Matrix Science header

ms_mascotoptions.hpp

00001 /*
00002 ##############################################################################
00003 # file: ms_mascotoptions.hpp                                                 #
00004 # 'msparser' toolkit                                                         #
00005 # Encapsulates "Options" section of "mascot.dat" file that describes most    #
00006 # important parameters                                                       #
00007 ##############################################################################
00008 # COPYRIGHT NOTICE                                                           #
00009 # Copyright 1998-2003 Matrix Science Limited  All Rights Reserved.           #
00010 #                                                                            #
00011 ##############################################################################
00012 #    $Archive:: /Mowse/ms_mascotresfile/include/ms_mascotoptions.hpp       $ #
00013 #     $Author: francoisr@matrixscience.com $ #
00014 #       $Date: 2021-05-21 16:59:53 +0100 $ #
00015 #   $Revision: 666210a89688eb394d284ca454da0ad70252e9db | MSPARSER_REL_2_8_1-0-gea32989045 $ #
00016 # $NoKeywords::                                                            $ #
00017 ##############################################################################
00018 */
00019 
00020 #ifndef MS_MASCOTOPTIONS_HPP
00021 #define MS_MASCOTOPTIONS_HPP
00022 
00023 
00024 #include <string>
00025 #include <vector>
00026 
00027 namespace matrix_science {
00032 #ifndef DOXYGEN_SHOULD_SKIP_THIS
00033     class MS_MASCOTRESFILE_API ms_blastaccession
00034     {
00035         friend class ms_datfile;
00036 
00037     public:
00038         ms_blastaccession();
00039         ms_blastaccession(const ms_blastaccession& src);
00040         ~ms_blastaccession();
00041 
00042         void defaultValues();
00043         void copyFrom(const ms_blastaccession* right);
00044 #ifndef SWIG
00045         ms_blastaccession& operator=(const ms_blastaccession& right);
00046 #endif
00047         bool isUseRegex() const;
00048         void setUseRegex(const bool flag);
00049 
00050         int getMinLength() const;
00051         void setMinLength(const int value);
00052 
00053         const char* getStart() const;
00054         const char* getStop() const;
00055 
00056     private:
00057 
00058         bool useRegex_;
00059         int  minLen_;
00060         char start_[255];
00061         char stop_[255];
00062     }; // class ms_blastaccession
00063 #endif
00064 
00066 
00090     class MS_MASCOTRESFILE_API ms_mascotoptions: public ms_customproperty
00091     {
00092         friend class ms_datfile;
00093 
00094     public:
00096 
00099         enum MS_REVIEW_COL
00100         {
00101             MS_REVIEW_COL_JOB               = 0x0000, 
00102             MS_REVIEW_COL_PID               = 0x0001, 
00103             MS_REVIEW_COL_DATABASE          = 0x0002, 
00104             MS_REVIEW_COL_USERNAME          = 0x0003, 
00105             MS_REVIEW_COL_USEREMAIL         = 0x0004, 
00106             MS_REVIEW_COL_TITLE             = 0x0005, 
00107             MS_REVIEW_COL_RESULTS_FILE      = 0x0006, 
00108             MS_REVIEW_COL_START_TIME        = 0x0007, 
00109             MS_REVIEW_COL_DURATION          = 0x0008, 
00110             MS_REVIEW_COL_STATUS            = 0x0009, 
00111             MS_REVIEW_COL_PRIORITY          = 0x000A, 
00112             MS_REVIEW_COL_SEARCHTYPE        = 0x000B, 
00113             MS_REVIEW_COL_ENZYMEUSED        = 0x000C, 
00114             MS_REVIEW_COL_IPADDRESS         = 0x000D, 
00115             MS_REVIEW_COL_USERID            = 0x000E, 
00116             MS_REVIEW_COL_PEAKLISTDATAFILE  = 0x000F, 
00117             MS_REVIEW_COL____LAST___        = 0x0010  
00118         };
00119 
00121 
00124         enum PERC_EXE_RT {
00125             PERC_EXE_RT_USE_DEFAULT = 1, 
00126             PERC_EXE_RT_FORCE_ON    = 2, 
00127             PERC_EXE_RT_FORCE_OFF   = 3  
00128         };
00129 
00131 
00156         enum DECOY_ALGORITHM {
00157             DECOY_ALGORITHM_NONE        = 0, 
00158             DECOY_PROTEIN_REVERSE       = 1, 
00159             DECOY_PEPTIDE_REVERSE       = 2, 
00160             DECOY_PROTEIN_RANDOM        = 3, 
00161             DECOY_PEPTIDE_RANDOM        = 4, 
00162             DECOY_PROTEIN_RANDOM_DIPEP  = 5, 
00163             DECOY_PEPTIDE_RANDOM_DIPEP  = 6, 
00164             DECOY_PROTEIN_SHUFFLE       = 7, 
00165             DECOY_PEPTIDE_SHUFFLE       = 8, 
00166 
00167             DECOY_PROTEIN_BASED_MASK    = 0x0001 
00168         };
00169 
00170 
00172 
00175         enum EXEC_AFTER_SEARCH
00176         {
00177             MAX_EXEC_AFTER_SEARCH = 10 
00178         };
00179 
00180         enum REPORTBUILDER_COL_ARR
00181         {
00182             MAX_REPORTBUILDER_COL_ARR = 10
00183         };
00184 
00186         enum NUMERICAL_VALUE_STORAGE
00187         {
00188             MASS_DECIMAL_PLACES = 6 
00189         };
00190 
00192         ms_mascotoptions();
00193 
00195         ms_mascotoptions(const ms_mascotoptions& src);
00196 
00198         ~ms_mascotoptions();
00199 
00201         void copyFrom(const ms_mascotoptions* right);
00202 
00203 #ifndef SWIG
00204 
00205         ms_mascotoptions& operator=(const ms_mascotoptions& right);
00206 #endif
00207 
00208         void defaultValues();
00209 
00211         bool isSectionAvailable() const;
00212 
00214         void setSectionAvailable(const bool value);
00215 
00217         bool isSaveLastQueryAsc() const;
00218 
00220         void setSaveLastQueryAsc(const bool flag);
00221 
00223         bool isSaveEveryLastQueryAsc() const;
00224 
00226         void setSaveEveryLastQueryAsc(const bool flag);
00227 
00229         std::string getLastQueryAscFile() const;
00230 
00232         void setLastQueryAscFile(const char* str);
00233 
00235         std::string getErrorLogFile() const;
00236 
00238         void setErrorLogFile(const char* str);
00239 
00241         std::string getSearchLogFile() const;
00242 
00244         void setSearchLogFile(const char* str);
00245 
00247         std::string getMonitorLogFile() const;
00248 
00250         void setMonitorLogFile(const char* str);
00251 
00253         std::string getInterFileBasePath() const;
00254 
00256         void setInterFileBasePath(const char* str);
00257 
00259         std::string getInterFileRelPath() const;
00260 
00262         void setInterFileRelPath(const char* str);
00263 
00265         std::string getMascotCmdLine() const;
00266 
00268         void setMascotCmdLine(const char* str);
00269 
00271         std::string getTestDirectory() const;
00272 
00274         void setTestDirectory(const char* str);
00275 
00277         std::string getMascotControlFile() const;
00278 
00280         void setMascotControlFile(const char* str);
00281 
00283         std::string getMascNodeCtrlFile() const;
00284 
00286         void setMascNodeCtrlFile(const char* str);
00287 
00289         std::string getMascotJobIdFile() const;
00290 
00292         void setMascotJobIdFile(const char* str);
00293 
00295         std::string getGetSeqJobIdFile() const;
00296 
00298         void setGetSeqJobIdFile(const char* str);
00299 
00301         int getUniqueJobStartNumber() const;
00302 
00304         void setUniqueJobStartNumber(const int value);
00305 
00307         std::string getResultsPerlScript() const;
00308 
00310         void setResultsPerlScript(const char* str);
00311 
00313         std::string getNoResultsScript() const;
00314 
00316         void setNoResultsScript(const char* str);
00317 
00319         std::string getResultsFullURL() const;
00320 
00322         void setResultsFullURL(const char* str);
00323 
00325         std::string getLogoImageFile() const;
00326 
00328         void setLogoImageFile(const char* str);
00329 
00331         int getMassDecimalPlaces() const;
00332 
00334         void setMassDecimalPlaces(const int value);
00335 
00337         int getIonsDecimalPlaces() const;
00338 
00340         void setIonsDecimalPlaces(const int value);
00341 
00343         int getIntensitySigFigs() const;
00344 
00346         void setIntensitySigFigs(const int value);
00347 
00349         bool isEmailUsersEnabled() const;
00350 
00352         void setEmailUsersEnabled(const bool value);
00353 
00355         bool isEmailErrorsEnabled() const;
00356 
00358         void setEmailErrorsEnabled(const bool value);
00359 
00361         int getMailTransport() const;
00362 
00364         void setMailTransport(const int value);
00365 
00367         std::string getEmailService() const;
00368 
00370         void setEmailService(const char* str);
00371 
00373         std::string getEmailPassword() const;
00374 
00376         void setEmailPassword(const char* str);
00377 
00379         std::string getEmailProfile() const;
00380 
00382         void setEmailProfile(const char* str);
00383 
00385         std::string getSendmailPath() const;
00386 
00388         void setSendmailPath(const char* str);
00389 
00391         std::string getEmailFromUser() const;
00392 
00394         void setEmailFromUser(const char* str);
00395 
00397         std::string getEmailFromTextName() const;
00398 
00400         void setEmailFromTextName(const char* str);
00401 
00403         int getEmailTimeOutPeriod() const;
00404 
00406         void setEmailTimeOutPeriod(const int value);
00407 
00409         int getMonitorEmailCheckFreq() const;
00410 
00412         void setMonitorEmailCheckFreq(const int value);
00413 
00415         std::string getMailTempFile() const;
00416 
00418         void setMailTempFile(const char* str);
00419 
00421         std::string getErrMessageEmailTo() const;
00422 
00424         void setErrMessageEmailTo(const char* str);
00425 
00427         int getMonitorTestTimeout() const;
00428 
00430         void setMonitorTestTimeout(const int value);
00431 
00433         std::string getNTMonitorGroup() const;
00434 
00436         void setNTMonitorGroup(const char* str);
00437 
00439         std::string getNTIUserGroup() const;
00440 
00442         void setNTIUserGroup(const char* str);
00443 
00445         int getUnixWebUserGroup() const;
00446 
00448         void setUnixWebUserGroup(const int value);
00449 
00451         bool isForkForUnixApache() const;
00452 
00454         void setForkForUnixApache(const bool value);
00455 
00457         int getSeparateLockMem() const;
00458 
00460         void setSeparateLockMem(const int value);
00461 
00463         std::string getFormVersion() const;
00464 
00466         void setFormVersion(const char* str);
00467 
00469         int getMaxSequenceLen() const;
00470 
00472         void setMaxSequenceLen(const int value);
00473 
00475         int getMaxConcurrentSearches() const;
00476 
00478         void setMaxConcurrentSearches(const int value);
00479 
00481         int getMaxSearchesPerUser() const;
00482 
00484         void setMaxSearchesPerUser(const int value);
00485 
00487         double getCentroidWidth() const;
00488 
00490         void setCentroidWidth(const double value);
00491 
00493         int getCentroidWidthCount() const;
00494 
00496         void setCentroidWidthCount(const int value);
00497 
00499         int getMaxDescriptionLen() const;
00500 
00502         void setMaxDescriptionLen(const int value);
00503 
00505         int getMaxNumPeptides() const;
00506 
00508         void setMaxNumPeptides(const int value);
00509 
00511         INT64 getVmemory() const;
00512 
00514         void setVmemory(const INT64 value);
00515 
00517         int getNumberOfReportNumberChoices() const;
00518 
00520         void clearReportNumberChoices();
00521 
00523         int getReportNumberChoice(const int index) const;
00524 
00526         void setReportNumberChoice(const int index, const int value);
00527 
00529         void appendReportNumberChoice(const int value);
00530 
00532         int getNumberOfTargetFDRPercentages() const;
00533 
00535         void clearTargetFDRPercentages();
00536 
00538         double getTargetFDRPercentage(const int index) const;
00539 
00541         void setTargetFDRPercentage(const int index, const double value, const bool makeDefault = false);
00542 
00544         void appendTargetFDRPercentage(const double value, const bool makeDefault = false);
00545 
00547         bool isDefaultTargetFDRPercentage(const int index) const;
00548 
00550         void setDefaultTargetFDRPercentage(const int index);
00551 
00553         int getReviewColWidth(const MS_REVIEW_COL index) const;
00554 
00556         void setReviewColWidth(const MS_REVIEW_COL index, const int value);
00557         
00559         bool getReviewColDisplay(const MS_REVIEW_COL index) const;
00560 
00562         void setReviewColDisplay(const MS_REVIEW_COL index, const bool value);
00563 
00565         std::string getReportBuilderColumnArrangement(const int index) const;
00566 
00568         int getMaxNumOfReportBuilderColumnArrangements() const;
00569 
00571         void setReportBuilderColumnArrangement(const int index, const std::string str);
00572 
00574         std::string getSpectrumViewerColourSchemeString(const std::string &name) const;
00575 
00577         std::vector<std::string> getSpectrumViewerColourSchemeNames() const;
00578 
00580         void setSpectrumViewerColourSchemeString(const std::string &name, const std::string &str, bool doCheck = true);
00581 
00583         std::string getSpectrumViewerDefaultColourSchemeName() const;
00584 
00586         void setSpectrumViewerDefaultColourSchemeName(const std::string &name);
00587 
00589         std::string getProxyType() const;
00590 
00592         void setProxyType(const std::string &value);
00593 
00595         bool isUseHTTPProxyForFTP() const;
00596 
00598         void setUseHTTPProxyForFTP(const bool value);
00599 
00601         bool isUseHTTPProxyForHTTPS() const;
00602 
00604         void setUseHTTPProxyForHTTPS(const bool value);
00605 
00607         std::string getProxyServer() const;
00608 
00610         void setProxyServer(const char* str);
00611 
00613         std::string getProxyUsername() const;
00614 
00616         void setProxyUsername(const char* str);
00617 
00619         std::string getProxyPassword() const;
00620 
00622         void setProxyPassword(const char* str);
00623 
00625         int getMinPepLenInPepSummary() const;
00626 
00628         void setMinPepLenInPepSummary(const int value);
00629 
00631         int getMaxQueries() const;
00632 
00634         void setMaxQueries(const int value);
00635 
00637         bool isShowSubsets() const;
00638 
00640         void setShowSubsets(const bool value);
00641 
00643         double getShowSubsets() const;
00644 
00646         void setShowSubsets(const double value);
00647 
00649         bool isRequireBoldRed() const;
00650 
00652         void setRequireBoldRed(const bool value);
00653 
00655         double getSigThreshold() const;
00656 
00658         void setSigThreshold(const double value);
00659 
00661         double getSiteAnalysisMD10Prob() const;
00662 
00664         void setSiteAnalysisMD10Prob(const double value);
00665 
00667         int getMaxVarMods() const;
00668 
00670         void setMaxVarMods(const int value);
00671 
00673         int getMaxEtVarMods() const;
00674 
00676         void setMaxEtVarMods(const int value);
00677 
00679         int getErrTolMaxAccessions() const;
00680 
00682         void setErrTolMaxAccessions(const int value);
00683 
00685         bool isLabelAll() const;
00686 
00688         void setLabelAll(const bool value);
00689 
00691         bool isShowAllFromErrorTolerant() const;
00692 
00694         void setShowAllFromErrorTolerant(const bool value);
00695 
00697         double getIgnoreIonsScoreBelow() const;
00698 
00700         void setIgnoreIonsScoreBelow(const double value);
00701 
00703         std::string getMonitorPidFile() const;
00704 
00706         void setMonitorPidFile(const char* str);
00707 
00709         bool isStoreModPermutations() const;
00710 
00712         void setStoreModPermutations(const bool value);
00713 
00715         int getProteinsInResultsFile() const;
00716 
00718         void setProteinsInResultsFile(const int value);
00719 
00721         std::string getMascotMessage() const;
00722 
00724         void setMascotMessage(const char* str);
00725 
00727         int getSplitNumberOfQueries() const;
00728 
00730         void setSplitNumberOfQueries(const int value);
00731 
00733         int getSplitDataFileSize() const;
00734 
00736         void setSplitDataFileSize(const int value);
00737 
00739         bool isMoveOldDbToOldDir() const;
00740 
00742         void setMoveOldDbToOldDir(const bool value);
00743 
00745         bool isRemoveOldIndexFiles() const;
00746 
00748         void setRemoveOldIndexFiles(const bool value);
00749 
00751         int getFeatureTableLength() const;
00752 
00754         void setFeatureTableLength(const int value);
00755 
00757         double getFeatureTableMinScore() const;
00758 
00760         void setFeatureTableMinScore(const double value);
00761 
00763         std::string getICATLight() const;
00764 
00766         void setICATLight(const char* modName);
00767 
00769         std::string getICATHeavy() const;
00770 
00772         void setICATHeavy(const char* modName);
00773 
00775         std::string getICATFilter() const;
00776 
00778         void setICATFilter(const char* filterString);
00779 
00781         std::string getICATQuantitationMethod() const;
00782 
00784         void setICATQuantitationMethod(const char* methodName);
00785 
00787         unsigned int getNumberOfIgnoreDupeAccessions() const;
00788 
00790         void clearIgnoreDupeAccessions();
00791 
00793         std::string getIgnoreDupeAccession(const unsigned int index) const;
00794 
00796         void setIgnoreDupeAccession(const unsigned int index, const std::string value);
00797 
00799         void appendIgnoreDupeAccession(const std::string value);
00800 
00802         bool isInIgnoreDupeAccessionList(const std::string value) const;
00803 
00805         int getUnixDirPerm() const;
00806 
00808         void setUnixDirPerm(const int value);
00809 
00811         bool isUnixDirPermDefined() const;
00812 
00814         int getMudpit() const;
00815 
00817         void setMudpit(const int value);
00818 
00820         double getPrecursorCutOutLowerLimit() const;
00821 
00823         void setPrecursorCutOutLowerLimit(const double value);
00824 
00826         double getPrecursorCutOutUpperLimit() const;
00827 
00829         void setPrecursorCutOutUpperLimit(const double value);
00830 
00832         bool isAutoSelectCharge() const;
00833 
00835         void setAutoSelectCharge(const bool value);
00836 
00838         std::string getTaxBrowserUrl() const;
00839 
00841         void setTaxBrowserUrl(const std::string value);
00842 
00844         int getMinPepLenInSearch() const;
00845 
00847         void setMinPepLenInSearch(const int value);
00848 
00850         int getMaxPepModArrangements() const;
00851 
00853         void setMaxPepModArrangements(const int value);
00854 
00856         int getMaxPepNumVarMods() const;
00857 
00859         void setMaxPepNumVarMods(const int value);
00860 
00862         int getMaxPepNumModifiedSites() const;
00863 
00865         void setMaxPepNumModifiedSites(const int value);
00866 
00868         bool isIteratePMFIntensities() const;
00869 
00871         void setIteratePMFIntensities(const bool value);
00872 
00874         double getMinEtagMassDelta() const;
00875 
00877         void setMinEtagMassDelta(const double value);
00878 
00880         double getMaxEtagMassDelta() const;
00881 
00883         void setMaxEtagMassDelta(const double value);
00884 
00886         std::string getResultsFileFormatVersion() const;
00887 
00889         void setResultsFileFormatVersion(const char *value);
00890 
00892         std::string getSortUnassigned() const;
00893 
00895         void setSortUnassigned(const std::string newValue);
00896 
00898         int getSelectSwitch() const;
00899 
00901         void setSelectSwitch(const int value);
00902 
00904         double getMudpitSwitch() const;
00905 
00907         void setMudpitSwitch(const double value);
00908 
00910         int getMaxDatabases() const;
00911 
00913         void setMaxDatabases(const int value);
00914 
00916         std::string getCacheDirectory() const;
00917 
00919         void setCacheDirectory(const char * value);
00920 
00922         std::string getResfileCache() const;
00923 
00925         void setResfileCache(const char * value);
00926 
00928         std::string getResultsCache() const;
00929 
00931         void setResultsCache(const char * value);
00932 
00934         bool isPercolator() const;
00935 
00937         void setPercolator(const bool value);
00938 
00940         std::string getPercolatorFeatures() const;
00941 
00943         void setPercolatorFeatures(std::string value);
00944 
00946         int getPercolatorMinQueries() const;
00947 
00949         void setPercolatorMinQueries(const int value);
00950 
00952         int getPercolatorMinSequences() const;
00953 
00955         void setPercolatorMinSequences(const int value);
00956 
00958         bool isPercolatorUseProteins() const;
00959 
00961         void setPercolatorUseProteins(const bool value);
00962 
00964         bool isPercolatorUseRT() const;
00965 
00967         void setPercolatorUseRT(const bool value);
00968 
00970         std::string getPercolatorExeFlags(bool anyRetentionTimes,
00971                                           const std::vector<std::string> percolatorFiles,
00972                                           const PERC_EXE_RT rt = PERC_EXE_RT_USE_DEFAULT) const;
00973 
00975         void setPercolatorExeFlags(const char * value);
00976 
00978         int getPercolatorTargetRankScoreThreshold() const;
00979 
00981         void setPercolatorTargetRankScoreThreshold(const int threshold);
00982 
00984         double getPercolatorTargetRankRelativeThreshold() const;
00985 
00987         void setPercolatorTargetRankRelativeThreshold(const double threshold);
00988 
00990         int getCreatePipThreads() const;
00991 
00993         void setCreatePipThreads(const int nThreads);
00994 
00996         int getCreatePipThreadBlockSize() const;
00997 
00999         void setCreatePipThreadBlockSize(const int blockSize);
01000 
01002         int getExecAfterSearch(const char               * szResultsFilePath,
01003                                std::vector<std::string> & commands,
01004                                std::vector<std::string> & titles,
01005                                std::vector<int>         & waitfor,
01006                                std::vector<int>         & logging,
01007                                std::vector<std::string> & additionalFlags,
01008                                const char               * sessionID = 0,
01009                                const char               * taskID = 0) const;
01010 
01012         void setExecAfterSearch(const int num, std::string value);
01013 
01015         std::string getResultsPerlScript_2() const;
01016 
01018         void setResultsPerlScript_2(std::string value);
01019 
01021         std::string getResultsFullURL_2() const;
01022 
01024         void setResultsFullURL_2(std::string value);
01025 
01027         int getProteinFamilySwitch() const;
01028 
01030         void setProteinFamilySwitch(const int value);
01031 
01033         int getDecoyTypeSpecific() const;
01034 
01036         void setDecoyTypeSpecific(const int value);
01037 
01039         int getDecoyTypeNoEnzyme() const;
01040 
01042         void setDecoyTypeNoEnzyme(const int value);
01043 
01045         int getSVGSpectrumSwitch() const;
01046 
01048         void setSVGSpectrumSwitch(const int value);
01049 
01051         int getDisplayNonSignificantMatches() const;
01052 
01054         void setDisplayNonSignificantMatches(const int value);
01055 
01057         std::string getCompressToolAA() const;
01058 
01060         void setCompressToolAA(const std::string value);
01061 
01063         std::string getCompressToolNA() const;
01064 
01066         void setCompressToolNA(const std::string value);
01067 
01069         std::string getCompressToolSL() const;
01070 
01072         void setCompressToolSL(const std::string value);
01073         
01075         std::string getCompressToolCommandLineFasta(DATABASE_TYPE dbType,
01076                                                const std::string & dbname,
01077                                                const std::string & dbpath) const; 
01078         
01080         std::string getCompressToolCommandLineLibrary(const std::string & logfilepath,
01081                                                       const std::string & inputfile,
01082                                                       const std::string & outputdirectory) const; 
01083 
01085         std::string getPepSearchTool() const;
01086 
01088         void setPepSearchTool(const std::string value);
01089         
01091         std::string getPepSearchToolCommandLine(const std::string & peptideToleranceUnit,
01092                                                 const double      & peptideTolerance,
01093                                                 const std::string & ionToleranceUnit,
01094                                                 const double      & ionTolerance,
01095                                                 const std::string & libraryDirectoryPath,
01096                                                 const std::string & inputFileRelativePath,
01097                                                 const std::string & outputFileRelativePath) const;
01098 
01100         int getSpectraPerLibraryBlock() const;
01101 
01103         void setSpectraPerLibraryBlock(const int value);
01104 
01106         int getCrawlerNumPeaksPer100Da() const;
01107 
01109         void setCrawlerNumPeaksPer100Da(const int value);        
01110 
01112         std::string getSearchSubmitMode() const;
01113 
01115         void setSearchSubmitMode(const std::string value);
01116 
01118         int getDechargeFragmentPeaks() const;
01119 
01121         void setDechargeFragmentPeaks(const int maxCharge);
01122 
01124 
01126         const ms_blastaccession* getGetSeqBlastAccession() const;
01127 
01129         void setGetSeqBlastAccession(const ms_blastaccession* value);
01130 
01131         // MatrixScience internal usage only
01132         int getMinPeakIteration() const;
01133 
01134         // MatrixScience internal usage only
01135         void setMinPeakIteration(const int value);
01136 
01137         // MatrixScience internal usage only
01138         bool isEncryptURL() const;
01139 
01140         // MatrixScience internal usage only
01141         void setEncryptURL(const bool value);
01142 
01143         // MatrixScience internal usage only
01144         std::string getPercolatorExeFlags() const;
01145 
01146         // MatrixScience internal usage only
01147         std::string getPercolatorRtFlags(const bool anyRetentionTimes, const bool useRT) const;
01148 
01149         // MatrixScience internal usage only
01150         std::string getExecAfterSearch(const int num) const;
01151 
01152         // MatrixScience internal usage only
01153         void checkExecAfterSearch(ms_errs & err);
01154 
01155         // MatrixScience internal usage only
01156         void checkReportBuilderColumnArrangement(ms_errs & err);
01157 
01158         // MatrixScience internal usage only
01159         void checkSpectrumViewerColourSchemes(ms_errs & err, bool addToList = true);
01160 
01162         bool isMatchOppositeCrosslinkPairs() const;
01163 
01165         void setMatchOppositeCrosslinkPairs(const bool value);
01166 
01168         int getMaxIntactCrosslinkPeptides() const;
01169 
01171         void setMaxIntactCrosslinkPeptides(const int value);
01172 
01174         bool isTransferParsingToNodes() const;
01175 
01177         void setTransferParsingToNodes(const bool value);
01178 
01180         int getMascotFileProcessingThreads() const;
01181 
01183         void setMascotFileProcessingThreads(const int value);
01184 
01186         int getInputFileParsingThreads() const;
01187 
01189         void setInputFileParsingThreads(const int value);
01190         
01192         int getChunkReadingThreads() const;
01193 
01195         void setChunkReadingThreads(const int value);
01196         
01198         int getChunkPreparationThreads() const;
01199 
01201         void setChunkPreparationThreads(const int value);
01202 
01203 #ifdef SUPPRESS_MS_CUSTOMPROPERTY_INHERITANCE
01204 #include "suppress_ms_customproperty.hpp"
01205 #endif
01206 
01207     private:
01208         void        synchronizeReportNumberChoices_();
01209         void        synchronizeIgnoreDupeAccession_();
01210         void        synchronizeTargetFDRPercentages_();
01211 
01212         bool        sectionAvailable_;
01213 
01214         bool        saveLastQueryAsc_;
01215         bool        saveEveryLastQueryAsc_;
01216         std::string lastQueryAscFile_;
01217 
01218         std::string errorLogFile_;
01219         std::string searchLogFile_;
01220         std::string monitorLogFile_;
01221         std::string interFileBasePath_;
01222         std::string interFileRelPath_;
01223 
01224         std::string mascotCmdLine_;
01225         std::string testDirectory_;
01226         std::string mascotControlFile_;
01227         std::string mascNodeCtrlFile_;
01228         std::string mascotJobIdFile_;
01229         std::string getSeqJobIdFile_;
01230         int         uniqueJobStartNumber_;
01231 
01232         std::string resultsPerlScript_;
01233         std::string noResultsScript_;
01234         std::string resultsFullURL_;
01235         std::string logoImageFile_;
01236 
01237         int         massDecimalPlaces_;
01238         int         ionsDecimalPlaces_;
01239         int         intensitySigFigs_;
01240 
01241         bool        emailUsersEnabled_;
01242         bool        emailErrorsEnabled_;
01243         int         mailTransport_;
01244         std::string emailService_;
01245         std::string emailPassword_;
01246         std::string emailProfile_;
01247         std::string sendmailPath_;
01248         std::string emailFromUser_;
01249         std::string emailFromTextName_;
01250         int         emailTimeOutPeriod_;
01251         int         monitorEmailCheckFreq_;
01252         std::string mailTempFile_;
01253         std::string errMessageEmailTo_;
01254 
01255         int         monitorTestTimeout_;
01256         std::string NTMonitorGroup_;
01257         std::string NTIUserGroup_;
01258         int         unixWebUserGroup_;
01259         bool        forkForUnixApache_;
01260         int         separateLockMem_;
01261 
01262         std::string formVersion_;
01263         int         maxSequenceLen_;
01264         int         maxConcurrentSearches_;
01265         int         maxSearchesPerUser_;
01266         double      centroidWidth_;
01267         int         centroidWidthCount_;
01268         int         maxDescriptionLen_;
01269         int         maxNumPeptides_;
01270         INT64       vmemory_;
01271 
01272         std::vector< int > reportNumberChoices_;
01273         std::vector< double > targetFDRPercentages_;
01274         int         defaultTargetFDRPercentagesIx_;
01275 
01276         int         reviewColWidths_[MS_REVIEW_COL____LAST___];
01277         bool        reviewColDisplay_[MS_REVIEW_COL____LAST___];
01278         std::vector<std::string> reportBuilderColArr_;
01279 
01280         std::string defaultColourSchemeName_;
01281         std::vector<std::string> colourSchemeNames_;
01282         std::vector<std::string> colourSchemeStrings_;
01283 
01284         std::string proxyType_;
01285         bool        useHTTPProxyForFTP_;
01286         bool        useHTTPProxyForHTTPS_;
01287         std::string proxy_server_;
01288         std::string proxy_username_;
01289         std::string proxy_password_;
01290 
01291         int         maxVarMods_;
01292         int         maxEtVarMods_;
01293         int         errTolMaxAccessions_;
01294         bool        labelAll_;
01295         bool        showAllFromErrorTolerant_;
01296 
01297         int         minPepLenInPepSummary_;
01298         int         maxPepModArrangements_;
01299         int         maxPepNumVarMods_;
01300         int         maxPepNumModifiedSites_;
01301         int         maxQueries_;
01302         double      showSubsets_;
01303         bool        requireBoldRed_;
01304         double      sigThreshold_;
01305         double      siteAnalysisMD10Prob_;
01306         double      ignoreIonsScoreBelow_;
01307 
01308         std::string monitorPidFile_;
01309         bool        storeModPermutations_;
01310         int         proteinsInResultsFile_;
01311         std::string mascotMessage_;
01312         int         splitNumberOfQueries_;
01313         int         splitDataFileSize_;
01314         bool        moveOldDbToOldDir_;
01315         bool        removeOldIndexFiles_;
01316 
01317         int         featureTableLength_;
01318         double      featureTableMinScore_;
01319 
01320         std::string ICATLight_;
01321         std::string ICATHeavy_;
01322         std::string ICATFilter_;
01323         std::string ICATQuantitationMethod_;
01324 
01325         int         UnixDirPerm_;
01326         bool        UnixDirPermDefined_;
01327         int         mudpit_;
01328 
01329         typedef std::vector<std::string> t_dupeAccs;
01330         t_dupeAccs ignoreDupeAccessions_;
01331 
01332         double      precursorCutOutLowerLimit_;
01333         double      precursorCutOutUpperLimit_;
01334 
01335         bool        autoSelectCharge_;
01336         std::string taxBrowserUrl_;
01337         int         minPepLenInSearch_;
01338         bool        iteratePMFIntensities_;
01339 
01340         double      minEtagMassDelta_;
01341         double      maxEtagMassDelta_;
01342 
01343         std::string resultsFileFormatVersion_;
01344         std::string sortUnassigned_;
01345         int         selectSwitch_;
01346         double      mudpitSwitch_;
01347 
01348         int         maxDatabases_;
01349         std::string cacheDirectory_;
01350 
01351         std::string resfileCache_;
01352         std::string resultsCache_;
01353 
01354         bool        percolator_;
01355         std::string percolatorFeatures_;
01356         int         percolatorMinQueries_;
01357         int         percolatorMinSequences_;
01358         bool        percolatorUseProteins_;
01359         bool        percolatorUseRT_;
01360         std::string percolatorExeFlags_;
01361         int percolatorTargetRankScoreThreshold_;
01362         double percolatorTargetRankRelativeThreshold_;
01363 
01364         int createPipThreads_;
01365         int createPipThreadBlockSize_;
01366 
01367         std::vector<std::string> execAfterSearch_;
01368         std::vector<std::string> execAfterSearchCommands_;
01369         std::vector<std::string> execAfterSearchTitles_;
01370         std::vector<int>         execAfterSearchWaitFor_;
01371         std::vector<int>         execAfterSearchLogging_;
01372         std::vector<std::string> execAfterSearchAdditionalFlags_;
01373         std::string resultsPerlScript_2_;
01374         std::string resultsFullURL_2_;
01375         int         proteinFamilySwitch_;
01376 
01377         int         decoyTypeSpecific_;
01378         int         decoyTypeNoEnzyme_;
01379 
01380         int         svgSpectrumSwitch_;
01381         int         displayNonSigMatches_;
01382 
01383         ms_blastaccession   getSeqBlastAccession_;
01384         int         minPeakIteration_;
01385         bool        encryptURL_;
01386         
01387         std::string compressToolAA_;
01388         std::string compressToolNA_;
01389         std::string compressToolSL_;
01390         std::string pepSearchTool_;
01391         int         spectraPerLibraryBlock_;
01392         int         crawlerNumPeaksPer100Da_;
01393         bool        matchOppositeCrosslinkPairs_;
01394         int         maxIntactCrosslinkPeptides_;
01395         std::string searchSubmitMode_;
01396         int         dechargeFragmentPeaks_;
01397         bool        transferParsingToNodes_; //internal Mascot debug option
01398         int         mascotFileProcessingThreads_;
01399         int         inputFileParsingThreads_; //internal Mascot debug option
01400         int         chunkReadingThreads_; //internal Mascot debug option
01401         int         chunkPreparationThreads_; //internal Mascot debug option
01402     }; // class ms_mascotoptions // end of config_group
01404 } // namespace matrix_science
01405 
01406 #endif // MS_MASCOTOPTIONS_HPP
01407 
01408 /*------------------------------- End of File -------------------------------*/

Copyright © 2022 Matrix Science Ltd.  All Rights Reserved. Generated on Thu Mar 31 2022 01:12:29