Download varDB ruby Free Java Code

.gitignore/*from   w ww  . j av a2 s  . com*/
.project
Gemfile
Gemfile.lock
README
Rakefile
app/controllers/admin_controller.rb
app/controllers/ajax_controller.rb
app/controllers/application_controller.rb
app/controllers/direct_controller.rb
app/controllers/explorer_controller.rb
app/controllers/pages_controller.rb
app/controllers/sequences_controller.rb
app/controllers/svg_controller.rb
app/controllers/tags_controller.rb
app/helpers/admin_helper.rb
app/helpers/ajax_helper.rb
app/helpers/application_helper.rb
app/helpers/explorer_helper.rb
app/helpers/pages_helper.rb
app/helpers/sequences_helper.rb
app/helpers/svg_helper.rb
app/helpers/tags_helper.rb
app/models/animal.rb
app/models/bacteria.rb
app/models/chain.rb
app/models/clan.rb
app/models/comment.rb
app/models/country.rb
app/models/disease.rb
app/models/drug.rb
app/models/family.rb
app/models/feedback.rb
app/models/filter.rb
app/models/fungus.rb
app/models/ortholog.rb
app/models/pathogen.rb
app/models/pfam.rb
app/models/protist.rb
app/models/query.treetop
app/models/query_helper.rb
app/models/ref.rb
app/models/resource.rb
app/models/sequence.rb
app/models/source.rb
app/models/structure.rb
app/models/subgroup.rb
app/models/tag.rb
app/models/taxon.rb
app/models/term.rb
app/models/user.rb
app/models/virus.rb
app/setup/setup.rb
app/views/admin/index.html.erb
app/views/ajax/.tmp_announcements.html.erb.4437~
app/views/ajax/.tmp_homepage.html.erb.97476~
app/views/ajax/announcements.html.erb
app/views/ajax/comments.html.erb
app/views/analysis/blastclust.html.erb
app/views/analysis/blastclustform.html.erb
app/views/analysis/codonalign.html.erb
app/views/analysis/codonusage.html.erb
app/views/analysis/codonusageform.html.erb
app/views/analysis/gblocks.html.erb
app/views/analysis/gblocksform.html.erb
app/views/analysis/hvalign.html.erb
app/views/analysis/hvcodons.html.erb
app/views/analysis/hvcodonsform.html.erb
app/views/analysis/netblast.html.erb
app/views/analysis/netblastform.html.erb
app/views/analysis/pal2nal.html.erb
app/views/analysis/pssm.html.erb
app/views/analysis/pssmform.html.erb
app/views/analysis/revtrans.html.erb
app/views/analysis/variability.html.erb
app/views/analysis/variabilityform.html.erb
app/views/blast/blast.html.erb
app/views/blast/hits.html.erb
app/views/blast/phiblast.html.erb
app/views/blast/psiblast.html.erb
app/views/devise/confirmations/new.html.erb
app/views/devise/mailer/confirmation_instructions.html.erb
app/views/devise/mailer/reset_password_instructions.html.erb
app/views/devise/mailer/unlock_instructions.html.erb
app/views/devise/passwords/edit.html.erb
app/views/devise/passwords/new.html.erb
app/views/devise/registrations/edit.html.erb
app/views/devise/registrations/new.html.erb
app/views/devise/sessions/new.html.erb
app/views/devise/shared/_links.erb
app/views/devise/unlocks/new.html.erb
app/views/explorer/.tmp_explorer.html.erb.79555~
app/views/explorer/explorer.html.erb
app/views/layouts/.tmp__analytics.html.erb.37976~
app/views/layouts/.tmp__comments.html.erb.86476~
app/views/layouts/.tmp__footer.html.erb.1507~
app/views/layouts/.tmp__header.html.erb.39942~
app/views/layouts/.tmp__map.html.erb.13935~
app/views/layouts/.tmp__navigation.html.erb.31159~
app/views/layouts/.tmp__navigation.html.erb.40278~
app/views/layouts/.tmp__navigation.html.erb.7833~
app/views/layouts/.tmp__scripts.html.erb.17840~
app/views/layouts/.tmp__scripts.html.erb.32466~
app/views/layouts/.tmp__scripts.html.erb.49827~
app/views/layouts/.tmp__scripts.html.erb.89456~
app/views/layouts/.tmp_application.html.erb.2693~
app/views/layouts/.tmp_application.html.erb.29542~
app/views/layouts/.tmp_application.html.erb.47222~
app/views/layouts/.tmp_application.html.erb.65651~
app/views/layouts/.tmp_application.html.erb.86680~
app/views/layouts/.tmp_contact.html.erb.82291~
app/views/layouts/.tmp_viewport.html.erb.85263~
app/views/layouts/_analytics.html.erb
app/views/layouts/_breadcrumbs.html.erb
app/views/layouts/_comments.html.erb
app/views/layouts/_footer.html.erb
app/views/layouts/_header.html.erb
app/views/layouts/_map.html.erb
app/views/layouts/_navigation.html.erb
app/views/layouts/_scripts.html.erb
app/views/layouts/application.html.erb
app/views/layouts/viewport.html.erb
app/views/pages/.tmp_contact.html.erb.14553~
app/views/pages/.tmp_contact.html.erb.94309~
app/views/pages/.tmp_families.html.erb.69571~
app/views/pages/.tmp_homepage.html.erb.25830~
app/views/pages/.tmp_homepage.html.erb.4780~
app/views/pages/.tmp_homepage.html.erb.54247~
app/views/pages/.tmp_homepage.html.erb.76869~
app/views/pages/.tmp_homepage.html.erb.77106~
app/views/pages/.tmp_homepage.html.erb.9870~
app/views/pages/antigenicvariation.html.erb
app/views/pages/database.html.erb
app/views/pages/disease.html.erb
app/views/pages/diseases.html.erb
app/views/pages/families.html.erb
app/views/pages/family.html.erb
app/views/pages/feedback.html.erb
app/views/pages/homepage.html.erb
app/views/pages/images.html.erb
app/views/pages/links.html.erb
app/views/pages/map.html.erb
app/views/pages/ortholog.html.erb
app/views/pages/pathogen.html.erb
app/views/pages/pathogens.html.erb
app/views/pages/pfam.html.erb
app/views/pages/pfams.html.erb
app/views/pages/references.html.erb
app/views/pages/sequence.html.erb
app/views/pages/structure.html.erb
app/views/pages/structures.html.erb
app/views/pages/terms.html.erb
app/views/pages/tutorials.html.erb
app/views/svg/.tmp_sequence.html.erb.85087~
app/views/svg/.tmp_sequence.html.erb.9496~
app/views/svg/sequence.html.erb
app/views/svg/sequence.svg.erb
app/views/users/login.html.erb
app/views/users/newuser.html.erb
config.ru
config/application.rb
config/boot.rb
config/database.yml
config/environment.rb
config/environments/development.rb
config/environments/production.rb
config/environments/test.rb
config/initializers/backtrace_silencers.rb
config/initializers/devise.rb
config/initializers/inflections.rb
config/initializers/mime_types.rb
config/initializers/mongo.rb
config/initializers/secret_token.rb
config/initializers/session_store.rb
config/locales/devise.en.yml
config/locales/en.yml
config/routes.rb
config/vardb.yml
db/migrate/20100927144637_devise_create_users.rb
db/seeds.rb
dev/.tmp_svg.html.9727~
dev/blast.rb
dev/browser.rb
dev/email.rb
dev/erb.rb
dev/excel.rb
dev/excel2.rb
dev/gblocks.aln
dev/gblocks.rb
dev/jexcelapi.rb
dev/pdb.rb
dev/pfam.rb
dev/pubmed.rb
dev/snplist.txt
dev/snps.txt
dev/svg.html
dev/system.rb
dev/taxa.rb
dev/treetop/arithmetic.treetop
dev/treetop/filter.rb
dev/treetop/paren_language.treetop
dev/treetop/query.treetop
dev/treetop/query2.treetop
dev/treetop/query3.treetop
dev/treetop/query4.treetop
dev/treetop/query5.treetop
dev/treetop/query6.treetop
dev/treetop/query7.treetop
dev/treetop/query8.treetop
dev/treetop/query9.treetop
dev/treetop/testquery.rb
dev/treetop/testtreetop.rb
doc/README_FOR_APP
doc/commands.txt
lib/sequence_loader.rb
lib/tasks/.gitkeep
public/404.html
public/422.html
public/500.html
public/favicon.ico
public/images/banner.png
public/images/bullet.gif
public/images/data-mining-small.jpg
public/images/data-mining.jpg
public/images/extjs/Thumbs.db
public/images/extjs/charts.swf
public/images/extjs/column_tree_icon.png
public/images/extjs/extanim32.gif
public/images/extjs/extjs-color-trigger.gif
public/images/extjs/extjs-color-trigger.png
public/images/extjs/extjs-header-bg.gif
public/images/extjs/extjs-information.png
public/images/extjs/extjs-lb-close-over.gif
public/images/extjs/extjs-lb-close.gif
public/images/extjs/extjs-lb-load.gif
public/images/extjs/extjs-lb-next.png
public/images/extjs/extjs-lb-prev.png
public/images/extjs/extjs-livegrid-loading.gif
public/images/extjs/extjs-lovcombo-checked.gif
public/images/extjs/extjs-lovcombo-unchecked.gif
public/images/extjs/extjs-xcheckboxgroup-invert-selection.png
public/images/extjs/extjs-xcheckboxgroup-select-all.png
public/images/extjs/extjs-xcheckboxgroup-select-none.png
public/images/extjs/itemselector/bottom2.gif
public/images/extjs/itemselector/down2.gif
public/images/extjs/itemselector/left2.gif
public/images/extjs/itemselector/right2.gif
public/images/extjs/itemselector/top2.gif
public/images/extjs/itemselector/up2.gif
public/images/extjs/s.gif
public/images/favicon.ico
public/images/figure-1.png
public/images/figure-2.png
public/images/figure-3.png
public/images/figure-4.png
public/images/figure-5.png
public/images/figure-6.png
public/images/figure-7.png
public/images/icons/Thumbs.db
public/images/icons/basket.png
public/images/icons/basket_put.png
public/images/icons/basket_remove.png
public/images/icons/chart_organisation.png
public/images/icons/email.png
public/images/icons/extjs-logindialog-locked.png
public/images/icons/feed.png
public/images/icons/fileupload.png
public/images/icons/page_white_acrobat.png
public/images/icons/page_white_excel.png
public/images/icons/silk-add.png
public/images/icons/silk-arrow_switch.png
public/images/icons/silk-cross.png
public/images/icons/silk-information.png
public/images/icons/silk-printer.png
public/images/icons/user_comment.png
public/images/loading.gif
public/images/malaria.jpg
public/images/openid.png
public/images/plasmodium_falciparum.jpg
public/images/small_logo.png
public/images/vardb-banner-home.png
public/javascripts/extensions/extjs-addcolumns.js
public/javascripts/extensions/extjs-bufferview.js
public/javascripts/extensions/extjs-color-field.js
public/javascripts/extensions/extjs-comboboxadd.js
public/javascripts/extensions/extjs-fileuploadfield.js
public/javascripts/extensions/extjs-formqtip.js
public/javascripts/extensions/extjs-formtooltips.js
public/javascripts/extensions/extjs-gridctxmenuplugin.js
public/javascripts/extensions/extjs-gridprinter.js
public/javascripts/extensions/extjs-itemselector.js
public/javascripts/extensions/extjs-lightbox.js
public/javascripts/extensions/extjs-lovcombo.js
public/javascripts/extensions/extjs-menu.js
public/javascripts/extensions/extjs-messagewindow.js
public/javascripts/extensions/extjs-multiselect.js
public/javascripts/extensions/extjs-pagesize.js
public/javascripts/extensions/extjs-progressbarpager.js
public/javascripts/extensions/extjs-propertygrid2.js
public/javascripts/extensions/extjs-remotevalidator.js
public/javascripts/extensions/extjs-rowexpander.js
public/javascripts/extensions/extjs-safari-fix.js
public/javascripts/extensions/extjs-select.js
public/javascripts/extensions/extjs-slidingpager.js
public/javascripts/extensions/extjs-textbox.js
public/javascripts/extensions/extjs-xcheckboxgroup.js
public/javascripts/extensions/files.txt
public/javascripts/extensions/g.bar-min.js
public/javascripts/extensions/g.dot-min.js
public/javascripts/extensions/g.line-min.js
public/javascripts/extensions/g.pie-min.js
public/javascripts/extensions/livegrid-all-debug.js
public/javascripts/extensions/raphael.js
public/javascripts/extensions/showdown.js
public/javascripts/kyoto/extjs/grid.js
public/javascripts/kyoto/extjs/selectlist.js
public/javascripts/kyoto/namespace.js
public/javascripts/kyoto/tags/applytagdialog.js
public/javascripts/kyoto/tags/newtagdialog.js
public/javascripts/kyoto/tags/tagcloud.js
public/javascripts/kyoto/tags/tags.js
public/javascripts/kyoto/users/login.js
public/javascripts/kyoto/utils.js
public/javascripts/kyoto/vardb/analysis/alignmentviewerform.js
public/javascripts/kyoto/vardb/analysis/blastclustform.js
public/javascripts/kyoto/vardb/analysis/codonalignform.js
public/javascripts/kyoto/vardb/analysis/codonusageform.js
public/javascripts/kyoto/vardb/analysis/codonusagetable.js
public/javascripts/kyoto/vardb/analysis/gblocksform.js
public/javascripts/kyoto/vardb/analysis/hvalignform.js
public/javascripts/kyoto/vardb/analysis/jalviewform.js
public/javascripts/kyoto/vardb/analysis/mafftform.js
public/javascripts/kyoto/vardb/analysis/oligorepform.js
public/javascripts/kyoto/vardb/analysis/selectonform.js
public/javascripts/kyoto/vardb/analysis/selectongrid.js
public/javascripts/kyoto/vardb/analysis/variabilityform.js
public/javascripts/kyoto/vardb/analysis/variabilitygrid.js
public/javascripts/kyoto/vardb/blast/blastform.js
public/javascripts/kyoto/vardb/blast/blastreader.js
public/javascripts/kyoto/vardb/blast/chainhitsgrid.js
public/javascripts/kyoto/vardb/blast/expander.js
public/javascripts/kyoto/vardb/blast/form.js
public/javascripts/kyoto/vardb/blast/grid.js
public/javascripts/kyoto/vardb/blast/netblastform.js
public/javascripts/kyoto/vardb/blast/netblastgrid.js
public/javascripts/kyoto/vardb/blast/phiblastform.js
public/javascripts/kyoto/vardb/blast/psiblastform.js
public/javascripts/kyoto/vardb/blast/results.js
public/javascripts/kyoto/vardb/explorer/accordian.js
public/javascripts/kyoto/vardb/explorer/aligndialog.js
public/javascripts/kyoto/vardb/explorer/alignmentgrid.js
public/javascripts/kyoto/vardb/explorer/alignmenttab.js
public/javascripts/kyoto/vardb/explorer/batchlookupdialog.js
public/javascripts/kyoto/vardb/explorer/blastclustdialog.js
public/javascripts/kyoto/vardb/explorer/bundlegrid.js
public/javascripts/kyoto/vardb/explorer/bundletab.js
public/javascripts/kyoto/vardb/explorer/cartgrid.js
public/javascripts/kyoto/vardb/explorer/carttab.js
public/javascripts/kyoto/vardb/explorer/copydialog.js
public/javascripts/kyoto/vardb/explorer/explorer.js
public/javascripts/kyoto/vardb/explorer/gagdialog.js
public/javascripts/kyoto/vardb/explorer/groupdialog.js
public/javascripts/kyoto/vardb/explorer/joindialog.js
public/javascripts/kyoto/vardb/explorer/joingrid.js
public/javascripts/kyoto/vardb/explorer/regexdialog.js
public/javascripts/kyoto/vardb/explorer/sequencegrid.js
public/javascripts/kyoto/vardb/explorer/taskgrid.js
public/javascripts/kyoto/vardb/explorer/toolbar.js
public/javascripts/kyoto/vardb/explorer/weblogo.js
public/javascripts/kyoto/vardb/popups/termpopup.js
public/javascripts/kyoto/vardb/svg/OLD1sequence.js
public/javascripts/kyoto/vardb/svg/OLD2sequence.js
public/javascripts/kyoto/vardb/svg/OLD3sequence.js
public/javascripts/kyoto/vardb/svg/OLD4sequence.js
public/javascripts/kyoto/vardb/svg/sequence.js
public/javascripts/kyoto/vardb/vardb.js
public/javascripts/kyoto/vardb/widgets/announcements.js
public/javascripts/kyoto/vardb/widgets/browsebycategory.js
public/javascripts/kyoto/vardb/widgets/comment.js
public/javascripts/kyoto/vardb/widgets/comments.js
public/javascripts/kyoto/vardb/widgets/feedback.js
public/javascripts/kyoto/vardb/widgets/mainmenu.js
public/javascripts/kyoto/vardb/widgets/navigation.js
public/javascripts/kyoto/vardb/widgets/sortdialog.js
public/javascripts/kyoto/widgets/selectcolumnsdialog.js
public/javascripts/kyoto/widgets/sortdialog.js
public/robots.txt
public/stylesheets/.gitkeep
public/stylesheets/extensions.css
public/stylesheets/global.css
public/stylesheets/sass/_consensus.scss
public/stylesheets/sass/_explorer.scss
public/stylesheets/sass/_extjs-color-field.scss
public/stylesheets/sass/_extjs-colview.scss
public/stylesheets/sass/_extjs-extensions.scss
public/stylesheets/sass/_extjs-fileuploadfield.scss
public/stylesheets/sass/_extjs-lightbox.scss
public/stylesheets/sass/_extjs-livegrid.scss
public/stylesheets/sass/_extjs-lockinggridview.scss
public/stylesheets/sass/_extjs-lovcombo.scss
public/stylesheets/sass/_general.scss
public/stylesheets/sass/_icons.scss
public/stylesheets/sass/_layout.scss
public/stylesheets/sass/_navigation.scss
public/stylesheets/sass/_table.scss
public/stylesheets/sass/_text.scss
public/stylesheets/sass/_yui-grids.scss
public/stylesheets/sass/extensions.scss
public/stylesheets/sass/global.scss
rails.README
script/rails
test/functional/ajax_controller_test.rb
test/functional/explorer_controller_test.rb
test/functional/pages_controller_test.rb
test/functional/sequences_controller_test.rb
test/functional/svg_controller_controller_test.rb
test/functional/tags_controller_test.rb
test/functional/users_controller_test.rb
test/performance/browsing_test.rb
test/test_helper.rb
test/unit/helpers/ajax_helper_test.rb
test/unit/helpers/explorer_helper_test.rb
test/unit/helpers/pages_helper_test.rb
test/unit/helpers/sequences_helper_test.rb
test/unit/helpers/svg_controller_helper_test.rb
test/unit/helpers/tags_helper_test.rb
test/unit/helpers/users_helper_test.rb
vendor/plugins/.gitkeep