| OpenMS 2.5.0

ProteinHit.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <vector>
38 #include <functional>
39 #include <set>
40 #include <map>
41
42 #include <OpenMS/CHEMISTRY/ResidueModification.h>
43 #include <OpenMS/CONCEPT/Types.h>
44 #include <OpenMS/DATASTRUCTURES/String.h>
45 #include <OpenMS/METADATA/MetaInfoInterface.h>
46
47 namespace OpenMS
48 {
57 class OPENMS_DLLAPI ProteinHit :
58 public MetaInfoInterface
59 {
60 public:
61 static const double COVERAGE_UNKNOWN; // == -1
62
64
65 class OPENMS_DLLAPI ProteinHitAccessionHash
67 {
68 public:
69 size_t operator()(const ProteinHit & p)
70 {
71 return std::hash<std::string>{}(p.getAccession());
72 }
73
74 };
75 class OPENMS_DLLAPI ProteinHitPtrAccessionHash
76 {
77 public:
78 size_t operator()(const ProteinHit * p)
79 {
80 return std::hash<std::string>{}(p->getAccession());
81 }
82
83 };
85
87
88 class OPENMS_DLLAPI ScoreMore
90 {
91 public:
92 template <typename Arg>
93 bool operator()(const Arg & a, const Arg & b)
94 {
95 #pragma clang diagnostic push
96 #pragma clang diagnostic ignored "-Wfloat-equal"
97 if (a.getScore() != b.getScore())
98 #pragma clang diagnostic pop
99 {
100 return a.getScore() > b.getScore();
101 }
102 return a.getAccession() > b.getAccession();
103 }
104
105 };
106
108 class OPENMS_DLLAPI ScoreLess
109 {
110 public:
111 template <typename Arg>
112 bool operator()(const Arg & a, const Arg & b)
113 {
114 #pragma clang diagnostic push
115 #pragma clang diagnostic ignored "-Wfloat-equal"
116 if (a.getScore() != b.getScore())
117 #pragma clang diagnostic pop
118 {
119 return a.getScore() < b.getScore();
120 }
121 return a.getAccession() < b.getAccession();
122 }
123
124 };
126
129
131 ProteinHit();
132
134 ProteinHit(double score, UInt rank, String accession, String sequence);
135
137 ProteinHit(const ProteinHit &) = default;
138
140 ProteinHit(ProteinHit&&) = default;
141
143
145 ProteinHit & operator=(const ProteinHit &) = default;
146
148 ProteinHit& operator=(ProteinHit&&) = default; // TODO: add noexcept (gcc 4.8 bug)
149
151 ProteinHit & operator=(const MetaInfoInterface & source);
152
154 bool operator==(const ProteinHit & rhs) const;
155
157 bool operator!=(const ProteinHit & rhs) const;
158
159
162
164 double getScore() const;
165
167 UInt getRank() const;
168
170 const String & getSequence() const;
171
173 const String & getAccession() const;
174
176 String getDescription() const;
177
179 double getCoverage() const;
180
182 void setScore(const double score);
183
185 void setRank(UInt newrank);
186
188 void setSequence(const String & sequence);
189
191 void setAccession(const String & accession);
192
194 void setDescription(const String & description);
195
197 void setCoverage(const double coverage);
198
200 const std::set<std::pair<Size, ResidueModification> >& getModifications() const;
201
203 void setModifications(std::set<std::pair<Size, ResidueModification> >& mods);
205
206 protected:
207 double score_;
208 UInt rank_;
209 String accession_;
210 String sequence_;
211 double coverage_;
212 std::set<std::pair<Size, ResidueModification> > modifications_;
213 };
214
215 } // namespace OpenMS
216
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ProteinHit::ScoreLess
Lesser predicate for scores of hits.
Definition: ProteinHit.h:108
OpenMS::ProteinHit::ProteinHitAccessionHash
Hash of a ProteinHit based on its accession only!
Definition: ProteinHit.h:66
OpenMS::ProteinHit::getAccession
const String & getAccession() const
returns the accession of the protein
OpenMS::ProteinHit::COVERAGE_UNKNOWN
static const double COVERAGE_UNKNOWN
Definition: ProteinHit.h:61
OpenMS::ProteinHit::ScoreLess::operator()
bool operator()(const Arg &a, const Arg &b)
Definition: ProteinHit.h:112
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:57
OpenMS::ProteinHit::ProteinHitAccessionHash::operator()
size_t operator()(const ProteinHit &p)
Definition: ProteinHit.h:69
OpenMS::ProteinHit::rank_
UInt rank_
the position(rank) where the hit appeared in the hit list
Definition: ProteinHit.h:208
OpenMS::ProteinHit::modifications_
std::set< std::pair< Size, ResidueModification > > modifications_
modified positions in a protein
Definition: ProteinHit.h:212
Types.h
String.h
OpenMS::ProteinHit::accession_
String accession_
the protein identifier
Definition: ProteinHit.h:209
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProteinHit::sequence_
String sequence_
the amino acid sequence of the protein hit
Definition: ProteinHit.h:210
OpenMS::ProteinHit::coverage_
double coverage_
coverage of the protein based upon the matched peptide sequences
Definition: ProteinHit.h:211
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
MetaInfoInterface.h
OpenMS::ProteinHit::score_
double score_
the score of the protein hit
Definition: ProteinHit.h:207
OpenMS::ProteinHit::ProteinHitPtrAccessionHash
Definition: ProteinHit.h:75
OpenMS::ProteinHit::ScoreMore::operator()
bool operator()(const Arg &a, const Arg &b)
Definition: ProteinHit.h:93
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
ResidueModification.h
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
OpenMS::ProteinHit::ProteinHitPtrAccessionHash::operator()
size_t operator()(const ProteinHit *p)
Definition: ProteinHit.h:78