sequenceserver 1.0.4 → 1.0.5

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Files changed (12) hide show
  1. checksums.yaml +4 -4
  2. data/Rakefile +18 -5
  3. data/lib/sequenceserver/blast/formatter.rb +3 -1
  4. data/lib/sequenceserver/version.rb +1 -1
  5. data/package.json +1 -1
  6. data/public/css/custom.css +1 -0
  7. data/public/dist/css/sequenceserver.min.css +1 -1
  8. data/public/dist/css/sequenceserver.min.css.gz +0 -0
  9. data/public/dist/js/sequenceserver.min.js +6 -12
  10. data/public/dist/js/sequenceserver.min.js.gz +0 -0
  11. data/sequenceserver.gemspec +4 -4
  12. metadata +4 -5
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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- metadata.gz: 9040c6020c1e07fdb573d72393de66c9db7fc48c
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- data.tar.gz: 6d42a977fd1d4a26528f60738b35c3155eb65c12
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+ metadata.gz: 71f03465e5e74fa9f0b75b6e4efe48973c9e2106
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+ data.tar.gz: 1536896d54e1c0e4d162b0733bd122c02f801a5e
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  SHA512:
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- metadata.gz: 5f23f8d52e26144ce797c833bcad02bb278da705aae2c6acd58d857973895c4845287d5b2fd2010ba1cd661f15a38a59437713a4fb2f8ee5dcba145d83767c26
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- data.tar.gz: d0d705074535ea97e6935e4e098aade727dad62b3aa641b3028da10309c959eb0b3a7726dfa02ec4f427b1317f42a23bb30eefbf24f24aad86523c92abe52b3e
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+ metadata.gz: 36b4279bdb6d19a33bed61906523039f87244a920fa0d2c57e6390cb7d1d734b6c8e69efa5c2fa261b4e0a54809170e99a53dc296d03c2c0a7f73bf941911d43
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+ data.tar.gz: 5e234b68af3b53b5c42c4c06ce59e666e79e638448210b73295ec3e363fb06c239fc88882ff88ede20d38651f375270e6bf8667e98f2be5b7fa7561998372cc5
data/Rakefile CHANGED
@@ -2,12 +2,25 @@ require 'rspec/core'
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  require 'rspec/core/rake_task'
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  require 'rubocop/rake_task'
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- desc 'Run RuboCop to generate HTML report'
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- RuboCop::RakeTask.new :rubocop
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-
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- desc 'Run main spec testing task'
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+ desc 'Run specs'
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  RSpec::Core::RakeTask.new(:spec) do |spec|
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  spec.pattern = FileList['spec/**/*_spec.rb']
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  end
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- task :default => [:spec, :rubocop]
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+ desc 'Run RuboCop'
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+ RuboCop::RakeTask.new :rubocop
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+
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+ desc 'Run GruntCop (bootlint, csslint, jshint)'
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+ task :gruntcop do
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+ system 'npm run-script cop'
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+ end
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+
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+ desc 'Run all cops'
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+ task :cop => [:rubocop, :gruntcop]
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+
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+ desc 'Concatenate and minify JS & CSS'
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+ task :build do
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+ system 'npm run-script build'
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+ end
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+
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+ task :default => [:spec, :cop, :build]
data/lib/sequenceserver/blast/formatter.rb CHANGED
@@ -41,7 +41,9 @@ module SequenceServer
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  " -outfmt '#{format} #{specifiers}'" \
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  " -out '#{file.path}' 2> /dev/null"
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  logger.debug("Executing: #{command}")
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- system(command, :chdir => (File.exist?(DOTDIR) && DOTDIR || Dir.pwd))
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+ Dir.chdir(File.exist?(DOTDIR) && DOTDIR || Dir.pwd) do
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+ system(command)
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+ end
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  end
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  def validate
data/lib/sequenceserver/version.rb CHANGED
@@ -1,4 +1,4 @@
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  # Define version number.
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  module SequenceServer
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- VERSION = '1.0.4'
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+ VERSION = '1.0.5'
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  end
data/package.json CHANGED
@@ -1,7 +1,7 @@
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  {
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  "name": "SequenceServer",
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  "description": "BLAST searching made easy!",
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- "version": "1.0.0-2",
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+ "version": "1.0.5",
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  "homepage": "http://www.sequenceserver.com",
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  "repository": "https://github.com/yannickwurm/sequenceserver",
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  "author": {
data/public/css/custom.css CHANGED
@@ -8,6 +8,7 @@
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  body {
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  font-size: 13px;
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  position: relative;
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+ font-family: "Open Sans","Helvetica Neue",Helvetica,Arial,sans-serif;
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  }
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  /**
data/public/dist/css/sequenceserver.min.css CHANGED
@@ -1 +1 @@
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c=a.style,d=a.currentStyle,e=ea.isNumeric(b)?"alpha(opacity="+100*b+")":"",f=d&&d.filter||c.filter||"";c.zoom=1,(b>=1||""===b)&&""===ea.trim(f.replace(fb,""))&&c.removeAttribute&&(c.removeAttribute("filter"),""===b||d&&!d.filter)||(c.filter=fb.test(f)?f.replace(fb,e):f+" "+e)}}),ea.cssHooks.marginRight=A(ca.reliableMarginRight,function(a,b){return b?ea.swap(a,{display:"inline-block"},bb,[a,"marginRight"]):void 0}),ea.each({margin:"",padding:"",border:"Width"},function(a,b){ea.cssHooks[a+b]={expand:function(c){for(var d=0,e={},f="string"==typeof c?c.split(" "):[c];4>d;d++)e[a+Ba[d]+b]=f[d]||f[d-2]||f[0];return e}},cb.test(a)||(ea.cssHooks[a+b].set=D)}),ea.fn.extend({css:function(a,b){return Da(this,function(a,b,c){var d,e,f={},g=0;if(ea.isArray(b)){for(d=ab(a),e=b.length;e>g;g++)f[b[g]]=ea.css(a,b[g],!1,d);return f}return void 0!==c?ea.style(a,b,c):ea.css(a,b)},a,b,arguments.length>1)},show:function(){return C(this,!0)},hide:function(){return 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c.finish})}}),ea.each(["toggle","show","hide"],function(a,b){var c=ea.fn[b];ea.fn[b]=function(a,d,e){return null==a||"boolean"==typeof a?c.apply(this,arguments):this.animate(I(b,!0),a,d,e)}}),ea.each({slideDown:I("show"),slideUp:I("hide"),slideToggle:I("toggle"),fadeIn:{opacity:"show"},fadeOut:{opacity:"hide"},fadeToggle:{opacity:"toggle"}},function(a,b){ea.fn[a]=function(a,c,d){return this.animate(b,a,c,d)}}),ea.timers=[],ea.fx.tick=function(){var a,b=ea.timers,c=0;for(nb=ea.now();c<b.length;c++)a=b[c],a()||b[c]!==a||b.splice(c--,1);b.length||ea.fx.stop(),nb=void 0},ea.fx.timer=function(a){ea.timers.push(a),a()?ea.fx.start():ea.timers.pop()},ea.fx.interval=13,ea.fx.start=function(){ob||(ob=setInterval(ea.fx.tick,ea.fx.interval))},ea.fx.stop=function(){clearInterval(ob),ob=null},ea.fx.speeds={slow:600,fast:200,_default:400},ea.fn.delay=function(a,b){return a=ea.fx?ea.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=oa.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=oa.createElement("select"),e=c.appendChild(oa.createElement("option")),a=b.getElementsByTagName("input")[0],d.style.cssText="top:1px",ca.getSetAttribute="t"!==b.className,ca.style=/top/.test(d.getAttribute("style")),ca.hrefNormalized="/a"===d.getAttribute("href"),ca.checkOn=!!a.value,ca.optSelected=e.selected,ca.enctype=!!oa.createElement("form").enctype,c.disabled=!0,ca.optDisabled=!e.disabled,a=oa.createElement("input"),a.setAttribute("value",""),ca.input=""===a.getAttribute("value"),a.value="t",a.setAttribute("type","radio"),ca.radioValue="t"===a.value}();var ub=/\r/g;ea.fn.extend({val:function(a){var b,c,d,e=this[0];return arguments.length?(d=ea.isFunction(a),this.each(function(c){var e;1===this.nodeType&&(e=d?a.call(this,c,ea(this).val()):a,null==e?e="":"number"==typeof e?e+="":ea.isArray(e)&&(e=ea.map(e,function(a){return null==a?"":a+""})),b=ea.valHooks[this.type]||ea.valHooks[this.nodeName.toLowerCase()],b&&"set"in b&&void 0!==b.set(this,e,"value")||(this.value=e))})):e?(b=ea.valHooks[e.type]||ea.valHooks[e.nodeName.toLowerCase()],b&&"get"in b&&void 0!==(c=b.get(e,"value"))?c:(c=e.value,"string"==typeof c?c.replace(ub,""):null==c?"":c)):void 0}}),ea.extend({valHooks:{option:{get:function(a){var b=ea.find.attr(a,"value");return null!=b?b:ea.trim(ea.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||(ca.optDisabled?c.disabled:null!==c.getAttribute("disabled"))||c.parentNode.disabled&&ea.nodeName(c.parentNode,"optgroup"))){if(b=ea(c).val(),f)return b;g.push(b)}return g},set:function(a,b){for(var c,d,e=a.options,f=ea.makeArray(b),g=e.length;g--;)if(d=e[g],ea.inArray(ea.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}}}}),ea.each(["radio","checkbox"],function(){ea.valHooks[this]={set:function(a,b){return ea.isArray(b)?a.checked=ea.inArray(ea(a).val(),b)>=0:void 0}},ca.checkOn||(ea.valHooks[this].get=function(a){return null===a.getAttribute("value")?"on":a.value})});var vb,wb,xb=ea.expr.attrHandle,yb=/^(?:checked|selected)$/i,zb=ca.getSetAttribute,Ab=ca.input;ea.fn.extend({attr:function(a,b){return Da(this,ea.attr,a,b,arguments.length>1)},removeAttr:function(a){return this.each(function(){ea.removeAttr(this,a)})}}),ea.extend({attr:function(a,b,c){var d,e,f=a.nodeType;return a&&3!==f&&8!==f&&2!==f?typeof a.getAttribute===xa?ea.prop(a,b,c):(1===f&&ea.isXMLDoc(a)||(b=b.toLowerCase(),d=ea.attrHooks[b]||(ea.expr.match.bool.test(b)?wb:vb)),void 0===c?d&&"get"in 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 0:a[ea.camelCase("default-"+b)]?b.toLowerCase():null}}),Ab&&zb||(ea.attrHooks.value={set:function(a,b,c){return ea.nodeName(a,"input")?void(a.defaultValue=b):vb&&vb.set(a,b,c)}}),zb||(vb={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}},xb.id=xb.name=xb.coords=function(a,b,c){var d;return c?void 0:(d=a.getAttributeNode(b))&&""!==d.value?d.value:null},ea.valHooks.button={get:function(a,b){var c=a.getAttributeNode(b);return c&&c.specified?c.value:void 0},set:vb.set},ea.attrHooks.contenteditable={set:function(a,b,c){vb.set(a,""===b?!1:b,c)}},ea.each(["width","height"],function(a,b){ea.attrHooks[b]={set:function(a,c){return""===c?(a.setAttribute(b,"auto"),c):void 0}}})),ca.style||(ea.attrHooks.style={get:function(a){return a.style.cssText||void 0},set:function(a,b){return a.style.cssText=b+""}});var Bb=/^(?:input|select|textarea|button|object)$/i,Cb=/^(?:a|area)$/i;ea.fn.extend({prop:function(a,b){return Da(this,ea.prop,a,b,arguments.length>1)},removeProp:function(a){return a=ea.propFix[a]||a,this.each(function(){try{this[a]=void 0,delete this[a]}catch(b){}})}}),ea.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||!ea.isXMLDoc(a),f&&(b=ea.propFix[b]||b,e=ea.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=ea.find.attr(a,"tabindex");return b?parseInt(b,10):Bb.test(a.nodeName)||Cb.test(a.nodeName)&&a.href?0:-1}}}}),ca.hrefNormalized||ea.each(["href","src"],function(a,b){ea.propHooks[b]={get:function(a){return a.getAttribute(b,4)}}}),ca.optSelected||(ea.propHooks.selected={get:function(a){var b=a.parentNode;return b&&(b.selectedIndex,b.parentNode&&b.parentNode.selectedIndex),null}}),ea.each(["tabIndex","readOnly","maxLength","cellSpacing","cellPadding","rowSpan","colSpan","useMap","frameBorder","contentEditable"],function(){ea.propFix[this.toLowerCase()]=this}),ca.enctype||(ea.propFix.enctype="encoding");var Db=/[\t\r\n\f]/g;ea.fn.extend({addClass:function(a){var b,c,d,e,f,g,h=0,i=this.length,j="string"==typeof a&&a;if(ea.isFunction(a))return this.each(function(b){ea(this).addClass(a.call(this,b,this.className))});if(j)for(b=(a||"").match(ta)||[];i>h;h++)if(c=this[h],d=1===c.nodeType&&(c.className?(" "+c.className+" ").replace(Db," "):" ")){for(f=0;e=b[f++];)d.indexOf(" "+e+" ")<0&&(d+=e+" ");g=ea.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;
5
-
6
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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 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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(a){window.location.href=b}).fail(function(a,b,c){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=$(c[0].nextSibling);c.remove(),e.remove(),d.empty().append(b)},h=function(a,b){a.forEach(j),b.forEach(i)},i=function(a){var b=a.id+"<small>&nbsp;"+a.title+"</small>",d=e+(new Date).getUTCMilliseconds();c.append($("<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,c,d){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(a){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(a){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(a){$("#sequence").val("").focus()}),SS.onedb(),$("#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()}}),$(document).on("click","#methods .dropdown-menu li",function(a){var b=$(this),c=$("#method"),d=c.text(),e=b.text();b.html(SS.decorate(d)),c.val(e).html(SS.decorate(e)),$("#methods").wiggle()}),$(".result").on("mousedown",".hitn > .page-header > h4",function(a){var b=$(this);b.on("mouseup mousemove",function c(a){"mouseup"===a.type?(b.attr("data-toggle","collapse"),b.find(".fa-chevron-down").toggleClass("fa-rotate-270")):b.attr("data-toggle",""),b.off("mouseup mousemove",c)})}),$(".result").on("click",".view-sequence",function(a){a.preventDefault(),a.stopPropagation(),a.target.disabled||SS.showSequenceViewer(a.target)}),$(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"}),$("#spinner").modal("hide")}).fail(function(a,b,c){SS.showErrorModal(a,function(){$("#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&nbsp;").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&nbsp;").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+=" &times; 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;$("#blast").on("sequence_type_changed database_type_changed",function(c){b=h(),_.isEqual(b,a)||(a=b,$(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}();
data/sequenceserver.gemspec CHANGED
@@ -17,10 +17,10 @@ interface for use locally or over the web.
17
17
  DESC
18
18
 
19
19
  # dependencies
20
- s.add_dependency('sinatra', '~> 1.4', '>= 1.4.5')
21
- s.add_dependency('json', '~> 1.8', '>= 1.8.2')
22
- s.add_dependency('ox', '~> 2.1', '>= 2.1.1')
23
- s.add_dependency('slop', '~> 3.6', '>= 3.6.0')
20
+ s.add_dependency('sinatra', '~> 1.4', '>= 1.4.5')
21
+ s.add_dependency('json_pure', '~> 1.8', '>= 1.8.2')
22
+ s.add_dependency('ox', '~> 2.1', '>= 2.1.1')
23
+ s.add_dependency('slop', '~> 3.6', '>= 3.6.0')
24
24
 
25
25
  s.add_development_dependency('rack-test', '~> 0.6', '>= 0.6.2')
26
26
  s.add_development_dependency('rspec', '~> 2.8', '>= 2.8.0')
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
4
+ version: 1.0.5
5
5
  platform: ruby
6
6
  authors:
7
7
  - Anurag Priyam
@@ -11,7 +11,7 @@ authors:
11
11
  autorequire:
12
12
  bindir: bin
13
13
  cert_chain: []
14
- date: 2015-05-18 00:00:00.000000000 Z
14
+ date: 2015-11-06 00:00:00.000000000 Z
15
15
  dependencies:
16
16
  - !ruby/object:Gem::Dependency
17
17
  name: sinatra
@@ -34,7 +34,7 @@ dependencies:
34
34
  - !ruby/object:Gem::Version
35
35
  version: 1.4.5
36
36
  - !ruby/object:Gem::Dependency
37
- name: json
37
+ name: json_pure
38
38
  requirement: !ruby/object:Gem::Requirement
39
39
  requirements:
40
40
  - - "~>"
@@ -684,9 +684,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
684
684
  version: '0'
685
685
  requirements: []
686
686
  rubyforge_project:
687
- rubygems_version: 2.4.2
687
+ rubygems_version: 2.2.5
688
688
  signing_key:
689
689
  specification_version: 4
690
690
  summary: BLAST search made easy!
691
691
  test_files: []
692
- has_rdoc: