protvista-uniprot 2.13.2 → 3.0.0

package/dist/es/__spec__/filter-config.spec.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/es/__spec__/filter-config.spec.js

@@ -0,0 +1,123 @@
+import { colorConfig, getFilteredVariants, } from '../filter-config';
+const transformedVariantPositions = [
+    {
+        variants: [
+            {
+                accession: 'A',
+                begin: 1,
+                end: 1,
+                start: 1,
+                tooltipContent: '',
+                sourceType: 'source',
+                variant: 'V',
+                protvistaFeatureId: 'id1',
+                xrefNames: [],
+                type: 'VARIANT',
+                wildType: 'A',
+                alternativeSequence: 'V',
+                consequenceType: 'disease',
+                clinicalSignificances: [
+                    {
+                        type: 'Variant of uncertain significance',
+                        sources: ['Ensembl'],
+                    },
+                ],
+                xrefs: [],
+                hasPredictions: false,
+            },
+            {
+                accession: 'B',
+                begin: 1,
+                end: 1,
+                start: 1,
+                tooltipContent: '',
+                sourceType: 'source',
+                variant: 'D',
+                protvistaFeatureId: 'id2',
+                xrefNames: [],
+                type: 'VARIANT',
+                wildType: 'A',
+                alternativeSequence: 'D',
+                consequenceType: 'disease',
+                xrefs: [],
+                hasPredictions: false,
+            },
+        ],
+    },
+    {
+        variants: [
+            {
+                accession: 'C',
+                begin: 2,
+                end: 2,
+                start: 2,
+                tooltipContent: '',
+                sourceType: 'source',
+                variant: 'V',
+                protvistaFeatureId: 'id1',
+                xrefNames: [],
+                type: 'VARIANT',
+                wildType: 'A',
+                alternativeSequence: 'V',
+                consequenceType: 'disease',
+                xrefs: [],
+                hasPredictions: false,
+            },
+        ],
+    },
+    {
+        variants: [
+            {
+                accession: 'D',
+                begin: 3,
+                end: 3,
+                start: 3,
+                tooltipContent: '',
+                sourceType: 'source',
+                variant: 'V',
+                protvistaFeatureId: 'id1',
+                xrefNames: [],
+                type: 'VARIANT',
+                wildType: 'A',
+                alternativeSequence: 'V',
+                consequenceType: 'disease',
+                siftScore: 0.5,
+                xrefs: [],
+                hasPredictions: false,
+            },
+        ],
+    },
+];
+describe('Variation filter config', () => {
+    test('it should filter according to the callback function', () => {
+        const filteredVariants = getFilteredVariants(transformedVariantPositions, (variant) => variant.accession === 'A');
+        expect(filteredVariants).toEqual([
+            {
+                variants: [transformedVariantPositions[0].variants[0]],
+            },
+            {
+                variants: [],
+            },
+            {
+                variants: [],
+            },
+        ]);
+    });
+    test('it should get the right colour for disease', () => {
+        const firstVariant = colorConfig(transformedVariantPositions[0].variants[0]);
+        expect(firstVariant).toEqual('#009e73');
+    });
+    test('it should get the right colour for non disease', () => {
+        const secondVariant = colorConfig(transformedVariantPositions[0].variants[1]);
+        expect(secondVariant).toEqual('#009e73');
+    });
+    test('it should get the right colour for other', () => {
+        const thirdVariant = colorConfig(transformedVariantPositions === null || transformedVariantPositions === void 0 ? void 0 : transformedVariantPositions[1].variants[0]);
+        expect(thirdVariant).toEqual('#009e73');
+    });
+    test('it should get the right colour for predicted', () => {
+        const thirdVariant = colorConfig(transformedVariantPositions[2].variants[0]);
+        expect(thirdVariant).toEqual('#009e73');
+    });
+});
+//# sourceMappingURL=filter-config.spec.js.map

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

@@ -0,0 +1 @@
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package/dist/es/adapters/__tests__/__mocks__/uniprotkb-entry-data.d.ts

@@ -0,0 +1,47 @@
+declare const data: {
+    accession: string;
+    id: string;
+    dbReferences: ({
+        type: string;
+        id: string;
+        properties?: undefined;
+    } | {
+        type: string;
+        id: string;
+        properties: {
+            method: string;
+            resolution: string;
+            chains?: undefined;
+            'match status'?: undefined;
+            'entry name'?: undefined;
+        };
+    } | {
+        type: string;
+        id: string;
+        properties: {
+            method: string;
+            chains: string;
+            resolution?: undefined;
+            'match status'?: undefined;
+            'entry name'?: undefined;
+        };
+    } | {
+        type: string;
+        id: string;
+        properties: {
+            'match status': string;
+            'entry name': string;
+            method?: undefined;
+            resolution?: undefined;
+            chains?: undefined;
+        };
+    })[];
+    sequence: {
+        version: number;
+        length: number;
+        mass: number;
+        modified: string;
+        sequence: string;
+    };
+};
+export default data;

package/dist/es/adapters/__tests__/__mocks__/uniprotkb-entry-data.js

@@ -0,0 +1,75 @@
+const data = {
+    accession: 'P01234',
+    id: 'A4_HUMAN_mocked',
+    dbReferences: [
+        {
+            type: 'UniGene',
+            id: 'Hs.434980',
+        },
+        {
+            type: 'PDB',
+            id: '1AAP',
+            properties: {
+                method: 'X-ray',
+                resolution: '1.50 A',
+            },
+        },
+        {
+            type: 'PDB',
+            id: '1AMB',
+            properties: {
+                method: 'NMR',
+                chains: 'A=672-699',
+            },
+        },
+        {
+            type: 'PDB',
+            id: '1AMC',
+            properties: {
+                method: 'NMR',
+                chains: 'A=672-699',
+            },
+        },
+        {
+            type: 'PDB',
+            id: '1AML',
+            properties: {
+                method: 'NMR',
+                chains: 'A=672-711',
+            },
+        },
+        {
+            type: 'PDB',
+            id: '1BA4',
+            properties: {
+                method: 'NMR',
+                chains: 'A=672-711',
+            },
+        },
+        {
+            type: 'PROSITE',
+            id: 'PS00280',
+            properties: {
+                'match status': '1',
+                'entry name': 'BPTI_KUNITZ_1',
+            },
+        },
+        {
+            type: 'PROSITE',
+            id: 'PS50279',
+            properties: {
+                'match status': '1',
+                'entry name': 'BPTI_KUNITZ_2',
+            },
+        },
+    ],
+    sequence: {
+        version: 3,
+        length: 770,
+        mass: 86943,
+        modified: '1991-11-01',
+        sequence: 'MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKFLHQERMDVCETHLHWHTVAKETCSEKSTNLHDYGMLLPCGIDKFRGVEFVCCPLAEESDNVDSADAEEDDSDVWWGGADTDYADGSEDKVVEVAEEEEVAEVEEEEADDDEDDEDGDEVEEEAEEPYEEATERTTSIATTTTTTTESVEEVVREVCSEQAETGPCRAMISRWYFDVTEGKCAPFFYGGCGGNRNNFDTEEYCMAVCGSAMSQSLLKTTQEPLARDPVKLPTTAASTPDAVDKYLETPGDENEHAHFQKAKERLEAKHRERMSQVMREWEEAERQAKNLPKADKKAVIQHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRPRHVFNMLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSLLYNVPAVAEEIQDEVDELLQKEQNYSDDVLANMISEPRISYGNDALMPSLTETKTTVELLPVNGEFSLDDLQPWHSFGADSVPANTENEVEPVDARPAADRGLTTRPGSGLTNIKTEEISEVKMDAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVITLVMLKKKQYTSIHHGVVEVDAAVTPEERHLSKMQQNGYENPTYKFFEQMQN',
+    },
+};
+export default data;
+//# sourceMappingURL=uniprotkb-entry-data.js.map

package/dist/es/adapters/__tests__/__mocks__/uniprotkb-entry-data.js.map

@@ -0,0 +1 @@
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package/dist/es/adapters/__tests__/structure-adapter.spec.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/es/adapters/__tests__/structure-adapter.spec.js

@@ -0,0 +1,14 @@
+import { getAllFeatureStructures, mergeOverlappingIntervals, } from '../structure-adapter';
+import entryData from './__mocks__/uniprotkb-entry-data';
+describe('structure data', () => {
+    it('should turn structures into features', () => {
+        const features = getAllFeatureStructures(entryData);
+        expect(features).toMatchSnapshot();
+    });
+    it('should merge Overlapping Intervals', () => {
+        const features = getAllFeatureStructures(entryData);
+        const overlapping = mergeOverlappingIntervals(features);
+        expect(overlapping).toMatchSnapshot();
+    });
+});
+//# sourceMappingURL=structure-adapter.spec.js.map

package/dist/es/adapters/__tests__/structure-adapter.spec.js.map

@@ -0,0 +1 @@
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package/dist/es/adapters/alphafold-confidence-adapter.d.ts

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

package/dist/es/{protvista-alphafold-confidence.js → adapters/alphafold-confidence-adapter.js}

@@ -1,4 +1,4 @@
-export const getConfidenceURLFromPayload = (data) => {
+const getConfidenceURLFromPayload = (data) => {
     var _a;
     const cifURL = (_a = data === null || data === void 0 ? void 0 : data[0]) === null || _a === void 0 ? void 0 : _a.cifUrl;
     return (cifURL === null || cifURL === void 0 ? void 0 : cifURL.length)
@@ -14,7 +14,7 @@ const loadConfidence = async (url) => {
         console.error('Could not load AlphaFold confidence', e);
     }
 };
-export const transformData = async (data, protein) => {
+const transformData = async (data, protein) => {
     const confidenceUrl = getConfidenceURLFromPayload(data);
     const { uniprotSequence } = (data === null || data === void 0 ? void 0 : data[0]) || {};
     if (confidenceUrl && uniprotSequence === protein.sequence.sequence) {
@@ -22,4 +22,5 @@ export const transformData = async (data, protein) => {
         return confidenceData === null || confidenceData === void 0 ? void 0 : confidenceData.confidenceCategory.join('');
     }
 };
-//# sourceMappingURL=protvista-alphafold-confidence.js.map
+export default transformData;
+//# sourceMappingURL=alphafold-confidence-adapter.js.map

package/dist/es/adapters/alphafold-confidence-adapter.js.map

@@ -0,0 +1 @@
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package/dist/es/adapters/alphamissense-heatmap-adapter.d.ts

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

package/dist/es/{protvista-alphamissense-heatmap.js → adapters/alphamissense-heatmap-adapter.js}

@@ -1,4 +1,4 @@
-import { cellSplitter, rowSplitter, } from './protvista-alphamissense-pathogenicity';
+import { cellSplitter, rowSplitter, } from './alphamissense-pathogenicity-adapter';
 const parseCSV = (rawText) => {
     const data = [];
     for (const [i, row] of rawText.split(rowSplitter).entries()) {
@@ -25,11 +25,12 @@ const loadAndParseAnnotations = async (url) => {
         console.error('Could not load AlphaMissense pathogenicity', e);
     }
 };
-export const transformData = async (data, protein) => {
+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
+export default transformData;
+//# sourceMappingURL=alphamissense-heatmap-adapter.js.map

package/dist/es/adapters/alphamissense-heatmap-adapter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"alphamissense-heatmap-adapter.js","sourceRoot":"","sources":["../../../src/adapters/alphamissense-heatmap-adapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,YAAY,EACZ,WAAW,GACZ,MAAM,uCAAuC,CAAC;AAG/C,MAAM,QAAQ,GAAG,CAAC,OAAe,EAAiC,EAAE;IAClE,MAAM,IAAI,GAAG,EAAE,CAAC;IAEhB,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,CAAC,EAAE,AAAD,EAAG,cAAc,EAAE,OAAO,EAAE,kBAAkB,CAAC,GACrD,GAAG,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC;QAE1B,IAAI,CAAC,IAAI,CAAC;YACR,MAAM,EAAE,CAAC,cAAc;YACvB,MAAM,EAAE,OAAO;YACf,KAAK,EAAE,CAAC,kBAAkB;SAC3B,CAAC,CAAC;KACJ;IACD,OAAO,IAAI,CAAC;AACd,CAAC,CAAC;AAEF,iBAAiB;AACjB,MAAM,uBAAuB,GAAG,KAAK,EACnC,GAAW,EAC6B,EAAE;IAC1C,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,aAAa,GAAG,KAAK,EACzB,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,WAAW,GAAG,MAAM,uBAAuB,CAAC,gBAAgB,CAAC,CAAC;QACpE,OAAO,WAAW,CAAC;KACpB;AACH,CAAC,CAAC;AAEF,eAAe,aAAa,CAAC"}

package/dist/es/adapters/alphamissense-pathogenicity-adapter.d.ts

@@ -0,0 +1,10 @@
+import { AlphafoldPayload } from './types/alphafold';
+export declare const rowSplitter: RegExp;
+export declare const cellSplitter: RegExp;
+type PartialProtein = {
+    sequence: {
+        sequence: string;
+    };
+};
+declare const transformData: (data: AlphafoldPayload, protein: PartialProtein) => Promise<string>;
+export default transformData;

package/dist/es/{protvista-alphamissense-pathogenicity.js → adapters/alphamissense-pathogenicity-adapter.js}

@@ -56,7 +56,7 @@ const loadAndParseAnnotations = async (url) => {
         console.error('Could not load AlphaMissense pathogenicity', e);
     }
 };
-export const transformData = async (data, protein) => {
+const transformData = async (data, protein) => {
     const { amAnnotationsUrl, uniprotSequence } = (data === null || data === void 0 ? void 0 : data[0]) || {};
     if (amAnnotationsUrl && uniprotSequence === protein.sequence.sequence) {
         const variationData = await loadAndParseAnnotations(amAnnotationsUrl);
@@ -64,4 +64,5 @@ export const transformData = async (data, protein) => {
         return variationData;
     }
 };
-//# sourceMappingURL=protvista-alphamissense-pathogenicity.js.map
+export default transformData;
+//# sourceMappingURL=alphamissense-pathogenicity-adapter.js.map

package/dist/es/adapters/alphamissense-pathogenicity-adapter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"alphamissense-pathogenicity-adapter.js","sourceRoot":"","sources":["../../../src/adapters/alphamissense-pathogenicity-adapter.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,aAAa,GAAG,KAAK,EACzB,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;AAEF,eAAe,aAAa,CAAC"}

package/dist/es/adapters/config/evidence.d.ts

@@ -0,0 +1,14 @@
+declare const ecoMap: ({
+    name: string;
+    description: string;
+    shortDescription: string;
+    acronym: string;
+    isManual: boolean;
+} | {
+    name: string;
+    description: string;
+    shortDescription: string;
+    acronym: string;
+    isManual?: undefined;
+})[];
+export default ecoMap;

package/dist/es/adapters/config/evidence.js

@@ -0,0 +1,101 @@
+const ecoMap = [
+    {
+        name: 'ECO:0000269',
+        description: 'Manual assertion based on experiment',
+        shortDescription: 'Publication',
+        acronym: 'EXP',
+        isManual: true,
+    },
+    {
+        name: 'ECO:0000303',
+        description: 'Manual assertion based on opinion',
+        shortDescription: 'Publication',
+        acronym: 'NAS',
+        isManual: true,
+    },
+    {
+        name: 'ECO:0000305',
+        description: 'Manual assertion inferred by curator',
+        shortDescription: 'Curated',
+        acronym: 'IC',
+        isManual: true,
+    },
+    {
+        name: 'ECO:0000250',
+        description: 'Manual assertion inferred from sequence similarity',
+        shortDescription: 'By similarity',
+        acronym: 'ISS',
+        isManual: true,
+    },
+    {
+        name: 'ECO:0000255',
+        description: 'Manual assertion according to rules',
+        shortDescription: 'Sequence Analysis',
+        acronym: 'ISM',
+        isManual: true,
+    },
+    {
+        name: 'ECO:0007744',
+        description: 'Manual assertion inferred from combination of experimental and computational evidence',
+        shortDescription: 'Combined sources',
+        acronym: 'MIXM',
+        isManual: true,
+    },
+    {
+        name: 'ECO:0000312',
+        description: 'Manual assertion inferred from database entries',
+        shortDescription: 'Imported',
+        acronym: 'MI',
+        isManual: true,
+    },
+    {
+        name: 'ECO:0000256',
+        description: 'Automatic assertion according to rules',
+        shortDescription: 'Automatic annotation',
+        acronym: 'AA',
+    },
+    {
+        name: 'ECO:0000259',
+        description: 'Automatic assertion inferred from signature match',
+        shortDescription: 'Automatic annotation',
+        acronym: 'AA',
+    },
+    {
+        name: 'ECO:0007829',
+        description: 'Automatic assertion inferred from combination of experimental and computational evidence',
+        shortDescription: 'Combined sources',
+        acronym: 'MIXA',
+    },
+    /* ECO:0007829 replaced ECO:0000213 from release 2022_02.
+      Some evidences still have the obsolete code. eg: https://www.ebi.ac.uk/proteins/api/antigen/P49841
+      It is better to show the evidence rather than being it empty */
+    {
+        name: 'ECO:0000213',
+        description: 'Automatic assertion inferred from combination of experimental and computational evidence',
+        shortDescription: 'Combined sources',
+        acronym: 'MIXA',
+    },
+    // ECO:0007744 replaced ECO:0000244 from release 2022_02. Same as above
+    {
+        name: 'ECO:0000244',
+        description: 'Manual assertion inferred from combination of experimental and computational evidence',
+        shortDescription: 'Combined sources',
+        acronym: 'MIXM',
+        isManual: true,
+    },
+    {
+        name: 'ECO:0000313',
+        description: 'Automatic assertion inferred from database entries',
+        shortDescription: 'Imported',
+        acronym: 'AI',
+    },
+    {
+        name: 'ECO:0000260',
+        description: 'Manual assertion inferred from signature match',
+        shortDescription: 'InterPro annotation',
+        acronym: 'SGNM',
+        isManual: true,
+    },
+];
+export default ecoMap;
+//# sourceMappingURL=evidence.js.map

package/dist/es/adapters/config/evidence.js.map

@@ -0,0 +1 @@
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package/dist/es/adapters/feature-adapter.d.ts

@@ -0,0 +1,2 @@
+declare const transformData: (data: any) => any[];
+export default transformData;

package/dist/es/adapters/feature-adapter.js

@@ -0,0 +1,18 @@
+import { renameProperties } from '../utils';
+import formatTooltip from '../tooltips/featureTooltip';
+const transformData = (data) => {
+    let transformedData = [];
+    const { features } = data;
+    if (features && features.length > 0) {
+        transformedData = features.map((feature) => {
+            return {
+                ...feature,
+                tooltipContent: formatTooltip(feature),
+            };
+        });
+        transformedData = renameProperties(transformedData);
+    }
+    return transformedData;
+};
+export default transformData;
+//# sourceMappingURL=feature-adapter.js.map

package/dist/es/adapters/feature-adapter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"feature-adapter.js","sourceRoot":"","sources":["../../../src/adapters/feature-adapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,gBAAgB,EAAE,MAAM,UAAU,CAAC;AAC5C,OAAO,aAAa,MAAM,4BAA4B,CAAC;AAEvD,MAAM,aAAa,GAAG,CAAC,IAAI,EAAE,EAAE;IAC7B,IAAI,eAAe,GAAG,EAAE,CAAC;IACzB,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC;IAC1B,IAAI,QAAQ,IAAI,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE;QACnC,eAAe,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC,OAAO,EAAE,EAAE;YACzC,OAAO;gBACL,GAAG,OAAO;gBACV,cAAc,EAAE,aAAa,CAAC,OAAO,CAAC;aACvC,CAAC;QACJ,CAAC,CAAC,CAAC;QACH,eAAe,GAAG,gBAAgB,CAAC,eAAe,CAAC,CAAC;KACrD;IACD,OAAO,eAAe,CAAC;AACzB,CAAC,CAAC;AAEF,eAAe,aAAa,CAAC"}

package/dist/es/adapters/interpro-adapter.d.ts

@@ -0,0 +1,2 @@
+declare const transformData: (data: any) => any;
+export default transformData;

package/dist/es/adapters/interpro-adapter.js

@@ -0,0 +1,60 @@
+import ColorHash from 'color-hash';
+// Copied from InterPro to replicate the same colours for the representative domains
+/* eslint-disable no-magic-numbers */
+const colorHash = new ColorHash({
+    hash: 'bkdr',
+    saturation: [0.65, 0.35, 0.5],
+    lightness: [0.65, 0.35, 0.5],
+});
+/* eslint-enable no-magic-numbers */
+const transformData = (data) => {
+    var _a;
+    try {
+        return (_a = data === null || data === void 0 ? void 0 : data.results) === null || _a === void 0 ? void 0 : _a.map(({ metadata, proteins }) => {
+            var _a;
+            return ({
+                ...metadata,
+                locations: proteins[0].entry_protein_locations,
+                start: proteins[0].entry_protein_locations
+                    ? Math.min(...proteins[0].entry_protein_locations.map((location) => Math.min(...location.fragments.map((fragment) => fragment.start))))
+                    : '',
+                end: proteins[0].entry_protein_locations
+                    ? Math.max(...(_a = proteins[0].entry_protein_locations) === null || _a === void 0 ? void 0 : _a.map((location) => Math.max(...location.fragments.map((fragment) => fragment.end))))
+                    : '',
+                color: colorHash.hex(metadata.accession.toLowerCase().split('').reverse().join('')),
+                tooltipContent: `
+        <h5>Accession</h5>
+        <p>
+        <a
+          target="_blank"
+          rel="noopener"
+          href="https://www.ebi.ac.uk/interpro/entry/${metadata.source_database}/${metadata.accession}/"
+        >
+        ${metadata.accession}
+        </a>
+        </p>
+        <h5>Name</h5>
+        <p>${metadata.name}</p>
+        ${metadata.integrated
+                    ? `<h5>Integrated into </h5>
+        <p>
+        <a
+          target="_blank"
+          rel="noopener"
+          href="https://www.ebi.ac.uk/interpro/entry/InterPro/${metadata.integrated}/"
+        >
+          ${metadata.integrated}
+        </a>
+        </p>`
+                    : ''}
+      `,
+                length: proteins[0].protein_length,
+            });
+        });
+    }
+    catch (error) {
+        throw new Error('Failed transforming the data');
+    }
+};
+export default transformData;
+//# sourceMappingURL=interpro-adapter.js.map

package/dist/es/adapters/interpro-adapter.js.map

@@ -0,0 +1 @@
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package/dist/es/adapters/proteomics-adapter.d.ts

@@ -0,0 +1,2 @@
+declare const transformData: (data: any) => any[];
+export default transformData;