raw_scoremat.c File Reference

#include <util/tables/raw_scoremat.h>
#include <ctype.h>
#include <string.h>
#include "sm_blosum45.c"
#include "sm_blosum50.c"
#include "sm_blosum62.c"
#include "sm_blosum80.c"
#include "sm_blosum90.c"
#include "sm_pam30.c"
#include "sm_pam70.c"
#include "sm_pam250.c"
#include "sm_identity.c"

Include dependency graph for raw_scoremat.c:

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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...
static int	s_NCBISM_StartsWith (const char *str, const char *pfx)
const SNCBIPackedScoreMatrix *	NCBISM_GetStandardMatrix (const char *name)

Variables
static const char	kNCBIstdaa [] = "-ABCDEFGHIKLMNPQRSTVWXYZU*OJ"

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().

s_NCBISM_StartsWith()

static int s_NCBISM_StartsWith ( const char *  str, const char *  pfx  )

static

Definition at line 121 of file raw_scoremat.c.

References str(), and tolower().

Referenced by NCBISM_GetStandardMatrix().

Variable Documentation

kNCBIstdaa

const char kNCBIstdaa[] = "-ABCDEFGHIKLMNPQRSTVWXYZU*OJ"

static

Definition at line 48 of file raw_scoremat.c.

Referenced by NCBISM_GetIndex(), and NCBISM_Unpack().