Search Toolkit Book for CRegion_similarity_Base
A biostruc similarity describes spatial features which are similar between two or more biostrucs. More...
#include <objects/mmdb3/Region_similarity_.hpp>
Inheritance diagram for CRegion_similarity_Base:
Collaboration diagram for CRegion_similarity_Base:
Public Types | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_dimension , e_biostruc_ids , e_similarity , e_transform } |
| typedef int | TDimension |
| typedef list< CRef< CBiostruc_id > > | TBiostruc_ids |
| typedef list< CRef< CRegion_pntrs > > | TSimilarity |
| typedef list< CRef< CTransform > > | TTransform |
| typedef Tparent::CMemberIndex< E_memberIndex, 5 > | 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 | |
| CRegion_similarity_Base (void) | |
| virtual | ~CRegion_similarity_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 | IsSetSimilarity (void) const |
| Check if a value has been assigned to Similarity data member. More... | |
| bool | CanGetSimilarity (void) const |
| Check if it is safe to call GetSimilarity method. More... | |
| void | ResetSimilarity (void) |
| Reset Similarity data member. More... | |
| const TSimilarity & | GetSimilarity (void) const |
| Get the Similarity member data. More... | |
| TSimilarity & | SetSimilarity (void) |
| Assign a value to Similarity 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... | |
| 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 |
Private Types | |
| typedef CSerialObject | Tparent |
Private Member Functions | |
| CRegion_similarity_Base (const CRegion_similarity_Base &) | |
| CRegion_similarity_Base & | operator= (const CRegion_similarity_Base &) |
Private Attributes | |
| Uint4 | m_set_State [1] |
| int | m_Dimension |
| list< CRef< CBiostruc_id > > | m_Biostruc_ids |
| list< CRef< CRegion_pntrs > > | m_Similarity |
| list< CRef< CTransform > > | m_Transform |
Additional Inherited Members | |
| 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) |
| 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
A biostruc similarity describes spatial features which are similar between two or more biostrucs.
Similarities are model dependent, and the model and coordinate set ids of the biostrucs must be specified. They do not necessarily map to a sequence alignment, as the regions referenced may be pieces of a surface or grid, and thus not uniquely mapable to particular chemical components.
Definition at line 84 of file Region_similarity_.hpp.
The documentation for this class was generated from the following files:
- include/objects/mmdb3/Region_similarity_.hpp
- src/objects/mmdb3/Region_similarity_.cpp
