libpappsomspp
Library for mass spectrometry
peptidenaturalisotopelist.h
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1/**
2 * \file pappsomspp/peptide/peptidenaturalisotopelist.h
3 * \date 8/3/2015
4 * \author Olivier Langella
5 * \brief peptide natural isotope model
6 */
7
8/*******************************************************************************
9 * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
10 *
11 * This file is part of the PAPPSOms++ library.
12 *
13 * PAPPSOms++ is free software: you can redistribute it and/or modify
14 * it under the terms of the GNU General Public License as published by
15 * the Free Software Foundation, either version 3 of the License, or
16 * (at your option) any later version.
17 *
18 * PAPPSOms++ is distributed in the hope that it will be useful,
19 * but WITHOUT ANY WARRANTY; without even the implied warranty of
20 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 * GNU General Public License for more details.
22 *
23 * You should have received a copy of the GNU General Public License
24 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25 *
26 * Contributors:
27 * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
28 *implementation
29 ******************************************************************************/
30
31#pragma once
32
33
34#include <list>
36
38#include "../exportinmportconfig.h"
39
40namespace pappso
41{
42
43class PeptideNaturalIsotopeList;
44typedef std::shared_ptr<const PeptideNaturalIsotopeList>
46
47
49{
50 private:
52 std::list<PeptideNaturalIsotopeSp> msp_peptide_natural_isotope_list;
53
54 public:
55 /** @brief compute the list of possible isotopes for a peptide
56 * @param peptide the peptide
57 * @param minimu_ratio_to_compute the limit under which we stop to compute
58 * because the ratio is too thin and not informative (default is 0.001). This
59 * limit is the same for each atom to survey : CHNOS
60 */
62 pappso_double minimum_ratio_to_compute = 0.001);
65 PeptideNaturalIsotopeListSp makePeptideNaturalIsotopeListSp() const;
66
67 typedef std::list<PeptideNaturalIsotopeSp>::const_iterator const_iterator;
68
69 const_iterator begin() const;
70
71 const_iterator end() const;
72
73 const std::map<unsigned int, pappso_double>
74 getIntensityRatioPerIsotopeNumber() const;
75
76 std::vector<PeptideNaturalIsotopeSp>
77 getByIsotopeNumber(unsigned int isotopeLevel, unsigned int charge) const;
78
79 /** @brief get the list of natural isotopes representing at least a minimum
80 * ratio of the whole isotope pattern
81 * @param charge gives the number of H+, important to take into account for
82 * isotope ratio
83 * @param precision the mass accuracy to take into acount each isotope (C13 !=
84 * H2)
85 * @param minimum_isotope_pattern_ratio the minimum ratio of the isotope
86 * pattern to represent
87 */
88 std::vector<PeptideNaturalIsotopeAverageSp>
89 getByIntensityRatio(unsigned int charge,
90 PrecisionPtr precision,
91 pappso_double minimum_isotope_pattern_ratio) const;
92
93
94 unsigned int size() const;
95 const PeptideInterfaceSp &getPeptideInterfaceSp() const;
96};
97
98
99} // namespace pappso
std::list< PeptideNaturalIsotopeSp >::const_iterator const_iterator
std::list< PeptideNaturalIsotopeSp > msp_peptide_natural_isotope_list
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< const PeptideInterface > PeptideInterfaceSp
double pappso_double
A type definition for doubles.
Definition: types.h:49
std::shared_ptr< const PeptideNaturalIsotopeList > PeptideNaturalIsotopeListSp
peptide natural isotope model