protvista-uniprot 2.12.2 → 2.13.0

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

@@ -1,7 +1,7 @@
 import { LitElement, html, svg, css } from 'lit-element';
 import { unsafeHTML } from 'lit-html/directives/unsafe-html.js';
 import { load } from 'data-loader';
-import ProtvistaStructure from 'protvista-structure';
+import NightingaleStructure from '@nightingale-elements/nightingale-structure';
 import ProtvistaDatatable from 'protvista-datatable';
 import { loadComponent } from './loadComponents';
 import loaderIcon from './icons/spinner.svg';
@@ -80,18 +80,45 @@ const AFMetaInfo = html `
     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=${sourceDB}">Foldseek</a>`;
+    return html `<a
+    href="${foldseekLink}?accession=${accession}&source=${sourceDB}"
+    >Foldseek</a
+  >`;
 };
 const styleId = 'protvista-styles';
 class ProtvistaUniprotStructure extends LitElement {
     constructor() {
         super();
-        loadComponent('protvista-structure', ProtvistaStructure);
+        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 {
@@ -99,6 +126,7 @@ class ProtvistaUniprotStructure extends LitElement {
             structureId: { type: String },
             data: { type: Object },
             loading: { type: Boolean },
+            colorTheme: { type: String },
         };
     }
     async connectedCallback() {
@@ -167,6 +195,12 @@ class ProtvistaUniprotStructure extends LitElement {
     }
     get cssStyle() {
         return css `
+      .protvista-uniprot-structure {
+        line-height: normal;
+      }
+      .theme-selection {
+        padding-bottom: 1rem;
+      }
       .protvista-uniprot-structure__structure {
         display: flex;
       }
@@ -174,7 +208,7 @@ class ProtvistaUniprotStructure extends LitElement {
         flex: 1;
         padding: 1rem;
       }
-      .protvista-uniprot-structure__structure protvista-structure {
+      .protvista-uniprot-structure__structure nightingale-structure {
         z-index: 40000;
         width: 100%;
         flex: 4;
@@ -209,91 +243,128 @@ class ProtvistaUniprotStructure extends LitElement {
     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">
           ${this.metaInfo
-            ? html `<div class="protvista-uniprot-structure__meta">
+            ? html ` <div class="protvista-uniprot-structure__meta">
+                <div class="theme-selection">
+                  Select color scale <br />
+                  <input
+                    type="radio"
+                    id="alphafold"
+                    name="colorScheme"
+                    value="alphafold"
+                    @click=${(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 ``}
           ${this.structureId
-            ? html `<protvista-structure
-                structureid=${this.structureId}
-                accession=${this.accession}
-              ></protvista-structure>`
+            ? html `<nightingale-structure
+                structure-id=${this.structureId}
+                protein-accession=${this.accession}
+                color-theme=${this.colorTheme}
+              ></nightingale-structure>`
             : html ``}
         </div>
-        <div class="class="protvista-uniprot-structure__table">
-        ${this.data && this.data.length
+        <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'
+                <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) => {
+                                ${PDBLinks.map((pdbLink) => {
                     return html `
-                                  <a href="${pdbLink.link}${id}"
-                                    >${pdbLink.name}</a
-                                  >
-                                `;
+                                    <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')}`
+                                >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>`
+                        </td>
+                      </tr>`)}
+                  </tbody>
+                </table>
+              </protvista-datatable>`
             : html ``}
-        ${this.loading
+          ${this.loading
             ? html `<div class="protvista-loader">
-              ${svg `${unsafeHTML(loaderIcon)}`}
-            </div>`
+                ${svg `${unsafeHTML(loaderIcon)}`}
+              </div>`
             : html ``}
-        ${!this.data && !this.loading
+          ${!this.data && !this.loading
             ? html `<div class="protvista-no-results">
-              No structure information available for ${this.accession}
-            </div>`
+                No structure information available for ${this.accession}
+              </div>`
             : html ``}
+        </div>
       </div>
     `;
     }

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

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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,oBAGN,MAAM,6CAA6C,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,sBAAsB,CAAC;AAChD,OAAO,YAAY,MAAM,wBAAwB,CAAC;AAElD,MAAM,QAAQ,GAAG;IACf,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,4CAA4C,EAAE;IACpE,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;AAC3D,MAAM,YAAY,GAAG,oCAAoC,CAAC;AAa1D,MAAM,cAAc,GAAG,CAAC,IAAmB,EAA4B,EAAE,CACvE,IAAI,CAAC,YAAY;KACd,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,KAAK,KAAK,CAAC;KACrC,IAAI,CAAC,CAAC,IAAI,EAAE,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,aAAa,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;KACpD,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE;IAC1B,IAAI,CAAC,UAAU,EAAE;QACf,OAAO;KACR;IACD,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,EAAE,GAAG,UAAU,CAAC;IAElD,IAAI,KAAK,CAAC;IACV,IAAI,SAAS,CAAC;IACd,IAAI,MAAM,EAAE;QACV,MAAM,MAAM,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QACjC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE;YACvB,CAAC,KAAK,EAAE,SAAS,CAAC,GAAG,MAAM,CAAC;SAC7B;KACF;IACD,MAAM,MAAM,GAA2B;QACrC,EAAE;QACF,MAAM,EAAE,KAAK;QACb,MAAM;QACN,UAAU,EAAE,CAAC,UAAU,IAAI,UAAU,KAAK,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,UAAU;QACtE,YAAY,EAAE,sDAAsD,EAAE,CAAC,WAAW,EAAE,MAAM;QAC1F,KAAK;QACL,SAAS;QACT,kBAAkB,EAAE,EAAE;KACvB,CAAC;IACF,OAAO,MAAM,CAAC;AAChB,CAAC,CAAC;KACD,MAAM,CACL,CACE,eAAmD,EACR,EAAE,CAC7C,eAAe,KAAK,SAAS,CAChC,CAAC;AAEN,MAAM,aAAa,GAAG,CAAC,IAAsB,EAA4B,EAAE,CACzE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;IACf,EAAE,EAAE,CAAC,CAAC,OAAO;IACb,MAAM,EAAE,WAAW;IACnB,MAAM,EAAE,WAAW;IACnB,SAAS,EAAE,GAAG,CAAC,CAAC,YAAY,IAAI,CAAC,CAAC,UAAU,EAAE;IAC9C,kBAAkB,EAAE,CAAC,CAAC,OAAO;IAC7B,YAAY,EAAE,CAAC,CAAC,MAAM;CACvB,CAAC,CAAC,CAAC;AAEN,MAAM,UAAU,GAAG,IAAI,CAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;CA2BtB,CAAC;AAEF,MAAM,UAAU,GAAG,IAAI,CAAA;;;;;;;;;;;;;;;;;;;;;;OAsBhB,CAAC;AAER,MAAM,WAAW,GAAG,CAAC,SAAS,EAAE,QAAQ,EAAE,EAAE;IAC1C,OAAO,IAAI,CAAA;YACD,YAAY,cAAc,SAAS,WAAW,QAAQ;;IAE9D,CAAC;AACL,CAAC,CAAC;AAEF,MAAM,OAAO,GAAG,kBAAkB,CAAC;AACnC,MAAM,yBAA0B,SAAQ,UAAU;IAQhD;QACE,KAAK,EAAE,CAAC;QACR,aAAa,CAAC,uBAAuB,EAAE,oBAAoB,CAAC,CAAC;QAC7D,aAAa,CAAC,qBAAqB,EAAE,kBAAkB,CAAC,CAAC;QACzD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC;QACpB,IAAI,CAAC,eAAe,GAAG,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACvD,IAAI,CAAC,SAAS,EAAE,CAAC;QACjB,IAAI,CAAC,UAAU,GAAG,WAAW,CAAC;IAChC,CAAC;IAED,MAAM,KAAK,UAAU;QACnB,OAAO;YACL,SAAS,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE;YAC3B,WAAW,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE;YAC7B,IAAI,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE;YACtB,OAAO,EAAE,EAAE,IAAI,EAAE,OAAO,EAAE;YAC1B,UAAU,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE;SAC7B,CAAC;IACJ,CAAC;IAED,KAAK,CAAC,iBAAiB;QACrB,KAAK,CAAC,iBAAiB,EAAE,CAAC;QAC1B,IAAI,CAAC,IAAI,CAAC,SAAS;YAAE,OAAO;QAC5B,4EAA4E;QAC5E,MAAM,MAAM,GAAG,+CAA+C,IAAI,CAAC,SAAS,EAAE,CAAC;QAC/E,MAAM,YAAY,GAAG,8CAA8C,IAAI,CAAC,SAAS,EAAE,CAAC;QAEpF,MAAM,OAAO,GAA2B,EAAE,CAAC;QAE3C,MAAM,OAAO,CAAC,GAAG,CACf,CAAC,MAAM,EAAE,YAAY,CAAC,CAAC,GAAG,CAAC,CAAC,GAAW,EAAE,EAAE,CACzC,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI,CACZ,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC;QACvC,8CAA8C;QAC9C,wBAAwB;QACxB,CAAC,KAAK,EAAE,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAC/B,CACF,CACF,CAAC;QAEF,IAAI,CAAC,OAAO,GAAG,KAAK,CAAC;QACrB,iCAAiC;QACjC,wBAAwB;QACxB,MAAM,OAAO,GAAG,cAAc,CAAC,OAAO,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC,CAAC;QACtD,MAAM,MAAM,GAAG,aAAa,CAAC,OAAO,CAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAC;QAC1D,MAAM,IAAI,GAAG,CAAC,GAAG,OAAO,EAAE,GAAG,MAAM,CAAC,CAAC;QACrC,IAAI,CAAC,IAAI,IAAI,CAAC,IAAI,CAAC,MAAM;YAAE,OAAO;QAElC,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;IACnB,CAAC;IAED,oBAAoB;QAClB,IAAI,CAAC,YAAY,EAAE,CAAC;IACtB,CAAC;IAED,OAAO;;QACL,MAAM,qBAAqB,GAAG,IAAI,CAAC,aAAa,CAC9C,qBAAqB,CACA,CAAC;QACxB,IAAI,CAAC,CAAA,qBAAqB,aAArB,qBAAqB,uBAArB,qBAAqB,CAAE,UAAU,CAAA,KAAI,MAAA,IAAI,CAAC,IAAI,0CAAG,CAAC,CAAC,CAAA,EAAE;YACxD,wCAAwC;YACxC,IAAI,CAAC,eAAe,CAAC,EAAE,EAAE,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC9C,qBAAqB,CAAC,UAAU,GAAG,IAAI,CAAC,WAAW,CAAC;SACrD;IACH,CAAC;IAED,SAAS;;QACP,uCAAuC;QACvC,oCAAoC;QACpC,kBAAkB;QAClB,IAAI,CAAC,QAAQ,CAAC,cAAc,CAAC,OAAO,CAAC,EAAE;YACrC,MAAM,QAAQ,GAAG,QAAQ,CAAC,aAAa,CAAC,OAAO,CAAC,CAAC;YACjD,QAAQ,CAAC,EAAE,GAAG,OAAO,CAAC;YACtB,QAAQ,CAAC,SAAS,GAAG;QACnB,YAAY,CAAC,QAAQ,EAAE;QACvB,IAAI,CAAC,QAAQ;OACd,CAAC;YACF,MAAA,QAAQ,CAAC,aAAa,CAAC,MAAM,CAAC,0CAAE,MAAM,CAAC,QAAQ,CAAC,CAAC;SAClD;IACH,CAAC;IAED,YAAY;QACV,MAAM,QAAQ,GAAG,QAAQ,CAAC,cAAc,CAAC,OAAO,CAAC,CAAC;QAClD,IAAI,QAAQ,EAAE;YACZ,QAAQ,CAAC,MAAM,EAAE,CAAC;SACnB;IACH,CAAC;IAED,eAAe,CAAC,EAAE,EAAE,EAAkB;QACpC,IAAI,CAAC,WAAW,GAAG,EAAE,CAAC;QACtB,IAAI,IAAI,CAAC,WAAW,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE;YACtC,IAAI,CAAC,QAAQ,GAAG,UAAU,CAAC;SAC5B;aAAM;YACL,IAAI,CA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package/dist/es/protvista-uniprot.d.ts

@@ -1,8 +1,5 @@
 import { LitElement } from 'lit-element';
-import ProtvistaTrackConfig from 'protvista-track';
 import _ProtvistaUniprotStructure from './protvista-uniprot-structure';
-import _DownloadPanel from './download-panel';
-import { NightingaleEvent } from './types/nightingale-components';
 export declare const transformDataFeatureAdapter: any;
 export declare const transformDataProteomicsAdapter: any;
 export declare const transformDataStructureAdapter: any;
@@ -10,6 +7,15 @@ export declare const transformDataVariationAdapter: (data: import("protvista-var
     sequence: string;
     variants: any[];
 };
+export declare const transformDataVariationGraphAdapter: (data: any) => {
+    name: string;
+    range: number[];
+    color: string;
+    values: {
+        position: number;
+        value: number;
+    }[];
+}[];
 export declare const transformDataInterproAdapter: any;
 export declare const transformDataProteomicsPTMApdapter: (data: {
     accession: string;
@@ -66,6 +72,11 @@ export declare const transformDataAlphaMissensePathogenicityAdapter: (data: impo
         sequence: string;
     };
 }) => Promise<string>;
+export declare const transformDataAlphaMissenseHeatmapAdapter: (data: import("./commonTypes").AlphafoldPayload, protein: {
+    sequence: {
+        sequence: string;
+    };
+}) => Promise<Record<string, string>[]>;
 export declare const filterConfig: {
     name: string;
     type: {
@@ -73,18 +84,18 @@ export declare const filterConfig: {
         text: string;
     };
     options: {
-        labels: string[];
-        colors: string[];
+        label: string;
+        color: string;
     };
+    filterPredicate: (variantPos: any) => any;
     filterData: (variants: ProtvistaVariationData) => {
         variants: ProtvistaVariant[];
     }[];
 }[];
-export declare const colorConfig: (variant: ProtvistaVariant) => string;
+export declare const colorConfig: (variant: any) => string;
 export declare const ProtvistaUniprotStructure: typeof _ProtvistaUniprotStructure;
-export declare const DownloadPanel: typeof _DownloadPanel;
-declare type TrackType = 'protvista-track' | 'protvista-variation' | 'protvista-variation-graph' | 'protvista-interpro-track' | 'protvista-coloured-sequence';
-declare type ProtvistaTrackConfig = {
+type TrackType = 'nightingale-track' | 'nightingale-interpro-track' | 'nightingale-colored-sequence' | 'nightingale-variation' | 'nightingale-linegraph-track' | 'nightingale-sequence-heatmap';
+type ProtvistaTrackConfig = {
     name: string;
     label: string;
     labelUrl?: string;
@@ -92,22 +103,21 @@ declare type ProtvistaTrackConfig = {
     trackType: TrackType;
     data: {
         url: string | string[];
-        adapter?: 'protvista-feature-adapter' | 'protvista-structure-adapter' | 'protvista-proteomics-adapter' | 'protvista-variation-adapter' | 'protvista-interpro-adapter';
+        adapter?: 'protvista-feature-adapter' | 'protvista-structure-adapter' | 'protvista-proteomics-adapter' | 'protvista-variation-adapter' | 'protvista-variation-graph-adapter' | 'protvista-interpro-adapter' | 'protvista-alphafold-confidence-adapter' | 'protvista-alphamissense-pathogenicity-adapter' | 'protvista-alphamissense-heatmap-adapter';
     }[];
     tooltip: string;
     color?: string;
     shape?: string;
     scale?: string;
-    filterComponent?: 'protvista-filter';
+    filterComponent?: 'nightingale-filter';
     'color-range'?: string;
 };
-export declare type DownloadConfig = {
+export type DownloadConfig = {
     type: string;
     url: string;
 }[];
 declare class ProtvistaUniprot extends LitElement {
     private openCategories;
-    private notooltip;
     private nostructure;
     private hasData;
     private loading;
@@ -117,6 +127,7 @@ declare class ProtvistaUniprot extends LitElement {
     private suspend?;
     private accession?;
     private sequence?;
+    private transformedVariants?;
     private config?;
     constructor();
     static get properties(): {
@@ -156,16 +167,16 @@ declare class ProtvistaUniprot extends LitElement {
     updated(changedProperties: Map<string, string>): void;
     _init(): void;
     connectedCallback(): void;
-    disconnectedCallback(): void;
-    _resetTooltip(e?: MouseEvent): void;
     loadEntry(accession: string): Promise<any>;
     /**
      * we need to use the light DOM.
      * */
     createRenderRoot(): this;
     render(): import("lit-element").TemplateResult;
-    updateTooltip(e: NightingaleEvent): Promise<void>;
     handleCategoryClick(e: MouseEvent): void;
+    groupByCategory(filters: any, category: any): any;
+    getFilter(filters: any, filterName: any): any;
+    handleFilterClick(e: CustomEvent): void;
     getCategoryTypesAsString(tracks: ProtvistaTrackConfig[]): string;
     getFilterComponent(forId: string): import("lit-element").TemplateResult;
     getTrack(trackType: TrackType, layout?: string, color?: string, shape?: string, id?: string, scale?: string, colorRange?: string): import("lit-element").TemplateResult;