protvista-uniprot 2.12.2 → 2.13.0

package/dist/es/protvista-uniprot.js

@@ -1,30 +1,31 @@
 import { LitElement, html, svg } from 'lit-element';
 import { unsafeHTML } from 'lit-html/directives/unsafe-html.js';
 import { frame } from 'timing-functions';
-// components
-import ProtvistaNavigation from 'protvista-navigation';
-import ProtvistaTooltip from 'protvista-tooltip';
-import ProtvistaTrackConfig from 'protvista-track';
-import ProtvistaColouredSequenceConfig from 'protvista-coloured-sequence';
-import ProtvistaInterproTrack from 'protvista-interpro-track';
-import ProtvistaSequence from 'protvista-sequence';
-import ProtvistaVariation from 'protvista-variation';
-import ProtvistaVariationGraph from 'protvista-variation-graph';
-import ProtvistaFilter from 'protvista-filter';
-import ProtvistaManager from 'protvista-manager';
+// Nightingale
+import NightingaleManager from '@nightingale-elements/nightingale-manager';
+import NightingaleNavigation from '@nightingale-elements/nightingale-navigation';
+import NightingaleSequence from '@nightingale-elements/nightingale-sequence';
+import NightingaleColoredSequence from '@nightingale-elements/nightingale-colored-sequence';
+import NightingaleTrack from '@nightingale-elements/nightingale-track';
+import NightingaleInterproTrack from '@nightingale-elements/nightingale-interpro-track';
+import NightingaleVariation from '@nightingale-elements/nightingale-variation';
+import NightingaleLinegraphTrack from '@nightingale-elements/nightingale-linegraph-track';
+import NightingaleSequenceHeatmap from '@nightingale-elements/nightingale-sequence-heatmap';
+import NightingaleFilter from '@nightingale-elements/nightingale-filter';
 import { load } from 'data-loader';
 // adapters
 import { transformData as _transformDataFeatureAdapter } from 'protvista-feature-adapter';
 import { transformData as _transformDataProteomicsAdapter } from 'protvista-proteomics-adapter';
 import { transformData as _transformDataStructureAdapter } from 'protvista-structure-adapter';
-import { transformData as _transformDataVariationAdapter } from 'protvista-variation-adapter';
+import { transformData as _transformDataVariationAdapter, } from 'protvista-variation-adapter';
+import { transformData as _transformDataVariationGraphAdapter } from './protvista-variation-graph-adapter';
 import { transformData as _transformDataInterproAdapter } from 'protvista-interpro-adapter';
 import { transformData as _transformDataProteomicsPTMApdapter } from './protvista-ptm-exchange';
 import { transformData as _transformDataAlphaFoldConfidenceAdapter } from './protvista-alphafold-confidence';
 import { transformData as _transformDataAlphaMissensePathogenicityAdapter } from './protvista-alphamissense-pathogenicity';
+import { transformData as _transformDataAlphaMissenseHeatmapAdapter } from './protvista-alphamissense-heatmap';
 import defaultConfig from './config.json';
 import _ProtvistaUniprotStructure from './protvista-uniprot-structure';
-import _DownloadPanel from './download-panel';
 import { loadComponent } from './loadComponents';
 import _filterConfig, { colorConfig as _colorConfig } from './filterConfig';
 import loaderIcon from './icons/spinner.svg';
@@ -34,37 +35,40 @@ export const transformDataFeatureAdapter = _transformDataFeatureAdapter;
 export const transformDataProteomicsAdapter = _transformDataProteomicsAdapter;
 export const transformDataStructureAdapter = _transformDataStructureAdapter;
 export const transformDataVariationAdapter = _transformDataVariationAdapter;
+export const transformDataVariationGraphAdapter = _transformDataVariationGraphAdapter;
 export const transformDataInterproAdapter = _transformDataInterproAdapter;
 export const transformDataProteomicsPTMApdapter = _transformDataProteomicsPTMApdapter;
 export const transformDataAlphaFoldConfidenceAdapter = _transformDataAlphaFoldConfidenceAdapter;
 export const transformDataAlphaMissensePathogenicityAdapter = _transformDataAlphaMissensePathogenicityAdapter;
+export const transformDataAlphaMissenseHeatmapAdapter = _transformDataAlphaMissenseHeatmapAdapter;
 export const filterConfig = _filterConfig;
 export const colorConfig = _colorConfig;
 export const ProtvistaUniprotStructure = _ProtvistaUniprotStructure;
-export const DownloadPanel = _DownloadPanel;
 const adapters = {
     'protvista-feature-adapter': transformDataFeatureAdapter,
     'protvista-interpro-adapter': transformDataInterproAdapter,
     'protvista-proteomics-adapter': transformDataProteomicsAdapter,
     'protvista-structure-adapter': transformDataStructureAdapter,
     'protvista-variation-adapter': transformDataVariationAdapter,
+    'protvista-variation-graph-adapter': transformDataVariationGraphAdapter,
     'protvista-proteomics-ptm-adapter': transformDataProteomicsPTMApdapter,
     'protvista-alphafold-confidence-adapter': transformDataAlphaFoldConfidenceAdapter,
     'protvista-alphamissense-pathogenicity-adapter': transformDataAlphaMissensePathogenicityAdapter,
+    'protvista-alphamissense-heatmap-adapter': transformDataAlphaMissenseHeatmapAdapter,
 };
 class ProtvistaUniprot extends LitElement {
     constructor() {
         super();
         this.displayCoordinates = {};
         this.openCategories = [];
-        this.notooltip = false;
         this.nostructure = false;
         this.hasData = false;
         this.loading = true;
         this.data = {};
         this.rawData = {};
         this.displayCoordinates = {};
-        this.addStyles();
+        (this.transformedVariants = { sequence: '', variants: [] }),
+            this.addStyles();
     }
     static get properties() {
         return {
@@ -88,17 +92,17 @@ class ProtvistaUniprot extends LitElement {
         (_a = document.querySelector('head')) === null || _a === void 0 ? void 0 : _a.append(styleTag);
     }
     registerWebComponents() {
-        loadComponent('protvista-navigation', ProtvistaNavigation);
-        loadComponent('protvista-tooltip', ProtvistaTooltip);
-        loadComponent('protvista-track', ProtvistaTrackConfig);
-        loadComponent('protvista-coloured-sequence', ProtvistaColouredSequenceConfig);
-        loadComponent('protvista-interpro-track', ProtvistaInterproTrack);
-        loadComponent('protvista-sequence', ProtvistaSequence);
-        loadComponent('protvista-variation', ProtvistaVariation);
-        loadComponent('protvista-variation-graph', ProtvistaVariationGraph);
-        loadComponent('protvista-filter', ProtvistaFilter);
-        loadComponent('protvista-manager', ProtvistaManager);
+        loadComponent('nightingale-navigation', NightingaleNavigation);
+        loadComponent('nightingale-track', NightingaleTrack);
+        loadComponent('nightingale-colored-sequence', NightingaleColoredSequence);
+        loadComponent('nightingale-interpro-track', NightingaleInterproTrack);
+        loadComponent('nightingale-sequence', NightingaleSequence);
+        loadComponent('nightingale-variation', NightingaleVariation);
+        loadComponent('nightingale-linegraph-track', NightingaleLinegraphTrack);
+        loadComponent('nightingale-filter', NightingaleFilter);
+        loadComponent('nightingale-manager', NightingaleManager);
         loadComponent('protvista-uniprot-structure', _ProtvistaUniprotStructure);
+        loadComponent('nightingale-sequence-heatmap', NightingaleSequenceHeatmap);
     }
     async _loadData() {
         const accession = this.accession;
@@ -166,11 +170,14 @@ class ProtvistaUniprot extends LitElement {
                     }
                     // 3. Assign track data
                     this.data[`${categoryName}-${trackName}`] = filteredData;
+                    if (trackName === 'variation') {
+                        this.transformedVariants = filteredData;
+                    }
                     return filteredData;
                 }));
                 this.data[categoryName] =
-                    trackType === 'protvista-variation-graph' ||
-                        trackType === 'protvista-coloured-sequence'
+                    trackType === 'nightingale-linegraph-track' ||
+                        trackType === 'nightingale-colored-sequence'
                         ? categoryData[0]
                         : categoryData.flat();
             }
@@ -208,16 +215,32 @@ class ProtvistaUniprot extends LitElement {
                     }
                 }
             }
+            if ((currentCategory === null || currentCategory === void 0 ? void 0 : currentCategory.name) === 'ALPHAMISSENSE_PATHOGENICITY' &&
+                currentCategory.tracks) {
+                for (const track of currentCategory.tracks) {
+                    if (track.trackType === 'nightingale-sequence-heatmap') {
+                        const heatmapComponent = this.querySelector('nightingale-sequence-heatmap');
+                        if (heatmapComponent) {
+                            const heatmapData = this.data[`${id}-${track.name}`];
+                            const xDomain = Array.from({ length: this.sequence.length }, (_, i) => i + 1);
+                            const yDomain = [
+                                ...new Set(heatmapData.map((hotMapItem) => hotMapItem.yValue)),
+                            ];
+                            heatmapComponent.setHeatmapData(xDomain, yDomain, heatmapData);
+                        }
+                    }
+                }
+            }
         });
     }
     updated(changedProperties) {
         super.updated(changedProperties);
-        const filterComponent = this.querySelector('protvista-filter');
+        const filterComponent = this.querySelector('nightingale-filter');
         if (filterComponent && filterComponent.filters !== filterConfig) {
             filterComponent.filters = filterConfig;
         }
-        const variationComponent = this.querySelector('protvista-variation');
-        if (variationComponent && variationComponent.colorConfig !== colorConfig) {
+        const variationComponent = this.querySelector('nightingale-variation');
+        if (variationComponent && (variationComponent === null || variationComponent === void 0 ? void 0 : variationComponent.colorConfig) !== colorConfig) {
             variationComponent.colorConfig = colorConfig;
         }
         if (changedProperties.has('suspend')) {
@@ -247,35 +270,14 @@ class ProtvistaUniprot extends LitElement {
         if (!this.suspend)
             this._init();
         this.addEventListener('change', (e) => {
-            var _a, _b, _c;
+            var _a, _b;
             if ((_a = e.detail) === null || _a === void 0 ? void 0 : _a.displaystart) {
                 this.displayCoordinates.start = e.detail.displaystart;
             }
             if ((_b = e.detail) === null || _b === void 0 ? void 0 : _b.displayend) {
                 this.displayCoordinates.end = e.detail.displayend;
             }
-            if (!this.notooltip) {
-                if (!((_c = e.detail) === null || _c === void 0 ? void 0 : _c.eventtype)) {
-                    this._resetTooltip();
-                }
-                else if (e.detail.eventtype === 'click') {
-                    this.updateTooltip(e);
-                }
-            }
         });
-        if (!this.notooltip) {
-            this.addEventListener('click', (e) => {
-                const target = e.target;
-                if (!target.closest('.feature') &&
-                    !target.closest('protvista-tooltip')) {
-                    const tooltip = this.querySelector('protvista-tooltip');
-                    if (tooltip) {
-                        tooltip.visible = false;
-                    }
-                }
-            });
-            document.addEventListener('click', this._resetTooltip);
-        }
         // Note: this doesn't seem to work
         this.addEventListener('load', () => {
             if (!this.hasData) {
@@ -289,20 +291,6 @@ class ProtvistaUniprot extends LitElement {
             }
         });
     }
-    disconnectedCallback() {
-        if (!this.notooltip) {
-            document.removeEventListener('click', this._resetTooltip);
-        }
-    }
-    _resetTooltip(e) {
-        var _a;
-        if (this && (!e || !((_a = e.target) === null || _a === void 0 ? void 0 : _a.closest('protvista-uniprot')))) {
-            const tooltip = this.querySelector('protvista-tooltip');
-            if (tooltip) {
-                tooltip.visible = false;
-            }
-        }
-    }
     async loadEntry(accession) {
         try {
             return await (await fetch(`https://www.ebi.ac.uk/proteins/api/proteins/${accession}`)).json();
@@ -334,28 +322,25 @@ class ProtvistaUniprot extends LitElement {
       </div>`;
         }
         return html `
-      <protvista-manager
-        attributes="length displaystart displayend highlight activefilters filters"
-        additionalsubscribers="protvista-structure"
+      <nightingale-manager
+        reflected-attributes="length display-start display-end highlight activefilters filters"
       >
         <div class="nav-container">
-          <div class="action-buttons">
-            <download-panel
-              accession="${this.accession}"
-              config="${JSON.stringify(this.config.download)}"
-            />
-          </div>
+          <div class="nav-track-label"></div>
           <div class="track-content">
-            <protvista-navigation
+            <nightingale-navigation
               length="${this.sequence.length}"
-            ></protvista-navigation>
-            <protvista-sequence
+              height="40"
+            ></nightingale-navigation>
+            <nightingale-sequence
               length="${this.sequence.length}"
+              height="40"
               sequence="${this.sequence}"
-              displaystart=${(_a = this.displayCoordinates) === null || _a === void 0 ? void 0 : _a.start}
-              displayend="${(_b = this.displayCoordinates) === null || _b === void 0 ? void 0 : _b.end}"
-              no-scroll
-            ></protvista-sequence>
+              display-start=${(_a = this.displayCoordinates) === null || _a === void 0 ? void 0 : _a.start}
+              display-end="${(_b = this.displayCoordinates) === null || _b === void 0 ? void 0 : _b.end}"
+              highlight-event="onclick"
+              use-ctrl-to-zoom
+            ></nightingale-sequence>
           </div>
         </div>
         ${this.config.categories.map((category) => this.data[category.name] &&
@@ -371,7 +356,7 @@ class ProtvistaUniprot extends LitElement {
                 <div
                   data-id="category_${category.name}"
                   class="aggregate-track-content track-content ${category.trackType ===
-                'protvista-coloured-sequence'
+                'nightingale-colored-sequence'
                 ? 'track-content__coloured-sequence'
                 : ''}"
                   .style="${this.openCategories.includes(category.name)
@@ -407,7 +392,7 @@ class ProtvistaUniprot extends LitElement {
                           <div
                             class="track-content"
                             class="track-content ${category.trackType ===
-                                'protvista-coloured-sequence'
+                                'nightingale-colored-sequence'
                                 ? 'track-content__coloured-sequence'
                                 : ''}"
                             data-id="track_${track.name}"
@@ -447,13 +432,15 @@ class ProtvistaUniprot extends LitElement {
         <div class="nav-container">
           <div class="credits"></div>
           <div class="track-content">
-            <protvista-sequence
+            <nightingale-sequence
               length="${this.sequence.length}"
+              height="40"
               sequence="${this.sequence}"
-              displaystart=${this.displayCoordinates.start}
-              displayend="${this.displayCoordinates.end}"
-              no-scroll
-            ></protvista-sequence>
+              display-start=${this.displayCoordinates.start}
+              display-end="${this.displayCoordinates.end}"
+              highlight-event="onclick"
+              use-ctrl-to-zoom
+            ></nightingale-sequence>
           </div>
         </div>
         ${!this.nostructure
@@ -463,29 +450,9 @@ class ProtvistaUniprot extends LitElement {
               ></protvista-uniprot-structure>
             `
             : ''}
-        <protvista-tooltip />
-      </protvista-manager>
+      </nightingale-manager>
     `;
     }
-    async updateTooltip(e) {
-        var _a, _b;
-        const d = (_a = e.detail) === null || _a === void 0 ? void 0 : _a.feature;
-        if (!d.tooltipContent) {
-            return;
-        }
-        const tooltip = this.querySelector('protvista-tooltip');
-        if (!tooltip) {
-            return;
-        }
-        tooltip.title = `${d.type} ${d.start}-${d.end}`;
-        tooltip.innerHTML = d.tooltipContent;
-        tooltip.visible = true;
-        if ((_b = e.detail) === null || _b === void 0 ? void 0 : _b.coords) {
-            const [x, y] = e.detail.coords;
-            tooltip.x = x;
-            tooltip.y = y;
-        }
-    }
     handleCategoryClick(e) {
         const target = e.target;
         const toggle = target.getAttribute('data-category-toggle');
@@ -498,84 +465,138 @@ class ProtvistaUniprot extends LitElement {
             this.openCategories = [...this.openCategories].filter((d) => d !== toggle);
         }
     }
+    groupByCategory(filters, category) {
+        return filters === null || filters === void 0 ? void 0 : filters.filter((f) => f.type.name === category);
+    }
+    getFilter(filters, filterName) {
+        var _a;
+        return (_a = filters === null || filters === void 0 ? void 0 : filters.filter((f) => f.name === filterName)) === null || _a === void 0 ? void 0 : _a[0];
+    }
+    handleFilterClick(e) {
+        var _a, _b;
+        const target = e.target;
+        const consequenceFilters = this.groupByCategory(target.filters, 'consequence');
+        const provenanceFilters = this.groupByCategory(target.filters, 'provenance');
+        const selectedFilters = (_a = e.detail) === null || _a === void 0 ? void 0 : _a.value;
+        if (selectedFilters) {
+            const selectedConsequenceFilters = selectedFilters
+                .map((f) => this.getFilter(consequenceFilters, f))
+                .filter(Boolean);
+            const selectedProvenanceFilters = selectedFilters
+                .map((f) => this.getFilter(provenanceFilters, f))
+                .filter(Boolean);
+            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)));
+            this.data['VARIATION-variation'] = {
+                ...this.data['VARIATION-variation'],
+                variants: filteredVariants,
+            };
+            this._loadDataInComponents();
+        }
+    }
     getCategoryTypesAsString(tracks) {
         return tracks.map((t) => t.filter).join(',');
     }
     getFilterComponent(forId) {
         return html `
-      <protvista-filter
+      <nightingale-filter
         style="minWidth: 20%"
         for="track-${forId}"
-      ></protvista-filter>
+        @change="${this.handleFilterClick}"
+      ></nightingale-filter>
     `;
     }
     getTrack(trackType, layout = '', color = '', shape = '', id = '', scale = '', colorRange = '') {
-        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o, _p, _q;
+        var _a, _b, _c, _d, _e, _f, _g, _h, _j, _k, _l, _m, _o, _p, _q, _r, _s, _t;
         // lit-html doesn't allow to have dynamic tag names, hence the switch/case
         // with repeated code
         switch (trackType) {
-            case 'protvista-track':
+            case 'nightingale-track':
                 return html `
-          <protvista-track
+          <nightingale-track
             length="${(_a = this.sequence) === null || _a === void 0 ? void 0 : _a.length}"
+            height="40"
             layout="${layout}"
             color="${color}"
             shape="${shape}"
-            displaystart="${(_b = this.displayCoordinates) === null || _b === void 0 ? void 0 : _b.start}"
-            displayend="${(_c = this.displayCoordinates) === null || _c === void 0 ? void 0 : _c.end}"
+            display-start="${(_b = this.displayCoordinates) === null || _b === void 0 ? void 0 : _b.start}"
+            display-end="${(_c = this.displayCoordinates) === null || _c === void 0 ? void 0 : _c.end}"
             id="track-${id}"
-            no-scroll
+            highlight-event="onclick"
+            use-ctrl-to-zoom
           >
-          </protvista-track>
+          </nightingale-track>
         `;
-            case 'protvista-interpro-track':
+            case 'nightingale-interpro-track':
                 return html `
-          <protvista-interpro-track
+          <nightingale-interpro-track
             length="${(_d = this.sequence) === null || _d === void 0 ? void 0 : _d.length}"
+            height="40"
             color="${color}"
             shape="${shape}"
-            displaystart="${(_e = this.displayCoordinates) === null || _e === void 0 ? void 0 : _e.start}"
-            displayend="${(_f = this.displayCoordinates) === null || _f === void 0 ? void 0 : _f.end}"
+            display-start="${(_e = this.displayCoordinates) === null || _e === void 0 ? void 0 : _e.start}"
+            display-end="${(_f = this.displayCoordinates) === null || _f === void 0 ? void 0 : _f.end}"
             id="track-${id}"
-            no-scroll
+            highlight-event="onclick"
+            use-ctrl-to-zoom
           >
-          </protvista-interpro-track>
+          </nightingale-interpro-track>
         `;
-            case 'protvista-variation':
+            case 'nightingale-variation':
                 return html `
-          <protvista-variation
+          <nightingale-variation
             length="${(_g = this.sequence) === null || _g === void 0 ? void 0 : _g.length}"
-            displaystart="${(_h = this.displayCoordinates) === null || _h === void 0 ? void 0 : _h.start}"
-            displayend="${(_j = this.displayCoordinates) === null || _j === void 0 ? void 0 : _j.end}"
+            height="500"
+            display-start="${(_h = this.displayCoordinates) === null || _h === void 0 ? void 0 : _h.start}"
+            display-end="${(_j = this.displayCoordinates) === null || _j === void 0 ? void 0 : _j.end}"
             id="track-${id}"
-            no-scroll
+            highlight-event="onclick"
+            use-ctrl-to-zoom
           >
-          </protvista-variation>
+          </nightingale-variation>
         `;
-            case 'protvista-variation-graph':
+            case 'nightingale-linegraph-track':
                 return html `
-          <protvista-variation-graph
+          <nightingale-linegraph-track
             length="${(_k = this.sequence) === null || _k === void 0 ? void 0 : _k.length}"
-            displaystart="${(_l = this.displayCoordinates) === null || _l === void 0 ? void 0 : _l.start}"
-            displayend="${(_m = this.displayCoordinates) === null || _m === void 0 ? void 0 : _m.end}"
+            height="50"
+            display-start="${(_l = this.displayCoordinates) === null || _l === void 0 ? void 0 : _l.start}"
+            display-end="${(_m = this.displayCoordinates) === null || _m === void 0 ? void 0 : _m.end}"
             id="track-${id}"
-            no-scroll
+            show-label-name
+            highlight-on-click
+            use-ctrl-to-zoom
           >
-          </protvista-variation-graph>
+          </nightingale-linegraph-track>
         `;
-            case 'protvista-coloured-sequence':
+            case 'nightingale-colored-sequence':
                 return html `
-          <protvista-coloured-sequence
+          <nightingale-colored-sequence
             length="${(_o = this.sequence) === null || _o === void 0 ? void 0 : _o.length}"
-            displaystart="${(_p = this.displayCoordinates) === null || _p === void 0 ? void 0 : _p.start}"
-            displayend="${(_q = this.displayCoordinates) === null || _q === void 0 ? void 0 : _q.end}"
+            display-start="${(_p = this.displayCoordinates) === null || _p === void 0 ? void 0 : _p.start}"
+            display-end="${(_q = this.displayCoordinates) === null || _q === void 0 ? void 0 : _q.end}"
             id="track-${id}"
             scale="${scale}"
-            color_range="${colorRange}"
+            color-range="${colorRange}"
             height="13"
-            no-scroll
+            highlight-event="onclick"
+            use-ctrl-to-zoom
+          >
+          </nightingale-colored-sequence>
+        `;
+            case 'nightingale-sequence-heatmap':
+                return html `
+          <nightingale-sequence-heatmap
+            id="track-${id}"
+            heatmap-id="seq-heatmap"
+            length="${(_r = this.sequence) === null || _r === void 0 ? void 0 : _r.length}"
+            display-start="${(_s = this.displayCoordinates) === null || _s === void 0 ? void 0 : _s.start}"
+            display-end="${(_t = this.displayCoordinates) === null || _t === void 0 ? void 0 : _t.end}"
+            highlight-event="onclick"
+            highlight-color="#EB3BFF66"
+            height="300"
+            use-ctrl-to-zoom
           >
-          </protvista-coloured-sequence>
+          </nightingale-sequence-heatmap>
         `;
             default:
                 console.warn('No Matching ProtvistaTrack Found.');

package/dist/es/protvista-uniprot.js.map

@@ -1 +1 @@
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package/dist/es/protvista-variation-graph-adapter.d.ts

@@ -0,0 +1,9 @@
+export declare const transformData: (data: any) => {
+    name: string;
+    range: number[];
+    color: string;
+    values: {
+        position: number;
+        value: number;
+    }[];
+}[];