vg::ZipCodeTree Class Reference

#include <zip_code_tree.hpp>

Classes
class	iterator
struct	oriented_seed_t
class	reverse_iterator
struct	seed_result_t
struct	tree_item_t
	One item in the zip code tree, representing a node or edge of the tree. More...

Public Types
enum	tree_item_type_t {   SEED =0, SNARL_START, SNARL_END, CHAIN_START,   CHAIN_END, EDGE, NODE_COUNT }
	The type of an item in the zip code tree. More...

Public Member Functions
	ZipCodeTree ()
size_t	get_tree_size () const
	Get the number of items in the tree. More...
tree_item_t	get_item_at_index (size_t index) const
	Access the values in the zip_code_tree. More...
iterator	begin () const
	Get an iterator over indexes of seeds in the tree, left to right. More...
iterator	end () const
	Get the end iterator for seeds in the tree, left to right. More...
reverse_iterator	look_back (const iterator &from, size_t distance_limit=std::numeric_limits< size_t >::max()) const
	Get a reverse iterator looking left from where a forward iterator is, up to a distance limit. More...
reverse_iterator	rend () const
	Get the reverse end iterator for looking back from seeds. More...
template<typename Minimizer >
void	print_self (const vector< Seed > *seeds, const VectorView< Minimizer > *minimizers) const
bool	node_is_invalid (nid_t id, const SnarlDistanceIndex &distance_index, size_t distance_limit=std::numeric_limits< size_t >::max()) const
bool	node_is_in_cyclic_snarl (nid_t id, const SnarlDistanceIndex &distance_index) const
	Is the node in a cyclic (non-dag) snarl? More...
void	validate_zip_tree (const SnarlDistanceIndex &distance_index, const vector< Seed > *seeds, size_t distance_limit=std::numeric_limits< size_t >::max()) const
	Check that the tree is correct. More...
void	validate_snarl (std::vector< tree_item_t >::const_iterator zip_iterator, const SnarlDistanceIndex &distance_index, const vector< Seed > *seeds, size_t distance_limit=std::numeric_limits< size_t >::max()) const
	Helper function for validate_zip_tree for just a snarl. More...
std::pair< size_t, size_t >	dag_and_non_dag_snarl_count (const vector< Seed > &seeds, const SnarlDistanceIndex &distance_index) const

Static Protected Member Functions
static bool	seed_is_reversed_at_depth (const Seed &seed, size_t depth, const SnarlDistanceIndex &distance_index)

Protected Attributes
vector< tree_item_t >	zip_code_tree

Private Types
typedef SnarlDistanceIndexClusterer::Seed	Seed

Friends
class	ZipCodeForest

Detailed Description

A ZipCodeTree represents of set of SnarlDistanceIndexCluserer::Seed's (seed alignments between a read and reference) as a tree structure. The tree represents the connectivity of the seeds, based on the distance index. Edges are labelled with distance values. The tree can be traversed to find distances between seeds

This provides an iterator that, given a seed and a distance limit, iterates through seeds that are reachable within the distance limit

The ZipCodeTree is built by the ZipCodeForest, which represents a collection of trees

Member Typedef Documentation

Seed

typedef SnarlDistanceIndexClusterer::Seed vg::ZipCodeTree::Seed

private

Member Enumeration Documentation

tree_item_type_t

enum vg::ZipCodeTree::tree_item_type_t

The type of an item in the zip code tree.

Enumerator
SEED
SNARL_START
SNARL_END
CHAIN_START
CHAIN_END
EDGE
NODE_COUNT

Constructor & Destructor Documentation

ZipCodeTree()

vg::ZipCodeTree::ZipCodeTree ( )

inline

Empty constructor ZipCodeTree's get filled in by ZipCodeForest's

Member Function Documentation

begin()

auto vg::ZipCodeTree::begin

(

)

const

Get an iterator over indexes of seeds in the tree, left to right.

dag_and_non_dag_snarl_count()

std::pair< size_t, size_t > vg::ZipCodeTree::dag_and_non_dag_snarl_count	(	const vector< Seed > &	seeds,
		const SnarlDistanceIndex &	distance_index
	)		const

Count the number of snarls involved in the tree Returns a pair of <dag count, non-dag count> Assumes that the tree has already been filled in

end()

auto vg::ZipCodeTree::end

(

)

const

Get the end iterator for seeds in the tree, left to right.

get_item_at_index()

tree_item_t vg::ZipCodeTree::get_item_at_index ( size_t  index ) const

inline

Access the values in the zip_code_tree.

get_tree_size()

size_t vg::ZipCodeTree::get_tree_size ( ) const

inline

Get the number of items in the tree.

look_back()

auto vg::ZipCodeTree::look_back	(	const iterator &	from,
		size_t	distance_limit = std::numeric_limits<size_t>::max()
	)		const

Get a reverse iterator looking left from where a forward iterator is, up to a distance limit.

node_is_in_cyclic_snarl()

bool vg::ZipCodeTree::node_is_in_cyclic_snarl	(	nid_t	id,
		const SnarlDistanceIndex &	distance_index
	)		const

Is the node in a cyclic (non-dag) snarl?

node_is_invalid()

bool vg::ZipCodeTree::node_is_invalid	(	nid_t	id,
		const SnarlDistanceIndex &	distance_index,
		size_t	distance_limit = std::numeric_limits<size_t>::max()
	)		const

Is the given node in a multicomponent chain, looping chain, or anything else that would cause it to not have exact distances? The distances are only guaranteed to be correct up to the given distance limit Cyclic snarls don't count as being invalid

print_self()

template<typename Minimizer >

void vg::ZipCodeTree::print_self	(	const vector< Seed > *	seeds,
		const VectorView< Minimizer > *	minimizers
	)		const

Print the zip code tree to stderr ( and ) are used for the starts and ends of snarls [ and ] are used for the starts and ends of chains seeds are printed as their positions

rend()

auto vg::ZipCodeTree::rend

(

)

const

Get the reverse end iterator for looking back from seeds.

seed_is_reversed_at_depth()

bool vg::ZipCodeTree::seed_is_reversed_at_depth ( const Seed &  seed, size_t  depth, const SnarlDistanceIndex &  distance_index  )

staticprotected

validate_snarl()

void vg::ZipCodeTree::validate_snarl	(	std::vector< tree_item_t >::const_iterator	zip_iterator,
		const SnarlDistanceIndex &	distance_index,
		const vector< Seed > *	seeds,
		size_t	distance_limit = std::numeric_limits<size_t>::max()
	)		const

Helper function for validate_zip_tree for just a snarl.

validate_zip_tree()

void vg::ZipCodeTree::validate_zip_tree	(	const SnarlDistanceIndex &	distance_index,
		const vector< Seed > *	seeds,
		size_t	distance_limit = std::numeric_limits<size_t>::max()
	)		const

Check that the tree is correct.

Friends And Related Function Documentation

ZipCodeForest

friend class ZipCodeForest

friend

Member Data Documentation

zip_code_tree

vector<tree_item_t> vg::ZipCodeTree::zip_code_tree

protected

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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