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Public Types | Public Member Functions

ms_mascotoptions Class Reference
[Mascot configuration files module]

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

#include <ms_mascotoptions.hpp>

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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.

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enum  EXEC_AFTER_SEARCH { MAX_EXEC_AFTER_SEARCH = 10 }
 

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

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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().

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enum  NUMERICAL_VALUE_STORAGE { MASS_DECIMAL_PLACES = 6 }
 

Definitions for storage of numerical values in files.

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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().

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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 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 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_mascotoptions *right)
 Can be used to create a copy of another object.
void defaultValues ()
 Initialises the instance with default values.
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 getDecoyTypeNoEnzyme () const
 Returns the value of DecoyTypeNoEnzyme.
int getDecoyTypeSpecific () const
 Returns the value of DecoyTypeSpecific.
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.
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 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 getMaxPepNumModifiableSites () const
 Returns value of the MaxPepNumModifiableSites.
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 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 getPreceedingComments () const
 Returns any comments preceeding the section.
double getPrecursorCutOutLowerLimit () const
 Gets the first PrecursorCutOut.
double getPrecursorCutOutUpperLimit () const
 Gets the second PrecursorCutOut.
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.
int getSelectSwitch () const
 Returns the value of SelectSwitch.
std::string getSendmailPath () const
 Returns the value of sendmailPath.
int getSeparateLockMem () const
 Returns the value of SeparateLockMem.
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 isAutoSelectCharge () const
 Returns the value of AutoSelectCharge.
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 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.
ms_mascotoptionsoperator= (const ms_mascotoptions &right)
 C++ style assignment operator.
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 setDecoyTypeNoEnzyme (const int value)
 Sets DecoyTypeNoEnzyme.
void setDecoyTypeSpecific (const int value)
 Sets DecoyTypeSpecific.
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 setMascotJobIdFile (const char *str)
 Sets MascotJobIdFile.
void setMascotMessage (const char *str)
 Sets MascotMessage.
void setMassDecimalPlaces (const int value)
 Sets MassDecimalPlaces.
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 setMaxNumPeptides (const int value)
 Sets MaxNumPeptides.
void setMaxPepModArrangements (const int value)
 Sets MaxPepModArrangements.
void setMaxPepNumModifiableSites (const int value)
 Sets MaxPepNumModifiableSites.
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 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 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 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 setSeparateLockMem (const int value)
 Sets SeparateLockMem.
void setShowAllFromErrorTolerant (const bool value)
 Sets ShowAllFromErrorTolerant.
void setShowSubsets (const double value)
 Sets ShowSubSets.
void setShowSubsets (const bool 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)
 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 setVmemory (const INT64 value)
 Sets Vmemory.

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:

More functionality is described in the documentation for ms_customproperty.

Examples:

config_mascotdat.cpp, and resfile_summary.cpp.


Member Enumeration Documentation

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 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)

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

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

Enumerator:
MAX_EXEC_AFTER_SEARCH 

The maximum value for setExecAfterSearch () abd getExecAfterSearch()

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

See Using enumerated values 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.

Definitions for storage of numerical values in files.

Enumerator:
MASS_DECIMAL_PLACES 

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

Definitions for retention time override when calling getPercolatorExeFlags().

See Using enumerated values 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

Default constructor.

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

ms_mascotoptions ( const ms_mascotoptions src )

Copying constructor.

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

Parameters:
srcreference to a valid ms_mascotoptions object

Member Function Documentation

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:
valueis the name of the database to add to the list.
void appendReportNumberChoice ( const int  value )

Append a value to the ReportNumberChoices list.

See getReportNumberChoice() for more information.

Parameters:
valueis the value to be appended to the list.
void appendTargetFDRPercentage ( const double  value,
const bool  makeDefault = false 
)

Append a value to the TargetFDRPercentages list.

See getTargetFDRPercentage() for more information.

Parameters:
valueis the value to be appended to the list.
makeDefaultcontrols whether the new element should be made the default item in the list.
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()
void clearReportNumberChoices (  )

Deletes all ReportNumberChoices values from the list.

See getNumberOfReportNumberChoices().

void clearTargetFDRPercentages (  )

Deletes all TargetFDRPercentages values from the list.

See getNumberOfTargetFDRPercentages().

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_mascotresfile::getCacheDirectory().

ParameterCacheDirectory
Permitted valuesAny 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.
double getCentroidWidth (  ) const

Returns the value of CentroidWidth.

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

ParameterCentroidWidth
Permitted valuesFloating point > 0 and less than 10.0
Default
(if no parameter in mascot.dat)
0.25
Value in mascot.dat0.25
Returns:
the width in Da.
int getCentroidWidthCount (  ) const

Returns the value of CentroidWidthCount.

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

ParameterCentroidWidthCount
Permitted valuesPositive integer > 0
Default
(if no parameter in mascot.dat)
1000
Value in mascot.dat1000
Returns:
the peak count threshold.
std::string getCompressToolAA (  ) const

Returns the value of CompressTool_AA.

Not implemented (at version 2.6)

See also:
getCompressToolSL(), getCompressToolNA() and getCompressToolCommandLineFasta()
ParameterCompressTool_AA
Permitted valuesAny 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
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:
dbTypeDatabase type, AA or NA
dbnameName of the database
dbpathFull path to the database file
Returns:
complete compress tool command line for a fasta
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:
logfilepathfull path to the log file that the tool will create. The contents of this file are inserted into the .stats file.
inputfilefull path to the input file. Typically an msp file, but could be any format supported by the tool.
outputdirectorypath 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
std::string getCompressToolNA (  ) const

Returns the value of CompressTool_NA.

Not implemented (at version 2.6)

See also:
getCompressToolSL() and getCompressToolAA() and getCompressToolCommandLineFasta()
ParameterCompressTool_NA
Permitted valuesAny 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
std::string getCompressToolSL (  ) const

Returns the value of CompressTool_NA.

See also:
getCompressToolAA(), getCompressToolNA() and getCompressToolCommandLineLibrary
ParameterCompressTool_SL
Permitted valuesAny 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
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.

ParameterCrawlerNumPeaksPer100Da
Permitted valuesAny integer > 0.
Default
(if no parameter in mascot.dat)
100
Value in mascot.dat100
Returns:
the number of peaks to choose from each 100 Da window
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 in Mascot 2.4

Only the following values are implemented in Mascot 2.4:

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().

ParameterDecoyTypeNoEnzyme
Permitted values1, 2, 3, 4, 5, 6, 7, 8
Default
(if no parameter in mascot.dat)
3
Value in mascot.dat3
Returns:
the decoy search type for a no-enzyme search.
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 in Mascot 2.4:

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().

ParameterDecoyTypeSpecific
Permitted values1, 2, 3, 4, 5, 6, 7, 8
Default
(if no parameter in mascot.dat)
1
Value in mascot.dat1
Returns:
the decoy search type for an ordinary search.
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.

ParameterDisplayNonSignificantMatches
Permitted values0, 1, 2
Default
(if no parameter in mascot.dat)
1
Value in mascot.dat0
Returns:
form control type for filtering out non-significant matches.
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().
ParameterEmailFromTextName
Permitted valuesAny text string
Default
(if no parameter in mascot.dat)
[empty]
Value in mascot.datMascot
Returns:
the name from which messages are sent.
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().
ParameterEmailFromUser
Permitted valuesAny non empty text string
Default
(if no parameter in mascot.dat)
[empty]
Value in mascot.datyour_id
Returns:
the email address from which messages are sent.
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().
ParameterEmailPassword
Permitted valuesAny text string
Default
(if no parameter in mascot.dat)
[empty]
Value in mascot.datyour_password
Returns:
the password for the email service.
std::string getEmailProfile (  ) const

Returns the value of EmailProfile.

EmailProfile is the MAPI profile name.

See also:
getMailTransport(), isEmailUsersEnabled(), isEmailErrorsEnabled().
ParameterEmailProfile
Permitted valuesAny non empty text string
Default
(if no parameter in mascot.dat)
[empty
Value in mascot.datyour_profile
Returns:
the name for the MAPI email profile.
std::string getEmailService (  ) const

Returns the value of EmailService.

EmailService is the service name (CMC only).

See also:
getMailTransport(), isEmailUsersEnabled(), isEmailErrorsEnabled().
ParameterEmailService
Permitted valuesAny text string
Default
(if no parameter in mascot.dat)
[empty]
Value in mascot.datyour_service
Returns:
the name of the CMC email service.
int getEmailTimeOutPeriod (  ) const

Returns the value of EmailTimeOutPeriod.

See isEmailUsersEnabled() for information on this parameter.

ParameterEmailTimeOutPeriod
Permitted valuesAny positive integer
Default
(if no parameter in mascot.dat)
120
Value in mascot.dat120
Returns:
The timeout period in seconds.
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().
ParameterErrMessageEmailTo
Permitted valuesAny text string
Default
(if no parameter in mascot.dat)
[empty]
Value in mascot.datadministrator@your.domain
Returns:
the email address to which messages are sent.
std::string getErrorLogFile (  ) const

Returns the value of ErrorLogFile.

This defines where error messages should be stored.

ParameterErrorLogFile
Permitted valuesAny 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.
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

ParameterErrTolMaxAccessions
Permitted valuesAny integer >= 0
Default
(if no parameter in mascot.dat)
0
Value in mascot.dat[not defined]
Returns:
the maximum number of accessions.
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.

ParameterExecAfterSearch_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_1 waitfor:0;logging:0, Creating percolator input, ../bin/ms-createpip.exe -i %resultfilepath -o %percolator_pip
ExecAfterSearch_2 waitfor:1;logging:0, Percolating, ../bin/percolator.exe $PercolatorExeFlags

The following flags may be specified:

flagAcceptable 'num'Description
waitfor0 or 1..10This command should not be run until the command specified by the waitfor has finished. A value of 0 indicates 'don't wait'.
logging0..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
percolator0 or 1This command will only be run if the search meets the criteria to percolate results. See Using Percolator scores
cgienv0 or 1Default 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.

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).

TagReplaced with
%resultfilepathThe passed szResultsFilePath
%resultfilenameThe filename part of the passed szResultsFilePath
%percolator_pipThe input file from ms_mascotresfile::staticGetPercolatorFileNames()
%percolator_decoy_popThe decoy output file from ms_mascotresfile::staticGetPercolatorFileNames()
%percolator_target_popThe target output file from ms_mascotresfile::staticGetPercolatorFileNames()
%session_idIs replaced by the passed sessionID parameter
%task_idIs replaced by the passed taskID parameter
$PercolatorExeFlagsThis 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:
szResultsFilePathis the path to the results file.
commandsis 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 classes in Perl, Java, Python and C#.
titlesis a vector containing the text to be output will the process is running. For example: "Creating XML output....". See Using STL classes in Perl, Java, Python and C#.
waitforis 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 classes in Perl, Java, Python and C#.
loggingis 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 classes in Perl, Java, Python and C#.
additionalFlagsis a vector of strings containing any flags apart from the waitfor or logging flag. See Using STL classes in Perl, Java, Python and C#.
sessionIDis the session identifier for the search. See ms_session::ms_session. This value is passed to the search engine using the --sessionID parameter.
taskIDis 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.
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.

ParameterFeatureTableLength
Permitted valuesAny 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.
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.

ParameterFeatureTableMinScore
Permitted valuesFloating 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.
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.

ParameterFormVersion
Permitted valuesAny non empty text string
Default
(if no parameter in mascot.dat)
1.01
Value in mascot.dat1.01
Returns:
the form version.
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.

ParameterGetSeqJobIdFile
Permitted valuesAny 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.
std::string getICATFilter (  ) const

Returns the value of ICATFilter.

Parameter ICATFilter gives a residue that ICAT modifications apply to.

ParameterICATFilter
Permitted valuesAny 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.
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.

ParameterICATHeavy
Permitted valuesAny 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.
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.

ParameterICATLight
Permitted valuesAny 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.
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.

ParameterICATQuantitationMethod
Permitted valuesAny non empty text string
Default
(if no parameter in mascot.dat)
ICAT
Value in mascot.datICAT ABI Cleavable [MD]
Returns:
the name of quantitation method to use.
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.

ParameterIgnoreDupeAccessions
Permitted valuestext strings delimted by tab, space and comma
Default
(if no parameter in mascot.dat)
EST_others
Value in mascot.datEST_others
Parameters:
indexis a 0 based index into the list of databases.
Returns:
the database name.
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.

ParameterIgnoreIonsScoreBelow
Permitted valuesAny floating point >= 0.0
Default
(if no parameter in mascot.dat)
0.0
Value in mascot.dat0.0
Returns:
the minimum ions score to be considered when generating search reports.
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.

ParameterIntensitySigFigs
Permitted values1 to 20
Default
(if no parameter in mascot.dat)
2
Value in mascot.dat4
Returns:
the number of significant figures to be used when saving values.
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
ParameterInterFileBasePath
Permitted valuesAny 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.
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.

ParameterInterFileRelPath
Permitted valuesAny 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.
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.

ParameterIonsDecimalPlaces
Permitted values1 to 20
Default
(if no parameter in mascot.dat)
2
Value in mascot.dat4
Returns:
the number of decimal places to be displayed.
std::string getLastQueryAscFile (  ) const

Returns the value of LastQueryAscFile.

See isSaveLastQueryAsc() for a detailed explanation.

ParameterLastQueryAscFile
Permitted valuesAny 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.
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.

ParameterLogoImageFile
Permitted valuesAny 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.
std::string getMailTempFile (  ) const

Returns the value of MailTempFile.

See isEmailUsersEnabled() for information on this parameter.

ParameterMailTempFile
Permitted valuesAny 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.
int getMailTransport (  ) const

Returns the value of MailTransport.

MailTransport should be set to one of the following values:

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().
ParameterMailTransport
Permitted values0 to 3 inclusive
Default
(if no parameter in mascot.dat)
2
Value in mascot.dat0
Returns:
a code defining the mail transport to be used.
std::string getMascNodeCtrlFile (  ) const

Returns the value of MascotNodeControlFile.

ParameterMascotNodeControlFile
Permitted valuesAny 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.
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.

ParameterMascotCmdLine
Permitted valuesAny 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.
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.

ParameterMascotControlFile
Permitted valuesAny 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.
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.

ParameterMascotJobIdFile
Permitted valuesAny 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.
std::string getMascotMessage (  ) const

Returns the value of MascotMessage.

Displays the specified message while a search is running.

ParameterMascotMessage
Permitted valuesAny 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.
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.

ParameterMassDecimalPlaces
Permitted values1 to 20
Default
(if no parameter in mascot.dat)
2
Value in mascot.dat4
Returns:
the number of decimal places to be displayed.
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.

See also ms_security_tasks::SECTASK_MAXCONCURRENTSEARCHES.

ParameterMaxConcurrentSearches
Permitted valuesAny integer > 0
Default
(if no parameter in mascot.dat)
10
Value in mascot.dat10
Returns:
the maximum number of concurrent searches.
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.

ParameterMaxDatabases
Permitted valuesAny integer > 64
Default
(if no parameter in mascot.dat)
64
Value in mascot.dat256
Returns:
an integer value specifying the limit.
int getMaxDescriptionLen (  ) const

Returns the value of MaxDescriptionLen.

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

ParameterMaxDescriptionLen
Permitted valuesAny positive integer
Default
(if no parameter in mascot.dat)
100
Value in mascot.dat250
Returns:
the maximum length.
double getMaxEtagMassDelta (  ) const

Returns the value of MaxEtagMassDelta.

See also:
getMinEtagMassDelta()
ParameterMaxEtagMassDelta
Permitted valuesAny floating point number
Default
(if no parameter in mascot.dat)
1770.0
Value in mascot.dat1770.0
Returns:
The maximum delta to be considered for an error tolerant match.
int getMaxEtVarMods (  ) const

Returns the value of MaxEtVarMods.

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

ParameterMaxEtVarMods
Permitted valuesAny 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.
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.
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.

ParameterMaxNumPeptides
Permitted valuesAny 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.
int getMaxPepModArrangements (  ) const

Returns the value of MaxPepModArrangements.

*** For future use only. Value currently ignored. ***

The maximum number of variable modification arrangements allowed for a single peptide. Arrangements are tested beginning with one modification, then two and so on up to however many modifications are applicable to the peptide. The number or modification permutations for some peptides can be very large. This value prevents the searches testing beyond the simpler and more probable arrangements.

A value of zero indicates no limit.

ParameterMaxModArrangements
Permitted valuesAny integer >= 0
Default
(if no parameter in mascot.dat)
256
Value in mascot.dat[not defined]
Returns:
the maximum number of variable modification arrangements allowed for a single peptide.
int getMaxPepNumModifiableSites (  ) const

Returns value of the MaxPepNumModifiableSites.

*** For future use only. Value currently ignored. ***

This parameter specifies the maximum number of sites that can be modified by variable modifications in a peptide.

A value of zero indicates no limit.

ParameterMaxPepNumModifiableSites
Permitted valuesAny non-negative integer
Default
(if no parameter in mascot.dat)
6
Value in mascot.dat[not defined]
Returns:
the maximum number of modifiable sites in a peptide
int getMaxPepNumVarMods (  ) const

Returns value of the MaxPepNumVarMods.

This parameter specifies the maximum number of variable modifications that can be used simultaneously in one peptide.

ParameterMaxPepNumVarMods
Permitted valuesAny non-negative integer
Default
(if no parameter in mascot.dat)
5
Value in mascot.dat5
Returns:
the maximum number of modifications in one peptide.
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.

ParameterMaxQueries
Permitted valuesInteger >= 10
Default
(if no parameter in mascot.dat)
10000
Value in mascot.dat1000000
Returns:
the maximum number of queries per search.
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.

ParameterMaxSearchesPerUser
Permitted valuesAny 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.
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).

ParameterMaxSequenceLen
Permitted valuesAny integer >= 100
Default
(if no parameter in mascot.dat)
50,000
Value in mascot.dat50,000
Returns:
the maximum sequence length.
int getMaxVarMods (  ) const

Returns the value of MaxVarMods.

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

ParameterMaxVarMods
Permitted valuesAny 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.
double getMinEtagMassDelta (  ) const

Returns the value of MinEtagMassDelta.

See also:
getMaxEtagMassDelta()
ParameterMinEtagMassDelta
Permitted valuesAny 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.
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.

ParameterMinPepLenInPepSummary
Permitted valuesInteger in range 1 to 9 inclusive
Default
(if no parameter in mascot.dat)
6
Value in mascot.dat7 (Was 5 in Mascot 2.3.02 and earlier)
Returns:
the minimum peptide length used to differentiate different proteins.
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.

ParameterMinPepLenInSearch
Permitted valuesAny non-negative integer
Default
(if no parameter in mascot.dat)
3
Value in mascot.dat5
Returns:
the minimum peptide length.
int getMonitorEmailCheckFreq (  ) const

Returns the value of MonitorEmailCheckFreq.

See isEmailUsersEnabled() for information on this parameter..

ParameterMonitorEmailCheckFreq
Permitted valuesAny positive integer
Default
(if no parameter in mascot.dat)
300
Value in mascot.dat300
Returns:
the frequency to check for sending emails in seconds.
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.

ParameterMonitorLogFile
Permitted valuesAny 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.
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.

ParameterMonitorPidFile
Permitted valuesAny 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
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.

ParameterMonitorTestTimeout
Permitted valuesAny positive integer
Default
(if no parameter in mascot.dat)
1200
Value in mascot.dat1200
Returns:
the timeout period in seconds.
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
ParameterMudpit
Permitted valuesAny integer
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
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.

ParameterMudpitSwitch
Permitted valuesAny floating point value > 0
Default
(if no parameter in mascot.dat)
0.001
Value in mascot.dat0.001
Returns:
The q/e value used to determine which protein scoring method to use.
std::string getNoResultsScript (  ) const

Returns the value of NoResultsScript.

See getResultsPerlScript() for more information.

ParameterNoResultsScript
Permitted valuesAny 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.
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"

ParameterNTIUserGroup
Permitted valuesAny non empty text string
Default
(if no parameter in mascot.dat)
Guests
Value in mascot.datUsers
Returns:
NTI user group
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.

ParameterNTMonitorGroup
Permitted valuesAny non empty text string
Default
(if no parameter in mascot.dat)
Administrators
Value in mascot.datAdministrators
Returns:
the name of the Administrators group.
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.

ParameterIgnoreDupeAccessions
Permitted valuestext strings delimted by tab, space and comma
Default
(if no parameter in mascot.dat)
EST_others
Value in mascot.datEST_others
Returns:
the number of items in the IgnoreDupeAccessions parameter.
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.

ParameterReportNumberChoices
Permitted valuesAny non empty text string
Default
(if no parameter in mascot.dat)
5,10,20,30,40,50
Value in mascot.datAUTO,5,10,20,30,50,100,200
Returns:
the number of integers in the list.
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.

ParameterTargetFDRPercentages
Permitted valuesAny non empty text string
Default
(if no parameter in mascot.dat)
0.1, 0.2, 0.5, 1+, 2, 5
Value in mascot.dat0.1, 0.2, 0.5, 1+, 2, 5
Returns:
the number of integers in the list.
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 parameterMeaning
mprecursor ion m/z within precursor ion m/z uncertainty
Ggeneric (no peak annotations or peptide peak weighting used)
aalternative peak matching in computing match factors
Ppeptide (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"

ParameterLibrarySearch
Permitted valuesAny 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.
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:
peptideToleranceUnitwill be Z or ZPPM, where 'Z' specifies Daltons.
peptideTolerancetolerance in the unit above.
ionToleranceUnitwill be M or MPPM, where 'M' specifies Daltons.
ionTolerancetolerance in the unit above.
libraryDirectoryPathfull path to the directory containing the spectral library 'database'.
inputFileRelativePathpath to the mgf file created by nph-mascot.exe.
outputFileRelativePathis 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.
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.

ParameterPercolatorExeFlags
Permitted valuesany 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:
anyRetentionTimesshould 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.
percolatorFilesis the parameter returned by ms_mascotresfile::getPercolatorFileNames().
rtone 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.
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.

ParameterPercolatorFeatures
Permitted valuesAny 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.datmScore,lgDScore, mrCalc, charge, dM, dMppm, absDM, absDMppm, isoDM, isoDMppm, mc, varmods, totInt, intMatchedTot,relIntMatchedTot
Returns:
the comma separated list of features.
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.

ParameterPercolatorMinQueries
Permitted valuesAny integer > 0
Default
(if no parameter in mascot.dat)
750
Value in mascot.dat750
(was 100 for Mascot Server versions 2.3 to 2.5.0)
Returns:
the minimum number of queries required to display percolator results.
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.

ParameterPercolatorMinSequences
Permitted valuesAny integer > 0
Default
(if no parameter in mascot.dat)
100
Value in mascot.dat100
Returns:
the minimum number of sequences.
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
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.

ParameterPrecursorCutOut
Permitted valuesAny 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.
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.

ParameterPrecursorCutOut
Permitted valuesAny 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.
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.

ParameterProteinFamilySwitch
Permitted valuesAny integer > 0
Default
(if no parameter in mascot.dat)
300
Value in mascot.dat300
Returns:
the number of MS-MS spectra required for displaying the Protein Family Summary report.
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.
ParameterProteinsInResultsFile
Permitted values1, 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.
std::string getProxyPassword (  ) const

Returns the value of proxy_password.

See getProxyServer().

Parameterproxy_password
Permitted valuesAny 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.
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()).

Parameterproxy_server
Permitted valuesAny text string
Default
(if no parameter in mascot.dat)
[empty]
Value in mascot.dat[commented out]# proxy_server myserver
Returns:
the proxy server name.
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.

ParameterProxyType
Permitted valuesNone, Registry, Specify, WPAD, Environment, Auto
Default
(if no parameter in mascot.dat)
Auto
Value in mascot.datAuto
Returns:
A string matching one of the ms_connection_settings::PROXY_TYPE values.
std::string getProxyUsername (  ) const

Returns the value of proxy_username.

See getProxyServer().

Parameterproxy_username
Permitted valuesAny 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.
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().
ParameterReportBuilderColumnArrangement_XXX
Permitted valuesA 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.datReportBuilderColumnArrangement_1 Standard:family,member,db,acc,score,mass,matches,matches-sig,sequences,sequences-sig,empai,frame,desc
Parameters:
indexA value between 1 and getMaxNumOfReportBuilderColumnArrangements(), inclusive.
Returns:
The column arrangement definition at that index, or the empty string if the arrangement does not exist.
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

ParameterReportNumberChoices
Permitted valuesAny non empty text string
Default
(if no parameter in mascot.dat)
5,10,20,30,40,50
Value in mascot.datAUTO,5,10,20,30,50,100,200
Parameters:
indexelement number from 0 to (getNumberOfReportNumberChoices()-1).
Returns:
an element of the list that corresponds to the given index.
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_mascotresfile::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_mascotresfile::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()
ParameterResfileCache
Permitted valuesComma, 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.datmaster_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_mascotresfile::RESFILE_USE_CACHE when creating a ms_mascotresfile object.
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()
ParameterResultsCache
Permitted valuesComma, 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.datmaster_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.
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.

ParameterResultsFileFormatVersion
Permitted valuesAny text string
Default
(if no parameter in mascot.dat)
[empty]
Value in mascot.dat[commented out] #ResultsFileFormatVersion 2.1
Returns:
the version string.
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.

ParameterResultsFullURL
Permitted valuesAny non empty text string
Default
(if no parameter in mascot.dat)
###URL###/cgi/master_results.pl
Value in mascot.dathttp://www.matrixscience.com/cgi/master_results.pl
Returns:
the url.
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.

ParameterResultsFullURL_2
Permitted valuesAny non empty text string
Default
(if no parameter in mascot.dat)
http://www.matrixscience.com/cgi/master_results_2.pl
Value in mascot.dathttp://www.matrixscience.com/cgi/master_results_2.pl
Returns:
the URL to use.
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.

ParameterResultsPerlScript
Permitted valuesAny 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.
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.

ParameterResultsPerlScript_2
Permitted valuesAny 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.
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().
ParameterReviewColDisplay
Permitted values1 (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.dat1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1
Parameters:
indexA value from the MS_REVIEW_COL enumeration.
Returns:
column display state for the given number
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().
ParameterReviewColWidths
Permitted valuesAny non empty text string
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.dat7, 8, 8, 27, 30, 100, 32, 25, 6, 13, 4, 4, 6, 16, 7, 32
Parameters:
indexA value from the MS_REVIEW_COL enumeration.
Returns:
column width for the given number.
std::string getSearchLogFile (  ) const

Returns the value of SearchLogFile.

This path defines where search log file should be stored.

ParameterSearchLogFile
Permitted valuesAny 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.
int getSelectSwitch (  ) const

Returns the value of SelectSwitch.

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

ParameterSelectSwitch
Permitted valuesAny integer >= 0
Default
(if no parameter in mascot.dat)
1000
Value in mascot.dat1000
Returns:
The minimum number of queries for a select summary.
std::string getSendmailPath (  ) const

Returns the value of sendmailPath.

sendmailPath is the path to sendmail or BLAT programs.

See also:
getMailTransport(), isEmailUsersEnabled(), isEmailErrorsEnabled().
ParametersendmailPath
Permitted valuesAny 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.
int getSeparateLockMem (  ) const

Returns the value of SeparateLockMem.

Setting this value to 1 indicates that ms-monitor.exe will run a separate program (ms-lockmem.exe) that will lock the memory blocks.

A value greater than 1 specifies the block size in Mb. For example, if there is a 1.5 Gb *.s00 file, and this parameter is set to 750, then two instances of ms-lockmem.exe will be run.

ParameterSeparateLockMem
Permitted valuesAny integer >= 0
Default
(if no parameter in mascot.dat)
0
Value in mascot.dat0
Returns:
the parameter specifying how to use ms-lockmem.exe.
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()
ParameterShowSubSets
Permitted valuesFloating 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()).
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.

ParameterSigThreshold
Permitted valuesFloating point 1e-18 to 1.0
Default
(if no parameter in mascot.dat)
0.05
Value in mascot.dat0.05
Returns:
the significance threshold.
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.

ParameterSiteAnalysisMD10Prob
Permitted valuesFloating point 1e-18 to 1.0
Default
(if no parameter in mascot.dat)
0.1
Value in mascot.dat0.1
Returns:
the MD10Score value.
std::string getSortUnassigned (  ) const

Returns the value of SortUnassigned.

ParameterSortUnassigned
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
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.

ParameterSpectraPerLibraryBlock
Permitted valuesAny integer > 0.
Default
(if no parameter in mascot.dat)
500000
Value in mascot.dat500000
Returns:
the maximum number of spectra before splitting into separate blocks
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.
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.

ParameterSpectrumViewerColourScheme_XXX
Permitted valuesA 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.datSpectrumViewerColourScheme_screen unmatched=black,internal_ion=orange,immonium_ion=orange,terminal_series_ion=red,terminal_series_ion_nl=orange,library_peak=blue
Parameters:
nameColour 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.
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()
ParameterSpectrumViewerDefaultColourScheme
Permitted valuescolour scheme name
Default
(if no parameter in mascot.dat)
screen
Value in mascot.datscreen
Returns:
The name of the default colour scheme.
int getSplitDataFileSize (  ) const

Returns the value of SplitDataFileSize.

See getSplitNumberOfQueries() for a description.

ParameterSplitDataFileSize
Permitted valuesAny integer > 0
Default
(if no parameter in mascot.dat)
10000000
Value in mascot.dat10000000
Returns:
the maximum size (bytes) of each chunk.
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.

ParameterSplitNumberOfQueries
Permitted valuesAny integer > 0
Default
(if no parameter in mascot.dat)
1000
Value in mascot.dat1000
Returns:
the maximum number of queries in each chunk.
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.

ParameterSVGSpectrumSwitch
Permitted values0-100000
Default
(if no parameter in mascot.dat)
2000
Value in mascot.dat2000
Returns:
cut-off point where Peptide View reverts to the static spectrum graphic
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:
indexelement number from 0 to (getNumberOfTargetFDRPercentages()-1).
Returns:
an element of the list that corresponds to the given index.
std::string getTaxBrowserUrl (  ) const

Returns value of the TaxBrowserUrl.

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

ParameterTaxBrowserUrl
Permitted valuesAny text string
Default
(if no parameter in mascot.dat)
[empty]
Value in mascot.dathttp://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=#TAXID#
Returns:
the URL.
std::string getTestDirectory (  ) const

Returns the value of TestDirectory.

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

ParameterTestDirectory
Permitted valuesAny non empty text string
Default
(if no parameter in mascot.dat)
../data/test
Value in mascot.dat../data/test
Returns:
the test directory.
int getUniqueJobStartNumber (  ) const

Returns the value of UniqueJobStartNumber.

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

ParameterUniqueJobStartNumber
Permitted valuesInteger >= 0
Default
(if no parameter in mascot.dat)
1234
Value in mascot.dat1234
Returns:
the start job number to be used if the job id file does not exist.
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()
ParameterUnixDirPerm
Permitted valuesAny integer in octal format
Default
(if no parameter in mascot.dat)
777 (octal)
Value in mascot.dat[not defined]
Returns:
the permissions flag.
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.

ParameterUnixWebUserGroup
Permitted valuesAny text string
Default
(if no parameter in mascot.dat)
-1
Value in mascot.dat[not defined]
Returns:
the id of the group.
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.

ParameterVmemory
Permitted values64 bit integer > -1
Default
(if no parameter in mascot.dat)
-1
Value in mascot.dat[not defined]
Returns:
the vmemory limit.
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).

ParameterAutoSelectCharge
Permitted values0 or 1
Default
(if no parameter in mascot.dat)
1
Value in mascot.dat1
Returns:
true if the auto selection of charge is enabled.
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:
indexelement number from 0 to (getNumberOfTargetFDRPercentages()-1).
Returns:
true if the element is marked as a default value.
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.

ParameterEmailErrorsEnabled
Permitted values0 or 1
Default
(if no parameter in mascot.dat)
0
Value in mascot.dat0
Returns:
true if error messages should be emailed to the Mascot server administrator.
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()
ParameterEmailUsersEnabled
Permitted values0 or 1
Default
(if no parameter in mascot.dat)
0
Value in mascot.dat0
Returns:
the flag indicating if emails with a link to results should be sent.
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.

ParameterForkForUnixApache
Permitted values0 or 1
Default
(if no parameter in mascot.dat)
0
Value in mascot.dat0
Returns:
true if the nph-mascot.exe process should be forked at startup
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.

ParameterIgnoreDupeAccessions
Permitted valuestext strings delimted by tab, space and comma
Default
(if no parameter in mascot.dat)
EST_others
Value in mascot.datEST_others
Parameters:
valueis the name of the databases to check.
Returns:
true if the database is in the list.
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.

ParameterIteratePMFIntensities
Permitted values0 or 1
Default
(if no parameter in mascot.dat)
1
Value in mascot.dat1
Returns:
TRUE if the parameter is set to 1 and FALSE otherwise.
bool isLabelAll (  ) const

Returns the value of LabelAll.

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.

ParameterLabelAll
Permitted values0 or 1
Default
(if no parameter in mascot.dat)
0
Value in mascot.dat0
Returns:
true if if all peaks that match a calculated mass value should be labelled in Peptide View.
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.

ParameterMoveOldDbToOldDir
Permitted values0 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
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.

ParameterPercolator
Permitted values0 or 1
Default
(if no parameter in mascot.dat)
0
Value in mascot.dat1
Returns:
true if percolated results should be opened by default.
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.

ParameterPercolatorUseProteins
Permitted values0 or 1
Default
(if no parameter in mascot.dat)
0
Value in mascot.dat0
Returns:
true if percolator should use protein features.
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.

ParameterPercolatorUseRT
Permitted values0 or 1
Default
(if no parameter in mascot.dat)
0
Value in mascot.dat0
Returns:
true if percolator should use retention times.
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.

ParameterRemoveOldIndexFiles
Permitted values0 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
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.

ParameterRequireBoldRed
Permitted values0 or 1
Default
(if no parameter in mascot.dat)
0
Value in mascot.dat0
Returns:
true if all proteins must contain a bold red peptide.
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().
ParameterSaveEveryLastQueryAsc
Permitted values0 or 1
Default
(if no parameter in mascot.dat)
1
Value in mascot.dat0
Returns:
true if the value in the file is '1'.
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().
ParameterSaveLastQueryAsc
Permitted values0 or 1
Default
(if no parameter in mascot.dat)
0
Value in mascot.dat0
Returns:
true if the value in the file is '1'.
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.
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.

ParameterShowAllFromErrorTolerant
Permitted values0 or 1
Default
(if no parameter in mascot.dat)
0
Value in mascot.dat0
Returns:
true if all matches should be displayed in manual error tolerant searches.
bool isShowSubsets (  ) const

Returns the value of ShowSubSets.

Deprecated:
See getShowSubsets().
ParameterShowSubSets
Permitted valuesFloating 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.
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.

ParameterStoreModPermutations
Permitted values0 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.
bool isUnixDirPermDefined (  ) const

Returns true if the UnixDirPerm value is defined.

See getUnixDirPerm().

ParameterUnixDirPerm
Permitted valuesAny 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.
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.

ParameterUseHTTPProxyForFTP
Permitted values0 or 1
Default
(if no parameter in mascot.dat)
0
Value in mascot.dat0
Returns:
true if FTP requests should use the HTTP proxy server.

This option is ignored for windows with auto proxy configuration enabled as it will be determined automatically. Applicable for linux auto proxy configuration.

void setAutoSelectCharge ( const bool  value )

Sets AutoSelectCharge.

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

Parameters:
valueis the new setting.
void setCacheDirectory ( const char *  value )

Sets CacheDirectory.

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

Parameters:
valueis the new cache directory.
void setCentroidWidth ( const double  value )

Sets CentroidWidth.

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

Parameters:
valueis the new centroid width.
void setCentroidWidthCount ( const int  value )

Sets CentroidWidthCount.

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

Parameters:
valueis the new peak count threshold.
void setCompressToolAA ( const std::string  value )

Sets CompressTool_AA.

For a description of this function, see getCompressToolAA()

Parameters:
valueis the new setting
void setCompressToolNA ( const std::string  value )

Sets CompressTool_NA.

For a description of this function, see getCompressToolNA()

Parameters:
valueis the new setting
void setCompressToolSL ( const std::string  value )

Sets CompressTool_NA.

For a description of this function, see getCompressToolSL()

Parameters:
valueis the new setting
void setDecoyTypeNoEnzyme ( const int  value )

Sets DecoyTypeNoEnzyme.

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

Parameters:
valueis the new setting.
void setDecoyTypeSpecific ( const int  value )

Sets DecoyTypeSpecific.

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

Parameters:
valueis the new setting.
void setDefaultTargetFDRPercentage ( const int  index )

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

See getTargetFDRPercentage() for more information.

Parameters:
indexis the index of the item to set. index must be between 0 and getNumberOfTargetFDRPercentages()-1.
void setDisplayNonSignificantMatches ( const int  value )

Sets DisplayNonSignificantMatches.

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

Parameters:
valueis the new setting. If it is not one of the permitted values, the setting remains unchanged.
void setEmailErrorsEnabled ( const bool  value )

Sets EmailErrorsEnabled.

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

Parameters:
valuespecified whether errors should be emailed.
void setEmailFromTextName ( const char *  str )

Sets EmailFromTextName.

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

Parameters:
stris the new name of the user from which email appears to come.
void setEmailFromUser ( const char *  str )

Sets EmailFromUser.

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

Parameters:
stris the new email address of the user from which email appears to come.
void setEmailPassword ( const char *  str )

Sets EmailPassword.

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

Parameters:
stris the new email password.
void setEmailProfile ( const char *  str )

Sets EmailPassword.

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

Parameters:
stris the new name of the email profile.
void setEmailService ( const char *  str )

Sets EmailService.

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

Parameters:
stris the new email service name.
void setEmailTimeOutPeriod ( const int  value )

Sets EmailTimeOutPeriod.

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

Parameters:
valueis the new timeout period.
void setEmailUsersEnabled ( const bool  value )

Sets EmailUsersEnabled.

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

Parameters:
valuespecifies whether users should be emailed.
void setErrMessageEmailTo ( const char *  str )

Sets ErrMessageEmailTo.

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

Parameters:
stris the new name of the person to send errors to.
void setErrorLogFile ( const char *  str )

Sets ErrorLogFile path.

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

Parameters:
stris the new name of the errorlog file.
void setErrTolMaxAccessions ( const int  value )

Sets ErrTolMaxAccessions.

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

Parameters:
valueis the new maximum.
void setExecAfterSearch ( const int  num,
std::string  value 
)

Sets ExecAfterSearch_XXX.

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

Parameters:
numis the 1 based number for the ExecAfterSearch_[num] parameter.
valueis the command to be run.
void setFeatureTableLength ( const int  value )

Sets FeatureTableLength.

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

Parameters:
valueis the new length.
void setFeatureTableMinScore ( const double  value )

Sets FeatureTableMinScore.

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

Parameters:
valueis the new minimum score.
void setForkForUnixApache ( const bool  value )

Sets ForkForUnixApache.

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

Parameters:
valuespecifies whether the fork command should be used.
void setFormVersion ( const char *  str )

Sets FormVersion.

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

Parameters:
stris the new version string.
void setGetSeqBlastAccession ( const ms_blastaccession *  value )

Sets GetSeqBlastAccession.

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

Parameters:
valueis the new setting.
void setGetSeqJobIdFile ( const char *  str )

Sets GetSeqJobIdFile.

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

Parameters:
stris the new name of the job id file.
void setICATFilter ( const char *  filterString )

Sets ICATFilter.

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

Parameters:
filterStringis the new name of the ICAT filter.
void setICATHeavy ( const char *  modName )

Sets ICATHeavy.

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

Parameters:
modNameis the new name of the heavy ICAT mod.
void setICATLight ( const char *  modName )

Sets ICATLight.

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

Parameters:
modNameis the new name of the light ICAT mod.
void setICATQuantitationMethod ( const char *  methodName )

Sets ICATQuantitationMethod.

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

Parameters:
methodNameis the new name of the quantitation method.
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:
indexis the index of the value to set. index must be between 0 and getNumberOfIgnoreDupeAccessions()-1.
valueis the value to set (the name of the database).
void setIgnoreIonsScoreBelow ( const double  value )

Sets IgnoreIonsScoreBelow.

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

Parameters:
valueis the new maximum.
void setIntensitySigFigs ( const int  value )

Sets IntensitySigFigs.

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

Parameters:
valueis the new number of significant figures.
void setInterFileBasePath ( const char *  str )

Sets InterFileBasePath.

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

Parameters:
stris the new path.
void setInterFileRelPath ( const char *  str )

Sets InterFileRelPath.

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

Parameters:
stris the new path.
void setIonsDecimalPlaces ( const int  value )

Sets IonsDecimalPlaces.

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

Parameters:
valueis the new number of decimal places.
void setIteratePMFIntensities ( const bool  value )

Sets IteratePMFIntensities.

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

Parameters:
valueis the new setting.
void setLabelAll ( const bool  value )

Sets LabelAll.

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

Parameters:
valuespecifies if all peaks that match a calculated mass value should be labelled in Peptide View.
void setLastQueryAscFile ( const char *  filename )

Sets LastQueryAscFile to the passed value.

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

Parameters:
filenameis the new name of the lastqueryasc file.
void setLogoImageFile ( const char *  str )

Sets LogoImageFile.

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

Parameters:
stris the new logo image file.
void setMailTempFile ( const char *  str )

Sets MailTempFile.

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

Parameters:
stris the new name of the temp file.
void setMailTransport ( const int  value )

Sets MailTransport.

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

Parameters:
valueis the new mail transport option.
void setMascNodeCtrlFile ( const char *  str )

Sets MascNodeCtrlFile.

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

Parameters:
stris the new name of the node control file.
void setMascotCmdLine ( const char *  str )

Sets MascotCmdLine.

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

Parameters:
stris the new path.
void setMascotControlFile ( const char *  str )

Sets MascotControlFile.

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

Parameters:
stris the new name of the control file.
void setMascotJobIdFile ( const char *  str )

Sets MascotJobIdFile.

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

Parameters:
stris the new name of the job id file.
void setMascotMessage ( const char *  str )

Sets MascotMessage.

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

Parameters:
stris the new message.
void setMassDecimalPlaces ( const int  value )

Sets MassDecimalPlaces.

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

Parameters:
valueis the new number of decimal places.
void setMaxConcurrentSearches ( const int  value )

Sets MaxConcurrentSearches.

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

Parameters:
valueis the new maximum value.
void setMaxDatabases ( const int  value )

Sets MaxDatabases.

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

Parameters:
valueis the new maximum number of databases.
void setMaxDescriptionLen ( const int  value )

Sets MaxDescriptionLen.

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

Parameters:
valueis the new maximum length.
void setMaxEtagMassDelta ( const double  value )

Sets MaxEtagMassDelta.

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

Parameters:
valueis the new maximum delta.
void setMaxEtVarMods ( const int  value )

Sets MaxEtVarMods.

For a description of this function, see getMaxEtVarMods()

Parameters:
valueis the new maximum in the range 0 to 31.
void setMaxNumPeptides ( const int  value )

Sets MaxNumPeptides.

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

Parameters:
valueis the new maximum value.
void setMaxPepModArrangements ( const int  value )

Sets MaxPepModArrangements.

For a description of this function, see getMaxPepModArrangements()

Parameters:
valueis the new maximum.
void setMaxPepNumModifiableSites ( const int  value )

Sets MaxPepNumModifiableSites.

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

Parameters:
valueis the new maximum number of modifiable sites.
void setMaxPepNumVarMods ( const int  value )

Sets MaxPepNumVarMods.

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

Parameters:
valueis the new maximum number of modifications.
void setMaxQueries ( const int  value )

Sets MaxQueries.

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

Parameters:
valueis the new maximum number of queries.
void setMaxSearchesPerUser ( const int  value )

Sets MaxSearchesPerUser.

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

Parameters:
valueis the maximum value.
void setMaxSequenceLen ( const int  value )

Sets MaxSequenceLen.

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

Parameters:
valueis the new maximum length.
void setMaxVarMods ( const int  value )

Sets MaxVarMods.

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

Parameters:
valueis the new maximum in the range 0 to 32.
void setMinEtagMassDelta ( const double  value )

Sets MinEtagMassDelta.

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

Parameters:
valueis the new minimum delta.
void setMinPepLenInPepSummary ( const int  value )

Sets MinPepLenInPepSummary.

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

Parameters:
valueis the new minimum length.
void setMinPepLenInSearch ( const int  value )

Sets MinPepLenInSearch.

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

Parameters:
valueis the new minimum setting.
void setMonitorEmailCheckFreq ( const int  value )

Sets MonitorEmailCheckFreq.

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

Parameters:
valueis the new time period.
void setMonitorLogFile ( const char *  str )

Sets MonitorLogFile.

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

Parameters:
stris the new name of the monitor log.
void setMonitorPidFile ( const char *  str )

Sets MonitorPidFile.

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

Parameters:
stris the new name of the pid file.
void setMonitorTestTimeout ( const int  value )

Sets MonitorTestTimeout.

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

Parameters:
valueis the new timeout period.
void setMoveOldDbToOldDir ( const bool  value )

Sets MoveOldDbToOldDir.

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

Parameters:
valueis the new setting.
void setMudpit ( const int  value )

Sets Mudpit.

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

Parameters:
valueis the new setting.
void setMudpitSwitch ( const double  value )

Sets MudpitSwitch.

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

Parameters:
valueis the new q/e value used to determine which protein scoring method to use.
void setNoResultsScript ( const char *  str )

Sets NoResultsScript.

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

Parameters:
stris the new name of the script.
void setNTIUserGroup ( const char *  str )

Sets NTIUserGroup.

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

Parameters:
stris the new name of the web user group.
void setNTMonitorGroup ( const char *  str )

Sets NTMonitorGroup.

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

Parameters:
stris the new name of the group used by ms-monitor.exe.
void setPepSearchTool ( const std::string  value )

Sets LibrarySearch.

For a description of this function, see getPepSearchTool()

Parameters:
valueis the new setting
void setPercolator ( const bool  value )

Sets Percolator.

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

Parameters:
valueTrue if percolated results should be opened by default.
void setPercolatorExeFlags ( const char *  value )

Sets PercolatorExeFlags.

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

Parameters:
valueis the new flags.
void setPercolatorFeatures ( std::string  value )

Sets PercolatorFeatures.

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

Parameters:
valueis the new list of features.
void setPercolatorMinQueries ( const int  value )

Sets PercolatorMinQueries.

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

Parameters:
valueis the new minimum number of queries.
void setPercolatorMinSequences ( const int  value )

Sets PercolatorMinSequences.

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

Parameters:
valueis the new minimum number of sequences.
void setPercolatorUseProteins ( const bool  value )

Sets PercolatorUseProteins.

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

Parameters:
valueis the new flag.
void setPercolatorUseRT ( const bool  value )

Sets PercolatorUseRT.

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

Parameters:
valueis the new flag.
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:
commentsany comments preceeding the section
void setPrecursorCutOutLowerLimit ( const double  value )

Sets the first PrecursorCutOut.

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

Parameters:
valueis the new lower limit.
void setPrecursorCutOutUpperLimit ( const double  value )

Sets the second PrecursorCutOut.

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

Parameters:
valueis the new upper limit.
void setProteinFamilySwitch ( const int  value )

Sets ProteinFamilySwitch.

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

Parameters:
valueis the new minimum number of spectra.
void setProteinsInResultsFile ( const int  value )

Sets ProteinsInResultsFile.

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

Parameters:
valueis the new setting.
void setProxyPassword ( const char *  str )

Sets proxy_password.

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

Parameters:
stris the new password.
void setProxyServer ( const char *  str )

Sets proxy_server.

For a description of this function, see getProxyServer.

Parameters:
stris the new proxy server address/name.
void setProxyType ( const std::string &  value )

Sets ProxyType.

For a description of this function, see getProxyServer.

Parameters:
valueA 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.
void setProxyUsername ( const char *  str )

Sets proxy_username.

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

Parameters:
stris the new proxy user name.
void setRemoveOldIndexFiles ( const bool  value )

Sets RemoveOldIndexFiles.

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

Parameters:
valueis the new setting.
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().

Parameters:
indexA value between 1 and getMaxNumOfReportBuilderColumnArrangements, inclusive.
strName, followed by colon, followed by comma-separated column arrangement string, e.g. "Mini:family,member,db,acc,score,mass,desc"
void setReportNumberChoice ( const int  index,
const int  value 
)

Sets an element of the ReportNumberChoices list by its index.

See getReportNumberChoice() for more information.

Parameters:
indexis the index of the item to set. index must be between 0 and getNumberOfReportNumberChoices()-1.
valueis the value it should be set to.
void setRequireBoldRed ( const bool  value )

Sets RequireBoldRed.

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

Parameters:
valuespecifies if proteins need a bold red peptide.
void setResfileCache ( const char *  value )

Sets ResfileCache.

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

Parameters:
valuea comma separated list of scripts that should specify ms_mascotresfile::RESFILE_USE_CACHE when creating a ms_mascotresfile object.
void setResultsCache ( const char *  value )

Sets ResultsCache.

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

Parameters:
valuea comma separated list of scripts that should specify ms_peptidesummary::MSPEPSUM_USE_CACHE when creating a ms_peptidesummary object.
void setResultsFileFormatVersion ( const char *  value )

Sets ResultsFileFormatVersion.

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

Parameters:
valueis the new version string.
void setResultsFullURL ( const char *  str )

Sets ResultsFullURL.

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

Parameters:
stris the new URL.
void setResultsFullURL_2 ( std::string  value )

Sets ResultsFullURL_2.

For a description of this function, see getResultsFullURL_2().

Parameters:
valueis the new perl script.
void setResultsPerlScript ( const char *  str )

Sets ResultsPerlScript.

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

Parameters:
stris the new name of the script.
void setResultsPerlScript_2 ( std::string  value )

Sets ResultsPerlScript_2.

For a description of this function, see getResultsPerlScript_2().

Parameters:
valueis the new perl script.
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().
Parameters:
indexis a value from the MS_REVIEW_COL enumeration.
valueis the new display state to set.
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().
Parameters:
indexis a value from the MS_REVIEW_COL enumeration.
valueis the new width to set.
void setSaveEveryLastQueryAsc ( const bool  flag )

Sets SaveEveryLastQueryAsc to 1 or 0.

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

Parameters:
flagis a boolean flag that corresponds to 1 (true) or 0 (false).
void setSaveLastQueryAsc ( const bool  flag )

Sets SaveLastQueryAsc to 1 or 0.

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

Parameters:
flagis a boolean flag that corresponds to 1 (true) or 0 (false).
void setSearchLogFile ( const char *  str )

Sets SearchLogFile.

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

Parameters:
stris the new name of the search log.
void setSelectSwitch ( const int  value )

Sets SelectSwitch.

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

Parameters:
valueis the new minimum number of queries for a select summary.
void setSendmailPath ( const char *  str )

Sets sendmailPath.

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

Parameters:
stris the new name of the sendmail program.
void setSeparateLockMem ( const int  value )

Sets SeparateLockMem.

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

Parameters:
valuespecifies whether ms-lockmem.exe should be called.
void setShowAllFromErrorTolerant ( const bool  value )

Sets ShowAllFromErrorTolerant.

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

Parameters:
valuespecifies if all matches should be displayed in manual error tolerant searches.
void setShowSubsets ( const double  value )

Sets ShowSubSets.

See getShowSubsets().

Parameters:
valueis 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.
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:
valueif set to true, 1.0 is used, otherwise 0.0 is used
void setSigThreshold ( const double  value )

Set the SigThreshold.

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

Parameters:
valueis the new default threshold value.
void setSiteAnalysisMD10Prob ( const double  value )

Set the SiteAnalysisMD10Prob.

For a description of this function, see getSiteAnalysisMD10Prob().

Parameters:
valueis the new default MD10Prob value.
void setSortUnassigned ( const std::string  value )

Sets SortUnassigned.

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

Parameters:
valueshould be one of:

  • scoredown - descending score
  • queryup - query order
  • intdown - intensity order
void setSpectraPerLibraryBlock ( const int  value )

Sets the number of spectra in a spectral library block.

For a description of this function, see getSpectraPerLibraryBlock()

Parameters:
valuemust be a number greater than zero
void setSpectrumViewerColourSchemeString ( const std::string &  name,
const std::string &  str 
)

Sets SpectrumViewerColourScheme.

If str is the empty string, the named colour scheme will be deleted.

For details, see getSpectrumViewerColourSchemeString().

Parameters:
nameColour scheme name; the defined names are returned by getSpectrumViewerColourSchemeNames().
strColour scheme specification as defined in getSpectrumViewerColourSchemeString(), or the empty string.
void setSpectrumViewerDefaultColourSchemeName ( const std::string &  name )

Sets the default colour scheme name (SpectrumViewerDefaultColourScheme).

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

Parameters:
nameColour scheme name, typically one of getSpectrumViewerColourSchemeNames().
void setSplitDataFileSize ( const int  value )

Sets SplitDataFileSize.

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

Parameters:
valueis the new file size to split at.
void setSplitNumberOfQueries ( const int  value )

Sets SplitNumberOfQueries.

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

Parameters:
valueis the new number of queries.
void setStoreModPermutations ( const bool  value )

Sets StoreModPermutations.

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

Parameters:
valueis the new setting.
void setSVGSpectrumSwitch ( const int  value )

Sets SVGSpectrumSwitch.

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

Parameters:
valueis the new setting.
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.

Parameters:
indexis the index of the item to set. index must be between 0 and getNumberOfTargetFDRPercentages()-1.
valueis the value it should be set to.
makeDefaultcontrols whether the new element should be made the default item in the list.
void setTaxBrowserUrl ( const std::string  value )

Sets TaxBrowserURL.

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

Parameters:
valueis the URL.
void setTestDirectory ( const char *  str )

Sets TestDirectory.

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

Parameters:
stris the new path.
void setUniqueJobStartNumber ( const int  value )

Sets UniqueJobStartNumber.

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

Parameters:
valueis the new job start number.
void setUnixDirPerm ( const int  value )

Sets UnixDirPerm.

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

Parameters:
valueis the new permissions.
void setUnixWebUserGroup ( const int  value )

Sets UnixWebUserGroup.

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

Parameters:
valueis the new setting for the web user group.
void setUseHTTPProxyForFTP ( const bool  value )

Sets UseHTTPProxyForFTP.

For a description of this function, see isUseHTTPProxyForFTP.

Parameters:
valueTrue if FTP requests should use HTTP proxy settings; false otherwise.
void setVmemory ( const INT64  value )

Sets Vmemory.

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

Parameters:
valueis the new value.

The documentation for this class was generated from the following files:
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:52