NCBI C++ ToolKit
|
Search Toolkit Book for CID2S_Chunk_Data_Base
CID2S_Chunk_Data_Base –. More...
#include <objects/seqsplit/ID2S_Chunk_Data_.hpp>
Classes | |
class | C_Id |
place of data to insert More... | |
Public Types | |
enum class | E_memberIndex { e__allMandatory = 0 , e_id , e_descr , e_annots , e_assembly , e_seq_map , e_seq_data , e_bioseqs } |
typedef C_Id | TId |
typedef CSeq_descr | TDescr |
typedef list< CRef< CSeq_annot > > | TAnnots |
typedef list< CRef< CSeq_align > > | TAssembly |
typedef list< CRef< CID2S_Sequence_Piece > > | TSeq_map |
typedef list< CRef< CID2S_Sequence_Piece > > | TSeq_data |
typedef list< CRef< CBioseq > > | TBioseqs |
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... | |
Public Member Functions | |
CID2S_Chunk_Data_Base (void) | |
virtual | ~CID2S_Chunk_Data_Base (void) |
DECLARE_INTERNAL_TYPE_INFO () | |
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 | IsSetDescr (void) const |
Seq-descr, for Bioseq and Bioseq-set Check if a value has been assigned to Descr data member. More... | |
bool | CanGetDescr (void) const |
Check if it is safe to call GetDescr method. More... | |
void | ResetDescr (void) |
Reset Descr data member. More... | |
const TDescr & | GetDescr (void) const |
Get the Descr member data. More... | |
void | SetDescr (TDescr &value) |
Assign a value to Descr data member. More... | |
TDescr & | SetDescr (void) |
Assign a value to Descr data member. More... | |
bool | IsSetAnnots (void) const |
Seq-annot, for Bioseq and Bioseq-set Check if a value has been assigned to Annots data member. More... | |
bool | CanGetAnnots (void) const |
Check if it is safe to call GetAnnots method. More... | |
void | ResetAnnots (void) |
Reset Annots data member. More... | |
const TAnnots & | GetAnnots (void) const |
Get the Annots member data. More... | |
TAnnots & | SetAnnots (void) |
Assign a value to Annots data member. More... | |
bool | IsSetAssembly (void) const |
assembly history Seq-align, for Bioseq 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... | |
TAssembly & | SetAssembly (void) |
Assign a value to Assembly data member. More... | |
bool | IsSetSeq_map (void) const |
sequence map, for Bioseq Check if a value has been assigned to Seq_map data member. More... | |
bool | CanGetSeq_map (void) const |
Check if it is safe to call GetSeq_map method. More... | |
void | ResetSeq_map (void) |
Reset Seq_map data member. More... | |
const TSeq_map & | GetSeq_map (void) const |
Get the Seq_map member data. More... | |
TSeq_map & | SetSeq_map (void) |
Assign a value to Seq_map data member. More... | |
bool | IsSetSeq_data (void) const |
sequence data, for Bioseq Check if a value has been assigned to Seq_data data member. More... | |
bool | CanGetSeq_data (void) const |
Check if it is safe to call GetSeq_data method. More... | |
void | ResetSeq_data (void) |
Reset Seq_data data member. More... | |
const TSeq_data & | GetSeq_data (void) const |
Get the Seq_data member data. More... | |
TSeq_data & | SetSeq_data (void) |
Assign a value to Seq_data data member. More... | |
bool | IsSetBioseqs (void) const |
Bioseq, for Bioseq-set Check if a value has been assigned to Bioseqs data member. More... | |
bool | CanGetBioseqs (void) const |
Check if it is safe to call GetBioseqs method. More... | |
void | ResetBioseqs (void) |
Reset Bioseqs data member. More... | |
const TBioseqs & | GetBioseqs (void) const |
Get the Bioseqs member data. More... | |
TBioseqs & | SetBioseqs (void) |
Assign a value to Bioseqs 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 CSerialObject | Tparent |
Private Member Functions | |
CID2S_Chunk_Data_Base (const CID2S_Chunk_Data_Base &) | |
CID2S_Chunk_Data_Base & | operator= (const CID2S_Chunk_Data_Base &) |
Private Attributes | |
Uint4 | m_set_State [1] |
CRef< TId > | m_Id |
CRef< TDescr > | m_Descr |
list< CRef< CSeq_annot > > | m_Annots |
list< CRef< CSeq_align > > | m_Assembly |
list< CRef< CID2S_Sequence_Piece > > | m_Seq_map |
list< CRef< CID2S_Sequence_Piece > > | m_Seq_data |
list< CRef< CBioseq > > | m_Bioseqs |
Additional Inherited Members | |
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 81 of file ID2S_Chunk_Data_.hpp.