| OpenMS 2.5.0

PeptideIndexing Member List

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

aaa_max_ | PeptideIndexing | protected
addHits_(AhoCorasickAmbiguous &fuzzyAC, const AhoCorasickAmbiguous::FuzzyACPattern &pattern, const AhoCorasickAmbiguous::PeptideDB &pep_DB, const String &prot, const String &full_prot, SignedSize idx_prot, Int offset, FoundProteinFunctor &func_threads) const | PeptideIndexing | inline protected
allow_unmatched_ | PeptideIndexing | protected
check_defaults_ | DefaultParamHandler | protected
CMD enum value | ProgressLogger |
current_logger_ | ProgressLogger | mutable protected
DATABASE_EMPTY enum value | PeptideIndexing |
decoy_string_ | PeptideIndexing | protected
DefaultParamHandler(const String &name) | DefaultParamHandler |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler |
defaults_ | DefaultParamHandler | protected
defaultsToParam_() | DefaultParamHandler | protected
endProgress() const | ProgressLogger |
enzyme_name_ | PeptideIndexing | protected
enzyme_specificity_ | PeptideIndexing | protected
error_name_ | DefaultParamHandler | protected
EXECUTION_OK enum value | PeptideIndexing |
ExitCodes enum name | PeptideIndexing |
getDecoyString() const | PeptideIndexing |
getDefaults() const | DefaultParamHandler |
getLogType() const | ProgressLogger |
getName() const | DefaultParamHandler |
getParameters() const | DefaultParamHandler |
getSubsections() const | DefaultParamHandler |
GUI enum value | ProgressLogger |
IL_equivalent_ | PeptideIndexing | protected
ILLEGAL_PARAMETERS enum value | PeptideIndexing |
isPrefix() const | PeptideIndexing |
keep_unreferenced_proteins_ | PeptideIndexing | protected
last_invoke_ | ProgressLogger | mutable protected
LogType enum name | ProgressLogger |
logTypeToFactoryName_(LogType type) | ProgressLogger | protected static
missing_decoy_action_ | PeptideIndexing | protected
mm_max_ | PeptideIndexing | protected
nextProgress() const | ProgressLogger |
NONE enum value | ProgressLogger |
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_IDS_EMPTY enum value | PeptideIndexing |
PeptideIndexing() | PeptideIndexing |
prefix_ | PeptideIndexing | protected
ProgressLogger() | ProgressLogger |
ProgressLogger(const ProgressLogger &other) | ProgressLogger |
recursion_depth_ | ProgressLogger | protected static
run(std::vector< FASTAFile::FASTAEntry > &proteins, std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids) | PeptideIndexing | inline
run(FASTAContainer< T > &proteins, std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids) | PeptideIndexing | inline
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 | PeptideIndexing |
updateMembers_() override | PeptideIndexing | protected virtual
warn_empty_defaults_ | DefaultParamHandler | protected
write_protein_description_ | PeptideIndexing | protected
write_protein_sequence_ | PeptideIndexing | protected
~DefaultParamHandler() | DefaultParamHandler | virtual
~PeptideIndexing() override | PeptideIndexing |
~ProgressLogger() | ProgressLogger |