/*************************************************************************
* *
* 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.v2;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.function.Predicate;
import java.util.stream.Collectors;
public class LcmsPeakSpectrum implements PeakSpectrum {
List<DetectedPeak> peaks;
public LcmsPeakSpectrum(List<DetectedPeak> peaks) {
this.peaks = peaks;
}
public LcmsPeakSpectrum(PeakSpectrum spectrum) {
this(spectrum.getAllPeaks());
}
public LcmsPeakSpectrum() {
this(new ArrayList<>());
}
public void addPeak(DetectedPeak peak) {
peaks.add(peak);
}
@Override
public List<DetectedPeak> getAllPeaks() {
return peaks;
}
@Override
public List<DetectedPeak> getPeaks(Predicate<DetectedPeak> filter) {
return peaks.stream().filter(filter).collect(Collectors.toList());
}
@Override
public List<DetectedPeak> getPeaksByMZ(Double mz, Double confidenceLevel) {
return getPeaks(peak -> peak.matchesMz(mz, confidenceLevel));
}
@Override
public List<DetectedPeak> getPeaksByTime(Double time, Double timeTolerance) {
return getPeaks(peak -> Math.abs(peak.getRetentionTime() - time) <= timeTolerance);
}
@Override
public List<DetectedPeak> getPeaksByMzTime(Double time, Double mz, Double confidenceLevel) {
return getPeaks(peak -> peak.matchesMzTime(mz, time, confidenceLevel));
}
@Override
public List<DetectedPeak> getNeighborhoodPeaks(DetectedPeak targetPeak, Double massTolerance, Double timeTolerance) {
return getNeighborhoodPeaks(targetPeak.getMz(), massTolerance, targetPeak.getRetentionTime(), timeTolerance);
}
@Override
public List<DetectedPeak> getNeighborhoodPeaks(Double mass, Double massTolerance, Double time, Double timeTolerance) {
return getPeaks(peak -> Math.abs(peak.getRetentionTime() - time) < timeTolerance &&
Math.abs(peak.getMz() - mass) < massTolerance);
}
@Override
public Map<String, List<DetectedPeak>> getPeaksByScanFile() {
return peaks.stream().collect(Collectors.groupingBy(DetectedPeak::getSourceScanFileId));
}
@Override
public List<DetectedPeak> getPeaks(String scanFileId) {
return getPeaks(peak -> peak.getSourceScanFileId().equals(scanFileId));
}
}