libpappsomspp
Library for mass spectrometry
Loading...
Searching...
No Matches
peptidespectrum.h
Go to the documentation of this file.
1
/**
2
* \file pappsomspp/processing/specglob/peptidespectrum.h
3
* \date 06/11/2023
4
* \author Olivier Langella
5
* \brief transform a peptide to SpecGlob spectrum
6
*
7
* C++ implementation of the SpecGlob algorithm described in :
8
* 1. Prunier, G. et al. Fast alignment of mass spectra in large proteomics
9
* datasets, capturing dissimilarities arising from multiple complex
10
* modifications of peptides. BMC Bioinformatics 24, 421 (2023).
11
*
12
* HAL Id : hal-04296170 , version 1
13
* Mot de passe : hxo20cl
14
* DOI : 10.1186/s12859-023-05555-y
15
*/
16
17
18
/*
19
* SpecGlobTool, Spectra to peptide alignment tool
20
* Copyright (C) 2023 Olivier Langella
21
* <olivier.langella@universite-paris-saclay.fr>
22
*
23
* This program is free software: you can redistribute it and/or modify
24
* it under the terms of the GNU General Public License as published by
25
* the Free Software Foundation, either version 3 of the License, or
26
* (at your option) any later version.
27
*
28
* This program is distributed in the hope that it will be useful,
29
* but WITHOUT ANY WARRANTY; without even the implied warranty of
30
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
31
* GNU General Public License for more details.
32
*
33
* You should have received a copy of the GNU General Public License
34
* along with this program. If not, see <http://www.gnu.org/licenses/>.
35
*
36
*/
37
38
#pragma once
39
40
#include "../../peptide/peptide.h"
41
#include <memory>
42
#include "../../exportinmportconfig.h"
43
44
namespace
pappso
45
{
46
namespace
specglob
47
{
48
struct
PeptideSpectrumDataPoint
49
{
50
double
mz
;
51
double
diff_mz
;
52
};
53
54
class
PeptideSpectrum
;
55
56
typedef
std::shared_ptr<const PeptideSpectrum>
PeptideSpectraCsp
;
57
/**
58
* @todo write docs
59
*/
60
class
PMSPP_LIB_DECL
PeptideSpectrum
61
:
public
std::vector<PeptideSpectrumDataPoint>
62
{
63
public
:
64
/**
65
* Default constructor
66
*/
67
PeptideSpectrum
(
const
pappso::PeptideSp
peptide_sp);
68
69
/**
70
* Copy constructor
71
*
72
* @param other TODO
73
*/
74
PeptideSpectrum
(
const
PeptideSpectrum
&other);
75
76
/**
77
* Destructor
78
*/
79
virtual
~PeptideSpectrum
();
80
81
std::vector<double> getMassList()
const
;
82
83
pappso::PeptideSp
getPeptideSp()
const
;
84
85
private
:
86
pappso::PeptideSp
msp_peptide
;
87
// std::vector<double> m_massList;
88
};
89
}
// namespace specglob
90
}
// namespace pappso
pappso::specglob::PeptideSpectrum
Definition
peptidespectrum.h:62
pappso::specglob::PeptideSpectrum::msp_peptide
pappso::PeptideSp msp_peptide
Definition
peptidespectrum.h:86
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition
exportinmportconfig.h:14
pappso::specglob::PeptideSpectraCsp
std::shared_ptr< const PeptideSpectrum > PeptideSpectraCsp
Definition
peptidespectrum.h:56
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition
aa.cpp:39
pappso::PeptideSp
std::shared_ptr< const Peptide > PeptideSp
Definition
aamodification.h:48
pappso::specglob::PeptideSpectrumDataPoint
Definition
peptidespectrum.h:49
pappso::specglob::PeptideSpectrumDataPoint::diff_mz
double diff_mz
Definition
peptidespectrum.h:51
pappso::specglob::PeptideSpectrumDataPoint::mz
double mz
Definition
peptidespectrum.h:50
pappsomspp
processing
specglob
peptidespectrum.h
Generated on Thu May 16 2024 09:01:17 for libpappsomspp by
1.9.8