Java tutorial
/** * Copyright Copyright 2014 Simon Andrews * * This file is part of BamQC. * * BamQC 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 3 of the License, or * (at your option) any later version. * * BamQC 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 BamQC; if not, write to the Free Software * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA */ /* * Changelog: * - Piero Dalle Pezze: Changed plot, changed data representation, added report, added y axis label, antialiasing, axes numbers resizing to avoid overlapping. * - Simon Andrews: Class creation. */ package uk.ac.babraham.BamQC.Modules; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; import java.util.Comparator; import javax.swing.JPanel; import javax.xml.stream.XMLStreamException; import org.apache.commons.math3.util.Precision; import net.sf.samtools.SAMRecord; import uk.ac.babraham.BamQC.DataTypes.Genome.AnnotationSet; import uk.ac.babraham.BamQC.DataTypes.Genome.Chromosome; import uk.ac.babraham.BamQC.Graphs.CompactScatterGraph; import uk.ac.babraham.BamQC.Graphs.ScatterGraph; import uk.ac.babraham.BamQC.Report.HTMLReportArchive; import uk.ac.babraham.BamQC.Sequence.SequenceFile; /** * @author Simon Andrews * @author Piero Dalle Pezze * */ public class ChromosomeReadDensity extends AbstractQCModule { private String[] chromosomeNames; private double[] readNumber; private double[] chromosomeLength; @Override public void processSequence(SAMRecord read) { } @Override public void processFile(SequenceFile file) { } @Override public void processAnnotationSet(AnnotationSet annotation) { //processAnnotationSetDeprecated(annotation); Chromosome[] chromosomes = annotation.chromosomeFactory().getAllChromosomes(); ArrayList<Chromosome> keptChromosomes = new ArrayList<Chromosome>(); for (int c = 0; c < chromosomes.length; c++) { if (chromosomes[c].seqCount() > 0) { keptChromosomes.add(chromosomes[c]); } } chromosomes = keptChromosomes.toArray(new Chromosome[0]); // Sort by chromosome length, replacing the Chromosome implementation of compare. Arrays.sort(chromosomes, new Comparator<Chromosome>() { @Override public int compare(Chromosome c1, Chromosome c2) { if (c1.length() < c2.length()) { return -1; } else if (c1.length() == c2.length()) { return 0; } return 1; } }); // recorded for the plot and text report readNumber = new double[chromosomes.length]; chromosomeLength = new double[chromosomes.length]; // recorded for the text report only chromosomeNames = new String[chromosomes.length]; for (int c = 0; c < chromosomes.length; c++) { // readNumber[c] = chromosomes[c].seqCount(); // chromosomeLength[c] = chromosomes[c].length(); chromosomeNames[c] = chromosomes[c].name(); readNumber[c] = Precision.round(Math.log(chromosomes[c].seqCount()), 2); chromosomeLength[c] = Precision.round(Math.log(chromosomes[c].length()), 2); } } @Override public JPanel getResultsPanel() { String title = "Chromosome Read Density ( hover the mouse on the blue dots for names )"; String xLabel = "Log Chromosome Length"; String yLabel = "Log Read Number"; if (readNumber.length < 1) { return new ScatterGraph(new double[1], new double[1], new String[1], xLabel, yLabel, title); } return new ScatterGraph(readNumber, chromosomeLength, chromosomeNames, xLabel, yLabel, title); } /* This simply plots the points without including empty spaces in between if these are found. */ @Deprecated public JPanel getOldResultsPanel() { String title = "Chromosome Read Density"; String[] xCategories; String xLabel = "Log Chromosome Length"; String yLabel = "Log Read Number"; double maxY = Double.MIN_VALUE, minY = Double.MAX_VALUE; if (readNumber.length < 1) { xCategories = new String[] { "Null" }; // Previously this was a bar graph // return new BarGraph(new double[1], 0d, maxY, xLabel, yLabel, xCategories, title); return new CompactScatterGraph(new double[1], 0d, maxY, xLabel, yLabel, xCategories, title); } xCategories = new String[chromosomeLength.length]; for (int i = 0; i < readNumber.length; i++) { if (maxY < readNumber[i]) { maxY = readNumber[i]; } else if (minY > readNumber[i]) { minY = readNumber[i]; } //System.out.println(chromosomeLength[i] + " " + readNumber[i]); } // temporarily replaced with 0 minY = 0; for (int i = 0; i < chromosomeLength.length; i++) { xCategories[i] = String.valueOf(chromosomeLength[i]); } // Previously this was a bar graph //return new BarGraph(readNumber, minY, maxY, xLabel, yLabel, xCategories, title); // This just plots the data as it is, without empty non-represented points. return new CompactScatterGraph(readNumber, minY, maxY + maxY * 0.1, xLabel, yLabel, xCategories, title); } @Override public String name() { return "Chromosome Read Density"; } @Override public String description() { return "Tells if the read density varies between chromosomes"; } @Override public void reset() { } @Override public boolean raisesError() { return false; } @Override public boolean raisesWarning() { return false; } @Override public boolean needsToSeeSequences() { return false; } @Override public boolean needsToSeeAnnotation() { return true; } @Override public boolean ignoreInReport() { if (ModuleConfig.getParam("ChromosomeReadDensity", "ignore") > 0 || chromosomeLength.length < 1) { return true; } return false; } @Override public void makeReport(HTMLReportArchive report) throws XMLStreamException, IOException { super.writeDefaultImage(report, "chromosome_density.png", "Chromsome Density Graph", 800, 600); StringBuffer sb = report.dataDocument(); sb.append("Chromosome_name\tChromosome_length_(log)\tRead_number_(log)\n"); for (int i = 0; i < chromosomeNames.length; i++) { sb.append(chromosomeNames[i]); sb.append("\t"); sb.append(chromosomeLength[i]); sb.append("\t"); sb.append(readNumber[i]); sb.append("\n"); } } public String[] getChromosomeNames() { return chromosomeNames; } public double[] getLogReadNumber() { return readNumber; } public double[] getLogChromosomeLength() { return chromosomeLength; } }