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NCBI C++ ToolKit: src/algo/blast/core/blast_setup.c Source File

(sbp ==

|| scoring_options ==

) {

}

(sbp->

) {

sbp->

, error_return);

(retval)

retval;

index <= query_info->last_context; index++) {

( scoring_options->

== 0 && scoring_options->

== 0 )

sbp->

, error_return);

}

(0 ==

(

, options->

)) {

}

(0 ==

(

, options->

)) {

}

(0 ==

(

, options->

)) {

}

(0 ==

(

, options->

)) {

snprintf(

,

(

),

,

}

(status == -2) {

snprintf(

,

(

),

, options->

);

( !sbp || !scoring_options ) {

( scoring_options->

== 0 && scoring_options->

== 0 )

snprintf(

,

(

),

,

context <= query_info->last_context; ++

) {

(sbp && sbp->

) {

query_info, blast_message);

query_info, blast_message);

index <= query_info->last_context;

valid_context_found =

;

}

(score_blk) {

(valid_context_found) {

filter_options_allocated =

;

(filter_options_allocated)

(filter_options_allocated) {

(lookup_segments) {

filter_maskloc, lookup_segments);

*

= filter_maskloc;

filter_maskloc =

;

program_number, sbpp, scale_factor,

blast_message, get_path);

(*blast_message ==

) {

(context_index != 0) {

);

(context_index < eff_len_options->num_searchspaces);

retval = eff_len_options->

[context_index];

alpha=0, beta=0;

(!query_info || !sbp)

db_length = eff_len_options->

;

(db_length == 0 &&

db_length = db_length/3;

db_num_seqs = eff_len_options->

;

index <= query_info->last_context;

index <= query_info->last_context;

index <= query_info->last_context;

length_adjustment = 0;

effective_search_space =

kbp = kbp_ptr[index];

( scoring_options->

== 0 && scoring_options->

== 0 )

alpha/kbp->

, beta,

query_length, db_length,

db_num_seqs, &length_adjustment);

(effective_search_space == 0) {

effective_db_length = db_length - ((

)db_num_seqs * length_adjustment);

(effective_db_length <= 0)

effective_db_length = 1;

effective_search_space = effective_db_length *

(query_length - length_adjustment);

(total_length && num_seqs);

(*total_length <= 0)

(*total_length > 0) {

max_subject_length;

min_subject_length;

total_length = -1;

(total_length <= 0)

dbl = total_length;

(total_length > 0) {

*eff_len_params, sbp, query_info,

)) != 0)

query_info, ext_params)) != 0)

min_subject_length/=3;

min_subject_length = (

) (total_length/num_seqs);

(min_subject_length <=0) {

query_info, min_subject_length,

(*ext_params)->options->compositionBasedStats,

max_subject_length, sbp, gap_align)) != 0) {

subject_length,

eff_len_params, sbp, query_info,

)) != 0)

subject_length, word_params);

(seqloc = *

; seqloc; seqloc = next_loc) {

next_loc = seqloc->next;

seqloc->ssr->left =

(0, seqloc->ssr->left - from);

seqloc->ssr->right =

(seqloc->ssr->right, to) - from;

(seqloc->ssr->left > seqloc->ssr->right) {

last_loc->next = seqloc->next;

}

(!head_loc) {

head_loc = last_loc = seqloc;

last_loc->

= seqloc;

last_loc = last_loc->

;

num_patterns = 0;

(query_info && pattern_blk);

(num_patterns == 0)

snprintf(

,

(

),

, pattern_blk->

);

(num_patterns ==

)

snprintf(

,

(

),

, pattern_blk->

);

(num_patterns < 0)

#define sfree(x)

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

BLAST filtering functions.

void BlastSetUp_MaskQuery(BLAST_SequenceBlk *query_blk, const BlastQueryInfo *query_info, const BlastMaskLoc *filter_maskloc, EBlastProgramType program_number)

Masks the sequence given a BlastMaskLoc.

BlastMaskLoc * BlastMaskLocFree(BlastMaskLoc *mask_loc)

Deallocate memory for a BlastMaskLoc structure as well as the BlastSeqLoc's pointed to.

Int2 BLAST_ComplementMaskLocations(EBlastProgramType program_number, const BlastQueryInfo *query_info, const BlastMaskLoc *mask_loc, BlastSeqLoc **complement_mask)

This function takes the list of mask locations (i.e., regions that should not be searched or not adde...

BlastSeqLoc * BlastSeqLocNodeFree(BlastSeqLoc *node)

Deallocate a single BlastSeqLoc structure and its contents, without following its next pointer.

Int2 BlastSetUp_GetFilteringLocations(BLAST_SequenceBlk *query_blk, const BlastQueryInfo *query_info, EBlastProgramType program_number, const SBlastFilterOptions *filter_options, BlastMaskLoc **filter_out, Blast_Message **blast_message)

Does preparation for filtering and then calls BlastSetUp_Filter.

Int2 BlastFilteringOptionsFromString(EBlastProgramType program_number, const char *instructions, SBlastFilterOptions **filtering_options, Blast_Message **blast_message)

Produces SBlastFilterOptions from a string that has been traditionally supported in blast.

Int2 BlastMaskLocProteinToDNA(BlastMaskLoc *mask_loc, const BlastQueryInfo *query_info)

Given a BlastMaskLoc with an array of lists of mask locations per protein frame, recalculates all mas...

Int2 BLAST_GapAlignStructNew(const BlastScoringParameters *score_params, const BlastExtensionParameters *ext_params, Uint4 max_subject_length, BlastScoreBlk *sbp, BlastGapAlignStruct **gap_align_ptr)

Initializes the BlastGapAlignStruct structure.

#define Blast_PerrorWithLocation(msg, error_code, context)

Convenient define to call the function Blast_PerrorEx.

#define BLASTERR_SUBJECT_LENGTH_INVALID

Subject seqs min avg length error.

Int2 Blast_MessageWrite(Blast_Message **blast_msg, EBlastSeverity severity, int context, const char *message)

Writes a message to a structure.

const int kBlastMessageNoContext

Declared in blast_message.h as extern const.

#define BLASTERR_MEMORY

System error: out of memory condition.

#define BLASTERR_INVALIDPARAM

Invalid parameter: possible programmer error or pre-condition not met.

#define BLAST_GAP_OPEN_MEGABLAST

default gap open penalty (megablast with greedy gapped alignment)

#define BLAST_GAP_EXTN_MEGABLAST

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

Boolean SBlastFilterOptionsMaskAtHash(const SBlastFilterOptions *filter_options)

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

SBlastFilterOptions * SBlastFilterOptionsFree(SBlastFilterOptions *filter_options)

Frees SBlastFilterOptions and all subservient structures.

#define BLAST_REWARD

default nucleotide match score

#define BLAST_PENALTY

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

Boolean BlastEffectiveLengthsOptions_IsSearchSpaceSet(const BlastEffectiveLengthsOptions *options)

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

BlastEffectiveLengthsParameters * BlastEffectiveLengthsParametersFree(BlastEffectiveLengthsParameters *parameters)

Deallocate memory for BlastEffectiveLengthsParameters*.

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

Calculate the raw values for the X-dropoff parameters.

BlastExtensionParameters * BlastExtensionParametersFree(BlastExtensionParameters *parameters)

Deallocate memory for BlastExtensionParameters.

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

Calculate scaled cutoff scores and gap penalties.

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

Allocate memory and initialize the BlastHitSavingParameters structure.

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

Updates cutoff scores in hit saving parameters.

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

Update BlastLinkHSPParameters, using calculated values of other parameters.

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

Update cutoff scores in BlastInitialWordParameters structure.

BlastScoringParameters * BlastScoringParametersFree(BlastScoringParameters *parameters)

Deallocate memory for BlastScoringParameters.

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

Allocate memory for BlastEffectiveLengthsParameters.

Boolean Blast_ProgramIsMapping(EBlastProgramType p)

Boolean Blast_QueryIsPssm(EBlastProgramType p)

Returns true if the query is PSSM.

Boolean Blast_ProgramIsPhiBlast(EBlastProgramType p)

Returns true if program is PHI-BLAST (i.e.

Boolean Blast_QueryIsTranslated(EBlastProgramType p)

Returns true if the query is translated.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

Boolean Blast_SubjectIsTranslated(EBlastProgramType p)

Returns true if the subject is translated.

Int8 BlastSeqSrcGetTotLenStats(const BlastSeqSrc *seq_src)

Get the total length of all sequences for calculation of expect value etc.

Int4 BlastSeqSrcGetSeqLen(const BlastSeqSrc *seq_src, void *oid)

Retrieve sequence length (number of residues/bases)

Int4 BlastSeqSrcGetNumSeqs(const BlastSeqSrc *seq_src)

Get the number of sequences contained in the sequence source.

Int8 BlastSeqSrcGetTotLen(const BlastSeqSrc *seq_src)

Get the total length of all sequences in the sequence source.

Int4 BlastSeqSrcGetNumSeqsStats(const BlastSeqSrc *seq_src)

Get the number of sequences used for calculation of expect values etc.

Int4 BlastSeqSrcGetMaxSeqLen(const BlastSeqSrc *seq_src)

Get the length of the longest sequence in the sequence source.

Int4 BlastSeqSrcGetMinSeqLen(const BlastSeqSrc *seq_src)

Get the length of the longest sequence in the sequence source.

static Int2 s_PHIScoreBlkFill(BlastScoreBlk *sbp, const BlastScoringOptions *options, Blast_Message **blast_message, GET_MATRIX_PATH get_path)

Fills a scoring block structure for a PHI BLAST search.

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

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

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

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

static Int2 s_JumperScoreBlkFill(BlastScoreBlk *sbp, const BlastQueryInfo *query_info, Blast_Message **error_return)

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

Initializes the score block structure.

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

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

static Int8 s_GetEffectiveSearchSpaceForContext(const BlastEffectiveLengthsOptions *eff_len_options, int context_index, Blast_Message **blast_message)

Return the search space appropriate for a given context from a list of tabulated search spaces.

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

"Main" setup routine for BLAST.

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

Blast_ScoreBlkKbpGappedCalc, fills the ScoreBlkPtr for a gapped search.

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

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

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

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

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

Adjusts the mask locations coordinates to a sequence interval.

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

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

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

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

Utilities initialize/setup BLAST.

char *(* GET_MATRIX_PATH)(const char *, Boolean)

callback to resolve the path to blast score matrices

Int2 Blast_GetNuclAlphaBeta(Int4 reward, Int4 penalty, Int4 gap_open, Int4 gap_extend, Blast_KarlinBlk *kbp, Boolean gapped_calculation, double *alpha, double *beta)

Extract the alpha and beta settings for these substitution and gap scores.

Int2 Blast_KarlinBlkGappedCalc(Blast_KarlinBlk *kbp, Int4 gap_open, Int4 gap_extend, const char *matrix_name, Blast_Message **error_return)

Fills in lambda, H, and K values, as calculated by Stephen Altschul in Methods in Enzy.

Blast_KarlinBlk * Blast_KarlinBlkNew(void)

Callocs a Blast_KarlinBlk.

Int2 BLAST_ScoreSetAmbigRes(BlastScoreBlk *sbp, char ambiguous_res)

Set the ambiguous residue (e.g, 'N', 'X') in the BlastScoreBlk*.

Int2 Blast_ScoreBlkKbpUngappedCalc(EBlastProgramType program, BlastScoreBlk *sbp, Uint1 *query, const BlastQueryInfo *query_info, Blast_Message **blast_message)

Calculate and fill the ungapped Karlin-Altschul parameters in the BlastScoreBlk structure (fields kbp...

Int2 Blast_GumbelBlkCalc(Blast_GumbelBlk *gbp, Int4 gap_open, Int4 gap_extend, const char *matrix_name, Blast_Message **error_return)

Fills in gumbel parameters to estimate p-value using FSC.

Int2 Blast_KarlinBlkNuclGappedCalc(Blast_KarlinBlk *kbp, Int4 gap_open, Int4 gap_extend, Int4 reward, Int4 penalty, Blast_KarlinBlk *kbp_ungap, Boolean *round_down, Blast_Message **error_return)

Retrieves Karlin-Altschul parameters from precomputed tables, given the substitution and gap scores.

Int2 Blast_ScoreBlkKbpIdealCalc(BlastScoreBlk *sbp)

Calculates the Karlin-Altschul parameters assuming standard residue compositions for the query and su...

void BLAST_GetAlphaBeta(const char *matrixName, double *alpha, double *beta, Boolean gapped, Int4 gap_open, Int4 gap_extend, const Blast_KarlinBlk *kbp_ungapped)

Extract the alpha and beta settings for this matrixName, and these gap open and gap extension costs.

Blast_ScoreFreq * Blast_ScoreFreqNew(Int4 score_min, Int4 score_max)

Creates a new structure to keep track of score frequencies for a scoring system.

Int2 Blast_KarlinBlkCopy(Blast_KarlinBlk *kbp_to, Blast_KarlinBlk *kbp_from)

Copies contents of one Karlin block to another.

Int4 BLAST_ComputeLengthAdjustment(double K, double logK, double alpha_d_lambda, double beta, Int4 query_length, Int8 db_length, Int4 db_num_seqs, Int4 *length_adjustment)

Computes the adjustment to the lengths of the query and database sequences that is used to compensate...

BlastScoreBlk * BlastScoreBlkNew(Uint1 alphabet, Int4 number_of_contexts)

Allocates and initializes BlastScoreBlk.

Int2 Blast_ScoreBlkMatrixFill(BlastScoreBlk *sbp, GET_MATRIX_PATH get_path)

This function fills in the BlastScoreBlk structure.

Various auxiliary BLAST utility functions.

Int2 BLAST_CreateMixedFrameDNATranslation(BLAST_SequenceBlk *query_blk, const BlastQueryInfo *query_info)

Initialize the mixed-frame sequence for out-of-frame gapped extension.

char * BLAST_StrToUpper(const char *string)

Returns a copy of the input string with all its characters turned to uppercase.

ncbi::TMaskedQueryRegions mask

#define BLASTNA_SEQ_CODE

Identifies the blastna alphabet, for use in blast only.

#define BLASTAA_SEQ_CODE

== Seq_code_ncbistdaa

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

int strcmp(const char *str1, const char *str2)

#define MIN(a, b)

returns smaller of a and b.

#define INT4_MAX

largest nubmer represented by signed int

void * BlastMemDup(const void *orig, size_t size)

Copies memory using memcpy and malloc.

Uint1 Boolean

bool replacment for C

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

#define NULLB

terminating byte of a char* string.

#define ASSERT

macro for assert.

#define MAX(a, b)

returns larger of a and b.

Int4 PHIGetPatternOccurrences(const SPHIPatternSearchBlk *pattern_blk, const BLAST_SequenceBlk *query, const BlastSeqLoc *location, Boolean is_dna, BlastQueryInfo *query_info)

Finds all pattern hits in a given query and saves them in the previously allocated SPHIQueryInfo stru...

SPHIQueryInfo * SPHIQueryInfoNew(void)

Allocates the pattern occurrences structure.

Structure to hold a sequence.

Uint1 * sequence

Sequence used for search (could be translation).

Int4 query_length

Length of this query, strand or frame.

Boolean is_valid

Determine if this context is valid or not.

Int4 length_adjustment

Length adjustment for boundary conditions.

Int8 eff_searchsp

Effective search space for this context.

Options for setting up effective lengths and search spaces.

Int8 * searchsp_eff

Search space to be used for statistical calculations (one such per query context)

Int8 db_length

Database length to be used for statistical calculations.

Int4 dbseq_num

Number of database sequences to be used for statistical calculations.

Int4 num_searchspaces

Number of elements in searchsp_eff, this must be equal to the number of contexts in the search.

Parameters for setting up effective lengths and search spaces.

Int8 real_db_length

Total database length to use in search space calculations.

Int4 real_num_seqs

Number of subject sequences to use for search space calculations.

BlastEffectiveLengthsOptions * options

User provided values for these parameters.

Options used for gapped extension These include: a.

Computed values used as parameters for gapped alignments.

Structure supporting the gapped alignment.

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

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

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

Structure for keeping the query masking information.

The query related information.

Int4 first_context

Index of the first element of the context array.

BlastContextInfo * contexts

Information per context.

struct SPHIQueryInfo * pattern_info

Counts of PHI BLAST pattern occurrences, used in PHI BLAST only.

Int4 last_context

Index of the last element of the context array.

Structure used for scoring calculations.

Blast_KarlinBlk ** kbp

Karlin-Altschul parameters.

Blast_ScoreFreq ** sfp

score frequencies for scoring matrix.

Boolean matrix_only_scoring

Score ungapped/gapped alignment only using the matrix parameters and with raw scores.

double scale_factor

multiplier for all cutoff and dropoff scores

Blast_KarlinBlk ** kbp_gap

K-A parameters for gapped alignments.

Boolean round_down

Score must be rounded down to nearest even score if odd.

char * name

name of scoring matrix.

Int4 penalty

penalty for mismatch in blastn.

Int4 number_of_contexts

Used by sfp and kbp, how large are these.

Boolean read_in_matrix

If TRUE, matrix is read in, otherwise produce one from penalty and reward above.

Boolean complexity_adjusted_scoring

Use cross_match-like complexity adjustment on raw scores.

Blast_KarlinBlk * kbp_ideal

Ideal values (for query with average database composition).

Blast_KarlinBlk ** kbp_gap_std

K-A parameters for std (not position-based) alignments.

Blast_KarlinBlk ** kbp_std

K-A parameters for ungapped alignments.

Int4 reward

reward for match in blastn.

Blast_KarlinBlk ** kbp_gap_psi

K-A parameters for psi alignments.

Blast_GumbelBlk * gbp

Gumbel parameters for FSC.

Scoring options block Used to produce the BlastScoreBlk structure This structure may be needed for lo...

Int2 penalty

Penalty for a mismatch.

Int4 gap_open

Extra penalty for starting a gap.

Int4 gap_extend

Penalty for each gap residue.

Int2 reward

Reward for a match.

Boolean gapped_calculation

gap-free search if FALSE

char * matrix

Name of the matrix containing all scores: needed for finding neighboring words.

Boolean is_ooframe

Should out-of-frame gapping be used in a translated search?

Boolean complexity_adjusted_scoring

Use cross_match-like complexity adjustment on raw scores.

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

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

struct BlastSeqLoc * next

next in linked list

Complete type definition of Blast Sequence Source ADT.

Int8 db_length

total length of database

Structure to hold the Karlin-Altschul parameters.

double paramC

for use in seed.

double K

K value used in statistics.

double Lambda

Lambda value used in statistics.

double H

H value used in statistics.

double logK

natural log of K value used in statistics

Structure to hold the a message from the core of the BLAST engine.

Options required for setting up the query sequence.

char * filter_string

DEPRECATED, filtering options above.

SBlastFilterOptions * filtering_options

structured options for all filtering offered from algo/blast/core for BLAST.

Structure containing all auxiliary information needed in a pattern search.

double patternProbability

Probability of this letter combination.

Int4 minPatternMatchLength

Minimum length of string to match this pattern.

char * pattern

Pattern used, saved here for error reporting.

char * pattern

Pattern used, saved here for formatting purposes.

double probability

Estimated probability of the pattern.

static CS_CONTEXT * context

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