JoinAlignerModule.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.alignment.joinaligner;

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.joinaligner.JoinAlignerMethod;
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;

/**
 * Join aligner module
 */
public class JoinAlignerModule implements MZmineProcessingModule {

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

  private static final String MODULE_NAME = "Join Aligner";
  private static final String MODULE_DESCRIPTION =
      "This module aligns features using a match score calculated based on the mass and retention time of each feature.";

  @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) {

    // Parameter values
    final FeatureTablesSelection featureTables =
        parameters.getParameter(JoinAlignerParameters.featureTables).getValue();
    final MaximumMzTolerance mzTolerance =
        parameters.getParameter(JoinAlignerParameters.mzTolerance).getValue();
    final RTTolerance rtTolerance =
        parameters.getParameter(JoinAlignerParameters.rtTolerance).getValue();
    Integer mzWeight = parameters.getParameter(JoinAlignerParameters.mzWeight).getValue();
    Integer rtWeight = parameters.getParameter(JoinAlignerParameters.rtWeight).getValue();
    Boolean requireSameAnnotation =
        parameters.getParameter(JoinAlignerParameters.requireSameAnnotation).getValue();
    Boolean requireSameCharge =
        parameters.getParameter(JoinAlignerParameters.requireSameCharge).getValue();
    final String featureTableName =
        parameters.getParameter(JoinAlignerParameters.featureTableName).getValue();

    // Default values
    if (mzWeight == null)
      mzWeight = 1;
    if (rtWeight == null)
      rtWeight = 1;
    if (requireSameAnnotation == null)
      requireSameAnnotation = false;
    if (requireSameCharge == null)
      requireSameCharge = false;

    final Boolean removeOldTable =
        parameters.getParameter(JoinAlignerParameters.removeOldTable).getValue();

    if (featureTables == null || featureTables.getMatchingFeatureTables().isEmpty()) {
      logger.warn("Match aligner module started with no feature table selected");
      return;
    }
    if (featureTables.getMatchingFeatureTables().size() == 1) {
      logger.warn("Match aligner module started with less than two feature table");
      return;
    }

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

    // New row filter method
    JoinAlignerMethod method = new JoinAlignerMethod(featureTables.getMatchingFeatureTables(),
        dataStore, mzTolerance, rtTolerance, mzWeight, rtWeight, requireSameCharge,
        requireSameAnnotation, featureTableName);

    MSDKTask newTask = new MSDKTask("Aligning feature tables", featureTableName, 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) {
        for (FeatureTable featureTable : featureTables.getMatchingFeatureTables()) {
          project.removeFeatureTable(featureTable);
        }
      }
    });

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

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

}