OpenMS
PeptideIndexing Member List

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

aaa_max_PeptideIndexingprotected
allow_nterm_protein_cleavage_PeptideIndexingprotected
AUTO_MODEPeptideIndexingstatic
check_defaults_DefaultParamHandlerprotected
CMD enum valueProgressLogger
current_logger_ProgressLoggermutableprotected
DATABASE_EMPTY enum valuePeptideIndexing
decoy_string_PeptideIndexingprotected
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
endProgress(UInt64 bytes_processed=0) constProgressLogger
enzyme_name_PeptideIndexingprotected
enzyme_specificity_PeptideIndexingprotected
error_name_DefaultParamHandlerprotected
EXECUTION_OK enum valuePeptideIndexing
ExitCodes enum namePeptideIndexing
getDecoyString() constPeptideIndexing
getDefaults() constDefaultParamHandler
getLogType() constProgressLogger
getName() constDefaultParamHandler
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
GUI enum valueProgressLogger
IL_equivalent_PeptideIndexingprotected
ILLEGAL_PARAMETERS enum valuePeptideIndexing
isPrefix() constPeptideIndexing
keep_unreferenced_proteins_PeptideIndexingprotected
last_invoke_ProgressLoggermutableprotected
LogType enum nameProgressLogger
logTypeToFactoryName_(LogType type)ProgressLoggerprotectedstatic
missing_decoy_action_PeptideIndexingprotected
MissingDecoy enum namePeptideIndexing
mm_max_PeptideIndexingprotected
names_of_missing_decoyPeptideIndexingstatic
names_of_unmatchedPeptideIndexingstatic
nextProgress() constProgressLogger
NONE enum valueProgressLogger
OpenMS::operator=(const DefaultParamHandler &rhs)DefaultParamHandler
OpenMS::ProgressLogger::operator=(const ProgressLogger &other)ProgressLogger
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
PEPTIDE_IDS_EMPTY enum valuePeptideIndexing
PeptideIndexing()PeptideIndexing
prefix_PeptideIndexingprotected
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
recursion_depth_ProgressLoggerprotectedstatic
run(std::vector< FASTAFile::FASTAEntry > &proteins, std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids)PeptideIndexing
run(FASTAContainer< TFI_File > &proteins, std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids)PeptideIndexing
run(FASTAContainer< TFI_Vector > &proteins, std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids)PeptideIndexing
run_(FASTAContainer< T > &proteins, std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids)PeptideIndexingprotected
setLogType(LogType type) constProgressLogger
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
setProgress(SignedSize value) constProgressLogger
startProgress(SignedSize begin, SignedSize end, const String &label) constProgressLogger
subsections_DefaultParamHandlerprotected
type_ProgressLoggermutableprotected
UNEXPECTED_RESULT enum valuePeptideIndexing
Unmatched enum namePeptideIndexing
unmatched_action_PeptideIndexingprotected
updateMembers_() overridePeptideIndexingprotectedvirtual
warn_empty_defaults_DefaultParamHandlerprotected
write_protein_description_PeptideIndexingprotected
write_protein_sequence_PeptideIndexingprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
~DefaultParamHandler()DefaultParamHandlervirtual
~PeptideIndexing() overridePeptideIndexing
~ProgressLogger()ProgressLoggervirtual