protvista-uniprot 2.7.5 → 2.8.2
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.
- package/dist/es/config.json +17 -2
- package/dist/es/index.d.ts +4 -1
- package/dist/es/protvista-uniprot-structure.d.ts +2 -0
- package/dist/es/protvista-uniprot-structure.js +68 -51
- package/dist/es/protvista-uniprot-structure.js.map +1 -1
- package/dist/es/protvista-uniprot.d.ts +4 -1
- package/dist/protvista-uniprot.js +81 -129
- package/dist/protvista-uniprot.js.LICENSE.txt +10 -10
- package/dist/protvista-uniprot.js.map +1 -1
- package/package.json +18 -18
- package/src/config.json +17 -2
- package/src/protvista-uniprot-structure.ts +81 -57
package/dist/es/config.json
CHANGED
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@@ -554,7 +554,7 @@
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"data": [
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{
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"adapter": "protvista-feature-adapter",
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"url": "
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"url": "https://www.ebi.ac.uk/proteins/api/mutagenesis/{accession}"
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}
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],
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"tooltip": "Site which has been experimentally altered by mutagenesis"
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@@ -566,7 +566,10 @@
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"label": "Proteomics",
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"trackType": "protvista-track",
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"adapter": "protvista-proteomics-adapter",
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-
"
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"urls": [
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"https://www.ebi.ac.uk/proteins/api/proteomics/{accession}",
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"https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}"
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],
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"tracks": [
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{
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"name": "unique",
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@@ -593,6 +596,18 @@
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}
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],
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"tooltip": ""
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},
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{
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"name": "proteomics-ptm",
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"label": "PTM",
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"trackType": "protvista-track",
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"data": [
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{
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"adapter": "protvista-proteomics-adapter",
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"url": "https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}"
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}
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],
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"tooltip": ""
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}
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]
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},
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package/dist/es/index.d.ts
CHANGED
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@@ -4,7 +4,10 @@ import _ProtvistaUniprotStructure from './protvista-uniprot-structure';
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export declare const transformDataFeatureAdapter: any;
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export declare const transformDataProteomicsAdapter: any;
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export declare const transformDataStructureAdapter: any;
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export declare const transformDataVariationAdapter: (data: import("protvista-variation-adapter/dist/es/variants").ProteinsAPIVariation) =>
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export declare const transformDataVariationAdapter: (data: import("protvista-variation-adapter/dist/es/variants").ProteinsAPIVariation) => {
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sequence: string;
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variants: any[];
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};
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export declare const transformDataInterproAdapter: any;
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export declare const ProtvistaUniprotStructure: typeof _ProtvistaUniprotStructure;
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export declare const DownloadPanel: typeof _DownloadPanel;
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@@ -6,6 +6,7 @@ declare type ProcessedStructureData = {
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resolution?: string;
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chain?: string;
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positions?: string;
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downloadLink?: string;
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protvistaFeatureId: string;
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};
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declare class ProtvistaUniprotStructure extends LitElement {
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@@ -31,6 +32,7 @@ declare class ProtvistaUniprotStructure extends LitElement {
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};
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connectedCallback(): Promise<void>;
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disconnectedCallback(): void;
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updated(): void;
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addStyles(): void;
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removeStyles(): void;
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onTableRowClick({ id }: {
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@@ -5,6 +5,7 @@ import ProtvistaStructure from 'protvista-structure';
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import ProtvistaDatatable from 'protvista-datatable';
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import { loadComponent } from './loadComponents';
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import loaderIcon from './icons/spinner.svg';
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import downloadIcon from './icons/download.svg';
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import loaderStyles from './styles/loader-styles';
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const PDBLinks = [
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{ name: 'PDB', link: 'https://www.ebi.ac.uk/pdbe-srv/view/entry/' },
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@@ -34,6 +35,7 @@ const processPDBData = (data) => data.dbReferences
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source: 'PDB',
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method,
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resolution: !resolution || resolution === '-' ? undefined : resolution,
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downloadLink: `https://www.ebi.ac.uk/pdbe/entry-files/download/pdb${id.toLowerCase()}.ent`,
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chain,
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positions,
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protvistaFeatureId: id,
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@@ -47,46 +49,8 @@ const processAFData = (data) => data.map((d) => ({
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method: 'Predicted',
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positions: `${d.uniprotStart}-${d.uniprotEnd}`,
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protvistaFeatureId: d.entryId,
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downloadLink: d.pdbUrl,
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}));
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const getColumnConfig = (accession) => ({
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source: {
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label: 'Source',
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resolver: ({ source }) => html `<strong>${source}</strong>`,
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},
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type: {
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label: 'Identifier',
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resolver: ({ id }) => id,
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},
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method: {
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label: 'Method',
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resolver: ({ method }) => method,
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},
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resolution: {
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label: 'Resolution',
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resolver: ({ resolution }) => resolution ? resolution.replace('A', 'Å') : '',
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},
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chain: {
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label: 'Chain',
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resolver: ({ chain }) => chain || '',
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},
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positions: {
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label: 'Positions',
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resolver: ({ positions }) => positions || '',
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},
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links: {
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label: 'Links',
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resolver: ({ source, id }) => {
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if (source === 'PDB') {
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return html `
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${PDBLinks.map((pdbLink) => {
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return html ` <a href="${pdbLink.link}${id}">${pdbLink.name}</a> `;
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}).reduce((prev, curr) => html ` ${prev} · ${curr} `)}
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`;
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}
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return html `<a href="${alphaFoldLink}${accession}">AlphaFold</a>`;
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},
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},
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});
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const AFMetaInfo = html `
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<strong>Model Confidence:</strong>
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<ul class="no-bullet">
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@@ -154,17 +118,18 @@ class ProtvistaUniprotStructure extends LitElement {
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if (!data || !data.length)
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return;
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this.data = data;
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const protvistaDatatableElt = this.querySelector('protvista-datatable');
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// Select the first element in the table
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this.onTableRowClick({ id: this.data[0].id });
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protvistaDatatableElt.columns = getColumnConfig(this.accession);
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protvistaDatatableElt.data = this.data;
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protvistaDatatableElt.rowClickEvent = this.onTableRowClick;
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protvistaDatatableElt.selectedid = this.structureId;
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}
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disconnectedCallback() {
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this.removeStyles();
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}
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updated() {
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const protvistaDatatableElt = this.querySelector('protvista-datatable');
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if (!protvistaDatatableElt.selectedid) {
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// Select the first element in the table
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this.onTableRowClick({ id: this.data[0].id });
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protvistaDatatableElt.selectedid = this.structureId;
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}
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}
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addStyles() {
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var _a;
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// We are not using static get styles()
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@@ -228,6 +193,9 @@ class ProtvistaUniprotStructure extends LitElement {
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width: 20px;
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height: 16px;
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}
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.download-link svg {
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width: 1rem;
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}
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`;
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}
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/**
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@@ -237,6 +205,7 @@ class ProtvistaUniprotStructure extends LitElement {
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return this;
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}
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render() {
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var _a;
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return html `
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<div class="protvista-uniprot-structure">
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<div class="protvista-uniprot-structure__structure">
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@@ -253,11 +222,59 @@ class ProtvistaUniprotStructure extends LitElement {
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: html ``}
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</div>
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<div class="class="protvista-uniprot-structure__table">
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<protvista-datatable
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<protvista-datatable noScrollToRow noDeselect filter-scroll>
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<table>
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<thead>
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<tr>
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<th data-filter="source">Source</th>
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<th>Identifier</th>
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<th data-filter="method">Method</th>
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<th>Resolution</th>
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<th>Chain</th>
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<th>Positions</th>
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<th>Links</th>
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<th><!--Download--></th>
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</tr>
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</thead>
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<tbody>
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${(_a = this.data) === null || _a === void 0 ? void 0 : _a.map(({ source, id, method, resolution, chain, positions, downloadLink, }) => html `<tr
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data-id="${id}"
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@click="${() => this.onTableRowClick({ id })}"
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>
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<td data-filter="source" data-filter-value="${source}">
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<strong>${source}</strong>
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</td>
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<td>${id}</td>
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<td data-filter="method" data-filter-value="${method}">
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${method}
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</td>
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<td>${resolution ? resolution.replace('A', 'Å') : ''}</td>
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<td>${chain || ''}</td>
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<td>${positions || ''}</td>
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<td>
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${source === 'PDB'
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? html `
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${PDBLinks.map((pdbLink) => {
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return html `
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<a href="${pdbLink.link}${id}">${pdbLink.name}</a>
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`;
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}).reduce((prev, curr) => html ` ${prev} · ${curr} `)}
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`
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: html `<a href="${alphaFoldLink}${this.accession}"
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>AlphaFold</a
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>`}
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</td>
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<td>
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${downloadLink
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? html `<a href="${downloadLink}" class="download-link"
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>${svg `${unsafeHTML(downloadIcon)}`}</a
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>`
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: ''}
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</td>
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</tr>`)}
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</tbody>
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</table>
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</protvista-datatable>
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${this.loading
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? html `<div class="protvista-loader">
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${svg `${unsafeHTML(loaderIcon)}`}
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"protvista-uniprot-structure.js","sourceRoot":"","sources":["../../src/protvista-uniprot-structure.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,IAAI,EAAE,GAAG,EAAkB,GAAG,EAAE,MAAM,aAAa,CAAC;AACzE,OAAO,EAAE,UAAU,EAAE,MAAM,oCAAoC,CAAC;AAChE,OAAO,EAAE,IAAI,EAAE,MAAM,aAAa,CAAC;AACnC,OAAO,kBAAkB,MAAM,qBAAqB,CAAC;AACrD,OAAO,kBAAkB,MAAM,qBAAqB,CAAC;AACrD,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AAEjD,OAAO,UAAU,MAAM,qBAAqB,CAAC;AAC7C,OAAO,YAAY,MAAM,wBAAwB,CAAC;AAOlD,MAAM,QAAQ,GAAG;IACf,EAAE,IAAI,EAAE,KAAK,EAAE,IAAI,EAAE,4CAA4C,EAAE;IACnE,EAAE,IAAI,EAAE,UAAU,EAAE,IAAI,EAAE,iCAAiC,EAAE;IAC7D,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,gCAAgC,EAAE;IACxD,EAAE,IAAI,EAAE,QAAQ,EAAE,IAAI,EAAE,+BAA+B,EAAE;CAC1D,CAAC;AACF,MAAM,aAAa,GAAG,oCAAoC,CAAC;
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+
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@@ -6,7 +6,10 @@ import { NightingaleEvent } from './types/nightingale-components';
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6
6
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export declare const transformDataFeatureAdapter: any;
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7
7
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export declare const transformDataProteomicsAdapter: any;
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8
8
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export declare const transformDataStructureAdapter: any;
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9
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-
export declare const transformDataVariationAdapter: (data: import("protvista-variation-adapter/dist/es/variants").ProteinsAPIVariation) =>
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9
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+
export declare const transformDataVariationAdapter: (data: import("protvista-variation-adapter/dist/es/variants").ProteinsAPIVariation) => {
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10
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+
sequence: string;
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11
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+
variants: any[];
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12
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+
};
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10
13
|
export declare const transformDataInterproAdapter: any;
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11
14
|
export declare const filterConfig: {
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12
15
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name: string;
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