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peptidenaturalisotopelist.h
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/**
* \file pappsomspp/peptide/peptidenaturalisotopelist.h
* \date 8/3/2015
* \author Olivier Langella
* \brief peptide natural isotope model
*/
/*******************************************************************************
* 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 <list>
#include "peptidenaturalisotope.h"
#include "peptidenaturalisotopeaverage.h"
#include "pappsomspp/export-import-config.h"
namespace pappso
{
class PeptideNaturalIsotopeList;
typedef std::shared_ptr<const PeptideNaturalIsotopeList>
PeptideNaturalIsotopeListSp;
class PMSPP_LIB_DECL PeptideNaturalIsotopeList
{
private:
const PeptideInterfaceSp msp_peptide;
std::list<PeptideNaturalIsotopeSp> msp_peptide_natural_isotope_list;
public:
/** @brief compute the list of possible isotopes for a peptide
* @param peptide the peptide
* @param minimu_ratio_to_compute the limit under which we stop to compute
* because the ratio is too thin and not informative (default is 0.001). This
* limit is the same for each atom to survey : CHNOS
*/
PeptideNaturalIsotopeList(const PeptideInterfaceSp &peptide,
pappso_double minimum_ratio_to_compute = 0.001);
PeptideNaturalIsotopeList(const PeptideNaturalIsotopeList &other);
~PeptideNaturalIsotopeList();
PeptideNaturalIsotopeListSp makePeptideNaturalIsotopeListSp() const;
typedef std::list<PeptideNaturalIsotopeSp>::const_iterator const_iterator;
const_iterator begin() const;
const_iterator end() const;
const std::map<unsigned int, pappso_double>
getIntensityRatioPerIsotopeNumber() const;
std::vector<PeptideNaturalIsotopeSp>
getByIsotopeNumber(unsigned int isotopeLevel, unsigned int charge) const;
/** @brief get the list of natural isotopes representing at least a minimum
* ratio of the whole isotope pattern
* @param charge gives the number of H+, important to take into account for
* isotope ratio
* @param precision the mass accuracy to take into acount each isotope (C13 !=
* H2)
* @param minimum_isotope_pattern_ratio the minimum ratio of the isotope
* pattern to represent
*/
std::vector<PeptideNaturalIsotopeAverageSp>
getByIntensityRatio(unsigned int charge,
PrecisionPtr precision,
pappso_double minimum_isotope_pattern_ratio) const;
unsigned int size() const;
const PeptideInterfaceSp &getPeptideInterfaceSp() const;
};
} // namespace pappso
pappso::PeptideNaturalIsotopeList
Definition peptidenaturalisotopelist.h:49
pappso::PeptideNaturalIsotopeList::getPeptideInterfaceSp
const PeptideInterfaceSp & getPeptideInterfaceSp() const
Definition peptidenaturalisotopelist.cpp:497
pappso::PeptideNaturalIsotopeList::msp_peptide
const PeptideInterfaceSp msp_peptide
Definition peptidenaturalisotopelist.h:51
pappso::PeptideNaturalIsotopeList::PeptideNaturalIsotopeList
PeptideNaturalIsotopeList(const PeptideInterfaceSp &peptide, pappso_double minimum_ratio_to_compute=0.001)
compute the list of possible isotopes for a peptide
Definition peptidenaturalisotopelist.cpp:38
pappso::PeptideNaturalIsotopeList::const_iterator
std::list< PeptideNaturalIsotopeSp >::const_iterator const_iterator
Definition peptidenaturalisotopelist.h:67
pappso::PeptideNaturalIsotopeList::end
const_iterator end() const
Definition peptidenaturalisotopelist.cpp:485
pappso::PeptideNaturalIsotopeList::makePeptideNaturalIsotopeListSp
PeptideNaturalIsotopeListSp makePeptideNaturalIsotopeListSp() const
Definition peptidenaturalisotopelist.cpp:260
pappso::PeptideNaturalIsotopeList::getByIntensityRatio
std::vector< PeptideNaturalIsotopeAverageSp > getByIntensityRatio(unsigned int charge, PrecisionPtr precision, pappso_double minimum_isotope_pattern_ratio) const
get the list of natural isotopes representing at least a minimum ratio of the whole isotope pattern
Definition peptidenaturalisotopelist.cpp:398
pappso::PeptideNaturalIsotopeList::msp_peptide_natural_isotope_list
std::list< PeptideNaturalIsotopeSp > msp_peptide_natural_isotope_list
Definition peptidenaturalisotopelist.h:52
pappso::PeptideNaturalIsotopeList::getIntensityRatioPerIsotopeNumber
const std::map< unsigned int, pappso_double > getIntensityRatioPerIsotopeNumber() const
Definition peptidenaturalisotopelist.cpp:276
pappso::PeptideNaturalIsotopeList::begin
const_iterator begin() const
Definition peptidenaturalisotopelist.cpp:479
pappso::PeptideNaturalIsotopeList::getByIsotopeNumber
std::vector< PeptideNaturalIsotopeSp > getByIsotopeNumber(unsigned int isotopeLevel, unsigned int charge) const
Definition peptidenaturalisotopelist.cpp:304
pappso::PeptideNaturalIsotopeList::size
unsigned int size() const
Definition peptidenaturalisotopelist.cpp:491
export-import-config.h
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition export-import-config.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:40
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition types.h:60
pappso::PrecisionPtr
const PrecisionBase * PrecisionPtr
Definition precision.h:122
pappso::PeptideNaturalIsotopeListSp
std::shared_ptr< const PeptideNaturalIsotopeList > PeptideNaturalIsotopeListSp
Definition peptidenaturalisotopelist.h:45
peptidenaturalisotope.h
peptidenaturalisotopeaverage.h