64 class GraphInferenceFunctor;
69 class ExtendedGraphInferenceFunctor;
72 struct GridSearchEvaluator;
91 std::vector<ProteinIdentification>& proteinIDs,
92 std::vector<PeptideIdentification>& peptideIDs,
93 bool greedy_group_resolution,
94 std::optional<const ExperimentalDesign> exp_des = std::optional<const ExperimentalDesign>());
109 bool greedy_group_resolution,
110 std::optional<const ExperimentalDesign> exp_des = std::optional<const ExperimentalDesign>());
120 std::vector<double>& alpha_search,
121 std::vector<double>& beta_search,
122 std::vector<double>& gamma_search
141 #ifdef INFERENCE_BENCH
142 std::vector<std::pair<double,Size>> debug_times_;
Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimenta...
Definition: BayesianProteinInferenceAlgorithm.h:52
void setScoreTypeAndSettings_(ProteinIdentification &proteinIDs)
set score type and settings for every ProteinID run processed
std::function< void(PeptideIdentification &)> checkConvertAndFilterPepHits_
Definition: BayesianProteinInferenceAlgorithm.h:137
void resetProteinScores_(ProteinIdentification &protein_id, bool keep_old_as_prior)
reset all protein scores to 0.0, save old ones as Prior MetaValue if requested
~BayesianProteinInferenceAlgorithm() override=default
Destructor.
GridSearch< double, double, double > initGridSearchFromParams_(std::vector< double > &alpha_search, std::vector< double > &beta_search, std::vector< double > &gamma_search)
read Param object and set the grid
void inferPosteriorProbabilities_(Internal::IDBoostGraph &ibg)
void inferPosteriorProbabilities(std::vector< ProteinIdentification > &proteinIDs, std::vector< PeptideIdentification > &peptideIDs, bool greedy_group_resolution, std::optional< const ExperimentalDesign > exp_des=std::optional< const ExperimentalDesign >())
Perform inference. Filter, build graph, run the private inferPosteriorProbabilities_ function....
BayesianProteinInferenceAlgorithm(unsigned int debug_lvl=0)
Constructor.
void inferPosteriorProbabilities(ConsensusMap &cmap, bool greedy_group_resolution, std::optional< const ExperimentalDesign > exp_des=std::optional< const ExperimentalDesign >())
Perform inference. Filter, build graph, run the private inferPosteriorProbabilities_ function....
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
unsigned int debug_lvl_
Definition: BayesianProteinInferenceAlgorithm.h:139
A container for consensus elements.
Definition: ConsensusMap.h:66
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
Definition: GridSearch.h:73
Creates and maintains a boost graph based on the OpenMS ID datastructures.
Definition: IDBoostGraph.h:57
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:39
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:27
Representation of a protein identification run.
Definition: ProteinIdentification.h:50
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19