Definitions used throughout BLAST. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_export.h>
#include <algo/blast/core/blast_program.h>

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Classes
union	BlastOffsetPair
	This symbol enables the verbose option in makeblastdb and other BLAST+ search command line applications, as well as the option to submit searches to the test server in NCBI for remote BLAST searches #define _BLAST_DEBUG 1. More...

struct	SSeqRange
	A structure containing two integers, used e.g. More...

struct	BlastSeqLoc
	Used to hold a set of positions, mostly used for filtering. More...

struct	BlastMaskLoc
	Structure for keeping the query masking information. More...

struct	BLAST_SequenceBlk
	Structure to hold a sequence. More...

struct	SPHIPatternInfo
	Information about a single pattern occurence in the query. More...

struct	SPHIQueryInfo
	In PHI BLAST, structure containing information about all pattern occurrences in query. More...

struct	SBlastTargetTranslation
	Information about target translations. More...

struct	SBlastProgress
	Progress monitoring structure. More...

Macros
#define	CODON_LENGTH 3
	Codons are always of length 3. More...

#define	DEFAULT_LONGEST_INTRON 122
	For translated gapped searches, this is the default value in nucleotides of longest_intron (for ungapped translated searches, the default value of longest_intron is zero, which causes a legacy method of HSP linking that does not use longest_intron to be invoked). More...

#define	COMPRESSION_RATIO 4
	Compression ratio of nucleotide bases (4 bases in 1 byte) More...

#define	NUM_FRAMES 6
	Number of frames to which we translate in translating searches. More...

#define	NUM_STRANDS 2
	Number of frames in a nucleotide sequence. More...

#define	GENCODE_STRLEN 64
	Length of the genetic code string. More...

#define	BLAST_CMP(a, b) ((a)>(b) ? 1 : ((a)<(b) ? -1 : 0))
	A macro expression that returns 1, 0, -1 if a is greater than, equal to or less than b, respectively. More...

#define	sfree(x) __sfree((void*)(void)&(x))
	Safe free a pointer: belongs to a higher level header. More...

Typedefs
typedef union BlastOffsetPair	BlastOffsetPair
	This symbol enables the verbose option in makeblastdb and other BLAST+ search command line applications, as well as the option to submit searches to the test server in NCBI for remote BLAST searches #define _BLAST_DEBUG 1. More...

typedef struct SSeqRange	SSeqRange
	A structure containing two integers, used e.g. More...

typedef struct BlastSeqLoc	BlastSeqLoc
	Used to hold a set of positions, mostly used for filtering. More...

typedef struct BlastMaskLoc	BlastMaskLoc
	Structure for keeping the query masking information. More...

typedef enum ESubjectMaskingType	ESubjectMaskingType
	Define the possible subject masking types. More...

typedef struct BLAST_SequenceBlk	BLAST_SequenceBlk
	Structure to hold a sequence. More...

typedef struct SPHIPatternInfo	SPHIPatternInfo
	Information about a single pattern occurence in the query. More...

typedef struct SPHIQueryInfo	SPHIQueryInfo
	In PHI BLAST, structure containing information about all pattern occurrences in query. More...

typedef struct SBlastTargetTranslation	SBlastTargetTranslation
	Information about target translations. More...

typedef enum EBlastStage	EBlastStage
	Enumeration for the stages in the BLAST search. More...

typedef struct SBlastProgress	SBlastProgress
	Progress monitoring structure. More...

typedef Boolean(*	TInterruptFnPtr) (SBlastProgress *progress_info)
	Prototype for function pointer to determine whether the BLAST search should proceed or be interrupted. More...

Enumerations
enum	ESubjectMaskingType { eNoSubjMasking , eSoftSubjMasking , eHardSubjMasking }
	Define the possible subject masking types. More...

enum	EBlastStage { eNone = 0x0 , ePrelimSearch = 0x1 << 0 , eTracebackSearch = 0x1 << 1 , eBoth = (ePrelimSearch \| eTracebackSearch) }
	Enumeration for the stages in the BLAST search. More...

Functions
void	__sfree (void **x)
	Implemented in blast_util.c. More...

SSeqRange	SSeqRangeNew (Int4 start, Int4 stop)
	Create a new SSeqRange structure with both fields initialized. More...

static NCBI_INLINE Boolean	SSeqRangeIntersectsWith (const SSeqRange a, const SSeqRange b)
	Determine if two ranges intersect. More...

Int4	SSeqRangeArrayLessThanOrEqual (const SSeqRange *ranges, Int4 num_ranges, Int4 target)
	Returns the index of the range, such that this element is the first range that either contains the target or if no such range exists, the index of the first range, such that the target is less than this range. More...

SBlastProgress *	SBlastProgressNew (void *user_data)
	Allocates and initializes a new SBlastProgress structure. More...

SBlastProgress *	SBlastProgressFree (SBlastProgress *progress_info)
	Deallocates a SBlastProgress structure. More...

void	SBlastProgressReset (SBlastProgress *progress_info)
	Resets the progress structure to its original state (as if newly allocated) for a fresh start without touching the user_data field. More...

Variables
const int	kDustLevel
	Level parameter used by dust. More...

const int	kDustWindow
	Window parameter used by dust. More...

const int	kDustLinker
	Parameter used by dust to link together close low-complexity segments. More...

const int	kSegWindow
	Window that SEG examines at once. More...

const double	kSegLocut
	Locut parameter for SEG. More...

const double	kSegHicut
	Hicut parameter for SEG. More...

const int	kUngappedHSPNumMax
	Maximum number of HPSs to be saved in an ungapped search. More...

Detailed Description

Definitions used throughout BLAST.

Definition in file blast_def.h.

Macro Definition Documentation

◆ BLAST_CMP

#define BLAST_CMP	(	a,
		b
	)	((a)>(b) ? 1 : ((a)<(b) ? -1 : 0))

A macro expression that returns 1, 0, -1 if a is greater than, equal to or less than b, respectively.

This macro evaluates its arguments more than once.

Definition at line 107 of file blast_def.h.

◆ CODON_LENGTH

#define CODON_LENGTH 3

Codons are always of length 3.

Definition at line 63 of file blast_def.h.

◆ COMPRESSION_RATIO

#define COMPRESSION_RATIO 4

Compression ratio of nucleotide bases (4 bases in 1 byte)

Definition at line 83 of file blast_def.h.

◆ DEFAULT_LONGEST_INTRON

#define DEFAULT_LONGEST_INTRON 122

For translated gapped searches, this is the default value in nucleotides of longest_intron (for ungapped translated searches, the default value of longest_intron is zero, which causes a legacy method of HSP linking that does not use longest_intron to be invoked).

The value 122 corresponds to 40 amino acids: 40 codons * 3 nucleotides per codon + up to 2 frame shifts. 40 amino acids is the maximum gap size in the untranslated sequence, so DEFAULT_LONGEST_INTRON makes these two gap sizes equal.

Definition at line 78 of file blast_def.h.

◆ GENCODE_STRLEN

#define GENCODE_STRLEN 64

Length of the genetic code string.

Definition at line 98 of file blast_def.h.

◆ NUM_FRAMES

#define NUM_FRAMES 6

Number of frames to which we translate in translating searches.

Definition at line 88 of file blast_def.h.

◆ NUM_STRANDS

#define NUM_STRANDS 2

Number of frames in a nucleotide sequence.

Definition at line 93 of file blast_def.h.

◆ sfree

#define sfree ( x ) __sfree((void**)(void*)&(x))

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

Definition at line 112 of file blast_def.h.

Typedef Documentation

◆ BLAST_SequenceBlk

typedef struct BLAST_SequenceBlk BLAST_SequenceBlk

Structure to hold a sequence.

◆ BlastMaskLoc

typedef struct BlastMaskLoc BlastMaskLoc

Structure for keeping the query masking information.

◆ BlastOffsetPair

typedef union BlastOffsetPair BlastOffsetPair

This symbol enables the verbose option in makeblastdb and other BLAST+ search command line applications, as well as the option to submit searches to the test server in NCBI for remote BLAST searches #define _BLAST_DEBUG 1.

Structure holding a pair of offsets. Used for storing offsets for the initial seeds. In most programs the offsets are query offset and subject offset of an initial word match. For PHI BLAST, the offsets are start and end of the pattern occurrence in subject, with no query information, because all pattern occurrences in subjects are aligned to all pattern occurrences in query.

◆ BlastSeqLoc

typedef struct BlastSeqLoc BlastSeqLoc

Used to hold a set of positions, mostly used for filtering.

oid holds the index of the query sequence.

◆ EBlastStage

typedef enum EBlastStage EBlastStage

Enumeration for the stages in the BLAST search.

◆ ESubjectMaskingType

typedef enum ESubjectMaskingType ESubjectMaskingType

Define the possible subject masking types.

◆ SBlastProgress

typedef struct SBlastProgress SBlastProgress

Progress monitoring structure.

This is updated by the engine to provided to the user as an argument to the user-supplied callback function (TInterruptFnPtr). This function then can assess whether the search should proceed or exit prematurely.

See also: TInterruptFnPtr

◆ SBlastTargetTranslation

typedef struct SBlastTargetTranslation SBlastTargetTranslation

Information about target translations.

◆ SPHIPatternInfo

typedef struct SPHIPatternInfo SPHIPatternInfo

Information about a single pattern occurence in the query.

◆ SPHIQueryInfo

typedef struct SPHIQueryInfo SPHIQueryInfo

In PHI BLAST, structure containing information about all pattern occurrences in query.

◆ SSeqRange

typedef struct SSeqRange SSeqRange

A structure containing two integers, used e.g.

for locations for the lookup table.

◆ TInterruptFnPtr

typedef Boolean(* TInterruptFnPtr) (SBlastProgress *progress_info)

Prototype for function pointer to determine whether the BLAST search should proceed or be interrupted.

If this function returns true, all processing must stop and the search must discard all interim results

Note: In order to avoid undue overhead, this function should not perform any time consuming operations and should always return (i.e.: it should never block)

Definition at line 354 of file blast_def.h.

Enumeration Type Documentation

◆ EBlastStage

enum EBlastStage

Enumeration for the stages in the BLAST search.

Enumerator
eNone	None specified.
ePrelimSearch	Preliminary stage.
eTracebackSearch	Traceback stage.
eBoth	Both preliminary and traceback stages.

Definition at line 324 of file blast_def.h.

◆ ESubjectMaskingType

enum ESubjectMaskingType

Define the possible subject masking types.

Enumerator
eNoSubjMasking
eSoftSubjMasking
eHardSubjMasking

Definition at line 235 of file blast_def.h.

Function Documentation

◆ __sfree()

void __sfree ( void ** x )

Implemented in blast_util.c.

See also: sfree

Definition at line 40 of file blast_util.c.

References free(), and NULL.

◆ SBlastProgressFree()

SBlastProgress* SBlastProgressFree ( SBlastProgress * progress_info )

Deallocates a SBlastProgress structure.

Implemented in blast_util.c

Definition at line 1397 of file blast_util.c.

References NULL, and sfree.

◆ SBlastProgressNew()

SBlastProgress* SBlastProgressNew ( void * user_data )

Allocates and initializes a new SBlastProgress structure.

Parameters

user_data user-provided data (not owned by the resulting structure) [in] Implemented in blast_util.c

Definition at line 1387 of file blast_util.c.

References calloc(), NULL, and SBlastProgress::user_data.

Referenced by CPrelimSearchThread::CPrelimSearchThread(), CBlastPrelimSearch::SetInterruptCallback(), and SplitQuery_CreateChunkData().

◆ SBlastProgressReset()

void SBlastProgressReset ( SBlastProgress * progress_info )

Resets the progress structure to its original state (as if newly allocated) for a fresh start without touching the user_data field.

Definition at line 1406 of file blast_util.c.

References ePrelimSearch, and SBlastProgress::stage.

Referenced by CPrelimSearchRunner::operator()().

◆ SSeqRangeArrayLessThanOrEqual()

Int4 SSeqRangeArrayLessThanOrEqual	(	const SSeqRange *	ranges,
		Int4	num_ranges,
		Int4	target
	)

Returns the index of the range, such that this element is the first range that either contains the target or if no such range exists, the index of the first range, such that the target is less than this range.

Precondition: ranges array is sorted on the starting coordinates (i.e.: SSeqRange::left)

Parameters

ranges	array of SSeqRange structures to search [in]
num_ranges	number of elements in the ranges array [in]
target	element to look for [in]

Returns: the index of interest in the ranges array or -1 if the function was called with invalid parameters

Definition at line 56 of file blast_util.c.

References b, and NULL.

Referenced by BOOST_AUTO_TEST_CASE().

◆ SSeqRangeIntersectsWith()

static NCBI_INLINE Boolean SSeqRangeIntersectsWith	(	const SSeqRange *	a,
		const SSeqRange *	b
	)

static

Determine if two ranges intersect.

Parameters

a	first range to compare [in]
b	second range to compare [in]

Returns: TRUE if they intersect, otherwise FALSE

Definition at line 173 of file blast_def.h.

References a, b, FALSE, and TRUE.

Referenced by BOOST_AUTO_TEST_CASE().

◆ SSeqRangeNew()

SSeqRange SSeqRangeNew	(	Int4	start,
		Int4	stop
	)

Create a new SSeqRange structure with both fields initialized.

Parameters

start	the start of the range [in]
stop	the end of the range [in]

Definition at line 47 of file blast_util.c.

References SSeqRange::left, and SSeqRange::right.

Referenced by BOOST_AUTO_TEST_CASE().

Variable Documentation

◆ kDustLevel

const int kDustLevel

extern

Level parameter used by dust.

Definition at line 46 of file blast_options.c.

Referenced by BlastFilteringOptionsToString(), s_MergeDustOptions(), and SDustOptionsNew().

◆ kDustLinker

const int kDustLinker

extern

Parameter used by dust to link together close low-complexity segments.

Definition at line 48 of file blast_options.c.

Referenced by BlastFilteringOptionsToString(), s_MergeDustOptions(), and SDustOptionsNew().

◆ kDustWindow

const int kDustWindow

extern

Window parameter used by dust.

Definition at line 47 of file blast_options.c.

Referenced by BlastFilteringOptionsToString(), s_MergeDustOptions(), and SDustOptionsNew().

◆ kSegHicut

const double kSegHicut

extern

Hicut parameter for SEG.

Definition at line 47 of file blast_seg.c.

Referenced by BlastFilteringOptionsToString(), SegMaskerApplication::Init(), s_MergeSegOptions(), SegParametersNewAa(), and SSegOptionsNew().

◆ kSegLocut

const double kSegLocut

extern

Locut parameter for SEG.

Definition at line 46 of file blast_seg.c.

Referenced by BlastFilteringOptionsToString(), SegMaskerApplication::Init(), s_MergeSegOptions(), SegParametersNewAa(), and SSegOptionsNew().

◆ kSegWindow

const int kSegWindow

extern

Window that SEG examines at once.

Definition at line 45 of file blast_seg.c.

Referenced by BlastFilteringOptionsToString(), SegMaskerApplication::Init(), s_MergeSegOptions(), SegParametersNewAa(), and SSegOptionsNew().

◆ kUngappedHSPNumMax

const int kUngappedHSPNumMax

extern

Maximum number of HPSs to be saved in an ungapped search.

Value defined in blast_options.c

Classes

Macros

Typedefs

Enumerations

Functions

Variables

Detailed Description

Macro Definition Documentation

◆ BLAST_CMP

◆ CODON_LENGTH

◆ COMPRESSION_RATIO

◆ DEFAULT_LONGEST_INTRON

◆ GENCODE_STRLEN

◆ NUM_FRAMES

◆ NUM_STRANDS

◆ sfree

Typedef Documentation

◆ BLAST_SequenceBlk

◆ BlastMaskLoc

◆ BlastOffsetPair

◆ BlastSeqLoc

◆ EBlastStage

◆ ESubjectMaskingType

◆ SBlastProgress

◆ SBlastTargetTranslation

◆ SPHIPatternInfo

◆ SPHIQueryInfo

◆ SSeqRange

◆ TInterruptFnPtr

Enumeration Type Documentation

◆ EBlastStage

◆ ESubjectMaskingType

Function Documentation

◆ __sfree()

◆ SBlastProgressFree()

◆ SBlastProgressNew()

◆ SBlastProgressReset()

◆ SSeqRangeArrayLessThanOrEqual()

◆ SSeqRangeIntersectsWith()

◆ SSeqRangeNew()

Variable Documentation

◆ kDustLevel

◆ kDustLinker

◆ kDustWindow

◆ kSegHicut

◆ kSegLocut

◆ kSegWindow

◆ kUngappedHSPNumMax