OpenMS  2.8.0
ConsensusIDAlgorithm.h
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31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Andreas Bertsch, Marc Sturm, Sven Nahnsen, Hendrik Weisser $
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34 
35 #pragma once
36 
39 
40 #include <map>
41 #include <vector>
42 
43 namespace OpenMS
44 {
59  class OPENMS_DLLAPI ConsensusIDAlgorithm :
60  public DefaultParamHandler
61  {
62  public:
73  void apply(std::vector<PeptideIdentification>& ids,
74  const std::map<String, String>& se_info,
75  Size number_of_runs = 0);
76 
77  void apply(std::vector<PeptideIdentification>& ids,
78  Size number_of_runs = 0);
79 
82 
83  protected:
84  struct HitInfo
85  {
87  std::vector<double> scores;
88  std::vector<String> types;
89  // in case too much information is stored, TD and evidence
90  // could be re-annotated with PeptideIndexer later
92  std::set<PeptideEvidence> evidence;
93  double final_score;
94  double support;
95  //TODO: we could gather spectrum_refs here as well,
96  // to support passing of spectrum_ref if ALL refs of a group are the same
97  // For now, we do it in the ConsensusID TOPP tool class in cases where we
98  // know that refs will be the same.
99  };
100 
102  typedef std::map<AASequence, HitInfo>
104 
107 
110 
112  double min_support_;
113 
116 
119 
122 
130  virtual void apply_(std::vector<PeptideIdentification>& ids,
131  const std::map<String, String>& se_info,
132  SequenceGrouping& results) = 0;
133 
135  void updateMembers_() override;
136 
138  void compareChargeStates_(Int& recorded_charge, Int new_charge,
139  const AASequence& peptide);
140 
141  private:
144 
147 
148  };
149 
150 } // namespace OpenMS
151 
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
Abstract base class for all ConsensusID algorithms (that calculate a consensus from multiple ID runs)...
Definition: ConsensusIDAlgorithm.h:61
void compareChargeStates_(Int &recorded_charge, Int new_charge, const AASequence &peptide)
Compare (and possibly update) charge state information.
Size considered_hits_
Number of peptide hits considered per ID run (input parameter)
Definition: ConsensusIDAlgorithm.h:106
ConsensusIDAlgorithm(const ConsensusIDAlgorithm &)
Not implemented.
std::set< PeptideEvidence > evidence
Definition: ConsensusIDAlgorithm.h:92
double support
Definition: ConsensusIDAlgorithm.h:94
String target_decoy
Definition: ConsensusIDAlgorithm.h:91
std::vector< double > scores
Definition: ConsensusIDAlgorithm.h:87
Size number_of_runs_
Number of ID runs.
Definition: ConsensusIDAlgorithm.h:109
double min_support_
Fraction of required support by other ID runs (input parameter)
Definition: ConsensusIDAlgorithm.h:112
bool count_empty_
Count empty runs in "min_support" calculation? (input parameter)
Definition: ConsensusIDAlgorithm.h:115
ConsensusIDAlgorithm & operator=(const ConsensusIDAlgorithm &)
Not implemented.
Int charge
Definition: ConsensusIDAlgorithm.h:86
std::map< AASequence, HitInfo > SequenceGrouping
Mapping: peptide sequence -> (charge, scores)
Definition: ConsensusIDAlgorithm.h:103
bool keep_old_scores_
Keep old scores?
Definition: ConsensusIDAlgorithm.h:118
ConsensusIDAlgorithm()
Default constructor.
double final_score
Definition: ConsensusIDAlgorithm.h:93
virtual void apply_(std::vector< PeptideIdentification > &ids, const std::map< String, String > &se_info, SequenceGrouping &results)=0
Consensus computation (to be implemented by subclasses).
void apply(std::vector< PeptideIdentification > &ids, Size number_of_runs=0)
void updateMembers_() override
Docu in base class.
std::vector< String > types
Definition: ConsensusIDAlgorithm.h:88
void apply(std::vector< PeptideIdentification > &ids, const std::map< String, String > &se_info, Size number_of_runs=0)
Calculates the consensus ID for a set of peptide identifications of one spectrum or (consensus) featu...
~ConsensusIDAlgorithm() override
Virtual destructor.
Definition: ConsensusIDAlgorithm.h:85
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:93
A more convenient string class.
Definition: String.h:60
int Int
Signed integer type.
Definition: Types.h:102
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47