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NCBI C++ ToolKit: include/algo/blast/core/blast_lookup.h Source File

31 #ifndef ALGO_BLAST_CORE__BLAST_LOOKUP__H 32 #define ALGO_BLAST_CORE__BLAST_LOOKUP__H 41 #define PV_ARRAY_TYPE Uint4 42 #define PV_ARRAY_BYTES 4 43 #define PV_ARRAY_BTS 5 44 #define PV_ARRAY_MASK 31 49 #define PV_SET(lookup, index, shift) \ 50  lookup[(index) >> (shift)] |= (PV_ARRAY_TYPE)1 << ((index) & PV_ARRAY_MASK) 55 #define PV_TEST(lookup, index, shift) \ 56  ( lookup[(index) >> (shift)] & \ 57  ((PV_ARRAY_TYPE)1 << ((index) & PV_ARRAY_MASK)) ) 103  for

(

i

= 0;

i

< wordsize;

i

++) {

104

index = (index << charsize) |

word

[

i

];

127  return

((index << charsize) |

word

[wordsize - 1]) &

mask

;

178  Int4

lut_word_length,

Definitions used throughout BLAST.

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

Add a single query offset to a generic lookup table.

BackboneCell * BackboneCellFree(BackboneCell *cell)

struct BackboneCell BackboneCell

Thin backbone cell for nucleotide lookup table with hashed words.

static NCBI_INLINE Int4 ComputeTableIndexIncremental(Int4 wordsize, Int4 charsize, Int4 mask, const Uint1 *word, Int4 index)

Given a word, compute its index value, reusing a previously computed index value.

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.

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.

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, Uint4 *pv_array)

Add all applicable query offsets to a hashed lookup table.

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

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

#define PV_ARRAY_TYPE

The pv_array 'native' type.

ncbi::TMaskedQueryRegions mask

uint8_t Uint1

1-byte (8-bit) unsigned integer

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

Type and macro definitions from C toolkit that are not defined in C++ toolkit.

#define NCBI_INLINE

"inline" seems to work on our remaining in-house compilers (WorkShop, Compaq, ICC,...

static PCRE2_SIZE * offsets

Structure to hold a sequence.

Thin backbone cell for nucleotide lookup table with hashed words.

struct BackboneCell * next

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

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