PrecursorIonSelection Member List

This is the complete list of members for PrecursorIonSelection, including all inherited members.

check_defaults_	DefaultParamHandler	protected
checkForRequiredUserParams_(FeatureMap &features)	PrecursorIonSelection	private
convertPeptideIdScores_(std::vector< PeptideIdentification > &pep_ids)	PrecursorIonSelection	private
DefaultParamHandler(const String &name)	DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)	DefaultParamHandler
defaults_	DefaultParamHandler	protected
defaultsToParam_()	DefaultParamHandler	protected
DEX enum value	PrecursorIonSelection
DOWNSHIFT enum value	PrecursorIonSelection
error_name_	DefaultParamHandler	protected
filterPeptideIds_(std::vector< PeptideIdentification > &pep_ids)	PrecursorIonSelection	private
filterProtIds_(std::vector< ProteinIdentification > &prot_ids)	PrecursorIonSelection	private
fraction_counter_	PrecursorIonSelection	private
getDefaults() const	DefaultParamHandler
getLPSolver()	PrecursorIonSelection	inline
getMaxScore() const	PrecursorIonSelection
getName() const	DefaultParamHandler
getNextPrecursors(FeatureMap &features, FeatureMap &next_features, UInt number)	PrecursorIonSelection
getNextPrecursors(std::vector< Int > &solution_indices, std::vector< PSLPFormulation::IndexTriple > &variable_indices, std::set< Int > &measured_variables, FeatureMap &features, FeatureMap &new_features, UInt step_size, PSLPFormulation &ilp)	PrecursorIonSelection
getNextPrecursorsSeq(FeatureMap &features, FeatureMap &next_features, UInt number, double &rt)	PrecursorIonSelection
getParameters() const	DefaultParamHandler
getPeptideProteinCounter()	PrecursorIonSelection	inline
getSubsections() const	DefaultParamHandler
ILP_IPS enum value	PrecursorIonSelection
IPS enum value	PrecursorIonSelection
max_iteration_	PrecursorIonSelection	private
max_score_	PrecursorIonSelection	private
min_pep_ids_	PrecursorIonSelection	private
mz_tolerance_	PrecursorIonSelection	private
mz_tolerance_unit_	PrecursorIonSelection	private
operator=(const DefaultParamHandler &rhs)	DefaultParamHandler	virtual
operator==(const DefaultParamHandler &rhs) const	DefaultParamHandler	virtual
param_	DefaultParamHandler	protected
PrecursorIonSelection()	PrecursorIonSelection
PrecursorIonSelection(const PrecursorIonSelection &source)	PrecursorIonSelection
prot_id_counter_	PrecursorIonSelection	private
rescore(FeatureMap &features, std::vector< PeptideIdentification > &new_pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, bool check_meta_values=true)	PrecursorIonSelection
rescore_(FeatureMap &features, std::vector< PeptideIdentification > &new_pep_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, PSProteinInference &protein_inference)	PrecursorIonSelection	private
reset()	PrecursorIonSelection
setLPSolver(LPWrapper::SOLVER solver)	PrecursorIonSelection	inline
setMaxScore(const double &max_score)	PrecursorIonSelection
setName(const String &name)	DefaultParamHandler
setParameters(const Param &param)	DefaultParamHandler
shiftDown_(FeatureMap &features, PrecursorIonSelectionPreprocessing &preprocessed_db, String protein_acc)	PrecursorIonSelection	private
shiftUp_(FeatureMap &features, PrecursorIonSelectionPreprocessing &preprocessed_db, String protein_acc)	PrecursorIonSelection	private
simulateILPBasedIPSRun_(FeatureMap &features, PeakMap &experiment, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, String output_path, String precursor_path="")	PrecursorIonSelection	private
simulateRun(FeatureMap &features, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, String path, PeakMap &experiment, String precursor_path="")	PrecursorIonSelection
simulateRun_(FeatureMap &features, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, String path, String precursor_path="")	PrecursorIonSelection	private
solver_	PrecursorIonSelection	private
sortByTotalScore(FeatureMap &features)	PrecursorIonSelection	inline
SPS enum value	PrecursorIonSelection
subsections_	DefaultParamHandler	protected
Type enum name	PrecursorIonSelection
type_	PrecursorIonSelection	private
updateMembers_() override	PrecursorIonSelection	privatevirtual
UPSHIFT enum value	PrecursorIonSelection
warn_empty_defaults_	DefaultParamHandler	protected
x_variable_number_	PrecursorIonSelection	private
~DefaultParamHandler()	DefaultParamHandler	virtual
~PrecursorIonSelection() override	PrecursorIonSelection