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PeptideIdentification.h
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34 
35 #ifndef OPENMS_METADATA_PEPTIDEIDENTIFICATION_H
36 #define OPENMS_METADATA_PEPTIDEIDENTIFICATION_H
37 
41 
42 #include <string>
43 #include <map>
44 
45 namespace OpenMS
46 {
63  class OPENMS_DLLAPI PeptideIdentification :
64  public MetaInfoInterface
65  {
66 public:
67 
70 
72 
76  virtual ~PeptideIdentification();
80  PeptideIdentification& operator=(const PeptideIdentification& source);
82  bool operator==(const PeptideIdentification& rhs) const;
84  bool operator!=(const PeptideIdentification& rhs) const;
86 
88  double getRT() const;
90  void setRT(double rt);
92  bool hasRT() const;
93 
95  double getMZ() const;
97  void setMZ(double mz);
99  bool hasMZ() const;
100 
102  const std::vector<PeptideHit>& getHits() const;
104  std::vector<PeptideHit>& getHits();
106  void insertHit(const PeptideHit& hit);
108  void setHits(const std::vector<PeptideHit>& hits);
109 
111  double getSignificanceThreshold() const;
113  void setSignificanceThreshold(double value);
114 
116  const String& getScoreType() const;
118  void setScoreType(const String& type);
119 
121  bool isHigherScoreBetter() const;
123  void setHigherScoreBetter(bool value);
124 
126  const String& getIdentifier() const;
128  void setIdentifier(const String& id);
129 
131  const String& getBaseName() const;
133  void setBaseName(const String& base_name);
134 
136  void assignRanks();
137 
143  void sort();
144 
146  bool empty() const;
147 
149 
150 
152  static std::vector<PeptideHit> getReferencingHits(const std::vector<PeptideHit>&, const std::set<String>& accession);
153 
156  const DataValue& getMetaValue(const String& name) const;
158  void setMetaValue(const String& name, const DataValue& value);
159 
160 
161 protected:
163  std::vector<PeptideHit> hits_;
168  double mz_;
169  double rt_;
170 
171  };
172 
173 } //namespace OpenMS
174 #endif // OPENMS_METADATA_PEPTIDEIDENTIFICATION_H
double significance_threshold_
the peptide significance threshold
Definition: PeptideIdentification.h:164
A more convenient string class.
Definition: String.h:57
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
String score_type_
The score type (Mascot, Sequest, e-value, p-value)
Definition: PeptideIdentification.h:165
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:57
std::vector< PeptideHit > hits_
A list containing the peptide hits.
Definition: PeptideIdentification.h:163
Representation of a peptide hit.
Definition: PeptideHit.h:55
double rt_
Definition: PeptideIdentification.h:169
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:56
PeptideHit HitType
Hit type definition.
Definition: PeptideIdentification.h:69
String id_
Identifier by which ProteinIdentification and PeptideIdentification are matched.
Definition: PeptideIdentification.h:162
double mz_
Definition: PeptideIdentification.h:168
String base_name_
Definition: PeptideIdentification.h:167
bool higher_score_better_
The score orientation.
Definition: PeptideIdentification.h:166
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:28 using doxygen 1.8.9.1