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

(diagnostics ==

) {

memcpy((

*)retval->

, (

*)diagnostics->

,

total_hits,

extended_hits,

(!ungapped_stats || total_hits == 0)

->ungapped_stat->lookup_hits;

->ungapped_stat->num_seqs_lookup_hits;

->ungapped_stat->init_extends;

->ungapped_stat->good_init_extends;

->ungapped_stat->num_seqs_passed;

->gapped_stat->seqs_ungapped_passed;

->gapped_stat->extensions;

->gapped_stat->good_extensions;

->gapped_stat->num_seqs_passed;

Definitions used throughout BLAST.

#define sfree(x)

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

BlastDiagnostics * Blast_DiagnosticsInitMT(MT_LOCK mt_lock)

Initialize the BlastDiagnostics structure for a multi-threaded search.

void Blast_UngappedStatsUpdate(BlastUngappedStats *ungapped_stats, Int4 total_hits, Int4 extended_hits, Int4 saved_hits)

Fill data in the ungapped hits diagnostics structure.

BlastDiagnostics * Blast_DiagnosticsFree(BlastDiagnostics *diagnostics)

Free the BlastDiagnostics structure and all substructures.

void Blast_DiagnosticsUpdate(BlastDiagnostics *global, BlastDiagnostics *local)

In a multi-threaded run, update global diagnostics data with the data coming from one of the prelimin...

BlastDiagnostics * Blast_DiagnosticsCopy(const BlastDiagnostics *diagnostics)

Free the BlastDiagnostics structure and all substructures.

BlastDiagnostics * Blast_DiagnosticsInit()

Initialize the BlastDiagnostics structure and all its substructures.

Various diagnostics (hit counts, etc.) returned from the BLAST engine.

int32_t Int4

4-byte (32-bit) signed integer

MT_LOCK MT_LOCK_Delete(MT_LOCK lk)

Decrement internal reference count by 1, and if it reaches 0, then destroy the handle,...

#define MT_LOCK_Do(lk, how)

Call "lk->handler(lk->data, how)".

@ eMT_Unlock

unlock critical section

@ eMT_Lock

lock critical section

Return statistics from the BLAST search.

BlastUngappedStats * ungapped_stat

Ungapped extension counts.

BlastRawCutoffs * cutoffs

Various raw values for the cutoffs.

BlastGappedStats * gapped_stat

Gapped extension counts.

MT_LOCK mt_lock

Mutex for updating diagnostics data in a multi-threaded search.

Structure containing hit counts from the gapped stage of a BLAST search.

Int4 good_extensions

Number of HSPs below the e-value threshold after gapped extension.

Int4 num_seqs_passed

Number of sequences with top HSP passing the e-value threshold.

Int4 seqs_ungapped_passed

Number of sequences with top HSP after ungapped extension passing the e-value threshold.

Int4 extensions

Total number of gapped extensions performed.

Structure holding raw cutoff and gap-x-drop values.

Int4 ungapped_cutoff

Minimal raw score for starting gapped extension.

Int4 x_drop_gap_final

Raw value of the x-dropoff for gapped extensions with traceback.

Int4 x_drop_gap

Raw value of the x-dropoff for preliminary gapped extensions.

Int4 x_drop_ungapped

Raw value of the x-dropoff for ungapped extensions.

Int4 cutoff_score

Cutoff score corresponding to given evalue.

Structure containing hit counts from the ungapped stage of a BLAST search.

Int4 num_seqs_lookup_hits

Number of sequences which had at least one lookup table hit.

Int8 lookup_hits

Number of successful lookup table hits.

Int4 init_extends

Number of initial words found and extended.

Int4 good_init_extends

Number of successful initial extensions, i.e.

Int4 num_seqs_passed

Number of sequences with at least one HSP saved after ungapped stage.

voidp calloc(uInt items, uInt size)

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