vg::ZipCodeTree::seed_iterator Class Reference

#include <zip_code_tree.hpp>

Public Member Functions
	seed_iterator (size_t start_index, const ZipCodeTree &ziptree)
	seed_iterator (const seed_iterator &other)=default
	seed_iterator (seed_iterator &&other)=default
seed_iterator &	operator= (const seed_iterator &other)=default
seed_iterator &	operator= (seed_iterator &&other)=default
seed_iterator &	operator++ ()
bool	operator== (const seed_iterator &other) const
bool	operator!= (const seed_iterator &other) const
	Compare for inequality.
tree_item_t	current_item () const
	What item does index point to?
vector< oriented_seed_t >	operator* () const
size_t	get_index () const
bool	get_right_to_left () const
stack< size_t >	get_chain_numbers () const

Private Attributes
const vector< tree_item_t > *	zip_code_tree
stack< size_t >	chain_numbers
	Within each parent snarl, which chain are we in?
size_t	index
	Where we are in the stored tree.
size_t	cyclic_snarl_nestedness
	How far inside of a cyclic snarl are we?
bool	right_to_left
vector< oriented_seed_t >	current_seeds
	Seeds at this position.

Friends
class	distance_iterator

Detailed Description

Iterator that visits seeds left to right in the tree's in-order traversal

Iteration flow

Each seed is visited from left to right, in the same order as get_all_seeds() would return them.

The first time any given seed is visited, right_to_left is true, indicating that a distance iterator should be set off going in the default direction of right to left.

Once the right-to-left step has been done, then the iterator decides whether to do a second, left-to-right step, with right_to_left set to false. This will happen if inside a cyclic snarl, even if not necessarily the direct parent. Calling ++() will toggle right_to_left instead of moving the internal iteration index. The next call to ++() would then reset right_to_left back to true, and finally advance the iterator rightward to the next seed.

For seeds not inside cyclic snarls, ++() will simply move rightward.

We need to traverse seeds in cyclic snarls in both directions because the chains are not necessarily traversed in a single direction, and are stored in an arbitrary orientation.

How to use this iterator

The intent of this iterator is to hide a lot of the fiddly bits required to iterate over a zip tree with cyclic and non-cyclic snarls. All a caller needs to do is

• call ++() to move to the next seed
• dereference the iterator to get the seeds at the current position
• create the distance iterator for this position by calling find_distances(seed_itr, distance_limit)

Seeds from both iterators will be automatically oriented based on the direction of traversal. That is, you can Just Trust Me (TM) for all seed orientations which iterators yield.

Constructor & Destructor Documentation

seed_iterator() [1/3]

vg::ZipCodeTree::seed_iterator::seed_iterator	(	size_t	start_index,
		const ZipCodeTree &	ziptree )

Make an iterator starting from start_index until the end of the given ziptree

seed_iterator() [2/3]

vg::ZipCodeTree::seed_iterator::seed_iterator ( const seed_iterator & other )

default

seed_iterator() [3/3]

vg::ZipCodeTree::seed_iterator::seed_iterator ( seed_iterator && other )

default

Member Function Documentation

current_item()

tree_item_t vg::ZipCodeTree::seed_iterator::current_item ( ) const

inline

What item does index point to?

get_chain_numbers()

stack< size_t > vg::ZipCodeTree::seed_iterator::get_chain_numbers ( ) const

inline

get_index()

size_t vg::ZipCodeTree::seed_iterator::get_index ( ) const

inline

get_right_to_left()

bool vg::ZipCodeTree::seed_iterator::get_right_to_left ( ) const

inline

operator!=()

bool vg::ZipCodeTree::seed_iterator::operator!= ( const seed_iterator & other ) const

inline

Compare for inequality.

operator*()

vector< oriented_seed_t > vg::ZipCodeTree::seed_iterator::operator* ( ) const

inline

Get the index and orientation of the seed we are currently at. Also return all other seeds on the same position

operator++()

auto vg::ZipCodeTree::seed_iterator::operator++

(

)

Advance right until we hit another seed or the end Automatically handle updating chain_numbers and cyclic_snarl_nestedness

operator=() [1/2]

seed_iterator & vg::ZipCodeTree::seed_iterator::operator= ( const seed_iterator & other )

default

operator=() [2/2]

seed_iterator & vg::ZipCodeTree::seed_iterator::operator= ( seed_iterator && other )

default

operator==()

bool vg::ZipCodeTree::seed_iterator::operator== ( const seed_iterator & other ) const

inline

Compare for equality to see if we hit end This just trusts that the two iterators are for the same tree

Friends And Related Symbol Documentation

distance_iterator

friend class distance_iterator

friend

Member Data Documentation

chain_numbers

stack<size_t> vg::ZipCodeTree::seed_iterator::chain_numbers

private

Within each parent snarl, which chain are we in?

current_seeds

vector<oriented_seed_t> vg::ZipCodeTree::seed_iterator::current_seeds

private

Seeds at this position.

cyclic_snarl_nestedness

size_t vg::ZipCodeTree::seed_iterator::cyclic_snarl_nestedness

private

How far inside of a cyclic snarl are we?

index

size_t vg::ZipCodeTree::seed_iterator::index

private

Where we are in the stored tree.

right_to_left

bool vg::ZipCodeTree::seed_iterator::right_to_left

private

Direction a distance iterator should be set off NOT the direction this iterator moves; a seed_iterator always moves left to right

zip_code_tree

const vector<tree_item_t>* vg::ZipCodeTree::seed_iterator::zip_code_tree

private

A pointer to the ziptree vector to let us look up distance matrices. Needs to be a pointer so the iterator can be assignable.

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

• src/zip_code_tree.hpp
• src/zip_code_tree.cpp