Definition at line 107 of file BlockProperty_.hpp.
◆ E_memberIndex [2/11] Enumerator e__allMandatory e_start e_stop e_minstart e_maxstop e_propertyDefinition at line 96 of file CoreBlock_.hpp.
◆ E_memberIndex [3/11] Enumerator e__allMandatory e_nblocks e_blocks e_loops e_isDiscontinuous e_insertionsDefinition at line 97 of file CoreDef_.hpp.
◆ E_memberIndex [4/11] ◆ E_memberIndex [5/11] ◆ E_memberIndex [6/11] Enumerator e__allMandatory e_isProtein e_identifier e_numRows e_numColumns e_rowLabels e_byRow e_query e_intermediateData e_finalDataDefinition at line 118 of file Pssm_.hpp.
◆ E_memberIndex [7/11] Enumerator e__allMandatory e_scores e_lambda e_kappa e_h e_scalingFactor e_lambdaUngapped e_kappaUngapped e_hUngapped e_wordScoreThresholdDefinition at line 143 of file PssmFinalData_.hpp.
◆ E_memberIndex [8/11] Enumerator e__allMandatory e_resFreqsPerPos e_weightedResFreqsPerPos e_freqRatios e_informationContent e_gaplessColumnWeights e_sigma e_intervalSizes e_numMatchingSeqs e_numIndeptObsrDefinition at line 100 of file PssmIntermediateData_.hpp.
◆ E_memberIndex [9/11] Enumerator e__allMandatory e_pseudocount e_rpsdbparams e_constraints e_bitScoreThresh e_bitScoreReportingThresh e_annotatedSitesDefinition at line 97 of file PssmParameters_.hpp.
◆ E_memberIndex [10/11] ◆ E_memberIndex [11/11] Enumerator e__allMandatory e_startPosition e_stopPosition e_description e_type e_aliases e_motif e_motifuseDefinition at line 95 of file Site_annot_.hpp.
◆ EType Enumerator eType_unassigned eType_thresholdscore threshold for heuristics
eType_minscoreobserved minimum score in CD
eType_maxscoreobserved maximum score in CD
eType_meanscoreobserved mean score in CD
eType_varianceobserved score variance
eType_namejust name the block
eType_is_optionalblock may not have to be used
eType_otherDefinition at line 86 of file BlockProperty_.hpp.
◆ CanGet() bool CSite_annot_set_Base::CanGet ( void ) const inlineCheck if it is safe to call Get method.
Definition at line 158 of file Site_annot_set_.hpp.
◆ CanGetAliases() bool CSite_annot_Base::CanGetAliases ( void ) const inlineCheck if it is safe to call GetAliases method.
Definition at line 604 of file Site_annot_.hpp.
◆ CanGetAnnotatedSites() bool CPssmParameters_Base::CanGetAnnotatedSites ( void ) const inline ◆ CanGetBitScoreReportingThresh() bool CPssmParameters_Base::CanGetBitScoreReportingThresh ( void ) const inline ◆ CanGetBitScoreThresh() bool CPssmParameters_Base::CanGetBitScoreThresh ( void ) const inline ◆ CanGetBlocks() bool CCoreDef_Base::CanGetBlocks ( void ) const inlineCheck if it is safe to call GetBlocks method.
Definition at line 363 of file CoreDef_.hpp.
◆ CanGetByRow() bool CPssm_Base::CanGetByRow ( void ) const inlineCheck if it is safe to call GetByRow method.
Definition at line 716 of file Pssm_.hpp.
◆ CanGetConstraints() bool CPssmParameters_Base::CanGetConstraints ( void ) const inline ◆ CanGetDescription() bool CSite_annot_Base::CanGetDescription ( void ) const inline ◆ CanGetFinalData() bool CPssm_Base::CanGetFinalData ( void ) const inlineCheck if it is safe to call GetFinalData method.
Definition at line 808 of file Pssm_.hpp.
References CPssm_Base::IsSetFinalData().
Referenced by CPssm_Base::GetFinalData(), CPssm::GetH(), CPssm::GetHUngapped(), CPssm::GetKappa(), CPssm::GetKappaUngapped(), CPssm::GetLambda(), CPssm::GetLambdaUngapped(), CPsiBl2SeqTestFixture::x_ReadPssmFromFile(), and CPsiBlastTestFixture::x_ReadPssmFromFile().
◆ CanGetFreqRatios() bool CPssmIntermediateData_Base::CanGetFreqRatios ( void ) const inlineCheck if it is safe to call GetFreqRatios method.
Definition at line 511 of file PssmIntermediateData_.hpp.
◆ CanGetGapExtend() bool CFormatRpsDbParameters_Base::CanGetGapExtend ( void ) const inline ◆ CanGetGaplessColumnWeights() bool CPssmIntermediateData_Base::CanGetGaplessColumnWeights ( void ) const inlineCheck if it is safe to call GetGaplessColumnWeights method.
Definition at line 561 of file PssmIntermediateData_.hpp.
◆ CanGetGapOpen() bool CFormatRpsDbParameters_Base::CanGetGapOpen ( void ) const inline ◆ CanGetH() bool CPssmFinalData_Base::CanGetH ( void ) const inline ◆ CanGetHUngapped() bool CPssmFinalData_Base::CanGetHUngapped ( void ) const inline ◆ CanGetIdentifier() bool CPssm_Base::CanGetIdentifier ( void ) const inline ◆ CanGetInformationContent() bool CPssmIntermediateData_Base::CanGetInformationContent ( void ) const inlineCheck if it is safe to call GetInformationContent method.
Definition at line 536 of file PssmIntermediateData_.hpp.
◆ CanGetInsertions() bool CCoreDef_Base::CanGetInsertions ( void ) const inlineCheck if it is safe to call GetInsertions method.
Definition at line 460 of file CoreDef_.hpp.
◆ CanGetIntermediateData() bool CPssm_Base::CanGetIntermediateData ( void ) const inline ◆ CanGetIntervalSizes() bool CPssmIntermediateData_Base::CanGetIntervalSizes ( void ) const inlineCheck if it is safe to call GetIntervalSizes method.
Definition at line 611 of file PssmIntermediateData_.hpp.
◆ CanGetIntvalue() bool CBlockProperty_Base::CanGetIntvalue ( void ) const inline ◆ CanGetIsDiscontinuous() bool CCoreDef_Base::CanGetIsDiscontinuous ( void ) const inline ◆ CanGetIsProtein() bool CPssm_Base::CanGetIsProtein ( void ) const inlineCheck if it is safe to call GetIsProtein method.
Definition at line 526 of file Pssm_.hpp.
◆ CanGetKappa() bool CPssmFinalData_Base::CanGetKappa ( void ) const inline ◆ CanGetKappaUngapped() bool CPssmFinalData_Base::CanGetKappaUngapped ( void ) const inline ◆ CanGetLambda() bool CPssmFinalData_Base::CanGetLambda ( void ) const inline ◆ CanGetLambdaUngapped() bool CPssmFinalData_Base::CanGetLambdaUngapped ( void ) const inline ◆ CanGetLoops() bool CCoreDef_Base::CanGetLoops ( void ) const inlineCheck if it is safe to call GetLoops method.
Definition at line 388 of file CoreDef_.hpp.
◆ CanGetMatrixName() bool CFormatRpsDbParameters_Base::CanGetMatrixName ( void ) const inline ◆ CanGetMaxlength() bool CLoopConstraint_Base::CanGetMaxlength ( void ) const inlineCheck if it is safe to call GetMaxlength method.
Definition at line 258 of file LoopConstraint_.hpp.
◆ CanGetMaxstop() bool CCoreBlock_Base::CanGetMaxstop ( void ) const inline ◆ CanGetMinlength() bool CLoopConstraint_Base::CanGetMinlength ( void ) const inlineCheck if it is safe to call GetMinlength method.
Definition at line 208 of file LoopConstraint_.hpp.
◆ CanGetMinstart() bool CCoreBlock_Base::CanGetMinstart ( void ) const inline ◆ CanGetMotif() bool CSite_annot_Base::CanGetMotif ( void ) const inline ◆ CanGetMotifuse() bool CSite_annot_Base::CanGetMotifuse ( void ) const inline ◆ CanGetNblocks() bool CCoreDef_Base::CanGetNblocks ( void ) const inline ◆ CanGetNumColumns() bool CPssm_Base::CanGetNumColumns ( void ) const inline ◆ CanGetNumIndeptObsr() bool CPssmIntermediateData_Base::CanGetNumIndeptObsr ( void ) const inlineCheck if it is safe to call GetNumIndeptObsr method.
Definition at line 661 of file PssmIntermediateData_.hpp.
◆ CanGetNumMatchingSeqs() bool CPssmIntermediateData_Base::CanGetNumMatchingSeqs ( void ) const inlineCheck if it is safe to call GetNumMatchingSeqs method.
Definition at line 636 of file PssmIntermediateData_.hpp.
◆ CanGetNumRows() bool CPssm_Base::CanGetNumRows ( void ) const inline ◆ CanGetParams() bool CPssmWithParameters_Base::CanGetParams ( void ) const inline ◆ CanGetProperty() bool CCoreBlock_Base::CanGetProperty ( void ) const inlineCheck if it is safe to call GetProperty method.
Definition at line 514 of file CoreBlock_.hpp.
◆ CanGetPseudocount() bool CPssmParameters_Base::CanGetPseudocount ( void ) const inline ◆ CanGetPssm() bool CPssmWithParameters_Base::CanGetPssm ( void ) const inline ◆ CanGetQuery() bool CPssm_Base::CanGetQuery ( void ) const inline ◆ CanGetResFreqsPerPos() bool CPssmIntermediateData_Base::CanGetResFreqsPerPos ( void ) const inlineCheck if it is safe to call GetResFreqsPerPos method.
Definition at line 461 of file PssmIntermediateData_.hpp.
◆ CanGetRowLabels() bool CPssm_Base::CanGetRowLabels ( void ) const inlineCheck if it is safe to call GetRowLabels method.
Definition at line 691 of file Pssm_.hpp.
◆ CanGetRpsdbparams() bool CPssmParameters_Base::CanGetRpsdbparams ( void ) const inline ◆ CanGetScalingFactor() bool CPssmFinalData_Base::CanGetScalingFactor ( void ) const inlineCheck if it is safe to call GetScalingFactor method.
Definition at line 712 of file PssmFinalData_.hpp.
◆ CanGetScores() bool CPssmFinalData_Base::CanGetScores ( void ) const inline ◆ CanGetSigma() bool CPssmIntermediateData_Base::CanGetSigma ( void ) const inlineCheck if it is safe to call GetSigma method.
Definition at line 586 of file PssmIntermediateData_.hpp.
◆ CanGetStart() bool CCoreBlock_Base::CanGetStart ( void ) const inline ◆ CanGetStartPosition() bool CSite_annot_Base::CanGetStartPosition ( void ) const inline ◆ CanGetStop() bool CCoreBlock_Base::CanGetStop ( void ) const inline ◆ CanGetStopPosition() bool CSite_annot_Base::CanGetStopPosition ( void ) const inline ◆ CanGetTextvalue() bool CBlockProperty_Base::CanGetTextvalue ( void ) const inline ◆ CanGetType() [1/2] bool CBlockProperty_Base::CanGetType ( void ) const inline ◆ CanGetType() [2/2] bool CSite_annot_Base::CanGetType ( void ) const inline ◆ CanGetWeightedResFreqsPerPos() bool CPssmIntermediateData_Base::CanGetWeightedResFreqsPerPos ( void ) const inlineCheck if it is safe to call GetWeightedResFreqsPerPos method.
Definition at line 486 of file PssmIntermediateData_.hpp.
◆ CanGetWordScoreThreshold() bool CPssmFinalData_Base::CanGetWordScoreThreshold ( void ) const inline ◆ CBlockProperty() [1/2] ◆ CBlockProperty() [2/2] CBlockProperty::CBlockProperty ( void ) inlineDefinition at line 86 of file BlockProperty.hpp.
◆ CBlockProperty_Base() [1/2] ◆ CBlockProperty_Base() [2/2] ◆ CCoreBlock() [1/2] ◆ CCoreBlock() [2/2] CCoreBlock::CCoreBlock ( void ) inlineDefinition at line 86 of file CoreBlock.hpp.
◆ CCoreBlock_Base() [1/2] ◆ CCoreBlock_Base() [2/2] ◆ CCoreDef() [1/2] ◆ CCoreDef() [2/2] CCoreDef::CCoreDef ( void ) inlineDefinition at line 86 of file CoreDef.hpp.
◆ CCoreDef_Base() [1/2] ◆ CCoreDef_Base() [2/2] ◆ CFormatRpsDbParameters_Base() [1/2] ◆ CFormatRpsDbParameters_Base() [2/2] END_CLASS_INFO CFormatRpsDbParameters_Base::CFormatRpsDbParameters_Base ( void ) ◆ CLoopConstraint() [1/2] ◆ CLoopConstraint() [2/2] ◆ CLoopConstraint_Base() [1/2] ◆ CLoopConstraint_Base() [2/2] ◆ CPssm_Base() [1/2] ◆ CPssm_Base() [2/2] ◆ CPssmFinalData() [1/2] ◆ CPssmFinalData() [2/2] CPssmFinalData::CPssmFinalData ( void ) inlineDefinition at line 86 of file PssmFinalData.hpp.
◆ CPssmFinalData_Base() [1/2] ◆ CPssmFinalData_Base() [2/2] ◆ CPssmIntermediateData() [1/2] ◆ CPssmIntermediateData() [2/2] ◆ CPssmIntermediateData_Base() [1/2] ◆ CPssmIntermediateData_Base() [2/2] END_CLASS_INFO CPssmIntermediateData_Base::CPssmIntermediateData_Base ( void ) ◆ CPssmParameters() [1/2] ◆ CPssmParameters() [2/2] ◆ CPssmParameters_Base() [1/2] ◆ CPssmParameters_Base() [2/2] ◆ CPssmWithParameters_Base() [1/2] ◆ CPssmWithParameters_Base() [2/2] END_CLASS_INFO CPssmWithParameters_Base::CPssmWithParameters_Base ( void ) ◆ CSite_annot() [1/2] ◆ CSite_annot() [2/2] CSite_annot::CSite_annot ( void ) inlineDefinition at line 86 of file Site_annot.hpp.
◆ CSite_annot_Base() [1/2] ◆ CSite_annot_Base() [2/2] ◆ CSite_annot_set() [1/2] ◆ CSite_annot_set() [2/2] ◆ CSite_annot_set_Base() [1/2] ◆ CSite_annot_set_Base() [2/2] ◆ DECLARE_INTERNAL_TYPE_INFO() [1/12] CBlockProperty_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [2/12] CCoreBlock_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [3/12] CCoreDef_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [4/12] CFormatRpsDbParameters_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [5/12] CLoopConstraint_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [6/12] CPssm_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [7/12] CPssmFinalData_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [8/12] CPssmIntermediateData_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [9/12] CPssmParameters_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [10/12] CPssmWithParameters_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [11/12] CSite_annot_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ DECLARE_INTERNAL_TYPE_INFO() [12/12] CSite_annot_set_Base::DECLARE_INTERNAL_TYPE_INFO ( ) ◆ EType()Access to EType's attributes (values, names) as defined in spec.
◆ Get() ◆ GetAliases() ◆ GetAnnotatedSites() ◆ GetBitScoreReportingThresh() ◆ GetBitScoreThresh() ◆ GetBlocks() ◆ GetByRow()Get the ByRow member data.
Definition at line 735 of file Pssm_.hpp.
References CPssm_Base::m_ByRow.
Referenced by ConvertPSSMToBLASTMatrix(), CScorematPssmConverter::GetFreqRatios(), CScorematPssmConverter::GetResidueFrequencies(), CScorematPssmConverter::GetScores(), CScorematPssmConverter::GetWeightedResidueFrequencies(), AlignmentManager::SavePairwiseFromMultiple(), CMakeProfileDBApp::x_CheckDelta(), CPssmEngine::x_PSIMatrix2Asn1(), CMakeProfileDBApp::x_RPSUpdatePSSM(), CMakeProfileDBApp::x_UpdateDelta(), and CMakeProfileDBApp::x_UpdateFreqRatios().
◆ GetConstraints() ◆ GetDescription() ◆ GetFinalData()Get the FinalData member data.
Definition at line 814 of file Pssm_.hpp.
References CPssm_Base::CanGetFinalData(), CPssm_Base::m_FinalData, and CSerialObject::ThrowUnassigned().
Referenced by BOOST_AUTO_TEST_CASE(), ConvertPSSMToBLASTMatrix(), CPsiBl2SeqTestFixture::CPsiBl2SeqTestFixture(), CPsiBlastTestFixture::CPsiBlastTestFixture(), CPssm::GetH(), CPssm::GetHUngapped(), CPssm::GetKappa(), CPssm::GetKappaUngapped(), CPssm::GetLambda(), CPssm::GetLambdaUngapped(), CScorematPssmConverter::GetScores(), PsiBlastComputePssmScores(), AlignmentManager::SavePairwiseFromMultiple(), CMakeProfileDBApp::x_MakeVol(), CMakeProfileDBApp::x_RPSAddFirstSequence(), CMakeProfileDBApp::x_RPSUpdatePSSM(), and CMakeProfileDBApp::x_RPSUpdateStatistics().
◆ GetFreqRatios() ◆ GetGapExtend() ◆ GetGaplessColumnWeights() ◆ GetGapOpen() ◆ GetH() ◆ GetHUngapped() ◆ GetIdentifier() ◆ GetInformationContent() ◆ GetInsertions() ◆ GetIntermediateData()Get the IntermediateData member data.
Definition at line 793 of file Pssm_.hpp.
References CPssm_Base::CanGetIntermediateData(), CPssm_Base::m_IntermediateData, and CSerialObject::ThrowUnassigned().
Referenced by BOOST_AUTO_TEST_CASE(), CScorematPssmConverter::GetFreqRatios(), CScorematPssmConverter::GetGaplessColumnWeights(), CScorematPssmConverter::GetInformationContent(), CScorematPssmConverter::GetIntervalSizes(), CScorematPssmConverter::GetNumMatchingSeqs(), CScorematPssmConverter::GetResidueFrequencies(), CScorematPssmConverter::GetSigma(), CScorematPssmConverter::GetWeightedResidueFrequencies(), CMakeProfileDBApp::x_CheckDelta(), CMakeProfileDBApp::x_CheckInputScoremat(), CMakeProfileDBApp::x_CreateDeltaList(), CMakeProfileDBApp::x_UpdateDelta(), and CMakeProfileDBApp::x_UpdateFreqRatios().
◆ GetIntervalSizes() ◆ GetIntvalue() ◆ GetIsDiscontinuous() ◆ GetIsProtein() ◆ GetKappa() ◆ GetKappaUngapped() ◆ GetLambda() ◆ GetLambdaUngapped() ◆ GetLoops() ◆ GetMatrixName() ◆ GetMaxlength() ◆ GetMaxstop() ◆ GetMinlength() ◆ GetMinstart() ◆ GetMotif() ◆ GetMotifuse() ◆ GetNblocks() ◆ GetNumColumns() ◆ GetNumIndeptObsr() ◆ GetNumMatchingSeqs() ◆ GetNumRows()Get the NumRows member data.
Definition at line 610 of file Pssm_.hpp.
References CPssm_Base::CanGetNumRows(), CPssm_Base::m_NumRows, and CSerialObject::ThrowUnassigned().
Referenced by BOOST_AUTO_TEST_CASE(), ConvertPSSMToBLASTMatrix(), CScorematPssmConverter::GetFreqRatios(), CScorematPssmConverter::GetResidueFrequencies(), CScorematPssmConverter::GetScores(), CScorematPssmConverter::GetWeightedResidueFrequencies(), PsiBlastComputePssmScores(), AlignmentManager::SavePairwiseFromMultiple(), CMakeProfileDBApp::x_CheckDelta(), CMakeProfileDBApp::x_CheckInputScoremat(), CMakeProfileDBApp::x_RPSUpdatePSSM(), CMakeProfileDBApp::x_UpdateDelta(), and CMakeProfileDBApp::x_UpdateFreqRatios().
◆ GetParams() ◆ GetProperty() ◆ GetPseudocount() ◆ GetPssm()Get the Pssm member data.
Definition at line 229 of file PssmWithParameters_.hpp.
References CPssmWithParameters_Base::m_Pssm, and CPssmWithParameters_Base::ResetPssm().
Referenced by BOOST_AUTO_TEST_CASE(), ConvertPSSMToBLASTMatrix(), CPsiBl2SeqTestFixture::CPsiBl2SeqTestFixture(), CPsiBlastTestFixture::CPsiBlastTestFixture(), ExtractPssmAncillaryData(), CPssmWithParameters::GetQuery(), CPssmWithParameters::HasQuery(), PsiBlastComputePssmScores(), s_AddSeqDataToPssm(), AlignmentManager::SavePairwiseFromMultiple(), PssmScorer::score(), CMakeProfileDBApp::x_CheckInputScoremat(), CMakeProfileDBApp::x_CreateDeltaList(), CMakeProfileDBApp::x_MakeVol(), CPsiBl2SeqTestFixture::x_ReadPssmFromFile(), CPsiBlastTestFixture::x_ReadPssmFromFile(), CDeltaBlastTestFixture::x_ReadSeqEntriesFromFile(), CPsiBl2SeqTestFixture::x_ReadSeqEntriesFromFile(), CPsiBlastTestFixture::x_ReadSeqEntriesFromFile(), CMakeProfileDBApp::x_RPSAddFirstSequence(), CMakeProfileDBApp::x_RPSUpdateStatistics(), CMakeProfileDBApp::x_UpdateCobalt(), CMakeProfileDBApp::x_UpdateDelta(), and CMakeProfileDBApp::x_UpdateFreqRatios().
◆ GetQuery() ◆ GetResFreqsPerPos() ◆ GetRowLabels() ◆ GetRpsdbparams() ◆ GetScalingFactor() ◆ GetScores() ◆ GetSigma() ◆ GetStart() ◆ GetStartPosition() ◆ GetStop() ◆ GetStopPosition() ◆ GetTextvalue() ◆ GetType() [1/2] ◆ GetType() [2/2] ◆ GetWeightedResFreqsPerPos() ◆ GetWordScoreThreshold() ◆ IsSet() bool CSite_annot_set_Base::IsSet ( void ) const inlineCheck if a value has been assigned to data member.
Data member is mandatory; its type is defined as 'typedef list< CRef< CSite_annot > > Tdata'
Definition at line 152 of file Site_annot_set_.hpp.
References CSite_annot_set_Base::m_set_State.
◆ IsSetAliases() bool CSite_annot_Base::IsSetAliases ( void ) const inlineadditional names for the annotation Check if a value has been assigned to Aliases data member.
Data member Aliases is optional; its type is defined as 'typedef list< string > TAliases'
Definition at line 598 of file Site_annot_.hpp.
References CSite_annot_Base::m_set_State.
◆ IsSetAnnotatedSites() bool CPssmParameters_Base::IsSetAnnotatedSites ( void ) const inline ◆ IsSetBitScoreReportingThresh() bool CPssmParameters_Base::IsSetBitScoreReportingThresh ( void ) const inline ◆ IsSetBitScoreThresh() bool CPssmParameters_Base::IsSetBitScoreThresh ( void ) const inline ◆ IsSetBlocks() bool CCoreDef_Base::IsSetBlocks ( void ) const inline ◆ IsSetByRow() bool CPssm_Base::IsSetByRow ( void ) const inlineare matrices stored row by row? Check if a value has been assigned to ByRow data member.
Data member ByRow is optional with default false; its type is defined as 'typedef bool TByRow'
Definition at line 710 of file Pssm_.hpp.
References CPssm_Base::m_set_State.
Referenced by CPssm_Base::SetByRow().
◆ IsSetConstraints() bool CPssmParameters_Base::IsSetConstraints ( void ) const inline ◆ IsSetDescription() bool CSite_annot_Base::IsSetDescription ( void ) const inline ◆ IsSetFinalData() bool CPssm_Base::IsSetFinalData ( void ) const inline ◆ IsSetFreqRatios() bool CPssmIntermediateData_Base::IsSetFreqRatios ( void ) const inline ◆ IsSetGapExtend() bool CFormatRpsDbParameters_Base::IsSetGapExtend ( void ) const inline ◆ IsSetGaplessColumnWeights() bool CPssmIntermediateData_Base::IsSetGaplessColumnWeights ( void ) const inlineRelative weight for columns of the PSSM without gaps to pseudocounts NOTE: this is needed for diagnostics information only (i.e.
: -out_ascii_pssm option in psiblast) Check if a value has been assigned to GaplessColumnWeights data member.
Data member GaplessColumnWeights is optional; its type is defined as 'typedef list< double > TGaplessColumnWeights'
Definition at line 555 of file PssmIntermediateData_.hpp.
References CPssmIntermediateData_Base::m_set_State.
◆ IsSetGapOpen() bool CFormatRpsDbParameters_Base::IsSetGapOpen ( void ) const inline ◆ IsSetH() bool CPssmFinalData_Base::IsSetH ( void ) const inline ◆ IsSetHUngapped() bool CPssmFinalData_Base::IsSetHUngapped ( void ) const inline ◆ IsSetIdentifier() bool CPssm_Base::IsSetIdentifier ( void ) const inline ◆ IsSetInformationContent() bool CPssmIntermediateData_Base::IsSetInformationContent ( void ) const inlineInformation content per position of the PSSM NOTE: this is needed for diagnostics information only (i.e.
: -out_ascii_pssm option in psiblast) Check if a value has been assigned to InformationContent data member.
Data member InformationContent is optional; its type is defined as 'typedef list< double > TInformationContent'
Definition at line 530 of file PssmIntermediateData_.hpp.
References CPssmIntermediateData_Base::m_set_State.
◆ IsSetInsertions() bool CCoreDef_Base::IsSetInsertions ( void ) const inlinepositions of long insertions Check if a value has been assigned to Insertions data member.
Data member Insertions is optional; its type is defined as 'typedef list< int > TInsertions'
Definition at line 454 of file CoreDef_.hpp.
References CCoreDef_Base::m_set_State.
◆ IsSetIntermediateData() bool CPssm_Base::IsSetIntermediateData ( void ) const inline ◆ IsSetIntervalSizes() bool CPssmIntermediateData_Base::IsSetIntervalSizes ( void ) const inlineLength of the aligned regions per position of the query sequence NOTE: this is needed for diagnostics information only (i.e.
: -out_ascii_pssm option in psiblast) Check if a value has been assigned to IntervalSizes data member.
Data member IntervalSizes is optional; its type is defined as 'typedef list< int > TIntervalSizes'
Definition at line 605 of file PssmIntermediateData_.hpp.
References CPssmIntermediateData_Base::m_set_State.
◆ IsSetIntvalue() bool CBlockProperty_Base::IsSetIntvalue ( void ) const inline ◆ IsSetIsDiscontinuous() bool CCoreDef_Base::IsSetIsDiscontinuous ( void ) const inline ◆ IsSetIsProtein() bool CPssm_Base::IsSetIsProtein ( void ) const inlineIs the this a protein or nucleotide scoring matrix? Check if a value has been assigned to IsProtein data member.
Data member IsProtein is optional with default true; its type is defined as 'typedef bool TIsProtein'
Definition at line 520 of file Pssm_.hpp.
References CPssm_Base::m_set_State.
Referenced by CPssm_Base::SetIsProtein().
◆ IsSetKappa() bool CPssmFinalData_Base::IsSetKappa ( void ) const inline ◆ IsSetKappaUngapped() bool CPssmFinalData_Base::IsSetKappaUngapped ( void ) const inline ◆ IsSetLambda() bool CPssmFinalData_Base::IsSetLambda ( void ) const inline ◆ IsSetLambdaUngapped() bool CPssmFinalData_Base::IsSetLambdaUngapped ( void ) const inline ◆ IsSetLoops() bool CCoreDef_Base::IsSetLoops ( void ) const inline(nblocks+1) constraints Check if a value has been assigned to Loops data member.
Data member Loops is mandatory; its type is defined as 'typedef list< CRef< CLoopConstraint > > TLoops'
Definition at line 382 of file CoreDef_.hpp.
References CCoreDef_Base::m_set_State.
◆ IsSetMatrixName() bool CFormatRpsDbParameters_Base::IsSetMatrixName ( void ) const inline ◆ IsSetMaxlength() bool CLoopConstraint_Base::IsSetMaxlength ( void ) const inline ◆ IsSetMaxstop() bool CCoreBlock_Base::IsSetMaxstop ( void ) const inline ◆ IsSetMinlength() bool CLoopConstraint_Base::IsSetMinlength ( void ) const inline ◆ IsSetMinstart() bool CCoreBlock_Base::IsSetMinstart ( void ) const inline ◆ IsSetMotif() bool CSite_annot_Base::IsSetMotif ( void ) const inline ◆ IsSetMotifuse() bool CSite_annot_Base::IsSetMotifuse ( void ) const inline ◆ IsSetNblocks() bool CCoreDef_Base::IsSetNblocks ( void ) const inline ◆ IsSetNumColumns() bool CPssm_Base::IsSetNumColumns ( void ) const inline ◆ IsSetNumIndeptObsr() bool CPssmIntermediateData_Base::IsSetNumIndeptObsr ( void ) const inline ◆ IsSetNumMatchingSeqs() bool CPssmIntermediateData_Base::IsSetNumMatchingSeqs ( void ) const inlineNumber of matching sequences per position of the PSSM (including the query) NOTE: this is needed for diagnostics information only (i.e.
: -out_ascii_pssm option in psiblast) Check if a value has been assigned to NumMatchingSeqs data member.
Data member NumMatchingSeqs is optional; its type is defined as 'typedef list< int > TNumMatchingSeqs'
Definition at line 630 of file PssmIntermediateData_.hpp.
References CPssmIntermediateData_Base::m_set_State.
◆ IsSetNumRows() bool CPssm_Base::IsSetNumRows ( void ) const inline ◆ IsSetParams() bool CPssmWithParameters_Base::IsSetParams ( void ) const inline ◆ IsSetProperty() bool CCoreBlock_Base::IsSetProperty ( void ) const inlineCheck if a value has been assigned to Property data member.
Data member Property is optional; its type is defined as 'typedef list< CRef< CBlockProperty > > TProperty'
Definition at line 508 of file CoreBlock_.hpp.
References CCoreBlock_Base::m_set_State.
◆ IsSetPseudocount() bool CPssmParameters_Base::IsSetPseudocount ( void ) const inline ◆ IsSetPssm() bool CPssmWithParameters_Base::IsSetPssm ( void ) const inlineThis field is applicable to PSI-BLAST and formatrpsdb.
When both the intermediate and final PSSM data are provided in this field, the final data (matrix of scores and associated statistical parameters) takes precedence and that data is used for further processing. The rationale for this is that the PSSM's scores and statistical parameters might have been calculated by other applications and it might not be possible to recreate it by using PSI-BLAST's PSSM engine. Check if a value has been assigned to Pssm data member.
Data member Pssm is mandatory; its type is defined as 'typedef CPssm TPssm'
Definition at line 217 of file PssmWithParameters_.hpp.
References CPssmWithParameters_Base::m_Pssm.
Referenced by CMakeProfileDBApp::x_CheckInputScoremat().
◆ IsSetQuery() bool CPssm_Base::IsSetQuery ( void ) const inline ◆ IsSetResFreqsPerPos() bool CPssmIntermediateData_Base::IsSetResFreqsPerPos ( void ) const inlineobserved residue frequencies (or counts) per position of the PSSM (prior to application of pseudocounts) Check if a value has been assigned to ResFreqsPerPos data member.
Data member ResFreqsPerPos is optional; its type is defined as 'typedef list< int > TResFreqsPerPos'
Definition at line 455 of file PssmIntermediateData_.hpp.
References CPssmIntermediateData_Base::m_set_State.
◆ IsSetRowLabels() bool CPssm_Base::IsSetRowLabels ( void ) const inlinerow-labels is given to note the order of residue types so that it can be cross-checked between applications.
If this field is not given, the matrix values are presented in order of the alphabet ncbistdaa is used for protein, ncbi4na for nucl. for proteins the values returned correspond to (-,-), (-,A), (-,B), (-,C) ... (A,-), (A,A), (A,B), (A,C) ... Check if a value has been assigned to RowLabels data member.
Data member RowLabels is optional; its type is defined as 'typedef list< string > TRowLabels'
Definition at line 685 of file Pssm_.hpp.
References CPssm_Base::m_set_State.
◆ IsSetRpsdbparams() bool CPssmParameters_Base::IsSetRpsdbparams ( void ) const inline ◆ IsSetScalingFactor() bool CPssmFinalData_Base::IsSetScalingFactor ( void ) const inlinescaling factor used to obtain more precision when building the PSSM.
(i.e.: scores are scaled by this value). By default, PSI-BLAST's PSSM engine generates PSSMs which are not scaled-up, however, if PSI-BLAST is given a PSSM which contains a scaled-up PSSM (indicated by having a scalingFactor greater than 1), then it will scale down the PSSM to perform the initial stages of the search with it. N.B.: When building RPS-BLAST databases, if formatrpsdb is provided scaled-up PSSMs, it will ensure that all PSSMs used to build the RPS-BLAST database are scaled by the same factor (otherwise, RPS-BLAST will silently produce incorrect results). Check if a value has been assigned to ScalingFactor data member.
Data member ScalingFactor is optional with default 1; its type is defined as 'typedef int TScalingFactor'
Definition at line 706 of file PssmFinalData_.hpp.
References CPssmFinalData_Base::m_set_State.
Referenced by CPssmFinalData_Base::SetScalingFactor(), CMakeProfileDBApp::x_MakeVol(), and CMakeProfileDBApp::x_RPSAddFirstSequence().
◆ IsSetScores() bool CPssmFinalData_Base::IsSetScores ( void ) const inlinePSSM's scores Check if a value has been assigned to Scores data member.
Data member Scores is mandatory; its type is defined as 'typedef list< int > TScores'
Definition at line 540 of file PssmFinalData_.hpp.
References CPssmFinalData_Base::m_set_State.
◆ IsSetSigma() bool CPssmIntermediateData_Base::IsSetSigma ( void ) const inlineUsed in sequence weights computation NOTE: this is needed for diagnostics information only (i.e.
: -out_ascii_pssm option in psiblast) Check if a value has been assigned to Sigma data member.
Data member Sigma is optional; its type is defined as 'typedef list< double > TSigma'
Definition at line 580 of file PssmIntermediateData_.hpp.
References CPssmIntermediateData_Base::m_set_State.
◆ IsSetStart() bool CCoreBlock_Base::IsSetStart ( void ) const inline ◆ IsSetStartPosition() bool CSite_annot_Base::IsSetStartPosition ( void ) const inline ◆ IsSetStop() bool CCoreBlock_Base::IsSetStop ( void ) const inline ◆ IsSetStopPosition() bool CSite_annot_Base::IsSetStopPosition ( void ) const inline ◆ IsSetTextvalue() bool CBlockProperty_Base::IsSetTextvalue ( void ) const inline ◆ IsSetType() [1/2] bool CBlockProperty_Base::IsSetType ( void ) const inline ◆ IsSetType() [2/2] bool CSite_annot_Base::IsSetType ( void ) const inline ◆ IsSetWeightedResFreqsPerPos() bool CPssmIntermediateData_Base::IsSetWeightedResFreqsPerPos ( void ) const inlineWeighted observed residue frequencies per position of the PSSM.
(N.B.: each position's weights should add up to 1.0). This field corresponds to f_i (f sub i) in equation 2 of Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005. NOTE: this is needed for diagnostics information only (i.e.: -out_ascii_pssm option in psiblast) Check if a value has been assigned to WeightedResFreqsPerPos data member.
Data member WeightedResFreqsPerPos is optional; its type is defined as 'typedef list< double > TWeightedResFreqsPerPos'
Definition at line 480 of file PssmIntermediateData_.hpp.
References CPssmIntermediateData_Base::m_set_State.
Referenced by BOOST_AUTO_TEST_CASE(), and CMakeProfileDBApp::x_CreateDeltaList().
◆ IsSetWordScoreThreshold() bool CPssmFinalData_Base::IsSetWordScoreThreshold ( void ) const inline ◆ operator const Tdata &() ◆ operator Tdata &() ◆ operator=() [1/21] ◆ operator=() [2/21] ◆ operator=() [3/21] ◆ operator=() [4/21] ◆ operator=() [5/21] ◆ operator=() [6/21] ◆ operator=() [7/21] ◆ operator=() [8/21] ◆ operator=() [9/21] ◆ operator=() [10/21] ◆ operator=() [11/21] ◆ operator=() [12/21] ◆ operator=() [13/21] ◆ operator=() [14/21] ◆ operator=() [15/21] ◆ operator=() [16/21] ◆ operator=() [17/21] ◆ operator=() [18/21] ◆ operator=() [19/21] ◆ operator=() [20/21] ◆ operator=() [21/21] ◆ Reset() [1/12] void CBlockProperty_Base::Reset ( void ) virtual ◆ Reset() [2/12] void CCoreBlock_Base::Reset ( void ) virtual ◆ Reset() [3/12] void CCoreDef_Base::Reset ( void ) virtual ◆ Reset() [4/12] void CFormatRpsDbParameters_Base::Reset ( void ) virtual ◆ Reset() [5/12] void CLoopConstraint_Base::Reset ( void ) virtual ◆ Reset() [6/12] void CPssm_Base::Reset ( void ) virtual ◆ Reset() [7/12] void CPssmFinalData_Base::Reset ( void ) virtual ◆ Reset() [8/12] void CPssmIntermediateData_Base::Reset ( void ) virtual ◆ Reset() [9/12] void CPssmParameters_Base::Reset ( void ) virtual ◆ Reset() [10/12] void CPssmWithParameters_Base::Reset ( void ) virtual ◆ Reset() [11/12] void CSite_annot_Base::Reset ( void ) virtual ◆ Reset() [12/12] void CSite_annot_set_Base::Reset ( void ) ◆ ResetAliases() void CSite_annot_Base::ResetAliases ( void ) ◆ ResetAnnotatedSites() void CPssmParameters_Base::ResetAnnotatedSites ( void ) ◆ ResetBitScoreReportingThresh() void CPssmParameters_Base::ResetBitScoreReportingThresh ( void ) inline ◆ ResetBitScoreThresh() void CPssmParameters_Base::ResetBitScoreThresh ( void ) inline ◆ ResetBlocks() void CCoreDef_Base::ResetBlocks ( void ) ◆ ResetByRow() void CPssm_Base::ResetByRow ( void ) inline ◆ ResetConstraints() void CPssmParameters_Base::ResetConstraints ( void ) ◆ ResetDescription() void CSite_annot_Base::ResetDescription ( void ) ◆ ResetFinalData() void CPssm_Base::ResetFinalData ( void ) ◆ ResetFreqRatios() void CPssmIntermediateData_Base::ResetFreqRatios ( void ) ◆ ResetGapExtend() void CFormatRpsDbParameters_Base::ResetGapExtend ( void ) inline ◆ ResetGaplessColumnWeights() void CPssmIntermediateData_Base::ResetGaplessColumnWeights ( void ) ◆ ResetGapOpen() void CFormatRpsDbParameters_Base::ResetGapOpen ( void ) inline ◆ ResetH() void CPssmFinalData_Base::ResetH ( void ) inline ◆ ResetHUngapped() void CPssmFinalData_Base::ResetHUngapped ( void ) inline ◆ ResetIdentifier() void CPssm_Base::ResetIdentifier ( void ) ◆ ResetInformationContent() void CPssmIntermediateData_Base::ResetInformationContent ( void ) ◆ ResetInsertions() void CCoreDef_Base::ResetInsertions ( void ) ◆ ResetIntermediateData() void CPssm_Base::ResetIntermediateData ( void ) ◆ ResetIntervalSizes() void CPssmIntermediateData_Base::ResetIntervalSizes ( void ) ◆ ResetIntvalue() void CBlockProperty_Base::ResetIntvalue ( void ) inline ◆ ResetIsDiscontinuous() void CCoreDef_Base::ResetIsDiscontinuous ( void ) inline ◆ ResetIsProtein() void CPssm_Base::ResetIsProtein ( void ) inline ◆ ResetKappa() void CPssmFinalData_Base::ResetKappa ( void ) inline ◆ ResetKappaUngapped() void CPssmFinalData_Base::ResetKappaUngapped ( void ) inline ◆ ResetLambda() void CPssmFinalData_Base::ResetLambda ( void ) inline ◆ ResetLambdaUngapped() void CPssmFinalData_Base::ResetLambdaUngapped ( void ) inline ◆ ResetLoops() void CCoreDef_Base::ResetLoops ( void ) ◆ ResetMatrixName() void CFormatRpsDbParameters_Base::ResetMatrixName ( void ) ◆ ResetMaxlength() void CLoopConstraint_Base::ResetMaxlength ( void ) inline ◆ ResetMaxstop() void CCoreBlock_Base::ResetMaxstop ( void ) inline ◆ ResetMinlength() void CLoopConstraint_Base::ResetMinlength ( void ) inline ◆ ResetMinstart() void CCoreBlock_Base::ResetMinstart ( void ) inline ◆ ResetMotif() void CSite_annot_Base::ResetMotif ( void ) ◆ ResetMotifuse() void CSite_annot_Base::ResetMotifuse ( void ) inline ◆ ResetNblocks() void CCoreDef_Base::ResetNblocks ( void ) inline ◆ ResetNumColumns() void CPssm_Base::ResetNumColumns ( void ) inline ◆ ResetNumIndeptObsr() void CPssmIntermediateData_Base::ResetNumIndeptObsr ( void ) ◆ ResetNumMatchingSeqs() void CPssmIntermediateData_Base::ResetNumMatchingSeqs ( void ) ◆ ResetNumRows() void CPssm_Base::ResetNumRows ( void ) inline ◆ ResetParams() void CPssmWithParameters_Base::ResetParams ( void ) ◆ ResetProperty() void CCoreBlock_Base::ResetProperty ( void ) ◆ ResetPseudocount() void CPssmParameters_Base::ResetPseudocount ( void ) inline ◆ ResetPssm() void CPssmWithParameters_Base::ResetPssm ( void ) ◆ ResetQuery() void CPssm_Base::ResetQuery ( void ) ◆ ResetResFreqsPerPos() void CPssmIntermediateData_Base::ResetResFreqsPerPos ( void ) ◆ ResetRowLabels() void CPssm_Base::ResetRowLabels ( void ) ◆ ResetRpsdbparams() void CPssmParameters_Base::ResetRpsdbparams ( void ) ◆ ResetScalingFactor() void CPssmFinalData_Base::ResetScalingFactor ( void ) inline ◆ ResetScores() void CPssmFinalData_Base::ResetScores ( void ) ◆ ResetSigma() void CPssmIntermediateData_Base::ResetSigma ( void ) ◆ ResetStart() void CCoreBlock_Base::ResetStart ( void ) inline ◆ ResetStartPosition() void CSite_annot_Base::ResetStartPosition ( void ) inline ◆ ResetStop() void CCoreBlock_Base::ResetStop ( void ) inline ◆ ResetStopPosition() void CSite_annot_Base::ResetStopPosition ( void ) inline ◆ ResetTextvalue() ◆ ResetType() [1/2] void CBlockProperty_Base::ResetType ( void ) inline ◆ ResetType() [2/2] void CSite_annot_Base::ResetType ( void ) inline ◆ ResetWeightedResFreqsPerPos() void CPssmIntermediateData_Base::ResetWeightedResFreqsPerPos ( void ) ◆ ResetWordScoreThreshold() void CPssmFinalData_Base::ResetWordScoreThreshold ( void ) inline ◆ Set() ◆ SetAliases() ◆ SetAnnotatedSites() [1/2] ◆ SetAnnotatedSites() [2/2] ◆ SetBitScoreReportingThresh() [1/2] ◆ SetBitScoreReportingThresh() [2/2] ◆ SetBitScoreThresh() [1/2] ◆ SetBitScoreThresh() [2/2] ◆ SetBlocks() ◆ SetByRow() [1/2] ◆ SetByRow() [2/2] ◆ SetConstraints() [1/2] ◆ SetConstraints() [2/2] ◆ SetDefaultByRow() void CPssm_Base::SetDefaultByRow ( void ) inline ◆ SetDefaultIsProtein() void CPssm_Base::SetDefaultIsProtein ( void ) inline ◆ SetDefaultMaxlength() void CLoopConstraint_Base::SetDefaultMaxlength ( void ) inline ◆ SetDefaultMinlength() void CLoopConstraint_Base::SetDefaultMinlength ( void ) inline ◆ SetDefaultScalingFactor() void CPssmFinalData_Base::SetDefaultScalingFactor ( void ) inline ◆ SetDescription() [1/3] ◆ SetDescription() [2/3] ◆ SetDescription() [3/3] ◆ SetFinalData() [1/2] ◆ SetFinalData() [2/2] ◆ SetFreqRatios() ◆ SetGapExtend() [1/2] ◆ SetGapExtend() [2/2] ◆ SetGaplessColumnWeights() ◆ SetGapOpen() [1/2] ◆ SetGapOpen() [2/2] ◆ SetH() [1/2] ◆ SetH() [2/2] ◆ SetHUngapped() [1/2] ◆ SetHUngapped() [2/2] ◆ SetIdentifier() [1/2] ◆ SetIdentifier() [2/2] ◆ SetInformationContent() ◆ SetInsertions() ◆ SetIntermediateData() [1/2] ◆ SetIntermediateData() [2/2] ◆ SetIntervalSizes() ◆ SetIntvalue() [1/2] ◆ SetIntvalue() [2/2] ◆ SetIsDiscontinuous() [1/2] ◆ SetIsDiscontinuous() [2/2] ◆ SetIsProtein() [1/2] ◆ SetIsProtein() [2/2] ◆ SetKappa() [1/2] ◆ SetKappa() [2/2] ◆ SetKappaUngapped() [1/2] ◆ SetKappaUngapped() [2/2] ◆ SetLambda() [1/2] ◆ SetLambda() [2/2] ◆ SetLambdaUngapped() [1/2] ◆ SetLambdaUngapped() [2/2] ◆ SetLoops() ◆ SetMatrixName() [1/3] ◆ SetMatrixName() [2/3] ◆ SetMatrixName() [3/3] ◆ SetMaxlength() [1/2] ◆ SetMaxlength() [2/2] ◆ SetMaxstop() [1/2] ◆ SetMaxstop() [2/2] ◆ SetMinlength() [1/2] ◆ SetMinlength() [2/2] ◆ SetMinstart() [1/2] ◆ SetMinstart() [2/2] ◆ SetMotif() [1/3] void CSite_annot_Base::SetMotif ( const TMotif & value ) inline ◆ SetMotif() [2/3] ◆ SetMotif() [3/3] ◆ SetMotifuse() [1/2] ◆ SetMotifuse() [2/2] ◆ SetNblocks() [1/2] ◆ SetNblocks() [2/2] ◆ SetNumColumns() [1/2] ◆ SetNumColumns() [2/2] ◆ SetNumIndeptObsr() ◆ SetNumMatchingSeqs() ◆ SetNumRows() [1/2] ◆ SetNumRows() [2/2] ◆ SetParams() [1/2] ◆ SetParams() [2/2] ◆ SetProperty() ◆ SetPseudocount() [1/2] ◆ SetPseudocount() [2/2] ◆ SetPssm() [1/2] ◆ SetPssm() [2/2] ◆ SetQuery() [1/2] ◆ SetQuery() [2/2] ◆ SetResFreqsPerPos() ◆ SetRowLabels() ◆ SetRpsdbparams() [1/2] ◆ SetRpsdbparams() [2/2] ◆ SetScalingFactor() [1/2] ◆ SetScalingFactor() [2/2] ◆ SetScores() ◆ SetSigma() ◆ SetStart() [1/2] ◆ SetStart() [2/2] ◆ SetStartPosition() [1/2] ◆ SetStartPosition() [2/2] ◆ SetStop() [1/2] ◆ SetStop() [2/2] ◆ SetStopPosition() [1/2] ◆ SetStopPosition() [2/2] ◆ SetTextvalue() [1/3] ◆ SetTextvalue() [2/3] ◆ SetTextvalue() [3/3] ◆ SetType() [1/4] ◆ SetType() [2/4] ◆ SetType() [3/4] ◆ SetType() [4/4] ◆ SetWeightedResFreqsPerPos() ◆ SetWordScoreThreshold() [1/2] ◆ SetWordScoreThreshold() [2/2] ◆ ~CBlockProperty() ◆ ~CBlockProperty_Base() CBlockProperty_Base::~CBlockProperty_Base ( void ) virtualDefinition at line 99 of file BlockProperty_.cpp.
◆ ~CCoreBlock() CCoreBlock::~CCoreBlock ( void )Definition at line 50 of file CoreBlock.cpp.
◆ ~CCoreBlock_Base() CCoreBlock_Base::~CCoreBlock_Base ( void ) virtualDefinition at line 88 of file CoreBlock_.cpp.
◆ ~CCoreDef() CCoreDef::~CCoreDef ( void )Definition at line 50 of file CoreDef.cpp.
◆ ~CCoreDef_Base() CCoreDef_Base::~CCoreDef_Base ( void ) virtualDefinition at line 101 of file CoreDef_.cpp.
◆ ~CFormatRpsDbParameters_Base() ◆ ~CLoopConstraint() ◆ ~CLoopConstraint_Base() CLoopConstraint_Base::~CLoopConstraint_Base ( void ) virtualDefinition at line 75 of file LoopConstraint_.cpp.
◆ ~CPssm_Base() CPssm_Base::~CPssm_Base ( void ) virtualDefinition at line 167 of file Pssm_.cpp.
◆ ~CPssmFinalData() ◆ ~CPssmFinalData_Base() CPssmFinalData_Base::~CPssmFinalData_Base ( void ) virtualDefinition at line 95 of file PssmFinalData_.cpp.
◆ ~CPssmIntermediateData() ◆ ~CPssmIntermediateData_Base() ◆ ~CPssmParameters() ◆ ~CPssmParameters_Base() CPssmParameters_Base::~CPssmParameters_Base ( void ) virtualDefinition at line 137 of file PssmParameters_.cpp.
◆ ~CPssmWithParameters_Base() ◆ ~CSite_annot() CSite_annot::~CSite_annot ( void )Definition at line 50 of file Site_annot.cpp.
◆ ~CSite_annot_Base() CSite_annot_Base::~CSite_annot_Base ( void ) virtualDefinition at line 103 of file Site_annot_.cpp.
◆ ~CSite_annot_set() ◆ ~CSite_annot_set_Base() CSite_annot_set_Base::~CSite_annot_set_Base ( void ) virtualDefinition at line 74 of file Site_annot_set_.cpp.
◆ m_Aliases list< string > CSite_annot_Base::m_Aliases private ◆ m_AnnotatedSites ◆ m_BitScoreReportingThresh double CPssmParameters_Base::m_BitScoreReportingThresh private ◆ m_BitScoreThresh double CPssmParameters_Base::m_BitScoreThresh private ◆ m_Blocks ◆ m_ByRow ◆ m_Constraints ◆ m_data ◆ m_Description string CSite_annot_Base::m_Description private ◆ m_FinalData ◆ m_FreqRatios list< double > CPssmIntermediateData_Base::m_FreqRatios private ◆ m_GapExtend int CFormatRpsDbParameters_Base::m_GapExtend private ◆ m_GaplessColumnWeights list< double > CPssmIntermediateData_Base::m_GaplessColumnWeights private ◆ m_GapOpen int CFormatRpsDbParameters_Base::m_GapOpen private ◆ m_H double CPssmFinalData_Base::m_H private ◆ m_HUngapped double CPssmFinalData_Base::m_HUngapped private ◆ m_Identifier ◆ m_InformationContent list< double > CPssmIntermediateData_Base::m_InformationContent private ◆ m_Insertions list< int > CCoreDef_Base::m_Insertions private ◆ m_IntermediateData ◆ m_IntervalSizes list< int > CPssmIntermediateData_Base::m_IntervalSizes private ◆ m_Intvalue int CBlockProperty_Base::m_Intvalue private ◆ m_IsDiscontinuous bool CCoreDef_Base::m_IsDiscontinuous private ◆ m_IsProtein bool CPssm_Base::m_IsProtein private ◆ m_Kappa double CPssmFinalData_Base::m_Kappa private ◆ m_KappaUngapped double CPssmFinalData_Base::m_KappaUngapped private ◆ m_Lambda double CPssmFinalData_Base::m_Lambda private ◆ m_LambdaUngapped double CPssmFinalData_Base::m_LambdaUngapped private ◆ m_Loops ◆ m_MatrixName string CFormatRpsDbParameters_Base::m_MatrixName private ◆ m_Maxlength int CLoopConstraint_Base::m_Maxlength private ◆ m_Maxstop int CCoreBlock_Base::m_Maxstop private ◆ m_Minlength int CLoopConstraint_Base::m_Minlength private ◆ m_Minstart int CCoreBlock_Base::m_Minstart private ◆ m_Motif string CSite_annot_Base::m_Motif private ◆ m_Motifuse int CSite_annot_Base::m_Motifuse private ◆ m_Nblocks int CCoreDef_Base::m_Nblocks private ◆ m_NumColumns int CPssm_Base::m_NumColumns private ◆ m_NumIndeptObsr list< double > CPssmIntermediateData_Base::m_NumIndeptObsr private ◆ m_NumMatchingSeqs list< int > CPssmIntermediateData_Base::m_NumMatchingSeqs private ◆ m_NumRows int CPssm_Base::m_NumRows private ◆ m_Params ◆ m_Property ◆ m_Pseudocount int CPssmParameters_Base::m_Pseudocount private ◆ m_Pssm CRef< TPssm > CPssmWithParameters_Base::m_Pssm private ◆ m_Query ◆ m_ResFreqsPerPos list< int > CPssmIntermediateData_Base::m_ResFreqsPerPos private ◆ m_RowLabels list< string > CPssm_Base::m_RowLabels private ◆ m_Rpsdbparams ◆ m_ScalingFactor int CPssmFinalData_Base::m_ScalingFactor private ◆ m_Scores list< int > CPssmFinalData_Base::m_Scores private ◆ m_set_State [1/12] Uint4 CBlockProperty_Base::m_set_State[1] private ◆ m_set_State [2/12] Uint4 CCoreBlock_Base::m_set_State[1] privateDefinition at line 302 of file CoreBlock_.hpp.
Referenced by CCoreBlock_Base::CCoreBlock_Base(), CCoreBlock_Base::IsSetMaxstop(), CCoreBlock_Base::IsSetMinstart(), CCoreBlock_Base::IsSetProperty(), CCoreBlock_Base::IsSetStart(), CCoreBlock_Base::IsSetStop(), CCoreBlock_Base::ResetMaxstop(), CCoreBlock_Base::ResetMinstart(), CCoreBlock_Base::ResetProperty(), CCoreBlock_Base::ResetStart(), CCoreBlock_Base::ResetStop(), CCoreBlock_Base::SetMaxstop(), CCoreBlock_Base::SetMinstart(), CCoreBlock_Base::SetProperty(), CCoreBlock_Base::SetStart(), and CCoreBlock_Base::SetStop().
◆ m_set_State [3/12] Uint4 CCoreDef_Base::m_set_State[1] privateDefinition at line 292 of file CoreDef_.hpp.
Referenced by CCoreDef_Base::CCoreDef_Base(), CCoreDef_Base::IsSetBlocks(), CCoreDef_Base::IsSetInsertions(), CCoreDef_Base::IsSetIsDiscontinuous(), CCoreDef_Base::IsSetLoops(), CCoreDef_Base::IsSetNblocks(), CCoreDef_Base::ResetBlocks(), CCoreDef_Base::ResetInsertions(), CCoreDef_Base::ResetIsDiscontinuous(), CCoreDef_Base::ResetLoops(), CCoreDef_Base::ResetNblocks(), CCoreDef_Base::SetBlocks(), CCoreDef_Base::SetInsertions(), CCoreDef_Base::SetIsDiscontinuous(), CCoreDef_Base::SetLoops(), and CCoreDef_Base::SetNblocks().
◆ m_set_State [4/12] Uint4 CFormatRpsDbParameters_Base::m_set_State[1] private ◆ m_set_State [5/12] Uint4 CLoopConstraint_Base::m_set_State[1] private ◆ m_set_State [6/12] Uint4 CPssm_Base::m_set_State[1] privateDefinition at line 498 of file Pssm_.hpp.
Referenced by CPssm_Base::CPssm_Base(), CPssm_Base::IsSetByRow(), CPssm_Base::IsSetIsProtein(), CPssm_Base::IsSetNumColumns(), CPssm_Base::IsSetNumRows(), CPssm_Base::IsSetRowLabels(), CPssm_Base::ResetByRow(), CPssm_Base::ResetIsProtein(), CPssm_Base::ResetNumColumns(), CPssm_Base::ResetNumRows(), CPssm_Base::ResetRowLabels(), CPssm_Base::SetByRow(), CPssm_Base::SetIsProtein(), CPssm_Base::SetNumColumns(), CPssm_Base::SetNumRows(), and CPssm_Base::SetRowLabels().
◆ m_set_State [7/12] Uint4 CPssmFinalData_Base::m_set_State[1] privateDefinition at line 518 of file PssmFinalData_.hpp.
Referenced by CPssmFinalData_Base::CPssmFinalData_Base(), CPssmFinalData_Base::IsSetH(), CPssmFinalData_Base::IsSetHUngapped(), CPssmFinalData_Base::IsSetKappa(), CPssmFinalData_Base::IsSetKappaUngapped(), CPssmFinalData_Base::IsSetLambda(), CPssmFinalData_Base::IsSetLambdaUngapped(), CPssmFinalData_Base::IsSetScalingFactor(), CPssmFinalData_Base::IsSetScores(), CPssmFinalData_Base::IsSetWordScoreThreshold(), CPssmFinalData_Base::ResetH(), CPssmFinalData_Base::ResetHUngapped(), CPssmFinalData_Base::ResetKappa(), CPssmFinalData_Base::ResetKappaUngapped(), CPssmFinalData_Base::ResetLambda(), CPssmFinalData_Base::ResetLambdaUngapped(), CPssmFinalData_Base::ResetScalingFactor(), CPssmFinalData_Base::ResetScores(), CPssmFinalData_Base::ResetWordScoreThreshold(), CPssmFinalData_Base::SetH(), CPssmFinalData_Base::SetHUngapped(), CPssmFinalData_Base::SetKappa(), CPssmFinalData_Base::SetKappaUngapped(), CPssmFinalData_Base::SetLambda(), CPssmFinalData_Base::SetLambdaUngapped(), CPssmFinalData_Base::SetScalingFactor(), CPssmFinalData_Base::SetScores(), and CPssmFinalData_Base::SetWordScoreThreshold().
◆ m_set_State [8/12] Uint4 CPssmIntermediateData_Base::m_set_State[1] privateDefinition at line 433 of file PssmIntermediateData_.hpp.
Referenced by CPssmIntermediateData_Base::CPssmIntermediateData_Base(), CPssmIntermediateData_Base::IsSetFreqRatios(), CPssmIntermediateData_Base::IsSetGaplessColumnWeights(), CPssmIntermediateData_Base::IsSetInformationContent(), CPssmIntermediateData_Base::IsSetIntervalSizes(), CPssmIntermediateData_Base::IsSetNumIndeptObsr(), CPssmIntermediateData_Base::IsSetNumMatchingSeqs(), CPssmIntermediateData_Base::IsSetResFreqsPerPos(), CPssmIntermediateData_Base::IsSetSigma(), CPssmIntermediateData_Base::IsSetWeightedResFreqsPerPos(), CPssmIntermediateData_Base::ResetFreqRatios(), CPssmIntermediateData_Base::ResetGaplessColumnWeights(), CPssmIntermediateData_Base::ResetInformationContent(), CPssmIntermediateData_Base::ResetIntervalSizes(), CPssmIntermediateData_Base::ResetNumIndeptObsr(), CPssmIntermediateData_Base::ResetNumMatchingSeqs(), CPssmIntermediateData_Base::ResetResFreqsPerPos(), CPssmIntermediateData_Base::ResetSigma(), CPssmIntermediateData_Base::ResetWeightedResFreqsPerPos(), CPssmIntermediateData_Base::SetFreqRatios(), CPssmIntermediateData_Base::SetGaplessColumnWeights(), CPssmIntermediateData_Base::SetInformationContent(), CPssmIntermediateData_Base::SetIntervalSizes(), CPssmIntermediateData_Base::SetNumIndeptObsr(), CPssmIntermediateData_Base::SetNumMatchingSeqs(), CPssmIntermediateData_Base::SetResFreqsPerPos(), CPssmIntermediateData_Base::SetSigma(), and CPssmIntermediateData_Base::SetWeightedResFreqsPerPos().
◆ m_set_State [9/12] Uint4 CPssmParameters_Base::m_set_State[1] private ◆ m_set_State [10/12] Uint4 CPssmWithParameters_Base::m_set_State[1] private ◆ m_set_State [11/12] Uint4 CSite_annot_Base::m_set_State[1] privateDefinition at line 390 of file Site_annot_.hpp.
Referenced by CSite_annot_Base::CSite_annot_Base(), CSite_annot_Base::IsSetAliases(), CSite_annot_Base::IsSetDescription(), CSite_annot_Base::IsSetMotif(), CSite_annot_Base::IsSetMotifuse(), CSite_annot_Base::IsSetStartPosition(), CSite_annot_Base::IsSetStopPosition(), CSite_annot_Base::IsSetType(), CSite_annot_Base::ResetAliases(), CSite_annot_Base::ResetDescription(), CSite_annot_Base::ResetMotif(), CSite_annot_Base::ResetMotifuse(), CSite_annot_Base::ResetStartPosition(), CSite_annot_Base::ResetStopPosition(), CSite_annot_Base::ResetType(), CSite_annot_Base::SetAliases(), CSite_annot_Base::SetDescription(), CSite_annot_Base::SetMotif(), CSite_annot_Base::SetMotifuse(), CSite_annot_Base::SetStartPosition(), CSite_annot_Base::SetStopPosition(), and CSite_annot_Base::SetType().
◆ m_set_State [12/12] Uint4 CSite_annot_set_Base::m_set_State[1] private ◆ m_Sigma list< double > CPssmIntermediateData_Base::m_Sigma private ◆ m_Start int CCoreBlock_Base::m_Start private ◆ m_StartPosition int CSite_annot_Base::m_StartPosition private ◆ m_Stop int CCoreBlock_Base::m_Stop private ◆ m_StopPosition int CSite_annot_Base::m_StopPosition private ◆ m_Textvalue string CBlockProperty_Base::m_Textvalue private ◆ m_Type [1/2] int CBlockProperty_Base::m_Type private ◆ m_Type [2/2] int CSite_annot_Base::m_Type private ◆ m_WeightedResFreqsPerPos list< double > CPssmIntermediateData_Base::m_WeightedResFreqsPerPos private ◆ m_WordScoreThreshold double CPssmFinalData_Base::m_WordScoreThreshold privateRetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4