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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/loc__edit_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/edit/loc_edit.cpp Source File

best_id = sid.AsFastaString();

from = seq_int.

();

f_from.

(&lab_from, from,

);

to = seq_int.

();

f_from.

(&lab_from, from,

);

+= lab_from +

+ lab_to;

(seq_loc.

()) {

(seq_loc.

()) {

list <CRef <CSeq_loc> >* seq_loc_ls;

(seq_loc.

()) {

seq_loc_ls = &(seq_loc.

().

());

(it == seq_loc.

().

().begin()) {

(seq_loc.

()) {

num_intervals = last_l.

();

last_l.

(num_intervals - 1);

& do_set_5_partial,

& do_clear_5_partial)

do_set_5_partial =

;

do_clear_5_partial =

;

do_set_5_partial =

;

confident =

;

(confident && !at_5) {

do_set_5_partial =

;

confident =

;

do_set_5_partial =

;

confident =

;

do_set_5_partial =

;

do_set_5_partial =

;

do_clear_5_partial =

;

confident =

;

do_clear_5_partial =

;

confident =

;

do_clear_5_partial =

;

do_set_5_partial || do_clear_5_partial;

& do_set_3_partial,

& do_clear_3_partial)

do_set_3_partial =

;

do_clear_3_partial =

;

do_set_3_partial =

;

confident =

;

(confident && !at_3) {

do_set_3_partial =

;

confident =

;

(at_3 && confident) {

do_set_3_partial =

;

confident =

;

do_set_3_partial =

;

do_clear_3_partial =

;

confident =

;

(!at_3 && confident) {

do_clear_3_partial =

;

confident =

;

do_clear_3_partial =

;

do_set_3_partial || do_clear_3_partial;

num_intervals = last_l.

();

last_l.

(num_intervals - 1);

(pos < loc_start) {

->Assign(*(loc.

()));

(*

,

(pos), loc_start - 1, strand));

}

(pos > loc_stop) {

->Assign(*(loc.

()));

*

, loc_stop + 1,

(pos), strand));

any_change =

;

do_set_5_partial =

;

do_clear_5_partial =

;

any_change |=

(feat, scope, do_set_5_partial, do_clear_5_partial);

(do_set_5_partial) {

}

(do_clear_5_partial) {

do_set_3_partial =

;

do_clear_3_partial =

;

any_change |=

(feat, scope, do_set_3_partial, do_clear_3_partial);

(do_set_3_partial) {

}

(do_clear_3_partial) {

changed =

;

changed =

;

((*it)->IsNull()) {

new_loc->

(orig_loc);

(subloc && !subloc->

()) {

new_loc->

().Set().push_back(add);

new_loc->

(orig_loc);

(orig_loc.

()) {

new_loc->

(orig_loc);

new_loc->

().Set().push_back(null_loc);

new_loc->

().Set().push_back(add);

((orig_frame + diff % 3) % 3) {

feat.

().SetCdregion().SetFrame(new_frame);

extend =

;

confident =

;

extend =

;

confident =

;

num_intervals = last_l.

();

last_l.

(num_intervals - 1);

& scope,

adjust_gene,

retranslate_cds)

new_feat->

(orig_feat);

new_gene->

(*old_gene);

gene_change =

;

interval.

(from);

}

(interval.

()) {

vector<int> new_pnts;

(vector<int>, it, new_pnts) {

(loc.

()) {

((*it)->IsSetLoc()) {

(loc.

()) {

CSeq_loc::TEquiv::Tdata::iterator it = loc.

().Set().begin();

(it != loc.

().Set().end()) {

it = loc.

().Set().erase(it);

}

(loc.

().

().size() == 0) {

CSeq_loc::TMix::Tdata::iterator it = loc.

().Set().begin();

(it != loc.

().Set().end()) {

it = loc.

().Set().erase(it);

(loc.

().

().size() == 1) {

}

(loc.

().

().size() == 0) {

loc.

().Assign(*sub);

loc.

().Assign(*sub);

& bCompleteCut,

cut_size = cut_to - cut_from + 1;

(feat_to < cut_from)

(feat_from >= cut_from && feat_to <= cut_to)

bCompleteCut =

;

trim5 += feat_from - feat_to + 1;

(feat_from > cut_to)

feat_from -= cut_size;

feat_to -= cut_size;

interval.

(feat_from);

interval.

(feat_to);

(feat_to > cut_to) {

feat_to -= cut_size;

diff = cut_from - 1 - feat_to;

feat_to = cut_from - 1;

(feat_from >= cut_from) {

diff = cut_to + 1 - feat_from;

feat_from = cut_to + 1;

feat_from -= cut_size;

interval.

(feat_from);

interval.

(feat_to);

& bCompleteCut,

(packint.

()) {

CPacked_seqint::Tdata::iterator it;

(it = packint.

().begin();

it != packint.

().end(); )

bDeleted =

;

bDeleted, this_trim, bAdjusted);

it = packint.

().erase(it);

(packint.

().empty()) {

(!packint.

()) {

bCompleteCut =

;

& bCompleteCut,

(mix.

()) {

CSeq_loc_mix::Tdata::iterator it;

(it = mix.

().begin();

it != mix.

().end(); )

bDeleted =

;

it = mix.

().erase(it);

(!mix.

() || mix.

().empty()) {

bCompleteCut =

;

& bCompleteCut,

diff = to - from + 1;

}

(from < pnt.

()) {

bCompleteCut =

;

& bCompleteCut,

& trim5,

& bAdjusted)

(

.IsSetPoints()) {

it =

.SetPoints().begin();

(it !=

.SetPoints().end()) {

diff = to - from + 1;

}

(from < *it) {

it =

.SetPoints().erase(it);

(

.SetPoints().empty()) {

bCompleteCut =

;

& bCompleteCut,

cutA =

, cutB =

;

bCompleteCut =

;

& bCompleteCut,

CSeq_loc_equiv::Tdata::iterator it = equiv.

().begin();

(it != equiv.

().end()) {

(this_trim5 > max_trim5) {

max_trim5 = this_trim5;

it = equiv.

().erase(it);

(equiv.

().empty()) {

bCompleteCut =

;

& bCompleteCut,

& trim5,

& bAdjusted)

(loc.

())

bCompleteCut, trim5, bAdjusted);

(!bCompleteCut) {

insert_size = insert_to - insert_from + 1;

(feat_to < insert_from)

(feat_from > insert_from) {

feat_from += insert_size;

feat_to += insert_size;

interval.

(feat_from);

interval.

(feat_to);

(feat_from <= insert_from && feat_to >= insert_from)

feat_to += insert_size;

interval.

(feat_to);

(packint.

()) {

CPacked_seqint::Tdata::iterator it;

(it = packint.

().begin();

it != packint.

().end(); it++)

(mix.

()) {

CSeq_loc_mix::Tdata::iterator it;

(it = mix.

().begin();

it != mix.

().end(); it++)

(insert_from < pnt.

()) {

diff = insert_to - insert_from + 1;

it = packpnt.

().begin();

(it != packpnt.

().end()) {

diff = to - from + 1;

CSeq_loc_equiv::Tdata::iterator it = equiv.

().begin();

(it != equiv.

().end()) {

(loc.

())

* seqid,

& cut,

options)

(feat_to < start) {

(feat_from < start && feat_to > stop) {

(feat_to > stop) {

(stop + 1 > feat_from) {

(feat_from < start) {

before.

(start - 1);

* seqid,

options)

(before_intervals.

()) {

reverse(before_intervals.

().begin(), before_intervals.

().end());

it = before_intervals.

().begin();

(it != before_intervals.

().end()) {

(int_from > stop && after_intervals.

() && !after_intervals.

().empty()) {

after_intervals.

().push_back(

(&sub_interval));

it = before_intervals.

().erase(it);

it = before_intervals.

().erase(it);

after_intervals.

().push_back(after);

reverse(after_intervals.

().begin(), after_intervals.

().end());

reverse(before_intervals.

().begin(), before_intervals.

().end());

start,

stop,

* seqid,

options)

(loc1.

())

seqid, cut, options);

(before_intervals.

().empty()) {

(!after_intervals->Set().empty()) {

(before_mix.

()) {

reverse(before_mix.

().begin(), before_mix.

().end());

it = before_mix.

().begin();

(it != before_mix.

().end()) {

(from > stop && after_mix->IsSet() && !after_mix->Get().empty()) {

after_mix->Set().push_back(

(&sub_loc));

it = before_mix.

().erase(it);

it = before_mix.

().erase(it);

after_mix->Set().push_back(after);

(after_mix->IsReverseStrand()) {

reverse(after_mix->Set().begin(), after_mix->Set().end());

reverse(before_mix.

().begin(), before_mix.

().end());

(before_mix.

().empty()) {

(!after_mix->Set().empty()) {

loc2.

().Assign(*after_mix);

add->

().Assign(*after_mix);

(before_equiv.

()) {

CSeq_loc_equiv::Tdata::iterator it;

(it = before_equiv.

().begin();

it != before_equiv.

().end(); )

it = before_equiv.

().erase(it);

after_equiv->Set().push_back(after);

(before_equiv.

().empty()) {

(!after_equiv->Set().empty()) {

loc2.

().Assign(*after_equiv);

add->

().Assign(*after_equiv);

CPacked_seqpnt::TPoints::iterator it = loc1.

().SetPoints().begin();

after_points.push_back(*it);

it = before_points.erase(it);

(!after_points.empty()) {

after->SetPoints().assign(after_points.begin(), after_points.end());

(before_points.empty()) {

CCdregion::TCode_break::iterator it = cdr.

().begin();

((*it)->IsSetLoc()) {

adjusted =

;

trimmed =

;

& bCompleteCut,

CCdregion::TCode_break::iterator it = cdr.

().begin();

((*it)->IsSetLoc()) {

(pint.

().size() < 2) {

any_change =

;

this_change =

;

(this_change) {

this_change =

;

CPacked_seqint::Tdata::iterator

= pint.

().begin();

CPacked_seqint::Tdata::iterator

=

;

(

!= pint.

().end()) {

((*a)->IsSetId() && (*b)->IsSetId() &&

(*a)->GetId().Equals((*b)->GetId()) &&

(*a)->IsSetFrom() && (*a)->IsSetTo() && (*a)->GetFrom() < (*a)->GetTo() &&

(*b)->IsSetFrom() && (*b)->IsSetTo() && (*b)->GetFrom() < (*b)->GetTo() &&

((*b)->GetTo() > (*a)->GetFrom()) {

->Reset(

->GetPointer());

this_change =

;

((*b)->GetTo() < (*a)->GetFrom()) {

->Reset(

->GetPointer());

this_change =

;

(this_strand != strand) {

any_change =

;

(mix.size() < 2) {

this_change =

;

(this_change) {

this_change =

;

CSeq_loc::TMix::Tdata::iterator

= mix.begin();

CSeq_loc::TMix::Tdata::iterator

=

;

(

!= mix.end()) {

a_strand == b_strand) {

->Reset(

->GetPointer());

this_change =

;

->Reset(

->GetPointer());

this_change =

;

any_change =

;

(loc.

()) {

((*it)->IsLiteral()) {

+= (*it)->GetLiteral().GetLength();

(!(*it)->GetLiteral().IsSetSeq_data()) {

}

((*it)->GetLiteral().GetSeq_data().IsGap()) {

}

((*it)->IsLoc()) {

(left >= last_gap_stop && left - last_gap_stop <= 3) {

extend_len = left - last_gap_stop;

extend_len = seq.

() - right - 1;

((*it)->IsLiteral()) {

(!(*it)->GetLiteral().IsSetSeq_data()) {

next_gap_start =

;

}

((*it)->GetLiteral().GetSeq_data().IsGap()) {

next_gap_start =

;

+= (*it)->GetLiteral().GetLength();

}

((*it)->IsLoc()) {

(

> right + 4) {

(next_gap_start > right && next_gap_start - right - 1 <= 3) {

extend_len = next_gap_start - right - 1;

extendable =

;

new_start = start - extend_len;

(start < seq->GetInst().

() - 1) {

new_start = start + extend_len;

(

it : related_features) {

it->SetLocation().Assign(*related_loc);

(it->IsSetData() && it->GetData().IsCdregion()) {

num_intervals = last_l.

();

last_l.

(num_intervals - 1);

extendable =

;

(stop < seq->GetInst().

() - 1) {

new_stop = stop + extend_len;

new_stop = stop - extend_len;

(

it : related_features) {

it->SetLocation().Assign(*related_loc);

(

(start, *seq, &scope, extend_len) && extend_len > 0) {

num_intervals = last_l.

();

last_l.

(num_intervals - 1);

any_change =

;

(

->GetData().IsCdregion()) {

vector<CRef<CSeq_feat> > related_features;

related_features.push_back(new_gene);

related_features.push_back(new_mRNA);

new_cds->

(*(

->GetOriginalSeq_feat()));

(adjusted_5prime || adjusted_3prime) {

geh.

(*(related_features.front()));

meh.

(*(related_features.back()));

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ 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.

TSeqPos GetLength(void) const

void GetLabel(string *label, TSeqPos pos, bool right=true) const

static CRef< CSeq_loc > ConvertToOrder(const CSeq_loc &orig_loc, bool &changed)

bool Interpret5Policy(const CSeq_feat &orig_feat, CScope &scope, bool &do_set_5_partial, bool &do_clear_5_partial) const

@ eMergePolicy_SingleInterval

static bool HasNulls(const CSeq_loc &orig_loc)

static bool Extend3(CSeq_feat &feat, CScope &scope)

static bool Extend5(CSeq_feat &feat, CScope &scope)

static CRef< CSeq_loc > ConvertToJoin(const CSeq_loc &orig_loc, bool &changed)

EPartialPolicy m_PartialPolicy3

static bool Is3AtEndOfSeq(const CSeq_loc &loc, CBioseq_Handle bsh)

static bool Is5AtEndOfSeq(const CSeq_loc &loc, CBioseq_Handle bsh)

EPartialPolicy m_PartialPolicy5

@ ePartialPolicy_eSetForFrame

@ ePartialPolicy_eSetAtEnd

@ ePartialPolicy_eNoChange

@ ePartialPolicy_eSetForBadEnd

@ ePartialPolicy_eClearForGoodEnd

@ ePartialPolicy_eClearNotAtEnd

EMergePolicy m_MergePolicy

bool Interpret3Policy(const CSeq_feat &orig_feat, CScope &scope, bool &do_set_3_partial, bool &do_clear_3_partial) const

bool ApplyPolicyToFeature(CSeq_feat &feat, CScope &scope) const

bool IsReverseStrand(void) const

ESubtype GetSubtype(void) const

CSeq_feat_EditHandle –.

namespace ncbi::objects::

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

bool IsReverseStrand(void) const

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

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static const char * pack(const char *fmt,...)

static const char location[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

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

Check if both objects contain the same values.

const string AsFastaString(void) const

CConstRef< CSeq_id > GetSeqId(void) const

E_SIC Compare(const CSeq_id &sid2) const

Compare() - more general.

@ e_YES

SeqIds compared, but are different.

void SetPacked_int(TPacked_int &v)

void InvalidateCache(void) const

Combine invalidation of all cached values.

void SetPacked_pnt(TPacked_pnt &v)

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.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

CConstRef< CSeq_loc > GetRangeAsSeq_loc(void) const

Get seq-loc for the current iterator position.

bool IsSetStrand(void) const

Get strand.

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

Check if strand is set for any/all part(s) of the seq-loc depending on the flag.

void SetPos(size_t pos)

Set iterator's position.

const CSeq_id * GetId(void) const

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

size_t GetSize(void) const

Get number of ranges.

TRange GetRange(void) const

Get the range.

void SetPartialStart(bool val, ESeqLocExtremes ext)

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

ENa_strand GetStrand(void) const

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

void GetLabel(string *label) const

Appends a label suitable for display (e.g., error messages) label must point to an existing string ob...

void SetPartialStop(bool val, ESeqLocExtremes ext)

void SetNull(void)

Override all setters to incorporate cache invalidation.

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

bool RetranslateCDS(const CSeq_feat &cds, CScope &scope)

RetranslateCDS A function to replace the protein Bioseq pointed to by cds.product with the current tr...

bool AdjustFeaturePartialFlagForLocation(CSeq_feat &new_feat)

AdjustFeaturePartialFlagForLocation A function to ensure that Seq-feat.partial is set if either end o...

bool AdjustForCDSPartials(const CSeq_feat &cds, CSeq_entry_Handle seh)

AdjustForCDSPartials A function to make all of the necessary related changes to a Seq-entry after the...

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,...

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

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

Returns the sequence::ECompare containment relationship between CSeq_locs.

CRef< CSeq_loc > Seq_loc_Merge(const CSeq_loc &loc, CSeq_loc::TOpFlags flags, CScope *scope)

Merge ranges in the seq-loc.

CRef< CSeq_loc > Seq_loc_Add(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Add two seq-locs.

@ fCompareOverlapping

Check if seq-locs are overlapping.

@ eSame

CSeq_locs contain each other.

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

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

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)

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

TSeqPos GetBioseqLength(void) const

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

TInst_Length GetInst_Length(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

void Replace(const CSeq_feat &new_feat) const

Replace the feature with new Seq-feat object.

const TInst & GetInst(void) const

CRef< C > Ref(C *object)

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

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

#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.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

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

Check if a string starts with a specified prefix value.

@ eNocase

Case insensitive compare.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From 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.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void ResetCode_break(void)

Reset Code_break data member.

const TLocation & GetLocation(void) const

Get the Location member data.

list< CRef< CCode_break > > TCode_break

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

TCode_break & SetCode_break(void)

Assign a value to Code_break data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

const TCode_break & GetCode_break(void) const

Get the Code_break member data.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

bool IsSetCode_break(void) const

individual exceptions Check if a value has been assigned to Code_break data member.

bool IsSetFrame(void) const

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

bool IsSetLocation(void) const

feature made from Check if a value has been assigned to Location data member.

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

bool IsSet(void) const

Check if a value has been assigned to data member.

void SetTo(TTo value)

Assign a value to To data member.

const TFuzz_from & GetFuzz_from(void) const

Get the Fuzz_from member data.

void SetPoint(TPoint value)

Assign a value to Point data member.

void SetId(TId &value)

Assign a value to Id data member.

void SetA(TA &value)

Assign a value to A data member.

bool IsSetId(void) const

WARNING: this used to be optional Check if a value has been assigned to Id data member.

void ResetFuzz_to(void)

Reset Fuzz_to data member.

bool IsMix(void) const

Check if variant Mix is selected.

bool CanGetFuzz_to(void) const

Check if it is safe to call GetFuzz_to method.

const TB & GetB(void) const

Get the B member data.

list< CRef< CSeq_interval > > Tdata

ENa_strand

strand of nucleic acid

const Tdata & Get(void) const

Get the member data.

bool CanGetStrand(void) const

Check if it is safe to call GetStrand method.

void ResetPoints(void)

Reset Points data member.

TStrand GetStrand(void) const

Get the Strand member data.

const TId & GetId(void) const

Get the Id member data.

bool IsSetPoint(void) const

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

bool IsSetPoints(void) const

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

bool IsPacked_pnt(void) const

Check if variant Packed_pnt is selected.

Tdata & Set(void)

Assign a value to data member.

const TPnt & GetPnt(void) const

Get the variant data.

TPoint GetPoint(void) const

Get the Point member data.

const TFuzz_to & GetFuzz_to(void) const

Get the Fuzz_to member data.

bool IsSetA(void) const

connection to a least one residue Check if a value has been assigned to A data member.

void SetStrand(TStrand value)

Assign a value to Strand data member.

bool IsSetStrand(void) const

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

TFrom GetFrom(void) const

Get the From member data.

bool CanGetTo(void) const

Check if it is safe to call GetTo method.

void SetFuzz(TFuzz &value)

Assign a value to Fuzz data member.

bool IsSetFuzz(void) const

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

list< CRef< CSeq_loc > > Tdata

bool IsEquiv(void) const

Check if variant Equiv is selected.

E_Choice Which(void) const

Which variant is currently selected.

const TId & GetId(void) const

Get the Id member data.

const TId & GetId(void) const

Get the Id member data.

bool IsSet(void) const

Check if a value has been assigned to data member.

void SetFrom(TFrom value)

Assign a value to From data member.

bool IsBond(void) const

Check if variant Bond is selected.

bool IsSetFuzz(void) const

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

const Tdata & Get(void) const

Get the member data.

const TPacked_pnt & GetPacked_pnt(void) const

Get the variant data.

void SetFuzz(TFuzz &value)

Assign a value to Fuzz data member.

const Tdata & Get(void) const

Get the member data.

void ResetFuzz_from(void)

Reset Fuzz_from data member.

const TEquiv & GetEquiv(void) const

Get the variant data.

TPoints & SetPoints(void)

Assign a value to Points data member.

list< CRef< CSeq_loc > > Tdata

vector< TSeqPos > TPoints

virtual void Reset(void)

Reset the whole object.

void SetFuzz_to(TFuzz_to &value)

Assign a value to Fuzz_to data member.

void SetFuzz_from(TFuzz_from &value)

Assign a value to Fuzz_from data member.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

const TA & GetA(void) const

Get the A member data.

bool IsSetTo(void) const

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

bool IsSet(void) const

Check if a value has been assigned to data member.

bool CanGetB(void) const

Check if it is safe to call GetB method.

bool IsSetStrand(void) const

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

Tdata & Set(void)

Assign a value to data member.

bool IsSetFuzz_to(void) const

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

void Reset(void)

Reset data member.

Tdata & Set(void)

Assign a value to data member.

void ResetFrom(void)

Reset From data member.

const TPoints & GetPoints(void) const

Get the Points member data.

TStrand GetStrand(void) const

Get the Strand member data.

bool IsSetId(void) const

WARNING: this used to be optional Check if a value has been assigned to Id data member.

TTo GetTo(void) const

Get the To member data.

bool IsSetFrom(void) const

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

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.

void SetB(TB &value)

Assign a value to B data member.

bool IsSetId(void) const

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

bool IsSetFuzz_from(void) const

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

const TFuzz & GetFuzz(void) const

Get the Fuzz member data.

const TMix & GetMix(void) const

Get the variant data.

void ResetTo(void)

Reset To data member.

bool IsPnt(void) const

Check if variant Pnt is selected.

bool IsSetB(void) const

other end may not be available Check if a value has been assigned to B data member.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

const TBond & GetBond(void) const

Get the variant data.

bool CanGetFrom(void) const

Check if it is safe to call GetFrom method.

bool CanGetFuzz_from(void) const

Check if it is safe to call GetFuzz_from method.

@ eNa_strand_both_rev

in reverse orientation

@ e_not_set

No variant selected.

@ e_Equiv

equivalent sets of locations

@ e_Empty

to NULL one Seq-id in a collection

@ e_Feat

indirect, through a Seq-feat

TRepr GetRepr(void) const

Get the Repr member data.

const TInst & GetInst(void) const

Get the Inst member data.

bool IsSetRepr(void) const

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

bool IsSetExt(void) const

extensions for special types Check if a value has been assigned to Ext data member.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TLength GetLength(void) const

Get the Length member data.

bool IsDelta(void) const

Check if variant Delta is selected.

const TExt & GetExt(void) const

Get the Ext member data.

const TDelta & GetDelta(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

list< CRef< CDelta_seq > > Tdata

@ eRepr_delta

sequence made by changes (delta) to others

unsigned int

A callback function used to compare two keys in a database.

CRef< CSeq_loc > SeqLocExtend5(const CSeq_loc &loc, TSeqPos pos, CScope *scope)

bool IsExtendableRight(TSeqPos right, const CBioseq &seq, CScope *scope, TSeqPos &extend_len)

bool IsExtendableLeft(TSeqPos left, const CBioseq &seq, CScope *scope, TSeqPos &extend_len)

void AdjustFrameFor5Extension(CSeq_feat &feat, size_t diff)

bool OkToAdjustLoc(const CSeq_interval &interval, const CSeq_id *seqid)

void SeqLocAdjustForInsert(CSeq_interval &interval, TSeqPos insert_from, TSeqPos insert_to, const CSeq_id *seqid)

void CdregionAdjustForTrim(CCdregion &cdr, TSeqPos from, TSeqPos to, const CSeq_id *seqid)

void ReverseComplementCDRegion(CCdregion &cdr, CScope &scope)

bool AdjustFeatureEnd3(CSeq_feat &cds, vector< CRef< CSeq_feat > > related_features, CScope &scope)

void FeatureAdjustForInsert(CSeq_feat &feat, TSeqPos from, TSeqPos to, const CSeq_id *seqid)

bool ExtendPartialFeatureEnds(CBioseq_Handle bsh)

bool s_StrandsConsistent(const CSeq_interval &a, const CSeq_interval &b)

void ReverseComplementFeature(CSeq_feat &feat, CScope &scope)

bool s_PPntCompareMinus(const TSeqPos &p1, const TSeqPos &p2)

string PrintSeqIntUseBestID(const CSeq_interval &seq_int, CScope &scope, bool range_only)

void TrnaAdjustForTrim(CTrna_ext &trna, TSeqPos from, TSeqPos to, const CSeq_id *seqid)

void SeqLocAdjustForTrim(CSeq_interval &interval, TSeqPos cut_from, TSeqPos cut_to, const CSeq_id *seqid, bool &bCompleteCut, TSeqPos &trim5, bool &bAdjusted)

void NormalizeLoc(CSeq_loc &loc)

bool CorrectIntervalOrder(CPacked_seqpnt &ppnt)

bool AdjustFeatureEnd5(CSeq_feat &cds, vector< CRef< CSeq_feat > > related_features, CScope &scope)

string PrintBestSeqId(const CSeq_id &sid, CScope &scope)

void TrnaAdjustForInsert(CTrna_ext &trna, TSeqPos from, TSeqPos to, const CSeq_id *seqid)

bool OneIdOneStrand(const CSeq_loc &loc, const CSeq_id **id, ENa_strand &strand)

void ReverseComplementLocation(CSeq_interval &interval, CScope &scope)

bool ApplyPolicyToFeature(const CLocationEditPolicy &policy, const CSeq_feat &orig_feat, CScope &scope, bool adjust_gene, bool retranslate_cds)

bool IsExtendable(const CSeq_feat &cds, CScope &scope)

string SeqLocPrintUseBestID(const CSeq_loc &seq_loc, CScope &scope, bool range_only)

CRef< CSeq_loc > SeqLocExtend3(const CSeq_loc &loc, TSeqPos pos, CScope *scope)

string PrintPntAndPntsUseBestID(const CSeq_loc &seq_loc, CScope &scope, bool range_only)

bool s_PPntComparePlus(const TSeqPos &p1, const TSeqPos &p2)

void FeatureAdjustForTrim(CSeq_feat &feat, TSeqPos from, TSeqPos to, const CSeq_id *seqid, bool &bCompleteCut, bool &bTrimmed)

void CdregionAdjustForInsert(CCdregion &cdr, TSeqPos from, TSeqPos to, const CSeq_id *seqid)

static const string strand_symbol[]

void ReverseComplementTrna(CTrna_ext &trna, CScope &scope)

CRef< CSeq_interval > SplitLocationForGap(CSeq_interval &before, TSeqPos start, TSeqPos stop, const CSeq_id *seqid, bool &cut, unsigned int options)

CRef< CSeq_loc > SeqLocExtend(const CSeq_loc &loc, size_t pos, CScope *scope)

@ eSplitLocOption_split_in_intron

@ eSplitLocOption_make_partial

@ eSplitLocOption_split_in_exon

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

Generic utility macros and templates for exploring NCBI objects.

bool seq_mac_is_sorted(Iter first, Iter last, Comp comp)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

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