Search Toolkit Book for UngappedAlignedBlock

#include <algo/structure/struct_util/su_block_multiple_alignment.hpp>

Inheritance diagram for UngappedAlignedBlock:

Collaboration diagram for UngappedAlignedBlock:

Public Member Functions
	UngappedAlignedBlock (const BlockMultipleAlignment *multiple)

bool	IsAligned (void) const

unsigned int	GetIndexAt (unsigned int blockColumn, unsigned int row, BlockMultipleAlignment::eUnalignedJustification justification=BlockMultipleAlignment::eCenter) const

char	GetCharacterAt (unsigned int blockColumn, unsigned int row) const

void	DeleteRow (unsigned int row)

void	DeleteRows (std::vector< bool > &removeRows, unsigned int nToRemove)

Block *	Clone (const BlockMultipleAlignment *newMultiple) const

	UngappedAlignedBlock (const BlockMultipleAlignment *multiple)

bool	IsAligned (void) const

int	GetIndexAt (unsigned int blockColumn, unsigned int row, BlockMultipleAlignment::eUnalignedJustification justification=BlockMultipleAlignment::eCenter) const

char	GetCharacterAt (unsigned int blockColumn, unsigned int row) const

void	DeleteRow (unsigned int row)

void	DeleteRows (std::vector< bool > &removeRows, unsigned int nToRemove)

Block *	Clone (const BlockMultipleAlignment *newMultiple) const

Public Member Functions inherited from Block
	Block ()

	Block (const Block &rhs)

	Block (int start, int len, int id)

	Block (int start, int len)

const Block &	operator= (const Block &rhs)

bool	operator< (const Block rhs) const

bool	operator== (const Block &rhs) const

bool	operator!= (const Block &rhs) const

bool	contain (const Block &rhs) const

bool	isIntersecting (const Block &rhs) const

bool	intersect (Block &rhs) const

Block	operator+ (const DeltaBlock &deltaBlock) const

DeltaBlock	operator- (const Block &object) const

int	getLen () const

int	getStart () const

int	getEnd () const

void	setEnd (int end)

int	getId () const

void	setId (int id)

Block	extend (int nExt, int cExt) const

void	extendSelf (int nExt, int cExt)

void	addOffset (int nExt)

bool	isValid () const

virtual	~Block (void)

bool	IsFrom (const BlockMultipleAlignment *alignment) const

const Range *	GetRangeOfRow (int row) const

void	SetRangeOfRow (unsigned int row, int from, int to)

void	AddRows (unsigned int nNewRows)

unsigned int	NSequences (void) const

bool	ReorderRows (const std::vector< unsigned int > &newOrder)

virtual	~Block (void)

bool	IsFrom (const BlockMultipleAlignment *alignment) const

const Range *	GetRangeOfRow (unsigned int row) const

void	SetRangeOfRow (unsigned int row, int from, int to)

void	AddRows (unsigned int nNewRows)

unsigned int	NSequences (void) const

Additional Inherited Members
Public Types inherited from Block
typedef set< Block >	SortedBlocks

Static Public Member Functions inherited from Block
static bool	concatenate (const SortedBlocks &blocks, Block &comBlock)

Public Attributes inherited from Block
unsigned int	m_width

unsigned int	width

Protected Types inherited from Block
typedef std::vector< Range >	RangeList

typedef std::vector< Range >	RangeList

Protected Member Functions inherited from Block
	Block (const BlockMultipleAlignment *multiple)

	Block (const BlockMultipleAlignment *multiple)

Protected Attributes inherited from Block
const BlockMultipleAlignment *	m_parentAlignment

RangeList	m_ranges

RangeList	ranges

const BlockMultipleAlignment *	parentAlignment

Detailed Description

Definition at line 320 of file su_block_multiple_alignment.hpp.

Constructor & Destructor Documentation

◆ UngappedAlignedBlock() [1/2]

UngappedAlignedBlock::UngappedAlignedBlock ( const BlockMultipleAlignment * multiple )

inline

Definition at line 323 of file su_block_multiple_alignment.hpp.

Referenced by Clone().

◆ UngappedAlignedBlock() [2/2]

UngappedAlignedBlock::UngappedAlignedBlock ( const BlockMultipleAlignment * multiple )

inline

Definition at line 393 of file block_multiple_alignment.hpp.

Member Function Documentation

◆ Clone() [1/2]

Block * UngappedAlignedBlock::Clone ( const BlockMultipleAlignment * newMultiple ) const

virtual

Implements Block.

Definition at line 1363 of file su_block_multiple_alignment.cpp.

References copy(), Block::GetRangeOfRow(), Block::m_width, Block::NSequences(), compile_time_bits::range(), row, and UngappedAlignedBlock().

◆ Clone() [2/2]

Block* UngappedAlignedBlock::Clone ( const BlockMultipleAlignment * newMultiple ) const

virtual

Implements Block.

◆ DeleteRow() [1/2]

void UngappedAlignedBlock::DeleteRow ( unsigned int row )

virtual

Implements Block.

Definition at line 1375 of file su_block_multiple_alignment.cpp.

References i, Block::m_ranges, r(), and row.

◆ DeleteRow() [2/2]

void UngappedAlignedBlock::DeleteRow ( unsigned int row )

virtual

Implements Block.

◆ DeleteRows() [1/2]

void UngappedAlignedBlock::DeleteRows	(	std::vector< bool > &	removeRows,
		unsigned int	nToRemove
	)

virtual

Implements Block.

Definition at line 1383 of file su_block_multiple_alignment.cpp.

References Block::m_ranges, and VectorRemoveElements().

◆ DeleteRows() [2/2]

void UngappedAlignedBlock::DeleteRows	(	std::vector< bool > &	removeRows,
		unsigned int	nToRemove
	)

virtual

Implements Block.

◆ GetCharacterAt() [1/2]

char UngappedAlignedBlock::GetCharacterAt	(	unsigned int	blockColumn,
		unsigned int	row
	)		const

Definition at line 1358 of file su_block_multiple_alignment.cpp.

References GetIndexAt(), BlockMultipleAlignment::GetSequenceOfRow(), Block::m_parentAlignment, Sequence::m_sequenceString, and row.

◆ GetCharacterAt() [2/2]

char UngappedAlignedBlock::GetCharacterAt	(	unsigned int	blockColumn,
		unsigned int	row
	)		const

◆ GetIndexAt() [1/2]

unsigned int UngappedAlignedBlock::GetIndexAt	(	unsigned int	blockColumn,
		unsigned int	row,
		BlockMultipleAlignment::eUnalignedJustification	justification = `BlockMultipleAlignment::eCenter`
	)		const

inlinevirtual

Implements Block.

Definition at line 327 of file su_block_multiple_alignment.hpp.

References Block::GetRangeOfRow(), and row.

Referenced by GetCharacterAt().

◆ GetIndexAt() [2/2]

int UngappedAlignedBlock::GetIndexAt	(	unsigned int	blockColumn,
		unsigned int	row,
		BlockMultipleAlignment::eUnalignedJustification	justification = `BlockMultipleAlignment::eCenter`
	)		const