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NCBI C++ ToolKit: src/objmgr/util/seq_align_util.cpp Source File

( loc.IsWhole() ) {

* orig_id = loc.GetId();

);

->Assign(*orig_id);

mapper.

(align,

);

: m_Align(align),

(scope)

);

);

);

( !

(**part_it, gen_offset) )

;

( !

(**part_it, gen_offset) )

;

(0, gen_to - gen_from);

( ch.

() ) {

);

static CRef< CScope > m_Scope

bool IsReverse(ENa_strand s)

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Seq-loc and seq-align mapper exceptions.

Exceptions for objmgr/util library.

const string & GetProductString(void)

bool x_Mismatch(TSeqPos mismatch_len)

bool x_AddExonPart(const CSpliced_exon_chunk &ch, TSeqPos &gen_offset)

void x_Match(TSeqPos gen_from, TSeqPos gen_to_open)

const CSeq_align & m_Align

bool x_AddExon(const CSpliced_exon &ex)

CProductStringBuilder(const CSeq_align &align, CScope &scope)

static SIZE_TYPE ReverseComplement(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define REVERSE_ITERATE(Type, Var, Cont)

ITERATE macro to reverse sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

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

void SetStrand(ENa_strand strand)

Set the strand for all of the location's ranges.

string GetProductString(const CSeq_align &align, CScope &scope)

Given a spliced-seg alignment with MismatchedBases user object, compose product sequence data.

CRef< CSeq_align > RemapAlignToLoc(const CSeq_align &align, CSeq_align::TDim row, const CSeq_loc &loc, CScope *scope)

Remap seq-align row to the seq-loc.

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

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

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

#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.

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

const TData & GetData(void) const

Get the Data member data.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

vector< CRef< CUser_field > > TData

bool IsSetParts(void) const

basic seqments always are in biologic order Check if a value has been assigned to Parts data member.

TMatch GetMatch(void) const

Get the variant data.

bool IsSetExt(void) const

extra info Check if a value has been assigned to Ext data member.

TGenomic_start GetGenomic_start(void) const

Get the Genomic_start member data.

TProduct_length GetProduct_length(void) const

Get the Product_length member data.

TProduct_type GetProduct_type(void) const

Get the Product_type member data.

TMismatch GetMismatch(void) const

Get the variant data.

list< CRef< CUser_object > > TExt

const TParts & GetParts(void) const

Get the Parts member data.

const TProduct_start & GetProduct_start(void) const

Get the Product_start member data.

const TProduct_end & GetProduct_end(void) const

Get the Product_end member data.

const TSpliced & GetSpliced(void) const

Get the variant data.

TGenomic_ins GetGenomic_ins(void) const

Get the variant data.

list< CRef< CSpliced_exon > > TExons

const TExons & GetExons(void) const

Get the Exons member data.

const TExt & GetExt(void) const

Get the Ext member data.

list< CRef< CSpliced_exon_chunk > > TParts

bool IsSetProduct_length(void) const

length of the product, in bases/residues from this (or from poly-a if present), a 3' unaligned length...

TGenomic_end GetGenomic_end(void) const

Get the Genomic_end member data.

bool IsSpliced(void) const

Check if variant Spliced is selected.

bool IsNucpos(void) const

Check if variant Nucpos is selected.

TProduct_ins GetProduct_ins(void) const

Get the variant data.

TNucpos GetNucpos(void) const

Get the variant data.

const TSegs & GetSegs(void) const

Get the Segs member data.

E_Choice Which(void) const

Which variant is currently selected.

@ e_Product_ins

insertion in product sequence (i.e. gap in the genomic sequence)

@ e_Diag

both sequences are represented, there is sufficient similarity between product and genomic sequences....

@ e_Genomic_ins

insertion in genomic sequence (i.e. gap in the product sequence)

@ e_Match

both sequences represented, product and genomic sequences match

@ e_Mismatch

both sequences represented, product and genomic sequences do not match

@ eProduct_type_transcript

ENa_strand

strand of nucleic acid

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

#define row(bind, expected)

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