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

(

->num_queries > 1) {

(hsp_list_array ==

)

(index = 0; index < hsp_list->

; index++) {

(!(tmp_hsp_list = hsp_list_array[query_index])) {

hsp_list_array[query_index] = tmp_hsp_list =

(tmp_hsp_list ==

)

(hsp_list_array);

tmp_hsp_list->

= hsp_list->

;

(index = 0; index <

->num_queries; index++) {

(hsp_list_array[index]) {

(!

->hitlist_array[index]) {

->hitlist_array[index] =

hsp_list_array[index]);

(hsp_list_array);

}

(hsp_list->

> 0) {

(!

->hitlist_array[0]) {

index, next_index;

(!hsplist_in || hsplist_in->

== 0)

(index = 0; index < hsplist_in->

; index = next_index) {

(next_index = index; next_index < hsplist_in->

;

hspcnt = next_index - index;

hsp_list->

= oid;

( ; index < next_index; ++index)

->params = params;

compositionBasedStats,

(hit_options ==

)

compositionBasedStats, gapped_calculation);

writer_info->

= params;

#define sfree(x)

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

#define BLAST_CMP(a, b)

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

int ScoreCompareHSPs(const void *h1, const void *h2)

Comparison callback function for sorting HSPs, first by score in descending order,...

Int4 BlastHspNumMax(Boolean gapped_calculation, const BlastHitSavingOptions *options)

Calculated the number of HSPs that should be saved.

BlastHitList * Blast_HitListNew(Int4 hitlist_size)

Allocate memory for a hit list of a given size.

BlastHSPList * Blast_HSPListNew(Int4 hsp_max)

Creates HSP list structure with a default size HSP array.

Boolean Blast_HSPListIsSortedByScore(const BlastHSPList *hsp_list)

Check if HSP list is sorted by score.

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.

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.

Various auxiliary BLAST utility functions.

int32_t Int4

4-byte (32-bit) signed integer

BlastHSPCollectorParams * BlastHSPCollectorParamsNew(const BlastHitSavingOptions *hit_options, Int4 compositionBasedStats, Boolean gapped_calculation)

The following are exported functions to be used by APP.

BlastHSPWriterInfo * BlastHSPCollectorInfoNew(BlastHSPCollectorParams *params)

WriterInfo to create a default writer: the collecter.

struct BlastHSPCollectorData BlastHSPCollectorData

Data structure used by the writer.

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

create the writer

BlastHSPCollectorParams * BlastHSPCollectorParamsFree(BlastHSPCollectorParams *opts)

Deallocates the BlastHSPCollectorParams structure passed in.

static BlastHSPWriter * s_BlastHSPCollectorFree(BlastHSPWriter *writer)

Free the writer.

static int s_BlastHSPCollectorRun_RPS(void *data, BlastHSPList *hsplist_in)

Perform writing task for RPS case For RPS BLAST saving procedure is different, because HSPs from diff...

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

The following are implementations for BlastHSPWriter ADT.

static int s_ScoreCompareHSPWithContext(const void *h1, const void *h2)

Callback used for sorting HSPs by score, with HSPs from different contexts segregated from each other...

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

Perform writing task ownership of the HSP list and sets the dereferenced pointer to NULL.

static int s_BlastHSPCollectorFinal(void *data, void *results)

Perform post-run clean-ups.

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

Uint1 Boolean

bool replacment for C

#define ASSERT

macro for assert.

Structure to hold a sequence.

Data structure used by the writer.

BlastHSPResults * results

place to store hits

BlastHSPCollectorParams * params

how many hits to save

Keeps prelim_hitlist_size and HitSavingOptions together.

EBlastProgramType program

program type

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.

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.

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.

Int4 context

Context number of query.

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

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.

voidp calloc(uInt items, uInt size)

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