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NCBI C++ ToolKit: src/algo/blast/core/blast_sw.c Source File

final_best_score;

gap_open_extend = gap_open + gap_extend;

(a_size < b_size) {

scores = gap_align->

;

memset(scores, 0, (b_size + 1) *

(

));

final_best_score = 0;

(

= 1;

<= a_size;

++) {

matrix_row = matrix[

-1];

matrix_row = matrix[

[

-1]];

(j = 1; j <= b_size; j++) {

best_score = scores[j].

- gap_extend;

(scores[j].best - gap_open_extend > best_score)

best_score = scores[j].

- gap_open_extend;

best_score = insert_score - gap_extend;

(row_score - gap_open_extend > best_score)

best_score = row_score - gap_open_extend;

insert_score = best_score;

best_score =

(scores[j-1].best + matrix_row[

[j-1]], 0);

(insert_score > best_score)

best_score = insert_score;

(scores[j].best_gap > best_score)

(best_score > final_best_score)

final_best_score = best_score;

scores[j-1].

= row_score;

row_score = best_score;

scores[j-1].

= row_score;

final_best_score;

final_best_score;

gap_open_extend = gap_open + gap_extend;

scores = gap_align->

;

memset(scores, 0, (a_size + 1) *

(

));

final_best_score = 0;

(

= 1;

<= b_size;

++) {

matrix_row = matrix[base_pair];

(j = 1; j <= a_size; j++) {

best_score = scores[j].

- gap_extend;

(scores[j].best - gap_open_extend > best_score)

best_score = scores[j].

- gap_open_extend;

best_score = insert_score - gap_extend;

(row_score - gap_open_extend > best_score)

best_score = row_score - gap_open_extend;

insert_score = best_score;

best_score =

(scores[j-1].best + matrix_row[

[j-1]], 0);

(insert_score > best_score)

best_score = insert_score;

(scores[j].best_gap > best_score)

(best_score > final_best_score)

final_best_score = best_score;

scores[j-1].

= row_score;

row_score = best_score;

scores[j-1].

= row_score;

final_best_score;

*traceback_row;

a_start, b_start;

curr_score = -best_score;

traceback_row =

+

* (b_size + 1);

(curr_score != 0) {

next_action = traceback_row[j];

curr_score += matrix[

-1][

[j-1]];

curr_score += matrix[

[

-1]][

[j-1]];

traceback_row -= b_size + 1;

curr_score -= gap_open;

curr_score -= gap_extend;

traceback_row -= b_size + 1;

curr_score -= gap_open;

curr_score -= gap_extend;

(

= prelim_tback->

- 1, j = 0;

>= 0;

--, j++) {

final_tback->

[j] = p->

;

a_start, b_start, template_hsp->

,

&final_tback, &new_hsp);

score_options, hit_options)) {

row_path_stop_i;

row_path_stop_j;

new_path_stop_i;

new_path_stop_j;

gap_open_extend = gap_open + gap_extend;

*traceback_array;

*traceback_row;

(a_size < b_size) {

traceback_array = (

*)

((a_size + 1) * (b_size + 1) *

traceback_row = traceback_array;

(

= 0;

<= b_size;

++)

traceback_row += b_size + 1;

(

= 1;

<= a_size;

++) {

matrix_row = matrix[

-1];

matrix_row = matrix[

[

-1]];

(j = 1; j <= b_size; j++) {

best_score = scores[j].

- gap_extend;

(scores[j].best - gap_open_extend > best_score) {

best_score = scores[j].

- gap_open_extend;

best_score = insert_score - gap_extend;

(row_score - gap_open_extend > best_score) {

best_score = row_score - gap_open_extend;

insert_score = best_score;

best_score =

(scores[j-1].best + matrix_row[

[j-1]], 0);

traceback_row[j] = script |

;

(insert_score > best_score) {

best_score = insert_score;

new_path_score = row_path_score;

new_path_stop_i = row_path_stop_i;

new_path_stop_j = row_path_stop_j;

(scores[j].best_gap >= best_score) {

(best_score == 0) {

(new_path_score >= cutoff) {

gap_open, gap_extend,

gap_align, new_path_stop_i,

new_path_stop_j, new_path_score,

hsp_list, swapped, template_hsp,

hit_params->

, start_shift);

(best_score > new_path_score) {

new_path_score = best_score;

new_path_stop_i =

;

scores[j-1].

= row_score;

row_score = best_score;

row_path_score = new_path_score;

row_path_stop_i = new_path_stop_i;

row_path_stop_j = new_path_stop_j;

scores[j-1].

= row_score;

(scores[j-1].path_score >= cutoff) {

gap_open, gap_extend,

gap_align, scores[j-1].path_stop_i,

scores[j-1].path_stop_j,

scores[j-1].path_score,

hsp_list, swapped, template_hsp,

hit_params->

, start_shift);

traceback_row += b_size + 1;

(

= 0;

< b_size;

++) {

(scores[

].best && scores[

].path_score >= cutoff) {

gap_open, gap_extend,

gap_align, scores[

].path_stop_i,

scores[

].path_stop_j,

scores[

].path_score,

hsp_list, swapped, template_hsp,

hit_params->

, start_shift);

(traceback_array);

cutoff_score = 0;

(!

|| !

|| !gap_align || !score_params || !ext_params ||

!hit_params || !init_hitlist || !hsp_list_ptr)

(*hsp_list_ptr ==

)

hsp_list = *hsp_list_ptr;

context <= query_info->last_context;

++) {

(rpsblast_pssms) {

(score >= cutoff_score) {

*hsp_list_ptr = hsp_list;

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

#define NUM_FRAMES

Number of frames to which we translate in translating searches.

Int2 Blast_HSPInit(Int4 query_start, Int4 query_end, Int4 subject_start, Int4 subject_end, Int4 query_gapped_start, Int4 subject_gapped_start, Int4 query_context, Int2 query_frame, Int2 subject_frame, Int4 score, GapEditScript **gap_edit, BlastHSP **ret_hsp)

Allocates BlastHSP and inits with information from input.

Int4 BlastHspNumMax(Boolean gapped_calculation, const BlastHitSavingOptions *options)

Calculated the number of HSPs that should be saved.

Boolean Blast_HSPTestIdentityAndLength(EBlastProgramType program_number, BlastHSP *hsp, const Uint1 *query, const Uint1 *subject, const BlastScoringOptions *score_options, const BlastHitSavingOptions *hit_options)

Calculates number of identities and alignment lengths of an HSP via Blast_HSPGetNumIdentities and det...

BlastHSPList * Blast_HSPListNew(Int4 hsp_max)

Creates HSP list structure with a default size HSP array.

BlastHSP * Blast_HSPFree(BlastHSP *hsp)

Deallocate memory for an HSP structure.

Int2 Blast_HSPListSaveHSP(BlastHSPList *hsp_list, BlastHSP *hsp)

Saves HSP information into a BlastHSPList structure.

void Blast_HSPAdjustSubjectOffset(BlastHSP *hsp, Int4 start_shift)

Adjusts offsets if partial sequence was used for extension.

Boolean Blast_ProgramIsRpsBlast(EBlastProgramType p)

Returns true if program is RPS-BLAST (i.e.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

static Int4 s_NuclSmithWaterman(const Uint1 *B, Int4 b_size, const Uint1 *A, Int4 a_size, Int4 gap_open, Int4 gap_extend, BlastGapAlignStruct *gap_align)

Compute the score of the best local alignment between two nucleotide sequences.

static Int4 s_SmithWatermanScoreOnly(const Uint1 *A, Int4 a_size, const Uint1 *B, Int4 b_size, Int4 gap_open, Int4 gap_extend, BlastGapAlignStruct *gap_align)

Compute the score of the best local alignment between two protein sequences.

#define SWAP_INT(A, B)

swap two integers

@ EDIT_START_GAP_B

open a gap in B

@ EDIT_GAP_IN_B

Insertion.

@ EDIT_GAP_IN_A

Deletion.

@ EDIT_START_GAP_A

open a gap in A

@ EDIT_OP_MASK

Mask for edit script operations.

#define SWAP_SEQS(A, B)

swap (pointers to) a pair of sequences

struct BlastGapSW BlastGapSW

Auxiliary structures for Smith-Waterman alignment with traceback.

static void s_GetTraceback(EBlastProgramType program_number, Uint1 *trace, const Uint1 *A, const Uint1 *B, Int4 b_size, Int4 gap_open, Int4 gap_extend, BlastGapAlignStruct *gap_align, Int4 a_end, Int4 b_end, Int4 best_score, BlastHSPList *hsp_list, Boolean swapped, BlastHSP *template_hsp, const BlastScoringOptions *score_options, const BlastHitSavingOptions *hit_options, Int4 start_shift)

Generate the traceback for a single local alignment between two (unpacked) sequences,...

Smith-Waterman alignment for use within the infrastructure of BLAST.

Various auxiliary BLAST utility functions.

Int4 BLAST_FrameToContext(Int2 frame, EBlastProgramType program)

Convert translation frame or strand into a context number suitable for indexing into the BlastQueryIn...

#define NCBI2NA_UNPACK_BASE(x, N)

Macro to extract base N from a byte x (N >= 0, N < 4)

void GapPrelimEditBlockAdd(GapPrelimEditBlock *edit_block, EGapAlignOpType op_type, Int4 num_ops)

Add a new operation to a preliminary edit block, possibly combining it with the last operation if the...

EGapAlignOpType

Operation types within the edit script.

@ eGapAlignIns

Insertion: a gap in subject.

@ eGapAlignSub

Substitution.

@ eGapAlignDel

Deletion: a gap in query.

GapEditScript * GapEditScriptNew(Int4 size)

Initialize the edit script structure.

void GapPrelimEditBlockReset(GapPrelimEditBlock *edit_block)

Reset a preliminary edit block without freeing it.

void SmithWatermanScoreWithTraceback(EBlastProgramType program_number, const Uint1 *A, Int4 a_size, const Uint1 *B, Int4 b_size, BlastHSP *template_hsp, BlastHSPList *hsp_list, const BlastScoringParameters *score_params, const BlastHitSavingParameters *hit_params, BlastGapAlignStruct *gap_align, Int4 start_shift, Int4 cutoff)

Find all local alignments between two (unpacked) sequences, using the Smith-Waterman algorithm,...

Int2 BLAST_SmithWatermanGetGappedScore(EBlastProgramType program_number, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, BLAST_SequenceBlk *subject, BlastGapAlignStruct *gap_align, const BlastScoringParameters *score_params, const BlastExtensionParameters *ext_params, const BlastHitSavingParameters *hit_params, const BlastInitialWordParameters *word_params, BlastInitHitList *init_hitlist, BlastHSPList **hsp_list_ptr, BlastGappedStats *gapped_stats, Boolean *fence_hit)

Performs score-only Smith-Waterman gapped alignment of the subject sequence with all contexts in the ...

uint8_t Uint1

1-byte (8-bit) unsigned integer

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

Uint1 Boolean

bool replacment for C

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

#define MAX(a, b)

returns larger of a and b.

Structure to hold a sequence.

The context related information.

Int4 query_length

Length of this query, strand or frame.

Boolean is_valid

Determine if this context is valid or not.

Int4 query_offset

Offset of this query, strand or frame in the concatenated super-query.

Int1 frame

Frame number (-1, -2, -3, 0, 1, 2, or 3)

Computed values used as parameters for gapped alignments.

Structure supporting the gapped alignment.

GapPrelimEditBlock * fwd_prelim_tback

traceback from right extensions

Boolean positionBased

Is this PSI-BLAST?

Int4 dp_mem_alloc

current number of structures allocated

BlastScoreBlk * sbp

Pointer to the scoring information block.

BlastGapDP * dp_mem

scratch structures for dynamic programming

Auxiliary structure for dynamic programming gapped extension.

Int4 best_gap

score of best path that ends in a gap at this position

Int4 best

score of best path that ends in a match at this position

Auxiliary structures for Smith-Waterman alignment with traceback.

Int4 path_stop_j

Offset (plus one) on the second sequence where path_score occurs.

Int4 path_score

The highest score that the alignment at this position has previously achieved.

Int4 best_gap

Score of best alignment at this position that ends in a gap.

Int4 path_stop_i

Offset (plus one) on the first sequence where path_score occurs.

Int4 best

Score of best alignment at this position.

Int4 cutoff_score

Raw cutoff score corresponding to the e-value provided by the user if no sum stats,...

Structure containing hit counts from the gapped stage of a BLAST search.

The structure to hold all HSPs for a given sequence after the gapped alignment.

Structure holding all information about an HSP.

BlastSeg query

Query sequence info.

Int4 context

Context number of query.

BlastSeg subject

Subject sequence info.

Options used when evaluating and saving hits These include: a.

Parameter block that contains a pointer to BlastHitSavingOptions and the values derived from it.

BlastGappedCutoffs * cutoffs

per-context gapped cutoff information

BlastHitSavingOptions * options

The original (unparsed) options.

Structure to hold all initial HSPs for a given subject sequence.

Parameter block that contains a pointer to BlastInitialWordOptions and the values derived from it.

The query related information.

Int4 first_context

Index of the first element of the context array.

BlastContextInfo * contexts

Information per context.

SPsiBlastScoreMatrix * psi_matrix

PSSM and associated data.

SBlastScoreMatrix * matrix

scoring matrix data

Scoring options block Used to produce the BlastScoreBlk structure This structure may be needed for lo...

Scoring parameters block Contains scoring-related information that is actually used for the blast sea...

Int4 gap_extend

Penalty for each gap residue (scaled version)

Int4 gap_open

Extra penalty for starting a gap (scaled version)

BlastScoringOptions * options

User-provided values for these params.

Int2 frame

Translation frame.

Edit script: linked list of correspondencies between two sequences.

Int4 * num

Array of number of operations.

EGapAlignOpType * op_type

Array of type of operation.

Preliminary version of GapEditBlock, used directly by the low- level dynamic programming routines.

GapPrelimEditScript * edit_ops

array of edit operations

Int4 num_ops

number of edit ops presently in use

A version of GapEditScript used to store initial results from the gapped alignment routines.

Int4 num

Number of operations.

EGapAlignOpType op_type

Type of operation.

int ** data

actual scoring matrix data, stored in row-major form

SBlastScoreMatrix * pssm

position-specific score matrix

static CS_CONTEXT * context

voidp calloc(uInt items, uInt size)

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