protvista-uniprot 2.13.2 → 3.0.1

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

@@ -0,0 +1,66 @@
+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

@@ -0,0 +1 @@
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package/dist/es/{protvista-ptm-exchange.d.ts → adapters/ptm-exchange-adapter.d.ts}

@@ -41,7 +41,7 @@ type DBReference = {
         [key: string]: string;
     };
 };
-export declare const transformData: (data: ProteomicsPtm) => {
+declare const transformData: (data: ProteomicsPtm) => {
     source: string;
     type: string;
     start: number;
@@ -50,4 +50,4 @@ export declare const transformData: (data: ProteomicsPtm) => {
     tooltipContent: string;
     color: any;
 }[];
-export {};
+export default transformData;

package/dist/es/{protvista-ptm-exchange.js → adapters/ptm-exchange-adapter.js}

@@ -65,7 +65,7 @@ const convertPtmExchangePtms = (ptms, aa, absolutePosition) => {
         color: ConfidenceScoreColors[confidenceScore] || 'black',
     };
 };
-export const transformData = (data) => {
+const transformData = (data) => {
     if (data) {
         const { features } = data;
         const absolutePositionToPtms = {};
@@ -97,4 +97,5 @@ export const transformData = (data) => {
     }
     return [];
 };
-//# sourceMappingURL=protvista-ptm-exchange.js.map
+export default transformData;
+//# sourceMappingURL=ptm-exchange-adapter.js.map

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

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

@@ -0,0 +1,4 @@
+export declare const getAllFeatureStructures: (data: any) => any;
+export declare const mergeOverlappingIntervals: (structures: any) => any[];
+declare const transformData: (data: any) => any[];
+export default transformData;

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

@@ -0,0 +1,89 @@
+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

@@ -0,0 +1 @@
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package/dist/es/adapters/types/alphafold.js

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

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

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

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

@@ -0,0 +1,7 @@
+import { ProteinsAPIVariation, Variant, VariationDatum } from '@nightingale-elements/nightingale-variation';
+export type TransformedVariant = VariationDatum & Variant;
+declare const transformData: (data: ProteinsAPIVariation) => {
+    sequence: string;
+    variants: TransformedVariant[];
+};
+export default transformData;

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

@@ -0,0 +1,31 @@
+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

@@ -0,0 +1 @@
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package/dist/es/{protvista-variation-graph-adapter.d.ts → adapters/variation-graph-adapter.d.ts}

@@ -1,4 +1,4 @@
-export declare const transformData: (data: any) => {
+declare const transformData: (data: any) => {
     name: string;
     range: number[];
     color: string;
@@ -7,3 +7,4 @@ export declare const transformData: (data: any) => {
         value: number;
     }[];
 }[];
+export default transformData;

package/dist/es/{protvista-variation-graph-adapter.js → adapters/variation-graph-adapter.js}

@@ -1,10 +1,10 @@
-export const transformData = (data) => {
+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(", "),
+                accession: (_a = variant.genomicLocation) === null || _a === void 0 ? void 0 : _a.join(', '),
                 start: variant.begin,
             });
         });
@@ -31,16 +31,23 @@ export const transformData = (data) => {
                 name: 'variant',
                 range: [0, Math.max(Math.max(...total), Math.max(...diseaseTotal))],
                 color: 'darkgrey',
-                values: [...total].map((value, index) => ({ position: index, value: value })),
+                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 })),
+                values: [...diseaseTotal].map((value, index) => ({
+                    position: index,
+                    value: value,
+                })),
             },
         ];
         return graphData;
     }
 };
-//# sourceMappingURL=protvista-variation-graph-adapter.js.map
+export default transformData;
+//# sourceMappingURL=variation-graph-adapter.js.map

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

@@ -0,0 +1 @@
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