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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/lookup__wrap_8c_source.html below:

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

lookup_segments, sbp, lookup_wrap_ptr,

rps_info, error_msg, seqsrc, 1);

*lookup_wrap_ptr = lookup_wrap =

( lookup_options->

) {

, lookup_segments, 0);

lookup_options, sbp);

num_table_entries;

lookup_options, num_table_entries,

max_q_off, &lut_width);

lookup_options, query_options,

num_table_entries, lut_width,

lookup_options, query_options, lut_width);

lookup_options, query_options, lut_width);

lookup_options, query_options, seqsrc,

lookup_options, query_options, lut_width);

(&lookup_wrap->

));

alphabet_size =

->alphabet_size;

(

->lut_type) {

offset_array_size;

(

->lut_type) {

offset_array_size;

Routines for creating protein BLAST lookup tables.

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

Create a new RPS blast lookup table.

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

Create a new compressed protein lookup table.

BlastCompressedAaLookupTable * BlastCompressedAaLookupTableDestruct(BlastCompressedAaLookupTable *lookup)

Free the compressed lookup table.

BlastAaLookupTable * BlastAaLookupTableDestruct(BlastAaLookupTable *lookup)

Free the lookup table.

BlastRPSLookupTable * RPSLookupTableDestruct(BlastRPSLookupTable *lookup)

Free the lookup table.

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

Index a protein query.

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.

#define sfree(x)

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

Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent ...

BLAST filtering functions.

void Blast_MaskUnsupportedAA(BLAST_SequenceBlk *seq, Uint1 min_invalid)

Mask protein letters that are currently unsupported.

Routines for creating nucleotide BLAST lookup tables.

BlastSmallNaLookupTable * BlastSmallNaLookupTableDestruct(BlastSmallNaLookupTable *lookup)

Free a small nucleotide lookup table.

Int4 BlastNaLookupTableNew(BLAST_SequenceBlk *query, BlastSeqLoc *locations, BlastNaLookupTable **lut, const LookupTableOptions *opt, const QuerySetUpOptions *query_options, Int4 lut_width)

Create a new nucleotide lookup table.

ELookupTableType BlastChooseNaLookupTable(const LookupTableOptions *lookup_options, Int4 approx_table_entries, Int4 query_length, Int4 *lut_width)

choose the type of nucleotide lookup table to be used for a blast search

BlastMBLookupTable * BlastMBLookupTableDestruct(BlastMBLookupTable *mb_lt)

Deallocate memory used by the Mega BLAST lookup table.

BlastNaHashLookupTable * BlastNaHashLookupTableDestruct(BlastNaHashLookupTable *lookup)

Free a nucleotide lookup table.

Int2 BlastMBLookupTableNew(BLAST_SequenceBlk *query, BlastSeqLoc *location, BlastMBLookupTable **mb_lt_ptr, const LookupTableOptions *lookup_options, const QuerySetUpOptions *query_options, Int4 approx_table_entries, Int4 lut_width, BlastSeqSrc *seqsrc)

Create the lookup table for Mega BLAST.

Int4 BlastNaHashLookupTableNew(BLAST_SequenceBlk *query, BlastSeqLoc *locations, BlastNaHashLookupTable **lut, const LookupTableOptions *opt, const QuerySetUpOptions *query_options, BlastSeqSrc *seqsrc, Uint4 num_threads)

Int4 BlastSmallNaLookupTableNew(BLAST_SequenceBlk *query, BlastSeqLoc *locations, BlastSmallNaLookupTable **lut, const LookupTableOptions *opt, const QuerySetUpOptions *query_options, Int4 lut_width)

Create a new small nucleotide lookup table.

BlastNaLookupTable * BlastNaLookupTableDestruct(BlastNaLookupTable *lookup)

Free a nucleotide lookup table.

@ eSmallNaLookupTable

lookup table for blastn with small query

@ eMixedMBLookupTable

use when some volumes are searched with index and some are not

@ eNaLookupTable

blastn lookup table

@ eMBLookupTable

megablast lookup table (includes both contiguous and discontiguous megablast)

@ eIndexedMBLookupTable

use database index as a lookup structure

@ ePhiNaLookupTable

nucleotide lookup table for phi-blast

@ eAaLookupTable

standard protein (blastp) lookup table

@ eCompressedAaLookupTable

compressed alphabet (blastp) lookup table

@ ePhiLookupTable

protein lookup table specialized for phi-blast

@ eRPSLookupTable

RPS lookup table (rpsblast and rpstblastn)

@ eNaHashLookupTable

used for 16-base words

RPS BLAST structure definitions.

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

#define BLASTAA_SIZE

Size of aminoacid alphabet.

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

Utility functions for lookup table generation.

Int4 EstimateNumTableEntries(BlastSeqLoc *location, Int4 *max_off)

Given a list of query locations, estimate the number of words that would need to be added to a lookup...

Int2 LookupTableWrapInit_MT(BLAST_SequenceBlk *query, const LookupTableOptions *lookup_options, const QuerySetUpOptions *query_options, BlastSeqLoc *lookup_segments, BlastScoreBlk *sbp, LookupTableWrap **lookup_wrap_ptr, const BlastRPSInfo *rps_info, Blast_Message **error_msg, BlastSeqSrc *seqsrc, Uint4 num_threads)

Create the lookup table for all query words (possibly multithreaded, depends on implementation).

Int4 GetOffsetArraySize(LookupTableWrap *lookup)

Determine the size of the offsets arrays to be filled by the ScanSubject function.

LookupTableWrap * LookupTableWrapFree(LookupTableWrap *lookup)

Deallocate memory for the lookup table.

Int2 LookupTableWrapInit(BLAST_SequenceBlk *query, const LookupTableOptions *lookup_options, const QuerySetUpOptions *query_options, BlastSeqLoc *lookup_segments, BlastScoreBlk *sbp, LookupTableWrap **lookup_wrap_ptr, const BlastRPSInfo *rps_info, Blast_Message **error_msg, BlastSeqSrc *seqsrc)

Create the lookup table for all query words.

Wrapper for all lookup tables used in BLAST.

#define OFFSET_ARRAY_SIZE

Default size of offset arrays filled in a single ScanSubject call.

Uint1 Boolean

bool replacment for C

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

#define INT2_MAX

largest number represented by signed (two byte) short

#define ASSERT

macro for assert.

Pseudo lookup table structure and database scanning functions used in PHI-BLAST.

SPHIPatternSearchBlk * SPHIPatternSearchBlkFree(SPHIPatternSearchBlk *pattern_blk)

Deallocate memory for the PHI BLAST lookup table.

Int2 SPHIPatternSearchBlkNew(char *pattern, Boolean is_dna, BlastScoreBlk *sbp, SPHIPatternSearchBlk **pattern_blk, Blast_Message **error_msg)

Initialize the pattern items structure, serving as a "pseudo" lookup table in a PHI BLAST search.

Structure to hold a sequence.

The basic lookup table structure for blastp searches.

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

The lookup table structure used for Mega BLAST.

The basic lookup table structure for blastn searches.

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.

Structure used for scoring calculations.

SPsiBlastScoreMatrix * psi_matrix

PSSM and associated data.

SBlastScoreMatrix * matrix

scoring matrix data

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

Complete type definition of Blast Sequence Source ADT.

Lookup table structure for blastn searches with small queries.

Structure to hold the a message from the core of the BLAST engine.

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

char * phi_pattern

PHI-BLAST pattern.

ELookupTableType lut_type

What kind of lookup table to construct?

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?

Options required for setting up the query sequence.

int ** data

actual scoring matrix data, stored in row-major form

Structure containing all auxiliary information needed in a pattern search.

SBlastScoreMatrix * pssm

position-specific score matrix

voidp calloc(uInt items, uInt size)

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