xtandemhyperscore.h
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/**
* \file pappsomspp/psm/xtandem/xtandemhyperscore.h
* \date 19/3/2015
* \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 "../../mzrange.h"
#include "../../peptide/peptidefragmention.h"
namespace pappso
{
class PMSPP_LIB_DECL XtandemHyperscore
{
public:
using AaFactorMap = std::map<char, pappso_double>;
XtandemHyperscore(const MassSpectrum &spectrum,
pappso::PeptideSp peptideSp,
unsigned int parent_charge,
PrecisionPtr precision,
std::list<PeptideIon> ion_list,
bool refine_spectrum_synthesis);
~XtandemHyperscore();
pappso_double getHyperscore() const;
unsigned int getMatchedIons(PeptideIon ion_type) const;
private:
bool _refine_spectrum_synthesis;
unsigned int
getXtandemPredictedIonIntensityFactor(const QString &sequence,
PeptideDirection ion_direction,
unsigned int ion_size) const;
pappso_double _proto_hyperscore;
std::map<PeptideIon, unsigned int> _ion_count;
static AaFactorMap _aa_ion_factor_y;
static AaFactorMap _aa_ion_factor_b;
};
} // namespace pappso
pappso::MassSpectrum
Class to represent a mass spectrum.
Definition: massspectrum.h:71
pappso::PrecisionBase
Definition: precision.h:44
pappso::XtandemHyperscore
Definition: xtandemhyperscore.h:43
pappso::XtandemHyperscore::_refine_spectrum_synthesis
bool _refine_spectrum_synthesis
Definition: xtandemhyperscore.h:58
pappso::XtandemHyperscore::_aa_ion_factor_y
static AaFactorMap _aa_ion_factor_y
Definition: xtandemhyperscore.h:68
pappso::XtandemHyperscore::_proto_hyperscore
pappso_double _proto_hyperscore
Definition: xtandemhyperscore.h:65
pappso::XtandemHyperscore::AaFactorMap
std::map< char, pappso_double > AaFactorMap
Definition: xtandemhyperscore.h:45
pappso::XtandemHyperscore::_aa_ion_factor_b
static AaFactorMap _aa_ion_factor_b
Definition: xtandemhyperscore.h:69
pappso::XtandemHyperscore::_ion_count
std::map< PeptideIon, unsigned int > _ion_count
Definition: xtandemhyperscore.h:66
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:385
pappso::PeptideSp
std::shared_ptr< const Peptide > PeptideSp
Definition: aamodification.h:47
pappso::PeptideDirection
PeptideDirection
Definition: peptide.h:46
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition: types.h:48