Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__lookup_8c_source.html below:

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

hits_in_chain = 0;

(backbone[index] ==

) {

chain[0] = chain_size;

chain[1] = hits_in_chain;

backbone[index] = chain;

chain = backbone[index];

chain_size = chain[0];

hits_in_chain = chain[1];

((hits_in_chain + 2) == chain_size) {

chain_size = chain_size * 2;

chain = (

*) realloc(chain, chain_size *

(

));

backbone[index] = chain;

chain[0] = chain_size;

chain[chain[1] + 2] = query_offset;

invalid_mask = 0xff << charsize;

(loc = locations; loc; loc = loc->

) {

(word_length > to - from + 1)

seq =

->sequence + from;

word_target = seq + lut_word_length;

(seq >= word_target) {

lut_word_length, charsize,

seq - lut_word_length,

- lut_word_length);

(*seq & invalid_mask)

word_target = seq + lut_word_length + 1;

(seq >= word_target) {

lut_word_length, charsize,

seq - lut_word_length,

- lut_word_length);

(

= 0;

< wordsize;

++) {

large_index = (large_index << charsize) | seq[

];

(backbone[index].num_offsets == 0) {

(

->next &&

->word != large_index) {

(

->word == large_index) {

lut_word_length,

invalid_mask = 0xff << charsize;

(loc = locations; loc; loc = loc->

) {

(word_length > to - from + 1)

seq =

->sequence + from;

word_target = seq + lut_word_length;

(seq >= word_target) {

lut_word_length, charsize,

seq - lut_word_length,

(*seq & invalid_mask)

word_target = seq + lut_word_length + 1;

(seq >= word_target) {

lut_word_length, charsize,

seq - lut_word_length,

#define sfree(x)

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

void BlastLookupAddWordHit(Int4 **backbone, Int4 wordsize, Int4 charsize, Uint1 *seq, Int4 query_offset)

Add a single query offset to a generic lookup table.

static Int2 s_AddWordHit(BackboneCell *backbone, Int4 *offsets, Int4 wordsize, Int4 charsize, Uint1 *seq, Int4 offset, TNaLookupHashFunction hash_func, Uint4 mask, PV_ARRAY_TYPE *pv_array)

BackboneCell * BackboneCellFree(BackboneCell *cell)

void BlastHashLookupIndexQueryExactMatches(BackboneCell *backbone, Int4 *offsets, Int4 word_length, Int4 charsize, Int4 lut_word_length, BLAST_SequenceBlk *query, BlastSeqLoc *locations, TNaLookupHashFunction hash_func, Uint4 mask, PV_ARRAY_TYPE *pv_array)

BackboneCell * BackboneCellNew(Uint4 word, Int4 offset)

Create a new cell for a given word and offset.

void BlastLookupIndexQueryExactMatches(Int4 **backbone, Int4 word_length, Int4 charsize, Int4 lut_word_length, BLAST_SequenceBlk *query, BlastSeqLoc *locations)

Add all applicable query offsets to a generic lookup table.

Int4 BackboneCellInit(BackboneCell *cell, Uint4 word, Int4 offset)

Initialize an olready allocated cell for a given word and offset.

Common definitions for protein and nucleotide lookup tables.

#define PV_ARRAY_BTS

bits-to-shift from lookup_index to pv_array index.

#define PV_TEST(lookup, index, shift)

Test the bit at position 'index' in the PV array bitfield within 'lookup'.

static NCBI_INLINE Int4 ComputeTableIndex(Int4 wordsize, Int4 charsize, const Uint1 *word)

Given a word, compute its index value from scratch.

Uint4(* TNaLookupHashFunction)(Uint1 *, Uint4)

Hash function type for the lookup table.

#define PV_ARRAY_TYPE

The pv_array 'native' type.

ncbi::TMaskedQueryRegions mask

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

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

int64_t Int8

8-byte (64-bit) signed integer

#define ASSERT

macro for assert.

static PCRE2_SIZE * offsets

Structure to hold a sequence.

Thin backbone cell for nucleotide lookup table with hashed words.

Used to hold a set of positions, mostly used for filtering.

SSeqRange * ssr

location data on the sequence.

struct BlastSeqLoc * next

next in linked list

Int4 left

left endpoint of range (zero based)

Int4 right

right endpoint of range (zero based)

voidp calloc(uInt items, uInt size)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4