[BioRuby-cvs] bioruby/lib/bio/sequence common.rb,1.1,1.2

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/sequence
In directory pub.open-bio.org:/tmp/cvs-serv1993/sequence

Modified Files:
	common.rb 
Log Message:
* added RDoc header with Ruby's license
* changed to use autoload
* subseq method is changed to raise exception when the start or end position
  is not a positive integer
* splicing method is renamed to splice
* splicing is made aliased to splice method


Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence/common.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** common.rb	23 Jan 2006 04:13:36 -0000	1.1
--- common.rb	6 Feb 2006 14:16:17 -0000	1.2
***************
*** 1,6 ****
--- 1,20 ----
+ #
+ # = bio/sequence/common.rb - common methods for biological sequence
+ #
+ # Copyright::   Copyright (C) 2006
+ #               Toshiaki Katayama <k at bioruby.org>
+ # License::     Ruby's
+ #
+ # $Id$
+ #
+ 
  module Bio
  
+   autoload :Locations, 'bio/location'
+ 
  class Sequence
  
+ # This module provides common methods for biological sequence classes
+ # which must inherit String.
  module Common
  
***************
*** 34,38 ****
    # Returns the subsequence of the self string.
    def subseq(s = 1, e = self.length)
!     return nil if s < 1 or e < 1
      s -= 1
      e -= 1
--- 48,52 ----
    # Returns the subsequence of the self string.
    def subseq(s = 1, e = self.length)
!     raise "Error: start/end position must be a positive integer" unless s > 0 and e > 0
      s -= 1
      e -= 1
***************
*** 134,140 ****
    # Receive a GenBank style position string and convert it to the Locations
    # objects to splice the sequence itself.  See also: bio/location.rb
!   #
!   # This method depends on Locations class, see bio/location.rb
!   def splicing(position)
      unless position.is_a?(Locations) then
        position = Locations.new(position)
--- 148,152 ----
    # Receive a GenBank style position string and convert it to the Locations
    # objects to splice the sequence itself.  See also: bio/location.rb
!   def splice(position)
      unless position.is_a?(Locations) then
        position = Locations.new(position)
***************
*** 155,158 ****
--- 167,171 ----
      return self.class.new(s)
    end
+   alias splicing splice
  
  end # Common