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NCBI C++ ToolKit: src/objects/seqalign/Spliced_seg.cpp Source File

(*

().begin())->GetProduct_strand();

(*

().begin())->GetGenomic_strand();

);

last_exon_gen_rev =

;

last_exon_prod_rev =

;

exon_gen_rev =

;

exon_gen_rev = aln_gen_rev;

(exon_it !=

().begin() && last_exon_gen_rev != exon_gen_rev)

;

last_exon_gen_rev = exon_gen_rev;

exon_prod_rev =

;

exon_prod_rev = aln_prod_rev;

(exon_it !=

().begin() && last_exon_prod_rev != exon_prod_rev)

;

last_exon_prod_rev = exon_prod_rev;

prod_start = pstart.

() ? pstart.GetNucpos() :

pstart.GetProtpos().GetAmin() * 3 + pstart.GetProtpos().GetFrame() - 1;

prod_end = pend.IsNucpos() ? pend.GetNucpos() :

pend.GetProtpos().GetAmin() * 3 + pend.GetProtpos().GetFrame() - 1;

(prod_end > last_prod_start)

;

(prod_start < last_prod_end)

;

last_prod_start = prod_start;

last_prod_end = prod_end;

internal_unaligned = 0;

CSpliced_seg::TExons::const_reverse_iterator it =

().rbegin();

CSpliced_seg::TExons::const_reverse_iterator

=

().rbegin();

CSpliced_seg::TExons::const_reverse_iterator end =

().rend();

(++it; it != end; ++it, ++

) {

internal_unaligned += (*it)->GetProduct_start().GetNucpos() -

(*prev)->GetProduct_end().GetNucpos() - 1;

(++it; it != end; ++it, ++

) {

curr_nuc = (*it)->GetProduct_start().AsSeqPos();

last_nuc = (*prev)->GetProduct_end().AsSeqPos();

internal_unaligned += curr_nuc - last_nuc - 1;

CSpliced_seg::TExons::const_iterator it =

().begin();

CSpliced_seg::TExons::const_iterator

=

().begin();

CSpliced_seg::TExons::const_iterator end =

().end();

(++it; it != end; ++it, ++

) {

internal_unaligned += (*it)->GetProduct_start().GetNucpos() -

(*prev)->GetProduct_end().GetNucpos() - 1;

(++it; it != end; ++it, ++

) {

curr_nuc = (*it)->GetProduct_start().AsSeqPos();

last_nuc = (*prev)->GetProduct_end().AsSeqPos();

internal_unaligned += curr_nuc - last_nuc - 1;

internal_unaligned;

product_position_limits.

((

? product_length * 3 : product_length) -1);

);

(poly_a > 0 &&

(poly_a) > product_position_limits.

()+1) {

);

product_position_limits.

(poly_a+1);

product_position_limits.

(poly_a-1);

);

(product_start > product_end) {

);

(product_start < product_position_limits.

() || product_position_limits.

() < product_end) {

);

);

);

);

);

);

product_plus =

;

(

&& !product_plus) {

);

(chunk.

()) {

chunk_product_len = chunk_genomic_len = chunk.

();

chunk_product_len = chunk_genomic_len = chunk.

();

chunk_product_len = chunk_genomic_len = chunk.

();

exon_product_len += chunk_product_len;

exon_genomic_len += chunk_genomic_len;

(exon_product_len != product_end - product_start + 1) {

);

(exon_genomic_len !=

);

exon_product_len = product_end - product_start + 1;

(exon_product_len != exon_genomic_len) {

);

);

((*exon_it)->GetProduct_start().GetNucpos(),

(*exon_it)->GetProduct_end().GetNucpos()));

((*exon_it)->GetProduct_start().GetProtpos().GetAmin(),

(*exon_it)->GetProduct_end().GetProtpos().GetAmin()));

);

((*exon_it)->GetGenomic_start(),

(*exon_it)->GetGenomic_end()));

);

vector<TSignedSeqPos>

vector<TSignedSeqPos> rv;

rv.reserve(lens.size());

rv.push_back((end + 1) -

);

rv.push_back(start +

);

vector<TSeqPos> product_lens;

vector<TSeqPos> genomic_lens;

product_lens.push_back(part.

());

genomic_lens.push_back(part.

());

}

(part.

()) {

product_lens.push_back(part.

());

genomic_lens.push_back(part.

());

genomic_lens.push_back(0);

product_lens.push_back(0);

runtime_error(

);

genomic_lens.push_back(

);

product_lens.push_back(

);

lens.reserve(product_lens.size());

(

= 0;

< product_lens.size(); ++

) {

lens.push_back(

(product_lens[

], genomic_lens[

]));

vector<TSignedSeqPos> product_starts;

vector<TSignedSeqPos> genomic_starts =

starts.reserve(product_starts.size() + genomic_starts.size());

(

= 0;

< lens.size(); ++

) {

starts.push_back(product_starts[

]);

starts.push_back(genomic_starts[

]);

(

= 0;

< lens.size(); ++

) {

strands.push_back(product_strand);

strands.push_back(genomic_strand);

product_strand, genomic_strand,

product_id, genomic_id);

ds_align->

().SetDenseg(*ds);

disc->

().SetDisc().Set().push_back(ds_align);

product_strand, genomic_strand,

product_id, genomic_id);

ds_align->

().SetDenseg(*ds);

disc->

().SetDisc().Set().push_back(ds_align);

);

bool IsReverse(ENa_strand s)

static vector< TSignedSeqPos > s_CalculateStarts(const vector< TSeqPos > &lens, ENa_strand strand, TSeqPos start, TSeqPos end)

static CRef< CDense_seg > s_ExonToDenseg(const CSpliced_exon &exon, ENa_strand product_strand, ENa_strand genomic_strand, const CSeq_id &product_id, const CSeq_id &genomic_id)

User-defined methods of the data storage class.

TWidths & SetWidths(void)

void Compact()

Join adjacent mergeable segments to create a more compact alignment.

TSeqRange GetRowSeq_range(CSeq_align::TDim row, bool always_as_nuc) const

Return exon's range within this row.

TSeqPos GetSeqStop(TDim row) const

CRange< TSeqPos > GetSeqRange(TDim row) const

GetSeqRange NB: In case the product-type is protein, these only return the amin part of Prot-pos.

bool IsConsistentBiologicalOrder(void) const

TSeqPos GetSeqStart(TDim row) const

void Validate(bool full_test=false) const

Validators.

ENa_strand GetSeqStrand(TDim row) const

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

CRef< CSeq_align > AsDiscSeg() const

Convert this alignment to a discontinuous segment.

TSeqPos InternalUnaligned(void) const

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define NCBI_THROW(exception_class, err_code, message)

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

C * SerialClone(const C &src)

Create on heap a clone of the source object.

static TThisType GetWhole(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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.

void SetTo(TTo value)

Assign a value to To data member.

bool IsSetProduct_strand(void) const

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

TLens & SetLens(void)

Assign a value to Lens data member.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

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.

list< CRef< CScore > > Tdata

bool IsSetProduct_strand(void) const

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

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

TGenomic_start GetGenomic_start(void) const

Get the Genomic_start member data.

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

bool IsMismatch(void) const

Check if variant Mismatch is selected.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

vector< ENa_strand > TStrands

TProduct_length GetProduct_length(void) const

Get the Product_length member data.

bool IsSetPoly_a(void) const

start of poly(A) tail on the transcript For sense transcripts: aligned product positions < poly-a <= ...

TScores & SetScores(void)

Assign a value to Scores data member.

TDiag GetDiag(void) const

Get the variant data.

vector< TSignedSeqPos > TStarts

TProduct_type GetProduct_type(void) const

Get the Product_type member data.

TMismatch GetMismatch(void) const

Get the variant data.

TGenomic_strand GetGenomic_strand(void) const

Get the Genomic_strand member data.

bool IsSetGenomic_strand(void) const

genomic-strand represents the strand of translation Check if a value has been assigned to Genomic_str...

bool CanGetProduct_strand(void) const

Check if it is safe to call GetProduct_strand method.

bool IsSetProduct_id(void) const

product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data ...

void SetType(TType value)

Assign a value to Type data member.

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.

bool IsSetProduct_id(void) const

product is either protein or transcript (cDNA) Check if a value has been assigned to Product_id data ...

bool IsGenomic_ins(void) const

Check if variant Genomic_ins is selected.

bool IsMatch(void) const

Check if variant Match is selected.

bool CanGetGenomic_strand(void) const

Check if it is safe to call GetGenomic_strand method.

TGenomic_ins GetGenomic_ins(void) const

Get the variant data.

bool IsSetGenomic_strand(void) const

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

const TScores & GetScores(void) const

Get the Scores member data.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

list< CRef< CSpliced_exon > > TExons

const TExons & GetExons(void) const

Get the Exons member data.

TGenomic_strand GetGenomic_strand(void) const

Get the Genomic_strand member data.

TProduct_strand GetProduct_strand(void) const

Get the Product_strand member data.

bool IsDiag(void) const

Check if variant Diag is selected.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

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...

bool CanGetProduct_strand(void) const

Check if it is safe to call GetProduct_strand method.

TPoly_a GetPoly_a(void) const

Get the Poly_a member data.

TGenomic_end GetGenomic_end(void) const

Get the Genomic_end member data.

const Tdata & Get(void) const

Get the member data.

TProduct_strand GetProduct_strand(void) const

Get the Product_strand member data.

TIds & SetIds(void)

Assign a value to Ids data member.

bool IsSetGenomic_id(void) const

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

bool IsProduct_ins(void) const

Check if variant Product_ins is selected.

bool IsNucpos(void) const

Check if variant Nucpos is selected.

TProduct_ins GetProduct_ins(void) const

Get the variant data.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

bool CanGetGenomic_strand(void) const

Check if it is safe to call GetGenomic_strand method.

bool IsSetGenomic_id(void) const

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

bool IsSetScores(void) const

scores for this exon Check if a value has been assigned to Scores data member.

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

@ eType_partial

mapping pieces together

@ eType_disc

discontinuous alignment

@ eProduct_type_transcript

ENa_strand

strand of nucleic acid

constexpr bool empty(list< Ts... >) noexcept

#define row(bind, expected)

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