#include <objtools/alnmgr/alnmap.hpp>

Inheritance diagram for CAlnMap:

Collaboration diagram for CAlnMap:

Classes
class	CAlnChunk

class	CAlnChunkVec

class	CNumSegWithOffset

Public Types
enum	ESegTypeFlags { fSeq = 0x0001 , fNotAlignedToSeqOnAnchor = 0x0002 , fInsert = fSeq \| fNotAlignedToSeqOnAnchor , fUnalignedOnRight = 0x0004 , fUnalignedOnLeft = 0x0008 , fNoSeqOnRight = 0x0010 , fNoSeqOnLeft = 0x0020 , fEndOnRight = 0x0040 , fEndOnLeft = 0x0080 , fUnaligned = 0x0100 , fUnalignedOnRightOnAnchor = 0x0200 , fUnalignedOnLeftOnAnchor = 0x0400 , fTypeIsSet = (TSegTypeFlags) 0x80000000 }

enum	EGetChunkFlags { fAllChunks = 0x0000 , fIgnoreUnaligned = 0x0001 , fInsertSameAsSeq = 0x0002 , fDeletionSameAsGap = 0x0004 , fIgnoreAnchor = fInsertSameAsSeq \| fDeletionSameAsGap , fIgnoreGaps = 0x0008 , fChunkSameAsSeg = 0x0010 , fSkipUnalignedGaps = 0x0020 , fSkipDeletions = 0x0040 , fSkipAllGaps = fSkipUnalignedGaps \| fSkipDeletions , fSkipInserts = 0x0080 , fSkipAlnSeq = 0x0100 , fSeqOnly = fSkipAllGaps \| fSkipInserts , fInsertsOnly = fSkipAllGaps \| fSkipAlnSeq , fAlnSegsOnly = fSkipInserts \| fSkipUnalignedGaps , fDoNotTruncateSegs = 0x0200 , fAddUnalignedChunks = 0x0400 }

enum	ESegmentTrimFlag { eSegment_Include , eSegment_Trim , eSegment_Remove }

typedef unsigned int	TSegTypeFlags

typedef CDense_seg::TDim	TDim

typedef TDim	TNumrow

typedef CRange< TSeqPos >	TRange

typedef CRange< TSignedSeqPos >	TSignedRange

typedef CDense_seg::TNumseg	TNumseg

typedef list< TSeqPos >	TSeqPosList

typedef int	TGetChunkFlags

typedef TNumseg	TNumchunk

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
	CAlnMap (const CDense_seg &ds)

	CAlnMap (const CDense_seg &ds, TNumrow anchor)

CRef< CSeq_align >	CreateAlignFromRange (const vector< TNumrow > &selected_rows, TSignedSeqPos aln_from, TSignedSeqPos aln_to, ESegmentTrimFlag seg_flag=eSegment_Trim)

	~CAlnMap (void)

const CDense_seg &	GetDenseg (void) const

TNumseg	GetNumSegs (void) const

TDim	GetNumRows (void) const

const CSeq_id &	GetSeqId (TNumrow row) const

bool	IsPositiveStrand (TNumrow row) const

bool	IsNegativeStrand (TNumrow row) const

int	StrandSign (TNumrow row) const

int	GetWidth (TNumrow row) const

TSignedSeqPos	GetSeqAlnStart (TNumrow row) const

TSignedSeqPos	GetSeqAlnStop (TNumrow row) const

TSignedRange	GetSeqAlnRange (TNumrow row) const

TSeqPos	GetSeqStart (TNumrow row) const

TSeqPos	GetSeqStop (TNumrow row) const

TRange	GetSeqRange (TNumrow row) const

TSignedSeqPos	GetStart (TNumrow row, TNumseg seg, int offset=0) const

TSignedSeqPos	GetStop (TNumrow row, TNumseg seg, int offset=0) const

TSignedRange	GetRange (TNumrow row, TNumseg seg, int offset=0) const

TSeqPos	GetLen (TNumseg seg, int offset=0) const

TSeqPos	GetSeqLen (TNumrow row, TNumseg seg, int offset=0) const

TSegTypeFlags	GetSegType (TNumrow row, TNumseg seg, int offset=0) const

TSegTypeFlags	GetTypeAtAlnPos (TNumrow row, TSeqPos aln_pos) const

TSeqPos	GetAlnStart (TNumseg seg) const

TSeqPos	GetAlnStop (TNumseg seg) const

TSeqPos	GetAlnStart (void) const

TSeqPos	GetAlnStop (void) const

bool	IsSetAnchor (void) const

TNumrow	GetAnchor (void) const

void	SetAnchor (TNumrow anchor)

void	UnsetAnchor (void)

TNumseg	GetSeg (TSeqPos aln_pos) const

TNumseg	GetRawSeg (TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

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

TSignedSeqPos	GetSeqPosFromSeqPos (TNumrow for_row, TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

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

void	GetResidueIndexMap (TNumrow row0, TNumrow row1, TRange aln_rng, vector< TSignedSeqPos > &result, TRange &rng0, TRange &rng1) const

CRef< CAlnChunkVec >	GetAlnChunks (TNumrow row, const TSignedRange &range, TGetChunkFlags flags=fAlnSegsOnly) const

CRef< CAlnChunkVec >	GetSeqChunks (TNumrow row, const TSignedRange &range, TGetChunkFlags flags=fAlnSegsOnly) 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

Static Public Member Functions
static bool	IsTypeInsert (TSegTypeFlags type)

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 vector< TSegTypeFlags >	TRawSegTypes

Protected Member Functions
void	x_GetChunks (CAlnChunkVec *vec, TNumrow row, TNumseg left_seg, TNumseg right_seg, TGetChunkFlags flags) const

	CAlnMap (const CAlnMap &value)

CAlnMap &	operator= (const CAlnMap &value)

void	x_Init (void)

void	x_CreateAlnStarts (void)

TRawSegTypes &	x_GetRawSegTypes () const

TSegTypeFlags	x_GetRawSegType (TNumrow row, TNumseg seg, int hint_idx=-1) const

TSegTypeFlags	x_SetRawSegType (TNumrow row, TNumseg seg) const

void	x_SetRawSegTypes (TNumrow row) const

CNumSegWithOffset	x_GetSegFromRawSeg (TNumseg seg) const

TNumseg	x_GetRawSegFromSeg (TNumseg seg) const

TSignedSeqPos	x_GetRawStart (TNumrow row, TNumseg seg) const

TSignedSeqPos	x_GetRawStop (TNumrow row, TNumseg seg) const

TSeqPos	x_GetLen (TNumrow row, TNumseg seg) const

const TNumseg &	x_GetSeqLeftSeg (TNumrow row) const

const TNumseg &	x_GetSeqRightSeg (TNumrow row) const

TSignedSeqPos	x_FindClosestSeqPos (TNumrow row, TNumseg seg, ESearchDirection dir, bool try_reverse_dir) const

bool	x_SkipType (TSegTypeFlags type, TGetChunkFlags flags) const

bool	x_CompareAdjacentSegTypes (TSegTypeFlags left_type, TSegTypeFlags right_type, TGetChunkFlags flags) const

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Protected Attributes
CConstRef< CDense_seg >	m_DS

TNumrow	m_NumRows

TNumseg	m_NumSegs

const CDense_seg::TIds &	m_Ids

const CDense_seg::TStarts &	m_Starts

const CDense_seg::TLens &	m_Lens

const CDense_seg::TStrands &	m_Strands

const CDense_seg::TScores &	m_Scores

const CDense_seg::TWidths &	m_Widths

TNumrow	m_Anchor

vector< TNumseg >	m_AlnSegIdx

vector< TNumseg >	m_SeqLeftSegs

vector< TNumseg >	m_SeqRightSegs

CDense_seg::TStarts	m_AlnStarts

vector< CNumSegWithOffset >	m_NumSegWithOffsets

TRawSegTypes *	m_RawSegTypes

Private Types
typedef CObject	TParent

Friends
CConstRef< CAlnChunk >	CAlnChunkVec::operator[] (TNumchunk i) const

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

Definition at line 44 of file alnmap.hpp.

Member Typedef Documentation

◆ TDim

typedef CDense_seg::TDim CAlnMap::TDim

Definition at line 68 of file alnmap.hpp.

◆ TGetChunkFlags

typedef int CAlnMap::TGetChunkFlags

Definition at line 110 of file alnmap.hpp.

◆ TNumchunk

typedef TNumseg CAlnMap::TNumchunk

Definition at line 112 of file alnmap.hpp.

◆ TNumrow

typedef TDim CAlnMap::TNumrow

Definition at line 69 of file alnmap.hpp.

◆ TNumseg

typedef CDense_seg::TNumseg CAlnMap::TNumseg

Definition at line 72 of file alnmap.hpp.

◆ TParent

typedef CObject CAlnMap::TParent

private

Definition at line 46 of file alnmap.hpp.

◆ TRange

typedef CRange<TSeqPos> CAlnMap::TRange

Definition at line 70 of file alnmap.hpp.

◆ TRawSegTypes

typedef vector<TSegTypeFlags> CAlnMap::TRawSegTypes

protected

Definition at line 342 of file alnmap.hpp.

◆ TSegTypeFlags

typedef unsigned int CAlnMap::TSegTypeFlags

Definition at line 50 of file alnmap.hpp.

◆ TSeqPosList

typedef list<TSeqPos> CAlnMap::TSeqPosList

Definition at line 73 of file alnmap.hpp.

◆ TSignedRange

typedef CRange<TSignedSeqPos> CAlnMap::TSignedRange

Definition at line 71 of file alnmap.hpp.

Member Enumeration Documentation

◆ EGetChunkFlags

enum CAlnMap::EGetChunkFlags

Enumerator
fAllChunks
fIgnoreUnaligned
fInsertSameAsSeq
fDeletionSameAsGap
fIgnoreAnchor
fIgnoreGaps
fChunkSameAsSeg
fSkipUnalignedGaps
fSkipDeletions
fSkipAllGaps
fSkipInserts
fSkipAlnSeq
fSeqOnly
fInsertsOnly
fAlnSegsOnly
fDoNotTruncateSegs
fAddUnalignedChunks

Definition at line 76 of file alnmap.hpp.

◆ ESegmentTrimFlag

enum CAlnMap::ESegmentTrimFlag

Enumerator
eSegment_Include
eSegment_Trim
eSegment_Remove

Definition at line 120 of file alnmap.hpp.

◆ ESegTypeFlags

enum CAlnMap::ESegTypeFlags

Enumerator
fSeq
fNotAlignedToSeqOnAnchor
fInsert
fUnalignedOnRight
fUnalignedOnLeft
fNoSeqOnRight
fNoSeqOnLeft
fEndOnRight
fEndOnLeft
fUnaligned
fUnalignedOnRightOnAnchor
fUnalignedOnLeftOnAnchor
fTypeIsSet

Definition at line 51 of file alnmap.hpp.

Constructor & Destructor Documentation

◆ CAlnMap() [1/3]

CAlnMap::CAlnMap ( const CDense_seg & ds )

inline

Definition at line 428 of file alnmap.hpp.

References x_CreateAlnStarts(), and x_Init().

◆ CAlnMap() [2/3]

CAlnMap::CAlnMap	(	const CDense_seg &	ds,
		TNumrow	anchor
	)

inline

Definition at line 447 of file alnmap.hpp.

References SetAnchor(), and x_Init().

◆ ~CAlnMap()

CAlnMap::~CAlnMap ( void )

inline

Definition at line 466 of file alnmap.hpp.

References m_RawSegTypes.

◆ CAlnMap() [3/3]

CAlnMap::CAlnMap ( const CAlnMap & value )

protected

Member Function Documentation

◆ CreateAlignFromRange()

CRef< CSeq_align > CAlnMap::CreateAlignFromRange	(	const vector< TNumrow > &	selected_rows,
		TSignedSeqPos	aln_from,
		TSignedSeqPos	aln_to,
		ESegmentTrimFlag	seg_flag = `eSegment_Trim`
	)

◆ GetAlnChunks()

CRef< CAlnMap::CAlnChunkVec > CAlnMap::GetAlnChunks	(	TNumrow	row,
		const TSignedRange &	range,
		TGetChunkFlags	flags = `fAlnSegsOnly`
	)		const

Definition at line 1002 of file alnmap.cpp.

References fDoNotTruncateSegs, flags, GetAlnStart(), GetAlnStop(), GetNumSegs(), GetSeg(), m_NumSegs, compile_time_bits::range(), x_GetChunks(), and x_GetRawSegFromSeg().

Referenced by CAlnMapPrinter::Chunks(), CAlignFormatUtil::GetAlignLengths(), CAlnVec::GetAlnSeqString(), and CSampleAlnmgrApplication::Run().

◆ GetAlnPosFromSeqPos()

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

Definition at line 527 of file alnmap.cpp.

References delta(), IAlnExplorer::eBackwards, IAlnExplorer::eForward, IAlnExplorer::eLeft, IAlnExplorer::eNone, IAlnExplorer::eRight, CAlnMap::CNumSegWithOffset::GetAlnSeg(), GetAlnStart(), GetAlnStop(), GetNumSegs(), CAlnMap::CNumSegWithOffset::GetOffset(), GetRawSeg(), GetWidth(), IsPositiveStrand(), len, m_AlnStarts, m_Lens, m_NumRows, m_Starts, plus(), x_GetLen(), and x_GetSegFromRawSeg().

Referenced by s_GetGermlineTranslation(), s_MapSlaveFeatureToMaster(), s_MaskQuerySeq(), CAlnVwrApp::View10(), and CIgBlast::x_AnnotateDomain().

◆ GetAlnStart() [1/2]

TSeqPos CAlnMap::GetAlnStart ( TNumseg seg ) const

inline

Definition at line 481 of file alnmap.hpp.

References m_AlnStarts.

Referenced by CAlnPos_CI::CAlnPos_CI(), CAlnMap::CAlnChunkVec::operator[](), s_MaskQuerySeq(), CAlnMapPrinter::Segments(), CAlnVwrApp::View10(), and CAlnVwrApp::View7().

◆ GetAlnStart() [2/2]

TSeqPos CAlnMap::GetAlnStart ( void ) const

inline

Definition at line 177 of file alnmap.hpp.

Referenced by CreateAlignFromRange(), GetAlnChunks(), GetAlnPosFromSeqPos(), CAlnVec::GetColumnVector(), GetSeqAlnStart(), and GetSeqPosFromAlnPos().

◆ GetAlnStop() [1/2]

TSeqPos CAlnMap::GetAlnStop ( TNumseg seg ) const

inline

◆ GetAlnStop() [2/2]

TSeqPos CAlnMap::GetAlnStop ( void ) const

inline

Definition at line 495 of file alnmap.hpp.

References GetNumSegs().

Referenced by CreateAlignFromRange(), GetAlnChunks(), GetAlnPosFromSeqPos(), CAlnVec::GetColumnVector(), CAlnVec::GetResidue(), GetResidueIndexMap(), GetSeqAlnStop(), GetSeqPosFromAlnPos(), and CAlnVec::GetWholeAlnSeqString().

◆ GetAnchor()

CAlnMap::TNumrow CAlnMap::GetAnchor ( void ) const

inline

Definition at line 530 of file alnmap.hpp.

References m_Anchor.

Referenced by CAlnPos_CI::operator++(), and CAlnPos_CI::operator--().

◆ GetDenseg()

const CDense_seg & CAlnMap::GetDenseg ( void ) const

inline

Definition at line 475 of file alnmap.hpp.

References m_DS.

Referenced by CAlnVecPrinter::ClustalStyle(), CPhyTreeCalc::GetSeqAlign(), CPhyTreeCalc::GetSeqIds(), CAlnVecPrinter::PopsetStyle(), CPhyTreeCalc::SetQuery(), CPhyTreeCalc::x_CreateValidAlign(), CGff3Writer::xAssignAlignmentDensegGap(), CGff3Writer::xAssignAlignmentDensegScores(), and CGff3FlybaseWriter::xAssignAlignmentDensegScores().

◆ GetLen()

TSeqPos CAlnMap::GetLen	(	TNumseg	seg,
		int	offset = `0`
	)		const

inline

Definition at line 621 of file alnmap.hpp.

References m_Lens, offset, and x_GetRawSegFromSeg().

Referenced by CreateAlignFromRange(), CAlnMapPrinter::CsvTable(), CScoreBuilder::GetBlastScoreDenseg(), CAlnVec::GetColumnVector(), CAlnPos_CI::operator++(), CAlnPos_CI::operator--(), CAlnVwrApp::View7(), CGff3Writer::xAssignAlignmentDensegTarget(), and CGff3FlybaseWriter::xAssignAlignmentDensegTarget().

◆ GetNumRows()

CAlnMap::TDim CAlnMap::GetNumRows ( void ) const

inline

◆ GetNumSegs()

CAlnMap::TNumseg CAlnMap::GetNumSegs ( void ) const

inline

◆ GetRange()

CAlnMap::TSignedRange CAlnMap::GetRange	(	TNumrow	row,
		TNumseg	seg,
		int	offset = `0`
	)		const

inline

Definition at line 653 of file alnmap.hpp.

References GetSeqLen(), GetStart(), and offset.

Referenced by CTestSingleAln_All::RunTest(), CCIGAR_Formatter::x_FormatLine(), and CGff3Writer::xAssignAlignmentDensegGap().

◆ GetRawSeg()

CAlnMap::TNumseg CAlnMap::GetRawSeg	(	TNumrow	row,
		TSeqPos	seq_pos,
		ESearchDirection	dir = `eNone`,
		bool	try_reverse_dir = `true`
	)		const

Definition at line 400 of file alnmap.cpp.

References IAlnExplorer::eBackwards, IAlnExplorer::eForward, IAlnExplorer::eLeft, IAlnExplorer::eNone, IAlnExplorer::eRight, GetSeqStart(), GetSeqStop(), IsPositiveStrand(), last(), m_NumRows, m_NumSegs, m_Starts, plus(), and x_GetLen().

Referenced by GetAlnPosFromSeqPos(), GetSeqChunks(), and GetSeqPosFromSeqPos().

◆ GetResidueIndexMap()

void CAlnMap::GetResidueIndexMap	(	TNumrow	row0,
		TNumrow	row1,
		TRange	aln_rng,
		vector< TSignedSeqPos > &	result,
		TRange &	rng0,
		TRange &	rng1
	)		const

Definition at line 757 of file alnmap.cpp.

References _ASSERT, delta(), GetAlnStop(), CRange_Base::GetFrom(), CRange_Base::GetTo(), NStr::IntToString(), IsPositiveStrand(), IsSetAnchor(), m_Lens, m_NumRows, m_NumSegs, m_Starts, NCBI_THROW, result, CRange_Base::SetFrom(), CRange_Base::SetTo(), ncbi::grid::netcache::search::fields::size, and string.

Referenced by CAlnVwrApp::View9().

◆ GetSeg()

CAlnMap::TNumseg CAlnMap::GetSeg ( TSeqPos aln_pos ) const

Definition at line 373 of file alnmap.cpp.

References m_AlnStarts, m_Lens, and x_GetRawSegFromSeg().

Referenced by CAlnPos_CI::CAlnPos_CI(), CreateAlignFromRange(), GetAlnChunks(), CAlnVec::GetColumnVector(), CAlnVec::GetResidue(), GetSeqPosFromAlnPos(), GetTypeAtAlnPos(), and CIgBlast::x_AnnotateDomain().

◆ GetSegType()

CAlnMap::TSegTypeFlags CAlnMap::GetSegType	(	TNumrow	row,
		TNumseg	seg,
		int	offset = `0`
	)		const

inline

Definition at line 503 of file alnmap.hpp.

References offset, x_GetRawSegFromSeg(), and x_GetRawSegType().

Referenced by CBuildAlnVecJob::Build(), CAlnVec::GetColumnVector(), CAlnVec::GetResidue(), GetTypeAtAlnPos(), CAlnMapPrinter::Segments(), CCIGAR_Formatter::x_FormatLine(), and CGff3Writer::xAssignAlignmentDensegGap().

◆ GetSeqAlnRange()

CAlnMap::TSignedRange CAlnMap::GetSeqAlnRange ( TNumrow row ) const

inline

Definition at line 691 of file alnmap.hpp.

References GetSeqAlnStart(), and GetSeqAlnStop().

Referenced by CAlignFormatUtil::GetAlignLengths().

◆ GetSeqAlnStart()

TSignedSeqPos CAlnMap::GetSeqAlnStart ( TNumrow row ) const

Definition at line 969 of file alnmap.cpp.

References GetAlnStart(), IsSetAnchor(), m_AlnSegIdx, m_NumRows, m_Starts, and x_GetSeqLeftSeg().

Referenced by GetSeqAlnRange(), and s_SetAirrAlignmentInfo().

◆ GetSeqAlnStop()

TSignedSeqPos CAlnMap::GetSeqAlnStop ( TNumrow row ) const

Definition at line 985 of file alnmap.cpp.

References GetAlnStop(), IsSetAnchor(), m_AlnSegIdx, m_NumRows, m_Starts, and x_GetSeqRightSeg().

Referenced by GetSeqAlnRange(), and s_SetAirrAlignmentInfo().

◆ GetSeqChunks()

CRef< CAlnMap::CAlnChunkVec > CAlnMap::GetSeqChunks	(	TNumrow	row,
		const TSignedRange &	range,
		TGetChunkFlags	flags = `fAlnSegsOnly`
	)		const

Definition at line 1039 of file alnmap.cpp.

References fDoNotTruncateSegs, flags, GetRawSeg(), GetSeqStart(), GetSeqStop(), IsPositiveStrand(), m_NumSegs, compile_time_bits::range(), x_GetChunks(), x_GetRawStart(), and x_GetRawStop().

Referenced by COligoSpecificityCheck::x_NW_alignment().

◆ GetSeqId()

const CSeq_id & CAlnMap::GetSeqId ( TNumrow row ) const

inline

Definition at line 645 of file alnmap.hpp.

References m_Ids.

Referenced by CBuildAlnVecJob::Build(), CAlnMapPrinter::CAlnMapPrinter(), CDisplaySeqalign::DisplaySeqalign(), CAlnVec::GetBioseqHandle(), s_DoNWalign(), CCIGAR_Formatter::x_FormatDensegRows(), CCIGAR_Formatter::x_FormatLine(), CApplyRNAITSDlg::x_GetRow(), CCIGAR_Formatter::x_GetRowById(), CMultiAlnPrinter::x_PrintFastaPlusGaps(), CMultiAlnPrinter::x_PrintNexus(), CMultiAlnPrinter::x_PrintPhylipInterleaved(), CMultiAlnPrinter::x_PrintPhylipSequential(), CGff3Writer::xAssignAlignmentDensegGap(), CGff3Writer::xAssignAlignmentDensegMethod(), CGff3Writer::xAssignAlignmentDensegSeqId(), CGff3FlybaseWriter::xAssignAlignmentDensegSeqId(), CGff3Writer::xAssignAlignmentDensegTarget(), CGff3FlybaseWriter::xAssignAlignmentDensegTarget(), CGff3Writer::xAssignAlignmentDensegType(), and CGff3Writer::xWriteAlignDenseg().

◆ GetSeqLen()

TSeqPos CAlnMap::GetSeqLen	(	TNumrow	row,
		TNumseg	seg,
		int	offset = `0`
	)		const

inline

Definition at line 628 of file alnmap.hpp.

References offset, x_GetLen(), and x_GetRawSegFromSeg().

Referenced by GetRange(), and GetStop().

◆ GetSeqPosFromAlnPos()

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

Definition at line 663 of file alnmap.cpp.

References delta(), IAlnExplorer::eNone, GetAlnStart(), GetAlnStop(), GetSeg(), GetStart(), GetWidth(), IsPositiveStrand(), x_FindClosestSeqPos(), x_GetLen(), and x_GetRawSegFromSeg().

Referenced by CContigAssembly::BestLocalSubAlignment(), CAlnVec::GetResidue(), CApplyRNAITSDlg::GetRNAITSList_AlignCoordFromDlg(), CAlnVecPrinter::PopsetStyle(), CTestSingleAln_All::RunTest(), s_MapSlaveFeatureToMaster(), and CAlnVwrApp::View10().

◆ GetSeqPosFromSeqPos()

TSignedSeqPos CAlnMap::GetSeqPosFromSeqPos	(	TNumrow	for_row,
		TNumrow	row,
		TSeqPos	seq_pos,
		ESearchDirection	dir = `eNone`,
		bool	try_reverse_dir = `true`
	)		const