Merge pull request #538 from ProteinsWebTeam/representative-domains-e…

…vetywhere

Representative domains everywhere

.prettierrc

@@ -4,7 +4,10 @@ overrides:
 - files: "*.css"
   options:
     singleQuote: false
-- files: "src/**/*.js"
+- files: 
+  - "src/**/*.js"
+  - "src/**/*.ts"
+  - "src/**/*.tsx"
   options:
     parser: typescript
     trailingComma: all

src/components/Protein/Isoforms/Viewer/index.tsx

@@ -9,6 +9,7 @@ import descriptionToPath from 'utils/processDescription/descriptionToPath';
 import NumberComponent from 'components/NumberComponent';
 import { groupByEntryType } from 'components/Related/DomainsOnProtein';
 import { byEntryType } from 'components/Related/DomainsOnProtein/DomainsOnProteinLoaded';
+import { selectRepresentativeDomains } from 'components/ProteinViewer/utils';
 import Loading from 'components/SimpleCommonComponents/Loading';
 
 import loadable from 'higherOrder/loadable';
@@ -58,17 +59,31 @@ const features2protvista = (features: FeatureMap) => {
   }
 
   const interpro = featArray.filter(({ accession }) =>
-    accession.toLowerCase().startsWith('ipr')
+    accession.toLowerCase().startsWith('ipr'),
   );
   const groups = groupByEntryType(interpro);
   const unintegrated = featArray.filter(
-    (f) => interpro.indexOf(f) === -1 && integrated.indexOf(f) === -1
+    (f) => interpro.indexOf(f) === -1 && integrated.indexOf(f) === -1,
   );
   const categories: Array<[string, unknown]> = [
     ...(Object.entries(groups) as Array<[string, unknown]>),
     ['unintegrated', unintegrated],
   ];
-  return categories.sort(byEntryType);
+
+  const sortedCategories = categories.sort(byEntryType);
+  const representativeDomains = selectRepresentativeDomains(
+    featArray,
+    'locations',
+  );
+
+  if (representativeDomains?.length) {
+    sortedCategories.splice(0, 0, [
+      'representative domains',
+      representativeDomains,
+    ]);
+  }
+
+  return sortedCategories;
 };
 type Props = {
   isoform?: string;
@@ -113,7 +128,7 @@ const Viewer = ({ isoform, data }: LoadedProps) => {
 
 const mapStateToProps = createSelector(
   (state: GlobalState) => state.customLocation.search,
-  ({ isoform }) => ({ isoform })
+  ({ isoform }) => ({ isoform }),
 );
 
 const getIsoformURL = createSelector(
@@ -123,7 +138,7 @@ const getIsoformURL = createSelector(
   (
     { protocol, hostname, port, root },
     { protein: { accession } },
-    { isoform }
+    { isoform },
   ) => {
     const description = {
       main: { key: 'protein' },
@@ -139,8 +154,8 @@ const getIsoformURL = createSelector(
         isoforms: isoform,
       },
     });
-  }
+  },
 );
 export default loadData({ getUrl: getIsoformURL, mapStateToProps } as Params)(
-  Viewer
+  Viewer,
 );

src/components/ProteinViewer/utils.ts

@@ -3,16 +3,21 @@ import { toPlural } from 'utils/pages/toPlural';
 import { NOT_MEMBER_DBS } from 'menuConfig';
 import { getTrackColor, EntryColorMode } from 'utils/entry-color';
 
-const selectRepresentativeDomains = (domains: Record<string, unknown>[]) => {
+export const selectRepresentativeDomains = (
+  domains: Record<string, unknown>[],
+  locationKey: string = 'entry_protein_locations',
+) => {
   const flatDomains = [];
   for (const domain of domains) {
-    const { accession, short_name, name, source_database, integrated } = domain;
-    for (const location of domain.entry_protein_locations as Array<ProtVistaLocation>) {
+    const { accession, short_name, name, source_database, integrated, chain } =
+      domain;
+    for (const location of domain[locationKey] as Array<ProtVistaLocation>) {
       for (const fragment of location.fragments) {
         const { start, end, representative } = fragment;
         if (representative) {
           flatDomains.push({
             accession,
+            chain,
             short_name,
             name,
             source_database,
@@ -31,15 +36,15 @@ const selectRepresentativeDomains = (domains: Record<string, unknown>[]) => {
 };
 export const useProcessData = <M = Metadata>(
   results: EndpointWithMatchesPayload<M, MatchI>[] | undefined,
-  endpoint: Endpoint
+  endpoint: Endpoint,
 ) =>
   useMemo(() => {
     return processData(results || [], endpoint);
   }, [results, endpoint]);
 
 const processData = <M = Metadata>(
   dataResults: EndpointWithMatchesPayload<M>[],
-  endpoint: Endpoint
+  endpoint: Endpoint,
 ) => {
   const results: Record<string, unknown>[] = [];
   for (const item of dataResults) {
@@ -50,29 +55,29 @@ const processData = <M = Metadata>(
         ...match,
         ...item.metadata,
         ...(item.extra_fields || {}),
-      }))
+      })),
     );
   }
   const interpro = results.filter(
     (entry) =>
       (entry as unknown as Metadata).source_database.toLowerCase() ===
-      'interpro'
+      'interpro',
   );
 
   const representativeDomains = selectRepresentativeDomains(results);
   const interproMap = new Map(
     interpro.map((ipro) => [
       `${ipro.accession}-${ipro.chain}-${ipro.protein}`,
       ipro,
-    ])
+    ]),
   );
   const integrated = results.filter((entry) => entry.integrated);
   const unintegrated = results.filter(
     (entry) =>
       interpro.concat(integrated).indexOf(entry) === -1 &&
       !NOT_MEMBER_DBS.has(
-        (entry as unknown as Metadata).source_database.toLowerCase()
-      )
+        (entry as unknown as Metadata).source_database.toLowerCase(),
+      ),
   );
   integrated.forEach((entry) => {
     const ipro: Record<string, unknown> & {
@@ -84,7 +89,7 @@ const processData = <M = Metadata>(
     if (ipro.children.indexOf(entry) === -1) ipro.children.push(entry);
   });
   integrated.sort((a, b) =>
-    a.chain ? (a.chain as string).localeCompare(b.chain as string) : -1
+    a.chain ? (a.chain as string).localeCompare(b.chain as string) : -1,
   );
   return {
     interpro,

src/components/Related/DomainEntriesOnStructure/__snapshots__/test.js.snap

@@ -3,10 +3,10 @@
 exports[`<EntriesOnStructure /> should render 1`] = `
 <React.Fragment>
   <div
-    className="row"
+    className="vf-stack vf-stack--400"
   >
     <div
-      className="columns"
+      className="vf-stack"
     >
       <h4
         id="protvista-A-p00735"

src/components/Related/DomainEntriesOnStructure/index.tsx

@@ -1,4 +1,4 @@
-import React from 'react';
+import React, { useMemo } from 'react';
 
 import Link from 'components/generic/Link';
 import Tooltip from 'components/SimpleCommonComponents/Tooltip';
@@ -50,7 +50,7 @@ export type DataForProteinChain = {
 
 const mergeData = (
   secondaryData: StructureLinkedObject[],
-  secondaryStructures?: SecondaryStructure[]
+  secondaryStructures?: SecondaryStructure[],
 ) => {
   const out: Record<string, Record<string, DataForProteinChain>> = {};
   for (const entry of secondaryData) {
@@ -119,7 +119,7 @@ const mergeData = (
         ({ entry_protein_locations, entry_structure_locations, ...child }) => ({
           ...child,
           locations: entry_structure_locations,
-        })
+        }),
       ),
       chain: entry.chain,
       protein: entry.protein,
@@ -131,7 +131,7 @@ const mergeData = (
   const chains = Object.keys(out).sort((a, b) => (a ? a.localeCompare(b) : -1));
   for (const chain of chains) {
     const proteins = Object.keys(out[chain]).sort((a, b) =>
-      a ? a.localeCompare(b) : -1
+      a ? a.localeCompare(b) : -1,
     );
     for (const protein of proteins) {
       entries.push(out[chain][protein]);
@@ -151,37 +151,71 @@ const tagChimericStructures = (data: DataForProteinChain[]) => {
   }
 };
 
+const getRepresentativesPerChain = (
+  representativeDomains?: Record<string, unknown>[],
+) => {
+  const representativesPerChain: Record<string, Array<MinimalFeature>> = {};
+  if (representativeDomains?.length) {
+    representativeDomains.forEach((domain) => {
+      if (domain.chain) {
+        if (!representativesPerChain[domain.chain as string])
+          representativesPerChain[domain.chain as string] = [];
+        representativesPerChain[domain.chain as string].push(
+          domain as MinimalFeature,
+        );
+      }
+    });
+  }
+  return representativesPerChain;
+};
+
 type Props = {
   structure: string;
   entries: StructureLinkedObject[];
   secondaryStructures?: SecondaryStructure[];
+  representativeDomains?: Record<string, unknown>[];
 };
 
 const EntriesOnStructure = ({
   entries,
   secondaryStructures,
   structure,
+  representativeDomains,
 }: Props) => {
-  const merged = mergeData(entries, secondaryStructures);
-  tagChimericStructures(merged);
+  const merged = useMemo(() => {
+    const data = mergeData(entries, secondaryStructures);
+    tagChimericStructures(data);
+    return data;
+  }, [entries, secondaryStructures]);
+  const representativesPerChain = useMemo(
+    () => getRepresentativesPerChain(representativeDomains),
+    [representativeDomains],
+  );
+
   return (
     <>
-      <div className={css('row')}>
+      <div className={css('vf-stack', 'vf-stack--400')}>
         {merged.map((e, i) => {
           const sequenceData = {
             accession: `${e.chain}-${structure}`,
             ...e.sequence,
           };
 
           const tracks = Object.entries(
-            e.data as Record<string, Array<Record<string, unknown>>>
+            e.data as Record<string, Array<Record<string, unknown>>>,
           ).sort(([a], [b]) => {
             if (a && a.toLowerCase() === 'chain') return -1;
             if (b && b.toLowerCase() === 'chain') return 1;
             return b ? b.localeCompare(a) : -1;
           });
+          if (representativesPerChain[e.chain]) {
+            tracks.splice(0, 0, [
+              'representative domains',
+              representativesPerChain[e.chain],
+            ]);
+          }
           return (
-            <div key={i} className={css('columns')}>
+            <div key={i} className={css('vf-stack')}>
               <h4 id={`protvista-${e.chain}-${e.protein.accession}`}>
                 Chain {e.chain}{' '}
                 {e.protein?.accession && (