Search Toolkit Book for CSeq_literal
#include <objects/seq/Seq_literal.hpp>
Inheritance diagram for CSeq_literal:
Collaboration diagram for CSeq_literal:
Public Types | |
| enum | EBridgeableStatus { e_NotAGap , e_Bridgeable , e_NotBridgeable , e_MaybeBridgeable } |
| Public Types inherited from CSeq_literal_Base | |
| enum class | E_memberIndex { e__allMandatory = 0 , e_length , e_fuzz , e_seq_data } |
| typedef TSeqPos | TLength |
| typedef CInt_fuzz | TFuzz |
| typedef CSeq_data | TSeq_data |
| typedef Tparent::CMemberIndex< E_memberIndex, 4 > | 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 | |
| CSeq_literal (void) | |
| ~CSeq_literal (void) | |
| EBridgeableStatus | GetBridgeability () const |
| EBridgeableStatus | IsBridgeable () const |
| Public Member Functions inherited from CSeq_literal_Base | |
| CSeq_literal_Base (void) | |
| virtual | ~CSeq_literal_Base (void) |
| DECLARE_INTERNAL_TYPE_INFO () | |
| bool | IsSetLength (void) const |
| must give a length 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 |
| could be unsure 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 | IsSetSeq_data (void) const |
| may have the data 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... | |
| 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 CSeq_literal_Base | Tparent |
Private Member Functions | |
| CSeq_literal (const CSeq_literal &value) | |
| CSeq_literal & | operator= (const CSeq_literal &value) |
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... | |
Detailed Description
Definition at line 53 of file Seq_literal.hpp.
Member Typedef Documentation
◆ Tparent
|
private |
Definition at line 55 of file Seq_literal.hpp.
Member Enumeration Documentation
◆ EBridgeableStatus
| Enumerator | |
|---|---|
| e_NotAGap | |
| e_Bridgeable | |
| e_NotBridgeable | |
| e_MaybeBridgeable | |
Definition at line 62 of file Seq_literal.hpp.
Constructor & Destructor Documentation
◆ CSeq_literal() [1/2]
|
inline |
Definition at line 81 of file Seq_literal.hpp.
◆ ~CSeq_literal()
| CSeq_literal::~CSeq_literal | ( | void | ) |
Definition at line 52 of file Seq_literal.cpp.
◆ CSeq_literal() [2/2]
|
private |
Member Function Documentation
◆ GetBridgeability()
| CSeq_literal::EBridgeableStatus CSeq_literal::GetBridgeability | ( | ) | const |
Definition at line 56 of file Seq_literal.cpp.
References e_Bridgeable, e_MaybeBridgeable, e_NotAGap, e_NotBridgeable, CSeq_gap_Base::eLinkage_linked, CSeq_gap_Base::eType_centromere, CSeq_gap_Base::eType_heterochromatin, CLinkage_evidence_Base::eType_paired_ends, CLinkage_evidence_Base::eType_pcr, CSeq_gap_Base::eType_short_arm, CSeq_gap_Base::eType_telomere, CLinkage_evidence_Base::eType_within_clone, CSeq_data_Base::GetGap(), CSeq_gap_Base::GetLinkage(), CSeq_gap_Base::GetLinkage_evidence(), CSeq_literal_Base::GetSeq_data(), CSeq_gap_Base::GetType(), IsGap(), CSeq_literal_Base::IsSetFuzz(), CSeq_gap_Base::IsSetLinkage(), CSeq_gap_Base::IsSetLinkage_evidence(), CSeq_literal_Base::IsSetSeq_data(), and ITERATE.
Referenced by IsBridgeable().
◆ IsBridgeable()
|
inline |
Definition at line 68 of file Seq_literal.hpp.
References GetBridgeability().
◆ operator=()
|
private |
The documentation for this class was generated from the following files:
- include/objects/seq/Seq_literal.hpp
- src/objects/seq/Seq_literal.cpp
