Deprecated List

Member ms_fragmentationrules::getFirstSerie ()

Use getFirstSeries().

Member ms_fragmentationrules::getLastSerie ()

Use getLastSeries().

Member ms_group::GROUPID_INTEGRA_SYSTEM

The Mascot Integra system group, only member is normally USERID_INTEGRA_SYSTEM. Users will never be able to log in as this user - it is only used from the Integra server.

Member ms_http_client_search::sessionId () const

Use getSessionID()

Member ms_license::ms_license (const char *filename)

Warning: This class just reads licenses for Mascot version 2.4.x and earlier

Member ms_license::ms_license ()

Warning: This class just reads licenses for Mascot version 2.4.x and earlier

Member ms_license::read_file ()

Warning: This class just reads licenses for Mascot version 2.4.x and earlier

Member ms_license::setFileName (const char *filename)

Warning: This class just reads licenses for Mascot version 2.4.x and earlier

Member ms_mascotoptions::getMudpit () const

For Mascot 2.2 and later, use getMudpitSwitch() and getSelectSwitch().

Member ms_mascotoptions::isShowSubsets () const

See getShowSubsets().

Member ms_mascotoptions::setShowSubsets (const bool value)

See setShowSubsets(const double).

Member ms_mascotresfile_dat::err

- use ms_errs::err instead

Member ms_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) const

This function is deprecated. All new code should use ms_mascotresfilebase::get_ms_mascotresults_params(const ms_mascotoptions &, ms_mascotresults_params &) instead, as all the parameters are encapsulated in the ms_mascotresults_params class.

Member ms_mascotresfilebase::getQuantitation (ms_quant_configfile *qfile) const =0

See getQuantitationMethod() which is generally easier to use.

Member ms_mascotresfilebase::setPercolatorFeatures (const char *percolatorFeatures, const char *additionalFeatures, const bool useRetentionTimes)

This function is deprecated and has been replaced with matrix_science::ms_mascotresfilebase::setPercolatorFeatures(const ms_mascotoptions&, const char*, const std::vector<std::string>&).

Member 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)

This function is deprecated and has been replaced with matrix_science::ms_mascotresfilebase::staticGetPercolatorFileNames(const char*, const char*, const ms_mascotoptions&, const char *, const std::vector<std::string>&, std::vector<std::string>&, std::vector<bool>&).

Member ms_mascotresults::FC_ALL_PEPTITDES

Unfortunate spelling error, please use FC_ALL_PEPTIDES which has an identical value.

Member ms_mascotresults::findProteinsByAccession (const int startHit, const std::string &str, const int dbIdx, FIND_COMPARE_FLAGS compareFlags, std::vector< std::string > &accessions, std::vector< int > &dbIndexes) const =0

See findProteins() with the ms_mascotresults::FT_PROTEIN_ACCESSION flag.

Member ms_mascotresults::findProteinsByDescription (const int startHit, const std::string &str, FIND_COMPARE_FLAGS compareFlags, std::vector< std::string > &accessions, std::vector< int > &dbIndexes) const =0

See findProteins() with the ms_mascotresults::FT_PROTEIN_DESCRIPTION flag.

Member ms_mascotresults::getProbOfPepBeingRandomMatch (const double score, const int query) const

Use getPeptideExpectationValue().

Member ms_mascotresults::getProbOfProteinBeingRandomMatch (const double score) const

Use getProteinExpectationValue().

Member ms_mascotresults::getQmatch (const int query) const

This method is deprecated in favour of ms_mascotresfilebase::getQmatch

Member ms_mascotresults::getQmatch (const int query, const ms_mascotresfile_dat::section sec) const

This method is deprecated in favour of ms_mascotresfilebase::getQmatch

Member ms_modification::copyMassFile (const ms_masses *massFile)

Do not use.

Member ms_ms1quant_charge_state::getBucket (int index, unsigned &scanId, double &area) const

see getBucket(const int, int, unsigned &, double &)

Member ms_ms1quant_time_align::getFinalResults () const

This function is deprecated and now calls the more accurately named getShiftsToConsensus()

Member ms_ms1quant_time_align::getFinalResults ()

This function is deprecated and now calls the more accurately named getShiftsToConsensus()

Member ms_ms1quantitation::getSummary () const

Use getPeptideSummary() instead.

Member ms_peptidesummary::getSrcRank (int q, int p) const

This method is only useful with files in dat28 format.

Member ms_peptidesummary::getSrcSection (int q, int p) const

This method is only useful with files in dat28 format.

Member ms_processors::getHyperThreadedCPUsMask () const

Use isPrimaryLogicalProcessor(), getCoreFromLogical() and getPhysicalFromLogical() instead.

Member ms_processors::getWhichAvailableForMascot () const

Use getWhichAvailableForMascot2<p> Use isLogicalCPUAvailableForMascot() instead.

Member ms_protein::getSimilarProteinDB () const

Use ms_protein::getSimilarProteins(), ms_mascotresults::getNextSimilarProtein() or ms_mascotresults::getNextSimilarProteinOf() instead.

Member ms_protein::getSimilarProteinName () const

Use ms_protein::getSimilarProteins(), ms_mascotresults::getNextSimilarProtein() or ms_mascotresults::getNextSimilarProteinOf() instead.

Member ms_quant_component::dropFileIndex ()

After version 2.7.2, multiple file indexes are supported per component

Member ms_quant_component::getFileIndex () const

After version 2.7.2, multiple file indexes are supported per component and this just returns the first one.

Member ms_quant_component::haveFileIndex () const

After version 2.7.2, multiple file indexes are supported per component

Member ms_quant_component::setFileIndex (const int file_index)

After version 2.7.2, multiple file indexes are supported per component and this just sets the first one.

Member ms_quant_integration::dropMassDelta ()

Not in use.

Member ms_quant_integration::dropMassDeltaUnit ()

Not in use.

Member ms_quant_integration::dropPrecursorRange ()

Do not use.

Member ms_quant_integration::dropProcessingOptions ()

Do not use.

Member ms_quant_integration::getMassDelta () const

Not in use.

Member ms_quant_integration::getMassDeltaSchemaType () const

Not in use.

Member ms_quant_integration::getMassDeltaUnit () const

Not in use.

Member ms_quant_integration::getMassDeltaUnitSchemaType () const

Not in use.

Member ms_quant_integration::getPrecursorRange () const

Do not use.

Member ms_quant_integration::getPrecursorRangeSchemaType () const

Do not use.

Member ms_quant_integration::getProcessingOptions () const

Do not use.

Member ms_quant_integration::getProcessingOptionsSchemaType () const

Do not use.

Member ms_quant_integration::haveMassDelta () const

Not in use.

Member ms_quant_integration::haveMassDeltaUnit () const

Not in use.

Member ms_quant_integration::havePrecursorRange () const

Do not use.

Member ms_quant_integration::haveProcessingOptions () const

Do not use.

Member ms_quant_integration::setMassDelta (const char *value)

Not in use.

Member ms_quant_integration::setMassDeltaUnit (const char *value)

Not in use.

Member ms_quant_integration::setPrecursorRange (const char *value)

Do not use.

Member ms_quant_integration::setProcessingOptions (const std::string value)

Do not use.

Member ms_quant_multiplex::dropIonSeries ()

Replaced with clearIonSeries().

Member ms_quant_multiplex::setIonSeries (const std::string ionSeries)

Replaced with appendIonSeries().

Member ms_quant_precursor::dropAllChargeStates ()

Moved to ms_quant_integration.

Moved to ms_quant_integration.

Member ms_quant_precursor::dropAllowElutionShift ()

Moved to ms_quant_integration.

Moved to ms_quant_integration.

Member ms_quant_precursor::getAllChargeStatesSchemaType () const

Moved to ms_quant_integration.

Member ms_quant_precursor::getAllowElutionShiftSchemaType () const

Moved to ms_quant_integration.

Member ms_quant_precursor::haveAllChargeStates () const

Moved to ms_quant_integration.

Member ms_quant_precursor::haveAllowElutionShift () const

Moved to ms_quant_integration.

Member ms_quant_precursor::isAllChargeStates () const

Moved to ms_quant_integration.

Member ms_quant_precursor::isAllowElutionShift () const

Moved to ms_quant_integration.

Member ms_security::getIntegraUsers () const

Mascot Integra is not supported in Mascot Parser 2.5 and later.

Member ms_security_options::getIntegraAppServerURL () const

Mascot Integra is not supported in Mascot Parser 2.5 and later.

Member ms_security_options::getIntegraDatabaseName () const

Mascot Integra is not supported in Mascot Parser 2.5 and later.

Member ms_security_options::getIntegraOracleServerName () const

Mascot Integra is not supported in Mascot Parser 2.5 and later.

Member ms_security_options::setIntegraAppServerURL (std::string newVal)

Mascot Integra is not supported in Mascot Parser 2.5 and later.

Member ms_security_options::setIntegraDatabaseName (std::string newVal)

Mascot Integra is not supported in Mascot Parser 2.5 and later.

Member ms_security_options::setIntegraOracleServerName (std::string newVal)

Mascot Integra is not supported in Mascot Parser 2.5 and later.

Member ms_security_tasks::MISECTASK_ACCESS

INSIGHT: Access to Mascot Insight.

Member ms_security_tasks::MISECTASK_ADDCUSTOMREPORT

INSIGHT: Add custom report to Mascot Insight.

Member ms_security_tasks::MISECTASK_ADDEXCLUSIONFILE

INSIGHT: Add BlastCluster exclusion file.

Member ms_security_tasks::MISECTASK_ADDIMPORTFILTER

INSIGHT: Add import assignment filter.

Member ms_security_tasks::MISECTASK_ADMIN

INSIGHT: Mascot Insight administration functions.

Member ms_security_tasks::MISECTASK_DELETECUSTOMREPORT

INSIGHT: Delete custom report Mascot Insight.

Member ms_security_tasks::MISECTASK_DELETEEXCLUSIONFILE

INSIGHT: Delete BlastCluster exclusion file.

Member ms_security_tasks::MISECTASK_PROTEINAPPROVAL

INSIGHT: Protein approval in Mascot Insight.

Member ms_security_tasks::MISECTASK_SENDNOTIFICATION

INSIGHT: Send notification.

Member ms_security_tasks::SECTASK_INTEGRASYSTEMACCOUNT

CLIENT: Integra system account.

Member ms_session::ms_session (const std::string userName, const std::string connectionID, const std::string database)

Mascot Integra is not supported in Mascot Parser 2.5 and later.

Member ms_user::USER_INTEGRA

Mascot Integra is not supported in Mascot Parser 2.5 and later. Login etc. is done through Mascot Insight.

Member ms_user::USERID_INTEGRA_SYSTEM

Mascot Integra is not supported in Mascot Parser 2.5 and later.