vg
tools for working with variation graphs
vg::MinimumDistanceIndex Member List

This is the complete list of members for vg::MinimumDistanceIndex, including all inherited members.

addNodesInRange(const HandleGraph *super_graph, int64_t min_distance, int64_t max_distance, SubHandleGraph &sub_graph, vector< tuple< handle_t, int64_t >> &start_nodes, hash_set< pair< id_t, bool >> &seen_nodes)vg::MinimumDistanceIndexprotected
calculateMaxIndex(const HandleGraph *graph, int64_t cap)vg::MinimumDistanceIndexprotected
calculateMinIndex(const HandleGraph *graph, const SnarlManager *snarl_manager, const Chain *chain, size_t parent_id, bool rev_in_parent, bool trivial_chain, size_t depth)vg::MinimumDistanceIndexprotected
chain_assignmentsvg::MinimumDistanceIndexprotected
chain_indexesvg::MinimumDistanceIndexprotected
chain_ranksvg::MinimumDistanceIndexprotected
ChainIndex classvg::MinimumDistanceIndexfriend
distToCommonAncestor(pair< size_t, bool > common_ancestor, pos_t &pos, bool rev) constvg::MinimumDistanceIndexprotected
file_headervg::MinimumDistanceIndexprotected
getChainAssignment(id_t i) constvg::MinimumDistanceIndexinlineprotected
getChainRank(id_t i) constvg::MinimumDistanceIndexinlineprotected
getPrimaryAssignment(id_t i) constvg::MinimumDistanceIndexinlineprotected
getPrimaryRank(id_t i) constvg::MinimumDistanceIndexinlineprotected
getSecondaryAssignment(id_t i) constvg::MinimumDistanceIndexinlineprotected
getSecondaryRank(id_t i) constvg::MinimumDistanceIndexinlineprotected
has_chainvg::MinimumDistanceIndexprotected
has_chain_bvvg::MinimumDistanceIndexprotected
has_secondary_snarlvg::MinimumDistanceIndexprotected
has_secondary_snarl_bvvg::MinimumDistanceIndexprotected
include_maximumvg::MinimumDistanceIndexprotected
load(istream &in)vg::MinimumDistanceIndex
max_distancesvg::MinimumDistanceIndexprotected
max_node_idvg::MinimumDistanceIndexprotected
maxDistance(pos_t pos1, pos_t pos2) constvg::MinimumDistanceIndex
min_distancesvg::MinimumDistanceIndexprotected
min_node_idvg::MinimumDistanceIndexprotected
minDistance(pos_t pos1, pos_t pos2) constvg::MinimumDistanceIndex
MinimumDistanceIndex(const HandleGraph *graph, const SnarlManager *snarl_manager, int64_t cap=0)vg::MinimumDistanceIndex
MinimumDistanceIndex(istream &in)vg::MinimumDistanceIndex
MinimumDistanceIndex()vg::MinimumDistanceIndex
minPos(vector< int64_t > vals)vg::MinimumDistanceIndexstatic
minPos(int64_t x, int64_t y)vg::MinimumDistanceIndexinlinestatic
populateSnarlIndex(const HandleGraph *graph, const SnarlManager *snarl_manager, const NetGraph &ng, const Snarl *snarl, bool snarl_rev_in_chain, size_t snarl_assignment, hash_set< pair< id_t, bool >> &all_nodes, size_t depth)vg::MinimumDistanceIndexprotected
primary_snarl_assignmentsvg::MinimumDistanceIndexprotected
primary_snarl_ranksvg::MinimumDistanceIndexprotected
printSelf()vg::MinimumDistanceIndex
printSnarlStats()vg::MinimumDistanceIndex
secondary_snarl_assignmentsvg::MinimumDistanceIndexprotected
secondary_snarl_ranksvg::MinimumDistanceIndexprotected
serialize(ostream &out) constvg::MinimumDistanceIndex
snarl_indexesvg::MinimumDistanceIndexprotected
SnarlIndex classvg::MinimumDistanceIndexfriend
SnarlSeedClusterer classvg::MinimumDistanceIndexfriend
subgraphInRange(const Path &path, const HandleGraph *super_graph, int64_t min_distance, int64_t max_distance, SubHandleGraph &sub_graph, bool look_forward)vg::MinimumDistanceIndex
TestMinDistanceIndex classvg::MinimumDistanceIndexfriend
tree_depthvg::MinimumDistanceIndexprotected