libpappsomspp
Library for mass spectrometry
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selfspectrum.h
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1/**
2 * \file pappsomspp/processing/specself/selfspectrum.h
3 * \date 23/03/2024
4 * \author Olivier Langella
5 * \brief spectrum self operations
6 */
7
8/*******************************************************************************
9 * Copyright (c) 2024 Olivier Langella
10 *<Olivier.Langella@universite-paris-saclay.fr>.
11 *
12 * This file is part of PAPPSOms++.
13 *
14 * PAPPSOms++ is free software: you can redistribute it and/or modify
15 * it under the terms of the GNU General Public License as published by
16 * the Free Software Foundation, either version 3 of the License, or
17 * (at your option) any later version.
18 *
19 * PAPPSOms++ is distributed in the hope that it will be useful,
20 * but WITHOUT ANY WARRANTY; without even the implied warranty of
21 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22 * GNU General Public License for more details.
23 *
24 * You should have received a copy of the GNU General Public License
25 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
26 *
27 ******************************************************************************/
28
29#pragma once
30
31#include "../../trace/trace.h"
32#include <boost/numeric/ublas/matrix.hpp>
34
35namespace pappso
36{
37namespace specself
38{
39
40typedef boost::numeric::ublas::matrix<SelfSpectrumDataPoint> SelfSpectrumMatrix;
41/**
42 * @todo write docs
43 */
45{
46 public:
47 /**
48 * Default constructor
49 */
50 SelfSpectrum(const pappso::AaStringCodeMassMatching &codec_mass_matching,
51 const Trace &trace);
52 /**
53 * Destructor
54 */
55 virtual ~SelfSpectrum();
56
57 void
58 setPrecursorMass(const pappso::AaStringCodeMassMatching &codec_mass_matching,
59 double precursor_mass);
60
61
63 const pappso::AaStringCodeMassMatching &codec_mass_matching,
64 const Aa &aa,
65 int quantifier);
66
67 const SelfSpectrumMatrix &getMatrix() const;
68 const Trace &getTrace() const;
69
70 private:
73};
74} // namespace specself
75} // namespace pappso
convert a list of mass to amino acid string codes
A simple container of DataPoint instances.
Definition trace.h:148
const SelfSpectrumMatrix & getMatrix() const
void setVariableModification(const pappso::AaStringCodeMassMatching &codec_mass_matching, const Aa &aa, int quantifier)
SelfSpectrumMatrix m_matrix
SelfSpectrum(const pappso::AaStringCodeMassMatching &codec_mass_matching, const Trace &trace)
void setPrecursorMass(const pappso::AaStringCodeMassMatching &codec_mass_matching, double precursor_mass)
const Trace & getTrace() const
boost::numeric::ublas::matrix< SelfSpectrumDataPoint > SelfSpectrumMatrix
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
spectrum self data points stored in the self spectrum matrix