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OpenPepXLLFAlgorithm Member List
This is the complete list of members for
OpenPepXLLFAlgorithm
, including all inherited members.
add_a_ions_
OpenPepXLLFAlgorithm
private
add_b_ions_
OpenPepXLLFAlgorithm
private
add_c_ions_
OpenPepXLLFAlgorithm
private
add_losses_
OpenPepXLLFAlgorithm
private
add_x_ions_
OpenPepXLLFAlgorithm
private
add_y_ions_
OpenPepXLLFAlgorithm
private
add_z_ions_
OpenPepXLLFAlgorithm
private
check_defaults_
DefaultParamHandler
protected
CMD
enum value
ProgressLogger
cross_link_mass_
OpenPepXLLFAlgorithm
private
cross_link_mass_mono_link_
OpenPepXLLFAlgorithm
private
cross_link_name_
OpenPepXLLFAlgorithm
private
cross_link_residue1_
OpenPepXLLFAlgorithm
private
cross_link_residue2_
OpenPepXLLFAlgorithm
private
current_logger_
ProgressLogger
mutable
protected
decoy_prefix_
OpenPepXLLFAlgorithm
private
decoy_string_
OpenPepXLLFAlgorithm
private
DefaultParamHandler
(const String &name)
DefaultParamHandler
DefaultParamHandler
(const DefaultParamHandler &rhs)
DefaultParamHandler
DefaultParamHandler
()
DefaultParamHandler
private
defaults_
DefaultParamHandler
protected
defaultsToParam_
()
DefaultParamHandler
protected
deisotope_mode_
OpenPepXLLFAlgorithm
private
endProgress
(UInt64 bytes_processed=0) const
ProgressLogger
enzyme_name_
OpenPepXLLFAlgorithm
private
error_name_
DefaultParamHandler
protected
EXECUTION_OK
enum value
OpenPepXLLFAlgorithm
ExitCodes
enum name
OpenPepXLLFAlgorithm
fixedModNames_
OpenPepXLLFAlgorithm
private
fragment_mass_tolerance_
OpenPepXLLFAlgorithm
private
fragment_mass_tolerance_unit_ppm_
OpenPepXLLFAlgorithm
private
fragment_mass_tolerance_xlinks_
OpenPepXLLFAlgorithm
private
getDefaults
() const
DefaultParamHandler
getLogType
() const
ProgressLogger
getName
() const
DefaultParamHandler
getParameters
() const
DefaultParamHandler
getSubsections
() const
DefaultParamHandler
GUI
enum value
ProgressLogger
ILLEGAL_PARAMETERS
enum value
OpenPepXLLFAlgorithm
INCOMPATIBLE_INPUT_DATA
enum value
OpenPepXLLFAlgorithm
last_invoke_
ProgressLogger
mutable
protected
LogType
enum name
ProgressLogger
logTypeToFactoryName_
(LogType type)
ProgressLogger
protected
static
max_precursor_charge_
OpenPepXLLFAlgorithm
private
max_variable_mods_per_peptide_
OpenPepXLLFAlgorithm
private
min_precursor_charge_
OpenPepXLLFAlgorithm
private
missed_cleavages_
OpenPepXLLFAlgorithm
private
nextProgress
() const
ProgressLogger
NONE
enum value
ProgressLogger
number_top_hits_
OpenPepXLLFAlgorithm
private
OpenPepXLLFAlgorithm
()
OpenPepXLLFAlgorithm
OpenMS::operator=
(const DefaultParamHandler &rhs)
DefaultParamHandler
OpenMS::ProgressLogger::operator=
(const ProgressLogger &other)
ProgressLogger
operator==
(const DefaultParamHandler &rhs) const
DefaultParamHandler
virtual
param_
DefaultParamHandler
protected
peptide_min_size_
OpenPepXLLFAlgorithm
private
precursor_correction_steps_
OpenPepXLLFAlgorithm
private
precursor_mass_tolerance_
OpenPepXLLFAlgorithm
private
precursor_mass_tolerance_unit_ppm_
OpenPepXLLFAlgorithm
private
ProgressLogger
()
ProgressLogger
ProgressLogger
(const ProgressLogger &other)
ProgressLogger
recursion_depth_
ProgressLogger
protected
static
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_
OpenPepXLLFAlgorithm
private
setLogType
(LogType type) const
ProgressLogger
setName
(const String &name)
DefaultParamHandler
setParameters
(const Param ¶m)
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
OpenPepXLLFAlgorithm
updateMembers_
() override
OpenPepXLLFAlgorithm
private
virtual
use_sequence_tags_
OpenPepXLLFAlgorithm
private
varModNames_
OpenPepXLLFAlgorithm
private
warn_empty_defaults_
DefaultParamHandler
protected
writeParametersToMetaValues
(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
DefaultParamHandler
static
~DefaultParamHandler
()
DefaultParamHandler
virtual
~OpenPepXLLFAlgorithm
() override
OpenPepXLLFAlgorithm
~ProgressLogger
()
ProgressLogger
virtual
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