Matrix Science header

ms_mascotoptions Member List

This is the complete list of members for ms_mascotoptions, including all inherited members.
appendIgnoreDupeAccession(const std::string value)ms_mascotoptions
appendReportNumberChoice(const int value)ms_mascotoptions
appendTargetFDRPercentage(const double value, const bool makeDefault=false)ms_mascotoptions
clearIgnoreDupeAccessions()ms_mascotoptions
clearReportNumberChoices()ms_mascotoptions
clearTargetFDRPercentages()ms_mascotoptions
copyFrom(const ms_mascotoptions *right)ms_mascotoptions
DECOY_ALGORITHM enum namems_mascotoptions
DECOY_ALGORITHM_NONE enum valuems_mascotoptions
DECOY_PEPTIDE_RANDOM enum valuems_mascotoptions
DECOY_PEPTIDE_RANDOM_DIPEP enum valuems_mascotoptions
DECOY_PEPTIDE_REVERSE enum valuems_mascotoptions
DECOY_PEPTIDE_SHUFFLE enum valuems_mascotoptions
DECOY_PROTEIN_BASED_MASK enum valuems_mascotoptions
DECOY_PROTEIN_RANDOM enum valuems_mascotoptions
DECOY_PROTEIN_RANDOM_DIPEP enum valuems_mascotoptions
DECOY_PROTEIN_REVERSE enum valuems_mascotoptions
DECOY_PROTEIN_SHUFFLE enum valuems_mascotoptions
defaultValues()ms_mascotoptions
EXEC_AFTER_SEARCH enum namems_mascotoptions
getCacheDirectory() const ms_mascotoptions
getCentroidWidth() const ms_mascotoptions
getCentroidWidthCount() const ms_mascotoptions
getCompressToolAA() const ms_mascotoptions
getCompressToolCommandLineFasta(DATABASE_TYPE dbType, const std::string &dbname, const std::string &dbpath) const ms_mascotoptions
getCompressToolCommandLineLibrary(const std::string &logfilepath, const std::string &inputfile, const std::string &outputdirectory) const ms_mascotoptions
getCompressToolNA() const ms_mascotoptions
getCompressToolSL() const ms_mascotoptions
getCrawlerNumPeaksPer100Da() const ms_mascotoptions
getDecoyTypeNoEnzyme() const ms_mascotoptions
getDecoyTypeSpecific() const ms_mascotoptions
getDisplayNonSignificantMatches() const ms_mascotoptions
getEmailFromTextName() const ms_mascotoptions
getEmailFromUser() const ms_mascotoptions
getEmailPassword() const ms_mascotoptions
getEmailProfile() const ms_mascotoptions
getEmailService() const ms_mascotoptions
getEmailTimeOutPeriod() const ms_mascotoptions
getErrMessageEmailTo() const ms_mascotoptions
getErrorLogFile() const ms_mascotoptions
getErrTolMaxAccessions() const ms_mascotoptions
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 ms_mascotoptions
getFeatureTableLength() const ms_mascotoptions
getFeatureTableMinScore() const ms_mascotoptions
getFormVersion() const ms_mascotoptions
getGetSeqBlastAccession() const ms_mascotoptions
getGetSeqJobIdFile() const ms_mascotoptions
getICATFilter() const ms_mascotoptions
getICATHeavy() const ms_mascotoptions
getICATLight() const ms_mascotoptions
getICATQuantitationMethod() const ms_mascotoptions
getIgnoreDupeAccession(const unsigned int index) const ms_mascotoptions
getIgnoreIonsScoreBelow() const ms_mascotoptions
getIntensitySigFigs() const ms_mascotoptions
getInterFileBasePath() const ms_mascotoptions
getInterFileRelPath() const ms_mascotoptions
getIonsDecimalPlaces() const ms_mascotoptions
getLastQueryAscFile() const ms_mascotoptions
getLogoImageFile() const ms_mascotoptions
getMailTempFile() const ms_mascotoptions
getMailTransport() const ms_mascotoptions
getMascNodeCtrlFile() const ms_mascotoptions
getMascotCmdLine() const ms_mascotoptions
getMascotControlFile() const ms_mascotoptions
getMascotJobIdFile() const ms_mascotoptions
getMascotMessage() const ms_mascotoptions
getMassDecimalPlaces() const ms_mascotoptions
getMaxConcurrentSearches() const ms_mascotoptions
getMaxDatabases() const ms_mascotoptions
getMaxDescriptionLen() const ms_mascotoptions
getMaxEtagMassDelta() const ms_mascotoptions
getMaxEtVarMods() const ms_mascotoptions
getMaxNumOfReportBuilderColumnArrangements() const ms_mascotoptions
getMaxNumPeptides() const ms_mascotoptions
getMaxPepModArrangements() const ms_mascotoptions
getMaxPepNumModifiableSites() const ms_mascotoptions
getMaxPepNumVarMods() const ms_mascotoptions
getMaxQueries() const ms_mascotoptions
getMaxSearchesPerUser() const ms_mascotoptions
getMaxSequenceLen() const ms_mascotoptions
getMaxVarMods() const ms_mascotoptions
getMinEtagMassDelta() const ms_mascotoptions
getMinPepLenInPepSummary() const ms_mascotoptions
getMinPepLenInSearch() const ms_mascotoptions
getMonitorEmailCheckFreq() const ms_mascotoptions
getMonitorLogFile() const ms_mascotoptions
getMonitorPidFile() const ms_mascotoptions
getMonitorTestTimeout() const ms_mascotoptions
getMudpit() const ms_mascotoptions
getMudpitSwitch() const ms_mascotoptions
getNoResultsScript() const ms_mascotoptions
getNTIUserGroup() const ms_mascotoptions
getNTMonitorGroup() const ms_mascotoptions
getNumberOfIgnoreDupeAccessions() const ms_mascotoptions
getNumberOfReportNumberChoices() const ms_mascotoptions
getNumberOfTargetFDRPercentages() const ms_mascotoptions
getPepSearchTool() const ms_mascotoptions
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 ms_mascotoptions
getPercolatorExeFlags(bool anyRetentionTimes, const std::vector< std::string > percolatorFiles, const PERC_EXE_RT rt=PERC_EXE_RT_USE_DEFAULT) const ms_mascotoptions
getPercolatorFeatures() const ms_mascotoptions
getPercolatorMinQueries() const ms_mascotoptions
getPercolatorMinSequences() const ms_mascotoptions
getPreceedingComments() const ms_customproperty
getPrecursorCutOutLowerLimit() const ms_mascotoptions
getPrecursorCutOutUpperLimit() const ms_mascotoptions
getProteinFamilySwitch() const ms_mascotoptions
getProteinsInResultsFile() const ms_mascotoptions
getProxyPassword() const ms_mascotoptions
getProxyServer() const ms_mascotoptions
getProxyType() const ms_mascotoptions
getProxyUsername() const ms_mascotoptions
getReportBuilderColumnArrangement(const int index) const ms_mascotoptions
getReportNumberChoice(const int index) const ms_mascotoptions
getResfileCache() const ms_mascotoptions
getResultsCache() const ms_mascotoptions
getResultsFileFormatVersion() const ms_mascotoptions
getResultsFullURL() const ms_mascotoptions
getResultsFullURL_2() const ms_mascotoptions
getResultsPerlScript() const ms_mascotoptions
getResultsPerlScript_2() const ms_mascotoptions
getReviewColDisplay(const MS_REVIEW_COL index) const ms_mascotoptions
getReviewColWidth(const MS_REVIEW_COL index) const ms_mascotoptions
getSearchLogFile() const ms_mascotoptions
getSelectSwitch() const ms_mascotoptions
getSendmailPath() const ms_mascotoptions
getSeparateLockMem() const ms_mascotoptions
getShowSubsets() const ms_mascotoptions
getSigThreshold() const ms_mascotoptions
getSiteAnalysisMD10Prob() const ms_mascotoptions
getSortUnassigned() const ms_mascotoptions
getSpectraPerLibraryBlock() const ms_mascotoptions
getSpectrumViewerColourSchemeNames() const ms_mascotoptions
getSpectrumViewerColourSchemeString(const std::string &name) const ms_mascotoptions
getSpectrumViewerDefaultColourSchemeName() const ms_mascotoptions
getSplitDataFileSize() const ms_mascotoptions
getSplitNumberOfQueries() const ms_mascotoptions
getSVGSpectrumSwitch() const ms_mascotoptions
getTargetFDRPercentage(const int index) const ms_mascotoptions
getTaxBrowserUrl() const ms_mascotoptions
getTestDirectory() const ms_mascotoptions
getUniqueJobStartNumber() const ms_mascotoptions
getUnixDirPerm() const ms_mascotoptions
getUnixWebUserGroup() const ms_mascotoptions
getVmemory() const ms_mascotoptions
isAutoSelectCharge() const ms_mascotoptions
isDefaultTargetFDRPercentage(const int index) const ms_mascotoptions
isEmailErrorsEnabled() const ms_mascotoptions
isEmailUsersEnabled() const ms_mascotoptions
isForkForUnixApache() const ms_mascotoptions
isInIgnoreDupeAccessionList(const std::string value) const ms_mascotoptions
isIteratePMFIntensities() const ms_mascotoptions
isLabelAll() const ms_mascotoptions
isMoveOldDbToOldDir() const ms_mascotoptions
isPercolator() const ms_mascotoptions
isPercolatorUseProteins() const ms_mascotoptions
isPercolatorUseRT() const ms_mascotoptions
isRemoveOldIndexFiles() const ms_mascotoptions
isRequireBoldRed() const ms_mascotoptions
isSaveEveryLastQueryAsc() const ms_mascotoptions
isSaveLastQueryAsc() const ms_mascotoptions
isSectionAvailable() const ms_mascotoptions
isShowAllFromErrorTolerant() const ms_mascotoptions
isShowSubsets() const ms_mascotoptions
isStoreModPermutations() const ms_mascotoptions
isUnixDirPermDefined() const ms_mascotoptions
isUseHTTPProxyForFTP() const ms_mascotoptions
MASS_DECIMAL_PLACES enum valuems_mascotoptions
MAX_EXEC_AFTER_SEARCH enum valuems_mascotoptions
ms_customproperty()ms_customproperty
ms_mascotoptions()ms_mascotoptions
ms_mascotoptions(const ms_mascotoptions &src)ms_mascotoptions
MS_REVIEW_COL enum namems_mascotoptions
MS_REVIEW_COL____LAST___ enum valuems_mascotoptions
MS_REVIEW_COL_DATABASE enum valuems_mascotoptions
MS_REVIEW_COL_DURATION enum valuems_mascotoptions
MS_REVIEW_COL_ENZYMEUSED enum valuems_mascotoptions
MS_REVIEW_COL_IPADDRESS enum valuems_mascotoptions
MS_REVIEW_COL_JOB enum valuems_mascotoptions
MS_REVIEW_COL_PEAKLISTDATAFILE enum valuems_mascotoptions
MS_REVIEW_COL_PID enum valuems_mascotoptions
MS_REVIEW_COL_PRIORITY enum valuems_mascotoptions
MS_REVIEW_COL_RESULTS_FILE enum valuems_mascotoptions
MS_REVIEW_COL_SEARCHTYPE enum valuems_mascotoptions
MS_REVIEW_COL_START_TIME enum valuems_mascotoptions
MS_REVIEW_COL_STATUS enum valuems_mascotoptions
MS_REVIEW_COL_TITLE enum valuems_mascotoptions
MS_REVIEW_COL_USEREMAIL enum valuems_mascotoptions
MS_REVIEW_COL_USERID enum valuems_mascotoptions
MS_REVIEW_COL_USERNAME enum valuems_mascotoptions
NUMERICAL_VALUE_STORAGE enum namems_mascotoptions
operator=(const ms_mascotoptions &right)ms_mascotoptions
PERC_EXE_RT enum namems_mascotoptions
PERC_EXE_RT_FORCE_OFF enum valuems_mascotoptions
PERC_EXE_RT_FORCE_ON enum valuems_mascotoptions
PERC_EXE_RT_USE_DEFAULT enum valuems_mascotoptions
setAutoSelectCharge(const bool value)ms_mascotoptions
setCacheDirectory(const char *value)ms_mascotoptions
setCentroidWidth(const double value)ms_mascotoptions
setCentroidWidthCount(const int value)ms_mascotoptions
setCompressToolAA(const std::string value)ms_mascotoptions
setCompressToolNA(const std::string value)ms_mascotoptions
setCompressToolSL(const std::string value)ms_mascotoptions
setCrawlerNumPeaksPer100Da(const int value)ms_mascotoptions
setDecoyTypeNoEnzyme(const int value)ms_mascotoptions
setDecoyTypeSpecific(const int value)ms_mascotoptions
setDefaultTargetFDRPercentage(const int index)ms_mascotoptions
setDisplayNonSignificantMatches(const int value)ms_mascotoptions
setEmailErrorsEnabled(const bool value)ms_mascotoptions
setEmailFromTextName(const char *str)ms_mascotoptions
setEmailFromUser(const char *str)ms_mascotoptions
setEmailPassword(const char *str)ms_mascotoptions
setEmailProfile(const char *str)ms_mascotoptions
setEmailService(const char *str)ms_mascotoptions
setEmailTimeOutPeriod(const int value)ms_mascotoptions
setEmailUsersEnabled(const bool value)ms_mascotoptions
setErrMessageEmailTo(const char *str)ms_mascotoptions
setErrorLogFile(const char *str)ms_mascotoptions
setErrTolMaxAccessions(const int value)ms_mascotoptions
setExecAfterSearch(const int num, std::string value)ms_mascotoptions
setFeatureTableLength(const int value)ms_mascotoptions
setFeatureTableMinScore(const double value)ms_mascotoptions
setForkForUnixApache(const bool value)ms_mascotoptions
setFormVersion(const char *str)ms_mascotoptions
setGetSeqBlastAccession(const ms_blastaccession *value)ms_mascotoptions
setGetSeqJobIdFile(const char *str)ms_mascotoptions
setICATFilter(const char *filterString)ms_mascotoptions
setICATHeavy(const char *modName)ms_mascotoptions
setICATLight(const char *modName)ms_mascotoptions
setICATQuantitationMethod(const char *methodName)ms_mascotoptions
setIgnoreDupeAccession(const unsigned int index, const std::string value)ms_mascotoptions
setIgnoreIonsScoreBelow(const double value)ms_mascotoptions
setIntensitySigFigs(const int value)ms_mascotoptions
setInterFileBasePath(const char *str)ms_mascotoptions
setInterFileRelPath(const char *str)ms_mascotoptions
setIonsDecimalPlaces(const int value)ms_mascotoptions
setIteratePMFIntensities(const bool value)ms_mascotoptions
setLabelAll(const bool value)ms_mascotoptions
setLastQueryAscFile(const char *str)ms_mascotoptions
setLogoImageFile(const char *str)ms_mascotoptions
setMailTempFile(const char *str)ms_mascotoptions
setMailTransport(const int value)ms_mascotoptions
setMascNodeCtrlFile(const char *str)ms_mascotoptions
setMascotCmdLine(const char *str)ms_mascotoptions
setMascotControlFile(const char *str)ms_mascotoptions
setMascotJobIdFile(const char *str)ms_mascotoptions
setMascotMessage(const char *str)ms_mascotoptions
setMassDecimalPlaces(const int value)ms_mascotoptions
setMaxConcurrentSearches(const int value)ms_mascotoptions
setMaxDatabases(const int value)ms_mascotoptions
setMaxDescriptionLen(const int value)ms_mascotoptions
setMaxEtagMassDelta(const double value)ms_mascotoptions
setMaxEtVarMods(const int value)ms_mascotoptions
setMaxNumPeptides(const int value)ms_mascotoptions
setMaxPepModArrangements(const int value)ms_mascotoptions
setMaxPepNumModifiableSites(const int value)ms_mascotoptions
setMaxPepNumVarMods(const int value)ms_mascotoptions
setMaxQueries(const int value)ms_mascotoptions
setMaxSearchesPerUser(const int value)ms_mascotoptions
setMaxSequenceLen(const int value)ms_mascotoptions
setMaxVarMods(const int value)ms_mascotoptions
setMinEtagMassDelta(const double value)ms_mascotoptions
setMinPepLenInPepSummary(const int value)ms_mascotoptions
setMinPepLenInSearch(const int value)ms_mascotoptions
setMonitorEmailCheckFreq(const int value)ms_mascotoptions
setMonitorLogFile(const char *str)ms_mascotoptions
setMonitorPidFile(const char *str)ms_mascotoptions
setMonitorTestTimeout(const int value)ms_mascotoptions
setMoveOldDbToOldDir(const bool value)ms_mascotoptions
setMudpit(const int value)ms_mascotoptions
setMudpitSwitch(const double value)ms_mascotoptions
setNoResultsScript(const char *str)ms_mascotoptions
setNTIUserGroup(const char *str)ms_mascotoptions
setNTMonitorGroup(const char *str)ms_mascotoptions
setPepSearchTool(const std::string value)ms_mascotoptions
setPercolator(const bool value)ms_mascotoptions
setPercolatorExeFlags(const char *value)ms_mascotoptions
setPercolatorFeatures(std::string value)ms_mascotoptions
setPercolatorMinQueries(const int value)ms_mascotoptions
setPercolatorMinSequences(const int value)ms_mascotoptions
setPercolatorUseProteins(const bool value)ms_mascotoptions
setPercolatorUseRT(const bool value)ms_mascotoptions
setPreceedingComments(const std::string &comments)ms_customproperty
setPrecursorCutOutLowerLimit(const double value)ms_mascotoptions
setPrecursorCutOutUpperLimit(const double value)ms_mascotoptions
setProteinFamilySwitch(const int value)ms_mascotoptions
setProteinsInResultsFile(const int value)ms_mascotoptions
setProxyPassword(const char *str)ms_mascotoptions
setProxyServer(const char *str)ms_mascotoptions
setProxyType(const std::string &value)ms_mascotoptions
setProxyUsername(const char *str)ms_mascotoptions
setRemoveOldIndexFiles(const bool value)ms_mascotoptions
setReportBuilderColumnArrangement(const int index, const std::string str)ms_mascotoptions
setReportNumberChoice(const int index, const int value)ms_mascotoptions
setRequireBoldRed(const bool value)ms_mascotoptions
setResfileCache(const char *value)ms_mascotoptions
setResultsCache(const char *value)ms_mascotoptions
setResultsFileFormatVersion(const char *value)ms_mascotoptions
setResultsFullURL(const char *str)ms_mascotoptions
setResultsFullURL_2(std::string value)ms_mascotoptions
setResultsPerlScript(const char *str)ms_mascotoptions
setResultsPerlScript_2(std::string value)ms_mascotoptions
setReviewColDisplay(const MS_REVIEW_COL index, const bool value)ms_mascotoptions
setReviewColWidth(const MS_REVIEW_COL index, const int value)ms_mascotoptions
setSaveEveryLastQueryAsc(const bool flag)ms_mascotoptions
setSaveLastQueryAsc(const bool flag)ms_mascotoptions
setSearchLogFile(const char *str)ms_mascotoptions
setSectionAvailable(const bool value)ms_mascotoptions
setSelectSwitch(const int value)ms_mascotoptions
setSendmailPath(const char *str)ms_mascotoptions
setSeparateLockMem(const int value)ms_mascotoptions
setShowAllFromErrorTolerant(const bool value)ms_mascotoptions
setShowSubsets(const bool value)ms_mascotoptions
setShowSubsets(const double value)ms_mascotoptions
setSigThreshold(const double value)ms_mascotoptions
setSiteAnalysisMD10Prob(const double value)ms_mascotoptions
setSortUnassigned(const std::string newValue)ms_mascotoptions
setSpectraPerLibraryBlock(const int value)ms_mascotoptions
setSpectrumViewerColourSchemeString(const std::string &name, const std::string &str)ms_mascotoptions
setSpectrumViewerDefaultColourSchemeName(const std::string &name)ms_mascotoptions
setSplitDataFileSize(const int value)ms_mascotoptions
setSplitNumberOfQueries(const int value)ms_mascotoptions
setStoreModPermutations(const bool value)ms_mascotoptions
setSVGSpectrumSwitch(const int value)ms_mascotoptions
setTargetFDRPercentage(const int index, const double value, const bool makeDefault=false)ms_mascotoptions
setTaxBrowserUrl(const std::string value)ms_mascotoptions
setTestDirectory(const char *str)ms_mascotoptions
setUniqueJobStartNumber(const int value)ms_mascotoptions
setUnixDirPerm(const int value)ms_mascotoptions
setUnixWebUserGroup(const int value)ms_mascotoptions
setUseHTTPProxyForFTP(const bool value)ms_mascotoptions
setVmemory(const INT64 value)ms_mascotoptions
~ms_customproperty()ms_customproperty
~ms_mascotoptions()ms_mascotoptions
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:52