#include <genesis/tree/formats/newick/input_iterator.hpp>

Detailed Description

Iterate an input stream and parse it as Newick trees.

This class allows to iterate over an input stream, iterpreting it as Newick trees, and yielding one such tree per iteration step. This is useful for processing large files without having to keep them fully in memory.

Example:

for( auto const& t : NewickInputIterator( from_file( "/path/to/trees.newick" ))) {
    std::cout << t.node_count() << "\n";
}

Alternatively, the following also works:

auto it = NewickInputIterator( from_file( "/path/to/trees.newick" ));
while( it ) {
    Tree const& t = *it;
    std::cout << t.node_count() << "\n";
    ++it;
}

Use functions such as utils::from_file() and utils::from_string() to conveniently get an input source that can be used here.

See NewickReader for a description of the expected format. In order to change the reading behaviour, a NewickReader object can be handed over from which the settings are copied.

Definition at line 76 of file tree/formats/newick/input_iterator.hpp.

Public Member Functions
	NewickInputIterator ()
	Create a default instance, with no input. More...

	NewickInputIterator (self_type &&)=default

	NewickInputIterator (self_type const &)=delete

	NewickInputIterator (std::shared_ptr< utils::BaseInputSource > source)
	Create an instance that reads from an input source, using a default NewickReader. More...

	NewickInputIterator (std::shared_ptr< utils::BaseInputSource > source, NewickReader const &settings)
	Create an instance that reads from an input source, using the settings of a given NewickReader. More...

	~NewickInputIterator ()=default

self_type &	begin ()
	Beginning of the iterator. More...

Tree const &	dereference () const

self_type	end ()
	End of the iterator. More...

void	increment ()

	operator bool () const
	Return true iff dereferencing is valid, i.e., iff there is a Tree available. More...

bool	operator!= (self_type const &other) const

Tree const &	operator* () const

self_type &	operator++ ()

Tree const *	operator-> () const

self_type &	operator= (self_type &&)=default

self_type &	operator= (self_type const &)=delete

bool	operator== (self_type const &other) const

Public Types
using	iterator_category = std::input_iterator_tag

using	self_type = NewickInputIterator

Constructor & Destructor Documentation

◆ NewickInputIterator() [1/5]

NewickInputIterator ( )

inline

Create a default instance, with no input.

Definition at line 94 of file tree/formats/newick/input_iterator.hpp.

◆ NewickInputIterator() [2/5]

NewickInputIterator ( std::shared_ptr< utils::BaseInputSource > source )

inlineexplicit

Create an instance that reads from an input source, using a default NewickReader.

Definition at line 103 of file tree/formats/newick/input_iterator.hpp.

◆ NewickInputIterator() [3/5]

NewickInputIterator	(	std::shared_ptr< utils::BaseInputSource >	source,
		NewickReader const &	settings
	)

inline

Create an instance that reads from an input source, using the settings of a given NewickReader.

Definition at line 119 of file tree/formats/newick/input_iterator.hpp.

◆ ~NewickInputIterator()

~NewickInputIterator ( )

default

◆ NewickInputIterator() [4/5]

NewickInputIterator ( self_type const & )

delete

◆ NewickInputIterator() [5/5]

NewickInputIterator ( self_type && )

default

Member Function Documentation

◆ begin()

self_type& begin ( )

inline

Beginning of the iterator.

This is a bit uncommon, as the iterator provides its own begin() and end() functions. We do this to allow the easy use case that is explained above.

Definition at line 190 of file tree/formats/newick/input_iterator.hpp.

◆ dereference()

Tree const& dereference ( ) const

inline

Definition at line 175 of file tree/formats/newick/input_iterator.hpp.

◆ end()

self_type end ( )

inline

End of the iterator.

Beginning of the iterator. This is a bit uncommon, as the iterator provides its own begin() and end() functions. We do this to allow the easy use case that is explained above.

Definition at line 200 of file tree/formats/newick/input_iterator.hpp.