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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 symmetric (int)
scoreReAlignBoth = 3, ///< Score for re-alignment both (int)
scoreAlignNative = 4, ///< Score for good alignment native (int)
scoreAlignSym = 5, ///< Score for good alignment symmetric (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 symmetric (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 symmetric mass
symmetric =
1, ///< new peak : computed symmetric 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
Definition experimentalspectrum.cpp:44
pappso::specglob::ScoreValueType
ScoreValueType
Definition types.h:57
pappso::specglob::ScoreValueType::scoreAlignNative
@ scoreAlignNative
Score for good alignment native (int).
Definition types.h:65
pappso::specglob::ScoreValueType::scoreReAlignSymNO
@ scoreReAlignSymNO
Score for re-alignment without offset symmetric (int).
Definition types.h:71
pappso::specglob::ScoreValueType::scoreNonAlign
@ scoreNonAlign
Score for non alignment (int).
Definition types.h:58
pappso::specglob::ScoreValueType::scoreAlignBoth
@ scoreAlignBoth
Score for good alignment both (int).
Definition types.h:67
pappso::specglob::ScoreValueType::scoreReAlignBoth
@ scoreReAlignBoth
Score for re-alignment both (int).
Definition types.h:62
pappso::specglob::ScoreValueType::scoreReAlignBothNO
@ scoreReAlignBothNO
Score for re-alignment without offset both (int).
Definition types.h:73
pappso::specglob::ScoreValueType::scoreReAlignSym
@ scoreReAlignSym
Score for re-alignment symmetric (int).
Definition types.h:61
pappso::specglob::ScoreValueType::scoreReAlignNative
@ scoreReAlignNative
Definition types.h:60
pappso::specglob::ScoreValueType::scoreAlignSym
@ scoreAlignSym
Score for good alignment symmetric (int).
Definition types.h:66
pappso::specglob::ScoreValueType::scoreReAlignNativeNO
@ scoreReAlignNativeNO
Score for re-alignment without offset native (int).
Definition types.h:69
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)
Definition types.h:49
pappso::specglob::SpectralAlignmentType::reAlign
@ reAlign
Re Alignment (1 - RE).
Definition types.h:51
pappso::specglob::SpectralAlignmentType::align
@ align
Alignment (2 - AL).
Definition types.h:52
pappso::specglob::ExperimentalSpectrumDataPointType
ExperimentalSpectrumDataPointType
Definition types.h:78
pappso::specglob::ExperimentalSpectrumDataPointType::synthetic
@ synthetic
does not correspond to existing peak, for computational purpose
Definition types.h:85
pappso::specglob::ExperimentalSpectrumDataPointType::native
@ native
Definition types.h:79
pappso::specglob::ExperimentalSpectrumDataPointType::both
@ both
both, the ion and the complement exists in the original spectrum
Definition types.h:83
pappso::specglob::ExperimentalSpectrumDataPointType::symmetric
@ symmetric
new peak : computed symmetric mass from a corresponding native peak
Definition types.h:81
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39