List of usage examples for java.awt Graphics2D getTransform
public abstract AffineTransform getTransform();
From source file:net.sf.maltcms.common.charts.api.overlay.SelectionOverlay.java
private void drawEntity(Shape entity, Graphics2D g2, Color fill, ChartPanel chartPanel, boolean scale) { if (entity != null) { Shape savedClip = g2.getClip(); Rectangle2D dataArea = chartPanel.getScreenDataArea(); Color c = g2.getColor();/*www. j a v a 2s . c o m*/ Composite comp = g2.getComposite(); g2.clip(dataArea); g2.setColor(fill); AffineTransform originalTransform = g2.getTransform(); Shape transformed = entity; if (scale) { transformed = scaleAtOrigin(entity, hoverScaleX, hoverScaleY).createTransformedShape(entity); } transformed = getTranslateInstance( entity.getBounds2D().getCenterX() - transformed.getBounds2D().getCenterX(), entity.getBounds2D().getCenterY() - transformed.getBounds2D().getCenterY()) .createTransformedShape(transformed); g2.setComposite(getInstance(AlphaComposite.SRC_OVER, fillAlpha)); g2.fill(transformed); g2.setColor(Color.DARK_GRAY); g2.draw(transformed); g2.setComposite(comp); g2.setColor(c); g2.setClip(savedClip); } }
From source file:net.sf.maltcms.chromaui.annotations.PeakAnnotationRenderer.java
private void drawEntity(Shape entity, Graphics2D g2, Color fill, Color stroke, ChartPanel chartPanel, boolean scale, float alpha) { if (entity != null) { //System.out.println("Drawing entity with bbox: "+entity.getBounds2D()); Shape savedClip = g2.getClip(); Rectangle2D dataArea = chartPanel.getScreenDataArea(); Color c = g2.getColor();//from www . j av a2 s.c o m Composite comp = g2.getComposite(); g2.clip(dataArea); g2.setColor(fill); g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); AffineTransform originalTransform = g2.getTransform(); Shape transformed = entity; FlatteningPathIterator iter = new FlatteningPathIterator( transformed.getPathIterator(new AffineTransform()), 1); Path2D.Float path = new Path2D.Float(); path.append(iter, false); g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, alpha)); g2.fill(path); if (stroke != null) { g2.setColor(stroke); g2.draw(path); } g2.setComposite(comp); g2.setColor(c); g2.setClip(savedClip); } else { Logger.getLogger(getClass().getName()).info("Entity is null!"); } }
From source file:com.epiq.bitshark.ui.FrequencyDomainMouseMarker.java
/** * Draws the annotation./*from www.j a va 2 s . c o m*/ * * @param g2 the graphics device. * @param plot the plot. * @param dataArea the data area. * @param domainAxis the domain axis. * @param rangeAxis the range axis. * @param rendererIndex the renderer index. * @param info if supplied, this info object will be populated with * entity information. */ @Override public void draw(Graphics2D g2, XYPlot plot, Rectangle2D dataArea, ValueAxis domainAxis, ValueAxis rangeAxis, int rendererIndex, PlotRenderingInfo info) { if (!visible) { return; } PlotOrientation orientation = plot.getOrientation(); RectangleEdge domainEdge = Plot.resolveDomainAxisLocation(plot.getDomainAxisLocation(), orientation); RectangleEdge rangeEdge = Plot.resolveRangeAxisLocation(plot.getRangeAxisLocation(), orientation); float j2DX = (float) domainAxis.valueToJava2D(this.x, dataArea, domainEdge); float j2DY = (float) rangeAxis.valueToJava2D(this.y, dataArea, rangeEdge); Rectangle2D displayArea = new Rectangle2D.Double(j2DX - this.displayWidth / 2.0, j2DY - this.displayHeight / 2.0, this.displayWidth, this.displayHeight); // here we change the AffineTransform so we can draw the annotation // to a larger area and scale it down into the display area // afterwards, the original transform is restored AffineTransform savedTransform = g2.getTransform(); Rectangle2D drawArea = new Rectangle2D.Double(0.0, 0.0, this.displayWidth * this.drawScaleFactor, this.displayHeight * this.drawScaleFactor); g2.scale(1 / this.drawScaleFactor, 1 / this.drawScaleFactor); g2.translate((j2DX - this.displayWidth / 2.0) * this.drawScaleFactor, (j2DY - this.displayHeight / 2.0) * this.drawScaleFactor); draw(g2, drawArea); g2.setTransform(savedTransform); String toolTip = getToolTipText(); String url = getURL(); if (toolTip != null || url != null) { addEntity(info, displayArea, rendererIndex, toolTip, url); } }
From source file:com.rapidminer.gui.new_plotter.engine.jfreechart.link_and_brush.LinkAndBrushChartPanel.java
@Override public void paintComponent(Graphics g) { super.paintComponent(g); if (getChart() == null) { return;//from w w w. ja v a 2 s. c om } Graphics2D g2 = (Graphics2D) g.create(); // first determine the size of the chart rendering area... Dimension size = getSize(); Insets insets = getInsets(); Rectangle2D available = new Rectangle2D.Double(insets.left, insets.top, size.getWidth() - insets.left - insets.right, size.getHeight() - insets.top - insets.bottom); // work out if scaling is required... boolean scale = false; double drawWidth = available.getWidth(); double drawHeight = available.getHeight(); setChartFieldValue(getChartFieldByName("scaleX"), 1.0); // this.scaleX = 1.0; setChartFieldValue(getChartFieldByName("scaleY"), 1.0); // this.scaleY = 1.0; if (drawWidth < getMinimumDrawWidth()) { setChartFieldValue(getChartFieldByName("scaleX"), drawWidth / getMinimumDrawWidth()); // this.scaleX = drawWidth / getMinimumDrawWidth(); drawWidth = getMinimumDrawWidth(); scale = true; } else if (drawWidth > getMaximumDrawWidth()) { setChartFieldValue(getChartFieldByName("scaleX"), drawWidth / getMaximumDrawWidth()); // this.scaleX = drawWidth / getMaximumDrawWidth(); drawWidth = getMaximumDrawWidth(); scale = true; } if (drawHeight < getMinimumDrawHeight()) { setChartFieldValue(getChartFieldByName("scaleY"), drawHeight / getMinimumDrawHeight()); // this.scaleY = drawHeight / getMinimumDrawHeight(); drawHeight = getMinimumDrawHeight(); scale = true; } else if (drawHeight > getMaximumDrawHeight()) { setChartFieldValue(getChartFieldByName("scaleY"), drawHeight / getMaximumDrawHeight()); // this.scaleY = drawHeight / getMaximumDrawHeight(); drawHeight = getMaximumDrawHeight(); scale = true; } Rectangle2D chartArea = new Rectangle2D.Double(0.0, 0.0, drawWidth, drawHeight); // are we using the chart buffer? if ((Boolean) getChartFieldValueByName("useBuffer")) { // do we need to resize the buffer? if ((getChartFieldValueByName("chartBuffer") == null) || ((Integer) getChartFieldValueByName("chartBufferWidth") != available.getWidth()) || ((Integer) getChartFieldValueByName("chartBufferHeight") != available.getHeight())) { setChartFieldValue(getChartFieldByName("chartBufferWidth"), (int) available.getWidth()); // this.chartBufferWidth = (int) available.getWidth(); setChartFieldValue(getChartFieldByName("chartBufferHeight"), (int) available.getHeight()); // this.chartBufferHeight = (int) available.getHeight(); GraphicsConfiguration gc = g2.getDeviceConfiguration(); setChartFieldValue(getChartFieldByName("chartBuffer"), gc.createCompatibleImage((Integer) getChartFieldValueByName("chartBufferWidth"), (Integer) getChartFieldValueByName("chartBufferHeight"), Transparency.TRANSLUCENT)); // this.chartBuffer = gc.createCompatibleImage(this.chartBufferWidth, // this.chartBufferHeight, Transparency.TRANSLUCENT); setRefreshBuffer(true); } // do we need to redraw the buffer? if (getRefreshBuffer()) { setRefreshBuffer(false); // clear the flag Rectangle2D bufferArea = new Rectangle2D.Double(0, 0, (Integer) getChartFieldValueByName("chartBufferWidth"), (Integer) getChartFieldValueByName("chartBufferHeight")); Graphics2D bufferG2 = (Graphics2D) ((Image) getChartFieldValueByName("chartBuffer")).getGraphics(); Rectangle r = new Rectangle(0, 0, (Integer) getChartFieldValueByName("chartBufferWidth"), (Integer) getChartFieldValueByName("chartBufferHeight")); bufferG2.setPaint(getBackground()); bufferG2.fill(r); if (scale) { AffineTransform saved = bufferG2.getTransform(); AffineTransform st = AffineTransform.getScaleInstance( (Double) getChartFieldValueByName("scaleX"), (Double) getChartFieldValueByName("scaleY")); bufferG2.transform(st); getChart().draw(bufferG2, chartArea, getAnchor(), getChartRenderingInfo()); bufferG2.setTransform(saved); } else { getChart().draw(bufferG2, bufferArea, getAnchor(), getChartRenderingInfo()); } } // zap the buffer onto the panel... g2.drawImage((Image) getChartFieldValueByName("chartBuffer"), insets.left, insets.top, this); } // or redrawing the chart every time... else { AffineTransform saved = g2.getTransform(); g2.translate(insets.left, insets.top); if (scale) { AffineTransform st = AffineTransform.getScaleInstance((Double) getChartFieldValueByName("scaleX"), (Double) getChartFieldValueByName("scaleY")); g2.transform(st); } getChart().draw(g2, chartArea, getAnchor(), getChartRenderingInfo()); g2.setTransform(saved); } Iterator iterator = ((List) getChartFieldValueByName("overlays")).iterator(); while (iterator.hasNext()) { Overlay overlay = (Overlay) iterator.next(); overlay.paintOverlay(g2, this); } // redraw the zoom rectangle (if present) - if useBuffer is false, // we use XOR so we can XOR the rectangle away again without redrawing // the chart drawZoomRectangle(g2, !(Boolean) getChartFieldValueByName("useBuffer")); g2.dispose(); setAnchor(null); setVerticalTraceLine(null); setHorizontalTraceLine(null); }
From source file:org.gvsig.remotesensing.scatterplot.chart.ScatterPlotDiagram.java
/** * Paints the component by drawing the chart to fill the entire component, * but allowing for the insets (which will be non-zero if a border has been * set for this component). To increase performance (at the expense of * memory), an off-screen buffer image can be used. * * @param g the graphics device for drawing on. *///from w w w. ja v a2s. co m public void paintComponent(Graphics g) { super.paintComponent(g); if (this.chart == null) { return; } Graphics2D g2 = (Graphics2D) g.create(); // first determine the size of the chart rendering area... Dimension size = getSize(); Insets insets = getInsets(); Rectangle2D available = new Rectangle2D.Double(insets.left, insets.top, size.getWidth() - insets.left - insets.right, size.getHeight() - insets.top - insets.bottom); // work out if scaling is required... boolean scale = false; double drawWidth = available.getWidth(); double drawHeight = available.getHeight(); this.scaleX = 1.0; this.scaleY = 1.0; if (drawWidth < this.minimumDrawWidth) { this.scaleX = drawWidth / this.minimumDrawWidth; drawWidth = this.minimumDrawWidth; scale = true; } else if (drawWidth > this.maximumDrawWidth) { this.scaleX = drawWidth / this.maximumDrawWidth; drawWidth = this.maximumDrawWidth; scale = true; } if (drawHeight < this.minimumDrawHeight) { this.scaleY = drawHeight / this.minimumDrawHeight; drawHeight = this.minimumDrawHeight; scale = true; } else if (drawHeight > this.maximumDrawHeight) { this.scaleY = drawHeight / this.maximumDrawHeight; drawHeight = this.maximumDrawHeight; scale = true; } Rectangle2D chartArea = new Rectangle2D.Double(0.0, 0.0, drawWidth, drawHeight); // are we using the chart buffer? if (this.useBuffer) { // if buffer is being refreshed, it needs clearing unless it is // new - use the following flag to track this... boolean clearBuffer = true; // do we need to resize the buffer? if ((this.chartBuffer == null) || (this.chartBufferWidth != available.getWidth()) || (this.chartBufferHeight != available.getHeight())) { this.chartBufferWidth = (int) available.getWidth(); this.chartBufferHeight = (int) available.getHeight(); this.chartBuffer = createImage(this.chartBufferWidth, this.chartBufferHeight); // GraphicsConfiguration gc = g2.getDeviceConfiguration(); // this.chartBuffer = gc.createCompatibleImage( // this.chartBufferWidth, this.chartBufferHeight, // Transparency.TRANSLUCENT); this.refreshBuffer = true; clearBuffer = false; // buffer is new, no clearing required } // do we need to redraw the buffer? if (this.refreshBuffer) { this.refreshBuffer = false; // clear the flag Rectangle2D bufferArea = new Rectangle2D.Double(0, 0, this.chartBufferWidth, this.chartBufferHeight); Graphics2D bufferG2 = (Graphics2D) this.chartBuffer.getGraphics(); if (clearBuffer) { bufferG2.clearRect(0, 0, this.chartBufferWidth, this.chartBufferHeight); } if (scale) { AffineTransform saved = bufferG2.getTransform(); AffineTransform st = AffineTransform.getScaleInstance(this.scaleX, this.scaleY); bufferG2.transform(st); this.chart.draw(bufferG2, chartArea, this.anchor, this.info); bufferG2.setTransform(saved); } else { this.chart.draw(bufferG2, bufferArea, this.anchor, this.info); } } g2.drawImage(this.chartBuffer, insets.left, insets.top, this); g2.draw((Shape) activeROI.getShapesList().get(1)); // Dibujar las rois que se encuentren activas } // or redrawing the chart every time... else { AffineTransform saved = g2.getTransform(); g2.translate(insets.left, insets.top); if (scale) { AffineTransform st = AffineTransform.getScaleInstance(this.scaleX, this.scaleY); g2.transform(st); } this.chart.draw(g2, chartArea, this.anchor, this.info); g2.drawImage(this.chartBuffer, insets.left, insets.top, this); // Se pintan las Roi activa drawsROIs(g2); g2.setTransform(saved); } g2.dispose(); this.anchor = null; }
From source file:MWC.GUI.JFreeChart.StepperChartPanel.java
/** * Paints the component by drawing the chart to fill the entire component, * but allowing for the insets (which will be non-zero if a border has been * set for this component). To increase performance (at the expense of * memory), an off-screen buffer image can be used. * * @param g the graphics device for drawing on. *///from w w w.j av a2 s.c o m public void paintWMFComponent(final Graphics g) { final Graphics2D g2 = (Graphics2D) g; // first determine the size of the chart rendering area... final Dimension size = getSize(); final Insets insets = getInsets(); available.setRect(insets.left, insets.top, size.getWidth() - insets.left - insets.right, size.getHeight() - insets.top - insets.bottom); // work out if scaling is required... boolean scale = false; double drawWidth = available.getWidth(); double drawHeight = available.getHeight(); double scaleX = 1.0; double scaleY = 1.0; if (drawWidth < this.getMinimumDrawWidth()) { scaleX = drawWidth / getMinimumDrawWidth(); drawWidth = getMinimumDrawWidth(); scale = true; } else if (drawWidth > this.getMaximumDrawWidth()) { scaleX = drawWidth / getMaximumDrawWidth(); drawWidth = getMaximumDrawWidth(); scale = true; } if (drawHeight < this.getMinimumDrawHeight()) { scaleY = drawHeight / getMinimumDrawHeight(); drawHeight = getMinimumDrawHeight(); scale = true; } else if (drawHeight > this.getMaximumDrawHeight()) { scaleY = drawHeight / getMaximumDrawHeight(); drawHeight = getMaximumDrawHeight(); scale = true; } chartArea.setRect(0.0, 0.0, drawWidth, drawHeight); final AffineTransform saved = g2.getTransform(); g2.translate(insets.left, insets.right); if (scale) { final AffineTransform st = AffineTransform.getScaleInstance(scaleX, scaleY); g2.transform(st); } getChart().draw(g2, chartArea, this.getChartRenderingInfo()); g2.setTransform(saved); }
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"); }/*ww w . j a v a2 s . com*/ 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:cn.pholance.datamanager.common.components.JRViewer.java
protected void paintPageError(Graphics2D grx) { AffineTransform origTransform = grx.getTransform(); AffineTransform transform = new AffineTransform(); transform.translate(1, 1);//from w ww .j a va 2 s .c om transform.scale(realZoom, realZoom); grx.transform(transform); try { drawPageError(grx); } finally { grx.setTransform(origTransform); } }
From source file:edu.uci.ics.jung.visualization.PluggableRenderer.java
/** * Labels the specified non-self-loop edge with the specified label. * Uses the font specified by this instance's * <code>EdgeFontFunction</code>. (If the font is unspecified, the existing * font for the graphics context is used.) Positions the * label between the endpoints according to the coefficient returned * by this instance's edge label closeness function. *//* w ww . ja v a2 s. c om*/ protected void labelEdge(Graphics2D g2d, Edge e, String label, int x1, int x2, int y1, int y2) { int distX = x2 - x1; int distY = y2 - y1; double totalLength = Math.sqrt(distX * distX + distY * distY); double closeness = edgeLabelClosenessFunction.getNumber(e).doubleValue(); int posX = (int) (x1 + (closeness) * distX); int posY = (int) (y1 + (closeness) * distY); int xDisplacement = (int) (LABEL_OFFSET * (distY / totalLength)); int yDisplacement = (int) (LABEL_OFFSET * (-distX / totalLength)); Component component = prepareRenderer(graphLabelRenderer, label, isPicked(e), e); Dimension d = component.getPreferredSize(); Shape edgeShape = edgeShapeFunction.getShape(e); double parallelOffset = 1; parallelOffset += parallelEdgeIndexFunction.getIndex(e); if (edgeShape instanceof Ellipse2D) { parallelOffset += edgeShape.getBounds().getHeight(); parallelOffset = -parallelOffset; } parallelOffset *= d.height; AffineTransform old = g2d.getTransform(); AffineTransform xform = new AffineTransform(old); xform.translate(posX + xDisplacement, posY + yDisplacement); double dx = x2 - x1; double dy = y2 - y1; if (graphLabelRenderer.isRotateEdgeLabels()) { double theta = Math.atan2(dy, dx); if (dx < 0) { theta += Math.PI; } xform.rotate(theta); } if (dx < 0) { parallelOffset = -parallelOffset; } xform.translate(-d.width / 2, -(d.height / 2 - parallelOffset)); g2d.setTransform(xform); rendererPane.paintComponent(g2d, component, screenDevice, 0, 0, d.width, d.height, true); g2d.setTransform(old); }
From source file:forseti.JUtil.java
public static synchronized Image generarImagenMensaje(String mensaje, String nombreFuente, int tamanioFuente) { Frame f = new Frame(); f.addNotify();/* w w w . j av a 2s . co m*/ GraphicsEnvironment env = GraphicsEnvironment.getLocalGraphicsEnvironment(); env.getAvailableFontFamilyNames(); Font fuente = new Font(nombreFuente, Font.PLAIN, tamanioFuente); FontMetrics medidas = f.getFontMetrics(fuente); int anchoMensaje = medidas.stringWidth(mensaje); int lineaBaseX = anchoMensaje / 10; int ancho = anchoMensaje + 2 * (lineaBaseX + tamanioFuente); int alto = tamanioFuente * 7 / 2; int lineaBaseY = alto * 8 / 10; Image imagenMensaje = f.createImage(ancho, alto); Graphics2D g2d = (Graphics2D) imagenMensaje.getGraphics(); g2d.setFont(fuente); g2d.translate(lineaBaseX, lineaBaseY); g2d.setPaint(Color.lightGray); AffineTransform origTransform = g2d.getTransform(); g2d.shear(-0.95, 0); g2d.scale(1, 3); g2d.drawString(mensaje, 0, 0); g2d.setTransform(origTransform); g2d.setPaint(Color.black); g2d.drawString(mensaje, 0, 0); return (imagenMensaje); }