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: villek $ #
00014 #       $Date: 2018/02/15 16:39:13 $ #
00015 #   $Revision: 1.58.2.1 $ #
00016 # $NoKeywords::                                                            $ #
00017 ##############################################################################
00018 */
00019 
00020 #ifndef MS_MASCOTOPTIONS_HPP
00021 #define MS_MASCOTOPTIONS_HPP
00022 
00023 #ifdef _WIN32
00024 #pragma warning(disable:4251)   // Don't want all classes to be exported
00025 #pragma warning(disable:4786)   // Debug symbols too long
00026 #   ifndef _MATRIX_USE_STATIC_LIB
00027 #       ifdef MS_MASCOTRESFILE_EXPORTS
00028 #           define MS_MASCOTRESFILE_API __declspec(dllexport)
00029 #       else
00030 #           define MS_MASCOTRESFILE_API __declspec(dllimport)
00031 #       endif
00032 #   else
00033 #       define MS_MASCOTRESFILE_API
00034 #   endif
00035 #else
00036 #   define MS_MASCOTRESFILE_API
00037 #endif
00038 
00039 // for the sake of #include <string>
00040 #ifdef __ALPHA_UNIX__
00041 #include <ctype.h>
00042 #endif
00043 #include <string>
00044 #include <vector>
00045 
00046 namespace matrix_science {
00051 #ifndef DOXYGEN_SHOULD_SKIP_THIS
00052     class MS_MASCOTRESFILE_API ms_blastaccession
00053     {
00054         friend class ms_datfile;
00055 
00056     public:
00057         ms_blastaccession();
00058         ms_blastaccession(const ms_blastaccession& src);
00059         ~ms_blastaccession();
00060 
00061         void defaultValues();
00062         void copyFrom(const ms_blastaccession* right);
00063 #ifndef SWIG
00064         ms_blastaccession& operator=(const ms_blastaccession& right);
00065 #endif
00066         bool isUseRegex() const;
00067         void setUseRegex(const bool flag);
00068 
00069         int getMinLength() const;
00070         void setMinLength(const int value);
00071 
00072         const char* getStart() const;
00073         const char* getStop() const;
00074 
00075     private:
00076 
00077         bool useRegex_;
00078         int  minLen_;
00079         char start_[255];
00080         char stop_[255];
00081     }; // class ms_blastaccession
00082 #endif
00083 
00085 
00109     class MS_MASCOTRESFILE_API ms_mascotoptions: public ms_customproperty
00110     {
00111         friend class ms_datfile;
00112 
00113     public:
00115 
00118         enum MS_REVIEW_COL
00119         {
00120             MS_REVIEW_COL_JOB               = 0x0000, 
00121             MS_REVIEW_COL_PID               = 0x0001, 
00122             MS_REVIEW_COL_DATABASE          = 0x0002, 
00123             MS_REVIEW_COL_USERNAME          = 0x0003, 
00124             MS_REVIEW_COL_USEREMAIL         = 0x0004, 
00125             MS_REVIEW_COL_TITLE             = 0x0005, 
00126             MS_REVIEW_COL_RESULTS_FILE      = 0x0006, 
00127             MS_REVIEW_COL_START_TIME        = 0x0007, 
00128             MS_REVIEW_COL_DURATION          = 0x0008, 
00129             MS_REVIEW_COL_STATUS            = 0x0009, 
00130             MS_REVIEW_COL_PRIORITY          = 0x000A, 
00131             MS_REVIEW_COL_SEARCHTYPE        = 0x000B, 
00132             MS_REVIEW_COL_ENZYMEUSED        = 0x000C, 
00133             MS_REVIEW_COL_IPADDRESS         = 0x000D, 
00134             MS_REVIEW_COL_USERID            = 0x000E, 
00135             MS_REVIEW_COL_PEAKLISTDATAFILE  = 0x000F, 
00136             MS_REVIEW_COL____LAST___        = 0x0010  
00137         };
00138 
00140 
00143         enum PERC_EXE_RT {
00144             PERC_EXE_RT_USE_DEFAULT = 1, 
00145             PERC_EXE_RT_FORCE_ON    = 2, 
00146             PERC_EXE_RT_FORCE_OFF   = 3  
00147         };
00148 
00150 
00175         enum DECOY_ALGORITHM {
00176             DECOY_ALGORITHM_NONE        = 0, 
00177             DECOY_PROTEIN_REVERSE       = 1, 
00178             DECOY_PEPTIDE_REVERSE       = 2, 
00179             DECOY_PROTEIN_RANDOM        = 3, 
00180             DECOY_PEPTIDE_RANDOM        = 4, 
00181             DECOY_PROTEIN_RANDOM_DIPEP  = 5, 
00182             DECOY_PEPTIDE_RANDOM_DIPEP  = 6, 
00183             DECOY_PROTEIN_SHUFFLE       = 7, 
00184             DECOY_PEPTIDE_SHUFFLE       = 8, 
00185 
00186             DECOY_PROTEIN_BASED_MASK    = 0x0001 
00187         };
00188 
00189 
00191 
00194         enum EXEC_AFTER_SEARCH
00195         {
00196             MAX_EXEC_AFTER_SEARCH = 10 
00197         };
00198 
00199         enum REPORTBUILDER_COL_ARR
00200         {
00201             MAX_REPORTBUILDER_COL_ARR = 10
00202         };
00203 
00205         enum NUMERICAL_VALUE_STORAGE
00206         {
00207             MASS_DECIMAL_PLACES = 6 
00208         };
00209 
00211         ms_mascotoptions();
00212 
00214         ms_mascotoptions(const ms_mascotoptions& src);
00215 
00217         ~ms_mascotoptions();
00218 
00220         void copyFrom(const ms_mascotoptions* right);
00221 
00222 #ifndef SWIG
00223 
00224         ms_mascotoptions& operator=(const ms_mascotoptions& right);
00225 #endif
00226 
00227         void defaultValues();
00228 
00230         bool isSectionAvailable() const;
00231 
00233         void setSectionAvailable(const bool value);
00234 
00236         bool isSaveLastQueryAsc() const;
00237 
00239         void setSaveLastQueryAsc(const bool flag);
00240 
00242         bool isSaveEveryLastQueryAsc() const;
00243 
00245         void setSaveEveryLastQueryAsc(const bool flag);
00246 
00248         std::string getLastQueryAscFile() const;
00249 
00251         void setLastQueryAscFile(const char* str);
00252 
00254         std::string getErrorLogFile() const;
00255 
00257         void setErrorLogFile(const char* str);
00258 
00260         std::string getSearchLogFile() const;
00261 
00263         void setSearchLogFile(const char* str);
00264 
00266         std::string getMonitorLogFile() const;
00267 
00269         void setMonitorLogFile(const char* str);
00270 
00272         std::string getInterFileBasePath() const;
00273 
00275         void setInterFileBasePath(const char* str);
00276 
00278         std::string getInterFileRelPath() const;
00279 
00281         void setInterFileRelPath(const char* str);
00282 
00284         std::string getMascotCmdLine() const;
00285 
00287         void setMascotCmdLine(const char* str);
00288 
00290         std::string getTestDirectory() const;
00291 
00293         void setTestDirectory(const char* str);
00294 
00296         std::string getMascotControlFile() const;
00297 
00299         void setMascotControlFile(const char* str);
00300 
00302         std::string getMascNodeCtrlFile() const;
00303 
00305         void setMascNodeCtrlFile(const char* str);
00306 
00308         std::string getMascotJobIdFile() const;
00309 
00311         void setMascotJobIdFile(const char* str);
00312 
00314         std::string getGetSeqJobIdFile() const;
00315 
00317         void setGetSeqJobIdFile(const char* str);
00318 
00320         int getUniqueJobStartNumber() const;
00321 
00323         void setUniqueJobStartNumber(const int value);
00324 
00326         std::string getResultsPerlScript() const;
00327 
00329         void setResultsPerlScript(const char* str);
00330 
00332         std::string getNoResultsScript() const;
00333 
00335         void setNoResultsScript(const char* str);
00336 
00338         std::string getResultsFullURL() const;
00339 
00341         void setResultsFullURL(const char* str);
00342 
00344         std::string getLogoImageFile() const;
00345 
00347         void setLogoImageFile(const char* str);
00348 
00350         int getMassDecimalPlaces() const;
00351 
00353         void setMassDecimalPlaces(const int value);
00354 
00356         int getIonsDecimalPlaces() const;
00357 
00359         void setIonsDecimalPlaces(const int value);
00360 
00362         int getIntensitySigFigs() const;
00363 
00365         void setIntensitySigFigs(const int value);
00366 
00368         bool isEmailUsersEnabled() const;
00369 
00371         void setEmailUsersEnabled(const bool value);
00372 
00374         bool isEmailErrorsEnabled() const;
00375 
00377         void setEmailErrorsEnabled(const bool value);
00378 
00380         int getMailTransport() const;
00381 
00383         void setMailTransport(const int value);
00384 
00386         std::string getEmailService() const;
00387 
00389         void setEmailService(const char* str);
00390 
00392         std::string getEmailPassword() const;
00393 
00395         void setEmailPassword(const char* str);
00396 
00398         std::string getEmailProfile() const;
00399 
00401         void setEmailProfile(const char* str);
00402 
00404         std::string getSendmailPath() const;
00405 
00407         void setSendmailPath(const char* str);
00408 
00410         std::string getEmailFromUser() const;
00411 
00413         void setEmailFromUser(const char* str);
00414 
00416         std::string getEmailFromTextName() const;
00417 
00419         void setEmailFromTextName(const char* str);
00420 
00422         int getEmailTimeOutPeriod() const;
00423 
00425         void setEmailTimeOutPeriod(const int value);
00426 
00428         int getMonitorEmailCheckFreq() const;
00429 
00431         void setMonitorEmailCheckFreq(const int value);
00432 
00434         std::string getMailTempFile() const;
00435 
00437         void setMailTempFile(const char* str);
00438 
00440         std::string getErrMessageEmailTo() const;
00441 
00443         void setErrMessageEmailTo(const char* str);
00444 
00446         int getMonitorTestTimeout() const;
00447 
00449         void setMonitorTestTimeout(const int value);
00450 
00452         std::string getNTMonitorGroup() const;
00453 
00455         void setNTMonitorGroup(const char* str);
00456 
00458         std::string getNTIUserGroup() const;
00459 
00461         void setNTIUserGroup(const char* str);
00462 
00464         int getUnixWebUserGroup() const;
00465 
00467         void setUnixWebUserGroup(const int value);
00468 
00470         bool isForkForUnixApache() const;
00471 
00473         void setForkForUnixApache(const bool value);
00474 
00476         int getSeparateLockMem() const;
00477 
00479         void setSeparateLockMem(const int value);
00480 
00482         std::string getFormVersion() const;
00483 
00485         void setFormVersion(const char* str);
00486 
00488         int getMaxSequenceLen() const;
00489 
00491         void setMaxSequenceLen(const int value);
00492 
00494         int getMaxConcurrentSearches() const;
00495 
00497         void setMaxConcurrentSearches(const int value);
00498 
00500         int getMaxSearchesPerUser() const;
00501 
00503         void setMaxSearchesPerUser(const int value);
00504 
00506         double getCentroidWidth() const;
00507 
00509         void setCentroidWidth(const double value);
00510 
00512         int getCentroidWidthCount() const;
00513 
00515         void setCentroidWidthCount(const int value);
00516 
00518         int getMaxDescriptionLen() const;
00519 
00521         void setMaxDescriptionLen(const int value);
00522 
00524         int getMaxNumPeptides() const;
00525 
00527         void setMaxNumPeptides(const int value);
00528 
00530         INT64 getVmemory() const;
00531 
00533         void setVmemory(const INT64 value);
00534 
00536         int getNumberOfReportNumberChoices() const;
00537 
00539         void clearReportNumberChoices();
00540 
00542         int getReportNumberChoice(const int index) const;
00543 
00545         void setReportNumberChoice(const int index, const int value);
00546 
00548         void appendReportNumberChoice(const int value);
00549 
00551         int getNumberOfTargetFDRPercentages() const;
00552 
00554         void clearTargetFDRPercentages();
00555 
00557         double getTargetFDRPercentage(const int index) const;
00558 
00560         void setTargetFDRPercentage(const int index, const double value, const bool makeDefault = false);
00561 
00563         void appendTargetFDRPercentage(const double value, const bool makeDefault = false);
00564 
00566         bool isDefaultTargetFDRPercentage(const int index) const;
00567 
00569         void setDefaultTargetFDRPercentage(const int index);
00570 
00572         int getReviewColWidth(const MS_REVIEW_COL index) const;
00573 
00575         void setReviewColWidth(const MS_REVIEW_COL index, const int value);
00576         
00578         bool getReviewColDisplay(const MS_REVIEW_COL index) const;
00579 
00581         void setReviewColDisplay(const MS_REVIEW_COL index, const bool value);
00582 
00584         std::string getReportBuilderColumnArrangement(const int index) const;
00585 
00587         int getMaxNumOfReportBuilderColumnArrangements() const;
00588 
00590         void setReportBuilderColumnArrangement(const int index, const std::string str);
00591 
00593         std::string getSpectrumViewerColourSchemeString(const std::string &name) const;
00594 
00596         std::vector<std::string> getSpectrumViewerColourSchemeNames() const;
00597 
00599         void setSpectrumViewerColourSchemeString(const std::string &name, const std::string &str);
00600 
00602         std::string getSpectrumViewerDefaultColourSchemeName() const;
00603 
00605         void setSpectrumViewerDefaultColourSchemeName(const std::string &name);
00606 
00608         std::string getProxyType() const;
00609 
00611         void setProxyType(const std::string &value);
00612 
00614         bool isUseHTTPProxyForFTP() const;
00615 
00617         void setUseHTTPProxyForFTP(const bool value);
00618 
00620         bool isUseHTTPProxyForHTTPS() const;
00621 
00623         void setUseHTTPProxyForHTTPS(const bool value);
00624 
00626         std::string getProxyServer() const;
00627 
00629         void setProxyServer(const char* str);
00630 
00632         std::string getProxyUsername() const;
00633 
00635         void setProxyUsername(const char* str);
00636 
00638         std::string getProxyPassword() const;
00639 
00641         void setProxyPassword(const char* str);
00642 
00644         int getMinPepLenInPepSummary() const;
00645 
00647         void setMinPepLenInPepSummary(const int value);
00648 
00650         int getMaxQueries() const;
00651 
00653         void setMaxQueries(const int value);
00654 
00656         bool isShowSubsets() const;
00657 
00659         void setShowSubsets(const bool value);
00660 
00662         double getShowSubsets() const;
00663 
00665         void setShowSubsets(const double value);
00666 
00668         bool isRequireBoldRed() const;
00669 
00671         void setRequireBoldRed(const bool value);
00672 
00674         double getSigThreshold() const;
00675 
00677         void setSigThreshold(const double value);
00678 
00680         double getSiteAnalysisMD10Prob() const;
00681 
00683         void setSiteAnalysisMD10Prob(const double value);
00684 
00686         int getMaxVarMods() const;
00687 
00689         void setMaxVarMods(const int value);
00690 
00692         int getMaxEtVarMods() const;
00693 
00695         void setMaxEtVarMods(const int value);
00696 
00698         int getErrTolMaxAccessions() const;
00699 
00701         void setErrTolMaxAccessions(const int value);
00702 
00704         bool isLabelAll() const;
00705 
00707         void setLabelAll(const bool value);
00708 
00710         bool isShowAllFromErrorTolerant() const;
00711 
00713         void setShowAllFromErrorTolerant(const bool value);
00714 
00716         double getIgnoreIonsScoreBelow() const;
00717 
00719         void setIgnoreIonsScoreBelow(const double value);
00720 
00722         std::string getMonitorPidFile() const;
00723 
00725         void setMonitorPidFile(const char* str);
00726 
00728         bool isStoreModPermutations() const;
00729 
00731         void setStoreModPermutations(const bool value);
00732 
00734         int getProteinsInResultsFile() const;
00735 
00737         void setProteinsInResultsFile(const int value);
00738 
00740         std::string getMascotMessage() const;
00741 
00743         void setMascotMessage(const char* str);
00744 
00746         int getSplitNumberOfQueries() const;
00747 
00749         void setSplitNumberOfQueries(const int value);
00750 
00752         int getSplitDataFileSize() const;
00753 
00755         void setSplitDataFileSize(const int value);
00756 
00758         bool isMoveOldDbToOldDir() const;
00759 
00761         void setMoveOldDbToOldDir(const bool value);
00762 
00764         bool isRemoveOldIndexFiles() const;
00765 
00767         void setRemoveOldIndexFiles(const bool value);
00768 
00770         int getFeatureTableLength() const;
00771 
00773         void setFeatureTableLength(const int value);
00774 
00776         double getFeatureTableMinScore() const;
00777 
00779         void setFeatureTableMinScore(const double value);
00780 
00782         std::string getICATLight() const;
00783 
00785         void setICATLight(const char* modName);
00786 
00788         std::string getICATHeavy() const;
00789 
00791         void setICATHeavy(const char* modName);
00792 
00794         std::string getICATFilter() const;
00795 
00797         void setICATFilter(const char* filterString);
00798 
00800         std::string getICATQuantitationMethod() const;
00801 
00803         void setICATQuantitationMethod(const char* methodName);
00804 
00806         unsigned int getNumberOfIgnoreDupeAccessions() const;
00807 
00809         void clearIgnoreDupeAccessions();
00810 
00812         std::string getIgnoreDupeAccession(const unsigned int index) const;
00813 
00815         void setIgnoreDupeAccession(const unsigned int index, const std::string value);
00816 
00818         void appendIgnoreDupeAccession(const std::string value);
00819 
00821         bool isInIgnoreDupeAccessionList(const std::string value) const;
00822 
00824         int getUnixDirPerm() const;
00825 
00827         void setUnixDirPerm(const int value);
00828 
00830         bool isUnixDirPermDefined() const;
00831 
00833         int getMudpit() const;
00834 
00836         void setMudpit(const int value);
00837 
00839         double getPrecursorCutOutLowerLimit() const;
00840 
00842         void setPrecursorCutOutLowerLimit(const double value);
00843 
00845         double getPrecursorCutOutUpperLimit() const;
00846 
00848         void setPrecursorCutOutUpperLimit(const double value);
00849 
00851         bool isAutoSelectCharge() const;
00852 
00854         void setAutoSelectCharge(const bool value);
00855 
00857         std::string getTaxBrowserUrl() const;
00858 
00860         void setTaxBrowserUrl(const std::string value);
00861 
00863         int getMinPepLenInSearch() const;
00864 
00866         void setMinPepLenInSearch(const int value);
00867 
00869         int getMaxPepModArrangements() const;
00870 
00872         void setMaxPepModArrangements(const int value);
00873 
00875         int getMaxPepNumVarMods() const;
00876 
00878         void setMaxPepNumVarMods(const int value);
00879 
00881         int getMaxPepNumModifiableSites() const;
00882 
00884         void setMaxPepNumModifiableSites(const int value);
00885 
00887         bool isIteratePMFIntensities() const;
00888 
00890         void setIteratePMFIntensities(const bool value);
00891 
00893         double getMinEtagMassDelta() const;
00894 
00896         void setMinEtagMassDelta(const double value);
00897 
00899         double getMaxEtagMassDelta() const;
00900 
00902         void setMaxEtagMassDelta(const double value);
00903 
00905         std::string getResultsFileFormatVersion() const;
00906 
00908         void setResultsFileFormatVersion(const char *value);
00909 
00911         std::string getSortUnassigned() const;
00912 
00914         void setSortUnassigned(const std::string newValue);
00915 
00917         int getSelectSwitch() const;
00918 
00920         void setSelectSwitch(const int value);
00921 
00923         double getMudpitSwitch() const;
00924 
00926         void setMudpitSwitch(const double value);
00927 
00929         int getMaxDatabases() const;
00930 
00932         void setMaxDatabases(const int value);
00933 
00935         std::string getCacheDirectory() const;
00936 
00938         void setCacheDirectory(const char * value);
00939 
00941         std::string getResfileCache() const;
00942 
00944         void setResfileCache(const char * value);
00945 
00947         std::string getResultsCache() const;
00948 
00950         void setResultsCache(const char * value);
00951 
00953         bool isPercolator() const;
00954 
00956         void setPercolator(const bool value);
00957 
00959         std::string getPercolatorFeatures() const;
00960 
00962         void setPercolatorFeatures(std::string value);
00963 
00965         int getPercolatorMinQueries() const;
00966 
00968         void setPercolatorMinQueries(const int value);
00969 
00971         int getPercolatorMinSequences() const;
00972 
00974         void setPercolatorMinSequences(const int value);
00975 
00977         bool isPercolatorUseProteins() const;
00978 
00980         void setPercolatorUseProteins(const bool value);
00981 
00983         bool isPercolatorUseRT() const;
00984 
00986         void setPercolatorUseRT(const bool value);
00987 
00989         std::string getPercolatorExeFlags(bool anyRetentionTimes,
00990                                           const std::vector<std::string> percolatorFiles,
00991                                           const PERC_EXE_RT rt = PERC_EXE_RT_USE_DEFAULT) const;
00992 
00994         void setPercolatorExeFlags(const char * value);
00995 
00997         int getExecAfterSearch(const char               * szResultsFilePath,
00998                                std::vector<std::string> & commands,
00999                                std::vector<std::string> & titles,
01000                                std::vector<int>         & waitfor,
01001                                std::vector<int>         & logging,
01002                                std::vector<std::string> & additionalFlags,
01003                                const char               * sessionID = 0,
01004                                const char               * taskID = 0) const;
01005 
01007         void setExecAfterSearch(const int num, std::string value);
01008 
01010         std::string getResultsPerlScript_2() const;
01011 
01013         void setResultsPerlScript_2(std::string value);
01014 
01016         std::string getResultsFullURL_2() const;
01017 
01019         void setResultsFullURL_2(std::string value);
01020 
01022         int getProteinFamilySwitch() const;
01023 
01025         void setProteinFamilySwitch(const int value);
01026 
01028         int getDecoyTypeSpecific() const;
01029 
01031         void setDecoyTypeSpecific(const int value);
01032 
01034         int getDecoyTypeNoEnzyme() const;
01035 
01037         void setDecoyTypeNoEnzyme(const int value);
01038 
01040         int getSVGSpectrumSwitch() const;
01041 
01043         void setSVGSpectrumSwitch(const int value);
01044 
01046         int getDisplayNonSignificantMatches() const;
01047 
01049         void setDisplayNonSignificantMatches(const int value);
01050 
01052         std::string getCompressToolAA() const;
01053 
01055         void setCompressToolAA(const std::string value);
01056 
01058         std::string getCompressToolNA() const;
01059 
01061         void setCompressToolNA(const std::string value);
01062 
01064         std::string getCompressToolSL() const;
01065 
01067         void setCompressToolSL(const std::string value);
01068         
01070         std::string getCompressToolCommandLineFasta(DATABASE_TYPE dbType,
01071                                                const std::string & dbname,
01072                                                const std::string & dbpath) const; 
01073         
01075         std::string getCompressToolCommandLineLibrary(const std::string & logfilepath,
01076                                                       const std::string & inputfile,
01077                                                       const std::string & outputdirectory) const; 
01078 
01080         std::string getPepSearchTool() const;
01081 
01083         void setPepSearchTool(const std::string value);
01084         
01086         std::string getPepSearchToolCommandLine(const std::string & peptideToleranceUnit,
01087                                                 const double      & peptideTolerance,
01088                                                 const std::string & ionToleranceUnit,
01089                                                 const double      & ionTolerance,
01090                                                 const std::string & libraryDirectoryPath,
01091                                                 const std::string & inputFileRelativePath,
01092                                                 const std::string & outputFileRelativePath) const;
01093 
01095         int getSpectraPerLibraryBlock() const;
01096 
01098         void setSpectraPerLibraryBlock(const int value);
01099 
01101         int getCrawlerNumPeaksPer100Da() const;
01102 
01104         void setCrawlerNumPeaksPer100Da(const int value);        
01105         
01106 
01108 
01110         const ms_blastaccession* getGetSeqBlastAccession() const;
01111 
01113         void setGetSeqBlastAccession(const ms_blastaccession* value);
01114 
01115         // MatrixScience internal usage only
01116         int getMinPeakIteration() const;
01117 
01118         // MatrixScience internal usage only
01119         void setMinPeakIteration(const int value);
01120 
01121         // MatrixScience internal usage only
01122         bool isEncryptURL() const;
01123 
01124         // MatrixScience internal usage only
01125         void setEncryptURL(const bool value);
01126 
01127         // MatrixScience internal usage only
01128         std::string getPercolatorExeFlags() const;
01129 
01130         // MatrixScience internal usage only
01131         std::string getExecAfterSearch(const int num) const;
01132 
01133         // MatrixScience internal usage only
01134         void checkExecAfterSearch(ms_errs & err);
01135 
01136         // MatrixScience internal usage only
01137         void checkReportBuilderColumnArrangement(ms_errs & err);
01138 
01139         // MatrixScience internal usage only
01140         void checkSpectrumViewerColourSchemes(ms_errs & err);
01141 
01142 #ifdef SUPPRESS_MS_CUSTOMPROPERTY_INHERITANCE
01143 #include "suppress_ms_customproperty.hpp"
01144 #endif
01145 
01146     private:
01147         void        synchronizeReportNumberChoices_();
01148         void        synchronizeIgnoreDupeAccession_();
01149         void        synchronizeTargetFDRPercentages_();
01150 
01151         bool        sectionAvailable_;
01152 
01153         bool        saveLastQueryAsc_;
01154         bool        saveEveryLastQueryAsc_;
01155         std::string lastQueryAscFile_;
01156 
01157         std::string errorLogFile_;
01158         std::string searchLogFile_;
01159         std::string monitorLogFile_;
01160         std::string interFileBasePath_;
01161         std::string interFileRelPath_;
01162 
01163         std::string mascotCmdLine_;
01164         std::string testDirectory_;
01165         std::string mascotControlFile_;
01166         std::string mascNodeCtrlFile_;
01167         std::string mascotJobIdFile_;
01168         std::string getSeqJobIdFile_;
01169         int         uniqueJobStartNumber_;
01170 
01171         std::string resultsPerlScript_;
01172         std::string noResultsScript_;
01173         std::string resultsFullURL_;
01174         std::string logoImageFile_;
01175 
01176         int         massDecimalPlaces_;
01177         int         ionsDecimalPlaces_;
01178         int         intensitySigFigs_;
01179 
01180         bool        emailUsersEnabled_;
01181         bool        emailErrorsEnabled_;
01182         int         mailTransport_;
01183         std::string emailService_;
01184         std::string emailPassword_;
01185         std::string emailProfile_;
01186         std::string sendmailPath_;
01187         std::string emailFromUser_;
01188         std::string emailFromTextName_;
01189         int         emailTimeOutPeriod_;
01190         int         monitorEmailCheckFreq_;
01191         std::string mailTempFile_;
01192         std::string errMessageEmailTo_;
01193 
01194         int         monitorTestTimeout_;
01195         std::string NTMonitorGroup_;
01196         std::string NTIUserGroup_;
01197         int         unixWebUserGroup_;
01198         bool        forkForUnixApache_;
01199         int         separateLockMem_;
01200 
01201         std::string formVersion_;
01202         int         maxSequenceLen_;
01203         int         maxConcurrentSearches_;
01204         int         maxSearchesPerUser_;
01205         double      centroidWidth_;
01206         int         centroidWidthCount_;
01207         int         maxDescriptionLen_;
01208         int         maxNumPeptides_;
01209         INT64       vmemory_;
01210 
01211         std::vector< int > reportNumberChoices_;
01212         std::vector< double > targetFDRPercentages_;
01213         int         defaultTargetFDRPercentagesIx_;
01214 
01215         int         reviewColWidths_[MS_REVIEW_COL____LAST___];
01216         bool        reviewColDisplay_[MS_REVIEW_COL____LAST___];
01217         std::vector<std::string> reportBuilderColArr_;
01218 
01219         std::string defaultColourSchemeName_;
01220         std::vector<std::string> colourSchemeNames_;
01221         std::vector<std::string> colourSchemeStrings_;
01222 
01223         std::string proxyType_;
01224         bool        useHTTPProxyForFTP_;
01225         bool        useHTTPProxyForHTTPS_;
01226         std::string proxy_server_;
01227         std::string proxy_username_;
01228         std::string proxy_password_;
01229 
01230         int         maxVarMods_;
01231         int         maxEtVarMods_;
01232         int         errTolMaxAccessions_;
01233         bool        labelAll_;
01234         bool        showAllFromErrorTolerant_;
01235 
01236         int         minPepLenInPepSummary_;
01237         int         maxPepModArrangements_;
01238         int         maxPepNumVarMods_;
01239         int         maxPepNumModifiableSites_;
01240         int         maxQueries_;
01241         double      showSubsets_;
01242         bool        requireBoldRed_;
01243         double      sigThreshold_;
01244         double      siteAnalysisMD10Prob_;
01245         double      ignoreIonsScoreBelow_;
01246 
01247         std::string monitorPidFile_;
01248         bool        storeModPermutations_;
01249         int         proteinsInResultsFile_;
01250         std::string mascotMessage_;
01251         int         splitNumberOfQueries_;
01252         int         splitDataFileSize_;
01253         bool        moveOldDbToOldDir_;
01254         bool        removeOldIndexFiles_;
01255 
01256         int         featureTableLength_;
01257         double      featureTableMinScore_;
01258 
01259         std::string ICATLight_;
01260         std::string ICATHeavy_;
01261         std::string ICATFilter_;
01262         std::string ICATQuantitationMethod_;
01263 
01264         int         UnixDirPerm_;
01265         bool        UnixDirPermDefined_;
01266         int         mudpit_;
01267 
01268         typedef std::vector<std::string> t_dupeAccs;
01269         t_dupeAccs ignoreDupeAccessions_;
01270 
01271         double      precursorCutOutLowerLimit_;
01272         double      precursorCutOutUpperLimit_;
01273 
01274         bool        autoSelectCharge_;
01275         std::string taxBrowserUrl_;
01276         int         minPepLenInSearch_;
01277         bool        iteratePMFIntensities_;
01278 
01279         double      minEtagMassDelta_;
01280         double      maxEtagMassDelta_;
01281 
01282         std::string resultsFileFormatVersion_;
01283         std::string sortUnassigned_;
01284         int         selectSwitch_;
01285         double      mudpitSwitch_;
01286 
01287         int         maxDatabases_;
01288         std::string cacheDirectory_;
01289 
01290         std::string resfileCache_;
01291         std::string resultsCache_;
01292 
01293         bool        percolator_;
01294         std::string percolatorFeatures_;
01295         int         percolatorMinQueries_;
01296         int         percolatorMinSequences_;
01297         bool        percolatorUseProteins_;
01298         bool        percolatorUseRT_;
01299         std::string percolatorExeFlags_;
01300         std::vector<std::string> execAfterSearch_;
01301         std::vector<std::string> execAfterSearchCommands_;
01302         std::vector<std::string> execAfterSearchTitles_;
01303         std::vector<int>         execAfterSearchWaitFor_;
01304         std::vector<int>         execAfterSearchLogging_;
01305         std::vector<std::string> execAfterSearchAdditionalFlags_;
01306         std::string resultsPerlScript_2_;
01307         std::string resultsFullURL_2_;
01308         int         proteinFamilySwitch_;
01309 
01310         int         decoyTypeSpecific_;
01311         int         decoyTypeNoEnzyme_;
01312 
01313         int         svgSpectrumSwitch_;
01314         int         displayNonSigMatches_;
01315 
01316         ms_blastaccession   getSeqBlastAccession_;
01317         int         minPeakIteration_;
01318         bool        encryptURL_;
01319         
01320         std::string compressToolAA_;
01321         std::string compressToolNA_;
01322         std::string compressToolSL_;
01323         std::string pepSearchTool_;
01324         int         spectraPerLibraryBlock_;
01325         int         crawlerNumPeaksPer100Da_;
01326     }; // class ms_mascotoptions // end of config_group
01328 } // namespace matrix_science
01329 
01330 #endif // MS_MASCOTOPTIONS_HPP
01331 
01332 /*------------------------------- End of File -------------------------------*/
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Sat Apr 14 2018 01:45:12