OpenMS  2.4.0
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();
79  PeptideIdentification& operator=(const PeptideIdentification& source);
81  bool operator==(const PeptideIdentification& rhs) const;
83  bool operator!=(const PeptideIdentification& rhs) const;
85 
87  double getRT() const;
89  void setRT(double rt);
91  bool hasRT() const;
92 
94  double getMZ() const;
96  void setMZ(double mz);
98  bool hasMZ() const;
99 
101  const std::vector<PeptideHit>& getHits() const;
103  std::vector<PeptideHit>& getHits();
105  void insertHit(const PeptideHit& hit);
107  void setHits(const std::vector<PeptideHit>& hits);
108 
110  double getSignificanceThreshold() const;
112  void setSignificanceThreshold(double value);
113 
115  const String& getScoreType() const;
117  void setScoreType(const String& type);
118 
120  bool isHigherScoreBetter() const;
122  void setHigherScoreBetter(bool value);
123 
125  const String& getIdentifier() const;
127  void setIdentifier(const String& id);
128 
130  const String& getBaseName() const;
132  void setBaseName(const String& base_name);
133 
135  const String getExperimentLabel() const;
137  void setExperimentLabel(const String& type);
138 
140  void assignRanks();
141 
147  void sort();
148 
154  void sortByRank();
155 
157  bool empty() const;
158 
160  static std::vector<PeptideHit> getReferencingHits(const std::vector<PeptideHit>&, const std::set<String>& accession);
161 
162 protected:
163 
165  std::vector<PeptideHit> hits_;
169  // hint: here is an alignment gap of 7 bytes <-- here --> use it when introducing new members with sizeof(m)<=4
171  double mz_;
172  double rt_;
173 
174  };
175 
176 } //namespace OpenMS
double significance_threshold_
the peptide significance threshold
Definition: PeptideIdentification.h:166
A more convenient string class.
Definition: String.h:57
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
String score_type_
The score type (Mascot, Sequest, e-value, p-value)
Definition: PeptideIdentification.h:167
std::vector< PeptideHit > hits_
A list containing the peptide hits.
Definition: PeptideIdentification.h:165
Representation of a peptide hit.
Definition: PeptideHit.h:54
double rt_
Definition: PeptideIdentification.h:172
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:55
PeptideHit HitType
Hit type definition.
Definition: PeptideIdentification.h:68
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
String id_
Identifier by which ProteinIdentification and PeptideIdentification are matched.
Definition: PeptideIdentification.h:164
double mz_
Definition: PeptideIdentification.h:171
String base_name_
Definition: PeptideIdentification.h:170
bool higher_score_better_
The score orientation.
Definition: PeptideIdentification.h:168
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62