NCBI C++ ToolKit
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Search Toolkit Book for CVariantPlacement
#include <objects/variation/VariantPlacement.hpp>
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... | |
Definition at line 65 of file VariantPlacement.hpp.