bio-nexml 0.0.1

data/Gemfile

@@ -0,0 +1,15 @@
+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.5.2"
+  gem "rcov", ">= 0"
+  gem "bio", ">= 1.4.1"
+  gem "libxml-ruby", ">= 1.1.4"
+end

data/Gemfile.lock

@@ -0,0 +1,24 @@
+GEM
+  remote: http://rubygems.org/
+  specs:
+    bio (1.4.1)
+    git (1.2.5)
+    jeweler (1.5.2)
+      bundler (~> 1.0.0)
+      git (>= 1.2.5)
+      rake
+    libxml-ruby (1.1.4)
+    rake (0.8.7)
+    rcov (0.9.9)
+    shoulda (2.11.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bio (>= 1.4.1)
+  bundler (~> 1.0.0)
+  jeweler (~> 1.5.2)
+  libxml-ruby (>= 1.1.4)
+  rcov
+  shoulda

data/LICENSE.txt

@@ -0,0 +1,20 @@
+Copyright (c) 2011 rvosa
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

@@ -0,0 +1,47 @@
+= bio-nexml
+
+NeXML is a file format for phylogenetic data. It is inspired by the modular
+architecture of the commonly-used NEXUS file format (hence the name) in that
+a NeXML instance document can contain:
+* sets of Operational Taxonomic Units (OTUs), i.e. the tips in phylogenetic
+  trees, and that which comparative observations are made on. Often these are
+  species ("taxa").
+* sets of phylogenetic trees (or reticulate trees, i.e. networks)
+* sets of comparative data, i.e. molecular sequences, morphological categorical
+  data, continuous data, and other types.
+
+The elements in a NeXML document can be annotated using RDFa
+(http://en.wikipedia.org/wiki/RDFa), which means that every object that can
+be parsed out of a NeXML document must be an object that, in turn, can be
+annotated with predicates (and their namespaces) and other objects (with,
+perhaps, their own namespaces). The advantage over previous file formats is
+that we can retain all metadata for all objects within one file, regardless
+where the metadata come from.
+
+NeXML can be transformed to RDF using an XSL stylesheet. As such, NeXML forms
+an intermediate format between traditional flat file formats (with predictable
+structure but no semantics) and RDF (with loose structure, but lots of
+semantics) that is both easy to work with, yet ready for the Semantic Web.
+
+To learn more, visit http://www.nexml.org
+
+== Contributing to bio-nexml
+ 
+* Check out the latest master to make sure the feature hasn't been implemented
+  or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it
+  and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a
+  future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to
+  have your own version, or is otherwise necessary, that is fine, but please
+  isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2011 rvosa. See LICENSE.txt for
+further details.
+

data/Rakefile

@@ -0,0 +1,55 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-nexml"
+  gem.homepage = "http://github.com/rvosa/bioruby-nexml"
+  gem.license = "MIT"
+  gem.summary = %Q{BioRuby plugin for reading and writing NeXML (http://nexml.org)}
+  gem.description = %Q{This plugin reads, writes and generates NeXML}
+  gem.email = "rutgeraldo@gmail.com"
+  gem.authors = ["rvosa"]
+  gem.add_runtime_dependency 'libxml-ruby', '1.1.4'
+  gem.add_development_dependency 'libxml-ruby', '1.1.4'
+  # Include your dependencies below. Runtime dependencies are required when using your gem,
+  # and development dependencies are only needed for development (ie running rake tasks, tests, etc)
+  #  gem.add_runtime_dependency 'jabber4r', '> 0.1'
+  #  gem.add_development_dependency 'rspec', '> 1.2.3'
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-nexml #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/TODO.txt

@@ -0,0 +1,6 @@
+* it would be good if objects could only be instantiated in the right nesting
+  order, e.g. you wouldn't do cell = Cell.new, but you'd do
+  cell = Row.create_cell and the nesting is automatically handled for you.
+  I think the way to do this is to require the containing object to be passed
+  (recursively) to the constructors, while create_foo internally does this,
+  passing self to the constructor.

data/VERSION

@@ -0,0 +1 @@
+0.0.1

data/bio-nexml.gemspec

@@ -0,0 +1,126 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{bio-nexml}
+  s.version = "0.0.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["rvosa"]
+  s.date = %q{2011-03-01}
+  s.description = %q{This plugin reads, writes and generates NeXML}
+  s.email = %q{rutgeraldo@gmail.com}
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "TODO.txt",
+    "VERSION",
+    "bio-nexml.gemspec",
+    "extconf.rb",
+    "lib/bio-nexml.rb",
+    "lib/bio.rb",
+    "lib/bio/db/nexml.rb",
+    "lib/bio/db/nexml/mapper.rb",
+    "lib/bio/db/nexml/mapper/framework.rb",
+    "lib/bio/db/nexml/mapper/inflection.rb",
+    "lib/bio/db/nexml/mapper/repository.rb",
+    "lib/bio/db/nexml/matrix.rb",
+    "lib/bio/db/nexml/parser.rb",
+    "lib/bio/db/nexml/schema/README.txt",
+    "lib/bio/db/nexml/schema/abstract.xsd",
+    "lib/bio/db/nexml/schema/characters/README.txt",
+    "lib/bio/db/nexml/schema/characters/abstractcharacters.xsd",
+    "lib/bio/db/nexml/schema/characters/characters.xsd",
+    "lib/bio/db/nexml/schema/characters/continuous.xsd",
+    "lib/bio/db/nexml/schema/characters/dna.xsd",
+    "lib/bio/db/nexml/schema/characters/protein.xsd",
+    "lib/bio/db/nexml/schema/characters/restriction.xsd",
+    "lib/bio/db/nexml/schema/characters/rna.xsd",
+    "lib/bio/db/nexml/schema/characters/standard.xsd",
+    "lib/bio/db/nexml/schema/external/sawsdl.xsd",
+    "lib/bio/db/nexml/schema/external/xhtml-datatypes-1.xsd",
+    "lib/bio/db/nexml/schema/external/xlink.xsd",
+    "lib/bio/db/nexml/schema/external/xml.xsd",
+    "lib/bio/db/nexml/schema/meta/README.txt",
+    "lib/bio/db/nexml/schema/meta/annotations.xsd",
+    "lib/bio/db/nexml/schema/meta/meta.xsd",
+    "lib/bio/db/nexml/schema/nexml.xsd",
+    "lib/bio/db/nexml/schema/taxa/README.txt",
+    "lib/bio/db/nexml/schema/taxa/taxa.xsd",
+    "lib/bio/db/nexml/schema/trees/README.txt",
+    "lib/bio/db/nexml/schema/trees/abstracttrees.xsd",
+    "lib/bio/db/nexml/schema/trees/network.xsd",
+    "lib/bio/db/nexml/schema/trees/tree.xsd",
+    "lib/bio/db/nexml/schema/trees/trees.xsd",
+    "lib/bio/db/nexml/taxa.rb",
+    "lib/bio/db/nexml/trees.rb",
+    "lib/bio/db/nexml/writer.rb",
+    "test/data/nexml/test.xml",
+    "test/test_bio-nexml.rb",
+    "test/unit/bio/db/nexml/tc_factory.rb",
+    "test/unit/bio/db/nexml/tc_mapper.rb",
+    "test/unit/bio/db/nexml/tc_matrix.rb",
+    "test/unit/bio/db/nexml/tc_parser.rb",
+    "test/unit/bio/db/nexml/tc_taxa.rb",
+    "test/unit/bio/db/nexml/tc_trees.rb",
+    "test/unit/bio/db/nexml/tc_writer.rb"
+  ]
+  s.homepage = %q{http://github.com/rvosa/bioruby-nexml}
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.4.2}
+  s.summary = %q{BioRuby plugin for reading and writing NeXML (http://nexml.org)}
+  s.test_files = [
+    "test/test_bio-nexml.rb",
+    "test/unit/bio/db/nexml/tc_factory.rb",
+    "test/unit/bio/db/nexml/tc_mapper.rb",
+    "test/unit/bio/db/nexml/tc_matrix.rb",
+    "test/unit/bio/db/nexml/tc_parser.rb",
+    "test/unit/bio/db/nexml/tc_taxa.rb",
+    "test/unit/bio/db/nexml/tc_trees.rb",
+    "test/unit/bio/db/nexml/tc_writer.rb"
+  ]
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_development_dependency(%q<libxml-ruby>, [">= 1.1.4"])
+      s.add_runtime_dependency(%q<libxml-ruby>, ["= 1.1.4"])
+      s.add_development_dependency(%q<libxml-ruby>, ["= 1.1.4"])
+    else
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_dependency(%q<libxml-ruby>, [">= 1.1.4"])
+      s.add_dependency(%q<libxml-ruby>, ["= 1.1.4"])
+      s.add_dependency(%q<libxml-ruby>, ["= 1.1.4"])
+    end
+  else
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.1"])
+    s.add_dependency(%q<libxml-ruby>, [">= 1.1.4"])
+    s.add_dependency(%q<libxml-ruby>, ["= 1.1.4"])
+    s.add_dependency(%q<libxml-ruby>, ["= 1.1.4"])
+  end
+end
+

data/extconf.rb

@@ -0,0 +1,2 @@
+require 'mkmf'
+create_makefile("bio-nexml")

data/lib/bio.rb

@@ -0,0 +1,321 @@
+#
+# = bio.rb - Loading all BioRuby modules
+#
+# Copyright::	Copyright (C) 2001-2007
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	The Ruby License
+#
+# $Id:$
+#
+
+module Bio
+
+  autoload :BIORUBY_VERSION, 'bio/version'
+  autoload :BIORUBY_EXTRA_VERSION, 'bio/version'
+  autoload :BIORUBY_VERSION_ID, 'bio/version'
+
+  ### Basic data types
+
+  ## Sequence
+
+  autoload :Sequence,       'bio/sequence'
+  ## below are described in bio/sequence.rb
+  #class Sequence
+  #  autoload :Common,  'bio/sequence/common'
+  #  autoload :NA,      'bio/sequence/na'
+  #  autoload :AA,      'bio/sequence/aa'
+  #  autoload :Generic, 'bio/sequence/generic'
+  #  autoload :Format,  'bio/sequence/format'
+  #  autoload :Adapter, 'bio/sequence/adapter'
+  #end
+
+  ## Locations/Location
+
+  autoload :Location,       'bio/location'
+  autoload :Locations,      'bio/location'
+
+  ## Features/Feature
+
+  autoload :Feature,        'bio/feature'
+  autoload :Features,       'bio/compat/features'
+
+  ## References/Reference
+
+  autoload :Reference,      'bio/reference'
+  autoload :References,     'bio/compat/references'
+
+  ## Pathway/Relation
+
+  autoload :Pathway,        'bio/pathway'
+  autoload :Relation,       'bio/pathway'
+
+  ## Alignment
+
+  autoload :Alignment,      'bio/alignment'
+
+  ## Tree
+  autoload :Tree, 'bio/tree'
+
+  ## Map
+  autoload :Map,            'bio/map'
+	
+  ### Constants
+
+  autoload :NucleicAcid,    'bio/data/na'
+  autoload :AminoAcid,      'bio/data/aa'
+  autoload :CodonTable,     'bio/data/codontable'
+
+
+  ### DB parsers
+
+  autoload :DB,             'bio/db'
+  autoload :NCBIDB,         'bio/db'
+  autoload :KEGGDB,         'bio/db'
+  autoload :EMBLDB,         'bio/db'
+
+  ## GenBank/RefSeq/DDBJ
+
+  autoload :GenBank,        'bio/db/genbank/genbank'
+  autoload :GenPept,        'bio/db/genbank/genpept'
+  autoload :RefSeq,         'bio/db/genbank/refseq'
+  autoload :DDBJ,           'bio/db/genbank/ddbj'
+  ## below are described in bio/db/genbank/ddbj.rb
+  #class DDBJ
+  #  autoload :XML,          'bio/io/ddbjxml'
+  #end
+
+  ## EMBL/TrEMBL/Swiss-Prot/SPTR
+
+  autoload :EMBL,           'bio/db/embl/embl'
+  autoload :SPTR,           'bio/db/embl/sptr'
+  autoload :TrEMBL,         'bio/db/embl/trembl'
+  autoload :UniProt,        'bio/db/embl/uniprot'
+  autoload :SwissProt,      'bio/db/embl/swissprot'
+
+  ## KEGG
+
+  class KEGG
+    autoload :GENOME,       'bio/db/kegg/genome'
+    autoload :GENES,        'bio/db/kegg/genes'
+    autoload :ENZYME,       'bio/db/kegg/enzyme'
+    autoload :COMPOUND,     'bio/db/kegg/compound'
+    autoload :DRUG,         'bio/db/kegg/drug'
+    autoload :GLYCAN,       'bio/db/kegg/glycan'
+    autoload :REACTION,     'bio/db/kegg/reaction'
+    autoload :BRITE,        'bio/db/kegg/brite'
+    autoload :CELL,         'bio/db/kegg/cell'
+    autoload :EXPRESSION,   'bio/db/kegg/expression'
+    autoload :ORTHOLOGY,    'bio/db/kegg/orthology'
+    autoload :KGML,         'bio/db/kegg/kgml'
+    autoload :Taxonomy,     'bio/db/kegg/taxonomy'
+  end
+
+  ## other formats
+
+  autoload :FastaFormat,    'bio/db/fasta'
+  autoload :FastaNumericFormat, 'bio/db/fasta/qual' # change to FastaFormat::Numeric ?
+  autoload :FastaDefline,       'bio/db/fasta/defline' # change to FastaFormat::Defline ?
+  autoload :Fastq,          'bio/db/fastq'
+  autoload :GFF,            'bio/db/gff'
+  autoload :AAindex,        'bio/db/aaindex'
+  autoload :AAindex1,       'bio/db/aaindex' # change to AAindex::AAindex1 ?
+  autoload :AAindex2,       'bio/db/aaindex' # change to AAindex::AAindex2 ?
+  autoload :TRANSFAC,       'bio/db/transfac'
+  autoload :PROSITE,        'bio/db/prosite'
+  autoload :LITDB,          'bio/db/litdb'
+  autoload :MEDLINE,        'bio/db/medline'
+  autoload :FANTOM,         'bio/db/fantom'
+  autoload :GO,             'bio/db/go'
+  autoload :PDB,            'bio/db/pdb'
+  autoload :NBRF,           'bio/db/nbrf'
+  autoload :REBASE,         'bio/db/rebase'
+  autoload :SOFT,           'bio/db/soft'
+  autoload :Lasergene,      'bio/db/lasergene'
+  autoload :SangerChromatogram, 'bio/db/sanger_chromatogram/chromatogram'
+  autoload :Scf,                'bio/db/sanger_chromatogram/scf'
+  autoload :Abif,               'bio/db/sanger_chromatogram/abif'
+
+  autoload :Newick,         'bio/db/newick'
+  autoload :Nexus,          'bio/db/nexus'
+
+  autoload :PhyloXML,       'bio/db/phyloxml/phyloxml_elements'
+  # Bio::Taxonomy will be moved to other file
+  autoload :Taxonomy,       'bio/db/phyloxml/phyloxml_elements'
+  ## below are described in bio/db/phyloxml/phyloxml_elements.rb
+  #module PhyloXML
+  #  autoload :Parser,       'bio/db/phyloxml/phyloxml_parser'
+  #  autoload :Writer,       'bio/db/phyloxml/phyloxml_writer'
+  #end
+
+  ### IO interface modules
+
+  autoload :Registry,       'bio/io/registry'
+  autoload :Fetch,          'bio/io/fetch'
+  autoload :SQL,            'bio/io/sql'
+  autoload :SOAPWSDL,       'bio/io/soapwsdl'
+  autoload :FlatFile,       'bio/io/flatfile'
+  autoload :FlatFileIndex,  'bio/io/flatfile/index' # chage to FlatFile::Index ?
+  ## below are described in bio/io/flatfile/index.rb
+  #class FlatFileIndex
+  #  autoload :Indexer,    'bio/io/flatfile/indexer'
+  #  autoload :BDBdefault, 'bio/io/flatfile/bdb'
+  #  autoload :BDBwrapper, 'bio/io/flatfile/bdb'
+  #  autoload :BDB_1,      'bio/io/flatfile/bdb'
+  #end
+
+  autoload :PubMed,         'bio/io/pubmed'
+  autoload :DAS,            'bio/io/das'
+  autoload :DBGET,          'bio/io/dbget'
+
+  autoload :Ensembl,        'bio/io/ensembl'
+  autoload :Hinv,           'bio/io/hinv'
+
+  ## below are described in bio/appl/blast.rb
+  #class Blast
+  #  autoload :Fastacmd,     'bio/io/fastacmd'
+  #end
+
+  class KEGG
+    autoload :API,          'bio/io/keggapi'
+  end
+
+  ## below are described in bio/db/genbank/ddbj.rb
+  #class DDBJ
+  #  autoload :XML,          'bio/io/ddbjxml'
+  #end
+
+  class HGC
+    autoload :HiGet,        'bio/io/higet'
+  end
+
+  class EBI
+    autoload :SOAP,         'bio/io/ebisoap'
+  end
+
+  autoload :NCBI,         'bio/io/ncbirest'
+  ## below are described in bio/io/ncbirest.rb
+  #class NCBI
+  #  autoload :SOAP,       'bio/io/ncbisoap'
+  #  autoload :REST,       'bio/io/ncbirest'
+  #end
+
+  autoload :TogoWS,       'bio/io/togows'
+
+  ### Applications
+
+  autoload :Fasta,          'bio/appl/fasta'
+  ## below are described in bio/appl/fasta.rb
+  #class Fasta
+  #  autoload :Report,       'bio/appl/fasta/format10'
+  #end
+
+  autoload :Blast,          'bio/appl/blast'
+  ## below are described in bio/appl/blast.rb
+  #class Blast
+  #  autoload :Fastacmd,     'bio/io/fastacmd'
+  #  autoload :Report,       'bio/appl/blast/report'
+  #  autoload :Default,      'bio/appl/blast/format0'
+  #  autoload :WU,           'bio/appl/blast/wublast'
+  #  autoload :Bl2seq,       'bio/appl/bl2seq/report'
+  #  autoload :RPSBlast,     'bio/appl/blast/rpsblast'
+  #  autoload :NCBIOptions,  'bio/appl/blast/ncbioptions'
+  #  autoload :Remote,       'bio/appl/blast/remote'
+  #end
+
+  autoload :HMMER,          'bio/appl/hmmer'
+  ## below are described in bio/appl/hmmer.rb
+  #class HMMER
+  #  autoload :Report,       'bio/appl/hmmer/report'
+  #end
+
+  autoload :EMBOSS,         'bio/appl/emboss'    # use bio/command, improve
+
+  autoload :PSORT,          'bio/appl/psort'
+  ## below are described in bio/appl/psort.rb
+  #class PSORT
+  #  class PSORT1
+  #    autoload :Report,       'bio/appl/psort/report'
+  #  end
+  #  class PSORT2
+  #    autoload :Report,       'bio/appl/psort/report'
+  #  end
+  #end
+
+  autoload :TMHMM,          'bio/appl/tmhmm/report'
+  autoload :TargetP,        'bio/appl/targetp/report'
+  autoload :SOSUI,          'bio/appl/sosui/report'
+  autoload :Genscan,        'bio/appl/genscan/report'
+
+  autoload :ClustalW,       'bio/appl/clustalw'
+  ## below are described in bio/appl/clustalw.rb
+  #class ClustalW
+  #  autoload :Report,       'bio/appl/clustalw/report'
+  #end
+
+  autoload :MAFFT,          'bio/appl/mafft'
+  ## below are described in bio/appl/mafft.rb
+  #class MAFFT
+  #  autoload :Report,       'bio/appl/mafft/report'
+  #end
+
+  autoload :Tcoffee,        'bio/appl/tcoffee'
+  autoload :Muscle,         'bio/appl/muscle'
+  autoload :Probcons,       'bio/appl/probcons'
+
+  autoload :Sim4,           'bio/appl/sim4'
+  ## below are described in bio/appl/sim4.rb
+  #class Sim4
+  #  autoload :Report,       'bio/appl/sim4/report'
+  #end
+  
+  autoload :Spidey,         'bio/appl/spidey/report'
+  autoload :Blat,           'bio/appl/blat/report'
+  
+  module GCG
+    autoload :Msf,          'bio/appl/gcg/msf'
+    autoload :Seq,          'bio/appl/gcg/seq'
+  end
+
+  module Phylip
+    autoload :PhylipFormat,   'bio/appl/phylip/alignment'
+    autoload :DistanceMatrix, 'bio/appl/phylip/distance_matrix'
+  end
+
+  autoload :Iprscan,        'bio/appl/iprscan/report'
+
+  autoload :PAML,           'bio/appl/paml/common'
+  ## below are described in bio/appl/paml/common.rb
+  # module PAML
+  #   autoload :Codeml,         'bio/appl/paml/codeml'
+  #   autoload :Baseml,         'bio/appl/paml/baseml'
+  #   autoload :Yn00,           'bio/appl/paml/yn00'
+  # end
+
+  ### Utilities
+
+  autoload :SiRNA,          'bio/util/sirna'
+  autoload :ColorScheme,    'bio/util/color_scheme'
+  autoload :ContingencyTable, 'bio/util/contingency_table'
+  autoload :RestrictionEnzyme, 'bio/util/restriction_enzyme'
+
+  ### Service libraries
+  autoload :Command,        'bio/command'
+
+  ### NeXML lib
+  autoload :NeXML,          'bio/db/nexml'
+
+  ### Provide BioRuby shell 'command' also as 'Bio.command' (like ChemRuby)
+
+  def self.method_missing(*args)
+    require 'bio/shell'
+    extend Bio::Shell
+    public_class_method(*Bio::Shell.private_instance_methods)
+    if Bio.respond_to?(args.first)
+      Bio.send(*args)
+    else
+      raise NameError
+    end
+  end
+
+end
+