Java tutorial
/* * Copyright 2006-2015 The MZmine 2 Development Team * * This file is part of MZmine 2. * * MZmine 2 is free software; you can redistribute it and/or modify it under the * terms of the GNU General Public License as published by the Free Software * Foundation; either version 2 of the License, or (at your option) any later * version. * * MZmine 2 is distributed in the hope that it will be useful, but WITHOUT ANY * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR * A PARTICULAR PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with * MZmine 2; if not, write to the Free Software Foundation, Inc., 51 Franklin St, * Fifth Floor, Boston, MA 02110-1301 USA */ package net.sf.mzmine.modules.visualization.twod; import java.awt.Color; import java.awt.Graphics2D; import java.awt.geom.Rectangle2D; import java.util.Date; import org.jfree.chart.axis.ValueAxis; import org.jfree.chart.plot.CrosshairState; import org.jfree.chart.plot.PlotRenderingInfo; import com.google.common.collect.Range; import java.awt.geom.Ellipse2D; import java.awt.geom.Point2D; import java.util.ArrayList; import java.util.Iterator; import java.util.List; import net.sf.mzmine.datamodel.DataPoint; /** * This class is responsible for drawing the actual data points. * modified by Owen Myers 2017 */ class PointTwoDXYPlot extends BaseXYPlot { PointTwoDXYPlot(TwoDDataSet dataset, Range<Double> rtRange, Range<Double> mzRange, ValueAxis domainAxis, ValueAxis rangeAxis) { super(dataset, rtRange, mzRange, domainAxis, rangeAxis); this.dataset = dataset; totalRTRange = rtRange; totalMZRange = mzRange; } public boolean render(final Graphics2D g2, final Rectangle2D dataArea, int index, PlotRenderingInfo info, CrosshairState crosshairState) { // if this is not TwoDDataSet if (index != 0) return super.render(g2, dataArea, index, info, crosshairState); // prepare some necessary constants final int x = (int) dataArea.getX(); final int y = (int) dataArea.getY(); final int width = (int) dataArea.getWidth(); final int height = (int) dataArea.getHeight(); final double imageRTMin = (double) getDomainAxis().getRange().getLowerBound(); final double imageRTMax = (double) getDomainAxis().getRange().getUpperBound(); final double imageRTStep = (imageRTMax - imageRTMin) / width; final double imageMZMin = (double) getRangeAxis().getRange().getLowerBound(); final double imageMZMax = (double) getRangeAxis().getRange().getUpperBound(); final double imageMZStep = (imageMZMax - imageMZMin) / height; // This if statement below keeps the min max values at the original values when the user // zooms in. We need some variables that scall as the box size so that the points we show // have better resolution the more someone zooms in. double dynamicImageRTMin = imageRTMin; double dynamicImageRTMax = imageRTMax; double dynamicImageMZMin = imageMZMin; double dynamicImageMZMax = imageMZMax; double dynamicImageRTStep = imageRTStep; double dynamicImageMZStep = imageMZStep; if ((zoomOutBitmap != null) && (imageRTMin == totalRTRange.lowerEndpoint()) && (imageRTMax == totalRTRange.upperEndpoint()) && (imageMZMin == totalMZRange.lowerEndpoint()) && (imageMZMax == totalMZRange.upperEndpoint()) && (zoomOutBitmap.getWidth() == width) && (zoomOutBitmap.getHeight() == height)) { g2.drawImage(zoomOutBitmap, x, y, null); return true; } // Save current time Date renderStartTime = new Date(); // prepare a bitmap of required size //BufferedImage image = new BufferedImage(width, height, //BufferedImage.TYPE_INT_ARGB); //ArrayList<DataPoint> listOfDataPoints = new ArrayList<DataPoint>(); //ArrayList<DataPoint> listOfRTValues = new ArrayList<DataPoint>(); ArrayList<DataPoint> listOfDataPoints; ArrayList<Double> listOfRTValues; // These two function must be run in this order Range<Double> rtRangeIn = Range.closed(getDomainAxis().getRange().getLowerBound(), getDomainAxis().getRange().getUpperBound()); Range<Double> mzRangeIn = Range.closed(getRangeAxis().getRange().getLowerBound(), getRangeAxis().getRange().getUpperBound()); listOfDataPoints = dataset.getCentroidedDataPointsInRTMZRange(rtRangeIn, mzRangeIn); listOfRTValues = dataset.getrtValuesInUserRange(); // points to be plotted List plotPoints = new ArrayList(); int count = 0; // Store the current mz,rt,int values so that they can be outputed to a file if we want //currentlyPlottedMZ = new ArrayList(); //for (Iterator dpIt = listOfDataPoints.iterator(); dpIt.hasNext();) { // make a list to keep track of the intesities of each for (DataPoint curDataPoint : listOfDataPoints) { //DataPoint curDataPoint = dpIt.next(); double currentRT = listOfRTValues.get(count).doubleValue(); double currentMZ = curDataPoint.getMZ(); plotPoints.add(new Point2D.Double(currentRT, currentMZ)); count += 1; //currentlyPlottedMZ.add() } // draw image points //for (int i = 0; i < width; i++) // for (int j = 0; j < height; j++) { // Color pointColor = paletteType.getColor(values[i][j]); // //image.setRGB(i, height - j - 1, pointColor.getRGB()); // points.add(new Point2D.Float(i,j)); // } count = 0; for (Iterator i = plotPoints.iterator(); i.hasNext();) { Point2D.Double pt = (Point2D.Double) i.next(); // using the ''dynamic'' min and max will make the resolution imporve as someone zooms // in //float xPlace = (pt.x-(float)dynamicImageRTMin)/((float)dynamicImageRTStep) + x; //float yPlace = (pt.y-(float)dynamicImageMZMin)/((float)dynamicImageMZStep) + y; double xPlace = (pt.x - dynamicImageRTMin) / (dynamicImageRTStep) + (double) x; double yPlace = (double) height - (pt.y - dynamicImageMZMin) / (dynamicImageMZStep) + (double) y; //get the current intensity // use the R, G B for the intensity double curIntensity = listOfDataPoints.get(count).getIntensity(); curIntensity = curIntensity / dataset.curMaxIntensity; //g2.setColor(Color.BLACK); Color pointColor = paletteType.getColor(curIntensity); g2.setColor(pointColor); Ellipse2D dot = new Ellipse2D.Double(xPlace - 1, yPlace - 1, 2, 2); g2.fill(dot); count += 1; } //float xPlace = ((float)42.0-(float)dynamicImageRTMin)/((float)dynamicImageRTStep)+x; //float yPlace = (float)height - ((float)201.02-(float)dynamicImageMZMin)/((float)dynamicImageMZStep)+y; //Ellipse2D dot = new Ellipse2D.Float(xPlace - 1, yPlace - 1, 2, 2); //g2.fill(dot); //g2.dispose(); // if we are zoomed out, save the values if ((imageRTMin == totalRTRange.lowerEndpoint()) && (imageRTMax == totalRTRange.upperEndpoint()) && (imageMZMin == totalMZRange.lowerEndpoint()) && (imageMZMax == totalMZRange.upperEndpoint())) { //zoomOutBitmap = image; } // Paint image //g2.drawImage(image, x, y, null); //g.setColor(Color.BLACK) Date renderFinishTime = new Date(); logger.finest("Finished rendering 2D visualizer, " + (renderFinishTime.getTime() - renderStartTime.getTime()) + " ms"); return true; } }