libpappsomspp
Library for mass spectrometry
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aastringcodemassmatching.h
Go to the documentation of this file.
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/**
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* \file pappsomspp/amino_acid/aastringcodemassmatching.h
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* \date 10/05/2023
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* \author Olivier Langella
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* \brief convert mass list to amino acid string code list
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*/
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/*******************************************************************************
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* Copyright (c) 2023 Olivier Langella <Olivier.Langella@u-psud.fr>.
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*
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* This file is part of PAPPSOms-tools.
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*
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* PAPPSOms-tools is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* PAPPSOms-tools is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
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*
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******************************************************************************/
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#pragma once
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#include "../exportinmportconfig.h"
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#include "
aastringcodec.h
"
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#include "../mzrange.h"
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namespace
pappso
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{
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/**
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* @brief
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*/
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class
PMSPP_LIB_DECL
AaStringCodeMassMatching
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{
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public
:
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/**
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* Default constructor
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*/
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AaStringCodeMassMatching
(
const
AaCode
&aa_code,
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std::size_t model_max_size,
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PrecisionPtr
precision);
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/**
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* Copy constructor
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*
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* @param other TODO
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*/
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AaStringCodeMassMatching
(
const
AaStringCodeMassMatching
&other);
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/**
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* Destructor
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*/
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~AaStringCodeMassMatching
();
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/** @brief get amino acid string code from mass delta list
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* mass delta is a list of masses differences found in a spectrum
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* see @file /pappsomspp/filers/filtepeakdelta.h functions
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*/
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std::vector<uint32_t>
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getAaCodeFromMassList(std::vector<double> &mass_list)
const
;
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/** @brief filter a list of amino acid string code
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* find elementary amino acids (one base only) in the list and retrieve 2 or
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* more amino acid string containing only basic aminio acid found
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*/
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std::vector<uint32_t> filterCodeList(std::vector<uint32_t> &code_list)
const
;
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private
:
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const
AaCode
&
m_aaCode
;
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AaStringCodec
m_aaCodec
;
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uint32_t m_base = 0;
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struct
aaCodeAndMassRange
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{
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std::uint32_t code = 0;
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double
mz_range_low = 0;
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double
mz
= 0;
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double
mz_range_up = 0;
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};
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std::vector<aaCodeAndMassRange>
m_codeMassList
;
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};
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}
// namespace pappso
aastringcodec.h
code and decodefrom amino acid string to integer
pappso::AaCode
collection of integer code for each amino acid 0 => null 1 to 20 => amino acid sorted by there mass (...
Definition
aacode.h:43
pappso::AaStringCodeMassMatching
Definition
aastringcodemassmatching.h:41
pappso::AaStringCodeMassMatching::m_codeMassList
std::vector< aaCodeAndMassRange > m_codeMassList
Definition
aastringcodemassmatching.h:92
pappso::AaStringCodeMassMatching::m_aaCodec
AaStringCodec m_aaCodec
Definition
aastringcodemassmatching.h:79
pappso::AaStringCodeMassMatching::m_aaCode
const AaCode & m_aaCode
Definition
aastringcodemassmatching.h:77
pappso::AaStringCodec
Definition
aastringcodec.h:52
pappso::PrecisionBase
Definition
precision.h:44
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::PrecisionUnit::mz
@ mz
pappso::AaStringCodeMassMatching::aaCodeAndMassRange
Definition
aastringcodemassmatching.h:85
pappsomspp
amino_acid
aastringcodemassmatching.h
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