Search Toolkit Book for CVariantPlacement
#include <objects/variation/VariantPlacement.hpp>
Inheritance diagram for CVariantPlacement:
Collaboration diagram for CVariantPlacement:
Public Member Functions | |
| CVariantPlacement (void) | |
| ~CVariantPlacement (void) | |
| Public Member Functions inherited from CVariantPlacement_Base | |
| CVariantPlacement_Base (void) | |
| virtual | ~CVariantPlacement_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetLoc (void) const |
| actual concrete placement we are considering Check if a value has been assigned to Loc data member. More... | |
| bool | CanGetLoc (void) const |
| Check if it is safe to call GetLoc method. More... | |
| void | ResetLoc (void) |
| Reset Loc data member. More... | |
| const TLoc & | GetLoc (void) const |
| Get the Loc member data. More... | |
| void | SetLoc (TLoc &value) |
| Assign a value to Loc data member. More... | |
| TLoc & | SetLoc (void) |
| Assign a value to Loc data member. More... | |
| bool | IsSetMol (void) const |
| Check if a value has been assigned to Mol data member. More... | |
| bool | CanGetMol (void) const |
| Check if it is safe to call GetMol method. More... | |
| void | ResetMol (void) |
| Reset Mol data member. More... | |
| TMol | GetMol (void) const |
| Get the Mol member data. More... | |
| void | SetMol (TMol value) |
| Assign a value to Mol data member. More... | |
| TMol & | SetMol (void) |
| Assign a value to Mol data member. More... | |
| bool | IsSetPlacement_method (void) const |
| Check if a value has been assigned to Placement_method data member. More... | |
| bool | CanGetPlacement_method (void) const |
| Check if it is safe to call GetPlacement_method method. More... | |
| void | ResetPlacement_method (void) |
| Reset Placement_method data member. More... | |
| TPlacement_method | GetPlacement_method (void) const |
| Get the Placement_method member data. More... | |
| void | SetPlacement_method (TPlacement_method value) |
| Assign a value to Placement_method data member. More... | |
| TPlacement_method & | SetPlacement_method (void) |
| Assign a value to Placement_method data member. More... | |
| bool | IsSetStart_offset (void) const |
| location refinements, describing offsets into introns from product coordinates. More... | |
| bool | CanGetStart_offset (void) const |
| Check if it is safe to call GetStart_offset method. More... | |
| void | ResetStart_offset (void) |
| Reset Start_offset data member. More... | |
| TStart_offset | GetStart_offset (void) const |
| Get the Start_offset member data. More... | |
| void | SetStart_offset (TStart_offset value) |
| Assign a value to Start_offset data member. More... | |
| TStart_offset & | SetStart_offset (void) |
| Assign a value to Start_offset data member. More... | |
| bool | IsSetStart_offset_fuzz (void) const |
| Check if a value has been assigned to Start_offset_fuzz data member. More... | |
| bool | CanGetStart_offset_fuzz (void) const |
| Check if it is safe to call GetStart_offset_fuzz method. More... | |
| void | ResetStart_offset_fuzz (void) |
| Reset Start_offset_fuzz data member. More... | |
| const TStart_offset_fuzz & | GetStart_offset_fuzz (void) const |
| Get the Start_offset_fuzz member data. More... | |
| void | SetStart_offset_fuzz (TStart_offset_fuzz &value) |
| Assign a value to Start_offset_fuzz data member. More... | |
| TStart_offset_fuzz & | SetStart_offset_fuzz (void) |
| Assign a value to Start_offset_fuzz data member. More... | |
| bool | IsSetStop_offset (void) const |
| Check if a value has been assigned to Stop_offset data member. More... | |
| bool | CanGetStop_offset (void) const |
| Check if it is safe to call GetStop_offset method. More... | |
| void | ResetStop_offset (void) |
| Reset Stop_offset data member. More... | |
| TStop_offset | GetStop_offset (void) const |
| Get the Stop_offset member data. More... | |
| void | SetStop_offset (TStop_offset value) |
| Assign a value to Stop_offset data member. More... | |
| TStop_offset & | SetStop_offset (void) |
| Assign a value to Stop_offset data member. More... | |
| bool | IsSetStop_offset_fuzz (void) const |
| Check if a value has been assigned to Stop_offset_fuzz data member. More... | |
| bool | CanGetStop_offset_fuzz (void) const |
| Check if it is safe to call GetStop_offset_fuzz method. More... | |
| void | ResetStop_offset_fuzz (void) |
| Reset Stop_offset_fuzz data member. More... | |
| const TStop_offset_fuzz & | GetStop_offset_fuzz (void) const |
| Get the Stop_offset_fuzz member data. More... | |
| void | SetStop_offset_fuzz (TStop_offset_fuzz &value) |
| Assign a value to Stop_offset_fuzz data member. More... | |
| TStop_offset_fuzz & | SetStop_offset_fuzz (void) |
| Assign a value to Stop_offset_fuzz data member. More... | |
| bool | IsSetFrame (void) const |
| 0-based position of bio-start relative to containing codon Check if a value has been assigned to Frame data member. More... | |
| bool | CanGetFrame (void) const |
| Check if it is safe to call GetFrame method. More... | |
| void | ResetFrame (void) |
| Reset Frame data member. More... | |
| TFrame | GetFrame (void) const |
| Get the Frame member data. More... | |
| void | SetFrame (TFrame value) |
| Assign a value to Frame data member. More... | |
| TFrame & | SetFrame (void) |
| Assign a value to Frame data member. More... | |
| bool | IsSetSeq (void) const |
| for situations in which a raw location isn't sufficient Check if a value has been assigned to Seq data member. More... | |
| bool | CanGetSeq (void) const |
| Check if it is safe to call GetSeq method. More... | |
| void | ResetSeq (void) |
| Reset Seq data member. More... | |
| const TSeq & | GetSeq (void) const |
| Get the Seq member data. More... | |
| void | SetSeq (TSeq &value) |
| Assign a value to Seq data member. More... | |
| TSeq & | SetSeq (void) |
| Assign a value to Seq data member. More... | |
| bool | IsSetAssembly (void) const |
| reference to the assembly (GenColl ID) for this location Check if a value has been assigned to Assembly data member. More... | |
| bool | CanGetAssembly (void) const |
| Check if it is safe to call GetAssembly method. More... | |
| void | ResetAssembly (void) |
| Reset Assembly data member. More... | |
| const TAssembly & | GetAssembly (void) const |
| Get the Assembly member data. More... | |
| void | SetAssembly (TAssembly &value) |
| Assign a value to Assembly data member. More... | |
| TAssembly & | SetAssembly (void) |
| Assign a value to Assembly data member. More... | |
| bool | IsSetHgvs_name (void) const |
| Check if a value has been assigned to Hgvs_name data member. More... | |
| bool | CanGetHgvs_name (void) const |
| Check if it is safe to call GetHgvs_name method. More... | |
| void | ResetHgvs_name (void) |
| Reset Hgvs_name data member. More... | |
| const THgvs_name & | GetHgvs_name (void) const |
| Get the Hgvs_name member data. More... | |
| void | SetHgvs_name (const THgvs_name &value) |
| Assign a value to Hgvs_name data member. More... | |
| void | SetHgvs_name (THgvs_name &&value) |
| THgvs_name & | SetHgvs_name (void) |
| Assign a value to Hgvs_name data member. More... | |
| bool | IsSetComment (void) const |
| the reference location for this variant Check if a value has been assigned to Comment data member. More... | |
| bool | CanGetComment (void) const |
| Check if it is safe to call GetComment method. More... | |
| void | ResetComment (void) |
| Reset Comment data member. More... | |
| const TComment & | GetComment (void) const |
| Get the Comment member data. More... | |
| void | SetComment (const TComment &value) |
| Assign a value to Comment data member. More... | |
| void | SetComment (TComment &&value) |
| TComment & | SetComment (void) |
| Assign a value to Comment data member. More... | |
| bool | IsSetExceptions (void) const |
| Check if a value has been assigned to Exceptions data member. More... | |
| bool | CanGetExceptions (void) const |
| Check if it is safe to call GetExceptions method. More... | |
| void | ResetExceptions (void) |
| Reset Exceptions data member. More... | |
| const TExceptions & | GetExceptions (void) const |
| Get the Exceptions member data. More... | |
| TExceptions & | SetExceptions (void) |
| Assign a value to Exceptions data member. More... | |
| bool | IsSetDbxrefs (void) const |
| e.g. More... | |
| bool | CanGetDbxrefs (void) const |
| Check if it is safe to call GetDbxrefs method. More... | |
| void | ResetDbxrefs (void) |
| Reset Dbxrefs data member. More... | |
| const TDbxrefs & | GetDbxrefs (void) const |
| Get the Dbxrefs member data. More... | |
| TDbxrefs & | SetDbxrefs (void) |
| Assign a value to Dbxrefs data member. More... | |
| bool | IsSetExt (void) const |
| for process-specific placement tags/labels Check if a value has been assigned to Ext data member. More... | |
| bool | CanGetExt (void) const |
| Check if it is safe to call GetExt method. More... | |
| void | ResetExt (void) |
| Reset Ext data member. More... | |
| const TExt & | GetExt (void) const |
| Get the Ext member data. More... | |
| TExt & | SetExt (void) |
| Assign a value to Ext data member. More... | |
| bool | IsSetGene_location (void) const |
| Same semantics as VariantProperties.gene-location, except placement-specific Check if a value has been assigned to Gene_location data member. More... | |
| bool | CanGetGene_location (void) const |
| Check if it is safe to call GetGene_location method. More... | |
| void | ResetGene_location (void) |
| Reset Gene_location data member. More... | |
| TGene_location | GetGene_location (void) const |
| Get the Gene_location member data. More... | |
| void | SetGene_location (TGene_location value) |
| Assign a value to Gene_location data member. More... | |
| TGene_location & | SetGene_location (void) |
| Assign a value to Gene_location data member. More... | |
| 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 TId & | GetId (void) const |
| Get the Id member data. More... | |
| void | SetId (TId &value) |
| Assign a value to Id data member. More... | |
| TId & | SetId (void) |
| Assign a value to Id data member. More... | |
| bool | IsSetParent_id (void) const |
| id of the placement from which this one was derived Check if a value has been assigned to Parent_id data member. More... | |
| bool | CanGetParent_id (void) const |
| Check if it is safe to call GetParent_id method. More... | |
| void | ResetParent_id (void) |
| Reset Parent_id data member. More... | |
| const TParent_id & | GetParent_id (void) const |
| Get the Parent_id member data. More... | |
| void | SetParent_id (TParent_id &value) |
| Assign a value to Parent_id data member. More... | |
| TParent_id & | SetParent_id (void) |
| Assign a value to Parent_id data member. More... | |
| bool | IsSetSo_terms (void) const |
| Sequence Ontology terms for this placement Check if a value has been assigned to So_terms data member. More... | |
| bool | CanGetSo_terms (void) const |
| Check if it is safe to call GetSo_terms method. More... | |
| void | ResetSo_terms (void) |
| Reset So_terms data member. More... | |
| const TSo_terms & | GetSo_terms (void) const |
| Get the So_terms member data. More... | |
| TSo_terms & | SetSo_terms (void) |
| Assign a value to So_terms 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 CVariantPlacement_Base | Tparent |
Private Member Functions | |
| CVariantPlacement (const CVariantPlacement &value) | |
| CVariantPlacement & | operator= (const CVariantPlacement &value) |
Additional Inherited Members | |
| Public Types inherited from CVariantPlacement_Base | |
| enum | EMol { eMol_unknown = 0 , eMol_genomic = 1 , eMol_cdna = 2 , eMol_rna = 3 , eMol_protein = 4 , eMol_mitochondrion = 5 } |
| enum | EPlacement_method { ePlacement_method_projected = 1 , ePlacement_method_asserted = 2 , ePlacement_method_aligned = 3 } |
| location flags More... | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_loc , e_mol , e_placement_method , e_start_offset , e_start_offset_fuzz , e_stop_offset , e_stop_offset_fuzz , e_frame , e_seq , e_assembly , e_hgvs_name , e_comment , e_exceptions , e_dbxrefs , e_ext , e_gene_location , e_id , e_parent_id , e_so_terms } |
| typedef CSeq_loc | TLoc |
| typedef int | TMol |
| typedef int | TPlacement_method |
| typedef int | TStart_offset |
| typedef CInt_fuzz | TStart_offset_fuzz |
| typedef int | TStop_offset |
| typedef CInt_fuzz | TStop_offset_fuzz |
| typedef int | TFrame |
| typedef CSeq_literal | TSeq |
| typedef CDbtag | TAssembly |
| typedef string | THgvs_name |
| typedef string | TComment |
| typedef list< CRef< CVariationException > > | TExceptions |
| typedef list< CRef< CDbtag > > | TDbxrefs |
| typedef list< CRef< CUser_object > > | TExt |
| typedef int | TGene_location |
| typedef CObject_id | TId |
| typedef CObject_id | TParent_id |
| typedef list< int > | TSo_terms |
| typedef Tparent::CMemberIndex< E_memberIndex, 20 > | 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 CVariantPlacement_Base | |
| static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | EMol (void) |
| Access to EMol's attributes (values, names) as defined in spec. More... | |
| static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | EPlacement_method (void) |
| Access to EPlacement_method'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 65 of file VariantPlacement.hpp.
The documentation for this class was generated from the following files:
- include/objects/variation/VariantPlacement.hpp
- src/objects/variation/VariantPlacement.cpp
