#include <util/tables/tables_export.h>
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Classes | |
| struct | SNCBIPackedScoreMatrix |
| struct | SNCBIFullScoreMatrix |
Macros | |
| #define | NCBI_FSM_DIM 128 |
| Recommended approach: unpack and index directly. More... | |
Typedefs | |
| typedef int | TNCBIScore |
| data types More... | |
| typedef struct SNCBIPackedScoreMatrix | SNCBIPackedScoreMatrix |
| typedef struct SNCBIFullScoreMatrix | SNCBIFullScoreMatrix |
Functions | |
| int | NCBISM_GetIndex (const SNCBIPackedScoreMatrix *sm, int aa) |
| Map a standard residue code into an index suitable for a particular packed score matrix. More... | |
| TNCBIScore | NCBISM_GetScore (const SNCBIPackedScoreMatrix *sm, int aa1, int aa2) |
| Look up an entry in a packed score matrix. More... | |
| void | NCBISM_Unpack (const SNCBIPackedScoreMatrix *psm, SNCBIFullScoreMatrix *fsm) |
| Expand a packed score matrix into an unpacked one, which callers can proceed to index directly by standard residue values (NCBIstdaa or case-insensitive NCBIeaa, which are conveniently disjoint) modulo gaps in coverage, for which the unpacked matrix will hold the packed one's default score. More... | |
| const SNCBIPackedScoreMatrix * | NCBISM_GetStandardMatrix (const char *name) |
Macro Definition Documentation
◆ NCBI_FSM_DIM
| #define NCBI_FSM_DIM 128 |
Recommended approach: unpack and index directly.
Definition at line 85 of file raw_scoremat.h.
Typedef Documentation
◆ SNCBIFullScoreMatrix
| typedef struct SNCBIFullScoreMatrix SNCBIFullScoreMatrix |
◆ SNCBIPackedScoreMatrix
| typedef struct SNCBIPackedScoreMatrix SNCBIPackedScoreMatrix |
◆ TNCBIScore
| typedef int TNCBIScore |
data types
Definition at line 45 of file raw_scoremat.h.
Function Documentation
◆ NCBISM_GetIndex()
| int NCBISM_GetIndex | ( | const SNCBIPackedScoreMatrix * | sm, |
| int | aa | ||
| ) |
Map a standard residue code into an index suitable for a particular packed score matrix.
Calling this function is not as fast as working with unpacked matrices, but avoids the overhead of producing them.
- Parameters
-
sm Packed score matrix of interest. aa Standard amino acid code; may be either NCBIstdaa or case-insensitive NCBIeaa (which are conveniently disjoint), modulo gaps in coverage. (The standard built-in matrices don't cover O or U.)
- Returns
- The corresponding index into sm, or -1 if it doesn't cover AA.
Definition at line 51 of file raw_scoremat.c.
References int, islower(), kNCBIstdaa, SNCBIPackedScoreMatrix::symbols, and toupper().
Referenced by NCBISM_GetScore().
◆ NCBISM_GetScore()
| TNCBIScore NCBISM_GetScore | ( | const SNCBIPackedScoreMatrix * | sm, |
| int | aa1, | ||
| int | aa2 | ||
| ) |
Look up an entry in a packed score matrix.
Calling this function is not as fast as working with unpacked matrices, but avoids the overhead of producing them.
- Parameters
-
sm Packed score matrix of interest. aa1,aa2 Standard amino acid code; may be either NCBIstdaa or case-insensitive NCBIeaa (which are conveniently disjoint), modulo gaps in coverage. (The standard built-in matrices don't cover O or U.)
- Returns
- The corresponding score (or the matrix's default if it doesn't cover both residues).
Definition at line 67 of file raw_scoremat.c.
References SNCBIPackedScoreMatrix::defscore, NCBISM_GetIndex(), SNCBIPackedScoreMatrix::scores, and SNCBIPackedScoreMatrix::symbols.
Referenced by BlastScoreBlkProteinMatrixLoad(), BOOST_AUTO_TEST_CASE(), and CPssmInputTestData::FindNonIdenticalHighScoringResidue().
◆ NCBISM_GetStandardMatrix()
| const SNCBIPackedScoreMatrix* NCBISM_GetStandardMatrix | ( | const char * | name | ) |
Definition at line 131 of file raw_scoremat.c.
References NCBISM_Blosum45, NCBISM_Blosum50, NCBISM_Blosum62, NCBISM_Blosum80, NCBISM_Blosum90, NCBISM_Identity, NCBISM_Pam250, NCBISM_Pam30, NCBISM_Pam70, NULL, s_NCBISM_StartsWith(), and util::strcmp().
Referenced by BlastScoreBlkProteinMatrixLoad(), CProteinAlignText::CProteinAlignText(), and CAlignFormatUtil::GetAsciiProteinMatrix().
◆ NCBISM_Unpack()
| void NCBISM_Unpack | ( | const SNCBIPackedScoreMatrix * | psm, |
| SNCBIFullScoreMatrix * | fsm | ||
| ) |
Expand a packed score matrix into an unpacked one, which callers can proceed to index directly by standard residue values (NCBIstdaa or case-insensitive NCBIeaa, which are conveniently disjoint) modulo gaps in coverage, for which the unpacked matrix will hold the packed one's default score.
(The standard built-in matrices don't cover O or U.)
- Parameters
-
sm Packed score matrix to expand. fsm Storage for the resulting full score matrix.
Definition at line 81 of file raw_scoremat.c.
References SNCBIPackedScoreMatrix::defscore, i, int, kNCBIstdaa, NCBI_FSM_DIM, SNCBIFullScoreMatrix::s, SNCBIPackedScoreMatrix::scores, SNCBIPackedScoreMatrix::symbols, and toupper().
Referenced by CAlnVec::CalculateScore(), CGeneralScoreMatrix::CGeneralScoreMatrix(), CProteinAlignText::CProteinAlignText(), CSubstMatrix::CSubstMatrix(), CAlignFormatUtil::GetAsciiProteinMatrix(), GetBLOSUM62Score(), ScoreMatrix::initialize(), CNWAligner::SetScoreMatrix(), CQualityScoringMethodAA::SetSubstitutionMatrix(), CCmdLineBlastXML2ReportData::x_FillScoreMatrix(), and CCmdLineBlastXMLReportData::x_FillScoreMatrix().
Variable Documentation
◆ NCBISM_Blosum45
|
extern |
The standard matrices.
Definition at line 92 of file sm_blosum45.c.
Referenced by CGeneralScoreMatrix::CGeneralScoreMatrix(), ScoreMatrix::initialize(), CMatrixScoringMethod::Load(), NCBISM_GetStandardMatrix(), s_BuiltInSM(), CCmdLineBlastXML2ReportData::x_FillScoreMatrix(), CCmdLineBlastXMLReportData::x_FillScoreMatrix(), CMultiAligner::x_SetScoreMatrix(), and x_SetScoreMatrix().
◆ NCBISM_Blosum50
|
extern |
Definition at line 92 of file sm_blosum50.c.
Referenced by NCBISM_GetStandardMatrix(), CCmdLineBlastXML2ReportData::x_FillScoreMatrix(), and CCmdLineBlastXMLReportData::x_FillScoreMatrix().
◆ NCBISM_Blosum62
|
extern |
Definition at line 92 of file sm_blosum62.c.
Referenced by BOOST_AUTO_TEST_CASE(), CAlnVec::CalculateScore(), CGeneralScoreMatrix::CGeneralScoreMatrix(), CQualityScoringMethodAA::CQualityScoringMethodAA(), CSubstMatrix::CSubstMatrix(), GetBLOSUM62Score(), ScoreMatrix::initialize(), CMatrixScoringMethod::Load(), NCBISM_GetStandardMatrix(), s_BuiltInSM(), s_RunBlast2NWSeq(), CPssmInputTestData::SetupMsaHasUnalignedRegion(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CCmdLineBlastXML2ReportData::x_FillScoreMatrix(), CCmdLineBlastXMLReportData::x_FillScoreMatrix(), CAppNWA::x_RunOnPair(), CMultiAligner::x_SetScoreMatrix(), and x_SetScoreMatrix().
◆ NCBISM_Blosum80
|
extern |
Definition at line 92 of file sm_blosum80.c.
Referenced by CGeneralScoreMatrix::CGeneralScoreMatrix(), ScoreMatrix::initialize(), CMatrixScoringMethod::Load(), NCBISM_GetStandardMatrix(), s_BuiltInSM(), CCmdLineBlastXML2ReportData::x_FillScoreMatrix(), CCmdLineBlastXMLReportData::x_FillScoreMatrix(), CMultiAligner::x_SetScoreMatrix(), and x_SetScoreMatrix().
◆ NCBISM_Blosum90
|
extern |
Definition at line 92 of file sm_blosum90.c.
Referenced by NCBISM_GetStandardMatrix(), CCmdLineBlastXML2ReportData::x_FillScoreMatrix(), and CCmdLineBlastXMLReportData::x_FillScoreMatrix().
◆ NCBISM_Identity
|
extern |
Definition at line 92 of file sm_identity.c.
Referenced by NCBISM_GetStandardMatrix(), CCmdLineBlastXML2ReportData::x_FillScoreMatrix(), and CCmdLineBlastXMLReportData::x_FillScoreMatrix().
◆ NCBISM_Pam250
|
extern |
Definition at line 92 of file sm_pam250.c.
Referenced by CGeneralScoreMatrix::CGeneralScoreMatrix(), ScoreMatrix::initialize(), CMatrixScoringMethod::Load(), NCBISM_GetStandardMatrix(), s_BuiltInSM(), CCmdLineBlastXML2ReportData::x_FillScoreMatrix(), CCmdLineBlastXMLReportData::x_FillScoreMatrix(), CMultiAligner::x_SetScoreMatrix(), and x_SetScoreMatrix().
◆ NCBISM_Pam30
|
extern |
Definition at line 92 of file sm_pam30.c.
Referenced by CGeneralScoreMatrix::CGeneralScoreMatrix(), ScoreMatrix::initialize(), CMatrixScoringMethod::Load(), NCBISM_GetStandardMatrix(), s_BuiltInSM(), CCmdLineBlastXML2ReportData::x_FillScoreMatrix(), CCmdLineBlastXMLReportData::x_FillScoreMatrix(), CMultiAligner::x_SetScoreMatrix(), and x_SetScoreMatrix().
◆ NCBISM_Pam70
|
extern |
Definition at line 92 of file sm_pam70.c.
Referenced by CGeneralScoreMatrix::CGeneralScoreMatrix(), ScoreMatrix::initialize(), CMatrixScoringMethod::Load(), NCBISM_GetStandardMatrix(), s_BuiltInSM(), CCmdLineBlastXML2ReportData::x_FillScoreMatrix(), CCmdLineBlastXMLReportData::x_FillScoreMatrix(), CMultiAligner::x_SetScoreMatrix(), and x_SetScoreMatrix().
