struct_dp.h File Reference

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#include <corelib/ncbi_limits.h>

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Classes
struct	DP_BlockInfo
struct	DP_AlignmentResult
struct	DP_MultipleAlignmentResults

Macros
#define	STRUCT_DP_FOUND_ALIGNMENT   1 /* found an alignment */
#define	STRUCT_DP_NO_ALIGNMENT   2 /* algorithm successful, but no significant alignment found */
#define	STRUCT_DP_PARAMETER_ERROR   3 /* error/inconsistency in function parameters */
#define	STRUCT_DP_ALGORITHM_ERROR   4 /* error encountered during algorithm execution */
#define	STRUCT_DP_OKAY   5 /* generic ok status */

Typedefs
typedef int(*	DP_BlockScoreFunction) (unsigned int block, unsigned int queryPos)
typedef unsigned int(*	DP_LoopPenaltyFunction) (unsigned int loopNumber, unsigned int loopLength)

Functions
DP_BlockInfo *	DP_CreateBlockInfo (unsigned int nBlocks)
void	DP_DestroyBlockInfo (DP_BlockInfo *blocks)
unsigned int	DP_CalculateMaxLoopLength (unsigned int nLoops, const unsigned int *loopLengths, double percentile, unsigned int extension, unsigned int cutoff)
void	DP_DestroyAlignmentResult (DP_AlignmentResult *alignment)
int	DP_GlobalBlockAlign (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, unsigned int queryFrom, unsigned int queryTo, DP_AlignmentResult **alignment)
int	DP_LocalBlockAlign (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, unsigned int queryFrom, unsigned int queryTo, DP_AlignmentResult **alignment)
void	DP_DestroyMultipleAlignmentResults (DP_MultipleAlignmentResults *alignments)
int	DP_MultipleLocalBlockAlign (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, unsigned int queryFrom, unsigned int queryTo, DP_MultipleAlignmentResults **alignments, unsigned int maxAlignments)
int	DP_GlobalBlockAlignGeneric (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, DP_LoopPenaltyFunction LoopScore, unsigned int queryFrom, unsigned int queryTo, DP_AlignmentResult **alignment)
int	DP_LocalBlockAlignGeneric (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, DP_LoopPenaltyFunction LoopScore, unsigned int queryFrom, unsigned int queryTo, DP_AlignmentResult **alignment)
int	DP_MultipleLocalBlockAlignGeneric (const DP_BlockInfo *blocks, DP_BlockScoreFunction BlockScore, DP_LoopPenaltyFunction LoopScore, unsigned int queryFrom, unsigned int queryTo, DP_MultipleAlignmentResults **alignments, unsigned int maxAlignments)

Variables
static const int	DP_NEGATIVE_INFINITY = kMin_Int
static const unsigned int	DP_POSITIVE_INFINITY = kMax_UInt
static const unsigned int	DP_UNFROZEN_BLOCK = kMax_UInt

Macro Definition Documentation

STRUCT_DP_ALGORITHM_ERROR

#define STRUCT_DP_ALGORITHM_ERROR   4 /* error encountered during algorithm execution */

Definition at line 47 of file struct_dp.h.

STRUCT_DP_FOUND_ALIGNMENT

#define STRUCT_DP_FOUND_ALIGNMENT   1 /* found an alignment */

Definition at line 44 of file struct_dp.h.

STRUCT_DP_NO_ALIGNMENT

#define STRUCT_DP_NO_ALIGNMENT   2 /* algorithm successful, but no significant alignment found */

Definition at line 45 of file struct_dp.h.

STRUCT_DP_OKAY

#define STRUCT_DP_OKAY   5 /* generic ok status */

Definition at line 48 of file struct_dp.h.

STRUCT_DP_PARAMETER_ERROR

#define STRUCT_DP_PARAMETER_ERROR   3 /* error/inconsistency in function parameters */

Definition at line 46 of file struct_dp.h.

Typedef Documentation

DP_BlockScoreFunction

typedef int(* DP_BlockScoreFunction) (unsigned int block, unsigned int queryPos)

Definition at line 98 of file struct_dp.h.

DP_LoopPenaltyFunction

typedef unsigned int(* DP_LoopPenaltyFunction) (unsigned int loopNumber, unsigned int loopLength)

Definition at line 157 of file struct_dp.h.

Function Documentation

DP_CalculateMaxLoopLength()

unsigned int DP_CalculateMaxLoopLength	(	unsigned int	nLoops,
		const unsigned int *	loopLengths,
		double	percentile,
		unsigned int	extension,
		unsigned int	cutoff
	)

Definition at line 881 of file block_align.cpp.

References int, and max().

Referenced by BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), AlignmentUtility::DoLeaveNOut(), and AlignmentUtility::DoLeaveOneOut().

DP_CreateBlockInfo()

DP_BlockInfo* DP_CreateBlockInfo

(

unsigned int

nBlocks

)

Definition at line 839 of file block_align.cpp.

References DP_BlockInfo::blockPositions, blocks, DP_BlockInfo::blockSizes, DP_UNFROZEN_BLOCK, DP_BlockInfo::freezeBlocks, i, DP_BlockInfo::maxLoops, and DP_BlockInfo::nBlocks.

Referenced by BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), AlignmentUtility::DoLeaveNOut(), AlignmentUtility::DoLeaveOneOut(), and DPApp::Run().

DP_DestroyAlignmentResult()

void DP_DestroyAlignmentResult

(

DP_AlignmentResult *

alignment

)

Definition at line 863 of file block_align.cpp.

References DP_AlignmentResult::blockPositions.

Referenced by BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), AlignmentUtility::DoLeaveNOut(), AlignmentUtility::DoLeaveOneOut(), and DPApp::Run().

DP_DestroyBlockInfo()

void DP_DestroyBlockInfo

(

DP_BlockInfo *

blocks

)

Definition at line 852 of file block_align.cpp.

References DP_BlockInfo::blockPositions, blocks, DP_BlockInfo::blockSizes, DP_BlockInfo::freezeBlocks, and DP_BlockInfo::maxLoops.

Referenced by BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), AlignmentUtility::DoLeaveNOut(), AlignmentUtility::DoLeaveOneOut(), and DPApp::Run().

DP_DestroyMultipleAlignmentResults()

void DP_DestroyMultipleAlignmentResults

(

DP_MultipleAlignmentResults *

alignments

)

Definition at line 871 of file block_align.cpp.

References DP_MultipleAlignmentResults::alignments, DP_AlignmentResult::blockPositions, i, and DP_MultipleAlignmentResults::nAlignments.

DP_GlobalBlockAlign()

int DP_GlobalBlockAlign	(	const DP_BlockInfo *	blocks,
		DP_BlockScoreFunction	BlockScore,
		unsigned int	queryFrom,
		unsigned int	queryTo,
		DP_AlignmentResult **	alignment
	)

Definition at line 659 of file block_align.cpp.

References blocks, DP_BlockInfo::blockSizes, CalculateGlobalMatrix(), ERROR_MESSAGE, i, if(), DP_BlockInfo::nBlocks, STRUCT_DP_OKAY, STRUCT_DP_PARAMETER_ERROR, TracebackGlobalAlignment(), and ValidateFrozenBlockPositions().

Referenced by BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), AlignmentUtility::DoLeaveNOut(), and AlignmentUtility::DoLeaveOneOut().

DP_GlobalBlockAlignGeneric()

int DP_GlobalBlockAlignGeneric	(	const DP_BlockInfo *	blocks,
		DP_BlockScoreFunction	BlockScore,
		DP_LoopPenaltyFunction	LoopScore,
		unsigned int	queryFrom,
		unsigned int	queryTo,
		DP_AlignmentResult **	alignment
	)

Definition at line 694 of file block_align.cpp.

References blocks, DP_BlockInfo::blockSizes, CalculateGlobalMatrixGeneric(), ERROR_MESSAGE, i, if(), DP_BlockInfo::nBlocks, STRUCT_DP_OKAY, STRUCT_DP_PARAMETER_ERROR, TracebackGlobalAlignment(), and ValidateFrozenBlockPositions().

DP_LocalBlockAlign()

int DP_LocalBlockAlign	(	const DP_BlockInfo *	blocks,
		DP_BlockScoreFunction	BlockScore,
		unsigned int	queryFrom,
		unsigned int	queryTo,
		DP_AlignmentResult **	alignment
	)

Definition at line 731 of file block_align.cpp.

References blocks, DP_BlockInfo::blockSizes, CalculateLocalMatrix(), DP_UNFROZEN_BLOCK, ERROR_MESSAGE, DP_BlockInfo::freezeBlocks, DP_BlockInfo::nBlocks, STRUCT_DP_OKAY, STRUCT_DP_PARAMETER_ERROR, TracebackLocalAlignment(), and WARNING_MESSAGE.

Referenced by BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), and DPApp::Run().

DP_LocalBlockAlignGeneric()

int DP_LocalBlockAlignGeneric	(	const DP_BlockInfo *	blocks,
		DP_BlockScoreFunction	BlockScore,
		DP_LoopPenaltyFunction	LoopScore,
		unsigned int	queryFrom,
		unsigned int	queryTo,
		DP_AlignmentResult **	alignment
	)

Definition at line 758 of file block_align.cpp.

References blocks, DP_BlockInfo::blockSizes, CalculateLocalMatrixGeneric(), DP_UNFROZEN_BLOCK, ERROR_MESSAGE, DP_BlockInfo::freezeBlocks, DP_BlockInfo::nBlocks, STRUCT_DP_OKAY, STRUCT_DP_PARAMETER_ERROR, TracebackLocalAlignment(), and WARNING_MESSAGE.

DP_MultipleLocalBlockAlign()

int DP_MultipleLocalBlockAlign	(	const DP_BlockInfo *	blocks,
		DP_BlockScoreFunction	BlockScore,
		unsigned int	queryFrom,
		unsigned int	queryTo,
		DP_MultipleAlignmentResults **	alignments,
		unsigned int	maxAlignments
	)

Definition at line 785 of file block_align.cpp.

References blocks, DP_BlockInfo::blockSizes, CalculateLocalMatrix(), DP_UNFROZEN_BLOCK, ERROR_MESSAGE, DP_BlockInfo::freezeBlocks, DP_BlockInfo::nBlocks, STRUCT_DP_OKAY, STRUCT_DP_PARAMETER_ERROR, TracebackMultipleLocalAlignments(), and WARNING_MESSAGE.

DP_MultipleLocalBlockAlignGeneric()

int DP_MultipleLocalBlockAlignGeneric	(	const DP_BlockInfo *	blocks,
		DP_BlockScoreFunction	BlockScore,
		DP_LoopPenaltyFunction	LoopScore,
		unsigned int	queryFrom,
		unsigned int	queryTo,
		DP_MultipleAlignmentResults **	alignments,
		unsigned int	maxAlignments
	)

Definition at line 812 of file block_align.cpp.

References blocks, DP_BlockInfo::blockSizes, CalculateLocalMatrixGeneric(), DP_UNFROZEN_BLOCK, ERROR_MESSAGE, DP_BlockInfo::freezeBlocks, DP_BlockInfo::nBlocks, STRUCT_DP_OKAY, STRUCT_DP_PARAMETER_ERROR, TracebackMultipleLocalAlignments(), and WARNING_MESSAGE.

Variable Documentation

DP_NEGATIVE_INFINITY

const int DP_NEGATIVE_INFINITY = kMin_Int

static

Definition at line 51 of file struct_dp.h.

Referenced by CalculateGlobalMatrix(), CalculateGlobalMatrixGeneric(), CalculateLocalMatrix(), CalculateLocalMatrixGeneric(), dpScoreFunction(), ScoreByBlosum62(), ScoreByPSSM(), TracebackGlobalAlignment(), TracebackLocalAlignment(), and TracebackMultipleLocalAlignments().

DP_POSITIVE_INFINITY

const unsigned int DP_POSITIVE_INFINITY = kMax_UInt

static

Definition at line 54 of file struct_dp.h.

Referenced by CalculateGlobalMatrixGeneric(), and CalculateLocalMatrixGeneric().

DP_UNFROZEN_BLOCK

const unsigned int DP_UNFROZEN_BLOCK = kMax_UInt

static

Definition at line 61 of file struct_dp.h.

Referenced by CalculateGlobalMatrix(), CalculateGlobalMatrixGeneric(), BlockAligner::CreateNewPairwiseAlignmentsByBlockAlignment(), DP_CreateBlockInfo(), DP_LocalBlockAlign(), DP_LocalBlockAlignGeneric(), DP_MultipleLocalBlockAlign(), DP_MultipleLocalBlockAlignGeneric(), FreezeBlocks(), and ValidateFrozenBlockPositions().