Structure and function definitions for BLAST parameter structures, which are internal to the CORE of BLAST. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_export.h>
#include <algo/blast/core/blast_program.h>
#include <algo/blast/core/blast_query_info.h>
#include <algo/blast/core/blast_options.h>
#include <algo/blast/core/blast_message.h>
#include <algo/blast/core/blast_stat.h>
#include <algo/blast/core/lookup_wrap.h>

Include dependency graph for blast_parameters.h:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Go to the SVN repository for this file.

Classes
struct	BlastUngappedCutoffs
	All the ungapped cutoff values that can change from context to context. More...

struct	BlastInitialWordParameters
	Parameter block that contains a pointer to BlastInitialWordOptions and the values derived from it. More...

struct	BlastExtensionParameters
	Computed values used as parameters for gapped alignments. More...

struct	BlastLinkHSPParameters
	Parameter block for linking HSPs with sum statistics. More...

struct	BlastGappedCutoffs
	All the gapped cutoff values that can change from context to context. More...

struct	BlastHitSavingParameters
	Parameter block that contains a pointer to BlastHitSavingOptions and the values derived from it. More...

struct	BlastScoringParameters
	Scoring parameters block Contains scoring-related information that is actually used for the blast search. More...

struct	BlastEffectiveLengthsParameters
	Parameters for setting up effective lengths and search spaces. More...

Macros
#define	BLAST_GAP_PROB 0.5
	Default parameters for linking HSPs. More...

#define	BLAST_GAP_PROB_GAPPED 1.0
	Gap probability for gapped search. More...

#define	BLAST_GAP_DECAY_RATE 0.5
	Gap decay rate for ungapped search. More...

#define	BLAST_GAP_DECAY_RATE_GAPPED 0.1
	Gap decay rate for gapped search. More...

#define	BLAST_GAP_SIZE 40
	Default gap size. More...

#define	BLAST_OVERLAP_SIZE 9
	Default overlap size. More...

#define	CUTOFF_E_BLASTN 0.05
	Expect values corresponding to the default cutoff scores for all ungapped and gapped blastn alignments. More...

#define	CUTOFF_E_BLASTP 1e-300
	default evalue (ungapped blastp) More...

#define	CUTOFF_E_BLASTX 1.0
	default evalue (ungapped blastx) More...

#define	CUTOFF_E_TBLASTN 1.0
	default evalue (ungapped tblastn) More...

#define	CUTOFF_E_TBLASTX 1e-300
	default evalue (tblastx) More...

#define	RESTRICTED_ALIGNMENT_WORST_EVALUE 10.0
	Because approximate gapped alignment adds extra overhead, it should be avoided if there is no performance benefit to using it. More...

Typedefs
typedef enum ESeedContainerType	ESeedContainerType
	specifies the data structures used for bookkeeping during computation of ungapped extensions More...

typedef struct BlastUngappedCutoffs	BlastUngappedCutoffs
	All the ungapped cutoff values that can change from context to context. More...

typedef struct BlastInitialWordParameters	BlastInitialWordParameters
	Parameter block that contains a pointer to BlastInitialWordOptions and the values derived from it. More...

typedef struct BlastExtensionParameters	BlastExtensionParameters
	Computed values used as parameters for gapped alignments. More...

typedef struct BlastLinkHSPParameters	BlastLinkHSPParameters
	Parameter block for linking HSPs with sum statistics. More...

typedef struct BlastGappedCutoffs	BlastGappedCutoffs
	All the gapped cutoff values that can change from context to context. More...

typedef struct BlastHitSavingParameters	BlastHitSavingParameters
	Parameter block that contains a pointer to BlastHitSavingOptions and the values derived from it. More...

typedef struct BlastScoringParameters	BlastScoringParameters
	Scoring parameters block Contains scoring-related information that is actually used for the blast search. More...

typedef struct BlastEffectiveLengthsParameters	BlastEffectiveLengthsParameters
	Parameters for setting up effective lengths and search spaces. More...

Enumerations
enum	ESeedContainerType { eDiagArray , eDiagHash , eMaxContainerType }
	specifies the data structures used for bookkeeping during computation of ungapped extensions More...

Functions
BlastInitialWordParameters *	BlastInitialWordParametersFree (BlastInitialWordParameters *parameters)
	Deallocate memory for BlastInitialWordParameters. More...

Int2	BlastInitialWordParametersNew (EBlastProgramType program_number, const BlastInitialWordOptions word_options, const BlastHitSavingParameters hit_params, const LookupTableWrap lookup_wrap, const BlastScoreBlk sbp, BlastQueryInfo query_info, Uint4 subject_length, BlastInitialWordParameters *parameters)
	Allocate memory for BlastInitialWordParameters and set x_dropoff. More...

Int2	BlastInitialWordParametersUpdate (EBlastProgramType program_number, const BlastHitSavingParameters hit_params, const BlastScoreBlk sbp, BlastQueryInfo query_info, Uint4 subject_length, BlastInitialWordParameters parameters)
	Update cutoff scores in BlastInitialWordParameters structure. More...

Int2	BlastExtensionParametersNew (EBlastProgramType blast_program, const BlastExtensionOptions options, BlastScoreBlk sbp, BlastQueryInfo query_info, BlastExtensionParameters *parameters)
	Calculate the raw values for the X-dropoff parameters. More...

BlastExtensionParameters *	BlastExtensionParametersFree (BlastExtensionParameters *parameters)
	Deallocate memory for BlastExtensionParameters. More...

BlastScoringParameters *	BlastScoringParametersFree (BlastScoringParameters *parameters)
	Deallocate memory for BlastScoringParameters. More...

Int2	BlastScoringParametersNew (const BlastScoringOptions options, BlastScoreBlk sbp, BlastScoringParameters **parameters)
	Calculate scaled cutoff scores and gap penalties. More...

BlastEffectiveLengthsParameters *	BlastEffectiveLengthsParametersFree (BlastEffectiveLengthsParameters *parameters)
	Deallocate memory for BlastEffectiveLengthsParameters*. More...

Int2	BlastEffectiveLengthsParametersNew (const BlastEffectiveLengthsOptions options, Int8 db_length, Int4 num_seqs, BlastEffectiveLengthsParameters *parameters)
	Allocate memory for BlastEffectiveLengthsParameters. More...

BlastLinkHSPParameters *	BlastLinkHSPParametersFree (BlastLinkHSPParameters *parameters)
	Deallocate memory for BlastLinkHSPParameters;. More...

Int2	BlastLinkHSPParametersNew (EBlastProgramType program_number, Boolean gapped_calculation, BlastLinkHSPParameters **link_hsp_params)
	Initialize the linking HSPs parameters with default values. More...

Int2	BlastLinkHSPParametersUpdate (const BlastInitialWordParameters word_params, const BlastHitSavingParameters hit_params, Boolean gapped_calculation)
	Update BlastLinkHSPParameters, using calculated values of other parameters. More...

BlastHitSavingParameters *	BlastHitSavingParametersFree (BlastHitSavingParameters *parameters)
	Deallocate memory for BlastHitSavingOptions*. More...

Int2	BlastHitSavingParametersNew (EBlastProgramType program_number, const BlastHitSavingOptions options, const BlastScoreBlk sbp, const BlastQueryInfo query_info, Int4 avg_subject_length, Int4 compositionBasedStats, BlastHitSavingParameters *parameters)
	Allocate memory and initialize the BlastHitSavingParameters structure. More...

Int2	BlastHitSavingParametersUpdate (EBlastProgramType program_number, const BlastScoreBlk sbp, const BlastQueryInfo query_info, Int4 avg_subject_length, Int4 compositionBasedStats, BlastHitSavingParameters *parameters)
	Updates cutoff scores in hit saving parameters. More...

void	CalculateLinkHSPCutoffs (EBlastProgramType program, BlastQueryInfo query_info, const BlastScoreBlk sbp, BlastLinkHSPParameters link_hsp_params, const BlastInitialWordParameters word_params, Int8 db_length, Int4 subject_length)
	Calculates cutoff scores and returns them. More...

void	printBlastScoringParameters (BlastScoringParameters *params)

void	printBlastInitialWordParamters (BlastInitialWordParameters word_params, BlastQueryInfo query_info)

void	printBlastExtensionParameters (BlastExtensionParameters *ext_params)

void	printBlastHitSavingParameters (BlastHitSavingParameters hit_params, BlastQueryInfo query_info)

void	printAllParameters (BlastHitSavingParameters hit_params, BlastExtensionParameters ext_params, BlastInitialWordParameters word_params, BlastQueryInfo query_info)

Detailed Description

Structure and function definitions for BLAST parameter structures, which are internal to the CORE of BLAST.

These parameters are normally set by:
   1.) reading the options in blast_options.[ch] to find user preferences
   2.) making intelligent choices based upon the program, user preferences, 
       and other data such as the sequence's length.

NOTE: These parameters should be set by calls in algo/blast/core, 
      preferrably to functions in this file. User preferences should be 
      controlled by the structures and functions in blast_options.[ch]. 
      The parameter structures belong to algo/blast/core, the options
      structures belong to the user.

Definition in file blast_parameters.h.

Macro Definition Documentation

◆ BLAST_GAP_DECAY_RATE

#define BLAST_GAP_DECAY_RATE 0.5

Gap decay rate for ungapped search.

Definition at line 68 of file blast_parameters.h.

◆ BLAST_GAP_DECAY_RATE_GAPPED

#define BLAST_GAP_DECAY_RATE_GAPPED 0.1

Gap decay rate for gapped search.

Definition at line 69 of file blast_parameters.h.

◆ BLAST_GAP_PROB

#define BLAST_GAP_PROB 0.5

Default parameters for linking HSPs.

Gap probability for ungapped search

Definition at line 66 of file blast_parameters.h.

◆ BLAST_GAP_PROB_GAPPED

#define BLAST_GAP_PROB_GAPPED 1.0

Gap probability for gapped search.

Definition at line 67 of file blast_parameters.h.

◆ BLAST_GAP_SIZE

#define BLAST_GAP_SIZE 40

Default gap size.

Definition at line 70 of file blast_parameters.h.

◆ BLAST_OVERLAP_SIZE

#define BLAST_OVERLAP_SIZE 9

Default overlap size.

Definition at line 71 of file blast_parameters.h.

◆ CUTOFF_E_BLASTN

#define CUTOFF_E_BLASTN 0.05

Expect values corresponding to the default cutoff scores for all ungapped and gapped blastn alignments.

default evalue (blastn)

Definition at line 76 of file blast_parameters.h.

◆ CUTOFF_E_BLASTP

#define CUTOFF_E_BLASTP 1e-300

default evalue (ungapped blastp)

Definition at line 77 of file blast_parameters.h.

◆ CUTOFF_E_BLASTX

#define CUTOFF_E_BLASTX 1.0

default evalue (ungapped blastx)

Definition at line 78 of file blast_parameters.h.

◆ CUTOFF_E_TBLASTN

#define CUTOFF_E_TBLASTN 1.0

default evalue (ungapped tblastn)

Definition at line 79 of file blast_parameters.h.

◆ CUTOFF_E_TBLASTX

#define CUTOFF_E_TBLASTX 1e-300

default evalue (tblastx)

Definition at line 80 of file blast_parameters.h.

◆ RESTRICTED_ALIGNMENT_WORST_EVALUE

#define RESTRICTED_ALIGNMENT_WORST_EVALUE 10.0

Because approximate gapped alignment adds extra overhead, it should be avoided if there is no performance benefit to using it.

To be benficial, most score-only gapped alignments should be the restricted kind, and we can only assure that if the e-value cutoff is not too generous

Definition at line 193 of file blast_parameters.h.

Typedef Documentation

◆ BlastEffectiveLengthsParameters

typedef struct BlastEffectiveLengthsParameters BlastEffectiveLengthsParameters

Parameters for setting up effective lengths and search spaces.

The real database size values to be used for statistical calculations, if there are no overriding values in options.

◆ BlastExtensionParameters

typedef struct BlastExtensionParameters BlastExtensionParameters

Computed values used as parameters for gapped alignments.

Note that currently the value of the X-dropoff parameter is fixed for all search contexts

◆ BlastGappedCutoffs

typedef struct BlastGappedCutoffs BlastGappedCutoffs

All the gapped cutoff values that can change from context to context.

◆ BlastHitSavingParameters

typedef struct BlastHitSavingParameters BlastHitSavingParameters

Parameter block that contains a pointer to BlastHitSavingOptions and the values derived from it.

◆ BlastInitialWordParameters

typedef struct BlastInitialWordParameters BlastInitialWordParameters

Parameter block that contains a pointer to BlastInitialWordOptions and the values derived from it.

◆ BlastLinkHSPParameters

typedef struct BlastLinkHSPParameters BlastLinkHSPParameters

Parameter block for linking HSPs with sum statistics.

◆ BlastScoringParameters

typedef struct BlastScoringParameters BlastScoringParameters

Scoring parameters block Contains scoring-related information that is actually used for the blast search.

◆ BlastUngappedCutoffs

typedef struct BlastUngappedCutoffs BlastUngappedCutoffs

All the ungapped cutoff values that can change from context to context.

◆ ESeedContainerType

typedef enum ESeedContainerType ESeedContainerType

specifies the data structures used for bookkeeping during computation of ungapped extensions

Enumeration Type Documentation

◆ ESeedContainerType

enum ESeedContainerType

specifies the data structures used for bookkeeping during computation of ungapped extensions

Enumerator
eDiagArray	use diagonal structures with array of last hits and levels.
eDiagHash	use hash table (blastn only)
eMaxContainerType	maximum value for this enumeration

Definition at line 85 of file blast_parameters.h.

Function Documentation

◆ BlastEffectiveLengthsParametersFree()

BlastEffectiveLengthsParameters* BlastEffectiveLengthsParametersFree ( BlastEffectiveLengthsParameters * parameters )

Deallocate memory for BlastEffectiveLengthsParameters*.

Parameters

parameters Structure to free [in]

Definition at line 570 of file blast_parameters.c.

References NULL, and sfree.

Referenced by BLAST_GapAlignSetUp(), Blast_RunPreliminarySearchWithInterrupt(), BOOST_AUTO_TEST_CASE(), LinkHspTestFixture::fillEffectiveLengths(), CBlastExtendTestFixture::fillEffectiveLengths(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_BlastRunFullSearchCleanUp(), SThreadLocalDataFree(), and CTracebackTestFixture::~CTracebackTestFixture().

◆ BlastEffectiveLengthsParametersNew()

Int2 BlastEffectiveLengthsParametersNew	(	const BlastEffectiveLengthsOptions *	options,
		Int8	db_length,
		Int4	num_seqs,
		BlastEffectiveLengthsParameters **	parameters
	)

Allocate memory for BlastEffectiveLengthsParameters.

Parameters

options	The user provided options [in]
db_length	The database length [in]
num_seqs	Number of sequences in database [in]
parameters	The parameters structure returned [out]

Definition at line 579 of file blast_parameters.c.

References calloc().

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

◆ BlastExtensionParametersFree()

BlastExtensionParameters* BlastExtensionParametersFree ( BlastExtensionParameters * parameters )

Deallocate memory for BlastExtensionParameters.

Parameters

parameters Structure to free [in]

Definition at line 493 of file blast_parameters.c.

References NULL, and sfree.

Referenced by BLAST_GapAlignSetUp(), Blast_RunPreliminarySearchWithInterrupt(), BOOST_AUTO_TEST_CASE(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_BlastRunFullSearchCleanUp(), LinkHspTestFixture::setupCutoffScores(), SThreadLocalDataFree(), and CTracebackTestFixture::~CTracebackTestFixture().

◆ BlastExtensionParametersNew()

Int2 BlastExtensionParametersNew	(	EBlastProgramType	blast_program,
		const BlastExtensionOptions *	options,
		BlastScoreBlk *	sbp,
		BlastQueryInfo *	query_info,
		BlastExtensionParameters **	parameters
	)

Calculate the raw values for the X-dropoff parameters.

Parameters

blast_program	Program number [in]
options	Already allocated extension options [in]
sbp	Structure containing statistical information [in]
query_info	Query information, needed only for determining the first context [in]
parameters	Extension parameters [out]

Definition at line 422 of file blast_parameters.c.

References ASSERT, Blast_ProgramIsRpsBlast(), calloc(), eBlastTypeBlastn, eBlastTypeMapping, BlastExtensionOptions::gap_x_dropoff, BlastExtensionParameters::gap_x_dropoff, BlastExtensionOptions::gap_x_dropoff_final, BlastExtensionParameters::gap_x_dropoff_final, BlastScoreBlk::kbp, BlastScoreBlk::kbp_gap, BlastScoreBlk::matrix_only_scoring, MAX, NCBIMATH_LN2, NULL, BlastExtensionParameters::options, s_BlastFindSmallestLambda(), s_BlastFindValidKarlinBlk(), and BlastScoreBlk::scale_factor.

Referenced by BLAST_GapAlignSetUp(), BOOST_AUTO_TEST_CASE(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), LinkHspTestFixture::setupCutoffScores(), and CBlastExtendTestFixture::setupStructures().

◆ BlastHitSavingParametersFree()

BlastHitSavingParameters* BlastHitSavingParametersFree ( BlastHitSavingParameters * parameters )

Deallocate memory for BlastHitSavingOptions*.

Parameters

parameters Structure to free [in]

Definition at line 718 of file blast_parameters.c.

References BlastHitSavingParameters::cutoffs, BlastHitSavingParameters::link_hsp_params, BlastHitSavingParameters::low_score, NULL, and sfree.

Referenced by Blast_RunPreliminarySearchWithInterrupt(), BOOST_AUTO_TEST_CASE(), LinkHspTestFixture::freeStructures(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_BlastRunFullSearchCleanUp(), TestFixture::SkipMaskedRangesCore(), SThreadLocalDataFree(), CBlastExtendTestFixture::~CBlastExtendTestFixture(), and CTracebackTestFixture::~CTracebackTestFixture().

◆ BlastHitSavingParametersNew()

Int2 BlastHitSavingParametersNew	(	EBlastProgramType	program_number,
		const BlastHitSavingOptions *	options,
		const BlastScoreBlk *	sbp,
		const BlastQueryInfo *	query_info,
		Int4	avg_subject_length,
		Int4	compositionBasedStats,
		BlastHitSavingParameters **	parameters
	)

Allocate memory and initialize the BlastHitSavingParameters structure.

Calculates the (raw) score cutoff given an expect value and puts it in the "cutoff_score" field of the returned BlastHitSavingParameters*

Parameters

program_number	Number of the BLAST program [in]
options	The given hit saving options [in]
sbp	Scoring block, needed for calculating score cutoff from e-value [in]
query_info	Query information, needed for calculating score cutoff from e-value [in]
avg_subject_length	average length of subject sequence [in]
compositionBasedStats	follows -t option in blastp [in]
parameters	Resulting parameters [out]

Definition at line 734 of file blast_parameters.c.

References ASSERT, Blast_QueryIsTranslated(), Blast_SubjectIsTranslated(), BlastHitSavingParametersUpdate(), BlastLinkHSPParametersFree(), BlastLinkHSPParametersNew(), calloc(), BlastHitSavingParameters::cutoffs, DEFAULT_LONGEST_INTRON, BlastHitSavingOptions::do_sum_stats, BlastHitSavingParameters::do_sum_stats, eBlastTypeTblastx, FALSE, BlastScoreBlk::kbp_gap, BlastQueryInfo::last_context, BlastHitSavingParameters::link_hsp_params, BlastHitSavingOptions::longest_intron, BlastLinkHSPParameters::longest_intron, BlastHitSavingParameters::low_score, BlastHitSavingOptions::low_score_perc, BlastHitSavingParameters::mask_level, MAX, NULL, BlastQueryInfo::num_queries, BlastHitSavingParameters::options, and TRUE.

Referenced by BLAST_GapAlignSetUp(), BOOST_AUTO_TEST_CASE(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), LinkHspTestFixture::setupCutoffScores(), CBlastExtendTestFixture::setupStructures(), and TestFixture::SkipMaskedRangesCore().

◆ BlastHitSavingParametersUpdate()

Int2 BlastHitSavingParametersUpdate	(	EBlastProgramType	program_number,
		const BlastScoreBlk *	sbp,
		const BlastQueryInfo *	query_info,
		Int4	avg_subject_length,
		Int4	compositionBasedStats,
		BlastHitSavingParameters *	parameters
	)

Updates cutoff scores in hit saving parameters.

Parameters

program_number	Number of the BLAST program [in]
sbp	Scoring block, needed for calculating score cutoff from e-value [in]
query_info	Query information, needed for calculating score cutoff from e-value [in]
avg_subject_length	average length of subject sequence, used in sum_stats mode [in]
compositionBasedStats	follows -t option in blastp [in]
parameters	Preallocated parameters [in] [out]

Definition at line 831 of file blast_parameters.c.

References ASSERT, BLAST_Cutoffs(), Blast_ProgramIsPhiBlast(), BLAST_SpougeEtoS(), context, BlastQueryInfo::contexts, BlastHitSavingOptions::cutoff_score, BlastGappedCutoffs::cutoff_score, BlastGappedCutoffs::cutoff_score_max, BlastHitSavingParameters::cutoff_score_min, BlastHitSavingParameters::cutoffs, eBlastTypeBlastn, eBlastTypeBlastp, eBlastTypeMapping, eBlastTypeRpsTblastn, BlastContextInfo::eff_searchsp, BlastHitSavingOptions::expect_value, FALSE, Blast_GumbelBlk::filled, BlastQueryInfo::first_context, for(), BlastLinkHSPParameters::gap_decay_rate, BlastScoreBlk::gbp, INT4_MAX, BlastContextInfo::is_valid, BlastScoreBlk::kbp, BlastScoreBlk::kbp_gap, BlastQueryInfo::last_context, BlastHitSavingParameters::link_hsp_params, BlastHitSavingOptions::mask_level, BlastHitSavingParameters::mask_level, BlastScoreBlk::matrix_only_scoring, MIN, NUM_FRAMES, BlastHitSavingParameters::options, BlastHitSavingParameters::prelim_evalue, BlastContextInfo::query_length, BlastContextInfo::query_offset, BlastHitSavingParameters::restricted_align, RESTRICTED_ALIGNMENT_WORST_EVALUE, s_BlastKarlinBlkIsValid(), s_PhiBlastCutoffScore(), BlastScoreBlk::scale_factor, and TRUE.

Referenced by BLAST_OneSubjectUpdateParameters(), BlastHitSavingParametersNew(), and BOOST_AUTO_TEST_CASE().

◆ BlastInitialWordParametersFree()

BlastInitialWordParameters* BlastInitialWordParametersFree ( BlastInitialWordParameters * parameters )

Deallocate memory for BlastInitialWordParameters.

Parameters

parameters Structure to free [in]

Definition at line 119 of file blast_parameters.c.

References BlastInitialWordParameters::cutoffs, NULL, and sfree.

Referenced by BLAST_PreliminarySearchEngine(), BOOST_AUTO_TEST_CASE(), LinkHspTestFixture::setupCutoffScores(), TestFixture::SkipMaskedRangesCore(), CBlastExtendTestFixture::~CBlastExtendTestFixture(), and NuclWordFinderTextFixture::~NuclWordFinderTextFixture().

◆ BlastInitialWordParametersNew()

Int2 BlastInitialWordParametersNew	(	EBlastProgramType	program_number,
		const BlastInitialWordOptions *	word_options,
		const BlastHitSavingParameters *	hit_params,
		const LookupTableWrap *	lookup_wrap,
		const BlastScoreBlk *	sbp,
		BlastQueryInfo *	query_info,
		Uint4	subject_length,
		BlastInitialWordParameters **	parameters
	)

Allocate memory for BlastInitialWordParameters and set x_dropoff.

Calling BlastInitialWordParametersNew calculates the raw x_dropoff from the bit x_dropoff and puts it into the x_dropoff field of BlastInitialWordParameters*. The container type is also set. For blastn queries over a certain length eDiagHash is set, otherwise it's eDiagArray. The extension method is also set via a call to s_GetBestExtensionMethod

Parameters

program_number	Type of BLAST program [in]
word_options	The initial word options [in]
hit_params	The hit saving options (needed to calculate cutoff score for ungapped extensions) [in]
lookup_wrap	contains lookup table so the proper extension method can be set [in]
sbp	Statistical (Karlin-Altschul) information [in]
query_info	Query information [in]
subject_length	Average subject sequence length [in]
parameters	Resulting parameters [out]

Definition at line 159 of file blast_parameters.c.

References ASSERT, Blast_ProgramIsNucleotide(), Blast_ProgramIsPhiBlast(), Blast_QueryIsPattern(), BlastInitialWordParametersUpdate(), calloc(), BlastInitialWordParameters::container_type, context, BlastQueryInfo::contexts, BlastInitialWordParameters::cutoffs, eBlastTypeBlastn, eBlastTypeMapping, eDiagArray, eDiagHash, FALSE, BlastQueryInfo::first_context, i, BlastContextInfo::is_valid, BlastScoreBlk::kbp, Blast_KarlinBlk::Lambda, BlastQueryInfo::last_context, BlastInitialWordParameters::matrix_only_scoring, BlastScoreBlk::matrix_only_scoring, NCBIMATH_LN2, BlastInitialWordParameters::nucl_score_table, BlastInitialWordParameters::options, BlastScoreBlk::penalty, BlastContextInfo::query_length, BlastContextInfo::query_offset, BlastScoreBlk::reward, s_BlastFindValidKarlinBlk(), s_BlastKarlinBlkIsValid(), BlastScoreBlk::scale_factor, table, TRUE, BlastInitialWordParameters::ungapped_extension, BlastInitialWordOptions::x_dropoff, and BlastUngappedCutoffs::x_dropoff_init.

Referenced by BLAST_PreliminarySearchEngine(), BOOST_AUTO_TEST_CASE(), s_GetInitialWordParameters(), LinkHspTestFixture::setupCutoffScores(), CBlastExtendTestFixture::setupStructures(), and TestFixture::SkipMaskedRangesCore().

◆ BlastInitialWordParametersUpdate()

Int2 BlastInitialWordParametersUpdate	(	EBlastProgramType	program_number,
		const BlastHitSavingParameters *	hit_params,
		const BlastScoreBlk *	sbp,
		BlastQueryInfo *	query_info,
		Uint4	subject_length,
		BlastInitialWordParameters *	parameters
	)

Update cutoff scores in BlastInitialWordParameters structure.

Parameters

program_number	Type of BLAST program [in]
hit_params	The hit saving parameters, needed to calculate cutoff score for ungapped extensions. The HSP linking cutoff might have to be adjusted here. [in] [out]
sbp	Statistical (Karlin-Altschul) information [in]
query_info	Query information [in]
subject_length	Average subject sequence length [in]
parameters	Preallocated parameters [in] [out]

Definition at line 280 of file blast_parameters.c.

References ASSERT, BLAST_Cutoffs(), context, BlastQueryInfo::contexts, BlastUngappedCutoffs::cutoff_score, BlastGappedCutoffs::cutoff_score_max, BlastInitialWordParameters::cutoff_score_min, BlastInitialWordParameters::cutoffs, BlastHitSavingParameters::cutoffs, eBlastTypeBlastn, eBlastTypeMapping, FALSE, BlastQueryInfo::first_context, BlastLinkHSPParameters::gap_decay_rate, BlastInitialWordOptions::gap_trigger, INT4_MAX, BlastContextInfo::is_valid, BlastScoreBlk::kbp_gap, BlastScoreBlk::kbp_std, Blast_KarlinBlk::Lambda, BlastHitSavingParameters::link_hsp_params, Blast_KarlinBlk::logK, BlastScoreBlk::matrix_only_scoring, MIN, NCBIMATH_LN2, BlastInitialWordParameters::options, BlastContextInfo::query_length, BlastUngappedCutoffs::reduced_nucl_cutoff_score, s_BlastKarlinBlkIsValid(), s_GetCutoffEvalue(), BlastScoreBlk::scale_factor, TRUE, BlastUngappedCutoffs::x_dropoff, BlastUngappedCutoffs::x_dropoff_init, and BlastInitialWordParameters::x_dropoff_max.

Referenced by BLAST_OneSubjectUpdateParameters(), and BlastInitialWordParametersNew().

◆ BlastLinkHSPParametersFree()

BlastLinkHSPParameters* BlastLinkHSPParametersFree ( BlastLinkHSPParameters * parameters )

Deallocate memory for BlastLinkHSPParameters;.

Parameters

parameters Structure to free [in]

Definition at line 592 of file blast_parameters.c.

References NULL, and sfree.

Referenced by BlastHitSavingParametersNew().

◆ BlastLinkHSPParametersNew()

Int2 BlastLinkHSPParametersNew	(	EBlastProgramType	program_number,
		Boolean	gapped_calculation,
		BlastLinkHSPParameters **	link_hsp_params
	)

Initialize the linking HSPs parameters with default values.

Parameters

program_number	Type of BLAST program [in]
gapped_calculation	Is this a gapped search? [in]
link_hsp_params	Initialized parameters structure [out]

Definition at line 598 of file blast_parameters.c.

References BLAST_GAP_DECAY_RATE, BLAST_GAP_DECAY_RATE_GAPPED, BLAST_GAP_PROB, BLAST_GAP_PROB_GAPPED, BLAST_GAP_SIZE, BLAST_OVERLAP_SIZE, calloc(), eBlastTypeBlastn, BlastLinkHSPParameters::gap_decay_rate, BlastLinkHSPParameters::gap_prob, BlastLinkHSPParameters::gap_size, and BlastLinkHSPParameters::overlap_size.

Referenced by BlastHitSavingParametersNew(), and LinkHspTestFixture::setupHitParams().

◆ BlastLinkHSPParametersUpdate()

Int2 BlastLinkHSPParametersUpdate	(	const BlastInitialWordParameters *	word_params,
		const BlastHitSavingParameters *	hit_params,
		Boolean	gapped_calculation
	)

Update BlastLinkHSPParameters, using calculated values of other parameters.

Parameters

word_params	Initial word parameters [in]
hit_params	Hit saving parameters, including the link HSP parameters [in] [out]
gapped_calculation	Is this a gapped search? [in]

Definition at line 625 of file blast_parameters.c.

References BlastInitialWordParameters::cutoff_score_min, BlastLinkHSPParameters::cutoff_small_gap, and BlastHitSavingParameters::link_hsp_params.

Referenced by BLAST_OneSubjectUpdateParameters(), BLAST_PreliminarySearchEngine(), and LinkHspTestFixture::setupCutoffScores().

◆ BlastScoringParametersFree()

BlastScoringParameters* BlastScoringParametersFree ( BlastScoringParameters * parameters )

Deallocate memory for BlastScoringParameters.

Parameters

parameters Structure to free [in]

Definition at line 500 of file blast_parameters.c.

References NULL, and sfree.

Referenced by BLAST_GapAlignSetUp(), Blast_RunPreliminarySearchWithInterrupt(), BOOST_AUTO_TEST_CASE(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_BlastRunFullSearchCleanUp(), SThreadLocalDataFree(), and CTracebackTestFixture::~CTracebackTestFixture().

◆ BlastScoringParametersNew()

Int2 BlastScoringParametersNew	(	const BlastScoringOptions *	options,
		BlastScoreBlk *	sbp,
		BlastScoringParameters **	parameters
	)

Calculate scaled cutoff scores and gap penalties.

Parameters

options	Already allocated scoring options [in]
sbp	Structure containing scale factor [in]
parameters	Scoring parameters [out]

Definition at line 542 of file blast_parameters.c.

References calloc(), BlastScoringOptions::gap_extend, BlastScoringParameters::gap_extend, BlastScoringOptions::gap_open, BlastScoringParameters::gap_open, NULL, BlastScoringParameters::options, BlastScoringOptions::penalty, BlastScoringParameters::penalty, BlastScoringOptions::reward, BlastScoringParameters::reward, BlastScoringParameters::scale_factor, BlastScoreBlk::scale_factor, BlastScoringOptions::shift_pen, and BlastScoringParameters::shift_pen.

Referenced by BLAST_GapAlignSetUp(), BOOST_AUTO_TEST_CASE(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), and CBlastExtendTestFixture::setupStructures().

◆ CalculateLinkHSPCutoffs()

void CalculateLinkHSPCutoffs	(	EBlastProgramType	program,
		BlastQueryInfo *	query_info,
		const BlastScoreBlk *	sbp,
		BlastLinkHSPParameters *	link_hsp_params,
		const BlastInitialWordParameters *	word_params,
		Int8	db_length,
		Int4	subject_length
	)

Calculates cutoff scores and returns them.

Equations provided by Stephen Altschul.

Parameters

program	BLAST program type [in]
query_info	Query(ies) information [in]
sbp	Scoring statistical parameters [in]
link_hsp_params	Parameters for linking HSPs [in] [out]
word_params	InitialWordParameters (cutoff_score used for small gaps) [in]
db_length	Total length of database (non-database search if 0) [in]
subject_length	Length of the subject sequence. [in]

Definition at line 998 of file blast_parameters.c.

References BLAST_GAP_PROB, BLAST_Nint(), Blast_SubjectIsTranslated(), CODON_LENGTH, BlastQueryInfo::contexts, BlastLinkHSPParameters::cutoff_big_gap, BlastInitialWordParameters::cutoff_score_min, BlastLinkHSPParameters::cutoff_small_gap, eBlastTypeRpsTblastn, BlastLinkHSPParameters::gap_decay_rate, BlastLinkHSPParameters::gap_prob, BlastLinkHSPParameters::gap_size, Blast_KarlinBlk::H, Blast_KarlinBlk::K, BlastScoreBlk::kbp, kEpsilon, Blast_KarlinBlk::Lambda, BlastQueryInfo::last_context, log, MAX, NULL, BlastLinkHSPParameters::overlap_size, BlastContextInfo::query_length, BlastContextInfo::query_offset, s_BlastFindSmallestLambda(), BlastScoreBlk::scale_factor, and window_size.

Referenced by BLAST_PreliminarySearchEngine(), BOOST_AUTO_TEST_CASE(), and LinkHspTestFixture::setupCutoffScores().

◆ printAllParameters()

void printAllParameters	(	BlastHitSavingParameters *	hit_params,
		BlastExtensionParameters *	ext_params,
		BlastInitialWordParameters *	word_params,
		BlastQueryInfo *	query_info
	)

Definition at line 1130 of file blast_parameters.c.

References printBlastExtensionParameters(), printBlastHitSavingParameters(), and printBlastInitialWordParamters().

◆ printBlastExtensionParameters()

void printBlastExtensionParameters ( BlastExtensionParameters * ext_params )

Definition at line 1105 of file blast_parameters.c.

References BlastExtensionParameters::gap_x_dropoff, and BlastExtensionParameters::gap_x_dropoff_final.

Referenced by printAllParameters().

◆ printBlastHitSavingParameters()

void printBlastHitSavingParameters	(	BlastHitSavingParameters *	hit_params,
		BlastQueryInfo *	query_info
	)

Definition at line 1113 of file blast_parameters.c.

References context, BlastQueryInfo::contexts, BlastGappedCutoffs::cutoff_score, BlastGappedCutoffs::cutoff_score_max, BlastHitSavingParameters::cutoff_score_min, BlastHitSavingParameters::cutoffs, BlastQueryInfo::first_context, and BlastContextInfo::is_valid.

Referenced by printAllParameters().

◆ printBlastInitialWordParamters()

void printBlastInitialWordParamters	(	BlastInitialWordParameters *	word_params,
		BlastQueryInfo *	query_info
	)

Definition at line 1085 of file blast_parameters.c.

References context, BlastQueryInfo::contexts, BlastUngappedCutoffs::cutoff_score, BlastInitialWordParameters::cutoff_score_min, BlastInitialWordParameters::cutoffs, BlastQueryInfo::first_context, BlastContextInfo::is_valid, BlastUngappedCutoffs::reduced_nucl_cutoff_score, BlastUngappedCutoffs::x_dropoff, BlastUngappedCutoffs::x_dropoff_init, and BlastInitialWordParameters::x_dropoff_max.

Referenced by printAllParameters().

◆ printBlastScoringParameters()

void printBlastScoringParameters ( BlastScoringParameters * params )

Classes

Macros

Typedefs

Enumerations

Functions

Detailed Description

Macro Definition Documentation

◆ BLAST_GAP_DECAY_RATE

◆ BLAST_GAP_DECAY_RATE_GAPPED

◆ BLAST_GAP_PROB

◆ BLAST_GAP_PROB_GAPPED

◆ BLAST_GAP_SIZE

◆ BLAST_OVERLAP_SIZE

◆ CUTOFF_E_BLASTN

◆ CUTOFF_E_BLASTP

◆ CUTOFF_E_BLASTX

◆ CUTOFF_E_TBLASTN

◆ CUTOFF_E_TBLASTX

◆ RESTRICTED_ALIGNMENT_WORST_EVALUE

Typedef Documentation

◆ BlastEffectiveLengthsParameters

◆ BlastExtensionParameters

◆ BlastGappedCutoffs

◆ BlastHitSavingParameters

◆ BlastInitialWordParameters

◆ BlastLinkHSPParameters

◆ BlastScoringParameters

◆ BlastUngappedCutoffs

◆ ESeedContainerType

Enumeration Type Documentation

◆ ESeedContainerType

Function Documentation

◆ BlastEffectiveLengthsParametersFree()

◆ BlastEffectiveLengthsParametersNew()

◆ BlastExtensionParametersFree()

◆ BlastExtensionParametersNew()

◆ BlastHitSavingParametersFree()

◆ BlastHitSavingParametersNew()

◆ BlastHitSavingParametersUpdate()

◆ BlastInitialWordParametersFree()

◆ BlastInitialWordParametersNew()

◆ BlastInitialWordParametersUpdate()

◆ BlastLinkHSPParametersFree()

◆ BlastLinkHSPParametersNew()

◆ BlastLinkHSPParametersUpdate()

◆ BlastScoringParametersFree()

◆ BlastScoringParametersNew()

◆ CalculateLinkHSPCutoffs()

◆ printAllParameters()

◆ printBlastExtensionParameters()

◆ printBlastHitSavingParameters()

◆ printBlastInitialWordParamters()

◆ printBlastScoringParameters()