libpappsomspp
Library for mass spectrometry
peptidefragment.h
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1 /**
2  * \file pappsomspp/peptide/peptidefragment.h
3  * \date 10/3/2015
4  * \author Olivier Langella
5  * \brief peptide fragment 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 
32 #pragma once
33 
34 
35 #include "peptide.h"
36 #include "../pappsoexception.h"
37 #include "../exportinmportconfig.h"
38 
39 namespace pappso
40 {
41 
42 
43 class PeptideFragment;
44 
45 typedef std::shared_ptr<const PeptideFragment> PeptideFragmentSp;
46 
48 {
49 
50  public:
51  PeptideFragment(const PeptideSp &sp_peptide,
52  PeptideDirection direction,
53  unsigned int size);
54  PeptideFragment(const PeptideFragment &other);
55  PeptideFragment(PeptideFragment &&toCopy); // move constructor
56  virtual ~PeptideFragment();
57 
58  virtual const PeptideSp &getPeptideSp() const;
59 
60  virtual unsigned int size() const override;
61  virtual const QString getSequence() const override;
62 
63  virtual pappso_double getMass() const override;
64  static const QString getPeptideIonDirectionName(PeptideDirection direction);
66 
67  virtual int getNumberOfAtom(AtomIsotopeSurvey atom) const override;
68  virtual int getNumberOfIsotope(Isotope isotope) const override;
69 
70  virtual bool isPalindrome() const override;
71 
72 
73  private:
76  const unsigned int m_size = 0;
77  // the aa modification to add on Nter or Cter aa (depending on peptide
78  // direction)
80 
81  pappso_double m_mass = 0;
82 };
83 
84 
85 } // namespace pappso
pappso::PeptideFragment::msp_peptide
const PeptideSp msp_peptide
Definition: peptidefragment.h:74
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition: types.h:48
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::Isotope
Isotope
Definition: types.h:91
peptide.h
peptide model
pappso::PeptideFragmentSp
std::shared_ptr< const PeptideFragment > PeptideFragmentSp
Definition: peptidefragment.h:43
pappso::PeptideInterface
Definition: peptideinterface.h:43
pappso::PeptideFragment::m_direction
const PeptideDirection m_direction
Definition: peptidefragment.h:75
pappso::getPeptideIonDirection
PeptideDirection getPeptideIonDirection(PeptideIon ion_type)
get the direction of a peptide ion
Definition: peptide.cpp:54
pappso::PeptideDirection
PeptideDirection
Definition: peptide.h:46
pappso::PeptideFragment::m_nterCterCleavage
AaModificationP m_nterCterCleavage
Definition: peptidefragment.h:79
pappso::PeptideSp
std::shared_ptr< const Peptide > PeptideSp
Definition: aamodification.h:47
pappso::PeptideFragment
Definition: peptidefragment.h:48
pappso::AaModification
Definition: aamodification.h:57
pappso::AtomIsotopeSurvey
AtomIsotopeSurvey
Definition: types.h:76