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CBioseqGaps_CI Class Reference

Search Toolkit Book for CBioseqGaps_CI

This iterates over the runs of Ns of each sequence. More...

#include <objmgr/util/sequence.hpp>

+ Inheritance diagram for CBioseqGaps_CI:
+ Collaboration diagram for CBioseqGaps_CI:

Classes

struct  Params
 The params that control the behavior of CBioseqGaps_CI. More...
 
struct  SCurrentGapInfo
 This indicates the state of the iterator right now. More...
 

Public Member Functions

 CBioseqGaps_CI (const CSeq_entry_Handle &entry_h, const Params &params=Params())
 This constructor initializes the iterator. More...
 
CBioseqGaps_CIoperator++ (void)
 Move the iterator forward to next gap (or the end, if there are no more to return) More...
 
 DECLARE_OPERATOR_BOOL (m_bioseq_CI)
 
const SCurrentGapInfooperator* (void) const
 Get information about the gap we're currently on. More...
 
const SCurrentGapInfooperator-> (void) const
 Get information about the gap we're currently on. 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...
 
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

enum  EFindNext { eFindNext_NotFound , eFindNext_Found }
 This indicates what happened when we tried to run x_FindNextGapOnBioseq. More...
 

Protected Member Functions

virtual const SCurrentGapInfox_GetCurrent (void) const
 This gives info on the gap we're currently on. More...
 
virtual void x_Next (void)
 This moves this iterator to the next relevant gap. More...
 
virtual void x_NextBioseq (void)
 This advances m_bioseq_CI although it has extra logic to terminate m_bioseq_CI if we've exceeded the number of bioseqs we can look for. More...
 
virtual EFindNext x_FindNextGapOnBioseq (const CBioseq_Handle &bioseq_h, const TSeqPos pos_to_start_looking, TSeqPos &out_pos_of_gap, TSeqPos &out_len_of_gap) const
 This finds the next gap on the bioseq, starting at given pos. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

CBioseq_CI m_bioseq_CI
 This points to the bioseq we're currently on. More...
 
SCurrentGapInfo m_infoOnCurrentGap
 This indicates information about the gap we're currently on. More...
 
Params m_Params
 This holds the params the caller gave when this object was initially created. More...
 

Additional Inherited Members

- 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 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...
 

Detailed Description

This iterates over the runs of Ns of each sequence.

Definition at line 1572 of file sequence.hpp.


The documentation for this class was generated from the following files:
Modified on Sun Jul 21 04:18:06 2024 by modify_doxy.py rev. 669887