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OpenPepXLAlgorithm Member List

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

add_a_ions_OpenPepXLAlgorithmprivate
add_b_ions_OpenPepXLAlgorithmprivate
add_c_ions_OpenPepXLAlgorithmprivate
add_losses_OpenPepXLAlgorithmprivate
add_x_ions_OpenPepXLAlgorithmprivate
add_y_ions_OpenPepXLAlgorithmprivate
add_z_ions_OpenPepXLAlgorithmprivate
check_defaults_DefaultParamHandlerprotected
CMD enum valueProgressLogger
cross_link_mass_iso_shift_OpenPepXLAlgorithmprivate
cross_link_mass_light_OpenPepXLAlgorithmprivate
cross_link_mass_mono_link_OpenPepXLAlgorithmprivate
cross_link_name_OpenPepXLAlgorithmprivate
cross_link_residue1_OpenPepXLAlgorithmprivate
cross_link_residue2_OpenPepXLAlgorithmprivate
current_logger_ProgressLoggermutableprotected
decoy_prefix_OpenPepXLAlgorithmprivate
decoy_string_OpenPepXLAlgorithmprivate
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
deisotope_mode_OpenPepXLAlgorithmprivate
endProgress(UInt64 bytes_processed=0) constProgressLogger
enzyme_name_OpenPepXLAlgorithmprivate
error_name_DefaultParamHandlerprotected
EXECUTION_OK enum valueOpenPepXLAlgorithm
ExitCodes enum nameOpenPepXLAlgorithm
fixedModNames_OpenPepXLAlgorithmprivate
fragment_mass_tolerance_OpenPepXLAlgorithmprivate
fragment_mass_tolerance_unit_ppm_OpenPepXLAlgorithmprivate
fragment_mass_tolerance_xlinks_OpenPepXLAlgorithmprivate
getDefaults() constDefaultParamHandler
getLogType() constProgressLogger
getName() constDefaultParamHandler
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
GUI enum valueProgressLogger
ILLEGAL_PARAMETERS enum valueOpenPepXLAlgorithm
INCOMPATIBLE_INPUT_DATA enum valueOpenPepXLAlgorithm
last_invoke_ProgressLoggermutableprotected
LogType enum nameProgressLogger
max_precursor_charge_OpenPepXLAlgorithmprivate
max_variable_mods_per_peptide_OpenPepXLAlgorithmprivate
min_precursor_charge_OpenPepXLAlgorithmprivate
missed_cleavages_OpenPepXLAlgorithmprivate
nextProgress() constProgressLogger
NONE enum valueProgressLogger
number_top_hits_OpenPepXLAlgorithmprivate
OpenPepXLAlgorithm()OpenPepXLAlgorithm
OpenMS::operator=(const DefaultParamHandler &rhs)DefaultParamHandler
OpenMS::ProgressLogger::operator=(const ProgressLogger &other)ProgressLogger
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
peptide_min_size_OpenPepXLAlgorithmprivate
precursor_correction_steps_OpenPepXLAlgorithmprivate
precursor_mass_tolerance_OpenPepXLAlgorithmprivate
precursor_mass_tolerance_unit_ppm_OpenPepXLAlgorithmprivate
preprocessPairs_(const PeakMap &spectra, const std::vector< std::pair< Size, Size > > &spectrum_pairs, const double cross_link_mass_iso_shift, double fragment_mass_tolerance, double fragment_mass_tolerance_xlinks, bool fragment_mass_tolerance_unit_ppm, bool deisotope)OpenPepXLAlgorithmprivatestatic
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
recursion_depth_ProgressLoggerprotectedstatic
run(PeakMap &unprocessed_spectra, ConsensusMap &cfeatures, std::vector< FASTAFile::FASTAEntry > &fasta_db, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, OPXLDataStructs::PreprocessedPairSpectra &preprocessed_pair_spectra, std::vector< std::pair< Size, Size > > &spectrum_pairs, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, PeakMap &spectra)OpenPepXLAlgorithm
setLogger(ProgressLoggerImpl *logger)ProgressLogger
setLogType(LogType type) constProgressLogger
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
setProgress(SignedSize value) constProgressLogger
startProgress(SignedSize begin, SignedSize end, const String &label) constProgressLogger
subsections_DefaultParamHandlerprotected
type_ProgressLoggermutableprotected
UNEXPECTED_RESULT enum valueOpenPepXLAlgorithm
updateMembers_() overrideOpenPepXLAlgorithmprivatevirtual
varModNames_OpenPepXLAlgorithmprivate
warn_empty_defaults_DefaultParamHandlerprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
~DefaultParamHandler()DefaultParamHandlervirtual
~OpenPepXLAlgorithm() overrideOpenPepXLAlgorithm
~ProgressLogger()ProgressLoggervirtual