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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 };
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
01132 int getMinPeakIteration() const;
01133
01134
01135 void setMinPeakIteration(const int value);
01136
01137
01138 bool isEncryptURL() const;
01139
01140
01141 void setEncryptURL(const bool value);
01142
01143
01144 std::string getPercolatorExeFlags() const;
01145
01146
01147 std::string getPercolatorRtFlags(const bool anyRetentionTimes, const bool useRT) const;
01148
01149
01150 std::string getExecAfterSearch(const int num) const;
01151
01152
01153 void checkExecAfterSearch(ms_errs & err);
01154
01155
01156 void checkReportBuilderColumnArrangement(ms_errs & err);
01157
01158
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_;
01398 int mascotFileProcessingThreads_;
01399 int inputFileParsingThreads_;
01400 int chunkReadingThreads_;
01401 int chunkPreparationThreads_;
01402 };
01404 }
01405
01406 #endif // MS_MASCOTOPTIONS_HPP
01407
01408