Team:EPF-Lausanne/PrimerDesignHelper.js

From 2012.igem.org

(Difference between revisions)

Revision as of 11:13, 28 July 2012

var DNA,__indexOf=Array.prototype.indexOf||function(a){for(var b=0,c=this.length;b<c;b++){if(b in this&&this[b]===a)return b}return-1};DNA=function(){function a(a){this.data=a}a.allowed=["A","C","G","T"];a.extendedAllowed=["A","C","G","T","R","Y","K","M","S","W","B","D","H","V","N"];a.RS={AatI:"AGGCCT",AatII:"GACGTC",AccI:"GTMKAC",AccIII:"TCCGGA",Acc65I:"GGTACC",AcsI:"RAATTY",AcyI:"GRCGYC",AflI:"GGWCC",AflII:"CTTAAG",AflIII:"ACRYGT",AgeI:"ACCGGT",AhaII:"GRCGYC",AhaIII:"TTTAAA",AluI:"AGCT",Alw44I:"GTGCAC",AlwNI:"CAGNNNCTG",AocI:"CCTNAGG",AosI:"TGCGCA",ApaI:"GGGCCC",ApaLI:"GTGCAC",ApoI:"RAATTY",ApyI:"CCWGG",AscI:"GGCGCGCC",AseI:"ATTAAT",AsnI:"ATTAAT",AspI:"GACNNNGTC",Asp700:"GAANNNNTTC",Asp718:"GGTACC",AspEI:"GACNNNNNGTC",AspHI:"GWGCWC",AsuII:"TTCGAA",AvaI:"CYCGRG",AvaII:"GGWCC",AviII:"TGCGCA",AvrII:"CCTAGG",BalI:"TGGCCA",BamHI:"GGATCC",BanI:"GGYRCC",BanII:"GRGCYC",BbrPI:"CACGTG",BclI:"TGATCA",BfaI:"CTAG",BfrI:"CTTAAG",BglI:"GCCNNNNNGGC",BglII:"AGATCT",BinI:"CCTAGG",BmyI:"GDGCHC",Bpu1102I:"GCTNAGC",BsaAI:"YACGTR",BsaBI:"GATNNNNATC",BsaHI:"GRCGYC",BsaJI:"CCNNGG",BseAI:"TCCGGA",BsePI:"GCGCGC",BsiEI:"CGRYCG",BsiWI:"CGTACG",BsiYI:"CCNNNNNNNGG",BslI:"CCNNNNNNNGG",Bsp1286I:"GDGCHC",Bsp1407I:"TGTACA",BspDI:"ATCGAT",BspEI:"TCCGGA",BspHI:"TCATGA",BspLU11I:"ACATGT",BsrFI:"RCCGGY",BssGI:"CCANNNNNNTGG",BssHII:"GCGCGC",Bst1107I:"GTATAC",BstBI:"TTCGAA",BstEII:"GGTNACC",BstNI:"CCWGG",BstUI:"CGCG",BstXI:"CCANNNNNNTGG",BstYI:"RGATCY",Bsu36I:"CCTNAGG",CelII:"GCTNAGC",CfoI:"GCGC",CfrI:"YGGCCR",Cfr10I:"RCCGGY",ClaI:"ATCGAT",DdeI:"CTNAG",DpnII:"GATC",DraI:"TTTAAA",DraII:"RGGNCCY",DraIII:"CACNNNGTG",DrdI:"GACNNNNNNGTC",DsaI:"CCRYGG",EaeI:"YGGCCR",EagI:"CGGCCG",Eam1105I:"GACNNNNNGTC",Ecl136II:"GAGCTC",EclXI:"CGGCCG",Eco47III:"AGCGCT",EcoNI:"CCTNNNNNAGG",EcoO109I:"RGGNCCY",EcoRI:"GAATTC",EcoRII:"CCWGG",EcoRV:"GATATC",EspI:"GCTNAGC",FnuDII:"CGCG",Fnu4HI:"GCNGC",FseI:"GGCCGGCC",FspI:"TGCGCA",HaeII:"RGCGCY",HaeIII:"GGCC",HgiAI:"GWGCWC",HhaI:"GCGC",HincII:"GTYRAC",HindII:"GTYRAC",HindIII:"AAGCTT",HinfI:"GANTC",HinPI:"GCGC",HpaI:"GTTAAC",HpaII:"CCGG",ItaI:"GCNGC",KasI:"GGCGCC",KpnI:"GGTACC",KspI:"CCGCGG",MaeI:"CTAG",MaeII:"ACGT",MaeIII:"GTNAC",MamI:"GATNNNNATC",MboI:"GATC",MfeI:"CAATTG",MluI:"ACGCGT",MluNI:"TGGCCA",MroI:"TCCGGA",MscI:"TGGCCA",MseI:"TTAA",MspI:"CCGG",MstI:"TGCGCA",MstII:"CCTNAGG",MunI:"CAATTG",MvaI:"CCWGG",MvnI:"CGCG",NaeI:"GCCGGC",NarI:"GGCGCC",NciI:"CCSGG",NcoI:"CCATGG",NdeI:"CATATG",NdeII:"GATC",NgoMI:"GCCGGC",NheI:"GCTAGC",NlaIII:"CATG",NlaIV:"GGNNCC",NotI:"GCGGCCGC",NruI:"TCGCGA",NsiI:"ATGCAT",NspBII:"CMGCKG",NspI:"RCATGY",NspII:"GDGCHC",NspV:"TTCGAA",PacI:"TTAATTAA",PaeR7I:"CTCGAG",PflMI:"CCANNNNNTGG",PinAI:"ACCGGT",PsiI:"TTATAA",PmaCI:"CACGTG",PmeI:"GTTTAAAC",PmlI:"CACGTG",PpuMI:"RGGWCCY",Psp1406I:"AACGTT",PstI:"CTGCAG",PvuI:"CGATCG",PvuII:"CAGCTG",RcaI:"TCATGA",RmaI:"CTAG",RsaI:"GTAC",RsrII:"CGGWCCG",SacI:"GAGCTC",SacII:"CCGCGG",SalI:"GTCGAC",SauI:"CCTNAGG",Sau3AI:"GATC",Sau96I:"GGNCC",ScaI:"AGTACT",ScrFI:"CCNGG",SexAI:"ACCWGGT",SfcI:"CTRYAG",SfiI:"GGCCNNNNNGGCC",SfuI:"TTCGAA",SgrAI:"CRCCGGYG",SmaI:"CCCGGG",SnaBI:"TACGTA",SnoI:"GTGCAC",SpeI:"ACTAGT",SphI:"GCATGC",SrfI:"GCCCGGGC",Sse8387I:"CCTGCAGG",SspI:"AATATT",SspBI:"TGTACA",SstI:"GAGCTC",SstII:"CCGCGG",StuI:"AGGCCT",StyI:"CCWWGG",SwaI:"ATTTAAAT",TaqI:"TCGA",TfiI:"GAWTC",ThaI:"CGCG",Tru9I:"TTAA",Tth111I:"GACNNNGTC",Van91I:"CCANNNNNTGG",XbaI:"TCTAGA",XcmI:"CCANNNNNNNNNTGG",XhoI:"CTCGAG",XhoII:"RGATCY",XmaI:"CCCGGG",XmaIII:"CGGCCG",XmnI:"GAANNNNTTC"};a.cutPositions={AatI:3,AatII:5,AccI:2,AccIII:1,Acc65I:1,AcsI:1,AcyI:2,AflI:1,AflII:1,AflIII:1,AgeI:1,AhaII:2,AhaIII:3,AluI:2,Alw44I:1,AlwNI:6,AocI:2,AosI:3,ApaI:5,ApaLI:1,ApoI:1,ApyI:0,AscI:2,AseI:2,AsnI:2,AspI:4,Asp700:5,Asp718:1,AspEI:6,AspHI:5,AsuII:2,AvaI:1,AvaII:1,AviII:3,AvrII:1,BalI:3,BamHI:1,BanI:1,BanII:5,BbrPI:3,BclI:1,BfaI:1,BfrI:1,BglI:7,BglII:1,BinI:1,BmyI:5,Bpu1102I:2,BsaAI:3,BsaBI:5,BsaHI:2,BsaJI:1,BseAI:1,BsePI:1,BsiEI:4,BsiWI:1,BsiYI:7,BslI:7,Bsp1286I:5,Bsp1407I:1,BspDI:2,BspEI:1,BspHI:1,BspLU11I:1,BsrFI:1,BssGI:8,BssHII:1,Bst1107I:3,BstBI:2,BstEII:1,BstNI:2,BstUI:2,BstXI:8,BstYI:1,Bsu36I:2,CelII:2,CfoI:3,CfrI:1,Cfr10I:1,ClaI:2,DdeI:1,DpnII:0,DraI:3,DraII:2,DraIII:6,DrdI:7,DsaI:1,EaeI:1,EagI:1,Eam1105I:6,Ecl136II:3,EclXI:1,Eco47III:3,EcoNI:5,EcoO109I:2,EcoRI:1,EcoRII:0,EcoRV:3,EspI:2,FnuDII:2,Fnu4HI:2,FseI:6,FspI:3,HaeII:5,HaeIII:2,HgiAI:5,HhaI:3,HincII:3,HindII:3,HindIII:1,HinfI:1,HinPI:1,HpaI:3,HpaII:1,ItaI:2,KasI:1,KpnI:5,KspI:4,MaeI:1,MaeII:1,MaeIII:0,MamI:5,MboI:0,MfeI:1,MluI:1,MluNI:3,MroI:1,MscI:3,MseI:1,MspI:1,MstI:3,MstII:2,MunI:1,MvaI:2,MvnI:2,NaeI:3,NarI:2,NciI:2,NcoI:1,NdeI:2,NdeII:0,NgoMI:1,NheI:1,NlaIII:4,NlaIV:3,NotI:2,NruI:3,NsiI:5,NspBII:3,NspI:5,NspII:5,NspV:2,PacI:5,PaeR7I:1,PflMI:7,PinAI:1,PsiI:3,PmaCI:3,PmeI:4,PmlI:3,PpuMI:2,Psp1406I:2,PstI:5,PvuI:4,PvuII:3,RcaI:1,RmaI:1,RsaI:2,RsrII:2,SacI:5,SacII:4,SalI:1,SauI:2,Sau3AI:0,Sau96I:1,ScaI:3,ScrFI:2,SexAI:1,SfcI:1,SfiI:8,SfuI:2,SgrAI:2,SmaI:3,SnaBI:3,SnoI:1,SpeI:1,SphI:5,SrfI:4,Sse8387I:6,SspI:3,SspBI:1,SstI:5,SstII:4,StuI:3,StyI:1,SwaI:4,TaqI:1,TfiI:1,ThaI:2,Tru9I:1,Tth111I:4,Van91I:7,XbaI:1,XcmI:8,XhoI:1,XhoII:1,XmaI:1,XmaIII:1,XmaCI:1,XmnI:5};a.RSFlipped=void 0;a.getRSFlipped=function(){var a,b,c,d,e,f;if(this.RSFlipped===void 0){this.RSFlipped={};e=this.RS;for(b in e){c=e[b];if(this.RSFlipped[c]){this.RSFlipped[c].push(b)}else{this.RSFlipped[c]=[b]}}f=this.RSFlipped;for(a in f){d=f[a];if(d.length<=2){this.RSFlipped[a]=d.join(" or ")}else{this.RSFlipped[a]=d.slice(0,d.length-1).join(", ")+" or "+d[d.length-1]}}}return this.RSFlipped};a.getCutPosition=function(b){var c,d,e;if(a.cutPositions[b]){return a.cutPositions[b]}else{e=a.cutPositions;for(c in e){d=e[c];if(c.toLowerCase()===b.toLowerCase())return d}return-1}};a.nucleotideMatches={A:["A","R","M","W","D","H","V","N"],C:["C","Y","M","S","B","H","V","N"],G:["G","R","K","S","B","D","V","N"],T:["T","Y","K","W","B","D","H","N"],R:["A","G"],Y:["C","T"],K:["G","T"],M:["A","C"],S:["C","G"],W:["A","T"],B:["C","G","T"],D:["A","G","T"],H:["A","C","T"],V:["A","C","G"],N:["A","C","G","T"]};a.fromString=function(b){var c,d,e,f,g;c=false;if(b!=null){g=this.RS;for(d in g){f=g[d];if(d.toLowerCase()===b.toLowerCase()){e=new a(f.split(""));c=true}}}else{b=""}if(!c)e=new a(b.toUpperCase().replace(/\s/ig,"").split(""));e.validateData();return e};a.fromRandom=function(b){var c,d;if(b===0||b==="0"||!b||b===void 0){return new a([])}else{c=function(){var c;c=[];for(d=1;1<=b?d<=b:d>=b;1<=b?d++:d--){c.push(a.allowed[Math.floor(Math.random()*a.allowed.length)])}return c}();return new a(c)}};a.prototype.validateData=function(b){if(b){if(this.data.some(function(b){return __indexOf.call(a.allowed,b)<0})){throw new Error("Invalid character encountered")}}else{if(this.data.some(function(b){return __indexOf.call(a.extendedAllowed,b)<0})){throw new Error("Invalid character encountered")}}};a.prototype.matches=function(b){var c;if(this.length()!==b.length())return false;c=_.zip(this.data,b.data);return _.all(c,function(b){var c,d,e,f,g,h,i,j;e=b[0],g=b[1];if(e===g){return true}else{if(__indexOf.call(a.allowed,e)>=0){return __indexOf.call(a.nucleotideMatches[e],g)>=0}if(__indexOf.call(a.allowed,g)>=0){return __indexOf.call(a.nucleotideMatches[g],e)>=0}f=a.nucleotideMatches[e];h=a.nucleotideMatches[g];for(c=0,i=f.length-1;0<=i?c<=i:c>=i;0<=i?c++:c--){for(d=0,j=h.length-1;0<=j?d<=j:d>=j;0<=j?d++:d--){if(f[c]===h[d])return true}}return false}})};a.prototype.findRS=function(b){var c,d,e,f,g,h;if(b==null)b=false;if(this.length()>15)return"";c=this.data.join("");e=a.getRSFlipped();if(e[c]){if(b){return e[c]}else{return e[c]+" (5' → 3': "+c+")"}}else{h=a.RS;for(g in h){d=h[g];f=a.fromString(g);if(this.matches(f)){if(b){d}else{d+" (5' → 3': "+c+")"}}}return""}};a.prototype.getCutPosition=function(){return a.getCutPosition(this.findRS(true))};a.prototype.containsRS=function(b){var c,d,e,f,g,h,i,j,k,l,m,n,o;d=[];for(k=0,m=b.length;k<m;k++){g=b[k];d.push(g.toLowerCase())}f=function(){var a;a=[];for(e=0;e<=10;e++){a.push("")}return a}();j=a.getRSFlipped();i=0;o=this.data;for(l=0,n=o.length;l<n;l++){c=o[l];for(e=4;e<=10;e++){f[e]+=c;if(e<=i)f[e]=f[e].substr(1);if(j[f[e]]){h=j[f[e]].toLowerCase().split(" ");if(_.some(d,function(a){return __indexOf.call(h,a)>=0})){return true}}}i++}return false};a.prototype.length=function(){return this.data.length};a.prototype.snip=function(b){if(b>=0&&b<=this.data.length){return new a(this.data.slice(0,b))}else{throw new Error("Invalid snip length (tried to snip a piece of length "+b+" in a sequence of "+this.length()+"bp)")}};a.prototype.reverseComplement=function(){var b,c,d,e,f,g,h;e=[];b=function(a){switch(a){case"A":return"T";case"T":return"A";case"C":return"G";case"G":return"C";default:throw new Error("Invalid character encountered ("+a+")")}};d=this.data.length-1;h=this.data;for(c=0,g=h.length;c<g;c++){f=h[c];e[d-c]=b(f)}return new a(e)};a.prototype.append=function(b){return new a(this.data.concat(b.data))};a.prototype.tm=function(){return TmCalc.calc(this.data)};a.prototype.toString=function(){return this.data.join("")};a.prototype.toJSON=function(){return this.toString()};a.prototype.clone=function(){return new a(this.data.slice(0))};return a}();var DNAInput,DNARSInput,DNASmallInput,Input,InputForm,NumberInput,RadioInput,SelectInput,Separator,Submit,TemperatureInput,__hasProp=Object.prototype.hasOwnProperty,__extends=function(a,b){function d(){this.constructor=a}for(var c in b){if(__hasProp.call(b,c))a[c]=b[c]}d.prototype=b.prototype;a.prototype=new d;a.__super__=b.prototype;return a};InputForm=function(){function a(b){this.update=b.update,this.submit=b.submit,this.name=b.name;this.id="inputform-"+a.i++;this.inputs=[];this.inputDict={};this.lastValue={}}a.i=0;a.create=function(b,c){var d;d=new a(b);c.forEach(function(a){return d.addInput(a)});return d};a.prototype.save=function(a){var b,c,d;try{if(JSON&&localStorage){c={};for(b in a){d=a[b];if(b==="leftRS"||b==="rightRS")d=d.rs;c[b]=d}return localStorage.setItem("values",JSON.stringify(c))}}catch(e){}};a.prototype.restore=function(){var a,b,c,d;try{if(JSON&&localStorage){b=localStorage.getItem("values");if(b!=null){b=JSON.parse(b);d=[];for(a in b){c=b[a];d.push(this.inputDict[a].value(c))}return d}}}catch(e){}};a.prototype.attach=function(a){$(a).append(this.generateDOM());$(".help-block").hide();this.restore();return this.updateCallback()};a.prototype.submitCallback=function(){var a,b,c,d,e;e=this.getFormData(),b=e.data,d=e.messages,c=e.error,a=e.changed;return typeof this.submit==="function"?this.submit(b,d,c):void 0};a.prototype.updateCallback=function(){var a,b,c,d,e;if(this.disableAuto)return;e=this.getFormData(),b=e.data,d=e.messages,c=e.error,a=e.changed;if(a){return typeof this.update==="function"?this.update(b,d,c):void 0}};a.prototype.getFormData=function(){var a,b,c,d;b={};d=[];c=false;this.inputs.forEach(function(a){var e;e=void 0;try{e=a.value()}catch(f){d.push("Error: "+f.message)}if(!a.validate(e)){c=true;d.push("The value of "+a.get("label")+" is invalid")}if(a.get("name")!=null)return b[a.get("name")]=e});a=false;if(!_.isEqual(this.lastValue,b)){a=true;this.inputs.forEach(function(a){if(a.visible(b)){return a.show()}else{return a.hide()}});this.lastValue=b;this.save(b)}return{data:b,messages:d,error:c,changed:a}};a.prototype.addInput=function(a){var b,c,d=this;if(a==="Separator"){this.inputs.push(new Separator);return}if(!window[a.type]instanceof Function){throw new Error("Passed input can't be instantiated")}b=function(){return d.updateCallback.apply(d,arguments)};if(a.type==="Submit"){b=function(){return d.submitCallback.apply(d,arguments)}}c=new window[a.type](b,a);if(!c instanceof Input)throw new Error("Object isn't an input");this.inputDict[a.name]=c;this.inputs.push(c);return this};a.prototype.get=function(a){return this.inputDict[a]};a.prototype.generateDOM=function(){var a,b,c=this;b=$("<form>").attr("id",this.id).attr("class","form-horizontal");if(this.name!=null){a=$("<fieldset>").append($("<legend>").text(this.name));b.append(a)}else{a=b}this.inputs.forEach(function(b){return a.append(b.generateDOM())});a.prepend($("

")).prepend($("

").attr("class","control-group "+this.rowClass).append($("<label>").attr("class","control-label").attr("for","help-checkbox").html("Show help blocks")).append($("

").attr("class","controls").append($("<input>").attr("class","input-medium").attr("type","checkbox").attr("checked",false).attr("id","help-checkbox").on("change",function(){if($("#help-checkbox").attr("checked")){return $(".help-block").show()}else{return $(".help-block").hide()}})))).prepend($("

").attr("class","control-group "+this.rowClass).append($("<label>").attr("class","control-label").attr("for","autoUpdate-checkbox").html("Automatically update results (CPU-heavy, but way more useable)")).append($("

").attr("class","controls").append($("<input>").attr("class","input-medium").attr("type","checkbox").attr("checked","checked").attr("id","autoUpdate-checkbox").on("change",function(){if($("#autoUpdate-checkbox").attr("checked")){return c.disableAuto=false}else{return c.disableAuto=true}}))));return b};return a}();Input=function(){function a(b,c,d){this.callback=b;this.data=c;this.rowClass=d!=null?d:"";this.id="input-"+a.i++;this.type="text"}a.i=0;a.prototype.generateDOM=function(){return $("

").attr("id","row-"+this.id).attr("class","control-group "+this.rowClass).append(this.generateLabelDOM()).append($("

").attr("class","controls").append(this.generateElementDOM()).append(this.generateHelpDOM()))};a.prototype.generateLabelDOM=function(){return $("<label>").attr("class","control-label").attr("for",this.id).html(this.data.label)};a.prototype.generateInputElementDOM=function(a,b,c,d){var e;e=$("<input>").attr("class","input-medium").attr("type",b).attr("id",a).on("change",d).on("keyup",d);e.val(c);return e};a.prototype.generateElementDOM=function(){return this.generateInputElementDOM(this.id,this.type,this.data.value,this.callback)};a.prototype.generateHelpDOM=function(a){if(a==null)a=this.data.help;if(a!=null&&a.length>0){return $("

").attr("class","help-block").html(a)}else{return $("<p>").attr("class","help-block").attr("style","display: none")}};a.prototype.get=function(a){return this.data[a]};a.prototype.visible=function(a){if(this.data.visible!=null){return this.data.visible(a)}else{return true}};a.prototype.hide=function(){return $("#row-"+this.id).hide()};a.prototype.show=function(){return $("#row-"+this.id).show()};a.prototype.value=function(a){if(a===void 0){return $("#"+this.id).val()}else{return $("#"+this.id).val(a)}};a.prototype.validate=function(a){return true};return a}();Separator=function(a){function b(){b.__super__.constructor.apply(this,arguments)}__extends(b,a);b.prototype.generateDOM=function(){return $("

").attr("id","row-"+this.id)};b.prototype.value=function(){};b.prototype.validate=function(){return true};return b}(Input);Submit=function(a){function b(){b.__super__.constructor.apply(this,arguments)}__extends(b,a);b.prototype.generateElementDOM=function(){return $("<input>").attr("type","submit").attr("value",this.data.value).attr("class","btn").click(this.callback,function(a){a.preventDefault();a.data(a);return false})};b.prototype.value=function(){};b.prototype.validate=function(){return true};return b}(Input);NumberInput=function(a){function b(){b.__super__.constructor.apply(this,arguments);this.type="number"}__extends(b,a);b.prototype.value=function(a){if(a===void 0){return parseInt(b.__super__.value.call(this),10)}else{return b.__super__.value.call(this,parseInt(a,10))}};b.prototype.validate=function(a){return!isNaN(a)};return b}(Input);TemperatureInput=function(a){function b(){b.__super__.constructor.apply(this,arguments)}__extends(b,a);b.prototype.generateElementDOM=function(){var a;a=b.__super__.generateElementDOM.call(this);return $("

").attr("class","input-append").append(a).append($("").attr("class","add-on").text("°C"))};return b}(NumberInput);DNAInput=function(a){function b(){b.__super__.constructor.apply(this,arguments)}__extends(b,a);b.prototype.generateElementDOM=function(){var a;a=$("<textarea>").attr("class","input-xlarge").attr("id",this.id).on("change",this.callback).on("keyup",this.callback);a.val(this.data.value);return a};b.prototype.value=function(a){if(a===void 0){return DNA.fromString(b.__super__.value.call(this))}else{return b.__super__.value.call(this,a.toString())}};b.prototype.validate=function(a){return a!==void 0};return b}(Input);DNASmallInput=function(a){function b(){b.__super__.constructor.apply(this,arguments)}__extends(b,a);b.prototype.generateElementDOM=function(){var a;a=b.__super__.generateElementDOM.call(this);return $("

").attr("class","input-prepend input-append").append($("").attr("class","add-on").text("5'")).append(this.generateInputElementDOM(this.id,"text",this.data.value,this.callback)).append($("").attr("class","add-on").text("3'"))};return b}(DNAInput);DNARSInput=function(a){function b(){b.__super__.constructor.apply(this,arguments)}__extends(b,a);b.prototype.generateElementDOM=function(){var a;a=b.__super__.generateElementDOM.call(this);return $("

").attr("class","input-prepend input-append").append($("").attr("class","add-on").text("5'")).append(this.generateInputElementDOM(this.id,"text",this.data.value,this.callback)).append($("").attr("class","add-on").text("3'")).append($("").attr("id",this.id+"-rs").attr("class","add-on").text("append 2"))};b.prototype.value=function(a){var c;c=b.__super__.value.call(this,a);if(c!=null&&c instanceof DNA){$("#"+this.id+"-rs").html(c.toString())}if(c===void 0)c=DNA.fromString("");return{dna:c,rs:$("#"+this.id).val()}};return b}(DNAInput);SelectInput=function(a){function b(a,c){b.__super__.constructor.apply(this,arguments);this.choices=c.choices}__extends(b,a);b.prototype.generateElementDOM=function(){var a,c,d=this;c=b.__super__.generateElementDOM.call(this);a=$("<select>").attr("class","input-medium").attr("id",this.id).on("change",this.callback).on("click",this.callback);this.choices.forEach(function(b){var c,d;c=b.name,d=b.value;return a.append($("<option>").attr("value",c).text(d))});return a};return b}(Input);RadioInput=function(a){function b(a,c){b.__super__.constructor.apply(this,arguments);this.choices=c.choices}__extends(b,a);b.prototype.generateElementDOM=function(){var a,c,d,e=this;d=b.__super__.generateElementDOM.call(this);a=$("

");c=0;this.choices.forEach(function(b){var c,d,f,g;g=b.name,f=b.label,d=b.help;c=$("<label>").attr("class","radio").text(f).prepend($("<input>").attr("checked",e.data.value===g).attr("type","radio").attr("id",e.id+"-"+g).attr("name",e.id).on("change",e.callback).on("click",e.callback)).append(e.generateHelpDOM(d));return a.append(c)});return a};b.prototype.value=function(a){var b,c=this;if(a===void 0){b={};this.choices.forEach(function(a){var d;d=a.name;return b[d]=$("#"+c.id+"-"+d).attr("checked")==="checked"});return b}else{if(a instanceof String){this.choices.forEach(function(b){var d;d=b.name;return $("#"+c.id+"-"+d).attr("checked",d===a)})}else{this.choices.forEach(function(b){var d;d=b.name;return $("#"+c.id+"-"+d).attr("checked",a[d])})}return a}};return b}(Input);$(function(){window.output=new Output("Primer 1 (Template:Primer1Tm°C, Template:Primer1TailLength + Template:Primer1Lengthbp): 5' → 3'
\n

{{primer1}}

\nPrimer 2 (Template:Primer2Tm°C, Template:Primer2TailLength + Template:Primer2Lengthbp): 5' → 3'
\n

{{primer2}}

\nAnnealing temperature: Template:AnnealingTm°C\n\n

\n

Messages

\nTemplate:Messages\n\n
\n

Digestion result

\nTemplate:RSDisplay:\n
\n

PCR Product

\nTemplate:DNADisplay:full\n");window.output.attach("#outputAttach");window.primerFinder=new PrimerFinder({output:function(a,b){window.output.setMessages(b);return window.output.set(a)}});window.form=InputForm.create({name:"Primer design helper",submit:function(a,b,c){return window.primerFinder.calc(a,b,c)},update:function(a,b,c){return window.primerFinder.calc(a,b,c)}},[{name:"dna",label:"DNA Sequence of interest",type:"DNAInput",value:"",help:"Most of the time you should just paste the DNA sequence (in the 5' → 3' direction) you want to extract/edit in this field"},{type:"Separator"},{name:"type",label:"Primer type",type:"RadioInput",choices:[{name:"normal",label:"Primers that extract the whole sequence",help:"Running a PCR using these primers will extract the entire sequence"},{name:"rs",label:"Add restriction sites",help:"Running a PCR using these primers will result in the sequence with added standardized restriction sites on both sides."},{name:"known",label:"Add a standard prefix/suffix to the sequence",help:"Running a PCR using these primers will result in the sequence with added standardized tails on both sides (for example for biobricking)."},{name:"custom",label:"Add custom tails to the sequence",help:"Running a PCR using these primers will result in the sequence with added tails on both sides."}],value:"normal"},{type:"Separator"},{name:"standardTail",label:"Standardized tails",type:"SelectInput",value:"biobrickGene",choices:[{name:"biobrickGene",value:"Biobrick (gene)"},{name:"biobrickOther",value:"Biobrick (other)"}],visible:function(a){var b;b=a.type;return b.known}},{name:"randomBases",label:"Random Bases",type:"NumberInput",value:"4",help:"This is the number of random bases will be added on both ends.",visible:function(a){var b;b=a.type;return b.rs}},{name:"leftRS",label:"Left restriction site",type:"DNARSInput",value:"",help:"You can also enter the name of the restriction enzyme (i.e. EcoRI).",visible:function(a){var b;b=a.type;return b.rs}},{name:"rightRS",label:"Right restriction site",type:"DNARSInput",value:"",help:"You can also enter the name of the restriction enzyme (i.e. EcoRI).",visible:function(a){var b;b=a.type;return b.rs}},{name:"leftTail",label:"Left tail",type:"DNASmallInput",value:"",visible:function(a){var b;b=a.type;return b.custom}},{name:"rightTail",label:"Right tail",type:"DNASmallInput",value:"",visible:function(a){var b;b=a.type;return b.custom}},{type:"Separator",visible:function(a){var b;b=a.type;return!b.normal}},{name:"tm",label:"Target Tm",type:"TemperatureInput",value:"50",help:"The program will try to create primers that have an annealing temperature close to this one."},{value:"Generate",type:"Submit"}]);return window.form.attach($("#formAttach"))});window.tails=[{name:"Biobrick (gene)",value:"biobrickGene",primer1Tail:"GTT TCT TCG AAT TCG CGG CCG CTT CTA G",primer2Tail:"GTT TCT TCC TGC AGC GGC CGC TAC TAG TA TTA TTA",messages:["Don't forget to include the first ATG and to exclude the stop codon!","The recommended minimum length of a BioBrick primer is 20bp","The recommended Tm of a BioBrick primer is between 55 and 65°C","Check that the following restriction sites are absent: EcoRI, SpeI, XbaI, PstI, NotI","Check out <a href='http://openwetware.org/wiki/Synthetic_Biology:BioBricks/Part_fabrication'>OpenWetWare's reference page</a>"],validate:function(a,b,c){var d,e;e=a.substr(0,3).toUpperCase();if(e!=="ATG")return"The starting ATG seems to be absent.";d=b.substr(0,3).toUpperCase();if(d==="TTA"||d==="TCA"||d==="CTA"){return"Remove the stop codons from the sequence!"}if(c.containsRS(["EcoRI","SpeI","XbaI","PstI","NotI"])){return"One of the following restriction sites is present (and shouldn't be): EcoRI, SpeI, XbaI, PstI, NotI"}return}},{name:"Biobrick (other)",value:"biobrickOther",primer1Tail:"GTT TCT TCG AAT TCG CGG CCG CTT CTA GAG",primer2Tail:"GTT TCT TCC TGC AGC GGC CGC TAC TAG TA",messages:["The recommended minimum length of a BioBrick primer is 20bp","The recommended Tm of a BioBrick primer is between 55 and 65°C","Check that the following restriction sites are absent: EcoRI, SpeI, XbaI, PstI, NotI","Check out <a href='http://openwetware.org/wiki/Synthetic_Biology:BioBricks/Part_fabrication'>OpenWetWare's reference page</a>"],validate:function(a,b,c){if(c.containsRS(["EcoRI","SpeI","XbaI","PstI","NotI"])){return"One of the following restriction sites is present (and shouldn't be): EcoRI, SpeI, XbaI, PstI, NotI"}return}}];var DNADisplay,Display,Output,RSDisplay,SelfDimerDisplay,__hasProp=Object.prototype.hasOwnProperty,__extends=function(a,b){function d(){this.constructor=a}for(var c in b){if(__hasProp.call(b,c))a[c]=b[c]}d.prototype=b.prototype;a.prototype=new d;a.__super__=b.prototype;return a};Output=function(){function a(b){this.template=b;this.id="output-"+a.i++;this.fields={};this.matches={};this.displays={};this.parsedTemplate=this.parseTemplate(this.template)}a.i=0;a.j=0;a.prototype.attach=function(a){var b,c,d,e,f,g;this.matches={};$(a).html(this.parsedTemplate);f=this.displays;g=[];for(d in f){e=f[d];g.push(function(){var a,d,f,g;g=[];for(a=0,d=e.length;a<d;a++){f=e[a],b=f.displayClass,c=f.displayObj;g.push(c.attach("."+b))}return g}())}return g};a.prototype.setMessages=function(a){var b;b=a;if(a.length===0)b=["No messages"];return this.getFields("_messages").html("

"+b.join("
")+"

")};a.prototype.wipe=function(){var a,b,c;c=this.fields;for(a in c){b=c[a];this.updateValue(a,void 0)}return this.fields={}};a.prototype.set=function(a){var b,c;for(b in a){c=a[b];this.updateValue(b,c)}this.updateValue("__all__",this.fields);return this.fields};a.prototype.updateValue=function(a,b){var c,d,e,f,g;if(this.fields[a]!==b){this.fields[a]=b;if(b!=null){this.getFields(a).html(b.toString())}else{this.getFields(a).html("")}}if(this.displays[a]!=null){f=this.displays[a];g=[];for(d=0,e=f.length;d<e;d++){c=f[d].displayObj;g.push(c.set(b))}return g}};a.prototype.getFields=function(a){if(!this.matches[a]){this.matches[a]=$("."+this.id+"-match-"+a)}return this.matches[a]};a.prototype.parseTemplate=function(a){var b,c,d,e,f,g,h,i,j,k,l,m,n,o;b=a[0];c=a[1];l=a+"";m=false;i=false;n=-1;k="";for(h=1,o=a.length-1;1<=o?h<=o:h>=o;1<=o?h++:h--){c=a[h];if(!m){if(b==="{"&&c==="{"){if(i){throw new Error("Invalid template, opened brackets in an already opened context")}k="";n=h;m=true;i=true}else if(b==="}"&&c==="}"){if(!i){throw new Error("Invalid template, closed unopened brackets")}g=k.indexOf(":");if(g>=0){d=k.substr(0,g);j=k.substr(g+1);if(j==="")j="__all__";e=this.id+"-display-"+d+"-"+j;l=l.replace("Template:"+k+"","");f=new window[d](j);if(!(this.displays[j]!=null))this.displays[j]=[];this.displays[j].push({displayClass:e,displayObj:f})}else{l=l.replace("Template:"+k+"","")}m=true;i=false}else{if(i)k+=b}}else{m=false}b=c}return l};return a}();Display=function(){function a(a){this.key=a;this.value=void 0}a.prototype.attach=function(a){throw new Error("Not implemented")};a.prototype.set=function(a){return this.value=a[this.key]};a.prototype.pad=function(a,b,c){var d;if(a==null)a="";if(b==null)b=5;if(c==null)c=false;a=a.toString();d=a.length;while(d=b){e.push(a.substr(c,b));d-=b;c+=b}if(d>0)e.push(a.substr(c));return e};return a}();DNADisplay=function(a){function b(a){var c,d=this;b.__super__.constructor.apply(this,arguments);this["class"]="dnadisplay-"+b.i++;this.objects=[];c=this;this.dom=$("
").attr("class",this["class"]).append($("<label>").append($("<input>").attr("class",this["class"]+"-toggleLines").attr("type","checkbox").attr("checked","on").on("change",function(){if($("."+d["class"]+"-toggleLines").attr("checked")){$("."+d["class"]+"-lines").hide();$("."+d["class"]+"-numberedLines").show()}else{$("."+d["class"]+"-lines").show();$("."+d["class"]+"-numberedLines").hide()}return})).append(" Line Numbers")).append($("
").attr("class",this["class"]+"-lines product").hide()).append($("<pre>").attr("class",this["class"]+"-numberedLines product"))}__extends(b,a);b.i=0;b.prototype.attach=function(a){$(a).append(this.dom);return this.objects=$("."+this["class"])};b.prototype.set=function(a){var b,c,d,e,f,g,h,i,j;h=60;e=6;i=40;d=this.wrap(a,h);f=this.wrap(a,i);g=[];for(b=0,j=f.length;b<j;b++){c=f[b];if(c.length>0){g[b]=this.pad(b*i+1,e,true)+" - "+this.pad((b+1)*i,e)+" "+c}}this.full=d.join("\n");this.fullNumbered=g.join("\n");$("."+this["class"]+"-lines").text(this.full);return $("."+this["class"]+"-numberedLines").text(this.fullNumbered)};return b}(Display);RSDisplay=function(a){function b(a){var c;b.__super__.constructor.apply(this,arguments);this["class"]="rsdisplay-"+b.i++;this.objects=[];c=this;this.dom=$("<div>").attr("class",this["class"]).append($("<pre>").attr("class",this["class"]+"-pre"))}__extends(b,a);b.i=0;b.prototype.attach=function(a){$(a).append(this.dom);return this.objects=$("."+this["class"])};b.prototype.set=function(a){var b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,A;s=a.rs,u=a.type,h=a.leftRS,p=a.rightRS;if(!u.rs){$("."+this["class"]+"-pre").html("Not applicable");return}i=h.rs;q=p.rs;e=s.left,m=s.right,d=s.full,l=s.randomBases;g=DNA.getCutPosition(i);if(g<0){h=DNA.fromString(e).findRS(true);g=DNA.getCutPosition(h)}else{h=i}if(h.length===0)h="?";o=DNA.getCutPosition(q);if(o<0){p=DNA.fromString(m).findRS(true);o=DNA.getCutPosition(p)}else{p=q}if(p.length===0)p="?";j=d.substr(0,l+e.length+10);r=d.substr(d.length-(l+m.length+10));if(l>6){j="..."+j.substr(l-3);r=r.substr(0,r.length-(l-3))+"...";l=6}f="";n="";c=function(a){switch(a){case"A":return"T";case"T":return"A";case"C":return"G";case"G":return"C";default:return a}};z=j.split("");for(v=0,x=z.length;v<x;v++){b=z[v];f+=c(b)}A=r.split("");for(w=0,y=A.length;w<y;w++){b=A[w];n+=c(b)}if(g>=0){k=Math.ceil(Math.abs(e.length/2-g))+1;j=j.substr(0,l+g)+this.pad("",k+1)+j.substr(l+g);f=f.substr(0,l+e.length-g)+this.pad("",k+1)+f.substr(l+e.length-g)}else{j=j.substr(0,l)+" "+j.substr(l,e.length)+" "+j.substr(l+e.length);f=f.substr(0,l)+" "+f.substr(l,e.length)+" "+f.substr(l+e.length)}if(o>=0){k=Math.ceil(Math.abs(m.length/2-o))+1;r=r.substr(0,r.length-(l+m.length-o))+this.pad("",k+1)+r.substr(r.length-(l+m.length-o));n=n.substr(0,n.length-(l+o))+this.pad("",k+1)+n.substr(n.length-(l+o))}else{r=r.substr(0,r.length-(l+m.length))+" "+r.substr(r.length-(l+m.length),m.length)+" "+r.substr(r.length-l);n=n.substr(0,n.length-(l+m.length))+" "+n.substr(n.length-(l+m.length),m.length)+" "+n.substr(n.length-l)}t=[];t.push("Left restriction site: "+h+(g<0?" (cutting site unknown)":""));t.push("Right restriction site: "+p+(o<0?" (cutting site unknown)":""));t.push("");t.push("5'"+this.pad("3'",j.length+r.length+1,true));t.push(j+"..."+r);t.push(f+"..."+n);t.push("3'"+this.pad("5'",j.length+r.length+1,true));return $("."+this["class"]+"-pre").text(t.join("\n"))};return b}(Display);SelfDimerDisplay=function(a){function b(a){var c,d=this;b.__super__.constructor.apply(this,arguments);this["class"]="selfdimerdisplay-"+RSDisplay.i++;this.objects=[];c=this;this.dom=$("<div>").attr("class",this["class"]).append($("<span>").text("This calculation is quite heavy and is done on demand. Press on the button to start the calculations:")).append("<br>").append($("<input>").attr("type","button").attr("value","Calculate").attr("class","btn").click(function(){return d.click()})).append("<br>").append("<br>").append($("<pre>").attr("class",this["class"]+"-pre").html("Press the calculate button to update this data"))}__extends(b,a);b.i=0;b.prototype.attach=function(a){$(a).append(this.dom);return this.objects=$("."+this["class"]+"-pre")};b.prototype.set=function(a){var b,c;b=a.primer1,c=a.primer2;if(b!==this.primer1||c!==this.primer2){this.primer1=b;this.primer2=c;return this.objects.html("Press the calculate button to update this data")}};b.prototype.click=function(){var a;a=this.generateReport("Primer 1",this.primer1)+"\n\n"+this.generateReport("Primer 2",this.primer2);return this.objects.html(a)};b.prototype.generateReport=function(a,b){var c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r;g=[];g.push(a+":");l=RNA.fromString(b);p=l.findKnots(),h=p.matches,d=p.folds;g.push("Amount of matches: "+h);k=_.zip(function(){r=[];for(var a=1,c=b.length;1<=c?a<=c:a>=c;1<=c?a++:a--){r.push(a)}return r}.apply(this),b.split(""));e="";f="";for(n=0,o=k.length;n<o;n++){j=k[n];i=j[0]+" ";c=this.pad(j[1],i.length-1,true)+" ";if(e.length+i.length>60){g.push(e);g.push(f);g.push("");e="";f=""}e+=c;f+=i}if(e.length>0){g.push(e);g.push(f);g.push("")}return g.join("\n")};return b}(Display);var Primer;Primer=function(){function a(a){if(a instanceof DNA){this.seq=a.clone()}else{this.seq=DNA.fromString(a)}this.tail1=new DNA([]);this.tail2=new DNA([]);this.randEdgeSize=0}a.minLength=8;a.maxLength=50;a.maxDiff=8;a.lastData="";a.lastTail1="";a.lastTail2="";a.lastTm=0;a.lastRandEdgeSize=-1;a.reset=function(){this.lastData="";this.lastTm=0;this.lastTail1="";this.lastTail2="";return this.lastRandEdgeSize=-1};a.prototype.setTails=function(a,b){this.tail1=a;this.tail2=b};a.prototype.addRandomEdges=function(a){this.randEdgeSize=a};a.prototype.isSameAsLast=function(b,c){return a.lastTail1.toString()===this.tail1.toString()&&a.lastTail2.toString()===this.tail2.toString()&&a.lastData===DNA.fromString(b).toString()&&a.lastTm===c&&a.lastRandEdgeSize===this.randEdgeSize};a.prototype.generate=function(b){var c,d,e,f,g,h,i,j,k,l,m,n,o,p;if(2*a.minLength>this.seq.length()){throw new Error("The given sequence is too short")}a.lastData=this.seq.toString();a.lastTm=b;a.lastTail1=this.tail1;a.lastTail2=this.tail2;a.lastRandEdgeSize=this.randEdgeSize;f=Math.min(Math.floor(this.seq.length()/2),a.maxLength);m=this.seq.reverseComplement();g=-1;h=0;i=-1;j=0;for(d=o=a.minLength;o<=f?d<=f:d>=f;o<=f?d++:d--){n=this.seq.snip(d).tm();c=Math.abs(n-b);if(c<=a.maxDiff&&(g===-1||Math.abs(h-b)>c)){g=d;h=n}if(n>=b)break}for(e=p=a.minLength;p<=f?e<=f:e>=f;p<=f?e++:e--){n=m.snip(e).tm();c=Math.abs(n-b);if(c<=a.maxDiff&&(i===-1||Math.abs(j-b)>c)){i=e;j=n}if(n>=b)break}if(g<0||i<0){throw new Error("Couldn't find a primer of correct length that satisfies the conditions")}k=DNA.fromRandom(this.randEdgeSize);l=DNA.fromRandom(this.randEdgeSize);return{rs:{left:this.tail1.toString(),right:this.tail2.toString(),randomBases:this.randEdgeSize,full:k.toString()+this.tail1.toString()+this.seq.toString()+this.tail2.reverseComplement().toString()+l.reverseComplement().toString()},primer1:k.toString()+" "+this.tail1.toString()+" "+this.seq.snip(g).toString(),primers:{primer1:k.toString()+this.tail1.toString()+this.seq.snip(g).toString(),primer2:l.toString()+this.tail2.toString()+m.snip(i).toString()},primer1NoTail:this.seq.snip(g).toString(),primer1Tm:h,primer1Length:g,primer1TailLength:k.length()+this.tail1.length(),primer2:l.toString()+" "+this.tail2.toString()+" "+m.snip(i).toString(),primer2NoTail:m.snip(i).toString(),primer2Tm:j,primer2Length:i,primer2TailLength:l.length()+this.tail2.length(),full:k.toString()+this.tail1.toString()+this.seq.toString()+this.tail2.reverseComplement().toString()+l.reverseComplement().toString()}};return a}();var PrimerFinder;PrimerFinder=function(){function a(a){this.output=a.output;this.defaults={primer1:"No data",primer1Tm:"?",primer1Length:0,primer2:"No data",primer2Tm:"?",primer2Length:0,annealingTm:"?"}}a.prototype.calc=function(a,b,c){var d,e,f,g,h,i,j,k,l,m,n,o,p,q,r;if(c){b=["A fatal error occured:"].concat(b);this.output(a,b);return}q=this.defaults;for(d in q){m=q[d];if(!(a[d]!=null))a[d]=m}try{g=new Primer(a.dna);n=function(a,b,c){};if(a.type.custom)g.setTails(a.leftTail,a.rightTail);if(a.type.rs){e=a.leftRS.dna.findRS();f=a.rightRS.dna.findRS();if(e!=null&&e.length>0){b.push("The left restriction site is "+e)}else{b.push("The left restriction site wasn't recognized")}if(f!=null&&f.length>0){b.push("The right restriction site is "+f)}else{b.push("The right restriction site wasn't recognized")}g.setTails(a.leftRS.dna,a.rightRS.dna.reverseComplement());g.addRandomEdges(a.randomBases);b.push("Click the 'Generate' button to regenerate the random bases added on the end of the primers.");b.push("In the case of a plasmid where the piece between A and B is cut out, and A is used for the primer 1 RS (and B for the second).\nThe generated primers will put the RS such that the given DNA starts at the A side and ends at the B side (in short,\nit will probably work as you expected, but still check what happens with some other tool).")}if(a.type.known){k="";l="";r=window.tails;for(o=0,p=r.length;o<p;o++){j=r[o];if(j.value===a.standardTail){k=j.primer1Tail;l=j.primer2Tail;if(j.messages!=null)b=[].concat(j.messages);if(j.validate!=null)n=j.validate}}g.setTails(DNA.fromString(k),DNA.fromString(l))}h=g.generate(a.tm);i=n(h.primer1NoTail,h.primer2NoTail,a.dna);if(i!=null)b.push(i);for(d in h){m=h[d];a[d]=m}b=b}catch(s){b=[s.message]}a.annealingTm=Math.min(a.primer1Tm,a.primer2Tm);if(Math.abs(a.primer1Tm-a.primer2Tm)>5){b.push("The difference between the primer's Tm is more than 5°C")}if(a.annealingTm>70){b.push("Consider using the two-step PCR protocol")}if(a.annealingTm>72){b.push("Annealing temperature shouldn't exceed 72°C");a.annealingTm=72}if(a.annealingTm<45){b.push("The annealing temperature should be more than 45°C")}return this.output(a,b)};return a}();var RNA;RNA=function(){function a(a){this.data=a;this.n=this.data.length;this.knots=void 0}a.fromDNA=function(b){return new a(b.data.map(function(a){switch(a){case"T":return"U";default:return a}}))};a.fromString=function(b){return a.fromDNA(DNA.fromString(b))};a.prototype.P=function(a,b){if(this.data[a]==="A"&&this.data[b]==="U"||this.data[a]==="U"&&this.data[b]==="C"){return 1}else if(this.data[a]==="G"&&this.data[b]==="C"||this.data[a]==="C"&&this.data[b]==="G"){return 1}else{return 0}};a.prototype.isTooSelfComplementary=function(){var a,b,c,d,e,f,g,h,i;h=this.findKnots(),d=h.matches,b=h.folds;for(f=0,g=b.length;f<g;f++){a=b[f];e=[];console.log(a);for(c=0,i=a.length-1;0<=i?c<=i:c>=i;0<=i?c++:c--){if(a[c]==="("){if(c>0&&a[c-1]==="("){e[e.length-1]+=this.data[c]}else{e[e.length]=this.data[c]}}}console.log(e)}return false};a.prototype.findKnots=function(a){var b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,A,B,C,D,E,F,G,H,I,J,K,L,M,N=this;if(a==null)a=2;if(this.knots!==void 0)return this.knots;g=function(){var a,b,c;c=[];for(a=1,b=N.n;1<=b?a<=b:a>=b;1<=b?a++:a--){c.push(".")}return c};b=[];for(n=0,D=this.n-1;0<=D?n<=D:n>=D;0<=D?n++:n--){i=[];for(o=0,F=this.n-1;0<=F?o<=F:o>=F;0<=F?o++:o--){i[o]=[g()]}b[n]=i}c=function(){var a,b;b=[];for(k=1,a=this.n;1<=a?k<=a:k>=a;1<=a?k++:k--){b.push(function(){var a,b;b=[];for(l=1,a=this.n;1<=a?l<=a:l>=a;1<=a?l++:l--){b.push(0)}return b}.call(this))}return b}.call(this);for(k=G=this.n-1;G<=0?k<=0:k>=0;G<=0?k++:k--){for(l=k,H=this.n-1;k<=H?l<=H:l>=H;k<=H?l++:l--){p=0;if(k<l-a){p=c[k+1][l-1]+this.P(k,l);j=[];I=b[k+1][l-1];for(v=0,z=I.length;v<z;v++){s=I[v];if(this.P(k,l)===1){s[k]="(";s[l]=")"}else{s[k]=".";s[l]="."}if(j.length<50)j.push(s)}for(m=k,J=l-1;k<=J?m<=J:m>=J;k<=J?m++:m--){u=c[k][m]+c[m+1][l];if(u>p){p=u;j=[]}if(u>=p){K=b[k][m];for(w=0,A=K.length;w<A;w++){e=K[w];L=b[m+1][l];for(x=0,B=L.length;x<B;x++){f=L[x];d=g(this.n);for(r=0;0<=m?r<=m:r>=m;0<=m?r++:r--){d[r]=e[r]}for(r=M=m+1;M<=l?r<=l:r>=l;M<=l?r++:r--){d[r]=f[r]}if(j.length<50)j.push(d)}}}}c[k][l]=p;b[k][l]=j}}}q=[];h={};E=b[0][this.n-1];for(y=0,C=E.length;y<C;y++){s=E[y];t=s.join("");if(h[t]===void 0){h[t]=true;q.push(t)}}return this.knots={matches:c[0][this.n-1],folds:q}};return a}();var TmCalc;TmCalc=function(){function a(){}a.maxCacheSize=500;a.cache={};a.calc=function(b){var c,d,e;if(!this.cache[b]){e=Math.round(this.calcFull(b)*10)/10;if(this.cache.length>=this.maxCacheSize){d=Object.keys(a.cache);c=d[Math.floor(Math.random()*d.length)];delete a.cache[c]}this.cache[b]=e}return this.cache[b]};a.complement=function(a){switch(a){case"A":return"T";case"T":return"A";case"C":return"G";case"G":return"C";default:throw new Error("Invalid character encountered ("+a+")")}};a.neighborH={AA:9.1,AT:8.6,TA:6,CA:5.8,GT:6.5,CT:7.8,GA:5.6,CG:11.9,GC:11.1,GG:11};a.getH=function(a,b){return this.get(this.neighborH,a,b)};a.neighborG={AA:1.9,AT:1.5,TA:.9,CA:1.9,GT:1.3,CT:1.6,GA:1.6,CG:3.6,GC:3.1,GG:3.1};a.getG=function(a,b){return this.get(this.neighborG,a,b)};a.neighborS={AA:24,AT:23.9,TA:16.9,CA:12.9,GT:17.3,CT:20.8,GA:13.5,CG:27.8,GC:26.7,GG:26.6};a.getS=function(a,b){return this.get(this.neighborS,a,b)};a.get=function(a,b,c){switch(b+c){case"AA":return a["AA"];case"TT":return a["AA"];case"AT":return a["AT"];case"TA":return a["TA"];case"TT":return a["TA"];case"CA":return 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@@ Line 1: / Line 1: @@
-/*
+var DNA,__indexOf=Array.prototype.indexOf||function(a){for(var b=0,c=this.length;b<c;b++){if(b in this&&this[b]===a)return b}return-1};DNA=function(){function a(a){this.data=a}a.allowed=["A","C","G","T"];a.extendedAllowed=["A","C","G","T","R","Y","K","M","S","W","B","D","H","V","N"];a.RS={AatI:"AGGCCT",AatII:"GACGTC",AccI:"GTMKAC",AccIII:"TCCGGA",Acc65I:"GGTACC",AcsI:"RAATTY",AcyI:"GRCGYC",AflI:"GGWCC",AflII:"CTTAAG",AflIII:"ACRYGT",AgeI:"ACCGGT",AhaII:"GRCGYC",AhaIII:"TTTAAA",AluI:"AGCT",Alw44I:"GTGCAC",AlwNI:"CAGNNNCTG",AocI:"CCTNAGG",AosI:"TGCGCA",ApaI:"GGGCCC",ApaLI:"GTGCAC",ApoI:"RAATTY",ApyI:"CCWGG",AscI:"GGCGCGCC",AseI:"ATTAAT",AsnI:"ATTAAT",AspI:"GACNNNGTC",Asp700:"GAANNNNTTC",Asp718:"GGTACC",AspEI:"GACNNNNNGTC",AspHI:"GWGCWC",AsuII:"TTCGAA",AvaI:"CYCGRG",AvaII:"GGWCC",AviII:"TGCGCA",AvrII:"CCTAGG",BalI:"TGGCCA",BamHI:"GGATCC",BanI:"GGYRCC",BanII:"GRGCYC",BbrPI:"CACGTG",BclI:"TGATCA",BfaI:"CTAG",BfrI:"CTTAAG",BglI:"GCCNNNNNGGC",BglII:"AGATCT",BinI:"CCTAGG",BmyI:"GDGCHC",Bpu1102I:"GCTNAGC",BsaAI:"YACGTR",BsaBI:"GATNNNNATC",BsaHI:"GRCGYC",BsaJI:"CCNNGG",BseAI:"TCCGGA",BsePI:"GCGCGC",BsiEI:"CGRYCG",BsiWI:"CGTACG",BsiYI:"CCNNNNNNNGG",BslI:"CCNNNNNNNGG",Bsp1286I:"GDGCHC",Bsp1407I:"TGTACA",BspDI:"ATCGAT",BspEI:"TCCGGA",BspHI:"TCATGA",BspLU11I:"ACATGT",BsrFI:"RCCGGY",BssGI:"CCANNNNNNTGG",BssHII:"GCGCGC",Bst1107I:"GTATAC",BstBI:"TTCGAA",BstEII:"GGTNACC",BstNI:"CCWGG",BstUI:"CGCG",BstXI:"CCANNNNNNTGG",BstYI:"RGATCY",Bsu36I:"CCTNAGG",CelII:"GCTNAGC",CfoI:"GCGC",CfrI:"YGGCCR",Cfr10I:"RCCGGY",ClaI:"ATCGAT",DdeI:"CTNAG",DpnII:"GATC",DraI:"TTTAAA",DraII:"RGGNCCY",DraIII:"CACNNNGTG",DrdI:"GACNNNNNNGTC",DsaI:"CCRYGG",EaeI:"YGGCCR",EagI:"CGGCCG",Eam1105I:"GACNNNNNGTC",Ecl136II:"GAGCTC",EclXI:"CGGCCG",Eco47III:"AGCGCT",EcoNI:"CCTNNNNNAGG",EcoO109I:"RGGNCCY",EcoRI:"GAATTC",EcoRII:"CCWGG",EcoRV:"GATATC",EspI:"GCTNAGC",FnuDII:"CGCG",Fnu4HI:"GCNGC",FseI:"GGCCGGCC",FspI:"TGCGCA",HaeII:"RGCGCY",HaeIII:"GGCC",HgiAI:"GWGCWC",HhaI:"GCGC",HincII:"GTYRAC",HindII:"GTYRAC",HindIII:"AAGCTT",HinfI:"GANTC",HinPI:"GCGC",HpaI:"GTTAAC",HpaII:"CCGG",ItaI:"GCNGC",KasI:"GGCGCC",KpnI:"GGTACC",KspI:"CCGCGG",MaeI:"CTAG",MaeII:"ACGT",MaeIII:"GTNAC",MamI:"GATNNNNATC",MboI:"GATC",MfeI:"CAATTG",MluI:"ACGCGT",MluNI:"TGGCCA",MroI:"TCCGGA",MscI:"TGGCCA",MseI:"TTAA",MspI:"CCGG",MstI:"TGCGCA",MstII:"CCTNAGG",MunI:"CAATTG",MvaI:"CCWGG",MvnI:"CGCG",NaeI:"GCCGGC",NarI:"GGCGCC",NciI:"CCSGG",NcoI:"CCATGG",NdeI:"CATATG",NdeII:"GATC",NgoMI:"GCCGGC",NheI:"GCTAGC",NlaIII:"CATG",NlaIV:"GGNNCC",NotI:"GCGGCCGC",NruI:"TCGCGA",NsiI:"ATGCAT",NspBII:"CMGCKG",NspI:"RCATGY",NspII:"GDGCHC",NspV:"TTCGAA",PacI:"TTAATTAA",PaeR7I:"CTCGAG",PflMI:"CCANNNNNTGG",PinAI:"ACCGGT",PsiI:"TTATAA",PmaCI:"CACGTG",PmeI:"GTTTAAAC",PmlI:"CACGTG",PpuMI:"RGGWCCY",Psp1406I:"AACGTT",PstI:"CTGCAG",PvuI:"CGATCG",PvuII:"CAGCTG",RcaI:"TCATGA",RmaI:"CTAG",RsaI:"GTAC",RsrII:"CGGWCCG",SacI:"GAGCTC",SacII:"CCGCGG",SalI:"GTCGAC",SauI:"CCTNAGG",Sau3AI:"GATC",Sau96I:"GGNCC",ScaI:"AGTACT",ScrFI:"CCNGG",SexAI:"ACCWGGT",SfcI:"CTRYAG",SfiI:"GGCCNNNNNGGCC",SfuI:"TTCGAA",SgrAI:"CRCCGGYG",SmaI:"CCCGGG",SnaBI:"TACGTA",SnoI:"GTGCAC",SpeI:"ACTAGT",SphI:"GCATGC",SrfI:"GCCCGGGC",Sse8387I:"CCTGCAGG",SspI:"AATATT",SspBI:"TGTACA",SstI:"GAGCTC",SstII:"CCGCGG",StuI:"AGGCCT",StyI:"CCWWGG",SwaI:"ATTTAAAT",TaqI:"TCGA",TfiI:"GAWTC",ThaI:"CGCG",Tru9I:"TTAA",Tth111I:"GACNNNGTC",Van91I:"CCANNNNNTGG",XbaI:"TCTAGA",XcmI:"CCANNNNNNNNNTGG",XhoI:"CTCGAG",XhoII:"RGATCY",XmaI:"CCCGGG",XmaIII:"CGGCCG",XmnI:"GAANNNNTTC"};a.cutPositions={AatI:3,AatII:5,AccI:2,AccIII:1,Acc65I:1,AcsI:1,AcyI:2,AflI:1,AflII:1,AflIII:1,AgeI:1,AhaII:2,AhaIII:3,AluI:2,Alw44I:1,AlwNI:6,AocI:2,AosI:3,ApaI:5,ApaLI:1,ApoI:1,ApyI:0,AscI:2,AseI:2,AsnI:2,AspI:4,Asp700:5,Asp718:1,AspEI:6,AspHI:5,AsuII:2,AvaI:1,AvaII:1,AviII:3,AvrII:1,BalI:3,BamHI:1,BanI:1,BanII:5,BbrPI:3,BclI:1,BfaI:1,BfrI:1,BglI:7,BglII:1,BinI:1,BmyI:5,Bpu1102I:2,BsaAI:3,BsaBI:5,BsaHI:2,BsaJI:1,BseAI:1,BsePI:1,BsiEI:4,BsiWI:1,BsiYI:7,BslI:7,Bsp1286I:5,Bsp1407I:1,BspDI:2,BspEI:1,BspHI:1,BspLU11I:1,BsrFI:1,BssGI:8,BssHII:1,Bst1107I:3,BstBI:2,BstEII:1,BstNI:2,BstUI:2,BstXI:8,BstYI:1,Bsu36I:2,CelII:2,CfoI:3,CfrI:1,Cfr10I:1,ClaI:2,DdeI:1,DpnII:0,DraI:3,DraII:2,DraIII:6,DrdI:7,DsaI:1,EaeI:1,EagI:1,Eam1105I:6,Ecl136II:3,EclXI:1,Eco47III:3,EcoNI:5,EcoO109I:2,EcoRI:1,EcoRII:0,EcoRV:3,EspI:2,FnuDII:2,Fnu4HI:2,FseI:6,FspI:3,HaeII:5,HaeIII:2,HgiAI:5,HhaI:3,HincII:3,HindII:3,HindIII:1,HinfI:1,HinPI:1,HpaI:3,HpaII:1,ItaI:2,KasI:1,KpnI:5,KspI:4,MaeI:1,MaeII:1,MaeIII:0,MamI:5,MboI:0,MfeI:1,MluI:1,MluNI:3,MroI:1,MscI:3,MseI:1,MspI:1,MstI:3,MstII:2,MunI:1,MvaI:2,MvnI:2,NaeI:3,NarI:2,NciI:2,NcoI:1,NdeI:2,NdeII:0,NgoMI:1,NheI:1,NlaIII:4,NlaIV:3,NotI:2,NruI:3,NsiI:5,NspBII:3,NspI:5,NspII:5,NspV:2,PacI:5,PaeR7I:1,PflMI:7,PinAI:1,PsiI:3,PmaCI:3,PmeI:4,PmlI:3,PpuMI:2,Psp1406I:2,PstI:5,PvuI:4,PvuII:3,RcaI:1,RmaI:1,RsaI:2,RsrII:2,SacI:5,SacII:4,SalI:1,SauI:2,Sau3AI:0,Sau96I:1,ScaI:3,ScrFI:2,SexAI:1,SfcI:1,SfiI:8,SfuI:2,SgrAI:2,SmaI:3,SnaBI:3,SnoI:1,SpeI:1,SphI:5,SrfI:4,Sse8387I:6,SspI:3,SspBI:1,SstI:5,SstII:4,StuI:3,StyI:1,SwaI:4,TaqI:1,TfiI:1,ThaI:2,Tru9I:1,Tth111I:4,Van91I:7,XbaI:1,XcmI:8,XhoI:1,XhoII:1,XmaI:1,XmaIII:1,XmaCI:1,XmnI:5};a.RSFlipped=void 0;a.getRSFlipped=function(){var a,b,c,d,e,f;if(this.RSFlipped===void 0){this.RSFlipped={};e=this.RS;for(b in e){c=e[b];if(this.RSFlipped[c]){this.RSFlipped[c].push(b)}else{this.RSFlipped[c]=[b]}}f=this.RSFlipped;for(a in f){d=f[a];if(d.length<=2){this.RSFlipped[a]=d.join(" or ")}else{this.RSFlipped[a]=d.slice(0,d.length-1).join(", ")+" or "+d[d.length-1]}}}return this.RSFlipped};a.getCutPosition=function(b){var c,d,e;if(a.cutPositions[b]){return a.cutPositions[b]}else{e=a.cutPositions;for(c in e){d=e[c];if(c.toLowerCase()===b.toLowerCase())return d}return-1}};a.nucleotideMatches={A:["A","R","M","W","D","H","V","N"],C:["C","Y","M","S","B","H","V","N"],G:["G","R","K","S","B","D","V","N"],T:["T","Y","K","W","B","D","H","N"],R:["A","G"],Y:["C","T"],K:["G","T"],M:["A","C"],S:["C","G"],W:["A","T"],B:["C","G","T"],D:["A","G","T"],H:["A","C","T"],V:["A","C","G"],N:["A","C","G","T"]};a.fromString=function(b){var c,d,e,f,g;c=false;if(b!=null){g=this.RS;for(d in g){f=g[d];if(d.toLowerCase()===b.toLowerCase()){e=new a(f.split(""));c=true}}}else{b=""}if(!c)e=new a(b.toUpperCase().replace(/\s/ig,"").split(""));e.validateData();return e};a.fromRandom=function(b){var c,d;if(b===0||b==="0"||!b||b===void 0){return new a([])}else{c=function(){var c;c=[];for(d=1;1<=b?d<=b:d>=b;1<=b?d++:d--){c.push(a.allowed[Math.floor(Math.random()*a.allowed.length)])}return c}();return new a(c)}};a.prototype.validateData=function(b){if(b){if(this.data.some(function(b){return __indexOf.call(a.allowed,b)<0})){throw new Error("Invalid character encountered")}}else{if(this.data.some(function(b){return __indexOf.call(a.extendedAllowed,b)<0})){throw new Error("Invalid character encountered")}}};a.prototype.matches=function(b){var c;if(this.length()!==b.length())return false;c=_.zip(this.data,b.data);return _.all(c,function(b){var c,d,e,f,g,h,i,j;e=b[0],g=b[1];if(e===g){return true}else{if(__indexOf.call(a.allowed,e)>=0){return __indexOf.call(a.nucleotideMatches[e],g)>=0}if(__indexOf.call(a.allowed,g)>=0){return __indexOf.call(a.nucleotideMatches[g],e)>=0}f=a.nucleotideMatches[e];h=a.nucleotideMatches[g];for(c=0,i=f.length-1;0<=i?c<=i:c>=i;0<=i?c++:c--){for(d=0,j=h.length-1;0<=j?d<=j:d>=j;0<=j?d++:d--){if(f[c]===h[d])return true}}return false}})};a.prototype.findRS=function(b){var c,d,e,f,g,h;if(b==null)b=false;if(this.length()>15)return"";c=this.data.join("");e=a.getRSFlipped();if(e[c]){if(b){return e[c]}else{return e[c]+" (5' → 3': "+c+")"}}else{h=a.RS;for(g in h){d=h[g];f=a.fromString(g);if(this.matches(f)){if(b){d}else{d+" (5' → 3': "+c+")"}}}return""}};a.prototype.getCutPosition=function(){return a.getCutPosition(this.findRS(true))};a.prototype.containsRS=function(b){var c,d,e,f,g,h,i,j,k,l,m,n,o;d=[];for(k=0,m=b.length;k<m;k++){g=b[k];d.push(g.toLowerCase())}f=function(){var a;a=[];for(e=0;e<=10;e++){a.push("")}return a}();j=a.getRSFlipped();i=0;o=this.data;for(l=0,n=o.length;l<n;l++){c=o[l];for(e=4;e<=10;e++){f[e]+=c;if(e<=i)f[e]=f[e].substr(1);if(j[f[e]]){h=j[f[e]].toLowerCase().split(" ");if(_.some(d,function(a){return __indexOf.call(h,a)>=0})){return true}}}i++}return false};a.prototype.length=function(){return this.data.length};a.prototype.snip=function(b){if(b>=0&&b<=this.data.length){return new a(this.data.slice(0,b))}else{throw new Error("Invalid snip length (tried to snip a piece of length "+b+" in a sequence of "+this.length()+"bp)")}};a.prototype.reverseComplement=function(){var b,c,d,e,f,g,h;e=[];b=function(a){switch(a){case"A":return"T";case"T":return"A";case"C":return"G";case"G":return"C";default:throw new Error("Invalid character encountered ("+a+")")}};d=this.data.length-1;h=this.data;for(c=0,g=h.length;c<g;c++){f=h[c];e[d-c]=b(f)}return new a(e)};a.prototype.append=function(b){return new a(this.data.concat(b.data))};a.prototype.tm=function(){return TmCalc.calc(this.data)};a.prototype.toString=function(){return this.data.join("")};a.prototype.toJSON=function(){return this.toString()};a.prototype.clone=function(){return new a(this.data.slice(0))};return a}();var DNAInput,DNARSInput,DNASmallInput,Input,InputForm,NumberInput,RadioInput,SelectInput,Separator,Submit,TemperatureInput,__hasProp=Object.prototype.hasOwnProperty,__extends=function(a,b){function d(){this.constructor=a}for(var c in b){if(__hasProp.call(b,c))a[c]=b[c]}d.prototype=b.prototype;a.prototype=new d;a.__super__=b.prototype;return a};InputForm=function(){function a(b){this.update=b.update,this.submit=b.submit,this.name=b.name;this.id="inputform-"+a.i++;this.inputs=[];this.inputDict={};this.lastValue={}}a.i=0;a.create=function(b,c){var d;d=new a(b);c.forEach(function(a){return d.addInput(a)});return d};a.prototype.save=function(a){var b,c,d;try{if(JSON&&localStorage){c={};for(b in a){d=a[b];if(b==="leftRS"||b==="rightRS")d=d.rs;c[b]=d}return localStorage.setItem("values",JSON.stringify(c))}}catch(e){}};a.prototype.restore=function(){var a,b,c,d;try{if(JSON&&localStorage){b=localStorage.getItem("values");if(b!=null){b=JSON.parse(b);d=[];for(a in b){c=b[a];d.push(this.inputDict[a].value(c))}return d}}}catch(e){}};a.prototype.attach=function(a){$(a).append(this.generateDOM());$(".help-block").hide();this.restore();return this.updateCallback()};a.prototype.submitCallback=function(){var a,b,c,d,e;e=this.getFormData(),b=e.data,d=e.messages,c=e.error,a=e.changed;return typeof this.submit==="function"?this.submit(b,d,c):void 0};a.prototype.updateCallback=function(){var a,b,c,d,e;if(this.disableAuto)return;e=this.getFormData(),b=e.data,d=e.messages,c=e.error,a=e.changed;if(a){return typeof this.update==="function"?this.update(b,d,c):void 0}};a.prototype.getFormData=function(){var a,b,c,d;b={};d=[];c=false;this.inputs.forEach(function(a){var e;e=void 0;try{e=a.value()}catch(f){d.push("Error: "+f.message)}if(!a.validate(e)){c=true;d.push("The value of "+a.get("label")+" is invalid")}if(a.get("name")!=null)return b[a.get("name")]=e});a=false;if(!_.isEqual(this.lastValue,b)){a=true;this.inputs.forEach(function(a){if(a.visible(b)){return a.show()}else{return a.hide()}});this.lastValue=b;this.save(b)}return{data:b,messages:d,error:c,changed:a}};a.prototype.addInput=function(a){var b,c,d=this;if(a==="Separator"){this.inputs.push(new Separator);return}if(!window[a.type]instanceof Function){throw new Error("Passed input can't be instantiated")}b=function(){return d.updateCallback.apply(d,arguments)};if(a.type==="Submit"){b=function(){return d.submitCallback.apply(d,arguments)}}c=new window[a.type](b,a);if(!c instanceof Input)throw new Error("Object isn't an input");this.inputDict[a.name]=c;this.inputs.push(c);return this};a.prototype.get=function(a){return this.inputDict[a]};a.prototype.generateDOM=function(){var a,b,c=this;b=$("<form>").attr("id",this.id).attr("class","form-horizontal");if(this.name!=null){a=$("<fieldset>").append($("<legend>").text(this.name));b.append(a)}else{a=b}this.inputs.forEach(function(b){return a.append(b.generateDOM())});a.prepend($("<hr>")).prepend($("<div>").attr("class","control-group "+this.rowClass).append($("<label>").attr("class","control-label").attr("for","help-checkbox").html("Show help blocks")).append($("<div>").attr("class","controls").append($("<input>").attr("class","input-medium").attr("type","checkbox").attr("checked",false).attr("id","help-checkbox").on("change",function(){if($("#help-checkbox").attr("checked")){return $(".help-block").show()}else{return $(".help-block").hide()}})))).prepend($("<div>").attr("class","control-group "+this.rowClass).append($("<label>").attr("class","control-label").attr("for","autoUpdate-checkbox").html("Automatically update results (CPU-heavy, but way more useable)")).append($("<div>").attr("class","controls").append($("<input>").attr("class","input-medium").attr("type","checkbox").attr("checked","checked").attr("id","autoUpdate-checkbox").on("change",function(){if($("#autoUpdate-checkbox").attr("checked")){return c.disableAuto=false}else{return c.disableAuto=true}}))));return b};return a}();Input=function(){function a(b,c,d){this.callback=b;this.data=c;this.rowClass=d!=null?d:"";this.id="input-"+a.i++;this.type="text"}a.i=0;a.prototype.generateDOM=function(){return $("<div>").attr("id","row-"+this.id).attr("class","control-group "+this.rowClass).append(this.generateLabelDOM()).append($("<div>").attr("class","controls").append(this.generateElementDOM()).append(this.generateHelpDOM()))};a.prototype.generateLabelDOM=function(){return $("<label>").attr("class","control-label").attr("for",this.id).html(this.data.label)};a.prototype.generateInputElementDOM=function(a,b,c,d){var e;e=$("<input>").attr("class","input-medium").attr("type",b).attr("id",a).on("change",d).on("keyup",d);e.val(c);return e};a.prototype.generateElementDOM=function(){return this.generateInputElementDOM(this.id,this.type,this.data.value,this.callback)};a.prototype.generateHelpDOM=function(a){if(a==null)a=this.data.help;if(a!=null&&a.length>0){return $("<p>").attr("class","help-block").html(a)}else{return $("<p>").attr("class","help-block").attr("style","display: none")}};a.prototype.get=function(a){return this.data[a]};a.prototype.visible=function(a){if(this.data.visible!=null){return this.data.visible(a)}else{return true}};a.prototype.hide=function(){return $("#row-"+this.id).hide()};a.prototype.show=function(){return $("#row-"+this.id).show()};a.prototype.value=function(a){if(a===void 0){return $("#"+this.id).val()}else{return $("#"+this.id).val(a)}};a.prototype.validate=function(a){return true};return a}();Separator=function(a){function b(){b.__super__.constructor.apply(this,arguments)}__extends(b,a);b.prototype.generateDOM=function(){return $("<hr>").attr("id","row-"+this.id)};b.prototype.value=function(){};b.prototype.validate=function(){return true};return b}(Input);Submit=function(a){function b(){b.__super__.constructor.apply(this,arguments)}__extends(b,a);b.prototype.generateElementDOM=function(){return $("<input>").attr("type","submit").attr("value",this.data.value).attr("class","btn").click(this.callback,function(a){a.preventDefault();a.data(a);return false})};b.prototype.value=function(){};b.prototype.validate=function(){return true};return b}(Input);NumberInput=function(a){function b(){b.__super__.constructor.apply(this,arguments);this.type="number"}__extends(b,a);b.prototype.value=function(a){if(a===void 0){return parseInt(b.__super__.value.call(this),10)}else{return b.__super__.value.call(this,parseInt(a,10))}};b.prototype.validate=function(a){return!isNaN(a)};return b}(Input);TemperatureInput=function(a){function b(){b.__super__.constructor.apply(this,arguments)}__extends(b,a);b.prototype.generateElementDOM=function(){var a;a=b.__super__.generateElementDOM.call(this);return $("<div>").attr("class","input-append").append(a).append($("<span>").attr("class","add-on").text("°C"))};return b}(NumberInput);DNAInput=function(a){function b(){b.__super__.constructor.apply(this,arguments)}__extends(b,a);b.prototype.generateElementDOM=function(){var a;a=$("<textarea>").attr("class","input-xlarge").attr("id",this.id).on("change",this.callback).on("keyup",this.callback);a.val(this.data.value);return a};b.prototype.value=function(a){if(a===void 0){return DNA.fromString(b.__super__.value.call(this))}else{return b.__super__.value.call(this,a.toString())}};b.prototype.validate=function(a){return a!==void 0};return b}(Input);DNASmallInput=function(a){function b(){b.__super__.constructor.apply(this,arguments)}__extends(b,a);b.prototype.generateElementDOM=function(){var a;a=b.__super__.generateElementDOM.call(this);return $("<div>").attr("class","input-prepend input-append").append($("<span>").attr("class","add-on").text("5'")).append(this.generateInputElementDOM(this.id,"text",this.data.value,this.callback)).append($("<span>").attr("class","add-on").text("3'"))};return b}(DNAInput);DNARSInput=function(a){function b(){b.__super__.constructor.apply(this,arguments)}__extends(b,a);b.prototype.generateElementDOM=function(){var a;a=b.__super__.generateElementDOM.call(this);return $("<div>").attr("class","input-prepend input-append").append($("<span>").attr("class","add-on").text("5'")).append(this.generateInputElementDOM(this.id,"text",this.data.value,this.callback)).append($("<span>").attr("class","add-on").text("3'")).append($("<span>").attr("id",this.id+"-rs").attr("class","add-on").text("append 2"))};b.prototype.value=function(a){var c;c=b.__super__.value.call(this,a);if(c!=null&&c instanceof DNA){$("#"+this.id+"-rs").html(c.toString())}if(c===void 0)c=DNA.fromString("");return{dna:c,rs:$("#"+this.id).val()}};return b}(DNAInput);SelectInput=function(a){function b(a,c){b.__super__.constructor.apply(this,arguments);this.choices=c.choices}__extends(b,a);b.prototype.generateElementDOM=function(){var a,c,d=this;c=b.__super__.generateElementDOM.call(this);a=$("<select>").attr("class","input-medium").attr("id",this.id).on("change",this.callback).on("click",this.callback);this.choices.forEach(function(b){var c,d;c=b.name,d=b.value;return a.append($("<option>").attr("value",c).text(d))});return a};return b}(Input);RadioInput=function(a){function b(a,c){b.__super__.constructor.apply(this,arguments);this.choices=c.choices}__extends(b,a);b.prototype.generateElementDOM=function(){var a,c,d,e=this;d=b.__super__.generateElementDOM.call(this);a=$("<div>");c=0;this.choices.forEach(function(b){var c,d,f,g;g=b.name,f=b.label,d=b.help;c=$("<label>").attr("class","radio").text(f).prepend($("<input>").attr("checked",e.data.value===g).attr("type","radio").attr("id",e.id+"-"+g).attr("name",e.id).on("change",e.callback).on("click",e.callback)).append(e.generateHelpDOM(d));return a.append(c)});return a};b.prototype.value=function(a){var b,c=this;if(a===void 0){b={};this.choices.forEach(function(a){var d;d=a.name;return b[d]=$("#"+c.id+"-"+d).attr("checked")==="checked"});return b}else{if(a instanceof String){this.choices.forEach(function(b){var d;d=b.name;return $("#"+c.id+"-"+d).attr("checked",d===a)})}else{this.choices.forEach(function(b){var d;d=b.name;return $("#"+c.id+"-"+d).attr("checked",a[d])})}return a}};return b}(Input);$(function(){window.output=new Output("Primer 1 (<b>{{primer1Tm}}°C</b>, {{primer1TailLength}} + {{primer1Length}}bp): 5' → 3'<br />\n<pre class='primer'>{{primer1}}</pre>\nPrimer 2 (<b>{{primer2Tm}}°C</b>, {{primer2TailLength}} + {{primer2Length}}bp): 5' → 3'<br />\n<pre class='primer'>{{primer2}}</pre>\n<b>Annealing temperature:</b> {{annealingTm}}°C\n\n<br /><br />\n<h3>Messages</h3>\n{{_messages}}\n\n<br />\n<h3>Digestion result</h3>\n{{RSDisplay:}}\n<br />\n<h3>PCR Product</h3>\n{{DNADisplay:full}}\n<!-- <br />\n<h3>Self Dimer</h3>\n{{SelfDimerDisplay:primers}} -->");window.output.attach("#outputAttach");window.primerFinder=new PrimerFinder({output:function(a,b){window.output.setMessages(b);return window.output.set(a)}});window.form=InputForm.create({name:"Primer design helper",submit:function(a,b,c){return window.primerFinder.calc(a,b,c)},update:function(a,b,c){return window.primerFinder.calc(a,b,c)}},[{name:"dna",label:"DNA Sequence of interest",type:"DNAInput",value:"",help:"Most of the time you should just paste the DNA sequence (in the 5' → 3' direction) you want to extract/edit in this field"},{type:"Separator"},{name:"type",label:"Primer type",type:"RadioInput",choices:[{name:"normal",label:"Primers that extract the whole sequence",help:"Running a PCR using these primers will extract the entire sequence"},{name:"rs",label:"Add restriction sites",help:"Running a PCR using these primers will result in the sequence with added standardized restriction sites on both sides."},{name:"known",label:"Add a standard prefix/suffix to the sequence",help:"Running a PCR using these primers will result in the sequence with added standardized tails on both sides (for example for biobricking)."},{name:"custom",label:"Add custom tails to the sequence",help:"Running a PCR using these primers will result in the sequence with added tails on both sides."}],value:"normal"},{type:"Separator"},{name:"standardTail",label:"Standardized tails",type:"SelectInput",value:"biobrickGene",choices:[{name:"biobrickGene",value:"Biobrick (gene)"},{name:"biobrickOther",value:"Biobrick (other)"}],visible:function(a){var b;b=a.type;return b.known}},{name:"randomBases",label:"Random Bases",type:"NumberInput",value:"4",help:"This is the number of random bases will be added on both ends.",visible:function(a){var b;b=a.type;return b.rs}},{name:"leftRS",label:"Left restriction site",type:"DNARSInput",value:"",help:"You can also enter the name of the restriction enzyme (i.e. EcoRI).",visible:function(a){var b;b=a.type;return b.rs}},{name:"rightRS",label:"Right restriction site",type:"DNARSInput",value:"",help:"You can also enter the name of the restriction enzyme (i.e. EcoRI).",visible:function(a){var b;b=a.type;return b.rs}},{name:"leftTail",label:"Left tail",type:"DNASmallInput",value:"",visible:function(a){var b;b=a.type;return b.custom}},{name:"rightTail",label:"Right tail",type:"DNASmallInput",value:"",visible:function(a){var b;b=a.type;return b.custom}},{type:"Separator",visible:function(a){var b;b=a.type;return!b.normal}},{name:"tm",label:"Target Tm",type:"TemperatureInput",value:"50",help:"The program will try to create primers that have an annealing temperature close to this one."},{value:"Generate",type:"Submit"}]);return window.form.attach($("#formAttach"))});window.tails=[{name:"Biobrick (gene)",value:"biobrickGene",primer1Tail:"GTT TCT TCG AAT TCG CGG CCG CTT CTA G",primer2Tail:"GTT TCT TCC TGC AGC GGC CGC TAC TAG TA TTA TTA",messages:["Don't forget to include the first ATG and to exclude the stop codon!","The recommended minimum length of a BioBrick primer is 20bp","The recommended Tm of a BioBrick primer is between 55 and 65°C","Check that the following restriction sites are absent: EcoRI, SpeI, XbaI, PstI, NotI","Check out <a href='http://openwetware.org/wiki/Synthetic_Biology:BioBricks/Part_fabrication'>OpenWetWare's reference page</a>"],validate:function(a,b,c){var d,e;e=a.substr(0,3).toUpperCase();if(e!=="ATG")return"<b>The starting ATG seems to be absent.</b>";d=b.substr(0,3).toUpperCase();if(d==="TTA"||d==="TCA"||d==="CTA"){return"<b>Remove the stop codons from the sequence!</b>"}if(c.containsRS(["EcoRI","SpeI","XbaI","PstI","NotI"])){return"<b>One of the following restriction sites is present (and shouldn't be): EcoRI, SpeI, XbaI, PstI, NotI</b>"}return}},{name:"Biobrick (other)",value:"biobrickOther",primer1Tail:"GTT TCT TCG AAT TCG CGG CCG CTT CTA GAG",primer2Tail:"GTT TCT TCC TGC AGC GGC CGC TAC TAG TA",messages:["The recommended minimum length of a BioBrick primer is 20bp","The recommended Tm of a BioBrick primer is between 55 and 65°C","Check that the following restriction sites are absent: EcoRI, SpeI, XbaI, PstI, NotI","Check out <a href='http://openwetware.org/wiki/Synthetic_Biology:BioBricks/Part_fabrication'>OpenWetWare's reference page</a>"],validate:function(a,b,c){if(c.containsRS(["EcoRI","SpeI","XbaI","PstI","NotI"])){return"<b>One of the following restriction sites is present (and shouldn't be): EcoRI, SpeI, XbaI, PstI, NotI</b>"}return}}];var DNADisplay,Display,Output,RSDisplay,SelfDimerDisplay,__hasProp=Object.prototype.hasOwnProperty,__extends=function(a,b){function d(){this.constructor=a}for(var c in b){if(__hasProp.call(b,c))a[c]=b[c]}d.prototype=b.prototype;a.prototype=new d;a.__super__=b.prototype;return a};Output=function(){function a(b){this.template=b;this.id="output-"+a.i++;this.fields={};this.matches={};this.displays={};this.parsedTemplate=this.parseTemplate(this.template)}a.i=0;a.j=0;a.prototype.attach=function(a){var b,c,d,e,f,g;this.matches={};$(a).html(this.parsedTemplate);f=this.displays;g=[];for(d in f){e=f[d];g.push(function(){var a,d,f,g;g=[];for(a=0,d=e.length;a<d;a++){f=e[a],b=f.displayClass,c=f.displayObj;g.push(c.attach("."+b))}return g}())}return g};a.prototype.setMessages=function(a){var b;b=a;if(a.length===0)b=["No messages"];return this.getFields("_messages").html("<ul><li>"+b.join("</li><li>")+"</li></ul>")};a.prototype.wipe=function(){var a,b,c;c=this.fields;for(a in c){b=c[a];this.updateValue(a,void 0)}return this.fields={}};a.prototype.set=function(a){var b,c;for(b in a){c=a[b];this.updateValue(b,c)}this.updateValue("__all__",this.fields);return this.fields};a.prototype.updateValue=function(a,b){var c,d,e,f,g;if(this.fields[a]!==b){this.fields[a]=b;if(b!=null){this.getFields(a).html(b.toString())}else{this.getFields(a).html("")}}if(this.displays[a]!=null){f=this.displays[a];g=[];for(d=0,e=f.length;d<e;d++){c=f[d].displayObj;g.push(c.set(b))}return g}};a.prototype.getFields=function(a){if(!this.matches[a]){this.matches[a]=$("."+this.id+"-match-"+a)}return this.matches[a]};a.prototype.parseTemplate=function(a){var b,c,d,e,f,g,h,i,j,k,l,m,n,o;b=a[0];c=a[1];l=a+"";m=false;i=false;n=-1;k="";for(h=1,o=a.length-1;1<=o?h<=o:h>=o;1<=o?h++:h--){c=a[h];if(!m){if(b==="{"&&c==="{"){if(i){throw new Error("Invalid template, opened brackets in an already opened context")}k="";n=h;m=true;i=true}else if(b==="}"&&c==="}"){if(!i){throw new Error("Invalid template, closed unopened brackets")}g=k.indexOf(":");if(g>=0){d=k.substr(0,g);j=k.substr(g+1);if(j==="")j="__all__";e=this.id+"-display-"+d+"-"+j;l=l.replace("{{"+k+"}}","<span class='"+e+"'></span>");f=new window[d](j);if(!(this.displays[j]!=null))this.displays[j]=[];this.displays[j].push({displayClass:e,displayObj:f})}else{l=l.replace("{{"+k+"}}","<span class='"+this.id+"-match-"+k+"'></span>")}m=true;i=false}else{if(i)k+=b}}else{m=false}b=c}return l};return a}();Display=function(){function a(a){this.key=a;this.value=void 0}a.prototype.attach=function(a){throw new Error("Not implemented")};a.prototype.set=function(a){return this.value=a[this.key]};a.prototype.pad=function(a,b,c){var d;if(a==null)a="";if(b==null)b=5;if(c==null)c=false;a=a.toString();d=a.length;while(d<b){if(c){a=" "+a}else{a+=" "}d++}return a};a.prototype.wrap=function(a,b){var c,d,e;if(a==null)a="";if(b==null)b=40;a=a.toString();d=a.length;e=[];c=0;while(d>=b){e.push(a.substr(c,b));d-=b;c+=b}if(d>0)e.push(a.substr(c));return e};return a}();DNADisplay=function(a){function b(a){var c,d=this;b.__super__.constructor.apply(this,arguments);this["class"]="dnadisplay-"+b.i++;this.objects=[];c=this;this.dom=$("<div>").attr("class",this["class"]).append($("<label>").append($("<input>").attr("class",this["class"]+"-toggleLines").attr("type","checkbox").attr("checked","on").on("change",function(){if($("."+d["class"]+"-toggleLines").attr("checked")){$("."+d["class"]+"-lines").hide();$("."+d["class"]+"-numberedLines").show()}else{$("."+d["class"]+"-lines").show();$("."+d["class"]+"-numberedLines").hide()}return})).append(" Line Numbers")).append($("<pre>").attr("class",this["class"]+"-lines product").hide()).append($("<pre>").attr("class",this["class"]+"-numberedLines product"))}__extends(b,a);b.i=0;b.prototype.attach=function(a){$(a).append(this.dom);return this.objects=$("."+this["class"])};b.prototype.set=function(a){var b,c,d,e,f,g,h,i,j;h=60;e=6;i=40;d=this.wrap(a,h);f=this.wrap(a,i);g=[];for(b=0,j=f.length;b<j;b++){c=f[b];if(c.length>0){g[b]=this.pad(b*i+1,e,true)+" - "+this.pad((b+1)*i,e)+"  "+c}}this.full=d.join("\n");this.fullNumbered=g.join("\n");$("."+this["class"]+"-lines").text(this.full);return $("."+this["class"]+"-numberedLines").text(this.fullNumbered)};return b}(Display);RSDisplay=function(a){function b(a){var c;b.__super__.constructor.apply(this,arguments);this["class"]="rsdisplay-"+b.i++;this.objects=[];c=this;this.dom=$("<div>").attr("class",this["class"]).append($("<pre>").attr("class",this["class"]+"-pre"))}__extends(b,a);b.i=0;b.prototype.attach=function(a){$(a).append(this.dom);return this.objects=$("."+this["class"])};b.prototype.set=function(a){var b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,A;s=a.rs,u=a.type,h=a.leftRS,p=a.rightRS;if(!u.rs){$("."+this["class"]+"-pre").html("Not applicable");return}i=h.rs;q=p.rs;e=s.left,m=s.right,d=s.full,l=s.randomBases;g=DNA.getCutPosition(i);if(g<0){h=DNA.fromString(e).findRS(true);g=DNA.getCutPosition(h)}else{h=i}if(h.length===0)h="?";o=DNA.getCutPosition(q);if(o<0){p=DNA.fromString(m).findRS(true);o=DNA.getCutPosition(p)}else{p=q}if(p.length===0)p="?";j=d.substr(0,l+e.length+10);r=d.substr(d.length-(l+m.length+10));if(l>6){j="..."+j.substr(l-3);r=r.substr(0,r.length-(l-3))+"...";l=6}f="";n="";c=function(a){switch(a){case"A":return"T";case"T":return"A";case"C":return"G";case"G":return"C";default:return a}};z=j.split("");for(v=0,x=z.length;v<x;v++){b=z[v];f+=c(b)}A=r.split("");for(w=0,y=A.length;w<y;w++){b=A[w];n+=c(b)}if(g>=0){k=Math.ceil(Math.abs(e.length/2-g))+1;j=j.substr(0,l+g)+this.pad("",k+1)+j.substr(l+g);f=f.substr(0,l+e.length-g)+this.pad("",k+1)+f.substr(l+e.length-g)}else{j=j.substr(0,l)+"  "+j.substr(l,e.length)+"  "+j.substr(l+e.length);f=f.substr(0,l)+"  "+f.substr(l,e.length)+"  "+f.substr(l+e.length)}if(o>=0){k=Math.ceil(Math.abs(m.length/2-o))+1;r=r.substr(0,r.length-(l+m.length-o))+this.pad("",k+1)+r.substr(r.length-(l+m.length-o));n=n.substr(0,n.length-(l+o))+this.pad("",k+1)+n.substr(n.length-(l+o))}else{r=r.substr(0,r.length-(l+m.length))+"  "+r.substr(r.length-(l+m.length),m.length)+"  "+r.substr(r.length-l);n=n.substr(0,n.length-(l+m.length))+"  "+n.substr(n.length-(l+m.length),m.length)+"  "+n.substr(n.length-l)}t=[];t.push("Left restriction site: "+h+(g<0?" (cutting site unknown)":""));t.push("Right restriction site: "+p+(o<0?" (cutting site unknown)":""));t.push("");t.push("5'"+this.pad("3'",j.length+r.length+1,true));t.push(j+"..."+r);t.push(f+"..."+n);t.push("3'"+this.pad("5'",j.length+r.length+1,true));return $("."+this["class"]+"-pre").text(t.join("\n"))};return b}(Display);SelfDimerDisplay=function(a){function b(a){var c,d=this;b.__super__.constructor.apply(this,arguments);this["class"]="selfdimerdisplay-"+RSDisplay.i++;this.objects=[];c=this;this.dom=$("<div>").attr("class",this["class"]).append($("<span>").text("This calculation is quite heavy and is done on demand. Press on the button to start the calculations:")).append("<br>").append($("<input>").attr("type","button").attr("value","Calculate").attr("class","btn").click(function(){return d.click()})).append("<br>").append("<br>").append($("<pre>").attr("class",this["class"]+"-pre").html("Press the calculate button to update this data"))}__extends(b,a);b.i=0;b.prototype.attach=function(a){$(a).append(this.dom);return this.objects=$("."+this["class"]+"-pre")};b.prototype.set=function(a){var b,c;b=a.primer1,c=a.primer2;if(b!==this.primer1||c!==this.primer2){this.primer1=b;this.primer2=c;return this.objects.html("Press the calculate button to update this data")}};b.prototype.click=function(){var a;a=this.generateReport("Primer 1",this.primer1)+"\n\n"+this.generateReport("Primer 2",this.primer2);return this.objects.html(a)};b.prototype.generateReport=function(a,b){var c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r;g=[];g.push(a+":");l=RNA.fromString(b);p=l.findKnots(),h=p.matches,d=p.folds;g.push("Amount of matches: "+h);k=_.zip(function(){r=[];for(var a=1,c=b.length;1<=c?a<=c:a>=c;1<=c?a++:a--){r.push(a)}return r}.apply(this),b.split(""));e="";f="";for(n=0,o=k.length;n<o;n++){j=k[n];i=j[0]+" ";c=this.pad(j[1],i.length-1,true)+" ";if(e.length+i.length>60){g.push(e);g.push(f);g.push("");e="";f=""}e+=c;f+=i}if(e.length>0){g.push(e);g.push(f);g.push("")}return g.join("\n")};return b}(Display);var Primer;Primer=function(){function a(a){if(a instanceof DNA){this.seq=a.clone()}else{this.seq=DNA.fromString(a)}this.tail1=new DNA([]);this.tail2=new DNA([]);this.randEdgeSize=0}a.minLength=8;a.maxLength=50;a.maxDiff=8;a.lastData="";a.lastTail1="";a.lastTail2="";a.lastTm=0;a.lastRandEdgeSize=-1;a.reset=function(){this.lastData="";this.lastTm=0;this.lastTail1="";this.lastTail2="";return this.lastRandEdgeSize=-1};a.prototype.setTails=function(a,b){this.tail1=a;this.tail2=b};a.prototype.addRandomEdges=function(a){this.randEdgeSize=a};a.prototype.isSameAsLast=function(b,c){return a.lastTail1.toString()===this.tail1.toString()&&a.lastTail2.toString()===this.tail2.toString()&&a.lastData===DNA.fromString(b).toString()&&a.lastTm===c&&a.lastRandEdgeSize===this.randEdgeSize};a.prototype.generate=function(b){var c,d,e,f,g,h,i,j,k,l,m,n,o,p;if(2*a.minLength>this.seq.length()){throw new Error("The given sequence is too short")}a.lastData=this.seq.toString();a.lastTm=b;a.lastTail1=this.tail1;a.lastTail2=this.tail2;a.lastRandEdgeSize=this.randEdgeSize;f=Math.min(Math.floor(this.seq.length()/2),a.maxLength);m=this.seq.reverseComplement();g=-1;h=0;i=-1;j=0;for(d=o=a.minLength;o<=f?d<=f:d>=f;o<=f?d++:d--){n=this.seq.snip(d).tm();c=Math.abs(n-b);if(c<=a.maxDiff&&(g===-1||Math.abs(h-b)>c)){g=d;h=n}if(n>=b)break}for(e=p=a.minLength;p<=f?e<=f:e>=f;p<=f?e++:e--){n=m.snip(e).tm();c=Math.abs(n-b);if(c<=a.maxDiff&&(i===-1||Math.abs(j-b)>c)){i=e;j=n}if(n>=b)break}if(g<0||i<0){throw new Error("Couldn't find a primer of correct length that satisfies the conditions")}k=DNA.fromRandom(this.randEdgeSize);l=DNA.fromRandom(this.randEdgeSize);return{rs:{left:this.tail1.toString(),right:this.tail2.toString(),randomBases:this.randEdgeSize,full:k.toString()+this.tail1.toString()+this.seq.toString()+this.tail2.reverseComplement().toString()+l.reverseComplement().toString()},primer1:k.toString()+" "+this.tail1.toString()+" "+this.seq.snip(g).toString(),primers:{primer1:k.toString()+this.tail1.toString()+this.seq.snip(g).toString(),primer2:l.toString()+this.tail2.toString()+m.snip(i).toString()},primer1NoTail:this.seq.snip(g).toString(),primer1Tm:h,primer1Length:g,primer1TailLength:k.length()+this.tail1.length(),primer2:l.toString()+" "+this.tail2.toString()+" "+m.snip(i).toString(),primer2NoTail:m.snip(i).toString(),primer2Tm:j,primer2Length:i,primer2TailLength:l.length()+this.tail2.length(),full:k.toString()+this.tail1.toString()+this.seq.toString()+this.tail2.reverseComplement().toString()+l.reverseComplement().toString()}};return a}();var PrimerFinder;PrimerFinder=function(){function a(a){this.output=a.output;this.defaults={primer1:"No data",primer1Tm:"?",primer1Length:0,primer2:"No data",primer2Tm:"?",primer2Length:0,annealingTm:"?"}}a.prototype.calc=function(a,b,c){var d,e,f,g,h,i,j,k,l,m,n,o,p,q,r;if(c){b=["A fatal error occured:"].concat(b);this.output(a,b);return}q=this.defaults;for(d in q){m=q[d];if(!(a[d]!=null))a[d]=m}try{g=new Primer(a.dna);n=function(a,b,c){};if(a.type.custom)g.setTails(a.leftTail,a.rightTail);if(a.type.rs){e=a.leftRS.dna.findRS();f=a.rightRS.dna.findRS();if(e!=null&&e.length>0){b.push("The left restriction site is "+e)}else{b.push("The left restriction site wasn't recognized")}if(f!=null&&f.length>0){b.push("The right restriction site is "+f)}else{b.push("The right restriction site wasn't recognized")}g.setTails(a.leftRS.dna,a.rightRS.dna.reverseComplement());g.addRandomEdges(a.randomBases);b.push("Click the 'Generate' button to regenerate the random bases added on the end of the primers.");b.push("In the case of a plasmid where the piece between A and B is cut out, and A is used for the primer 1 RS (and B for the second).\nThe generated primers will put the RS such that the given DNA starts at the A side and ends at the B side (in short,\nit will probably work as you expected, but still check what happens with some other tool).")}if(a.type.known){k="";l="";r=window.tails;for(o=0,p=r.length;o<p;o++){j=r[o];if(j.value===a.standardTail){k=j.primer1Tail;l=j.primer2Tail;if(j.messages!=null)b=[].concat(j.messages);if(j.validate!=null)n=j.validate}}g.setTails(DNA.fromString(k),DNA.fromString(l))}h=g.generate(a.tm);i=n(h.primer1NoTail,h.primer2NoTail,a.dna);if(i!=null)b.push(i);for(d in h){m=h[d];a[d]=m}b=b}catch(s){b=[s.message]}a.annealingTm=Math.min(a.primer1Tm,a.primer2Tm);if(Math.abs(a.primer1Tm-a.primer2Tm)>5){b.push("The difference between the primer's Tm is more than 5°C")}if(a.annealingTm>70){b.push("Consider using the two-step PCR protocol")}if(a.annealingTm>72){b.push("Annealing temperature shouldn't exceed 72°C");a.annealingTm=72}if(a.annealingTm<45){b.push("The annealing temperature should be more than 45°C")}return this.output(a,b)};return a}();var RNA;RNA=function(){function a(a){this.data=a;this.n=this.data.length;this.knots=void 0}a.fromDNA=function(b){return new a(b.data.map(function(a){switch(a){case"T":return"U";default:return a}}))};a.fromString=function(b){return a.fromDNA(DNA.fromString(b))};a.prototype.P=function(a,b){if(this.data[a]==="A"&&this.data[b]==="U"||this.data[a]==="U"&&this.data[b]==="C"){return 1}else if(this.data[a]==="G"&&this.data[b]==="C"||this.data[a]==="C"&&this.data[b]==="G"){return 1}else{return 0}};a.prototype.isTooSelfComplementary=function(){var a,b,c,d,e,f,g,h,i;h=this.findKnots(),d=h.matches,b=h.folds;for(f=0,g=b.length;f<g;f++){a=b[f];e=[];console.log(a);for(c=0,i=a.length-1;0<=i?c<=i:c>=i;0<=i?c++:c--){if(a[c]==="("){if(c>0&&a[c-1]==="("){e[e.length-1]+=this.data[c]}else{e[e.length]=this.data[c]}}}console.log(e)}return false};a.prototype.findKnots=function(a){var b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,A,B,C,D,E,F,G,H,I,J,K,L,M,N=this;if(a==null)a=2;if(this.knots!==void 0)return this.knots;g=function(){var a,b,c;c=[];for(a=1,b=N.n;1<=b?a<=b:a>=b;1<=b?a++:a--){c.push(".")}return c};b=[];for(n=0,D=this.n-1;0<=D?n<=D:n>=D;0<=D?n++:n--){i=[];for(o=0,F=this.n-1;0<=F?o<=F:o>=F;0<=F?o++:o--){i[o]=[g()]}b[n]=i}c=function(){var a,b;b=[];for(k=1,a=this.n;1<=a?k<=a:k>=a;1<=a?k++:k--){b.push(function(){var a,b;b=[];for(l=1,a=this.n;1<=a?l<=a:l>=a;1<=a?l++:l--){b.push(0)}return b}.call(this))}return b}.call(this);for(k=G=this.n-1;G<=0?k<=0:k>=0;G<=0?k++:k--){for(l=k,H=this.n-1;k<=H?l<=H:l>=H;k<=H?l++:l--){p=0;if(k<l-a){p=c[k+1][l-1]+this.P(k,l);j=[];I=b[k+1][l-1];for(v=0,z=I.length;v<z;v++){s=I[v];if(this.P(k,l)===1){s[k]="(";s[l]=")"}else{s[k]=".";s[l]="."}if(j.length<50)j.push(s)}for(m=k,J=l-1;k<=J?m<=J:m>=J;k<=J?m++:m--){u=c[k][m]+c[m+1][l];if(u>p){p=u;j=[]}if(u>=p){K=b[k][m];for(w=0,A=K.length;w<A;w++){e=K[w];L=b[m+1][l];for(x=0,B=L.length;x<B;x++){f=L[x];d=g(this.n);for(r=0;0<=m?r<=m:r>=m;0<=m?r++:r--){d[r]=e[r]}for(r=M=m+1;M<=l?r<=l:r>=l;M<=l?r++:r--){d[r]=f[r]}if(j.length<50)j.push(d)}}}}c[k][l]=p;b[k][l]=j}}}q=[];h={};E=b[0][this.n-1];for(y=0,C=E.length;y<C;y++){s=E[y];t=s.join("");if(h[t]===void 0){h[t]=true;q.push(t)}}return this.knots={matches:c[0][this.n-1],folds:q}};return a}();var TmCalc;TmCalc=function(){function a(){}a.maxCacheSize=500;a.cache={};a.calc=function(b){var c,d,e;if(!this.cache[b]){e=Math.round(this.calcFull(b)*10)/10;if(this.cache.length>=this.maxCacheSize){d=Object.keys(a.cache);c=d[Math.floor(Math.random()*d.length)];delete a.cache[c]}this.cache[b]=e}return this.cache[b]};a.complement=function(a){switch(a){case"A":return"T";case"T":return"A";case"C":return"G";case"G":return"C";default:throw new Error("Invalid character encountered ("+a+")")}};a.neighborH={AA:9.1,AT:8.6,TA:6,CA:5.8,GT:6.5,CT:7.8,GA:5.6,CG:11.9,GC:11.1,GG:11};a.getH=function(a,b){return this.get(this.neighborH,a,b)};a.neighborG={AA:1.9,AT:1.5,TA:.9,CA:1.9,GT:1.3,CT:1.6,GA:1.6,CG:3.6,GC:3.1,GG:3.1};a.getG=function(a,b){return this.get(this.neighborG,a,b)};a.neighborS={AA:24,AT:23.9,TA:16.9,CA:12.9,GT:17.3,CT:20.8,GA:13.5,CG:27.8,GC:26.7,GG:26.6};a.getS=function(a,b){return this.get(this.neighborS,a,b)};a.get=function(a,b,c){switch(b+c){case"AA":return a["AA"];case"TT":return a["AA"];case"AT":return a["AT"];case"TA":return a["TA"];case"TT":return a["TA"];case"CA":return a["CA"];case"TG":return a["CA"];case"GT":return a["GT"];case"AC":return a["GT"];case"CT":return a["CT"];case"AG":return a["CT"];case"GA":return a["GA"];case"TC":return a["GA"];case"CG":return a["CG"];case"TC":return a["CG"];case"GC":return a["GC"];case"TC":return a["GC"];case"GG":return a["GG"];case"CC":return a["GG"];default:throw new Error("No idea what happened... (tried getting "+b+c+")")}};a.calcFull=function(a){var b,c,d,e,f,g,h,i,j,k,l,m,n,o;k=0;j=-(5+.4);l=0;m=500*.01;i=50*.01;b=1.987;g=a[0];for(f=1,o=a.length-1;1<=o?f<=o:f>=o;1<=o?f++:f--){h=a[f];k-=this.getH(g,h);j-=this.getG(g,h);l-=this.getS(g,h);g=h}c=1e3*k;d=l;e=-10.8;n=m/4*1e-6;return c/(e+d+b*Math.log(n/10))-273.15+16.6*Math.log(i/10)/Math.LN10};return a}();(function(){function a(b,c,d){if(b===c)return 0!==b||1/b==1/c;if(null==b||null==c)return b===c;b._chain&&(b=b._wrapped);c._chain&&(c=c._wrapped);if(b.isEqual&&v.isFunction(b.isEqual))return b.isEqual(c);if(c.isEqual&&v.isFunction(c.isEqual))return c.isEqual(b);var e=i.call(b);if(e!=i.call(c))return!1;switch(e){case"[object String]":return b==""+c;case"[object Number]":return b!=+b?c!=+c:0==b?1/b==1/c:b==+c;case"[object Date]":case"[object Boolean]":return+b==+c;case"[object RegExp]":return b.source==c.source&&b.global==c.global&&b.multiline==c.multiline&&b.ignoreCase==c.ignoreCase}if("object"!=typeof b||"object"!=typeof 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-Immutable class that makes it possible to work with (very simplified) DNA sequences
-*/
-var DNA,
-  __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; };
-DNA = (function() {
-  DNA.allowed = ["A", "C", "G", "T"];
-  DNA.extendedAllowed = ["A", "C", "G", "T", "R", "Y", "K", "M", "S", "W", "B", "D", "H", "V", "N"];
-  DNA.RS = {
-    AatI: "AGGCCT",
-    AatII: "GACGTC",
-    AccI: "GTMKAC",
-    AccIII: "TCCGGA",
-    Acc65I: "GGTACC",
-    AcsI: "RAATTY",
-    AcyI: "GRCGYC",
-    AflI: "GGWCC",
-    AflII: "CTTAAG",
-    AflIII: "ACRYGT",
-    AgeI: "ACCGGT",
-    AhaII: "GRCGYC",
-    AhaIII: "TTTAAA",
-    AluI: "AGCT",
-    Alw44I: "GTGCAC",
-    AlwNI: "CAGNNNCTG",
-    AocI: "CCTNAGG",
-    AosI: "TGCGCA",
-    ApaI: "GGGCCC",
-    ApaLI: "GTGCAC",
-    ApoI: "RAATTY",
-    ApyI: "CCWGG",
-    AscI: "GGCGCGCC",
-    AseI: "ATTAAT",
-    AsnI: "ATTAAT",
-    AspI: "GACNNNGTC",
-    Asp700: "GAANNNNTTC",
-    Asp718: "GGTACC",
-    AspEI: "GACNNNNNGTC",
-    AspHI: "GWGCWC",
-    AsuII: "TTCGAA",
-    AvaI: "CYCGRG",
-    AvaII: "GGWCC",
-    AviII: "TGCGCA",
-    AvrII: "CCTAGG",
-    BalI: "TGGCCA",
-    BamHI: "GGATCC",
-    BanI: "GGYRCC",
-    BanII: "GRGCYC",
-    BbrPI: "CACGTG",
-    BclI: "TGATCA",
-    BfaI: "CTAG",
-    BfrI: "CTTAAG",
-    BglI: "GCCNNNNNGGC",
-    BglII: "AGATCT",
-    BinI: "CCTAGG",
-    BmyI: "GDGCHC",
-    Bpu1102I: "GCTNAGC",
-    BsaAI: "YACGTR",
-    BsaBI: "GATNNNNATC",
-    BsaHI: "GRCGYC",
-    BsaJI: "CCNNGG",
-    BseAI: "TCCGGA",
-    BsePI: "GCGCGC",
-    BsiEI: "CGRYCG",
-    BsiWI: "CGTACG",
-    BsiYI: "CCNNNNNNNGG",
-    BslI: "CCNNNNNNNGG",
-    Bsp1286I: "GDGCHC",
-    Bsp1407I: "TGTACA",
-    BspDI: "ATCGAT",
-    BspEI: "TCCGGA",
-    BspHI: "TCATGA",
-    BspLU11I: "ACATGT",
-    BsrFI: "RCCGGY",
-    BssGI: "CCANNNNNNTGG",
-    BssHII: "GCGCGC",
-    Bst1107I: "GTATAC",
-    BstBI: "TTCGAA",
-    BstEII: "GGTNACC",
-    BstNI: "CCWGG",
-    BstUI: "CGCG",
-    BstXI: "CCANNNNNNTGG",
-    BstYI: "RGATCY",
-    Bsu36I: "CCTNAGG",
-    CelII: "GCTNAGC",
-    CfoI: "GCGC",
-    CfrI: "YGGCCR",
-    Cfr10I: "RCCGGY",
-    ClaI: "ATCGAT",
-    DdeI: "CTNAG",
-    DpnII: "GATC",
-    DraI: "TTTAAA",
-    DraII: "RGGNCCY",
-    DraIII: "CACNNNGTG",
-    DrdI: "GACNNNNNNGTC",
-    DsaI: "CCRYGG",
-    EaeI: "YGGCCR",
-    EagI: "CGGCCG",
-    Eam1105I: "GACNNNNNGTC",
-    Ecl136II: "GAGCTC",
-    EclXI: "CGGCCG",
-    Eco47III: "AGCGCT",
-    EcoNI: "CCTNNNNNAGG",
-    EcoO109I: "RGGNCCY",
-    EcoRI: "GAATTC",
-    EcoRII: "CCWGG",
-    EcoRV: "GATATC",
-    EspI: "GCTNAGC",
-    FnuDII: "CGCG",
-    Fnu4HI: "GCNGC",
-    FseI: "GGCCGGCC",
-    FspI: "TGCGCA",
-    HaeII: "RGCGCY",
-    HaeIII: "GGCC",
-    HgiAI: "GWGCWC",
-    HhaI: "GCGC",
-    HincII: "GTYRAC",
-    HindII: "GTYRAC",
-    HindIII: "AAGCTT",
-    HinfI: "GANTC",
-    HinPI: "GCGC",
-    HpaI: "GTTAAC",
-    HpaII: "CCGG",
-    ItaI: "GCNGC",
-    KasI: "GGCGCC",
-    KpnI: "GGTACC",
-    KspI: "CCGCGG",
-    MaeI: "CTAG",
-    MaeII: "ACGT",
-    MaeIII: "GTNAC",
-    MamI: "GATNNNNATC",
-    MboI: "GATC",
-    MfeI: "CAATTG",
-    MluI: "ACGCGT",
-    MluNI: "TGGCCA",
-    MroI: "TCCGGA",
-    MscI: "TGGCCA",
-    MseI: "TTAA",
-    MspI: "CCGG",
-    MstI: "TGCGCA",
-    MstII: "CCTNAGG",
-    MunI: "CAATTG",
-    MvaI: "CCWGG",
-    MvnI: "CGCG",
-    NaeI: "GCCGGC",
-    NarI: "GGCGCC",
-    NciI: "CCSGG",
-    NcoI: "CCATGG",
-    NdeI: "CATATG",
-    NdeII: "GATC",
-    NgoMI: "GCCGGC",
-    NheI: "GCTAGC",
-    NlaIII: "CATG",
-    NlaIV: "GGNNCC",
-    NotI: "GCGGCCGC",
-    NruI: "TCGCGA",
-    NsiI: "ATGCAT",
-    NspBII: "CMGCKG",
-    NspI: "RCATGY",
-    NspII: "GDGCHC",
-    NspV: "TTCGAA",
-    PacI: "TTAATTAA",
-    PaeR7I: "CTCGAG",
-    PflMI: "CCANNNNNTGG",
-    PinAI: "ACCGGT",
-    PsiI: "TTATAA",
-    PmaCI: "CACGTG",
-    PmeI: "GTTTAAAC",
-    PmlI: "CACGTG",
-    PpuMI: "RGGWCCY",
-    Psp1406I: "AACGTT",
-    PstI: "CTGCAG",
-    PvuI: "CGATCG",
-    PvuII: "CAGCTG",
-    RcaI: "TCATGA",
-    RmaI: "CTAG",
-    RsaI: "GTAC",
-    RsrII: "CGGWCCG",
-    SacI: "GAGCTC",
-    SacII: "CCGCGG",
-    SalI: "GTCGAC",
-    SauI: "CCTNAGG",
-    Sau3AI: "GATC",
-    Sau96I: "GGNCC",
-    ScaI: "AGTACT",
-    ScrFI: "CCNGG",
-    SexAI: "ACCWGGT",
-    SfcI: "CTRYAG",
-    SfiI: "GGCCNNNNNGGCC",
-    SfuI: "TTCGAA",
-    SgrAI: "CRCCGGYG",
-    SmaI: "CCCGGG",
-    SnaBI: "TACGTA",
-    SnoI: "GTGCAC",
-    SpeI: "ACTAGT",
-    SphI: "GCATGC",
-    SrfI: "GCCCGGGC",
-    Sse8387I: "CCTGCAGG",
-    SspI: "AATATT",
-    SspBI: "TGTACA",
-    SstI: "GAGCTC",
-    SstII: "CCGCGG",
-    StuI: "AGGCCT",
-    StyI: "CCWWGG",
-    SwaI: "ATTTAAAT",
-    TaqI: "TCGA",
-    TfiI: "GAWTC",
-    ThaI: "CGCG",
-    Tru9I: "TTAA",
-    Tth111I: "GACNNNGTC",
-    Van91I: "CCANNNNNTGG",
-    XbaI: "TCTAGA",
-    XcmI: "CCANNNNNNNNNTGG",
-    XhoI: "CTCGAG",
-    XhoII: "RGATCY",
-    XmaI: "CCCGGG",
-    XmaIII: "CGGCCG",
-    XmaCI: "CCCGGG",
-    XmnI: "GAANNNNTTC"
-  };
-  DNA.RSFlipped = void 0;
-  DNA.getRSFlipped = function() {
-    var name, seq, _ref;
-    if (this.RSFlipped === void 0) {
-      this.RSFlipped = {};
-      _ref = this.RS;
-      for (name in _ref) {
-        seq = _ref[name];
-        if (this.RSFlipped[seq]) {
-          this.RSFlipped[seq] += " / " + name;
-        } else {
-          this.RSFlipped[seq] = name;
-        }
-      }
-    }
-    return this.RSFlipped;
-  };
-  DNA.nucleotideMatches = {
-    A: ["A", "R", "M", "W", "D", "H", "V", "N"],
-    C: ["C", "Y", "M", "S", "B", "H", "V", "N"],
-    G: ["G", "R", "K", "S", "B", "D", "V", "N"],
-    T: ["T", "Y", "K", "W", "B", "D", "H", "N"],
-    R: ["A", "G"],
-    Y: ["C", "T"],
-    K: ["G", "T"],
-    M: ["A", "C"],
-    S: ["C", "G"],
-    W: ["A", "T"],
-    B: ["C", "G", "T"],
-    D: ["A", "G", "T"],
-    H: ["A", "C", "T"],
-    V: ["A", "C", "G"],
-    N: ["A", "C", "G", "T"]
-  };
-  DNA.fromString = function(data) {
-    var found, name, seq, sequence, _ref;
-    found = false;
-    _ref = this.RS;
-    for (name in _ref) {
-      sequence = _ref[name];
-      if (name.toLowerCase() === data.toLowerCase()) {
-        seq = new DNA(sequence.split(''));
-        found = true;
-      }
-    }
-    if (!found) {
-      seq = new DNA(data.toUpperCase().replace(/\s/ig, "").split(''));
-    }
-    seq.validateData();
-    return seq;
-  };
-  DNA.fromRandom = function(length) {
-    var data, i;
-    if (length === 0 || length === "0" || !length || length === void 0) {
-      return new DNA([]);
-    } else {
-      data = (function() {
-        var _i, _results;
-        _results = [];
-        for (i = _i = 1; 1 <= length ? _i <= length : _i >= length; i = 1 <= length ? ++_i : --_i) {
-          _results.push(DNA.allowed[Math.floor(Math.random() * DNA.allowed.length)]);
-        }
-        return _results;
-      })();
-      return new DNA(data);
-    }
-  };
-  /*
-    The constructor assumes the data has been validated (for performance reasons -> premature and non-consequent
-    optimization ^^). Anyway, the DNA.fromString function is probably what you were looking for!
-  */
-  function DNA(data) {
-    this.data = data;
-  }
-  DNA.prototype.validateData = function(strict) {
-    if (strict) {
-      if (this.data.some(function(x) {
-        return __indexOf.call(DNA.allowed, x) < 0;
-      })) {
-        throw new Error("Invalid character encountered");
-      }
-    } else {
-      if (this.data.some(function(x) {
-        return __indexOf.call(DNA.extendedAllowed, x) < 0;
-      })) {
-        throw new Error("Invalid character encountered");
-      }
-    }
-  };
-  DNA.prototype.matches = function(seq2) {
-    var combined;
-    if (this.length() !== seq2.length()) {
-      return false;
-    }
-    combined = _.zip(this.data, seq2.data);
-    return _.all(combined, function(_arg) {
-      var i, j, n1, n1Matches, n2, n2Matches, _i, _j, _ref, _ref1;
-      n1 = _arg[0], n2 = _arg[1];
-      if (n1 === n2) {
-        return true;
-      } else {
-        if (__indexOf.call(DNA.allowed, n1) >= 0) {
-          return __indexOf.call(DNA.nucleotideMatches[n1], n2) >= 0;
-        }
-        if (__indexOf.call(DNA.allowed, n2) >= 0) {
-          return __indexOf.call(DNA.nucleotideMatches[n2], n1) >= 0;
-        }
-        n1Matches = DNA.nucleotideMatches[n1];
-        n2Matches = DNA.nucleotideMatches[n2];
-        for (i = _i = 0, _ref = n1Matches.length - 1; 0 <= _ref ? _i <= _ref : _i >= _ref; i = 0 <= _ref ? ++_i : --_i) {
-          for (j = _j = 0, _ref1 = n2Matches.length - 1; 0 <= _ref1 ? _j <= _ref1 : _j >= _ref1; j = 0 <= _ref1 ? ++_j : --_j) {
-            if (n1Matches[i] === n2Matches[j]) {
-              return true;
-            }
-          }
-        }
-        return false;
-      }
-    });
-  };
-  DNA.prototype.findRS = function() {
-    var key, name, rs, seq, _ref;
-    key = this.data.join("");
-    rs = DNA.getRSFlipped();
-    if (rs[key]) {
-      return rs[key] + " (" + key + ")";
-    } else {
-      _ref = DNA.RS;
-      for (seq in _ref) {
-        name = _ref[seq];
-        if (this.matches(DNA.fromString(seq))) {
-          return name + " (" + seq + ")";
-        }
-      }
-      return "";
-    }
-  };
-  DNA.prototype.length = function() {
-    return this.data.length;
-  };
-  DNA.prototype.snip = function(length) {
-    if (length >= 0 && length <= this.data.length) {
-      return new DNA(this.data.slice(0, length));
-    } else {
-      throw new Error("Invalid snip length (tried to snip a piece of length " + length + " in a sequence of " + this.length() + "bp)");
-    }
-  };
-  DNA.prototype.reverseComplement = function() {
-    var complement, k, l, revCompl, v, _i, _len, _ref;
-    revCompl = [];
-    complement = function(x) {
-      switch (x) {
-        case "A":
-          return "T";
-        case "T":
-          return "A";
-        case "C":
-          return "G";
-        case "G":
-          return "C";
-        default:
-          throw new Error("Invalid character encountered (" + x + ")");
-      }
-    };
-    l = this.data.length - 1;
-    _ref = this.data;
-    for (k = _i = 0, _len = _ref.length; _i < _len; k = ++_i) {
-      v = _ref[k];
-      revCompl[l - k] = complement(v);
-    }
-    return new DNA(revCompl);
-  };
-  DNA.prototype.append = function(seqToAdd) {
-    return new DNA(this.data.concat(seqToAdd.data));
-  };
-  DNA.prototype.tm = function() {
-    return TmCalc.calc(this.data);
-  };
-  DNA.prototype.toString = function() {
-    return this.data.join("");
-  };
-  return DNA;
-})();
-window.tails = [
-	{
-		name: "Biobrick (gene)",
-		value: "biobrickGene",
-		primer1Tail: "GTT TCT TCG AAT TCG CGG CCG CTT CTA G",
-		primer2Tail: "GTT TCT TCC TGC AGC GGC CGC TAC TAG TA TTA TTA",
-		messages: [
-			"Don't forget to include the first ATG and to exclude the stop codon!",
-			"The recommended minimum length of a BioBrick primer is 20bp",
-			"The recommended Tm of a BioBrick primer is between 55 and 65 °C",
-			"Check that the following restriction sites are absent: EcoRI, SpeI, XbaI, PstI, NotI",
-			"Check out <a href='http://openwetware.org/wiki/Synthetic_Biology:BioBricks/Part_fabrication'>OpenWetWare's reference page</a>"
-		],
-		validate: function(primer1, primer2){
-			var start = primer1.substr(0, 3).toUpperCase();
-			if(start != "ATG"){
-				return "<b>The starting ATG seems to be absent.</b>"
-			}
-			var end = primer2.substr(0, 3).toUpperCase();
-			//         TAA             TGA             TAG
-			if(end == "TTA" || end == "TCA" || end == "CTA"){
-				return "<b>Remove the stop codons from the sequence!</b>"
-			}
-		}
-	},
-	{
-		name: "Biobrick (other)",
-		value: "biobrickOther",
-		primer1Tail: "GTT TCT TCG AAT TCG CGG CCG CTT CTA GAG",
-		primer2Tail: "GTT TCT TCC TGC AGC GGC CGC TAC TAG TA",
-		messages: [
-			"The recommended minimum length of a BioBrick primer is 20bp",
-			"The recommended Tm of a BioBrick primer is between 55 and 65 °C",
-			"Check that the following restriction sites are absent: EcoRI, SpeI, XbaI, PstI, NotI",
-			"Check out <a href='http://openwetware.org/wiki/Synthetic_Biology:BioBricks/Part_fabrication'>OpenWetWare's reference page</a>"
-		]
-	}
-];
-window.calc = function(){
-	var data = document.getElementById("data").value;
-	var isNormal = document.getElementById("primerTypeNormal").checked;
-	var isCustom = document.getElementById("primerTypeCustom").checked;
-	var isRS = document.getElementById("primerTypeRestrictionSites").checked;
-	var isKnown = document.getElementById("primerTypeKnownTail").checked;
-	var isNumbered = document.getElementById("toggleLines").checked;
-	var goalTm = document.getElementById("goalTm").value;
-	try{
-		var messages = [];
-		var toAdd = {};
-		var p = new Primer(data);
-		var validate = function(primer1, primer2){};
-		if(isCustom){
-			p.setTails(DNA.fromString(document.getElementById("primer1Tail").value), DNA.fromString(document.getElementById("primer2Tail").value));
-		}
-		if(isRS){
-			var rs1 = DNA.fromString(document.getElementById("primer1RS").value);
-			var rs2 = DNA.fromString(document.getElementById("primer2RS").value);
-			var match1 = rs1.findRS();
-			var match2 = rs2.findRS();
-			toAdd.primer1RSMatch = match1.length > 0 ? "- "+match1 : "";
-			toAdd.primer2RSMatch = match2.length > 0 ? "- "+match2 : "";
-			p.setTails(rs1, rs2.reverseComplement());
-			p.addRandomEdges(document.getElementById("primerRandBases").value);
-			messages.push("Click the 'Calculate' button to regenerate the random bases added on the end of the primers.");
-			messages.push(
-				"In the case of a plasmid where the piece between A and B is cut out, and A is used for the primer 1 RS (and B for the second). "
-				+ "The generated primers will put the RS such that the given DNA starts at the A side and ends at the B side (in short, "
-				+ "it will probably work as you expected, but still check what happens with some other tool)."
-			);
-		}
-		if(isKnown){
-			var selected = $("#knownTailSelect").val();
-			var tail1 = "";
-			var tail2 = "";
-			for(var i = 0; i < window.tails.length; i++){
-				if(window.tails[i].value == selected){
-					tail1 = window.tails[i].primer1Tail;
-					tail2 = window.tails[i].primer2Tail;
-					if(window.tails[i].messages)
-						messages = [].concat(window.tails[i].messages);
-					if(window.tails[i].validate)
-						validate = window.tails[i].validate;
-				}
-			}
-			p.setTails(DNA.fromString(tail1), DNA.fromString(tail2));
-		}
-		//if(!p.isSameAsLast(data, goalTm) || window.isCurrentlyNumbered != isNumbered){
-		window.isCurrentlyNumbered = isNumbered;
-		var primers = p.generate(goalTm);
-		for(var key in toAdd){
-			primers[key] = toAdd[key];
-		}
-		var result = validate(primers.primer1NoTail, primers.primer2NoTail);
-		if(result)
-			messages.push(result);
-		if(messages.length > 0){
-			window.output({
-				primers: primers,
-				messages: messages,
-				numbered: isNumbered
-			});
-		}else{
-			window.output({
-				primers: primers,
-				numbered: isNumbered
-			});
-		}
-		//}
-	}catch(e){
-		window.output({
-			error: e.message,
-			numbered: isNumbered
-		});
-	}
-};
-window.isCurrentlyNumbered = -1;
-window.output = function(options){
-	var output = {
-		message: [],
-		primer1: "No data",
-		primer1Temp: "NaN",
-		primer1bp: "NaN",
-		primer1Tailbp: "NaN",
-		primer1RSMatch: "",
-		primer2: "No data",
-		primer2Temp: "NaN",
-		primer2bp: "NaN",
-		primer2Tailbp: "NaN",
-		primer2RSMatch: "",
-		full: "",
-		numbered: false
-	};
-	if(options.numbered){
-		output.numbered = options.numbered;
-	}
-	if(options.error){
-		output.message.push(options.error);
-	}
-	if(options.messages){
-		output.message = output.message.concat(options.messages);
-	}
-	if(options.primers){
-		for(var key in options.primers){
-			if(key == "message"){
-				output[key].push(options.primers[key]);
-			}else{
-				output[key] = options.primers[key];
-			}
-		}
-	}
-	if(Math.abs(output.primer1Temp - output.primer2Temp) > 5){
-		output.message.push("The difference is more than 5 °C");
-	}
-	if(Math.min(output.primer1Temp, output.primer2Temp) > 72){
-		output.message.push("Consider using the two-step PCR protocol");
-	}
-	if(Math.min(output.primer1Temp, output.primer2Temp) > 72){
-		output.message.push("Annealing temperature shouldn't exceed 72 °C");
-	}
-	if(Math.min(output.primer1Temp, output.primer2Temp) < 45){
-		output.message.push("The annealing temperature should be more than 45 °C");
-	}
-	document.getElementById("primer1RSMatch").innerHTML = output.primer1RSMatch;
-	document.getElementById("primer2RSMatch").innerHTML = output.primer2RSMatch;
-	document.getElementById("messages").innerHTML = output.message.length > 0 ? "<ul><li>"+output.message.join("</li><li>")+"</li></ul>" : "";
-	document.getElementById("primer1").innerHTML = output.primer1;
-	document.getElementById("primer1Temp").innerHTML = output.primer1Temp;
-	document.getElementById("primer1bp").innerHTML = output.primer1Tailbp != 0 && output.primer1Tailbp != "NaN" ? output.primer1Tailbp+" + "+output.primer1bp : output.primer1bp;
-	document.getElementById("primer2").innerHTML = output.primer2;
-	document.getElementById("primer2Temp").innerHTML = output.primer2Temp;
-	document.getElementById("primer2bp").innerHTML = output.primer2Tailbp != 0 && output.primer2Tailbp != "NaN" ? output.primer2Tailbp+" + "+output.primer2bp : output.primer2bp;
-	document.getElementById("annealingTemp").innerHTML = Math.min(72, Math.min(output.primer1Temp, output.primer2Temp));
-	var width = 80;
-	var lines = window.wrap(output.full, width);
-	var outputLines = [];
-	if(output.numbered){
-		for(var i = 0; i < lines.length; i++){
-			outputLines[i] = window.pad(i*width+1, 6, true)+" - "+window.pad((i+1)*width, 6)+"  "+lines[i];
-		}
-	}else{
-		outputLines = lines;
-	}
-	document.getElementById("finalResult").innerHTML = outputLines.join("\n");
-};
-window.pad = function(str, width, right){
-	str += "";
-	while(str.length < width){
-		if(right){
-			str = " "+str;
-		}else{
-			str += " ";
-		}
-	}
-	return str;
-}
-window.wrap = function(str, width){
-	var chunks = [];
-	var i = 0, l = str.length;
-	while(i < l){
-		if(i + width >= l){
-			chunks.push(str.substr(i, l-i));
-		}else{
-			chunks.push(str.substr(i, width));
-		}
-		i += width;
-	}
-	return chunks;
-};
-window.updateRadioElements = function(){
-	if(document.getElementById('primerTypeRestrictionSites').checked){
-		$('#restrictionSiteRow').show();
-	}else{
-		$('#restrictionSiteRow').hide();
-	}
-	if(document.getElementById('primerTypeCustom').checked){
-		$('#customRow').show();
-	}else{
-		$('#customRow').hide();
-	}
-	if(document.getElementById('primerTypeKnownTail').checked){
-		$('#knownTailRow').show();
-	}else{
-		$('#knownTailRow').hide();
-	}
-};var Primer;
-Primer = (function() {
-  Primer.minLength = 8;
-  Primer.maxLength = 50;
-  Primer.maxDiff = 8;
-  Primer.lastData = "";
-  Primer.lastTail1 = "";
-  Primer.lastTail2 = "";
-  Primer.lastTm = 0;
-  Primer.lastRandEdgeSize = -1;
-  Primer.reset = function() {
-    this.lastData = "";
-    this.lastTm = 0;
-    this.lastTail1 = "";
-    this.lastTail2 = "";
-    return this.lastRandEdgeSize = -1;
-  };
-  function Primer(data) {
-    this.seq = DNA.fromString(data);
-    this.tail1 = new DNA([]);
-    this.tail2 = new DNA([]);
-    this.randEdgeSize = 0;
-  }
-  Primer.prototype.setTails = function(tail1, tail2) {
-    this.tail1 = tail1;
-    this.tail2 = tail2;
-  };
-  Primer.prototype.addRandomEdges = function(randEdgeSize) {
-    this.randEdgeSize = randEdgeSize;
-  };
-  Primer.prototype.isSameAsLast = function(data, tm) {
-    return Primer.lastTail1.toString() === this.tail1.toString() && Primer.lastTail2.toString() === this.tail2.toString() && Primer.lastData === DNA.fromString(data).toString() && Primer.lastTm === tm && Primer.lastRandEdgeSize === this.randEdgeSize;
-  };
-  Primer.prototype.generate = function(goal) {
-    var diff, l1, l2, maxLength, primer1Length, primer1Temp, primer2Length, primer2Temp, rand1, rand2, revCompl, temp, _i, _j, _ref, _ref1;
-    if (2 * Primer.minLength > this.seq.length()) {
-      throw new Error("The given sequence is too short");
-    }
-    Primer.lastData = this.seq.toString();
-    Primer.lastTm = goal;
-    Primer.lastTail1 = this.tail1;
-    Primer.lastTail2 = this.tail2;
-    Primer.lastRandEdgeSize = this.randEdgeSize;
-    maxLength = Math.min(Math.floor(this.seq.length() / 2), Primer.maxLength);
-    revCompl = this.seq.reverseComplement();
-    primer1Length = -1;
-    primer1Temp = 0;
-    primer2Length = -1;
-    primer2Temp = 0;
-    for (l1 = _i = _ref = Primer.minLength; _ref <= maxLength ? _i <= maxLength : _i >= maxLength; l1 = _ref <= maxLength ? ++_i : --_i) {
-      temp = this.seq.snip(l1).tm();
-      diff = Math.abs(temp - goal);
-      if (diff <= Primer.maxDiff && (primer1Length === -1 || Math.abs(primer1Temp - goal) > diff)) {
-        primer1Length = l1;
-        primer1Temp = temp;
-      }
-      if (temp >= goal) {
-        break;
-      }
-    }
-    for (l2 = _j = _ref1 = Primer.minLength; _ref1 <= maxLength ? _j <= maxLength : _j >= maxLength; l2 = _ref1 <= maxLength ? ++_j : --_j) {
-      temp = revCompl.snip(l2).tm();
-      diff = Math.abs(temp - goal);
-      if (diff <= Primer.maxDiff && (primer2Length === -1 || Math.abs(primer2Temp - goal) > diff)) {
-        primer2Length = l2;
-        primer2Temp = temp;
-      }
-      if (temp >= goal) {
-        break;
-      }
-    }
-    if (primer1Length < 0 || primer2Length < 0) {
-      throw new Error("Couldn't find a primer of correct length that satisfies the conditions");
-    }
-    rand1 = DNA.fromRandom(this.randEdgeSize);
-    rand2 = DNA.fromRandom(this.randEdgeSize);
-    return {
-      primer1: rand1.toString() + " " + this.tail1.toString() + " " + this.seq.snip(primer1Length).toString(),
-      primer1NoTail: this.seq.snip(primer1Length).toString(),
-      primer1Temp: primer1Temp,
-      primer1bp: primer1Length,
-      primer1Tailbp: rand1.length() + this.tail1.length(),
-      primer2: rand2.toString() + " " + this.tail2.toString() + " " + revCompl.snip(primer2Length).toString(),
-      primer2NoTail: revCompl.snip(primer2Length).toString(),
-      primer2Temp: primer2Temp,
-      primer2bp: primer2Length,
-      primer2Tailbp: rand2.length() + this.tail2.length(),
-      full: rand1.toString() + this.tail1.toString() + this.seq.toString() + this.tail2.reverseComplement().toString() + rand2.reverseComplement().toString()
-    };
-  };
-  return Primer;
-})();
-var RNA;
-RNA = (function() {
-  RNA.fromDNA = function(dna) {
-    return new RNA(dna.data.map(function(x) {
-      switch (x) {
-        case "T":
-          return "U";
-        default:
-          return x;
-      }
-    }));
-  };
-  RNA.fromString = function(data) {
-    return RNA.fromDNA(DNA.fromString(data));
-  };
-  /*
-    Note: Just like for the DNA class, you probably didn't want to use the constructor. Use fromDNA or fromString instead!
-  */
-  function RNA(data) {
-    this.data = data;
-    this.n = this.data.length;
-    this.knots = void 0;
-  }
-  RNA.prototype.P = function(i, j) {
-    if ((this.data[i] === "A" && this.data[j] === "U") || (this.data[i] === "U" && this.data[j] === "C")) {
-      return 1;
-    } else if ((this.data[i] === "G" && this.data[j] === "C") || (this.data[i] === "C" && this.data[j] === "G")) {
-      return 1;
-    } else {
-      return 0;
-    }
-  };
-  RNA.prototype.isTooSelfComplementary = function() {
-    var matches;
-    matches = this.findKnots().matches;
-    return (matches / (this.n / 2)) > 0.5;
-  };
-  RNA.prototype.findKnots = function(minSize) {
-    var HM, M, a, a1, a2, createSolution, hashSet, hm, hs, i, j, k, l, m, max, output, p, sol, str, tmp, _i, _j, _k, _l, _len, _len1, _len2, _len3, _m, _n, _o, _p, _q, _r, _ref, _ref1, _ref2, _ref3, _ref4, _ref5, _ref6, _ref7, _ref8, _ref9, _s,
-      _this = this;
-    if (minSize == null) {
-      minSize = 2;
-    }
-    if (this.knots !== void 0) {
-      return this.knots;
-    }
-    createSolution = function() {
-      var i, _i, _ref, _results;
-      _results = [];
-      for (i = _i = 1, _ref = _this.n; 1 <= _ref ? _i <= _ref : _i >= _ref; i = 1 <= _ref ? ++_i : --_i) {
-        _results.push(".");
-      }
-      return _results;
-    };
-    HM = [];
-    for (l = _i = 0, _ref = this.n - 1; 0 <= _ref ? _i <= _ref : _i >= _ref; l = 0 <= _ref ? ++_i : --_i) {
-      hm = [];
-      for (m = _j = 0, _ref1 = this.n - 1; 0 <= _ref1 ? _j <= _ref1 : _j >= _ref1; m = 0 <= _ref1 ? ++_j : --_j) {
-        hm[m] = [createSolution()];
-      }
-      HM[l] = hm;
-    }
-    M = (function() {
-      var _k, _ref2, _results;
-      _results = [];
-      for (i = _k = 1, _ref2 = this.n; 1 <= _ref2 ? _k <= _ref2 : _k >= _ref2; i = 1 <= _ref2 ? ++_k : --_k) {
-        _results.push((function() {
-          var _l, _ref3, _results1;
-          _results1 = [];
-          for (j = _l = 1, _ref3 = this.n; 1 <= _ref3 ? _l <= _ref3 : _l >= _ref3; j = 1 <= _ref3 ? ++_l : --_l) {
-            _results1.push(0);
-          }
-          return _results1;
-        }).call(this));
-      }
-      return _results;
-    }).call(this);
-    for (i = _k = _ref2 = this.n - 1; _ref2 <= 0 ? _k <= 0 : _k >= 0; i = _ref2 <= 0 ? ++_k : --_k) {
-      for (j = _l = i, _ref3 = this.n - 1; i <= _ref3 ? _l <= _ref3 : _l >= _ref3; j = i <= _ref3 ? ++_l : --_l) {
-        max = 0;
-        if (i < j - minSize) {
-          max = M[i + 1][j - 1] + this.P(i, j);
-          hs = [];
-          _ref4 = HM[i + 1][j - 1];
-          for (_m = 0, _len = _ref4.length; _m < _len; _m++) {
-            sol = _ref4[_m];
-            if (this.P(i, j) === 1) {
-              sol[i] = "(";
-              sol[j] = ")";
-            } else {
-              sol[i] = ".";
-              sol[j] = ".";
-            }
-            if (hs.length < 50) {
-              hs.push(sol);
-            }
-          }
-          for (k = _n = i, _ref5 = j - 1; i <= _ref5 ? _n <= _ref5 : _n >= _ref5; k = i <= _ref5 ? ++_n : --_n) {
-            tmp = M[i][k] + M[k + 1][j];
-            if (tmp > max) {
-              max = tmp;
-              hs = [];
-            }
-            if (tmp >= max) {
-              _ref6 = HM[i][k];
-              for (_o = 0, _len1 = _ref6.length; _o < _len1; _o++) {
-                a1 = _ref6[_o];
-                _ref7 = HM[k + 1][j];
-                for (_p = 0, _len2 = _ref7.length; _p < _len2; _p++) {
-                  a2 = _ref7[_p];
-                  a = createSolution(this.n);
-                  for (p = _q = 0; 0 <= k ? _q <= k : _q >= k; p = 0 <= k ? ++_q : --_q) {
-                    a[p] = a1[p];
-                  }
-                  for (p = _r = _ref8 = k + 1; _ref8 <= j ? _r <= j : _r >= j; p = _ref8 <= j ? ++_r : --_r) {
-                    a[p] = a2[p];
-                  }
-                  if (hs.length < 50) {
-                    hs.push(a);
-                  }
-                }
-              }
-            }
-          }
-          M[i][j] = max;
-          HM[i][j] = hs;
-        }
-      }
-    }
-    output = [];
-    hashSet = {};
-    _ref9 = HM[0][this.n - 1];
-    for (_s = 0, _len3 = _ref9.length; _s < _len3; _s++) {
-      sol = _ref9[_s];
-      str = sol.join("");
-      if (hashSet[str] === void 0) {
-        hashSet[str] = true;
-        output.push(str);
-      }
-    }
-    return this.knots = {
-      matches: M[0][this.n - 1],
-      folds: output
-    };
-  };
-  return RNA;
-})();
-/*
-Container class that helps with Tm calculations. It has been seperated to enable easy improvements to the
-algorithm.
-*/
-var TmCalc;
-TmCalc = (function() {
-  function TmCalc() {}
-  TmCalc.maxCacheSize = 500;
-  TmCalc.cache = {};
-  TmCalc.calc = function(data) {
-    var key, keys, result;
-    if (!this.cache[data]) {
-      result = Math.round(this.calcFull(data) * 10) / 10;
-      if (this.cache.length >= this.maxCacheSize) {
-        keys = Object.keys(TmCalc.cache);
-        key = keys[Math.floor(Math.random() * keys.length)];
-        delete TmCalc.cache[key];
-      }
-      this.cache[data] = result;
-    }
-    return this.cache[data];
-  };
-  TmCalc.complement = function(n) {
-    switch (n) {
-      case "A":
-        return "T";
-      case "T":
-        return "A";
-      case "C":
-        return "G";
-      case "G":
-        return "C";
-      default:
-        throw new Error("Invalid character encountered (" + n + ")");
-    }
-  };
-  TmCalc.neighborH = {
-    AA: 9.1,
-    AT: 8.6,
-    TA: 6.0,
-    CA: 5.8,
-    GT: 6.5,
-    CT: 7.8,
-    GA: 5.6,
-    CG: 11.9,
-    GC: 11.1,
-    GG: 11.0
-  };
-  TmCalc.getH = function(n1, n2) {
-    return this.get(this.neighborH, n1, n2);
-  };
-  TmCalc.neighborG = {
-    AA: 1.9,
-    AT: 1.5,
-    TA: 0.9,
-    CA: 1.9,
-    GT: 1.3,
-    CT: 1.6,
-    GA: 1.6,
-    CG: 3.6,
-    GC: 3.1,
-    GG: 3.1
-  };
-  TmCalc.getG = function(n1, n2) {
-    return this.get(this.neighborG, n1, n2);
-  };
-  TmCalc.neighborS = {
-    AA: 24.0,
-    AT: 23.9,
-    TA: 16.9,
-    CA: 12.9,
-    GT: 17.3,
-    CT: 20.8,
-    GA: 13.5,
-    CG: 27.8,
-    GC: 26.7,
-    GG: 26.6
-  };
-  TmCalc.getS = function(n1, n2) {
-    return this.get(this.neighborS, n1, n2);
-  };
-  TmCalc.get = function(searchVar, n1, n2) {
-    switch (n1 + n2) {
-      case "AA":
-        return searchVar["AA"];
-      case "TT":
-        return searchVar["AA"];
-      case "AT":
-        return searchVar["AT"];
-      case "TA":
-        return searchVar["TA"];
-      case "TT":
-        return searchVar["TA"];
-      case "CA":
-        return searchVar["CA"];
-      case "TG":
-        return searchVar["CA"];
-      case "GT":
-        return searchVar["GT"];
-      case "AC":
-        return searchVar["GT"];
-      case "CT":
-        return searchVar["CT"];
-      case "AG":
-        return searchVar["CT"];
-      case "GA":
-        return searchVar["GA"];
-      case "TC":
-        return searchVar["GA"];
-      case "CG":
-        return searchVar["CG"];
-      case "TC":
-        return searchVar["CG"];
-      case "GC":
-        return searchVar["GC"];
-      case "TC":
-        return searchVar["GC"];
-      case "GG":
-        return searchVar["GG"];
-      case "CC":
-        return searchVar["GG"];
-      default:
-        throw new Error("No idea what happened... (tried getting " + n1 + n2 + ")");
-    }
-  };
-  TmCalc.calcFull = function(data) {
-    /* See (Breslauer et al. 1986): http://www.pnas.org/content/83/11/3746.full.pdf
-    */
-    var R, dh, ds, dsinit, i, n1, n2, naConc, predG, predH, predS, primerConc, primerc_local, _i, _ref;
-    predH = 0;
-    predG = -(5 + 0.4);
-    predS = 0;
-    primerConc = 500 * 10e-3;
-    naConc = 50 * 10e-3;
-    R = 1.987;
-    n1 = data[0];
-    for (i = _i = 1, _ref = data.length - 1; 1 <= _ref ? _i <= _ref : _i >= _ref; i = 1 <= _ref ? ++_i : --_i) {
-      n2 = data[i];
-      predH -= this.getH(n1, n2);
-      predG -= this.getG(n1, n2);
-      predS -= this.getS(n1, n2);
-      n1 = n2;
-    }
-    dh = 1000 * predH;
-    ds = predS;
-    dsinit = -10.8;
-    primerc_local = primerConc / 4 * 1e-6;
-    return dh / (dsinit + ds + R * Math.log(primerc_local / 10)) - 273.15 + 16.6 * Math.log(naConc / 10) / Math.LN10;
-  };
-  /* Again, old
-  @calcFull: (data, options) ->
-    ##
-    For more details see: http://www.basic.northwestern.edu/biotools/oligocalc.html
-    ##
-    freq = @calcFrequencies(data)
-    if not options
-      options = {}
-    if not options.Na
-      options.Na = 0.05
-    GC = freq["G"] + freq["C"]
-    AT = freq["A"] + freq["T"]
-    N = data.length
-    if N < 14
-      AT*2 + GC*4 - 16.6*Math.log(0.050)/Math.log(10) + 16.6*Math.log(options.Na)/Math.log(10)
-    else if N < 50 #18
-.5 + (41 * GC/N) - (820/N) + 16.6*Math.log(options.Na)/Math.log(10)
-    #else if N < 50
-    #  81.5 + (41 * GC/N) - (500/N) + 16.6*Math.log(options.Na) - 0.62*options.F
-    else
-.8 + 18.5*Math.log(options.Na)/Math.log(10) + (58.4 * GC/N) + (11.8 * (GC/N) * (GC/N)) - (820/N)
-  @calcFrequencies: (data) ->
-    freq = {A: 0, C: 0, G: 0, T: 0}
-    data.forEach (x) ->
-      freq[x]++
-    freq
-  */
-  return TmCalc;
-})();
-/* Old version (not very accurate):
-  @calc: (data) ->
-    Math.round(@calcFull(data)*100)/100
-  @calcFull: (data) ->
-    freq = @calcFrequencies(data)
-    if data.length < 14
-* (freq["G"] + freq["C"]) + 2 * (freq["A"] + freq["T"])
-    else
-.9 + 41 * (freq["G"] + freq["C"] - 16.4)/data.length
-  @calcFrequencies: (data) ->
-    freq = {A: 0, C: 0, G: 0, T: 0}
-    data.forEach (x) ->
-      freq[x]++
-    freq
-*/
-// Underscore.js 1.3.3
-// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
-// Underscore is freely distributable under the MIT license.
-// Portions of Underscore are inspired or borrowed from Prototype,
-// Oliver Steele's Functional, and John Resig's Micro-Templating.
-// For all details and documentation:
-// http://documentcloud.github.com/underscore
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