Java tutorial
/* * Copyright 2007-2013 VTT Biotechnology * This file is part of Guineu. * * Guineu 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. * * Guineu 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 * Guineu; if not, write to the Free Software Foundation, Inc., 51 Franklin St, * Fifth Floor, Boston, MA 02110-1301 USA */ package guineu.modules.filter.Alignment.RANSAC; import guineu.main.GuineuCore; import java.awt.BasicStroke; import java.awt.Color; import java.awt.Font; import java.awt.Shape; import java.awt.geom.Ellipse2D; import java.text.NumberFormat; import java.util.ArrayList; import java.util.Collections; import java.util.List; import org.apache.commons.math.analysis.polynomials.PolynomialFunction; import org.apache.commons.math.optimization.OptimizationException; import org.apache.commons.math.optimization.fitting.PolynomialFitter; import org.apache.commons.math.optimization.general.GaussNewtonOptimizer; import org.apache.commons.math.stat.regression.SimpleRegression; import org.jfree.chart.ChartFactory; import org.jfree.chart.ChartPanel; import org.jfree.chart.JFreeChart; import org.jfree.chart.axis.NumberAxis; import org.jfree.chart.labels.XYToolTipGenerator; import org.jfree.chart.plot.DatasetRenderingOrder; import org.jfree.chart.plot.PlotOrientation; import org.jfree.chart.plot.XYPlot; import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer; import org.jfree.chart.title.LegendTitle; import org.jfree.chart.title.TextTitle; import org.jfree.data.xy.XYSeries; import org.jfree.data.xy.XYSeriesCollection; import org.jfree.ui.RectangleInsets; public class AlignmentRansacPlot extends ChartPanel { // peak labels color private static final Color labelsColor = Color.darkGray; // grid color private static final Color gridColor = Color.lightGray; // crosshair (selection) color private static final Color crossHairColor = Color.gray; // crosshair stroke private static final BasicStroke crossHairStroke = new BasicStroke(1, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL, 1.0f, new float[] { 5, 3 }, 0); // data points shape private static final Shape dataPointsShape = new Ellipse2D.Double(-2, -2, 5, 5); // titles private static final Font titleFont = new Font("SansSerif", Font.BOLD, 12); private TextTitle chartTitle; // legend private LegendTitle legend; private static final Font legendFont = new Font("SansSerif", Font.PLAIN, 11); private XYToolTipGenerator toolTipGenerator; private XYSeriesCollection dataset; private JFreeChart chart; private XYPlot plot; private NumberFormat rtFormat = GuineuCore.getRTFormat(); public AlignmentRansacPlot() { super(null, true); dataset = new XYSeriesCollection(); chart = ChartFactory.createXYLineChart("", null, null, dataset, PlotOrientation.VERTICAL, true, true, false); chart.setBackgroundPaint(Color.white); setChart(chart); // title chartTitle = chart.getTitle(); chartTitle.setMargin(5, 0, 0, 0); chartTitle.setFont(titleFont); // legend constructed by ChartFactory legend = chart.getLegend(); legend.setItemFont(legendFont); // legend.setFrame(BlockBorder.NONE); // set the plot properties plot = chart.getXYPlot(); plot.setBackgroundPaint(Color.white); plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0)); plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD); // set grid properties plot.setDomainGridlinePaint(gridColor); plot.setRangeGridlinePaint(gridColor); // set crosshair (selection) properties plot.setDomainCrosshairVisible(true); plot.setRangeCrosshairVisible(true); plot.setDomainCrosshairPaint(crossHairColor); plot.setRangeCrosshairPaint(crossHairColor); plot.setDomainCrosshairStroke(crossHairStroke); plot.setRangeCrosshairStroke(crossHairStroke); // set default renderer properties XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer(); renderer.setBaseLinesVisible(false); renderer.setBaseShapesVisible(true); renderer.setSeriesShape(0, dataPointsShape); renderer.setSeriesShape(1, dataPointsShape); renderer.setSeriesLinesVisible(2, true); renderer.setSeriesShapesVisible(2, false); renderer.setSeriesPaint(0, Color.RED); renderer.setSeriesPaint(1, Color.GRAY); renderer.setSeriesPaint(2, Color.BLUE); renderer.setBaseItemLabelPaint(labelsColor); plot.setRenderer(renderer); } /** * Remove all series from the chart */ public void removeSeries() { dataset.removeAllSeries(); } /** * Add new serie. * @param v Vector with the alignments * @param Name Name of the type of lipids in this alignment */ public void addSeries(List<AlignStructMol> data, String title, boolean linear) { try { chart.setTitle(title); XYSeries s1 = new XYSeries("Aligned pairs"); XYSeries s2 = new XYSeries("Non-aligned pairs"); XYSeries s3 = new XYSeries("Model"); PolynomialFunction function = getPolynomialFunction(data, linear); for (AlignStructMol point : data) { if (point.Aligned) { s1.add((Double) point.row1.getVar("getRT"), (Double) point.row2.getVar("getRT")); } else { s2.add((Double) point.row1.getVar("getRT"), (Double) point.row2.getVar("getRT")); } try { s3.add(function.value((Double) point.row2.getVar("getRT")), (Double) point.row2.getVar("getRT")); } catch (Exception e) { } } this.dataset.addSeries(s1); this.dataset.addSeries(s2); this.dataset.addSeries(s3); } catch (Exception e) { } } private PolynomialFunction getPolynomialFunction(List<AlignStructMol> list, boolean linear) { List<RTs> data = new ArrayList<RTs>(); for (AlignStructMol m : list) { if (m.Aligned) { data.add(new RTs(m.RT2, m.RT)); } } data = this.smooth(data); Collections.sort(data, new RTs()); double[] xval = new double[data.size()]; double[] yval = new double[data.size()]; int i = 0; for (RTs rt : data) { xval[i] = rt.RT; yval[i++] = rt.RT2; } int degree = 2; if (linear) { degree = 1; } PolynomialFitter fitter = new PolynomialFitter(degree, new GaussNewtonOptimizer(true)); for (RTs rt : data) { fitter.addObservedPoint(1, rt.RT, rt.RT2); } try { return fitter.fit(); } catch (OptimizationException ex) { return null; } } private List<RTs> smooth(List<RTs> list) { // Add points to the model in between of the real points to smooth the regression model Collections.sort(list, new RTs()); for (int i = 0; i < list.size() - 1; i++) { RTs point1 = list.get(i); RTs point2 = list.get(i + 1); if (point1.RT < point2.RT - 2) { SimpleRegression regression = new SimpleRegression(); regression.addData(point1.RT, point1.RT2); regression.addData(point2.RT, point2.RT2); double rt = point1.RT + 1; while (rt < point2.RT) { RTs newPoint = new RTs(rt, regression.predict(rt)); list.add(newPoint); rt++; } } } return list; } public void printAlignmentChart(String axisTitleX, String axisTitleY) { try { toolTipGenerator = new AlignmentPreviewTooltipGenerator(axisTitleX, axisTitleY); plot.getRenderer().setBaseToolTipGenerator(toolTipGenerator); NumberAxis xAxis = new NumberAxis(axisTitleX); xAxis.setNumberFormatOverride(rtFormat); xAxis.setAutoRangeIncludesZero(false); plot.setDomainAxis(xAxis); NumberAxis yAxis = new NumberAxis(axisTitleY); yAxis.setNumberFormatOverride(rtFormat); yAxis.setAutoRangeIncludesZero(false); plot.setRangeAxis(yAxis); } catch (Exception e) { } } }