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locationsaver.h
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/**
* \file pappsomspp/processing/specpeptidoms/locationsaver.h
* \date 24/03/2025
* \author Aurélien Berthier
* \brief save protein subsequences for alignment
*
* 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>
*
*
>>>>>>> main:src/pappsomspp/processing/specpeptidoms/locationsaver.h
* 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 <cstddef>
#include <vector>
#include <algorithm>
#include <QString>
#include "spomsprotein.h"
#include "pappsomspp/export-import-config.h"
namespace pappso
{
namespace specpeptidoms
{
struct Location
{
// std::vector<uint8_t> prot_sequence;
/** @brief convenient function to get peptide sequence from location
*/
QString getPeptideString() const;
/** @brief start position of the subsequence
*/
std::size_t beginning;
/** @brief length of the subsequence
*/
std::size_t length;
/** index of the alignment tree
*/
int tree;
/** @TODO number of matching peak ?
*/
int score;
/** @brief Protein accession
*/
const SpOMSProtein *proteinPtr;
};
class PMSPP_LIB_DECL LocationSaver
{
public:
/**
* Constructor
*/
LocationSaver();
/**
* Destructor
*/
~LocationSaver();
/**
* @brief Adds a location to the locations heap. If a saved location has the same tree_id, it will
* replace it. Otherwise, it replaces the location with the lowest score.
*/
void addLocation(std::size_t beginning,
std::size_t length,
int tree,
int score,
const SpOMSProtein *protein_ptr);
/**
* @brief Returns a vector containing the saved locations.
* @return vector of Location of size MAX_SAVED_ALIGNMENTS
*/
std::vector<Location> getLocations() const;
/**
* @brief Creates a new alignment tree and returns its id
*/
std::size_t getNextTree();
/**
* @brief Returns the minimum score for a location with the provided tree_id to be saved in the
* heap.
*/
int getMinScore(int tree_id) const;
void resetLocationSaver();
private:
static bool locationCompare(const Location &loc1, const Location &loc2);
std::vector<Location> m_locations_heap;
std::vector<int> m_tree_scores;
std::vector<bool> m_tree_in_heap;
};
} // namespace specpeptidoms
} // namespace pappso
pappso::specpeptidoms::LocationSaver::getMinScore
int getMinScore(int tree_id) const
Returns the minimum score for a location with the provided tree_id to be saved in the heap.
Definition locationsaver.cpp:151
pappso::specpeptidoms::LocationSaver::m_tree_scores
std::vector< int > m_tree_scores
Definition locationsaver.h:124
pappso::specpeptidoms::LocationSaver::resetLocationSaver
void resetLocationSaver()
Definition locationsaver.cpp:186
pappso::specpeptidoms::LocationSaver::locationCompare
static bool locationCompare(const Location &loc1, const Location &loc2)
Definition locationsaver.cpp:75
pappso::specpeptidoms::LocationSaver::LocationSaver
LocationSaver()
Definition locationsaver.cpp:59
pappso::specpeptidoms::LocationSaver::addLocation
void addLocation(std::size_t beginning, std::size_t length, int tree, int score, const SpOMSProtein *protein_ptr)
Adds a location to the locations heap. If a saved location has the same tree_id, it will replace it....
Definition locationsaver.cpp:82
pappso::specpeptidoms::LocationSaver::m_tree_in_heap
std::vector< bool > m_tree_in_heap
Definition locationsaver.h:125
pappso::specpeptidoms::LocationSaver::getLocations
std::vector< Location > getLocations() const
Returns a vector containing the saved locations.
Definition locationsaver.cpp:126
pappso::specpeptidoms::LocationSaver::m_locations_heap
std::vector< Location > m_locations_heap
Definition locationsaver.h:123
pappso::specpeptidoms::LocationSaver::getNextTree
std::size_t getNextTree()
Creates a new alignment tree and returns its id.
Definition locationsaver.cpp:143
pappso::specpeptidoms::SpOMSProtein
Definition spomsprotein.h:38
export-import-config.h
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition export-import-config.h:14
pappso::specpeptidoms
Definition correctiontree.h:40
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
spomsprotein.h
pappso::specpeptidoms::Location
Definition locationsaver.h:49
pappso::specpeptidoms::Location::tree
int tree
Definition locationsaver.h:67
pappso::specpeptidoms::Location::length
std::size_t length
length of the subsequence
Definition locationsaver.h:62
pappso::specpeptidoms::Location::getPeptideString
QString getPeptideString() const
convenient function to get peptide sequence from location
Definition locationsaver.cpp:44
pappso::specpeptidoms::Location::beginning
std::size_t beginning
start position of the subsequence
Definition locationsaver.h:58
pappso::specpeptidoms::Location::proteinPtr
const SpOMSProtein * proteinPtr
Protein accession.
Definition locationsaver.h:75
pappso::specpeptidoms::Location::score
int score
Definition locationsaver.h:71