genevalidatorapp 1.4.12

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Files changed (72) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +24 -0
  3. data/.travis.yml +7 -0
  4. data/Gemfile +4 -0
  5. data/GeneValidatorApp.gemspec +50 -0
  6. data/LICENSE.txt +661 -0
  7. data/README.md +101 -0
  8. data/Rakefile +14 -0
  9. data/bin/genevalidatorapp +122 -0
  10. data/config.ru +3 -0
  11. data/lib/GeneValidatorApp.rb +321 -0
  12. data/lib/GeneValidatorApp/config.rb +86 -0
  13. data/lib/GeneValidatorApp/database.rb +114 -0
  14. data/lib/GeneValidatorApp/genevalidator.rb +241 -0
  15. data/lib/GeneValidatorApp/logger.rb +24 -0
  16. data/lib/GeneValidatorApp/version.rb +3 -0
  17. data/public/GeneValidator/.gitkeep +0 -0
  18. data/public/web_files/css/bootstrap.min.css +7 -0
  19. data/public/web_files/css/bootstrap1.min.css +7 -0
  20. data/public/web_files/css/custom.css +521 -0
  21. data/public/web_files/css/custom.min.css +3 -0
  22. data/public/web_files/css/font-awesome.min.css +4 -0
  23. data/public/web_files/fonts/FontAwesome.otf +0 -0
  24. data/public/web_files/fonts/fontawesome-webfont.eot +0 -0
  25. data/public/web_files/fonts/fontawesome-webfont.svg +504 -0
  26. data/public/web_files/fonts/fontawesome-webfont.ttf +0 -0
  27. data/public/web_files/fonts/fontawesome-webfont.woff +0 -0
  28. data/public/web_files/img/gene.png +0 -0
  29. data/public/web_files/js/bionode-seq.min.js +1 -0
  30. data/public/web_files/js/bootstrap.min.js +6 -0
  31. data/public/web_files/js/d3.v3.min.js +5 -0
  32. data/public/web_files/js/genevalidator.js +282 -0
  33. data/public/web_files/js/genevalidator.min.js +1 -0
  34. data/public/web_files/js/jquery.cookie.min.js +1 -0
  35. data/public/web_files/js/jquery.min.js +4 -0
  36. data/public/web_files/js/jquery.tablesorter.min.js +5 -0
  37. data/public/web_files/js/jquery.validate.min.js +4 -0
  38. data/public/web_files/js/plots.js +744 -0
  39. data/public/web_files/js/plots.min.js +1 -0
  40. data/spec/app_spec.rb +107 -0
  41. data/spec/database/funky_ids/funky_ids.fa +10 -0
  42. data/spec/database/funky_ids/funky_ids.fa.nhr +0 -0
  43. data/spec/database/funky_ids/funky_ids.fa.nin +0 -0
  44. data/spec/database/funky_ids/funky_ids.fa.nog +0 -0
  45. data/spec/database/funky_ids/funky_ids.fa.nsd +9 -0
  46. data/spec/database/funky_ids/funky_ids.fa.nsi +0 -0
  47. data/spec/database/funky_ids/funky_ids.fa.nsq +0 -0
  48. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta +6449 -0
  49. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr +0 -0
  50. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin +0 -0
  51. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog +0 -0
  52. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psd +2378 -0
  53. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi +0 -0
  54. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq +0 -0
  55. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta +5486 -0
  56. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr +0 -0
  57. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin +0 -0
  58. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog +0 -0
  59. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsd +946 -0
  60. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsi +0 -0
  61. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq +0 -0
  62. data/spec/database/unformatted/Cardiocondyla_obscurior/Cobs1.4.proteins.fa +148303 -0
  63. data/spec/database/without_parse_seqids/without_parse_seqids.fa +10 -0
  64. data/spec/database/without_parse_seqids/without_parse_seqids.fa.phr +0 -0
  65. data/spec/database/without_parse_seqids/without_parse_seqids.fa.pin +0 -0
  66. data/spec/database/without_parse_seqids/without_parse_seqids.fa.psq +0 -0
  67. data/spec/database_spec.rb +37 -0
  68. data/spec/empty_config.yml +0 -0
  69. data/views/500.slim +5 -0
  70. data/views/index.slim +66 -0
  71. data/views/layout.slim +85 -0
  72. metadata +337 -0
@@ -0,0 +1 @@
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"]);
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+ /*!
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+ * Bootstrap v3.1.1 (http://getbootstrap.com)
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+ * Copyright 2011-2014 Twitter, Inc.
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+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
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+ */
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@@ -0,0 +1,282 @@
1
+ $(document).ready(function() {
2
+ 'use strict';
3
+ checkCollapseState();
4
+ keepFooterFixedToBottom();
5
+ addSeqValidation();
6
+ inputValidation();
7
+
8
+ $(document).bind('keydown', function (e) {
9
+ if (e.ctrlKey && e.keyCode === 13 ) {
10
+ $('#input').trigger('submit');
11
+ }
12
+ });
13
+ });
14
+
15
+ // Looks for a cookie (called 'GeneValidator_adv_params_status') to check the state of the adv_params box when it was last closed.
16
+ // This function is called upon as soon as the website is loaded;
17
+ function checkCollapseState() {
18
+ 'use strict';
19
+ if ($.cookie('GeneValidator_adv_params_status')){
20
+ var adv_params_status = $.cookie('GeneValidator_adv_params_status');
21
+ if (adv_params_status === 'open') {
22
+ var btn = document.getElementById('adv_params_btn');
23
+ btn.innerHTML = '<i class="fa fa-pencil-square-o"></i>&nbsp;&nbsp;Hide Advanced Parameters';
24
+ $('#adv_params').addClass('in');
25
+ }
26
+ }
27
+ }
28
+
29
+ // This function simply ensures that the footer stays to fixed to the bottom of the window
30
+ function keepFooterFixedToBottom() {
31
+ 'use strict';
32
+ $('#mainbody').css({'margin-bottom': (($('#footer').height()) + 15)+'px'});
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+ $(window).resize(function(){
34
+ $('#mainbody').css({'margin-bottom': (($('#footer').height()) + 15)+'px'});
35
+ });
36
+ }
37
+
38
+ // Creates a custom Validation for Jquery Validation plugin...
39
+ // It ensures that sequences are either protein or DNA data...
40
+ // If there are multiple sequences, ensures that they are of the same type
41
+ // It utilises the checkType function (further below)...
42
+ function addSeqValidation() {
43
+ 'use strict';
44
+ jQuery.validator.addMethod('checkInputType', function(value, element) {
45
+ var types = [];
46
+ if (value.charAt(0) === '>') {
47
+ var seqs_array = value.split('>');
48
+ for (var i = 1; i < seqs_array.length; i++) {
49
+ var lines = seqs_array[i].split('\n');
50
+ if (lines.length !== 0) {
51
+ var clean_lines = jQuery.grep(lines,function(n){ return(n); });
52
+ if (clean_lines.length !== 0){
53
+ clean_lines.shift();
54
+ var seq = clean_lines.join('');
55
+ var type = checkType(seq, 0.9);
56
+ types.push(type);
57
+ if ((type !== 'protein') && (type !== 'dna') && (type !== 'rna')) {
58
+ return false;
59
+ }
60
+ }
61
+ }
62
+ }
63
+ var firstType = types[0];
64
+ for (var j = 0; j < types.length; j++) {
65
+ if (types[j] !== firstType){
66
+ return false;
67
+ }
68
+ }
69
+ return true;
70
+ } else {
71
+ var type = checkType(value, 0.9);
72
+ if ((type !== 'protein') && (type !== 'dna') && (type !== 'rna')) {
73
+ return false;
74
+ } else {
75
+ return true;
76
+ }
77
+ }
78
+ }, '* 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. ');
79
+ }
80
+
81
+
82
+ // A function that validates the input - Utilises Jquery.Validator.js
83
+ function inputValidation() {
84
+ 'use strict';
85
+ var maxCharacters = $('#seq').attr('data-maxCharacters'); // returns a number or undefined
86
+ $('#input').validate({
87
+ rules: {
88
+ seq: {
89
+ minlength: 5,
90
+ required: true,
91
+ checkInputType: true,
92
+ maxlength: maxCharacters // when undefined, maxlength is unlimited
93
+ },
94
+ 'validations[]': {
95
+ required: true,
96
+ },
97
+ },
98
+ highlight: function(element) {
99
+ $(element).closest('.form-group').addClass('has-error');
100
+ },
101
+ unhighlight: function(element) {
102
+ $(element).closest('.form-group').removeClass('has-error');
103
+ },
104
+ errorElement: 'span',
105
+ errorClass: 'help-block',
106
+ errorPlacement: function(error, element) {
107
+ if (element.parent().parent().attr('id') === 'validations_group') {
108
+ var helpText = document.getElementById('lastValidation');
109
+ error.insertAfter(helpText);
110
+ } else {
111
+ if (element.parent('.input-group').length) {
112
+ error.insertAfter(element.parent());
113
+ } else {
114
+ error.insertAfter(element);
115
+ }
116
+ }
117
+ },
118
+ submitHandler: function(form) {
119
+ $('#spinner').modal({
120
+ backdrop: 'static',
121
+ keyboard: 'false'
122
+ });
123
+ ajaxFunction();
124
+ }
125
+ });
126
+ }
127
+
128
+ // Sends the data within the form to the Server
129
+ function ajaxFunction() {
130
+ 'use strict';
131
+ $.ajax({
132
+ type: 'POST',
133
+ url: $('#input').attr('action'),
134
+ data: $('#input').serialize(),
135
+ success: function(response){
136
+ $('#results_box').show();
137
+ $('#output').html(response);
138
+ initTableSorter(); // initiate the table sorter
139
+ $("[data-toggle='tooltip']").tooltip(); // Initiate the tooltips
140
+ removeEmptyColumns(); // Remove Unwanted Columns
141
+
142
+ $('#mainbody').css({'background-color': '#fff'});
143
+ $('#search').css({'background-color': '#F5F5F5'});
144
+ $('#results').css({'border-top': '3px solid #DBDBDB'});
145
+ $('#search').css({'margin-bottom': '0'});
146
+
147
+ $('#spinner').modal('hide'); // remove progress notification
148
+ },
149
+ error: function (e, status) {
150
+ var errorMessage;
151
+ if (e.status == 500) {
152
+ errorMessage = e.responseText;
153
+ $('#results_box').show();
154
+ $('#output').html(errorMessage);
155
+ $('#spinner').modal('hide'); // remove progress notification
156
+ } else {
157
+ errorMessage = e.responseText;
158
+ $('#results_box').show();
159
+ $('#output').html('There seems to be an unidentified Error.');
160
+ $('#spinner').modal('hide'); // remove progress notification
161
+ }
162
+ }
163
+ });
164
+ }
165
+
166
+ // Table sortert Initialiser
167
+ // Contains a custom parser that allows the Stars to be sorted.
168
+ function initTableSorter() {
169
+ 'use strict';
170
+ $.tablesorter.addParser({
171
+ id: 'star_scores',
172
+ is: function(s) {return false;},
173
+ format: function(s, table, cell, cellIndex) {
174
+ var $cell = $(cell);
175
+ if (cellIndex === 1) {
176
+ return $cell.attr('data-score') || s;
177
+ }
178
+ return s;
179
+ },
180
+ parsed: false,
181
+ type: 'numeric'
182
+ });
183
+
184
+ $('table').tablesorter({
185
+ headers: {
186
+ 1 : { sorter: 'star_scores' }
187
+ },
188
+ sortList: [[0,0]],
189
+ });
190
+ }
191
+
192
+ // Remove empty colums that are not used for that type of input data...
193
+ function removeEmptyColumns() {
194
+ 'use strict';
195
+ $('#sortable_table tr th').each(function(i) {
196
+ var tds = $(this).parents('table') // Select all tds in column
197
+ .find('tr td:nth-child(' + (i + 1) + ')');
198
+ // Check if all cells in the column are empty
199
+ if ($(this).hasClass( 'chart-column' )) {
200
+ } else {
201
+ if ($(this).text().trim() == '') {
202
+ //hide header
203
+ $(this).hide();
204
+ //hide cells
205
+ tds.hide();
206
+ }
207
+ }
208
+ });
209
+ }
210
+
211
+ // Function is called each time the Adv. Params button is pressed...
212
+ function changeAdvParamsBtnText() {
213
+ 'use strict';
214
+ var btn = document.getElementById('adv_params_btn');
215
+ if (btn.innerHTML === '<i class="fa fa-pencil-square-o"></i>&nbsp;&nbsp;Show Advanced Parameters') {
216
+ btn.innerHTML = '<i class="fa fa-pencil-square-o"></i>&nbsp;&nbsp;Hide Advanced Parameters';
217
+ $('#adv_params').collapse('show');
218
+ $.cookie('GeneValidator_adv_params_status', 'open');
219
+ }
220
+ else {
221
+ btn.innerHTML = '<i class="fa fa-pencil-square-o"></i>&nbsp;&nbsp;Show Advanced Parameters';
222
+ $('#adv_params').collapse('hide');
223
+ $.cookie('GeneValidator_adv_params_status', 'closed');
224
+ }
225
+ }
226
+
227
+ // Changes the input to an examplar dna or protein sequence...
228
+ function examplarSequence(type){
229
+ 'use strict';
230
+ var dna = '>Insulin\n' +
231
+ 'ATGGCTCTCTGGATCCGGTCGCTGCCTCTCCTGGCCCTTCTTGCTCTTTCTGGCCCTGGGATCAGCCACGCAGCTGCCAACCAGCACCTCTGTGGCTCCCACTTGGTTGAGGCTCTCTACCTGGTGTGTGGGGAGCGGGGTTTCTTCTACTCCCCCAAAACACGGCGGGACGTTGAGCAGCCTCTAGTGAACGGTCCCCTGCATGGCGAGGTGGGAGAGCTGCCGTTCCAGCATGAGGAATACCAGAAAGTCAAGCGAGGCATCGTTGAGCAATGCTGTGAAAACCCGTGCTCCCTCTACCAACTGGAAAACTACTGCAACTAG\n' +
232
+ '>Insulin (with a duplication)\n' +
233
+ 'ATGGCTCTCTGGATCCGGTCGCTGCCTCTCCTGGCCCTTCTTGCTCTTTCTGGCCCTGGGATCAGCCACGCAGCTGCCAACCAGCACCTCTGTGGCTCCCACTTGGTTGAGGCTCTCTACCTGGTGTGTGGGGAGCGGGGTTTCTTCTACTCCCCCAAAACACGGCGGGACGTTGAGCAGCCTCTAGTGAACGGTCCCCTGCATGGCGAGGTGGGAGAGCTGCCGTTCCAGCATGAGGAATACCAGACAGCACCTCTGTGGCTCCCACTTGGTTGAGGCTCTCTACCTGGTGTGTGGGGAGCGGGGTTTCTTCTACTCCCCCAAAACACGGCGGGACGTTGAGCAGCCTCTAGTGAACGGTCCCCTGCATGGCGAGGTGGGAGAGCTGCCGTTCCAGCATGAGGAATACCAGAAAGTCAAGCGAGGCATCGTTGAGCAATGCTGTGAAAACCCGTGCTCCCTCTACCAACTGGAAAACTACTGCAACTAG';
234
+ var protein = '>Methylmalonyl-CoA carboxyltransferase 12S \n' +
235
+ 'MAENNNLKLASTMEGRVEQLAEQRQVIEAGGGERRVEKQHSQGKQTARERLNNLLDPHSFDEVGAFRKHRTTLFGMDKAVVPADGVVTGRGTILGRPVHAASQDFTVMGGSAGETQSTKVVETMEQALLTGTPFLFFYDSGGARIQEGIDSLSGYGKMFFANVKLSGVVPQIAIIAGPCAGGASYSPALTDFIIMTKKAHMFITGPQVIKSVTGEDVTADELGGAEAHMAISGNIHFVAEDDDAAELIAKKLLSFLPQNNTEEASFVNPNNDVSPNTELRDIVPIDGKKGYDVRDVIAKIVDWGDYLEVKAGYATNLVTAFARVNGRSVGIVANQPSVMSGCLDINASDKAAEFVNFCDSFNIPLVQLVDVPGFLPGVQQEYGGIIRHGAKMLYAYSEATVPKITVVLRKAYGGSYLAMCNRDLGADAVYAWPSAEIAVMGAEGAANVIFRKEIKAADDPDAMRAEKIEEYQNAFNTPYVAAARGQVDDVIDPADTRRKIASALEMYATKRQTRPAKKPWKLPLLSEEEIMADEEEKDLMIATLNKRVASLESELGSLQSDTQGVTEDVLTAISAVAAYLGNDGSAEVVHFAPSPNWVREGRRALQNHSIR\n' +
236
+ '>locus=Si_gnF\n' +
237
+ 'MWFPVVLLLLVGVAVAMPDHEHAWEPQNEYQYSVFVRTLTGVDTLKQQYTGIQLKGVLVIQVKSEELLQAKYINPRYAHIHQELSNGPYSKIPEENLEYRDIPMSGKPFEIKLKHGVIRDLLFDRNVPTWEVNMLKGIVGQLQIDTQGENAIDSQSTQIPSNSEPSSATFKAMEDSVGGKCEVLYEITPLPQHVAQTRPDRVPMSSVPSKGHHYEVKKLKNYEKCQERQLYHYGMDVKMTKENMMKRNKVVSELSTTHIVITGTLKSFTIQSTEMKNEITVQPESSDSPIGTVYSITKLTLAKINKISNSWFGPLELSNVESTGNLVYIFNNPFSDSEQRRVGQPSISRNSEQENSLETKKRSFHSHSSSSSSSSSSSSEEENESVMQSKASLRNIFMAPNVPLLPYFIGFKGKTIMKSNEHNVMQLAKDLLLQIAKEIQNPSEGYENTLEKYVNLKNLIRTMDRKQYTELEQYVSQFNKATVEGENAWYTLRDAVVHAGTGPAFVTIENWLKSGQVKGEEAAELLSKIPKSVHQPTPDYIKEFFKLIKSSVVTQQEYVNVSAPLAFAELLRNNYVVPSYYPVHSFGRMTLKGNEEIDNYISYLANQLQQGYLENNTQKIQTFIFALGVTAHPKIISVFEPYLEGKLPTTKYQRMLMVAALYDLSRDIPKLVGPIFYKLYMNENEAHEVRCMAVQQFILTDPPMITLQRVAKYTNYDQSDQVNSAVKSTLNSIINTKRPEWRNLANKARSVRYLVNPKNYDTWYSKGYYIDFENWVFKGLNVKMVASNDAVLPRYVYVGLDSIFNFLRKPTFEVGYAVSSYRQVYDLINELWNSYQFEEMREKSQGSRVEKLAQELKIKSGQKNNLEGHVLFNSVYGSMVYPYDKHRIREAVAALKKLLTSDSKLKTTAFNNFEKIVSFPMEMGVPFVYSFELPVFVKSEINFKKGEPITSRSGVYETLFCNRVQKRFGFIAPFEYQNYIAGIDKNGIMRVPLKYETNIDIKQKNFALKIHPNIPQSGTSTGLTHYSVVPFTTRQNIFNLQPVSNEGNTRPVITSEIHKMTKEKGPFSIKIESDTTKKESVLEDIVTGISKSSNSNNERYMKIDTTFESKQVAKCEIQIDMTFDAVTIHGKNQQPSHKEMQHHSKLDWKPNSKERREEIVNVLSAGLKSGTVFVADVSFSLPRLQDNTYVFTVGSVRSNIDQKLRHYFYVNTNAAQEVKYELCYSQEVQYAYPTPLNFEYAINNEPKDKLKGVLRYGRTCNTGNEIVITGSSSQSPQLRDMIENSSITKQCMEEIQKGKKSVRTCNKATDVAQVRDQLNFHIDASQLSEIRQKYDQVIGLLNYTNLSQYNVQQNSETNTIVVQNPWVMVPTVQEPWYRWAIKPSESQRQSEIDVLLDEVSQPSCTLDNDKILTFDNQLYNVQLGKCKHVLLTTYPQDSHNRRNYIPESSKVAVLAKDTDNDSRNVYVWLGNLEIELKKVGNDLKVAINGQNVEIPEKGHQESNGNEIIFEIVQLPDGSLSVISEKYGITVIFDGKHVRLYANGATYRNAIRGLCGNYDSRRDNDFLTPKNCLLTKPEEFAATYAMTNENCQGPAPENKRKAEGAMCIEVPEQQQMNVISDREAGRMMTEGGNWGYHQSNRKKEHGQDSKRGHGHKKYNQKDSQEGGSNESQYRKKHNIVYRTRVVEMDDKICFTTTPVPGCLQDTRPVERVPKKYDLYCLSKNNESMDLKRRVEEGAKPDFTQKPVNKIQNFQIPVSCSAA';
238
+
239
+ if (type === 'dna'){
240
+ document.getElementById('seq').value = dna;
241
+ } else if (type === 'protein') {
242
+ document.getElementById('seq').value = protein;
243
+ }
244
+ }
245
+
246
+ // FROM BIONODE-Seq - See https://github.com/bionode/bionode-seq
247
+ // Checks whether a sequence is a protein or dna sequence...
248
+ function checkType(sequence, threshold, length, index) {
249
+ 'use strict';
250
+ if (threshold === undefined) {
251
+ threshold = 0.9;
252
+ }
253
+ if (length === undefined) {
254
+ length = 10000;
255
+ }
256
+ if (index === undefined) {
257
+ index = 1;
258
+ }
259
+ var seq = sequence.slice(index - 1, length);
260
+
261
+ var dnaSeq = seq.replace(/N/gi,'');
262
+ var dnaTotal = dnaSeq.length;
263
+ var acgMatch = ((dnaSeq.match(/[ACG]/gi) || []).length) / dnaTotal;
264
+ var tMatch = ((dnaSeq.match(/[T]/gi) || []).length) / dnaTotal;
265
+ var uMatch = ((dnaSeq.match(/[U]/gi) || []).length) / dnaTotal;
266
+
267
+ var proteinSeq = seq.replace(/X/gi,'');
268
+ var proteinTotal = proteinSeq.length;
269
+ var proteinMatch = ((seq.match(/[ARNDCQEGHILKMFPSTWYV\*]/gi) || []).length) / proteinTotal;
270
+
271
+ if (((acgMatch + tMatch) >= threshold) || ((acgMatch + uMatch) >= threshold)) {
272
+ if (tMatch >= uMatch) {
273
+ return 'dna';
274
+ } else if (uMatch >= tMatch) {
275
+ return 'rna';
276
+ } else {
277
+ return 'dna';
278
+ }
279
+ } else if (proteinMatch >= threshold) {
280
+ return 'protein';
281
+ }
282
+ }
@@ -0,0 +1 @@
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 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@@ -0,0 +1,4 @@
1
+ /*! jQuery Validation Plugin - v1.13.0 - 7/1/2014
2
+ * http://jqueryvalidation.org/
3
+ * Copyright (c) 2014 Jörn Zaefferer; Licensed MIT */
4
+ !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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c})}),b)},a.extend(a.validator,{defaults:{messages:{},groups:{},rules:{},errorClass:"error",validClass:"valid",errorElement:"label",focusInvalid:!0,errorContainer:a([]),errorLabelContainer:a([]),onsubmit:!0,ignore:":hidden",ignoreTitle:!1,onfocusin:function(a){this.lastActive=a,this.settings.focusCleanup&&!this.blockFocusCleanup&&(this.settings.unhighlight&&this.settings.unhighlight.call(this,a,this.settings.errorClass,this.settings.validClass),this.hideThese(this.errorsFor(a)))},onfocusout:function(a){this.checkable(a)||!(a.name in this.submitted)&&this.optional(a)||this.element(a)},onkeyup:function(a,b){(9!==b.which||""!==this.elementValue(a))&&(a.name in this.submitted||a===this.lastElement)&&this.element(a)},onclick:function(a){a.name in this.submitted?this.element(a):a.parentNode.name in this.submitted&&this.element(a.parentNode)},highlight:function(b,c,d){"radio"===b.type?this.findByName(b.name).addClass(c).removeClass(d):a(b).addClass(c).removeClass(d)},unhighlight:function(b,c,d){"radio"===b.type?this.findByName(b.name).removeClass(c).addClass(d):a(b).removeClass(c).addClass(d)}},setDefaults:function(b){a.extend(a.validator.defaults,b)},messages:{required:"This field is required.",remote:"Please fix this field.",email:"Please enter a valid email address.",url:"Please enter a valid URL.",date:"Please enter a valid date.",dateISO:"Please enter a valid date ( ISO ).",number:"Please enter a valid number.",digits:"Please enter only digits.",creditcard:"Please enter a valid credit card number.",equalTo:"Please enter the same value again.",maxlength:a.validator.format("Please enter no more than {0} characters."),minlength:a.validator.format("Please enter at least {0} characters."),rangelength:a.validator.format("Please enter a value between {0} and {1} characters long."),range:a.validator.format("Please enter a value between {0} and {1}."),max:a.validator.format("Please enter a value less than or equal to {0}."),min:a.validator.format("Please enter a value greater than or equal to {0}.")},autoCreateRanges:!1,prototype:{init:function(){function b(b){var c=a.data(this[0].form,"validator"),d="on"+b.type.replace(/^validate/,""),e=c.settings;e[d]&&!this.is(e.ignore)&&e[d].call(c,this[0],b)}this.labelContainer=a(this.settings.errorLabelContainer),this.errorContext=this.labelContainer.length&&this.labelContainer||a(this.currentForm),this.containers=a(this.settings.errorContainer).add(this.settings.errorLabelContainer),this.submitted={},this.valueCache={},this.pendingRequest=0,this.pending={},this.invalid={},this.reset();var c,d=this.groups={};a.each(this.settings.groups,function(b,c){"string"==typeof c&&(c=c.split(/\s/)),a.each(c,function(a,c){d[c]=b})}),c=this.settings.rules,a.each(c,function(b,d){c[b]=a.validator.normalizeRule(d)}),a(this.currentForm).validateDelegate(":text, [type='password'], [type='file'], select, textarea, [type='number'], [type='search'] ,[type='tel'], [type='url'], [type='email'], [type='datetime'], [type='date'], [type='month'], [type='week'], [type='time'], [type='datetime-local'], [type='range'], [type='color'], [type='radio'], [type='checkbox']","focusin focusout keyup",b).validateDelegate("select, option, [type='radio'], [type='checkbox']","click",b),this.settings.invalidHandler&&a(this.currentForm).bind("invalid-form.validate",this.settings.invalidHandler),a(this.currentForm).find("[required], [data-rule-required], .required").attr("aria-required","true")},form:function(){return this.checkForm(),a.extend(this.submitted,this.errorMap),this.invalid=a.extend({},this.errorMap),this.valid()||a(this.currentForm).triggerHandler("invalid-form",[this]),this.showErrors(),this.valid()},checkForm:function(){this.prepareForm();for(var a=0,b=this.currentElements=this.elements();b[a];a++)this.check(b[a]);return this.valid()},element:function(b){var c=this.clean(b),d=this.validationTargetFor(c),e=!0;return this.lastElement=d,void 0===d?delete this.invalid[c.name]:(this.prepareElement(d),this.currentElements=a(d),e=this.check(d)!==!1,e?delete this.invalid[d.name]:this.invalid[d.name]=!0),a(b).attr("aria-invalid",!e),this.numberOfInvalids()||(this.toHide=this.toHide.add(this.containers)),this.showErrors(),e},showErrors:function(b){if(b){a.extend(this.errorMap,b),this.errorList=[];for(var c in b)this.errorList.push({message:b[c],element:this.findByName(c)[0]});this.successList=a.grep(this.successList,function(a){return!(a.name in b)})}this.settings.showErrors?this.settings.showErrors.call(this,this.errorMap,this.errorList):this.defaultShowErrors()},resetForm:function(){a.fn.resetForm&&a(this.currentForm).resetForm(),this.submitted={},this.lastElement=null,this.prepareForm(),this.hideErrors(),this.elements().removeClass(this.settings.errorClass).removeData("previousValue").removeAttr("aria-invalid")},numberOfInvalids:function(){return this.objectLength(this.invalid)},objectLength:function(a){var b,c=0;for(b in a)c++;return c},hideErrors:function(){this.hideThese(this.toHide)},hideThese:function(a){a.not(this.containers).text(""),this.addWrapper(a).hide()},valid:function(){return 0===this.size()},size:function(){return this.errorList.length},focusInvalid:function(){if(this.settings.focusInvalid)try{a(this.findLastActive()||this.errorList.length&&this.errorList[0].element||[]).filter(":visible").focus().trigger("focusin")}catch(b){}},findLastActive:function(){var b=this.lastActive;return b&&1===a.grep(this.errorList,function(a){return a.element.name===b.name}).length&&b},elements:function(){var b=this,c={};return a(this.currentForm).find("input, select, textarea").not(":submit, :reset, :image, [disabled]").not(this.settings.ignore).filter(function(){return!this.name&&b.settings.debug&&window.console&&console.error("%o has no name assigned",this),this.name in c||!b.objectLength(a(this).rules())?!1:(c[this.name]=!0,!0)})},clean:function(b){return a(b)[0]},errors:function(){var b=this.settings.errorClass.split(" ").join(".");return a(this.settings.errorElement+"."+b,this.errorContext)},reset:function(){this.successList=[],this.errorList=[],this.errorMap={},this.toShow=a([]),this.toHide=a([]),this.currentElements=a([])},prepareForm:function(){this.reset(),this.toHide=this.errors().add(this.containers)},prepareElement:function(a){this.reset(),this.toHide=this.errorsFor(a)},elementValue:function(b){var c,d=a(b),e=b.type;return"radio"===e||"checkbox"===e?a("input[name='"+b.name+"']:checked").val():"number"===e&&"undefined"!=typeof b.validity?b.validity.badInput?!1:d.val():(c=d.val(),"string"==typeof c?c.replace(/\r/g,""):c)},check:function(b){b=this.validationTargetFor(this.clean(b));var c,d,e,f=a(b).rules(),g=a.map(f,function(a,b){return b}).length,h=!1,i=this.elementValue(b);for(d in f){e={method:d,parameters:f[d]};try{if(c=a.validator.methods[d].call(this,i,b,e.parameters),"dependency-mismatch"===c&&1===g){h=!0;continue}if(h=!1,"pending"===c)return void(this.toHide=this.toHide.not(this.errorsFor(b)));if(!c)return this.formatAndAdd(b,e),!1}catch(j){throw this.settings.debug&&window.console&&console.log("Exception occurred when checking element "+b.id+", check the '"+e.method+"' method.",j),j}}if(!h)return this.objectLength(f)&&this.successList.push(b),!0},customDataMessage:function(b,c){return a(b).data("msg"+c.charAt(0).toUpperCase()+c.substring(1).toLowerCase())||a(b).data("msg")},customMessage:function(a,b){var c=this.settings.messages[a];return c&&(c.constructor===String?c:c[b])},findDefined:function(){for(var a=0;a<arguments.length;a++)if(void 0!==arguments[a])return arguments[a];return void 0},defaultMessage:function(b,c){return this.findDefined(this.customMessage(b.name,c),this.customDataMessage(b,c),!this.settings.ignoreTitle&&b.title||void 0,a.validator.messages[c],"<strong>Warning: No message defined for "+b.name+"</strong>")},formatAndAdd:function(b,c){var d=this.defaultMessage(b,c.method),e=/\$?\{(\d+)\}/g;"function"==typeof d?d=d.call(this,c.parameters,b):e.test(d)&&(d=a.validator.format(d.replace(e,"{$1}"),c.parameters)),this.errorList.push({message:d,element:b,method:c.method}),this.errorMap[b.name]=d,this.submitted[b.name]=d},addWrapper:function(a){return this.settings.wrapper&&(a=a.add(a.parent(this.settings.wrapper))),a},defaultShowErrors:function(){var 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 $.validator.format instead."};var b,c={};a.ajaxPrefilter?a.ajaxPrefilter(function(a,b,d){var e=a.port;"abort"===a.mode&&(c[e]&&c[e].abort(),c[e]=d)}):(b=a.ajax,a.ajax=function(d){var e=("mode"in d?d:a.ajaxSettings).mode,f=("port"in d?d:a.ajaxSettings).port;return"abort"===e?(c[f]&&c[f].abort(),c[f]=b.apply(this,arguments),c[f]):b.apply(this,arguments)}),a.extend(a.fn,{validateDelegate:function(b,c,d){return this.bind(c,function(c){var e=a(c.target);return e.is(b)?d.apply(e,arguments):void 0})}})});
@@ -0,0 +1,744 @@
1
+ function showDiv(source, target){
2
+ 'use strict';
3
+ if (window.chrome && (window.location.protocol === 'file:') ) {
4
+ if (($('#browser-alert').length) === 0) {
5
+ $('#browseralertText').html('<stong>Sorry, this feature is not supported in your browser.');
6
+ $('#browseralert').modal();
7
+ }
8
+ return;
9
+ }
10
+ var explanationId = '#' + target + 'explanation';
11
+
12
+ if ( $(explanationId).length) {
13
+ $(explanationId).remove();
14
+ }
15
+
16
+ var button = document.getElementById(target);
17
+ if (source.status === 'pressed'){
18
+ button.style.display = 'none';
19
+ $(button).parent().parent().hide();
20
+ } else {
21
+ d3.select('#'.concat(target)).selectAll('svg').remove();
22
+ button.style.display = 'block';
23
+ $(button).parent().parent().show();
24
+ var pressedButtons = document.querySelectorAll('td');
25
+ for (var i = 0; i < pressedButtons.length; i++) {
26
+ if (pressedButtons[i].status === 'pressed') {
27
+ pressedButtons[i].status = 'released';
28
+ }
29
+ }
30
+ }
31
+
32
+ if (source.status=='pressed') {
33
+ source.status='released';
34
+ } else {
35
+ source.status='pressed';
36
+ }
37
+ }
38
+
39
+ function AddExplanation(source, target){
40
+ 'use strict';
41
+ var row = '#' + target +'row';
42
+ var approach_html = '<p><b>Approach:</b> ' + source.getAttribute("data-approach") + '</p>';
43
+ var explanation_html = '<p><b>Explanation:</b> ' + source.getAttribute("data-explanation") + '</p>';
44
+ var conclusion_html = '<p><b>Conclusion:</b> ' + source.getAttribute("data-conclusion") + '</p>';
45
+
46
+ var explain = $('<div id="' + target + 'explanation" class="alert alert-info explanation_alert" role="alert">' + approach_html + explanation_html + conclusion_html + '</div>');
47
+ if (source.status === 'pressed') {
48
+ $(row).prepend(explain);
49
+ }
50
+ }
51
+
52
+ function addPlot(target, filename, type, title, footer, xtitle, ytitle, aux1, aux2){
53
+ 'use strict';
54
+ var legend;
55
+ if (footer === '') {
56
+ legend = [];
57
+ } else {
58
+ legend = footer.split(';');
59
+ }
60
+
61
+ switch(type) {
62
+ case 'scatter':
63
+ plot_scatter(filename, target, title, footer, xtitle, ytitle, aux1, aux2);
64
+ break;
65
+ case 'bars':
66
+ plot_bars(filename, target, title, legend, xtitle, ytitle, aux1);
67
+ break;
68
+ case 'simplebars':
69
+ plot_simple_bars(filename, target, title, legend, xtitle, ytitle);
70
+ break;
71
+ case 'lines':
72
+ if (aux2 !== '') {
73
+ aux2 = aux2.split(',');
74
+ }
75
+ plot_lines(filename, target, title, legend, xtitle, ytitle, aux1, aux2);
76
+ break;
77
+ case 'align':
78
+ if (aux2 !== '') {
79
+ aux2 = aux2.split(',');
80
+ }
81
+ plot_align(filename, target, title, legend, xtitle, ytitle, aux1, aux2);
82
+ break;
83
+ default:
84
+ break;
85
+ }
86
+ }
87
+
88
+ function color_beautification(color){
89
+ 'use strict';
90
+ switch(color){
91
+ case 'red':
92
+ return d3.rgb(189,54,47);
93
+ case 'blue':
94
+ return d3.rgb(58,135,173);
95
+ case 'green':
96
+ return d3.rgb(70,136,71);
97
+ case 'yellow':
98
+ return d3.rgb(255,255,51);
99
+ case 'orange':
100
+ return d3.rgb(248,148,6);
101
+ case 'violet':
102
+ return d3.rgb(153,0,153);
103
+ case 'gray':
104
+ return d3.rgb(160,160,160);
105
+ default:
106
+ return color;
107
+ }
108
+ }
109
+
110
+ // bars plot
111
+ function plot_bars(filename, target, title, footer, xTitle, yTitle, bar){
112
+ var margin = {top: 70, right: 50, bottom: 75, left: 50},
113
+ width = 600 - margin.left - margin.right,
114
+ height = 500 - margin.top - margin.bottom;
115
+ var legend_width = 15
116
+
117
+ var svg = d3.select("#".concat(target)).append("svg")
118
+ .attr("width", width + margin.left + margin.right)
119
+ .attr("height", height + margin.top + margin.bottom)
120
+ .append("g")
121
+ .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
122
+
123
+ svg.append("text")
124
+ .attr("x", (width / 2))
125
+ .attr("y", -45)
126
+ .attr("text-anchor", "middle")
127
+ .style("font-size", "16px")
128
+ .text(title);
129
+
130
+ var colors = new Array("orange", "blue", "green", "yellow", "brown");
131
+ var no_colors = colors.length
132
+
133
+ var padding = 100
134
+
135
+ d3.json(filename, function(error, alldata) {
136
+
137
+ flattened_data = [].concat.apply([], alldata)
138
+ var yMax = d3.max(flattened_data, function(d) { return d.value; }) + 3
139
+ var y = d3.scale.linear()
140
+ .domain([0, yMax + yMax/10])
141
+ .range([height, 0]);
142
+
143
+ var xMin = d3.min(flattened_data, function(d) { return d.key; })
144
+ if (bar!=undefined){
145
+ var xMin = Math.min(xMin, bar);
146
+ }
147
+
148
+ var xMax = d3.max(flattened_data, function(d) { return d.key; })
149
+ if (bar!=undefined){
150
+ var xMax = Math.max(xMax, bar);
151
+ }
152
+
153
+ var x = d3.scale.linear()
154
+ .domain([xMin-padding, xMax+padding])
155
+ .range([13, width]);
156
+
157
+ var xAxis = d3.svg.axis()
158
+ .scale(x)
159
+ .orient("bottom")
160
+ .ticks(8)
161
+
162
+ var yAxis = d3.svg.axis()
163
+ .scale(y)
164
+ .orient("left")
165
+ .tickFormat(d3.format("d"))
166
+ .ticks(8)
167
+
168
+ svg.append("g")
169
+ .attr("class", "x axis")
170
+ .attr("transform", "translate(0," + height + ")")
171
+ .call(xAxis)
172
+ .append("text")
173
+ .attr("class", "label")
174
+ .attr("x", (width-xTitle.length)/2-50)
175
+ .attr("y", 35)
176
+ .style("text-anchor", "start")
177
+ .text(xTitle)
178
+
179
+ svg.append("g")
180
+ .attr("class", "y axis")
181
+ .call(yAxis)
182
+ .append("text")
183
+ .attr("class", "label")
184
+ .attr("transform", "rotate(-90)")
185
+ .attr("x", -(height+yTitle.length)/2-50)
186
+ .attr("y", -40)
187
+ .style("text-anchor", "start")
188
+ .text(yTitle)
189
+
190
+ alldata.map( function(data, i) {
191
+
192
+ color = colors[i % (no_colors - 1)];
193
+ svg.selectAll(".bar")
194
+ .data(data)
195
+ .enter().append("rect")
196
+ .attr("x", function(d) { return x(d.key); })
197
+ .attr("width", 6)
198
+ .attr("y", function(d) { return y(d.value); })
199
+ .attr("height", function(d) { return height - y(d.value); })
200
+ .attr("fill", function(d) { if (d.main == true) return color_beautification("red"); return color_beautification("blue");});
201
+ });
202
+
203
+ if (bar!=undefined){
204
+ svg.append("rect")
205
+ .attr("x", x(bar))
206
+ .attr("width", 4)
207
+ .attr("y", y(yMax + yMax/10))
208
+ .style("opacity",0.6)
209
+ .attr("height", height - y(yMax + yMax/8))
210
+ .attr("fill", color_beautification("black"));
211
+
212
+ svg.append("text")
213
+ .attr("transform", "rotate(-90)")
214
+ .attr("x", -yMax/10 - 35)
215
+ .attr("y", x(bar) - 5)
216
+ .text("query");
217
+ }
218
+ });
219
+
220
+ var offset = 0
221
+ var total_len = 0
222
+ for (var i = 0; i < footer.length; i++) {
223
+ var array = footer[i].split(",");
224
+ total_len = total_len + array[0].length*8 + 15;
225
+ }
226
+
227
+ for (var i = 0; i < footer.length; i++) {
228
+
229
+ var array = footer[i].split(",");
230
+ svg.append("rect")
231
+ .attr("x", (width-total_len)/2 + offset)
232
+ .attr("y", -30)
233
+ .attr("width", 10)
234
+ .attr("height", 10)
235
+ .style("fill", color_beautification(array[1].replace(/\s+/g, '')))
236
+
237
+ svg.append("text")
238
+ .attr("x", (width-total_len)/2 + offset + 15)
239
+ .attr("y", -20)
240
+ .text(array[0]);
241
+ offset = offset + array[0].length*8 + 15
242
+
243
+ }
244
+
245
+
246
+
247
+ }
248
+
249
+ // bars plot
250
+ function plot_simple_bars(filename, target, title, footer, xTitle, yTitle){
251
+ 'use strict';
252
+
253
+ var margin = {top: 70, right: 50, bottom: 75, left: 50},
254
+ width = 600 - margin.left - margin.right,
255
+ height = 500 - margin.top - margin.bottom;
256
+ var legend_width = 15
257
+
258
+ var svg = d3.select("#".concat(target)).append("svg")
259
+ .attr("width", width + margin.left + margin.right)
260
+ .attr("height", height + margin.top + margin.bottom)
261
+ .append("g")
262
+ .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
263
+
264
+ svg.append("text")
265
+ .attr("x", (width / 2))
266
+ .attr("y", -45)
267
+ .attr("text-anchor", "middle")
268
+ .style("font-size", "16px")
269
+ .text(title);
270
+
271
+ var colors = new Array("orange", "blue", "green", "yellow", "brown");
272
+ var no_colors = colors.length
273
+
274
+ var padding = 0
275
+
276
+ d3.json(filename, function(error, alldata) {
277
+
278
+ flattened_data = [].concat.apply([], alldata)
279
+ var yMax = d3.max(flattened_data, function(d) { return d.value; }) + 3
280
+ var y = d3.scale.linear()
281
+ .domain([0, yMax])
282
+ .range([height, 0]);
283
+
284
+ var xMin = d3.min(flattened_data, function(d) { return d.key; })
285
+ var xMax = d3.max(flattened_data, function(d) { return d.key; })
286
+
287
+ var x = d3.scale.linear()
288
+ .domain([xMin-padding, xMax+padding])
289
+ .range([13, width]);
290
+
291
+ var xAxis = d3.svg.axis()
292
+ .scale(x)
293
+ .orient("bottom")
294
+ .ticks(8)
295
+
296
+ var yAxis = d3.svg.axis()
297
+ .scale(y)
298
+ .orient("left")
299
+ .tickFormat(d3.format("d"))
300
+ .ticks(8)
301
+
302
+ svg.append("g")
303
+ .attr("class", "x axis")
304
+ .attr("transform", "translate(0," + height + ")")
305
+ .call(xAxis)
306
+ .append("text")
307
+ .attr("class", "label")
308
+ .attr("x", (width-xTitle.length)/2-50)
309
+ .attr("y", 35)
310
+ .style("text-anchor", "start")
311
+ .text(xTitle)
312
+
313
+ svg.append("g")
314
+ .attr("class", "y axis")
315
+ .call(yAxis)
316
+ .append("text")
317
+ .attr("class", "label")
318
+ .attr("transform", "rotate(-90)")
319
+ .attr("x", -(height+yTitle.length)/2-50)
320
+ .attr("y", -40)
321
+ .style("text-anchor", "start")
322
+ .text(yTitle)
323
+
324
+ alldata.map( function(data, i) {
325
+
326
+ color = colors[i % (no_colors - 1)];
327
+ svg.selectAll(".bar")
328
+ .data(data)
329
+ .enter().append("rect")
330
+ .attr("x", function(d) { return x(d.key); })
331
+ .attr("width", 6)
332
+ .attr("y", function(d) { return y(d.value); })
333
+ .attr("height", function(d) { return height - y(d.value); })
334
+ .attr("fill", function(d) { if (d.main == true) return color_beautification("red"); return color_beautification("blue");});
335
+ });
336
+
337
+ });
338
+
339
+ }
340
+
341
+
342
+ // scatter plot
343
+ // ecuation of the line: slope * x + yLine
344
+ function plot_scatter(filename, target, title, footer, xTitle, yTitle, yLine, slope){
345
+ 'use strict';
346
+
347
+ var margin = {top: 50, right: 30, bottom: 75, left: 50},
348
+ width = 500 - margin.left - margin.right,
349
+ height = 500 - margin.top - margin.bottom;
350
+
351
+ var x = d3.scale.linear()
352
+ .range([0, width]);
353
+ var y = d3.scale.linear()
354
+ .range([height, 0]);
355
+
356
+ var color = d3.scale.category10();
357
+
358
+ var xAxis = d3.svg.axis()
359
+ .scale(x)
360
+ .orient("bottom")
361
+ .ticks(8);
362
+ var yAxis = d3.svg.axis()
363
+ .scale(y)
364
+ .orient("left")
365
+ .tickFormat(d3.format("d"))
366
+ .ticks(8);
367
+
368
+ var svg = d3.select("#".concat(target)).append("svg")
369
+ .attr("width", width + margin.left + margin.right)
370
+ .attr("height", height + margin.top + margin.bottom)
371
+ .append("g")
372
+ .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
373
+
374
+ svg.append("text")
375
+ .attr("x", (width / 2))
376
+ .attr("y", -25)
377
+ .attr("text-anchor", "middle")
378
+ .style("font-size", "16px")
379
+ .text(title);
380
+
381
+ svg.append("text")
382
+ .attr("x", (width / 2))
383
+ .attr("y", height+ 55)
384
+ .attr("text-anchor", "middle")
385
+ .style("font-size", "12px")
386
+ .text(footer);
387
+
388
+ d3.json(filename, function(error, data) {
389
+
390
+ var xMax = d3.max(data, function(d) { return d.x; })
391
+ var xMin = d3.min(data, function(d) { return d.x; })
392
+ var yMax = d3.max(data, function(d) { return d.y; })
393
+ var yMin = d3.min(data, function(d) { return d.y; })
394
+ x.domain(d3.extent(data, function(d) { return d.x; })).nice();
395
+ y.domain(d3.extent(data, function(d) { return d.y; })).nice();
396
+
397
+ svg.append("g")
398
+ .attr("class", "x axis")
399
+ .attr("transform", "translate(0," + height + ")")
400
+ .call(xAxis)
401
+ .append("text")
402
+ .attr("class", "label")
403
+ .attr("x", (width-xTitle.length)/2-50)
404
+ .attr("y", 35)
405
+ .style("text-anchor", "start")
406
+ .text(xTitle)
407
+
408
+ svg.append("g")
409
+ .attr("class", "y axis")
410
+ .call(yAxis)
411
+ .append("text")
412
+ .attr("class", "label")
413
+ .attr("transform", "rotate(-90)")
414
+ .attr("x", -(height+yTitle.length)/2-50)
415
+ .attr("y", -40)
416
+ .style("text-anchor", "start")
417
+ .text(yTitle)
418
+
419
+ svg.selectAll(".dot")
420
+ .data(data)
421
+ .enter().append("circle")
422
+ //.attr("class", "dot")
423
+ .attr("r", 2)
424
+ .attr("cx", function(d) { return x(d.x); })
425
+ .attr("cy", function(d) { return y(d.y); })
426
+ .style("fill", function(d) { return color_beautification("red"); })
427
+ .style("opacity",0.6);
428
+
429
+ if ((slope!=undefined && slope != "") && (yLine!=undefined && yLine != "")){
430
+
431
+ yLine = parseFloat(yLine.replace(",", "."));
432
+ var xMaxValue = xMax
433
+ var yMaxValue = yLine + slope * xMax
434
+ if (yMaxValue > yMax){
435
+ xMaxValue = (yMax-yLine)/slope
436
+ yMaxValue = yMax
437
+ }
438
+
439
+ if (yMaxValue < yMin){
440
+ xMaxValue = (yMin-yLine)/slope
441
+ yMaxValue = yMin
442
+ }
443
+
444
+ var xMinValue = xMin
445
+ var yMinValue = yLine + slope * xMin
446
+ if (yMinValue > yMax){
447
+ xMinValue = (yMax-yLine)/slope
448
+ yMinValue = yMin
449
+ }
450
+
451
+ if (yMinValue < yMin){
452
+ xMinValue = (yMin-yLine)/slope
453
+ yMinValue = yMin
454
+ }
455
+
456
+ svg.append("line")
457
+ .attr("x1", x(xMinValue))
458
+ .attr("y1", y(yMinValue))
459
+ .attr("x2", x(xMaxValue))
460
+ .attr("y2", y(yMaxValue))
461
+ .attr("stroke-width", 2)
462
+ .attr("stroke", "black")
463
+ }
464
+
465
+
466
+ });
467
+ }
468
+
469
+ // line plot
470
+ // maximum 80 lines
471
+ function plot_lines(filename, target, title, footer, xTitle, yTitle, no_lines, yValues){
472
+ 'use strict';
473
+ var margin = {top: 70, right: 50, bottom: 75, left: 50},
474
+ width = 600 - margin.left - margin.right,
475
+ height = 500 - margin.top - margin.bottom;
476
+ var legend_width = 17
477
+
478
+ var x = d3.scale.linear()
479
+ .range([0, width]);
480
+ var y = d3.scale.linear()
481
+ .range([height, 0]);
482
+
483
+ var color = d3.scale.category10();
484
+
485
+ if (title === 'Open Reading Frames in all 6 Frames') {
486
+ var xAxis = d3.svg.axis()
487
+ .scale(x)
488
+ .orient("bottom")
489
+ .ticks(0);
490
+ } else {
491
+ var xAxis = d3.svg.axis()
492
+ .scale(x)
493
+ .orient("bottom")
494
+ .ticks(5);
495
+ }
496
+
497
+ var yAxis = d3.svg.axis()
498
+ .scale(y)
499
+ .orient("left")
500
+ .ticks(5)
501
+
502
+ var svg = d3.select("#".concat(target)).append("svg")
503
+ .attr("width", width + margin.left + margin.right)
504
+ .attr("height", height + margin.top + margin.bottom)
505
+ .append("g")
506
+ .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
507
+
508
+ svg.append("text")
509
+ .attr("x", (width / 2))
510
+ .attr("y", -35)
511
+ .attr("text-anchor", "middle")
512
+ .style("font-size", "16px")
513
+ .text(title);
514
+
515
+ d3.json(filename, function(error, data) {
516
+
517
+ var idx = -1
518
+
519
+ x.domain([0, d3.max(data, function(d) { return d.stop; })]);
520
+ y.domain(d3.extent(data, function(d) { return d.y; })).nice();
521
+
522
+ svg.append("g")
523
+ .attr("class", "x axis")
524
+ .attr("transform", "translate(0," + (height + height/no_lines) + ")")
525
+ .call(xAxis)
526
+ .append("text")
527
+ .attr("class", "label")
528
+ .attr("x", (width-xTitle.length)/2-50)
529
+ .attr("y", 35)
530
+ .style("text-anchor", "start")
531
+ .text(xTitle)
532
+
533
+ if (yValues != ""){
534
+ svg.append("g")
535
+ .attr("class", "y axis")
536
+ .call(yAxis
537
+ .ticks(yValues.length)
538
+ .tickFormat(function (d) {
539
+ idx = idx + 1;
540
+ return yValues[idx];
541
+ }))
542
+ .append("text")
543
+ .attr("class", "label")
544
+ .attr("transform", "rotate(-90)")
545
+ .attr("x", -(height+yTitle.length)/2-50)
546
+ .attr("y", -40)
547
+ .style("text-anchor", "start")
548
+ .text(yTitle)
549
+ }
550
+ else{
551
+ svg.append("g")
552
+ .attr("class", "y axis")
553
+ .call(yAxis)
554
+ .append("text")
555
+ .attr("class", "label")
556
+ .attr("transform", "rotate(-90)")
557
+ .attr("x", -(height+yTitle.length)/2)
558
+ .attr("y", -40)
559
+ .style("text-anchor", "start")
560
+ .text(yTitle)
561
+ }
562
+
563
+ svg.selectAll(".dot")
564
+ .data(data)
565
+ .enter().append("line")
566
+ .attr("x1", function(d) { return x(d.start); })
567
+ .attr("y1", function(d) { return y(d.y); })
568
+ .attr("x2", function(d) { return x(d.stop); })
569
+ .attr("x2", function(d) { return x(d.stop); })
570
+ .attr("y2", function(d) { return y(d.y); })
571
+ .attr("stroke-width", function(d) {
572
+ if (d.dotted == undefined) {
573
+ if (d.color == "red" ) {
574
+ return height/no_lines/2.5
575
+ } else {
576
+ return height/no_lines
577
+ }
578
+ } else {
579
+ return height/no_lines/5
580
+ }
581
+ })
582
+ .style("stroke-dasharray", function(d) { if (d.dotted == undefined) return ("0, 0"); return ("2, 6");})
583
+ .attr("stroke", function(d) { return color_beautification(d.color); })
584
+ });
585
+
586
+ // add legend
587
+ var legend = svg.append("g")
588
+ .attr("class", "legend")
589
+ .attr("height", 100)
590
+ .attr("width", 100)
591
+ .attr('transform', 'translate(-20,50)')
592
+
593
+ var h = 0
594
+
595
+ var offset = 40
596
+ var total_len = 0
597
+ for (var i = 0; i < footer.length; i++) {
598
+ var array = footer[i].split(",");
599
+ total_len = total_len + array[0].length*8 + 15;
600
+ }
601
+
602
+ for (var i = 0; i < footer.length; i++) {
603
+
604
+ var array = footer[i].split(",");
605
+ svg.append("rect")
606
+ .attr("x", (width-total_len)/2 + offset)
607
+ .attr("y", -30)
608
+ .attr("width", 10)
609
+ .attr("height", 10)
610
+ .style("fill", color_beautification(array[1].replace(/\s+/g, '')))
611
+
612
+ svg.append("text")
613
+ .attr("x", (width-total_len)/2 + offset + 15)
614
+ .attr("y", -20)
615
+ .text(array[0]);
616
+ offset = offset + array[0].length*8 + 15
617
+
618
+ }
619
+ }
620
+
621
+ // line plot
622
+ // maximum 80 lines
623
+ function plot_align(filename, target, title, footer, xTitle, yTitle, no_lines, yValues){
624
+ 'use strict';
625
+
626
+ var margin = {top: 75, right: 50, bottom: 75, left: 150},
627
+ width = 600 - margin.left - margin.right,
628
+ height = 300 - margin.top - margin.bottom;
629
+ var legend_width = 17
630
+
631
+ var x = d3.scale.linear()
632
+ .range([0, width]);
633
+ var y = d3.scale.linear()
634
+ .range([height, 0]);
635
+
636
+ var color = d3.scale.category10();
637
+
638
+ var xAxis = d3.svg.axis()
639
+ .scale(x)
640
+ .orient("bottom")
641
+ .ticks(5);
642
+
643
+ var yAxis = d3.svg.axis()
644
+ .scale(y)
645
+ .orient("left")
646
+ .ticks(5)
647
+
648
+ var svg = d3.select("#".concat(target)).append("svg")
649
+ .style("vertical-align", "top")
650
+ .attr("width", width + margin.left + margin.right)
651
+ .attr("height", height + margin.top + margin.bottom)
652
+ .append("g")
653
+ .attr("transform", "translate(" + margin.left + "," + margin.top + ")");
654
+
655
+ svg.append("text")
656
+ .attr("x", (width / 2))
657
+ .attr("y", -35)
658
+ .attr("text-anchor", "middle")
659
+ .style("font-size", "16px")
660
+ .text(title);
661
+
662
+ d3.json(filename, function(error, data) {
663
+
664
+ var idx = -1
665
+
666
+ x.domain([0, d3.max(data, function(d) { return d.stop; })]);
667
+ y.domain(d3.extent(data, function(d) { return d.y; })).nice();
668
+
669
+ svg.append("g")
670
+ .attr("class", "x axis")
671
+ .attr("transform", "translate(0," + (height+height/no_lines) + ")")
672
+ .call(xAxis)
673
+ .append("text")
674
+ .attr("class", "label")
675
+ .attr("x", (width-xTitle.length)/2-50)
676
+ .attr("y", 35)
677
+ .style("text-anchor", "start")
678
+ .text(xTitle)
679
+
680
+ if (yValues != ""){
681
+ svg.append("g")
682
+ .attr("class", "y axis")
683
+ .call(yAxis
684
+ .ticks(yValues.length)
685
+ .tickFormat(function (d) {
686
+ idx = idx + 1;
687
+ return yValues[idx];
688
+ }))
689
+ .append("text")
690
+ .attr("class", "label")
691
+ .attr("transform", "rotate(-90)")
692
+ .attr("x", -(height+yTitle.length)/2-50)
693
+ .attr("y", -40)
694
+ .style("text-anchor", "start")
695
+ .text(yTitle)
696
+ }
697
+ else{
698
+ svg.append("g")
699
+ .attr("class", "y axis")
700
+ .call(yAxis)
701
+ .append("text")
702
+ .attr("class", "label")
703
+ .attr("transform", "rotate(-90)")
704
+ .attr("x", -(height+yTitle.length)/2-50)
705
+ .attr("y", -40)
706
+ .style("text-anchor", "start")
707
+ .text(yTitle)
708
+ }
709
+
710
+ svg.selectAll(".dot")
711
+ .data(data)
712
+ .enter().append("line")
713
+ .attr("x1", function(d) { return x(d.start); })
714
+ .attr("y1", function(d) { return y(d.y); })
715
+ .attr("x2", function(d) { return x(d.stop); })
716
+ .attr("y2", function(d) { return y(d.y); })
717
+ .attr("stroke-width", function(d) { if (d.height == -1) return height/no_lines; return (height/no_lines * d.height) ; })
718
+ .attr("stroke", function(d) { return color_beautification(d.color); })
719
+ });
720
+
721
+ var offset = 0
722
+ var total_len = 0
723
+ for (var i = 0; i < footer.length; i++) {
724
+ var array = footer[i].split(",");
725
+ total_len = total_len + array[0].length*8 + 15;
726
+ }
727
+
728
+ for (var i = 0; i < footer.length; i++) {
729
+
730
+ var array = footer[i].split(",");
731
+ svg.append("rect")
732
+ .attr("x", (width-total_len)/2 + offset)
733
+ .attr("y", -30)
734
+ .attr("width", 10)
735
+ .attr("height", 10)
736
+ .style("fill", color_beautification(array[1].replace(/\s+/g, '')))
737
+
738
+ svg.append("text")
739
+ .attr("x", (width-total_len)/2 + offset + 15)
740
+ .attr("y", -20)
741
+ .text(array[0]);
742
+ offset = offset + array[0].length*8 + 15
743
+ }
744
+ }