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

(p->sid == list->

) {

(sid < tmp_hit_list->hsplist_current);

best_list = p->

;

(

=0;

< list->

; ++id) {

->sid = list->

;

->end =

->begin +

->len;

(q=

, p=best_list; p && p->

<

->begin; q=p, p=p->next);

(qid=0; qid<

->num_queries; ++qid) {

(best_list[qid]) {

(!

->hitlist_array[qid]) {

, qid, qlen, begin, end, lenA, lenB, scoreA, scoreB, overhang;

allowed_begin, allowed_end;

denA, evalueA, evalueB, param_overhang, param_s;

(!hsp_list)

0;

param_overhang = params->

;

(

=0;

<hsp_list->

; ++

) {

scoreA = hsp->

;

denA = 1.0 * scoreA / lenA / param_s;

(p=best_list[qid]; p && p->

< end; p=p->

);

( ; p && p->

<= begin; p=p->

) {

&& evalueB <= evalueA

&& 1.0 * scoreB / lenB > denA)

overhang = 2.0 * lenA * param_overhang / (1.0 - 2.0 * param_overhang);

allowed_begin = begin - overhang;

allowed_end = end + overhang;

overhang = lenA * param_overhang;

denA = 1.0 * scoreA / lenA * param_s;

(q=

, p=best_list[qid]; p && p->

< allowed_begin; q=p, p=p->

);

(; p && p->begin < allowed_end; ) {

scoreB = p->hsp->score;

overhang = (p->end - p->begin - lenB)/2;

evalueB= p->hsp->evalue;

( p->begin + overhang >= begin

&& p->end - overhang <= end

&& evalueB >= evalueA

&& 1.0 * scoreB / lenB < denA)

best_list[qid] = p->

;

(q=

, p=best_list[qid]; p && p->

< begin; q=p, p=p->

);

->sid = hsp_list->

;

, qid, begin, end, lenA, lenB, scoreA, scoreB, overhang;

allowed_begin, allowed_end;

denA, evalueA, evalueB, param_overhang, param_s;

(!hsp_list)

0;

param_overhang = params->

;

(

=0;

<hsp_list->

; ++

) {

scoreA = hsp->

;

denA = 1.0 * scoreA / lenA / param_s;

(p=best_list[qid]; p && p->

< end; p=p->

);

( ; p && p->

< begin; p=p->

) {

&& evalueB <= evalueA

&& 1.0 * scoreB / lenB > denA)

overhang = 2.0 * lenA * param_overhang / (1.0 - 2.0 * param_overhang);

allowed_begin = begin - overhang;

allowed_end = end + overhang;

overhang = lenA * param_overhang;

denA = 1.0 * scoreA / lenA * param_s;

(q=

, p=best_list[qid]; p && p->

< allowed_begin; q=p, p=p->

);

(; p && p->begin < allowed_end; ) {

scoreB = p->hsp->score;

overhang = (p->end - p->begin - lenB)/2;

evalueB= p->hsp->evalue;

( p->begin + overhang >= begin

&& p->end - overhang <= end

&& evalueB >= evalueA

&& 1.0 * scoreB / lenB < denA)

best_list[qid] = p->

;

(q=

, p=best_list[qid]; p && p->

< begin; q=p, p=p->

);

(! query_info)

;

.params = params;

.query_info = query_info;

qid, sid, num_list;

(qid = 0; qid <

->num_queries; ++qid) {

(!(

->hitlist_array[qid]))

;

num_list =

->hitlist_array[qid]->hsplist_count;

(sid = 0; sid < num_list; ++sid) {

->hitlist_array[qid]->hsplist_array[sid]);

->hitlist_array[qid]->hsplist_array[sid] =

;

->hitlist_array[qid]->hsplist_count = 0;

(! query_info)

;

.params = params;

.query_info = query_info;

compositionBasedStats,

compositionBasedStats, gapped_calculation);

writer_info->

= params;

pipe_info->

= params;

#define sfree(x)

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

BlastHitList * Blast_HitListFree(BlastHitList *hitlist)

Deallocate memory for the hit list.

Int4 BlastHspNumMax(Boolean gapped_calculation, const BlastHitSavingOptions *options)

Calculated the number of HSPs that should be saved.

Int2 Blast_HSPResultsSortByEvalue(BlastHSPResults *results)

Sort each hit list in the BLAST results by best e-value.

BlastHitList * Blast_HitListNew(Int4 hitlist_size)

Allocate memory for a hit list of a given size.

Int2 Blast_HitListSortByEvalue(BlastHitList *hit_list)

Sort BlastHitLIst bon evalue.

BlastHSPList * Blast_HSPListNew(Int4 hsp_max)

Creates HSP list structure with a default size HSP array.

BlastHSP * Blast_HSPFree(BlastHSP *hsp)

Deallocate memory for an HSP structure.

Int2 Blast_HSPListSaveHSP(BlastHSPList *hsp_list, BlastHSP *hsp)

Saves HSP information into a BlastHSPList structure.

Int4 GetPrelimHitlistSize(Int4 hitlist_size, Int4 compositionBasedStats, Boolean gapped_calculation)

BlastHSPList * Blast_HSPListFree(BlastHSPList *hsp_list)

Deallocate memory for an HSP list structure as well as all it's components.

void Blast_HSPListSortByScore(BlastHSPList *hsp_list)

Sort the HSPs in an HSP list by score.

Int2 Blast_HitListUpdate(BlastHitList *hit_list, BlastHSPList *hsp_list)

Insert a new HSP list into the hit list.

Utilities for dealing with BLAST HSPs in the core of BLAST.

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.

Int4 Blast_GetQueryIndexFromContext(Int4 context, EBlastProgramType program)

Given a context from BLAST engine core, return the query index.

Int4 BlastQueryInfoGetQueryLength(const BlastQueryInfo *qinfo, EBlastProgramType program, Int4 query_index)

Obtains the sequence length for a given query in the query, without taking into consideration any app...

Various auxiliary BLAST utility functions.

int32_t Int4

4-byte (32-bit) signed integer

static int s_BlastHSPBestHitFinal(void *data, void *hsp_results)

Perform post-run clean-ups Blast_HSPListFree(hsp_list);.

static BlastHSPWriter * s_BlastHSPBestHitFree(BlastHSPWriter *writer)

Free the writer.

static BlastHSPWriter * s_BlastHSPBestHitNew(void *params, BlastQueryInfo *query_info, BLAST_SequenceBlk *sequence)

create the writer

static int s_BlastHSPBestHitRun(void *data, BlastHSPList *hsp_list)

Perform writing task, will save best hits to best_list.

BlastHSPPipeInfo * BlastHSPBestHitPipeInfoNew(BlastHSPBestHitParams *params)

static int s_ExportToHitlist(int qid, BlastHSPBestHitData *bh_data, BlastHitList *hit_list)

Export best_list to hitlist.

static BlastHSPPipe * s_BlastHSPBestHitPipeNew(void *params, BlastQueryInfo *query_info)

create the pipe

static int s_BlastHSPBestHitPipeRun(void *data, BlastHSPResults *results)

The pipe version of best-hit writer.

BlastHSPWriterInfo * BlastHSPBestHitInfoNew(BlastHSPBestHitParams *params)

WriterInfo and PipeInfo to create a best hit writer/pipe.

struct BlastHSPBestHitData BlastHSPBestHitData

static int s_BlastHSPBestHitInit(void *data, void *hsp_results)

The following are implementations for BlastHSPWriter ADT.

static BlastHSPPipe * s_BlastHSPBestHitPipeFree(BlastHSPPipe *pipe)

Free the pipe.

struct LinkedHSP_BH LinkedHSP_BH

linked list of HSPs used to keep best hits for each query.

static int s_BlastHSPBestHitRun_RPS(void *data, BlastHSPList *hsp_list)

Perform writing task for RPS blast, will save best hits to best_list.

BlastHSPBestHitParams * BlastHSPBestHitParamsFree(BlastHSPBestHitParams *opts)

Deallocates the BlastHSPBestHitParams structure passed in.

BlastHSPBestHitParams * BlastHSPBestHitParamsNew(const BlastHitSavingOptions *hit_options, const BlastHSPBestHitOptions *best_hit_opts, Int4 compositionBasedStats, Boolean gapped_calculation)

The following are exported functions to be used by APP.

static int s_ImportFromHitlist(int qid, BlastHSPBestHitData *bh_data, BlastHitList *hit_list)

Import hitlist to best_list (assuming all hsps are besthits)

Implementation of a number of BlastHSPWriters to save hits from a BLAST search, and subsequently retu...

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

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.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

Structure to hold a sequence.

Int1 frame

Frame number (-1, -2, -3, 0, 1, 2, or 3)

Int4 * max_hsps

max number of hsps to hold before pruning

BlastQueryInfo * query_info

query info

Int4 * num_hsps

field to record the number of hsps in each list

BlastHSPBestHitParams * params

parameters to control overhang

LinkedHSP_BH ** best_list

buffer to store best hits

Options for the Best Hit HSP collection algorithm.

Keeps parameters used in best hit algorithm.

double score_edge

fraction of score margin in condition 4

double overhang

overhang used in condition 1.

Int4 hsp_num_max

number of HSPs to save per db sequence.

Int4 prelim_hitlist_size

number of hits saved during preliminary part of search.

EBlastProgramType program

program type.

The structure to hold all HSPs for a given sequence after the gapped alignment.

Int4 oid

The ordinal id of the subject sequence this HSP list is for.

Int4 hspcnt

Number of HSPs saved.

BlastHSP ** hsp_array

Array of pointers to individual HSPs.

Int4 query_index

Index of the query which this HSPList corresponds to.

A wrap of data structure used to create a pipe.

BlastHSPPipeNewFn NewFnPtr

struct BlastHSPPipeInfo * next

the next pipe inf in chain

ADT definition of BlastHSPPipe.

void * data

data structure

BlastHSPPipe * next

the next pipe in chain

BlastHSPPipeRunFn RunFnPtr

BlastHSPPipeFreeFn FreeFnPtr

The structure to contain all BLAST results, for multiple queries.

A wrap of data structure used to create a writer.

BlastHSPWriterNewFn NewFnPtr

ADT definition of BlastHSPWriter.

void * data

data structure

BlastHSPWriterFinalFn FinalFnPtr

BlastHSPWriterFreeFn FreeFnPtr

BlastHSPWriterRunFn RunFnPtr

BlastHSPWriterInitFn InitFnPtr

Structure holding all information about an HSP.

double evalue

This HSP's e-value.

BlastSeg query

Query sequence info.

Int4 context

Context number of query.

Int4 score

This HSP's raw score.

The structure to contain all BLAST results for one query sequence.

BlastHSPList ** hsplist_array

Array of HSP lists for individual database hits.

Int4 hsplist_count

Filled size of the HSP lists array.

Int4 hsplist_current

Number of allocated HSP list arrays.

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

EBlastProgramType program_number

indicates blastn, blastp, etc.

Int4 hitlist_size

Maximal number of database sequences to return results for.

The query related information.

BlastContextInfo * contexts

Information per context.

Int4 offset

Start of hsp.

linked list of HSPs used to keep best hits for each query.

struct LinkedHSP_BH * next

voidp calloc(uInt items, uInt size)

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