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NCBI C++ ToolKit: CChem_graph_alignment_Base Class Reference
A biostruc alignment establishes an equivalence of nodes in the chemical graphs of two or more biostrucs. More...
CChem_graph_alignment_Base (void) virtual ~CChem_graph_alignment_Base (void) DECLARE_INTERNAL_TYPE_INFO () bool IsSetDimension (void) const Check if a value has been assigned to Dimension data member. More...
bool CanGetDimension (void) const Check if it is safe to call GetDimension method. More...
void ResetDimension (void) Reset Dimension data member. More...
void SetDefaultDimension (void) Assign default value to Dimension data member. More...
TDimension GetDimension (void) const Get the Dimension member data. More...
void SetDimension (TDimension value) Assign a value to Dimension data member. More...
TDimension & SetDimension (void) Assign a value to Dimension data member. More...
bool IsSetBiostruc_ids (void) const Check if a value has been assigned to Biostruc_ids data member. More...
bool CanGetBiostruc_ids (void) const Check if it is safe to call GetBiostruc_ids method. More...
void ResetBiostruc_ids (void) Reset Biostruc_ids data member. More...
const TBiostruc_ids & GetBiostruc_ids (void) const Get the Biostruc_ids member data. More...
TBiostruc_ids & SetBiostruc_ids (void) Assign a value to Biostruc_ids data member. More...
bool IsSetAlignment (void) const Check if a value has been assigned to Alignment data member. More...
bool CanGetAlignment (void) const Check if it is safe to call GetAlignment method. More...
void ResetAlignment (void) Reset Alignment data member. More...
const TAlignment & GetAlignment (void) const Get the Alignment member data. More...
TAlignment & SetAlignment (void) Assign a value to Alignment data member. More...
bool IsSetDomain (void) const Check if a value has been assigned to Domain data member. More...
bool CanGetDomain (void) const Check if it is safe to call GetDomain method. More...
void ResetDomain (void) Reset Domain data member. More...
const TDomain & GetDomain (void) const Get the Domain member data. More...
TDomain & SetDomain (void) Assign a value to Domain data member. More...
bool IsSetTransform (void) const Check if a value has been assigned to Transform data member. More...
bool CanGetTransform (void) const Check if it is safe to call GetTransform method. More...
void ResetTransform (void) Reset Transform data member. More...
const TTransform & GetTransform (void) const Get the Transform member data. More...
TTransform & SetTransform (void) Assign a value to Transform data member. More...
bool IsSetAligndata (void) const Check if a value has been assigned to Aligndata data member. More...
bool CanGetAligndata (void) const Check if it is safe to call GetAligndata method. More...
void ResetAligndata (void) Reset Aligndata data member. More...
const TAligndata & GetAligndata (void) const Get the Aligndata member data. More...
TAligndata & SetAligndata (void) Assign a value to Aligndata data member. More...
virtual void Reset (void) Reset the whole object. More...
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...
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...
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
A biostruc alignment establishes an equivalence of nodes in the chemical graphs of two or more biostrucs.
This may be mapped to a sequence alignment in the case of biopolymers. The 'dimension' component indicates the number of participants in the alignment. For pairwise alignments, such as VAST structure-structure alignments, the dimension will be always 2, with biostruc-ids, alignment, and domain each containing two entries for an aligned pair. The 'alignment' component contains a pair of Chem-graph-pntrs specifying a like number of corresponding residues in each structure. The 'domain' component specifies a region of each structure considered in the alignment. Only one transform (for the second structure) and one aligndata (for the pair) are provided for each VAST alignment.
For multiple alignments, a set of components are treated as parallel arrays of length 'dimension'. The 'transform' component moves each structure to align it with the structure specified as the first element in the "parallel" array, so necessarily the first transform is a NULL transform. Align-stats are placeholders for scores.
CChem_graph_alignment_Base –
Definition at line 98 of file Chem_graph_alignment_.hpp.
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