RegionWindowIterator< ForwardIterator, InputType, DataType > Class Template Reference

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

Detailed Description

template<class ForwardIterator, class InputType, class DataType = InputType>
class genesis::population::RegionWindowIterator< ForwardIterator, InputType, DataType >

Iterator for Windows representing regions of a genome.

This class allows to iterate a set of regions, each in a window.

The template parameters are:

• ForwardIterator: The underlying data iterator.
• InputType: The input data type that the basis iterator provided (that is, the input iterator from which the region window takes its data),
• DataType: The data type of the Window::Data that is stored in Window::Entry. The functor entry_input_function needs to be provided to convert from InputType to this DataType.

The three functors

• entry_input_function,
• chromosome_function, and
• position_function

have to be set prior to the iteration. All other settings are option and/or defaulted to reasonable values.

The class streams through both the input data and the region list in a single pass. This makes it algorithmically complex, but is a good compromise between the memory footprint needed for storing data of multiple windows at the same time and processing speed for only having to read the input once.

Definition at line 84 of file region_window_iterator.hpp.

Public Member Functions
	RegionWindowIterator (ForwardIterator begin, ForwardIterator end)
	RegionWindowIterator (RegionWindowIterator &&)=default
	RegionWindowIterator (RegionWindowIterator const &)=default
	~RegionWindowIterator ()=default
RegionWindowIterator &	operator= (RegionWindowIterator &&)=default
RegionWindowIterator &	operator= (RegionWindowIterator const &)=default

Public Types
using	const_reference = value_type const &
using	Entry = typename Window::Entry
using	iterator_category = std::input_iterator_tag
using	reference = value_type &
using	self_type = RegionWindowIterator< ForwardIterator, InputType, DataType >
using	settings_type = RegionWindowIteratorSettings< InputType, DataType >
using	value_type = Window
using	Window = ::genesis::population::Window< DataType >

Public Attributes
std::function< std::string(InputType const &)>	chromosome_function
	Functor that yields the current chromosome, given the input iterator data. More...
std::function< DataType(InputType const &)>	entry_input_function
	Functor to convert from the underlying input iterator that provides the data for the region window to the data that is stored per window. More...
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	Iterator
	Internal iterator over the data. More...

Constructor & Destructor Documentation

RegionWindowIterator() [1/3]

RegionWindowIterator ( ForwardIterator  begin, ForwardIterator  end  )

inline

Definition at line 409 of file region_window_iterator.hpp.

~RegionWindowIterator()

~RegionWindowIterator ( )

default

RegionWindowIterator() [2/3]

RegionWindowIterator ( RegionWindowIterator< ForwardIterator, InputType, DataType > const &  )

default

RegionWindowIterator() [3/3]

RegionWindowIterator ( RegionWindowIterator< ForwardIterator, InputType, DataType > &&  )

default

Member Function Documentation

operator=() [1/2]

RegionWindowIterator& operator= ( RegionWindowIterator< ForwardIterator, InputType, DataType > &&  )

default

operator=() [2/2]

RegionWindowIterator& operator= ( RegionWindowIterator< ForwardIterator, InputType, DataType > const &  )

default

Member Typedef Documentation

const_reference

using const_reference = value_type const&

Definition at line 102 of file region_window_iterator.hpp.

Entry

using Entry = typename Window::Entry

Definition at line 96 of file region_window_iterator.hpp.

iterator_category

using iterator_category = std::input_iterator_tag

Definition at line 106 of file region_window_iterator.hpp.

reference

using reference = value_type&

Definition at line 101 of file region_window_iterator.hpp.

self_type

using self_type = RegionWindowIterator<ForwardIterator, InputType, DataType>

Definition at line 99 of file region_window_iterator.hpp.

settings_type

using settings_type = RegionWindowIteratorSettings<InputType, DataType>

Definition at line 98 of file region_window_iterator.hpp.

value_type

using value_type = Window

Definition at line 100 of file region_window_iterator.hpp.

Window

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

Definition at line 95 of file region_window_iterator.hpp.

Member Data Documentation

chromosome_function

std::function<std::string( InputType const& )> chromosome_function

Functor that yields the current chromosome, given the input iterator data.

Definition at line 439 of file region_window_iterator.hpp.

entry_input_function

std::function<DataType( InputType const& )> entry_input_function

Functor to convert from the underlying input iterator that provides the data for the region window to the data that is stored per window.

Definition at line 434 of file region_window_iterator.hpp.

position_function

std::function<size_t( InputType const& )> position_function

Functor that yields the current position on the chromosome, given the input iterator data.

Definition at line 445 of file region_window_iterator.hpp.

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

• region_window_iterator.hpp