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CAlignResultsSet Class Reference

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#include <algo/align/ngalign/result_set.hpp>

+ Inheritance diagram for CAlignResultsSet:
+ Collaboration diagram for CAlignResultsSet:

Public Types

typedef map< string, CRef< CQuerySet > > TQueryToSubjectSet
- 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

 CAlignResultsSet ()
 CAlignResultsSet (bool AllowDupes)
 CAlignResultsSet (CRef< objects::CGC_Assembly > Gencoll, bool AllowDupes=false)
 CAlignResultsSet (const blast::CSearchResultSet &BlastResults)
TQueryToSubjectSetGet ()
const TQueryToSubjectSetGet () const
bool QueryExists (const objects::CSeq_id &Id) const
CRef< CQuerySetGetQuerySet (const objects::CSeq_id &Id)
CConstRef< CQuerySetGetQuerySet (const objects::CSeq_id &Id) const
CRef< objects::CSeq_align_set > ToSeqAlignSet () const
CRef< objects::CSeq_align_set > ToBestSeqAlignSet () const
void Insert (CRef< CQuerySet > QuerySet)
void Insert (CRef< CAlignResultsSet > AlignSet)
void Insert (const blast::CSearchResultSet &BlastResults)
void Insert (CRef< objects::CSeq_align > Alignment)
void Insert (const objects::CSeq_align_set &AlignSet)
size_t size () const
bool empty () 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

Private Member Functions

void DropQuery (const objects::CSeq_id &Id)

Private Attributes

bool m_AllowDupes
TQueryToSubjectSet m_QueryMap
CRef< objects::CGC_Assembly > m_GenColl


class CSplitSeqAlignMerger

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 121 of file result_set.hpp.

Member Typedef Documentation

◆ TQueryToSubjectSet

Definition at line 124 of file result_set.hpp.

Constructor & Destructor Documentation

◆ CAlignResultsSet() [1/4]

CAlignResultsSet::CAlignResultsSet ( )

Definition at line 481 of file result_set.cpp.

◆ CAlignResultsSet() [2/4]

CAlignResultsSet::CAlignResultsSet ( bool  AllowDupes)

Definition at line 486 of file result_set.cpp.

References m_AllowDupes.

◆ CAlignResultsSet() [3/4]

CAlignResultsSet::CAlignResultsSet ( CRef< objects::CGC_Assembly >  Gencoll,
bool  AllowDupes = false 

◆ CAlignResultsSet() [4/4]

CAlignResultsSet::CAlignResultsSet ( const blast::CSearchResultSet &  BlastResults)

Definition at line 499 of file result_set.cpp.

References Insert().

Member Function Documentation

◆ DropQuery()

void CAlignResultsSet::DropQuery ( const objects::CSeq_id &  Id)

◆ empty()

bool CAlignResultsSet::empty ( ) const

Definition at line 152 of file result_set.hpp.

References map_checker< Container >::empty(), and m_QueryMap.

◆ Get() [1/2]

TQueryToSubjectSet& CAlignResultsSet::Get ( )

Definition at line 132 of file result_set.hpp.

References m_QueryMap.

◆ Get() [2/2]

const TQueryToSubjectSet& CAlignResultsSet::Get ( ) const

Definition at line 133 of file result_set.hpp.

References m_QueryMap.

◆ GetQuerySet() [1/2]

CRef<CQuerySet> CAlignResultsSet::GetQuerySet ( const objects::CSeq_id &  Id)

◆ GetQuerySet() [2/2]

CConstRef<CQuerySet> CAlignResultsSet::GetQuerySet ( const objects::CSeq_id &  Id) const

◆ Insert() [1/5]

void CAlignResultsSet::Insert ( const blast::CSearchResultSet &  BlastResults)

◆ Insert() [2/5]

void CAlignResultsSet::Insert ( const objects::CSeq_align_set &  AlignSet)

◆ Insert() [3/5]

void CAlignResultsSet::Insert ( CRef< CAlignResultsSet AlignSet)

Definition at line 600 of file result_set.cpp.

References Insert(), and ITERATE.

◆ Insert() [4/5]

void CAlignResultsSet::Insert ( CRef< CQuerySet QuerySet)

◆ Insert() [5/5]

void CAlignResultsSet::Insert ( CRef< objects::CSeq_align >  Alignment)

◆ QueryExists()

bool CAlignResultsSet::QueryExists ( const objects::CSeq_id &  Id) const

◆ size()

size_t CAlignResultsSet::size ( ) const

Definition at line 151 of file result_set.hpp.

References m_QueryMap, and map_checker< Container >::size().

◆ ToBestSeqAlignSet()

CRef< CSeq_align_set > CAlignResultsSet::ToBestSeqAlignSet ( ) const

◆ ToSeqAlignSet()

CRef< CSeq_align_set > CAlignResultsSet::ToSeqAlignSet ( ) const

Definition at line 543 of file result_set.cpp.

References ITERATE, m_QueryMap, and Out().

Friends And Related Function Documentation

◆ CSplitSeqAlignMerger

friend class CSplitSeqAlignMerger

Definition at line 164 of file result_set.hpp.

Member Data Documentation

◆ m_AllowDupes

bool CAlignResultsSet::m_AllowDupes

Definition at line 156 of file result_set.hpp.

Referenced by CAlignResultsSet(), and Insert().

◆ m_GenColl

CRef<objects::CGC_Assembly> CAlignResultsSet::m_GenColl

Definition at line 160 of file result_set.hpp.

Referenced by Insert().

◆ m_QueryMap

TQueryToSubjectSet CAlignResultsSet::m_QueryMap

The documentation for this class was generated from the following files:
Modified on Fri May 24 14:50:12 2024 by rev. 669887