lib/bio/nwk.rb in bio-nwk-0.1.0 vs lib/bio/nwk.rb in bio-nwk-0.1.1

@@ -118,9 +118,37 @@
       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
+
+    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) if edge.distance < 0
+    end
+  end
+
   private
   def translate
     #  TRANSLATE
     #    1	Hamster,
     puts "\tTRANSLATE"