protvista-uniprot 4.2.0 → 4.2.1

package/dist/types/adapters/types/interpro.d.ts

@@ -8,7 +8,7 @@ type Result = {
     metadata: Metadata;
     proteins: Protein[];
 };
-type Metadata = {
+export type Metadata = {
     accession: string;
     name: string;
     source_database: string;

package/dist/types/index.d.ts

@@ -1,7 +1,7 @@
 import { default as ProtvistaUniprot } from './protvista-uniprot';
 export { default as filterConfig, colorConfig } from './filter-config';
-export { default as getFeatureTooltip } from './tooltips/featureTooltip';
-export { default as getStructureTooltip } from './tooltips/structureTooltip';
-export { default as getVariationTooltip } from './tooltips/variationTooltip';
+export { default as getFeatureTooltip } from './tooltips/feature-tooltip';
+export { default as getStructureTooltip } from './tooltips/structure-tooltip';
+export { default as getVariationTooltip } from './tooltips/variation-tooltip';
 export { default as ProtvistaUniprotStructure } from './protvista-uniprot-structure';
 export default ProtvistaUniprot;

package/dist/types/tooltips/interpro-tooltip.d.ts

@@ -0,0 +1,3 @@
+import { Metadata } from '../adapters/types/interpro';
+declare const formatTooltip: (start: number | "", end: number | "", metadata: Metadata) => string;
+export default formatTooltip;

package/dist/types/tooltips/{ptmTooltip.d.ts → ptm-tooltip.d.ts}

@@ -1,5 +1,5 @@
 import { PTM } from '../adapters/ptm-exchange-adapter';
 export declare const phosphorylate: (aa: string) => string;
 export declare const sumoylate: (aa: string) => string;
-declare const formatTooltip: (ptms: PTM[], aa: string, confidenceScore: string) => string;
+declare const formatTooltip: (title: string, ptms: PTM[], aa: string, confidenceScore: string) => string;
 export default formatTooltip;

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "protvista-uniprot",
   "description": "ProtVista tool for the UniProt website",
-  "version": "4.2.0",
+  "version": "4.2.1",
   "files": [
     "dist",
     "src"

package/src/adapters/feature-adapter.ts

@@ -1,5 +1,5 @@
 import { renameProperties } from '../utils';
-import formatTooltip from '../tooltips/featureTooltip';
+import formatTooltip from '../tooltips/feature-tooltip';
 
 const transformData = (data) => {
   let transformedData = [];

package/src/adapters/interpro-adapter.ts

@@ -1,5 +1,7 @@
 import ColorHash from 'color-hash';
 
+import formatTooltip from '../tooltips/interpro-tooltip';
+
 import { InterProProteinSearch, TransformedInterPro } from './types/interpro';
 
 // Copied from InterPro to replicate the same colours for the representative domains
@@ -11,58 +13,35 @@ const colorHash = new ColorHash({
 
 const transformData = (data: InterProProteinSearch): TransformedInterPro => {
   try {
-    return data?.results?.map(({ metadata, proteins }) => ({
-      ...metadata,
-      locations: proteins[0].entry_protein_locations,
-      start: proteins[0].entry_protein_locations
+    return data?.results?.map(({ metadata, proteins }) => {
+      const 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
+        : '';
+
+      const end = proteins[0].entry_protein_locations
         ? Math.max(
             ...proteins[0].entry_protein_locations?.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,
-    }));
+        : '';
+
+      return {
+        ...metadata,
+        locations: proteins[0].entry_protein_locations,
+        start,
+        end,
+        color: colorHash.hex(
+          metadata.accession.toLowerCase().split('').reverse().join('')
+        ),
+        tooltipContent: formatTooltip(start, end, metadata),
+        length: proteins[0].protein_length,
+      };
+    });
   } catch (error) {
     throw new Error('Failed transforming the data');
   }

package/src/adapters/proteomics-adapter.ts

@@ -1,5 +1,5 @@
 import { renameProperties } from '../utils';
-import formatTooltip from '../tooltips/featureTooltip';
+import formatTooltip from '../tooltips/feature-tooltip';
 
 const proteomicsTrackProperties = (feature, taxId) => {
   return {
@@ -64,7 +64,10 @@ const transformData = (data) => {
       }, []);
     } else {
       adaptedData = data.features.map((feature) => {
-        return Object.assign(feature, proteomicsTrackProperties(feature, data.taxid));
+        return Object.assign(
+          feature,
+          proteomicsTrackProperties(feature, data.taxid)
+        );
       });
     }
 

package/src/adapters/ptm-exchange-adapter.ts

@@ -1,4 +1,4 @@
-import formatTooltip from "../tooltips/ptmTooltip";
+import formatTooltip from '../tooltips/ptm-tooltip';
 
 type ProteomicsPtm = {
   accession: string;
@@ -82,7 +82,12 @@ const convertPtmExchangePtms = (
     start: absolutePosition,
     end: absolutePosition,
     shape: 'triangle',
-    tooltipContent: formatTooltip(ptms, aa, confidenceScore),
+    tooltipContent: formatTooltip(
+      `MOD_RES_LS ${absolutePosition}-${absolutePosition}`,
+      ptms,
+      aa,
+      confidenceScore
+    ),
     color:
       (confidenceScore && ConfidenceScoreColors[confidenceScore]) || 'black',
   };

package/src/adapters/rna-editing-adapter.ts

@@ -1,7 +1,7 @@
 import { AminoAcid } from '@nightingale-elements/nightingale-variation';
 
 import { RnaEditing, TransformedRnaEditing } from './types/rna-editing';
-import formatTooltip from '../tooltips/rnaEditingTooltip';
+import formatTooltip from '../tooltips/rna-editing-tooltip';
 
 const transformData = ({
   sequence,

package/src/adapters/structure-adapter.ts

@@ -1,4 +1,4 @@
-import formatTooltip from '../tooltips/structureTooltip';
+import formatTooltip from '../tooltips/structure-tooltip';
 
 const featureType = 'PDBE_COVER';
 const featureCategory = 'STRUCTURE_COVERAGE';

package/src/adapters/types/interpro.ts

@@ -10,7 +10,7 @@ type Result = {
   proteins: Protein[];
 };
 
-type Metadata = {
+export type Metadata = {
   accession: string;
   name: string;
   source_database: string;

package/src/adapters/variation-adapter.ts

@@ -7,7 +7,7 @@ import {
   VariationDatum,
 } from '@nightingale-elements/nightingale-variation';
 
-import formatTooltip from '../tooltips/variationTooltip';
+import formatTooltip from '../tooltips/variation-tooltip';
 
 export type TransformedVariant = VariationDatum & Variant;
 

package/src/index.ts

@@ -1,7 +1,7 @@
 export { default as filterConfig, colorConfig } from './filter-config';
-export { default as getFeatureTooltip } from './tooltips/featureTooltip';
-export { default as getStructureTooltip } from './tooltips/structureTooltip';
-export { default as getVariationTooltip } from './tooltips/variationTooltip';
+export { default as getFeatureTooltip } from './tooltips/feature-tooltip';
+export { default as getStructureTooltip } from './tooltips/structure-tooltip';
+export { default as getVariationTooltip } from './tooltips/variation-tooltip';
 export { default as ProtvistaUniprotStructure } from './protvista-uniprot-structure';
 import ProtvistaUniprot from './protvista-uniprot';
 export default ProtvistaUniprot;

package/src/tooltips/{featureTooltip.ts → feature-tooltip.ts}

@@ -1,5 +1,5 @@
 import ecoMap from '../adapters/config/evidence';
-import { phosphorylate, sumoylate } from './ptmTooltip';
+import { phosphorylate, sumoylate } from './ptm-tooltip';
 
 const taxIdToPeptideAtlasBuildData = {
   '36329': { build: '542', organism: 'Plasmodium' },

package/src/tooltips/interpro-tooltip.ts

@@ -0,0 +1,43 @@
+import { Metadata } from '../adapters/types/interpro';
+
+const formatTooltip = (
+  start: number | '',
+  end: number | '',
+  metadata: Metadata
+) => `
+      ${
+        start && end
+          ? `<h4>InterPro Representative Domain ${start}-${end}</h4><hr />`
+          : ''
+      }
+        <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>`
+            : ''
+        }
+      `;
+
+export default formatTooltip;

package/src/tooltips/{ptmTooltip.ts → ptm-tooltip.ts}

@@ -33,7 +33,7 @@ export const sumoylate = (aa: string) => {
   return '';
 };
 
-const formatTooltip = (ptms: PTM[], aa: string, confidenceScore: string): string => {
+const formatTooltip = (title: string, ptms: PTM[], aa: string, confidenceScore: string): string => {
     const evidences = [
         ...ptms.flatMap(({ dbReferences }) =>
           dbReferences?.flatMap(({ id }) => [id])
@@ -55,6 +55,11 @@ const formatTooltip = (ptms: PTM[], aa: string, confidenceScore: string): string
       }
       
   return `
+  ${
+    title
+      ? `<h4>${title}</h4><hr />`
+      : ''
+  }
   <h5>Description</h5><p>${
     modification === 'Phosphorylation' ? phosphorylate(aa) : sumoylate(aa)
   }</p>

package/src/tooltips/{variationTooltip.ts → variation-tooltip.ts}

@@ -7,7 +7,7 @@ import {
 } from '@nightingale-elements/nightingale-variation';
 import groupBy from 'lodash-es/groupBy';
 
-import { formatXrefs, getEvidenceFromCodes } from './featureTooltip';
+import { formatXrefs, getEvidenceFromCodes } from './feature-tooltip';
 
 const getDiseaseAssociations = (associations: Association[]): string =>
   associations