#include <objects/seqalign/Dense_seg.hpp>

Inheritance diagram for CDense_seg:

Collaboration diagram for CDense_seg:

Classes
class	CReserveHook

Public Types
typedef vector< int >	TWidths

Public Types inherited from CDense_seg_Base
enum class	E_memberIndex { e__allMandatory = 0 , e_dim , e_numseg , e_ids , e_starts , e_lens , e_strands , e_scores }

typedef int	TDim

typedef int	TNumseg

typedef vector< CRef< CSeq_id > >	TIds

typedef vector< TSignedSeqPos >	TStarts

typedef vector< TSeqPos >	TLens

typedef vector< ENa_strand >	TStrands

typedef vector< CRef< CScore > >	TScores

typedef Tparent::CMemberIndex< E_memberIndex, 8 >	TmemberIndex

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
	CDense_seg (void)

	~CDense_seg (void)

void	Assign (const CSerialObject &obj, ESerialRecursionMode how=eRecursive)
	overloaded Assign() More...

bool	IsSetWidths (void) const

bool	CanGetWidths (void) const

void	ResetWidths (void)

const TWidths &	GetWidths (void) const

TWidths &	SetWidths (void)

TDim	CheckNumRows (void) const

TNumseg	CheckNumSegs (void) const

void	Validate (bool full_test=false) const

CRange< TSeqPos >	GetSeqRange (TDim row) const

TSeqPos	GetSeqStart (TDim row) const

TSeqPos	GetSeqStop (TDim row) const

const CSeq_id &	GetSeq_id (TDim row) const

ENa_strand	GetSeqStrand (TDim row) const

void	Reverse (void)
	Reverse the segments' orientation. More...

void	SwapRows (TDim row1, TDim row2)
	Swap two rows (changing order, not content) More...

CRef< CDense_seg >	FillUnaligned () const
	Create a new dense-seg with added all unaligned pieces (implicit inserts), if any, between segments. More...

CRef< CDense_seg >	ExtractSlice (TDim row, TSeqPos from, TSeqPos to) const
	Extract a slice of the alignment that includes the specified range. More...

CRef< CDense_seg >	ExtractRows (const vector< TDim > &rows) const
	Extract specified rows of the alignment, in specified order. More...

void	Compact ()
	Join adjacent mergeable segments to create a more compact alignment. More...

void	OrderAdjacentGaps ()
	Order adjacent gaps, so that the side with sequence is in row-decending order. More...

void	RemovePureGapSegs ()
	Remove any segments in which every row has a gap (these can arise when ExtractRows is used) More...

void	TrimEndGaps ()
	Trim leading/training gaps if possible. More...

void	OffsetRow (TDim row, TSignedSeqPos offset)
	Offset row's coords. More...

void	RemapToLoc (TDim row, const CSeq_loc &loc, bool ignore_strand=false)

void	FromTranscript (TSeqPos query_start, ENa_strand query_strand, TSeqPos subj_start, ENa_strand subj_strand, const string &transcript)
	Initialize from pairwise alignment transcript (a string representation produced by CNWAligner) More...

CRef< CSeq_interval >	CreateRowSeq_interval (TDim row) const

Public Member Functions inherited from CDense_seg_Base
	CDense_seg_Base (void)

virtual	~CDense_seg_Base (void)

	DECLARE_INTERNAL_TYPE_INFO ()

bool	IsSetDim (void) const
	dimensionality Check if a value has been assigned to Dim data member. More...

bool	CanGetDim (void) const
	Check if it is safe to call GetDim method. More...

void	ResetDim (void)
	Reset Dim data member. More...

void	SetDefaultDim (void)
	Assign default value to Dim data member. More...

TDim	GetDim (void) const
	Get the Dim member data. More...

void	SetDim (TDim value)
	Assign a value to Dim data member. More...

TDim &	SetDim (void)
	Assign a value to Dim data member. More...

bool	IsSetNumseg (void) const
	number of segments here Check if a value has been assigned to Numseg data member. More...

bool	CanGetNumseg (void) const
	Check if it is safe to call GetNumseg method. More...

void	ResetNumseg (void)
	Reset Numseg data member. More...

TNumseg	GetNumseg (void) const
	Get the Numseg member data. More...

void	SetNumseg (TNumseg value)
	Assign a value to Numseg data member. More...

TNumseg &	SetNumseg (void)
	Assign a value to Numseg data member. More...

bool	IsSetIds (void) const
	sequences in order Check if a value has been assigned to Ids data member. More...

bool	CanGetIds (void) const
	Check if it is safe to call GetIds method. More...

void	ResetIds (void)
	Reset Ids data member. More...

const TIds &	GetIds (void) const
	Get the Ids member data. More...

TIds &	SetIds (void)
	Assign a value to Ids data member. More...

bool	IsSetStarts (void) const
	start OFFSETS in ids order within segs Check if a value has been assigned to Starts data member. More...

bool	CanGetStarts (void) const
	Check if it is safe to call GetStarts method. More...

void	ResetStarts (void)
	Reset Starts data member. More...

const TStarts &	GetStarts (void) const
	Get the Starts member data. More...

TStarts &	SetStarts (void)
	Assign a value to Starts data member. More...

bool	IsSetLens (void) const
	lengths in ids order within segs Check if a value has been assigned to Lens data member. More...

bool	CanGetLens (void) const
	Check if it is safe to call GetLens method. More...

void	ResetLens (void)
	Reset Lens data member. More...

const TLens &	GetLens (void) const
	Get the Lens member data. More...

TLens &	SetLens (void)
	Assign a value to Lens data member. More...

bool	IsSetStrands (void) const
	Check if a value has been assigned to Strands data member. More...

bool	CanGetStrands (void) const
	Check if it is safe to call GetStrands method. More...

void	ResetStrands (void)
	Reset Strands data member. More...

const TStrands &	GetStrands (void) const
	Get the Strands member data. More...

TStrands &	SetStrands (void)
	Assign a value to Strands data member. More...

bool	IsSetScores (void) const
	score for each seg Check if a value has been assigned to Scores data member. More...

bool	CanGetScores (void) const
	Check if it is safe to call GetScores method. More...

void	ResetScores (void)
	Reset Scores data member. More...

const TScores &	GetScores (void) const
	Get the Scores member data. More...

TScores &	SetScores (void)
	Assign a value to Scores data member. More...

virtual void	Reset (void)
	Reset the whole object. More...

Public Member Functions inherited from CSerialObject
	CSerialObject (void)

virtual	~CSerialObject (void)

virtual const CTypeInfo *	GetThisTypeInfo (void) const =0

virtual bool	Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
	Check if both objects contain the same values. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

void	ThrowUnassigned (TMemberIndex index) const

void	ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const

bool	HasNamespaceName (void) const
	Check if object data type has namespace name. More...

const string &	GetNamespaceName (void) const
	Get namespace name. More...

bool	HasNamespacePrefix (void) const
	Check if data type has namespace prefix. More...

const string &	GetNamespacePrefix (void) const
	Get namespace prefix. 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...

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	SetReserveHooks (CObjectIStream &in)

static void	SetGlobalReserveHooks (void)

Static Public Member Functions inherited from CSerialObject
static void	SetVerifyDataThread (ESerialVerifyData verify)

static void	SetVerifyDataGlobal (ESerialVerifyData verify)

static string	UnassignedString (void)

static CStringUTF8	UnassignedStringUTF8 (void)

static char	UnassignedByte (void)

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 Member Functions
TNumseg	x_FindSegment (TDim row, TSignedSeqPos pos) const

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

Private Types
typedef CDense_seg_Base	Tparent

Private Member Functions
	CDense_seg (const CDense_seg &value)

CDense_seg &	operator= (const CDense_seg &value)

Private Attributes
Uint4	m_set_State1 [1]

TWidths	m_Widths

Additional Inherited Members
Static Public Attributes inherited from CSerialObject
static const char *	ms_UnassignedStr = "<unassigned>"

static const char	ms_UnassignedByte = char(0xcd)

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 60 of file Dense_seg.hpp.

Member Typedef Documentation

◆ Tparent

typedef CDense_seg_Base CDense_seg::Tparent

private

Definition at line 62 of file Dense_seg.hpp.

◆ TWidths

typedef vector<int> CDense_seg::TWidths

Definition at line 73 of file Dense_seg.hpp.

Constructor & Destructor Documentation

◆ CDense_seg() [1/2]

CDense_seg::CDense_seg ( void )

◆ ~CDense_seg()

CDense_seg::~CDense_seg ( void )

Definition at line 57 of file Dense_seg.cpp.

◆ CDense_seg() [2/2]

CDense_seg::CDense_seg ( const CDense_seg & value )

private

Member Function Documentation

◆ Assign()

void CDense_seg::Assign	(	const CSerialObject &	obj,
		ESerialRecursionMode	how = `eRecursive`
	)

virtual

◆ CanGetWidths()

bool CDense_seg::CanGetWidths ( void ) const

inline

Definition at line 203 of file Dense_seg.hpp.

◆ CheckNumRows()

CDense_seg::TDim CDense_seg::CheckNumRows ( void ) const

Definition at line 92 of file Dense_seg.cpp.

References CDense_seg_Base::GetDim(), CDense_seg_Base::GetIds(), NCBI_THROW, and ncbi::grid::netcache::search::fields::size.

Referenced by CSeq_align::CheckNumRows(), ExtractRows(), FillUnaligned(), GetSeqStrand(), RemapToLoc(), RemovePureGapSegs(), and Validate().

◆ CheckNumSegs()

CDense_seg::TNumseg CDense_seg::CheckNumSegs ( void ) const

Definition at line 109 of file Dense_seg.cpp.

References CDense_seg_Base::GetDim(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), GetWidths(), and NCBI_THROW.

Referenced by BuildAlignDataSource(), ExtractRows(), FillUnaligned(), GetSeqStart(), GetSeqStop(), RemapToLoc(), RemovePureGapSegs(), and Validate().

◆ Compact()

void CDense_seg::Compact ( )

Join adjacent mergeable segments to create a more compact alignment.

Definition at line 432 of file Dense_seg.cpp.

References ASSERT_CONSISTENCY, eNa_strand_minus, CDense_seg_Base::GetDim(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), i, CDense_seg_Base::IsSetStrands(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), and ncbi::grid::netcache::search::fields::size.

Referenced by ExtractRows(), s_ExonToDenseg(), CMacroFunction_RemoveSegGaps::s_RemoveSegGaps(), s_TestAlignmentFromMSAs(), CInversionMergeAligner::x_CreateDiscAlignment(), CUnorderedSplitter::x_MakeAlignmentPairUnique(), and CTreeAlignMerger::x_MakeSeqAlign().

◆ CreateRowSeq_interval()

CRef< CSeq_interval > CDense_seg::CreateRowSeq_interval ( TDim row ) const

◆ ExtractRows()

CRef< CDense_seg > CDense_seg::ExtractRows ( const vector< TDim > & rows ) const

Extract specified rows of the alignment, in specified order.

The result is compacted with Compact, but may contain segments in which all rows have gaps, which can be removed with RemovePureGapSegs. The rows in the new alignment are in the order given by the rows parameter. Thus, this can also be used for permuting the order of rows.