Search Toolkit Book for CGC_Replicon
#include <objects/genomecoll/GC_Replicon.hpp>
Inheritance diagram for CGC_Replicon:
Collaboration diagram for CGC_Replicon:
Public Member Functions | |
| CGC_Replicon (void) | |
| ~CGC_Replicon (void) | |
| CConstRef< CGC_AssemblyUnit > | GetAssemblyUnit () const |
| Access the assembly unit the sequence belongs to. More... | |
| CConstRef< CGC_Assembly > | GetFullAssembly () const |
| Access the most specific full assembly the replicon belongs to This is needed because assemblies are packaged as sets of assemblies; knowing the unit is not always enough. More... | |
| string | GetMoleculeLocation () const |
| string | GetMoleculeType () const |
| string | GetMoleculeLabel () const |
| Public Member Functions inherited from CGC_Replicon_Base | |
| CGC_Replicon_Base (void) | |
| virtual | ~CGC_Replicon_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetName (void) const |
| name for this molecule the official name, Check if a value has been assigned to Name data member. More... | |
| bool | CanGetName (void) const |
| Check if it is safe to call GetName method. More... | |
| void | ResetName (void) |
| Reset Name data member. More... | |
| const TName & | GetName (void) const |
| Get the Name member data. More... | |
| void | SetName (const TName &value) |
| Assign a value to Name data member. More... | |
| void | SetName (TName &&value) |
| TName & | SetName (void) |
| Assign a value to Name data member. More... | |
| bool | IsSetLocal_name (void) const |
| If the chromosome has a different name in this assembly. More... | |
| bool | CanGetLocal_name (void) const |
| Check if it is safe to call GetLocal_name method. More... | |
| void | ResetLocal_name (void) |
| Reset Local_name data member. More... | |
| const TLocal_name & | GetLocal_name (void) const |
| Get the Local_name member data. More... | |
| void | SetLocal_name (const TLocal_name &value) |
| Assign a value to Local_name data member. More... | |
| void | SetLocal_name (TLocal_name &&value) |
| TLocal_name & | SetLocal_name (void) |
| Assign a value to Local_name data member. More... | |
| bool | IsSetSequence (void) const |
| Check if a value has been assigned to Sequence data member. More... | |
| bool | CanGetSequence (void) const |
| Check if it is safe to call GetSequence method. More... | |
| void | ResetSequence (void) |
| Reset Sequence data member. More... | |
| const TSequence & | GetSequence (void) const |
| Get the Sequence member data. More... | |
| void | SetSequence (TSequence &value) |
| Assign a value to Sequence data member. More... | |
| TSequence & | SetSequence (void) |
| Assign a value to Sequence 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 |
Protected Attributes | |
| CGC_Assembly * | m_Assembly |
| CGC_AssemblyUnit * | m_AssemblyUnit |
Private Types | |
| typedef CGC_Replicon_Base | Tparent |
Private Member Functions | |
| CGC_Replicon (const CGC_Replicon &value) | |
| CGC_Replicon & | operator= (const CGC_Replicon &value) |
Friends | |
| class | CGC_Assembly |
| class | CGC_AssemblyUnit |
Additional Inherited Members | |
| Public Types inherited from CGC_Replicon_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_name , e_local_name , e_sequence } |
| typedef string | TName |
| typedef string | TLocal_name |
| typedef C_Sequence | TSequence |
| 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... | |
| 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
Definition at line 53 of file GC_Replicon.hpp.
Member Typedef Documentation
◆ Tparent
|
private |
Definition at line 55 of file GC_Replicon.hpp.
Constructor & Destructor Documentation
◆ CGC_Replicon() [1/2]
| CGC_Replicon::CGC_Replicon | ( | void | ) |
Definition at line 54 of file GC_Replicon.cpp.
◆ ~CGC_Replicon()
| CGC_Replicon::~CGC_Replicon | ( | void | ) |
Definition at line 61 of file GC_Replicon.cpp.
◆ CGC_Replicon() [2/2]
|
private |
Member Function Documentation
◆ GetAssemblyUnit()
| CConstRef< CGC_AssemblyUnit > CGC_Replicon::GetAssemblyUnit | ( | ) | const |
Access the assembly unit the sequence belongs to.
Definition at line 67 of file GC_Replicon.cpp.
References m_AssemblyUnit.
◆ GetFullAssembly()
| CConstRef< CGC_Assembly > CGC_Replicon::GetFullAssembly | ( | ) | const |
Access the most specific full assembly the replicon belongs to This is needed because assemblies are packaged as sets of assemblies; knowing the unit is not always enough.
Access the assembly the sequence belongs to.
Definition at line 74 of file GC_Replicon.cpp.
References m_Assembly.
◆ GetMoleculeLabel()
| string CGC_Replicon::GetMoleculeLabel | ( | ) | const |
Definition at line 114 of file GC_Replicon.cpp.
References CUser_field_Base::GetData(), CUser_object::GetField(), CUser_field_Base::C_Data::GetStr(), kEmptyStr, and x_GetMolLocTypeUserObj().
◆ GetMoleculeLocation()
| string CGC_Replicon::GetMoleculeLocation | ( | ) | const |
Definition at line 96 of file GC_Replicon.cpp.
References CUser_field_Base::GetData(), CUser_object::GetField(), CUser_field_Base::C_Data::GetStr(), kEmptyStr, and x_GetMolLocTypeUserObj().
◆ GetMoleculeType()
| string CGC_Replicon::GetMoleculeType | ( | ) | const |
Definition at line 105 of file GC_Replicon.cpp.
References CUser_field_Base::GetData(), CUser_object::GetField(), CUser_field_Base::C_Data::GetStr(), kEmptyStr, and x_GetMolLocTypeUserObj().
◆ operator=()
|
private |
Friends And Related Function Documentation
◆ CGC_Assembly
|
friend |
Definition at line 56 of file GC_Replicon.hpp.
◆ CGC_AssemblyUnit
|
friend |
Definition at line 57 of file GC_Replicon.hpp.
Member Data Documentation
◆ m_Assembly
|
protected |
Definition at line 77 of file GC_Replicon.hpp.
Referenced by GetFullAssembly(), and CGC_Assembly::x_Index().
◆ m_AssemblyUnit
|
protected |
Definition at line 78 of file GC_Replicon.hpp.
Referenced by GetAssemblyUnit(), and CGC_Assembly::x_Index().
The documentation for this class was generated from the following files:
- include/objects/genomecoll/GC_Replicon.hpp
- src/objects/genomecoll/GC_Replicon.cpp
