#include <util/tables/tables_export.h>

Include dependency graph for raw_scoremat.h:

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Classes
struct	SNCBIPackedScoreMatrix
struct	SNCBIFullScoreMatrix
Defines
#define	NCBI_FSM_DIM 128
	Recommended approach: unpack and index directly.
Typedefs
typedef signed char	TNCBIScore
	data types
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.
TNCBIScore	NCBISM_GetScore (const SNCBIPackedScoreMatrix *sm, int aa1, int aa2)
	Look up an entry in a packed score matrix.
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.
const SNCBIPackedScoreMatrix *	NCBISM_GetStandardMatrix (const char *name)
Variables
const SNCBIPackedScoreMatrix	NCBISM_Blosum45
	The standard matrices.
const SNCBIPackedScoreMatrix	NCBISM_Blosum50
const SNCBIPackedScoreMatrix	NCBISM_Blosum62
const SNCBIPackedScoreMatrix	NCBISM_Blosum80
const SNCBIPackedScoreMatrix	NCBISM_Blosum90
const SNCBIPackedScoreMatrix	NCBISM_Pam30
const SNCBIPackedScoreMatrix	NCBISM_Pam70
const SNCBIPackedScoreMatrix	NCBISM_Pam250

Define Documentation

#define NCBI_FSM_DIM 128

Recommended approach: unpack and index directly.

Definition at line 85 of file raw_scoremat.h.

Referenced by CAlnVec::CalculateScore(), CQualityScoringMethod::CalculateScores(), NCBISM_Unpack(), CSplicedAligner16::ScoreFromTranscript(), CSplicedAligner32::ScoreFromTranscript(), CPSSMAligner::ScoreFromTranscript(), CNWAligner::ScoreFromTranscript(), CSplicedAligner16::x_Align(), CSplicedAligner32::x_Align(), CBandAligner::x_Align(), CNWAligner::x_Align(), CMMAligner::x_RunBtm(), CMMAligner::x_RunTerm(), and CMMAligner::x_RunTop().

Typedef Documentation

typedef struct SNCBIFullScoreMatrix SNCBIFullScoreMatrix

typedef struct SNCBIPackedScoreMatrix SNCBIPackedScoreMatrix

typedef signed char TNCBIScore

data types

Definition at line 45 of file raw_scoremat.h.

Function Documentation

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 50 of file raw_scoremat.c.

References kNCBIstdaa, and SNCBIPackedScoreMatrix::symbols.

Referenced by 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 66 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().

const SNCBIPackedScoreMatrix* NCBISM_GetStandardMatrix ( const char * name )

Definition at line 125 of file raw_scoremat.c.

References NCBISM_Blosum45, NCBISM_Blosum50, NCBISM_Blosum62, NCBISM_Blosum80, NCBISM_Blosum90, NCBISM_Pam250, NCBISM_Pam30, NCBISM_Pam70, s_NCBISM_StartsWith(), and util::strcmp().

Referenced by BlastScoreBlkProteinMatrixLoad(), CProteinAlignText::CProteinAlignText(), CScore_TblastnScore::Get(), and CAlignFormatUtil::GetAsciiProteinMatrix().

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: