Default implementation of the BlastHSPWriter interface to save hits from a BLAST search, and subsequently return them in sorted order. More...

#include <algo/blast/core/hspfilter_collector.h>
#include <algo/blast/core/blast_util.h>
#include "blast_hits_priv.h"

Include dependency graph for hspfilter_collector.c:

Go to the source code of this file.

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Classes
struct	BlastHSPCollectorData
	Data structure used by the writer. More...

Typedefs
typedef struct BlastHSPCollectorData	BlastHSPCollectorData
	Data structure used by the writer. More...

Functions
static int	s_BlastHSPCollectorInit (void data, void hsp_results)
	The following are implementations for BlastHSPWriter ADT. More...

static int	s_BlastHSPCollectorFinal (void data, void results)
	Perform post-run clean-ups. More...

static int	s_BlastHSPCollectorRun (void data, BlastHSPList hsp_list)
	Perform writing task ownership of the HSP list and sets the dereferenced pointer to NULL. More...

static int	s_ScoreCompareHSPWithContext (const void h1, const void h2)
	Callback used for sorting HSPs by score, with HSPs from different contexts segregated from each other. More...

static int	s_BlastHSPCollectorRun_RPS (void data, BlastHSPList hsplist_in)
	Perform writing task for RPS case For RPS BLAST saving procedure is different, because HSPs from different subjects are bundled in one HSP list ownership of the HSP list and sets the dereferenced pointer to NULL. More...

static BlastHSPWriter *	s_BlastHSPCollectorFree (BlastHSPWriter *writer)
	Free the writer. More...

static BlastHSPWriter *	s_BlastHSPCollectorNew (void params, BlastQueryInfo query_info, BLAST_SequenceBlk *sequence)
	create the writer More...

BlastHSPCollectorParams *	BlastHSPCollectorParamsNew (const BlastHitSavingOptions *hit_options, Int4 compositionBasedStats, Boolean gapped_calculation)
	The following are exported functions to be used by APP. More...

BlastHSPCollectorParams *	BlastHSPCollectorParamsFree (BlastHSPCollectorParams *opts)
	Deallocates the BlastHSPCollectorParams structure passed in. More...

BlastHSPWriterInfo *	BlastHSPCollectorInfoNew (BlastHSPCollectorParams *params)
	WriterInfo to create a default writer: the collecter. More...

Detailed Description

Default implementation of the BlastHSPWriter interface to save hits from a BLAST search, and subsequently return them in sorted order.

Definition in file hspfilter_collector.c.

Typedef Documentation

◆ BlastHSPCollectorData

typedef struct BlastHSPCollectorData BlastHSPCollectorData

Data structure used by the writer.

Function Documentation

◆ BlastHSPCollectorInfoNew()

BlastHSPWriterInfo* BlastHSPCollectorInfoNew ( BlastHSPCollectorParams * params )

WriterInfo to create a default writer: the collecter.

Parameters

params The collector parameters.

Returns: pointer to WriterInfo

Definition at line 353 of file hspfilter_collector.c.

References malloc(), BlastHSPWriterInfo::NewFnPtr, BlastHSPWriterInfo::params, and s_BlastHSPCollectorNew().

Referenced by BOOST_AUTO_TEST_CASE(), CSetupFactory::CreateHspWriter(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), testHSPStream(), CTracebackSearchTestFixture::x_GetSampleHspStream(), CTracebackSearchTestFixture::x_GetSelfHitHspStream(), and CTracebackTestFixture::x_MakeStream().

◆ BlastHSPCollectorParamsFree()

BlastHSPCollectorParams* BlastHSPCollectorParamsFree ( BlastHSPCollectorParams * opts )

Deallocates the BlastHSPCollectorParams structure passed in.

Parameters

opts	structure to deallocate [in]

Returns: NULL

Definition at line 344 of file hspfilter_collector.c.

References NULL, and sfree.

Referenced by BlastHSPCullingParamsNew().

◆ BlastHSPCollectorParamsNew()

BlastHSPCollectorParams* BlastHSPCollectorParamsNew	(	const BlastHitSavingOptions *	hit_options,
		Int4	compositionBasedStats,
		Boolean	gapped_calculation
	)

The following are exported functions to be used by APP.

Sets up parameter set for use by collector.

Definition at line 325 of file hspfilter_collector.c.

References BlastHspNumMax(), GetPrelimHitlistSize(), BlastHitSavingOptions::hitlist_size, BlastHSPCollectorParams::hsp_num_max, malloc(), NULL, BlastHSPCollectorParams::prelim_hitlist_size, BlastHSPCollectorParams::program, and BlastHitSavingOptions::program_number.

Referenced by BlastHSPCullingParamsNew(), BOOST_AUTO_TEST_CASE(), CSetupFactory::CreateHspWriter(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), testHSPStream(), CTracebackSearchTestFixture::x_GetSampleHspStream(), CTracebackSearchTestFixture::x_GetSelfHitHspStream(), and CTracebackTestFixture::x_MakeStream().

◆ s_BlastHSPCollectorFinal()

static int s_BlastHSPCollectorFinal	(	void *	data,
		void *	results
	)

static

Perform post-run clean-ups.

Parameters

data	The buffered data structure [in]
results	The HSP results to propagate [in][out]

Definition at line 68 of file hspfilter_collector.c.

References data, NULL, and BlastHSPCollectorData::results.

Referenced by s_BlastHSPCollectorNew().

◆ s_BlastHSPCollectorFree()

static BlastHSPWriter* s_BlastHSPCollectorFree ( BlastHSPWriter * writer )

static

Free the writer.

Parameters

writer The writer to free [in]

Returns: NULL.

Definition at line 279 of file hspfilter_collector.c.

References BlastHSPWriter::data, data, NULL, and sfree.

Referenced by s_BlastHSPCollectorNew().

◆ s_BlastHSPCollectorInit()

static int s_BlastHSPCollectorInit	(	void *	data,
		void *	hsp_results
	)

static

The following are implementations for BlastHSPWriter ADT.

Perform pre-run stage-specific initialization

Parameters

data	The internal data structure [in][out]
results	The HSP results to operate on [in]

Definition at line 54 of file hspfilter_collector.c.

References data, BlastHSPCollectorData::results, and results.

Referenced by s_BlastHSPCollectorNew().

◆ s_BlastHSPCollectorNew()

static BlastHSPWriter* s_BlastHSPCollectorNew	(	void *	params,
		BlastQueryInfo *	query_info,
		BLAST_SequenceBlk *	sequence
	)

static

create the writer

Parameters

params	Pointer to the hit paramters [in]
query_info	BlastQueryInfo (not used) [in]

Returns: writer

Definition at line 295 of file hspfilter_collector.c.

References Blast_ProgramIsRpsBlast(), BlastHSPWriter::data, data, BlastHSPWriter::FinalFnPtr, BlastHSPWriter::FreeFnPtr, BlastHSPWriter::InitFnPtr, malloc(), NULL, BlastHSPCollectorParams::program, BlastHSPWriter::RunFnPtr, s_BlastHSPCollectorFinal(), s_BlastHSPCollectorFree(), s_BlastHSPCollectorInit(), s_BlastHSPCollectorRun(), and s_BlastHSPCollectorRun_RPS().

Referenced by BlastHSPCollectorInfoNew().

◆ s_BlastHSPCollectorRun()

static int s_BlastHSPCollectorRun	(	void *	data,
		BlastHSPList *	hsp_list
	)

static

Perform writing task ownership of the HSP list and sets the dereferenced pointer to NULL.

Parameters

data	To store results to [in][out]
hsp_list	Pointer to the HSP list to save in the collector. [in]

Definition at line 82 of file hspfilter_collector.c.

References Blast_GetQueryIndexFromContext(), Blast_HitListNew(), Blast_HitListUpdate(), Blast_HSPListFree(), Blast_HSPListIsSortedByScore(), Blast_HSPListNew(), Blast_HSPListSaveHSP(), calloc(), BlastHSP::context, data, ErrPostEx, BlastHSPList::hsp_array, BlastHSPCollectorParams::hsp_num_max, BlastHSPList::hspcnt, NULL, BlastHSPList::oid, BlastHSPCollectorData::params, BlastHSPCollectorParams::prelim_hitlist_size, BlastHSPCollectorParams::program, BlastHSPCollectorData::results, results, SEV_WARNING, and sfree.

Referenced by s_BlastHSPCollectorNew().

◆ s_BlastHSPCollectorRun_RPS()

static int s_BlastHSPCollectorRun_RPS	(	void *	data,
		BlastHSPList *	hsplist_in
	)

static

Perform writing task for RPS case For RPS BLAST saving procedure is different, because HSPs from different subjects are bundled in one HSP list ownership of the HSP list and sets the dereferenced pointer to NULL.

Parameters

data	To store results to [in][out]
hsp_list	Pointer to the HSP list to save in the collector. [in]

Definition at line 204 of file hspfilter_collector.c.

References ASSERT, Blast_HitListNew(), Blast_HitListUpdate(), Blast_HSPListFree(), Blast_HSPListIsSortedByScore(), Blast_HSPListNew(), Blast_HSPListSaveHSP(), Blast_ProgramIsRpsBlast(), BlastHSP::context, data, BlastHSPList::hsp_array, BlastHSPList::hspcnt, BlastHSPList::oid, BlastHSPCollectorData::params, BlastHSPCollectorParams::prelim_hitlist_size, BlastHSPCollectorParams::program, BlastHSPList::query_index, BlastHSPCollectorData::results, results, and s_ScoreCompareHSPWithContext().

Referenced by s_BlastHSPCollectorNew().

◆ s_ScoreCompareHSPWithContext()

static int s_ScoreCompareHSPWithContext	(	const void *	h1,
		const void *	h2
	)

static

Callback used for sorting HSPs by score, with HSPs from different contexts segregated from each other.

Definition at line 174 of file hspfilter_collector.c.

References BLAST_CMP, BlastHSP::context, result, and ScoreCompareHSPs().

Referenced by s_BlastHSPCollectorRun_RPS().

Classes

Typedefs

Functions

Detailed Description

Typedef Documentation

◆ BlastHSPCollectorData

Function Documentation

◆ BlastHSPCollectorInfoNew()

◆ BlastHSPCollectorParamsFree()

◆ BlastHSPCollectorParamsNew()

◆ s_BlastHSPCollectorFinal()

◆ s_BlastHSPCollectorFree()

◆ s_BlastHSPCollectorInit()

◆ s_BlastHSPCollectorNew()

◆ s_BlastHSPCollectorRun()

◆ s_BlastHSPCollectorRun_RPS()

◆ s_ScoreCompareHSPWithContext()