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CAlnMix Class Reference

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#include <objtools/alnmgr/alnmix.hpp>

+ Inheritance diagram for CAlnMix:
+ Collaboration diagram for CAlnMix:

Public Types

enum  EAddFlags { fCalcScore = 0x01 , fForceTranslation = 0x02 , fPreserveRows = 0x04 }
 
enum  EMergeFlags {
  fTruncateOverlaps = 0x0001 , fNegativeStrand = 0x0002 , fGapJoin = 0x0004 , fMinGap = 0x0008 ,
  fRemoveLeadTrailGaps = 0x0010 , fSortSeqsByScore = 0x0020 , fSortInputByScore = 0x0040 , fQuerySeqMergeOnly = 0x0080 ,
  fFillUnalignedRegions = 0x0100 , fAllowTranslocation = 0x0200
}
 
typedef CAlnMixMatches::TCalcScoreMethod TCalcScoreMethod
 
typedef int TAddFlags
 
typedef vector< CConstRef< CDense_seg > > TConstDSs
 
typedef vector< CConstRef< CSeq_align > > TConstAlns
 
typedef int TMergeFlags
 
- 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

 CAlnMix (void)
 
 CAlnMix (CScope &scope, TCalcScoreMethod calc_score=0)
 
 ~CAlnMix (void)
 
void Add (const CDense_seg &ds, TAddFlags flags=0)
 
void Add (const CSeq_align &aln, TAddFlags flags=0)
 
CScopeGetScope (void) const
 
const TConstDSsGetInputDensegs (void) const
 
const TConstAlnsGetInputSeqAligns (void) const
 
void Merge (TMergeFlags flags=0)
 
const CDense_segGetDenseg (void) const
 
const CSeq_alignGetSeqAlign (void) 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
 
- Public Member Functions inherited from CTaskProgressReporter
 CTaskProgressReporter ()
 Constructor. More...
 
void SetTaskProgressCallback (ITaskProgressCallback *callback)
 Hook a callback to a task. More...
 

Private Types

typedef map< void *, CConstRef< CDense_seg > > TConstDSsMap
 
typedef map< void *, CConstRef< CSeq_align > > TConstAlnsMap
 

Private Member Functions

 CAlnMix (const CAlnMix &value)
 
CAlnMixoperator= (const CAlnMix &value)
 
void x_Init (void)
 
void x_Reset (void)
 
virtual void ChooseSeqId (CSeq_id &id1, const CSeq_id &id2)
 
CRef< CDense_segx_ExtendDSWithWidths (const CDense_seg &ds)
 

Private Attributes

CRef< CScopem_Scope
 
TCalcScoreMethod x_CalculateScore
 
TConstDSs m_InputDSs
 
TConstAlns m_InputAlns
 
TConstDSsMap m_InputDSsMap
 
TConstAlnsMap m_InputAlnsMap
 
TAddFlags m_AddFlags
 
CRef< CAlnMixSequencesm_AlnMixSequences
 
CRef< CAlnMixMatchesm_AlnMixMatches
 
CRef< CAlnMixMergerm_AlnMixMerger
 

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...
 
- Protected Member Functions inherited from CTaskProgressReporter
void x_SetTaskName (const string &name)
 Methods for reporting task progress. More...
 
void x_SetTaskCompleted (int completed)
 
void x_SetTaskTotal (int total)
 
bool x_InterruptTask ()
 Check if the task should be interrupted. More...
 
ITaskProgressCallbackx_GetTaskProgressCallback () const
 Callback accessor. More...
 

Detailed Description

Definition at line 51 of file alnmix.hpp.

Member Typedef Documentation

◆ TAddFlags

Definition at line 82 of file alnmix.hpp.

◆ TCalcScoreMethod

typedef CAlnMixMatches::TCalcScoreMethod CAlnMix::TCalcScoreMethod

Definition at line 58 of file alnmix.hpp.

◆ TConstAlns

Definition at line 91 of file alnmix.hpp.

◆ TConstAlnsMap

typedef map<void *, CConstRef<CSeq_align> > CAlnMix::TConstAlnsMap
private

Definition at line 134 of file alnmix.hpp.

◆ TConstDSs

Definition at line 90 of file alnmix.hpp.

◆ TConstDSsMap

typedef map<void *, CConstRef<CDense_seg> > CAlnMix::TConstDSsMap
private

Definition at line 133 of file alnmix.hpp.

◆ TMergeFlags

Definition at line 114 of file alnmix.hpp.

Member Enumeration Documentation

◆ EAddFlags

Enumerator
fCalcScore 
fForceTranslation 
fPreserveRows 

Definition at line 69 of file alnmix.hpp.

◆ EMergeFlags

Enumerator
fTruncateOverlaps 
fNegativeStrand 
fGapJoin 
fMinGap 
fRemoveLeadTrailGaps 
fSortSeqsByScore 
fSortInputByScore 
fQuerySeqMergeOnly 
fFillUnalignedRegions 
fAllowTranslocation 

Definition at line 100 of file alnmix.hpp.

Constructor & Destructor Documentation

◆ CAlnMix() [1/3]

CAlnMix::CAlnMix ( void  )

Definition at line 52 of file alnmix.cpp.

References x_Init().

◆ CAlnMix() [2/3]

CAlnMix::CAlnMix ( CScope scope,
TCalcScoreMethod  calc_score = 0 
)

Definition at line 59 of file alnmix.cpp.

References CAlnVec::CalculateScore(), x_CalculateScore, and x_Init().

◆ ~CAlnMix()

CAlnMix::~CAlnMix ( void  )

Definition at line 71 of file alnmix.cpp.

◆ CAlnMix() [3/3]

CAlnMix::CAlnMix ( const CAlnMix value)
private

Member Function Documentation

◆ Add() [1/2]

void CAlnMix::Add ( const CDense_seg ds,
TAddFlags  flags = 0 
)

◆ Add() [2/2]

void CAlnMix::Add ( const CSeq_align aln,
TAddFlags  flags = 0 
)

◆ ChooseSeqId()

void CAlnMix::ChooseSeqId ( CSeq_id id1,
const CSeq_id id2 
)
privatevirtual

◆ GetDenseg()

const CDense_seg & CAlnMix::GetDenseg ( void  ) const

◆ GetInputDensegs()

const CAlnMix::TConstDSs & CAlnMix::GetInputDensegs ( void  ) const
inline

Definition at line 174 of file alnmix.hpp.

References m_InputDSs.

◆ GetInputSeqAligns()

const CAlnMix::TConstAlns & CAlnMix::GetInputSeqAligns ( void  ) const
inline

Definition at line 181 of file alnmix.hpp.

References m_InputAlns.

Referenced by CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile().

◆ GetScope()

CScope & CAlnMix::GetScope ( void  ) const
inline

Definition at line 167 of file alnmix.hpp.

Referenced by CBuildAlnVecJob::Build(), and CAlignDataSource::x_Init().

◆ GetSeqAlign()

const CSeq_align & CAlnMix::GetSeqAlign ( void  ) const

◆ Merge()

void CAlnMix::Merge ( TMergeFlags  flags = 0)

◆ operator=()

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

◆ x_ExtendDSWithWidths()

CRef< CDense_seg > CAlnMix::x_ExtendDSWithWidths ( const CDense_seg ds)
private

◆ x_Init()

void CAlnMix::x_Init ( void  )
private

◆ x_Reset()

void CAlnMix::x_Reset ( void  )
private

Definition at line 88 of file alnmix.cpp.

References m_AlnMixMerger, and CAlnMixMerger::Reset().

Referenced by Add().

Member Data Documentation

◆ m_AddFlags

TAddFlags CAlnMix::m_AddFlags
private

Definition at line 153 of file alnmix.hpp.

Referenced by Add().

◆ m_AlnMixMatches

CRef<CAlnMixMatches> CAlnMix::m_AlnMixMatches
private

Definition at line 156 of file alnmix.hpp.

Referenced by Add(), Merge(), and x_Init().

◆ m_AlnMixMerger

CRef<CAlnMixMerger> CAlnMix::m_AlnMixMerger
private

Definition at line 157 of file alnmix.hpp.

Referenced by GetDenseg(), GetSeqAlign(), Merge(), x_Init(), and x_Reset().

◆ m_AlnMixSequences

CRef<CAlnMixSequences> CAlnMix::m_AlnMixSequences
private

Definition at line 155 of file alnmix.hpp.

Referenced by Add(), ChooseSeqId(), Merge(), x_ExtendDSWithWidths(), and x_Init().

◆ m_InputAlns

TConstAlns CAlnMix::m_InputAlns
private

Definition at line 149 of file alnmix.hpp.

Referenced by Add(), and GetInputSeqAligns().

◆ m_InputAlnsMap

TConstAlnsMap CAlnMix::m_InputAlnsMap
private

Definition at line 151 of file alnmix.hpp.

Referenced by Add().

◆ m_InputDSs

TConstDSs CAlnMix::m_InputDSs
private

Definition at line 148 of file alnmix.hpp.

Referenced by Add(), and GetInputDensegs().

◆ m_InputDSsMap

TConstDSsMap CAlnMix::m_InputDSsMap
private

Definition at line 150 of file alnmix.hpp.

Referenced by Add().

◆ m_Scope

CRef<CScope> CAlnMix::m_Scope
mutableprivate

Definition at line 146 of file alnmix.hpp.

Referenced by Add(), and x_Init().

◆ x_CalculateScore

TCalcScoreMethod CAlnMix::x_CalculateScore
private

Definition at line 147 of file alnmix.hpp.

Referenced by Add(), CAlnMix(), and x_Init().


The documentation for this class was generated from the following files:
Modified on Fri Sep 20 14:58:28 2024 by modify_doxy.py rev. 669887