protvista-uniprot 3.0.1 → 3.0.8

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (85) hide show
  1. package/README.md +20 -14
  2. package/dist/protvista-uniprot.mjs +368 -0
  3. package/dist/{protvista-uniprot.js.map → protvista-uniprot.mjs.map} +1 -1
  4. package/package.json +18 -10
  5. package/src/adapters/ptm-exchange-adapter.ts +1 -1
  6. package/src/config.json +0 -18
  7. package/src/tooltips/featureTooltip.ts +6 -6
  8. package/dist/es/__spec__/filter-config.spec.js +0 -123
  9. package/dist/es/__spec__/filter-config.spec.js.map +0 -1
  10. package/dist/es/adapters/__tests__/__mocks__/uniprotkb-entry-data.js +0 -75
  11. package/dist/es/adapters/__tests__/__mocks__/uniprotkb-entry-data.js.map +0 -1
  12. package/dist/es/adapters/__tests__/structure-adapter.spec.js +0 -14
  13. package/dist/es/adapters/__tests__/structure-adapter.spec.js.map +0 -1
  14. package/dist/es/adapters/alphafold-confidence-adapter.js +0 -26
  15. package/dist/es/adapters/alphafold-confidence-adapter.js.map +0 -1
  16. package/dist/es/adapters/alphamissense-heatmap-adapter.js +0 -36
  17. package/dist/es/adapters/alphamissense-heatmap-adapter.js.map +0 -1
  18. package/dist/es/adapters/alphamissense-pathogenicity-adapter.js +0 -68
  19. package/dist/es/adapters/alphamissense-pathogenicity-adapter.js.map +0 -1
  20. package/dist/es/adapters/config/evidence.js +0 -101
  21. package/dist/es/adapters/config/evidence.js.map +0 -1
  22. package/dist/es/adapters/feature-adapter.js +0 -18
  23. package/dist/es/adapters/feature-adapter.js.map +0 -1
  24. package/dist/es/adapters/interpro-adapter.js +0 -60
  25. package/dist/es/adapters/interpro-adapter.js.map +0 -1
  26. package/dist/es/adapters/proteomics-adapter.js +0 -66
  27. package/dist/es/adapters/proteomics-adapter.js.map +0 -1
  28. package/dist/es/adapters/ptm-exchange-adapter.js +0 -101
  29. package/dist/es/adapters/ptm-exchange-adapter.js.map +0 -1
  30. package/dist/es/adapters/structure-adapter.js +0 -89
  31. package/dist/es/adapters/structure-adapter.js.map +0 -1
  32. package/dist/es/adapters/types/alphafold.js +0 -2
  33. package/dist/es/adapters/types/alphafold.js.map +0 -1
  34. package/dist/es/adapters/variation-adapter.js +0 -31
  35. package/dist/es/adapters/variation-adapter.js.map +0 -1
  36. package/dist/es/adapters/variation-graph-adapter.js +0 -53
  37. package/dist/es/adapters/variation-graph-adapter.js.map +0 -1
  38. package/dist/es/config.json +0 -811
  39. package/dist/es/filter-config.js +0 -157
  40. package/dist/es/filter-config.js.map +0 -1
  41. package/dist/es/index.js +0 -8
  42. package/dist/es/index.js.map +0 -1
  43. package/dist/es/protvista-uniprot-structure.js +0 -379
  44. package/dist/es/protvista-uniprot-structure.js.map +0 -1
  45. package/dist/es/protvista-uniprot.js +0 -594
  46. package/dist/es/protvista-uniprot.js.map +0 -1
  47. package/dist/es/styles/loader-styles.js +0 -20
  48. package/dist/es/styles/loader-styles.js.map +0 -1
  49. package/dist/es/styles/protvista-styles.js +0 -89
  50. package/dist/es/styles/protvista-styles.js.map +0 -1
  51. package/dist/es/tooltips/featureTooltip.js +0 -160
  52. package/dist/es/tooltips/featureTooltip.js.map +0 -1
  53. package/dist/es/tooltips/structureTooltip.js +0 -15
  54. package/dist/es/tooltips/structureTooltip.js.map +0 -1
  55. package/dist/es/tooltips/variationTooltip.js +0 -82
  56. package/dist/es/tooltips/variationTooltip.js.map +0 -1
  57. package/dist/es/utils.js +0 -28
  58. package/dist/es/utils.js.map +0 -1
  59. package/dist/protvista-uniprot.js +0 -368
  60. /package/dist/{protvista-uniprot.js.LICENSE.txt → protvista-uniprot.mjs.LICENSE.txt} +0 -0
  61. /package/dist/{es → types}/__spec__/filter-config.spec.d.ts +0 -0
  62. /package/dist/{es → types}/adapters/__tests__/__mocks__/uniprotkb-entry-data.d.ts +0 -0
  63. /package/dist/{es → types}/adapters/__tests__/structure-adapter.spec.d.ts +0 -0
  64. /package/dist/{es → types}/adapters/alphafold-confidence-adapter.d.ts +0 -0
  65. /package/dist/{es → types}/adapters/alphamissense-heatmap-adapter.d.ts +0 -0
  66. /package/dist/{es → types}/adapters/alphamissense-pathogenicity-adapter.d.ts +0 -0
  67. /package/dist/{es → types}/adapters/config/evidence.d.ts +0 -0
  68. /package/dist/{es → types}/adapters/feature-adapter.d.ts +0 -0
  69. /package/dist/{es → types}/adapters/interpro-adapter.d.ts +0 -0
  70. /package/dist/{es → types}/adapters/proteomics-adapter.d.ts +0 -0
  71. /package/dist/{es → types}/adapters/ptm-exchange-adapter.d.ts +0 -0
  72. /package/dist/{es → types}/adapters/structure-adapter.d.ts +0 -0
  73. /package/dist/{es → types}/adapters/types/alphafold.d.ts +0 -0
  74. /package/dist/{es → types}/adapters/variation-adapter.d.ts +0 -0
  75. /package/dist/{es → types}/adapters/variation-graph-adapter.d.ts +0 -0
  76. /package/dist/{es → types}/filter-config.d.ts +0 -0
  77. /package/dist/{es → types}/index.d.ts +0 -0
  78. /package/dist/{es → types}/protvista-uniprot-structure.d.ts +0 -0
  79. /package/dist/{es → types}/protvista-uniprot.d.ts +0 -0
  80. /package/dist/{es → types}/styles/loader-styles.d.ts +0 -0
  81. /package/dist/{es → types}/styles/protvista-styles.d.ts +0 -0
  82. /package/dist/{es → types}/tooltips/featureTooltip.d.ts +0 -0
  83. /package/dist/{es → types}/tooltips/structureTooltip.d.ts +0 -0
  84. /package/dist/{es → types}/tooltips/variationTooltip.d.ts +0 -0
  85. /package/dist/{es → types}/utils.d.ts +0 -0
@@ -1,594 +0,0 @@
1
- var __decorate = (this && this.__decorate) || function (decorators, target, key, desc) {
2
- var c = arguments.length, r = c < 3 ? target : desc === null ? desc = Object.getOwnPropertyDescriptor(target, key) : desc, d;
3
- if (typeof Reflect === "object" && typeof Reflect.decorate === "function") r = Reflect.decorate(decorators, target, key, desc);
4
- else for (var i = decorators.length - 1; i >= 0; i--) if (d = decorators[i]) r = (c < 3 ? d(r) : c > 3 ? d(target, key, r) : d(target, key)) || r;
5
- return c > 3 && r && Object.defineProperty(target, key, r), r;
6
- };
7
- import { LitElement, html, svg } from 'lit';
8
- // eslint-disable-next-line @typescript-eslint/no-unused-vars
9
- import { customElement } from 'lit/decorators.js';
10
- import { unsafeHTML } from 'lit/directives/unsafe-html.js';
11
- import { frame } from 'timing-functions';
12
- // Nightingale
13
- import NightingaleManager from '@nightingale-elements/nightingale-manager';
14
- import NightingaleNavigation from '@nightingale-elements/nightingale-navigation';
15
- import NightingaleSequence from '@nightingale-elements/nightingale-sequence';
16
- import NightingaleColoredSequence from '@nightingale-elements/nightingale-colored-sequence';
17
- import NightingaleTrack from '@nightingale-elements/nightingale-track';
18
- import NightingaleInterproTrack from '@nightingale-elements/nightingale-interpro-track';
19
- import NightingaleVariation from '@nightingale-elements/nightingale-variation';
20
- import NightingaleLinegraphTrack from '@nightingale-elements/nightingale-linegraph-track';
21
- import NightingaleSequenceHeatmap from '@nightingale-elements/nightingale-sequence-heatmap';
22
- import NightingaleFilter from '@nightingale-elements/nightingale-filter';
23
- // adapters
24
- import featureAdapter from './adapters/feature-adapter';
25
- import proteomicsAdapter from './adapters/proteomics-adapter';
26
- import structureAdapter from './adapters/structure-adapter';
27
- import variationAdapter from './adapters/variation-adapter';
28
- import interproAdapter from './adapters/interpro-adapter';
29
- import variationGraphAdapter from './adapters/variation-graph-adapter';
30
- import proteomicsPTMApdapter from './adapters/ptm-exchange-adapter';
31
- import alphaFoldConfidenceAdapter from './adapters/alphafold-confidence-adapter';
32
- import alphaMissensePathogenicityAdapter from './adapters/alphamissense-pathogenicity-adapter';
33
- import alphaMissenseHeatmapAdapter from './adapters/alphamissense-heatmap-adapter';
34
- import ProtvistaUniprotStructure from './protvista-uniprot-structure';
35
- import { fetchAll, loadComponent } from './utils';
36
- import filterConfig, { colorConfig } from './filter-config';
37
- import defaultConfig from './config.json';
38
- import loaderIcon from './icons/spinner.svg';
39
- import protvistaStyles from './styles/protvista-styles';
40
- import loaderStyles from './styles/loader-styles';
41
- const adapters = {
42
- 'feature-adapter': featureAdapter,
43
- 'interpro-adapter': interproAdapter,
44
- 'proteomics-adapter': proteomicsAdapter,
45
- 'structure-adapter': structureAdapter,
46
- 'variation-adapter': variationAdapter,
47
- 'variation-graph-adapter': variationGraphAdapter,
48
- 'proteomics-ptm-adapter': proteomicsPTMApdapter,
49
- 'alphafold-confidence-adapter': alphaFoldConfidenceAdapter,
50
- 'alphamissense-pathogenicity-adapter': alphaMissensePathogenicityAdapter,
51
- 'alphamissense-heatmap-adapter': alphaMissenseHeatmapAdapter,
52
- };
53
- let ProtvistaUniprot = class ProtvistaUniprot extends LitElement {
54
- constructor() {
55
- super();
56
- this.displayCoordinates = {};
57
- this.openCategories = [];
58
- this.nostructure = false;
59
- this.hasData = false;
60
- this.loading = true;
61
- this.data = {};
62
- this.rawData = {};
63
- this.displayCoordinates = {};
64
- (this.transformedVariants = { sequence: '', variants: [] }),
65
- this.addStyles();
66
- }
67
- static get properties() {
68
- return {
69
- suspend: { type: Boolean, reflect: true },
70
- accession: { type: String, reflect: true },
71
- sequence: { type: String },
72
- data: { type: Object },
73
- openCategories: { type: Array },
74
- config: { type: Object },
75
- notooltip: { type: Boolean, reflect: true },
76
- nostructure: { type: Boolean, reflect: true },
77
- };
78
- }
79
- addStyles() {
80
- var _a;
81
- // We are not using static get styles()
82
- // as we are not using the shadowDOM
83
- // because of Mol*
84
- const styleTag = document.createElement('style');
85
- styleTag.innerHTML = `${protvistaStyles.toString()} ${loaderStyles.toString()}`;
86
- (_a = document.querySelector('head')) === null || _a === void 0 ? void 0 : _a.append(styleTag);
87
- }
88
- registerWebComponents() {
89
- loadComponent('nightingale-navigation', NightingaleNavigation);
90
- loadComponent('nightingale-track', NightingaleTrack);
91
- loadComponent('nightingale-colored-sequence', NightingaleColoredSequence);
92
- loadComponent('nightingale-interpro-track', NightingaleInterproTrack);
93
- loadComponent('nightingale-sequence', NightingaleSequence);
94
- loadComponent('nightingale-variation', NightingaleVariation);
95
- loadComponent('nightingale-linegraph-track', NightingaleLinegraphTrack);
96
- loadComponent('nightingale-filter', NightingaleFilter);
97
- loadComponent('nightingale-manager', NightingaleManager);
98
- loadComponent('protvista-uniprot-structure', ProtvistaUniprotStructure);
99
- loadComponent('nightingale-sequence-heatmap', NightingaleSequenceHeatmap);
100
- }
101
- async _loadData() {
102
- const accession = this.accession;
103
- if (accession && this.config) {
104
- // Get the list of unique urls
105
- const urls = this.config.categories.flatMap(({ tracks }) => tracks.flatMap(({ data }) => data[0].url));
106
- // Get the data for all urls and store it
107
- this.rawData = await fetchAll([...new Set(urls)], (url) => url.replace('{accession}', accession));
108
- // Some endpoints return empty arrays, while most fail 🙄
109
- this.hasData =
110
- this.hasData ||
111
- Object.values(this.rawData).some((d) => { var _a; return !!((_a = d === null || d === void 0 ? void 0 : d.features) === null || _a === void 0 ? void 0 : _a.length); });
112
- // Now iterate over tracks and categories, transforming the data
113
- // and assigning it as adequate
114
- for (const { name: categoryName, tracks, trackType } of this.config
115
- .categories) {
116
- const categoryData = await Promise.all(tracks.map(async ({ data: dataConfig, name: trackName, filter }) => {
117
- const { url, adapter } = dataConfig[0]; // TODO handle array
118
- const trackData = (Array.isArray(url) ? url : [url]).map((url) => this.rawData[url] || []);
119
- if (!trackData ||
120
- (adapter === 'variation-adapter' && trackData[0].length === 0)) {
121
- return;
122
- }
123
- // 1. Convert data
124
- let transformedData = adapter
125
- ? await adapters[adapter].apply(null, trackData)
126
- : trackData;
127
- if (adapter === 'interpro-adapter') {
128
- const representativeDomains = [];
129
- transformedData === null || transformedData === void 0 ? void 0 : transformedData.forEach((feature) => {
130
- var _a;
131
- (_a = feature.locations) === null || _a === void 0 ? void 0 : _a.forEach((location) => {
132
- var _a;
133
- (_a = location.fragments) === null || _a === void 0 ? void 0 : _a.forEach((fragment) => {
134
- if (fragment.representative) {
135
- representativeDomains.push({
136
- ...feature,
137
- type: 'InterPro Representative Domain',
138
- start: fragment.start,
139
- end: fragment.end,
140
- });
141
- }
142
- });
143
- });
144
- });
145
- transformedData = representativeDomains;
146
- }
147
- // 2. Filter raw data if filter is specified
148
- const filteredData = Array.isArray(transformedData) && filter
149
- ? transformedData.filter(({ type }) => type === filter)
150
- : transformedData;
151
- if (!filteredData) {
152
- return;
153
- }
154
- // 3. Assign track data
155
- this.data[`${categoryName}-${trackName}`] = filteredData;
156
- if (trackName === 'variation') {
157
- this.transformedVariants = filteredData;
158
- }
159
- return filteredData;
160
- }));
161
- this.data[categoryName] =
162
- trackType === 'nightingale-linegraph-track' ||
163
- trackType === 'nightingale-colored-sequence'
164
- ? categoryData[0]
165
- : categoryData.flat();
166
- }
167
- }
168
- this.loading = false;
169
- this.requestUpdate(); // Why?
170
- }
171
- async _loadDataInComponents() {
172
- await frame();
173
- Object.entries(this.data).forEach(([id, data]) => {
174
- var _a, _b;
175
- const element = document.getElementById(`track-${id}`);
176
- // set data if it hasn't changed
177
- if (element && element.data !== data) {
178
- element.data = data;
179
- }
180
- const currentCategory = (_a = this.config) === null || _a === void 0 ? void 0 : _a.categories.find(({ name }) => name === id);
181
- if (currentCategory &&
182
- currentCategory.tracks &&
183
- data &&
184
- // Check there's data and special case for variants
185
- // NOTE: should refactor variation-adapter
186
- // to return a list of variants and set the sequence
187
- // on protvista-variation separately
188
- (data.length > 0 || ((_b = data.variants) === null || _b === void 0 ? void 0 : _b.length))) {
189
- // Make category element visible
190
- const categoryElt = document.getElementById(`category_${currentCategory.name}`);
191
- if (categoryElt) {
192
- categoryElt.style.display = 'flex';
193
- }
194
- for (const track of currentCategory.tracks) {
195
- const elementTrack = document.getElementById(`track-${id}-${track.name}`);
196
- if (elementTrack) {
197
- elementTrack.data = this.data[`${id}-${track.name}`];
198
- }
199
- }
200
- }
201
- if ((currentCategory === null || currentCategory === void 0 ? void 0 : currentCategory.name) === 'ALPHAMISSENSE_PATHOGENICITY' &&
202
- currentCategory.tracks) {
203
- for (const track of currentCategory.tracks) {
204
- if (track.trackType === 'nightingale-sequence-heatmap') {
205
- const heatmapComponent = this.querySelector('nightingale-sequence-heatmap');
206
- if (heatmapComponent) {
207
- const heatmapData = this.data[`${id}-${track.name}`];
208
- const xDomain = Array.from({ length: this.sequence.length }, (_, i) => i + 1);
209
- const yDomain = [
210
- ...new Set(heatmapData.map((hotMapItem) => hotMapItem.yValue)),
211
- ];
212
- heatmapComponent.setHeatmapData(xDomain, yDomain, heatmapData);
213
- }
214
- }
215
- }
216
- }
217
- });
218
- }
219
- updated(changedProperties) {
220
- super.updated(changedProperties);
221
- const filterComponent = this.querySelector('nightingale-filter');
222
- if (filterComponent && filterComponent.filters !== filterConfig) {
223
- filterComponent.filters = filterConfig;
224
- }
225
- const variationComponent = this.querySelector('nightingale-variation');
226
- if (variationComponent && (variationComponent === null || variationComponent === void 0 ? void 0 : variationComponent.colorConfig) !== colorConfig) {
227
- variationComponent.colorConfig = colorConfig;
228
- }
229
- if (changedProperties.has('suspend')) {
230
- if (this.suspend)
231
- return;
232
- this._init();
233
- }
234
- this._loadDataInComponents();
235
- }
236
- _init() {
237
- if (!this.config) {
238
- this.config = defaultConfig;
239
- }
240
- if (!this.accession)
241
- return;
242
- this.loadEntry(this.accession).then((entryData) => {
243
- var _a;
244
- this.sequence = entryData.sequence.sequence;
245
- this.displayCoordinates = { start: 1, end: (_a = this.sequence) === null || _a === void 0 ? void 0 : _a.length };
246
- // We need to get the length of the protein before rendering it
247
- });
248
- this._loadData();
249
- }
250
- connectedCallback() {
251
- super.connectedCallback();
252
- this.registerWebComponents();
253
- if (!this.suspend)
254
- this._init();
255
- this.addEventListener('change', (e) => {
256
- var _a, _b;
257
- if ((_a = e.detail) === null || _a === void 0 ? void 0 : _a.displaystart) {
258
- this.displayCoordinates.start = e.detail.displaystart;
259
- }
260
- if ((_b = e.detail) === null || _b === void 0 ? void 0 : _b.displayend) {
261
- this.displayCoordinates.end = e.detail.displayend;
262
- }
263
- });
264
- // Note: this doesn't seem to work
265
- this.addEventListener('load', () => {
266
- if (!this.hasData) {
267
- this.dispatchEvent(new CustomEvent('protvista-event', {
268
- detail: {
269
- hasData: true,
270
- },
271
- bubbles: true,
272
- }));
273
- this.hasData = true;
274
- }
275
- });
276
- }
277
- async loadEntry(accession) {
278
- try {
279
- return await (await fetch(`https://www.ebi.ac.uk/proteins/api/proteins/${accession}`)).json();
280
- }
281
- catch (e) {
282
- console.error(`Couldn't load UniProt entry`, e);
283
- }
284
- }
285
- /**
286
- * we need to use the light DOM.
287
- * */
288
- createRenderRoot() {
289
- return this;
290
- }
291
- render() {
292
- var _a, _b;
293
- // Component isn't ready
294
- if (!this.sequence || !this.config || this.suspend) {
295
- return html ``;
296
- }
297
- if (this.loading) {
298
- return html `<div class="protvista-loader">
299
- ${svg `${unsafeHTML(loaderIcon)}`}
300
- </div>`;
301
- }
302
- if (!this.hasData) {
303
- return html `<div class="protvista-no-results">
304
- No feature data available for ${this.accession}
305
- </div>`;
306
- }
307
- return html `
308
- <nightingale-manager
309
- reflected-attributes="length display-start display-end highlight activefilters filters"
310
- >
311
- <div class="nav-container">
312
- <div class="nav-track-label"></div>
313
- <div class="track-content">
314
- <nightingale-navigation
315
- length="${this.sequence.length}"
316
- height="40"
317
- ></nightingale-navigation>
318
- <nightingale-sequence
319
- length="${this.sequence.length}"
320
- height="40"
321
- sequence="${this.sequence}"
322
- display-start=${(_a = this.displayCoordinates) === null || _a === void 0 ? void 0 : _a.start}
323
- display-end="${(_b = this.displayCoordinates) === null || _b === void 0 ? void 0 : _b.end}"
324
- highlight-event="onclick"
325
- use-ctrl-to-zoom
326
- ></nightingale-sequence>
327
- </div>
328
- </div>
329
- ${this.config.categories.map((category) => this.data[category.name] &&
330
- html `
331
- <div class="category" id="category_${category.name}">
332
- <div
333
- class="category-label"
334
- data-category-toggle="${category.name}"
335
- @click="${this.handleCategoryClick}"
336
- >
337
- ${category.label}
338
- </div>
339
- <div
340
- data-id="category_${category.name}"
341
- class="aggregate-track-content track-content ${category.trackType ===
342
- 'nightingale-colored-sequence'
343
- ? 'track-content__coloured-sequence'
344
- : ''}"
345
- .style="${this.openCategories.includes(category.name)
346
- ? 'opacity:0'
347
- : 'opacity:1'}"
348
- >
349
- ${this.data[category.name] &&
350
- this.getTrack(category.trackType, 'non-overlapping', category.color, category.shape, category.name, category.scale, category['color-range'])}
351
- </div>
352
- </div>
353
-
354
- <!-- Expanded Categories -->
355
- ${category.tracks &&
356
- category.tracks.map((track) => {
357
- if (this.openCategories.includes(category.name)) {
358
- const trackData = this.data[`${category.name}-${track.name}`];
359
- return trackData &&
360
- ((Array.isArray(trackData) && trackData.length) ||
361
- Object.keys(trackData).length)
362
- ? html `
363
- <div class="category__track" id="track_${track.name}">
364
- <div class="track-label" title="${track.tooltip}">
365
- ${(track.filterComponent &&
366
- this.getFilterComponent(`${category.name}-${track.name}`)) ||
367
- (track.labelUrl &&
368
- html `<a
369
- target="_blank"
370
- href="${track.labelUrl.replace('{accession}', this.accession)}"
371
- >${track.label}</a
372
- >`) ||
373
- track.label}
374
- </div>
375
- <div
376
- class="track-content"
377
- class="track-content ${category.trackType ===
378
- 'nightingale-colored-sequence'
379
- ? 'track-content__coloured-sequence'
380
- : ''}"
381
- data-id="track_${track.name}"
382
- >
383
- ${this.getTrack(track.trackType, 'non-overlapping', track.color || category.color, track.shape || category.shape, `${category.name}-${track.name}`, track.scale || category.scale, track['color-range'] || category['color-range'])}
384
- </div>
385
- </div>
386
- `
387
- : '';
388
- }
389
- })}
390
- ${!category.tracks
391
- ? this.data[category.name].map((item) => {
392
- if (this.openCategories.includes(category.name)) {
393
- if (!item || !item.accession)
394
- return '';
395
- return html `
396
- <div
397
- class="category__track"
398
- id="track_${item.accession}"
399
- >
400
- <div class="track-label" title="${item.accession}">
401
- ${item.accession}
402
- </div>
403
- <div
404
- class="track-content"
405
- data-id="track_${item.accession}"
406
- >
407
- ${this.getTrack(category.trackType, 'non-overlapping', category.color, category.shape, `${category.name}-${item.accession}`, category.scale, category['color-range'])}
408
- </div>
409
- </div>
410
- `;
411
- }
412
- })
413
- : ''}
414
- `)}
415
- <div class="nav-container">
416
- <div class="credits"></div>
417
- <div class="track-content">
418
- <nightingale-sequence
419
- length="${this.sequence.length}"
420
- height="40"
421
- sequence="${this.sequence}"
422
- display-start=${this.displayCoordinates.start}
423
- display-end="${this.displayCoordinates.end}"
424
- highlight-event="onclick"
425
- use-ctrl-to-zoom
426
- ></nightingale-sequence>
427
- </div>
428
- </div>
429
- ${!this.nostructure
430
- ? html `
431
- <protvista-uniprot-structure
432
- accession="${this.accession || ''}"
433
- ></protvista-uniprot-structure>
434
- `
435
- : ''}
436
- </nightingale-manager>
437
- `;
438
- }
439
- handleCategoryClick(e) {
440
- const target = e.target;
441
- const toggle = target.getAttribute('data-category-toggle');
442
- if (toggle && !target.classList.contains('open')) {
443
- target.classList.add('open');
444
- this.openCategories = [...this.openCategories, toggle];
445
- }
446
- else {
447
- target.classList.remove('open');
448
- this.openCategories = [...this.openCategories].filter((d) => d !== toggle);
449
- }
450
- }
451
- groupByCategory(filters, category) {
452
- return filters === null || filters === void 0 ? void 0 : filters.filter((f) => f.type.name === category);
453
- }
454
- getFilter(filters, filterName) {
455
- var _a;
456
- return (_a = filters === null || filters === void 0 ? void 0 : filters.filter((f) => f.name === filterName)) === null || _a === void 0 ? void 0 : _a[0];
457
- }
458
- handleFilterClick(e) {
459
- var _a, _b;
460
- const target = e.target;
461
- const consequenceFilters = this.groupByCategory(target.filters, 'consequence');
462
- const provenanceFilters = this.groupByCategory(target.filters, 'provenance');
463
- const selectedFilters = (_a = e.detail) === null || _a === void 0 ? void 0 : _a.value;
464
- if (selectedFilters) {
465
- const selectedConsequenceFilters = selectedFilters
466
- .map((f) => this.getFilter(consequenceFilters, f))
467
- .filter(Boolean);
468
- const selectedProvenanceFilters = selectedFilters
469
- .map((f) => this.getFilter(provenanceFilters, f))
470
- .filter(Boolean);
471
- const filteredVariants = (_b = this.transformedVariants.variants) === null || _b === void 0 ? void 0 : _b.filter((variant) => selectedConsequenceFilters.some((filter) => filter.filterPredicate(variant))).filter((variant) => selectedProvenanceFilters.some((filter) => filter.filterPredicate(variant)));
472
- this.data['VARIATION-variation'] = {
473
- ...this.data['VARIATION-variation'],
474
- variants: filteredVariants,
475
- };
476
- this._loadDataInComponents();
477
- }
478
- }
479
- getCategoryTypesAsString(tracks) {
480
- return tracks.map((t) => t.filter).join(',');
481
- }
482
- getFilterComponent(forId) {
483
- return html `
484
- <nightingale-filter
485
- style="minWidth: 20%"
486
- for="track-${forId}"
487
- @change="${this.handleFilterClick}"
488
- ></nightingale-filter>
489
- `;
490
- }
491
- getTrack(trackType, layout = '', color = '', shape = '', id = '', scale = '', colorRange = '') {
492
- var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o, _p, _q, _r, _s, _t;
493
- // lit-html doesn't allow to have dynamic tag names, hence the switch/case
494
- // with repeated code
495
- switch (trackType) {
496
- case 'nightingale-track':
497
- return html `
498
- <nightingale-track
499
- length="${(_a = this.sequence) === null || _a === void 0 ? void 0 : _a.length}"
500
- height="40"
501
- layout="${layout}"
502
- color="${color}"
503
- shape="${shape}"
504
- display-start="${(_b = this.displayCoordinates) === null || _b === void 0 ? void 0 : _b.start}"
505
- display-end="${(_c = this.displayCoordinates) === null || _c === void 0 ? void 0 : _c.end}"
506
- id="track-${id}"
507
- highlight-event="onclick"
508
- use-ctrl-to-zoom
509
- >
510
- </nightingale-track>
511
- `;
512
- case 'nightingale-interpro-track':
513
- return html `
514
- <nightingale-interpro-track
515
- length="${(_d = this.sequence) === null || _d === void 0 ? void 0 : _d.length}"
516
- height="40"
517
- color="${color}"
518
- shape="${shape}"
519
- display-start="${(_e = this.displayCoordinates) === null || _e === void 0 ? void 0 : _e.start}"
520
- display-end="${(_f = this.displayCoordinates) === null || _f === void 0 ? void 0 : _f.end}"
521
- id="track-${id}"
522
- highlight-event="onclick"
523
- use-ctrl-to-zoom
524
- >
525
- </nightingale-interpro-track>
526
- `;
527
- case 'nightingale-variation':
528
- return html `
529
- <nightingale-variation
530
- length="${(_g = this.sequence) === null || _g === void 0 ? void 0 : _g.length}"
531
- height="500"
532
- display-start="${(_h = this.displayCoordinates) === null || _h === void 0 ? void 0 : _h.start}"
533
- display-end="${(_j = this.displayCoordinates) === null || _j === void 0 ? void 0 : _j.end}"
534
- id="track-${id}"
535
- highlight-event="onclick"
536
- use-ctrl-to-zoom
537
- >
538
- </nightingale-variation>
539
- `;
540
- case 'nightingale-linegraph-track':
541
- return html `
542
- <nightingale-linegraph-track
543
- length="${(_k = this.sequence) === null || _k === void 0 ? void 0 : _k.length}"
544
- height="50"
545
- display-start="${(_l = this.displayCoordinates) === null || _l === void 0 ? void 0 : _l.start}"
546
- display-end="${(_m = this.displayCoordinates) === null || _m === void 0 ? void 0 : _m.end}"
547
- id="track-${id}"
548
- show-label-name
549
- highlight-on-click
550
- use-ctrl-to-zoom
551
- >
552
- </nightingale-linegraph-track>
553
- `;
554
- case 'nightingale-colored-sequence':
555
- return html `
556
- <nightingale-colored-sequence
557
- length="${(_o = this.sequence) === null || _o === void 0 ? void 0 : _o.length}"
558
- display-start="${(_p = this.displayCoordinates) === null || _p === void 0 ? void 0 : _p.start}"
559
- display-end="${(_q = this.displayCoordinates) === null || _q === void 0 ? void 0 : _q.end}"
560
- id="track-${id}"
561
- scale="${scale}"
562
- color-range="${colorRange}"
563
- height="13"
564
- highlight-event="onclick"
565
- use-ctrl-to-zoom
566
- >
567
- </nightingale-colored-sequence>
568
- `;
569
- case 'nightingale-sequence-heatmap':
570
- return html `
571
- <nightingale-sequence-heatmap
572
- id="track-${id}"
573
- heatmap-id="seq-heatmap"
574
- length="${(_r = this.sequence) === null || _r === void 0 ? void 0 : _r.length}"
575
- display-start="${(_s = this.displayCoordinates) === null || _s === void 0 ? void 0 : _s.start}"
576
- display-end="${(_t = this.displayCoordinates) === null || _t === void 0 ? void 0 : _t.end}"
577
- highlight-event="onclick"
578
- highlight-color="#EB3BFF66"
579
- height="300"
580
- use-ctrl-to-zoom
581
- >
582
- </nightingale-sequence-heatmap>
583
- `;
584
- default:
585
- console.warn('No Matching ProtvistaTrack Found.');
586
- break;
587
- }
588
- }
589
- };
590
- ProtvistaUniprot = __decorate([
591
- customElement('protvista-uniprot')
592
- ], ProtvistaUniprot);
593
- export default ProtvistaUniprot;
594
- //# sourceMappingURL=protvista-uniprot.js.map
@@ -1 +0,0 @@
1
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@@ -1,20 +0,0 @@
1
- import { css } from 'lit';
2
- export default css `
3
- .protvista-loader {
4
- display: flex;
5
- justify-content: center;
6
- padding: 4rem 0;
7
- }
8
- .protvista-loader svg {
9
- height: 100px;
10
- }
11
-
12
- .protvista-no-results {
13
- background-color: #e4e8eb;
14
- display: flex;
15
- justify-content: center;
16
- padding: 1rem;
17
- font-size: 0.8rem;
18
- }
19
- `;
20
- //# sourceMappingURL=loader-styles.js.map
@@ -1 +0,0 @@
1
- {"version":3,"file":"loader-styles.js","sourceRoot":"","sources":["../../../src/styles/loader-styles.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,GAAG,EAAE,MAAM,KAAK,CAAC;AAE1B,eAAe,GAAG,CAAA;;;;;;;;;;;;;;;;;CAiBjB,CAAC"}