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types.h
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/**
* \file pappsomspp/processing/specglob/types.h
* \date 14/11/2023
* \author Olivier Langella
* \brief SpecGlobTool types definition
*
* C++ implementation of the SpecGlob algorithm described in :
* 1. Prunier, G. et al. Fast alignment of mass spectra in large proteomics
* datasets, capturing dissimilarities arising from multiple complex
* modifications of peptides. BMC Bioinformatics 24, 421 (2023).
*
* HAL Id : hal-04296170 , version 1
* Mot de passe : hxo20cl
* DOI : 10.1186/s12859-023-05555-y
*
* ANR founded project :
* https://anr.fr/Project-ANR-18-CE45-0004
*/
/*
* SpecGlobTool, Spectra to peptide alignment tool
* Copyright (C) 2023 Olivier Langella
* <olivier.langella@universite-paris-saclay.fr>
*
* This program is free software: you can redistribute ipetide to spectrum
* alignmentt 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
namespace pappso
{
namespace specglob
{
enum class SpectralAlignmentType : std::uint8_t
{
nonAlign =
0, ///< the type of alignment to put in origin matrix NON Alignment (0 - NA)
reAlign = 1, ///< Re Alignment (1 - RE)
align = 2, ///< Alignment (2 - AL)
};
enum class ScoreValueType : std::uint8_t
{
scoreNonAlign = 0, ///< Score for non alignment (int)
scoreReAlignNative = 1, ////algorithm< Score for re-alignment native (int)
scoreReAlignSym = 2, ///< Score for re-alignment symetric (int)
scoreReAlignBoth = 3, ///< Score for re-alignment both (int)
scoreAlignNative = 4, ///< Score for good alignment native (int)
scoreAlignSym = 5, ///< Score for good alignment symetric (int)
scoreAlignBoth = 6, ///< Score for good alignment both (int)
scoreReAlignNativeNO =
7, ///< Score for re-alignment without offset native (int)
scoreReAlignSymNO =
8, ///< Score for re-alignment without offset symetric (int)
scoreReAlignBothNO = 9, ///< Score for re-alignment without offset both (int)
};
enum class ExperimentalSpectrumDataPointType : std::uint8_t
{
native = 0, ///< native peak, but has no mz counterpart (the complement ion),
///< we had to compute the symetric mass
symetric =
1, ///< new peak : computed symetric mass from a corresponding native peak
both =
2, ///< both, the ion and the complement exists in the original spectrum
synthetic =
3, ///< does not correspond to existing peak, for computational purpose
};
} // namespace specglob
} // namespace pappso
pappso::specglob::ScoreValueType
ScoreValueType
Definition types.h:57
pappso::specglob::ScoreValueType::scoreAlignNative
@ scoreAlignNative
Score for good alignment native (int)
pappso::specglob::ScoreValueType::scoreReAlignSymNO
@ scoreReAlignSymNO
Score for re-alignment without offset symetric (int)
pappso::specglob::ScoreValueType::scoreNonAlign
@ scoreNonAlign
Score for non alignment (int)
pappso::specglob::ScoreValueType::scoreAlignBoth
@ scoreAlignBoth
Score for good alignment both (int)
pappso::specglob::ScoreValueType::scoreReAlignBoth
@ scoreReAlignBoth
Score for re-alignment both (int)
pappso::specglob::ScoreValueType::scoreReAlignBothNO
@ scoreReAlignBothNO
Score for re-alignment without offset both (int)
pappso::specglob::ScoreValueType::scoreReAlignSym
@ scoreReAlignSym
Score for re-alignment symetric (int)
pappso::specglob::ScoreValueType::scoreReAlignNative
@ scoreReAlignNative
pappso::specglob::ScoreValueType::scoreAlignSym
@ scoreAlignSym
Score for good alignment symetric (int)
pappso::specglob::ScoreValueType::scoreReAlignNativeNO
@ scoreReAlignNativeNO
Score for re-alignment without offset native (int)
pappso::specglob::SpectralAlignmentType
SpectralAlignmentType
Definition types.h:48
pappso::specglob::SpectralAlignmentType::nonAlign
@ nonAlign
the type of alignment to put in origin matrix NON Alignment (0 - NA)
pappso::specglob::SpectralAlignmentType::reAlign
@ reAlign
Re Alignment (1 - RE)
pappso::specglob::SpectralAlignmentType::align
@ align
Alignment (2 - AL)
pappso::specglob::ExperimentalSpectrumDataPointType
ExperimentalSpectrumDataPointType
Definition types.h:78
pappso::specglob::ExperimentalSpectrumDataPointType::symetric
@ symetric
new peak : computed symetric mass from a corresponding native peak
pappso::specglob::ExperimentalSpectrumDataPointType::synthetic
@ synthetic
does not correspond to existing peak, for computational purpose
pappso::specglob::ExperimentalSpectrumDataPointType::native
@ native
pappso::specglob::ExperimentalSpectrumDataPointType::both
@ both
both, the ion and the complement exists in the original spectrum
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39