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< Uint8 > | TCounter |
| 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_type & | SetParent_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 TParentid & | GetParentid (void) const |
| Get the Parentid member data. More... | |
| void | SetParentid (TParentid &value) |
| Assign a value to Parentid data member. More... | |
| TParentid & | SetParentid (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 TSeqannot & | GetSeqannot (void) const |
| Get the Seqannot member data. More... | |
| void | SetSeqannot (TSeqannot &value) |
| Assign a value to Seqannot data member. More... | |
| TSeqannot & | SetSeqannot (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 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 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_Base & | operator= (const CDomain_parent_Base &) |
Private Attributes | |
| Uint4 | m_set_State [1] |
| int | m_Parent_type |
| CRef< TParentid > | m_Parentid |
| CRef< TSeqannot > | m_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.
Definition at line 88 of file Domain_parent_.hpp.
The documentation for this class was generated from the following files:
- include/objects/cdd/Domain_parent_.hpp
- src/objects/cdd/Domain_parent_.cpp
