Sequence Representations

Collaboration diagram for Sequence Representations:

Classes
class	CSeqMap
	CSeqMap –. More...
class	CSeqMap::CSegment
class	CSeqMap::SPosLessSegment
class	CSeqMapSwitchPoint
class	CSeqVector
	CSeqVector –. More...
class	CNcbi2naRandomizer
	CNcbi2naRandomizer –. More...

Typedefs
typedef TSeqPos	TSeqPosition
typedef TSeqPos	TSeqLength
typedef CSeq_inst::TMol	CSeqMap::TMol
typedef CSeqMap_CI	CSeqMap::const_iterator
typedef int	CSeqMap::TFlags
typedef vector< CSegment >	CSeqMap::TSegments
typedef Uint1	CSeqMap::THasSegments
typedef bool	CSeqMap::TChanged
typedef pair< TSeqPos, TSeqPos >	CSeqMapSwitchPoint::TInsertDelete
typedef map< TSeqPos, TInsertDelete >	CSeqMapSwitchPoint::TDifferences
typedef vector< CRef< CSeqMapSwitchPoint > >	TSeqMapSwitchPoints
typedef list< CRef< CSeq_align > >	TSeqMapSwitchAligns
typedef CBioseq_Handle::EVectorCoding	CSeqVector::EVectorCoding
typedef CSeqVector_CI	CSeqVector::const_iterator
typedef CMutex	CSeqVector::TMutex
typedef TMutex::TWriteLockGuard	CSeqVector::TMutexGuard
typedef CSeq_inst::TMol	CSeqVector::TMol

Enumerations
enum	CSeqMap::ESegmentType {   CSeqMap::eSeqGap , CSeqMap::eSeqData , CSeqMap::eSeqSubMap , CSeqMap::eSeqRef ,   CSeqMap::eSeqEnd , CSeqMap::eSeqChunk , CSeqMap::eSeqLiteral }
enum	CSeqMap::EFlags {   CSeqMap::fFindData = (1<<0) , CSeqMap::fFindGap = (1<<1) , CSeqMap::fFindLeafRef = (1<<2) , CSeqMap::fFindInnerRef = (1<<3) ,   CSeqMap::fFindExactLevel = (1<<4) , CSeqMap::fIgnoreUnresolved = (1<<5) , CSeqMap::fByFeaturePolicy = (1<<6) , CSeqMap::fBySequenceClass = (1<<7) ,   CSeqMap::fFindRef = (fFindLeafRef | fFindInnerRef) , CSeqMap::fFindAny = fFindData | fFindGap | fFindRef , CSeqMap::fFindAnyLeaf = fFindData | fFindGap | fFindLeafRef , CSeqMap::fDefaultFlags = fFindAnyLeaf }
	Segment type flags. More...
enum	{ CNcbi2naRandomizer::kRandomizerPosMask = 0x3f , CNcbi2naRandomizer::kRandomDataSize = kRandomizerPosMask + 1 , CNcbi2naRandomizer::kRandomValue = 16 }

Functions
	CSeqMap::~CSeqMap (void)
size_t	CSeqMap::GetSegmentsCount (void) const
TSeqPos	CSeqMap::GetLength (CScope *scope) const
TMol	CSeqMap::GetMol (void) const
const_iterator	CSeqMap::begin (CScope *scope) const
	STL style methods. More...
const_iterator	CSeqMap::end (CScope *scope) const
CSeqMap_CI	CSeqMap::Begin (CScope *scope) const
	NCBI style methods. More...
CSeqMap_CI	CSeqMap::End (CScope *scope) const
CSeqMap_CI	CSeqMap::FindSegment (TSeqPos pos, CScope *scope) const
	Find segment containing the position. More...
CSeqMap_CI	CSeqMap::BeginResolved (CScope *scope) const
CSeqMap_CI	CSeqMap::BeginResolved (CScope *scope, const SSeqMapSelector &selector) const
CSeqMap_CI	CSeqMap::EndResolved (CScope *scope) const
CSeqMap_CI	CSeqMap::EndResolved (CScope *scope, const SSeqMapSelector &selector) const
CSeqMap_CI	CSeqMap::FindResolved (CScope *scope, TSeqPos pos, const SSeqMapSelector &selector) const
CSeqMap_CI	CSeqMap::ResolvedRangeIterator (CScope *scope, TSeqPos from, TSeqPos length, ENa_strand strand=eNa_strand_plus, size_t maxResolve=size_t(-1), TFlags flags=fDefaultFlags) const
	Iterate segments in the range with specified strand coordinates. More...
bool	CSeqMap::HasSegmentOfType (ESegmentType type) const
size_t	CSeqMap::CountSegmentsOfType (ESegmentType type) const
bool	CSeqMap::CanResolveRange (CScope *scope, const SSeqMapSelector &sel) const
bool	CSeqMap::CanResolveRange (CScope *scope, TSeqPos from, TSeqPos length, ENa_strand strand=eNa_strand_plus, size_t maxResolve=size_t(-1), TFlags flags=fDefaultFlags) const
static CRef< CSeqMap >	CSeqMap::CreateSeqMapForBioseq (const CBioseq &seq)
static CRef< CSeqMap >	CSeqMap::CreateSeqMapForSeq_loc (const CSeq_loc &loc, CScope *scope)
static CConstRef< CSeqMap >	CSeqMap::GetSeqMapForSeq_loc (const CSeq_loc &loc, CScope *scope)
CRef< CSeqMap >	CSeqMap::CloneFor (const CBioseq &seq) const
	CSeqMap::CSeqMap (const CSeqMap &sm)
void	CSeqMap::SetRegionInChunk (CTSE_Chunk_Info &chunk, TSeqPos pos, TSeqPos length)
void	CSeqMap::LoadSeq_data (TSeqPos pos, TSeqPos len, const CSeq_data &data)
void	CSeqMap::SetSegmentGap (const CSeqMap_CI &seg, TSeqPos length)
void	CSeqMap::SetSegmentGap (const CSeqMap_CI &seg, TSeqPos length, CSeq_data &gap_data)
void	CSeqMap::SetSegmentData (const CSeqMap_CI &seg, TSeqPos length, CSeq_data &data)
void	CSeqMap::SetSegmentRef (const CSeqMap_CI &seg, TSeqPos length, const CSeq_id_Handle &ref_id, TSeqPos ref_pos, bool ref_minus_strand)
CSeqMap_CI	CSeqMap::InsertSegmentGap (const CSeqMap_CI &seg, TSeqPos length)
	Insert new gap into sequence map. More...
CSeqMap_CI	CSeqMap::RemoveSegment (const CSeqMap_CI &seg)
	Delete segment from sequence map. More...
void	CSeqMap::SetRepr (CSeq_inst::TRepr repr)
void	CSeqMap::ResetRepr (void)
void	CSeqMap::SetMol (CSeq_inst::TMol mol)
void	CSeqMap::ResetMol (void)
bool	CSeqMap::HasZeroGapAt (TSeqPos pos, CScope *scope=0) const
	Returns true if there is zero-length gap at position. More...
	CSeqMap::CSegment::CSegment (ESegmentType seg_type=eSeqEnd, TSeqPos length=kInvalidSeqPos, bool unknown_len=false)
	CSeqMap::CSegment::CSegment (const CSegment &seg)
CSegment &	CSeqMap::CSegment::operator= (const CSegment &seg)
bool	CSeqMap::CSegment::IsSetData (void) const
bool	CSeqMap::SPosLessSegment::operator() (TSeqPos pos, const CSegment &seg)
bool	CSeqMap::SPosLessSegment::operator() (const CSegment &seg, TSeqPos pos)
bool	CSeqMap::SPosLessSegment::operator() (const CSegment &seg1, const CSegment &seg2)
	CSeqMap::CSeqMap (CSeqMap *parent, size_t index)
	CSeqMap::CSeqMap (void)
	CSeqMap::CSeqMap (const CSeq_loc &ref)
	CSeqMap::CSeqMap (TSeqPos len)
	CSeqMap::CSeqMap (const CSeq_inst &inst)
void	CSeqMap::x_AddEnd (void)
void	CSeqMap::x_AddSegment (ESegmentType type, TSeqPos len, bool unknown_len=false)
void	CSeqMap::x_AddSegment (ESegmentType type, TSeqPos len, const CObject *object)
void	CSeqMap::x_AddSegment (ESegmentType type, const CObject *object, TSeqPos refPos, TSeqPos len, ENa_strand strand=eNa_strand_plus)
void	CSeqMap::x_AddGap (TSeqPos len, bool unknown_len)
void	CSeqMap::x_AddGap (TSeqPos len, bool unknown_len, const CSeq_data &gap_data)
void	CSeqMap::x_AddGap (TSeqPos len, bool unknown_len, const CSeq_literal &gap_data)
void	CSeqMap::x_Add (CSeqMap *submap)
void	CSeqMap::x_Add (const CSeq_data &data, TSeqPos len)
void	CSeqMap::x_Add (const CPacked_seqint &seq)
void	CSeqMap::x_Add (const CPacked_seqpnt &seq)
void	CSeqMap::x_Add (const CSeq_loc_mix &seq)
void	CSeqMap::x_Add (const CSeq_loc_equiv &seq)
void	CSeqMap::x_Add (const CSeq_literal &seq)
void	CSeqMap::x_Add (const CDelta_seq &seq)
void	CSeqMap::x_Add (const CSeq_loc &seq)
void	CSeqMap::x_Add (const CSeq_id &seq)
void	CSeqMap::x_Add (const CSeq_point &seq)
void	CSeqMap::x_Add (const CSeq_interval &seq)
void	CSeqMap::x_AddUnloadedSeq_data (TSeqPos len)
void	CSeqMap::ResolveAll (void) const
CSeqMap &	CSeqMap::operator= (const CSeqMap &)
size_t	CSeqMap::x_GetLastEndSegmentIndex (void) const
size_t	CSeqMap::x_GetFirstEndSegmentIndex (void) const
const CSegment &	CSeqMap::x_GetSegment (size_t index) const
void	CSeqMap::x_GetSegmentException (size_t index) const
CSegment &	CSeqMap::x_SetSegment (size_t index)
size_t	CSeqMap::x_FindSegment (TSeqPos position, CScope *scope) const
TSeqPos	CSeqMap::x_GetSegmentLength (size_t index, CScope *scope) const
TSeqPos	CSeqMap::x_GetSegmentPosition (size_t index, CScope *scope) const
TSeqPos	CSeqMap::x_GetSegmentEndPosition (size_t index, CScope *scope) const
TSeqPos	CSeqMap::x_ResolveSegmentLength (size_t index, CScope *scope) const
TSeqPos	CSeqMap::x_ResolveSegmentPosition (size_t index, CScope *scope) const
void	CSeqMap::x_StartEditing (void)
bool	CSeqMap::x_IsChanged (void) const
void	CSeqMap::x_SetChanged (size_t index)
bool	CSeqMap::x_UpdateSeq_inst (CSeq_inst &inst)
bool	CSeqMap::x_DoUpdateSeq_inst (CSeq_inst &inst)
const CBioseq_Info &	CSeqMap::x_GetBioseqInfo (const CSegment &seg, CScope *scope) const
CConstRef< CSeqMap >	CSeqMap::x_GetSubSeqMap (const CSegment &seg, CScope *scope, bool resolveExternal=false) const
const CSeq_data &	CSeqMap::x_GetSeq_data (const CSegment &seg) const
CConstRef< CSeq_literal >	CSeqMap::x_GetSeq_literal (const CSegment &seg) const
const CSeq_id &	CSeqMap::x_GetRefSeqid (const CSegment &seg) const
TSeqPos	CSeqMap::x_GetRefPosition (const CSegment &seg) const
bool	CSeqMap::x_GetRefMinusStrand (const CSegment &seg) const
void	CSeqMap::x_LoadObject (const CSegment &seg) const
CRef< CTSE_Chunk_Info >	CSeqMap::x_GetChunkToLoad (const CSegment &seg) const
const CObject *	CSeqMap::x_GetObject (const CSegment &seg) const
void	CSeqMap::x_SetObject (CSegment &seg, const CObject &obj)
void	CSeqMap::x_SetChunk (CSegment &seg, CTSE_Chunk_Info &chunk)
void	CSeqMap::x_SetSeq_data (size_t index, CSeq_data &data)
void	CSeqMap::x_SetSubSeqMap (size_t index, CSeqMap_Delta_seqs *subMap)
void	CSeqMap::x_SetSegmentGap (size_t index, TSeqPos length, CSeq_data *gap_data=0)
void	CSeqMap::x_SetSegmentData (size_t index, TSeqPos length, CSeq_data &data)
void	CSeqMap::x_SetSegmentRef (size_t index, TSeqPos length, const CSeq_id &ref_id, TSeqPos ref_pos, bool ref_minus_strand)
int	CSeqMap::x_GetSequenceClass (void) const
TInsertDelete	CSeqMapSwitchPoint::GetDifferences (TSeqPos new_pos, TSeqPos add=0) const
int	CSeqMapSwitchPoint::GetLengthDifference (TSeqPos new_pos, TSeqPos add=0) const
int	CSeqMapSwitchPoint::GetSequenceDifference (TSeqPos new_pos, TSeqPos add=0) const
TSeqPos	CSeqMapSwitchPoint::GetInsert (TSeqPos pos) const
TSeqPos	CSeqMapSwitchPoint::GetLeftInPlaceInsert (void) const
TSeqPos	CSeqMapSwitchPoint::GetRightInPlaceInsert (void) const
void	CSeqMapSwitchPoint::ChangeSwitchPoint (TSeqPos pos, TSeqPos add)
void	CSeqMapSwitchPoint::InsertInPlace (TSeqPos add_left, TSeqPos add_right)
bool	CSeqMapSwitchPoint::operator< (const CSeqMapSwitchPoint &p) const
CRef< CSeqMapSwitchPoint >	GetSwitchPoint (const CBioseq_Handle &seq, const CSeq_align &align)
TSeqMapSwitchPoints	GetAllSwitchPoints (const CBioseq_Handle &seq, const TSeqMapSwitchAligns &aligns)
TSeqMapSwitchPoints	GetAllSwitchPoints (const CBioseq_Handle &seq)
	CSeqVector::CSeqVector (void)
	CSeqVector::CSeqVector (const CBioseq_Handle &bioseq, EVectorCoding coding=CBioseq_Handle::eCoding_Ncbi, ENa_strand strand=eNa_strand_unknown)
	CSeqVector::CSeqVector (const CSeqMap &seqMap, CScope &scope, EVectorCoding coding=CBioseq_Handle::eCoding_Ncbi, ENa_strand strand=eNa_strand_unknown)
	CSeqVector::CSeqVector (const CSeqMap &seqMap, const CTSE_Handle &top_tse, EVectorCoding coding=CBioseq_Handle::eCoding_Ncbi, ENa_strand strand=eNa_strand_unknown)
	CSeqVector::CSeqVector (const CSeq_loc &loc, CScope &scope, EVectorCoding coding=CBioseq_Handle::eCoding_Ncbi, ENa_strand strand=eNa_strand_unknown)
	CSeqVector::CSeqVector (const CSeq_loc &loc, const CTSE_Handle &top_tse, EVectorCoding coding=CBioseq_Handle::eCoding_Ncbi, ENa_strand strand=eNa_strand_unknown)
	CSeqVector::CSeqVector (const CBioseq &bioseq, CScope *scope=0, EVectorCoding coding=CBioseq_Handle::eCoding_Ncbi, ENa_strand strand=eNa_strand_unknown)
	CSeqVector::CSeqVector (const CSeqVector &vec)
virtual	CSeqVector::~CSeqVector (void)
CSeqVector &	CSeqVector::operator= (const CSeqVector &vec)
bool	CSeqVector::empty (void) const
TSeqPos	CSeqVector::size (void) const
TMutex &	CSeqVector::GetMutex (void) const
	Get mutex for a few non-MT-safe methods to make them MT-safe at a cost of performance. More...
TResidue	CSeqVector::operator[] (TSeqPos pos) const
	0-based array of residues Note: this method is not MT-safe, do not call it in parallel with other, even MT-safe method. More...
bool	CSeqVector::IsInGap (TSeqPos pos) const
	true if sequence at 0-based position 'pos' has gap Note: this method is not MT-safe, do not call it in parallel with other, even MT-safe method. More...
TSeqPos	CSeqVector::GetGapSizeForward (TSeqPos pos) const
	returns number of gap symbols ahead including base at position 'pos' returns 0 if the position is not in gap More...
CConstRef< CSeq_literal >	CSeqVector::GetGapSeq_literal (TSeqPos pos) const
	returns gap Seq-literal object ref returns null if it's not a gap or an unspecified gap More...
bool	CSeqVector::CanGetRange (TSeqPos start, TSeqPos stop) const
	Check if the sequence data is available for the interval [start, stop). More...
bool	CSeqVector::CanGetRange (const const_iterator &start, const const_iterator &stop) const
void	CSeqVector::GetSeqData (TSeqPos start, TSeqPos stop, string &buffer) const
	Fill the buffer string with the sequence data for the interval [start, stop). More...
void	CSeqVector::GetSeqData (const const_iterator &start, const const_iterator &stop, string &buffer) const
void	CSeqVector::GetPackedSeqData (string &buffer, TSeqPos start=0, TSeqPos stop=kInvalidSeqPos)
TMol	CSeqVector::GetSequenceType (void) const
bool	CSeqVector::IsProtein (void) const
bool	CSeqVector::IsNucleotide (void) const
CScope &	CSeqVector::GetScope (void) const
const CSeqMap &	CSeqVector::GetSeqMap (void) const
ENa_strand	CSeqVector::GetStrand (void) const
void	CSeqVector::SetStrand (ENa_strand strand)
TCoding	CSeqVector::GetCoding (void) const
	Target sequence coding. More...
void	CSeqVector::SetCoding (TCoding coding)
void	CSeqVector::SetIupacCoding (void)
	Set coding to either Iupacaa or Iupacna depending on molecule type. More...
void	CSeqVector::SetNcbiCoding (void)
	Set coding to either Ncbi8aa or Ncbi8na depending on molecule type. More...
void	CSeqVector::SetCoding (EVectorCoding coding)
	Set coding to either Iupac or Ncbi8xx. More...
TResidue	CSeqVector::GetGapChar (ECaseConversion case_cvt=eCaseConversion_none) const
	Return gap symbol corresponding to the selected coding. More...
const_iterator	CSeqVector::begin (void) const
const_iterator	CSeqVector::end (void) const
void	CSeqVector::SetRandomizeAmbiguities (void)
	Randomization of ambiguities and gaps in ncbi2na coding. More...
void	CSeqVector::SetRandomizeAmbiguities (Uint4 seed)
void	CSeqVector::SetRandomizeAmbiguities (CRandom &random_gen)
void	CSeqVector::SetRandomizeAmbiguities (CRef< INcbi2naRandomizer > randomizer)
void	CSeqVector::SetNoAmbiguities (void)
void	CSeqVector::x_InitSequenceType (void)
CSeqVector_CI &	CSeqVector::x_GetIterator (TSeqPos pos) const
CSeqVector_CI *	CSeqVector::x_CreateIterator (TSeqPos pos) const
void	CSeqVector::x_ResetIterator (void) const
void	CSeqVector::x_InitRandomizer (CRandom &random_gen)
void	CSeqVector::x_GetPacked8SeqData (string &dst_str, TSeqPos src_pos, TSeqPos src_end)
void	CSeqVector::x_GetPacked4naSeqData (string &dst_str, TSeqPos src_pos, TSeqPos src_end)
void	CSeqVector::x_GetPacked2naSeqData (string &dst_str, TSeqPos src_pos, TSeqPos src_end)
	CNcbi2naRandomizer::CNcbi2naRandomizer (CRandom &gen)
	CNcbi2naRandomizer::~CNcbi2naRandomizer (void)
void	CNcbi2naRandomizer::RandomizeData (char *buffer, size_t count, TSeqPos pos)
	Convert count unpacked bases in buffer 4na -> 2na with randomization. More...

Variables
atomic< TSeqPos >	CSeqMap::CSegment::m_Position
atomic< TSeqPos >	CSeqMap::CSegment::m_Length
bool	CSeqMap::CSegment::m_UnknownLength
char	CSeqMap::CSegment::m_SegType
char	CSeqMap::CSegment::m_ObjType
bool	CSeqMap::CSegment::m_RefMinusStrand
TSeqPos	CSeqMap::CSegment::m_RefPosition
CConstRef< CObject >	CSeqMap::CSegment::m_RefObject
CBioseq_Info *	CSeqMap::m_Bioseq
vector< CSegment >	CSeqMap::m_Segments
atomic< size_t >	CSeqMap::m_Resolved
CRef< CObject >	CSeqMap::m_Delta
TMol	CSeqMap::m_Mol
atomic< THasSegments >	CSeqMap::m_HasSegments
TChanged	CSeqMap::m_Changed
atomic< TSeqPos >	CSeqMap::m_SeqLength
CMutex	CSeqMap::m_SeqMap_Mtx
CBioseq_Handle	CSeqMapSwitchPoint::m_Master
TSeqPos	CSeqMapSwitchPoint::m_MasterPos
CConstRef< CSeq_align >	CSeqMapSwitchPoint::m_FirstAlign
CSeq_id_Handle	CSeqMapSwitchPoint::m_LeftId
TSeqPos	CSeqMapSwitchPoint::m_LeftPos
bool	CSeqMapSwitchPoint::m_LeftMinusStrand
CSeq_id_Handle	CSeqMapSwitchPoint::m_RightId
TSeqPos	CSeqMapSwitchPoint::m_RightPos
bool	CSeqMapSwitchPoint::m_RightMinusStrand
CRange< TSeqPos >	CSeqMapSwitchPoint::m_MasterRange
CRange< TSeqPos >	CSeqMapSwitchPoint::m_ExactMasterRange
TDifferences	CSeqMapSwitchPoint::m_LeftDifferences
TDifferences	CSeqMapSwitchPoint::m_RightDifferences
CHeapScope	CSeqVector::m_Scope
CConstRef< CSeqMap >	CSeqVector::m_SeqMap
CTSE_Handle	CSeqVector::m_TSE
TSeqPos	CSeqVector::m_Size
TMol	CSeqVector::m_Mol
ENa_strand	CSeqVector::m_Strand
TCoding	CSeqVector::m_Coding
CRef< INcbi2naRandomizer >	CSeqVector::m_Randomizer
TMutex	CSeqVector::m_IteratorMutex
AutoPtr< CSeqVector_CI >	CSeqVector::m_Iterator
char	CNcbi2naRandomizer::m_FixedTable [16]
char	CNcbi2naRandomizer::m_RandomTable [16][kRandomDataSize]

Friends
class	CSeqMap::CSegment
class	CSeqMap::SPosLessSegment
class	CSeqMap::CSeqMap_SeqPoss
class	CSeqMap::CBioseq_Info
class	CSeqMap::CSeqMap_CI
class	CSeqMap::CSeqMap_CI_SegmentInfo
class	CSeqVector::CBioseq_Handle
class	CSeqVector::CSeqVector_CI

Detailed Description

Typedef Documentation

const_iterator [1/2]

typedef CSeqMap_CI CSeqMap::const_iterator

Definition at line 107 of file seq_map.hpp.

const_iterator [2/2]

typedef CSeqVector_CI CSeqVector::const_iterator

Definition at line 68 of file seq_vector.hpp.

EVectorCoding

typedef CBioseq_Handle::EVectorCoding CSeqVector::EVectorCoding

Definition at line 67 of file seq_vector.hpp.

TChanged

typedef bool CSeqMap::TChanged

protected

Definition at line 400 of file seq_map.hpp.

TDifferences

typedef map<TSeqPos, TInsertDelete> CSeqMapSwitchPoint::TDifferences

Definition at line 89 of file seq_map_switch.hpp.

TFlags

typedef int CSeqMap::TFlags

Definition at line 142 of file seq_map.hpp.

THasSegments

typedef Uint1 CSeqMap::THasSegments

protected

Definition at line 397 of file seq_map.hpp.

TInsertDelete

typedef pair<TSeqPos, TSeqPos> CSeqMapSwitchPoint::TInsertDelete

Definition at line 87 of file seq_map_switch.hpp.

TMol [1/2]

typedef CSeq_inst::TMol CSeqMap::TMol

Definition at line 106 of file seq_map.hpp.

TMol [2/2]

typedef CSeq_inst::TMol CSeqVector::TMol

Definition at line 141 of file seq_vector.hpp.

TMutex

typedef CMutex CSeqVector::TMutex

Definition at line 69 of file seq_vector.hpp.

TMutexGuard

typedef TMutex::TWriteLockGuard CSeqVector::TMutexGuard

Definition at line 70 of file seq_vector.hpp.

TSegments

typedef vector<CSegment> CSeqMap::TSegments

protected

Definition at line 382 of file seq_map.hpp.

TSeqLength

typedef TSeqPos TSeqLength

Definition at line 74 of file seq_map.hpp.

TSeqMapSwitchAligns

typedef list<CRef<CSeq_align> > TSeqMapSwitchAligns

Definition at line 129 of file seq_map_switch.hpp.

TSeqMapSwitchPoints

typedef vector<CRef<CSeqMapSwitchPoint> > TSeqMapSwitchPoints

Definition at line 128 of file seq_map_switch.hpp.

TSeqPosition

typedef TSeqPos TSeqPosition

Definition at line 73 of file seq_map.hpp.

Enumeration Type Documentation

anonymous enum

anonymous enum

private

Enumerator
kRandomizerPosMask
kRandomDataSize
kRandomValue

Definition at line 230 of file seq_vector.hpp.

EFlags

enum CSeqMap::EFlags

Segment type flags.

Enumerator
fFindData
fFindGap
fFindLeafRef
fFindInnerRef
fFindExactLevel
fIgnoreUnresolved
fByFeaturePolicy
fBySequenceClass
fFindRef
fFindAny
fFindAnyLeaf
fDefaultFlags

Definition at line 128 of file seq_map.hpp.

ESegmentType

enum CSeqMap::ESegmentType

Enumerator
eSeqGap	gap
eSeqData	real sequence data
eSeqSubMap	sub seqmap
eSeqRef	reference to Bioseq
eSeqEnd
eSeqChunk
eSeqLiteral	used only in m_ObjType for gap segments

Definition at line 96 of file seq_map.hpp.

Function Documentation

begin() [1/2]

CSeqMap::const_iterator CSeqMap::begin

(

CScope *

scope

)

const

STL style methods.

Definition at line 818 of file seq_map.cpp.

References CSeqMap::Begin().

Referenced by GetAllSwitchPoints(), GetSwitchPoint(), and CDemoApp::Run().

Begin()

CSeqMap_CI CSeqMap::Begin

(

CScope *

scope

)

const

NCBI style methods.

Definition at line 799 of file seq_map.cpp.

References CSeqMap::CSeqMap_CI.

Referenced by CSeqMap::begin(), CTestSingleAln_All::RunTest(), and s_AgpWrite().

begin() [2/2]

CSeqVector_CI CSeqVector::begin ( void  ) const

inline

Definition at line 298 of file seq_vector.hpp.

References CSeqVector::CSeqVector_CI.

Referenced by CSplignFormatter::AsAlignmentText(), BOOST_AUTO_TEST_CASE(), CNewCleanup_imp::CdRegionEC(), CChain::CollectTrustedmRNAsProts(), CAnnotCompare::CompareFeats(), Does3primerAbutGap(), Does5primerAbutGap(), ExtendCDSToStopCodon(), ExtendToStopCodon(), CCleanup::ExtendToStopCodon(), variation::FindSSRLoc(), CInternalStopFinder::FindStartStopRanges(), CInternalStopFinder::GetCDSNucleotideSequence(), CExtendCDSToStop::GetCommand(), CBlastSeqVectorOM::GetCompressedPlusStrand(), CPostProcessUtils::GetLiteralAtLoc(), s_GetPolyA_genomic_priming(), CSeqTranslator::TranslateToProtein(), variation_ref::CHgvsParser::CContext::Validate(), CAgpFastaComparator::CTmpSeqVecStorage::WriteData(), CGapAnalysis::x_AddGapsFromBases(), CFeatureItem::x_AddQualsProt(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CFeaturePropagator::x_ExtendToStopCodon(), CVariationUtilities::x_GetAlleleFromLoc(), variation_ref::CVariationUtil::x_GetLiteralAtLoc(), variation::CVariationUtil::x_GetLiteralAtLoc(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), variation::CVariationUtil::x_InferNAfromAA(), variation_ref::CHgvsParser::x_LocToSeqStr(), variation::CHgvsParser::x_LocToSeqStr(), variation_ref::CVariationUtil::x_ProtToPrecursor(), and CValidError_graph::x_ValidateGraphValues().

BeginResolved() [1/2]

CSeqMap_CI CSeqMap::BeginResolved

(

CScope *

scope

)

const

Definition at line 837 of file seq_map.cpp.

References CSeqMap::CSeqMap_CI, kMax_UInt, and SSeqMapSelector::SetResolveCount().

Referenced by CBioseq_Handle::ContainsSegment(), CFlatGatherer::x_DoMultipleSections(), and CMasterContext::x_SetBaseName().

BeginResolved() [2/2]

CSeqMap_CI CSeqMap::BeginResolved	(	CScope *	scope,
		const SSeqMapSelector &	selector
	)		const

Definition at line 830 of file seq_map.cpp.

References CSeqMap::CSeqMap_CI.

CanGetRange() [1/2]

bool CSeqVector::CanGetRange ( const const_iterator &  start, const const_iterator &  stop  ) const

inline

Definition at line 364 of file seq_vector.hpp.

References CSeqVector::CanGetRange(), and CSeqVector_CI::GetPos().

CanGetRange() [2/2]

bool CSeqVector::CanGetRange	(	TSeqPos	start,
		TSeqPos	stop
	)		const

Check if the sequence data is available for the interval [start, stop).

Definition at line 292 of file seq_vector.cpp.

References CSeqVector_CI::CanGetRange(), CSeqVector::GetMutex(), and CSeqVector::x_GetIterator().

Referenced by CSeqVector::CanGetRange(), CSeqVector::GetPackedSeqData(), CBioseqIndex::GetSequence(), CFeatureIndex::GetSequence(), CDemoApp::Run(), and CAgpFastaComparator::x_Process().

CanResolveRange() [1/2]

bool CSeqMap::CanResolveRange	(	CScope *	scope,
		const SSeqMapSelector &	sel
	)		const

Definition at line 986 of file seq_map.cpp.

References _ASSERT, SSeqMapSelector::AddUsedTSE(), ConstRef(), CSeqMap::eSeqRef, CSeqMap::fFindAnyLeaf, Get(), AutoPtr< X, Del >::get(), CScope::GetBioseqHandles(), CDataLoader::GetChunks(), CSeqMap::GetLength(), CSeqMap_CI::GetLength(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefSeqid(), CSeqMap_CI::GetType(), i, kInvalidSeqPos, SSeqMapSelector::m_Length, SSeqMapSelector::m_LinkUsedTSE, SSeqMapSelector::m_MaxResolveCount, SSeqMapSelector::m_Position, CSeqMap_CI::m_Selector, SSeqMapSelector::m_TopTSE, CSeqMap_CI_SegmentInfo::m_TSE, SSeqMapSelector::SetFlags(), SSeqMapSelector::SetResolveCount(), ct::sort(), CSeqMap::x_GetChunkToLoad(), CSeqMap_CI::x_GetSegment(), CSeqMap_CI::x_GetSegmentInfo(), CSeqMap_CI::x_GetSeqMap(), and SSeqMapSelector::x_HasLimitTSE().

Referenced by CSeqVector_CI::CanGetRange(), CSeqMap::CanResolveRange(), CAsn2FastaApp::HandleSeqEntry(), LoadSequencesToScope(), and CFastaOstream::WriteSequence().

CanResolveRange() [2/2]

bool CSeqMap::CanResolveRange	(	CScope *	scope,
		TSeqPos	from,
		TSeqPos	length,
		ENa_strand	strand = eNa_strand_plus,
		size_t	maxResolve = size_t(-1),
		TFlags	flags = fDefaultFlags
	)		const

Definition at line 949 of file seq_map.cpp.

References CSeqMap::CanResolveRange(), depth, flags, SSeqMapSelector::SetFlags(), SSeqMapSelector::SetRange(), SSeqMapSelector::SetResolveCount(), and SSeqMapSelector::SetStrand().

ChangeSwitchPoint()

void CSeqMapSwitchPoint::ChangeSwitchPoint	(	TSeqPos	pos,
		TSeqPos	add
	)

Definition at line 498 of file seq_map_switch.cpp.

References _ASSERT, CSeqMap::eSeqRef, CSeqMap::FindSegment(), CRange_Base::GetFrom(), CSeqMapSwitchPoint::GetInsert(), CSeqMap_CI::GetLength(), CSeqMapSwitchPoint::GetLengthDifference(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefMinusStrand(), CSeqMap_CI::GetRefPosition(), CSeqMap_CI::GetRefSeqid(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqMap(), CRange_Base::GetTo(), CSeqMap_CI::GetType(), len, CSeqMapSwitchPoint::m_LeftId, CSeqMapSwitchPoint::m_LeftMinusStrand, CSeqMapSwitchPoint::m_LeftPos, CSeqMapSwitchPoint::m_Master, CSeqMapSwitchPoint::m_MasterPos, CSeqMapSwitchPoint::m_MasterRange, CSeqMapSwitchPoint::m_RightId, CSeqMapSwitchPoint::m_RightMinusStrand, CSeqMapSwitchPoint::m_RightPos, NCBI_THROW, and CSeqMap::SetSegmentRef().

CloneFor()

CRef< CSeqMap > CSeqMap::CloneFor

(

const CBioseq &

seq

)

const

Definition at line 1128 of file seq_map.cpp.

References CSeqMap::CreateSeqMapForBioseq().

CNcbi2naRandomizer()

CNcbi2naRandomizer::CNcbi2naRandomizer

(

CRandom &

gen

)

Definition at line 63 of file seq_vector.cpp.

References gen, i, CNcbi2naRandomizer::kRandomDataSize, CNcbi2naRandomizer::kRandomValue, CNcbi2naRandomizer::m_FixedTable, CNcbi2naRandomizer::m_RandomTable, rnd(), and bm::set_bit().

CountSegmentsOfType()

size_t CSeqMap::CountSegmentsOfType

(

ESegmentType

type

)

const

Definition at line 895 of file seq_map.cpp.

References count, ITERATE, and CSeqMap::m_Segments.

CreateSeqMapForBioseq()

CRef< CSeqMap > CSeqMap::CreateSeqMapForBioseq ( const CBioseq &  seq )

static

Definition at line 1122 of file seq_map.cpp.

References CSeqMap::CSeqMap(), CBioseq_Base::GetInst(), and Ref().

Referenced by CDiscrepancyContext::BuildSeqSummary(), CSeqMap::CloneFor(), and CBioseq_Info::GetSeqMap().

CreateSeqMapForSeq_loc()

CRef< CSeqMap > CSeqMap::CreateSeqMapForSeq_loc ( const CSeq_loc &  loc, CScope *  scope  )

static

Definition at line 1134 of file seq_map.cpp.

References CSeqMap::CSeqMap(), CSeq_inst_Base::eMol_not_set, CSeqMap::eSeqEnd, CSeqMap::eSeqRef, CScope::GetBioseqHandle(), CBioseq_Handle::GetSequenceType(), i, CSeqMap::m_Mol, CSeqMap::CSegment::m_SegType, CSeqMap::x_GetRefSeqid(), and CSeqMap::x_GetSegment().

Referenced by GetSequenceFromLoc(), CAsn2FastaApp::HandleSeqEntry(), s_CreateGapMapIter(), s_SeqMapForHandle(), and CFlatGatherer::x_GatherReferences().

CSegment() [1/2]

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

inline

Definition at line 87 of file seq_map.cpp.

CSegment() [2/2]

CSeqMap::CSegment::CSegment ( ESegmentType  seg_type = eSeqEnd, TSeqPos  length = kInvalidSeqPos, bool  unknown_len = false  )

inline

Definition at line 72 of file seq_map.cpp.

CSeqMap() [1/6]

CSeqMap::CSeqMap ( const CSeq_inst &  inst )

protected

Definition at line 202 of file seq_map.cpp.

References CSeq_ext_Base::e_Delta, CSeq_ext_Base::e_Map, CSeq_ext_Base::e_Ref, CSeq_ext_Base::e_Seg, CSeq_inst_Base::eRepr_map, CSeq_inst_Base::eRepr_not_set, CSeq_inst_Base::eRepr_virtual, CDelta_ext_Base::Get(), CSeg_ext_Base::Get(), CSeq_ext_Base::GetDelta(), CSeq_inst_Base::GetExt(), CSeq_inst_Base::GetLength(), CSeq_inst_Base::GetMol(), CSeq_ext_Base::GetRef(), CSeq_inst_Base::GetRepr(), CSeq_ext_Base::GetSeg(), CSeq_inst_Base::GetSeq_data(), CSeq_data_Base::IsGap(), CSeq_inst_Base::IsSetExt(), CSeq_inst_Base::IsSetLength(), CSeq_inst_Base::IsSetMol(), CSeq_inst_Base::IsSetSeq_data(), ITERATE, kInvalidSeqPos, CSeqMap::m_Mol, CSeqMap::m_SeqLength, NCBI_THROW, CSeq_ext_Base::Which(), CSeqMap::x_Add(), CSeqMap::x_AddEnd(), and CSeqMap::x_AddGap().

CSeqMap() [2/6]

CSeqMap::CSeqMap ( const CSeq_loc &  ref )

protected

Definition at line 141 of file seq_map.cpp.

References CSeqMap::x_Add(), and CSeqMap::x_AddEnd().

CSeqMap() [3/6]

CSeqMap::CSeqMap

(

const CSeqMap &

sm

)

Definition at line 182 of file seq_map.cpp.

References CSeqMap::eSeqChunk, CSeqMap::eSeqGap, CSeqMap::m_Segments, and NON_CONST_ITERATE.

CSeqMap() [4/6]

CSeqMap::CSeqMap ( CSeqMap *  parent, size_t  index  )

protected

Definition at line 130 of file seq_map.cpp.

CSeqMap() [5/6]

CSeqMap::CSeqMap ( TSeqPos  len )

protected

Definition at line 168 of file seq_map.cpp.

References CSeqMap::x_AddEnd(), and CSeqMap::x_AddGap().

CSeqMap() [6/6]

CSeqMap::CSeqMap ( void  )

protected

Definition at line 119 of file seq_map.cpp.

Referenced by CSeqMap::CreateSeqMapForBioseq(), CSeqMap::CreateSeqMapForSeq_loc(), and CSeqMap::GetSeqMapForSeq_loc().

CSeqVector() [1/8]

CSeqVector::CSeqVector	(	const CBioseq &	bioseq,
		CScope *	scope = 0,
		EVectorCoding	coding = CBioseq_Handle::eCoding_Ncbi,
		ENa_strand	strand = eNa_strand_unknown
	)

Definition at line 225 of file seq_vector.cpp.

References CBioseq_Base::GetInst(), CSeqMap::GetLength(), CSeq_inst_Base::GetMol(), CSeqVector::m_Mol, CSeqVector::m_SeqMap, CSeqVector::m_Size, and CSeqVector::SetCoding().

CSeqVector() [2/8]

CSeqVector::CSeqVector ( const CBioseq_Handle &  bioseq, EVectorCoding  coding = CBioseq_Handle::eCoding_Ncbi, ENa_strand  strand = eNa_strand_unknown  )

explicit

Definition at line 152 of file seq_vector.cpp.

References CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetSequenceType(), CSeqVector::m_Mol, CSeqVector::m_Size, and CSeqVector::SetCoding().

CSeqVector() [3/8]

CSeqVector::CSeqVector	(	const CSeq_loc &	loc,
		const CTSE_Handle &	top_tse,
		EVectorCoding	coding = CBioseq_Handle::eCoding_Ncbi,
		ENa_strand	strand = eNa_strand_unknown
	)

Definition at line 211 of file seq_vector.cpp.

References CSeqMap::GetLength(), CSeqMap::GetMol(), CSeqVector::m_Mol, CSeqVector::m_Scope, CSeqVector::m_SeqMap, CSeqVector::m_Size, and CSeqVector::SetCoding().

CSeqVector() [4/8]

CSeqVector::CSeqVector	(	const CSeq_loc &	loc,
		CScope &	scope,
		EVectorCoding	coding = CBioseq_Handle::eCoding_Ncbi,
		ENa_strand	strand = eNa_strand_unknown
	)

Definition at line 193 of file seq_vector.cpp.

References CScope::GetBioseqHandle(), CSeq_loc::GetId(), CSeqMap::GetLength(), CSeqMap::GetMol(), CSeqVector::m_Mol, CSeqVector::m_Scope, CSeqVector::m_SeqMap, CSeqVector::m_Size, CSeqVector::m_TSE, and CSeqVector::SetCoding().

CSeqVector() [5/8]

CSeqVector::CSeqVector	(	const CSeqMap &	seqMap,
		const CTSE_Handle &	top_tse,
		EVectorCoding	coding = CBioseq_Handle::eCoding_Ncbi,
		ENa_strand	strand = eNa_strand_unknown
	)

Definition at line 179 of file seq_vector.cpp.

References CSeqMap::GetLength(), CSeqMap::GetMol(), CSeqVector::m_Mol, CSeqVector::m_Scope, CSeqVector::m_SeqMap, CSeqVector::m_Size, and CSeqVector::SetCoding().

CSeqVector() [6/8]

CSeqVector::CSeqVector	(	const CSeqMap &	seqMap,
		CScope &	scope,
		EVectorCoding	coding = CBioseq_Handle::eCoding_Ncbi,
		ENa_strand	strand = eNa_strand_unknown
	)

Definition at line 166 of file seq_vector.cpp.

References CSeqMap::GetLength(), CSeqMap::GetMol(), CSeqVector::m_Mol, CSeqVector::m_Scope, CSeqVector::m_SeqMap, CSeqVector::m_Size, and CSeqVector::SetCoding().

CSeqVector() [7/8]

CSeqVector::CSeqVector

(

const CSeqVector &

vec

)

Definition at line 140 of file seq_vector.cpp.

CSeqVector() [8/8]

CSeqVector::CSeqVector

(

void

)

Definition at line 134 of file seq_vector.cpp.

empty()

bool CSeqVector::empty ( void  ) const

inline

Definition at line 284 of file seq_vector.hpp.

References CSeqVector::m_Size.

Referenced by CSeqVectorCache::GetSeq(), CSeqVectorCache::PrefetchSequence(), CGapFeatValidator::Validate(), CSingleFeatValidator::x_CalculateLocationGaps(), CSingleFeatValidator::x_IsMostlyNs(), and CSingleFeatValidator::x_ValidateRptUnitVal().

end() [1/2]

CSeqMap::const_iterator CSeqMap::end

(

CScope *

scope

)

const

Definition at line 824 of file seq_map.cpp.

References CSeqMap::End().

Referenced by CDemoApp::Run().

End()

CSeqMap_CI CSeqMap::End

(

CScope *

scope

)

const

Definition at line 805 of file seq_map.cpp.

References CSeqMap::CSeqMap_CI, and kMax_UInt.

Referenced by CSeqMap::end().

end() [2/2]

CSeqVector_CI CSeqVector::end ( void  ) const

inline

Definition at line 305 of file seq_vector.hpp.

References CSeqVector::CSeqVector_CI, and CSeqVector::size().

Referenced by CSplignFormatter::AsAlignmentText(), BOOST_AUTO_TEST_CASE(), CNewCleanup_imp::CdRegionEC(), CChain::CollectTrustedmRNAsProts(), CAnnotCompare::CompareFeats(), variation::FindSSRLoc(), CInternalStopFinder::FindStartStopRanges(), CInternalStopFinder::GetCDSNucleotideSequence(), CBlastSeqVectorOM::GetCompressedPlusStrand(), CPostProcessUtils::GetLiteralAtLoc(), GetProteinWeight(), s_GetPolyA_genomic_priming(), variation_ref::CHgvsParser::CContext::Validate(), CAgpFastaComparator::CTmpSeqVecStorage::WriteData(), CFeatureItem::x_AddQualsProt(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CVariationUtilities::x_GetAlleleFromLoc(), variation_ref::CVariationUtil::x_GetLiteralAtLoc(), variation::CVariationUtil::x_GetLiteralAtLoc(), CFeatureGenerator::SImplementation::x_HandleRnaExceptions(), variation::CVariationUtil::x_InferNAfromAA(), variation_ref::CHgvsParser::x_LocToSeqStr(), variation::CHgvsParser::x_LocToSeqStr(), variation_ref::CVariationUtil::x_ProtToPrecursor(), and CValidError_graph::x_ValidateGraphValues().

EndResolved() [1/2]

CSeqMap_CI CSeqMap::EndResolved

(

CScope *

scope

)

const

Definition at line 845 of file seq_map.cpp.

References CSeqMap::CSeqMap_CI, kMax_UInt, and SSeqMapSelector::SetResolveCount().

EndResolved() [2/2]

CSeqMap_CI CSeqMap::EndResolved	(	CScope *	scope,
		const SSeqMapSelector &	selector
	)		const

Definition at line 853 of file seq_map.cpp.

References CSeqMap::CSeqMap_CI, and kMax_UInt.

FindResolved()

CSeqMap_CI CSeqMap::FindResolved	(	CScope *	scope,
		TSeqPos	pos,
		const SSeqMapSelector &	selector
	)		const

Definition at line 860 of file seq_map.cpp.

References CSeqMap::CSeqMap_CI.

FindSegment()

CSeqMap_CI CSeqMap::FindSegment	(	TSeqPos	pos,
		CScope *	scope
	)		const

Find segment containing the position.

Definition at line 812 of file seq_map.cpp.

References CSeqMap::CSeqMap_CI.

Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint(), CSequenceAmbigTrimmer::x_CountAmbigInRange(), CSequenceAmbigTrimmer::x_EdgeSeqMapGapAdjust(), and CBioseqGaps_CI::x_FindNextGapOnBioseq().

GetAllSwitchPoints() [1/2]

TSeqMapSwitchPoints GetAllSwitchPoints

(

const CBioseq_Handle &

seq

)

Definition at line 647 of file seq_map_switch.cpp.

References GetAllSwitchPoints(), CSeq_hist_Base::GetAssembly(), and CBioseq_Handle::GetInst_Hist().

GetAllSwitchPoints() [2/2]

TSeqMapSwitchPoints GetAllSwitchPoints	(	const CBioseq_Handle &	seq,
		const TSeqMapSwitchAligns &	aligns
	)

Definition at line 619 of file seq_map_switch.cpp.

References CSeqMap::begin(), CSeqMap::eSeqRef, CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqMap(), CSeqMap_CI::GetType(), info, ITERATE, and NCBI_THROW.

Referenced by GetAllSwitchPoints(), and CSGSwitchPointJob::x_Execute().

GetCoding()

CSeqVector::TCoding CSeqVector::GetCoding ( void  ) const

inline

Target sequence coding.

CSeq_data::e_not_set – do not convert sequence (use GetCoding() to check the real coding).

Definition at line 312 of file seq_vector.hpp.

References CSeqVector::m_Coding.

Referenced by g_ConvertDeltaToRawSeq(), CSeqVector::GetGapChar(), CSeqVector::GetPackedSeqData(), CValidError_bioseq::x_CalculateNsStretchAndTotal(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), CSeqVector::x_GetPacked8SeqData(), CPromote::x_PromoteRna(), and CSequenceAmbigTrimmer::x_SliceBioseq().

GetDifferences()

CSeqMapSwitchPoint::TInsertDelete CSeqMapSwitchPoint::GetDifferences	(	TSeqPos	new_pos,
		TSeqPos	add = 0
	)		const

Definition at line 437 of file seq_map_switch.cpp.

References CSeqMapSwitchPoint::m_LeftDifferences, CSeqMapSwitchPoint::m_MasterPos, and CSeqMapSwitchPoint::m_RightDifferences.

Referenced by CSeqMapSwitchPoint::GetLengthDifference(), and CSeqMapSwitchPoint::GetSequenceDifference().

GetGapChar()

CSeqVector::TResidue CSeqVector::GetGapChar ( ECaseConversion  case_cvt = eCaseConversion_none ) const

inline

Return gap symbol corresponding to the selected coding.

Definition at line 318 of file seq_vector.hpp.

References CSeqVector::GetCoding(), and CSeqVectorTypes::sx_GetGapChar().

Referenced by CAlnVec::GetGapChar(), CGapAnalysis::x_AddGapsFromBases(), CBioseqGaps_CI::x_FindNextGapOnBioseq(), CSeqVector::x_GetPacked4naSeqData(), CSeqVector::x_GetPacked8SeqData(), and CFastaOstream::x_WriteSequence().

GetGapSeq_literal()

CConstRef< CSeq_literal > CSeqVector::GetGapSeq_literal

(

TSeqPos

pos

)

const

returns gap Seq-literal object ref returns null if it's not a gap or an unspecified gap

Definition at line 285 of file seq_vector.cpp.

References CSeqVector_CI::GetGapSeq_literal(), CSeqVector::GetMutex(), and CSeqVector::x_GetIterator().

Referenced by CDemoApp::Run().

GetGapSizeForward()

TSeqPos CSeqVector::GetGapSizeForward

(

TSeqPos

pos

)

const

returns number of gap symbols ahead including base at position 'pos' returns 0 if the position is not in gap

Definition at line 278 of file seq_vector.cpp.

References CSeqVector_CI::GetGapSizeForward(), CSeqVector::GetMutex(), and CSeqVector::x_GetIterator().

Referenced by CDemoApp::Run().

GetInsert()

TSeqPos CSeqMapSwitchPoint::GetInsert

(

TSeqPos

pos

)

const

Definition at line 450 of file seq_map_switch.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), CRange_Base::GetFrom(), CRange_Base::GetTo(), CSeqMapSwitchPoint::m_LeftDifferences, CSeqMapSwitchPoint::m_Master, CSeqMapSwitchPoint::m_MasterPos, CSeqMapSwitchPoint::m_MasterRange, CSeqMapSwitchPoint::m_RightDifferences, NCBI_THROW, and offset.

Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint().

GetLeftInPlaceInsert()

TSeqPos CSeqMapSwitchPoint::GetLeftInPlaceInsert

(

void

)

const

Definition at line 478 of file seq_map_switch.cpp.

References map_checker< Container >::begin(), map_checker< Container >::empty(), and CSeqMapSwitchPoint::m_LeftDifferences.

Referenced by CSeqMapSwitchPoint::InsertInPlace().

GetLength()

TSeqPos CSeqMap::GetLength ( CScope *  scope ) const

inline

Definition at line 482 of file seq_map.hpp.

References kInvalidSeqPos, CSeqMap::m_SeqLength, CSeqMap::x_GetLastEndSegmentIndex(), and CSeqMap::x_GetSegmentPosition().

Referenced by AgpWrite(), CSeqMap::CanResolveRange(), CSeqVector::CSeqVector(), CBioseq_Handle::GetBioseqLength(), CBioseq_Info::GetInst_Length(), CSeqMap::HasZeroGapAt(), CSeqMap::x_DoUpdateSeq_inst(), CSeqVector_CI::x_GetSize(), CSeqMap::x_ResolveSegmentLength(), and CSeqMap_CI::x_Select().

GetLengthDifference()

int CSeqMapSwitchPoint::GetLengthDifference ( TSeqPos  new_pos, TSeqPos  add = 0  ) const

inline

Definition at line 95 of file seq_map_switch.hpp.

References CSeqMapSwitchPoint::GetDifferences().

Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint().

GetMol()

CSeqMap::TMol CSeqMap::GetMol ( void  ) const

inline

Definition at line 492 of file seq_map.hpp.

References CSeqMap::m_Mol.

Referenced by CSeqVector::CSeqVector(), and CDemoApp::Run().

GetMutex()

CSeqVector::TMutex & CSeqVector::GetMutex ( void  ) const

inline

Get mutex for a few non-MT-safe methods to make them MT-safe at a cost of performance.

Definition at line 263 of file seq_vector.hpp.

References CSeqVector::m_IteratorMutex.

Referenced by CSeqVector::CanGetRange(), CSeqVector::GetGapSeq_literal(), CSeqVector::GetGapSizeForward(), CSeqVector::GetSeqData(), CSeqVector::operator=(), CDemoApp::Run(), and CSeqVector::x_ResetIterator().

GetPackedSeqData()

void CSeqVector::GetPackedSeqData	(	string &	buffer,
		TSeqPos	start = 0,
		TSeqPos	stop = kInvalidSeqPos
	)

Definition at line 311 of file seq_vector.cpp.

References CSeqVector::CanGetRange(), CSeq_data_Base::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeq_data_Base::e_Ncbi2na, CSeq_data_Base::e_Ncbi4na, CSeq_data_Base::e_Ncbi8aa, CSeq_data_Base::e_Ncbi8na, CSeq_data_Base::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, CSeqVector::GetCoding(), CSeqVector::m_TSE, min(), NCBI_THROW_FMT, CSeqVector::size(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), and CSeqVector::x_GetPacked8SeqData().

Referenced by CBlastSequenceSource::GetSeq(), and CSequenceAmbigTrimmer::x_SliceBioseq().

GetRightInPlaceInsert()

TSeqPos CSeqMapSwitchPoint::GetRightInPlaceInsert

(

void

)

const

Definition at line 488 of file seq_map_switch.cpp.

References map_checker< Container >::begin(), map_checker< Container >::empty(), and CSeqMapSwitchPoint::m_RightDifferences.

Referenced by CSeqMapSwitchPoint::InsertInPlace().

GetScope()

CScope & CSeqVector::GetScope ( void  ) const

inline

Definition at line 330 of file seq_vector.hpp.

References CSeqVector::m_Scope.

Referenced by GetMismatches(), CSequenceAmbigTrimmer::x_CountAmbigInRange(), CSequenceAmbigTrimmer::x_EdgeSeqMapGapAdjust(), and CCDSTranslationProblems::x_GetTranslationMismatches().

GetSegmentsCount()

size_t CSeqMap::GetSegmentsCount ( void  ) const

inline

Definition at line 426 of file seq_map.hpp.

References CSeqMap::m_Segments.

Referenced by s_AgpWrite(), and CSeqMap::x_DoUpdateSeq_inst().

GetSeqData() [1/2]

void CSeqVector::GetSeqData ( const const_iterator &  start, const const_iterator &  stop, string &  buffer  ) const

inline

Definition at line 372 of file seq_vector.hpp.

References buffer, CSeqVector_CI::GetPos(), and CSeqVector::GetSeqData().

GetSeqData() [2/2]

void CSeqVector::GetSeqData	(	TSeqPos	start,
		TSeqPos	stop,
		string &	buffer
	)		const

Fill the buffer string with the sequence data for the interval [start, stop).

Definition at line 304 of file seq_vector.cpp.

References buffer, CSeqVector::GetMutex(), CSeqVector_CI::GetSeqData(), and CSeqVector::x_GetIterator().

Referenced by CSAM_CIGAR_Formatter::AddRow(), CAdjustForConsensusSpliceSite::AdjustCDS(), CAdjustForConsensusSpliceSite::AdjustCDSEnds(), CExpandGaps::apply(), CSplignFormatter::AsAlignmentText(), CContigAssembly::BandedGlobalAlignment(), BOOST_AUTO_TEST_CASE(), CEquivRangeBuilder::CalcMatches(), CAlnVec::CalculateScore(), CPrefetchSeqData::Execute(), ExtendLocationForTranslExcept(), CFindRSites::Find(), variation::FindSSRLoc(), CInternalStopFinder::FindStartStopRanges(), COrf::FindStrongKozakUOrfs(), CFlatAnticodonQVal::Format(), g_ConvertDeltaToRawSeq(), CScore_SegPct::Get(), CScore_Entropy::Get(), NSnp::GetAlleles(), CAlnVec::GetAlnSeqString(), CSparseAlignment::GetAlnSeqString(), CDensegGraphicDataSource::GetAlnSeqString(), CSparseAln::GetAlnSeqString(), CProjectedMappingInfo::GetAnchorSequence(), CInternalStopFinder::GetCDSNucleotideSequence(), CAlnVec::GetColumnVector(), CAddGlobalCodeBreak::GetCommand(), CEditSequenceEnds::GetCommand(), CBlastSeqVectorOM::GetCompressedPlusStrand(), GetDNASequence(), CEditSequence::GetFeatures(), CSimpleOM::GetIupac(), CPostProcessUtils::GetLiteralAtLoc(), GetLoc(), GetProteinString(), CAlnVec::GetResidue(), CPaintAlignment::GetSegments(), CSeqVectorCache::GetSeq(), CSeqVector::GetSeqData(), GetSeqsStatus(), CAlnWriter::GetSeqString(), CGuiObjectInfoSeq_align::GetSeqString(), CDensegGraphicDataSource::GetSeqString(), CAlnVec::GetSeqString(), CAlnMixSeq::GetSeqString(), CSparseAln::GetSeqString(), CSparseAlignment::GetSeqString(), CBioseqIndex::GetSequence(), CFeatureIndex::GetSequence(), CEditingActionFeatTranslation::GetValue(), sequpd::HaveIdenticalResidues(), CAlignCollapser::CPartialString::Init(), IsExtendableLeft(), IsExtendableRight(), CGuiObjectInfoSeq_align::IsPolyA(), CSeqTextDataSourceInterval::LookForSpliceJunctions(), CRestoreRNAediting::OnApply(), CFlatFileSeqBlockIterator::operator*(), CTabularFormatter_MismatchPositions::Print(), RemoteFetchLongNucleotideBioseq(), CHitMatrixSeqGraph::Render(), RetrievePartsOfLargeChromosome(), CAlnVec::RetrieveSegmentSequences(), CDemoApp::Run(), CSampleObjmgrApplication::Run(), CTestSingleAln_All::RunTest(), CTestTranscript_PolyA::RunTest(), s_CdsStartCodon(), s_CdsStopCodon(), s_CodonVariation(), CUpdateSeq_Input::s_ConvertDeltaToRawBioseq(), s_CountAmbiguities(), s_DumpSequences_wRange(), CSequenceUpdater::s_ExtendOneEndOfSequence(), ApplyCDSFrame::s_FindMatchingFrame(), CMacroFunction_ApplyCDSFrame::s_FindMatchingFrame(), s_GetPolyA_genomic_priming(), s_GetQuerySequence(), s_GetSplicedSegIdentityMismatch(), s_OrfExtension(), s_RunBlast2NWSeq(), ScanForCpGs(), SeqLocToBioseq(), CSeqUtils::SeqLocToBioseq(), CIgBlastTabularInfo::SetAirrFormatData(), CMultAlign::SetGenomic(), CIgBlastTabularInfo::SetIgAnnotation(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CCDSTranslationPanel::TransferDataToWindow(), TrimStopsFromCompleteCDS(), UpdateSeqLength(), CAssemblyGapValidator::Validate(), CGapFeatValidator::Validate(), variation_ref::CHgvsParser::CContext::Validate(), CProductStringBuilder::x_AddExon(), CFeatureItem::x_AddFTableAnticodon(), CFeatureItem::x_AddQualsProt(), CFeatureItem::x_AddQualsRna(), CFeatureItem::x_AddQualTranslation(), CAdjustForConsensusSpliceSite::x_AdjustCDS3End(), CAdjustForConsensusSpliceSite::x_AdjustCDS5End(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CSingleFeatValidator::x_CalculateLocationGaps(), CSGAlignStatJob::x_CollectAlignStats(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CWriteDB_Impl::x_CookSequence(), CFeatureGenerator::SImplementation::x_CreateCdsFeature(), CSGAlignStatJob::x_CreatePileUpGraphs(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CURLTooltipHandler::x_DisplayForwardStrandRegion(), CURLTooltipHandler::x_DisplayReverseStrandRegion(), CCpgSearchJob::x_DoSearch(), COrfSearchJob::x_DoSearch(), CCdsGlyph::x_Draw(), CAlignGlyph::x_DrawAlignRowSequence(), CCdsGlyph::x_DrawProjectedProtSeq(), CCdsGlyph::x_DrawProtSeqWithMapping(), CFeatGlyph::x_DrawRNAProductSequence(), CAlignGlyph::x_DrawUnalignedRowSequence(), CSFTranslationJob::x_Execute(), CSequenceUpdater::x_ExtendOneEnd(), CVariationUtilities::x_GetAlleleFromLoc(), CDensegGraphicDataSource::x_GetAlnStringFromCigar(), variation_ref::CVariationUtil::x_GetLiteralAtLoc(), variation::CVariationUtil::x_GetLiteralAtLoc(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), CCrossPanelIR::x_GetSequence(), x_GetSequence(), CSequenceSearchJob::x_GetSequence(), CGuiObjectInfoSeq_feat::x_GetSplicedSeqTitle(), CPrimaryItem::x_GetStrForPrimary(), CPsiBlastInputData::x_GetSubjectSequence(), CCDSTranslationProblems::x_GetTranslExceptProblems(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), variation::CVariationUtil::x_InferNAfromAA(), CSingleFeatValidator::x_IsMostlyNs(), CSplign::x_LoadSequence(), variation_ref::CHgvsParser::x_LocToSeqStr(), variation::CHgvsParser::x_LocToSeqStr(), CSequenceUpdater::x_PatchSequence(), CAgpFastaComparator::x_Process(), CSplignApp::x_ProcessPair(), CPromote::x_PromoteRna(), variation_ref::CVariationUtil::x_ProtToPrecursor(), CUpdateSeq_Input::x_ReadAccession(), CSequenceTrack::x_RenderSequence(), CFastaSeqBlockItem::x_RenderText(), CSequenceUpdater::x_ReplaceSequence(), CInstancedAligner::x_RunMMGlobal(), CSequenceSearchJob::x_SearchSequence(), CVectorTrimPanel::x_SetSeqData(), CUnorderedSplitter::x_SplitSeqData(), CCdregionValidator::x_ValidateConflict(), CCdregionValidator::x_ValidateFeatComment(), CSingleFeatValidator::x_ValidateReplaceQual(), CSingleFeatValidator::x_ValidateRptUnitVal(), and CVcfWriter::x_WriteFeature().

GetSeqMap()

const CSeqMap & CSeqVector::GetSeqMap ( void  ) const

inline

Definition at line 324 of file seq_vector.hpp.

References CSeqVector::m_SeqMap.

Referenced by CSeqTranslator::TranslateToProtein(), CSequenceAmbigTrimmer::x_CountAmbigInRange(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CSequenceAmbigTrimmer::x_EdgeSeqMapGapAdjust(), and CBioseqGaps_CI::x_FindNextGapOnBioseq().

GetSeqMapForSeq_loc()

CConstRef< CSeqMap > CSeqMap::GetSeqMapForSeq_loc ( const CSeq_loc &  loc, CScope *  scope  )

static

Definition at line 1162 of file seq_map.cpp.

References ConstRef(), CSeqMap::CSeqMap(), CSeq_inst_Base::eMol_not_set, CSeqMap::eSeqEnd, CSeqMap::eSeqRef, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetId(), CSeq_loc_Base::GetInt(), CBioseq_Handle::GetSeqMap(), CBioseq_Handle::GetSequenceType(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), CSeq_loc_Base::GetWhole(), i, CSeq_loc_Base::IsInt(), IsReverse(), CSeq_interval_Base::IsSetStrand(), CSeq_loc_Base::IsWhole(), CSeqMap::m_Mol, CSeqMap::CSegment::m_SegType, CSeqMap::x_GetRefSeqid(), and CSeqMap::x_GetSegment().

Referenced by CFeatGapInfo::CollectGaps(), CSplign::x_LoadSequence(), and CSplign::x_RunOnCompartment().

GetSequenceDifference()

int CSeqMapSwitchPoint::GetSequenceDifference ( TSeqPos  new_pos, TSeqPos  add = 0  ) const

inline

Definition at line 101 of file seq_map_switch.hpp.

References CSeqMapSwitchPoint::GetDifferences().

GetSequenceType()

CSeqVector::TMol CSeqVector::GetSequenceType ( void  ) const

inline

Definition at line 343 of file seq_vector.hpp.

References CSeqVector::m_Mol.

Referenced by CScoreBuilder::GetBlastScoreDenseg(), CSeqVector::IsNucleotide(), CSeqVector::IsProtein(), and CSequenceAmbigTrimmer::x_CountAmbigInRange().

GetStrand()

ENa_strand CSeqVector::GetStrand ( void  ) const

inline

Definition at line 336 of file seq_vector.hpp.

References CSeqVector::m_Strand.

Referenced by CIntronValidator::Validate(), and CBlastSeqVectorOM::x_SetStrand().

GetSwitchPoint()

CRef<CSeqMapSwitchPoint> GetSwitchPoint	(	const CBioseq_Handle &	seq,
		const CSeq_align &	align
	)

Definition at line 585 of file seq_map_switch.cpp.

References CSeqMap::begin(), CSeqMap::eSeqRef, CSeqMap_CI::GetRefSeqid(), CBioseq_Handle::GetScope(), CBioseq_Handle::GetSeqMap(), CSeqMap_CI::GetType(), info, and NCBI_THROW.

HasSegmentOfType()

bool CSeqMap::HasSegmentOfType

(

ESegmentType

type

)

const

Definition at line 882 of file seq_map.cpp.

References bool, flags, ITERATE, CSeqMap::m_HasSegments, and CSeqMap::m_Segments.

Referenced by CAnnot_Collector::x_CollectSegments(), CSeqMap::x_DoUpdateSeq_inst(), CAnnot_Collector::x_Initialize(), and CAnnot_Collector::x_SearchSegments().

HasZeroGapAt()

bool CSeqMap::HasZeroGapAt	(	TSeqPos	pos,
		CScope *	scope = 0
	)		const

Returns true if there is zero-length gap at position.

Checks referenced sequences too.

Parameters

pos	Sequence position to check
scope	Optional scope for segments resolution

Definition at line 907 of file seq_map.cpp.

References _ASSERT, CSeqMap::eSeqGap, CSeqMap::eSeqRef, CSeqMap::GetLength(), CSeqMap::HasZeroGapAt(), CSeqMap::CSegment::m_Length, CSeqMap::CSegment::m_Position, CSeqMap::CSegment::m_RefMinusStrand, CSeqMap::CSegment::m_RefPosition, CSeqMap::CSegment::m_SegType, CSeqMap::x_FindSegment(), CSeqMap::x_GetFirstEndSegmentIndex(), CSeqMap::x_GetLastEndSegmentIndex(), CSeqMap::x_GetSegment(), and CSeqMap::x_GetSubSeqMap().

Referenced by CSeqMap::HasZeroGapAt(), and CSeqVector_CI::HasZeroGapBefore().

InsertInPlace()

void CSeqMapSwitchPoint::InsertInPlace	(	TSeqPos	add_left,
		TSeqPos	add_right
	)

Definition at line 570 of file seq_map_switch.cpp.

References CSeqMapSwitchPoint::GetLeftInPlaceInsert(), CSeqMapSwitchPoint::GetRightInPlaceInsert(), CSeqMapSwitchPoint::m_Master, and NCBI_THROW.

InsertSegmentGap()

CSeqMap_CI CSeqMap::InsertSegmentGap	(	const CSeqMap_CI &	seg,
		TSeqPos	length
	)

Insert new gap into sequence map.

Parameters

seg	Iterator pointing to the place where new gap will be inserted. Becomes invalid after the call.

Returns

New iterator pointing to the new segment.

Definition at line 723 of file seq_map.cpp.

References _ASSERT, CSeqMap::CSeqMap_CI, CSeqMap::eSeqGap, CSeqMap::CSegment::m_Position, CSeqMap::m_Resolved, CSeqMap::m_Segments, CSeqMap::m_SeqMap_Mtx, CSeqMap_CI_SegmentInfo::x_GetIndex(), CSeqMap_CI::x_GetSegmentInfo(), CSeqMap::x_GetSegmentPosition(), CSeqMap_CI_SegmentInfo::x_GetSeqMap(), CSeqMap::x_SetChanged(), CSeqMap::x_SetSegment(), and CSeqMap::x_StartEditing().

Referenced by CSeqMap_I::InsertGap().

IsInGap()

bool CSeqVector::IsInGap ( TSeqPos  pos ) const

inline

true if sequence at 0-based position 'pos' has gap Note: this method is not MT-safe, do not call it in parallel with other, even MT-safe method.

It will be MT-safe to call this method after locking GetMutex().

Definition at line 277 of file seq_vector.hpp.

References CSeqVector_CI::IsInGap(), and CSeqVector::x_GetIterator().

Referenced by CConvertGapsBySize::apply(), CExpandGaps::apply(), CCombineAdjacentGaps::apply_impl(), CheckBioseqEndsForNAndGap(), CAddLinkageToGaps::GetCommand(), HasBadProteinStart(), CAlignCollapser::InitContig(), CSpliceProblems::ReadAcceptorSpliceSite(), CSpliceProblems::ReadDonorSpliceSite(), CDemoApp::Run(), s_AfterIsGap(), s_BeforeIsGap(), s_CheckPosNOrGap(), s_PartialAtGapOrNs(), s_PosIsNNotGap(), StartAbutsGap(), StopAbutsGap(), CSeqTranslator::TranslateToProtein(), CIntronValidator::Validate(), CGapFeatValidator::Validate(), CValidError_bioseq::ValidateDelta(), CValidError_bioseq::x_CalculateNsStretchAndTotal(), CCdregionValidator::x_CheckPosNOrGap(), CCDSTranslationProblems::x_Is5AtEndSpliceSiteOrGap(), CReportTrim::x_IsThereGapNotAtTheEnd(), and CFeatureGenerator::SImplementation::x_MapFeature().

IsNucleotide()

bool CSeqVector::IsNucleotide ( void  ) const

inline

Definition at line 357 of file seq_vector.hpp.

References CSeqVector::GetSequenceType(), and CSeq_inst::IsNa().

Referenced by CheckBioseqEndsForNAndGap(), CSequenceDataTester::x_CompareSequenceData(), CSequenceAmbigTrimmer::x_CountAmbigInRange(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CSequenceAmbigTrimmer::x_EdgeSeqMapGapAdjust(), variation_ref::CVariationUtil::x_GetLiteralAtLoc(), variation::CVariationUtil::x_GetLiteralAtLoc(), CAlnVec::x_GetSeqVector(), and CSparseAln::x_GetSeqVector().

IsProtein()

bool CSeqVector::IsProtein ( void  ) const

inline

Definition at line 350 of file seq_vector.hpp.

References CSeqVector::GetSequenceType(), and CSeq_inst::IsAa().

Referenced by CPostProcessUtils::GetLiteralAtLoc(), s_ReadAndTestQueryFromString(), SeqLocToBioseq(), CSeqUtils::SeqLocToBioseq(), CSeqVector::SetIupacCoding(), CSeqVector::SetNcbiCoding(), CFastaOstream::Write(), CFastaOstream::WriteSequence(), CSequenceDataTester::x_CompareSequenceData(), CSequenceAmbigTrimmer::x_CountAmbigInRange(), CSequenceAmbigTrimmer::x_EdgeSeqMapGapAdjust(), variation_ref::CVariationUtil::x_GetLiteralAtLoc(), variation::CVariationUtil::x_GetLiteralAtLoc(), CAlnVec::x_GetSeqVector(), CSparseAln::x_GetSeqVector(), CSequenceDataTester::x_TestSingleNucleotide_Remote(), CSequenceDataTester::x_TestSingleProtein_Remote(), and CFastaOstream::x_WriteSequence().

IsSetData()

bool CSeqMap::CSegment::IsSetData ( void  ) const

inline

Definition at line 418 of file seq_map.hpp.

References CSeqMap::eSeqData, CSeqMap::CSegment::m_ObjType, and CSeqMap::CSegment::m_SegType.

Referenced by CSeqMap_CI_SegmentInfo::IsSetData().

LoadSeq_data()

void CSeqMap::LoadSeq_data	(	TSeqPos	pos,
		TSeqPos	len,
		const CSeq_data &	data
	)

Definition at line 764 of file seq_map.cpp.

References data, len, CSeqMap::CSegment::m_Length, CSeqMap::CSegment::m_Position, NCBI_THROW, CSeqMap::x_FindSegment(), CSeqMap::x_GetSegment(), and CSeqMap::x_SetSeq_data().

Referenced by CTSE_Default_Assigner::LoadSequence().

operator()() [1/3]

bool CSeqMap::SPosLessSegment::operator() ( const CSegment &  seg, TSeqPos  pos  )

inline

Definition at line 275 of file seq_map.hpp.

References CSeqMap::CSegment::m_Length, and CSeqMap::CSegment::m_Position.

operator()() [2/3]

bool CSeqMap::SPosLessSegment::operator() ( const CSegment &  seg1, const CSegment &  seg2  )

inline

Definition at line 279 of file seq_map.hpp.

References CSeqMap::CSegment::m_Length, and CSeqMap::CSegment::m_Position.

operator()() [3/3]

bool CSeqMap::SPosLessSegment::operator() ( TSeqPos  pos, const CSegment &  seg  )

inline

Definition at line 271 of file seq_map.hpp.

References CSeqMap::CSegment::m_Length, and CSeqMap::CSegment::m_Position.

operator<()

bool CSeqMapSwitchPoint::operator< ( const CSeqMapSwitchPoint &  p ) const

inline

Definition at line 114 of file seq_map_switch.hpp.

References _ASSERT, CSeqMapSwitchPoint::m_Master, and CSeqMapSwitchPoint::m_MasterPos.

operator=() [1/3]

CSeqMap::CSegment & CSeqMap::CSegment::operator= ( const CSegment &  seg )

inline

Definition at line 101 of file seq_map.cpp.

References CSeqMap::CSegment::m_Length, CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_Position, CSeqMap::CSegment::m_RefMinusStrand, CSeqMap::CSegment::m_RefObject, CSeqMap::CSegment::m_RefPosition, CSeqMap::CSegment::m_SegType, and CSeqMap::CSegment::m_UnknownLength.

operator=() [2/3]

CSeqMap& CSeqMap::operator= ( const CSeqMap &  )

private

operator=() [3/3]

CSeqVector & CSeqVector::operator=

(

const CSeqVector &

vec

)

Definition at line 244 of file seq_vector.cpp.

References CSeqVector::GetMutex(), CSeqVector::m_Coding, CSeqVector::m_Iterator, CSeqVector::m_Mol, CSeqVector::m_Scope, CSeqVector::m_SeqMap, CSeqVector::m_Size, CSeqVector::m_Strand, CSeqVector::m_TSE, and AutoPtr< X, Del >::reset().

operator[]()

CSeqVector::TResidue CSeqVector::operator[] ( TSeqPos  pos ) const

inline

0-based array of residues Note: this method is not MT-safe, do not call it in parallel with other, even MT-safe method.

It will be MT-safe to call this method after locking GetMutex().

Definition at line 270 of file seq_vector.hpp.

References CSeqVector::x_GetIterator().

RandomizeData()

void CNcbi2naRandomizer::RandomizeData ( char *  buffer, size_t  count, TSeqPos  pos  )

virtual

Convert count unpacked bases in buffer 4na -> 2na with randomization.

The argument pos will contain position of the buffer in the sequence, and can be used to give the same random base at the same ambiguous position.

Implements INcbi2naRandomizer.

Definition at line 112 of file seq_vector.cpp.

References count, data, CNcbi2naRandomizer::kRandomizerPosMask, CNcbi2naRandomizer::kRandomValue, CNcbi2naRandomizer::m_FixedTable, and CNcbi2naRandomizer::m_RandomTable.

RemoveSegment()

CSeqMap_CI CSeqMap::RemoveSegment

(

const CSeqMap_CI &

seg

)

Delete segment from sequence map.

Parameters

seg	Iterator pointing to the segment to be deleted. Becomes invalid after the call.

Returns

New iterator pointing to the next segment.

Definition at line 740 of file seq_map.cpp.

References _ASSERT, CSeqMap::CSeqMap_CI, CSeqMap::eSeqEnd, CSeqMap::CSegment::m_Position, CSeqMap::m_Resolved, CSeqMap::m_Segments, CSeqMap::CSegment::m_SegType, CSeqMap::m_SeqMap_Mtx, NCBI_THROW, CSeqMap_CI_SegmentInfo::x_GetIndex(), CSeqMap_CI::x_GetSegmentInfo(), CSeqMap::x_GetSegmentPosition(), CSeqMap_CI_SegmentInfo::x_GetSeqMap(), CSeqMap::x_SetChanged(), CSeqMap::x_SetSegment(), and CSeqMap::x_StartEditing().

Referenced by CSeqMap_I::Remove().

ResetMol()

void CSeqMap::ResetMol

(

void

)

Definition at line 1625 of file seq_map.cpp.

References CSeq_inst_Base::eMol_not_set, and CSeqMap::m_Mol.

Referenced by CBioseq_Info::ResetInst_Mol().

ResetRepr()

void CSeqMap::ResetRepr

(

void

)

Definition at line 1614 of file seq_map.cpp.

Referenced by CBioseq_Info::ResetInst_Repr().

ResolveAll()

void CSeqMap::ResolveAll ( void  ) const

private

ResolvedRangeIterator()

CSeqMap_CI CSeqMap::ResolvedRangeIterator	(	CScope *	scope,
		TSeqPos	from,
		TSeqPos	length,
		ENa_strand	strand = eNa_strand_plus,
		size_t	maxResolve = size_t(-1),
		TFlags	flags = fDefaultFlags
	)		const

Iterate segments in the range with specified strand coordinates.

Definition at line 868 of file seq_map.cpp.

References CSeqMap::CSeqMap_CI, flags, SSeqMapSelector::SetFlags(), SSeqMapSelector::SetRange(), SSeqMapSelector::SetResolveCount(), and SSeqMapSelector::SetStrand().

Referenced by CFeatGapInfo::CollectGaps(), CTextItemSeq_loc::CreateObject(), CGapInfo< CBlastTabular >::IntersectsNonBridgeableGap(), CDemoApp::Run(), TrimSeqData(), CComponentSearchJob::x_DoSearch(), CSplign::x_RunOnCompartment(), CVectorTrimPanel::x_SetSeqData(), and CSequenceAmbigTrimmer::x_SliceBioseq().

SetCoding() [1/2]

void CSeqVector::SetCoding

(

EVectorCoding

coding

)

Set coding to either Iupac or Ncbi8xx.

Definition at line 1293 of file seq_vector.cpp.

References CSeq_data_Base::e_not_set, CBioseq_Handle::eCoding_Iupac, CBioseq_Handle::eCoding_Ncbi, CSeqVector::SetCoding(), CSeqVector::SetIupacCoding(), and CSeqVector::SetNcbiCoding().

SetCoding() [2/2]

void CSeqVector::SetCoding

(

TCoding

coding

)

Definition at line 1272 of file seq_vector.cpp.

References CSeqVector::m_Coding, and CSeqVector::x_ResetIterator().

Referenced by CAdjustForConsensusSpliceSite::AdjustCDS(), CAdjustForConsensusSpliceSite::AdjustCDSEnds(), CCDSTranslationProblems::CalculateTranslationProblems(), CSeqVector::CSeqVector(), CPrefetchSeqData::Execute(), CScore_SegPct::Get(), GetMismatches(), GetProteinString(), GetProteinWeight(), GetProteinWeights(), CBlastSequenceSource::GetSeq(), CBioseqIndex::GetSequence(), CFeatureIndex::GetSequence(), CEditingActionFeatTranslation::GetValue(), MakeSeqVectorForResidueCounting(), CRestoreRNAediting::OnApply(), CUpdateSeq_Input::s_ConvertDeltaToRawBioseq(), ApplyCDSFrame::s_FindMatchingFrame(), CMacroFunction_ApplyCDSFrame::s_FindMatchingFrame(), s_GetQuerySequence(), CBlastSeqVectorOM::SetCoding(), CSeqVector::SetCoding(), CSeqVector::SetIupacCoding(), CSeqVector::SetNcbiCoding(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CCDSTranslationPanel::TransferDataToWindow(), TrimStopsFromCompleteCDS(), CFastaOstream::Write(), CFastaOstream::WriteSequence(), CFeatureItem::x_AddQualsProt(), CFeatureItem::x_AddQualsRna(), CFeatureItem::x_AddQualTranslation(), CFeaturePropagator::x_CdsStopAtStopCodon(), CSequenceDataTester::x_CompareSequenceData(), COrfSearchJob::x_DoSearch(), CSequenceItem::x_GatherInfo(), CAlnVec::x_GetSeqVector(), CSparseAln::x_GetSeqVector(), CPsiBlastInputData::x_GetSubjectSequence(), CSequenceUpdater::x_ReplaceSequence(), CSequenceDataTester::x_TestSingleNucleotide_Remote(), CSequenceDataTester::x_TestSingleProtein_Remote(), CCdregionValidator::x_ValidateConflict(), and CValidError_graph::x_ValidateGraphValues().

SetIupacCoding()

void CSeqVector::SetIupacCoding

(

void

)

Set coding to either Iupacaa or Iupacna depending on molecule type.

Definition at line 1281 of file seq_vector.cpp.

References CSeq_data_Base::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeqVector::IsProtein(), and CSeqVector::SetCoding().

Referenced by CContigAssembly::BandedGlobalAlignment(), CSimpleOM::GetIupac(), CCodingPropensity::GetScore(), CHitMatrixSeqGraph::Render(), CLocalFinderApp::Run(), CTestSingleAln_All::RunTest(), CTestTranscript_PolyA::RunTest(), CTestTranscript_Orfs::RunTest(), s_CdsStartCodon(), s_CdsStopCodon(), s_CompareProtProdToTrans(), s_CountAmbiguities(), s_InframeUpstreamStart(), s_InframeUpstreamStop(), s_OrfExtension(), s_PrematureStopCodon(), s_ReadAndTestQueryFromString(), CSeqVector::SetCoding(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CAlnVec::x_GetSeqVector(), CSparseAln::x_GetSeqVector(), and CFastaSeqBlockItem::x_RenderText().

SetMol()

void CSeqMap::SetMol

(

CSeq_inst::TMol

mol

)

Definition at line 1619 of file seq_map.cpp.

References CSeqMap::m_Mol.

Referenced by CBioseq_Info::SetInst_Mol().

SetNcbiCoding()

void CSeqVector::SetNcbiCoding

(

void

)

Set coding to either Ncbi8aa or Ncbi8na depending on molecule type.

Definition at line 1287 of file seq_vector.cpp.

References CSeq_data_Base::e_Ncbi4na, CSeq_data_Base::e_Ncbistdaa, CSeqVector::IsProtein(), and CSeqVector::SetCoding().

Referenced by CFindRSites::Find(), and CSeqVector::SetCoding().

SetNoAmbiguities()

void CSeqVector::SetNoAmbiguities

(

void

)

Definition at line 1345 of file seq_vector.cpp.

References CSeqVector::SetRandomizeAmbiguities().

SetRandomizeAmbiguities() [1/4]

void CSeqVector::SetRandomizeAmbiguities

(

CRandom &

random_gen

)

Definition at line 1323 of file seq_vector.cpp.

References CSeqVector::x_InitRandomizer().

SetRandomizeAmbiguities() [2/4]

void CSeqVector::SetRandomizeAmbiguities

(

CRef< INcbi2naRandomizer >

randomizer

)

Definition at line 1336 of file seq_vector.cpp.

References CSeqVector::m_Randomizer, and CSeqVector::x_ResetIterator().

SetRandomizeAmbiguities() [3/4]

void CSeqVector::SetRandomizeAmbiguities

(

Uint4

seed

)

Definition at line 1316 of file seq_vector.cpp.

References seed, and CSeqVector::x_InitRandomizer().

SetRandomizeAmbiguities() [4/4]

void CSeqVector::SetRandomizeAmbiguities

(

void

)

Randomization of ambiguities and gaps in ncbi2na coding.

Definition at line 1309 of file seq_vector.cpp.

References CSeqVector::x_InitRandomizer().

Referenced by CBlastSequenceSource::GetSeq(), CSeqVector::SetNoAmbiguities(), and CSeqVector::x_InitRandomizer().

SetRegionInChunk()

void CSeqMap::SetRegionInChunk	(	CTSE_Chunk_Info &	chunk,
		TSeqPos	pos,
		TSeqPos	length
	)

Definition at line 1438 of file seq_map.cpp.

References _ASSERT, CSeqMap::eSeqData, CSeqMap::eSeqGap, kInvalidSeqPos, literal(), CSeqMap::CSegment::m_Length, CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_Position, CSeqMap::CSegment::m_RefObject, CSeqMap::m_Resolved, CSeqMap::CSegment::m_SegType, CSeqMap::m_SeqLength, CSeqMap::m_SeqMap_Mtx, NCBI_THROW, CSeqMap::x_FindSegment(), CSeqMap::x_GetLastEndSegmentIndex(), CSeqMap::x_GetSegmentException(), CSeqMap::x_GetSeq_literal(), CSeqMap::x_SetChunk(), and CSeqMap::x_SetSegment().

Referenced by CTSE_Default_Assigner::AddSeq_data().

SetRepr()

void CSeqMap::SetRepr

(

CSeq_inst::TRepr

repr

)

Definition at line 1609 of file seq_map.cpp.

Referenced by CBioseq_Info::SetInst_Repr().

SetSegmentData()

void CSeqMap::SetSegmentData	(	const CSeqMap_CI &	seg,
		TSeqPos	length,
		CSeq_data &	data
	)

Definition at line 713 of file seq_map.cpp.

References _ASSERT, data, CSeqMap_CI_SegmentInfo::x_GetIndex(), CSeqMap_CI::x_GetSegmentInfo(), CSeqMap_CI_SegmentInfo::x_GetSeqMap(), and CSeqMap::x_SetSegmentData().

Referenced by CSeqMap_I::InsertData(), and CSeqMap_I::SetSeq_data().

SetSegmentGap() [1/2]

void CSeqMap::SetSegmentGap	(	const CSeqMap_CI &	seg,
		TSeqPos	length
	)

Definition at line 694 of file seq_map.cpp.

References _ASSERT, CSeqMap_CI_SegmentInfo::x_GetIndex(), CSeqMap_CI::x_GetSegmentInfo(), CSeqMap_CI_SegmentInfo::x_GetSeqMap(), and CSeqMap::x_SetSegmentGap().

Referenced by CSeqMap_I::SetGap().

SetSegmentGap() [2/2]

void CSeqMap::SetSegmentGap	(	const CSeqMap_CI &	seg,
		TSeqPos	length,
		CSeq_data &	gap_data
	)

Definition at line 703 of file seq_map.cpp.

References _ASSERT, CSeqMap_CI_SegmentInfo::x_GetIndex(), CSeqMap_CI::x_GetSegmentInfo(), CSeqMap_CI_SegmentInfo::x_GetSeqMap(), and CSeqMap::x_SetSegmentGap().

SetSegmentRef()

void CSeqMap::SetSegmentRef	(	const CSeqMap_CI &	seg,
		TSeqPos	length,
		const CSeq_id_Handle &	ref_id,
		TSeqPos	ref_pos,
		bool	ref_minus_strand
	)

Definition at line 682 of file seq_map.cpp.

References _ASSERT, CSeq_id_Handle::GetSeqId(), CSeqMap_CI_SegmentInfo::x_GetIndex(), CSeqMap_CI::x_GetSegmentInfo(), CSeqMap_CI_SegmentInfo::x_GetSeqMap(), and CSeqMap::x_SetSegmentRef().

Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint(), CSeqMap_I::InsertRef(), and CSeqMap_I::SetRef().

SetStrand()

void CSeqVector::SetStrand

(

ENa_strand

strand

)

Definition at line 1263 of file seq_vector.cpp.

References CSeqVector::m_Strand, and CSeqVector::x_ResetIterator().

size()

TSeqPos CSeqVector::size ( void  ) const

inline

Definition at line 291 of file seq_vector.hpp.

References CSeqVector::m_Size.

Referenced by CAdjustForConsensusSpliceSite::AdjustCDS(), CAdjustForConsensusSpliceSite::AdjustCDSEnds(), CContigAssembly::BandedGlobalAlignment(), BOOST_AUTO_TEST_CASE(), CEquivRangeBuilder::CalcMatches(), CalculateEffectiveTranslationLengths(), CAlnVec::CalculateScore(), CCDSTranslationProblems::CalculateTranslationProblems(), CdsTrnaOverlapStr(), CheckBioseqEndsForNAndGap(), Does3primerAbutGap(), CSeqVector::end(), ExtendCDSToStopCodon(), ExtendToStopCodon(), CCleanup::ExtendToStopCodon(), CFindRSites::Find(), CInternalStopFinder::FindStartStopRanges(), COrf::FindStrongKozakUOrfs(), CFlatAnticodonQVal::Format(), CAlnVec::GetAlnSeqString(), CSparseAlignment::GetAlnSeqString(), CSparseAln::GetAlnSeqString(), CAlnVec::GetColumnVector(), CAddGlobalCodeBreak::GetCommand(), CExtendCDSToStop::GetCommand(), GetDNASequence(), CSimpleOM::GetIupac(), GetLoc(), GetMRNATranslationProblems(), CSRSearch::getNMer(), CSeqVector::GetPackedSeqData(), CNucProp::GetPercentGC(), CProtProp::GetProteinPI(), GetProteinWeights(), CAlnVec::GetResidue(), CCodingPropensity::GetScore(), CBlastSequenceSource::GetSeq(), CBlastSequenceSource::GetSeqLength(), CSeqVectorCache::GetSeqSize(), GetSeqsStatus(), CAlnVec::GetSeqString(), CAlnMixSeq::GetSeqString(), CSparseAln::GetSeqString(), CSparseAlignment::GetSeqString(), CBioseqIndex::GetSequence(), CFeatureIndex::GetSequence(), CEditingActionFeatTranslation::GetValue(), HasBadProteinStart(), CBlastBioseqMaker::HasSequence(), CAlignCollapser::InitContig(), CRestoreRNAediting::OnApply(), CTabularFormatter_MismatchPositions::Print(), RetrievePartsOfLargeChromosome(), CAlnVec::RetrieveSegmentSequences(), CDemoApp::Run(), CSampleObjmgrApplication::Run(), CTestSingleAln_All::RunTest(), CTestTranscript_PolyA::RunTest(), s_CdsStopCodon(), s_CodonVariation(), s_CompareProtProdToTrans(), s_CountAmbiguities(), s_DumpSequences_wRange(), ApplyCDSFrame::s_FindMatchingFrame(), CMacroFunction_ApplyCDSFrame::s_FindMatchingFrame(), s_GetKozakStrength(), s_GetQuerySequence(), s_PartialAtGapOrNs(), s_PosIsNNotGap(), s_PrematureStopCodon(), s_ReadAndTestQueryFromString(), s_RunBlast2NWSeq(), ScanForCpGs(), CSeqSearch::Search(), CSRSearch_Impl< index_t >::search(), CSRSearch_Impl< index_t >::searchOneMismatch(), SeqLocToBioseq(), CSeqUtils::SeqLocToBioseq(), CMultAlign::SetGenomic(), SSeqDB_SVCISource::SSeqDB_SVCISource(), StopAbutsGap(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CCDSTranslationPanel::TransferDataToWindow(), CSeqTranslator::TranslateToProtein(), TrimStopsFromCompleteCDS(), CGapFeatValidator::Validate(), CFeatureItem::x_AddQualsRna(), CFeatureItem::x_AddQualTranslation(), CSingleFeatValidator::x_CalculateLocationGaps(), CValidError_bioseq::x_CalculateNsStretchAndTotal(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CSequenceDataTester::x_CompareSequenceData(), CWriteDB_Impl::x_ComputeSeqLength(), CWriteDB_Impl::x_CookSequence(), CCDSTranslationProblems::x_CountTerminalXs(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CURLTooltipHandler::x_DisplayForwardStrandRegion(), CURLTooltipHandler::x_DisplayReverseStrandRegion(), CCpgSearchJob::x_DoSearch(), COrfSearchJob::x_DoSearch(), CCdsGlyph::x_Draw(), CCdsGlyph::x_DrawProjectedProtSeq(), CCdsGlyph::x_DrawProtSeqWithMapping(), CFeatGlyph::x_DrawRNAProductSequence(), CFeaturePropagator::x_ExtendToStopCodon(), CBioseqGaps_CI::x_FindNextGapOnBioseq(), CBaseCountItem::x_GatherInfo(), CGuiObjectInfoSeq_feat::x_GetProductSequence(), x_GetSequence(), CGuiObjectInfoSeq_feat::x_GetSplicedSeqTitle(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), CSingleFeatValidator::x_IsMostlyNs(), CSplign::x_LoadSequence(), CFeatureGenerator::SImplementation::x_MapFeature(), CSplignApp::x_ProcessPair(), CPromote::x_PromoteRna(), CInstancedAligner::x_RunMMGlobal(), CSequenceSearchJob::x_SearchSequence(), CFeatureGenerator::SImplementation::x_SetComment(), CReportEntry::x_SetSequence(), CSeqVector_CI::x_SetVector(), CBlastSeqVectorOM::x_Size(), CUnorderedSplitter::x_SplitSeqData(), CSequenceDataTester::x_TestSingleNucleotide_Remote(), CSequenceDataTester::x_TestSingleProtein_Remote(), CCdregionValidator::x_ValidateConflict(), CSingleFeatValidator::x_ValidateReplaceQual(), and CSingleFeatValidator::x_ValidateRptUnitVal().

x_Add() [1/12]

void CSeqMap::x_Add ( const CDelta_seq &  seq )

protected

Definition at line 1422 of file seq_map.cpp.

References CDelta_seq_Base::e_Literal, CDelta_seq_Base::e_Loc, CDelta_seq_Base::GetLiteral(), CDelta_seq_Base::GetLoc(), NCBI_THROW, CDelta_seq_Base::Which(), and CSeqMap::x_Add().

x_Add() [2/12]

void CSeqMap::x_Add ( const CPacked_seqint &  seq )

protected

Definition at line 1321 of file seq_map.cpp.

References CPacked_seqint_Base::Get(), ITERATE, and CSeqMap::x_Add().

x_Add() [3/12]

void CSeqMap::x_Add ( const CPacked_seqpnt &  seq )

protected

Definition at line 1330 of file seq_map.cpp.

References eNa_strand_unknown, CSeqMap::eSeqRef, CPacked_seqpnt_Base::GetId(), CPacked_seqpnt_Base::GetPoints(), CPacked_seqpnt_Base::GetStrand(), CPacked_seqpnt_Base::IsSetStrand(), ITERATE, and CSeqMap::x_AddSegment().

x_Add() [4/12]

void CSeqMap::x_Add ( const CSeq_data &  data, TSeqPos  len  )

protected

Definition at line 1287 of file seq_map.cpp.

References data, CSeqMap::eSeqData, len, and CSeqMap::x_AddSegment().

x_Add() [5/12]

void CSeqMap::x_Add ( const CSeq_id &  seq )

protected

Definition at line 1309 of file seq_map.cpp.

References CSeqMap::eSeqRef, kInvalidSeqPos, and CSeqMap::x_AddSegment().

x_Add() [6/12]

void CSeqMap::x_Add ( const CSeq_interval &  seq )

protected

Definition at line 1301 of file seq_map.cpp.

References eNa_strand_unknown, CSeqMap::eSeqRef, CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetId(), CSeq_interval::GetLength(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::IsSetStrand(), and CSeqMap::x_AddSegment().

x_Add() [7/12]

void CSeqMap::x_Add ( const CSeq_literal &  seq )

protected

Definition at line 1359 of file seq_map.cpp.

References CSeq_literal_Base::CanGetFuzz(), CInt_fuzz_Base::eLim_unk, CSeq_literal_Base::GetFuzz(), CSeq_literal_Base::GetLength(), CInt_fuzz_Base::GetLim(), CSeq_literal_Base::GetSeq_data(), CSeq_data_Base::IsGap(), CInt_fuzz_Base::IsLim(), CSeq_literal_Base::IsSetSeq_data(), CSeqMap::x_Add(), and CSeqMap::x_AddGap().

x_Add() [8/12]

void CSeqMap::x_Add ( const CSeq_loc &  seq )

protected

Definition at line 1380 of file seq_map.cpp.

References CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, CSeq_loc_Base::GetEquiv(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSeq_loc_Base::GetWhole(), NCBI_THROW, CSeq_loc_Base::Which(), CSeqMap::x_Add(), and CSeqMap::x_AddGap().

x_Add() [9/12]

void CSeqMap::x_Add ( const CSeq_loc_equiv &  seq )

protected

Definition at line 1350 of file seq_map.cpp.

References CSeq_loc_equiv_Base::Get(), ITERATE, and CSeqMap::x_Add().

x_Add() [10/12]

void CSeqMap::x_Add ( const CSeq_loc_mix &  seq )

protected

Definition at line 1341 of file seq_map.cpp.

References CSeq_loc_mix_Base::Get(), ITERATE, and CSeqMap::x_Add().

x_Add() [11/12]

void CSeqMap::x_Add ( const CSeq_point &  seq )

protected

Definition at line 1293 of file seq_map.cpp.

References eNa_strand_unknown, CSeqMap::eSeqRef, CSeq_point_Base::GetId(), CSeq_point_Base::GetPoint(), CSeq_point_Base::GetStrand(), CSeq_point_Base::IsSetStrand(), and CSeqMap::x_AddSegment().

x_Add() [12/12]

void CSeqMap::x_Add ( CSeqMap *  submap )

protected

Referenced by CSeqMap::CSeqMap(), and CSeqMap::x_Add().

x_AddEnd()

void CSeqMap::x_AddEnd ( void  )

protected

Definition at line 1242 of file seq_map.cpp.

References CSeqMap::eSeqEnd, kInvalidSeqPos, CSeqMap::CSegment::m_Position, CSeqMap::m_Segments, and CSeqMap::x_AddSegment().

Referenced by CSeqMap::CSeqMap().

x_AddGap() [1/3]

void CSeqMap::x_AddGap ( TSeqPos  len, bool  unknown_len  )

protected

Definition at line 1255 of file seq_map.cpp.

References CSeqMap::eSeqGap, len, and CSeqMap::x_AddSegment().

Referenced by CSeqMap::CSeqMap(), and CSeqMap::x_Add().

x_AddGap() [2/3]

void CSeqMap::x_AddGap ( TSeqPos  len, bool  unknown_len, const CSeq_data &  gap_data  )

protected

Definition at line 1261 of file seq_map.cpp.

References CSeqMap::eSeqData, CSeqMap::eSeqGap, len, CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_RefObject, CSeqMap::m_Segments, and CSeqMap::x_AddSegment().

x_AddGap() [3/3]

void CSeqMap::x_AddGap ( TSeqPos  len, bool  unknown_len, const CSeq_literal &  gap_data  )

protected

Definition at line 1271 of file seq_map.cpp.

References CSeqMap::eSeqGap, CSeqMap::eSeqLiteral, len, CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_RefObject, CSeqMap::m_Segments, and CSeqMap::x_AddSegment().

x_AddSegment() [1/3]

void CSeqMap::x_AddSegment ( ESegmentType  type, const CObject *  object, TSeqPos  refPos, TSeqPos  len, ENa_strand  strand = eNa_strand_plus  )

protected

Definition at line 1229 of file seq_map.cpp.

References IsReverse(), len, CSeqMap::CSegment::m_RefMinusStrand, CSeqMap::CSegment::m_RefPosition, CSeqMap::m_Segments, and CSeqMap::x_AddSegment().

x_AddSegment() [2/3]

void CSeqMap::x_AddSegment ( ESegmentType  type, TSeqPos  len, bool  unknown_len = false  )

inlineprotected

Definition at line 1212 of file seq_map.cpp.

References CSeqMap::CSegment, len, and CSeqMap::m_Segments.

Referenced by CSeqMap::x_Add(), CSeqMap::x_AddEnd(), CSeqMap::x_AddGap(), CSeqMap::x_AddSegment(), and CSeqMap::x_AddUnloadedSeq_data().

x_AddSegment() [3/3]

void CSeqMap::x_AddSegment ( ESegmentType  type, TSeqPos  len, const CObject *  object  )

protected

Definition at line 1220 of file seq_map.cpp.

References len, CSeqMap::CSegment::m_RefObject, CSeqMap::m_Segments, CConstRef< C, Locker >::Reset(), and CSeqMap::x_AddSegment().

x_AddUnloadedSeq_data()

void CSeqMap::x_AddUnloadedSeq_data ( TSeqPos  len )

protected

Definition at line 1281 of file seq_map.cpp.

References CSeqMap::eSeqData, len, and CSeqMap::x_AddSegment().

x_CreateIterator()

CSeqVector_CI * CSeqVector::x_CreateIterator ( TSeqPos  pos ) const

private

Definition at line 261 of file seq_vector.cpp.

References CSeqVector::CSeqVector_CI, CSeqVector::m_Iterator, and AutoPtr< X, Del >::reset().

Referenced by CSeqVector::x_GetIterator().

x_DoUpdateSeq_inst()

bool CSeqMap::x_DoUpdateSeq_inst ( CSeq_inst &  inst )

protected

Definition at line 1494 of file seq_map.cpp.

References _ASSERT, data, delta(), CInt_fuzz_Base::eLim_unk, eNa_strand_minus, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_virtual, CSeqMap::eSeqData, CSeqMap::eSeqGap, CSeqMap::eSeqLiteral, CSeqMap::eSeqRef, CSeq_inst_Base::GetExt(), CSeqMap::GetLength(), CSeqMap::GetSegmentsCount(), CSeqMap::HasSegmentOfType(), CSeq_ext_Base::IsSeg(), CSeq_inst_Base::IsSetExt(), CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_RefMinusStrand, CSeqMap::CSegment::m_RefPosition, CSeqMap::CSegment::m_SegType, CSeqMap::CSegment::m_UnknownLength, CSeq_inst_Base::ResetExt(), CSeq_literal_Base::ResetFuzz(), CSeq_interval_Base::ResetFuzz_from(), CSeq_interval_Base::ResetFuzz_to(), CSeq_inst_Base::ResetSeq_data(), CSeq_literal_Base::ResetSeq_data(), CSeq_interval_Base::ResetStrand(), CSeq_inst_Base::SetExt(), CSeq_interval_Base::SetFrom(), CSeq_literal_Base::SetFuzz(), CSeq_interval_Base::SetId(), CSeq_loc::SetInt(), CSeq_inst_Base::SetLength(), CSeq_literal_Base::SetLength(), CDelta_seq_Base::SetLiteral(), CDelta_seq_Base::SetLoc(), CSeq_inst_Base::SetRepr(), CSeq_inst_Base::SetSeq_data(), CSeq_literal_Base::SetSeq_data(), CSeq_interval_Base::SetStrand(), CSeq_interval_Base::SetTo(), CSeqMap::x_GetFirstEndSegmentIndex(), CSeqMap::x_GetLastEndSegmentIndex(), CSeqMap::x_GetRefSeqid(), CSeqMap::x_GetSegmentLength(), CSeqMap::x_GetSeq_data(), CSeqMap::x_GetSeq_literal(), and CSeqMap::x_SetSegment().

Referenced by CSeqMap::x_UpdateSeq_inst().

x_FindSegment()

size_t CSeqMap::x_FindSegment ( TSeqPos  position, CScope *  scope  ) const

protected

Definition at line 403 of file seq_map.cpp.

References kInvalidSeqPos, CSeqMap::CSegment::m_Position, CSeqMap::m_Resolved, CSeqMap::m_Segments, CSeqMap::m_SeqMap_Mtx, NCBI_THROW, CSeqMap::x_GetLastEndSegmentIndex(), CSeqMap::x_GetSegment(), and CSeqMap::x_GetSegmentLength().

Referenced by CSeqMap::HasZeroGapAt(), CSeqMap::LoadSeq_data(), CSeqMap::SetRegionInChunk(), and CSeqMap_CI::x_Push().

x_GetBioseqInfo()

const CBioseq_Info & CSeqMap::x_GetBioseqInfo ( const CSegment &  seg, CScope *  scope  ) const

protected

Definition at line 319 of file seq_map.cpp.

References CTSE_Info::FindBioseq(), CScope::GetBioseqHandle(), CSeq_id_Handle::GetHandle(), CTSE_Info_Object::GetTSE_Info(), CSeqMap::m_Bioseq, NCBI_THROW_FMT, CBioseq_Handle::x_GetInfo(), and CSeqMap::x_GetRefSeqid().

Referenced by CSeqMap::x_GetSubSeqMap(), and CSeqMap::x_ResolveSegmentLength().

x_GetChunkToLoad()

CRef< CTSE_Chunk_Info > CSeqMap::x_GetChunkToLoad ( const CSegment &  seg ) const

protected

Definition at line 461 of file seq_map.cpp.

References _ASSERT, CSeqMap::eSeqChunk, CConstRef< C, Locker >::GetPointer(), kInvalidSeqPos, CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_Position, CSeqMap::CSegment::m_RefObject, CSeqMap::CSegment::m_SegType, CSeqMap::m_SeqMap_Mtx, and CTSE_Chunk_Info::NotLoaded().

Referenced by CSeqMap::CanResolveRange().

x_GetFirstEndSegmentIndex()

size_t CSeqMap::x_GetFirstEndSegmentIndex ( void  ) const

inlineprotected

Definition at line 440 of file seq_map.hpp.

Referenced by CSeqMap::HasZeroGapAt(), CSeqMap::x_DoUpdateSeq_inst(), CSeqMap_CI_SegmentInfo::x_Move(), and CSeqMap_CI::x_Push().

x_GetIterator()

CSeqVector_CI & CSeqVector::x_GetIterator ( TSeqPos  pos ) const

inlineprivate

Definition at line 249 of file seq_vector.hpp.

References AutoPtr< X, Del >::get(), CSeqVector::m_Iterator, CSeqVector_CI::SetPos(), and CSeqVector::x_CreateIterator().

Referenced by CSeqVector::CanGetRange(), CSeqVector::GetGapSeq_literal(), CSeqVector::GetGapSizeForward(), CSeqVector::GetSeqData(), CSeqVector::IsInGap(), and CSeqVector::operator[]().

x_GetLastEndSegmentIndex()

size_t CSeqMap::x_GetLastEndSegmentIndex ( void  ) const

inlineprotected

Definition at line 433 of file seq_map.hpp.

References CSeqMap::m_Segments.

Referenced by CSeqMap::GetLength(), CSeqMap::HasZeroGapAt(), CSeqMap::SetRegionInChunk(), CSeqMap::x_DoUpdateSeq_inst(), CSeqMap::x_FindSegment(), CSeqMap_CI_SegmentInfo::x_Move(), CSeqMap_CI::x_Push(), and CSeqMap::x_ResolveSegmentPosition().

x_GetObject()

const CObject * CSeqMap::x_GetObject ( const CSegment &  seg ) const

protected

Definition at line 481 of file seq_map.cpp.

References CConstRef< C, Locker >::GetPointer(), CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_RefObject, CSeqMap::CSegment::m_SegType, NCBI_THROW, and CSeqMap::x_LoadObject().

Referenced by CSeqMap::x_GetRefSeqid(), CSeqMap::x_GetSeq_data(), and CSeqMap::x_GetSubSeqMap().

x_GetPacked2naSeqData()

void CSeqVector::x_GetPacked2naSeqData ( string &  dst_str, TSeqPos  src_pos, TSeqPos  src_end  )

private

Definition at line 983 of file seq_vector.cpp.

References _ASSERT, count, data, CSeq_data_Base::e_Ncbi2na, CSeq_data_Base::e_Ncbi4na, CSeqVectorTypes::eCaseConversion_none, CSeqMap::eSeqGap, CSeqMap::fDefaultFlags, CSeqVector::GetCoding(), CSeqMap_CI::GetEndPosition(), CRef< C, Locker >::GetPointer(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefData(), CSeqMap_CI::GetRefEndPosition(), CSeqMap_CI::GetRefMinusStrand(), CSeqMap_CI::GetRefPosition(), CHeapScope::GetScopeOrNull(), CSeqMap_CI::GetType(), kMax_UInt, CSeqVector::m_Randomizer, CSeqVector::m_Scope, CSeqVector::m_SeqMap, CSeqVector::m_Strand, CSeqVector::m_TSE, min(), NCBI_THROW, NCBI_THROW_FMT, SSeqMapSelector::SetLinkUsedTSE(), SSeqMapSelector::SetStrand(), CSeqVectorTypes::sm_TrivialTable, CSeqVectorTypes::sx_GetConvertTable(), CSeqVectorTypes::sx_GetGapChar(), table, x_Append2To2(), x_AppendAnyTo2(), and x_AppendRandomTo2().

Referenced by CSeqVector::GetPackedSeqData().

x_GetPacked4naSeqData()

void CSeqVector::x_GetPacked4naSeqData ( string &  dst_str, TSeqPos  src_pos, TSeqPos  src_end  )

private

Definition at line 912 of file seq_vector.cpp.

References _ASSERT, count, data, CSeqVectorTypes::eCaseConversion_none, CSeqMap::eSeqGap, CSeqMap::fDefaultFlags, CSeqVector::GetCoding(), CSeqMap_CI::GetEndPosition(), CSeqVector::GetGapChar(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefData(), CSeqMap_CI::GetRefEndPosition(), CSeqMap_CI::GetRefMinusStrand(), CSeqMap_CI::GetRefPosition(), CHeapScope::GetScopeOrNull(), CSeqMap_CI::GetType(), kMax_UInt, CSeqVector::m_Scope, CSeqVector::m_SeqMap, CSeqVector::m_Strand, CSeqVector::m_TSE, min(), NCBI_THROW_FMT, SSeqMapSelector::SetLinkUsedTSE(), SSeqMapSelector::SetStrand(), CSeqVectorTypes::sm_TrivialTable, CSeqVectorTypes::sx_GetConvertTable(), table, x_Append4To4(), x_AppendAnyTo4(), and x_AppendGapTo4().

Referenced by CSeqVector::GetPackedSeqData().

x_GetPacked8SeqData()

void CSeqVector::x_GetPacked8SeqData ( string &  dst_str, TSeqPos  src_pos, TSeqPos  src_end  )

private

Definition at line 821 of file seq_vector.cpp.

References _ASSERT, _DEBUG_ARG, count, data, CSeq_data_Base::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeq_data_Base::e_Ncbi8aa, CSeq_data_Base::e_Ncbi8na, CSeq_data_Base::e_Ncbieaa, CSeq_data_Base::e_Ncbistdaa, CSeqVectorTypes::eCaseConversion_none, CSeqMap::eSeqGap, CSeqMap::fDefaultFlags, CSeqVector::GetCoding(), CSeqMap_CI::GetEndPosition(), CSeqVector::GetGapChar(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefData(), CSeqMap_CI::GetRefEndPosition(), CSeqMap_CI::GetRefMinusStrand(), CSeqMap_CI::GetRefPosition(), CHeapScope::GetScopeOrNull(), CSeqMap_CI::GetType(), kMax_UInt, CSeqVector::m_Scope, CSeqVector::m_SeqMap, CSeqVector::m_Strand, CSeqVector::m_TSE, min(), NCBI_THROW_FMT, SSeqMapSelector::SetLinkUsedTSE(), SSeqMapSelector::SetStrand(), CSeqVectorTypes::sm_TrivialTable, CSeqVectorTypes::sx_GetConvertTable(), table, x_Append8To8(), x_AppendAnyTo8(), and x_AppendGapTo8().

Referenced by CSeqVector::GetPackedSeqData().

x_GetRefMinusStrand()

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

protected

Definition at line 793 of file seq_map.cpp.

References CSeqMap::CSegment::m_RefMinusStrand.

x_GetRefPosition()

TSeqPos CSeqMap::x_GetRefPosition ( const CSegment &  seg ) const

protected

Definition at line 787 of file seq_map.cpp.

References CSeqMap::CSegment::m_RefPosition.

x_GetRefSeqid()

const CSeq_id & CSeqMap::x_GetRefSeqid ( const CSegment &  seg ) const

protected

Definition at line 777 of file seq_map.cpp.

References CSeqMap::eSeqRef, CSeqMap::CSegment::m_SegType, NCBI_THROW, and CSeqMap::x_GetObject().

Referenced by CSeqMap::CreateSeqMapForSeq_loc(), CSeqMap::GetSeqMapForSeq_loc(), CSeqMap::x_DoUpdateSeq_inst(), CSeqMap::x_GetBioseqInfo(), and CSeqMap::x_ResolveSegmentLength().

x_GetSegment()

const CSeqMap::CSegment & CSeqMap::x_GetSegment ( size_t  index ) const

inlineprotected

Definition at line 447 of file seq_map.hpp.

References _ASSERT, and CSeqMap::m_Segments.

Referenced by CSeqMap::CreateSeqMapForSeq_loc(), CSeqMap::GetSeqMapForSeq_loc(), CSeqMap::HasZeroGapAt(), CSeqMap::LoadSeq_data(), CSeqMap::x_FindSegment(), CSeqMap_CI_SegmentInfo::x_GetSegment(), CSeqMap::x_GetSegmentLength(), CSeqMap_CI_SegmentInfo::x_Move(), CSeqMap::x_ResolveSegmentLength(), and CSeqMap::x_ResolveSegmentPosition().

x_GetSegmentEndPosition()

TSeqPos CSeqMap::x_GetSegmentEndPosition ( size_t  index, CScope *  scope  ) const

inlineprotected

Definition at line 475 of file seq_map.hpp.

References CSeqMap::x_GetSegmentLength(), and CSeqMap::x_GetSegmentPosition().

Referenced by CSeqMap_CI::x_Push().

x_GetSegmentException()

void CSeqMap::x_GetSegmentException ( size_t  index ) const

protected

Definition at line 305 of file seq_map.cpp.

References NCBI_THROW.

Referenced by CSeqMap::SetRegionInChunk(), and CSeqMap::x_ResolveSegmentPosition().

x_GetSegmentLength()

TSeqPos CSeqMap::x_GetSegmentLength ( size_t  index, CScope *  scope  ) const

inlineprotected

Definition at line 464 of file seq_map.hpp.

References kInvalidSeqPos, CSeqMap::CSegment::m_Length, CSeqMap::x_GetSegment(), and CSeqMap::x_ResolveSegmentLength().

Referenced by CSeqMap::x_DoUpdateSeq_inst(), CSeqMap::x_FindSegment(), CSeqMap::x_GetSegmentEndPosition(), CSeqMap_CI_SegmentInfo::x_Move(), CSeqMap_CI::x_Push(), and CSeqMap::x_ResolveSegmentPosition().

x_GetSegmentPosition()

TSeqPos CSeqMap::x_GetSegmentPosition ( size_t  index, CScope *  scope  ) const

inlineprotected

Definition at line 455 of file seq_map.hpp.

References CSeqMap::m_Resolved, CSeqMap::m_Segments, and CSeqMap::x_ResolveSegmentPosition().

Referenced by CSeqMap::GetLength(), CSeqMap::InsertSegmentGap(), CSeqMap::RemoveSegment(), CSeqMap::x_GetSegmentEndPosition(), CSeqMap_CI_SegmentInfo::x_Move(), and CSeqMap_CI::x_Push().

x_GetSeq_data()

const CSeq_data & CSeqMap::x_GetSeq_data ( const CSegment &  seg ) const

protected

Definition at line 544 of file seq_map.cpp.

References CSeqMap::eSeqData, CSeqMap::eSeqGap, CSeqMap::eSeqLiteral, literal(), CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_RefObject, CSeqMap::CSegment::m_SegType, NCBI_THROW, and CSeqMap::x_GetObject().

Referenced by CSeqMap_CI::GetRefData(), and CSeqMap::x_DoUpdateSeq_inst().

x_GetSeq_literal()

CConstRef< CSeq_literal > CSeqMap::x_GetSeq_literal ( const CSegment &  seg ) const

protected

Definition at line 563 of file seq_map.cpp.

References ConstRef(), CSeqMap::eSeqLiteral, CSeqMap::CSegment::m_ObjType, and CSeqMap::CSegment::m_RefObject.

Referenced by CSeqMap_CI::GetRefGapLiteral(), CSeqMap::SetRegionInChunk(), and CSeqMap::x_DoUpdateSeq_inst().

x_GetSequenceClass()

int CSeqMap::x_GetSequenceClass ( void  ) const

protected

Definition at line 588 of file seq_map.cpp.

References CBioseq_Handle::eSequenceClass_none, CBioseq_Info::GetSequenceClass(), and CSeqMap::m_Bioseq.

Referenced by CSeqMap_CI_SegmentInfo::x_GetSequenceClass().

x_GetSubSeqMap()

CConstRef< CSeqMap > CSeqMap::x_GetSubSeqMap ( const CSegment &  seg, CScope *  scope, bool  resolveExternal = false  ) const

protected

Definition at line 523 of file seq_map.cpp.

References CSeqMap::eSeqRef, CSeqMap::eSeqSubMap, CSeqMap::CSegment::m_SegType, CConstRef< C, Locker >::Reset(), CSeqMap::x_GetBioseqInfo(), and CSeqMap::x_GetObject().

Referenced by CSeqMap::HasZeroGapAt(), and CSeqMap::x_ResolveSegmentLength().

x_InitRandomizer()

void CSeqVector::x_InitRandomizer ( CRandom &  random_gen )

private

Definition at line 1329 of file seq_vector.cpp.

References CSeqVector::SetRandomizeAmbiguities().

Referenced by CSeqVector::SetRandomizeAmbiguities().

x_InitSequenceType()

void CSeqVector::x_InitSequenceType ( void  )

private

x_IsChanged()

bool CSeqMap::x_IsChanged ( void  ) const

inlineprotected

Definition at line 499 of file seq_map.hpp.

References CSeqMap::m_Changed.

Referenced by CSeqMap::x_UpdateSeq_inst().

x_LoadObject()

void CSeqMap::x_LoadObject ( const CSegment &  seg ) const

protected

Definition at line 442 of file seq_map.cpp.

References _ASSERT, CSeqMap::eSeqChunk, CConstRef< C, Locker >::GetPointer(), kInvalidSeqPos, CTSE_Chunk_Info::Load(), CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_Position, CSeqMap::CSegment::m_RefObject, CSeqMap::CSegment::m_SegType, and CSeqMap::m_SeqMap_Mtx.

Referenced by CSeqMap::x_GetObject().

x_ResetIterator()

void CSeqVector::x_ResetIterator ( void  ) const

private

Definition at line 269 of file seq_vector.cpp.

References AutoPtr< X, Del >::get(), CSeqVector::GetMutex(), CSeqVector::m_Iterator, and AutoPtr< X, Del >::reset().

Referenced by CSeqVector::SetCoding(), CSeqVector::SetRandomizeAmbiguities(), and CSeqVector::SetStrand().

x_ResolveSegmentLength()

TSeqPos CSeqMap::x_ResolveSegmentLength ( size_t  index, CScope *  scope  ) const

protected

Definition at line 343 of file seq_map.cpp.

References CSeqMap::eSeqRef, CSeqMap::eSeqSubMap, CTSE_Info::FindMatchingBioseq(), CBioseq_Info::GetBioseqLength(), CSeq_id_Handle::GetHandle(), CSeqMap::GetLength(), CTSE_Info_Object::GetTSE_Info(), kInvalidSeqPos, CSeqMap::m_Bioseq, CSeqMap::CSegment::m_Length, CSeqMap::CSegment::m_SegType, NCBI_THROW, CSeqMap::x_GetBioseqInfo(), CSeqMap::x_GetRefSeqid(), CSeqMap::x_GetSegment(), and CSeqMap::x_GetSubSeqMap().

Referenced by CSeqMap::x_GetSegmentLength().

x_ResolveSegmentPosition()

TSeqPos CSeqMap::x_ResolveSegmentPosition ( size_t  index, CScope *  scope  ) const

protected

Definition at line 376 of file seq_map.cpp.

References kInvalidSeqPos, CSeqMap::CSegment::m_Position, CSeqMap::m_Resolved, CSeqMap::m_Segments, CSeqMap::m_SeqMap_Mtx, NCBI_THROW, CSeqMap::x_GetLastEndSegmentIndex(), CSeqMap::x_GetSegment(), CSeqMap::x_GetSegmentException(), and CSeqMap::x_GetSegmentLength().

Referenced by CSeqMap::x_GetSegmentPosition().

x_SetChanged()

void CSeqMap::x_SetChanged ( size_t  index )

protected

Definition at line 597 of file seq_map.cpp.

References kInvalidSeqPos, CSeqMap::m_Bioseq, CSeqMap::m_Changed, CSeqMap::m_HasSegments, CSeqMap::CSegment::m_Position, CSeqMap::m_Resolved, CSeqMap::m_SeqLength, CBioseq_Info::x_SetChangedSeqMap(), and CSeqMap::x_SetSegment().

Referenced by CSeqMap::InsertSegmentGap(), CSeqMap::RemoveSegment(), CSeqMap::x_SetSegmentData(), CSeqMap::x_SetSegmentGap(), and CSeqMap::x_SetSegmentRef().

x_SetChunk()

void CSeqMap::x_SetChunk ( CSegment &  seg, CTSE_Chunk_Info &  chunk  )

protected

Definition at line 508 of file seq_map.cpp.

References CSeqMap::eSeqChunk, CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_RefObject, CSeqMap::CSegment::m_SegType, NCBI_THROW, and CConstRef< C, Locker >::Reset().

Referenced by CSeqMap::SetRegionInChunk().

x_SetObject()

void CSeqMap::x_SetObject ( CSegment &  seg, const CObject &  obj  )

protected

Definition at line 493 of file seq_map.cpp.

References CSeqMap::m_Changed, CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_RefObject, CSeqMap::CSegment::m_SegType, CSeqMap::m_SeqMap_Mtx, NCBI_THROW, and CConstRef< C, Locker >::Reset().

Referenced by CSeqMap::x_SetSeq_data().

x_SetSegment()

CSeqMap::CSegment & CSeqMap::x_SetSegment ( size_t  index )

protected

Definition at line 312 of file seq_map.cpp.

References _ASSERT, and CSeqMap::m_Segments.

Referenced by CSeqMap::InsertSegmentGap(), CSeqMap::RemoveSegment(), CSeqMap::SetRegionInChunk(), CSeqMap::x_DoUpdateSeq_inst(), CSeqMap::x_SetChanged(), CSeqMap::x_SetSegmentData(), CSeqMap::x_SetSegmentGap(), CSeqMap::x_SetSegmentRef(), and CSeqMap::x_SetSeq_data().

x_SetSegmentData()

void CSeqMap::x_SetSegmentData ( size_t  index, TSeqPos  length, CSeq_data &  data  )

protected

Definition at line 647 of file seq_map.cpp.

References data, CSeqMap::eSeqData, CSeqMap::eSeqGap, CSeqMap::CSegment::m_Length, CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_RefObject, CSeqMap::CSegment::m_SegType, CSeqMap::m_SeqMap_Mtx, CSeqMap::x_SetChanged(), CSeqMap::x_SetSegment(), and CSeqMap::x_StartEditing().

Referenced by CSeqMap::SetSegmentData().

x_SetSegmentGap()

void CSeqMap::x_SetSegmentGap ( size_t  index, TSeqPos  length, CSeq_data *  gap_data = 0  )

protected

Definition at line 626 of file seq_map.cpp.

References CSeqMap::eSeqData, CSeqMap::eSeqGap, CSeq_data_Base::IsGap(), CSeqMap::CSegment::m_Length, CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_RefObject, CSeqMap::CSegment::m_SegType, CSeqMap::m_SeqMap_Mtx, NCBI_THROW, CSeqMap::x_SetChanged(), CSeqMap::x_SetSegment(), and CSeqMap::x_StartEditing().

Referenced by CSeqMap::SetSegmentGap().

x_SetSegmentRef()

void CSeqMap::x_SetSegmentRef ( size_t  index, TSeqPos  length, const CSeq_id &  ref_id, TSeqPos  ref_pos, bool  ref_minus_strand  )

protected

Definition at line 662 of file seq_map.cpp.

References CSeqMap::eSeqRef, CConstRef< C, Locker >::GetPointer(), CSeqMap::CSegment::m_Length, CSeqMap::CSegment::m_ObjType, CSeqMap::CSegment::m_RefMinusStrand, CSeqMap::CSegment::m_RefObject, CSeqMap::CSegment::m_RefPosition, CSeqMap::CSegment::m_SegType, CSeqMap::m_SeqMap_Mtx, CSeqMap::x_SetChanged(), CSeqMap::x_SetSegment(), and CSeqMap::x_StartEditing().

Referenced by CSeqMap::SetSegmentRef().

x_SetSeq_data()

void CSeqMap::x_SetSeq_data ( size_t  index, CSeq_data &  data  )

protected

Definition at line 572 of file seq_map.cpp.

References data, ERR_POST, CSeqMap::eSeqData, CSeqMap::eSeqGap, CSeqMap::CSegment::m_SegType, NCBI_THROW, CSeqMap::x_SetObject(), and CSeqMap::x_SetSegment().

Referenced by CSeqMap::LoadSeq_data().

x_SetSubSeqMap()

void CSeqMap::x_SetSubSeqMap ( size_t  index, CSeqMap_Delta_seqs *  subMap  )

protected

Definition at line 537 of file seq_map.cpp.

References NCBI_THROW.

x_StartEditing()

void CSeqMap::x_StartEditing ( void  )

protected

Definition at line 613 of file seq_map.cpp.

References CDataSource::CanBeEdited(), CTSE_Info_Object::GetDataSource(), CSeqMap::m_Bioseq, and NCBI_THROW.

Referenced by CSeqMap::InsertSegmentGap(), CSeqMap::RemoveSegment(), CSeqMap::x_SetSegmentData(), CSeqMap::x_SetSegmentGap(), and CSeqMap::x_SetSegmentRef().

x_UpdateSeq_inst()

bool CSeqMap::x_UpdateSeq_inst ( CSeq_inst &  inst )

inlineprotected

Definition at line 506 of file seq_map.hpp.

References CSeqMap::m_Changed, CSeqMap::x_DoUpdateSeq_inst(), and CSeqMap::x_IsChanged().

Referenced by CBioseq_Info::x_DoUpdate().

~CNcbi2naRandomizer()

CNcbi2naRandomizer::~CNcbi2naRandomizer

(

void

)

Definition at line 107 of file seq_vector.cpp.

~CSeqMap()

CSeqMap::~CSeqMap

(

void

)

Definition at line 297 of file seq_map.cpp.

References _ASSERT, CSeqMap::m_Bioseq, CSeqMap::m_Resolved, and CSeqMap::m_Segments.

~CSeqVector()

CSeqVector::~CSeqVector ( void  )

virtual

Definition at line 239 of file seq_vector.cpp.

Variable Documentation

m_Bioseq

CBioseq_Info* CSeqMap::m_Bioseq

protected

Definition at line 380 of file seq_map.hpp.

Referenced by CBioseq_Info::GetSeqMap(), CBioseq_Info::x_AttachMap(), CSeqMap::x_GetBioseqInfo(), CSeqMap::x_GetSequenceClass(), CBioseq_Info::x_ResetSeqMap(), CSeqMap::x_ResolveSegmentLength(), CSeqMap::x_SetChanged(), CBioseq_Info::x_SetObject(), CSeqMap::x_StartEditing(), and CSeqMap::~CSeqMap().

m_Changed

TChanged CSeqMap::m_Changed

protected

Definition at line 401 of file seq_map.hpp.

Referenced by CSeqMap::x_IsChanged(), CSeqMap::x_SetChanged(), CSeqMap::x_SetObject(), and CSeqMap::x_UpdateSeq_inst().

m_Coding

TCoding CSeqVector::m_Coding

private

Definition at line 205 of file seq_vector.hpp.

Referenced by CSeqVector::GetCoding(), CSeqVector::operator=(), CSeqVector::SetCoding(), and CSeqVector_CI::x_SetVector().

m_Delta

CRef<CObject> CSeqMap::m_Delta

protected

Definition at line 391 of file seq_map.hpp.

m_ExactMasterRange

CRange<TSeqPos> CSeqMapSwitchPoint::m_ExactMasterRange

Definition at line 82 of file seq_map_switch.hpp.

m_FirstAlign

CConstRef<CSeq_align> CSeqMapSwitchPoint::m_FirstAlign

Definition at line 67 of file seq_map_switch.hpp.

m_FixedTable

char CNcbi2naRandomizer::m_FixedTable[16]

private

Definition at line 236 of file seq_vector.hpp.

Referenced by CNcbi2naRandomizer::CNcbi2naRandomizer(), and CNcbi2naRandomizer::RandomizeData().

m_HasSegments

atomic<THasSegments> CSeqMap::m_HasSegments

mutableprotected

Definition at line 398 of file seq_map.hpp.

Referenced by CSeqMap::HasSegmentOfType(), and CSeqMap::x_SetChanged().

m_Iterator

AutoPtr<CSeqVector_CI> CSeqVector::m_Iterator

mutableprivate

Definition at line 209 of file seq_vector.hpp.

Referenced by CSeqVector::operator=(), CSeqVector::x_CreateIterator(), CSeqVector::x_GetIterator(), and CSeqVector::x_ResetIterator().

m_IteratorMutex

TMutex CSeqVector::m_IteratorMutex

mutableprivate

Definition at line 208 of file seq_vector.hpp.

Referenced by CSeqVector::GetMutex().

m_LeftDifferences

TDifferences CSeqMapSwitchPoint::m_LeftDifferences

Definition at line 90 of file seq_map_switch.hpp.

Referenced by CSeqMapSwitchPoint::GetDifferences(), CSeqMapSwitchPoint::GetInsert(), and CSeqMapSwitchPoint::GetLeftInPlaceInsert().

m_LeftId

CSeq_id_Handle CSeqMapSwitchPoint::m_LeftId

Definition at line 70 of file seq_map_switch.hpp.

Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint().

m_LeftMinusStrand

bool CSeqMapSwitchPoint::m_LeftMinusStrand

Definition at line 72 of file seq_map_switch.hpp.

Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint().

m_LeftPos

TSeqPos CSeqMapSwitchPoint::m_LeftPos

Definition at line 71 of file seq_map_switch.hpp.

Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint().

m_Length

atomic<TSeqPos> CSeqMap::CSegment::m_Length

mutable

Definition at line 255 of file seq_map.hpp.

Referenced by CSeqMap_CI_SegmentInfo::GetRefPosition(), CSeqMap::HasZeroGapAt(), CSeqMap_CI_SegmentInfo::InRange(), CSeqMap::LoadSeq_data(), CSeqMap::SPosLessSegment::operator()(), CSeqMap::CSegment::operator=(), CSeqMap::SetRegionInChunk(), CSeqMap_CI_SegmentInfo::x_GetLevelRealEnd(), CSeqMap::x_GetSegmentLength(), CSeqMap_CI_SegmentInfo::x_Move(), CSeqMap::x_ResolveSegmentLength(), CSeqMap::x_SetSegmentData(), CSeqMap::x_SetSegmentGap(), and CSeqMap::x_SetSegmentRef().

m_Master

CBioseq_Handle CSeqMapSwitchPoint::m_Master

Definition at line 62 of file seq_map_switch.hpp.

Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint(), CSeqMapSwitchPoint::GetInsert(), CSeqMapSwitchPoint::InsertInPlace(), and CSeqMapSwitchPoint::operator<().

m_MasterPos

TSeqPos CSeqMapSwitchPoint::m_MasterPos

Definition at line 64 of file seq_map_switch.hpp.

Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint(), CSeqMapSwitchPoint::GetDifferences(), CSeqMapSwitchPoint::GetInsert(), and CSeqMapSwitchPoint::operator<().

m_MasterRange

CRange<TSeqPos> CSeqMapSwitchPoint::m_MasterRange

Definition at line 80 of file seq_map_switch.hpp.

Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint(), and CSeqMapSwitchPoint::GetInsert().

m_Mol [1/2]

TMol CSeqMap::m_Mol

protected

Definition at line 394 of file seq_map.hpp.

Referenced by CSeqMap::CreateSeqMapForSeq_loc(), CSeqMap::CSeqMap(), CSeqMap::GetMol(), CSeqMap::GetSeqMapForSeq_loc(), CSeqMap::ResetMol(), and CSeqMap::SetMol().

m_Mol [2/2]

TMol CSeqVector::m_Mol

private

Definition at line 203 of file seq_vector.hpp.

Referenced by CSeqVector::CSeqVector(), CSeqVector::GetSequenceType(), and CSeqVector::operator=().

m_ObjType

char CSeqMap::CSegment::m_ObjType

Definition at line 260 of file seq_map.hpp.

Referenced by CSeqMap::CSegment::IsSetData(), CSeqMap::CSegment::operator=(), CSeqMap::SetRegionInChunk(), CSeqMap::x_AddGap(), CSeqMap::x_DoUpdateSeq_inst(), CSeqMap::x_GetChunkToLoad(), CSeqMap::x_GetObject(), CSeqMap::x_GetSeq_data(), CSeqMap::x_GetSeq_literal(), CSeqMap::x_LoadObject(), CSeqMap::x_SetChunk(), CSeqMap::x_SetObject(), CSeqMap::x_SetSegmentData(), CSeqMap::x_SetSegmentGap(), and CSeqMap::x_SetSegmentRef().

m_Position

atomic<TSeqPos> CSeqMap::CSegment::m_Position

mutable

Definition at line 253 of file seq_map.hpp.

Referenced by CSeqMap_CI::CSeqMap_CI(), CSeqMap_CI_SegmentInfo::GetRefPosition(), CSeqMap::HasZeroGapAt(), CSeqMap_CI_SegmentInfo::InRange(), CSeqMap::InsertSegmentGap(), CSeqMap::LoadSeq_data(), CSeqMap::SPosLessSegment::operator()(), CSeqMap::CSegment::operator=(), CSeqMap::RemoveSegment(), CSeqMap::SetRegionInChunk(), CSeqMap::x_AddEnd(), CSeqMap::x_FindSegment(), CSeqMap::x_GetChunkToLoad(), CSeqMap_CI_SegmentInfo::x_GetLevelRealEnd(), CSeqMap_CI_SegmentInfo::x_GetLevelRealPos(), CSeqMap::x_LoadObject(), CSeqMap_CI_SegmentInfo::x_Move(), CSeqMap::x_ResolveSegmentPosition(), and CSeqMap::x_SetChanged().

m_Randomizer

CRef<INcbi2naRandomizer> CSeqVector::m_Randomizer

private

Definition at line 206 of file seq_vector.hpp.

Referenced by CSeqVector::SetRandomizeAmbiguities(), CSeqVector::x_GetPacked2naSeqData(), and CSeqVector_CI::x_SetVector().

m_RandomTable

char CNcbi2naRandomizer::m_RandomTable[16][kRandomDataSize]

private

Definition at line 237 of file seq_vector.hpp.

Referenced by CNcbi2naRandomizer::CNcbi2naRandomizer(), and CNcbi2naRandomizer::RandomizeData().

m_RefMinusStrand

bool CSeqMap::CSegment::m_RefMinusStrand

Definition at line 263 of file seq_map.hpp.

Referenced by CSeqMap_CI_SegmentInfo::GetRefMinusStrand(), CSeqMap_CI_SegmentInfo::GetRefPosition(), CSeqMap::HasZeroGapAt(), CSeqMap::CSegment::operator=(), CSeqMap::x_AddSegment(), CSeqMap::x_DoUpdateSeq_inst(), CSeqMap::x_GetRefMinusStrand(), and CSeqMap::x_SetSegmentRef().

m_RefObject

CConstRef<CObject> CSeqMap::CSegment::m_RefObject

Definition at line 265 of file seq_map.hpp.

Referenced by CSeqMap::CSegment::operator=(), CSeqMap::SetRegionInChunk(), CSeqMap::x_AddGap(), CSeqMap::x_AddSegment(), CSeqMap::x_GetChunkToLoad(), CSeqMap::x_GetObject(), CSeqMap::x_GetSeq_data(), CSeqMap::x_GetSeq_literal(), CSeqMap::x_LoadObject(), CSeqMap::x_SetChunk(), CSeqMap::x_SetObject(), CSeqMap::x_SetSegmentData(), CSeqMap::x_SetSegmentGap(), and CSeqMap::x_SetSegmentRef().

m_RefPosition

TSeqPos CSeqMap::CSegment::m_RefPosition

Definition at line 264 of file seq_map.hpp.

Referenced by CSeqMap_CI_SegmentInfo::GetRefPosition(), CSeqMap::HasZeroGapAt(), CSeqMap::CSegment::operator=(), CSeqMap::x_AddSegment(), CSeqMap::x_DoUpdateSeq_inst(), CSeqMap::x_GetRefPosition(), and CSeqMap::x_SetSegmentRef().

m_Resolved

atomic<size_t> CSeqMap::m_Resolved

mutableprotected

Definition at line 388 of file seq_map.hpp.

Referenced by CSeqMap::InsertSegmentGap(), CSeqMap::RemoveSegment(), CSeqMap::SetRegionInChunk(), CSeqMap::x_FindSegment(), CSeqMap::x_GetSegmentPosition(), CSeqMap::x_ResolveSegmentPosition(), CSeqMap::x_SetChanged(), and CSeqMap::~CSeqMap().

m_RightDifferences

TDifferences CSeqMapSwitchPoint::m_RightDifferences

Definition at line 90 of file seq_map_switch.hpp.

Referenced by CSeqMapSwitchPoint::GetDifferences(), CSeqMapSwitchPoint::GetInsert(), and CSeqMapSwitchPoint::GetRightInPlaceInsert().

m_RightId

CSeq_id_Handle CSeqMapSwitchPoint::m_RightId

Definition at line 75 of file seq_map_switch.hpp.

Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint().

m_RightMinusStrand

bool CSeqMapSwitchPoint::m_RightMinusStrand

Definition at line 77 of file seq_map_switch.hpp.

Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint().

m_RightPos

TSeqPos CSeqMapSwitchPoint::m_RightPos

Definition at line 76 of file seq_map_switch.hpp.

Referenced by CSeqMapSwitchPoint::ChangeSwitchPoint().

m_Scope

CHeapScope CSeqVector::m_Scope

private

Definition at line 199 of file seq_vector.hpp.

Referenced by CSeqVector::CSeqVector(), CSeqVector::GetScope(), CSeqVector::operator=(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), CSeqVector::x_GetPacked8SeqData(), and CSeqVector_CI::x_SetVector().

m_Segments

vector<CSegment> CSeqMap::m_Segments

protected

Definition at line 385 of file seq_map.hpp.

Referenced by CSeqMap::CountSegmentsOfType(), CSeqMap::CSeqMap(), CSeqMap::GetSegmentsCount(), CSeqMap::HasSegmentOfType(), CSeqMap::InsertSegmentGap(), CSeqMap::RemoveSegment(), CSeqMap::x_AddEnd(), CSeqMap::x_AddGap(), CSeqMap::x_AddSegment(), CSeqMap::x_FindSegment(), CSeqMap::x_GetLastEndSegmentIndex(), CSeqMap::x_GetSegment(), CSeqMap::x_GetSegmentPosition(), CSeqMap::x_ResolveSegmentPosition(), CSeqMap::x_SetSegment(), and CSeqMap::~CSeqMap().

m_SegType

char CSeqMap::CSegment::m_SegType

Definition at line 259 of file seq_map.hpp.

Referenced by CSeqMap::CreateSeqMapForSeq_loc(), CSeqMap::GetSeqMapForSeq_loc(), CSeqMap::HasZeroGapAt(), CSeqMap::CSegment::IsSetData(), CSeqMap::CSegment::operator=(), CSeqMap::RemoveSegment(), CSeqMap::SetRegionInChunk(), CSeqMap::x_DoUpdateSeq_inst(), CSeqMap_CI::x_Found(), CSeqMap::x_GetChunkToLoad(), CSeqMap::x_GetObject(), CSeqMap::x_GetRefSeqid(), CSeqMap::x_GetSeq_data(), CSeqMap::x_GetSubSeqMap(), CSeqMap::x_LoadObject(), CSeqMap_CI::x_Push(), CSeqMap_CI::x_RefTSEMatch(), CSeqMap::x_ResolveSegmentLength(), CSeqMap::x_SetChunk(), CSeqMap::x_SetObject(), CSeqMap::x_SetSegmentData(), CSeqMap::x_SetSegmentGap(), CSeqMap::x_SetSegmentRef(), and CSeqMap::x_SetSeq_data().

m_SeqLength

atomic<TSeqPos> CSeqMap::m_SeqLength

mutableprotected

Definition at line 404 of file seq_map.hpp.

Referenced by CSeqMap::CSeqMap(), CSeqMap::GetLength(), CSeqMap::SetRegionInChunk(), and CSeqMap::x_SetChanged().

m_SeqMap

CConstRef<CSeqMap> CSeqVector::m_SeqMap

private

Definition at line 200 of file seq_vector.hpp.

Referenced by CSeqVector::CSeqVector(), CSeqVector::GetSeqMap(), CSeqVector::operator=(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), CSeqVector::x_GetPacked8SeqData(), and CSeqVector_CI::x_SetVector().

m_SeqMap_Mtx

CMutex CSeqMap::m_SeqMap_Mtx

mutableprotected

Definition at line 407 of file seq_map.hpp.

Referenced by CSeqMap::InsertSegmentGap(), CSeqMap::RemoveSegment(), CSeqMap::SetRegionInChunk(), CSeqMap::x_FindSegment(), CSeqMap::x_GetChunkToLoad(), CSeqMap::x_LoadObject(), CSeqMap::x_ResolveSegmentPosition(), CSeqMap::x_SetObject(), CSeqMap::x_SetSegmentData(), CSeqMap::x_SetSegmentGap(), and CSeqMap::x_SetSegmentRef().

m_Size

TSeqPos CSeqVector::m_Size

private

Definition at line 202 of file seq_vector.hpp.

Referenced by CSeqVector::CSeqVector(), CSeqVector::empty(), CSeqVector::operator=(), and CSeqVector::size().

m_Strand

ENa_strand CSeqVector::m_Strand

private

Definition at line 204 of file seq_vector.hpp.

Referenced by CSeqVector::GetStrand(), CSeqVector::operator=(), CSeqVector::SetStrand(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), CSeqVector::x_GetPacked8SeqData(), and CSeqVector_CI::x_SetVector().

m_TSE

CTSE_Handle CSeqVector::m_TSE

private

Definition at line 201 of file seq_vector.hpp.

Referenced by CSeqVector::CSeqVector(), CSeqVector::GetPackedSeqData(), CSeqVector::operator=(), CSeqVector::x_GetPacked2naSeqData(), CSeqVector::x_GetPacked4naSeqData(), CSeqVector::x_GetPacked8SeqData(), and CSeqVector_CI::x_SetVector().

m_UnknownLength

bool CSeqMap::CSegment::m_UnknownLength

Definition at line 256 of file seq_map.hpp.

Referenced by CSeqMap_CI::IsUnknownLength(), CSeqMap::CSegment::operator=(), and CSeqMap::x_DoUpdateSeq_inst().

Friends

CBioseq_Handle

friend class CBioseq_Handle

friend

Definition at line 178 of file seq_vector.hpp.

CBioseq_Info

friend class CBioseq_Info

friend

Definition at line 238 of file seq_map.hpp.

CSegment

friend class CSegment

friend

Definition at line 235 of file seq_map.hpp.

Referenced by CSeqMap::x_AddSegment().

CSeqMap_CI

friend class CSeqMap_CI

friend

Definition at line 409 of file seq_map.hpp.

Referenced by CSeqMap::Begin(), CSeqMap::BeginResolved(), CSeqMap::End(), CSeqMap::EndResolved(), CSeqMap::FindResolved(), CSeqMap::FindSegment(), CSeqMap::InsertSegmentGap(), CSeqMap::RemoveSegment(), and CSeqMap::ResolvedRangeIterator().

CSeqMap_CI_SegmentInfo

friend class CSeqMap_CI_SegmentInfo

friend

Definition at line 410 of file seq_map.hpp.

CSeqMap_SeqPoss

friend class CSeqMap_SeqPoss

friend

Definition at line 237 of file seq_map.hpp.

CSeqVector_CI

friend class CSeqVector_CI

friend

Definition at line 179 of file seq_vector.hpp.

Referenced by CSeqVector::begin(), CSeqVector::end(), and CSeqVector::x_CreateIterator().

SPosLessSegment

friend class SPosLessSegment

friend

Definition at line 236 of file seq_map.hpp.