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 | inlineprotected |
allow_unmatched_ | PeptideIndexing | protected |
check_defaults_ | DefaultParamHandler | protected |
CMD enum value | ProgressLogger | |
current_logger_ | ProgressLogger | mutableprotected |
DATABASE_EMPTY enum value | PeptideIndexing | |
decoy_string_ | PeptideIndexing | protected |
DefaultParamHandler(const String &name) | DefaultParamHandler | |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
DefaultParamHandler() | DefaultParamHandler | private |
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 | mutableprotected |
LogType enum name | ProgressLogger | |
logTypeToFactoryName_(LogType type) | ProgressLogger | protectedstatic |
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 | protectedstatic |
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 ¶m) | DefaultParamHandler | |
setProgress(SignedSize value) const | ProgressLogger | |
startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
subsections_ | DefaultParamHandler | protected |
type_ | ProgressLogger | mutableprotected |
UNEXPECTED_RESULT enum value | PeptideIndexing | |
updateMembers_() override | PeptideIndexing | protectedvirtual |
warn_empty_defaults_ | DefaultParamHandler | protected |
write_protein_description_ | PeptideIndexing | protected |
write_protein_sequence_ | PeptideIndexing | protected |
~DefaultParamHandler() | DefaultParamHandler | virtual |
~PeptideIndexing() override | PeptideIndexing | |
~ProgressLogger() | ProgressLogger | |