MobiDB lite standardization

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

@@ -142,38 +142,10 @@ const Viewer = ({ isoform, data }: LoadedProps) => {
   const { accession, length, sequence, features } = data.payload;
   const dataProtvista = features2protvista(features);
 
-  const mainTracks = [
-    'alphafold confidence',
-    'family',
-    'domain',
-    'pathogenic and likely pathogenic variants',
-    'intrinsically disordered regions',
-    'spurious proteins',
-    'residues',
-  ];
-
-  const hideCategories = {
-    'secondary structure': false,
-    family: false,
-    domain: false,
-    repeat: false,
-    'conserved site': false,
-    'active site': false,
-    'binding site': false,
-    ptm: false,
-    'match conservation': false,
-    'coiled-coils, signal peptides, transmembrane regions': false,
-    'short linear motifs': false,
-    'pfam-n': false,
-    funfam: false,
-  };
-
   return (
     <div className={css('isoform-panel')}>
       <IsoformHeader accession={accession} length={length} />
       <ProteinViewer
-        mainTracks={mainTracks}
-        hideCategories={hideCategories}
         protein={{ sequence, length: sequence.length }}
         data={dataProtvista}
         title="Entry matches to this isoform"

src/components/ProteinViewer/index.tsx

@@ -17,7 +17,11 @@ import {
   FeatureLocation,
 } from '@nightingale-elements/nightingale-track';
 
-import { typeNameToSectionName, standardizePTMData } from './utils';
+import {
+  typeNameToSectionName,
+  standardizePTMData,
+  firstHideCategories,
+} from './utils';
 
 import {
   useFloating,
@@ -111,16 +115,9 @@ type Props = PropsWithChildren<{
   conservationError?: string;
   /** TO include loading animation in the header */
   loading: boolean;
-
   viewerType: string;
-
   changeSettingsRaw: typeof changeSettingsRaw;
-
   showMoreSettings: boolean;
-
-  mainTracks: string[];
-
-  hideCategories: Record<string, boolean>;
 }>;
 
 interface LoadedProps extends Props, LoadDataProps<RootAPIPayload, 'Base'> {}
@@ -153,9 +150,7 @@ const switchCategoryVisibilityShowMore = (
 };
 
 export const ProteinViewer = ({
-  mainTracks,
   viewerType,
-  hideCategories,
   protein,
   title,
   data,
@@ -170,10 +165,19 @@ export const ProteinViewer = ({
 }: LoadedProps) => {
   const [isPrinting, setPrinting] = useState(false);
 
+  const mainTracks = [
+    'alphafold confidence',
+    'domain',
+    'family',
+    'active site',
+    'conserved site',
+    'intrinsically disordered regions',
+  ];
+
   /// STATE
   const [showMore, setShowMore] = useState(showMoreSettings);
   const [hideCategory, setHideCategory] =
-    useState<CategoryVisibility>(hideCategories);
+    useState<CategoryVisibility>(firstHideCategories);
   const categoryRefs = useRef<ExpandedHandle[]>([]);
   const [_, setOverTooltip, overTooltipRef] = useStateRef(false);
   const arrowRef = useRef(null);
@@ -245,7 +249,7 @@ export const ProteinViewer = ({
       If the representative track is not available, nothing would be shown. This prevents it, showing all the matches anyway.
     */
     const changeVisibilityFor: string[] = [];
-    ['familiy', 'domain'].forEach((type) => {
+    ['family', 'domain'].forEach((type) => {
       const entries = data.find(([entryType]) => entryType === type)?.[1] || [];
       const hasRep = (entries as ExtendedFeature[]).some(
         (entry) => entry.representative === true,
@@ -357,7 +361,7 @@ export const ProteinViewer = ({
                     }
 
                     // Transform PTM data to track-like data
-                    else if (type == 'ptm') {
+                    if (type == 'ptm') {
                       entries = standardizePTMData(entries, protein);
                     }
 

src/components/ProteinViewer/utils.ts

@@ -30,6 +30,23 @@ export const typeNameToSectionName: Record<string, string> = {
   'external sources': 'External Sources',
 };
 
+export const firstHideCategories = {
+  'secondary structure': false,
+  family: false,
+  domain: false,
+  repeat: false,
+  'conserved site': false,
+  residues: false,
+  'active site': false,
+  'binding site': false,
+  ptm: false,
+  'match conservation': false,
+  'coiled-coils, signal peptides, transmembrane regions': false,
+  'short linear motifs': false,
+  'pfam-n': false,
+  funfam: false,
+};
+
 export type PTM = {
   position: number;
   name: string;
@@ -176,7 +193,7 @@ const processData = <M = Metadata>(
   };
 };
 
-const ptmFeaturesFragments = (features: PTMFeature[]): PTMFragment[] => {
+export const ptmFeaturesFragments = (features: PTMFeature[]): PTMFragment[] => {
   const ptmFragments: PTMFragment[] = [];
 
   features.map((feature) => {
@@ -236,13 +253,19 @@ export const standardizePTMData = (
       locations: [{ fragments: fragments }],
     };
 
+    console.log('f', newFeature);
+
     ptmsEntriesGroupedByModification.push(newFeature);
   });
 
+  console.log('here', ptmsEntriesGroupedByModification);
+
   // PTMs coming from InterPro and external API should be in the same section but require different processing due to different structure (see above)
   entries = ptmsEntriesGroupedByModification.concat(
     entries.filter((entry) => entry.source_database === 'interpro'),
   );
 
+  console.log('final', entries);
+
   return [...entries];
 };

src/components/Related/DomainEntriesOnStructure/ProteinViewerLoaded/index.tsx

@@ -55,30 +55,11 @@ const ProteinViewerLoaded = ({
     };
   });
 
-  // List of "main" tracks to be displayed, the rest are hidden by default
-  const mainTracks = [
-    'secondary structure',
-    'family',
-    'domain',
-    'conserved site',
-    'active site',
-  ];
-
-  const hideCategories = {
-    'secondary structure': false,
-    family: false,
-    domain: false,
-    'conserved site': false,
-    'active site': false,
-  };
-
   const enrichedTracks = [...tracks];
 
   return (
     <div ref={protvistaEl}>
       <ProteinViewer
-        mainTracks={mainTracks}
-        hideCategories={hideCategories}
         protein={protein}
         data={enrichedTracks}
         id={id}

src/components/Related/DomainsOnProtein/DomainsOnProteinLoaded/index.tsx

@@ -175,6 +175,7 @@ const standardizeMobiDBFeatureStructure = (
     tempFeature.locations = slicedTempFeatureLocations;
     newFeatures.push(tempFeature);
   });
+
   return newFeatures;
 };
 
@@ -307,8 +308,6 @@ const DomainsOnProteinLoaded = ({
     (mainData as ProteinEntryPayload).metadata ||
     (mainData as { payload: ProteinEntryPayload }).payload.metadata;
 
-  let mainTracks: string[] = [];
-  let hideCategories: Record<string, boolean> = {};
   let flattenedData = undefined;
 
   if (dataConfidence)
@@ -375,22 +374,22 @@ const DomainsOnProteinLoaded = ({
       dataMerged['unintegrated'] = [...filteredUnintegrated];
     }
 
-    console.log(accessionsToRemoveFromUnintegrated);
-
-    // Create PTM section
-    if (dataMerged['intrinsically_disordered_regions']) {
-      dataMerged['intrinsically_disordered_regions'] =
-        standardizeMobiDBFeatureStructure(
-          dataMerged['intrinsically_disordered_regions'] as ExtendedFeature[],
-        );
-    }
-
     let proteinViewerData = proteinViewerReorganization(
       dataFeatures,
       dataMerged as ProteinViewerDataObject<MinimalFeature>,
     );
     proteinViewerData = sectionsReorganization(proteinViewerData);
 
+    // Create PTM section
+    if (proteinViewerData['intrinsically_disordered_regions']) {
+      proteinViewerData['intrinsically_disordered_regions'] =
+        standardizeMobiDBFeatureStructure(
+          proteinViewerData[
+            'intrinsically_disordered_regions'
+          ] as ExtendedFeature[],
+        );
+    }
+
     // Sort data by match position, but exclude PIRSR, which is sorted in proteinViewerReorganization
     Object.entries(
       proteinViewerData as ProteinViewerDataObject<ExtendedFeature>,
@@ -420,65 +419,12 @@ const DomainsOnProteinLoaded = ({
         dataMerged[representativeToSection[track]] = dataMerged[
           representativeToSection[track]
         ].concat(dataMerged[track]);
+
+        // Remove representative_x track
+        dataMerged[track] = [];
       }
     });
-
-    mainTracks = [
-      'alphafold confidence',
-      'family',
-      'domain',
-      'pathogenic and likely pathogenic variants',
-      'intrinsically disordered regions',
-      'spurious proteins',
-      'residues',
-      'unintegrated',
-      'other features',
-      'other residues',
-    ];
-
-    hideCategories = {
-      'secondary structure': false,
-      family: false,
-      domain: false,
-      repeat: false,
-      'conserved site': false,
-      'active site': false,
-      'binding site': false,
-      ptm: false,
-      'match conservation': false,
-      'coiled-coils, signal peptides, transmembrane regions': false,
-      'short linear motifs': false,
-      'pfam-n': false,
-      funfam: false,
-    };
   } else {
-    mainTracks = [
-      'alphafold confidence',
-      'family',
-      'domain',
-      'pathogenic and likely pathogenic variants',
-      'intrinsically disordered regions',
-      'spurious proteins',
-      'residues',
-    ];
-
-    hideCategories = {
-      'secondary structure': false,
-      family: false,
-      domain: false,
-      repeat: false,
-      'conserved site': false,
-      residues: false,
-      'active site': false,
-      'binding site': false,
-      ptm: false,
-      'match conservation': false,
-      'coiled-coils, signal peptides, transmembrane regions': false,
-      'short linear motifs': false,
-      'pfam-n': false,
-      funfam: false,
-    };
-
     flattenedData = flattenTracksObject(dataMerged);
   }
 
@@ -493,8 +439,6 @@ const DomainsOnProteinLoaded = ({
         handleConservationLoad={handleConservationLoad}
         conservationError={conservationError}
         loading={loading}
-        mainTracks={mainTracks}
-        hideCategories={hideCategories}
       >
         {children}
       </ProteinViewer>

src/components/Structure/ViewerAndEntries/ProteinViewerForAlphafold/index.tsx

@@ -151,31 +151,14 @@ const ProteinViewerForAlphafold = ({
   if (dataConfidence) addConfidenceTrack(dataConfidence, protein, groups);
   const tracks = flattenTracksObject(groups);
 
-  const mainTracks = [
-    'alphafold confidence',
-    'domain',
-    'family',
-    'active site',
-    'conserved site',
-  ];
-
   if (!dataProtein.payload?.metadata) return null;
 
-  const hideCategories = {
-    domain: false,
-    family: false,
-    'active site': false,
-    'conserved site': false,
-  };
-
   return (
     <div ref={trackRef}>
       <ProteinViewer
         viewerType={'structures'}
         protein={dataProtein.payload.metadata}
         data={tracks}
-        mainTracks={mainTracks}
-        hideCategories={hideCategories}
         title="Protein domains"
         showOptions={!isSplitScreen}
       />