46 void apply(std::vector<PeptideIdentification>& ids,
const std::map<String, String>& se_info,
Size number_of_runs = 0);
48 void apply(std::vector<PeptideIdentification>& ids,
Size number_of_runs = 0);
98 virtual void apply_(std::vector<PeptideIdentification>& ids,
const std::map<String, String>& se_info,
SequenceGrouping& results) = 0;
Representation of a peptide/protein sequence.
Definition: AASequence.h:86
Abstract base class for all ConsensusID algorithms (that calculate a consensus from multiple ID runs)...
Definition: ConsensusIDAlgorithm.h:34
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:74
std::set< PeptideEvidence > evidence
Definition: ConsensusIDAlgorithm.h:61
double support
Definition: ConsensusIDAlgorithm.h:63
String target_decoy
Definition: ConsensusIDAlgorithm.h:60
std::vector< double > scores
Definition: ConsensusIDAlgorithm.h:56
Size number_of_runs_
Number of ID runs.
Definition: ConsensusIDAlgorithm.h:77
double min_support_
Fraction of required support by other ID runs (input parameter)
Definition: ConsensusIDAlgorithm.h:80
bool count_empty_
Count empty runs in "min_support" calculation? (input parameter)
Definition: ConsensusIDAlgorithm.h:83
Int charge
Definition: ConsensusIDAlgorithm.h:55
std::map< AASequence, HitInfo > SequenceGrouping
Mapping: peptide sequence -> (charge, scores)
Definition: ConsensusIDAlgorithm.h:71
bool keep_old_scores_
Keep old scores?
Definition: ConsensusIDAlgorithm.h:86
ConsensusIDAlgorithm()
Default constructor.
double final_score
Definition: ConsensusIDAlgorithm.h:62
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.
ConsensusIDAlgorithm(const ConsensusIDAlgorithm &)=delete
Not implemented.
std::vector< String > types
Definition: ConsensusIDAlgorithm.h:57
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 & operator=(const ConsensusIDAlgorithm &)=delete
Not implemented.
~ConsensusIDAlgorithm() override
Virtual destructor.
Definition: ConsensusIDAlgorithm.h:54
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
A more convenient string class.
Definition: String.h:34
int Int
Signed integer type.
Definition: Types.h:72
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19