| OpenMS 2.5.0

PeptideEvidence.h
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2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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10 // * Redistributions in binary form must reproduce the above copyright
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/Types.h>
38 #include <OpenMS/DATASTRUCTURES/String.h>
39
40 namespace OpenMS
41 {
42
50 class OPENMS_DLLAPI PeptideEvidence
51 {
52 public:
53 static const int UNKNOWN_POSITION; // == -1
54
55 // Note: we use 0 as position of the N-terminus while e.g. mzTab or other formats start counting at 1.
56 static const int N_TERMINAL_POSITION;
57 static const char UNKNOWN_AA; // PeptideEvidence::UNKNOWN_AA = 'X';
58
59 // Note: we use '[' and ']' instead of e.g. '-' as in mzTab specification
60 static const char N_TERMINAL_AA;
61 static const char C_TERMINAL_AA;
62
64 PeptideEvidence();
65
67 PeptideEvidence(const String& accession, Int start, Int end, char aa_before, char aa_after);
68
70 PeptideEvidence(const PeptideEvidence&) = default;
71
73 PeptideEvidence(PeptideEvidence&&) noexcept = default;
74
76 ~PeptideEvidence() {}
78
80 PeptideEvidence& operator=(const PeptideEvidence&) = default;
82 PeptideEvidence& operator=(PeptideEvidence&&) = default; // TODO: add noexcept (gcc 4.8 bug)
83
85 bool operator==(const PeptideEvidence& rhs) const;
86
88 bool operator<(const PeptideEvidence& rhs) const;
89
91 bool operator!=(const PeptideEvidence& rhs) const;
92
94 bool hasValidLimits() const;
95
97 const String& getProteinAccession() const;
98
100 void setProteinAccession(const String& s);
101
103 void setStart(const Int a);
104
106 Int getStart() const;
107
109 void setEnd(const Int a);
110
112 Int getEnd() const;
113
115 void setAABefore(const char acid);
116
118 char getAABefore() const;
119
121 void setAAAfter(const char acid);
122
124 char getAAAfter() const;
125
126 protected:
127 String accession_;
128
129 Int start_;
130
131 Int end_;
132
133 char aa_before_;
134
135 char aa_after_;
136 };
137
138 }
139
OpenMS::PeptideEvidence::aa_after_
char aa_after_
Definition: PeptideEvidence.h:135
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::PeptideEvidence::UNKNOWN_AA
static const char UNKNOWN_AA
Definition: PeptideEvidence.h:57
OpenMS::PeptideEvidence::accession_
String accession_
Definition: PeptideEvidence.h:127
OpenMS::PeptideEvidence::start_
Int start_
Definition: PeptideEvidence.h:129
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::PeptideEvidence::end_
Int end_
Definition: PeptideEvidence.h:131
OpenMS::PeptideEvidence
Representation of a peptide evidence.
Definition: PeptideEvidence.h:50
OpenMS::PeptideEvidence::C_TERMINAL_AA
static const char C_TERMINAL_AA
Definition: PeptideEvidence.h:61
Types.h
OpenMS::PeptideEvidence::N_TERMINAL_POSITION
static const int N_TERMINAL_POSITION
Definition: PeptideEvidence.h:56
String.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::PeptideEvidence::N_TERMINAL_AA
static const char N_TERMINAL_AA
Definition: PeptideEvidence.h:60
int
OpenMS::PeptideEvidence::aa_before_
char aa_before_
Definition: PeptideEvidence.h:133
OpenMS::PeptideEvidence::UNKNOWN_POSITION
static const int UNKNOWN_POSITION
Definition: PeptideEvidence.h:53
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806