NCBI C++ ToolKit
Public Member Functions | Private Types | Private Member Functions | List of all members
CStd_seg Class Reference

Represents ASN.1 type Std-seg defined in file seqalign.asn

Search Toolkit Book for CStd_seg

#include <objects/seqalign/Std_seg.hpp>

+ Inheritance diagram for CStd_seg:
+ Collaboration diagram for CStd_seg:

Public Member Functions

 CStd_seg (void)
 
 ~CStd_seg (void)
 
TDim CheckNumRows (void) const
 
void Validate (bool full_test=false) const
 
TSignedSeqPos GetSeqStart (TDim row) const
 
TSignedSeqPos GetSeqStop (TDim row) const
 
CRange< TSignedSeqPosGetSeqRange (TDim row) const
 
void SwapRows (TDim row1, TDim row2)
 Swap two rows (changing *order*, not content) More...
 
void OffsetRow (TDim row, TSignedSeqPos offset)
 Offset row's coords. More...
 
void RemapToLoc (TDim row, const CSeq_loc &dst_loc, bool ignore_strand=false)
 
CRef< CSeq_locCreateRowSeq_loc (TDim row) const
 
- Public Member Functions inherited from CStd_seg_Base
 CStd_seg_Base (void)
 
virtual ~CStd_seg_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetDim (void) const
 dimensionality Check if a value has been assigned to Dim data member. More...
 
bool CanGetDim (void) const
 Check if it is safe to call GetDim method. More...
 
void ResetDim (void)
 Reset Dim data member. More...
 
void SetDefaultDim (void)
 Assign default value to Dim data member. More...
 
TDim GetDim (void) const
 Get the Dim member data. More...
 
void SetDim (TDim value)
 Assign a value to Dim data member. More...
 
TDimSetDim (void)
 Assign a value to Dim data member. More...
 
bool IsSetIds (void) const
 Check if a value has been assigned to Ids data member. More...
 
bool CanGetIds (void) const
 Check if it is safe to call GetIds method. More...
 
void ResetIds (void)
 Reset Ids data member. More...
 
const TIdsGetIds (void) const
 Get the Ids member data. More...
 
TIdsSetIds (void)
 Assign a value to Ids data member. More...
 
bool IsSetLoc (void) const
 Check if a value has been assigned to Loc data member. More...
 
bool CanGetLoc (void) const
 Check if it is safe to call GetLoc method. More...
 
void ResetLoc (void)
 Reset Loc data member. More...
 
const TLocGetLoc (void) const
 Get the Loc member data. More...
 
TLocSetLoc (void)
 Assign a value to Loc data member. More...
 
bool IsSetScores (void) const
 Check if a value has been assigned to Scores data member. More...
 
bool CanGetScores (void) const
 Check if it is safe to call GetScores method. More...
 
void ResetScores (void)
 Reset Scores data member. More...
 
const TScoresGetScores (void) const
 Get the Scores member data. More...
 
TScoresSetScores (void)
 Assign a value to Scores 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 CStd_seg_Base Tparent
 

Private Member Functions

 CStd_seg (const CStd_seg &value)
 
CStd_segoperator= (const CStd_seg &value)
 

Additional Inherited Members

- Public Types inherited from CStd_seg_Base
enum class  E_memberIndex {
  e__allMandatory = 0 , e_dim , e_ids , e_loc ,
  e_scores
}
 
typedef int TDim
 
typedef vector< CRef< CSeq_id > > TIds
 
typedef vector< CRef< CSeq_loc > > TLoc
 
typedef vector< CRef< CScore > > TScores
 
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 53 of file Std_seg.hpp.

Member Typedef Documentation

◆ Tparent

Definition at line 55 of file Std_seg.hpp.

Constructor & Destructor Documentation

◆ CStd_seg() [1/2]

CStd_seg::CStd_seg ( void  )
inline

Definition at line 98 of file Std_seg.hpp.

◆ ~CStd_seg()

CStd_seg::~CStd_seg ( void  )

Definition at line 53 of file Std_seg.cpp.

◆ CStd_seg() [2/2]

CStd_seg::CStd_seg ( const CStd_seg value)
private

Member Function Documentation

◆ CheckNumRows()

CStd_seg::TDim CStd_seg::CheckNumRows ( void  ) const

◆ CreateRowSeq_loc()

CRef< CSeq_loc > CStd_seg::CreateRowSeq_loc ( TDim  row) const

◆ GetSeqRange()

CRange< TSignedSeqPos > CStd_seg::GetSeqRange ( TDim  row) const

◆ GetSeqStart()

TSignedSeqPos CStd_seg::GetSeqStart ( TDim  row) const

◆ GetSeqStop()

TSignedSeqPos CStd_seg::GetSeqStop ( TDim  row) const

◆ OffsetRow()

void CStd_seg::OffsetRow ( TDim  row,
TSignedSeqPos  offset 
)

◆ operator=()

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

◆ RemapToLoc()

void CStd_seg::RemapToLoc ( TDim  row,
const CSeq_loc dst_loc,
bool  ignore_strand = false 
)

◆ SwapRows()

void CStd_seg::SwapRows ( TDim  row1,
TDim  row2 
)

◆ Validate()

void CStd_seg::Validate ( bool  full_test = false) const

Definition at line 122 of file Std_seg.cpp.

References CheckNumRows().


The documentation for this class was generated from the following files:
Modified on Thu Apr 11 15:20:27 2024 by modify_doxy.py rev. 669887