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

entire_slp->

().Assign(query_id);

&

(*target_seqloc),

(*masked_loc)->GetFrom(),

(*masked_loc)->GetTo()));

query_masks->

(*seq_interval);

query_masks.

(mapper->

(*query_masks));

(orig_query_mask.

() && !orig_query_mask->

()) {

query_masks->

(kTopFlags, 0);

orig_query_mask.

(query_masks);

(orig_query_mask->

() || orig_query_mask->

()) {

orig_query_mask.

();

(orig_query_mask->

()) {

orig_query_mask.

->scope, query_id,

->mask, level, window,

(

= 0;

< queries.

();

++)

masks, level, window, linker);

Declares the CBlastNucleotideOptionsHandle class.

Definitions of special type used in BLAST.

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

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.

void SetMaskedRegions(size_type i, TMaskedQueryRegions mqr)

Assign a list of masked regions to one query.

CRef< objects::CSeq_loc > GetMasks(size_type i) const

Convenience method to get a CSeq_loc representing the masking locations.

Looks for low complexity parts of sequences according to the symmetric version of DUST algorithm.

CRef< objects::CPacked_seqint > GetMaskedInts(objects::CSeq_id &seq_id, const sequence_type &seq)

Mask a sequence and return result as a CPacked_seqint instance.

Collection of masked regions for a single query sequence.

Calls sym dust lib in algo/dustmask and returns CSeq_locs for use by BLAST.

int GetDustFilteringLinker() const

Get linker parameter for dust.

static CRef< CSeq_loc_Mapper > s_CreateSeqLocMapper(CSeq_id &query_id, const CSeq_loc *target_seqloc, CScope *scope)

Auxiliary function to create CSeq_loc_Mapper from a copy of the target Seq-loc.

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...

bool GetDustFiltering() const

Is dust filtering enabled?

int GetDustFilteringLevel() const

Get level parameter for dust.

void s_CombineDustMasksWithUserProvidedMasks(CSeqVector &data, CConstRef< CSeq_loc > seqloc, CRef< CScope > scope, CRef< CSeq_id > query_id, CRef< CSeq_loc > &orig_query_mask, Uint4 level, Uint4 window, Uint4 linker)

int GetDustFilteringWindow() const

Get window parameter for dust.

void Blast_FindDustFilterLoc(TSeqLocVector &queries, const CBlastNucleotideOptionsHandle *nucl_handle)

Finds dust locations for a given set of sequences by calling the the symmetric dust lib.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

void SetDiagFilter(EDiagFilter what, const char *filter_str)

Set diagnostic filter.

@ eDiagFilter_Post

for all non-TRACE, non-FATAL

void ChangeToPackedInt(void)

Works only if location is currently an interval, point, packed-int (handled trivially),...

CRef< CSeq_loc > Merge(TOpFlags flags, ISynonymMapper *syn_mapper) const

All functions create and return a new seq-loc object.

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

uint32_t Uint4

4-byte (32-bit) unsigned integer

#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.

bool IsEmpty(void) const

Check if variant Empty is selected.

list< CRef< CSeq_interval > > Tdata

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsNull(void) const

Check if variant Null is selected.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

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