PeakFinderModule.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.gapfilling.peakfinder;

import java.util.Collection;

import javax.annotation.Nonnull;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import io.github.msdk.datamodel.datastore.DataPointStore;
import io.github.msdk.datamodel.datastore.DataPointStoreFactory;
import io.github.msdk.datamodel.featuretables.FeatureTable;
import io.github.msdk.features.gapfilling.GapFillingMethod;
import io.github.msdk.util.tolerances.MaximumMzTolerance;
import io.github.msdk.util.tolerances.RTTolerance;
import io.github.mzmine.modules.MZmineProcessingModule;
import io.github.mzmine.parameters.ParameterSet;
import io.github.mzmine.parameters.parametertypes.selectors.FeatureTablesSelection;
import io.github.mzmine.project.MZmineProject;
import io.github.mzmine.taskcontrol.MSDKTask;
import javafx.concurrent.Task;

/**
 * Gap filling module
 */
public class PeakFinderModule implements MZmineProcessingModule {

  private Logger logger = LoggerFactory.getLogger(this.getClass());

  private static final String MODULE_NAME = "Peak Finder";
  private static final String MODULE_DESCRIPTION =
      "This module fills the missing gaps in the feature list by searching for a peak in the original raw data.";

  @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) {

    // Parameters
    final FeatureTablesSelection featureTables =
        parameters.getParameter(PeakFinderParameters.featureTables).getValue();
    final MaximumMzTolerance mzTolerance =
        parameters.getParameter(PeakFinderParameters.mzTolerance).getValue();
    final RTTolerance rtTolerance =
        parameters.getParameter(PeakFinderParameters.rtTolerance).getValue();
    final Boolean isIntensityTolSet =
        parameters.getParameter(PeakFinderParameters.intensityTolerance).getValue();
    Double intensityTolerance = parameters.getParameter(PeakFinderParameters.intensityTolerance)
        .getEmbeddedParameter().getValue();
    final String nameSuffix = parameters.getParameter(PeakFinderParameters.nameSuffix).getValue();
    final Boolean removeOldTable =
        parameters.getParameter(PeakFinderParameters.removeOldTable).getValue();

    if (featureTables == null || featureTables.getMatchingFeatureTables().isEmpty()) {
      logger.warn("Peak finder module started with no feature table selected");
      return;
    }

    // Add a task for each feature table
    for (FeatureTable featureTable : featureTables.getMatchingFeatureTables()) {

      // Create the data structures
      DataPointStore dataStore = DataPointStoreFactory.getMemoryDataStore();

      // If intensity tolerance is not active then set the
      // intensityTolerance value to a very high value to avoid any
      // filtering the peak shape
      if (isIntensityTolSet == null || !isIntensityTolSet)
        intensityTolerance = Double.MAX_VALUE;

      // New feature filter task
      GapFillingMethod method = new GapFillingMethod(featureTable, dataStore, mzTolerance,
          rtTolerance, intensityTolerance, nameSuffix);

      MSDKTask newTask = new MSDKTask("Gap filling feature table", featureTable.getName(), method);

      // Add the feature table to the project
      newTask.setOnSucceeded(e -> {
        FeatureTable newFeatureTable = method.getResult();
        project.addFeatureTable(newFeatureTable);

        // If selected, remove old feature table
        if (removeOldTable != null && removeOldTable) {
          project.removeFeatureTable(featureTable);
        }
      });

      // Add the task to the queue
      tasks.add(newTask);

    }
  }

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

}