OpenMS  2.5.0
PrecursorIonSelection Member List

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

check_defaults_DefaultParamHandlerprotected
checkForRequiredUserParams_(FeatureMap &features)PrecursorIonSelectionprivate
convertPeptideIdScores_(std::vector< PeptideIdentification > &pep_ids)PrecursorIonSelectionprivate
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
DEX enum valuePrecursorIonSelection
DOWNSHIFT enum valuePrecursorIonSelection
error_name_DefaultParamHandlerprotected
filterPeptideIds_(std::vector< PeptideIdentification > &pep_ids)PrecursorIonSelectionprivate
filterProtIds_(std::vector< ProteinIdentification > &prot_ids)PrecursorIonSelectionprivate
fraction_counter_PrecursorIonSelectionprivate
getDefaults() constDefaultParamHandler
getLPSolver()PrecursorIonSelectioninline
getMaxScore() constPrecursorIonSelection
getName() constDefaultParamHandler
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() constDefaultParamHandler
getPeptideProteinCounter()PrecursorIonSelectioninline
getSubsections() constDefaultParamHandler
ILP_IPS enum valuePrecursorIonSelection
IPS enum valuePrecursorIonSelection
max_iteration_PrecursorIonSelectionprivate
max_score_PrecursorIonSelectionprivate
min_pep_ids_PrecursorIonSelectionprivate
mz_tolerance_PrecursorIonSelectionprivate
mz_tolerance_unit_PrecursorIonSelectionprivate
operator=(const DefaultParamHandler &rhs)DefaultParamHandlervirtual
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
PrecursorIonSelection()PrecursorIonSelection
PrecursorIonSelection(const PrecursorIonSelection &source)PrecursorIonSelection
prot_id_counter_PrecursorIonSelectionprivate
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)PrecursorIonSelectionprivate
reset()PrecursorIonSelection
setLPSolver(LPWrapper::SOLVER solver)PrecursorIonSelectioninline
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)PrecursorIonSelectionprivate
shiftUp_(FeatureMap &features, PrecursorIonSelectionPreprocessing &preprocessed_db, String protein_acc)PrecursorIonSelectionprivate
simulateILPBasedIPSRun_(FeatureMap &features, PeakMap &experiment, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids, PrecursorIonSelectionPreprocessing &preprocessed_db, String output_path, String precursor_path="")PrecursorIonSelectionprivate
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="")PrecursorIonSelectionprivate
solver_PrecursorIonSelectionprivate
sortByTotalScore(FeatureMap &features)PrecursorIonSelectioninline
SPS enum valuePrecursorIonSelection
subsections_DefaultParamHandlerprotected
Type enum namePrecursorIonSelection
type_PrecursorIonSelectionprivate
updateMembers_() overridePrecursorIonSelectionprivatevirtual
UPSHIFT enum valuePrecursorIonSelection
warn_empty_defaults_DefaultParamHandlerprotected
x_variable_number_PrecursorIonSelectionprivate
~DefaultParamHandler()DefaultParamHandlervirtual
~PrecursorIonSelection() overridePrecursorIonSelection