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

offset_array_size,

init_hitlist, ungapped_stats);

init_hitlist, ungapped_stats);

offset_array_size,

init_hitlist, ungapped_stats);

init_hitlist, ungapped_stats);

first_offset = 0;

hsp_q, hsp_s, hsp_len;

last_hit, s_last_off, diff;

diag_offset, diag_coord, diag_mask;

hits_extended = 0;

diag_offset = diag->

;

wordsize =

->wordsize;

last_offset =

->length - wordsize;

(first_offset <= last_offset) {

(

= 0;

<

->num_buckets; ++

) {

(j = 0; j < hits; ++j) {

diag_coord = (query_offset - subject_offset) & diag_mask;

(diag_array[diag_coord].flag) {

((

) (subject_offset + diag_offset) <

diag_array[diag_coord].last_hit) {

subject_offset + diag_offset;

diag_array[diag_coord].

= 0;

last_hit = diag_array[diag_coord].

- diag_offset;

diff = subject_offset - last_hit;

(diff >= window) {

subject_offset + diag_offset;

(diff < wordsize) {

subject_offset, query_offset,

dropoff, &hsp_q, &hsp_s,

wordsize, &right_extend,

query_offset, subject_offset,

diag_array[diag_coord].

= 1;

s_last_off - (wordsize - 1) + diag_offset;

subject_offset + diag_offset;

ungapped_hsps->

);

hsp_q, hsp_s, hsp_len = 0;

last_hit, s_last_off, diff;

diag_offset, diag_coord, diag_mask;

hits_extended = 0;

diag_offset = diag->

;

wordsize =

->word_length;

use_pssm =

->use_pssm;

wordsize =

->word_length;

scan_range[1] =

->seq_ranges[0].left;

scan_range[2] =

->seq_ranges[0].right - wordsize;

(scan_range[2] < scan_range[1])

scan_range[2] = scan_range[1];

(scan_range[1] <= scan_range[2]) {

hits = scansub(lookup_wrap,

,

offset_pairs, array_size, scan_range);

(

= 0;

< hits; ++

) {

query_offset = offset_pairs[

].qs_offsets.q_off;

subject_offset = offset_pairs[

].qs_offsets.s_off;

diag_coord = (query_offset - subject_offset) & diag_mask;

(diag_array[diag_coord].flag) {

((

) (subject_offset + diag_offset) <

diag_array[diag_coord].last_hit) {

subject_offset + diag_offset;

diag_array[diag_coord].

= 0;

last_hit = diag_array[diag_coord].

- diag_offset;

diff = subject_offset - last_hit;

(diff >= window) {

subject_offset + diag_offset;

(diff < wordsize) {

(query_offset - diff <

subject_offset + diag_offset;

cutoffs = word_params->

+ curr_context;

subject_offset, query_offset,

wordsize, &right_extend,

query_offset, subject_offset, hsp_len,

diag_array[diag_coord].

= 1;

s_last_off - (wordsize - 1) + diag_offset;

subject_offset + diag_offset;

ungapped_hsps->

);

first_offset = 0;

hsp_q, hsp_s, hsp_len;

diag_offset, diag_coord, diag_mask, diff;

hits_extended = 0;

diag_offset = diag->

;

wordsize =

->wordsize;

last_offset =

->length - wordsize;

(first_offset <= last_offset) {

(

= 0;

<

->num_buckets;

++) {

(j = 0; j < hits; ++j) {

diag_coord = (subject_offset - query_offset) & diag_mask;

diff = subject_offset -

(diag_array[diag_coord].

- diag_offset);

subject_offset, query_offset,

dropoff, &hsp_q, &hsp_s,

&hsp_len, wordsize,

,

(score >= cutoff) {

query_offset, subject_offset,

s_last_off - (wordsize - 1) + diag_offset;

ungapped_hsps->

);

hsp_q, hsp_s, hsp_len;

diag_offset, diag_coord, diag_mask, diff;

hits_extended = 0;

diag_offset = diag->

;

wordsize =

->word_length;

use_pssm =

->use_pssm;

wordsize =

->word_length;

scan_range[1] =

->seq_ranges[0].left;

scan_range[2] =

->seq_ranges[0].right - wordsize;

(scan_range[1] <= scan_range[2]) {

hits = scansub(lookup_wrap,

,

offset_pairs, array_size, scan_range);

(

= 0;

< hits; ++

) {

query_offset = offset_pairs[

].qs_offsets.q_off;

subject_offset = offset_pairs[

].qs_offsets.s_off;

diag_coord = (subject_offset - query_offset) & diag_mask;

diff = subject_offset -

(diag_array[diag_coord].

- diag_offset);

subject_offset, query_offset,

&hsp_q, &hsp_s, &hsp_len,

wordsize, use_pssm, &s_last_off);

query_offset, subject_offset, hsp_len,

s_last_off - (wordsize - 1) + diag_offset;

ungapped_hsps->

);

score = maxscore;

s =

->sequence + s_off;

q =

->sequence + q_off;

(

= 0;

<

;

++) {

score += matrix[q[

]][s[

]];

(score > maxscore) {

(score <= 0 || (maxscore - score) >= dropoff)

*length = best_i + 1;

*s_last_off = s_off +

;

score = maxscore;

=

(s_off, q_off);

s =

->sequence + s_off -

;

q =

->sequence + q_off -

;

(

=

;

>= 0;

--) {

score += matrix[q[

]][s[

]];

(score > maxscore) {

((maxscore - score) >= dropoff)

*length =

- best_i + 1;

score = maxscore;

=

(

->length - s_off, query_size - q_off);

s =

->sequence + s_off;

(

= 0;

<

;

++) {

score += matrix[q_off +

][s[

]];

(score > maxscore) {

(score <= 0 || (maxscore - score) >= dropoff)

*length = best_i + 1;

*s_last_off = s_off +

;

score = maxscore;

=

(s_off, q_off);

s =

->sequence + s_off -

;

(

=

;

>= 0;

--) {

score += matrix[q_off -

+

][s[

]];

(score > maxscore) {

((maxscore - score) >= dropoff)

*length =

- best_i + 1;

score = 0, left_score, total_score, sum = 0;

left_disp = 0, right_disp = 0;

q_left_off = q_off, q_right_off =

q_off + word_size, q_best_left_off = q_off;

s_left_off, s_right_off;

init_hit_width = 0;

(

= 0;

< word_size;

++) {

sum += matrix[q_off +

][s[s_off +

]];

sum += matrix[q[q_off +

]][s[s_off +

]];

q_best_left_off = q_left_off;

q_right_off = q_off +

;

}

(sum <= 0) {

q_left_off = q_off +

+ 1;

init_hit_width = q_right_off - q_left_off + 1;

q_left_off = q_best_left_off;

s_left_off = q_left_off + (s_off - q_off);

s_right_off = q_right_off + (s_off - q_off);

s_left_off - 1, q_left_off - 1,

dropoff, &left_disp, score);

s_right_off + 1, q_right_off + 1,

dropoff, &right_disp, left_score,

s_left_off - 1, q_left_off - 1,

dropoff, &left_disp, score);

s_right_off + 1, q_right_off + 1,

dropoff, &right_disp, left_score,

*hsp_q = q_left_off - left_disp;

*hsp_s = s_left_off - left_disp;

*hsp_len = left_disp + right_disp + init_hit_width;

left_d = 0, right_d = 0;

left_score = 0, right_score = 0;

(

= 0;

< word_size;

++) {

score += matrix[q_right_off +

][s[s_right_off +

]];

score += matrix[q[q_right_off +

]][s[s_right_off +

]];

(score > left_score) {

q_right_off += right_d;

s_right_off += right_d;

*right_extend =

;

*s_last_off = s_right_off;

s_right_off - 1, q_right_off - 1,

dropoff, &left_d, 0);

s_right_off - 1, q_right_off - 1,

dropoff, &left_d, 0);

(left_d >= (s_right_off - s_left_off)) {

*right_extend =

;

s_right_off, q_right_off,

dropoff, &right_d, left_score,

s_right_off, q_right_off,

dropoff, &right_d, left_score,

*hsp_q = q_right_off - left_d;

*hsp_s = s_right_off - left_d;

*hsp_len = left_d + right_d;

(left_score, right_score);

static Int4 s_BlastAaExtendOneHit(Int4 **matrix, const BLAST_SequenceBlk *subject, const BLAST_SequenceBlk *query, Int4 s_off, Int4 q_off, Int4 dropoff, Int4 *hsp_q, Int4 *hsp_s, Int4 *hsp_len, Int4 word_size, Boolean use_pssm, Int4 *s_last_off)

Perform a one-hit extension.

static Int2 s_BlastRPSWordFinder_OneHit(const BLAST_SequenceBlk *subject, const BLAST_SequenceBlk *query, const LookupTableWrap *lookup_wrap, Blast_ExtendWord *ewp, Int4 **matrix, Int4 cutoff, Int4 dropoff, BlastInitHitList *ungapped_hsps, BlastUngappedStats *ungapped_stats)

Scan a subject sequence for word hits and trigger one-hit extensions (spcialized for RPS blast).

static Int4 s_BlastAaExtendLeft(Int4 **matrix, const BLAST_SequenceBlk *subject, const BLAST_SequenceBlk *query, Int4 s_off, Int4 q_off, Int4 dropoff, Int4 *length, Int4 maxscore)

Beginning at s_off and q_off in the subject and query, respectively, extend to the left until the cum...

static Int4 s_BlastPSSMExtendRight(Int4 **matrix, const BLAST_SequenceBlk *subject, Int4 query_size, Int4 s_off, Int4 q_off, Int4 dropoff, Int4 *length, Int4 maxscore, Int4 *s_last_off)

Identical to BlastAaExtendRight, except the score matrix is position-specific.

static Int2 s_BlastAaWordFinder_OneHit(const BLAST_SequenceBlk *subject, const BLAST_SequenceBlk *query, const LookupTableWrap *lookup_wrap, Blast_ExtendWord *ewp, Int4 **matrix, const BlastInitialWordParameters *word_params, BlastQueryInfo *query_info, BlastOffsetPair *offset_pairs, Int4 array_size, BlastInitHitList *ungapped_hsps, BlastUngappedStats *ungapped_stats)

Scan a subject sequence for word hits and trigger one-hit extensions.

static Int2 s_BlastAaWordFinder_TwoHit(const BLAST_SequenceBlk *subject, const BLAST_SequenceBlk *query, const LookupTableWrap *lookup_wrap, Blast_ExtendWord *ewp, Int4 **matrix, const BlastInitialWordParameters *word_params, BlastQueryInfo *query_info, BlastOffsetPair *offset_pairs, Int4 array_size, BlastInitHitList *ungapped_hsps, BlastUngappedStats *ungapped_stats)

Scan a subject sequence for word hits and trigger two-hit extensions.

static Int4 s_BlastPSSMExtendLeft(Int4 **matrix, const BLAST_SequenceBlk *subject, Int4 s_off, Int4 q_off, Int4 dropoff, Int4 *length, Int4 maxscore)

Identical to BlastAaExtendLeft, except the query is represented by a position-specific score matrix.

Int2 BlastAaWordFinder(BLAST_SequenceBlk *subject, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, LookupTableWrap *lut_wrap, Int4 **matrix, const BlastInitialWordParameters *word_params, Blast_ExtendWord *ewp, BlastOffsetPair *offset_pairs, Int4 offset_array_size, BlastInitHitList *init_hitlist, BlastUngappedStats *ungapped_stats)

Scan a subject sequence for word hits (blastp)

static Int4 s_BlastAaExtendRight(Int4 **matrix, const BLAST_SequenceBlk *subject, const BLAST_SequenceBlk *query, Int4 s_off, Int4 q_off, Int4 dropoff, Int4 *length, Int4 maxscore, Int4 *s_last_off)

Beginning at s_off and q_off in the subject and query, respectively, extend to the right until the cu...

static Int2 s_BlastRPSWordFinder_TwoHit(const BLAST_SequenceBlk *subject, const BLAST_SequenceBlk *query, const LookupTableWrap *lookup_wrap, Blast_ExtendWord *ewp, Int4 **matrix, Int4 cutoff, Int4 dropoff, BlastInitHitList *ungapped_hsps, BlastUngappedStats *ungapped_stats)

Scan a subject sequence for word hits and trigger two-hit extensions (specialized for RPS blast).

Int2 BlastRPSWordFinder(BLAST_SequenceBlk *subject, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, LookupTableWrap *lut_wrap, Int4 **matrix, const BlastInitialWordParameters *word_params, Blast_ExtendWord *ewp, BlastOffsetPair *offset_pairs, Int4 offset_array_size, BlastInitHitList *init_hitlist, BlastUngappedStats *ungapped_stats)

Scan a subject sequence for word hits (rpsblast and rpstblastn)

static Int4 s_BlastAaExtendTwoHit(Int4 **matrix, const BLAST_SequenceBlk *subject, const BLAST_SequenceBlk *query, Int4 s_left_off, Int4 s_right_off, Int4 q_right_off, Int4 dropoff, Int4 *hsp_q, Int4 *hsp_s, Int4 *hsp_len, Boolean use_pssm, Int4 word_size, Boolean *right_extend, Int4 *s_last_off)

Perform a two-hit extension.

Protein ungapped extension code.

Routines for creating protein BLAST lookup tables.

Routines for creating protein BLAST lookup tables.

Int4 BlastRPSScanSubject(const LookupTableWrap *lookup_wrap, const BLAST_SequenceBlk *sequence, Int4 *offset)

Scans the RPS query sequence from "offset" to the end of the sequence.

Int4(* TAaScanSubjectFunction)(const LookupTableWrap *lookup_wrap, const BLAST_SequenceBlk *subject, BlastOffsetPair *offset_pairs, Int4 max_hits, Int4 *s_range)

Generic prototype for nucleotide subject scanning routines.

#define NUM_FRAMES

Number of frames to which we translate in translating searches.

void Blast_UngappedStatsUpdate(BlastUngappedStats *ungapped_stats, Int4 total_hits, Int4 extended_hits, Int4 saved_hits)

Fill data in the ungapped hits diagnostics structure.

void Blast_InitHitListSortByScore(BlastInitHitList *init_hitlist)

Sort array of initial HSPs by score.

Int2 Blast_ExtendWordExit(Blast_ExtendWord *ewp, Int4 subject_length)

Update the word extension structure after scanning of each subject sequence.

void BlastSaveInitHsp(BlastInitHitList *ungapped_hsps, Int4 q_start, Int4 s_start, Int4 q_off, Int4 s_off, Int4 len, Int4 score)

Add a new initial (ungapped) HSP to an initial hit list.

@ eAaLookupTable

standard protein (blastp) lookup table

Int4 BSearchContextInfo(Int4 n, const BlastQueryInfo *A)

Search BlastContextInfo structures for the specified offset.

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...

static int lookup(const char *name, const struct lookup_int *table)

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

uint32_t Uint4

4-byte (32-bit) unsigned integer

while(yy_chk[yy_base[yy_current_state]+yy_c] !=yy_current_state)

#define MIN(a, b)

returns smaller of a and b.

Uint1 Boolean

bool replacment for C

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

#define ASSERT

macro for assert.

#define MAX(a, b)

returns larger of a and b.

Structure containing parameters needed for initial word extension.

DiagStruct * hit_level_array

Array to hold latest hits and their lengths for all diagonals.

Int4 diag_mask

Used to mask off everything above min_diag_length (mask = min_diag_length-1).

Boolean multiple_hits

Used by BlastExtendWordNew to decide whether or not to prepare the structure for multiple-hit type se...

Int4 window

The "window" size, within which two (or more) hits must be found in order to be extended.

Int4 offset

"offset" added to query and subject position so that "last_hit" doesn't have to be zeroed out every t...

Structure to hold a sequence.

The basic lookup table structure for blastp searches.

The lookup table structure for protein searches using a compressed alphabet.

Int4 query_offset

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

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

Int4 total

Total number of hits currently saved.

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

BlastUngappedCutoffs * cutoffs

cutoff values (one per context)

The query related information.

BlastContextInfo * contexts

Information per context.

The basic lookup table structure for RPS blast searches.

All the ungapped cutoff values that can change from context to context.

Int4 cutoff_score

Cutoff score for saving ungapped hits.

Int4 x_dropoff

Raw X-dropoff value used in the ungapped extension.

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

Structure for keeping initial word extension information.

BLAST_DiagTable * diag_table

Diagonal array and related parameters.

Structure for keeping last hit information for a diagonal.

signed int last_hit

Offset of the last hit.

unsigned int flag

Reset the next extension?

Wrapper structure for different types of BLAST lookup tables.

void * lut

Pointer to the actual lookup table structure.

ELookupTableType lut_type

What kind of a lookup table it is?

structure used for bucket sorting offsets retrieved from the RPS blast lookup table.

Int4 num_filled

number of offset pairs currently in bucket

BlastOffsetPair * offset_pairs

list of offset pairs

This symbol enables the verbose option in makeblastdb and other BLAST+ search command line applicatio...

Uint4 q_off

Query offset.

Uint4 s_off

Subject offset.

struct BlastOffsetPair::@6 qs_offsets

Query/subject offset pair.

static CS_CONTEXT * context

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