CSparseAln Class Reference

Search Toolkit Book for CSparseAln

Sparse alignment. More...

#include <objtools/alnmgr/sparse_aln.hpp>

Inheritance diagram for CSparseAln:

Collaboration diagram for CSparseAln:

Public Types
enum	EConstants { kDefaultGenCode = 1 }
typedef CPairwiseAln::TRng	TRng
typedef CPairwiseAln::TAlnRng	TAlnRng
typedef CPairwiseAln::TAlnRngColl	TAlnRngColl
typedef CAnchoredAln::TDim	TDim
	Synonym of TNumrow. More...
typedef CSeq_data::E_Choice	TCoding
typedef pair< int, int >	TFrames
	Get start and stop frames for the selected row/range. More...
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 Types inherited from IAlnExplorer
enum	EAlignType {   fDNA = 0x01 , fProtein = 0x02 , fMixed = 0x04 , fHomogenous = fDNA | fProtein ,   fInvalid = 0x80000000 }
enum	ESearchDirection {   eNone , eBackwards , eForward , eLeft ,   eRight }
	Position search options. More...
enum	ESortState { eUnSorted , eAscending , eDescending , eNotSupported }
typedef int	TNumrow
typedef objects::CSeqVector::TResidue	TResidue
typedef CRange< TSeqPos >	TRange
typedef CRange< TSignedSeqPos >	TSignedRange

Public Member Functions
	CSparseAln (const CAnchoredAln &anchored_aln, objects::CScope &scope)
	Constructor. More...
virtual	~CSparseAln (void)
	Destructor. More...
void	SetGapChar (TResidue gap_char)
	Gap character modifier. More...
CRef< objects::CScope >	GetScope (void) const
	Scope accessor. More...
TDim	GetDim (void) const
	Alignment dimension (number of sequence rows in the alignment) More...
TNumrow	GetNumRows (void) const
	Synonym of the above. More...
const objects::CSeq_id &	GetSeqId (TNumrow row) const
	Get seq-id for the row. More...
TRng	GetAlnRange (void) const
	Get whole alignment range. More...
const TAlnRngColl &	GetAlignCollection (TNumrow row)
	Get pairwise alignment for the row. More...
bool	IsSetAnchor (void) const
	Check if anchor is set - always true for sparse alignments. More...
TNumrow	GetAnchor (void) const
	Get anchor row index. More...
TSignedRange	GetSeqAlnRange (TNumrow row) const
	Get sequence range in alignment coords (strand ignored). More...
TSignedSeqPos	GetSeqAlnStart (TNumrow row) const
TSignedSeqPos	GetSeqAlnStop (TNumrow row) const
TRange	GetSeqRange (TNumrow row) const
	Get sequence range in sequence coords. More...
TSeqPos	GetSeqStart (TNumrow row) const
TSeqPos	GetSeqStop (TNumrow row) const
bool	IsPositiveStrand (TNumrow row) const
	Check direction of the row. More...
bool	IsNegativeStrand (TNumrow row) const
TSignedSeqPos	GetAlnPosFromSeqPos (TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const
	Map sequence position to alignment coordinates. More...
TSignedSeqPos	GetSeqPosFromAlnPos (TNumrow for_row, TSeqPos aln_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const
TCoding	GetNaCoding (void) const
	Get sequence coding for nucleotides. More...
TCoding	GetAaCoding (void) const
	Get sequence coding for proteins. More...
void	SetNaCoding (TCoding coding)
	Set sequence coding for nucleotides. If not set, Iupacna coding is used. More...
void	SetAaCoding (TCoding coding)
	Set sequence coding for proteins. If not set, Iupacaa coding is used. More...
string &	GetSeqString (TNumrow row, string &buffer, TSeqPos seq_from, TSeqPos seq_to, bool force_translation=false) const
	Fetch sequence data for the given row and range. More...
string &	GetSeqString (TNumrow row, string &buffer, const TRange &rq_seq_rng, bool force_translation=false) const
	Fetch sequence data for the given row and range. More...
string &	GetAlnSeqString (TNumrow row, string &buffer, const TSignedRange &rq_aln_rng, bool force_translation=false) const
	Fetch alignment sequence data. More...
const objects::CBioseq_Handle &	GetBioseqHandle (TNumrow row) const
	Get bioseq handle for the row. More...
virtual IAlnSegmentIterator *	CreateSegmentIterator (TNumrow row, const TSignedRange &range, IAlnSegmentIterator::EFlags flags) const
	Create segment iterator. More...
bool	IsTranslated (void) const
	Wheather the alignment is translated (heterogenous), e.g. nuc-prot. More...
int	GetBaseWidth (TNumrow row) const
	Get base width for the sequence (1 for nucleotides, 3 for proteins). More...
TSignedSeqPos	AlnPosToNativeSeqPos (TNumrow row, TSignedSeqPos aln_pos) const
	Convert alignment (genomic) coordinate on the selected row to real sequence position. More...
int	AlnPosToNativeFrame (TNumrow row, TSignedSeqPos aln_pos) const
	For protein sequences get frame for the specified coordinated. More...
TSignedSeqPos	NativeSeqPosToAlnPos (TNumrow row, TSignedSeqPos seq_pos, int frame=0) const
	Convert sequence position to alignment (genomic) coordinate. More...
template<class _TRange >
_TRange	AlnRangeToNativeSeqRange (TNumrow row, _TRange aln_range) const
	Convert alignment range (genomic coordinates) on the selected row to real sequence range. More...
template<class _TRange >
TFrames	AlnRangeToNativeFrames (TNumrow row, _TRange aln_range) const
template<class _TRange >
_TRange	NativeSeqRangeToAlnRange (TNumrow row, _TRange seq_range, TFrames frames=TFrames(0, 0)) const
	Convert sequence range to alignment range (genomic coordinates). More...
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

Static Public Member Functions
static void	TranslateNAToAA (const string &na, string &aa, int gen_code=kDefaultGenCode)
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)

Protected Types
typedef CAnchoredAln::TPairwiseAlnVector	TPairwiseAlnVector

Protected Member Functions
void	x_Build (const CAnchoredAln &src_align)
CSeqVector &	x_GetSeqVector (TNumrow row) const
int	x_GetGenCode (TNumrow row) const
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Protected Attributes
CRef< CAnchoredAln >	m_Aln
CRef< objects::CScope >	m_Scope
TRng	m_FirstRange
vector< TRng >	m_SecondRanges
TResidue	m_GapChar
vector< objects::CBioseq_Handle >	m_BioseqHandles
vector< CRef< CSeqVector > >	m_SeqVectors
TCoding	m_NaCoding
TCoding	m_AaCoding
bool	m_AnchorDirect

Friends
class	CSparse_CI

Additional Inherited Members
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

Sparse alignment.

Definition at line 50 of file sparse_aln.hpp.

Member Typedef Documentation

TAlnRng

typedef CPairwiseAln::TAlnRng CSparseAln::TAlnRng

Definition at line 54 of file sparse_aln.hpp.

TAlnRngColl

typedef CPairwiseAln::TAlnRngColl CSparseAln::TAlnRngColl

Definition at line 55 of file sparse_aln.hpp.

TCoding

typedef CSeq_data::E_Choice CSparseAln::TCoding

Definition at line 133 of file sparse_aln.hpp.

TDim

typedef CAnchoredAln::TDim CSparseAln::TDim

Synonym of TNumrow.

Definition at line 56 of file sparse_aln.hpp.

TFrames

typedef pair<int, int> CSparseAln::TFrames

Get start and stop frames for the selected row/range.

0 - no frame (native coordinates are genomic) 1..3 - frame value for protein coordinates

Definition at line 275 of file sparse_aln.hpp.

TPairwiseAlnVector

typedef CAnchoredAln::TPairwiseAlnVector CSparseAln::TPairwiseAlnVector

protected

Definition at line 308 of file sparse_aln.hpp.

TRng

typedef CPairwiseAln::TRng CSparseAln::TRng

Definition at line 53 of file sparse_aln.hpp.

Member Enumeration Documentation

EConstants

enum CSparseAln::EConstants

Enumerator
kDefaultGenCode

Definition at line 216 of file sparse_aln.hpp.

Constructor & Destructor Documentation

CSparseAln()

CSparseAln::CSparseAln	(	const CAnchoredAln &	anchored_aln,
		objects::CScope &	scope
	)

Constructor.

Parameters

anchored_aln	Input CAnchoredAln object. Should be built using BuildAln function for the alignment coordinates to be correct.
scope	CScope used to fetch sequence data.

See also

BuildAln

Definition at line 52 of file sparse_aln.cpp.

References x_Build().

~CSparseAln()

CSparseAln::~CSparseAln ( void  )

virtual

Destructor.

Definition at line 64 of file sparse_aln.cpp.

Member Function Documentation

AlnPosToNativeFrame()

int CSparseAln::AlnPosToNativeFrame ( TNumrow  row, TSignedSeqPos  aln_pos  ) const

inline

For protein sequences get frame for the specified coordinated.

For genomic sequences always returns 0.

Definition at line 242 of file sparse_aln.hpp.

References GetBaseWidth(), and row.

AlnPosToNativeSeqPos()

TSignedSeqPos CSparseAln::AlnPosToNativeSeqPos ( TNumrow  row, TSignedSeqPos  aln_pos  ) const

inline

Convert alignment (genomic) coordinate on the selected row to real sequence position.

Definition at line 235 of file sparse_aln.hpp.

References GetBaseWidth(), and row.

AlnRangeToNativeFrames()

template<class _TRange >

TFrames CSparseAln::AlnRangeToNativeFrames ( TNumrow  row, _TRange  aln_range  ) const

inline

Definition at line 277 of file sparse_aln.hpp.

References GetBaseWidth(), and row.

Referenced by DumpSparseAln(), and CAlnTestApp::Run().

AlnRangeToNativeSeqRange()

template<class _TRange >

_TRange CSparseAln::AlnRangeToNativeSeqRange ( TNumrow  row, _TRange  aln_range  ) const

inline

Convert alignment range (genomic coordinates) on the selected row to real sequence range.

NOTE: Need to use template since there are many range types: TRng, TAlnRng, TRange, TSignedRange etc.

Definition at line 265 of file sparse_aln.hpp.

References GetBaseWidth(), and row.

Referenced by CheckSparseAln(), DumpSparseAln(), and CAlnTestApp::Run().

CreateSegmentIterator()

IAlnSegmentIterator * CSparseAln::CreateSegmentIterator ( TNumrow  row, const TSignedRange &  range, IAlnSegmentIterator::EFlags  flags  ) const

virtual

Create segment iterator.

Parameters

row	Row to iterate segments for.
range	Range to iterate.
flags	Iterator flags.

See also

CSparse_CI

IAlnSegmentIterator

Definition at line 710 of file sparse_aln.cpp.

References _ASSERT, CSparse_CI, GetDim(), CAnchoredAln::GetPairwiseAlns(), GetSeqId(), NStr::IntToString(), m_Aln, NCBI_THROW, compile_time_bits::range(), and row.

Referenced by CAlignmentSmear::AddAlignment(), CSparseRowHandle::CreateSegmentIterator(), CSparseMultiDataSource::CreateSegmentIterator(), CSparseAlnGraphicDataSource::CreateSegmentIterator(), CAlnBuildApp::PrintAnchoredAln(), and CAlnTestApp::Run().

GetAaCoding()

TCoding CSparseAln::GetAaCoding ( void  ) const

inline

Get sequence coding for proteins.

Definition at line 137 of file sparse_aln.hpp.

References m_AaCoding.

GetAlignCollection()

const CSparseAln::TAlnRngColl & CSparseAln::GetAlignCollection

(

TNumrow

row

)

Get pairwise alignment for the row.

Definition at line 257 of file sparse_aln.cpp.

References _ASSERT, GetDim(), CAnchoredAln::GetPairwiseAlns(), m_Aln, and row.

GetAlnPosFromSeqPos()

TSignedSeqPos CSparseAln::GetAlnPosFromSeqPos	(	TNumrow	row,
		TSeqPos	seq_pos,
		ESearchDirection	dir = eNone,
		bool	try_reverse_dir = true
	)		const

Map sequence position to alignment coordinates.

Parameters

row	Alignment row where the input position is defined.
seq_pos	Input position
dir	In case the input position can not be mapped to the alignment coordinates (e.g. the position is inside an unaligned range), try to search for the neares alignment position in the specified direction.
try_reverse_dir	Not implemented

Definition at line 373 of file sparse_aln.cpp.

References _ASSERT, GetCollectionSearchDirection(), GetDim(), CAnchoredAln::GetPairwiseAlns(), m_Aln, and row.

Referenced by CSparseMultiDataSource::GetAlnFromSeq(), CSparseMultiDataSource::GetAlnPosFromSeqPos(), CSparseAlnGraphicDataSource::GetAlnPosFromSeqPos(), CSparseRowHandle::GetAlnPosFromSeqPos(), CSparseAlnGraphicDataSource::GetSeqPosFromSeqPos(), and CValidError_align::x_ValidateAlignPercentIdentity().

GetAlnRange()

CSparseAln::TRng CSparseAln::GetAlnRange

(

void

)

const

Get whole alignment range.

Definition at line 238 of file sparse_aln.cpp.

References m_FirstRange.

Referenced by CAlignmentSmear::AddAlignment(), CheckSparseAln(), DumpSparseAln(), CSparseAlnGraphicDataSource::GetAlnRange(), CSparseMultiDataSource::GetAlnStart(), CSparseAlnGraphicDataSource::GetAlnStart(), CSparseMultiDataSource::GetAlnStop(), CSparseAlnGraphicDataSource::GetAlnStop(), CAlnBuildApp::PrintAnchoredAln(), CTreeBuilderJob::x_Divergence(), and CValidError_align::x_ValidateAlignPercentIdentity().

GetAlnSeqString()

string & CSparseAln::GetAlnSeqString	(	TNumrow	row,
		string &	buffer,
		const TSignedRange &	rq_aln_rng,
		bool	force_translation = false
	)		const

Fetch alignment sequence data.

Unaligned ranges of the selected row are filled with gap char.

Parameters

row	Alignment row to fetch sequence for.
buffer	Output buffer.
aln_rng	Alignment range.
force_translation	Force nucleotide to protein sequence translation.

Returns

Reference to the output buffer.

Definition at line 552 of file sparse_aln.cpp.

References _ASSERT, buffer, CAlignRangeCollectionList< TAlnRange >::empty(), COpenRange< Position >::Empty(), IAlnSegmentIterator::eSkipInserts, IAlnSegment::GetAlnRange(), GetDim(), CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), CAnchoredAln::GetPairwiseAlns(), IAlnSegment::GetRange(), CPairwiseAln::GetSecondBaseWidth(), CPairwiseAln::GetSecondId(), GetSeqAlnRange(), CSeqVector::GetSeqData(), GetSeqId(), COpenRange< Position >::GetToOpen(), NStr::IntToString(), IsPositiveStrand(), COpenRange< Position >::IsWhole(), kInvalidSeqPos, len, m_Aln, m_AnchorDirect, m_GapChar, min(), NCBI_THROW, row, COpenRange< Position >::SetOpen(), CSeqVector::size(), TranslateNAToAA(), x_GetGenCode(), and x_GetSeqVector().

Referenced by CheckSparseAln(), DumpSparseAln(), CSparseRowHandle::GetAlnSeqString(), CSparseMultiDataSource::GetAlnSeqString(), CSparseAlnGraphicDataSource::GetAlnSeqString(), CAlnBuildApp::PrintAnchoredAln(), CTreeBuilderJob::x_Divergence(), and CValidError_align::x_ValidateAlignPercentIdentity().

GetAnchor()

TNumrow CSparseAln::GetAnchor ( void  ) const

inline

Get anchor row index.

Definition at line 95 of file sparse_aln.hpp.

References CAnchoredAln::GetAnchorRow(), and m_Aln.

Referenced by CAlignmentSmear::AddAlignment(), CheckSparseAln(), DumpSparseAln(), CSparseMultiDataSource::GetAnchor(), CSparseAlnGraphicDataSource::GetAnchor(), TestIterators(), and TestSparseIt().

GetBaseWidth()

int CSparseAln::GetBaseWidth ( TNumrow  row ) const

inline

Get base width for the sequence (1 for nucleotides, 3 for proteins).

Definition at line 225 of file sparse_aln.hpp.

References _ASSERT, GetDim(), CAnchoredAln::GetPairwiseAlns(), m_Aln, and row.

Referenced by AlnPosToNativeFrame(), AlnPosToNativeSeqPos(), AlnRangeToNativeFrames(), AlnRangeToNativeSeqRange(), CheckSparseAln(), DumpSparseAln(), CSparseRowHandle::GetBaseWidth(), CSparseMultiDataSource::GetBaseWidth(), CSparseAlnGraphicDataSource::GetBaseWidth(), CSparseRowHandle::IsNucProtAlignment(), NativeSeqPosToAlnPos(), NativeSeqRangeToAlnRange(), and CAlnTestApp::Run().

GetBioseqHandle()

const CBioseq_Handle & CSparseAln::GetBioseqHandle

(

TNumrow

row

)

const

Get bioseq handle for the row.

Throw exception if the handle can not be obtained.

Definition at line 396 of file sparse_aln.cpp.

References _ASSERT, GetDim(), GetSeqId(), m_BioseqHandles, m_Scope, NCBI_THROW, and row.

Referenced by CBuildSparseAlnJob::Build(), CSparseRowHandle::GetBioseqHandle(), CSparseMultiDataSource::GetBioseqHandle(), CSparseAlnGraphicDataSource::GetBioseqHandle(), CSparseAlnGraphicDataSource::GetSeqLength(), CSparseRowHandle::UsesAATranslation(), CTreeBuilderJob::x_CreateProjectItems(), x_GetGenCode(), and x_GetSeqVector().

GetDim()

CSparseAln::TDim CSparseAln::GetDim

(

void

)

const

Alignment dimension (number of sequence rows in the alignment)

Definition at line 69 of file sparse_aln.cpp.

References CAnchoredAln::GetDim(), and m_Aln.

Referenced by BuildAlignDataSource(), CheckSparseAln(), CreateSegmentIterator(), DumpSparseAln(), GetAlignCollection(), GetAlnPosFromSeqPos(), GetAlnSeqString(), GetBaseWidth(), GetBioseqHandle(), GetNumRows(), GetSeqAlnRange(), GetSeqAlnStart(), GetSeqAlnStop(), GetSeqId(), GetSeqPosFromAlnPos(), GetSeqRange(), GetSeqStart(), GetSeqStop(), GetSeqString(), IsNegativeStrand(), IsPositiveStrand(), CValidError_align::IsTpaAlignment(), IsTranslated(), CAlnBuildApp::PrintAnchoredAln(), CAlnTestApp::Run(), x_GetSeqVector(), and CValidError_align::x_ValidateAlignPercentIdentity().

GetNaCoding()

TCoding CSparseAln::GetNaCoding ( void  ) const

inline

Get sequence coding for nucleotides.

Definition at line 135 of file sparse_aln.hpp.

References m_NaCoding.

GetNumRows()

TNumrow CSparseAln::GetNumRows ( void  ) const

inline

Synonym of the above.

Definition at line 80 of file sparse_aln.hpp.

References GetDim().

Referenced by CAlignmentSmear::AddAlignment(), CBuildSparseAlnJob::Build(), CheckSparseAln(), DumpSparseAln(), CSparseMultiDataSource::GetAlignType(), CSparseMultiDataSource::GetNumRows(), CSparseAlnGraphicDataSource::GetNumRows(), CSparseRowHandle::IsNucProtAlignment(), TestIterators(), CSparseMultiDataSource::x_CreateHandles(), CTreeBuilderJob::x_CreateProjectItems(), and CTreeBuilderJob::x_Divergence().

GetScope()

CRef< CScope > CSparseAln::GetScope

(

void

)

const

Scope accessor.

Definition at line 250 of file sparse_aln.cpp.

References m_Scope.

Referenced by CSparseMultiDataSource::GetAlignType(), and CSparseRowHandle::GetScope().

GetSeqAlnRange()

CSparseAln::TSignedRange CSparseAln::GetSeqAlnRange

(

TNumrow

row

)

const

Get sequence range in alignment coords (strand ignored).

Definition at line 285 of file sparse_aln.cpp.

References _ASSERT, GetDim(), GetSeqAlnStart(), GetSeqAlnStop(), and row.

Referenced by DumpSparseAln(), GetAlnSeqString(), CSparseRowHandle::GetSeqAlnRange(), CSparseAlnGraphicDataSource::GetSeqAlnRange(), CAlnBuildApp::PrintAnchoredAln(), and CAlnTestApp::Run().

GetSeqAlnStart()

TSignedSeqPos CSparseAln::GetSeqAlnStart

(

TNumrow

row

)

const

Definition at line 271 of file sparse_aln.cpp.

References _ASSERT, GetDim(), CAnchoredAln::GetPairwiseAlns(), m_Aln, and row.

Referenced by CheckSparseAln(), DumpSparseAln(), GetSeqAlnRange(), CSparseRowHandle::GetSeqAlnStart(), CSparseMultiDataSource::GetSeqFromAln(), and CValidError_align::x_ValidateAlignPercentIdentity().

GetSeqAlnStop()

TSignedSeqPos CSparseAln::GetSeqAlnStop

(

TNumrow

row

)

const

Definition at line 278 of file sparse_aln.cpp.

References _ASSERT, GetDim(), CAnchoredAln::GetPairwiseAlns(), m_Aln, and row.

Referenced by CheckSparseAln(), DumpSparseAln(), GetSeqAlnRange(), CSparseRowHandle::GetSeqAlnStop(), CSparseMultiDataSource::GetSeqFromAln(), and CValidError_align::x_ValidateAlignPercentIdentity().

GetSeqId()

const CSeq_id & CSparseAln::GetSeqId

(

TNumrow

row

)

const

Get seq-id for the row.

Definition at line 264 of file sparse_aln.cpp.

References _ASSERT, GetDim(), CAnchoredAln::GetPairwiseAlns(), m_Aln, and row.

Referenced by CheckSparseAln(), CreateSegmentIterator(), DumpSparseAln(), CSparseMultiDataSource::GetAlignType(), GetAlnSeqString(), GetBioseqHandle(), CSparseRowHandle::GetSeq_id(), CSparseMultiDataSource::GetSeqId(), CSparseAlnGraphicDataSource::GetSeqId(), CValidError_align::IsTpaAlignment(), CAlnBuildApp::PrintAnchoredAln(), and TestIterators().

GetSeqPosFromAlnPos()

TSignedSeqPos CSparseAln::GetSeqPosFromAlnPos	(	TNumrow	for_row,
		TSeqPos	aln_pos,
		ESearchDirection	dir = eNone,
		bool	try_reverse_dir = true
	)		const

Definition at line 385 of file sparse_aln.cpp.

References _ASSERT, GetCollectionSearchDirection(), GetDim(), CAnchoredAln::GetPairwiseAlns(), m_Aln, and row.

Referenced by CSparseMultiDataSource::GetSeqFromAln(), CSparseMultiDataSource::GetSeqPosFromAlnPos(), CSparseAlnGraphicDataSource::GetSeqPosFromAlnPos(), CSparseRowHandle::GetSeqPosFromAlnPos(), CAlnBuildApp::PrintAnchoredAln(), TestSparseIt(), and CValidError_align::x_ValidateAlignPercentIdentity().

GetSeqRange()

CSparseAln::TRange CSparseAln::GetSeqRange

(

TNumrow

row

)

const

Get sequence range in sequence coords.

Definition at line 306 of file sparse_aln.cpp.

References _ASSERT, GetDim(), GetSeqStart(), GetSeqStop(), and row.

Referenced by CheckSparseAln(), DumpSparseAln(), and GetSeqString().

GetSeqStart()

TSeqPos CSparseAln::GetSeqStart

(

TNumrow

row

)

const

Definition at line 292 of file sparse_aln.cpp.

References _ASSERT, GetDim(), m_SecondRanges, and row.

Referenced by CSparseMultiDataSource::GetAlnFromSeq(), GetSeqRange(), CSparseRowHandle::GetSeqStart(), CSparseMultiDataSource::GetSeqStart(), and CSparseAlnGraphicDataSource::GetSeqStart().

GetSeqStop()

TSeqPos CSparseAln::GetSeqStop

(

TNumrow

row

)

const

Definition at line 299 of file sparse_aln.cpp.

References _ASSERT, GetDim(), m_SecondRanges, and row.

Referenced by CSparseMultiDataSource::GetAlnFromSeq(), GetSeqRange(), CSparseRowHandle::GetSeqStop(), CSparseMultiDataSource::GetSeqStop(), and CSparseAlnGraphicDataSource::GetSeqStop().

GetSeqString() [1/2]

string & CSparseAln::GetSeqString	(	TNumrow	row,
		string &	buffer,
		const TRange &	rq_seq_rng,
		bool	force_translation = false
	)		const

Fetch sequence data for the given row and range.

Parameters

row	Alignment row to fetch sequence for.
buffer	Output buffer.
seq_rng	Sequence range.
force_translation	Force nucleotide to protein sequence translation.

Returns

Reference to the output buffer.

Definition at line 505 of file sparse_aln.cpp.

References _ASSERT, buffer, GetDim(), CRange_Base::GetFrom(), CAnchoredAln::GetPairwiseAlns(), CSeqVector::GetSeqData(), GetSeqRange(), COpenRange< Position >::GetToOpen(), IsPositiveStrand(), COpenRange< Position >::IsWhole(), m_Aln, m_GapChar, row, ncbi::grid::netcache::search::fields::size, CSeqVector::size(), TranslateNAToAA(), x_GetGenCode(), and x_GetSeqVector().

GetSeqString() [2/2]

string & CSparseAln::GetSeqString	(	TNumrow	row,
		string &	buffer,
		TSeqPos	seq_from,
		TSeqPos	seq_to,
		bool	force_translation = false
	)		const

Fetch sequence data for the given row and range.

Parameters

row	Alignment row to fetch sequence for.
buffer	Output buffer.
seq_from	Start sequence position.
seq_to	End sequence position.
force_translation	Force nucleotide to protein sequence translation.

Returns

Reference to the output buffer.

Definition at line 496 of file sparse_aln.cpp.

References buffer, and row.

Referenced by CheckSparseAln(), DumpSparseAln(), CSparseRowHandle::GetSeqString(), and CSparseMultiDataSource::GetSeqString().

IsNegativeStrand()

bool CSparseAln::IsNegativeStrand

(

TNumrow

row

)

const

Definition at line 321 of file sparse_aln.cpp.

References _ASSERT, CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::fMixedDir, CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::fReversed, GetDim(), CAnchoredAln::GetPairwiseAlns(), m_Aln, m_AnchorDirect, and row.

Referenced by CSparseRowHandle::IsNegativeStrand(), CSparseMultiDataSource::IsNegativeStrand(), and CSparseAlnGraphicDataSource::IsNegativeStrand().

IsPositiveStrand()

bool CSparseAln::IsPositiveStrand

(

TNumrow

row

)

const

Check direction of the row.

Definition at line 313 of file sparse_aln.cpp.

References _ASSERT, CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::fDirect, CAlignRangeCollectionList< CAlignRange< TSignedSeqPos > >::fMixedDir, GetDim(), CAnchoredAln::GetPairwiseAlns(), m_Aln, m_AnchorDirect, and row.

Referenced by GetAlnSeqString(), GetSeqString(), CSparseMultiDataSource::IsPositiveStrand(), CSparseAlnGraphicDataSource::IsPositiveStrand(), and x_GetSeqVector().

IsSetAnchor()

bool CSparseAln::IsSetAnchor ( void  ) const

inline

Check if anchor is set - always true for sparse alignments.

Definition at line 92 of file sparse_aln.hpp.

Referenced by CSparseMultiDataSource::IsSetAnchor().

IsTranslated()

bool CSparseAln::IsTranslated

(

void

)

const

Wheather the alignment is translated (heterogenous), e.g. nuc-prot.

Definition at line 329 of file sparse_aln.cpp.

References GetDim(), CAnchoredAln::GetPairwiseAlns(), m_Aln, and row.

NativeSeqPosToAlnPos()

TSignedSeqPos CSparseAln::NativeSeqPosToAlnPos ( TNumrow  row, TSignedSeqPos  seq_pos, int  frame = 0  ) const

inline

Convert sequence position to alignment (genomic) coordinate.

Optional frame can be used with protein positions.

Definition at line 250 of file sparse_aln.hpp.

References GetBaseWidth(), and row.

NativeSeqRangeToAlnRange()

template<class _TRange >

_TRange CSparseAln::NativeSeqRangeToAlnRange ( TNumrow  row, _TRange  seq_range, TFrames  frames = TFrames(0, 0)  ) const

inline

Convert sequence range to alignment range (genomic coordinates).

Optional frames argument can be provided for protein ranges. NOTE: Need to use template since there are many range types: TRng, TAlnRng, TRange, TSignedRange etc.

Definition at line 290 of file sparse_aln.hpp.

References GetBaseWidth(), and row.

SetAaCoding()

void CSparseAln::SetAaCoding ( TCoding  coding )

inline

Set sequence coding for proteins. If not set, Iupacaa coding is used.

Definition at line 141 of file sparse_aln.hpp.

References m_AaCoding.

SetGapChar()

void CSparseAln::SetGapChar

(

TResidue

gap_char

)

Gap character modifier.

Definition at line 244 of file sparse_aln.cpp.

References m_GapChar.

Referenced by CSparseMultiDataSource::SetGapChar(), CTreeBuilderJob::x_CreateProjectItems(), and CTreeBuilderJob::x_Divergence().

SetNaCoding()

void CSparseAln::SetNaCoding ( TCoding  coding )

inline

Set sequence coding for nucleotides. If not set, Iupacna coding is used.

Definition at line 139 of file sparse_aln.hpp.

References m_NaCoding.

TranslateNAToAA()

void CSparseAln::TranslateNAToAA ( const string &  na, string &  aa, int  gen_code = kDefaultGenCode  )

static

Definition at line 463 of file sparse_aln.cpp.

References CTrans_table::GetCodonResidue(), CGen_code_table::GetTransTable(), i, and CTrans_table::NextCodonState().

Referenced by GetAlnSeqString(), GetSeqString(), and CAlnSpanVertModel::x_PopulateRows().

x_Build()

void CSparseAln::x_Build ( const CAnchoredAln &  src_align )

protected

Definition at line 99 of file sparse_aln.cpp.

References _ASSERT, CAlignRangeCollectionList< TAlnRange >::begin(), COpenRange< Position >::CombineWith(), SGapRange::direct, CAlignRangeCollectionList< TAlnRange >::empty(), CAlignRangeCollectionList< TAlnRange >::end(), CAlignRangeCollectionList< TAlnRange >::fInvalid, CAlignRangeCollectionList< TAlnRange >::fOverlap, SGapRange::from, CAlignRangeCollectionList< TAlnRange >::fUnsorted, CAnchoredAln::GetAnchorRow(), CAnchoredAln::GetDim(), CAlignRange< Position >::GetFirstFrom(), CPairwiseAln::GetFirstId(), CAlignRange< Position >::GetFirstToOpen(), CAlignRangeCollectionList< TAlnRange >::GetFlags(), CAlignRangeCollectionList< TAlnRange >::GetInsertions(), CAlignRange< Position >::GetLength(), CAnchoredAln::GetPairwiseAlns(), CAnchoredAln::GetScore(), CAlignRange< Position >::GetSecondFrom(), CPairwiseAln::GetSecondId(), CAlignRangeCollExtender< TColl >::GetSecondRange(), CAlignRange< Position >::GetSecondToOpen(), i, CAlignRange< Position >::IsDirect(), CAlignRange< Position >::IsFirstDirect(), SGapRange::len, m_Aln, m_AnchorDirect, m_BioseqHandles, m_FirstRange, m_SecondRanges, m_SeqVectors, NON_CONST_ITERATE, CRef< C, Locker >::Reset(), row, SGapRange::row, SGapRange::second_from, CAnchoredAln::SetAnchorRow(), CAnchoredAln::SetDim(), CAlignRange< Position >::SetDirect(), CAlignRange< Position >::SetFirstDirect(), CAlignRange< Position >::SetFirstFrom(), CAlignRange< Position >::SetLength(), CAnchoredAln::SetPairwiseAlns(), CAnchoredAln::SetScore(), CAlignRange< Position >::SetSecondFrom(), SGapRange::shift, and CAlignRangeCollExtender< TColl >::UpdateIndex().

Referenced by CSparseAln().

x_GetGenCode()

int CSparseAln::x_GetGenCode ( TNumrow  row ) const

protected

Definition at line 446 of file sparse_aln.cpp.

References GetBioseqHandle(), GetBioSource(), CBioSource::GetGenCode(), GetOrg_refOrNull(), kDefaultGenCode, and row.

Referenced by GetAlnSeqString(), and GetSeqString().

x_GetSeqVector()

CSeqVector & CSparseAln::x_GetSeqVector ( TNumrow  row ) const

protected

Definition at line 411 of file sparse_aln.cpp.

References _ASSERT, CSeq_data_Base::e_not_set, CBioseq_Handle::eCoding_Iupac, CBioseq_Handle::eStrand_Minus, CBioseq_Handle::eStrand_Plus, GetBioseqHandle(), GetDim(), CSeqVector::IsNucleotide(), IsPositiveStrand(), CSeqVector::IsProtein(), m_AaCoding, m_NaCoding, m_SeqVectors, row, CSeqVector::SetCoding(), and CSeqVector::SetIupacCoding().

Referenced by GetAlnSeqString(), and GetSeqString().

Friends And Related Function Documentation

CSparse_CI

friend class CSparse_CI

friend

Definition at line 302 of file sparse_aln.hpp.

Referenced by CreateSegmentIterator().

Member Data Documentation

m_AaCoding

TCoding CSparseAln::m_AaCoding

protected

Definition at line 319 of file sparse_aln.hpp.

Referenced by GetAaCoding(), SetAaCoding(), and x_GetSeqVector().

m_Aln

CRef<CAnchoredAln> CSparseAln::m_Aln

protected

Definition at line 310 of file sparse_aln.hpp.

Referenced by CreateSegmentIterator(), GetAlignCollection(), GetAlnPosFromSeqPos(), GetAlnSeqString(), GetAnchor(), GetBaseWidth(), GetDim(), GetSeqAlnStart(), GetSeqAlnStop(), GetSeqId(), GetSeqPosFromAlnPos(), GetSeqString(), IsNegativeStrand(), IsPositiveStrand(), IsTranslated(), and x_Build().

m_AnchorDirect

bool CSparseAln::m_AnchorDirect

protected

Definition at line 321 of file sparse_aln.hpp.

Referenced by GetAlnSeqString(), IsNegativeStrand(), IsPositiveStrand(), and x_Build().

m_BioseqHandles

vector<objects::CBioseq_Handle> CSparseAln::m_BioseqHandles

mutableprotected

Definition at line 315 of file sparse_aln.hpp.

Referenced by GetBioseqHandle(), and x_Build().

m_FirstRange

TRng CSparseAln::m_FirstRange

protected

Definition at line 312 of file sparse_aln.hpp.

Referenced by GetAlnRange(), and x_Build().

m_GapChar

TResidue CSparseAln::m_GapChar

protected

Definition at line 314 of file sparse_aln.hpp.

Referenced by GetAlnSeqString(), GetSeqString(), and SetGapChar().

m_NaCoding

TCoding CSparseAln::m_NaCoding

protected

Definition at line 318 of file sparse_aln.hpp.

Referenced by GetNaCoding(), SetNaCoding(), and x_GetSeqVector().

m_Scope

CRef<objects::CScope> CSparseAln::m_Scope

mutableprotected

Definition at line 311 of file sparse_aln.hpp.

Referenced by GetBioseqHandle(), and GetScope().

m_SecondRanges

vector<TRng> CSparseAln::m_SecondRanges

protected

Definition at line 313 of file sparse_aln.hpp.

Referenced by GetSeqStart(), GetSeqStop(), and x_Build().

m_SeqVectors

vector<CRef<CSeqVector> > CSparseAln::m_SeqVectors

mutableprotected

Definition at line 316 of file sparse_aln.hpp.

Referenced by x_Build(), and x_GetSeqVector().

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

• include/objtools/alnmgr/sparse_aln.hpp
• src/objtools/alnmgr/sparse_aln.cpp