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.
DEFAULT_OPTIONS | = | { :indent => ' ' } | default options |
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) |
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.
# 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
Adds a node to the tree. Returns self. If the node already exists, it does nothing.
# File lib/bio/tree.rb, line 389 389: def add_node(node) 390: @pathway.graph[node] ||= {} 391: self 392: end
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.
# 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
Gets all ancestral nodes of the node. If root isn‘t specified or root is nil, @root is used. Returns an array of Nodes. The result is unspecified for cyclic trees.
# 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
Gets the adjacent children nodes of the node. If root isn‘t specified or root is nil, @root is used. Returns an array of Nodes. The result is unspecified for cyclic trees.
# 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
Removes all edges connected with the node. Returns self. If the node does not exist, raises IndexError.
# 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
Replaces each edge by each block‘s return value. Returns self.
# 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
Replaces each node by each block‘s return value. Returns self.
# 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
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.
# 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
Gets all descendent nodes of the node. If root isn‘t specified or root is nil, @root is used. Returns an array of Nodes. The result is unspecified for cyclic trees.
# 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
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.
# 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
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.
# 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
Iterates over each edge from node1 to node2. The result is unspecified for cyclic trees.
# 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
Iterates over each node of this tree.
# File lib/bio/tree.rb, line 293 293: def each_node(&x) #:yields: node 294: @pathway.graph.each_key(&x) 295: self 296: end
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.
# 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
Returns edge1 + edge2
# 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
# 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
# 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
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).
# 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
Gets node name
# 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
If the node exists, returns true. Otherwise, returns false.
# File lib/bio/tree.rb, line 396 396: def include?(node) 397: @pathway.graph[node] ? true : false 398: end
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.
# 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
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 Nodes. The result is unspecified for cyclic trees.
# 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
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.
# 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
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.
# File lib/bio/tree.rb, line 353 353: def out_degree(source) 354: h = @pathway.graph[source] 355: h ? h.size : 0 356: end
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.
# 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
Returns formatted text (or something) of the tree Currently supported format is: :newick, :nhx
# 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
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). |
# 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
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: ’ ’) |
# 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
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.
# 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
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.
# 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
# Removes an edge between source and target. # Returns self. # If the edge does not exist, raises IndexError. +
# 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
Removes each edge if the block returns not nil. Returns self.
# 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
Removes each node if the block returns not nil. All edges connected with the removed nodes are also removed. Returns self.
# 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
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.
# 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
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.
# 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
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.
# 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