OpenMS  2.5.0
PeptideIdentification.h
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34 
35 #pragma once
36 
40 
41 #include <string>
42 #include <map>
43 
44 namespace OpenMS
45 {
62  class OPENMS_DLLAPI PeptideIdentification :
63  public MetaInfoInterface
64  {
65 public:
66 
69 
71 
75  virtual ~PeptideIdentification() noexcept;
79  PeptideIdentification(PeptideIdentification&&) noexcept = default;
80 
82  PeptideIdentification& operator=(const PeptideIdentification&) = default;
84  PeptideIdentification& operator=(PeptideIdentification&&) = default; // TODO: add noexcept (gcc 4.8 bug)
86  bool operator==(const PeptideIdentification& rhs) const;
88  bool operator!=(const PeptideIdentification& rhs) const;
90 
92  double getRT() const;
94  void setRT(double rt);
96  bool hasRT() const;
97 
99  double getMZ() const;
101  void setMZ(double mz);
103  bool hasMZ() const;
104 
106  const std::vector<PeptideHit>& getHits() const;
108  std::vector<PeptideHit>& getHits();
110  void insertHit(const PeptideHit& hit);
112  void insertHit(PeptideHit&& hit);
114  void setHits(const std::vector<PeptideHit>& hits);
115 
117  double getSignificanceThreshold() const;
119  void setSignificanceThreshold(double value);
120 
122  const String& getScoreType() const;
124  void setScoreType(const String& type);
125 
127  bool isHigherScoreBetter() const;
129  void setHigherScoreBetter(bool value);
130 
132  const String& getIdentifier() const;
134  void setIdentifier(const String& id);
135 
137  const String& getBaseName() const;
139  void setBaseName(const String& base_name);
140 
142  const String getExperimentLabel() const;
144  void setExperimentLabel(const String& type);
145 
147  void assignRanks();
148 
154  void sort();
155 
161  void sortByRank();
162 
164  bool empty() const;
165 
167  static std::vector<PeptideHit> getReferencingHits(const std::vector<PeptideHit>&, const std::set<String>& accession);
168 
169 protected:
170 
171  String id_;
172  std::vector<PeptideHit> hits_;
173  double significance_threshold_;
174  String score_type_;
175  bool higher_score_better_;
176  // hint: here is an alignment gap of 7 bytes <-- here --> use it when introducing new members with sizeof(m)<=4
177  String base_name_;
178  double mz_;
179  double rt_;
180 
181  };
182 
183 } //namespace OpenMS
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
PeptideHit.h
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
ProteinHit.h
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
MetaInfoInterface.h
OpenMS::PeptideIdentification::HitType
PeptideHit HitType
Hit type definition.
Definition: PeptideIdentification.h:68
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54