RubyGems - bio - Versions diffs - 1.4.2 → 1.4.3 - Mend

bio 1.4.2 → 1.4.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (139) hide show

data/.travis.yml +66 -0
data/ChangeLog +989 -4524
data/KNOWN_ISSUES.rdoc +67 -2
data/README.rdoc +89 -23
data/README_DEV.rdoc +93 -2
data/RELEASE_NOTES.rdoc +167 -95
data/Rakefile +199 -7
data/bioruby.gemspec +27 -12
data/bioruby.gemspec.erb +6 -3
data/doc/ChangeLog-before-1.4.2 +5013 -0
data/doc/RELEASE_NOTES-1.4.2.rdoc +132 -0
data/doc/Tutorial.rd +21 -3
data/doc/Tutorial.rd.html +20 -12
data/etc/bioinformatics/seqdatabase.ini +13 -196
data/gemfiles/Gemfile.travis-jruby1.8 +7 -0
data/gemfiles/Gemfile.travis-jruby1.9 +10 -0
data/gemfiles/Gemfile.travis-ruby1.8 +7 -0
data/gemfiles/Gemfile.travis-ruby1.9 +10 -0
data/gemfiles/modify-Gemfile.rb +28 -0
data/gemfiles/prepare-gemspec.rb +25 -0
data/lib/bio/alignment.rb +1 -1
data/lib/bio/appl/bl2seq/report.rb +3 -3
data/lib/bio/appl/blast/ddbj.rb +0 -3
data/lib/bio/appl/blast/format0.rb +4 -22
data/lib/bio/appl/blast/genomenet.rb +33 -16
data/lib/bio/appl/blast/ncbioptions.rb +8 -3
data/lib/bio/appl/blast/remote.rb +6 -5
data/lib/bio/appl/blast/report.rb +10 -6
data/lib/bio/appl/blast/rpsblast.rb +3 -2
data/lib/bio/appl/blast/wublast.rb +3 -3
data/lib/bio/command.rb +118 -36
data/lib/bio/data/na.rb +1 -1
data/lib/bio/db/embl/embl.rb +74 -0
data/lib/bio/db/embl/format_embl.rb +0 -4
data/lib/bio/db/fasta.rb +57 -45
data/lib/bio/db/fasta/defline.rb +1 -1
data/lib/bio/db/fasta/format_fasta.rb +0 -4
data/lib/bio/db/fasta/format_qual.rb +0 -5
data/lib/bio/db/fastq/format_fastq.rb +0 -1
data/lib/bio/db/genbank/format_genbank.rb +0 -4
data/lib/bio/db/gff.rb +41 -12
data/lib/bio/db/kegg/genes.rb +3 -3
data/lib/bio/db/kegg/kgml.rb +465 -64
data/lib/bio/db/newick.rb +0 -244
data/lib/bio/db/pdb.rb +1 -4
data/lib/bio/db/pdb/atom.rb +3 -2
data/lib/bio/db/pdb/chain.rb +2 -3
data/lib/bio/db/pdb/chemicalcomponent.rb +3 -2
data/lib/bio/db/pdb/model.rb +2 -2
data/lib/bio/db/pdb/pdb.rb +2 -1
data/lib/bio/db/pdb/residue.rb +2 -2
data/lib/bio/db/pdb/utils.rb +7 -4
data/lib/bio/db/phyloxml/phyloxml_parser.rb +52 -5
data/lib/bio/feature.rb +2 -3
data/lib/bio/io/flatfile/autodetection.rb +1 -1
data/lib/bio/io/flatfile/buffer.rb +84 -0
data/lib/bio/sequence.rb +6 -4
data/lib/bio/sequence/aa.rb +3 -5
data/lib/bio/sequence/adapter.rb +6 -6
data/lib/bio/sequence/common.rb +3 -3
data/lib/bio/sequence/compat.rb +2 -7
data/lib/bio/sequence/dblink.rb +6 -5
data/lib/bio/sequence/format.rb +0 -6
data/lib/bio/sequence/format_raw.rb +0 -4
data/lib/bio/sequence/generic.rb +3 -4
data/lib/bio/sequence/na.rb +4 -6
data/lib/bio/sequence/quality_score.rb +2 -0
data/lib/bio/sequence/sequence_masker.rb +3 -0
data/lib/bio/shell/core.rb +1 -0
data/lib/bio/tree.rb +1 -2
data/lib/bio/tree/output.rb +264 -0
data/lib/bio/util/restriction_enzyme.rb +1 -3
data/lib/bio/util/restriction_enzyme/analysis.rb +8 -5
data/lib/bio/util/restriction_enzyme/analysis_basic.rb +4 -3
data/lib/bio/util/restriction_enzyme/cut_symbol.rb +3 -2
data/lib/bio/util/restriction_enzyme/dense_int_array.rb +3 -0
data/lib/bio/util/restriction_enzyme/double_stranded.rb +3 -4
data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +3 -4
data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +3 -4
data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +3 -4
data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +3 -4
data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +3 -4
data/lib/bio/util/restriction_enzyme/range/cut_range.rb +3 -4
data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +3 -4
data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +3 -4
data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +3 -4
data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +3 -4
data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +3 -4
data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +3 -4
data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +3 -4
data/lib/bio/util/restriction_enzyme/single_strand.rb +3 -3
data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +3 -4
data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +3 -4
data/lib/bio/util/restriction_enzyme/sorted_num_array.rb +3 -0
data/lib/bio/util/restriction_enzyme/string_formatting.rb +3 -4
data/lib/bio/version.rb +11 -2
data/sample/seqdatabase.ini +210 -0
data/test/bioruby_test_helper.rb +37 -12
data/test/data/KEGG/test.kgml +37 -0
data/test/data/command/echoarg2.bat +0 -0
data/test/data/command/echoarg2.sh +4 -0
data/test/functional/bio/test_command.rb +58 -28
data/test/{functional → network}/bio/appl/blast/test_remote.rb +0 -0
data/test/{functional → network}/bio/appl/test_blast.rb +0 -0
data/test/{functional → network}/bio/appl/test_pts1.rb +0 -0
data/test/{functional → network}/bio/io/test_ddbjrest.rb +0 -0
data/test/{functional → network}/bio/io/test_ensembl.rb +0 -0
data/test/{functional → network}/bio/io/test_pubmed.rb +0 -0
data/test/{functional → network}/bio/io/test_soapwsdl.rb +0 -0
data/test/{functional → network}/bio/io/test_togows.rb +0 -0
data/test/network/bio/test_command.rb +35 -0
data/test/runner.rb +16 -6
data/test/unit/bio/appl/blast/test_report.rb +119 -0
data/test/unit/bio/appl/blast/test_rpsblast.rb +1 -0
data/test/unit/bio/data/test_na.rb +1 -1
data/test/unit/bio/db/embl/test_embl.rb +2 -7
data/test/unit/bio/db/embl/test_embl_rel89.rb +2 -7
data/test/unit/bio/db/fasta/test_defline.rb +1 -1
data/test/unit/bio/db/genbank/test_genpept.rb +1 -1
data/test/unit/bio/db/kegg/test_drug.rb +1 -1
data/test/unit/bio/db/kegg/test_genome.rb +1 -1
data/test/unit/bio/db/kegg/test_glycan.rb +1 -1
data/test/unit/bio/db/kegg/test_kgml.rb +1022 -0
data/test/unit/bio/db/sanger_chromatogram/test_abif.rb +2 -1
data/test/unit/bio/db/sanger_chromatogram/test_scf.rb +4 -2
data/test/unit/bio/db/test_newick.rb +2 -0
data/test/unit/bio/db/test_phyloxml.rb +54 -2
data/test/unit/bio/db/test_phyloxml_writer.rb +15 -9
data/test/unit/bio/db/test_soft.rb +1 -1
data/test/unit/bio/io/flatfile/test_autodetection.rb +6 -0
data/test/unit/bio/io/flatfile/test_buffer.rb +141 -0
data/test/unit/bio/sequence/test_common.rb +36 -4
data/test/unit/bio/sequence/test_na.rb +1 -1
data/test/unit/bio/test_command.rb +9 -4
data/test/unit/bio/test_sequence.rb +2 -2
data/test/unit/bio/test_tree.rb +11 -11
data/test/unit/bio/util/test_restriction_enzyme.rb +1 -1
metadata +1428 -655
data/rdoc.zsh +0 -8

data/lib/bio/util/restriction_enzyme.rb CHANGED

@@ -5,12 +5,10 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id:$
-#
 module Bio
-  autoload :REBASE, 'bio/db/rebase'
+  autoload :REBASE, 'bio/db/rebase' unless const_defined?(:REBASE)
 # = Description
 #

data/lib/bio/util/restriction_enzyme/analysis.rb CHANGED

@@ -5,17 +5,20 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: analysis.rb,v 1.20 2007/07/16 19:28:48 k Exp $
-#
-require 'bio/util/restriction_enzyme'
-require 'bio/util/restriction_enzyme/analysis_basic'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class Analysis
+  #--
+  # require "analysis_basic.rb" here to avoid cyclic require
+  #++
+  require 'bio/util/restriction_enzyme/analysis_basic'
   # See cut instance method
   def self.cut( sequence, *args )
     self.new.cut( sequence, *args )

data/lib/bio/util/restriction_enzyme/analysis_basic.rb CHANGED

@@ -5,13 +5,14 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: analysis_basic.rb,v 1.16 2007/07/16 19:28:48 k Exp $
-#
 require 'set'  # for method create_enzyme_actions
-require 'bio/util/restriction_enzyme'
+require 'bio/sequence'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class Analysis

data/lib/bio/util/restriction_enzyme/cut_symbol.rb CHANGED

@@ -5,10 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: cut_symbol.rb,v 1.6 2007/07/16 19:28:48 k Exp $
-#
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 # = Usage

data/lib/bio/util/restriction_enzyme/dense_int_array.rb CHANGED

@@ -8,6 +8,9 @@
 #
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
   # a class to store integer numbers, containing many contiguous

data/lib/bio/util/restriction_enzyme/double_stranded.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: double_stranded.rb,v 1.11 2007/07/16 19:28:48 k Exp $
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 # A pair of SingleStrand and SingleStrandComplement objects with methods to

data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: aligned_strands.rb,v 1.6 2007/07/16 19:28:48 k Exp $
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class DoubleStranded

data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: cut_location_pair.rb,v 1.9 2007/07/16 19:28:48 k Exp $
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class DoubleStranded

data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: cut_location_pair_in_enzyme_notation.rb,v 1.7 2007/07/16 19:28:48 k Exp $
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class DoubleStranded

data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: cut_locations.rb,v 1.6 2007/07/16 19:28:48 k Exp $
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class DoubleStranded

data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: cut_locations_in_enzyme_notation.rb,v 1.7 2007/07/16 19:28:48 k Exp $
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class DoubleStranded

data/lib/bio/util/restriction_enzyme/range/cut_range.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: cut_range.rb,v 1.4 2007/07/16 19:28:48 k Exp $
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class Range

data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: cut_ranges.rb,v 1.5 2007/07/16 19:28:48 k Exp $
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class Range

data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: horizontal_cut_range.rb,v 1.5 2007/07/16 19:28:48 k Exp $
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class Range

data/lib/bio/util/restriction_enzyme/range/sequence_range.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id:$
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class Range

data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id:$
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class Range
 class SequenceRange

data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id:$
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class Range
 class SequenceRange

data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: fragments.rb,v 1.5 2007/07/16 19:28:48 k Exp $
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class Range
 class SequenceRange

data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: vertical_cut_range.rb,v 1.5 2007/07/16 19:28:48 k Exp $
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class Range

data/lib/bio/util/restriction_enzyme/single_strand.rb CHANGED

@@ -5,13 +5,13 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id:$
-#
-require 'bio/util/restriction_enzyme'
 require 'bio/sequence'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 # A single strand of restriction enzyme sequence pattern with a 5' to 3'

data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: cut_locations_in_enzyme_notation.rb,v 1.7 2007/07/16 19:28:48 k Exp $
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 class SingleStrand

data/lib/bio/util/restriction_enzyme/single_strand_complement.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: single_strand_complement.rb,v 1.5 2007/07/16 19:28:48 k Exp $
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 # A single strand of restriction enzyme sequence pattern with a 3' to 5' orientation.

data/lib/bio/util/restriction_enzyme/sorted_num_array.rb CHANGED

@@ -7,6 +7,9 @@
 #
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
   # a class to store sorted numerics.

data/lib/bio/util/restriction_enzyme/string_formatting.rb CHANGED

@@ -5,12 +5,11 @@
 # Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
 # License::   The Ruby License
 #
-#  $Id: string_formatting.rb,v 1.6 2007/07/16 19:28:48 k Exp $
-#
-require 'bio/util/restriction_enzyme'
 module Bio
+require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
 class RestrictionEnzyme
 module StringFormatting

data/lib/bio/version.rb CHANGED

@@ -1,7 +1,7 @@
 #
 # = bio/version.rb - BioRuby version information
 #
-# Copyright::	Copyright (C) 2001-2009
+# Copyright::	Copyright (C) 2001-2012
 #		Toshiaki Katayama <k@bioruby.org>,
 #               Naohisa Goto <ng@bioruby.org>
 # License::	The Ruby License
@@ -10,10 +10,19 @@
 module Bio
   # BioRuby version (Array containing Integer)
-  BIORUBY_VERSION = [1, 4, 2].extend(Comparable).freeze
+  BIORUBY_VERSION = [1, 4, 3].extend(Comparable).freeze
   # Extra version specifier (String or nil).
   # Existance of the value indicates pre-release version or modified version.
+  #
+  # nil                 :: Release version.
+  # ".0000"..".4999"    :: Release version with patches.
+  # ".5000"             :: Development unstable version.
+  # ".5001"..".8999"    :: Pre-alpha version.
+  # "-alphaN" (N=0..99) :: Alpha version.
+  # "-preN"   (N=0..99) :: Pre-release test version.
+  # "-rcN"    (N=0..99) :: Release candidate version.
+  #
   BIORUBY_EXTRA_VERSION = nil
   # Version identifier, including extra version string (String)

data/sample/seqdatabase.ini ADDED

@@ -0,0 +1,210 @@
+VERSION=1.00
+[embl]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=embl
+[embl-upd]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=embl-upd
+[embl_biofetch]
+protocol=biofetch
+location=http://www.ebi.ac.uk/cgi-bin/dbfetch
+dbname=embl
+[embl_biosql]
+protocol=biosql
+location=localhost
+dbname=biosql
+driver=postgres
+user=hack
+pass=
+biodbname=embl
+[embl_biocorba]
+protocol=bsane-corba
+location=sqldbsrv.ior
+[embl_xembl]
+protocol=xembl
+location=http://www.ebi.ac.uk/xembl/XEMBL.wsdl
+format=Bsml
+[embl_flat]
+protcol=flat
+location=/export/database/
+dbname=embl
+[genbank_bdb]
+protcol=flat
+location=/export/database/
+dbname=genbank
+[swissprot]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=swissprot
+[swissprot-upd]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=swissprot-upd
+[swissprot_biofetch]
+protocol=biofetch
+location=http://www.ebi.ac.uk/cgi-bin/dbfetch
+dbname=swall
+[swissprot_biosql]
+protocol=biosql
+location=db.bioruby.org
+dbname=biosql
+driver=mysql
+user=root
+pass=
+biodbname=sp
+[genbank]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=genbank
+[genbank-upd]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=genbank-upd
+[genbank_biosql]
+protocol=biosql
+location=db.bioruby.org
+dbname=biosql
+driver=mysql
+user=root
+pass=
+biodbname=gb
+[refseq]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=refseq
+[refseq_biosql]
+protocol=biosql
+location=db.bioruby.org
+dbname=biosql
+driver=mysql
+user=
+pass=
+biodbname=rs
+[kegg-pathway]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=pathway
+[kegg-genome]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=genome
+[kegg-genes]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=genes
+[kegg-vgenes]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=vgenes
+[aaindex]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=aaindex
+[blocks]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=blocks
+[enzyme]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=enzyme
+[epd]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=epd
+[litdb]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=litdb
+[omim]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=omim
+[pdb]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=pdb
+[pdbstr]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=pdbstr
+[pfam]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=pfam
+[pir]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=pir
+[pmd]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=pmd
+[prf]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=prf
+[prints]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=prints
+[prodom]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=prodom
+[prosdoc]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=prosdoc
+[prosite]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=prosite
+[transfac]
+protocol=biofetch
+location=http://bioruby.org/cgi-bin/biofetch.rb
+dbname=transfac