[BioRuby-cvs] bioruby/lib/bio/db newick.rb,1.5,1.6

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory dev.open-bio.org:/tmp/cvs-serv19837/lib/bio/db

Modified Files:
	newick.rb 
Log Message:
Bio::Tree#output_phylip_distance_matrix(...) and
Bio::Tree#output(:phylip_distance_matrix, ...) are added
to output phylip-style distance matrix as a string.


Index: newick.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/newick.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** newick.rb	13 Dec 2006 17:29:17 -0000	1.5
--- newick.rb	15 Dec 2006 14:59:25 -0000	1.6
***************
*** 206,209 ****
--- 206,211 ----
        when :nhx
          output_nhx(*arg, &block)
+       when :phylip_distance_matrix
+         output_phylip_distance_matrix(*arg, &block)
        else
          raise 'Unknown format'
***************
*** 211,214 ****
--- 213,235 ----
      end
  
+     #---
+     # This method isn't suitable to written in this file?
+     #+++
+ 
+     # 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.
+     def output_phylip_distance_matrix(nodes = nil, options = {})
+       nodes = self.leaves unless nodes
+       names = nodes.collect do |x|
+         y = get_node_name(x)
+         y = sprintf("%x", x.__id__.abs) if y.empty?
+         y
+       end
+       m = self.distance_matrix(nodes)
+       Bio::Phylip::DistanceMatrix.generate(m, names, options)
+     end
+ 
    end #class Tree