LocalMaxCentroidingModule.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.rawdata.centroiding.localmaxima;

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.rawdata.RawDataFile;
import io.github.msdk.rawdata.centroiding.LocalMaximaCentroidingAlgorithm;
import io.github.msdk.rawdata.centroiding.MSDKCentroidingMethod;
import io.github.mzmine.modules.MZmineProcessingModule;
import io.github.mzmine.parameters.ParameterSet;
import io.github.mzmine.parameters.parametertypes.selectors.RawDataFilesSelection;
import io.github.mzmine.project.MZmineProject;
import io.github.mzmine.taskcontrol.MSDKTask;
import javafx.concurrent.Task;

/**
 * Local maxima centroiding
 */
public class LocalMaxCentroidingModule implements MZmineProcessingModule {

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

  private static final String MODULE_NAME = "Local maxima centroiding";
  private static final String MODULE_DESCRIPTION = "Local maxima centroiding";

  @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 rawDataFiles =
        parameters.getParameter(LocalMaxCentroidingParameters.dataFiles).getValue();
    final String suffix = parameters.getParameter(LocalMaxCentroidingParameters.suffix).getValue();

    if (rawDataFiles == null || rawDataFiles.getMatchingRawDataFiles().isEmpty()) {
      logger.warn("Centroiding module started with no raw data files selected");
      return;
    }

    for (RawDataFile rawDataFile : rawDataFiles.getMatchingRawDataFiles()) {

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

      final String newName = rawDataFile.getName() + " " + suffix;
      LocalMaximaCentroidingAlgorithm algorithm = new LocalMaximaCentroidingAlgorithm(dataStore);

      MSDKCentroidingMethod method = new MSDKCentroidingMethod(rawDataFile, algorithm, dataStore);

      MSDKTask newTask =
          new MSDKTask("Local maxima centroiding method", rawDataFile.getName(), method);

      // Add the feature table to the project
      newTask.setOnSucceeded(e -> {
        RawDataFile newRawFile = method.getResult();
        newRawFile.setName(newName);
        project.addFile(newRawFile);
      });

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

    }

  }

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