* Copyright 2006-2018 The MZmine 2 Development Team
 * This file is part of MZmine 2.
 * MZmine 2 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 2 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 2; if not,
 * write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301
 * USA

package net.sf.mzmine.modules.masslistmethods.shoulderpeaksfilter;

import java.util.Arrays;
import java.util.Iterator;
import java.util.TreeSet;

import net.sf.mzmine.datamodel.DataPoint;
import net.sf.mzmine.parameters.ParameterSet;
import net.sf.mzmine.util.DataPointSorter;
import net.sf.mzmine.util.SortingDirection;
import net.sf.mzmine.util.SortingProperty;

public class ShoulderPeaksFilter {

  public static DataPoint[] filterMassValues(DataPoint[] mzPeaks, ParameterSet parameters) {

    double resolution =

    PeakModel peakModel = null;

    // Try to create an instance of the peak model
    try {
      PeakModelType type =
      if (type == null)
        type = PeakModelType.GAUSS;
      Class<?> modelClass = type.getModelClass();
      peakModel = (PeakModel) modelClass.newInstance();
    } catch (Exception e) {

    // If peakModel is null, just don't do any filtering
    if (peakModel == null)
      return mzPeaks;

    // Create a tree set of detected mzPeaks sorted by MZ in ascending order
    TreeSet<DataPoint> finalMZPeaks =
        new TreeSet<DataPoint>(new DataPointSorter(SortingProperty.MZ, SortingDirection.Ascending));

    // Create a tree set of candidate mzPeaks sorted by intensity in
    // descending order.
    TreeSet<DataPoint> candidatePeaks = new TreeSet<DataPoint>(
        new DataPointSorter(SortingProperty.Intensity, SortingDirection.Descending));

    while (candidatePeaks.size() > 0) {

      // Always take the biggest (intensity) peak
      DataPoint currentCandidate = candidatePeaks.first();

      // Add this candidate to the final tree set sorted by MZ and remove
      // from tree set sorted by intensity

      // Remove from tree set sorted by intensity all FTMS shoulder peaks,
      // taking as a main peak the current candidate
      removeLateralPeaks(currentCandidate, candidatePeaks, peakModel, resolution);


    return finalMZPeaks.toArray(new DataPoint[0]);

   * This function remove peaks encountered in the lateral of a main peak (currentCandidate) that
   * are considered as garbage, for example FTMS shoulder peaks.
   * First calculates a peak model (Gauss, Lorenzian, etc) defined by peakModelName parameter, with
   * the same position (m/z) and height (intensity) of the currentCandidate, and the defined
   * resolution (resolution parameter). Second search and remove all the lateral peaks that are
   * under the curve of the modeled peak.
  private static void removeLateralPeaks(DataPoint currentCandidate, TreeSet<DataPoint> candidates,
      PeakModel peakModel, double resolution) {

    // We set our peak model with same position(m/z), height(intensity) and
    // resolution of the current peak
    peakModel.setParameters(currentCandidate.getMZ(), currentCandidate.getIntensity(), resolution);

    // We search over all peak candidates and remove all of them that are
    // under the curve defined by our peak model
    Iterator<DataPoint> candidatesIterator = candidates.iterator();
    while (candidatesIterator.hasNext()) {

      DataPoint lateralCandidate = candidatesIterator.next();

      // Condition in x domain (m/z)
      if ((lateralCandidate.getIntensity() < peakModel.getIntensity(lateralCandidate.getMZ()))) {