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

diag_array_length;

diag_array_length = 1;

diag_array_length = diag_array_length << 1;

diag_table->

= diag_array_length-1;

(

= 0;

<

;

++) {

diag_struct_array[

].

= 0;

(index = 0; index < init_hitlist->

; ++index)

init_hitlist->

= 0;

(init_hitlist ==

)

(init_hitlist);

(index = 0; index < init_hitlist->

- 1; ++index) {

&init_hsp_array[index + 1]) > 0)

num = init_hitlist->

;

(num >= num_avail) {

realloc(match_array, num_avail *

(

));

init_hitlist->

++;

ungapped_data->

= q_start;

ungapped_data->

= s_start;

ungapped_data->

= score;

#define sfree(x)

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

#define BLAST_CMP(a, b)

A macro expression that returns 1, 0, -1 if a is greater than, equal to or less than b,...

static int score_compare_match(const void *v1, const void *v2)

Callback for sorting an array of initial HSP structures (not pointers to structures!...

void BlastInitHitListReset(BlastInitHitList *init_hitlist)

Free the ungapped data substructures and reset initial HSP count to 0.

BlastInitHitList * BLAST_InitHitListNew(void)

Allocate memory for the BlastInitHitList structure.

Boolean BLAST_SaveInitialHit(BlastInitHitList *init_hitlist, Int4 q_off, Int4 s_off, BlastUngappedData *ungapped_data)

Save the initial hit data into the initial hit list structure.

static BLAST_DiagHash * s_BlastDiagHashFree(BLAST_DiagHash *hash_table)

Deallocate memory for the hash table 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 BlastInitHitListMove(BlastInitHitList *dst, BlastInitHitList *src)

Move the contents of a BlastInitHitList structure.

static BLAST_DiagTable * s_BlastDiagTableNew(Int4 qlen, Boolean multiple_hits, Int4 window_size)

Allocates memory for the BLAST_DiagTable*.

static BLAST_DiagTable * s_BlastDiagTableFree(BLAST_DiagTable *diag_table)

Deallocate memory for the diagonal table structure.

Blast_ExtendWord * BlastExtendWordFree(Blast_ExtendWord *ewp)

Deallocate memory for the word extension structure.

Boolean Blast_InitHitListIsSortedByScore(BlastInitHitList *init_hitlist)

Check if array of initial HSPs is sorted by score.

static void s_BlastInitHitListClean(BlastInitHitList *hi)

empty an init hitlist but do not deallocate the base structure

BlastInitHitList * BLAST_InitHitListFree(BlastInitHitList *init_hitlist)

Free memory for the BlastInitList structure.

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.

static Int4 s_BlastDiagClear(BLAST_DiagTable *diag)

Reset the diagonal array structure.

Int2 BlastExtendWordNew(Uint4 query_length, const BlastInitialWordParameters *word_params, Blast_ExtendWord **ewp_ptr)

Initializes the word extension structure.

Ungapped extension structures that are common to nucleotide and protein extension routines.

#define DIAGHASH_CHAIN_LENGTH

Default hash chain length.

#define DIAGHASH_NUM_BUCKETS

Number of hash buckets in BLAST_DiagHash.

#define MIN_INIT_HITLIST_SIZE

Minimal size of an array of initial word hits, allocated up front.

The structures and functions in blast_options.

@ eDiagHash

use hash table (blastn only)

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

#define INT4_MAX

largest nubmer represented by signed int

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.

Track initial word matches using hashing with chaining.

Int4 window

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

Uint4 occupancy

Number of occupied elements.

Uint4 capacity

Total number of elements.

DiagHashCell * chain

Array of data cells.

Uint4 * backbone

Array of offsets to heads of chains.

Int4 offset

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

Uint4 num_buckets

Number of buckets to be used for storing hit offsets.

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_array_length

Smallest power of 2 longer than query length.

Int4 diag_mask

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

Uint1 * hit_len_array

Array to hold the lengthof the latest hit.

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 the initial HSP information.

BlastUngappedData * ungapped_data

Pointer to a structure holding ungapped alignment information.

BlastOffsetPair offsets

Offsets in query and subject, or, in PHI BLAST, start and end of pattern in subject.

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

Int4 allocated

Available size of the offsets array.

Int4 total

Total number of hits currently saved.

Boolean do_not_reallocate

Can the init_hsp_array be reallocated?

BlastInitHSP * init_hsp_array

Array of offset pairs, possibly with scores.

Int4 window_size

Maximal allowed distance between 2 hits in case 2 hits are required to trigger the extension.

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

BlastInitialWordOptions * options

The original (unparsed) options.

ESeedContainerType container_type

How to store offset pairs for initial seeds?

Structure to hold ungapped alignment information.

Int4 score

Score of the ungapped alignment.

Int4 length

Length of the ungapped alignment.

Int4 q_start

Start of the ungapped alignment in query.

Int4 s_start

Start of the ungapped alignment in subject.

Structure for keeping initial word extension information.

BLAST_DiagHash * hash_table

Hash table and related parameters.

BLAST_DiagTable * diag_table

Diagonal array and related parameters.

Structure for keeping last hit information for a diagonal in a hash table, when eRight or eRightAndLe...

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?

Uint4 q_off

Query offset.

Uint4 s_off

Subject offset.

struct BlastOffsetPair::@6 qs_offsets

Query/subject offset pair.

voidp calloc(uInt items, uInt size)

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