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

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

Detailed Description

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

Stream for Windows contaiing a queue of entries, i.e., sliding Windows of a fixed number of selected positions in a genome.

With each step of the iteration, a window of entries of the underlying input stream is yielded. The window contains count() many selected entries (entries that we want to consider), which is based on the result of the user-provided entry_selection_function() functor. Any entries of the underlying stream for which entry_selection_function() returns false are still included in the windows, but do not count towards the total count() of entries that we want in the window. This is meant as a way for instance to create windows of n SNP positions, while also being able to retain all non-SNP entries, if they are needed for the downstream algorithm that is using the windows.

If no such extra positions should be included in the window (e.g., if we only want the SNPs), an approriate filter needs to be applied beforhand to the input stream, for instance by adding it to the VariantInputStream that is typically used as input stream here, so that these entries are removed already before being assembled into windows here.

The way the windowing then works is as follows: Any window contains count() many selected entries, as well as all not-selected entries that come before each of these selected entries. For instance, x marking selected (for which entry_selection_function returns true), and - marking non-selected entries, and with non-overlapping windows of size 2 (stride == count == 2), we get the following windows:

---x--x---x-xx---x-xx-x--x----x-x-x---x--
[     ][    ][   ][ ][   ][     ][      ]

where brackets mark each window as a closed interval. This is only considering entries based on them being selected or not - their position on the chromosome is not considerered here at all, which also means that any missing data does not affect this - it will just appear as jumps in the positions when iterating the windows, but as this windowing approach here is not based on these positions, there is no other effect.

Notice the special last case here: the last window also contains the trailing non-selected positions. This is done so that these positions are part of some window. This is also the case if the last window contains fewer entries than the count(), which happens if the number of selected entries in the chromosome is not a multiple of the count() (which is very likely).

The default helper functions to make an instance of this window stream, make_default_queue_window_stream() and make_default_queue_window_view_stream() set the entry_selection_function() so that all entries are selected. On the other hand, the specialized versions of these functions for underlying data of type Variant, make_passing_variant_queue_window_stream() and make_passing_variant_queue_window_view_stream() instead set the entry_selection_function() so that only Variants are selected for which the Variant::status is passing. Thus, for instance, if the underlying data stream has filters applied to it using the VariantFilterNumericalParams, this can be used to filter for SNPs. See there for details.

During the stream iteration, when incrementing the iterator, we move forward stride() many entries, which can correspond to an arbitrary number of positions in the genome, depending on how far the entries are spread out. Hence, any filtering on positions in the genome should be done beforehand on the inputs, so that only those entries are used by this stream that are meant to be selected.

The four functors

have to be set in the class prior to starting the iteration, as well as the count() of how many entries shall be used in each iteration. All other settings are optional and/or defaulted to reasonable values.

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

For helper functions that take care of setting up this class for the most common use cases:

See also: make_queue_window_stream(); make_default_queue_window_stream(); make_default_queue_window_view_stream(); make_passing_variant_queue_window_stream(); make_passing_variant_queue_window_view_stream()

Definition at line 131 of file queue_window_stream.hpp.

Public Member Functions
	QueueWindowStream (InputStreamIterator begin, InputStreamIterator end, size_t count=0, size_t stride=0)

	QueueWindowStream (QueueWindowStream &&)=default

	QueueWindowStream (QueueWindowStream const &)=default

virtual	~QueueWindowStream () override=default

size_t	count () const

self_type &	count (size_t value)
	Number of selected entries in each Window. More...

QueueWindowStream &	operator= (QueueWindowStream &&)=default

QueueWindowStream &	operator= (QueueWindowStream const &)=default

size_t	stride () const

self_type &	stride (size_t value)
	Stride of the Window, that is, how many entries to move forward with each iteration. 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 = QueueWindowStream< 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

std::function< bool(InputType const &)>	entry_selection_function
	Functor that takes an entry of the underlying input stream and returns whether that entry should be selected towards the window size count() or not. More...

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

◆ QueueWindowStream() [1/3]

QueueWindowStream	(	InputStreamIterator	begin,
		InputStreamIterator	end,
		size_t	count = `0`,
		size_t	stride = `0`
	)

inline

Definition at line 715 of file queue_window_stream.hpp.

◆ ~QueueWindowStream()

virtual ~QueueWindowStream ( )

overridevirtualdefault

◆ QueueWindowStream() [2/3]

QueueWindowStream ( QueueWindowStream< InputStreamIterator, DataType > const & )

default

◆ QueueWindowStream() [3/3]

QueueWindowStream ( QueueWindowStream< InputStreamIterator, DataType > && )

default

Member Function Documentation

◆ count() [1/2]

size_t count ( ) const

inline

Definition at line 752 of file queue_window_stream.hpp.

◆ count() [2/2]

self_type& count ( size_t value )

inline

Number of selected entries in each Window.

The count has to be > 0. This is the number of selected entries that are put into each Window. Typically, we process, e.g., variant positions only - in that case, the count() is the number of Variants in each Window. This depends on the entry_selection_function(), see there for details on how the selection of entries works.

Definition at line 746 of file queue_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 784 of file queue_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 793 of file queue_window_stream.hpp.

◆ operator=() [1/2]

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

default

◆ operator=() [2/2]

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

default

◆ stride() [1/2]

size_t stride ( ) const

inline

Definition at line 772 of file queue_window_stream.hpp.

◆ stride() [2/2]

self_type& stride ( size_t value )

inline

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

The stride his is the shift towards the next interval, determining how many entries are dropped from the beginning and added to the end of each Window when iterating. It has to be <= count. If stride is set to 0 (default), it is set automatically to the count() when starting the iteration, meaning that each Window contains the next count() many new entries from the underlying input iterator.

Definition at line 766 of file queue_window_stream.hpp.

Member Typedef Documentation

◆ base_type

using base_type = BaseWindowStream<InputStreamIterator, DataType>

Definition at line 140 of file queue_window_stream.hpp.

◆ const_reference

using const_reference = value_type const&

Definition at line 150 of file queue_window_stream.hpp.

◆ Entry

using Entry = typename Window::Entry

Definition at line 143 of file queue_window_stream.hpp.

◆ InputType

using InputType = typename InputStreamIterator::value_type

Definition at line 144 of file queue_window_stream.hpp.

◆ iterator_category

using iterator_category = std::input_iterator_tag

Definition at line 146 of file queue_window_stream.hpp.

◆ pointer

using pointer = value_type*

Definition at line 148 of file queue_window_stream.hpp.

◆ reference

using reference = value_type&

Definition at line 149 of file queue_window_stream.hpp.

◆ self_type

using self_type = QueueWindowStream<InputStreamIterator, DataType>

Definition at line 139 of file queue_window_stream.hpp.

◆ value_type

using value_type = Window

Definition at line 147 of file queue_window_stream.hpp.

◆ Window

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

Definition at line 142 of file queue_window_stream.hpp.

Member Data Documentation

◆ DerivedIterator

friend DerivedIterator

Definition at line 732 of file queue_window_stream.hpp.

◆ entry_selection_function

std::function<bool( InputType const& )> entry_selection_function

Functor that takes an entry of the underlying input stream and returns whether that entry should be selected towards the window size count() or not.

Any entry that is selected (the function here returning true) will be used to fill the window and are considered for the count() of entries per window. Entries for which the function returns false are also enqueued in the window, but do not count towards the number of entries in the window.

Definition at line 165 of file queue_window_stream.hpp.

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

queue_window_stream.hpp

Detailed Description

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

Public Member Functions

Public Types

Public Attributes

Classes

Protected Member Functions

Constructor & Destructor Documentation

◆ QueueWindowStream() [1/3]

◆ ~QueueWindowStream()

◆ QueueWindowStream() [2/3]

◆ QueueWindowStream() [3/3]

Member Function Documentation

◆ count() [1/2]

◆ count() [2/2]

◆ get_begin_iterator_()

◆ get_end_iterator_()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ stride() [1/2]

◆ stride() [2/2]

Member Typedef Documentation

◆ base_type

◆ const_reference

◆ Entry

◆ InputType

◆ iterator_category

◆ pointer

◆ reference

◆ self_type

◆ value_type

◆ Window

Member Data Documentation

◆ DerivedIterator

◆ entry_selection_function

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