, including all inherited members.
| anyMSMS() const | ms_mascotresfile | |
| anyPeptideSummaryMatches(const section sec=SEC_PEPTIDES) const | ms_mascotresfile | |
| anyPMF() const | ms_mascotresfile | |
| anySQ() const | ms_mascotresfile | |
| anyTag() const | ms_mascotresfile | |
| appendErrors(ms_errs &errs) | ms_mascotresfile | |
| matrix_science::ms_errors::appendErrors(const ms_errors &src) | ms_errors | |
| appendResfile(const char *filename, int flags=RESFILE_USE_PARENT_PARAMS, const char *cacheDirectory=0) | ms_mascotresfile | |
| clearAllErrors() | ms_errors | |
| copyFrom(const ms_errors *right) | ms_errors | |
| doesSectionExist(const section sec) const | ms_mascotresfile | |
| enumerateQuerySectionKeys(const int query, const int num, int *pPreviousNum=0, OFFSET64_T *pPreviousOffset=0) const | ms_mascotresfile | |
| enumerateSectionKeys(const section sec, const int num, int *pPreviousNum=0, OFFSET64_T *pPreviousOffset=0) const | ms_mascotresfile | |
| err enum name | ms_mascotresfile | |
| ERR_ACCINPEPTIDESTR enum value | ms_mascotresfile | |
| ERR_ADDPEPTIDES enum value | ms_mascotresfile | |
| ERR_CANNOT_APPEND_RESFILE enum value | ms_mascotresfile | |
| ERR_CANNOT_APPEND_RESFILE_NO_FNAMES enum value | ms_mascotresfile | |
| ERR_CDB_64_BIT_REMAKE enum value | ms_mascotresfile | |
| ERR_CDB_BEING_CREATED enum value | ms_mascotresfile | |
| ERR_CDB_FAIL_LOCK enum value | ms_mascotresfile | |
| ERR_CDB_FAIL_REMOVE enum value | ms_mascotresfile | |
| ERR_CDB_FAIL_UNLOCK enum value | ms_mascotresfile | |
| ERR_CDB_INCOMPLETE_NO_RETRY enum value | ms_mascotresfile | |
| ERR_CDB_INCOMPLETE_RETRY enum value | ms_mascotresfile | |
| ERR_CDB_OLD_VER_NO_RETRY enum value | ms_mascotresfile | |
| ERR_CDB_OLD_VER_RETRY enum value | ms_mascotresfile | |
| ERR_CDB_SOURCE_CHANGE_NO_RETRY enum value | ms_mascotresfile | |
| ERR_CDB_SOURCE_CHANGE_RETRY enum value | ms_mascotresfile | |
| ERR_CDB_TOO_LARGE enum value | ms_mascotresfile | |
| ERR_DUPE_ACCESSION enum value | ms_mascotresfile | |
| ERR_DUPLICATE_KEY enum value | ms_mascotresfile | |
| ERR_FAIL_CDB_INIT enum value | ms_mascotresfile | |
| ERR_FAIL_CLOSE_FILE enum value | ms_mascotresfile | |
| ERR_FAIL_MK_CACHE_DIR enum value | ms_mascotresfile | |
| ERR_FAIL_MK_CDB_FILE enum value | ms_mascotresfile | |
| ERR_FAIL_OPEN_DAT_FILE enum value | ms_mascotresfile | |
| ERR_INVALID_CACHE_DIR enum value | ms_mascotresfile | |
| ERR_INVALID_CDB_FILE enum value | ms_mascotresfile | |
| ERR_INVALID_NUMQUERIES enum value | ms_mascotresfile | |
| ERR_INVALID_PROTDB enum value | ms_mascotresfile | |
| ERR_INVALID_RESFILE enum value | ms_mascotresfile | |
| ERR_MALFORMED_DRANGE enum value | ms_mascotresfile | |
| ERR_MALFORMED_ERR_TOL enum value | ms_mascotresfile | |
| ERR_MALFORMED_TAG enum value | ms_mascotresfile | |
| ERR_MALFORMED_TERMS enum value | ms_mascotresfile | |
| ERR_MISSING_CDB_FILE enum value | ms_mascotresfile | |
| ERR_MISSING_PERCOLATOR_FILE enum value | ms_mascotresfile | |
| ERR_MISSINGENTRY enum value | ms_mascotresfile | |
| ERR_MISSINGHIT enum value | ms_mascotresfile | |
| ERR_MISSINGSECTION enum value | ms_mascotresfile | |
| ERR_MISSINGSECTIONEND enum value | ms_mascotresfile | |
| ERR_NEED_64_BIT enum value | ms_mascotresfile | |
| ERR_NO_ERR_TOL_PARENT enum value | ms_mascotresfile | |
| ERR_NO_ERROR enum value | ms_mascotresfile | |
| ERR_NO_UNIGENE_FILE enum value | ms_mascotresfile | |
| ERR_NOMEM enum value | ms_mascotresfile | |
| ERR_NOSUCHFILE enum value | ms_mascotresfile | |
| ERR_NULL_ACC_PEP_SUM enum value | ms_mascotresfile | |
| ERR_NULL_ACC_PROT_SUM enum value | ms_mascotresfile | |
| ERR_OLDRESULTSFILE enum value | ms_mascotresfile | |
| ERR_PEPSUMMPEPGET enum value | ms_mascotresfile | |
| ERR_PEPTIDESTR enum value | ms_mascotresfile | |
| ERR_PROTSUMM enum value | ms_mascotresfile | |
| ERR_PROTSUMMPEP enum value | ms_mascotresfile | |
| ERR_QUERYOUTOFRANGE enum value | ms_mascotresfile | |
| ERR_READINGFILE enum value | ms_mascotresfile | |
| ERR_RESULTS_NOT_CREATED enum value | ms_mascotresfile | |
| ERR_UNASSIGNED_PROG enum value | ms_mascotresfile | |
| ERR_UNASSIGNED_RANGE enum value | ms_mascotresfile | |
| ERR_UNASSIGNED_UNK enum value | ms_mascotresfile | |
| ERR_UNIGENE_MULTIDB enum value | ms_mascotresfile | |
| ERR_WRITE_CDB_FILE enum value | ms_mascotresfile | |
| FLAGS enum name | ms_mascotresfile | |
| get_ms_mascotresults_params(const ms_mascotoptions &opts, unsigned int *gpFlags, double *gpMinProbability, int *gpMaxHitsToReport, double *gpIgnoreIonsScoreBelow, unsigned int *gpMinPepLenInPepSummary, bool *gpUsePeptideSummary, unsigned int *gpFlags2) const | ms_mascotresfile | |
| get_ms_mascotresults_params(const ms_mascotoptions &opts, ms_mascotresults_params ¶ms) const | ms_mascotresfile | |
| getCacheDirectory(bool processed=true) const | ms_mascotresfile | |
| getCacheFileName() const | ms_mascotresfile | |
| getCrosslinkingMethod(ms_crosslinking_method *method) const | ms_mascotresfile | |
| getDatabaseType(const int idx) const | ms_mascotresfile | |
| getDate() const | ms_mascotresfile | [inline] |
| getDecoyTypeForDB(const int idx=1) const | ms_mascotresfile | |
| getEnzyme(ms_enzymefile *efile, const char *enzymeFileName=0) const | ms_mascotresfile | |
| getErrorHandler() const | ms_errors | |
| getErrorNumber(const int num=-1) const | ms_mascotresfile | |
| getErrorString(const int num) const | ms_mascotresfile | |
| getExecTime() const | ms_mascotresfile | [inline] |
| getFastaPath(int idx=1) const | ms_mascotresfile | |
| getFastaVer(int idx=1) const | ms_mascotresfile | |
| getFileName(const int id=1) const | ms_mascotresfile | |
| getJobNumber(const int resfileID=1) const | ms_mascotresfile | |
| getKeepAlive(KA_TASK &kaTask, int &kaPercentage, std::string &kaAccession, int &kaHit, int &kaQuery, std::string &kaText) const | ms_mascotresfile | |
| getLastError() const | ms_mascotresfile | |
| getLastErrorString() const | ms_mascotresfile | |
| getMascotVer() const | ms_mascotresfile | [inline] |
| getMasses(ms_masses *masses) const | ms_mascotresfile | |
| getMonoLinkModification(const int modNum, const int monoLink) const | ms_mascotresfile | |
| getMSParserVersion() const | ms_mascotresfile | |
| getMultiFileQueryNumber(const int localQuery, const int fileId) const | ms_mascotresfile | |
| getNumberOfErrors() const | ms_mascotresfile | |
| getNumberOfResfiles() const | ms_mascotresfile | |
| getNumEtSeqsSearched(const int idx=0) const | ms_mascotresfile | |
| getNumHits(const section sec=SEC_SUMMARY) const | ms_mascotresfile | |
| getNumLibraryEntries(const int idx=0) const | ms_mascotresfile | |
| getNumQueries(const int resfileID=0) const | ms_mascotresfile | |
| getNumResidues(const int idx=0) const | ms_mascotresfile | |
| getNumSeqs(const int idx=0) const | ms_mascotresfile | |
| getNumSeqsAfterTax(const int idx=0) const | ms_mascotresfile | |
| getObservedCharge(const int query, const bool decoy=false) const | ms_mascotresfile | |
| getObservedIntensity(const int query) const | ms_mascotresfile | |
| getObservedMass(const int query) const | ms_mascotresfile | |
| getObservedMrValue(const int query, const bool decoy=false) const | ms_mascotresfile | |
| getPercolatorFileNames() const | ms_mascotresfile | |
| getProgressInfo(bool forPeptideSummary=false) const | ms_mascotresfile | |
| getQuantitation(ms_quant_configfile *qfile) const | ms_mascotresfile | |
| getQuantitationMethod(ms_quant_method *qmethod) const | ms_mascotresfile | |
| getQuerySectionValue(const int query, const char *key, char *str, int maxLen) const | ms_mascotresfile | |
| getQuerySectionValueDouble(const int query, const char *key) const | ms_mascotresfile | |
| getQuerySectionValueInt(const int query, const char *key) const | ms_mascotresfile | |
| getQuerySectionValueStr(const int query, const char *key) const | ms_mascotresfile | |
| getReferenceDatabaseNumberOfSL(const int idx) const | ms_mascotresfile | |
| getRepeatSearchString(const int query, const bool fullQuery=false) const | ms_mascotresfile | |
| getResfile(int id) const | ms_mascotresfile | |
| getSectionName(const section sec) | ms_mascotresfile | [static] |
| getSectionValue(const section sec, const char *key, char *str, int maxLen) const | ms_mascotresfile | |
| getSectionValueDouble(const section sec, const char *key) const | ms_mascotresfile | |
| getSectionValueInt(const section sec, const char *key) const | ms_mascotresfile | |
| getSectionValueStr(const section sec, const char *key) const | ms_mascotresfile | |
| getSLDatabaseNumbersOfReference(const int idx) const | ms_mascotresfile | |
| getSLFragmentTolerance(int idx=1) const | ms_mascotresfile | |
| getSLFragmentToleranceUnit(int idx=1) const | ms_mascotresfile | |
| getSrcQueryAndFileIdForMultiFile(const int q, int &gsqNewQuery, int &gsqFileId) const | ms_mascotresfile | |
| getTaxonomy(ms_taxonomyfile *tfile) const | ms_mascotresfile | |
| getUnimod(ms_umod_configfile *ufile, bool useSchemaFromResfile=false) const | ms_mascotresfile | |
| getUnimodXL(ms_umod_configfile *ufile, bool useSchemaFromResfile=false) const | ms_mascotresfile | |
| getUniqueTaskID() const | ms_mascotresfile | |
| getXMLschemaFilePath(XML_SCHEMA XMLschema) const | ms_mascotresfile | |
| isDatabaseTypeAvailable() const | ms_mascotresfile | |
| isErrorTolerant() const | ms_mascotresfile | |
| isMSMS() const | ms_mascotresfile | |
| isPMF() const | ms_mascotresfile | |
| isSQ() const | ms_mascotresfile | |
| isValid() const | ms_errors | |
| KA_ASSIGNPROTEINS_AP enum value | ms_mascotresfile | |
| KA_CREATECACHE_CC enum value | ms_mascotresfile | |
| KA_CREATEINDEX_CI enum value | ms_mascotresfile | |
| KA_GROUPPROTEINS_GP enum value | ms_mascotresfile | |
| KA_LAST enum value | ms_mascotresfile | |
| KA_QUANTITATION enum value | ms_mascotresfile | |
| KA_READFILE_RF enum value | ms_mascotresfile | |
| KA_TASK enum name | ms_mascotresfile | |
| KA_THRESHFORFDR_FDR enum value | ms_mascotresfile | |
| KA_UNASSIGNEDLIST_UL enum value | ms_mascotresfile | |
| ms_errors() | ms_errors | |
| ms_mascotresfile(const char *szFileName, const int keepAliveInterval=0, const char *keepAliveText="<!-- %d seconds -->\n", const unsigned int flags=RESFILE_NOFLAG, const char *cacheDirectory="../data/cache/%Y/%m", const char *XMLschemaDirectory=0, ms_progress_info *progressMonitor=0) | ms_mascotresfile | |
| outputKeepAlive() const | ms_mascotresfile | |
| params() const | ms_mascotresfile | [inline] |
| PERCOLATOR_FILE_NAMES enum name | ms_mascotresfile | |
| PERCOLATOR_INPUT_FILE enum value | ms_mascotresfile | |
| PERCOLATOR_OUTPUT_DECOY enum value | ms_mascotresfile | |
| PERCOLATOR_OUTPUT_TARGET enum value | ms_mascotresfile | |
| resetKeepAlive(const int keepAliveInterval, const char *keepAliveText, const bool propagateToAppended=true, const bool resetStartTime=false) | ms_mascotresfile | |
| RESFILE_CACHE_IGNORE_ACC_DUPES enum value | ms_mascotresfile | |
| RESFILE_CACHE_IGNORE_DATE_CHANGE enum value | ms_mascotresfile | |
| RESFILE_NOFLAG enum value | ms_mascotresfile | |
| RESFILE_USE_CACHE enum value | ms_mascotresfile | |
| RESFILE_USE_PARENT_PARAMS enum value | ms_mascotresfile | |
| SEC_CROSSLINK_PEPTIDES enum value | ms_mascotresfile | |
| SEC_CROSSLINK_SUMMARY enum value | ms_mascotresfile | |
| SEC_CROSSLINKING enum value | ms_mascotresfile | |
| SEC_DECOYMIXTURE enum value | ms_mascotresfile | |
| SEC_DECOYPEPTIDES enum value | ms_mascotresfile | |
| SEC_DECOYPROTEINS enum value | ms_mascotresfile | |
| SEC_DECOYSUMMARY enum value | ms_mascotresfile | |
| SEC_ENZYME enum value | ms_mascotresfile | |
| SEC_ERRTOLDECOYPEPTIDES enum value | ms_mascotresfile | |
| SEC_ERRTOLDECOYSUMMARY enum value | ms_mascotresfile | |
| SEC_ERRTOLPEPTIDES enum value | ms_mascotresfile | |
| SEC_ERRTOLSUMMARY enum value | ms_mascotresfile | |
| SEC_HEADER enum value | ms_mascotresfile | |
| SEC_INDEX enum value | ms_mascotresfile | |
| SEC_LIBRARYPEPTIDES enum value | ms_mascotresfile | |
| SEC_LIBRARYSUMMARY enum value | ms_mascotresfile | |
| SEC_MASSES enum value | ms_mascotresfile | |
| SEC_MIXTURE enum value | ms_mascotresfile | |
| SEC_NUMSECTIONS enum value | ms_mascotresfile | |
| SEC_PARAMETERS enum value | ms_mascotresfile | |
| SEC_PEPTIDES enum value | ms_mascotresfile | |
| SEC_PROTEINS enum value | ms_mascotresfile | |
| SEC_QUANTITATION enum value | ms_mascotresfile | |
| SEC_QUERY1 enum value | ms_mascotresfile | |
| SEC_SPECTRAL_LIBRARY enum value | ms_mascotresfile | |
| SEC_SUMMARY enum value | ms_mascotresfile | |
| SEC_TAXONOMY enum value | ms_mascotresfile | |
| SEC_UNIMOD enum value | ms_mascotresfile | |
| SEC_UNIMOD_XL enum value | ms_mascotresfile | |
| section enum name | ms_mascotresfile | |
| setPercolatorFeatures(const char *percolatorFeatures, const char *additionalFeatures, const bool useRetentionTimes) | ms_mascotresfile | |
| setPercolatorFeatures(const ms_mascotoptions &options, const char *additionalFeatures) | ms_mascotresfile | |
| setXMLschemaFilePath(XML_SCHEMA XMLschema, const char *path) | ms_mascotresfile | |
| staticGetPercolatorFileNames(const char *szDatFileName, const char *cacheDirectory, const char *percolatorFeatures, const char *additionalFeatures, const bool useRetentionTimes, std::vector< std::string > &filenames, std::vector< bool > &exists) | ms_mascotresfile | [static] |
| staticGetPercolatorFileNames(const char *szDatFileName, const char *cacheDirectory, const ms_mascotoptions &options, const char *additionalFeatures, std::vector< std::string > &filenames, std::vector< bool > &exists) | ms_mascotresfile | [static] |
| versionGreaterOrEqual(int major, int minor, int revision) const | ms_mascotresfile | |
| willCreateCache(const char *szFileName, const unsigned int flags, const char *cacheDirectory, std::string *cacheFileName) | ms_mascotresfile | [static] |
| willCreateCache(const char *szFileName, const ms_mascotoptions &opts, const char *applicationName, std::string &resfileCacheFileName, unsigned int &cacheStatus) | ms_mascotresfile | [static] |
| XML_SCHEMA enum name | ms_mascotresfile | |
| XML_SCHEMA_CROSSLINKING enum value | ms_mascotresfile | |
| XML_SCHEMA_DIRECTORY enum value | ms_mascotresfile | |
| XML_SCHEMA_LAST enum value | ms_mascotresfile | |
| XML_SCHEMA_QUANTITATION enum value | ms_mascotresfile | |
| XML_SCHEMA_UNIMOD enum value | ms_mascotresfile | |
| ~ms_errors() | ms_errors | |
