[BioRuby-cvs] bioruby/lib/bio tree.rb,1.2,1.3

[Naohisa Goto]

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

Modified Files:
	tree.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: tree.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/tree.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** tree.rb	13 Dec 2006 15:46:28 -0000	1.2
--- tree.rb	13 Dec 2006 16:29:37 -0000	1.3
***************
*** 1,4 ****
  #
! # = bio/phylogenetictree.rb - phylogenetic tree data structure class
  #
  # Copyright::   Copyright (C) 2006
--- 1,4 ----
  #
! # = bio/tree.rb - phylogenetic tree data structure class
  #
  # Copyright::   Copyright (C) 2006
***************
*** 21,25 ****
    #
    # This is alpha version. Incompatible changes may be made frequently.
!   class PhylogeneticTree
  
      # Error when there are no path between specified nodes
--- 21,25 ----
    #
    # This is alpha version. Incompatible changes may be made frequently.
!   class Tree
  
      # Error when there are no path between specified nodes
***************
*** 255,259 ****
      # Creates a new phylogenetic tree.
      # When no arguments are given, it creates a new empty tree.
!     # When a PhylogeneticTree object is given, it copies the tree.
      # Note that the  new tree shares Node and Edge objects
      # with the given tree.
--- 255,259 ----
      # 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.
***************
*** 499,503 ****
      # _nodes_ must be an array of nodes.
      # Nodes that do not exist in the original tree are ignored.
!     # Returns a PhylogeneticTree object.
      # Note that the sub-tree shares Node and Edge objects
      # with the original tree.
--- 499,503 ----
      # _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.
***************
*** 524,528 ****
      # _nodes_ must be an array of nodes.
      # Nodes that do not exist in the original tree are ignored.
!     # Returns a PhylogeneticTree object.
      # The result is unspecified for cyclic trees.
      # Note that the sub-tree shares Node and Edge objects
--- 524,528 ----
      # _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
***************
*** 551,555 ****
      # If the same edge exists, the edge in _other_ is used.
      # Returns self.
!     # The result is unspecified if _other_ isn't a PhylogeneticTree object.
      # Note that the Node and Edge objects in the _other_ tree are
      # shared in the concatinated tree.
--- 551,555 ----
      # 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.
***************
*** 816,820 ****
        self
      end
!   end #class PhylogeneticTree
  end #module Bio
  
--- 816,820 ----
        self
      end
!   end #class Tree
  end #module Bio