#include <genesis/population/window/interval_window_stream.hpp>

Inherits BaseWindowStream< InputStreamIterator, typename InputStreamIterator::value_type >.

Detailed Description

template<class InputStreamIterator, class DataType = typename InputStreamIterator::value_type>
class genesis::population::IntervalWindowStream< InputStreamIterator, DataType >

Stream for sliding Windows of fixed sized intervals over the chromosomes of a genome.

The three functors

have to be set in the class prior to starting the iteration, as well as the width(). All other settings are optional and/or defaulted to reasonable values. See make_interval_window_stream() and make_default_interval_window_stream() for helper functions that take care of this for most of our data types.

See BaseWindowStream for more details on the three functors, the template parameters, and general usage examples of the class.

See also: make_interval_window_stream(); make_default_interval_window_stream()

Definition at line 74 of file interval_window_stream.hpp.

Public Member Functions
	IntervalWindowStream (InputStreamIterator begin, InputStreamIterator end, size_t width=0, size_t stride=0)

	IntervalWindowStream (IntervalWindowStream &&)=default

	IntervalWindowStream (IntervalWindowStream const &)=default

virtual	~IntervalWindowStream () override=default

bool	emit_leading_empty_windows () const

self_type &	emit_leading_empty_windows (bool value)
	Select whether the iterator produces empty windows in the beginning of each chromosome, before the first actual position that is reported by the underlying data. More...

IntervalWindowStream &	operator= (IntervalWindowStream &&)=default

IntervalWindowStream &	operator= (IntervalWindowStream const &)=default

size_t	stride () const

self_type &	stride (size_t value)
	Stride of the Window, that is, how many positions to move forward with each iteration. More...

size_t	width () const

self_type &	width (size_t value)
	Width of the Window, that is, the fixed length along the chromosome. More...

Public Member Functions inherited from BaseWindowStream< InputStreamIterator, typename InputStreamIterator::value_type >
	BaseWindowStream (BaseWindowStream &&)=default

	BaseWindowStream (BaseWindowStream const &)=default

	BaseWindowStream (InputStreamIterator begin, InputStreamIterator end)

virtual	~BaseWindowStream ()=default

self_type &	add_begin_callback (std::function< void()> const &callback)
	Add a callback function that is executed when beginning the iteration. More...

self_type &	add_end_callback (std::function< void()> const &callback)
	Add a callback function that is executed when the end of the iteration is reached. More...

self_type &	add_on_enter_observer (std::function< void(typename ::genesis::population::Window< typename InputStreamIterator::value_type > const &)> const &observer)
	Add a observer function that is executed once for each window during the iteration, when entering the window during the iteration. More...

self_type &	add_on_leave_observer (std::function< void(typename ::genesis::population::Window< typename InputStreamIterator::value_type > const &)> const &observer)
	Add a observer function that is executed once for each window during the iteration, when leaving the window during the iteration. More...

Iterator	begin ()

self_type &	clear_callbacks ()
	Clear all functions that have been added via add_begin_callback() and add_end_callback(). More...

self_type &	clear_observers ()
	Clear all functions that are executed on incrementing to the next element. More...

Iterator	end ()

BaseWindowStream &	operator= (BaseWindowStream &&)=default

BaseWindowStream &	operator= (BaseWindowStream const &)=default

Public Types
using	base_type = BaseWindowStream< InputStreamIterator, DataType >

using	const_reference = value_type const &

using	Entry = typename Window::Entry

using	InputType = typename InputStreamIterator::value_type

using	iterator_category = std::input_iterator_tag

using	pointer = value_type *

using	reference = value_type &

using	self_type = IntervalWindowStream< InputStreamIterator, DataType >

using	value_type = Window

using	Window = ::genesis::population::Window< DataType >

Public Types inherited from BaseWindowStream< InputStreamIterator, typename InputStreamIterator::value_type >
using	const_reference = value_type const &

using	DataType = typename InputStreamIterator::value_type

using	InputStreamType = InputStreamIterator

using	InputType = typename InputStreamIterator::value_type

using	iterator_category = std::input_iterator_tag

using	pointer = value_type *

using	reference = value_type &

using	self_type = BaseWindowStream< InputStreamIterator, DataType, typename ::genesis::population::Window< typename InputStreamIterator::value_type > >

using	value_type = typename ::genesis::population::Window< typename InputStreamIterator::value_type >

Public Attributes
friend	DerivedIterator

Public Attributes inherited from BaseWindowStream< InputStreamIterator, typename InputStreamIterator::value_type >
std::function< std::string(InputType const &)>	chromosome_function
	Functor that yields the current chromosome, given the input stream data. More...

std::function< DataType(InputType const &)>	entry_input_function
	Functor to convert from the underlying input stream that provides the data to fill the windows to the data that is stored per window. More...

friend	Iterator

std::function< size_t(InputType const &)>	position_function
	Functor that yields the current position on the chromosome, given the input stream data. More...

Classes
class	DerivedIterator
	Internal iterator that produces Windows. More...

Protected Member Functions
std::unique_ptr< typename BaseWindowStream< InputStreamIterator, DataType >::BaseIterator >	get_begin_iterator_ () override final
	Get the begin iterator. More...

std::unique_ptr< typename BaseWindowStream< InputStreamIterator, DataType >::BaseIterator >	get_end_iterator_ () override final
	Get the end iterator. More...

Protected Member Functions inherited from BaseWindowStream< InputStreamIterator, typename InputStreamIterator::value_type >
	BaseWindowStream ()=default

Constructor & Destructor Documentation

◆ IntervalWindowStream() [1/3]

IntervalWindowStream	(	InputStreamIterator	begin,
		InputStreamIterator	end,
		size_t	width = `0`,
		size_t	stride = `0`
	)

inline

Definition at line 368 of file interval_window_stream.hpp.

◆ ~IntervalWindowStream()

virtual ~IntervalWindowStream ( )

overridevirtualdefault

◆ IntervalWindowStream() [2/3]

IntervalWindowStream ( IntervalWindowStream< InputStreamIterator, DataType > const & )

default

◆ IntervalWindowStream() [3/3]

IntervalWindowStream ( IntervalWindowStream< InputStreamIterator, DataType > && )

default

Member Function Documentation

◆ emit_leading_empty_windows() [1/2]

bool emit_leading_empty_windows ( ) const

inline

Definition at line 442 of file interval_window_stream.hpp.

◆ emit_leading_empty_windows() [2/2]

self_type& emit_leading_empty_windows ( bool value )

inline

Select whether the iterator produces empty windows in the beginning of each chromosome, before the first actual position that is reported by the underlying data.

Say the underlying iterator has the first Variant (or whatever datatype it iterates over) at position 1020 for a chromosome, and we use a window size of 100. If this setting is set to true, the iterator will emit 10 empty windows before reaching this position. If set to false, it will skip these, and start at position 1001, which is the first one that would have been reached by striding along the chromosome.

Definition at line 436 of file interval_window_stream.hpp.

◆ get_begin_iterator_()

std::unique_ptr<typename BaseWindowStream<InputStreamIterator, DataType>::BaseIterator> get_begin_iterator_ ( )

inlinefinaloverrideprotectedvirtual

Get the begin iterator.

Needs to be implemented by the derived class, to give the correct derived BaseIterator instance.

Implements BaseWindowStream< InputStreamIterator, typename InputStreamIterator::value_type >.

Definition at line 454 of file interval_window_stream.hpp.

◆ get_end_iterator_()

std::unique_ptr<typename BaseWindowStream<InputStreamIterator, DataType>::BaseIterator> get_end_iterator_ ( )

inlinefinaloverrideprotectedvirtual

Get the end iterator.

Needs to be implemented by the derived class, to give the correct derived BaseIterator instance.

Implements BaseWindowStream< InputStreamIterator, typename InputStreamIterator::value_type >.

Definition at line 463 of file interval_window_stream.hpp.

◆ operator=() [1/2]

IntervalWindowStream& operator= ( IntervalWindowStream< InputStreamIterator, DataType > && )

default

◆ operator=() [2/2]

IntervalWindowStream& operator= ( IntervalWindowStream< InputStreamIterator, DataType > const & )

default

◆ stride() [1/2]

size_t stride ( ) const

inline

Definition at line 421 of file interval_window_stream.hpp.

◆ stride() [2/2]

self_type& stride ( size_t value )

inline

Stride of the Window, that is, how many positions to move forward with each iteration.

The stride his is the shift towards the next interval, determining how the first and last position in each Window change. It has to be <= width. If stride is set to 0 (default), it is set automatically to the width when starting the iteration.

Definition at line 415 of file interval_window_stream.hpp.