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peptiderawfragmentmasses.h
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/**
* \file pappsomspp/peptide/peptiderawfragmentmasses.h
* \date 16/7/2016
* \author Olivier Langella
* \brief class dedicated to raw mass computations of peptide products
* (fragments)
*/
/*******************************************************************************
* Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.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/>.
*
* Contributors:
* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
*implementation
******************************************************************************/
#pragma once
#include "peptide.h"
#include "../massspectrum/massspectrum.h"
namespace pappso
{
enum class RawFragmentationMode : std::int8_t
{
full = 0,
proline_effect = 1
};
struct SimplePeakIonMatch
{
DataPoint peak;
PeptideIon ion_type;
unsigned int ion_size;
unsigned int ion_charge;
pappso_double ion_mz;
};
class PMSPP_LIB_DECL PeptideRawFragmentMasses
{
using ionDeltatMzMassMap = pappso_double[20];
private:
static ionDeltatMzMassMap m_ionDeltaMz;
/** \brief cumulative Nter masses (without internal Nter modification)
* */
std::vector<pappso_double> m_cumulativeNterMasses;
/** \brief cumulative Cter masses (without internal Cter modification)
* */
std::vector<pappso_double> m_cumulativeCterMasses;
public:
PeptideRawFragmentMasses(const Peptide &peptide, RawFragmentationMode mode);
~PeptideRawFragmentMasses();
void pushBackIonMasses(std::vector<pappso_double> &mass_list,
PeptideIon ion_type) const;
void pushBackIonMz(std::vector<pappso_double> &mass_list,
PeptideIon ion_type,
unsigned int charge) const;
void pushBackMatchSpectrum(std::vector<SimplePeakIonMatch> &peak_match_list,
const MassSpectrum &spectrum,
PrecisionPtr precision,
PeptideIon ion_type,
unsigned int charge) const;
static pappso_double getDeltaMass(PeptideIon ion_type);
};
} // namespace pappso
pappso::MassSpectrum
Class to represent a mass spectrum.
Definition massspectrum.h:73
pappso::PeptideRawFragmentMasses
Definition peptiderawfragmentmasses.h:60
pappso::PeptideRawFragmentMasses::ionDeltatMzMassMap
pappso_double[20] ionDeltatMzMassMap
Definition peptiderawfragmentmasses.h:61
pappso::PeptideRawFragmentMasses::m_cumulativeCterMasses
std::vector< pappso_double > m_cumulativeCterMasses
cumulative Cter masses (without internal Cter modification)
Definition peptiderawfragmentmasses.h:72
pappso::PeptideRawFragmentMasses::m_cumulativeNterMasses
std::vector< pappso_double > m_cumulativeNterMasses
cumulative Nter masses (without internal Nter modification)
Definition peptiderawfragmentmasses.h:68
pappso::PeptideRawFragmentMasses::m_ionDeltaMz
static ionDeltatMzMassMap m_ionDeltaMz
Definition peptiderawfragmentmasses.h:64
pappso::Peptide
Definition peptide.h:100
pappso::PrecisionBase
Definition precision.h:44
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::PeptideIon
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition types.h:432
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition types.h:50
pappso::RawFragmentationMode
RawFragmentationMode
Definition peptiderawfragmentmasses.h:43
pappso::RawFragmentationMode::full
@ full
pappso::RawFragmentationMode::proline_effect
@ proline_effect
peptide.h
peptide model
pappso::DataPoint
Definition datapoint.h:22
pappso::SimplePeakIonMatch
Definition peptiderawfragmentmasses.h:50
pappso::SimplePeakIonMatch::ion_mz
pappso_double ion_mz
Definition peptiderawfragmentmasses.h:55
pappso::SimplePeakIonMatch::ion_type
PeptideIon ion_type
Definition peptiderawfragmentmasses.h:52
pappso::SimplePeakIonMatch::ion_charge
unsigned int ion_charge
Definition peptiderawfragmentmasses.h:54
pappso::SimplePeakIonMatch::ion_size
unsigned int ion_size
Definition peptiderawfragmentmasses.h:53
pappso::SimplePeakIonMatch::peak
DataPoint peak
Definition peptiderawfragmentmasses.h:51