73 void apply(std::vector<PeptideIdentification>& ids,
74 const std::map<String, String>& se_info,
75 Size number_of_runs = 0);
77 void apply(std::vector<PeptideIdentification>& ids,
78 Size number_of_runs = 0);
102 typedef std::map<AASequence, HitInfo>
130 virtual void apply_(std::vector<PeptideIdentification>& ids,
131 const std::map<String, String>& se_info,
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