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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/feature__edit_8cpp_source.html below:

NCBI C++ ToolKit: src/objmgr/util/feature_edit.cpp Source File

trimmed_cb->

(code_break);

trimmed_ext->Assign(trna_ext);

set_partial =

;

trimmed_loc->

(loc);

set_partial =

;

(new_sf->

().SetCdregion().IsSetCode_break()) {

list<CRef<CCode_break>>& code_breaks = new_sf->

().SetCdregion().SetCode_break();

(code_breaks.empty()) {

new_sf->

().SetCdregion().ResetCode_break();

(

code_break : code_breaks) {

cb_to = code_break->GetLoc().GetTotalRange().GetTo();

(

code_break : code_breaks) {

cb_from = code_break->GetLoc().GetTotalRange().GetFrom();

(cb_from < from) {

(

.IsSetExt() &&

.GetExt().IsTRNA()) {

not_partial =

;

code_break.

(*cb_loc);

set_partial,

partial_start =

;

partial_stop =

;

(

loc_it(*loc); loc_it; ++loc_it) {

& current_range = loc_it.GetRange();

current_from = current_range.GetFrom();

current_to = current_range.GetTo();

current_seqid->

(loc_it.GetSeq_id());

((current_to < from) ||

(current_from > to)) {

(current_to < from) {

partial_start =

;

(current_from > to) {

partial_stop =

;

(current_from < from) {

partial_start =

;

(current_to > to) {

partial_stop =

;

(loc->

() || !set_partial) {

(partial_start, partial_stop);

(trimmed_loc.

()) {

(trimmed_loc.

()) {

length += pSubInt->GetLength();

(trimmed_loc.

()) {

(

pSubLoc : trimmed_loc.

().

()) {

pTrimmedInt->SetInt().SetId().Assign(loc_it.

());

pTrimmedInt->SetInt().SetFrom(from);

pTrimmedInt->SetInt().SetTo(to);

(feat_from < from) {

(from - feat_from);

(feat_to - to);

(new_frame == 1) {

(new_frame == 2) {

(from <= ac_from && to >= ac_to) {

(from > ac_to || to < ac_from) {

set_partial=

;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

static CRef< CSeq_feat > Apply(const CSeq_feat &feat, const CRange< TSeqPos > &range)

static void x_TrimCodeBreak(TSeqPos from, TSeqPos to, CCode_break &cod_break)

static CCdregion::EFrame GetCdsFrame(const CSeq_feat &cds_feature, const CRange< TSeqPos > &range)

static TSeqPos x_GetStartOffset(const CSeq_feat &feat, TSeqPos from, TSeqPos to)

static TSeqPos x_GetFrame(const CCdregion &cdregion)

static CCdregion::EFrame x_GetNewFrame(TSeqPos offset, const CCdregion &region)

static void x_TrimTrnaExt(TSeqPos from, TSeqPos to, CTrna_ext &ext)

static void x_UpdateFrame(TSeqPos offset, CCdregion &cdregion)

static void x_TrimLocation(TSeqPos from, TSeqPos to, bool set_partial, CRef< CSeq_loc > &loc)

ESubtype GetSubtype(void) const

namespace ncbi::objects::

TSeqPos GetLength(void) const

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

Include a standard set of the NCBI C++ Toolkit most basic headers.

static TSeqPos s_GetTrimmedLength(const CSeq_loc &trimmed_loc)

unsigned int TSeqPos

Type for sequence locations and lengths.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

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

Set object to copy of another one.

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

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

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.

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

Override Assign() to incorporate cache invalidation.

TRange GetTotalRange(void) const

CRef< CSeq_loc > Subtract(const CSeq_loc &other, TOpFlags flags, ISynonymMapper *syn_mapper, ILengthGetter *len_getter) const

Subtract seq-loc from this, merge/sort resulting ranges depending on flags.

void SetPartialStart(bool val, ESeqLocExtremes ext)

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

CRef< CSeq_loc > Intersect(const CSeq_loc &other, TOpFlags flags, ISynonymMapper *syn_mapper) const

Find the intersection with the seq-loc, merge/sort resulting ranges depending on flags.

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

CRef< C > Ref(C *object)

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

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

bool NotEmpty(void) const

TThisType IntersectionWith(const TThisType &r) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TAnticodon & GetAnticodon(void) const

Get the Anticodon member data.

bool IsSetAnticodon(void) const

location of anticodon Check if a value has been assigned to Anticodon data member.

void SetAnticodon(TAnticodon &value)

Assign a value to Anticodon data member.

void ResetAnticodon(void)

Reset Anticodon data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TLoc & GetLoc(void) const

Get the Loc member data.

void SetPartial(TPartial value)

Assign a value to Partial data member.

const TLocation & GetLocation(void) const

Get the Location member data.

void ResetLoc(void)

Reset Loc data member.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

void ResetFrame(void)

Reset Frame data member.

void SetData(TData &value)

Assign a value to Data data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

void SetFrame(TFrame value)

Assign a value to Frame data member.

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

bool IsMix(void) const

Check if variant Mix is selected.

bool IsEmpty(void) const

Check if variant Empty is selected.

const Tdata & Get(void) const

Get the member data.

bool IsPacked_pnt(void) const

Check if variant Packed_pnt is selected.

const Tdata & Get(void) const

Get the member data.

const TPacked_pnt & GetPacked_pnt(void) const

Get the variant data.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

const TPoints & GetPoints(void) const

Get the Points member data.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

bool IsNull(void) const

Check if variant Null is selected.

const TMix & GetMix(void) const

Get the variant data.

bool IsPnt(void) const

Check if variant Pnt is selected.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

SOutsideRange(const CRange< TSeqPos > &range)

bool operator()(const CRef< CCode_break > &code_break)

CRange< TSeqPos > m_Range

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