OpenMS  2.5.0
OpenPepXLLFAlgorithm Member List

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

add_a_ions_OpenPepXLLFAlgorithmprivate
add_b_ions_OpenPepXLLFAlgorithmprivate
add_c_ions_OpenPepXLLFAlgorithmprivate
add_losses_OpenPepXLLFAlgorithmprivate
add_x_ions_OpenPepXLLFAlgorithmprivate
add_y_ions_OpenPepXLLFAlgorithmprivate
add_z_ions_OpenPepXLLFAlgorithmprivate
check_defaults_DefaultParamHandlerprotected
CMD enum valueProgressLogger
cross_link_mass_OpenPepXLLFAlgorithmprivate
cross_link_mass_mono_link_OpenPepXLLFAlgorithmprivate
cross_link_name_OpenPepXLLFAlgorithmprivate
cross_link_residue1_OpenPepXLLFAlgorithmprivate
cross_link_residue2_OpenPepXLLFAlgorithmprivate
current_logger_ProgressLoggermutableprotected
decoy_prefix_OpenPepXLLFAlgorithmprivate
decoy_string_OpenPepXLLFAlgorithmprivate
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
deisotope_mode_OpenPepXLLFAlgorithmprivate
endProgress() constProgressLogger
enzyme_name_OpenPepXLLFAlgorithmprivate
error_name_DefaultParamHandlerprotected
EXECUTION_OK enum valueOpenPepXLLFAlgorithm
ExitCodes enum nameOpenPepXLLFAlgorithm
fixedModNames_OpenPepXLLFAlgorithmprivate
fragment_mass_tolerance_OpenPepXLLFAlgorithmprivate
fragment_mass_tolerance_unit_ppm_OpenPepXLLFAlgorithmprivate
fragment_mass_tolerance_xlinks_OpenPepXLLFAlgorithmprivate
getDefaults() constDefaultParamHandler
getLogType() constProgressLogger
getName() constDefaultParamHandler
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
GUI enum valueProgressLogger
ILLEGAL_PARAMETERS enum valueOpenPepXLLFAlgorithm
INCOMPATIBLE_INPUT_DATA enum valueOpenPepXLLFAlgorithm
last_invoke_ProgressLoggermutableprotected
LogType enum nameProgressLogger
logTypeToFactoryName_(LogType type)ProgressLoggerprotectedstatic
max_precursor_charge_OpenPepXLLFAlgorithmprivate
max_variable_mods_per_peptide_OpenPepXLLFAlgorithmprivate
min_precursor_charge_OpenPepXLLFAlgorithmprivate
missed_cleavages_OpenPepXLLFAlgorithmprivate
nextProgress() constProgressLogger
NONE enum valueProgressLogger
number_top_hits_OpenPepXLLFAlgorithmprivate
OpenPepXLLFAlgorithm()OpenPepXLLFAlgorithm
OpenMS::operator=(const DefaultParamHandler &rhs)DefaultParamHandlervirtual
OpenMS::ProgressLogger::operator=(const ProgressLogger &other)ProgressLogger
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
peptide_min_size_OpenPepXLLFAlgorithmprivate
precursor_correction_steps_OpenPepXLLFAlgorithmprivate
precursor_mass_tolerance_OpenPepXLLFAlgorithmprivate
precursor_mass_tolerance_unit_ppm_OpenPepXLLFAlgorithmprivate
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
recursion_depth_ProgressLoggerprotectedstatic
run(PeakMap &unprocessed_spectra, std::vector< FASTAFile::FASTAEntry > &fasta_db, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, PeakMap &spectra)OpenPepXLLFAlgorithm
sequence_tag_min_length_OpenPepXLLFAlgorithmprivate
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 valueOpenPepXLLFAlgorithm
updateMembers_() overrideOpenPepXLLFAlgorithmprivatevirtual
use_sequence_tags_OpenPepXLLFAlgorithmprivate
varModNames_OpenPepXLLFAlgorithmprivate
warn_empty_defaults_DefaultParamHandlerprotected
~DefaultParamHandler()DefaultParamHandlervirtual
~OpenPepXLLFAlgorithm() overrideOpenPepXLLFAlgorithm
~ProgressLogger()ProgressLogger
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