An instance of this class represents all the parameters specified in the Options section of mascot.dat. More...

#include <ms_mascotoptions.hpp>

Inheritance diagram for ms_mascotoptions:

Collaboration diagram for ms_mascotoptions:

Public Types
enum	DECOY_ALGORITHM { DECOY_ALGORITHM_NONE = 0 , DECOY_PROTEIN_REVERSE = 1 , DECOY_PEPTIDE_REVERSE = 2 , DECOY_PROTEIN_RANDOM = 3 , DECOY_PEPTIDE_RANDOM = 4 , DECOY_PROTEIN_RANDOM_DIPEP = 5 , DECOY_PEPTIDE_RANDOM_DIPEP = 6 , DECOY_PROTEIN_SHUFFLE = 7 , DECOY_PEPTIDE_SHUFFLE = 8 , DECOY_PROTEIN_BASED_MASK = 0x0001 }
	Definitions for how the decoy sequences are generated. More...

enum	EXEC_AFTER_SEARCH { MAX_EXEC_AFTER_SEARCH = 10 }
	Definitions for the ExecAfterSearch_XXX lines in the Options section of mascot.dat. More...

enum	MS_REVIEW_COL { MS_REVIEW_COL_JOB = 0x0000 , MS_REVIEW_COL_PID = 0x0001 , MS_REVIEW_COL_DATABASE = 0x0002 , MS_REVIEW_COL_USERNAME = 0x0003 , MS_REVIEW_COL_USEREMAIL = 0x0004 , MS_REVIEW_COL_TITLE = 0x0005 , MS_REVIEW_COL_RESULTS_FILE = 0x0006 , MS_REVIEW_COL_START_TIME = 0x0007 , MS_REVIEW_COL_DURATION = 0x0008 , MS_REVIEW_COL_STATUS = 0x0009 , MS_REVIEW_COL_PRIORITY = 0x000A , MS_REVIEW_COL_SEARCHTYPE = 0x000B , MS_REVIEW_COL_ENZYMEUSED = 0x000C , MS_REVIEW_COL_IPADDRESS = 0x000D , MS_REVIEW_COL_USERID = 0x000E , MS_REVIEW_COL_PEAKLISTDATAFILE = 0x000F , MS_REVIEW_COL____LAST___ = 0x0010 }
	Definitions for columns in `ms-review.exe` for use with getReviewColWidth() and getReviewColDisplay(). More...

enum	NUMERICAL_VALUE_STORAGE { MASS_DECIMAL_PLACES = 6 }
	Definitions for storage of numerical values in files. More...

enum	PERC_EXE_RT { PERC_EXE_RT_USE_DEFAULT = 1 , PERC_EXE_RT_FORCE_ON = 2 , PERC_EXE_RT_FORCE_OFF = 3 }
	Definitions for retention time override when calling getPercolatorExeFlags(). More...

Public Member Functions
	ms_mascotoptions ()
	Default constructor.

	ms_mascotoptions (const ms_mascotoptions &src)
	Copying constructor.

	~ms_mascotoptions ()
	Destructor.

void	appendIgnoreDupeAccession (const std::string value)
	Appends a database to the list databases that shouldn't be checked for duplicate accessions.

void	appendProperty (const char name, const char value, const char *delimiter, const bool bFirstPlace=false)
	Adds a new property with the given parameters.

void	appendReportNumberChoice (const int value)
	Append a value to the ReportNumberChoices list.

void	appendTargetFDRPercentage (const double value, const bool makeDefault=false)
	Append a value to the TargetFDRPercentages list.

void	appendText (const char *line, const bool bFirstPlace=false)
	Adds a new non-parsed property.

void	clearIgnoreDupeAccessions ()
	Clears the list of databases that shouldn't be checked for duplicate accessions.

void	clearReportNumberChoices ()
	Deletes all ReportNumberChoices values from the list.

void	clearTargetFDRPercentages ()
	Deletes all TargetFDRPercentages values from the list.

void	copyFrom (const ms_customproperty *src)
	Copies all properties and comments from another instance.

void	copyFrom (const ms_mascotoptions *right)
	Can be used to create a copy of another object.

void	defaultValues ()
	Initialises the instance with default values.

void	delNonEmpty ()
	Deletes all non-comment properties.

void	delProp (const char *name)
	Deletes all properties with the specified name.

void	delPropByNumber (const int index)
	Deletes a single property with the specified number only.

void	delPropStart (const char *nameBeginning)
	Deletes all properties whose names start with the given string.

int	findProperty (const char *name, const int startFrom=0) const
	Searches the list for a property with the given name.

int	findPropertyBeginning (const char *nameBeginning, const int startFrom=0) const
	Searches the list for a property with the partially matching name.

std::string	getCacheDirectory () const
	Returns the value of CacheDirectory.

double	getCentroidWidth () const
	Returns the value of CentroidWidth.

int	getCentroidWidthCount () const
	Returns the value of CentroidWidthCount.

std::string	getCompressToolAA () const
	Returns the value of CompressTool_AA.

std::string	getCompressToolCommandLineFasta (DATABASE_TYPE dbType, const std::string &dbname, const std::string &dbpath) const
	Get command line to compress fasta, eg ms-compress.exe.

std::string	getCompressToolCommandLineLibrary (const std::string &logfilepath, const std::string &inputfile, const std::string &outputdirectory) const
	Get command line to compress library, eg lib2nistcl.exe.

std::string	getCompressToolNA () const
	Returns the value of CompressTool_NA.

std::string	getCompressToolSL () const
	Returns the value of CompressTool_NA.

int	getCrawlerNumPeaksPer100Da () const
	Returns the number of peaks to output in each 100 Da window for the library crawler.

int	getCreatePipThreadBlockSize () const
	Returns the value of CreatePipThreadBlockSize.

int	getCreatePipThreads () const
	Returns the value of CreatePipThreads.

int	getDechargeFragmentPeaks () const
	Return the maximum fragment ion charge state to be decharged.

int	getDecoyTypeNoEnzyme () const
	Returns the value of DecoyTypeNoEnzyme.

int	getDecoyTypeSpecific () const
	Returns the value of DecoyTypeSpecific.

std::string	getDefaultDelimiter () const
	Return current default delimiter string used for parsing/storing properties.

std::string	getDelimiterByNumber (const int index) const
	Returns a specific delimiter used for the property.

int	getDisplayNonSignificantMatches () const
	Returns the value of DisplayNonSignificantMatches.

std::string	getEmailFromTextName () const
	Returns the value of EmailFromTextName.

std::string	getEmailFromUser () const
	Returns the value of EmailFromUser.

std::string	getEmailPassword () const
	Returns the value of EmailPassword.

std::string	getEmailProfile () const
	Returns the value of EmailProfile.

std::string	getEmailService () const
	Returns the value of EmailService.

int	getEmailTimeOutPeriod () const
	Returns the value of EmailTimeOutPeriod.

std::string	getErrMessageEmailTo () const
	Returns the value of ErrMessageEmailTo.

std::string	getErrorLogFile () const
	Returns the value of ErrorLogFile.

int	getErrTolMaxAccessions () const
	Returns the value of ErrTolMaxAccessions.

int	getExecAfterSearch (const char szResultsFilePath, std::vector< std::string > &commands, std::vector< std::string > &titles, std::vector< int > &waitfor, std::vector< int > &logging, std::vector< std::string > &additionalFlags, const char sessionID=0, const char *taskID=0) const
	Returns the values of the ExecAfterSearch_XXX parameters.

int	getFeatureTableLength () const
	Returns the value of FeatureTableLength.

double	getFeatureTableMinScore () const
	Returns the value of FeatureTableMinScore.

std::string	getFormVersion () const
	Returns the value of FormVersion.

const ms_blastaccession *	getGetSeqBlastAccession () const
	Returns GetSeqBlastAccession.

std::string	getGetSeqJobIdFile () const
	Returns the value of GetSeqJobIdFile.

std::string	getICATFilter () const
	Returns the value of ICATFilter.

std::string	getICATHeavy () const
	Returns the value of ICATHeavy.

std::string	getICATLight () const
	Returns the value of ICATLight.

std::string	getICATQuantitationMethod () const
	Returns the value of name of the ICATQuantitationMethod.

std::string	getIgnoreDupeAccession (const unsigned int index) const
	Returns one of the list databases that shouldn't be checked for duplicate accessions.

double	getIgnoreIonsScoreBelow () const
	Returns the value of IgnoreIonsScoreBelow.

int	getIntensitySigFigs () const
	Returns the value of IntensitySigFigs.

std::string	getInterFileBasePath () const
	Returns the value of InterFileBasePath.

std::string	getInterFileRelPath () const
	Returns the value of InterFileRelPath.

int	getIonsDecimalPlaces () const
	Returns the value of IonsDecimalPlaces.

std::string	getLastQueryAscFile () const
	Returns the value of LastQueryAscFile.

std::string	getLogoImageFile () const
	Returns the value of LogoImageFile.

std::string	getMailTempFile () const
	Returns the value of MailTempFile.

int	getMailTransport () const
	Returns the value of MailTransport.

std::string	getMascNodeCtrlFile () const
	Returns the value of MascotNodeControlFile.

std::string	getMascotCmdLine () const
	Returns the value of MascotCmdLine.

std::string	getMascotControlFile () const
	Returns the value of MascotControlFile.

int	getMascotFileProcessingThreads () const
	Returns the value of MascotFileProcessingThreads.

std::string	getMascotJobIdFile () const
	Returns the value of MascotJobIdFile.

std::string	getMascotMessage () const
	Returns the value of MascotMessage.

int	getMassDecimalPlaces () const
	Returns the value of MassDecimalPlaces.

int	getMaxConcurrentSearches () const
	Returns the value of MaxConcurrentSearches.

int	getMaxDatabases () const
	Returns the value of MaxDatabases.

int	getMaxDescriptionLen () const
	Returns the value of MaxDescriptionLen.

double	getMaxEtagMassDelta () const
	Returns the value of MaxEtagMassDelta.

int	getMaxEtVarMods () const
	Returns the value of MaxEtVarMods.

int	getMaxIntactCrosslinkPeptides () const
	Returns the value of MaxIntactCrosslinkPeptides.

int	getMaxNumOfReportBuilderColumnArrangements () const
	Returns the maximum number of column arrangements allowed.

int	getMaxNumPeptides () const
	Returns the value of MaxNumPeptides.

int	getMaxPepModArrangements () const
	Returns the value of MaxPepModArrangements.

int	getMaxPepNumModifiedSites () const
	Returns value of the MaxPepNumModifiedSites.

int	getMaxPepNumVarMods () const
	Returns value of the MaxPepNumVarMods.

int	getMaxQueries () const
	Returns the value of MaxQueries.

int	getMaxSearchesPerUser () const
	Returns the value of MaxSearchesPerUser.

int	getMaxSequenceLen () const
	Returns the value of MaxSequenceLen.

int	getMaxVarMods () const
	Returns the value of MaxVarMods.

double	getMinEtagMassDelta () const
	Returns the value of MinEtagMassDelta.

int	getMinPepLenInPepSummary () const
	Returns the value of MinPepLenInPepSummary.

int	getMinPepLenInSearch () const
	Returns value of the MinPepLenInSearch.

int	getMonitorEmailCheckFreq () const
	Returns the value of MonitorEmailCheckFreq.

std::string	getMonitorLogFile () const
	Returns the value of MonitorLogFile.

std::string	getMonitorPidFile () const
	Returns the value of MonitorPidFile.

int	getMonitorTestTimeout () const
	Returns the value of MonitorTestTimeout.

int	getMudpit () const
	Returns the value of Mudpit.

double	getMudpitSwitch () const
	Returns the value of MudpitSwitch.

std::string	getNoResultsScript () const
	Returns the value of NoResultsScript.

std::string	getNTIUserGroup () const
	Returns the value of NTIUserGroup.

std::string	getNTMonitorGroup () const
	Returns the value of NTMonitorGroup.

unsigned int	getNumberOfIgnoreDupeAccessions () const
	Returns the number of databases that shouldn't be checked for duplicate accessions.

int	getNumberOfProperties () const
	Returns a total number of property/comment entries.

int	getNumberOfReportNumberChoices () const
	Returns the values of ReportNumberChoices.

int	getNumberOfTargetFDRPercentages () const
	Returns the values of TargetFDRPercentages.

std::string	getPepSearchTool () const
	Returns the value of LibrarySearch.

std::string	getPepSearchToolCommandLine (const std::string &peptideToleranceUnit, const double &peptideTolerance, const std::string &ionToleranceUnit, const double &ionTolerance, const std::string &libraryDirectoryPath, const std::string &inputFileRelativePath, const std::string &outputFileRelativePath) const
	Get command line to search a library, eg MSPepSearch.exe.

std::string	getPercolatorExeFlags (bool anyRetentionTimes, const std::vector< std::string > percolatorFiles, const PERC_EXE_RT rt=PERC_EXE_RT_USE_DEFAULT) const
	Returns the value of PercolatorExeFlags.

std::string	getPercolatorFeatures () const
	Returns the value of PercolatorFeatures.

int	getPercolatorMinQueries () const
	Returns the value of PercolatorMinQueries.

int	getPercolatorMinSequences () const
	Returns the value of PercolatorMinSequences.

std::string	getPercolatorRtFlags (const bool anyRetentionTimes, const bool useRT) const
	Returns PercolatorExeFlags with the `-D` flag optionally removed if there are no retention times.

double	getPercolatorTargetRankRelativeThreshold () const
	Returns the value of PercolatorTargetRankRelativeThreshold.

int	getPercolatorTargetRankScoreThreshold () const
	Returns the value of PercolatorTargetRankScoreThreshold.

std::string	getPreceedingComments () const
	Returns any comments preceeding the section.

double	getPrecursorCutOutLowerLimit () const
	Gets the first PrecursorCutOut.

double	getPrecursorCutOutUpperLimit () const
	Gets the second PrecursorCutOut.

std::string	getPropertyName (const int index) const
	Returns a property name for a given index.

std::string	getPropValStringByName (const char *name) const
	Retrieves property value by name.

std::string	getPropValStringByNumber (const int index) const
	Retrieves property raw text values by number.

int	getProteinFamilySwitch () const
	Returns the value of ProteinFamilySwitch.

int	getProteinsInResultsFile () const
	Returns the value of ProteinsInResultsFile.

std::string	getProxyPassword () const
	Returns the value of proxy_password.

std::string	getProxyServer () const
	Returns the value of proxy_server.

std::string	getProxyType () const
	Returns the value of ProxyType.

std::string	getProxyUsername () const
	Returns the value of proxy_username.

std::string	getReportBuilderColumnArrangement (const int index) const
	Returns ReportBuilderColumnArrangement by number.

int	getReportNumberChoice (const int index) const
	Returns an element of the ReportNumberChoices list by its number.

std::string	getResfileCache () const
	Returns the value of ResfileCache.

std::string	getResultsCache () const
	Returns the value of ResultsCache.

std::string	getResultsFileFormatVersion () const
	Returns the value of ResultsFileFormatVersion.

std::string	getResultsFullURL () const
	Returns the value of ResultsFullURL.

std::string	getResultsFullURL_2 () const
	Returns the value of ResultsFullURL_2.

std::string	getResultsPerlScript () const
	Returns the value of ResultsPerlScript.

std::string	getResultsPerlScript_2 () const
	Returns the value of ResultsPerlScript_2.

bool	getReviewColDisplay (const MS_REVIEW_COL index) const
	Returns ReviewColDisplay by number.

int	getReviewColWidth (const MS_REVIEW_COL index) const
	Returns ReviewColWidths by number.

std::string	getSearchLogFile () const
	Returns the value of SearchLogFile.

std::string	getSearchSubmitAcceptedFileTypes () const
	Returns a list of accepted input file types in the Mascot search form.

std::string	getSearchSubmitDefaultPeptideCharge () const
	Returns the value in the CHARGE parameter when the peptide charge control is hidden in the search form.

std::string	getSearchSubmitMode () const
	Returns the Mascot search submission mode.

std::string	getSearchSubmitOutputFormat () const
	Returns the Mascot search submission output format.

int	getSelectSwitch () const
	Returns the value of SelectSwitch.

std::string	getSendmailPath () const
	Returns the value of sendmailPath.

double	getShowSubsets () const
	Returns the value of ShowSubSets.

double	getSigThreshold () const
	Returns the value of SigThreshold.

double	getSiteAnalysisMD10Prob () const
	Returns the value of SiteAnalysisMD10Prob.

std::string	getSortUnassigned () const
	Returns the value of SortUnassigned.

int	getSpectraPerLibraryBlock () const
	Returns the number of spectra in a spectral library block.

std::vector< std::string >	getSpectrumViewerColourSchemeNames () const
	Returns the names of all colour schemes (SpectrumViewerColourScheme).

std::string	getSpectrumViewerColourSchemeString (const std::string &name) const
	Returns SpectrumViewerColourScheme by name.

std::string	getSpectrumViewerDefaultColourSchemeName () const
	Return the name of the default colour scheme (SpectrumViewerDefaultColourScheme).

int	getSplitDataFileSize () const
	Returns the value of SplitDataFileSize.

int	getSplitNumberOfQueries () const
	Returns the value of SplitNumberOfQueries.

int	getSVGSpectrumSwitch () const
	Returns the value of SVGSpectrumSwitch.

double	getTargetFDRPercentage (const int index) const
	Returns an element of the TargetFDRPercentages list by its number.

std::string	getTaxBrowserUrl () const
	Returns value of the TaxBrowserUrl.

std::string	getTestDirectory () const
	Returns the value of TestDirectory.

int	getUniqueJobStartNumber () const
	Returns the value of UniqueJobStartNumber.

int	getUnixDirPerm () const
	Returns the value of UnixDirPerm.

int	getUnixWebUserGroup () const
	Returns the value of UnixWebUserGroup.

INT64	getVmemory () const
	Returns the value of Vmemory.

bool	isAlwaysCreateDat28ResultsFile () const
	Returns the value of AlwaysCreateDat28ResultsFile.

bool	isAlwaysEnableAutoDecoySearch () const
	Returns true if Mascot always runs an automatic target-decoy search.

bool	isAutoSelectCharge () const
	Returns the value of AutoSelectCharge.

bool	isCreateLegacyModAndSubstitutionFiles () const
	Returns true if Mascot Monitor creates legacy files containing modification definitions.

bool	isDefaultTargetFDRPercentage (const int index) const
	Returns true if the element of TargetFDRPercentages is a default value.

bool	isEmailErrorsEnabled () const
	Returns the value of EmailErrorsEnabled.

bool	isEmailUsersEnabled () const
	Returns the value of EmailUsersEnabled.

bool	isForkForUnixApache () const
	Returns the value of ForkForUnixApache.

bool	isInIgnoreDupeAccessionList (const std::string value) const
	Checks to see if the passed database name is in the list databases that shouldn't be checked for duplicate accessions.

bool	isIteratePMFIntensities () const
	Returns value of the IteratePMFIntensities.

bool	isLabelAll () const
	Returns the value of LabelAll.

bool	isMatchOppositeCrosslinkPairs () const
	Returns the value of MatchOppositeCrosslinkPairs.

bool	isMoveOldDbToOldDir () const
	Returns the value of MoveOldDbToOldDir.

bool	isPercolator () const
	Returns the value of Percolator.

bool	isPercolatorUseProteins () const
	Returns the value of PercolatorUseProteins.

bool	isPercolatorUseRT () const
	Returns the value of PercolatorUseRT.

bool	isRemoveOldIndexFiles () const
	Returns the value of RemoveOldIndexFiles.

bool	isRequireBoldRed () const
	Returns the value of RequireBoldRed.

bool	isSaveEveryLastQueryAsc () const
	Returns the value of SaveEveryLastQueryAsc.

bool	isSaveLastQueryAsc () const
	Returns the value of SaveLastQueryAsc.

bool	isSectionAvailable () const
	Indicates whether the section has been actually read from the file.

bool	isShowAllFromErrorTolerant () const
	Returns the value of ShowAllFromErrorTolerant.

bool	isShowSubsets () const
	Returns the value of ShowSubSets.

bool	isStoreModPermutations () const
	Returns the value of StoreModPermutations.

bool	isUnixDirPermDefined () const
	Returns true if the UnixDirPerm value is defined.

bool	isUseHTTPProxyForFTP () const
	Returns the value of UseHTTPProxyForFTP.

bool	isUseHTTPProxyForHTTPS () const
	Returns the value of UseHTTPProxyForHTTPS.

ms_mascotoptions &	operator= (const ms_mascotoptions &right)
	C++ style assignment operator.

void	setAlwaysCreateDat28ResultsFile (const bool value)
	Sets the value of AlwaysCreateDat28ResultsFile.

void	setAlwaysEnableAutoDecoySearch (const bool value)
	Sets AlwaysEnableAutoDecoySearch.

void	setAutoSelectCharge (const bool value)
	Sets AutoSelectCharge.

void	setCacheDirectory (const char *value)
	Sets CacheDirectory.

void	setCentroidWidth (const double value)
	Sets CentroidWidth.

void	setCentroidWidthCount (const int value)
	Sets CentroidWidthCount.

void	setCompressToolAA (const std::string value)
	Sets CompressTool_AA.

void	setCompressToolNA (const std::string value)
	Sets CompressTool_NA.

void	setCompressToolSL (const std::string value)
	Sets CompressTool_NA.

void	setCrawlerNumPeaksPer100Da (const int value)
	Sets the number of peaks to output in each 100 Da window for the library crawler.

void	setCreateLegacyModAndSubstitutionFiles (const bool value)
	Sets an option for backwards compatibility with very old software.

void	setCreatePipThreadBlockSize (const int blockSize)
	Sets CreatePipThreadBlockSize.

void	setCreatePipThreads (const int nThreads)
	Sets CreatePipThreads.

void	setDechargeFragmentPeaks (const int maxCharge)
	Sets the maximum fragment ion charge state to be decharged.

void	setDecoyTypeNoEnzyme (const int value)
	Sets DecoyTypeNoEnzyme.

void	setDecoyTypeSpecific (const int value)
	Sets DecoyTypeSpecific.

void	setDefaultDelimiter (const char *delim)
	Allows to set a specific delimiter string to be used when no property-specific delimiter is supplied.

void	setDefaultTargetFDRPercentage (const int index)
	Makes an element of TargetFDRPercentages at the given index the default value.

void	setDisplayNonSignificantMatches (const int value)
	Sets DisplayNonSignificantMatches.

void	setEmailErrorsEnabled (const bool value)
	Sets EmailErrorsEnabled.

void	setEmailFromTextName (const char *str)
	Sets EmailFromTextName.

void	setEmailFromUser (const char *str)
	Sets EmailFromUser.

void	setEmailPassword (const char *str)
	Sets EmailPassword.

void	setEmailProfile (const char *str)
	Sets EmailPassword.

void	setEmailService (const char *str)
	Sets EmailService.

void	setEmailTimeOutPeriod (const int value)
	Sets EmailTimeOutPeriod.

void	setEmailUsersEnabled (const bool value)
	Sets EmailUsersEnabled.

void	setErrMessageEmailTo (const char *str)
	Sets ErrMessageEmailTo.

void	setErrorLogFile (const char *str)
	Sets ErrorLogFile path.

void	setErrTolMaxAccessions (const int value)
	Sets ErrTolMaxAccessions.

void	setExecAfterSearch (const int num, std::string value)
	Sets ExecAfterSearch_XXX.

void	setFeatureTableLength (const int value)
	Sets FeatureTableLength.

void	setFeatureTableMinScore (const double value)
	Sets FeatureTableMinScore.

void	setForkForUnixApache (const bool value)
	Sets ForkForUnixApache.

void	setFormVersion (const char *str)
	Sets FormVersion.

void	setGetSeqBlastAccession (const ms_blastaccession *value)
	Sets GetSeqBlastAccession.

void	setGetSeqJobIdFile (const char *str)
	Sets GetSeqJobIdFile.

void	setICATFilter (const char *filterString)
	Sets ICATFilter.

void	setICATHeavy (const char *modName)
	Sets ICATHeavy.

void	setICATLight (const char *modName)
	Sets ICATLight.

void	setICATQuantitationMethod (const char *methodName)
	Sets ICATQuantitationMethod.

void	setIgnoreDupeAccession (const unsigned int index, const std::string value)
	Sets an item in the IgnoreDupeAccessions list by its index.

void	setIgnoreIonsScoreBelow (const double value)
	Sets IgnoreIonsScoreBelow.

void	setIntensitySigFigs (const int value)
	Sets IntensitySigFigs.

void	setInterFileBasePath (const char *str)
	Sets InterFileBasePath.

void	setInterFileRelPath (const char *str)
	Sets InterFileRelPath.

void	setIonsDecimalPlaces (const int value)
	Sets IonsDecimalPlaces.

void	setIteratePMFIntensities (const bool value)
	Sets IteratePMFIntensities.

void	setLabelAll (const bool value)
	Sets LabelAll.

void	setLastQueryAscFile (const char *str)
	Sets LastQueryAscFile to the passed value.

void	setLogoImageFile (const char *str)
	Sets LogoImageFile.

void	setMailTempFile (const char *str)
	Sets MailTempFile.

void	setMailTransport (const int value)
	Sets MailTransport.

void	setMascNodeCtrlFile (const char *str)
	Sets MascNodeCtrlFile.

void	setMascotCmdLine (const char *str)
	Sets MascotCmdLine.

void	setMascotControlFile (const char *str)
	Sets MascotControlFile.

void	setMascotFileProcessingThreads (const int value)
	Sets MascotFileProcessingThreads.

void	setMascotJobIdFile (const char *str)
	Sets MascotJobIdFile.

void	setMascotMessage (const char *str)
	Sets MascotMessage.

void	setMassDecimalPlaces (const int value)
	Sets MassDecimalPlaces.

void	setMatchOppositeCrosslinkPairs (const bool value)
	Sets MatchOppositeCrosslinkPairs.

void	setMaxConcurrentSearches (const int value)
	Sets MaxConcurrentSearches.

void	setMaxDatabases (const int value)
	Sets MaxDatabases.

void	setMaxDescriptionLen (const int value)
	Sets MaxDescriptionLen.

void	setMaxEtagMassDelta (const double value)
	Sets MaxEtagMassDelta.

void	setMaxEtVarMods (const int value)
	Sets MaxEtVarMods.

void	setMaxIntactCrosslinkPeptides (const int value)
	Sets MaxIntactCrosslinkPeptides.

void	setMaxNumPeptides (const int value)
	Sets MaxNumPeptides.

void	setMaxPepModArrangements (const int value)
	Sets MaxPepModArrangements.

void	setMaxPepNumModifiedSites (const int value)
	Sets MaxPepNumModifiedSites.

void	setMaxPepNumVarMods (const int value)
	Sets MaxPepNumVarMods.

void	setMaxQueries (const int value)
	Sets MaxQueries.

void	setMaxSearchesPerUser (const int value)
	Sets MaxSearchesPerUser.

void	setMaxSequenceLen (const int value)
	Sets MaxSequenceLen.

void	setMaxVarMods (const int value)
	Sets MaxVarMods.

void	setMinEtagMassDelta (const double value)
	Sets MinEtagMassDelta.

void	setMinPepLenInPepSummary (const int value)
	Sets MinPepLenInPepSummary.

void	setMinPepLenInSearch (const int value)
	Sets MinPepLenInSearch.

void	setMonitorEmailCheckFreq (const int value)
	Sets MonitorEmailCheckFreq.

void	setMonitorLogFile (const char *str)
	Sets MonitorLogFile.

void	setMonitorPidFile (const char *str)
	Sets MonitorPidFile.

void	setMonitorTestTimeout (const int value)
	Sets MonitorTestTimeout.

void	setMoveOldDbToOldDir (const bool value)
	Sets MoveOldDbToOldDir.

void	setMudpit (const int value)
	Sets Mudpit.

void	setMudpitSwitch (const double value)
	Sets MudpitSwitch.

void	setNoResultsScript (const char *str)
	Sets NoResultsScript.

void	setNTIUserGroup (const char *str)
	Sets NTIUserGroup.

void	setNTMonitorGroup (const char *str)
	Sets NTMonitorGroup.

void	setPepSearchTool (const std::string value)
	Sets LibrarySearch.

void	setPercolator (const bool value)
	Sets Percolator.

void	setPercolatorExeFlags (const char *value)
	Sets PercolatorExeFlags.

void	setPercolatorFeatures (std::string value)
	Sets PercolatorFeatures.

void	setPercolatorMinQueries (const int value)
	Sets PercolatorMinQueries.

void	setPercolatorMinSequences (const int value)
	Sets PercolatorMinSequences.

void	setPercolatorTargetRankRelativeThreshold (const double threshold)
	Sets PercolatorTargetRankRelativeThreshold.

void	setPercolatorTargetRankScoreThreshold (const int threshold)
	Sets PercolatorTargetRankScoreThreshold.

void	setPercolatorUseProteins (const bool value)
	Sets PercolatorUseProteins.

void	setPercolatorUseRT (const bool value)
	Sets PercolatorUseRT.

void	setPreceedingComments (const std::string &comments)
	Sets any comments preceeding the section.

void	setPrecursorCutOutLowerLimit (const double value)
	Sets the first PrecursorCutOut.

void	setPrecursorCutOutUpperLimit (const double value)
	Sets the second PrecursorCutOut.

void	setPropertyName (const int index, const char *name)
	Changes name of the property with the given index.

void	setPropValBoolByName (const char *name, const bool value, const bool bFirstPlace=false)
	Changes a boolean value of the first entry with the given name or creates a new property if it is not found.

void	setPropValCharByName (const char *name, const char value, const bool bFirstPlace=false)
	Changes a single character value of the first entry with the given name or creates a new property if it is not found.

void	setPropValFloatByName (const char *name, const double value, const bool bFirstPlace=false)
	Changes an floating point value of the first entry with the given name or creates a new property if it is not found.

void	setPropValInt64ByName (const char *name, const INT64 value, const bool bFirstPlace=false)
	Changes a long 64-bit integer value of the first entry with the given name or creates a new property if it is not found.

void	setPropValIntByName (const char *name, const int value, const bool bFirstPlace=false)
	Changes an integer value of the first entry with the given name or creates a new property if it is not found.

void	setPropValStringByName (const char name, const char value, const bool bFirstPlace=false)
	Changes a string value of the first entry with the given name or creates a new property if it is not found.

void	setPropValStringByNumber (const int index, const char *value)
	Changes an string value of an existing property with the given index.

void	setProteinFamilySwitch (const int value)
	Sets ProteinFamilySwitch.

void	setProteinsInResultsFile (const int value)
	Sets ProteinsInResultsFile.

void	setProxyPassword (const char *str)
	Sets proxy_password.

void	setProxyServer (const char *str)
	Sets proxy_server.

void	setProxyType (const std::string &value)
	Sets ProxyType.

void	setProxyUsername (const char *str)
	Sets proxy_username.

void	setRemoveOldIndexFiles (const bool value)
	Sets RemoveOldIndexFiles.

void	setReportBuilderColumnArrangement (const int index, const std::string str)
	Sets ReportBuilderColumnArrangement.

void	setReportNumberChoice (const int index, const int value)
	Sets an element of the ReportNumberChoices list by its index.

void	setRequireBoldRed (const bool value)
	Sets RequireBoldRed.

void	setResfileCache (const char *value)
	Sets ResfileCache.

void	setResultsCache (const char *value)
	Sets ResultsCache.

void	setResultsFileFormatVersion (const char *value)
	Sets ResultsFileFormatVersion.

void	setResultsFullURL (const char *str)
	Sets ResultsFullURL.

void	setResultsFullURL_2 (std::string value)
	Sets ResultsFullURL_2.

void	setResultsPerlScript (const char *str)
	Sets ResultsPerlScript.

void	setResultsPerlScript_2 (std::string value)
	Sets ResultsPerlScript_2.

void	setReviewColDisplay (const MS_REVIEW_COL index, const bool value)
	Sets ReviewColDisplay.

void	setReviewColWidth (const MS_REVIEW_COL index, const int value)
	Sets ReviewColWidths.

void	setSaveEveryLastQueryAsc (const bool flag)
	Sets SaveEveryLastQueryAsc to 1 or 0.

void	setSaveLastQueryAsc (const bool flag)
	Sets SaveLastQueryAsc to 1 or 0.

void	setSearchLogFile (const char *str)
	Sets SearchLogFile.

void	setSearchSubmitAcceptedFileTypes (const std::string value)
	Sets the accepted input file types in the Mascot search form.

void	setSearchSubmitDefaultPeptideCharge (const std::string value)
	Sets the default peptide charge when not specified in the input file.

void	setSearchSubmitMode (const std::string value)
	Sets the Mascot search submission mode.

void	setSearchSubmitOutputFormat (const std::string value)
	Sets the Mascot search submission output format.

void	setSectionAvailable (const bool value)
	Changes availability of the section, i.e. whether it should be saved in a file.

void	setSelectSwitch (const int value)
	Sets SelectSwitch.

void	setSendmailPath (const char *str)
	Sets sendmailPath.

void	setShowAllFromErrorTolerant (const bool value)
	Sets ShowAllFromErrorTolerant.

void	setShowSubsets (const bool value)
	Sets ShowSubSets.

void	setShowSubsets (const double value)
	Sets ShowSubSets.

void	setSigThreshold (const double value)
	Set the SigThreshold.

void	setSiteAnalysisMD10Prob (const double value)
	Set the SiteAnalysisMD10Prob.

void	setSortUnassigned (const std::string newValue)
	Sets SortUnassigned.

void	setSpectraPerLibraryBlock (const int value)
	Sets the number of spectra in a spectral library block.

void	setSpectrumViewerColourSchemeString (const std::string &name, const std::string &str, bool doCheck=true)
	Sets SpectrumViewerColourScheme.

void	setSpectrumViewerDefaultColourSchemeName (const std::string &name)
	Sets the default colour scheme name (SpectrumViewerDefaultColourScheme).

void	setSplitDataFileSize (const int value)
	Sets SplitDataFileSize.

void	setSplitNumberOfQueries (const int value)
	Sets SplitNumberOfQueries.

void	setStoreModPermutations (const bool value)
	Sets StoreModPermutations.

void	setSVGSpectrumSwitch (const int value)
	Sets SVGSpectrumSwitch.

void	setTargetFDRPercentage (const int index, const double value, const bool makeDefault=false)
	Sets an element of the TargetFDRPercentages list by its index.

void	setTaxBrowserUrl (const std::string value)
	Sets TaxBrowserURL.

void	setTestDirectory (const char *str)
	Sets TestDirectory.

void	setUniqueJobStartNumber (const int value)
	Sets UniqueJobStartNumber.

void	setUnixDirPerm (const int value)
	Sets UnixDirPerm.

void	setUnixWebUserGroup (const int value)
	Sets UnixWebUserGroup.

void	setUseHTTPProxyForFTP (const bool value)
	Sets UseHTTPProxyForFTP.

void	setUseHTTPProxyForHTTPS (const bool value)
	Sets UseHTTPProxyForHTTPS.

void	setVmemory (const INT64 value)
	Sets Vmemory.

bool	uncommentProp (const int index, const char *delimeter=0)
	Uncomments a line in the configuration file.

Detailed Description

An instance of this class represents all the parameters specified in the Options section of mascot.dat.

An instance of this class is created and populated in ms_datfile.

It can also be created separately and initialized with default values. One can create an instance of the class or copy from another instance in order to pass it then as an options containing object.

For detailed information on any of the options please consult Mascot manual.

Also get yourselves acquainted with the base class ms_customproperty. It facilitates the following tasks:

Retrieving an unsupported property.
Retrieving a raw/text/XML property representation.
Checking for existence of a certain property rather than dealing with its default value.
Accessing commented lines in a section.

More functionality is described in the documentation for ms_customproperty.

Examples: config_mascotdat.cpp, and resfile_summary.cpp.

Member Enumeration Documentation

◆ DECOY_ALGORITHM

enum DECOY_ALGORITHM

Definitions for how the decoy sequences are generated.

In Mascot 2.4 and later, DecoyTypeSpecific and DecoyTypeNoEnzyme control how the decoy database is generated. The strategies are based on the classification by G. Wang, et al. (2009), "Decoy Methods for Assessing False Positives and False Discovery Rates in Shotgun Proteomics", Anal Chem. 81(1):146-159 (doi: 10.1021/ac801664q).

There are four protein based strategies and four peptide based strategies.

The peptide based strategies are not supported for getDecoyTypeNoEnzyme() and if specified in mascot.dat, the corresponding protein based strategy will be returned.

For the peptide based strategies, with a semi-specific search, the protein sequences are generated in the same way as if the search was fully specific, rather than preserving the terminii of the non-specific terminus. A similar rule is applied for missed cleavages: i.e. the two residues either side of the missed cleavage site will be the same as in the target sequence.

This value is returned by getDecoyTypeSpecific() and getDecoyTypeNoEnzyme() See Using enumerated values and static const ints in Perl, Java, Python and C#.

Enumerator
DECOY_ALGORITHM_NONE	(0) No algorithm defined. An invalid value.
DECOY_PROTEIN_REVERSE	(1) Reverse the sequence of each protein entry. For a nucleic acid database, the bases are reversed before translation.
DECOY_PEPTIDE_REVERSE	(2) Digest each protein sequence into peptides, then reverse the resulting peptide sequences, but keep the same terminal residues.
DECOY_PROTEIN_RANDOM	(3) For each protein entry, generate a random sequence of the same length, with the composition based on the average composition of the whole database. This is the default in Mascot 2.3 and earlier. For nucleic acid databases, the randomised sequence is generated before translation.
DECOY_PEPTIDE_RANDOM	(4) Digest each protein sequence into peptides, then generate a random sequence for each peptide, as for DECOY_PROTEIN_RANDOM, but keep the same terminal residues and don't introduce new cutting sites. If this option is specified and a nucleic acid database is searched, DECOY_PROTEIN_RANDOM is used.
DECOY_PROTEIN_RANDOM_DIPEP	(5) Protein sequence randomization based on dipeptide frequency (randomDipep): for each protein, an amino acid is randomly chosen according to their frequency distribution as the N-terminal. Each amino acid generated thereafter is based on the occurrence frequency of each dipeptide that starts with its preceding neighboring amino acid. Decoy sequences created this way are expected to have similar amino acid composition and nearest-neighbor frequencies of the target database. (Not implemented in Mascot 2.4).
DECOY_PEPTIDE_RANDOM_DIPEP	(6) Digest each protein sequence into peptides, but generate random dipeptide sequences for each peptide as in DECOY_PROTEIN_RANDOM_DIPEP, keeping the same terminal residues. (Not implemented in Mascot 2.4).
DECOY_PROTEIN_SHUFFLE	(7) Randomise the order of amino acids in each protein sequence using the STL random_shuffle algorithm: http://www.cplusplus.com/reference/algorithm/random_shuffle/ .
DECOY_PEPTIDE_SHUFFLE	(8) Digest each protein sequence into peptides, but shuffle their sequence as in DECOY_PROTEIN_SHUFFLE, excluding the terminus residue.
DECOY_PROTEIN_BASED_MASK	If the value AND'ed with this is '1', then the algorithm is protein based. (Protein based strategies have value 1,3,5,7)

◆ EXEC_AFTER_SEARCH

enum EXEC_AFTER_SEARCH

Definitions for the ExecAfterSearch_XXX lines in the Options section of mascot.dat.

See Using enumerated values and static const ints in Perl, Java, Python and C#.

Enumerator
MAX_EXEC_AFTER_SEARCH	The maximum value for setExecAfterSearch () abd getExecAfterSearch()

◆ MS_REVIEW_COL

enum MS_REVIEW_COL

Definitions for columns in ms-review.exe for use with getReviewColWidth() and getReviewColDisplay().

See Using enumerated values and static const ints in Perl, Java, Python and C#.

Enumerator
MS_REVIEW_COL_JOB	The job number column.
MS_REVIEW_COL_PID	The process ID column.
MS_REVIEW_COL_DATABASE	The database name column.
MS_REVIEW_COL_USERNAME	The USERNAME column.
MS_REVIEW_COL_USEREMAIL	The USEREMAIL column.
MS_REVIEW_COL_TITLE	The search title (COM) column.
MS_REVIEW_COL_RESULTS_FILE	The results file name column.
MS_REVIEW_COL_START_TIME	The job start time and date column.
MS_REVIEW_COL_DURATION	The job duration column (seconds).
MS_REVIEW_COL_STATUS	The job status column - normally 'User read res'.
MS_REVIEW_COL_PRIORITY	The job priority column (0 = normal priority).
MS_REVIEW_COL_SEARCHTYPE	The job search type column (PMF, MIS or SQ).
MS_REVIEW_COL_ENZYMEUSED	The job enzyme used column (Yes or No).
MS_REVIEW_COL_IPADDRESS	The IP address from where the search was submitted.
MS_REVIEW_COL_USERID	The USERID of the user who submitted the search.
MS_REVIEW_COL_PEAKLISTDATAFILE	The name of the data file.
MS_REVIEW_COL____LAST___	Placeholder.

◆ NUMERICAL_VALUE_STORAGE

enum NUMERICAL_VALUE_STORAGE

Definitions for storage of numerical values in files.

Enumerator
MASS_DECIMAL_PLACES	Decimal places used when storing mass values as strings in files.

◆ PERC_EXE_RT

enum PERC_EXE_RT

Definitions for retention time override when calling getPercolatorExeFlags().

See Using enumerated values and static const ints in Perl, Java, Python and C#.

Enumerator
PERC_EXE_RT_USE_DEFAULT	Use the default value in `mascot.dat`.
PERC_EXE_RT_FORCE_ON	Override the value in `mascot.dat`, forcing the use of retention times.
PERC_EXE_RT_FORCE_OFF	Override the value in `mascot.dat`, turning off the use of retention times.

Constructor & Destructor Documentation

◆ ms_mascotoptions() [1/2]

ms_mascotoptions ( )

Default constructor.

See ms_datfile::getMascotOptions() for the most common way to create an ms_mascotoptions object.

◆ ms_mascotoptions() [2/2]

ms_mascotoptions ( const ms_mascotoptions & src )

Copying constructor.

See ms_datfile::getMascotOptions() for the most common way to create an ms_mascotoptions object.

Parameters

src	reference to a valid ms_mascotoptions object

Member Function Documentation

◆ appendIgnoreDupeAccession()

void appendIgnoreDupeAccession ( const std::string value )

Appends a database to the list databases that shouldn't be checked for duplicate accessions.

When FASTA files are compressed, they are checked to ensure that there are no duplicate accession strings. For a large EST database with many millions of entries, this can take up a lot of memory. Adding a database to the list of values for the IgnoreDupeAccessions entry in mascot.dat prevents this database from being tested.

Add a database to the list.

Parameters

value is the name of the database to add to the list.

◆ appendProperty()

void appendProperty	(	const char *	name,
		const char *	value,
		const char *	delimiter,
		const bool	bFirstPlace = `false`
	)

inherited

Adds a new property with the given parameters.

Parameters

name	a property name to use.
value	a property value to use.
delimiter	a specific delimiter or an empty string for a default one to be used.
bFirstPlace	forces a new property to be put on top of the list.

◆ appendReportNumberChoice()

void appendReportNumberChoice ( const int value )

Append a value to the ReportNumberChoices list.

See getReportNumberChoice() for more information. If the provided value is not valid, the existing value will be kept.

Parameters

value is the value to be appended to the list.

◆ appendTargetFDRPercentage()

void appendTargetFDRPercentage	(	const double	value,
		const bool	makeDefault = `false`
	)

Append a value to the TargetFDRPercentages list.

See getTargetFDRPercentage() for more information. If the provided value is not valid, the list will be unchanged.

Parameters

value	is the value to be appended to the list.
makeDefault	controls whether the new element should be made the default item in the list.

◆ appendText()

void appendText	(	const char *	l,
		const bool	bFirstPlace = `false`
	)

inherited

Adds a new non-parsed property.

All property elements will be retrieved from the first parameter. Before calling this method, a specific default delimiter can be set using setDefaultDelimiter().

Parameters

l	raw text representation of the property to be parsed.
bFirstPlace	forces a new property to be put on top of the list.

◆ clearIgnoreDupeAccessions()

void clearIgnoreDupeAccessions ( )

Clears the list of databases that shouldn't be checked for duplicate accessions.

When FASTA files are compressed, they are checked to ensure that there are no duplicate accession strings. For a large EST database with many millions of entries, this can take up a lot of memory. Adding a database to the list of values for the IgnoreDupeAccessions entry in mascot.dat prevents this database from being tested.

See also: getNumberOfIgnoreDupeAccessions(), getIgnoreDupeAccession()

◆ clearReportNumberChoices()

void clearReportNumberChoices ( )

Deletes all ReportNumberChoices values from the list.

See getNumberOfReportNumberChoices().

◆ clearTargetFDRPercentages()

void clearTargetFDRPercentages ( )

Deletes all TargetFDRPercentages values from the list.

See getNumberOfTargetFDRPercentages().

◆ delProp()

void delProp ( const char * str )

inherited

Deletes all properties with the specified name.

Parameters

str	Property name to find a match and then delete.

◆ delPropStart()

void delPropStart ( const char * str )

inherited

Deletes all properties whose names start with the given string.

Parameters

str	Beginning a first part of the property name to delete.

◆ findProperty()

int findProperty	(	const char *	name,
		const int	startFrom = `0`
	)		const

inherited

Searches the list for a property with the given name.

If no property found with the given name -1 will be returned. There may be several property entries in the list with the same name.

Parameters

name	a property name to be found.
startFrom	a minimal property index to start search from.

Returns: a property index or -1 if no property found.

◆ findPropertyBeginning()

int findPropertyBeginning	(	const char *	nameBeginning,
		const int	startFrom = `0`
	)		const

inherited

Searches the list for a property with the partially matching name.

If no property found with the given name part -1 will be returned. There may be several property entries in the list whose names start with the given string.

Parameters

nameBeginning	first part of a property name to be found.
startFrom	a minimal property index to start search from.

Returns: a property index or -1 if no property found.

◆ getCacheDirectory()

std::string getCacheDirectory ( ) const

Returns the value of CacheDirectory.

See Caching Mascot Results.

The value returned by this function may have an 'encoded' string which requires interpretation by the calling application. For this reason, it is normally easier to call ms_mascotresfilebase::getCacheDirectory().

Parameter	CacheDirectory
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../data/cache/%Y/%m
Value in mascot.dat	../data/cache/%Y/%m

Returns: the directory.

◆ getCentroidWidth()

double getCentroidWidth ( ) const

Returns the value of CentroidWidth.

The width in Daltons of the sliding window used for re-centroiding profile data.

Parameter	CentroidWidth
Permitted values	Floating point > 0 and less than 10.0
Default (if no parameter in mascot.dat)	0.25
Value in mascot.dat	0.25

Returns: the width in Da.

◆ getCentroidWidthCount()

int getCentroidWidthCount ( ) const

Returns the value of CentroidWidthCount.

Centroiding is applied to a scan when the number of peaks in the scan exceeds CentroidWidthCount.

Parameter	CentroidWidthCount
Permitted values	Positive integer > 0
Default (if no parameter in mascot.dat)	1000
Value in mascot.dat	1000

Returns: the peak count threshold.

◆ getCompressToolAA()

std::string getCompressToolAA ( ) const

Returns the value of CompressTool_AA.

Not implemented (at version 2.6)

Parameter	CompressTool_AA
Permitted values	Any non empty text string. Should contain $dbname and $dbpath
Default (if no parameter in mascot.dat)	"../bin/ms-compress.exe $dbname $dbpath"
Value in mascot.dat	"../bin/ms-compress.exe $dbname $dbpath"

Returns: raw compress tool command line from mascot.dat

◆ getCompressToolCommandLineFasta()

std::string getCompressToolCommandLineFasta	(	DATABASE_TYPE	dbType,
		const std::string &	dbname,
		const std::string &	dbpath
	)		const

Get command line to compress fasta, eg ms-compress.exe.

CURRENTLY NOT IN USE

Parameters

dbType	Database type, AA or NA
dbname	Name of the database
dbpath	Full path to the database file

Returns: complete compress tool command line for a fasta

◆ getCompressToolCommandLineLibrary()

std::string getCompressToolCommandLineLibrary	(	const std::string &	logfilepath,
		const std::string &	inputfile,
		const std::string &	outputdirectory
	)		const

Get command line to compress library, eg lib2nistcl.exe.

This function is called by ms-monitor.exe to get the command line required to compress (or otherwise prepare) a spectral library. It calls getCompressToolSL which contains a number of 'tags' which need to be replaced with search specific parameters. In theory, any tool could be used instead of lib2nistcl.exe . This function replaces the following tags with the corresponding variable passed to this function:

$logfile is replaced with logfilepath
$inputfile is replaced with inputfile
$outputdirectory is replaced with outputdirectory

See also: getCompressToolSL()

Parameters

logfilepath	full path to the log file that the tool will create. The contents of this file are inserted into the .stats file.
inputfile	full path to the input file. Typically an msp file, but could be any format supported by the tool.
outputdirectory	path to the output directory. For lib2nistcl, this is a directory, but it could be a filename.

Returns: complete compress tool command line for a spectral library

◆ getCompressToolNA()

std::string getCompressToolNA ( ) const

Returns the value of CompressTool_NA.

Not implemented (at version 2.6)

Parameter	CompressTool_NA
Permitted values	Any non empty text string. Should contain $dbname and $dbpath
Default (if no parameter in mascot.dat)	"../bin/ms-compress.exe $dbname $dbpath"
Value in mascot.dat	"../bin/ms-compress.exe $dbname $dbpath"

Returns: raw compress tool command line from mascot.dat

◆ getCompressToolSL()

std::string getCompressToolSL ( ) const

Returns the value of CompressTool_NA.

Parameter	CompressTool_SL
Permitted values	Any non empty text string. Should contain $logfile, $inputfile and $outputdirectory
Default (if no parameter in mascot.dat)	"../bin/NIST/lib2nistcl/lib2nistcl.exe -log9 $logfile -msp2peplib $inputfile $outputdirectory"
Value in mascot.dat	"../bin/NIST/lib2nistcl/lib2nistcl.exe -log9 $logfile -msp2peplib $inputfile $outputdirectory"

Returns: raw compress tool command line from mascot.dat

◆ getCrawlerNumPeaksPer100Da()

int getCrawlerNumPeaksPer100Da ( ) const

Returns the number of peaks to output in each 100 Da window for the library crawler.

The number of highest-intensity peaks to choose from each 100 Da window of the observed spectrum when creating the library spectrum.

Parameter	CrawlerNumPeaksPer100Da
Permitted values	Any integer > 0.
Default (if no parameter in mascot.dat)	100
Value in mascot.dat	100

Returns: the number of peaks to choose from each 100 Da window

◆ getCreatePipThreadBlockSize()

int getCreatePipThreadBlockSize ( ) const

Returns the value of CreatePipThreadBlockSize.

Mascot 2.8 and later parallelises the calculation of the Percolator features. Each thread calculates the features in blocks of queries whose size is specified by this option. This option is not implemented in Mascot 2.7 and earlier.

See Using Percolator scores for further information.

Permitted values	An integer greater than 0
Default (if no parameter in mascot.dat)	2000
Value in mascot.dat	2000

Returns: Number of queries processed by each thread.

◆ getCreatePipThreads()

int getCreatePipThreads ( ) const

Returns the value of CreatePipThreads.

Mascot 2.8 and later parallelises the calculation of the Percolator features. If the value of this option is set to -1, all available threads will be used. This option is not implemented in Mascot 2.7 and earlier.

See Using Percolator scores for further information.

Permitted values	Any iteger greater or equal to -1
Default (if no parameter in mascot.dat)	4
Value in mascot.dat	4

Returns: Number of threads used in ms-createpip.exe.

◆ getDechargeFragmentPeaks()

int getDechargeFragmentPeaks ( ) const

Return the maximum fragment ion charge state to be decharged.

Fragment ion peak charges can be specified in Mascot Generic Format. Mascot Server only looks for 1+ and 2+ fragment ions, so higher charge states will not be matched unless they are de-charged.

If the charge specified for a particular fragment in the MGF file is less than or equal to the value returned by this function, then the m/z value will be decharged to the singly charged MH+ value before searching.

Some instruments will never produce very high charge states, but the peak detection software may incorrectly report a very high charge state. Setting this value to a sensible maximum charge state will prevent decharging of these fragment peaks. A value of zero will prevent any decharging.

Parameter	DechargeFragmentPeaks
Permitted values	Zero or a positive integer
Default (if no parameter in mascot.dat)	10
Value in mascot.dat	10

Returns: currently defined value.

◆ getDecoyTypeNoEnzyme()

int getDecoyTypeNoEnzyme ( ) const

Returns the value of DecoyTypeNoEnzyme.

Mascot 2.2 introduced automatic decoy searches. Any search can be run simultaneously against a randomised decoy database, which is generated on the fly.

See ms_mascotoptions::DECOY_ALGORITHM for a description of the possible values. However, only PROTEIN based strategies are supported for no-enzyme searches.

Only the following values are implemented for no-enzyme searches:

ms_mascotoptions::DECOY_PROTEIN_REVERSE
ms_mascotoptions::DECOY_PROTEIN_RANDOM (default)
ms_mascotoptions::DECOY_PROTEIN_SHUFFLE

The other values may be implemented in future versions of Mascot and are thus reserved values. Setting DecoyTypeNoEnzyme to any of them will select the default strategy (3).

For a search with an enzyme specified, see getDecoyTypeSpecific().

Parameter	DecoyTypeNoEnzyme
Permitted values	1, 2, 3, 4, 5, 6, 7, 8
Default (if no parameter in mascot.dat)	3
Value in mascot.dat	3

Returns: the decoy search type for a no-enzyme search.

◆ getDecoyTypeSpecific()

int getDecoyTypeSpecific ( ) const

Returns the value of DecoyTypeSpecific.

Mascot 2.2 introduced automatic decoy searches. Any search can be run simultaneously against a randomised decoy database, which is generated on the fly.

See ms_mascotoptions::DECOY_ALGORITHM for a description of the possible values.

Only the following values are implemented:

ms_mascotoptions::DECOY_PROTEIN_REVERSE (default)
ms_mascotoptions::DECOY_PEPTIDE_REVERSE
ms_mascotoptions::DECOY_PROTEIN_RANDOM
ms_mascotoptions::DECOY_PEPTIDE_RANDOM
ms_mascotoptions::DECOY_PROTEIN_SHUFFLE
ms_mascotoptions::DECOY_PEPTIDE_SHUFFLE

The other values may be implemented in future versions of Mascot and are thus reserved values. Setting DecoyTypeSpecific to any of them will select the default strategy (1).

For a search with no enzyme specified, see getDecoyTypeNoEnzyme().

Parameter	DecoyTypeSpecific
Permitted values	1, 2, 3, 4, 5, 6, 7, 8
Default (if no parameter in mascot.dat)	1
Value in mascot.dat	2

Returns: the decoy search type for an ordinary search.

◆ getDefaultDelimiter()

std::string getDefaultDelimiter ( ) const

inherited

Return current default delimiter string used for parsing/storing properties.

Returns: default delimiter

◆ getDelimiterByNumber()

std::string getDelimiterByNumber ( const int index ) const

inherited

Returns a specific delimiter used for the property.

Parameters

index Index for which to get a delimiter

Returns: corresponding delimiter

◆ getDisplayNonSignificantMatches()

int getDisplayNonSignificantMatches ( ) const

Returns the value of DisplayNonSignificantMatches.

In Mascot 2.5 and earlier, the search reports show an input field for "Ignore ions score below". The control allows filtering out non-significant or uninteresting peptide matches by score or expect value.

In Mascot 2.6 and later, the search reports show either a checkbox for "Display non-significant matches" or the edit field from previous versions, depending on the value of DisplayNonSignificantMatches: if 0 or 1, display the checkbox, and if 2, display the edit field. Additionally, 0 means the checkbox is unchecked by default and 1 means checked.

Parameter	DisplayNonSignificantMatches
Permitted values	0, 1, 2
Default (if no parameter in mascot.dat)	1
Value in mascot.dat	0

Returns: form control type for filtering out non-significant matches.

◆ getEmailFromTextName()

std::string getEmailFromTextName ( ) const

Returns the value of EmailFromTextName.

The EmailFromTextName value is the text name of the sender of all messages For example, if the email is from "Mascot Server <sender@somewhere.com>", then "Mascot Server" is the EmailFromTextName value. The default value of 'your_domain' in earlier versions of mascot.dat was somewhat confusing.

Used by all e-mail configurations.

See also: getEmailFromUser(), getMailTransport(), isEmailUsersEnabled(), isEmailErrorsEnabled().

Parameter	EmailFromTextName
Permitted values	Any text string
Default (if no parameter in mascot.dat)	[empty]
Value in mascot.dat	Mascot

Returns: the name from which messages are sent.

◆ getEmailFromUser()

std::string getEmailFromUser ( ) const

Returns the value of EmailFromUser.

EmailFromUser is the email address which will appear in the From field of the email message. Used by all e-mail configurations.

See also: getMailTransport(), isEmailUsersEnabled(), isEmailErrorsEnabled().

Parameter	EmailFromUser
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	[empty]
Value in mascot.dat	your_id

Returns: the email address from which messages are sent.

◆ getEmailPassword()

std::string getEmailPassword ( ) const

Returns the value of EmailPassword.

EmailPassword is the password (if any) required to log onto MAPI or CMC.

See also: getMailTransport(), isEmailUsersEnabled(), isEmailErrorsEnabled().

Parameter	EmailPassword
Permitted values	Any text string
Default (if no parameter in mascot.dat)	[empty]
Value in mascot.dat	your_password

Returns: the password for the email service.

◆ getEmailProfile()

std::string getEmailProfile ( ) const

Returns the value of EmailProfile.

EmailProfile is the MAPI profile name.

See also: getMailTransport(), isEmailUsersEnabled(), isEmailErrorsEnabled().

Parameter	EmailProfile
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	[empty]
Value in mascot.dat	your_profile

Returns: the name for the MAPI email profile.

◆ getEmailService()

std::string getEmailService ( ) const

Returns the value of EmailService.

EmailService is the service name (CMC only).

See also: getMailTransport(), isEmailUsersEnabled(), isEmailErrorsEnabled().

Parameter	EmailService
Permitted values	Any text string
Default (if no parameter in mascot.dat)	[empty]
Value in mascot.dat	your_service

Returns: the name of the CMC email service.

◆ getEmailTimeOutPeriod()

int getEmailTimeOutPeriod ( ) const

Returns the value of EmailTimeOutPeriod.

See isEmailUsersEnabled() for information on this parameter.

Parameter	EmailTimeOutPeriod
Permitted values	Any positive integer
Default (if no parameter in mascot.dat)	120
Value in mascot.dat	120

Returns: The timeout period in seconds.

◆ getErrMessageEmailTo()

std::string getErrMessageEmailTo ( ) const

Returns the value of ErrMessageEmailTo.

If EmailErrorsEnabled is set to 1, serious error messages will be emailed to ErrMessageEmailTo.

See also: isEmailErrorsEnabled().

Parameter	ErrMessageEmailTo
Permitted values	Any text string
Default (if no parameter in mascot.dat)	[empty]
Value in mascot.dat	admin.nosp@m.istr.nosp@m.ator@.nosp@m.your.nosp@m..doma.nosp@m.in

Returns: the email address to which messages are sent.

◆ getErrorLogFile()

std::string getErrorLogFile ( ) const

Returns the value of ErrorLogFile.

This defines where error messages should be stored.

Parameter	ErrorLogFile
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../logs/errorlog.txt
Value in mascot.dat	[not defined]

Returns: the full (or relative) path to the errorlog file.

◆ getErrTolMaxAccessions()

int getErrTolMaxAccessions ( ) const

Returns the value of ErrTolMaxAccessions.

The maximum number of accessions allowed for an 'old style' error-tolerant search.

A value of zero indicates no limit

Parameter	ErrTolMaxAccessions
Permitted values	Any integer >= 0
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	[not defined]

Returns: the maximum number of accessions.

◆ getExecAfterSearch()

int getExecAfterSearch	(	const char *	szResultsFilePath,
		std::vector< std::string > &	commands,
		std::vector< std::string > &	titles,
		std::vector< int > &	waitfor,
		std::vector< int > &	logging,
		std::vector< std::string > &	additionalFlags,
		const char *	sessionID = `0`,
		const char *	taskID = `0`
	)		const

Returns the values of the ExecAfterSearch_XXX parameters.

After each search, a number of 'user' programs can be run. For example, Percolator may be run after each search.

Parameter	ExecAfterSearch_XXX
Permitted values	Text string of the format: `flag:num[;flag:num], title string, command` where flag:num can be one or more of flag:value pairs from the table below title string is the (optional) text output by nph-mascot while the process is running. For example "Percolating...". The title must not contain a comma! command should be a unix/windows command string. It may contain one or more of tags as described below
Default (if no parameter in mascot.dat)	[empty]
Value in mascot.dat	`ExecAfterSearch_2 waitfor:0;logging:0;percolator:1, Percolating, ../bin/percolator.exe $PercolatorExeFlags`

The following flags may be specified:

flag	Acceptable 'num'	Description
waitfor	0 or 1..10	This command should not be run until the command specified by the waitfor has finished. A value of 0 indicates 'don't wait'.
logging	0..3	The values indicate the level of logging. Messages are put into errorlog.txt: 0 - No logging 1 - Log successful commands (return code 0) 2 - Log unsuccessful commands (return code not 0) 3 - Log successful and unsuccessful commands
percolator	0 or 1	This command will only be run if Percolator is set to 1 in mascot.dat and if the search meets the criteria to percolate results. See Using Percolator scores
cgienv	0 or 1	Default is 1. When nph-mascot.exe runs the command specified, it uses spawn/exec so all the same environment variables available to nph-mascot.exe are set. When this includes cgi environment variables, it can cause confusion and problems for some perl scripts such as export_dat.pl, where the script behaves differently when running as cgi process. Setting this flag to 0 ensures that all the cgi environment variables, such as =CONTENT_LENGTH= and =SCRIPT_NAME= are cleared before the process is run.

For consistency with ms_mascotresfilebase::staticGetPercolatorFileNames() and ms_mascotresfilebase::setPercolatorFeatures(), it is important to set PercolatorExeFlags correctly before calling this method. Otherwise, this method may generate a pip or pop filename different from setPercolatorFeatures().

    bool anyRT = (whether any query has RTINSECONDS);
    std::string percolatorFlags = options.getPercolatorRtFlags(anyRT, options.isPercolatorUseRT());
    options.setPercolatorExeFlags(percolatorFlags.c_str());

The following tags will be replaced. (Note that it would potentially be unsafe to add a tag for a value that can be entered by the user in a search form, e.g. a user could enter cat /etc/passwd as their username).

Tag	Replaced with
%resultfilepath	The passed szResultsFilePath
%resultfilename	The filename part of the passed szResultsFilePath
%percolator_pip	The input file from ms_mascotresfilebase::staticGetPercolatorFileNames()
%percolator_decoy_pop	The decoy output file from ms_mascotresfilebase::staticGetPercolatorFileNames()
%percolator_target_pop	The target output file from ms_mascotresfilebase::staticGetPercolatorFileNames()
%session_id	Is replaced by the passed sessionID parameter
%task_id	Is replaced by the passed taskID parameter
$PercolatorExeFlags	This flag is not replaced by this function! nph-mascot calls getPercolatorExeFlags() to replace it.

A set of vectors is returned from this function. Currently, each vector will have 10 entries, corresponding to ExecAfterSearch_1 ... ExecAfterSearch_10, but this value may be increased in future. The calling application should use the size of the vectors rather than hardcode the number 10. Note that many (or all) of the commands may be empty.

Parameters

szResultsFilePath	is the path to the results file.
commands	is a vector, containing the list of commands to be run. the flags and titles will have been stripped from the command, and any tags in the commands will have been replaced by values as described above. See Using STL vector classes vectori, vectord and VectorString in Perl, Java, Python and C#.
titles	is a vector containing the text to be output will the process is running. For example: "Creating XML output....". See Using STL vector classes vectori, vectord and VectorString in Perl, Java, Python and C#.
waitfor	is a vector of integers containing the dependency for each commands to be run. A value of 0 indicates that the command should be run immediately without waiting for another one to finish. See Using STL vector classes vectori, vectord and VectorString in Perl, Java, Python and C#.
logging	is a vector of integers containing the logging level for each commands to be run. A value of 0 indicates that no entries should be added to the `errorlog.txt` file. See Using STL vector classes vectori, vectord and VectorString in Perl, Java, Python and C#.
additionalFlags	is a vector of strings containing any flags apart from the waitfor or logging flag. See Using STL vector classes vectori, vectord and VectorString in Perl, Java, Python and C#.
sessionID	is the session identifier for the search. See ms_session::ms_session. This value is passed to the search engine using the `–sessionID` parameter.
taskID	is the task identifier for the search and is normally obtained by calling `ms-searchcontrol.exe` or `client.pl`. It is passed to `nph-mascot.exe` using the `–taskID` parameter.

Returns: the total number of commands to be run. This is not the same as the size of the vectors as the vectors may contain empty values.

◆ getFeatureTableLength()

int getFeatureTableLength ( ) const

Returns the value of FeatureTableLength.

If a nucleic acid sequence is longer than FeatureTableLength parameter value, the protein view report will automatically switch to feature table mode and output the matches as a GenBank feature table.

Parameter	FeatureTableLength
Permitted values	Any integer > 0
Default (if no parameter in mascot.dat)	30,000
Value in mascot.dat	[not defined]

Returns: the length at which to switch to a feature table.

◆ getFeatureTableMinScore()

double getFeatureTableMinScore ( ) const

Returns the value of FeatureTableMinScore.

By default, only matches with significant scores (p < 0.05) are output. A different score threshold can be specified using the parameter FeatureTableMinScore.

Parameter	FeatureTableMinScore
Permitted values	Floating point > 0
Default (if no parameter in mascot.dat)	13.0
Value in mascot.dat	[not defined]

Returns: the minimum score to be shown in a feature table.

◆ getFormVersion()

std::string getFormVersion ( ) const

Returns the value of FormVersion.

Mascot users may save search forms off-line, or submit searches using scripts or private forms. When the search engine is upgraded, there is the possibility that old scripts or forms may contain invalid or obsolete parameters. If a search is submitted to Mascot without a version number, or if the version number is lower than that specified by FormVersion, a warning will be included in the results file and in the master results report.

Parameter	FormVersion
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	1.01
Value in mascot.dat	1.01

Returns: the form version.

◆ getGetSeqJobIdFile()

std::string getGetSeqJobIdFile ( ) const

Returns the value of GetSeqJobIdFile.

GetSeqJobIdFile contains the next available job number for the ms-getseq.exe utility. These numbers wrap around at 999 and do not appear in the search logs. If this file is deleted, the next job number will be reset to 1 and a new jobId-file created automatically.

Parameter	GetSeqJobIdFile
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../data/getseq.job
Value in mascot.dat	../data/getseq.job

Returns: the path to the getseq.job file.

◆ getICATFilter()

std::string getICATFilter ( ) const

Returns the value of ICATFilter.

Parameter ICATFilter gives a residue that ICAT modifications apply to.

Parameter	ICATFilter
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	"C"
Value in mascot.dat	[not defined]

Returns: the filter string used as a comp command.

◆ getICATHeavy()

std::string getICATHeavy ( ) const

Returns the value of ICATHeavy.

The ICATHeavy parameter is the name of ICAT heavy modification. The full modification definition can be found in mod_file.

Parameter	ICATHeavy
Permitted values	Any text string
Default (if no parameter in mascot.dat)	ICAT_heavy
Value in mascot.dat	[not defined]

Returns: the name of the heavy ICAT modification.

◆ getICATLight()

std::string getICATLight ( ) const

Returns the value of ICATLight.

The ICATLight parameter is the name of ICAT light modification. The full modification definition can be found in mod_file.

Parameter	ICATLight
Permitted values	Any text string
Default (if no parameter in mascot.dat)	ICAT_light
Value in mascot.dat	[not defined]

Returns: the name of the light ICAT modification.

◆ getICATQuantitationMethod()

std::string getICATQuantitationMethod ( ) const

Returns the value of name of the ICATQuantitationMethod.

The ICATQuantitationMethod parameter is the name of the quantitation method to use if the old 'ICAT' checkbox is clicked for Mascot 2.2 and later. Just for backward compatibility.

Parameter	ICATQuantitationMethod
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	ICAT
Value in mascot.dat	ICAT ABI Cleavable [MD]

Returns: the name of quantitation method to use.

◆ getIgnoreDupeAccession()

std::string getIgnoreDupeAccession ( const unsigned int index ) const

Returns one of the list databases that shouldn't be checked for duplicate accessions.

When FASTA files are compressed, they are checked to ensure that there are no duplicate accession strings. For a large EST database with many millions of entries, this can take up a lot of memory. Adding a database to the list of values for the IgnoreDupeAccessions entry in mascot.dat prevents this database from being tested.

Parameter	IgnoreDupeAccessions
Permitted values	text strings delimted by tab, space and comma
Default (if no parameter in mascot.dat)	EST_others
Value in mascot.dat	EST_others

Parameters

index is a 0 based index into the list of databases.

Returns: the database name.

◆ getIgnoreIonsScoreBelow()

double getIgnoreIonsScoreBelow ( ) const

Returns the value of IgnoreIonsScoreBelow.

Any ions score lower than this value will be set to zero and ignored. The parameter is a floating point number.

Parameter	IgnoreIonsScoreBelow
Permitted values	Any floating point >= 0.0
Default (if no parameter in mascot.dat)	0.0
Value in mascot.dat	0.0

Returns: the minimum ions score to be considered when generating search reports.

◆ getIntensitySigFigs()

int getIntensitySigFigs ( ) const

Returns the value of IntensitySigFigs.

The precision of intensity values written to the result file is determined by IntensitySigFigs.

The default in the mascot.dat suppplied with version 2.2 and later is 4.

Parameter	IntensitySigFigs
Permitted values	1 to 20
Default (if no parameter in mascot.dat)	2
Value in mascot.dat	4

Returns: the number of significant figures to be used when saving values.

◆ getInterFileBasePath()

std::string getInterFileBasePath ( ) const

Returns the value of InterFileBasePath.

Mascot output files are written to a path given by:

   InterFileBasePath/InterFileRelPath/yyyymmdd/Fnnnnnn.dat

Here yyyymmdd is the current ISO date, and nnnnnn is a sequential job number. The path is split into a base path and a relative path as seen by the CGI scripts so that the search engine can pass a file path to (say) master_results.pl as:

   InterFileRelPath/yyyymmdd/Fnnnnnn.dat

Parameter	InterFileBasePath
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	C:/InetPub/Mascot/data for Windows and /usr/local/mascot/data for all other platforms
Value in mascot.dat	###ROOT###/data

Returns: the path to the Mascot output files.

◆ getInterFileRelPath()

std::string getInterFileRelPath ( ) const

Returns the value of InterFileRelPath.

One of the critical values that determine a location for storing intermediate files.

See getInterFileBasePath() for further information.

Parameter	InterFileRelPath
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../data
Value in mascot.dat	../data

Returns: the relative path to Mascot results files.

◆ getIonsDecimalPlaces()

int getIonsDecimalPlaces ( ) const

Returns the value of IonsDecimalPlaces.

Mascot calculates all masses to an accuracy of 1/65535 Daltons. By default, values are displayed to two decimal places, which is probably too few for most modern instruments. The default in the mascot.dat suppplied with version 2.2 and later is 4.

The displayed precision of fragment ion masses in reports can be altered by changing the values of IonsDecimalPlaces.

Parameter	IonsDecimalPlaces
Permitted values	1 to 20
Default (if no parameter in mascot.dat)	2
Value in mascot.dat	4

Returns: the number of decimal places to be displayed.

◆ getLastQueryAscFile()

std::string getLastQueryAscFile ( ) const

Returns the value of LastQueryAscFile.

See isSaveLastQueryAsc() for a detailed explanation.

Parameter	LastQueryAscFile
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../logs/lastquery.asc
Value in mascot.dat	../logs/lastquery.asc

Returns: the full pathname of the file.

◆ getLogoImageFile()

std::string getLogoImageFile ( ) const

Returns the value of LogoImageFile.

This is the URL of the Matrix Science logo, used at the top of a search progress report. You can customise this by substituting the URL of your own logo. For optimum appearance, the image should be 88 pixels wide and 31 pixels high.

Parameter	LogoImageFile
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../images/88x31_logo_white.gif
Value in mascot.dat	../images/88x31_logo_white.gif

Returns: the path to an image file.

◆ getMailTempFile()

std::string getMailTempFile ( ) const

Returns the value of MailTempFile.

See isEmailUsersEnabled() for information on this parameter.

Parameter	MailTempFile
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	C:/TEMP/MXXXXXX
Value in mascot.dat	/var/tmp/MXXXXXX

Returns: the location of temp files created for sending emails.

◆ getMailTransport()

int getMailTransport ( ) const

Returns the value of MailTransport.

MailTransport should be set to one of the following values:

0 for CMC. See getEmailService(), getEmailPassword()
1 for MAPI. See getEmailProfile(), getEmailPassword()
2 for sendmail (Unix only). See getSendmailPath()
3 for Blat. See getSendmailPath().

E-mail functionality has to be enabled by one of the following parameters: isEmailUsersEnabled(), isEmailErrorsEnabled().

Other parameters are common for all e-mail transports.

See also: getEmailFromUser(), getEmailFromTextName(), getErrMessageEmailTo(), getMailTempFile().

Parameter	MailTransport
Permitted values	0 to 3 inclusive
Default (if no parameter in mascot.dat)	2
Value in mascot.dat	0

Returns: a code defining the mail transport to be used.

◆ getMascNodeCtrlFile()

std::string getMascNodeCtrlFile ( ) const

Returns the value of MascotNodeControlFile.

Parameter	MascotNodeControlFile
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../data/mascotnode.control
Value in mascot.dat	../data/mascotnode.control

Returns: the path to the mascotnode.control file.

◆ getMascotCmdLine()

std::string getMascotCmdLine ( ) const

Returns the value of MascotCmdLine.

Filepath to the mascot executable. This is used by ms-monitor.exe when running the test search.

Parameter	MascotCmdLine
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../cgi/nph-mascot.exe
Value in mascot.dat	../cgi/nph-mascot.exe

Returns: the absolute or relative patch to nph-mascot.exe.

Examples: config_mascotdat.cpp.

◆ getMascotControlFile()

std::string getMascotControlFile ( ) const

Returns the value of MascotControlFile.

MascotControlFile contains critical internal parameters. This file must be memory mapped and locked to provide interprocess communication between different Mascot components.

Parameter	MascotControlFile
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../data/mascot.control
Value in mascot.dat	../data/mascot.control

Returns: the path to the mascot.control file.

◆ getMascotFileProcessingThreads()

int getMascotFileProcessingThreads ( ) const

Returns the value of MascotFileProcessingThreads.

MascotFileProcessingThreads specifies the number of threads used for pre-processing the input data at the beginning of the search, and for file processing at the beginning and end of each chunk. This setting does not affect the number of threads used for the search proper, which is determined by the number of licensed CPUs. If the value is -1 (automatic), the search will use the maximum number of threads authorised by the license, while respecting the configuration from Database Manager.

Parameter	MascotFileProcessingThreads
Permitted values	Any integer > 0, or -1 for automatic.
Default (if no parameter in mascot.dat)	4
Value in mascot.dat	[not defined]

Returns: the number of threads to use to process files

◆ getMascotJobIdFile()

std::string getMascotJobIdFile ( ) const

Returns the value of MascotJobIdFile.

MascotJobIdFile contains the next available job number. If this file is deleted, the next job number will be initialised to the value given by UniqueJobStartNumber, and a new jobId file created automatically.

Parameter	MascotJobIdFile
Permitted values	Any non empty text stringg
Default (if no parameter in mascot.dat)	../data/mascot.job
Value in mascot.dat	../data/mascot.job

Returns: the path to the mascot.job file.

◆ getMascotMessage()

std::string getMascotMessage ( ) const

Returns the value of MascotMessage.

Displays the specified message while a search is running.

Parameter	MascotMessage
Permitted values	Any text string
Default (if no parameter in mascot.dat)	[empty]
Value in mascot.dat	[not defined]

Returns: the message to be displayed for all searches.

◆ getMassDecimalPlaces()

int getMassDecimalPlaces ( ) const

Returns the value of MassDecimalPlaces.

Mascot calculates all masses to an accuracy of 1/65535 Daltons. By default, values are displayed to two decimal places, which is probably too few for most modern instruments. The default in the mascot.dat suppplied with version 2.2 and later is 4.

The displayed precision of peptide masses in reports can be altered by changing the values of MassDecimalPlaces.

Parameter	MassDecimalPlaces
Permitted values	1 to 20
Default (if no parameter in mascot.dat)	2
Value in mascot.dat	4

Returns: the number of decimal places to be displayed.

◆ getMaxConcurrentSearches()

int getMaxConcurrentSearches ( ) const

Returns the value of MaxConcurrentSearches.

This parameter limits the maximum number of concurrent searches so as to avoid overloading the Mascot server.

Parameter	MaxConcurrentSearches
Permitted values	Any integer > 0
Default (if no parameter in mascot.dat)	10
Value in mascot.dat	10

Returns: the maximum number of concurrent searches.

◆ getMaxDatabases()

int getMaxDatabases ( ) const

Returns the value of MaxDatabases.

Maximum number of databases that can be configured without re-starting monitor. Older versions of Mascot had a fixed limit of 64, which is a default value. Avoid specifying very large number as this will consume more physical memory and disk space unnecessarily.

Parameter	MaxDatabases
Permitted values	Any integer > 64
Default (if no parameter in mascot.dat)	64
Value in mascot.dat	256

Returns: an integer value specifying the limit.

◆ getMaxDescriptionLen()

int getMaxDescriptionLen ( ) const

Returns the value of MaxDescriptionLen.

Long FASTA title (description) lines will be truncated at this number of characters.

Parameter	MaxDescriptionLen
Permitted values	Any positive integer
Default (if no parameter in mascot.dat)	100
Value in mascot.dat	250

Returns: the maximum length.

◆ getMaxEtagMassDelta()

double getMaxEtagMassDelta ( ) const

Returns the value of MaxEtagMassDelta.

See also: getMinEtagMassDelta()

Parameter	MaxEtagMassDelta
Permitted values	Any floating point number
Default (if no parameter in mascot.dat)	1770.0
Value in mascot.dat	1770.0

Returns: The maximum delta to be considered for an error tolerant match.

◆ getMaxEtVarMods()

int getMaxEtVarMods ( ) const

Returns the value of MaxEtVarMods.

The maximum number of variable modifications allowed in an error-tolerant search.

Parameter	MaxEtVarMods
Permitted values	Any integer in the range 0 to 31
Default (if no parameter in mascot.dat)	2
Value in mascot.dat	[not defined]

Returns: the maximum number of variable modifications for the first pass search.

◆ getMaxIntactCrosslinkPeptides()

int getMaxIntactCrosslinkPeptides ( ) const

Returns the value of MaxIntactCrosslinkPeptides.

The maximum number of intact crosslink peptides to consider for a crosslink search. All regular peptides are still considered in the search and are not affected by this parameter.

Parameter	MaxIntactCrosslinkPeptides
Permitted values	Any integer > 0.
Default (if no parameter in mascot.dat)	1000000
Value in mascot.dat	1000000

Returns: the maximum number of crosslink peptides to consider for matching

◆ getMaxNumOfReportBuilderColumnArrangements()

int getMaxNumOfReportBuilderColumnArrangements ( ) const

Returns the maximum number of column arrangements allowed.

The maximum number of column arrangements defined in mascot.dat is limited. If security is enabled, each user can save additional column arrangements in user preferences.

Returns: Maximum number of column arrangements.

◆ getMaxNumPeptides()

int getMaxNumPeptides ( ) const

Returns the value of MaxNumPeptides.

The maximum number of peptides which can be expected from the enzymatic digest of a single entry.

If this value is not defined in mascot.dat than the value is calculated from getMaxSequenceLen() / 4

In general, this should not be defined in mascot.dat.

Parameter	MaxNumPeptides
Permitted values	Any positive integer
Default (if no parameter in mascot.dat)	[not defined]
Value in mascot.dat	[not defined]

Returns: the maximum number of peptides to be considered in a search.

◆ getMaxPepModArrangements()

int getMaxPepModArrangements ( ) const

Returns the value of MaxPepModArrangements.

Mascot iterates over the variable modifications of a peptide in the following way:

Choose a (sub)set of variable modifications, up to a limit of MaxPepNumVarMods.
Choose the number of instances for each modification that fits the precursor mass within precursor tolerance. Total number of instances is limited by MaxPepNumModifiedSites.
Assign the selected modification instances on modifiable sites. Each assignment is an arrangement of the modification instances. Repeat until the arrangements are exhausted or MaxPepModArrangements is reached.

The number of arrangements for some peptides can be very large.

A value of zero indicates maximum.

This parameter is new in Mascot 2.7. Previous versions had no specific upper limit, although in many cases iteration ended before about 16-20 arrangements had been sampled.

Parameter	MaxModArrangements
Permitted values	Any integer >= 0 and <= 1000000
Default (if no parameter in mascot.dat)	64
Value in mascot.dat	64

Returns: the maximum number of variable modification arrangements allowed for a single peptide.

◆ getMaxPepNumModifiedSites()

int getMaxPepNumModifiedSites ( ) const

Returns value of the MaxPepNumModifiedSites.

Mascot iterates over the variable modifications of a peptide in the following way:

Choose a (sub)set of variable modifications, up to a limit of MaxPepNumVarMods.
Choose the number of instances for each modification that fits the precursor mass within precursor tolerance. Total number of instances is limited by MaxPepNumModifiedSites.
Assign the selected modification instances on modifiable sites. Each assignment is an arrangement of the modification instances. Repeat until the arrangements are exhausted or MaxPepModArrangements is reached.

A value of zero indicates maximum.

This parameter is new in Mascot 2.7. Previous versions had no configurable upper limit.

Parameter	MaxPepNumModifiedSites
Permitted values	Any integer >= 0 and <= 10000
Default (if no parameter in mascot.dat)	5
Value in mascot.dat	5

Returns: the maximum number of modified sites in a peptide

◆ getMaxPepNumVarMods()

int getMaxPepNumVarMods ( ) const

Returns value of the MaxPepNumVarMods.

Mascot iterates over the variable modifications of a peptide in the following way:

Choose a (sub)set of variable modifications, up to a limit of MaxPepNumVarMods.
Choose the number of instances for each modification that fits the precursor mass within precursor tolerance. Total number of instances is limited by MaxPepNumModifiedSites.
Assign the selected modification instances on modifiable sites. Each assignment is an arrangement of the modification instances. Repeat until the arrangements are exhausted or MaxPepModArrangements is reached.

A value of zero indicates maximum.

Parameter	MaxPepNumVarMods
Permitted values	Any integer >= 0 and <= 10000
Default (if no parameter in mascot.dat)	3
Value in mascot.dat	3

Returns: the maximum number of modifications in one peptide.

◆ getMaxQueries()

int getMaxQueries ( ) const

Returns the value of MaxQueries.

The maximum number of mass values (PMF) or MS/MS spectra (MIS) allowed in a single search.

Parameter	MaxQueries
Permitted values	Integer >= 10
Default (if no parameter in mascot.dat)	10000
Value in mascot.dat	1000000

Returns: the maximum number of queries per search.

◆ getMaxSearchesPerUser()

int getMaxSearchesPerUser ( ) const

Returns the value of MaxSearchesPerUser.

Sets the maximum number of concurrent searches from a single IP-address.

A value of 0 means no limit.

Parameter	MaxSearchesPerUser
Permitted values	Any integer >= 0
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	[not defined]

Returns: the maximum number of concurrent searches per user.

◆ getMaxSequenceLen()

int getMaxSequenceLen ( ) const

Returns the value of MaxSequenceLen.

This parameters defines the maximum length of a database entry in characters, (bases for nucleic acids or residues for amino acids databases respectively).

Parameter	MaxSequenceLen
Permitted values	Any integer >= 100
Default (if no parameter in mascot.dat)	80,000
Value in mascot.dat	80,000

Returns: the maximum sequence length.

◆ getMaxVarMods()

int getMaxVarMods ( ) const

Returns the value of MaxVarMods.

The maximum number of variable modifications allowed in a standard search.

Parameter	MaxVarMods
Permitted values	Any integer in the range 0 to 32
Default (if no parameter in mascot.dat)	9
Value in mascot.dat	[not defined]

Returns: the maximum number of variable modifications.

◆ getMinEtagMassDelta()

double getMinEtagMassDelta ( ) const

Returns the value of MinEtagMassDelta.

See also: getMaxEtagMassDelta()

Parameter	MinEtagMassDelta
Permitted values	Any floating point number
Default (if no parameter in mascot.dat)	-130.0
Value in mascot.dat	-130.0

Returns: The minimum delta to be considered for an error tolerant match.

◆ getMinPepLenInPepSummary()

int getMinPepLenInPepSummary ( ) const

Returns the value of MinPepLenInPepSummary.

In a Peptide Summary report, two proteins are reported as distinct matches if the peptide matches to one protein are not identical to or a sub-set of the peptide matches to the other protein. Since matches to very short peptides are usually random, peptides shorter than MinPepLenInPepSummary are not considered in this comparison.

Parameter	MinPepLenInPepSummary
Permitted values	Any integer greater than zero
Default (if no parameter in mascot.dat)	7
Value in mascot.dat	7 (Was 5 in Mascot 2.3.02 and earlier)

Returns: the minimum peptide length used to differentiate different proteins.

◆ getMinPepLenInSearch()

int getMinPepLenInSearch ( ) const

Returns value of the MinPepLenInSearch.

This parameter specifies the minimal length of a peptide to be accepted as a match to any query in all searches. Use this parameter if you see too many short peptides in a result file that constitute mostly meaningless matches.

Parameter	MinPepLenInSearch
Permitted values	Any non-negative integer
Default (if no parameter in mascot.dat)	3
Value in mascot.dat	5

Returns: the minimum peptide length.

◆ getMonitorEmailCheckFreq()

int getMonitorEmailCheckFreq ( ) const

Returns the value of MonitorEmailCheckFreq.

See isEmailUsersEnabled() for information on this parameter..

Parameter	MonitorEmailCheckFreq
Permitted values	Any positive integer
Default (if no parameter in mascot.dat)	300
Value in mascot.dat	300

Returns: the frequency to check for sending emails in seconds.

◆ getMonitorLogFile()

std::string getMonitorLogFile ( ) const

Returns the value of MonitorLogFile.

This path defines where monitor log file should be placed. The ms-monitor.exe service/daemon writes to this file.

Parameter	MonitorLogFile
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../logs/monitor.log
Value in mascot.dat	[not defined]

Returns: the relative or absolute path to the monitor log.

◆ getMonitorPidFile()

std::string getMonitorPidFile ( ) const

Returns the value of MonitorPidFile.

The name for the file which holds the process ID number for ms-monitor.exe. Unix only.

Parameter	MonitorPidFile
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../bin/monitor.pid
Value in mascot.dat	[not defined]

Returns: monitor pid file name

◆ getMonitorTestTimeout()

int getMonitorTestTimeout ( ) const

Returns the value of MonitorTestTimeout.

A time-out is applied to the test searches used to validate a new database. If the test search on a new database does not produce a valid result within the number of seconds specified by MonitorTestTimeout, the problem is assumed to be with the new database, and the exchange process is halted.

Parameter	MonitorTestTimeout
Permitted values	Any positive integer
Default (if no parameter in mascot.dat)	1200
Value in mascot.dat	1200

Returns: the timeout period in seconds.

◆ getMudpit()

int getMudpit ( ) const

Returns the value of Mudpit.

Deprecated:: For Mascot 2.2 and later, use getMudpitSwitch() and getSelectSwitch().

Gets the number of queries at which the protein scoring switches to MudPIT mode.

See also: ms_mascotresults::MSRES_MUDPIT_PROTEIN_SCORE

Parameter	Mudpit
Permitted values	Any integer>0
Default (if no parameter in mascot.dat)	1000
Value in mascot.dat	[not defined]

Returns: number of queries at which scoring switches to MudPIT mode

◆ getMudpitSwitch()

double getMudpitSwitch ( ) const

Returns the value of MudpitSwitch.

A ratio of the number of queries divided by the number of entries in the database is used to determine when to switch between the two methods of protein scoring. The default value for SelectSwitch is 0.001. If q/e < 0.001, then standard protein scoring is used. If it is higher than 0.001, then MudPIT protein scoring is used.

If the user never wants to see MudPIT scoring, then this should be set to a large value, e.g. 1000

In the standard reports, the _server_mudpit_switch flag can be passed as a url parameter to override this setting.

This parameter, and getSelectSwitch() replaced the single value returned by getMudpit() in Mascot 2.1 and earlier.

See also ms_protein::getScore() for a description of standard and MudPIT protein scoring.

Parameter	MudpitSwitch
Permitted values	Any floating point value > 0
Default (if no parameter in mascot.dat)	0.001
Value in mascot.dat	0.001

Returns: The q/e value used to determine which protein scoring method to use.

◆ getNoResultsScript()

std::string getNoResultsScript ( ) const

Returns the value of NoResultsScript.

See getResultsPerlScript() for more information.

Parameter	NoResultsScript
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../cgi/master_results.pl
Value in mascot.dat	../cgi/master_results.pl

Returns: the url for the no results script.

◆ getNTIUserGroup()

std::string getNTIUserGroup ( ) const

Returns the value of NTIUserGroup.

See getNTMonitorGroup() for information on this parameter.

The default in mascot.dat since mascot 2.3.0 is "Users". Earlier versions had the default as "Guests"

Parameter	NTIUserGroup
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	Guests
Value in mascot.dat	Users

Returns: NTI user group

◆ getNTMonitorGroup()

std::string getNTMonitorGroup ( ) const

Returns the value of NTMonitorGroup.

Under Windows NT, the Mascot service is generally run using the Local System account. It has to create, write and read the memory mapped files. The CGI scripts (such as nph-mascot.exe) are run by the Web server, and will be run using a different user name with different permissions from the service. These programs also need to be able to read and write to these files.

For example, with the Microsoft Web server (IIS), a new user with the name IUSR_<name_of_pc> is created when the server is installed, and the scripts are run using this user name. The installation program sets these values appropriately. Other Web servers may use different user names, with different permissions.

NTMonitorGroup is used to define one of the groups that the administrator belongs to. In most cases, this can be left at the default of Administrators.

NTIUserGroup is the name of one of the groups that the user name used to run the CGI scripts belongs to.

Parameter	NTMonitorGroup
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	Administrators
Value in mascot.dat	Administrators

Returns: the name of the Administrators group.

◆ getNumberOfIgnoreDupeAccessions()

unsigned int getNumberOfIgnoreDupeAccessions ( ) const

Returns the number of databases that shouldn't be checked for duplicate accessions.

When fasta files are compressed, they are checked to ensure that there are no duplicate accession strings. For a large EST database with many millions of entries, this can take up a lot of memory. Adding a database to the list of values for the IgnoreDupeAccessions entry in mascot.dat prevents this database from being tested.

Parameter	IgnoreDupeAccessions
Permitted values	text strings delimted by tab, space and comma
Default (if no parameter in mascot.dat)	EST_others
Value in mascot.dat	EST_others

Returns: the number of items in the IgnoreDupeAccessions parameter.

◆ getNumberOfProperties()

int getNumberOfProperties ( ) const

inherited

Returns a total number of property/comment entries.

Returns: Number of property/comment entries

◆ getNumberOfReportNumberChoices()

int getNumberOfReportNumberChoices ( ) const

Returns the values of ReportNumberChoices.

If present, ReportNumberChoices list will define the choices provided in the search form Report top drop down list box. If not, this member will return zero.

getReportNumberChoice() member is used to retrieve individual elements of the list.

The default value in mascot.dat is AUTO,5,10,20,30,50,100,200, so this function would return 8 for that case.

Parameter	ReportNumberChoices
Permitted values	Any integer > 0, or -1.
Default (if no parameter in mascot.dat)	5,10,20,30,40,50
Value in mascot.dat	AUTO,5,10,20,30,50,100,200

Returns: the number of integers in the list.

◆ getNumberOfTargetFDRPercentages()

int getNumberOfTargetFDRPercentages ( ) const

Returns the values of TargetFDRPercentages.

If present, the TargetFDRPercentages list will define the choices available in a Protein Family Summary report of a decoy search. Each item in the list is a percentage (e.g. 2.5 means 2.5% or 0.025). If the option is not present, this function will return 0.

An element in the list can be marked as the default value. Use getTargetFDRPercentage() to retrieve individual elements of the list, and isDefaultTargetFDRPercentage() to find out if an element is marked as the default element.

The default value in mascot.dat is 0.1, 0.2, 0.5, 1+, 2, 5, so this function would return 6 in the default case. The postfix "+" means that, in this case, 1 is the default value.

Parameter	TargetFDRPercentages
Permitted values	Any number >0
Default (if no parameter in mascot.dat)	0.1, 0.2, 0.5, 1+, 2, 5
Value in mascot.dat	0.1, 0.2, 0.5, 1+, 2, 5

Returns: the number of integers in the list.

◆ getPepSearchTool()

std::string getPepSearchTool ( ) const

Returns the value of LibrarySearch.

See also: setPepSearchTool() and getPepSearchToolCommandLine()

Introduced in version 2.6.0.

In version 2.6.1, "m G" was replaced with "m a P" where:

MSPepSearch parameter	Meaning
m	precursor ion m/z within precursor ion m/z uncertainty
G	generic (no peak annotations or peptide peak weighting used)
a	alternative peak matching in computing match factors
P	peptide (use peak annotations and peak weighting)

And, in 2.6.1, we made sure that every library spectrum has properly annotated peaks, and not just a "?"

Also, in 2.6.1, "/HITS 100" was changed to "/HITS 10"

Parameter	LibrarySearch
Permitted values	Any non empty text string.
Default (if no parameter in mascot.dat)	../bin/NIST/mspepsearch/MSPepSearch.exe m a P $peptidetoleranceunit $peptidetolerance $iontoleranceunit $iontolerance /LIB $libname /INP $inputfile /OUTTAB $outputfile /HITS 10 /MinMF 0 /NumCompared /OutPrecursorMz /OutDeltaPrecursorMz /OutSpecNum
Value in mascot.dat	../bin/NIST/mspepsearch/MSPepSearch.exe m a P $peptidetoleranceunit $peptidetolerance $iontoleranceunit $iontolerance /LIB $libname /INP $inputfile /OUTTAB $outputfile /HITS 10 /MinMF 0 /NumCompared /OutPrecursorMz /OutDeltaPrecursorMz /OutSpecNum

Returns: the value of LibrarySearch.

◆ getPepSearchToolCommandLine()

std::string getPepSearchToolCommandLine	(	const std::string &	peptideToleranceUnit,
		const double &	peptideTolerance,
		const std::string &	ionToleranceUnit,
		const double &	ionTolerance,
		const std::string &	libraryDirectoryPath,
		const std::string &	inputFileRelativePath,
		const std::string &	outputFileRelativePath
	)		const

Get command line to search a library, eg MSPepSearch.exe.

This function is called by nph-mascot.exe to get the command line required to invoke the spectral library search tool. It calls getPepSearchTool which contains a number of 'tags' which need to be replaced with search specific parameters. In theory, any search tool that accepts an MGF file and outputs a CSV file could be used instead of MSPepSearch. This function replaces the following tags with the corresponding variable passed to this function:

$peptidetoleranceunit is replaced with peptideToleranceUnit
$peptidetolerance is replaced with peptideTolerance
$iontoleranceunit is replaced with ionToleranceUnit
$iontolerance is replaced with ionTolerance
$libname is replaced with libraryDirectoryPath
$inputfile is replaced with inputFileRelativePath
$outputfile is replaced with outputFileRelativePath

See also: getPepSearchTool() and setPepSearchTool()

Parameters

peptideToleranceUnit	will be Z or ZPPM, where 'Z' specifies Daltons.
peptideTolerance	tolerance in the unit above.
ionToleranceUnit	will be M or MPPM, where 'M' specifies Daltons.
ionTolerance	tolerance in the unit above.
libraryDirectoryPath	full path to the directory containing the spectral library 'database'.
inputFileRelativePath	path to the mgf file created by nph-mascot.exe.
outputFileRelativePath	is the path to the results file produced by the library search tool that will be read by nph-mascot.exe.

Returns: complete pep search tool command line for the specified spectral library.

◆ getPercolatorExeFlags()

std::string getPercolatorExeFlags	(	bool	anyRetentionTimes,
		const std::vector< std::string >	percolatorFiles,
		const PERC_EXE_RT	rt = `PERC_EXE_RT_USE_DEFAULT`
	)		const

Returns the value of PercolatorExeFlags.

See Using Percolator scores for further information.

Parameter	PercolatorExeFlags
Permitted values	any string
Default (if no parameter in mascot.dat)	-i 10 -D 14 -v 0
Value in mascot.dat	-i 10 -D 14 -v 0

This function will create a string of the form

  -i 10 -D 14 -v 0 -j [percolator_input_file] -B [percolator_decoy_file] -r [percolator_target_file]

If anyRetentionTimes is true and either forceUseRT or the return from isPercolatorUseRT() is true, then the -D [num] option will be retained, otherwise the -D [num] option will be removed from the PercolatorExeFlags parameters.

Parameters

anyRetentionTimes	should be set to true if there are any retention times in the results file. It is normally safe to just check the first query and if ms_inputquery::getRetentionTimes() returns an empty string, then set this parameter to false.
percolatorFiles	is the parameter returned by ms_mascotresfilebase::getPercolatorFileNames().
rt	one of the ms_mascotoptions::PERC_EXE_RT enumerations may be specified to override the value in mascot.dat that is returned by calling isPercolatorUseRT().

Returns: the flags and options to be used when calling percolator.exe.

◆ getPercolatorFeatures()

std::string getPercolatorFeatures ( ) const

Returns the value of PercolatorFeatures.

Returns a list of features that should be considered when running percolator.

To see the list of available features, run ms-createpip.exe –help. See Using Percolator scores for further information.

Parameter	PercolatorFeatures
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	mScore,lgDScore, mrCalc, charge, dM, dMppm, absDM, absDMppm, isoDM, isoDMppm, mc, varmods, totInt, intMatchedTot,relIntMatchedTot
Value in mascot.dat	mScore,lgDScore, mrCalc, charge, dM, dMppm, absDM, absDMppm, isoDM, isoDMppm, mc, varmods, totInt, intMatchedTot,relIntMatchedTot

Returns: the comma separated list of features.

◆ getPercolatorMinQueries()

int getPercolatorMinQueries ( ) const

Returns the value of PercolatorMinQueries.

Percolator requires a 'reasonable' number of ms-ms spectra to perform well, and this parameter specifies that minimum. If the number of queries is below this value, percolator results will not be made available.

See Using Percolator scores for further information.

Parameter	PercolatorMinQueries
Permitted values	Any integer > 0
Default (if no parameter in mascot.dat)	750
Value in mascot.dat	750 (was 100 for Mascot Server versions 2.3 to 2.5.0)

Returns: the minimum number of queries required to display percolator results.

◆ getPercolatorMinSequences()

int getPercolatorMinSequences ( ) const

Returns the value of PercolatorMinSequences.

Percolator requires a 'reasonable' number of sequences to perform well, and this parameter specifies that minimum. If the number of sequences searched is below this value, percolator results will not be made available.

See Using Percolator scores for further information.

Parameter	PercolatorMinSequences
Permitted values	Any integer > 0
Default (if no parameter in mascot.dat)	100
Value in mascot.dat	100

Returns: the minimum number of sequences.

◆ getPercolatorRtFlags()

std::string getPercolatorRtFlags	(	const bool	anyRetentionTimes,
		const bool	useRT
	)		const

Returns PercolatorExeFlags with the -D flag optionally removed if there are no retention times.

Note: This method is only needed when using getExecAfterSearch() or ms_mascotresfilebase::staticGetPercolatorFileNames(). In all other cases, please use getPercolatorExeFlags().

Returns: the raw value of the PercolatorExeFlags_XXX parameter in the mascot.dat file. If anyRetentionTimes is true and useRT is true, then the -D [num] option will be retained, otherwise the -D [num] option will be removed from the PercolatorExeFlags parameters.

◆ getPercolatorTargetRankRelativeThreshold()

double getPercolatorTargetRankRelativeThreshold ( ) const

Returns the value of PercolatorTargetRankRelativeThreshold.

For a description of this function, see getPercolatorTargetRankScoreThreshold().

See Using Percolator scores for further information.

Permitted values	A real number in [0, 1]
Default (if no parameter in mascot.dat)	0.2
Value in mascot.dat	0.2

Returns: Minimum relative score difference with rank 1 match.

◆ getPercolatorTargetRankScoreThreshold()

int getPercolatorTargetRankScoreThreshold ( ) const

Returns the value of PercolatorTargetRankScoreThreshold.

Mascot 2.8 and later exports rank 1 matches plus further ranks from target if score > PercolatorTargetRankScoreThreshold and the relative difference from rank 1 score < PercolatorTargetRankRelativeThreshold. This option is not implemented in Mascot 2.7 and earlier.

See Using Percolator scores for further information.

Parameter	PercolatorTargetRankScoreThreshold
Permitted values	Positive integers
Default (if no parameter in mascot.dat)	20
Value in mascot.dat	20

Returns: Minimum score for matches whose rank is greater than 1.

◆ getPreceedingComments()

std::string getPreceedingComments ( ) const

inherited

Returns any comments preceeding the section.

Sections in the mascot.dat file may have comments preceeding them. In most cases, these comments need to stay 'attached' to the section.

Multiple line comments are supported by having a single string with newline characters

See also: setPreceedingComments()

Returns: any comments preceeding the section

◆ getPrecursorCutOutLowerLimit()

double getPrecursorCutOutLowerLimit ( ) const

Gets the first PrecursorCutOut.

This parameter defines boundaries for cut-out window for precursor m/z value. It consists of two numbers - the lower limit and the upper limit for precursor m/z window. If both numbers are the same (i.e. if the window is of zero-length) Mascot uses a "smart" mechanism for filtering out peptide m/z from MS-spectra.

Parameter	PrecursorCutOut
Permitted values	Any 2 comma separated floating point numbers
Default (if no parameter in mascot.dat)	"-1, -1"
Value in mascot.dat	"-1, -1"

Returns: the first of the two values.

◆ getPrecursorCutOutUpperLimit()

double getPrecursorCutOutUpperLimit ( ) const

Gets the second PrecursorCutOut.

This parameter defines boundaries for cut-out window for precursor m/z value. It consists of two numbers - the lower limit and the upper limit for precursor m/z window. If both numbers are the same (i.e. if the window is of zero-length) Mascot uses a "smart" mechanism for filtering out peptide m/z from MS-spectra.

Parameter	PrecursorCutOut
Permitted values	Any 2 comma separated floating point numbers
Default (if no parameter in mascot.dat)	"-1, -1"
Value in mascot.dat	"-1, -1"

Returns: the second of the two values.

◆ getPropertyName()

std::string getPropertyName ( const int index ) const

inherited

Returns a property name for a given index.

Parameters

index property number from 0 to (getNumberOfProperties()-1).

Returns: Rroperty name of an empty string for comments.

◆ getPropValStringByName()

std::string getPropValStringByName ( const char * name ) const

inherited

Retrieves property value by name.

Don't use this method for comments as they all have empty name. Also note that there might be several entries corresponding to the same name . – only the first value will be returned. If in doubt use findProperty() and getPropValStringByNumber() instead.

Parameters

name	Name for which to get a property value

Returns: corresponding property value

◆ getPropValStringByNumber()

std::string getPropValStringByNumber ( const int index ) const

inherited

Retrieves property raw text values by number.

Parameters

index Index for which to get a property value

Returns: corresponding property value

◆ getProteinFamilySwitch()

int getProteinFamilySwitch ( ) const

Returns the value of ProteinFamilySwitch.

For Mascot 2.3 and later, if a search has greater than or equal the number of MS-MS spectra defined by getProteinFamilySwitch(), then the script defined by getResultsPerlScript_2() is run.

Parameter	ProteinFamilySwitch
Permitted values	Any integer > 0
Default (if no parameter in mascot.dat)	300
Value in mascot.dat	300

Returns: the number of MS-MS spectra required for displaying the Protein Family Summary report.

◆ getProteinsInResultsFile()

int getProteinsInResultsFile ( ) const

Returns the value of ProteinsInResultsFile.

Determines the number of protein title lines saved to each results file. Possible values are:

1 - as in Mascot 1.7 and earlier, only proteins that appear in the Summary section will appear in the Proteins section.
2 - include proteins with at least one top ranking peptide match to a peptide of length greater than or equal to MinPepLengthInPepSummary (see getMinPepLenInPepSummary()).
3 - include all proteins.

Parameter	ProteinsInResultsFile
Permitted values	1, 2 or 3
Default (if no parameter in mascot.dat)	2
Value in mascot.dat	[not defined]

Returns: a value defining which protein descriptions should be stored in the results file.

◆ getProxyPassword()

std::string getProxyPassword ( ) const

Returns the value of proxy_password.

See getProxyServer().

Parameter	proxy_password
Permitted values	Any text string
Default (if no parameter in mascot.dat)	[empty]
Value in mascot.dat	[commented out]# proxy_password mypassword

Returns: the password for the proxy server user.

◆ getProxyServer()

std::string getProxyServer ( ) const

Returns the value of proxy_server.

This parameter allows a proxy server to be defined.

Other parameters defining proxy server are proxy_username (getProxyUsername()) and proxy_password (getProxyPassword()).

Parameter	proxy_server
Permitted values	Any text string
Default (if no parameter in mascot.dat)	[empty]
Value in mascot.dat	[commented out]# proxy_server myserver

Returns: the proxy server name.

◆ getProxyType()

std::string getProxyType ( ) const

Returns the value of ProxyType.

Proxy server settings can be specified in a number of ways depending on the operating system and local network policies. See ms_connection_settings::PROXY_TYPE for a description. The proxy type value in mascot.dat is case-insensitive; for example, all of none, None and NONE mean ms_connection_settings::PROXY_TYPE_NO_PROXY.

This parameter was introduced in Mascot Server 2.5. The default in Mascot Server 2.4 and earlier is equivalent to Specify. If proxy_server is not given in mascot.dat, the default in 2.4 is None.

Parameter	ProxyType
Permitted values	None, Registry, Specify, WPAD, Environment, Auto
Default (if no parameter in mascot.dat)	Auto
Value in mascot.dat	Auto

Returns: A string matching one of the ms_connection_settings::PROXY_TYPE values.

◆ getProxyUsername()

std::string getProxyUsername ( ) const

Returns the value of proxy_username.

See getProxyServer().

Parameter	proxy_username
Permitted values	Any text string
Default (if no parameter in mascot.dat)	[empty]
Value in mascot.dat	[commented out]# proxy_username myusername

Returns: the username for proxy server.

◆ getReportBuilderColumnArrangement()

std::string getReportBuilderColumnArrangement ( const int index ) const

Returns ReportBuilderColumnArrangement by number.

Set the column arrangement at the given index. Column arrangements are used by Report Builder (introduced in Mascot 2.4) to provide a default list of columns to show. These can be selected from a dropdown list in the report.

Each column arrangement is of the form

  Name:[columns]

where Name is the column arrangement name (e.g. Standard) and [columns] is a comma-separated list of column names, as used by Report Builder. The following is the standard list of column names, available in every report:

  family
  member
  db
  acc
  score
  mass
  matches
  matches-sig
  sequences
  sequences-sig
  empai
  frame
  desc

(frame will not be shown in the report if the search is against an amino acid database.) Quantitation methods add additional column names, but these are generated from the quantitation ratio names. The easiest way to create a column arrangement string is to arrange the columns in Report Builder, then "export" the column arrangement as a string and copy it into mascot.dat.

See also: setReportBuilderColumnArrangement().

Parameter	ReportBuilderColumnArrangement_XXX
Permitted values	A name followed by colon followed by column arrangement string (see above)
Default (if no parameter in mascot.dat)	`ReportBuilderColumnArrangement_1 Standard:family,member,db,acc,score,mass,matches,matches-sig,sequences,sequences-sig,empai,frame,desc`
Value in mascot.dat	`ReportBuilderColumnArrangement_1 Standard:family,member,db,acc,score,mass,matches,matches-sig,sequences,sequences-sig,empai,frame,desc`

Parameters

index A value between 1 and getMaxNumOfReportBuilderColumnArrangements(), inclusive.

Returns: The column arrangement definition at that index, or the empty string if the arrangement does not exist.

◆ getReportNumberChoice()

int getReportNumberChoice ( const int index ) const

Returns an element of the ReportNumberChoices list by its number.

The function returns -1 in case of AUTO string. For more information on the ReportNumberChoices parameter see getNumberOfReportNumberChoices().

The default value in mascot.dat is AUTO,5,10,20,30,50,100,200, so this function would return 5 for an index value of 1

Parameter	ReportNumberChoices
Permitted values	Any integer > 0, or -1.
Default (if no parameter in mascot.dat)	5,10,20,30,40,50
Value in mascot.dat	AUTO,5,10,20,30,50,100,200

Parameters

index element number from 0 to (getNumberOfReportNumberChoices()-1).

Returns: an element of the list that corresponds to the given index. Returns 0 if the provided index is not valid.

◆ getResfileCache()

std::string getResfileCache ( ) const

Returns the value of ResfileCache.

See Caching Mascot Results.

This parameter is rather counter-intuitive! A script or application running on the Mascot server has a choice of whether or not to specify ms_mascotresfilebase::RESFILE_USE_CACHE. Each Mascot script calls this function which returns a comma separated list of scripts and executable programs. The script then searches for its own name, and if it finds it, then it will specify the ms_mascotresfilebase::RESFILE_USE_CACHE flag. Mascot parser does not use this parameter internally – it is up to each script to use it.

A user can disable/enable the use of the cache for one or more scripts by adding them to the list in mascot.dat.

See also: getResultsCache()

Parameter	ResfileCache
Permitted values	Comma, space or tab delimeted string. May be empty
Default (if no parameter in mascot.dat)	`master_results.pl,master_results_2.pl,peptide_view.pl,protein_view.pl,export_dat.pl,export_dat_2.pl,ms-createpip.exe,MSAnatomiser.class,mi_getpeaklist.pl,msms_gif.pl,nph-mascot.exe,ms-searchcontrol.exe,client.pl`
Value in mascot.dat	`master_results.pl,master_results_2.pl,peptide_view.pl,protein_view.pl,export_dat.pl,export_dat_2.pl,ms-createpip.exe,MSAnatomiser.class,mi_getpeaklist.pl,msms_gif.pl,nph-mascot.exe,ms-searchcontrol.exe,client.pl`

Returns: a comma separated list of scripts that should specify ms_mascotresfilebase::RESFILE_USE_CACHE when creating a ms_mascotresfilebase object.

◆ getResultsCache()

std::string getResultsCache ( ) const

Returns the value of ResultsCache.

See Caching Mascot Results.

This parameter is rather counter intuitive! A script or application running on the Mascot server has a choice of whether or not to specify ms_peptidesummary::MSPEPSUM_USE_CACHE. Each Mascot script calls this function which returns a comma separated list of scripts and executable programs. The script then searches for its own name, and if it finds it, then it will specify the ms_peptidesummary::MSPEPSUM_USE_CACHE flag. Mascot parser does not use this parameter internally – it is up to each script to use it.

A user can disable/enable the use of the cache for one or more scripts by adding them to the list in mascot.dat.

See also: getResfileCache()

Parameter	ResultsCache
Permitted values	Comma, space or tab delimeted string. May be empty
Default (if no parameter in mascot.dat)	`master_results.pl,master_results_2.pl,peptide_view.pl,protein_view.pl,export_dat.pl,export_dat_2.pl,MSAnatomiser.class,mi_getpeaklist.pl,nph-mascot.exe,ms-searchcontrol.exe`
Value in mascot.dat	`master_results.pl,master_results_2.pl,peptide_view.pl,protein_view.pl,export_dat.pl,export_dat_2.pl,MSAnatomiser.class,mi_getpeaklist.pl,nph-mascot.exe,ms-searchcontrol.exe`

Returns: a comma separated list of scripts that should specify ms_peptidesummary::MSPEPSUM_USE_CACHE when creating a ms_peptidesummary object.

◆ getResultsFileFormatVersion()

std::string getResultsFileFormatVersion ( ) const

Returns the value of ResultsFileFormatVersion.

Currently only one value choice is supported: "2.1". Specifiying this value will force Mascot to produce result file compatible with ver. 2.1. An empty or any other value means current version result file format.

Be careful, however, when submitting to Mascot a search which explicitly requires new functionality. In this case Mascot will decide whether to output results in the requested or the current format.

Parameter	ResultsFileFormatVersion
Permitted values	Any text string
Default (if no parameter in mascot.dat)	[empty]
Value in mascot.dat	[commented out] #ResultsFileFormatVersion 2.1

Returns: the version string.

◆ getResultsFullURL()

std::string getResultsFullURL ( ) const

Returns the value of ResultsFullURL.

The ResultsFullURL entry is used when results are emailed to a user. Since the email will probably be received on another system, the URL used needs to have the full name including the Web server.

Parameter	ResultsFullURL
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	###URL###/cgi/master_results.pl
Value in mascot.dat	http://www.matrixscience.com/cgi/master_results.pl

Returns: the url.

◆ getResultsFullURL_2()

std::string getResultsFullURL_2 ( ) const

Returns the value of ResultsFullURL_2.

For Mascot 2.3 and later, if a search has greater than or equal the number of MS-MS spectra defined by getProteinFamilySwitch(), then this URL is used to send results by email.

Parameter	ResultsFullURL_2
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	http://www.matrixscience.com/cgi/master_results_2.pl
Value in mascot.dat	http://www.matrixscience.com/cgi/master_results_2.pl

Returns: the URL to use.

◆ getResultsPerlScript()

std::string getResultsPerlScript ( ) const

Returns the value of ResultsPerlScript.

There are URLs (not disk paths) of the scripts to be called by the search engine at the completion of a search. A successful search calls ResultsPerlScript, while a search that didn't find any hits calls NoResultsScript. In the scripts supplied with Mascot, for Mascot 2.2 and earlier, both eventualities are handled by a single script: master_results.pl.

Parameter	ResultsPerlScript
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../cgi/master_results.pl
Value in mascot.dat	../cgi/master_results.pl

Returns: the url for the results script.

◆ getResultsPerlScript_2()

std::string getResultsPerlScript_2 ( ) const

Returns the value of ResultsPerlScript_2.

For Mascot 2.3 and later, if a search has greater than or equal the number of MS-MS spectra defined by getProteinFamilySwitch(), this script is run.

Parameter	ResultsPerlScript_2
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../cgi/master_results_2.pl
Value in mascot.dat	../cgi/master_results_2.pl

Returns: the script to run.

◆ getReviewColDisplay()

bool getReviewColDisplay ( const MS_REVIEW_COL index ) const

Returns ReviewColDisplay by number.

End users can specify the display states in mascot.dat to suit their requirements, for example if they want to hide by default some columns.

See also: setReviewColDisplay().

Parameter	ReviewColDisplay
Permitted values	1 (true) for display, 0 (false) for hide
Default (if no parameter in mascot.dat)	1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1
Value in mascot.dat	1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1

Parameters

index A value from the MS_REVIEW_COL enumeration.

Returns: column display state for the given number

◆ getReviewColWidth()

int getReviewColWidth ( const MS_REVIEW_COL index ) const

Returns ReviewColWidths by number.

End users can specify the widths in mascot.dat to suit their requirements, for example if they use long titles.

See also: setReviewColWidth().

Parameter	ReviewColWidths
Permitted values	Positive integer >0
Default (if no parameter in mascot.dat)	7, 8, 8, 27, 30, 100, 32, 25, 6, 13, 4, 4, 6, 16, 7, 32
Value in mascot.dat	7, 8, 8, 27, 30, 100, 32, 25, 6, 13, 4, 4, 6, 16, 7, 32

Parameters

index A value from the MS_REVIEW_COL enumeration.

Returns: column width for the given number.

◆ getSearchLogFile()

std::string getSearchLogFile ( ) const

Returns the value of SearchLogFile.

This path defines where search log file should be stored.

Parameter	SearchLogFile
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../logs/searches.log
Value in mascot.dat	[not defined]

Returns: the relative or absolute path to the searches log.

◆ getSearchSubmitAcceptedFileTypes()

std::string getSearchSubmitAcceptedFileTypes ( ) const

Returns a list of accepted input file types in the Mascot search form.

Returns accepted input the file formats of searches submitted through the search form.

The setting SearchSubmitAcceptedFileTypes is a list of input file formats selectable in the browser-based search form (search_form.pl). The default is MGF (Mascot generic) and mzML. Mascot supports other file formats, most of which are no longer in use.

The full list of file types is:

Mascot generic
Sequest (.DTA)
Finnigan (.ASC)
Micromass (.PKL)
PerSeptive (.PKS)
PerSeptive (.PKM)
Sciex API III
Bruker reportfile
Bruker (.XML)
mzData (.XML)
mzML (.mzML)

Parameter	SearchSubmitOutputFormat
Permitted values	A comma-separated list of the supported file formats
Default (if no parameter in mascot.dat)	Mascot generic,mzML (.mzML)
Value in mascot.dat	Mascot generic,mzML (.mzML)

Returns: currently defined value.

◆ getSearchSubmitDefaultPeptideCharge()

std::string getSearchSubmitDefaultPeptideCharge ( ) const

Returns the value in the CHARGE parameter when the peptide charge control is hidden in the search form.

Parameter	SearchSubmitDefaultPeptideCharge
Permitted values	One of the following: `8-` `7-` `6-` `5-` `4-` `3-` `2-` `2-, 3- and 4-` `2- and 3-` `2-` `1-, 2- and 3-` `1-` `Mr` `1+` `1+, 2+ and 3+` `2+` `2+ and 3+` `2+, 3+ and 4+` `3+` `4+` `5+` `6+` `7+` `8+`
Default (if no parameter in mascot.dat)	2+, 3+ and 4+
Value in mascot.dat	2+, 3+ and 4+

Returns: currently defined value.

◆ getSearchSubmitMode()

std::string getSearchSubmitMode ( ) const

Returns the Mascot search submission mode.

In Mascot 2.5 and later, searches submitted through the search form report progress feedback asynchronously. Once the input file is uploaded, Mascot redirects from the search form to a separate search progress page.

If SearchSubmitMode is async, Mascot behaves as described above. If the value is direct, progress is reported directly by the nph-mascot.exe executable as in Mascot 2.4 and earlier. The downside of "direct" mode is that closing the web browser may kill the search.

Parameter	SearchSubmitMode
Permitted values	async or direct
Default (if no parameter in mascot.dat)	asynchronous
Value in mascot.dat	[not defined]

Returns: currently defined value.

◆ getSearchSubmitOutputFormat()

std::string getSearchSubmitOutputFormat ( ) const

Returns the Mascot search submission output format.

Returns the file format of searches submitted through the search form.

In Mascot 3.0 and later, searches submitted through the search form default to the new Mascot Search Results (MSR) file format. This is a relational database saved as an SQLite file and fully supported from Parser 3.0 onward.

If SearchSubmitOutputFormat is msr, Mascot behaves as described above. If the value is dat28, Mascot will write results in the old text-based .dat format compatible with Mascot Server 2.8. Choosing dat28 is only relevant if your application submits searches through the web based search form, and then reads the file directly from the 'daily' directory on the Mascot server. If you download search results using the client.pl or export_dat_2.pl API, set SearchSubmitOutputFormat to msr – the scripts automatically convert from MSR to .dat as needed.

If SearchSubmitOutputFormat is dat28,msr, then Mascot writes the results in two files, one in .dat format and one in MSR format. This combination doubles the amount of disk space used by new searches and is only recommended for testing purposes.

Parameter	SearchSubmitOutputFormat
Permitted values	dat28 or msr or dat28,msr
Default (if no parameter in mascot.dat)	msr
Value in mascot.dat	msr

Returns: currently defined value.

◆ getSelectSwitch()

int getSelectSwitch ( ) const

Returns the value of SelectSwitch.

This function and getMudpitSwitch() replaced the single function getMudpit() in Mascot 2.1 and earlier.

Parameter	SelectSwitch
Permitted values	Any integer >= 0
Default (if no parameter in mascot.dat)	1000
Value in mascot.dat	1000

Returns: The minimum number of queries for a select summary.

◆ getSendmailPath()

std::string getSendmailPath ( ) const

Returns the value of sendmailPath.

sendmailPath is the path to sendmail or BLAT programs.

See also: getMailTransport(), isEmailUsersEnabled(), isEmailErrorsEnabled().

Parameter	sendmailPath
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	/usr/lib/sendmail
Value in mascot.dat	/usr/lib/sendmail

Returns: the full or relative path to sendmail or BLAT.

◆ getShowSubsets()

double getShowSubsets ( ) const

Returns the value of ShowSubSets.

If you have a primary hit with (say) 100 peptide matches, you are very interested in sub-set proteins with 99 matches but not if they only have 1 or 2 matches. These are the sub-set hits that clutter up the report if Show Sub-sets is checked in Mascot 2.1 and earlier. If you have a primary hit with (say) 2 peptide matches, you are more likely to be interested in sub-set proteins with just 1 match.

A value of 1 indicates that all proteins with a subset of matches should be reported. A value of 0 indicates that no subsets will be reported.

See also: ms_mascotresults::setSubsetsThreshold()

Parameter	ShowSubSets
Permitted values	Floating point in range 0 to 1 inclusive
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	[not defined]

Returns: The fractional score required for a protein to be counted as a subset. Its score must be greater than or equal to main_protein_score * (1 - getShowSubsets()).

◆ getSigThreshold()

double getSigThreshold ( ) const

Returns the value of SigThreshold.

Significance threshold used in results reports.

This global default can be overridden on an individual report URL be appending &_sigthreshold=X, where X is the significance threshold.

Parameter	SigThreshold
Permitted values	Floating point 1e-18 to 1.0
Default (if no parameter in mascot.dat)	0.05
Value in mascot.dat	0.05

Returns: the significance threshold.

◆ getSiteAnalysisMD10Prob()

double getSiteAnalysisMD10Prob ( ) const

Returns the value of SiteAnalysisMD10Prob.

SiteAnalysisMD10Prob is used in calculating relative probabilities of modification assignments in Peptide View. It defines the factor in probability that a peptide score difference of 10 corresponds to. The default is 0.1, which means a score difference of 10 corresponds to a factor of 10 in probability. Similarly, 0.05 corresponds to a factor of 20.

Parameter	SiteAnalysisMD10Prob
Permitted values	Floating point 1e-18 to 1.0
Default (if no parameter in mascot.dat)	0.1
Value in mascot.dat	0.1

Returns: the MD10Score value.

◆ getSortUnassigned()

std::string getSortUnassigned ( ) const

Returns the value of SortUnassigned.

Parameter	SortUnassigned
Permitted values	"scoredown", "queryup" or "intdown"
Default (if no parameter in mascot.dat)	scoredown
Value in mascot.dat	[not defined]

Returns

The returned value will be one of:

scoredown - descending score
queryup - query order
intdown - intensity order

◆ getSpectraPerLibraryBlock()

int getSpectraPerLibraryBlock ( ) const

Returns the number of spectra in a spectral library block.

The NIST spectral library tools have a limit of about 600k spectra. Mascot deals with larger files by splitting them up into chunks each with the maximum number of spectra specified by this value.

Parameter	SpectraPerLibraryBlock
Permitted values	Any integer > 0.
Default (if no parameter in mascot.dat)	500000
Value in mascot.dat	500000

Returns: the maximum number of spectra before splitting into separate blocks

◆ getSpectrumViewerColourSchemeNames()

std::vector< std::string > getSpectrumViewerColourSchemeNames ( ) const

Returns the names of all colour schemes (SpectrumViewerColourScheme).

See also: getSpectrumViewerColourSchemeString()

Returns: A vector of colour scheme names defined in mascot.dat.

◆ getSpectrumViewerColourSchemeString()

std::string getSpectrumViewerColourSchemeString ( const std::string & name ) const

Returns SpectrumViewerColourScheme by name.

Spectrum Viewer colour schemes were added in Mascot 2.6, and they allow you to choose different peak colours in Peptide View.

Colour scheme name must contain ASCII letters and numbers only; no special characters are allowed.

Each colour scheme is a comma-separated list of key=value pairs, where the key is a peak class and value is either a colour name or an RGB value. The permitted peak classes are:

unmatched
internal_ion
immonium_ion
terminal_series_ion
terminal_series_ion_nl
library_peak

The colour is either one of the 16 HTML 4.01 colour names:

white
silver
gray
black
red
maroon
yellow
olive
lime
green
aqua
teal
blue
navy
fuchsia
purple
orange

Or an RGB value in standard CSS format, #rrggbb. For example, pure red is #ff0000. Letter case does not matter in colour names or hexadecimal digits.

Note that "orange" is not an HTML 4.01 colour name. It is accepted as a special exception, since it is a valid colour name in CSS 2.1.

Parameter	SpectrumViewerColourScheme_XXX
Permitted values	A comma-separated list of key=value pairs (see above)
Default (if no parameter in mascot.dat)	`SpectrumViewerColourScheme_screen unmatched=black,internal_ion=orange,immonium_ion=orange,terminal_series_ion=red,terminal_series_ion_nl=orange,library_peak=blue`
Value in mascot.dat	`SpectrumViewerColourScheme_screen unmatched=black,internal_ion=orange,immonium_ion=orange,terminal_series_ion=red,terminal_series_ion_nl=orange,library_peak=blue`

Parameters

name	Colour scheme name; the defined names are returned by getSpectrumViewerColourSchemeNames().

Returns: The colour scheme string, or the empty string if the colour scheme does not exist.

◆ getSpectrumViewerDefaultColourSchemeName()

std::string getSpectrumViewerDefaultColourSchemeName ( ) const

Return the name of the default colour scheme (SpectrumViewerDefaultColourScheme).

The colour scheme used in Peptide View by default is the scheme named here.

See also: getSpectrumViewerColourSchemeString()

Parameter	SpectrumViewerDefaultColourScheme
Permitted values	colour scheme name
Default (if no parameter in mascot.dat)	screen
Value in mascot.dat	screen

Returns: The name of the default colour scheme.

◆ getSplitDataFileSize()

int getSplitDataFileSize ( ) const

Returns the value of SplitDataFileSize.

See getSplitNumberOfQueries() for a description.

Parameter	SplitDataFileSize
Permitted values	Any integer > 0
Default (if no parameter in mascot.dat)	20000000
Value in mascot.dat	20000000

Returns: the maximum size (bytes) of each chunk.

◆ getSplitNumberOfQueries()

int getSplitNumberOfQueries ( ) const

Returns the value of SplitNumberOfQueries.

Used in conjunction with SplitDataFileSize parameter. When large amount of spectra is submitted the input file is split into several chunks. Each chunk contains no more than SplitNumberOfQueries queries and no more than SplitDataFileSize bytes long.

Parameter	SplitNumberOfQueries
Permitted values	Any integer > 0
Default (if no parameter in mascot.dat)	2000
Value in mascot.dat	2000

Returns: the maximum number of queries in each chunk.

◆ getSVGSpectrumSwitch()

int getSVGSpectrumSwitch ( ) const

Returns the value of SVGSpectrumSwitch.

Mascot 2.5 introduced SVG-based graphics in Peptide View. Since the graphics is rendered in the browser, spectra with a large number of peaks may cause Peptide View to load much slower than in Mascot 2.4 and ealier.

SVGSpectrumSwitch is the cut-off point where Peptide View reverts to the static spectrum graphic used in Mascot 2.4 and earlier. If the spectrum has more peaks than SVGSpectrumSwitch, the old graphic is used; otherwise the new SVG-based graphic is shown. In particular, if you set SVGSpectrumSwitch to 0, the new SVG-based graphic is never shown. If you set it to the maximum value (100000), the SVG-based graphic is always shown.

Parameter	SVGSpectrumSwitch
Permitted values	0-100000
Default (if no parameter in mascot.dat)	2000
Value in mascot.dat	2000

Returns: cut-off point where Peptide View reverts to the static spectrum graphic

◆ getTargetFDRPercentage()

double getTargetFDRPercentage ( const int index ) const

Returns an element of the TargetFDRPercentages list by its number.

For more information on the TargetFDRPercentages parameter see getNumberOfTargetFDRPercentages().

Parameters

index element number from 0 to (getNumberOfTargetFDRPercentages()-1).

Returns: an element of the list that corresponds to the given index. Returns 0 if the index is not valid.

◆ getTaxBrowserUrl()

std::string getTaxBrowserUrl ( ) const

Returns value of the TaxBrowserUrl.

The URL used in reports to retrieve taxonomy information for a Protein View report.

Parameter	TaxBrowserUrl
Permitted values	Any text string
Default (if no parameter in mascot.dat)	[empty]
Value in mascot.dat	http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=#TAXID#

Returns: the URL.

◆ getTestDirectory()

std::string getTestDirectory ( ) const

Returns the value of TestDirectory.

TestDirectory contains the input files used by Monitor to test new sequence databases.

Parameter	TestDirectory
Permitted values	Any non empty text string
Default (if no parameter in mascot.dat)	../data/test
Value in mascot.dat	../data/test

Returns: the test directory.

◆ getUniqueJobStartNumber()

int getUniqueJobStartNumber ( ) const

Returns the value of UniqueJobStartNumber.

See getMascotJobIdFile() for explanations on usage of this parameter.

Parameter	UniqueJobStartNumber
Permitted values	Integer >= 0
Default (if no parameter in mascot.dat)	1234
Value in mascot.dat	1234

Returns: the start job number to be used if the job id file does not exist.

◆ getUnixDirPerm()

int getUnixDirPerm ( ) const

Returns the value of UnixDirPerm.

Specify the Unix permissions for the 'daily' result file directories and the logs directory. For example, 775 makes each directory world readable but not writeable.

See also: getUnixWebUserGroup()

Parameter	UnixDirPerm
Permitted values	Any integer in octal format
Default (if no parameter in mascot.dat)	777 (octal)
Value in mascot.dat	[not defined]

Returns: the permissions flag.

◆ getUnixWebUserGroup()

int getUnixWebUserGroup ( ) const

Returns the value of UnixWebUserGroup.

The paramater UnixWebUserGroup, if present, will restrict access to the files created by ms-monitor.exe, and hence improve system security. UnixWebUserGroup parameter value is the id of the group used by the web server to run CGI programs.

With Apache, the group name will generally be nobody or apache and you will need to ascertain the group number from the group file. For other Web servers, check the documentation that comes with the server to find out which user name is used for running CGI programs.

A value of -2 can be used if the same user name is used to run Web server scripts as runs ms-monitor.exe. In this case, the files created by ms-monitor.exe will not be world accessible, and chown is not used on the files to change ownership.

Parameter	UnixWebUserGroup
Permitted values	Any text string
Default (if no parameter in mascot.dat)	-1
Value in mascot.dat	[not defined]

Returns: the id of the group.

◆ getVmemory()

INT64 getVmemory ( ) const

Returns the value of Vmemory.

Alpha Tru64 only. When setting resource limits for address space, this is the maximum number of bytes requested. If a value of -1 is specified, then the maximum system value is requested.

Parameter	Vmemory
Permitted values	64 bit integer >= -1
Default (if no parameter in mascot.dat)	-1
Value in mascot.dat	[not defined]

Returns: the vmemory limit.

◆ isAlwaysCreateDat28ResultsFile()

bool isAlwaysCreateDat28ResultsFile ( ) const

Returns the value of AlwaysCreateDat28ResultsFile.

This option is only intended for backwards compatibility with third-party software.

If AlwaysCreateDat28ResultsFile is set to 0, the file format for search results defaults to Mascot Search Results (MSR). The task ID is associated with the filename F001234.msr. If set to 1, then nph-mascot.exe writes search results in two files, F001234.msr (MSR) and F001234.dat (dat28). The task ID is associated with the filename F001234.dat.

The behaviour can be overriden by the client program by using the -format argument when submitting the search to nph-mascot.exe. The behaviour can also be overriden in the Mascot search form with getSearchSubmitOutputFormat(). The setting AlwaysCreateDat28ResultsFile should only be used if these alternatives are infeasible.

Parameter	AlwaysCreateDat28ResultsFile
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	[not defined]

Returns: true if Mascot searches should always create a result file in dat28 format

◆ isAlwaysEnableAutoDecoySearch()

bool isAlwaysEnableAutoDecoySearch ( ) const

Returns true if Mascot always runs an automatic target-decoy search.

Controls whether to run an automatic decoy search. Before Mascot Server 3.0, an automatic target-decoy search was only run if the search parameter DECOY=1 is set. From Mascot Server 3.0, if AlwaysEnableAutoDecoySearch is 1 (default), nph-mascot.exe defaults to DECOY=1 unless overridden by the DECOY search parameter. The Decoy checkbox is not shown in the browser-based search form. A decoy search is only omitted for unsupported search types (currently spectral library searches and intact crosslink searches).

If set to 0, the Decoy checkbox is shown in the browser-based search form and defaults to unchecked, and nph-mascot.exe defaults to DECOY=0 unless overridden by the DECOY search parameter.

Parameter	AlwaysEnableAutoDecoySearch
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	1
Value in mascot.dat	1

Returns: true if nph-mascot.exe should always write a dat28 (.dat) file

◆ isAutoSelectCharge()

bool isAutoSelectCharge ( ) const

Returns the value of AutoSelectCharge.

When this parameter is set to 1 only the charge state that gives the best ion score is reported for each query. Otherwise, each query will be transformed and split into several queries (one for each possible charge state).

Parameter	AutoSelectCharge
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	1
Value in mascot.dat	1

Returns: true if the auto selection of charge is enabled.

◆ isCreateLegacyModAndSubstitutionFiles()

bool isCreateLegacyModAndSubstitutionFiles ( ) const

Returns true if Mascot Monitor creates legacy files containing modification definitions.

This option is meant for backwards compatibility with very old third-party software. Mascot Server 2.1 and earlier saved modification definitions in three files, ../config/mod_file, ../config_masses and ../config/substitutions. Since Unimod support was added in Mascot Server 2.2, these files have been automatically generated from unimod.xml.

Set the option to true (1) and Mascot Monitor will create the legacy files. Note that this option may be removed in a future Mascot release.

Parameter	CreateLegacyModAndSubstitutionFiles
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	[not defined]

Returns: true if Mascot Monitor should create obsolete mod_file, substitutions and masses files

◆ isDefaultTargetFDRPercentage()

bool isDefaultTargetFDRPercentage ( const int index ) const

Returns true if the element of TargetFDRPercentages is a default value.

For more information on the TargetFDRPercentages parameter see getNumberOfTargetFDRPercentages().

Parameters

index element number from 0 to (getNumberOfTargetFDRPercentages()-1).

Returns: true if the element is marked as a default value.

◆ isEmailErrorsEnabled()

bool isEmailErrorsEnabled ( ) const

Returns the value of EmailErrorsEnabled.

Serious error messages can be emailed to an administrator. This facility can be enabled by setting EmailErrorsEnabled to 1 or disabled by setting it to 0.

Error messages that are considered serious are identified in the file errors.html. This file can be found in the root directory of the installation CD-ROM.

A number of other parameters are required to send e-mail messages. See isEmailUsersEnabled(), getErrMessageEmailTo(), and getMailTransport() for more information.

Parameter	EmailErrorsEnabled
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	0

Returns: true if error messages should be emailed to the Mascot server administrator.

◆ isEmailUsersEnabled()

bool isEmailUsersEnabled ( ) const

Returns the value of EmailUsersEnabled.

When the search engine executes as a CGI application, email can be used to send the results of a search to a user who accidentally or deliberately disconnected before the search was complete. This facility can be enabled by setting EmailUsersEnabled to 1 or disabled by setting it to 0.

If EmailUsersEnabled is set to 1, search results will be emailed to a user if their web browser does not respond within the number of seconds specified in EmailTimeOutPeriod following the completion of a search. See getEmailTimeOutPeriod().

Email messages can be sent in batches at intervals specified by MonitorEmailCheckFreq (in seconds). See getMonitorEmailCheckFreq().

MailTempFile is the name of the temporary file used to store email messages until they can be sent. See getMailTempFile().

A number of other parameters are used to define how email should be sent. You can find some more information about other parameters in the the Mascot installation and setup manual.

See also: getMailTransport()

Parameter	EmailUsersEnabled
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	0

Returns: the flag indicating if emails with a link to results should be sent.

◆ isForkForUnixApache()

bool isForkForUnixApache ( ) const

Returns the value of ForkForUnixApache.

If a user presses Stop or goes to another page in their browser when a search is running, then the intended behaviour is that the search should continue, and the user be emailed with their results.

However, when running some versions of Apache under Unix, the search is terminated by Apache when the connection to the browser is lost. To stop this from happening, set this value to 1.

Windows versions of Mascot prior to 2.5.1 also used this parameter and attempted to emulate a 'fork' after the search started. However, with Windows 7 and later versions, this was very unreliable and the functionality was removed from the Windows version of nph-mascot.exe in Mascot Server version 2.5.1. However, this Mascot Parser function still returns the value in mascot.dat for both Windows and Linux.

Parameter	ForkForUnixApache
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	0

Returns: true if the nph-mascot.exe process should be forked at startup

◆ isInIgnoreDupeAccessionList()

bool isInIgnoreDupeAccessionList ( const std::string value ) const

Checks to see if the passed database name is in the list databases that shouldn't be checked for duplicate accessions.

When FASTA files are compressed, they are checked to ensure that there are no duplicate accession strings. For a large EST database with many millions of entries, this can take up a lot of memory. Adding a database to the list of values for the IgnoreDupeAccessions entry in mascot.dat prevents this database from being tested.

Parameter	IgnoreDupeAccessions
Permitted values	text strings delimted by tab, space and comma
Default (if no parameter in mascot.dat)	EST_others
Value in mascot.dat	EST_others

Parameters

value is the name of the databases to check.

Returns: true if the database is in the list.

◆ isIteratePMFIntensities()

bool isIteratePMFIntensities ( ) const

Returns value of the IteratePMFIntensities.

The IteratePMFIntensities parameter is used in order to switch off iterative PMF scoring. If the parameter is set to 1 mascot will try to use only as many queries for scoring as necessary to achieve the best PMF score.

Parameter	IteratePMFIntensities
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	1
Value in mascot.dat	1

Returns: TRUE if the parameter is set to 1 and FALSE otherwise.

◆ isLabelAll()

bool isLabelAll ( ) const

obsolete

Returns the value of LabelAll.

LabelAll is obsolete. Peptide View in Mascot 3.0 and later always shows all annotated peaks.

If LabelAll is set to 1, the initial display in Peptide View is the one in which all peaks that match a calculated mass value are labelled.

Parameter	LabelAll
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	0

Returns: true if if all peaks that match a calculated mass value should be labelled in Peptide View.

◆ isMatchOppositeCrosslinkPairs()

bool isMatchOppositeCrosslinkPairs ( ) const

Returns the value of MatchOppositeCrosslinkPairs.

Mascot 2.7 and later support intact crosslinking. Normally Mascot only stores a match to the alpha-beta pair, where the alpha has the higher Mr, longer sequence or is alphabetically first (in this order).

If this setting is 1, both alpha-beta and beta-alpha matches are stored in the results file. Enabling the setting is only useful for debugging purposes.

Parameter	MatchOppositeCrosslinkPairs
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	[not defined]

Returns: true if for each crosslink pair, the opposite combination should also be considered for matching

◆ isMoveOldDbToOldDir()

bool isMoveOldDbToOldDir ( ) const

Returns the value of MoveOldDbToOldDir.

After a successful database swap, the old fasta file and old reference file are moved to the ../old directory unless this is set to 0 in which case the files are simply deleted.

Parameter	MoveOldDbToOldDir
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	1
Value in mascot.dat	[not defined]

Returns: true if old fasta and reference files are moved to the old directory

◆ isPercolator()

bool isPercolator ( ) const

Returns the value of Percolator.

Returns true if percolated results should be opened by default.

See Using Percolator scores for further information.

Parameter	Percolator
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	1

Returns: true if percolated results should be opened by default.

◆ isPercolatorUseProteins()

bool isPercolatorUseProteins ( ) const

Returns the value of PercolatorUseProteins.

Percolator can use the assignment of proteins to peptides to improve specificity. However, this is risky in some situations so can be switched off.

Currently not supported

See Using Percolator scores for further information.

Parameter	PercolatorUseProteins
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	0

Returns: true if percolator should use protein features.

◆ isPercolatorUseRT()

bool isPercolatorUseRT ( ) const

Returns the value of PercolatorUseRT.

Percolator can use retention times of peptides to improve specificity. However, this is risky in some situations so can be switched off.

See Using Percolator scores for further information.

Parameter	PercolatorUseRT
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	0

Returns: true if percolator should use retention times.

◆ isRemoveOldIndexFiles()

bool isRemoveOldIndexFiles ( ) const

Returns the value of RemoveOldIndexFiles.

After a successful database swap, the compressed files in the current directory are deleted unless this is set to 0.

Parameter	RemoveOldIndexFiles
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	1
Value in mascot.dat	[not defined]

Returns: true if compressed files in the current directory are deleted after a swap

◆ isRequireBoldRed()

bool isRequireBoldRed ( ) const

Returns the value of RequireBoldRed.

If RequireBoldRed is set to 1 in a Peptide Summary report, only protein matches which have one or more 'bold red' peptide matches will be listed. That is, proteins that include at least one top ranking peptide match that has not already appeared in the report.

Not used for the Protein Family Summary report and when ms_mascotresults::MSRES_CLUSTER_PROTEINS is specified.

Parameter	RequireBoldRed
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	0

Returns: true if all proteins must contain a bold red peptide.

◆ isSaveEveryLastQueryAsc()

bool isSaveEveryLastQueryAsc ( ) const

Returns the value of SaveEveryLastQueryAsc.

If set to 1, the Mascot input file will be saved for any search that fails to complete because it generates a fatal error. The name of the output file follows the same naming convention as a normal Mascot output file, except for the additional suffix .inp. If a search goes to completion, this file is deleted as soon as the normal output file has been written to disk.

See also: isSaveLastQueryAsc(), getLastQueryAscFile().

Parameter	SaveEveryLastQueryAsc
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	1
Value in mascot.dat	0

Returns: true if the value in the file is '1'.

◆ isSaveLastQueryAsc()

bool isSaveLastQueryAsc ( ) const

Returns the value of SaveLastQueryAsc.

SaveLastQueryAsc is a flag which controls whether the most recent input file to Mascot (i.e. the MIME format file containing MS data and search parameters) should be saved to disk (1) or not (0). This can be a useful debugging tool when writing scripts or forms to submit searches to Mascot.

If SaveLastQueryAsc is set to 1, the name of the file is determined by LastQueryAscFile.

Each new search overwrites this file.

See also: isSaveEveryLastQueryAsc(), getLastQueryAscFile().

Parameter	SaveLastQueryAsc
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	0

Returns: true if the value in the file is '1'.

◆ isSectionAvailable()

bool isSectionAvailable ( ) const

Indicates whether the section has been actually read from the file.

The Options section is unavailable until it has been read from the file. This function doesn't normally need to be used by client applications.

Returns: true if the seciton is available.

Examples: config_mascotdat.cpp.

◆ isShowAllFromErrorTolerant()

bool isShowAllFromErrorTolerant ( ) const

Returns the value of ShowAllFromErrorTolerant.

If ShowAllFromErrorTolerant is set to 0, result resports of manual error tolerant searches show only those matches that satisfy two criteria: (i) the score must be at least as high as the match for the same query in the original "parent" search, (ii) the score equals or exceeds the identity threshold for the same query in the original "parent" search. Setting ShowAllFromErrorTolerant to 1 causes all matches to be displayed.

Parameter	ShowAllFromErrorTolerant
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	0

Returns: true if all matches should be displayed in manual error tolerant searches.

◆ isShowSubsets()

bool isShowSubsets ( ) const

Returns the value of ShowSubSets.

Deprecated:: See getShowSubsets().

Parameter	ShowSubSets
Permitted values	Floating point in range 0 to 1 inclusive
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	[not defined]

Returns: true if the return from getShowSubsets is greater than 0.

◆ isStoreModPermutations()

bool isStoreModPermutations ( ) const

Returns the value of StoreModPermutations.

If set to 0, only the highest scoring permutation of variable modifications for each unique peptide sequence is retained in the list of the top 10 ions scores. If set to 1, then different permutations of variable modifications are treated as independent matches, creating the possibility that all 10 top ions scores correspond to the same primary sequence.

Parameter	StoreModPermutations
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	1
Value in mascot.dat	[not defined]

Returns: true if peptides with different modification permuatation should be stored.

◆ isUnixDirPermDefined()

bool isUnixDirPermDefined ( ) const

Returns true if the UnixDirPerm value is defined.

See getUnixDirPerm().

Parameter	UnixDirPerm
Permitted values	Any integer in octal format
Default (if no parameter in mascot.dat)	777 (octal)
Value in mascot.dat	[not defined]

Returns: true if there is a value in mascot.dat.

◆ isUseHTTPProxyForFTP()

bool isUseHTTPProxyForFTP ( ) const

Returns the value of UseHTTPProxyForFTP.

This parameter allows making FTP requests through the HTTP proxy. Note that the HTTP proxy server must explicitly support such "tunneling".

The default is false. You should only alter the setting if FTP requests fail.

Parameter	UseHTTPProxyForFTP
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	0

Returns: true if FTP requests should use the HTTP proxy server.

This option is ignored on Windows if auto proxy configuration is enabled.

◆ isUseHTTPProxyForHTTPS()

bool isUseHTTPProxyForHTTPS ( ) const

Returns the value of UseHTTPProxyForHTTPS.

This parameter allows making HTTPS requests through the HTTP proxy. Note that the HTTP proxy server must explicitly support such "tunneling".

The default is false. You should only alter the setting if HTTPS requests fail.

Parameter	UseHTTPProxyForHTTPS
Permitted values	0 or 1
Default (if no parameter in mascot.dat)	0
Value in mascot.dat	0

Returns: true if HTTPS requests should use the HTTP proxy server.

This option is ignored on Windows if auto proxy configuration is enabled.

◆ setAlwaysCreateDat28ResultsFile()

void setAlwaysCreateDat28ResultsFile ( const bool value )

Sets the value of AlwaysCreateDat28ResultsFile.

For a description of this function, see isAlwaysCreateDat28ResultsFile().

Parameters

value is the new setting.

◆ setAlwaysEnableAutoDecoySearch()

void setAlwaysEnableAutoDecoySearch ( const bool value )

Sets AlwaysEnableAutoDecoySearch.

For a description of this function, see isAlwaysEnableAutoDecoySearch().

Parameters

value is the new setting.

◆ setAutoSelectCharge()

void setAutoSelectCharge ( const bool value )

Sets AutoSelectCharge.

For a description of this function, see isAutoSelectCharge().

Parameters

value is the new setting.

◆ setCacheDirectory()

void setCacheDirectory ( const char * value )

Sets CacheDirectory.

For a description of this function, see getCacheDirectory(). If the provided value is null, the existing value will be kept.

Parameters

value is the new cache directory.

◆ setCentroidWidth()

void setCentroidWidth ( const double value )

Sets CentroidWidth.

For a description of this function, see getCentroidWidth(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new centroid width.

◆ setCentroidWidthCount()

void setCentroidWidthCount ( const int value )

Sets CentroidWidthCount.

For a description of this function, see getCentroidWidthCount(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new peak count threshold.

◆ setCompressToolAA()

void setCompressToolAA ( const std::string value )

Sets CompressTool_AA.

For a description of this function, see getCompressToolAA() If the provided value is not valid, the existing value will be kept.

Parameters

value is the new setting

◆ setCompressToolNA()

void setCompressToolNA ( const std::string value )

Sets CompressTool_NA.

For a description of this function, see getCompressToolNA() If the provided value is not valid, the existing value will be kept.

Parameters

value is the new setting

◆ setCompressToolSL()

void setCompressToolSL ( const std::string value )

Sets CompressTool_NA.

For a description of this function, see getCompressToolSL() If the provided value is not valid, the existing value will be kept.

Parameters

value is the new setting

◆ setCrawlerNumPeaksPer100Da()

void setCrawlerNumPeaksPer100Da ( const int value )

Sets the number of peaks to output in each 100 Da window for the library crawler.

Sets the number of peaks to output in each 100 Da window for the library crawler If the provided value is not valid, the existing value will be kept.

Parameters

value must be a number greater than zero

◆ setCreateLegacyModAndSubstitutionFiles()

void setCreateLegacyModAndSubstitutionFiles ( const bool value )

Sets an option for backwards compatibility with very old software.

For a description of this function, see isCreateLegacyModAndSubstitutionFiles().

Parameters

value is the new setting.

◆ setCreatePipThreadBlockSize()

void setCreatePipThreadBlockSize ( const int blockSize )

Sets CreatePipThreadBlockSize.

For a description of this function, see getCreatePipThreadBlockSize(). If the provided value is not valid, the existing value will be kept.

Parameters

blockSize is .

◆ setCreatePipThreads()

void setCreatePipThreads ( const int nThreads )

Sets CreatePipThreads.

For a description of this function, see getCreatePipThreads(). If the provided value is not valid, the existing value will be kept.

Parameters

nThreads is the number of threads used to generate the Percolator input file.

◆ setDechargeFragmentPeaks()

void setDechargeFragmentPeaks ( const int maxCharge )

Sets the maximum fragment ion charge state to be decharged.

For a description of this function, see getDechargeFragmentPeaks(). If the provided value is not valid, the existing value will be kept.

Parameters

maxCharge must be zero or a positive integer

◆ setDecoyTypeNoEnzyme()

void setDecoyTypeNoEnzyme ( const int value )

Sets DecoyTypeNoEnzyme.

For a description of this function, see getDecoyTypeNoEnzyme(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new setting.

◆ setDecoyTypeSpecific()

void setDecoyTypeSpecific ( const int value )

Sets DecoyTypeSpecific.

For a description of this function, see getDecoyTypeSpecific(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new setting.

◆ setDefaultDelimiter()

void setDefaultDelimiter ( const char * delim )

inherited

Allows to set a specific delimiter string to be used when no property-specific delimiter is supplied.

Parameters

delim String to set the default delimiter

◆ setDefaultTargetFDRPercentage()

void setDefaultTargetFDRPercentage ( const int index )

Makes an element of TargetFDRPercentages at the given index the default value.

See getTargetFDRPercentage() for more information. If the provided index is not valid, the existing value will be kept.

Parameters

index is the index of the item to set. index must be between 0 and getNumberOfTargetFDRPercentages()-1.

◆ setDisplayNonSignificantMatches()

void setDisplayNonSignificantMatches ( const int value )

Sets DisplayNonSignificantMatches.

For a description of this function, see getDisplayNonSignificantMatches().

Parameters

value is the new setting. If it is not one of the permitted values, the setting remains unchanged.

◆ setEmailErrorsEnabled()

void setEmailErrorsEnabled ( const bool value )

Sets EmailErrorsEnabled.

For a description of this function, see isEmailErrorsEnabled().

Parameters

value specified whether errors should be emailed.

◆ setEmailFromTextName()

void setEmailFromTextName ( const char * str )

Sets EmailFromTextName.

For a description of this function, see getEmailFromTextName(). If the provided value is null, the existing value will be kept.

Parameters

str	is the new name of the user from which email appears to come.

◆ setEmailFromUser()

void setEmailFromUser ( const char * str )

Sets EmailFromUser.

For a description of this function, see getEmailFromUser(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new email address of the user from which email appears to come.

◆ setEmailPassword()

void setEmailPassword ( const char * str )

Sets EmailPassword.

For a description of this function, see getEmailPassword(). If the provided value is null, the existing value will be kept.

Parameters

str	is the new email password.

◆ setEmailProfile()

void setEmailProfile ( const char * str )

Sets EmailPassword.

For a description of this function, see getEmailProfile(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new name of the email profile.

◆ setEmailService()

void setEmailService ( const char * str )

Sets EmailService.

For a description of this function, see getEmailService(). If the provided value is null, the existing value will be kept.

Parameters

str	is the new email service name.

◆ setEmailTimeOutPeriod()

void setEmailTimeOutPeriod ( const int value )

Sets EmailTimeOutPeriod.

For a description of this function, see getEmailTimeOutPeriod(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new timeout period.

◆ setEmailUsersEnabled()

void setEmailUsersEnabled ( const bool value )

Sets EmailUsersEnabled.

For a description of this function, see isEmailUsersEnabled().

Parameters

value specifies whether users should be emailed.

◆ setErrMessageEmailTo()

void setErrMessageEmailTo ( const char * str )

Sets ErrMessageEmailTo.

For a description of this function, see getErrMessageEmailTo(). If the provided value is null, the existing value will be kept.

Parameters

str	is the new name of the person to send errors to.

◆ setErrorLogFile()

void setErrorLogFile ( const char * str )

Sets ErrorLogFile path.

For a description of this function, see getErrorLogFile(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new name of the errorlog file.

◆ setErrTolMaxAccessions()

void setErrTolMaxAccessions ( const int value )

Sets ErrTolMaxAccessions.

For a description of this function, see getErrTolMaxAccessions(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new maximum.

◆ setExecAfterSearch()

void setExecAfterSearch	(	const int	num,
		std::string	value
	)

Sets ExecAfterSearch_XXX.

For a description of this function, see getExecAfterSearch(). If the provided value is not valid, the existing value will be kept.

Parameters

num	is the 1 based number for the `ExecAfterSearch_[num]` parameter.
value	is the command to be run.

◆ setFeatureTableLength()

void setFeatureTableLength ( const int value )

Sets FeatureTableLength.

For a description of this function, see getFeatureTableLength(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new length.

◆ setFeatureTableMinScore()

void setFeatureTableMinScore ( const double value )

Sets FeatureTableMinScore.

For a description of this function, see getFeatureTableMinScore(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new minimum score.

◆ setForkForUnixApache()

void setForkForUnixApache ( const bool value )

Sets ForkForUnixApache.

For a description of this function, see isForkForUnixApache().

Parameters

value specifies whether the fork command should be used.

◆ setFormVersion()

void setFormVersion ( const char * str )

Sets FormVersion.

For a description of this function, see getFormVersion(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new version string.

◆ setGetSeqBlastAccession()

void setGetSeqBlastAccession ( const ms_blastaccession * value )

Sets GetSeqBlastAccession.

For a description of this function, see getGetSeqBlastAccession(). If the provided value is null, the existing value will be kept.

Parameters

value is the new setting.

◆ setGetSeqJobIdFile()

void setGetSeqJobIdFile ( const char * str )

Sets GetSeqJobIdFile.

For a description of this function, see getGetSeqJobIdFile(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new name of the job id file.

◆ setICATFilter()

void setICATFilter ( const char * filterString )

Sets ICATFilter.

For a description of this function, see getICATFilter(). If the provided value is not valid, the existing value will be kept.

Parameters

filterString is the new name of the ICAT filter.

◆ setICATHeavy()

void setICATHeavy ( const char * modName )

Sets ICATHeavy.

For a description of this function, see getICATHeavy(). If the provided value is null, the existing value will be kept.

Parameters

modName is the new name of the heavy ICAT mod.

◆ setICATLight()

void setICATLight ( const char * modName )

Sets ICATLight.

For a description of this function, see getICATLight(). If the provided value is null, the existing value will be kept.

Parameters

modName is the new name of the light ICAT mod.

◆ setICATQuantitationMethod()

void setICATQuantitationMethod ( const char * methodName )

Sets ICATQuantitationMethod.

For a description of this function, see getICATQuantitationMethod(). If the provided value is not valid, the existing value will be kept.

Parameters

methodName is the new name of the quantitation method.

◆ setIgnoreDupeAccession()

void setIgnoreDupeAccession	(	const unsigned int	index,
		const std::string	value
	)

Sets an item in the IgnoreDupeAccessions list by its index.

See getIgnoreDupeAccession() and isInIgnoreDupeAccessionList() for details.

This method sets the value at the given index.

Parameters

index	is the index of the value to set. index must be between 0 and getNumberOfIgnoreDupeAccessions()-1.
value	is the value to set (the name of the database).

◆ setIgnoreIonsScoreBelow()

void setIgnoreIonsScoreBelow ( const double value )

Sets IgnoreIonsScoreBelow.

For a description of this function, see getIgnoreIonsScoreBelow(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new maximum.

◆ setIntensitySigFigs()

void setIntensitySigFigs ( const int value )

Sets IntensitySigFigs.

For a description of this function, see getIntensitySigFigs(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new number of significant figures.

◆ setInterFileBasePath()

void setInterFileBasePath ( const char * str )

Sets InterFileBasePath.

For a description of this function, see getInterFileBasePath(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new path.

◆ setInterFileRelPath()

void setInterFileRelPath ( const char * str )

Sets InterFileRelPath.

For a description of this function, see getInterFileRelPath(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new path.

◆ setIonsDecimalPlaces()

void setIonsDecimalPlaces ( const int value )

Sets IonsDecimalPlaces.

For a description of this function, see getIonsDecimalPlaces(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new number of decimal places.

◆ setIteratePMFIntensities()

void setIteratePMFIntensities ( const bool value )

Sets IteratePMFIntensities.

For a description of this function, see isIteratePMFIntensities().

Parameters

value is the new setting.

◆ setLabelAll()

void setLabelAll ( const bool value )

obsolete

Sets LabelAll.

For a description of this function, see isLabelAll().

Parameters

value specifies if all peaks that match a calculated mass value should be labelled in Peptide View.

◆ setLastQueryAscFile()

void setLastQueryAscFile ( const char * filename )

Sets LastQueryAscFile to the passed value.

For a description of this function, see isSaveLastQueryAsc(). If the provided value is not valid, the existing value will be kept.

Parameters

filename is the new name of the lastqueryasc file.

◆ setLogoImageFile()

void setLogoImageFile ( const char * str )

Sets LogoImageFile.

For a description of this function, see getLogoImageFile(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new logo image file.

◆ setMailTempFile()

void setMailTempFile ( const char * str )

Sets MailTempFile.

For a description of this function, see getMailTempFile(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new name of the temp file.

◆ setMailTransport()

void setMailTransport ( const int value )

Sets MailTransport.

For a description of this function, see getMailTransport(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new mail transport option.

◆ setMascNodeCtrlFile()

void setMascNodeCtrlFile ( const char * str )

Sets MascNodeCtrlFile.

For a description of this function, see getMascNodeCtrlFile(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new name of the node control file.

◆ setMascotCmdLine()

void setMascotCmdLine ( const char * str )

Sets MascotCmdLine.

For a description of this function, see getMascotCmdLine(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new path.

◆ setMascotControlFile()

void setMascotControlFile ( const char * str )

Sets MascotControlFile.

For a description of this function, see getMascotControlFile(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new name of the control file.

◆ setMascotFileProcessingThreads()

void setMascotFileProcessingThreads ( const int value )

Sets MascotFileProcessingThreads.

For a description of this function, see getMascotFileProcessingThreads() If the provided value is not valid, the existing value will be kept.

Parameters

value must be a number greater than zero or -1

◆ setMascotJobIdFile()

void setMascotJobIdFile ( const char * str )

Sets MascotJobIdFile.

For a description of this function, see getMascotJobIdFile(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new name of the job id file.

◆ setMascotMessage()

void setMascotMessage ( const char * str )

Sets MascotMessage.

For a description of this function, see getMascotMessage(). If the provided value is null, the existing value will be kept.

Parameters

str	is the new message.

◆ setMassDecimalPlaces()

void setMassDecimalPlaces ( const int value )

Sets MassDecimalPlaces.

For a description of this function, see getMassDecimalPlaces(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new number of decimal places.

◆ setMatchOppositeCrosslinkPairs()

void setMatchOppositeCrosslinkPairs ( const bool value )

Sets MatchOppositeCrosslinkPairs.

For a description of this function, see isMatchOppositeCrosslinkPairs().

Parameters

value is the new setting.

◆ setMaxConcurrentSearches()

void setMaxConcurrentSearches ( const int value )

Sets MaxConcurrentSearches.

For a description of this function, see getMaxConcurrentSearches(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new maximum value.

◆ setMaxDatabases()

void setMaxDatabases ( const int value )

Sets MaxDatabases.

For a description of this function, see getMaxDatabases(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new maximum number of databases.

◆ setMaxDescriptionLen()

void setMaxDescriptionLen ( const int value )

Sets MaxDescriptionLen.

For a description of this function, see getMaxDescriptionLen(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new maximum length.

◆ setMaxEtagMassDelta()

void setMaxEtagMassDelta ( const double value )

Sets MaxEtagMassDelta.

For a description of this function, see getMaxEtagMassDelta().

Parameters

value is the new maximum delta.

◆ setMaxEtVarMods()

void setMaxEtVarMods ( const int value )

Sets MaxEtVarMods.

For a description of this function, see getMaxEtVarMods()

Parameters

value is the new maximum in the range 0 to 31.

◆ setMaxIntactCrosslinkPeptides()

void setMaxIntactCrosslinkPeptides ( const int value )

Sets MaxIntactCrosslinkPeptides.

For a description of this function, see getMaxIntactCrosslinkPeptides() If the provided value is not valid, the existing value will be kept.

Parameters

value must be a number greater than zero

◆ setMaxNumPeptides()

void setMaxNumPeptides ( const int value )

Sets MaxNumPeptides.

For a description of this function, see getMaxNumPeptides().

Parameters

value is the new maximum value.

◆ setMaxPepModArrangements()

void setMaxPepModArrangements ( const int value )

Sets MaxPepModArrangements.

For a description of this function, see getMaxPepModArrangements() If the provided value is not valid, the existing value will be kept.

Parameters

value is the new maximum.

◆ setMaxPepNumModifiedSites()

void setMaxPepNumModifiedSites ( const int value )

Sets MaxPepNumModifiedSites.

For a description of this function, see getMaxPepNumModifiedSites(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new maximum number of modified sites.

◆ setMaxPepNumVarMods()

void setMaxPepNumVarMods ( const int value )

Sets MaxPepNumVarMods.

For a description of this function, see getMaxPepNumVarMods(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new maximum number of modifications.

◆ setMaxQueries()

void setMaxQueries ( const int value )

Sets MaxQueries.

For a description of this function, see getMaxQueries(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new maximum number of queries.

◆ setMaxSearchesPerUser()

void setMaxSearchesPerUser ( const int value )

Sets MaxSearchesPerUser.

For a description of this function, see getMaxSearchesPerUser(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the maximum value.

◆ setMaxSequenceLen()

void setMaxSequenceLen ( const int value )

Sets MaxSequenceLen.

For a description of this function, see getMaxSequenceLen(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new maximum length.

◆ setMaxVarMods()

void setMaxVarMods ( const int value )

Sets MaxVarMods.

For a description of this function, see getMaxVarMods().

Parameters

value is the new maximum in the range 0 to 32.

◆ setMinEtagMassDelta()

void setMinEtagMassDelta ( const double value )

Sets MinEtagMassDelta.

For a description of this function, see getMinEtagMassDelta().

Parameters

value is the new minimum delta.

◆ setMinPepLenInPepSummary()

void setMinPepLenInPepSummary ( const int value )

Sets MinPepLenInPepSummary.

For a description of this function, see getMinPepLenInPepSummary(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new minimum length.

◆ setMinPepLenInSearch()

void setMinPepLenInSearch ( const int value )

Sets MinPepLenInSearch.

For a description of this function, see getMinPepLenInSearch(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new minimum setting.

◆ setMonitorEmailCheckFreq()

void setMonitorEmailCheckFreq ( const int value )

Sets MonitorEmailCheckFreq.

For a description of this function, see getMonitorEmailCheckFreq(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new time period.

◆ setMonitorLogFile()

void setMonitorLogFile ( const char * str )

Sets MonitorLogFile.

For a description of this function, see getMonitorLogFile(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new name of the monitor log.

◆ setMonitorPidFile()

void setMonitorPidFile ( const char * str )

Sets MonitorPidFile.

For a description of this function, see getMonitorPidFile(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new name of the pid file.

◆ setMonitorTestTimeout()

void setMonitorTestTimeout ( const int value )

Sets MonitorTestTimeout.

For a description of this function, see getMonitorTestTimeout(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new timeout period.

◆ setMoveOldDbToOldDir()

void setMoveOldDbToOldDir ( const bool value )

Sets MoveOldDbToOldDir.

For a description of this function, see isMoveOldDbToOldDir().

Parameters

value is the new setting.

◆ setMudpit()

void setMudpit ( const int value )

Sets Mudpit.

For a description of this function, see getMudpit(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new setting.

◆ setMudpitSwitch()

void setMudpitSwitch ( const double value )

Sets MudpitSwitch.

For a description of this function, see getMudpitSwitch(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new q/e value used to determine which protein scoring method to use.

◆ setNoResultsScript()

void setNoResultsScript ( const char * str )

Sets NoResultsScript.

For a description of this function, see getNoResultsScript(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new name of the script.

◆ setNTIUserGroup()

void setNTIUserGroup ( const char * str )

Sets NTIUserGroup.

For a description of this function, see getNTIUserGroup(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new name of the web user group.

◆ setNTMonitorGroup()

void setNTMonitorGroup ( const char * str )

Sets NTMonitorGroup.

For a description of this function, see getNTMonitorGroup(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new name of the group used by `ms-monitor.exe`.

◆ setPepSearchTool()

void setPepSearchTool ( const std::string value )

Sets LibrarySearch.

For a description of this function, see getPepSearchTool() If the provided value is not valid, the existing value will be kept.

Parameters

value is the new setting

◆ setPercolator()

void setPercolator ( const bool value )

Sets Percolator.

For a description of this function, see isPercolator().

Parameters

value True if percolated results should be opened by default.

◆ setPercolatorExeFlags()

void setPercolatorExeFlags ( const char * value )

Sets PercolatorExeFlags.

For a description of this function, see getPercolatorExeFlags(). If the provided value is null, the existing value will be kept.

Parameters

value is the new flags.

◆ setPercolatorFeatures()

void setPercolatorFeatures ( std::string value )

Sets PercolatorFeatures.

For a description of this function, see getPercolatorFeatures(). If the provided value is empty, the existing value will be kept.

Parameters

value is the new list of features.

◆ setPercolatorMinQueries()

void setPercolatorMinQueries ( const int value )

Sets PercolatorMinQueries.

For a description of this function, see getPercolatorMinQueries(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new minimum number of queries.

◆ setPercolatorMinSequences()

void setPercolatorMinSequences ( const int value )

Sets PercolatorMinSequences.

For a description of this function, see getPercolatorMinSequences(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new minimum number of sequences.

◆ setPercolatorTargetRankRelativeThreshold()

void setPercolatorTargetRankRelativeThreshold ( const double threshold )

Sets PercolatorTargetRankRelativeThreshold.

For a description of this function, see getPercolatorTargetRankScoreThreshold(). If the provided value is not valid, the existing value will be kept.

Parameters

threshold is the minimum relative score difference with rank 1 match.

◆ setPercolatorTargetRankScoreThreshold()

void setPercolatorTargetRankScoreThreshold ( const int threshold )

Sets PercolatorTargetRankScoreThreshold.

For a description of this function, see getPercolatorTargetRankScoreThreshold(). If the provided value is not valid, the existing value will be kept.

Parameters

threshold is the minimum score to include a match in the pip file.

◆ setPercolatorUseProteins()

void setPercolatorUseProteins ( const bool value )

Sets PercolatorUseProteins.

For a description of this function, see isPercolatorUseProteins().

Parameters

value is the new flag.

◆ setPercolatorUseRT()

void setPercolatorUseRT ( const bool value )

Sets PercolatorUseRT.

For a description of this function, see isPercolatorUseRT().

Parameters

value is the new flag.

◆ setPreceedingComments()

void setPreceedingComments ( const std::string & comments )

inherited

Sets any comments preceeding the section.

Sections in the mascot.dat file may have comments preceeding them. In most cases, these comments need to stay 'attached' to the section.

Multiple line comments are supported by having a single string with newline characters

See also: getPreceedingComments()

Parameters

comments any comments preceeding the section

◆ setPrecursorCutOutLowerLimit()

void setPrecursorCutOutLowerLimit ( const double value )

Sets the first PrecursorCutOut.

For a description of this function, see getPrecursorCutOutLowerLimit().

Parameters

value is the new lower limit.

◆ setPrecursorCutOutUpperLimit()

void setPrecursorCutOutUpperLimit ( const double value )

Sets the second PrecursorCutOut.

For a description of this function, see getPrecursorCutOutUpperLimit().

Parameters

value is the new upper limit.

◆ setPropertyName()

void setPropertyName	(	const int	index,
		const char *	name
	)

inherited

Changes name of the property with the given index.

Parameters

index	property number from 0 to (getNumberOfProperties()-1).
name	new name to be given to the property.

◆ setPropValBoolByName()

void setPropValBoolByName	(	const char *	name,
		const bool	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a boolean value of the first entry with the given name or creates a new property if it is not found.

A new value will be converted into 1 (for TRUE) or 0 (for FALSE) character.

Parameters

name	a name of the property to find or add.
value	a new boolean value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValCharByName()

void setPropValCharByName	(	const char *	name,
		const char	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a single character value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new single character value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValFloatByName()

void setPropValFloatByName	(	const char *	name,
		const double	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes an floating point value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new floating point value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValInt64ByName()

void setPropValInt64ByName	(	const char *	name,
		const INT64	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a long 64-bit integer value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new long 64-bit integer value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValIntByName()

void setPropValIntByName	(	const char *	name,
		const int	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes an integer value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new integer value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValStringByName()

void setPropValStringByName	(	const char *	name,
		const char *	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a string value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new string value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValStringByNumber()

void setPropValStringByNumber	(	const int	index,
		const char *	str
	)

inherited

Changes an string value of an existing property with the given index.

Parameters

index	an index of an existing property.
str	String value for the property.

◆ setProteinFamilySwitch()

void setProteinFamilySwitch ( const int value )

Sets ProteinFamilySwitch.

For a description of this function, see getProteinFamilySwitch(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new minimum number of spectra.

◆ setProteinsInResultsFile()

void setProteinsInResultsFile ( const int value )

Sets ProteinsInResultsFile.

For a description of this function, see getProteinsInResultsFile(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new setting.

◆ setProxyPassword()

void setProxyPassword ( const char * str )

Sets proxy_password.

For a description of this function, see getProxyPassword(). If the provided value is null, the existing value will be kept.

Parameters

str	is the new password.

◆ setProxyServer()

void setProxyServer ( const char * str )

Sets proxy_server.

For a description of this function, see getProxyServer. If the provided value is null, the existing value will be kept.

Parameters

str	is the new proxy server address/name.

◆ setProxyType()

void setProxyType ( const std::string & value )

Sets ProxyType.

For a description of this function, see getProxyServer.

Parameters

value A case-insensitive string matching one of the ms_connection_settings::PROXY_TYPE values. If value matches none of them, proxy type is set to Auto.

◆ setProxyUsername()

void setProxyUsername ( const char * str )

Sets proxy_username.

For a description of this function, see getProxyUsername(). If the provided value is null, the existing value will be kept.

Parameters

str	is the new proxy user name.

◆ setRemoveOldIndexFiles()

void setRemoveOldIndexFiles ( const bool value )

Sets RemoveOldIndexFiles.

For a description of this function, see isRemoveOldIndexFiles().

Parameters

value is the new setting.

◆ setReportBuilderColumnArrangement()

void setReportBuilderColumnArrangement	(	const int	index,
		const std::string	str
	)

Sets ReportBuilderColumnArrangement.

Set the column arrangement string at index to the given value. If str is the empty string, the column arrangement at that index will be deleted.

For details, see getReportBuilderColumnArrangement(). If the provided index or value is not valid, the list will be unchanged.

Parameters

index	A value between 1 and getMaxNumOfReportBuilderColumnArrangements, inclusive.
str	Name, followed by colon, followed by comma-separated column arrangement string, e.g. `"Mini:family,member,db,acc,score,mass,desc"`

◆ setReportNumberChoice()

void setReportNumberChoice	(	const int	index,
		const int	value
	)

Sets an element of the ReportNumberChoices list by its index.

See getReportNumberChoice() for more information. If the provided index or value is not valid, the existing value will be kept.

Parameters

index	is the index of the item to set. index must be between 0 and getNumberOfReportNumberChoices()-1.
value	is the value it should be set to.

◆ setRequireBoldRed()

void setRequireBoldRed ( const bool value )

Sets RequireBoldRed.

For a description of this function, see isRequireBoldRed().

Parameters

value specifies if proteins need a bold red peptide.

◆ setResfileCache()

void setResfileCache ( const char * value )

Sets ResfileCache.

For a description of this function, see getResfileCache(). If the provided value is null, the existing value will be kept.

Parameters

value a comma separated list of scripts that should specify ms_mascotresfilebase::RESFILE_USE_CACHE when creating a ms_mascotresfilebase object.

◆ setResultsCache()

void setResultsCache ( const char * value )

Sets ResultsCache.

For a description of this function, see getResultsCache(). If the provided value is null, the existing value will be kept.

Parameters

value a comma separated list of scripts that should specify ms_peptidesummary::MSPEPSUM_USE_CACHE when creating a ms_peptidesummary object.

◆ setResultsFileFormatVersion()

void setResultsFileFormatVersion ( const char * value )

Sets ResultsFileFormatVersion.

For a description of this function, see getResultsFileFormatVersion(). If the provided value is null, the existing value will be kept.

Parameters

value is the new version string.

◆ setResultsFullURL()

void setResultsFullURL ( const char * str )

Sets ResultsFullURL.

For a description of this function, see getResultsFullURL(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new URL.

◆ setResultsFullURL_2()

void setResultsFullURL_2 ( std::string value )

Sets ResultsFullURL_2.

For a description of this function, see getResultsFullURL_2(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new perl script.

◆ setResultsPerlScript()

void setResultsPerlScript ( const char * str )

Sets ResultsPerlScript.

For a description of this function, see getResultsPerlScript(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new name of the script.

◆ setResultsPerlScript_2()

void setResultsPerlScript_2 ( std::string value )

Sets ResultsPerlScript_2.

For a description of this function, see getResultsPerlScript_2(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new perl script.

◆ setReviewColDisplay()

void setReviewColDisplay	(	const MS_REVIEW_COL	index,
		const bool	value
	)

Sets ReviewColDisplay.

End users can specify the display states in mascot.dat to suit their requirements, for example if they want to hide some columns by default.

See also: getReviewColDisplay(). If the provided index is not valid, the list will be unchanged.

Parameters

index	is a value from the MS_REVIEW_COL enumeration.
value	is the new display state to set.

◆ setReviewColWidth()

void setReviewColWidth	(	const MS_REVIEW_COL	index,
		const int	value
	)

Sets ReviewColWidths.

End users can specify the widths in mascot.dat to suit their requirements, for example if they use long titles.

See also: getReviewColWidth(). If the provided index or value is not valid, the list will be unchanged.

Parameters

index	is a value from the MS_REVIEW_COL enumeration.
value	is the new width to set.

◆ setSaveEveryLastQueryAsc()

void setSaveEveryLastQueryAsc ( const bool flag )

Sets SaveEveryLastQueryAsc to 1 or 0.

For a description of this function, see isSaveEveryLastQueryAsc().

Parameters

flag	is a boolean flag that corresponds to 1 (true) or 0 (false).

◆ setSaveLastQueryAsc()

void setSaveLastQueryAsc ( const bool flag )

Sets SaveLastQueryAsc to 1 or 0.

For a description of this function, see isSaveLastQueryAsc().

Parameters

flag	is a boolean flag that corresponds to 1 (true) or 0 (false).

◆ setSearchLogFile()

void setSearchLogFile ( const char * str )

Sets SearchLogFile.

For a description of this function, see getSearchLogFile(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new name of the search log.

◆ setSearchSubmitAcceptedFileTypes()

void setSearchSubmitAcceptedFileTypes ( const std::string value )

Sets the accepted input file types in the Mascot search form.

For a description of this function, see getSearchSubmitAcceptedFileTypes(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new setting

◆ setSearchSubmitDefaultPeptideCharge()

void setSearchSubmitDefaultPeptideCharge ( const std::string value )

Sets the default peptide charge when not specified in the input file.

For a description of this function, see getSearchSubmitDefaultPeptideCharge(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new setting

◆ setSearchSubmitMode()

void setSearchSubmitMode ( const std::string value )

Sets the Mascot search submission mode.

For a description of this function, see getSearchSubmitMode(). If the provided value is not valid, the existing value will be kept.

Parameters

value must be either "asynchronous" or "direct".

◆ setSearchSubmitOutputFormat()

void setSearchSubmitOutputFormat ( const std::string value )

Sets the Mascot search submission output format.

For a description of this function, see getSearchSubmitOutputFormat(). If the provided value is not valid, the existing value will be kept.

Parameters

value must be either "dat28" or "msr" or "dat28,msr".

◆ setSelectSwitch()

void setSelectSwitch ( const int value )

Sets SelectSwitch.

For a description of this function, see getSelectSwitch(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new minimum number of queries for a select summary.

◆ setSendmailPath()

void setSendmailPath ( const char * str )

Sets sendmailPath.

For a description of this function, see getSendmailPath(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new name of the sendmail program.

◆ setShowAllFromErrorTolerant()

void setShowAllFromErrorTolerant ( const bool value )

Sets ShowAllFromErrorTolerant.

For a description of this function, see isShowAllFromErrorTolerant().

Parameters

value specifies if all matches should be displayed in manual error tolerant searches.

◆ setShowSubsets() [1/2]

void setShowSubsets ( const bool value )

Sets ShowSubSets.

Deprecated:: See setShowSubsets(const double).

Simply calls setShowSubsets(const double) with a value of 0.0 or 1.0.

Parameters

value if set to true, 1.0 is used, otherwise 0.0 is used

◆ setShowSubsets() [2/2]

void setShowSubsets ( const double value )

Sets ShowSubSets.

See getShowSubsets().

Parameters

value is the fractional score required for a protein to be counted as a subset. Its score must be greater than or equal to main_protein_score * (1-getShowSubsets()). A value between 0 and 1 (inclusive) is required and the default value is 0.

◆ setSigThreshold()

void setSigThreshold ( const double value )

Set the SigThreshold.

For a description of this function, see getSigThreshold(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new default threshold value.

◆ setSiteAnalysisMD10Prob()

void setSiteAnalysisMD10Prob ( const double value )

Set the SiteAnalysisMD10Prob.

For a description of this function, see getSiteAnalysisMD10Prob(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new default MD10Prob value.

◆ setSortUnassigned()

void setSortUnassigned ( const std::string value )

Sets SortUnassigned.

For a description of this function, see getSortUnassigned(). If the provided value is not valid, the existing value will be kept.

Parameters

value

should be one of:

scoredown - descending score
queryup - query order
intdown - intensity order

◆ setSpectraPerLibraryBlock()

void setSpectraPerLibraryBlock ( const int value )

Sets the number of spectra in a spectral library block.

For a description of this function, see getSpectraPerLibraryBlock() If the provided value is not valid, the existing value will be kept.

Parameters

value must be a number greater than zero

◆ setSpectrumViewerColourSchemeString()

void setSpectrumViewerColourSchemeString	(	const std::string &	name,
		const std::string &	str,
		bool	doCheck = `true`
	)

Sets SpectrumViewerColourScheme.

If str is the empty string, the named colour scheme will be deleted.

For details, see getSpectrumViewerColourSchemeString(). If the provided name or value is not valid, the list will be unchanged.

Parameters

name	Colour scheme name; the defined names are returned by getSpectrumViewerColourSchemeNames().
str	Colour scheme specification as defined in getSpectrumViewerColourSchemeString(), or the empty string.
doCheck	Whether the method should check if the colour scheme is of the correct format, default to true.

◆ setSpectrumViewerDefaultColourSchemeName()

void setSpectrumViewerDefaultColourSchemeName ( const std::string & name )

Sets the default colour scheme name (SpectrumViewerDefaultColourScheme).

For a description of this function, see getSpectrumViewerDefaultColourSchemeName(). If the provided default name is not in the list of current names, the value will not be changed.

Parameters

name	Colour scheme name, typically one of getSpectrumViewerColourSchemeNames().

◆ setSplitDataFileSize()

void setSplitDataFileSize ( const int value )

Sets SplitDataFileSize.

For a description of this function, see getSplitDataFileSize(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new file size to split at.

◆ setSplitNumberOfQueries()

void setSplitNumberOfQueries ( const int value )

Sets SplitNumberOfQueries.

For a description of this function, see getSplitNumberOfQueries(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new number of queries.

◆ setStoreModPermutations()

void setStoreModPermutations ( const bool value )

Sets StoreModPermutations.

For a description of this function, see isStoreModPermutations().

Parameters

value is the new setting.

◆ setSVGSpectrumSwitch()

void setSVGSpectrumSwitch ( const int value )

Sets SVGSpectrumSwitch.

For a description of this function, see getSVGSpectrumSwitch(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new setting.

◆ setTargetFDRPercentage()

void setTargetFDRPercentage	(	const int	index,
		const double	value,
		const bool	makeDefault = `false`
	)

Sets an element of the TargetFDRPercentages list by its index.

See getTargetFDRPercentage() for more information. If the provided index or value is not valid, the list will be unchanged.

Parameters

index	is the index of the item to set. index must be between 0 and getNumberOfTargetFDRPercentages()-1.
value	is the value it should be set to.
makeDefault	controls whether the new element should be made the default item in the list.

◆ setTaxBrowserUrl()

void setTaxBrowserUrl ( const std::string value )

Sets TaxBrowserURL.

For a description of this function, see getTaxBrowserUrl().

Parameters

value is the URL.

◆ setTestDirectory()

void setTestDirectory ( const char * str )

Sets TestDirectory.

For a description of this function, see getTestDirectory(). If the provided value is not valid, the existing value will be kept.

Parameters

str	is the new path.

◆ setUniqueJobStartNumber()

void setUniqueJobStartNumber ( const int value )

Sets UniqueJobStartNumber.

For a description of this function, see getUniqueJobStartNumber(). If the provided value is negative, the existing value will be kept.

Parameters

value is the new job start number.

◆ setUnixDirPerm()

void setUnixDirPerm ( const int value )

Sets UnixDirPerm.

For a description of this function, see getUnixDirPerm(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new permissions.

◆ setUnixWebUserGroup()

void setUnixWebUserGroup ( const int value )

Sets UnixWebUserGroup.

For a description of this function, see getUnixWebUserGroup().

Parameters

value is the new setting for the web user group.

◆ setUseHTTPProxyForFTP()

void setUseHTTPProxyForFTP ( const bool value )

Sets UseHTTPProxyForFTP.

For a description of this function, see isUseHTTPProxyForFTP.

Parameters

value True if FTP requests should use HTTP proxy settings; false otherwise.

◆ setUseHTTPProxyForHTTPS()

void setUseHTTPProxyForHTTPS ( const bool value )

Sets UseHTTPProxyForHTTPS.

For a description of this function, see isUseHTTPProxyForHTTPS.

Parameters

value True if HTTPS requests should use HTTP proxy settings; false otherwise.

◆ setVmemory()

void setVmemory ( const INT64 value )

Sets Vmemory.

For a description of this function, see getVmemory(). If the provided value is not valid, the existing value will be kept.

Parameters

value is the new value.

◆ uncommentProp()

bool uncommentProp	(	const int	index,
		const char *	delimeter = `0`
	)

inherited

Uncomments a line in the configuration file.

Removes a # and any white space. Finds the delimeter and extracts the property name and value.

Parameters

index	must be a value between 0 and getNumberOfProperties().
delimeter	will often be a space. If not supplied, the default delimeter will be used.

Returns: true if the delimiter was found, false otherwise

The documentation for this class was generated from the following files:

ms_mascotoptions.hpp
ms_mascotoptions.cpp

Public Types

Public Member Functions

Detailed Description

Member Enumeration Documentation

◆ DECOY_ALGORITHM

◆ EXEC_AFTER_SEARCH

◆ MS_REVIEW_COL

◆ NUMERICAL_VALUE_STORAGE

◆ PERC_EXE_RT

Constructor & Destructor Documentation

◆ ms_mascotoptions() [1/2]

◆ ms_mascotoptions() [2/2]

Member Function Documentation

◆ appendIgnoreDupeAccession()

◆ appendProperty()

◆ appendReportNumberChoice()

◆ appendTargetFDRPercentage()

◆ appendText()

◆ clearIgnoreDupeAccessions()

◆ clearReportNumberChoices()

◆ clearTargetFDRPercentages()

◆ delProp()

◆ delPropStart()

◆ findProperty()

◆ findPropertyBeginning()

◆ getCacheDirectory()

◆ getCentroidWidth()

◆ getCentroidWidthCount()

◆ getCompressToolAA()

◆ getCompressToolCommandLineFasta()

◆ getCompressToolCommandLineLibrary()

◆ getCompressToolNA()

◆ getCompressToolSL()

◆ getCrawlerNumPeaksPer100Da()

◆ getCreatePipThreadBlockSize()

◆ getCreatePipThreads()

◆ getDechargeFragmentPeaks()

◆ getDecoyTypeNoEnzyme()

◆ getDecoyTypeSpecific()

◆ getDefaultDelimiter()

◆ getDelimiterByNumber()

◆ getDisplayNonSignificantMatches()

◆ getEmailFromTextName()

◆ getEmailFromUser()

◆ getEmailPassword()

◆ getEmailProfile()

◆ getEmailService()

◆ getEmailTimeOutPeriod()

◆ getErrMessageEmailTo()

◆ getErrorLogFile()

◆ getErrTolMaxAccessions()

◆ getExecAfterSearch()

◆ getFeatureTableLength()

◆ getFeatureTableMinScore()

◆ getFormVersion()

◆ getGetSeqJobIdFile()

◆ getICATFilter()

◆ getICATHeavy()

◆ getICATLight()

◆ getICATQuantitationMethod()

◆ getIgnoreDupeAccession()

◆ getIgnoreIonsScoreBelow()

◆ getIntensitySigFigs()

◆ getInterFileBasePath()

◆ getInterFileRelPath()

◆ getIonsDecimalPlaces()

◆ getLastQueryAscFile()

◆ getLogoImageFile()

◆ getMailTempFile()

◆ getMailTransport()

◆ getMascNodeCtrlFile()

◆ getMascotCmdLine()

◆ getMascotControlFile()

◆ getMascotFileProcessingThreads()

◆ getMascotJobIdFile()

◆ getMascotMessage()

◆ getMassDecimalPlaces()

◆ getMaxConcurrentSearches()

◆ getMaxDatabases()

◆ getMaxDescriptionLen()