OpenMS
FLASHExtenderAlgorithm Member List

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

calculatePrecursorMass_(const ProteinHit &hit, const std::map< int, std::vector< Size >> &best_path_map, HitInformation &hi)FLASHExtenderAlgorithmprivate
check_defaults_DefaultParamHandlerprotected
CMD enum valueProgressLogger
connectBetweenTags_(std::set< Size > &visited_tag_edges, HitInformation &hi, std::map< Size, std::tuple< double, double >> &sinks, Size vertex, double truncation_mass, double cumulative_shift, std::map< Size, std::map< int, int >> &node_max_score_map, const std::vector< std::vector< int >> &tag_edges, int max_mod_cntr_for_last_mode, bool use_tags)FLASHExtenderAlgorithmprivate
constructDAG_(std::set< Size > &sinks, HitInformation &hi, const std::vector< std::vector< int >> &tag_edges, int max_mod_cntr_for_last_mode, bool use_tags)FLASHExtenderAlgorithmprivate
current_logger_ProgressLoggermutableprotected
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
defineNodes_(const DeconvolvedSpectrum &dspec, HitInformation &hi, double max_mass)FLASHExtenderAlgorithmprivate
endProgress(UInt64 bytes_processed=0) constProgressLogger
error_name_DefaultParamHandlerprotected
extendBetweenTags_(std::map< Size, std::tuple< double, double >> &sinks, HitInformation &hi, Size start_vertex, int end_node_index, int end_pro_index, int diagonal_counter, double truncation_mass, double cumulative_mod_mass, std::map< Size, std::map< int, int >> &node_max_score_map, int max_mod_cntr_for_last_mode)FLASHExtenderAlgorithmprivate
FLASHExtenderAlgorithm()FLASHExtenderAlgorithm
FLASHExtenderAlgorithm(const FLASHExtenderAlgorithm &)=defaultFLASHExtenderAlgorithm
FLASHExtenderAlgorithm(FLASHExtenderAlgorithm &&other)=defaultFLASHExtenderAlgorithm
getDefaults() constDefaultParamHandler
getLogType() constProgressLogger
getModifiedAACount_(const std::vector< Size > &path) constFLASHExtenderAlgorithmprivate
getModNumber_(Size vertex) constFLASHExtenderAlgorithmprivate
getName() constDefaultParamHandler
getNodeIndex_(Size vertex, Size pro_mass_size) constFLASHExtenderAlgorithmprivate
getParameters() constDefaultParamHandler
getProIndex_(Size vertex, Size pro_mass_size) constFLASHExtenderAlgorithmprivate
getProMasses_(const ProteinHit &hit, std::vector< double > &pro_masses, int mode)FLASHExtenderAlgorithmprivatestatic
getProteinLength_(const std::vector< Size > &path, const std::vector< double > &pro_masses) constFLASHExtenderAlgorithmprivate
getProteinMassSpan_(const std::vector< Size > &path, const std::vector< double > &pro_masses) constFLASHExtenderAlgorithmprivate
getProteoforms(std::vector< ProteinHit > &hits) constFLASHExtenderAlgorithminline
getScore_(Size vertex) constFLASHExtenderAlgorithmprivate
getSpecMassSpan_(const std::vector< Size > &path, const MSSpectrum &node_spec, int pro_mass_size) constFLASHExtenderAlgorithmprivate
getSubsections() constDefaultParamHandler
getVertex_(int node_index, int pro_index, int score, int num_mod, Size pro_mass_size) constFLASHExtenderAlgorithmprivate
given_precursor_mass_FLASHExtenderAlgorithmprivate
GUI enum valueProgressLogger
hasProteoforms() constFLASHExtenderAlgorithminline
ion_types_str_FLASHExtenderAlgorithmprivate
last_invoke_ProgressLoggermutableprotected
LogType enum nameProgressLogger
max_extension_stretch_FLASHExtenderAlgorithmprivate
max_mod_cntr_FLASHExtenderAlgorithmprivate
max_mod_mass_FLASHExtenderAlgorithmprivate
max_path_score_FLASHExtenderAlgorithmprivate
min_path_score_FLASHExtenderAlgorithmprivate
mod_map_FLASHExtenderAlgorithmprivate
multi_ion_scoreFLASHExtenderAlgorithmstatic
nextProgress() constProgressLogger
NONE enum valueProgressLogger
operator=(const FLASHExtenderAlgorithm &other)FLASHExtenderAlgorithm
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs)DefaultParamHandler
OpenMS::ProgressLogger::operator=(const ProgressLogger &other)ProgressLogger
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
prefix_shifts_FLASHExtenderAlgorithmprivate
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
proteoform_hits_FLASHExtenderAlgorithmprivate
recursion_depth_ProgressLoggerprotectedstatic
run(std::vector< ProteinHit > &hits, const std::vector< FLASHHelperClasses::Tag > &tags, const DeconvolvedSpectrum &dspec, const MSSpectrum &spec, double ppm, bool multiple_hits_per_spec)FLASHExtenderAlgorithm
run_(const ProteinHit &hit, HitInformation &hi, const std::vector< FLASHHelperClasses::Tag > &matched_tags, std::map< int, std::vector< Size >> &all_paths_per_mode, int max_mod_cntr_for_last_mode)FLASHExtenderAlgorithmprivate
setDefaultParams_()FLASHExtenderAlgorithmprotected
setLogger(ProgressLoggerImpl *logger)ProgressLogger
setLogType(LogType type) constProgressLogger
setModificationMap(const std::map< double, std::vector< ResidueModification >> &mod_map)FLASHExtenderAlgorithminline
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
setProgress(SignedSize value) constProgressLogger
start_pro_indices_FLASHExtenderAlgorithmprivate
startProgress(SignedSize begin, SignedSize end, const String &label) constProgressLogger
subsections_DefaultParamHandlerprotected
suffix_shifts_FLASHExtenderAlgorithmprivate
tags_FLASHExtenderAlgorithmprivate
tol_FLASHExtenderAlgorithmprivate
type_ProgressLoggermutableprotected
updateMembers_() overrideFLASHExtenderAlgorithmprotectedvirtual
warn_empty_defaults_DefaultParamHandlerprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
~DefaultParamHandler()DefaultParamHandlervirtual
~FLASHExtenderAlgorithm() override=defaultFLASHExtenderAlgorithm
~ProgressLogger()ProgressLoggervirtual