Matrix Science Mascot Parser toolkit
 
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ms_mascotresfilebase Member List

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

anyCrosslinkedMatches(const bool isDecoy=false) const =0ms_mascotresfilebasepure virtual
anyErrorTolerantMatches(const bool isDecoy=false) const =0ms_mascotresfilebasepure virtual
anyFastaMatches(const bool isDecoy=false) const =0ms_mascotresfilebasepure virtual
anyMSMS() const =0ms_mascotresfilebasepure virtual
anyPMF() const =0ms_mascotresfilebasepure virtual
anySpectralLibraryMatches(const bool isDecoy=false) const =0ms_mascotresfilebasepure virtual
anySQ() const =0ms_mascotresfilebasepure virtual
anyTag() const =0ms_mascotresfilebasepure virtual
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)=0ms_mascotresfilebasepure virtual
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
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 =0ms_mascotresfilebasepure virtual
getCacheFileName() const =0ms_mascotresfilebasepure virtual
getCrosslinking(ms_crosslinking_configfile *crosslinkingFile) const =0ms_mascotresfilebaseprotectedpure virtual
getCrosslinkingMethod(ms_crosslinking_method *method) constms_mascotresfilebase
getDatabaseType(const int idx) const =0ms_mascotresfilebasepure virtual
getDate() const =0ms_mascotresfilebasepure virtual
getDecoyTypeForDB(const int idx=1) const =0ms_mascotresfilebasepure virtual
getEnzyme(ms_enzymefile *efile, const char *enzymeFileName=0) const =0ms_mascotresfilebasepure virtual
getErrorHandler() constms_errors
getErrorInfoAsString(const int num) constms_mascotresfilebaseprotected
getErrorNumber(const int num=-1) constms_mascotresfilebase
getErrorString(const int num) constms_mascotresfilebase
getExecTime() const =0ms_mascotresfilebasepure virtual
getFastaPath(int idx=1) const =0ms_mascotresfilebasepure virtual
getFastaVer(int idx=1) const =0ms_mascotresfilebasepure virtual
getFileName(const int id=1) const =0ms_mascotresfilebasepure virtual
getFirstPassThreshold() const =0ms_mascotresfilebasepure virtual
getHeaderKeyValues(std::vector< std::string > &keys, std::vector< std::string > &values) const =0ms_mascotresfilebasepure virtual
getHeaderValue(const std::string &key) const =0ms_mascotresfilebasepure virtual
getInputQuery(const int queryNum) const =0ms_mascotresfilebasepure virtual
getJobNumber(const int resfileID=1) const =0ms_mascotresfilebasepure virtual
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 =0ms_mascotresfilebasepure virtual
getMascotVer() const =0ms_mascotresfilebasepure virtual
getMasses(ms_masses *masses) constms_mascotresfilebase
getMassesKeyValues(std::vector< std::string > &keys, std::vector< double > &values) const =0ms_mascotresfilebasepure virtual
getMassValue(const std::string &key) const =0ms_mascotresfilebasepure virtual
getMonoLinkModification(const int modNum, const int monoLink) constms_mascotresfilebase
getMSParserVersion() constms_mascotresfilebase
getMultiFileQueryNumber(const int localQuery, const int fileId) const =0ms_mascotresfilebasepure virtual
getNumberOfErrors() constms_mascotresfilebase
getNumberOfResfiles() const =0ms_mascotresfilebasepure virtual
getNumEtSeqsSearched(const int idx=0) const =0ms_mascotresfilebasepure virtual
getNumLibraryEntries(const int idx=0) const =0ms_mascotresfilebasepure virtual
getNumQueries(const int resfileID=0) const =0ms_mascotresfilebasepure virtual
getNumResidues(const int idx=0) const =0ms_mascotresfilebasepure virtual
getNumSeqs(const int idx=0) const =0ms_mascotresfilebasepure virtual
getNumSeqsAfterTax(const int idx=0) const =0ms_mascotresfilebasepure virtual
getObservedCharge(const int query, const bool decoy=false) const =0ms_mascotresfilebasepure virtual
getObservedIntensity(const int query) const =0ms_mascotresfilebasepure virtual
getObservedMass(const int query) const =0ms_mascotresfilebasepure virtual
getObservedMrValue(const int query, const bool decoy=false) const =0ms_mascotresfilebasepure virtual
getPercolatorFileNames() constms_mascotresfilebase
getProgressInfo(bool forPeptideSummary=false) constms_mascotresfilebase
getQmatch(const int query, const ms_peptide::PSM_TYPE pepType) const =0ms_mascotresfilebasepure virtual
getQplughole(const int query, const ms_peptide::PSM_TYPE pepType) const =0ms_mascotresfilebasepure virtual
getQuantitation(ms_quant_configfile *qfile) const =0ms_mascotresfilebasepure virtual
getQuantitationMethod(ms_quant_method *qmethod) constms_mascotresfilebase
getReferenceDatabaseNumberOfSL(const int idx) const =0ms_mascotresfilebasepure virtual
getRepeatSearchString(const int query, const bool fullQuery=false) const =0ms_mascotresfilebasepure virtual
getResfile(int id) const =0ms_mascotresfilebasepure virtual
getSearchParameter(const std::string &key) const =0ms_mascotresfilebasepure virtual
getSearchParametersKeyValues(std::vector< std::string > &keys, std::vector< std::string > &values) const =0ms_mascotresfilebasepure virtual
getSLDatabaseNumbersOfReference(const int idx) const =0ms_mascotresfilebasepure virtual
getSLExecCommand(int idx=1) const =0ms_mascotresfilebasepure virtual
getSLFragmentTolerance(int idx=1) const =0ms_mascotresfilebasepure virtual
getSLFragmentToleranceUnit(int idx=1) const =0ms_mascotresfilebasepure virtual
getSrcQueryAndFileIdForMultiFile(const int q, int &gsqNewQuery, int &gsqFileId) const =0ms_mascotresfilebasepure virtual
getTaxonomy(ms_taxonomyfile *tfile) const =0ms_mascotresfilebasepure virtual
getUnimod(ms_umod_configfile *ufile, bool useSchemaFromResfile=false) const =0ms_mascotresfilebasepure virtual
getUnimodXL(ms_umod_configfile *ufile, bool useSchemaFromResfile=false) const =0ms_mascotresfilebasepure virtual
getUniqueTaskID() const =0ms_mascotresfilebasepure virtual
getXMLschemaFilePath(XML_SCHEMA XMLschema) constms_mascotresfilebase
hasEnzyme() const =0ms_mascotresfilebasepure virtual
hasQuantitation() const =0ms_mascotresfilebasepure virtual
hasRT() const =0ms_mascotresfilebasepure virtual
isDatabaseTypeAvailable() const =0ms_mascotresfilebasepure virtual
isErrorTolerant() const =0ms_mascotresfilebasepure virtual
isMSMS() const =0ms_mascotresfilebasepure virtual
isPMF() const =0ms_mascotresfilebasepure virtual
isSQ() const =0ms_mascotresfilebasepure virtual
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_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
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