Matrix Science Mascot Parser toolkit
 
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ms_mascotresfile_dat Member List

This is the complete list of members for ms_mascotresfile_dat, including all inherited members.

anyCrosslinkedMatches(const bool isDecoy=false) const overridems_mascotresfile_datvirtual
anyErrorTolerantMatches(const bool isDecoy=false) const overridems_mascotresfile_datvirtual
anyFastaMatches(const bool isDecoy=false) const overridems_mascotresfile_datvirtual
anyMSMS() const overridems_mascotresfile_datvirtual
anyPeptideSummaryMatches(const section sec=SEC_PEPTIDES) constms_mascotresfile_dat
anyPMF() const overridems_mascotresfile_datvirtual
anySpectralLibraryMatches(const bool isDecoy=false) const overridems_mascotresfile_datvirtual
anySQ() const overridems_mascotresfile_datvirtual
anyTag() const overridems_mascotresfile_datvirtual
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) overridems_mascotresfile_datvirtual
clearAllErrors()ms_errors
copyFrom(const ms_errors *right)ms_errors
createResfile(const char *szFileName, const int keepAliveInterval=0, const char *keepAliveText="<!-- %d seconds -->\n", const unsigned int flags=matrix_science::ms_mascotresfilebase::RESFILE_NOFLAG, const char *cacheDirectory="../data/cache/%Y/%m", const char *XMLschemaDirectory=0, matrix_science::ms_progress_info *progressMonitor=0)ms_mascotresfilebasestatic
doesSectionExist(const section sec) constms_mascotresfile_dat
enumerateQuerySectionKeys(const int query, const int num, int *pPreviousNum=0, OFFSET64_T *pPreviousOffset=0) constms_mascotresfile_dat
enumerateSectionKeys(const section sec, const int num, int *pPreviousNum=0, OFFSET64_T *pPreviousOffset=0) constms_mascotresfile_dat
err enum namems_mascotresfile_dat
ERR_ACCINPEPTIDESTR enum valuems_mascotresfile_dat
ERR_ADDPEPTIDES enum valuems_mascotresfile_dat
ERR_CANNOT_APPEND_RESFILE enum valuems_mascotresfile_dat
ERR_CANNOT_APPEND_RESFILE_NO_FNAMES enum valuems_mascotresfile_dat
ERR_CDB_64_BIT_REMAKE enum valuems_mascotresfile_dat
ERR_CDB_BEING_CREATED enum valuems_mascotresfile_dat
ERR_CDB_FAIL_LOCK enum valuems_mascotresfile_dat
ERR_CDB_FAIL_REMOVE enum valuems_mascotresfile_dat
ERR_CDB_FAIL_UNLOCK enum valuems_mascotresfile_dat
ERR_CDB_INCOMPLETE_NO_RETRY enum valuems_mascotresfile_dat
ERR_CDB_INCOMPLETE_RETRY enum valuems_mascotresfile_dat
ERR_CDB_OLD_VER_NO_RETRY enum valuems_mascotresfile_dat
ERR_CDB_OLD_VER_RETRY enum valuems_mascotresfile_dat
ERR_CDB_SOURCE_CHANGE_NO_RETRY enum valuems_mascotresfile_dat
ERR_CDB_SOURCE_CHANGE_RETRY enum valuems_mascotresfile_dat
ERR_CDB_TOO_LARGE enum valuems_mascotresfile_dat
ERR_DUPE_ACCESSION enum valuems_mascotresfile_dat
ERR_DUPLICATE_KEY enum valuems_mascotresfile_dat
ERR_FAIL_CDB_INIT enum valuems_mascotresfile_dat
ERR_FAIL_CLOSE_FILE enum valuems_mascotresfile_dat
ERR_FAIL_MK_CACHE_DIR enum valuems_mascotresfile_dat
ERR_FAIL_MK_CDB_FILE enum valuems_mascotresfile_dat
ERR_FAIL_OPEN_DAT_FILE enum valuems_mascotresfile_dat
ERR_INVALID_CACHE_DIR enum valuems_mascotresfile_dat
ERR_INVALID_CDB_FILE enum valuems_mascotresfile_dat
ERR_INVALID_NUMQUERIES enum valuems_mascotresfile_dat
ERR_INVALID_PROTDB enum valuems_mascotresfile_dat
ERR_INVALID_RESFILE enum valuems_mascotresfile_dat
ERR_MALFORMED_DRANGE enum valuems_mascotresfile_dat
ERR_MALFORMED_ERR_TOL enum valuems_mascotresfile_dat
ERR_MALFORMED_TAG enum valuems_mascotresfile_dat
ERR_MALFORMED_TERMS enum valuems_mascotresfile_dat
ERR_MISSING_CDB_FILE enum valuems_mascotresfile_dat
ERR_MISSING_PERCOLATOR_FILE enum valuems_mascotresfile_dat
ERR_MISSINGENTRY enum valuems_mascotresfile_dat
ERR_MISSINGHIT enum valuems_mascotresfile_dat
ERR_MISSINGSECTION enum valuems_mascotresfile_dat
ERR_MISSINGSECTIONEND enum valuems_mascotresfile_dat
ERR_NEED_64_BIT enum valuems_mascotresfile_dat
ERR_NO_ERR_TOL_PARENT enum valuems_mascotresfile_dat
ERR_NO_ERROR enum valuems_mascotresfile_dat
ERR_NO_UNIGENE_FILE enum valuems_mascotresfile_dat
ERR_NOMEM enum valuems_mascotresfile_dat
ERR_NOSUCHFILE enum valuems_mascotresfile_dat
ERR_NULL_ACC_PEP_SUM enum valuems_mascotresfile_dat
ERR_NULL_ACC_PROT_SUM enum valuems_mascotresfile_dat
ERR_OLDRESULTSFILE enum valuems_mascotresfile_dat
ERR_PEPSUMMPEPGET enum valuems_mascotresfile_dat
ERR_PEPTIDESTR enum valuems_mascotresfile_dat
ERR_PROTSUMM enum valuems_mascotresfile_dat
ERR_PROTSUMMPEP enum valuems_mascotresfile_dat
ERR_QUERYOUTOFRANGE enum valuems_mascotresfile_dat
ERR_READINGFILE enum valuems_mascotresfile_dat
ERR_RESULTS_NOT_CREATED enum valuems_mascotresfile_dat
ERR_UNASSIGNED_PROG enum valuems_mascotresfile_dat
ERR_UNASSIGNED_RANGE enum valuems_mascotresfile_dat
ERR_UNASSIGNED_UNK enum valuems_mascotresfile_dat
ERR_UNIGENE_MULTIDB enum valuems_mascotresfile_dat
ERR_WRITE_CDB_FILE enum valuems_mascotresfile_dat
FLAGS enum namems_mascotresfilebase
get_ms_mascotresults_params(const ms_mascotoptions &opts, ms_mascotresults_params &params) constms_mascotresfilebase
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) constms_mascotresfilebase
getCacheDirectory(bool processed=true) const overridems_mascotresfile_datvirtual
getCacheFileName() const overridems_mascotresfile_datvirtual
getCrosslinking(ms_crosslinking_configfile *crosslinkingFile) const overridems_mascotresfile_datprotectedvirtual
getCrosslinkingMethod(ms_crosslinking_method *method) constms_mascotresfilebase
getDatabaseType(const int idx) const overridems_mascotresfile_datvirtual
getDate() const overridems_mascotresfile_datinlinevirtual
getDecoyTypeForDB(const int idx=1) const overridems_mascotresfile_datvirtual
getEnzyme(ms_enzymefile *efile, const char *enzymeFileName=0) const overridems_mascotresfile_datvirtual
getErrorHandler() constms_errors
getErrorInfoAsString(const int num) constms_mascotresfilebaseprotected
getErrorNumber(const int num=-1) constms_mascotresfilebase
getErrorString(const int num) constms_mascotresfilebase
getExecTime() const overridems_mascotresfile_datinlinevirtual
getFastaPath(int idx=1) const overridems_mascotresfile_datvirtual
getFastaVer(int idx=1) const overridems_mascotresfile_datvirtual
getFileName(const int id=1) const overridems_mascotresfile_datvirtual
getFirstPassThreshold() const overridems_mascotresfile_datvirtual
getHeaderKeyValues(std::vector< std::string > &keys, std::vector< std::string > &values) const overridems_mascotresfile_datvirtual
getHeaderValue(const std::string &key) const overridems_mascotresfile_datvirtual
getInputQuery(const int queryNum) const overridems_mascotresfile_datvirtual
getJobNumber(const int resfileID=1) const overridems_mascotresfile_datvirtual
getKeepAlive(KA_TASK &kaTask, int &kaPercentage, std::string &kaAccession, int &kaHit, int &kaQuery, std::string &kaText) constms_mascotresfilebase
getLastError() constms_mascotresfilebase
getLastErrorString() constms_mascotresfilebase
getLibraryMods(std::vector< std::string > &modNames, std::vector< double > &modDeltas) const overridems_mascotresfile_datvirtual
getMascotVer() const overridems_mascotresfile_datinlinevirtual
getMasses(ms_masses *masses) constms_mascotresfilebase
getMassesKeyValues(std::vector< std::string > &keys, std::vector< double > &values) const overridems_mascotresfile_datvirtual
getMassValue(const std::string &key) const overridems_mascotresfile_datvirtual
getMonoLinkModification(const int modNum, const int monoLink) constms_mascotresfilebase
getMSParserVersion() constms_mascotresfilebase
getMultiFileQueryNumber(const int localQuery, const int fileId) const overridems_mascotresfile_datvirtual
getNumberOfErrors() constms_mascotresfilebase
getNumberOfResfiles() const overridems_mascotresfile_datvirtual
getNumEtSeqsSearched(const int idx=0) const overridems_mascotresfile_datvirtual
getNumHits(const section sec=SEC_SUMMARY) constms_mascotresfile_dat
getNumLibraryEntries(const int idx=0) const overridems_mascotresfile_datvirtual
getNumQueries(const int resfileID=0) const overridems_mascotresfile_datvirtual
getNumResidues(const int idx=0) const overridems_mascotresfile_datvirtual
getNumSeqs(const int idx=0) const overridems_mascotresfile_datvirtual
getNumSeqsAfterTax(const int idx=0) const overridems_mascotresfile_datvirtual
getObservedCharge(const int query, const bool decoy=false) const overridems_mascotresfile_datvirtual
getObservedIntensity(const int query) const overridems_mascotresfile_datvirtual
getObservedMass(const int query) const overridems_mascotresfile_datvirtual
getObservedMrValue(const int query, const bool decoy=false) const overridems_mascotresfile_datvirtual
getPeptideSection(const ms_peptide::PSM_TYPE pepType)ms_mascotresfile_datstatic
getPercolatorFileNames() constms_mascotresfilebase
getProgressInfo(bool forPeptideSummary=false) constms_mascotresfilebase
getQmatch(const int query, const ms_peptide::PSM_TYPE pepType) const overridems_mascotresfile_datvirtual
getQplughole(const int query, const ms_peptide::PSM_TYPE pepType) const overridems_mascotresfile_datvirtual
getQuantitation(ms_quant_configfile *qfile) const overridems_mascotresfile_datvirtual
getQuantitationMethod(ms_quant_method *qmethod) constms_mascotresfilebase
getQuerySectionValue(const int query, const char *key, char *str, int maxLen) constms_mascotresfile_dat
getQuerySectionValueDouble(const int query, const char *key) constms_mascotresfile_dat
getQuerySectionValueInt(const int query, const char *key) constms_mascotresfile_dat
getQuerySectionValueStr(const int query, const char *key) constms_mascotresfile_dat
getReferenceDatabaseNumberOfSL(const int idx) const overridems_mascotresfile_datvirtual
getRepeatSearchString(const int query, const bool fullQuery=false) const overridems_mascotresfile_datvirtual
getResfile(int id) const overridems_mascotresfile_datvirtual
getSearchParameter(const std::string &key) const overridems_mascotresfile_datvirtual
getSearchParametersKeyValues(std::vector< std::string > &keys, std::vector< std::string > &values) const overridems_mascotresfile_datvirtual
getSectionName(const section sec)ms_mascotresfile_datstatic
getSectionValue(const section sec, const char *key, char *str, int maxLen) constms_mascotresfile_dat
getSectionValueDouble(const section sec, const char *key) constms_mascotresfile_dat
getSectionValueInt(const section sec, const char *key) constms_mascotresfile_dat
getSectionValueStr(const section sec, const char *key) constms_mascotresfile_dat
getSLDatabaseNumbersOfReference(const int idx) const overridems_mascotresfile_datvirtual
getSLExecCommand(int idx=1) const overridems_mascotresfile_datvirtual
getSLFragmentTolerance(int idx=1) const overridems_mascotresfile_datvirtual
getSLFragmentToleranceUnit(int idx=1) const overridems_mascotresfile_datvirtual
getSrcQueryAndFileIdForMultiFile(const int q, int &gsqNewQuery, int &gsqFileId) const overridems_mascotresfile_datvirtual
getSummarySection(const ms_peptide::PSM_TYPE pepType)ms_mascotresfile_datstatic
getTaxonomy(ms_taxonomyfile *tfile) const overridems_mascotresfile_datvirtual
getUnimod(ms_umod_configfile *ufile, bool useSchemaFromResfile=false) const overridems_mascotresfile_datvirtual
getUnimodXL(ms_umod_configfile *ufile, bool useSchemaFromResfile=false) const overridems_mascotresfile_datvirtual
getUniqueTaskID() const overridems_mascotresfile_datvirtual
getXMLschemaFilePath(XML_SCHEMA XMLschema) constms_mascotresfilebase
hasEnzyme() const overridems_mascotresfile_datvirtual
hasQuantitation() const overridems_mascotresfile_datvirtual
hasRT() const overridems_mascotresfile_datvirtual
isDatabaseTypeAvailable() const overridems_mascotresfile_datvirtual
isErrorTolerant() const overridems_mascotresfile_datvirtual
isMSMS() const overridems_mascotresfile_datvirtual
isPMF() const overridems_mascotresfile_datvirtual
isSQ() const overridems_mascotresfile_datvirtual
isValid() constms_errors
KA_ASSIGNPROTEINS_AP enum valuems_mascotresfilebase
KA_CREATECACHE_CC enum valuems_mascotresfilebase
KA_CREATEINDEX_CI enum valuems_mascotresfilebase
KA_GROUPPROTEINS_GP enum valuems_mascotresfilebase
KA_LAST enum valuems_mascotresfilebase
KA_QUANTITATION enum valuems_mascotresfilebase
KA_READFILE_RF enum valuems_mascotresfilebase
KA_TASK enum namems_mascotresfilebase
KA_THRESHFORFDR_FDR enum valuems_mascotresfilebase
KA_UNASSIGNEDLIST_UL enum valuems_mascotresfilebase
ms_errors()ms_errors
ms_mascotresfile_dat(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_dat
ms_mascotresfilebase(const char *szFileName, const int keepAliveInterval=0, const char *keepAliveText="<!-- %d seconds -->\n", const unsigned int flags=RESFILE_NOFLAG, const char *cacheDirectory=0, const char *XMLschemaDirectory=0, ms_progress_info *progressMonitor=0)ms_mascotresfilebase
outputKeepAlive() constms_mascotresfilebase
params() constms_mascotresfilebaseinline
PERCOLATOR_FILE_NAMES enum namems_mascotresfilebase
PERCOLATOR_INPUT_FILE enum valuems_mascotresfilebase
PERCOLATOR_OUTPUT_DECOY enum valuems_mascotresfilebase
PERCOLATOR_OUTPUT_TARGET enum valuems_mascotresfilebase
resetKeepAlive(const int keepAliveInterval, const char *keepAliveText, const bool propagateToAppended=true, const bool resetStartTime=false)ms_mascotresfilebase
RESFILE_CACHE_IGNORE_ACC_DUPES enum valuems_mascotresfilebase
RESFILE_CACHE_IGNORE_DATE_CHANGE enum valuems_mascotresfilebase
RESFILE_DAT28 enum valuems_mascotresfilebase
RESFILE_MSR enum valuems_mascotresfilebase
RESFILE_NOFLAG enum valuems_mascotresfilebase
RESFILE_TYPE enum namems_mascotresfilebase
RESFILE_UNKNOWN enum valuems_mascotresfilebase
RESFILE_USE_CACHE enum valuems_mascotresfilebase
RESFILE_USE_PARENT_PARAMS enum valuems_mascotresfilebase
resfileType(const std::string &fileName)ms_mascotresfilebasestatic
SEC_CROSSLINK_PEPTIDES enum valuems_mascotresfile_dat
SEC_CROSSLINK_SUMMARY enum valuems_mascotresfile_dat
SEC_CROSSLINKING enum valuems_mascotresfile_dat
SEC_DECOYMIXTURE enum valuems_mascotresfile_dat
SEC_DECOYPEPTIDES enum valuems_mascotresfile_dat
SEC_DECOYPROTEINS enum valuems_mascotresfile_dat
SEC_DECOYSUMMARY enum valuems_mascotresfile_dat
SEC_ENZYME enum valuems_mascotresfile_dat
SEC_ERRTOLDECOYPEPTIDES enum valuems_mascotresfile_dat
SEC_ERRTOLDECOYSUMMARY enum valuems_mascotresfile_dat
SEC_ERRTOLPEPTIDES enum valuems_mascotresfile_dat
SEC_ERRTOLSUMMARY enum valuems_mascotresfile_dat
SEC_HEADER enum valuems_mascotresfile_dat
SEC_INDEX enum valuems_mascotresfile_dat
SEC_LIBRARYPEPTIDES enum valuems_mascotresfile_dat
SEC_LIBRARYSUMMARY enum valuems_mascotresfile_dat
SEC_MASSES enum valuems_mascotresfile_dat
SEC_MIXTURE enum valuems_mascotresfile_dat
SEC_NUMSECTIONS enum valuems_mascotresfile_dat
SEC_PARAMETERS enum valuems_mascotresfile_dat
SEC_PEPTIDES enum valuems_mascotresfile_dat
SEC_PROTEINS enum valuems_mascotresfile_dat
SEC_QUANTITATION enum valuems_mascotresfile_dat
SEC_QUERY1 enum valuems_mascotresfile_dat
SEC_SPECTRAL_LIBRARY enum valuems_mascotresfile_dat
SEC_SUMMARY enum valuems_mascotresfile_dat
SEC_TAXONOMY enum valuems_mascotresfile_dat
SEC_UNIMOD enum valuems_mascotresfile_dat
SEC_UNIMOD_XL enum valuems_mascotresfile_dat
section enum namems_mascotresfile_dat
setErrorInfoFromString(const std::string &e)ms_mascotresfilebaseprotected
setPercolatorFeatures(const char *percolatorFeatures, const char *additionalFeatures, const bool useRetentionTimes)ms_mascotresfilebase
setPercolatorFeatures(const ms_mascotoptions &options, const char *additionalFeatures, const std::vector< std::string > &adapterParameters=std::vector< std::string >())ms_mascotresfilebase
setXMLschemaFilePath(XML_SCHEMA XMLschema, const char *path)ms_mascotresfilebase
staticGetPercolatorFileNames(const char *szFileName, const char *cacheDirectory, const char *percolatorFeatures, const char *additionalFeatures, const bool useRetentionTimes, std::vector< std::string > &filenames, std::vector< bool > &exists)ms_mascotresfilebasestatic
staticGetPercolatorFileNames(const char *szFileName, const char *cacheDirectory, const ms_mascotoptions &options, const char *additionalFeatures, const std::vector< std::string > &adapterParameters, std::vector< std::string > &filenames, std::vector< bool > &exists)ms_mascotresfilebasestatic
versionGreaterOrEqual(int major, int minor, int revision) constms_mascotresfilebase
willCreateCache(const char *szFileName, const unsigned int flags, const char *cacheDirectory, std::string *cacheFileName)ms_mascotresfilebasestatic
willCreateCache(const char *szFileName, const ms_mascotoptions &opts, const char *applicationName, std::string &resfileCacheFileName, unsigned int &cacheStatus)ms_mascotresfilebasestatic
XML_SCHEMA enum namems_mascotresfilebase
XML_SCHEMA_CROSSLINKING enum valuems_mascotresfilebase
XML_SCHEMA_DIRECTORY enum valuems_mascotresfilebase
XML_SCHEMA_LAST enum valuems_mascotresfilebase
XML_SCHEMA_QUANTITATION enum valuems_mascotresfilebase
XML_SCHEMA_UNIMOD enum valuems_mascotresfilebase
~ms_errors()ms_errors