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NCBI C++ ToolKit: src/objtools/writers/aln_writer.cpp Source File

uFlags) :

uFlags) :

);

);

num_rows = denseg.

();

num_segs = denseg.

();

(

=0;

<num_rows; ++

)

);

(

seg=0; seg<num_segs; ++seg)

start = denseg.

()[seg*num_rows +

];

defline =

+ best_id;

);

);

(length >= 0) ? length : -length;

prev_genomic_id;

prev_product_id;

exon->IsSetGenomic_id() ?

exon->GetGenomic_id() :

exon->IsSetProduct_id() ?

exon->GetProduct_id() :

exon->IsSetGenomic_strand() ?

exon->GetGenomic_strand() :

default_genomic_strand;

exon->IsSetProduct_strand() ?

exon->GetProduct_strand() :

default_product_strand;

genomic_start = exon->GetGenomic_start();

genomic_end = exon->GetGenomic_end();

(genomic_end < genomic_start) {

);

genomic_length = genomic_end - genomic_start;

product_start = exon->GetProduct_start().AsSeqPos();

product_end = exon->GetProduct_end().AsSeqPos();

(product_end < product_start) {

);

product_length = product_end - product_start;

);

(genomic_bsh, genomic_range, genomic_strand, genomic_seq);

);

(product_bsh, product_range, product_strand, product_seq);

(exon->IsSetParts()) {

(product_type, exon->GetParts(), genomic_seq, product_seq);

(product_length != genomic_length) {

);

& genomic_seq,

& product_seq)

(exon_chunks.empty()) {

genomic_string;

product_string;

res_width =

interval_width = 0;

chunk_type = exon_chunk->Which();

(chunk_type) {

(chunk_type) {

interval_width = exon_chunk->GetMatch();

interval_width = exon_chunk->GetMismatch();

interval_width = exon_chunk->GetDiag();

genomic_string.append(genomic_seq, genomic_pos, interval_width);

product_string.append(product_seq, product_pos, (interval_width + (res_width-1))/res_width);

genomic_pos += interval_width;

product_pos += interval_width/res_width;

interval_width = exon_chunk->GetGenomic_ins();

genomic_string.append(genomic_seq, genomic_pos, interval_width);

product_string.append(interval_width/res_width,

);

genomic_pos += interval_width;

interval_width = exon_chunk->GetProduct_ins();

genomic_string.append(interval_width,

);

product_string.append(product_seq, product_pos, interval_width/res_width);

product_pos += interval_width/res_width;

genomic_seq = genomic_string;

product_seq = product_string;

(start >= seq_plus.size()) {

);

seq_plus.substr(start,

);

num_segs = sparse_align.

();

(

seg=0; seg<num_segs; ++seg) {

= sparse_align.

()[seg];

(

seg=0; seg<num_segs; ++seg) {

= sparse_align.

()[seg];

(defline.back() ==

&& defline.size() > 1)

length = defline.size();

<< defline.substr(0,length-1) <<

;

<< defline <<

;

(pos < seqdata.size()) {

);

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.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

unsigned int s_ProductLength(const CProduct_pos &start, const CProduct_pos &end)

void ProcessSeqId(const CSeq_id &id, CBioseq_Handle &bsh, CRange< TSeqPos > &range)

bool WriteSparseAlign(const CSparse_align &sparse_aln)

void WriteContiguous(const string &defline, const string &seqdata)

bool WriteSplicedExons(const list< CRef< CSpliced_exon >> &exons, CSpliced_seg::TProduct_type product_type, CRef< CSeq_id > default_genomic_id, ENa_strand default_genomic_strand, CRef< CSeq_id > default_product_id, ENa_strand default_product_strand)

CAlnWriter(CScope &scope, CNcbiOstream &ostr, unsigned int uFlags)

void GetSeqString(CBioseq_Handle bsh, const CRange< TSeqPos > &range, ENa_strand strand, string &seq)

bool WriteAlignSparseSeg(const CSparse_seg &sparse_seg)

bool WriteAlign(const CSeq_align &align, const string &name="", const string &descr="") override

Write a raw Seq-align to the internal output stream.

string GetSegString(const string &seq_plus, CSeqUtil::ECoding coding, ENa_strand strand, int start, size_t len)

void AddGaps(CSpliced_seg::TProduct_type product_type, const CSpliced_exon::TParts &exon_chunks, string &genomic_seq, string &product_seq)

bool WriteAlignSplicedSeg(const CSpliced_seg &spliced_seg)

string GetBestId(const CSeq_id &)

bool WriteAlignDenseSeg(const CDense_seg &denseg)

const CSeq_id & GetSeq_id(TDim row) const

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

Defines and provides stubs for a general interface to a variety of file formatters.

bool GetBestId(CSeq_id_Handle idh, CScope &scope, string &best_id) const

unique_ptr< CGenbankIdResolve > mpIdResolve

#define NCBI_THROW(exception_class, err_code, message)

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

const string AsFastaString(void) const

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

@ eFasta

Tagged ID in NCBI's traditional FASTA style.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

bool IsNucleotide(void) const

TSeqPos GetBioseqLength(void) const

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ 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).

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

TThisType & SetToOpen(position_type toOpen)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static const char label[]

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

bool CanGetDim(void) const

Check if it is safe to call GetDim method.

const TDenseg & GetDenseg(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetStrands(void) const

Check if a value has been assigned to Strands data member.

bool IsSetProduct_strand(void) const

should be 'plus' or 'minus' Check if a value has been assigned to Product_strand data member.

const TStarts & GetStarts(void) const

Get the Starts member data.

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

const TLens & GetLens(void) const

Get the Lens member data.

bool CanGetNumseg(void) const

Check if it is safe to call GetNumseg method.

const TFirst_id & GetFirst_id(void) const

Get the First_id member data.

TProduct_type GetProduct_type(void) const

Get the Product_type member data.

TGenomic_strand GetGenomic_strand(void) const

Get the Genomic_strand member data.

bool CanGetIds(void) const

Check if it is safe to call GetIds method.

const TSpliced & GetSpliced(void) const

Get the variant data.

TDim GetDim(void) const

Get the Dim member data.

bool IsSetGenomic_strand(void) const

Check if a value has been assigned to Genomic_strand data member.

const TLens & GetLens(void) const

Get the Lens member data.

const TExons & GetExons(void) const

Get the Exons member data.

bool IsSetSecond_strands(void) const

Check if a value has been assigned to Second_strands data member.

const TFirst_starts & GetFirst_starts(void) const

Get the First_starts member data.

TNumseg GetNumseg(void) const

Get the Numseg member data.

bool IsSetExons(void) const

set of segments involved each segment corresponds to one exon exons are always in biological order Ch...

const TSecond_strands & GetSecond_strands(void) const

Get the Second_strands member data.

list< CRef< CSpliced_exon_chunk > > TParts

const TSecond_id & GetSecond_id(void) const

Get the Second_id member data.

bool CanGetStarts(void) const

Check if it is safe to call GetStarts method.

TNumseg GetNumseg(void) const

Get the Numseg member data.

TProduct_strand GetProduct_strand(void) const

Get the Product_strand member data.

const TSparse & GetSparse(void) const

Get the variant data.

const TRows & GetRows(void) const

Get the Rows member data.

const TStrands & GetStrands(void) const

Get the Strands member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool CanGetLens(void) const

Check if it is safe to call GetLens method.

bool IsSetGenomic_id(void) const

Check if a value has been assigned to Genomic_id data member.

@ 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

@ e_not_set

No variant selected.

@ eProduct_type_transcript

ENa_strand

strand of nucleic acid

#define row(bind, expected)

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