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NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/recompute_intervals.cpp Source File

(ival.GetFrom() > 3) {

ival.SetFrom(ival.GetFrom() - 3);

(ival.GetTo() <

- 4) {

ival.SetTo(ival.GetTo() + 3);

modified =

;

& cds = fi->GetOriginalFeature();

(

exception&)

found_start_codon =

;

found_stop_codon =

;

(alignment && alignment->IsSetSegs() && alignment->GetSegs().IsSpliced())

seq_id->Assign(*match_loc->GetId());

(objects::CSpliced_seg::TExons, exon_it, alignment->GetSegs().GetSpliced().GetExons())

exon(

objects::CSeq_loc(*seq_id, (*exon_it)->GetGenomic_start(), (*exon_it)->GetGenomic_end()));

((*exon_it)->IsSetGenomic_strand())

exon->SetStrand((*exon_it)->GetGenomic_strand());

cds_loc->SetMix().Set().push_back(exon);

(objects::CSpliced_seg::TModifiers, mod_it, alignment->GetSegs().GetSpliced().GetModifiers())

((*mod_it)->IsStart_codon_found())

found_start_codon = (*mod_it)->GetStart_codon_found();

((*mod_it)->IsStop_codon_found())

found_stop_codon = (*mod_it)->GetStop_codon_found();

(!cds_loc->IsMix())

(cds_loc->GetMix().Get().size() == 1)

cds_loc->Assign(*exon);

(!found_start_codon)

(found_stop_codon)

(cds_loc->IsMix())

new_gene->Assign(*gene);

->Assign(*(cds_loc->GetId()));

new_gene_loc->SetInt(*new_int);

new_gene->SetLocation().Assign(*new_gene_loc);

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

CLocalRange< TOffset > TRange

define for the fundamental building block of sequence ranges

Output filtering parameters.

@ ePassThrough

all zeroes - no filtering

spliced protein to genomic alignment

CRef< objects::CSeq_align > FindAlignment(objects::CScope &scope, const objects::CSeq_id &protein, const objects::CSeq_loc &genomic, CProSplignOutputOptions output_options=CProSplignOutputOptions())

Aligns protein to a region on genomic sequence.

static void ExtendIntervalToEnd(objects::CSeq_interval &ival, size_t len)

static CRef< CCmdComposite > apply(CSeq_entry_Handle tse, bool update_genes)

namespace ncbi::objects::

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

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

Set object to copy of another one.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

bool IsPartialStop(ESeqLocExtremes ext) const

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

@ eSame

CSeq_locs contain each other.

CConstRef< CSeq_feat > GetOverlappingGene(const CSeq_loc &loc, CScope &scope, ETransSplicing eTransSplicing=eTransSplicing_Auto)

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

TSeqPos GetBioseqLength(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

TInst_Length GetInst_Length(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

const TLocation & GetLocation(void) const

Get the Location member data.

const TProduct & GetProduct(void) const

Get the Product member data.

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