[BioRuby-cvs] bioruby/lib/bio/db newick.rb,1.3,1.4

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory dev.open-bio.org:/tmp/cvs-serv8729/lib/bio/db

Modified Files:
	newick.rb 
Log Message:
Bio::PhylogeneticTree is renamed to Bio::Tree and
filenames are also renamed from phylogenetictree.rb to tree.rb and
from test_phylogenetictree.rb to test_tree.rb.


Index: newick.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/newick.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** newick.rb	13 Dec 2006 15:55:29 -0000	1.3
--- newick.rb	13 Dec 2006 16:29:37 -0000	1.4
***************
*** 10,17 ****
  #
  
! require 'bio/phylogenetictree'
  
  module Bio
!   class PhylogeneticTree
  
      #---
--- 10,17 ----
  #
  
! require 'bio/tree'
  
  module Bio
!   class Tree
  
      #---
***************
*** 211,215 ****
      end
  
!   end #class PhylogeneticTree
  
    #---
--- 211,215 ----
      end
  
!   end #class Tree
  
    #---
***************
*** 228,236 ****
      class ParseError < RuntimeError; end
  
!     # same as Bio::PhylogeneticTree::Edge
!     Edge = Bio::PhylogeneticTree::Edge
  
!     # same as Bio::PhylogeneticTree::Node
!     Node = Bio::PhylogeneticTree::Node
  
      # Creates a new Newick object.
--- 228,236 ----
      class ParseError < RuntimeError; end
  
!     # same as Bio::Tree::Edge
!     Edge = Bio::Tree::Edge
  
!     # same as Bio::Tree::Node
!     Node = Bio::Tree::Node
  
      # Creates a new Newick object.
***************
*** 262,266 ****
  
      # Gets the tree.
!     # Returns a Bio::PhylogeneticTree object.
      def tree
        if !defined?(@tree)
--- 262,266 ----
  
      # Gets the tree.
!     # Returns a Bio::Tree object.
      def tree
        if !defined?(@tree)
***************
*** 475,479 ****
        end
        # Let the tree into instance variables
!       tree = Bio::PhylogeneticTree.new
        tree.instance_eval {
          @pathway.relations.concat(edges)
--- 475,479 ----
        end
        # Let the tree into instance variables
!       tree = Bio::Tree.new
        tree.instance_eval {
          @pathway.relations.concat(edges)