libpappsomspp
Library for mass spectrometry
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 
36 #include "../exportinmportconfig.h"
37 #include "peptidefragment.h"
38 
39 
40 namespace pappso
41 {
42 
43 
44 class PeptideFragmentIon;
45 
46 typedef 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:386
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:77
double pappso_double
A type definition for doubles.
Definition: types.h:49
Isotope
Definition: types.h:92
std::shared_ptr< const PeptideFragment > PeptideFragmentSp
peptide fragment model