NCBI C++ ToolKit
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Represents ASN.1 type GC-AssemblyUnit defined in file genome_collection.asn

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CGC_AssemblyUnit_Base –. More...

#include <objects/genomecoll/GC_AssemblyUnit_.hpp>

+ Inheritance diagram for CGC_AssemblyUnit_Base:
+ Collaboration diagram for CGC_AssemblyUnit_Base:

Public Types

enum  EClass { eClass_haploid_unit = 1 , eClass_alt_loci = 2 , eClass_assembly_patch = 3 , eClass_other = 255 }
 'class' defines the semantics of how to interpret this item More...
 
enum class  E_memberIndex {
  e__allMandatory = 0 , e_id , e_class , e_desc ,
  e_mols , e_other_sequences , e_stats , e_unplaced_stats ,
  e_unplaced_unlocalized_stats
}
 
typedef list< CRef< CDbtag > > TId
 
typedef int TClass
 
typedef CGC_AssemblyDesc TDesc
 
typedef list< CRef< CGC_Replicon > > TMols
 
typedef list< CRef< CGC_TaggedSequences > > TOther_sequences
 
typedef CGC_SequenceStats TStats
 
typedef list< CRef< CGC_Scaf_stats > > TUnplaced_stats
 
typedef list< CRef< CGC_Scaf_stats > > TUnplaced_unlocalized_stats
 
typedef Tparent::CMemberIndex< E_memberIndex, 9 > 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...
 

Public Member Functions

 CGC_AssemblyUnit_Base (void)
 
virtual ~CGC_AssemblyUnit_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetId (void) const
 The identifier of this assembly Contains: GenColl internal id, GenColl accession.version, AGP id, UCSC name, Ensembl name Types of DbTags used: db "GenColl", tag id <assembly-release-id> db "GenColl", tag str <assembly-accession.version> db "AGP", tag id <agp-sumbission-id> db "GenColl_Chain", tag id <assembly-chain-id> "Ensembl_name" and "UCSC_name" will not appear in the Unit level since these organizations do not define assembly-units. More...
 
bool CanGetId (void) const
 Check if it is safe to call GetId method. More...
 
void ResetId (void)
 Reset Id data member. More...
 
const TIdGetId (void) const
 Get the Id member data. More...
 
TIdSetId (void)
 Assign a value to Id data member. More...
 
bool IsSetClass (void) const
 Check if a value has been assigned to Class data member. More...
 
bool CanGetClass (void) const
 Check if it is safe to call GetClass method. More...
 
void ResetClass (void)
 Reset Class data member. More...
 
TClass GetClass (void) const
 Get the Class member data. More...
 
void SetClass (TClass value)
 Assign a value to Class data member. More...
 
TClassSetClass (void)
 Assign a value to Class data member. More...
 
bool IsSetDesc (void) const
 descriptors live in a shared data block Check if a value has been assigned to Desc data member. More...
 
bool CanGetDesc (void) const
 Check if it is safe to call GetDesc method. More...
 
void ResetDesc (void)
 Reset Desc data member. More...
 
const TDescGetDesc (void) const
 Get the Desc member data. More...
 
void SetDesc (TDesc &value)
 Assign a value to Desc data member. More...
 
TDescSetDesc (void)
 Assign a value to Desc data member. More...
 
bool IsSetMols (void) const
 collections of molecules for this assembly Check if a value has been assigned to Mols data member. More...
 
bool CanGetMols (void) const
 Check if it is safe to call GetMols method. More...
 
void ResetMols (void)
 Reset Mols data member. More...
 
const TMolsGetMols (void) const
 Get the Mols member data. More...
 
TMolsSetMols (void)
 Assign a value to Mols data member. More...
 
bool IsSetOther_sequences (void) const
 On primary assembly-unit: here will be the unplaced sequences On alt-loci: list of sequences aligned/unaligned to primary unit Check if a value has been assigned to Other_sequences data member. More...
 
bool CanGetOther_sequences (void) const
 Check if it is safe to call GetOther_sequences method. More...
 
void ResetOther_sequences (void)
 Reset Other_sequences data member. More...
 
const TOther_sequencesGetOther_sequences (void) const
 Get the Other_sequences member data. More...
 
TOther_sequencesSetOther_sequences (void)
 Assign a value to Other_sequences data member. More...
 
bool IsSetStats (void) const
 statistics "stats" field holds stats for all chromosomes combined: ordered/unordered scaffolds "unplaced-stats" holds stats for ChrUn which is omitted from "stats" Check if a value has been assigned to Stats data member. More...
 
bool CanGetStats (void) const
 Check if it is safe to call GetStats method. More...
 
void ResetStats (void)
 Reset Stats data member. More...
 
const TStatsGetStats (void) const
 Get the Stats member data. More...
 
void SetStats (TStats &value)
 Assign a value to Stats data member. More...
 
TStatsSetStats (void)
 Assign a value to Stats data member. More...
 
bool IsSetUnplaced_stats (void) const
 Check if a value has been assigned to Unplaced_stats data member. More...
 
bool CanGetUnplaced_stats (void) const
 Check if it is safe to call GetUnplaced_stats method. More...
 
void ResetUnplaced_stats (void)
 Reset Unplaced_stats data member. More...
 
const TUnplaced_statsGetUnplaced_stats (void) const
 Get the Unplaced_stats member data. More...
 
TUnplaced_statsSetUnplaced_stats (void)
 Assign a value to Unplaced_stats data member. More...
 
bool IsSetUnplaced_unlocalized_stats (void) const
 Check if a value has been assigned to Unplaced_unlocalized_stats data member. More...
 
bool CanGetUnplaced_unlocalized_stats (void) const
 Check if it is safe to call GetUnplaced_unlocalized_stats method. More...
 
void ResetUnplaced_unlocalized_stats (void)
 Reset Unplaced_unlocalized_stats data member. More...
 
const TUnplaced_unlocalized_statsGetUnplaced_unlocalized_stats (void) const
 Get the Unplaced_unlocalized_stats member data. More...
 
TUnplaced_unlocalized_statsSetUnplaced_unlocalized_stats (void)
 Assign a value to Unplaced_unlocalized_stats 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
 

Static Public Member Functions

static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() EClass (void)
 Access to EClass'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

 CGC_AssemblyUnit_Base (const CGC_AssemblyUnit_Base &)
 
CGC_AssemblyUnit_Baseoperator= (const CGC_AssemblyUnit_Base &)
 

Private Attributes

Uint4 m_set_State [1]
 
list< CRef< CDbtag > > m_Id
 
int m_Class
 
CRef< TDescm_Desc
 
list< CRef< CGC_Replicon > > m_Mols
 
list< CRef< CGC_TaggedSequences > > m_Other_sequences
 
CRef< TStatsm_Stats
 
list< CRef< CGC_Scaf_stats > > m_Unplaced_stats
 
list< CRef< CGC_Scaf_stats > > m_Unplaced_unlocalized_stats
 

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

CGC_AssemblyUnit_Base –.

Definition at line 81 of file GC_AssemblyUnit_.hpp.


The documentation for this class was generated from the following files:
Modified on Sun Apr 21 03:40:57 2024 by modify_doxy.py rev. 669887