Here is a list of all documented class members with links to the class documentation for each member:
- s -
- S_NOT_STARTED
: ms_progress_info
- S_RUNNING
: ms_progress_info
- S_RUNNING_INDETERMINATE
: ms_progress_info
- S_STOPPED_BREAK
: ms_progress_info
- S_STOPPED_COMPLETE
: ms_progress_info
- S_STOPPED_FAIL
: ms_progress_info
- SAR_FAIL_CHMOD
: ms_fileutilities
- SAR_FAIL_CHOWN
: ms_fileutilities
- SAR_FAIL_GET_NAMED_SECURITY_INFO
: ms_fileutilities
- SAR_FAIL_SET_ENTRIES_IN_ACL
: ms_fileutilities
- SAR_FAIL_SET_NAMED_SECURITY_INFO
: ms_fileutilities
- SAR_SUCCESS
: ms_fileutilities
- save_buffer()
: ms_crosslinking_configfile
, ms_quant_configfile
, ms_umod_configfile
- save_file()
: ms_crosslinking_configfile
, ms_datfile
, ms_enzymefile
, ms_fragrulesfile
, ms_masses
, ms_modfile
, ms_quant_configfile
, ms_taxonomyfile
, ms_umod_configfile
- saveAs()
: ms_spectral_lib_file
- saveBoolParam()
: ms_session
- saveCdbFile()
: ms_ms1quantitation
, ms_ms2quantitation
- saveDoubleParam()
: ms_session
- saveFileOffsetForKey()
: ms_tinycdb
- saveIntForKey()
: ms_tinycdb
- saveIntParam()
: ms_session
- saveLongParam()
: ms_session
- saveStringParam()
: ms_group
, ms_session
, ms_user
- saveTimeParam()
: ms_session
- saveToFile()
: ms_security_tasks
- saveToString()
: ms_modfile
- saveValueForKey()
: ms_tinycdb
- saveXmlFile()
: ms_ms1quantitation
, ms_ms2quantitation
- SCORE
: ms_mascotresults
- SearchStatusCode
: ms_http_client_search
- SEC_CROSSLINK_PEPTIDES
: ms_mascotresfile
- SEC_CROSSLINK_SUMMARY
: ms_mascotresfile
- SEC_CROSSLINKING
: ms_mascotresfile
- SEC_DECOYMIXTURE
: ms_mascotresfile
- SEC_DECOYPEPTIDES
: ms_mascotresfile
- SEC_DECOYPROTEINS
: ms_mascotresfile
- SEC_DECOYSUMMARY
: ms_mascotresfile
- SEC_ENZYME
: ms_mascotresfile
- SEC_ERRTOLDECOYPEPTIDES
: ms_mascotresfile
- SEC_ERRTOLDECOYSUMMARY
: ms_mascotresfile
- SEC_ERRTOLPEPTIDES
: ms_mascotresfile
- SEC_ERRTOLSUMMARY
: ms_mascotresfile
- SEC_HEADER
: ms_mascotresfile
- SEC_INDEX
: ms_mascotresfile
- SEC_LIBRARYPEPTIDES
: ms_mascotresfile
- SEC_LIBRARYSUMMARY
: ms_mascotresfile
- SEC_MASSES
: ms_mascotresfile
- SEC_MIXTURE
: ms_mascotresfile
- SEC_NUMSECTIONS
: ms_mascotresfile
- SEC_PARAMETERS
: ms_mascotresfile
- SEC_PEPTIDES
: ms_mascotresfile
- SEC_PROTEINS
: ms_mascotresfile
- SEC_QUANTITATION
: ms_mascotresfile
- SEC_QUERY1
: ms_mascotresfile
- SEC_SPECTRAL_LIBRARY
: ms_mascotresfile
- SEC_SUMMARY
: ms_mascotresfile
- SEC_TAXONOMY
: ms_mascotresfile
- SEC_UNIMOD
: ms_mascotresfile
- SEC_UNIMOD_XL
: ms_mascotresfile
- SECTASK_ACCESSDBSETUP
: ms_security_tasks
- SECTASK_ADMINPAGES
: ms_security_tasks
- SECTASK_ALLFASTA
: ms_security_tasks
- SECTASK_ALLOWMSMS
: ms_security_tasks
- SECTASK_ALLOWMSMSNOENZYME
: ms_security_tasks
- SECTASK_ALLOWPMF
: ms_security_tasks
- SECTASK_ALLOWPMFNOENZYME
: ms_security_tasks
- SECTASK_ALLOWSPOOFOTHERUSER
: ms_security_tasks
- SECTASK_BIOTOOLSBATCH
: ms_security_tasks
- SECTASK_DAEMONCLIENT
: ms_security_tasks
- SECTASK_DATAURLMAXSIZE
: ms_security_tasks
- SECTASK_DATAURLPROTOCOLS
: ms_security_tasks
- SECTASK_DENYQUANT
: ms_security_tasks
- SECTASK_DISTILLERCLIENT
: ms_security_tasks
- SECTASK_DOWNLOAD_DISTILLER_XML
: ms_security_tasks
- SECTASK_EDITCONFIG
: ms_security_tasks
- SECTASK_INTEGRASYSTEMACCOUNT
: ms_security_tasks
- SECTASK_KILLALLTASK
: ms_security_tasks
- SECTASK_KILLTASKINGROUP
: ms_security_tasks
- SECTASK_MAXCONCURRENTSEARCHES
: ms_security_tasks
- SECTASK_MAXETACCESSIONS
: ms_security_tasks
- SECTASK_MAXETVARMODS
: ms_security_tasks
- SECTASK_MAXEXECUTIONTIME
: ms_security_tasks
- SECTASK_MAXFASTAFILES
: ms_security_tasks
- SECTASK_MAXJOBPRIORITY
: ms_security_tasks
- SECTASK_MAXNOENZQUERIES
: ms_security_tasks
- SECTASK_MAXQUERIES
: ms_security_tasks
- SECTASK_MAXVARMODS
: ms_security_tasks
- SECTASK_MODIFYOWNPROFILE
: ms_security_tasks
- SECTASK_MSSTATUSEXECLUSTER
: ms_security_tasks
- SECTASK_MSSTATUSEXERETRYDB
: ms_security_tasks
- SECTASK_NAMEDFASTA
: ms_security_tasks
- SECTASK_SEEALLSEARCHESWITHUSERID
: ms_security_tasks
- SECTASK_SEEOLDSEARCHES
: ms_security_tasks
- SECTASK_SEESEARCHINANYGROUP
: ms_security_tasks
- SECTASK_SEESEARCHINGROUP
: ms_security_tasks
- SECTASK_SPOOFNAMEDGROUPSONLY
: ms_security_tasks
- SECTASK_UPLOAD_DISTILLER_XML
: ms_security_tasks
- SECTASK_USEMSREVIEWEXE
: ms_security_tasks
- SECTASK_USEMSSTATUSEXE
: ms_security_tasks
- SECTASK_VIEWCONFIG
: ms_security_tasks
- SECTASK_VIEWCONFIGUSINGMSSTATUS
: ms_security_tasks
- section
: ms_mascotresfile
- SEQDB_INSTALL
: ms_datfile
- SEQDB_INSTALL_CURRENT_RULES
: ms_datfile
- SEQDB_INSTALL_CUSTOMISED
: ms_datfile
- SEQDB_INSTALL_EXISTING_LARGER
: ms_datfile
- SEQDB_INSTALL_INACTIVE
: ms_datfile
- SEQDB_INSTALL_INVALID_CONFIG
: ms_datfile
- SEQDB_INSTALL_INVALID_DBNAME
: ms_datfile
- SEQDB_INSTALL_MISSING_CONFIG
: ms_datfile
- SEQDB_INSTALL_MUST_UPDATE_CFG
: ms_datfile
- SEQDB_INSTALL_OLD_RULES
: ms_datfile
- SEQDB_INSTALL_SHOULD_QUERY_USER
: ms_datfile
- SEQDB_INSTALL_WRONG_WILDCARD
: ms_datfile
- SequenceShowOptions
: ms_http_client_session
- serverVersionNewerOrSameAs()
: ms_distiller_data_search
- sessionId()
: ms_http_client_search
- set()
: ms_linker_site_vector
, ms_peptide_quant_key_vector
- setAbort()
: ms_http_helper_progress
- setAccession()
: ms_quant_normalisation_protein
- setAccessionParseRuleIndex()
: ms_databaseoptions
- setAccessionRefParseRuleIndex()
: ms_databaseoptions
- setAccessions()
: ms_crosslinking_method
- setAccessRights()
: ms_fileutilities
- setAccFromSpeciesLine()
: ms_taxonomyrules
- setAccountEnabled()
: ms_user
- setActive()
: ms_databaseoptions
- setAllChargeStates()
: ms_quant_integration
- setAllChargeStatesThreshold()
: ms_quant_integration
- setAllowElutionShift()
: ms_quant_integration
- setAllowMassTimeMatch()
: ms_quant_precursor
- setAnnotation()
: ms_spectral_lib_peak
- setAnnotationLevel()
: ms_spectral_lib_peak_list
- setAPI()
: ms_errs
- setApproved()
: ms_umod_modification
- setAutoSelectCharge()
: ms_mascotoptions
- setAvailable()
: ms_parserule
- setAvailableModifications()
: ms_aahelper
- setAverage()
: ms_quant_moverz
, ms_quant_protocol
- setAverageNumPeptides()
: ms_ms1quantitation
- setAverageReferenceProtein()
: ms_ms1quantitation
- setAverageSelection()
: ms_ms1quantitation
- setAvgeMass()
: ms_umod_aminoacid
, ms_umod_composition
, ms_umod_element
, ms_umod_modbrick
- setBaseUrl()
: ms_http_client
- setBreak()
: ms_progress_info
- setCacheDirectory()
: ms_mascotoptions
- setCarbonMass()
: ms_masses
- setCentroidWidth()
: ms_mascotoptions
- setCentroidWidthCount()
: ms_mascotoptions
- setCharged2Plus()
: ms_fragmentationrules
- setCharged3Plus()
: ms_fragmentationrules
- setCheckNodesAliveFreq()
: ms_clusterparams
- setChopSource()
: ms_parserule_plus
- setClassification()
: ms_umod_specificity
- setClusterParams()
: ms_datfile
- setCode()
: ms_umod_neutralloss
- setCoefficient()
: ms_quant_numerator
- setColsToOutput()
: ms_logger
- setColumnDown()
: ms_matrix
- setColumnUp()
: ms_matrix
- setCombinedReportRatio()
: ms_ms2quantitation
- setCombineRepeats()
: ms_errs
- setCommandStr()
: ms_cronjob
- setComp()
: ms_quant_method
- setCompositionString()
: ms_umod_composition
- setCompressToolAA()
: ms_mascotoptions
- setCompressToolNA()
: ms_mascotoptions
- setCompressToolSL()
: ms_mascotoptions
- setConcatRefFileLines()
: ms_taxonomyrules
- setConnectionSettings()
: ms_crosslinking_configfile
, ms_datfile
, ms_enzymefile
, ms_fragrulesfile
, ms_http_client
, ms_masses
, ms_modfile
, ms_quant_configfile
, ms_taxonomyfile
, ms_umod_configfile
- setConnectionTimeout()
: ms_connection_settings
- setConstrainSearch()
: ms_quant_method
- setContent()
: ms_quant_correction
, ms_quant_numerator
, ms_quant_unmodified
- setCR()
: ms_matrix
- setCrawlerNumPeaksPer100Da()
: ms_mascotoptions
- setCreatePipThreadBlockSize()
: ms_mascotoptions
- setCreatePipThreads()
: ms_mascotoptions
- setCronEnabled()
: ms_cronoptions
- setCronJob()
: ms_cronoptions
- setCronOptions()
: ms_datfile
- setCTerminusMass()
: ms_modification
- setCtermModification()
: ms_masses
- setDatabaseName()
: ms_crosslinking_accession
- setDatabases()
: ms_datfile
- setDateTimeModified()
: ms_umod_modification
- setDateTimePosted()
: ms_umod_modification
- setDayOfMonth()
: ms_cronjob
- setDayOfWeek()
: ms_cronjob
- setDB()
: ms_protein
- setDBLevelTaxId()
: ms_taxonomyrules
- setDBType()
: ms_databaseoptions
- setDechargeFragmentPeaks()
: ms_mascotoptions
- setDecoyTypeNoEnzyme()
: ms_mascotoptions
- setDecoyTypeSpecific()
: ms_mascotoptions
- setDefaultDelimiter()
: ms_customproperty
- setDefaultMonitor()
: ms_loggingmonitor
- setDefaultNodeHomeDir()
: ms_clusterparams
- setDefaultNodeHomeDirFromMaster()
: ms_clusterparams
- setDefaultNodeOS()
: ms_clusterparams
- setDefaultPasswordExpiryTime()
: ms_security_options
- setDefaultPort()
: ms_clusterparams
- setDefaultRule()
: ms_taxonomyrules
- setDefaultTargetFDRPercentage()
: ms_mascotoptions
- setDelta()
: ms_modification
, ms_quant_localdef
, ms_umod_modification
- setDescription()
: ms_crosslinking_method
, ms_quant_method
, ms_umod_neutralloss
, ms_xml_parameter
- setDescriptionLineSep()
: ms_taxonomyrules
- setDescriptionParseRuleIndex()
: ms_databaseoptions
- setDisplayNonSignificantMatches()
: ms_mascotoptions
- setDoThisRuleFirst()
: ms_taxonomyrules
- setElectronMass()
: ms_masses
- setElement()
: ms_quant_correction
- setElutionProfileCorrelationThreshold()
: ms_quant_integration
- setElutionTimeDelta()
: ms_quant_integration
- setElutionTimeDeltaUnit()
: ms_quant_integration
- setEmailAddress()
: ms_user
- setEmailErrorsEnabled()
: ms_mascotoptions
- setEmailFromTextName()
: ms_mascotoptions
- setEmailFromUser()
: ms_mascotoptions
- setEmailPassword()
: ms_mascotoptions
- setEmailProfile()
: ms_mascotoptions
- setEmailService()
: ms_mascotoptions
- setEmailTimeOutPeriod()
: ms_mascotoptions
- setEmailUsersEnabled()
: ms_mascotoptions
- setEnabled()
: ms_clusterparams
, ms_cronjob
, ms_taxonomyrules
- setEncryptedPassword()
: ms_user
- setEntry()
: ms_wwwoptions
- setEnzyme()
: ms_aahelper
- setEnzymes()
: ms_mascotfiles
- setErrMessageEmailTo()
: ms_mascotoptions
- setErrorLevel()
: ms_taxonomyrules
- setErrorLogFile()
: ms_mascotoptions
- setErrTolMaxAccessions()
: ms_mascotoptions
- setExcludeInternalLabel()
: ms_quant_multiplex
- setExcludeIsobaricFragments()
: ms_quant_multiplex
- setExecAfterSearch()
: ms_mascotoptions
- setFeatureTableLength()
: ms_mascotoptions
- setFeatureTableMinScore()
: ms_mascotoptions
- setFileIndex()
: ms_quant_component
- setFileName()
: ms_crosslinking_configfile
, ms_datfile
, ms_enzymefile
, ms_fragrulesfile
, ms_license
, ms_masses
, ms_modfile
, ms_quant_configfile
, ms_taxonomyfile
, ms_taxspeciesfiles
, ms_taxnodesfiles
, ms_umod_configfile
- setFileTypeToSearch()
: ms_parserule_plus
- setFilters()
: ms_crosslinking_method
- setFindFileTimeout()
: ms_datfile
- setFlag()
: ms_mascotresults_params
, ms_quant_neutralloss
, ms_umod_neutralloss
- setFlag2()
: ms_mascotresults_params
- setFlags()
: ms_mascotresults_params
- setFlags2()
: ms_mascotresults_params
- setForkForUnixApache()
: ms_mascotoptions
- setFormat()
: ms_taxspeciesfiles
, ms_taxnodesfiles
- setFormVersion()
: ms_mascotoptions
- setFrequencies()
: ms_mascotfiles
- setFromRefFile()
: ms_taxonomyrules
- setFromSubstitutions()
: ms_modfile
- setFullName()
: ms_user
, ms_umod_aminoacid
, ms_umod_element
, ms_umod_modbrick
, ms_umod_modification
- setGetSeqBlastAccession()
: ms_mascotoptions
- setGetSeqJobIdFile()
: ms_mascotoptions
- setGroupOfPoster()
: ms_umod_modification
- setHeaderComments()
: ms_datfile
- setHidden()
: ms_modification
, ms_umod_specificity
- setHitRatioExcluded()
: ms_ms1quant_match
- setHitRatioOutlier()
: ms_ms1quant_match
- setHostName()
: ms_computeraddress
, ms_wwwentry
- setHour()
: ms_cronjob
- setHttpPassword()
: ms_connection_settings
- setHttpProtocol()
: ms_connection_settings
- setHttpUsername()
: ms_connection_settings
- setHydrogenMass()
: ms_masses
- setICATFilter()
: ms_mascotoptions
- setICATHeavy()
: ms_mascotoptions
- setICATLight()
: ms_mascotoptions
- setICATQuantitationMethod()
: ms_mascotoptions
- setID()
: ms_group
, ms_user
- setIdentifier()
: ms_taxonomyrules
- setIgnoreDupeAccession()
: ms_mascotoptions
- setIgnoreIonsScoreBelow()
: ms_mascotoptions
, ms_mascotresults_params
- setIndependent()
: ms_enzyme
- setIndexFileName()
: ms_tinycdb
- setInErrorTolerant()
: ms_modification
- setInetAddress()
: ms_computeraddress
- setInLongList()
: ms_modification
- setInShortList()
: ms_modification
- setIntegraAppServerURL()
: ms_security_options
- setIntegraDatabaseName()
: ms_security_options
- setIntegraOracleServerName()
: ms_security_options
- setIntegration()
: ms_quant_method
- setIntensityNormalisationBase()
: ms_ms2quantitation
- setIntensitySigFigs()
: ms_mascotoptions
- setInterFileBasePath()
: ms_mascotoptions
- setInterFileRelPath()
: ms_mascotoptions
- setIonIntensityThreshold()
: ms_quant_multiplex
- setIonsDecimalPlaces()
: ms_mascotoptions
- setIonSeries()
: ms_quant_multiplex
- setIPCLogfile()
: ms_clusterparams
- setIPCLogging()
: ms_clusterparams
- setIPCTimeout()
: ms_clusterparams
- setIsolatedPrecursor()
: ms_quant_quality
- setIsolatedPrecursorThreshold()
: ms_quant_quality
- setIteratePMFIntensities()
: ms_mascotoptions
- setLabelAll()
: ms_mascotoptions
- setLastModificationTime()
: ms_fileutilities
- setLastQueryAscFile()
: ms_mascotoptions
- setLibraryOptions()
: ms_datfile
- setLinkers()
: ms_crosslinking_method
- setLocalModsStr()
: ms_peptide
- setLocalRefFile()
: ms_databaseoptions
- setLockMemory()
: ms_databaseoptions
- setLogFileName()
: ms_cronoptions
, ms_security_options
- setLoggingFile()
: ms_errs
- setLoggingLevel()
: ms_cronoptions
, ms_errs
, ms_security_options
- setLogMask()
: ms_loggingmonitor
- setLogoImageFile()
: ms_mascotoptions
- setMailTempFile()
: ms_mascotoptions
- setMailTransport()
: ms_mascotoptions
- setMajorVersion()
: ms_umod_configfile
- setMascNodeCtrlFile()
: ms_mascotoptions
- setMascotCmdLine()
: ms_mascotoptions
- setMascotControlFile()
: ms_mascotoptions
- setMascotFileProcessingThreads()
: ms_mascotoptions
- setMascotFiles()
: ms_datfile
- setMascotJobIdFile()
: ms_mascotoptions
- setMascotMessage()
: ms_mascotoptions
- setMascotNodeRebootScript()
: ms_clusterparams
- setMascotNodeScript()
: ms_clusterparams
- setMascotOptions()
: ms_datfile
- setMassDecimalPlaces()
: ms_mascotoptions
- setMassDelta()
: ms_quant_integration
- setMassDeltaUnit()
: ms_quant_integration
- setMasses()
: ms_aahelper
- setMassFile()
: ms_modification
, ms_modfile
- setMasterComputer()
: ms_clusterparams
- setMatchedIon()
: ms_fragment
- setMatchedRho()
: ms_quant_integration
- setMatchOppositeCrosslinkPairs()
: ms_mascotoptions
- setMaxConcurrentSearches()
: ms_mascotoptions
- setMaxDatabases()
: ms_mascotoptions
- setMaxDescriptionLen()
: ms_mascotoptions
- setMaxEtagMassDelta()
: ms_mascotoptions
- setMaxEtVarMods()
: ms_mascotoptions
- setMaxHitsToReport()
: ms_mascotresults_params
- setMaxIntactCrosslinkPeptides()
: ms_mascotoptions
- setMaxInternalMass()
: ms_fragmentationrules
- setMaxNumPeptides()
: ms_mascotoptions
- setMaxPepModArrangements()
: ms_mascotoptions
- setMaxPepNumModifiedSites()
: ms_mascotoptions
- setMaxPepNumVarMods()
: ms_mascotoptions
- setMaxQueries()
: ms_mascotoptions
- setMaxSearchesPerUser()
: ms_mascotoptions
- setMaxSequenceLen()
: ms_mascotoptions
- setMaxVarMods()
: ms_mascotoptions
- setMemoryMapFiles()
: ms_databaseoptions
- setMethod()
: ms_quant_outliers
, ms_quant_integration
, ms_quant_normalisation
- setMinEtagMassDelta()
: ms_mascotoptions
- setMinimumA1()
: ms_quant_quality
- setMinimumPasswordLength()
: ms_security_options
- setMinInternalMass()
: ms_fragmentationrules
- setMinIonPairs()
: ms_quant_multiplex
- setMinNumPeptides()
: ms_quant_method
, ms_quantitation
- setMinNumSigUniqueSequences()
: ms_mascotresults_params
- setMinorVersion()
: ms_umod_configfile
- setMinPepLenInPepSummary()
: ms_mascotoptions
- setMinPepLenInPeptideSummary()
: ms_mascotresults_params
- setMinPepLenInSearch()
: ms_mascotoptions
- setMinPrecursorCharge()
: ms_quant_quality
- setMinProbability()
: ms_mascotresults_params
- setMinute()
: ms_cronjob
- setMiscNotes()
: ms_umod_modification
, ms_umod_specificity
- setMitochondrialTranslation()
: ms_taxonomyrules
- setMode()
: ms_quant_modgroup
- setModFileName()
: ms_crosslinking_does_not_pair_with
, ms_crosslinking_linker
- setModifications()
: ms_mascotfiles
, ms_quant_satellite
- setModificationType()
: ms_modification
- setMonitorEmailCheckFreq()
: ms_mascotoptions
- setMonitorLogFile()
: ms_mascotoptions
- setMonitorPidFile()
: ms_mascotoptions
- setMonitorTestTimeout()
: ms_mascotoptions
- setMonoisotopic()
: ms_quant_moverz
- setMonoMass()
: ms_umod_element
, ms_umod_aminoacid
, ms_umod_composition
, ms_umod_modbrick
- setMonthOfYear()
: ms_cronjob
- setMoveOldDbToOldDir()
: ms_mascotoptions
- setMoverz()
: ms_quant_component
- setMudpit()
: ms_mascotoptions
- setMudpitSwitch()
: ms_mascotoptions
- setMultiplex()
: ms_quant_protocol
- setName()
: ms_group
, ms_quant_method
, ms_crosslinking_method
, ms_databaseoptions
, ms_dbprocessors
, ms_quant_component
, ms_quant_modgroup
, ms_quant_numerator
, ms_quant_ratio
, ms_user
, ms_wwwentry
, ms_xml_parameter
- setNameOfDB()
: ms_parserule_plus
- setNeutralLoss()
: ms_modification
- setNew()
: ms_quant_isotope
- setNitrogenMass()
: ms_masses
- setNodeListFile()
: ms_mascotfiles
- setNodeSequenceDatabaseDir()
: ms_clusterparams
- setNoResultsScript()
: ms_mascotoptions
- setNormalisation()
: ms_quant_method
- setNTerminusMass()
: ms_modification
- setNtermModification()
: ms_masses
- setNTIUserGroup()
: ms_mascotoptions
- setNTMonitorGroup()
: ms_mascotoptions
- setNull()
: ms_quant_protocol
- setNumber()
: ms_quant_element
, ms_umod_elemref
- setNumberOfThreads()
: ms_databaseoptions
- setNumPeptides()
: ms_quant_average
- setOld()
: ms_quant_isotope
- setOutliers()
: ms_quant_method
- setOxygenMass()
: ms_masses
- setPairsWith()
: ms_umod_neutralloss
- setParams()
: ms_security_task
- setParseOptions()
: ms_datfile
- setParseRule()
: ms_wwwentry
, ms_parseoptions
- setPassword()
: ms_user
- setPasswordExpiry()
: ms_user
- setPath()
: ms_wwwentry
, ms_databaseoptions
- setPepNeutralLoss()
: ms_modification
- setPepSearchTool()
: ms_mascotoptions
- setPepThresholdType()
: ms_quant_quality
- setPepThresholdValue()
: ms_quant_quality
- setPeptideIsBold()
: ms_protein
- setPeptideRatioExcluded()
: ms_quantitation
, ms_customquantitation
, ms_ms2quantitation
- setPeptideRatioIncluded()
: ms_customquantitation
, ms_ms2quantitation
, ms_quantitation
- setPeptideRatioNormalisationBase()
: ms_quantitation
- setPeptides()
: ms_quant_normalisation
- setPeptideShowCheckbox()
: ms_protein
- setPercolator()
: ms_mascotoptions
- setPercolatorExeFlags()
: ms_mascotoptions
- setPercolatorFeatures()
: ms_mascotoptions
, ms_mascotresfile
- setPercolatorMinQueries()
: ms_mascotoptions
- setPercolatorMinSequences()
: ms_mascotoptions
- setPercolatorTargetRankRelativeThreshold()
: ms_mascotoptions
- setPercolatorTargetRankScoreThreshold()
: ms_mascotoptions
- setPercolatorUseProteins()
: ms_mascotoptions
- setPercolatorUseRT()
: ms_mascotoptions
- setPermittedTasks()
: ms_group
, ms_session
- setPort()
: ms_computeraddress
- setPortNumber()
: ms_wwwentry
- setPosition()
: ms_umod_specificity
, ms_quant_specificity
, ms_quant_unmodified
- setPreceedingComments()
: ms_customproperty
, ms_databaseoptions
- setPrecursor()
: ms_quant_protocol
- setPrecursorCutOutLowerLimit()
: ms_mascotoptions
- setPrecursorCutOutUpperLimit()
: ms_mascotoptions
- setPrecursorRange()
: ms_quant_integration
- setPrivacyEnabled()
: ms_umod_modification
- setPrivate()
: ms_umod_modification
- setProcessingOptions()
: ms_quant_integration
- setProcessors()
: ms_datfile
- setPropertyName()
: ms_customproperty
- setPropValBoolByName()
: ms_customproperty
- setPropValCharByName()
: ms_customproperty
- setPropValFloatByName()
: ms_customproperty
- setPropValInt64ByName()
: ms_customproperty
- setPropValIntByName()
: ms_customproperty
- setPropValStringByName()
: ms_customproperty
- setPropValStringByNumber()
: ms_customproperty
- setProteinFamilySwitch()
: ms_mascotoptions
- setProteinRatioType()
: ms_ms2quantitation
, ms_customquantitation
, ms_quant_method
, ms_quantitation
- setProteins()
: ms_quant_normalisation
- setProteinsInResultsFile()
: ms_mascotoptions
- setProtocol()
: ms_quant_method
- setProtScoreType()
: ms_quant_method
- setProxyPassword()
: ms_mascotoptions
, ms_connection_settings
- setProxyServer()
: ms_connection_settings
, ms_mascotoptions
- setProxyServerType()
: ms_connection_settings
- setProxyType()
: ms_mascotoptions
- setProxyUsername()
: ms_connection_settings
, ms_mascotoptions
- setQuality()
: ms_quant_method
- setQuantNormalisation()
: ms_ms2quantitation
- setQuantOutliers()
: ms_quantitation
, ms_customquantitation
, ms_ms2quantitation
- setQuickRefSearch()
: ms_taxonomyrules
- setRC()
: ms_matrix
- setRecordID()
: ms_umod_modification
- setRedirectPolicy()
: ms_connection_settings
- setReferenceAccession()
: ms_quant_average
- setReferenceAmount()
: ms_quant_average
- setReferenceDatabase()
: ms_quant_average
- setReferenceFasta()
: ms_libraryoptions
- setRemoveOldIndexFiles()
: ms_mascotoptions
- setReplicate()
: ms_quant_protocol
- setReportBuilderColumnArrangement()
: ms_mascotoptions
- setReportDetail()
: ms_quant_method
- setReporter()
: ms_quant_protocol
- setReporterTol()
: ms_quant_reporter
- setReporterTolUnit()
: ms_quant_reporter
- setReportNumberChoice()
: ms_mascotoptions
- setReportRatioInFile()
: ms_ms2quantitation
- setReqPepNeutralLoss()
: ms_modification
- setRequireBoldRed()
: ms_mascotoptions
, ms_quant_method
- setRequired()
: ms_quant_modgroup
, ms_quant_pepneutralloss
- setResfileCache()
: ms_mascotoptions
- setResidueMasses()
: ms_masses
- setResidueModification()
: ms_masses
- setResultsCache()
: ms_mascotoptions
- setResultsFileFormatVersion()
: ms_mascotoptions
- setResultsFullURL()
: ms_mascotoptions
- setResultsFullURL_2()
: ms_mascotoptions
- setResultsPerlScript()
: ms_mascotoptions
- setResultsPerlScript_2()
: ms_mascotoptions
- setReviewColDisplay()
: ms_mascotoptions
- setReviewColWidth()
: ms_mascotoptions
- setRow()
: ms_treecluster
- setRule()
: ms_parserule_plus
- setRuleStr()
: ms_parserule
- setSatellite()
: ms_quant_component
- setSaveEveryLastQueryAsc()
: ms_mascotoptions
- setSaveLastQueryAsc()
: ms_mascotoptions
- setSchemaDirectory()
: ms_quant_configfile
- setSchemaFileName()
: ms_crosslinking_configfile
, ms_quant_configfile
, ms_umod_configfile
- setScope()
: ms_crosslinking_method
- setSearchLogFile()
: ms_mascotoptions
- setSearchSubmitMode()
: ms_mascotoptions
- setSecsToWaitForNodeAtStartup()
: ms_clusterparams
- setSectionAvailable()
: ms_cronoptions
, ms_libraryoptions
, ms_parseoptions
, ms_wwwoptions
, ms_processoroptions
, ms_taxonomyrules
, ms_unigeneoptions
, ms_mascotoptions
, ms_databases
, ms_clusterparams
- setSecurityEnabled()
: ms_security_options
- setSelection()
: ms_quant_average
- setSelectSwitch()
: ms_mascotoptions
- setSemiSpecific()
: ms_enzyme
- setSendmailPath()
: ms_mascotoptions
- setSeparateLockMem()
: ms_mascotoptions
- setSequence()
: ms_quant_normalisation_peptide
- setSeriesUsed()
: ms_fragmentationrules
- setSessionID()
: ms_connection_settings
- setSessionTimeout()
: ms_security_options
- setSettings()
: ms_crosslinking_method
- setShift()
: ms_quant_correction
- setShowAllFromErrorTolerant()
: ms_mascotoptions
- setShowSubsets()
: ms_mascotoptions
- setShowSubSets()
: ms_quant_method
- setSigThreshold()
: ms_mascotoptions
- setSigThresholdValue()
: ms_quant_method
- setSimpleRatio()
: ms_quant_integration
- setSingleHit()
: ms_mascotresults_params
- setSinglyCharged()
: ms_fragmentationrules
- setSite()
: ms_umod_specificity
, ms_quant_specificity
, ms_quant_unmodified
- setSiteAnalysisMD10Prob()
: ms_mascotoptions
- setSortUnassigned()
: ms_mascotoptions
- setSource()
: ms_umod_xref
, ms_quant_integration
- setSpecGroup()
: ms_umod_specificity
- setSpeciesFormatRegex()
: ms_taxonomyrules
- setSpectraPerLibraryBlock()
: ms_mascotoptions
- setSpectrumViewerColourSchemeString()
: ms_mascotoptions
- setSpectrumViewerDefaultColourSchemeName()
: ms_mascotoptions
- setSplitDataFileSize()
: ms_mascotoptions
- setSplitNumberOfQueries()
: ms_mascotoptions
- setSrcDatabaseRule()
: ms_taxonomyrules
- setStoreModPermutations()
: ms_mascotoptions
- setStrategy()
: ms_crosslinking_method
- setStrRule()
: ms_taxonomyrules
- setSubsetsThreshold()
: ms_mascotresults
- setSummedModsStr()
: ms_peptide
- setSVGSpectrumSwitch()
: ms_mascotoptions
- setSymbol()
: ms_umod_elemref
, ms_quant_element
- setTargetFDR()
: ms_mascotresults_params
- setTargetFDRPercentage()
: ms_mascotoptions
- setTargetFDRType()
: ms_mascotresults_params
- setTaxBrowserUrl()
: ms_mascotoptions
- setTaxonomyParseRuleIndex()
: ms_databaseoptions
- setTaxonomyRules()
: ms_datfile
- setTestDirectory()
: ms_mascotoptions
- setText()
: ms_umod_xref
- setThreeLetter()
: ms_umod_aminoacid
- setTitle()
: ms_umod_modification
, ms_enzyme
, ms_modification
, ms_fragmentationrules
, ms_umod_aminoacid
, ms_taxonomychoice
, ms_umod_modbrick
, ms_quant_localdef
, ms_umod_element
- setTitleSource()
: ms_modification
- setToleranceInDa()
: ms_libraryoptions
- setToleranceInPPM()
: ms_libraryoptions
- setTotalIntensity()
: ms_quant_quality
- setTotalIntensityThreshold()
: ms_quant_quality
- setType()
: ms_wwwentry
, ms_quant_correction
- setUnigeneIndexFile()
: ms_mascotresults_params
- setUniGeneOptions()
: ms_datfile
- setUniqueJobStartNumber()
: ms_mascotoptions
- setUniquePepseq()
: ms_quant_quality
- setUnixDirPerm()
: ms_mascotoptions
- setUnixWebUserGroup()
: ms_mascotoptions
- setUrl()
: ms_umod_xref
- setUseHTTPProxyForFTP()
: ms_connection_settings
, ms_mascotoptions
- setUseHTTPProxyForHTTPS()
: ms_connection_settings
, ms_mascotoptions
- setUsePeptideSummary()
: ms_mascotresults_params
- setUserAgent()
: ms_connection_settings
- setUsernameOfPoster()
: ms_umod_modification
- setUserType()
: ms_user
- setUseSessionCookies()
: ms_security_options
- setValue()
: ms_http_client_mime
, ms_crosslinking_monolink
, ms_xml_parameter
, ms_crosslinking_accession
- setValueWithFilename()
: ms_http_client_mime
- setVarModsStr()
: ms_peptide
- setVerifySessionIPAddress()
: ms_security_options
- setVmemory()
: ms_mascotoptions
- setWWWOptions()
: ms_datfile
- setXicMaxWidth()
: ms_quant_integration
- setXicSmoothing()
: ms_quant_integration
- setXicThreshold()
: ms_quant_integration
- setXMLschemaFilePath()
: ms_mascotresfile
- sev_debug1
: ms_log
- sev_debug2
: ms_log
- sev_debug3
: ms_log
- sev_fatal
: ms_log
- sev_info
: ms_log
- sev_warn
: ms_log
- severityAsText()
: ms_loggingmonitor
- SHOW_ALL
: ms_http_client_session
- SHOW_LENGTH
: ms_http_client_session
- SHOW_NONE
: ms_http_client_session
- SHOW_PI
: ms_http_client_session
- SHOW_REFERENCE
: ms_http_client_session
- SHOW_SEQUENCE
: ms_http_client_session
- SHOW_TITLE
: ms_http_client_session
- showInLongList()
: ms_umod_specificity
- showInShortList()
: ms_umod_specificity
- size()
: ms_linker_site_vector
, ms_peptide_quant_key_vector
- sizei()
: ms_matrix
- sizej()
: ms_matrix
- snedecorsCriticalValue()
: ms_quant_stats
- sortBy
: ms_mascotresults
- sortedMedian()
: ms_quant_stats
- sortModifications()
: ms_modfile
- sortPeptides()
: ms_protein
- sortUsers()
: ms_security
- Source_e
: ms_loggingmonitor
- SRC_ALL
: ms_loggingmonitor
- SRC_APPLICATION
: ms_loggingmonitor
- SRC_DENOVOLIB
: ms_loggingmonitor
- SRC_MASCOTSERVER
: ms_loggingmonitor
- SRC_MDRO
: ms_loggingmonitor
- SRC_MSPARSER
: ms_loggingmonitor
- SRC_MSQUANTLIB
: ms_loggingmonitor
- SRC_PURIFIERAPI
: ms_loggingmonitor
- SRC_PURIFIERAPP
: ms_loggingmonitor
- SRC_VENDORSTART
: ms_loggingmonitor
- SS_ASSIGNED
: ms_http_client_search
- SS_COMPLETE
: ms_http_client_search
- SS_ERROR
: ms_http_client_search
- SS_QUEUED
: ms_http_client_search
- SS_RUNNING
: ms_http_client_search
- SS_SEARCH_CONTROL_ERROR
: ms_http_client_search
- SS_UNKNOWN
: ms_http_client_search
- startIteratePeptides()
: ms_aahelper
- staticGetPercolatorFileNames()
: ms_mascotresfile
- STATUS
: ms_progress_info
- stopIteratePeptides()
: ms_aahelper
- stripLastFolder()
: ms_fileutilities
- studentsCriticalValue()
: ms_quant_stats
- submitSearch()
: ms_http_client_session
- sum()
: ms_quant_stats
- sumsq()
: ms_quant_stats
- swap()
: ms_linker_site_vector
, ms_peptide_quant_key_vector
- swilk()
: ms_shapiro_wilk
- systemError()
: ms_http_helper_return
- systemids
: ms_user
, ms_group