neurohmmerapp 0.0.1

data/public/src/css/bootstrap1.min.css

@@ -0,0 +1,7 @@
+@import url("//fonts.googleapis.com/css?family=Lato:400,700,400italic");/*!
+ * bootswatch v3.3.1+2
+ * Homepage: http://bootswatch.com
+ * Copyright 2012-2014 Thomas Park
+ * Licensed under MIT
+ * Based on Bootstrap
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data/public/src/css/custom.css

@@ -0,0 +1,189 @@
+html {
+  /* This is required in order to make the footer stick to the bottom..*/
+  /* There is a js function that controls the bottom margin...*/
+  position: relative;
+  min-height: 100%;
+}
+
+body {
+  margin: 0;
+  margin-top: 60px;
+  background-color:#F5F5F5;
+}
+
+section {
+  width: 100%;
+  padding: 0 5%;
+  display: table;
+  margin: 0;
+  max-width: none;
+  padding-bottom: 35px;
+}
+
+.nav-container {
+  width:100%;
+  padding: 0 5%;
+  margin: 0;
+}
+
+.navbar-brand {
+  padding-left: 0;
+}
+
+footer {
+  bottom: 0;
+  width: 100%;
+  margin: 0 auto;
+  position: absolute;
+  border-top: 2px solid #DBDBDB;
+  padding-top:10px;
+}
+
+
+/* Navbar
+-------------------------------------------------- */
+.navbar-nav>li>a, .navbar-brand {
+  line-height: 27px;
+}
+
+.navbar-brand a {
+  color:#fff;
+}
+
+.navbar-brand a:hover {
+  text-decoration: none;
+}
+
+.navbar-nav > li > a.nav_github_icon {
+  padding-top: 0;
+  padding-bottom: 0;
+}
+
+.fa-github {
+  color: #fff;
+  padding-top: 18px;
+  padding-bottom: 18px;
+}
+
+h1 .small {
+  color: #2C3E50;
+}
+
+.input_seq-label {
+  font-size: 26px;
+}
+
+#np_example {
+  cursor: pointer;
+}
+
+#adv_params_btn {
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+  margin-top: 5px;
+}
+
+#input_btn {
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+  margin-top: 20px;
+}
+
+.show_examples_text {
+  font-size: 17px;
+  text-align: center;
+}
+
+.control-label{
+  font-size: 1.25em;
+  font-weight: normal;
+}
+
+label, .radio label, .checkbox label, .help-block {
+  font-size: 0.9em;
+  font-weight: inherit;
+}
+
+.checkbox.inline.no_indent+.checkbox.inline.no_indent {
+  margin-left: 0;
+  margin-right: 10px;
+
+}
+.checkbox.inline.no_indent:last-child {
+  margin-right: 0px;
+}
+
+label.checkbox-inline.no_indent {
+  margin-left: 0;
+  margin-right: 10px;
+}
+
+label.radio-inline.no_indent {
+  margin-left: 0;
+  margin-right: 10px;
+}
+
+#results_header {
+  margin-top: 0;
+  margin-bottom: 30px;
+}
+
+#results_link_btn {
+  margin-top: 0;
+  margin-right: -15px;
+}
+
+/* NeuroHmmer Results...
+-------------------------------------------------- */
+p {
+  margin:0 0 10.5px;
+  word-break: break-all;
+}
+.id {
+  font-weight:bold;
+}
+.sequence {
+  font-family:Courier New, Courier, Mono;
+}
+.clv {
+  color:#00B050;
+  font-weight:bold;
+}
+.clv_i {
+  color:#00B050;
+  font-weight: bold;
+  background-color:#FFE4B5;
+}
+.gly {
+  color:#FF0000;
+  font-weight:bold;
+}
+.hsp {
+  background-color:#FFE4B5;
+}
+
+
+/* Responsive CSS
+___________________________*/
+
+@media (min-width: 768px) {
+  #adv_params_btn {
+    float:left !important;
+    margin-top: 5px;
+  }
+
+  #input_btn {
+    float:right !important;
+    margin-top: -43px;
+  }
+
+  .show_examples_text {
+    text-align: left;
+  }
+
+  .container{
+    width:90%;
+  }
+}

data/public/src/css/custom.min.css

@@ -0,0 +1 @@
+.fa-github,.navbar-brand a{color:#fff}html{position:relative;min-height:100%}body{margin:60px 0 0;background-color:#F5F5F5}.clv_i,.hsp{background-color:#FFE4B5}section{width:100%;padding:0 5% 35px;display:table;margin:0;max-width:none}.nav-container{width:100%;padding:0 5%;margin:0}.navbar-brand{padding-left:0}footer{bottom:0;width:100%;margin:0 auto;position:absolute;border-top:2px solid #DBDBDB;padding-top:10px}#adv_params_btn,#input_btn{display:block;margin-left:auto;margin-right:auto}.navbar-brand,.navbar-nav>li>a{line-height:27px}.navbar-brand a:hover{text-decoration:none}.navbar-nav>li>a.nav_github_icon{padding-top:0;padding-bottom:0}.fa-github{padding-top:18px;padding-bottom:18px}h1 .small{color:#2C3E50}.clv,.clv_i{color:#00B050}.input_seq-label{font-size:26px}#np_example{cursor:pointer}#adv_params_btn{margin-top:5px}#input_btn{margin-top:20px}.show_examples_text{font-size:17px;text-align:center}.control-label{font-size:1.25em;font-weight:400}.checkbox label,.help-block,.radio label,label{font-size:.9em;font-weight:inherit}.clv,.clv_i,.gly,.id{font-weight:700}.checkbox.inline.no_indent+.checkbox.inline.no_indent{margin-left:0;margin-right:10px}.checkbox.inline.no_indent:last-child{margin-right:0}label.checkbox-inline.no_indent,label.radio-inline.no_indent{margin-left:0;margin-right:10px}#results_header{margin-top:0;margin-bottom:30px}#results_link_btn{margin-top:0;margin-right:-15px}p{margin:0 0 10.5px;word-break:break-all}.sequence{font-family:Courier New,Courier,Mono}.gly{color:red}@media (min-width:768px){#adv_params_btn{float:left!important;margin-top:5px}#input_btn{float:right!important;margin-top:-43px}.show_examples_text{text-align:left}.container{width:90%}}

data/public/src/css/font-awesome.min.css

@@ -0,0 +1,4 @@
+/*!
+ *  Font Awesome 4.1.0 by @davegandy - http://fontawesome.io - @fontawesome
+ *  License - http://fontawesome.io/license (Font: SIL OFL 1.1, CSS: MIT License)
+ */@font-face{font-family:'FontAwesome';src:url('../fonts/fontawesome-webfont.eot?v=4.1.0');src:url('../fonts/fontawesome-webfont.eot?#iefix&v=4.1.0') format('embedded-opentype'),url('../fonts/fontawesome-webfont.woff?v=4.1.0') format('woff'),url('../fonts/fontawesome-webfont.ttf?v=4.1.0') format('truetype'),url('../fonts/fontawesome-webfont.svg?v=4.1.0#fontawesomeregular') 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data/public/src/js/bionode-seq.min.js

@@ -0,0 +1 @@
+require=function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s}({1:[function(require,module,exports){var seq=module.exports;var _baseMatrix={A:"T",C:"G",W:"S",M:"K",R:"Y",B:"V",D:"H"};var _dnaComplementBasesMatrix=Object.create(_baseMatrix);var _rnaComplementBasesMatrix=Object.create(_baseMatrix);var _transcribeBasesMatrix=Object.create(_baseMatrix);var _translateCodonsMatrix={GCU:"A",GCC:"A",GCA:"A",GCG:"A",CGU:"R",CGC:"R",CGA:"R",CGG:"R",AGA:"R",AGG:"R",AAU:"N",AAC:"N",GAU:"D",GAC:"D",UGU:"C",UGC:"C",CAA:"Q",CAG:"Q",GAA:"E",GAG:"E",GGU:"G",GGC:"G",GGA:"G",GGG:"G",CAU:"H",CAC:"H",AUU:"I",AUC:"I",AUA:"I",UUA:"L",UUG:"L",CUU:"L",CUC:"L",CUA:"L",CUG:"L",AAA:"K",AAG:"K",AUG:"M",UUU:"F",UUC:"F",CCU:"P",CCC:"P",CCA:"P",CCG:"P",UCU:"S",UCC:"S",UCA:"S",UCG:"S",AGU:"S",AGC:"S",ACU:"T",ACC:"T",ACA:"T",ACG:"T",UGG:"W",UAU:"Y",UAC:"Y",GUU:"V",GUC:"V",GUA:"V",GUG:"V",UAA:"*",UGA:"*",UAG:"*",XAA:"X",XAC:"X",XAG:"X",XAU:"X",XCA:"X",XCC:"X",XCG:"X",XCU:"X",XGA:"X",XGC:"X",XGG:"X",XGU:"X",XUA:"X",XUC:"X",XUG:"X",XUU:"X",XAX:"X",XCX:"X",XGX:"X",XUX:"X",XXA:"X",XXC:"X",XXG:"X",XXU:"X",XXX:"X",gcu:"a",gcc:"a",gca:"a",gcg:"a",cgu:"r",cgc:"r",cga:"r",cgg:"r",aga:"r",agg:"r",aau:"n",aac:"n",gau:"d",gac:"d",ugu:"c",ugc:"c",caa:"q",cag:"q",gaa:"e",gag:"e",ggu:"g",ggc:"g",gga:"g",ggg:"g",cau:"h",cac:"h",auu:"i",auc:"i",aua:"i",uua:"l",uug:"l",cuu:"l",cuc:"l",cua:"l",cug:"l",aaa:"k",aag:"k",aug:"m",uuu:"f",uuc:"f",ccu:"p",ccc:"p",cca:"p",ccg:"p",ucu:"s",ucc:"s",uca:"s",ucg:"s",agu:"s",agc:"s",acu:"t",acc:"t",aca:"t",acg:"t",ugg:"w",uau:"y",uac:"y",guu:"v",guc:"v",gua:"v",gug:"v",uaa:"*",uga:"*",uag:"*",xaa:"x",xac:"x",xag:"x",xau:"x",xca:"x",xcc:"x",xcg:"x",xcu:"x",xga:"x",xgc:"x",xgg:"x",xgu:"x",xua:"x",xuc:"x",xug:"x",xuu:"x",xax:"x",xcx:"x",xgx:"x",xux:"x",xxa:"x",xxc:"x",xxg:"x",xxu:"x",xxx:"x"};_rnaComplementBasesMatrix["A"]="U";delete _rnaComplementBasesMatrix["T"];_transcribeBasesMatrix["A"]="U";mirrorAndLowerCaseMatrices([_dnaComplementBasesMatrix,_rnaComplementBasesMatrix,_transcribeBasesMatrix]);_transcribeBasesMatrix["T"]="A";_transcribeBasesMatrix["t"]="a";function mirrorAndLowerCaseMatrices(matricesArray){matricesArray.forEach(function(matrix){for(var k in matrix){var v=matrix[k];matrix[k.toLowerCase()]=v.toLowerCase();matrix[v]=k;matrix[v.toLowerCase()]=k.toLowerCase()}})}seq.checkType=function(sequence,threshold,length,index){if(threshold===undefined){threshold=.9}if(length===undefined){length=1e4}if(index===undefined){index=1}var seq=sequence.slice(index-1,length);var dnaSeq=seq.replace(/N/gi,"");var dnaTotal=dnaSeq.length;var acgMatch=(dnaSeq.match(/[ACG]/gi)||[]).length/dnaTotal;var tMatch=(dnaSeq.match(/[T]/gi)||[]).length/dnaTotal;var uMatch=(dnaSeq.match(/[U]/gi)||[]).length/dnaTotal;var proteinSeq=seq.replace(/X/gi,"");var proteinTotal=proteinSeq.length;var proteinMatch=(seq.match(/[ARNDCQEGHILKMFPSTWYV\*]/gi)||[]).length/proteinTotal;if(acgMatch+tMatch>=threshold||acgMatch+uMatch>=threshold){if(tMatch>=uMatch){return"dna"}else if(uMatch>=tMatch){return"rna"}else{return"dna"}}else if(proteinMatch>=threshold){return"protein"}};seq.createComplementBase=function(sequenceType){var complementBasesMatrix=sequenceType==="rna"||sequenceType==="ambiguousRna"?_rnaComplementBasesMatrix:_dnaComplementBasesMatrix;var getComplementBase=function(base){var complement=complementBasesMatrix[base];return complement||base};return getComplementBase};seq.reverse=function(sequence){return sequence.split("").reverse().join("")};seq.complement=function(sequence,reverse){var reverse=reverse||false;var sequenceType=seq.checkType(sequence);var getComplementBase=seq.createComplementBase(sequenceType);if(reverse){return sequence.split("").reverse().map(getComplementBase).join("")}else{return sequence.split("").map(getComplementBase).join("")}};seq.reverseComplement=function(sequence){return seq.complement(sequence,true)};seq.getTranscribedBase=function(base){return _transcribeBasesMatrix[base]||base};seq.getTranslatedAA=function(codon){return _translateCodonsMatrix[codon]};seq.removeIntrons=function(sequence,exonsRanges){var sequenceWithoutIntrons="";var exonsRangesSorted=exonsRanges.sort(function(a,b){return a[0]-b[0]});exonsRangesSorted.forEach(function(exonRange){sequenceWithoutIntrons+=sequence.substring(exonRange[0],exonRange[1])});return sequenceWithoutIntrons};seq.transcribe=function(sequence,exonsRanges){if(exonsRanges){var sequenceWithoutIntrons=seq.removeIntrons(sequence,exonsRanges);sequence=sequenceWithoutIntrons}var sequenceType=seq.checkType(sequence);if(sequenceType==="dna"||sequenceType==="ambiguousDna"){return sequence.replace(/t/g,"u").replace(/T/g,"U")}else if(sequenceType==="rna"||sequenceType==="ambiguousRna"){return sequence.replace(/u/g,"t").replace(/U/g,"T")}};seq.translate=function(sequence,exonsRanges){if(exonsRanges){var sequenceWithoutIntrons=seq.removeIntrons(sequence,exonsRanges);sequence=sequenceWithoutIntrons}var sequenceType=seq.checkType(sequence);var rna;if(sequenceType==="protein"){return sequence}else if(sequenceType==="dna"||sequenceType==="ambiguousDna"){if(sequenceType==="ambiguousDna")sequence.replace(/[wsmkrybdhv]/g,"x").replace(/[WSMKRYBDHV]/g,"X");rna=seq.transcribe(sequence,exonsRanges)}else if(sequenceType==="rna"||sequenceType==="ambiguousRna"){if(sequenceType==="ambiguousRna")sequence.replace(/[wsmkrybdhv]/g,"x").replace(/[WSMKRYBDHV]/g,"X");rna=sequence}return rna.match(/.{1,3}/g).map(seq.getTranslatedAA).join("")};seq.reverseExons=function(exonsRanges,referenceLength){var reversedExonsRanges=[];exonsRanges.forEach(function(exonRange){var start=referenceLength-exonRange[1];var stop=referenceLength-exonRange[0];reversedExonsRanges.push([start,stop])});return reversedExonsRanges};seq.findNonCanonicalSplices=function(sequence,exonsRanges){var nonCanonicalSplices=[];var exonsRangesSorted=exonsRanges.sort(function(a,b){return a[0]-b[0]});exonsRangesSorted.forEach(checkNonCanonicalIntron);function checkNonCanonicalIntron(exonRange,i){var donor=exonRange;var acceptor=exonsRangesSorted[i+1];if(!acceptor)return null;var intronRange=[donor[1],acceptor[0]];var intronStartBases=sequence.slice(intronRange[0],intronRange[0]+2).toLowerCase().replace("t","u");var intronStopBases=sequence.slice(intronRange[1]-2,intronRange[1]).toLowerCase();if(intronStartBases!=="gu")nonCanonicalSplices.push(intronRange[0]);if(intronStopBases!=="ag")nonCanonicalSplices.push(intronRange[1])}return nonCanonicalSplices};seq.checkCanonicalTranslationStartSite=function(sequence){return sequence.substring(0,3).toLowerCase().replace("t","u")==="aug"};seq.getReadingFrames=function(sequence){var reverse=seq.reverseComplement(sequence);return[sequence,sequence.substring(1),sequence.substring(2),reverse,reverse.substring(1),reverse.substring(2)]};seq.getOpenReadingFrames=function(sequence){var sequenceType=seq.checkType(sequence);var stopCodons;if(sequenceType==="dna"||sequenceType==="ambiguousDna"){stopCodons=["TAA","TGA","TAG","taa","tga","tag"]}else if(sequenceType==="rna"||sequenceType==="ambiguousRna"){stopCodons=["UAA","UGA","UAG","uaa","uga","uag"]}var openReadingFrames=[];var openReadingFrame="";sequence.match(/.{1,3}/g).forEach(function(codon){openReadingFrame+=codon;if(stopCodons.indexOf(codon)!==-1&&openReadingFrame.length>0){openReadingFrames.push(openReadingFrame);openReadingFrame=""}});openReadingFrames.push(openReadingFrame);return openReadingFrames};seq.getAllOpenReadingFrames=function(sequence){var readingFrames=seq.getReadingFrames(sequence);var allOpenReadingFrames=readingFrames.map(seq.getOpenReadingFrames);return allOpenReadingFrames};seq.findLongestOpenReadingFrame=function(sequence,frameSymbol){var frameSymbols=["+1","+2","+3","-1","-2","-3"];if(frameSymbol){var framePosition=frameSymbols.indexOf(frameSymbol);var readingFrame=seq.getReadingFrames(sequence)[framePosition];var openReadingFrames=seq.getOpenReadingFrames(readingFrame);var longestOpenReadingFrame=getLongestOpenReadingFrame(openReadingFrames);return longestOpenReadingFrame}else{var longestOpenReadingFrames=seq.getAllOpenReadingFrames(sequence).map(getLongestOpenReadingFrame);var longestOpenReadingFrame=getLongestOpenReadingFrame(longestOpenReadingFrames.slice());var framePosition=longestOpenReadingFrames.indexOf(longestOpenReadingFrame);var frameSymbol=frameSymbols[framePosition];return[longestOpenReadingFrame,frameSymbol]}function sortReadingFrames(a,b){var aSort=a.length;var bSort=b.length;if(bSort-aSort===0){var aStartCodon=a.slice(0,3).toUpperCase().replace("T","U");var bStartCodon=b.slice(0,3).toUpperCase().replace("T","U");if(aStartCodon==="AUG"){aSort++}if(bStartCodon==="AUG"){bSort++}}return bSort-aSort}function getLongestOpenReadingFrame(array){return array.sort(sortReadingFrames)[0]}}},{}],"bionode-seq":[function(require,module,exports){module.exports=require("./lib/bionode-seq")},{"./lib/bionode-seq":1}]},{},["bionode-seq"]);