CAlignRange Represents an element of pairwise alignment of two sequences. More...

#include <util/align_range.hpp>

Public Types
enum	EFlags { fReversed = 0x01 , fFirstRev = 0x02 }

typedef Position	position_type

typedef CAlignRange< Position >	TThisType

typedef CRange< Position >	TRange

Public Member Functions
	CAlignRange (void)

	CAlignRange (position_type first_from, position_type second_from, position_type len, bool direct=true, bool first_direct=true)

bool	IsDirect () const

bool	IsReversed () const

bool	IsFirstDirect () const

bool	IsFirstReversed () const

position_type	GetFirstFrom (void) const

position_type	GetFirstToOpen (void) const

position_type	GetFirstTo (void) const

position_type	GetSecondFrom (void) const

position_type	GetSecondToOpen (void) const

position_type	GetSecondTo (void) const

TRange	GetFirstRange () const

TRange	GetSecondRange () const

bool	Empty (void) const

bool	NotEmpty (void) const

position_type	GetLength (void) const

TThisType &	SetFirstFrom (position_type from)

TThisType &	SetSecondFrom (position_type second_from)

TThisType &	SetLength (position_type len)

TThisType &	Set (position_type first_from, position_type second_from, position_type len)

void	SetDirect (bool direct=true)

void	SetReversed (bool reversed=true)

void	SetFirstDirect (bool direct=true)

void	SetFirstReversed (bool reversed=true)

bool	operator== (const TThisType &r) const

bool	operator!= (const TThisType &r) const

position_type	GetSecondPosByFirstPos (position_type pos) const

position_type	GetFirstPosBySecondPos (position_type pos) const

bool	FirstContains (position_type pos) const

bool	SecondContains (position_type pos) const

TThisType	IntersectionWith (const CRange< position_type > &r) const
	Intersection. More...

TThisType &	IntersectWith (const CRange< position_type > &r)

TThisType &	IntersectSecondWith (const CRange< position_type > &r)

bool	IntersectingWith (const CRange< position_type > &r) const

bool	IsAbutting (const TThisType &r) const

TThisType &	CombineWithAbutting (const TThisType &r)

TThisType	CombinationWithAbutting (const TThisType &r) const

Static Public Member Functions
static position_type	GetEmptyFrom (void)

static position_type	GetEmptyToOpen (void)

static position_type	GetEmptyTo (void)

static position_type	GetEmptyLength (void)

static TThisType	GetEmpty (void)

static position_type	GetPositionMin (void)

static position_type	GetPositionMax (void)

Private Attributes
position_type	m_FirstFrom

position_type	m_SecondFrom
	start More...

position_type	m_Length
	start on the aligned sequence More...

int	m_Flags
	length of the segment More...

Detailed Description

template<class Position>
class CAlignRange< Position >

CAlignRange Represents an element of pairwise alignment of two sequences.

CAlignRange := [from_1, to_open_1), [from_2, to_open_2), direction where: from_1 <= to_open_1, from_2 <= to_open_2 (to_open_1 - from_1) == (to_open_2 - from_2) mapping: if direct from_1 -> from_2, to_1 -> to_2 if reversed from_1 -> to_2, to_1 -> from_2

Definition at line 62 of file align_range.hpp.

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

include/util/align_range.hpp

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

template<class Position> class CAlignRange< Position >

template<class Position>
class CAlignRange< Position >