sequenceserver 1.0.1 → 1.0.2
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- checksums.yaml +4 -4
- data/lib/sequenceserver.rb +26 -28
- data/lib/sequenceserver/server.rb +63 -0
- data/lib/sequenceserver/version.rb +1 -1
- data/public/dist/css/sequenceserver.min.css +1 -1
- data/public/dist/css/sequenceserver.min.css.gz +0 -0
- data/public/dist/js/sequenceserver.min.js +17 -11
- data/public/dist/js/sequenceserver.min.js.gz +0 -0
- data/public/js/jquery.t.js +14 -0
- data/sequenceserver.gemspec +0 -1
- metadata +3 -22
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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metadata.gz:
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4
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data.tar.gz:
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3
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metadata.gz: c7a9114ec438ee4afd588e18a35b3c3afd576ba9
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4
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data.tar.gz: 8b85ab9e90c977a8670e1523a0269c7a54ec375e
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5
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SHA512:
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metadata.gz:
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data.tar.gz:
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6
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metadata.gz: 710d4315a1fc708d92b409fa72123b34b5d4b72f3fcc889cc622091644e3281537f95d0ba198aab2ad136399c5ab8722277d4a836bb928e339e0946a4582652d
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7
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data.tar.gz: e9c49ebda9ec0be9e4e9b35e7f5b21d773ac258045a3d6ddae175ee7df1108d0ff1a1de0f2b59a059e91d71020718615dedb7cda244e5d5d115913c4e379431a
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data/lib/sequenceserver.rb
CHANGED
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@@ -1,10 +1,10 @@
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1
1
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require 'English'
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2
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-
require 'thin'
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2
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4
3
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require 'sequenceserver/version'
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4
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require 'sequenceserver/exceptions'
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require 'sequenceserver/config'
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require 'sequenceserver/logger'
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7
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require 'sequenceserver/server'
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require 'sequenceserver/search'
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require 'sequenceserver/sequence'
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require 'sequenceserver/database'
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@@ -14,7 +14,7 @@ require 'sequenceserver/routes'
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14
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# Top level module / namespace.
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module SequenceServer
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# Use a fixed minimum version of BLAST+
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-
MINIMUM_BLAST_VERSION
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MINIMUM_BLAST_VERSION = '2.2.30+'
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class << self
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def environment
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@@ -52,35 +52,33 @@ module SequenceServer
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# Run SequenceServer as a self-hosted server using Thin webserver.
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def run
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check_host
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-
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-
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-
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use Rack::CommonLogger if SequenceServer.verbose?
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run SequenceServer
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end
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61
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server.silent = true
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server.backend.start do
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puts '** SequenceServer is ready.'
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puts " Go to #{server_url} in your browser and start BLASTing!"
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65
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puts ' Press CTRL+C to quit.'
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66
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open_in_browser(server_url)
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67
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[:INT, :TERM].each do |sig|
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trap sig do
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server.stop!
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puts
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puts '** Thank you for using SequenceServer :).'
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puts ' Please cite: '
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puts ' Priyam, Woodcroft, Rai & Wurm,'
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puts ' SequenceServer (in prep).'
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end
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end
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-
end
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rescue
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puts '** Oops! There was an error.'
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Server.run(self)
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rescue Errno::EADDRINUSE
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puts "** Could not bind to port #{config[:port]}."
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puts " Is SequenceServer already accessible at #{server_url}?"
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puts ' Try running SequenceServer on another port, like so:'
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puts ' No? Try running SequenceServer on another port, like so:'
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puts
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puts ' sequenceserver -p 4570.'
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rescue Errno::EACCES
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puts "** Need root privilege to bind to port #{config[:port]}."
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puts ' It is not advisable to run SequenceServer as root.'
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puts ' Please use Apache/Nginx to bind to a privileged port.'
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puts ' Instructions available on http://sequenceserver.com.'
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end
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68
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def on_start
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puts '** SequenceServer is ready.'
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puts " Go to #{server_url} in your browser and start BLASTing!"
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puts ' Press CTRL+C to quit.'
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open_in_browser(server_url)
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end
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def on_stop
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puts
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puts '** Thank you for using SequenceServer :).'
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puts ' Please cite: '
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puts ' Priyam, Woodcroft, Rai & Wurm,'
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puts ' SequenceServer (in prep).'
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82
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end
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# Rack-interface.
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@@ -0,0 +1,63 @@
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1
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require 'rack/handler/webrick'
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module SequenceServer
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# Simple wrapper around WEBrick and Rack::Handler::WEBrick to host
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# SequenceServer standalone.
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class Server
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class << self
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def run(*args)
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new(*args).start
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end
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end
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def initialize(app)
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@app = app
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end
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attr_reader :app
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# Start server. Raises Errno::EADDRINUSE if port is in use by another
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# process. Raises Errno::EACCES if binding to the port requires root
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# privilege.
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def start
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setup_signal_handlers
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@server = WEBrick::HTTPServer.new(options)
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@server.mount '/', Rack::Handler::WEBrick, app
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@server.start
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end
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# Stop server.
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def stop
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@server.shutdown
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end
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# Options Hash passed to WEBrick::HTTPServer.
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# rubocop:disable Metrics/AbcSize
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def options
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@options ||= {
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:BindAddress => app.config[:host],
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:Port => app.config[:port],
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:StartCallback => proc { app.on_start },
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:StopCallback => proc { app.on_stop },
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:OutputBufferSize => 5,
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:AccessLog => [[logdev, WEBrick::AccessLog::COMMON_LOG_FORMAT]],
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:Logger => WEBrick::Log.new(logdev)
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}
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end
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# rubocop:enable Metrics/AbcSize
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private
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def setup_signal_handlers
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[:INT, :TERM].each do |sig|
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trap sig do
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stop
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end
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end
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end
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def logdev
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@logdev ||= app.verbose? ? STDERR : '/dev/null'
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end
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end
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end
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@@ -1 +1 @@
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1
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-
html{font-family:sans-serif;-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%}body{margin:0}article,aside,details,figcaption,figure,footer,header,hgroup,main,menu,nav,section,summary{display:block}audio,canvas,progress,video{display:inline-block;vertical-align:baseline}audio:not([controls]){display:none;height:0}[hidden],template{display:none}a{background-color:transparent}a:active,a:hover{outline:0}b,strong{font-weight:700}dfn{font-style:italic}h1{margin:.67em 0}mark{background:#ff0;color:#000}sub,sup{font-size:75%;line-height:0;position:relative;vertical-align:baseline}sup{top:-.5em}sub{bottom:-.25em}img{border:0}svg:not(:root){overflow:hidden}hr{-moz-box-sizing:content-box;-webkit-box-sizing:content-box;box-sizing:content-box;height:0}pre{overflow:auto}code,kbd,pre,samp{font-size:1em}button,input,optgroup,select,textarea{color:inherit;font:inherit;margin:0}button{overflow:visible}button,select{text-transform:none}button,html 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c=a.style,d=a.currentStyle,e=eb.isNumeric(b)?"alpha(opacity="+100*b+")":"",f=d&&d.filter||c.filter||"";c.zoom=1,(b>=1||""===b)&&""===eb.trim(f.replace(fc,""))&&c.removeAttribute&&(c.removeAttribute("filter"),""===b||d&&!d.filter)||(c.filter=fc.test(f)?f.replace(fc,e):f+" "+e)}}),eb.cssHooks.marginRight=A(cb.reliableMarginRight,function(a,b){return b?eb.swap(a,{display:"inline-block"},bc,[a,"marginRight"]):void 0}),eb.each({margin:"",padding:"",border:"Width"},function(a,b){eb.cssHooks[a+b]={expand:function(c){for(var d=0,e={},f="string"==typeof c?c.split(" "):[c];4>d;d++)e[a+Bb[d]+b]=f[d]||f[d-2]||f[0];return e}},cc.test(a)||(eb.cssHooks[a+b].set=D)}),eb.fn.extend({css:function(a,b){return Db(this,function(a,b,c){var d,e,f={},g=0;if(eb.isArray(b)){for(d=ac(a),e=b.length;e>g;g++)f[b[g]]=eb.css(a,b[g],!1,d);return f}return void 0!==c?eb.style(a,b,c):eb.css(a,b)},a,b,arguments.length>1)},show:function(){return C(this,!0)},hide:function(){return 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b=M(this,eb.extend({},a),f);(e||eb._data(this,"finish"))&&b.stop(!0)};return g.finish=g,e||f.queue===!1?this.each(g):this.queue(f.queue,g)},stop:function(a,b,c){var d=function(a){var b=a.stop;delete a.stop,b(c)};return"string"!=typeof a&&(c=b,b=a,a=void 0),b&&a!==!1&&this.queue(a||"fx",[]),this.each(function(){var b=!0,e=null!=a&&a+"queueHooks",f=eb.timers,g=eb._data(this);if(e)g[e]&&g[e].stop&&d(g[e]);else for(e in g)g[e]&&g[e].stop&&rc.test(e)&&d(g[e]);for(e=f.length;e--;)f[e].elem!==this||null!=a&&f[e].queue!==a||(f[e].anim.stop(c),b=!1,f.splice(e,1));(b||!c)&&eb.dequeue(this,a)})},finish:function(a){return a!==!1&&(a=a||"fx"),this.each(function(){var b,c=eb._data(this),d=c[a+"queue"],e=c[a+"queueHooks"],f=eb.timers,g=d?d.length:0;for(c.finish=!0,eb.queue(this,a,[]),e&&e.stop&&e.stop.call(this,!0),b=f.length;b--;)f[b].elem===this&&f[b].queue===a&&(f[b].anim.stop(!0),f.splice(b,1));for(b=0;g>b;b++)d[b]&&d[b].finish&&d[b].finish.call(this);delete c.finish})}}),eb.each(["toggle","show","hide"],function(a,b){var c=eb.fn[b];eb.fn[b]=function(a,d,e){return null==a||"boolean"==typeof a?c.apply(this,arguments):this.animate(I(b,!0),a,d,e)}}),eb.each({slideDown:I("show"),slideUp:I("hide"),slideToggle:I("toggle"),fadeIn:{opacity:"show"},fadeOut:{opacity:"hide"},fadeToggle:{opacity:"toggle"}},function(a,b){eb.fn[a]=function(a,c,d){return this.animate(b,a,c,d)}}),eb.timers=[],eb.fx.tick=function(){var a,b=eb.timers,c=0;for(nc=eb.now();c<b.length;c++)a=b[c],a()||b[c]!==a||b.splice(c--,1);b.length||eb.fx.stop(),nc=void 0},eb.fx.timer=function(a){eb.timers.push(a),a()?eb.fx.start():eb.timers.pop()},eb.fx.interval=13,eb.fx.start=function(){oc||(oc=setInterval(eb.fx.tick,eb.fx.interval))},eb.fx.stop=function(){clearInterval(oc),oc=null},eb.fx.speeds={slow:600,fast:200,_default:400},eb.fn.delay=function(a,b){return a=eb.fx?eb.fx.speeds[a]||a:a,b=b||"fx",this.queue(b,function(b,c){var d=setTimeout(b,a);c.stop=function(){clearTimeout(d)}})},function(){var a,b,c,d,e;b=ob.createElement("div"),b.setAttribute("className","t"),b.innerHTML=" <link/><table></table><a href='/a'>a</a><input type='checkbox'/>",d=b.getElementsByTagName("a")[0],c=ob.createElement("select"),e=c.appendChild(ob.createElement("option")),a=b.getElementsByTagName("input")[0],d.style.cssText="top:1px",cb.getSetAttribute="t"!==b.className,cb.style=/top/.test(d.getAttribute("style")),cb.hrefNormalized="/a"===d.getAttribute("href"),cb.checkOn=!!a.value,cb.optSelected=e.selected,cb.enctype=!!ob.createElement("form").enctype,c.disabled=!0,cb.optDisabled=!e.disabled,a=ob.createElement("input"),a.setAttribute("value",""),cb.input=""===a.getAttribute("value"),a.value="t",a.setAttribute("type","radio"),cb.radioValue="t"===a.value}();var uc=/\r/g;eb.fn.extend({val:function(a){var b,c,d,e=this[0];return arguments.length?(d=eb.isFunction(a),this.each(function(c){var e;1===this.nodeType&&(e=d?a.call(this,c,eb(this).val()):a,null==e?e="":"number"==typeof e?e+="":eb.isArray(e)&&(e=eb.map(e,function(a){return null==a?"":a+""})),b=eb.valHooks[this.type]||eb.valHooks[this.nodeName.toLowerCase()],b&&"set"in b&&void 0!==b.set(this,e,"value")||(this.value=e))})):e?(b=eb.valHooks[e.type]||eb.valHooks[e.nodeName.toLowerCase()],b&&"get"in b&&void 0!==(c=b.get(e,"value"))?c:(c=e.value,"string"==typeof c?c.replace(uc,""):null==c?"":c)):void 0}}),eb.extend({valHooks:{option:{get:function(a){var b=eb.find.attr(a,"value");return null!=b?b:eb.trim(eb.text(a))}},select:{get:function(a){for(var b,c,d=a.options,e=a.selectedIndex,f="select-one"===a.type||0>e,g=f?null:[],h=f?e+1:d.length,i=0>e?h:f?e:0;h>i;i++)if(c=d[i],!(!c.selected&&i!==e||(cb.optDisabled?c.disabled:null!==c.getAttribute("disabled"))||c.parentNode.disabled&&eb.nodeName(c.parentNode,"optgroup"))){if(b=eb(c).val(),f)return b;g.push(b)}return g},set:function(a,b){for(var c,d,e=a.options,f=eb.makeArray(b),g=e.length;g--;)if(d=e[g],eb.inArray(eb.valHooks.option.get(d),f)>=0)try{d.selected=c=!0}catch(h){d.scrollHeight}else d.selected=!1;return c||(a.selectedIndex=-1),e}}}}),eb.each(["radio","checkbox"],function(){eb.valHooks[this]={set:function(a,b){return eb.isArray(b)?a.checked=eb.inArray(eb(a).val(),b)>=0:void 0}},cb.checkOn||(eb.valHooks[this].get=function(a){return null===a.getAttribute("value")?"on":a.value})});var vc,wc,xc=eb.expr.attrHandle,yc=/^(?:checked|selected)$/i,zc=cb.getSetAttribute,Ac=cb.input;eb.fn.extend({attr:function(a,b){return Db(this,eb.attr,a,b,arguments.length>1)},removeAttr:function(a){return this.each(function(){eb.removeAttr(this,a)})}}),eb.extend({attr:function(a,b,c){var d,e,f=a.nodeType;return a&&3!==f&&8!==f&&2!==f?typeof a.getAttribute===xb?eb.prop(a,b,c):(1===f&&eb.isXMLDoc(a)||(b=b.toLowerCase(),d=eb.attrHooks[b]||(eb.expr.match.bool.test(b)?wc:vc)),void 0===c?d&&"get"in d&&null!==(e=d.get(a,b))?e:(e=eb.find.attr(a,b),null==e?void 0:e):null!==c?d&&"set"in d&&void 0!==(e=d.set(a,c,b))?e:(a.setAttribute(b,c+""),c):void eb.removeAttr(a,b)):void 0},removeAttr:function(a,b){var c,d,e=0,f=b&&b.match(tb);if(f&&1===a.nodeType)for(;c=f[e++];)d=eb.propFix[c]||c,eb.expr.match.bool.test(c)?Ac&&zc||!yc.test(c)?a[d]=!1:a[eb.camelCase("default-"+c)]=a[d]=!1:eb.attr(a,c,""),a.removeAttribute(zc?c:d)},attrHooks:{type:{set:function(a,b){if(!cb.radioValue&&"radio"===b&&eb.nodeName(a,"input")){var c=a.value;return a.setAttribute("type",b),c&&(a.value=c),b}}}}}),wc={set:function(a,b,c){return b===!1?eb.removeAttr(a,c):Ac&&zc||!yc.test(c)?a.setAttribute(!zc&&eb.propFix[c]||c,c):a[eb.camelCase("default-"+c)]=a[c]=!0,c}},eb.each(eb.expr.match.bool.source.match(/\w+/g),function(a,b){var c=xc[b]||eb.find.attr;xc[b]=Ac&&zc||!yc.test(b)?function(a,b,d){var e,f;return d||(f=xc[b],xc[b]=e,e=null!=c(a,b,d)?b.toLowerCase():null,xc[b]=f),e}:function(a,b,c){return c?void 0:a[eb.camelCase("default-"+b)]?b.toLowerCase():null}}),Ac&&zc||(eb.attrHooks.value={set:function(a,b,c){return eb.nodeName(a,"input")?void(a.defaultValue=b):vc&&vc.set(a,b,c)}}),zc||(vc={set:function(a,b,c){var d=a.getAttributeNode(c);return d||a.setAttributeNode(d=a.ownerDocument.createAttribute(c)),d.value=b+="","value"===c||b===a.getAttribute(c)?b:void 0}},xc.id=xc.name=xc.coords=function(a,b,c){var d;return c?void 0:(d=a.getAttributeNode(b))&&""!==d.value?d.value:null},eb.valHooks.button={get:function(a,b){var c=a.getAttributeNode(b);return c&&c.specified?c.value:void 0},set:vc.set},eb.attrHooks.contenteditable={set:function(a,b,c){vc.set(a,""===b?!1:b,c)}},eb.each(["width","height"],function(a,b){eb.attrHooks[b]={set:function(a,c){return""===c?(a.setAttribute(b,"auto"),c):void 0}}})),cb.style||(eb.attrHooks.style={get:function(a){return a.style.cssText||void 0},set:function(a,b){return a.style.cssText=b+""}});var Bc=/^(?:input|select|textarea|button|object)$/i,Cc=/^(?:a|area)$/i;eb.fn.extend({prop:function(a,b){return Db(this,eb.prop,a,b,arguments.length>1)},removeProp:function(a){return a=eb.propFix[a]||a,this.each(function(){try{this[a]=void 0,delete this[a]}catch(b){}})}}),eb.extend({propFix:{"for":"htmlFor","class":"className"},prop:function(a,b,c){var d,e,f,g=a.nodeType;return a&&3!==g&&8!==g&&2!==g?(f=1!==g||!eb.isXMLDoc(a),f&&(b=eb.propFix[b]||b,e=eb.propHooks[b]),void 0!==c?e&&"set"in e&&void 0!==(d=e.set(a,c,b))?d:a[b]=c:e&&"get"in e&&null!==(d=e.get(a,b))?d:a[b]):void 0},propHooks:{tabIndex:{get:function(a){var b=eb.find.attr(a,"tabindex");return b?parseInt(b,10):Bc.test(a.nodeName)||Cc.test(a.nodeName)&&a.href?0:-1}}}}),cb.hrefNormalized||eb.each(["href","src"],function(a,b){eb.propHooks[b]={get:function(a){return a.getAttribute(b,4)}}}),cb.optSelected||(eb.propHooks.selected={get:function(a){var b=a.parentNode;return b&&(b.selectedIndex,b.parentNode&&b.parentNode.selectedIndex),null}}),eb.each(["tabIndex","readOnly","maxLength","cellSpacing","cellPadding","rowSpan","colSpan","useMap","frameBorder","contentEditable"],function(){eb.propFix[this.toLowerCase()]=this}),cb.enctype||(eb.propFix.enctype="encoding");var Dc=/[\t\r\n\f]/g;eb.fn.extend({addClass:function(a){var b,c,d,e,f,g,h=0,i=this.length,j="string"==typeof a&&a;if(eb.isFunction(a))return this.each(function(b){eb(this).addClass(a.call(this,b,this.className))});if(j)for(b=(a||"").match(tb)||[];i>h;h++)if(c=this[h],d=1===c.nodeType&&(c.className?(" "+c.className+" ").replace(Dc," "):" ")){for(f=0;e=b[f++];)d.indexOf(" "+e+" ")<0&&(d+=e+" ");g=eb.trim(d),c.className!==g&&(c.className=g)}return this},removeClass:function(a){var b,c,d,e,f,g,h=0,i=this.length,j=0===arguments.length||"string"==typeof a&&a;
|
|
4
|
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d&&null!==(e=d.get(a,b))?e:(e=ea.find.attr(a,b),null==e?void 0:e):null!==c?d&&"set"in d&&void 0!==(e=d.set(a,c,b))?e:(a.setAttribute(b,c+""),c):void ea.removeAttr(a,b)):void 0},removeAttr:function(a,b){var c,d,e=0,f=b&&b.match(ta);if(f&&1===a.nodeType)for(;c=f[e++];)d=ea.propFix[c]||c,ea.expr.match.bool.test(c)?Ab&&zb||!yb.test(c)?a[d]=!1:a[ea.camelCase("default-"+c)]=a[d]=!1:ea.attr(a,c,""),a.removeAttribute(zb?c:d)},attrHooks:{type:{set:function(a,b){if(!ca.radioValue&&"radio"===b&&ea.nodeName(a,"input")){var c=a.value;return a.setAttribute("type",b),c&&(a.value=c),b}}}}}),wb={set:function(a,b,c){return b===!1?ea.removeAttr(a,c):Ab&&zb||!yb.test(c)?a.setAttribute(!zb&&ea.propFix[c]||c,c):a[ea.camelCase("default-"+c)]=a[c]=!0,c}},ea.each(ea.expr.match.bool.source.match(/\w+/g),function(a,b){var c=xb[b]||ea.find.attr;xb[b]=Ab&&zb||!yb.test(b)?function(a,b,d){var e,f;return d||(f=xb[b],xb[b]=e,e=null!=c(a,b,d)?b.toLowerCase():null,xb[b]=f),e}:function(a,b,c){return c?void 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|
5
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+
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|
6
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+
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7
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+
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5
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|
|
9
|
+
|
|
10
|
+
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hits."}),b.disable().removeAttr("href")},SS.updateDownloadFastaOfSelectedLink=function(){var a=$(".hitn :checkbox:checked").length,b=$(".download-fasta-of-selected"),c=b.find("span");if(a>=1&&30>=a){var d=$(".hitn :checkbox:checked").map(function(){return this.value}).get();return void b.enable().attr("href",SS.generateURI(d,b.data().databases)).tooltip({title:a+" hit(s) selected."}).find("span").html(a)}0===a&&(c.empty(),b.tooltip({title:"No hit selected."})),a>30&&b.tooltip({title:"Can't download more than 30 hits."}),b.disable().removeAttr("href")},SS.updateSequenceViewerLinks=function(){var a=1e4;$(".view-sequence").each(function(){var b=$(this),c=b.closest(".hitn");c.data().hitLen>a&&b.disable().removeAttr("href").tooltip({title:"Sequence too long to show. Please view it locally after download."})})},SS.setupTooltips=function(){$(".pos-label").each(function(){$(this).tooltip({placement:"right"})}),$(".downloads a").each(function(){$(this).tooltip()})},SS.setupDownloadLinks=function(){$(".download").on("click",function(a){if(a.preventDefault(),a.stopPropagation(),!a.target.disabled){var b=this.href;$.get(b).done(function(){window.location.href=b}).fail(function(a){SS.showErrorModal(a,function(){})})}})},SS.generateURI=function(a,b){a=encodeURIComponent(a.join(" ")),b=encodeURIComponent(b);var c="get_sequence/?sequence_ids="+a+"&database_ids="+b+"&download=fasta";return c},SS.showErrorModal=function(a,b){setTimeout(function(){b(),a.responseText?$("#error").html(a.responseText).modal():$("#error-no-response").modal()},500)},SS.init=function(){this.$sequence=$("#sequence"),this.$sequenceFile=$("#sequence-file"),this.$sequenceControls=$(".sequence-controls"),SS.blast.init()}}(),SS.selectHit=function(a){if(a&&a.value){var b=$($(a).data("target"));a.checked?b.addClass("glow").find(":checkbox").not(a).check():b.removeClass("glow").find(":checkbox").not(a).uncheck(),this.updateDownloadFastaOfSelectedLink()}},SS.showSequenceViewer=function(){var a=$("#sequence-viewer"),b=$(".spinner",a),c=$(".modal-body",a),d=$(".modal-footer",a),e="biojs-vis-sequence",f=function(e){c.empty(),d.empty(),g(e),b.show(),a.modal("show")},g=function(a){var b=a.parent().clone(),c=b.find(".view-sequence"),e=$(c[0].nextSibling);c.remove(),e.remove(),d.empty().append(b)},h=function(a,b){a.forEach(j),b.forEach(i)},i=function(a){var b=a.id+"<small> "+a.title+"</small>",d=e+(new Date).getUTCMilliseconds();c.append($("<div/>").addClass("fastan").append($("<div/>").addClass("page-header").append($("<h4/>").html(b)),$("<div/>").attr("id",d).addClass(e).addClass("page-content")));var f=new Sequence({sequence:a.value,target:d,format:"PRIDE",columns:{size:40,spacedEach:5},formatOptions:{title:!1,footer:!1}});f.hideFormatSelector()},j=function(a){c.append($("<div/>").addClass("page-header").append($("<h4/>").html(a[0])),$("<div/>").addClass("page-content").append($("<pre/>").addClass("pre-reset").html(a[1])),$("<br>"))};return function(c){var d=$(c);f(d);var e=d.attr("href");$.getJSON(e).done(function(a){h(a.error_msgs,a.sequences),b.hide()}).fail(function(b){SS.showErrorModal(b,function(){a.modal("hide")})})}}(),$(document).ready(function(){SS.init();var a,b=$(".dnd-overlay"),c=$("#sequence"),d=function(a){$(".dnd-error").hide(),$("#"+a+"-notification").show(),b.effect("fade",2500)};$(document).on("dragenter",function(a){if(!$.modalActive){var d=a.originalEvent.dataTransfer,e=d.types&&(d.types.indexOf&&-1!=d.types.indexOf("Files")||d.types.contains&&d.types.contains("application/x-moz-file"));e&&($(".dnd-error").hide(),b.stop(!0,!0),b.show(),d.effectAllowed="copy",""===c.val()?($(".dnd-overlay-overwrite").hide(),$(".dnd-overlay-drop").show("drop",{direction:"down"},"fast")):($(".dnd-overlay-drop").hide(),$(".dnd-overlay-overwrite").show("drop",{direction:"down"},"fast")))}}).on("dragleave",".dnd-overlay",function(){b.hide(),$(".dnd-overlay-drop").hide(),$(".dnd-overlay-overwrite").hide()}).on("dragover",".dnd-overlay",function(a){a.originalEvent.dataTransfer.dropEffect="copy",a.preventDefault()}).on("drop",".dnd-overlay",function(a){a.preventDefault(),a.stopPropagation();var c=$("#sequence"),e=$("#sequence-file");c.focus();var f=a.originalEvent.dataTransfer.files;if(f.length>1)return void d("dnd-multi");var g=f[0];if(g.size>10485760)return void d("dnd-large-file");var h=new FileReader;h.onload=function(a){var f=a.target.result;SS.FASTA_FORMAT.test(f)?(c.val(f),e.text(g.name),b.hide()):d("dnd-format")},h.onerror=function(){d("dnd-format")},h.readAsText(g)}),SS.$sequence.change(function(){if(SS.$sequence.val()){var a=SS.$sequence[0].offsetWidth-SS.$sequence[0].clientWidth;SS.$sequenceControls.css("right",a+17),SS.$sequenceControls.removeClass("hidden")}else SS.$sequenceFile.empty(),SS.$sequenceControls.addClass("hidden"),SS.$sequence.parent().removeClass("has-error")}),$("#btn-sequence-clear").click(function(){$("#sequence").val("").focus()}),SS.onedb(),$("#methods").tooltip({title:function(){var a=$(".databases input:checkbox:checked");return 0===a.length?"You must select one or more databases above before you can run a search!":void 0}}),$("#method").tooltip({title:function(){var a="Click to BLAST or press Ctrl+Enter.";return 0!==$(this).siblings().length&&(a+=" Click dropdown button on the right for other BLAST algorithms that can be used."),a},delay:{show:1e3,hide:0}}),$(document).bind("keydown",function(a){a.ctrlKey&&13===a.keyCode&&!$("#method").is(":disabled")&&$("#method").trigger("submit")}),$("#sequence").on("sequence_type_changed",function(b,c){clearTimeout(a),$(this).parent().removeClass("has-error"),$(".notifications .active").hide().removeClass("active"),c&&($("#"+c+"-sequence-notification").show("drop",{direction:"up"}).addClass("active"),a=setTimeout(function(){$(".notifications .active").hide("drop",{direction:"up"}).removeClass("active")},5e3),"mixed"===c&&$(this).parent().addClass("has-error"))}),$("body").click(function(){$(".notifications .active").hide("drop",{direction:"up"}).removeClass("active")}),$(".databases").on("database_type_changed",function(a,b){switch(b){case"protein":$(".databases.nucleotide input:checkbox").disable(),$(".databases.nucleotide .checkbox").addClass("disabled");break;case"nucleotide":$(".databases.protein input:checkbox").disable(),$(".databases.protein .checkbox").addClass("disabled");break;default:$(".databases input:checkbox").enable(),$(".databases .checkbox").removeClass("disabled")}}),$("form").on("blast_method_changed",function(a,b){if($("#method").disable().val("").html("blast"),$("#methods").removeClass("input-group").children().not("#method").remove(),b.length>0){var c=b.shift();$("#method").enable().val(c).html(SS.decorate(c)),b.length>=1&&$("#methods").addClass("input-group").append($("<div/>").addClass("input-group-btn").append($("<button/>").attr("type","button").addClass("btn btn-primary dropdown-toggle").attr("data-toggle","dropdown").append($("<span/>").addClass("caret")),$("<ul/>").addClass("dropdown-menu dropdown-menu-right").append($.map(b,function(a){return $("<li/>").html(SS.decorate(a))})))),$("#methods").wiggle()}}),$(document).on("click","#methods .dropdown-menu li",function(){var a=$(this),b=$("#method"),c=b.text(),d=a.text();a.html(SS.decorate(c)),b.val(d).html(SS.decorate(d)),$("#methods").wiggle()}),$(".result").on("mousedown",".hitn > .page-header > h4",function(){var a=$(this);a.on("mouseup mousemove",function b(c){"mouseup"===c.type?(a.attr("data-toggle","collapse"),a.find(".fa-chevron-down").toggleClass("fa-rotate-270")):a.attr("data-toggle",""),a.off("mouseup mousemove",b)})}),$(".result").on("click",".view-sequence",function(a){a.preventDefault(),a.stopPropagation(),a.target.disabled||SS.showSequenceViewer(a.target)}),$(document).on("change",".hitn :checkbox",function(a){a.stopPropagation(),SS.selectHit(this)}),$("#blast").submit(function(){var a=$(this).attr("action"),b=a.indexOf("#"),c=a.slice(0,b),d=a.slice(b,a.length);location.hash="",$("#spinner").modal();var e=$(this).serialize()+"&method="+$("#method").val();return $.post(c,e).done(function(a){$(".result").html(a).show();var b=$(".sidebar");0!==b.length&&b.affix({offset:{top:b.offset().top}}).width(b.width()),location.hash=d,SS.generateGraphicalOverview(),SS.updateDownloadFastaOfAllLink(),SS.updateDownloadFastaOfSelectedLink(),SS.updateSequenceViewerLinks(),SS.setupTooltips(),SS.setupDownloadLinks(),$("body").scrollspy({target:".sidebar"}),$("#spinner").modal("hide")}).fail(function(a){SS.showErrorModal(a,function(){$("#spinner").modal("hide")})}),!1}),SS.$sequence.poll()}),function(a){var b=function(){a('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true","white-space":"nowrap"})},c=function(b){a("a",b).click(function(b){b.preventDefault(),b.stopPropagation(),window.location.hash=a(this).attr("href")})},d=function(b,c,d,e){var f=a(window).width(),g=_.debounce(function(){if(f!==a(window).width()){var g=b.find(".ghit > g").length;a.graphIt(b,c,g,d,e),f=a(window).width()}},125);a(window).resize(g)},e=function(c,d,e){var f,g,h,i,j=20,k=function(){f=c.data().hitCount,g=c.find(".ghit > g").length},l=function(b,c){c.append(a("<button/>").addClass("btn btn-link more").attr("type","button").attr("data-parent-query",b.attr("id")).html("View More ").append(a("<i/>").addClass("fa fa-angle-double-down")),a("<button/>").addClass("btn btn-link less").attr("type","button").attr("data-parent-query",b.attr("id")).html("View Less ").append(a("<i/>").addClass("fa fa-angle-double-up"))),h=a(".less",c),i=a(".more",c)},m=function(){k(),f===j||j>g?(h.hide(),i.hide()):g===f?(i.hide(),h.show()):g===j?(h.hide(),i.show()):(h.show(),i.show())};e===!0&&(l(c,d),m()),i.on("click",function(e){k(),a.graphIt(c,d,g,j),m(),b(),e.stopPropagation()}),h.on("click",function(e){k();var f=g-j;f>=j?(a.graphIt(c,d,g,-j),m()):0!==f&&(a.graphIt(c,d,g,j-g),m()),b(),e.stopPropagation()})},f=function(b,c,d){var e,f=[];return e=b.find(".hitn").slice(0,c+d),e.map(function(){var b=a(this),c=[];b.find(".hsp").each(function(){var b=[];b=a(this).data(),b.hspId=this.id,c.push(b)}),c.hitId=b.attr("id"),c.hitDef=b.data().hitDef,c.hitEvalue=b.data().hitEvalue,f.push(c)}),f},g=function(a,b,c,d){var e=a.append("g").attr("transform","translate(0,"+(d-b.margin-1.25*b.legend)+")");e.append("rect").attr("x",7*(c-2*b.margin)/10).attr("width",2*(c-4*b.margin)/10).attr("height",b.legend).attr("fill","url(#legend-grad)"),e.append("text").attr("transform","translate(0, "+b.legend+")").attr("x",6*(c-2*b.margin)/10-b.margin/2).text("Weaker hits"),e.append("text").attr("transform","translate(0, "+b.legend+")").attr("x",9*(c-2*b.margin)/10+b.margin/2).text("Stronger hits"),a.append("linearGradient").attr("id","legend-grad").selectAll("stop").data([{offset:"0%",color:"#ccc"},{offset:"50%",color:"#888"},{offset:"100%",color:"#000"}]).enter().append("stop").attr("offset",function(a){return a.offset}).attr("stop-color",function(a){return a.color})};a.extend({graphIt:function(h,i,j,k,l){var m={barHeight:4,barPadding:5,legend:10,margin:20},n=a.extend(m,l),o=f(h,j,k);if(o.length<1)return!1;0!==j&&i.find("svg").remove();var p=h.data().queryLen,q=h.attr("id"),r=i.width(),s=o.length*(n.barHeight+n.barPadding)+5*n.margin+3*n.legend,t=d3.select(i[0]).selectAll("svg").data([o]).enter().insert("svg",":first-child").attr("width",r).attr("height",s).append("g").attr("transform","translate("+n.margin/4+", "+n.margin/4+")"),u=d3.scale.linear().range([0,r-n.margin]);u.domain([1,p]);var v=u.ticks(11);v.pop();var w=d3.svg.axis().scale(u).orient("top").tickValues(v.concat([1,p]));t.append("g").attr("transform","translate(0, "+n.margin+")").append("g").attr("class","x axis").call(w);var x=d3.scale.ordinal().rangeBands([0,s-3*n.margin-2*n.legend],.3);x.domain(o.map(function(a){return a.hitId}));var y=d3.scale.log().domain([d3.min([1e-5,d3.min(o.map(function(a){return 0===parseFloat(a.hitEvalue)?void 0:a.hitEvalue}))]),d3.max(o.map(function(a){return a.hitEvalue}))]).range([40,150]);t.append("g").attr("class","ghit").attr("transform","translate(0, "+(2*n.margin-n.legend)+")").selectAll(".hits").data(o).enter().append("g").attr("data-toggle","tooltip").attr("title",function(a){var b=/(\d*\.\d*)e?([+-]\d*)?/,c=b.exec(a.hitEvalue),d=parseFloat(c[1]).toFixed(3),e=a.hitDef+"<br><strong>E value:</strong> "+d;return void 0!==c[2]&&(e+=" × 10<sup>"+c[2]+"</sup>"),e}).each(function(a,b){var c=b+1,d=a,e=a.hitId,f=a.length;d3.select(this).selectAll(".hsp").data(a).enter().append("a").each(function(a,b){var g=x(e)+n.barHeight/2,h=d3.rgb(y(d.hitEvalue),y(d.hitEvalue),y(d.hitEvalue));f>b+1&&(d[b].hspEnd<=d[b+1].hspStart?d3.select(this.parentNode).append("line").attr("x1",u(d[b].hspEnd)).attr("y1",g).attr("x2",u(d[b+1].hspStart)).attr("y2",g).attr("stroke",h):d[b].hspStart>d[b+1].hspEnd&&d3.select(this.parentNode).append("line").attr("x1",u(d[b+1].hspEnd)).attr("y1",g).attr("x2",u(d[b].hspStart)).attr("y2",g).attr("stroke",h)),d3.select(this).attr("xlink:href","#"+q+"_hit_"+c).append("rect").attr("x",function(a){return u(a.hspStart)}).attr("y",x(e)).attr("width",function(a){return u(a.hspEnd-a.hspStart+1)}).attr("height",n.barHeight).attr("fill",d3.rgb(h))})}),o.length>1&&g(t,n,r,s),0===j&&(e(h,i,!0),d(h,i,j,l)),b(),c(i)}})}(jQuery),SS.blast=function(){var a=function(a){if(a=a.replace(/[^A-Z]/gi,""),a=a.replace(/[NX]/gi,""),a.length<10)return void 0;var b,c,d;for(b=0,c=.9*a.length,d=0;d<a.length;d++)a[d].match(/[ACGTU]/i)&&(b+=1);return b>c?"nucleotide":"protein"},b=function(){var b,c,d,e=$("#sequence").val().split(/>.*/);for(d=0;d<e.length;d++)if(c=a(e[d]))if(b){if(c!==b)return"mixed"}else b=c;return b},c=function(){return $(".databases input:checked").data("type")},d=function(){return $("#sequence").val()&&$(".databases input:checked").val()?!0:!1},e=function(){var a,c;$("#sequence").change(function(){c=b(),c&&c===a||(a=c,$(this).trigger("sequence_type_changed",a))})},f=function(){var a,b=c();$(".databases input").change(function(){a=c(),a!=b&&(b=a,$(this).trigger("database_type_changed",b))})},g=function(){var a,b;$("#blast").on("sequence_type_changed database_type_changed",function(){b=h(),_.isEqual(b,a)||(a=b,$(this).trigger("blast_method_changed",[a.slice()]))})},h=function(){if(!d())return[];var a=c(),e=b();switch(a){case"protein":switch(e){case void 0:return["blastp","blastx"];case"protein":return["blastp"];case"nucleotide":return["blastx"]}break;case"nucleotide":switch(e){case void 0:return["tblastn","blastn","tblastx"];case"protein":return["tblastn"];case"nucleotide":return["blastn","tblastx"]}}return[]},i=function(){return void 0};return i.init=function(){e(),f(),g()},i}();
|
|
Binary file
|
data/public/js/jquery.t.js
CHANGED
|
@@ -16,6 +16,18 @@
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|
|
16
16
|
});
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|
17
17
|
};
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|
18
18
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|
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19
|
+
var setupResponsiveness = function ($queryDiv, $graphDiv, index, opts) {
|
|
20
|
+
var currentWidth = $(window).width();
|
|
21
|
+
var debounced_draw = _.debounce(function () {
|
|
22
|
+
if (currentWidth !== $(window).width()) {
|
|
23
|
+
var shownHits = $queryDiv.find('.ghit > g').length;
|
|
24
|
+
$.graphIt($queryDiv, $graphDiv, shownHits, index, opts);
|
|
25
|
+
currentWidth = $(window).width();
|
|
26
|
+
}
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|
27
|
+
}, 125);
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|
28
|
+
$(window).resize(debounced_draw);
|
|
29
|
+
};
|
|
30
|
+
|
|
19
31
|
var graphControls = function ($queryDiv, $graphDiv, isInit) {
|
|
20
32
|
var MIN_HITS_TO_SHOW = 20;
|
|
21
33
|
|
|
@@ -342,6 +354,8 @@
|
|
|
342
354
|
// been drawn for first time.
|
|
343
355
|
if (index === 0) {
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|
344
356
|
graphControls($queryDiv, $graphDiv, true);
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|
357
|
+
// Redraw the SVG on a browser resize...
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|
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|
+
setupResponsiveness($queryDiv, $graphDiv, index, opts);
|
|
345
359
|
}
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360
|
// Refresh tooltip each time graph is redrawn.
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361
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setupTooltip();
|
data/sequenceserver.gemspec
CHANGED
|
@@ -17,7 +17,6 @@ interface for use locally or over the web.
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|
|
17
17
|
DESC
|
|
18
18
|
|
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19
19
|
# dependencies
|
|
20
|
-
s.add_dependency('thin', '~> 1.6', '>= 1.6.2')
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|
21
20
|
s.add_dependency('sinatra', '~> 1.4', '>= 1.4.5')
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|
22
21
|
s.add_dependency('json', '~> 1.8', '>= 1.8.2')
|
|
23
22
|
s.add_dependency('ox', '~> 2.1', '>= 2.1.1')
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: sequenceserver
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 1.0.
|
|
4
|
+
version: 1.0.2
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Anurag Priyam
|
|
@@ -11,28 +11,8 @@ authors:
|
|
|
11
11
|
autorequire:
|
|
12
12
|
bindir: bin
|
|
13
13
|
cert_chain: []
|
|
14
|
-
date: 2015-03-
|
|
14
|
+
date: 2015-03-23 00:00:00.000000000 Z
|
|
15
15
|
dependencies:
|
|
16
|
-
- !ruby/object:Gem::Dependency
|
|
17
|
-
name: thin
|
|
18
|
-
requirement: !ruby/object:Gem::Requirement
|
|
19
|
-
requirements:
|
|
20
|
-
- - "~>"
|
|
21
|
-
- !ruby/object:Gem::Version
|
|
22
|
-
version: '1.6'
|
|
23
|
-
- - ">="
|
|
24
|
-
- !ruby/object:Gem::Version
|
|
25
|
-
version: 1.6.2
|
|
26
|
-
type: :runtime
|
|
27
|
-
prerelease: false
|
|
28
|
-
version_requirements: !ruby/object:Gem::Requirement
|
|
29
|
-
requirements:
|
|
30
|
-
- - "~>"
|
|
31
|
-
- !ruby/object:Gem::Version
|
|
32
|
-
version: '1.6'
|
|
33
|
-
- - ">="
|
|
34
|
-
- !ruby/object:Gem::Version
|
|
35
|
-
version: 1.6.2
|
|
36
16
|
- !ruby/object:Gem::Dependency
|
|
37
17
|
name: sinatra
|
|
38
18
|
requirement: !ruby/object:Gem::Requirement
|
|
@@ -298,6 +278,7 @@ files:
|
|
|
298
278
|
- lib/sequenceserver/routes.rb
|
|
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279
|
- lib/sequenceserver/search.rb
|
|
300
280
|
- lib/sequenceserver/sequence.rb
|
|
281
|
+
- lib/sequenceserver/server.rb
|
|
301
282
|
- lib/sequenceserver/version.rb
|
|
302
283
|
- package.json
|
|
303
284
|
- public/css/bootstrap.min.css
|