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NCBI C++ ToolKit: src/algo/sequence/internal_stops.cpp Source File

: scope(a_scope), generator(a_scope)

starts.

(

->first.GetFrom());

make_pair(starts, stops);

pair<TStarts, set<TSeqRange> >

pair<bool, bool> trim_by_contig(

,

);

=

(

, ((stop > start ? genomic_length : 0) - (stop - start +1))/2);

(start <= 2 && !is_circular) {

trim_by_contig.first =

;

(stop >= genomic_length-3 && !is_circular) {

trim_by_contig.second =

;

start = is_circular ? start + genomic_length : 0;

(stop >= genomic_length) {

stop = is_circular ? stop - genomic_length : genomic_length-1;

query_loc->

(*spl.

().front()->CreateRowSeq_interval(0, spl));

(seq.size() % 3 != 0) {

->Set().push_back(c_e);

kUnknownState = tbl.

(

,

,

);

codon =

;

(

== kUnknownState)

query_loc->

().SetFrom((k-3)/3);

query_loc->

().SetTo((k-3)/3);

query_loc->

().SetFrom(k-3);

query_loc->

().SetTo(k-1);

starts[

(mapped_pos, mapped_pos2)] = codon;

(gaps !=

) {

region_loc->

().SetFrom(0);

region_loc->

().SetTo(genomic_length-1);

->Assign(*region_loc->

());

(

s: region_seq) {

}

(gap_end == k) {

lcl_query_loc->

().SetFrom(gap_begin);

lcl_query_loc->

().SetTo(gap_end-1);

mapped_loc = lcl_mapper.

(*lcl_query_loc);

(trim_by_contig.first) {

(!gaps->

() && gaps->

()->GetFrom()==0) {

gap_stop = gaps->

()->GetTo();

(!gaps->

() && gaps->

()->GetTo()==0) {

gap_stop = gaps->

()->GetFrom();

(trim_by_contig.second) {

gap_start = genomic_length;

(!gaps->

() && gaps->rbegin()->GetTo()==genomic_length-1) {

gap_start = gaps->rbegin()->GetFrom();

(!gaps->

() && gaps->rbegin()->GetFrom()==genomic_length-1) {

gap_start = gaps->rbegin()->GetTo();

make_pair(starts, stops);

next_prod_start = 0;

cds_ranges.push_back(loc_ci.GetRange());

cds_ranges.back().SetTo(cds_ranges.back().GetTo()-3);

prod_pos_start = (*exon)->GetProduct_start().AsSeqPos();

subject_loc->

(*(*exon)->CreateRowSeq_interval(1, spliced_seg));

(next_prod_start < prod_pos_start) {

mRNA.append(prod_pos_start - next_prod_start,

);

next_prod_start = prod_pos_start;

((*exon)->IsSetParts()) {

pair<int, int> chunk =

(**part_it);

prod_pos_start += chunk.second;

(chunk.first == 0) {

(next_prod_start < prod_pos_start) {

mRNA.append(prod_pos_start - next_prod_start,

);

next_prod_start = prod_pos_start;

}

(chunk.second > 0) {

(next_prod_start < prod_pos_start) {

mRNA.append(subject_seq, subj_pos+chunk.second-(prod_pos_start - next_prod_start), prod_pos_start - next_prod_start);

next_prod_start = prod_pos_start;

subj_pos += chunk.first;

mRNA.append(subject_seq);

next_prod_start += subject_seq.size();

(cds_ranges.front().IsWhole()) {

(

&range : cds_ranges) {

(range.GetFrom() >= mRNA.size()) {

cds_seq += mRNA.substr(range.GetFrom(), range.GetLength());

(chunk.

()) {

make_pair(

, 0);

make_pair(0,

);

make_pair(

,

);

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

CConstRef< objects::CSeq_align > AdjustAlignment(const objects::CSeq_align &align, TSeqRange range, EProductPositionsMode mode=eForceProductFrom0)

void SetFlags(TFeatureGeneratorFlags)

void SetAllowedUnaligned(TSeqPos)

CConstRef< objects::CSeq_align > CleanAlignment(const objects::CSeq_align &align)

Clean an alignment according to our best guess of its biological representation.

static const CTrans_table & GetTransTable(int id)

string GetCDSNucleotideSequence(const CSeq_align &align)

set< TSeqPos > FindStops(const CSeq_align &align)

pair< map< TSeqRange, string >, set< TSeqRange > > FindStartStopRanges(const CSeq_align &align, int padding=0, set< TSignedSeqRange > *gaps=nullptr)

bool HasInternalStops(const CSeq_align &align)

pair< set< TSeqPos >, set< TSeqPos > > FindStartsStops(const CSeq_align &align, int padding=0)

CFeatureGenerator generator

CInternalStopFinder(CScope &scope)

CRef< CSeq_loc > CreateRowSeq_loc(TDim row) const

const CSeq_id & GetSeq_id(TDim row) const

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

bool IsOrfStart(int state) const

static int SetCodonState(unsigned char ch1, unsigned char ch2, unsigned char ch3)

static int NextCodonState(int state, unsigned char ch)

bool IsOrfStop(int state) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

CMappedFeat GetCdsOnMrna(const objects::CSeq_id &rna_id, CScope &scope)

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.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define NCBI_USER_THROW(message)

Throw a quick-and-dirty runtime exception of type 'CException' with the given error message and error...

#define NCBI_THROW(exception_class, err_code, message)

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

#define MSerial_AsnText

I/O stream manipulators –.

ENa_strand GetStrand(void) const

Get the location's strand.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

CRef< CSeq_loc > Merge(TOpFlags flags, ISynonymMapper *syn_mapper) const

All functions create and return a new seq-loc object.

CPacked_seqint::TRanges TRanges

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

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.

TSeqPos GetBioseqLength(void) const

TInst_Topology GetInst_Topology(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

const CSeq_loc & GetLocation(void) const

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

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

const_iterator begin(void) const

const_iterator end(void) const

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

CRange< TSignedSeqPos > TSignedSeqRange

static TThisType GetWhole(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TMatch GetMatch(void) const

Get the variant data.

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

TDiag GetDiag(void) const

Get the variant data.

TProduct_type GetProduct_type(void) const

Get the Product_type member data.

TMismatch GetMismatch(void) const

Get the variant 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.

list< CRef< CSpliced_exon_chunk > > TParts

bool IsSpliced(void) const

Check if variant Spliced is selected.

TProduct_ins GetProduct_ins(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

pair< int, int > ChunkSize(const CSpliced_exon_chunk &chunk)

map< TSeqRange, string > TStarts

int GetGeneticCode(const CBioseq_Handle &bsh)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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