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

Inherits BaseWindowIterator< ForwardIterator, typename ForwardIterator::value_type >.

Detailed Description

template<class ForwardIterator, class DataType = typename ForwardIterator::value_type>
class genesis::population::SlidingIntervalWindowIterator< ForwardIterator, DataType >

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

Definition at line 66 of file sliding_interval_window_iterator.hpp.

Public Member Functions
	SlidingIntervalWindowIterator (ForwardIterator begin, ForwardIterator end)

	SlidingIntervalWindowIterator (SlidingIntervalWindowIterator &&)=default

	SlidingIntervalWindowIterator (SlidingIntervalWindowIterator const &)=default

	~SlidingIntervalWindowIterator ()=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...

SlidingIntervalWindowIterator &	operator= (SlidingIntervalWindowIterator &&)=default

SlidingIntervalWindowIterator &	operator= (SlidingIntervalWindowIterator 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 BaseWindowIterator< ForwardIterator, typename ForwardIterator::value_type >
	BaseWindowIterator (BaseWindowIterator &&)=default

	BaseWindowIterator (BaseWindowIterator const &)=default

	BaseWindowIterator (ForwardIterator begin, ForwardIterator end)

	~BaseWindowIterator ()=default

Iterator	begin ()

Iterator	end ()

BaseWindowIterator &	operator= (BaseWindowIterator &&)=default

BaseWindowIterator &	operator= (BaseWindowIterator const &)=default

Public Types
using	base_type = BaseWindowIterator< ForwardIterator, DataType >

using	const_reference = value_type const &

using	Entry = typename Window::Entry

using	InputType = typename ForwardIterator::value_type

using	iterator_category = std::input_iterator_tag

using	pointer = value_type *

using	reference = value_type &

using	self_type = SlidingIntervalWindowIterator< ForwardIterator, DataType >

using	value_type = Window

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

Public Types inherited from BaseWindowIterator< ForwardIterator, typename ForwardIterator::value_type >
using	const_reference = value_type const &

using	Entry = typename Window::Entry

using	InputType = typename ForwardIterator::value_type

using	iterator_category = std::input_iterator_tag

using	pointer = value_type *

using	reference = value_type &

using	self_type = BaseWindowIterator< ForwardIterator, typename ForwardIterator::value_type >

using	value_type = Window

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

Public Attributes
friend	DerivedIterator

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

std::function< typename ForwardIterator::value_type(InputType const &)>	entry_input_function
	Functor to convert from the underlying input iterator 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 iterator data. More...

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

Protected Member Functions
std::unique_ptr< typename BaseWindowIterator< ForwardIterator, DataType >::BaseIterator >	get_begin_iterator_ () override final

std::unique_ptr< typename BaseWindowIterator< ForwardIterator, DataType >::BaseIterator >	get_end_iterator_ () override final

Constructor & Destructor Documentation

◆ SlidingIntervalWindowIterator() [1/3]

SlidingIntervalWindowIterator	(	ForwardIterator	begin,
		ForwardIterator	end
	)

inline

Definition at line 344 of file sliding_interval_window_iterator.hpp.

◆ ~SlidingIntervalWindowIterator()

~SlidingIntervalWindowIterator ( )

default

◆ SlidingIntervalWindowIterator() [2/3]

SlidingIntervalWindowIterator ( SlidingIntervalWindowIterator< ForwardIterator, DataType > const & )

default

◆ SlidingIntervalWindowIterator() [3/3]

SlidingIntervalWindowIterator ( SlidingIntervalWindowIterator< ForwardIterator, DataType > && )

default

Member Function Documentation

◆ emit_leading_empty_windows() [1/2]

bool emit_leading_empty_windows ( ) const

inline

Definition at line 415 of file sliding_interval_window_iterator.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 409 of file sliding_interval_window_iterator.hpp.

◆ get_begin_iterator_()

std::unique_ptr<typename BaseWindowIterator<ForwardIterator, DataType>::BaseIterator> get_begin_iterator_ ( )

inlinefinaloverrideprotectedvirtual

Implements BaseWindowIterator< ForwardIterator, typename ForwardIterator::value_type >.

Definition at line 427 of file sliding_interval_window_iterator.hpp.

◆ get_end_iterator_()

std::unique_ptr<typename BaseWindowIterator<ForwardIterator, DataType>::BaseIterator> get_end_iterator_ ( )

inlinefinaloverrideprotectedvirtual

Implements BaseWindowIterator< ForwardIterator, typename ForwardIterator::value_type >.

Definition at line 436 of file sliding_interval_window_iterator.hpp.

◆ operator=() [1/2]

SlidingIntervalWindowIterator& operator= ( SlidingIntervalWindowIterator< ForwardIterator, DataType > && )

default

◆ operator=() [2/2]

SlidingIntervalWindowIterator& operator= ( SlidingIntervalWindowIterator< ForwardIterator, DataType > const & )

default

◆ stride() [1/2]

size_t stride ( ) const

inline

Definition at line 394 of file sliding_interval_window_iterator.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 388 of file sliding_interval_window_iterator.hpp.