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
39namespace pappso
40{
41
42
43class PeptideFragment;
44
45typedef 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
const PeptideSp msp_peptide
AaModificationP m_nterCterCleavage
const PeptideDirection m_direction
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
PeptideDirection getPeptideIonDirection(PeptideIon ion_type)
get the direction of a peptide ion
Definition: peptide.cpp:70
std::shared_ptr< const Peptide > PeptideSp
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 model