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

list<CConstRef<CSeq_align> > align_list;

align_product_idh = canonical;

(feat_idh.

(align_product_idh)) {

(align_list.size() > 1) {

(!ignore_errors) {

& annot_name)

(!annot_name.empty()) {

(annot_name ==

) {

& annot_name,

feature::CFeatTree feat_tree;

feat_tree.AddFeatures(feat_it);

);

);

(

prod_feat_it(mrna_bsh, mrna_sel); prod_feat_it; ++prod_feat_it) {

);

prod_cd_feat = *prod_feat_it;

*projected_mrna_loc);

changes[mrna_eh] = new_mrna_feat;

changes[cds_eh] = new_cds_feat;

(

mit = changes.

(); mit != changes.

(); mit++) {

mit->first.Replace(*mit->second);

ESeqLocExtremes

Used to determine the meaning of a location's Start/Stop positions.

@ eExtreme_Biological

5' and 3'

static void CreateMicroIntrons(objects::CScope &scope, objects::CBioseq_Handle bsh, const string &annot_name="", TSeqRange *range=NULL, bool ignore_errors=false)

static CRef< objects::CSeq_loc > s_ProjectCDS(const objects::CSeq_align &spliced_aln, const objects::CSeq_loc &product_cds_loc, bool convert_overlaps=true)

Similar to s_ProjectRNA(...) Postcondition: seq-vector of the returned loc is of exact same length an...

static CRef< objects::CSeq_loc > s_ProjectRNA(const objects::CSeq_align &spliced_aln, CConstRef< objects::CSeq_loc > product_cds_loc=CConstRef< objects::CSeq_loc >(NULL), size_t unaligned_ends_partialness_thr=kDefaultAllowedUnaligned)

Project RNA, preserving discontinuities in the CDS.

static void x_SetAnnotName(objects::SAnnotSelector &sel, const string &annot_name)

const CSeq_id & GetSeq_id(TDim row) const

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

CSeq_feat_EditHandle –.

namespace ncbi::objects::

const_iterator begin() const

const_iterator end() const

#define NCBI_THROW(exception_class, err_code, message)

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

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

Set object to copy of another one.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

bool MatchesTo(const CSeq_id_Handle &h) const

True if *this matches to h.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

string AsString(void) const

void SetTruncatedStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (tl/tr - indicating removed parts of the seq-loc)

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

ENa_strand GetStrand(void) const

Get the location's strand.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

bool IsTruncatedStop(ESeqLocExtremes ext) const

bool IsTruncatedStart(ESeqLocExtremes ext) const

check if parts of the seq-loc are missing

const CSeq_id * GetId(void) const

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

void SetPartialStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval)

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

void SetTruncatedStop(bool val, ESeqLocExtremes ext)

TSeqPos GetStop(ESeqLocExtremes ext) const

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CBioseq_EditHandle GetEditHandle(const CBioseq_Handle &seq)

Get editable Biosec handle by regular one.

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

virtual CSeq_id_Handle GetProductId(void) const

CSeq_id_Handle GetProductId(void) const

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

const CSeq_loc & GetLocation(void) const

SAnnotSelector & ResetAnnotsNames(void)

Select annotations from all Seq-annots.

SAnnotSelector & SetAdaptiveDepth(bool value=true)

SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower...

SAnnotSelector & IncludeNamedAnnotAccession(const string &acc, int zoom_level=0)

SAnnotSelector & IncludeFeatType(TFeatType type)

Include feature type in the search.

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to look for.

SAnnotSelector & ExcludeUnnamedAnnots(void)

Add unnamed annots to set of annots names to exclude.

SAnnotSelector & AddUnnamedAnnots(void)

Add unnamed annots to set of annots names to look for.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

void SetLocation(TLocation &value)

Assign a value to Location data member.

const TLocation & GetLocation(void) const

Get the Location member data.

static void InheritPartialness(const CSeq_loc &src, CSeq_loc &dest)

CConstRef< CSeq_align > GetAlignmentForRna(const CMappedFeat &a_feat, CScope &a_scope, bool ignore_errors)

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