Class | Bio::Tree
In: | lib/bio/db/newick.rb lib/bio/tree.rb
Parent: | Object

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.

### Methods

add_edge add_node adjacency_matrix adjacent_nodes ancestors children clear clear_node collect_edge! collect_node! concat descendents distance distance_matrix each_edge each_edge_in_path each_node each_out_edge edges get_edge get_edge_distance get_edge_distance_string get_edge_merged get_node_bootstrap get_node_bootstrap_string get_node_by_name get_node_name include? insert_node leaves lowest_common_ancestor new newick nodes number_of_edges number_of_nodes out_degree out_edges output output_newick output_nhx output_phylip_distance_matrix parent path remove_edge remove_edge_if remove_node remove_node_if remove_nonsense_nodes subtree subtree_with_all_paths total_distance

### Classes and Modules

Class Bio::Tree::Edge
Class Bio::Tree::NoPathError
Class Bio::Tree::Node

### Constants

DEFAULT_OPTIONS | = | { :indent => ' ' } |  | default options

### Attributes

options | [RW] | tree options; mainly used for tree output
root | [RW] | root node of this tree (even if unrooted tree, it is used by some methods)

### Public Class methods

new(tree = nil)

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.

[Source]

         # File lib/bio/tree.rb, line 259
    259:     def initialize(tree = nil)
    260:       # creates an undirected adjacency list graph
    261:       @pathway = Bio::Pathway.new([], true)
    262:       @root = nil
    263:       @options = {}
    264:       self.concat(tree) if tree
    265:     end

### Public Instance methods

add_edge(source, target, edge = Edge.new)

Adds a new edge to the tree. Returns the newly added edge. If the edge already exists, it is overwritten with new one.

[Source]

         # File lib/bio/tree.rb, line 368
    368:     def add_edge(source, target, edge = Edge.new)
    369:       @pathway.append(Bio::Relation.new(source, target, edge))
    370:       edge
    371:     end

add_node(node)

Adds a node to the tree. Returns self. If the node already exists, it does nothing.

[Source]

         # File lib/bio/tree.rb, line 389
    389:     def add_node(node)
    390:       @pathway.graph[node] ||= {}
    391:       self
    392:     end

adjacency_matrix(nodes = nil, default_value = nil, diagonal_value = nil) {|source, target, edge| ...}

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.

[Source]

         # File lib/bio/tree.rb, line 760
    760:     def adjacency_matrix(nodes = nil,
    761:                          default_value = nil,
    762:                          diagonal_value = nil) #:yields: source, target, edge
    763:       nodes ||= self.nodes
    764:       size = nodes.size
    765:       hash = {}
    766:       nodes.each_with_index { |x, i| hash[x] = i }
    767:       # prepares an matrix
    768:       matrix = Array.new(size, nil)
    769:       matrix.collect! { |x| Array.new(size, default_value) }
    770:       (0...size).each { |i| matrix[i][i] = diagonal_value }
    771:       # fills the matrix from each edge
    772:       self.each_edge do |source, target, edge|
    773:         i_source = hash[source]
    774:         i_target = hash[target]
    775:         if i_source and i_target then
    776:           val = block_given? ? (yield source, target, edge) : edge
    777:           matrix[i_source][i_target] = val
    778:           matrix[i_target][i_source] = val
    779:         end
    780:       end
    781:       Matrix.rows(matrix, false)
    782:     end

adjacent_nodes(node)

Returns an array of adjacent nodes of the given node.

[Source]

         # File lib/bio/tree.rb, line 319
    319:     def adjacent_nodes(node)
    320:       h = @pathway.graph[node]
    321:       h ? h.keys : []
    322:     end

ancestors(node, root = nil)

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.

[Source]

         # File lib/bio/tree.rb, line 695
    695:     def ancestors(node, root = nil)
    696:       root ||= @root
    697:       (self.path(root, node) - [ node ]).reverse
    698:     end

children(node, root = nil)

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.

[Source]

         # File lib/bio/tree.rb, line 638
    638:     def children(node, root = nil)
    639:       root ||= @root
    640:       path = self.path(root, node)
    641:       result = self.adjacent_nodes(node)
    642:       result -= path
    643:       result
    644:     end

clear()

Clears all nodes and edges. Returns self. Note that options and root are also cleared.

[Source]

         # File lib/bio/tree.rb, line 277
    277:     def clear
    278:       initialize
    279:       self
    280:     end

clear_node(node)

Removes all edges connected with the node. Returns self. If the node does not exist, raises IndexError.

[Source]

         # File lib/bio/tree.rb, line 403
    403:     def clear_node(node)
    404:       unless self.include?(node)
    405:         raise IndexError, 'the node does not exist'
    406:       end
    407:       @pathway.relations.delete_if do |rel|
    408:         rel.node.include?(node)
    409:       end
    410:       @pathway.graph[node].each_key do |k|
    411:         @pathway.graph[k].delete(node)
    412:       end
    413:       @pathway.graph[node].clear
    414:       self
    415:     end

collect_edge!( {|source, target, edge| ...}

Replaces each edge by each block‘s return value. Returns self.

[Source]

         # File lib/bio/tree.rb, line 507
    507:     def collect_edge! #:yields: source, target, edge
    508:       @pathway.relations.each do |rel|
    509:         newedge = yield rel.node[0], rel.node[1], rel.relation
    510:         rel.relation = newedge
    511:         @pathway.append(rel, false)
    512:       end
    513:       self
    514:     end

collect_node!( {|node| ...}

Replaces each node by each block‘s return value. Returns self.

[Source]

         # File lib/bio/tree.rb, line 487
    487:     def collect_node! #:yields: node
    488:       tr = {}
    489:       self.each_node do |node|
    490:         tr[node] = yield node
    491:       end
    492:       # replaces nodes in @pathway.relations
    493:       @pathway.relations.each do |rel|
    494:         rel.node.collect! { |node| tr[node] }
    495:       end
    496:       # re-generates @pathway from relations
    497:       @pathway.to_list
    498:       # adds orphan nodes
    499:       tr.each_value do |newnode|
    500:         @pathway.graph[newnode] ||= {}
    501:       end
    502:       self
    503:     end

concat(other)

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.

[Source]

         # File lib/bio/tree.rb, line 574
    574:     def concat(other)
    575:       #raise TypeError unless other.kind_of?(self.class)
    576:       other.each_node do |node|
    577:         self.add_node(node)
    578:       end
    579:       other.each_edge do |node1, node2, edge|
    580:         self.add_edge(node1, node2, edge)
    581:       end
    582:       self
    583:     end

descendents(node, root = nil)

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.

[Source]

         # File lib/bio/tree.rb, line 650
    650:     def descendents(node, root = nil)
    651:       root ||= @root
    652:       distance, route = @pathway.breadth_first_search(root)
    653:       d = distance[node]
    654:       result = []
    655:       distance.each do |key, val|
    656:         if val > d then
    657:           x = key
    658:           while x = route[x]
    659:             if x == node then
    660:               result << key
    661:               break
    662:             end
    663:             break if distance[x] <= d
    664:           end
    665:         end
    666:       end
    667:       result
    668:     end

distance(node1, node2)

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.

[Source]

         # File lib/bio/tree.rb, line 617
    617:     def distance(node1, node2)
    618:       distance = 0
    619:       self.each_edge_in_path(node1, node2) do |source, target, edge|
    620:         distance += get_edge_distance(edge)
    621:       end
    622:       distance
    623:     end

distance_matrix(nodes = nil)

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.

[Source]

         # File lib/bio/tree.rb, line 731
    731:     def distance_matrix(nodes = nil)
    732:       nodes ||= self.leaves
    733:       matrix = []
    734:       nodes.each_index do |i|
    735:         row = []
    736:         nodes.each_index do |j|
    737:           if i == j then
    738:             distance = 0
    739:           elsif r = matrix[j] and val = r[i] then
    740:             distance = val
    741:           else
    742:             distance = (self.distance(nodes[i], nodes[j]) rescue nil)
    743:           end
    744:           row << distance
    745:         end
    746:         matrix << row
    747:       end
    748:       Matrix.rows(matrix, false)
    749:     end

each_edge( {|source, target, edge| ...}

Iterates over each edges of this tree.

[Source]

         # File lib/bio/tree.rb, line 299
    299:     def each_edge #:yields: source, target, edge
    300:       @pathway.relations.each do |rel|
    301:         yield rel.node[0], rel.node[1], rel.relation
    302:       end
    303:       self
    304:     end

each_edge_in_path(node1, node2) {|source, target, edge| ...}

Iterates over each edge from node1 to node2. The result is unspecified for cyclic trees.

[Source]

         # File lib/bio/tree.rb, line 603
    603:     def each_edge_in_path(node1, node2)
    604:       path = self.path(node1, node2)
    605:       source = path.shift
    606:       path.each do |target|
    607:         edge = self.get_edge(source, target)
    608:         yield source, target, edge
    609:         source = target
    610:       end
    611:       self
    612:     end

each_node() {|node| ...}

Iterates over each node of this tree.

[Source]

         # File lib/bio/tree.rb, line 293
    293:     def each_node(&x) #:yields: node
    294:       @pathway.graph.each_key(&x)
    295:       self
    296:     end

each_out_edge(source) {|source, target, edge| ...}

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.

[Source]

         # File lib/bio/tree.rb, line 343
    343:     def each_out_edge(source) #:yields: source, target, edge
    344:       h = @pathway.graph[source]
    345:       h.each { |key, val| yield source, key, val } if h
    346:       self
    347:     end

edges()

Returns all edges an array of [ node0, node1, edge ]

[Source]

         # File lib/bio/tree.rb, line 307
    307:     def edges
    308:       @pathway.relations.collect do |rel|
    309:         [ rel.node[0], rel.node[1], rel.relation ]
    310:       end
    311:     end

get_edge(source, target)

Returns an edge from source to target. If source and target are not adjacent nodes, returns nil.

[Source]

         # File lib/bio/tree.rb, line 360
    360:     def get_edge(source, target)
    361:       h = @pathway.graph[source]
    362:       h ? h[target] : nil
    363:     end

get_edge_distance(edge)

Gets distance value from the given edge. Returns float or any other numeric value or nil.

[Source]

         # File lib/bio/tree.rb, line 101
    101:     def get_edge_distance(edge)
    102:       begin
    103:         dist = edge.distance
    104:       rescue NoMethodError
    105:         dist = edge
    106:       end
    107:       dist
    108:     end

get_edge_distance_string(edge)

Gets distance string from the given edge. Returns a string or nil.

[Source]

         # File lib/bio/tree.rb, line 112
    112:     def get_edge_distance_string(edge)
    113:       begin
    114:         dist = edge.distance_string
    115:       rescue NoMethodError
    116:         dist = (edge ? edge.to_s : nil)
    117:       end
    118:       dist
    119:     end

get_edge_merged(edge1, edge2)

Returns edge1 + edge2

[Source]

         # File lib/bio/tree.rb, line 122
    122:     def get_edge_merged(edge1, edge2)
    123:       dist1 = get_edge_distance(edge1)
    124:       dist2 = get_edge_distance(edge2)
    125:       if dist1 and dist2 then
    126:         Edge.new(dist1 + dist2)
    127:       elsif dist1 then
    128:         Edge.new(dist1)
    129:       elsif dist2 then
    130:         Edge.new(dist2)
    131:       else
    132:         Edge.new
    133:       end
    134:     end

get_node_bootstrap(node)

[Source]

         # File lib/bio/tree.rb, line 238
    238:     def get_node_bootstrap(node)
    239:       begin
    240:         node.bootstrap
    241:       rescue NoMethodError
    242:         nil
    243:       end
    244:     end

get_node_bootstrap_string(node)

[Source]

         # File lib/bio/tree.rb, line 246
    246:     def get_node_bootstrap_string(node)
    247:       begin
    248:         node.bootstrap_string
    249:       rescue NoMethodError
    250:         nil
    251:       end
    252:     end

get_node_by_name(str)

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).

[Source]

         # File lib/bio/tree.rb, line 377
    377:     def get_node_by_name(str)
    378:       self.each_node do |node|
    379:         if get_node_name(node) == str
    380:           return node
    381:         end
    382:       end
    383:       nil
    384:     end

get_node_name(node)

Gets node name

[Source]

         # File lib/bio/tree.rb, line 230
    230:     def get_node_name(node)
    231:       begin
    232:         node.name
    233:       rescue NoMethodError
    234:         node.to_s
    235:       end
    236:     end

include?(node)

If the node exists, returns true. Otherwise, returns false.

[Source]

         # File lib/bio/tree.rb, line 396
    396:     def include?(node)
    397:       @pathway.graph[node] ? true : false
    398:     end

insert_node(node1, node2, new_node, new_distance = nil)

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.

[Source]

         # File lib/bio/tree.rb, line 827
    827:     def insert_node(node1, node2, new_node, new_distance = nil)
    828:       unless edge = self.get_edge(node1, node2) then
    829:         raise IndexError, 'nodes not found or two nodes are not adjacent'
    830:       end
    831:       new_edge = Edge.new(new_distance)
    832:       self.remove_edge(node1, node2)
    833:       self.add_edge(node1, new_node, new_edge)
    834:       if new_distance and old_distance = get_edge_distance(edge) then
    835:         old_distance -= new_distance
    836:         begin
    837:           edge.distance = old_distance
    838:         rescue NoMethodError
    839:           edge = old_distance
    840:         end
    841:       end
    842:       self.add_edge(new_node, node2, edge)
    843:       self
    844:     end

leaves(node = nil, root = nil)

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.

[Source]

         # File lib/bio/tree.rb, line 676
    676:     def leaves(node = nil, root = nil)
    677:       unless node then
    678:         nodes = []
    679:         self.each_node do |x|
    680:           nodes << x if self.out_degree(x) == 1
    681:         end
    682:         return nodes
    683:       else
    684:         root ||= @root
    685:         self.descendents(node, root).find_all do |x|
    686:           self.adjacent_nodes(x).size == 1
    687:         end
    688:       end
    689:     end

lowest_common_ancestor(node1, node2, root = nil)

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.

[Source]

         # File lib/bio/tree.rb, line 704
    704:     def lowest_common_ancestor(node1, node2, root = nil)
    705:       root ||= @root
    706:       distance, route = @pathway.breadth_first_search(root)
    707:       x = node1; r1 = []
    708:       begin; r1 << x; end while x = route[x]
    709:       x = node2; r2 = []
    710:       begin; r2 << x; end while x = route[x]
    711:       return (r1 & r2).first
    712:     end

newick(options = {})

Alias for output_newick

nodes()

Returns all nodes as an array.

[Source]

         # File lib/bio/tree.rb, line 283
    283:     def nodes
    284:       @pathway.graph.keys
    285:     end

number_of_edges()

Returns number of edges in the tree.

[Source]

         # File lib/bio/tree.rb, line 314
    314:     def number_of_edges
    315:       @pathway.relations.size
    316:     end

number_of_nodes()

Number of nodes.

[Source]

         # File lib/bio/tree.rb, line 288
    288:     def number_of_nodes
    289:       @pathway.nodes
    290:     end

out_degree(source)

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.

[Source]

         # File lib/bio/tree.rb, line 353
    353:     def out_degree(source)
    354:       h = @pathway.graph[source]
    355:       h ? h.size : 0
    356:     end

out_edges(source)

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.

[Source]

         # File lib/bio/tree.rb, line 329
    329:     def out_edges(source)
    330:       h = @pathway.graph[source]
    331:       if h
    332:         h.collect { |key, val| [ source, key, val ] }
    333:       else
    334:         []
    335:       end
    336:     end

output(format, *arg, &block)

Returns formatted text (or something) of the tree Currently supported format is: :newick, :nhx

[Source]

         # File lib/bio/db/newick.rb, line 235
    235:     def output(format, *arg, &block)
    236:       case format
    237:       when :newick
    238:         output_newick(*arg, &block)
    239:       when :nhx
    240:         output_nhx(*arg, &block)
    241:       when :phylip_distance_matrix
    242:         output_phylip_distance_matrix(*arg, &block)
    243:       else
    244:         raise 'Unknown format'
    245:       end
    246:     end

output_newick(options = {}) {|node1, node2| ...}

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).

[Source]

         # File lib/bio/db/newick.rb, line 203
    203:     def output_newick(options = {}, &block) #:yields: node1, node2
    204:       root = @root
    205:       root ||= self.nodes.first
    206:       return '();' unless root
    207:       __to_newick([], root, 0, :__to_newick_format_leaf, options, &block) +
    208:         __to_newick_format_leaf(root, Edge.new, options) +
    209:         ";\n"
    210:     end

output_nhx(options = {}) {|node1, node2| ...}

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: ’ ’)

[Source]

         # File lib/bio/db/newick.rb, line 223
    223:     def output_nhx(options = {}, &block) #:yields: node1, node2
    224:       root = @root
    225:       root ||= self.nodes.first
    226:       return '();' unless root
    227:       __to_newick([], root, 0,
    228:                   :__to_newick_format_leaf_NHX, options, &block) +
    229:         __to_newick_format_leaf_NHX(root, Edge.new, options) +
    230:         ";\n"
    231:     end

output_phylip_distance_matrix(nodes = nil, options = {})

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.

[Source]

         # File lib/bio/db/newick.rb, line 256
    256:     def output_phylip_distance_matrix(nodes = nil, options = {})
    257:       nodes = self.leaves unless nodes
    258:       names = nodes.collect do |x|
    259:         y = get_node_name(x)
    260:         y = sprintf("%x", x.__id__.abs) if y.empty?
    261:         y
    262:       end
    263:       m = self.distance_matrix(nodes)
    264:       Bio::Phylip::DistanceMatrix.generate(m, names, options)
    265:     end

parent(node, root = nil)

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.

[Source]

         # File lib/bio/tree.rb, line 629
    629:     def parent(node, root = nil)
    630:       root ||= @root
    631:       self.path(root, node)[-2]
    632:     end

path(node1, node2)

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.

[Source]

         # File lib/bio/tree.rb, line 590
    590:     def path(node1, node2)
    591:       raise IndexError, 'node1 not found' unless @pathway.graph[node1]
    592:       raise IndexError, 'node2 not found' unless @pathway.graph[node2]
    593:       return [ node1 ] if node1 == node2
    594:       step, path = @pathway.bfs_shortest_path(node1, node2)
    595:       unless path[0] == node1 and path[-1] == node2 then
    596:         raise NoPathError, 'node1 and node2 are not connected'
    597:       end
    598:       path
    599:     end

remove_edge(source, target)

# Removes an edge between source and target. # Returns self. # If the edge does not exist, raises IndexError. +

[Source]

         # File lib/bio/tree.rb, line 448
    448:     def remove_edge(source, target)
    449:       unless self.get_edge(source, target) then
    450:         raise IndexError, 'edge not found'
    451:       end
    452:       fwd = [ source, target ]
    453:       rev = [ target, source ]
    454:       @pathway.relations.delete_if do |rel|
    455:         rel.node == fwd or rel.node == rev
    456:       end
    457:       h = @pathway.graph[source]
    458:       h.delete(target) if h
    459:       h = @pathway.graph[target]
    460:       h.delete(source) if h
    461:       self
    462:     end

remove_edge_if( {|source, target, edge| ...}

Removes each edge if the block returns not nil. Returns self.

[Source]

         # File lib/bio/tree.rb, line 466
    466:     def remove_edge_if #:yields: source, target, edge
    467:       removed_rel = []
    468:       @pathway.relations.delete_if do |rel|
    469:         if yield rel.node[0], rel.node[1], edge then
    470:           removed_rel << rel
    471:           true
    472:         end
    473:       end
    474:       removed_rel.each do |rel|
    475:         source = rel[0]
    476:         target = rel[1]
    477:         h = @pathway.graph[source]
    478:         h.delete(target) if h
    479:         h = @pathway.graph[target]
    480:         h.delete(source) if h
    481:       end
    482:       self
    483:     end

remove_node(node)

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.

[Source]

         # File lib/bio/tree.rb, line 421
    421:     def remove_node(node)
    422:       self.clear_node(node)
    423:       @pathway.graph.delete(node)
    424:       self
    425:     end

remove_node_if() {|node then self.clear_node(node)| ...}

Removes each node if the block returns not nil. All edges connected with the removed nodes are also removed. Returns self.

[Source]

         # File lib/bio/tree.rb, line 430
    430:     def remove_node_if
    431:       all = self.nodes
    432:       all.each do |node|
    433:         if yield node then
    434:           self.clear_node(node)
    435:           @pathway.graph.delete(node)
    436:         end
    437:       end
    438:       self
    439:     end

remove_nonsense_nodes()

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.

[Source]

         # File lib/bio/tree.rb, line 790
    790:     def remove_nonsense_nodes
    791:       hash = {}
    792:       self.each_node do |node|
    793:         hash[node] = true if @pathway.graph[node].size == 2
    794:       end
    795:       hash.each_key do |node|
    796:         adjs = @pathway.graph[node].keys
    797:         edges = @pathway.graph[node].values
    798:         new_edge = get_edge_merged(edges[0], edges[1])
    799:         @pathway.graph[adjs[0]].delete(node)
    800:         @pathway.graph[adjs[1]].delete(node)
    801:         @pathway.graph.delete(node)
    802:         @pathway.append(Bio::Relation.new(adjs[0], adjs[1], new_edge))
    803:       end
    804:       #@pathway.to_relations
    805:       @pathway.relations.reject! do |rel|
    806:         hash[rel.node[0]] or hash[rel.node[1]]
    807:       end
    808:       return hash.keys
    809:     end

subtree(nodes)

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.

[Source]

         # File lib/bio/tree.rb, line 522
    522:     def subtree(nodes)
    523:       nodes = nodes.find_all do |x|
    524:         @pathway.graph[x]
    525:       end
    526:       return self.class.new if nodes.empty?
    527:       # creates subtree
    528:       new_tree = self.class.new
    529:       nodes.each do |x|
    530:         new_tree.add_node(x)
    531:       end
    532:       self.each_edge do |node1, node2, edge|
    533:         if new_tree.include?(node1) and new_tree.include?(node2) then
    534:           new_tree.add_edge(node1, node2, edge)
    535:         end
    536:       end
    537:       return new_tree
    538:     end

subtree_with_all_paths(nodes)

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.

[Source]

         # File lib/bio/tree.rb, line 548
    548:     def subtree_with_all_paths(nodes)
    549:       hash = {}
    550:       nodes.each { |x| hash[x] = true }
    551:       nodes.each_index do |i|
    552:         node1 = nodes[i]
    553:         (0...i).each do |j|
    554:           node2 = nodes[j]
    555:           unless node1 == node2 then
    556:             begin
    557:               path = self.path(node1, node2)
    558:             rescue IndexError, NoPathError
    559:               path = []
    560:             end
    561:             path.each { |x| hash[x] = true }
    562:           end
    563:         end
    564:       end
    565:       self.subtree(hash.keys)
    566:     end

total_distance()

Returns total distance of all edges. It would raise error if some edges didn‘t contain distance values.

[Source]

         # File lib/bio/tree.rb, line 716
    716:     def total_distance
    717:       distance = 0
    718:       self.each_edge do |source, target, edge|
    719:         distance += get_edge_distance(edge)
    720:       end
    721:       distance
    722:     end

[Validate]