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NCBI C++ ToolKit: include/objmgr/seq_map_ci.hpp Source File

GetRefPosition(

)

;

GetRefMinusStrand(

)

;

& x_GetSeqMap(

)

;

x_GetIndex(

)

;

IsSetData(

)

;

x_Move(

minusStrand,

* scope);

x_GetLevelRealPos(

)

;

x_GetLevelRealEnd(

)

;

x_GetLevelPos(

)

;

x_GetLevelEnd(

)

;

x_GetSkipBefore(

)

;

x_GetSkipAfter(

)

;

x_CalcLength(

)

;

x_GetTopOffset(

)

;

x_GetSequenceClass(

)

;

m_Position = range.

();

m_MaxResolveCount = res_cnt;

m_LinkUsedTSE = link;

m_LinkUsedTSE =

;

m_LinkUsedTSE =

;

m_UsedTSEs = &used_tses;

m_MaxResolveCount;

GetResolveCount() > 0;

IsInvalid(

)

;

Next(

resolveExternal =

);

GetFlags(

)

;

GetDepth(

)

;

GetPosition(

)

;

IsUnknownLength(

)

;

GetEndPosition(

)

;

IsSetData(

)

;

& GetData(

)

;

& GetRefData(

)

;

GetRefPosition(

)

;

GetRefEndPosition(

)

;

GetRefMinusStrand(

)

;

FeaturePolicyWasApplied(

)

;

& seqmap,

index,

(

resolveExternal);

ref_minus_strand =

);

ref_minus_strand =

);

SetSequence(

&

,

m_MinusStrand(

), m_SequenceClass(-1)

!(*

== seg);

!(*

> seg);

!(*

< seg);

bool IsReverse(ENa_strand s)

CScope * GetScopeOrNull(void) const

Non-const iterator over CSeqMap (allows to edit the sequence).

bool operator<(const CEquivRange &A, const CEquivRange &B)

bool operator==(const CEquivRange &A, const CEquivRange &B)

SBlastSequence GetSequence(const objects::CSeq_loc &sl, EBlastEncoding encoding, objects::CScope *scope, objects::ENa_strand strand=objects::eNa_strand_plus, ESentinelType sentinel=eSentinels, std::string *warnings=NULL)

Retrieves a sequence using the object manager.

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

CExpression operator>=(CREATED, time_point)

CExpression operator<=(time_point, CREATED)

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

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

bool IsValid(const CSeq_point &pt, CScope *scope)

Checks that point >= 0 and point < length of Bioseq.

TSeqPos x_GetLevelRealPos(void) const

TSeqPos GetEndPosition(void) const

return end position of current segment in sequence (exclusive)

int x_GetSequenceClass(void) const

bool operator>=(const CSeqMap_CI &seg) const

SSeqMapSelector & SetResolveCount(size_t res_cnt)

Set max depth of resolving seq-map.

SSeqMapSelector & SetLinkUsedTSE(const CTSE_Handle &top_tse)

CSeqMap_CI_SegmentInfo TSegmentInfo

size_t GetResolveCount(void) const

CSeqMap_CI & operator--(void)

const CSeqMap::CSegment & x_GetSegment(void) const

void x_Select(const CConstRef< CSeqMap > &seqMap, const SSeqMapSelector &selector, TSeqPos pos)

bool CanResolve(void) const

bool operator==(const CSeqMap_CI &seg) const

CSeqMap_CI & operator++(void)

bool Next(bool resolveExternal=true)

go to next/next segment, return false if no more segments if no_resolve_current == true,...

SSeqMapSelector & SetLinkUsedTSE(bool link=true)

TSeqPos x_CalcLength(void) const

SSeqMapSelector & SetBySequenceClass(void)

size_t x_GetIndex(void) const

SSeqMapSelector m_Selector

TSeqPos GetRefPosition(void) const

bool operator<=(const CSeqMap_CI &seg) const

SSeqMapSelector & SetPosition(TSeqPos pos)

Find segment containing the position.

const TSegmentInfo & x_GetSegmentInfo(void) const

CScope * GetScope(void) const

bool IsSetData(void) const

SSeqMapSelector & SetFlags(TFlags flags)

Select segment type(s)

CConstRef< CSeqMap > m_SeqMap

TSeqPos x_GetTopOffset(void) const

const CSeqMap & x_GetSeqMap(void) const

const CSeqMap::CSegment & x_GetSegment(void) const

TSeqPos GetRefPosition(void) const

TSeqPos x_GetLevelEnd(void) const

TSeqPos x_GetSkipAfter(void) const

bool x_RefTSEMatch(const CSeqMap::CSegment &seg) const

const CSeqMap & x_GetSeqMap(void) const

CSeqMap_CI_SegmentInfo(void)

bool operator!=(const CSeqMap_CI &seg) const

bool GetRefMinusStrand(void) const

vector< TSegmentInfo > TStack

TSeqPos x_GetSkipBefore(void) const

CSeqMap::ESegmentType GetType(void) const

bool GetRefMinusStrand(void) const

DECLARE_OPERATOR_BOOL(IsValid())

bool x_CanResolve(const CSeqMap::CSegment &seg) const

CBioseq_Handle x_GetBioseq(const CSeq_id &seq_id) const

TSeqPos x_GetLevelPos(void) const

bool IsSetData(void) const

void x_UpdateLength(void)

bool m_FeaturePolicyWasApplied

SSeqMapSelector & SetRange(TSeqPos start, TSeqPos length)

Set range for iterator.

CSeqMap::ESegmentType GetType(void) const

SSeqMapSelector::TFlags TFlags

bool operator<(const CSeqMap_CI &seg) const

size_t x_GetIndex(void) const

bool FeaturePolicyWasApplied(void) const

SSeqMapSelector & SetLinkUsedTSE(vector< CTSE_Handle > &used_tses)

TSeqPos GetRefEndPosition(void) const

SSeqMapSelector & SetRange(const TRange &range)

Set range for iterator - CRange<> version.

TFlags GetFlags(void) const

vector< CTSE_Handle > * m_UsedTSEs

bool x_Push(TSeqPos offset, bool resolveExternal)

SSeqMapSelector & SetStrand(ENa_strand strand)

Set strand to iterate over.

bool IsInvalid(void) const

TSeqPos x_GetLevelRealEnd(void) const

TSeqPos GetPosition(void) const

return position of current segment in sequence

const CSeqMap::CSegment & x_GetNextSegment(void) const

bool operator>(const CSeqMap_CI &seg) const

SSeqMapSelector & SetByFeaturePolicy(void)

TSeqPos GetLength(void) const

return length of current segment

bool x_HasLimitTSE(void) const

size_t GetDepth(void) const

return the depth of current segment

const CTSE_Handle & GetUsingTSE(void) const

void x_Resolve(TSeqPos pos)

atomic< TSeqPos > m_Position

const CSegment & x_GetSegment(size_t index) const

bool IsSetData(void) const

atomic< TSeqPos > m_Length

int8_t Int1

1-byte (8-bit) signed integer

position_type GetLength(void) 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.

bool operator!=(const CNCBI_IPAddr &lhs, unsigned int rhs)

#define NCBI_XOBJMGR_EXPORT

TFrom GetFrom(void) const

Get the From member data.

ENa_strand

strand of nucleic acid

E_Choice

Choice variants.

bool InRange(TModelUnit z, TModelUnit z1, TModelUnit z2)

S & operator--(CNetRef< S > &r, int)

Selector used in CSeqMap methods returning iterators.

bool operator>(const typename tree< T, tree_node_allocator >::iterator_base &one, const typename tree< T, tree_node_allocator >::iterator_base &two)

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