Index

_

__add__() (bg.multicolor.Multicolor method) __eq__() (bg.edge.BGEdge method) (bg.genome.BGGenome method) (bg.multicolor.Multicolor method) __ge__() (bg.multicolor.Multicolor method) __gt__() (bg.multicolor.Multicolor method) __hash__() (bg.genome.BGGenome method) __iadd__() (bg.multicolor.Multicolor method) __init__() (bg.breakpoint_graph.BreakpointGraph method) (bg.edge.BGEdge method) (bg.kbreak.KBreak method) (bg.multicolor.Multicolor method) __isub__() (bg.multicolor.Multicolor method) __le__() (bg.genome.BGGenome method) (bg.multicolor.Multicolor method) __lt__() (bg.genome.BGGenome method) (bg.multicolor.Multicolor method) __mul__() (bg.multicolor.Multicolor method) __sub__() (bg.multicolor.Multicolor method) _BGEdge__vertex_json_id() (bg.edge.BGEdge static method) _BGTree__get_node_by_name() (bg.tree.BGTree method) _BGTree__get_v_tree_consistent_leaf_based_hashable_multicolors() (bg.tree.BGTree method) _BGTree__has_edge() (bg.tree.BGTree method) _BGTree__has_node() (bg.tree.BGTree method) _BGTree__update_consistent_multicolors() (bg.tree.BGTree method)

_BGTree__vertex_is_leaf() (bg.tree.BGTree method) _BreakpointGraph__add_bgedge() (bg.breakpoint_graph.BreakpointGraph method) _BreakpointGraph__delete_all_bgedges_between_two_vertices() (bg.breakpoint_graph.BreakpointGraph method) _BreakpointGraph__delete_bgedge() (bg.breakpoint_graph.BreakpointGraph method) _BreakpointGraph__edges() (bg.breakpoint_graph.BreakpointGraph method) _BreakpointGraph__edges_between_two_vertices() (bg.breakpoint_graph.BreakpointGraph method) _BreakpointGraph__get_edge_by_two_vertices() (bg.breakpoint_graph.BreakpointGraph method) _BreakpointGraph__get_edges_by_vertex() (bg.breakpoint_graph.BreakpointGraph method) _BreakpointGraph__get_vertex_by_name() (bg.breakpoint_graph.BreakpointGraph method) _BreakpointGraph__merge_all_bgedges_between_two_vertices() (bg.breakpoint_graph.BreakpointGraph method) _BreakpointGraph__split_all_edges_between_two_vertices() (bg.breakpoint_graph.BreakpointGraph method) _BreakpointGraph__split_bgedge() (bg.breakpoint_graph.BreakpointGraph method) _BreakpointGraph__update() (bg.breakpoint_graph.BreakpointGraph method) _GRIMMReader__assign_vertex_pair() (bg.grimm.GRIMMReader static method) _Multicolor__delete() (bg.multicolor.Multicolor method) _Multicolor__left_merge() (bg.multicolor.Multicolor static method) _Multicolor__merge() (bg.multicolor.Multicolor class method)

A

add_bgedge() (bg.breakpoint_graph.BreakpointGraph method) add_edge() (bg.breakpoint_graph.BreakpointGraph method) (bg.tree.BGTree method)

append() (bg.tree.BGTree method) apply_kbreak() (bg.breakpoint_graph.BreakpointGraph method)

B

bg.breakpoint_graph (module) bg.distances (module) bg.edge (module) bg.genome (module) bg.grimm (module) bg.kbreak (module) bg.multicolor (module) bg.tree (module) bg.utils (module) bg.vertices (module) BGEdge (class in bg.edge)

BGEdge.BGEdgeJSONSchema (class in bg.edge) bgedge_is_tree_consistent() (bg.tree.BGTree method) bgedge_is_vtree_consistent() (bg.tree.BGTree method) BGGenome (class in bg.genome) BGGenome.BGGenomeJSONSchema (class in bg.genome) BGTree (class in bg.tree) BGVertex (class in bg.vertices) BlockVertex (class in bg.vertices) BlockVertex.BlockVertexJSONSchema (class in bg.vertices) BreakpointGraph (class in bg.breakpoint_graph)

C

colors (bg.multicolor.Multicolor attribute) colors_json_ids (bg.edge.BGEdge attribute)

connected_components_subgraphs() (bg.breakpoint_graph.BreakpointGraph method)

D

delete() (bg.multicolor.Multicolor method) delete_all_edges_between_two_vertices() (bg.breakpoint_graph.BreakpointGraph method)

delete_bgedge() (bg.breakpoint_graph.BreakpointGraph method) delete_edge() (bg.breakpoint_graph.BreakpointGraph method)

E

edges() (bg.breakpoint_graph.BreakpointGraph method) (bg.tree.BGTree method)

edges_between_two_vertices() (bg.breakpoint_graph.BreakpointGraph method)

F

from_json() (bg.breakpoint_graph.BreakpointGraph class method) (bg.edge.BGEdge class method) (bg.genome.BGGenome class method) (bg.vertices.BlockVertex class method) (bg.vertices.InfinityVertex class method)

G

get_breakpoint_graph() (bg.grimm.GRIMMReader static method) get_distance() (bg.tree.BGTree method) get_edge_by_two_vertices() (bg.breakpoint_graph.BreakpointGraph method) get_edges_by_vertex() (bg.breakpoint_graph.BreakpointGraph method) get_edges_from_parsed_data() (bg.grimm.GRIMMReader static method)

get_node_by_name() (bg.tree.BGTree method) get_tree_consistent_multicolors() (bg.tree.BGTree method) get_vertex_by_name() (bg.breakpoint_graph.BreakpointGraph method) get_vtree_consistent_multicolors() (bg.tree.BGTree method) GRIMMReader (class in bg.grimm)

H

has_edge() (bg.tree.BGTree method) has_node() (bg.tree.BGTree method)

hashable_representation (bg.multicolor.Multicolor attribute)

I

InfinityVertex (class in bg.vertices) InfinityVertex.InfinityVertexJSONSchema (class in bg.vertices) intersect() (bg.multicolor.Multicolor method) is_block_vertex (bg.vertices.BlockVertex attribute) is_comment_string() (bg.grimm.GRIMMReader static method)

is_genome_declaration_string() (bg.grimm.GRIMMReader static method) is_infinity_vertex (bg.vertices.InfinityVertex attribute) is_irregular_vertex (bg.vertices.InfinityVertex attribute) is_regular_vertex (bg.vertices.BlockVertex attribute)

J

json_id (bg.genome.BGGenome attribute)

json_schema_name (bg.edge.BGEdge attribute) (bg.genome.BGGenome attribute)

K

KBreak (class in bg.kbreak)

L

left_merge() (bg.multicolor.Multicolor class method)

M

merge() (bg.breakpoint_graph.BreakpointGraph class method) (bg.edge.BGEdge class method) (bg.multicolor.Multicolor class method) merge_all_edges() (bg.breakpoint_graph.BreakpointGraph method) merge_all_edges_between_two_vertices() (bg.breakpoint_graph.BreakpointGraph method)

Multicolor (class in bg.multicolor) multicolor_is_tree_consistent() (bg.tree.BGTree method) multicolor_is_vtree_consistent() (bg.tree.BGTree method)

N

name (bg.vertices.InfinityVertex attribute)

nodes() (bg.breakpoint_graph.BreakpointGraph method) (bg.tree.BGTree method)

P

parse_data_string() (bg.grimm.GRIMMReader static method)

parse_genome_declaration_string() (bg.grimm.GRIMMReader static method)

R

root (bg.tree.BGTree attribute)

S

similarity_score() (bg.multicolor.Multicolor static method) split_all_edges() (bg.breakpoint_graph.BreakpointGraph method) split_all_edges_between_two_vertices() (bg.breakpoint_graph.BreakpointGraph method)

split_bgedge() (bg.breakpoint_graph.BreakpointGraph method) split_colors() (bg.multicolor.Multicolor class method) split_edge() (bg.breakpoint_graph.BreakpointGraph method)

T

to_json() (bg.breakpoint_graph.BreakpointGraph method) (bg.edge.BGEdge method) (bg.genome.BGGenome method) tree_consistent_multicolors (bg.tree.BGTree attribute)

tree_consistent_multicolors_set (bg.tree.BGTree attribute)

U

update() (bg.breakpoint_graph.BreakpointGraph method) (bg.multicolor.Multicolor method)

V

valid_kbreak_matchings() (bg.kbreak.KBreak static method) vertex1_json_id (bg.edge.BGEdge attribute) vertex2_json_id (bg.edge.BGEdge attribute)

vtree_consistent_multicolors (bg.tree.BGTree attribute) vtree_consistent_multicolors_set (bg.tree.BGTree attribute)