peptidenaturalisotopeaverage.h
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/*******************************************************************************
* Copyright (c) 2015 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 <vector>
#include "../exportinmportconfig.h"
#include "peptidenaturalisotope.h"
namespace pappso
{
class PeptideNaturalIsotopeList;
class PeptideNaturalIsotopeAverage;
typedef std::shared_ptr<const PeptideNaturalIsotopeAverage>
PeptideNaturalIsotopeAverageSp;
class PMSPP_LIB_DECL PeptideNaturalIsotopeAverage
{
public:
PeptideNaturalIsotopeAverage(const PeptideInterfaceSp &peptide,
unsigned int askedIsotopeRank,
unsigned int isotopeLevel,
unsigned int charge,
PrecisionPtr precision);
PeptideNaturalIsotopeAverage(const PeptideNaturalIsotopeList &isotopeList,
unsigned int askedIsotopeRank,
unsigned int isotopeLevel,
unsigned int charge,
PrecisionPtr precision);
PeptideNaturalIsotopeAverage(const PeptideNaturalIsotopeAverage &other);
~PeptideNaturalIsotopeAverage();
PeptideNaturalIsotopeAverageSp makePeptideNaturalIsotopeAverageSp() const;
pappso_double getMz() const;
pappso_double getIntensityRatio() const;
unsigned int getCharge() const;
unsigned int getIsotopeNumber() const;
unsigned int getIsotopeRank() const;
const std::vector<PeptideNaturalIsotopeSp> &getComponents() const;
const PeptideInterfaceSp &getPeptideInterfaceSp() const;
PrecisionPtr getPrecision() const;
virtual bool matchPeak(pappso_double peak_mz) const final;
bool isEmpty() const;
private:
void recursiveDepletion(std::vector<PeptideNaturalIsotopeSp> &v_isotope_list,
unsigned int rank);
private:
const PeptideInterfaceSp mcsp_peptideSp;
std::vector<PeptideNaturalIsotopeSp> m_peptideNaturalIsotopeSpList;
pappso_double m_averageMz;
pappso_double m_abundanceRatio;
unsigned int m_isotopeLevel;
unsigned int m_isotopeRank = 1;
unsigned int m_z;
PrecisionPtr mp_precision = nullptr;
};
} // namespace pappso
pappso::PeptideNaturalIsotopeAverage
Definition: peptidenaturalisotopeaverage.h:43
pappso::PeptideNaturalIsotopeAverage::m_peptideNaturalIsotopeSpList
std::vector< PeptideNaturalIsotopeSp > m_peptideNaturalIsotopeSpList
Definition: peptidenaturalisotopeaverage.h:78
pappso::PeptideNaturalIsotopeAverage::m_abundanceRatio
pappso_double m_abundanceRatio
Definition: peptidenaturalisotopeaverage.h:81
pappso::PeptideNaturalIsotopeAverage::mcsp_peptideSp
const PeptideInterfaceSp mcsp_peptideSp
Definition: peptidenaturalisotopeaverage.h:77
pappso::PeptideNaturalIsotopeAverage::m_isotopeLevel
unsigned int m_isotopeLevel
Definition: peptidenaturalisotopeaverage.h:82
pappso::PeptideNaturalIsotopeAverage::m_averageMz
pappso_double m_averageMz
Definition: peptidenaturalisotopeaverage.h:80
pappso::PeptideNaturalIsotopeAverage::m_z
unsigned int m_z
Definition: peptidenaturalisotopeaverage.h:84
pappso::PeptideNaturalIsotopeList
Definition: peptidenaturalisotopelist.h:49
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::PeptideInterfaceSp
std::shared_ptr< const PeptideInterface > PeptideInterfaceSp
Definition: peptideinterface.h:38
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition: types.h:48
pappso::PeptideNaturalIsotopeAverageSp
std::shared_ptr< const PeptideNaturalIsotopeAverage > PeptideNaturalIsotopeAverageSp
Definition: peptidenaturalisotopeaverage.h:37
peptidenaturalisotope.h
peptide natural isotope model