RubyGems - bio - Versions diffs - 1.0.0 → 1.1.0 - Mend

bio 1.0.0 → 1.1.0

Files changed (340) hide show

data/bin/bioruby +14 -122
data/bin/br_biofetch.rb +2 -2
data/bin/br_bioflat.rb +2 -2
data/bin/br_biogetseq.rb +2 -2
data/bin/br_pmfetch.rb +3 -3
data/doc/Changes-0.7.rd +77 -0
data/doc/KEGG_API.rd +523 -232
data/doc/KEGG_API.rd.ja +529 -207
data/doc/Tutorial.rd +48 -11
data/lib/bio.rb +59 -6
data/lib/bio/alignment.rb +713 -103
data/lib/bio/appl/bl2seq/report.rb +2 -18
data/lib/bio/appl/blast.rb +108 -91
data/lib/bio/appl/blast/format0.rb +33 -18
data/lib/bio/appl/blast/format8.rb +6 -20
data/lib/bio/appl/blast/report.rb +293 -429
data/lib/bio/appl/blast/rexml.rb +8 -22
data/lib/bio/appl/blast/wublast.rb +21 -12
data/lib/bio/appl/blast/xmlparser.rb +180 -183
data/lib/bio/appl/blat/report.rb +127 -30
data/lib/bio/appl/clustalw.rb +87 -59
data/lib/bio/appl/clustalw/report.rb +20 -22
data/lib/bio/appl/emboss.rb +113 -20
data/lib/bio/appl/fasta.rb +173 -198
data/lib/bio/appl/fasta/format10.rb +244 -347
data/lib/bio/appl/gcg/msf.rb +212 -0
data/lib/bio/appl/gcg/seq.rb +195 -0
data/lib/bio/appl/genscan/report.rb +5 -23
data/lib/bio/appl/hmmer.rb +8 -45
data/lib/bio/appl/hmmer/report.rb +2 -20
data/lib/bio/appl/iprscan/report.rb +374 -0
data/lib/bio/appl/mafft.rb +87 -50
data/lib/bio/appl/mafft/report.rb +151 -44
data/lib/bio/appl/muscle.rb +52 -0
data/lib/bio/appl/phylip/alignment.rb +129 -0
data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
data/lib/bio/appl/probcons.rb +41 -0
data/lib/bio/appl/psort.rb +89 -96
data/lib/bio/appl/psort/report.rb +6 -22
data/lib/bio/appl/pts1.rb +263 -0
data/lib/bio/appl/sim4.rb +26 -36
data/lib/bio/appl/sim4/report.rb +2 -18
data/lib/bio/appl/sosui/report.rb +5 -20
data/lib/bio/appl/spidey/report.rb +2 -2
data/lib/bio/appl/targetp/report.rb +4 -20
data/lib/bio/appl/tcoffee.rb +55 -0
data/lib/bio/appl/tmhmm/report.rb +4 -20
data/lib/bio/command.rb +235 -64
data/lib/bio/data/aa.rb +21 -26
data/lib/bio/data/codontable.rb +2 -20
data/lib/bio/data/na.rb +19 -4
data/lib/bio/db.rb +27 -12
data/lib/bio/db/aaindex.rb +2 -20
data/lib/bio/db/embl/common.rb +4 -21
data/lib/bio/db/embl/embl.rb +33 -85
data/lib/bio/db/embl/sptr.rb +612 -302
data/lib/bio/db/embl/swissprot.rb +10 -29
data/lib/bio/db/embl/trembl.rb +10 -29
data/lib/bio/db/embl/uniprot.rb +10 -29
data/lib/bio/db/fantom.rb +15 -20
data/lib/bio/db/fasta.rb +3 -3
data/lib/bio/db/genbank/common.rb +37 -46
data/lib/bio/db/genbank/ddbj.rb +6 -18
data/lib/bio/db/genbank/genbank.rb +47 -186
data/lib/bio/db/genbank/genpept.rb +4 -17
data/lib/bio/db/genbank/refseq.rb +4 -17
data/lib/bio/db/gff.rb +103 -35
data/lib/bio/db/go.rb +4 -20
data/lib/bio/db/kegg/brite.rb +26 -36
data/lib/bio/db/kegg/compound.rb +81 -85
data/lib/bio/db/kegg/drug.rb +98 -0
data/lib/bio/db/kegg/enzyme.rb +133 -110
data/lib/bio/db/kegg/expression.rb +2 -20
data/lib/bio/db/kegg/genes.rb +208 -238
data/lib/bio/db/kegg/genome.rb +164 -285
data/lib/bio/db/kegg/glycan.rb +114 -157
data/lib/bio/db/kegg/keggtab.rb +242 -303
data/lib/bio/db/kegg/kgml.rb +117 -160
data/lib/bio/db/kegg/orthology.rb +112 -0
data/lib/bio/db/kegg/reaction.rb +54 -69
data/lib/bio/db/kegg/taxonomy.rb +331 -0
data/lib/bio/db/lasergene.rb +209 -0
data/lib/bio/db/litdb.rb +3 -27
data/lib/bio/db/medline.rb +228 -249
data/lib/bio/db/nbrf.rb +3 -3
data/lib/bio/db/newick.rb +510 -0
data/lib/bio/db/nexus.rb +1854 -0
data/lib/bio/db/pdb.rb +5 -17
data/lib/bio/db/pdb/atom.rb +2 -18
data/lib/bio/db/pdb/chain.rb +2 -18
data/lib/bio/db/pdb/chemicalcomponent.rb +2 -18
data/lib/bio/db/pdb/model.rb +2 -18
data/lib/bio/db/pdb/pdb.rb +73 -34
data/lib/bio/db/pdb/residue.rb +4 -20
data/lib/bio/db/pdb/utils.rb +2 -18
data/lib/bio/db/prosite.rb +403 -422
data/lib/bio/db/rebase.rb +84 -40
data/lib/bio/db/soft.rb +404 -0
data/lib/bio/db/transfac.rb +5 -17
data/lib/bio/feature.rb +106 -52
data/lib/bio/io/das.rb +32 -42
data/lib/bio/io/dbget.rb +2 -20
data/lib/bio/io/ddbjxml.rb +77 -138
data/lib/bio/io/ebisoap.rb +158 -0
data/lib/bio/io/ensembl.rb +229 -0
data/lib/bio/io/fastacmd.rb +89 -82
data/lib/bio/io/fetch.rb +163 -96
data/lib/bio/io/flatfile.rb +170 -73
data/lib/bio/io/flatfile/bdb.rb +3 -16
data/lib/bio/io/flatfile/index.rb +2 -2
data/lib/bio/io/flatfile/indexer.rb +3 -2
data/lib/bio/io/higet.rb +12 -31
data/lib/bio/io/keggapi.rb +210 -269
data/lib/bio/io/ncbisoap.rb +155 -0
data/lib/bio/io/pubmed.rb +169 -147
data/lib/bio/io/registry.rb +4 -20
data/lib/bio/io/soapwsdl.rb +43 -38
data/lib/bio/io/sql.rb +242 -305
data/lib/bio/location.rb +407 -285
data/lib/bio/map.rb +410 -0
data/lib/bio/pathway.rb +558 -695
data/lib/bio/reference.rb +272 -75
data/lib/bio/sequence.rb +255 -13
data/lib/bio/sequence/aa.rb +71 -10
data/lib/bio/sequence/common.rb +187 -33
data/lib/bio/sequence/compat.rb +59 -4
data/lib/bio/sequence/format.rb +54 -7
data/lib/bio/sequence/generic.rb +3 -3
data/lib/bio/sequence/na.rb +328 -26
data/lib/bio/shell.rb +11 -4
data/lib/bio/shell/core.rb +221 -160
data/lib/bio/shell/demo.rb +18 -15
data/lib/bio/shell/interface.rb +14 -12
data/lib/bio/shell/irb.rb +95 -0
data/lib/bio/shell/object.rb +45 -26
data/lib/bio/shell/plugin/blast.rb +42 -0
data/lib/bio/shell/plugin/codon.rb +22 -14
data/lib/bio/shell/plugin/das.rb +58 -0
data/lib/bio/shell/plugin/emboss.rb +2 -2
data/lib/bio/shell/plugin/entry.rb +22 -11
data/lib/bio/shell/plugin/flatfile.rb +2 -2
data/lib/bio/shell/plugin/keggapi.rb +13 -6
data/lib/bio/shell/plugin/midi.rb +4 -4
data/lib/bio/shell/plugin/obda.rb +2 -2
data/lib/bio/shell/plugin/psort.rb +56 -0
data/lib/bio/shell/plugin/seq.rb +35 -8
data/lib/bio/shell/plugin/soap.rb +87 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/bioruby_generator.rb +29 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_classes.rhtml +4 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_log.rhtml +27 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_methods.rhtml +11 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_modules.rhtml +4 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/_variables.rhtml +7 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-bg.gif +0 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-console.png +0 -0
data/lib/bio/shell/rails/{public/images/icon.png → vendor/plugins/generators/bioruby/templates/bioruby-gem.png} +0 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby-link.gif +0 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.css +369 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby.rhtml +47 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_controller.rb +144 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_helper.rb +47 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/commands.rhtml +8 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/history.rhtml +10 -0
data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/index.rhtml +22 -0
data/lib/bio/shell/script.rb +25 -0
data/lib/bio/shell/setup.rb +109 -0
data/lib/bio/shell/web.rb +70 -58
data/lib/bio/tree.rb +850 -0
data/lib/bio/util/color_scheme.rb +84 -107
data/lib/bio/util/color_scheme/buried.rb +5 -24
data/lib/bio/util/color_scheme/helix.rb +5 -24
data/lib/bio/util/color_scheme/hydropathy.rb +5 -24
data/lib/bio/util/color_scheme/nucleotide.rb +5 -24
data/lib/bio/util/color_scheme/strand.rb +5 -24
data/lib/bio/util/color_scheme/taylor.rb +5 -24
data/lib/bio/util/color_scheme/turn.rb +5 -24
data/lib/bio/util/color_scheme/zappo.rb +5 -24
data/lib/bio/util/contingency_table.rb +70 -43
data/lib/bio/util/restriction_enzyme.rb +228 -0
data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
data/lib/bio/util/restriction_enzyme/single_strand.rb +199 -0
data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
data/lib/bio/util/sirna.rb +4 -22
data/sample/color_scheme_na.rb +4 -12
data/sample/enzymes.rb +78 -0
data/sample/goslim.rb +5 -13
data/sample/psortplot_html.rb +4 -12
data/test/data/blast/2.2.15.blastp.m7 +876 -0
data/test/data/embl/AB090716.embl.rel89 +63 -0
data/test/data/fasta/example1.txt +75 -0
data/test/data/fasta/example2.txt +21 -0
data/test/data/iprscan/merged.raw +32 -0
data/test/data/iprscan/merged.txt +74 -0
data/test/data/soft/GDS100_partial.soft +92 -0
data/test/data/soft/GSE3457_family_partial.soft +874 -0
data/test/functional/bio/io/test_ensembl.rb +103 -0
data/test/functional/bio/io/test_soapwsdl.rb +5 -17
data/test/unit/bio/appl/bl2seq/test_report.rb +2 -2
data/test/unit/bio/appl/blast/test_report.rb +3 -16
data/test/unit/bio/appl/blast/test_xmlparser.rb +4 -16
data/test/unit/bio/appl/genscan/test_report.rb +3 -16
data/test/unit/bio/appl/hmmer/test_report.rb +3 -16
data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
data/test/unit/bio/appl/mafft/test_report.rb +63 -0
data/test/unit/bio/appl/sosui/test_report.rb +3 -16
data/test/unit/bio/appl/targetp/test_report.rb +3 -16
data/test/unit/bio/appl/test_blast.rb +3 -16
data/test/unit/bio/appl/test_fasta.rb +4 -16
data/test/unit/bio/appl/test_pts1.rb +140 -0
data/test/unit/bio/appl/tmhmm/test_report.rb +3 -16
data/test/unit/bio/data/test_aa.rb +4 -17
data/test/unit/bio/data/test_codontable.rb +3 -16
data/test/unit/bio/data/test_na.rb +3 -3
data/test/unit/bio/db/embl/test_common.rb +3 -16
data/test/unit/bio/db/embl/test_embl.rb +3 -16
data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
data/test/unit/bio/db/embl/test_sptr.rb +1548 -41
data/test/unit/bio/db/embl/test_uniprot.rb +3 -16
data/test/unit/bio/db/kegg/test_genes.rb +3 -16
data/test/unit/bio/db/pdb/test_pdb.rb +7 -24
data/test/unit/bio/db/test_aaindex.rb +2 -2
data/test/unit/bio/db/test_fasta.rb +3 -16
data/test/unit/bio/db/test_gff.rb +3 -16
data/test/unit/bio/db/test_lasergene.rb +95 -0
data/test/unit/bio/db/test_newick.rb +56 -0
data/test/unit/bio/db/test_nexus.rb +360 -0
data/test/unit/bio/db/test_prosite.rb +5 -18
data/test/unit/bio/db/test_rebase.rb +11 -25
data/test/unit/bio/db/test_soft.rb +138 -0
data/test/unit/bio/io/test_ddbjxml.rb +5 -17
data/test/unit/bio/io/test_ensembl.rb +109 -0
data/test/unit/bio/io/test_fastacmd.rb +3 -16
data/test/unit/bio/io/test_flatfile.rb +237 -0
data/test/unit/bio/io/test_soapwsdl.rb +4 -17
data/test/unit/bio/sequence/test_aa.rb +3 -3
data/test/unit/bio/sequence/test_common.rb +3 -16
data/test/unit/bio/sequence/test_compat.rb +3 -16
data/test/unit/bio/sequence/test_na.rb +29 -3
data/test/unit/bio/shell/plugin/test_seq.rb +8 -8
data/test/unit/bio/test_alignment.rb +16 -27
data/test/unit/bio/test_command.rb +242 -25
data/test/unit/bio/test_db.rb +3 -16
data/test/unit/bio/test_feature.rb +4 -16
data/test/unit/bio/test_location.rb +4 -16
data/test/unit/bio/test_map.rb +230 -0
data/test/unit/bio/test_pathway.rb +4 -16
data/test/unit/bio/test_reference.rb +2 -2
data/test/unit/bio/test_sequence.rb +7 -19
data/test/unit/bio/test_shell.rb +3 -16
data/test/unit/bio/test_tree.rb +593 -0
data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +100 -0
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
data/test/unit/bio/util/test_color_scheme.rb +6 -18
data/test/unit/bio/util/test_contingency_table.rb +6 -18
data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
data/test/unit/bio/util/test_sirna.rb +3 -16
metadata +228 -169
data/doc/BioRuby.rd.ja +0 -225
data/doc/Design.rd.ja +0 -341
data/doc/TODO.rd.ja +0 -138
data/lib/bio/appl/fasta/format6.rb +0 -37
data/lib/bio/db/kegg/cell.rb +0 -88
data/lib/bio/db/kegg/ko.rb +0 -178
data/lib/bio/shell/rails/Rakefile +0 -10
data/lib/bio/shell/rails/app/controllers/application.rb +0 -4
data/lib/bio/shell/rails/app/controllers/shell_controller.rb +0 -94
data/lib/bio/shell/rails/app/helpers/application_helper.rb +0 -3
data/lib/bio/shell/rails/app/models/shell_connection.rb +0 -30
data/lib/bio/shell/rails/app/views/layouts/shell.rhtml +0 -37
data/lib/bio/shell/rails/app/views/shell/history.rhtml +0 -5
data/lib/bio/shell/rails/app/views/shell/index.rhtml +0 -2
data/lib/bio/shell/rails/app/views/shell/show.rhtml +0 -13
data/lib/bio/shell/rails/config/boot.rb +0 -19
data/lib/bio/shell/rails/config/database.yml +0 -85
data/lib/bio/shell/rails/config/environment.rb +0 -53
data/lib/bio/shell/rails/config/environments/development.rb +0 -19
data/lib/bio/shell/rails/config/environments/production.rb +0 -19
data/lib/bio/shell/rails/config/environments/test.rb +0 -19
data/lib/bio/shell/rails/config/routes.rb +0 -19
data/lib/bio/shell/rails/doc/README_FOR_APP +0 -2
data/lib/bio/shell/rails/public/404.html +0 -8
data/lib/bio/shell/rails/public/500.html +0 -8
data/lib/bio/shell/rails/public/dispatch.cgi +0 -10
data/lib/bio/shell/rails/public/dispatch.fcgi +0 -24
data/lib/bio/shell/rails/public/dispatch.rb +0 -10
data/lib/bio/shell/rails/public/favicon.ico +0 -0
data/lib/bio/shell/rails/public/images/rails.png +0 -0
data/lib/bio/shell/rails/public/index.html +0 -277
data/lib/bio/shell/rails/public/javascripts/controls.js +0 -750
data/lib/bio/shell/rails/public/javascripts/dragdrop.js +0 -584
data/lib/bio/shell/rails/public/javascripts/effects.js +0 -854
data/lib/bio/shell/rails/public/javascripts/prototype.js +0 -1785
data/lib/bio/shell/rails/public/robots.txt +0 -1
data/lib/bio/shell/rails/public/stylesheets/main.css +0 -187
data/lib/bio/shell/rails/script/about +0 -3
data/lib/bio/shell/rails/script/breakpointer +0 -3
data/lib/bio/shell/rails/script/console +0 -3
data/lib/bio/shell/rails/script/destroy +0 -3
data/lib/bio/shell/rails/script/generate +0 -3
data/lib/bio/shell/rails/script/performance/benchmarker +0 -3
data/lib/bio/shell/rails/script/performance/profiler +0 -3
data/lib/bio/shell/rails/script/plugin +0 -3
data/lib/bio/shell/rails/script/process/reaper +0 -3
data/lib/bio/shell/rails/script/process/spawner +0 -3
data/lib/bio/shell/rails/script/process/spinner +0 -3
data/lib/bio/shell/rails/script/runner +0 -3
data/lib/bio/shell/rails/script/server +0 -42
data/lib/bio/shell/rails/test/test_helper.rb +0 -28

data/lib/bio/shell/rails/app/controllers/application.rb DELETED

@@ -1,4 +0,0 @@
-# Filters added to this controller will be run for all controllers in the application.
-# Likewise, all the methods added will be available for all controllers.
-class ApplicationController < ActionController::Base
-end

data/lib/bio/shell/rails/app/controllers/shell_controller.rb DELETED

@@ -1,94 +0,0 @@
-class DocumentRegistry
-  @@registry = []
-  def self.[](class_name)
-    @@registry.each do |block|
-      url = block.call(class_name)
-      return url if url
-    end
-    ""
-  end
-  def self.register &block
-    @@registry.push(block)
-  end
-end
-DocumentRegistry.register() do |class_name|
-  if m = /Bio::(.+)/.match(class_name)
-    "http://bioruby.org/rdoc/classes/Bio/#{m[1].split('::').join('/')}.html"
-  else
-    false
-  end
-end
-DocumentRegistry.register do |class_name|
-  if m = /Chem::(.+)/.match(class_name)
-    "http://chemruby.org/rdoc/classes/Chem/#{m[1].split('::').join('/')}.html"
-  else
-    false
-  end
-end
-DocumentRegistry.register do |class_name|
-  "http://www.ruby-doc.org/core/classes/#{class_name.split('::').join('/')}.html"
-end
-class ShellController < ApplicationController
-  layout 'shell'  #, :except => [:rss_feed, :rss_with_content]
-  def index
-    setup
-  end
-  def show
-    setup
-    @obj = $drb_server[params[:id]]
-    if @obj.nil?
-      @inheritance = "<h1>Unknown local variable! : #{params[:var]}</h1>"
-    else
-      @inheritance = get_inheritance @obj.class
-      if @obj.respond_to?(:to_html)
-        @contents = @obj.to_html
-      else
-        @contents = "Undefined :to_html"
-      end
-    end
-    @title = params[:id]
-  end
-=begin
-  def history
-    setup
-    @history = File.read("session/history")
-  end
-=end
-  private
-  def setup
-    @local_vars = $drb_server.registry
-  end
-  def get_inheritance obj
-    #    mods = obj.included_modules - [PP::ObjectMixin, Bio::Shell, WEBrick]
-    mods = obj.included_modules
-    module_links = mods.collect{|m|
-      " [<a href=#{DocumentRegistry[m.to_s]}>#{m.to_s}</a>] "
-    }.join("|")
-    inherit = []
-    loop do
-      inherit.push(" [<a href=#{DocumentRegistry[obj.to_s]}>#{obj.to_s}</a>] ")
-      break if obj == Object
-      obj = obj.superclass
-    end
-    "<table><tr><th>Inheritance</th><td>" +  inherit.join(" &lt; ") + "</td></tr>" +
-      "<tr><th>Mix-in</th><td>" + module_links + "</td</tr></table>"
-  end
-end

data/lib/bio/shell/rails/app/helpers/application_helper.rb DELETED

@@ -1,3 +0,0 @@
-# Methods added to this helper will be available to all templates in the application.
-module ApplicationHelper
-end

data/lib/bio/shell/rails/app/models/shell_connection.rb DELETED

@@ -1,30 +0,0 @@
-# Model object for rails
-class ShellConnection
-# include DRb::DRbObservable
-  attr_reader :registry
-  def puts_remote(str)
-    STDOUT.puts(str)
-  end
-  def initialize
-    @connected = false
-    @registry = {}
-  end
-  def [] o_id
-    @registry[o_id]
-  end
-  def []=(name, obj)
-    @registry[name] = obj
-  end
-  def delete(name)
-    @registry.delete(name)
-  end
-end

data/lib/bio/shell/rails/app/views/layouts/shell.rhtml DELETED

@@ -1,37 +0,0 @@
-<html>
-<head>
-  <title>BioRuby shell on Rails</title>
-  <link href="/stylesheets/main.css" media="screen" rel="Stylesheet" type="text/css" />
-</head>
-<body>
-<div id="side">
-  <img src="/images/icon.png">
-  <br>
-<!--
-  <h2>Status</h2>
-  <ul><li><%= @connected ? "Not Connected" : "Connected" %></li></ul>
-  <h2>History</h2>
-  <ul>
-    <li>
-      <%= link_to "History", :action => "history" %>
-    </li>
-  </ul>
--->
-  <h2>Local variables</h2>
-  <ul>
-  <% @local_vars.each do |idx, var| %>
-  <li><%= link_to idx, {:action => "show", :id => idx}%></li>
-  <% end %>
-  </ul>
-</div>
-<div id="banner">
-  BioRuby shell on Rails
-</div>
-<div id="main">
-  <%= @content_for_layout %>
-</div>
-</body>

data/lib/bio/shell/rails/app/views/shell/history.rhtml DELETED

@@ -1,5 +0,0 @@
-<!-- this file is temprally not used -- see shell_controller.rb#history -->
-<pre>
-<%= @history %>
-</pre>

data/lib/bio/shell/rails/app/views/shell/index.rhtml DELETED

	@@ -1,2 +0,0 @@
1	-
2	- <h2>Connected!</h2>

data/lib/bio/shell/rails/app/views/shell/show.rhtml DELETED

@@ -1,13 +0,0 @@
-<%= @inheritance %>
-<%= @contents %>
-<%= form_tag(:action => "show")%>
-<!--
-<table>
-  <tr><th>Memo</th></tr>
-  <tr><td><input type="submit"></td></tr>
-</table>
--->
-<%= end_form_tag %>

data/lib/bio/shell/rails/config/boot.rb DELETED

@@ -1,19 +0,0 @@
-# Don't change this file. Configuration is done in config/environment.rb and config/environments/*.rb
-unless defined?(RAILS_ROOT)
-  root_path = File.join(File.dirname(__FILE__), '..')
-  unless RUBY_PLATFORM =~ /mswin32/
-    require 'pathname'
-    root_path = Pathname.new(root_path).cleanpath(true).to_s
-  end
-  RAILS_ROOT = root_path
-end
-if File.directory?("#{RAILS_ROOT}/vendor/rails")
-  require "#{RAILS_ROOT}/vendor/rails/railties/lib/initializer"
-else
-  require 'rubygems'
-  require 'initializer'
-end
-Rails::Initializer.run(:set_load_path)

data/lib/bio/shell/rails/config/database.yml DELETED

@@ -1,85 +0,0 @@
-# MySQL (default setup).  Versions 4.1 and 5.0 are recommended.
-#
-# Get the fast C bindings:
-#   gem install mysql
-#   (on OS X: gem install mysql -- --include=/usr/local/lib)
-# And be sure to use new-style password hashing:
-#   http://dev.mysql.com/doc/refman/5.0/en/old-client.html
-development:
-  adapter: mysql
-  database: kumamushi_development
-  username: root
-  password:
-  socket: /tmp/mysql.sock
-  # Connect on a TCP socket.  If omitted, the adapter will connect on the
-  # domain socket given by socket instead.
-  #host: localhost
-  #port: 3306
-# Warning: The database defined as 'test' will be erased and
-# re-generated from your development database when you run 'rake'.
-# Do not set this db to the same as development or production.
-test:
-  adapter: mysql
-  database: kumamushi_test
-  username: root
-  password:
-  socket: /tmp/mysql.sock
-production:
-  adapter: mysql
-  database: kumamushi_production
-  username: root
-  password:
-  socket: /tmp/mysql.sock
-# PostgreSQL versions 7.4 - 8.1
-#
-# Get the C bindings:
-#   gem install postgres
-# or use the pure-Ruby bindings on Windows:
-#   gem install postgres-pr
-postgresql_example:
-  adapter: postgresql
-  database: kumamushi_development
-  username: kumamushi
-  password:
-  # Connect on a TCP socket.  Omitted by default since the client uses a
-  # domain socket that doesn't need configuration.
-  #host: remote-database
-  #port: 5432
-  # Schema search path.  The server defaults to $user,public
-  #schema_search_path: myapp,sharedapp,public
-  # Character set encoding.  The server defaults to sql_ascii.
-  #encoding: UTF8
-  # Minimum log levels, in increasing order:
-  #   debug5, debug4, debug3, debug2, debug1,
-  #   info, notice, warning, error, log, fatal, or panic
-  # The server defaults to notice.
-  #min_messages: warning
-# SQLite version 2.x
-#   gem install sqlite-ruby
-sqlite_example:
-  adapter: sqlite
-  database: db/development.sqlite2
-# SQLite version 3.x
-#   gem install sqlite3-ruby
-sqlite3_example:
-  adapter: sqlite3
-  database: db/development.sqlite3
-# In-memory SQLite 3 database.  Useful for tests.
-sqlite3_in_memory_example:
-  adapter: sqlite3
-  database: ":memory:"

data/lib/bio/shell/rails/config/environment.rb DELETED

@@ -1,53 +0,0 @@
-# Be sure to restart your web server when you modify this file.
-# Uncomment below to force Rails into production mode when
-# you don't control web/app server and can't set it the proper way
-# ENV['RAILS_ENV'] ||= 'production'
-# Bootstrap the Rails environment, frameworks, and default configuration
-require File.join(File.dirname(__FILE__), 'boot')
-Rails::Initializer.run do |config|
-  # Settings in config/environments/* take precedence those specified here
-  # Skip frameworks you're not going to use
-  # config.frameworks -= [ :action_web_service, :action_mailer ]
-  # Add additional load paths for your own custom dirs
-  # config.load_paths += %W( #{RAILS_ROOT}/extras )
-  # Force all environments to use the same logger level
-  # (by default production uses :info, the others :debug)
-  # config.log_level = :debug
-  # Use the database for sessions instead of the file system
-  # (create the session table with 'rake create_sessions_table')
-  # config.action_controller.session_store = :active_record_store
-  # Enable page/fragment caching by setting a file-based store
-  # (remember to create the caching directory and make it readable to the application)
-  # config.action_controller.fragment_cache_store = :file_store, "#{RAILS_ROOT}/cache"
-  # Activate observers that should always be running
-  # config.active_record.observers = :cacher, :garbage_collector
-  # Make Active Record use UTC-base instead of local time
-  # config.active_record.default_timezone = :utc
-  # Use Active Record's schema dumper instead of SQL when creating the test database
-  # (enables use of different database adapters for development and test environments)
-  # config.active_record.schema_format = :ruby
-  # See Rails::Configuration for more options
-end
-# Add new inflection rules using the following format
-# (all these examples are active by default):
-# Inflector.inflections do |inflect|
-#   inflect.plural /^(ox)$/i, '\1en'
-#   inflect.singular /^(ox)en/i, '\1'
-#   inflect.irregular 'person', 'people'
-#   inflect.uncountable %w( fish sheep )
-# end
-# Include your application configuration below

data/lib/bio/shell/rails/config/environments/development.rb DELETED

@@ -1,19 +0,0 @@
-# Settings specified here will take precedence over those in config/environment.rb
-# In the development environment your application's code is reloaded on
-# every request.  This slows down response time but is perfect for development
-# since you don't have to restart the webserver when you make code changes.
-config.cache_classes     = false
-# Log error messages when you accidentally call methods on nil.
-config.whiny_nils        = true
-# Enable the breakpoint server that script/breakpointer connects to
-config.breakpoint_server = true
-# Show full error reports and disable caching
-config.action_controller.consider_all_requests_local = true
-config.action_controller.perform_caching             = false
-# Don't care if the mailer can't send
-config.action_mailer.raise_delivery_errors = false

data/lib/bio/shell/rails/config/environments/production.rb DELETED

@@ -1,19 +0,0 @@
-# Settings specified here will take precedence over those in config/environment.rb
-# The production environment is meant for finished, "live" apps.
-# Code is not reloaded between requests
-config.cache_classes = true
-# Use a different logger for distributed setups
-# config.logger        = SyslogLogger.new
-# Full error reports are disabled and caching is turned on
-config.action_controller.consider_all_requests_local = false
-config.action_controller.perform_caching             = true
-# Enable serving of images, stylesheets, and javascripts from an asset server
-# config.action_controller.asset_host                  = "http://assets.example.com"
-# Disable delivery errors if you bad email addresses should just be ignored
-# config.action_mailer.raise_delivery_errors = false

data/lib/bio/shell/rails/config/environments/test.rb DELETED

@@ -1,19 +0,0 @@
-# Settings specified here will take precedence over those in config/environment.rb
-# The test environment is used exclusively to run your application's
-# test suite.  You never need to work with it otherwise.  Remember that
-# your test database is "scratch space" for the test suite and is wiped
-# and recreated between test runs.  Don't rely on the data there!
-config.cache_classes = true
-# Log error messages when you accidentally call methods on nil.
-config.whiny_nils    = true
-# Show full error reports and disable caching
-config.action_controller.consider_all_requests_local = true
-config.action_controller.perform_caching             = false
-# Tell ActionMailer not to deliver emails to the real world.
-# The :test delivery method accumulates sent emails in the
-# ActionMailer::Base.deliveries array.
-config.action_mailer.delivery_method = :test

data/lib/bio/shell/rails/config/routes.rb DELETED

@@ -1,19 +0,0 @@
-ActionController::Routing::Routes.draw do |map|
-  # Add your own custom routes here.
-  # The priority is based upon order of creation: first created -> highest priority.
-  # Here's a sample route:
-  # map.connect 'products/:id', :controller => 'catalog', :action => 'view'
-  # Keep in mind you can assign values other than :controller and :action
-  # You can have the root of your site routed by hooking up ''
-  # -- just remember to delete public/index.html.
-  # map.connect '', :controller => "welcome"
-  # Allow downloading Web Service WSDL as a file with an extension
-  # instead of a file named 'wsdl'
-  map.connect ':controller/service.wsdl', :action => 'wsdl'
-  # Install the default route as the lowest priority.
-  map.connect ':controller/:action/:id'
-end

data/lib/bio/shell/rails/doc/README_FOR_APP DELETED

	@@ -1,2 +0,0 @@
1	- Use this README file to introduce your application and point to useful places in the API for learning more.
2	- Run "rake appdoc" to generate API documentation for your models and controllers.