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NCBI C++ ToolKit: src/gui/widgets/aln_multiple/sparse_row_handle.cpp Source File

try_reverse_dir)

try_reverse_dir)

TSignedSeqPos GetSeqAlnStart(TNumrow row) const

TNumrow GetNumRows(void) const

Synonym of the above.

int GetBaseWidth(TNumrow row) const

Get base width for the sequence (1 for nucleotides, 3 for proteins).

TSignedSeqPos GetSeqAlnStop(TNumrow row) const

TSeqPos GetSeqStop(TNumrow row) const

virtual IAlnSegmentIterator * CreateSegmentIterator(TNumrow row, const TSignedRange &range, IAlnSegmentIterator::EFlags flags) const

Create segment iterator.

string & GetAlnSeqString(TNumrow row, string &buffer, const TSignedRange &rq_aln_rng, bool force_translation=false) const

Fetch alignment sequence data.

TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

Map sequence position to alignment coordinates.

TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

const objects::CBioseq_Handle & GetBioseqHandle(TNumrow row) const

Get bioseq handle for the row.

TSeqPos GetSeqStart(TNumrow row) const

TSignedRange GetSeqAlnRange(TNumrow row) const

Get sequence range in alignment coords (strand ignored).

CRef< objects::CScope > GetScope(void) const

Scope accessor.

string & GetSeqString(TNumrow row, string &buffer, TSeqPos seq_from, TSeqPos seq_to, bool force_translation=false) const

Fetch sequence data for the given row and range.

bool IsNegativeStrand(TNumrow row) const

const objects::CSeq_id & GetSeqId(TNumrow row) const

Get seq-id for the row.

virtual size_t GetBaseWidth() const

virtual bool CanGetBioseqHandle() const

virtual ~CSparseRowHandle()

virtual TSignedSeqPos GetSeqStart() const

virtual TSignedSeqPos GetSeqAlnStart() const

virtual IAlnExplorer::TSignedRange GetSeqAlnRange() const

virtual TSignedSeqPos GetAlnPosFromSeqPos(TSeqPos seq_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const

virtual TSignedSeqPos GetSeqAlnStop() const

virtual TSignedSeqPos GetSeqPosFromAlnPos(TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const

const string & GetText() const

virtual TSignedSeqPos GetSeqStop() const

virtual string & GetSeqString(string &buffer, const IAlnExplorer::TRange &seq_rng) const

virtual IAlnSegmentIterator * CreateSegmentIterator(const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flag) const

virtual string & GetAlnSeqString(string &buffer, const IAlnExplorer::TSignedRange &aln_rng) const

virtual bool IsNegativeStrand() const

bool UsesAATranslation() const

virtual objects::CScope & GetScope() const

CSparseRowHandle(CSparseAln &aln, TNumrow row)

CSparseRowHandle.

virtual const objects::CBioseq_Handle & GetBioseqHandle() const

virtual bool IsNucProtAlignment() const

virtual int GetGenCode() const

virtual TNumrow GetRowNum() const

virtual bool CanGetSeqString() const

virtual const objects::CSeq_id & GetSeq_id() const

IAlnExplorer::TNumrow TNumrow

ESearchDirection

Position search options.

Alignment segment iterator interface.

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

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

static bool IsVDBAccession(const string &acc)

Check if string starts with ("SRA", "SRR", "DRR", "ERR")

static int GetGenCode(const objects::CBioseq_Handle &handle)

Returns Bioseq's Genetic Code.

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define row(bind, expected)

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