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

Inherits BaseWindowStream< InputStreamIterator, typename InputStreamIterator::value_type, ::genesis::population::WindowView< typename InputStreamIterator::value_type > >.

Detailed Description

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

Stream for traversing each chromosome as a whole, with an inner WindowView iterator over the positions of each chromosome.

With each step of the iteration, an inner WindowView iterator is yielded that traverses all positions on a chromosome of the underlying input data stream. Then, when incrementing the main iterator, we move forward to the next chromosome.

This class is merely meant as a simplification over manually keeping track of the current chromosome, for example when computing a statistic for whole chromosomes, so that those algorithms do not need to take care of when to produce their output. Instead, they can simply use this class, and produce output at each step of the main iterator. This class contains a quite unfortunate amount of boiler plate, but hopefully makes downstream algorithms easier to write.

The three functors

have to be set in the class prior to starting the iteration for the chromosome iterator. See make_chromosome_window_stream() and make_default_chromosome_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. This class here however does not derive from the BaseWindowStream over normal Windows, but behaves in a similar way - with the exception that it does not produce Windows in each step of the iteration, as we do not want to keep the positions of a whole chromosome in memory. Hence, instead, it yields a WindowView iterator, directly streaming over the positions of the chromosome, without keeping all data in memory.

See also: make_chromosome_window_stream(); make_default_chromosome_window_stream()

Definition at line 90 of file chromosome_window_stream.hpp.

Public Member Functions
	ChromosomeWindowStream (ChromosomeWindowStream &&)=default

	ChromosomeWindowStream (ChromosomeWindowStream const &)=default

	ChromosomeWindowStream (InputStreamIterator begin, InputStreamIterator end)

virtual	~ChromosomeWindowStream () override=default

ChromosomeWindowStream &	operator= (ChromosomeWindowStream &&)=default

ChromosomeWindowStream &	operator= (ChromosomeWindowStream const &)=default

std::shared_ptr< genesis::sequence::SequenceDict >	sequence_dict () const
	Get the currently set sequence dictionary used for the chromosome lengths. More...

self_type &	sequence_dict (std::shared_ptr< genesis::sequence::SequenceDict > value)
	Set a sequence dictionary to be used for the chromosome lengths. More...

Public Member Functions inherited from BaseWindowStream< InputStreamIterator, typename InputStreamIterator::value_type, ::genesis::population::WindowView< 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(::genesis::population::WindowView< 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(::genesis::population::WindowView< 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, WindowViewType >

using	const_reference = value_type const &

using	InputType = typename InputStreamIterator::value_type

using	iterator_category = std::input_iterator_tag

using	pointer = value_type *

using	reference = value_type &

using	self_type = ChromosomeWindowStream< InputStreamIterator, DataType >

using	value_type = WindowViewType

using	WindowViewType = ::genesis::population::WindowView< DataType >

Public Types inherited from BaseWindowStream< InputStreamIterator, typename InputStreamIterator::value_type, ::genesis::population::WindowView< 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, ::genesis::population::WindowView< typename InputStreamIterator::value_type > >

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

Public Attributes
friend	DerivedIterator

Public Attributes inherited from BaseWindowStream< InputStreamIterator, typename InputStreamIterator::value_type, ::genesis::population::WindowView< 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 WindowViews. More...

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

std::unique_ptr< typename base_type::BaseIterator >	get_end_iterator_ () override final
	Get the end iterator. More...

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

Constructor & Destructor Documentation

◆ ChromosomeWindowStream() [1/3]

ChromosomeWindowStream	(	InputStreamIterator	begin,
		InputStreamIterator	end
	)

inline

Definition at line 362 of file chromosome_window_stream.hpp.

◆ ~ChromosomeWindowStream()

virtual ~ChromosomeWindowStream ( )

overridevirtualdefault

◆ ChromosomeWindowStream() [2/3]

ChromosomeWindowStream ( ChromosomeWindowStream< InputStreamIterator, DataType > const & )

default

◆ ChromosomeWindowStream() [3/3]

ChromosomeWindowStream ( ChromosomeWindowStream< InputStreamIterator, DataType > && )

default

Member Function Documentation

◆ get_begin_iterator_()

std::unique_ptr<typename base_type::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, ::genesis::population::WindowView< typename InputStreamIterator::value_type > >.

Definition at line 414 of file chromosome_window_stream.hpp.

◆ get_end_iterator_()

std::unique_ptr<typename base_type::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, ::genesis::population::WindowView< typename InputStreamIterator::value_type > >.

Definition at line 423 of file chromosome_window_stream.hpp.

◆ operator=() [1/2]

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

default

◆ operator=() [2/2]

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

default

◆ sequence_dict() [1/2]

std::shared_ptr<genesis::sequence::SequenceDict> sequence_dict ( ) const

inline

Get the currently set sequence dictionary used for the chromosome lengths.

Definition at line 385 of file chromosome_window_stream.hpp.

◆ sequence_dict() [2/2]

self_type& sequence_dict ( std::shared_ptr< genesis::sequence::SequenceDict > value )

inline

Set a sequence dictionary to be used for the chromosome lengths.

By default, we use the chromosome positions as given in the data to set the Window first and last positions. When setting a SequenceDict here, we use lengths as provided instead, throwing an exception should the dict not contain a chromosome of the input.

To un-set the dictionary, simply call this function with a nullptr.

Definition at line 401 of file chromosome_window_stream.hpp.