quorum 0.1.0
Sign up to get free protection for your applications and to get access to all the features.
- data/.gitignore +10 -0
- data/.rspec +1 -0
- data/Gemfile +15 -0
- data/Gemfile.lock +170 -0
- data/MIT-LICENSE +20 -0
- data/README.rdoc +318 -0
- data/Rakefile +31 -0
- data/app/assets/images/quorum/.gitkeep +0 -0
- data/app/assets/images/quorum/bg.png +0 -0
- data/app/assets/images/quorum/knight_rider.gif +0 -0
- data/app/assets/images/quorum/ui-bg_flat_0_aaaaaa_40x100.png +0 -0
- data/app/assets/images/quorum/ui-bg_flat_75_ffffff_40x100.png +0 -0
- data/app/assets/images/quorum/ui-bg_glass_55_fbf9ee_1x400.png +0 -0
- data/app/assets/images/quorum/ui-bg_glass_65_ffffff_1x400.png +0 -0
- data/app/assets/images/quorum/ui-bg_glass_75_dadada_1x400.png +0 -0
- data/app/assets/images/quorum/ui-bg_glass_75_e6e6e6_1x400.png +0 -0
- data/app/assets/images/quorum/ui-bg_highlight-soft_75_cccccc_1x100.png +0 -0
- data/app/assets/images/quorum/ui-bg_inset-soft_95_fef1ec_1x100.png +0 -0
- data/app/assets/images/quorum/ui-icons_222222_256x240.png +0 -0
- data/app/assets/images/quorum/ui-icons_2e83ff_256x240.png +0 -0
- data/app/assets/images/quorum/ui-icons_454545_256x240.png +0 -0
- data/app/assets/images/quorum/ui-icons_888888_256x240.png +0 -0
- data/app/assets/images/quorum/ui-icons_cd0a0a_256x240.png +0 -0
- data/app/assets/javascripts/quorum/application.js +13 -0
- data/app/assets/javascripts/quorum/jobs.js +386 -0
- data/app/assets/stylesheets/quorum/application.css +224 -0
- data/app/assets/stylesheets/quorum/jobs.css +72 -0
- data/app/assets/stylesheets/quorum/jquery-ui-1.8.16.custom.css +568 -0
- data/app/assets/stylesheets/quorum/tipsy.css +25 -0
- data/app/controllers/quorum/application_controller.rb +5 -0
- data/app/controllers/quorum/jobs_controller.rb +102 -0
- data/app/helpers/quorum/application_helper.rb +4 -0
- data/app/models/quorum/blastn_job.rb +111 -0
- data/app/models/quorum/blastn_job_report.rb +7 -0
- data/app/models/quorum/blastp_job.rb +111 -0
- data/app/models/quorum/blastp_job_report.rb +7 -0
- data/app/models/quorum/blastx_job.rb +111 -0
- data/app/models/quorum/blastx_job_report.rb +7 -0
- data/app/models/quorum/job.rb +164 -0
- data/app/models/quorum/tblastn_job.rb +111 -0
- data/app/models/quorum/tblastn_job_report.rb +7 -0
- data/app/views/layouts/quorum/application.html.erb +15 -0
- data/app/views/quorum/jobs/_blastn_form.html.erb +71 -0
- data/app/views/quorum/jobs/_blastp_form.html.erb +71 -0
- data/app/views/quorum/jobs/_blastx_form.html.erb +71 -0
- data/app/views/quorum/jobs/_tblastn_form.html.erb +71 -0
- data/app/views/quorum/jobs/new.html.erb +45 -0
- data/app/views/quorum/jobs/show.html.erb +183 -0
- data/app/views/shared/_error_messages.html.erb +10 -0
- data/config/locales/en.yml +8 -0
- data/config/routes.rb +9 -0
- data/db/migrate/20111031204518_create_jobs.rb +12 -0
- data/db/migrate/20111031204701_create_blastn_jobs.rb +19 -0
- data/db/migrate/20111031204719_create_blastx_jobs.rb +19 -0
- data/db/migrate/20111031204733_create_blastp_jobs.rb +19 -0
- data/db/migrate/20111031204754_create_tblastn_jobs.rb +19 -0
- data/db/migrate/20111031204846_create_blastn_job_reports.rb +34 -0
- data/db/migrate/20111031204903_create_blastx_job_reports.rb +34 -0
- data/db/migrate/20111031204922_create_blastp_job_reports.rb +34 -0
- data/db/migrate/20111031204941_create_tblastn_job_reports.rb +34 -0
- data/lib/generators/quorum/install_generator.rb +68 -0
- data/lib/generators/quorum/styles_generator.rb +18 -0
- data/lib/generators/quorum/views_generator.rb +18 -0
- data/lib/generators/templates/README +25 -0
- data/lib/generators/templates/blast.rb +412 -0
- data/lib/generators/templates/logger.rb +43 -0
- data/lib/generators/templates/quorum_initializer.rb +36 -0
- data/lib/generators/templates/quorum_settings.yml +157 -0
- data/lib/generators/templates/search +141 -0
- data/lib/generators/templates/trollop.rb +781 -0
- data/lib/quorum/engine.rb +5 -0
- data/lib/quorum/helpers.rb +17 -0
- data/lib/quorum/sequence.rb +89 -0
- data/lib/quorum/version.rb +3 -0
- data/lib/quorum.rb +89 -0
- data/lib/tasks/blastdb/README +17 -0
- data/lib/tasks/blastdb/build_blast_db.rb +222 -0
- data/lib/tasks/quorum_resque.rake +3 -0
- data/lib/tasks/quorum_tasks.rake +50 -0
- data/lib/workers/quorum.rb +45 -0
- data/quorum.gemspec +29 -0
- data/script/rails +6 -0
- data/spec/data/nucl_prot_seqs.txt +36 -0
- data/spec/data/nucl_seqs.txt +32 -0
- data/spec/data/prot_seqs.txt +4 -0
- data/spec/data/seqs.docx +0 -0
- data/spec/data/seqs_not_fa.txt +16 -0
- data/spec/data/tmp/test.tgz +0 -0
- data/spec/dummy/Rakefile +7 -0
- data/spec/dummy/app/assets/javascripts/application.js +9 -0
- data/spec/dummy/app/assets/stylesheets/application.css +7 -0
- data/spec/dummy/app/controllers/application_controller.rb +3 -0
- data/spec/dummy/app/helpers/application_helper.rb +2 -0
- data/spec/dummy/app/mailers/.gitkeep +0 -0
- data/spec/dummy/app/models/.gitkeep +0 -0
- data/spec/dummy/app/models/blast.rb +2 -0
- data/spec/dummy/app/views/layouts/application.html.erb +14 -0
- data/spec/dummy/config/application.rb +46 -0
- data/spec/dummy/config/boot.rb +10 -0
- data/spec/dummy/config/environment.rb +20 -0
- data/spec/dummy/config/environments/development.rb +30 -0
- data/spec/dummy/config/environments/production.rb +60 -0
- data/spec/dummy/config/environments/test.rb +42 -0
- data/spec/dummy/config/initializers/backtrace_silencers.rb +7 -0
- data/spec/dummy/config/initializers/inflections.rb +10 -0
- data/spec/dummy/config/initializers/mime_types.rb +5 -0
- data/spec/dummy/config/initializers/quorum_initializer.rb +36 -0
- data/spec/dummy/config/initializers/resque.rb +1 -0
- data/spec/dummy/config/initializers/secret_token.rb +7 -0
- data/spec/dummy/config/initializers/session_store.rb +8 -0
- data/spec/dummy/config/initializers/wrap_parameters.rb +14 -0
- data/spec/dummy/config/locales/en.yml +5 -0
- data/spec/dummy/config/locales/quorum.en.yml +8 -0
- data/spec/dummy/config/quorum_settings.yml +145 -0
- data/spec/dummy/config/routes.rb +9 -0
- data/spec/dummy/config.ru +4 -0
- data/spec/dummy/db/schema.rb +214 -0
- data/spec/dummy/lib/assets/.gitkeep +0 -0
- data/spec/dummy/log/.gitkeep +0 -0
- data/spec/dummy/public/404.html +26 -0
- data/spec/dummy/public/422.html +26 -0
- data/spec/dummy/public/500.html +26 -0
- data/spec/dummy/public/favicon.ico +0 -0
- data/spec/dummy/quorum/bin/search +141 -0
- data/spec/dummy/quorum/blastdb/test/contigs.fa +2 -0
- data/spec/dummy/quorum/blastdb/test/peptides.fa +2 -0
- data/spec/dummy/quorum/blastdb/test.nhd +1 -0
- data/spec/dummy/quorum/blastdb/test.nhi +0 -0
- data/spec/dummy/quorum/blastdb/test.nhr +0 -0
- data/spec/dummy/quorum/blastdb/test.nin +0 -0
- data/spec/dummy/quorum/blastdb/test.nog +0 -0
- data/spec/dummy/quorum/blastdb/test.nsd +1 -0
- data/spec/dummy/quorum/blastdb/test.nsi +0 -0
- data/spec/dummy/quorum/blastdb/test.nsq +0 -0
- data/spec/dummy/quorum/blastdb/test.phd +1 -0
- data/spec/dummy/quorum/blastdb/test.phi +0 -0
- data/spec/dummy/quorum/blastdb/test.phr +0 -0
- data/spec/dummy/quorum/blastdb/test.pin +0 -0
- data/spec/dummy/quorum/blastdb/test.pog +0 -0
- data/spec/dummy/quorum/blastdb/test.psd +1 -0
- data/spec/dummy/quorum/blastdb/test.psi +0 -0
- data/spec/dummy/quorum/blastdb/test.psq +0 -0
- data/spec/dummy/quorum/lib/logger.rb +43 -0
- data/spec/dummy/quorum/lib/search_tools/blast.rb +412 -0
- data/spec/dummy/quorum/lib/trollop.rb +781 -0
- data/spec/dummy/script/rails +6 -0
- data/spec/models/blastn_job_report_spec.rb +13 -0
- data/spec/models/blastn_job_spec.rb +103 -0
- data/spec/models/blastp_job_report_spec.rb +13 -0
- data/spec/models/blastp_job_spec.rb +103 -0
- data/spec/models/blastx_job_report_spec.rb +13 -0
- data/spec/models/blastx_job_spec.rb +103 -0
- data/spec/models/job_spec.rb +40 -0
- data/spec/models/tblastn_job_report_spec.rb +13 -0
- data/spec/models/tblastn_job_spec.rb +103 -0
- data/spec/quorum/quorum_sequence_spec.rb +64 -0
- data/spec/quorum_installed_spec.rb +64 -0
- data/spec/requests/jobs_spec.rb +138 -0
- data/spec/spec_helper.rb +45 -0
- data/spec/tasks/blastdb_rake_spec.rb +119 -0
- data/spec/templates/blast_spec.rb +8 -0
- data/spec/templates/logger_spec.rb +35 -0
- data/vendor/assets/javascripts/jquery.tipsy.js +241 -0
- data/vendor/assets/javascripts/underscore-min.js +30 -0
- metadata +325 -0
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module Quorum
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class TblastnJob < ActiveRecord::Base
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before_save :set_optional_params, :set_blast_dbs
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belongs_to :job
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has_many :tblastn_job_reports,
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:dependent => :destroy,
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:foreign_key => :tblastn_job_id,
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:primary_key => :job_id
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attr_accessible :expectation, :max_score, :min_bit_score,
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:filter, :gapped_alignments, :gap_opening_penalty,
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:gap_extension_penalty, :gap_opening_extension, :queue,
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:blast_dbs
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validates_format_of :expectation,
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:with => /^[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/,
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:message => " - Valid formats (12, 32.05, 43e-123)",
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:allow_blank => true
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validates_numericality_of :max_score,
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:only_integer => true,
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:allow_blank => true
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validates_numericality_of :min_bit_score,
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:only_integer => true,
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:allow_blank => true
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validates_numericality_of :gap_opening_penalty,
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:only_integer => true,
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:allow_blank => true
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validates_numericality_of :gap_extension_penalty,
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:only_integer => true,
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:allow_blank => true
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validates_presence_of :blast_dbs, :if => :queue
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validate :gap_opening_extension_exists
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#
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# Gapped alignment helper.
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#
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def gapped_alignment?
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self.gapped_alignments
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end
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#
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# Valid gap opening and extension values.
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#
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def gap_opening_extension_values
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[
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['--Select--', ''],
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['32767, 32767', '32767,32767'],
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['11, 2', '11,2'],
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['10, 2', '10,2'],
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['9, 2', '9,2'],
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['8, 2', '8,2'],
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['7, 2', '7,2'],
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['6, 2', '6,2'],
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['13, 1', '13,1'],
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['12, 1', '12,1'],
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['11, 1', '11,1'],
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['10, 1', '10,1'],
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['9, 1', '9,1']
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]
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end
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#
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# Virtual attribute getter.
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#
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def gap_opening_extension
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[gap_opening_penalty, gap_extension_penalty].join(',')
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end
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#
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# Virtual attribute setter.
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#
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def gap_opening_extension=(value)
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v = value.split(',')
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self.gap_opening_penalty = v.first
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self.gap_extension_penalty = v.last
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end
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private
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def set_blast_dbs
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if self.blast_dbs.present?
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self.blast_dbs = self.blast_dbs.join(';')
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end
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end
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def set_optional_params
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self.expectation = "5e-20" if self.expectation.blank?
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self.max_score ||= 25
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self.min_bit_score ||= 0
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unless self.gapped_alignments
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self.gap_opening_penalty = 0
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self.gap_extension_penalty = 0
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end
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end
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#
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# Add error if gapped_alignment? without gap_opening_extension.
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#
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def gap_opening_extension_exists
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if gap_opening_extension.split(',').blank? && gapped_alignment?
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errors.add(
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:gap_opening_extension,
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" - Please select a value."
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)
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end
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end
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end
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end
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<!DOCTYPE html>
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<html>
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<head>
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<title>Quorum</title>
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<%= stylesheet_link_tag "quorum/application" %>
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<%= javascript_include_tag "quorum/application" %>
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<%= csrf_meta_tags %>
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</head>
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<body>
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<% flash.each do |name, msg| %>
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<%= content_tag :div, msg, :id => name %>
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<% end %>
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<%= yield %>
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</body>
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</html>
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<%= f.fields_for :blastn_job do |n| %>
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<p>
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<strong>blastn</strong>
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<%= n.check_box :queue %>
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</p>
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<div id="blastn" class="toggle">
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<table class="options">
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<tr>
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<td>
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<label>Database(s)</label>
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</td>
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<td>
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<%= n.select :blast_dbs, @blast_dbs[:blastn], {}, { :multiple => true } %>
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</td>
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<td>
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<%= n.label :filter, "DUST" %>
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</td>
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<td>
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<%= n.check_box :filter %>
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</td>
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</tr>
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<tr>
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<td>
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<%= n.label :expectation %>
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</td>
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<td>
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<%= n.text_field :expectation, :size => 15, :title => "5e-20",
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:class => "auto-hint" %>
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</td>
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<td>
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<%= n.label :min_bit_score %>
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</td>
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<td>
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<%= n.text_field :min_bit_score, :size => 15, :title => "0",
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:class => "auto-hint" %>
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</td>
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</tr>
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<tr>
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<td>
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<%= n.label :max_score %>
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</td>
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<td>
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<%= n.text_field :max_score, :size => 15, :title => "25",
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:class => "auto-hint" %>
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</td>
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<td>
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<%= n.label :gapped_alignments %>
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</td>
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<td>
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<%= n.select :gapped_alignments, [['No', false], ['Yes', true]] %>
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</td>
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</tr>
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<tr>
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<td>
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<%= n.label :gap_opening_extension %>
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</td>
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<td>
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<%=
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n.select :gap_opening_extension,
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options_for_select(
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@job.blastn_job.gap_opening_extension_values,
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@job.blastn_job.gap_opening_extension
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)
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%>
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</td>
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<td></td>
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<td></td>
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</tr>
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</table>
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</div>
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<% end %>
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<%= f.fields_for :blastp_job do |n| %>
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<p>
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<strong>blastp</strong>
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<%= n.check_box :queue %>
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</p>
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<div id="blastp" class="toggle">
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<table class="options">
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<tr>
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<td>
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<label>Database(s)</label>
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</td>
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<td>
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<%= n.select :blast_dbs, @blast_dbs[:blastp], {}, { :multiple => true } %>
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</td>
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<td>
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+
<%= n.label :filter, "SEG" %>
|
17
|
+
</td>
|
18
|
+
<td>
|
19
|
+
<%= n.check_box :filter %>
|
20
|
+
</td>
|
21
|
+
</tr>
|
22
|
+
<tr>
|
23
|
+
<td>
|
24
|
+
<%= n.label :expectation %>
|
25
|
+
</td>
|
26
|
+
<td>
|
27
|
+
<%= n.text_field :expectation, :size => 15, :title => "5e-20",
|
28
|
+
:class => "auto-hint" %>
|
29
|
+
</td>
|
30
|
+
<td>
|
31
|
+
<%= n.label :min_bit_score %>
|
32
|
+
</td>
|
33
|
+
<td>
|
34
|
+
<%= n.text_field :min_bit_score, :size => 15, :title => "0",
|
35
|
+
:class => "auto-hint" %>
|
36
|
+
</td>
|
37
|
+
</tr>
|
38
|
+
<tr>
|
39
|
+
<td>
|
40
|
+
<%= n.label :max_score %>
|
41
|
+
</td>
|
42
|
+
<td>
|
43
|
+
<%= n.text_field :max_score, :size => 15, :title => "25",
|
44
|
+
:class => "auto-hint" %>
|
45
|
+
</td>
|
46
|
+
<td>
|
47
|
+
<%= n.label :gapped_alignments %>
|
48
|
+
</td>
|
49
|
+
<td>
|
50
|
+
<%= n.select :gapped_alignments, [['No', false], ['Yes', true]] %>
|
51
|
+
</td>
|
52
|
+
</tr>
|
53
|
+
<tr>
|
54
|
+
<td>
|
55
|
+
<%= n.label :gap_opening_extension %>
|
56
|
+
</td>
|
57
|
+
<td>
|
58
|
+
<%=
|
59
|
+
n.select :gap_opening_extension,
|
60
|
+
options_for_select(
|
61
|
+
@job.blastn_job.gap_opening_extension_values,
|
62
|
+
@job.blastn_job.gap_opening_extension
|
63
|
+
)
|
64
|
+
%>
|
65
|
+
</td>
|
66
|
+
<td></td>
|
67
|
+
<td></td>
|
68
|
+
</tr>
|
69
|
+
</table>
|
70
|
+
</div>
|
71
|
+
<% end %>
|
@@ -0,0 +1,71 @@
|
|
1
|
+
<%= f.fields_for :blastx_job do |n| %>
|
2
|
+
<p>
|
3
|
+
<strong>blastx</strong>
|
4
|
+
<%= n.check_box :queue %>
|
5
|
+
</p>
|
6
|
+
<div id="blastx" class="toggle">
|
7
|
+
<table class="options">
|
8
|
+
<tr>
|
9
|
+
<td>
|
10
|
+
<label>Database(s)</label>
|
11
|
+
</td>
|
12
|
+
<td>
|
13
|
+
<%= n.select :blast_dbs, @blast_dbs[:blastx], {}, { :multiple => true } %>
|
14
|
+
</td>
|
15
|
+
<td>
|
16
|
+
<%= n.label :filter, "SEG" %>
|
17
|
+
</td>
|
18
|
+
<td>
|
19
|
+
<%= n.check_box :filter %>
|
20
|
+
</td>
|
21
|
+
</tr>
|
22
|
+
<tr>
|
23
|
+
<td>
|
24
|
+
<%= n.label :expectation %>
|
25
|
+
</td>
|
26
|
+
<td>
|
27
|
+
<%= n.text_field :expectation, :size => 15, :title => "5e-20",
|
28
|
+
:class => "auto-hint" %>
|
29
|
+
</td>
|
30
|
+
<td>
|
31
|
+
<%= n.label :min_bit_score %>
|
32
|
+
</td>
|
33
|
+
<td>
|
34
|
+
<%= n.text_field :min_bit_score, :size => 15, :title => "0",
|
35
|
+
:class => "auto-hint" %>
|
36
|
+
</td>
|
37
|
+
</tr>
|
38
|
+
<tr>
|
39
|
+
<td>
|
40
|
+
<%= n.label :max_score %>
|
41
|
+
</td>
|
42
|
+
<td>
|
43
|
+
<%= n.text_field :max_score, :size => 15, :title => "25",
|
44
|
+
:class => "auto-hint" %>
|
45
|
+
</td>
|
46
|
+
<td>
|
47
|
+
<%= n.label :gapped_alignments %>
|
48
|
+
</td>
|
49
|
+
<td>
|
50
|
+
<%= n.select :gapped_alignments, [['No', false], ['Yes', true]] %>
|
51
|
+
</td>
|
52
|
+
</tr>
|
53
|
+
<tr>
|
54
|
+
<td>
|
55
|
+
<%= n.label :gap_opening_extension %>
|
56
|
+
</td>
|
57
|
+
<td>
|
58
|
+
<%=
|
59
|
+
n.select :gap_opening_extension,
|
60
|
+
options_for_select(
|
61
|
+
@job.blastn_job.gap_opening_extension_values,
|
62
|
+
@job.blastn_job.gap_opening_extension
|
63
|
+
)
|
64
|
+
%>
|
65
|
+
</td>
|
66
|
+
<td></td>
|
67
|
+
<td></td>
|
68
|
+
</tr>
|
69
|
+
</table>
|
70
|
+
</div>
|
71
|
+
<% end %>
|
@@ -0,0 +1,71 @@
|
|
1
|
+
<%= f.fields_for :tblastn_job do |n| %>
|
2
|
+
<p>
|
3
|
+
<strong>tblastn</strong>
|
4
|
+
<%= n.check_box :queue %>
|
5
|
+
</p>
|
6
|
+
<div id="tblastn" class="toggle">
|
7
|
+
<table class="options">
|
8
|
+
<tr>
|
9
|
+
<td>
|
10
|
+
<label>Database(s)</label>
|
11
|
+
</td>
|
12
|
+
<td>
|
13
|
+
<%= n.select :blast_dbs, @blast_dbs[:tblastn], {}, { :multiple => true } %>
|
14
|
+
</td>
|
15
|
+
<td>
|
16
|
+
<%= n.label :filter, "SEG" %>
|
17
|
+
</td>
|
18
|
+
<td>
|
19
|
+
<%= n.check_box :filter %>
|
20
|
+
</td>
|
21
|
+
</tr>
|
22
|
+
<tr>
|
23
|
+
<td>
|
24
|
+
<%= n.label :expectation %>
|
25
|
+
</td>
|
26
|
+
<td>
|
27
|
+
<%= n.text_field :expectation, :size => 15, :title => "5e-20",
|
28
|
+
:class => "auto-hint" %>
|
29
|
+
</td>
|
30
|
+
<td>
|
31
|
+
<%= n.label :min_bit_score %>
|
32
|
+
</td>
|
33
|
+
<td>
|
34
|
+
<%= n.text_field :min_bit_score, :size => 15, :title => "0",
|
35
|
+
:class => "auto-hint" %>
|
36
|
+
</td>
|
37
|
+
</tr>
|
38
|
+
<tr>
|
39
|
+
<td>
|
40
|
+
<%= n.label :max_score %>
|
41
|
+
</td>
|
42
|
+
<td>
|
43
|
+
<%= n.text_field :max_score, :size => 15, :title => "25",
|
44
|
+
:class => "auto-hint" %>
|
45
|
+
</td>
|
46
|
+
<td>
|
47
|
+
<%= n.label :gapped_alignments %>
|
48
|
+
</td>
|
49
|
+
<td>
|
50
|
+
<%= n.select :gapped_alignments, [['No', false], ['Yes', true]] %>
|
51
|
+
</td>
|
52
|
+
</tr>
|
53
|
+
<tr>
|
54
|
+
<td>
|
55
|
+
<%= n.label :gap_opening_extension %>
|
56
|
+
</td>
|
57
|
+
<td>
|
58
|
+
<%=
|
59
|
+
n.select :gap_opening_extension,
|
60
|
+
options_for_select(
|
61
|
+
@job.blastn_job.gap_opening_extension_values,
|
62
|
+
@job.blastn_job.gap_opening_extension
|
63
|
+
)
|
64
|
+
%>
|
65
|
+
</td>
|
66
|
+
<td></td>
|
67
|
+
<td></td>
|
68
|
+
</tr>
|
69
|
+
</table>
|
70
|
+
</div>
|
71
|
+
<% end %>
|
@@ -0,0 +1,45 @@
|
|
1
|
+
<div id="new">
|
2
|
+
<h1>Quorum Search</h1>
|
3
|
+
<%= form_for @job, :html => {:id => "quorum_job"} do |f| %>
|
4
|
+
<%= render "shared/error_messages", :target => @job %>
|
5
|
+
<div>
|
6
|
+
<%= f.text_area :sequence,
|
7
|
+
:title => "Paste nucleic and amino acid FASTA sequence(s) here or upload a file below.",
|
8
|
+
:class => "auto-hint" %>
|
9
|
+
</div>
|
10
|
+
<div>
|
11
|
+
<%= f.file_field :sequence_file %>
|
12
|
+
</div>
|
13
|
+
<!-- Search Algorithms -->
|
14
|
+
<!-- Comment out an alorithm below to remove it from the form. -->
|
15
|
+
|
16
|
+
<!-- blastn -->
|
17
|
+
<%= render :partial => "blastn_form", :locals => {
|
18
|
+
:f => f, :blast_dbs => @blast_dbs } %>
|
19
|
+
|
20
|
+
<!-- blastx -->
|
21
|
+
<%= render :partial => "blastx_form", :locals => {
|
22
|
+
:f => f, :blast_dbs => @blast_dbs } %>
|
23
|
+
|
24
|
+
<!-- tblastn -->
|
25
|
+
<%= render :partial => "tblastn_form", :locals => {
|
26
|
+
:f => f, :blast_dbs => @blast_dbs } %>
|
27
|
+
|
28
|
+
<!-- blastp -->
|
29
|
+
<%= render :partial => "blastp_form", :locals => {
|
30
|
+
:f => f, :blast_dbs => @blast_dbs } %>
|
31
|
+
|
32
|
+
<!-- End Search Algorithms -->
|
33
|
+
<div>
|
34
|
+
<%= f.submit "Submit" %>
|
35
|
+
<%= submit_tag "Reset", :name => "reset",
|
36
|
+
:type => "button", :id => "quorum_job_reset" %>
|
37
|
+
</div>
|
38
|
+
<% end %>
|
39
|
+
</div>
|
40
|
+
<div id="quorum">
|
41
|
+
<hr class="big" />
|
42
|
+
<p>
|
43
|
+
Powered by <%= link_to "Quorum", "https://github.com/ncgr/quorum" %>
|
44
|
+
</p>
|
45
|
+
</div>
|
@@ -0,0 +1,183 @@
|
|
1
|
+
<div id="show">
|
2
|
+
<h1>Search Results</h1>
|
3
|
+
<p class="small right"><%= link_to raw("Search Again »"), :jobs %></p>
|
4
|
+
<!-- Tabs -->
|
5
|
+
<!-- To remove an algorithm from the view, simply comment out the -->
|
6
|
+
<!-- div#tabs ul li and corresponding div#tabs-(tab number) -->
|
7
|
+
<div id="tabs">
|
8
|
+
<ul>
|
9
|
+
<li><a href="#tabs-1">Blastn</a></li>
|
10
|
+
<li><a href="#tabs-2">Blastx</a></li>
|
11
|
+
<li><a href="#tabs-3">Tblastn</a></li>
|
12
|
+
<li><a href="#tabs-4">Blastp</a></li>
|
13
|
+
</ul>
|
14
|
+
|
15
|
+
<!-- Search results per algorithm -->
|
16
|
+
<div id="tabs-1">
|
17
|
+
<h2>Blastn</h2>
|
18
|
+
<div id="blastn-results">
|
19
|
+
Searching... <%= image_tag "quorum/knight_rider.gif" %>
|
20
|
+
</div>
|
21
|
+
</div>
|
22
|
+
|
23
|
+
<div id="tabs-2">
|
24
|
+
<h2>Blastx</h2>
|
25
|
+
<div id="blastx-results">
|
26
|
+
Searching... <%= image_tag "quorum/knight_rider.gif" %>
|
27
|
+
</div>
|
28
|
+
</div>
|
29
|
+
|
30
|
+
<div id="tabs-3">
|
31
|
+
<h2>Tblastn</h2>
|
32
|
+
<div id="tblastn-results">
|
33
|
+
Searching... <%= image_tag "quorum/knight_rider.gif" %>
|
34
|
+
</div>
|
35
|
+
</div>
|
36
|
+
|
37
|
+
<div id="tabs-4">
|
38
|
+
<h2>Blastp</h2>
|
39
|
+
<div id="blastp-results">
|
40
|
+
Searching... <%= image_tag "quorum/knight_rider.gif" %>
|
41
|
+
</div>
|
42
|
+
</div>
|
43
|
+
</div>
|
44
|
+
<!-- End Tabs -->
|
45
|
+
<p class="small right"><%= link_to raw("Search Again »"), :jobs %></p>
|
46
|
+
|
47
|
+
<!-- Detailed report element -->
|
48
|
+
<div id="detailed_report_dialog" title="Quorum Report Details"></div>
|
49
|
+
</div>
|
50
|
+
<div id="quorum">
|
51
|
+
<hr class="big" />
|
52
|
+
<p>
|
53
|
+
Powered by <%= link_to "Quorum", "https://github.com/ncgr/quorum" %>
|
54
|
+
</p>
|
55
|
+
</div>
|
56
|
+
|
57
|
+
<!-- Blast Results Template -->
|
58
|
+
<script type="text/template" id="blast_template">
|
59
|
+
{{ if (data[0].results === false) { }}
|
60
|
+
<p><strong>Your search returned 0 hits.</strong></p>
|
61
|
+
{{ } else { }}
|
62
|
+
<table class="results">
|
63
|
+
<tr>
|
64
|
+
<th>Query Accession</th>
|
65
|
+
<th>Query Length</th>
|
66
|
+
<th>Hit Length</th>
|
67
|
+
<th>Qstrand / Hstrand</th>
|
68
|
+
<th>Hit Accession</th>
|
69
|
+
<th>Hit Description</th>
|
70
|
+
<th>Alignment Length</th>
|
71
|
+
<th>
|
72
|
+
<a class="bit-score"
|
73
|
+
onclick="openWindow(
|
74
|
+
'http://www.ncbi.nlm.nih.gov/books/NBK21106/def-item/app8/',
|
75
|
+
'Bit Score',
|
76
|
+
800,
|
77
|
+
300
|
78
|
+
)">
|
79
|
+
Bit Score
|
80
|
+
</a>
|
81
|
+
</th>
|
82
|
+
<th>
|
83
|
+
<a class="e-value"
|
84
|
+
onclick="openWindow(
|
85
|
+
'http://www.ncbi.nlm.nih.gov/books/NBK21106/def-item/app42/',
|
86
|
+
'E-value',
|
87
|
+
800,
|
88
|
+
300
|
89
|
+
)">
|
90
|
+
E-value
|
91
|
+
</a>
|
92
|
+
</th>
|
93
|
+
</tr>
|
94
|
+
{{ var i = 1; var style = "" }}
|
95
|
+
{{ _.each(data, function(v) { }}
|
96
|
+
{{ i % 2 == 0 ? style = "even" : style = "odd" }}
|
97
|
+
{{ var qstrand = v.query_frame }}
|
98
|
+
{{ var hstrand = v.hit_frame }}
|
99
|
+
<tr class="{{= style }}">
|
100
|
+
<td>{{= v.query }}</td>
|
101
|
+
<td class="right">{{= v.query_len }}</td>
|
102
|
+
<td class="right">{{= v.hit_len }}</td>
|
103
|
+
<td>{{= formatStrand(qstrand, hstrand) }}</td>
|
104
|
+
<td>{{= v.hit_id }}</td>
|
105
|
+
<td>{{= v.hit_def.trunc(20) }}</td>
|
106
|
+
<td class="right">{{= v.align_len }}</td>
|
107
|
+
<td class="right">{{= v.bit_score }}</td>
|
108
|
+
<td class="right">
|
109
|
+
<a class="detailed_report"
|
110
|
+
onclick="viewDetailedReport(
|
111
|
+
<%= @jobs.id %>,
|
112
|
+
{{= v.id }},
|
113
|
+
'{{= v.query }}',
|
114
|
+
'{{= algo }}')">
|
115
|
+
{{= v.evalue }}
|
116
|
+
</a>
|
117
|
+
</td>
|
118
|
+
</tr>
|
119
|
+
{{ i++ }}
|
120
|
+
{{ }); }}
|
121
|
+
</table>
|
122
|
+
{{ } }}
|
123
|
+
</script>
|
124
|
+
|
125
|
+
<!-- Detailed Report Template -->
|
126
|
+
<script type="text/template" id="detailed_report_template">
|
127
|
+
<h3>Query Accession {{= query }}</h3>
|
128
|
+
{{ _.each(data, function(v) { }}
|
129
|
+
{{ var id = v.id }}
|
130
|
+
{{ var qseq = v.qseq }}
|
131
|
+
{{ var midline = v.midline }}
|
132
|
+
{{ var hseq = v.hseq }}
|
133
|
+
{{ var q_from = v.query_from }}
|
134
|
+
{{ var q_to = v.query_to }}
|
135
|
+
{{ var h_from = v.hit_from }}
|
136
|
+
{{ var h_to = v.hit_to }}
|
137
|
+
{{ var qstrand = v.query_frame }}
|
138
|
+
{{ var hstrand = v.hit_frame }}
|
139
|
+
{{ var hsp_group = v.hsp_group }}
|
140
|
+
<div id="{{= id }}">
|
141
|
+
<p class="small">{{= displayHspLinks(id, hsp_group, data) }}</p>
|
142
|
+
<p class="small">Hit Accession: {{= v.hit_id }}</p>
|
143
|
+
<p class="small">Hit Description: {{= v.hit_def }}</p>
|
144
|
+
<table class="report_details">
|
145
|
+
<tr>
|
146
|
+
<td>E-value: {{= v.evalue }}</td>
|
147
|
+
<td>Bit Score: {{= v.bit_score }}</td>
|
148
|
+
<td></td>
|
149
|
+
</tr>
|
150
|
+
<tr>
|
151
|
+
<td>Alignment Length: {{= v.align_len }}</td>
|
152
|
+
<td>Qstrand / Hstrand: {{= formatStrand(qstrand, hstrand) }}</td>
|
153
|
+
<td></td>
|
154
|
+
</tr>
|
155
|
+
<tr>
|
156
|
+
<td>Query Length: {{= v.query_len }}</td>
|
157
|
+
<td>Query From: {{= v.query_from }}</td>
|
158
|
+
<td>Query To: {{= v.query_to }}</td>
|
159
|
+
</tr>
|
160
|
+
<tr>
|
161
|
+
<td>Hit Length: {{= v.hit_len }}</td>
|
162
|
+
<td>Hit From: {{= v.hit_from }}</td>
|
163
|
+
<td>Hit To: {{= v.hit_to }}</td>
|
164
|
+
</tr>
|
165
|
+
</table>
|
166
|
+
{{= formatSequenceReport(qseq, midline, hseq, q_from, q_to, h_from, h_to, algo) }}
|
167
|
+
</div>
|
168
|
+
<hr />
|
169
|
+
{{ }); }}
|
170
|
+
</script>
|
171
|
+
|
172
|
+
<script type="text/javascript">
|
173
|
+
$(function() {
|
174
|
+
//
|
175
|
+
// Asynchronously poll Quorum for search results.
|
176
|
+
//
|
177
|
+
// pollResults(id, interval)
|
178
|
+
// id: Job.id
|
179
|
+
// interval: poll interval in milliseconds. 5000 default.
|
180
|
+
//
|
181
|
+
pollResults(<%= @jobs.id %>);
|
182
|
+
});
|
183
|
+
</script>
|
@@ -0,0 +1,10 @@
|
|
1
|
+
<% if target.errors.any? %>
|
2
|
+
<div id="error_explanation">
|
3
|
+
<h2><%= pluralize(target.errors.count, "error") %> prohibited this record from being saved:</h2>
|
4
|
+
<ul>
|
5
|
+
<% target.errors.full_messages.each do |msg| %>
|
6
|
+
<li><%= msg %></li>
|
7
|
+
<% end %>
|
8
|
+
</ul>
|
9
|
+
</div>
|
10
|
+
<% end %>
|