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/vendor/plugins/generators/bioruby/templates/bioruby.rhtml ADDED

@@ -0,0 +1,47 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<title>BioRuby shell on Rails</title>
+<%= stylesheet_link_tag "bioruby.css" %>
+<%= javascript_include_tag :defaults %>
+</head>
+<body>
+<div id="content">
+ <div id="side">
+  <div class="title">Project</div>
+  <ul>
+   <li><%= link_to "#{File.basename(project_workdir)}", "file://#{project_workdir}" %>
+  </ul>
+  <div class="title">Functions</div>
+  <ul>
+    <li><%= link_to "Console", :action => "index" %></li>
+    <li><%= link_to "History", :action => "history" %></li>
+    <li><%= link_to "Commands", :action => "commands" %></li>
+  </ul>
+  <div class="title">Local variables</div>
+  <%= render :partial => "variables" %>
+  <br>
+  <a href="http://bioruby.org/"><img src="/images/bioruby-link.gif" border=0></a>
+ </div><!-- side -->
+ <div id="title">
+  <p class="titletop">BioRuby shell on Rails</p>
+  <p class="titlesub">Web interface for the BioRuby library</p>
+ </div><!-- title -->
+ <div id="main">
+<%= yield %>
+ </div><!-- main -->
+</div><!-- content -->
+</body>
+</html>

data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_controller.rb ADDED

@@ -0,0 +1,144 @@
+class BiorubyController < ApplicationController
+  HIDE_METHODS = Object.methods + [ "singleton_method_added" ]
+  HIDE_MODULES = [
+    Base64::Deprecated, Base64, PP::ObjectMixin, Bio::Shell,
+  ]
+  HIDE_MODULES << WEBrick if defined?(WEBrick)
+  HIDE_VARIABLES = [
+    "_", "irb", "_erbout",
+  ]
+  SECURITY_NOTICE = "For security purposes, this functionality is only available to local requests."
+  def index
+    unless local_request?
+      flash[:notice] = SECURITY_NOTICE
+    end
+  end
+  def evaluate
+    if local_request?
+      begin
+        @script = params[:script].strip
+        # write out to history
+        Bio::Shell.store_history(@script)
+        # evaluate ruby script
+        @result = eval(@script, Bio::Shell.cache[:binding])
+        # *TODO* need to handle with output of print/puts/p/pp etc. here
+        @output = nil
+      rescue
+        @result = $!
+        @output = nil
+      end
+    else
+      @result = SECURITY_NOTICE
+      @output = nil
+    end
+    @number = Bio::Shell.cache[:results].store(@script, @result, @output)
+    render :update do |page|
+      render_log(page)
+    end
+  end
+  def list_methods
+    number = params[:number].to_i
+    script, result, output = Bio::Shell.cache[:results].restore(number)
+    @class = result.class
+    @methods = (result.methods - HIDE_METHODS).sort
+    render :update do |page|
+      page.replace_html "methods_#{number}", :partial => "methods"
+      page.visual_effect :toggle_blind, "methods_#{number}", :duration => 0.5
+    end
+  end
+  def list_classes
+    number = params[:number].to_i
+    script, result, output = Bio::Shell.cache[:results].restore(number)
+    class_name = result.class
+    @class = class_name
+    @classes = []
+    loop do
+      @classes.unshift(class_name)
+      if class_name == Object
+        break
+      else
+        class_name = class_name.superclass
+      end
+    end
+    render :update do |page|
+      page.replace_html "classes_#{number}", :partial => "classes"
+      page.visual_effect :toggle_blind, "classes_#{number}", :duration => 0.5
+    end
+  end
+  def list_modules
+    number = params[:number].to_i
+    script, result, output = Bio::Shell.cache[:results].restore(number)
+    @class = result.class
+    @modules = result.class.included_modules - HIDE_MODULES
+    render :update do |page|
+      page.replace_html "modules_#{number}", :partial => "modules"
+      page.visual_effect :toggle_blind, "modules_#{number}", :duration => 0.5
+    end
+  end
+  def reload_script
+    number = params[:number].to_i
+    script, result, output = Bio::Shell.cache[:results].restore(number)
+    render :update do |page|
+      page.replace_html :script, script
+    end
+  end
+  def results
+    if Bio::Shell.cache[:results].number > 0
+      limit = params[:limit].to_i
+      max_num = Bio::Shell.cache[:results].number
+      min_num = [ max_num - limit + 1, 1 ].max
+      min_num = 1 if limit == 0
+      render :update do |page|
+        # delete all existing results in the current DOM for clean up
+        page.select(".log").each do |element|
+          #page.hide element
+          page.remove element
+        end
+        # add selected results to the current DOM
+        min_num.upto(max_num) do |@number|
+          #page.show "log_#{@number}"
+          @script, @result, @output = Bio::Shell.cache[:results].restore(@number)
+          if @script
+            render_log(page)
+          end
+        end
+      end
+    end
+  end
+  def commands
+    @bioruby_commands = Bio::Shell.private_instance_methods.sort
+  end
+  def history
+    @history = File.readlines(Bio::Shell.history_file)
+  end
+end

data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/bioruby_helper.rb ADDED

@@ -0,0 +1,47 @@
+module BiorubyHelper
+  include Bio::Shell
+  def project_workdir
+    if Bio::Shell.cache[:savedir].match(/\.bioruby$/)
+      Bio::Shell.cache[:workdir]
+    else
+      Bio::Shell.cache[:savedir]
+    end
+  end
+  def have_results
+    Bio::Shell.cache[:results].number > 0
+  end
+  def local_variables
+    eval("local_variables", Bio::Shell.cache[:binding]) -
+      BiorubyController::HIDE_VARIABLES
+  end
+  def render_log(page)
+    page.insert_html :top, :logs, :partial => "log"
+    page.replace_html "variables", :partial => "variables"
+    page.hide "methods_#{@number}"
+    page.hide "classes_#{@number}"
+    page.hide "modules_#{@number}"
+  end
+  def reference_link(class_or_module)
+    name = class_or_module.to_s
+    case name
+    when /Bio::(.+)/
+      path = $1.split('::').join('/')
+      url = "http://bioruby.org/rdoc/classes/Bio/#{path}.html"
+    when /Chem::(.+)/
+      path = $1.split('::').join('/')
+      url = "http://chemruby.org/rdoc/classes/Chem/#{path}.html"
+    else
+      path = name.split('::').join('/')
+      url = "http://www.ruby-doc.org/core/classes/#{path}.html"
+    end
+    return "<a href='#{url}'>#{name}</a>"
+  end
+end

data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/commands.rhtml ADDED

@@ -0,0 +1,8 @@
+<div id="command">
+<h2>BioRuby shell commands</h2>
+<ul>
+  <% @bioruby_commands.each do |cmd| %>
+  <li><%= cmd %></li>
+  <% end %>
+</ul>
+</div>

data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/history.rhtml ADDED

@@ -0,0 +1,10 @@
+<div id="history">
+<h2>Command history</h2>
+<% @history.each do |line| %>
+<%   if line[/^# /] %>
+<div class="histtime"><%= line %></div>
+<%   else %>
+<div class="histline"><%= line %></div>
+<%   end %>
+<% end %>
+</div>

data/lib/bio/shell/rails/vendor/plugins/generators/bioruby/templates/index.rhtml ADDED

@@ -0,0 +1,22 @@
+<div id="console">
+<%- if flash[:notice] -%>
+<div id="notice"><p><%= flash[:notice] %></p></div><br>
+<%- end -%>
+<%= form_remote_tag(:url => {:action => "evaluate"}, :position => "top") %>
+<b>BioRuby script:</b>
+<textarea id="script" name="script" rows=10 cols=80></textarea><br>
+<input type="submit" value="Evaluate">
+<input type="reset" value="Clear">
+&nbsp;&nbsp;
+Show [
+<%= link_to_remote "All",      :url => {:action => "results", :limit => 0} %> |
+<%= link_to_remote "Last 5",   :url => {:action => "results", :limit => 5} %> |
+<%= link_to_remote "Previous", :url => {:action => "results", :limit => 1} %>
+] or
+<%= link_to "Hide", :action => "index" %>
+results<br>
+<%= end_form_tag %>
+</div>
+<div id="logs">
+</div>

data/lib/bio/shell/script.rb ADDED

@@ -0,0 +1,25 @@
+#
+# = bio/shell/script.rb - script mode for the BioRuby shell
+#
+# Copyright::   Copyright (C) 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: script.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
+#
+module Bio::Shell
+  class Script
+    def initialize(script)
+      Bio::Shell.cache[:binding] = TOPLEVEL_BINDING
+      Bio::Shell.load_session
+      eval(File.read(script), TOPLEVEL_BINDING)
+      exit
+    end
+  end # Script
+end

data/lib/bio/shell/setup.rb ADDED

@@ -0,0 +1,109 @@
+#
+# = bio/shell/setup.rb - setup initial environment for the BioRuby shell
+#
+# Copyright::   Copyright (C) 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: setup.rb,v 1.8 2007/06/28 11:21:40 k Exp $
+#
+require 'getoptlong'
+class Bio::Shell::Setup
+  def initialize
+    check_ruby_version
+    # command line options
+    getoptlong
+    # setup working directory
+    savedir = setup_savedir
+    # load configuration and plugins
+    Bio::Shell.configure(savedir)
+    # set default to irb mode
+    Bio::Shell.cache[:mode] = @mode || :irb
+    case Bio::Shell.cache[:mode]
+    when :web
+      # setup rails server
+      Bio::Shell::Web.new
+    when :irb
+      # setup irb server
+      Bio::Shell::Irb.new
+    when :script
+      # run bioruby shell script
+      Bio::Shell::Script.new(@script)
+    end
+  end
+  def check_ruby_version
+    if RUBY_VERSION < "1.8.2"
+      raise "BioRuby shell runs on Ruby version >= 1.8.2"
+    end
+  end
+  # command line argument (working directory or bioruby shell script file)
+  def getoptlong
+    opts = GetoptLong.new
+    opts.set_options(
+      [ '--rails',   '-r',  GetoptLong::NO_ARGUMENT ],
+      [ '--web',     '-w',  GetoptLong::NO_ARGUMENT ],
+      [ '--console', '-c',  GetoptLong::NO_ARGUMENT ],
+      [ '--irb',     '-i',  GetoptLong::NO_ARGUMENT ]
+    )
+    opts.each_option do |opt, arg|
+      case opt
+      when /--rails/, /--web/
+        @mode = :web
+      when /--console/, /--irb/
+        @mode = :irb
+      end
+    end
+  end
+  def setup_savedir
+    arg = ARGV.shift
+    # Options after the '--' argument are not parsed by GetoptLong and
+    # are passed to irb or rails.  This hack preserve the first option
+    # when working directory of the project is not given.
+    if arg and arg[/^-/]
+      ARGV.unshift arg
+      arg = nil
+    end
+    if arg.nil?
+      # run in the current directory
+      if File.exist?(Bio::Shell::Core::HISTORY)
+        savedir = Dir.pwd
+      else
+        savedir = File.join(ENV['HOME'].to_s, ".bioruby")
+        install_savedir(savedir)
+      end
+    elsif File.file?(arg)
+      # run file as a bioruby shell script
+      savedir = File.join(File.dirname(arg), "..")
+      @script = arg
+      @mode = :script
+    else
+      # run in new or existing directory
+      if arg[/^#{File::SEPARATOR}/]
+        savedir = arg
+      else
+        savedir = File.join(Dir.pwd, arg)
+      end
+      install_savedir(savedir)
+    end
+    return savedir
+  end
+  def install_savedir(savedir)
+    FileUtils.makedirs(savedir)
+  end
+end # Setup

data/lib/bio/shell/web.rb CHANGED

@@ -4,86 +4,98 @@
 # Copyright::   Copyright (C) 2006
 #               Nobuya Tanaka <t@chemruby.org>,
 #               Toshiaki Katayama <k@bioruby.org>
-# License::     Ruby's
+# License::     The Ruby License
 #
-# $Id: web.rb,v 1.1 2006/02/27 09:22:42 k Exp $
+# $Id: web.rb,v 1.5 2007/06/26 08:38:38 k Exp $
 #
 module Bio::Shell
-  private
+  class Web
-  def rails_directory_setup
-    server = "script/server"
-    unless File.exists?(server)
-      require 'fileutils'
-      basedir = File.dirname(__FILE__)
-      print "Copying web server files ... "
-      FileUtils.cp_r("#{basedir}/rails/.", ".")
-      puts "done"
+    def initialize
+      Bio::Shell.cache[:binding] = binding
+      Bio::Shell.cache[:results] ||= Results.new
+      install_rails
+      setup_rails
+      start_rails
     end
-  end
-  def rails_server_setup
-    require 'open3'
-    $web_server = Open3.popen3(server)
+    private
-    $web_error_log = File.open("log/web-error.log", "a")
-    $web_server[2].reopen($web_error_log)
+    def setup_rails
+      puts
+      puts ">>>"
+      puts ">>>  open http://localhost:3000/bioruby"
+      puts ">>>"
+      puts
+      puts '(You can change the port number by adding "-- -p 4000" option)'
+      puts
+    end
-    while line = $web_server[1].gets
-      if line[/druby:\/\/localhost/]
-        uri = line.chomp
-        puts uri if $DEBUG
-        break
+    def install_rails
+      savedir = Bio::Shell.cache[:savedir]
+      path = File.join(savedir, "script", "generate")
+      unless File.exist?(path)
+        puts "Installing Rails application for BioRuby shell ... "
+        system("rails #{savedir}")
+        puts "done"
+      end
+      path = File.join(savedir, "app", "controllers", "bioruby_controller.rb")
+      unless File.exist?(path)
+        basedir = File.dirname(__FILE__)
+        puts "Installing Rails plugin for BioRuby shell ... "
+        FileUtils.cp_r("#{basedir}/rails/.", savedir)
+        Dir.chdir(savedir) do
+          system("./script/generate bioruby shell")
+        end
+        puts "done"
       end
     end
-    $web_access_log = File.open("log/web-access.log", "a")
-    $web_server[1].reopen($web_access_log)
-    return uri
-  end
+    def start_rails
+      begin
+        Bio::Shell.cache[:rails] = Thread.new do
+          Dir.chdir(Bio::Shell.cache[:savedir]) do
+            require './config/boot'
+            require 'commands/server'
+          end
+        end
+      end
+    end
-  def web
-    return if $web_server
+    class Results
+      attr_accessor :number, :script, :result, :output
-    require 'drb/drb'
-    # $SAFE = 1   # disable eval() and friends
+      def initialize
+        @number = 0
+        @script = []
+        @result = []
+        @output = []
+      end
-    rails_directory_setup
-    #uri = rails_server_setup
-    uri = 'druby://localhost:81064' # baioroji-
+      def store(script, result, output)
+        @number += 1
+        @script[@number] = script
+        @result[@number] = result
+        @output[@number] = output
+        return @number
+      end
-    $drb_server = DRbObject.new_with_uri(uri)
-    $drb_server.puts_remote("Connected")
+      def restore(number)
+        return @script[number], @result[number], @output[number]
+      end
+    end
-    puts "Connected to server #{uri}"
-    puts "Open http://localhost:3000/shell/"
+  end
-    io = IRB.conf[:MAIN_CONTEXT].io
+  private
-    io.class.class_eval do
-      alias_method :shell_original_gets, :gets
-    end
+  # *TODO* stop irb and start rails?
+  #def web
+  #end
-    def io.gets
-      bind = IRB.conf[:MAIN_CONTEXT].workspace.binding
-      vars = eval("local_variables", bind)
-      vars.each do |var|
-        next if var == "_"
-        if val = eval("#{var}", bind)
-          $drb_server[var] = val
-        else
-          $drb_server.delete(var)
-        end
-      end
-      line = shell_original_gets
-      line
-    end
-  end
 end