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

.m_TransSplicing = trans_splcing;

( loc.

() ) {

.m_PrevId.Reset();

.m_PrevId && h &&

.m_PrevId != h ) {

( pos1 >= 0 && pos2 >= 0 &&

(pos2-pos1) > 1 ) {

backw = pos2 < pos1;

backw2 =

(strand) != minus2;

( backw1 == backw && backw2 == backw ) {

dir = backw ? -1: 1;

(

pos = pos1+dir; pos != pos2; pos += dir ) {

.m_PrevStrand = strand;

.m_PrevRange = range;

( it2 !=

() && it1->second.IntersectingWith(it2->second) ) {

( it2 !=

() && it1->second.GetOverlappingRange()

.IntersectingWith(it2->second.GetOverlappingRange()) ) {

(it.GetRefSeqid(), it.GetRefMinusStrand());

bool IsReverse(ENa_strand s)

ENa_strand Reverse(ENa_strand s)

User-defined methods of the data storage class.

const CSeqMap & GetSeqMap(void) const

const TId & GetId(void) const

CHandleRange::TRange TRange

void AddLocation(const CSeq_loc &loc, ETransSplicing trans_splcing=eNoTransSplicing)

void AddRanges(const CSeq_id_Handle &h, const CHandleRange &hr)

bool TotalRangeIntersectingWith(const CHandleRangeMap &rmap) const

bool IntersectingWithMap(const CHandleRangeMap &rmap) const

void AddRange(const CSeq_id_Handle &h, const TRange &range, ENa_strand strand)

bool IntersectingWithLoc(const CSeq_loc &loc) const

CConstRef< CMasterSeqSegments > m_MasterSeq

TLocMap::const_iterator const_iterator

const_iterator end(void) const

void AddRange(TRange range, ENa_strand strand)

int AddSegment(const CSeq_id_Handle &id, bool minus_strand)

bool GetMinusStrand(int seg) const

list< CRef< CSeq_id > > TIds2

~CMasterSeqSegments(void)

vector< CSeq_id_Handle > TIds

int GetSegmentCount(void) const

void AddSegments(const CSeqMap &seq)

void AddSegmentIds(int idx, const TIds &ids)

void AddSegmentId(int idx, const CSeq_id_Handle &id)

int FindSeg(const CSeq_id_Handle &h) const

const CSeq_id_Handle & GetHandle(int seg) const

pair< CSeq_id_Handle, bool > TSeg

const CTSE_Info & GetTSE_Info(void) const

CConstRef< CBioseq_Info > FindMatchingBioseq(const CSeq_id_Handle &id) const

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

struct parameters_t * pb[]

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

static TThisType GetEmpty(void)

static TThisType GetWhole(void)

#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.

const TB & GetB(void) const

Get the B member data.

list< CRef< CSeq_interval > > Tdata

ENa_strand

strand of nucleic acid

TStrand GetStrand(void) const

Get the Strand member data.

const TPnt & GetPnt(void) const

Get the variant data.

TPoint GetPoint(void) const

Get the Point member data.

const TWhole & GetWhole(void) const

Get the variant data.

bool IsSetStrand(void) const

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

list< CRef< CSeq_loc > > Tdata

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.

TStrand GetStrand(void) const

Get the Strand member data.

const Tdata & Get(void) const

Get the member data.

const TPacked_pnt & GetPacked_pnt(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TEquiv & GetEquiv(void) const

Get the variant data.

list< CRef< CSeq_loc > > Tdata

vector< TSeqPos > TPoints

const TA & GetA(void) const

Get the A member data.

const TEmpty & GetEmpty(void) const

Get the variant data.

bool IsSetStrand(void) const

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

const TPoints & GetPoints(void) const

Get the Points member data.

const TInt & GetInt(void) const

Get the variant data.

const TMix & GetMix(void) const

Get the variant data.

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.

@ 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

CHandleRange::TRange TRange

ETransSplicing m_TransSplicing

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