NCBI C++ ToolKit
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CMasterSeqSegments Class Reference

Search Toolkit Book for CMasterSeqSegments

#include <objmgr/impl/handle_range_map.hpp>

+ Inheritance diagram for CMasterSeqSegments:
+ Collaboration diagram for CMasterSeqSegments:

Public Types

typedef vector< CSeq_id_HandleTIds
 
typedef list< CRef< CSeq_id > > TIds2
 
- 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

 CMasterSeqSegments (void)
 
 CMasterSeqSegments (const CBioseq_Info &seq)
 
 ~CMasterSeqSegments (void)
 
void AddSegments (const CSeqMap &seq)
 
int AddSegment (const CSeq_id_Handle &id, bool minus_strand)
 
void AddSegmentId (int idx, const CSeq_id_Handle &id)
 
void AddSegmentIds (int idx, const TIds &ids)
 
void AddSegmentIds (int idx, const TIds2 &ids)
 
void AddSegmentIds (const TIds &ids)
 
void AddSegmentIds (const TIds2 &ids)
 
int GetSegmentCount (void) const
 
int FindSeg (const CSeq_id_Handle &h) const
 
bool GetMinusStrand (int seg) const
 
const CSeq_id_HandleGetHandle (int seg) const
 
- 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...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. 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 Types

typedef pair< CSeq_id_Handle, boolTSeg
 
typedef vector< TSegTSegSet
 
typedef map< CSeq_id_Handle, intTId2Seg
 

Protected Attributes

TSegSet m_SegSet
 
TId2Seg m_Id2Seg
 

Private Member Functions

 CMasterSeqSegments (const CMasterSeqSegments &)
 
void operator= (const CMasterSeqSegments &)
 

Additional Inherited Members

- 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 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 49 of file handle_range_map.hpp.

Member Typedef Documentation

◆ TId2Seg

Definition at line 76 of file handle_range_map.hpp.

◆ TIds

Definition at line 59 of file handle_range_map.hpp.

◆ TIds2

Definition at line 60 of file handle_range_map.hpp.

◆ TSeg

typedef pair<CSeq_id_Handle, bool> CMasterSeqSegments::TSeg
protected

Definition at line 74 of file handle_range_map.hpp.

◆ TSegSet

typedef vector<TSeg> CMasterSeqSegments::TSegSet
protected

Definition at line 75 of file handle_range_map.hpp.

Constructor & Destructor Documentation

◆ CMasterSeqSegments() [1/3]

CMasterSeqSegments::CMasterSeqSegments ( void  )

Definition at line 349 of file handle_range_map.cpp.

◆ CMasterSeqSegments() [2/3]

CMasterSeqSegments::CMasterSeqSegments ( const CBioseq_Info seq)

◆ ~CMasterSeqSegments()

CMasterSeqSegments::~CMasterSeqSegments ( void  )

Definition at line 354 of file handle_range_map.cpp.

◆ CMasterSeqSegments() [3/3]

CMasterSeqSegments::CMasterSeqSegments ( const CMasterSeqSegments )
private

Member Function Documentation

◆ AddSegment()

int CMasterSeqSegments::AddSegment ( const CSeq_id_Handle id,
bool  minus_strand 
)

Definition at line 373 of file handle_range_map.cpp.

References AddSegmentId(), GetSegmentCount(), and m_SegSet.

Referenced by AddSegments().

◆ AddSegmentId()

void CMasterSeqSegments::AddSegmentId ( int  idx,
const CSeq_id_Handle id 
)

Definition at line 382 of file handle_range_map.cpp.

References m_Id2Seg.

Referenced by AddSegment(), and AddSegmentIds().

◆ AddSegmentIds() [1/4]

void CMasterSeqSegments::AddSegmentIds ( const TIds ids)

Definition at line 404 of file handle_range_map.cpp.

References AddSegmentIds(), FindSeg(), and ITERATE.

◆ AddSegmentIds() [2/4]

void CMasterSeqSegments::AddSegmentIds ( const TIds2 ids)

Definition at line 416 of file handle_range_map.cpp.

References AddSegmentIds(), FindSeg(), CSeq_id_Handle::GetHandle(), and ITERATE.

◆ AddSegmentIds() [3/4]

void CMasterSeqSegments::AddSegmentIds ( int  idx,
const TIds ids 
)

◆ AddSegmentIds() [4/4]

void CMasterSeqSegments::AddSegmentIds ( int  idx,
const TIds2 ids 
)

Definition at line 396 of file handle_range_map.cpp.

References AddSegmentId(), CSeq_id_Handle::GetHandle(), and ITERATE.

◆ AddSegments()

void CMasterSeqSegments::AddSegments ( const CSeqMap seq)

◆ FindSeg()

int CMasterSeqSegments::FindSeg ( const CSeq_id_Handle h) const

◆ GetHandle()

const CSeq_id_Handle & CMasterSeqSegments::GetHandle ( int  seg) const

Definition at line 443 of file handle_range_map.cpp.

References _ASSERT, and m_SegSet.

Referenced by CHandleRangeMap::AddRange(), and CMasterSeqSegments().

◆ GetMinusStrand()

bool CMasterSeqSegments::GetMinusStrand ( int  seg) const

Definition at line 450 of file handle_range_map.cpp.

References _ASSERT, and m_SegSet.

Referenced by CHandleRangeMap::AddRange().

◆ GetSegmentCount()

int CMasterSeqSegments::GetSegmentCount ( void  ) const
inline

Definition at line 66 of file handle_range_map.hpp.

References int, and m_SegSet.

Referenced by AddSegment(), and CMasterSeqSegments().

◆ operator=()

void CMasterSeqSegments::operator= ( const CMasterSeqSegments )
private

Member Data Documentation

◆ m_Id2Seg

TId2Seg CMasterSeqSegments::m_Id2Seg
protected

Definition at line 79 of file handle_range_map.hpp.

Referenced by AddSegmentId(), and FindSeg().

◆ m_SegSet

TSegSet CMasterSeqSegments::m_SegSet
protected

Definition at line 78 of file handle_range_map.hpp.

Referenced by AddSegment(), GetHandle(), GetMinusStrand(), and GetSegmentCount().


The documentation for this class was generated from the following files:
Modified on Tue May 21 10:57:46 2024 by modify_doxy.py rev. 669887