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

(kbp->

> 0 && kbp->

> 0 && kbp->

> 0);

(kbp_in && query_info && kbp_ret);

(

=query_info->

; i<=query_info->last_context;

++) {

*kbp_ret = kbp_in[

];

min_lambda = (double)

;

(kbp_in && query_info);

(

=query_info->

; i<=query_info->last_context;

++) {

(min_lambda > kbp_in[

]->Lambda)

min_lambda = kbp_in[

]->

;

*kbp_out = kbp_in[

];

(min_lambda > 0.0);

subject_length,

kQueryLenForHashTable = 8000;

context <= query_info->last_context; ++

) {

hit_params, sbp, query_info, subject_length, p);

(

= 0;

< 256;

++) {

(

& 3) score += penalty;

score += reward;

((

>> 2) & 3) score += penalty;

score += reward;

((

>> 4) & 3) score += penalty;

score += reward;

(

>> 6) score += penalty;

score += reward;

gap_decay_rate = 0.0;

gapped_calculation =

;

context <= query_info->last_context; ++

) {

(query_length > 0);

(

)query_length)*((

)subj_length),

, gap_decay_rate);

new_cutoff =

(new_cutoff, gap_trigger);

new_cutoff = gap_trigger;

new_cutoff =

(new_cutoff,

(new_cutoff < cutoff_min) {

cutoff_min = new_cutoff;

(xdrop_max < curr_cutoffs->x_dropoff)

( params ==

)

printf(

);

printf(

);

printf(

);

printf(

);

printf(

, options->

);

printf(

, options->

);

printf(

, options->

);

printf(

, options->

);

printf(

, options->

);

printf(

, options->

);

printf(

, options->

);

printf(

, options->

);

printf(

, params->

);

printf(

, params->

);

printf(

, params->

);

printf(

, params->

);

printf(

, params->

);

printf(

, params->

);

(score_options ==

)

(*parameters)->real_db_length = db_length;

(*parameters)->real_num_seqs = num_seqs;

(!link_hsp_params)

*link_hsp_params = params;

(!word_params || !hit_params)

(gapped_calculation) {

evalue = pattern_space*paramC*(1+Lambda*score)*

kMaxIter=20;

effNumPatterns = 0;

(iteration=0; iteration<kMaxIter; iteration++)

targetScore = (lowScore+highScore)/2;

lowScore = targetScore;

highScore = targetScore;

((highScore-lowScore) <= 1)

avg_subj_length,

compositionBasedStats,

gapped_calculation =

;

(options->

&& gapped_calculation && avg_subj_length <= 0)

max_protein_gap;

(gapped_calculation) {

}

(max_protein_gap <= 0) {

(max_protein_gap, 0);

avg_subj_length, compositionBasedStats, params);

avg_subject_length,

compositionBasedStats,

}

(sbp->

) {

kbp_array = sbp->

;

gapped_calculation =

;

context <= query_info->last_context; ++

) {

context <= query_info->last_context; ++

) {

context <= query_info->last_context; ++

) {

cbs_stretch = (compositionBasedStats > 1) ? 5 : 1;

evalue_hsp = 1.0;

searchsp = (

)

(avg_qlen, avg_subject_length) *

(

)avg_subject_length;

context <= query_info->last_context; ++

) {

context <= query_info->last_context; ++

) {

cutoff_min =

(cutoff_min,

db_length,

subject_length)

gap_prob, gap_decay_rate, x_variable, y_variable;

(!link_hsp_params)

((double) subject_length))/(kbp->

));

query_length = query_length - expected_length;

subject_length = subject_length - expected_length;

query_length =

(query_length, 1);

subject_length =

(subject_length, 1);

(db_length > subject_length) {

y_variable =

((

) (db_length)/(

) subject_length)*(kbp->

)/

y_variable =

((

) (subject_length + expected_length)/

(

) subject_length)*(kbp->

)/(gap_decay_rate);

search_sp = ((

) query_length)* ((

) subject_length);

x_variable = 0.25*y_variable*((double) search_sp);

x_variable /= (1.0 - gap_prob +

);

x_variable /= (gap_prob +

);

printf(

);

printf(

, word_params->

);

printf(

);

context <= query_info->last_context; ++

)

printf(

);

printf(

, ext_params->

);

printf(

);

context <= query_info->last_context; ++

)

#define sfree(x)

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

#define CODON_LENGTH

Codons are always of length 3.

#define NUM_FRAMES

Number of frames to which we translate in translating searches.

#define DEFAULT_LONGEST_INTRON

For translated gapped searches, this is the default value in nucleotides of longest_intron (for ungap...

Structures and API used for saving BLAST hits.

Int4 PhiBlastGetEffectiveNumberOfPatterns(const BlastQueryInfo *query_info)

Count the number of occurrences of pattern in sequence, which do not overlap by more than half the pa...

#define BLASTERR_NOVALIDKARLINALTSCHUL

Could not calculate Karlin-Altschul statistics for any context.

Routines for creating nucleotide BLAST lookup tables.

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

Updates cutoff scores in hit saving parameters.

BlastHitSavingParameters * BlastHitSavingParametersFree(BlastHitSavingParameters *parameters)

Deallocate memory for BlastHitSavingOptions*.

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

Calculate scaled cutoff scores and gap penalties.

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

Calculate the raw values for the X-dropoff parameters.

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

Initialize the linking HSPs parameters with default values.

BlastEffectiveLengthsParameters * BlastEffectiveLengthsParametersFree(BlastEffectiveLengthsParameters *parameters)

Deallocate memory for BlastEffectiveLengthsParameters*.

void printBlastScoringParameters(BlastScoringParameters *params)

static double s_BlastFindSmallestLambda(Blast_KarlinBlk **kbp_in, const BlastQueryInfo *query_info, Blast_KarlinBlk **kbp_out)

Returns the smallest lambda value from a collection of Karlin-Altchul blocks.

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

Allocate memory and initialize the BlastHitSavingParameters structure.

static Int2 s_BlastFindValidKarlinBlk(Blast_KarlinBlk **kbp_in, const BlastQueryInfo *query_info, Blast_KarlinBlk **kbp_ret)

Returns the first valid Karlin-Altchul block from the list of blocks.

BlastInitialWordParameters * BlastInitialWordParametersFree(BlastInitialWordParameters *parameters)

Deallocate memory for BlastInitialWordParameters.

BlastExtensionParameters * BlastExtensionParametersFree(BlastExtensionParameters *parameters)

Deallocate memory for BlastExtensionParameters.

void printBlastHitSavingParameters(BlastHitSavingParameters *hit_params, BlastQueryInfo *query_info)

static double s_GetEstimatedPhiExpect(int score, const BlastQueryInfo *query_info, const BlastScoreBlk *sbp, int effNumPatterns)

Returns the estimated expect value for the pattern match with a given scoring alignment.

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

Allocate memory for BlastInitialWordParameters and set x_dropoff.

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

static double s_GetCutoffEvalue(EBlastProgramType program)

Compute the default cutoff expect value for ungapped extensions.

BlastLinkHSPParameters * BlastLinkHSPParametersFree(BlastLinkHSPParameters *parameters)

Deallocate memory for BlastLinkHSPParameters;.

static Boolean s_BlastKarlinBlkIsValid(const Blast_KarlinBlk *kbp)

Returns true if the Karlin-Altschul block doesn't have its lambda, K, and H fields set to negative va...

static Int4 s_PhiBlastCutoffScore(double ethresh, const BlastQueryInfo *query_info, const BlastScoreBlk *sbp)

Estimates a cutoff score for use in preliminary gapped stage of phiblast.

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

Update BlastLinkHSPParameters, using calculated values of other parameters.

void printBlastInitialWordParamters(BlastInitialWordParameters *word_params, BlastQueryInfo *query_info)

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

Calculates cutoff scores and returns them.

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

Update cutoff scores in BlastInitialWordParameters structure.

void printBlastExtensionParameters(BlastExtensionParameters *ext_params)

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.

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

#define RESTRICTED_ALIGNMENT_WORST_EVALUE

Because approximate gapped alignment adds extra overhead, it should be avoided if there is no perform...

#define CUTOFF_E_BLASTP

default evalue (ungapped blastp)

#define CUTOFF_E_BLASTN

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

#define BLAST_GAP_SIZE

Default gap size.

@ eDiagHash

use hash table (blastn only)

@ eDiagArray

use diagonal structures with array of last hits and levels.

#define BLAST_GAP_PROB

Default parameters for linking HSPs.

#define BLAST_GAP_DECAY_RATE_GAPPED

Gap decay rate for gapped search.

#define CUTOFF_E_BLASTX

default evalue (ungapped blastx)

#define BLAST_GAP_PROB_GAPPED

Gap probability for gapped search.

#define BLAST_GAP_DECAY_RATE

Gap decay rate for ungapped search.

#define CUTOFF_E_TBLASTX

default evalue (tblastx)

#define BLAST_OVERLAP_SIZE

Default overlap size.

#define CUTOFF_E_TBLASTN

default evalue (ungapped tblastn)

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.

Boolean Blast_ProgramIsNucleotide(EBlastProgramType p)

Boolean Blast_QueryIsPattern(EBlastProgramType p)

Boolean Blast_ProgramIsRpsBlast(EBlastProgramType p)

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

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.

const double kEpsilon

Small constant to test against 0.

Int4 BLAST_SpougeEtoS(double E, Blast_KarlinBlk *kbp, Blast_GumbelBlk *gbp, Int4 qlen, Int4 slen)

Estimate the score for a specified expect value.

Int2 BLAST_Cutoffs(Int4 *S, double *E, Blast_KarlinBlk *kbp, Int8 searchsp, Boolean dodecay, double gap_decay_rate)

Calculate the cutoff score from the expected number of HSPs or vice versa.

static const char * expect

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

uint64_t Uint8

8-byte (64-bit) unsigned integer

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

for(len=0;yy_str[len];++len)

Prototypes for portable math library (ported from C Toolkit)

#define NCBIMATH_LN2

Natural log(2)

long BLAST_Nint(double x)

Nearest integer.

#define MIN(a, b)

returns smaller of a and b.

#define INT4_MAX

largest nubmer represented by signed int

Uint1 Boolean

bool replacment for C

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

#define ASSERT

macro for assert.

#define MAX(a, b)

returns larger of a and b.

Int4 query_length

Length of this query, strand or frame.

Boolean is_valid

Determine if this context is valid or not.

Int4 query_offset

Offset of this query, strand or frame in the concatenated super-query.

Int8 eff_searchsp

Effective search space for this context.

Options for setting up effective lengths and search spaces.

Parameters for setting up effective lengths and search spaces.

Options used for gapped extension These include: a.

double gap_x_dropoff_final

X-dropoff value for the final gapped extension (in bits)

double gap_x_dropoff

X-dropoff value for gapped extension (in bits)

Computed values used as parameters for gapped alignments.

BlastExtensionOptions * options

The original (unparsed) options.

Int4 gap_x_dropoff_final

X-dropoff value for the final gapped extension (raw)

Int4 gap_x_dropoff

X-dropoff value for gapped extension (raw)

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

Int4 cutoff_score

Raw cutoff score corresponding to the e-value provided by the user if no sum stats,...

Int4 cutoff_score_max

Raw cutoff score corresponding to the e-value provided by user, cutoff_score must be <= this.

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

Int4 longest_intron

The longest distance between HSPs allowed for combining via sum statistics with uneven gaps.

double low_score_perc

Low-score option.

double expect_value

The expect value cut-off threshold for an HSP, or a combined hit if sum statistics is used.

Int4 cutoff_score

The (raw) score cut-off threshold.

Int4 mask_level

Only keep the highest scoring HSP when more than one HSP overlaps the same region of the query by mor...

Boolean do_sum_stats

Force sum statistics to be used to combine HSPs, TRUE by default for all ungapped searches and transl...

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

BlastGappedCutoffs * cutoffs

per-context gapped cutoff information

Int4 mask_level

Only keep the highest scoring HSP when more than one HSP overlaps the same region of the query by mor...

Boolean restricted_align

TRUE if approximate score-only gapped alignment is used.

Int4 cutoff_score_min

smallest cutoff score across all contexts

Boolean do_sum_stats

TRUE if sum stats will be used.

Int4 * low_score

lowest ungapped score that can trigger a gapped alignment if the histlist is already full.

double prelim_evalue

evalue for preliminary search (may be higher for CBS).

BlastLinkHSPParameters * link_hsp_params

Parameters for linking HSPs with sum statistics; linking is not done if NULL.

BlastHitSavingOptions * options

The original (unparsed) options.

Options needed for initial word finding and processing.

double gap_trigger

Score in bits for starting gapped extension.

double x_dropoff

X-dropoff value (in bits) for the ungapped extension.

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

BlastUngappedCutoffs * cutoffs

cutoff values (one per context)

Boolean ungapped_extension

Should an ungapped extension be performed?

BlastInitialWordOptions * options

The original (unparsed) options.

Boolean matrix_only_scoring

Use the scoring matrix ( not table ) to score ungapped and gapped alignments -RMH-.

Int4 cutoff_score_min

smallest cutoff score across all contexts

Int4 x_dropoff_max

largest X-drop cutoff across all contexts

ESeedContainerType container_type

How to store offset pairs for initial seeds?

Int4 nucl_score_table[256]

the combined score of all match/mismatch combinations for aligning four bases

Parameter block for linking HSPs with sum statistics.

double gap_decay_rate

Decay rate for linking HSPs and calculating cutoff scores.

double gap_prob

Probability of decay for linking HSPs.

Int4 cutoff_big_gap

Cutoff sum score for linked HSPs with big gaps.

Int4 cutoff_small_gap

Cutoff sum score for linked HSPs with small gaps.

Int4 overlap_size

Maximal overlap allowed in successive linked HSPs.

Int4 longest_intron

Length of a longest intron for uneven gap linking of HSPs.

Int4 gap_size

Small gap size for linking HSPs.

The query related information.

Int4 first_context

Index of the first element of the context array.

BlastContextInfo * contexts

Information per context.

int num_queries

Number of query sequences.

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.

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.

Int4 penalty

penalty for mismatch in blastn.

Blast_KarlinBlk ** kbp_std

K-A parameters for ungapped alignments.

Int4 reward

reward for match in blastn.

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.

EBlastProgramType program_number

indicates blastn, blastp, etc.

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_path

Directory path to where matrices are stored.

Int4 shift_pen

Penalty for shifting a frame in out-of-frame gapping.

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...

double scale_factor

multiplier for all cutoff scores

Int4 gap_extend

Penalty for each gap residue (scaled version)

Int2 penalty

Penalty for a mismatch.

Int4 shift_pen

Penalty for shifting a frame in out-of-frame gapping (scaled version)

Int4 gap_open

Extra penalty for starting a gap (scaled version)

BlastScoringOptions * options

User-provided values for these params.

Int2 reward

Reward for a match.

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

Int4 reduced_nucl_cutoff_score

for blastn, a reduced cutoff score for use with approximate ungapped alignments

Int4 x_dropoff_init

Raw X-dropoff value specified by the bit score in BlastInitialWordOptions.

Int4 cutoff_score

Cutoff score for saving ungapped hits.

Int4 x_dropoff

Raw X-dropoff value used in the ungapped extension.

Boolean filled

flag indicate the values of gbp are prepared

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

Wrapper structure for different types of BLAST lookup tables.

double probability

Estimated probability of the pattern.

static CS_CONTEXT * context

voidp calloc(uInt items, uInt size)

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