NCBI C++ ToolKit
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CSparse_align Class Reference

Represents ASN.1 type Sparse-align defined in file seqalign.asn

Search Toolkit Book for CSparse_align

#include <objects/seqalign/Sparse_align.hpp>

+ Inheritance diagram for CSparse_align:
+ Collaboration diagram for CSparse_align:

Public Types

typedef int TDim
 types More...
 
- Public Types inherited from CSparse_align_Base
enum class  E_memberIndex {
  e__allMandatory = 0 , e_first_id , e_second_id , e_numseg ,
  e_first_starts , e_second_starts , e_lens , e_second_strands ,
  e_seg_scores
}
 
typedef CSeq_id TFirst_id
 
typedef CSeq_id TSecond_id
 
typedef int TNumseg
 
typedef vector< intTFirst_starts
 
typedef vector< intTSecond_starts
 
typedef vector< TSeqPosTLens
 
typedef vector< ENa_strandTSecond_strands
 
typedef vector< CRef< CScore > > TSeg_scores
 
typedef Tparent::CMemberIndex< E_memberIndex, 9 > 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...
 

Public Member Functions

 CSparse_align (void)
 
 ~CSparse_align (void)
 
void Validate (bool full_test=false) const
 Validators. More...
 
TDim CheckNumRows (void) const
 
TNumseg CheckNumSegs (void) const
 
- Public Member Functions inherited from CSparse_align_Base
 CSparse_align_Base (void)
 
virtual ~CSparse_align_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetFirst_id (void) const
 Check if a value has been assigned to First_id data member. More...
 
bool CanGetFirst_id (void) const
 Check if it is safe to call GetFirst_id method. More...
 
void ResetFirst_id (void)
 Reset First_id data member. More...
 
const TFirst_idGetFirst_id (void) const
 Get the First_id member data. More...
 
void SetFirst_id (TFirst_id &value)
 Assign a value to First_id data member. More...
 
TFirst_idSetFirst_id (void)
 Assign a value to First_id data member. More...
 
bool IsSetSecond_id (void) const
 Check if a value has been assigned to Second_id data member. More...
 
bool CanGetSecond_id (void) const
 Check if it is safe to call GetSecond_id method. More...
 
void ResetSecond_id (void)
 Reset Second_id data member. More...
 
const TSecond_idGetSecond_id (void) const
 Get the Second_id member data. More...
 
void SetSecond_id (TSecond_id &value)
 Assign a value to Second_id data member. More...
 
TSecond_idSetSecond_id (void)
 Assign a value to Second_id data member. More...
 
bool IsSetNumseg (void) const
 number of segments Check if a value has been assigned to Numseg data member. More...
 
bool CanGetNumseg (void) const
 Check if it is safe to call GetNumseg method. More...
 
void ResetNumseg (void)
 Reset Numseg data member. More...
 
TNumseg GetNumseg (void) const
 Get the Numseg member data. More...
 
void SetNumseg (TNumseg value)
 Assign a value to Numseg data member. More...
 
TNumsegSetNumseg (void)
 Assign a value to Numseg data member. More...
 
bool IsSetFirst_starts (void) const
 starts on the first sequence [numseg] Check if a value has been assigned to First_starts data member. More...
 
bool CanGetFirst_starts (void) const
 Check if it is safe to call GetFirst_starts method. More...
 
void ResetFirst_starts (void)
 Reset First_starts data member. More...
 
const TFirst_startsGetFirst_starts (void) const
 Get the First_starts member data. More...
 
TFirst_startsSetFirst_starts (void)
 Assign a value to First_starts data member. More...
 
bool IsSetSecond_starts (void) const
 starts on the second sequence [numseg] Check if a value has been assigned to Second_starts data member. More...
 
bool CanGetSecond_starts (void) const
 Check if it is safe to call GetSecond_starts method. More...
 
void ResetSecond_starts (void)
 Reset Second_starts data member. More...
 
const TSecond_startsGetSecond_starts (void) const
 Get the Second_starts member data. More...
 
TSecond_startsSetSecond_starts (void)
 Assign a value to Second_starts data member. More...
 
bool IsSetLens (void) const
 lengths of segments [numseg] Check if a value has been assigned to Lens data member. More...
 
bool CanGetLens (void) const
 Check if it is safe to call GetLens method. More...
 
void ResetLens (void)
 Reset Lens data member. More...
 
const TLensGetLens (void) const
 Get the Lens member data. More...
 
TLensSetLens (void)
 Assign a value to Lens data member. More...
 
bool IsSetSecond_strands (void) const
 Check if a value has been assigned to Second_strands data member. More...
 
bool CanGetSecond_strands (void) const
 Check if it is safe to call GetSecond_strands method. More...
 
void ResetSecond_strands (void)
 Reset Second_strands data member. More...
 
const TSecond_strandsGetSecond_strands (void) const
 Get the Second_strands member data. More...
 
TSecond_strandsSetSecond_strands (void)
 Assign a value to Second_strands data member. More...
 
bool IsSetSeg_scores (void) const
 per-segment scores Check if a value has been assigned to Seg_scores data member. More...
 
bool CanGetSeg_scores (void) const
 Check if it is safe to call GetSeg_scores method. More...
 
void ResetSeg_scores (void)
 Reset Seg_scores data member. More...
 
const TSeg_scoresGetSeg_scores (void) const
 Get the Seg_scores member data. More...
 
TSeg_scoresSetSeg_scores (void)
 Assign a value to Seg_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 CSparse_align_Base Tparent
 

Private Member Functions

 CSparse_align (const CSparse_align &value)
 
CSparse_alignoperator= (const CSparse_align &value)
 

Additional Inherited Members

- 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 Sparse_align.hpp.

Member Typedef Documentation

◆ TDim

types

Definition at line 68 of file Sparse_align.hpp.

◆ Tparent

Definition at line 60 of file Sparse_align.hpp.

Constructor & Destructor Documentation

◆ CSparse_align() [1/2]

CSparse_align::CSparse_align ( void  )
inline

Definition at line 88 of file Sparse_align.hpp.

◆ ~CSparse_align()

CSparse_align::~CSparse_align ( void  )

Definition at line 49 of file Sparse_align.cpp.

◆ CSparse_align() [2/2]

CSparse_align::CSparse_align ( const CSparse_align value)
private

Member Function Documentation

◆ CheckNumRows()

TDim CSparse_align::CheckNumRows ( void  ) const
inline

Definition at line 72 of file Sparse_align.hpp.

Referenced by Validate().

◆ CheckNumSegs()

CSparse_align::TNumseg CSparse_align::CheckNumSegs ( void  ) const

◆ operator=()

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

◆ Validate()

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

Validators.

Definition at line 54 of file Sparse_align.cpp.

References CheckNumRows(), and CheckNumSegs().


The documentation for this class was generated from the following files:
Modified on Mon May 27 04:36:44 2024 by modify_doxy.py rev. 669887