libpappsomspp
Library for mass spectrometry
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protein.h
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1/**
2 * \file pappsomspp/protein/protein.h
3 * \date 2/7/2015
4 * \author Olivier Langella
5 * \brief object to handle a protein
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#include <QString>
35#include <memory>
36#include "../types.h"
37#include "../exportinmportconfig.h"
38
39namespace pappso
40{
41
42
43class Protein;
44
45/** \brief shared pointer on a Protein object
46 */
47typedef std::shared_ptr<const Protein> ProteinSp;
48
50{
51 private:
52 /** \brief free text to describe the protein */
54 /** \brief a single unique identifier of the protein (usually the first word
55 * of description) */
56 QString m_accession;
57 /** \brief the amino acid sequence */
58 QString m_sequence;
59 /** \brief number of amino acid */
60 unsigned int m_length = 0;
61
62 static QRegularExpression m_removeTranslationStopRegExp;
63
64 public:
65 Protein();
66 Protein(const QString &description, const QString &sequence);
67 Protein(const Protein &protein);
68 ProteinSp makeProteinSp() const;
69
70 bool operator==(const Protein &other) const;
71 ~Protein();
72
73 const QString &getSequence() const;
74
75 void setSequence(const QString &sequence);
76
77 const QString &getAccession() const;
78
79 virtual void setAccession(const QString &accession);
80
81 const QString &getDescription() const;
82
83 void setDescription(const QString &description);
84
85 /** \brief remove * characters at the end of the sequence
86 */
87 Protein &removeTranslationStop();
88
89 /** \brief reverse characters in the sequence
90 */
91 Protein &reverse();
92
93 /** \brief protein amino acid sequence size
94 */
95 unsigned int size() const;
96
97 /** \brief get monoisotopic mass of ProteinSp Protein::makeProteinSp() const
98 */
99 pappso_double getMass() const;
100};
101
102
103} // namespace pappso
QString m_sequence
the amino acid sequence
Definition protein.h:58
static QRegularExpression m_removeTranslationStopRegExp
Definition protein.h:62
QString m_accession
a single unique identifier of the protein (usually the first word of description)
Definition protein.h:56
QString m_description
free text to describe the protein
Definition protein.h:53
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
double pappso_double
A type definition for doubles.
Definition types.h:50
std::shared_ptr< const Protein > ProteinSp
shared pointer on a Protein object
Definition protein.h:47
bool operator==(Aa const &l, Aa const &r)
Definition aa.cpp:341