blast_setup.h File Reference

Utilities initialize/setup BLAST. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_export.h>
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/blast_query_info.h>
#include <algo/blast/core/blast_options.h>
#include <algo/blast/core/blast_parameters.h>
#include <algo/blast/core/blast_message.h>
#include <algo/blast/core/blast_stat.h>
#include <algo/blast/core/blast_gapalign.h>
#include <algo/blast/core/pattern.h>

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Functions
Int2	BLAST_MainSetUp (EBlastProgramType program_number, const QuerySetUpOptions *qsup_options, const BlastScoringOptions *scoring_options, BLAST_SequenceBlk *query_blk, const BlastQueryInfo *query_info, double scale_factor, BlastSeqLoc **lookup_segments, BlastMaskLoc **mask, BlastScoreBlk **sbpp, Blast_Message **blast_message, GET_MATRIX_PATH get_path)
	"Main" setup routine for BLAST. More...
Int2	Blast_ScoreBlkKbpGappedCalc (BlastScoreBlk *sbp, const BlastScoringOptions *scoring_options, EBlastProgramType program, const BlastQueryInfo *query_info, Blast_Message **error_return)
	Blast_ScoreBlkKbpGappedCalc, fills the ScoreBlkPtr for a gapped search. More...
Int2	BLAST_CalcEffLengths (EBlastProgramType program_number, const BlastScoringOptions *scoring_options, const BlastEffectiveLengthsParameters *eff_len_params, const BlastScoreBlk *sbp, BlastQueryInfo *query_info, Blast_Message **blast_message)
	Function to calculate effective query length and db length as well as effective search space. More...
Int2	BLAST_GapAlignSetUp (EBlastProgramType program_number, const BlastSeqSrc *seq_src, const BlastScoringOptions *scoring_options, const BlastEffectiveLengthsOptions *eff_len_options, const BlastExtensionOptions *ext_options, const BlastHitSavingOptions *hit_options, BlastQueryInfo *query_info, BlastScoreBlk *sbp, BlastScoringParameters **score_params, BlastExtensionParameters **ext_params, BlastHitSavingParameters **hit_params, BlastEffectiveLengthsParameters **eff_len_params, BlastGapAlignStruct **gap_align)
	Set up the auxiliary structures for gapped alignment / traceback only. More...
Int2	BLAST_OneSubjectUpdateParameters (EBlastProgramType program_number, Uint4 subject_length, const BlastScoringOptions *scoring_options, BlastQueryInfo *query_info, const BlastScoreBlk *sbp, BlastHitSavingParameters *hit_params, BlastInitialWordParameters *word_params, BlastEffectiveLengthsParameters *eff_len_params)
	Recalculates the parameters that depend on an individual sequence, if this is not a database search. More...
Int2	Blast_ScoreBlkMatrixInit (EBlastProgramType program_number, const BlastScoringOptions *scoring_options, BlastScoreBlk *sbp, GET_MATRIX_PATH get_path)
	Initializes the substitution matrix in the BlastScoreBlk according to the scoring options specified. More...
Int2	BlastSetup_ScoreBlkInit (BLAST_SequenceBlk *query_blk, const BlastQueryInfo *query_info, const BlastScoringOptions *scoring_options, EBlastProgramType program_number, BlastScoreBlk **sbpp, double scale_factor, Blast_Message **blast_message, GET_MATRIX_PATH get_path)
	Initializes the score block structure. More...
void	BlastSeqLoc_RestrictToInterval (BlastSeqLoc **mask, Int4 from, Int4 to)
	Adjusts the mask locations coordinates to a sequence interval. More...
Int2	Blast_SetPHIPatternInfo (EBlastProgramType program, const SPHIPatternSearchBlk *pattern_blk, const BLAST_SequenceBlk *query, const BlastSeqLoc *lookup_segments, BlastQueryInfo *query_info, Blast_Message **blast_message)
	In a PHI BLAST search, adds pattern information to the BlastQueryInfo structure. More...
void	BLAST_GetSubjectTotals (const BlastSeqSrc *seqsrc, Int8 *total_length, Int4 *num_seqs)
	Auxiliary function to retrieve the subject's number of sequences and total length. More...
Int2	BlastSetup_Validate (const BlastQueryInfo *query_info, const BlastScoreBlk *score_blk)
	Validation function for the setup of queries for the BLAST search. More...

Detailed Description

Utilities initialize/setup BLAST.

Definition in file blast_setup.h.

Function Documentation

BLAST_CalcEffLengths()

Int2 BLAST_CalcEffLengths	(	EBlastProgramType	program_number,
		const BlastScoringOptions *	scoring_options,
		const BlastEffectiveLengthsParameters *	eff_len_params,
		const BlastScoreBlk *	sbp,
		BlastQueryInfo *	query_info,
		Blast_Message **	blast_message
	)

Function to calculate effective query length and db length as well as effective search space.

Parameters

program_number	blastn, blastp, blastx, etc. [in]
scoring_options	options for scoring. [in]
eff_len_params	Used to calculate effective lengths [in]
sbp	Karlin-Altschul parameters [out]
query_info	The query information block, which stores the effective search spaces for all queries [in] [out]
blast_message	Error message [out]

Definition at line 699 of file blast_setup.c.

References BLAST_ComputeLengthAdjustment(), BLAST_GetAlphaBeta(), Blast_GetNuclAlphaBeta(), BLAST_PENALTY, Blast_ProgramIsMapping(), Blast_ProgramIsPhiBlast(), BLAST_REWARD, Blast_SubjectIsTranslated(), BlastEffectiveLengthsOptions_IsSearchSpaceSet(), BlastQueryInfo::contexts, BlastEffectiveLengthsOptions::db_length, BlastEffectiveLengthsOptions::dbseq_num, eBlastTypeBlastn, BlastContextInfo::eff_searchsp, BlastQueryInfo::first_context, BlastScoringOptions::gap_extend, BlastScoringOptions::gap_open, BlastScoringOptions::gapped_calculation, BlastContextInfo::is_valid, Blast_KarlinBlk::K, BlastScoreBlk::kbp, BlastScoreBlk::kbp_gap_std, BlastScoreBlk::kbp_std, Blast_KarlinBlk::Lambda, BlastContextInfo::length_adjustment, Blast_KarlinBlk::logK, BlastScoreBlk::name, BlastEffectiveLengthsParameters::options, BlastScoringOptions::penalty, BlastContextInfo::query_length, BlastEffectiveLengthsParameters::real_db_length, BlastEffectiveLengthsParameters::real_num_seqs, BlastScoringOptions::reward, and s_GetEffectiveSearchSpaceForContext().

Referenced by BLAST_GapAlignSetUp(), BLAST_OneSubjectUpdateParameters(), BOOST_AUTO_TEST_CASE(), CEffectiveSearchSpaceCalculator::CEffectiveSearchSpaceCalculator(), LinkHspTestFixture::fillEffectiveLengths(), CBlastExtendTestFixture::fillEffectiveLengths(), and CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest().

BLAST_GapAlignSetUp()

Int2 BLAST_GapAlignSetUp	(	EBlastProgramType	program_number,
		const BlastSeqSrc *	seq_src,
		const BlastScoringOptions *	scoring_options,
		const BlastEffectiveLengthsOptions *	eff_len_options,
		const BlastExtensionOptions *	ext_options,
		const BlastHitSavingOptions *	hit_options,
		BlastQueryInfo *	query_info,
		BlastScoreBlk *	sbp,
		BlastScoringParameters **	score_params,
		BlastExtensionParameters **	ext_params,
		BlastHitSavingParameters **	hit_params,
		BlastEffectiveLengthsParameters **	eff_len_params,
		BlastGapAlignStruct **	gap_align
	)

Set up the auxiliary structures for gapped alignment / traceback only.

Parameters

program_number	blastn, blastp, blastx, etc. [in]
seq_src	Sequence source information, with callbacks to get sequences, their lengths, etc. [in]
scoring_options	options for scoring. [in]
eff_len_options	Options overriding real database sizes for calculating effective lengths [in]
ext_options	options for gapped extension. [in]
hit_options	options for saving hits. [in]
query_info	The query information block [in]
sbp	Contains scoring information. [in]
score_params	Parameters for scoring [out]
ext_params	Parameters for gapped extension [out]
hit_params	Parameters for saving hits [out]
eff_len_params	Parameters for search space calculations [out]
gap_align	Gapped alignment information and allocated memory [out]

Definition at line 888 of file blast_setup.c.

References BLAST_CalcEffLengths(), BLAST_GapAlignStructNew(), Blast_SubjectIsTranslated(), BlastEffectiveLengthsParametersFree(), BlastEffectiveLengthsParametersNew(), BLASTERR_SUBJECT_LENGTH_INVALID, BlastExtensionParametersFree(), BlastExtensionParametersNew(), BlastHitSavingParametersNew(), BlastScoringParametersFree(), BlastScoringParametersNew(), BlastSeqSrcGetMaxSeqLen(), BlastSeqSrcGetMinSeqLen(), BlastSeqSrcGetNumSeqs(), BlastSeqSrcGetNumSeqsStats(), BlastSeqSrcGetSeqLen(), BlastSeqSrcGetTotLen(), BlastSeqSrcGetTotLenStats(), BlastEffectiveLengthsOptions::db_length, Blast_GumbelBlk::db_length, BlastScoreBlk::gbp, and NULL.

Referenced by Blast_RunFullSearch(), Blast_RunPreliminarySearchWithInterrupt(), SThreadLocalDataArraySetup(), and CTracebackTestFixture::x_SetupGapAlign().

BLAST_GetSubjectTotals()

void BLAST_GetSubjectTotals	(	const BlastSeqSrc *	seqsrc,
		Int8 *	total_length,
		Int4 *	num_seqs
	)

Auxiliary function to retrieve the subject's number of sequences and total length.

Note

In the case of a Blast2Sequences search, this function assumes a single sequence and returns the length of the first sequence only

Definition at line 853 of file blast_setup.c.

References ASSERT, BlastSeqSrcGetNumSeqs(), BlastSeqSrcGetNumSeqsStats(), BlastSeqSrcGetSeqLen(), BlastSeqSrcGetTotLen(), and BlastSeqSrcGetTotLenStats().

BLAST_MainSetUp()

Int2 BLAST_MainSetUp	(	EBlastProgramType	program_number,
		const QuerySetUpOptions *	qsup_options,
		const BlastScoringOptions *	scoring_options,
		BLAST_SequenceBlk *	query_blk,
		const BlastQueryInfo *	query_info,
		double	scale_factor,
		BlastSeqLoc **	lookup_segments,
		BlastMaskLoc **	mask,
		BlastScoreBlk **	sbpp,
		Blast_Message **	blast_message,
		GET_MATRIX_PATH	get_path
	)

"Main" setup routine for BLAST.

Calculates all information for BLAST search that is dependent on the ASN.1 structures.

Parameters

program_number	Type of BLAST program (0=blastn, ...). [in]
qsup_options	options for query setup. [in]
scoring_options	options for scoring. [in]
query_blk	BLAST_SequenceBlk* for the query. [in]
query_info	The query information block [in]
scale_factor	Multiplier for cutoff and dropoff scores [in]
lookup_segments	Start/stop locations for non-masked query segments [out]
mask	masking locations. [out]
sbpp	Contains scoring information. [out]
blast_message	error or warning [out]
get_path	callback function to get matrix path [in]

Definition at line 563 of file blast_setup.c.

References ASSERT, BLAST_ComplementMaskLocations(), BLAST_CreateMixedFrameDNATranslation(), Blast_PerrorWithLocation, Blast_QueryIsTranslated(), BlastFilteringOptionsFromString(), BlastMaskLocFree(), BlastMaskLocProteinToDNA(), BlastSetUp_GetFilteringLocations(), BlastSetUp_MaskQuery(), BlastSetup_ScoreBlkInit(), BlastSetup_Validate(), eBlastTypeBlastx, FALSE, QuerySetUpOptions::filter_string, QuerySetUpOptions::filtering_options, BlastScoringOptions::is_ooframe, kBlastMessageNoContext, mask, NULL, SBlastFilterOptionsFree(), SBlastFilterOptionsMaskAtHash(), and TRUE.

Referenced by BOOST_AUTO_TEST_CASE(), CSetupFactory::CreateScoreBlock(), and CTracebackTestFixture::x_SetupMain().

BLAST_OneSubjectUpdateParameters()

Int2 BLAST_OneSubjectUpdateParameters	(	EBlastProgramType	program_number,
		Uint4	subject_length,
		const BlastScoringOptions *	scoring_options,
		BlastQueryInfo *	query_info,
		const BlastScoreBlk *	sbp,
		BlastHitSavingParameters *	hit_params,
		BlastInitialWordParameters *	word_params,
		BlastEffectiveLengthsParameters *	eff_len_params
	)

Recalculates the parameters that depend on an individual sequence, if this is not a database search.

Parameters

program_number	BLAST program [in]
subject_length	Length of the current subject sequence [in]
scoring_options	Scoring options [in]
query_info	The query information structure. Effective lengths are recalculated here. [in] [out]
sbp	Scoring statistical parameters [in]
hit_params	Parameters for saving hits. Score cutoffs are recalculated here [in] [out]
word_params	Parameters for ungapped extension. Score cutoffs are recalculated here [in] [out]
eff_len_params	Parameters for effective lengths calculation. Reset with the current sequence data [in] [out]

Definition at line 1001 of file blast_setup.c.

References BLAST_CalcEffLengths(), BlastHitSavingParametersUpdate(), BlastInitialWordParametersUpdate(), BlastLinkHSPParametersUpdate(), BlastScoringOptions::gapped_calculation, NULL, and BlastEffectiveLengthsParameters::real_db_length.

Referenced by BLAST_ComputeTraceback_MT(), and BLAST_PreliminarySearchEngine().

Blast_ScoreBlkKbpGappedCalc()

Int2 Blast_ScoreBlkKbpGappedCalc	(	BlastScoreBlk *	sbp,
		const BlastScoringOptions *	scoring_options,
		EBlastProgramType	program,
		const BlastQueryInfo *	query_info,
		Blast_Message **	error_return
	)

Blast_ScoreBlkKbpGappedCalc, fills the ScoreBlkPtr for a gapped search.

Should be moved to blast_stat.c in the future.

Parameters

sbp	Contains fields to be set, should not be NULL. [out]
scoring_options	Scoring_options [in]
program	Used to set fields on sbp [in]
query_info	Query information containing context information [in]
error_return	Pointer to structure for returning errors. [in][out]

Returns

Status.

Definition at line 41 of file blast_setup.c.

References Blast_GumbelBlkCalc(), Blast_KarlinBlkCopy(), Blast_KarlinBlkGappedCalc(), Blast_KarlinBlkNew(), Blast_KarlinBlkNuclGappedCalc(), BLAST_PENALTY, Blast_PerrorWithLocation, Blast_QueryIsPssm(), BLAST_REWARD, BLASTERR_INVALIDPARAM, BlastQueryInfo::contexts, eBlastTypeBlastn, eBlastTypeMapping, BlastQueryInfo::first_context, BlastScoringOptions::gap_extend, BlastScoringOptions::gap_open, BlastScoreBlk::gbp, BlastContextInfo::is_valid, BlastScoreBlk::kbp_gap, BlastScoreBlk::kbp_gap_psi, BlastScoreBlk::kbp_gap_std, BlastScoreBlk::kbp_std, BlastScoreBlk::name, NULL, BlastScoringOptions::penalty, BlastScoringOptions::reward, and BlastScoreBlk::round_down.

Referenced by BlastSetup_ScoreBlkInit(), LinkHspTestFixture::setupScoreBlk(), and CBlastExtendTestFixture::setupStructures().

Blast_ScoreBlkMatrixInit()

Int2 Blast_ScoreBlkMatrixInit	(	EBlastProgramType	program_number,
		const BlastScoringOptions *	scoring_options,
		BlastScoreBlk *	sbp,
		GET_MATRIX_PATH	get_path
	)

Initializes the substitution matrix in the BlastScoreBlk according to the scoring options specified.

Parameters

program_number	Used to set fields on sbp [in]
scoring_options	Scoring_options [in]
sbp	Contains fields to be set, should not be NULL. [out]
get_path	callback function to get matrix path [in]

Definition at line 330 of file blast_setup.c.

References BLAST_PENALTY, BLAST_REWARD, Blast_ScoreBlkMatrixFill(), BLAST_ScoreSetAmbigRes(), BLAST_StrToUpper(), buffer, eBlastTypeBlastn, eBlastTypeMapping, FALSE, BlastScoringOptions::matrix, BlastScoreBlk::matrix_only_scoring, BlastScoreBlk::name, NULLB, BlastScoringOptions::penalty, BlastScoreBlk::penalty, BlastScoreBlk::read_in_matrix, BlastScoringOptions::reward, BlastScoreBlk::reward, strdup, and TRUE.

Referenced by AascanTestFixture::AascanTestFixture(), BlastSetup_ScoreBlkInit(), BOOST_AUTO_TEST_CASE(), CompressedAascanTestFixture::CompressedAascanTestFixture(), CompressedAalookupTestFixture::FillLookupTable(), AalookupTestFixture::FillLookupTable(), NuclWordFinderTextFixture::setupScoreBlk(), LinkHspTestFixture::setupScoreBlk(), CBlastExtendTestFixture::setupStructures(), and CScoreBuilder::x_Initialize().

Blast_SetPHIPatternInfo()

Int2 Blast_SetPHIPatternInfo	(	EBlastProgramType	program,
		const SPHIPatternSearchBlk *	pattern_blk,
		const BLAST_SequenceBlk *	query,
		const BlastSeqLoc *	lookup_segments,
		BlastQueryInfo *	query_info,
		Blast_Message **	blast_message
	)

In a PHI BLAST search, adds pattern information to the BlastQueryInfo structure.

Parameters

program	Type of PHI BLAST program [in]
pattern_blk	Auxiliary pattern items structure [in]
query	Query sequence [in]
lookup_segments	Locations on query sequence to find pattern on [in]
query_info	Query information structure, where pattern occurrences will be saved. [in][out]
blast_message	will be filled in if pattern not found on query [in][out]

Returns

Status, 0 on success, -1 on error.

Definition at line 1065 of file blast_setup.c.

References ASSERT, Blast_MessageWrite(), Blast_ProgramIsPhiBlast(), BlastMemDup(), buffer, BlastQueryInfo::contexts, eBlastSevWarning, eBlastTypePhiBlastn, INT4_MAX, kBlastMessageNoContext, BlastContextInfo::length_adjustment, SPHIPatternSearchBlk::minPatternMatchLength, SPHIQueryInfo::pattern, SPHIPatternSearchBlk::pattern, BlastQueryInfo::pattern_info, SPHIPatternSearchBlk::patternProbability, PHIGetPatternOccurrences(), SPHIQueryInfo::probability, query, and SPHIQueryInfoNew().

Referenced by CSetupFactory::CreateLookupTable(), and CPhiblastTestFixture::x_FindQueryOccurrences().

BlastSeqLoc_RestrictToInterval()

void BlastSeqLoc_RestrictToInterval	(	BlastSeqLoc **	mask,
		Int4	from,
		Int4	to
	)

Adjusts the mask locations coordinates to a sequence interval.

Removes those mask locations that do not intersect the interval. Can do this either for all queries or only for the first one.

Parameters

mask	Structure containing a mask location. [in] [out]
from	Starting offset of a sequence interval [in]
to	Ending offset of a sequence interval [in]

Definition at line 1030 of file blast_setup.c.

References BlastSeqLocNodeFree(), mask, MAX, MIN, BlastSeqLoc::next, and NULL.

Referenced by BOOST_AUTO_TEST_CASE(), s_GetRestrictedBlastSeqLocs(), and s_RestrictSeqLocs_Multiframe().

BlastSetup_ScoreBlkInit()

Int2 BlastSetup_ScoreBlkInit	(	BLAST_SequenceBlk *	query_blk,
		const BlastQueryInfo *	query_info,
		const BlastScoringOptions *	scoring_options,
		EBlastProgramType	program_number,
		BlastScoreBlk **	sbpp,
		double	scale_factor,
		Blast_Message **	blast_message,
		GET_MATRIX_PATH	get_path
	)

Initializes the score block structure.

Parameters

query_blk	Query sequence(s) [in]
query_info	Additional query information [in]
scoring_options	Scoring options [in]
program_number	BLAST program type [in]
sbpp	Initialized score block [out]
scale_factor	Matrix scaling factor for this search [in]
blast_message	Error message [out]
get_path	callback function to get matrix path [in]

Definition at line 456 of file blast_setup.c.

References ASSERT, Blast_PerrorWithLocation, Blast_ProgramIsMapping(), Blast_ProgramIsPhiBlast(), Blast_ScoreBlkKbpGappedCalc(), Blast_ScoreBlkKbpUngappedCalc(), Blast_ScoreBlkMatrixInit(), BLASTAA_SEQ_CODE, BLASTERR_MEMORY, BLASTNA_SEQ_CODE, BlastScoreBlkNew(), BlastScoringOptions::complexity_adjusted_scoring, BlastScoreBlk::complexity_adjusted_scoring, eBlastTypeBlastn, eBlastTypeMapping, BlastScoringOptions::gapped_calculation, BlastScoreBlk::gbp, kBlastMessageNoContext, BlastScoreBlk::kbp_gap, BlastQueryInfo::last_context, NULL, s_JumperScoreBlkFill(), s_PHIScoreBlkFill(), BlastScoreBlk::scale_factor, BLAST_SequenceBlk::sequence, and sfree.

Referenced by BLAST_MainSetUp(), BOOST_AUTO_TEST_CASE(), CPhiblastTestFixture::CPhiblastTestFixture(), InitializeBlastScoreBlk(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), TestFixture::SetUpLookupTable(), CPssmEngine::x_InitializeScoreBlock(), and CSeedTop::x_MakeScoreBlk().

BlastSetup_Validate()

Int2 BlastSetup_Validate	(	const BlastQueryInfo *	query_info,
		const BlastScoreBlk *	score_blk
	)

Validation function for the setup of queries for the BLAST search.

Parameters

query_info	properly set up BlastQueryInfo structure [in]
score_blk	optional properly set up BlastScoreBlk structure (may be NULL)[in]

Returns

If no valid queries are found, 1 is returned, otherwise 0.

Definition at line 535 of file blast_setup.c.

References ASSERT, BlastQueryInfo::contexts, FALSE, BlastQueryInfo::first_context, BlastContextInfo::is_valid, BlastScoreBlk::kbp, BlastScoreBlk::kbp_gap, NULL, BlastScoreBlk::sfp, and TRUE.

Referenced by BLAST_MainSetUp(), and SetupQueries_OMF().