deepprotenum.h
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/**
* \file pappsomspp/psm/deepprot/deepprotenum.h
* \date 22/1/2021
* \author Olivier Langella <olivier.langella@universite-paris-saclay.fr>
* \brief base type definition to use in DeepProt
*
* DeepProt is the C++ implementation of the SpecOMS algorithm
*
*/
/*******************************************************************************
* Copyright (c) 2021 Olivier Langella
*<olivier.langella@universite-paris-saclay.fr>.
*
* This file is part of the PAPPSOms++ library.
*
* PAPPSOms++ 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.
*
* PAPPSOms++ 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 PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
#pragma once
#include "../../exportinmportconfig.h"
#include <QString>
namespace pappso
{
/** @brief definition of different class of PSMs used by DeepProt
*/
enum class DeepProtMatchType : std::uint8_t
{
uncategorized = 0, ///< precursor mass was not compared
ZeroMassDelta = 1, ///< peptide candidate is in precursor mz range
ZeroMassDeltaMissedCleavage =
2, ///< peptide candidate with missed cleavage is in precursor mz range
ZeroMassDeltaSemiTryptic =
3, ///< semi tryptic peptide candidate is in precursor mz range
DeltaPosition = 4, ///< spectrum shifter on peptide candidate has detected a
///< position for the mass delta
NoDeltaPosition = 5, ///< spectrum shifter on peptide candidate has not
///< detected a position for the mass delta
last = 6
};
/** @brief definition of different status for potential peptide candidates on
* the same spectrum
*/
enum class DeepProtPeptideCandidateStatus : std::uint8_t
{
unmodified = 0, ///< precursor mass was not compared
ZeroMassDelta = 1,
CterRemoval = 2,
NterRemoval = 3,
MissedCleavage = 4,
DeltaPosition = 5,
NoDeltaPosition = 6,
last = 7
};
class PMSPP_LIB_DECL DeepProtEnumStr
{
public:
static const QString toString(DeepProtMatchType match_type);
static const QString toString(DeepProtPeptideCandidateStatus status);
static DeepProtPeptideCandidateStatus
DeepProtPeptideCandidateStatusFromString(const QString &name);
static DeepProtMatchType DeepProtMatchTypeFromString(const QString &name);
};
} // namespace pappso
pappso::DeepProtEnumStr
Definition: deepprotenum.h:73
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition: exportinmportconfig.h:14
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
pappso::DeepProtMatchType
DeepProtMatchType
definition of different class of PSMs used by DeepProt
Definition: deepprotenum.h:42
pappso::DeepProtMatchType::ZeroMassDeltaMissedCleavage
@ ZeroMassDeltaMissedCleavage
peptide candidate with missed cleavage is in precursor mz range
pappso::DeepProtMatchType::uncategorized
@ uncategorized
precursor mass was not compared
pappso::DeepProtMatchType::NoDeltaPosition
@ NoDeltaPosition
pappso::DeepProtMatchType::DeltaPosition
@ DeltaPosition
pappso::DeepProtMatchType::last
@ last
pappso::DeepProtMatchType::ZeroMassDelta
@ ZeroMassDelta
peptide candidate is in precursor mz range
pappso::DeepProtMatchType::ZeroMassDeltaSemiTryptic
@ ZeroMassDeltaSemiTryptic
semi tryptic peptide candidate is in precursor mz range
pappso::DeepProtPeptideCandidateStatus
DeepProtPeptideCandidateStatus
definition of different status for potential peptide candidates on the same spectrum
Definition: deepprotenum.h:61
pappso::DeepProtPeptideCandidateStatus::CterRemoval
@ CterRemoval
pappso::DeepProtPeptideCandidateStatus::unmodified
@ unmodified
precursor mass was not compared
pappso::DeepProtPeptideCandidateStatus::NoDeltaPosition
@ NoDeltaPosition
pappso::DeepProtPeptideCandidateStatus::MissedCleavage
@ MissedCleavage
pappso::DeepProtPeptideCandidateStatus::DeltaPosition
@ DeltaPosition
pappso::DeepProtPeptideCandidateStatus::last
@ last
pappso::DeepProtPeptideCandidateStatus::ZeroMassDelta
@ ZeroMassDelta
pappso::DeepProtPeptideCandidateStatus::NterRemoval
@ NterRemoval