#include <objects/seqloc/Seq_loc.hpp>

Inheritance diagram for CSeq_loc:

Collaboration diagram for CSeq_loc:

Classes
class	ISubLocFilter
	Used as a helper for determining which pieces of a CSeq_loc to compare. More...

Public Types
enum	ECompareFlags { fCompare_Default = 0 , fCompare_Strand = 1 }
	Flags for location comparison. More...

enum	EOpFlags { 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 , fSort = 1<<5 , fSortAndMerge_All = fSort \| fMerge_All }
	CSeq_loc operations. More...

typedef CSeq_loc_Base	Tparent

typedef CPacked_seqpnt_Base::TPoints	TPoints

typedef CPacked_seqint_Base::Tdata	TIntervals

typedef CSeq_loc_mix_Base::Tdata	TLocations

typedef CSeq_id	TId

typedef ENa_strand	TStrand

typedef TSeqPos	TPoint

typedef CPacked_seqint::TRanges	TRanges

typedef CRange< TSeqPos >	TRange
	See related functions in objmgr/util/seq_loc_util.hpp: More...

typedef int	TCompareFlags

typedef int	TOpFlags

typedef CSeq_loc_CI	const_iterator
	Make CSeq_loc look like an STL container. More...

Public Types inherited from CSeq_loc_Base
enum	E_Choice { e_not_set = 0 , e_Null , e_Empty , e_Whole , e_Int , e_Packed_int , e_Pnt , e_Packed_pnt , e_Mix , e_Equiv , e_Bond , e_Feat }
	Choice variants. More...

enum	E_ChoiceStopper { e_MaxChoice = 12 }
	Maximum+1 value of the choice variant enumerator. More...

typedef CSeq_id	TEmpty

typedef CSeq_id	TWhole

typedef CSeq_interval	TInt

typedef CPacked_seqint	TPacked_int

typedef CSeq_point	TPnt

typedef CPacked_seqpnt	TPacked_pnt

typedef CSeq_loc_mix	TMix

typedef CSeq_loc_equiv	TEquiv

typedef CSeq_bond	TBond

typedef CFeat_id	TFeat

Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	CSeq_loc (void)
	constructors More...

	CSeq_loc (E_Choice index)

	CSeq_loc (TId &id, TPoint point, TStrand strand=eNa_strand_unknown)

	CSeq_loc (TId &id, const TPoints &points, TStrand strand=eNa_strand_unknown)

	CSeq_loc (TId &id, TPoint from, TPoint to, TStrand strand=eNa_strand_unknown)

	CSeq_loc (TId &id, TRanges ivals, TStrand strand=eNa_strand_unknown)

virtual	~CSeq_loc (void)

TRange	GetTotalRange (void) const

void	InvalidateTotalRangeCache (void) const

bool	IsSetStrand (EIsSetStrand flag=eIsSetStrand_Any) const
	Check if strand is set for any/all part(s) of the seq-loc depending on the flag. More...

ENa_strand	GetStrand (void) const
	Get the location's strand. More...

bool	IsReverseStrand (void) const
	Return true if all ranges have reverse strand. More...

void	FlipStrand (void)
	Flip the strand (e.g. plus to minus) More...

void	SetStrand (ENa_strand strand)
	Set the strand for all of the location's ranges. More...

void	ResetStrand (void)
	Reset the strand on this location. More...

TSeqPos	GetStart (ESeqLocExtremes ext) const
	Return start and stop positions of the seq-loc. More...

TSeqPos	GetStop (ESeqLocExtremes ext) const

TSeqPos	GetCircularLength (TSeqPos seq_len) const
	Special case for circular sequences. More...

void	GetLabel (string *label) const
	Appends a label suitable for display (e.g., error messages) label must point to an existing string object Method just returns if label is null. More...

bool	IsPartialStart (ESeqLocExtremes ext) const
	check start or stop of location for e_Lim fuzz More...

bool	IsPartialStop (ESeqLocExtremes ext) const

void	SetPartialStart (bool val, ESeqLocExtremes ext)
	set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval) More...

void	SetPartialStop (bool val, ESeqLocExtremes ext)

bool	IsTruncatedStart (ESeqLocExtremes ext) const
	check if parts of the seq-loc are missing More...

bool	IsTruncatedStop (ESeqLocExtremes ext) const

void	SetTruncatedStart (bool val, ESeqLocExtremes ext)
	set / remove e_Lim fuzz on start or stop (tl/tr - indicating removed parts of the seq-loc) More...

void	SetTruncatedStop (bool val, ESeqLocExtremes ext)

const CSeq_id *	GetId (void) const
	Get the id of the location return NULL if has multiple ids or no id at all. More...

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. More...

void	InvalidateIdCache (void) const

void	SetId (CSeq_id &id)
	set the 'id' field in all parts of this location More...

void	SetId (const CSeq_id &id)

void	InvalidateCache (void) const
	Combine invalidation of all cached values. More...

virtual void	Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
	Override Assign() to incorporate cache invalidation. More...

void	SetNull (void)
	Override all setters to incorporate cache invalidation. More...

void	SetEmpty (TEmpty &v)

TEmpty &	SetEmpty (void)

void	SetWhole (TWhole &v)

TWhole &	SetWhole (void)

void	SetInt (TInt &v)

TInt &	SetInt (void)

void	SetPacked_int (TPacked_int &v)

TPacked_int &	SetPacked_int (void)

void	SetPnt (TPnt &v)

TPnt &	SetPnt (void)

void	SetPacked_pnt (TPacked_pnt &v)

TPacked_pnt &	SetPacked_pnt (void)

void	SetMix (TMix &v)

TMix &	SetMix (void)

void	SetEquiv (TEquiv &v)

TEquiv &	SetEquiv (void)

void	SetBond (TBond &v)

TBond &	SetBond (void)

void	SetFeat (TFeat &v)

TFeat &	SetFeat (void)

void	PostRead (void) const
	Invalidate id/range cache after deserialization. More...

int	Compare (const CSeq_loc &loc) const

int	Compare (const CSeq_loc &loc, TCompareFlags flags) const
	Compare locations by total range for each seq-id. More...

int	CompareSubLoc (const CSeq_loc &loc, ENa_strand strand, const ISubLocFilter *filter=NULL) const
	Compare first-level sub-locations sequentially to order them by biological "complexity". More...

void	Add (const CSeq_loc &other)
	Simple adding of seq-locs. More...

void	ChangeToMix (void)

void	ChangeToPackedInt (void)
	Works only if location is currently an interval, point, packed-int (handled trivially), or a mix built recursively from these. More...

CRef< CSeq_loc >	Merge (TOpFlags flags, ISynonymMapper *syn_mapper) const
	All functions create and return a new seq-loc object. More...

CRef< CSeq_loc >	Add (const CSeq_loc &other, TOpFlags flags, ISynonymMapper *syn_mapper) const
	Add seq-loc, merge/sort resulting ranges depending on flags. More...

CRef< CSeq_loc >	Subtract (const CSeq_loc &other, TOpFlags flags, ISynonymMapper syn_mapper, ILengthGetter len_getter) const
	Subtract seq-loc from this, merge/sort resulting ranges depending on flags. More...

CRef< CSeq_loc >	Intersect (const CSeq_loc &other, TOpFlags flags, ISynonymMapper *syn_mapper) const
	Find the intersection with the seq-loc, merge/sort resulting ranges depending on flags. More...

const_iterator	begin (void) const

const_iterator	end (void) const

Public Member Functions inherited from CSeq_loc_Base
	CSeq_loc_Base (void)

virtual	~CSeq_loc_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

virtual void	Reset (void)
	Reset the whole object. More...

virtual void	ResetSelection (void)
	Reset the selection (set it to e_not_set). More...

E_Choice	Which (void) const
	Which variant is currently selected. More...

void	CheckSelected (E_Choice index) const
	Verify selection, throw exception if it differs from the expected. More...

void	ThrowInvalidSelection (E_Choice index) const
	Throw 'InvalidSelection' exception. More...

void	Select (E_Choice index, EResetVariant reset=eDoResetVariant)
	Select the requested variant if needed. More...

void	Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
	Select the requested variant if needed, allocating CObject variants from memory pool. More...

bool	IsNull (void) const
	Check if variant Null is selected. More...

void	SetNull (void)
	Select the variant. More...

bool	IsEmpty (void) const
	Check if variant Empty is selected. More...

const TEmpty &	GetEmpty (void) const
	Get the variant data. More...

TEmpty &	SetEmpty (void)
	Select the variant. More...

void	SetEmpty (TEmpty &value)
	Select the variant and set its data. More...

bool	IsWhole (void) const
	Check if variant Whole is selected. More...

const TWhole &	GetWhole (void) const
	Get the variant data. More...

TWhole &	SetWhole (void)
	Select the variant. More...

void	SetWhole (TWhole &value)
	Select the variant and set its data. More...

bool	IsInt (void) const
	Check if variant Int is selected. More...

const TInt &	GetInt (void) const
	Get the variant data. More...

TInt &	SetInt (void)
	Select the variant. More...

void	SetInt (TInt &value)
	Select the variant and set its data. More...

bool	IsPacked_int (void) const
	Check if variant Packed_int is selected. More...

const TPacked_int &	GetPacked_int (void) const
	Get the variant data. More...

TPacked_int &	SetPacked_int (void)
	Select the variant. More...

void	SetPacked_int (TPacked_int &value)
	Select the variant and set its data. More...

bool	IsPnt (void) const
	Check if variant Pnt is selected. More...

const TPnt &	GetPnt (void) const
	Get the variant data. More...

TPnt &	SetPnt (void)
	Select the variant. More...

void	SetPnt (TPnt &value)
	Select the variant and set its data. More...

bool	IsPacked_pnt (void) const
	Check if variant Packed_pnt is selected. More...

const TPacked_pnt &	GetPacked_pnt (void) const
	Get the variant data. More...

TPacked_pnt &	SetPacked_pnt (void)
	Select the variant. More...

void	SetPacked_pnt (TPacked_pnt &value)
	Select the variant and set its data. More...

bool	IsMix (void) const
	Check if variant Mix is selected. More...

const TMix &	GetMix (void) const
	Get the variant data. More...

TMix &	SetMix (void)
	Select the variant. More...

void	SetMix (TMix &value)
	Select the variant and set its data. More...

bool	IsEquiv (void) const
	Check if variant Equiv is selected. More...

const TEquiv &	GetEquiv (void) const
	Get the variant data. More...

TEquiv &	SetEquiv (void)
	Select the variant. More...

void	SetEquiv (TEquiv &value)
	Select the variant and set its data. More...

bool	IsBond (void) const
	Check if variant Bond is selected. More...

const TBond &	GetBond (void) const
	Get the variant data. More...

TBond &	SetBond (void)
	Select the variant. More...

void	SetBond (TBond &value)
	Select the variant and set its data. More...

bool	IsFeat (void) const
	Check if variant Feat is selected. More...

const TFeat &	GetFeat (void) const
	Get the variant data. More...

TFeat &	SetFeat (void)
	Select the variant. More...

void	SetFeat (TFeat &value)
	Select the variant and set its data. More...

Public Member Functions inherited from CSerialObject
	CSerialObject (void)

virtual	~CSerialObject (void)

virtual const CTypeInfo *	GetThisTypeInfo (void) const =0

virtual bool	Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
	Check if both objects contain the same values. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

void	ThrowUnassigned (TMemberIndex index) const

void	ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const

bool	HasNamespaceName (void) const
	Check if object data type has namespace name. More...

const string &	GetNamespaceName (void) const
	Get namespace name. More...

bool	HasNamespacePrefix (void) const
	Check if data type has namespace prefix. More...

const string &	GetNamespacePrefix (void) const
	Get namespace prefix. More...

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...

bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...

bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...

bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...

bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...

void	AddReference (void) const
	Add reference to object. More...

void	RemoveReference (void) const
	Remove reference to object. More...

void	ReleaseReference (void) const
	Remove reference without deleting object. More...

virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...

virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...

void *	operator new (size_t size)
	Define new operator for memory allocation. More...

void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...

void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...

void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...

void *	operator new (size_t size, void *place)
	Define new operator. More...

void	operator delete (void ptr, void place)
	Define delete operator. More...

void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...

void	operator delete (void ptr, CObjectMemoryPool place)
	Define delete operator. More...

Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)

virtual	~CDebugDumpable (void)

void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const

void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const

void	DumpToConsole (void) const

Private Types
enum	{ kDirtyCache = -2 , kSeveralIds = -3 }

Private Member Functions
	CSeq_loc (const CSeq_loc &)

CSeq_loc &	operator= (const CSeq_loc &)

TRange	x_UpdateTotalRange (void) const

TRange	x_CalculateTotalRangeCheckId (const CSeq_id *&id) const

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

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

void	x_ChangeToMix (const CSeq_loc &other)

void	x_ChangeToPackedInt (const CSeq_interval &other)

void	x_ChangeToPackedInt (const CSeq_loc &other)

void	x_ChangeToPackedPnt (const CSeq_loc &other)

int	x_CompareSingleId (const CSeq_loc &loc, const CSeq_id id1, const CSeq_id id2, TCompareFlags flags) const
	Compare single-id locations, or throw an exception if any location is multi-id. More...

Private Attributes
atomic< TSeqPos >	m_TotalRangeCacheFrom

atomic< TSeqPos >	m_TotalRangeCacheToOpen

atomic< const CSeq_id * >	m_IdCache

Additional Inherited Members
Static Public Member Functions inherited from CSeq_loc_Base
static string	SelectionName (E_Choice index)
	Retrieve selection name (for diagnostic purposes). More...

Static Public Member Functions inherited from CSerialObject
static void	SetVerifyDataThread (ESerialVerifyData verify)

static void	SetVerifyDataGlobal (ESerialVerifyData verify)

static string	UnassignedString (void)

static CStringUTF8	UnassignedStringUTF8 (void)

static char	UnassignedByte (void)

Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Static Public Attributes inherited from CSerialObject
static const char *	ms_UnassignedStr = "<unassigned>"

static const char	ms_UnassignedByte = char(0xcd)

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 93 of file Seq_loc.hpp.

The documentation for this class was generated from the following files:

include/objects/seqloc/Seq_loc.hpp
src/objects/seqloc/Seq_loc.cpp

Classes

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description