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spomsprotein.h
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/*
* Copyright (c) 2025 Aurélien Berthier
* <aurelien.berthier@ls2n.fr>
*
* This program 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.
*
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
*/
#pragma once
#include "pappsomspp/core/protein/protein.h"
#include "pappsomspp/core/amino_acid/aacode.h"
#include "pappsomspp/export-import-config.h"
namespace pappso
{
namespace specpeptidoms
{
struct SpOMSAa
{
std::uint8_t code;
pappso::Enums::AminoAcidChar aa;
double mass;
};
class PMSPP_LIB_DECL SpOMSProtein : public std::vector<SpOMSAa>
{
public:
SpOMSProtein(const QString &description, const QString &sequence, const AaCode &aa_code);
virtual ~SpOMSProtein();
const QString getAccession() const;
const QString &getCompleteDescription() const;
const QString &getSequence() const;
std::vector<SpOMSAa> sliced(std::size_t position, std::size_t length) const;
private:
QString m_description;
QString m_sequence;
};
} // namespace specpeptidoms
} // namespace pappso
aacode.h
pappso::AaCode
collection of integer code for each amino acid 0 => null 1 to 20 => amino acid sorted by there mass (...
Definition aacode.h:44
pappso::specpeptidoms::SpOMSProtein::getSequence
const QString & getSequence() const
Definition spomsprotein.cpp:58
pappso::specpeptidoms::SpOMSProtein::SpOMSProtein
SpOMSProtein(const QString &description, const QString &sequence, const AaCode &aa_code)
Definition spomsprotein.cpp:26
pappso::specpeptidoms::SpOMSProtein::getCompleteDescription
const QString & getCompleteDescription() const
Definition spomsprotein.cpp:65
pappso::specpeptidoms::SpOMSProtein::getAccession
const QString getAccession() const
Definition spomsprotein.cpp:52
pappso::specpeptidoms::SpOMSProtein::m_description
QString m_description
Definition spomsprotein.h:52
pappso::specpeptidoms::SpOMSProtein::sliced
std::vector< SpOMSAa > sliced(std::size_t position, std::size_t length) const
Definition spomsprotein.cpp:71
pappso::specpeptidoms::SpOMSProtein::m_sequence
QString m_sequence
Definition spomsprotein.h:53
export-import-config.h
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition export-import-config.h:14
pappso::Enums::AminoAcidChar
AminoAcidChar
Definition types.h:196
pappso::specpeptidoms
Definition correctiontree.h:40
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
protein.h
pappso::specpeptidoms::SpOMSAa
Definition spomsprotein.h:31
pappso::specpeptidoms::SpOMSAa::code
std::uint8_t code
Definition spomsprotein.h:32
pappso::specpeptidoms::SpOMSAa::aa
pappso::Enums::AminoAcidChar aa
Definition spomsprotein.h:33
pappso::specpeptidoms::SpOMSAa::mass
double mass
Definition spomsprotein.h:34