/*************************************************************************
* *
* 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.List;
import java.util.Map;
import java.util.function.Predicate;
/**
* Interface representing a collection of detected peaks.
* Example use case: representation of the output of a peak calling algorithm
*/
public interface PeakSpectrum {
/**
* Get all detected peaks in the spectrum
*/
List<DetectedPeak> getAllPeaks();
/**
* Get all peaks in the spectrum that satisfy a given predicate
* @param filter input Predicate
* @return a list of detectedpeaks
*/
List<DetectedPeak> getPeaks(Predicate<DetectedPeak> filter); // generic API, supports other getPeaks() methods
/*
* All following APIs are supported by the above getPeaks.
*/
/*
* Retrieval of peaks around a given mz and/or time value, with a certain confidence level
*/
List<DetectedPeak> getPeaksByMZ(Double mz, Double confidenceLevel);
List<DetectedPeak> getPeaksByTime(Double time, Double confidenceLevel);
List<DetectedPeak> getPeaksByMzTime(Double time, Double mz, Double confidenceLevel);
/*
* Retrieval of peaks around a given mz and/or time value, with a given mz/time tolerance
*/
List<DetectedPeak> getNeighborhoodPeaks(DetectedPeak targetPeak, Double mzTolerance, Double timeTolerance);
List<DetectedPeak> getNeighborhoodPeaks(Double mz, Double mzTolerance, Double time, Double timeTolerance);
/**
* Partition the spectrum by scan file id.
* @return a mapping between scan files and their corresponding detected peaks.
*/
Map<String, List<DetectedPeak>> getPeaksByScanFile();
/**
* Extract a list of peaks corresponding to a given scan file
* @param scanFileId id of the desired scan file
* @return the corresponding PeakSpectrum
*/
List<DetectedPeak> getPeaks(String scanFileId);
}