NCBI C++ ToolKit
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Represents ASN.1 type Domain-parent defined in file cdd.asn

Search Toolkit Book for CDomain_parent_Base

the Domain-parent records an evolutionary relationship which may not be as simple as a classical parent-child relationship in a typical hierarchy, i.e. More...

#include <objects/cdd/Domain_parent_.hpp>

+ Inheritance diagram for CDomain_parent_Base:
+ Collaboration diagram for CDomain_parent_Base:

Public Types

enum  EParent_type {
  eParent_type_classical = 0 , eParent_type_fusion = 1 , eParent_type_deletion = 2 , eParent_type_permutation = 3 ,
  eParent_type_other = 255
}
 
enum class  E_memberIndex { e__allMandatory = 0 , e_parent_type , e_parentid , e_seqannot }
 
typedef int TParent_type
 
typedef CCdd_id TParentid
 
typedef CSeq_annot TSeqannot
 
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

 CDomain_parent_Base (void)
 
virtual ~CDomain_parent_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetParent_type (void) const
 Check if a value has been assigned to Parent_type data member. More...
 
bool CanGetParent_type (void) const
 Check if it is safe to call GetParent_type method. More...
 
void ResetParent_type (void)
 Reset Parent_type data member. More...
 
TParent_type GetParent_type (void) const
 Get the Parent_type member data. More...
 
void SetParent_type (TParent_type value)
 Assign a value to Parent_type data member. More...
 
TParent_typeSetParent_type (void)
 Assign a value to Parent_type data member. More...
 
bool IsSetParentid (void) const
 identify the section parent by accession Check if a value has been assigned to Parentid data member. More...
 
bool CanGetParentid (void) const
 Check if it is safe to call GetParentid method. More...
 
void ResetParentid (void)
 Reset Parentid data member. More...
 
const TParentidGetParentid (void) const
 Get the Parentid member data. More...
 
void SetParentid (TParentid &value)
 Assign a value to Parentid data member. More...
 
TParentidSetParentid (void)
 Assign a value to Parentid data member. More...
 
bool IsSetSeqannot (void) const
 contains the sequence alignment linking CD alignment models, should align the masters/representatives of each CD Check if a value has been assigned to Seqannot data member. More...
 
bool CanGetSeqannot (void) const
 Check if it is safe to call GetSeqannot method. More...
 
void ResetSeqannot (void)
 Reset Seqannot data member. More...
 
const TSeqannotGetSeqannot (void) const
 Get the Seqannot member data. More...
 
void SetSeqannot (TSeqannot &value)
 Assign a value to Seqannot data member. More...
 
TSeqannotSetSeqannot (void)
 Assign a value to Seqannot 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 NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EParent_type (void)
 Access to EParent_type'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 CSerialObject Tparent
 

Private Member Functions

 CDomain_parent_Base (const CDomain_parent_Base &)
 
CDomain_parent_Baseoperator= (const CDomain_parent_Base &)
 

Private Attributes

Uint4 m_set_State [1]
 
int m_Parent_type
 
CRef< TParentidm_Parentid
 
CRef< TSeqannotm_Seqannot
 

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

the Domain-parent records an evolutionary relationship which may not be as simple as a classical parent-child relationship in a typical hierarchy, i.e.

where a CD is merely a specific subgroup ("child") of a more general diverse alignment model ("parent"). A CD alignment model may be the result of an ancient fusion event, combining two or more domains into a bigger unit which has subsequently undergone a divergent evolutionary process similar to what may have happened to a single "domain". A CD alignment model may also reflect the result of a deletion event, where a specific subgroup lacks part of a (set of) domain(s), but where the part present is found to be highly similar to a putative "parent", with some added evidence for an actual deletion, like from the distribution of truncated copies in phylogenetic lineages. Deletion events which affect different parts of a set of duplicated domain architectures may be indistinguishable from actual fission events, which means that we may want to represent the latter as deletions after duplication and do not need a special case for fissions.

CDomain_parent_Base

Definition at line 88 of file Domain_parent_.hpp.


The documentation for this class was generated from the following files:
Modified on Sat May 25 14:22:55 2024 by modify_doxy.py rev. 669887