#include <objtools/alnmgr/alnmerger.hpp>

Inheritance diagram for CAlnMixMerger:

Collaboration diagram for CAlnMixMerger:

Public Types
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	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< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Public Member Functions
	CAlnMixMerger (CRef< CAlnMixMatches > &aln_mix_matches, TCalcScoreMethod calc_score=0)

void	Reset ()

void	Merge (TMergeFlags flags=0)

const CDense_seg &	GetDenseg (void) const

const CSeq_align &	GetSeqAlign (void) const

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (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
enum	ESecondRowFits { eSecondRowFitsOk , eForceSeparateRow , eInconsistentStrand , eInconsistentFrame , eFirstRowOverlapBelow , eFirstRowOverlapAbove , eInconsistentOverlap , eSecondRowOverlap , eSecondRowInconsistency , eTranslocation , eIgnoreMatch }

typedef int	TSecondRowFits

typedef vector< CRef< CAlnMixMatch > >	TMatches

typedef vector< CRef< CAlnMixSeq > >	TSeqs

typedef map< pair< CAlnMixSeq , CAlnMixSeq >, CDiagRangeCollection >	TPlanes

Private Member Functions
void	x_Reset (void)

void	x_Merge (void)

void	x_CreateDenseg (void)

void	x_SetSeqFrame (CAlnMixMatch match, CAlnMixSeq &seq)

TSecondRowFits	x_SecondRowFits (CAlnMixMatch *match) const

Private Attributes
const size_t &	m_DsCnt

CRef< CDense_seg >	m_DS

CRef< CSeq_align >	m_Aln

TMergeFlags	m_MergeFlags

CRef< CAlnMixMatches >	m_AlnMixMatches

TMatches &	m_Matches

CRef< CAlnMixSequences >	m_AlnMixSequences

TSeqs &	m_Seqs

vector< CRef< CAlnMixSeq > > &	m_Rows

list< CRef< CAlnMixSeq > > &	m_ExtraRows

CRef< CAlnMixSegments >	m_AlnMixSegments

size_t	m_MatchIdx

bool	m_SingleRefseq

bool	m_IndependentDSs

TCalcScoreMethod	x_CalculateScore

TPlanes	m_Planes

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...

ITaskProgressCallback *	x_GetTaskProgressCallback () const
	Callback accessor. More...

Detailed Description

Definition at line 56 of file alnmerger.hpp.

Member Typedef Documentation

◆ TCalcScoreMethod

typedef CAlnMixMatches::TCalcScoreMethod CAlnMixMerger::TCalcScoreMethod

Definition at line 62 of file alnmerger.hpp.

◆ TMatches

typedef vector<CRef<CAlnMixMatch> > CAlnMixMerger::TMatches

private

Definition at line 119 of file alnmerger.hpp.

◆ TMergeFlags

typedef int CAlnMixMerger::TMergeFlags

Definition at line 84 of file alnmerger.hpp.

◆ TPlanes

typedef map<pair<CAlnMixSeq*, CAlnMixSeq*>, CDiagRangeCollection> CAlnMixMerger::TPlanes

private

Definition at line 122 of file alnmerger.hpp.

◆ TSecondRowFits

typedef int CAlnMixMerger::TSecondRowFits

private

Definition at line 114 of file alnmerger.hpp.

◆ TSeqs

typedef vector<CRef<CAlnMixSeq> > CAlnMixMerger::TSeqs

private

Definition at line 120 of file alnmerger.hpp.

Member Enumeration Documentation

◆ EMergeFlags

enum CAlnMixMerger::EMergeFlags

Enumerator
fTruncateOverlaps
fNegativeStrand
fGapJoin
fMinGap
fRemoveLeadTrailGaps
fSortSeqsByScore
fSortInputByScore
fQuerySeqMergeOnly
fFillUnalignedRegions
fAllowTranslocation

Definition at line 71 of file alnmerger.hpp.

◆ ESecondRowFits

enum CAlnMixMerger::ESecondRowFits

private

Enumerator
eSecondRowFitsOk
eForceSeparateRow
eInconsistentStrand
eInconsistentFrame
eFirstRowOverlapBelow
eFirstRowOverlapAbove
eInconsistentOverlap
eSecondRowOverlap
eSecondRowInconsistency
eTranslocation
eIgnoreMatch

Definition at line 101 of file alnmerger.hpp.

Constructor & Destructor Documentation

◆ CAlnMixMerger()

CAlnMixMerger::CAlnMixMerger	(	CRef< CAlnMixMatches > &	aln_mix_matches,
		TCalcScoreMethod	calc_score = `0`
	)

Definition at line 48 of file alnmerger.cpp.

Member Function Documentation

◆ GetDenseg()

const CDense_seg & CAlnMixMerger::GetDenseg ( void ) const

inline

Definition at line 159 of file alnmerger.hpp.

References m_DS, and NCBI_THROW.

Referenced by CAlnMix::GetDenseg().

◆ GetSeqAlign()

const CSeq_align & CAlnMixMerger::GetSeqAlign ( void ) const

inline

Definition at line 171 of file alnmerger.hpp.

References m_Aln, and NCBI_THROW.

Referenced by CAlnMix::GetSeqAlign().

◆ Merge()

void CAlnMixMerger::Merge ( TMergeFlags flags = 0 )

Definition at line 85 of file alnmerger.cpp.

References flags, m_DS, m_DsCnt, m_MergeFlags, NCBI_THROW, Reset(), and x_Merge().

Referenced by CAlnMix::Merge().

◆ Reset()

void CAlnMixMerger::Reset ( void )

Definition at line 65 of file alnmerger.cpp.

References m_Aln, m_AlnMixSegments, m_DS, m_ExtraRows, m_Rows, CAlnMixSegments::m_Segments, m_Seqs, m_SingleRefseq, NON_CONST_ITERATE, and CRef< C, Locker >::Reset().

Referenced by Merge(), x_Merge(), and CAlnMix::x_Reset().

◆ x_CreateDenseg()

void CAlnMixMerger::x_CreateDenseg ( void )

private

Definition at line 1156 of file alnmerger.cpp.

References _ASSERT, eNa_strand_minus, eNa_strand_plus, CSeq_align_Base::eType_not_set, CAlnMixMatches::fForceTranslation, i, int, ITERATE, kInvalidSeqPos, CAlnMixMatches::m_AddFlags, m_Aln, m_AlnMixMatches, m_AlnMixSegments, CAlnMixMatches::m_ContainsAA, CAlnMixMatches::m_ContainsNA, m_DS, m_Rows, CAlnMixSegments::m_Segments, NULL, offset, CDense_seg_Base::SetDim(), CSeq_align_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), CSeq_align_Base::SetType(), CDense_seg::SetWidths(), CDense_seg::Validate(), CTaskProgressReporter::x_SetTaskCompleted(), CTaskProgressReporter::x_SetTaskName(), and CTaskProgressReporter::x_SetTaskTotal().

Referenced by x_Merge().

◆ x_Merge()

void CAlnMixMerger::x_Merge ( void )

private

Definition at line 101 of file alnmerger.cpp.

References _ASSERT, CAlignRangeCollection< TAlnRange >::begin(), map_checker< Container >::begin(), CAlnMixSegments::Build(), CAlnMixSequences::BuildRows(), CDiagRangeCollection::Diff(), eIgnoreMatch, CAlignRangeCollection< TAlnRange >::empty(), map_checker< Container >::end(), eSecondRowFitsOk, eTranslocation, fFillUnalignedRegions, CAlnMixMatches::fForceTranslation, fGapJoin, CAlnMixSegments::FillUnalignedRegions(), map_checker< Container >::find(), first(), fMinGap, fNegativeStrand, fQuerySeqMergeOnly, fRemoveLeadTrailGaps, fTruncateOverlaps, CAlignRange< Position >::GetFirstFrom(), CAlignRange< Position >::GetLength(), CAlignRange< Position >::GetSecondFrom(), CAlignRangeCollection< TAlnRange >::insert(), ITERATE, len, map_checker< Container >::lower_bound(), CAlnMixMatches::m_AddFlags, m_AlnMixMatches, m_AlnMixSegments, m_AlnMixSequences, CAlnMixSeq::m_BioseqHandle, CAlnMixSeq::m_ChildIdx, CAlnMixMatches::m_ContainsAA, CAlnMixMatches::m_ContainsNA, m_DsCnt, CAlnMixSegment::m_DsIdx, CAlnMixSeq::m_DsIdx, CAlnMixSeq::m_ExtraRowIdx, m_ExtraRows, CAlnMixSeq::m_Frame, m_IndependentDSs, CAlnMixSegment::m_Len, m_Matches, m_MatchIdx, CAlnMixSeq::m_MatchList, m_MergeFlags, m_Planes, CAlnMixSeq::m_PositiveStrand, CAlnMixSeq::m_RefBy, CAlnMixSeq::m_SeqId, CAlnMixSeq::m_SeqIdx, m_Seqs, m_SingleRefseq, CAlnMixSegment::m_StartIts, CAlnMixSeq::m_Width, match(), NCBI_THROW, NON_CONST_ITERATE, Reset(), CAlnMixSegment::SetStartIterator(), CAlnMixSeq::SetStarts(), map_checker< Container >::size(), CAlnMixSegment::StartItsConsistencyCheck(), x_CreateDenseg(), CTaskProgressReporter::x_InterruptTask(), x_SecondRowFits(), x_SetSeqFrame(), CTaskProgressReporter::x_SetTaskCompleted(), and CTaskProgressReporter::x_SetTaskTotal().

Referenced by Merge().

◆ x_Reset()

void CAlnMixMerger::x_Reset ( void )

private

◆ x_SecondRowFits()

CAlnMixMerger::TSecondRowFits CAlnMixMerger::x_SecondRowFits ( CAlnMixMatch * match ) const

private

◆ x_SetSeqFrame()

void CAlnMixMerger::x_SetSeqFrame	(	CAlnMixMatch *	match,
		CAlnMixSeq *&	seq
	)

private

Definition at line 1269 of file alnmerger.cpp.

References map_checker< Container >::empty(), fQuerySeqMergeOnly, CAlnMixSeq::GetStarts(), CAlnMixSeq::m_BioseqHandle, CAlnMixSeq::m_ChildIdx, CAlnMixSeq::m_DsIdx, CAlnMixSeq::m_ExtraRow, CAlnMixSeq::m_ExtraRowIdx, m_ExtraRows, CAlnMixSeq::m_Frame, m_MergeFlags, CAlnMixSeq::m_PositiveStrand, CAlnMixSeq::m_SeqId, CAlnMixSeq::m_SeqIdx, CAlnMixSeq::m_Width, and match().

Referenced by x_Merge().

Member Data Documentation

◆ m_Aln

CRef<CSeq_align> CAlnMixMerger::m_Aln

private

Definition at line 127 of file alnmerger.hpp.

Referenced by GetSeqAlign(), Reset(), and x_CreateDenseg().

◆ m_AlnMixMatches

CRef<CAlnMixMatches> CAlnMixMerger::m_AlnMixMatches

private

Definition at line 131 of file alnmerger.hpp.

Referenced by x_CreateDenseg(), and x_Merge().

◆ m_AlnMixSegments

CRef<CAlnMixSegments> CAlnMixMerger::m_AlnMixSegments

private

Definition at line 139 of file alnmerger.hpp.

Referenced by Reset(), x_CreateDenseg(), and x_Merge().

◆ m_AlnMixSequences

CRef<CAlnMixSequences> CAlnMixMerger::m_AlnMixSequences

private

Definition at line 134 of file alnmerger.hpp.

Referenced by x_Merge().

◆ m_DS

CRef<CDense_seg> CAlnMixMerger::m_DS

private

Definition at line 126 of file alnmerger.hpp.

Referenced by GetDenseg(), Merge(), Reset(), and x_CreateDenseg().

◆ m_DsCnt

const size_t& CAlnMixMerger::m_DsCnt

private

Definition at line 124 of file alnmerger.hpp.

Referenced by Merge(), and x_Merge().

◆ m_ExtraRows

list<CRef<CAlnMixSeq> >& CAlnMixMerger::m_ExtraRows

private

Definition at line 137 of file alnmerger.hpp.

Referenced by Reset(), x_Merge(), and x_SetSeqFrame().

◆ m_IndependentDSs

bool CAlnMixMerger::m_IndependentDSs

private

Definition at line 144 of file alnmerger.hpp.

Referenced by x_Merge(), and x_SecondRowFits().

◆ m_Matches

TMatches& CAlnMixMerger::m_Matches

private

Definition at line 132 of file alnmerger.hpp.

Referenced by x_Merge().

◆ m_MatchIdx

size_t CAlnMixMerger::m_MatchIdx

private

Definition at line 141 of file alnmerger.hpp.

Referenced by x_Merge().

◆ m_MergeFlags

TMergeFlags CAlnMixMerger::m_MergeFlags

private

Definition at line 129 of file alnmerger.hpp.

Referenced by Merge(), x_Merge(), x_SecondRowFits(), and x_SetSeqFrame().

◆ m_Planes

TPlanes CAlnMixMerger::m_Planes

private

Definition at line 148 of file alnmerger.hpp.

Referenced by x_Merge().

◆ m_Rows

vector<CRef<CAlnMixSeq> >& CAlnMixMerger::m_Rows

private

Definition at line 136 of file alnmerger.hpp.

Referenced by Reset(), and x_CreateDenseg().

◆ m_Seqs

TSeqs& CAlnMixMerger::m_Seqs

private

Definition at line 135 of file alnmerger.hpp.

Referenced by Reset(), and x_Merge().

◆ m_SingleRefseq

bool CAlnMixMerger::m_SingleRefseq

private

Definition at line 143 of file alnmerger.hpp.

Referenced by Reset(), and x_Merge().

◆ x_CalculateScore

TCalcScoreMethod CAlnMixMerger::x_CalculateScore

private

Definition at line 146 of file alnmerger.hpp.

The documentation for this class was generated from the following files:

include/objtools/alnmgr/alnmerger.hpp
src/objtools/alnmgr/alnmerger.cpp

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TCalcScoreMethod

◆ TMatches

◆ TMergeFlags

◆ TPlanes

◆ TSecondRowFits

◆ TSeqs

Member Enumeration Documentation

◆ EMergeFlags

◆ ESecondRowFits

Constructor & Destructor Documentation

◆ CAlnMixMerger()

Member Function Documentation

◆ GetDenseg()

◆ GetSeqAlign()

◆ Merge()

◆ Reset()

◆ x_CreateDenseg()

◆ x_Merge()

◆ x_Reset()

◆ x_SecondRowFits()

◆ x_SetSeqFrame()

Member Data Documentation

◆ m_Aln

◆ m_AlnMixMatches

◆ m_AlnMixSegments

◆ m_AlnMixSequences

◆ m_DS

◆ m_DsCnt

◆ m_ExtraRows

◆ m_IndependentDSs

◆ m_Matches

◆ m_MatchIdx

◆ m_MergeFlags

◆ m_Planes

◆ m_Rows

◆ m_Seqs

◆ m_SingleRefseq

◆ x_CalculateScore