/*************************************************************************
* *
* 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);
}
}
}