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NCBI C++ ToolKit: src/algo/blast/api/repeats_filter_cxx.cpp Source File

(loc = loc_list; loc; loc = loc->

) {

((*itr)->GetSegs().IsDenseg());

& seg = (*itr)->GetSegs().GetDenseg();

kNumSegments = seg.

();

kNumDim = seg.

();

(kNumSegments*kNumDim == (

) starts.size());

(kNumSegments == (

) lengths.size());

(kNumSegments*kNumDim == (

) strands.size());

left(0), right(0);

(strands[0] == strands[1]) {

left = starts.front();

right = starts[(kNumSegments-1)*2] + lengths[kNumSegments-1] - 1;

left = starts[(kNumSegments-1)*2];

right = starts.front() + lengths.front() - 1;

(

query_index = 0; query_index <

.size(); ++query_index) {

(

.GetSeqAlign().Empty() ||

.GetSeqAlign()->IsEmpty()) {

[query_index].mask.Reset(filter_seqloc);

(

qindex = 0; qindex <

.Size(); ++qindex) {

(

.GetSeqAlign().Empty() ||

.GetSeqAlign()->IsEmpty()) {

TFrameSet& used = frames->ListFrames();

(TFrameSet, itr, used) {

pplast = & (*pplast)->

;

.GetScope(qindex),

.SetMaskedRegions(qindex, filter_seqloc);

vector< CRef<CSeq_loc> > lcase_mask_v;

lcase_mask_v.reserve(

.size());

(

index = 0; index <

.size(); ++index) {

lcase_mask_v.push_back(

[index].

);

blaster(query_factory, repeat_opts, target_db);

(

index = 0; index <

.size(); ++index) {

[index].mask.Reset(lcase_mask_v[index]);

(

= 0;

< queries.

(); ++

) {

blaster(query_factory, repeat_opts, target_db);

Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to ...

BLAST filtering functions.

#define REPEATS_SEARCH_GAP_OPEN

Default gap opening cost.

#define REPEATS_SEARCH_WORD_SIZE

Default word size.

#define REPEATS_SEARCH_REWARD

Default match reward.

#define REPEATS_SEARCH_XDROP_FINAL

Default X-dropoff for gapped extension with traceback.

#define REPEATS_SEARCH_PENALTY

Default mismatch penalty.

void BlastSeqLocCombine(BlastSeqLoc **mask_loc, Int4 link_value)

Go through all mask locations in one sequence and combine any that overlap, deallocating the unneeded...

#define REPEATS_SEARCH_GAP_EXTEND

Default gap extension cost.

BlastSeqLoc * BlastSeqLocFree(BlastSeqLoc *loc)

Deallocate all BlastSeqLoc objects in a chain.

BlastSeqLoc * BlastSeqLocNew(BlastSeqLoc **head, Int4 from, Int4 to)

Create and initialize a new sequence interval.

#define REPEAT_MASK_LINK_VALUE

Largest gap allowed to be filled between repeat mask intervals.

#define REPEATS_SEARCH_MINSCORE

Default score cutoff.

#define REPEATS_SEARCH_XDROP_UNGAPPED

Default X-dropoff for ungapped extension.

Structures and API used for saving BLAST hits.

Declares the CBlastNucleotideOptionsHandle class.

EBlastProgramType

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

Declaration of ADT to retrieve sequences for the BLAST engine.

Internal auxiliary setup classes/functions for C++ BLAST APIs.

Definitions of special type used in BLAST.

ncbi::TMaskedQueryRegions mask

Handle to the nucleotide-nucleotide options to the BLAST algorithm.

Handle to the options to the BLAST algorithm.

Collection of BlastSeqLoc lists for filtering processing.

void AddQuery(CRef< CBlastSearchQuery > q)

Add a query to the set.

CRef< objects::CScope > GetScope(size_type i) const

Get the scope containing a query by index.

size_type Size() const

Returns the number of queries found in this query vector.

CConstRef< objects::CSeq_loc > GetQuerySeqLoc(size_type i) const

Get the query Seq-loc for a query by index.

Class to perform a BLAST search on local BLAST databases Note that PHI-BLAST can be run using this cl...

NCBI C++ Object Manager dependant implementation of IQueryFactory.

Search Results for All Queries.

Search Results for One Query.

Collection of masked regions for a single query sequence.

static void s_SeqAlignToBlastSeqLoc(const CSeq_align_set &alignment, BlastSeqLoc **locs)

Build a list of BlastSeqLoc's from a set of Dense-seg contained in a Seq-align-set.

BlastSeqLoc * CSeqLoc2BlastSeqLoc(const objects::CSeq_loc *slp)

Converts a CSeq_loc into a BlastSeqLoc structure used in NewBlast.

TMaskedQueryRegions PackedSeqLocToMaskedQueryRegions(CConstRef< objects::CSeq_loc > sloc, EBlastProgramType program, bool assume_both_strands=false)

Auxiliary function to convert a Seq-loc describing masked query regions to a TMaskedQueryRegions obje...

void SetMatchReward(int r)

Sets MatchReward.

CRef< CSearchResultSet > Run()

Executes the search.

void SetTraditionalBlastnDefaults()

Sets TraditionalBlastnDefaults.

void SetMismatchPenalty(int p)

Sets MismatchPenalty.

static CRef< CBlastOptionsHandle > s_CreateRepeatsSearchOptions()

Create an options handle with the defaults set for a search for repeats.

static CSeq_loc * s_BlastSeqLoc2CSeqloc(const CSeq_loc &query, CScope *scope, BlastSeqLoc *loc_list)

Convert a list of mask locations to a CSeq_loc object.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

void SetXDropoff(double x)

Sets XDropoff.

bool GetRepeatFiltering() const

Is repeat filtering enabled?

TMaskedQueryRegions s_BlastSeqLoc2MaskedRegions(const CSeq_loc &query, CScope *scope, BlastSeqLoc *loc_list, EBlastProgramType program)

Convert a list of mask locations to TMaskedQueryRegions.

void Blast_FindRepeatFilterLoc(TSeqLocVector &query_loc, const CBlastOptionsHandle *opts_handle)

Finds repeats locations for a given set of sequences.

void SetGapXDropoffFinal(double x)

Sets GapXDropoffFinal.

void SetGapExtensionCost(int e)

Sets GapExtensionCost.

bool GetMBIndexLoaded() const

const char * GetRepeatFilteringDB() const

Get the repeat filtering database.

void SetWordSize(int ws)

Sets WordSize.

static void s_FillMaskLocFromBlastResults(TSeqLocVector &query, const CSearchResultSet &results)

Fills the mask locations in the query SSeqLoc structures, as if it was a lower case mask,...

void SetDustFiltering(bool val)

Enable dust filtering.

void SetCutoffScore(int s)

Sets CutoffScore.

void SetGapOpeningCost(int g)

Sets GapOpeningCost.

@ eBlastDbIsNucleotide

nucleotide

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void SetPacked_int(TPacked_int &v)

void SetNull(void)

Override all setters to incorporate cache invalidation.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

TObjectType * Release(void)

Release a reference to the object and return a pointer to the object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

const TStarts & GetStarts(void) const

Get the Starts member data.

vector< ENa_strand > TStrands

const TLens & GetLens(void) const

Get the Lens member data.

vector< TSignedSeqPos > TStarts

TDim GetDim(void) const

Get the Dim member data.

TNumseg GetNumseg(void) const

Get the Numseg member data.

list< CRef< CSeq_align > > Tdata

const TStrands & GetStrands(void) const

Get the Strands member data.

const Tdata & Get(void) const

Get the member data.

Main class to perform a BLAST search on the local machine.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

C++ implementation of repeats filtering for C++ BLAST.

Implementation of the BlastSeqSrc interface using the C++ BLAST databases API.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

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

SSeqRange * ssr

location data on the sequence.

struct BlastSeqLoc * next

next in linked list

Structure to represent a single sequence to be fed to BLAST.

Int4 left

left endpoint of range (zero based)

Int4 right

right endpoint of range (zero based)

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