Matrix Science header

ms_mascotresfile Member List

This is the complete list of members for ms_mascotresfile, including all inherited members.
anyMSMS()ms_mascotresfile
anyPeptideSummaryMatches(const section sec=SEC_PEPTIDES)ms_mascotresfile
anyPMF()ms_mascotresfile
anySQ()ms_mascotresfile
anyTag()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 namems_mascotresfile
ERR_ACCINPEPTIDESTR enum valuems_mascotresfile
ERR_ADDPEPTIDES enum valuems_mascotresfile
ERR_CANNOT_APPEND_RESFILE enum valuems_mascotresfile
ERR_CANNOT_APPEND_RESFILE_NO_FNAMES enum valuems_mascotresfile
ERR_CDB_64_BIT_REMAKE enum valuems_mascotresfile
ERR_CDB_BEING_CREATED enum valuems_mascotresfile
ERR_CDB_FAIL_LOCK enum valuems_mascotresfile
ERR_CDB_FAIL_REMOVE enum valuems_mascotresfile
ERR_CDB_FAIL_UNLOCK enum valuems_mascotresfile
ERR_CDB_INCOMPLETE_NO_RETRY enum valuems_mascotresfile
ERR_CDB_INCOMPLETE_RETRY enum valuems_mascotresfile
ERR_CDB_OLD_VER_NO_RETRY enum valuems_mascotresfile
ERR_CDB_OLD_VER_RETRY enum valuems_mascotresfile
ERR_CDB_SOURCE_CHANGE_NO_RETRY enum valuems_mascotresfile
ERR_CDB_SOURCE_CHANGE_RETRY enum valuems_mascotresfile
ERR_CDB_TOO_LARGE enum valuems_mascotresfile
ERR_DUPE_ACCESSION enum valuems_mascotresfile
ERR_DUPLICATE_KEY enum valuems_mascotresfile
ERR_FAIL_CDB_INIT enum valuems_mascotresfile
ERR_FAIL_CLOSE_FILE enum valuems_mascotresfile
ERR_FAIL_MK_CACHE_DIR enum valuems_mascotresfile
ERR_FAIL_MK_CDB_FILE enum valuems_mascotresfile
ERR_FAIL_OPEN_DAT_FILE enum valuems_mascotresfile
ERR_INVALID_CACHE_DIR enum valuems_mascotresfile
ERR_INVALID_CDB_FILE enum valuems_mascotresfile
ERR_INVALID_NUMQUERIES enum valuems_mascotresfile
ERR_INVALID_PROTDB enum valuems_mascotresfile
ERR_INVALID_RESFILE enum valuems_mascotresfile
ERR_MALFORMED_DRANGE enum valuems_mascotresfile
ERR_MALFORMED_ERR_TOL enum valuems_mascotresfile
ERR_MALFORMED_TAG enum valuems_mascotresfile
ERR_MALFORMED_TERMS enum valuems_mascotresfile
ERR_MISSING_CDB_FILE enum valuems_mascotresfile
ERR_MISSING_PERCOLATOR_FILE enum valuems_mascotresfile
ERR_MISSINGENTRY enum valuems_mascotresfile
ERR_MISSINGHIT enum valuems_mascotresfile
ERR_MISSINGSECTION enum valuems_mascotresfile
ERR_MISSINGSECTIONEND enum valuems_mascotresfile
ERR_NEED_64_BIT enum valuems_mascotresfile
ERR_NO_ERR_TOL_PARENT enum valuems_mascotresfile
ERR_NO_ERROR enum valuems_mascotresfile
ERR_NO_UNIGENE_FILE enum valuems_mascotresfile
ERR_NOMEM enum valuems_mascotresfile
ERR_NOSUCHFILE enum valuems_mascotresfile
ERR_NULL_ACC_PEP_SUM enum valuems_mascotresfile
ERR_NULL_ACC_PROT_SUM enum valuems_mascotresfile
ERR_OLDRESULTSFILE enum valuems_mascotresfile
ERR_PEPSUMMPEPGET enum valuems_mascotresfile
ERR_PEPTIDESTR enum valuems_mascotresfile
ERR_PROTSUMM enum valuems_mascotresfile
ERR_PROTSUMMPEP enum valuems_mascotresfile
ERR_QUERYOUTOFRANGE enum valuems_mascotresfile
ERR_READINGFILE enum valuems_mascotresfile
ERR_RESULTS_NOT_CREATED enum valuems_mascotresfile
ERR_UNASSIGNED_PROG enum valuems_mascotresfile
ERR_UNASSIGNED_RANGE enum valuems_mascotresfile
ERR_UNASSIGNED_UNK enum valuems_mascotresfile
ERR_UNIGENE_MULTIDB enum valuems_mascotresfile
ERR_WRITE_CDB_FILE enum valuems_mascotresfile
FLAGS enum namems_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)ms_mascotresfile
get_ms_mascotresults_params(const ms_mascotoptions &opts, ms_mascotresults_params &params)ms_mascotresfile
getCacheDirectory(bool processed=true) const ms_mascotresfile
getCacheFileName() 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
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)ms_mascotresfile
getObservedIntensity(const int query)ms_mascotresfile
getObservedMass(const int query)ms_mascotresfile
getObservedMrValue(const int query, const bool decoy=false)ms_mascotresfile
getPercolatorFileNames() 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)ms_mascotresfile
getResfile(int id) const ms_mascotresfile
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
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 valuems_mascotresfile
KA_CREATECACHE_CC enum valuems_mascotresfile
KA_CREATEINDEX_CI enum valuems_mascotresfile
KA_GROUPPROTEINS_GP enum valuems_mascotresfile
KA_LAST enum valuems_mascotresfile
KA_QUANTITATION enum valuems_mascotresfile
KA_READFILE_RF enum valuems_mascotresfile
KA_TASK enum namems_mascotresfile
KA_THRESHFORFDR_FDR enum valuems_mascotresfile
KA_UNASSIGNEDLIST_UL enum valuems_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_mascotresfile
outputKeepAlive() const ms_mascotresfile
params() const ms_mascotresfile [inline]
PERCOLATOR_FILE_NAMES enum namems_mascotresfile
PERCOLATOR_INPUT_FILE enum valuems_mascotresfile
PERCOLATOR_OUTPUT_DECOY enum valuems_mascotresfile
PERCOLATOR_OUTPUT_TARGET enum valuems_mascotresfile
resetKeepAlive(const int keepAliveInterval, const char *keepAliveText, const bool propagateToAppended=true, const bool resetStartTime=false)ms_mascotresfile
RESFILE_CACHE_IGNORE_ACC_DUPES enum valuems_mascotresfile
RESFILE_CACHE_IGNORE_DATE_CHANGE enum valuems_mascotresfile
RESFILE_NOFLAG enum valuems_mascotresfile
RESFILE_USE_CACHE enum valuems_mascotresfile
RESFILE_USE_PARENT_PARAMS enum valuems_mascotresfile
SEC_DECOYMIXTURE enum valuems_mascotresfile
SEC_DECOYPEPTIDES enum valuems_mascotresfile
SEC_DECOYPROTEINS enum valuems_mascotresfile
SEC_DECOYSUMMARY enum valuems_mascotresfile
SEC_ENZYME enum valuems_mascotresfile
SEC_ERRTOLPEPTIDES enum valuems_mascotresfile
SEC_ERRTOLSUMMARY enum valuems_mascotresfile
SEC_HEADER enum valuems_mascotresfile
SEC_INDEX enum valuems_mascotresfile
SEC_LIBRARYPEPTIDES enum valuems_mascotresfile
SEC_LIBRARYSUMMARY enum valuems_mascotresfile
SEC_MASSES enum valuems_mascotresfile
SEC_MIXTURE enum valuems_mascotresfile
SEC_NUMSECTIONS enum valuems_mascotresfile
SEC_PARAMETERS enum valuems_mascotresfile
SEC_PEPTIDES enum valuems_mascotresfile
SEC_PROTEINS enum valuems_mascotresfile
SEC_QUANTITATION enum valuems_mascotresfile
SEC_QUERY1 enum valuems_mascotresfile
SEC_SPECTRAL_LIBRARY enum valuems_mascotresfile
SEC_SUMMARY enum valuems_mascotresfile
SEC_TAXONOMY enum valuems_mascotresfile
SEC_UNIMOD enum valuems_mascotresfile
section enum namems_mascotresfile
setPercolatorFeatures(const char *percolatorFeatures, const char *additionalFeatures, const bool useRetentionTimes)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]
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]
XML_SCHEMA enum namems_mascotresfile
XML_SCHEMA_DIRECTORY enum valuems_mascotresfile
XML_SCHEMA_LAST enum valuems_mascotresfile
XML_SCHEMA_QUANTITATION enum valuems_mascotresfile
XML_SCHEMA_UNIMOD enum valuems_mascotresfile
~ms_errors()ms_errors
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:52