Matrix Science header

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

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::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::err
- use ms_errs::err instead

Member ms_mascotresfile::getQuantitation (ms_quant_configfile *qfile) const
See getQuantitationMethod() which is generally easier to use.

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_modification::copyMassFile (const ms_masses *massFile)
Do not use.

Member ms_processors::getHyperThreadedCPUsMask () const
Use isPrimaryLogicalProcessor(), getCoreFromLogical() and getPhysicalFromLogical() instead.

Member ms_processors::getWhichAvailableForMascot () const
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_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::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.
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:51