MsSpectrumPlotModule.java

/*
 * Copyright 2006-2015 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.msspectrum;

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

import javax.annotation.Nonnull;

import com.google.common.base.Preconditions;
import com.google.common.collect.Range;

import io.github.msdk.datamodel.msspectra.MsSpectrum;
import io.github.msdk.datamodel.rawdata.MsScan;
import io.github.msdk.datamodel.rawdata.RawDataFile;
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.RawDataFilesSelection;
import io.github.mzmine.parameters.parametertypes.selectors.ScanSelection;
import io.github.mzmine.project.MZmineProject;
import io.github.mzmine.util.MsScanUtils;
import javafx.application.Platform;
import javafx.concurrent.Task;
import javafx.fxml.FXMLLoader;
import javafx.scene.Parent;

/**
 * MS spectrum plot
 */
public class MsSpectrumPlotModule implements MZmineRunnableModule {

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

  private static final @Nonnull String MODULE_NAME = "MS spectrum plot";
  private static final @Nonnull String MODULE_DESCRIPTION = "MS spectrum plot";

  @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 RawDataFilesSelection fileSelection =
        parameters.getParameter(MsSpectrumPlotParameters.inputFiles).getValue();

    final Integer scanNumber =
        parameters.getParameter(MsSpectrumPlotParameters.scanNumber).getValue();

    Preconditions.checkNotNull(fileSelection);
    Preconditions.checkNotNull(scanNumber);

    final ScanSelection scanSelection =
        new ScanSelection(Range.singleton(scanNumber), null, null, null, null, null);

    final List<RawDataFile> dataFiles = fileSelection.getMatchingRawDataFiles();

    // Add the window to the desktop only if we actually have any raw
    // data to show.
    boolean weHaveData = false;
    for (RawDataFile dataFile : dataFiles) {
      if (!scanSelection.getMatchingScans(dataFile).isEmpty()) {
        weHaveData = true;
        break;
      }
    }
    if (!weHaveData) {
      MZmineGUI.displayMessage("Scan not found");
      return;
    }

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

      Parent node = loader.load();
      MZmineGUI.addWindow(node, "MS spectrum");
      MsSpectrumPlotWindowController controller = loader.getController();

      Platform.runLater(() -> {
        for (RawDataFile dataFile : dataFiles) {
          for (MsScan scan : scanSelection.getMatchingScans(dataFile)) {
            String title = MsScanUtils.createSingleLineMsScanDescription(scan);
            controller.addSpectrum(scan, title);
          }
        }
      });

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

  }

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

  public static void showNewSpectrumWindow(@Nonnull MsScan scan) {
    try {
      URL mainFXML = MsSpectrumPlotModule.class.getResource(PLOT_FXML);
      FXMLLoader loader = new FXMLLoader(mainFXML);
      Parent node = loader.load();
      String title = MsScanUtils.createSingleLineMsScanDescription(scan);
      MZmineGUI.addWindow(node, title);
      MsSpectrumPlotWindowController controller = loader.getController();
      controller.addSpectrum(scan, title);

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

  public static void showNewSpectrumWindow(@Nonnull MsSpectrum spectrum, @Nonnull String name) {
    try {
      URL mainFXML = MsSpectrumPlotModule.class.getResource(PLOT_FXML);
      FXMLLoader loader = new FXMLLoader(mainFXML);

      Parent node = loader.load();
      MZmineGUI.addWindow(node, name);
      MsSpectrumPlotWindowController controller = loader.getController();
      controller.addSpectrum(spectrum, name);

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

}