Boolean(* TInterruptFnPtr)(SBlastProgress *progress_info)
Prototype for function pointer to determine whether the BLAST search should proceed or be interrupted...
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
Structures and functions prototypes used for BLAST gapped extension.
Declaration of ADT to save and retrieve lists of HSPs in the BLAST engine.
Structure and function definitions for BLAST parameter structures, which are internal to the CORE of ...
EBlastProgramType
Defines the engine's notion of the different applications of the BLAST algorithm.
SThreadLocalData * SThreadLocalDataFree(SThreadLocalData *tld)
Deallocate the SThreadLocalData structure passed in.
struct SThreadLocalData SThreadLocalData
Data structure to support MT traceback: this encapsulates the data that each thread modifies.
void SThreadLocalDataArrayTrim(SThreadLocalDataArray *array, Uint4 actual_num_threads)
Reduce the size of the array structure passed in to match the value of the actual_num_threads paramet...
Int2 SThreadLocalDataArraySetup(SThreadLocalDataArray *array, EBlastProgramType program, const BlastScoringOptions *score_options, const BlastEffectiveLengthsOptions *eff_len_options, const BlastExtensionOptions *ext_options, const BlastHitSavingOptions *hit_options, BlastQueryInfo *query_info, BlastScoreBlk *sbp, const BlastSeqSrc *seqsrc)
Set up a newly allocated SThreadLocalDataArray object so it can be used by multiple threads.
SThreadLocalDataArray * SThreadLocalDataArrayFree(SThreadLocalDataArray *array)
Deallocate the SThreadLocalDataArray structure passed in.
SThreadLocalData * SThreadLocalDataNew()
Allocate a new SThreadLocalData structure.
Int2 BLAST_ComputeTraceback_MT(EBlastProgramType program_number, BlastHSPStream *hsp_stream, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, SThreadLocalDataArray *thread_data, const BlastDatabaseOptions *db_options, const PSIBlastOptions *psi_options, const BlastRPSInfo *rps_info, SPHIPatternSearchBlk *pattern_blk, BlastHSPResults **results, TInterruptFnPtr interrupt_search, SBlastProgress *progress_info)
Identical in function to BLAST_ComputeTraceback, but this performs its task in a multi-threaded manne...
SThreadLocalDataArray * SThreadLocalDataArrayNew(Uint4 num_threads)
Allocate a new SThreadLocalDataArray structure.
BlastHSPResults * SThreadLocalDataArrayConsolidateResults(SThreadLocalDataArray *array)
Extracts a single, consolidated BlastHSPResults structure from its input for single threaded processi...
struct SThreadLocalDataArray SThreadLocalDataArray
int16_t Int2
2-byte (16-bit) signed integer
uint32_t Uint4
4-byte (32-bit) unsigned integer
Structure to hold a sequence.
Options used to create the ReadDBFILE structure Include database name and various information for res...
Options for setting up effective lengths and search spaces.
Parameters for setting up effective lengths and search spaces.
Options used for gapped extension These include: a.
Computed values used as parameters for gapped alignments.
Structure supporting the gapped alignment.
The structure to contain all BLAST results, for multiple queries.
Default implementation of BlastHSPStream.
Options used when evaluating and saving hits These include: a.
Parameter block that contains a pointer to BlastHitSavingOptions and the values derived from it.
The query related information.
The RPS engine uses this structure to access all of the RPS blast related data (assumed to be collect...
Structure used for scoring calculations.
Scoring options block Used to produce the BlastScoreBlk structure This structure may be needed for lo...
Scoring parameters block Contains scoring-related information that is actually used for the blast sea...
Complete type definition of Blast Sequence Source ADT.
Options used in protein BLAST only (PSI, PHI, RPS and translated BLAST) Some of these possibly should...
Progress monitoring structure.
Structure containing all auxiliary information needed in a pattern search.
Data structure to support MT traceback: this encapsulates the data that each thread modifies.
BlastGapAlignStruct * gap_align
BlastHitSavingParameters * hit_params
Hit saving parameters.
BlastScoringParameters * score_params
Scoring parameters, allocated anew in BLAST_GapAlignSetUp.
BlastSeqSrc * seqsrc
BlastSeqSrc so that each thread can set its own partial fetching.
BlastExtensionParameters * ext_params
Gapped extension parameters, allocated anew in BLAST_GapAlignSetUp.
BlastHSPResults * results
Structure to store results from this thread.
BlastEffectiveLengthsParameters * eff_len_params
Parameters for effective lengths calculations.
BlastQueryInfo * query_info
The effective search space is modified.
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