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xtandemhyperscorebis.h
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/**
* \file pappsomspp/psm/xtandem/xtandemhyperscorebis.h
* \date 8/9/2016
* \author Olivier Langella
* \brief computation of the X!Tandem hyperscore
*/
/*******************************************************************************
* 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 "../../massspectrum/massspectrum.h"
#include "../../peptide/peptide.h"
namespace pappso
{
class XtandemHyperscoreBis
{
using AaFactorMap = std::map<char, pappso_double>;
private:
unsigned int getXtandemPredictedIonIntensityFactor(const QString &sequence,
PeptideIon ion_type,
unsigned int size) const;
bool m_isRefineSpectrumSynthesis;
PrecisionPtr mp_precision;
std::vector<PeptideIon> m_ionList;
unsigned int m_totalMatchedIons = 0;
unsigned int m_ionCount[PEPTIDE_ION_TYPE_COUNT] = {0};
pappso_double m_protoHyperscore;
static AaFactorMap m_aaIonFactorY;
static AaFactorMap m_aaIonFactorBb;
public:
XtandemHyperscoreBis(bool refine_spectrum_synthesis,
PrecisionPtr precision,
const std::vector<PeptideIon> &ion_list);
~XtandemHyperscoreBis();
pappso_double getHyperscore() const;
unsigned int getMatchedIons(PeptideIon ion_type) const;
void reset();
bool computeXtandemHyperscore(const MassSpectrum &spectrum,
const Peptide &peptide,
unsigned int parent_charge);
unsigned int getTotalMatchedIons() const;
};
} // namespace pappso
pappso::MassSpectrum
Class to represent a mass spectrum.
Definition massspectrum.h:73
pappso::Peptide
Definition peptide.h:100
pappso::PrecisionBase
Definition precision.h:44
pappso::XtandemHyperscoreBis
Definition xtandemhyperscorebis.h:41
pappso::XtandemHyperscoreBis::getTotalMatchedIons
unsigned int getTotalMatchedIons() const
Definition xtandemhyperscorebis.cpp:263
pappso::XtandemHyperscoreBis::getXtandemPredictedIonIntensityFactor
unsigned int getXtandemPredictedIonIntensityFactor(const QString &sequence, PeptideIon ion_type, unsigned int size) const
Definition xtandemhyperscorebis.cpp:208
pappso::XtandemHyperscoreBis::m_protoHyperscore
pappso_double m_protoHyperscore
Definition xtandemhyperscorebis.h:56
pappso::XtandemHyperscoreBis::reset
void reset()
Definition xtandemhyperscorebis.cpp:74
pappso::XtandemHyperscoreBis::m_isRefineSpectrumSynthesis
bool m_isRefineSpectrumSynthesis
Definition xtandemhyperscorebis.h:48
pappso::XtandemHyperscoreBis::m_aaIonFactorY
static AaFactorMap m_aaIonFactorY
Definition xtandemhyperscorebis.h:58
pappso::XtandemHyperscoreBis::AaFactorMap
std::map< char, pappso_double > AaFactorMap
Definition xtandemhyperscorebis.h:42
pappso::XtandemHyperscoreBis::computeXtandemHyperscore
bool computeXtandemHyperscore(const MassSpectrum &spectrum, const Peptide &peptide, unsigned int parent_charge)
Definition xtandemhyperscorebis.cpp:85
pappso::XtandemHyperscoreBis::mp_precision
PrecisionPtr mp_precision
Definition xtandemhyperscorebis.h:49
pappso::XtandemHyperscoreBis::m_ionCount
unsigned int m_ionCount[PEPTIDE_ION_TYPE_COUNT]
Definition xtandemhyperscorebis.h:53
pappso::XtandemHyperscoreBis::m_ionList
std::vector< PeptideIon > m_ionList
Definition xtandemhyperscorebis.h:50
pappso::XtandemHyperscoreBis::~XtandemHyperscoreBis
~XtandemHyperscoreBis()
Definition xtandemhyperscorebis.cpp:62
pappso::XtandemHyperscoreBis::getHyperscore
pappso_double getHyperscore() const
Definition xtandemhyperscorebis.cpp:269
pappso::XtandemHyperscoreBis::getMatchedIons
unsigned int getMatchedIons(PeptideIon ion_type) const
Definition xtandemhyperscorebis.cpp:67
pappso::XtandemHyperscoreBis::m_aaIonFactorBb
static AaFactorMap m_aaIonFactorBb
Definition xtandemhyperscorebis.h:59
pappso::XtandemHyperscoreBis::m_totalMatchedIons
unsigned int m_totalMatchedIons
Definition xtandemhyperscorebis.h:52
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
PEPTIDE_ION_TYPE_COUNT
#define PEPTIDE_ION_TYPE_COUNT
only useful for internal use DO not change this value : it is used to define static array size
Definition types.h:452