Class: Bio::Tree
Overview
This is the class for phylogenetic tree. It stores a phylogenetic tree.
Internally, it is based on Bio::Pathway class. However, users cannot handle Bio::Pathway object directly.
This is alpha version. Incompatible changes may be made frequently.
Defined Under Namespace
Classes: Edge, NoPathError, Node
Constant Summary collapse
- DEFAULT_OPTIONS =
default options
{ :indent => ' ' }
Instance Attribute Summary collapse
-
#options ⇒ Object
tree options; mainly used for tree output.
-
#root ⇒ Object
root node of this tree (even if unrooted tree, it is used by some methods).
Instance Method Summary collapse
-
#add_edge(source, target, edge = Edge.new) ⇒ Object
Adds a new edge to the tree.
-
#add_node(node) ⇒ Object
Adds a node to the tree.
-
#adjacency_matrix(nodes = nil, default_value = nil, diagonal_value = nil) ⇒ Object
Shows the adjacency matrix representation of the tree.
-
#adjacent_nodes(node) ⇒ Object
Returns an array of adjacent nodes of the given node.
-
#ancestors(node, root = nil) ⇒ Object
Gets all ancestral nodes of the node.
-
#children(node, root = nil) ⇒ Object
Gets the adjacent children nodes of the node.
-
#clear ⇒ Object
Clears all nodes and edges.
-
#clear_node(node) ⇒ Object
Removes all edges connected with the node.
-
#collect_edge! ⇒ Object
Replaces each edge by each block’s return value.
-
#collect_node! ⇒ Object
Replaces each node by each block’s return value.
-
#concat(other) ⇒ Object
Concatenates the other tree.
-
#descendents(node, root = nil) ⇒ Object
Gets all descendent nodes of the node.
-
#distance(node1, node2) ⇒ Object
Returns distance between node1 and node2.
-
#distance_matrix(nodes = nil) ⇒ Object
Calculates distance matrix of given nodes.
-
#each_edge ⇒ Object
Iterates over each edges of this tree.
-
#each_edge_in_path(node1, node2) ⇒ Object
Iterates over each edge from node1 to node2.
-
#each_node(&x) ⇒ Object
Iterates over each node of this tree.
-
#each_out_edge(source) ⇒ Object
Iterates over each connected edges of the given node.
-
#edges ⇒ Object
Returns all edges an array of [ node0, node1, edge ].
-
#get_edge(source, target) ⇒ Object
Returns an edge from source to target.
-
#get_edge_distance(edge) ⇒ Object
Gets distance value from the given edge.
-
#get_edge_distance_string(edge) ⇒ Object
Gets distance string from the given edge.
-
#get_edge_merged(edge1, edge2) ⇒ Object
Returns edge1 + edge2.
- #get_node_bootstrap(node) ⇒ Object
- #get_node_bootstrap_string(node) ⇒ Object
-
#get_node_by_name(str) ⇒ Object
Finds a node in the tree by given name and returns the node.
-
#get_node_name(node) ⇒ Object
Gets node name.
-
#include?(node) ⇒ Boolean
If the node exists, returns true.
-
#initialize(tree = nil) ⇒ Tree
constructor
Creates a new phylogenetic tree.
-
#insert_node(node1, node2, new_node, new_distance = nil) ⇒ Object
Insert a new node between adjacent nodes node1 and node2.
-
#leaves(node = nil, root = nil) ⇒ Object
If node is nil, returns an array of all leaves (nodes connected with one edge).
-
#lowest_common_ancestor(node1, node2, root = nil) ⇒ Object
Gets the lowest common ancestor of the two nodes.
-
#nodes ⇒ Object
Returns all nodes as an array.
-
#number_of_edges ⇒ Object
Returns number of edges in the tree.
-
#number_of_nodes ⇒ Object
Number of nodes.
-
#out_degree(source) ⇒ Object
Returns number of edges in the given node.
-
#out_edges(source) ⇒ Object
Returns all connected edges with adjacent nodes.
-
#output(format, *arg, &block) ⇒ Object
Returns formatted text (or something) of the tree Currently supported format is: :newick, :nhx.
-
#output_newick(options = {}, &block) ⇒ Object
(also: #newick)
Returns a newick formatted string.
-
#output_nhx(options = {}, &block) ⇒ Object
Returns a NHX (New Hampshire eXtended) formatted string.
-
#output_phylip_distance_matrix(nodes = nil, options = {}) ⇒ Object
Generates phylip-style distance matrix as a string.
-
#parent(node, root = nil) ⇒ Object
Gets the parent node of the node.
-
#path(node1, node2) ⇒ Object
Gets path from node1 to node2.
-
#remove_edge(source, target) ⇒ Object
Removes an edge between source and target.
-
#remove_edge_if ⇒ Object
Removes each edge if the block returns not nil.
-
#remove_node(node) ⇒ Object
Removes the given node from the tree.
-
#remove_node_if ⇒ Object
Removes each node if the block returns not nil.
-
#remove_nonsense_nodes ⇒ Object
Removes all nodes that are not branches nor leaves.
-
#subtree(nodes) ⇒ Object
Gets the sub-tree consisted of given nodes.
-
#subtree_with_all_paths(nodes) ⇒ Object
Gets the sub-tree consisted of given nodes and all internal nodes connected between given nodes.
-
#total_distance ⇒ Object
Returns total distance of all edges.
Constructor Details
#initialize(tree = nil) ⇒ Tree
Creates a new phylogenetic tree. When no arguments are given, it creates a new empty tree. When a Tree object is given, it copies the tree. Note that the new tree shares Node and Edge objects with the given tree.
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# File 'lib/bio/tree.rb', line 257 def initialize(tree = nil) # creates an undirected adjacency list graph @pathway = Bio::Pathway.new([], true) @root = nil @options = {} self.concat(tree) if tree end |
Instance Attribute Details
#options ⇒ Object
tree options; mainly used for tree output
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# File 'lib/bio/tree.rb', line 270 def @options end |
Instance Method Details
#add_edge(source, target, edge = Edge.new) ⇒ Object
Adds a new edge to the tree. Returns the newly added edge. If the edge already exists, it is overwritten with new one.
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# File 'lib/bio/tree.rb', line 366 def add_edge(source, target, edge = Edge.new) @pathway.append(Bio::Relation.new(source, target, edge)) edge end |
#add_node(node) ⇒ Object
Adds a node to the tree. Returns self. If the node already exists, it does nothing.
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# File 'lib/bio/tree.rb', line 387 def add_node(node) @pathway.graph[node] ||= {} self end |
#adjacency_matrix(nodes = nil, default_value = nil, diagonal_value = nil) ⇒ Object
Shows the adjacency matrix representation of the tree. It shows matrix only for given nodes. If nodes is nil or is ommitted, it acts the same as tree.adjacency_matrix(tree.nodes). If a block is given, for each edge, it yields source, target, and edge, and uses the returned value of the block. Without blocks, it uses edge. Returns a matrix object.
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# File 'lib/bio/tree.rb', line 758 def adjacency_matrix(nodes = nil, default_value = nil, diagonal_value = nil) #:yields: source, target, edge nodes ||= self.nodes size = nodes.size hash = {} nodes.each_with_index { |x, i| hash[x] = i } # prepares an matrix matrix = Array.new(size, nil) matrix.collect! { |x| Array.new(size, default_value) } (0...size).each { |i| matrix[i][i] = diagonal_value } # fills the matrix from each edge self.each_edge do |source, target, edge| i_source = hash[source] i_target = hash[target] if i_source and i_target then val = block_given? ? (yield source, target, edge) : edge matrix[i_source][i_target] = val matrix[i_target][i_source] = val end end Matrix.rows(matrix, false) end |
#adjacent_nodes(node) ⇒ Object
Returns an array of adjacent nodes of the given node.
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# File 'lib/bio/tree.rb', line 317 def adjacent_nodes(node) h = @pathway.graph[node] h ? h.keys : [] end |
#ancestors(node, root = nil) ⇒ Object
Gets all ancestral nodes of the node. If root isn’t specified or root is nil
, @root is used. Returns an array of Node
s. The result is unspecified for cyclic trees.
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# File 'lib/bio/tree.rb', line 693 def ancestors(node, root = nil) root ||= @root (self.path(root, node) - [ node ]).reverse end |
#children(node, root = nil) ⇒ Object
Gets the adjacent children nodes of the node. If root isn’t specified or root is nil
, @root is used. Returns an array of Node
s. The result is unspecified for cyclic trees.
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# File 'lib/bio/tree.rb', line 636 def children(node, root = nil) root ||= @root path = self.path(root, node) result = self.adjacent_nodes(node) result -= path result end |
#clear ⇒ Object
Clears all nodes and edges. Returns self. Note that options and root are also cleared.
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# File 'lib/bio/tree.rb', line 275 def clear initialize self end |
#clear_node(node) ⇒ Object
Removes all edges connected with the node. Returns self. If the node does not exist, raises IndexError.
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# File 'lib/bio/tree.rb', line 401 def clear_node(node) unless self.include?(node) raise IndexError, 'the node does not exist' end @pathway.relations.delete_if do |rel| rel.node.include?(node) end @pathway.graph[node].each_key do |k| @pathway.graph[k].delete(node) end @pathway.graph[node].clear self end |
#collect_edge! ⇒ Object
Replaces each edge by each block’s return value. Returns self.
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# File 'lib/bio/tree.rb', line 505 def collect_edge! #:yields: source, target, edge @pathway.relations.each do |rel| newedge = yield rel.node[0], rel.node[1], rel.relation rel.relation = newedge @pathway.append(rel, false) end self end |
#collect_node! ⇒ Object
Replaces each node by each block’s return value. Returns self.
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# File 'lib/bio/tree.rb', line 485 def collect_node! #:yields: node tr = {} self.each_node do |node| tr[node] = yield node end # replaces nodes in @pathway.relations @pathway.relations.each do |rel| rel.node.collect! { |node| tr[node] } end # re-generates @pathway from relations @pathway.to_list # adds orphan nodes tr.each_value do |newnode| @pathway.graph[newnode] ||= {} end self end |
#concat(other) ⇒ Object
Concatenates the other tree. If the same edge exists, the edge in other is used. Returns self. The result is unspecified if other isn’t a Tree object. Note that the Node and Edge objects in the other tree are shared in the concatinated tree.
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# File 'lib/bio/tree.rb', line 572 def concat(other) #raise TypeError unless other.kind_of?(self.class) other.each_node do |node| self.add_node(node) end other.each_edge do |node1, node2, edge| self.add_edge(node1, node2, edge) end self end |
#descendents(node, root = nil) ⇒ Object
Gets all descendent nodes of the node. If root isn’t specified or root is nil
, @root is used. Returns an array of Node
s. The result is unspecified for cyclic trees.
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# File 'lib/bio/tree.rb', line 648 def descendents(node, root = nil) root ||= @root distance, route = @pathway.breadth_first_search(root) d = distance[node] result = [] distance.each do |key, val| if val > d then x = key while x = route[x] if x == node then result << key break end break if distance[x] <= d end end end result end |
#distance(node1, node2) ⇒ Object
Returns distance between node1 and node2. It would raise error if the edges didn’t contain distance values. The result is unspecified for cyclic trees.
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# File 'lib/bio/tree.rb', line 615 def distance(node1, node2) distance = 0 self.each_edge_in_path(node1, node2) do |source, target, edge| distance += get_edge_distance(edge) end distance end |
#distance_matrix(nodes = nil) ⇒ Object
Calculates distance matrix of given nodes. If nodes is nil, or is ommited, it acts the same as tree.distance_matrix(tree.leaves). Returns a matrix object. The result is unspecified for cyclic trees. Note 1: The diagonal values of the matrix are 0. Note 2: If the distance cannot be calculated, nil will be set.
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# File 'lib/bio/tree.rb', line 729 def distance_matrix(nodes = nil) nodes ||= self.leaves matrix = [] nodes.each_index do |i| row = [] nodes.each_index do |j| if i == j then distance = 0 elsif r = matrix[j] and val = r[i] then distance = val else distance = (self.distance(nodes[i], nodes[j]) rescue nil) end row << distance end matrix << row end Matrix.rows(matrix, false) end |
#each_edge ⇒ Object
Iterates over each edges of this tree.
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# File 'lib/bio/tree.rb', line 297 def each_edge #:yields: source, target, edge @pathway.relations.each do |rel| yield rel.node[0], rel.node[1], rel.relation end self end |
#each_edge_in_path(node1, node2) ⇒ Object
Iterates over each edge from node1 to node2. The result is unspecified for cyclic trees.
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# File 'lib/bio/tree.rb', line 601 def each_edge_in_path(node1, node2) path = self.path(node1, node2) source = path.shift path.each do |target| edge = self.get_edge(source, target) yield source, target, edge source = target end self end |
#each_node(&x) ⇒ Object
Iterates over each node of this tree.
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# File 'lib/bio/tree.rb', line 291 def each_node(&x) #:yields: node @pathway.graph.each_key(&x) self end |
#each_out_edge(source) ⇒ Object
Iterates over each connected edges of the given node. Returns self.
The reason why the method name is “each_out_edge” is that it comes from the Boost Graph Library.
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# File 'lib/bio/tree.rb', line 341 def each_out_edge(source) #:yields: source, target, edge h = @pathway.graph[source] h.each { |key, val| yield source, key, val } if h self end |
#edges ⇒ Object
Returns all edges an array of [ node0, node1, edge ]
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# File 'lib/bio/tree.rb', line 305 def edges @pathway.relations.collect do |rel| [ rel.node[0], rel.node[1], rel.relation ] end end |
#get_edge(source, target) ⇒ Object
Returns an edge from source to target. If source and target are not adjacent nodes, returns nil.
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# File 'lib/bio/tree.rb', line 358 def get_edge(source, target) h = @pathway.graph[source] h ? h[target] : nil end |
#get_edge_distance(edge) ⇒ Object
Gets distance value from the given edge. Returns float or any other numeric value or nil.
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# File 'lib/bio/tree.rb', line 101 def get_edge_distance(edge) begin dist = edge.distance rescue NoMethodError dist = edge end dist end |
#get_edge_distance_string(edge) ⇒ Object
Gets distance string from the given edge. Returns a string or nil.
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# File 'lib/bio/tree.rb', line 112 def get_edge_distance_string(edge) begin dist = edge.distance_string rescue NoMethodError dist = (edge ? edge.to_s : nil) end dist end |
#get_edge_merged(edge1, edge2) ⇒ Object
Returns edge1 + edge2
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# File 'lib/bio/tree.rb', line 122 def get_edge_merged(edge1, edge2) dist1 = get_edge_distance(edge1) dist2 = get_edge_distance(edge2) if dist1 and dist2 then Edge.new(dist1 + dist2) elsif dist1 then Edge.new(dist1) elsif dist2 then Edge.new(dist2) else Edge.new end end |
#get_node_bootstrap(node) ⇒ Object
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# File 'lib/bio/tree.rb', line 236 def get_node_bootstrap(node) begin node.bootstrap rescue NoMethodError nil end end |
#get_node_bootstrap_string(node) ⇒ Object
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# File 'lib/bio/tree.rb', line 244 def get_node_bootstrap_string(node) begin node.bootstrap_string rescue NoMethodError nil end end |
#get_node_by_name(str) ⇒ Object
Finds a node in the tree by given name and returns the node. If the node does not found, returns nil. If multiple nodes with the same name exist, the result would be one of those (unspecified).
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# File 'lib/bio/tree.rb', line 375 def get_node_by_name(str) self.each_node do |node| if get_node_name(node) == str return node end end nil end |
#get_node_name(node) ⇒ Object
Gets node name
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# File 'lib/bio/tree.rb', line 228 def get_node_name(node) begin node.name rescue NoMethodError node.to_s end end |
#include?(node) ⇒ Boolean
If the node exists, returns true. Otherwise, returns false.
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# File 'lib/bio/tree.rb', line 394 def include?(node) @pathway.graph[node] ? true : false end |
#insert_node(node1, node2, new_node, new_distance = nil) ⇒ Object
Insert a new node between adjacent nodes node1 and node2. The old edge between node1 and node2 are changed to the edge between new_node and node2. The edge between node1 and new_node is newly created.
If new_distance is specified, the distance between node1 and new_node is set to new_distance, and distance between new_node and node2 is set to tree.get_edge(node1, node2).distance - new_distance
.
Returns self. If node1 and node2 are not adjacent, raises IndexError.
If new_node already exists in the tree, the tree would become circular. In addition, if the edge between new_node and node1 (or node2) already exists, it will be erased.
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# File 'lib/bio/tree.rb', line 825 def insert_node(node1, node2, new_node, new_distance = nil) unless edge = self.get_edge(node1, node2) then raise IndexError, 'nodes not found or two nodes are not adjacent' end new_edge = Edge.new(new_distance) self.remove_edge(node1, node2) self.add_edge(node1, new_node, new_edge) if new_distance and old_distance = get_edge_distance(edge) then old_distance -= new_distance begin edge.distance = old_distance rescue NoMethodError edge = old_distance end end self.add_edge(new_node, node2, edge) self end |
#leaves(node = nil, root = nil) ⇒ Object
If node is nil, returns an array of all leaves (nodes connected with one edge). Otherwise, gets all descendent leaf nodes of the node. If root isn’t specified or root is nil
, @root is used. Returns an array of Node
s. The result is unspecified for cyclic trees.
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# File 'lib/bio/tree.rb', line 674 def leaves(node = nil, root = nil) unless node then nodes = [] self.each_node do |x| nodes << x if self.out_degree(x) == 1 end return nodes else root ||= @root self.descendents(node, root).find_all do |x| self.adjacent_nodes(x).size == 1 end end end |
#lowest_common_ancestor(node1, node2, root = nil) ⇒ Object
Gets the lowest common ancestor of the two nodes. If root isn’t specified or root is nil
, @root is used. Returns a Node
object or nil. The result is unspecified for cyclic trees.
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# File 'lib/bio/tree.rb', line 702 def lowest_common_ancestor(node1, node2, root = nil) root ||= @root distance, route = @pathway.breadth_first_search(root) x = node1; r1 = [] begin; r1 << x; end while x = route[x] x = node2; r2 = [] begin; r2 << x; end while x = route[x] return (r1 & r2).first end |
#nodes ⇒ Object
Returns all nodes as an array.
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# File 'lib/bio/tree.rb', line 281 def nodes @pathway.graph.keys end |
#number_of_edges ⇒ Object
Returns number of edges in the tree.
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# File 'lib/bio/tree.rb', line 312 def number_of_edges @pathway.relations.size end |
#number_of_nodes ⇒ Object
Number of nodes.
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# File 'lib/bio/tree.rb', line 286 def number_of_nodes @pathway.nodes end |
#out_degree(source) ⇒ Object
Returns number of edges in the given node.
The reason why the method name is “out_degree” is that it comes from the Boost Graph Library.
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# File 'lib/bio/tree.rb', line 351 def out_degree(source) h = @pathway.graph[source] h ? h.size : 0 end |
#out_edges(source) ⇒ Object
Returns all connected edges with adjacent nodes. Returns an array of the array [ source, target, edge ].
The reason why the method name is “out_edges” is that it comes from the Boost Graph Library.
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# File 'lib/bio/tree.rb', line 327 def out_edges(source) h = @pathway.graph[source] if h h.collect { |key, val| [ source, key, val ] } else [] end end |
#output(format, *arg, &block) ⇒ Object
Returns formatted text (or something) of the tree Currently supported format is: :newick, :nhx
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# File 'lib/bio/db/newick.rb', line 235 def output(format, *arg, &block) case format when :newick output_newick(*arg, &block) when :nhx output_nhx(*arg, &block) when :phylip_distance_matrix output_phylip_distance_matrix(*arg, &block) else raise 'Unknown format' end end |
#output_newick(options = {}, &block) ⇒ Object Also known as: newick
Returns a newick formatted string. If block is given, the order of the node is sorted (as the same manner as Enumerable#sort).
Available options:
:indent
-
indent string; set false to disable (default: ‘ ’)
:bootstrap_style
-
:disabled
disables bootstrap representations.:traditional
for traditional style.:molphy
for Molphy style (default).
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# File 'lib/bio/db/newick.rb', line 203 def output_newick( = {}, &block) #:yields: node1, node2 root = @root root ||= self.nodes.first return '();' unless root __to_newick([], root, 0, :__to_newick_format_leaf, , &block) + __to_newick_format_leaf(root, Edge.new, ) + ";\n" end |
#output_nhx(options = {}, &block) ⇒ Object
Returns a NHX (New Hampshire eXtended) formatted string. If block is given, the order of the node is sorted (as the same manner as Enumerable#sort).
Available options:
:indent
-
indent string; set false to disable (default: ‘ ’)
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# File 'lib/bio/db/newick.rb', line 223 def output_nhx( = {}, &block) #:yields: node1, node2 root = @root root ||= self.nodes.first return '();' unless root __to_newick([], root, 0, :__to_newick_format_leaf_NHX, , &block) + __to_newick_format_leaf_NHX(root, Edge.new, ) + ";\n" end |
#output_phylip_distance_matrix(nodes = nil, options = {}) ⇒ Object
Generates phylip-style distance matrix as a string. if nodes is not given, all leaves in the tree are used. If the names of some of the given (or default) nodes are not defined or are empty, the names are automatically generated.
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# File 'lib/bio/db/newick.rb', line 256 def output_phylip_distance_matrix(nodes = nil, = {}) nodes = self.leaves unless nodes names = nodes.collect do |x| y = get_node_name(x) y = sprintf("%x", x.__id__.abs) if y.empty? y end m = self.distance_matrix(nodes) Bio::Phylip::DistanceMatrix.generate(m, names, ) end |
#parent(node, root = nil) ⇒ Object
Gets the parent node of the node. If root isn’t specified or root is nil
, @root is used. Returns an Node
object or nil. The result is unspecified for cyclic trees.
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# File 'lib/bio/tree.rb', line 627 def parent(node, root = nil) root ||= @root self.path(root, node)[-2] end |
#path(node1, node2) ⇒ Object
Gets path from node1 to node2. Retruns an array of nodes, including node1 and node2. If node1 and/or node2 do not exist, IndexError is raised. If node1 and node2 are not connected, NoPathError is raised. The result is unspecified for cyclic trees.
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# File 'lib/bio/tree.rb', line 588 def path(node1, node2) raise IndexError, 'node1 not found' unless @pathway.graph[node1] raise IndexError, 'node2 not found' unless @pathway.graph[node2] return [ node1 ] if node1 == node2 step, path = @pathway.bfs_shortest_path(node1, node2) unless path[0] == node1 and path[-1] == node2 then raise NoPathError, 'node1 and node2 are not connected' end path end |
#remove_edge(source, target) ⇒ Object
Removes an edge between source and target. Returns self. If the edge does not exist, raises IndexError.
If two or more edges exists between source and target, all of them are removed. +++
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# File 'lib/bio/tree.rb', line 446 def remove_edge(source, target) unless self.get_edge(source, target) then raise IndexError, 'edge not found' end fwd = [ source, target ] rev = [ target, source ] @pathway.relations.delete_if do |rel| rel.node == fwd or rel.node == rev end h = @pathway.graph[source] h.delete(target) if h h = @pathway.graph[target] h.delete(source) if h self end |
#remove_edge_if ⇒ Object
Removes each edge if the block returns not nil. Returns self.
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# File 'lib/bio/tree.rb', line 464 def remove_edge_if #:yields: source, target, edge removed_rel = [] @pathway.relations.delete_if do |rel| if yield rel.node[0], rel.node[1], edge then removed_rel << rel true end end removed_rel.each do |rel| source = rel[0] target = rel[1] h = @pathway.graph[source] h.delete(target) if h h = @pathway.graph[target] h.delete(source) if h end self end |
#remove_node(node) ⇒ Object
Removes the given node from the tree. All edges connected with the node are also removed. Returns self. If the node does not exist, raises IndexError.
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# File 'lib/bio/tree.rb', line 419 def remove_node(node) self.clear_node(node) @pathway.graph.delete(node) self end |
#remove_node_if ⇒ Object
Removes each node if the block returns not nil. All edges connected with the removed nodes are also removed. Returns self.
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# File 'lib/bio/tree.rb', line 428 def remove_node_if all = self.nodes all.each do |node| if yield node then self.clear_node(node) @pathway.graph.delete(node) end end self end |
#remove_nonsense_nodes ⇒ Object
Removes all nodes that are not branches nor leaves. That is, removes nodes connected with exactly two edges. For each removed node, two adjacent edges are merged and a new edge are created. Returns removed nodes. Note that orphan nodes are still kept unchanged.
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# File 'lib/bio/tree.rb', line 788 def remove_nonsense_nodes hash = {} self.each_node do |node| hash[node] = true if @pathway.graph[node].size == 2 end hash.each_key do |node| adjs = @pathway.graph[node].keys edges = @pathway.graph[node].values new_edge = get_edge_merged(edges[0], edges[1]) @pathway.graph[adjs[0]].delete(node) @pathway.graph[adjs[1]].delete(node) @pathway.graph.delete(node) @pathway.append(Bio::Relation.new(adjs[0], adjs[1], new_edge)) end #@pathway.to_relations @pathway.relations.reject! do |rel| hash[rel.node[0]] or hash[rel.node[1]] end return hash.keys end |
#subtree(nodes) ⇒ Object
Gets the sub-tree consisted of given nodes. nodes must be an array of nodes. Nodes that do not exist in the original tree are ignored. Returns a Tree object. Note that the sub-tree shares Node and Edge objects with the original tree.
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# File 'lib/bio/tree.rb', line 520 def subtree(nodes) nodes = nodes.find_all do |x| @pathway.graph[x] end return self.class.new if nodes.empty? # creates subtree new_tree = self.class.new nodes.each do |x| new_tree.add_node(x) end self.each_edge do |node1, node2, edge| if new_tree.include?(node1) and new_tree.include?(node2) then new_tree.add_edge(node1, node2, edge) end end return new_tree end |
#subtree_with_all_paths(nodes) ⇒ Object
Gets the sub-tree consisted of given nodes and all internal nodes connected between given nodes. nodes must be an array of nodes. Nodes that do not exist in the original tree are ignored. Returns a Tree object. The result is unspecified for cyclic trees. Note that the sub-tree shares Node and Edge objects with the original tree.
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# File 'lib/bio/tree.rb', line 546 def subtree_with_all_paths(nodes) hash = {} nodes.each { |x| hash[x] = true } nodes.each_index do |i| node1 = nodes[i] (0...i).each do |j| node2 = nodes[j] unless node1 == node2 then begin path = self.path(node1, node2) rescue IndexError, NoPathError path = [] end path.each { |x| hash[x] = true } end end end self.subtree(hash.keys) end |
#total_distance ⇒ Object
Returns total distance of all edges. It would raise error if some edges didn’t contain distance values.
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# File 'lib/bio/tree.rb', line 714 def total_distance distance = 0 self.each_edge do |source, target, edge| distance += get_edge_distance(edge) end distance end |