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

compressed_alphabet_size,

*scaled_compress_table =

->scaled_compress_table;

(

= 0;

< wordsize;

++) {

ch = scaled_compress_table[word[

]];

index = index / compressed_alphabet_size + ch;

Int2 RPSLookupTableNew(const BlastRPSInfo *rps_info, BlastRPSLookupTable **lut)

Create a new RPS blast lookup table.

struct BlastCompressedAaLookupTable BlastCompressedAaLookupTable

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

#define COMPRESSED_HITS_PER_OVERFLOW_CELL

number of query offsets to store in an overflow cell

struct AaLookupSmallboneCell AaLookupSmallboneCell

structure defining one cell of the small (i.e., use short) lookup table

Int4 BlastCompressedAaLookupTableNew(BLAST_SequenceBlk *query, BlastSeqLoc *locations, BlastCompressedAaLookupTable **lut, const LookupTableOptions *opt, BlastScoreBlk *sbp)

Create a new compressed protein lookup table.

struct CompressedLookupBackboneCell CompressedLookupBackboneCell

structure for hashtable of indexed query offsets

BlastCompressedAaLookupTable * BlastCompressedAaLookupTableDestruct(BlastCompressedAaLookupTable *lookup)

Free the compressed lookup table.

BlastAaLookupTable * BlastAaLookupTableDestruct(BlastAaLookupTable *lookup)

Free the lookup table.

#define COMPRESSED_HITS_PER_BACKBONE_CELL

number of query offsets to store in a backbone cell

BlastRPSLookupTable * RPSLookupTableDestruct(BlastRPSLookupTable *lookup)

Free the lookup table.

struct CompressedMixedOffsets CompressedMixedOffsets

"alternative" structure of CompressedLookupBackboneCell storage

void BlastAaLookupIndexQuery(BlastAaLookupTable *lookup, Int4 **matrix, BLAST_SequenceBlk *query, BlastSeqLoc *unmasked_regions, Int4 query_bias)

Index a protein query.

#define AA_HITS_PER_CELL

maximum number of hits in one lookup table cell

struct RPSBucket RPSBucket

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

struct CompressedOverflowCell CompressedOverflowCell

cell in list for holding query offsets

struct RPSBackboneCell RPSBackboneCell

structure defining one cell of the RPS lookup table

struct BlastAaLookupTable BlastAaLookupTable

The basic lookup table structure for blastp searches.

struct AaLookupBackboneCell AaLookupBackboneCell

structure defining one cell of the compacted lookup table

struct BlastRPSLookupTable BlastRPSLookupTable

The basic lookup table structure for RPS blast searches.

#define RPS_HITS_PER_CELL

maximum number of hits in an RPS backbone cell; this may be redundant (have the same value as AA_HITS...

Int4 BlastAaLookupFinalize(BlastAaLookupTable *lookup, EBoneType bone_type)

Pack the data structures comprising a protein lookup table into their final form.

Int4 BlastAaLookupTableNew(const LookupTableOptions *opt, BlastAaLookupTable **lut)

Create a new protein lookup table.

static NCBI_INLINE Int4 s_ComputeCompressedIndex(Int4 wordsize, const Uint1 *word, Int4 compressed_alphabet_size, Int4 *skip, BlastCompressedAaLookupTable *lookup)

Convert a word to use a compressed alphabet.

Definitions used throughout BLAST.

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

Common definitions for protein and nucleotide lookup tables.

#define PV_ARRAY_TYPE

The pv_array 'native' type.

The structures and functions in blast_options.

RPS BLAST structure definitions.

Definitions and prototypes used by blast_stat.c to calculate BLAST statistics.

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

uint16_t Uint2

2-byte (16-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,...

Uint1 Boolean

bool replacment for C

structure defining one cell of the compacted lookup table

union AaLookupBackboneCell::@3 payload

union that specifies either entries stored right on the backbone if fewer than AA_HITS_PER_CELL are p...

Int4 entries[3]

if the number of hits for this cell is AA_HITS_PER_CELL or less, the hits are all stored directly in ...

Int4 overflow_cursor

integer offset into the overflow array where the list of hits for this cell begins

Int4 num_used

number of hits stored for this cell

structure defining one cell of the small (i.e., use short) lookup table

union AaLookupSmallboneCell::@4 payload

union that specifies either entries stored right on the backbone if fewer than AA_HITS_PER_CELL are p...

Uint2 num_used

number of hits stored for this cell

Int4 overflow_cursor

integer offset into the overflow array where the list of hits for this cell begins

Uint2 entries[3]

if the number of hits for this cell is AA_HITS_PER_CELL or less, the hits are all stored directly in ...

Structure to hold a sequence.

The basic lookup table structure for blastp searches.

void * thick_backbone

may point to BackboneCell, SmallboneCell, or TinyboneCell.

Int4 mask

part of index to mask off, that is, top (wordsize*charsize) bits should be discarded.

Int4 ** thin_backbone

the "thin" backbone.

Boolean use_pssm

if TRUE, lookup table construction will assume that the underlying score matrix is position- specific

Int4 lut_word_length

Length in bases of a word indexed by the lookup table.

Int4 charsize

number of bits for a base/residue

void * scansub_callback

function for scanning subject sequences

EBoneType bone_type

type of bone used: 0: normal backbone (using Int4) 1: small backbone (using Uint2) will be determined...

PV_ARRAY_TYPE * pv

Presence vector bitfield; bit positions that are set indicate that the corresponding thick backbone c...

Int4 neighbor_matches

the number of neighboring words found while indexing the queries, used for informational/ debugging p...

Int4 threshold

the score threshold for neighboring words

Int4 overflow_size

Number of elements in the overflow array.

Int4 alphabet_size

number of letters in the alphabet

Int4 word_length

Length in letters of the full word match required to trigger extension.

Int4 longest_chain

length of the longest chain on the backbone

void * overflow

may point to Int4 or Uint2, the overflow array for the compacted lookup table

Int4 backbone_size

number of cells in the backbone

Int4 exact_matches

the number of exact matches found while indexing the queries, used for informational/ debugging purpo...

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

Int4 pv_array_bts

bit-to-shift value for PV array indicies

Int4 longest_chain

length of the longest chain on the backbone

void * scansub_callback

function for scanning subject sequences

Int4 threshold

the score threshold for neighboring words

Int4 neighbor_matches

the number of neighboring words found while indexing the queries, used for informational/ debugging p...

Int4 exact_matches

the number of exact matches found while indexing the queries, used for informational/ debugging purpo...

Int4 alphabet_size

number of letters in the alphabet

PV_ARRAY_TYPE * pv

Presence vector bitfield; bit positions that are set indicate that the corresponding thick backbone c...

Int4 reciprocal_alphabet_size

2^32 / compressed_alphabet_size

Uint1 * compress_table

translation table (protein->compressed)

Int4 * scaled_compress_table

scaled version of compress_table

CompressedLookupBackboneCell * backbone

hashtable for storing indexed query offsets

Int4 compressed_alphabet_size

letters in the compressed alphabet

Int4 word_length

Length in letters of the full word match required to trigger extension.

Int4 curr_overflow_bank

current bank to fill-up

Int4 backbone_size

number of cells in the backbone

CompressedOverflowCell ** overflow_banks

array of batches of query offsets that are too numerous to fit in backbone cells

Int4 curr_overflow_cell

occupied cells in the current bank

The RPS engine uses this structure to access all of the RPS blast related data (assumed to be collect...

The basic lookup table structure for RPS blast searches.

Int4 * overflow

the overflow array for the compacted lookup table

RPSBucket * bucket_array

list of buckets

Int4 num_buckets

number of buckets used to sort offsets retrieved from the lookup table

RPSBackboneCell * rps_backbone

the lookup table used for RPS blast

Int4 overflow_size

Number of elements in the overflow array.

Int4 mask

part of index to mask off, that is, top (wordsize*charsize) bits should be discarded.

Int4 charsize

number of bits for a base/residue

Int4 alphabet_size

number of letters in the alphabet

Int4 num_profiles

Number of profiles in RPS database.

Int4 wordsize

number of full bytes in a full word

PV_ARRAY_TYPE * pv

Presence vector bitfield; bit positions that are set indicate that the corresponding thick backbone c...

Int4 backbone_size

number of cells in the backbone

Int4 * rps_seq_offsets

array of start offsets for each RPS DB seq.

Int4 ** rps_pssm

Pointer to memory-mapped RPS Blast profile file.

Structure used for scoring calculations.

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

structure for hashtable of indexed query offsets

Int4 query_offsets[4]

storage for query offsets local to the backbone cell

CompressedMixedOffsets overflow_list

storage for remote query offsets

union CompressedLookupBackboneCell::@5 payload

structure for holding the list of query offsets

"alternative" structure of CompressedLookupBackboneCell storage

Int4 query_offsets[4 -2]

the query offsets stored locally

CompressedOverflowCell * head

head of linked list of cells of query offsets stored off the backbone

cell in list for holding query offsets

struct CompressedOverflowCell * next

pointer to next cell

Int4 query_offsets[4]

the query offsets stored in the cell

Options needed to construct a lookup table Also needed: query sequence and query length.

structure defining one cell of the RPS lookup table

Int4 num_used

number of hits in this cell

Int4 entries[3]

if the number of hits in this cell is RPS_HITS_PER_CELL or less, all hits go into this array.

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

Int4 num_filled

number of offset pairs currently in bucket

Int4 num_alloc

max number of offset pairs bucket can hold

BlastOffsetPair * offset_pairs

list of offset pairs

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

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