sequenceserver 2.0.0.beta3 → 2.0.0.beta4

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Files changed (87) hide show
  1. checksums.yaml +5 -5
  2. data/.eslintrc.json +36 -0
  3. data/.rubocop.yml +1 -1
  4. data/.travis.yml +53 -20
  5. data/AppImage/recipe.yml +15 -0
  6. data/AppImage/sequenceserver.desktop +8 -0
  7. data/AppImage/sequenceserver.png +0 -0
  8. data/AppImage/sequenceserver.sh +11 -0
  9. data/README.md +79 -46
  10. data/bin/sequenceserver +4 -4
  11. data/lib/sequenceserver/version.rb +1 -1
  12. data/package.json +2 -0
  13. data/public/css/grapher.css +3 -0
  14. data/public/css/sequenceserver.css +17 -6
  15. data/public/css/sequenceserver.min.css +3 -3
  16. data/public/js/circos.js +515 -491
  17. data/public/js/grapher.js +12 -6
  18. data/public/js/hits_overview.js +321 -308
  19. data/public/js/hsp.js +12 -7
  20. data/public/js/length_distribution.js +241 -234
  21. data/public/js/report.js +196 -174
  22. data/public/js/search.js +3 -3
  23. data/public/js/sequenceserver.js +9 -9
  24. data/public/js/utils.js +17 -10
  25. data/public/js/visualisation_helpers.js +77 -77
  26. data/public/sequenceserver-report.min.js +17 -17
  27. data/public/sequenceserver-search.min.js +1 -1
  28. data/public/vendor/github/nicgirault/circosJs@1.7.0/dist/circosJS.js +1 -5
  29. data/sequenceserver.gemspec +1 -2
  30. data/spec/blast_versions/blast_2.2.30/blast_2.2.30_spec.rb +13 -13
  31. data/spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb +555 -25
  32. data/spec/blast_versions/blast_2.2.31/blast_2.2.31_spec.rb +13 -13
  33. data/spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.rb +558 -24
  34. data/spec/blast_versions/blast_2.3.0/blast_2.3.0_spec.rb +13 -13
  35. data/spec/blast_versions/blast_2.3.0/import_spec_capybara_local_2.3.0.rb +561 -26
  36. data/spec/blast_versions/blast_2.4.0/blast_2.4.0_spec.rb +13 -13
  37. data/spec/blast_versions/blast_2.4.0/import_spec_capybara_local_2.4.0.rb +561 -25
  38. data/spec/blast_versions/blast_2.5.0/blast_2.5.0_spec.rb +13 -13
  39. data/spec/blast_versions/blast_2.5.0/import_spec_capybara_local_2.5.0.rb +558 -24
  40. data/spec/blast_versions/blast_2.6.0/blast_2.6.0_spec.rb +13 -13
  41. data/spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb +559 -24
  42. data/spec/blast_versions/blast_2.7.1/blast_2.7.1_spec.rb +13 -13
  43. data/spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb +559 -28
  44. data/spec/blast_versions/blast_2.8.1/blast_2.8.1_spec.rb +13 -13
  45. data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb +559 -27
  46. data/spec/blast_versions/blast_2.9.0/blast_2.9.0_spec.rb +13 -13
  47. data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb +557 -25
  48. data/spec/blast_versions/diamond_0.9.24/diamond_0.9.24_spec.rb +13 -13
  49. data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb +219 -21
  50. data/spec/capybara_spec.rb +25 -28
  51. data/spec/download_helper.rb +6 -3
  52. data/spec/sequences/MH011443_1_gi_1486783306_gb_MH011443_1.txt +6 -0
  53. data/spec/sequences/MH011443_1_gi_1486783307_gb_AYF55702_1.txt +6 -0
  54. data/spec/sequences/MH011443_1_gi_1528997474_gb_MH447967_1.txt +30 -0
  55. data/spec/sequences/MH011443_1_sp_P04637_P53_HUMAN.txt +6 -0
  56. data/spec/sequences/alignment-35_hits_diamond_blastp.txt +210 -0
  57. data/spec/sequences/alignment-35_hits_diamond_blastx.txt +210 -0
  58. data/spec/sequences/alignment-3_hits.txt +18 -0
  59. data/spec/sequences/alignment-40_hits_blastn.txt +246 -0
  60. data/spec/sequences/alignment-40_hits_blastp.txt +240 -0
  61. data/spec/sequences/alignment-40_hits_blastp_2.2.30.txt +240 -0
  62. data/spec/sequences/alignment-40_hits_blastx.txt +240 -0
  63. data/spec/sequences/alignment-40_hits_tblastn.txt +240 -0
  64. data/spec/sequences/alignment-40_hits_tblastn_2.2.30.txt +240 -0
  65. data/spec/sequences/alignment-40_hits_tblastx.txt +2664 -0
  66. data/spec/sequences/alignment-4_hits.txt +24 -0
  67. data/spec/sequences/alignment-4_hits_blastn.txt +24 -0
  68. data/spec/sequences/alignment-4_hits_blastp.txt +24 -0
  69. data/spec/sequences/alignment-4_hits_blastp_2.2.30.txt +24 -0
  70. data/spec/sequences/alignment-4_hits_blastx.txt +24 -0
  71. data/spec/sequences/alignment-4_hits_diamond_blastp.txt +24 -0
  72. data/spec/sequences/alignment-4_hits_diamond_blastx.txt +24 -0
  73. data/spec/sequences/alignment-4_hits_tblastn.txt +24 -0
  74. data/spec/sequences/alignment-4_hits_tblastn_2.2.30.txt +24 -0
  75. data/spec/sequences/alignment-4_hits_tblastx.txt +318 -0
  76. data/spec/sequences/sp_P04637_P53_HUMAN_gi_1099170394_ref_XP_018868681_1.txt +6 -0
  77. data/spec/sequences/sp_P04637_P53_HUMAN_gi_120407068_ref_NP_000537_3.txt +6 -0
  78. data/spec/sequences/sp_P04637_P53_HUMAN_gi_1484127324_gb_MG595988_1.txt +6 -0
  79. data/spec/sequences/sp_P04637_P53_HUMAN_gi_395440626_gb_JQ694049_1.txt +6 -0
  80. data/spec/sequences/sp_P04637_P53_HUMAN_sp_P04637_P53_HUMAN.txt +6 -0
  81. data/spec/spec_helper.rb +3 -3
  82. metadata +67 -57
  83. data/.eslintrc +0 -213
  84. data/Rakefile +0 -8
  85. data/spec/dotdir/blast_2.4.0/blastn/TBLASTN_XML_2.4.0.xml +0 -1181
  86. data/spec/dotdir/blast_2.5.0/blastn/BLASTN_LONG_XML_2.5.0.xml +0 -18813
  87. data/spec/import_spec_capybara_local.rb +0 -61
data/public/js/search.js CHANGED
@@ -689,7 +689,7 @@ var Databases = React.createClass({
689
689
 
690
690
  // JSX.
691
691
  return (
692
- <div className={columnClass}>
692
+ <div className={columnClass} key={"DB_"+category}>
693
693
  <div className="panel panel-default">
694
694
  <div className="panel-heading">
695
695
  <h4 style={{display: "inline"}}>{panelTitle}</h4> &nbsp;&nbsp;
@@ -700,9 +700,9 @@ var Databases = React.createClass({
700
700
  </div>
701
701
  <ul className={"list-group databases " + category}>
702
702
  {
703
- _.map(this.databases(category), _.bind(function (database) {
703
+ _.map(this.databases(category), _.bind(function (database,index) {
704
704
  return (
705
- <li className="list-group-item">
705
+ <li className="list-group-item" key={"DB_"+category+index}>
706
706
  { this.renderDatabase(database) }
707
707
  </li>
708
708
  );
@@ -52,14 +52,14 @@ import 'webshim';
52
52
  $.fn._tooltip = $.fn.tooltip;
53
53
  $.fn.tooltip = function (options) {
54
54
  return this
55
- ._tooltip('destroy')
56
- ._tooltip($.extend({
57
- container: 'body',
58
- placement: 'left',
59
- delay: {
60
- show: 1000
61
- }
62
- }, options));
55
+ ._tooltip('destroy')
56
+ ._tooltip($.extend({
57
+ container: 'body',
58
+ placement: 'left',
59
+ delay: {
60
+ show: 1000
61
+ }
62
+ }, options));
63
63
  };
64
64
 
65
65
  /**
@@ -84,7 +84,7 @@ import 'webshim';
84
84
  * Used for wiggling BLAST button.
85
85
  */
86
86
  $.fn.wiggle = function () {
87
- this.finish().effect("bounce", {
87
+ this.finish().effect('bounce', {
88
88
  direction: 'left',
89
89
  distance: 24,
90
90
  times: 4,
data/public/js/utils.js CHANGED
@@ -10,8 +10,8 @@ var Utils = {
10
10
  {
11
11
  return (
12
12
  <a href={link.url} className={link.class} target='_blank'>
13
- {link.icon && <i className={"fa " + link.icon}></i>}
14
- {" " + link.title + " "}
13
+ {link.icon && <i className={'fa ' + link.icon}></i>}
14
+ {' ' + link.title + ' '}
15
15
  </a>
16
16
  );
17
17
  }
@@ -24,28 +24,35 @@ var Utils = {
24
24
 
25
25
  // Formats an array of two elements as "first (last)".
26
26
  format_2_tuple: function (tuple) {
27
- return (tuple[0] + " (" + tuple[tuple.length - 1] + ")");
27
+ return (tuple[0] + ' (' + tuple[tuple.length - 1] + ')');
28
28
  },
29
29
 
30
30
  /**
31
31
  * Returns fraction as percentage
32
32
  */
33
- inPercentage: function (num , den) {
34
- return `${(num * 100.0 / den).toFixed(2)}%`;
33
+ inPercentage: function (num, den) {
34
+ var x = (num * 100.0 / den).toFixed(2);
35
+ if (x % 1 == 0) {
36
+ x = parseInt(x, 10);
37
+ return `${x}%`;
38
+ }
39
+ else {
40
+ return `${x}%`;
41
+ }
35
42
  },
36
43
 
37
44
  /**
38
45
  * Returns fractional representation as String.
39
46
  */
40
47
  inFraction: function (num , den) {
41
- return num + "/" + den;
48
+ return num + '/' + den;
42
49
  },
43
50
 
44
51
  /**
45
52
  * Returns given Float as String formatted to two decimal places.
46
53
  */
47
54
  inTwoDecimal: function (num) {
48
- return num.toFixed(2)
55
+ return num.toFixed(2);
49
56
  },
50
57
 
51
58
  /**
@@ -55,19 +62,19 @@ var Utils = {
55
62
  inExponential: function (num) {
56
63
  // Nothing to do if num is 0.
57
64
  if (num === 0) {
58
- return 0
65
+ return 0;
59
66
  }
60
67
 
61
68
  // Round to two decimal places if in the rane [1..10).
62
69
  if (num >= 1 && num < 10)
63
70
  {
64
- return this.inTwoDecimal(num)
71
+ return this.inTwoDecimal(num);
65
72
  }
66
73
 
67
74
  // Return numbers in the range [0..1) and [10..Inf] in
68
75
  // scientific format.
69
76
  var exp = num.toExponential(2);
70
- var parts = exp.split("e");
77
+ var parts = exp.split('e');
71
78
  var base = parts[0];
72
79
  var power = parts[1];
73
80
  return <span>{base} &times; 10<sup>{power}</sup></span>;
@@ -1,20 +1,20 @@
1
1
  import _ from 'underscore';
2
2
 
3
3
  export function get_colors_for_evalue(evalue, hits) {
4
- var colors = d3.scale
5
- .log()
6
- .domain([
7
- d3.min([1e-5, d3.min(hits.map(function (d) {
8
- if (parseFloat(d.evalue) === 0.0) return undefined;
9
- return d.evalue;
10
- }))]),
11
- d3.max(hits.map(function (d) {
12
- return d.evalue;
13
- }))
14
- ])
15
- .range([40,150]);
16
- var rgb = colors(evalue);
17
- return d3.rgb(rgb, rgb , rgb);
4
+ var colors = d3.scale
5
+ .log()
6
+ .domain([
7
+ d3.min([1e-5, d3.min(hits.map(function (d) {
8
+ if (parseFloat(d.evalue) === 0.0) return undefined;
9
+ return d.evalue;
10
+ }))]),
11
+ d3.max(hits.map(function (d) {
12
+ return d.evalue;
13
+ }))
14
+ ])
15
+ .range([40,150]);
16
+ var rgb = colors(evalue);
17
+ return d3.rgb(rgb, rgb , rgb);
18
18
  }
19
19
 
20
20
  export function toLetters(num) {
@@ -32,76 +32,76 @@ export function toLetters(num) {
32
32
  * Borrowed from Kablammo. Modified by Priyam based on https://github.com/mbostock/d3/issues/1722.
33
33
  */
34
34
  export function tick_formatter(scale, seq_type) {
35
- var ticks = scale.ticks();
36
- var prefix = d3.formatPrefix(ticks[ticks.length - 1]);
37
- var suffixes = {amino_acid: 'aa', nucleic_acid: 'bp'};
35
+ var ticks = scale.ticks();
36
+ var prefix = d3.formatPrefix(ticks[ticks.length - 1]);
37
+ var suffixes = {amino_acid: 'aa', nucleic_acid: 'bp'};
38
38
 
39
- var digits = 0;
40
- var format;
41
- var _ticks;
42
- while (true) {
43
- format = d3.format('.' + digits + 'f');
44
- _ticks = scale.ticks().map(function (d) {
45
- return format(prefix.scale(d));
46
- });
47
- if (_ticks.length === _.uniq(_ticks).length) {
48
- break;
49
- }
50
- digits++;
51
- }
39
+ var digits = 0;
40
+ var format;
41
+ var _ticks;
42
+ while (true) {
43
+ format = d3.format('.' + digits + 'f');
44
+ _ticks = scale.ticks().map(function (d) {
45
+ return format(prefix.scale(d));
46
+ });
47
+ if (_ticks.length === _.uniq(_ticks).length) {
48
+ break;
49
+ }
50
+ digits++;
51
+ }
52
52
 
53
- return function (d) {
54
- if (!prefix.symbol || d === scale.domain()[0]) {
55
- return (d + ' ' + suffixes[seq_type]);
56
- }
57
- else {
58
- return (format(prefix.scale(d)) +
53
+ return function (d) {
54
+ if (!prefix.symbol || d === scale.domain()[0]) {
55
+ return (d + ' ' + suffixes[seq_type]);
56
+ }
57
+ else {
58
+ return (format(prefix.scale(d)) +
59
59
  ' ' + prefix.symbol + suffixes[seq_type]);
60
- }
61
- };
60
+ }
61
+ };
62
62
  }
63
63
 
64
64
  export function get_seq_type(algorithm) {
65
- var SEQ_TYPES = {
66
- blastn: {
67
- query_seq_type: 'nucleic_acid',
68
- subject_seq_type: 'nucleic_acid'
69
- },
70
- blastp: {
71
- query_seq_type: 'amino_acid',
72
- subject_seq_type: 'amino_acid'
73
- },
74
- blastx: {
75
- query_seq_type: 'nucleic_acid',
76
- subject_seq_type: 'amino_acid'
77
- },
78
- tblastx: {
79
- query_seq_type: 'nucleic_acid',
80
- subject_seq_type: 'nucleic_acid'
81
- },
82
- tblastn: {
83
- query_seq_type: 'amino_acid',
84
- subject_seq_type: 'nucleic_acid'
85
- }
86
- };
87
- return SEQ_TYPES[algorithm];
65
+ var SEQ_TYPES = {
66
+ blastn: {
67
+ query_seq_type: 'nucleic_acid',
68
+ subject_seq_type: 'nucleic_acid'
69
+ },
70
+ blastp: {
71
+ query_seq_type: 'amino_acid',
72
+ subject_seq_type: 'amino_acid'
73
+ },
74
+ blastx: {
75
+ query_seq_type: 'nucleic_acid',
76
+ subject_seq_type: 'amino_acid'
77
+ },
78
+ tblastx: {
79
+ query_seq_type: 'nucleic_acid',
80
+ subject_seq_type: 'nucleic_acid'
81
+ },
82
+ tblastn: {
83
+ query_seq_type: 'amino_acid',
84
+ subject_seq_type: 'nucleic_acid'
85
+ }
86
+ };
87
+ return SEQ_TYPES[algorithm];
88
88
  }
89
89
 
90
90
  export function prettify_evalue(evalue) {
91
- var matches = evalue.toString().split("e");
92
- var base = matches[0];
93
- var power = matches[1];
91
+ var matches = evalue.toString().split('e');
92
+ var base = matches[0];
93
+ var power = matches[1];
94
94
 
95
- if (power)
96
- {
97
- var s = parseFloat(base).toFixed(2);
98
- var element = '<span>'+s+' &times; 10<sup>'+power+'</sup></span>';
99
- return element;
100
- }
101
- else {
102
- if (!(base % 1==0))
103
- return parseFloat(base).toFixed(2);
104
- else
105
- return base;
106
- }
107
- }
95
+ if (power)
96
+ {
97
+ var s = parseFloat(base).toFixed(2);
98
+ var element = '<span>'+s+' &times; 10<sup>'+power+'</sup></span>';
99
+ return element;
100
+ }
101
+ else {
102
+ if (!(base % 1==0))
103
+ return parseFloat(base).toFixed(2);
104
+ else
105
+ return base;
106
+ }
107
+ }
@@ -1,19 +1,19 @@
1
1
  !function(a){function b(a,b,e){return 4===arguments.length?c.apply(this,arguments):void d(a,{declarative:!0,deps:b,declare:e})}function c(a,b,c,e){d(a,{declarative:!1,deps:b,executingRequire:c,execute:e})}function d(a,b){b.name=a,a in o||(o[a]=b),b.normalizedDeps=b.deps}function e(a,b){if(b[a.groupIndex]=b[a.groupIndex]||[],-1==p.call(b[a.groupIndex],a)){b[a.groupIndex].push(a);for(var c=0,d=a.normalizedDeps.length;d>c;c++){var f=a.normalizedDeps[c],g=o[f];if(g&&!g.evaluated){var h=a.groupIndex+(g.declarative!=a.declarative);if(void 0===g.groupIndex||g.groupIndex<h){if(void 0!==g.groupIndex&&(b[g.groupIndex].splice(p.call(b[g.groupIndex],g),1),0==b[g.groupIndex].length))throw new TypeError("Mixed dependency cycle detected");g.groupIndex=h}e(g,b)}}}}function f(a){var b=o[a];b.groupIndex=0;var c=[];e(b,c);for(var d=!!b.declarative==c.length%2,f=c.length-1;f>=0;f--){for(var g=c[f],i=0;i<g.length;i++){var k=g[i];d?h(k):j(k)}d=!d}}function g(a){return 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d.y(a,c,b)}).interpolate(b.interpolation),a.append("path").datum(function(a){return a.values}).attr("class","line").attr("d",e).attr("opacity",function(a){return a.opacity||b.opacity}).attr("stroke-width",function(a){return a.thickness||b.thickness}).attr("stroke",function(a){return a.color||b.color}).attr("fill",function(a){var c,d;return d=a.fill||b.fill,c=a.fill_color||b.fill_color,d?c:"none"})},this},e.Scatter=function(){return e.Track.call(this),this.parseData=e.parsePositionValueData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",d),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){var e;return e=a.selectAll(".point").data(function(a){return a.values}).enter().append("path").attr("class","point").attr("opacity",function(a){return a.opacity||b.opacity}).attr("d",d3.svg.symbol().type(b.glyph.shape).size(b.glyph.size)).attr("transform",function(a){return function(a){return"translate("+d.x(a,c,b)+","+d.y(a,c,b)+") rotate("+360*d.theta(a.position,c.blocks[a.block_id])/(2*Math.PI)+")"}}(this)).attr("stroke",function(a){return a.glyph_strokeColor||b.glyph.strokeColor}).attr("stroke-width",function(a){return a.glyph_strokeWidth||b.glyph.strokeWidth}).attr("fill",function(a){var c,d;return d=a.glyph_fill||b.glyph.fill,c=a.glyph_color||b.glyph.color,d?c:"none"})},this},e.Stack=function(){return e.Track.call(this),this.parseData=e.parseSpanValueData,this.build=function(a,b,c,d,e){return this.loadData(c,a),this.conf=this.processConf(b,this.defaultConf,this.meta,a,this),this.buildLayers(this.data,this.conf.margin),this.applyRules(b.rules,this.data)},this.buildLayers=function(a,b){var c,d,e,f,g,h,i,j,k,l,m,n,o;for(f in a)for(c=a[f],c.values=c.values.sort(function(a,b){return a.start<b.start?-1:a.start===b.start&&a.end>b.end?-1:a.start===b.start&&a.end===b.end?0:1}),j=[],o=c.values,g=0,k=o.length;g<k;g++){for(d=o[g],n=!1,e=m=0,l=j.length;m<l;e=++m)if(i=j[e],h=i.slice(0).pop(),h.end+b<d.start){i.push(d),d.layer=e,n=!0;break}n||(d.layer=j.length),n||j.push([d])}},this.applyRules=function(a,b){var c,d,e,f,g,h,i;a=a||[],g=[];for(e in b)i=b[e],g.push(function(){var b,e;b=i.layers,e=[];for(d in b)f=b[d],e.push(function(){var b,e,g;for(g=[],b=0,e=f.length;b<e;b++)c=f[b],g.push(function(){var b,e,f;for(f=[],e=0,b=a.length;e<b;e++)h=a[e],h.condition(i.parent,c,d)?f.push(c[h.parameter]=h.value):f.push(void 0);return f}());return g}());return e}());return g},this.datumRadialPosition=function(a){return function(b){var c,d,e;return e=(a.conf.thickness+a.conf.radialMargin)*b.layer,d=e+a.conf.thickness,"out"===a.conf.direction?[a.conf.innerRadius+e,Math.min(a.conf.innerRadius+d,a.conf.outerRadius)]:"in"===a.conf.direction?[Math.max(a.conf.outerRadius-d,a.conf.innerRadius),a.conf.outerRadius-e]:"center"===a.conf.direction?(c=Math.floor((a.conf.outerRadius+a.conf.innerRadius)/2),e=(a.conf.thickness+a.conf.radialMargin)*Math.floor(b.layer/2),d=e+a.conf.thickness,b.layer%2===0?[c+e,c+d]:[c-e-a.conf.radialMargin,c-d-a.conf.radialMargin]):void 0}}(this),this.datumInnerRadius=function(a){return function(b,c,d){return a.datumRadialPosition(b,c,d)[0]}}(this),this.datumOuterRadius=function(a){return function(b,c,d){return a.datumRadialPosition(b,c,d)[1]}}(this),this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",f.colorPalette),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){var e;return e=a.selectAll(".tile").data(function(a){return a.values}).enter().append("path").attr("class","tile").attr("d",d3.svg.arc().innerRadius(d.datumInnerRadius).outerRadius(d.datumOuterRadius).startAngle(function(a){return d.theta(a.start,c.blocks[a.block_id])}).endAngle(function(a){return d.theta(a.end,c.blocks[a.block_id])})),e.attr("opacity",function(a){return a.opacity||b.opacity}),e.attr("stroke-width",function(a){return a.strokeWidth||b.strokeWidth}),e.attr("stroke",function(a){return a.strokeColor||b.strokeColor}),e.attr("fill",function(a){return a.color||b.color}),e.attr("class",function(a){var c;if(c=a.usePalette||b.usePalette)return"q"+d.ratio(a.value,b.cmin,b.cmax,b.colorPaletteSize,b.colorPaletteReverse,b.logScale)+"-"+b.colorPaletteSize}),e},this},e.Text=function(){return e.Track.call(this),this.parseData=e.parsePositionTextData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",d),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){var e,f,g,h;g=a.selectAll("g").data(function(a){return a.values}).enter().append("g").append("text").text(function(a){return a.value}).attr("transform",function(a){var e;return e=360*d.theta(a.position,c.blocks[a.block_id])/(2*Math.PI)-90,"rotate("+e+")translate("+b.innerRadius+",0)"}),f=b.style;for(e in f)h=f[e],g.style(e,h);return g},this},e.Track=function(){return this.build=function(a,b,c){return this.dispatch=d3.dispatch("mouseover","mouseout"),this.loadData(c,a),this.conf=this.processConf(b,this.defaultConf,this.meta,a,this),this.applyRules(b.rules,this.data)},this.loadData=function(a,b){var c,d,e,f,g,h;for(e={},g=b._layout.data,d=0,f=g.length;d<f;d++)c=g[d],e[c.id]=c.len;return h=this.parseData(a,e),this.data=h.data,this.meta=h.meta},this.processConf=function(a,b,c,d,f){var g;return a=e.mixConf(a,Object.assign({},b)),a=f.computeMinMax(a,c),0===a.innerRadius&&0===a.outerRadius&&(g=d.smartBorders(),a.innerRadius=g.in,a.outerRadius=g.out),a},this.applyRules=function(a,b){var c,d,e,f,g,h;a=a||[],f=[];for(e in b)h=b[e],f.push(function(){var b,e;b=h.values,e=[];for(d in b)c=b[d],e.push(function(){var b,e,f;for(f=[],b=0,e=a.length;b<e;b++)g=a[b],g.condition(h.key,c,d)?f.push(c[g.parameter]=g.value):f.push(void 0);return f}());return e}());return f},this.computeMinMax=function(a,b){return a.cmin="smart"===a.min?b.min:a.min,a.cmax="smart"===a.max?b.max:a.max,a},this.ratio=function(a,b,c,d,e,f){var g,h,i;return h=f?2.3:1,b===c||a===b&&!e||a===c&&e?0:a===c||a===b&&e?d-1:(g=(a-b)/(c-b),i=Math.exp(1/h*Math.log(g)),e&&(i=1-i),Math.floor(d*i))},this.render=function(a){return function(b,c,d){var f,g,h,i;return c.select("."+d).remove(),i=c.append("g").attr("class",d).attr("z-index",a.conf.zIndex),f=a.renderDatumContainer(b,i,d,a.data,a.conf),(null!=(g=a.conf.axes)?g.display:void 0)&&a.renderAxes(f,a.conf,b._layout,a.data),h=a.renderDatum(f,a.conf,b._layout,a),null!=a.conf.tooltipContent&&e.registerTooltip(b,a,h,a.conf),h.on("mouseover",function(b,c,d){return a.dispatch.mouseover(b,c,d)}),h.on("mouseout",function(b,c,d){
4
- return a.dispatch.mouseout(b,c,d)})}}(this),this.renderBlock=function(a,b,c,d){var e,f;return f=d.outerRadius-d.innerRadius,e=a.selectAll(".block").data(b).enter().append("g").attr("class","block").attr("transform",function(a){return"rotate("+360*c.blocks[a.key].start/(2*Math.PI)+")"}),d.backgrounds&&e.selectAll(".background").data(d.backgrounds).enter().append("path").attr("class","background").attr("fill",function(a){return a.color}).attr("opacity",function(a){return a.opacity||1}).attr("d",d3.svg.arc().innerRadius(function(a){return"in"===d.direction?d.outerRadius-f*a.start:d.innerRadius+f*a.start}).outerRadius(function(a){return"in"===d.direction?d.outerRadius-f*a.end:d.innerRadius+f*a.end}).startAngle(function(a,b,c){return 0}).endAngle(function(a,d,e){return c.blocks[b[e].key].end-c.blocks[b[e].key].start})),e},this.renderAxes=function(a,b,c,d){var e,f,g;return"pixel"===b.axes.minor.spacingType&&(e=function(){var a,c,d,e,f;for(f=[],g=a=c=b.innerRadius,d=b.outerRadius,e=b.axes.minor.spacing;e>0?a<=d:a>=d;g=a+=e)f.push(g);return f}()),f=d3.svg.arc().innerRadius(function(a){return a}).outerRadius(function(a){return a}).startAngle(0).endAngle(function(a,b,e){var f;return f=c.blocks[d[e].key],f.end-f.start}),a.selectAll(".axis").data(e).enter().append("path").attr("opacity",b.opacity).attr("class","axis").attr("d",f).attr("stroke-width",function(a,c){return c%b.axes.major.spacing===0?b.axes.major.thickness:b.axes.minor.thickness}).attr("stroke",function(a,c){return c%b.axes.major.spacing===0?b.axes.major.color:b.axes.minor.color})},this.theta=function(a,b){return a/b.len*(b.end-b.start)},this.x=function(a){return function(b,c,d){var e,f,g;return f=a.ratio(b.value,d.cmin,d.cmax,d.outerRadius-d.innerRadius,!1,d.logscale),g="in"===d.direction?d.outerRadius-f:d.innerRadius+f,e=a.theta(b.position,c.blocks[b.block_id])-Math.PI/2,g*Math.cos(e)}}(this),this.y=function(a){return function(b,c,d){var e,f,g;return f=a.ratio(b.value,d.cmin,d.cmax,d.outerRadius-d.innerRadius,!1,d.logscale),g="in"===d.direction?d.outerRadius-f:d.innerRadius+f,e=a.theta(b.position,c.blocks[b.block_id])-Math.PI/2,g*Math.sin(e)}}(this),this.ratio=function(a,b,c,d,e,f){var g,h,i;return h=f?2.3:1,b===c||a===b&&!e||a===c&&e?0:a===c||a===b&&e?d-1:(g=(a-b)/(c-b),i=Math.exp(1/h*Math.log(g)),e&&(i=1-i),Math.floor(d*i))},this},e.renderLayout=function(a,b,c){var d,f,g,h;if(f=c._layout.conf,b.select(".cs-layout").remove(),h=b.append("g").attr("class","cs-layout").attr("z-index",f.zIndex).on("click",f.onClick),d=h.selectAll("g").data(c._layout.data).enter().append("g").attr("class",function(a){return a.id}).attr("opacity",f.opacity),g=a.svg.arc().innerRadius(f.innerRadius).outerRadius(f.outerRadius).cornerRadius(f.cornerRadius).startAngle(function(a){return a.start}).endAngle(function(a){return a.end}),d.append("path").attr("d",g).attr("fill",function(a){return a.color}).attr("id",function(a){return a.id}),f.labels.display&&e.renderLayoutLabels(f,a,d),f.ticks.display)return e.renderLayoutTicks(f,h,a,c)},e.renderLayoutLabels=function(a,b,c){var d,e,f;return f=a.innerRadius+a.labels.radialOffset,e=b.svg.arc().innerRadius(f).outerRadius(f).startAngle(function(a,b){return a.start}).endAngle(function(a,b){return a.end}),c.append("path").attr("fill","none").attr("stroke","none").attr("d",e).attr("id",function(a){return"arc-label"+a.id}),d=c.append("text").attr("font-size",a.labels.size).attr("text-anchor","middle"),d.append("textPath").attr("startOffset","25%").attr("xlink:href",function(a){return"#arc-label"+a.id}).style("fill",a.labels.color).text(function(a){var b=a.end-a.start;return a.label.slice(0,Math.floor(21*b))+".."})},e.renderLayoutTicks=function(a,b,c,d){var e,f,g;return e=function(b){var d,e;d=(b.end-b.start)/b.len,b.end-b.start>1.57?e=8:b.end-b.start>.785?e=4:b.end-b.start>.3925?e=2:b.end-b.start>0&&(e=0);var f=[],g={angle:0*d+b.start,label:0};f.push(g);var h=c.scale.linear().domain([1,b.len]).range([b.start,b.end]),i=h.ticks(e).length;h.ticks(e).map(function(c,e){var g=(c*d+b.start,b.len*d+b.start,{angle:c*d+b.start,label:c/a.ticks.labelDenominator+a.ticks.labelSuffix});f.push(g)}),f.splice(i,1);var g={angle:b.len*d+b.start-.006,label:b.len/a.ticks.labelDenominator+a.ticks.labelSuffix};return f.push(g),f},f=function(b,c){return a.ticks.labels===!1?null:a.ticks.labelDisplay0===!1&&0===c?null:c%a.ticks.labelSpacing?null:0===c?b/a.ticks.labelDenominator:b/a.ticks.labelDenominator+a.ticks.labelSuffix},g=b.append("g").selectAll("g").data(d._layout.data).enter().append("g").selectAll("g").data(e).enter().append("g").attr("transform",function(b){return"rotate("+(180*b.angle/Math.PI-90)+")translate("+a.outerRadius+",0)"}),g.append("line").attr("x1",0).attr("y1",1).attr("x2",function(b,c){return a.ticks.size.major}).attr("y2",1).style("stroke",a.ticks.color),g.append("text").attr("x",8).attr("dy",".35em").attr("transform",function(a){return a.angle>Math.PI?"rotate(180)translate(-16)":null}).attr("text-anchor",function(a){return a.angle>Math.PI?"end":null}).attr("font-size",a.ticks.labelSize).style("fill",a.ticks.labelColor).text(function(a){return a.label})},e.Core.prototype.render=function(a,b){var c,d,g,h,i,j,k,l,m,n;if("undefined"==typeof a&&(h=!0,a=[]),b){d=this.tracks;for(l in d){k=d[l];for(c in k)j=k[c],i.select("."+c).remove()}}i=d3.select(this.conf.container).attr("width",this.conf.width).attr("height",this.conf.height),n=i.select(".all"),n.empty()&&(n=i.append("g").attr("class","all").attr("transform","translate("+parseInt(this.conf.width/2)+","+parseInt(this.conf.height/2)+")")),g=this.tracks;for(l in g){k=g[l];for(c in k)j=k[c],(h||f.call(a,c)>=0)&&j.render(this,n,c)}return(h||f.call(a,"layout")>=0)&&e.renderLayout(d3,n,this),m=i.selectAll(".all > g").remove(),m[0].sort(function(a,b){return parseInt(a.getAttribute("z-index"))<parseInt(b.getAttribute("z-index"))?-1:parseInt(a.getAttribute("z-index"))>parseInt(b.getAttribute("z-index"))?1:0}),i.select(".all").selectAll("g").data(m[0]).enter().append(function(a){return a}),this},e.Core.prototype.defaultConf={width:700,height:700,container:"circos",defaultTrackWidth:10},e.Layout.prototype.defaultConf={innerRadius:250,outerRadius:300,cornerRadius:5,gap:.04,opacity:1,labels:{position:"center",display:!0,size:14,color:"#000",radialOffset:20},ticks:{display:!0,color:"grey",spacing:1e7,labels:!0,labelSpacing:10,labelSuffix:"Mb",labelDenominator:1e6,labelDisplay0:!0,labelSize:10,labelColor:"#000",labelFont:"default",majorSpacing:5,size:{minor:2,major:5}},onClick:null,onMouseOver:null,zIndex:100},e.axes={display:!1,minor:{spacing:5,spacingType:"pixel",color:"#d3d3d3",thickness:2},major:{spacing:5,color:"#000000",thickness:2}},e.Heatmap.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",colorPalette:"YlGnBu",colorPaletteSize:9,colorPaletteReverse:!1,logScale:!1,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Histogram.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",direction:"out",colorPaletteSize:9,colorPalette:"YlGnBu",usePalette:!0,colorPaletteReverse:!1,color:"#fd6a62",logScale:!1,axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Chord.prototype.defaultConf={colorPaletteSize:9,colorPalette:"PuBuGn",usePalette:!0,colorPaletteReverse:!1,color:"#fd6a62",opacity:.7,min:"smart",max:"smart",logScale:!1,rules:[],backgrounds:[],zIndex:1,tooltipContent:null},e.Scatter.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",direction:"out",logScale:!1,glyph:{color:"#fd6a62",fill:!0,size:15,shape:"circle",strokeColor:"#d3d3d3",strokeWidth:2},axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Line.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",direction:"out",logScale:!1,color:"#fd6a62",fill:!0,fill_color:"#d3d3d3",thickness:2,max_gap:1e7,interpolation:"linear",axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Stack.prototype.defaultConf={innerRadius:0,outerRadius:0,colorPaletteSize:9,colorPalette:"PuBuGn",usePalette:!0,colorPaletteReverse:!1,color:"#fd6a62",min:"smart",max:"smart",direction:"out",logScale:!1,color:"#fd6a62",thickness:10,radialMargin:2,margin:2,strokeWidth:1,strokeColor:"#000000",axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Highlight.prototype.defaultConf={innerRadius:0,outerRadius:0,defaultColor:"#fd6a62",opacity:.5,rules:[],zIndex:101,strokeColor:"#d3d3d3",strokeWidth:0,tooltipContent:null},e.Text.prototype.defaultConf={innerRadius:0,outerRadius:0,rules:[],backgrounds:[],zIndex:1,style:{},tooltipContent:null},e.registerTooltip=function(a,b,c,d){return b.tip=d3.tip().direction("s").offset([20,0]).html(d.tooltipContent),c.call(b.tip),b.dispatch.on("mouseover",function(a,c,d){return b.tip.attr("class","d3-tip appear").show(a)}),b.dispatch.on("mouseout",function(a,c,d){return b.tip.attr("class","d3-tip").show(a),b.tip.hide()})}}),c.registerDynamic("c",["b"],!0,function(a,b,c){this||self;c.exports=a("b")}),c.register("d",["10","11","12","13","e","f","c"],function(a){var b,c,d,e,f,g,h,i,j;return{setters:[function(a){b=a.default},function(a){c=a},function(a){d=a.default},function(a){e=a.default},function(a){f=a.default},function(a){g=a.default},function(a){h=a.default}],execute:function(){i=function(){function a(b,d){e(this,a),this.queries=d.queries,this.svgContainer=b,this.seq_type=c.get_seq_type(d.program),this.initiate()}return d(a,null,[{key:"name",value:function(){return"Circos"}},{key:"className",value:function(){return"circos"}},{key:"collapseId",value:function(a){return"circos-collapse"}},{key:"dataName",value:function(a){return"Circos-visualisation"}}]),d(a,[{key:"initiate",value:function(){this.width=this.svgContainer.width(),this.height=600,this.innerRadius=200,this.outerRadius=230,this.query_arr=[],this.hit_arr=[],this.layout_arr=[],this.chords_arr=[],this.hsp_count=50,this.denominator=100,this.spacing=20,this.labelSpacing=10;var a={amino_acid:"aa",nucleic_acid:"bp"};this.construct_layout(),this.iterator_for_edits(),this.hit_arr=g.uniq(this.hit_arr),this.handle_spacing();var b=f.formatPrefix(this.max_length);this.suffix=" "+b.symbol+a[this.seq_type.subject_seq_type],"k"==b.symbol?this.denominator=1e3:"M"==b.symbol?(this.denominator=1e6,this.spacing=1e6,this.labelSpacing=2e5):"g"==b.symbol&&(this.denominator=1e9),f.select(this.svgContainer[0]).insert("svg",":first-child").attr("class","circosContainer"),this.create_instance(this.svgContainer,this.width,this.height),this.chords_arr.length&&this.layout_arr.length?this.instance_render():this.render_error(),this.setupTooltip()}},{key:"iterator_for_edits",value:function(){this.max_length=this.calculate_max_length(),this.hit_arr.length>10&&this.complex_layout_edits()}},{key:"construct_layout",value:function(){var a=0,b=32,c=this.queries.length,d=Math.min(b/2,c),e=(b-d)/d;this.new_layout=[],this.data=g.map(this.queries,g.bind(function(b){if(a<d){var c=b.id,f=b.length,h={len:f,color:"#8dd3c7",label:c,id:"Query_"+this.clean_id(b.id),ori_id:c};this.layout_arr.push(h);g.map(b.hits,g.bind(function(a){if(a.number<e){g.map(a.hsps,g.bind(function(c){if(g.indexOf(this.hit_arr,a.id)==-1){var d=a.id,e=a.length;this.hit_arr.push(a.id);var f={len:e,color:"#80b1d3",label:d,id:"Hit_"+this.clean_id(a.id),ori_id:d};this.layout_arr.push(f)}var h=["Query_"+this.clean_id(b.id),c.qstart,c.qend,"Hit_"+this.clean_id(a.id),c.sstart,c.send,a.number,c];return this.chords_arr.push(h),c},this));return a}},this))}return this.query_arr.push(b.id),b},this))}},{key:"rearrange_new_layout",value:function(){g.each(this.new_layout,g.bind(function(a){var b=a.id.slice(0,3);"Que"==b&&this.layout_arr.push(a)},this)),g.each(this.new_layout,g.bind(function(a){var b=a.id.slice(0,3);"Hit"==b&&this.layout_arr.push(a)},this))}},{key:"complex_layout_edits",value:function(){this.delete_from_layout=[],this.delete_from_chords=[],g.each(this.layout_arr,g.bind(function(a,b){var c=(a.len/this.max_length).toFixed(3);a.label;c<.1&&"Que"!=a.id.slice(0,3)&&(this.delete_from_layout.push(a),this.hit_arr.slice(g.indexOf(this.hit_arr,a.label),1))},this))}},{key:"check_in_chords_arr",value:function(a,b,c){var d=0;g.each(this.chords_arr,g.bind(function(c){"Que"==b&&c[0]!=a&&d++},this)),d==this.chords_arr.length&&(console.log("no record found "+a),this.delete_arr.push(c))}},{key:"find_index_of_hit",value:function(a){var b;return g.each(this.queries,g.bind(function(c){g.each(c.hits,g.bind(function(c){var d="Hit_"+this.clean_id(c.id);a==d&&(b=c.id)},this))},this)),g.indexOf(this.layout_arr,b)}},{key:"edit_labels",value:function(){console.log("label edits"),g.each(this.layout_arr,g.bind(function(a){var b=(a.len/this.max_length).toFixed(3),c=a.label;b<.41?a.label="..":c.length>10?a.label=c.slice(0,2)+"...":a.label=a.ori_id},this))}},{key:"calculate_multipliers",value:function(){var a=0,b=0;g.each(this.query_arr,g.bind(function(b){g.each(this.data,g.bind(function(c){b==c.id&&(a+=c.length)},this))},this)),g.each(this.data,g.bind(function(a){g.each(a.hits,g.bind(function(a){var c=g.indexOf(this.hit_arr,a.id);c>=0&&(b+=a.length)},this))},this));var c=(a+b)/2;console.log("mid sum "+c+" hit_sum "+b+" query_sum "+a),this.query_multiplier=(c/a).toFixed(3),this.hit_multiplier=(c/b).toFixed(3),console.log("query "+this.query_multiplier+" hit "+this.hit_multiplier)}},{key:"handle_spacing",value:function(){this.max_length>16e3?this.spacing=200:this.max_length>12e3?this.spacing=150:this.max_length>8e3?this.spacing=100:this.max_length>4e3?this.spacing=75:this.max_length>1800&&(this.spacing=50)}},{key:"calculate_max_length",value:function(){var a=0;return g.each(this.layout_arr,function(b){a<b.len&&(a=b.len)}),a}},{key:"clean_id",value:function(a){return a.replace(/[^a-zA-Z0-9]/g,"")}},{key:"create_instance",value:function(a,b,c){this.instance=new h({container:".circosContainer",width:b,height:c}),this.chord_layout(),this.instance_layout()}},{key:"chord_layout",value:function(){return this.chords_arr.length>32?this.paletteSize=32:this.paletteSize=this.chords_arr.length,{usePalette:!0,colorPaletteSize:this.paletteSize,colorPalette:"RdYlBu",opacity:.85}}},{key:"instance_layout",value:function(){return{innerRadius:this.innerRadius,outerRadius:this.outerRadius,cornerRadius:1,labels:{display:!0,size:"10px",radialOffset:10},ticks:{display:!0,spacing:this.spacing,labelSpacing:this.labelSpacing,labelDenominator:this.denominator,labelSuffix:this.suffix,labelSize:"10px",majorSpacing:this.labelSpacing,size:{minor:0,major:4}}}}},{key:"instance_render",value:function(){this.instance.layout(this.instance_layout(),this.layout_arr),this.instance.chord("chord1",this.chord_layout(),this.chords_arr),this.instance.render()}},{key:"render_error",value:function(){this.svgContainer.find("svg").remove(),this.svg=f.select(this.svgContainer[0]).insert("svg",":first-child").attr("width",this.svgContainer.width()).attr("height",this.svgContainer.height()).append("g").attr("class","circos-error").attr("transform","translate("+this.svgContainer.width()/2+","+this.svgContainer.height()/2+")").append("text").attr("text-anchor","start").attr("dy","-0.25em").attr("x",-175).style("font-size","14px").text("Circos looks great with less than 16 queries")}},{key:"layoutReset",value:function(){this.layoutHide=[],g.each(this.layout_arr,function(a){$("."+a.id).css("opacity",1)})}},{key:"chordsReset",value:function(){this.chordsHide=[],g.each(this.chords_arr,function(a){var b=a[1]+a[2],c=a[4]+a[5];$("#"+a[0]+"_"+b+"_"+a[3]+"_"+c).show()})}},{key:"chordsCheck",value:function(a,b){g.each(this.chords_arr,g.bind(function(c,d){"Que"==b&&c[0]==a&&(this.chordsHide.push(d),this.layoutHide.push(c[3])),"Hit"==b&&c[3]==a&&(this.chordsHide.push(d),this.layoutHide.push(c[0]))},this))}},{key:"chordsClean",value:function(){g.each(this.chords_arr,g.bind(function(a,b){if(g.indexOf(this.chordsHide,b)==-1){var c=a[1]+a[2],d=a[4]+a[5];$("#"+a[0]+"_"+c+"_"+a[3]+"_"+d).hide()}},this))}},{key:"layoutClean",value:function(){g.each(this.layout_arr,g.bind(function(a,b){g.indexOf(this.layoutHide,a.id)==-1&&$("."+a.id).css("opacity",.1)},this))}},{key:"setupTooltip",value:function(){var a={};$(".circos-distribution").on("click",g.bind(function(b){b.stopPropagation(),this.layoutReset(),this.chordsReset(),a={}},this)),g.each(this.query_arr,g.bind(function(b,c){this.chordsHide=[],this.layoutHide=[],b&&$(".circos-distribution .Query_"+this.clean_id(b)).attr("data-toggle","tooltip").attr("title",b).on("click",g.bind(function(d){if(d.stopPropagation(),a[c]!=b){a[c]=b;var e="Query_"+this.clean_id(b);this.layoutHide.push(e),this.chordsCheck(e,"Que"),this.chordsClean(),this.layoutClean()}else a[c]=0,this.layoutReset(),this.chordsReset()},this))},this)),g.each(this.hit_arr,g.bind(function(b,c){this.chordsHide=[],this.layoutHide=[],b&&$(".circos .Hit_"+this.clean_id(b)).attr("data-toggle","tooltip").attr("title",b).on("click",g.bind(function(d){if(d.stopPropagation(),a[c]!=b){a[c]=b;var e="Hit_"+this.clean_id(b);this.layoutHide.push(e),this.chordsCheck(e,"Hit"),this.chordsClean(),this.layoutClean()}else a[c]=0,this.layoutReset(),this.chordsReset()},this))},this)),$('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true",delay:0,"white-space":"nowrap"})}},{key:"ratioCalculate",value:function(a,b,c,d,e,f){var g,h,i;return h=f?2.3:1,b===c||a===b&&!e||a===c&&e?0:a===c||a===b&&e?d-1:(g=(a-b)/(c-b),i=Math.exp(1/h*Math.log(g)),e&&(i=1-i),Math.floor(d*i))}},{key:"drawLegend",value:function(){this.ratioHSP=[],g.each(this.chords_arr,g.bind(function(a){var b={number:a[6],evalue:a[7].evalue};this.ratioHSP.push(b)},this));var a=f.min(this.ratioHSP,function(a){return a.number}),b=f.max(this.ratioHSP,function(a){return a.number});console.log("chords_arr "+this.chords_arr.length),console.log("ratioHSP test "+this.ratioHSP.length),console.log("paletteSize "+this.paletteSize),console.log("min "+a+" max "+b),this.legend=f.select(this.svgContainer[0]).insert("svg",":first-child").attr("height",20).attr("width",30*this.ratioHSP.length).attr("transform","translate(10, 10)").append("g").attr("class","RdYlBu").attr("transform","translate(10, 0)");this.legend.selectAll(".bar").data(this.ratioHSP).enter().append("g").attr("class","g").attr("transform",function(a,b){return"translate("+30*b+",0)"}).append("rect").attr("class",g.bind(function(c,d){var e=this.ratioCalculate(c.number,a,b,this.paletteSize,!1,!1);return console.log("calc ratio "+e),"q"+e+"-"+this.paletteSize},this)).attr("data-toggle","tooltip").attr("title",function(a){return a.evalue}).attr("x",1).attr("width",30).attr("height",20),f.scale.linear().domain([0,250]).range([0,100])}}]),a}(),j=b(i),a("default",j)}}}),c.register("14",["10","11","12","13","e","f"],function(a){var b,c,d,e,f,g,h,i;return{setters:[function(a){b=a.default},function(a){c=a},function(a){d=a.default},function(a){e=a.default},function(a){f=a.default},function(a){g=a.default}],execute:function(){h=function(){function a(b,c){e(this,a),this.svg_container=b,$queryDiv=b.parents(".resultn"),hits=this.extractData(c.query.hits,c.query.number),this.graphIt($queryDiv,b,0,20,null,hits)}return d(a,null,[{key:"name",value:function(){return"Graphical overview of hits"}},{key:"className",value:function(){return"alignment-overview"}},{key:"collapseId",value:function(a){return"alignment_"+a.query.number}},{key:"dataName",value:function(a){return"Alignment-Overview-"+a.query.id}}]),d(a,[{key:"extractData",value:function(a,b){var c=[];return a.map(function(a){var d=[],e=a.hsps;g.each(e,function(c){var e={};e.hspEvalue=c.evalue,e.hspStart=c.qstart,e.hspEnd=c.qend,e.hspFrame=c.sframe,e.hspId="Query_"+b+"_hit_"+a.number+"_hsp_"+c.number,d.push(e)}),d.hitId=a.id,d.hitDef="Query_"+b+"_hit_"+a.number,d.hitEvalue=a.evalue,c.push(d)}),c}},{key:"setupTooltip",value:function(){this.svg_container.find('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true",delay:0,"white-space":"nowrap"})}},{key:"setupClick",value:function(a){$("a",a).click(function(a){a.preventDefault(),a.stopPropagation(),window.location.hash=$(this).attr("href")})}},{key:"graphControls",value:function(a,b,c,d,e){var f,h,i,j,k=20,l=function(){f=e.length,h=a.find(".ghit > g").length},m=function(a,b){b.append($("<button/>").addClass("btn btn-link more").attr("type","button").attr("data-parent-query",a.attr("id")).html("View More&nbsp;").append($("<i/>").html("&nbsp;&nbsp;").addClass("fa fa-angle-double-down")),$("<button/>").addClass("btn btn-link less").attr("type","button").attr("data-parent-query",a.attr("id")).html("View Less&nbsp;").append($("<i/>").html("&nbsp;&nbsp;").addClass("fa fa-angle-double-up"))),i=$(".less",b),j=$(".more",b)},n=function(){l(),f===k||h<k?(i.hide(),j.hide()):h===f?(j.hide(),i.show()):h===k?(i.hide(),j.show()):(i.show(),j.show())};c===!0&&(m(a,b),n()),j.on("click",g.bind(function(c){l(),this.graphIt(a,b,h,k,d,e),n(),this.setupTooltip(),c.stopPropagation()},this)),i.on("click",g.bind(function(c){l();var f=h-k;f>=k?(this.graphIt(a,b,h,-k,d,e),n()):0!==f&&(this.graphIt(a,b,h,k-h,d,e),n()),this.setupTooltip(),c.stopPropagation()},this))}},{key:"drawLegend",value:function(a,b,c,d,e){var f=a.append("g").attr("transform","translate(0,"+(d-1.88*b.margin)+")");f.append("rect").attr("x",7*(c-2*b.margin)/10).attr("width",2*(c-4*b.margin)/10).attr("height",b.legend).attr("fill","url(#legend-grad)"),f.append("text").attr("class"," legend-text").attr("transform","translate(0, "+b.legend+")").attr("x",6*(c-2*b.margin)/10-b.margin/2).text("Weaker hits"),f.append("text").attr("class"," legend-text").attr("transform","translate(0, "+b.legend+")").attr("x",9*(c-2*b.margin)/10+b.margin/2).text("Stronger hits"),a.append("linearGradient").attr("id","legend-grad").selectAll("stop").data([{offset:"0%",color:"#ccc"},{offset:"50%",color:"#888"},{offset:"100%",color:"#000"}]).enter().append("stop").attr("offset",function(a){return a.offset}).attr("stop-color",function(a){return a.color})}},{key:"graphIt",value:function(a,b,d,e,g,h){var i={barHeight:3,legend:h.length>1?3:0,margin:20},j=$.extend(i,g),k=h.slice(0,d+e);if(k.length<1)return!1;0!==d&&b.find("svg").remove();var l=a.data().queryLen,m=a.attr("id"),n=b.width(),o=k.length*j.barHeight+2*j.legend+5*j.margin,p={blastn:"nucleic_acid",blastp:"amino_acid",blastx:"nucleic_acid",tblastx:"nucleic_acid",tblastn:"amino_acid"},q=f.select(b[0]).selectAll("svg").data([k]).enter().insert("svg",":first-child").attr("width",n).attr("height",o).append("g").attr("transform","translate("+j.margin/2+", "+1.5*j.margin+")"),r=f.scale.linear().range([0,n-j.margin]);r.domain([1,l]);var s=a.data().algorithm,t=c.tick_formatter(r,p[s]),u=r.ticks(11);u.pop();var v=f.svg.axis().scale(r).orient("top").tickValues(u.concat([1,l])).tickFormat(t),w=q.append("g").attr("transform","translate(0, "+j.margin+")").append("g").attr("class","x axis").call(v);w.selectAll("text").attr("x","25px").attr("y","2px").attr("transform","rotate(-90)");var x=f.scale.ordinal().rangeBands([0,o-3*j.margin-2*j.legend],.3);x.domain(k.map(function(a){return a.hitId}));var y=f.scale.log().domain([f.min([1e-5,f.min(k.map(function(a){if(0!==parseFloat(a.hitEvalue))return a.hitEvalue}))]),f.max(k.map(function(a){return a.hitEvalue}))]).range([40,150]);q.append("g").attr("class","ghit").attr("transform","translate(0, "+1.65*(j.margin-j.legend)+")").selectAll(".hits").data(k).enter().append("g").each(function(a,b){f.select(this).selectAll(".hsp").data(a).enter().append("a").each(function(d,e){var g=x(a.hitId)+j.barHeight/2,h=f.rgb(y(d.hspEvalue),y(d.hspEvalue),y(d.hspEvalue));e+1<a.length&&(a[e].hspEnd<=a[e+1].hspStart?f.select(this.parentNode).append("line").attr("x1",r(a[e].hspEnd)).attr("y1",g).attr("x2",r(a[e+1].hspStart)).attr("y2",g).attr("stroke",h):a[e].hspStart>a[e+1].hspEnd&&f.select(this.parentNode).append("line").attr("x1",r(a[e+1].hspEnd)).attr("y1",g).attr("x2",r(a[e].hspStart)).attr("y2",g).attr("stroke",h)),f.select(this).attr("xlink:href","#"+m+"_hit_"+(b+1)).append("rect").attr("data-toggle","tooltip").attr("title",a.hitId+"<br><strong>E value:</strong> "+c.prettify_evalue(d.hspEvalue)).attr("class","bar").attr("x",function(a){return r(a.hspStart)}).attr("y",x(a.hitId)).attr("width",function(a){return r(a.hspEnd-a.hspStart+1)}).attr("height",j.barHeight).attr("fill",f.rgb(h))})}),k.length>1&&this.drawLegend(q,j,n,o,h),0===d&&this.graphControls(a,b,!0,g,h),this.setupTooltip(),this.setupClick(b)}}]),a}(),i=b(h),a("default",i)}}}),c.register("15",["10","11","12","13","e","f"],function(a){var b,c,d,e,f,g,h,i;return{setters:[function(a){b=a.default},function(a){c=a},function(a){d=a.default},function(a){e=a.default},function(a){f=a.default},function(a){g=a.default}],execute:function(){h=function(){function a(b,d){e(this,a),this.query=d.query,this._seq_type=c.get_seq_type(d.algorithm),this.svg_container=b,this._margin={top:30,right:25,bottom:55,left:12.5},this.initiate(b.width(),b.height())}return d(a,null,[{key:"name",value:function(){return"Length distribution of hits"}},{key:"className",value:function(){return"length-distribution"}},{key:"collapseId",value:function(a){return"length_"+a.query.number}},{key:"dataName",value:function(a){return"length-distribution-"+a.query.id}}]),d(a,[{key:"initiate",value:function(a,b){this._width=a-this._margin.left-this._margin.right,this._height=b-this._margin.top-this._margin.bottom,this.svg=f.select(this.svg_container[0]).insert("svg",":first-child").attr("width",this._width+this._margin.right+this._margin.left).attr("height",this._height+this._margin.top+this._margin.bottom).append("g").attr("transform","translate("+this._margin.left+","+this._margin.top+")"),this.hit_lengths(),this.define_scale_and_bins(),this.update_data(),this.draw()}},{key:"draw",value:function(){this.draw_rectangles(),this.draw_query_line(),this.draw_axes(),this.setupTooltip()}},{key:"define_scale_and_bins",value:function(){this._scale_x=f.scale.linear().domain([0,1.05*f.max([this.query.length,f.max(this._data)])]).range([0,this._width]),this._bins=f.layout.histogram().range(this._scale_x.domain()).bins(this._scale_x.ticks(50))(this._data),this._scale_y=f.scale.linear().domain([0,f.max(this._bins,function(a){return a.length})]).range([this._height,0])}},{key:"hit_lengths",value:function(){this._data=g.map(this.query.hits,g.iteratee("length"))}},{key:"setupTooltip",value:function(){this.svg_container.find('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true",delay:0,"white-space":"nowrap"})}},{key:"setupResponsiveness",value:function(){var a=$(window).width();console.log("cureent "+a);var b=g.debounce(g.bind(function(){a!=$(window).width()&&(console.log("redraw initiated "+this._height),this.draw(),a=$(window).width())},this),125);$(window).resize(b)}},{key:"tick_formatter",value:function(a){var b=this._scale_x.ticks(),c=f.format(".1f"),d=f.formatPrefix(b[b.length-1]),e={amino_acid:"aa",nucleic_acid:"bp"};return function(f){if(0!==f)return g.indexOf(b,f)>=0?"aa"==e[a]?f+" "+e[a]:c(d.scale(f))+" "+d.symbol+e[a]:void 0}}},{key:"update_data",value:function(){var a=this,b=[];this._bins.map(function(d){var e=[];d.reverse();var f=d.length;d.map(function(b,h){var 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0,formatSelectorVisible:!0},eventTypes:["onSelectionChanged","onSelectionChange","onAnnotationClicked"],getId:function(){return this.opt.id},_headerDiv:null,_contentDiv:null,_initialize:function(){void 0!==this.opt.width&&this._container.width(this.opt.width),void 0!==this.opt.height&&this._container.height(this.opt.height),this._buildFormatSelector(),this._contentDiv=jQuery("<div/>").appendTo(this._container),this._highlights=this.opt.highlights,this._annotations=this.opt.annotations;var a="sequenceTip"+this.opt.target;jQuery('<div id="'+a+'"></div>').css({position:"absolute","z-index":"999999",color:"#fff","font-size":"12px",width:"auto",display:"none"}).addClass("tooltip").appendTo("body").hide(),this.opt._tooltip=document.getElementById(a),this.opt.sequence?this._redraw():this.opt.id?this._requestSequence(this.opt.id):this.clearSequence("No sequence available","../biojs/css/images/warning_icon.png")},setSequence:function(a,b){a.match(/^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 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0;this.opt.sequence="",this.opt.id="",this._highlights=[],this._highlightsCount=0,this.opt.selection={start:0,end:0},this._annotations=[],this._contentDiv.children().remove(),this._headerDiv.hide(),void 0!==a&&(c=jQuery("<div>"+a+"</div>").appendTo(this._contentDiv).addClass("message"),void 0!==b&&c.css({background:'transparent url("'+b+'") no-repeat center left',"padding-left":"20px"}))},setSelection:function(a,b){if(a>b){var c=b;b=a,a=c}a==this.opt.selection.start&&b==this.opt.selection.end||(this._setSelection(a,b),this.trigger(j,{start:a,end:b}))},_buildFormatSelector:function(){var a=this;this._headerDiv=jQuery("<div></div>").appendTo(this._container),this._headerDiv.append("Format: "),this._formatSelector=jQuery('<select> <option value="FASTA">FASTA</option><option value="CODATA">CODATA</option><option value="PRIDE">PRIDE</option><option value="RAW">RAW</option></select>').appendTo(a._headerDiv),this._formatSelector.change(function(b){a.opt.format=jQuery(this).val(),a._redraw()}),this._formatSelector.val(a.opt.format),this.formatSelectorVisible(this.opt.formatSelectorVisible)},addHighlight:function(a){var b="-1",c="",d="",e={};return a instanceof Object&&a.start<=a.end&&(c="string"==typeof a.color?a.color:this.opt.highlightFontColor,d="string"==typeof a.background?a.background:this.opt.highlightBackgroundColor,b="string"==typeof a.id?a.id:new Number(this._highlightsCount++).toString(),e={start:a.start,end:a.end,color:c,background:d,id:b},this._highlights.push(e),this._applyHighlight(e),this._restoreSelection(a.start,a.end)),b},_applyHighlight:function(a){for(var b=this._contentDiv.find(".sequence"),c=a.start-1;c<a.end;c++)zindex=jQuery(b[c]).css("z-index"),"auto"==zindex?(z=1,o=1):(z=0,o=.5),jQuery(b[c]).css({color:a.color,"background-color":a.background,"z-index":z,opacity:o}).addClass("highlighted")},_applyHighlights:function(a){for(var b in a)this._applyHighlight(a[b])},_restoreHighlights:function(c,d){var e=this._highlights;this._applyHighlight({start:c,end:d,color:this.opt.fontColor,background:this.opt.backgroundColor});for(var f in e)e[f].start>d||e[f].end<c||(a=e[f].start<c?c:e[f].start,
13
- b=e[f].end>d?d:e[f].end,this._applyHighlight({start:a,end:b,color:e[f].color,background:e[f].background}))},_restoreSelection:function(c,d){var e=this.opt.selection;c>e.end||d<e.start||(a=c<e.start?e.start:c,b=d>e.end?e.end:d,this._applyHighlight({start:a,end:b,color:this.opt.selectionFontColor,background:this.opt.selectionColor}))},removeHighlight:function(a){var b=this._highlights;for(i in b)if(b[i].id==a){start=b[i].start,end=b[i].end,b.splice(i,1),this._restoreHighlights(start,end),this._restoreSelection(start,end);break}},removeAllHighlights:function(){this._highlights=[],this._restoreHighlights(1,this.opt.sequence.length),this._restoreSelection(1,this.opt.sequence.length)},setFormat:function(a){this.opt.format!=a.toUpperCase()&&(this.opt.format=a.toUpperCase(),this._redraw());var b=this;this._headerDiv.find("option").each(function(){jQuery(this).val()==b.opt.format.toUpperCase()&&jQuery(this).attr("selected","selected")})},setNumCols:function(a){this.opt.columns.size=a,this._redraw()},formatSelectorVisible:function(a){a?this._headerDiv.show():this._headerDiv.hide()},showFormatSelector:function(){this._headerDiv.show()},hideFormatSelector:function(){this._headerDiv.hide()},hide:function(){this._headerDiv.hide(),this._contentDiv.hide()},show:function(){this._headerDiv.show(),this._contentDiv.show()},_setSelection:function(a,b){var c=this.opt.selection,d={};c.start==a?c.end<b?(d.start=c.end,d.end=b):this._restoreHighlights(b+1,c.end):c.end==b?c.start>a?(d.start=a,d.end=c.start):this._restoreHighlights(c.start,a-1):(this._restoreHighlights(c.start,c.end),d.start=a,d.end=b),c.start=a,c.end=b},_repaintSelection:function(){var a=this.opt.selection;this._setSelection(0,0),this._setSelection(a.start,a.end)},_redraw:function(){this._contentDiv.children().remove(),"RAW"==this.opt.format?this._drawRaw():"CODATA"==this.opt.format?this._drawCodata():"FASTA"==this.opt.format?this._drawFasta():(this.opt.format="PRIDE",this._drawPride()),this._applyHighlights(this._highlights),this._repaintSelection(),this._addSpanEvents()},_drawFasta:function(){var a=this.opt.sequence.toUpperCase().split(""),b=jQuery("<pre></pre>").appendTo(this._contentDiv),c=">"+this.opt.id+" "+a.length+" bp<br/>",d=this.opt.columns.size;this.opt.sequence.length<this.opt.columns.size&&(d=this.opt.sequence.length);var e={numCols:d,numColsForSpace:0};c+=this._drawSequence(a,e),b.html(c),this._drawAnnotations(e)},_drawCodata:function(){var a=this.opt.sequence.toUpperCase().split("");if(void 0!==this.opt.formatOptions&&void 0!==this.opt.formatOptions.title&&0!=this.opt.formatOptions.title){var b=d("<pre/>").addClass("header").appendTo(this._contentDiv);b.html("ENTRY "+this.opt.id+"<br/>SEQUENCE<br/>")}var c=this.opt.columns.size;this.opt.sequence.length<this.opt.columns.size&&(c=this.opt.sequence.length);var e={numLeft:!0,numLeftSize:7,numLeftPad:" ",numTop:!0,numTopEach:5,numCols:c,numColsForSpace:0,spaceBetweenChars:!0};if(this._drawSequence(a,e),void 0!==this.opt.formatOptions&&void 0!==this.opt.formatOptions.footer&&0!=this.opt.formatOptions.footer){var f=d("<pre/>").addClass("footer").appendTo(this._contentDiv);f.html("<br/>///")}this._drawAnnotations(e)},_drawAnnotations:function(a){var b=this,c=this.opt.sequence.toLowerCase().split(""),d=this._annotations,e="",f="",g="";a.numLeft&&(e+=this._formatIndex(" ",a.numLeftSize+2," "));for(var h=0;h<c.length;h+=a.numCols){f="";for(var i in d)d[i].id=this.getId()+"_"+i,g=this._getHTMLRowAnnot(h+1,d[i],a),g.length>0&&(f+="<br/>",f+=e,f+=g,f+="<br/>");var j=a.numCols,l=c.length-h;l<j&&(j=l),a.numRight?jQuery(f).insertAfter("div#"+b.opt.target+" div pre span#numRight_"+this.getId()+"_"+(h+j)):jQuery(f).insertAfter("div#"+b.opt.target+" div pre span#"+this.getId()+"_"+(h+j))}jQuery(this._contentDiv).find(".annotation").each(function(){b._addToolTip(this,function(){return b._getAnnotationString(jQuery(this).attr("id"))}),jQuery(this).mouseover(function(a){jQuery(".annotation."+jQuery(a.target).attr("id")).each(function(){jQuery(this).css("background-color",jQuery(this).attr("color"))})}).mouseout(function(){jQuery(".annotation").css("background-color","transparent")}).click(function(a){for(var c=void 0,d=jQuery(a.target).attr("id"),e=0;e<b._annotations.length;e++)b._annotations[e].id!=d||(c=b._annotations[e].name);b.trigger(k,{name:c})})})},_getAnnotationString:function(a){var b=this._annotations[a.substr(a.indexOf("_")+1)];return b.name+"<br/>"+(b.html?b.html:"")},_getHTMLRowAnnot:function(a,b,c){for(var d="border-left:1px solid; border-bottom:1px solid; border-color:",e="border-bottom:1px solid; border-color:",f="border-bottom:1px solid; border-right:1px solid; border-color:",g="border-left:1px solid; border-right:1px solid; border-bottom:1px solid; border-color:",h=[],i=a+c.numCols,j=c.spaceBetweenChars?" 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a=this.opt.sequence.toUpperCase().split(""),b=this.opt.columns.size;this.opt.sequence.length<this.opt.columns.size&&(b=this.opt.sequence.length),opt={numLeft:!0,numLeftSize:5,numLeftPad:" ",numRight:!1,numRightSize:5,numRightPad:"",numCols:b,numColsForSpace:this.opt.columns.spacedEach},this._drawSequence(a,opt),this._drawAnnotations(opt)},_drawSequence:function(a,b){var c="",e="",f="\n",g="";if(b.numTop){e+='<span class="numTop pos-marker">';var h=b.spaceBetweenChars?2*b.numTopEach:b.numTopEach;b.numLeft&&(e+=this._formatIndex(" ",b.numLeftSize," ")),e+=this._formatIndex(" ",h," ");for(var i=b.numTopEach;i<b.numCols;i+=b.numTopEach)e+=this._formatIndex(i,h," ",!0);e+="</span>"}b.numLeft&&(c+='<span id="numLeft_'+this.getId()+'_0"',c+='class="pos-marker">',c+=this._formatIndex(1,b.numLeftSize,b.numLeftPad),c+=" ",c+="</span>",c+="\n");for(var j=1,k=1;k<=a.length;k++)if(k%b.numCols==0){g+='<span class="sequence" id="'+this.getId()+"_"+k+'">'+a[k-1]+"</span>",b.numRight&&(f+='<span 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b.numTop&&d("<pre/>").html(e).addClass("indT").css({color:"#aaa"}).appendTo(this._contentDiv),b.numLeft&&d("<pre/>").html(c).addClass("indL").css({color:"#aaa",display:"inline-block"}).appendTo(this._contentDiv),d("<pre/>").html(g).addClass("seqF").css({display:"inline-block"}).appendTo(this._contentDiv),b.numRight&&d("<pre/>").html(f).addClass("indR").css({color:"#aaa",display:"inline-block"}).appendTo(this._contentDiv),g},_formatIndex:function(a,b,c,d){var e=a.toString(),f="",g=b-e.length;if(g>0){for(;g-- >0;)f+="<span>"+c+"</span>";e=d?a+f:f+a}return e},_addSpanEvents:function(){var a,b,c=this,d=!1;c._contentDiv.find(".sequence").each(function(){jQuery(this).mousedown(function(){var e=jQuery(this).attr("id");b=parseInt(e.substr(e.indexOf("_")+1)),a=b,c._setSelection(a,b),d=!0,c.trigger(h,{start:c.opt.selection.start,end:c.opt.selection.end})}).mouseover(function(){var e=jQuery(this).attr("id");b=parseInt(e.substr(e.indexOf("_")+1)),d&&(b>a?c._setSelection(a,b):c._setSelection(b,a),c.trigger(h,{start:c.opt.selection.start,end:c.opt.selection.end}))}).mouseup(function(){d=!1,c.trigger(j,{start:c.opt.selection.start,end:c.opt.selection.end})}),c._addToolTip.call(c,this,function(){return d?"["+c.opt.selection.start+", "+c.opt.selection.end+"]":b})}).css("cursor","pointer")},_addToolTip:function(a,b){var c=this.opt._tooltip;jQuery(a).mouseover(function(d){var e=jQuery(d.target).offset();jQuery(c).is(":visible")||jQuery(c).css({"background-color":"#000",padding:"3px 10px 3px 10px",top:e.top+jQuery(d.target).height()+"px",left:e.left+jQuery(d.target).width()+"px"}).animate({opacity:"0.85"},10).html(b.call(a)).show()}).mouseout(function(){jQuery(c).hide()})},addAnnotation:function(a){this._annotations.push(a),this._redraw()},removeAnnotation:function(a){for(var b=0;b<this._annotations.length;b++)if(a!=this._annotations[b].name){this._annotations.splice(b,1),this._redraw();break}},removeAllAnnotations:function(){this._annotations=[],this._redraw()}}),c("biojs-events").mixin(Sequence.prototype),e.exports=Sequence},{"biojs-events":2,"jquery-browser-plugin":20,"js-class":22}],2:[function(a,b,c){var d=a("backbone-events-standalone");d.onAll=function(a,b){return this.on("all",a,b),this},d.oldMixin=d.mixin,d.mixin=function(a){d.oldMixin(a);for(var b=["onAll"],c=0;c<b.length;c++){var e=b[c];a[e]=this[e]}return a},b.exports=d},{"backbone-events-standalone":4}],3:[function(a,b,c){!function(){function a(){return{keys:g||function(a){if("object"!=typeof a&&"function"!=typeof a||null===a)throw new TypeError("keys() called on a non-object");var b,c=[];for(b in a)a.hasOwnProperty(b)&&(c[c.length]=b);return c},uniqueId:function(a){var b=++k+"";return a?a+b:b},has:function(a,b){return 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this.fetchResults(),this.updateCycle=0,{search_id:"",program:"",program_version:"",submitted_at:"",num_queries:0,queries:[],querydb:[],params:[],stats:[]}},fetchResults:function(){function a(){$.getJSON(location.pathname+".json").complete(function(d){switch(d.status){case 202:var e;e=1===b.length?b[0]:b.shift(),setTimeout(a,e);break;case 200:c.updateState(d.responseJSON);break;case 404:case 400:case 500:l(d.responseJSON)}})}var b=[200,400,800,1200,2e3,3e3,5e3],c=this;a()},updateState:function(a){var b=a.queries;a.num_queries=b.length,a.veryBig=b.length>250,a.queries=b.splice(0,50),this.setState(a);var c=function a(){b.length>0?(this.setState({queries:this.state.queries.concat(b.splice(0,50))}),setTimeout(a.bind(this),500)):this.componentFinishedUpdating()};setTimeout(c.bind(this),500)},render:function(){return this.isResultAvailable()?this.resultsJSX():this.loadingJSX()},loadingJSX:function(){return e.createElement("div",{className:"row"},e.createElement("div",{className:"col-md-6 col-md-offset-3 text-center"},e.createElement("h1",null,e.createElement("i",{className:"fa fa-cog fa-spin"}),"  BLAST-ing"),e.createElement("p",null,e.createElement("br",null),"This can take some time depending on the size of your query and database(s). The page will update automatically when BLAST is done.",e.createElement("br",null),e.createElement("br",null),"You can bookmark the page and come back to it later or share the link with someone.")))},resultsJSX:function(){return e.createElement("div",{className:"row"},this.shouldShowSidebar()&&e.createElement("div",{className:"col-md-3 hidden-sm hidden-xs"},e.createElement(t,{data:this.state,shouldShowIndex:this.shouldShowIndex()})),e.createElement("div",{className:this.shouldShowSidebar()?"col-md-9":"col-md-12"},this.overviewJSX(),this.isHitsAvailable()?e.createElement(h,{queries:this.state.queries,program:this.state.program,collapsed:"true"}):e.createElement("span",null),g.map(this.state.queries,g.bind(function(a){return e.createElement(p,{key:"Query_"+a.id,program:this.state.program,querydb:this.state.querydb,query:a,num_queries:this.state.num_queries,veryBig:this.state.veryBig,selectHit:this.selectHit,imported_xml:this.state.imported_xml})},this))))},overviewJSX:function(){return e.createElement("div",{className:"overview"},e.createElement("pre",{className:"pre-reset"},this.state.program_version,this.state.submitted_at&&"; query submitted on "+this.state.submitted_at,e.createElement("br",null),"Databases (",this.state.stats.nsequences," sequences, ",this.state.stats.ncharacters," characters): ",this.state.querydb.map(function(a){return a.title}).join(", "),e.createElement("br",null),"Parameters: ",g.map(this.state.params,function(a,b){return b+" "+a}).join(", ")))},isResultAvailable:function(){return this.state.queries.length>=1},isHitsAvailable:function(){var a=0;return g.each(this.state.queries,function(b){0==b.hits.length&&a++}),!(a==this.state.queries.length)},shouldShowSidebar:function(){return!(1==this.state.queries.length&&0==this.state.queries[0].hits.length)},shouldShowIndex:function(){return this.state.queries.length<=8},componentDidMount:function(){this.preventCollapseOnSelection()},componentDidUpdate:function(){this.updateCycle+=1,1===this.updateCycle&&this.affixSidebar()},componentFinishedUpdating:function(){this.shouldShowIndex()&&this.setupScrollSpy()},preventCollapseOnSelection:function(){$("body").on("mousedown",".hit > .section-header > h4",function(a){var b=$(this);b.on("mouseup mousemove",function a(c){if("mouseup"===c.type){b.attr("data-toggle","collapse");var d=$("#"+b.attr("data-target"));d.toggleClass("in"),b.find(".fa-chevron-down").toggleClass("fa-rotate-270")}else b.attr("data-toggle","");b.off("mouseup mousemove",a)})})},affixSidebar:function(){var a=$(".sidebar");a.affix({offset:{top:a.offset().top}})},setupScrollSpy:function(){$("body").scrollspy({target:".sidebar"})},selectHit:function(a){var b=$("#"+a),c=$(".hit-links :checkbox:checked").length;if(b&&b.val()){var d=$(b.data("target"));if(b.is(":checked")?(d.find(".section-content").addClass("glow"),$(".download-alignment-of-selected").enable(),$(".download-fasta-of-selected").enable()):d.find(".section-content").removeClass("glow"),c>=1){var e=$(".download-fasta-of-selected"),f=$(".download-alignment-of-selected");e.find(".text-bold").html(c),f.find(".text-bold").html(c)}if(0==c){var e=$(".download-fasta-of-selected"),f=$(".download-alignment-of-selected");e.addClass("disabled").find(".text-bold").html(""),f.addClass("disabled").find(".text-bold").html("")}}}}),p=e.createClass({displayName:"Query",domID:function(){return"Query_"+this.props.query.number},numhits:function(){return this.props.query.hits.length},render:function(){return e.createElement("div",{className:"resultn",id:this.domID(),"data-query-len":this.props.query.length,"data-algorithm":this.props.program},e.createElement("div",{className:"section-header"},e.createElement("h3",null,"Query= ",this.props.query.id," ",e.createElement("small",null,this.props.query.title)),e.createElement("span",{className:"label label-reset pos-label",title:"Query"+this.props.query.number+".","data-toggle":"tooltip"},this.props.query.number+"/"+this.props.num_queries)),this.numhits()&&e.createElement("div",{className:"section-content"},e.createElement(c,{key:"GO_"+this.props.query.number,query:this.props.query,program:this.props.program,collapsed:this.props.veryBig}),e.createElement(d,{key:"LD_"+this.props.query.id,query:this.props.query,algorithm:this.props.program,collapsed:"true"}),e.createElement(q,{key:"HT_"+this.props.query.number,query:this.props.query,imported_xml:this.props.imported_xml}),e.createElement("div",{id:"hits"},g.map(this.props.query.hits,g.bind(function(a){return e.createElement(r,{hit:a,key:"HIT_"+a.number,algorithm:this.props.program,querydb:this.props.querydb,query:this.props.query,imported_xml:this.props.imported_xml,selectHit:this.props.selectHit})},this))))||e.createElement("div",{className:"section-content"},e.createElement("p",null,"Query length: ",this.props.query.length),e.createElement("br",null),e.createElement("br",null),e.createElement("p",null,e.createElement("strong",null," ****** No hits found ****** "))))},shouldComponentUpdate:function(a,b){if(!this.props.query)return!0}}),q=e.createClass({displayName:"HitsTable",mixins:[f],render:function(){var a=g.every(this.props.query.hits,function(a){return""!==a.sciname});return e.createElement("table",{className:"table table-hover table-condensed tabular-view"},e.createElement("thead",null,e.createElement("th",{className:"text-left"},"#"),e.createElement("th",null,"Similar sequences"),a&&e.createElement("th",{className:"text-left"},"Species"),!this.props.imported_xml&&e.createElement("th",{className:"text-right"},"Query coverage (%)"),e.createElement("th",{className:"text-right"},"Total score"),e.createElement("th",{className:"text-right"},"E value"),e.createElement("th",{className:"text-right","data-toggle":"tooltip","data-placement":"left",title:"Total identity of all hsps / total length of all hsps"},"Identity (%)")),e.createElement("tbody",null,g.map(this.props.query.hits,g.bind(function(b){return e.createElement("tr",{key:b.number},e.createElement("td",{className:"text-left"},b.number+"."),e.createElement("td",null,e.createElement("a",{href:"#Query_"+this.props.query.number+"_hit_"+b.number},b.id)),a&&e.createElement("td",{className:"text-left"},b.sciname),!this.props.imported_xml&&e.createElement("td",{className:"text-right"},b.qcovs),e.createElement("td",{className:"text-right"},b.score),e.createElement("td",{className:"text-right"},this.inExponential(b.hsps[0].evalue)),e.createElement("td",{className:"text-right"},b.identity))},this))))}}),r=e.createClass({displayName:"Hit",mixins:[f],accession:function(){return this.props.hit.accession},length:function(){return this.props.hit.length},domID:function(){return"Query_"+this.props.query.number+"_hit_"+this.props.hit.number},databaseIDs:function(){return g.map(this.props.querydb,g.iteratee("id"))},showSequenceViewer:function(a){this.setState({showSequenceViewer:!0}),a&&a.preventDefault()},hideSequenceViewer:function(){this.setState({showSequenceViewer:!1})},viewSequenceLink:function(){return encodeURI("get_sequence/?sequence_ids="+this.accession()+"&database_ids="+this.databaseIDs())},downloadFASTA:function(a){var b=[this.accession()];m(b,this.databaseIDs())},downloadAlignment:function(a){var b=g.map(this.props.hit.hsps,g.bind(function(a){return a.query_id=this.props.query.id,a.hit_id=this.props.hit.id,a},this)),c=new j;c.export_alignments(b,this.props.query.id+"_"+this.props.hit.id)},getInitialState:function(){return{showSequenceViewer:!1}},viewSequenceButton:function(){return this.length()>1e4?e.createElement("button",{className:"btn btn-link view-sequence disabled",title:"Sequence too long",disabled:"true"},e.createElement("i",{className:"fa fa-eye"})," Sequence"):e.createElement("button",{
19
- className:"btn btn-link view-sequence",onClick:this.showSequenceViewer},e.createElement("i",{className:"fa fa-eye"})," Sequence")},render:function(){return e.createElement("div",{className:"hit",id:this.domID(),"data-hit-def":this.props.hit.id,"data-hit-evalue":this.props.hit.evalue,"data-hit-len":this.props.hit.length},e.createElement("div",{className:"section-header"},e.createElement("h4",{"data-toggle":"collapse","data-target":this.domID()+"_content"},e.createElement("i",{className:"fa fa-chevron-down"})," ",e.createElement("span",null,this.props.hit.id," ",e.createElement("small",null,this.props.hit.title))),e.createElement("span",{className:"label label-reset pos-label",title:"Query "+this.props.query.number+". Hit "+this.props.hit.number+" of "+this.props.query.hits.length+".","data-toggle":"tooltip"},this.props.hit.number+"/"+this.props.query.hits.length)),e.createElement("div",{id:this.domID()+"_content",className:"section-content collapse in"},this.hitLinks(),e.createElement(i,{key:"kablammo"+this.props.query.id,query:this.props.query,hit:this.props.hit,algorithm:this.props.algorithm}),this.hspListJSX()))},hitLinks:function(){return e.createElement("div",{className:"hit-links"},e.createElement("label",null,e.createElement("input",{type:"checkbox",id:this.domID()+"_checkbox",value:this.accession(),onChange:function(){this.props.selectHit(this.domID()+"_checkbox")}.bind(this),"data-target":"#"+this.domID()})," Select"),!this.props.imported_xml&&[e.createElement("span",null," | "),this.viewSequenceButton(),this.state.showSequenceViewer&&e.createElement(s,{url:this.viewSequenceLink(),onHide:this.hideSequenceViewer})],!this.props.imported_xml&&[e.createElement("span",null," | "),e.createElement("button",{className:"btn btn-link download-fa",onClick:this.downloadFASTA},e.createElement("i",{className:"fa fa-download"})," FASTA")],e.createElement("span",null," | "),e.createElement("button",{className:"btn btn-link download-aln",onClick:this.downloadAlignment},e.createElement("i",{className:"fa fa-download"})," Alignment"),g.map(this.props.hit.links,g.bind(function(a){return[e.createElement("span",null," | "),this.a(a)]},this)))},hspListJSX:function(){var a=this;return e.createElement("div",{className:"hsps"},this.props.hit.hsps.map(function(b){return e.createElement(k,{key:b.number,algorithm:a.props.algorithm,queryNumber:a.props.query.number,hitNumber:a.props.hit.number,hsp:b})},this))}}),s=function(){var a=e.createClass({displayName:"Viewer",widgetClass:"biojs-vis-sequence",render:function(){return this.widgetID=this.widgetClass+"-"+(new Date).getUTCMilliseconds(),e.createElement("div",{className:"fastan"},e.createElement("div",{className:"section-header"},e.createElement("h4",null,this.props.sequence.id,e.createElement("small",null,"  ",this.props.sequence.title))),e.createElement("div",{className:"section-content"},e.createElement("div",{className:this.widgetClass,id:this.widgetID})))},componentDidMount:function(){var a=new Sequence({sequence:this.props.sequence.value,target:this.widgetID,format:"PRIDE",columns:{size:40,spacedEach:0},formatOptions:{title:!1,footer:!1}});a.hideFormatSelector()}});return e.createClass({show:function(){this.modal().modal("show")},modal:function(){return $(e.findDOMNode(this.refs.modal))},resultsJSX:function(){return e.createElement("div",{className:"modal-body"},g.map(this.state.error_msgs,g.bind(function(a){return e.createElement("div",{className:"fastan"},e.createElement("div",{className:"section-header"},e.createElement("h4",null,a[0])),e.createElement("div",{className:"section-content"},e.createElement("pre",{className:"pre-reset"},a[1])))},this)),g.map(this.state.sequences,g.bind(function(b){return e.createElement(a,{sequence:b})},this)))},loadingJSX:function(){return e.createElement("div",{className:"modal-body text-center"},e.createElement("i",{className:"fa fa-spinner fa-3x fa-spin"}))},getInitialState:function(){return{error_msgs:[],sequences:[],requestCompleted:!1}},render:function(){return e.createElement("div",{className:"modal sequence-viewer",ref:"modal",tabIndex:"-1"},e.createElement("div",{className:"modal-dialog"},e.createElement("div",{className:"modal-content"},e.createElement("div",{className:"modal-header"},e.createElement("h3",null,"View sequence")),this.state.requestCompleted&&this.resultsJSX()||this.loadingJSX())))},componentDidMount:function(){this.show(),$.getJSON(this.props.url).done(g.bind(function(a){this.setState({sequences:a.sequences,error_msgs:a.error_msgs,requestCompleted:!0})},this)).fail(function(a,b,c){l(a,function(){this.hide()})}),this.modal().on("hidden.bs.modal",this.props.onHide)}})}(),t=e.createClass({displayName:"SideBar",downloadFastaOfAll:function(){var a=$(".hit-links :checkbox").map(function(){return this.value}).get(),b=g.map(this.props.data.querydb,g.iteratee("id"));return m(a,b),!1},downloadFastaOfSelected:function(){var a=$(".hit-links :checkbox:checked").map(function(){return this.value}).get(),b=g.map(this.props.data.querydb,g.iteratee("id"));return m(a,b),!1},downloadAlignmentOfAll:function(){var a=$(".hit-links :checkbox").map(function(){return this.value}).get(),b=[],c=new j;return g.each(this.props.data.queries,g.bind(function(a){g.each(a.hits,function(c){g.each(c.hsps,function(d){d.hit_id=c.id,d.query_id=a.id,b.push(d)})})},this)),console.log("len "+b.length),c.export_alignments(b,"alignment-"+a.length+"_hits"),!1},downloadAlignmentOfSelected:function(){var a=$(".hit-links :checkbox:checked").map(function(){return this.value}).get(),b=[],c=new j;return console.log("check "+a.toString()),g.each(this.props.data.queries,g.bind(function(c){g.each(c.hits,function(d){g.indexOf(a,d.accession)!=-1&&g.each(d.hsps,function(a){a.hit_id=d.id,a.query_id=c.id,b.push(a)})})},this)),c.export_alignments(b,"alignment-"+a.length+"_hits"),!1},render:function(){return e.createElement("div",{className:"sidebar"},this.props.shouldShowIndex&&this.index(),this.downloads())},index:function(){return e.createElement("div",{className:"index"},e.createElement("div",{className:"section-header"},e.createElement("h4",null,this.summary())),e.createElement("ul",{className:"nav hover-reset active-bold"},g.map(this.props.data.queries,g.bind(function(a){return e.createElement("li",{key:"Side_bar_"+a.id},e.createElement("a",{className:"nowrap-ellipsis hover-bold",href:"#Query_"+a.number,title:"Query= "+a.id+" "+a.title},"Query= "+a.id))},this))))},summary:function(){var a=this.props.data.program,b=this.props.data.queries.length,c=this.props.data.querydb.length;return a.toUpperCase()+": "+b+" "+(b>1?"queries":"query")+", "+c+" "+(c>1?"databases":"database")},downloads:function(){return e.createElement("div",{className:"downloads"},e.createElement("div",{className:"section-header"},e.createElement("h4",null,"Download FASTA, XML, TSV")),e.createElement("ul",{className:"nav"},!this.props.data.imported_xml&&e.createElement("li",null,e.createElement("a",{href:"#",className:"btn-link download-fasta-of-all",onClick:this.downloadFastaOfAll},"FASTA of all hits")),!this.props.data.imported_xml&&e.createElement("li",null,e.createElement("a",{href:"#",className:"btn-link download-fasta-of-selected disabled",onClick:this.downloadFastaOfSelected},"FASTA of ",e.createElement("span",{className:"text-bold"})," selected hit(s)")),e.createElement("li",null,e.createElement("a",{href:"#",className:"btn-link download-alignment-of-all",onClick:this.downloadAlignmentOfAll},"Alignment of all hits")),e.createElement("li",null,e.createElement("a",{href:"#",className:"btn-link download-alignment-of-selected disabled",onClick:this.downloadAlignmentOfSelected},"Alignment of ",e.createElement("span",{className:"text-bold"})," selected hit(s)")),!this.props.data.imported_xml&&e.createElement("li",null,e.createElement("a",{className:"download","data-toggle":"tooltip",title:"15 columns: query and subject ID; scientific name, alignment length, mismatches, gaps, identity, start and end coordinates, e value, bitscore, query coverage per subject and per HSP.",href:"download/"+this.props.data.search_id+".std_tsv"},"Standard tabular report")),!this.props.data.imported_xml&&e.createElement("li",null,e.createElement("a",{className:"download","data-toggle":"tooltip",title:"44 columns: query and subject ID, GI, accessions, and length; alignment details; taxonomy details of subject sequence(s) and query coverage per subject and per HSP.",href:"download/"+this.props.data.search_id+".full_tsv"},"Full tabular report")),!this.props.data.imported_xml&&e.createElement("li",null,e.createElement("a",{className:"download","data-toggle":"tooltip",title:"Results in XML format.",href:"download/"+this.props.data.search_id+".xml"},"Full XML report"))))}}),e.render(e.createElement(n,null),document.getElementById("view"))}}})})(function(a){a()});
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i)k=i[f],this.blocks[k.id].start=k.offset/j*(2*Math.PI-c*d)+f*d,this.blocks[k.id].end=(k.offset+k.len)/j*(2*Math.PI-c*d)+f*d,k.start=k.offset/j*(2*Math.PI-c*d)+f*d,k.end=(k.offset+k.len)/j*(2*Math.PI-c*d)+f*d;return this.getAngle=function(a,b){var c;return c=this.blocks[a].start/this._size,"deg"===b?360*c:"rad"===b?2*c*Math.PI:null},this.summary=function(){var a,b,c,d,e;for(c={},e=this._data,b=0,d=e.length;b<d;b++)a=e[b],c[a.id]=a.len;return c},this},e.Core.prototype.heatmap=function(a,b,c){var d;return d=new e.Heatmap,d.build(this,b,c),this.tracks.heatmaps[a]=d,this},e.Core.prototype.histogram=function(a,b,c){var d;return d=new e.Histogram,d.build(this,b,c),this.tracks.histograms[a]=d,this},e.Core.prototype.chord=function(a,b,c){var d;return d=new e.Chord,d.build(this,b,c),this.tracks.chords[a]=d,this},e.Core.prototype.scatter=function(a,b,c){var d;return d=new e.Scatter,d.build(this,b,c),this.tracks.scatters[a]=d,this},e.Core.prototype.line=function(a,b,c){var d;return d=new e.Line,d.build(this,b,c),this.tracks.lines[a]=d,this},e.Core.prototype.stack=function(a,b,c){var d;return d=new e.Stack,d.build(this,b,c),this.tracks.stacks[a]=d,this},e.Core.prototype.highlight=function(a,b,c){var d;return d=new e.Highlight,d.build(this,b,c),this.tracks.highlights[a]=d,this},e.Core.prototype.text=function(a,b,c){var d;return d=new e.Text,d.build(this,b,c),this.tracks.texts[a]=d,this},e.Chord=function(){return e.Track.call(this),this.parseData=e.parseChordData,this.applyRules=function(a,b){var c,d,e,f,g;for(a=a||[],f=[],d=0,e=b.length;d<e;d++)c=b[d],f.push(function(){var b,d,e;for(e=[],d=0,b=a.length;d<b;d++)g=a[d],g.condition(c)?e.push(c[g.parameter]=g.value):e.push(void 0);return e}());return f},this.getSource=function(a){return function(a,b){var c,d,e,f;return a=a.source,c=b.blocks[a.id],f=c.start+a.start/c.len*(c.end-c.start),d=c.start+a.end/c.len*(c.end-c.start),e={radius:b.conf.innerRadius,startAngle:f,endAngle:d}}}(this),this.getTarget=function(a){return function(a,b){var c,d,e,f;return a=a.target,c=b.blocks[a.id],f=c.start+a.start/c.len*(c.end-c.start),d=c.start+a.end/c.len*(c.end-c.start),e={radius:b.conf.innerRadius,startAngle:f,endAngle:d}}}(this),this.dimChords=function(a,b,c,d){a.selectAll("path").style("opacity",function(a,b){return d==b?1:0})},this.resetChords=function(a,b){a.selectAll("path").style("opacity",b.opacity)},this.renderChords=function(a,b,c,d,e,f,g,h){var i,j;return j=a.append("g").attr("class",c.colorPalette),i=j.selectAll(".chord").data(d).enter().append("path").attr("class","chord").attr("d",d3.svg.chord().source(function(a){return g(a,e)}).target(function(a){return h(a,e)})).attr("opacity",function(a){return c.opacity}).attr("id",function(a){return a.source.id+"_"+a.target.id}).on("mouseover",function(a){return function(b,d,e){return a.dimChords(j,b,c,d),a.dispatch.mouseover(b,d,e)}}(this)).on("mouseout",function(a){return function(b,d,e){return a.resetChords(j,c),a.dispatch.mouseout(b,d,e)}}(this)),c.usePalette?i.attr("class",function(a){return"q"+f(a.value,c.cmin,c.cmax,c.colorPaletteSize,c.colorPaletteReverse,c.logScale)+"-"+c.colorPaletteSize}):i.attr("fill",function(a){return a.color||c.color}),i},this.render=function(a){return function(b,c,d){var f,g;if(c.select("."+d).remove(),g=c.append("g").attr("class",d).attr("z-index",a.conf.zIndex),f=a.renderChords(g,d,a.conf,a.data,b._layout,a.ratio,a.getSource,a.getTarget),null!=a.conf.tooltipContent)return e.registerTooltip(b,a,f,a.conf)}}(this),this},e.Heatmap=function(){return e.Track.call(this),this.parseData=e.parseSpanValueData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",f.colorPalette),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){return a.selectAll("tile").data(function(a){return a.values}).enter().append("path").attr("class","tile").attr("opacity",function(a){return a.opacity||b.opacity}).attr("d",d3.svg.arc().innerRadius(b.innerRadius).outerRadius(b.outerRadius).startAngle(function(a,b){return d.theta(a.start,c.blocks[a.block_id])}).endAngle(function(a,b){return d.theta(a.end,c.blocks[a.block_id])})).attr("class",function(a){return"q"+d.ratio(a.value,b.cmin,b.cmax,b.colorPaletteSize,b.colorPaletteReverse,b.logScale)+"-"+b.colorPaletteSize})},this},e.Highlight=function(){return e.Track.call(this),this.parseData=e.parseSpanStringData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g;return g=a.renderBlock(c,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){return a.selectAll("tile").data(function(a){return a.values}).enter().append("path").attr("class","tile").attr("d",d3.svg.arc().innerRadius(b.innerRadius).outerRadius(b.outerRadius).startAngle(function(a,b){return d.theta(a.start,c.blocks[a.block_id])}).endAngle(function(a,b){return d.theta(a.end,c.blocks[a.block_id])})).attr("fill",function(a){return a.value||b.color}).attr("opacity",function(a){return a.opacity||b.opacity}).attr("stroke-width",function(a){return a.strokeWidth||b.strokeWidth}).attr("stroke",function(a){return a.strokeColor||b.strokeColor})},this},e.Histogram=function(){return e.Track.call(this),this.parseData=e.parseSpanValueData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",a.conf.colorPalette),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,e){var f;return f=a.selectAll(".bin").data(function(a){return a.values}).enter().append("path").attr("class","bin").attr("opacity",function(a){return a.opacity||b.opacity}).attr("d",d3.svg.arc().innerRadius(function(a){var c;return"in"===b.direction?(c=e.ratio(a.value,b.cmin,b.cmax,b.outerRadius-b.innerRadius,!1,b.logscale),b.outerRadius-c):b.innerRadius}).outerRadius(function(a){var c;return"out"===b.direction?(c=e.ratio(a.value,b.cmin,b.cmax,b.outerRadius-b.innerRadius,!1,b.logscale),b.innerRadius+c):b.outerRadius}).startAngle(function(a){return e.theta(a.start,c.blocks[a.block_id])}).endAngle(function(a){return e.theta(a.end,c.blocks[a.block_id])})),b.usePalette?f.attr("class",function(a){return"q"+e.ratio(a.value,b.cmin,b.cmax,b.colorPaletteSize,b.colorPaletteReverse,b.logScale)+"-"+b.colorPaletteSize}):f.attr("fill",d.color||b.color),f},this},e.Line=function(){return e.Track.call(this),this.parseData=e.parsePositionValueData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",d),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){var e;return e=d3.svg.line().x(function(a){return d.x(a,c,b)}).y(function(a){return d.y(a,c,b)}).interpolate(b.interpolation),a.append("path").datum(function(a){return a.values}).attr("class","line").attr("d",e).attr("opacity",function(a){return a.opacity||b.opacity}).attr("stroke-width",function(a){return a.thickness||b.thickness}).attr("stroke",function(a){return a.color||b.color}).attr("fill",function(a){var c,d;return d=a.fill||b.fill,c=a.fill_color||b.fill_color,d?c:"none"})},this},e.Scatter=function(){return e.Track.call(this),this.parseData=e.parsePositionValueData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",d),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){var e;return e=a.selectAll(".point").data(function(a){return a.values}).enter().append("path").attr("class","point").attr("opacity",function(a){return a.opacity||b.opacity}).attr("d",d3.svg.symbol().type(b.glyph.shape).size(b.glyph.size)).attr("transform",function(a){return function(a){return"translate("+d.x(a,c,b)+","+d.y(a,c,b)+") rotate("+360*d.theta(a.position,c.blocks[a.block_id])/(2*Math.PI)+")"}}(this)).attr("stroke",function(a){return a.glyph_strokeColor||b.glyph.strokeColor}).attr("stroke-width",function(a){return a.glyph_strokeWidth||b.glyph.strokeWidth}).attr("fill",function(a){var c,d;return d=a.glyph_fill||b.glyph.fill,c=a.glyph_color||b.glyph.color,d?c:"none"})},this},e.Stack=function(){return e.Track.call(this),this.parseData=e.parseSpanValueData,this.build=function(a,b,c,d,e){return this.loadData(c,a),this.conf=this.processConf(b,this.defaultConf,this.meta,a,this),this.buildLayers(this.data,this.conf.margin),this.applyRules(b.rules,this.data)},this.buildLayers=function(a,b){var c,d,e,f,g,h,i,j,k,l,m,n,o;for(f in a)for(c=a[f],c.values=c.values.sort(function(a,b){return a.start<b.start?-1:a.start===b.start&&a.end>b.end?-1:a.start===b.start&&a.end===b.end?0:1}),j=[],o=c.values,g=0,k=o.length;g<k;g++){for(d=o[g],n=!1,e=m=0,l=j.length;m<l;e=++m)if(i=j[e],h=i.slice(0).pop(),h.end+b<d.start){i.push(d),d.layer=e,n=!0;break}n||(d.layer=j.length),n||j.push([d])}},this.applyRules=function(a,b){var c,d,e,f,g,h,i;a=a||[],g=[];for(e in b)i=b[e],g.push(function(){var b,e;b=i.layers,e=[];for(d in b)f=b[d],e.push(function(){var b,e,g;for(g=[],b=0,e=f.length;b<e;b++)c=f[b],g.push(function(){var b,e,f;for(f=[],e=0,b=a.length;e<b;e++)h=a[e],h.condition(i.parent,c,d)?f.push(c[h.parameter]=h.value):f.push(void 0);return f}());return g}());return e}());return g},this.datumRadialPosition=function(a){return function(b){var c,d,e;return e=(a.conf.thickness+a.conf.radialMargin)*b.layer,d=e+a.conf.thickness,"out"===a.conf.direction?[a.conf.innerRadius+e,Math.min(a.conf.innerRadius+d,a.conf.outerRadius)]:"in"===a.conf.direction?[Math.max(a.conf.outerRadius-d,a.conf.innerRadius),a.conf.outerRadius-e]:"center"===a.conf.direction?(c=Math.floor((a.conf.outerRadius+a.conf.innerRadius)/2),e=(a.conf.thickness+a.conf.radialMargin)*Math.floor(b.layer/2),d=e+a.conf.thickness,b.layer%2===0?[c+e,c+d]:[c-e-a.conf.radialMargin,c-d-a.conf.radialMargin]):void 0}}(this),this.datumInnerRadius=function(a){return function(b,c,d){return a.datumRadialPosition(b,c,d)[0]}}(this),this.datumOuterRadius=function(a){return function(b,c,d){return a.datumRadialPosition(b,c,d)[1]}}(this),this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",f.colorPalette),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){var e;return e=a.selectAll(".tile").data(function(a){return a.values}).enter().append("path").attr("class","tile").attr("d",d3.svg.arc().innerRadius(d.datumInnerRadius).outerRadius(d.datumOuterRadius).startAngle(function(a){return d.theta(a.start,c.blocks[a.block_id])}).endAngle(function(a){return d.theta(a.end,c.blocks[a.block_id])})),e.attr("opacity",function(a){return a.opacity||b.opacity}),e.attr("stroke-width",function(a){return a.strokeWidth||b.strokeWidth}),e.attr("stroke",function(a){return a.strokeColor||b.strokeColor}),e.attr("fill",function(a){return a.color||b.color}),e.attr("class",function(a){var c;if(c=a.usePalette||b.usePalette)return"q"+d.ratio(a.value,b.cmin,b.cmax,b.colorPaletteSize,b.colorPaletteReverse,b.logScale)+"-"+b.colorPaletteSize}),e},this},e.Text=function(){return e.Track.call(this),this.parseData=e.parsePositionTextData,this.renderDatumContainer=function(a){return function(b,c,d,e,f){var g,h;return h=c.append("g").attr("class",d),g=a.renderBlock(h,e,b._layout,f)}}(this),this.renderDatum=function(a,b,c,d){var e,f,g,h;g=a.selectAll("g").data(function(a){return a.values}).enter().append("g").append("text").text(function(a){return a.value}).attr("transform",function(a){var e;return e=360*d.theta(a.position,c.blocks[a.block_id])/(2*Math.PI)-90,"rotate("+e+")translate("+b.innerRadius+",0)"}),f=b.style;for(e in f)h=f[e],g.style(e,h);return g},this},e.Track=function(){return this.build=function(a,b,c){return this.dispatch=d3.dispatch("mouseover","mouseout"),this.loadData(c,a),this.conf=this.processConf(b,this.defaultConf,this.meta,a,this),this.applyRules(b.rules,this.data)},this.loadData=function(a,b){var c,d,e,f,g,h;for(e={},g=b._layout.data,d=0,f=g.length;d<f;d++)c=g[d],e[c.id]=c.len;return h=this.parseData(a,e),this.data=h.data,this.meta=h.meta},this.processConf=function(a,b,c,d,f){var g;return a=e.mixConf(a,Object.assign({},b)),a=f.computeMinMax(a,c),0===a.innerRadius&&0===a.outerRadius&&(g=d.smartBorders(),a.innerRadius=g.in,a.outerRadius=g.out),a},this.applyRules=function(a,b){var c,d,e,f,g,h;a=a||[],f=[];for(e in b)h=b[e],f.push(function(){var b,e;b=h.values,e=[];for(d in b)c=b[d],e.push(function(){var b,e,f;for(f=[],b=0,e=a.length;b<e;b++)g=a[b],g.condition(h.key,c,d)?f.push(c[g.parameter]=g.value):f.push(void 0);return f}());return e}());return f},this.computeMinMax=function(a,b){return a.cmin="smart"===a.min?b.min:a.min,a.cmax="smart"===a.max?b.max:a.max,a},this.ratio=function(a,b,c,d,e,f){var g,h,i;return h=f?2.3:1,b===c||a===b&&!e||a===c&&e?0:a===c||a===b&&e?d-1:(g=(a-b)/(c-b),i=Math.exp(1/h*Math.log(g)),e&&(i=1-i),Math.floor(d*i))},this.render=function(a){return function(b,c,d){var f,g,h,i;return c.select("."+d).remove(),i=c.append("g").attr("class",d).attr("z-index",a.conf.zIndex),f=a.renderDatumContainer(b,i,d,a.data,a.conf),(null!=(g=a.conf.axes)?g.display:void 0)&&a.renderAxes(f,a.conf,b._layout,a.data),h=a.renderDatum(f,a.conf,b._layout,a),null!=a.conf.tooltipContent&&e.registerTooltip(b,a,h,a.conf),h.on("mouseover",function(b,c,d){return a.dispatch.mouseover(b,c,d)}),h.on("mouseout",function(b,c,d){return a.dispatch.mouseout(b,c,d)})}}(this),this.renderBlock=function(a,b,c,d){var e,f;return f=d.outerRadius-d.innerRadius,e=a.selectAll(".block").data(b).enter().append("g").attr("class","block").attr("transform",function(a){
4
+ return"rotate("+360*c.blocks[a.key].start/(2*Math.PI)+")"}),d.backgrounds&&e.selectAll(".background").data(d.backgrounds).enter().append("path").attr("class","background").attr("fill",function(a){return a.color}).attr("opacity",function(a){return a.opacity||1}).attr("d",d3.svg.arc().innerRadius(function(a){return"in"===d.direction?d.outerRadius-f*a.start:d.innerRadius+f*a.start}).outerRadius(function(a){return"in"===d.direction?d.outerRadius-f*a.end:d.innerRadius+f*a.end}).startAngle(function(a,b,c){return 0}).endAngle(function(a,d,e){return c.blocks[b[e].key].end-c.blocks[b[e].key].start})),e},this.renderAxes=function(a,b,c,d){var e,f,g;return"pixel"===b.axes.minor.spacingType&&(e=function(){var a,c,d,e,f;for(f=[],g=a=c=b.innerRadius,d=b.outerRadius,e=b.axes.minor.spacing;e>0?a<=d:a>=d;g=a+=e)f.push(g);return f}()),f=d3.svg.arc().innerRadius(function(a){return a}).outerRadius(function(a){return a}).startAngle(0).endAngle(function(a,b,e){var f;return f=c.blocks[d[e].key],f.end-f.start}),a.selectAll(".axis").data(e).enter().append("path").attr("opacity",b.opacity).attr("class","axis").attr("d",f).attr("stroke-width",function(a,c){return c%b.axes.major.spacing===0?b.axes.major.thickness:b.axes.minor.thickness}).attr("stroke",function(a,c){return c%b.axes.major.spacing===0?b.axes.major.color:b.axes.minor.color})},this.theta=function(a,b){return a/b.len*(b.end-b.start)},this.x=function(a){return function(b,c,d){var e,f,g;return f=a.ratio(b.value,d.cmin,d.cmax,d.outerRadius-d.innerRadius,!1,d.logscale),g="in"===d.direction?d.outerRadius-f:d.innerRadius+f,e=a.theta(b.position,c.blocks[b.block_id])-Math.PI/2,g*Math.cos(e)}}(this),this.y=function(a){return function(b,c,d){var e,f,g;return f=a.ratio(b.value,d.cmin,d.cmax,d.outerRadius-d.innerRadius,!1,d.logscale),g="in"===d.direction?d.outerRadius-f:d.innerRadius+f,e=a.theta(b.position,c.blocks[b.block_id])-Math.PI/2,g*Math.sin(e)}}(this),this.ratio=function(a,b,c,d,e,f){var g,h,i;return h=f?2.3:1,b===c||a===b&&!e||a===c&&e?0:a===c||a===b&&e?d-1:(g=(a-b)/(c-b),i=Math.exp(1/h*Math.log(g)),e&&(i=1-i),Math.floor(d*i))},this},e.renderLayout=function(a,b,c){var d,f,g,h;if(f=c._layout.conf,b.select(".cs-layout").remove(),h=b.append("g").attr("class","cs-layout").attr("z-index",f.zIndex).on("click",f.onClick),d=h.selectAll("g").data(c._layout.data).enter().append("g").attr("class",function(a){return a.id}).attr("opacity",f.opacity),g=a.svg.arc().innerRadius(f.innerRadius).outerRadius(f.outerRadius).cornerRadius(f.cornerRadius).startAngle(function(a){return a.start}).endAngle(function(a){return a.end}),d.append("path").attr("d",g).attr("fill",function(a){return a.color}).attr("id",function(a){return a.id}),f.labels.display&&e.renderLayoutLabels(f,a,d),f.ticks.display)return e.renderLayoutTicks(f,h,a,c)},e.renderLayoutLabels=function(a,b,c){var d,e,f;return f=a.innerRadius+a.labels.radialOffset,e=b.svg.arc().innerRadius(f).outerRadius(f).startAngle(function(a,b){return a.start}).endAngle(function(a,b){return a.end}),c.append("path").attr("fill","none").attr("stroke","none").attr("d",e).attr("id",function(a){return"arc-label"+a.id}),d=c.append("text").attr("font-size",a.labels.size).attr("text-anchor","middle"),d.append("textPath").attr("startOffset","25%").attr("xlink:href",function(a){return"#arc-label"+a.id}).style("fill",a.labels.color).text(function(a){var b=a.end-a.start;return a.label.slice(0,Math.floor(21*b))+".."})},e.renderLayoutTicks=function(a,b,c,d){var e,f,g;return e=function(b){var d,e;d=(b.end-b.start)/b.len,b.end-b.start>1.57?e=8:b.end-b.start>.785?e=4:b.end-b.start>.3925?e=2:b.end-b.start>0&&(e=0);var f=[],g={angle:0*d+b.start,label:0};f.push(g);var h=c.scale.linear().domain([1,b.len]).range([b.start,b.end]),i=h.ticks(e).length;h.ticks(e).map(function(c,e){var g=(c*d+b.start,b.len*d+b.start,{angle:c*d+b.start,label:c/a.ticks.labelDenominator+a.ticks.labelSuffix});f.push(g)}),f.splice(i,1);var g={angle:b.len*d+b.start-.006,label:b.len/a.ticks.labelDenominator+a.ticks.labelSuffix};return f.push(g),f},f=function(b,c){return a.ticks.labels===!1?null:a.ticks.labelDisplay0===!1&&0===c?null:c%a.ticks.labelSpacing?null:0===c?b/a.ticks.labelDenominator:b/a.ticks.labelDenominator+a.ticks.labelSuffix},g=b.append("g").selectAll("g").data(d._layout.data).enter().append("g").selectAll("g").data(e).enter().append("g").attr("transform",function(b){return"rotate("+(180*b.angle/Math.PI-90)+")translate("+a.outerRadius+",0)"}),g.append("line").attr("x1",0).attr("y1",1).attr("x2",function(b,c){return a.ticks.size.major}).attr("y2",1).style("stroke",a.ticks.color),g.append("text").attr("x",8).attr("dy",".35em").attr("transform",function(a){return a.angle>Math.PI?"rotate(180)translate(-16)":null}).attr("text-anchor",function(a){return a.angle>Math.PI?"end":null}).attr("font-size",a.ticks.labelSize).style("fill",a.ticks.labelColor).text(function(a){return a.label})},e.Core.prototype.render=function(a,b){var c,d,g,h,i,j,k,l,m,n;if("undefined"==typeof a&&(h=!0,a=[]),b){d=this.tracks;for(l in d){k=d[l];for(c in k)j=k[c],i.select("."+c).remove()}}i=d3.select(this.conf.container).attr("width",this.conf.width).attr("height",this.conf.height),n=i.select(".all"),n.empty()&&(n=i.append("g").attr("class","all").attr("transform","translate("+parseInt(this.conf.width/2)+","+parseInt(this.conf.height/2)+")")),g=this.tracks;for(l in g){k=g[l];for(c in k)j=k[c],(h||f.call(a,c)>=0)&&j.render(this,n,c)}return(h||f.call(a,"layout")>=0)&&e.renderLayout(d3,n,this),m=i.selectAll(".all > g").remove(),m[0].sort(function(a,b){return parseInt(a.getAttribute("z-index"))<parseInt(b.getAttribute("z-index"))?-1:parseInt(a.getAttribute("z-index"))>parseInt(b.getAttribute("z-index"))?1:0}),i.select(".all").selectAll("g").data(m[0]).enter().append(function(a){return a}),this},e.Core.prototype.defaultConf={width:700,height:700,container:"circos",defaultTrackWidth:10},e.Layout.prototype.defaultConf={innerRadius:250,outerRadius:300,cornerRadius:5,gap:.04,opacity:1,labels:{position:"center",display:!0,size:14,color:"#000",radialOffset:20},ticks:{display:!0,color:"grey",spacing:1e7,labels:!0,labelSpacing:10,labelSuffix:"Mb",labelDenominator:1e6,labelDisplay0:!0,labelSize:10,labelColor:"#000",labelFont:"default",majorSpacing:5,size:{minor:2,major:5}},onClick:null,onMouseOver:null,zIndex:100},e.axes={display:!1,minor:{spacing:5,spacingType:"pixel",color:"#d3d3d3",thickness:2},major:{spacing:5,color:"#000000",thickness:2}},e.Heatmap.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",colorPalette:"YlGnBu",colorPaletteSize:9,colorPaletteReverse:!1,logScale:!1,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Histogram.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",direction:"out",colorPaletteSize:9,colorPalette:"YlGnBu",usePalette:!0,colorPaletteReverse:!1,color:"#fd6a62",logScale:!1,axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Chord.prototype.defaultConf={colorPaletteSize:9,colorPalette:"PuBuGn",usePalette:!0,colorPaletteReverse:!1,color:"#fd6a62",opacity:.7,min:"smart",max:"smart",logScale:!1,rules:[],backgrounds:[],zIndex:1,tooltipContent:null},e.Scatter.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",direction:"out",logScale:!1,glyph:{color:"#fd6a62",fill:!0,size:15,shape:"circle",strokeColor:"#d3d3d3",strokeWidth:2},axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Line.prototype.defaultConf={innerRadius:0,outerRadius:0,min:"smart",max:"smart",direction:"out",logScale:!1,color:"#fd6a62",fill:!0,fill_color:"#d3d3d3",thickness:2,max_gap:1e7,interpolation:"linear",axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Stack.prototype.defaultConf={innerRadius:0,outerRadius:0,colorPaletteSize:9,colorPalette:"PuBuGn",usePalette:!0,colorPaletteReverse:!1,color:"#fd6a62",min:"smart",max:"smart",direction:"out",logScale:!1,color:"#fd6a62",thickness:10,radialMargin:2,margin:2,strokeWidth:1,strokeColor:"#000000",axes:e.axes,rules:[],backgrounds:[],zIndex:1,opacity:1,tooltipContent:null},e.Highlight.prototype.defaultConf={innerRadius:0,outerRadius:0,defaultColor:"#fd6a62",opacity:.5,rules:[],zIndex:101,strokeColor:"#d3d3d3",strokeWidth:0,tooltipContent:null},e.Text.prototype.defaultConf={innerRadius:0,outerRadius:0,rules:[],backgrounds:[],zIndex:1,style:{},tooltipContent:null},e.registerTooltip=function(a,b,c,d){return b.tip=d3.tip().direction("s").offset([20,0]).html(d.tooltipContent),c.call(b.tip),b.dispatch.on("mouseover",function(a,c,d){return b.tip.attr("class","d3-tip appear").show(a)}),b.dispatch.on("mouseout",function(a,c,d){return b.tip.attr("class","d3-tip").show(a),b.tip.hide()})}}),c.registerDynamic("c",["b"],!0,function(a,b,c){this||self;c.exports=a("b")}),c.register("d",["10","11","12","13","14","e","f","c"],function(a){var b,c,d,e,f,g,h,i,j,k;return{setters:[function(a){b=a.default},function(a){c=a},function(a){d=a.default},function(a){e=a.default},function(a){f=a.default},function(a){g=a.default},function(a){h=a.default},function(a){i=a.default}],execute:function(){j=function(){function a(b,d){var e=this;f(this,a),this.queries=[],d.queries.forEach(function(a){a.hits.length>0&&e.queries.push(a)}),this.svgContainer=b,this.seq_type=c.get_seq_type(d.program),this.algorithm=d.program,this.initiate()}return e(a,null,[{key:"name",value:function(){return"Chord diagram: queries and their top hits"}},{key:"className",value:function(){return"circos"}},{key:"collapseId",value:function(a){return"circos-collapse"}},{key:"dataName",value:function(a){return"Circos-visualisation"}}]),e(a,[{key:"initiate",value:function(){this.width=this.svgContainer.width(),this.height=600,this.innerRadius=200,this.outerRadius=230,this.query_arr=[],this.hit_arr=[],this.layout_arr=[],this.chords_arr=[],this.hsp_count=50,this.denominator=1,this.spacing=20,this.labelSpacing=10;var a={amino_acid:"aa",nucleic_acid:"bp"};this.construct_layout(),this.iterator_for_edits(),this.hit_arr=h.uniq(this.hit_arr),this.handle_spacing();var b=g.formatPrefix(this.max_length);this.suffix=" "+b.symbol+a[this.seq_type.subject_seq_type],"k"==b.symbol?this.denominator=1e3:"M"==b.symbol?(this.denominator=1e6,this.spacing=1e6,this.labelSpacing=2e5):"g"==b.symbol&&(this.denominator=1e9),g.select(this.svgContainer[0]).insert("svg",":first-child").attr("class","circosContainer"),this.create_instance(this.svgContainer,this.width,this.height),this.chords_arr.length&&this.layout_arr.length?this.instance_render():this.render_error(),this.setupTooltip()}},{key:"iterator_for_edits",value:function(){this.max_length=this.calculate_max_length(),this.hit_arr.length>10&&this.complex_layout_edits()}},{key:"construct_layout",value:function(){var a=0,b=32,c=this.queries.length,d=Math.min(b/2,c),e=(b-d)/d;this.new_layout=[],this.data=h.map(this.queries,h.bind(function(b){if(a<d){var c=b.id,f=b.length,g={len:f,color:"#8dd3c7",label:c,id:"Query_"+this.clean_id(b.id),ori_id:c};this.layout_arr.push(g);h.map(b.hits,h.bind(function(a){if(a.number<e){h.map(a.hsps,h.bind(function(c){if(h.indexOf(this.hit_arr,a.id)==-1){var d=a.id,e=a.length;this.hit_arr.push(a.id);var f={len:e,color:"#80b1d3",label:d,id:"Hit_"+this.clean_id(a.id),ori_id:d};this.layout_arr.push(f)}var g=["Query_"+this.clean_id(b.id),c.qstart,c.qend,"Hit_"+this.clean_id(a.id),c.sstart,c.send,a.number,c];return this.chords_arr.push(g),c},this));return a}},this))}return this.query_arr.push(b.id),b},this))}},{key:"rearrange_new_layout",value:function(){h.each(this.new_layout,h.bind(function(a){var b=a.id.slice(0,3);"Que"==b&&this.layout_arr.push(a)},this)),h.each(this.new_layout,h.bind(function(a){var b=a.id.slice(0,3);"Hit"==b&&this.layout_arr.push(a)},this))}},{key:"complex_layout_edits",value:function(){this.delete_from_layout=[],this.delete_from_chords=[],h.each(this.layout_arr,h.bind(function(a,b){var c=(a.len/this.max_length).toFixed(3);a.label;c<.1&&"Que"!=a.id.slice(0,3)&&(this.delete_from_layout.push(a),this.hit_arr.slice(h.indexOf(this.hit_arr,a.label),1))},this))}},{key:"check_in_chords_arr",value:function(a,b,c){var d=0;h.each(this.chords_arr,h.bind(function(c){"Que"==b&&c[0]!=a&&d++},this)),d==this.chords_arr.length&&(console.log("no record found "+a),this.delete_arr.push(c))}},{key:"find_index_of_hit",value:function(a){var b;return h.each(this.queries,h.bind(function(c){h.each(c.hits,h.bind(function(c){var d="Hit_"+this.clean_id(c.id);a==d&&(b=c.id)},this))},this)),h.indexOf(this.layout_arr,b)}},{key:"edit_labels",value:function(){console.log("label edits"),h.each(this.layout_arr,h.bind(function(a){var b=(a.len/this.max_length).toFixed(3),c=a.label;b<.41?a.label="..":c.length>10?a.label=c.slice(0,2)+"...":a.label=a.ori_id},this))}},{key:"calculate_multipliers",value:function(){var a=0,b=0;h.each(this.query_arr,h.bind(function(b){h.each(this.data,h.bind(function(c){b==c.id&&(a+=c.length)},this))},this)),h.each(this.data,h.bind(function(a){h.each(a.hits,h.bind(function(a){var c=h.indexOf(this.hit_arr,a.id);c>=0&&(b+=a.length)},this))},this));var c=(a+b)/2;console.log("mid sum "+c+" hit_sum "+b+" query_sum "+a),this.query_multiplier=(c/a).toFixed(3),this.hit_multiplier=(c/b).toFixed(3),console.log("query "+this.query_multiplier+" hit "+this.hit_multiplier)}},{key:"handle_spacing",value:function(){this.max_length>16e3?this.spacing=200:this.max_length>12e3?this.spacing=150:this.max_length>8e3?this.spacing=100:this.max_length>4e3?this.spacing=75:this.max_length>1800&&(this.spacing=50)}},{key:"calculate_max_length",value:function(){var a=0;return h.each(this.layout_arr,function(b){a<b.len&&(a=b.len)}),a}},{key:"clean_id",value:function(a){return a.replace(/[^a-zA-Z0-9]/g,"")}},{key:"create_instance",value:function(a,b,c){this.instance=new i({container:".circosContainer",width:b,height:c}),this.chord_layout(),this.instance_layout()}},{key:"chord_layout",value:function(){return this.chords_arr.length>32?this.paletteSize=32:this.paletteSize=this.chords_arr.length,{usePalette:!0,colorPaletteSize:this.paletteSize,colorPalette:"RdYlBu",opacity:.85}}},{key:"instance_layout",value:function(){return{innerRadius:this.innerRadius,outerRadius:this.outerRadius,cornerRadius:1,labels:{display:!0,size:"10px",radialOffset:10},ticks:{display:!0,spacing:this.spacing,labelSpacing:this.labelSpacing,labelDenominator:this.denominator,labelSuffix:this.suffix,labelSize:"10px",majorSpacing:this.labelSpacing,size:{minor:0,major:4}}}}},{key:"instance_render",value:function(){this.instance.layout(this.instance_layout(),this.layout_arr),this.instance.chord("chord1",this.chord_layout(),this.chords_arr),this.instance.render()}},{key:"render_error",value:function(){this.svgContainer.find("svg").remove(),this.svg=g.select(this.svgContainer[0]).insert("svg",":first-child").attr("width",this.svgContainer.width()).attr("height",this.svgContainer.height()).append("g").attr("class","circos-error").attr("transform","translate("+this.svgContainer.width()/2+","+this.svgContainer.height()/2+")").append("text").attr("text-anchor","start").attr("dy","-0.25em").attr("x",-175).style("font-size","14px").text("Circos looks great with less than 16 queries")}},{key:"layoutReset",value:function(){this.layoutHide=[],h.each(this.layout_arr,function(a){$("."+a.id).css("opacity",1)})}},{key:"chordsReset",value:function(){this.chordsHide=[],h.each(this.chords_arr,function(a){var b=a[1]+a[2],c=a[4]+a[5];$("#"+a[0]+"_"+b+"_"+a[3]+"_"+c).show()})}},{key:"chordsCheck",value:function(a,b){h.each(this.chords_arr,h.bind(function(c,d){"Que"==b&&c[0]==a&&(this.chordsHide.push(d),this.layoutHide.push(c[3])),"Hit"==b&&c[3]==a&&(this.chordsHide.push(d),this.layoutHide.push(c[0]))},this))}},{key:"chordsClean",value:function(){h.each(this.chords_arr,h.bind(function(a,b){if(h.indexOf(this.chordsHide,b)==-1){var c=a[1]+a[2],d=a[4]+a[5];$("#"+a[0]+"_"+c+"_"+a[3]+"_"+d).hide()}},this))}},{key:"layoutClean",value:function(){h.each(this.layout_arr,h.bind(function(a,b){h.indexOf(this.layoutHide,a.id)==-1&&$("."+a.id).css("opacity",.1)},this))}},{key:"setupTooltip",value:function(){var a={};$(".circos-distribution").on("click",h.bind(function(b){b.stopPropagation(),this.layoutReset(),this.chordsReset(),a={}},this)),h.each(this.query_arr,h.bind(function(b,c){this.chordsHide=[],this.layoutHide=[],b&&$(".circos .Query_"+this.clean_id(b)).attr("data-toggle","tooltip").attr("title",b).on("click",h.bind(function(d){if(d.stopPropagation(),a[c]!=b){a[c]=b;var e="Query_"+this.clean_id(b);this.layoutHide.push(e),this.chordsCheck(e,"Que"),this.chordsClean(),this.layoutClean()}else a[c]=0,this.layoutReset(),this.chordsReset()},this))},this)),h.each(this.hit_arr,h.bind(function(b,c){this.chordsHide=[],this.layoutHide=[],b&&$(".circos .Hit_"+this.clean_id(b)).attr("data-toggle","tooltip").attr("title",b).on("click",h.bind(function(d){if(d.stopPropagation(),a[c]!=b){a[c]=b;var e="Hit_"+this.clean_id(b);this.layoutHide.push(e),this.chordsCheck(e,"Hit"),this.chordsClean(),this.layoutClean()}else a[c]=0,this.layoutReset(),this.chordsReset()},this))},this));var b=this.algorithm;h.each(this.chords_arr,function(a){$("#"+a[0]+"_"+a[3]).attr("data-toggle","tooltip").attr("title",function(){var e="E value: "+c.prettify_evalue(a[7].evalue)+(", Identities: "+d.inPercentage(a[7].identity,a[7].length));return"blastn"!=b&&(e+="<br>Positives: "+d.inPercentage(a[7].positives,a[7].length)),e+=", Gaps: "+d.inPercentage(a[7].gaps,a[7].length)})}),$('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true",delay:0,"white-space":"nowrap"})}},{key:"ratioCalculate",value:function(a,b,c,d,e,f){var g,h,i;return h=f?2.3:1,b===c||a===b&&!e||a===c&&e?0:a===c||a===b&&e?d-1:(g=(a-b)/(c-b),i=Math.exp(1/h*Math.log(g)),e&&(i=1-i),Math.floor(d*i))}},{key:"drawLegend",value:function(){this.ratioHSP=[],h.each(this.chords_arr,h.bind(function(a){var b={number:a[6],evalue:a[7].evalue};this.ratioHSP.push(b)},this));var a=g.min(this.ratioHSP,function(a){return a.number}),b=g.max(this.ratioHSP,function(a){return a.number});console.log("chords_arr "+this.chords_arr.length),console.log("ratioHSP test "+this.ratioHSP.length),console.log("paletteSize "+this.paletteSize),console.log("min "+a+" max "+b),this.legend=g.select(this.svgContainer[0]).insert("svg",":first-child").attr("height",20).attr("width",30*this.ratioHSP.length).attr("transform","translate(10, 10)").append("g").attr("class","RdYlBu").attr("transform","translate(10, 0)");this.legend.selectAll(".bar").data(this.ratioHSP).enter().append("g").attr("class","g").attr("transform",function(a,b){return"translate("+30*b+",0)"}).append("rect").attr("class",h.bind(function(c,d){var e=this.ratioCalculate(c.number,a,b,this.paletteSize,!1,!1);return console.log("calc ratio "+e),"q"+e+"-"+this.paletteSize},this)).attr("data-toggle","tooltip").attr("title",function(a){return a.evalue}).attr("x",1).attr("width",30).attr("height",20),g.scale.linear().domain([0,250]).range([0,100])}}]),a}(),k=b(j),a("default",k)}}}),c.register("15",["10","11","12","13","14","e","f"],function(a){var b,c,d,e,f,g,h,i,j;return{setters:[function(a){b=a.default},function(a){c=a},function(a){d=a.default},function(a){e=a.default},function(a){f=a.default},function(a){g=a.default},function(a){h=a.default}],execute:function(){i=function(){function a(b,c){f(this,a),this.svg_container=b,$queryDiv=b.parents(".resultn"),hits=this.extractData(c.query.hits,c.query.number),this.graphIt($queryDiv,b,0,20,null,hits)}return e(a,null,[{key:"name",value:function(){return"Graphical overview of hits"}},{key:"className",value:function(){return"alignment-overview"}},{key:"collapseId",value:function(a){return"alignment_"+a.query.number}},{key:"dataName",value:function(a){return"Alignment-Overview-"+a.query.id}}]),e(a,[{key:"extractData",value:function(a,b){var c=[];return a.map(function(a){var d=[],e=a.hsps;h.each(e,function(c){var e={};e.hspEvalue=c.evalue,e.hspStart=c.qstart,e.hspEnd=c.qend,e.hspFrame=c.sframe,e.hspId="Query_"+b+"_hit_"+a.number+"_hsp_"+c.number,e.hspIdentity=c.identity,e.hspGaps=c.gaps,e.hspPositives=c.positives,e.hspLength=c.length,d.push(e)}),d.hitId=a.id,d.hitDef="Query_"+b+"_hit_"+a.number,d.hitEvalue=a.evalue,c.push(d)}),c}},{key:"setupTooltip",value:function(){this.svg_container.find('[data-toggle="tooltip"]').tooltip({placement:"top",container:"body",html:"true",delay:0,"white-space":"nowrap"})}},{key:"setupClick",value:function(a){$("a",a).click(function(a){a.preventDefault(),a.stopPropagation(),window.location.hash=$(this).attr("href")})}},{key:"graphControls",value:function(a,b,c,d,e){var f,g,i,j,k=20,l=function(){f=e.length,g=a.find(".ghit > g").length},m=function(a,b){b.append($("<button/>").addClass("btn btn-link more").attr("type","button").attr("data-parent-query",a.attr("id")).html("View More&nbsp;").append($("<i/>").html("&nbsp;&nbsp;").addClass("fa 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this.props.query.hits.length},render:function(){return g.createElement("div",{className:"resultn",id:this.domID(),"data-query-len":this.props.query.length,"data-algorithm":this.props.program},this.headerJSX(),this.numhits()&&this.hitsListJSX()||this.noHitsJSX())},headerJSX:function(){var a="length: "+this.queryLength().toLocaleString();return this.props.showQueryCrumbs&&(a="query "+this.props.query.number+", "+a),g.createElement("div",{className:"section-header"},g.createElement("h3",null,"Query= ",this.props.query.id," ",g.createElement("small",null,this.props.query.title)),g.createElement("span",{className:"label label-reset pos-label"},a))},hitsListJSX:function(){return g.createElement("div",{className:"section-content"},g.createElement(d,{key:"GO_"+this.props.query.number,query:this.props.query,program:this.props.program,collapsed:this.props.veryBig}),g.createElement(e,{key:"LD_"+this.props.query.id,query:this.props.query,algorithm:this.props.program,collapsed:"true"}),g.createElement(q,{key:"HT_"+this.props.query.number,query:this.props.query,imported_xml:this.props.imported_xml}),g.createElement("div",{id:"hits"},h.map(this.props.query.hits,h.bind(function(a){return g.createElement(r,{key:"HIT_"+a.number,hit:a,algorithm:this.props.program,querydb:this.props.querydb,query:this.props.query,imported_xml:this.props.imported_xml,selectHit:this.props.selectHit,showHitCrumbs:this.numhits()>1,showQueryCrumbs:this.props.showQueryCrumbs})},this))))},noHitsJSX:function(){return g.createElement("div",{className:"section-content"},g.createElement("br",null),g.createElement("p",null,g.createElement("strong",null," ****** No hits found ****** 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g.createElement("tr",{key:b.number},g.createElement("td",{className:"text-left"},b.number+"."),g.createElement("td",null,g.createElement("a",{
19
+ href:"#Query_"+this.props.query.number+"_hit_"+b.number},b.id)),a&&g.createElement("td",{className:"text-left"},b.sciname),!this.props.imported_xml&&g.createElement("td",{className:"text-right"},b.qcovs),g.createElement("td",{className:"text-right"},b.score),g.createElement("td",{className:"text-right"},this.inExponential(b.hsps[0].evalue)),g.createElement("td",{className:"text-right"},b.identity))},this))))}}),r=g.createClass({displayName:"Hit",mixins:[c],accession:function(){return this.props.hit.accession},hitLength:function(){return this.props.hit.length},domID:function(){return"Query_"+this.props.query.number+"_hit_"+this.props.hit.number},databaseIDs:function(){return h.map(this.props.querydb,h.iteratee("id"))},showSequenceViewer:function(a){this.setState({showSequenceViewer:!0}),a&&a.preventDefault()},hideSequenceViewer:function(){this.setState({showSequenceViewer:!1})},viewSequenceLink:function(){return 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pos-label"},a))},contentJSX:function(){return g.createElement("div",{id:this.domID()+"_content",className:"section-content collapse in"},this.hitLinks(),g.createElement(j,{key:"kablammo"+this.props.query.id,query:this.props.query,hit:this.props.hit,algorithm:this.props.algorithm}),this.hspListJSX())},hitLinks:function(){return g.createElement("div",{className:"hit-links"},g.createElement("label",null,g.createElement("input",{type:"checkbox",id:this.domID()+"_checkbox",value:this.accession(),onChange:function(){this.props.selectHit(this.domID()+"_checkbox")}.bind(this),"data-target":"#"+this.domID()})," Select"),!this.props.imported_xml&&[g.createElement("span",null," | "),this.viewSequenceButton(),this.state.showSequenceViewer&&g.createElement(s,{url:this.viewSequenceLink(),onHide:this.hideSequenceViewer})],!this.props.imported_xml&&[g.createElement("span",null," | "),g.createElement("button",{className:"btn btn-link download-fa",onClick:this.downloadFASTA},g.createElement("i",{className:"fa fa-download"})," FASTA")],g.createElement("span",null," | "),g.createElement("button",{className:"btn btn-link download-aln",onClick:this.downloadAlignment},g.createElement("i",{className:"fa fa-download"})," Alignment"),h.map(this.props.hit.links,h.bind(function(a){return[g.createElement("span",null," | "),this.a(a)]},this)))},hspListJSX:function(){var a=this;return g.createElement("div",{className:"hsps"},this.props.hit.hsps.map(function(b){return g.createElement(f,{key:b.number,algorithm:a.props.algorithm,queryNumber:a.props.query.number,hitNumber:a.props.hit.number,hsp:b})},this))}}),s=function(){var a=g.createClass({displayName:"Viewer",widgetClass:"biojs-vis-sequence",render:function(){return this.widgetID=this.widgetClass+"-"+(new Date).getUTCMilliseconds(),g.createElement("div",{className:"fastan"},g.createElement("div",{className:"section-header"},g.createElement("h4",null,this.props.sequence.id,g.createElement("small",null,"  ",this.props.sequence.title))),g.createElement("div",{className:"section-content"},g.createElement("div",{className:this.widgetClass,id:this.widgetID})))},componentDidMount:function(){var a=new Sequence({sequence:this.props.sequence.value,target:this.widgetID,format:"PRIDE",columns:{size:40,spacedEach:0},formatOptions:{title:!1,footer:!1}});a.hideFormatSelector()}});return g.createClass({show:function(){this.modal().modal("show")},modal:function(){return $(g.findDOMNode(this.refs.modal))},resultsJSX:function(){return g.createElement("div",{className:"modal-body"},h.map(this.state.error_msgs,h.bind(function(a){return 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sequence")),this.state.requestCompleted&&this.resultsJSX()||this.loadingJSX())))},componentDidMount:function(){this.show(),$.getJSON(this.props.url).done(h.bind(function(a){this.setState({sequences:a.sequences,error_msgs:a.error_msgs,requestCompleted:!0})},this)).fail(function(a,b,c){l(a,function(){this.hide()})}),this.modal().on("hidden.bs.modal",this.props.onHide)}})}(),t=g.createClass({displayName:"SideBar",downloadFastaOfAll:function(){var a=$(".hit-links :checkbox").map(function(){return this.value}).get(),b=h.map(this.props.data.querydb,h.iteratee("id"));return m(a,b),!1},downloadFastaOfSelected:function(){var a=$(".hit-links :checkbox:checked").map(function(){return this.value}).get(),b=h.map(this.props.data.querydb,h.iteratee("id"));return m(a,b),!1},downloadAlignmentOfAll:function(){var a=$(".hit-links :checkbox").map(function(){return this.value}).get(),b=[],c=new k;return h.each(this.props.data.queries,h.bind(function(a){h.each(a.hits,function(c){h.each(c.hsps,function(d){d.hit_id=c.id,d.query_id=a.id,b.push(d)})})},this)),console.log("len "+b.length),c.export_alignments(b,"alignment-"+a.length+"_hits"),!1},downloadAlignmentOfSelected:function(){var a=$(".hit-links :checkbox:checked").map(function(){return this.value}).get(),b=[],c=new k;return console.log("check "+a.toString()),h.each(this.props.data.queries,h.bind(function(c){h.each(c.hits,function(d){h.indexOf(a,d.accession)!=-1&&h.each(d.hsps,function(a){a.hit_id=d.id,a.query_id=c.id,b.push(a)})})},this)),c.export_alignments(b,"alignment-"+a.length+"_hits"),!1},render:function(){return g.createElement("div",{className:"sidebar"},this.props.shouldShowIndex&&this.index(),this.downloads())},index:function(){return g.createElement("div",{className:"index"},g.createElement("div",{className:"section-header"},g.createElement("h4",null,this.summary())),g.createElement("ul",{className:"nav hover-reset 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Please try one sequence at a time."))}}),l=d.createClass({displayName:"Databases",getInitialState:function(){return{type:"",databases:[]}},databases:function(a){return a?c.select(this.props.databases,function(b){return b.type===a}):this.props.databases.slice()},nselected:function(){return $('input[name="databases[]"]:checked').length},categories:function(){return c.uniq(c.map(this.props.databases,c.iteratee("type"))).sort()},handleClick:function(a){var b=this.nselected()?a.type:"";this.setState({type:b})},handleToggle:function(a,b){switch(a){case"[Select all]":$("."+b+" .database input:not(:checked)").click();break;case"[Deselect all]":$("."+b+" .database input:checked").click()}},render:function(){return d.createElement("div",{className:"form-group databases-container"},c.map(this.categories(),this.renderDatabases))},renderDatabases:function(a){var b=a[0].toUpperCase()+a.substring(1).toLowerCase()+" databases",e=1===this.categories().length?"col-md-12":"col-md-6",f="[Select all]",g="btn btn-link",h=this.databases(a).length>1,i=this.state.type&&this.state.type!==a;return h&&i&&(g+=" disabled"),h||(g+=" hidden"),this.nselected()===this.databases(a).length&&(f="[Deselect all]"),d.createElement("div",{className:e},d.createElement("div",{className:"panel panel-default"},d.createElement("div",{className:"panel-heading"},d.createElement("h4",{style:{display:"inline"}},b),"   ",d.createElement("button",{type:"button",className:g,disabled:i,onClick:function(){this.handleToggle(f,a)}.bind(this)},f)),d.createElement("ul",{className:"list-group databases "+a},c.map(this.databases(a),c.bind(function(a){return d.createElement("li",{className:"list-group-item"},this.renderDatabase(a))},this)))))},renderDatabase:function(a){var b=this.state.type&&this.state.type!==a.type;return d.createElement("label",{className:b&&"disabled database"||"database"},d.createElement("input",{type:"checkbox",name:"databases[]",value:a.id,"data-type":a.type,disabled:b,onChange:c.bind(function(){this.handleClick(a)},this)})," "+(a.title||a.name))},componentDidUpdate:function(){this.databases()&&1===this.databases().length&&($(".databases").find("input").prop("checked",!0),this.handleClick(this.databases()[0])),this.props.onDatabaseTypeChanged(this.state.type)}}),m=d.createClass({displayName:"Options",updateBox:function(a){this.setState({preOpts:a.target.value})},getInitialState:function(){return{preOpts:""}},render:function(){return d.createElement("div",{className:"col-md-8"},d.createElement("div",{className:"form-group"},d.createElement("div",{className:"col-md-12"},d.createElement("div",{className:"input-group"},d.createElement("label",{className:"control-label",htmlFor:"advanced"},"Advanced parameters:"),d.createElement("input",{type:"text",className:"form-control",name:"advanced",id:"advanced",title:"View, and enter advanced parameters.",placeholder:"eg: -evalue 1.0e-5 -num_alignments 100",value:this.state.preOpts,onChange:this.updateBox}),d.createElement("div",{className:"input-group-addon cursor-pointer","data-toggle":"modal","data-target":"#help"},d.createElement("i",{className:"fa fa-question"}))))))}}),n=d.createClass({displayName:"SearchButton",inputGroup:function(){return $(d.findDOMNode(this.refs.inputGroup))},submitButton:function(){return $(d.findDOMNode(this.refs.submitButton))},initTooltip:function(){this.inputGroup().tooltip({trigger:"manual",title:c.bind(function(){return this.state.hasQuery||this.state.hasDatabases?this.state.hasQuery&&!this.state.hasDatabases?"You must select one or more databases above before you can run a search!":!this.state.hasQuery&&this.state.hasDatabases?"You must enter a query sequence above before you can run a search!":void 0:"You must enter a query sequence and select one or more databases above before you can run a search!"},this)}),this.submitButton().tooltip({title:c.bind(function(){var a="Click to BLAST or press Ctrl+Enter.";return this.state.methods.length>1&&(a+=" Click dropdown button on the right for other BLAST algorithms that can be used."),a},this)})},showTooltip:function(){this.inputGroup()._tooltip("show")},hideTooltip:function(){this.inputGroup()._tooltip("hide")},changeAlgorithm:function(a){var b=this.state.methods.slice();b.splice(b.indexOf(a),1),b.unshift(a),this.setState({methods:b})},decorate:function(a){return a.match(/(.?)(blast)(.?)/).slice(1).map(function(a,b){if(a)return"blast"!==a?d.createElement("strong",{key:a},a):a})},getInitialState:function(){return{methods:[],hasQuery:!1,hasDatabases:!1}},render:function(){var a=this.state.methods,b=a[0],e=a.length>1;return d.createElement("div",{className:"col-md-4"},d.createElement("div",{className:"form-group"},d.createElement("div",{className:"col-md-12"},d.createElement("div",{className:e&&"input-group",id:"methods",ref:"inputGroup",onMouseOver:this.showTooltip,onMouseOut:this.hideTooltip},d.createElement("button",{type:"submit",className:"btn btn-primary form-control text-uppercase",id:"method",ref:"submitButton",name:"method",value:b,disabled:!b},this.decorate(b||"blast")),e&&d.createElement("div",{className:"input-group-btn"},d.createElement("button",{className:"btn btn-primary dropdown-toggle","data-toggle":"dropdown"},d.createElement("span",{className:"caret"})),d.createElement("ul",{className:"dropdown-menu dropdown-menu-right"},c.map(a.slice(1),c.bind(function(a){return d.createElement("li",{key:a,className:"text-uppercase",onClick:c.bind(function(){this.changeAlgorithm(a)},this)},a)},this))))))))},componentDidMount:function(){this.initTooltip()},shouldComponentUpdate:function(a,b){return!c.isEqual(b.methods,this.state.methods)},componentDidUpdate:function(){this.state.methods.length>0?(this.inputGroup().wiggle(),this.props.onAlgoChanged(this.state.methods[0])):this.props.onAlgoChanged("")}}),d.render(d.createElement(e,null),document.getElementById("view"))}}})})(function(a){a()});
11
+ id:"protein-sequence-notification",style:{display:"none"}},d.createElement("div",{className:"alert-info col-md-6 col-md-offset-3"},"Detected: amino-acid sequence(s)."))}}),j=d.createClass({displayName:"NucleotideNotification",render:function(){return d.createElement("div",{className:"notification row",id:"nucleotide-sequence-notification",style:{display:"none"}},d.createElement("div",{className:"alert-info col-md-6 col-md-offset-3"},"Detected: nucleotide sequence(s)."))}}),k=d.createClass({displayName:"MixedNotification",render:function(){return d.createElement("div",{className:"notification row",id:"mixed-sequence-notification",style:{display:"none"}},d.createElement("div",{className:"alert-danger col-md-10 col-md-offset-1"},"Detected: mixed nucleotide and amino-acid sequences. We can't handle that. Please try one sequence at a time."))}}),l=d.createClass({displayName:"Databases",getInitialState:function(){return{type:"",databases:[]}},databases:function(a){return a?c.select(this.props.databases,function(b){return b.type===a}):this.props.databases.slice()},nselected:function(){return $('input[name="databases[]"]:checked').length},categories:function(){return c.uniq(c.map(this.props.databases,c.iteratee("type"))).sort()},handleClick:function(a){var b=this.nselected()?a.type:"";this.setState({type:b})},handleToggle:function(a,b){switch(a){case"[Select all]":$("."+b+" .database input:not(:checked)").click();break;case"[Deselect all]":$("."+b+" .database input:checked").click()}},render:function(){return d.createElement("div",{className:"form-group databases-container"},c.map(this.categories(),this.renderDatabases))},renderDatabases:function(a){var b=a[0].toUpperCase()+a.substring(1).toLowerCase()+" databases",e=1===this.categories().length?"col-md-12":"col-md-6",f="[Select all]",g="btn btn-link",h=this.databases(a).length>1,i=this.state.type&&this.state.type!==a;return h&&i&&(g+=" disabled"),h||(g+=" hidden"),this.nselected()===this.databases(a).length&&(f="[Deselect all]"),d.createElement("div",{className:e,key:"DB_"+a},d.createElement("div",{className:"panel panel-default"},d.createElement("div",{className:"panel-heading"},d.createElement("h4",{style:{display:"inline"}},b),"   ",d.createElement("button",{type:"button",className:g,disabled:i,onClick:function(){this.handleToggle(f,a)}.bind(this)},f)),d.createElement("ul",{className:"list-group databases "+a},c.map(this.databases(a),c.bind(function(b,c){return d.createElement("li",{className:"list-group-item",key:"DB_"+a+c},this.renderDatabase(b))},this)))))},renderDatabase:function(a){var b=this.state.type&&this.state.type!==a.type;return d.createElement("label",{className:b&&"disabled database"||"database"},d.createElement("input",{type:"checkbox",name:"databases[]",value:a.id,"data-type":a.type,disabled:b,onChange:c.bind(function(){this.handleClick(a)},this)})," "+(a.title||a.name))},componentDidUpdate:function(){this.databases()&&1===this.databases().length&&($(".databases").find("input").prop("checked",!0),this.handleClick(this.databases()[0])),this.props.onDatabaseTypeChanged(this.state.type)}}),m=d.createClass({displayName:"Options",updateBox:function(a){this.setState({preOpts:a.target.value})},getInitialState:function(){return{preOpts:""}},render:function(){return d.createElement("div",{className:"col-md-8"},d.createElement("div",{className:"form-group"},d.createElement("div",{className:"col-md-12"},d.createElement("div",{className:"input-group"},d.createElement("label",{className:"control-label",htmlFor:"advanced"},"Advanced parameters:"),d.createElement("input",{type:"text",className:"form-control",name:"advanced",id:"advanced",title:"View, and enter advanced parameters.",placeholder:"eg: -evalue 1.0e-5 -num_alignments 100",value:this.state.preOpts,onChange:this.updateBox}),d.createElement("div",{className:"input-group-addon cursor-pointer","data-toggle":"modal","data-target":"#help"},d.createElement("i",{className:"fa fa-question"}))))))}}),n=d.createClass({displayName:"SearchButton",inputGroup:function(){return $(d.findDOMNode(this.refs.inputGroup))},submitButton:function(){return $(d.findDOMNode(this.refs.submitButton))},initTooltip:function(){this.inputGroup().tooltip({trigger:"manual",title:c.bind(function(){return this.state.hasQuery||this.state.hasDatabases?this.state.hasQuery&&!this.state.hasDatabases?"You must select one or more databases above before you can run a search!":!this.state.hasQuery&&this.state.hasDatabases?"You must enter a query sequence above before you can run a search!":void 0:"You must enter a query sequence and select one or more databases above before you can run a search!"},this)}),this.submitButton().tooltip({title:c.bind(function(){var a="Click to BLAST or press Ctrl+Enter.";return this.state.methods.length>1&&(a+=" Click dropdown button on the right for other BLAST algorithms that can be used."),a},this)})},showTooltip:function(){this.inputGroup()._tooltip("show")},hideTooltip:function(){this.inputGroup()._tooltip("hide")},changeAlgorithm:function(a){var b=this.state.methods.slice();b.splice(b.indexOf(a),1),b.unshift(a),this.setState({methods:b})},decorate:function(a){return a.match(/(.?)(blast)(.?)/).slice(1).map(function(a,b){if(a)return"blast"!==a?d.createElement("strong",{key:a},a):a})},getInitialState:function(){return{methods:[],hasQuery:!1,hasDatabases:!1}},render:function(){var a=this.state.methods,b=a[0],e=a.length>1;return d.createElement("div",{className:"col-md-4"},d.createElement("div",{className:"form-group"},d.createElement("div",{className:"col-md-12"},d.createElement("div",{className:e&&"input-group",id:"methods",ref:"inputGroup",onMouseOver:this.showTooltip,onMouseOut:this.hideTooltip},d.createElement("button",{type:"submit",className:"btn btn-primary form-control text-uppercase",id:"method",ref:"submitButton",name:"method",value:b,disabled:!b},this.decorate(b||"blast")),e&&d.createElement("div",{className:"input-group-btn"},d.createElement("button",{className:"btn btn-primary dropdown-toggle","data-toggle":"dropdown"},d.createElement("span",{className:"caret"})),d.createElement("ul",{className:"dropdown-menu dropdown-menu-right"},c.map(a.slice(1),c.bind(function(a){return d.createElement("li",{key:a,className:"text-uppercase",onClick:c.bind(function(){this.changeAlgorithm(a)},this)},a)},this))))))))},componentDidMount:function(){this.initTooltip()},shouldComponentUpdate:function(a,b){return!c.isEqual(b.methods,this.state.methods)},componentDidUpdate:function(){this.state.methods.length>0?(this.inputGroup().wiggle(),this.props.onAlgoChanged(this.state.methods[0])):this.props.onAlgoChanged("")}}),d.render(d.createElement(e,null),document.getElementById("view"))}}})})(function(a){a()});
@@ -623,12 +623,8 @@ circosJS.Chord = function() {
623
623
  return getTarget(d, layout);
624
624
  })).attr('opacity', function(d) {
625
625
  return conf.opacity;
626
- }).attr('data-toggle','tooltip').attr('title',function(d) {
627
- return 'Identity '+d.hsp.identity+'<br> Evalue '+d.hsp.evalue;
628
626
  }).attr('id',function (d) {
629
- var slen = d.source.start + d.source.end;
630
- var tlen = d.target.start + d.target.end;
631
- return d.source.id+'_'+slen+'_'+d.target.id+'_'+tlen;
627
+ return d.source.id+'_'+d.target.id
632
628
  }).on('mouseover', (function(_this) {
633
629
  return function(d, i, j) {
634
630
  _this.dimChords(track, d, conf, i);
@@ -27,9 +27,8 @@ Gem::Specification.new do |s|
27
27
  s.add_development_dependency('capybara', '~> 3.15', '>= 3.15.1')
28
28
  s.add_development_dependency('capybara-screenshot', '~> 1.0', '>= 1.0.23')
29
29
  s.add_development_dependency('rack-test', '~> 1.0', '>= 1.0.0')
30
- s.add_development_dependency('rake', '~> 10.3', '>= 10.3.2')
31
30
  s.add_development_dependency('rspec', '~> 3.7', '>= 3.7.0')
32
- s.add_development_dependency('sauce_whisk', '~> 0.0', '>= 0.0.19')
31
+ s.add_development_dependency('rubocop', '~> 0.75', '>= 0.75.1')
33
32
  s.add_development_dependency('selenium-webdriver', '~> 3.142', '>= 3.142.3')
34
33
  s.add_development_dependency('simplecov', '~> 0.17.0', '>= 0.17.0')
35
34
 
@@ -32,9 +32,9 @@ module SequenceServer
32
32
  no_hits_report = BLAST::Report.new(no_hits)
33
33
 
34
34
  it 'will return queries with valid length' do
35
- hits_report.queries.first.length.should be_a Fixnum
35
+ hits_report.queries.first.length.should be_a Integer
36
36
  hits_report.queries.first.length.should satisfy { |n| n > 0 }
37
- no_hits_report.queries.first.length.should be_a Fixnum
37
+ no_hits_report.queries.first.length.should be_a Integer
38
38
  no_hits_report.queries.first.length.should satisfy { |n| n > 0 }
39
39
  end
40
40
 
@@ -79,45 +79,45 @@ module SequenceServer
79
79
  # Test Random HSPs to ensure that all the values from HSP struct are valid.
80
80
  it 'have correct alignment values' do
81
81
  hits_report.queries.last.hits.first.hsps.last.bit_score.should be_a Float
82
- hits_report.queries.last.hits.first.hsps.last.score.should be_a Fixnum
82
+ hits_report.queries.last.hits.first.hsps.last.score.should be_a Integer
83
83
 
84
84
  hits_report.queries.first.hits.first.hsps.first.evalue.should be_a Float
85
85
  hits_report.queries.first.hits.first.hsps.first.evalue
86
86
  .should_not satisfy { |n| n < 0 }
87
87
 
88
- hits_report.queries.first.hits.last.hsps.first.qstart.should be_a Fixnum
88
+ hits_report.queries.first.hits.last.hsps.first.qstart.should be_a Integer
89
89
  hits_report.queries.first.hits.last.hsps.first.qstart
90
90
  .should_not satisfy { |n| n < 0 }
91
91
 
92
- hits_report.queries.first.hits.last.hsps.first.qend.should be_a Fixnum
92
+ hits_report.queries.first.hits.last.hsps.first.qend.should be_a Integer
93
93
  hits_report.queries.first.hits.last.hsps.first.qend
94
94
  .should_not satisfy { |n| n < 0 }
95
95
 
96
- hits_report.queries.last.hits.last.hsps.last.sstart.should be_a Fixnum
96
+ hits_report.queries.last.hits.last.hsps.last.sstart.should be_a Integer
97
97
  hits_report.queries.last.hits.last.hsps.last.sstart
98
98
  .should_not satisfy { |n| n < 0 }
99
99
 
100
- hits_report.queries.first.hits.first.hsps.last.send.should be_a Fixnum
100
+ hits_report.queries.first.hits.first.hsps.last.send.should be_a Integer
101
101
  hits_report.queries.first.hits.first.hsps.last.send
102
102
  .should_not satisfy { |n| n < 0 }
103
103
 
104
- hits_report.queries.first.hits.first.hsps.last.qframe.should be_a Fixnum
105
- hits_report.queries.first.hits.first.hsps.last.sframe.should be_a Fixnum
104
+ hits_report.queries.first.hits.first.hsps.last.qframe.should be_a Integer
105
+ hits_report.queries.first.hits.first.hsps.last.sframe.should be_a Integer
106
106
 
107
- hits_report.queries.first.hits.first.hsps.last.identity.should be_a Fixnum
107
+ hits_report.queries.first.hits.first.hsps.last.identity.should be_a Integer
108
108
  hits_report.queries.first.hits.first.hsps.last.identity
109
109
  .should_not satisfy { |n| n < 0 }
110
110
 
111
- hits_report.queries.first.hits.first.hsps.last.gaps.should be_a Fixnum
111
+ hits_report.queries.first.hits.first.hsps.last.gaps.should be_a Integer
112
112
  hits_report.queries.first.hits.first.hsps.last.gaps
113
113
  .should_not satisfy { |n| n < 0 }
114
114
 
115
115
  hits_report.queries.first.hits.first.hsps.last.positives
116
- .should be_a Fixnum
116
+ .should be_a Integer
117
117
  hits_report.queries.first.hits.first.hsps.last.positives
118
118
  .should_not satisfy { |n| n < 0 }
119
119
 
120
- hits_report.queries.first.hits.first.hsps.last.length.should be_a Fixnum
120
+ hits_report.queries.first.hits.first.hsps.last.length.should be_a Integer
121
121
  hits_report.queries.first.hits.first.hsps.last.length
122
122
  .should satisfy { |n| n > 0 }
123
123
 
@@ -1,51 +1,581 @@
1
- require 'spec_helper'
2
- require 'sauce_whisk'
3
- require 'capybara/rspec'
4
- require 'selenium-webdriver'
1
+ describe 'report generated from imported XML', type: :feature, js: true do
2
+ # Test suite to test features of imported XML report. Fasta files used for
3
+ # testing consist of TP53 and COX41 protein/nucleotide sequences for
4
+ # reproducibility. Each query was limited to 20 hits to not to overload the
5
+ # test suite. BLAST 2.2.30 displays hits in a different order than versions
6
+ # 2.2.31 upwards for protein queries (BLASTP, TBLASTN), hence the test takes
7
+ # different files for comparison.
5
8
 
6
- RSpec.configure do |config|
7
- config.include Capybara::DSL
8
- end
9
+ # BLASTP test scenarios
10
+ it 'loads BLASTP XML and tests hit alignment and sidebar Alignment download' do
11
+ access_by_uuid('blast_2.2.30/blastp')
12
+ # Click on the first hit Alignment download button on the page and wait for
13
+ # the download to finish.
14
+
15
+ page.execute_script("$('.download-aln:eq(0)').click()")
16
+ wait_for_download
17
+ expect(File.basename(downloaded_file)).to eq('sp_P04637_P53_HUMAN_gi_120407068_ref_NP_000537_3.txt')
18
+ expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sp_P04637_P53_HUMAN_gi_120407068_ref_NP_000537_3.txt'))
19
+
20
+ clear_downloads
21
+
22
+ # Click on the Alignment of all hits download and compare the downloaded
23
+ # content
24
+
25
+ page.click_link('Alignment of all hits')
26
+ wait_for_download
27
+ expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
28
+ expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_blastp_2.2.30.txt'))
9
29
 
10
- describe 'report generated from imported XML', :js => true do
11
- before do |scenario|
12
- Capybara.app = SequenceServer.init
13
- Capybara.server = :webrick
14
- Capybara.javascript_driver = :selenium
15
- Capybara.default_max_wait_time = 20
30
+ clear_downloads
16
31
 
17
- Capybara.register_driver :selenium do |app|
18
- options = ::Selenium::WebDriver::Firefox::Options.new
19
- options.args << '--headless'
20
- Capybara::Selenium::Driver.new(app, browser: :firefox, options: options)
21
- end
32
+ # Check the cheboxes of indicted hits and click on the download of Alignment
33
+ # of selected hits and compare the downloaded content
34
+
35
+ page.check('Query_1_hit_1_checkbox')
36
+ page.check('Query_1_hit_2_checkbox')
37
+ page.check('Query_2_hit_1_checkbox')
38
+ page.check('Query_2_hit_2_checkbox')
39
+ page.click_link('Alignment of 4 selected hit(s)')
40
+ wait_for_download
41
+
42
+ expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
43
+ expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_blastp_2.2.30.txt'))
22
44
  end
23
45
 
24
- # Fasta files used for testing consist of TP53 and COX41 protein/nucleotide sequences for reproducibility.
25
- # Import xml files generated by blast 2.2.30
26
- it 'loads BLASTP xml output' do
46
+ it 'loads BLASTP XML and tests alignment overiview and hit PNG/SVG download' do
27
47
  access_by_uuid('blast_2.2.30/blastp')
48
+
49
+ # Click on the PNG/SVG download button of the alignment overview and compare
50
+ # the downloaded content.
51
+
52
+ page.execute_script("$('.export-to-png:eq(0)').click()")
53
+ wait_for_download
54
+ expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.png')
55
+
56
+ clear_downloads
57
+
58
+ page.execute_script("$('.export-to-svg:eq(0)').click()")
59
+ wait_for_download
60
+ expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.svg')
61
+
62
+ clear_downloads
63
+
64
+ # Click on the PNG/SVG download button of the first hit available and
65
+ # compare the downloaded content.
66
+ page.execute_script("$('.export-to-png:eq(1)').click()")
67
+ wait_for_download
68
+ expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_120407068_ref_NP_000537_3.png')
69
+
70
+ clear_downloads
71
+
72
+ page.execute_script("$('.export-to-svg:eq(1)').click()")
73
+ wait_for_download
74
+ expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_120407068_ref_NP_000537_3.svg')
75
+ page.should have_content('BLASTP')
76
+ end
77
+
78
+ it 'loads BLASTP XML and tests Circos download' do
79
+ access_by_uuid('blast_2.2.30/blastp')
80
+
81
+ # Click on the Circos expanding button, wait for animation, click on the
82
+ # download of PNG/SVG file and test that it initiated a file download in a
83
+ # right format.
84
+ page.should have_content('Chord diagram: queries and their top hits')
85
+ page.execute_script("$('.circos > .grapher-header > h5').click()")
86
+ sleep 1
87
+
88
+ page.execute_script("$('.export-to-png:eq(0)').click()")
89
+ wait_for_download
90
+ expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
91
+ clear_downloads
92
+
93
+ page.execute_script("$('.export-to-svg:eq(0)').click()")
94
+ wait_for_download
95
+ expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
96
+ end
97
+
98
+ it 'loads BLASTP XML and tests Length distribution download' do
99
+ access_by_uuid('blast_2.2.30/blastp')
100
+
101
+ # Click on the Length distribution expanding button, wait for animation,
102
+ # click on the download of PNG/SVG file and test that it initiated a file
103
+ # download in a right format.
104
+ page.should have_content('Length distribution of hits')
105
+ page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
106
+ sleep 1
107
+
108
+ page.execute_script("$('.export-to-png:eq(1)').click()")
109
+ wait_for_download
110
+ expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.png')
111
+
112
+ clear_downloads
113
+
114
+ page.execute_script("$('.export-to-svg:eq(1)').click()")
115
+ wait_for_download
116
+ expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.svg')
117
+ end
118
+
119
+ # BLASTX test scenarios
120
+
121
+ it 'loads BLASTX XML and tests hit alignment and sidebar Alignment download' do
122
+ access_by_uuid('blast_2.2.30/blastx')
123
+
124
+ # Click on the first Alignment download button on the page and wait for the
125
+ # download to finish.
126
+ page.execute_script("$('.download-aln:eq(0)').click()")
127
+ wait_for_download
128
+ expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1486783307_gb_AYF55702_1.txt')
129
+ expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/MH011443_1_gi_1486783307_gb_AYF55702_1.txt'))
130
+
131
+ clear_downloads
132
+
133
+ # Click on the Alignment of all hits download and compare the downloaded
134
+ # content
135
+
136
+ page.click_link('Alignment of all hits')
137
+ wait_for_download
138
+ expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
139
+ expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_blastx.txt'))
140
+
141
+ clear_downloads
142
+
143
+ # Select four hit checkboxes and click on the Alignment of selected hits.
144
+ # Compare the downloaded content.
145
+ page.check('Query_1_hit_3_checkbox')
146
+ page.check('Query_1_hit_4_checkbox')
147
+ page.check('Query_2_hit_3_checkbox')
148
+ page.check('Query_2_hit_4_checkbox')
149
+ page.click_link('Alignment of 4 selected hit(s)')
150
+ wait_for_download
151
+
152
+ expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
153
+ expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_blastx.txt'))
154
+
155
+ page.should have_content('BLASTX')
28
156
  end
29
157
 
30
- it 'loads BLASTX xml output' do
158
+ it 'loads BLASTX XML and tests hit PNG/SVG download' do
31
159
  access_by_uuid('blast_2.2.30/blastx')
160
+
161
+ # Click on the PNG/SVG download button of the alignment overview and compare
162
+ # the downloaded content.
163
+ page.execute_script("$('.export-to-png:eq(0)').click()")
164
+ wait_for_download
165
+ expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
166
+
167
+ clear_downloads
168
+
169
+ page.execute_script("$('.export-to-svg:eq(0)').click()")
170
+ wait_for_download
171
+ expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
172
+
173
+ clear_downloads
174
+
175
+ # Click on the PNG/SVG download button of the first hit available and
176
+ # compare the downloaded content.
177
+ page.execute_script("$('.export-to-png:eq(1)').click()")
178
+ wait_for_download
179
+ expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783307_gb_AYF55702_1.png')
180
+
181
+ clear_downloads
182
+
183
+ page.execute_script("$('.export-to-svg:eq(1)').click()")
184
+ wait_for_download
185
+ expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783307_gb_AYF55702_1.svg')
186
+ page.should have_content('BLASTX')
32
187
  end
33
188
 
34
- it 'loads BLASTN xml output' do
189
+ it 'loads BLASTX XML and tests Circos download' do
190
+ access_by_uuid('blast_2.2.30/blastx')
191
+ # Click on the Circos expanding button, wait for animation, click on the
192
+ # download of PNG/SVG file and test that it initiated a file download in a
193
+ # right format.
194
+
195
+ page.should have_content('Chord diagram: queries and their top hits')
196
+ page.execute_script("$('.circos > .grapher-header > h5').click()")
197
+ sleep 1
198
+
199
+ page.execute_script("$('.export-to-png:eq(0)').click()")
200
+ wait_for_download
201
+ expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
202
+ clear_downloads
203
+
204
+ page.execute_script("$('.export-to-svg:eq(0)').click()")
205
+ wait_for_download
206
+ expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
207
+ end
208
+
209
+ it 'loads BLASTX XML and tests Length distribution download' do
210
+ access_by_uuid('blast_2.2.30/blastx')
211
+ # Click on the Length distribution expanding button, wait for animation,
212
+ # click on the download of PNG/SVG file and test that it initiated a file
213
+ # download in a right format.
214
+
215
+ page.should have_content('Length distribution of hits')
216
+ page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
217
+ sleep 1
218
+
219
+ page.execute_script("$('.export-to-png:eq(1)').click()")
220
+ wait_for_download
221
+ expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
222
+
223
+ clear_downloads
224
+
225
+ page.execute_script("$('.export-to-svg:eq(1)').click()")
226
+ wait_for_download
227
+ expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
228
+ end
229
+
230
+ # BLASTN Test scenarios
231
+
232
+ it 'loads BLASTN XML and tests hit alignment and sidebar Alignment download' do
35
233
  access_by_uuid('blast_2.2.30/blastn')
234
+
235
+ # Click on the first Alignment download button on the page and wait for the
236
+ # download to finish.
237
+
238
+ page.execute_script("$('.download-aln:eq(0)').click()")
239
+ wait_for_download
240
+ expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1486783306_gb_MH011443_1.txt')
241
+ expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/MH011443_1_gi_1486783306_gb_MH011443_1.txt'))
242
+
243
+ clear_downloads
244
+
245
+ # Click on the Alignment of all hits download and compare the downloaded
246
+ # content
247
+
248
+ page.click_link('Alignment of all hits')
249
+ wait_for_download
250
+ expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
251
+ expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_blastn.txt'))
252
+
253
+ clear_downloads
254
+
255
+ # Select four hit checkboxes and click on the Alignment of selected hits.
256
+ # Compare the downloaded content.
257
+ page.check('Query_1_hit_5_checkbox')
258
+ page.check('Query_1_hit_6_checkbox')
259
+ page.check('Query_2_hit_5_checkbox')
260
+ page.check('Query_2_hit_6_checkbox')
261
+ page.click_link('Alignment of 4 selected hit(s)')
262
+ wait_for_download
263
+
264
+ expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
265
+ expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_blastn.txt'))
266
+ page.should have_content('BLASTN')
267
+ end
268
+
269
+ it 'loads BLASTN XML and tests alignment overview and hit PNG/SVG download' do
270
+ access_by_uuid('blast_2.2.30/blastn')
271
+
272
+ # Click on the PNG/SVG download button of the alignment overview and compare
273
+ # the downloaded content.
274
+ page.execute_script("$('.export-to-png:eq(0)').click()")
275
+ wait_for_download
276
+ expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
277
+
278
+ clear_downloads
279
+
280
+ page.execute_script("$('.export-to-svg:eq(0)').click()")
281
+ wait_for_download
282
+ expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
283
+
284
+ clear_downloads
285
+ # Click on the PNG download button of the first hit available and compare
286
+ # the downloaded content.
287
+
288
+ page.execute_script("$('.export-to-png:eq(2)').click()")
289
+ wait_for_download
290
+ expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1528997474_gb_MH447967_1.png')
291
+
292
+ clear_downloads
293
+
294
+ # Click on the SVG download button of the first hit available and compare
295
+ # the downloaded content.
296
+
297
+ page.execute_script("$('.export-to-svg:eq(2)').click()")
298
+ wait_for_download
299
+ expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1528997474_gb_MH447967_1.svg')
300
+ page.should have_content('BLASTN')
36
301
  end
37
302
 
38
- it 'loads TBLASTN xml output' do
303
+ it 'loads BLASTN XML and tests Circos download' do
304
+ access_by_uuid('blast_2.2.30/blastn')
305
+ # Click on the Circos expanding button, wait for animation, click on the
306
+ # download of PNG/SVG file and test that it initiated a file download in a
307
+ # right format.
308
+
309
+ page.should have_content('Chord diagram: queries and their top hits')
310
+ page.execute_script("$('.circos > .grapher-header > h5').click()")
311
+ sleep 1
312
+
313
+ page.execute_script("$('.export-to-png:eq(0)').click()")
314
+ wait_for_download
315
+ expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
316
+ clear_downloads
317
+
318
+ page.execute_script("$('.export-to-svg:eq(0)').click()")
319
+ wait_for_download
320
+ expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
321
+ end
322
+
323
+ it 'loads BLASTN XML and tests Length distribution download' do
324
+ access_by_uuid('blast_2.2.30/blastn')
325
+ # Click on the Length distribution expanding button, wait for animation,
326
+ # click on the download of PNG/SVG file and test that it initiated a file
327
+ # download in a right format.
328
+
329
+ page.should have_content('Length distribution of hits')
330
+ page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
331
+ sleep 1
332
+
333
+ page.execute_script("$('.export-to-png:eq(1)').click()")
334
+ wait_for_download
335
+ expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
336
+ clear_downloads
337
+
338
+ page.execute_script("$('.export-to-svg:eq(1)').click()")
339
+ wait_for_download
340
+ expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
341
+ end
342
+
343
+ # TBLASTN Test scenarios
344
+
345
+ it 'loads TBLASTN XML and tests hit alignment and sidebar Alignment download' do
39
346
  access_by_uuid('blast_2.2.30/tblastn')
347
+
348
+ # Click on the first Alignment download button on the page and wait for the
349
+ # download to finish.
350
+
351
+ page.execute_script("$('.download-aln:eq(0)').click()")
352
+ wait_for_download
353
+ expect(File.basename(downloaded_file)).to eq('sp_P04637_P53_HUMAN_gi_1484127324_gb_MG595988_1.txt')
354
+ expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/sp_P04637_P53_HUMAN_gi_1484127324_gb_MG595988_1.txt'))
355
+
356
+ clear_downloads
357
+
358
+ # Click on the Alignment of all hits download and compare the downloaded
359
+ # content
360
+
361
+ page.click_link('Alignment of all hits')
362
+ wait_for_download
363
+ expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
364
+ expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_tblastn_2.2.30.txt'))
365
+
366
+ clear_downloads
367
+
368
+ # Select four hit checkboxes and click on the Alignment of selected hits.
369
+ # Compare the downloaded content.
370
+ page.check('Query_1_hit_7_checkbox')
371
+ page.check('Query_1_hit_8_checkbox')
372
+ page.check('Query_2_hit_7_checkbox')
373
+ page.check('Query_2_hit_8_checkbox')
374
+ page.click_link('Alignment of 4 selected hit(s)')
375
+ wait_for_download
376
+
377
+ expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
378
+ expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_tblastn_2.2.30.txt'))
379
+ page.should have_content('TBLASTN')
40
380
  end
41
381
 
42
- it 'loads TBLASTX xml output' do
382
+ it 'loads TBLASTN XML and tests alignment overview and hit PNG/SVG download' do
383
+ access_by_uuid('blast_2.2.30/tblastn')
384
+
385
+ # Click on the PNG/SVG download button of the alignment overview and compare
386
+ # the downloaded content.
387
+
388
+ page.execute_script("$('.export-to-png:eq(0)').click()")
389
+ wait_for_download
390
+ expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.png')
391
+
392
+ clear_downloads
393
+
394
+ page.execute_script("$('.export-to-svg:eq(0)').click()")
395
+ wait_for_download
396
+ expect(File.basename(downloaded_file)).to eq('Alignment-Overview-sp_P04637_P53_HUMAN.svg')
397
+
398
+ clear_downloads
399
+
400
+ # Click on the PNG download button of the first hit available and compare
401
+ # the downloaded content.
402
+
403
+ page.execute_script("$('.export-to-png:eq(1)').click()")
404
+ wait_for_download
405
+ expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_1484127324_gb_MG595988_1.png')
406
+
407
+ clear_downloads
408
+
409
+ # Click on the SVG download button of the first hit available and compare
410
+ # the downloaded content.
411
+
412
+ page.execute_script("$('.export-to-svg:eq(1)').click()")
413
+ wait_for_download
414
+ expect(File.basename(downloaded_file)).to eq('Kablammo-sp_P04637_P53_HUMAN-gi_1484127324_gb_MG595988_1.svg')
415
+ page.should have_content('TBLASTN')
416
+ end
417
+
418
+ it 'loads TBLASTN XML and tests Circos download' do
419
+ access_by_uuid('blast_2.2.30/tblastn')
420
+ # Click on the Circos expanding button, wait for animation, click on the
421
+ # download of PNG/SVG file and test that it initiated a file download in a
422
+ # right format.
423
+
424
+ page.should have_content('Chord diagram: queries and their top hits')
425
+ page.execute_script("$('.circos > .grapher-header > h5').click()")
426
+ sleep 1
427
+
428
+ page.execute_script("$('.export-to-png:eq(0)').click()")
429
+ wait_for_download
430
+ expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
431
+
432
+ clear_downloads
433
+
434
+ page.execute_script("$('.export-to-svg:eq(0)').click()")
435
+ wait_for_download
436
+ expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
437
+ end
438
+
439
+ it 'loads TBLASTN XML and tests Length distribution download' do
440
+ access_by_uuid('blast_2.2.30/tblastn')
441
+ # Click on the Length distribution expanding button, wait for animation,
442
+ # click on the download of PNG/SVG file and test that it initiated a file
443
+ # download in a right format.
444
+
445
+ page.should have_content('Length distribution of hits')
446
+ page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
447
+ sleep 1
448
+
449
+ page.execute_script("$('.export-to-png:eq(1)').click()")
450
+ wait_for_download
451
+ expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.png')
452
+
453
+ clear_downloads
454
+
455
+ page.execute_script("$('.export-to-svg:eq(1)').click()")
456
+ wait_for_download
457
+ expect(File.basename(downloaded_file)).to eq('length-distribution-sp_P04637_P53_HUMAN.svg')
458
+ end
459
+
460
+ # TBLASTX Test scenarios
461
+
462
+ it 'loads TBLASTX XML and tests hit alignment and sidebar Alignment download' do
463
+ access_by_uuid('blast_2.2.30/tblastx')
464
+ # Click on the first Alignment download button on the page and wait for the
465
+ # download to finish.
466
+
467
+ page.execute_script("$('.download-aln:eq(1)').click()")
468
+ wait_for_download
469
+ expect(File.basename(downloaded_file)).to eq('MH011443_1_gi_1528997474_gb_MH447967_1.txt')
470
+ expect(File.read(downloaded_file)). to eq(File.read('spec/sequences/MH011443_1_gi_1528997474_gb_MH447967_1.txt'))
471
+
472
+ clear_downloads
473
+
474
+ # Click on the Alignment of all hits download and compare the downloaded
475
+ # content
476
+
477
+ page.click_link('Alignment of all hits')
478
+ wait_for_download
479
+ expect(File.basename(downloaded_file)).to eq('alignment-40_hits.txt')
480
+ expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-40_hits_tblastx.txt'))
481
+
482
+ clear_downloads
483
+
484
+ # Select four hit checkboxes and click on the Alignment of selected hits.
485
+ # Compare the downloaded content.
486
+ page.check('Query_1_hit_9_checkbox')
487
+ page.check('Query_1_hit_10_checkbox')
488
+ page.check('Query_2_hit_9_checkbox')
489
+ page.check('Query_2_hit_10_checkbox')
490
+ page.click_link('Alignment of 4 selected hit(s)')
491
+ wait_for_download
492
+
493
+ expect(File.basename(downloaded_file)).to eq('alignment-4_hits.txt')
494
+ expect(File.read(downloaded_file)).to eq(File.read('spec/sequences/alignment-4_hits_tblastx.txt'))
495
+ page.should have_content('TBLASTX')
496
+ end
497
+
498
+ it 'loads TBLASTX XML and tests hit PNG/SVG download' do
499
+ access_by_uuid('blast_2.2.30/tblastx')
500
+
501
+ # Click on the PNG/SVG download button of the alignment overview and compare
502
+ # the downloaded content.
503
+ page.execute_script("$('.export-to-png:eq(0)').click()")
504
+ wait_for_download
505
+ expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.png')
506
+
507
+ clear_downloads
508
+
509
+ page.execute_script("$('.export-to-svg:eq(0)').click()")
510
+ wait_for_download
511
+ expect(File.basename(downloaded_file)).to eq('Alignment-Overview-MH011443_1.svg')
512
+
513
+ clear_downloads
514
+
515
+ # Click on the PNG download button of the first hit available and compare
516
+ # the downloaded content.
517
+
518
+ page.execute_script("$('.export-to-png:eq(1)').click()")
519
+ wait_for_download
520
+ expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783306_gb_MH011443_1.png')
521
+
522
+ clear_downloads
523
+
524
+ # Click on the SVG download button of the first hit available and compare
525
+ # the downloaded content.
526
+
527
+ page.execute_script("$('.export-to-svg:eq(1)').click()")
528
+ wait_for_download
529
+ expect(File.basename(downloaded_file)).to eq('Kablammo-MH011443_1-gi_1486783306_gb_MH011443_1.svg')
530
+ page.should have_content('TBLASTX')
531
+ end
532
+
533
+ it 'loads TBLASTX XML and tests Circos download' do
534
+ access_by_uuid('blast_2.2.30/tblastx')
535
+ # Click on the Circos expanding button, wait for animation, click on the
536
+ # download of PNG/SVG file and test that it initiated a file download in a
537
+ # right format.
538
+
539
+ page.should have_content('Chord diagram: queries and their top hits')
540
+ page.execute_script("$('.circos > .grapher-header > h5').click()")
541
+ sleep 1
542
+
543
+ page.execute_script("$('.export-to-png:eq(0)').click()")
544
+ wait_for_download
545
+ expect(File.basename(downloaded_file)).to eq('Circos-visualisation.png')
546
+
547
+ clear_downloads
548
+
549
+ page.execute_script("$('.export-to-svg:eq(0)').click()")
550
+ wait_for_download
551
+ expect(File.basename(downloaded_file)).to eq('Circos-visualisation.svg')
552
+ end
553
+
554
+ it 'loads TBLASTX XML and tests Length distribution download' do
43
555
  access_by_uuid('blast_2.2.30/tblastx')
556
+ # Click on the Length distribution expanding button, wait for animation,
557
+ # click on the download of PNG/SVG file and test that it initiated a file
558
+ # download in a right format.
559
+
560
+ page.should have_content('Length distribution of hits')
561
+ page.execute_script("$('.length-distribution > .grapher-header > h5').click()")
562
+ sleep 1
563
+
564
+ page.execute_script("$('.export-to-png:eq(1)').click()")
565
+ wait_for_download
566
+ expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.png')
567
+
568
+ clear_downloads
569
+
570
+ page.execute_script("$('.export-to-svg:eq(1)').click()")
571
+ wait_for_download
572
+ expect(File.basename(downloaded_file)).to eq('length-distribution-MH011443_1.svg')
44
573
  end
45
574
 
46
575
  ## Helpers ##
47
576
 
48
577
  def access_by_uuid(id)
578
+ # Method to access the XML report in the browser
49
579
  url = url_encode(id)
50
580
  visit "/#{url}"
51
581
  page.should have_content('Query')