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NCBI C++ ToolKit: include/objtools/alnmgr/sparse_aln.hpp Source File

objects::CScope& scope);

GetDim(

)

;

objects::CSeq_id&

(TNumrow

)

;

TRng GetAlnRange(

)

;

TAlnRngColl& GetAlignCollection(TNumrow

);

m_Aln->GetAnchorRow();

TSignedRange GetSeqAlnRange(TNumrow

)

;

IsPositiveStrand(TNumrow

)

;

IsNegativeStrand(TNumrow

)

;

ESearchDirection dir =

,

try_reverse_dir =

)

;

ESearchDirection dir =

,

try_reverse_dir =

)

;

& GetSeqString(TNumrow

,

force_translation =

)

;

& GetSeqString(TNumrow

,

& rq_seq_rng,

force_translation =

)

;

& GetAlnSeqString(TNumrow

,

TSignedRange& rq_aln_rng,

force_translation =

)

;

objects::CBioseq_Handle& GetBioseqHandle(TNumrow

)

;

CreateSegmentIterator(TNumrow

,

TSignedRange& range,

IsTranslated(

)

;

TranslateNAToAA(

& na,

& aa,

gen_code = kDefaultGenCode);

w = m_Aln->GetPairwiseAlns()[

]->GetSecondBaseWidth();

aln_pos/GetBaseWidth(

);

w = GetBaseWidth(

);

(w == 3) ? aln_pos % 3 + 1 : 0;

w = GetBaseWidth(

);

(w == 3 && frame) ret += frame - 1;

<

_TRange>

(aln_range.Empty() || aln_range.IsWhole())

aln_range;

w = GetBaseWidth(

);

_TRange(aln_range.GetFrom()/w, aln_range.GetToOpen()/w - 1);

<

_TRange>

(aln_range.Empty() || aln_range.IsWhole())

(0, 0);

w = GetBaseWidth(

);

(w == 1)

(0, 0);

(aln_range.GetFrom() % w + 1, aln_range.GetTo() % w + 1);

<

_TRange>

(seq_range.Empty() || seq_range.IsWhole())

seq_range;

w = GetBaseWidth(

);

from_frame = frames.first ? frames.first - 1 : 0;

to_frame = frames.second ? frames.second - 1 : 0;

_TRange(seq_range.GetFrom()*w + from_frame, seq_range.GetToOpen()*w + to_frame - 1);

class CAlignRangeCollectionList<TAlignRange> represent a sorted collection of TAlignRange.

CAlignRange Represents an element of pairwise alignment of two sequences.

Query-anchored alignment can be 2 or multi-dimentional.

vector< CRef< CPairwiseAln > > TPairwiseAlnVector

CPairwiseAln::TAlnRng TAlnRng

CSeq_data::E_Choice TCoding

bool IsSetAnchor(void) const

Check if anchor is set - always true for sparse alignments.

TNumrow GetNumRows(void) const

Synonym of the above.

CAnchoredAln::TPairwiseAlnVector TPairwiseAlnVector

int GetBaseWidth(TNumrow row) const

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

TCoding GetNaCoding(void) const

Get sequence coding for nucleotides.

pair< int, int > TFrames

Get start and stop frames for the selected row/range.

CAnchoredAln::TDim TDim

Synonym of TNumrow.

CPairwiseAln::TAlnRngColl TAlnRngColl

CRef< CAnchoredAln > m_Aln

_TRange AlnRangeToNativeSeqRange(TNumrow row, _TRange aln_range) const

Convert alignment range (genomic coordinates) on the selected row to real sequence range.

TCoding GetAaCoding(void) const

Get sequence coding for proteins.

TSignedSeqPos AlnPosToNativeSeqPos(TNumrow row, TSignedSeqPos aln_pos) const

Convert alignment (genomic) coordinate on the selected row to real sequence position.

void SetNaCoding(TCoding coding)

Set sequence coding for nucleotides. If not set, Iupacna coding is used.

TFrames AlnRangeToNativeFrames(TNumrow row, _TRange aln_range) const

vector< objects::CBioseq_Handle > m_BioseqHandles

vector< TRng > m_SecondRanges

void SetAaCoding(TCoding coding)

Set sequence coding for proteins. If not set, Iupacaa coding is used.

CRef< objects::CScope > m_Scope

TNumrow GetAnchor(void) const

Get anchor row index.

_TRange NativeSeqRangeToAlnRange(TNumrow row, _TRange seq_range, TFrames frames=TFrames(0, 0)) const

Convert sequence range to alignment range (genomic coordinates).

int AlnPosToNativeFrame(TNumrow row, TSignedSeqPos aln_pos) const

For protein sequences get frame for the specified coordinated.

vector< CRef< CSeqVector > > m_SeqVectors

TSignedSeqPos NativeSeqPosToAlnPos(TNumrow row, TSignedSeqPos seq_pos, int frame=0) const

Convert sequence position to alignment (genomic) coordinate.

Implementation of IAlnSegmentIterator for CSparseAln.

Alignment explorer interface.

objects::CSeqVector::TResidue TResidue

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.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_XALNMGR_EXPORT

E_Choice

Choice variants.

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

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

#define row(bind, expected)

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