[BioRuby-cvs] bioruby/lib/bio/db/embl sptr.rb,1.30,1.31

[Mitsuteru C. Nakao]

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv9706

Modified Files:
	sptr.rb 
Log Message:
* Removed example codes (if __FILE__ == $0 ... end).
* Changed license (LGPL -> Ruby's).


Index: sptr.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/sptr.rb,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** sptr.rb	28 Jan 2006 06:40:38 -0000	1.30
--- sptr.rb	14 Apr 2006 05:52:28 -0000	1.31
***************
*** 2,7 ****
  # = bio/db/embl/sptr.rb - UniProt/SwissProt and TrEMBL database class
  # 
! # Copyright::   Copyright (C) 2001-2005 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     LGPL
  #
  # $Id$
--- 2,7 ----
  # = bio/db/embl/sptr.rb - UniProt/SwissProt and TrEMBL database class
  # 
! # Copyright::   Copyright (C) 2001-2006 Mitsuteru C. Nakao <n at bioruby.org>
! # License::     Ruby's
  #
  # $Id$
***************
*** 32,53 ****
  #   http://www.expasy.org/sprot/userman.html
  #
! #--
! #
! #  This library is free software; you can redistribute it and/or
! #  modify it under the terms of the GNU Lesser General Public
! #  License as published by the Free Software Foundation; either
! #  version 2 of the License, or (at your option) any later version.
! #
! #  This library is distributed in the hope that it will be useful,
! #  but WITHOUT ANY WARRANTY; without even the implied warranty of
! #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
! #  Lesser General Public License for more details.
! #
! #  You should have received a copy of the GNU Lesser General Public
! #  License along with this library; if not, write to the Free Software
! #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
! #
! #++
! #
  
  require 'bio/db'
--- 32,36 ----
  #   http://www.expasy.org/sprot/userman.html
  #
! 
  
  require 'bio/db'
***************
*** 760,841 ****
  
  
- if __FILE__ == $0
-   # Usage: ruby __FILE__ uniprot_sprot.dat 
-   # Usage: ruby __FILE__ uniprot_sprot.dat | egrep '^RuntimeError'
- 
-   begin
-     require 'pp'
-     alias pp p
-   rescue LoadError
-   end
- 
-   def cmd(cmd, tag = nil, ent = $ent)
-     puts " ==> #{cmd} "
-     puts Bio::SPTR.new(ent).get(tag) if tag
-     begin
-       p eval(cmd)
-     rescue RuntimeError
-       puts "RuntimeError(#{Bio::SPTR.new($ent).entry_id})}: #{$!} "
-     end
-     puts
-   end
- 
- 
-   while $ent = $<.gets(Bio::SPTR::RS)
-     
-     cmd "Bio::SPTR.new($ent).entry_id"
- 
-     cmd "Bio::SPTR.new($ent).id_line", 'ID'
-     cmd "Bio::SPTR.new($ent).entry"
-     cmd "Bio::SPTR.new($ent).entry_name"
-     cmd "Bio::SPTR.new($ent).molecule"
-     cmd "Bio::SPTR.new($ent).sequence_length"
- 
-     cmd "Bio::SPTR.new($ent).ac", 'AC'
-     cmd "Bio::SPTR.new($ent).accession"
- 
- 
-     cmd "Bio::SPTR.new($ent).gn", 'GN'
-     cmd "Bio::SPTR.new($ent).gene_name"
-     cmd "Bio::SPTR.new($ent).gene_names"
- 
-     cmd "Bio::SPTR.new($ent).dt", "DT"
-     ['created','annotation','sequence'].each do |key|
-       cmd "Bio::SPTR.new($ent).dt('#{key}')"
-     end
- 
-     cmd "Bio::SPTR.new($ent).de", 'DE'
-     cmd "Bio::SPTR.new($ent).definition"
-     cmd "Bio::SPTR.new($ent).protein_name"
-     cmd "Bio::SPTR.new($ent).synonyms"
- 
-     cmd "Bio::SPTR.new($ent).kw", 'KW'
- 
-     cmd "Bio::SPTR.new($ent).os", 'OS'
- 
-     cmd "Bio::SPTR.new($ent).oc", 'OC'
- 
-     cmd "Bio::SPTR.new($ent).og", 'OG'
- 
-     cmd "Bio::SPTR.new($ent).ox", 'OX'
- 
-     cmd "Bio::SPTR.new($ent).ref", 'R'
- 
-     cmd "Bio::SPTR.new($ent).cc", 'CC'
-     cmd "Bio::SPTR.new($ent).cc('ALTERNATIVE PRODUCTS')"
-     cmd "Bio::SPTR.new($ent).cc('DATABASE')"
-     cmd "Bio::SPTR.new($ent).cc('MASS SPECTOMETRY')"
- 
-     cmd "Bio::SPTR.new($ent).dr", 'DR'
- 
-     cmd "Bio::SPTR.new($ent).ft", 'FT'
-     cmd "Bio::SPTR.new($ent).ft['DOMAIN']"
- 
-     cmd "Bio::SPTR.new($ent).sq", "SQ"
-     cmd "Bio::SPTR.new($ent).seq"
-   end
- 
- end
- 
  
  =begin
--- 743,746 ----