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CGC_Replicon Class Reference

Represents ASN.1 type GC-Replicon defined in file genome_collection.asn

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#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_AssemblyUnitGetAssemblyUnit () const
 Access the assembly unit the sequence belongs to. More...
 
CConstRef< CGC_AssemblyGetFullAssembly () 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 TNameGetName (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)
 
TNameSetName (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_nameGetLocal_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_nameSetLocal_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 TSequenceGetSequence (void) const
 Get the Sequence member data. More...
 
void SetSequence (TSequence &value)
 Assign a value to Sequence data member. More...
 
TSequenceSetSequence (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 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
 

Protected Attributes

CGC_Assemblym_Assembly
 
CGC_AssemblyUnitm_AssemblyUnit
 

Private Types

typedef CGC_Replicon_Base Tparent
 

Private Member Functions

 CGC_Replicon (const CGC_Replicon &value)
 
CGC_Repliconoperator= (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< Uint8TCounter
 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

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]

CGC_Replicon::CGC_Replicon ( const CGC_Replicon value)
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

◆ GetMoleculeLocation()

string CGC_Replicon::GetMoleculeLocation ( ) const

◆ GetMoleculeType()

string CGC_Replicon::GetMoleculeType ( ) const

◆ operator=()

CGC_Replicon& CGC_Replicon::operator= ( const CGC_Replicon value)
private

Friends And Related Function Documentation

◆ CGC_Assembly

friend class CGC_Assembly
friend

Definition at line 56 of file GC_Replicon.hpp.

◆ CGC_AssemblyUnit

friend class CGC_AssemblyUnit
friend

Definition at line 57 of file GC_Replicon.hpp.

Member Data Documentation

◆ m_Assembly

CGC_Assembly* CGC_Replicon::m_Assembly
protected

Definition at line 77 of file GC_Replicon.hpp.

Referenced by GetFullAssembly(), and CGC_Assembly::x_Index().

◆ m_AssemblyUnit

CGC_AssemblyUnit* CGC_Replicon::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:
Modified on Wed Feb 21 09:56:24 2024 by modify_doxy.py rev. 669887