genevalidatorapp 1.4.12

data/public/web_files/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"]);

data/public/web_files/js/bootstrap.min.js

@@ -0,0 +1,6 @@
+/*!
+ * Bootstrap v3.1.1 (http://getbootstrap.com)
+ * Copyright 2011-2014 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */
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data/public/web_files/js/genevalidator.js

@@ -0,0 +1,282 @@
+$(document).ready(function() {
+  'use strict';
+  checkCollapseState();
+  keepFooterFixedToBottom();
+  addSeqValidation();
+  inputValidation();
+
+  $(document).bind('keydown', function (e) {
+    if (e.ctrlKey && e.keyCode === 13 ) {
+      $('#input').trigger('submit');
+    }
+  });
+});
+
+// Looks for a cookie (called 'GeneValidator_adv_params_status') to check the state of the adv_params box when it was last closed. 
+//  This function is called upon as soon as the website is loaded;  
+function checkCollapseState() {
+  'use strict';
+  if ($.cookie('GeneValidator_adv_params_status')){
+    var adv_params_status = $.cookie('GeneValidator_adv_params_status');
+    if (adv_params_status === 'open') {
+      var btn = document.getElementById('adv_params_btn');
+      btn.innerHTML = '<i class="fa fa-pencil-square-o"></i>&nbsp;&nbsp;Hide Advanced Parameters';
+      $('#adv_params').addClass('in');
+    }
+  }
+}
+
+// This function simply ensures that the footer stays to fixed to the bottom of the window
+function keepFooterFixedToBottom() {
+  'use strict';
+  $('#mainbody').css({'margin-bottom': (($('#footer').height()) + 15)+'px'});
+  $(window).resize(function(){
+      $('#mainbody').css({'margin-bottom': (($('#footer').height()) + 15)+'px'});
+  });
+}
+
+// Creates a custom Validation for Jquery Validation plugin...
+// It ensures that sequences are either protein or DNA data...
+// If there are multiple sequences, ensures that they are of the same type
+// It utilises the checkType function (further below)...
+function addSeqValidation() {
+  'use strict';
+  jQuery.validator.addMethod('checkInputType', function(value, element) {
+    var types = [];
+    if (value.charAt(0) === '>') {
+      var seqs_array = value.split('>');
+      for (var i = 1; i < seqs_array.length; i++) {
+        var lines = seqs_array[i].split('\n');
+        if (lines.length !== 0) {
+          var clean_lines = jQuery.grep(lines,function(n){ return(n); });
+          if (clean_lines.length !== 0){
+            clean_lines.shift();
+            var seq = clean_lines.join('');
+            var type = checkType(seq, 0.9);
+            types.push(type);
+            if ((type !== 'protein') && (type !== 'dna') && (type !== 'rna')) {
+              return false;
+            }
+          }
+        } 
+      }
+      var firstType = types[0];
+      for (var j = 0; j < types.length; j++) {
+        if (types[j] !== firstType){
+          return false;
+        }
+      }
+      return true;
+    } else {
+      var type = checkType(value, 0.9);
+      if ((type !== 'protein') && (type !== 'dna') && (type !== 'rna')) {
+        return false;
+      } else {
+        return true;
+      }
+    }
+  }, '* The Input must be either DNA or protein sequence(s). Please ensure that your sequences do not contains any non-letter character(s). If there are multiple sequences, ensure that they are all of one type. ');
+}
+
+
+// A function that validates the input - Utilises Jquery.Validator.js
+function inputValidation() {
+  'use strict';
+  var maxCharacters = $('#seq').attr('data-maxCharacters'); // returns a number or undefined
+  $('#input').validate({
+    rules: {
+        seq: {
+            minlength: 5,
+            required: true,
+            checkInputType: true,
+            maxlength: maxCharacters // when undefined, maxlength is unlimited
+        },
+        'validations[]': {
+           required: true,
+        },
+    },
+    highlight: function(element) {
+        $(element).closest('.form-group').addClass('has-error');
+    },
+    unhighlight: function(element) {
+        $(element).closest('.form-group').removeClass('has-error');
+    },
+    errorElement: 'span',
+    errorClass: 'help-block',
+    errorPlacement: function(error, element) {
+        if (element.parent().parent().attr('id') === 'validations_group') {
+          var helpText = document.getElementById('lastValidation');
+          error.insertAfter(helpText);
+        } else {
+          if (element.parent('.input-group').length) {
+              error.insertAfter(element.parent());
+          } else {
+              error.insertAfter(element);
+          }
+        }
+    },
+    submitHandler: function(form) {
+      $('#spinner').modal({
+        backdrop: 'static',
+        keyboard: 'false'
+      });
+      ajaxFunction();
+    }
+  });
+}
+
+// Sends the data within the form to the Server
+function ajaxFunction() {
+  'use strict';
+  $.ajax({
+    type: 'POST',
+    url: $('#input').attr('action'),
+    data: $('#input').serialize(),
+    success: function(response){
+      $('#results_box').show();
+      $('#output').html(response);
+      initTableSorter(); // initiate the table sorter
+      $("[data-toggle='tooltip']").tooltip(); // Initiate the tooltips
+      removeEmptyColumns(); // Remove Unwanted Columns
+
+      $('#mainbody').css({'background-color': '#fff'});
+      $('#search').css({'background-color': '#F5F5F5'});
+      $('#results').css({'border-top': '3px solid #DBDBDB'});
+      $('#search').css({'margin-bottom': '0'});
+      
+      $('#spinner').modal('hide'); // remove progress notification
+    },
+    error: function (e, status) {
+      var errorMessage;
+      if (e.status == 500) {
+        errorMessage = e.responseText;
+        $('#results_box').show();
+        $('#output').html(errorMessage);
+        $('#spinner').modal('hide'); // remove progress notification
+      } else {
+        errorMessage = e.responseText;
+        $('#results_box').show();
+        $('#output').html('There seems to be an unidentified Error.');
+        $('#spinner').modal('hide'); // remove progress notification
+      }
+    }
+  });
+}
+
+//  Table sortert Initialiser 
+//   Contains a custom parser that allows the Stars to be sorted. 
+function initTableSorter() {
+  'use strict';
+  $.tablesorter.addParser({
+    id: 'star_scores',
+    is: function(s) {return false;},
+    format: function(s, table, cell, cellIndex) {
+      var $cell = $(cell);
+      if (cellIndex === 1) {
+        return $cell.attr('data-score') || s;
+      } 
+      return s;
+    },
+    parsed: false,
+    type: 'numeric'
+  });
+
+  $('table').tablesorter({
+    headers: {
+      1 : { sorter: 'star_scores' }
+    },
+    sortList: [[0,0]],
+  });
+}
+
+// Remove empty colums that are not used for that type of input data...
+function removeEmptyColumns() {
+  'use strict';
+  $('#sortable_table tr th').each(function(i) {
+    var tds = $(this).parents('table') // Select all tds in column
+    .find('tr td:nth-child(' + (i + 1) + ')');
+    // Check if all cells in the column are empty
+    if ($(this).hasClass( 'chart-column' )) {
+    } else {
+      if ($(this).text().trim() == '') { 
+        //hide header
+        $(this).hide();
+        //hide cells
+        tds.hide();
+      }
+    }
+  });
+}
+
+// Function is called each time the Adv. Params button is pressed...
+function changeAdvParamsBtnText() {
+  'use strict';
+  var btn = document.getElementById('adv_params_btn');
+  if (btn.innerHTML === '<i class="fa fa-pencil-square-o"></i>&nbsp;&nbsp;Show Advanced Parameters') {
+    btn.innerHTML = '<i class="fa fa-pencil-square-o"></i>&nbsp;&nbsp;Hide Advanced Parameters';
+    $('#adv_params').collapse('show');
+    $.cookie('GeneValidator_adv_params_status', 'open');
+  }
+  else {
+    btn.innerHTML = '<i class="fa fa-pencil-square-o"></i>&nbsp;&nbsp;Show Advanced Parameters';
+    $('#adv_params').collapse('hide');
+    $.cookie('GeneValidator_adv_params_status', 'closed');
+  }
+}
+
+// Changes the input to an examplar dna or protein sequence...
+function examplarSequence(type){
+  'use strict';
+  var dna = '>Insulin\n' +
+                'ATGGCTCTCTGGATCCGGTCGCTGCCTCTCCTGGCCCTTCTTGCTCTTTCTGGCCCTGGGATCAGCCACGCAGCTGCCAACCAGCACCTCTGTGGCTCCCACTTGGTTGAGGCTCTCTACCTGGTGTGTGGGGAGCGGGGTTTCTTCTACTCCCCCAAAACACGGCGGGACGTTGAGCAGCCTCTAGTGAACGGTCCCCTGCATGGCGAGGTGGGAGAGCTGCCGTTCCAGCATGAGGAATACCAGAAAGTCAAGCGAGGCATCGTTGAGCAATGCTGTGAAAACCCGTGCTCCCTCTACCAACTGGAAAACTACTGCAACTAG\n' +
+                '>Insulin (with a duplication)\n' +
+                'ATGGCTCTCTGGATCCGGTCGCTGCCTCTCCTGGCCCTTCTTGCTCTTTCTGGCCCTGGGATCAGCCACGCAGCTGCCAACCAGCACCTCTGTGGCTCCCACTTGGTTGAGGCTCTCTACCTGGTGTGTGGGGAGCGGGGTTTCTTCTACTCCCCCAAAACACGGCGGGACGTTGAGCAGCCTCTAGTGAACGGTCCCCTGCATGGCGAGGTGGGAGAGCTGCCGTTCCAGCATGAGGAATACCAGACAGCACCTCTGTGGCTCCCACTTGGTTGAGGCTCTCTACCTGGTGTGTGGGGAGCGGGGTTTCTTCTACTCCCCCAAAACACGGCGGGACGTTGAGCAGCCTCTAGTGAACGGTCCCCTGCATGGCGAGGTGGGAGAGCTGCCGTTCCAGCATGAGGAATACCAGAAAGTCAAGCGAGGCATCGTTGAGCAATGCTGTGAAAACCCGTGCTCCCTCTACCAACTGGAAAACTACTGCAACTAG';
+  var protein = '>Methylmalonyl-CoA carboxyltransferase 12S \n' +
+                'MAENNNLKLASTMEGRVEQLAEQRQVIEAGGGERRVEKQHSQGKQTARERLNNLLDPHSFDEVGAFRKHRTTLFGMDKAVVPADGVVTGRGTILGRPVHAASQDFTVMGGSAGETQSTKVVETMEQALLTGTPFLFFYDSGGARIQEGIDSLSGYGKMFFANVKLSGVVPQIAIIAGPCAGGASYSPALTDFIIMTKKAHMFITGPQVIKSVTGEDVTADELGGAEAHMAISGNIHFVAEDDDAAELIAKKLLSFLPQNNTEEASFVNPNNDVSPNTELRDIVPIDGKKGYDVRDVIAKIVDWGDYLEVKAGYATNLVTAFARVNGRSVGIVANQPSVMSGCLDINASDKAAEFVNFCDSFNIPLVQLVDVPGFLPGVQQEYGGIIRHGAKMLYAYSEATVPKITVVLRKAYGGSYLAMCNRDLGADAVYAWPSAEIAVMGAEGAANVIFRKEIKAADDPDAMRAEKIEEYQNAFNTPYVAAARGQVDDVIDPADTRRKIASALEMYATKRQTRPAKKPWKLPLLSEEEIMADEEEKDLMIATLNKRVASLESELGSLQSDTQGVTEDVLTAISAVAAYLGNDGSAEVVHFAPSPNWVREGRRALQNHSIR\n' +
+                '>locus=Si_gnF\n' +
+                'MWFPVVLLLLVGVAVAMPDHEHAWEPQNEYQYSVFVRTLTGVDTLKQQYTGIQLKGVLVIQVKSEELLQAKYINPRYAHIHQELSNGPYSKIPEENLEYRDIPMSGKPFEIKLKHGVIRDLLFDRNVPTWEVNMLKGIVGQLQIDTQGENAIDSQSTQIPSNSEPSSATFKAMEDSVGGKCEVLYEITPLPQHVAQTRPDRVPMSSVPSKGHHYEVKKLKNYEKCQERQLYHYGMDVKMTKENMMKRNKVVSELSTTHIVITGTLKSFTIQSTEMKNEITVQPESSDSPIGTVYSITKLTLAKINKISNSWFGPLELSNVESTGNLVYIFNNPFSDSEQRRVGQPSISRNSEQENSLETKKRSFHSHSSSSSSSSSSSSEEENESVMQSKASLRNIFMAPNVPLLPYFIGFKGKTIMKSNEHNVMQLAKDLLLQIAKEIQNPSEGYENTLEKYVNLKNLIRTMDRKQYTELEQYVSQFNKATVEGENAWYTLRDAVVHAGTGPAFVTIENWLKSGQVKGEEAAELLSKIPKSVHQPTPDYIKEFFKLIKSSVVTQQEYVNVSAPLAFAELLRNNYVVPSYYPVHSFGRMTLKGNEEIDNYISYLANQLQQGYLENNTQKIQTFIFALGVTAHPKIISVFEPYLEGKLPTTKYQRMLMVAALYDLSRDIPKLVGPIFYKLYMNENEAHEVRCMAVQQFILTDPPMITLQRVAKYTNYDQSDQVNSAVKSTLNSIINTKRPEWRNLANKARSVRYLVNPKNYDTWYSKGYYIDFENWVFKGLNVKMVASNDAVLPRYVYVGLDSIFNFLRKPTFEVGYAVSSYRQVYDLINELWNSYQFEEMREKSQGSRVEKLAQELKIKSGQKNNLEGHVLFNSVYGSMVYPYDKHRIREAVAALKKLLTSDSKLKTTAFNNFEKIVSFPMEMGVPFVYSFELPVFVKSEINFKKGEPITSRSGVYETLFCNRVQKRFGFIAPFEYQNYIAGIDKNGIMRVPLKYETNIDIKQKNFALKIHPNIPQSGTSTGLTHYSVVPFTTRQNIFNLQPVSNEGNTRPVITSEIHKMTKEKGPFSIKIESDTTKKESVLEDIVTGISKSSNSNNERYMKIDTTFESKQVAKCEIQIDMTFDAVTIHGKNQQPSHKEMQHHSKLDWKPNSKERREEIVNVLSAGLKSGTVFVADVSFSLPRLQDNTYVFTVGSVRSNIDQKLRHYFYVNTNAAQEVKYELCYSQEVQYAYPTPLNFEYAINNEPKDKLKGVLRYGRTCNTGNEIVITGSSSQSPQLRDMIENSSITKQCMEEIQKGKKSVRTCNKATDVAQVRDQLNFHIDASQLSEIRQKYDQVIGLLNYTNLSQYNVQQNSETNTIVVQNPWVMVPTVQEPWYRWAIKPSESQRQSEIDVLLDEVSQPSCTLDNDKILTFDNQLYNVQLGKCKHVLLTTYPQDSHNRRNYIPESSKVAVLAKDTDNDSRNVYVWLGNLEIELKKVGNDLKVAINGQNVEIPEKGHQESNGNEIIFEIVQLPDGSLSVISEKYGITVIFDGKHVRLYANGATYRNAIRGLCGNYDSRRDNDFLTPKNCLLTKPEEFAATYAMTNENCQGPAPENKRKAEGAMCIEVPEQQQMNVISDREAGRMMTEGGNWGYHQSNRKKEHGQDSKRGHGHKKYNQKDSQEGGSNESQYRKKHNIVYRTRVVEMDDKICFTTTPVPGCLQDTRPVERVPKKYDLYCLSKNNESMDLKRRVEEGAKPDFTQKPVNKIQNFQIPVSCSAA';
+
+  if (type === 'dna'){
+    document.getElementById('seq').value = dna;
+  } else if (type === 'protein') {
+    document.getElementById('seq').value = protein;
+  }
+}
+
+// FROM BIONODE-Seq - See https://github.com/bionode/bionode-seq
+// Checks whether a sequence is a protein or dna sequence...
+function checkType(sequence, threshold, length, index) {
+  'use strict';
+  if (threshold === undefined) {
+    threshold = 0.9;
+  }
+  if (length === undefined) {
+    length = 10000;
+  }
+  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';
+  }
+}

data/public/web_files/js/genevalidator.min.js

@@ -0,0 +1 @@
+function checkCollapseState(){"use strict";if($.cookie("GeneValidator_adv_params_status")){var G=$.cookie("GeneValidator_adv_params_status");if("open"===G){var T=document.getElementById("adv_params_btn");T.innerHTML='<i class="fa fa-pencil-square-o"></i>&nbsp;&nbsp;Hide Advanced Parameters',$("#adv_params").addClass("in")}}}function keepFooterFixedToBottom(){"use strict";$("#mainbody").css({"margin-bottom":$("#footer").height()+15+"px"}),$(window).resize(function(){$("#mainbody").css({"margin-bottom":$("#footer").height()+15+"px"})})}function addSeqValidation(){"use strict";jQuery.validator.addMethod("checkInputType",function(G,T){var A=[];if(">"===G.charAt(0)){for(var e=G.split(">"),C=1;C<e.length;C++){var t=e[C].split("\n");if(0!==t.length){var a=jQuery.grep(t,function(G){return G});if(0!==a.length){a.shift();var n=a.join(""),r=checkType(n,.9);if(A.push(r),"protein"!==r&&"dna"!==r&&"rna"!==r)return!1}}}for(var V=A[0],s=0;s<A.length;s++)if(A[s]!==V)return!1;return!0}var r=checkType(G,.9);return"protein"!==r&&"dna"!==r&&"rna"!==r?!1:!0},"* The Input must be either DNA or protein sequence(s). Please ensure that your sequences do not contains any non-letter character(s). If there are multiple sequences, ensure that they are all of one type. ")}function inputValidation(){"use strict";var G=$("#seq").attr("data-maxCharacters");$("#input").validate({rules:{seq:{minlength:5,required:!0,checkInputType:!0,maxlength:G},"validations[]":{required:!0}},highlight:function(G){$(G).closest(".form-group").addClass("has-error")},unhighlight:function(G){$(G).closest(".form-group").removeClass("has-error")},errorElement:"span",errorClass:"help-block",errorPlacement:function(G,T){if("validations_group"===T.parent().parent().attr("id")){var A=document.getElementById("lastValidation");G.insertAfter(A)}else G.insertAfter(T.parent(".input-group").length?T.parent():T)},submitHandler:function(G){$("#spinner").modal({backdrop:"static",keyboard:"false"}),ajaxFunction()}})}function ajaxFunction(){"use strict";$.ajax({type:"POST",url:$("#input").attr("action"),data:$("#input").serialize(),success:function(G){$("#results_box").show(),$("#output").html(G),initTableSorter(),$("[data-toggle='tooltip']").tooltip(),removeEmptyColumns(),$("#mainbody").css({"background-color":"#fff"}),$("#search").css({"background-color":"#F5F5F5"}),$("#results").css({"border-top":"3px solid #DBDBDB"}),$("#search").css({"margin-bottom":"0"}),$("#spinner").modal("hide")},error:function(G,T){var A;500==G.status?(A=G.responseText,$("#results_box").show(),$("#output").html(A),$("#spinner").modal("hide")):(A=G.responseText,$("#results_box").show(),$("#output").html("There seems to be an unidentified Error."),$("#spinner").modal("hide"))}})}function initTableSorter(){"use strict";$.tablesorter.addParser({id:"star_scores",is:function(G){return!1},format:function(G,T,A,e){var C=$(A);return 1===e?C.attr("data-score")||G:G},parsed:!1,type:"numeric"}),$("table").tablesorter({headers:{1:{sorter:"star_scores"}},sortList:[[0,0]]})}function removeEmptyColumns(){"use strict";$("#sortable_table tr th").each(function(G){var T=$(this).parents("table").find("tr td:nth-child("+(G+1)+")");$(this).hasClass("chart-column")||""==$(this).text().trim()&&($(this).hide(),T.hide())})}function changeAdvParamsBtnText(){"use strict";var G=document.getElementById("adv_params_btn");'<i class="fa fa-pencil-square-o"></i>&nbsp;&nbsp;Show Advanced Parameters'===G.innerHTML?(G.innerHTML='<i class="fa fa-pencil-square-o"></i>&nbsp;&nbsp;Hide Advanced Parameters',$("#adv_params").collapse("show"),$.cookie("GeneValidator_adv_params_status","open")):(G.innerHTML='<i class="fa fa-pencil-square-o"></i>&nbsp;&nbsp;Show Advanced Parameters',$("#adv_params").collapse("hide"),$.cookie("GeneValidator_adv_params_status","closed"))}function examplarSequence(G){"use strict";var T=">Insulin\nATGGCTCTCTGGATCCGGTCGCTGCCTCTCCTGGCCCTTCTTGCTCTTTCTGGCCCTGGGATCAGCCACGCAGCTGCCAACCAGCACCTCTGTGGCTCCCACTTGGTTGAGGCTCTCTACCTGGTGTGTGGGGAGCGGGGTTTCTTCTACTCCCCCAAAACACGGCGGGACGTTGAGCAGCCTCTAGTGAACGGTCCCCTGCATGGCGAGGTGGGAGAGCTGCCGTTCCAGCATGAGGAATACCAGAAAGTCAAGCGAGGCATCGTTGAGCAATGCTGTGAAAACCCGTGCTCCCTCTACCAACTGGAAAACTACTGCAACTAG\n>Insulin (with a duplication)\nATGGCTCTCTGGATCCGGTCGCTGCCTCTCCTGGCCCTTCTTGCTCTTTCTGGCCCTGGGATCAGCCACGCAGCTGCCAACCAGCACCTCTGTGGCTCCCACTTGGTTGAGGCTCTCTACCTGGTGTGTGGGGAGCGGGGTTTCTTCTACTCCCCCAAAACACGGCGGGACGTTGAGCAGCCTCTAGTGAACGGTCCCCTGCATGGCGAGGTGGGAGAGCTGCCGTTCCAGCATGAGGAATACCAGACAGCACCTCTGTGGCTCCCACTTGGTTGAGGCTCTCTACCTGGTGTGTGGGGAGCGGGGTTTCTTCTACTCCCCCAAAACACGGCGGGACGTTGAGCAGCCTCTAGTGAACGGTCCCCTGCATGGCGAGGTGGGAGAGCTGCCGTTCCAGCATGAGGAATACCAGAAAGTCAAGCGAGGCATCGTTGAGCAATGCTGTGAAAACCCGTGCTCCCTCTACCAACTGGAAAACTACTGCAACTAG",A=">Methylmalonyl-CoA carboxyltransferase 12S 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data/public/web_files/js/jquery.cookie.min.js

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data/public/web_files/js/jquery.min.js

@@ -0,0 +1,4 @@
+/*! jQuery v2.1.1 | (c) 2005, 2014 jQuery Foundation, Inc. | jquery.org/license */
+!function(a,b){"object"==typeof module&&"object"==typeof module.exports?module.exports=a.document?b(a,!0):function(a){if(!a.document)throw new Error("jQuery requires a window with a document");return b(a)}:b(a)}("undefined"!=typeof window?window:this,function(a,b){var c=[],d=c.slice,e=c.concat,f=c.push,g=c.indexOf,h={},i=h.toString,j=h.hasOwnProperty,k={},l=a.document,m="2.1.1",n=function(a,b){return new n.fn.init(a,b)},o=/^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g,p=/^-ms-/,q=/-([\da-z])/gi,r=function(a,b){return b.toUpperCase()};n.fn=n.prototype={jquery:m,constructor:n,selector:"",length:0,toArray:function(){return d.call(this)},get:function(a){return null!=a?0>a?this[a+this.length]:this[a]:d.call(this)},pushStack:function(a){var b=n.merge(this.constructor(),a);return b.prevObject=this,b.context=this.context,b},each:function(a,b){return n.each(this,a,b)},map:function(a){return this.pushStack(n.map(this,function(b,c){return a.call(b,c,b)}))},slice:function(){return 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data/public/web_files/js/jquery.tablesorter.min.js

@@ -0,0 +1,5 @@
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data/public/web_files/js/jquery.validate.min.js

@@ -0,0 +1,4 @@
+/*! jQuery Validation Plugin - v1.13.0 - 7/1/2014
+ * http://jqueryvalidation.org/
+ * Copyright (c) 2014 Jörn Zaefferer; Licensed MIT */
+!function(a){"function"==typeof define&&define.amd?define(["jquery"],a):a(jQuery)}(function(a){a.extend(a.fn,{validate:function(b){if(!this.length)return void(b&&b.debug&&window.console&&console.warn("Nothing selected, can't validate, returning nothing."));var c=a.data(this[0],"validator");return c?c:(this.attr("novalidate","novalidate"),c=new a.validator(b,this[0]),a.data(this[0],"validator",c),c.settings.onsubmit&&(this.validateDelegate(":submit","click",function(b){c.settings.submitHandler&&(c.submitButton=b.target),a(b.target).hasClass("cancel")&&(c.cancelSubmit=!0),void 0!==a(b.target).attr("formnovalidate")&&(c.cancelSubmit=!0)}),this.submit(function(b){function d(){var d;return c.settings.submitHandler?(c.submitButton&&(d=a("<input type='hidden'/>").attr("name",c.submitButton.name).val(a(c.submitButton).val()).appendTo(c.currentForm)),c.settings.submitHandler.call(c,c.currentForm,b),c.submitButton&&d.remove(),!1):!0}return 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a,b,c;for(a=0;this.errorList[a];a++)c=this.errorList[a],this.settings.highlight&&this.settings.highlight.call(this,c.element,this.settings.errorClass,this.settings.validClass),this.showLabel(c.element,c.message);if(this.errorList.length&&(this.toShow=this.toShow.add(this.containers)),this.settings.success)for(a=0;this.successList[a];a++)this.showLabel(this.successList[a]);if(this.settings.unhighlight)for(a=0,b=this.validElements();b[a];a++)this.settings.unhighlight.call(this,b[a],this.settings.errorClass,this.settings.validClass);this.toHide=this.toHide.not(this.toShow),this.hideErrors(),this.addWrapper(this.toShow).show()},validElements:function(){return this.currentElements.not(this.invalidElements())},invalidElements:function(){return a(this.errorList).map(function(){return this.element})},showLabel:function(b,c){var d,e,f,g=this.errorsFor(b),h=this.idOrName(b),i=a(b).attr("aria-describedby");g.length?(g.removeClass(this.settings.validClass).addClass(this.settings.errorClass),g.html(c)):(g=a("<"+this.settings.errorElement+">").attr("id",h+"-error").addClass(this.settings.errorClass).html(c||""),d=g,this.settings.wrapper&&(d=g.hide().show().wrap("<"+this.settings.wrapper+"/>").parent()),this.labelContainer.length?this.labelContainer.append(d):this.settings.errorPlacement?this.settings.errorPlacement(d,a(b)):d.insertAfter(b),g.is("label")?g.attr("for",h):0===g.parents("label[for='"+h+"']").length&&(f=g.attr("id"),i?i.match(new RegExp("\b"+f+"\b"))||(i+=" "+f):i=f,a(b).attr("aria-describedby",i),e=this.groups[b.name],e&&a.each(this.groups,function(b,c){c===e&&a("[name='"+b+"']",this.currentForm).attr("aria-describedby",g.attr("id"))}))),!c&&this.settings.success&&(g.text(""),"string"==typeof this.settings.success?g.addClass(this.settings.success):this.settings.success(g,b)),this.toShow=this.toShow.add(g)},errorsFor:function(b){var c=this.idOrName(b),d=a(b).attr("aria-describedby"),e="label[for='"+c+"'], label[for='"+c+"'] *";return d&&(e=e+", #"+d.replace(/\s+/g,", #")),this.errors().filter(e)},idOrName:function(a){return this.groups[a.name]||(this.checkable(a)?a.name:a.id||a.name)},validationTargetFor:function(a){return this.checkable(a)&&(a=this.findByName(a.name).not(this.settings.ignore)[0]),a},checkable:function(a){return/radio|checkbox/i.test(a.type)},findByName:function(b){return a(this.currentForm).find("[name='"+b+"']")},getLength:function(b,c){switch(c.nodeName.toLowerCase()){case"select":return a("option:selected",c).length;case"input":if(this.checkable(c))return this.findByName(c.name).filter(":checked").length}return b.length},depend:function(a,b){return this.dependTypes[typeof a]?this.dependTypes[typeof a](a,b):!0},dependTypes:{"boolean":function(a){return a},string:function(b,c){return!!a(b,c.form).length},"function":function(a,b){return a(b)}},optional:function(b){var c=this.elementValue(b);return!a.validator.methods.required.call(this,c,b)&&"dependency-mismatch"},startRequest:function(a){this.pending[a.name]||(this.pendingRequest++,this.pending[a.name]=!0)},stopRequest:function(b,c){this.pendingRequest--,this.pendingRequest<0&&(this.pendingRequest=0),delete this.pending[b.name],c&&0===this.pendingRequest&&this.formSubmitted&&this.form()?(a(this.currentForm).submit(),this.formSubmitted=!1):!c&&0===this.pendingRequest&&this.formSubmitted&&(a(this.currentForm).triggerHandler("invalid-form",[this]),this.formSubmitted=!1)},previousValue:function(b){return a.data(b,"previousValue")||a.data(b,"previousValue",{old:null,valid:!0,message:this.defaultMessage(b,"remote")})}},classRuleSettings:{required:{required:!0},email:{email:!0},url:{url:!0},date:{date:!0},dateISO:{dateISO:!0},number:{number:!0},digits:{digits:!0},creditcard:{creditcard:!0}},addClassRules:function(b,c){b.constructor===String?this.classRuleSettings[b]=c:a.extend(this.classRuleSettings,b)},classRules:function(b){var c={},d=a(b).attr("class");return d&&a.each(d.split(" "),function(){this in a.validator.classRuleSettings&&a.extend(c,a.validator.classRuleSettings[this])}),c},attributeRules:function(b){var c,d,e={},f=a(b),g=b.getAttribute("type");for(c in a.validator.methods)"required"===c?(d=b.getAttribute(c),""===d&&(d=!0),d=!!d):d=f.attr(c),/min|max/.test(c)&&(null===g||/number|range|text/.test(g))&&(d=Number(d)),d||0===d?e[c]=d:g===c&&"range"!==g&&(e[c]=!0);return e.maxlength&&/-1|2147483647|524288/.test(e.maxlength)&&delete e.maxlength,e},dataRules:function(b){var c,d,e={},f=a(b);for(c in a.validator.methods)d=f.data("rule"+c.charAt(0).toUpperCase()+c.substring(1).toLowerCase()),void 0!==d&&(e[c]=d);return e},staticRules:function(b){var c={},d=a.data(b.form,"validator");return d.settings.rules&&(c=a.validator.normalizeRule(d.settings.rules[b.name])||{}),c},normalizeRules:function(b,c){return a.each(b,function(d,e){if(e===!1)return void delete b[d];if(e.param||e.depends){var f=!0;switch(typeof e.depends){case"string":f=!!a(e.depends,c.form).length;break;case"function":f=e.depends.call(c,c)}f?b[d]=void 0!==e.param?e.param:!0:delete b[d]}}),a.each(b,function(d,e){b[d]=a.isFunction(e)?e(c):e}),a.each(["minlength","maxlength"],function(){b[this]&&(b[this]=Number(b[this]))}),a.each(["rangelength","range"],function(){var c;b[this]&&(a.isArray(b[this])?b[this]=[Number(b[this][0]),Number(b[this][1])]:"string"==typeof b[this]&&(c=b[this].replace(/[\[\]]/g,"").split(/[\s,]+/),b[this]=[Number(c[0]),Number(c[1])]))}),a.validator.autoCreateRanges&&(b.min&&b.max&&(b.range=[b.min,b.max],delete b.min,delete b.max),b.minlength&&b.maxlength&&(b.rangelength=[b.minlength,b.maxlength],delete b.minlength,delete b.maxlength)),b},normalizeRule:function(b){if("string"==typeof b){var c={};a.each(b.split(/\s/),function(){c[this]=!0}),b=c}return b},addMethod:function(b,c,d){a.validator.methods[b]=c,a.validator.messages[b]=void 0!==d?d:a.validator.messages[b],c.length<3&&a.validator.addClassRules(b,a.validator.normalizeRule(b))},methods:{required:function(b,c,d){if(!this.depend(d,c))return"dependency-mismatch";if("select"===c.nodeName.toLowerCase()){var e=a(c).val();return e&&e.length>0}return this.checkable(c)?this.getLength(b,c)>0:a.trim(b).length>0},email:function(a,b){return this.optional(b)||/^[a-zA-Z0-9.!#$%&'*+\/=?^_`{|}~-]+@[a-zA-Z0-9](?:[a-zA-Z0-9-]{0,61}[a-zA-Z0-9])?(?:\.[a-zA-Z0-9](?:[a-zA-Z0-9-]{0,61}[a-zA-Z0-9])?)*$/.test(a)},url:function(a,b){return this.optional(b)||/^(https?|s?ftp):\/\/(((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&'\(\)\*\+,;=]|:)*@)?(((\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5])\.(\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5])\.(\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5])\.(\d|[1-9]\d|1\d\d|2[0-4]\d|25[0-5]))|((([a-z]|\d|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(([a-z]|\d|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])*([a-z]|\d|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])))\.)+(([a-z]|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(([a-z]|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])*([a-z]|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])))\.?)(:\d*)?)(\/((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&'\(\)\*\+,;=]|:|@)+(\/(([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&'\(\)\*\+,;=]|:|@)*)*)?)?(\?((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&'\(\)\*\+,;=]|:|@)|[\uE000-\uF8FF]|\/|\?)*)?(#((([a-z]|\d|-|\.|_|~|[\u00A0-\uD7FF\uF900-\uFDCF\uFDF0-\uFFEF])|(%[\da-f]{2})|[!\$&'\(\)\*\+,;=]|:|@)|\/|\?)*)?$/i.test(a)},date:function(a,b){return this.optional(b)||!/Invalid|NaN/.test(new Date(a).toString())},dateISO:function(a,b){return this.optional(b)||/^\d{4}[\/\-](0?[1-9]|1[012])[\/\-](0?[1-9]|[12][0-9]|3[01])$/.test(a)},number:function(a,b){return this.optional(b)||/^-?(?:\d+|\d{1,3}(?:,\d{3})+)?(?:\.\d+)?$/.test(a)},digits:function(a,b){return this.optional(b)||/^\d+$/.test(a)},creditcard:function(a,b){if(this.optional(b))return"dependency-mismatch";if(/[^0-9 \-]+/.test(a))return!1;var c,d,e=0,f=0,g=!1;if(a=a.replace(/\D/g,""),a.length<13||a.length>19)return!1;for(c=a.length-1;c>=0;c--)d=a.charAt(c),f=parseInt(d,10),g&&(f*=2)>9&&(f-=9),e+=f,g=!g;return e%10===0},minlength:function(b,c,d){var e=a.isArray(b)?b.length:this.getLength(a.trim(b),c);return this.optional(c)||e>=d},maxlength:function(b,c,d){var e=a.isArray(b)?b.length:this.getLength(a.trim(b),c);return this.optional(c)||d>=e},rangelength:function(b,c,d){var e=a.isArray(b)?b.length:this.getLength(a.trim(b),c);return this.optional(c)||e>=d[0]&&e<=d[1]},min:function(a,b,c){return this.optional(b)||a>=c},max:function(a,b,c){return this.optional(b)||c>=a},range:function(a,b,c){return this.optional(b)||a>=c[0]&&a<=c[1]},equalTo:function(b,c,d){var e=a(d);return this.settings.onfocusout&&e.unbind(".validate-equalTo").bind("blur.validate-equalTo",function(){a(c).valid()}),b===e.val()},remote:function(b,c,d){if(this.optional(c))return"dependency-mismatch";var e,f,g=this.previousValue(c);return this.settings.messages[c.name]||(this.settings.messages[c.name]={}),g.originalMessage=this.settings.messages[c.name].remote,this.settings.messages[c.name].remote=g.message,d="string"==typeof d&&{url:d}||d,g.old===b?g.valid:(g.old=b,e=this,this.startRequest(c),f={},f[c.name]=b,a.ajax(a.extend(!0,{url:d,mode:"abort",port:"validate"+c.name,dataType:"json",data:f,context:e.currentForm,success:function(d){var f,h,i,j=d===!0||"true"===d;e.settings.messages[c.name].remote=g.originalMessage,j?(i=e.formSubmitted,e.prepareElement(c),e.formSubmitted=i,e.successList.push(c),delete e.invalid[c.name],e.showErrors()):(f={},h=d||e.defaultMessage(c,"remote"),f[c.name]=g.message=a.isFunction(h)?h(b):h,e.invalid[c.name]=!0,e.showErrors(f)),g.valid=j,e.stopRequest(c,j)}},d)),"pending")}}}),a.format=function(){throw"$.format has been deprecated. Please use $.validator.format instead."};var b,c={};a.ajaxPrefilter?a.ajaxPrefilter(function(a,b,d){var e=a.port;"abort"===a.mode&&(c[e]&&c[e].abort(),c[e]=d)}):(b=a.ajax,a.ajax=function(d){var e=("mode"in d?d:a.ajaxSettings).mode,f=("port"in d?d:a.ajaxSettings).port;return"abort"===e?(c[f]&&c[f].abort(),c[f]=b.apply(this,arguments),c[f]):b.apply(this,arguments)}),a.extend(a.fn,{validateDelegate:function(b,c,d){return this.bind(c,function(c){var e=a(c.target);return e.is(b)?d.apply(e,arguments):void 0})}})});

data/public/web_files/js/plots.js

@@ -0,0 +1,744 @@
+function showDiv(source, target){
+  'use strict';
+  if (window.chrome && (window.location.protocol === 'file:') ) {
+    if (($('#browser-alert').length) === 0) {
+      $('#browseralertText').html('<stong>Sorry, this feature is not supported in your browser.');
+      $('#browseralert').modal();
+    }
+    return;
+  }
+  var explanationId = '#' + target + 'explanation';
+
+  if ( $(explanationId).length) {
+    $(explanationId).remove();
+  }
+
+  var button = document.getElementById(target);
+  if (source.status === 'pressed'){
+    button.style.display = 'none';
+    $(button).parent().parent().hide();
+  } else {
+    d3.select('#'.concat(target)).selectAll('svg').remove();    
+    button.style.display = 'block';
+    $(button).parent().parent().show();
+    var pressedButtons = document.querySelectorAll('td');
+    for (var i = 0; i < pressedButtons.length; i++) {
+      if (pressedButtons[i].status === 'pressed') {
+        pressedButtons[i].status = 'released';
+      }
+    }
+  }
+
+  if (source.status=='pressed') {
+    source.status='released';
+  } else {
+    source.status='pressed';
+  }
+}
+
+function AddExplanation(source, target){
+  'use strict';
+  var row = '#' + target +'row';
+  var approach_html = '<p><b>Approach:</b> ' + source.getAttribute("data-approach") + '</p>';
+  var explanation_html = '<p><b>Explanation:</b> ' + source.getAttribute("data-explanation") + '</p>';
+  var conclusion_html = '<p><b>Conclusion:</b> ' + source.getAttribute("data-conclusion") + '</p>';
+
+  var explain = $('<div id="' + target + 'explanation" class="alert alert-info explanation_alert" role="alert">' + approach_html + explanation_html + conclusion_html + '</div>');
+  if (source.status === 'pressed') {
+    $(row).prepend(explain);
+  }
+}
+
+function addPlot(target, filename, type, title, footer, xtitle, ytitle, aux1, aux2){
+  'use strict';
+  var legend;
+  if (footer === '') {
+    legend = [];
+  } else {
+    legend = footer.split(';');
+  }
+
+  switch(type) {
+    case 'scatter':
+      plot_scatter(filename, target, title, footer, xtitle, ytitle, aux1, aux2);
+      break;
+    case 'bars':
+      plot_bars(filename, target, title, legend, xtitle, ytitle, aux1);
+      break;
+    case 'simplebars':
+      plot_simple_bars(filename, target, title, legend, xtitle, ytitle);
+      break;
+    case 'lines':
+      if (aux2 !== '') {
+        aux2 = aux2.split(',');
+      }
+      plot_lines(filename, target, title, legend, xtitle, ytitle, aux1, aux2);
+      break;
+    case 'align':
+      if (aux2 !== '') {
+        aux2 = aux2.split(',');
+      }
+      plot_align(filename, target, title, legend, xtitle, ytitle, aux1, aux2);
+      break;
+    default:
+      break;
+  }
+}
+
+function color_beautification(color){
+  'use strict';
+  switch(color){
+    case 'red':
+      return d3.rgb(189,54,47);
+    case 'blue':
+      return d3.rgb(58,135,173);
+    case 'green':
+      return d3.rgb(70,136,71);
+    case 'yellow':
+      return d3.rgb(255,255,51);
+    case 'orange':
+      return d3.rgb(248,148,6);
+    case 'violet':
+      return d3.rgb(153,0,153);
+    case 'gray':
+      return d3.rgb(160,160,160);
+    default:
+      return color;
+  }
+}
+
+// bars plot
+function plot_bars(filename, target, title, footer, xTitle, yTitle, bar){
+  var margin = {top: 70, right: 50, bottom: 75, left: 50},
+    width = 600 - margin.left - margin.right,
+    height = 500 - margin.top - margin.bottom;      
+  var legend_width = 15
+
+  var svg = d3.select("#".concat(target)).append("svg")
+    .attr("width", width + margin.left + margin.right)
+    .attr("height", height + margin.top + margin.bottom)
+    .append("g")
+    .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+    
+  svg.append("text")
+    .attr("x", (width / 2))             
+    .attr("y", -45)
+    .attr("text-anchor", "middle")  
+    .style("font-size", "16px") 
+    .text(title);   
+    
+  var colors = new Array("orange", "blue", "green", "yellow", "brown");
+  var no_colors = colors.length
+
+  var padding = 100
+
+  d3.json(filename, function(error, alldata) {
+    
+    flattened_data = [].concat.apply([], alldata)           
+    var yMax = d3.max(flattened_data, function(d) { return d.value; }) + 3
+    var y = d3.scale.linear()
+      .domain([0, yMax + yMax/10])
+      .range([height, 0]);
+
+    var xMin = d3.min(flattened_data, function(d) { return d.key; })
+    if (bar!=undefined){
+      var xMin = Math.min(xMin, bar); 
+    }
+ 
+    var xMax = d3.max(flattened_data, function(d) { return d.key; })
+    if (bar!=undefined){
+      var xMax = Math.max(xMax, bar); 
+    }
+
+    var x = d3.scale.linear()
+      .domain([xMin-padding, xMax+padding])
+      .range([13, width]);
+
+    var xAxis = d3.svg.axis()
+      .scale(x)
+      .orient("bottom")
+      .ticks(8)
+
+    var yAxis = d3.svg.axis()
+      .scale(y)
+      .orient("left")
+      .tickFormat(d3.format("d"))
+      .ticks(8)
+
+    svg.append("g")
+        .attr("class", "x axis")
+        .attr("transform", "translate(0," + height + ")")
+        .call(xAxis)
+      .append("text")
+        .attr("class", "label")
+        .attr("x", (width-xTitle.length)/2-50)
+        .attr("y", 35)
+        .style("text-anchor", "start")
+        .text(xTitle)
+
+     svg.append("g")
+         .attr("class", "y axis")
+        .call(yAxis)
+      .append("text")
+        .attr("class", "label")
+        .attr("transform", "rotate(-90)")
+        .attr("x", -(height+yTitle.length)/2-50)
+        .attr("y", -40)
+        .style("text-anchor", "start")
+        .text(yTitle)
+        
+    alldata.map( function(data, i) {
+     
+      color = colors[i % (no_colors - 1)];
+      svg.selectAll(".bar")
+        .data(data)
+        .enter().append("rect")
+          .attr("x", function(d) { return x(d.key); })
+          .attr("width", 6)
+          .attr("y", function(d) { return y(d.value); })
+          .attr("height", function(d) { return height - y(d.value); })
+          .attr("fill", function(d) { if (d.main == true) return color_beautification("red"); return color_beautification("blue");});
+    }); 
+
+    if (bar!=undefined){
+      svg.append("rect")
+        .attr("x", x(bar))
+        .attr("width", 4)
+        .attr("y", y(yMax + yMax/10))
+        .style("opacity",0.6)
+        .attr("height", height - y(yMax + yMax/8))
+        .attr("fill", color_beautification("black"));
+
+      svg.append("text")
+        .attr("transform", "rotate(-90)")
+        .attr("x", -yMax/10 - 35)
+        .attr("y", x(bar) - 5)
+          .text("query");
+        }   
+  });
+
+  var offset = 0
+  var total_len = 0
+  for (var i = 0; i < footer.length; i++) {
+  var array = footer[i].split(","); 
+  total_len = total_len + array[0].length*8 + 15;
+  }
+
+  for (var i = 0; i < footer.length; i++) {
+
+  var array = footer[i].split(","); 
+  svg.append("rect")
+      .attr("x", (width-total_len)/2 + offset)             
+      .attr("y", -30)
+      .attr("width", 10)
+      .attr("height", 10)
+      .style("fill", color_beautification(array[1].replace(/\s+/g, '')))
+    
+  svg.append("text")
+      .attr("x", (width-total_len)/2 + offset + 15)             
+      .attr("y", -20)
+      .text(array[0]);
+    offset = offset + array[0].length*8 + 15
+
+  }
+
+
+
+}   
+
+// bars plot
+function plot_simple_bars(filename, target, title, footer, xTitle, yTitle){
+  'use strict';
+
+  var margin = {top: 70, right: 50, bottom: 75, left: 50},
+    width = 600 - margin.left - margin.right,
+    height = 500 - margin.top - margin.bottom;      
+  var legend_width = 15
+
+  var svg = d3.select("#".concat(target)).append("svg")
+    .attr("width", width + margin.left + margin.right)
+    .attr("height", height + margin.top + margin.bottom)
+    .append("g")
+      .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+    
+  svg.append("text")
+    .attr("x", (width / 2))             
+    .attr("y", -45)
+    .attr("text-anchor", "middle")  
+    .style("font-size", "16px") 
+    .text(title);   
+    
+  var colors = new Array("orange", "blue", "green", "yellow", "brown");
+  var no_colors = colors.length
+
+    var padding = 0
+
+  d3.json(filename, function(error, alldata) {
+    
+    flattened_data = [].concat.apply([], alldata)           
+    var yMax = d3.max(flattened_data, function(d) { return d.value; }) + 3
+    var y = d3.scale.linear()
+           .domain([0, yMax])
+           .range([height, 0]);
+
+    var xMin = d3.min(flattened_data, function(d) { return d.key; })
+        var xMax = d3.max(flattened_data, function(d) { return d.key; })
+
+    var x = d3.scale.linear()
+           .domain([xMin-padding, xMax+padding])
+           .range([13, width]);
+
+    var xAxis = d3.svg.axis()
+        .scale(x)
+        .orient("bottom")
+      .ticks(8)
+
+      var yAxis = d3.svg.axis()
+      .scale(y)
+      .orient("left")
+      .tickFormat(d3.format("d"))
+      .ticks(8)
+
+    svg.append("g")
+        .attr("class", "x axis")
+        .attr("transform", "translate(0," + height + ")")
+        .call(xAxis)
+      .append("text")
+        .attr("class", "label")
+        .attr("x", (width-xTitle.length)/2-50)
+        .attr("y", 35)
+        .style("text-anchor", "start")
+        .text(xTitle)
+
+     svg.append("g")
+         .attr("class", "y axis")
+        .call(yAxis)
+      .append("text")
+        .attr("class", "label")
+        .attr("transform", "rotate(-90)")
+        .attr("x", -(height+yTitle.length)/2-50)
+        .attr("y", -40)
+        .style("text-anchor", "start")
+        .text(yTitle)
+        
+    alldata.map( function(data, i) {
+     
+      color = colors[i % (no_colors - 1)];
+      svg.selectAll(".bar")
+        .data(data)
+        .enter().append("rect")
+          .attr("x", function(d) { return x(d.key); })
+          .attr("width", 6)
+          .attr("y", function(d) { return y(d.value); })
+          .attr("height", function(d) { return height - y(d.value); })
+          .attr("fill", function(d) { if (d.main == true) return color_beautification("red"); return color_beautification("blue");});
+    }); 
+
+  });
+
+}
+
+
+// scatter plot
+// ecuation of the line: slope * x + yLine
+function plot_scatter(filename, target, title, footer, xTitle, yTitle, yLine, slope){
+  'use strict';
+
+  var margin = {top: 50, right: 30, bottom: 75, left: 50},
+    width = 500 - margin.left - margin.right,
+    height = 500 - margin.top - margin.bottom;      
+
+  var x = d3.scale.linear()
+    .range([0, width]);
+  var y = d3.scale.linear()
+    .range([height, 0]);
+
+  var color = d3.scale.category10();
+
+  var xAxis = d3.svg.axis()
+    .scale(x)
+    .orient("bottom")
+    .ticks(8);
+  var yAxis = d3.svg.axis()
+    .scale(y)
+    .orient("left")
+    .tickFormat(d3.format("d"))
+    .ticks(8);
+
+  var svg = d3.select("#".concat(target)).append("svg")
+    .attr("width", width + margin.left + margin.right)
+    .attr("height", height + margin.top + margin.bottom)
+    .append("g")
+      .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+    
+  svg.append("text")
+    .attr("x", (width / 2))             
+    .attr("y", -25)
+    .attr("text-anchor", "middle")  
+    .style("font-size", "16px") 
+    .text(title);   
+
+  svg.append("text")
+    .attr("x", (width / 2))             
+    .attr("y", height+ 55)
+    .attr("text-anchor", "middle")  
+    .style("font-size", "12px") 
+    .text(footer);  
+
+  d3.json(filename, function(error, data) {
+
+      var xMax = d3.max(data, function(d) { return d.x; })
+      var xMin = d3.min(data, function(d) { return d.x; })
+      var yMax = d3.max(data, function(d) { return d.y; })
+      var yMin = d3.min(data, function(d) { return d.y; })
+    x.domain(d3.extent(data, function(d) { return d.x; })).nice();
+    y.domain(d3.extent(data, function(d) { return d.y; })).nice();
+
+    svg.append("g")
+      .attr("class", "x axis")
+      .attr("transform", "translate(0," + height + ")")
+      .call(xAxis)
+    .append("text")
+      .attr("class", "label")
+      .attr("x", (width-xTitle.length)/2-50)
+      .attr("y", 35)
+      .style("text-anchor", "start")
+      .text(xTitle)
+
+    svg.append("g")
+      .attr("class", "y axis")
+      .call(yAxis)
+    .append("text")
+      .attr("class", "label")
+      .attr("transform", "rotate(-90)")
+      .attr("x", -(height+yTitle.length)/2-50)
+      .attr("y", -40)
+      .style("text-anchor", "start")
+      .text(yTitle)
+
+    svg.selectAll(".dot")
+      .data(data)
+    .enter().append("circle")
+      //.attr("class", "dot")
+      .attr("r", 2)
+      .attr("cx", function(d) { return x(d.x); })
+      .attr("cy", function(d) { return y(d.y); })
+      .style("fill", function(d) { return color_beautification("red"); })
+      .style("opacity",0.6);
+
+       if ((slope!=undefined && slope != "") && (yLine!=undefined && yLine != "")){
+
+        yLine = parseFloat(yLine.replace(",", "."));
+        var xMaxValue = xMax
+        var yMaxValue = yLine + slope * xMax
+        if (yMaxValue > yMax){
+            xMaxValue = (yMax-yLine)/slope
+            yMaxValue = yMax
+        }
+
+        if (yMaxValue < yMin){
+            xMaxValue = (yMin-yLine)/slope
+            yMaxValue = yMin
+        }
+
+        var xMinValue = xMin
+        var yMinValue = yLine + slope * xMin
+        if (yMinValue > yMax){
+            xMinValue = (yMax-yLine)/slope
+            yMinValue = yMin
+        }
+
+        if (yMinValue < yMin){
+            xMinValue = (yMin-yLine)/slope
+            yMinValue = yMin
+        }
+
+        svg.append("line")
+          .attr("x1", x(xMinValue))
+          .attr("y1", y(yMinValue))
+          .attr("x2", x(xMaxValue))
+          .attr("y2", y(yMaxValue))
+          .attr("stroke-width", 2)
+          .attr("stroke", "black")
+      }
+
+
+  });
+}
+
+// line plot
+// maximum 80 lines
+function plot_lines(filename, target, title, footer, xTitle, yTitle, no_lines, yValues){
+  'use strict';
+  var margin = {top: 70, right: 50, bottom: 75, left: 50},
+    width = 600 - margin.left - margin.right,
+    height = 500 - margin.top - margin.bottom;      
+    var legend_width = 17   
+
+  var x = d3.scale.linear()
+    .range([0, width]);
+  var y = d3.scale.linear()
+    .range([height, 0]);
+
+  var color = d3.scale.category10();
+
+  if (title === 'Open Reading Frames in all 6 Frames') {  
+    var xAxis = d3.svg.axis()
+      .scale(x)
+      .orient("bottom")
+      .ticks(0); 
+  } else {
+    var xAxis = d3.svg.axis()
+      .scale(x)
+      .orient("bottom")
+      .ticks(5);
+  }
+
+  var yAxis = d3.svg.axis()
+    .scale(y)
+    .orient("left")
+    .ticks(5)
+
+  var svg = d3.select("#".concat(target)).append("svg")
+    .attr("width", width + margin.left + margin.right)
+    .attr("height", height + margin.top + margin.bottom)
+    .append("g")
+    .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+    
+  svg.append("text")
+    .attr("x", (width / 2))             
+    .attr("y", -35)
+    .attr("text-anchor", "middle")  
+    .style("font-size", "16px") 
+    .text(title);   
+
+  d3.json(filename, function(error, data) {
+
+    var idx = -1
+
+    x.domain([0, d3.max(data, function(d) { return d.stop; })]);
+    y.domain(d3.extent(data, function(d) { return d.y; })).nice();
+
+    svg.append("g")
+      .attr("class", "x axis")
+      .attr("transform", "translate(0," + (height + height/no_lines) + ")")
+      .call(xAxis)
+    .append("text")
+      .attr("class", "label")
+      .attr("x", (width-xTitle.length)/2-50)
+      .attr("y", 35)
+      .style("text-anchor", "start")
+      .text(xTitle)
+      
+      if (yValues != ""){
+      svg.append("g")
+        .attr("class", "y axis")
+        .call(yAxis
+            .ticks(yValues.length)
+        .tickFormat(function (d) {                     
+               idx = idx + 1;
+           return yValues[idx];
+          }))
+      .append("text")
+        .attr("class", "label")
+        .attr("transform", "rotate(-90)")
+        .attr("x", -(height+yTitle.length)/2-50)
+        .attr("y", -40)
+        .style("text-anchor", "start")
+        .text(yTitle)
+    }
+    else{
+      svg.append("g")
+        .attr("class", "y axis")
+        .call(yAxis)
+      .append("text")
+        .attr("class", "label")
+        .attr("transform", "rotate(-90)")
+        .attr("x", -(height+yTitle.length)/2)
+        .attr("y", -40)
+        .style("text-anchor", "start")
+        .text(yTitle)
+    }
+
+    svg.selectAll(".dot")
+      .data(data)
+    .enter().append("line")
+          .attr("x1", function(d) { return x(d.start); })
+          .attr("y1", function(d) { return y(d.y); })                 
+          .attr("x2", function(d) { return x(d.stop); })
+          .attr("x2", function(d) { return x(d.stop); })
+          .attr("y2", function(d) { return y(d.y); })                 
+          .attr("stroke-width", function(d) {
+          if (d.dotted == undefined) {
+            if (d.color == "red" ) {
+              return height/no_lines/2.5
+            } else {
+              return height/no_lines
+            }
+          } else {
+            return height/no_lines/5
+          }
+          })
+          .style("stroke-dasharray", function(d) { if (d.dotted == undefined) return ("0, 0"); return ("2, 6");}) 
+          .attr("stroke", function(d) { return color_beautification(d.color); })
+  });
+
+  // add legend   
+  var legend = svg.append("g")
+    .attr("class", "legend")
+    .attr("height", 100)
+    .attr("width", 100)
+      .attr('transform', 'translate(-20,50)')    
+    
+  var h = 0
+
+  var offset = 40
+  var total_len = 0
+  for (var i = 0; i < footer.length; i++) {
+  var array = footer[i].split(","); 
+  total_len = total_len + array[0].length*8 + 15;
+  }
+
+  for (var i = 0; i < footer.length; i++) {
+
+  var array = footer[i].split(","); 
+  svg.append("rect")
+      .attr("x", (width-total_len)/2 + offset)             
+      .attr("y", -30)
+      .attr("width", 10)
+      .attr("height", 10)
+      .style("fill", color_beautification(array[1].replace(/\s+/g, '')))
+    
+  svg.append("text")
+      .attr("x", (width-total_len)/2 + offset + 15)             
+      .attr("y", -20)
+      .text(array[0]);
+    offset = offset + array[0].length*8 + 15
+
+  }
+}
+
+// line plot
+// maximum 80 lines
+function plot_align(filename, target, title, footer, xTitle, yTitle, no_lines, yValues){
+  'use strict';
+
+  var margin = {top: 75, right: 50, bottom: 75, left: 150},
+    width = 600 - margin.left - margin.right,
+    height = 300 - margin.top - margin.bottom;      
+    var legend_width = 17   
+
+  var x = d3.scale.linear()
+    .range([0, width]);
+  var y = d3.scale.linear()
+    .range([height, 0]);
+
+  var color = d3.scale.category10();
+
+  var xAxis = d3.svg.axis()
+    .scale(x)
+    .orient("bottom")
+    .ticks(5);
+
+  var yAxis = d3.svg.axis()
+    .scale(y)
+    .orient("left")
+    .ticks(5)
+
+  var svg = d3.select("#".concat(target)).append("svg")
+    .style("vertical-align", "top") 
+    .attr("width", width + margin.left + margin.right)
+    .attr("height", height + margin.top + margin.bottom)
+    .append("g")
+    .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
+    
+  svg.append("text")
+    .attr("x", (width / 2))             
+    .attr("y", -35)
+    .attr("text-anchor", "middle")  
+    .style("font-size", "16px") 
+    .text(title);   
+
+  d3.json(filename, function(error, data) {
+
+    var idx = -1
+
+    x.domain([0, d3.max(data, function(d) { return d.stop; })]);
+    y.domain(d3.extent(data, function(d) { return d.y; })).nice();
+
+    svg.append("g")
+      .attr("class", "x axis")
+      .attr("transform", "translate(0," + (height+height/no_lines) + ")")
+      .call(xAxis)
+    .append("text")
+      .attr("class", "label")
+      .attr("x", (width-xTitle.length)/2-50)
+      .attr("y", 35)
+      .style("text-anchor", "start")
+      .text(xTitle)
+      
+      if (yValues != ""){
+      svg.append("g")
+        .attr("class", "y axis")
+        .call(yAxis
+            .ticks(yValues.length)
+        .tickFormat(function (d) {                     
+               idx = idx + 1;
+           return yValues[idx];
+          }))
+      .append("text")
+        .attr("class", "label")
+        .attr("transform", "rotate(-90)")
+        .attr("x", -(height+yTitle.length)/2-50)
+        .attr("y", -40)
+        .style("text-anchor", "start")
+        .text(yTitle)
+    }
+    else{
+      svg.append("g")
+        .attr("class", "y axis")
+        .call(yAxis)
+      .append("text")
+        .attr("class", "label")
+        .attr("transform", "rotate(-90)")
+        .attr("x", -(height+yTitle.length)/2-50)
+        .attr("y", -40)
+        .style("text-anchor", "start")
+        .text(yTitle)
+    }
+
+    svg.selectAll(".dot")
+      .data(data)
+    .enter().append("line")
+          .attr("x1", function(d) { return x(d.start); })
+          .attr("y1", function(d) { return y(d.y); })                 
+          .attr("x2", function(d) { return x(d.stop); })
+          .attr("y2", function(d) { return y(d.y); })                 
+          .attr("stroke-width", function(d) { if (d.height == -1) return height/no_lines; return (height/no_lines * d.height) ; })
+          .attr("stroke", function(d) { return color_beautification(d.color); })
+  });
+
+  var offset = 0
+  var total_len = 0
+  for (var i = 0; i < footer.length; i++) {
+  var array = footer[i].split(","); 
+  total_len = total_len + array[0].length*8 + 15;
+  }
+
+  for (var i = 0; i < footer.length; i++) {
+
+  var array = footer[i].split(","); 
+  svg.append("rect")
+      .attr("x", (width-total_len)/2 + offset)             
+      .attr("y", -30)
+      .attr("width", 10)
+      .attr("height", 10)
+      .style("fill", color_beautification(array[1].replace(/\s+/g, '')))
+    
+  svg.append("text")
+      .attr("x", (width-total_len)/2 + offset + 15)             
+      .attr("y", -20)
+      .text(array[0]);
+    offset = offset + array[0].length*8 + 15
+  }
+}