nwk.rb in bio-nwk-0.1.4

- old
+ new

@@ -5,93 +5,105 @@
 
 class Bio::Tree
   DELIMITER = ';'
   attr_accessor :tip2index, :index2tip
 
+
   def tips(node)
     rv = Array.new
     if node.isTip?(self)
       rv = [node]
     else
       rv = descendents(node).select{|n|children(n).empty?}
     end
     return(rv)
   end
 
+
   def all_nodes_of_subtree(node)
     [leaves(node), tips(node)].flatten
   end
 
+
   def cleanName!
     allTips.each do |tip|
       tip.name.gsub!(' ', '_')
     end
   end
 
+
   def twoTaxaNode(node)
     if node.isTip?(self)
       return(node)
     else
       return children(node).map{|child|tips(child).sort_by{|i|i.name}.shift}.sort_by{|i|i.name}
     end
   end
+
   
   def twoTaxaNodeName(node)
     if node.isTip?(self)
       return(node.name)
     else
       return children(node).map{|child|tips(child).sort_by{|i|i.name}.shift}.sort_by{|i|i.name}.map{|i|i.name}
     end
   end
 
+
   def twoTaxaNodeNameStr(node, sep='|')
     a = twoTaxaNodeName(node)
     if a.is_a?(Array)
       return(a.join(sep))
     else
       return(a)
     end
   end
 
+
   def sisters(node)
     if node == root
       return([])
     else
       return(children(parent(node)).select{|i|i!=node})
     end
   end
 
+
   def sister(node)
     return(sisters(node)[0])
   end
 
+
   def internal_nodes
     a = Array.new
     nodes.each do |node|
       if not node.isTip?(self)
         a << node
       end
     end
     return(a)
   end
 
+
   def allSubtreeRepresentatives
     arr = Array.new
     nodes.each do |node|
       arr << tips(node)
     end
     return(arr)
   end
 
+
   def allTips
     a = Array.new
     nodes.each do |node|
       a << node if node.isTip?(self)
     end
     return(a)
   end
 
+
   def outputNexus(isTranslate=false, isTip2Index=false)
     puts "#NEXUS"
     puts
     puts "BEGIN TREES;"
     translate if isTranslate
@@ -99,58 +111,65 @@
     puts ["\t"+'TREE TREE1', cleanNewick()].join('= ')
     puts ['ENDBLOCK', DELIMITER].join('')
     newickIndexToTip if isTip2Index
   end
 
+
   def cleanNewick
     output = output_newick
     output.gsub!(/[\n\s]/, '')
     output.gsub!(/[']/, '')
     return(output)
   end
 
+
   def tipToIndex
     @tip2index = Hash.new
     @index2tip = Hash.new
     allTips.each_with_index do |tip, index|
       @tip2index[tip.name.gsub(' ','_')] = (index+1).to_s
       @index2tip[(index+1).to_s] = tip.name
     end
   end
 
+
   def newickTipToIndex()
     tipToIndex
     allTips.each do |tip|
       index = @tip2index[tip.name.gsub(' ', '_')]
       tip.name = (index).to_s
     end
   end
 
+
   def newickIndexToTip()
     tipToIndex if @index2tip.empty?
     allTips.each do |tip|
       index = tip.name
       tip.name = @index2tip[index]
     end
   end
 
+
   def getAlldistances()
     distances = Array.new
     each_edge do |node0, node1, edge|
       next if node0 == root or node1 == root
       distances << edge.distance
     end
     return(distances)
   end
 
+
   def normalizeBranchLength!()
     min, max = getAlldistances().minmax
     each_edge do |node0, node1, edge|
       edge.distance = (edge.distance-min+1e-10).to_f/(max-min)
     end
   end
 
+
   def normalizeBranchLengthGainAndLoss!()
     min, max = getAlldistances().select{|i|i>=0}.minmax
     each_edge do |node0, node1, edge|
       edge.distance = (edge.distance-min+1e-10).to_f/(max-min) + 1 if edge.distance >= 0
     end
@@ -159,10 +178,31 @@
     each_edge do |node0, node1, edge|
       edge.distance = (edge.distance-min+1e-10).to_f/(max-min) if edge.distance < 0
     end
   end
 
+
+  def getNameTipRela()
+    tip2name, name2tip = [Hash.new, Hash.new]
+    allTips.each do |tip|
+      tip2name[tip] = tip.name
+      name2tip[tip.name] = tip
+    end
+    return([name2tip, tip2name])
+  end
+
+
+  def getNameNodeRela()
+    node2name, name2node = [Hash.new, Hash.new]
+    nodes.each do |node|
+      node2name[node] = node.name
+      name2node[node.name] = node
+    end
+    return([name2node, node2name])
+  end
+
+
   private
   def translate
     #  TRANSLATE
     #    1	Hamster,
     puts "\tTRANSLATE"
@@ -209,6 +249,7 @@
   first_line = `head -1 #{tree_file}`.chomp
   tree_txt = `tail -1 #{tree_file}`.chomp
   treeio = Bio::Newick.new(tree_txt).tree
   return([first_line, treeio])
 end
+
 