Here is a list of all documented class members with links to the class documentation for each member:
- g -
- geometricMean()
: ms_quant_stats
- geometricStandardDeviation()
: ms_quant_stats
- get()
: ms_peptide_quant_key_vector
, ms_spectral_lib_entry
, ms_linker_site_vector
- get_ms_mascotresults_params()
: ms_mascotresfile
, ms_distiller_data
, ms_mascotresfile
- getA()
: ms_fitexy_result
- getAbsoluteValue()
: ms_ms1quant_match_component
- getACCESSION()
: ms_searchparams
- getAccession()
: ms_protein
, ms_protein_quant_ratio
, ms_quant_normalisation_protein
- getAccessionByNumber()
: ms_crosslinking_accessions
- getAccessionFromNumber()
: ms_spectral_lib_file
- getAccessionParseRuleIndex()
: ms_databaseoptions
- getAccessionRefParseRuleIndex()
: ms_databaseoptions
- getAccessions()
: ms_crosslinking_method
- getAccessionSchemaType()
: ms_crosslinking_accessions
, ms_quant_normalisation_protein
- getAccessionsSchemaType()
: ms_crosslinking_method
- getAccFromSpeciesLine()
: ms_taxonomyrules
- getActiveKeys()
: ms_protein_quant_ratio
- getAllChargeStatesSchemaType()
: ms_quant_integration
, ms_quant_precursor
- getAllChargeStatesThreshold()
: ms_quant_integration
- getAllChargeStatesThresholdSchemaType()
: ms_quant_integration
- getAllCustomParamsForUser()
: ms_security
- getAllFamilyMembersWithThisPepMatch()
: ms_mascotresults
, ms_peptidesummary
, ms_proteinsummary
- getAllGroupIDs()
: ms_security
- getAllMatchedIons()
: ms_fragment
- getAllMods()
: ms_spectral_lib_file
- getAllowElutionShiftSchemaType()
: ms_quant_integration
, ms_quant_precursor
- getAllowMassTimeMatchSchemaType()
: ms_quant_precursor
- getAllParamsAsString()
: ms_security_task
- getAllProteinsWithThisPepMatch()
: ms_peptidesummary
, ms_proteinsummary
, ms_mascotresults
- getAllUserIDs()
: ms_security
, ms_group
- getAllUSERParams()
: ms_searchparams
- getAllValuesFromKey()
: ms_tinycdb
- getAlphaVarModsStrLength()
: ms_linker_site_vector
- getAltName()
: ms_umod_modification
- getAltNameSchemaType()
: ms_umod_modification
- getAmbiguityString()
: ms_peptide
- getAminoAcidByName()
: ms_umod_configfile
- getAminoAcidByNumber()
: ms_umod_configfile
- getAnnotation()
: ms_spectral_lib_peak
- getAnyMatch()
: ms_peptide
- getAnyProteinTermination()
: ms_peptide
- getApprovedSchemaType()
: ms_umod_modification
- getAutoDetectNumThreads()
: ms_processors
- getAvePeptideIdentityThreshold()
: ms_mascotresults
- getAverage()
: ms_quant_moverz
, ms_quant_protocol
- getAveragePeptideIntensity()
: ms_ms1quantitation
- getAverageResults()
: ms_ms1quantitation
- getAverageSchemaType()
: ms_quant_moverz
, ms_quant_protocol
- getAvgeMass()
: ms_umod_aminoacid
, ms_umod_composition
, ms_umod_element
, ms_umod_modbrick
- getAvgeMassAsNumber()
: ms_umod_element
- getAvgeMassSchemaType()
: ms_umod_aminoacid
, ms_umod_composition
, ms_umod_element
, ms_umod_modbrick
- getB()
: ms_fitexy_result
- getBetaVarModsStrLength()
: ms_linker_site_vector
- getBoolParam()
: ms_session
- getBucket()
: ms_ms1quant_charge_state
- getBucketWidth()
: ms_ms1quant_charge_state
- getCacheDirectory()
: ms_mascotoptions
, ms_mascotresfile
- getCacheFileName()
: ms_distiller_data_search
, ms_mascotresfile
, ms_peptidesummary
- getCacheFilename()
: ms_distiller_master_search
, ms_peptidesummary
- getCacheStreamName()
: ms_distiller_data_quant
- getCarbonMass()
: ms_searchparams
, ms_masses
- getCentroidWidth()
: ms_mascotoptions
- getCentroidWidthCount()
: ms_mascotoptions
- getCHARGE()
: ms_searchparams
- getCharge()
: ms_fragment
, ms_inputquery
, ms_peptide
, ms_peptide_quant_key
, ms_spectral_lib_entry
- getChargeState()
: ms_ms1quant_match
- getChargeStateData()
: ms_ms1quant_match
- getChargeType()
: ms_ms1quant_match
- getCheckNodesAliveFreq()
: ms_clusterparams
- getChecksum()
: ms_spectral_lib_peak_list
- getChecksumFromNumber()
: ms_spectral_lib_file
- getChi2()
: ms_fitexy_result
- getChopSource()
: ms_parserule_plus
- getChromosome()
: ms_unigene_entry
- getClassification()
: ms_umod_specificity
- getClassificationSchemaType()
: ms_umod_specificity
- getCLE()
: ms_searchparams
- getCleave()
: ms_enzyme
- getClusterParams()
: ms_datfile
- getCode()
: ms_modification
, ms_umod_neutralloss
- getCodeFromXml()
: ms_ms1quant_match
, ms_ms1quant_match_ratio
, ms_ms1quant_peptide_status
, ms_xic
- getCodeInfo()
: ms_ms1quant_match_ratio
- getCodeSchemaType()
: ms_umod_neutralloss
- getCoefficient()
: ms_quant_numerator
- getCoefficientSchemaType()
: ms_quant_numerator
- getColsToOutput()
: ms_logger
- getColumn()
: ms_fragment
- getCOM()
: ms_searchparams
- getCombinedPeptideSummaryCacheStreamName()
: ms_distiller_master_search
- getCombinedReportRatio()
: ms_ms2quantitation
- getCombinedReportRatioNames()
: ms_ms2quantitation
- getCombineRepeats()
: ms_errs
- getCommandStr()
: ms_cronjob
- getComment()
: ms_spectral_lib_entry
- getCommentField()
: ms_spectral_lib_entry
- getComp()
: ms_inputquery
, ms_quant_method
- getComponent()
: ms_protein
, ms_ms1quant_match
, ms_ms1quant_match_component
, ms_ms1quant_peptide_status
- getComponentByName()
: ms_quant_method
- getComponentByNumber()
: ms_quant_method
- getComponentIntensities()
: ms_ms2quantitation
- getComponentIntensity()
: ms_peptidesummary
, ms_proteinsummary
, ms_mascotresults
- getComponentProtein()
: ms_peptidesummary
, ms_mascotresults
- getComponentSchemaType()
: ms_quant_method
- getComponentStr()
: ms_peptide
- getComponentString()
: ms_peptidesummary
, ms_proteinsummary
, ms_mascotresults
- getCompositionString()
: ms_umod_composition
- getCompositionStringSchemaType()
: ms_umod_composition
- getCompressToolAA()
: ms_mascotoptions
- getCompressToolCommandLineFasta()
: ms_mascotoptions
- getCompressToolCommandLineLibrary()
: ms_mascotoptions
- getCompressToolNA()
: ms_mascotoptions
- getCompressToolSL()
: ms_mascotoptions
- getCompSchemaType()
: ms_quant_method
- getConciseLabelFreeVarMods()
: ms_ms1quant_match
- getConnectionSettings()
: ms_crosslinking_configfile
, ms_datfile
, ms_enzymefile
, ms_fragrulesfile
, ms_masses
, ms_modfile
, ms_quant_configfile
, ms_taxonomyfile
, ms_umod_configfile
- getConnectionTimeout()
: ms_connection_settings
- getConsensusData()
: ms_spectral_lib_peak
- getConstantName()
: ms_security_task
- getConstrainSearchSchemaType()
: ms_quant_method
- getContent()
: ms_quant_correction
, ms_quant_numerator
, ms_quant_unmodified
- getContentSchemaType()
: ms_quant_correction
, ms_quant_numerator
, ms_quant_unmodified
- getCoreFromLogical()
: ms_processors
- getCorrectedMaxSPPwidth()
: ms_ms1quant_charge_state
- getCorrectedMinSPPwidth()
: ms_ms1quant_charge_state
- getCorrectedSPPwidth()
: ms_ms1quant_charge_state
- getCorrection()
: ms_quant_component
- getCorrectionMatrix()
: ms_ms1quant_match
- getCorrectionSchemaType()
: ms_quant_component
- getCount()
: ms_http_client_mime
- getCoverage()
: ms_protein
- getCR()
: ms_matrix
- getCrawlerNumPeaksPer100Da()
: ms_mascotoptions
- getCreatePipThreadBlockSize()
: ms_mascotoptions
- getCreatePipThreads()
: ms_mascotoptions
- getCreateSummaryProgress()
: ms_mascotresults
- getCronJob()
: ms_cronoptions
- getCronOptions()
: ms_datfile
- getCROSSLINKING()
: ms_searchparams
- getCrosslinkingMethod()
: ms_mascotresfile
, ms_peptidesummary
- getCtermDelta()
: ms_masses
- getCterminalMass()
: ms_masses
- getCTerminusMass()
: ms_modification
- getCTermMass()
: ms_searchparams
- getCtermNeutralLoss()
: ms_masses
- getCurrentBytes()
: ms_http_helper_progress
- getCutterType()
: ms_enzyme
- getCytoBand()
: ms_unigene_entry
- getDatabase()
: ms_databases
, ms_processoroptions
- getDatabaseName()
: ms_crosslinking_accession
- getDatabaseNameSchemaType()
: ms_crosslinking_accession
- getDatabases()
: ms_datfile
- getDatabaseType()
: ms_mascotresfile
- getDataSourceId()
: ms_ms1quant_match
- getDATAURL()
: ms_searchparams
- getDate()
: ms_mascotresfile
- getDateTimeModified()
: ms_umod_modification
- getDateTimeModifiedSchemaType()
: ms_umod_modification
- getDateTimePosted()
: ms_umod_modification
- getDateTimePostedSchemaType()
: ms_umod_modification
- getDatfile()
: ms_distiller_data
- getDB()
: ms_searchparams
, ms_protein
, ms_protein_quant_ratio
- getDBLevelTaxId()
: ms_taxonomyrules
- getDBType()
: ms_databaseoptions
- getDechargeFragmentPeaks()
: ms_mascotoptions
- getDECOY()
: ms_searchparams
- getDecoyTypeForDB()
: ms_mascotresfile
- getDecoyTypeNoEnzyme()
: ms_mascotoptions
- getDecoyTypeSpecific()
: ms_mascotoptions
- getDefaultDelimiter()
: ms_customproperty
- getDefaultMonitor()
: ms_loggingmonitor
- getDefaultNodeHomeDir()
: ms_clusterparams
- getDefaultNodeHomeDirFromMaster()
: ms_clusterparams
- getDefaultNodeOS()
: ms_clusterparams
- getDefaultPasswordExpiryTime()
: ms_security_options
- getDefaultPort()
: ms_clusterparams
- getDefaultRule()
: ms_taxonomyrules
- getDefaultSchemaFileName()
: ms_crosslinking_configfile
, ms_umod_configfile
- getDelimiterByNumber()
: ms_customproperty
- getDelta()
: ms_peptide
, ms_modification
, ms_quant_localdef
, ms_spectral_lib_peak
, ms_umod_modification
- getDeltaSchemaType()
: ms_quant_localdef
, ms_umod_modification
- getDenominatorByName()
: ms_quant_ratio
- getDenominatorByNumber()
: ms_quant_ratio
- getDenominatorSchemaType()
: ms_quant_ratio
- getDescription()
: ms_progress_info
, ms_quant_method
, ms_security_task
, ms_umod_neutralloss
, ms_xml_parameter
, ms_crosslinking_method
- getDescriptionLineSep()
: ms_taxonomyrules
- getDescriptionParseRuleIndex()
: ms_databaseoptions
- getDescriptionSchemaType()
: ms_crosslinking_method
, ms_crosslinking_parameter
, ms_quant_method
, ms_quant_parameter
, ms_umod_neutralloss
, ms_xml_parameter
- getDiffsAsText()
: ms_security_tasks
- getDiscoveredErrTolModDeltas()
: ms_mascotresults
- getDiscoveredErrTolModNames()
: ms_mascotresults
- getDiscoveredLocalModDeltas()
: ms_mascotresults
- getDiscoveredLocalModNames()
: ms_mascotresults
- getDisplayIntensity()
: ms_ms1quant_match
- getDisplayNonSignificantMatches()
: ms_mascotoptions
- getDistillerProjectStreamName()
: ms_distiller_data
- getDistillerResfileTimestamp()
: ms_distiller_data
- getDistillerVersion()
: ms_distiller_data
- getDistinctPeptide()
: ms_protein
- getDistributor()
: ms_license
- getDoesNotPairWithByNumber()
: ms_crosslinking_linker
- getDoesNotPairWithSchemaType()
: ms_crosslinking_linker
- getDoThisRuleFirst()
: ms_taxonomyrules
- getDoubleParam()
: ms_session
- getDoubleParams()
: ms_security_task
- getElectronMass()
: ms_searchparams
, ms_masses
- getElement()
: ms_quant_composition
, ms_quant_correction
- getElementByName()
: ms_umod_configfile
- getElementByNumber()
: ms_umod_configfile
- getElementSchemaType()
: ms_quant_composition
, ms_quant_correction
- getElemRef()
: ms_umod_aminoacid
, ms_umod_composition
, ms_umod_modbrick
- getElemRefSchemaType()
: ms_umod_aminoacid
, ms_umod_composition
, ms_umod_modbrick
- getElutionProfileCorrelationThreshold()
: ms_quant_integration
- getElutionProfileCorrelationThresholdSchemaType()
: ms_quant_integration
- getElutionTimeDelta()
: ms_quant_integration
- getElutionTimeDeltaSchemaType()
: ms_quant_integration
- getElutionTimeDeltaUnit()
: ms_quant_integration
- getElutionTimeDeltaUnitSchemaType()
: ms_quant_integration
- getElutionTimeShift()
: ms_xic
- getEmailAddress()
: ms_session
, ms_user
- getEmailFromTextName()
: ms_mascotoptions
- getEmailFromUser()
: ms_mascotoptions
- getEmailPassword()
: ms_mascotoptions
- getEmailProfile()
: ms_mascotoptions
- getEmailService()
: ms_mascotoptions
- getEmailTimeOutPeriod()
: ms_mascotoptions
- getEncryptedPassword()
: ms_user
- getEnd()
: ms_fragment
- getEndDate()
: ms_license
- getEndIndex()
: ms_xic
- getEndScanId()
: ms_xic
- getEntry()
: ms_wwwoptions
- getEntryByName()
: ms_taxonomyfile
- getEntryByNumber()
: ms_taxonomyfile
- getEntryFromNumber()
: ms_spectral_lib_file
- getEntryFromNumberAsText()
: ms_spectral_lib_file
- getEnzyme()
: ms_aahelper
, ms_mascotresfile
- getEnzymeByName()
: ms_enzymefile
- getEnzymeByNumber()
: ms_enzymefile
- getEnzymes()
: ms_mascotfiles
- getErrMessageEmailTo()
: ms_mascotoptions
- getError()
: ms_distiller_search_status
- getErrorCode()
: ms_shapiro_wilk
- getErrorHandler()
: ms_errors
- getErrorLevel()
: ms_taxonomyrules
- getErrorLogFile()
: ms_mascotoptions
- getErrorNumber()
: ms_errs
, ms_mascotresfile
- getErrorRepeats()
: ms_errs
- getErrorSeverity()
: ms_errs
- getErrorString()
: ms_errs
, ms_mascotresfile
- getErrorText()
: ms_http_helper_return
- getERRORTOLERANT()
: ms_searchparams
- getErrorType()
: ms_http_helper_return
- getErrTolMaxAccessions()
: ms_mascotoptions
- getErrTolModDelta()
: ms_mascotresults
- getErrTolModMasterNeutralLoss()
: ms_mascotresults
- getErrTolModMasterString()
: ms_peptidesummary
, ms_proteinsummary
, ms_mascotresults
- getErrTolModName()
: ms_mascotresults
- getErrTolModNeutralLoss()
: ms_mascotresults
- getErrTolModPepNeutralLoss()
: ms_mascotresults
- getErrTolModPepString()
: ms_peptidesummary
, ms_proteinsummary
, ms_mascotresults
- getErrTolModReqPepNeutralLoss()
: ms_mascotresults
- getErrTolModReqPepString()
: ms_peptidesummary
, ms_proteinsummary
, ms_mascotresults
- getErrTolModSlaveNeutralLoss()
: ms_mascotresults
- getErrTolModSlaveString()
: ms_peptidesummary
, ms_proteinsummary
, ms_mascotresults
- getErrTolModString()
: ms_peptidesummary
, ms_proteinsummary
, ms_mascotresults
- getErrTolParentFilename()
: ms_searchparams
- getErrTolPeptide()
: ms_distiller_data_search
- getErrTolProbabilityThreshold()
: ms_mascotresults
- getExcludedKeys()
: ms_protein_quant_ratio
- getExcludeInternalLabelSchemaType()
: ms_quant_multiplex
- getExcludeIsobaricFragmentsSchemaType()
: ms_quant_multiplex
- getExcludeTaxonomy()
: ms_taxonomychoice
- getExclusion()
: ms_quant_method
- getExclusionSchemaType()
: ms_quant_method
- getExecAfterSearch()
: ms_mascotoptions
- getExecTime()
: ms_mascotresfile
- getExpectationValue()
: ms_peptide
- getExpress()
: ms_unigene_entry
- getFastaPath()
: ms_mascotresfile
- getFastaVer()
: ms_mascotresfile
- getFeatures()
: ms_license
- getFeatureTableLength()
: ms_mascotoptions
- getFeatureTableMinScore()
: ms_mascotoptions
- getFileIndex()
: ms_quant_component
- getFileIndexSchemaType()
: ms_quant_component
- getFilename()
: ms_http_client_mime
- getFILENAME()
: ms_searchparams
- getFileName()
: ms_crosslinking_configfile
, ms_datfile
, ms_enzymefile
, ms_fragrulesfile
, ms_license
, ms_mascotresfile
, ms_masses
, ms_modfile
, ms_quant_configfile
, ms_spectral_lib_entry
, ms_spectral_lib_file
, ms_taxonomyfile
, ms_taxspeciesfiles
, ms_taxnodesfiles
, ms_umod_configfile
- getFileOffset()
: ms_unigene_entry
- getFileOffsetFromKey()
: ms_tinycdb
- getFileSize()
: ms_fileutilities
- getFileTypeToSearch()
: ms_parserule_plus
- getFilters()
: ms_crosslinking_method
- getFiltersSchemaType()
: ms_crosslinking_method
- getFindFileTimeout()
: ms_datfile
- getFirstProtAppearedIn()
: ms_peptide
- getFirstSerie()
: ms_fragmentationrules
- getFirstSeries()
: ms_fragmentationrules
- getFirstXicScanId()
: ms_ms1quant_match
- getFitexy()
: ms_ms1quant_match_ratio
- getFixedMods()
: ms_aahelper
- getFixedModsDelta()
: ms_searchparams
- getFixedModsName()
: ms_searchparams
- getFixedModsNeutralLoss()
: ms_searchparams
- getFixedModsResidues()
: ms_searchparams
- getFlags()
: ms_mascotresults
, ms_mascotresults_params
- getFlags2()
: ms_mascotresults
, ms_mascotresults_params
- getFlagSchemaType()
: ms_quant_neutralloss
, ms_umod_neutralloss
- getFORMAT()
: ms_searchparams
- getFormat()
: ms_spectral_lib_file
, ms_taxspeciesfiles
, ms_taxnodesfiles
- getFORMVER()
: ms_searchparams
- getFormVersion()
: ms_mascotoptions
- getFragmentByNumber()
: ms_fragmentvector
- getFragResidueMass()
: ms_masses
- getFragRulesFile()
: ms_distiller_data
- getFrame()
: ms_protein
- getFrequencies()
: ms_mascotfiles
- getFromUnimod()
: ms_modification
- getFullName()
: ms_user
, ms_umod_aminoacid
, ms_umod_element
, ms_umod_modbrick
, ms_umod_modification
- getFullNameSchemaType()
: ms_umod_aminoacid
, ms_umod_element
, ms_umod_modbrick
, ms_umod_modification
- getFullUserName()
: ms_session
- getGencodeFile()
: ms_taxonomyrules
- getGene()
: ms_unigene_entry
- getGetSeqBlastAccession()
: ms_mascotoptions
- getGetSeqJobIdFile()
: ms_mascotoptions
- getGroup()
: ms_security
- getGroupFromID()
: ms_security
- getGrouping()
: ms_protein
- getGroupOfPoster()
: ms_umod_modification
- getGroupOfPosterSchemaType()
: ms_umod_modification
- getHavePeakList()
: ms_distiller_sub_project
- getHeaderComments()
: ms_datfile
- getHeaderLine()
: ms_logger
- getHeaderValue()
: ms_http_helper
- getHiddenSchemaType()
: ms_umod_specificity
- getHit()
: ms_peptidesummary
, ms_mascotresults
, ms_ms1quant_match
, ms_ms1quantitation
- getHitNumber()
: ms_protein
- getHomologyThreshold()
: ms_mascotresults
- getHomologyThresholdForHistogram()
: ms_mascotresults
- getHostName()
: ms_computeraddress
, ms_wwwentry
- getHT_IDFromLogical()
: ms_processors
- getHttpPassword()
: ms_connection_settings
- getHttpProtocol()
: ms_connection_settings
- getHttpStatusCode()
: ms_http_helper_return
- getHttpUsername()
: ms_connection_settings
- getHydrogenMass()
: ms_searchparams
, ms_masses
- getHyperThreadedCPUsMask()
: ms_processors
- getHyperThreadingState()
: ms_processors
- getHypothesisPvalue()
: ms_protein_quant_ratio
- getICAT()
: ms_searchparams
- getICATFilter()
: ms_mascotoptions
- getICATHeavy()
: ms_mascotoptions
- getICATLight()
: ms_mascotoptions
- getICATQuantitationMethod()
: ms_mascotoptions
- getID()
: ms_unigene_entry
, ms_peptide_quant_key
, ms_group
, ms_session
, ms_security_task
, ms_user
- getId()
: ms_distiller_master_search
, ms_distiller_search_status
, ms_distiller_sub_project
- getIdentifier()
: ms_taxonomyrules
- getIgnore()
: ms_quant_localdef
, ms_umod_modification
- getIgnoredQPs()
: ms_protein
- getIgnoreDupeAccession()
: ms_mascotoptions
- getIgnoreIonsScoreBelow()
: ms_mascotoptions
, ms_mascotresults_params
- getIgnoreMass()
: ms_modification
- getIgnoreSchemaType()
: ms_quant_localdef
, ms_umod_modification
- getIncludeTaxonomy()
: ms_taxonomychoice
- getIndex()
: ms_inputquery
- getIndexFileName()
: ms_tinycdb
- getInetAddress()
: ms_computeraddress
- getINSTRUMENT()
: ms_inputquery
, ms_searchparams
- getInstrumentByName()
: ms_fragrulesfile
- getInstrumentByNumber()
: ms_fragrulesfile
- getInstrumentName()
: ms_fragrulesfile
- getIntactLinks()
: ms_peptide
- getIntegraAppServerURL()
: ms_security_options
- getIntegraDatabaseName()
: ms_security_options
- getIntegraOracleServerName()
: ms_security_options
- getIntegration()
: ms_quant_method
- getIntegrationSchemaType()
: ms_quant_method
- getIntegraUsers()
: ms_security
- getIntensity()
: ms_spectral_lib_peak
- getIntensityNormalisationBase()
: ms_ms2quantitation
- getIntensitySigFigs()
: ms_mascotoptions
- getInterFileBasePath()
: ms_mascotoptions
- getInterFileRelPath()
: ms_mascotoptions
- getINTERMEDIATE()
: ms_searchparams
- getIntFromKey()
: ms_tinycdb
- getIntMax()
: ms_inputquery
- getIntMin()
: ms_inputquery
- getIntParam()
: ms_session
- getIonIntensityThreshold()
: ms_quant_multiplex
- getIonIntensityThresholdSchemaType()
: ms_quant_multiplex
- getIonMobility()
: ms_inputquery
- getIonsDecimalPlaces()
: ms_mascotoptions
- getIonSeries()
: ms_quant_multiplex
- getIonSeriesSchemaType()
: ms_quant_multiplex
- getIonsIntensity()
: ms_peptide
- getIonsScore()
: ms_peptide
, ms_peptidesummary
, ms_proteinsummary
, ms_mascotresults
- getIonsScoreCorrected()
: ms_mascotresults
- getIonsScoreHistogram()
: ms_mascotresults
- getIPAddress()
: ms_session
- getIPCLogfile()
: ms_clusterparams
- getIPCLogging()
: ms_clusterparams
- getIPCTimeout()
: ms_clusterparams
- getIsDatabaseActive()
: ms_http_client
- getIsFromErrorTolerant()
: ms_peptide
- getIsFromLibrary()
: ms_peptide
- getIsolatedPrecursorSchemaType()
: ms_quant_quality
- getIsolatedPrecursorThreshold()
: ms_quant_quality
- getIsolatedPrecursorThresholdSchemaType()
: ms_quant_quality
- getIsotope()
: ms_quant_component
- getIsotopeSchemaType()
: ms_quant_component
- getIsPermitted()
: ms_http_client_session
- getIsSecurityEnabled()
: ms_http_client
- getIsWebAuthenticationEnabled()
: ms_http_client
- getIsXmlUploadedList()
: ms_http_client_session
- getIT_MODS()
: ms_inputquery
, ms_searchparams
- getItemFromId()
: ms_obofile
- getITOL()
: ms_searchparams
- getITOLU()
: ms_searchparams
- getJobNumber()
: ms_mascotresfile
- getKeepAlive()
: ms_mascotresfile
- getKey()
: ms_ms1quant_match
, ms_peptide_quant_ratio
- getLabel()
: ms_fragment
- getLabelFree()
: ms_ms1quantitation
- getLabelFreeVarMods()
: ms_ms1quant_match
- getLastAccessed()
: ms_session
- getLastError()
: ms_errs
, ms_errors
, ms_mascotresfile
- getLastErrorString()
: ms_errs
, ms_errors
, ms_mascotresfile
- getLastModificationTime()
: ms_fileutilities
- getLastQueryAscFile()
: ms_mascotoptions
- getLastSerie()
: ms_fragmentationrules
- getLastSeries()
: ms_fragmentationrules
- getLastXicScanId()
: ms_ms1quant_match
- getLessThanMinPepLen()
: ms_peptide
- getLIBRARY_SEARCH()
: ms_searchparams
- getLibraryEntryId()
: ms_peptidesummary
- getLibraryModDelta()
: ms_searchparams
- getLibraryModName()
: ms_searchparams
- getLibraryModString()
: ms_peptidesummary
, ms_proteinsummary
, ms_mascotresults
- getLibraryName()
: ms_libraryoptions
- getLibraryOptions()
: ms_datfile
- getLICENSE()
: ms_searchparams
- getLicensee()
: ms_license
- getLicenseString()
: ms_license
- getLicenseVersion()
: ms_license
- getLine()
: ms_spectral_lib_entry
- getLinkerByNumber()
: ms_crosslinking_linkers
- getLinkerMass()
: ms_linker_site
- getLinkers()
: ms_crosslinking_method
- getLinkerSchemaType()
: ms_crosslinking_linkers
- getLinkersSchemaType()
: ms_crosslinking_method
- getLinkFrom()
: ms_linker_site
- getLinkTo()
: ms_linker_site
- getLoaded()
: ms_distiller_data_search
- getLoadedSearchIndex()
: ms_distiller_data
- getLoadUnassigned()
: ms_distiller_data_search
- getLocalDefinition()
: ms_quant_modgroup
- getLocalDefinitionSchemaType()
: ms_quant_modgroup
- getLocalModifications()
: ms_quant_method
- getLocalModsNlStr()
: ms_peptide
- getLocalModsStr()
: ms_peptide
- getLocalVarModName()
: ms_inputquery
- getLocus()
: ms_inputquery
- getLocusLink()
: ms_unigene_entry
- getLogEventsHandler()
: ms_loggingmonitor
- getLogFilename()
: ms_file_logger
- getLogFileName()
: ms_cronoptions
, ms_security_options
- getLoggingFileName()
: ms_errs
- getLoggingLevel()
: ms_cronoptions
, ms_errs
, ms_log
, ms_security_options
- getLogMask()
: ms_loggingmonitor
- getLogoImageFile()
: ms_mascotoptions
- getLongestPeptideLen()
: ms_protein
- getLongestSigPeptideLen()
: ms_protein
- getLongParam()
: ms_session
- getLongParams()
: ms_security_task
- getLoopLinks()
: ms_peptide
- getMailTempFile()
: ms_mascotoptions
- getMailTransport()
: ms_mascotoptions
- getMajorVersion()
: ms_crosslinking_configfile
, ms_quant_configfile
, ms_umod_configfile
- getMascNodeCtrlFile()
: ms_mascotoptions
- getMascotCmdLine()
: ms_mascotoptions
- getMascotControlFile()
: ms_mascotoptions
- getMascotFileProcessingThreads()
: ms_mascotoptions
- getMascotFiles()
: ms_datfile
- getMascotJobIdFile()
: ms_mascotoptions
- getMascotMessage()
: ms_mascotoptions
- getMascotNodeRebootScript()
: ms_clusterparams
- getMascotNodeScript()
: ms_clusterparams
- getMascotOptions()
: ms_datfile
- getMascotSearchURL()
: ms_distiller_data_search
- getMascotSecurityOptions()
: ms_security
- getMascotServerURL()
: ms_distiller_data_search
- getMascotVer()
: ms_mascotresfile
- getMass()
: ms_fragment
- getMASS()
: ms_searchparams
- getMassDecimalPlaces()
: ms_mascotoptions
- getMassDelta()
: ms_quant_integration
- getMassDeltaSchemaType()
: ms_quant_integration
- getMassDeltaUnit()
: ms_quant_integration
- getMassDeltaUnitSchemaType()
: ms_quant_integration
- getMasses()
: ms_aahelper
, ms_mascotresfile
, ms_protein
- getMassesWithinTolerance()
: ms_fragmentvector
- getMassFile()
: ms_modification
, ms_modfile
- getMassMax()
: ms_inputquery
- getMassMin()
: ms_inputquery
- getMassType()
: ms_searchparams
- getMasterComputer()
: ms_clusterparams
- getMasterProjectStreamName()
: ms_distiller_master_project
- getMatch()
: ms_ms1quantitation
- getMatchedFraction()
: ms_ms1quant_charge_state
- getMatchedIonIntensity()
: ms_fragment
- getMatchedIonMass()
: ms_fragment
- getMatchedRho()
: ms_ms1quant_charge_state
, ms_quant_integration
- getMatchedRhoSchemaType()
: ms_quant_integration
- getMatchForHit()
: ms_ms1quantitation
- getMaxAlignment()
: ms_ms1quant_charge_state
- getMaxConcurrentSearches()
: ms_mascotoptions
- getMaxDatabases()
: ms_mascotoptions
- getMaxDescriptionLen()
: ms_mascotoptions
- getMaxEtagMassDelta()
: ms_mascotoptions
- getMaxEtVarMods()
: ms_mascotoptions
- getMaxHitsToReport()
: ms_mascotresults_params
- getMaxIntactCrosslinkPeptides()
: ms_mascotoptions
- getMaxInternalMass()
: ms_fragmentationrules
, ms_inputquery
, ms_searchparams
- getMaxNumOfReportBuilderColumnArrangements()
: ms_mascotoptions
- getMaxNumPeptides()
: ms_mascotoptions
- getMaxPepModArrangements()
: ms_mascotoptions
- getMaxPepNumModifiedSites()
: ms_mascotoptions
- getMaxPepNumVarMods()
: ms_mascotoptions
- getMaxPeptideIdentityThreshold()
: ms_mascotresults
- getMaxQueries()
: ms_mascotoptions
- getMaxRankValue()
: ms_mascotresults
- getMaxSearchesPerUser()
: ms_mascotoptions
- getMaxSequenceLen()
: ms_mascotoptions
- getMaxTaxonomyRules()
: ms_datfile
- getMaxVarMods()
: ms_mascotoptions
- getMD5Sum()
: ms_fileutilities
- getMemberNumber()
: ms_protein
- getMessageSource()
: ms_log
- getMethod()
: ms_quant_integration
, ms_quant_normalisation
, ms_quant_outliers
- getMethodByName()
: ms_crosslinking_configfile
, ms_quant_configfile
- getMethodByNumber()
: ms_crosslinking_configfile
, ms_quant_configfile
- getMethodSchemaType()
: ms_quant_integration
, ms_quant_normalisation
, ms_quant_outliers
- getMinEtagMassDelta()
: ms_mascotoptions
- getMinimumA1()
: ms_quant_quality
- getMinimumA1SchemaType()
: ms_quant_quality
- getMinimumPasswordLength()
: ms_security_options
- getMinInternalMass()
: ms_fragmentationrules
, ms_inputquery
, ms_searchparams
- getMinIonPairs()
: ms_quant_multiplex
- getMinIonPairsSchemaType()
: ms_quant_multiplex
- getMinNumPeptides()
: ms_quant_method
, ms_quantitation
- getMinNumPeptidesSchemaType()
: ms_quant_method
- getMinNumSigUniqueSequences()
: ms_mascotresults_params
- getMinorVersion()
: ms_crosslinking_configfile
, ms_quant_configfile
, ms_umod_configfile
- getMinPepLenInPepSummary()
: ms_distiller_data_search
, ms_mascotoptions
, ms_mascotresults
- getMinPepLenInPeptideSummary()
: ms_mascotresults_params
- getMinPepLenInSearch()
: ms_mascotoptions
- getMinPrecursorCharge()
: ms_quant_quality
- getMinPrecursorChargeSchemaType()
: ms_quant_quality
- getMinProbability()
: ms_mascotresults_params
- getMinProbabilityForSLScore()
: ms_peptidesummary
- getMiscNotes()
: ms_umod_modification
, ms_umod_specificity
- getMiscNotesSchemaType()
: ms_umod_modification
, ms_umod_specificity
- getMissed()
: ms_aahelper
- getMissedCleavages()
: ms_peptide
- getModBrickByName()
: ms_umod_configfile
- getModBrickByNumber()
: ms_umod_configfile
- getMode()
: ms_quant_modgroup
- getModeSchemaType()
: ms_quant_modgroup
- getModFile()
: ms_quant_modgroup
- getModFileList()
: ms_umod_configfile
, ms_umod_modification
- getModFileName()
: ms_crosslinking_does_not_pair_with
, ms_crosslinking_linker
- getModFileNameSchemaType()
: ms_crosslinking_does_not_pair_with
, ms_crosslinking_linker
- getModFileSchemaType()
: ms_quant_modgroup
- getModificationByName()
: ms_modvector
, ms_modfile
, ms_umod_configfile
- getModificationByNumber()
: ms_modvector
, ms_modfile
, ms_umod_configfile
- getModificationGroupByName()
: ms_quant_component
, ms_quant_method
- getModificationGroupByNumber()
: ms_quant_component
, ms_quant_method
- getModificationGroupSchemaType()
: ms_quant_component
, ms_quant_method
- getModifications()
: ms_mascotfiles
, ms_quant_satellite
- getModificationsSchemaType()
: ms_quant_satellite
- getModificationType()
: ms_modification
- getModifiedResidue()
: ms_modification
- getMODS()
: ms_searchparams
- getMods()
: ms_spectral_lib_entry
- getModsFromNumber()
: ms_spectral_lib_file
- getMonitorEmailCheckFreq()
: ms_mascotoptions
- getMonitorLogFile()
: ms_mascotoptions
- getMonitorPidFile()
: ms_mascotoptions
- getMonitorTestTimeout()
: ms_mascotoptions
- getMonoisotopic()
: ms_quant_moverz
- getMonoisotopicSchemaType()
: ms_quant_moverz
- getMonoLinkByNumber()
: ms_crosslinking_linker
- getMonoLinkModification()
: ms_mascotresfile
- getMonoLinkSchemaType()
: ms_crosslinking_linker
- getMonoLinkStr()
: ms_peptide
- getMonoLinkTitle()
: ms_modification
- getMonoMass()
: ms_umod_aminoacid
, ms_umod_composition
, ms_umod_element
, ms_umod_modbrick
- getMonoMassAsNumber()
: ms_umod_element
- getMonoMassSchemaType()
: ms_umod_aminoacid
, ms_umod_composition
, ms_umod_element
, ms_umod_modbrick
- getMoverz()
: ms_ms1quant_match_component
, ms_quant_component
- getMoverzSchemaType()
: ms_quant_component
- getMrCalc()
: ms_peptide
- getMrExperimental()
: ms_peptide
- getMSParserVersion()
: ms_mascotresfile
- getMudpit()
: ms_mascotoptions
- getMudpitSwitch()
: ms_mascotoptions
- getMULTI_SITE_MODS()
: ms_searchparams
- getMultiFileQueryNumber()
: ms_mascotresfile
- getMultiplex()
: ms_quant_protocol
- getMultiplexSchemaType()
: ms_quant_protocol
- getMultithreadedName()
: ms_processors
- getMW()
: ms_spectral_lib_entry
- getMz()
: ms_spectral_lib_peak
- getName()
: ms_crosslinking_method
, ms_databaseoptions
, ms_distiller_sub_project
, ms_http_client_mime
, ms_dbprocessors
, ms_quant_component
, ms_quant_method
, ms_quant_modgroup
, ms_quant_numerator
, ms_quant_ratio
, ms_group
, ms_user
, ms_spectral_lib_entry
, ms_wwwentry
, ms_xml_parameter
- getNameOfDB()
: ms_parserule_plus
- getNameSchemaType()
: ms_crosslinking_method
, ms_crosslinking_parameter
, ms_quant_component
, ms_quant_method
, ms_quant_modgroup
, ms_quant_numerator
, ms_quant_parameter
, ms_quant_ratio
, ms_xml_parameter
- getNeutralLoss()
: ms_fragment
, ms_modification
, ms_quant_specificity
, ms_umod_specificity
- getNeutralLossRequired()
: ms_modification
- getNeutralLossSchemaType()
: ms_quant_specificity
, ms_umod_specificity
- getNew()
: ms_quant_isotope
- getNewSchemaType()
: ms_quant_isotope
- getNextFamilyProtein()
: ms_mascotresults
- getNextPeptide()
: ms_aahelper
- getNextSimilarProtein()
: ms_mascotresults
- getNextSimilarProteinOf()
: ms_mascotresults
- getNextSubsetProtein()
: ms_mascotresults
- getNextSubsetProteinOf()
: ms_mascotresults
- getNitrogenMass()
: ms_searchparams
, ms_masses
- getNoBreakDescLineIf()
: ms_taxonomyrules
- getNodeListFile()
: ms_mascotfiles
- getNodeSequenceDatabaseDir()
: ms_clusterparams
- getNodesFile()
: ms_taxonomyrules
- getNonMudpitScore()
: ms_protein
- getNoResultsScript()
: ms_mascotoptions
- getNormalisation()
: ms_quant_method
- getNormalisationSchemaType()
: ms_quant_method
- getNormalityPvalue()
: ms_protein_quant_ratio
- getNotes()
: ms_security_task
- getNtermDelta()
: ms_masses
- getNterminalMass()
: ms_masses
- getNTerminusMass()
: ms_modification
- getNTermMass()
: ms_searchparams
- getNtermNeutralLoss()
: ms_masses
- getNTIUserGroup()
: ms_mascotoptions
- getNTMonitorGroup()
: ms_mascotoptions
- getNum13C()
: ms_peptide
- getNumAccessions()
: ms_unigene_entry
- getNumAvailableToProcess()
: ms_processors
- getNumber()
: ms_quant_element
, ms_umod_elemref
- getNumberOfAccessionDBTypes()
: ms_peptidesummary
- getNumberOfAccessions()
: ms_crosslinking_accessions
- getNumberOfAltNames()
: ms_umod_modification
- getNumberOfAminoAcids()
: ms_umod_configfile
- getNumberOfBuckets()
: ms_ms1quant_charge_state
- getNumberOfComponents()
: ms_quant_method
- getNumberOfCorrections()
: ms_quant_component
- getNumberOfCronJobs()
: ms_cronoptions
- getNumberOfCutters()
: ms_enzyme
- getNumberOfDatabases()
: ms_databases
, ms_searchparams
, ms_processoroptions
- getNumberOfDenominators()
: ms_quant_ratio
- getNumberOfDoesNotPairWiths()
: ms_crosslinking_linker
- getNumberOfElements()
: ms_quant_composition
, ms_umod_configfile
- getNumberOfElemRefs()
: ms_umod_aminoacid
, ms_umod_composition
, ms_umod_modbrick
- getNumberOfEntries()
: ms_obofile
, ms_taxonomyfile
, ms_wwwoptions
- getNumberOfEnzymes()
: ms_enzymefile
- getNumberOfErrors()
: ms_errs
, ms_mascotresfile
- getNumberOfExcludeTaxonomies()
: ms_taxonomychoice
- getNumberOfExclusions()
: ms_quant_method
- getNumberOfFamilyAccessionDBTypes()
: ms_peptidesummary
- getNumberOfFamilyMembers()
: ms_mascotresults
- getNumberOfFragments()
: ms_fragmentvector
- getNumberOfGencodeFiles()
: ms_taxonomyrules
- getNumberOfHits()
: ms_mascotresults
- getNumberOfIgnoreDupeAccessions()
: ms_mascotoptions
- getNumberOfIgnoreMasses()
: ms_modification
- getNumberOfIgnores()
: ms_quant_localdef
, ms_umod_modification
- getNumberOfIncludeTaxonomies()
: ms_taxonomychoice
- getNumberOfInstruments()
: ms_fragrulesfile
- getNumberOfIonSeries()
: ms_quant_multiplex
- getNumberOfIsotopes()
: ms_quant_component
- getNumberOfLibraries()
: ms_libraryoptions
- getNumberOfLibraryMods()
: ms_searchparams
- getNumberOfLinkedPeptides()
: ms_peptide
- getNumberOfLinkers()
: ms_crosslinking_linkers
- getNumberOfLocalDefinitions()
: ms_quant_modgroup
- getNumberOfLocalVarMods()
: ms_inputquery
- getNumberOfMethods()
: ms_crosslinking_configfile
, ms_quant_configfile
- getNumberOfModBricks()
: ms_umod_configfile
- getNumberOfModFiles()
: ms_quant_modgroup
- getNumberOfModificationGroups()
: ms_quant_component
, ms_quant_method
- getNumberOfModifications()
: ms_modvector
, ms_modfile
, ms_umod_configfile
- getNumberOfModifiedResidues()
: ms_modification
- getNumberOfMonoLinks()
: ms_crosslinking_linker
- getNumberOfNeutralLosses()
: ms_quant_specificity
, ms_umod_specificity
- getNumberOfNoBreakDescLineIf()
: ms_taxonomyrules
- getNumberOfNodesFiles()
: ms_taxonomyrules
- getNumberOfNumerators()
: ms_quant_ratio
- getNumberOfParameters()
: ms_xml_parameters
, ms_crosslinking_parameters
, ms_quant_parameters
- getNumberOfParseRules()
: ms_parseoptions
- getNumberOfPeaks()
: ms_inputquery
- getNumberOfPepNeutralLosses()
: ms_umod_specificity
, ms_quant_specificity
- getNumberOfPeptides()
: ms_quant_normalisation_peptides
- getNumberOfPerDbSrcRules()
: ms_taxonomyrules
- getNumberOfPrefixRemoves()
: ms_taxonomyrules
- getNumberOfProcessors()
: ms_processoroptions
- getNumberOfProperties()
: ms_customproperty
- getNumberOfProteins()
: ms_quant_normalisation_proteins
- getNumberOfReportNumberChoices()
: ms_mascotoptions
- getNumberOfReportRatios()
: ms_quant_method
- getNumberOfResfiles()
: ms_mascotresfile
- getNumberOfSeqs()
: ms_quant_method
- getNumberOfSpeciesFiles()
: ms_taxonomyrules
- getNumberOfSpecificities()
: ms_quant_localdef
, ms_umod_modification
- getNumberOfStrFiles()
: ms_taxonomyrules
- getNumberOfSubClusters()
: ms_clusterparams
- getNumberOfSubtasks()
: ms_progress_info
- getNumberOfSuffixRemoves()
: ms_taxonomyrules
- getNumberOfTargetFDRPercentages()
: ms_mascotoptions
- getNumberOfTasks()
: ms_security_tasks
- getNumberOfThreads()
: ms_databaseoptions
, ms_dbprocessors
- getNumberOfUnassigned()
: ms_mascotresults
- getNumberOfUnmodified()
: ms_quant_modgroup
- getNumberOfXrefs()
: ms_umod_modification
- getNumberSchemaType()
: ms_quant_element
, ms_umod_elemref
- getNumComponents()
: ms_ms1quant_match
, ms_protein
- getNumCores()
: ms_processors
- getNumDecoyHitsAboveHomology()
: ms_mascotresults
- getNumDecoyHitsAboveIdentity()
: ms_mascotresults
- getNumDiscoveredErrTolMods()
: ms_mascotresults
- getNumDiscoveredFixedMods()
: ms_mascotresults
- getNumDiscoveredIntactLinks()
: ms_mascotresults
- getNumDiscoveredLibraryMods()
: ms_mascotresults
- getNumDiscoveredLocalMods()
: ms_mascotresults
- getNumDiscoveredNonSpecCleavage()
: ms_mascotresults
- getNumDiscoveredVariableMods()
: ms_mascotresults
- getNumDisplayPeptides()
: ms_protein
- getNumDistinctPeptideRepeats()
: ms_protein
- getNumDistinctPeptides()
: ms_protein
- getNumEntries()
: ms_spectral_lib_file
- getNumeratorByName()
: ms_quant_ratio
- getNumeratorByNumber()
: ms_quant_ratio
- getNumeratorSchemaType()
: ms_quant_ratio
- getNumEtSeqsSearched()
: ms_mascotresfile
- getNumGroups()
: ms_ms1quantitation
- getNumHits()
: ms_mascotresfile
, ms_ms1quant_match
, ms_ms1quantitation
- getNumHitsAboveHomology()
: ms_mascotresults
- getNumHitsAboveIdentity()
: ms_mascotresults
- getNumIonsMatched()
: ms_peptide
- getNumLibraryEntries()
: ms_mascotresfile
- getNumLogEventsHandlers()
: ms_loggingmonitor
- getNumLogicalPerPhysical()
: ms_processors
- getNumMatches()
: ms_ms1quantitation
- getNumMatchesForGroup()
: ms_ms1quantitation
- getNumMatchesForHit()
: ms_ms1quantitation
- getNumObservedForEmPAI()
: ms_protein
- getNumOnSystem()
: ms_processors
- getNumPeaks()
: ms_spectral_lib_peak_list
, ms_spectral_lib_entry
- getNumPeptideRatios()
: ms_ms1quant_match
- getNumPeptides()
: ms_quant_average
, ms_protein
, ms_ms1quant_match_component
- getNumPeptidesSchemaType()
: ms_quant_average
- getNumPeptideStatuses()
: ms_ms1quantitation
- getNumPhysicalOnSystem()
: ms_processors
- getNumPmfQueriesUsed()
: ms_proteinsummary
- getNumPoints()
: ms_xic
- getNumProcessorGroups()
: ms_processors
- getNumProcessorsLicensed()
: ms_license
- getNumProteinFamilies()
: ms_ms1quantitation
- getNumProteins()
: ms_peptide
- getNumQueries()
: ms_mascotresfile
- getNumRanges()
: ms_ms1quant_match_component
- getNumResidues()
: ms_spectral_lib_file
, ms_mascotresfile
- getNumSearches()
: ms_distiller_master_project
, ms_distiller_search_status_list
- getNumSeqs()
: ms_mascotresfile
- getNumSeqsAfterTax()
: ms_mascotresfile
- getNumSubprojects()
: ms_distiller_master_project
- getNumSubsearches()
: ms_distiller_master_search
- getNumUsed()
: ms_inputquery
- getNumVals()
: ms_inputquery
- getObserved()
: ms_peptide
- getObservedCharge()
: ms_mascotresfile
- getObservedIntensity()
: ms_mascotresfile
- getObservedMass()
: ms_mascotresfile
- getObservedMrValue()
: ms_mascotresfile
- getOld()
: ms_quant_isotope
- getOldSchemaType()
: ms_quant_isotope
- getOpaqueString()
: ms_peptide_quant_key
- getOpaqueStringAndID()
: ms_peptide_quant_key
- getOsName()
: ms_http_client
- getOutlierKeys()
: ms_protein_quant_ratio
- getOutliers()
: ms_quant_method
- getOutliersSchemaType()
: ms_quant_method
- getOVERVIEW()
: ms_searchparams
- getOxygenMass()
: ms_searchparams
, ms_masses
- getPairsWith()
: ms_modification
, ms_umod_neutralloss
- getPairsWithSchemaType()
: ms_umod_neutralloss
- getParameterByName()
: ms_crosslinking_parameters
, ms_quant_parameters
- getParameterByNumber()
: ms_crosslinking_parameters
, ms_quant_parameters
- getParameterSchemaType()
: ms_crosslinking_filters
, ms_crosslinking_parameters
, ms_crosslinking_scope
, ms_quant_parameters
, ms_xml_parameters
, ms_crosslinking_settings
- getParams()
: ms_session
- getParent()
: ms_taxonomytree
- getParseOptions()
: ms_datfile
- getParseRule()
: ms_parseoptions
, ms_wwwentry
- getPasswordExpiry()
: ms_user
- getPath()
: ms_databaseoptions
, ms_wwwentry
- getPeak()
: ms_spectral_lib_peak_list
- getPeakAnnotationLevel()
: ms_spectral_lib_peak_list
- getPeakEndIndex()
: ms_xic
- getPeakEndScanId()
: ms_xic
- getPeakIntensity()
: ms_inputquery
- getPeakList()
: ms_spectral_lib_entry
, ms_inputquery
- getPeakListChecksum()
: ms_spectral_lib_entry
- getPeakListObject()
: ms_spectral_lib_entry
- getPeakMass()
: ms_inputquery
- getPeakStartIndex()
: ms_xic
- getPeakStartScanId()
: ms_xic
- getPeakState()
: ms_xic
- getPeaksUsedFromIons1()
: ms_peptide
- getPeaksUsedFromIons2()
: ms_peptide
- getPeaksUsedFromIons3()
: ms_peptide
- getPEP_ISOTOPE_ERROR()
: ms_searchparams
- getPepEnd()
: ms_aahelper
- getPepIdentThreshProtected()
: ms_mascotresults
- getPepNeutralLoss()
: ms_modification
, ms_quant_specificity
, ms_umod_specificity
- getPepNeutralLossSchemaType()
: ms_quant_specificity
, ms_umod_specificity
- getPepNumber()
: ms_protein
- getPepSearchTool()
: ms_mascotoptions
- getPepSearchToolCommandLine()
: ms_mascotoptions
- getPepStart()
: ms_aahelper
- getPepsWithSameScore()
: ms_peptidesummary
, ms_mascotresults
, ms_proteinsummary
- getPepThresholdType()
: ms_quant_quality
- getPepThresholdTypeSchemaType()
: ms_quant_quality
- getPepThresholdValue()
: ms_quant_quality
- getPepThresholdValueSchemaType()
: ms_quant_quality
- getPeptide()
: ms_peptidesummary
, ms_proteinsummary
, ms_mascotresults
, ms_quant_normalisation_peptides
, ms_proteinsummary
- getPeptideAmbiguityRanks()
: ms_peptidesummary
- getPeptideComponentID()
: ms_protein
- getPeptideDuplicate()
: ms_protein
- getPeptideEnd()
: ms_protein
- getPeptideExpectationValue()
: ms_mascotresults
- getPeptideFrame()
: ms_protein
- getPeptideIdentityThreshold()
: ms_mascotresults
- getPeptideIonsScore()
: ms_protein
- getPeptideIsBold()
: ms_protein
- getPeptideKey()
: ms_ms1quant_match_component
- getPeptideLength()
: ms_peptide
- getPeptideMultiplicity()
: ms_protein
- getPeptideP()
: ms_protein
- getPeptideQuantKeys()
: ms_quantitation
- getPeptideQuery()
: ms_protein
- getPeptideRatio()
: ms_customquantitation
, ms_ms1quant_match
, ms_ms2quantitation
, ms_quantitation
- getPeptideRatioNormalisationBase()
: ms_quantitation
- getPeptideResidueAfter()
: ms_protein
- getPeptideResidueBefore()
: ms_protein
- getPeptides()
: ms_quant_normalisation
- getPeptideSchemaType()
: ms_quant_normalisation_peptides
- getPeptideShowCheckbox()
: ms_protein
- getPeptidesSchemaType()
: ms_quant_normalisation
- getPeptideStart()
: ms_protein
- getPeptideStatus()
: ms_ms1quantitation
- getPeptideStr()
: ms_peptide
- getPeptideString()
: ms_ms1quant_match
- getPeptideSubstring()
: ms_fragment
- getPeptideSummaryCacheStreamName()
: ms_distiller_search_status
- getPeptideSummaryFlags()
: ms_distiller_data_search
- getPeptideSummaryFlags2()
: ms_distiller_data_search
- getPeptideThreshold()
: ms_mascotresults
- getPepTol()
: ms_inputquery
- getPepTolString()
: ms_inputquery
- getPepTolUnits()
: ms_inputquery
- getPercolator()
: ms_distiller_data_search
- getPercolatorExeFlags()
: ms_mascotoptions
- getPercolatorFeatures()
: ms_mascotoptions
- getPercolatorFileNames()
: ms_mascotresfile
- getPercolatorMinQueries()
: ms_mascotoptions
- getPercolatorMinSequences()
: ms_mascotoptions
- getPercolatorScores()
: ms_peptide
- getPercolatorTargetRankRelativeThreshold()
: ms_mascotoptions
- getPercolatorTargetRankScoreThreshold()
: ms_mascotoptions
- getPercolatorUseProteins()
: ms_distiller_data_search
- getPercolatorUseRT()
: ms_distiller_data_search
- getPerDbSrcRule()
: ms_taxonomyrules
- getPerfectObservedMatrix()
: ms_ms1quant_match
- getPermittedTasks()
: ms_group
, ms_session
- getPermittedTasksForUser()
: ms_security
- getPFA()
: ms_searchparams
- getPhysicalFromLogical()
: ms_processors
- getPoint()
: ms_xic
- getPort()
: ms_computeraddress
- getPortNumber()
: ms_wwwentry
- getPosition()
: ms_quant_specificity
, ms_quant_unmodified
, ms_umod_specificity
- getPositionSchemaType()
: ms_quant_specificity
, ms_quant_unmodified
, ms_umod_specificity
- getPreceedingComments()
: ms_customproperty
, ms_databaseoptions
- getPRECURSOR()
: ms_searchparams
- getPrecursor()
: ms_quant_protocol
- getPrecursorChargeFromNumber()
: ms_spectral_lib_file
- getPrecursorCutOutLowerLimit()
: ms_mascotoptions
- getPrecursorCutOutUpperLimit()
: ms_mascotoptions
- getPrecursorMZ()
: ms_spectral_lib_entry
- getPrecursorMZFromNumber()
: ms_spectral_lib_file
- getPrecursorRange()
: ms_quant_integration
- getPrecursorRangeSchemaType()
: ms_quant_integration
- getPrecursorSchemaType()
: ms_quant_protocol
- getPredictionMatrix()
: ms_ms1quant_match
- getPrefixRemove()
: ms_taxonomyrules
- getPrettyRank()
: ms_peptide
- getPrimaryNlStr()
: ms_peptide
- getProbabilityThreshold()
: ms_mascotresults
- getProbFromScore()
: ms_mascotresults
- getProbOfPepBeingRandomMatch()
: ms_mascotresults
- getProbOfProteinBeingRandomMatch()
: ms_mascotresults
- getProcessingOptions()
: ms_quant_integration
- getProcessingOptionsSchemaType()
: ms_quant_integration
- getProcessor()
: ms_processoroptions
- getProcessorName()
: ms_processors
- getProcessors()
: ms_datfile
- getProgress()
: ms_progress_info
- getProgressInfo()
: ms_mascotresfile
, ms_quantitation
- getProjectRelativePath()
: ms_distiller_sub_project
- getPropertyName()
: ms_customproperty
- getProportion()
: ms_http_helper_progress
- getPropValStringByName()
: ms_customproperty
- getPropValStringByNumber()
: ms_customproperty
- getProtein()
: ms_quant_normalisation_proteins
, ms_peptide
, ms_mascotresults
, ms_peptidesummary
- getProteinDescription()
: ms_mascotresults
- getProteinEmPAI()
: ms_peptidesummary
, ms_mascotresults
- getProteinExpectationValue()
: ms_mascotresults
- getProteinFamilySwitch()
: ms_mascotoptions
- getProteinGrouping()
: ms_distiller_data_search
- getProteinMass()
: ms_mascotresults
- getProteinRatio()
: ms_ms1quantitation
, ms_ms2quantitation
, ms_customquantitation
, ms_ms1quantitation
, ms_quantitation
, ms_ms2quantitation
- getProteinRatioSample()
: ms_quantitation
- getProteinRatioType()
: ms_quant_method
- getProteinRatioTypeSchemaType()
: ms_quant_method
- getProteins()
: ms_quant_normalisation
, ms_peptide
- getProteinSchemaType()
: ms_quant_normalisation_proteins
- getProteinScoreCutoff()
: ms_peptidesummary
, ms_proteinsummary
, ms_mascotresults
- getProteinScoreForHistogram()
: ms_mascotresults
- getProteinsInResultsFile()
: ms_mascotoptions
- getProteinsSchemaType()
: ms_quant_normalisation
- getProteinSummaryHit()
: ms_protein
- getProteinsWithThisPepMatch()
: ms_peptidesummary
, ms_proteinsummary
, ms_mascotresults
- getProteinTaxonomyIDs()
: ms_mascotresults
- getProteinThreshold()
: ms_mascotresults
- getProtocol()
: ms_quant_method
- getProtocolSchemaType()
: ms_quant_method
- getProtScoreType()
: ms_quant_method
- getProtScoreTypeSchemaType()
: ms_quant_method
- getProxyConfig()
: ms_http_helper
- getProxyPassword()
: ms_connection_settings
, ms_mascotoptions
- getProxyServer()
: ms_connection_settings
, ms_mascotoptions
- getProxyServerType()
: ms_connection_settings
- getProxyType()
: ms_mascotoptions
- getProxyUserAndPassword()
: ms_connection_settings
- getProxyUsername()
: ms_connection_settings
, ms_mascotoptions
- getPValue()
: ms_shapiro_wilk
- getQ()
: ms_fitexy_result
- getQmatch()
: ms_spectral_lib_file
, ms_mascotresults
- getQuality()
: ms_ms1quant_match_ratio
, ms_quant_method
- getQualitySchemaType()
: ms_quant_method
- getQuant()
: ms_distiller_data
- getQuantCount()
: ms_distiller_data
- getQuantForSearch()
: ms_distiller_data
- getQUANTITATION()
: ms_searchparams
- getQuantitation()
: ms_mascotresfile
- getQuantitationComponentForPeptide()
: ms_peptidesummary
, ms_proteinsummary
, ms_mascotresults
- getQuantitationDatasources()
: ms_ms1quantitation
- getQuantitationMethod()
: ms_mascotresfile
, ms_quantitation
- getQuantMethod()
: ms_peptidesummary
, ms_distiller_data
- getQuantMethodXml()
: ms_distiller_data_search
- getQUE()
: ms_searchparams
- getQuery()
: ms_peptide
, ms_ms1quant_peptide_status
- getQueryAndRank()
: ms_peptide_quant_key
- getQueryList()
: ms_peptidesummary
- getQuerySectionValue()
: ms_mascotresfile
- getQuerySectionValueDouble()
: ms_mascotresfile
- getQuerySectionValueInt()
: ms_mascotresfile
- getQuerySectionValueStr()
: ms_mascotresfile
- getQuickRefSearch()
: ms_taxonomyrules
- getRange()
: ms_ms1quant_match_component
- getRank()
: ms_peptide
, ms_ms1quant_peptide_status
- getRatioName()
: ms_peptide_quant_ratio
, ms_protein_quant_ratio
, ms_ms1quant_match_ratio
- getRawAbsolutePath()
: ms_distiller_sub_project
- getRawfile()
: ms_inputquery
- getRawFormat()
: ms_distiller_sub_project
- getRawRelativePath()
: ms_distiller_sub_project
- getRawSampleNumber()
: ms_distiller_sub_project
- getRawScans()
: ms_inputquery
- getRC()
: ms_matrix
- getReadableLabelFreeVarMods()
: ms_ms1quant_match
- getReadableVarMods()
: ms_ms1quantitation
, ms_mascotresults
- getReadableVarModsConcise()
: ms_ms1quantitation
- getRecordID()
: ms_umod_modification
- getRecordIDSchemaType()
: ms_umod_modification
- getRedirectPolicy()
: ms_connection_settings
- getReferenceAccession()
: ms_quant_average
- getReferenceAccessionSchemaType()
: ms_quant_average
- getReferenceAmount()
: ms_quant_average
- getReferenceAmountSchemaType()
: ms_quant_average
- getReferenceDatabase()
: ms_quant_average
- getReferenceDatabaseNumberOfSL()
: ms_mascotresfile
- getReferenceDatabaseSchemaType()
: ms_quant_average
- getReferenceFasta()
: ms_libraryoptions
- getReferenceFastaTaxonomyTitle()
: ms_libraryoptions
- getReferenceHitId()
: ms_ms1quant_average_results
- getReferenceMemberNumber()
: ms_ms1quant_average_results
- getRegionEndIndex()
: ms_xic
- getRegionEndScanId()
: ms_xic
- getRegionStartIndex()
: ms_xic
- getRegionStartScanId()
: ms_xic
- getRelativeMass()
: ms_ms1quant_match_component
- getRepeatSearchString()
: ms_mascotresfile
- getRepEntryByName()
: ms_wwwoptions
- getReplicate()
: ms_quant_protocol
- getReplicateSchemaType()
: ms_quant_protocol
- getREPORT()
: ms_searchparams
- getReportBuilderColumnArrangement()
: ms_mascotoptions
- getReportDetailSchemaType()
: ms_quant_method
- getReporter()
: ms_quant_protocol
- getReporterSchemaType()
: ms_quant_protocol
- getReporterTol()
: ms_quant_reporter
- getReporterTolSchemaType()
: ms_quant_reporter
- getReporterTolUnit()
: ms_quant_reporter
- getReporterTolUnitSchemaType()
: ms_quant_reporter
- getReportNumberChoice()
: ms_mascotoptions
- getReportRatioByName()
: ms_quant_method
- getReportRatioByNumber()
: ms_quant_method
- getReportRatioFromFile()
: ms_ms2quantitation
- getReportRatioNamesInFile()
: ms_ms2quantitation
- getReportRatioSchemaType()
: ms_quant_method
- getReporttop()
: ms_distiller_data_search
- getREPTYPE()
: ms_searchparams
- getReqPepNeutralLoss()
: ms_modification
- getRequestData()
: ms_http_helper_handles
- getRequireBoldRed()
: ms_distiller_data_search
- getRequireBoldRedSchemaType()
: ms_quant_method
- getRequiredSchemaFileNames()
: ms_distiller_data
- getRequiredSchemaType()
: ms_quant_pepneutralloss
, ms_quant_modgroup
- getResfile()
: ms_mascotresults
, ms_mascotresfile
- getResfileCache()
: ms_mascotoptions
- getResfileStreamName()
: ms_distiller_search_status
- getResidueMass()
: ms_masses
, ms_modification
, ms_searchparams
- getRestrict()
: ms_enzyme
- getResult()
: ms_shapiro_wilk
- getResultsCache()
: ms_mascotoptions
- getResultsFile()
: ms_distiller_subsearch
, ms_distiller_search_status
- getResultsFileFormatVersion()
: ms_mascotoptions
- getResultsFileName()
: ms_http_client_search
- getResultsFullURL()
: ms_mascotoptions
- getResultsFullURL_2()
: ms_mascotoptions
- getResultsListStreamName()
: ms_distiller_sub_project
- getResultsParameters()
: ms_mascotresults
- getResultsPerlScript()
: ms_mascotoptions
- getResultsPerlScript_2()
: ms_mascotoptions
- getResultsStreamName()
: ms_distiller_data_quant
- getRetentionTimes()
: ms_inputquery
- getReviewColDisplay()
: ms_mascotoptions
- getReviewColWidth()
: ms_mascotoptions
- getRMSDeltas()
: ms_protein
- getRt()
: ms_ms1quant_match_range
- getRtPeakEnd()
: ms_xic
- getRtPeakStart()
: ms_xic
- getRtRegionEnd()
: ms_xic
- getRtRegionStart()
: ms_xic
- getRule()
: ms_parserule_plus
- getRULES()
: ms_searchparams
, ms_inputquery
- getRuleStr()
: ms_parserule
- getSampleSize()
: ms_protein_quant_ratio
- getSARExtendedErrorCode()
: ms_fileutilities
- getSatellite()
: ms_quant_component
- getSatelliteSchemaType()
: ms_quant_component
- getScan()
: ms_ms1quant_match_range
- getScanNumbers()
: ms_inputquery
- getSchemaDirectory()
: ms_quant_configfile
- getSchemaFileName()
: ms_crosslinking_configfile
, ms_umod_configfile
, ms_quant_configfile
- getSchemaType()
: ms_umod_aminoacid
, ms_quant_normalisation_peptide
, ms_crosslinking_accessions
, ms_crosslinking_filters
, ms_xml_parameter
, ms_crosslinking_monolink
, ms_crosslinking_settings
, ms_quant_composition
, ms_xml_parameters
, ms_quant_localdef
, ms_crosslinking_parameters
, ms_umod_modification
, ms_quant_multiplex
, ms_quant_normalisation
, ms_quant_normalisation_peptides
, ms_quant_outliers
, ms_umod_neutralloss
, ms_umod_specificity
, ms_umod_composition
, ms_quant_replicate
, ms_umod_modbrick
, ms_quant_unmodified
, ms_umod_elemref
, ms_umod_element
, ms_quant_satellite
, ms_quant_protocol
, ms_quant_specificity
, ms_quant_quality
, ms_quant_reporter
, ms_quant_ratio
, ms_quant_parameters
, ms_quant_normalisation_protein
, ms_quant_pepneutralloss
, ms_quant_precursor
, ms_quant_normalisation_proteins
, ms_quant_parameter
, ms_quant_numerator
, ms_quant_method
, ms_quant_modgroup
, ms_quant_moverz
, ms_quant_integration
, ms_quant_average
, ms_quant_neutralloss
, ms_quant_isotope
, ms_quant_component
, ms_quant_correction
, ms_quant_element
, ms_crosslinking_linker
, ms_crosslinking_scope
, ms_crosslinking_linkers
, ms_crosslinking_parameter
, ms_crosslinking_method
, ms_crosslinking_does_not_pair_with
, ms_umod_xref
, ms_crosslinking_accession
- getScope()
: ms_crosslinking_method
- getScopeSchemaType()
: ms_crosslinking_method
- getScore()
: ms_protein
- getScoreExpectCutOff()
: ms_distiller_data_search
- getScoreWithET()
: ms_protein
- getScoring()
: ms_distiller_data_search
- getSearch()
: ms_distiller_master_project
, ms_distiller_data
, ms_distiller_search_status_list
- getSEARCH()
: ms_searchparams
- getSearchCount()
: ms_distiller_data
- getSearchLogFile()
: ms_mascotoptions
- getSearchStatusListStreamName()
: ms_distiller_search_status_list
- getSearchSubmitMode()
: ms_mascotoptions
- getSearchTaskID()
: ms_http_client_search
- getSecsToWaitForNodeAtStartup()
: ms_clusterparams
- getSectionName()
: ms_mascotresfile
- getSectionValue()
: ms_mascotresfile
- getSectionValueDouble()
: ms_mascotresfile
- getSectionValueInt()
: ms_mascotresfile
- getSectionValueStr()
: ms_mascotresfile
- getSEG()
: ms_searchparams
- getSelection()
: ms_quant_average
- getSelectionSchemaType()
: ms_quant_average
- getSelectSwitch()
: ms_mascotoptions
- getSendmailPath()
: ms_mascotoptions
- getSeparateLockMem()
: ms_mascotoptions
- getSeq()
: ms_quant_method
, ms_inputquery
- getSeqEntryByName()
: ms_wwwoptions
- getSeqSchemaType()
: ms_quant_method
- getSequence()
: ms_spectral_lib_entry
, ms_quant_normalisation_peptide
- getSequenceFile()
: ms_http_client_session
- getSequenceFromNumber()
: ms_spectral_lib_file
- getSequenceMass()
: ms_mascotresults
- getSequenceSchemaType()
: ms_quant_normalisation_peptide
- getSeriesDescription()
: ms_fragmentationrules
- getSeriesName()
: ms_fragmentationrules
, ms_fragment
- getSeriesUsedStr()
: ms_peptide
- getServer()
: ms_distiller_search_status
- getSessionID()
: ms_http_client_session
, ms_http_client_search
, ms_connection_settings
- getSessionTimeout()
: ms_security_options
- getSettings()
: ms_crosslinking_method
- getSettingsSchemaType()
: ms_crosslinking_method
- getShift()
: ms_quant_correction
- getShiftSchemaType()
: ms_quant_correction
- getShowSamesets()
: ms_distiller_data_search
- getShowSamesetsFamily()
: ms_distiller_data_search
- getShowSubset()
: ms_distiller_data_search
- getShowSubsetFamily()
: ms_distiller_data_search
- getShowSubsets()
: ms_mascotoptions
- getShowSubSets()
: ms_quant_method
- getShowSubSetsSchemaType()
: ms_quant_method
- getSigmaA()
: ms_fitexy_result
- getSigmaB()
: ms_fitexy_result
- getSigmaX()
: ms_fitexy_result
- getSigmaY()
: ms_fitexy_result
- getSignificanceThreshold()
: ms_distiller_data_search
- getSigThreshold()
: ms_mascotoptions
- getSigThresholdValue()
: ms_quant_method
- getSigThresholdValueSchemaType()
: ms_quant_method
- getSimilarProteinDB()
: ms_protein
- getSimilarProteinName()
: ms_protein
- getSimilarProteins()
: ms_protein
- getSimpleRatioSchemaType()
: ms_quant_integration
- getSingleHit()
: ms_mascotresults_params
- getSite()
: ms_quant_unmodified
, ms_quant_specificity
, ms_umod_specificity
- getSiteAnalysisMD10Prob()
: ms_mascotoptions
- getSiteFrom()
: ms_linker_site
- getSiteSchemaType()
: ms_umod_specificity
, ms_quant_specificity
, ms_quant_unmodified
- getSiteTo()
: ms_linker_site
- getSkippedKeys()
: ms_protein_quant_ratio
- getSLDatabaseNumbersOfReference()
: ms_mascotresfile
- getSLFragmentTolerance()
: ms_mascotresfile
- getSLFragmentToleranceUnit()
: ms_mascotresfile
- getSLThresholdFromMinProbability()
: ms_peptidesummary
- getSortedFinitePeptideRatioValues()
: ms_ms2quantitation
, ms_quantitation
, ms_customquantitation
- getSortUnassigned()
: ms_mascotoptions
- getSource()
: ms_umod_xref
, ms_quant_integration
- getSourceSchemaType()
: ms_quant_integration
, ms_umod_xref
- getSpecGroup()
: ms_umod_specificity
- getSpecGroupSchemaType()
: ms_umod_specificity
- getSpeciesFile()
: ms_taxonomyrules
- getSpeciesFormatRegex()
: ms_taxonomyrules
- getSpecificity()
: ms_umod_modification
, ms_quant_localdef
- getSpecificityBySite()
: ms_umod_modification
- getSpecificityBySiteAndPosition()
: ms_umod_modification
- getSpecificitySchemaType()
: ms_quant_localdef
, ms_umod_modification
- getSpectralLibraryDisplayOption()
: ms_distiller_data_search
- getSpectraPerLibraryBlock()
: ms_mascotoptions
- getSpectrumViewerColourSchemeNames()
: ms_mascotoptions
- getSpectrumViewerColourSchemeString()
: ms_mascotoptions
- getSpectrumViewerDefaultColourSchemeName()
: ms_mascotoptions
- getSplitDataFileSize()
: ms_mascotoptions
- getSplitNumberOfQueries()
: ms_mascotoptions
- getSpoofableUsers()
: ms_session
- getSrcDatabaseRule()
: ms_taxonomyrules
- getSrcQueryAndFileIdForMultiFile()
: ms_mascotresfile
- getSrcRank()
: ms_peptidesummary
- getSrcSection()
: ms_peptidesummary
- getStandardDeviation()
: ms_protein_quant_ratio
- getStandardError()
: ms_protein_quant_ratio
- getStart()
: ms_fragment
- getStartDate()
: ms_license
- getStartIndex()
: ms_xic
- getStartScanId()
: ms_xic
- getStatsInformation()
: ms_spectral_lib_file
- getStatus()
: ms_http_client_search
, ms_progress_info
, ms_ms1quant_match_ratio
, ms_ms1quant_peptide_status
- getStatusList()
: ms_ms1quant_match_ratio
- getStatusMsg()
: ms_distiller_search_status
- getStrategy()
: ms_crosslinking_method
- getStrategySchemaType()
: ms_crosslinking_method
- getStreamNumber()
: ms_distiller_data_quant
- getStrFile()
: ms_taxonomyrules
- getStringIons1()
: ms_inputquery
- getStringIons2()
: ms_inputquery
- getStringIons3()
: ms_inputquery
- getStringParam()
: ms_session
, ms_user
, ms_group
, ms_user
, ms_group
, ms_session
- getStringParams()
: ms_security_task
- getStringTitle()
: ms_inputquery
- getStrRule()
: ms_taxonomyrules
- getSUBCLUSTER()
: ms_searchparams
- getSubClusterID()
: ms_clusterparams
- getSubClusterMaxCPU()
: ms_clusterparams
- getSubmitTime()
: ms_distiller_search_status
- getSubproject()
: ms_distiller_master_project
- getSubsearch()
: ms_distiller_master_search
- getSubtaskProgress()
: ms_progress_info
- getSuffixRemove()
: ms_taxonomyrules
- getSummary()
: ms_ms1quantitation
- getSummedModsNlStr()
: ms_peptide
- getSummedModsStr()
: ms_peptide
, ms_ms1quant_match_component
- getSVGSpectrumSwitch()
: ms_mascotoptions
- getSymbol()
: ms_umod_elemref
, ms_quant_element
- getSymbolSchemaType()
: ms_umod_elemref
, ms_quant_element
- getSystemError()
: ms_http_helper_return
- getTag()
: ms_inputquery
- getTagDeltaRangeEnd()
: ms_mascotresults
, ms_proteinsummary
, ms_peptidesummary
- getTagDeltaRangeStart()
: ms_peptidesummary
, ms_proteinsummary
, ms_mascotresults
- getTagEnd()
: ms_mascotresults
- getTagSeries()
: ms_mascotresults
- getTagStart()
: ms_mascotresults
- getTagString()
: ms_peptidesummary
, ms_mascotresults
, ms_proteinsummary
- getTARGET_FDR_PERCENT()
: ms_searchparams
- getTargetFDR()
: ms_mascotresults_params
- getTargetFDRPercentage()
: ms_mascotoptions
- getTargetFDRType()
: ms_mascotresults_params
- getTask()
: ms_security_tasks
- getTaskFromID()
: ms_security_tasks
- getTaskId()
: ms_distiller_search_status
, ms_distiller_data_quant
, ms_distiller_subsearch
, ms_distiller_data_search
- getTasks()
: ms_security
- getTaxBrowserUrl()
: ms_mascotoptions
- getTaxIDArray()
: ms_taxonomytree
- getTaxonomy()
: ms_mascotresfile
- getTAXONOMY()
: ms_searchparams
- getTaxonomyParseRuleIndex()
: ms_databaseoptions
- getTaxonomyRules()
: ms_datfile
- getTerminalResiduesString()
: ms_proteinsummary
, ms_peptidesummary
, ms_mascotresults
- getTestDirectory()
: ms_mascotoptions
- getText()
: ms_umod_xref
- getTextSchemaType()
: ms_umod_xref
- getThreadProcessorID()
: ms_dbprocessors
- getThreeLetter()
: ms_umod_aminoacid
- getThreeLetterSchemaType()
: ms_umod_aminoacid
- getThresholdForFDRAboveHomology()
: ms_mascotresults
- getThresholdForFDRAboveIdentity()
: ms_mascotresults
- getTimeout()
: ms_session
- getTimeParam()
: ms_session
- getTitle()
: ms_umod_aminoacid
, ms_umod_modbrick
, ms_quant_localdef
, ms_unigene_entry
, ms_distiller_search_status
, ms_umod_element
, ms_distiller_subsearch
, ms_fragmentationrules
, ms_taxonomychoice
, ms_modification
, ms_enzyme
, ms_umod_modification
- getTitleSchemaType()
: ms_umod_element
, ms_umod_modification
, ms_quant_localdef
, ms_umod_aminoacid
, ms_umod_modbrick
- getTOL()
: ms_searchparams
- getToleranceInDa()
: ms_libraryoptions
- getToleranceInDalton()
: ms_mascotresults
- getToleranceInPPM()
: ms_libraryoptions
- getTOLU()
: ms_searchparams
- getTotal()
: ms_progress_info
- getTotalBytes()
: ms_http_helper_progress
- getTotalIntensity()
: ms_ms1quant_charge_state
- getTotalIntensitySchemaType()
: ms_quant_quality
- getTotalIntensityThreshold()
: ms_quant_quality
- getTotalIntensityThresholdSchemaType()
: ms_quant_quality
- getTotalIonsIntensity()
: ms_inputquery
- getTotalSeriesOutput()
: ms_fragmentationrules
- getTreeClusterNodes()
: ms_peptidesummary
, ms_mascotresults
- getType()
: ms_quant_correction
, ms_quant_protocol
, ms_security_task
, ms_wwwentry
, ms_distiller_sub_project
- getTypeSchemaType()
: ms_quant_correction
- getUnassigned()
: ms_mascotresults
- getUnassignedIsBold()
: ms_mascotresults
- getUnassignedShowCheckbox()
: ms_mascotresults
- getUnigeneForAccession()
: ms_unigene
- getUnigeneIndexFile()
: ms_mascotresults_params
- getUniGeneOptions()
: ms_datfile
- getUnimod()
: ms_mascotresfile
- getUnimodXL()
: ms_mascotresfile
- getUniqueJobStartNumber()
: ms_mascotoptions
- getUniquePepseqSchemaType()
: ms_quant_quality
- getUniqueTaskID()
: ms_mascotresfile
- getUnixDirPerm()
: ms_mascotoptions
- getUnixWebUserGroup()
: ms_mascotoptions
- getUnmatchedAnnotationStr()
: ms_spectral_lib_peak
- getUnmatchedMasses()
: ms_protein
- getUnmodified()
: ms_quant_modgroup
- getUnmodifiedSchemaType()
: ms_quant_modgroup
- getUnnormalisedAveragePeptideRatio()
: ms_customquantitation
- getUnZipped()
: ms_zip
- getUnZippedLen()
: ms_zip
- getUrl()
: ms_umod_xref
- getUrlSchemaType()
: ms_umod_xref
- getUser()
: ms_security
- getUserAgent()
: ms_connection_settings
- getUSEREMAIL()
: ms_searchparams
- getUSERField()
: ms_searchparams
- getUserFromID()
: ms_security
- getUserID()
: ms_session
- getUSERID()
: ms_searchparams
- getUserName()
: ms_session
- getUSERNAME()
: ms_searchparams
- getUsernameOfPoster()
: ms_umod_modification
- getUsernameOfPosterSchemaType()
: ms_umod_modification
- getUserType()
: ms_session
, ms_user
- getUseSessionCookies()
: ms_security_options
- getUseTimeShift()
: ms_xic
- getValue()
: ms_xml_parameter
, ms_crosslinking_accession
, ms_protein_quant_ratio
, ms_peptide_quant_ratio
, ms_ms1quant_match_ratio
, ms_crosslinking_monolink
, ms_http_client_mime
- getValueFromKey()
: ms_tinycdb
- getValueSchemaType()
: ms_crosslinking_monolink
, ms_xml_parameter
, ms_crosslinking_parameter
, ms_crosslinking_accession
, ms_quant_parameter
- getVarModIdxFrom()
: ms_linker_site
- getVarModIdxOfLinkedSite()
: ms_linker_site_vector
- getVarModIdxTo()
: ms_linker_site
- getVarMods()
: ms_ms1quant_match
, ms_aahelper
- getVarModsDelta()
: ms_searchparams
- getVarModsName()
: ms_searchparams
- getVarModsNeutralLoss()
: ms_searchparams
- getVarModsNeutralLosses()
: ms_searchparams
- getVarModsPepNeutralLoss()
: ms_searchparams
- getVarModsReqPepNeutralLoss()
: ms_searchparams
- getVarModsStr()
: ms_peptide
, ms_ms1quant_match_component
- getVector()
: ms_fragmentvector
- getVerifySessionIPAddress()
: ms_security_options
- getVersion()
: ms_http_client
- getVmemory()
: ms_mascotoptions
- getWeight()
: ms_peptide_quant_ratio
- getWhichAvailableForMascot()
: ms_processors
- getWhichAvailableForMascot2()
: ms_processors
- getWWWOptions()
: ms_datfile
- getXic()
: ms_ms1quant_match_component
- getXicMaxWidth()
: ms_quant_integration
- getXicMaxWidthSchemaType()
: ms_quant_integration
- getXicSmoothing()
: ms_quant_integration
- getXicSmoothingSchemaType()
: ms_quant_integration
- getXicThreshold()
: ms_quant_integration
- getXicThresholdSchemaType()
: ms_quant_integration
- getXmlCode()
: ms_ms1quant_peptide_status
, ms_ms1quant_match
, ms_xic
, ms_ms1quant_match_ratio
- getXMLschemaFilePath()
: ms_mascotresfile
- getXref()
: ms_umod_modification
- getXrefSchemaType()
: ms_umod_modification
- getZipped()
: ms_zip
- getZippedLen()
: ms_zip
- GROUP
: ms_protein
- GROUP_COMPLETE
: ms_protein
- GROUP_FAMILY
: ms_protein
- GROUP_NO
: ms_protein
- GROUP_SUBSET
: ms_protein
- GROUP_UNKNOWN
: ms_protein
- GROUPID_ADMINISTRATORS
: ms_group
- GROUPID_DAEMONS
: ms_group
- GROUPID_GUESTS
: ms_group
- GROUPID_INTEGRA_SYSTEM
: ms_group
- GROUPID_LAST
: ms_group
- GROUPID_POWERUSERS
: ms_group