protvista-uniprot 3.0.0 → 3.0.7

package/dist/es/filter-config.js

@@ -1,157 +0,0 @@
-const scaleColors = {
-    UPDiseaseColor: '#990000',
-    UPNonDiseaseColor: '#99cc00',
-    predictedColor: '#4c8acd',
-    othersColor: '#009e73',
-};
-const consequences = {
-    uncertain: [/uncertain/i, /conflicting/i, /unclassified/i, /risk factor/i],
-};
-const significanceMatches = (clinicalSignificance, values) => clinicalSignificance.some(({ type }) => {
-    return values.some((rx) => rx.test(type));
-});
-export const getFilteredVariants = (variants, callbackFilter) => variants.map((variant) => {
-    const matchingVariants = variant.variants.filter((variantPos) => callbackFilter(variantPos));
-    return {
-        ...variant,
-        variants: [...matchingVariants],
-    };
-});
-const filterPredicates = {
-    disease: (variantPos) => { var _a; return (_a = variantPos.association) === null || _a === void 0 ? void 0 : _a.some((association) => association.disease); },
-    predicted: (variantPos) => variantPos.hasPredictions,
-    nonDisease: (variantPos) => {
-        var _a;
-        return (_a = variantPos.association) === null || _a === void 0 ? void 0 : _a.some((association) => association.disease === false);
-    },
-    uncertain: (variantPos) => (typeof variantPos.clinicalSignificances === 'undefined' &&
-        !variantPos.hasPredictions) ||
-        (variantPos.clinicalSignificances &&
-            significanceMatches(variantPos.clinicalSignificances, consequences.uncertain)),
-    UniProt: (variantPos) => variantPos.xrefNames &&
-        (variantPos.xrefNames.includes('uniprot') ||
-            variantPos.xrefNames.includes('UniProt')),
-    ClinVar: (variantPos) => variantPos.xrefNames &&
-        (variantPos.xrefNames.includes('ClinVar') ||
-            variantPos.xrefNames.includes('clinvar')),
-    LSS: (variantPos) => variantPos.sourceType === 'large_scale_study' ||
-        variantPos.sourceType === 'mixed',
-};
-const filterConfig = [
-    {
-        name: 'disease',
-        type: {
-            name: 'consequence',
-            text: 'Filter Consequence',
-        },
-        options: {
-            label: 'Likely pathogenic or pathogenic',
-            color: scaleColors.UPDiseaseColor,
-        },
-        filterPredicate: filterPredicates['disease'],
-        filterData: (variants) => getFilteredVariants(variants, filterPredicates['disease']),
-    },
-    {
-        name: 'predicted',
-        type: {
-            name: 'consequence',
-            text: 'Filter Consequence',
-        },
-        options: {
-            label: 'Predicted consequence',
-            color: scaleColors.predictedColor,
-        },
-        filterPredicate: filterPredicates['predicted'],
-        filterData: (variants) => getFilteredVariants(variants, filterPredicates['predicted']),
-    },
-    {
-        name: 'nonDisease',
-        type: {
-            name: 'consequence',
-            text: 'Filter Consequence',
-        },
-        options: {
-            label: 'Likely benign or benign',
-            color: scaleColors.UPNonDiseaseColor,
-        },
-        filterPredicate: filterPredicates['nonDisease'],
-        filterData: (variants) => getFilteredVariants(variants, filterPredicates['nonDisease']),
-    },
-    {
-        name: 'uncertain',
-        type: {
-            name: 'consequence',
-            text: 'Filter Consequence',
-        },
-        options: {
-            label: 'Uncertain significance',
-            color: scaleColors.othersColor,
-        },
-        filterPredicate: filterPredicates['uncertain'],
-        filterData: (variants) => getFilteredVariants(variants, filterPredicates['uncertain']),
-    },
-    {
-        name: 'UniProt',
-        type: {
-            name: 'provenance',
-            text: 'Filter Provenance',
-        },
-        options: {
-            label: 'UniProt reviewed',
-            color: '#9f9f9f',
-        },
-        filterPredicate: filterPredicates['UniProt'],
-        filterData: (variants) => getFilteredVariants(variants, filterPredicates['UniProt']),
-    },
-    {
-        name: 'ClinVar',
-        type: {
-            name: 'provenance',
-            text: 'Filter Provenance',
-        },
-        options: {
-            label: 'ClinVar',
-            color: '#9f9f9f',
-        },
-        filterPredicate: filterPredicates['ClinVar'],
-        filterData: (variants) => getFilteredVariants(variants, filterPredicates['ClinVar']),
-    },
-    {
-        name: 'LSS',
-        type: {
-            name: 'provenance',
-            text: 'Filter Provenance',
-        },
-        options: {
-            label: 'Large scale studies',
-            color: '#9f9f9f',
-        },
-        filterPredicate: filterPredicates['LSS'],
-        filterData: (variants) => getFilteredVariants(variants, filterPredicates['LSS']),
-    },
-];
-const countVariantsForFilter = (filterName, variant) => {
-    const variantWrapper = [{ variants: [variant] }];
-    const filter = filterConfig.find((filter) => filter.name === filterName);
-    if (filter) {
-        return filter.filterData(variantWrapper)[0].variants.length > 0;
-    }
-    return false;
-};
-export const colorConfig = (variant) => {
-    if (countVariantsForFilter('disease', variant)) {
-        return scaleColors.UPDiseaseColor;
-    }
-    else if (countVariantsForFilter('nonDisease', variant)) {
-        return scaleColors.UPNonDiseaseColor;
-    }
-    else if (countVariantsForFilter('uncertain', variant)) {
-        return scaleColors.othersColor;
-    }
-    else if (countVariantsForFilter('predicted', variant)) {
-        return scaleColors.predictedColor;
-    }
-    return scaleColors.othersColor;
-};
-export default filterConfig;
-//# sourceMappingURL=filter-config.js.map

package/dist/es/filter-config.js.map

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package/dist/es/index.d.ts

@@ -1,7 +0,0 @@
-import ProtvistaUniprot from './protvista-uniprot';
-import ProtvistaUniprotStructure from './protvista-uniprot-structure';
-import filterConfig, { colorConfig } from './filter-config';
-import getFeatureTooltip from './tooltips/featureTooltip';
-import getStructureTooltip from './tooltips/structureTooltip';
-import getVariationTooltip from './tooltips/variationTooltip';
-export { ProtvistaUniprot as default, ProtvistaUniprotStructure, filterConfig, colorConfig, getFeatureTooltip, getStructureTooltip, getVariationTooltip, };

package/dist/es/index.js

@@ -1,8 +0,0 @@
-import ProtvistaUniprot from './protvista-uniprot';
-import ProtvistaUniprotStructure from './protvista-uniprot-structure';
-import filterConfig, { colorConfig } from './filter-config';
-import getFeatureTooltip from './tooltips/featureTooltip';
-import getStructureTooltip from './tooltips/structureTooltip';
-import getVariationTooltip from './tooltips/variationTooltip';
-export { ProtvistaUniprot as default, ProtvistaUniprotStructure, filterConfig, colorConfig, getFeatureTooltip, getStructureTooltip, getVariationTooltip, };
-//# sourceMappingURL=index.js.map

package/dist/es/index.js.map

@@ -1 +0,0 @@
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package/dist/es/protvista-uniprot-structure.js

@@ -1,379 +0,0 @@
-var __decorate = (this && this.__decorate) || function (decorators, target, key, desc) {
-    var c = arguments.length, r = c < 3 ? target : desc === null ? desc = Object.getOwnPropertyDescriptor(target, key) : desc, d;
-    if (typeof Reflect === "object" && typeof Reflect.decorate === "function") r = Reflect.decorate(decorators, target, key, desc);
-    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;
-    return c > 3 && r && Object.defineProperty(target, key, r), r;
-};
-import { LitElement, html, svg, css } from 'lit';
-// eslint-disable-next-line @typescript-eslint/no-unused-vars
-import { customElement } from 'lit/decorators.js';
-import { unsafeHTML } from 'lit/directives/unsafe-html.js';
-import NightingaleStructure from '@nightingale-elements/nightingale-structure';
-import ProtvistaDatatable from 'protvista-datatable';
-import { fetchAll, loadComponent } from './utils';
-import loaderIcon from './icons/spinner.svg';
-import downloadIcon from './icons/download.svg';
-import loaderStyles from './styles/loader-styles';
-const PDBLinks = [
-    { name: 'PDBe', link: 'https://www.ebi.ac.uk/pdbe-srv/view/entry/' },
-    { name: 'RCSB-PDB', link: 'https://www.rcsb.org/structure/' },
-    { name: 'PDBj', link: 'https://pdbj.org/mine/summary/' },
-    { name: 'PDBsum', link: 'https://www.ebi.ac.uk/pdbsum/' },
-];
-const alphaFoldLink = 'https://alphafold.ebi.ac.uk/entry/';
-const foldseekLink = `https://search.foldseek.com/search`;
-const processPDBData = (data) => data.dbReferences
-    .filter((xref) => xref.type === 'PDB')
-    .sort((refA, refB) => refA.id.localeCompare(refB.id))
-    .map(({ id, properties }) => {
-    if (!properties) {
-        return;
-    }
-    const { chains, resolution, method } = properties;
-    let chain;
-    let positions;
-    if (chains) {
-        const tokens = chains.split('=');
-        if (tokens.length === 2) {
-            [chain, positions] = tokens;
-        }
-    }
-    const output = {
-        id,
-        source: 'PDB',
-        method,
-        resolution: !resolution || resolution === '-' ? undefined : resolution,
-        downloadLink: `https://www.ebi.ac.uk/pdbe/entry-files/download/pdb${id.toLowerCase()}.ent`,
-        chain,
-        positions,
-        protvistaFeatureId: id,
-    };
-    return output;
-})
-    .filter((transformedItem) => transformedItem !== undefined);
-const processAFData = (data) => data.map((d) => ({
-    id: d.entryId,
-    source: 'AlphaFold',
-    method: 'Predicted',
-    positions: `${d.uniprotStart}-${d.uniprotEnd}`,
-    protvistaFeatureId: d.entryId,
-    downloadLink: d.pdbUrl,
-}));
-const AFMetaInfo = html `
-  <strong>Model Confidence:</strong>
-  <ul class="no-bullet">
-    <li>
-      <span class="af-legend" style="background-color: rgb(0, 83, 214)"></span>
-      Very high (pLDDT > 90)
-    </li>
-    <li>
-      <span
-        class="af-legend"
-        style="background-color: rgb(101, 203, 243)"
-      ></span>
-      Confident (90 > pLDDT > 70)
-    </li>
-    <li>
-      <span class="af-legend" style="background-color:rgb(255, 219, 19)"></span>
-      Low (70 > pLDDT > 50)
-    </li>
-    <li>
-      <span class="af-legend" style="background-color:rgb(255, 125, 69)"></span>
-      Very low (pLDDT < 50)
-    </li>
-  </ul>
-  <p class="small">
-    AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
-    Some regions with low pLDDT may be unstructured in isolation.
-  </p>
-`;
-const AMMetaInfo = html `<strong>Model Pathogenicity:</strong>
-  <ul class="no-bullet">
-    <li>
-      <span class="af-legend" style="background-color: rgb(154, 19, 26)"></span>
-      Likely pathogenic (score > 0.564)
-    </li>
-    <li>
-      <span
-        class="af-legend"
-        style="background-color: rgb(168, 169, 173)"
-      ></span>
-      Uncertain (0.564 >= score >= 0.34)
-    </li>
-    <li>
-      <span class="af-legend" style="background-color: rgb(61, 84, 147)"></span>
-      Likely benign (score < 0.34)
-    </li>
-  </ul>
-  <p class="small">
-    The displayed colour for each residue is the average AlphaMissense
-    pathogenicity score across all possible amino acid substitutions at that
-    position.
-  </p>`;
-const foldseekURL = (accession, sourceDB) => {
-    return html `<a
-    href="${foldseekLink}?accession=${accession}&source=${sourceDB}"
-    >Foldseek</a
-  >`;
-};
-const styleId = 'protvista-styles';
-let ProtvistaUniprotStructure = class ProtvistaUniprotStructure extends LitElement {
-    constructor() {
-        super();
-        loadComponent('nightingale-structure', NightingaleStructure);
-        loadComponent('protvista-datatable', ProtvistaDatatable);
-        this.loading = true;
-        this.onTableRowClick = this.onTableRowClick.bind(this);
-        this.addStyles();
-        this.colorTheme = 'alphafold';
-    }
-    static get properties() {
-        return {
-            accession: { type: String },
-            structureId: { type: String },
-            data: { type: Object },
-            loading: { type: Boolean },
-            colorTheme: { type: String },
-        };
-    }
-    async connectedCallback() {
-        super.connectedCallback();
-        if (!this.accession)
-            return;
-        // https://www.ebi.ac.uk/pdbe/api/mappings/best_structures/${this.accession}
-        const pdbUrl = `https://www.ebi.ac.uk/proteins/api/proteins/${this.accession}`;
-        const alphaFoldURl = `https://alphafold.ebi.ac.uk/api/prediction/${this.accession}`;
-        const rawData = await fetchAll([pdbUrl, alphaFoldURl]);
-        this.loading = false;
-        // TODO: return if no data at all
-        // if (!payload) return;
-        const pdbData = processPDBData(rawData[pdbUrl] || []);
-        const afData = processAFData(rawData[alphaFoldURl] || []);
-        const data = [...pdbData, ...afData];
-        if (!data || !data.length)
-            return;
-        this.data = data;
-    }
-    disconnectedCallback() {
-        this.removeStyles();
-    }
-    updated() {
-        var _a;
-        const protvistaDatatableElt = this.querySelector('protvista-datatable');
-        if (!(protvistaDatatableElt === null || protvistaDatatableElt === void 0 ? void 0 : protvistaDatatableElt.selectedid) && ((_a = this.data) === null || _a === void 0 ? void 0 : _a[0])) {
-            // Select the first element in the table
-            this.onTableRowClick({ id: this.data[0].id });
-            protvistaDatatableElt.selectedid = this.structureId;
-        }
-    }
-    addStyles() {
-        var _a;
-        // We are not using static get styles()
-        // as we are not using the shadowDOM
-        // because of Mol*
-        if (!document.getElementById(styleId)) {
-            const styleTag = document.createElement('style');
-            styleTag.id = styleId;
-            styleTag.innerHTML = `
-      ${loaderStyles.toString()}
-      ${this.cssStyle}
-      `;
-            (_a = document.querySelector('head')) === null || _a === void 0 ? void 0 : _a.append(styleTag);
-        }
-    }
-    removeStyles() {
-        const styleTag = document.getElementById(styleId);
-        if (styleTag) {
-            styleTag.remove();
-        }
-    }
-    onTableRowClick({ id }) {
-        this.structureId = id;
-        if (this.structureId.startsWith('AF-')) {
-            this.metaInfo = AFMetaInfo;
-        }
-        else {
-            this.metaInfo = undefined;
-        }
-    }
-    get cssStyle() {
-        return css `
-      .protvista-uniprot-structure {
-        line-height: normal;
-      }
-      .theme-selection {
-        padding-bottom: 1rem;
-      }
-      .protvista-uniprot-structure__structure {
-        display: flex;
-      }
-      .protvista-uniprot-structure__meta {
-        flex: 1;
-        padding: 1rem;
-      }
-      .protvista-uniprot-structure__structure nightingale-structure {
-        z-index: 40000;
-        width: 100%;
-        flex: 4;
-      }
-      .protvista-uniprot-structure__meta .small {
-        font-size: 0.75rem;
-      }
-      .protvista-uniprot-structure__meta .no-bullet {
-        list-style: none;
-        padding: 0;
-        margin: 0;
-      }
-      .protvista-uniprot-structure__meta .no-bullet li {
-        padding: 0;
-        margin: 0.5rem 0;
-      }
-      .protvista-uniprot-structure__meta .af-legend::before {
-        content: '';
-        margin: 0;
-        display: inline-block;
-        width: 20px;
-        height: 16px;
-      }
-      .download-link svg {
-        width: 1rem;
-      }
-    `;
-    }
-    /**
-     * we need to use the light DOM.
-     * */
-    createRenderRoot() {
-        return this;
-    }
-    toggleColorTheme(e) {
-        this.colorTheme = e.target.value;
-        if (e.target.value === 'alphafold') {
-            this.metaInfo = AFMetaInfo;
-        }
-        else {
-            this.metaInfo = AMMetaInfo;
-        }
-    }
-    render() {
-        var _a;
-        return html `
-      <div class="protvista-uniprot-structure">
-        <div class="protvista-uniprot-structure__structure">
-          ${this.metaInfo
-            ? html ` <div class="protvista-uniprot-structure__meta">
-                <div class="theme-selection">
-                  Select color scale <br />
-                  <input
-                    type="radio"
-                    id="alphafold"
-                    name="colorScheme"
-                    value="alphafold"
-                    @click=${(e) => this.toggleColorTheme(e)}
-                    checked
-                  />
-                  <label for="alphafold">Confidence</label><br />
-                  <input
-                    type="radio"
-                    id="alphamissense"
-                    name="colorScheme"
-                    value="alphamissense"
-                    @click=${(e) => this.toggleColorTheme(e)}
-                  />
-                  <label for="alphamissense">Pathogenecity</label><br />
-                </div>
-                ${this.metaInfo}
-              </div>`
-            : html ``}
-          ${this.structureId
-            ? html `<nightingale-structure
-                structure-id=${this.structureId}
-                protein-accession=${this.accession}
-                color-theme=${this.colorTheme}
-              ></nightingale-structure>`
-            : html ``}
-        </div>
-        <div class="protvista-uniprot-structure__table">
-          ${this.data && this.data.length
-            ? html `<protvista-datatable noScrollToRow noDeselect filter-scroll>
-                <table>
-                  <thead>
-                    <tr>
-                      <th data-filter="source">Source</th>
-                      <th>Identifier</th>
-                      <th data-filter="method">Method</th>
-                      <th>Resolution</th>
-                      <th>Chain</th>
-                      <th>Positions</th>
-                      <th>Links</th>
-                      <th><!--Download--></th>
-                    </tr>
-                  </thead>
-                  <tbody>
-                    ${(_a = this.data) === null || _a === void 0 ? void 0 : _a.map(({ source, id, method, resolution, chain, positions, downloadLink, }) => html `<tr
-                        data-id="${id}"
-                        @click="${() => this.onTableRowClick({ id })}"
-                      >
-                        <td data-filter="source" data-filter-value="${source}">
-                          <strong>${source}</strong>
-                        </td>
-                        <td>${id}</td>
-                        <td data-filter="method" data-filter-value="${method}">
-                          ${method}
-                        </td>
-                        <td>
-                          ${resolution ? resolution.replace('A', 'Å') : ''}
-                        </td>
-                        <td>${chain || ''}</td>
-                        <td>${positions || ''}</td>
-                        <td>
-                          ${source === 'PDB'
-                ? html `
-                                ${PDBLinks.map((pdbLink) => {
-                    return html `
-                                    <a href="${pdbLink.link}${id}"
-                                      >${pdbLink.name}</a
-                                    >
-                                  `;
-                }).reduce((prev, curr) => html ` ${prev} · ${curr} `)}
-                              `
-                : html `<a href="${alphaFoldLink}${this.accession}"
-                                >AlphaFold</a
-                              >`}
-                        </td>
-                        <td>
-                          ${downloadLink
-                ? html `<a
-                                  href="${downloadLink}"
-                                  class="download-link"
-                                  >${svg `${unsafeHTML(downloadIcon)}`}</a
-                                >
-                                ·
-                                ${foldseekURL(source === 'PDB' ? id : this.accession, source === 'PDB' ? 'PDB' : 'AlphaFoldDB')}`
-                : ''}
-                        </td>
-                      </tr>`)}
-                  </tbody>
-                </table>
-              </protvista-datatable>`
-            : html ``}
-          ${this.loading
-            ? html `<div class="protvista-loader">
-                ${svg `${unsafeHTML(loaderIcon)}`}
-              </div>`
-            : html ``}
-          ${!this.data && !this.loading
-            ? html `<div class="protvista-no-results">
-                No structure information available for ${this.accession}
-              </div>`
-            : html ``}
-        </div>
-      </div>
-    `;
-    }
-};
-ProtvistaUniprotStructure = __decorate([
-    customElement('protvista-uniprot-structure')
-], ProtvistaUniprotStructure);
-export default ProtvistaUniprotStructure;
-//# sourceMappingURL=protvista-uniprot-structure.js.map

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

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