io.github.mzmine.modules.plots.chromatogram.ChromatogramPlotModule.java Source code

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Here is the source code for io.github.mzmine.modules.plots.chromatogram.ChromatogramPlotModule.java

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/*
 * Copyright 2006-2016 The MZmine 3 Development Team
 * 
 * This file is part of MZmine 3.
 * 
 * MZmine 3 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 3 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 3; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA
 */

package io.github.mzmine.modules.plots.chromatogram;

import java.net.URL;
import java.util.Collection;
import java.util.List;
import java.util.concurrent.ScheduledThreadPoolExecutor;

import javax.annotation.Nonnull;

import com.google.common.collect.Range;

import io.github.msdk.datamodel.Chromatogram;
import io.github.msdk.datamodel.ChromatogramType;
import io.github.msdk.datamodel.MsScan;
import io.github.msdk.datamodel.RawDataFile;
import io.github.msdk.datamodel.datastore.DataPointStore;
import io.github.msdk.datamodel.datastore.DataPointStoreFactory;
import io.github.msdk.rawdata.xic.MSDKXICMethod;
import io.github.mzmine.gui.MZmineGUI;
import io.github.mzmine.modules.MZmineRunnableModule;
import io.github.mzmine.parameters.ParameterSet;
import io.github.mzmine.parameters.parametertypes.selectors.ScanSelection;
import io.github.mzmine.project.MZmineProject;
import javafx.application.Platform;
import javafx.concurrent.Task;
import javafx.fxml.FXMLLoader;
import javafx.scene.Parent;

/**
 * Chromatogram plot
 */
public class ChromatogramPlotModule implements MZmineRunnableModule {

    private static final String PLOT_FXML = "ChromatogramPlotWindow.fxml";

    private static final @Nonnull String MODULE_NAME = "TIC/XIC visualizer";
    private static final @Nonnull String MODULE_DESCRIPTION = "TIC/XIC visualizer."; // TODO

    private static final ScheduledThreadPoolExecutor threadPool = new ScheduledThreadPoolExecutor(4);

    @Override
    public @Nonnull String getName() {
        return MODULE_NAME;
    }

    @Override
    public @Nonnull String getDescription() {
        return MODULE_DESCRIPTION;
    }

    @Override
    public void runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters,
            @Nonnull Collection<Task<?>> tasks) {

        final List<RawDataFile> dataFiles = parameters.getParameter(ChromatogramPlotParameters.inputFiles)
                .getValue().getMatchingRawDataFiles();
        final ScanSelection scanSelection = parameters.getParameter(ChromatogramPlotParameters.scanSelection)
                .getValue();
        final ChromatogramPlotType plotType = parameters.getParameter(ChromatogramPlotParameters.plotType)
                .getValue();
        final Range<Double> mzRange = parameters.getParameter(ChromatogramPlotParameters.mzRange).getValue();

        try {
            // Load the main window
            URL mainFXML = this.getClass().getResource(PLOT_FXML);
            FXMLLoader loader = new FXMLLoader(mainFXML);

            Parent node = loader.load();
            MZmineGUI.addWindow(node, "Chromatogram");
            ChromatogramPlotWindowController controller = loader.getController();

            for (RawDataFile dataFile : dataFiles) {

                // Load the actual data in a separate thread to avoid blocking
                // the GUI
                threadPool.execute(() -> {
                    try {
                        DataPointStore store = DataPointStoreFactory.getMemoryDataStore();
                        List<MsScan> scans = scanSelection.getMatchingScans(dataFile);
                        ChromatogramType chromatogramType = ChromatogramType.TIC;
                        if (plotType == ChromatogramPlotType.BASEPEAK)
                            chromatogramType = ChromatogramType.BPC;
                        MSDKXICMethod xicExtractor = new MSDKXICMethod(dataFile, scans, mzRange, chromatogramType,
                                store);
                        Chromatogram chromatogram = xicExtractor.execute();
                        String title = dataFile.getName() + " " + chromatogramType + " [" + mzRange.lowerEndpoint()
                                + "-" + mzRange.upperEndpoint() + " m/z]";
                        Platform.runLater(() -> controller.addChromatogram(chromatogram, title));
                    } catch (Exception e) {
                        e.printStackTrace();
                    }

                });
            }

        } catch (Exception e) {
            e.printStackTrace();
        }

    }

    @Override
    public @Nonnull Class<? extends ParameterSet> getParameterSetClass() {
        return ChromatogramPlotParameters.class;
    }

}