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CGapEdit Class Reference

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#include <gui/objutils/gap_edit.hpp>

+ Inheritance diagram for CGapEdit:
+ Collaboration diagram for CGapEdit:

Public Member Functions

 CGapEdit (CBioseq_Handle &bh, const TSeqPos from, const TSeqPos length)
 
CBioseq_Handle GetBioseq_Handle () const
 
TSeqPos GetFrom (void) const
 
- Public Member Functions inherited from CSeq_literal
 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...
 
TLengthSetLength (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 TFuzzGetFuzz (void) const
 Get the Fuzz member data. More...
 
void SetFuzz (TFuzz &value)
 Assign a value to Fuzz data member. More...
 
TFuzzSetFuzz (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_dataGetSeq_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_dataSetSeq_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 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
 

Protected Attributes

CBioseq_Handle m_BH
 
TSeqPos m_From
 

Additional Inherited Members

- Public Types inherited from CSeq_literal
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< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. 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...
 

Detailed Description

Definition at line 48 of file gap_edit.hpp.

Constructor & Destructor Documentation

◆ CGapEdit()

CGapEdit::CGapEdit ( CBioseq_Handle bh,
const TSeqPos  from,
const TSeqPos  length 
)
inline

Definition at line 51 of file gap_edit.hpp.

Member Function Documentation

◆ GetBioseq_Handle()

CBioseq_Handle CGapEdit::GetBioseq_Handle ( ) const
inline

Definition at line 56 of file gap_edit.hpp.

Referenced by CConvertSelectedGaps::apply_impl(), and CEditSelectedGaps::apply_impl().

◆ GetFrom()

TSeqPos CGapEdit::GetFrom ( void  ) const
inline

Definition at line 57 of file gap_edit.hpp.

Referenced by CConvertSelectedGaps::apply_impl(), and CEditSelectedGaps::apply_impl().

Member Data Documentation

◆ m_BH

CBioseq_Handle CGapEdit::m_BH
protected

Definition at line 60 of file gap_edit.hpp.

◆ m_From

TSeqPos CGapEdit::m_From
protected

Definition at line 61 of file gap_edit.hpp.


The documentation for this class was generated from the following file:
Modified on Thu Feb 29 12:19:02 2024 by modify_doxy.py rev. 669887