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correctiontree.h
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/**
* \file pappsomspp/processing/specpeptidoms/correctiontree.h
* \date 24/03/2025
* \author Aurélien Berthier
* \brief save corrections to apply
*
* C++ implementation of the SpecPeptidOMS algorithm described in :
* (1) Benoist, É.; Jean, G.; Rogniaux, H.; Fertin, G.; Tessier, D. SpecPeptidOMS Directly and
* Rapidly Aligns Mass Spectra on Whole Proteomes and Identifies Peptides That Are Not Necessarily
* Tryptic: Implications for Peptidomics. J. Proteome Res. 2025.
* https://doi.org/10.1021/acs.jproteome.4c00870.
*/
/*
* Copyright (c) 2025 Aurélien Berthier
* <aurelien.berthier@ls2n.fr>
*
* 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/>.
*/
#pragma once
#include <vector>
#include <memory>
namespace pappso
{
namespace specpeptidoms
{
class CorrectionTree;
typedef std::shared_ptr<CorrectionTree> CorrectionTreeSp;
class CorrectionTree
{
public:
CorrectionTree();
~CorrectionTree();
void addPeaks(std::size_t peak1, std::size_t peak2);
std::vector<std::vector<std::size_t>> getPeaks() const;
private:
std::size_t peak;
CorrectionTreeSp msp_left, msp_right;
CorrectionTree(std::size_t peak);
};
} // namespace specpeptidoms
} // namespace pappso
pappso::specpeptidoms::CorrectionTree
Definition correctiontree.h:45
pappso::specpeptidoms::CorrectionTree::getPeaks
std::vector< std::vector< std::size_t > > getPeaks() const
Definition correctiontree.cpp:64
pappso::specpeptidoms::CorrectionTree::msp_left
CorrectionTreeSp msp_left
Definition correctiontree.h:56
pappso::specpeptidoms::CorrectionTree::peak
std::size_t peak
Definition correctiontree.h:55
pappso::specpeptidoms::CorrectionTree::CorrectionTree
CorrectionTree()
Definition correctiontree.cpp:36
pappso::specpeptidoms::CorrectionTree::msp_right
CorrectionTreeSp msp_right
Definition correctiontree.h:56
pappso::specpeptidoms::CorrectionTree::addPeaks
void addPeaks(std::size_t peak1, std::size_t peak2)
Definition correctiontree.cpp:49
pappso::specpeptidoms::CorrectionTree::~CorrectionTree
~CorrectionTree()
Definition correctiontree.cpp:44
pappso::specpeptidoms
Definition correctiontree.h:40
pappso::specpeptidoms::CorrectionTreeSp
std::shared_ptr< CorrectionTree > CorrectionTreeSp
Definition correctiontree.h:42
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39