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NCBI C++ ToolKit: include/algo/blast/api/sseqloc.hpp Source File

: seqloc(), scope(),

(), ignore_strand_in_mask(

),

(

objects::CSeq_loc* sl, objects::CScope* s)

: seqloc(sl), scope(s),

(0), ignore_strand_in_mask(

),

(

objects::CSeq_loc& sl, objects::CScope& s)

: seqloc(&sl), scope(&s),

(0), ignore_strand_in_mask(

),

(

objects::CSeq_loc* sl, objects::CScope* s,

objects::CSeq_loc* m,

ignore_mask_strand =

)

: seqloc(sl), scope(s),

(m),

ignore_strand_in_mask(ignore_mask_strand),

(m !=

&& ignore_strand_in_mask) {

->ResetStrand();

(

objects::CSeq_loc& sl, objects::CScope& s,

objects::CSeq_loc& m,

ignore_mask_strand =

)

: seqloc(&sl), scope(&s),

(&m),

ignore_strand_in_mask(ignore_mask_strand),

(ignore_strand_in_mask) {

->ResetStrand();

objects::CScope & sc)

objects::CScope & sc,

.push_back(sli);

);

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

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

#define BLAST_GENETIC_CODE

Default genetic code for query and/or database.

ncbi::TMaskedQueryRegions mask

Defines BLAST error codes (user errors included)

bool Empty() const

Returns true if this query vector is empty.

const_iterator end() const

Returns const_iterator to end of container, provided to facilitate STL-style iteration.

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.

TMaskedQueryRegions GetMaskedRegions(size_type i) const

Get the masked regions for a query by number.

void clear()

Clears the contents of this object.

const_iterator begin() const

Returns const_iterator to beginning of container, provided to facilitate STL-style iteration.

size_type Size() const

Returns the number of queries found in this query vector.

vector< value_type >::size_type size_type

size_type type definition

size_type size() const

Identical to Size, provided to facilitate STL-style iteration.

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.

vector< CRef< CBlastSearchQuery > > m_Queries

The set of queries used for a search.

void AddMask(size_type i, CRef< CSeqLocInfo > sli)

Add a masked region to the set for a query.

vector< value_type >::const_iterator const_iterator

const_iterator type definition

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

Convenience method to get a CSeq_loc representing the masking locations.

void push_back(const value_type &element)

Add a value to the back of this container.

CRef< CBlastSearchQuery > value_type

CRef< CBlastSearchQuery > operator[](size_type i) const

Get the CBlastSearchQuery object at index i.

CRef< CBlastSearchQuery > GetBlastSearchQuery(size_type i) const

Get the CBlastSearchQuery object at index i.

void x_Validate()

Currently we only support whole or int. Throw exception otherwise.

CBlastSearchQuery()

Default constructor.

void SetGeneticCodeId(Uint4 gc_id)

Get the genetic code id.

Uint4 genetic_code_id

Genetic code id if this sequence should be translated.

CRef< objects::CScope > scope

This scope contains the query.

TMaskedQueryRegions mask

These regions of the query are masked.

CConstRef< objects::CSeq_loc > seqloc

The Seq-loc representing the query.

CConstRef< objects::CSeq_id > GetQueryId() const

Get the query Seq-id.

void SetMaskedRegions(TMaskedQueryRegions mqr)

Set the masked query regions.

CBlastSearchQuery(const objects::CSeq_loc &sl, objects::CScope &sc, TMaskedQueryRegions m)

Constructor.

TSeqPos GetLength() const

Get the length of the sequence represented by this object.

CBlastSearchQuery(const objects::CSeq_loc &sl, objects::CScope &sc)

Constructor.

CRef< objects::CScope > GetScope() const

Get the query CScope.

Uint4 GetGeneticCodeId() const

Get the genetic code id.

TMaskedQueryRegions GetMaskedRegions() const

Get the masked query regions.

void AddMask(CRef< CSeqLocInfo > sli)

Masked a region of this query.

CConstRef< objects::CSeq_loc > GetQuerySeqLoc() const

Get the query Seq-loc.

Collection of masked regions for a single query sequence.

Include a standard set of the NCBI C++ Toolkit most basic headers.

CRef< objects::CBioseq_set > TSeqLocVector2Bioseqs(const TSeqLocVector &input)

Convert a TSeqLocVector to a CBioseq_set.

CRef< objects::CSeq_loc > MaskedQueryRegionsToPackedSeqLoc(const TMaskedQueryRegions &sloc)

Interface to build a CSeq-loc from a TMaskedQueryRegion; note that conversion conversion in this dire...

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

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

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

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

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

bool ignore_strand_in_mask

This member dictates how the strand in the mask member is interpreted.

Uint4 genetic_code_id

Genetic code id if this sequence should be translated.

SSeqLoc()

Default constructor.

SSeqLoc(const objects::CSeq_loc *sl, objects::CScope *s, objects::CSeq_loc *m, bool ignore_mask_strand=true)

Parameterized constructor.

CConstRef< objects::CSeq_loc > seqloc

Seq-loc describing the sequence to use as query/subject to BLAST The types of Seq-loc currently suppo...

CRef< objects::CScope > scope

Scope where the sequence referenced can be found by the toolkit's object manager.

SSeqLoc(const objects::CSeq_loc *sl, objects::CScope *s)

Parameterized constructor.

CRef< objects::CSeq_loc > mask

Seq-loc describing regions to mask in the seqloc field Acceptable types of Seq-loc are Seq-interval a...

SSeqLoc(const objects::CSeq_loc &sl, objects::CScope &s)

Parameterized constructor.

SSeqLoc(const objects::CSeq_loc &sl, objects::CScope &s, objects::CSeq_loc &m, bool ignore_mask_strand=true)

Parameterized constructor.

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