NCBI C++ ToolKit
Public Types | Public Member Functions | Static Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members

Represents ASN.1 type Bioseq-set defined in file seqset.asn

Search Toolkit Book for CBioseq_set_Base

*** Sequence Collections ******************************** * just a collection More...

#include <objects/seqset/Bioseq_set_.hpp>

+ Inheritance diagram for CBioseq_set_Base:
+ Collaboration diagram for CBioseq_set_Base:

Public Types

enum  EClass {
  eClass_not_set = 0 , eClass_nuc_prot = 1 , eClass_segset = 2 , eClass_conset = 3 ,
  eClass_parts = 4 , eClass_gibb = 5 , eClass_gi = 6 , eClass_genbank = 7 ,
  eClass_pir = 8 , eClass_pub_set = 9 , eClass_equiv = 10 , eClass_swissprot = 11 ,
  eClass_pdb_entry = 12 , eClass_mut_set = 13 , eClass_pop_set = 14 , eClass_phy_set = 15 ,
  eClass_eco_set = 16 , eClass_gen_prod_set = 17 , eClass_wgs_set = 18 , eClass_named_annot = 19 ,
  eClass_named_annot_prod = 20 , eClass_read_set = 21 , eClass_paired_end_reads = 22 , eClass_small_genome_set = 23 ,
  eClass_other = 255
}
 
enum class  E_memberIndex {
  e__allMandatory = 0 , e_id , e_coll , e_level ,
  e_class , e_release , e_date , e_descr ,
  e_seq_set , e_annot
}
 
typedef CObject_id TId
 
typedef CDbtag TColl
 
typedef int TLevel
 
typedef EClass TClass
 
typedef string TRelease
 
typedef CDate TDate
 
typedef CSeq_descr TDescr
 
typedef list< CRef< CSeq_entry > > TSeq_set
 
typedef list< CRef< CSeq_annot > > TAnnot
 
typedef Tparent::CMemberIndex< E_memberIndex, 10 > 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

 CBioseq_set_Base (void)
 
virtual ~CBioseq_set_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetId (void) const
 Check if a value has been assigned to Id data member. 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...
 
void SetId (TId &value)
 Assign a value to Id data member. More...
 
TIdSetId (void)
 Assign a value to Id data member. More...
 
bool IsSetColl (void) const
 to identify a collection Check if a value has been assigned to Coll data member. More...
 
bool CanGetColl (void) const
 Check if it is safe to call GetColl method. More...
 
void ResetColl (void)
 Reset Coll data member. More...
 
const TCollGetColl (void) const
 Get the Coll member data. More...
 
void SetColl (TColl &value)
 Assign a value to Coll data member. More...
 
TCollSetColl (void)
 Assign a value to Coll data member. More...
 
bool IsSetLevel (void) const
 nesting level Check if a value has been assigned to Level data member. More...
 
bool CanGetLevel (void) const
 Check if it is safe to call GetLevel method. More...
 
void ResetLevel (void)
 Reset Level data member. More...
 
TLevel GetLevel (void) const
 Get the Level member data. More...
 
void SetLevel (TLevel value)
 Assign a value to Level data member. More...
 
TLevelSetLevel (void)
 Assign a value to Level 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...
 
void SetDefaultClass (void)
 Assign default value to 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 IsSetRelease (void) const
 Check if a value has been assigned to Release data member. More...
 
bool CanGetRelease (void) const
 Check if it is safe to call GetRelease method. More...
 
void ResetRelease (void)
 Reset Release data member. More...
 
const TReleaseGetRelease (void) const
 Get the Release member data. More...
 
void SetRelease (const TRelease &value)
 Assign a value to Release data member. More...
 
void SetRelease (TRelease &&value)
 
TReleaseSetRelease (void)
 Assign a value to Release data member. More...
 
bool IsSetDate (void) const
 Check if a value has been assigned to Date data member. More...
 
bool CanGetDate (void) const
 Check if it is safe to call GetDate method. More...
 
void ResetDate (void)
 Reset Date data member. More...
 
const TDateGetDate (void) const
 Get the Date member data. More...
 
void SetDate (TDate &value)
 Assign a value to Date data member. More...
 
TDateSetDate (void)
 Assign a value to Date data member. More...
 
bool IsSetDescr (void) const
 Check if a value has been assigned to Descr data member. More...
 
bool CanGetDescr (void) const
 Check if it is safe to call GetDescr method. More...
 
void ResetDescr (void)
 Reset Descr data member. More...
 
const TDescrGetDescr (void) const
 Get the Descr member data. More...
 
void SetDescr (TDescr &value)
 Assign a value to Descr data member. More...
 
TDescrSetDescr (void)
 Assign a value to Descr data member. More...
 
bool IsSetSeq_set (void) const
 Check if a value has been assigned to Seq_set data member. More...
 
bool CanGetSeq_set (void) const
 Check if it is safe to call GetSeq_set method. More...
 
void ResetSeq_set (void)
 Reset Seq_set data member. More...
 
const TSeq_setGetSeq_set (void) const
 Get the Seq_set member data. More...
 
TSeq_setSetSeq_set (void)
 Assign a value to Seq_set data member. More...
 
bool IsSetAnnot (void) const
 Check if a value has been assigned to Annot data member. More...
 
bool CanGetAnnot (void) const
 Check if it is safe to call GetAnnot method. More...
 
void ResetAnnot (void)
 Reset Annot data member. More...
 
const TAnnotGetAnnot (void) const
 Get the Annot member data. More...
 
TAnnotSetAnnot (void)
 Assign a value to Annot 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

 CBioseq_set_Base (const CBioseq_set_Base &)
 
CBioseq_set_Baseoperator= (const CBioseq_set_Base &)
 

Private Attributes

Uint4 m_set_State [1]
 
CRef< TIdm_Id
 
CRef< TCollm_Coll
 
int m_Level
 
EClass m_Class
 
string m_Release
 
CRef< TDatem_Date
 
CRef< TDescrm_Descr
 
list< CRef< CSeq_entry > > m_Seq_set
 
list< CRef< CSeq_annot > > m_Annot
 

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

*** Sequence Collections ******************************** * just a collection

CBioseq_set_Base

Definition at line 85 of file Bioseq_set_.hpp.


The documentation for this class was generated from the following files:
Modified on Mon Apr 22 04:01:43 2024 by modify_doxy.py rev. 669887