net.sf.mzmine.modules.rawdatamethods.rawdataimport.fileformats.AgilentCsvReadTask.java Source code

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Here is the source code for net.sf.mzmine.modules.rawdatamethods.rawdataimport.fileformats.AgilentCsvReadTask.java

Source

/*
 * 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.rawdatamethods.rawdataimport.fileformats;

import java.io.File;
import java.util.Scanner;

import net.sf.mzmine.datamodel.DataPoint;
import net.sf.mzmine.datamodel.MZmineProject;
import net.sf.mzmine.datamodel.PolarityType;
import net.sf.mzmine.datamodel.RawDataFile;
import net.sf.mzmine.datamodel.RawDataFileWriter;
import net.sf.mzmine.datamodel.impl.SimpleDataPoint;
import net.sf.mzmine.datamodel.impl.SimpleScan;
import net.sf.mzmine.project.impl.RawDataFileImpl;
import net.sf.mzmine.taskcontrol.AbstractTask;
import net.sf.mzmine.taskcontrol.TaskStatus;
import net.sf.mzmine.util.ScanUtils;

import com.google.common.collect.Range;

public class AgilentCsvReadTask extends AbstractTask {

    protected String dataSource;
    private File file;
    private MZmineProject project;
    private RawDataFileImpl newMZmineFile;
    private RawDataFile finalRawDataFile;

    private int totalScans, parsedScans;

    /**
     * Creates a new AgilentCSVReadTask
     * 
     * @param file
     *            A File instance containing the file to be read
     */
    public AgilentCsvReadTask(MZmineProject project, File fileToOpen, RawDataFileWriter newMZmineFile) {
        this.project = project;
        this.file = fileToOpen;
        this.newMZmineFile = (RawDataFileImpl) newMZmineFile;
    }

    /**
     * Reads the file.
     */
    public void run() {

        setStatus(TaskStatus.PROCESSING);
        Scanner scanner;

        try {

            scanner = new Scanner(this.file);

            this.dataSource = this.getMetaData(scanner, "file name");

            String[] range = this.getMetaData(scanner, "mass range").split(",");
            newMZmineFile.setMZRange(1, Range.closed(Double.parseDouble(range[0]), Double.parseDouble(range[1])));
            range = this.getMetaData(scanner, "time range").split(",");
            newMZmineFile.setRTRange(1, Range.closed(Double.parseDouble(range[0]), Double.parseDouble(range[1])));
            totalScans = Integer.parseInt(this.getMetaData(scanner, "number of spectra"));

            // advance to the spectrum data...
            while (!scanner.nextLine().trim().equals("[spectra]")) {
            }

            scanner.useDelimiter(",");

            for (parsedScans = 0; parsedScans < totalScans; parsedScans++) {

                if (isCanceled()) {
                    return;
                } // if the task is canceled.

                double retentionTime = scanner.nextDouble();
                int msLevel = scanner.nextInt(); // not sure about this value
                scanner.next();
                scanner.next();
                int charge = (scanner.next().equals("+") ? 1 : -1);
                scanner.next();

                int spectrumSize = scanner.nextInt();
                DataPoint[] dataPoints = new DataPoint[spectrumSize];
                for (int j = 0; j < spectrumSize; j++) {
                    dataPoints[j] = new SimpleDataPoint(scanner.nextDouble(), scanner.nextDouble());
                }
                newMZmineFile.addScan(
                        new SimpleScan(null, parsedScans + 1, msLevel, retentionTime, 0.0, charge, null, dataPoints,
                                ScanUtils.detectSpectrumType(dataPoints), PolarityType.UNKNOWN, "", null));

                scanner.nextLine();
            }

            finalRawDataFile = newMZmineFile.finishWriting();
            project.addFile(finalRawDataFile);

        } catch (Exception e) {
            setErrorMessage(e.getMessage());
            this.setStatus(TaskStatus.ERROR);
            return;
        }

        this.setStatus(TaskStatus.FINISHED);

    }

    /**
     * Reads meta information on the file. This must be called with the keys in
     * order, as it does not reset the scanner position after reading.
     * 
     * @param scanner
     *            The Scanner which is reading this AgilentCSV file.
     * @param key
     *            The key for the metadata to return the value of.
     */
    private String getMetaData(Scanner scanner, String key) {
        String line = "";
        while (!line.trim().startsWith(key) && scanner.hasNextLine()) {
            line = scanner.nextLine();
            if (line.trim().startsWith(key))
                return line.split(",", 2)[1].trim();
        }
        return null;
    }

    /**
     * @see net.sf.mzmine.taskcontrol.Task#getFinishedPercentage()
     */
    @Override
    public double getFinishedPercentage() {
        return totalScans == 0 ? 0 : (double) parsedScans / totalScans;
    }

    @Override
    public String getTaskDescription() {
        return "Opening file " + file;
    }

}