OpenMS  3.0.0
PeptideEvidence.h
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31 // $Maintainer: Timo Sachsenberg $
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34 
35 #pragma once
36 
37 #include <OpenMS/CONCEPT/Types.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 
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 
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:
128 
130 
132 
134 
135  char aa_after_;
136  };
137 
138 }
139 
Types.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::PeptideEvidence::aa_before_
char aa_before_
Definition: PeptideEvidence.h:133
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::PeptideEvidence::end_
Int end_
Definition: PeptideEvidence.h:131
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS::PeptideEvidence::N_TERMINAL_AA
static const char N_TERMINAL_AA
Definition: PeptideEvidence.h:60
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::PeptideEvidence::UNKNOWN_POSITION
static const int UNKNOWN_POSITION
Definition: PeptideEvidence.h:53
OpenMS::PeptideEvidence::aa_after_
char aa_after_
Definition: PeptideEvidence.h:135
OpenMS::PeptideEvidence::UNKNOWN_AA
static const char UNKNOWN_AA
Definition: PeptideEvidence.h:57
OpenMS::PeptideEvidence
Representation of a peptide evidence.
Definition: PeptideEvidence.h:50
OpenMS::PeptideEvidence::N_TERMINAL_POSITION
static const int N_TERMINAL_POSITION
Definition: PeptideEvidence.h:56
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::PeptideEvidence::C_TERMINAL_AA
static const char C_TERMINAL_AA
Definition: PeptideEvidence.h:61
String.h
OpenMS::PeptideEvidence::accession_
String accession_
Definition: PeptideEvidence.h:127
OpenMS::PeptideEvidence::start_
Int start_
Definition: PeptideEvidence.h:129