[BioRuby-cvs] bioruby/lib/bio/db/genbank common.rb, 1.7, 1.8 genbank.rb, 0.36, 0.37

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/db/genbank
In directory pub.open-bio.org:/tmp/cvs-serv26190/lib/bio/db/genbank

Modified Files:
	common.rb genbank.rb 
Log Message:
* fixed typo in methodname (s/varnacular_name/vernacular_name/) by Trevor Wennblom
* Bio::GenBank#gc method is removed as it can be calculated by Bio::Sequence::NA #gc and the method is changed to return int istead of float in BioRuby v0.7


Index: genbank.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/genbank.rb,v
retrieving revision 0.36
retrieving revision 0.37
diff -C2 -d -r0.36 -r0.37
*** genbank.rb	23 Oct 2005 07:20:37 -0000	0.36
--- genbank.rb	14 Nov 2005 05:43:43 -0000	0.37
***************
*** 2,6 ****
  # bio/db/genbank/genbank.rb - GenBank database class
  #
! #   Copyright (C) 2000-2004 KATAYAMA Toshiaki <k at bioruby.org>
  #
  #  This library is free software; you can redistribute it and/or
--- 2,6 ----
  # bio/db/genbank/genbank.rb - GenBank database class
  #
! #   Copyright (C) 2000-2005 KATAYAMA Toshiaki <k at bioruby.org>
  #
  #  This library is free software; you can redistribute it and/or
***************
*** 118,127 ****
    end
  
-   def gc
-     num_gc = basecount('g') + basecount('c')
-     num_at = basecount('a') + basecount('t')
-     return format("%.1f", num_gc * 100.0 / (num_at + num_gc)).to_f
-   end
- 
  end # GenBank
  end # Bio
--- 118,121 ----
***************
*** 186,190 ****
    p gb.source
    p gb.common_name
!   p gb.varnacular_name
    p gb.organism
    p gb.taxonomy
--- 180,184 ----
    p gb.source
    p gb.common_name
!   p gb.vernacular_name
    p gb.organism
    p gb.taxonomy
***************
*** 203,207 ****
    p gb.basecount('a')
    p gb.basecount('A')
-   p gb.gc
  
    puts "## ORIGIN"
--- 197,200 ----
***************
*** 292,296 ****
  
  --- Bio::GenBank#common_name -> String
! --- Bio::GenBank#varnacular_name -> String
  --- Bio::GenBank#organism -> String
  --- Bio::GenBank#taxonomy -> String
--- 285,289 ----
  
  --- Bio::GenBank#common_name -> String
! --- Bio::GenBank#vernacular_name -> String
  --- Bio::GenBank#organism -> String
  --- Bio::GenBank#taxonomy -> String
***************
*** 299,303 ****
  
  The 'common_name' method is same as source['common_name'].
! The 'varnacular_name' method is an alias for the 'common_name'.
  The 'organism' method is same as source['organism'].
  The 'taxonomy' method is same as source['taxonomy'].
--- 292,296 ----
  
  The 'common_name' method is same as source['common_name'].
! The 'vernacular_name' method is an alias for the 'common_name'.
  The 'organism' method is same as source['organism'].
  The 'taxonomy' method is same as source['taxonomy'].
***************
*** 337,344 ****
  count of the base as a Fixnum.  The base can be one of 'a', 't', 'g',
  'c', and 'o' (others).
- 
- --- Bio::GenBank#gc -> Float
- 
- Returns the average G+C% content of the sequence as a Float.
  
  === ORIGIN
--- 330,333 ----

Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/common.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** common.rb	23 Oct 2005 07:20:36 -0000	1.7
--- common.rb	14 Nov 2005 05:43:43 -0000	1.8
***************
*** 115,119 ****
      source['common_name']
    end
!   alias varnacular_name common_name
  
    def organism
--- 115,119 ----
      source['common_name']
    end
!   alias vernacular_name common_name
  
    def organism