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CDense_diag Class Reference

Represents ASN.1 type Dense-diag defined in file seqalign.asn

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#include <objects/seqalign/Dense_diag.hpp>

+ Inheritance diagram for CDense_diag:
+ Collaboration diagram for CDense_diag:

Public Member Functions

 CDense_diag (void)
 
 ~CDense_diag (void)
 
TDim CheckNumRows (void) const
 Validators. More...
 
void Validate () const
 
CRange< TSeqPosGetSeqRange (TDim row) const
 GetSeqRange. More...
 
TSeqPos GetSeqStart (TDim row) const
 
TSeqPos GetSeqStop (TDim row) const
 
ENa_strand GetSeqStrand (TDim row) const
 
void OffsetRow (TDim row, TSignedSeqPos offset)
 Offset row's coords. More...
 
CRef< CSeq_intervalCreateRowSeq_interval (TDim row) const
 
- Public Member Functions inherited from CDense_diag_Base
 CDense_diag_Base (void)
 
virtual ~CDense_diag_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
 sequences in order 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 IsSetStarts (void) const
 start OFFSETS in ids order Check if a value has been assigned to Starts data member. More...
 
bool CanGetStarts (void) const
 Check if it is safe to call GetStarts method. More...
 
void ResetStarts (void)
 Reset Starts data member. More...
 
const TStartsGetStarts (void) const
 Get the Starts member data. More...
 
TStartsSetStarts (void)
 Assign a value to Starts data member. More...
 
bool IsSetLen (void) const
 len of aligned segments Check if a value has been assigned to Len data member. More...
 
bool CanGetLen (void) const
 Check if it is safe to call GetLen method. More...
 
void ResetLen (void)
 Reset Len data member. More...
 
TLen GetLen (void) const
 Get the Len member data. More...
 
void SetLen (TLen value)
 Assign a value to Len data member. More...
 
TLenSetLen (void)
 Assign a value to Len data member. More...
 
bool IsSetStrands (void) const
 Check if a value has been assigned to Strands data member. More...
 
bool CanGetStrands (void) const
 Check if it is safe to call GetStrands method. More...
 
void ResetStrands (void)
 Reset Strands data member. More...
 
const TStrandsGetStrands (void) const
 Get the Strands member data. More...
 
TStrandsSetStrands (void)
 Assign a value to Strands 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 CDense_diag_Base Tparent
 

Private Member Functions

 CDense_diag (const CDense_diag &value)
 
CDense_diagoperator= (const CDense_diag &value)
 

Additional Inherited Members

- Public Types inherited from CDense_diag_Base
enum class  E_memberIndex {
  e__allMandatory = 0 , e_dim , e_ids , e_starts ,
  e_len , e_strands , e_scores
}
 
typedef int TDim
 
typedef vector< CRef< CSeq_id > > TIds
 
typedef vector< TSeqPosTStarts
 
typedef TSeqPos TLen
 
typedef vector< ENa_strandTStrands
 
typedef vector< CRef< CScore > > TScores
 
typedef Tparent::CMemberIndex< E_memberIndex, 7 > 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 58 of file Dense_diag.hpp.

Member Typedef Documentation

◆ Tparent

Definition at line 60 of file Dense_diag.hpp.

Constructor & Destructor Documentation

◆ CDense_diag() [1/2]

CDense_diag::CDense_diag ( void  )
inline

Definition at line 93 of file Dense_diag.hpp.

◆ ~CDense_diag()

CDense_diag::~CDense_diag ( void  )

Definition at line 53 of file Dense_diag.cpp.

◆ CDense_diag() [2/2]

CDense_diag::CDense_diag ( const CDense_diag value)
private

Member Function Documentation

◆ CheckNumRows()

CDense_diag::TDim CDense_diag::CheckNumRows ( void  ) const
inline

◆ CreateRowSeq_interval()

CRef< CSeq_interval > CDense_diag::CreateRowSeq_interval ( TDim  row) const

◆ GetSeqRange()

CRange< TSeqPos > CDense_diag::GetSeqRange ( TDim  row) const
inline

GetSeqRange.

Definition at line 118 of file Dense_diag.hpp.

References GetSeqStart(), and GetSeqStop().

◆ GetSeqStart()

TSeqPos CDense_diag::GetSeqStart ( TDim  row) const
inline

Definition at line 99 of file Dense_diag.hpp.

References CDense_diag_Base::GetDim(), CDense_diag_Base::GetStarts(), and NCBI_THROW.

Referenced by GetSeqRange(), and GetSeqStop().

◆ GetSeqStop()

TSeqPos CDense_diag::GetSeqStop ( TDim  row) const
inline

Definition at line 111 of file Dense_diag.hpp.

References CDense_diag_Base::GetLen(), and GetSeqStart().

Referenced by GetSeqRange().

◆ GetSeqStrand()

ENa_strand CDense_diag::GetSeqStrand ( TDim  row) const

◆ OffsetRow()

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

◆ operator=()

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

◆ Validate()

void CDense_diag::Validate ( void  ) const

The documentation for this class was generated from the following files:
Modified on Tue Feb 27 05:57:01 2024 by modify_doxy.py rev. 669887