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< Uint8 > | TCounter |
| 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 TPublic & | GetPublic (void) const |
| Get the Public member data. More... | |
| void | SetPublic (TPublic &value) |
| Assign a value to Public data member. More... | |
| TPublic & | SetPublic (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 TGpipe & | GetGpipe (void) const |
| Get the Gpipe member data. More... | |
| void | SetGpipe (TGpipe &value) |
| Assign a value to Gpipe data member. More... | |
| TGpipe & | SetGpipe (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 TGi & | GetGi (void) const |
| Get the Gi member data. More... | |
| void | SetGi (TGi &value) |
| Assign a value to Gi data member. More... | |
| TGi & | SetGi (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... | |
| TSimilarity & | SetSimilarity (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 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 |
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_Base & | operator= (const CGC_SeqIdAlias_Base &) |
Private Attributes | |
| Uint4 | m_set_State [1] |
| CRef< TPublic > | m_Public |
| CRef< TGpipe > | m_Gpipe |
| CRef< TGi > | m_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.
Definition at line 78 of file GC_SeqIdAlias_.hpp.
The documentation for this class was generated from the following files:
- include/objects/genomecoll/GC_SeqIdAlias_.hpp
- src/objects/genomecoll/GC_SeqIdAlias_.cpp
