[BioRuby-cvs] bioruby/lib/bio/shell/plugin flatfile.rb,1.3,1.4

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv29978/lib/bio/shell/plugin

Modified Files:
	flatfile.rb 
Log Message:
* converted to RDoc
* changed to private methods
* convert_to_fasta method is renamed to save_fasta
* bioflat_index method is renamed to flatindex
* bioflat_search method is renamed to flatsearch


Index: flatfile.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/flatfile.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** flatfile.rb	5 Oct 2005 08:56:14 -0000	1.3
--- flatfile.rb	5 Nov 2005 08:36:24 -0000	1.4
***************
*** 1,6 ****
  #
! #  bio/shell/plugin/flatfile.rb - plugin for flatfile database
  #
! #   Copyright (C) 2005 KATAYAMA Toshiaki <k at bioruby.org>
  #
  #  This library is free software; you can redistribute it and/or
--- 1,12 ----
  #
! # = bio/shell/plugin/flatfile.rb - plugin for flatfile database
  #
! # Copyright::	Copyright (C) 2005
! #		Toshiaki Katayama <k at bioruby.org>
! # Lisence::	LGPL
! #
! # $Id$
! #
! #--
  #
  #  This library is free software; you can redistribute it and/or
***************
*** 18,22 ****
  #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #  $Id$
  #
  
--- 24,28 ----
  #  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
  #
! #++
  #
  
***************
*** 25,28 ****
--- 31,36 ----
  module Bio::Shell
  
+   private
+ 
    def flatauto(filename)
      if block_given?
***************
*** 40,44 ****
    end
  
!   def convert_to_fasta(fastafile, *flatfiles)
      puts "Saving fasta file (#{fastafile}) ... "
      File.open(fastafile, "w") do |fasta|
--- 48,52 ----
    end
  
!   def save_fasta(fastafile, *flatfiles)
      puts "Saving fasta file (#{fastafile}) ... "
      File.open(fastafile, "w") do |fasta|
***************
*** 56,60 ****
    end
  
!   def bioflat_index(dbname, *flatfiles)
      prefix = Core::SAVEDIR + Core::BIOFLAT
      unless File.directory?(prefix)
--- 64,68 ----
    end
  
!   def flatindex(dbname, *flatfiles)
      prefix = Core::SAVEDIR + Core::BIOFLAT
      unless File.directory?(prefix)
***************
*** 72,76 ****
    end
  
!   def bioflat_search(dbname, keyword)
      dir = Core::SAVEDIR + Core::BIOFLAT + dbname.to_s
      Bio::FlatFileIndex.open(dir) do |db|
--- 80,84 ----
    end
  
!   def flatsearch(dbname, keyword)
      dir = Core::SAVEDIR + Core::BIOFLAT + dbname.to_s
      Bio::FlatFileIndex.open(dir) do |db|
***************
*** 85,88 ****
--- 93,97 ----
    end
  
+ =begin
    def bioflat_namespaces(dbname)
      dir = Core::SAVEDIR + Core::BIOFLAT + dbname.to_s
***************
*** 91,94 ****
--- 100,104 ----
      db.close
    end
+ =end
  
  end