#include <ncbi_pch.hpp>#include <corelib/ncbistd.hpp>#include <corelib/ncbistre.hpp>#include <serial/serial.hpp>#include <serial/objostrasn.hpp>#include <algo/blast/api/pssm_input.hpp>#include <algo/blast/api/pssm_engine.hpp>#include <algo/blast/api/blast_aux.hpp>#include <algo/blast/core/blast_encoding.h>#include <objects/scoremat/scoremat__.hpp>#include <algo/structure/struct_util/su_pssm.hpp>#include <algo/structure/struct_util/su_block_multiple_alignment.hpp>#include <algo/structure/struct_util/su_sequence_set.hpp>#include "su_private.hpp"
Include dependency graph for su_pssm.cpp:
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Classes | |
| class | SU_PSSMInput |
Macros | |
| #define | PTHROW(stream) NCBI_THROW(CException, eUnknown, stream) |
Functions | |
| USING_SCOPE (objects) | |
| USING_SCOPE (blast) | |
| static int | Round (double Num) |
| int | GetPSSMScoreOfCharWithAverageOfBZ (const BLAST_Matrix *matrix, unsigned int pssmIndex, char resChar) |
| static const string | NCBIStdaaResidues ("-ABCDEFGHIKLMNPQRSTVWXYZU*OJ") |
| unsigned char | LookupNCBIStdaaNumberFromCharacter (char r) |
| char | LookupCharacterFromNCBIStdaaNumber (unsigned char n) |
| static void | FillInAlignmentData (const BlockMultipleAlignment *bma, PSIMsa *data) |
| double | GetStandardProbability (char ch) |
| static double | CalculateInformationContent (const PSIMsa *data, bool ignoreMaster) |
| static BLAST_Matrix * | ConvertPSSMToBLASTMatrix (const CPssmWithParameters &pssm) |
| BLAST_Matrix * | CreateBlastMatrix (const BlockMultipleAlignment *bma) |
Variables | |
| USING_NCBI_SCOPE | |
Macro Definition Documentation
◆ PTHROW
| #define PTHROW | ( | stream | ) | NCBI_THROW(CException, eUnknown, stream) |
Definition at line 61 of file su_pssm.cpp.
Function Documentation
◆ CalculateInformationContent()
Definition at line 296 of file su_pssm.cpp.
References data, GetStandardProbability(), log, LookupCharacterFromNCBIStdaaNumber(), LookupNCBIStdaaNumberFromCharacter(), out(), r(), and TRACE_MESSAGE.
Referenced by SU_PSSMInput::SU_PSSMInput().
◆ ConvertPSSMToBLASTMatrix()
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static |
Definition at line 441 of file su_pssm.cpp.
References BLAST_SCORE_MIN, BLAST_Matrix::columns, columns, ERROR_MESSAGE, CPssm_Base::GetByRow(), CPssm_Base::GetFinalData(), CPssm_Base::GetIsProtein(), CPssmFinalData_Base::GetKappa(), CPssm_Base::GetNumColumns(), CPssm_Base::GetNumRows(), CPssmWithParameters_Base::GetPssm(), CPssmFinalData_Base::GetScores(), i, int, BLAST_Matrix::is_prot, CPssm_Base::IsSetFinalData(), CPssmFinalData_Base::IsSetKappa(), BLAST_Matrix::karlinK, BLAST_Matrix::matrix, BLAST_Matrix::name, NULL, out(), PTHROW, r(), and BLAST_Matrix::rows.
Referenced by CreateBlastMatrix().
◆ CreateBlastMatrix()
| BLAST_Matrix* CreateBlastMatrix | ( | const BlockMultipleAlignment * | bma | ) |
Definition at line 509 of file su_pssm.cpp.
References ConvertPSSMToBLASTMatrix(), eNoOwnership, ERROR_MESSAGE, input(), NULL, out(), and CPssmEngine::Run().
Referenced by BlockMultipleAlignment::GetPSSM().
◆ FillInAlignmentData()
|
static |
Definition at line 150 of file su_pssm.cpp.
References b, blocks, column, data, BlockMultipleAlignment::GetBlockList(), BlockMultipleAlignment::GetMaster(), Block::GetRangeOfRow(), BlockMultipleAlignment::GetSequenceOfRow(), int, PSIMsaCell::is_aligned, Sequence::Length(), PSIMsaCell::letter, LookupNCBIStdaaNumberFromCharacter(), Sequence::m_sequenceString, BlockMultipleAlignment::NRows(), PTHROW, compile_time_bits::range(), and row.
Referenced by SU_PSSMInput::SU_PSSMInput().
◆ GetPSSMScoreOfCharWithAverageOfBZ()
| int GetPSSMScoreOfCharWithAverageOfBZ | ( | const BLAST_Matrix * | matrix, |
| unsigned int | pssmIndex, | ||
| char | resChar | ||
| ) |
Definition at line 96 of file su_pssm.cpp.
References LookupNCBIStdaaNumberFromCharacter(), BLAST_Matrix::matrix, and Round().
Referenced by AlignmentUtility::DoLeaveNOut(), AlignmentUtility::DoLeaveOneOut(), ScoreByPSSM(), and AlignmentUtility::ScoreRowByPSSM().
◆ GetStandardProbability()
| double GetStandardProbability | ( | char | ch | ) |
Definition at line 271 of file su_pssm.cpp.
Referenced by ConservationColorer::CalculateBasicConservationColors(), CalculateInformationContent(), and BlockMultipleAlignment::OptimizeBlock().
◆ LookupCharacterFromNCBIStdaaNumber()
| char LookupCharacterFromNCBIStdaaNumber | ( | unsigned char | n | ) |
Definition at line 142 of file su_pssm.cpp.
Referenced by CalculateInformationContent(), GetStandardProbability(), and SU_PSSMInput::SU_PSSMInput().
◆ LookupNCBIStdaaNumberFromCharacter()
| unsigned char LookupNCBIStdaaNumberFromCharacter | ( | char | r | ) |
Definition at line 125 of file su_pssm.cpp.
Referenced by CalculateInformationContent(), FillInAlignmentData(), GetPSSMScoreOfCharWithAverageOfBZ(), and SU_PSSMInput::SU_PSSMInput().
◆ NCBIStdaaResidues()
Referenced by LookupCharacterFromNCBIStdaaNumber(), and LookupNCBIStdaaNumberFromCharacter().
◆ Round()
Definition at line 88 of file su_pssm.cpp.
Referenced by mu::ParserInt::Abs(), mu::ParserInt::Add(), mu::ParserInt::And(), mu::ParserInt::Div(), mu::ParserInt::Equal(), GetPSSMScoreOfCharWithAverageOfBZ(), mu::ParserInt::Greater(), mu::ParserInt::GreaterEq(), mu::ParserInt::Ite(), mu::ParserInt::Less(), mu::ParserInt::LessEq(), mu::ParserInt::LogAnd(), mu::ParserInt::LogOr(), mu::ParserInt::LogXor(), mu::ParserInt::Mod(), mu::ParserInt::Mul(), mu::ParserInt::Not(), mu::ParserInt::NotEqual(), mu::ParserInt::Or(), mu::ParserInt::Shl(), mu::ParserInt::Shr(), mu::ParserInt::Sign(), mu::ParserInt::Sub(), and mu::ParserInt::UnaryMinus().
◆ USING_SCOPE() [1/2]
| USING_SCOPE | ( | blast | ) |
◆ USING_SCOPE() [2/2]
| USING_SCOPE | ( | objects | ) |
Variable Documentation
◆ USING_NCBI_SCOPE
| USING_NCBI_SCOPE |
Definition at line 52 of file su_pssm.cpp.
