| OpenMS 2.5.0

OpenPepXLAlgorithm Member List

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

add_a_ions_ | OpenPepXLAlgorithm | private
add_b_ions_ | OpenPepXLAlgorithm | private
add_c_ions_ | OpenPepXLAlgorithm | private
add_losses_ | OpenPepXLAlgorithm | private
add_x_ions_ | OpenPepXLAlgorithm | private
add_y_ions_ | OpenPepXLAlgorithm | private
add_z_ions_ | OpenPepXLAlgorithm | private
check_defaults_ | DefaultParamHandler | protected
CMD enum value | ProgressLogger |
cross_link_mass_iso_shift_ | OpenPepXLAlgorithm | private
cross_link_mass_light_ | OpenPepXLAlgorithm | private
cross_link_mass_mono_link_ | OpenPepXLAlgorithm | private
cross_link_name_ | OpenPepXLAlgorithm | private
cross_link_residue1_ | OpenPepXLAlgorithm | private
cross_link_residue2_ | OpenPepXLAlgorithm | private
current_logger_ | ProgressLogger | mutable protected
decoy_prefix_ | OpenPepXLAlgorithm | private
decoy_string_ | OpenPepXLAlgorithm | private
DefaultParamHandler(const String &name) | DefaultParamHandler |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler |
defaults_ | DefaultParamHandler | protected
defaultsToParam_() | DefaultParamHandler | protected
deisotope_mode_ | OpenPepXLAlgorithm | private
endProgress() const | ProgressLogger |
enzyme_name_ | OpenPepXLAlgorithm | private
error_name_ | DefaultParamHandler | protected
EXECUTION_OK enum value | OpenPepXLAlgorithm |
ExitCodes enum name | OpenPepXLAlgorithm |
fixedModNames_ | OpenPepXLAlgorithm | private
fragment_mass_tolerance_ | OpenPepXLAlgorithm | private
fragment_mass_tolerance_unit_ppm_ | OpenPepXLAlgorithm | private
fragment_mass_tolerance_xlinks_ | OpenPepXLAlgorithm | private
getDefaults() const | DefaultParamHandler |
getLogType() const | ProgressLogger |
getName() const | DefaultParamHandler |
getParameters() const | DefaultParamHandler |
getSubsections() const | DefaultParamHandler |
GUI enum value | ProgressLogger |
ILLEGAL_PARAMETERS enum value | OpenPepXLAlgorithm |
INCOMPATIBLE_INPUT_DATA enum value | OpenPepXLAlgorithm |
last_invoke_ | ProgressLogger | mutable protected
LogType enum name | ProgressLogger |
logTypeToFactoryName_(LogType type) | ProgressLogger | protected static
max_precursor_charge_ | OpenPepXLAlgorithm | private
max_variable_mods_per_peptide_ | OpenPepXLAlgorithm | private
min_precursor_charge_ | OpenPepXLAlgorithm | private
missed_cleavages_ | OpenPepXLAlgorithm | private
nextProgress() const | ProgressLogger |
NONE enum value | ProgressLogger |
number_top_hits_ | OpenPepXLAlgorithm | private
OpenPepXLAlgorithm() | OpenPepXLAlgorithm |
OpenMS::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual
OpenMS::ProgressLogger::operator=(const ProgressLogger &other) | ProgressLogger |
operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual
param_ | DefaultParamHandler | protected
peptide_min_size_ | OpenPepXLAlgorithm | private
precursor_correction_steps_ | OpenPepXLAlgorithm | private
precursor_mass_tolerance_ | OpenPepXLAlgorithm | private
precursor_mass_tolerance_unit_ppm_ | OpenPepXLAlgorithm | private
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) | OpenPepXLAlgorithm | private static
ProgressLogger() | ProgressLogger |
ProgressLogger(const ProgressLogger &other) | ProgressLogger |
recursion_depth_ | ProgressLogger | protected static
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 |
setLogType(LogType type) const | ProgressLogger |
setName(const String &name) | DefaultParamHandler |
setParameters(const Param &param) | DefaultParamHandler |
setProgress(SignedSize value) const | ProgressLogger |
startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger |
subsections_ | DefaultParamHandler | protected
type_ | ProgressLogger | mutable protected
UNEXPECTED_RESULT enum value | OpenPepXLAlgorithm |
updateMembers_() override | OpenPepXLAlgorithm | private virtual
varModNames_ | OpenPepXLAlgorithm | private
warn_empty_defaults_ | DefaultParamHandler | protected
~DefaultParamHandler() | DefaultParamHandler | virtual
~OpenPepXLAlgorithm() override | OpenPepXLAlgorithm |
~ProgressLogger() | ProgressLogger |