RowFilterModule.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.rowfilter;

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.rowfilter.RowFilterMethod;
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;

/**
 * Row filter module
 */
public class RowFilterModule implements MZmineProcessingModule {

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

  private static final String MODULE_NAME = "Row filter";
  private static final String MODULE_DESCRIPTION =
      "This module removes certain rows 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 filterByMz = parameters.getParameter(RowFilterParameters.mzRange).getValue();
    Boolean filterByRt = parameters.getParameter(RowFilterParameters.rtRange).getValue();
    Boolean filterByDuration =
        parameters.getParameter(RowFilterParameters.durationRange).getValue();
    Boolean filterByCount = parameters.getParameter(RowFilterParameters.minCount).getValue();
    Boolean filterByIsotopes = parameters.getParameter(RowFilterParameters.minIsotopes).getValue();
    Boolean filterByIonAnnotation =
        parameters.getParameter(RowFilterParameters.ionAnnotation).getValue();
    Boolean requireAnnotation =
        parameters.getParameter(RowFilterParameters.requireAnnotation).getValue();

    // Default values
    if (filterByMz == null)
      filterByMz = false;
    if (filterByRt == null)
      filterByRt = false;
    if (filterByDuration == null)
      filterByDuration = false;
    if (filterByCount == null)
      filterByCount = false;
    if (filterByIsotopes == null)
      filterByIsotopes = false;
    if (filterByIonAnnotation == null)
      filterByIonAnnotation = false;
    if (requireAnnotation == null)
      requireAnnotation = false;

    // Embedded values
    final Range<Double> mzRange =
        parameters.getParameter(RowFilterParameters.mzRange).getEmbeddedParameter().getValue();
    final Range<Double> rtRange =
        parameters.getParameter(RowFilterParameters.rtRange).getEmbeddedParameter().getValue();
    final Range<Double> durationRange = parameters.getParameter(RowFilterParameters.durationRange)
        .getEmbeddedParameter().getValue();
    Double minCount =
        parameters.getParameter(RowFilterParameters.minCount).getEmbeddedParameter().getValue();
    final Integer minIsotopes =
        parameters.getParameter(RowFilterParameters.minIsotopes).getEmbeddedParameter().getValue();
    final String ionAnnotation = parameters.getParameter(RowFilterParameters.ionAnnotation)
        .getEmbeddedParameter().getValue();

    // Remove duplicate parameters
    Boolean removeDuplicates =
        parameters.getParameter(RowFilterParameters.removeDuplicates).getValue();
    final MaximumMzTolerance duplicateMzTolerance =
        parameters.getParameter(RowFilterParameters.removeDuplicates).getEmbeddedParameters()
            .getParameter(DuplicateFilterParameters.mzTolerance).getValue();
    final RTTolerance duplicateRtTolerance =
        parameters.getParameter(RowFilterParameters.removeDuplicates).getEmbeddedParameters()
            .getParameter(DuplicateFilterParameters.rtTolerance).getValue();
    Boolean duplicateRequireSameID = parameters.getParameter(RowFilterParameters.removeDuplicates)
        .getEmbeddedParameters().getParameter(DuplicateFilterParameters.requireSameID).getValue();

    // Default values
    if (removeDuplicates == null)
      removeDuplicates = false;
    if (duplicateRequireSameID == null)
      duplicateRequireSameID = false;

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

    if (featureTables == null || featureTables.getMatchingFeatureTables().isEmpty()) {
      logger.warn("Row filter 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();

      // Handle < 1 values for minCount
      if (minCount == null)
        minCount = 0d;
      if (minCount < 1)
        minCount = featureTable.getSamples().size() * minCount;
      // Round value down to nearest hole number
      int intMinCount = (int) (long) (double) minCount;

      // New row filter method
      RowFilterMethod method = new RowFilterMethod(featureTable, dataStore, nameSuffix, filterByMz,
          filterByRt, filterByDuration, filterByCount, filterByIsotopes, filterByIonAnnotation,
          requireAnnotation, mzRange, rtRange, durationRange, intMinCount, minIsotopes,
          ionAnnotation, removeDuplicates, duplicateMzTolerance, duplicateRtTolerance,
          duplicateRequireSameID);

      MSDKTask newTask =
          new MSDKTask("Row filtering features in 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 RowFilterParameters.class;
  }

}