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NCBI C++ ToolKit: include/objects/seqloc/Seq_loc.hpp Source File

GetTotalRange(

)

;

InvalidateTotalRangeCache(

)

;

IsReverseStrand(

)

;

FlipStrand(

);

ResetStrand(

);

(

*&

,

may_throw =

)

;

InvalidateIdCache(

)

;

SetId(

&

);

InvalidateCache(

)

;

PostRead(

)

;

fCompare_Default = 0,

ChangeToMix(

);

ChangeToPackedInt(

);

fStrand_Ignore = 1<<0,

fMerge_Contained = 1<<1,

fMerge_AbuttingOnly = 1<<2,

fMerge_Abutting = fMerge_AbuttingOnly | fMerge_Contained,

fMerge_OverlappingOnly = 1<<3,

fMerge_Overlapping = fMerge_OverlappingOnly | fMerge_Contained,

fMerge_All = fMerge_Abutting | fMerge_Overlapping,

fMerge_SingleRange = 1<<4,

fSortAndMerge_All = fSort | fMerge_All

x_UpdateTotalRange(

)

;

x_CalculateTotalRangeCheckId(

*&

)

;

x_CheckId(

*&

,

may_throw =

)

;

may_throw =

)

;

x_ChangeToMix(

& other);

x_ChangeToPackedInt(

& other);

x_ChangeToPackedPnt(

& other);

IsInBond(

)

;

IsBondA(

)

;

IsBondB(

)

;

pair<CSeq_loc_CI, CSeq_loc_CI> GetBondRange(

)

;

HasEquivSets(

)

;

IsInEquivSet(

)

;

GetEquivSetsCount(

)

;

pair<CSeq_loc_CI, CSeq_loc_CI> GetEquivSetRange(

level = 0)

;

pair<CSeq_loc_CI, CSeq_loc_CI> GetEquivPartRange(

level = 0)

;

& GetSeq_id(

)

;

GetRange(

)

;

IsSetStrand(

)

;

& GetEmbeddingSeq_loc(

)

;

* GetFuzzFrom(

)

;

* GetFuzzTo (

)

;

IsPoint(

)

;

GetSize(

)

;

GetPos(

)

;

SetPos(

pos);

x_IsValid(

)

;

* x_GetIteratorType(

)

;

x_CheckValid(

* where)

;

x_ThrowNotValid(

* where)

;

HasChanges(

)

;

MakeSeq_loc(EMakeType make_type = eMake_CompactType)

;

InsertInterval(

,

(from, to), strand);

InsertInterval(

,

(from, to), strand);

SetRange(

& range);

ResetStrand(

);

ResetFuzzFrom(

);

ResetFuzzTo(

);

ResetFuzz(

);

pair<CSeq_loc_I, CSeq_loc_I> GetEquivSetRange(

level = 0)

;

pair<CSeq_loc_I, CSeq_loc_I> GetEquivPartRange(

level = 0)

;

SetEquivMode(EEquivMode

);

SetEquivMode(eEquiv_new_equiv);

SetEquivMode(eEquiv_new_part);

SetEquivMode(eEquiv_none);

EEquivMode GetEquivMode(

)

;

RemoveBond(

);

MakeBondA(

);

MakeBondAB(

);

MakeBondB(

);

x_IsValidForInsert(

)

;

x_CheckValidForInsert(

* where)

;

* x_GetIteratorType(

)

;

( my_id ==

) {

.store(my_id, memory_order_release);

bool IsReverse(ENa_strand s)

ESeqLocExtremes

Used to determine the meaning of a location's Start/Stop positions.

EIsSetStrand

Flag used by IsSetStrand() to switch between any/all modes.

@ eIsSetStrand_Any

Check if any part has strand.

CLocalRange< TOffset > TRange

define for the fundamental building block of sequence ranges

vector< CRange< TSeqPos > > TRanges

Used as a helper for determining which pieces of a CSeq_loc to compare.

*** Sequence locations ********************************** *

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

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

Base class for all serializable objects.

Interface for getting bioseq length.

Interface for mapping IDs to the best synonym.

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

bool Empty(const CNcbiOstrstream &src)

unsigned int TSeqPos

Type for sequence locations and lengths.

EErrCode

Error types that an application can generate.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

ESerialRecursionMode

How to assign and compare child sub-objects of serial objects.

#define NCBISER_HAVE_POST_READ(Class)

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

@ eRecursive

Recursively.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

string GetLabel(const CSeq_id &id)

void InvalidateIdCache(void) const

void Rewind(void)

Reset the iterator to the initial state.

DECLARE_OPERATOR_BOOL(x_IsValid())

void InvalidateCache(void) const

Combine invalidation of all cached values.

bool x_IsValid(void) const

CSeq_loc_CI & operator++(void)

ENa_strand GetStrand(void) const

Get the location's strand.

void x_CheckValidForInsert(const char *where) const

CRange< TSeqPos > TRange

See related functions in objmgr/util/seq_loc_util.hpp:

bool x_UpdateId(const CSeq_id *&total_id, const CSeq_id *id, bool may_throw=true) const

virtual ~ILengthGetter(void)

bool IsReverseStrand(void) const

Return true if all ranges have reverse strand.

EEmptyFlag

Options for empty locations processing.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

atomic< TSeqPos > m_TotalRangeCacheFrom

size_t GetPos(void) const

Get iterator's position.

CSeq_loc_mix_Base::Tdata TLocations

void RemoveEquiv(size_t level=0)

Remove equiv set, all pieces that are part of the set will be preserved as independent pieces.

void StartNewEquiv(void)

Change equiv modification mode to add new equiv set for the next insert operation.

void x_CheckValid(const char *where) const

EMakeType

Options for creation modified locations Bond and equiv types are preserved if possible.

TRange GetTotalRange(void) const

EOpFlags

CSeq_loc operations.

CSeq_loc_CI const_iterator

Make CSeq_loc look like an STL container.

virtual CSeq_id_Handle GetBestSynonym(const CSeq_id &id)=0

CSeq_loc_I InsertEmpty(const CSeq_id &id)

Insert new element before the current one (.

void StopEquiv(void)

Change equiv modification mode to normal behavior that will only update existing equiv sets.

pair< CConstRef< CInt_fuzz >, CConstRef< CInt_fuzz > > m_Fuzz

bool IsSetStrand(void) const

Get strand.

CSeq_loc_I InsertInterval(const CSeq_id_Handle &id, TSeqPos from, TSeqPos to, ENa_strand strand=eNa_strand_unknown)

Insert new element before the current one (.

CSeq_id_Handle GetSeq_id_Handle(void) const

void SetSeq_id(const CSeq_id &id)

Set seq_id of the current location.

bool IsWhole(void) const

True if the current location is a whole sequence.

const CInt_fuzz * GetFuzzFrom(void) const

bool x_IsValidForInsert(void) const

CSeq_loc_I InsertInterval(const CSeq_id &id, TSeqPos from, TSeqPos to, ENa_strand strand=eNa_strand_unknown)

Insert new element before the current one (.

const CInt_fuzz * GetFuzzTo(void) const

const CSeq_loc_CI & operator*() const

CSeq_loc_I InsertInterval(const CSeq_id &id, const TRange &range, ENa_strand strand=eNa_strand_unknown)

Insert new element before the current one (.

CSeq_loc_I InsertPoint(const CSeq_id &id, TSeqPos pos, ENa_strand strand=eNa_strand_unknown)

Insert new element before the current one (.

bool CheckId(const CSeq_id *&id, bool may_throw=true) const

check that the 'id' field in all parts of the location is the same as the specifies id.

void MakeEquivPartBreak(size_t level=0)

Create equiv set with one part from current position to the position pointed by end_it argument exclu...

virtual ~ISynonymMapper(void)

void StartNewEquivPart(void)

Change equiv modification mode to add new equiv part for the next insert operation.

void MakeEquiv(const CSeq_loc_I &end_it)

Create equiv set with one part from current position to the position pointed by end_it argument exclu...

CPacked_seqint_Base::Tdata TIntervals

ECompareFlags

Flags for location comparison.

bool IsEmpty(void) const

True if the current location is empty.

CRef< CSeq_loc_CI_Impl > m_Impl

#define DEFINE_NCBI_SEQ_LOC_SETTERS(x)

CPacked_seqint::TRanges TRanges

const CSeq_id * GetId(void) const

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

CPacked_seqpnt_Base::TPoints TPoints

atomic< const CSeq_id * > m_IdCache

virtual bool operator()(const CSeq_id *id) const =0

CSeq_id_Handle m_IdHandle

TRange GetRange(void) const

Get the range.

void InvalidateTotalRangeCache(void) const

virtual TSeqPos GetLength(const CSeq_id &id)=0

void x_ThrowNotValid(const char *where) const

const SSeq_loc_CI_RangeInfo & x_GetRangeInfo(void) const

EEquivMode

This enum defines a way equiv sets are expanded or created when one of Insert*() methods is called.

ENa_strand GetStrand(void) const

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

TRange x_UpdateTotalRange(void) const

void SetStrand(ENa_strand strand)

bool IsPoint(void) const

True if the current location is a single point.

CSeq_loc(void)

constructors

NCBI_EXCEPTION_DEFAULT(CSeqLocException, CException)

atomic< TSeqPos > m_TotalRangeCacheToOpen

CConstRef< CSeq_id > m_Id

void SetNull(void)

Override all setters to incorporate cache invalidation.

CConstRef< CSeq_loc > m_Loc

CSeq_loc_I InsertWhole(const CSeq_id &id)

Insert new element before the current one (.

CSeq_loc(const CSeq_loc &)

bool x_CheckId(const CSeq_id *&id, bool may_throw=true) const

@ eEquiv_new_part

New equiv part will be started with the inserted element.

@ eEquiv_new_equiv

A new equiv set will be created, even if the insertion point is already inside of an existing equiv,...

@ eEquiv_append

If the insertion point is just after any equiv part, including the last one in an equiv,...

@ eEquiv_none

By default no equiv sets are created or expanded except if insertion point is completely inside of an...

@ eMultipleId

Seq-loc on multiple ids when one id is required.

@ eNotSet

Seq-loc is not set.

@ eIncomatible

Seq-loc type is incompatible with operation.

@ eBadLocation

Seq-loc is incorrectly formed.

@ eOutOfRange

parameter is out of valid range

@ eBadIterator

Seq-loc iterator is in bad state.

@ eUnsupported

Seq-loc has data that is not supported yet.

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.

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

Returns the sequence::ECompare containment relationship between CSeq_locs.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

position_type GetLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

#define NCBI_SEQLOC_EXPORT

static const char label[]

TWhole & SetWhole(void)

Select the variant.

TEquiv & SetEquiv(void)

Select the variant.

bool IsEmpty(void) const

Check if variant Empty is selected.

list< CRef< CSeq_interval > > Tdata

ENa_strand

strand of nucleic acid

TFeat & SetFeat(void)

Select the variant.

void SetNull(void)

Select the variant.

TPacked_pnt & SetPacked_pnt(void)

Select the variant.

TMix & SetMix(void)

Select the variant.

list< CRef< CSeq_loc > > Tdata

TBond & SetBond(void)

Select the variant.

TPnt & SetPnt(void)

Select the variant.

TEmpty & SetEmpty(void)

Select the variant.

vector< TSeqPos > TPoints

CSeq_loc_Base & operator=(const CSeq_loc_Base &)

TInt & SetInt(void)

Select the variant.

bool IsWhole(void) const

Check if variant Whole is selected.

E_Choice

Choice variants.

TPacked_int & SetPacked_int(void)

Select the variant.

void CheckId(const string &seqId, const vector< SLineInfo > &orderedIds, int idCount, int lineNum, bool firstBlock)

const CharType(& source)[N]

void Merge(wxMenu &menu_1, const wxMenu &menu_2)

merges all items form menu_2 into menu_1, preserving the structure if possible

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