Definitions used throughout BLAST.
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
The structures and functions in blast_options.
ELookupTableType
Types of the lookup table.
RPS BLAST structure definitions.
Declaration of ADT to retrieve sequences for the BLAST engine.
Definitions and prototypes used by blast_stat.c to calculate BLAST statistics.
static int lookup(const char *name, const struct lookup_int *table)
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
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.
struct LookupTableWrap LookupTableWrap
Wrapper structure for different types of BLAST lookup tables.
Boolean(* T_Lookup_Callback)(const LookupTableWrap *, Int4, Int4)
Function pointer type to check the presence of index->q_off pair.
Type and macro definitions from C toolkit that are not defined in C++ toolkit.
Structure to hold a sequence.
The RPS engine uses this structure to access all of the RPS blast related data (assumed to be collect...
Structure used for scoring calculations.
Used to hold a set of positions, mostly used for filtering.
Complete type definition of Blast Sequence Source ADT.
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.
Wrapper structure for different types of BLAST lookup tables.
void * lookup_callback
function used to look up an index->q_off pair
void * lut
Pointer to the actual lookup table structure.
void * end_search_indication
function used to report that a thread is done iterating over the database in preliminary search
void * check_index_oid
function used to check if seeds for a given oid are present
ELookupTableType lut_type
What kind of a lookup table it is?
void * read_indexed_db
function used to retrieve hits from an indexed database
Options required for setting up the query sequence.
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