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selfspectrum.h
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/**
* \file pappsomspp/processing/specself/selfspectrum.h
* \date 23/03/2024
* \author Olivier Langella
* \brief spectrum self operations
*/
/*******************************************************************************
* Copyright (c) 2024 Olivier Langella
*<Olivier.Langella@universite-paris-saclay.fr>.
*
* This file is part of PAPPSOms++.
*
* 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/>.
*
******************************************************************************/
#pragma once
#include "../../trace/trace.h"
#include <boost/numeric/ublas/matrix.hpp>
#include "selfspectrumdatapoint.h"
namespace pappso
{
namespace specself
{
typedef boost::numeric::ublas::matrix<SelfSpectrumDataPoint> SelfSpectrumMatrix;
/**
* @todo write docs
*/
class SelfSpectrum
{
public:
/**
* Default constructor
*/
SelfSpectrum(const pappso::AaStringCodeMassMatching &codec_mass_matching,
const Trace &trace);
/**
* Destructor
*/
virtual ~SelfSpectrum();
void
setPrecursorMass(const pappso::AaStringCodeMassMatching &codec_mass_matching,
double precursor_mass);
void setVariableModification(
const pappso::AaStringCodeMassMatching &codec_mass_matching,
const Aa &aa,
int quantifier);
const SelfSpectrumMatrix &getMatrix() const;
const Trace &getTrace() const;
private:
Trace m_trace;
SelfSpectrumMatrix m_matrix;
};
} // namespace specself
} // namespace pappso
pappso::AaStringCodeMassMatching
convert a list of mass to amino acid string codes
Definition aastringcodemassmatching.h:41
pappso::Aa
Definition aa.h:45
pappso::Trace
A simple container of DataPoint instances.
Definition trace.h:148
pappso::specself::SelfSpectrum
Definition selfspectrum.h:45
pappso::specself::SelfSpectrum::getMatrix
const SelfSpectrumMatrix & getMatrix() const
Definition selfspectrum.cpp:66
pappso::specself::SelfSpectrum::setVariableModification
void setVariableModification(const pappso::AaStringCodeMassMatching &codec_mass_matching, const Aa &aa, int quantifier)
Definition selfspectrum.cpp:101
pappso::specself::SelfSpectrum::~SelfSpectrum
virtual ~SelfSpectrum()
Definition selfspectrum.cpp:61
pappso::specself::SelfSpectrum::m_matrix
SelfSpectrumMatrix m_matrix
Definition selfspectrum.h:72
pappso::specself::SelfSpectrum::m_trace
Trace m_trace
Definition selfspectrum.h:71
pappso::specself::SelfSpectrum::setPrecursorMass
void setPrecursorMass(const pappso::AaStringCodeMassMatching &codec_mass_matching, double precursor_mass)
Definition selfspectrum.cpp:80
pappso::specself::SelfSpectrum::getTrace
const Trace & getTrace() const
Definition selfspectrum.cpp:73
pappso::specself::SelfSpectrumMatrix
boost::numeric::ublas::matrix< SelfSpectrumDataPoint > SelfSpectrumMatrix
Definition selfspectrum.h:40
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
selfspectrumdatapoint.h
spectrum self data points stored in the self spectrum matrix