bio 1.0.0 → 1.1.0

data/lib/bio/db/embl/swissprot.rb

@@ -1,14 +1,20 @@
 #
 # = bio/db/embl/swissprot.rb - SwissProt database class
 # 
-# Copyright::   Copyright (C) 2001, 2002 KATAYAMA Toshiaki <k@bioruby.org>
-# License::     LGPL
+# Copyright::   Copyright (C) 2001, 2002 Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
 #
-#  $Id: swissprot.rb,v 1.4 2006/01/28 06:40:38 nakao Exp $
+#  $Id: swissprot.rb,v 1.7 2007/04/05 23:35:40 trevor Exp $
 #
+
+require 'bio/db/embl/sptr'
+
+module Bio
+
 # == Description
 # 
-# Name space for SwissProt specific methods.
+# Parser class for SwissProt database entry. See also Bio::SPTR class.
+# This class holds name space for SwissProt specific methods.
 #
 # SwissProt (before UniProtKB/SwissProt) specific methods are defined in 
 # this class. Shared methods for UniProtKB/SwissProt and TrEMBL classes 
@@ -28,31 +34,6 @@
 # * Swiss-Prot Protein Knowledgebase User Manual
 #   http://au.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/embl/sptr'
-
-module Bio
-
-# Parser class for SwissProt database entry.
-# See also Bio::SPTR class.
 class SwissProt < SPTR
   # Nothing to do (SwissProt format is abstracted in SPTR)
 end

data/lib/bio/db/embl/trembl.rb

@@ -1,14 +1,20 @@
 #
 # = bio/db/embl/trembl.rb - TrEMBL database class
 # 
-# Copyright::   Copyright (C) 2001, 2002 KATAYAMA Toshiaki <k@bioruby.org>
-# License::     LGPL
+# Copyright::  Copyright (C) 2001, 2002 Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
 #
-#  $Id: trembl.rb,v 1.4 2006/01/28 06:40:38 nakao Exp $
+# $Id: trembl.rb,v 1.7 2007/04/05 23:35:40 trevor Exp $
 #
+
+require 'bio/db/embl/sptr'
+
+module Bio
+
 # == Description
 #
-# Name space for TrEMBL specific methods.
+# Parser class for TrEMBL database entry. See also Bio::SPTR class.
+# This class holds name space for TrEMBL specific methods.
 #
 # UniProtKB/SwissProt specific methods are defined in this class. 
 # Shared methods for UniProtKB/SwissProt and TrEMBL classes are 
@@ -28,31 +34,6 @@
 # * TrEMBL Computer-annotated supplement to Swiss-Prot User Manual
 #   http://au.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/embl/sptr'
-
-module Bio
-
-# Parser class for TrEMBL database entry.
-# See also Bio::SPTR class.
 class TrEMBL < SPTR
   # Nothing to do (TrEMBL format is abstracted in SPTR)
 end

data/lib/bio/db/embl/uniprot.rb

@@ -1,14 +1,20 @@
 #
 # = bio/db/embl/uniprot.rb - UniProt database class
 # 
-# Copyright::   Copyright (C) 2005 KATAYAMA Toshiaki <k@bioruby.org>
-# License::     LGPL
+# Copyright::  Copyright (C) 2005 Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
 #
-#  $Id: uniprot.rb,v 1.2 2006/01/28 06:40:39 nakao Exp $
+#  $Id: uniprot.rb,v 1.5 2007/04/05 23:35:40 trevor Exp $
 #
+
+require 'bio/db/embl/sptr'
+
+module Bio
+
 # == Description
 # 
-# Name space for UniProtKB/SwissProt specific methods.
+# Parser class for SwissProt database entry.# See also Bio::SPTR class.
+# This class holds name space for UniProtKB/SwissProt specific methods.
 #
 # UniProtKB/SwissProt specific methods are defined in this class. 
 # Shared methods for UniProtKB/SwissProt and TrEMBL classes are 
@@ -27,32 +33,7 @@
 #
 # * The UniProtKB/SwissProt/TrEMBL User Manual
 #   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/embl/sptr'
-
-module Bio
-
-# Parser class for SwissProt database entry.
-# See also Bio::SPTR class.
 class UniProt < SPTR
   # Nothing to do (UniProt format is abstracted in SPTR)
 end

data/lib/bio/db/fantom.rb

@@ -1,23 +1,10 @@
 #
 # bio/db/fantom.rb - RIKEN FANTOM2 database classes
 #
-#   Copyright (C) 2003 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
+# Copyright:: Copyright (C) 2003 GOTO Naohisa <ng@bioruby.org> 
+# License::   The Ruby License
 #
-#  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: fantom.rb,v 1.11 2005/09/26 13:00:06 k Exp $
+#  $Id: fantom.rb,v 1.14 2007/04/05 23:35:40 trevor Exp $
 #
 
 begin
@@ -28,6 +15,7 @@ require 'uri'
 require 'net/http'
 
 require 'bio/db'
+require 'bio/command'
 #require 'bio/sequence'
 
 module Bio
@@ -45,11 +33,18 @@ module Bio
       addr = 'fantom.gsc.riken.go.jp'
       port = 80
       path = "/db/maxml/maxmlseq.cgi?masterid=#{URI.escape(idstr.to_s)}&style=xml"
-      proxy = URI.parse(http_proxy.to_s)
       xml = ''
-      Net::HTTP.start(addr, port, proxy.host, proxy.port) do |http|
-        response, = http.get(path)
-        xml = response.body
+      if http_proxy then
+        proxy = URI.parse(http_proxy.to_s)
+        Net::HTTP.start(addr, port, proxy.host, proxy.port) do |http|
+          response, = http.get(path)
+          xml = response.body
+        end
+      else
+        Bio::Command.start_http(addr, port) do |http|
+          response, = http.get(path)
+          xml = response.body
+        end
       end
       xml
     end

data/lib/bio/db/fasta.rb

@@ -3,10 +3,10 @@
 #
 # Copyright::  Copyright (C) 2001, 2002
 #              GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>,
-#              KATAYAMA Toshiaki <k@bioruby.org>
-# Lisence::    Ruby's
+#              Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
 #
-# $Id: fasta.rb,v 1.25 2006/02/22 08:44:46 ngoto Exp $
+# $Id: fasta.rb,v 1.28 2007/04/05 23:35:40 trevor Exp $
 # 
 # == Description
 # 

data/lib/bio/db/genbank/common.rb

@@ -1,29 +1,27 @@
 #
-# bio/db/genbank/common.rb - Common methods for GenBank style database classes
+# = bio/db/genbank/common.rb - Common methods for GenBank style database classes
 #
-#   Copyright (C) 2004 KATAYAMA Toshiaki <k@bioruby.org>
+# Copyright::  Copyright (C) 2004 Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
 #
-#  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: common.rb,v 1.9 2005/12/07 11:23:51 k Exp $
+# $Id: common.rb,v 1.11 2007/04/05 23:35:40 trevor Exp $
 #
 
 require 'bio/db'
 
 module Bio
 class NCBIDB
+
+# == Description
+# 
+# This module defines a common framework among GenBank, GenPept, RefSeq, and
+# DDBJ.  For more details, see the documentations in each genbank/*.rb files.
+# 
+# == References
+# 
+# * ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt
+# * http://www.ncbi.nlm.nih.gov/collab/FT/index.html
+#
 module Common
 
   DELIMITER	= RS = "\n//\n"
@@ -33,61 +31,68 @@ module Common
     super(entry, TAGSIZE)
   end
 
-  # LOCUS  -- Locus class must be defined in child classes
+  # LOCUS -- Locus class must be defined in child classes.
+  def locus
+    # must be overrided in each subclass
+  end
 
-  # DEFINITION
+  # DEFINITION -- Returns contents of the DEFINITION record as a String.
   def definition
     field_fetch('DEFINITION')
   end
 
 
-  # ACCESSION
+  # ACCESSION -- Returns contents of the ACCESSION record as an Array.
   def accessions
     accession.split(/\s+/)
   end
 
 
-  # VERSION
+  # VERSION -- Returns contents of the VERSION record as an Array of Strings.
   def versions
     @data['VERSION'] ||= fetch('VERSION').split(/\s+/)
   end
 
+  # Returns the first part of the VERSION record as "ACCESSION.VERSION" String.
   def acc_version
     versions.first.to_s
   end
 
+  # Returns the ACCESSION part of the acc_version.
   def accession
     acc_version.split(/\./).first.to_s
   end
 
+  # Returns the VERSION part of the acc_version as a Fixnum
   def version
     acc_version.split(/\./).last.to_i
   end
 
+  # Returns the second part of the VERSION record as a "GI:#######" String.
   def gi
     versions.last
   end
 
 
-  # NID
+  # NID -- Returns contents of the NID record as a String.
   def nid
     field_fetch('NID')
   end
 
 
-  # KEYWORDS
+  # KEYWORDS -- Returns contents of the KEYWORDS record as an Array of Strings.
   def keywords
     @data['KEYWORDS'] ||= fetch('KEYWORDS').chomp('.').split(/; /)
   end
 
 
-  # SEGMENT
+  # SEGMENT -- Returns contents of the SEGMENT record as a "m/n" form String.
   def segment
     @data['SEGMENT'] ||= fetch('SEGMENT').scan(/\d+/).join("/")
   end
 
 
-  # SOURCE
+  # SOURCE -- Returns contents of the SOURCE record as a Hash.
   def source
     unless @data['SOURCE']
       name, org = get('SOURCE').split('ORGANISM')
@@ -126,7 +131,8 @@ module Common
   end
 
 
-  # REFERENCE
+  # REFERENCE -- Returns contents of the REFERENCE records as an Array of
+  # Bio::Reference objects.
   def references
     unless @data['REFERENCE']
       ary = []
@@ -173,13 +179,14 @@ module Common
   end
 
 
-  # COMMENT
+  # COMMENT -- Returns contents of the COMMENT record as a String.
   def comment
     field_fetch('COMMENT')
   end
 
 
-  # FEATURES
+  # FEATURES -- Returns contents of the FEATURES record as a Bio::Features
+  # object.
   def features
     unless @data['FEATURES']
       ary = []
@@ -233,7 +240,7 @@ module Common
   end
 
 
-  # ORIGIN
+  # ORIGIN -- Returns contents of the ORIGIN record as a String.
   def origin
     unless @data['ORIGIN']
       ori, seqstr = get('ORIGIN').split("\n", 2)
@@ -276,24 +283,8 @@ module Common
   end
 
 end # Common 
+
 end # GenBank
 end # Bio
 
 
-=begin
-
-= Bio::GenBank::Common
-
-This module defines a common framework among GenBank, GenPept, RefSeq, and
-DDBJ.  For more details, see the documentations in each genbank/*.rb files.
-
-
-== SEE ALSO
-
-* ((<URL:ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt>))
-* ((<URL:http://www.ncbi.nlm.nih.gov/collab/FT/index.html>))
-
-=end
-
-
-

data/lib/bio/db/genbank/ddbj.rb

@@ -1,23 +1,10 @@
 #
-# bio/db/genbank/ddbj.rb - DDBJ database class
+# = bio/db/genbank/ddbj.rb - DDBJ database class
 #
-#   Copyright (C) 2000-2004 KATAYAMA Toshiaki <k@bioruby.org>
+# Copyright::  Copyright (C) 2000-2004 Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
 #
-#  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: ddbj.rb,v 1.7 2005/09/09 16:02:04 ngoto Exp $
+# $Id: ddbj.rb,v 1.9 2007/04/05 23:35:40 trevor Exp $
 #
 
 require 'bio/db/genbank/genbank'
@@ -29,6 +16,7 @@ class DDBJ < GenBank
   autoload :XML,          'bio/io/ddbjxml'
 
   # Nothing to do (DDBJ database format is completely same as GenBank)
-end
+
+end # DDBJ
 
 end # Bio