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

1 #ifndef OBJECTS_OBJMGR___SEQ_MAP__HPP 2 #define OBJECTS_OBJMGR___SEQ_MAP__HPP 81 class

CSeqMap_Delta_seqs;

111 size_t

GetSegmentsCount(

void

)

const

;

114 TMol

GetMol(

void

)

const

;

131

fFindLeafRef = (1<<2),

132

fFindInnerRef = (1<<3),

133

fFindExactLevel = (1<<4),

134

fIgnoreUnresolved = (1<<5),

135

fByFeaturePolicy= (1<<6),

136

fBySequenceClass= (1<<7),

137

fFindRef = (fFindLeafRef | fFindInnerRef),

138

fFindAny = fFindData | fFindGap | fFindRef,

139

fFindAnyLeaf = fFindData | fFindGap | fFindLeafRef,

140

fDefaultFlags = fFindAnyLeaf

159 size_t

maxResolve =

size_t

(-1),

166 bool

CanResolveRange(

CScope

* scope,

170 size_t

maxResolve =

size_t

(-1),

200 bool

ref_minus_strand);

218 void

ResetRepr(

void

);

220 void

ResetMol(

void

);

237 friend class

CSeqMap_SeqPoss;

245 bool

unknown_len =

false

);

250 bool

IsSetData(

void

)

const

;

292 void

x_AddEnd(

void

);

293 void

x_AddSegment(ESegmentType

type

295 bool

unknown_len =

false

);

297 void

x_AddSegment(ESegmentType

type

const CObject

object

300 void

x_AddGap(

TSeqPos len

bool

unknown_len);

312 void

x_Add(

const CSeq_id

& seq);

326 size_t

x_GetLastEndSegmentIndex(

void

)

const

;

327 size_t

x_GetFirstEndSegmentIndex(

void

)

const

;

329 const CSegment

& x_GetSegment(

size_t

index)

const

;

330 void

x_GetSegmentException(

size_t

index)

const

;

331 CSegment

& x_SetSegment(

size_t

index);

333 size_t

x_FindSegment(

TSeqPos

position,

CScope

* scope)

const

;

335 TSeqPos

x_GetSegmentLength(

size_t

index,

CScope

* scope)

const

;

336 TSeqPos

x_GetSegmentPosition(

size_t

index,

CScope

* scope)

const

;

337 TSeqPos

x_GetSegmentEndPosition(

size_t

index,

CScope

* scope)

const

;

338 TSeqPos

x_ResolveSegmentLength(

size_t

index,

CScope

* scope)

const

;

339 TSeqPos

x_ResolveSegmentPosition(

size_t

index,

CScope

* scope)

const

;

341 void

x_StartEditing(

void

);

342 bool

x_IsChanged(

void

)

const

;

343 void

x_SetChanged(

size_t

index);

344 bool

x_UpdateSeq_inst(

CSeq_inst

& inst);

345 bool

x_DoUpdateSeq_inst(

CSeq_inst

& inst);

350 bool

resolveExternal =

false

)

const

;

355 bool

x_GetRefMinusStrand(

const CSegment

& seg)

const

;

357 void

x_LoadObject(

const CSegment

& seg)

const

;

364 void

x_SetSubSeqMap(

size_t

index, CSeqMap_Delta_seqs* subMap);

366 void

x_SetSegmentGap(

size_t

index,

369 void

x_SetSegmentData(

size_t

index,

372 void

x_SetSegmentRef(

size_t

index,

376 bool

ref_minus_strand);

378 int

x_GetSequenceClass(

void

)

const

;

unsigned int TSeqPos

Type for sequence locations and lengths.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

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

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

atomic< TSeqPos > m_SeqLength

CSeqMap_CI const_iterator

bool operator()(TSeqPos pos, const CSegment &seg)

bool x_IsChanged(void) const

TSeqPos x_ResolveSegmentPosition(size_t index, CScope *scope) const

atomic< TSeqPos > m_Position

atomic< THasSegments > m_HasSegments

bool operator()(const CSegment &seg, TSeqPos pos)

atomic< size_t > m_Resolved

const CSegment & x_GetSegment(size_t index) const

size_t x_GetLastEndSegmentIndex(void) const

bool x_UpdateSeq_inst(CSeq_inst &inst)

vector< CSegment > m_Segments

TSeqPos x_GetSegmentLength(size_t index, CScope *scope) const

size_t x_GetFirstEndSegmentIndex(void) const

TSeqPos x_GetSegmentPosition(size_t index, CScope *scope) const

TSeqPos x_GetSegmentEndPosition(size_t index, CScope *scope) const

bool operator()(const CSegment &seg1, const CSegment &seg2)

bool IsSetData(void) const

void x_Add(CSeqMap *submap)

vector< CSegment > TSegments

CConstRef< CObject > m_RefObject

EFlags

Segment type flags.

atomic< TSeqPos > m_Length

TSeqPos GetLength(CScope *scope) const

bool x_DoUpdateSeq_inst(CSeq_inst &inst)

void ResolveAll(void) const

size_t GetSegmentsCount(void) const

TSeqPos x_ResolveSegmentLength(size_t index, CScope *scope) const

@ eSeqData

real sequence data

@ eSeqRef

reference to Bioseq

CObject & operator=(const CObject &src) THROWS_NONE

Assignment operator.

uint8_t Uint1

1-byte (8-bit) unsigned integer

#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.

#define NCBI_XOBJMGR_EXPORT

ENa_strand

strand of nucleic acid

ERepr

representation class

EMol

molecule class in living organism

Multi-threading â mutexes; rw-locks; semaphore.

Selector used in CSeqMap methods returning iterators.

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