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CSeq_gap Class Reference

Represents ASN.1 type Seq-gap defined in file seq.asn

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#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_CStrTGapTypeMap
 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< Uint8TCounter
 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...
 
TTypeSetType (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...
 
TLinkageSetLinkage (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_evidenceGetLinkage_evidence (void) const
 Get the Linkage_evidence member data. More...
 
TLinkage_evidenceSetLinkage_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 CTypeInfoGetThisTypeInfo (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 stringGetNamespaceName (void) const
 Get namespace name. More...
 
bool HasNamespacePrefix (void) const
 Check if data type has namespace prefix. More...
 
const stringGetNamespacePrefix (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...
 
CObjectoperator= (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 SGapTypeInfoNameToGapTypeInfo (const CTempString &sName)
 From a gap-type string, get the SGapTypeInfo, insensitive to case, etc. More...
 
static const TGapTypeMapGetNameToGapTypeInfoMap (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_gapoperator= (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

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

Definition at line 61 of file Seq_gap.hpp.

Member Enumeration Documentation

◆ 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.

Constructor & Destructor Documentation

◆ CSeq_gap() [1/2]

CSeq_gap::CSeq_gap ( void  )
inline

Definition at line 118 of file Seq_gap.hpp.

◆ ~CSeq_gap()

CSeq_gap::~CSeq_gap ( void  )

Definition at line 74 of file Seq_gap.cpp.

◆ CSeq_gap() [2/2]

CSeq_gap::CSeq_gap ( const CSeq_gap value)
private

Member Function Documentation

◆ AddLinkageEvidence()

bool CSeq_gap::AddLinkageEvidence ( CLinkage_evidence::TType  evidence_type)

◆ ChangeType()

void CSeq_gap::ChangeType ( TType  linkage_type)

◆ GetNameToGapTypeInfoMap()

const CSeq_gap::TGapTypeMap & CSeq_gap::GetNameToGapTypeInfoMap ( void  )
static

◆ NameToGapTypeInfo()

const CSeq_gap::SGapTypeInfo * CSeq_gap::NameToGapTypeInfo ( const CTempString sName)
static

From a gap-type string, get the SGapTypeInfo, insensitive to case, etc.

This is NOT quite the same as calling find on the TGapTypeMap.

Returns
NULL if not found

Definition at line 158 of file Seq_gap.cpp.

References CStaticArraySearchBase< KeyValueGetter, KeyCompare >::end(), CStaticArraySearchBase< KeyValueGetter, KeyCompare >::find(), GetNameToGapTypeInfoMap(), and NULL.

Referenced by CFeatureTableReader::MakeGap(), and CFastaReader::ParseGapLine().

◆ operator=()

CSeq_gap& CSeq_gap::operator= ( const CSeq_gap value)
private

◆ SetLinkageTypeLinkedRepeat()

void CSeq_gap::SetLinkageTypeLinkedRepeat ( CLinkage_evidence::TType  evidence_type)

◆ SetLinkageTypeScaffold()

void CSeq_gap::SetLinkageTypeScaffold ( CLinkage_evidence::TType  evidence_type)

The documentation for this class was generated from the following files:
Modified on Sun Apr 14 05:28:28 2024 by modify_doxy.py rev. 669887