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:35
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:75
std::set< PeptideEvidence > evidence
Definition: ConsensusIDAlgorithm.h:62
double support
Definition: ConsensusIDAlgorithm.h:64
String target_decoy
Definition: ConsensusIDAlgorithm.h:61
std::vector< double > scores
Definition: ConsensusIDAlgorithm.h:57
Size number_of_runs_
Number of ID runs.
Definition: ConsensusIDAlgorithm.h:78
void apply(PeptideIdentificationList &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...
double min_support_
Fraction of required support by other ID runs (input parameter)
Definition: ConsensusIDAlgorithm.h:81
bool count_empty_
Count empty runs in "min_support" calculation? (input parameter)
Definition: ConsensusIDAlgorithm.h:84
Int charge
Definition: ConsensusIDAlgorithm.h:56
std::map< AASequence, HitInfo > SequenceGrouping
Mapping: peptide sequence -> (charge, scores)
Definition: ConsensusIDAlgorithm.h:72
void apply(PeptideIdentificationList &ids, Size number_of_runs=0)
bool keep_old_scores_
Keep old scores?
Definition: ConsensusIDAlgorithm.h:87
ConsensusIDAlgorithm()
Default constructor.
double final_score
Definition: ConsensusIDAlgorithm.h:63
void updateMembers_() override
Docu in base class.
ConsensusIDAlgorithm(const ConsensusIDAlgorithm &)=delete
Not implemented.
std::vector< String > types
Definition: ConsensusIDAlgorithm.h:58
virtual void apply_(PeptideIdentificationList &ids, const std::map< String, String > &se_info, SequenceGrouping &results)=0
Consensus computation (to be implemented by subclasses).
ConsensusIDAlgorithm & operator=(const ConsensusIDAlgorithm &)=delete
Not implemented.
~ConsensusIDAlgorithm() override
Virtual destructor.
Definition: ConsensusIDAlgorithm.h:55
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
Container for peptide identifications from multiple spectra.
Definition: PeptideIdentificationList.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