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NCBI C++ ToolKit: include/gui/widgets/aln_multiple/alnmulti_ds.hpp Source File

&

()

= 0;

try_reverse_dir =

)

= 0;

try_reverse_dir =

)

= 0;

objects::CSeq_id&

()

= 0;

m_fExtOrgLookup =

;

& GetOrgLabel(

fExtOrgLookup =

)

;

(

fExtOrgLookup =

)

;

GetTaxonomy(

& taxonomy,

fExtOrgLookup =

)

;

m_fExtOrgLookup =

;

m_TaxId = 0;

try_reverse_dir =

)

= 0;

try_reverse_dir =

)

= 0;

Class CConsensusRow - Simple interface to a row that represents the consensus for rendering purposes.

IAlnExplorer::TSignedRange TSignedRange

const IAlignRowHandle & GetHandle() const

void SetHandle(const IAlignRowHandle *h)

CConsensusRow(const IAlignRowHandle *handle)

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

const IAlignRowHandle * m_Handle

virtual string & GetStringAtPos(string &buffer, TSignedSeqPos aln_pos) const

Data notification relay class, sends data change notifications to the subscribed listener.

IAlignRowHandle provides an abstract way to access alignment row data.

virtual bool UsesAATranslation() const =0

virtual int GetMismatches() const

virtual ~IAlignRowHandle()

virtual TSignedSeqPos GetSeqStart() const =0

virtual void GetHost(string &value) const

virtual bool CanGetBioseqHandle() const =0

virtual bool IsAnchor() const

virtual TSignedSeqPos GetSeqAlnStart() const =0

virtual int GetGenCode() const =0

virtual const objects::CBioseq_Handle & GetBioseqHandle() const =0

virtual const objects::CSeq_id & GetSeq_id() const =0

virtual bool CanGetSeqString() const =0

virtual void GetCountry(string &value) const

IAlnExplorer::TNumrow TNumrow

virtual double GetPctCoverage() const

virtual bool IsNucProtAlignment() const =0

virtual double GetPctIdentity() const

virtual size_t GetBaseWidth() const =0

virtual IAlnExplorer::TSignedRange GetSeqAlnRange() const =0

virtual TSeqPos GetSeqLength() const

virtual TSignedSeqPos GetSeqPosFromAlnPos(TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

virtual TNumrow GetRowNum() const =0

virtual string & GetAlnSeqString(string &buffer, const IAlnExplorer::TSignedRange &aln_rng) const =0

virtual TSignedSeqPos GetSeqAlnStop() const =0

virtual TSignedSeqPos GetSeqStop() const =0

virtual void GetCollectionDate(string &value) const

virtual string & GetSeqString(string &buffer, const IAlnExplorer::TRange &seq_rng) const =0

virtual void GetIsolationSource(string &value) const

virtual bool IsNegativeStrand() const =0

IAlnExplorer::TResidue TResidue

void UseExternalOrganismLookup(bool f)

virtual TSignedSeqPos GetAlnPosFromSeqPos(TSeqPos seq_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

virtual IAlnSegmentIterator * CreateSegmentIterator(const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flags) const =0

virtual void GetGeneSymbol(string &value) const

virtual bool IsConsensus() const

virtual const string & GetText() const =0

objects::CSeqVector::TResidue TResidue

ESearchDirection

Position search options.

@ eRight

Towards higher aln coord (always to the right)

IAlnMultiDataSource - interface to a data source representing an abstract multiple alignment.

virtual IAlnExplorer::EAlignType GetAlignType() const =0

virtual void SetGapChar(TResidue gap_char)=0

virtual void GetAlnFromSeq(TNumrow row, const TRangeColl &seq_coll, TRangeColl &aln_coll) const =0

virtual TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

virtual const IAlignRowHandle * GetRowHandle(TNumrow row) const =0

virtual bool IsDataReadSync() const

virtual bool IsPositiveStrand(TNumrow row) const =0

virtual TSeqPos GetAlnStart(void) const =0

virtual TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

virtual bool CanGetId(TNumrow row) const =0

virtual int GetConsensusRow() const =0

returns index of the Consensus row or -1 if it doesn't exist

CRangeCollection< TSeqPos > TRangeColl

virtual bool CanChangeAnchor(void) const =0

virtual void GetSeqFromAln(TNumrow row, const TRangeColl &aln_coll, TRangeColl &seq_coll) const =0

IAlnExplorer::TResidue TResidue

virtual IAlnSegmentIterator * CreateSegmentIterator(TNumrow row, const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flags) const =0

IAlnExplorer::TNumrow TNumrow

virtual TNumrow GetNumRows(void) const =0

number of rows in alignment

virtual TSeqPos GetAlnStop(void) const =0

virtual bool SetAnchor(TNumrow anchor)=0

virtual TSeqPos GetSeqStop(TNumrow row) const =0

virtual TSeqPos GetSeqStart(TNumrow row) const =0

virtual bool IsSetAnchor(void) const =0

Anchoring methods.

virtual const objects::CSeq_id & GetSeqId(TNumrow row) const =0

virtual TNumrow GetAnchor(void) const =0

virtual bool CanCreateConsensus()=0

virtual bool UnsetAnchor(void)=0

virtual void SetCreateConsensus(bool b)=0

IAlnExplorer::ESearchDirection TSearchDirection

virtual bool IsNegativeStrand(TNumrow row) const =0

virtual bool IsEmpty() const =0

virtual void CreateConsensus()=0

virtual string & GetAlnSeqString(TNumrow row, string &buffer, const IAlnExplorer::TSignedRange &aln_range) const =0

Alignment segment iterator interface.

string GetSeqIdString(const CSeq_id &id)

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

int GetSeqLength(const CBioseq &bioseq)

bool IsConsensus(const CRef< CSeq_id > &seqId)

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_GUIWIDGETS_ALNMULTIPLE_EXPORT

const GenericPointer< typename T::ValueType > T2 value

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

#define row(bind, expected)

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