content: /*************************************************************************
  *                                                                        *
  *  This file is part of the 20n/act project.                             *
  *  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
  *  Copyright (C) 2017 20n Labs, Inc.                                     *
  *                                                                        *
  *  Please direct all queries to act@20n.com.                             *
  *                                                                        *
  *  This program 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 3 of the License, or     *
  *  (at your option) any later version.                                   *
  *                                                                        *
  *  This program 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 this program.  If not, see <http://www.gnu.org/licenses/>. *
  *                                                                        *
  *************************************************************************/
  
  package com.act.lcms.db.analysis;
  
  import com.act.lcms.db.io.report.IonAnalysisInterchangeModel;
  import org.apache.commons.lang3.tuple.Pair;
  
  import java.util.List;
  import java.util.stream.Collectors;
  
  public class HitOrMissReplicateFilterAndTransformer extends HitOrMissFilterAndTransformer<List<IonAnalysisInterchangeModel.HitOrMiss>> {
  
    public static final Integer TIME_TOLERANCE_IN_SECONDS = 5;
    // The peak statistic could be intensity, SNR or time.
    public static final Double LOWEST_POSSIBLE_VALUE_FOR_PEAK_STATISTIC = 0.0;
    public static String NIL_PLOT = "NIL_PLOT";
    public static final Integer REPRESENTATIVE_INDEX = 0;
  
    /**
     * This function takes in a list of molecules from multiple replicates over the same time and alignes the peaks across
     * these replicates. If the peaks can be aligned, the function reports the min statistic across those peaks, else it
     * defaults to a low statistic.
     * @param oneOrMoreReplicates
     * @return A pair of transformed HitOrMiss molecule and whether to save the result in the final model.
     */
    public Pair<IonAnalysisInterchangeModel.HitOrMiss, Boolean> apply(List<IonAnalysisInterchangeModel.HitOrMiss> oneOrMoreReplicates) {
  
      List<Double> intensityValues = oneOrMoreReplicates.stream().map(molecule -> molecule.getIntensity()).collect(Collectors.toList());
      List<Double> snrValues = oneOrMoreReplicates.stream().map(molecule -> molecule.getSnr()).collect(Collectors.toList());
      List<Double> timeValues = oneOrMoreReplicates.stream().map(molecule -> molecule.getTime()).collect(Collectors.toList());
  
      IonAnalysisInterchangeModel.HitOrMiss result = new IonAnalysisInterchangeModel.HitOrMiss();
      result.setInchi(oneOrMoreReplicates.get(REPRESENTATIVE_INDEX).getInchi());
      result.setIon(oneOrMoreReplicates.get(REPRESENTATIVE_INDEX).getIon());
      result.setPlot(NIL_PLOT);
  
      // We get the min and max time to calculate how much do the replicates deviate in time for the same signal. If
      // the deviation in the time axis is greater than our tolerance, we know the signal is bad.
      Double minTime = timeValues.stream().reduce(Double.MAX_VALUE, (accum, newVal) -> Math.min(accum, newVal));
      Double maxTime = timeValues.stream().reduce(Double.MIN_VALUE, (accum, newVal) -> Math.max(accum, newVal));
  
      if (maxTime - minTime < TIME_TOLERANCE_IN_SECONDS) {
        Double minIntensity = intensityValues.stream().reduce(Double.MAX_VALUE, (accum, newVal) -> Math.min(accum, newVal));
  
        Integer indexOfMinIntensityReplicate = intensityValues.indexOf(minIntensity);
  
        // The SNR and Time values will be the copy of the replicate with the lowest intensity value.
        result.setSnr(snrValues.get(indexOfMinIntensityReplicate));
        result.setIntensity(minIntensity);
        result.setTime(timeValues.get(indexOfMinIntensityReplicate));
  
        return Pair.of(result, DO_NOT_THROW_OUT_MOLECULE);
      } else {
        // TODO: We can just throw out such molecules.
        result.setSnr(LOWEST_POSSIBLE_VALUE_FOR_PEAK_STATISTIC);
        result.setIntensity(LOWEST_POSSIBLE_VALUE_FOR_PEAK_STATISTIC);
        result.setTime(LOWEST_POSSIBLE_VALUE_FOR_PEAK_STATISTIC);
  
        return Pair.of(result, DO_NOT_THROW_OUT_MOLECULE);
      }
    }
  }
  