vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem Struct Reference

Classes
struct	SnarlTreeChild

Public Member Functions
	SnarlTreeNodeProblem (net_handle_t net, size_t read_count, size_t seed_count, const SnarlDistanceIndex &distance_index, const SeedCache *seed, size_t zipcode_depth)
	SnarlTreeNodeProblem (net_handle_t net, size_t read_count, size_t seed_count, bool is_reversed_in_parent, size_t node_length, size_t prefix_sum, size_t component, const SeedCache *seed, size_t zipcode_depth)
void	set_chain_values (const SnarlDistanceIndex &distance_index)
void	set_snarl_values (const SnarlDistanceIndex &distance_index)

Public Attributes
hash_set< pair< size_t, size_t > >	read_cluster_heads
vector< SnarlTreeChild >	children
pair< size_t, size_t >	read_best_left = make_pair(std::numeric_limits<size_t>::max(), std::numeric_limits<size_t>::max())
pair< size_t, size_t >	read_best_right = make_pair(std::numeric_limits<size_t>::max(), std::numeric_limits<size_t>::max())
size_t	fragment_best_left = std::numeric_limits<size_t>::max()
size_t	fragment_best_right = std::numeric_limits<size_t>::max()
size_t	distance_start_left = std::numeric_limits<size_t>::max()
size_t	distance_start_right = std::numeric_limits<size_t>::max()
size_t	distance_end_left = std::numeric_limits<size_t>::max()
size_t	distance_end_right = std::numeric_limits<size_t>::max()
net_handle_t	containing_net_handle
net_handle_t	parent_net_handle
net_handle_t	grandparent_net_handle
const SeedCache *	seed
size_t	zipcode_depth
size_t	node_length = std::numeric_limits<size_t>::max()
size_t	prefix_sum_value = std::numeric_limits<size_t>::max()
size_t	chain_component_start = 0
size_t	chain_component_end = 0
size_t	loop_left = std::numeric_limits<size_t>::max()
size_t	loop_right = std::numeric_limits<size_t>::max()
bool	has_parent_handle = false
bool	has_grandparent_handle = false
bool	is_reversed_in_parent = false
bool	is_trivial_chain = false
bool	is_looping_chain = false

Constructor & Destructor Documentation

SnarlTreeNodeProblem() [1/2]

vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeNodeProblem ( net_handle_t  net, size_t  read_count, size_t  seed_count, const SnarlDistanceIndex &  distance_index, const SeedCache *  seed, size_t  zipcode_depth  )

inline

SnarlTreeNodeProblem() [2/2]

vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::SnarlTreeNodeProblem ( net_handle_t  net, size_t  read_count, size_t  seed_count, bool  is_reversed_in_parent, size_t  node_length, size_t  prefix_sum, size_t  component, const SeedCache *  seed, size_t  zipcode_depth  )

inline

Member Function Documentation

set_chain_values()

void vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::set_chain_values ( const SnarlDistanceIndex &  distance_index )

inline

set_snarl_values()

void vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::set_snarl_values ( const SnarlDistanceIndex &  distance_index )

inline

Member Data Documentation

chain_component_end

size_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::chain_component_end = 0

chain_component_start

size_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::chain_component_start = 0

children

vector<SnarlTreeChild> vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::children

containing_net_handle

net_handle_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::containing_net_handle

distance_end_left

size_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::distance_end_left = std::numeric_limits<size_t>::max()

distance_end_right

size_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::distance_end_right = std::numeric_limits<size_t>::max()

distance_start_left

size_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::distance_start_left = std::numeric_limits<size_t>::max()

distance_start_right

size_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::distance_start_right = std::numeric_limits<size_t>::max()

fragment_best_left

size_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::fragment_best_left = std::numeric_limits<size_t>::max()

fragment_best_right

size_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::fragment_best_right = std::numeric_limits<size_t>::max()

grandparent_net_handle

net_handle_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::grandparent_net_handle

has_grandparent_handle

bool vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::has_grandparent_handle = false

has_parent_handle

bool vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::has_parent_handle = false

is_looping_chain

bool vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::is_looping_chain = false

is_reversed_in_parent

bool vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::is_reversed_in_parent = false

is_trivial_chain

bool vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::is_trivial_chain = false

loop_left

size_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::loop_left = std::numeric_limits<size_t>::max()

loop_right

size_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::loop_right = std::numeric_limits<size_t>::max()

node_length

size_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::node_length = std::numeric_limits<size_t>::max()

parent_net_handle

net_handle_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::parent_net_handle

prefix_sum_value

size_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::prefix_sum_value = std::numeric_limits<size_t>::max()

read_best_left

pair<size_t, size_t> vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::read_best_left = make_pair(std::numeric_limits<size_t>::max(), std::numeric_limits<size_t>::max())

read_best_right

pair<size_t, size_t> vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::read_best_right = make_pair(std::numeric_limits<size_t>::max(), std::numeric_limits<size_t>::max())

read_cluster_heads

hash_set<pair<size_t, size_t> > vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::read_cluster_heads

seed

const SeedCache* vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::seed

zipcode_depth

size_t vg::SnarlDistanceIndexClusterer::SnarlTreeNodeProblem::zipcode_depth

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

• src/snarl_seed_clusterer.hpp