NCBI C++ ToolKit
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Search Toolkit Book for CSeq_inst_Base
*** Instances of sequences ******************************* * the sequence data itself More...
#include <objects/seq/Seq_inst_.hpp>
Public Member Functions | |
CSeq_inst_Base (void) | |
virtual | ~CSeq_inst_Base (void) |
DECLARE_INTERNAL_TYPE_INFO () | |
bool | IsSetRepr (void) const |
Check if a value has been assigned to Repr data member. More... | |
bool | CanGetRepr (void) const |
Check if it is safe to call GetRepr method. More... | |
void | ResetRepr (void) |
Reset Repr data member. More... | |
TRepr | GetRepr (void) const |
Get the Repr member data. More... | |
void | SetRepr (TRepr value) |
Assign a value to Repr data member. More... | |
TRepr & | SetRepr (void) |
Assign a value to Repr 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 | IsSetLength (void) const |
length of sequence in residues Check if a value has been assigned to Length data member. More... | |
bool | CanGetLength (void) const |
Check if it is safe to call GetLength method. More... | |
void | ResetLength (void) |
Reset Length data member. More... | |
TLength | GetLength (void) const |
Get the Length member data. More... | |
void | SetLength (TLength value) |
Assign a value to Length data member. More... | |
TLength & | SetLength (void) |
Assign a value to Length data member. More... | |
bool | IsSetFuzz (void) const |
length uncertainty Check if a value has been assigned to Fuzz data member. More... | |
bool | CanGetFuzz (void) const |
Check if it is safe to call GetFuzz method. More... | |
void | ResetFuzz (void) |
Reset Fuzz data member. More... | |
const TFuzz & | GetFuzz (void) const |
Get the Fuzz member data. More... | |
void | SetFuzz (TFuzz &value) |
Assign a value to Fuzz data member. More... | |
TFuzz & | SetFuzz (void) |
Assign a value to Fuzz data member. More... | |
bool | IsSetTopology (void) const |
Check if a value has been assigned to Topology data member. More... | |
bool | CanGetTopology (void) const |
Check if it is safe to call GetTopology method. More... | |
void | ResetTopology (void) |
Reset Topology data member. More... | |
void | SetDefaultTopology (void) |
Assign default value to Topology data member. More... | |
TTopology | GetTopology (void) const |
Get the Topology member data. More... | |
void | SetTopology (TTopology value) |
Assign a value to Topology data member. More... | |
TTopology & | SetTopology (void) |
Assign a value to Topology data member. More... | |
bool | IsSetStrand (void) const |
Check if a value has been assigned to Strand data member. More... | |
bool | CanGetStrand (void) const |
Check if it is safe to call GetStrand method. More... | |
void | ResetStrand (void) |
Reset Strand data member. More... | |
TStrand | GetStrand (void) const |
Get the Strand member data. More... | |
void | SetStrand (TStrand value) |
Assign a value to Strand data member. More... | |
TStrand & | SetStrand (void) |
Assign a value to Strand data member. More... | |
bool | IsSetSeq_data (void) const |
the sequence 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... | |
void | SetSeq_data (TSeq_data &value) |
Assign a value to Seq_data data member. More... | |
TSeq_data & | SetSeq_data (void) |
Assign a value to Seq_data data member. More... | |
bool | IsSetExt (void) const |
extensions for special types 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... | |
void | SetExt (TExt &value) |
Assign a value to Ext data member. More... | |
TExt & | SetExt (void) |
Assign a value to Ext data member. More... | |
bool | IsSetHist (void) const |
sequence history Check if a value has been assigned to Hist data member. More... | |
bool | CanGetHist (void) const |
Check if it is safe to call GetHist method. More... | |
void | ResetHist (void) |
Reset Hist data member. More... | |
const THist & | GetHist (void) const |
Get the Hist member data. More... | |
void | SetHist (THist &value) |
Assign a value to Hist data member. More... | |
THist & | SetHist (void) |
Assign a value to Hist 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() | ERepr (void) |
Access to ERepr's attributes (values, names) as defined in spec. More... | |
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() | ETopology (void) |
Access to ETopology's attributes (values, names) as defined in spec. More... | |
static const NCBI_NS_NCBI::CEnumeratedTypeValues *ENUM_METHOD_NAME() | EStrand (void) |
Access to EStrand'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 | |
CSeq_inst_Base (const CSeq_inst_Base &) | |
CSeq_inst_Base & | operator= (const CSeq_inst_Base &) |
Private Attributes | |
Uint4 | m_set_State [1] |
ERepr | m_Repr |
EMol | m_Mol |
TSeqPos | m_Length |
CRef< TFuzz > | m_Fuzz |
ETopology | m_Topology |
EStrand | m_Strand |
CRef< TSeq_data > | m_Seq_data |
CRef< TExt > | m_Ext |
CRef< THist > | m_Hist |
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... | |
*** Instances of sequences ******************************* * the sequence data itself
Definition at line 78 of file Seq_inst_.hpp.