| appendIgnoreDupeAccession(const std::string value) | ms_mascotoptions | |
| appendProperty(const char *name, const char *value, const char *delimiter, const bool bFirstPlace=false) | ms_customproperty | |
| appendReportNumberChoice(const int value) | ms_mascotoptions | |
| appendTargetFDRPercentage(const double value, const bool makeDefault=false) | ms_mascotoptions | |
| appendText(const char *line, const bool bFirstPlace=false) | ms_customproperty | |
| clearIgnoreDupeAccessions() | ms_mascotoptions | |
| clearReportNumberChoices() | ms_mascotoptions | |
| clearTargetFDRPercentages() | ms_mascotoptions | |
| copyFrom(const ms_mascotoptions *right) | ms_mascotoptions | |
| matrix_science::ms_customproperty::copyFrom(const ms_customproperty *src) | ms_customproperty | |
| DECOY_ALGORITHM enum name | ms_mascotoptions | |
| DECOY_ALGORITHM_NONE enum value | ms_mascotoptions | |
| DECOY_PEPTIDE_RANDOM enum value | ms_mascotoptions | |
| DECOY_PEPTIDE_RANDOM_DIPEP enum value | ms_mascotoptions | |
| DECOY_PEPTIDE_REVERSE enum value | ms_mascotoptions | |
| DECOY_PEPTIDE_SHUFFLE enum value | ms_mascotoptions | |
| DECOY_PROTEIN_BASED_MASK enum value | ms_mascotoptions | |
| DECOY_PROTEIN_RANDOM enum value | ms_mascotoptions | |
| DECOY_PROTEIN_RANDOM_DIPEP enum value | ms_mascotoptions | |
| DECOY_PROTEIN_REVERSE enum value | ms_mascotoptions | |
| DECOY_PROTEIN_SHUFFLE enum value | ms_mascotoptions | |
| defaultValues() | ms_mascotoptions | |
| delNonEmpty() | ms_customproperty | |
| delProp(const char *name) | ms_customproperty | |
| delPropByNumber(const int index) | ms_customproperty | |
| delPropStart(const char *nameBeginning) | ms_customproperty | |
| EXEC_AFTER_SEARCH enum name | ms_mascotoptions | |
| findProperty(const char *name, const int startFrom=0) const | ms_customproperty | |
| findPropertyBeginning(const char *nameBeginning, const int startFrom=0) const | ms_customproperty | |
| 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 | |
| getCreatePipThreadBlockSize() const | ms_mascotoptions | |
| getCreatePipThreads() const | ms_mascotoptions | |
| getDechargeFragmentPeaks() const | ms_mascotoptions | |
| getDecoyTypeNoEnzyme() const | ms_mascotoptions | |
| getDecoyTypeSpecific() const | ms_mascotoptions | |
| getDefaultDelimiter() const | ms_customproperty | |
| getDelimiterByNumber(const int index) const | ms_customproperty | |
| 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 | |
| getMascotFileProcessingThreads() 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 | |
| getMaxIntactCrosslinkPeptides() const | ms_mascotoptions | |
| getMaxNumOfReportBuilderColumnArrangements() const | ms_mascotoptions | |
| getMaxNumPeptides() const | ms_mascotoptions | |
| getMaxPepModArrangements() const | ms_mascotoptions | |
| getMaxPepNumModifiedSites() 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 | |
| getNumberOfProperties() const | ms_customproperty | |
| 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 | |
| getPercolatorRtFlags(const bool anyRetentionTimes, const bool useRT) const | ms_mascotoptions | |
| getPercolatorTargetRankRelativeThreshold() const | ms_mascotoptions | |
| getPercolatorTargetRankScoreThreshold() const | ms_mascotoptions | |
| getPreceedingComments() const | ms_customproperty | |
| getPrecursorCutOutLowerLimit() const | ms_mascotoptions | |
| getPrecursorCutOutUpperLimit() const | ms_mascotoptions | |
| getPropertyName(const int index) const | ms_customproperty | |
| getPropValStringByName(const char *name) const | ms_customproperty | |
| getPropValStringByNumber(const int index) const | ms_customproperty | |
| 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 | |
| getSearchSubmitAcceptedFileTypes() const | ms_mascotoptions | |
| getSearchSubmitDefaultPeptideCharge() const | ms_mascotoptions | |
| getSearchSubmitMode() const | ms_mascotoptions | |
| getSearchSubmitOutputFormat() const | ms_mascotoptions | |
| getSelectSwitch() const | ms_mascotoptions | |
| getSendmailPath() 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 | |
| isAlwaysCreateDat28ResultsFile() const | ms_mascotoptions | |
| isAlwaysEnableAutoDecoySearch() const | ms_mascotoptions | |
| isAutoSelectCharge() const | ms_mascotoptions | |
| isClientResultFileMimeRefining() const | ms_mascotoptions | |
| isCreateLegacyModAndSubstitutionFiles() 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 | |
| isMatchOppositeCrosslinkPairs() 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 | |
| isUseHTTPProxyForHTTPS() const | ms_mascotoptions | |
| MASS_DECIMAL_PLACES enum value | ms_mascotoptions | |
| MAX_EXEC_AFTER_SEARCH enum value | ms_mascotoptions | |
| ms_customproperty() | ms_customproperty | |
| ms_mascotoptions() | ms_mascotoptions | |
| ms_mascotoptions(const ms_mascotoptions &src) | ms_mascotoptions | |
| MS_REVIEW_COL enum name | ms_mascotoptions | |
| MS_REVIEW_COL____LAST___ enum value | ms_mascotoptions | |
| MS_REVIEW_COL_DATABASE enum value | ms_mascotoptions | |
| MS_REVIEW_COL_DURATION enum value | ms_mascotoptions | |
| MS_REVIEW_COL_ENZYMEUSED enum value | ms_mascotoptions | |
| MS_REVIEW_COL_IPADDRESS enum value | ms_mascotoptions | |
| MS_REVIEW_COL_JOB enum value | ms_mascotoptions | |
| MS_REVIEW_COL_PEAKLISTDATAFILE enum value | ms_mascotoptions | |
| MS_REVIEW_COL_PID enum value | ms_mascotoptions | |
| MS_REVIEW_COL_PRIORITY enum value | ms_mascotoptions | |
| MS_REVIEW_COL_RESULTS_FILE enum value | ms_mascotoptions | |
| MS_REVIEW_COL_SEARCHTYPE enum value | ms_mascotoptions | |
| MS_REVIEW_COL_START_TIME enum value | ms_mascotoptions | |
| MS_REVIEW_COL_STATUS enum value | ms_mascotoptions | |
| MS_REVIEW_COL_TITLE enum value | ms_mascotoptions | |
| MS_REVIEW_COL_USEREMAIL enum value | ms_mascotoptions | |
| MS_REVIEW_COL_USERID enum value | ms_mascotoptions | |
| MS_REVIEW_COL_USERNAME enum value | ms_mascotoptions | |
| NUMERICAL_VALUE_STORAGE enum name | ms_mascotoptions | |
| operator=(const ms_mascotoptions &right) | ms_mascotoptions | |
| PERC_EXE_RT enum name | ms_mascotoptions | |
| PERC_EXE_RT_FORCE_OFF enum value | ms_mascotoptions | |
| PERC_EXE_RT_FORCE_ON enum value | ms_mascotoptions | |
| PERC_EXE_RT_USE_DEFAULT enum value | ms_mascotoptions | |
| setAlwaysCreateDat28ResultsFile(const bool value) | ms_mascotoptions | |
| setAlwaysEnableAutoDecoySearch(const bool value) | ms_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 | |
| setClientResultFileMimeRefining(const bool 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 | |
| setCreateLegacyModAndSubstitutionFiles(const bool value) | ms_mascotoptions | |
| setCreatePipThreadBlockSize(const int blockSize) | ms_mascotoptions | |
| setCreatePipThreads(const int nThreads) | ms_mascotoptions | |
| setDechargeFragmentPeaks(const int maxCharge) | ms_mascotoptions | |
| setDecoyTypeNoEnzyme(const int value) | ms_mascotoptions | |
| setDecoyTypeSpecific(const int value) | ms_mascotoptions | |
| setDefaultDelimiter(const char *delim) | ms_customproperty | |
| 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 | |
| setMascotFileProcessingThreads(const int value) | ms_mascotoptions | |
| setMascotJobIdFile(const char *str) | ms_mascotoptions | |
| setMascotMessage(const char *str) | ms_mascotoptions | |
| setMassDecimalPlaces(const int value) | ms_mascotoptions | |
| setMatchOppositeCrosslinkPairs(const bool 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 | |
| setMaxIntactCrosslinkPeptides(const int value) | ms_mascotoptions | |
| setMaxNumPeptides(const int value) | ms_mascotoptions | |
| setMaxPepModArrangements(const int value) | ms_mascotoptions | |
| setMaxPepNumModifiedSites(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 | |
| setPercolatorTargetRankRelativeThreshold(const double threshold) | ms_mascotoptions | |
| setPercolatorTargetRankScoreThreshold(const int threshold) | 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 | |
| setPropertyName(const int index, const char *name) | ms_customproperty | |
| setPropValBoolByName(const char *name, const bool value, const bool bFirstPlace=false) | ms_customproperty | |
| setPropValCharByName(const char *name, const char value, const bool bFirstPlace=false) | ms_customproperty | |
| setPropValFloatByName(const char *name, const double value, const bool bFirstPlace=false) | ms_customproperty | |
| setPropValInt64ByName(const char *name, const INT64 value, const bool bFirstPlace=false) | ms_customproperty | |
| setPropValIntByName(const char *name, const int value, const bool bFirstPlace=false) | ms_customproperty | |
| setPropValStringByName(const char *name, const char *value, const bool bFirstPlace=false) | ms_customproperty | |
| setPropValStringByNumber(const int index, const char *value) | ms_customproperty | |
| 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 | |
| setSearchSubmitAcceptedFileTypes(const std::string value) | ms_mascotoptions | |
| setSearchSubmitDefaultPeptideCharge(const std::string value) | ms_mascotoptions | |
| setSearchSubmitMode(const std::string value) | ms_mascotoptions | |
| setSearchSubmitOutputFormat(const std::string value) | ms_mascotoptions | |
| setSectionAvailable(const bool value) | ms_mascotoptions | |
| setSelectSwitch(const int value) | ms_mascotoptions | |
| setSendmailPath(const char *str) | 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, bool doCheck=true) | 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 | |
| setUseHTTPProxyForHTTPS(const bool value) | ms_mascotoptions | |
| setVmemory(const INT64 value) | ms_mascotoptions | |
| uncommentProp(const int index, const char *delimeter=0) | ms_customproperty | |
| ~ms_customproperty() | ms_customproperty | |
| ~ms_mascotoptions() | ms_mascotoptions | |