NCBI C++ ToolKit
Public Types | Public Member Functions | Static Public Member Functions | Private Types | Private Member Functions | Private Attributes | Static Private Attributes | List of all members

Search Toolkit Book for CSeq_align_Base::C_Segs

alignment data More...

#include <objects/seqalign/Seq_align_.hpp>

+ Inheritance diagram for CSeq_align_Base::C_Segs:
+ Collaboration diagram for CSeq_align_Base::C_Segs:

Public Types

enum  E_Choice {
  e_not_set = 0 , e_Dendiag , e_Denseg , e_Std ,
  e_Packed , e_Disc , e_Spliced , e_Sparse
}
 Choice variants. More...
 
enum  E_ChoiceStopper { e_MaxChoice = 8 }
 Maximum+1 value of the choice variant enumerator. More...
 
typedef list< CRef< CDense_diag > > TDendiag
 
typedef CDense_seg TDenseg
 
typedef list< CRef< CStd_seg > > TStd
 
typedef CPacked_seg TPacked
 
typedef CSeq_align_set TDisc
 
typedef CSpliced_seg TSpliced
 
typedef CSparse_seg TSparse
 
- 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< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 

Public Member Functions

 C_Segs (void)
 
 ~C_Segs (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
void Reset (void)
 Reset the whole object. More...
 
void ResetSelection (void)
 Reset the selection (set it to e_not_set). More...
 
E_Choice Which (void) const
 Which variant is currently selected. More...
 
void CheckSelected (E_Choice index) const
 Verify selection, throw exception if it differs from the expected. More...
 
void ThrowInvalidSelection (E_Choice index) const
 Throw 'InvalidSelection' exception. More...
 
void Select (E_Choice index, EResetVariant reset=eDoResetVariant)
 Select the requested variant if needed. More...
 
void Select (E_Choice index, EResetVariant reset, CObjectMemoryPool *pool)
 Select the requested variant if needed, allocating CObject variants from memory pool. More...
 
bool IsDendiag (void) const
 Check if variant Dendiag is selected. More...
 
const TDendiagGetDendiag (void) const
 Get the variant data. More...
 
TDendiagSetDendiag (void)
 Select the variant. More...
 
bool IsDenseg (void) const
 Check if variant Denseg is selected. More...
 
const TDensegGetDenseg (void) const
 Get the variant data. More...
 
TDensegSetDenseg (void)
 Select the variant. More...
 
void SetDenseg (TDenseg &value)
 Select the variant and set its data. More...
 
bool IsStd (void) const
 Check if variant Std is selected. More...
 
const TStdGetStd (void) const
 Get the variant data. More...
 
TStdSetStd (void)
 Select the variant. More...
 
bool IsPacked (void) const
 Check if variant Packed is selected. More...
 
const TPackedGetPacked (void) const
 Get the variant data. More...
 
TPackedSetPacked (void)
 Select the variant. More...
 
void SetPacked (TPacked &value)
 Select the variant and set its data. More...
 
bool IsDisc (void) const
 Check if variant Disc is selected. More...
 
const TDiscGetDisc (void) const
 Get the variant data. More...
 
TDiscSetDisc (void)
 Select the variant. More...
 
void SetDisc (TDisc &value)
 Select the variant and set its data. More...
 
bool IsSpliced (void) const
 Check if variant Spliced is selected. More...
 
const TSplicedGetSpliced (void) const
 Get the variant data. More...
 
TSplicedSetSpliced (void)
 Select the variant. More...
 
void SetSpliced (TSpliced &value)
 Select the variant and set its data. More...
 
bool IsSparse (void) const
 Check if variant Sparse is selected. More...
 
const TSparseGetSparse (void) const
 Get the variant data. More...
 
TSparseSetSparse (void)
 Select the variant. More...
 
void SetSparse (TSparse &value)
 Select the variant and set its data. More...
 
- Public Member Functions inherited from CSerialObject
 CSerialObject (void)
 
virtual ~CSerialObject (void)
 
virtual const CTypeInfoGetThisTypeInfo (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 stringGetNamespaceName (void) const
 Get namespace name. More...
 
bool HasNamespacePrefix (void) const
 Check if data type has namespace prefix. More...
 
const stringGetNamespacePrefix (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...
 
CObjectoperator= (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 string SelectionName (E_Choice index)
 Retrieve selection name (for diagnostic purposes). 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

 C_Segs (const C_Segs &)
 
C_Segsoperator= (const C_Segs &)
 
void DoSelect (E_Choice index, CObjectMemoryPool *pool=0)
 

Private Attributes

E_Choice m_choice
 
union {
   NCBI_NS_NCBI::CUnionBuffer< TDendiag >   CSeq_align_Base::C_Segs::m_Dendiag
 
   NCBI_NS_NCBI::CUnionBuffer< TStd >   CSeq_align_Base::C_Segs::m_Std
 
   NCBI_NS_NCBI::CSerialObject *   CSeq_align_Base::C_Segs::m_object
 
}; 
 

Static Private Attributes

static const char *const sm_SelectionNames []
 

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...
 

Detailed Description

alignment data

C_Segs

Definition at line 117 of file Seq_align_.hpp.


The documentation for this class was generated from the following files:
Modified on Sun Apr 14 05:28:44 2024 by modify_doxy.py rev. 669887