ChromatogramPlotModule.java

/*
 * 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.chromatograms.Chromatogram;
import io.github.msdk.datamodel.chromatograms.ChromatogramType;
import io.github.msdk.datamodel.datastore.DataPointStore;
import io.github.msdk.datamodel.datastore.DataPointStoreFactory;
import io.github.msdk.datamodel.rawdata.MsScan;
import io.github.msdk.datamodel.rawdata.RawDataFile;
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;
  }

}