bio 0.7.1 → 1.0.0

data/lib/bio/io/brdb.rb

@@ -1,103 +0,0 @@
-#
-# bio/io/brdb.rb - BioRuby-DB access module
-#
-#   Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
-#
-#  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
-#
-#  $Id: brdb.rb,v 1.4 2005/09/26 13:00:08 k Exp $
-#
-
-begin
-  require 'dbi'
-rescue LoadError
-end
-
-module Bio
-
-  class BRDB
-
-    def initialize(*args)
-      @brdb = args
-    end
-
-    def fetch(db_table, entry_id)
-      DBI.connect(*@brdb) do |dbh|
-        query = "select * from #{db_table} where id = ?"
-        dbh.execute(query, entry_id).fetch_all
-      end
-    end
-
-    def insert(db_table, values)
-      if values.is_a?(Array)
-        values = values.map{ |x| '"' + DBI.quote(x) + '"' }.join(",")
-      end
-      DBI.connect(*@brdb) do |dbh|
-        query = "insert into #{db_table} values (?);"
-        dbh.execute(query, values)
-      end
-    end
-
-    def update(db_table, entry_id, values)
-      if values.is_a?(Hash)
-        values = values.to_a.map{ |k, v| "#{k}='#{DBI.quote(v)}'" }.join(',')
-      end
-      DBI.connect(*@brdb) do |dbh|
-        query = "update #{db_table} set ? where id = ?"
-        dbh.execute(query, values, entry_id)
-      end
-    end
-
-    def search(db_table, field, keyword)
-    end
-
-  end
-
-end
-
-
-if __FILE__ == $0
-  begin
-    require 'pp'
-    alias p pp
-  rescue LoadError
-  end
-
-  db    = 'dbi:Mysql:host=db.bioruby.org;database=genbank'
-  user  = 'root'
-
-  serv = Bio::BRDB.new(db, user)
-
-  serv.fetch('ent', 'AA2CG').each do |row|
-    p row.to_h
-  end
-  serv.fetch('ft', 'AA2CG').each do |row|
-    p row.to_h
-  end
-end
-
-
-=begin
-
-= Bio::BRDB
-
---- Bio::BRDB.new(*args)
-
---- Bio::BRDB#close
---- Bio::BRDB#fetch(db_table, entry_id)
---- Bio::BRDB#update(db_table, entry_id, hash)
---- Bio::BRDB#insert(db_table, ary)
-
-=end

data/lib/bioruby.rb

@@ -1,34 +0,0 @@
-#
-# = bioruby.rb - Loading all BioRuby modules and setup for shell programming
-#
-# Copyright::	Copyright (C) 2005
-#		Toshiaki Katayama <k@bioruby.org>
-# License::	LGPL
-#
-# $Id: bioruby.rb,v 1.1 2005/12/07 05:12:06 k Exp $
-#
-#--
-#
-#  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/shell'
-
-include Bio::Shell
-
-Bio::Shell.setup
-