Inheritance diagram for ymir::NoGapAlignmentVector:

Public Member Functions
bool	isMismatch (seq_len_t i, seq_len_t j) const

error_num_t	numMismatches (seq_len_t i, seq_len_t start, seq_len_t end) const


void	addAlignment (seg_index_t id, seq_len_t p_start, seq_len_t t_start, seq_len_t size)
	Add a new alignment to the vector. More...

void	addAlignment (seg_index_t id, seq_len_t p_start, seq_len_t t_start, const events_storage_t &vec)

Public Member Functions inherited from ymir::AlignmentVectorBase
bool	operator== (const AlignmentVectorBase &other)

bool	operator!= (const AlignmentVectorBase &other)

void	extend (const AlignmentVectorBase &other)

size_t	size () const

void	finish ()

void	clear ()

seq_len_t	pattern_start (seq_len_t i) const

seq_len_t	text_start (seq_len_t i) const

seq_len_t	len (seq_len_t i) const

seq_len_t	id (seq_len_t i) const

Additional Inherited Members
Public Types inherited from ymir::AlignmentVectorBase
typedef std::vector< bool >	events_storage_t

Static Public Attributes inherited from ymir::AlignmentVectorBase
static const size_t	default_start_reserve_size = 20

static const size_t	default_events_reserve_size = 600

Protected Attributes inherited from ymir::AlignmentVectorBase
std::vector< seq_len_t >	_data

events_storage_t	_events
	Vector of 4-tpuples - pattern start, text start, alignment length and a text ID.

std::vector< size_t >	_starts

Member Function Documentation

void ymir::NoGapAlignmentVector::addAlignment	(	seg_index_t	id,
		seq_len_t	p_start,
		seq_len_t	t_start,
		seq_len_t	size
	)

inline

Add a new alignment to the vector.

Parameters

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

Public Member Functions