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CSeq_point Class Reference

Represents ASN.1 type Seq-point defined in file seqloc.asn

Search Toolkit Book for CSeq_point

#include <objects/seqloc/Seq_point.hpp>

+ Inheritance diagram for CSeq_point:
+ Collaboration diagram for CSeq_point:

Public Member Functions

 CSeq_point (void)
 
 CSeq_point (TId &id, TPoint point, TStrand strand=eNa_strand_unknown)
 
 ~CSeq_point (void)
 
bool IsPartialStart (ESeqLocExtremes ext) const
 
bool IsPartialStop (ESeqLocExtremes ext) const
 
void SetPartialStart (bool val, ESeqLocExtremes ext)
 
void SetPartialStop (bool val, ESeqLocExtremes ext)
 
bool IsTruncatedStart (ESeqLocExtremes ext) const
 check if parts of the seq-loc are missing More...
 
bool IsTruncatedStop (ESeqLocExtremes ext) const
 
void SetTruncatedStart (bool val, ESeqLocExtremes ext)
 set / remove e_Lim fuzz on start or stop (tl/tr - indicating removed parts of the seq-loc) More...
 
void SetTruncatedStop (bool val, ESeqLocExtremes ext)
 
bool IsLeftOf (void) const
 
bool IsRightOf (void) const
 
void SetLeftOf (bool val)
 
void SetRightOf (bool val)
 
void FlipStrand (void)
 
- Public Member Functions inherited from CSeq_point_Base
 CSeq_point_Base (void)
 
virtual ~CSeq_point_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetPoint (void) const
 Check if a value has been assigned to Point data member. More...
 
bool CanGetPoint (void) const
 Check if it is safe to call GetPoint method. More...
 
void ResetPoint (void)
 Reset Point data member. More...
 
TPoint GetPoint (void) const
 Get the Point member data. More...
 
void SetPoint (TPoint value)
 Assign a value to Point data member. More...
 
TPointSetPoint (void)
 Assign a value to Point 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...
 
TStrandSetStrand (void)
 Assign a value to Strand data member. More...
 
bool IsSetId (void) const
 WARNING: this used to be optional 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 TIdGetId (void) const
 Get the Id member data. More...
 
void SetId (TId &value)
 Assign a value to Id data member. More...
 
TIdSetId (void)
 Assign a value to Id data member. More...
 
bool IsSetFuzz (void) const
 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...
 
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
 

Private Types

typedef CSeq_point_Base Tparent
 

Private Member Functions

 CSeq_point (const CSeq_point &value)
 
CSeq_pointoperator= (const CSeq_point &value)
 
bool x_IsMinusStrand (void) const
 

Additional Inherited Members

- Public Types inherited from CSeq_point_Base
enum class  E_memberIndex {
  e__allMandatory = 0 , e_point , e_strand , e_id ,
  e_fuzz
}
 
typedef TSeqPos TPoint
 
typedef ENa_strand TStrand
 
typedef CSeq_id TId
 
typedef CInt_fuzz TFuzz
 
typedef Tparent::CMemberIndex< E_memberIndex, 5 > 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 50 of file Seq_point.hpp.

Member Typedef Documentation

◆ Tparent

Definition at line 52 of file Seq_point.hpp.

Constructor & Destructor Documentation

◆ CSeq_point() [1/3]

CSeq_point::CSeq_point ( void  )
inline

Definition at line 103 of file Seq_point.hpp.

◆ CSeq_point() [2/3]

CSeq_point::CSeq_point ( TId id,
TPoint  point,
TStrand  strand = eNa_strand_unknown 
)
inline

◆ ~CSeq_point()

CSeq_point::~CSeq_point ( void  )

Definition at line 48 of file Seq_point.cpp.

◆ CSeq_point() [3/3]

CSeq_point::CSeq_point ( const CSeq_point value)
private

Member Function Documentation

◆ FlipStrand()

void CSeq_point::FlipStrand ( void  )

◆ IsLeftOf()

bool CSeq_point::IsLeftOf ( void  ) const

◆ IsPartialStart()

bool CSeq_point::IsPartialStart ( ESeqLocExtremes  ext) const

◆ IsPartialStop()

bool CSeq_point::IsPartialStop ( ESeqLocExtremes  ext) const

◆ IsRightOf()

bool CSeq_point::IsRightOf ( void  ) const

◆ IsTruncatedStart()

bool CSeq_point::IsTruncatedStart ( ESeqLocExtremes  ext) const

◆ IsTruncatedStop()

bool CSeq_point::IsTruncatedStop ( ESeqLocExtremes  ext) const

◆ operator=()

CSeq_point& CSeq_point::operator= ( const CSeq_point value)
private

◆ SetLeftOf()

void CSeq_point::SetLeftOf ( bool  val)

◆ SetPartialStart()

void CSeq_point::SetPartialStart ( bool  val,
ESeqLocExtremes  ext 
)

◆ SetPartialStop()

void CSeq_point::SetPartialStop ( bool  val,
ESeqLocExtremes  ext 
)

◆ SetRightOf()

void CSeq_point::SetRightOf ( bool  val)

◆ SetTruncatedStart()

void CSeq_point::SetTruncatedStart ( bool  val,
ESeqLocExtremes  ext 
)

set / remove e_Lim fuzz on start or stop (tl/tr - indicating removed parts of the seq-loc)

Definition at line 147 of file Seq_point.cpp.

References eExtreme_Biological, CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, IsTruncatedStart(), CSeq_point_Base::ResetFuzz(), CSeq_point_Base::SetFuzz(), CInt_fuzz_Base::SetLim(), val, and x_IsMinusStrand().

Referenced by CSeq_loc::SetTruncatedStart().

◆ SetTruncatedStop()

void CSeq_point::SetTruncatedStop ( bool  val,
ESeqLocExtremes  ext 
)

◆ x_IsMinusStrand()

bool CSeq_point::x_IsMinusStrand ( void  ) const
private

The documentation for this class was generated from the following files:
Modified on Wed May 29 18:36:39 2024 by modify_doxy.py rev. 669887