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 GC-SeqIdAlias defined in file genome_collection.asn

Search Toolkit Book for CGC_SeqIdAlias_Base

Seq-id-alias a sequence has multiple seq-ids - refseq, genbank, local and each one has both gi and accession.version We cannot provide them as simply a list of seq-ids since it will be unclear which gi goes with which accession, therefore we group the related ones as alias pair. More...

#include <objects/genomecoll/GC_SeqIdAlias_.hpp>

+ Inheritance diagram for CGC_SeqIdAlias_Base:
+ Collaboration diagram for CGC_SeqIdAlias_Base:

Public Types

enum  ESimilarity { eSimilarity_unknown = 0 , eSimilarity_identical = 1 , eSimilarity_different = 255 }
 
enum class  E_memberIndex {
  e__allMandatory = 0 , e_public , e_gpipe , e_gi ,
  e_similarity
}
 
typedef CSeq_id TPublic
 
typedef CSeq_id TGpipe
 
typedef CSeq_id TGi
 
typedef int TSimilarity
 
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< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CGC_SeqIdAlias_Base (void)
 
virtual ~CGC_SeqIdAlias_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetPublic (void) const
 the refseq/genbank accession Check if a value has been assigned to Public data member. More...
 
bool CanGetPublic (void) const
 Check if it is safe to call GetPublic method. More...
 
void ResetPublic (void)
 Reset Public data member. More...
 
const TPublicGetPublic (void) const
 Get the Public member data. More...
 
void SetPublic (TPublic &value)
 Assign a value to Public data member. More...
 
TPublicSetPublic (void)
 Assign a value to Public data member. More...
 
bool IsSetGpipe (void) const
 the gpipe accession Check if a value has been assigned to Gpipe data member. More...
 
bool CanGetGpipe (void) const
 Check if it is safe to call GetGpipe method. More...
 
void ResetGpipe (void)
 Reset Gpipe data member. More...
 
const TGpipeGetGpipe (void) const
 Get the Gpipe member data. More...
 
void SetGpipe (TGpipe &value)
 Assign a value to Gpipe data member. More...
 
TGpipeSetGpipe (void)
 Assign a value to Gpipe data member. More...
 
bool IsSetGi (void) const
 optional since not all sequences have GIs Similarity: relationship between this synonym to main seqid of the GC-Sequence Can be expanded to multiple level of identicality can use bitmap to flag ambiguity between different levels Check if a value has been assigned to Gi data member. More...
 
bool CanGetGi (void) const
 Check if it is safe to call GetGi method. More...
 
void ResetGi (void)
 Reset Gi data member. More...
 
const TGiGetGi (void) const
 Get the Gi member data. More...
 
void SetGi (TGi &value)
 Assign a value to Gi data member. More...
 
TGiSetGi (void)
 Assign a value to Gi 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...
 
TSimilarity GetSimilarity (void) const
 Get the Similarity member data. More...
 
void SetSimilarity (TSimilarity value)
 Assign a value to Similarity data member. More...
 
TSimilaritySetSimilarity (void)
 Assign a value to Similarity 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() ESimilarity (void)
 Access to ESimilarity'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_SeqIdAlias_Base (const CGC_SeqIdAlias_Base &)
 
CGC_SeqIdAlias_Baseoperator= (const CGC_SeqIdAlias_Base &)
 

Private Attributes

Uint4 m_set_State [1]
 
CRef< TPublicm_Public
 
CRef< TGpipem_Gpipe
 
CRef< TGim_Gi
 
int m_Similarity
 

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

Seq-id-alias a sequence has multiple seq-ids - refseq, genbank, local and each one has both gi and accession.version We cannot provide them as simply a list of seq-ids since it will be unclear which gi goes with which accession, therefore we group the related ones as alias pair.

CGC_SeqIdAlias_Base

Definition at line 78 of file GC_SeqIdAlias_.hpp.


The documentation for this class was generated from the following files:
Modified on Wed May 22 11:35:26 2024 by modify_doxy.py rev. 669887