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

bio 1.0.0 → 1.1.0

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 (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.