#include <objects/seq/Seq_gap.hpp>

Inheritance diagram for CSeq_gap:

Collaboration diagram for CSeq_gap:

Classes
struct	SGapTypeInfo
	Holds information about a given gap-type string. More...

Public Types
enum	ELinkEvid { eLinkEvid_UnspecifiedOnly , eLinkEvid_Forbidden , eLinkEvid_Required }
	indicates which linkage-evidences a given gap-type can accept, if any More...

typedef CStaticArrayMap< const char *, SGapTypeInfo, PCase_CStr >	TGapTypeMap
	Map a gap-type string to its information Note that PCase_CStr, which means direct lookup is NOT insensitive to case, etc. More...

Public Types inherited from CSeq_gap_Base
enum	EType { eType_unknown = 0 , eType_fragment = 1 , eType_clone = 2 , eType_short_arm = 3 , eType_heterochromatin = 4 , eType_centromere = 5 , eType_telomere = 6 , eType_repeat = 7 , eType_contig = 8 , eType_scaffold = 9 , eType_contamination = 10 , eType_other = 255 }

enum	ELinkage { eLinkage_unlinked = 0 , eLinkage_linked = 1 , eLinkage_other = 255 }

enum class	E_memberIndex { e__allMandatory = 0 , e_type , e_linkage , e_linkage_evidence }

typedef int	TType

typedef int	TLinkage

typedef list< CRef< CLinkage_evidence > >	TLinkage_evidence

typedef Tparent::CMemberIndex< E_memberIndex, 4 >	TmemberIndex

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_gap (void)

	~CSeq_gap (void)

void	ChangeType (TType linkage_type)

void	SetLinkageTypeScaffold (CLinkage_evidence::TType evidence_type)

void	SetLinkageTypeLinkedRepeat (CLinkage_evidence::TType evidence_type)

bool	AddLinkageEvidence (CLinkage_evidence::TType evidence_type)

Public Member Functions inherited from CSeq_gap_Base
	CSeq_gap_Base (void)

virtual	~CSeq_gap_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetType (void) const
	Check if a value has been assigned to Type data member. More...

bool	CanGetType (void) const
	Check if it is safe to call GetType method. More...

void	ResetType (void)
	Reset Type data member. More...

TType	GetType (void) const
	Get the Type member data. More...

void	SetType (TType value)
	Assign a value to Type data member. More...

TType &	SetType (void)
	Assign a value to Type data member. More...

bool	IsSetLinkage (void) const
	Check if a value has been assigned to Linkage data member. More...

bool	CanGetLinkage (void) const
	Check if it is safe to call GetLinkage method. More...

void	ResetLinkage (void)
	Reset Linkage data member. More...

TLinkage	GetLinkage (void) const
	Get the Linkage member data. More...

void	SetLinkage (TLinkage value)
	Assign a value to Linkage data member. More...

TLinkage &	SetLinkage (void)
	Assign a value to Linkage data member. More...

bool	IsSetLinkage_evidence (void) const
	Check if a value has been assigned to Linkage_evidence data member. More...

bool	CanGetLinkage_evidence (void) const
	Check if it is safe to call GetLinkage_evidence method. More...

void	ResetLinkage_evidence (void)
	Reset Linkage_evidence data member. More...

const TLinkage_evidence &	GetLinkage_evidence (void) const
	Get the Linkage_evidence member data. More...

TLinkage_evidence &	SetLinkage_evidence (void)
	Assign a value to Linkage_evidence data member. More...

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

Public Member Functions inherited from CSerialObject
	CSerialObject (void)

virtual	~CSerialObject (void)

virtual const CTypeInfo *	GetThisTypeInfo (void) const =0

virtual void	Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
	Set object to copy of another one. More...

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

Static Public Member Functions
static const SGapTypeInfo *	NameToGapTypeInfo (const CTempString &sName)
	From a gap-type string, get the SGapTypeInfo, insensitive to case, etc. More...

static const TGapTypeMap &	GetNameToGapTypeInfoMap (void)
	This is for if the user needs to get the gap-type string to SGapTypeInfo info directly (For example, to iterate through all possible types). More...

Static Public Member Functions inherited from CSeq_gap_Base
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	EType (void)
	Access to EType's attributes (values, names) as defined in spec. More...

static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME()	ELinkage (void)
	Access to ELinkage's attributes (values, names) as defined in spec. 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)

Private Types
typedef CSeq_gap_Base	Tparent

Private Member Functions
	CSeq_gap (const CSeq_gap &value)

CSeq_gap &	operator= (const CSeq_gap &value)

Additional Inherited Members
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 59 of file Seq_gap.hpp.

Member Typedef Documentation

◆ TGapTypeMap

typedef CStaticArrayMap<const char *, SGapTypeInfo, PCase_CStr> CSeq_gap::TGapTypeMap

Map a gap-type string to its information Note that PCase_CStr, which means direct lookup is NOT insensitive to case, etc.

Definition at line 93 of file Seq_gap.hpp.

◆ Tparent

typedef CSeq_gap_Base CSeq_gap::Tparent

private

Definition at line 61 of file Seq_gap.hpp.

Member Enumeration Documentation

◆ ELinkEvid

enum CSeq_gap::ELinkEvid

indicates which linkage-evidences a given gap-type can accept, if any

Enumerator
eLinkEvid_UnspecifiedOnly	only the "unspecified" linkage-evidence is allowed
eLinkEvid_Forbidden	no linkage-evidence is allowed
eLinkEvid_Required	any linkage-evidence is allowed, and at least one is required

Definition at line 75 of file Seq_gap.hpp.