shore::dp_multialigner_pipe< RefIter, QryIter, Scoring > Class Template Reference

Dynamic programming aligner (multiple reference sequences). More...

Inheritance diagram for shore::dp_multialigner_pipe< RefIter, QryIter, Scoring >:

Public Types
typedef dp_sequence< QryIter >	append_type
typedef dp_alignment< RefIter, QryIter, Scoring >	current_type
typedef buffer_chain < current_type >	buffer_chain_type
Public Types inherited from shore::pipe_facade< dp_multialigner_pipe< RefIter, QryIter, Scoring >, dp_sequence< QryIter >, dp_alignment< RefIter, QryIter, Scoring > >
typedef dp_sequence< QryIter >	append_type
typedef dp_alignment< RefIter, QryIter, Scoring >	current_type
Public Types inherited from shore::buffer_chain< dp_alignment< RefIter, QryIter, Scoring > >
typedef plugin< dp_alignment < RefIter, QryIter, Scoring > >	plugin_type

Public Member Functions
	dp_multialigner_pipe (const dp_aligner_config &c)
	Construct from end alignment modes.
	dp_multialigner_pipe (const dp_multialigner_pipe &other)
	~dp_multialigner_pipe ()
	Destructor.
void	add_ref (RefIter rb, RefIter re, const int id)
	Set the reference sequence.
const Scoring &	get_scoring () const
	Get the current scoring matrix.
void	set_scoring (const Scoring &matrix)
	Set the scoring matrix.
Public Member Functions inherited from shore::pipe_facade< dp_multialigner_pipe< RefIter, QryIter, Scoring >, dp_sequence< QryIter >, dp_alignment< RefIter, QryIter, Scoring > >
	pipe_facade (const pipe_facade &t)
	Copy constructor: need to bind the slots to the correct object.
void	disconnect_inputs ()
	Disconnect all connected upstream pipeline elements.
void	disconnect_outputs ()
	Disconnect all connected downstream pipeline elements.
signal< const dp_alignment < RefIter, QryIter, Scoring > & > &	sigdata ()
signal< void > &	sigflush ()
slot< const dp_sequence < QryIter > & > &	slotdata ()
slot< void > &	slotflush ()
slot< void > &	slotfreeze ()
slot< void > &	slotthaw ()
signal< void > &	sigfreeze ()
signal< void > &	sigthaw ()
Public Member Functions inherited from shore::buffer_chain< dp_alignment< RefIter, QryIter, Scoring > >
	buffer_chain ()
	Constructor - initialize empty buffer chain.
	~buffer_chain ()
	Destructor - free all buffers.
void	add_plugin (plugin_type *const p)
	Add a plugin object.
void	clear_plugins ()
	Remove all plugin objects.

Friends
class	pipeline_core_access

Additional Inherited Members
Protected Types inherited from shore::pipe_facade< dp_multialigner_pipe< RefIter, QryIter, Scoring >, dp_sequence< QryIter >, dp_alignment< RefIter, QryIter, Scoring > >
typedef pipe_facade < dp_multialigner_pipe < RefIter, QryIter, Scoring > , dp_sequence< QryIter > , dp_alignment< RefIter, QryIter, Scoring >, false >	facade_type
Protected Member Functions inherited from shore::pipe_facade< dp_multialigner_pipe< RefIter, QryIter, Scoring >, dp_sequence< QryIter >, dp_alignment< RefIter, QryIter, Scoring > >
void	emit (const dp_alignment< RefIter, QryIter, Scoring > &d)
	Called by derived classes to emit data to downstream pipeline elements. More...
Protected Member Functions inherited from shore::buffer_chain< dp_alignment< RefIter, QryIter, Scoring > >
bool	buffer_chain_ready () const
	Check if there is an element ready to be retrieved.
dp_alignment< RefIter, QryIter, Scoring > &	buffer_chain_push ()
	Get an empty buffer.
bool	buffer_chain_prepare ()
	Apply plugins after having initialized a new buffer.
bool	buffer_chain_flush (const bool undo_last_push)
	Indicate that no more data will be added. More...
const dp_alignment< RefIter, QryIter, Scoring > &	buffer_chain_front () const
	Get the contents of the first buffer.
bool	buffer_chain_waiting () const
	Check that the buffer chain is neither ready nor flushed.
bool	buffer_chain_pop ()
	Discard the buffer holding the first element.
void	buffer_chain_reset ()
	Clear all data and reset the state of the buffer chain.
dp_alignment< RefIter, QryIter, Scoring > *	buffer_chain_swap (dp_alignment< RefIter, QryIter, Scoring > *buf)
	Exchange the last pushed buffer with an external one. More...

Detailed Description

template<typename RefIter, typename QryIter = RefIter, typename Scoring = typename dp_traits<typename std::iterator_traits<RefIter>::value_type, typename std::iterator_traits<QryIter>::value_type>::scoring_type>
class shore::dp_multialigner_pipe< RefIter, QryIter, Scoring >

Dynamic programming aligner (multiple reference sequences).

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

• shore/algo/align.hpp