FeatureFilterModule.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.filtering.featurefilter;

import java.util.Collection;

import javax.annotation.Nonnull;

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

import com.google.common.collect.Range;

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.filtering.FeatureFilterMethod;
import io.github.mzmine.gui.MZmineGUI;
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;

/**
 * Feature filter module
 */
public class FeatureFilterModule implements MZmineProcessingModule {

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

  private static final String MODULE_NAME = "Feature filter";
  private static final String MODULE_DESCRIPTION =
      "This module removes certain features based on given restrictions.";

  @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) {

    // Boolean values
    Boolean filterByDuration = parameters.getParameter(FeatureFilterParameters.duration).getValue();
    Boolean filterByArea = parameters.getParameter(FeatureFilterParameters.area).getValue();
    Boolean filterByHeight = parameters.getParameter(FeatureFilterParameters.height).getValue();
    Boolean filterByDataPoints =
        parameters.getParameter(FeatureFilterParameters.dataPoints).getValue();
    Boolean filterByFWHM = parameters.getParameter(FeatureFilterParameters.fwhm).getValue();
    Boolean filterByTailingFactor =
        parameters.getParameter(FeatureFilterParameters.tailingFactor).getValue();
    Boolean filterByAsymmetryFactor =
        parameters.getParameter(FeatureFilterParameters.asymmetryFactor).getValue();

    // Default values
    if (filterByDuration == null)
      filterByDuration = false;
    if (filterByArea == null)
      filterByArea = false;
    if (filterByHeight == null)
      filterByHeight = false;
    if (filterByDataPoints == null)
      filterByDataPoints = false;
    if (filterByFWHM == null)
      filterByFWHM = false;
    if (filterByTailingFactor == null)
      filterByTailingFactor = false;
    if (filterByAsymmetryFactor == null)
      filterByAsymmetryFactor = false;

    // Embedded values
    final Range<Double> durationRange =
        parameters.getParameter(FeatureFilterParameters.duration).getEmbeddedParameter().getValue();
    final Range<Double> areaRange =
        parameters.getParameter(FeatureFilterParameters.area).getEmbeddedParameter().getValue();
    final Range<Double> heightRange =
        parameters.getParameter(FeatureFilterParameters.height).getEmbeddedParameter().getValue();
    final Range<Integer> dataPointsRange = parameters
        .getParameter(FeatureFilterParameters.dataPoints).getEmbeddedParameter().getValue();
    final Range<Double> fwhmRange =
        parameters.getParameter(FeatureFilterParameters.fwhm).getEmbeddedParameter().getValue();
    final Range<Double> tailingFactorRange = parameters
        .getParameter(FeatureFilterParameters.tailingFactor).getEmbeddedParameter().getValue();
    final Range<Double> asymmetryFactorRange = parameters
        .getParameter(FeatureFilterParameters.asymmetryFactor).getEmbeddedParameter().getValue();

    // Other values
    final FeatureTablesSelection featureTables =
        parameters.getParameter(FeatureFilterParameters.featureTables).getValue();
    final Boolean removeOldTable =
        parameters.getParameter(FeatureFilterParameters.removeOldTable).getValue();
    final String nameSuffix =
        parameters.getParameter(FeatureFilterParameters.nameSuffix).getValue();

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

    // Check if at least one filter is selected
    if (!filterByDuration && !filterByArea && !filterByHeight && !filterByDataPoints
        && !filterByFWHM && !filterByTailingFactor && !filterByAsymmetryFactor) {
      MZmineGUI.displayMessage("Feature filter module started with no filter selected.");
      logger.warn("Feature filter module started with no filter selected.");
      return;
    }

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

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

      // New feature filter task
      FeatureFilterMethod method = new FeatureFilterMethod(featureTable, dataStore,
          filterByDuration, filterByArea, filterByHeight, filterByDataPoints, filterByFWHM,
          filterByTailingFactor, filterByAsymmetryFactor, durationRange, areaRange, heightRange,
          dataPointsRange, fwhmRange, tailingFactorRange, asymmetryFactorRange, nameSuffix);

      MSDKTask newTask =
          new MSDKTask("Filtering features in tables", 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 FeatureFilterParameters.class;
  }

}