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types.h
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/**
* \file pappsomspp/processing/specpeptidoms/types.h
* \date 24/03/2025
* \author Aurélien Berthier
*
* 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 "../../amino_acid/aa.h"
namespace pappso
{
namespace specpeptidoms
{
// const std::unordered_map<pappso::Aa, double> aaMasses;
enum class ScoreType : std::uint8_t
{
foundDouble = 0,
found = 1,
foundShiftDouble = 2,
foundShift = 3,
notFound = 4,
init = 5,
};
enum class AlignType
{
found,
shift,
perfectShift,
notFound,
init
};
const uint MAX_SAVED_ALIGNMENTS(5);
const uint ALIGNMENT_SURPLUS(5);
const int MIN_ALIGNMENT_SCORE(15);
const uint MAX_RETURNED_RESULTS(2);
const uint TOL_PEAKS_MISSING(4);
const uint TOL_PEAKS_MISSING_FIRST_COLUMN(5);
const float ALIGNMENT_FILTER(0.9);
} // namespace specpeptidoms
} // namespace pappso
aa.h
pappso::specpeptidoms
Definition correctiontree.h:40
pappso::specpeptidoms::AlignType
AlignType
Definition types.h:51
pappso::specpeptidoms::AlignType::shift
@ shift
Definition types.h:53
pappso::specpeptidoms::AlignType::perfectShift
@ perfectShift
Definition types.h:54
pappso::specpeptidoms::ALIGNMENT_SURPLUS
const uint ALIGNMENT_SURPLUS(5)
pappso::specpeptidoms::MAX_SAVED_ALIGNMENTS
const uint MAX_SAVED_ALIGNMENTS(5)
pappso::specpeptidoms::MIN_ALIGNMENT_SCORE
const int MIN_ALIGNMENT_SCORE(15)
pappso::specpeptidoms::TOL_PEAKS_MISSING
const uint TOL_PEAKS_MISSING(4)
pappso::specpeptidoms::MAX_RETURNED_RESULTS
const uint MAX_RETURNED_RESULTS(2)
pappso::specpeptidoms::ALIGNMENT_FILTER
const float ALIGNMENT_FILTER(0.9)
pappso::specpeptidoms::ScoreType
ScoreType
Definition types.h:41
pappso::specpeptidoms::ScoreType::foundDouble
@ foundDouble
Definition types.h:42
pappso::specpeptidoms::ScoreType::notFound
@ notFound
Definition types.h:46
pappso::specpeptidoms::ScoreType::found
@ found
Definition types.h:43
pappso::specpeptidoms::ScoreType::foundShift
@ foundShift
Definition types.h:45
pappso::specpeptidoms::ScoreType::foundShiftDouble
@ foundShiftDouble
Definition types.h:44
pappso::specpeptidoms::ScoreType::init
@ init
Definition types.h:47
pappso::specpeptidoms::TOL_PEAKS_MISSING_FIRST_COLUMN
const uint TOL_PEAKS_MISSING_FIRST_COLUMN(5)
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
pappso::uint
unsigned int uint
Definition types.h:67