Detailed Description

template<class ForwardIterator, class DataType = typename ForwardIterator::value_type>
class genesis::population::SlidingVariantsWindowIterator< 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_variants_window_iterator.hpp.

Public Member Functions
	SlidingVariantsWindowIterator (ForwardIterator begin, ForwardIterator end)

	SlidingVariantsWindowIterator (SlidingVariantsWindowIterator &&)=default

	SlidingVariantsWindowIterator (SlidingVariantsWindowIterator const &)=default

	~SlidingVariantsWindowIterator ()=default

SlidingVariantsWindowIterator &	operator= (SlidingVariantsWindowIterator &&)=default

SlidingVariantsWindowIterator &	operator= (SlidingVariantsWindowIterator 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 = SlidingVariantsWindowIterator< 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

◆ SlidingVariantsWindowIterator() [1/3]

SlidingVariantsWindowIterator	(	ForwardIterator	begin,
		ForwardIterator	end
	)

inline

Definition at line 248 of file sliding_variants_window_iterator.hpp.

◆ ~SlidingVariantsWindowIterator()

~SlidingVariantsWindowIterator ( )

default

◆ SlidingVariantsWindowIterator() [2/3]

SlidingVariantsWindowIterator ( SlidingVariantsWindowIterator< ForwardIterator, DataType > const & )

default

◆ SlidingVariantsWindowIterator() [3/3]

SlidingVariantsWindowIterator ( SlidingVariantsWindowIterator< ForwardIterator, DataType > && )

default

Member Function Documentation

◆ 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 310 of file sliding_variants_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 319 of file sliding_variants_window_iterator.hpp.

◆ operator=() [1/2]

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

default

◆ operator=() [2/2]

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

default

◆ stride() [1/2]

size_t stride ( ) const

inline

Definition at line 298 of file sliding_variants_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 292 of file sliding_variants_window_iterator.hpp.