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:       _init_cache
    265:       self.concat(tree) if tree
    266:     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 381
    381:     def add_edge(source, target, edge = Edge.new)
    382:       _clear_cache
    383:       @pathway.append(Bio::Relation.new(source, target, edge))
    384:       edge
    385:     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 403
    403:     def add_node(node)
    404:       _clear_cache
    405:       @pathway.graph[node] ||= {}
    406:       self
    407:     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 823
    823:     def adjacency_matrix(nodes = nil,
    824:                          default_value = nil,
    825:                          diagonal_value = nil) #:yields: source, target, edge
    826:       nodes ||= self.nodes
    827:       size = nodes.size
    828:       hash = {}
    829:       nodes.each_with_index { |x, i| hash[x] = i }
    830:       # prepares an matrix
    831:       matrix = Array.new(size, nil)
    832:       matrix.collect! { |x| Array.new(size, default_value) }
    833:       (0...size).each { |i| matrix[i][i] = diagonal_value }
    834:       # fills the matrix from each edge
    835:       self.each_edge do |source, target, edge|
    836:         i_source = hash[source]
    837:         i_target = hash[target]
    838:         if i_source and i_target then
    839:           val = block_given? ? (yield source, target, edge) : edge
    840:           matrix[i_source][i_target] = val
    841:           matrix[i_target][i_source] = val
    842:         end
    843:       end
    844:       Matrix.rows(matrix, false)
    845:     end

adjacent_nodes(node)

Returns an array of adjacent nodes of the given node.

[Source]

         # File lib/bio/tree.rb, line 332
    332:     def adjacent_nodes(node)
    333:       h = @pathway.graph[node]
    334:       h ? h.keys : []
    335:     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 758
    758:     def ancestors(node, root = nil)
    759:       root ||= @root
    760:       (self.path(root, node) - [ node ]).reverse
    761:     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 702
    702:     def children(node, root = nil)
    703:       root ||= @root
    704:       c = self.adjacent_nodes(node)
    705:       c.delete(self.parent(node, root))
    706:       c
    707:     end

clear()

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

[Source]

         # File lib/bio/tree.rb, line 290
    290:     def clear
    291:       initialize
    292:       self
    293:     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 418
    418:     def clear_node(node)
    419:       unless self.include?(node)
    420:         raise IndexError, 'the node does not exist'
    421:       end
    422:       _clear_cache
    423:       @pathway.relations.delete_if do |rel|
    424:         rel.node.include?(node)
    425:       end
    426:       @pathway.graph[node].each_key do |k|
    427:         @pathway.graph[k].delete(node)
    428:       end
    429:       @pathway.graph[node].clear
    430:       self
    431:     end

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

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

[Source]

         # File lib/bio/tree.rb, line 528
    528:     def collect_edge! #:yields: source, target, edge
    529:       _clear_cache
    530:       @pathway.relations.each do |rel|
    531:         newedge = yield rel.node[0], rel.node[1], rel.relation
    532:         rel.relation = newedge
    533:         @pathway.append(rel, false)
    534:       end
    535:       self
    536:     end

collect_node!( {|node| ...}

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

[Source]

         # File lib/bio/tree.rb, line 507
    507:     def collect_node! #:yields: node
    508:       _clear_cache
    509:       tr = {}
    510:       self.each_node do |node|
    511:         tr[node] = yield node
    512:       end
    513:       # replaces nodes in @pathway.relations
    514:       @pathway.relations.each do |rel|
    515:         rel.node.collect! { |node| tr[node] }
    516:       end
    517:       # re-generates @pathway from relations
    518:       @pathway.to_list
    519:       # adds orphan nodes
    520:       tr.each_value do |newnode|
    521:         @pathway.graph[newnode] ||= {}
    522:       end
    523:       self
    524:     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 596
    596:     def concat(other)
    597:       #raise TypeError unless other.kind_of?(self.class)
    598:       _clear_cache
    599:       other.each_node do |node|
    600:         self.add_node(node)
    601:       end
    602:       other.each_edge do |node1, node2, edge|
    603:         self.add_edge(node1, node2, edge)
    604:       end
    605:       self
    606:     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 713
    713:     def descendents(node, root = nil)
    714:       root ||= @root
    715:       distance, route = @pathway.breadth_first_search(root)
    716:       d = distance[node]
    717:       result = []
    718:       distance.each do |key, val|
    719:         if val > d then
    720:           x = key
    721:           while x = route[x]
    722:             if x == node then
    723:               result << key
    724:               break
    725:             end
    726:             break if distance[x] <= d
    727:           end
    728:         end
    729:       end
    730:       result
    731:     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 641
    641:     def distance(node1, node2)
    642:       distance = 0
    643:       self.each_edge_in_path(node1, node2) do |source, target, edge|
    644:         distance += get_edge_distance(edge)
    645:       end
    646:       distance
    647:     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 794
    794:     def distance_matrix(nodes = nil)
    795:       nodes ||= self.leaves
    796:       matrix = []
    797:       nodes.each_index do |i|
    798:         row = []
    799:         nodes.each_index do |j|
    800:           if i == j then
    801:             distance = 0
    802:           elsif r = matrix[j] and val = r[i] then
    803:             distance = val
    804:           else
    805:             distance = (self.distance(nodes[i], nodes[j]) rescue nil)
    806:           end
    807:           row << distance
    808:         end
    809:         matrix << row
    810:       end
    811:       Matrix.rows(matrix, false)
    812:     end

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

Iterates over each edges of this tree.

[Source]

         # File lib/bio/tree.rb, line 312
    312:     def each_edge #:yields: source, target, edge
    313:       @pathway.relations.each do |rel|
    314:         yield rel.node[0], rel.node[1], rel.relation
    315:       end
    316:       self
    317:     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 627
    627:     def each_edge_in_path(node1, node2)
    628:       path = self.path(node1, node2)
    629:       source = path.shift
    630:       path.each do |target|
    631:         edge = self.get_edge(source, target)
    632:         yield source, target, edge
    633:         source = target
    634:       end
    635:       self
    636:     end

each_node() {|node| ...}

Iterates over each node of this tree.

[Source]

         # File lib/bio/tree.rb, line 306
    306:     def each_node(&x) #:yields: node
    307:       @pathway.graph.each_key(&x)
    308:       self
    309:     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 356
    356:     def each_out_edge(source) #:yields: source, target, edge
    357:       h = @pathway.graph[source]
    358:       h.each { |key, val| yield source, key, val } if h
    359:       self
    360:     end

edges()

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

[Source]

         # File lib/bio/tree.rb, line 320
    320:     def edges
    321:       @pathway.relations.collect do |rel|
    322:         [ rel.node[0], rel.node[1], rel.relation ]
    323:       end
    324:     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 373
    373:     def get_edge(source, target)
    374:       h = @pathway.graph[source]
    375:       h ? h[target] : nil
    376:     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 391
    391:     def get_node_by_name(str)
    392:       self.each_node do |node|
    393:         if get_node_name(node) == str
    394:           return node
    395:         end
    396:       end
    397:       nil
    398:     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 411
    411:     def include?(node)
    412:       @pathway.graph[node] ? true : false
    413:     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 891
    891:     def insert_node(node1, node2, new_node, new_distance = nil)
    892:       unless edge = self.get_edge(node1, node2) then
    893:         raise IndexError, 'nodes not found or two nodes are not adjacent'
    894:       end
    895:       _clear_cache
    896:       new_edge = Edge.new(new_distance)
    897:       self.remove_edge(node1, node2)
    898:       self.add_edge(node1, new_node, new_edge)
    899:       if new_distance and old_distance = get_edge_distance(edge) then
    900:         old_distance -= new_distance
    901:         begin
    902:           edge.distance = old_distance
    903:         rescue NoMethodError
    904:           edge = old_distance
    905:         end
    906:       end
    907:       self.add_edge(new_node, node2, edge)
    908:       self
    909:     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 739
    739:     def leaves(node = nil, root = nil)
    740:       unless node then
    741:         nodes = []
    742:         self.each_node do |x|
    743:           nodes << x if self.out_degree(x) == 1
    744:         end
    745:         return nodes
    746:       else
    747:         root ||= @root
    748:         self.descendents(node, root).find_all do |x|
    749:           self.adjacent_nodes(x).size == 1
    750:         end
    751:       end
    752:     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 767
    767:     def lowest_common_ancestor(node1, node2, root = nil)
    768:       root ||= @root
    769:       distance, route = @pathway.breadth_first_search(root)
    770:       x = node1; r1 = []
    771:       begin; r1 << x; end while x = route[x]
    772:       x = node2; r2 = []
    773:       begin; r2 << x; end while x = route[x]
    774:       return (r1 & r2).first
    775:     end

newick(options = {})

Alias for output_newick

nodes()

Returns all nodes as an array.

[Source]

         # File lib/bio/tree.rb, line 296
    296:     def nodes
    297:       @pathway.graph.keys
    298:     end

number_of_edges()

Returns number of edges in the tree.

[Source]

         # File lib/bio/tree.rb, line 327
    327:     def number_of_edges
    328:       @pathway.relations.size
    329:     end

number_of_nodes()

Number of nodes.

[Source]

         # File lib/bio/tree.rb, line 301
    301:     def number_of_nodes
    302:       @pathway.nodes
    303:     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 366
    366:     def out_degree(source)
    367:       h = @pathway.graph[source]
    368:       h ? h.size : 0
    369:     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 342
    342:     def out_edges(source)
    343:       h = @pathway.graph[source]
    344:       if h
    345:         h.collect { |key, val| [ source, key, val ] }
    346:       else
    347:         []
    348:       end
    349:     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 688
    688:     def parent(node, root = nil)
    689:       root ||= @root
    690:       raise IndexError, 'can not get parent for unrooted tree' unless root
    691:       unless ret = _get_cached_parent(node, root) then
    692:         ret = self.path(root, node)[-2]
    693:         _cache_parent(node, ret, root)
    694:       end
    695:       ret
    696:     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 613
    613:     def path(node1, node2)
    614:       raise IndexError, 'node1 not found' unless @pathway.graph[node1]
    615:       raise IndexError, 'node2 not found' unless @pathway.graph[node2]
    616:       return [ node1 ] if node1 == node2
    617:       return [ node1, node2 ] if @pathway.graph[node1][node2]
    618:       step, path = @pathway.bfs_shortest_path(node1, node2)
    619:       unless path[0] == node1 and path[-1] == node2 then
    620:         raise NoPathError, 'node1 and node2 are not connected'
    621:       end
    622:       path
    623:     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 466
    466:     def remove_edge(source, target)
    467:       unless self.get_edge(source, target) then
    468:         raise IndexError, 'edge not found'
    469:       end
    470:       _clear_cache
    471:       fwd = [ source, target ]
    472:       rev = [ target, source ]
    473:       @pathway.relations.delete_if do |rel|
    474:         rel.node == fwd or rel.node == rev
    475:       end
    476:       h = @pathway.graph[source]
    477:       h.delete(target) if h
    478:       h = @pathway.graph[target]
    479:       h.delete(source) if h
    480:       self
    481:     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 485
    485:     def remove_edge_if #:yields: source, target, edge
    486:       _clear_cache
    487:       removed_rel = []
    488:       @pathway.relations.delete_if do |rel|
    489:         if yield rel.node[0], rel.node[1], edge then
    490:           removed_rel << rel
    491:           true
    492:         end
    493:       end
    494:       removed_rel.each do |rel|
    495:         source = rel[0]
    496:         target = rel[1]
    497:         h = @pathway.graph[source]
    498:         h.delete(target) if h
    499:         h = @pathway.graph[target]
    500:         h.delete(source) if h
    501:       end
    502:       self
    503:     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 437
    437:     def remove_node(node)
    438:       #_clear_cache #done in clear_node(node)
    439:       self.clear_node(node)
    440:       @pathway.graph.delete(node)
    441:       self
    442:     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 447
    447:     def remove_node_if
    448:       #_clear_cache #done in clear_node(node)
    449:       all = self.nodes
    450:       all.each do |node|
    451:         if yield node then
    452:           self.clear_node(node)
    453:           @pathway.graph.delete(node)
    454:         end
    455:       end
    456:       self
    457:     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 853
    853:     def remove_nonsense_nodes
    854:       _clear_cache
    855:       hash = {}
    856:       self.each_node do |node|
    857:         hash[node] = true if @pathway.graph[node].size == 2
    858:       end
    859:       hash.each_key do |node|
    860:         adjs = @pathway.graph[node].keys
    861:         edges = @pathway.graph[node].values
    862:         new_edge = get_edge_merged(edges[0], edges[1])
    863:         @pathway.graph[adjs[0]].delete(node)
    864:         @pathway.graph[adjs[1]].delete(node)
    865:         @pathway.graph.delete(node)
    866:         @pathway.append(Bio::Relation.new(adjs[0], adjs[1], new_edge))
    867:       end
    868:       #@pathway.to_relations
    869:       @pathway.relations.reject! do |rel|
    870:         hash[rel.node[0]] or hash[rel.node[1]]
    871:       end
    872:       return hash.keys
    873:     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 544
    544:     def subtree(nodes)
    545:       nodes = nodes.find_all do |x|
    546:         @pathway.graph[x]
    547:       end
    548:       return self.class.new if nodes.empty?
    549:       # creates subtree
    550:       new_tree = self.class.new
    551:       nodes.each do |x|
    552:         new_tree.add_node(x)
    553:       end
    554:       self.each_edge do |node1, node2, edge|
    555:         if new_tree.include?(node1) and new_tree.include?(node2) then
    556:           new_tree.add_edge(node1, node2, edge)
    557:         end
    558:       end
    559:       return new_tree
    560:     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 570
    570:     def subtree_with_all_paths(nodes)
    571:       hash = {}
    572:       nodes.each { |x| hash[x] = true }
    573:       nodes.each_index do |i|
    574:         node1 = nodes[i]
    575:         (0...i).each do |j|
    576:           node2 = nodes[j]
    577:           unless node1 == node2 then
    578:             begin
    579:               path = self.path(node1, node2)
    580:             rescue IndexError, NoPathError
    581:               path = []
    582:             end
    583:             path.each { |x| hash[x] = true }
    584:           end
    585:         end
    586:       end
    587:       self.subtree(hash.keys)
    588:     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 779
    779:     def total_distance
    780:       distance = 0
    781:       self.each_edge do |source, target, edge|
    782:         distance += get_edge_distance(edge)
    783:       end
    784:       distance
    785:     end

[Validate]