A library for working with phylogenetic and population genetic data.
v0.32.0
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RegionWindowStream< InputStreamIterator, DataType > Class Template Referencefinal

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

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

Detailed Description

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

Stream for Windows representing regions of a genome.

This class allows to iterate a set of regions, each yielded to the caller as a Window. That is, with each step of the iteration of this class, one region (interval) of the input region list is yielded as a Window, containing the data of the input InputStreamIterator (which is of type DataType). These regions can for example be genes, linkage blocks, or other genomic intervals of interest. Each can have an arbitrary length, and the can potentially be overlapping or be nested.

The three functors

have to be set prior to the iteration. All other settings are option and/or defaulted to reasonable values. See make_region_window_stream() and make_default_region_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, and general usage examples of the class.

See also
make_region_window_stream()
make_default_region_window_stream()

Definition at line 89 of file region_window_stream.hpp.

Public Member Functions

 RegionWindowStream (InputStreamIterator begin, InputStreamIterator end, std::shared_ptr< GenomeRegionList > region_list)
 
 RegionWindowStream (RegionWindowStream &&)=default
 
 RegionWindowStream (RegionWindowStream const &)=default
 
virtual ~RegionWindowStream () override=default
 
RegionWindowStream & operator= (RegionWindowStream &&)=default
 
RegionWindowStream & operator= (RegionWindowStream const &)=default
 
bool skip_empty_regions () const
 
self_type & skip_empty_regions (bool value)
 
- 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 = RegionWindowStream< 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
 
- 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

◆ RegionWindowStream() [1/3]

RegionWindowStream ( InputStreamIterator  begin,
InputStreamIterator  end,
std::shared_ptr< GenomeRegionList >  region_list 
)
inline

Definition at line 732 of file region_window_stream.hpp.

◆ ~RegionWindowStream()

virtual ~RegionWindowStream ( )
overridevirtualdefault

◆ RegionWindowStream() [2/3]

RegionWindowStream ( RegionWindowStream< InputStreamIterator, DataType > const &  )
default

◆ RegionWindowStream() [3/3]

RegionWindowStream ( RegionWindowStream< InputStreamIterator, DataType > &&  )
default

Member Function Documentation

◆ 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 778 of file region_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 787 of file region_window_stream.hpp.

◆ operator=() [1/2]

RegionWindowStream& operator= ( RegionWindowStream< InputStreamIterator, DataType > &&  )
default

◆ operator=() [2/2]

RegionWindowStream& operator= ( RegionWindowStream< InputStreamIterator, DataType > const &  )
default

◆ skip_empty_regions() [1/2]

bool skip_empty_regions ( ) const
inline

Definition at line 766 of file region_window_stream.hpp.

◆ skip_empty_regions() [2/2]

self_type& skip_empty_regions ( bool  value)
inline

Definition at line 760 of file region_window_stream.hpp.

Member Typedef Documentation

◆ base_type

using base_type = BaseWindowStream<InputStreamIterator, DataType>

Definition at line 98 of file region_window_stream.hpp.

◆ const_reference

using const_reference = value_type const&

Definition at line 108 of file region_window_stream.hpp.

◆ Entry

using Entry = typename Window::Entry

Definition at line 101 of file region_window_stream.hpp.

◆ InputType

using InputType = typename InputStreamIterator::value_type

Definition at line 102 of file region_window_stream.hpp.

◆ iterator_category

using iterator_category = std::input_iterator_tag

Definition at line 104 of file region_window_stream.hpp.

◆ pointer

using pointer = value_type*

Definition at line 106 of file region_window_stream.hpp.

◆ reference

using reference = value_type&

Definition at line 107 of file region_window_stream.hpp.

◆ self_type

using self_type = RegionWindowStream<InputStreamIterator, DataType>

Definition at line 97 of file region_window_stream.hpp.

◆ value_type

using value_type = Window

Definition at line 105 of file region_window_stream.hpp.

◆ Window

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

Definition at line 100 of file region_window_stream.hpp.

Member Data Documentation

◆ DerivedIterator

friend DerivedIterator

Definition at line 754 of file region_window_stream.hpp.

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