20#ifndef MS_MASCOTOPTIONS_HPP
21#define MS_MASCOTOPTIONS_HPP
27namespace matrix_science {
32#ifndef DOXYGEN_SHOULD_SKIP_THIS
33 class MS_MASCOTRESFILE_API ms_blastaccession
35 friend class ms_datfile;
39 ms_blastaccession(
const ms_blastaccession& src);
43 void copyFrom(
const ms_blastaccession* right);
45 ms_blastaccession& operator=(
const ms_blastaccession& right);
47 bool isUseRegex()
const;
48 void setUseRegex(
const bool flag);
50 int getMinLength()
const;
51 void setMinLength(
const int value);
53 const char* getStart()
const;
54 const char* getStop()
const;
101 MS_REVIEW_COL_JOB = 0x0000,
102 MS_REVIEW_COL_PID = 0x0001,
103 MS_REVIEW_COL_DATABASE = 0x0002,
104 MS_REVIEW_COL_USERNAME = 0x0003,
105 MS_REVIEW_COL_USEREMAIL = 0x0004,
106 MS_REVIEW_COL_TITLE = 0x0005,
107 MS_REVIEW_COL_RESULTS_FILE = 0x0006,
108 MS_REVIEW_COL_START_TIME = 0x0007,
109 MS_REVIEW_COL_DURATION = 0x0008,
110 MS_REVIEW_COL_STATUS = 0x0009,
111 MS_REVIEW_COL_PRIORITY = 0x000A,
112 MS_REVIEW_COL_SEARCHTYPE = 0x000B,
113 MS_REVIEW_COL_ENZYMEUSED = 0x000C,
114 MS_REVIEW_COL_IPADDRESS = 0x000D,
115 MS_REVIEW_COL_USERID = 0x000E,
116 MS_REVIEW_COL_PEAKLISTDATAFILE = 0x000F,
117 MS_REVIEW_COL____LAST___ = 0x0010
125 PERC_EXE_RT_USE_DEFAULT = 1,
126 PERC_EXE_RT_FORCE_ON = 2,
127 PERC_EXE_RT_FORCE_OFF = 3
157 DECOY_ALGORITHM_NONE = 0,
158 DECOY_PROTEIN_REVERSE = 1,
159 DECOY_PEPTIDE_REVERSE = 2,
160 DECOY_PROTEIN_RANDOM = 3,
161 DECOY_PEPTIDE_RANDOM = 4,
162 DECOY_PROTEIN_RANDOM_DIPEP = 5,
163 DECOY_PEPTIDE_RANDOM_DIPEP = 6,
164 DECOY_PROTEIN_SHUFFLE = 7,
165 DECOY_PEPTIDE_SHUFFLE = 8,
167 DECOY_PROTEIN_BASED_MASK = 0x0001
177 MAX_EXEC_AFTER_SEARCH = 10
180 enum REPORTBUILDER_COL_ARR
182 MAX_REPORTBUILDER_COL_ARR = 10
188 MASS_DECIMAL_PLACES = 6
208 void defaultValues();
211 bool isSectionAvailable()
const;
214 void setSectionAvailable(
const bool value);
217 bool isSaveLastQueryAsc()
const;
220 void setSaveLastQueryAsc(
const bool flag);
223 bool isSaveEveryLastQueryAsc()
const;
226 void setSaveEveryLastQueryAsc(
const bool flag);
229 std::string getLastQueryAscFile()
const;
232 void setLastQueryAscFile(
const char* str);
235 std::string getErrorLogFile()
const;
238 void setErrorLogFile(
const char* str);
241 std::string getSearchLogFile()
const;
244 void setSearchLogFile(
const char* str);
247 std::string getMonitorLogFile()
const;
250 void setMonitorLogFile(
const char* str);
253 std::string getInterFileBasePath()
const;
256 void setInterFileBasePath(
const char* str);
259 std::string getInterFileRelPath()
const;
262 void setInterFileRelPath(
const char* str);
265 std::string getMascotCmdLine()
const;
268 void setMascotCmdLine(
const char* str);
271 std::string getTestDirectory()
const;
274 void setTestDirectory(
const char* str);
277 std::string getMascotControlFile()
const;
280 void setMascotControlFile(
const char* str);
283 std::string getMascNodeCtrlFile()
const;
286 void setMascNodeCtrlFile(
const char* str);
289 std::string getMascotJobIdFile()
const;
292 void setMascotJobIdFile(
const char* str);
295 std::string getGetSeqJobIdFile()
const;
298 void setGetSeqJobIdFile(
const char* str);
301 int getUniqueJobStartNumber()
const;
304 void setUniqueJobStartNumber(
const int value);
307 std::string getResultsPerlScript()
const;
310 void setResultsPerlScript(
const char* str);
313 std::string getNoResultsScript()
const;
316 void setNoResultsScript(
const char* str);
319 std::string getResultsFullURL()
const;
322 void setResultsFullURL(
const char* str);
325 std::string getLogoImageFile()
const;
328 void setLogoImageFile(
const char* str);
331 int getMassDecimalPlaces()
const;
334 void setMassDecimalPlaces(
const int value);
337 int getIonsDecimalPlaces()
const;
340 void setIonsDecimalPlaces(
const int value);
343 int getIntensitySigFigs()
const;
346 void setIntensitySigFigs(
const int value);
349 bool isEmailUsersEnabled()
const;
352 void setEmailUsersEnabled(
const bool value);
355 bool isEmailErrorsEnabled()
const;
358 void setEmailErrorsEnabled(
const bool value);
361 int getMailTransport()
const;
364 void setMailTransport(
const int value);
367 std::string getEmailService()
const;
370 void setEmailService(
const char* str);
373 std::string getEmailPassword()
const;
376 void setEmailPassword(
const char* str);
379 std::string getEmailProfile()
const;
382 void setEmailProfile(
const char* str);
385 std::string getSendmailPath()
const;
388 void setSendmailPath(
const char* str);
391 std::string getEmailFromUser()
const;
394 void setEmailFromUser(
const char* str);
397 std::string getEmailFromTextName()
const;
400 void setEmailFromTextName(
const char* str);
403 int getEmailTimeOutPeriod()
const;
406 void setEmailTimeOutPeriod(
const int value);
409 int getMonitorEmailCheckFreq()
const;
412 void setMonitorEmailCheckFreq(
const int value);
415 std::string getMailTempFile()
const;
418 void setMailTempFile(
const char* str);
421 std::string getErrMessageEmailTo()
const;
424 void setErrMessageEmailTo(
const char* str);
427 int getMonitorTestTimeout()
const;
430 void setMonitorTestTimeout(
const int value);
433 std::string getNTMonitorGroup()
const;
436 void setNTMonitorGroup(
const char* str);
439 std::string getNTIUserGroup()
const;
442 void setNTIUserGroup(
const char* str);
445 int getUnixWebUserGroup()
const;
448 void setUnixWebUserGroup(
const int value);
451 bool isForkForUnixApache()
const;
454 void setForkForUnixApache(
const bool value);
457 std::string getFormVersion()
const;
460 void setFormVersion(
const char* str);
463 int getMaxSequenceLen()
const;
466 void setMaxSequenceLen(
const int value);
469 int getMaxConcurrentSearches()
const;
472 void setMaxConcurrentSearches(
const int value);
475 int getMaxSearchesPerUser()
const;
478 void setMaxSearchesPerUser(
const int value);
481 double getCentroidWidth()
const;
484 void setCentroidWidth(
const double value);
487 int getCentroidWidthCount()
const;
490 void setCentroidWidthCount(
const int value);
493 int getMaxDescriptionLen()
const;
496 void setMaxDescriptionLen(
const int value);
499 int getMaxNumPeptides()
const;
502 void setMaxNumPeptides(
const int value);
505 INT64 getVmemory()
const;
508 void setVmemory(
const INT64 value);
511 int getNumberOfReportNumberChoices()
const;
514 void clearReportNumberChoices();
517 int getReportNumberChoice(
const int index)
const;
520 void setReportNumberChoice(
const int index,
const int value);
523 void appendReportNumberChoice(
const int value);
526 int getNumberOfTargetFDRPercentages()
const;
529 void clearTargetFDRPercentages();
532 double getTargetFDRPercentage(
const int index)
const;
535 void setTargetFDRPercentage(
const int index,
const double value,
const bool makeDefault =
false);
538 void appendTargetFDRPercentage(
const double value,
const bool makeDefault =
false);
541 bool isDefaultTargetFDRPercentage(
const int index)
const;
544 void setDefaultTargetFDRPercentage(
const int index);
547 int getReviewColWidth(
const MS_REVIEW_COL index)
const;
550 void setReviewColWidth(
const MS_REVIEW_COL index,
const int value);
553 bool getReviewColDisplay(
const MS_REVIEW_COL index)
const;
556 void setReviewColDisplay(
const MS_REVIEW_COL index,
const bool value);
559 std::string getReportBuilderColumnArrangement(
const int index)
const;
562 int getMaxNumOfReportBuilderColumnArrangements()
const;
565 void setReportBuilderColumnArrangement(
const int index,
const std::string str);
568 std::string getSpectrumViewerColourSchemeString(
const std::string &name)
const;
571 std::vector<std::string> getSpectrumViewerColourSchemeNames()
const;
574 void setSpectrumViewerColourSchemeString(
const std::string &name,
const std::string &str,
bool doCheck =
true);
577 std::string getSpectrumViewerDefaultColourSchemeName()
const;
580 void setSpectrumViewerDefaultColourSchemeName(
const std::string &name);
583 std::string getProxyType()
const;
586 void setProxyType(
const std::string &value);
589 bool isUseHTTPProxyForFTP()
const;
592 void setUseHTTPProxyForFTP(
const bool value);
595 bool isUseHTTPProxyForHTTPS()
const;
598 void setUseHTTPProxyForHTTPS(
const bool value);
601 std::string getProxyServer()
const;
604 void setProxyServer(
const char* str);
607 std::string getProxyUsername()
const;
610 void setProxyUsername(
const char* str);
613 std::string getProxyPassword()
const;
616 void setProxyPassword(
const char* str);
619 int getMinPepLenInPepSummary()
const;
622 void setMinPepLenInPepSummary(
const int value);
625 int getMaxQueries()
const;
628 void setMaxQueries(
const int value);
631 bool isShowSubsets()
const;
634 void setShowSubsets(
const bool value);
637 double getShowSubsets()
const;
640 void setShowSubsets(
const double value);
643 bool isRequireBoldRed()
const;
646 void setRequireBoldRed(
const bool value);
649 double getSigThreshold()
const;
652 void setSigThreshold(
const double value);
655 double getSiteAnalysisMD10Prob()
const;
658 void setSiteAnalysisMD10Prob(
const double value);
661 int getMaxVarMods()
const;
664 void setMaxVarMods(
const int value);
667 int getMaxEtVarMods()
const;
670 void setMaxEtVarMods(
const int value);
673 int getErrTolMaxAccessions()
const;
676 void setErrTolMaxAccessions(
const int value);
679 bool isLabelAll()
const;
682 void setLabelAll(
const bool value);
685 bool isShowAllFromErrorTolerant()
const;
688 void setShowAllFromErrorTolerant(
const bool value);
691 double getIgnoreIonsScoreBelow()
const;
694 void setIgnoreIonsScoreBelow(
const double value);
697 std::string getMonitorPidFile()
const;
700 void setMonitorPidFile(
const char* str);
703 bool isStoreModPermutations()
const;
706 void setStoreModPermutations(
const bool value);
709 int getProteinsInResultsFile()
const;
712 void setProteinsInResultsFile(
const int value);
715 std::string getMascotMessage()
const;
718 void setMascotMessage(
const char* str);
721 int getSplitNumberOfQueries()
const;
724 void setSplitNumberOfQueries(
const int value);
727 int getSplitDataFileSize()
const;
730 void setSplitDataFileSize(
const int value);
733 bool isMoveOldDbToOldDir()
const;
736 void setMoveOldDbToOldDir(
const bool value);
739 bool isRemoveOldIndexFiles()
const;
742 void setRemoveOldIndexFiles(
const bool value);
745 int getFeatureTableLength()
const;
748 void setFeatureTableLength(
const int value);
751 double getFeatureTableMinScore()
const;
754 void setFeatureTableMinScore(
const double value);
757 std::string getICATLight()
const;
760 void setICATLight(
const char* modName);
763 std::string getICATHeavy()
const;
766 void setICATHeavy(
const char* modName);
769 std::string getICATFilter()
const;
772 void setICATFilter(
const char* filterString);
775 std::string getICATQuantitationMethod()
const;
778 void setICATQuantitationMethod(
const char* methodName);
781 unsigned int getNumberOfIgnoreDupeAccessions()
const;
784 void clearIgnoreDupeAccessions();
787 std::string getIgnoreDupeAccession(
const unsigned int index)
const;
790 void setIgnoreDupeAccession(
const unsigned int index,
const std::string value);
793 void appendIgnoreDupeAccession(
const std::string value);
796 bool isInIgnoreDupeAccessionList(
const std::string value)
const;
799 int getUnixDirPerm()
const;
802 void setUnixDirPerm(
const int value);
805 bool isUnixDirPermDefined()
const;
808 int getMudpit()
const;
811 void setMudpit(
const int value);
814 double getPrecursorCutOutLowerLimit()
const;
817 void setPrecursorCutOutLowerLimit(
const double value);
820 double getPrecursorCutOutUpperLimit()
const;
823 void setPrecursorCutOutUpperLimit(
const double value);
826 bool isAutoSelectCharge()
const;
829 void setAutoSelectCharge(
const bool value);
832 std::string getTaxBrowserUrl()
const;
835 void setTaxBrowserUrl(
const std::string value);
838 int getMinPepLenInSearch()
const;
841 void setMinPepLenInSearch(
const int value);
844 int getMaxPepModArrangements()
const;
847 void setMaxPepModArrangements(
const int value);
850 int getMaxPepNumVarMods()
const;
853 void setMaxPepNumVarMods(
const int value);
856 int getMaxPepNumModifiedSites()
const;
859 void setMaxPepNumModifiedSites(
const int value);
862 bool isIteratePMFIntensities()
const;
865 void setIteratePMFIntensities(
const bool value);
868 double getMinEtagMassDelta()
const;
871 void setMinEtagMassDelta(
const double value);
874 double getMaxEtagMassDelta()
const;
877 void setMaxEtagMassDelta(
const double value);
880 std::string getResultsFileFormatVersion()
const;
883 void setResultsFileFormatVersion(
const char *value);
886 std::string getSortUnassigned()
const;
889 void setSortUnassigned(
const std::string newValue);
892 int getSelectSwitch()
const;
895 void setSelectSwitch(
const int value);
898 double getMudpitSwitch()
const;
901 void setMudpitSwitch(
const double value);
904 int getMaxDatabases()
const;
907 void setMaxDatabases(
const int value);
910 std::string getCacheDirectory()
const;
913 void setCacheDirectory(
const char * value);
916 std::string getResfileCache()
const;
919 void setResfileCache(
const char * value);
922 std::string getResultsCache()
const;
925 void setResultsCache(
const char * value);
928 bool isPercolator()
const;
931 void setPercolator(
const bool value);
934 std::string getPercolatorFeatures()
const;
937 void setPercolatorFeatures(std::string value);
940 int getPercolatorMinQueries()
const;
943 void setPercolatorMinQueries(
const int value);
946 int getPercolatorMinSequences()
const;
949 void setPercolatorMinSequences(
const int value);
952 bool isPercolatorUseProteins()
const;
955 void setPercolatorUseProteins(
const bool value);
958 bool isPercolatorUseRT()
const;
961 void setPercolatorUseRT(
const bool value);
964 std::string getPercolatorExeFlags(
bool anyRetentionTimes,
965 const std::vector<std::string> percolatorFiles,
966 const PERC_EXE_RT rt = PERC_EXE_RT_USE_DEFAULT)
const;
969 void setPercolatorExeFlags(
const char * value);
972 int getPercolatorTargetRankScoreThreshold()
const;
975 void setPercolatorTargetRankScoreThreshold(
const int threshold);
978 double getPercolatorTargetRankRelativeThreshold()
const;
981 void setPercolatorTargetRankRelativeThreshold(
const double threshold);
984 int getCreatePipThreads()
const;
987 void setCreatePipThreads(
const int nThreads);
990 int getCreatePipThreadBlockSize()
const;
993 void setCreatePipThreadBlockSize(
const int blockSize);
996 int getExecAfterSearch(
const char * szResultsFilePath,
997 std::vector<std::string> & commands,
998 std::vector<std::string> & titles,
999 std::vector<int> & waitfor,
1000 std::vector<int> & logging,
1001 std::vector<std::string> & additionalFlags,
1002 const char * sessionID = 0,
1003 const char * taskID = 0)
const;
1006 void setExecAfterSearch(
const int num, std::string value);
1009 std::string getResultsPerlScript_2()
const;
1012 void setResultsPerlScript_2(std::string value);
1015 std::string getResultsFullURL_2()
const;
1018 void setResultsFullURL_2(std::string value);
1021 int getProteinFamilySwitch()
const;
1024 void setProteinFamilySwitch(
const int value);
1027 int getDecoyTypeSpecific()
const;
1030 void setDecoyTypeSpecific(
const int value);
1033 int getDecoyTypeNoEnzyme()
const;
1036 void setDecoyTypeNoEnzyme(
const int value);
1039 int getSVGSpectrumSwitch()
const;
1042 void setSVGSpectrumSwitch(
const int value);
1045 int getDisplayNonSignificantMatches()
const;
1048 void setDisplayNonSignificantMatches(
const int value);
1051 std::string getCompressToolAA()
const;
1054 void setCompressToolAA(
const std::string value);
1057 std::string getCompressToolNA()
const;
1060 void setCompressToolNA(
const std::string value);
1063 std::string getCompressToolSL()
const;
1066 void setCompressToolSL(
const std::string value);
1069 std::string getCompressToolCommandLineFasta(
DATABASE_TYPE dbType,
1070 const std::string & dbname,
1071 const std::string & dbpath)
const;
1074 std::string getCompressToolCommandLineLibrary(
const std::string & logfilepath,
1075 const std::string & inputfile,
1076 const std::string & outputdirectory)
const;
1079 std::string getPepSearchTool()
const;
1082 void setPepSearchTool(
const std::string value);
1085 std::string getPepSearchToolCommandLine(
const std::string & peptideToleranceUnit,
1086 const double & peptideTolerance,
1087 const std::string & ionToleranceUnit,
1088 const double & ionTolerance,
1089 const std::string & libraryDirectoryPath,
1090 const std::string & inputFileRelativePath,
1091 const std::string & outputFileRelativePath)
const;
1094 int getSpectraPerLibraryBlock()
const;
1097 void setSpectraPerLibraryBlock(
const int value);
1100 int getCrawlerNumPeaksPer100Da()
const;
1103 void setCrawlerNumPeaksPer100Da(
const int value);
1106 std::string getSearchSubmitMode()
const;
1109 void setSearchSubmitMode(
const std::string value);
1112 int getDechargeFragmentPeaks()
const;
1115 void setDechargeFragmentPeaks(
const int maxCharge);
1118 std::string getSearchSubmitOutputFormat()
const;
1121 void setSearchSubmitOutputFormat(
const std::string value);
1124 bool isAlwaysCreateDat28ResultsFile()
const;
1127 void setAlwaysCreateDat28ResultsFile(
const bool value);
1130 bool isCreateLegacyModAndSubstitutionFiles()
const;
1133 void setCreateLegacyModAndSubstitutionFiles(
const bool value);
1136 bool isAlwaysEnableAutoDecoySearch()
const;
1139 void setAlwaysEnableAutoDecoySearch(
const bool value);
1142 std::string getSearchSubmitAcceptedFileTypes()
const;
1145 void setSearchSubmitAcceptedFileTypes(
const std::string value);
1148 std::string getSearchSubmitDefaultPeptideCharge()
const;
1151 void setSearchSubmitDefaultPeptideCharge(
const std::string value);
1156 const ms_blastaccession* getGetSeqBlastAccession()
const;
1159 void setGetSeqBlastAccession(
const ms_blastaccession* value);
1162 int getMinPeakIteration()
const;
1165 void setMinPeakIteration(
const int value);
1168 bool isEncryptURL()
const;
1171 void setEncryptURL(
const bool value);
1174 std::string getPercolatorExeFlags()
const;
1177 std::string getPercolatorRtFlags(
const bool anyRetentionTimes,
const bool useRT)
const;
1180 std::string getExecAfterSearch(
const int num)
const;
1183 void checkExecAfterSearch(
ms_errs & err);
1186 void checkReportBuilderColumnArrangement(
ms_errs & err);
1189 void checkSpectrumViewerColourSchemes(
ms_errs & err,
bool addToList =
true);
1192 bool isMatchOppositeCrosslinkPairs()
const;
1195 void setMatchOppositeCrosslinkPairs(
const bool value);
1198 int getMaxIntactCrosslinkPeptides()
const;
1201 void setMaxIntactCrosslinkPeptides(
const int value);
1204 bool isTransferParsingToNodes()
const;
1207 void setTransferParsingToNodes(
const bool value);
1210 int getMascotFileProcessingThreads()
const;
1213 void setMascotFileProcessingThreads(
const int value);
1216 int getInputFileParsingThreads()
const;
1219 void setInputFileParsingThreads(
const int value);
1222 int getChunkReadingThreads()
const;
1225 void setChunkReadingThreads(
const int value);
1228 int getChunkPreparationThreads()
const;
1231 void setChunkPreparationThreads(
const int value);
1234 bool isMsrSqlQueriesInTransactions()
const;
1237 void setMsrSqlQueriesInTransactions(
const bool value);
1240 bool getAllowEmbeddedConfigInMimeInput()
const;
1243 void setAllowEmbeddedConfigInMimeInput(
const bool value);
1246#ifdef SUPPRESS_MS_CUSTOMPROPERTY_INHERITANCE
1247#include "suppress_ms_customproperty.hpp"
1251 void synchronizeReportNumberChoices_();
1252 void synchronizeIgnoreDupeAccession_();
1253 void synchronizeTargetFDRPercentages_();
1255 bool sectionAvailable_;
1257 bool saveLastQueryAsc_;
1258 bool saveEveryLastQueryAsc_;
1259 std::string lastQueryAscFile_;
1261 std::string errorLogFile_;
1262 std::string searchLogFile_;
1263 std::string monitorLogFile_;
1264 std::string interFileBasePath_;
1265 std::string interFileRelPath_;
1267 std::string mascotCmdLine_;
1268 std::string testDirectory_;
1269 std::string mascotControlFile_;
1270 std::string mascNodeCtrlFile_;
1271 std::string mascotJobIdFile_;
1272 std::string getSeqJobIdFile_;
1273 int uniqueJobStartNumber_;
1275 std::string resultsPerlScript_;
1276 std::string noResultsScript_;
1277 std::string resultsFullURL_;
1278 std::string logoImageFile_;
1280 int massDecimalPlaces_;
1281 int ionsDecimalPlaces_;
1282 int intensitySigFigs_;
1284 bool emailUsersEnabled_;
1285 bool emailErrorsEnabled_;
1287 std::string emailService_;
1288 std::string emailPassword_;
1289 std::string emailProfile_;
1290 std::string sendmailPath_;
1291 std::string emailFromUser_;
1292 std::string emailFromTextName_;
1293 int emailTimeOutPeriod_;
1294 int monitorEmailCheckFreq_;
1295 std::string mailTempFile_;
1296 std::string errMessageEmailTo_;
1298 int monitorTestTimeout_;
1299 std::string NTMonitorGroup_;
1300 std::string NTIUserGroup_;
1301 int unixWebUserGroup_;
1302 bool forkForUnixApache_;
1304 std::string formVersion_;
1305 int maxSequenceLen_;
1306 int maxConcurrentSearches_;
1307 int maxSearchesPerUser_;
1308 double centroidWidth_;
1309 int centroidWidthCount_;
1310 int maxDescriptionLen_;
1311 int maxNumPeptides_;
1314 std::vector< int > reportNumberChoices_;
1315 std::vector< double > targetFDRPercentages_;
1316 int defaultTargetFDRPercentagesIx_;
1318 int reviewColWidths_[MS_REVIEW_COL____LAST___];
1319 bool reviewColDisplay_[MS_REVIEW_COL____LAST___];
1320 std::vector<std::string> reportBuilderColArr_;
1322 std::string defaultColourSchemeName_;
1323 std::vector<std::string> colourSchemeNames_;
1324 std::vector<std::string> colourSchemeStrings_;
1326 std::string proxyType_;
1327 bool useHTTPProxyForFTP_;
1328 bool useHTTPProxyForHTTPS_;
1329 std::string proxy_server_;
1330 std::string proxy_username_;
1331 std::string proxy_password_;
1335 int errTolMaxAccessions_;
1337 bool showAllFromErrorTolerant_;
1339 int minPepLenInPepSummary_;
1340 int maxPepModArrangements_;
1341 int maxPepNumVarMods_;
1342 int maxPepNumModifiedSites_;
1344 double showSubsets_;
1345 bool requireBoldRed_;
1346 double sigThreshold_;
1347 double siteAnalysisMD10Prob_;
1348 double ignoreIonsScoreBelow_;
1350 std::string monitorPidFile_;
1351 bool storeModPermutations_;
1352 int proteinsInResultsFile_;
1353 std::string mascotMessage_;
1354 int splitNumberOfQueries_;
1355 int splitDataFileSize_;
1356 bool moveOldDbToOldDir_;
1357 bool removeOldIndexFiles_;
1359 int featureTableLength_;
1360 double featureTableMinScore_;
1362 std::string ICATLight_;
1363 std::string ICATHeavy_;
1364 std::string ICATFilter_;
1365 std::string ICATQuantitationMethod_;
1368 bool UnixDirPermDefined_;
1371 typedef std::vector<std::string> t_dupeAccs;
1372 t_dupeAccs ignoreDupeAccessions_;
1374 double precursorCutOutLowerLimit_;
1375 double precursorCutOutUpperLimit_;
1377 bool autoSelectCharge_;
1378 std::string taxBrowserUrl_;
1379 int minPepLenInSearch_;
1380 bool iteratePMFIntensities_;
1382 double minEtagMassDelta_;
1383 double maxEtagMassDelta_;
1385 std::string resultsFileFormatVersion_;
1386 std::string sortUnassigned_;
1388 double mudpitSwitch_;
1391 std::string cacheDirectory_;
1393 std::string resfileCache_;
1394 std::string resultsCache_;
1397 std::string percolatorFeatures_;
1398 int percolatorMinQueries_;
1399 int percolatorMinSequences_;
1400 bool percolatorUseProteins_;
1401 bool percolatorUseRT_;
1402 std::string percolatorExeFlags_;
1403 int percolatorTargetRankScoreThreshold_;
1404 double percolatorTargetRankRelativeThreshold_;
1406 int createPipThreads_;
1407 int createPipThreadBlockSize_;
1409 std::vector<std::string> execAfterSearch_;
1410 std::vector<std::string> execAfterSearchCommands_;
1411 std::vector<std::string> execAfterSearchTitles_;
1412 std::vector<int> execAfterSearchWaitFor_;
1413 std::vector<int> execAfterSearchLogging_;
1414 std::vector<std::string> execAfterSearchAdditionalFlags_;
1415 std::string resultsPerlScript_2_;
1416 std::string resultsFullURL_2_;
1417 int proteinFamilySwitch_;
1419 int decoyTypeSpecific_;
1420 int decoyTypeNoEnzyme_;
1422 int svgSpectrumSwitch_;
1423 int displayNonSigMatches_;
1425 ms_blastaccession getSeqBlastAccession_;
1426 int minPeakIteration_;
1429 std::string compressToolAA_;
1430 std::string compressToolNA_;
1431 std::string compressToolSL_;
1432 std::string pepSearchTool_;
1433 int spectraPerLibraryBlock_;
1434 int crawlerNumPeaksPer100Da_;
1435 bool matchOppositeCrosslinkPairs_;
1436 int maxIntactCrosslinkPeptides_;
1437 std::string searchSubmitMode_;
1438 int dechargeFragmentPeaks_;
1439 std::string searchSubmitOutputFormat_;
1440 bool alwaysCreateDat28ResultsFile_;
1441 bool transferParsingToNodes_;
1442 int mascotFileProcessingThreads_;
1443 int inputFileParsingThreads_;
1444 int chunkReadingThreads_;
1445 int chunkPreparationThreads_;
1446 bool msrSqlQueriesInTransactions_;
1447 bool allowEmbeddedConfigInMimeInput_;
1448 bool createLegacyModAndSubstitutionFiles_;
1449 bool alwaysEnableAutoDecoySearch_;
1450 std::string searchSubmitAcceptedFileTypes_;
1451 std::string searchSubmitDefaultPeptideCharge_;
The class is used as a base for property-containing classes, such as ms_mascotoptions.
Definition: ms_customproperty.hpp:91
Encapsulates the mascot.dat file that contains the most important parameters.
Definition: ms_datfile.hpp:47
All errors are collected in an instance of this class.
Definition: ms_errors.hpp:37
An instance of this class represents all the parameters specified in the Options section of mascot....
Definition: ms_mascotoptions.hpp:91
PERC_EXE_RT
Definitions for retention time override when calling getPercolatorExeFlags().
Definition: ms_mascotoptions.hpp:124
EXEC_AFTER_SEARCH
Definitions for the ExecAfterSearch_XXX lines in the Options section of mascot.dat.
Definition: ms_mascotoptions.hpp:176
NUMERICAL_VALUE_STORAGE
Definitions for storage of numerical values in files.
Definition: ms_mascotoptions.hpp:187
MS_REVIEW_COL
Definitions for columns in ms-review.exe for use with getReviewColWidth() and getReviewColDisplay().
Definition: ms_mascotoptions.hpp:100
DECOY_ALGORITHM
Definitions for how the decoy sequences are generated.
Definition: ms_mascotoptions.hpp:156
DATABASE_TYPE
Definition: ms_databaseoptions.hpp:39
1.9.6