protvista-uniprot 3.0.0 → 3.0.7

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

@@ -1,60 +0,0 @@
-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

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

@@ -1,66 +0,0 @@
-import { renameProperties } from '../utils';
-import formatTooltip from '../tooltips/featureTooltip';
-const proteomicsTrackProperties = (feature) => {
-    return {
-        category: 'PROTEOMICS',
-        type: feature.unique ? 'unique' : 'non_unique',
-        tooltipContent: formatTooltip(feature),
-    };
-};
-const transformData = (data) => {
-    let adaptedData = [];
-    if (data && data.length !== 0) {
-        /* Important: The PTM map is a temporary patch until multiple modifications are shown in the peptide. At this point, only 'phospho' sites are of interest.
-          Once they are available in the data, there is no need for the below merging */
-        // To merge PTM data present in same residue in a same length peptide, have a map [key: start-end-phospho site 1-... phosphosite n, value: corresponding feature elements]
-        const ptmMap = {};
-        data.features.forEach((feature) => {
-            let ft = `${feature.begin}-${feature.end}`;
-            if (feature.ptms) {
-                feature.ptms.forEach((ptm) => {
-                    ft += `-${ptm.position}`;
-                });
-                ptmMap[ft] = ft in ptmMap ? [...ptmMap[ft], feature] : [feature];
-            }
-        });
-        // The else part alone is enough if the PTM information need not be merged.
-        if (Object.keys(ptmMap).length) {
-            adaptedData = Object.values(ptmMap).map((features) => {
-                // Only the dbReferences have to be merged as the rest is all the same
-                const mergedDbReferences = [];
-                features.forEach((feature) => {
-                    feature.ptms.forEach((ptm) => {
-                        ptm.dbReferences.forEach((dbReference) => {
-                            mergedDbReferences.push(dbReference);
-                        });
-                    });
-                });
-                const mergedFeatures = {
-                    type: features[0].type,
-                    begin: features[0].begin,
-                    end: features[0].end,
-                    xrefs: features[0].xrefs,
-                    evidences: features[0].evidences,
-                    peptide: features[0].peptide,
-                    unique: features[0].unique,
-                    ptms: features[0].ptms.map((ptm) => ({
-                        name: ptm.name,
-                        position: ptm.position,
-                        sources: ptm.sources,
-                        dbReferences: mergedDbReferences,
-                    })),
-                };
-                return Object.assign(mergedFeatures, proteomicsTrackProperties(mergedFeatures));
-            }, []);
-        }
-        else {
-            adaptedData = data.features.map((feature) => {
-                return Object.assign(feature, proteomicsTrackProperties(feature));
-            });
-        }
-        adaptedData = renameProperties(adaptedData);
-    }
-    return adaptedData;
-};
-export default transformData;
-//# sourceMappingURL=proteomics-adapter.js.map

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

@@ -1 +0,0 @@
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package/dist/es/adapters/ptm-exchange-adapter.js

@@ -1,101 +0,0 @@
-var ConfidenceScoreColors;
-(function (ConfidenceScoreColors) {
-    ConfidenceScoreColors["Gold"] = "#c39b00";
-    ConfidenceScoreColors["Silver"] = "#8194a1";
-    ConfidenceScoreColors["Bronze"] = "#a65708";
-})(ConfidenceScoreColors || (ConfidenceScoreColors = {}));
-const aaToPhosphorylated = {
-    R: 'Phosphoarginine',
-    C: 'Phosphocysteine',
-    H: 'Phosphohistidine',
-    S: 'Phosphoserine',
-    T: 'Phosphothreonine',
-    Y: 'Phosphotyrosine',
-};
-const phosphorylate = (aa) => {
-    const AA = aa.toUpperCase();
-    if (AA in aaToPhosphorylated) {
-        return aaToPhosphorylated[AA];
-    }
-    console.error(`${AA} not a valid amino acid for phosphorylation`);
-    return '';
-};
-const convertPtmExchangePtms = (ptms, aa, absolutePosition) => {
-    const evidences = [
-        ...ptms.flatMap(({ dbReferences }) => dbReferences === null || dbReferences === void 0 ? void 0 : dbReferences.flatMap(({ id }) => [id])),
-    ];
-    const confidenceScores = new Set(ptms.flatMap(({ dbReferences }) => dbReferences === null || dbReferences === void 0 ? void 0 : dbReferences.map(({ properties }) => properties['Confidence score'])));
-    let confidenceScore;
-    if (!confidenceScores.size) {
-        console.log('PTM has no confidence score');
-    }
-    else if (confidenceScores.size > 1) {
-        console.error(`PTM has a mixture of confidence scores: ${Array.from(confidenceScores)}`);
-    }
-    else {
-        [confidenceScore] = confidenceScores;
-    }
-    const tooltip = `
-  <h5>Description</h5><p>${phosphorylate(aa)}</p>
-  ${confidenceScore
-        ? `<h5 data-article-id="mod_res_large_scale#confidence-score">Confidence Score</h5><p>${confidenceScore}</p>`
-        : ''}
-  ${evidences
-        ? `<h5>Evidence</h5><ul>${evidences
-            .map((id) => {
-            const datasetID = id === 'Glue project' ? 'PXD012174' : id;
-            return `<li title='${datasetID}' style="padding: .25rem 0">${datasetID}&nbsp;
-              (<a href="https://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>`
-                : ''}
-              `;
-        })
-            .join('')}</ul>`
-        : ''}
-  `;
-    return {
-        source: 'PTMeXchange',
-        type: 'MOD_RES_LS',
-        start: absolutePosition,
-        end: absolutePosition,
-        shape: 'triangle',
-        tooltipContent: tooltip,
-        color: ConfidenceScoreColors[confidenceScore] || 'black',
-    };
-};
-const transformData = (data) => {
-    if (data) {
-        const { features } = data;
-        const absolutePositionToPtms = {};
-        if (features) {
-            for (const feature of features) {
-                for (const ptm of feature.ptms) {
-                    const absolutePosition = +feature.begin + ptm.position - 1;
-                    if (!Number.isFinite(absolutePosition)) {
-                        console.error(`Encountered infinite number: +feature.begin + ptm.position - 1 = ${+feature.begin} + ${ptm.position} - 1`);
-                        // eslint-disable-next-line no-continue
-                        continue;
-                    }
-                    const aa = feature.peptide[ptm.position - 1];
-                    if (absolutePosition in absolutePositionToPtms) {
-                        if (absolutePositionToPtms[absolutePosition].aa !== aa) {
-                            console.error(`One PTM has different amino acid values: [${absolutePositionToPtms[absolutePosition].aa}, ${aa}]`);
-                        }
-                        else {
-                            absolutePositionToPtms[absolutePosition].ptms.push(ptm);
-                        }
-                    }
-                    else {
-                        absolutePositionToPtms[absolutePosition] = { ptms: [ptm], aa };
-                    }
-                }
-            }
-            return Object.entries(absolutePositionToPtms).map(([absolutePosition, { ptms, aa }]) => convertPtmExchangePtms(ptms, aa, +absolutePosition));
-        }
-    }
-    return [];
-};
-export default transformData;
-//# sourceMappingURL=ptm-exchange-adapter.js.map

package/dist/es/adapters/ptm-exchange-adapter.js.map

@@ -1 +0,0 @@
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package/dist/es/adapters/structure-adapter.js

@@ -1,89 +0,0 @@
-import formatTooltip from '../tooltips/structureTooltip';
-const featureType = 'PDBE_COVER';
-const featureCategory = 'STRUCTURE_COVERAGE';
-const capitalizeFirstLetter = (word) => {
-    return word.charAt(0).toUpperCase() + word.slice(1);
-};
-const getDescription = (properties) => {
-    return Object.keys(properties).reduce((accumulator, propertyKey) => `${accumulator}${capitalizeFirstLetter(propertyKey)}: ${properties[propertyKey]}. `, '');
-};
-const parseChainString = (value) => {
-    const posEqual = value.indexOf('=');
-    const posDash = value.indexOf('-');
-    if (posEqual === -1 || posDash === -1) {
-        return { start: 0, end: 0 };
-    }
-    return {
-        start: +value.slice(posEqual + 1, posDash),
-        end: +value.slice(posDash + 1),
-    };
-};
-// Iterate over references and extract chain start and end
-export const getAllFeatureStructures = (data) => {
-    return data.dbReferences
-        .filter((reference) => {
-        return reference.type === 'PDB';
-    })
-        .map((structureReference) => {
-        const parsedChain = structureReference.properties.chains
-            ? parseChainString(structureReference.properties.chains)
-            : { start: 0, end: 0 };
-        return {
-            type: featureType,
-            category: featureCategory,
-            structures: [
-                {
-                    description: getDescription(structureReference.properties),
-                    start: parsedChain.start,
-                    end: parsedChain.end,
-                    source: {
-                        id: structureReference.id,
-                        url: `http://www.ebi.ac.uk/pdbe-srv/view/entry/${structureReference.id}`,
-                    },
-                },
-            ],
-            start: parsedChain.start,
-            end: parsedChain.end,
-        };
-    });
-};
-export const mergeOverlappingIntervals = (structures) => {
-    if (!structures || structures.length <= 0) {
-        return [];
-    }
-    // Sort by start position
-    const sortedStructures = structures.sort((a, b) => a.start - b.start);
-    const mergedIntervals = [];
-    sortedStructures.forEach((structure) => {
-        const lastItem = mergedIntervals[mergedIntervals.length - 1];
-        if (!lastItem ||
-            // If item doesn't overlap, push it
-            lastItem.end < structure.start) {
-            mergedIntervals.push(structure);
-        }
-        // If the end is bigger update the last one
-        else if (lastItem.end < structure.end) {
-            lastItem.end = structure.end;
-            lastItem.structures.push(structure.structures[0]);
-        }
-        // Otherwise just add to last item
-        else {
-            lastItem.structures.push(structure.structures[0]);
-        }
-    });
-    return mergedIntervals;
-};
-const transformData = (data) => {
-    let transformedData = [];
-    if (data && data.length !== 0) {
-        const allFeatureStructures = getAllFeatureStructures(data);
-        transformedData = mergeOverlappingIntervals(allFeatureStructures);
-        transformedData.forEach((feature) => {
-            /* eslint-disable no-param-reassign */
-            feature.tooltipContent = formatTooltip(feature);
-        });
-    }
-    return transformedData;
-};
-export default transformData;
-//# sourceMappingURL=structure-adapter.js.map

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

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package/dist/es/adapters/types/alphafold.js

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=alphafold.js.map

package/dist/es/adapters/types/alphafold.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"alphafold.js","sourceRoot":"","sources":["../../../../src/adapters/types/alphafold.ts"],"names":[],"mappings":""}

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

@@ -1,31 +0,0 @@
-import { AminoAcid, } from '@nightingale-elements/nightingale-variation';
-import formatTooltip from '../tooltips/variationTooltip';
-const getSourceType = (xrefs, sourceType) => {
-    const xrefNames = xrefs ? xrefs.map((ref) => ref.name) : [];
-    if (sourceType === 'uniprot' || sourceType === 'mixed') {
-        xrefNames.push('uniprot');
-    }
-    return xrefNames;
-};
-const transformData = (data) => {
-    const { sequence, features } = data;
-    const variants = features.map((variant) => {
-        var _a;
-        return ({
-            ...variant,
-            accession: (_a = variant.genomicLocation) === null || _a === void 0 ? void 0 : _a.join(', '),
-            variant: variant.alternativeSequence
-                ? variant.alternativeSequence
-                : AminoAcid.Empty,
-            start: +variant.begin,
-            xrefNames: getSourceType(variant.xrefs, variant.sourceType),
-            hasPredictions: variant.predictions && variant.predictions.length > 0,
-            tooltipContent: formatTooltip(variant),
-        });
-    });
-    if (!variants)
-        return null;
-    return { sequence, variants };
-};
-export default transformData;
-//# sourceMappingURL=variation-adapter.js.map

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

@@ -1 +0,0 @@
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package/dist/es/adapters/variation-graph-adapter.js

@@ -1,53 +0,0 @@
-const transformData = (data) => {
-    if (data.sequence && data.features.length) {
-        const variants = data.features.map((variant) => {
-            var _a;
-            return ({
-                ...variant,
-                accession: (_a = variant.genomicLocation) === null || _a === void 0 ? void 0 : _a.join(', '),
-                start: variant.begin,
-            });
-        });
-        const total = new Uint8ClampedArray(data.sequence.length);
-        const diseaseTotal = new Uint8ClampedArray(data.sequence.length);
-        for (const { start, association } of variants) {
-            const index = +start;
-            // skip if the variant is outside of bounds
-            // eslint-disable-next-line no-continue
-            if (index < 1 || index > data.sequence.length)
-                continue;
-            // eslint-disable-next-line no-plusplus
-            total[index]++;
-            // eslint-disable-next-line no-continue
-            if (!association)
-                continue;
-            const hasDisease = association.find((association) => association.disease === true);
-            // eslint-disable-next-line no-plusplus
-            if (hasDisease)
-                diseaseTotal[index]++;
-        }
-        const graphData = [
-            {
-                name: 'variant',
-                range: [0, Math.max(Math.max(...total), Math.max(...diseaseTotal))],
-                color: 'darkgrey',
-                values: [...total].map((value, index) => ({
-                    position: index,
-                    value: value,
-                })),
-            },
-            {
-                name: 'disease causing variant',
-                range: [0, Math.max(Math.max(...total), Math.max(...diseaseTotal))],
-                color: 'red',
-                values: [...diseaseTotal].map((value, index) => ({
-                    position: index,
-                    value: value,
-                })),
-            },
-        ];
-        return graphData;
-    }
-};
-export default transformData;
-//# sourceMappingURL=variation-graph-adapter.js.map

package/dist/es/adapters/variation-graph-adapter.js.map

@@ -1 +0,0 @@
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