bio 1.0.0 → 1.1.0
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- 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
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class BiorubyGenerator < Rails::Generator::Base
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def manifest
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record do |m|
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m.directory 'app/controllers'
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m.directory 'app/helpers'
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m.directory 'app/views/bioruby'
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m.directory 'app/views/layouts'
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m.directory 'public/images'
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m.directory 'public/stylesheets'
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m.file 'bioruby_controller.rb', 'app/controllers/bioruby_controller.rb'
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+
m.file 'bioruby_helper.rb', 'app/helpers/bioruby_helper.rb'
|
12
|
+
m.file '_methods.rhtml', 'app/views/bioruby/_methods.rhtml'
|
13
|
+
m.file '_classes.rhtml', 'app/views/bioruby/_classes.rhtml'
|
14
|
+
m.file '_modules.rhtml', 'app/views/bioruby/_modules.rhtml'
|
15
|
+
m.file '_log.rhtml', 'app/views/bioruby/_log.rhtml'
|
16
|
+
m.file '_variables.rhtml', 'app/views/bioruby/_variables.rhtml'
|
17
|
+
m.file 'commands.rhtml', 'app/views/bioruby/commands.rhtml'
|
18
|
+
m.file 'history.rhtml', 'app/views/bioruby/history.rhtml'
|
19
|
+
m.file 'index.rhtml', 'app/views/bioruby/index.rhtml'
|
20
|
+
m.file 'bioruby.rhtml', 'app/views/layouts/bioruby.rhtml'
|
21
|
+
m.file 'bioruby-gem.png', 'public/images/bioruby-gem.png'
|
22
|
+
m.file 'bioruby-link.gif', 'public/images/bioruby-link.gif'
|
23
|
+
m.file 'bioruby-bg.gif', 'public/images/bioruby-bg.gif'
|
24
|
+
m.file 'bioruby-console.png', 'public/images/bioruby-console.png'
|
25
|
+
m.file 'bioruby.css', 'public/stylesheets/bioruby.css'
|
26
|
+
end
|
27
|
+
end
|
28
|
+
end
|
29
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+
|
@@ -0,0 +1,27 @@
|
|
1
|
+
<div id="log_<%= @number %>" class="log">
|
2
|
+
<div class="input">
|
3
|
+
Input: [<%= link_to_remote @number, :url => {:action => "reload_script", :number => @number} %>]
|
4
|
+
<pre class="script">
|
5
|
+
<%=h @script %>
|
6
|
+
</pre>
|
7
|
+
<div class="output">
|
8
|
+
Result:
|
9
|
+
[<%= link_to_remote "methods", :url => {:action => "list_methods", :number => @number} %>]
|
10
|
+
[<%= link_to_remote "classes", :url => {:action => "list_classes", :number => @number} %>]
|
11
|
+
[<%= link_to_remote "modules", :url => {:action => "list_modules", :number => @number} %>]
|
12
|
+
<div id="methods_<%= @number %>" class="methods"></div>
|
13
|
+
<div id="classes_<%= @number %>" class="classes"></div>
|
14
|
+
<div id="modules_<%= @number %>" class="modules"></div>
|
15
|
+
<pre class="result">
|
16
|
+
<%=h @result %>
|
17
|
+
</pre>
|
18
|
+
<% if @output %>
|
19
|
+
Output:
|
20
|
+
<pre class="output">
|
21
|
+
<%=h @output %>
|
22
|
+
</pre>
|
23
|
+
<% end %>
|
24
|
+
</div>
|
25
|
+
</div>
|
26
|
+
</div>
|
27
|
+
|
Binary file
|
Binary file
|
File without changes
|
Binary file
|
@@ -0,0 +1,369 @@
|
|
1
|
+
/* body */
|
2
|
+
|
3
|
+
body {
|
4
|
+
margin: 0;
|
5
|
+
color: #555555;
|
6
|
+
background: url("/images/bioruby-bg.gif") repeat-y center;
|
7
|
+
font-family: "trebuchet ms", verdana, arial, helvetica, sans-serif;
|
8
|
+
font-size: 12px;
|
9
|
+
}
|
10
|
+
|
11
|
+
div#content {
|
12
|
+
width: 750px;
|
13
|
+
height: auto;
|
14
|
+
margin: 0 auto 0 auto;
|
15
|
+
text-align: left;
|
16
|
+
}
|
17
|
+
|
18
|
+
/* title */
|
19
|
+
|
20
|
+
div#title {
|
21
|
+
width: 550px;
|
22
|
+
padding-right: 200px;
|
23
|
+
margin-bottom: 20px;
|
24
|
+
text-align: left;
|
25
|
+
background: url("/images/bioruby-gem.png") no-repeat left bottom;
|
26
|
+
}
|
27
|
+
|
28
|
+
div#title .titletop {
|
29
|
+
color: #736451;
|
30
|
+
font-size: 30px;
|
31
|
+
font-weight: normal;
|
32
|
+
text-align: left;
|
33
|
+
text-indent: 70px;
|
34
|
+
margin: 0;
|
35
|
+
padding: 0;
|
36
|
+
padding-top: 20px;
|
37
|
+
margin-bottom: 10px;
|
38
|
+
}
|
39
|
+
|
40
|
+
div#title .titlesub {
|
41
|
+
color: #000000;
|
42
|
+
font-size: 15px;
|
43
|
+
font-weight: normal;
|
44
|
+
text-align: left;
|
45
|
+
text-indent: 70px;
|
46
|
+
margin: 0;
|
47
|
+
padding: 0;
|
48
|
+
border-bottom: 1px solid #eeeeee;
|
49
|
+
}
|
50
|
+
|
51
|
+
/* main */
|
52
|
+
|
53
|
+
div#main {
|
54
|
+
width: 550px;
|
55
|
+
background-color: #ffffff;
|
56
|
+
padding-top: 0px;
|
57
|
+
padding-left: 10px;
|
58
|
+
}
|
59
|
+
|
60
|
+
div#notice {
|
61
|
+
background-color: #fcc;
|
62
|
+
border: 1px solid #f00;
|
63
|
+
}
|
64
|
+
|
65
|
+
div#notice p {
|
66
|
+
margin: 0;
|
67
|
+
padding: 10px;
|
68
|
+
}
|
69
|
+
|
70
|
+
pre {
|
71
|
+
color: #6e8377;
|
72
|
+
background-color: #eaedeb;
|
73
|
+
border-color: #6e8377;
|
74
|
+
border-style: dashed;
|
75
|
+
border-width: 1px;
|
76
|
+
padding: 5px;
|
77
|
+
width: 500px;
|
78
|
+
overflow: auto;
|
79
|
+
}
|
80
|
+
|
81
|
+
div.log {
|
82
|
+
width: 500px;
|
83
|
+
margin-top: 15px;
|
84
|
+
padding-top: 5px;
|
85
|
+
border-top: 1px dotted #333333;
|
86
|
+
}
|
87
|
+
|
88
|
+
div.log div.input pre.script {
|
89
|
+
background-color: #ffffeb;
|
90
|
+
border-style: solid;
|
91
|
+
}
|
92
|
+
|
93
|
+
div.log div.output div.methods {
|
94
|
+
padding: 5px;
|
95
|
+
background-color: #ffffdd;
|
96
|
+
border: 1px solid #ffcc00;
|
97
|
+
}
|
98
|
+
|
99
|
+
div.log div.output div.classes {
|
100
|
+
padding: 5px;
|
101
|
+
background-color: #ccffcc;
|
102
|
+
border: 1px solid #00ff00;
|
103
|
+
}
|
104
|
+
|
105
|
+
div.log div.output div.modules {
|
106
|
+
padding: 5px;
|
107
|
+
background-color: #ffcccc;
|
108
|
+
border: 1px solid #ff0000;
|
109
|
+
}
|
110
|
+
|
111
|
+
div.log div.output pre.result {
|
112
|
+
border-style: dashed;
|
113
|
+
}
|
114
|
+
|
115
|
+
div.log div.output pre.output {
|
116
|
+
border-style: dashed;
|
117
|
+
}
|
118
|
+
|
119
|
+
div.log hr.log {
|
120
|
+
border-style: dotted none none none;
|
121
|
+
border-top-width: 1px;
|
122
|
+
border-color: #6e8377;
|
123
|
+
width: 200px;
|
124
|
+
height: 1px;
|
125
|
+
}
|
126
|
+
|
127
|
+
/* side */
|
128
|
+
|
129
|
+
div#side {
|
130
|
+
width: 150px;
|
131
|
+
float: right;
|
132
|
+
margin-top: 20px;
|
133
|
+
text-align: left;
|
134
|
+
font-size: 12px;
|
135
|
+
color: #e44268;
|
136
|
+
}
|
137
|
+
|
138
|
+
div#side div.title {
|
139
|
+
font-weight: normal;
|
140
|
+
color: #e44268;
|
141
|
+
text-align: left;
|
142
|
+
border-width: 0px 0px 1px 0px;
|
143
|
+
border-bottom: 1px solid #e44268;
|
144
|
+
}
|
145
|
+
|
146
|
+
div#side a:link {
|
147
|
+
color: #ffffff;
|
148
|
+
text-decoration: none;
|
149
|
+
}
|
150
|
+
|
151
|
+
div#side a:visited {
|
152
|
+
color: #ffffff;
|
153
|
+
text-decoration: none;
|
154
|
+
}
|
155
|
+
|
156
|
+
div#side a:hover {
|
157
|
+
color: #cccccc;
|
158
|
+
text-decoration: underline;
|
159
|
+
}
|
160
|
+
|
161
|
+
div#side ol,ul {
|
162
|
+
margin: 10px;
|
163
|
+
padding-left: 10px;
|
164
|
+
}
|
165
|
+
|
166
|
+
div#side li {
|
167
|
+
color: #e44268;
|
168
|
+
}
|
169
|
+
|
170
|
+
div#side img {
|
171
|
+
padding: 5px;
|
172
|
+
}
|
173
|
+
|
174
|
+
/* history */
|
175
|
+
|
176
|
+
div#history {
|
177
|
+
width: 500px;
|
178
|
+
}
|
179
|
+
|
180
|
+
div#history div.histtime {
|
181
|
+
background-color: #eaedeb;
|
182
|
+
padding: 5px;
|
183
|
+
}
|
184
|
+
|
185
|
+
div#history div.histline {
|
186
|
+
background-color: #ffffeb;
|
187
|
+
padding: 5px;
|
188
|
+
font-family: monospace;
|
189
|
+
white-space: pre;
|
190
|
+
}
|
191
|
+
|
192
|
+
/* command */
|
193
|
+
|
194
|
+
div#command {
|
195
|
+
width: 500px;
|
196
|
+
}
|
197
|
+
|
198
|
+
/* image */
|
199
|
+
|
200
|
+
img {
|
201
|
+
/* centering */
|
202
|
+
display: block;
|
203
|
+
margin-left: auto;
|
204
|
+
margin-right: auto;
|
205
|
+
border: 0px;
|
206
|
+
}
|
207
|
+
|
208
|
+
/* em */
|
209
|
+
|
210
|
+
em {
|
211
|
+
color: #6e8377;
|
212
|
+
font-style: normal;
|
213
|
+
}
|
214
|
+
|
215
|
+
/* link */
|
216
|
+
|
217
|
+
a {
|
218
|
+
text-decoration: none;
|
219
|
+
}
|
220
|
+
|
221
|
+
a:link {
|
222
|
+
color: #669933;
|
223
|
+
}
|
224
|
+
|
225
|
+
a:visited {
|
226
|
+
color: #669933;
|
227
|
+
}
|
228
|
+
|
229
|
+
a:hover {
|
230
|
+
text-decoration: underline;
|
231
|
+
}
|
232
|
+
|
233
|
+
/* header */
|
234
|
+
|
235
|
+
h1 {
|
236
|
+
font-size: 180%;
|
237
|
+
color: #ffffff;
|
238
|
+
background-color: #6e8377;
|
239
|
+
line-height: 64px;
|
240
|
+
text-align: left;
|
241
|
+
padding-left: 20px;
|
242
|
+
}
|
243
|
+
|
244
|
+
h2 {
|
245
|
+
font-size: 160%;
|
246
|
+
color: #6e8377;
|
247
|
+
border-color: #b9c3be;
|
248
|
+
border-style: dashed;
|
249
|
+
border-width: 0px 0px 1px 0px;
|
250
|
+
}
|
251
|
+
|
252
|
+
h3 {
|
253
|
+
font-size: 140%;
|
254
|
+
color: #6e8377;
|
255
|
+
border-color: #b9c3be;
|
256
|
+
border-style: dotted;
|
257
|
+
border-width: 0px 0px 1px 0px;
|
258
|
+
}
|
259
|
+
|
260
|
+
h4 {
|
261
|
+
font-size: 130%;
|
262
|
+
color: #6e8377;
|
263
|
+
border-color: #b9c3be;
|
264
|
+
border-style: solid;
|
265
|
+
border-width: 0px 0px 1px 0px;
|
266
|
+
}
|
267
|
+
|
268
|
+
h5 {
|
269
|
+
font-size: 120%;
|
270
|
+
color: #6e8377;
|
271
|
+
}
|
272
|
+
|
273
|
+
h6 {
|
274
|
+
font-size: 110%;
|
275
|
+
color: #6e8377;
|
276
|
+
}
|
277
|
+
|
278
|
+
/* list */
|
279
|
+
|
280
|
+
dt {
|
281
|
+
color: #6e8377;
|
282
|
+
border-color: #b9c3be;
|
283
|
+
border-style: dashed;
|
284
|
+
border-width: 1px;
|
285
|
+
padding: 5px;
|
286
|
+
}
|
287
|
+
|
288
|
+
ul {
|
289
|
+
color: #6e8377;
|
290
|
+
}
|
291
|
+
|
292
|
+
/* table */
|
293
|
+
|
294
|
+
table {
|
295
|
+
border: 1px solid #cccccc;
|
296
|
+
border-collapse: collapse;
|
297
|
+
}
|
298
|
+
|
299
|
+
th {
|
300
|
+
vertical-align: top;
|
301
|
+
padding: 5px;
|
302
|
+
}
|
303
|
+
|
304
|
+
td {
|
305
|
+
vertical-align: top;
|
306
|
+
padding: 5px;
|
307
|
+
}
|
308
|
+
|
309
|
+
div#method_list table {
|
310
|
+
border: none;
|
311
|
+
}
|
312
|
+
|
313
|
+
|
314
|
+
/* form */
|
315
|
+
|
316
|
+
input {
|
317
|
+
background-color: #FFFFFF;
|
318
|
+
padding: 2px;
|
319
|
+
font-size: 10px;
|
320
|
+
color: #666666;
|
321
|
+
border: 1px solid #611022;
|
322
|
+
margin-bottom: 2px;
|
323
|
+
}
|
324
|
+
|
325
|
+
input[type=submit] {
|
326
|
+
background-color: #FFFFFF;
|
327
|
+
padding: 2px;
|
328
|
+
font-size: 10px;
|
329
|
+
color: #ffffff;
|
330
|
+
border: 1px solid #611022;
|
331
|
+
background-color: #E44268;
|
332
|
+
margin-bottom: 2px;
|
333
|
+
}
|
334
|
+
|
335
|
+
/* textarea */
|
336
|
+
|
337
|
+
textarea {
|
338
|
+
background: url("/images/bioruby-console.png") no-repeat center;
|
339
|
+
background-color: #eaedeb;
|
340
|
+
font-family: monospace;
|
341
|
+
font-size: 12px;
|
342
|
+
overflow: auto;
|
343
|
+
width: 500px;
|
344
|
+
padding: 5px;
|
345
|
+
}
|
346
|
+
|
347
|
+
|
348
|
+
/* blockquote */
|
349
|
+
|
350
|
+
blockquote {
|
351
|
+
color: #6e8377;
|
352
|
+
background-color: #eaedeb;
|
353
|
+
border-color: #6e8377;
|
354
|
+
border-style: dashed;
|
355
|
+
border-width: 1px;
|
356
|
+
}
|
357
|
+
|
358
|
+
/* media */
|
359
|
+
|
360
|
+
@media print {
|
361
|
+
div#main { margin-left: 0px; }
|
362
|
+
div#side { display: none; }
|
363
|
+
}
|
364
|
+
|
365
|
+
@media screen {
|
366
|
+
div#main { margin-left: 0px; }
|
367
|
+
div#side { display: block; }
|
368
|
+
}
|
369
|
+
|