatterPlotDisplay.getPopupMenu().add(createCopyDataToClipboardMenuItem()); return scatterPlotDisplay; }
From source file:ucar.unidata.idv.control.chart.MyScatterPlot.java
/** * Draws the fast scatter plot on a Java 2D graphics device (such as the * screen or a printer)./*from ww w . j a va 2 s. c o m*/ * a * @param g2 the graphics device. * @param dataArea the data area * @param index which data set * @param info collects chart drawing information (<code>null</code> * permitted). * @param crosshairState crosshairState * * @return did something */ public boolean render(Graphics2D g2, Rectangle2D dataArea, int index, PlotRenderingInfo info, CrosshairState crosshairState) { if (index >= series.size()) { return false; } XYDataset dataset = getDataset(index); g2.setStroke(new BasicStroke()); // getRendererForDataset(dataset).getSeriesStroke(0)); ScatterPlotChartWrapper.MyRenderer renderer = (ScatterPlotChartWrapper.MyRenderer) getRendererForDataset( dataset); g2.setPaint(renderer.getSeriesPaint(0)); int shape = renderer.shape; PlotOrientation orientation = getOrientation(); int seenCnt = 0; int xx = (int) dataArea.getMinX(); int ww = (int) dataArea.getWidth(); int yy = (int) dataArea.getMaxY(); int hh = (int) dataArea.getHeight(); ValueAxis rangeAxis = getRangeAxisForDataset(index); ValueAxis domainAxis = getDomainAxisForDataset(index); double domainMin = domainAxis.getLowerBound(); double domainLength = domainAxis.getUpperBound() - domainMin; double rangeMin = rangeAxis.getLowerBound(); double rangeLength = rangeAxis.getUpperBound() - rangeMin; int boxWidth = 6; double[][] data = (double[][]) series.get(index); double[] d1 = data[0]; double[] d2 = data[1]; int size = d1.length; Hashtable seen = new Hashtable(); int lastX = 0; int lastY = 0; //TODO: Check for clipping //TODO: Try to create a GeneralPath with the points //and cal g2.draw just once GeneralPath path = new GeneralPath(); long t1 = System.currentTimeMillis(); for (int i = 0; i < size; i++) { int transX = (int) (xx + ww * (d1[i] - domainMin) / domainLength); int transY = (int) (yy - hh * (d2[i] - rangeMin) / rangeLength); Object key = transX + "_" + transY; if (seen.get(key) != null) { seenCnt++; continue; } seen.put(key, key); if (crosshairState != null) { crosshairState.updateCrosshairPoint(d1[i], d2[i], transX, transY, orientation); } switch (shape) { case LineState.SHAPE_VLINE: if (i > 1) { g2.drawLine(lastX, lastY, transX, transY); } lastX = transX; lastY = transY; case LineState.SHAPE_POINT: path.append(new Rectangle((int) transX, (int) transY, 1, 1), false); break; case LineState.SHAPE_LARGEPOINT: path.append(new Rectangle((int) transX, (int) transY, 2, 2), false); break; case LineState.SHAPE_RECTANGLE: path.append( new Rectangle((int) transX - boxWidth / 2, (int) transY - boxWidth / 2, boxWidth, boxWidth), false); break; case LineState.SHAPE_X: g2.drawLine(transX - boxWidth / 2, transY - boxWidth / 2, transX + boxWidth - boxWidth / 2, transY + boxWidth - boxWidth / 2); g2.drawLine(transX + boxWidth - boxWidth / 2, transY - boxWidth / 2, transX - boxWidth / 2, transY + boxWidth - boxWidth / 2); break; case LineState.SHAPE_PLUS: g2.drawLine(transX + boxWidth / 2, transY, transX + boxWidth / 2, transY + boxWidth); g2.drawLine(transX, transY + boxWidth / 2, transX + boxWidth, transY + boxWidth / 2); break; } } g2.fill(path); long t2 = System.currentTimeMillis(); // System.out.println ("time:" + (t2-t1)); return true; }
From source file:org.gumtree.vis.awt.time.TimePlotPanel.java
@Override protected void drawToolTipFollower(Graphics2D g2, int x, int y) { Rectangle2D dataArea = getScreenDataArea(); if (((int) dataArea.getMinX() <= x) && (x <= (int) dataArea.getMaxX()) && ((int) dataArea.getMinY() <= y) && (y <= (int) dataArea.getMaxY())) { Date date = new Date((long) getChartX()); String text = ""; SimpleDateFormat format = new SimpleDateFormat("EEE d MMM HH:mm:ss"); StringBuffer buffer = new StringBuffer(); format.format(date, buffer, new FieldPosition(0)); text = buffer.toString();/* ww w .j av a 2 s. c o m*/ text = "(" + text + String.format(", %.2f)", getChartY()); int xLoc = x + 10; int yLoc = y + 20; double width = text.length() * 5.5; double height = 15; if (xLoc + width > dataArea.getMaxX()) { xLoc = (int) (x - width); } if (yLoc + height > dataArea.getMaxY()) { yLoc = (int) (y - height); } Rectangle2D toolTipArea = new Rectangle2D.Double(xLoc, yLoc, width, height); g2.setColor(Color.white); g2.fill(toolTipArea); g2.setColor(Color.black); g2.drawString(text, xLoc + 3, yLoc + 11); } }
From source file:com.rapidminer.gui.new_plotter.engine.jfreechart.link_and_brush.LinkAndBrushChartPanel.java
@Override public void zoom(Rectangle2D selection) { // get the origin of the zoom selection in the Java2D space used for // drawing the chart (that is, before any scaling to fit the panel) Point2D selectOrigin = translateScreenToJava2D( new Point((int) Math.ceil(selection.getX()), (int) Math.ceil(selection.getY()))); PlotRenderingInfo plotInfo = getChartRenderingInfo().getPlotInfo(); Rectangle2D scaledDataArea = getScreenDataArea((int) selection.getCenterX(), (int) selection.getCenterY()); if ((selection.getHeight() > 0) && (selection.getWidth() > 0)) { double hLower = (selection.getMinX() - scaledDataArea.getMinX()) / scaledDataArea.getWidth(); double hUpper = (selection.getMaxX() - scaledDataArea.getMinX()) / scaledDataArea.getWidth(); double vLower = (scaledDataArea.getMaxY() - selection.getMaxY()) / scaledDataArea.getHeight(); double vUpper = (scaledDataArea.getMaxY() - selection.getMinY()) / scaledDataArea.getHeight(); Plot p = getChart().getPlot();//from w w w.ja va 2 s. co m if (p instanceof LinkAndBrushPlot) { PlotOrientation orientation = null; if (p instanceof XYPlot) { XYPlot xyPlot = (XYPlot) p; orientation = xyPlot.getOrientation(); } if (p instanceof CategoryPlot) { CategoryPlot categoryPlot = (CategoryPlot) p; orientation = categoryPlot.getOrientation(); } // here we tweak the notify flag on the plot so that only // one notification happens even though we update multiple // axes... boolean savedNotify = p.isNotify(); p.setNotify(false); LinkAndBrushPlot LABPlot = (LinkAndBrushPlot) p; List<Pair<Integer, Range>> zoomedDomainAxisRanges = new LinkedList<Pair<Integer, Range>>(); List<Pair<Integer, Range>> zoomedRangeAxisRanges = new LinkedList<Pair<Integer, Range>>(); if (orientation == PlotOrientation.HORIZONTAL) { zoomedDomainAxisRanges .addAll(LABPlot.calculateDomainAxesZoom(vLower, vUpper, zoomOnLinkAndBrushSelection)); zoomedRangeAxisRanges.addAll(LABPlot.calculateRangeAxesZoom(hLower, hUpper, plotInfo, selectOrigin, zoomOnLinkAndBrushSelection)); } else { zoomedDomainAxisRanges .addAll(LABPlot.calculateDomainAxesZoom(hLower, hUpper, zoomOnLinkAndBrushSelection)); zoomedRangeAxisRanges.addAll(LABPlot.calculateRangeAxesZoom(vLower, vUpper, plotInfo, selectOrigin, zoomOnLinkAndBrushSelection)); } p.setNotify(savedNotify); if (zoomOnLinkAndBrushSelection) { informLinkAndBrushSelectionListeners(new LinkAndBrushSelection(SelectionType.ZOOM_IN, zoomedDomainAxisRanges, zoomedRangeAxisRanges)); } else { informLinkAndBrushSelectionListeners(new LinkAndBrushSelection(SelectionType.SELECTION, zoomedDomainAxisRanges, zoomedRangeAxisRanges)); } } else { super.zoom(selection); } } }
From source file:com.rapidminer.gui.plotter.charts.WeightBasedSymbolAxis.java
/** * Draws the grid bands for the axis when it is at the top or bottom of the plot. * // w ww . j av a 2 s .c o m * @param g2 * the graphics device. * @param plotArea * the area within which the chart should be drawn. * @param dataArea * the area within which the plot should be drawn (a subset of the drawArea). * @param firstGridBandIsDark * True: the first grid band takes the color of <CODE>gridBandPaint<CODE>. * False: the second grid band takes the * color of <CODE>gridBandPaint<CODE>. * @param ticks * the ticks. */ @Override protected void drawGridBandsHorizontal(Graphics2D g2, Rectangle2D plotArea, Rectangle2D dataArea, boolean firstGridBandIsDark, List ticks) { double yy = dataArea.getY(); double xx1, xx2; // gets the outline stroke width of the plot double outlineStrokeWidth; if (getPlot().getOutlineStroke() != null) { outlineStrokeWidth = ((BasicStroke) getPlot().getOutlineStroke()).getLineWidth(); } else { outlineStrokeWidth = 1d; } Iterator iterator = ticks.iterator(); ValueTick tick; Rectangle2D band; while (iterator.hasNext()) { tick = (ValueTick) iterator.next(); int weightIndex = (int) tick.getValue(); xx1 = valueToJava2D(tick.getValue() - 0.5d, dataArea, RectangleEdge.BOTTOM); xx2 = valueToJava2D(tick.getValue() + 0.5d, dataArea, RectangleEdge.BOTTOM); g2.setColor(PlotterAdapter.getWeightColor(this.weights[weightIndex], this.maxWeight)); band = new Rectangle2D.Double(xx1, yy + outlineStrokeWidth, xx2 - xx1, dataArea.getMaxY() - yy - outlineStrokeWidth); g2.fill(band); } g2.setPaintMode(); }
From source file:org.proteosuite.FastScatterPlot.java
/** * Draws the fast scatter plot on a Java 2D graphics device (such as the * screen or a printer)./*ww w .java2 s .c o m*/ * * @param g2 the graphics device. * @param area the area within which the plot (including axis labels) * should be drawn. * @param anchor the anchor point (<code>null</code> permitted). * @param parentState the state from the parent plot, if there is one. * @param info collects chart drawing information (<code>null</code> * permitted). */ public void draw(Graphics2D g2, Rectangle2D area, Point2D anchor, PlotState parentState, PlotRenderingInfo info) { // set up info collection... if (info != null) { info.setPlotArea(area); } // adjust the drawing area for plot insets (if any)... RectangleInsets insets = getInsets(); insets.trim(area); AxisSpace space = new AxisSpace(); space = this.domainAxis.reserveSpace(g2, this, area, RectangleEdge.BOTTOM, space); space = this.rangeAxis.reserveSpace(g2, this, area, RectangleEdge.LEFT, space); Rectangle2D dataArea = space.shrink(area, null); if (info != null) { info.setDataArea(dataArea); } // draw the plot background and axes... drawBackground(g2, dataArea); AxisState domainAxisState = null; AxisState rangeAxisState = null; if (this.domainAxis != null) { domainAxisState = this.domainAxis.draw(g2, dataArea.getMaxY(), area, dataArea, RectangleEdge.BOTTOM, info); } if (this.rangeAxis != null) { rangeAxisState = this.rangeAxis.draw(g2, dataArea.getMinX(), area, dataArea, RectangleEdge.LEFT, info); } drawDomainGridlines(g2, dataArea, domainAxisState.getTicks()); drawRangeGridlines(g2, dataArea, rangeAxisState.getTicks()); Shape originalClip = g2.getClip(); Composite originalComposite = g2.getComposite(); g2.clip(dataArea); g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, getForegroundAlpha())); render(g2, dataArea, info, null); g2.setClip(originalClip); g2.setComposite(originalComposite); drawOutline(g2, dataArea); }
From source file:it.unibo.alchemist.model.implementations.actions.SocialForceAgent.java
/** * Method used to retrieve the obstacle edge nearest to the pedestrian * /*from w ww . j a v a 2 s . c om*/ * @param myx * - the current pedestrian x-coordinate position * @param myy * - the current pedestrian y-coordinate position * @param bounds * - the rectangle obstacle bounds * @return nearest - an array containing two Continuous2DEuclidean object * representing nearest edge vertices */ private Continuous2DEuclidean[] getNearestEdge(final double myx, final double myy, final Rectangle2D bounds) { Continuous2DEuclidean[] nearest = null; final double minX = bounds.getMinX(); final double maxX = bounds.getMaxX(); final double minY = bounds.getMinY(); final double maxY = bounds.getMaxY(); if (myx > minX && myx < maxX) { if (myy > maxY) { // above the obstacle nearest = new Continuous2DEuclidean[] { new Continuous2DEuclidean(bounds.getMinX(), bounds.getMaxY()), new Continuous2DEuclidean(bounds.getMaxX(), bounds.getMaxY()) }; } else if (myy < minY) { // under the obstacle nearest = new Continuous2DEuclidean[] { new Continuous2DEuclidean(bounds.getMinX(), bounds.getMinY()), new Continuous2DEuclidean(bounds.getMaxX(), bounds.getMinY()) }; } } else if (myy > minY && myy < maxY) { if (myx < minX) { // to the left the obstacle nearest = new Continuous2DEuclidean[] { new Continuous2DEuclidean(bounds.getMinX(), bounds.getMaxY()), new Continuous2DEuclidean(bounds.getMinX(), bounds.getMinY()) }; } else if (myx > maxX) { // to the right the obstacle nearest = new Continuous2DEuclidean[] { new Continuous2DEuclidean(bounds.getMaxX(), bounds.getMaxY()), new Continuous2DEuclidean(bounds.getMaxX(), bounds.getMinY()) }; } } return nearest; }
From source file:com.github.lindenb.jvarkit.tools.misc.BamCmpCoverage.java
@Override public Collection<Throwable> call() throws Exception { if (getOutputFile() == null) { return wrapException("output image file not defined"); }//from ww w . j a v a 2 s . c o m if (this.imgageSize < 1) { return wrapException("Bad image size:" + this.imgageSize); } if (this.minDepth < 0) { return wrapException("Bad min depth : " + this.minDepth); } if (this.minDepth >= this.maxDepth) { return wrapException("Bad min<max depth : " + this.minDepth + "<" + this.maxDepth); } if (this.getBedFile() != null) { readBedFile(this.getBedFile()); } if (regionStr != null && this.intervals != null) { return wrapException("bed and interval both defined."); } final SamRecordFilter filter = new SamRecordFilter() { @Override public boolean filterOut(SAMRecord first, SAMRecord second) { return filterOut(first); } @Override public boolean filterOut(SAMRecord rec) { if (rec.getReadUnmappedFlag()) return true; if (rec.isSecondaryOrSupplementary()) return true; if (rec.getDuplicateReadFlag()) return true; if (rec.getNotPrimaryAlignmentFlag()) return true; if (rec.getReadFailsVendorQualityCheckFlag()) return true; if (rec.getMappingQuality() == 0) return true; /* ignore non-overlapping BED, already checked with QuertInterval if( intervals!=null && ! intervals.containsOverlapping( new Interval(rec.getReferenceName(), rec.getAlignmentStart(), rec.getAlignmentEnd())) ) { return true; } */ return false; } }; Set<File> files = new HashSet<File>(); try { SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT); srf.disable(SamReaderFactory.Option.EAGERLY_DECODE); srf.disable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS); srf.disable(SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS); final List<String> args = this.getInputFiles(); for (String arg : args) { File f = new File(arg); if (f.getName().endsWith(".list")) { LOG.info("Reading BAM list from " + f); BufferedReader in = IOUtils.openFileForBufferedReading(f); String line; while ((line = in.readLine()) != null) { if (line.trim().isEmpty() || line.startsWith("#")) continue; files.add(new File(line)); } in.close(); } else { files.add(f); } } if (files.isEmpty()) { return wrapException("No BAM defined"); } Comparator<SAMRecord> comparator = new Comparator<SAMRecord>() { @Override public int compare(SAMRecord samRecord1, SAMRecord samRecord2) { final int refIndex1 = samRecord1.getReferenceIndex(); final int refIndex2 = samRecord2.getReferenceIndex(); if (refIndex1 == -1) { return (refIndex2 == -1 ? 0 : 1); } else if (refIndex2 == -1) { return -1; } final int cmp = refIndex1 - refIndex2; if (cmp != 0) { return cmp; } return samRecord1.getAlignmentStart() - samRecord2.getAlignmentStart(); } }; List<SamReader> readers = new ArrayList<SamReader>(files.size()); List<CloseableIterator<SAMRecord>> iterators = new ArrayList<CloseableIterator<SAMRecord>>( files.size()); Set<String> samples = new TreeSet<String>(); SAMSequenceDictionary dict = null; /* will be initialized below once, if needed */ QueryInterval queryIntervalArray[] = null; //scan samples names for (File bamFile : files) { SamReader r = srf.open(bamFile); readers.add(r); SAMFileHeader h = r.getFileHeader(); if (h.getSortOrder() != SortOrder.coordinate) { r.close(); return wrapException("file " + bamFile + " not sorted on coordinate"); } if (dict == null) { dict = h.getSequenceDictionary(); } else if (!SequenceUtil.areSequenceDictionariesEqual(dict, h.getSequenceDictionary())) { return wrapException("Found more than one dictint sequence dictionary"); } //fill query interval once List<QueryInterval> queryIntervals = new ArrayList<>(); if (regionStr != null && queryIntervalArray == null) { int colon = regionStr.indexOf(':'); String chrom; int chromStart; int chromEnd; if (colon == -1) { chrom = regionStr; } else { chrom = regionStr.substring(0, colon); } SAMSequenceRecord ssr = dict.getSequence(chrom); if (ssr == null) { return wrapException("Chromosome " + chrom + " not present in dictionary"); } int hyphen = regionStr.indexOf('-', colon + 1); if (hyphen != -1) { chromStart = Integer.parseInt(regionStr.substring(colon + 1, hyphen)); chromEnd = Integer.parseInt(regionStr.substring(hyphen + 1)); } else { chromStart = 0; chromEnd = ssr.getSequenceLength() - 1; } if (chromStart < 0 || chromEnd < chromStart) { return wrapException("bad position in " + regionStr); } queryIntervals.add(new QueryInterval(ssr.getSequenceIndex(), chromStart, chromEnd)); } if (this.intervals != null && queryIntervalArray == null) { for (Interval interval : this.intervals.keySet()) { SAMSequenceRecord ssr = dict.getSequence(interval.getContig()); if (ssr == null) { return wrapException( "Chromosome " + interval.getContig() + " not present in dictionary"); } queryIntervals.add( new QueryInterval(ssr.getSequenceIndex(), interval.getStart(), interval.getEnd())); } } if (!queryIntervals.isEmpty() && queryIntervalArray == null) { Collections.sort(queryIntervals); queryIntervalArray = queryIntervals.toArray(new QueryInterval[queryIntervals.size()]); } for (SAMReadGroupRecord rg : h.getReadGroups()) { String sample = rg.getSample(); if (sample == null) continue; samples.add(sample); } CloseableIterator<SAMRecord> reciterator = null; if (queryIntervalArray == null) { reciterator = r.iterator(); } else { reciterator = r.query(queryIntervalArray, false); } reciterator = new FilteringIterator(reciterator, filter); iterators.add(reciterator); } //free GC queryIntervalArray = null; LOG.info("Samples:" + samples.size()); for (String sample : samples) { this.sample2column.put(sample, this.sample2column.size()); } //create merging sam-reader MergingSamRecordIterator iter = new MergingSamRecordIterator(comparator, iterators); //create image LOG.info("Creating image " + this.imgageSize + "x" + this.imgageSize); this.image = new BufferedImage(this.imgageSize, this.imgageSize, BufferedImage.TYPE_INT_RGB); Graphics2D g = this.image.createGraphics(); this.marginWidth = this.imgageSize * 0.05; double drawingWidth = (this.imgageSize - 1) - marginWidth; this.sampleWidth = drawingWidth / samples.size(); //g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g.setColor(Color.WHITE); g.fillRect(0, 0, this.imgageSize, this.imgageSize); g.setColor(Color.BLACK); Hershey hershey = new Hershey(); for (String sample_x : samples) { double labelHeight = marginWidth; if (labelHeight > 50) labelHeight = 50; g.setColor(Color.BLACK); hershey.paint(g, sample_x, marginWidth + sample2column.get(sample_x) * sampleWidth, marginWidth - labelHeight, sampleWidth * 0.9, labelHeight * 0.9); AffineTransform old = g.getTransform(); AffineTransform tr = AffineTransform.getTranslateInstance(marginWidth, marginWidth + sample2column.get(sample_x) * sampleWidth); tr.rotate(Math.PI / 2); g.setTransform(tr); hershey.paint(g, sample_x, 0.0, 0.0, sampleWidth * 0.9, labelHeight * 0.9); //g.drawString(this.tabixFile.getFile().getName(),0,0); g.setTransform(old); for (String sample_y : samples) { Rectangle2D rect = new Rectangle2D.Double( marginWidth + sample2column.get(sample_x) * sampleWidth, marginWidth + sample2column.get(sample_y) * sampleWidth, sampleWidth, sampleWidth); g.setColor(Color.BLUE); g.draw(new Line2D.Double(rect.getMinX(), rect.getMinY(), rect.getMaxX(), rect.getMaxY())); g.setColor(Color.BLACK); g.draw(rect); } } //ceate bit-array BitSampleMatrix bitMatrix = new BitSampleMatrix(samples.size()); //preivous chrom //int prev_tid=-1; BufferedList<Depth> depthList = new BufferedList<Depth>(); g.setColor(Color.BLACK); SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(dict); LOG.info("Scanning bams..."); while (iter.hasNext()) { SAMRecord rec = iter.next(); if (filter.filterOut(rec)) continue; progress.watch(rec); SAMReadGroupRecord gr = rec.getReadGroup(); if (gr == null) continue; String sample = gr.getSample(); if (sample == null) continue; int sample_id = this.sample2column.get(sample); Cigar cigar = rec.getCigar(); if (cigar == null) continue; int refPos = rec.getAlignmentStart(); /* cleanup front pos */ while (!depthList.isEmpty()) { Depth front = depthList.getFirst(); if (front.tid != rec.getReferenceIndex().intValue() || front.pos < refPos) { paint(bitMatrix, front); depthList.removeFirst(); continue; } else { break; } } for (CigarElement ce : cigar.getCigarElements()) { CigarOperator op = ce.getOperator(); if (!op.consumesReferenceBases()) continue; if (op.consumesReadBases()) { for (int i = 0; i < ce.getLength(); ++i) { Depth depth = null; int pos = refPos + i; //ignore non-overlapping BED if (this.intervals != null && !this.intervals .containsOverlapping(new Interval(rec.getReferenceName(), pos, pos))) { continue; } else if (depthList.isEmpty()) { depth = new Depth(); depth.pos = pos; depth.tid = rec.getReferenceIndex(); depthList.add(depth); } else if (depthList.getLast().pos < pos) { Depth prev = depthList.getLast(); while (prev.pos < pos) { depth = new Depth(); depth.pos = prev.pos + 1; depth.tid = rec.getReferenceIndex(); depthList.add(depth); prev = depth; } depth = prev; } else { int lastPos = depthList.get(depthList.size() - 1).pos; int distance = lastPos - pos; int indexInList = (depthList.size() - 1) - (distance); if (indexInList < 0) { //can appen when BED declared and partially overlap the read continue; } depth = depthList.get((depthList.size() - 1) - (distance)); if (depth.pos != pos) { return wrapException(" " + pos + " vs " + depth.pos + " " + lastPos); } } depth.depths[sample_id]++; } } refPos += ce.getLength(); } } while (!depthList.isEmpty()) { //paint(g,depthList.remove(0)); paint(bitMatrix, depthList.remove(0)); } progress.finish(); iter.close(); //paint bitset for (int x = 0; x < bitMatrix.n_samples; ++x) { for (int y = 0; y < bitMatrix.n_samples; ++y) { LOG.info("Painting...(" + x + "/" + y + ")"); paint(g, bitMatrix.get(x, y)); } } g.dispose(); //close readers for (SamReader r : readers) r.close(); //save file LOG.info("saving " + getOutputFile()); if (getOutputFile().getName().toLowerCase().endsWith(".png")) { ImageIO.write(this.image, "PNG", getOutputFile()); } else { ImageIO.write(this.image, "JPG", getOutputFile()); } return Collections.emptyList(); } catch (Exception err) { return wrapException(err); } finally { } }
From source file:Polygon2D.java
/** * Constructs and initializes a <code>Polygon2D</code> from the specified * Rectangle2D./*from w w w.j a va 2 s.c o m*/ * @param rec the Rectangle2D * @exception NullPointerException rec is <code>null</code>. */ public Polygon2D(Rectangle2D rec) { if (rec == null) { throw new IndexOutOfBoundsException("null Rectangle"); } npoints = 4; xpoints = new float[4]; ypoints = new float[4]; xpoints[0] = (float) rec.getMinX(); ypoints[0] = (float) rec.getMinY(); xpoints[1] = (float) rec.getMaxX(); ypoints[1] = (float) rec.getMinY(); xpoints[2] = (float) rec.getMaxX(); ypoints[2] = (float) rec.getMaxY(); xpoints[3] = (float) rec.getMinX(); ypoints[3] = (float) rec.getMaxY(); calculatePath(); }