Matrix representation of an alignment. More...

Public Member Functions
	dp_alignment_matrix ()
	Constructor: init scoring matrix and alignment matrix maxima.

void	reset_maxima ()
	Clear recorded score maxima.

void	resize (const size_t ref_size, const size_t qry_size)
	Change the size.

int	get_score (const AlignmentMode right_ends) const
	Get the score given the right ends would be aligned accordingly.

size_t	num_global_max () const
	Number of fields with the global maximum score (i.e. locally aligned right ends).

size_t	num_ref_max () const
	Number of fields with the maximum score for a globally aligned (right end) reference.

size_t	num_qry_max () const
	Number of fields with the maximum score for a globally aligned (right end) query.

int	global_max () const
	Get the global maximum score (i.e. locally aligned right ends).

int	ref_max () const
	Get the maximum score for a globally (right end) reference.

int	qry_max () const
	Get the maximum score for a globally (right end) query.

iterator	begin ()

const_iterator	last () const
	Get the iterator to the field in the lower right corner.

const_iterator	global_max_pos (size_t index) const
	Get an iterator to a field with the global maximum value.

const_iterator	ref_max_pos (size_t index) const
	Get an iterator to a field with the reference maximum value.

const_iterator	qry_max_pos (size_t index) const
	Get an iterator to a field with the query maximum value.

template<typename RefIter , typename QryIter >
void	print (std::ostream &os, RefIter ir, QryIter iq) const
	Print.

Detailed Description

Matrix representation of an alignment.

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

Public Member Functions