blast_gapalign_priv.h File Reference

Private interface for blast_gapalign.c. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/gapinfo.h>
#include <algo/blast/core/blast_gapalign.h>
#include <algo/blast/core/blast_stat.h>
#include <algo/blast/core/blast_parameters.h>

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Classes
struct	BlastInitHSPNode
	A node in a path through blast unagpped alignments. More...
struct	ChainingStruct
	Workspace used for chaining. More...

Macros
#define	HSP_MAX_WINDOW   11
	Window size used to scan HSP for highest score region, where gapped extension starts. More...
#define	MB_HSP_CLOSE(q1, s1, q2, s2, c)   (ABS(((q1)-(s1)) - ((q2)-(s2))) < c)
	Are the two HSPs within a given number of diagonals from each other? More...

Typedefs
typedef struct BlastInitHSPNode	BlastInitHSPNode
	A node in a path through blast unagpped alignments. More...
typedef struct ChainingStruct	ChainingStruct
	Workspace used for chaining. More...

Functions
Int4	ALIGN_EX (const Uint1 *A, const Uint1 *B, Int4 M, Int4 N, Int4 *a_offset, Int4 *b_offset, GapPrelimEditBlock *edit_block, BlastGapAlignStruct *gap_align, const BlastScoringParameters *scoringParams, Int4 query_offset, Boolean reversed, Boolean reverse_sequence, Boolean *hit_fence)
	Low level function to perform dynamic programming gapped extension with traceback. More...
Int4	Blast_SemiGappedAlign (const Uint1 *A, const Uint1 *B, Int4 M, Int4 N, Int4 *a_offset, Int4 *b_offset, Boolean score_only, GapPrelimEditBlock *edit_block, BlastGapAlignStruct *gap_align, const BlastScoringParameters *score_params, Int4 query_offset, Boolean reversed, Boolean reverse_sequence, Boolean *fence_hit)
	Low level function to perform gapped extension in one direction with or without traceback. More...
GapEditScript *	Blast_PrelimEditBlockToGapEditScript (GapPrelimEditBlock *rev_prelim_tback, GapPrelimEditBlock *fwd_prelim_tback)
	Convert the initial list of traceback actions from a non-OOF gapped alignment into a blast edit script. More...
void	RPSPsiMatrixAttach (BlastScoreBlk *sbp, Int4 **rps_pssm, Int4 alphabet_size)
	Modify a BlastScoreBlk structure so that it can be used in RPS-BLAST. More...
void	RPSPsiMatrixDetach (BlastScoreBlk *sbp)
	Remove the artificially built SPsiBlastScoreMatrix structure allocated by RPSPsiMatrixAttach. More...
ChainingStruct *	ChainingStructNew (void)
ChainingStruct *	ChainingStructFree (ChainingStruct *ch)

Detailed Description

Private interface for blast_gapalign.c.

Definition in file blast_gapalign_priv.h.

Macro Definition Documentation

HSP_MAX_WINDOW

#define HSP_MAX_WINDOW   11

Window size used to scan HSP for highest score region, where gapped extension starts.

Definition at line 120 of file blast_gapalign_priv.h.

MB_HSP_CLOSE

#define MB_HSP_CLOSE	(		q1,
			s1,
			q2,
			s2,
			c
	)		(ABS(((q1)-(s1)) - ((q2)-(s2))) < c)

Are the two HSPs within a given number of diagonals from each other?

Definition at line 123 of file blast_gapalign_priv.h.

Typedef Documentation

BlastInitHSPNode

typedef struct BlastInitHSPNode BlastInitHSPNode

A node in a path through blast unagpped alignments.

ChainingStruct

typedef struct ChainingStruct ChainingStruct

Workspace used for chaining.

Function Documentation

ALIGN_EX()

Int4 ALIGN_EX	(	const Uint1 *	A,
		const Uint1 *	B,
		Int4	M,
		Int4	N,
		Int4 *	a_offset,
		Int4 *	b_offset,
		GapPrelimEditBlock *	edit_block,
		BlastGapAlignStruct *	gap_align,
		const BlastScoringParameters *	scoringParams,
		Int4	query_offset,
		Boolean	reversed,
		Boolean	reverse_sequence,
		Boolean *	hit_fence
	)

Low level function to perform dynamic programming gapped extension with traceback.

Parameters

A	The query sequence [in]
B	The subject sequence [in]
M	Maximal extension length in query [in]
N	Maximal extension length in subject [in]
a_offset	Resulting starting offset in query [out]
b_offset	Resulting starting offset in subject [out]
edit_block	Structure to hold traceback generated [out]
gap_align	Structure holding various information and allocated memory for the gapped alignment [in]
scoringParams	Parameters related to scoring [in]
query_offset	The starting offset in query [in]
reversed	Has the sequence been reversed? Used for psi-blast [in]
reverse_sequence	Do reverse the sequence [in]
hit_fence	If NULL, set to TRUE if the extension encountered sequence letters that indicate finding a region of B that is uninitialized [out]

Returns

The best alignment score found.

Definition at line 374 of file blast_gapalign.c.

References A, B, BlastGapDP::best, BlastGapDP::best_gap, SBlastScoreMatrix::data, done, BlastGapAlignStruct::dp_mem, BlastGapAlignStruct::dp_mem_alloc, FENCE_SENTRY, BlastScoringParameters::gap_extend, BlastScoringParameters::gap_open, BlastGapAlignStruct::gap_x_dropoff, GapPrelimEditBlockAdd(), i, M, malloc(), BlastScoreBlk::matrix, MAX, MININT, N, NULL, BlastGapAlignStruct::positionBased, BlastScoreBlk::psi_matrix, SPsiBlastScoreMatrix::pssm, s_GapGetState(), s_GapPurgeState(), BlastGapAlignStruct::sbp, SCRIPT_EXTEND_GAP_A, SCRIPT_EXTEND_GAP_B, SCRIPT_GAP_IN_A, SCRIPT_GAP_IN_B, SCRIPT_OP_MASK, SCRIPT_SUB, sfree, GapStateArrayStruct::state_array, BlastGapAlignStruct::state_struct, and GapStateArrayStruct::used.

Referenced by BLAST_GappedAlignmentWithTraceback(), Blast_SemiGappedAlign(), and s_SWFindFinalEndsUsingXdrop().

Blast_PrelimEditBlockToGapEditScript()

GapEditScript* Blast_PrelimEditBlockToGapEditScript	(	GapPrelimEditBlock *	rev_prelim_tback,
		GapPrelimEditBlock *	fwd_prelim_tback
	)

Convert the initial list of traceback actions from a non-OOF gapped alignment into a blast edit script.

Note that this routine assumes the input edit blocks have not been reversed or rearranged by calling code

Parameters

rev_prelim_tback	Traceback from extension to the left [in]
fwd_prelim_tback	Traceback from extension to the right [in]

Returns

Pointer to the resulting edit script, or NULL if there are no traceback actions specified

Definition at line 2481 of file blast_gapalign.c.

References GapPrelimEditBlock::edit_ops, FALSE, GapEditScriptNew(), i, NULL, GapEditScript::num, GapPrelimEditScript::num, GapPrelimEditBlock::num_ops, GapEditScript::op_type, GapPrelimEditScript::op_type, ncbi::grid::netcache::search::fields::size, and TRUE.

Referenced by BLAST_GappedAlignmentWithTraceback(), BLAST_GreedyGappedAlignment(), PHIGappedAlignmentWithTraceback(), s_BlastOOFTracebackToGapEditScript(), and s_NewAlignmentUsingXdrop().

Blast_SemiGappedAlign()

Int4 Blast_SemiGappedAlign	(	const Uint1 *	A,
		const Uint1 *	B,
		Int4	M,
		Int4	N,
		Int4 *	a_offset,
		Int4 *	b_offset,
		Boolean	score_only,
		GapPrelimEditBlock *	edit_block,
		BlastGapAlignStruct *	gap_align,
		const BlastScoringParameters *	score_params,
		Int4	query_offset,
		Boolean	reversed,
		Boolean	reverse_sequence,
		Boolean *	fence_hit
	)

Low level function to perform gapped extension in one direction with or without traceback.

Parameters

A	The query sequence [in]
B	The subject sequence [in]
M	Maximal extension length in query [in]
N	Maximal extension length in subject [in]
a_offset	Resulting starting offset in query [out]
b_offset	Resulting starting offset in subject [out]
score_only	Only find the score, without saving traceback [in]
edit_block	Structure to hold generated traceback [out]
gap_align	Structure holding various information and allocated memory for the gapped alignment [in]
score_params	Parameters related to scoring [in]
query_offset	The starting offset in query [in]
reversed	Has the sequence been reversed? Used for psi-blast [in]
reverse_sequence	Do reverse the sequence [in]
fence_hit	If NULL, set to TRUE if the extension encountered sequence letters that indicate finding a region of B that is uninitialized [out]

Returns

The best alignment score found.

Definition at line 736 of file blast_gapalign.c.

References A, ALIGN_EX(), B, BlastGapDP::best, BlastGapDP::best_gap, SBlastScoreMatrix::data, BlastGapAlignStruct::dp_mem, BlastGapAlignStruct::dp_mem_alloc, BlastScoringParameters::gap_extend, BlastScoringParameters::gap_open, BlastGapAlignStruct::gap_x_dropoff, i, M, malloc(), BlastScoreBlk::matrix, MAX, MININT, N, NULL, BlastGapAlignStruct::positionBased, BlastScoreBlk::psi_matrix, SPsiBlastScoreMatrix::pssm, BlastGapAlignStruct::sbp, and sfree.

Referenced by PHIGappedAlignmentWithTraceback(), s_BlastProtGappedAlignment(), and s_PHIGappedAlignment().

ChainingStructFree()

ChainingStruct* ChainingStructFree

(

ChainingStruct *

ch

)

Definition at line 3442 of file blast_gapalign.c.

References free(), ChainingStruct::nodes, and NULL.

Referenced by BLAST_GapAlignStructFree(), and ChainingStructNew().

ChainingStructNew()

ChainingStruct* ChainingStructNew

(

void

)

Definition at line 3455 of file blast_gapalign.c.

References calloc(), ChainingStructFree(), malloc(), ChainingStruct::nodes, NULL, and ChainingStruct::num_allocated.

Referenced by BLAST_GapAlignStructNew().

RPSPsiMatrixAttach()

void RPSPsiMatrixAttach	(	BlastScoreBlk *	sbp,
		Int4 **	rps_pssm,
		Int4	alphabet_size
	)

Modify a BlastScoreBlk structure so that it can be used in RPS-BLAST.

This involves allocating a SPsiBlastScoreMatrix structure so that the PSSMs memory mapped from the RPS-BLAST database files can be assigned to that structure.

Parameters

sbp	BlastScoreBlk structure to modify [in|out]
rps_pssm	PSSMs in RPS-BLAST database to use [in]
alphabet_size	Elements in one pssm row [in]

Definition at line 895 of file blast_traceback.c.

References ASSERT, calloc(), SBlastScoreMatrix::data, SBlastScoreMatrix::nrows, BlastScoreBlk::psi_matrix, and SPsiBlastScoreMatrix::pssm.

Referenced by s_RPSGapAlignDataPrepare(), and s_RPSPreliminarySearchEngine().

RPSPsiMatrixDetach()

void RPSPsiMatrixDetach

(

BlastScoreBlk *

sbp

)

Remove the artificially built SPsiBlastScoreMatrix structure allocated by RPSPsiMatrixAttach.

Parameters

sbp	BlastScoreBlk structure to modify [in|out]

Definition at line 916 of file blast_traceback.c.

References ASSERT, SBlastScoreMatrix::data, SPsiBlastScoreMatrix::freq_ratios, NULL, BlastScoreBlk::psi_matrix, SPsiBlastScoreMatrix::pssm, and sfree.

Referenced by s_RPSComputeTraceback(), and s_RPSPreliminarySearchEngine().