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/* Immutable class that makes it possible to work with (very simplified) DNA sequences */ var DNA, __indexOf = Array.prototype.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", XmnI: "GAANNNNTTC" }; DNA.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 }; DNA.RSFlipped = void 0; DNA.getRSFlipped = function() { var key, name, seq, value, _ref, _ref2; if (this.RSFlipped === void 0) { this.RSFlipped = {}; _ref = this.RS; for (name in _ref) { seq = _ref[name]; if (this.RSFlipped[seq]) { this.RSFlipped[seq].push(name); } else { this.RSFlipped[seq] = [name]; } } _ref2 = this.RSFlipped; for (key in _ref2) { value = _ref2[key]; if (value.length <= 2) { this.RSFlipped[key] = value.join(" or "); } else { this.RSFlipped[key] = value.slice(0, value.length - 1).join(", ") + " or " + value[value.length - 1]; } } } return this.RSFlipped; }; DNA.getCutPosition = function(rs) { var k, v, _ref; if (DNA.cutPositions[rs]) { return DNA.cutPositions[rs]; } else { _ref = DNA.cutPositions; for (k in _ref) { v = _ref[k]; if (k.toLowerCase() === rs.toLowerCase()) return v; } return -1; } }; 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; if (data != null) { _ref = this.RS; for (name in _ref) { sequence = _ref[name]; if (name.toLowerCase() === data.toLowerCase()) { seq = new DNA(sequence.split('')); found = true; } } } else { data = ""; } 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 _results; _results = []; for (i = 1; 1 <= length ? i <= length : i >= length; 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, _ref, _ref2; 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 = 0, _ref = n1Matches.length - 1; 0 <= _ref ? i <= _ref : i >= _ref; 0 <= _ref ? i++ : i--) { for (j = 0, _ref2 = n2Matches.length - 1; 0 <= _ref2 ? j <= _ref2 : j >= _ref2; 0 <= _ref2 ? j++ : j--) { if (n1Matches[i] === n2Matches[j]) return true; } } return false; } }); }; DNA.prototype.findRS = function(nameOnly) { var key, name, rs, rsDNA, seq, _ref; if (nameOnly == null) nameOnly = false; if (this.length() > 15) return ""; key = this.data.join(""); rs = DNA.getRSFlipped(); if (rs[key]) { if (nameOnly) { return rs[key]; } else { return rs[key] + " (5' &rarr; 3': " + key + ")"; } } else { _ref = DNA.RS; for (seq in _ref) { name = _ref[seq]; rsDNA = DNA.fromString(seq); if (this.matches(rsDNA)) { if (nameOnly) { name; } else { name + " (5' &rarr; 3': " + key + ")"; } } } return ""; } }; DNA.prototype.getCutPosition = function() { return DNA.getCutPosition(this.findRS(true)); }; DNA.prototype.containsRS = function(names) { var c, comparisons, i, lengths, name, parts, pos, rs, _i, _j, _len, _len2, _ref; comparisons = []; for (_i = 0, _len = names.length; _i < _len; _i++) { name = names[_i]; comparisons.push(name.toLowerCase()); } lengths = (function() { var _results; _results = []; for (i = 0; i <= 10; i++) { _results.push(""); } return _results; })(); rs = DNA.getRSFlipped(); pos = 0; _ref = this.data; for (_j = 0, _len2 = _ref.length; _j < _len2; _j++) { c = _ref[_j]; for (i = 4; i <= 10; i++) { lengths[i] += c; if (i <= pos) lengths[i] = lengths[i].substr(1); if (rs[lengths[i]]) { parts = rs[lengths[i]].toLowerCase().split(" "); if (_.some(comparisons, function(obj) { return __indexOf.call(parts, obj) >= 0; })) { return true; } } } pos++; } return false; }; 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, _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 = 0, _len = _ref.length; k < _len; k++) { 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(""); }; DNA.prototype.toJSON = function() { return this.toString(); }; DNA.prototype.clone = function() { return new DNA(this.data.slice(0)); }; return DNA; })(); var DNAInput, DNARSInput, DNASmallInput, Input, InputForm, NumberInput, RadioInput, SelectInput, Separator, Submit, TemperatureInput, __hasProp = Object.prototype.hasOwnProperty, __extends = function(child, parent) { for (var key in parent) { if (__hasProp.call(parent, key)) child[key] = parent[key]; } function ctor() { this.constructor = child; } ctor.prototype = parent.prototype; child.prototype = new ctor; child.__super__ = parent.prototype; return child; }; InputForm = (function() { InputForm.i = 0; /* [{ name: "tm", readableName: "Tm", type: "TemperatureInput", label: "Tm" }] */ InputForm.create = function(options, objects) { var f; f = new InputForm(options); objects.forEach(function(x) { return f.addInput(x); }); return f; }; function InputForm(_arg) { this.update = _arg.update, this.submit = _arg.submit, this.name = _arg.name; this.id = "inputform-" + InputForm.i++; this.inputs = []; this.inputDict = {}; this.lastValue = {}; } InputForm.prototype.save = function(data) { var k, tempData, v; try { if (JSON && localStorage) { tempData = {}; for (k in data) { v = data[k]; if (k === "leftRS" || k === "rightRS") v = v.rs; tempData[k] = v; } return localStorage.setItem("values", JSON.stringify(tempData)); } } catch (e) { } }; InputForm.prototype.restore = function() { var k, oldVals, v, _results; try { if (JSON && localStorage) { oldVals = localStorage.getItem("values"); if (oldVals != null) { oldVals = JSON.parse(oldVals); _results = []; for (k in oldVals) { v = oldVals[k]; _results.push(this.inputDict[k].value(v)); } return _results; } } } catch (e) { } }; InputForm.prototype.attach = function(elem) { $(elem).append(this.generateDOM()); $(".help-block").hide(); this.restore(); return this.updateCallback(); }; InputForm.prototype.submitCallback = function() { var changed, data, error, messages, _ref; _ref = this.getFormData(), data = _ref.data, messages = _ref.messages, error = _ref.error, changed = _ref.changed; return typeof this.submit === "function" ? this.submit(data, messages, error) : void 0; }; InputForm.prototype.updateCallback = function() { var changed, data, error, messages, _ref; if (this.disableAuto) return; _ref = this.getFormData(), data = _ref.data, messages = _ref.messages, error = _ref.error, changed = _ref.changed; if (changed) { return typeof this.update === "function" ? this.update(data, messages, error) : void 0; } }; InputForm.prototype.getFormData = function() { var changed, data, error, messages; data = {}; messages = []; error = false; this.inputs.forEach(function(x) { var val; val = void 0; try { val = x.value(); } catch (e) { messages.push("Error: " + e.message); } if (!x.validate(val)) { error = true; messages.push("The value of " + x.get("label") + " is invalid"); } if (x.get("name") != null) return data[x.get("name")] = val; }); changed = false; if (!_.isEqual(this.lastValue, data)) { changed = true; this.inputs.forEach(function(x) { if (x.visible(data)) { return x.show(); } else { return x.hide(); } }); this.lastValue = data; this.save(data); } return { data: data, messages: messages, error: error, changed: changed }; }; InputForm.prototype.addInput = function(input) { var callback, inputObj, _this = this; if (input === "Separator") { this.inputs.push(new Separator()); return; } if (!window[input.type] instanceof Function) { throw new Error("Passed input can't be instantiated"); } callback = function() { return _this.updateCallback.apply(_this, arguments); }; if (input.type === "Submit") { callback = function() { return _this.submitCallback.apply(_this, arguments); }; } inputObj = new window[input.type](callback, input); if (!inputObj instanceof Input) throw new Error("Object isn't an input"); this.inputDict[input.name] = inputObj; this.inputs.push(inputObj); return this; }; InputForm.prototype.get = function(field) { return this.inputDict[field]; }; InputForm.prototype.generateDOM = function() { var fieldset, form, _this = this; form = $("<form>").attr("id", this.id).attr("class", "form-horizontal"); if (this.name != null) { fieldset = $("<fieldset>").append($("<legend>").text(this.name)); form.append(fieldset); } else { fieldset = form; } this.inputs.forEach(function(input) { return fieldset.append(input.generateDOM()); }); fieldset.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 _this.disableAuto = false; } else { return _this.disableAuto = true; } })))); return form; }; return InputForm; })(); Input = (function() { Input.i = 0; function Input(callback, data, rowClass) { this.callback = callback; this.data = data; this.rowClass = rowClass != null ? rowClass : ""; this.id = "input-" + Input.i++; this.type = "text"; } Input.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())); }; Input.prototype.generateLabelDOM = function() { return $("<label>").attr("class", "control-label").attr("for", this.id).html(this.data.label); }; Input.prototype.generateInputElementDOM = function(id, type, value, callback) { var element; element = $("<input>").attr("class", "input-medium").attr("type", type).attr("id", id).on("change", callback).on("keyup", callback); element.val(value); return element; }; Input.prototype.generateElementDOM = function() { return this.generateInputElementDOM(this.id, this.type, this.data.value, this.callback); }; Input.prototype.generateHelpDOM = function(helpData) { if (helpData == null) helpData = this.data.help; if ((helpData != null) && helpData.length > 0) { return $("<p>").attr("class", "help-block").html(helpData); } else { return $("<p>").attr("class", "help-block").attr("style", "display: none"); } }; Input.prototype.get = function(key) { return this.data[key]; }; Input.prototype.visible = function(vals) { if (this.data.visible != null) { return this.data.visible(vals); } else { return true; } }; Input.prototype.hide = function() { return $("#row-" + this.id).hide(); }; Input.prototype.show = function() { return $("#row-" + this.id).show(); }; Input.prototype.value = function(value) { if (value === void 0) { return $("#" + this.id).val(); } else { return $("#" + this.id).val(value); } }; Input.prototype.validate = function(val) { return true; }; return Input; })(); Separator = (function(_super) { __extends(Separator, _super); function Separator() { Separator.__super__.constructor.apply(this, arguments); } Separator.prototype.generateDOM = function() { return $("<hr>").attr("id", "row-" + this.id); }; Separator.prototype.value = function() {}; Separator.prototype.validate = function() { return true; }; return Separator; })(Input); Submit = (function(_super) { __extends(Submit, _super); function Submit() { Submit.__super__.constructor.apply(this, arguments); } Submit.prototype.generateElementDOM = function() { return $("<input>").attr("type", "submit").attr("value", this.data.value).attr("class", "btn").click(this.callback, function(e) { e.preventDefault(); e.data(e); return false; }); }; Submit.prototype.value = function() {}; Submit.prototype.validate = function() { return true; }; return Submit; })(Input); NumberInput = (function(_super) { __extends(NumberInput, _super); function NumberInput() { NumberInput.__super__.constructor.apply(this, arguments); this.type = "number"; } NumberInput.prototype.value = function(value) { if (value === void 0) { return parseInt(NumberInput.__super__.value.call(this), 10); } else { return NumberInput.__super__.value.call(this, parseInt(value, 10)); } }; NumberInput.prototype.validate = function(val) { return !isNaN(val); }; return NumberInput; })(Input); TemperatureInput = (function(_super) { __extends(TemperatureInput, _super); function TemperatureInput() { TemperatureInput.__super__.constructor.apply(this, arguments); } TemperatureInput.prototype.generateElementDOM = function() { var input; input = TemperatureInput.__super__.generateElementDOM.call(this); return $("<div>").attr("class", "input-append").append(input).append($("<span>").attr("class", "add-on").text("\u00B0C")); }; return TemperatureInput; })(NumberInput); DNAInput = (function(_super) { __extends(DNAInput, _super); function DNAInput() { DNAInput.__super__.constructor.apply(this, arguments); } DNAInput.prototype.generateElementDOM = function() { var textarea; textarea = $("<textarea>").attr("class", "input-xlarge").attr("id", this.id).on("change", this.callback).on("keyup", this.callback); textarea.val(this.data.value); return textarea; }; DNAInput.prototype.value = function(value) { if (value === void 0) { return DNA.fromString(DNAInput.__super__.value.call(this)); } else { return DNAInput.__super__.value.call(this, value.toString()); } }; DNAInput.prototype.validate = function(val) { return val !== void 0; }; return DNAInput; })(Input); DNASmallInput = (function(_super) { __extends(DNASmallInput, _super); function DNASmallInput() { DNASmallInput.__super__.constructor.apply(this, arguments); } DNASmallInput.prototype.generateElementDOM = function() { var input; input = DNASmallInput.__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 DNASmallInput; })(DNAInput); DNARSInput = (function(_super) { __extends(DNARSInput, _super); function DNARSInput() { DNARSInput.__super__.constructor.apply(this, arguments); } DNARSInput.prototype.generateElementDOM = function() { var input; input = DNARSInput.__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")); }; DNARSInput.prototype.value = function(value) { var val; val = DNARSInput.__super__.value.call(this, value); if ((val != null) && val instanceof DNA) { $("#" + this.id + "-rs").html(val.toString()); } if (val === void 0) val = DNA.fromString(""); return { dna: val, rs: $("#" + this.id).val() }; }; return DNARSInput; })(DNAInput); SelectInput = (function(_super) { __extends(SelectInput, _super); function SelectInput(callback, obj) { SelectInput.__super__.constructor.apply(this, arguments); this.choices = obj.choices; } SelectInput.prototype.generateElementDOM = function() { var container, input, _this = this; input = SelectInput.__super__.generateElementDOM.call(this); container = $("<select>").attr("class", "input-medium").attr("id", this.id).on("change", this.callback).on("click", this.callback); this.choices.forEach(function(_arg) { var name, value; name = _arg.name, value = _arg.value; return container.append($("<option>").attr("value", name).text(value)); }); return container; }; return SelectInput; })(Input); RadioInput = (function(_super) { __extends(RadioInput, _super); function RadioInput(callback, obj) { RadioInput.__super__.constructor.apply(this, arguments); this.choices = obj.choices; } RadioInput.prototype.generateElementDOM = function() { var container, i, input, _this = this; input = RadioInput.__super__.generateElementDOM.call(this); container = $("<div>"); i = 0; this.choices.forEach(function(_arg) { var elem, help, label, name; name = _arg.name, label = _arg.label, help = _arg.help; elem = $("<label>").attr("class", "radio").text(label).prepend($("<input>").attr("checked", _this.data.value === name).attr("type", "radio").attr("id", _this.id + "-" + name).attr("name", _this.id).on("change", _this.callback).on("click", _this.callback)).append(_this.generateHelpDOM(help)); return container.append(elem); }); return container; }; RadioInput.prototype.value = function(value) { var output, _this = this; if (value === void 0) { output = {}; this.choices.forEach(function(_arg) { var name; name = _arg.name; return output[name] = $("#" + _this.id + "-" + name).attr("checked") === "checked"; }); return output; } else { if (value instanceof String) { this.choices.forEach(function(_arg) { var name; name = _arg.name; return $("#" + _this.id + "-" + name).attr("checked", name === value); }); } else { this.choices.forEach(function(_arg) { var name; name = _arg.name; return $("#" + _this.id + "-" + name).attr("checked", value[name]); }); } return value; } }; return RadioInput; })(Input); $(function() { window.output = new Output("Primer 1 (<b>{{primer1Tm}}\u00B0C</b>, {{primer1TailLength}} + {{primer1Length}}bp): 5' &rarr; 3'<br />\n<pre class='primer'>{{primer1}}</pre>\nPrimer 2 (<b>{{primer2Tm}}\u00B0C</b>, {{primer2TailLength}} + {{primer2Length}}bp): 5' &rarr; 3'<br />\n<pre class='primer'>{{primer2}}</pre>\n<b>Annealing temperature:</b> {{annealingTm}}\u00B0C\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(data, messages) { window.output.setMessages(messages); return window.output.set(data); } }); window.form = InputForm.create({ name: "Primer design helper", submit: function(data, messages, error) { return window.primerFinder.calc(data, messages, error); }, update: function(data, messages, error) { return window.primerFinder.calc(data, messages, error); } }, [ { 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' &rarr; 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(_arg) { var type; type = _arg.type; return type.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(_arg) { var type; type = _arg.type; return type.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(_arg) { var type; type = _arg.type; return type.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(_arg) { var type; type = _arg.type; return type.rs; } }, { name: "leftTail", label: "Left tail", type: "DNASmallInput", value: "", visible: function(_arg) { var type; type = _arg.type; return type.custom; } }, { name: "rightTail", label: "Right tail", type: "DNASmallInput", value: "", visible: function(_arg) { var type; type = _arg.type; return type.custom; } }, { type: "Separator", visible: function(_arg) { var type; type = _arg.type; return !type.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\u00B0C", "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, dna) { var end, start; start = primer1.substr(0, 3).toUpperCase(); if (start !== "ATG") return "<b>The starting ATG seems to be absent.</b>"; end = primer2.substr(0, 3).toUpperCase(); if (end === "TTA" || end === "TCA" || end === "CTA") { return "<b>Remove the stop codons from the sequence!</b>"; } if (dna.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\u00B0C", "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, dna) { if (dna.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(child, parent) { for (var key in parent) { if (__hasProp.call(parent, key)) child[key] = parent[key]; } function ctor() { this.constructor = child; } ctor.prototype = parent.prototype; child.prototype = new ctor; child.__super__ = parent.prototype; return child; }; Output = (function() { Output.i = 0; Output.j = 0; function Output(template) { this.template = template; this.id = "output-" + Output.i++; this.fields = {}; this.matches = {}; this.displays = {}; this.parsedTemplate = this.parseTemplate(this.template); } Output.prototype.attach = function(elem) { var displayClass, displayObj, k, v, _ref, _results; this.matches = {}; $(elem).html(this.parsedTemplate); _ref = this.displays; _results = []; for (k in _ref) { v = _ref[k]; _results.push((function() { var _i, _len, _ref2, _results2; _results2 = []; for (_i = 0, _len = v.length; _i < _len; _i++) { _ref2 = v[_i], displayClass = _ref2.displayClass, displayObj = _ref2.displayObj; _results2.push(displayObj.attach("." + displayClass)); } return _results2; })()); } return _results; }; Output.prototype.setMessages = function(messages) { var output; output = messages; if (messages.length === 0) output = ["No messages"]; return this.getFields("_messages").html("<ul><li>" + output.join("</li><li>") + "</li></ul>"); }; Output.prototype.wipe = function() { var k, v, _ref; _ref = this.fields; for (k in _ref) { v = _ref[k]; this.updateValue(k, void 0); } return this.fields = {}; }; Output.prototype.set = function(values) { var k, v; for (k in values) { v = values[k]; this.updateValue(k, v); } this.updateValue("__all__", this.fields); return this.fields; }; Output.prototype.updateValue = function(k, v) { var displayObj, _i, _len, _ref, _results; if (this.fields[k] !== v) { this.fields[k] = v; if (v != null) { this.getFields(k).html(v.toString()); } else { this.getFields(k).html(""); } } if (this.displays[k] != null) { _ref = this.displays[k]; _results = []; for (_i = 0, _len = _ref.length; _i < _len; _i++) { displayObj = _ref[_i].displayObj; _results.push(displayObj.set(v)); } return _results; } }; Output.prototype.getFields = function(name) { if (!this.matches[name]) { this.matches[name] = $("." + this.id + "-match-" + name); } return this.matches[name]; }; Output.prototype.parseTemplate = function(template) { var c1, c2, display, displayClass, displayObj, displayPart, i, inName, key, name, output, skipNext, started, _ref; c1 = template[0]; c2 = template[1]; output = template + ""; skipNext = false; inName = false; started = -1; name = ""; for (i = 1, _ref = template.length - 1; 1 <= _ref ? i <= _ref : i >= _ref; 1 <= _ref ? i++ : i--) { c2 = template[i]; if (!skipNext) { if (c1 === "{" && c2 === "{") { if (inName) { throw new Error("Invalid template, opened brackets in an already opened context"); } name = ""; started = i; skipNext = true; inName = true; } else if (c1 === "}" && c2 === "}") { if (!inName) { throw new Error("Invalid template, closed unopened brackets"); } displayPart = name.indexOf(":"); if (displayPart >= 0) { display = name.substr(0, displayPart); key = name.substr(displayPart + 1); if (key === "") key = "__all__"; displayClass = this.id + "-display-" + display + "-" + key; output = output.replace("{{" + name + "}}", "<span class='" + displayClass + "'></span>"); displayObj = new window[display](key); if (!(this.displays[key] != null)) this.displays[key] = []; this.displays[key].push({ displayClass: displayClass, displayObj: displayObj }); } else { output = output.replace("{{" + name + "}}", "<span class='" + this.id + "-match-" + name + "'></span>"); } skipNext = true; inName = false; } else { if (inName) name += c1; } } else { skipNext = false; } c1 = c2; } return output; }; return Output; })(); Display = (function() { function Display(key) { this.key = key; this.value = void 0; } Display.prototype.attach = function(id) { throw new Error("Not implemented"); }; Display.prototype.set = function(values) { return this.value = values[this.key]; }; Display.prototype.pad = function(str, width, padLeft) { var length; if (str == null) str = ""; if (width == null) width = 5; if (padLeft == null) padLeft = false; str = str.toString(); length = str.length; while (length < width) { if (padLeft) { str = " " + str; } else { str += " "; } length++; } return str; }; Display.prototype.wrap = function(str, width) { var i, length, output; if (str == null) str = ""; if (width == null) width = 40; str = str.toString(); length = str.length; output = []; i = 0; while (length >= width) { output.push(str.substr(i, width)); length -= width; i += width; } if (length > 0) output.push(str.substr(i)); return output; }; return Display; })(); DNADisplay = (function(_super) { __extends(DNADisplay, _super); DNADisplay.i = 0; function DNADisplay(key) { var that, _this = this; DNADisplay.__super__.constructor.apply(this, arguments); this["class"] = "dnadisplay-" + DNADisplay.i++; this.objects = []; that = this; this.dom = $("<div>").attr("class", this["class"]).append($("<label>").append($("<input>").attr("class", this["class"] + "-toggleLines").attr("type", "checkbox").attr("checked", "on").on("change", function() { if ($("." + _this["class"] + "-toggleLines").attr("checked")) { $("." + _this["class"] + "-lines").hide(); $("." + _this["class"] + "-numberedLines").show(); } else { $("." + _this["class"] + "-lines").show(); $("." + _this["class"] + "-numberedLines").hide(); } return; })).append(" Line Numbers")).append($("<pre>").attr("class", this["class"] + "-lines product").hide()).append($("<pre>").attr("class", this["class"] + "-numberedLines product")); } DNADisplay.prototype.attach = function(elem) { $(elem).append(this.dom); return this.objects = $("." + this["class"]); }; DNADisplay.prototype.set = function(value) { var i, line, lines, numberWidth, numberedLines, outputLines, width, widthNumbered, _len; width = 60; numberWidth = 6; widthNumbered = 40; lines = this.wrap(value, width); numberedLines = this.wrap(value, widthNumbered); outputLines = []; for (i = 0, _len = numberedLines.length; i < _len; i++) { line = numberedLines[i]; if (line.length > 0) { outputLines[i] = this.pad(i * widthNumbered + 1, numberWidth, true) + " - " + this.pad((i + 1) * widthNumbered, numberWidth) + " " + line; } } this.full = lines.join("\n"); this.fullNumbered = outputLines.join("\n"); $("." + this["class"] + "-lines").text(this.full); return $("." + this["class"] + "-numberedLines").text(this.fullNumbered); }; return DNADisplay; })(Display); RSDisplay = (function(_super) { __extends(RSDisplay, _super); RSDisplay.i = 0; function RSDisplay(key) { var that; RSDisplay.__super__.constructor.apply(this, arguments); this["class"] = "rsdisplay-" + RSDisplay.i++; this.objects = []; that = this; this.dom = $("<div>").attr("class", this["class"]).append($("<pre>").attr("class", this["class"] + "-pre")); } RSDisplay.prototype.attach = function(elem) { $(elem).append(this.dom); return this.objects = $("." + this["class"]); }; RSDisplay.prototype.set = function(_arg) { var c, complement, full, left, leftCompStr, leftCut, leftRS, leftRSInput, leftStr, overhang, randomBases, right, rightCompStr, rightCut, rightRS, rightRSInput, rightStr, rs, text, type, _i, _j, _len, _len2, _ref, _ref2; rs = _arg.rs, type = _arg.type, leftRS = _arg.leftRS, rightRS = _arg.rightRS; if (!type.rs) { $("." + this["class"] + "-pre").html("Not applicable"); return; } leftRSInput = leftRS.rs; rightRSInput = rightRS.rs; left = rs.left, right = rs.right, full = rs.full, randomBases = rs.randomBases; leftCut = DNA.getCutPosition(leftRSInput); if (leftCut < 0) { leftRS = DNA.fromString(left).findRS(true); leftCut = DNA.getCutPosition(leftRS); } else { leftRS = leftRSInput; } if (leftRS.length === 0) leftRS = "?"; rightCut = DNA.getCutPosition(rightRSInput); if (rightCut < 0) { rightRS = DNA.fromString(right).findRS(true); rightCut = DNA.getCutPosition(rightRS); } else { rightRS = rightRSInput; } if (rightRS.length === 0) rightRS = "?"; leftStr = full.substr(0, randomBases + left.length + 10); rightStr = full.substr(full.length - (randomBases + right.length + 10)); if (randomBases > 6) { leftStr = "..." + leftStr.substr(randomBases - 3); rightStr = rightStr.substr(0, rightStr.length - (randomBases - 3)) + "..."; randomBases = 6; } leftCompStr = ""; rightCompStr = ""; complement = function(c) { switch (c) { case "A": return "T"; case "T": return "A"; case "C": return "G"; case "G": return "C"; default: return c; } }; _ref = leftStr.split(""); for (_i = 0, _len = _ref.length; _i < _len; _i++) { c = _ref[_i]; leftCompStr += complement(c); } _ref2 = rightStr.split(""); for (_j = 0, _len2 = _ref2.length; _j < _len2; _j++) { c = _ref2[_j]; rightCompStr += complement(c); } if (leftCut >= 0) { overhang = Math.ceil(Math.abs(left.length / 2 - leftCut)) + 1; leftStr = leftStr.substr(0, randomBases + leftCut) + this.pad("", overhang + 1) + leftStr.substr(randomBases + leftCut); leftCompStr = leftCompStr.substr(0, randomBases + left.length - leftCut) + this.pad("", overhang + 1) + leftCompStr.substr(randomBases + left.length - leftCut); } else { leftStr = leftStr.substr(0, randomBases) + " " + leftStr.substr(randomBases, left.length) + " " + leftStr.substr(randomBases + left.length); leftCompStr = leftCompStr.substr(0, randomBases) + " " + leftCompStr.substr(randomBases, left.length) + " " + leftCompStr.substr(randomBases + left.length); } if (rightCut >= 0) { overhang = Math.ceil(Math.abs(right.length / 2 - rightCut)) + 1; rightStr = rightStr.substr(0, rightStr.length - (randomBases + right.length - rightCut)) + this.pad("", overhang + 1) + rightStr.substr(rightStr.length - (randomBases + right.length - rightCut)); rightCompStr = rightCompStr.substr(0, rightCompStr.length - (randomBases + rightCut)) + this.pad("", overhang + 1) + rightCompStr.substr(rightCompStr.length - (randomBases + rightCut)); } else { rightStr = rightStr.substr(0, rightStr.length - (randomBases + right.length)) + " " + rightStr.substr(rightStr.length - (randomBases + right.length), right.length) + " " + rightStr.substr(rightStr.length - randomBases); rightCompStr = rightCompStr.substr(0, rightCompStr.length - (randomBases + right.length)) + " " + rightCompStr.substr(rightCompStr.length - (randomBases + right.length), right.length) + " " + rightCompStr.substr(rightCompStr.length - randomBases); } text = []; text.push("Left restriction site: " + leftRS + (leftCut < 0 ? " (cutting site unknown)" : "")); text.push("Right restriction site: " + rightRS + (rightCut < 0 ? " (cutting site unknown)" : "")); text.push(""); text.push("5'" + this.pad("3'", leftStr.length + rightStr.length + 1, true)); text.push(leftStr + "..." + rightStr); text.push(leftCompStr + "..." + rightCompStr); text.push("3'" + this.pad("5'", leftStr.length + rightStr.length + 1, true)); return $("." + this["class"] + "-pre").text(text.join("\n")); }; return RSDisplay; })(Display); SelfDimerDisplay = (function(_super) { __extends(SelfDimerDisplay, _super); SelfDimerDisplay.i = 0; function SelfDimerDisplay(key) { var that, _this = this; SelfDimerDisplay.__super__.constructor.apply(this, arguments); this["class"] = "selfdimerdisplay-" + RSDisplay.i++; this.objects = []; that = 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($("<input>").attr("type", "button").attr("value", "Calculate").attr("class", "btn").click(function() { return _this.click(); })).append("<br>").append("<br>").append($("<pre>").attr("class", this["class"] + "-pre").html("Press the calculate button to update this data")); } SelfDimerDisplay.prototype.attach = function(elem) { $(elem).append(this.dom); return this.objects = $("." + this["class"] + "-pre"); }; SelfDimerDisplay.prototype.set = function(_arg) { var primer1, primer2; primer1 = _arg.primer1, primer2 = _arg.primer2; if (primer1 !== this.primer1 || primer2 !== this.primer2) { this.primer1 = primer1; this.primer2 = primer2; return this.objects.html("Press the calculate button to update this data"); } }; SelfDimerDisplay.prototype.click = function() { var report; report = this.generateReport("Primer 1", this.primer1) + "\n\n" + this.generateReport("Primer 2", this.primer2); return this.objects.html(report); }; SelfDimerDisplay.prototype.generateReport = function(name, primer) { var character, folds, lineC, lineN, lines, matches, number, p, pairs, rna, _i, _j, _len, _ref, _ref2, _results; lines = []; lines.push(name + ":"); rna = RNA.fromString(primer); _ref = rna.findKnots(), matches = _ref.matches, folds = _ref.folds; lines.push("Amount of matches: " + matches); pairs = _.zip((function() { _results = []; for (var _i = 1, _ref2 = primer.length; 1 <= _ref2 ? _i <= _ref2 : _i >= _ref2; 1 <= _ref2 ? _i++ : _i--){ _results.push(_i); } return _results; }).apply(this), primer.split("")); lineC = ""; lineN = ""; for (_j = 0, _len = pairs.length; _j < _len; _j++) { p = pairs[_j]; number = p[0] + " "; character = this.pad(p[1], number.length - 1, true) + " "; if (lineC.length + number.length > 60) { lines.push(lineC); lines.push(lineN); lines.push(""); lineC = ""; lineN = ""; } lineC += character; lineN += number; } if (lineC.length > 0) { lines.push(lineC); lines.push(lineN); lines.push(""); } return lines.join("\n"); }; return SelfDimerDisplay; })(Display); 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) { if (data instanceof DNA) { this.seq = data.clone(); } else { 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, _ref, _ref2; 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 = _ref = Primer.minLength; _ref <= maxLength ? l1 <= maxLength : l1 >= maxLength; _ref <= maxLength ? l1++ : l1--) { 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 = _ref2 = Primer.minLength; _ref2 <= maxLength ? l2 <= maxLength : l2 >= maxLength; _ref2 <= maxLength ? l2++ : l2--) { 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 { rs: { left: this.tail1.toString(), right: this.tail2.toString(), randomBases: this.randEdgeSize, full: rand1.toString() + this.tail1.toString() + this.seq.toString() + this.tail2.reverseComplement().toString() + rand2.reverseComplement().toString() }, primer1: rand1.toString() + " " + this.tail1.toString() + " " + this.seq.snip(primer1Length).toString(), primers: { primer1: rand1.toString() + this.tail1.toString() + this.seq.snip(primer1Length).toString(), primer2: rand2.toString() + this.tail2.toString() + revCompl.snip(primer2Length).toString() }, primer1NoTail: this.seq.snip(primer1Length).toString(), primer1Tm: primer1Temp, primer1Length: primer1Length, primer1TailLength: rand1.length() + this.tail1.length(), primer2: rand2.toString() + " " + this.tail2.toString() + " " + revCompl.snip(primer2Length).toString(), primer2NoTail: revCompl.snip(primer2Length).toString(), primer2Tm: primer2Temp, primer2Length: primer2Length, primer2TailLength: rand2.length() + this.tail2.length(), full: rand1.toString() + this.tail1.toString() + this.seq.toString() + this.tail2.reverseComplement().toString() + rand2.reverseComplement().toString() }; }; return Primer; })(); var PrimerFinder; PrimerFinder = (function() { function PrimerFinder(_arg) { this.output = _arg.output; this.defaults = { primer1: "No data", primer1Tm: "?", primer1Length: 0, primer2: "No data", primer2Tm: "?", primer2Length: 0, annealingTm: "?" }; } PrimerFinder.prototype.calc = function(data, messages, error) { var k, match1, match2, p, primers, result, tail, tail1, tail2, v, validate, _i, _len, _ref, _ref2; if (error) { messages = ["A fatal error occured:"].concat(messages); this.output(data, messages); return; } _ref = this.defaults; for (k in _ref) { v = _ref[k]; if (!(data[k] != null)) data[k] = v; } try { p = new Primer(data.dna); validate = function(primer1, primer2, dna) {}; if (data.type.custom) p.setTails(data.leftTail, data.rightTail); if (data.type.rs) { match1 = data.leftRS.dna.findRS(); match2 = data.rightRS.dna.findRS(); if ((match1 != null) && match1.length > 0) { messages.push("The left restriction site is " + match1); } else { messages.push("The left restriction site wasn't recognized"); } if ((match2 != null) && match2.length > 0) { messages.push("The right restriction site is " + match2); } else { messages.push("The right restriction site wasn't recognized"); } p.setTails(data.leftRS.dna, data.rightRS.dna.reverseComplement()); p.addRandomEdges(data.randomBases); messages.push("Click the 'Generate' 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).\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 (data.type.known) { tail1 = ""; tail2 = ""; _ref2 = window.tails; for (_i = 0, _len = _ref2.length; _i < _len; _i++) { tail = _ref2[_i]; if (tail.value === data.standardTail) { tail1 = tail.primer1Tail; tail2 = tail.primer2Tail; if (tail.messages != null) messages = [].concat(tail.messages); if (tail.validate != null) validate = tail.validate; } } p.setTails(DNA.fromString(tail1), DNA.fromString(tail2)); } primers = p.generate(data.tm); result = validate(primers.primer1NoTail, primers.primer2NoTail, data.dna); if (result != null) messages.push(result); for (k in primers) { v = primers[k]; data[k] = v; } messages = messages; } catch (e) { messages = [e.message]; } data.annealingTm = Math.min(data.primer1Tm, data.primer2Tm); if (Math.abs(data.primer1Tm - data.primer2Tm) > 5) { messages.push("The difference between the primer's Tm is more than 5\u00B0C"); } if (data.annealingTm > 70) { messages.push("Consider using the two-step PCR protocol"); } if (data.annealingTm > 72) { messages.push("Annealing temperature shouldn't exceed 72\u00B0C"); data.annealingTm = 72; } if (data.annealingTm < 45) { messages.push("The annealing temperature should be more than 45\u00B0C"); } return this.output(data, messages); }; return PrimerFinder; })(); 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 fold, folds, i, matches, seq, _i, _len, _ref, _ref2; _ref = this.findKnots(), matches = _ref.matches, folds = _ref.folds; for (_i = 0, _len = folds.length; _i < _len; _i++) { fold = folds[_i]; seq = []; console.log(fold); for (i = 0, _ref2 = fold.length - 1; 0 <= _ref2 ? i <= _ref2 : i >= _ref2; 0 <= _ref2 ? i++ : i--) { if (fold[i] === "(") { if (i > 0 && fold[i - 1] === "(") { seq[seq.length - 1] += this.data[i]; } else { seq[seq.length] = this.data[i]; } } } console.log(seq); } return false; }; 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, _len2, _len3, _len4, _ref, _ref10, _ref2, _ref3, _ref4, _ref5, _ref6, _ref7, _ref8, _ref9, _this = this; if (minSize == null) minSize = 2; if (this.knots !== void 0) return this.knots; createSolution = function() { var i, _ref, _results; _results = []; for (i = 1, _ref = _this.n; 1 <= _ref ? i <= _ref : i >= _ref; 1 <= _ref ? i++ : i--) { _results.push("."); } return _results; }; HM = []; for (l = 0, _ref = this.n - 1; 0 <= _ref ? l <= _ref : l >= _ref; 0 <= _ref ? l++ : l--) { hm = []; for (m = 0, _ref2 = this.n - 1; 0 <= _ref2 ? m <= _ref2 : m >= _ref2; 0 <= _ref2 ? m++ : m--) { hm[m] = [createSolution()]; } HM[l] = hm; } M = (function() { var _ref3, _results; _results = []; for (i = 1, _ref3 = this.n; 1 <= _ref3 ? i <= _ref3 : i >= _ref3; 1 <= _ref3 ? i++ : i--) { _results.push((function() { var _ref4, _results2; _results2 = []; for (j = 1, _ref4 = this.n; 1 <= _ref4 ? j <= _ref4 : j >= _ref4; 1 <= _ref4 ? j++ : j--) { _results2.push(0); } return _results2; }).call(this)); } return _results; }).call(this); for (i = _ref3 = this.n - 1; _ref3 <= 0 ? i <= 0 : i >= 0; _ref3 <= 0 ? i++ : i--) { for (j = i, _ref4 = this.n - 1; i <= _ref4 ? j <= _ref4 : j >= _ref4; i <= _ref4 ? j++ : j--) { max = 0; if (i < j - minSize) { max = M[i + 1][j - 1] + this.P(i, j); hs = []; _ref5 = HM[i + 1][j - 1]; for (_i = 0, _len = _ref5.length; _i < _len; _i++) { sol = _ref5[_i]; if (this.P(i, j) === 1) { sol[i] = "("; sol[j] = ")"; } else { sol[i] = "."; sol[j] = "."; } if (hs.length < 50) hs.push(sol); } for (k = i, _ref6 = j - 1; i <= _ref6 ? k <= _ref6 : k >= _ref6; i <= _ref6 ? k++ : k--) { tmp = M[i][k] + M[k + 1][j]; if (tmp > max) { max = tmp; hs = []; } if (tmp >= max) { _ref7 = HM[i][k]; for (_j = 0, _len2 = _ref7.length; _j < _len2; _j++) { a1 = _ref7[_j]; _ref8 = HM[k + 1][j]; for (_k = 0, _len3 = _ref8.length; _k < _len3; _k++) { a2 = _ref8[_k]; a = createSolution(this.n); for (p = 0; 0 <= k ? p <= k : p >= k; 0 <= k ? p++ : p--) { a[p] = a1[p]; } for (p = _ref9 = k + 1; _ref9 <= j ? p <= j : p >= j; _ref9 <= j ? p++ : p--) { a[p] = a2[p]; } if (hs.length < 50) hs.push(a); } } } } M[i][j] = max; HM[i][j] = hs; } } } output = []; hashSet = {}; _ref10 = HM[0][this.n - 1]; for (_l = 0, _len4 = _ref10.length; _l < _len4; _l++) { sol = _ref10[_l]; 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, _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 = 1, _ref = data.length - 1; 1 <= _ref ? i <= _ref : i >= _ref; 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 #18 100.5 + (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 79.8 + 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; 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