Here is a list of all documented class members with links to the class documentation for each member:
- c -
- CACHE_MISSING_RESFILE
: ms_peptidesummary
- CACHE_STATUS
: ms_peptidesummary
- calcFragments()
: ms_aahelper
- calcFragmentsEx()
: ms_aahelper
- calcPeptideMZ()
: ms_aahelper
- calculate()
: ms_shapiro_wilk
- calculateGeometricMeanRatio()
: ms_quantitation
- calculateMedianRatio()
: ms_quantitation
- calculateNormalMeanPvalue()
: ms_quant_stats
- calculateNormalMedianPvalue()
: ms_quant_stats
- calculateNormalWeightedPvalue()
: ms_quant_stats
- calculateWeightedGeometricMeanRatio()
: ms_quantitation
- cancelCreateSummary()
: ms_mascotresults
- canCleave()
: ms_enzyme
- canResultsFileBeViewed()
: ms_session
- changePassword()
: ms_http_client
- ChangePasswordResultCode
: ms_http_client
- chargeType
: ms_ms1quant_match
- CHARGETYPE_ALL
: ms_ms1quant_match
- CHARGETYPE_ORIGINAL
: ms_ms1quant_match
- checkSeqDBInstallRequest()
: ms_datfile
- chisqLowerCriticalValue()
: ms_quant_stats
- chisqUpperCriticalValue()
: ms_quant_stats
- clear()
: ms_linker_site_vector
, ms_peptide_quant_key_vector
, ms_progress_info
- clearAccessions()
: ms_crosslinking_accessions
- clearAllCutters()
: ms_enzyme
- clearAllErrors()
: ms_errors
, ms_errs
- clearAltNames()
: ms_umod_modification
- clearAminoAcids()
: ms_umod_configfile
- clearAnnotation()
: ms_spectral_lib_entry
, ms_spectral_lib_peak
, ms_spectral_lib_peak_list
- clearComponents()
: ms_quant_method
- clearCorrections()
: ms_quant_component
- clearCronJobs()
: ms_cronoptions
- clearDatabases()
: ms_databases
, ms_processoroptions
- clearDBLevelTaxId()
: ms_taxonomyrules
- clearDenominators()
: ms_quant_ratio
- clearDoesNotPairWiths()
: ms_crosslinking_linker
- clearElements()
: ms_quant_composition
, ms_umod_configfile
- clearElemRefs()
: ms_umod_aminoacid
, ms_umod_composition
, ms_umod_modbrick
- clearEntries()
: ms_taxonomyfile
, ms_wwwoptions
- clearEnzymes()
: ms_enzymefile
- clearExcludeTaxonomies()
: ms_taxonomychoice
- clearExclusions()
: ms_quant_method
- clearFragments()
: ms_fragmentvector
- clearGencodeFiles()
: ms_taxonomyrules
- clearHeaderFields()
: ms_quantitation
- clearHitRatioExcluded()
: ms_ms1quant_match
- clearHitRatioOutlier()
: ms_ms1quant_match
- clearIgnoreDupeAccessions()
: ms_mascotoptions
- clearIgnoreMasses()
: ms_modification
- clearIgnores()
: ms_umod_modification
, ms_quant_localdef
- clearIncludeTaxonomies()
: ms_taxonomychoice
- clearInstruments()
: ms_fragrulesfile
- clearIonSeries()
: ms_quant_multiplex
- clearIsotopes()
: ms_quant_component
- clearLinkers()
: ms_crosslinking_linkers
- clearLocalDefinitions()
: ms_quant_modgroup
- clearMatchedIon()
: ms_fragment
- clearMethods()
: ms_crosslinking_configfile
, ms_quant_configfile
- clearModBricks()
: ms_umod_configfile
- clearModFiles()
: ms_quant_modgroup
- clearModificationGroups()
: ms_quant_component
, ms_quant_method
- clearModifications()
: ms_modvector
, ms_modfile
, ms_umod_configfile
- clearModifiedResidues()
: ms_modification
- clearMonoLinks()
: ms_crosslinking_linker
- clearNeutralLosses()
: ms_quant_specificity
, ms_umod_specificity
- clearNoBreakDescLineIf()
: ms_taxonomyrules
- clearNodesFiles()
: ms_taxonomyrules
- clearNumerators()
: ms_quant_ratio
- clearParam()
: ms_group
, ms_session
, ms_user
- clearParameters()
: ms_crosslinking_parameters
, ms_quant_parameters
, ms_xml_parameters
- clearParams()
: ms_security_task
- clearParseRules()
: ms_parseoptions
- clearPepNeutralLosses()
: ms_quant_specificity
, ms_umod_specificity
- clearPeptideQuantKeys()
: ms_customquantitation
- clearPeptideRatios()
: ms_customquantitation
- clearPeptides()
: ms_quant_normalisation_peptides
- clearPerDbSrcRules()
: ms_taxonomyrules
- clearPrefixRemoves()
: ms_taxonomyrules
- clearProcessors()
: ms_processoroptions
- clearProteins()
: ms_quant_normalisation_proteins
- clearRawFileFields()
: ms_quantitation
- clearReloadableInfo()
: ms_peptide
- clearReportNumberChoices()
: ms_mascotoptions
- clearReportRatios()
: ms_quant_method
- clearSampleValues()
: ms_shapiro_wilk
- clearSeqs()
: ms_quant_method
- clearSeries()
: ms_fragmentationrules
- clearSpeciesFiles()
: ms_taxonomyrules
- clearSpecificities()
: ms_quant_localdef
, ms_umod_modification
- clearSubClusters()
: ms_clusterparams
- clearSuffixRemoves()
: ms_taxonomyrules
- clearTargetFDRPercentages()
: ms_mascotoptions
- clearThreads()
: ms_dbprocessors
- clearUnmodified()
: ms_quant_modgroup
- clearXrefs()
: ms_umod_modification
- closeHandles()
: ms_http_helper_handles
- closeIndexFile()
: ms_tinycdb
- cluster()
: ms_treecluster
- CMD_ARGUMENT_PARSE_COLLISION
: ms_fileutilities
- CMD_ARGUMENT_PARSE_INVALIDCHAR
: ms_fileutilities
- CMD_ARGUMENT_PARSE_OK
: ms_fileutilities
- CMD_ARGUMENT_PARSE_RESULT
: ms_fileutilities
- CMD_ARGUMENT_PARSE_UNBALANCED
: ms_fileutilities
- CMPXML_IGN_COL_SIZE_EQ_ONE
: ms_fileutilities
- CMPXML_IGN_DBL_DIFF_100_PPM
: ms_fileutilities
- CMPXML_IGN_DBL_DIFF_10_PPM
: ms_fileutilities
- CMPXML_IGN_DBL_DIFF_1_PPM
: ms_fileutilities
- CMPXML_IGN_DBL_IDENTICAL
: ms_fileutilities
- CMPXML_IGN_FILE_URL
: ms_fileutilities
- CMPXML_IGN_INF_999999
: ms_fileutilities
- CMPXML_IGN_RAWFILE_NAME
: ms_fileutilities
- CMPXML_IGN_TODAY_DATE
: ms_fileutilities
- CMPXML_NO_FLAG
: ms_fileutilities
- CMPXML_STRIP_TRAILING_ZEROS
: ms_fileutilities
- COL_ASC_TIME
: ms_logger
- COL_HEADERS
: ms_logger
- COL_IP_ADDRESS
: ms_logger
- COL_ISO8601_TIME
: ms_logger
- COL_LOGGER_DEFAULTS
: ms_logger
- COL_MSG
: ms_logger
- COL_MSG_NUM_DEC
: ms_logger
- COL_MSG_NUM_HEX
: ms_logger
- COL_MSG_SOURCE_TXT
: ms_logger
- COL_QUOTES
: ms_logger
- COL_SEVERITY_NUM
: ms_logger
- COL_SEVERITY_TXT
: ms_logger
- COL_SRC_FILE
: ms_logger
- COL_SRC_LINENUM
: ms_logger
- COL_THREAD_ID
: ms_logger
- COL_TSV
: ms_logger
- columnMatrix()
: ms_matrix
- compareXmlFiles()
: ms_fileutilities
- compareXMLFiles_flags
: ms_fileutilities
- COMPATIBLE
: ms_quant_method
- COMPATIBLE_DIFF_INTEGRATION_PARAM
: ms_quant_method
- COMPATIBLE_DIFF_LOCAL_MOD
: ms_quant_method
- COMPATIBLE_DIFF_NUM_COMPONENTS
: ms_quant_method
- COMPATIBLE_DIFF_NUM_ISOTOPES
: ms_quant_method
- COMPATIBLE_DIFF_NUM_LOCAL_MODS
: ms_quant_method
- COMPATIBLE_DIFF_NUM_MOD_GROUPS
: ms_quant_method
- COMPATIBLE_DIFF_NUM_MODS
: ms_quant_method
- COMPATIBLE_DIFF_PROTOCOL
: ms_quant_method
- COMPATIBLE_MISSING_COMPONENT
: ms_quant_method
- COMPATIBLE_MISSING_INTEGRATION
: ms_quant_method
- COMPATIBLE_MISSING_INTEGRATION_PARAM
: ms_quant_method
- COMPATIBLE_MISSING_MOD
: ms_quant_method
- COMPATIBLE_MISSING_MOD_GROUP
: ms_quant_method
- compressMore()
: ms_zip
- connectionSettings()
: ms_http_client
, ms_http_helper
- containsVarModIdx()
: ms_linker_site_vector
- convertFromLogLevel()
: ms_errs
- convertToLogLevel()
: ms_errs
- copyFrom()
: ms_quant_normalisation_peptides
, ms_crosslinking_accessions
, ms_crosslinking_linker
, ms_quant_numerator
, ms_peptide_quant_ratio
, ms_quant_neutralloss
, ms_umod_neutralloss
, ms_quant_ratio
, ms_quant_normalisation
, ms_crosslinking_parameter
, ms_quant_precursor
, ms_quant_pepneutralloss
, ms_umod_neutralloss
, ms_customproperty
, ms_umod_specificity
, ms_quant_multiplex
, ms_quant_normalisation_proteins
, ms_distiller_data
, ms_quant_parameter
, ms_distiller_master_project
, ms_quant_parameters
, ms_taxonomytree
, ms_datfile
, ms_umod_modbrick
, ms_crosslinking_scope
, ms_fragmentationrules
, ms_quant_specificity
, ms_quant_localdef
, ms_quant_satellite
, ms_http_client_search
, ms_umod_xref
, ms_quant_unmodified
, ms_processors
, ms_license
, ms_spectral_lib_peak
, ms_spectral_lib_entry
, ms_quant_protocol
, ms_quant_replicate
, ms_wwwentry
, ms_umod_specificity
, ms_protein
, ms_masses
, ms_taxspeciesfiles
, ms_taxonomyfile
, ms_http_helper
, ms_modvector
, ms_xic
, ms_taxnodesfiles
, ms_errors
, ms_parserule
, ms_umod_neutralloss
, ms_taxonomyrules
, ms_databases
, ms_spectral_lib_peak_list
, ms_crosslinking_parameters
, ms_wwwoptions
, ms_crosslinking_linkers
, ms_quant_average
, ms_umod_composition
, ms_crosslinking_accession
, ms_cronoptions
, ms_quant_configfile
, ms_aahelper
, ms_processoroptions
, ms_crosslinking_settings
, ms_crosslinking_method
, ms_zip
, ms_crosslinking_monolink
, ms_crosslinking_does_not_pair_with
, ms_treecluster
, ms_quant_moverz
, ms_umod_composition
, ms_umod_modification
, ms_umod_configfile
, ms_umod_modification
, ms_computeraddress
, ms_quant_normalisation_protein
, ms_crosslinking_filters
, ms_crosslinking_configfile
, ms_umod_modification
, ms_quant_outliers
, ms_clusterparams
, ms_unigeneoptions
, ms_umod_aminoacid
, ms_quant_isotope
, ms_quant_modgroup
, ms_umod_element
, ms_dbprocessors
, ms_umod_elemref
, ms_fragment
, ms_quant_integration
, ms_http_client
, ms_quant_reporter
, ms_libraryoptions
, ms_modfile
, ms_mascotfiles
, ms_security_options
, ms_mascotresults_params
, ms_xml_parameter
, ms_modvector
, ms_taxonomychoice
, ms_obofile
, ms_databaseoptions
, ms_quant_quality
, ms_parserule_plus
, ms_protein_quant_ratio
, ms_cronjob
, ms_quant_composition
, ms_quant_element
, ms_quant_method
, ms_umod_elemref
, ms_quant_correction
, ms_connection_settings
, ms_quant_normalisation_peptide
, ms_quant_component
, ms_distiller_search_status_list
, ms_mascotoptions
, ms_modfile
, ms_peptide_quant_key_vector
, ms_parseoptions
, ms_peptide
, ms_fragrulesfile
, ms_fragmentvector
, ms_linker_site
, ms_linker_site_vector
, ms_modification
, ms_masses
, ms_enzyme
, ms_http_client_session
, ms_enzymefile
- copyMassFile()
: ms_modification
- countDistinctPeptides()
: ms_ms2quantitation
, ms_ms1quantitation
, ms_quantitation
- CP_BADNEWPASSWORD
: ms_http_client
- CP_INCORRECTPASSWORD
: ms_http_client
- CP_SUCCESS
: ms_http_client
- CP_UNKNOWNUSER
: ms_http_client
- CP_UNSPECIFIEDERROR
: ms_http_client
- createCrosslinkedPeptide()
: ms_aahelper
- createDefaults()
: ms_security
- createDirectory()
: ms_fileutilities
- createMissingComponents()
: ms_quant_helper
- createPeptide()
: ms_aahelper
- createSummary()
: ms_peptidesummary
, ms_mascotresults
- createUnassignedList()
: ms_mascotresults
- CTERM_CUTTER
: ms_enzyme
- cuttertype
: ms_enzyme