Search Toolkit Book for CGC_AssemblySet
#include <objects/genomecoll/GC_AssemblySet.hpp>
Inheritance diagram for CGC_AssemblySet:
Collaboration diagram for CGC_AssemblySet:
Public Member Functions | |
| CGC_AssemblySet (void) | |
| ~CGC_AssemblySet (void) | |
| string | GetAccession () const |
| Public Member Functions inherited from CGC_AssemblySet_Base | |
| CGC_AssemblySet_Base (void) | |
| virtual | ~CGC_AssemblySet_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetId (void) const |
| The identifier of this assembly examples: GC internal id, Assembly-accession.version 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> db "UCSC_name", tag str <UCSC identifier for assembly> db "Ensembl_name",tag str <Ensembl identifier for assembly> 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 TId & | GetId (void) const |
| Get the Id member data. More... | |
| TId & | SetId (void) |
| Assign a value to Id data member. More... | |
| bool | IsSetSet_type (void) const |
| Check if a value has been assigned to Set_type data member. More... | |
| bool | CanGetSet_type (void) const |
| Check if it is safe to call GetSet_type method. More... | |
| void | ResetSet_type (void) |
| Reset Set_type data member. More... | |
| TSet_type | GetSet_type (void) const |
| Get the Set_type member data. More... | |
| void | SetSet_type (TSet_type value) |
| Assign a value to Set_type data member. More... | |
| TSet_type & | SetSet_type (void) |
| Assign a value to Set_type 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... | |
| TClass & | SetClass (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 TDesc & | GetDesc (void) const |
| Get the Desc member data. More... | |
| void | SetDesc (TDesc &value) |
| Assign a value to Desc data member. More... | |
| TDesc & | SetDesc (void) |
| Assign a value to Desc data member. More... | |
| bool | IsSetPrimary_assembly (void) const |
| we contain hierarchically a set of assemblies Check if a value has been assigned to Primary_assembly data member. More... | |
| bool | CanGetPrimary_assembly (void) const |
| Check if it is safe to call GetPrimary_assembly method. More... | |
| void | ResetPrimary_assembly (void) |
| Reset Primary_assembly data member. More... | |
| const TPrimary_assembly & | GetPrimary_assembly (void) const |
| Get the Primary_assembly member data. More... | |
| void | SetPrimary_assembly (TPrimary_assembly &value) |
| Assign a value to Primary_assembly data member. More... | |
| TPrimary_assembly & | SetPrimary_assembly (void) |
| Assign a value to Primary_assembly data member. More... | |
| bool | IsSetMore_assemblies (void) const |
| Check if a value has been assigned to More_assemblies data member. More... | |
| bool | CanGetMore_assemblies (void) const |
| Check if it is safe to call GetMore_assemblies method. More... | |
| void | ResetMore_assemblies (void) |
| Reset More_assemblies data member. More... | |
| const TMore_assemblies & | GetMore_assemblies (void) const |
| Get the More_assemblies member data. More... | |
| TMore_assemblies & | SetMore_assemblies (void) |
| Assign a value to More_assemblies data member. More... | |
| bool | IsSetStats (void) const |
| statistics "stats" field holds stats for all chromosomes combined: 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 TStats & | GetStats (void) const |
| Get the Stats member data. More... | |
| void | SetStats (TStats &value) |
| Assign a value to Stats data member. More... | |
| TStats & | SetStats (void) |
| Assign a value to 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 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 |
Private Types | |
| typedef CGC_AssemblySet_Base | Tparent |
Private Member Functions | |
| CGC_AssemblySet (const CGC_AssemblySet &value) | |
| CGC_AssemblySet & | operator= (const CGC_AssemblySet &value) |
Additional Inherited Members | |
| Public Types inherited from CGC_AssemblySet_Base | |
| enum | ESet_type { eSet_type_full_assembly = 0 , eSet_type_assembly_set = 100 , eSet_type_other = 255 } |
| set type: Assembly-Sets can be of 2 categories More... | |
| enum | EClass { eClass_full_assembly = 0 , eClass_haploid = 1 , eClass_haploid_with_alt_loci = 2 , eClass_diploid = 3 , eClass_unresolved_diploid = 4 , eClass_alternate_haplotype = 5 , eClass_alternate_pseudohaplotype = 6 , eClass_annotation_target_set = 101 , eClass_analysis_set = 102 , eClass_other = 255 } |
| 'class' defines the semantics of how to interpret this item More... | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_id , e_set_type , e_class , e_desc , e_primary_assembly , e_more_assemblies , e_stats } |
| typedef list< CRef< CDbtag > > | TId |
| typedef int | TSet_type |
| typedef int | TClass |
| typedef CGC_AssemblyDesc | TDesc |
| typedef CGC_Assembly | TPrimary_assembly |
| typedef list< CRef< CGC_Assembly > > | TMore_assemblies |
| typedef CGC_SequenceStats | TStats |
| typedef Tparent::CMemberIndex< E_memberIndex, 8 > | 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... | |
| Static Public Member Functions inherited from CGC_AssemblySet_Base | |
| static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | ESet_type (void) |
| Access to ESet_type's attributes (values, names) as defined in spec. More... | |
| 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) |
| 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_AssemblySet.hpp.
Member Typedef Documentation
◆ Tparent
|
private |
Definition at line 55 of file GC_AssemblySet.hpp.
Constructor & Destructor Documentation
◆ CGC_AssemblySet() [1/2]
|
inline |
Definition at line 75 of file GC_AssemblySet.hpp.
◆ ~CGC_AssemblySet()
| CGC_AssemblySet::~CGC_AssemblySet | ( | void | ) |
Definition at line 50 of file GC_AssemblySet.cpp.
◆ CGC_AssemblySet() [2/2]
|
private |
Member Function Documentation
◆ GetAccession()
| string CGC_AssemblySet::GetAccession | ( | ) | const |
◆ operator=()
|
private |
The documentation for this class was generated from the following files:
- include/objects/genomecoll/GC_AssemblySet.hpp
- src/objects/genomecoll/GC_AssemblySet.cpp
