libpappsomspp
Library for mass spectrometry
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peptidefragmention.h
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1/**
2 * \file pappsomspp/peptide/peptidefragmention.h
3 * \date 10/3/2015
4 * \author Olivier Langella
5 * \brief peptide ion 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 <QColor>
35
37#include "peptidefragment.h"
38
39
40namespace pappso
41{
42
43
44class PeptideFragmentIon;
45
46typedef std::shared_ptr<const PeptideFragmentIon> PeptideFragmentIonSp;
47
48
50{
51
52 public:
53 PeptideFragmentIon(const PeptideFragmentSp &sp_fragment,
54 PeptideIon ion_type,
55 unsigned int number_of_neutral_phospho_loss);
56 PeptideFragmentIon(const PeptideFragmentSp &sp_fragment, PeptideIon ion_type);
58 PeptideFragmentIon(PeptideFragmentIon &&toCopy); // move constructor
59 virtual ~PeptideFragmentIon();
60
61 PeptideFragmentIonSp makePeptideFragmentIonSp() const;
62
63 virtual unsigned int size() const override;
64 virtual const QString getSequence() const override;
65 virtual const PeptideFragmentSp &getPeptideFragmentSp() const;
66 virtual int getNumberOfAtom(AtomIsotopeSurvey atom) const override;
67
68 virtual int getNumberOfIsotope(Isotope isotope) const override;
69
70 virtual const QString getName() const override;
71
72 pappso_double getMass() const override;
73
74 const QString getPeptideIonName() const;
75
76 /** @brief get a complete ion name string
77 * @param charge
78 * */
79 const QString getCompletePeptideIonName(unsigned int charge) const;
80
82 static const QString getPeptideIonName(PeptideIon ion_type);
83
84 static const QColor getPeptideIonColor(PeptideIon ion_type);
85
86 PeptideIon getPeptideIonType() const;
88 unsigned int getNumberOfNeutralPhosphoLoss() const;
89
90
91 virtual bool isPalindrome() const override;
92
93
94 private:
97
98 pappso_double m_mass = 0;
99
100 // number of neutral phospho loss. this only occurs on MOD:00696
101 // it loses MOD:00696 + H2O
102 unsigned int m_neutralPhosphoLossNumber = 0;
103};
104
105
106} // namespace pappso
const PeptideFragmentSp msp_fragment
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition types.h:432
PeptideDirection getPeptideIonDirection(PeptideIon ion_type)
get the direction of a peptide ion
Definition peptide.cpp:70
std::shared_ptr< const PeptideFragmentIon > PeptideFragmentIonSp
PeptideDirection
Definition peptide.h:46
AtomIsotopeSurvey
Definition types.h:89
double pappso_double
A type definition for doubles.
Definition types.h:50
Isotope
Definition types.h:104
std::shared_ptr< const PeptideFragment > PeptideFragmentSp
peptide fragment model