guineu.modules.filter.report.RTShift.ReportTask.java Source code

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Here is the source code for guineu.modules.filter.report.RTShift.ReportTask.java

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/*
 * 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.report.RTShift;

import com.csvreader.CsvReader;
import guineu.data.Dataset;
import guineu.data.PeakListRow;
import guineu.data.LCMSColumnName;
import guineu.parameters.SimpleParameterSet;
import guineu.taskcontrol.AbstractTask;
import guineu.taskcontrol.TaskStatus;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.jfree.chart.ChartFactory;
import org.jfree.chart.ChartUtilities;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.axis.NumberAxis;
import org.jfree.chart.plot.CategoryPlot;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.renderer.category.LineAndShapeRenderer;
import org.jfree.data.category.CategoryDataset;
import org.jfree.data.category.DefaultCategoryDataset;

/**
 *
 * @author scsandra
 */
public class ReportTask extends AbstractTask {

    private Dataset dataset;
    private String fileName;
    private String reportFileName;
    private List<String> sampleNames;
    private double totalRows, processedRows;

    public ReportTask(Dataset simpleDataset, SimpleParameterSet parameters) {
        this.dataset = simpleDataset;
        this.fileName = parameters.getParameter(ReportParameters.filename).getValue().getAbsolutePath();
        this.reportFileName = parameters.getParameter(ReportParameters.reportFilename).getValue().getAbsolutePath();
        this.sampleNames = new ArrayList<String>();
        this.totalRows = dataset.getNumberRows();
        this.processedRows = 0;
    }

    public String getTaskDescription() {
        return "Report RT deviation... ";
    }

    public double getFinishedPercentage() {
        return processedRows / totalRows;
    }

    public void cancel() {
        setStatus(TaskStatus.CANCELED);
    }

    public void run() {
        try {
            setStatus(TaskStatus.PROCESSING);
            readFile();
            saveRTCharts();
            setStatus(TaskStatus.FINISHED);
        } catch (Exception e) {
            setStatus(TaskStatus.ERROR);
            errorMessage = e.toString();
            return;
        }
    }

    /**
     * Read the file with the name of the samples in order
     * @throws java.lang.Exception
     */
    private void readFile() throws Exception {
        FileReader fr = null;
        try {
            fr = new FileReader(new File(fileName));
        } catch (Exception e) {
            throw e;
        }
        CsvReader reader = new CsvReader(fr);
        String splitRow[];
        while (reader.readRecord()) {
            splitRow = reader.getValues();
            this.sampleNames.add(splitRow[0]);
        }
        reader.close();
        fr.close();
    }

    /**
     * For each selected row a chart is created and saved.
     */
    private void saveRTCharts() {
        for (PeakListRow row : dataset.getRows()) {
            if (row.isSelected() && getStatus() == TaskStatus.PROCESSING) {
                CategoryDataset data = createSampleDataset(row);
                String lipidName = "MZ: " + String.valueOf(row.getVar(LCMSColumnName.MZ.getGetFunctionName()))
                        + "RT: " + String.valueOf(row.getVar(LCMSColumnName.RT.getGetFunctionName()));
                createChart(data, lipidName);
            }
            this.processedRows++;
        }
    }

    /**
     * Create the chart and save it into a png file.
     * @param dataset
     * @param lipidName
     */
    private void createChart(CategoryDataset dataset, String lipidName) {
        try {

            JFreeChart chart = ChartFactory.createLineChart("RT shift", "Samples", "RT", dataset,
                    PlotOrientation.VERTICAL, false, false, false);

            // Chart characteristics
            CategoryPlot plot = (CategoryPlot) chart.getPlot();
            final NumberAxis axis = (NumberAxis) plot.getRangeAxis();
            axis.setAutoRangeIncludesZero(false);
            axis.setAutoRangeMinimumSize(1.0);
            LineAndShapeRenderer categoryRenderer = new LineAndShapeRenderer();
            categoryRenderer.setSeriesLinesVisible(0, false);
            categoryRenderer.setSeriesShapesVisible(0, true);
            plot.setRenderer(categoryRenderer);

            // Save all the charts in the folder choosen by the user
            ChartUtilities.saveChartAsPNG(new File(this.reportFileName + "/RT Shift:" + lipidName + ".png"), chart,
                    1000, (500));
        } catch (IOException ex) {
            Logger.getLogger(ReportTask.class.getName()).log(Level.SEVERE, null, ex);
        }

    }

    /**
     * Create the dataset for the chart. Each sample represents
     * one category.
     * @param row The intensities and general data of one metabolite
     * @return CategoryDataset
     */
    private CategoryDataset createSampleDataset(PeakListRow row) {

        DefaultCategoryDataset data = new DefaultCategoryDataset();
        int cont = 1;
        for (String sampleName : sampleNames) {
            try {
                sampleName += "01.CDF peak retention time";
                double value = (Double) row.getPeak(sampleName);
                data.addValue(value, cont + " => " + sampleName, String.valueOf(cont));
                cont++;
            } catch (Exception e) {
            }
        }

        return data;
    }
}