IsotopePatternPlotModule.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.isotopepattern;

import java.util.Collection;

import javax.annotation.Nonnull;

import com.google.common.base.Preconditions;

import io.github.msdk.datamodel.msspectra.MsSpectrum;
import io.github.msdk.spectra.isotopepattern.IsotopePatternGeneratorAlgorithm;
import io.github.mzmine.modules.MZmineRunnableModule;
import io.github.mzmine.modules.plots.msspectrum.MsSpectrumPlotModule;
import io.github.mzmine.parameters.ParameterSet;
import io.github.mzmine.project.MZmineProject;
import javafx.concurrent.Task;

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

  private static final @Nonnull String MODULE_NAME = "Isotope pattern plot";
  private static final @Nonnull String MODULE_DESCRIPTION = "Isotope pattern 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 String formula = parameters.getParameter(IsotopePatternPlotParameters.formula).getValue();
    final Double mzTolerance =
        parameters.getParameter(IsotopePatternPlotParameters.mzTolerance).getValue();
    final Double minAbundance =
        parameters.getParameter(IsotopePatternPlotParameters.minAbundance).getValue();
    final Double normalizedIntensity =
        parameters.getParameter(IsotopePatternPlotParameters.normalizedIntensity).getValue();

    Preconditions.checkNotNull(formula);
    Preconditions.checkNotNull(mzTolerance);
    Preconditions.checkNotNull(minAbundance);
    Preconditions.checkNotNull(normalizedIntensity);

    final MsSpectrum pattern = IsotopePatternGeneratorAlgorithm.generateIsotopes(formula,
        minAbundance, normalizedIntensity.floatValue(), mzTolerance);

    MsSpectrumPlotModule.showNewSpectrumWindow(pattern, formula);

  }

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

}