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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seqinfosrc__bioseq_8cpp_source.html below:

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

: m_DataSource(bss, is_prot)

list< CRef<CSeq_id> > retval;

retval.push_back(seqid);

vector<TSeqRange>&

,

Auxiliary functions for BLAST.

Collection of masked regions for a single query sequence.

CRef< CBioseq_set > x_BioseqSetFromBioseq(const CBioseq &bioseq)

Auxiliary function to convert a CBioseq into a CRef<CBioseq_set>

virtual CConstRef< objects::CSeq_loc > GetSeqLoc(int index) const

Return the CSeq_loc associated with a sequence.

CBlastQuerySourceBioseqSet m_DataSource

virtual list< CRef< objects::CSeq_id > > GetId(Uint4 index) const

Retrieve a sequence identifier given its index in the vector.

CBioseqSeqInfoSrc(const objects::CBioseq &bs, bool is_prot)

Parametrized constructor.

virtual TSeqPos GetLength(int index) const

Return the length of a sequence.

virtual Uint4 GetLength(Uint4 index) const

Retrieve sequence length given its index in the vector.

virtual bool HasGiList() const

Is the subject restricted by a GI list? (Always returns false).

virtual size_t Size() const

Returns the size of the underlying container of sequences.

virtual bool GetMasks(Uint4 index, const TSeqRange &target_range, TMaskedSubjRegions &retval) const

Retrieves the subject masks for the corresponding index.

CConstRef< objects::CSeq_loc > CreateWholeSeqLocFromIds(const list< CRef< objects::CSeq_id > > seqids)

Create a single CSeq_loc of type whole from the first id in the list.

virtual TSeqPos Size() const

Return the number of elements in the sequence container.

virtual CConstRef< objects::CSeq_loc > GetSeqLoc(Uint4 index) const

Retrieve a sequence identifier given its index in the vector.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

bool NotEmpty(void) const THROWS_NONE

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

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef 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.

Defines a concrete strategy for the IBlastSeqInfoSrc interface for sequence identifiers retrieval fro...

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