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/css/sequenceserver.min.css CHANGED
@@ -1,8 +1,8 @@
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.q25-32{fill:var(--z)}svg .RdYlBu .q26-32{fill:var(--aa)}svg .RdYlBu .q27-32{fill:var(--ab)}svg .RdYlBu .q28-32{fill:var(--ac)}svg .RdYlBu .q29-32{fill:var(--ad)}svg .RdYlBu .q30-32{fill:var(--ae)}svg .RdYlBu .q31-32{fill:var(--af)}@font-face{font-family:'Source Sans Pro';font-style:normal;font-weight:400;src:local('Source Sans Pro'),local('SourceSansPro-Regular'),url(../fonts/Source_Sans_Pro_400.woff2) format('woff2'),url(../fonts/Source_Sans_Pro_400.woff) format('woff'),url(../fonts/Source_Sans_Pro_400.ttf) format('truetype'),url(../fonts/Source_Sans_Pro_400.svg) format('svg'),url(../fonts/Source_Sans_Pro_400.eot) format('embedded-opentype')}@font-face{font-family:'Source Sans Pro';font-style:normal;font-weight:700;src:local('Source Sans Pro Bold'),local('SourceSansPro-Bold'),url(../fonts/Source_Sans_Pro_700.woff2) format('woff2'),url(../fonts/Source_Sans_Pro_700.woff) format('woff'),url(../fonts/Source_Sans_Pro_700.ttf) format('truetype'),url(../fonts/Source_Sans_Pro_700.svg) format('svg'),url(../fonts/Source_Sans_Pro_700.eot) format('embedded-opentype')}body{font-family:"Source Sans Pro","Helvetica Neue",Helvetica,Arial,sans-serif;position:relative;color:#000}.btn-link:hover,a:hover{text-decoration:none}textarea{resize:vertical;min-height:214px}label{cursor:pointer;font-weight:400}small{color:inherit!important}.disabled{color:#ccc}.btn-link[disabled]:hover,a.disabled:hover{color:#ccc;cursor:not-allowed}#methods li,.cursor-pointer,.hit h4{cursor:pointer}.navbar{border-radius:0;border-bottom:1px solid #eee}.navbar-brand{height:auto;padding:20px 15px;font-size:32px;color:#333}.navbar-brand>small{font-size:50%}.navbar-nav>li>a{padding:24px 15px;font-size:14px;color:#333}.section-header{border-bottom:1px solid #ddd;padding-bottom:5px;display:table;width:100%}.section-header>*{display:table-cell}.section-header>:first-child{width:100%}.section-content{padding:5px 0 0}.panel{border:none;-webkit-box-shadow:none;-moz-box-shadow:none;box-shadow:none}.panel 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pre:hover{background-color:#FFC}label[for=advanced]{font-size:16px;display:table-cell;width:1%;white-space:nowrap;vertical-align:middle;padding:5px 12px 5px 0}input[name=advanced]{border-top-left-radius:4px!important;border-bottom-left-radius:4px!important}input[type=checkbox]{vertical-align:top}#method{letter-spacing:1px}#methods li{text-align:center;padding-top:4px;padding-bottom:4px;letter-spacing:1px}.dropdown-menu li{border-bottom:1px solid #ccc}.dropdown-menu li:last-child{border-bottom:0}.sidebar>div{margin-top:20px}.sidebar h4{font-size:14px}.sidebar li a{padding:7px 10px}.sidebar.affix{margin-top:0;top:0}@media (min-width:992px){.sidebar.affix{width:212.5px}}@media (min-width:1200px){.sidebar.affix{width:262.5px}}.overview{margin:20px 0}.resultn{margin-bottom:25px}.graphical-overview{font-size:12px;text-align:center}.graphical-overview .btn{padding-top:0;padding-bottom:0}.tabular-view{margin-top:14px;margin-left:6px;margin-bottom:14px}.hit{padding-top:14px;margin-top:4px}.hit:first-child{padding-top:0}.hit h4 span{cursor:text}.hit>p{margin-top:0;margin-bottom:0}.hsps{padding:0 0 10px 10px}.hsp{padding-bottom:14px}.hsp:last-child{padding-bottom:0}.hsp-stats{font-size:12px}.hsp .hsp-lines{margin-top:5px;font-size:10px;letter-spacing:1.2px}.hsp .hsp-coords{color:#6e6e6e}.hit-links *{padding-left:3px;letter-spacing:1px;vertical-align:baseline}.btn-link{border:none;padding:0;letter-spacing:1px}.fastan>.section-header{padding-bottom:8px}.fastan>.section-content{padding-top:8px;padding-left:0}.footer a:first-child{vertical-align:super}.dnd-overlay{position:absolute;top:51px;left:0;right:0;bottom:0;z-index:1000;background-color:rgba(255,255,255,.75)}.dnd-overlay *{pointer-events:none}.dnd-overlay-container{padding-top:72px}.dnd-overlay-container p{font-size:48px}.glow{border-left:2px solid #f0ad4e}.downloads a{cursor:pointer}
data/public/js/circos.js CHANGED
@@ -4,524 +4,548 @@ import circosJs from 'nicgirault/circosJs';
4
4
 
5
5
  import Grapher from './grapher';
6
6
  import * as Helpers from './visualisation_helpers';
7
+ import Utils from './utils';
7
8
 
8
9
  class Graph {
9
- static name() {
10
- return 'Circos';
11
- }
12
-
13
- static className() {
14
- return 'circos';
15
- }
16
-
17
- static collapseId(props) {
18
- return 'circos-collapse';
19
- }
20
-
21
- static dataName(props) {
22
- return 'Circos-visualisation';
23
- }
24
-
25
- constructor($svgContainer, props) {
26
- this.queries = props.queries;
27
- this.svgContainer = $svgContainer;
28
- this.seq_type = Helpers.get_seq_type(props.program);
29
- this.initiate();
30
- }
31
-
32
- initiate() {
33
- // this.width = 700;
34
- this.width = this.svgContainer.width();
35
- this.height = 600;
36
- this.innerRadius = 200;
37
- this.outerRadius = 230;
38
- this.query_arr = [];
39
- this.hit_arr = [];
40
- this.layout_arr = [];
41
- this.chords_arr = [];
42
- // this.max_length = 0;
43
- this.hsp_count = 50;
44
- this.denominator = 100;
45
- this.spacing = 20;
46
- this.labelSpacing = 10;
47
- var suffixes = {amino_acid: 'aa', nucleic_acid: 'bp'};
48
- this.construct_layout();
49
- this.iterator_for_edits();
50
- this.hit_arr = _.uniq(this.hit_arr);
51
- this.handle_spacing();
52
- var prefix = d3.formatPrefix(this.max_length);
53
- this.suffix = ' '+prefix.symbol+suffixes[this.seq_type.subject_seq_type];
54
- if (prefix.symbol == 'k') {
55
- this.denominator = 1000;
56
- } else if (prefix.symbol == 'M') {
57
- this.denominator = 1000000;
58
- this.spacing = 1000000;
59
- this.labelSpacing = 200000;
60
- } else if (prefix.symbol == 'g') {
61
- this.denominator = 1000000000;
10
+ static name() {
11
+ return 'Chord diagram: queries and their top hits';
62
12
  }
63
- d3.select(this.svgContainer[0]).insert('svg',':first-child')
64
- .attr('class','circosContainer');
65
- this.create_instance(this.svgContainer, this.width, this.height);
66
- if (this.chords_arr.length && this.layout_arr.length) {
67
- this.instance_render();
68
- } else {
69
- this.render_error();
13
+
14
+ static className() {
15
+ return 'circos';
70
16
  }
71
- this.setupTooltip();
72
- // this.drawLegend();
73
- }
74
17
 
75
- iterator_for_edits() {
76
- this.max_length = this.calculate_max_length();
77
- if (this.hit_arr.length > 10) {
78
- this.complex_layout_edits();
18
+ static collapseId(props) {
19
+ return 'circos-collapse';
79
20
  }
80
- }
81
-
82
- // Generate both layout_arr and chords_arr with top hsps set by this.hsp_count
83
- construct_layout() {
84
- var hsp_count = 0;
85
- var query_count = 0;
86
- var num_karyotype = 32;
87
- var num_queries = this.queries.length;
88
- var x = Math.min(num_karyotype / 2, num_queries);
89
- var num_hits = (num_karyotype - x) / x;
90
- this.new_layout = [];
91
- this.data = _.map(this.queries, _.bind(function (query) {
92
- if (query_count < x) {
93
- var label = query.id;
94
- var len = query.length;
95
- var item1 = {'len': len, 'color': '#8dd3c7', 'label': label, 'id': 'Query_'+this.clean_id(query.id), 'ori_id': label};
96
- this.layout_arr.push(item1);
97
- var hit_details = _.map(query.hits, _.bind(function(hit) {
98
- if (hit.number < num_hits) {
99
- var hsp_details = _.map(hit.hsps, _.bind(function (hsp) {
100
-
101
- if (_.indexOf(this.hit_arr, hit.id) == -1) {
102
- var label = hit.id;
103
- var len = hit.length;
104
- this.hit_arr.push(hit.id);
105
- var item2 = {'len': len, 'color': '#80b1d3', 'label': label, 'id': 'Hit_'+this.clean_id(hit.id), 'ori_id': label};
106
- this.layout_arr.push(item2);
107
- }
108
-
109
- var item3 = ['Query_'+this.clean_id(query.id), hsp.qstart, hsp.qend, 'Hit_'+this.clean_id(hit.id), hsp.sstart, hsp.send, hit.number, hsp];
110
- this.chords_arr.push(item3);
111
- return hsp;
112
- }, this));
113
- return hit;
114
- }
115
- }, this));
116
- }
117
- this.query_arr.push(query.id);
118
- return query;
119
- }, this));
120
- }
121
-
122
- // rearraging hit and query karyotypes to have all query in one place
123
- rearrange_new_layout() {
124
- _.each(this.new_layout, _.bind(function(obj) {
125
- var id = (obj.id).slice(0,3);
126
- if (id == 'Que') {
127
- this.layout_arr.push(obj);
128
- }
129
- }, this));
130
- _.each(this.new_layout, _.bind(function(obj) {
131
- var id = (obj.id).slice(0,3);
132
- if (id == 'Hit') {
133
- this.layout_arr.push(obj);
134
- }
135
- }, this));
136
- }
137
-
138
- // label edits along with deleting hits which are too small to display
139
- complex_layout_edits() {
140
- this.delete_from_layout = [];
141
- this.delete_from_chords = [];
142
- _.each(this.layout_arr, _.bind(function (obj, index) {
143
- var rel_length = (obj.len / this.max_length).toFixed(3);
144
- var label = obj.label;
145
- if (rel_length < 0.1 && (obj.id).slice(0,3) != 'Que') {
146
- this.delete_from_layout.push(obj);
147
- this.hit_arr.slice(_.indexOf(this.hit_arr, obj.label), 1); // corresponding delete from hit_arr
148
- }
149
- }, this));
150
- }
151
-
152
- // get the chords_arr index based on hit or query id
153
- check_in_chords_arr(id, type, index) {
154
- var count = 0;
155
- _.each(this.chords_arr, _.bind(function (obj) {
156
- if (type == 'Que') {
157
- if (obj[0] != id) {
158
- count++
159
- }
160
- }
161
- }, this))
162
- if (count == this.chords_arr.length) {
163
- console.log('no record found '+id);
164
- this.delete_arr.push(index);
21
+
22
+ static dataName(props) {
23
+ return 'Circos-visualisation';
24
+ }
25
+
26
+ constructor($svgContainer, props) {
27
+ this.queries = [];
28
+ props.queries.forEach(query => {
29
+ if (query.hits.length > 0) {
30
+ this.queries.push(query);
31
+ }
32
+ });
33
+ this.svgContainer = $svgContainer;
34
+ this.seq_type = Helpers.get_seq_type(props.program);
35
+ this.algorithm = props.program;
36
+ this.initiate();
165
37
  }
166
- }
167
-
168
- // get index of hit_arr based on id
169
- find_index_of_hit(id) {
170
- var found;
171
- _.each(this.queries, _.bind(function (query) {
172
- _.each(query.hits, _.bind(function(hit) {
173
- var check_id = 'Hit_'+this.clean_id(hit.id)
174
- if (id == check_id) {
175
- found = hit.id;
38
+
39
+ initiate() {
40
+ // this.width = 700;
41
+ this.width = this.svgContainer.width();
42
+ this.height = 600;
43
+ this.innerRadius = 200;
44
+ this.outerRadius = 230;
45
+ this.query_arr = [];
46
+ this.hit_arr = [];
47
+ this.layout_arr = [];
48
+ this.chords_arr = [];
49
+ // this.max_length = 0;
50
+ this.hsp_count = 50;
51
+ this.denominator = 1;
52
+ this.spacing = 20;
53
+ this.labelSpacing = 10;
54
+ var suffixes = {amino_acid: 'aa', nucleic_acid: 'bp'};
55
+ this.construct_layout();
56
+ this.iterator_for_edits();
57
+ this.hit_arr = _.uniq(this.hit_arr);
58
+ this.handle_spacing();
59
+ var prefix = d3.formatPrefix(this.max_length);
60
+ this.suffix = ' '+prefix.symbol+suffixes[this.seq_type.subject_seq_type];
61
+ if (prefix.symbol == 'k') {
62
+ this.denominator = 1000;
63
+ } else if (prefix.symbol == 'M') {
64
+ this.denominator = 1000000;
65
+ this.spacing = 1000000;
66
+ this.labelSpacing = 200000;
67
+ } else if (prefix.symbol == 'g') {
68
+ this.denominator = 1000000000;
176
69
  }
177
- }, this))
178
- }, this));
179
- return _.indexOf(this.layout_arr, found);
180
- }
181
-
182
- edit_labels() {
183
- console.log('label edits');
184
- _.each(this.layout_arr, _.bind(function (obj) {
185
- var rel_length = (obj.len / this.max_length).toFixed(3);
186
- var label = obj.label;
187
- if (rel_length < 0.41) {
188
- obj.label = '..';
189
- } else if (label.length > 10) {
190
- obj.label = label.slice(0,2) + '...';
191
- } else {
192
- obj.label = obj.ori_id;
193
- }
194
- }, this));
195
- }
196
-
197
- calculate_multipliers() {
198
- var sum_query_length = 0;
199
- var sum_hit_length = 0;
200
- _.each(this.query_arr, _.bind(function (id) {
201
- _.each(this.data, _.bind(function (query) {
202
- if (id == query.id) {
203
- sum_query_length += query.length;
70
+ d3.select(this.svgContainer[0]).insert('svg',':first-child')
71
+ .attr('class','circosContainer');
72
+ this.create_instance(this.svgContainer, this.width, this.height);
73
+ if (this.chords_arr.length && this.layout_arr.length) {
74
+ this.instance_render();
75
+ } else {
76
+ this.render_error();
204
77
  }
205
- }, this));
206
- }, this));
207
-
208
- _.each(this.data, _.bind(function (query) {
209
- _.each(query.hits, _.bind(function (hit) {
210
- var index = _.indexOf(this.hit_arr, hit.id);
211
- if (index >= 0) {
212
- sum_hit_length += hit.length;
78
+ this.setupTooltip();
79
+ // this.drawLegend();
80
+ }
81
+
82
+ iterator_for_edits() {
83
+ this.max_length = this.calculate_max_length();
84
+ if (this.hit_arr.length > 10) {
85
+ this.complex_layout_edits();
213
86
  }
214
- }, this));
215
- }, this));
216
- var mid_sum = (sum_query_length + sum_hit_length) / 2;
217
- console.log('mid sum '+mid_sum+' hit_sum '+sum_hit_length+' query_sum '+sum_query_length);
218
- this.query_multiplier = (mid_sum / sum_query_length).toFixed(3);
219
- this.hit_multiplier = (mid_sum / sum_hit_length).toFixed(3);
220
- console.log('query '+this.query_multiplier+' hit '+this.hit_multiplier);
221
- }
222
-
223
- handle_spacing() {
224
- if (this.max_length > 16000) {
225
- this.spacing = 200;
226
- } else if (this.max_length > 12000) {
227
- this.spacing = 150;
228
- } else if (this.max_length > 8000) {
229
- this.spacing = 100;
230
- } else if (this.max_length > 4000) {
231
- this.spacing = 75;
232
- } else if (this.max_length > 1800) {
233
- this.spacing = 50;
234
87
  }
235
- }
236
-
237
- calculate_max_length() {
238
- var max = 0;
239
- _.each(this.layout_arr, function(obj) {
240
- if (max < obj.len) {
241
- max = obj.len;
242
- }
243
- })
244
- return max;
245
- }
246
-
247
- clean_id(id) {
248
- return id.replace(/[^a-zA-Z0-9]/g, '');
249
- }
250
-
251
- create_instance(container, width, height) {
252
- this.instance = new circosJs({
253
- container: '.circosContainer',
254
- width: width,
255
- height: height
256
- });
257
- this.chord_layout();
258
- this.instance_layout();
259
- }
260
-
261
- chord_layout() {
262
- if (this.chords_arr.length > 32) {
263
- this.paletteSize = 32;
264
- } else {
265
- this.paletteSize = this.chords_arr.length;
88
+
89
+ // Generate both layout_arr and chords_arr with top hsps set by this.hsp_count
90
+ construct_layout() {
91
+ var hsp_count = 0;
92
+ var query_count = 0;
93
+ var num_karyotype = 32;
94
+ var num_queries = this.queries.length;
95
+ var x = Math.min(num_karyotype / 2, num_queries);
96
+ var num_hits = (num_karyotype - x) / x;
97
+ this.new_layout = [];
98
+ this.data = _.map(this.queries, _.bind(function (query) {
99
+ if (query_count < x) {
100
+ var label = query.id;
101
+ var len = query.length;
102
+ var item1 = {'len': len, 'color': '#8dd3c7', 'label': label, 'id': 'Query_'+this.clean_id(query.id), 'ori_id': label};
103
+ this.layout_arr.push(item1);
104
+ var hit_details = _.map(query.hits, _.bind(function(hit) {
105
+ if (hit.number < num_hits) {
106
+ var hsp_details = _.map(hit.hsps, _.bind(function (hsp) {
107
+
108
+ if (_.indexOf(this.hit_arr, hit.id) == -1) {
109
+ var label = hit.id;
110
+ var len = hit.length;
111
+ this.hit_arr.push(hit.id);
112
+ var item2 = {'len': len, 'color': '#80b1d3', 'label': label, 'id': 'Hit_'+this.clean_id(hit.id), 'ori_id': label};
113
+ this.layout_arr.push(item2);
114
+ }
115
+
116
+ var item3 = ['Query_'+this.clean_id(query.id), hsp.qstart, hsp.qend, 'Hit_'+this.clean_id(hit.id), hsp.sstart, hsp.send, hit.number, hsp];
117
+ this.chords_arr.push(item3);
118
+ return hsp;
119
+ }, this));
120
+ return hit;
121
+ }
122
+ }, this));
123
+ }
124
+ this.query_arr.push(query.id);
125
+ return query;
126
+ }, this));
266
127
  }
267
- return {
268
- usePalette: true,
269
- colorPaletteSize: this.paletteSize,
270
- // color: 'rgb(0,0,0)',
271
- colorPalette: 'RdYlBu', // colors of chords based on last value in chords
272
- // tooltipContent: 'Hiten',
273
- opacity: 0.85 // add opacity to ribbons
128
+
129
+ // rearraging hit and query karyotypes to have all query in one place
130
+ rearrange_new_layout() {
131
+ _.each(this.new_layout, _.bind(function(obj) {
132
+ var id = (obj.id).slice(0,3);
133
+ if (id == 'Que') {
134
+ this.layout_arr.push(obj);
135
+ }
136
+ }, this));
137
+ _.each(this.new_layout, _.bind(function(obj) {
138
+ var id = (obj.id).slice(0,3);
139
+ if (id == 'Hit') {
140
+ this.layout_arr.push(obj);
141
+ }
142
+ }, this));
274
143
  }
275
- }
276
-
277
- instance_layout() {
278
- return {
279
- innerRadius: this.innerRadius,
280
- outerRadius: this.outerRadius,
281
- cornerRadius: 1, // rounding at edges of karyotypes
282
- labels: {
283
- display: true,
284
- size: '10px',
285
- radialOffset: 10
286
- },
287
- ticks: {
288
- display: true,
289
- spacing: this.spacing, // the ticks values to display
290
- labelSpacing: this.labelSpacing, // ticks value apper in interval
291
- labelDenominator: this.denominator, // divide the value by this value
292
- labelSuffix: this.suffix,
293
- labelSize: '10px',
294
- majorSpacing: this.labelSpacing, // major ticks apper in interval
295
- size: {
296
- minor: 0, // to remove minor ticks
297
- major: 4
144
+
145
+ // label edits along with deleting hits which are too small to display
146
+ complex_layout_edits() {
147
+ this.delete_from_layout = [];
148
+ this.delete_from_chords = [];
149
+ _.each(this.layout_arr, _.bind(function (obj, index) {
150
+ var rel_length = (obj.len / this.max_length).toFixed(3);
151
+ var label = obj.label;
152
+ if (rel_length < 0.1 && (obj.id).slice(0,3) != 'Que') {
153
+ this.delete_from_layout.push(obj);
154
+ this.hit_arr.slice(_.indexOf(this.hit_arr, obj.label), 1); // corresponding delete from hit_arr
155
+ }
156
+ }, this));
157
+ }
158
+
159
+ // get the chords_arr index based on hit or query id
160
+ check_in_chords_arr(id, type, index) {
161
+ var count = 0;
162
+ _.each(this.chords_arr, _.bind(function (obj) {
163
+ if (type == 'Que') {
164
+ if (obj[0] != id) {
165
+ count++;
166
+ }
167
+ }
168
+ }, this));
169
+ if (count == this.chords_arr.length) {
170
+ console.log('no record found '+id);
171
+ this.delete_arr.push(index);
298
172
  }
299
- }
300
173
  }
301
- }
302
-
303
- instance_render() {
304
- this.instance.layout(this.instance_layout(),this.layout_arr);
305
- this.instance.chord('chord1',this.chord_layout(),this.chords_arr);
306
- this.instance.render();
307
- }
308
-
309
- render_error() {
310
- this.svgContainer.find('svg').remove();
311
- this.svg = d3.select(this.svgContainer[0]).insert('svg',':first-child')
312
- .attr('width', this.svgContainer.width())
313
- .attr('height', this.svgContainer.height())
314
- .append('g')
315
- .attr('class', 'circos-error')
316
- .attr('transform','translate('+this.svgContainer.width() / 2+','+this.svgContainer.height()/2+')')
317
- .append('text')
318
- .attr('text-anchor','start')
319
- .attr('dy','-0.25em')
320
- .attr('x', -175)
321
- .style("font-size", "14px")
322
- .text('Circos looks great with less than 16 queries')
323
- }
324
-
325
- layoutReset() {
326
- this.layoutHide = [];
327
- _.each(this.layout_arr, function(obj) {
328
- $("."+obj.id).css("opacity", 1);
329
- });
330
- }
331
-
332
- chordsReset() {
333
- this.chordsHide = [];
334
- _.each(this.chords_arr, function (obj) {
335
- var slen = obj[1] + obj[2];
336
- var tlen = obj[4] + obj[5];
337
- $("#"+obj[0]+"_"+slen+"_"+obj[3]+"_"+tlen).show();
338
- });
339
- }
340
-
341
- chordsCheck(id, type) {
342
- _.each(this.chords_arr, _.bind(function (obj, index) {
343
- if (type == 'Que') {
344
- if (obj[0] == id) {
345
- this.chordsHide.push(index);
346
- this.layoutHide.push(obj[3]);
174
+
175
+ // get index of hit_arr based on id
176
+ find_index_of_hit(id) {
177
+ var found;
178
+ _.each(this.queries, _.bind(function (query) {
179
+ _.each(query.hits, _.bind(function(hit) {
180
+ var check_id = 'Hit_'+this.clean_id(hit.id);
181
+ if (id == check_id) {
182
+ found = hit.id;
183
+ }
184
+ }, this));
185
+ }, this));
186
+ return _.indexOf(this.layout_arr, found);
187
+ }
188
+
189
+ edit_labels() {
190
+ console.log('label edits');
191
+ _.each(this.layout_arr, _.bind(function (obj) {
192
+ var rel_length = (obj.len / this.max_length).toFixed(3);
193
+ var label = obj.label;
194
+ if (rel_length < 0.41) {
195
+ obj.label = '..';
196
+ } else if (label.length > 10) {
197
+ obj.label = label.slice(0,2) + '...';
198
+ } else {
199
+ obj.label = obj.ori_id;
200
+ }
201
+ }, this));
202
+ }
203
+
204
+ calculate_multipliers() {
205
+ var sum_query_length = 0;
206
+ var sum_hit_length = 0;
207
+ _.each(this.query_arr, _.bind(function (id) {
208
+ _.each(this.data, _.bind(function (query) {
209
+ if (id == query.id) {
210
+ sum_query_length += query.length;
211
+ }
212
+ }, this));
213
+ }, this));
214
+
215
+ _.each(this.data, _.bind(function (query) {
216
+ _.each(query.hits, _.bind(function (hit) {
217
+ var index = _.indexOf(this.hit_arr, hit.id);
218
+ if (index >= 0) {
219
+ sum_hit_length += hit.length;
220
+ }
221
+ }, this));
222
+ }, this));
223
+ var mid_sum = (sum_query_length + sum_hit_length) / 2;
224
+ console.log('mid sum '+mid_sum+' hit_sum '+sum_hit_length+' query_sum '+sum_query_length);
225
+ this.query_multiplier = (mid_sum / sum_query_length).toFixed(3);
226
+ this.hit_multiplier = (mid_sum / sum_hit_length).toFixed(3);
227
+ console.log('query '+this.query_multiplier+' hit '+this.hit_multiplier);
228
+ }
229
+
230
+ handle_spacing() {
231
+ if (this.max_length > 16000) {
232
+ this.spacing = 200;
233
+ } else if (this.max_length > 12000) {
234
+ this.spacing = 150;
235
+ } else if (this.max_length > 8000) {
236
+ this.spacing = 100;
237
+ } else if (this.max_length > 4000) {
238
+ this.spacing = 75;
239
+ } else if (this.max_length > 1800) {
240
+ this.spacing = 50;
347
241
  }
348
- }
349
- if (type == 'Hit') {
350
- if (obj[3] == id) {
351
- this.chordsHide.push(index);
352
- this.layoutHide.push(obj[0]);
242
+ }
243
+
244
+ calculate_max_length() {
245
+ var max = 0;
246
+ _.each(this.layout_arr, function(obj) {
247
+ if (max < obj.len) {
248
+ max = obj.len;
249
+ }
250
+ });
251
+ return max;
252
+ }
253
+
254
+ clean_id(id) {
255
+ return id.replace(/[^a-zA-Z0-9]/g, '');
256
+ }
257
+
258
+ create_instance(container, width, height) {
259
+ this.instance = new circosJs({
260
+ container: '.circosContainer',
261
+ width: width,
262
+ height: height
263
+ });
264
+ this.chord_layout();
265
+ this.instance_layout();
266
+ }
267
+
268
+ chord_layout() {
269
+ if (this.chords_arr.length > 32) {
270
+ this.paletteSize = 32;
271
+ } else {
272
+ this.paletteSize = this.chords_arr.length;
353
273
  }
354
- }
355
- }, this))
356
- }
357
-
358
- chordsClean() {
359
- _.each(this.chords_arr, _.bind(function (obj, index) {
360
- if (_.indexOf(this.chordsHide, index) == -1) {
361
- var slen = obj[1] + obj[2];
362
- var tlen = obj[4] + obj[5];
363
- $("#"+obj[0]+"_"+slen+"_"+obj[3]+"_"+tlen).hide();
364
- }
365
- }, this))
366
- }
367
-
368
- layoutClean() {
369
- _.each(this.layout_arr, _.bind(function(obj, index) {
370
- if(_.indexOf(this.layoutHide, obj.id) == -1) {
371
- $("."+obj.id).css("opacity",0.1);
372
- }
373
- }, this))
374
- }
375
-
376
- setupTooltip() {
377
- var selected = {};
378
- $('.circos-distribution').on('click', _.bind(function(event) {
379
- event.stopPropagation();
380
- this.layoutReset();
381
- this.chordsReset();
382
- selected = {};
383
- }, this));
384
- _.each(this.query_arr, _.bind(function (id, index) {
385
- this.chordsHide = [];
386
- this.layoutHide = [];
387
- if (id) {
388
- $(".circos-distribution .Query_"+this.clean_id(id)).attr('data-toggle','tooltip')
389
- .attr('title',id)
390
- .on('click', _.bind(function (event) {
391
- event.stopPropagation();
274
+ return {
275
+ usePalette: true,
276
+ colorPaletteSize: this.paletteSize,
277
+ // color: 'rgb(0,0,0)',
278
+ colorPalette: 'RdYlBu', // colors of chords based on last value in chords
279
+ // tooltipContent: 'Hiten',
280
+ opacity: 0.85 // add opacity to ribbons
281
+ };
282
+ }
283
+
284
+ instance_layout() {
285
+ return {
286
+ innerRadius: this.innerRadius,
287
+ outerRadius: this.outerRadius,
288
+ cornerRadius: 1, // rounding at edges of karyotypes
289
+ labels: {
290
+ display: true,
291
+ size: '10px',
292
+ radialOffset: 10
293
+ },
294
+ ticks: {
295
+ display: true,
296
+ spacing: this.spacing, // the ticks values to display
297
+ labelSpacing: this.labelSpacing, // ticks value apper in interval
298
+ labelDenominator: this.denominator, // divide the value by this value
299
+ labelSuffix: this.suffix,
300
+ labelSize: '10px',
301
+ majorSpacing: this.labelSpacing, // major ticks apper in interval
302
+ size: {
303
+ minor: 0, // to remove minor ticks
304
+ major: 4
305
+ }
306
+ }
307
+ };
308
+ }
309
+
310
+ instance_render() {
311
+ this.instance.layout(this.instance_layout(),this.layout_arr);
312
+ this.instance.chord('chord1',this.chord_layout(),this.chords_arr);
313
+ this.instance.render();
314
+ }
315
+
316
+ render_error() {
317
+ this.svgContainer.find('svg').remove();
318
+ this.svg = d3.select(this.svgContainer[0]).insert('svg',':first-child')
319
+ .attr('width', this.svgContainer.width())
320
+ .attr('height', this.svgContainer.height())
321
+ .append('g')
322
+ .attr('class', 'circos-error')
323
+ .attr('transform','translate('+this.svgContainer.width() / 2+','+this.svgContainer.height()/2+')')
324
+ .append('text')
325
+ .attr('text-anchor','start')
326
+ .attr('dy','-0.25em')
327
+ .attr('x', -175)
328
+ .style('font-size', '14px')
329
+ .text('Circos looks great with less than 16 queries');
330
+ }
331
+
332
+ layoutReset() {
333
+ this.layoutHide = [];
334
+ _.each(this.layout_arr, function(obj) {
335
+ $('.'+obj.id).css('opacity', 1);
336
+ });
337
+ }
338
+
339
+ chordsReset() {
340
+ this.chordsHide = [];
341
+ _.each(this.chords_arr, function (obj) {
342
+ var slen = obj[1] + obj[2];
343
+ var tlen = obj[4] + obj[5];
344
+ $('#'+obj[0]+'_'+slen+'_'+obj[3]+'_'+tlen).show();
345
+ });
346
+ }
347
+
348
+ chordsCheck(id, type) {
349
+ _.each(this.chords_arr, _.bind(function (obj, index) {
350
+ if (type == 'Que') {
351
+ if (obj[0] == id) {
352
+ this.chordsHide.push(index);
353
+ this.layoutHide.push(obj[3]);
354
+ }
355
+ }
356
+ if (type == 'Hit') {
357
+ if (obj[3] == id) {
358
+ this.chordsHide.push(index);
359
+ this.layoutHide.push(obj[0]);
360
+ }
361
+ }
362
+ }, this));
363
+ }
364
+
365
+ chordsClean() {
366
+ _.each(this.chords_arr, _.bind(function (obj, index) {
367
+ if (_.indexOf(this.chordsHide, index) == -1) {
368
+ var slen = obj[1] + obj[2];
369
+ var tlen = obj[4] + obj[5];
370
+ $('#'+obj[0]+'_'+slen+'_'+obj[3]+'_'+tlen).hide();
371
+ }
372
+ }, this));
373
+ }
374
+
375
+ layoutClean() {
376
+ _.each(this.layout_arr, _.bind(function(obj, index) {
377
+ if(_.indexOf(this.layoutHide, obj.id) == -1) {
378
+ $('.'+obj.id).css('opacity',0.1);
379
+ }
380
+ }, this));
381
+ }
382
+
383
+ setupTooltip() {
384
+ var selected = {};
385
+ $('.circos-distribution').on('click', _.bind(function(event) {
386
+ event.stopPropagation();
387
+ this.layoutReset();
388
+ this.chordsReset();
389
+ selected = {};
390
+ }, this));
391
+ _.each(this.query_arr, _.bind(function (id, index) {
392
+ this.chordsHide = [];
393
+ this.layoutHide = [];
394
+ if (id) {
395
+ $('.circos .Query_'+this.clean_id(id)).attr('data-toggle','tooltip')
396
+ .attr('title',id)
397
+ .on('click', _.bind(function (event) {
398
+ event.stopPropagation();
392
399
  if (selected[index] != id) {
393
- selected[index] = id;
394
- var cleaned_id = "Query_"+this.clean_id(id);
395
- this.layoutHide.push(cleaned_id);
396
- this.chordsCheck(cleaned_id, "Que");
397
- this.chordsClean();
398
- this.layoutClean();
400
+ selected[index] = id;
401
+ var cleaned_id = 'Query_' + this.clean_id(id);
402
+ this.layoutHide.push(cleaned_id);
403
+ this.chordsCheck(cleaned_id, 'Que');
404
+ this.chordsClean();
405
+ this.layoutClean();
399
406
  } else {
400
- selected[index] = 0;
401
- this.layoutReset();
402
- this.chordsReset();
407
+ selected[index] = 0;
408
+ this.layoutReset();
409
+ this.chordsReset();
403
410
  }
404
- }, this));
405
- }
406
- }, this))
407
- _.each(this.hit_arr, _.bind(function(id, index) {
408
- this.chordsHide = [];
409
- this.layoutHide = [];
410
- if (id) {
411
- $(".circos .Hit_"+this.clean_id(id)).attr('data-toggle','tooltip')
411
+ }, this));
412
+ }
413
+ }, this));
414
+ _.each(this.hit_arr, _.bind(function(id, index) {
415
+ this.chordsHide = [];
416
+ this.layoutHide = [];
417
+ if (id) {
418
+ $('.circos .Hit_'+this.clean_id(id)).attr('data-toggle','tooltip')
412
419
  .attr('title',id)
413
420
  .on('click', _.bind(function (event) {
414
421
  event.stopPropagation();
415
- if (selected[index] != id) {
416
- selected[index] = id;
417
- var cleaned_id = "Hit_"+this.clean_id(id);
418
- this.layoutHide.push(cleaned_id);
419
- this.chordsCheck(cleaned_id, "Hit");
420
- this.chordsClean();
421
- this.layoutClean();
422
- } else {
423
- selected[index] = 0;
424
- this.layoutReset();
425
- this.chordsReset();
426
- }
422
+ if (selected[index] != id) {
423
+ selected[index] = id;
424
+ var cleaned_id = 'Hit_' + this.clean_id(id);
425
+ this.layoutHide.push(cleaned_id);
426
+ this.chordsCheck(cleaned_id, 'Hit');
427
+ this.chordsClean();
428
+ this.layoutClean();
429
+ } else {
430
+ selected[index] = 0;
431
+ this.layoutReset();
432
+ this.chordsReset();
433
+ }
427
434
  }, this));
428
- }
429
- }, this));
430
- $('[data-toggle="tooltip"]').tooltip({
431
- 'placement': 'top',
432
- 'container': 'body',
433
- 'html': 'true',
434
- 'delay': 0,
435
- 'white-space': 'nowrap'
436
- });
437
- }
438
-
439
- ratioCalculate(value, min, max, scope, reverse, logScale) {
440
- var fraction, scaleLogBase, x;
441
- scaleLogBase = logScale ? 2.3 : 1;
442
- if (min === max || (value === min && !reverse) || (value === max && reverse)) {
443
- return 0;
444
- }
445
- if (value === max || (value === min && reverse)) {
446
- return scope - 1;
435
+ }
436
+ }, this));
437
+ var algorithm = this.algorithm;
438
+ _.each(this.chords_arr, function (obj) {
439
+ $('#' + obj[0] + '_' + obj[3])
440
+ .attr('data-toggle', 'tooltip')
441
+ .attr('title', function () {
442
+ // E value and identity.
443
+ var alt_tooltip = 'E value: ' + Helpers.prettify_evalue(obj[7].evalue) +
444
+ `, Identities: ${Utils.inPercentage(obj[7].identity, obj[7].length)}`;
445
+ // Positives (for protein alignment).
446
+ if (algorithm != 'blastn') {
447
+ alt_tooltip += `<br>Positives: ${Utils.inPercentage(obj[7].positives, obj[7].length)}`;
448
+ }
449
+ // Gaps. My understanding is that identities and gaps should add up to 100%.
450
+ alt_tooltip += `, Gaps: ${Utils.inPercentage(obj[7].gaps, obj[7].length)}`;
451
+ return alt_tooltip;
452
+ });
453
+ });
454
+ $('[data-toggle="tooltip"]').tooltip({
455
+ 'placement': 'top',
456
+ 'container': 'body',
457
+ 'html': 'true',
458
+ 'delay': 0,
459
+ 'white-space': 'nowrap'
460
+ });
447
461
  }
448
- fraction = (value - min) / (max - min);
449
- x = Math.exp(1 / scaleLogBase * Math.log(fraction));
450
- if (reverse) {
451
- x = 1 - x;
462
+
463
+ ratioCalculate(value, min, max, scope, reverse, logScale) {
464
+ var fraction, scaleLogBase, x;
465
+ scaleLogBase = logScale ? 2.3 : 1;
466
+ if (min === max || (value === min && !reverse) || (value === max && reverse)) {
467
+ return 0;
468
+ }
469
+ if (value === max || (value === min && reverse)) {
470
+ return scope - 1;
471
+ }
472
+ fraction = (value - min) / (max - min);
473
+ x = Math.exp(1 / scaleLogBase * Math.log(fraction));
474
+ if (reverse) {
475
+ x = 1 - x;
476
+ }
477
+ return Math.floor(scope * x);
452
478
  }
453
- return Math.floor(scope * x);
454
- }
455
-
456
- drawLegend() {
457
- this.ratioHSP = [];
458
- _.each(this.chords_arr, _.bind(function (obj) {
459
- var item = {number: obj[6], evalue: obj[7].evalue}
460
- this.ratioHSP.push(item);
461
- }, this));
462
- var min = d3.min(this.ratioHSP, function(d) {
463
- return d.number;
464
- });
465
- var max = d3.max(this.ratioHSP, function(d) {
466
- return d.number;
467
- });
468
- console.log('chords_arr '+this.chords_arr.length);
469
- console.log('ratioHSP test '+this.ratioHSP.length);
470
- console.log('paletteSize '+this.paletteSize);
471
- console.log('min '+min+' max '+max);
472
- this.legend = d3.select(this.svgContainer[0]).insert('svg', ':first-child')
473
- .attr('height', 20)
474
- .attr('width', this.ratioHSP.length * 30)
475
- .attr('transform','translate(10, 10)')
476
- .append('g')
477
- .attr('class','RdYlBu')
478
- .attr('transform','translate(10, 0)');
479
-
480
- var bar = this.legend.selectAll('.bar')
481
- .data(this.ratioHSP)
482
- .enter().append('g')
483
- .attr('class','g')
484
- .attr('transform', function(d, i) {
485
- return 'translate('+i * 30+',0)';
486
- })
487
- .append('rect')
488
- .attr('class',_.bind(function(d,i) {
489
- var s = this.ratioCalculate(d.number,min,max,this.paletteSize, false, false);
490
- console.log('calc ratio '+s);
491
- return 'q'+s+"-"+this.paletteSize;
492
- }, this))
493
- .attr('data-toggle','tooltip')
494
- .attr('title', function (d) {
495
- return d.evalue;
496
- })
497
- .attr('x', 1)
498
- .attr('width', 30)
499
- .attr('height', 20);
500
- // .attr('fill','#43ff21');
501
479
 
502
- var scale = d3.scale.linear()
503
- .domain([0, 250])
504
- .range([0, 100]);
480
+ drawLegend() {
481
+ this.ratioHSP = [];
482
+ _.each(this.chords_arr, _.bind(function (obj) {
483
+ var item = {number: obj[6], evalue: obj[7].evalue};
484
+ this.ratioHSP.push(item);
485
+ }, this));
486
+ var min = d3.min(this.ratioHSP, function(d) {
487
+ return d.number;
488
+ });
489
+ var max = d3.max(this.ratioHSP, function(d) {
490
+ return d.number;
491
+ });
492
+ console.log('chords_arr '+this.chords_arr.length);
493
+ console.log('ratioHSP test '+this.ratioHSP.length);
494
+ console.log('paletteSize '+this.paletteSize);
495
+ console.log('min '+min+' max '+max);
496
+ this.legend = d3.select(this.svgContainer[0]).insert('svg', ':first-child')
497
+ .attr('height', 20)
498
+ .attr('width', this.ratioHSP.length * 30)
499
+ .attr('transform','translate(10, 10)')
500
+ .append('g')
501
+ .attr('class','RdYlBu')
502
+ .attr('transform','translate(10, 0)');
503
+
504
+ var bar = this.legend.selectAll('.bar')
505
+ .data(this.ratioHSP)
506
+ .enter().append('g')
507
+ .attr('class','g')
508
+ .attr('transform', function(d, i) {
509
+ return 'translate('+i * 30+',0)';
510
+ })
511
+ .append('rect')
512
+ .attr('class',_.bind(function(d,i) {
513
+ var s = this.ratioCalculate(d.number,min,max,this.paletteSize, false, false);
514
+ console.log('calc ratio '+s);
515
+ return 'q'+s+'-'+this.paletteSize;
516
+ }, this))
517
+ .attr('data-toggle','tooltip')
518
+ .attr('title', function (d) {
519
+ return d.evalue;
520
+ })
521
+ .attr('x', 1)
522
+ .attr('width', 30)
523
+ .attr('height', 20);
524
+ // .attr('fill','#43ff21');
505
525
 
506
- // this.legend.append('rect')
507
- // .attr('x', 7*14)
508
- // .attr('width', 2*10)
509
- // .attr('height', 10)
510
- // .attr('fill','#43ff21');
511
- //
512
- // this.legend.append('text')
513
- // .attr('class','text-legend')
514
- // .attr('transform','translate('+10+',0)')
515
- // .attr('x',6*14)
516
- // .text('Weaker Hits');
517
- //
518
- // this.legend.append('text')
519
- // .attr('class','text-legend')
520
- // .attr('transform','translate('+10+',0)')
521
- // .attr('x',9*14)
522
- // .text('Stronger Hits');
523
-
524
- // bar.selectAll('rect')
526
+ var scale = d3.scale.linear()
527
+ .domain([0, 250])
528
+ .range([0, 100]);
529
+
530
+ // this.legend.append('rect')
531
+ // .attr('x', 7*14)
532
+ // .attr('width', 2*10)
533
+ // .attr('height', 10)
534
+ // .attr('fill','#43ff21');
535
+ //
536
+ // this.legend.append('text')
537
+ // .attr('class','text-legend')
538
+ // .attr('transform','translate('+10+',0)')
539
+ // .attr('x',6*14)
540
+ // .text('Weaker Hits');
541
+ //
542
+ // this.legend.append('text')
543
+ // .attr('class','text-legend')
544
+ // .attr('transform','translate('+10+',0)')
545
+ // .attr('x',9*14)
546
+ // .text('Stronger Hits');
547
+
548
+ // bar.selectAll('rect')
525
549
 
526
550
 
527
551
  // this.legend.append('rect')
@@ -529,7 +553,7 @@ class Graph {
529
553
  // .attr('width', 10)
530
554
  // .attr('height', 10)
531
555
  // .attr('fill','#232323');
532
- }
556
+ }
533
557
  }
534
558
 
535
559
  var Circos = Grapher(Graph);