The structures and functions in blast_options. 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_def.h>
#include <algo/blast/core/blast_message.h>

Include dependency graph for blast_options.h:

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Go to the source code of this file.

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Classes
struct	LookupTableOptions
	Options needed to construct a lookup table Also needed: query sequence and query length. More...

struct	SDustOptions
	Options for dust algorithm, applies only to nucl. More...

struct	SSegOptions
	Options for SEG algorithm, applies only to protein-protein comparisons. More...

struct	SRepeatFilterOptions
	Filtering options for organsim specific repeats filtering. More...

struct	SWindowMaskerOptions
	Filtering options for organism-specific filtering with Window Masker. More...

struct	SReadQualityOptions
	Filtering options for mapping next-generation sequences. More...

struct	SBlastFilterOptions
	All filtering options. More...

struct	QuerySetUpOptions
	Options required for setting up the query sequence. More...

struct	BlastInitialWordOptions
	Options needed for initial word finding and processing. More...

struct	BlastExtensionOptions
	Options used for gapped extension These include: a. More...

struct	BlastHSPBestHitOptions
	Options for the Best Hit HSP collection algorithm. More...

struct	BlastHSPCullingOptions
	Options for the HSP culling algorithm. More...

struct	BlastHSPSubjectBestHitOptions

struct	BlastHSPFilteringOptions
	Structure containing the HSP filtering/writing options. More...

struct	BlastHitSavingOptions
	Options used when evaluating and saving hits These include: a. More...

struct	BlastScoringOptions
	Scoring options block Used to produce the BlastScoreBlk structure This structure may be needed for lookup table construction (proteins only), and for evaluating alignments. More...

struct	BlastEffectiveLengthsOptions
	Options for setting up effective lengths and search spaces. More...

struct	PSIBlastOptions
	Options used in protein BLAST only (PSI, PHI, RPS and translated BLAST) Some of these possibly should be transfered elsewhere. More...

struct	BlastDatabaseOptions
	Options used to create the ReadDBFILE structure Include database name and various information for restricting the database to a subset. More...

Macros
#define	BLAST_WINDOW_SIZE_PROT 40
	Some default values (used when creating blast options block and for command-line program defaults. More...

#define	BLAST_WINDOW_SIZE_NUCL 0
	default window size (blastn) More...

#define	BLAST_WINDOW_SIZE_MEGABLAST 0
	default window size (contiguous megablast) More...

#define	BLAST_WINDOW_SIZE_DISC 40
	default window size (discontiguous megablast) More...

#define	BLAST_SCAN_RANGE_NUCL 0
	default scan range (blastn) More...

#define	BLAST_WORDSIZE_PROT 3
	length of word to trigger an extension. More...

#define	BLAST_WORDSIZE_NUCL 11
	default word size (blastn) More...

#define	BLAST_WORDSIZE_MEGABLAST 28
	default word size (contiguous megablast; for discontig megablast the word size is explicitly overridden) More...

#define	BLAST_WORDSIZE_MAPPER 18
	default word size for mapping rna-seq to a genome More...

#define	BLAST_DEFAULT_MATRIX "BLOSUM62"
	Default matrix name: BLOSUM62. More...

#define	BLAST_GAP_OPEN_PROT 11
	Protein gap costs are the defaults for the BLOSUM62 scoring matrix. More...

#define	BLAST_GAP_OPEN_NUCL 5
	default gap open penalty (blastn) More...

#define	BLAST_GAP_OPEN_MEGABLAST 0
	default gap open penalty (megablast with greedy gapped alignment) More...

#define	BLAST_GAP_OPEN_MAPPER 0

#define	BLAST_GAP_EXTN_PROT 1
	cost to extend a gap. More...

#define	BLAST_GAP_EXTN_NUCL 2
	default gap open penalty (blastn) More...

#define	BLAST_GAP_EXTN_MEGABLAST 0
	default gap open penalty (megablast) with greedy gapped alignment) More...

#define	BLAST_GAP_EXTN_MAPPER 4

#define	BLAST_WORD_THRESHOLD_BLASTP 11
	neighboring word score thresholds; a threshold of zero means that only query and subject words that match exactly will go into the BLAST lookup table when it is generated More...

#define	BLAST_WORD_THRESHOLD_BLASTP_FAST 20

#define	BLAST_WORD_THRESHOLD_BLASTP_WD_SZ_6 21

#define	BLAST_WORD_THRESHOLD_BLASTP_WD_SZ_7 20.25

#define	BLAST_WORD_THRESHOLD_BLASTN 0
	default threshold (blastn) More...

#define	BLAST_WORD_THRESHOLD_BLASTX 12
	default threshold (blastx) More...

#define	BLAST_WORD_THRESHOLD_TBLASTN 13
	default neighboring threshold (tblastn/rpstblastn) More...

#define	BLAST_WORD_THRESHOLD_TBLASTX 13
	default threshold (tblastx) More...

#define	BLAST_WORD_THRESHOLD_MEGABLAST 0
	default threshold (megablast) More...

#define	BLAST_UNGAPPED_X_DROPOFF_PROT 7
	default dropoff for ungapped extension; ungapped extensions will stop when the score for the extension has dropped from the current best score by at least this much More...

#define	BLAST_UNGAPPED_X_DROPOFF_NUCL 20
	ungapped dropoff score for blastn (and megablast) More...

#define	BLAST_GAP_X_DROPOFF_PROT 15
	default dropoff for preliminary gapped extensions More...

#define	BLAST_GAP_X_DROPOFF_NUCL 30
	default dropoff for non-greedy nucleotide gapped extensions More...

#define	BLAST_GAP_X_DROPOFF_GREEDY 25
	default dropoff for greedy nucleotide gapped extensions More...

#define	BLAST_GAP_X_DROPOFF_TBLASTX 0
	default dropoff for tblastx More...

#define	BLAST_GAP_TRIGGER_PROT 22.0
	default bit score that will trigger gapped extension More...

#define	BLAST_GAP_TRIGGER_NUCL 27.0
	default bit score that will trigger a gapped extension for blastn More...

#define	BLAST_GAP_X_DROPOFF_FINAL_PROT 25
	default dropoff for the final gapped extension with traceback More...

#define	BLAST_GAP_X_DROPOFF_FINAL_NUCL 100
	default dropoff for nucleotide gapped extensions) More...

#define	BLAST_GAP_X_DROPOFF_FINAL_TBLASTX 0
	default dropoff for tblastx More...

#define	BLAST_PENALTY -3
	default reward and penalty (only applies to blastn/megablast) More...

#define	BLAST_REWARD 1
	default nucleotide match score More...

#define	BLAST_PENALTY_MAPPER -4

#define	BLAST_REWARD_MAPPER 1

#define	BLAST_EXPECT_VALUE 10.0
	Default parameters for saving hits. More...

#define	BLAST_HITLIST_SIZE 500
	Number of database sequences to save hits for. More...

#define	PSI_INCLUSION_ETHRESH 0.002
	Defaults for PSI-BLAST and DELTA-BLAST options. More...

#define	PSI_PSEUDO_COUNT_CONST 0
	Pseudo-count constant for PSI-BLAST. More...

#define	DELTA_INCLUSION_ETHRESH 0.05
	Inclusion threshold for DELTA-BLAST. More...

#define	BLAST_GENETIC_CODE 1
	Default genetic code for query and/or database. More...

#define	MAX_DB_WORD_COUNT_MAPPER 30
	Default max frequency for a database word. More...

#define	MAGICBLAST_MAX_INSERT_SIZE_SPLICED 1000000
	Default maximum insert size: distance on the subject between reads that belong to a pair, for spliced and non-spliced alignments. More...

#define	MAGICBLAST_MAX_INSERT_SIZE_NONSPLICED 100000

#define	kDefaultRepeatFilterDb "repeat/repeat_9606"
	Default value for repeats database filtering. More...

#define	DEFAULT_SUBJECT_BESTHIT_PROT_MAX_RANGE_DIFF 3

#define	DEFAULT_SUBJECT_BESTHIT_NUCL_MAX_RANGE_DIFF 3

Typedefs
typedef struct LookupTableOptions	LookupTableOptions
	Options needed to construct a lookup table Also needed: query sequence and query length. More...

typedef struct SDustOptions	SDustOptions
	Options for dust algorithm, applies only to nucl. More...

typedef struct SSegOptions	SSegOptions
	Options for SEG algorithm, applies only to protein-protein comparisons. More...

typedef struct SRepeatFilterOptions	SRepeatFilterOptions
	Filtering options for organsim specific repeats filtering. More...

typedef struct SWindowMaskerOptions	SWindowMaskerOptions
	Filtering options for organism-specific filtering with Window Masker. More...

typedef struct SReadQualityOptions	SReadQualityOptions
	Filtering options for mapping next-generation sequences. More...

typedef struct SBlastFilterOptions	SBlastFilterOptions
	All filtering options. More...

typedef struct QuerySetUpOptions	QuerySetUpOptions
	Options required for setting up the query sequence. More...

typedef struct BlastInitialWordOptions	BlastInitialWordOptions
	Options needed for initial word finding and processing. More...

typedef enum EBlastPrelimGapExt	EBlastPrelimGapExt
	The algorithm to be used for preliminary gapped extensions. More...

typedef enum EBlastTbackExt	EBlastTbackExt
	The algorithm to be used for final gapped extensions with traceback. More...

typedef struct BlastExtensionOptions	BlastExtensionOptions
	Options used for gapped extension These include: a. More...

typedef struct BlastHSPBestHitOptions	BlastHSPBestHitOptions
	Options for the Best Hit HSP collection algorithm. More...

typedef struct BlastHSPCullingOptions	BlastHSPCullingOptions
	Options for the HSP culling algorithm. More...

typedef struct BlastHSPSubjectBestHitOptions	BlastHSPSubjectBestHitOptions

typedef struct BlastHSPFilteringOptions	BlastHSPFilteringOptions
	Structure containing the HSP filtering/writing options. More...

typedef struct BlastHitSavingOptions	BlastHitSavingOptions
	Options used when evaluating and saving hits These include: a. More...

typedef struct BlastScoringOptions	BlastScoringOptions
	Scoring options block Used to produce the BlastScoreBlk structure This structure may be needed for lookup table construction (proteins only), and for evaluating alignments. More...

typedef struct BlastEffectiveLengthsOptions	BlastEffectiveLengthsOptions
	Options for setting up effective lengths and search spaces. More...

typedef struct PSIBlastOptions	PSIBlastOptions
	Options used in protein BLAST only (PSI, PHI, RPS and translated BLAST) Some of these possibly should be transfered elsewhere. More...

typedef struct BlastDatabaseOptions	BlastDatabaseOptions
	Options used to create the ReadDBFILE structure Include database name and various information for restricting the database to a subset. More...

typedef enum EFilterOptions	EFilterOptions
	Types of filtering options. More...

Enumerations
enum	ELookupTableType { eMBLookupTable , eSmallNaLookupTable , eNaLookupTable , eAaLookupTable , eCompressedAaLookupTable , ePhiLookupTable , ePhiNaLookupTable , eRPSLookupTable , eIndexedMBLookupTable , eMixedMBLookupTable , eNaHashLookupTable }
	Types of the lookup table. More...

enum	EBlastPrelimGapExt { eDynProgScoreOnly , eGreedyScoreOnly , eJumperWithTraceback , eSmithWatermanScoreOnly }
	The algorithm to be used for preliminary gapped extensions. More...

enum	EBlastTbackExt { eDynProgTbck , eGreedyTbck , eSmithWatermanTbck , eSmithWatermanTbckFull }
	The algorithm to be used for final gapped extensions with traceback. More...

enum	EFilterOptions { eSeg , eDust , eRepeats , eDustRepeats , eEmpty }
	Types of filtering options. More...

Functions
SDustOptions *	SDustOptionsFree (SDustOptions *dust_options)
	Frees SDustOptions. More...

Int2	SDustOptionsNew (SDustOptions **dust_options)
	Allocates memory for SDustOptions, fills in defaults. More...

SSegOptions *	SSegOptionsFree (SSegOptions *seg_options)
	Frees SSegOptions. More...

Int2	SSegOptionsNew (SSegOptions **seg_options)
	Allocates memory for SSegOptions, fills in defaults. More...

Int2	SRepeatFilterOptionsResetDB (SRepeatFilterOptions *repeat_options, const char dbname)
	Resets name of db for repeat filtering. More...

Int2	SWindowMaskerOptionsResetDB (SWindowMaskerOptions *winmask_options, const char dbname)
	Resets name of db for window masker filtering. More...

SRepeatFilterOptions *	SRepeatFilterOptionsFree (SRepeatFilterOptions *repeat_options)
	Frees SRepeatFilterOptions. More...

SWindowMaskerOptions *	SWindowMaskerOptionsFree (SWindowMaskerOptions *winmask_options)
	Frees SWindowMaskerOptions. More...

Int2	SRepeatFilterOptionsNew (SRepeatFilterOptions **repeat_options)
	Allocates memory for SRepeatFilterOptions, fills in defaults. More...

Int2	SWindowMaskerOptionsNew (SWindowMaskerOptions **winmask_options)
	Allocates memory for SWindowMaskerOptions, fills in defaults. More...

Int2	SReadQualityOptionsNew (SReadQualityOptions **read_quality_options)
	Allocates memory for SReadQualityOptions, fills in defaults. More...

SReadQualityOptions *	SReadQualityOptionsFree (SReadQualityOptions *read_quality_options)
	Frees memory for SReadQualityOptions. More...

SBlastFilterOptions *	SBlastFilterOptionsFree (SBlastFilterOptions *filter_options)
	Frees SBlastFilterOptions and all subservient structures. More...

Int2	SBlastFilterOptionsMerge (SBlastFilterOptions *combined, const SBlastFilterOptions opt1, const SBlastFilterOptions *opt2)
	Merges two sets of options together, taking the non-default one as preferred. More...

Int2	SBlastFilterOptionsNew (SBlastFilterOptions **filter_options, EFilterOptions type)
	Allocates memory for SBlastFilterOptions and. More...

Boolean	SBlastFilterOptionsNoFiltering (const SBlastFilterOptions *filter_options)
	Queries whether no masking is required. More...

Boolean	SBlastFilterOptionsMaskAtHash (const SBlastFilterOptions *filter_options)
	Queries whether masking should be done only for the lookup table or for the entire search. More...

Int2	SBlastFilterOptionsValidate (EBlastProgramType program_number, const SBlastFilterOptions filter_options, Blast_Message *blast_message)
	Validates filter options to ensure that program and options are consistent and that options have valid values. More...

QuerySetUpOptions *	BlastQuerySetUpOptionsFree (QuerySetUpOptions *options)
	Deallocate memory for QuerySetUpOptions. More...

Int2	BlastQuerySetUpOptionsNew (QuerySetUpOptions **options)
	Allocate memory for QuerySetUpOptions and fill with default values. More...

Int2	BLAST_FillQuerySetUpOptions (QuerySetUpOptions options, EBlastProgramType program, const char filter_string, Uint1 strand_option)
	Fill non-default contents of the QuerySetUpOptions. More...

BlastInitialWordOptions *	BlastInitialWordOptionsFree (BlastInitialWordOptions *options)
	Deallocate memory for BlastInitialWordOptions. More...

Int2	BlastInitialWordOptionsNew (EBlastProgramType program, BlastInitialWordOptions **options)
	Allocate memory for BlastInitialWordOptions and fill with default values. More...

Int2	BlastInitialWordOptionsValidate (EBlastProgramType program_number, const BlastInitialWordOptions options, Blast_Message *blast_msg)
	Validate correctness of the initial word options. More...

Int2	BLAST_FillInitialWordOptions (BlastInitialWordOptions *options, EBlastProgramType program, Int4 window_size, double xdrop_ungapped)
	Fill non-default values in the BlastInitialWordOptions structure. More...

BlastExtensionOptions *	BlastExtensionOptionsFree (BlastExtensionOptions *options)
	Deallocate memory for BlastExtensionOptions. More...

Int2	BlastExtensionOptionsNew (EBlastProgramType program, BlastExtensionOptions **options, Boolean gapped)
	Allocate memory for BlastExtensionOptions and fill with default values. More...

Int2	BLAST_FillExtensionOptions (BlastExtensionOptions *options, EBlastProgramType program, Int4 greedy, double x_dropoff, double x_dropoff_final)
	Fill non-default values in the BlastExtensionOptions structure. More...

Int2	BlastExtensionOptionsValidate (EBlastProgramType program_number, const BlastExtensionOptions options, Blast_Message *blast_msg)
	Validate contents of BlastExtensionOptions. More...

BlastScoringOptions *	BlastScoringOptionsFree (BlastScoringOptions *options)
	Deallocate memory for BlastScoringOptions. More...

Int2	BlastScoringOptionsNew (EBlastProgramType program, BlastScoringOptions **options)
	Allocate memory for BlastScoringOptions and fill with default values. More...

Int2	BLAST_FillScoringOptions (BlastScoringOptions options, EBlastProgramType program, Boolean greedy_extension, Int4 penalty, Int4 reward, const char matrix, Int4 gap_open, Int4 gap_extend)
	Fill non-default values in the BlastScoringOptions structure. More...

Int2	BlastScoringOptionsValidate (EBlastProgramType program_number, const BlastScoringOptions options, Blast_Message *blast_msg)
	Validate contents of BlastScoringOptions. More...

Int2	BlastScoringOptionsDup (BlastScoringOptions *new_opt, const BlastScoringOptions old_opt)
	Produces copy of "old" options, with new memory allocated. More...

Int2	BlastScoringOptionsSetMatrix (BlastScoringOptions opts, const char matrix_name)
	Resets matrix name option. More...

BlastEffectiveLengthsOptions *	BlastEffectiveLengthsOptionsFree (BlastEffectiveLengthsOptions *options)
	Deallocate memory for BlastEffectiveLengthsOptions*. More...

Int2	BlastEffectiveLengthsOptionsNew (BlastEffectiveLengthsOptions **options)
	Allocate memory for BlastEffectiveLengthsOptions* and fill with default values. More...

Boolean	BlastEffectiveLengthsOptions_IsSearchSpaceSet (const BlastEffectiveLengthsOptions *options)
	Return true if the search spaces is set for any of the queries in the search. More...

Int2	BLAST_FillEffectiveLengthsOptions (BlastEffectiveLengthsOptions options, Int4 dbseq_num, Int8 db_length, Int8 searchsp_eff, Int4 num_searchsp)
	Fill the non-default values in the BlastEffectiveLengthsOptions structure. More...

Int2	LookupTableOptionsNew (EBlastProgramType program, LookupTableOptions **options)
	Allocate memory for lookup table options and fill with default values. More...

Int2	BLAST_FillLookupTableOptions (LookupTableOptions *options, EBlastProgramType program, Boolean is_megablast, double threshold, Int4 word_size)
	Allocate memory for lookup table options and fill with default values. More...

LookupTableOptions *	LookupTableOptionsFree (LookupTableOptions *options)
	Deallocates memory for LookupTableOptions*. More...

Int2	LookupTableOptionsValidate (EBlastProgramType program_number, const LookupTableOptions options, Blast_Message *blast_msg)
	Validate LookupTableOptions. More...

BlastHitSavingOptions *	BlastHitSavingOptionsFree (BlastHitSavingOptions *options)
	Deallocate memory for BlastHitSavingOptions. More...

Int2	BlastHitSavingOptionsValidate (EBlastProgramType program_number, const BlastHitSavingOptions options, Blast_Message *blast_msg)
	Validate BlastHitSavingOptions. More...

Int2	BlastHitSavingOptionsNew (EBlastProgramType program, BlastHitSavingOptions **options, Boolean gapped_calculation)
	Allocate memory for BlastHitSavingOptions. More...

Int2	BLAST_FillHitSavingOptions (BlastHitSavingOptions *options, double evalue, Int4 hitlist_size, Boolean is_gapped, Int4 culling_limit, Int4 min_diag_separation)
	Allocate memory for BlastHitSavingOptions. More...

Int2	PSIBlastOptionsNew (PSIBlastOptions **psi_options)
	Initialize default options for PSI BLAST. More...

Int2	PSIBlastOptionsValidate (const PSIBlastOptions psi_options, Blast_Message *blast_msg)
	Validates the PSI BLAST options so that they have sane values. More...

PSIBlastOptions *	PSIBlastOptionsFree (PSIBlastOptions *psi_options)
	Deallocate PSI BLAST options. More...

BlastHSPBestHitOptions *	BlastHSPBestHitOptionsNew (double overhang, double score_edge)
	Allocate and initialize a BlastHSPBestHitOptions structure. More...

Int2	BlastHSPBestHitOptionsValidate (const BlastHSPFilteringOptions *opts)
	Validate the best hit algorithm parameters (if any) in the. More...

BlastHSPBestHitOptions *	BlastHSPBestHitOptionsFree (BlastHSPBestHitOptions *opt)
	Deallocate a BlastHSPBestHitOptions structure. More...

BlastHSPCullingOptions *	BlastHSPCullingOptionsNew (int max)
	Allocate a new object for culling options. More...

Int2	BlastHSPCullingOptionsValidate (const BlastHSPFilteringOptions *opts)
	Validate culling options. More...

BlastHSPCullingOptions *	BlastHSPCullingOptionsFree (BlastHSPCullingOptions *culling_opts)
	Deallocates culling options structure. More...

BlastHSPFilteringOptions *	BlastHSPFilteringOptionsNew ()
	Allocate and initialize a BlastHSPFilteringOptions structure. More...

Int2	BlastHSPFilteringOptions_AddBestHit (BlastHSPFilteringOptions filt_opts, BlastHSPBestHitOptions *opts, EBlastStage stage)
	Add the best hit options. More...

Int2	BlastHSPFilteringOptions_AddCulling (BlastHSPFilteringOptions filt_opts, BlastHSPCullingOptions *opts, EBlastStage stage)
	Validates the BlastHSPFilteringOptions structure. More...

Int2	BlastHSPFilteringOptionsValidate (const BlastHSPFilteringOptions *opts)
	Validates the BlastHSPFilteringOptions structure. More...

BlastHSPFilteringOptions *	BlastHSPFilteringOptionsFree (BlastHSPFilteringOptions *opts)
	Deallocate a BlastHSPFilteringOptions structure. More...

Int2	BlastDatabaseOptionsNew (BlastDatabaseOptions **db_options)
	Allocates the BlastDatabase options structure and sets the default database genetic code value (BLAST_GENETIC_CODE). More...

BlastDatabaseOptions *	BlastDatabaseOptionsFree (BlastDatabaseOptions *db_options)
	Deallocate database options. More...

Int2	BLAST_InitDefaultOptions (EBlastProgramType blast_program, LookupTableOptions lookup_options, QuerySetUpOptions query_setup_options, BlastInitialWordOptions word_options, BlastExtensionOptions ext_options, BlastHitSavingOptions hit_options, BlastScoringOptions score_options, BlastEffectiveLengthsOptions eff_len_options, PSIBlastOptions protein_options, BlastDatabaseOptions **db_options)
	Initialize all the BLAST search options structures with the default values. More...

Int2	BLAST_ValidateOptions (EBlastProgramType program_number, const BlastExtensionOptions ext_options, const BlastScoringOptions score_options, const LookupTableOptions lookup_options, const BlastInitialWordOptions word_options, const BlastHitSavingOptions hit_options, Blast_Message *blast_msg)
	Validate all options. More...

Int2	BLAST_GetSuggestedThreshold (EBlastProgramType program_number, const char matrixName, double threshold)
	Get thresholds for word-finding suggested by Stephen Altschul. More...

Int2	BLAST_GetSuggestedWindowSize (EBlastProgramType program_number, const char matrixName, Int4 window_size)
	Get window sizes for two hit algorithm suggested by Stephen Altschul. More...

BlastHSPSubjectBestHitOptions *	BlastHSPSubjectBestHitOptionsNew (Boolean isProtein)
	Allocate a new object for subject besthit options. More...

Int2	BlastHSPSubjectBestHitOptionsValidate (const BlastHSPFilteringOptions *opts)
	Validate subject besthit options. More...

BlastHSPSubjectBestHitOptions *	BlastHSPSubjectBestHitOptionsFree (BlastHSPSubjectBestHitOptions *subject_besthit_opts)
	Deallocates subject besthit structure. More...

Int2	BlastHSPFilteringOptions_AddSubjectBestHit (BlastHSPFilteringOptions filt_opts, BlastHSPSubjectBestHitOptions *subject_besthit)

Variables
const double	kPSSM_NoImpalaScaling
	Value used to indicate that no IMPALA-style scaling should be performed when scaling a PSSM. More...

Detailed Description

The structures and functions in blast_options.

[ch] should be used to specify user preferences. The options structures should not be changed by the BLAST code but rather be read to determine user preferences. When possible these structures should be passed in as "const".

Definition in file blast_options.h.

Macro Definition Documentation

◆ BLAST_DEFAULT_MATRIX

#define BLAST_DEFAULT_MATRIX "BLOSUM62"

Default matrix name: BLOSUM62.

Definition at line 77 of file blast_options.h.

◆ BLAST_EXPECT_VALUE

#define BLAST_EXPECT_VALUE 10.0

Default parameters for saving hits.

by default, alignments whose expect value exceeds this number are discarded

Definition at line 159 of file blast_options.h.

◆ BLAST_GAP_EXTN_MAPPER

#define BLAST_GAP_EXTN_MAPPER 4

Definition at line 98 of file blast_options.h.

◆ BLAST_GAP_EXTN_MEGABLAST

#define BLAST_GAP_EXTN_MEGABLAST 0

default gap open penalty (megablast) with greedy gapped alignment)

Definition at line 96 of file blast_options.h.

◆ BLAST_GAP_EXTN_NUCL

#define BLAST_GAP_EXTN_NUCL 2

default gap open penalty (blastn)

Definition at line 94 of file blast_options.h.

◆ BLAST_GAP_EXTN_PROT

#define BLAST_GAP_EXTN_PROT 1

cost to extend a gap.

default gap open penalty (all protein searches)

Definition at line 93 of file blast_options.h.

◆ BLAST_GAP_OPEN_MAPPER

#define BLAST_GAP_OPEN_MAPPER 0

Definition at line 89 of file blast_options.h.

◆ BLAST_GAP_OPEN_MEGABLAST

#define BLAST_GAP_OPEN_MEGABLAST 0

default gap open penalty (megablast with greedy gapped alignment)

Definition at line 88 of file blast_options.h.

◆ BLAST_GAP_OPEN_NUCL

#define BLAST_GAP_OPEN_NUCL 5

default gap open penalty (blastn)

Definition at line 86 of file blast_options.h.

◆ BLAST_GAP_OPEN_PROT

#define BLAST_GAP_OPEN_PROT 11

Protein gap costs are the defaults for the BLOSUM62 scoring matrix.

More gap costs are listed in BLASTOptionSetGapParams cost for the existence of a gap. default gap open penalty (all protein searches)

Definition at line 85 of file blast_options.h.

◆ BLAST_GAP_TRIGGER_NUCL

#define BLAST_GAP_TRIGGER_NUCL 27.0

default bit score that will trigger a gapped extension for blastn

Definition at line 141 of file blast_options.h.

◆ BLAST_GAP_TRIGGER_PROT

#define BLAST_GAP_TRIGGER_PROT 22.0

default bit score that will trigger gapped extension

default bit score that will trigger a gapped extension for all protein- based searches

Definition at line 139 of file blast_options.h.

◆ BLAST_GAP_X_DROPOFF_FINAL_NUCL

#define BLAST_GAP_X_DROPOFF_FINAL_NUCL 100

default dropoff for nucleotide gapped extensions)

Definition at line 147 of file blast_options.h.

◆ BLAST_GAP_X_DROPOFF_FINAL_PROT

#define BLAST_GAP_X_DROPOFF_FINAL_PROT 25

default dropoff for the final gapped extension with traceback

default dropoff (all protein- based gapped extensions)

Definition at line 145 of file blast_options.h.

◆ BLAST_GAP_X_DROPOFF_FINAL_TBLASTX

#define BLAST_GAP_X_DROPOFF_FINAL_TBLASTX 0

default dropoff for tblastx

Definition at line 148 of file blast_options.h.

◆ BLAST_GAP_X_DROPOFF_GREEDY

#define BLAST_GAP_X_DROPOFF_GREEDY 25

default dropoff for greedy nucleotide gapped extensions

Definition at line 133 of file blast_options.h.

◆ BLAST_GAP_X_DROPOFF_NUCL

#define BLAST_GAP_X_DROPOFF_NUCL 30

default dropoff for non-greedy nucleotide gapped extensions

Definition at line 131 of file blast_options.h.

◆ BLAST_GAP_X_DROPOFF_PROT

#define BLAST_GAP_X_DROPOFF_PROT 15

default dropoff for preliminary gapped extensions

default dropoff (all protein- based gapped extensions)

Definition at line 129 of file blast_options.h.

◆ BLAST_GAP_X_DROPOFF_TBLASTX

#define BLAST_GAP_X_DROPOFF_TBLASTX 0

default dropoff for tblastx

Definition at line 134 of file blast_options.h.

◆ BLAST_GENETIC_CODE

#define BLAST_GENETIC_CODE 1

Default genetic code for query and/or database.

Use the standard genetic code for converting groups of three nucleotide bases to protein letters

Definition at line 170 of file blast_options.h.

◆ BLAST_HITLIST_SIZE

#define BLAST_HITLIST_SIZE 500

Number of database sequences to save hits for.

Definition at line 161 of file blast_options.h.

◆ BLAST_PENALTY

#define BLAST_PENALTY -3

default reward and penalty (only applies to blastn/megablast)

default nucleotide mismatch score

Definition at line 151 of file blast_options.h.

◆ BLAST_PENALTY_MAPPER

#define BLAST_PENALTY_MAPPER -4

Definition at line 154 of file blast_options.h.

◆ BLAST_REWARD

#define BLAST_REWARD 1

default nucleotide match score

Definition at line 152 of file blast_options.h.

◆ BLAST_REWARD_MAPPER

#define BLAST_REWARD_MAPPER 1

Definition at line 155 of file blast_options.h.

◆ BLAST_SCAN_RANGE_NUCL

#define BLAST_SCAN_RANGE_NUCL 0

default scan range (blastn)

Definition at line 63 of file blast_options.h.

◆ BLAST_UNGAPPED_X_DROPOFF_NUCL

#define BLAST_UNGAPPED_X_DROPOFF_NUCL 20

ungapped dropoff score for blastn (and megablast)

Definition at line 125 of file blast_options.h.

◆ BLAST_UNGAPPED_X_DROPOFF_PROT

#define BLAST_UNGAPPED_X_DROPOFF_PROT 7

default dropoff for ungapped extension; ungapped extensions will stop when the score for the extension has dropped from the current best score by at least this much

ungapped dropoff score for all searches except blastn

Definition at line 123 of file blast_options.h.

◆ BLAST_WINDOW_SIZE_DISC

#define BLAST_WINDOW_SIZE_DISC 40

default window size (discontiguous megablast)

Definition at line 62 of file blast_options.h.

◆ BLAST_WINDOW_SIZE_MEGABLAST

#define BLAST_WINDOW_SIZE_MEGABLAST 0

default window size (contiguous megablast)

Definition at line 60 of file blast_options.h.

◆ BLAST_WINDOW_SIZE_NUCL

#define BLAST_WINDOW_SIZE_NUCL 0

default window size (blastn)

Definition at line 58 of file blast_options.h.

◆ BLAST_WINDOW_SIZE_PROT

#define BLAST_WINDOW_SIZE_PROT 40

Some default values (used when creating blast options block and for command-line program defaults.

When changing these defaults, please remember to update the defaults in the command-line programs "window" between hits to trigger an extension. default window (all protein searches)

Definition at line 57 of file blast_options.h.

◆ BLAST_WORD_THRESHOLD_BLASTN

#define BLAST_WORD_THRESHOLD_BLASTN 0

default threshold (blastn)

Definition at line 111 of file blast_options.h.

◆ BLAST_WORD_THRESHOLD_BLASTP

#define BLAST_WORD_THRESHOLD_BLASTP 11

neighboring word score thresholds; a threshold of zero means that only query and subject words that match exactly will go into the BLAST lookup table when it is generated

default neighboring threshold (blastp and for rpsblast at RPS-BLAST database creation time)

Definition at line 106 of file blast_options.h.

◆ BLAST_WORD_THRESHOLD_BLASTP_FAST

#define BLAST_WORD_THRESHOLD_BLASTP_FAST 20

Definition at line 107 of file blast_options.h.

◆ BLAST_WORD_THRESHOLD_BLASTP_WD_SZ_6

#define BLAST_WORD_THRESHOLD_BLASTP_WD_SZ_6 21

Definition at line 108 of file blast_options.h.

◆ BLAST_WORD_THRESHOLD_BLASTP_WD_SZ_7

#define BLAST_WORD_THRESHOLD_BLASTP_WD_SZ_7 20.25

Definition at line 109 of file blast_options.h.

◆ BLAST_WORD_THRESHOLD_BLASTX

#define BLAST_WORD_THRESHOLD_BLASTX 12

default threshold (blastx)

Definition at line 112 of file blast_options.h.

◆ BLAST_WORD_THRESHOLD_MEGABLAST

#define BLAST_WORD_THRESHOLD_MEGABLAST 0

default threshold (megablast)

Definition at line 116 of file blast_options.h.

◆ BLAST_WORD_THRESHOLD_TBLASTN

#define BLAST_WORD_THRESHOLD_TBLASTN 13

default neighboring threshold (tblastn/rpstblastn)

Definition at line 114 of file blast_options.h.

◆ BLAST_WORD_THRESHOLD_TBLASTX

#define BLAST_WORD_THRESHOLD_TBLASTX 13

default threshold (tblastx)

Definition at line 115 of file blast_options.h.

◆ BLAST_WORDSIZE_MAPPER

#define BLAST_WORDSIZE_MAPPER 18

default word size for mapping rna-seq to a genome

Definition at line 74 of file blast_options.h.

◆ BLAST_WORDSIZE_MEGABLAST

#define BLAST_WORDSIZE_MEGABLAST 28

default word size (contiguous megablast; for discontig megablast the word size is explicitly overridden)

Definition at line 71 of file blast_options.h.

◆ BLAST_WORDSIZE_NUCL

#define BLAST_WORDSIZE_NUCL 11

default word size (blastn)

Definition at line 67 of file blast_options.h.

◆ BLAST_WORDSIZE_PROT

#define BLAST_WORDSIZE_PROT 3

length of word to trigger an extension.

default word size (all protein searches)

Definition at line 66 of file blast_options.h.

◆ DEFAULT_SUBJECT_BESTHIT_NUCL_MAX_RANGE_DIFF

#define DEFAULT_SUBJECT_BESTHIT_NUCL_MAX_RANGE_DIFF 3

Definition at line 1212 of file blast_options.h.

◆ DEFAULT_SUBJECT_BESTHIT_PROT_MAX_RANGE_DIFF

#define DEFAULT_SUBJECT_BESTHIT_PROT_MAX_RANGE_DIFF 3

Definition at line 1211 of file blast_options.h.

◆ DELTA_INCLUSION_ETHRESH

#define DELTA_INCLUSION_ETHRESH 0.05

Inclusion threshold for DELTA-BLAST.

Definition at line 165 of file blast_options.h.

◆ kDefaultRepeatFilterDb

#define kDefaultRepeatFilterDb "repeat/repeat_9606"

Default value for repeats database filtering.

Definition at line 246 of file blast_options.h.

◆ MAGICBLAST_MAX_INSERT_SIZE_NONSPLICED

#define MAGICBLAST_MAX_INSERT_SIZE_NONSPLICED 100000

Definition at line 179 of file blast_options.h.

◆ MAGICBLAST_MAX_INSERT_SIZE_SPLICED

#define MAGICBLAST_MAX_INSERT_SIZE_SPLICED 1000000

Default maximum insert size: distance on the subject between reads that belong to a pair, for spliced and non-spliced alignments.

Definition at line 178 of file blast_options.h.

◆ MAX_DB_WORD_COUNT_MAPPER

#define MAX_DB_WORD_COUNT_MAPPER 30

Default max frequency for a database word.

Words with higher frequency will be masked in the lookup table.

Definition at line 174 of file blast_options.h.

◆ PSI_INCLUSION_ETHRESH

#define PSI_INCLUSION_ETHRESH 0.002

Defaults for PSI-BLAST and DELTA-BLAST options.

Inclusion threshold for PSI BLAST

Definition at line 163 of file blast_options.h.

◆ PSI_PSEUDO_COUNT_CONST

#define PSI_PSEUDO_COUNT_CONST 0

Pseudo-count constant for PSI-BLAST.

Definition at line 164 of file blast_options.h.

Typedef Documentation

◆ BlastDatabaseOptions

typedef struct BlastDatabaseOptions BlastDatabaseOptions

Options used to create the ReadDBFILE structure Include database name and various information for restricting the database to a subset.

◆ BlastEffectiveLengthsOptions

typedef struct BlastEffectiveLengthsOptions BlastEffectiveLengthsOptions

Options for setting up effective lengths and search spaces.

The values are those the user has specified to override the real sizes.

◆ BlastExtensionOptions

typedef struct BlastExtensionOptions BlastExtensionOptions

Options used for gapped extension These include: a.

Penalties for various types of gapping; b. Drop-off values for the extension algorithms tree exploration; c. Parameters identifying what kind of extension algorithm(s) should be used.

◆ BlastHitSavingOptions

typedef struct BlastHitSavingOptions BlastHitSavingOptions

Options used when evaluating and saving hits These include: a.

Restrictions on the number of hits to be saved; b. Restrictions on the quality and positions of hits to be saved; c. Parameters used to evaluate the quality of hits.

◆ BlastHSPBestHitOptions

typedef struct BlastHSPBestHitOptions BlastHSPBestHitOptions

Options for the Best Hit HSP collection algorithm.

◆ BlastHSPCullingOptions

typedef struct BlastHSPCullingOptions BlastHSPCullingOptions

Options for the HSP culling algorithm.

◆ BlastHSPFilteringOptions

typedef struct BlastHSPFilteringOptions BlastHSPFilteringOptions

Structure containing the HSP filtering/writing options.

◆ BlastHSPSubjectBestHitOptions

typedef struct BlastHSPSubjectBestHitOptions BlastHSPSubjectBestHitOptions

◆ BlastInitialWordOptions

typedef struct BlastInitialWordOptions BlastInitialWordOptions

Options needed for initial word finding and processing.

◆ BlastScoringOptions

typedef struct BlastScoringOptions BlastScoringOptions

Scoring options block Used to produce the BlastScoreBlk structure This structure may be needed for lookup table construction (proteins only), and for evaluating alignments.

◆ EBlastPrelimGapExt

typedef enum EBlastPrelimGapExt EBlastPrelimGapExt

The algorithm to be used for preliminary gapped extensions.

◆ EBlastTbackExt

typedef enum EBlastTbackExt EBlastTbackExt

The algorithm to be used for final gapped extensions with traceback.

◆ EFilterOptions

typedef enum EFilterOptions EFilterOptions

Types of filtering options.

◆ LookupTableOptions

typedef struct LookupTableOptions LookupTableOptions

Options needed to construct a lookup table Also needed: query sequence and query length.

◆ PSIBlastOptions

typedef struct PSIBlastOptions PSIBlastOptions

Options used in protein BLAST only (PSI, PHI, RPS and translated BLAST) Some of these possibly should be transfered elsewhere.

◆ QuerySetUpOptions

typedef struct QuerySetUpOptions QuerySetUpOptions

Options required for setting up the query sequence.

◆ SBlastFilterOptions

typedef struct SBlastFilterOptions SBlastFilterOptions

All filtering options.

◆ SDustOptions

typedef struct SDustOptions SDustOptions

Options for dust algorithm, applies only to nucl.

-nucl. comparisons. value of less than zero means default value will be applied.

◆ SReadQualityOptions

typedef struct SReadQualityOptions SReadQualityOptions

Filtering options for mapping next-generation sequences.

◆ SRepeatFilterOptions

typedef struct SRepeatFilterOptions SRepeatFilterOptions

Filtering options for organsim specific repeats filtering.

Currently this consist of only the db name but could be expanded in the future to include other types of filtering or other options.

◆ SSegOptions

typedef struct SSegOptions SSegOptions

Options for SEG algorithm, applies only to protein-protein comparisons.

value of less than zero means default value will be applied.

◆ SWindowMaskerOptions

typedef struct SWindowMaskerOptions SWindowMaskerOptions

Filtering options for organism-specific filtering with Window Masker.

The taxid and filename are alternative means of choosing which Window Masker database to use.

Enumeration Type Documentation

◆ EBlastPrelimGapExt

enum EBlastPrelimGapExt

The algorithm to be used for preliminary gapped extensions.

Enumerator
eDynProgScoreOnly	standard affine gapping
eGreedyScoreOnly	Greedy extension (megaBlast)
eJumperWithTraceback	Jumper extension (mapping)
eSmithWatermanScoreOnly	Score-only smith-waterman.

Definition at line 310 of file blast_options.h.

◆ EBlastTbackExt

enum EBlastTbackExt

The algorithm to be used for final gapped extensions with traceback.

Enumerator
eDynProgTbck	standard affine gapping
eGreedyTbck	Greedy extension (megaBlast)
eSmithWatermanTbck	Smith-waterman finds optimal scores, then ALIGN_EX to find alignment.
eSmithWatermanTbckFull	Smith-waterman to find all alignments.

Definition at line 320 of file blast_options.h.

◆ EFilterOptions

enum EFilterOptions

Types of filtering options.

Enumerator
eSeg	low-complexity for proteins.
eDust	low-complexity for nucleotides.
eRepeats	Repeat filtering for nucleotides.
eDustRepeats	Repeat and dust filtering for nucleotides.
eEmpty	no filtering at all.

Definition at line 677 of file blast_options.h.

◆ ELookupTableType

enum ELookupTableType

Types of the lookup table.

Enumerator
eMBLookupTable	megablast lookup table (includes both contiguous and discontiguous megablast)
eSmallNaLookupTable	lookup table for blastn with small query
eNaLookupTable	blastn lookup table
eAaLookupTable	standard protein (blastp) lookup table
eCompressedAaLookupTable	compressed alphabet (blastp) lookup table
ePhiLookupTable	protein lookup table specialized for phi-blast
ePhiNaLookupTable	nucleotide lookup table for phi-blast
eRPSLookupTable	RPS lookup table (rpsblast and rpstblastn)
eIndexedMBLookupTable	use database index as a lookup structure
eMixedMBLookupTable	use when some volumes are searched with index and some are not
eNaHashLookupTable	used for 16-base words

Definition at line 187 of file blast_options.h.

Function Documentation

◆ BLAST_FillEffectiveLengthsOptions()

Int2 BLAST_FillEffectiveLengthsOptions	(	BlastEffectiveLengthsOptions *	options,
		Int4	dbseq_num,
		Int8	db_length,
		Int8 *	searchsp_eff,
		Int4	num_searchsp
	)

Fill the non-default values in the BlastEffectiveLengthsOptions structure.

Parameters

options	The options [in] [out]
dbseq_num	Number of sequences in the database (if zero real value will be used) [in]
db_length	Total length of the database (if zero real value will be used) [in]
*searchsp_eff	Array of effective search spaces (the real value will be used for elements that are 0). If array contains one element, all contexts use this value. If array has multiple elements, the number must match the number of contexts in the search [in]
num_searchsp	The number of elements in searchsp_eff [in]

Definition at line 1038 of file blast_options.c.

References BLASTERR_INVALIDPARAM, BLASTERR_MEMORY, BlastEffectiveLengthsOptions::db_length, BlastEffectiveLengthsOptions::dbseq_num, NULL, BlastEffectiveLengthsOptions::num_searchspaces, and BlastEffectiveLengthsOptions::searchsp_eff.

Referenced by BOOST_AUTO_TEST_CASE(), and CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest().

◆ BLAST_FillExtensionOptions()

Int2 BLAST_FillExtensionOptions	(	BlastExtensionOptions *	options,
		EBlastProgramType	program,
		Int4	greedy,
		double	x_dropoff,
		double	x_dropoff_final
	)

Fill non-default values in the BlastExtensionOptions structure.

Parameters

options	The options structure [in] [out]
program	Program number (blastn, blastp, etc.) [in]
greedy	In how many stages of the search greedy alignment is used (values 0, 1, 2)? FIXME [in]
x_dropoff	X-dropoff parameter value for preliminary gapped extensions [in]
x_dropoff_final	X-dropoff parameter value for final gapped extensions with traceback [in]

Definition at line 699 of file blast_options.c.

References BLAST_GAP_X_DROPOFF_FINAL_NUCL, BLAST_GAP_X_DROPOFF_GREEDY, BLAST_GAP_X_DROPOFF_NUCL, Blast_ProgramIsNucleotide(), Blast_QueryIsPssm(), Blast_SubjectIsTranslated(), BLASTERR_INVALIDPARAM, BlastExtensionOptions::compositionBasedStats, eCompositionBasedStats, eDynProgScoreOnly, eDynProgTbck, eGreedyScoreOnly, eGreedyTbck, BlastExtensionOptions::ePrelimGapExt, BlastExtensionOptions::eTbackExt, BlastExtensionOptions::gap_x_dropoff, BlastExtensionOptions::gap_x_dropoff_final, and MAX.

◆ BLAST_FillHitSavingOptions()

Int2 BLAST_FillHitSavingOptions	(	BlastHitSavingOptions *	options,
		double	evalue,
		Int4	hitlist_size,
		Boolean	is_gapped,
		Int4	culling_limit,
		Int4	min_diag_separation
	)

Allocate memory for BlastHitSavingOptions.

Parameters

options	The options [in] [out]
evalue	The expected value threshold [in]
hitlist_size	How many database sequences to save per query? [in]
is_gapped	is this a gapped alignment? [in]
culling_limit	Number of higher-scoring HSPs that must contain the query range of an HSP before that HSP is declared to be redundant (ignored if zero) [in]
min_diag_separation	Delete HSPs whose endpoints are at most this many diagonals from a higher-scoring HSP. If zero, delete HSPs whose query and subject ranges are enveloped by those of a higher-scoring HSP [in]

Definition at line 1482 of file blast_options.c.

References BLASTERR_INVALIDPARAM, BlastHitSavingOptions::culling_limit, BlastHitSavingOptions::expect_value, BlastHitSavingOptions::hitlist_size, BlastHitSavingOptions::hsp_filt_opt, INT4_MAX, BlastHitSavingOptions::max_edit_distance, BlastHitSavingOptions::min_diag_separation, and NULL.

◆ BLAST_FillInitialWordOptions()

Int2 BLAST_FillInitialWordOptions	(	BlastInitialWordOptions *	options,
		EBlastProgramType	program,
		Int4	window_size,
		double	xdrop_ungapped
	)

Fill non-default values in the BlastInitialWordOptions structure.

Parameters

options	The options structure [in] [out]
program	Program number (blastn, blastp, etc.) [in]
window_size	Size of a largest window between 2 words for the two-hit version [in]
xdrop_ungapped	The value of the X-dropoff for ungapped extensions [in]

Definition at line 634 of file blast_options.c.

References BLASTERR_INVALIDPARAM, BlastInitialWordOptions::window_size, window_size, and BlastInitialWordOptions::x_dropoff.

◆ BLAST_FillLookupTableOptions()

Int2 BLAST_FillLookupTableOptions	(	LookupTableOptions *	options,
		EBlastProgramType	program,
		Boolean	is_megablast,
		double	threshold,
		Int4	word_size
	)

Allocate memory for lookup table options and fill with default values.

Parameters

options	The options [in] [out]
program	Program number (blastn, blastp, etc.) [in]
is_megablast	Megablast (instead of blastn) if TRUE [in]
threshold	Threshold value for finding neighboring words (fractional values are allowed, though unless the engine scales up alignment scores a fractional threshold will be rounded down) [in]
word_size	Number of matched residues in an initial word [in]

Definition at line 1129 of file blast_options.c.

References Blast_ProgramIsRpsBlast(), BLAST_WORDSIZE_MAPPER, BLAST_WORDSIZE_MEGABLAST, BLAST_WORDSIZE_NUCL, BLASTERR_INVALIDPARAM, eAaLookupTable, eBlastTypeBlastn, eBlastTypeBlastp, eBlastTypeBlastx, eBlastTypeMapping, eBlastTypeTblastn, eCompressedAaLookupTable, eMBLookupTable, eNaHashLookupTable, eNaLookupTable, eRPSLookupTable, LookupTableOptions::lut_type, LookupTableOptions::max_db_word_count, MAX_DB_WORD_COUNT_MAPPER, LookupTableOptions::threshold, and LookupTableOptions::word_size.

Referenced by AascanTestFixture::AascanTestFixture(), BOOST_AUTO_TEST_CASE(), CompressedAascanTestFixture::CompressedAascanTestFixture(), CompressedAalookupTestFixture::FillLookupTable(), AalookupTestFixture::FillLookupTable(), TestFixture::SetUpLookupTable(), and CMakeProfileDBApp::x_RPSAddFirstSequence().

◆ BLAST_FillQuerySetUpOptions()

Int2 BLAST_FillQuerySetUpOptions	(	QuerySetUpOptions *	options,
		EBlastProgramType	program,
		const char *	filter_string,
		Uint1	strand_option
	)

Fill non-default contents of the QuerySetUpOptions.

Parameters

options	The options structure [in] [out]
program	Program number (blastn, blastp, etc.) [in]
filter_string	Parsable string of filtering options [in]
strand_option	which strand to search [in]

Definition at line 534 of file blast_options.c.

References BLASTERR_INVALIDPARAM, BlastFilteringOptionsFromString(), eBlastTypeBlastn, eBlastTypeBlastx, eBlastTypeMapping, eBlastTypePhiBlastn, eBlastTypeTblastx, QuerySetUpOptions::filter_string, QuerySetUpOptions::filtering_options, NULL, SBlastFilterOptionsFree(), sfree, and QuerySetUpOptions::strand_option.

Referenced by CMakeProfileDBApp::x_RPSAddFirstSequence().

◆ BLAST_FillScoringOptions()

Int2 BLAST_FillScoringOptions	(	BlastScoringOptions *	options,
		EBlastProgramType	program,
		Boolean	greedy_extension,
		Int4	penalty,
		Int4	reward,
		const char *	matrix,
		Int4	gap_open,
		Int4	gap_extend
	)

Fill non-default values in the BlastScoringOptions structure.

Parameters

options	The options structure [in] [out]
program	Program number (blastn, blastp, etc.) [in]
greedy_extension	Is greedy extension algorithm used? [in]
penalty	Mismatch penalty score (blastn only) [in]
reward	Match reward score (blastn only) [in]
matrix	Name of the BLAST matrix (all except blastn) [in]
gap_open	Extra cost for opening a gap [in]
gap_extend	Cost of a gap [in]

Definition at line 823 of file blast_options.c.

References BLAST_GAP_EXTN_MEGABLAST, BLAST_GAP_EXTN_NUCL, BLAST_GAP_OPEN_MEGABLAST, BLAST_GAP_OPEN_NUCL, Blast_ProgramIsNucleotide(), BLASTERR_INVALIDPARAM, BlastScoringOptionsSetMatrix(), BlastScoringOptions::gap_extend, BlastScoringOptions::gap_open, BlastScoringOptions::penalty, BlastScoringOptions::program_number, and BlastScoringOptions::reward.

Referenced by AascanTestFixture::AascanTestFixture(), BOOST_AUTO_TEST_CASE(), CompressedAascanTestFixture::CompressedAascanTestFixture(), CompressedAalookupTestFixture::FillLookupTable(), AalookupTestFixture::FillLookupTable(), TestFixture::SetUpLookupTable(), and CScoreBuilder::x_Initialize().

◆ BLAST_GetSuggestedThreshold()

Int2 BLAST_GetSuggestedThreshold	(	EBlastProgramType	program_number,
		const char *	matrixName,
		double *	threshold
	)

Get thresholds for word-finding suggested by Stephen Altschul.

Parameters

program_number	Type of blast program: blastn, blastp, blastx, tblastn, tblastx) [in]
matrixName	matrix, e.g., BLOSUM62 [in]
threshold	returns suggested value [in\|out]

Returns: zero on success

Definition at line 1174 of file blast_options.c.

References Blast_QueryIsTranslated(), Blast_SubjectIsTranslated(), BLASTERR_INVALIDPARAM, eBlastTypeBlastn, eBlastTypeMapping, NULL, strcasecmp, and TRUE.

Referenced by BOOST_AUTO_TEST_CASE(), and CWordThresholdArg::ExtractAlgorithmOptions().

◆ BLAST_GetSuggestedWindowSize()

Int2 BLAST_GetSuggestedWindowSize	(	EBlastProgramType	program_number,
		const char *	matrixName,
		Int4 *	window_size
	)

Get window sizes for two hit algorithm suggested by Stephen Altschul.

Parameters

program_number	Type of blast program: blastn, blastp, blastx, tblastn, tblastx) [in]
matrixName	matrix, e.g., BLOSUM62 [in]
window_size	returns suggested value [in\|out]

Returns: zero on success

Definition at line 1211 of file blast_options.c.

References BLASTERR_INVALIDPARAM, eBlastTypeBlastn, eBlastTypeMapping, NULL, strcasecmp, and window_size.

Referenced by BOOST_AUTO_TEST_CASE(), and CWindowSizeArg::ExtractAlgorithmOptions().

◆ BLAST_InitDefaultOptions()

Int2 BLAST_InitDefaultOptions	(	EBlastProgramType	blast_program,
		LookupTableOptions **	lookup_options,
		QuerySetUpOptions **	query_setup_options,
		BlastInitialWordOptions **	word_options,
		BlastExtensionOptions **	ext_options,
		BlastHitSavingOptions **	hit_options,
		BlastScoringOptions **	score_options,
		BlastEffectiveLengthsOptions **	eff_len_options,
		PSIBlastOptions **	protein_options,
		BlastDatabaseOptions **	db_options
	)

Initialize all the BLAST search options structures with the default values.

Parameters

blast_program	Type of blast program: blastn, blastp, blastx, tblastn, tblastx) [in]
lookup_options	Lookup table options [out]
query_setup_options	Query options [out]
word_options	Initial word processing options [out]
ext_options	Extension options [out]
hit_options	Hit saving options [out]
score_options	Scoring options [out]
eff_len_options	Effective length options [out]
protein_options	Protein BLAST options [out]
db_options	BLAST database options [out]

Definition at line 1638 of file blast_options.c.

References BlastDatabaseOptionsNew(), BlastEffectiveLengthsOptionsNew(), BlastExtensionOptionsNew(), BlastHitSavingOptionsNew(), BlastInitialWordOptionsNew(), BlastQuerySetUpOptionsNew(), BlastScoringOptionsNew(), LookupTableOptionsNew(), and PSIBlastOptionsNew().

◆ BLAST_ValidateOptions()

Int2 BLAST_ValidateOptions	(	EBlastProgramType	program_number,
		const BlastExtensionOptions *	ext_options,
		const BlastScoringOptions *	score_options,
		const LookupTableOptions *	lookup_options,
		const BlastInitialWordOptions *	word_options,
		const BlastHitSavingOptions *	hit_options,
		Blast_Message **	blast_msg
	)

◆ BlastDatabaseOptionsFree()

BlastDatabaseOptions* BlastDatabaseOptionsFree ( BlastDatabaseOptions * db_options )

Deallocate database options.

Definition at line 1628 of file blast_options.c.

References NULL, and sfree.

Referenced by BOOST_AUTO_TEST_CASE().

◆ BlastDatabaseOptionsNew()

Int2 BlastDatabaseOptionsNew ( BlastDatabaseOptions ** db_options )

Allocates the BlastDatabase options structure and sets the default database genetic code value (BLAST_GENETIC_CODE).

Genetic code string in ncbistdaa must be populated by client code

Definition at line 1608 of file blast_options.c.

References BLAST_GENETIC_CODE, BLASTERR_INVALIDPARAM, BLASTERR_MEMORY, calloc(), BlastDatabaseOptions::genetic_code, and NULL.

Referenced by BLAST_InitDefaultOptions(), and CBlastOptionsLocal::CBlastOptionsLocal().

◆ BlastEffectiveLengthsOptions_IsSearchSpaceSet()

Boolean BlastEffectiveLengthsOptions_IsSearchSpaceSet ( const BlastEffectiveLengthsOptions * options )

Return true if the search spaces is set for any of the queries in the search.

Parameters

options The options to examine [in]

Definition at line 1020 of file blast_options.c.

References FALSE, i, NULL, BlastEffectiveLengthsOptions::num_searchspaces, BlastEffectiveLengthsOptions::searchsp_eff, and TRUE.

Referenced by BLAST_CalcEffLengths().

◆ BlastEffectiveLengthsOptionsFree()

BlastEffectiveLengthsOptions* BlastEffectiveLengthsOptionsFree ( BlastEffectiveLengthsOptions * options )

Deallocate memory for BlastEffectiveLengthsOptions*.

Parameters

options Structure to free [in]

Definition at line 990 of file blast_options.c.

References NULL, BlastEffectiveLengthsOptions::searchsp_eff, and sfree.

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

◆ BlastEffectiveLengthsOptionsNew()

Int2 BlastEffectiveLengthsOptionsNew ( BlastEffectiveLengthsOptions ** options )

Allocate memory for BlastEffectiveLengthsOptions* and fill with default values.

Parameters

options The options that are being returned [out]

Definition at line 1003 of file blast_options.c.

References BLASTERR_INVALIDPARAM, BLASTERR_MEMORY, calloc(), and NULL.

Referenced by BLAST_InitDefaultOptions(), BOOST_AUTO_TEST_CASE(), CBlastOptionsLocal::CBlastOptionsLocal(), CEffectiveSearchSpacesMemento::CEffectiveSearchSpacesMemento(), LinkHspTestFixture::fillEffectiveLengths(), CBlastExtendTestFixture::fillEffectiveLengths(), and CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest().

◆ BlastExtensionOptionsFree()

BlastExtensionOptions* BlastExtensionOptionsFree ( BlastExtensionOptions * options )

Deallocate memory for BlastExtensionOptions.

Parameters

options Structure to free [in]

Definition at line 650 of file blast_options.c.

References NULL, and sfree.

Referenced by BOOST_AUTO_TEST_CASE(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), LinkHspTestFixture::setupCutoffScores(), TestFixture::TearDownLookupTable(), testHSPStream(), and CBlastExtendTestFixture::~CBlastExtendTestFixture().

◆ BlastExtensionOptionsNew()

Int2 BlastExtensionOptionsNew	(	EBlastProgramType	program,
		BlastExtensionOptions **	options,
		Boolean	gapped
	)

Allocate memory for BlastExtensionOptions and fill with default values.

Parameters

program	Program number (blastn, blastp, etc.) [in]
options	The options that are being returned [out]
gapped	The search is gapped [in]

Definition at line 660 of file blast_options.c.

References BLAST_GAP_X_DROPOFF_FINAL_NUCL, BLAST_GAP_X_DROPOFF_FINAL_PROT, BLAST_GAP_X_DROPOFF_NUCL, BLAST_GAP_X_DROPOFF_PROT, Blast_ProgramIsNucleotide(), Blast_QueryIsPssm(), Blast_SubjectIsTranslated(), BLASTERR_MEMORY, calloc(), eCompositionBasedStats, eDynProgScoreOnly, eDynProgTbck, eNoCompositionBasedStats, and NULL.

Referenced by BLAST_InitDefaultOptions(), BOOST_AUTO_TEST_CASE(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), LinkHspTestFixture::setupCutoffScores(), TestFixture::SetUpLookupTable(), CBlastExtendTestFixture::setupStructures(), and testHSPStream().

◆ BlastExtensionOptionsValidate()

Int2 BlastExtensionOptionsValidate	(	EBlastProgramType	program_number,
		const BlastExtensionOptions *	options,
		Blast_Message **	blast_msg
	)

Validate contents of BlastExtensionOptions.

Parameters

program_number	Type of BLAST program [in]
options	Options to be validated [in]
blast_msg	Describes any validation problems found [out]

Definition at line 740 of file blast_options.c.

References Blast_MessageWrite(), BLASTERR_INVALIDPARAM, BLASTERR_OPTION_PROGRAM_INVALID, BLASTERR_OPTION_VALUE_INVALID, eBlastSevWarning, eBlastTypeBlastn, eBlastTypeMapping, eGreedyScoreOnly, eGreedyTbck, BlastExtensionOptions::ePrelimGapExt, eSmithWatermanScoreOnly, eSmithWatermanTbckFull, BlastExtensionOptions::eTbackExt, kBlastMessageNoContext, and NULL.

Referenced by BLAST_ValidateOptions().

◆ BlastHitSavingOptionsFree()

BlastHitSavingOptions* BlastHitSavingOptionsFree ( BlastHitSavingOptions * options )

Deallocate memory for BlastHitSavingOptions.

Parameters

options Structure to free [in]

Definition at line 1433 of file blast_options.c.

References BlastHSPFilteringOptionsFree(), BlastHitSavingOptions::hsp_filt_opt, NULL, and sfree.

Referenced by BOOST_AUTO_TEST_CASE(), LinkHspTestFixture::freeStructures(), s_GetBestHitParams(), s_GetCullingParams(), TestFixture::TearDownLookupTable(), testHSPStream(), and CBlastExtendTestFixture::~CBlastExtendTestFixture().

◆ BlastHitSavingOptionsNew()

Int2 BlastHitSavingOptionsNew	(	EBlastProgramType	program,
		BlastHitSavingOptions **	options,
		Boolean	gapped_calculation
	)

Allocate memory for BlastHitSavingOptions.

Parameters

program	Program number (blastn, blastp, etc.) [in]
options	The options that are being returned [out]
gapped_calculation	is this search gapped? [in]

Definition at line 1444 of file blast_options.c.

References BLAST_EXPECT_VALUE, BLAST_HITLIST_SIZE, Blast_QueryIsTranslated(), Blast_SubjectIsTranslated(), BLASTERR_INVALIDPARAM, calloc(), eBlastTypeRpsTblastn, FALSE, INT4_MAX, NULL, and TRUE.

Referenced by BLAST_InitDefaultOptions(), BOOST_AUTO_TEST_CASE(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), s_GetBestHitParams(), s_GetCullingParams(), LinkHspTestFixture::setupCutoffScores(), TestFixture::SetUpLookupTable(), CBlastExtendTestFixture::setupStructures(), and testHSPStream().

◆ BlastHitSavingOptionsValidate()

Int2 BlastHitSavingOptionsValidate	(	EBlastProgramType	program_number,
		const BlastHitSavingOptions *	options,
		Blast_Message **	blast_msg
	)

Validate BlastHitSavingOptions.

Parameters

program_number	BLAST program [in]
options	The options that have are being returned [in]
blast_msg	Describes any validation problems found [out]

Definition at line 1505 of file blast_options.c.

References Blast_MessageWrite(), BLASTERR_INVALIDPARAM, BLASTERR_OPTION_PROGRAM_INVALID, BLASTERR_OPTION_VALUE_INVALID, BlastHSPFilteringOptionsValidate(), BlastHitSavingOptions::culling_limit, BlastHitSavingOptions::cutoff_score, eBlastSevError, eBlastTypeBlastx, eBlastTypeMapping, eBlastTypePsiTblastn, eBlastTypeTblastn, BlastHitSavingOptions::expect_value, BlastHitSavingOptions::hitlist_size, BlastHitSavingOptions::hsp_filt_opt, kBlastMessageNoContext, BlastHitSavingOptions::longest_intron, and NULL.

Referenced by BLAST_ValidateOptions().

◆ BlastHSPBestHitOptionsFree()

BlastHSPBestHitOptions* BlastHSPBestHitOptionsFree ( BlastHSPBestHitOptions * opt )

Deallocate a BlastHSPBestHitOptions structure.

Parameters

opt	object to be deallocated. [in]

Definition at line 1846 of file blast_options.c.

References NULL, and sfree.

Referenced by BlastHSPFilteringOptionsFree(), and s_GetBestHitParams().

◆ BlastHSPBestHitOptionsNew()

BlastHSPBestHitOptions* BlastHSPBestHitOptionsNew	(	double	overhang,
		double	score_edge
	)

Allocate and initialize a BlastHSPBestHitOptions structure.

Definition at line 1814 of file blast_options.c.

References calloc(), BlastHSPBestHitOptions::overhang, and BlastHSPBestHitOptions::score_edge.

Referenced by s_GetBestHitParams(), CBlastOptionsLocal::SetBestHitOverhang(), and CBlastOptionsLocal::SetBestHitScoreEdge().

◆ BlastHSPBestHitOptionsValidate()

Int2 BlastHSPBestHitOptionsValidate ( const BlastHSPFilteringOptions * opts )

Validate the best hit algorithm parameters (if any) in the.

Parameters

opts	BlastHSPFilteringOptions structure

Returns: 0 on success, else non-zero

Definition at line 1824 of file blast_options.c.

References BlastHSPFilteringOptions::best_hit, kBestHit_OverhangMax, kBestHit_OverhangMin, kBestHit_ScoreEdgeMax, kBestHit_ScoreEdgeMin, BlastHSPBestHitOptions::overhang, and BlastHSPBestHitOptions::score_edge.

Referenced by BlastHSPFilteringOptionsValidate().

◆ BlastHSPCullingOptionsFree()

BlastHSPCullingOptions* BlastHSPCullingOptionsFree ( BlastHSPCullingOptions * culling_opts )

Deallocates culling options structure.

Parameters

culling_opts object to be deallocated. [in]

Definition at line 1878 of file blast_options.c.

References NULL, and sfree.

Referenced by BlastHSPFilteringOptionsFree(), and s_GetCullingParams().

◆ BlastHSPCullingOptionsNew()

BlastHSPCullingOptions* BlastHSPCullingOptionsNew ( int max )

Allocate a new object for culling options.

Parameters

max	number of HSPs that may be aligned to one part of query [in]

Definition at line 1855 of file blast_options.c.

References calloc(), max(), and BlastHSPCullingOptions::max_hits.

Referenced by s_GetCullingParams(), and CBlastOptionsLocal::SetCullingLimit().

◆ BlastHSPCullingOptionsValidate()

Int2 BlastHSPCullingOptionsValidate ( const BlastHSPFilteringOptions * opts )

Validate culling options.

Parameters

opts	BlastHSPFilteringOptions structure

Returns: 0 on success, else non-zero

Definition at line 1864 of file blast_options.c.

References BlastHSPFilteringOptions::culling_opts, and BlastHSPCullingOptions::max_hits.

Referenced by BlastHSPFilteringOptionsValidate().

◆ BlastHSPFilteringOptions_AddBestHit()

Int2 BlastHSPFilteringOptions_AddBestHit	(	BlastHSPFilteringOptions *	filt_opts,
		BlastHSPBestHitOptions **	opts,
		EBlastStage	stage
	)

Add the best hit options.

Responsibility for best_hit is taken over by the BlastHSPFilteringOptions

Parameters

filt_opts	HSP filtering options [in]
best_hit	Best Hit algorithm options. Ownership of this is taken by the BlastHSPFilteringOptions structure [in\|out]

Definition at line 1895 of file blast_options.c.

References BlastHSPFilteringOptions::best_hit, BlastHSPFilteringOptions::best_hit_stage, and NULL.

Referenced by CBlastOptionsLocal::SetBestHitOverhang(), and CBlastOptionsLocal::SetBestHitScoreEdge().

◆ BlastHSPFilteringOptions_AddCulling()

Int2 BlastHSPFilteringOptions_AddCulling	(	BlastHSPFilteringOptions *	filt_opts,
		BlastHSPCullingOptions **	opts,
		EBlastStage	stage
	)

Validates the BlastHSPFilteringOptions structure.

Definition at line 1911 of file blast_options.c.

References BlastHSPFilteringOptions::culling_opts, BlastHSPFilteringOptions::culling_stage, and NULL.

Referenced by CBlastOptionsLocal::SetCullingLimit().

◆ BlastHSPFilteringOptions_AddSubjectBestHit()

Int2 BlastHSPFilteringOptions_AddSubjectBestHit	(	BlastHSPFilteringOptions *	filt_opts,
		BlastHSPSubjectBestHitOptions **	subject_besthit
	)

Definition at line 1998 of file blast_options.c.

References NULL, and BlastHSPFilteringOptions::subject_besthit_opts.

Referenced by CBlastOptionsLocal::SetSubjectBestHit().

◆ BlastHSPFilteringOptionsFree()

BlastHSPFilteringOptions* BlastHSPFilteringOptionsFree ( BlastHSPFilteringOptions * opts )

Deallocate a BlastHSPFilteringOptions structure.

Definition at line 1950 of file blast_options.c.

References BlastHSPFilteringOptions::best_hit, BlastHSPBestHitOptionsFree(), BlastHSPCullingOptionsFree(), BlastHSPSubjectBestHitOptionsFree(), BlastHSPFilteringOptions::culling_opts, NULL, sfree, and BlastHSPFilteringOptions::subject_besthit_opts.

Referenced by BlastHitSavingOptionsFree().

◆ BlastHSPFilteringOptionsNew()

BlastHSPFilteringOptions* BlastHSPFilteringOptionsNew ( )

Allocate and initialize a BlastHSPFilteringOptions structure.

Definition at line 1888 of file blast_options.c.

References calloc().

Referenced by CBlastOptionsLocal::SetBestHitOverhang(), CBlastOptionsLocal::SetBestHitScoreEdge(), CBlastOptionsLocal::SetCullingLimit(), and CBlastOptionsLocal::SetSubjectBestHit().

◆ BlastHSPFilteringOptionsValidate()

Int2 BlastHSPFilteringOptionsValidate ( const BlastHSPFilteringOptions * opts )

Validates the BlastHSPFilteringOptions structure.

Definition at line 1927 of file blast_options.c.

References BlastHSPFilteringOptions::best_hit_stage, BlastHSPBestHitOptionsValidate(), BlastHSPCullingOptionsValidate(), BlastHSPFilteringOptions::culling_stage, ePrelimSearch, FALSE, and TRUE.

Referenced by BlastHitSavingOptionsValidate().

◆ BlastHSPSubjectBestHitOptionsFree()

BlastHSPSubjectBestHitOptions* BlastHSPSubjectBestHitOptionsFree ( BlastHSPSubjectBestHitOptions * subject_besthit_opts )

Deallocates subject besthit structure.

Parameters

subject_besthit object to be deallocated. [in]

Definition at line 1988 of file blast_options.c.

References NULL, and sfree.

Referenced by BlastHSPFilteringOptionsFree(), and BOOST_AUTO_TEST_CASE().

◆ BlastHSPSubjectBestHitOptionsNew()

BlastHSPSubjectBestHitOptions* BlastHSPSubjectBestHitOptionsNew ( Boolean isProtein )

Allocate a new object for subject besthit options.

@params isProtein true if protein alignment [in]

Definition at line 1963 of file blast_options.c.

References calloc(), DEFAULT_SUBJECT_BESTHIT_NUCL_MAX_RANGE_DIFF, DEFAULT_SUBJECT_BESTHIT_PROT_MAX_RANGE_DIFF, and BlastHSPSubjectBestHitOptions::max_range_diff.

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastOptionsLocal::SetSubjectBestHit().

◆ BlastHSPSubjectBestHitOptionsValidate()

Int2 BlastHSPSubjectBestHitOptionsValidate ( const BlastHSPFilteringOptions * opts )

Validate subject besthit options.

Parameters

opts	BlastHSPFilteringOptions structure

Returns: 0 on success, else non-zero

Definition at line 1977 of file blast_options.c.

References BlastHSPFilteringOptions::subject_besthit_opts.

◆ BlastInitialWordOptionsFree()

BlastInitialWordOptions* BlastInitialWordOptionsFree ( BlastInitialWordOptions * options )

Deallocate memory for BlastInitialWordOptions.

Parameters

options Structure to free [in]

Definition at line 562 of file blast_options.c.

References NULL, and sfree.

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

◆ BlastInitialWordOptionsNew()

Int2 BlastInitialWordOptionsNew	(	EBlastProgramType	program,
		BlastInitialWordOptions **	options
	)

Allocate memory for BlastInitialWordOptions and fill with default values.

Parameters

program	Program number (blastn, blastp, etc.) [in]
options	The options that have are being returned [out]

Definition at line 573 of file blast_options.c.

References BLAST_GAP_TRIGGER_NUCL, BLAST_GAP_TRIGGER_PROT, Blast_ProgramIsNucleotide(), BLAST_SCAN_RANGE_NUCL, BLAST_UNGAPPED_X_DROPOFF_NUCL, BLAST_UNGAPPED_X_DROPOFF_PROT, BLAST_WINDOW_SIZE_NUCL, BLAST_WINDOW_SIZE_PROT, BLASTERR_MEMORY, calloc(), and NULL.

Referenced by BLAST_InitDefaultOptions(), BOOST_AUTO_TEST_CASE(), LinkHspTestFixture::setupCutoffScores(), NuclWordFinderTextFixture::setupExtendWord(), TestFixture::SetUpLookupTable(), and CBlastExtendTestFixture::setupStructures().

◆ BlastInitialWordOptionsValidate()

Int2 BlastInitialWordOptionsValidate	(	EBlastProgramType	program_number,
		const BlastInitialWordOptions *	options,
		Blast_Message **	blast_msg
	)

Validate correctness of the initial word options.

Parameters

program_number	Type of BLAST program [in]
options	Initial word options [in]
blast_msg	Describes any validation problems found [out]

Returns: Validation status

Definition at line 601 of file blast_options.c.

References ASSERT, Blast_MessageWrite(), Blast_ProgramIsPhiBlast(), BLASTERR_OPTION_VALUE_INVALID, eBlastSevError, eBlastTypeBlastn, eBlastTypeMapping, kBlastMessageNoContext, BlastInitialWordOptions::scan_range, BlastInitialWordOptions::window_size, and BlastInitialWordOptions::x_dropoff.

Referenced by BLAST_ValidateOptions().

◆ BlastQuerySetUpOptionsFree()

QuerySetUpOptions* BlastQuerySetUpOptionsFree ( QuerySetUpOptions * options )

Deallocate memory for QuerySetUpOptions.

Parameters

options Structure to free [in]

Definition at line 501 of file blast_options.c.

References QuerySetUpOptions::filter_string, QuerySetUpOptions::filtering_options, NULL, SBlastFilterOptionsFree(), and sfree.

Referenced by BOOST_AUTO_TEST_CASE(), s_GetInitialWordParameters(), LinkHspTestFixture::setupCutoffScores(), TestFixture::SetUpLookupTable(), CMakeProfileDBApp::x_RPS_DbClose(), and CMakeProfileDBApp::CRPS_DbInfo::~CRPS_DbInfo().

◆ BlastQuerySetUpOptionsNew()

Int2 BlastQuerySetUpOptionsNew ( QuerySetUpOptions ** options )

Allocate memory for QuerySetUpOptions and fill with default values.

Parameters

options The options that have are being returned [out]

Definition at line 514 of file blast_options.c.

References BLAST_GENETIC_CODE, BLASTERR_INVALIDPARAM, BLASTERR_MEMORY, calloc(), eEmpty, NULL, and SBlastFilterOptionsNew().

Referenced by BLAST_InitDefaultOptions(), BOOST_AUTO_TEST_CASE(), CBlastOptionsLocal::CBlastOptionsLocal(), s_GetInitialWordParameters(), LinkHspTestFixture::setupCutoffScores(), TestFixture::SetUpLookupTable(), and CMakeProfileDBApp::x_RPSAddFirstSequence().

◆ BlastScoringOptionsDup()

Int2 BlastScoringOptionsDup	(	BlastScoringOptions **	new_opt,
		const BlastScoringOptions *	old_opt
	)

Produces copy of "old" options, with new memory allocated.

Parameters

new_opt	Contains copied BlastScoringOptions upon return [out]
old_opt	BlastScoringOptions to be copied [in]

Definition at line 956 of file blast_options.c.

References BLASTERR_INVALIDPARAM, BLASTERR_MEMORY, BlastMemDup(), BlastScoringOptions::matrix, BlastScoringOptions::matrix_path, NULL, and strdup.

Referenced by CBlastOptionsLocal::x_Copy_CBlastScoringOptions().

◆ BlastScoringOptionsFree()

BlastScoringOptions* BlastScoringOptionsFree ( BlastScoringOptions * options )

Deallocate memory for BlastScoringOptions.

Parameters

options Structure to free [in]

Definition at line 774 of file blast_options.c.

References BlastScoringOptions::matrix, BlastScoringOptions::matrix_path, NULL, and sfree.

Referenced by BOOST_AUTO_TEST_CASE(), CompressedAalookupTestFixture::FillLookupTable(), AalookupTestFixture::FillLookupTable(), LinkHspTestFixture::setupCutoffScores(), LinkHspTestFixture::setupLinkHspInputBlastn(), LinkHspTestFixture::setupLinkHspInputTblastn(), TestFixture::SetUpLookupTable(), NuclWordFinderTextFixture::setupScoreBlk(), LinkHspTestFixture::setupScoreBlk(), testHSPStream(), CScoreBuilder::x_Initialize(), AascanTestFixture::~AascanTestFixture(), CBlastExtendTestFixture::~CBlastExtendTestFixture(), and CompressedAascanTestFixture::~CompressedAascanTestFixture().

◆ BlastScoringOptionsNew()

Int2 BlastScoringOptionsNew	(	EBlastProgramType	program,
		BlastScoringOptions **	options
	)

Allocate memory for BlastScoringOptions and fill with default values.

Parameters

program	Program number (blastn, blastp, etc.) [in]
options	The options that are being returned [out]

Definition at line 788 of file blast_options.c.

References BLAST_DEFAULT_MATRIX, BLAST_GAP_EXTN_NUCL, BLAST_GAP_EXTN_PROT, BLAST_GAP_OPEN_NUCL, BLAST_GAP_OPEN_PROT, BLAST_PENALTY, Blast_ProgramIsNucleotide(), BLAST_REWARD, BLASTERR_INVALIDPARAM, calloc(), eBlastTypeTblastx, FALSE, INT2_MAX, NULL, strdup, and TRUE.

Referenced by AascanTestFixture::AascanTestFixture(), BLAST_InitDefaultOptions(), BOOST_AUTO_TEST_CASE(), CompressedAascanTestFixture::CompressedAascanTestFixture(), CPhiblastTestFixture::CPhiblastTestFixture(), CompressedAalookupTestFixture::FillLookupTable(), AalookupTestFixture::FillLookupTable(), InitializeBlastScoreBlk(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), TestFixture::SetUpLookupTable(), NuclWordFinderTextFixture::setupScoreBlk(), LinkHspTestFixture::setupScoreBlk(), CBlastExtendTestFixture::setupStructures(), testHSPStream(), CScoreBuilder::x_Initialize(), CPssmEngine::x_InitializeScoreBlock(), and CSeedTop::x_MakeScoreBlk().

◆ BlastScoringOptionsSetMatrix()

Int2 BlastScoringOptionsSetMatrix	(	BlastScoringOptions *	opts,
		const char *	matrix_name
	)

Resets matrix name option.

Automatically converts the name to upper case.

Parameters

opts	Options structure to update. [in] [out]
matrix_name	New matrix name. If NULL, old matrix name is left as is. [in]

Definition at line 974 of file blast_options.c.

References i, BlastScoringOptions::matrix, sfree, strdup, and toupper().

Referenced by BLAST_FillScoringOptions(), and CPssmEngine::x_InitializeScoreBlock().

◆ BlastScoringOptionsValidate()

Int2 BlastScoringOptionsValidate	(	EBlastProgramType	program_number,
		const BlastScoringOptions *	options,
		Blast_Message **	blast_msg
	)

Validate contents of BlastScoringOptions.

Parameters

program_number	Type of BLAST program [in]
options	Options to be validated [in]
blast_msg	Describes any validation problems found [out]

Definition at line 862 of file blast_options.c.

References BLAST_CheckRewardPenaltyScores(), Blast_KarlinBlkGappedLoadFromTables(), Blast_MessageWrite(), BLAST_PrintAllowedValues(), BLAST_PrintMatrixMessage(), Blast_ProgramIsMapping(), Blast_ProgramIsNucleotide(), Blast_ProgramIsRpsBlast(), BLASTERR_INVALIDPARAM, BLASTERR_OPTION_PROGRAM_INVALID, BLASTERR_OPTION_VALUE_INVALID, buffer, eBlastSevError, eBlastSevWarning, eBlastTypeBlastp, eBlastTypeBlastx, eBlastTypeTblastn, eBlastTypeTblastx, BlastScoringOptions::gap_extend, BlastScoringOptions::gap_open, BlastScoringOptions::gapped_calculation, BlastScoringOptions::is_ooframe, kBlastMessageNoContext, BlastScoringOptions::matrix, NULL, BlastScoringOptions::penalty, BlastScoringOptions::reward, and sfree.

Referenced by BLAST_ValidateOptions().

◆ LookupTableOptionsFree()

LookupTableOptions* LookupTableOptionsFree ( LookupTableOptions * options )

Deallocates memory for LookupTableOptions*.

Parameters

options Structure to free [in]

Definition at line 1063 of file blast_options.c.

References NULL, LookupTableOptions::phi_pattern, and sfree.

Referenced by BOOST_AUTO_TEST_CASE(), s_GetInitialWordParameters(), LinkHspTestFixture::setupCutoffScores(), TestFixture::SetUpLookupTable(), AalookupTestFixture::~AalookupTestFixture(), AascanTestFixture::~AascanTestFixture(), CompressedAalookupTestFixture::~CompressedAalookupTestFixture(), CompressedAascanTestFixture::~CompressedAascanTestFixture(), and CMakeProfileDBApp::CRPS_DbInfo::~CRPS_DbInfo().

◆ LookupTableOptionsNew()

Int2 LookupTableOptionsNew	(	EBlastProgramType	program,
		LookupTableOptions **	options
	)

Allocate memory for lookup table options and fill with default values.

Parameters

program	Program number (blastn, blastp, etc.) [in]
options	The options that are being returned [out]

Definition at line 1077 of file blast_options.c.

References BLAST_WORD_THRESHOLD_BLASTP, BLAST_WORD_THRESHOLD_BLASTX, BLAST_WORD_THRESHOLD_TBLASTN, BLAST_WORD_THRESHOLD_TBLASTX, BLAST_WORDSIZE_MEGABLAST, BLAST_WORDSIZE_PROT, BLASTERR_INVALIDPARAM, calloc(), eAaLookupTable, eBlastTypeBlastn, eBlastTypeBlastp, eBlastTypeBlastx, eBlastTypeMapping, eBlastTypePhiBlastn, eBlastTypePhiBlastp, eBlastTypeRpsBlast, eBlastTypeRpsTblastn, eBlastTypeTblastn, eBlastTypeTblastx, eMBLookupTable, ePhiLookupTable, ePhiNaLookupTable, eRPSLookupTable, if(), MAX_DB_WORD_COUNT_MAPPER, and NULL.

Referenced by AascanTestFixture::AascanTestFixture(), BLAST_InitDefaultOptions(), BOOST_AUTO_TEST_CASE(), CompressedAascanTestFixture::CompressedAascanTestFixture(), CompressedAalookupTestFixture::FillLookupTable(), AalookupTestFixture::FillLookupTable(), s_GetInitialWordParameters(), LinkHspTestFixture::setupCutoffScores(), TestFixture::SetUpLookupTable(), CPhiblastTestFixture::setUpLookupTable(), CSeedTop::x_MakeLookupTable(), and CMakeProfileDBApp::x_RPSAddFirstSequence().

◆ LookupTableOptionsValidate()

Int2 LookupTableOptionsValidate	(	EBlastProgramType	program_number,
		const LookupTableOptions *	options,
		Blast_Message **	blast_msg
	)

Validate LookupTableOptions.

Parameters

program_number	BLAST program [in]
options	The options that have are being returned [in]
blast_msg	Describes any validation problems found [out]

Definition at line 1284 of file blast_options.c.

References ASSERT, Blast_MessageWrite(), Blast_ProgramIsNucleotide(), Blast_ProgramIsPhiBlast(), Blast_ProgramIsRpsBlast(), Blast_QueryIsPattern(), BLASTERR_INVALIDPARAM, BLASTERR_OPTION_PROGRAM_INVALID, BLASTERR_OPTION_VALUE_INVALID, buffer, LookupTableOptions::db_filter, DBSEQ_CHUNK_OVERLAP, DIM, eBlastSevError, eBlastTypeBlastn, eBlastTypeBlastp, eBlastTypeBlastx, eBlastTypeMapping, eBlastTypePsiBlast, eBlastTypeTblastn, eCompressedAaLookupTable, eMBLookupTable, kBlastMessageNoContext, LookupTableOptions::lut_type, LookupTableOptions::mb_template_length, LookupTableOptions::mb_template_type, NULL, LookupTableOptions::phi_pattern, s_DiscWordOptionsValidate(), LookupTableOptions::threshold, and LookupTableOptions::word_size.

Referenced by BLAST_ValidateOptions().

◆ PSIBlastOptionsFree()

PSIBlastOptions* PSIBlastOptionsFree ( PSIBlastOptions * psi_options )

Deallocate PSI BLAST options.

Definition at line 1602 of file blast_options.c.

References NULL, and sfree.

Referenced by BOOST_AUTO_TEST_CASE(), CPssmInputTestData::CPssmInputTestData(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), CdPssmInput::~CdPssmInput(), CPssmInputFlankingGaps::~CPssmInputFlankingGaps(), CPssmInputTestData::~CPssmInputTestData(), and SU_PSSMInput::~SU_PSSMInput().

◆ PSIBlastOptionsNew()

Int2 PSIBlastOptionsNew ( PSIBlastOptions ** psi_options )

Initialize default options for PSI BLAST.

Parameters

psi_options pointer to pointer where structure will be allocated [in]

Returns: 1 in case of memory allocation failure or if psi_options is NULL, 0 in case of success

Definition at line 1554 of file blast_options.c.

References BLASTERR_INVALIDPARAM, BLASTERR_MEMORY, calloc(), FALSE, PSIBlastOptions::ignore_unaligned_positions, PSIBlastOptions::impala_scaling_factor, PSIBlastOptions::inclusion_ethresh, kPSSM_NoImpalaScaling, PSIBlastOptions::nsg_compatibility_mode, NULL, PSIBlastOptions::pseudo_count, PSI_INCLUSION_ETHRESH, PSI_PSEUDO_COUNT_CONST, TRUE, and PSIBlastOptions::use_best_alignment.

Referenced by BLAST_InitDefaultOptions(), BOOST_AUTO_TEST_CASE(), CBlastOptionsLocal::CBlastOptionsLocal(), CdPssmInput::CdPssmInput(), CPssmInputFlankingGaps::CPssmInputFlankingGaps(), CPssmInputTestData::CPssmInputTestData(), CPssmInputWithNoCDs::CPssmInputWithNoCDs(), CPssmCddInputTest::CreatePssmInput(), PsiBlastComputePssmFromAlignment(), CDeltaBlast::Run(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), SU_PSSMInput::SU_PSSMInput(), and CPsiBlastArgs::x_CreatePssmFromMsa().

◆ PSIBlastOptionsValidate()

Int2 PSIBlastOptionsValidate	(	const PSIBlastOptions *	psi_options,
		Blast_Message **	blast_msg
	)

Validates the PSI BLAST options so that they have sane values.

Parameters

psi_options	structure to validate [in]
blast_msg	Describes any validation problems found [out]

Returns: 0 on success 1 on failure

Definition at line 1577 of file blast_options.c.

References Blast_MessageWrite(), eBlastSevError, PSIBlastOptions::inclusion_ethresh, kBlastMessageNoContext, and PSIBlastOptions::pseudo_count.

Referenced by s_Validate().

◆ SBlastFilterOptionsFree()

SBlastFilterOptions* SBlastFilterOptionsFree ( SBlastFilterOptions * filter_options )

Frees SBlastFilterOptions and all subservient structures.

Parameters

filter_options object to free

Returns: NULL pointer

Definition at line 204 of file blast_options.c.

References SBlastFilterOptions::dustOptions, NULL, SBlastFilterOptions::readQualityOptions, SBlastFilterOptions::repeatFilterOptions, SDustOptionsFree(), SBlastFilterOptions::segOptions, sfree, SReadQualityOptionsFree(), SRepeatFilterOptionsFree(), SSegOptionsFree(), SWindowMaskerOptionsFree(), and SBlastFilterOptions::windowMaskerOptions.

Referenced by BLAST_FillQuerySetUpOptions(), BLAST_MainSetUp(), BlastQuerySetUpOptionsFree(), BOOST_AUTO_TEST_CASE(), s_DoSegSequenceData(), CBlastOptionsLocal::SetFilterString(), and CFilteringMemento::~CFilteringMemento().

◆ SBlastFilterOptionsMaskAtHash()

Boolean SBlastFilterOptionsMaskAtHash ( const SBlastFilterOptions * filter_options )

Queries whether masking should be done only for the lookup table or for the entire search.

Parameters

filter_options the object to be queried [in]

Returns: TRUE or FALSE, FALSE if filter_options is NULL.

Definition at line 433 of file blast_options.c.

References FALSE, SBlastFilterOptions::mask_at_hash, and NULL.

Referenced by BLAST_MainSetUp(), BlastFilteringOptionsToString(), and s_HasMaskAtHashEnabled().

◆ SBlastFilterOptionsMerge()

Int2 SBlastFilterOptionsMerge	(	SBlastFilterOptions **	combined,
		const SBlastFilterOptions *	opt1,
		const SBlastFilterOptions *	opt2
	)

Merges two sets of options together, taking the non-default one as preferred.

if both are non-default then one or the other is taken.

Parameters

combined	object that is returned [in\|out]
opt1	first set of options [in]
opt2	second set of options [in]

Returns: zero on success.

Definition at line 390 of file blast_options.c.

References SBlastFilterOptions::dustOptions, eEmpty, SBlastFilterOptions::mask_at_hash, NULL, SBlastFilterOptions::repeatFilterOptions, s_MergeDustOptions(), s_MergeRepeatOptions(), s_MergeSegOptions(), s_MergeWindowMaskerOptions(), SBlastFilterOptionsNew(), SBlastFilterOptions::segOptions, TRUE, and SBlastFilterOptions::windowMaskerOptions.

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastOptionsLocal::SetFilterString().

◆ SBlastFilterOptionsNew()

Int2 SBlastFilterOptionsNew	(	SBlastFilterOptions **	filter_options,
		EFilterOptions	type
	)

Allocates memory for SBlastFilterOptions and.

Parameters

filter_options	options that are being returned [in\|out]
type	specify either dust or seg (now) with EFilterOptions [in]

Returns: zero on sucess

Definition at line 224 of file blast_options.c.

References calloc(), eDust, eDustRepeats, eRepeats, eSeg, FALSE, SDustOptionsNew(), SRepeatFilterOptionsNew(), and SSegOptionsNew().

Referenced by BlastFilteringOptionsFromString(), BlastQuerySetUpOptionsNew(), BOOST_AUTO_TEST_CASE(), CFilteringMemento::CFilteringMemento(), and SBlastFilterOptionsMerge().

◆ SBlastFilterOptionsNoFiltering()

Boolean SBlastFilterOptionsNoFiltering ( const SBlastFilterOptions * filter_options )

Queries whether no masking is required.

Parameters

filter_options the object to be queried [in]

Returns: TRUE if no filtering is required or argument is NULL, FALSE otherwise

Definition at line 422 of file blast_options.c.

References SBlastFilterOptions::dustOptions, NULL, SBlastFilterOptions::repeatFilterOptions, SBlastFilterOptions::segOptions, TRUE, and SBlastFilterOptions::windowMaskerOptions.

◆ SBlastFilterOptionsValidate()

Int2 SBlastFilterOptionsValidate	(	EBlastProgramType	program_number,
		const SBlastFilterOptions *	filter_options,
		Blast_Message **	blast_message
	)

Validates filter options to ensure that program and options are consistent and that options have valid values.

Parameters

program_number	Program number (blastn, blastp, etc.) [in]
filter_options	options to add to [in]
blast_message	error or warning (optional) [out]

Returns: zero on success

Definition at line 441 of file blast_options.c.

References Blast_MessageWrite(), BLASTERR_INVALIDPARAM, BLASTERR_OPTION_PROGRAM_INVALID, SRepeatFilterOptions::database, SBlastFilterOptions::dustOptions, eBlastSevError, eBlastSevWarning, eBlastTypeBlastn, eBlastTypeMapping, kBlastMessageNoContext, NULL, SBlastFilterOptions::repeatFilterOptions, and SBlastFilterOptions::segOptions.

Referenced by BlastSetUp_Filter().

◆ SDustOptionsFree()

SDustOptions* SDustOptionsFree ( SDustOptions * dust_options )

Frees SDustOptions.

Parameters

dust_options object to free

Returns: NULL pointer

Definition at line 50 of file blast_options.c.

References NULL, and sfree.

Referenced by BlastFilteringOptionsFromString(), BOOST_AUTO_TEST_CASE(), SBlastFilterOptionsFree(), and CBlastOptionsLocal::SetDustFiltering().

◆ SDustOptionsNew()

Int2 SDustOptionsNew ( SDustOptions ** dust_options )

Allocates memory for SDustOptions, fills in defaults.

Parameters

dust_options options that are being returned [in|out]

Returns: zero on sucess

Definition at line 57 of file blast_options.c.

References kDustLevel, kDustLinker, kDustWindow, malloc(), and NULL.

Referenced by BlastFilteringOptionsFromString(), BOOST_AUTO_TEST_CASE(), s_MergeDustOptions(), SBlastFilterOptionsNew(), CBlastOptionsLocal::SetDustFiltering(), CBlastOptionsLocal::SetDustFilteringLevel(), CBlastOptionsLocal::SetDustFilteringLinker(), and CBlastOptionsLocal::SetDustFilteringWindow().

◆ SReadQualityOptionsFree()

SReadQualityOptions* SReadQualityOptionsFree ( SReadQualityOptions * read_quality_options )

Frees memory for SReadQualityOptions.

Definition at line 177 of file blast_options.c.

References free(), and NULL.

Referenced by SBlastFilterOptionsFree(), and CBlastOptionsLocal::SetReadQualityFiltering().

◆ SReadQualityOptionsNew()

Int2 SReadQualityOptionsNew ( SReadQualityOptions ** read_quality_options )

Allocates memory for SReadQualityOptions, fills in defaults.

Parameters

read_quality_ptions options that are being returned [in|out]

Returns: zero on sucess

Definition at line 187 of file blast_options.c.

References calloc().

Referenced by CBlastOptionsLocal::SetReadMaxFractionAmbiguous(), CBlastOptionsLocal::SetReadMinDimerEntropy(), and CBlastOptionsLocal::SetReadQualityFiltering().

◆ SRepeatFilterOptionsFree()

SRepeatFilterOptions* SRepeatFilterOptionsFree ( SRepeatFilterOptions * repeat_options )

Frees SRepeatFilterOptions.

Parameters

repeat_options object to free [in]

Returns: NULL pointer

Definition at line 117 of file blast_options.c.

References SRepeatFilterOptions::database, NULL, and sfree.

Referenced by BlastFilteringOptionsFromString(), BOOST_AUTO_TEST_CASE(), SBlastFilterOptionsFree(), CBlastOptionsLocal::SetFilterString(), and CBlastOptionsLocal::SetRepeatFiltering().

◆ SRepeatFilterOptionsNew()

Int2 SRepeatFilterOptionsNew ( SRepeatFilterOptions ** repeat_options )

Allocates memory for SRepeatFilterOptions, fills in defaults.

Parameters

repeat_options options that are being returned [in|out]

Returns: zero on sucess

Definition at line 127 of file blast_options.c.

References BLASTERR_MEMORY, calloc(), kDefaultRepeatFilterDb, NULL, and strdup.

Referenced by BlastFilteringOptionsFromString(), s_MergeRepeatOptions(), SBlastFilterOptionsNew(), CBlastOptionsLocal::SetRepeatFiltering(), and SRepeatFilterOptionsResetDB().

◆ SRepeatFilterOptionsResetDB()

Int2 SRepeatFilterOptionsResetDB	(	SRepeatFilterOptions **	repeat_options,
		const char *	dbname
	)

Resets name of db for repeat filtering.

Parameters

repeat_options	already allocated options constaining field to be reset [in\|out]
dbname	name of the database(s) [in]

Returns: zero on sucess

Definition at line 142 of file blast_options.c.

References NULL, sfree, SRepeatFilterOptionsNew(), and strdup.

Referenced by BOOST_AUTO_TEST_CASE(), s_MergeRepeatOptions(), and CBlastOptionsLocal::SetRepeatFilteringDB().

◆ SSegOptionsFree()

SSegOptions* SSegOptionsFree ( SSegOptions * seg_options )

Frees SSegOptions.

Parameters

seg_options object to free [in]

Returns: NULL pointer

Definition at line 70 of file blast_options.c.

References NULL, and sfree.

Referenced by BlastFilteringOptionsFromString(), SBlastFilterOptionsFree(), and CBlastOptionsLocal::SetSegFiltering().

◆ SSegOptionsNew()

Int2 SSegOptionsNew ( SSegOptions ** seg_options )

Allocates memory for SSegOptions, fills in defaults.

[in|out]

Parameters

seg_options options that are being returned [in|out]

Returns: zero on sucess

Definition at line 77 of file blast_options.c.

References kSegHicut, kSegLocut, kSegWindow, malloc(), and NULL.

Referenced by BlastFilteringOptionsFromString(), s_MergeSegOptions(), SBlastFilterOptionsNew(), CBlastOptionsLocal::SetSegFiltering(), CBlastOptionsLocal::SetSegFilteringHicut(), CBlastOptionsLocal::SetSegFilteringLocut(), and CBlastOptionsLocal::SetSegFilteringWindow().

◆ SWindowMaskerOptionsFree()

SWindowMaskerOptions* SWindowMaskerOptionsFree ( SWindowMaskerOptions * winmask_options )

Frees SWindowMaskerOptions.

Parameters

winmask_options object to free [in]

Returns: NULL pointer

Definition at line 104 of file blast_options.c.

References SWindowMaskerOptions::database, NULL, and sfree.

Referenced by BlastFilteringOptionsFromString(), and SBlastFilterOptionsFree().

◆ SWindowMaskerOptionsNew()

Int2 SWindowMaskerOptionsNew ( SWindowMaskerOptions ** winmask_options )

Allocates memory for SWindowMaskerOptions, fills in defaults.

Parameters

winmask_options options that are being returned [in|out]

Returns: zero on sucess

Definition at line 90 of file blast_options.c.

References BLASTERR_MEMORY, calloc(), and NULL.

Referenced by BlastFilteringOptionsFromString(), s_MergeWindowMaskerOptions(), CBlastOptionsLocal::SetWindowMaskerDatabase(), CBlastOptionsLocal::SetWindowMaskerTaxId(), and SWindowMaskerOptionsResetDB().

◆ SWindowMaskerOptionsResetDB()

Int2 SWindowMaskerOptionsResetDB	(	SWindowMaskerOptions **	winmask_options,
		const char *	dbname
	)

Resets name of db for window masker filtering.

Parameters

winmask_options	options block constaining field to be reset [in\|out]
dbname	name of the database(s) [in]

Returns: zero on sucess

Definition at line 158 of file blast_options.c.

References NULL, sfree, strdup, and SWindowMaskerOptionsNew().

Referenced by s_MergeWindowMaskerOptions(), and CBlastOptionsLocal::SetWindowMaskerDatabase().

Variable Documentation

◆ kPSSM_NoImpalaScaling

const double kPSSM_NoImpalaScaling

extern

Value used to indicate that no IMPALA-style scaling should be performed when scaling a PSSM.

Definition at line 43 of file blast_options.c.

Referenced by _PSICreateAndScalePssmFromFrequencyRatios(), IPssmInputFreqRatios::GetImpalaScaleFactor(), PSIBlastOptionsNew(), and CPssmEngine::x_PSIMatrix2Asn1().

Classes

Macros

Typedefs

Enumerations

Functions

Variables

Detailed Description

Macro Definition Documentation

◆ BLAST_DEFAULT_MATRIX

◆ BLAST_EXPECT_VALUE

◆ BLAST_GAP_EXTN_MAPPER

◆ BLAST_GAP_EXTN_MEGABLAST

◆ BLAST_GAP_EXTN_NUCL

◆ BLAST_GAP_EXTN_PROT

◆ BLAST_GAP_OPEN_MAPPER

◆ BLAST_GAP_OPEN_MEGABLAST

◆ BLAST_GAP_OPEN_NUCL

◆ BLAST_GAP_OPEN_PROT

◆ BLAST_GAP_TRIGGER_NUCL

◆ BLAST_GAP_TRIGGER_PROT

◆ BLAST_GAP_X_DROPOFF_FINAL_NUCL

◆ BLAST_GAP_X_DROPOFF_FINAL_PROT

◆ BLAST_GAP_X_DROPOFF_FINAL_TBLASTX

◆ BLAST_GAP_X_DROPOFF_GREEDY

◆ BLAST_GAP_X_DROPOFF_NUCL

◆ BLAST_GAP_X_DROPOFF_PROT

◆ BLAST_GAP_X_DROPOFF_TBLASTX

◆ BLAST_GENETIC_CODE

◆ BLAST_HITLIST_SIZE

◆ BLAST_PENALTY

◆ BLAST_PENALTY_MAPPER

◆ BLAST_REWARD

◆ BLAST_REWARD_MAPPER

◆ BLAST_SCAN_RANGE_NUCL

◆ BLAST_UNGAPPED_X_DROPOFF_NUCL

◆ BLAST_UNGAPPED_X_DROPOFF_PROT

◆ BLAST_WINDOW_SIZE_DISC

◆ BLAST_WINDOW_SIZE_MEGABLAST

◆ BLAST_WINDOW_SIZE_NUCL

◆ BLAST_WINDOW_SIZE_PROT

◆ BLAST_WORD_THRESHOLD_BLASTN

◆ BLAST_WORD_THRESHOLD_BLASTP

◆ BLAST_WORD_THRESHOLD_BLASTP_FAST

◆ BLAST_WORD_THRESHOLD_BLASTP_WD_SZ_6

◆ BLAST_WORD_THRESHOLD_BLASTP_WD_SZ_7

◆ BLAST_WORD_THRESHOLD_BLASTX

◆ BLAST_WORD_THRESHOLD_MEGABLAST

◆ BLAST_WORD_THRESHOLD_TBLASTN

◆ BLAST_WORD_THRESHOLD_TBLASTX

◆ BLAST_WORDSIZE_MAPPER

◆ BLAST_WORDSIZE_MEGABLAST

◆ BLAST_WORDSIZE_NUCL

◆ BLAST_WORDSIZE_PROT

◆ DEFAULT_SUBJECT_BESTHIT_NUCL_MAX_RANGE_DIFF

◆ DEFAULT_SUBJECT_BESTHIT_PROT_MAX_RANGE_DIFF

◆ DELTA_INCLUSION_ETHRESH

◆ kDefaultRepeatFilterDb

◆ MAGICBLAST_MAX_INSERT_SIZE_NONSPLICED

◆ MAGICBLAST_MAX_INSERT_SIZE_SPLICED

◆ MAX_DB_WORD_COUNT_MAPPER

◆ PSI_INCLUSION_ETHRESH

◆ PSI_PSEUDO_COUNT_CONST

Typedef Documentation

◆ BlastDatabaseOptions

◆ BlastEffectiveLengthsOptions

◆ BlastExtensionOptions

◆ BlastHitSavingOptions

◆ BlastHSPBestHitOptions

◆ BlastHSPCullingOptions

◆ BlastHSPFilteringOptions

◆ BlastHSPSubjectBestHitOptions

◆ BlastInitialWordOptions

◆ BlastScoringOptions

◆ EBlastPrelimGapExt

◆ EBlastTbackExt

◆ EFilterOptions

◆ LookupTableOptions

◆ PSIBlastOptions

◆ QuerySetUpOptions

◆ SBlastFilterOptions