sequenceserver 0.8.6 → 0.8.7.beta1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 497b668eaeb852effdb0181e176e37c7c8fe746f
+  data.tar.gz: 1999260fc36d0d0defccbe80123f5dc85650f6a5
+SHA512:
+  metadata.gz: 00b1a531ab3dae22b949581e8d2d73ef0948b12186284701dac14e90aa790f959c0b19f3c6daaa8b4d88e6f7b8fa5099fb7c632e7335b612b5bdaf1b4b17beca
+  data.tar.gz: 4600be84bc18e1ac2e93f11340355a867292bcec70d6c79758a6a9d6e88b75080870fea5e39c9faeaff0029bcc20187adb2daff2e52c3a92ef119767f1e127e7

data/lib/profile_code.rb

@@ -0,0 +1,217 @@
+require 'ruby-prof'
+
+$:.unshift '.'
+
+#require 'sinatra/base'
+require 'yaml'
+require 'logger'
+require 'fileutils'
+require 'sequenceserver/helpers'
+require 'sequenceserver/blast'
+require 'sequenceserver/sequencehelpers'
+require 'sequenceserver/sinatralikeloggerformatter'
+require 'sequenceserver/customisation'
+require 'sequenceserver/version'
+
+require 'sequenceserver'
+
+
+query = '>1111883
+GCTGGCGGCGTGCCTAACACATGTAAGTCGAACGGGACTGGGGGCAACTCCAGTTCAGTG
+GCAGACGGGTGCGTAACACGTGAGCAACTTGTCCGACGGCGGGGGATAGCCGGCCCAACG
+GCCGGGTAATACCGCGTACGCTCGTTTAGGGACATCCCTGAATGAGGAAAGCCGTAAGGC
+ACCGACGGAGAGGCTCGCGGCCTATCAGCTAGTTGGCGGGGTAACGGCCCACCAAGGCGA
+CGACGGGTAGCTGGTCTGAGAGGATGGCCAGCCACATTGGGACTGAGACACGGCCCAGAC
+TCCTACGGGAGGCAGCAGTGGGGAATCTTGCGCAATGGCCGCAAGGCTGACGCAGCGACG
+CCGCGTGTGGGATGACGGCCTTCGGGTTGTAAACCACTGTCGGGAGGAACGAATACTCGG
+CTAGTCCGAGGGTGACGGTACCTCCAAAGGAAGCACCGGCTAACTCCGTGCCAGCAGCCG
+CGGTAATACGGAGGGTGCGAGCGTTGTCCGGAATCACTGGGCGTAAAGGGCGCGTAGGTG
+GCCCGTTAAGTGGCTGGTGAAATCCCGGGGCTCAACTCCGGGGCTGCCGGTCAGACTGGC
+GAGCTAGAGCACGGTAGGGGCAGATGGAATTCCCGGTGTAGCGGTGGAATGCGTAGATAT
+CGGGAAGAATACCAGTGGCGAAGGCGTTCTGCTGGGCCGTTGCTGACACTGAGGCGCGAC
+AGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGGACACT
+AGACGTCGGGGGGAGCGACCCTCCCGGTGTCGTCGCTAACGCAGTAAGTGTCCCGCCTGG
+GGAGTACGGCCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGA
+GCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACCTGGGCTTGACATGCTGGTGCA
+AGCCGGTGGAAACATCGGCCCCTCTTCGGAGCGCCAGCACAGGTGCTGCATGGCTGTCGT
+CAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACTCTCGCTCCCAGT
+TGCCAGCGGTTCGGCCGGGGACTCTGGGGGGACTGCCGGCGTTAAGCCGGAGGAAGGTGG
+GGACGACGTCAAGTCATCATGGCCCTTACGTCCAGGGCGACACACGTGCTACAATGCCTG
+GTACAGCGCGTCGCGAACTCGCAAGAGGGAGCCAATCGCCAAAAGCCGGGCTAAGTTCGG
+ATTGTCGTCTGCAACTCGACGGCATGAAGCCGGAATCGCTAGTAATCGCGGATCAGCCAC
+GCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGCCATGGAAGCCGGA
+GGGACCCGAAACCGGTGGGCCAACCGCAAGGGGGCAGCCGTCTAAGGT'
+
+#blastn -db '/home/ben/git/sequenceserver/db/97_otus.fasta' -query '/tmp/sequenceserver_query20140119-10926-qt2ecp'  -task blastn  -num_threads 1 -html
+method        = 'blastn'#params['method']
+databases     = ['/home/ben/git/sequenceserver/db/97_otus.fasta']#params[:databases]
+sequence      = query #params[:sequence]
+advanced_opts = '-max_target_seqs 1'#params['advanced']
+
+# evaluate empty sequence as nil, otherwise as fasta
+#      sequence = sequence.empty? ? nil : to_fasta(sequence)
+
+# blastn implies blastn, not megablast; but let's not interfere if a user
+# specifies `task` herself
+if method == 'blastn' and not advanced_opts =~ /task/
+  #advanced_opts << ' -task blastn '
+end
+
+
+# run blast and log
+blast = SequenceServer::Blast.new(method, sequence, databases.join(' '), advanced_opts)
+blast.run!
+puts('Ran: ' + blast.command)
+
+
+    def format_blast_results(result, databases)
+      formatted_result = ''
+      @all_retrievable_ids = []
+      string_of_used_databases = databases.join(' ')
+      blast_database_number = 0
+      line_number = 0
+      started_query = false
+      finished_database_summary = false
+      finished_alignments = false
+      reference_string = ''
+      database_summary_string = ''
+      result.each do |line|
+        line_number += 1
+        next if line_number <= 5 #skip the first 5 lines
+
+        # Add the reference to the end, not the start, of the blast result
+        if line_number >= 7 and line_number <= 15
+          reference_string += line
+          next
+        end
+
+        if !finished_database_summary and line_number > 15
+          database_summary_string += line
+          finished_database_summary = true if line.match(/total letters/)
+          next
+        end
+
+        # Remove certain lines from the output
+        skipped_lines = [/^<\/BODY>/,/^<\/HTML>/,/^<\/PRE>/]
+        skip = false
+        skipped_lines.each do |skippy|
+        #  $stderr.puts "`#{line}' matches #{skippy}?"
+          if skippy.match(line)
+            skip = true
+         #   $stderr.puts 'yes'
+          else
+          #  $stderr.puts 'no'
+          end
+        end
+        next if skip
+
+        # Remove the javascript inclusion
+        line.gsub!(/^<script src=\"blastResult.js\"><\/script>/, '')
+
+        if line.match(/^>/) # If line to possibly replace
+          # Reposition the anchor to the end of the line, so that it both still works and
+          # doesn't interfere with the diagnostic space at the beginning of the line.
+          #
+          # There are two cases:
+          #
+          # database formatted _with_ -parse_seqids
+          line.gsub!(/^>(.+)(<a.*><\/a>)(.*)/, '>\1\3\2')
+          #
+          # database formatted _without_ -parse_seqids
+          line.gsub!(/^>(<a.*><\/a>)(.*)/, '>\2\1')
+
+          # get hit coordinates -- useful for linking to genome browsers
+          hit_length      = result[line_number..-1].index{|l| l =~ />lcl|Lambda/}
+          hit_coordinates = result[line_number, hit_length].grep(/Sbjct/).
+            map(&:split).map{|l| [l[1], l[-1]]}.flatten.map(&:to_i).minmax
+
+          # Create the hyperlink (if required)
+          formatted_result += construct_sequence_hyperlink_line(line, databases, hit_coordinates)
+        else
+          # Surround each query's result in <div> tags so they can be coloured by CSS
+          if matches = line.match(/^<b>Query=<\/b> (.*)/) # If starting a new query, then surround in new <div> tag, and finish the last one off
+            line = "<div class=\"resultn\" id=\"#{matches[1]}\">\n<h3>Query= #{matches[1]}</h3><pre>"
+            unless blast_database_number == 0
+              line = "</pre></div>\n#{line}"
+            end
+            blast_database_number += 1
+          elsif line.match(/^  Database: /) and !finished_alignments
+            formatted_result += "</div>\n<pre>#{database_summary_string}\n\n"
+            finished_alignments = true
+          end
+          formatted_result += line
+        end
+      end
+      formatted_result << "</pre>"
+
+      link_to_fasta_of_all = "/get_sequence/?id=#{@all_retrievable_ids.join(' ')}&db=#{string_of_used_databases}"
+      # #dbs must be sep by ' '
+      retrieval_text       = @all_retrievable_ids.empty? ? '' : "<a href='#{url(link_to_fasta_of_all)}'>FASTA of #{@all_retrievable_ids.length} retrievable hit(s)</a>"
+
+      "<h2>Results</h2>"+
+      retrieval_text +
+      "<br/><br/>" +
+      formatted_result +
+      "<br/>" +
+      "<pre>#{reference_string.strip}</pre>"
+    end
+
+    def construct_sequence_hyperlink_line(line, databases, hit_coordinates)
+      matches = line.match(/^>(.+)/)
+      sequence_id = matches[1]
+
+      link = nil
+
+      # If a custom sequence hyperlink method has been defined,
+      # use that.
+      options = {
+        :sequence_id => sequence_id,
+        :databases => databases,
+        :hit_coordinates => hit_coordinates
+      }
+
+      # First precedence: construct the whole line to be customised
+      if self.respond_to?(:construct_custom_sequence_hyperlinking_line)
+        settings.log.debug("Using custom hyperlinking line creator with sequence #{options.inspect}")
+        link_line = construct_custom_sequence_hyperlinking_line(options)
+        unless link_line.nil?
+          return link_line
+        end
+      end
+
+      # If we have reached here, custom construction of the
+      # whole line either wasn't defined, or returned nil
+      # (indicating failure)
+      if self.respond_to?(:construct_custom_sequence_hyperlink)
+ #       settings.log.debug("Using custom hyperlink creator with sequence #{options.inspect}")
+        link = construct_custom_sequence_hyperlink(options)
+      else
+#        settings.log.debug("Using standard hyperlink creator with sequence `#{options.inspect}'")
+        link = construct_standard_sequence_hyperlink(options)
+      end
+
+      # Return the BLAST output line with the link in it
+      if link.nil?
+  #      settings.log.debug('No link added link for: `'+ sequence_id +'\'')
+        return line
+      else
+        settings.log.debug('Added link for: `'+ sequence_id +'\''+ link)
+        return "><a href='#{url(link)}' target='_blank'>#{sequence_id}</a> \n"
+      end
+
+    end
+
+    # Advanced options are specified by the user. Here they are checked for interference with SequenceServer operations.
+    # raise ArgumentError if an error has occurred, otherwise return without value
+    def validate_advanced_parameters(advanced_options)
+      raise ArgumentError, "Invalid characters detected in the advanced options" unless advanced_options =~ /\A[a-z0-9\-_\. ']*\Z/i
+      disallowed_options = %w(-out -html -outfmt -db -query)
+      disallowed_options.each do |o|
+        raise ArgumentError, "The advanced BLAST option \"#{o}\" is used internally by SequenceServer and so cannot be specified by the you" if advanced_options =~ /#{o}/i
+      end
+    end
+
+puts format_blast_results(blast.result, databases)
+
+
+

data/lib/sequenceserver.rb

@@ -337,8 +337,8 @@ module SequenceServer
 <em>#{found_sequences_count > sequenceids.length ? 'more' : 'less'}</em>
 sequence than expected.</strong></p>
 
-<p>This is likely due to a problem with how databases are formatted. 
-<strong>Please share this text with the person managing this website so 
+<p>This is likely due to a problem with how databases are formatted.
+<strong>Please share this text with the person managing this website so
 they can resolve the issue.</strong></p>
 
 <p> You requested #{sequenceids.length} sequence#{sequenceids.length > 1 ? 's' : ''}
@@ -375,7 +375,10 @@ HEADER
     end
 
     def format_blast_results(result, databases)
-      formatted_result = ''
+      # Constructing the result in an Array and then calling Array#join is much faster than
+      # building up a String and using +=, as older versions of SeqServ did.
+      formatted_results = []
+
       @all_retrievable_ids = []
       string_of_used_databases = databases.join(' ')
       blast_database_number = 0
@@ -436,7 +439,7 @@ HEADER
             map(&:split).map{|l| [l[1], l[-1]]}.flatten.map(&:to_i).minmax
 
           # Create the hyperlink (if required)
-          formatted_result += construct_sequence_hyperlink_line(line, databases, hit_coordinates)
+          formatted_results << construct_sequence_hyperlink_line(line, databases, hit_coordinates)
         else
           # Surround each query's result in <div> tags so they can be coloured by CSS
           if matches = line.match(/^<b>Query=<\/b> (.*)/) # If starting a new query, then surround in new <div> tag, and finish the last one off
@@ -446,13 +449,13 @@ HEADER
             end
             blast_database_number += 1
           elsif line.match(/^  Database: /) and !finished_alignments
-            formatted_result += "</div>\n<pre>#{database_summary_string}\n\n"
+            formatted_results << "</div>\n<pre>#{database_summary_string}\n\n"
             finished_alignments = true
           end
-          formatted_result += line
+          formatted_results << line
         end
       end
-      formatted_result << "</pre>"
+      formatted_results << "</pre>"
 
       link_to_fasta_of_all = "/get_sequence/?id=#{@all_retrievable_ids.join(' ')}&db=#{string_of_used_databases}"
       # #dbs must be sep by ' '
@@ -461,7 +464,7 @@ HEADER
       "<h2>Results</h2>"+
       retrieval_text +
       "<br/><br/>" +
-      formatted_result +
+      formatted_results.join +
       "<br/>" +
       "<pre>#{reference_string.strip}</pre>"
     end

data/sequenceserver.gemspec

@@ -1,7 +1,7 @@
 Gem::Specification.new do |s|
   # meta
   s.name        = 'sequenceserver'
-  s.version     = '0.8.6'
+  s.version     = '0.8.7.beta1'
   s.authors     = ['Anurag Priyam', 'Ben J Woodcroft', 'Yannick Wurm']
   s.email       = 'anurag08priyam@gmail.com'
   s.homepage    = 'http://sequenceserver.com'

data/tests/test_ui.rb~

@@ -0,0 +1,104 @@
+require 'rspec'
+require 'watir-webdriver'
+require 'headless'
+
+# These shared examples should work for
+shared_examples_for 'a browser' do
+  let(:seqserv_url){'http://localhost:4567'}
+
+  it 'should simply go the seqserv webpage' do
+    b.goto seqserv_url
+    b.url.gsub(/\/$/,'').should eq(seqserv_url)
+    b.ready_state.should eq('complete')
+  end
+
+  it 'should do a simple blastp' do
+    b.goto seqserv_url
+
+    # Nucleotide database should be available
+    b.checkbox(:value => 'e205221dd32dc53ebfc9fb48cbdecd9e').enabled?.should eq(true)
+
+    # First up the blast button should be disabled
+    b.button(:id => 'method').text.should eq('BLAST')
+    b.button(:id => 'method').enabled?.should eq(false)
+
+    # Pick a protein blast database
+    b.checkbox(:value => '6669b1c88665158621afc06407ce88ea').set
+    b.checkbox(:value => '6669b1c88665158621afc06407ce88ea').checked?.should eq(true)
+
+    # nuc dbs now disabled
+    b.checkbox(:value => 'e205221dd32dc53ebfc9fb48cbdecd9e').enabled?.should eq(false)
+
+    # The blast button should still be disabled
+    b.button(:id => 'method').text.should eq('BLAST')
+    b.button(:id => 'method').enabled?.should eq(false)
+
+    # Give a sequence we know should hit
+    b.textarea(:name => 'sequence').set 'YTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLA'
+
+    #blast butn now active
+    b.button(:id => 'method').text.should eq('BLASTP')
+    b.button(:id => 'method').enabled?.should eq(true)
+
+    # Run the blast
+    b.button(:id => 'method').click
+
+    while b.div(:id => 'result').text.include?('Waiting for BLAST to be run')
+    end
+
+    # blast should have worked
+    b.div(:id => 'result').text.include?('Sequences producing significant alignments: ').should eq(true)
+  end
+end
+
+#####################################################################################
+#+++++++++++ Below is admin code, hopefully not necessary to mess around with to test new UI specs
+
+# NOT thread-safe, at least because of the interaction with headless
+class BrowserAdmin
+  def self.setup_browser(type)
+    case type
+    when :firefox then
+      Watir::Browser.new :firefox
+    when :chrome then
+      Watir::Browser.new :chrome
+    when :headless_firefox then
+      @headless = Headless.new
+      @headless.start
+      Watir::Browser.new :firefox
+    when :headless_chrome then
+      @headless = Headless.new
+      @headless.start
+      Watir::Browser.new :chrome
+    else
+      raise "Unknown browser type asked for: #{type.inspect}"
+    end
+  end
+
+  def self.teardown_browser(browser)
+    browser.close
+
+    # Re-head again, but maybe this makes no difference
+    @headless.destroy unless @headless.nil?
+    @headless = nil
+  end
+end
+
+
+describe 'ui' do
+  [:firefox, :chrome, :headless_firefox, :headless_chrome].each do |bro|
+    context bro.to_s do
+      it_behaves_like 'a browser' do
+        browser = nil
+        before do
+          browser = BrowserAdmin.setup_browser bro
+        end
+        after do
+          BrowserAdmin.teardown_browser browser
+        end
+        let(:b){browser}
+      end
+    end
+  end
+end
+

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 0.8.6
-  prerelease: 
+  version: 0.8.7.beta1
 platform: ruby
 authors:
 - Anurag Priyam
@@ -11,224 +10,216 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-28 00:00:00.000000000 Z
+date: 2014-01-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.2'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.2'
 - !ruby/object:Gem::Dependency
   name: sinatra
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 1.3.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 1.3.0
 - !ruby/object:Gem::Dependency
   name: ptools
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: minitest
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rack-test
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: watir-webdriver
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: headless
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-description: ! 'SequenceServer lets you rapidly set up a BLAST+ server with an intuitive
-  user interface for use locally or over the web.
-
-'
+description: |
+  SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.
 email: anurag08priyam@gmail.com
 executables:
 - sequenceserver
 extensions: []
 extra_rdoc_files: []
 files:
-- lib/sequenceserver/sequencehelpers.rb
-- lib/sequenceserver/customisation.rb
+- Gemfile
+- LICENSE.Apache.txt
+- LICENSE.txt
+- README.txt
+- bin/sequenceserver
+- config.ru
+- example.config.yml
+- lib/profile_code.rb
+- lib/sequenceserver.rb
 - lib/sequenceserver/blast.rb
+- lib/sequenceserver/customisation.rb
 - lib/sequenceserver/database.rb
-- lib/sequenceserver/version.rb
+- lib/sequenceserver/database_formatter.rb
 - lib/sequenceserver/helpers.rb
+- lib/sequenceserver/sequencehelpers.rb
 - lib/sequenceserver/sinatralikeloggerformatter.rb
-- lib/sequenceserver/database_formatter.rb
-- lib/sequenceserver.rb
-- views/_options.erb
-- views/500.erb
-- views/search.erb
-- public/js/jquery.activity.js
-- public/js/sequenceserver.js
-- public/js/jquery.js
-- public/js/jquery-scrollspy.js
-- public/js/sequenceserver.blast.js
-- public/js/bootstrap.dropdown.js
-- public/js/store.min.js
-- public/js/bootstrap.modal.js
-- public/js/bootstrap.transition.js
-- public/js/jquery-ui.js
-- public/js/jquery.enablePlaceholder.min.js
+- lib/sequenceserver/version.rb
+- public/css/beige.css.css
+- public/css/bootstrap.dropdown.css
+- public/css/bootstrap.icons.css
 - public/css/bootstrap.min.css
 - public/css/bootstrap.modal.css
-- public/css/bootstrap.icons.css
-- public/css/bootstrap.dropdown.css
-- public/css/beige.css.css
 - public/css/custom.css
 - public/img/glyphicons-halflings-white.png
 - public/img/glyphicons-halflings.png
-- tests/ui.specs.todo
-- tests/test_sequenceserver_blast.rb
-- tests/test_ui.rb
-- tests/test_sequencehelpers.rb
-- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.psq
-- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.pin
-- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.phr
-- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta
+- public/js/bootstrap.dropdown.js
+- public/js/bootstrap.modal.js
+- public/js/bootstrap.transition.js
+- public/js/jquery-scrollspy.js
+- public/js/jquery-ui.js
+- public/js/jquery.activity.js
+- public/js/jquery.enablePlaceholder.min.js
+- public/js/jquery.js
+- public/js/sequenceserver.blast.js
+- public/js/sequenceserver.js
+- public/js/store.min.js
+- sequenceserver.gemspec
+- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta
 - tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nhr
 - tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nin
 - tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta.nsq
-- tests/database/nucleotide/Sinvicta2-2-3.cdna.subset.fasta
+- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta
+- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.phr
+- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.pin
+- tests/database/protein/Sinvicta2-2-3.prot.subset.fasta.psq
 - tests/run
-- config.ru
-- example.config.yml
-- LICENSE.txt
-- LICENSE.Apache.txt
-- README.txt
-- Gemfile
-- sequenceserver.gemspec
-- bin/sequenceserver
+- tests/test_sequencehelpers.rb
+- tests/test_sequenceserver_blast.rb
+- tests/test_ui.rb
+- tests/test_ui.rb~
+- tests/ui.specs.todo
+- views/500.erb
+- views/_options.erb
+- views/search.erb
 homepage: http://sequenceserver.com
 licenses:
 - SequenceServer (custom)
-post_install_message: ! "\n------------------------------------------------------------------------\n
-  \ Thank you for installing SequenceServer :)!\n\n  To launch SequenceServer execute
-  'sequenceserver' from command line.\n\n    $ sequenceserver\n\n\n  Visit http://sequenceserver.com
-  for more.\n------------------------------------------------------------------------\n\n"
+metadata: {}
+post_install_message: |2+
+
+  ------------------------------------------------------------------------
+    Thank you for installing SequenceServer :)!
+
+    To launch SequenceServer execute 'sequenceserver' from command line.
+
+      $ sequenceserver
+
+
+    Visit http://sequenceserver.com for more.
+  ------------------------------------------------------------------------
+
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.23
+rubygems_version: 2.2.0.rc.1
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: BLAST search made easy!
 test_files: []