| OpenMS 2.5.0

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 | private virtual
UPSHIFT enum value | PrecursorIonSelection |
warn_empty_defaults_ | DefaultParamHandler | protected
x_variable_number_ | PrecursorIonSelection | private
~DefaultParamHandler() | DefaultParamHandler | virtual
~PrecursorIonSelection() override | PrecursorIonSelection |