protvista-uniprot 2.12.2 → 2.13.0

package/dist/es/filterConfig.js

@@ -17,6 +17,26 @@ export const getFilteredVariants = (variants, callbackFilter) => variants.map((v
         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',
@@ -25,10 +45,11 @@ const filterConfig = [
             text: 'Filter Consequence',
         },
         options: {
-            labels: ['Likely pathogenic or pathogenic'],
-            colors: [scaleColors.UPDiseaseColor],
+            label: 'Likely pathogenic or pathogenic',
+            color: scaleColors.UPDiseaseColor,
         },
-        filterData: (variants) => getFilteredVariants(variants, (variantPos) => { var _a; return (_a = variantPos.association) === null || _a === void 0 ? void 0 : _a.some((association) => association.disease); }),
+        filterPredicate: filterPredicates['disease'],
+        filterData: (variants) => getFilteredVariants(variants, filterPredicates['disease']),
     },
     {
         name: 'predicted',
@@ -37,10 +58,11 @@ const filterConfig = [
             text: 'Filter Consequence',
         },
         options: {
-            labels: ['Predicted consequence'],
-            colors: [scaleColors.predictedColor],
+            label: 'Predicted consequence',
+            color: scaleColors.predictedColor,
         },
-        filterData: (variants) => getFilteredVariants(variants, (variantPos) => variantPos.hasPredictions),
+        filterPredicate: filterPredicates['predicted'],
+        filterData: (variants) => getFilteredVariants(variants, filterPredicates['predicted']),
     },
     {
         name: 'nonDisease',
@@ -49,13 +71,11 @@ const filterConfig = [
             text: 'Filter Consequence',
         },
         options: {
-            labels: ['Likely benign or benign'],
-            colors: [scaleColors.UPNonDiseaseColor],
+            label: 'Likely benign or benign',
+            color: scaleColors.UPNonDiseaseColor,
         },
-        filterData: (variants) => getFilteredVariants(variants, (variantPos) => {
-            var _a;
-            return (_a = variantPos.association) === null || _a === void 0 ? void 0 : _a.some((association) => association.disease === false);
-        }),
+        filterPredicate: filterPredicates['nonDisease'],
+        filterData: (variants) => getFilteredVariants(variants, filterPredicates['nonDisease']),
     },
     {
         name: 'uncertain',
@@ -64,13 +84,11 @@ const filterConfig = [
             text: 'Filter Consequence',
         },
         options: {
-            labels: ['Uncertain significance'],
-            colors: [scaleColors.othersColor],
+            label: 'Uncertain significance',
+            color: scaleColors.othersColor,
         },
-        filterData: (variants) => getFilteredVariants(variants, (variantPos) => (typeof variantPos.clinicalSignificances === 'undefined' &&
-            !variantPos.hasPredictions) ||
-            (variantPos.clinicalSignificances &&
-                significanceMatches(variantPos.clinicalSignificances, consequences.uncertain))),
+        filterPredicate: filterPredicates['uncertain'],
+        filterData: (variants) => getFilteredVariants(variants, filterPredicates['uncertain']),
     },
     {
         name: 'UniProt',
@@ -79,12 +97,11 @@ const filterConfig = [
             text: 'Filter Provenance',
         },
         options: {
-            labels: ['UniProt reviewed'],
-            colors: ['#9f9f9f'],
+            label: 'UniProt reviewed',
+            color: '#9f9f9f',
         },
-        filterData: (variants) => getFilteredVariants(variants, (variantPos) => variantPos.xrefNames &&
-            (variantPos.xrefNames.includes('uniprot') ||
-                variantPos.xrefNames.includes('UniProt'))),
+        filterPredicate: filterPredicates['UniProt'],
+        filterData: (variants) => getFilteredVariants(variants, filterPredicates['UniProt']),
     },
     {
         name: 'ClinVar',
@@ -93,12 +110,11 @@ const filterConfig = [
             text: 'Filter Provenance',
         },
         options: {
-            labels: ['ClinVar'],
-            colors: ['#9f9f9f'],
+            label: 'ClinVar',
+            color: '#9f9f9f',
         },
-        filterData: (variants) => getFilteredVariants(variants, (variantPos) => variantPos.xrefNames &&
-            (variantPos.xrefNames.includes('ClinVar') ||
-                variantPos.xrefNames.includes('clinvar'))),
+        filterPredicate: filterPredicates['ClinVar'],
+        filterData: (variants) => getFilteredVariants(variants, filterPredicates['ClinVar']),
     },
     {
         name: 'LSS',
@@ -107,11 +123,11 @@ const filterConfig = [
             text: 'Filter Provenance',
         },
         options: {
-            labels: ['Large scale studies'],
-            colors: ['#9f9f9f'],
+            label: 'Large scale studies',
+            color: '#9f9f9f',
         },
-        filterData: (variants) => getFilteredVariants(variants, (variantPos) => variantPos.sourceType === 'large_scale_study' ||
-            variantPos.sourceType === 'mixed'),
+        filterPredicate: filterPredicates['LSS'],
+        filterData: (variants) => getFilteredVariants(variants, filterPredicates['LSS']),
     },
 ];
 const countVariantsForFilter = (filterName, variant) => {

package/dist/es/filterConfig.js.map

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+{"version":3,"file":"filterConfig.js","sourceRoot":"","sources":["../../src/filterConfig.ts"],"names":[],"mappings":"AAEA,MAAM,WAAW,GAAG;IAClB,cAAc,EAAE,SAAS;IACzB,iBAAiB,EAAE,SAAS;IAC5B,cAAc,EAAE,SAAS;IACzB,WAAW,EAAE,SAAS;CACvB,CAAC;AAEF,MAAM,YAAY,GAAG;IACnB,SAAS,EAAE,CAAC,YAAY,EAAE,cAAc,EAAE,eAAe,EAAE,cAAc,CAAC;CAC3E,CAAC;AAEF,MAAM,mBAAmB,GAAG,CAC1B,oBAA4C,EAC5C,MAAgB,EAChB,EAAE,CACF,oBAAoB,CAAC,IAAI,CAAC,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE;IACrC,OAAO,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC;AAC5C,CAAC,CAAC,CAAC;AAEL,MAAM,CAAC,MAAM,mBAAmB,GAAG,CACjC,QAAgC,EAChC,cAAsD,EACtD,EAAE,CACF,QAAQ,CAAC,GAAG,CAAC,CAAC,OAAO,EAAE,EAAE;IACvB,MAAM,gBAAgB,GAAG,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,UAAU,EAAE,EAAE,CAC9D,cAAc,CAAC,UAAU,CAAC,CAC3B,CAAC;IACF,OAAO;QACL,GAAG,OAAO;QACV,QAAQ,EAAE,CAAC,GAAG,gBAAgB,CAAC;KAChC,CAAC;AACJ,CAAC,CAAC,CAAC;AAEL,MAAM,gBAAgB,GAAG;IACvB,OAAO,EAAE,CAAC,UAAU,EAAE,EAAE,WACtB,OAAA,MAAA,UAAU,CAAC,WAAW,0CAAE,IAAI,CAAC,CAAC,WAAW,EAAE,EAAE,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA,EAAA;IACpE,SAAS,EAAE,CAAC,UAAU,EAAE,EAAE,CAAC,UAAU,CAAC,cAAc;IACpD,UAAU,EAAE,CAAC,UAAU,EAAE,EAAE;;QACzB,OAAA,MAAA,UAAU,CAAC,WAAW,0CAAE,IAAI,CAC1B,CAAC,WAAW,EAAE,EAAE,CAAC,WAAW,CAAC,OAAO,KAAK,KAAK,CAC/C,CAAA;KAAA;IACH,SAAS,EAAE,CAAC,UAAU,EAAE,EAAE,CACxB,CAAC,OAAO,UAAU,CAAC,qBAAqB,KAAK,WAAW;QACtD,CAAC,UAAU,CAAC,cAAc,CAAC;QAC7B,CAAC,UAAU,CAAC,qBAAqB;YAC/B,mBAAmB,CACjB,UAAU,CAAC,qBAAqB,EAChC,YAAY,CAAC,SAAS,CACvB,CAAC;IACN,OAAO,EAAE,CAAC,UAAU,EAAE,EAAE,CACtB,UAAU,CAAC,SAAS;QACpB,CAAC,UAAU,CAAC,SAAS,CAAC,QAAQ,CAAC,SAAS,CAAC;YACvC,UAAU,CAAC,SAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;IAC7C,OAAO,EAAE,CAAC,UAAU,EAAE,EAAE,CACtB,UAAU,CAAC,SAAS;QACpB,CAAC,UAAU,CAAC,SAAS,CAAC,QAAQ,CAAC,SAAS,CAAC;YACvC,UAAU,CAAC,SAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;IAC7C,GAAG,EAAE,CAAC,UAAU,EAAE,EAAE,CAClB,UAAU,CAAC,UAAU,KAAK,mBAAmB;QAC7C,UAAU,CAAC,UAAU,KAAK,OAAO;CACpC,CAAC;AAEF,MAAM,YAAY,GAAG;IACnB;QACE,IAAI,EAAE,SAAS;QACf,IAAI,EAAE;YACJ,IAAI,EAAE,aAAa;YACnB,IAAI,EAAE,oBAAoB;SAC3B;QACD,OAAO,EAAE;YACP,KAAK,EAAE,iCAAiC;YACxC,KAAK,EAAE,WAAW,CAAC,cAAc;SAClC;QACD,eAAe,EAAE,gBAAgB,CAAC,SAAS,CAAC;QAC5C,UAAU,EAAE,CAAC,QAAgC,EAAE,EAAE,CAC/C,mBAAmB,CAAC,QAAQ,EAAE,gBAAgB,CAAC,SAAS,CAAC,CAAC;KAC7D;IACD;QACE,IAAI,EAAE,WAAW;QACjB,IAAI,EAAE;YACJ,IAAI,EAAE,aAAa;YACnB,IAAI,EAAE,oBAAoB;SAC3B;QACD,OAAO,EAAE;YACP,KAAK,EAAE,uBAAuB;YAC9B,KAAK,EAAE,WAAW,CAAC,cAAc;SAClC;QACD,eAAe,EAAE,gBAAgB,CAAC,WAAW,CAAC;QAC9C,UAAU,EAAE,CAAC,QAAgC,EAAE,EAAE,CAC/C,mBAAmB,CAAC,QAAQ,EAAE,gBAAgB,CAAC,WAAW,CAAC,CAAC;KAC/D;IACD;QACE,IAAI,EAAE,YAAY;QAClB,IAAI,EAAE;YACJ,IAAI,EAAE,aAAa;YACnB,IAAI,EAAE,oBAAoB;SAC3B;QACD,OAAO,EAAE;YACP,KAAK,EAAE,yBAAyB;YAChC,KAAK,EAAE,WAAW,CAAC,iBAAiB;SACrC;QACD,eAAe,EAAE,gBAAgB,CAAC,YAAY,CAAC;QAC/C,UAAU,EAAE,CAAC,QAAgC,EAAE,EAAE,CAC/C,mBAAmB,CAAC,QAAQ,EAAE,gBAAgB,CAAC,YAAY,CAAC,CAAC;KAChE;IACD;QACE,IAAI,EAAE,WAAW;QACjB,IAAI,EAAE;YACJ,IAAI,EAAE,aAAa;YACnB,IAAI,EAAE,oBAAoB;SAC3B;QACD,OAAO,EAAE;YACP,KAAK,EAAE,wBAAwB;YAC/B,KAAK,EAAE,WAAW,CAAC,WAAW;SAC/B;QACD,eAAe,EAAE,gBAAgB,CAAC,WAAW,CAAC;QAC9C,UAAU,EAAE,CAAC,QAAgC,EAAE,EAAE,CAC/C,mBAAmB,CAAC,QAAQ,EAAE,gBAAgB,CAAC,WAAW,CAAC,CAAC;KAC/D;IACD;QACE,IAAI,EAAE,SAAS;QACf,IAAI,EAAE;YACJ,IAAI,EAAE,YAAY;YAClB,IAAI,EAAE,mBAAmB;SAC1B;QACD,OAAO,EAAE;YACP,KAAK,EAAE,kBAAkB;YACzB,KAAK,EAAE,SAAS;SACjB;QACD,eAAe,EAAE,gBAAgB,CAAC,SAAS,CAAC;QAC5C,UAAU,EAAE,CAAC,QAAgC,EAAE,EAAE,CAC/C,mBAAmB,CAAC,QAAQ,EAAE,gBAAgB,CAAC,SAAS,CAAC,CAAC;KAC7D;IACD;QACE,IAAI,EAAE,SAAS;QACf,IAAI,EAAE;YACJ,IAAI,EAAE,YAAY;YAClB,IAAI,EAAE,mBAAmB;SAC1B;QACD,OAAO,EAAE;YACP,KAAK,EAAE,SAAS;YAChB,KAAK,EAAE,SAAS;SACjB;QACD,eAAe,EAAE,gBAAgB,CAAC,SAAS,CAAC;QAC5C,UAAU,EAAE,CAAC,QAAgC,EAAE,EAAE,CAC/C,mBAAmB,CAAC,QAAQ,EAAE,gBAAgB,CAAC,SAAS,CAAC,CAAC;KAC7D;IACD;QACE,IAAI,EAAE,KAAK;QACX,IAAI,EAAE;YACJ,IAAI,EAAE,YAAY;YAClB,IAAI,EAAE,mBAAmB;SAC1B;QACD,OAAO,EAAE;YACP,KAAK,EAAE,qBAAqB;YAC5B,KAAK,EAAE,SAAS;SACjB;QACD,eAAe,EAAE,gBAAgB,CAAC,KAAK,CAAC;QACxC,UAAU,EAAE,CAAC,QAAgC,EAAE,EAAE,CAC/C,mBAAmB,CAAC,QAAQ,EAAE,gBAAgB,CAAC,KAAK,CAAC,CAAC;KACzD;CACF,CAAC;AAEF,MAAM,sBAAsB,GAAG,CAC7B,UAAgE,EAChE,OAAyB,EACzB,EAAE;IACF,MAAM,cAAc,GAAG,CAAC,EAAE,QAAQ,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;IACjD,MAAM,MAAM,GAAG,YAAY,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,IAAI,KAAK,UAAU,CAAC,CAAC;IACzE,IAAI,MAAM,EAAE;QACV,OAAO,MAAM,CAAC,UAAU,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC;KACjE;IACD,OAAO,KAAK,CAAC;AACf,CAAC,CAAC;AAEF,MAAM,CAAC,MAAM,WAAW,GAAG,CAAC,OAAY,EAAE,EAAE;IAC1C,IAAI,sBAAsB,CAAC,SAAS,EAAE,OAAO,CAAC,EAAE;QAC9C,OAAO,WAAW,CAAC,cAAc,CAAC;KACnC;SAAM,IAAI,sBAAsB,CAAC,YAAY,EAAE,OAAO,CAAC,EAAE;QACxD,OAAO,WAAW,CAAC,iBAAiB,CAAC;KACtC;SAAM,IAAI,sBAAsB,CAAC,WAAW,EAAE,OAAO,CAAC,EAAE;QACvD,OAAO,WAAW,CAAC,WAAW,CAAC;KAChC;SAAM,IAAI,sBAAsB,CAAC,WAAW,EAAE,OAAO,CAAC,EAAE;QACvD,OAAO,WAAW,CAAC,cAAc,CAAC;KACnC;IACD,OAAO,WAAW,CAAC,WAAW,CAAC;AACjC,CAAC,CAAC;AAEF,eAAe,YAAY,CAAC"}

package/dist/es/index.d.ts

@@ -1,5 +1,4 @@
 import ProtvistaUniprot from './protvista-uniprot';
-import _DownloadPanel from './download-panel';
 import _ProtvistaUniprotStructure from './protvista-uniprot-structure';
 export declare const transformDataFeatureAdapter: any;
 export declare const transformDataProteomicsAdapter: any;
@@ -10,5 +9,4 @@ export declare const transformDataVariationAdapter: (data: import("protvista-var
 };
 export declare const transformDataInterproAdapter: any;
 export declare const ProtvistaUniprotStructure: typeof _ProtvistaUniprotStructure;
-export declare const DownloadPanel: typeof _DownloadPanel;
 export default ProtvistaUniprot;

package/dist/es/index.js

@@ -1,6 +1,5 @@
 import { loadComponent } from './loadComponents';
 import ProtvistaUniprot from './protvista-uniprot';
-import _DownloadPanel from './download-panel';
 import _ProtvistaUniprotStructure from './protvista-uniprot-structure';
 import { transformDataFeatureAdapter as _transformDataFeatureAdapter } from './protvista-uniprot';
 import { transformDataProteomicsAdapter as _transformDataProteomicsAdapter } from './protvista-uniprot';
@@ -13,9 +12,7 @@ export const transformDataStructureAdapter = _transformDataStructureAdapter;
 export const transformDataVariationAdapter = _transformDataVariationAdapter;
 export const transformDataInterproAdapter = _transformDataInterproAdapter;
 export const ProtvistaUniprotStructure = _ProtvistaUniprotStructure;
-export const DownloadPanel = _DownloadPanel;
 loadComponent('protvista-uniprot', ProtvistaUniprot);
-loadComponent('download-panel', _DownloadPanel);
 loadComponent('protvista-uniprot-structure', _ProtvistaUniprotStructure);
 export default ProtvistaUniprot;
 //# sourceMappingURL=index.js.map

package/dist/es/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AAEjD,OAAO,gBAAgB,MAAM,qBAAqB,CAAC;AACnD,OAAO,0BAA0B,MAAM,+BAA+B,CAAC;AAEvE,OAAO,EAAE,2BAA2B,IAAI,4BAA4B,EAAE,MAAM,qBAAqB,CAAC;AAClG,OAAO,EAAE,8BAA8B,IAAI,+BAA+B,EAAE,MAAM,qBAAqB,CAAC;AACxG,OAAO,EAAE,6BAA6B,IAAI,8BAA8B,EAAE,MAAM,qBAAqB,CAAC;AACtG,OAAO,EAAE,6BAA6B,IAAI,8BAA8B,EAAE,MAAM,qBAAqB,CAAC;AACtG,OAAO,EAAE,4BAA4B,IAAI,6BAA6B,EAAE,MAAM,qBAAqB,CAAC;AAEpG,MAAM,CAAC,MAAM,2BAA2B,GAAG,4BAA4B,CAAC;AACxE,MAAM,CAAC,MAAM,8BAA8B,GAAG,+BAA+B,CAAC;AAC9E,MAAM,CAAC,MAAM,6BAA6B,GAAG,8BAA8B,CAAC;AAC5E,MAAM,CAAC,MAAM,6BAA6B,GAAG,8BAA8B,CAAC;AAC5E,MAAM,CAAC,MAAM,4BAA4B,GAAG,6BAA6B,CAAC;AAC1E,MAAM,CAAC,MAAM,yBAAyB,GAAG,0BAA0B,CAAC;AAEpE,aAAa,CAAC,mBAAmB,EAAE,gBAAgB,CAAC,CAAC;AACrD,aAAa,CAAC,6BAA6B,EAAE,0BAA0B,CAAC,CAAC;AAEzE,eAAe,gBAAgB,CAAC"}

package/dist/es/protvista-alphafold-confidence.d.ts

@@ -1,6 +1,6 @@
 import { AlphafoldPayload } from './commonTypes';
 export declare const getConfidenceURLFromPayload: (data: AlphafoldPayload) => string;
-declare type PartialProtein = {
+type PartialProtein = {
     sequence: {
         sequence: string;
     };

package/dist/es/protvista-alphamissense-heatmap.d.ts

@@ -0,0 +1,8 @@
+import { AlphafoldPayload } from './commonTypes';
+type PartialProtein = {
+    sequence: {
+        sequence: string;
+    };
+};
+export declare const transformData: (data: AlphafoldPayload, protein: PartialProtein) => Promise<Record<string, string>[]>;
+export {};

package/dist/es/protvista-alphamissense-heatmap.js

@@ -0,0 +1,35 @@
+import { cellSplitter, rowSplitter, } from './protvista-alphamissense-pathogenicity';
+const parseCSV = (rawText) => {
+    const data = [];
+    for (const [i, row] of rawText.split(rowSplitter).entries()) {
+        if (i === 0 || !row) {
+            continue;
+        }
+        const [, , positionString, mutated, pathogenicityScore] = row.match(cellSplitter);
+        data.push({
+            xValue: +positionString,
+            yValue: mutated,
+            score: +pathogenicityScore,
+        });
+    }
+    return data;
+};
+// Load and parse
+const loadAndParseAnnotations = async (url) => {
+    try {
+        const payload = await fetch(url);
+        const rawCSV = await payload.text();
+        return parseCSV(rawCSV);
+    }
+    catch (e) {
+        console.error('Could not load AlphaMissense pathogenicity', e);
+    }
+};
+export const transformData = async (data, protein) => {
+    const { amAnnotationsUrl, uniprotSequence } = (data === null || data === void 0 ? void 0 : data[0]) || {};
+    if (amAnnotationsUrl && uniprotSequence === protein.sequence.sequence) {
+        const heatmapData = await loadAndParseAnnotations(amAnnotationsUrl);
+        return heatmapData;
+    }
+};
+//# sourceMappingURL=protvista-alphamissense-heatmap.js.map

package/dist/es/protvista-alphamissense-heatmap.js.map

@@ -0,0 +1 @@
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package/dist/es/protvista-alphamissense-pathogenicity.d.ts

@@ -1,5 +1,7 @@
 import { AlphafoldPayload } from './commonTypes';
-declare type PartialProtein = {
+export declare const rowSplitter: RegExp;
+export declare const cellSplitter: RegExp;
+type PartialProtein = {
     sequence: {
         sequence: string;
     };

package/dist/es/protvista-alphamissense-pathogenicity.js

@@ -4,8 +4,8 @@
 // pathogenic: [0.5646,0.9999]: 0.564 < x
 const benign = 0.34;
 const pathogenic = 0.564;
-const rowSplitter = /\s*\n\s*/;
-const cellSplitter = /^(.)(\d+)(.),(.+),(\w+)$/;
+export const rowSplitter = /\s*\n\s*/;
+export const cellSplitter = /^(.)(\d+)(.),(.+),(\w+)$/;
 const parseCSV = (rawText) => {
     const positions = [];
     for (const [i, row] of rawText.split(rowSplitter).entries()) {

package/dist/es/protvista-alphamissense-pathogenicity.js.map

@@ -1 +1 @@
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+{"version":3,"file":"protvista-alphamissense-pathogenicity.js","sourceRoot":"","sources":["../../src/protvista-alphamissense-pathogenicity.ts"],"names":[],"mappings":"AAEA,oBAAoB;AACpB,oCAAoC;AACpC,8CAA8C;AAC9C,yCAAyC;AACzC,MAAM,MAAM,GAAG,IAAI,CAAC;AACpB,MAAM,UAAU,GAAG,KAAK,CAAC;AAEzB,MAAM,CAAC,MAAM,WAAW,GAAG,UAAU,CAAC;AACtC,MAAM,CAAC,MAAM,YAAY,GAAG,0BAA0B,CAAC;AAUvD,MAAM,QAAQ,GAAG,CAAC,OAAe,EAAU,EAAE;IAC3C,MAAM,SAAS,GAAsB,EAAE,CAAC;IACxC,KAAK,MAAM,CAAC,CAAC,EAAE,GAAG,CAAC,IAAI,OAAO,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,OAAO,EAAE,EAAE;QAC3D,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,EAAE;YACnB,SAAS;SACV;QACD,MAAM,CACJ,AADK,EAEL,QAAQ,EACR,cAAc,EACd,OAAO,EACP,kBAAkB,EAClB,kBAAkB,EACnB,GAAG,GAAG,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC;QAC5B,MAAM,QAAQ,GAAG,CAAC,cAAc,CAAC;QACjC,MAAM,KAAK,GAAG,QAAQ,GAAG,CAAC,CAAC;QAC3B,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,EAAE;YACrB,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC;SACvB;QACD,SAAS,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC;YACpB,QAAQ;YACR,QAAQ;YACR,OAAO;YACP,kBAAkB,EAAE,CAAC,kBAAkB;YACvC,kBAAkB;SACnB,CAAC,CAAC;KACJ;IAED,MAAM,GAAG,GAAG,EAAE,CAAC;IACf,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE;QAChC,IAAI,MAAM,GAAG,GAAG,CAAC;QACjB,UAAU;QACV,0BAA0B;QAC1B,iEAAiE;QACjE,KAAK;QACL,UAAU;QACV,MAAM,KAAK,GACT,QAAQ,CAAC,MAAM,CACb,CAAC,GAAG,EAAE,SAAS,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,SAAS,CAAC,kBAAkB,EACvD,CAAC,CACF,GAAG,QAAQ,CAAC,MAAM,CAAC;QACtB,IAAI,KAAK,GAAG,UAAU,EAAE;YACtB,MAAM,GAAG,GAAG,CAAC;SACd;aAAM,IAAI,KAAK,GAAG,MAAM,EAAE;YACzB,MAAM,GAAG,GAAG,CAAC;SACd;QACD,GAAG,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;KAClB;IAED,OAAO,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;AACtB,CAAC,CAAC;AAEF,iBAAiB;AACjB,MAAM,uBAAuB,GAAG,KAAK,EAAE,GAAW,EAAmB,EAAE;IACrE,IAAI;QACF,MAAM,OAAO,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC;QACjC,MAAM,MAAM,GAAG,MAAM,OAAO,CAAC,IAAI,EAAE,CAAC;QACpC,OAAO,QAAQ,CAAC,MAAM,CAAC,CAAC;KACzB;IAAC,OAAO,CAAC,EAAE;QACV,OAAO,CAAC,KAAK,CAAC,4CAA4C,EAAE,CAAC,CAAC,CAAC;KAChE;AACH,CAAC,CAAC;AAQF,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,EAChC,IAAsB,EACtB,OAAuB,EACvB,EAAE;IACF,MAAM,EAAE,gBAAgB,EAAE,eAAe,EAAE,GAAG,CAAA,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAG,CAAC,CAAC,KAAI,EAAE,CAAC;IAC9D,IAAI,gBAAgB,IAAI,eAAe,KAAK,OAAO,CAAC,QAAQ,CAAC,QAAQ,EAAE;QACrE,MAAM,aAAa,GAAG,MAAM,uBAAuB,CAAC,gBAAgB,CAAC,CAAC;QACtE,sDAAsD;QACtD,OAAO,aAAa,CAAC;KACtB;AACH,CAAC,CAAC"}

package/dist/es/protvista-ptm-exchange.d.ts

@@ -1,4 +1,4 @@
-declare type ProteomicsPtm = {
+type ProteomicsPtm = {
     accession: string;
     entryName: string;
     sequence: string;
@@ -6,7 +6,7 @@ declare type ProteomicsPtm = {
     taxid: number;
     features: ProteomicsPtmFeature[];
 };
-declare type ProteomicsPtmFeature = {
+type ProteomicsPtmFeature = {
     type: string;
     begin: string;
     end: string;
@@ -16,26 +16,26 @@ declare type ProteomicsPtmFeature = {
     unique: boolean;
     ptms: PTM[];
 };
-declare type Evidence = {
+type Evidence = {
     code: string;
     source: Source;
 };
-declare type Source = {
+type Source = {
     id: string;
     url: string;
 };
-declare type Xref = {
+type Xref = {
     name: string;
     id: string;
     url: string;
 };
-declare type PTM = {
+type PTM = {
     name: string;
     position: number;
     sources: string[];
     dbReferences: DBReference[];
 };
-declare type DBReference = {
+type DBReference = {
     id: string;
     properties: {
         [key: string]: string;

package/dist/es/protvista-ptm-exchange.js

@@ -37,16 +37,18 @@ const convertPtmExchangePtms = (ptms, aa, absolutePosition) => {
     }
     const tooltip = `
   <h5>Description</h5><p>${phosphorylate(aa)}</p>
-  ${confidenceScore ? `<h5 data-article-id="mod_res_large_scale#confidence-score">Confidence Score</h5><p>${confidenceScore}</p>` : ''}
+  ${confidenceScore
+        ? `<h5 data-article-id="mod_res_large_scale#confidence-score">Confidence Score</h5><p>${confidenceScore}</p>`
+        : ''}
   ${evidences
         ? `<h5>Evidence</h5><ul>${evidences
             .map((id) => {
             const datasetID = id === 'Glue project' ? 'PXD012174' : id;
             return `<li title='${datasetID}' style="padding: .25rem 0">${datasetID}&nbsp;
-              (<a href="https://www.ebi.ac.uk/pride/archive/projects/${id}" style="color:#FFF" target="_blank">PRIDE</a>)
+              (<a href="https://proteomecentral.proteomexchange.org/dataset/${datasetID}" style="color:#FFF" target="_blank">ProteomeXchange</a>)
               </li>
-              ${id === 'Glue project' ?
-                `<li title="publication" style="padding: .25rem 0">Publication:&nbsp;31819260&nbsp;(<a href="https://pubmed.ncbi.nlm.nih.gov/31819260" style="color:#FFF" target="_blank">PubMed</a>)</li>`
+              ${id === 'Glue project'
+                ? `<li title="publication" style="padding: .25rem 0">Publication:&nbsp;31819260&nbsp;(<a href="https://pubmed.ncbi.nlm.nih.gov/31819260" style="color:#FFF" target="_blank">PubMed</a>)</li>`
                 : ''}
               `;
         })

package/dist/es/protvista-ptm-exchange.js.map

@@ -1 +1 @@
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package/dist/es/protvista-uniprot-structure.d.ts

@@ -1,5 +1,5 @@
 import { LitElement, TemplateResult } from 'lit-element';
-declare type ProcessedStructureData = {
+type ProcessedStructureData = {
     id: string;
     source: 'PDB' | 'AlphaFold';
     method: string;
@@ -14,6 +14,7 @@ declare class ProtvistaUniprotStructure extends LitElement {
     data?: ProcessedStructureData[];
     structureId?: string;
     metaInfo?: TemplateResult;
+    colorTheme?: string;
     private loading?;
     constructor();
     static get properties(): {
@@ -29,6 +30,9 @@ declare class ProtvistaUniprotStructure extends LitElement {
         loading: {
             type: BooleanConstructor;
         };
+        colorTheme: {
+            type: StringConstructor;
+        };
     };
     connectedCallback(): Promise<void>;
     disconnectedCallback(): void;
@@ -43,6 +47,7 @@ declare class ProtvistaUniprotStructure extends LitElement {
      * we need to use the light DOM.
      * */
     createRenderRoot(): this;
+    toggleColorTheme(e: any): void;
     render(): TemplateResult;
 }
 export default ProtvistaUniprotStructure;