jbrowse-plugin-protein3d 0.4.6 → 0.4.7

package/dist/LaunchProteinView/components/TranscriptSelector.js

@@ -19,21 +19,18 @@ export default function TranscriptSelector({ val, setVal, isoforms, isoformSeque
             nonMatches.push(f);
         }
     }
-    matches.sort((a, b) => isoformSequences[b.id()].seq.length -
-        isoformSequences[a.id()].seq.length);
-    nonMatches.sort((a, b) => isoformSequences[b.id()].seq.length -
-        isoformSequences[a.id()].seq.length);
+    const byLengthDesc = (a, b) => isoformSequences[b.id()].seq.length - isoformSequences[a.id()].seq.length;
     return (React.createElement(TextField, { value: val ?? '', onChange: event => {
             setVal(event.target.value);
         }, label: "Choose transcript isoform", select: true, disabled: disabled },
-        matches.map(f => (React.createElement(MenuItem, { value: f.id(), key: f.id() },
+        matches.toSorted(byLengthDesc).map(f => (React.createElement(MenuItem, { value: f.id(), key: f.id() },
             geneName,
             " - ",
             getTranscriptDisplayName(f),
             " (",
             isoformSequences[f.id()].seq.length,
             "aa) (matches structure residues)"))),
-        nonMatches.map(f => (React.createElement(MenuItem, { value: f.id(), key: f.id() },
+        nonMatches.toSorted(byLengthDesc).map(f => (React.createElement(MenuItem, { value: f.id(), key: f.id() },
             geneName,
             " - ",
             getTranscriptDisplayName(f),

package/dist/LaunchProteinView/services/foldseekApi.js

@@ -81,8 +81,7 @@ export async function pollFoldseekStatus(ticketId) {
     return result;
 }
 export async function getFoldseekResults(ticketId) {
-    const result = await jsonfetch(`https://search.foldseek.com/api/result/${ticketId}/0`);
-    return result;
+    return jsonfetch(`https://search.foldseek.com/api/result/${ticketId}/0`);
 }
 export async function waitForFoldseekResults(ticketId, onStatusChange) {
     const maxAttempts = 180;

package/dist/LaunchProteinView/services/lookupMethods.js

@@ -32,7 +32,7 @@ function buildXrefQuery(id) {
 }
 async function searchUniProt(query, size = 10) {
     const url = `https://rest.uniprot.org/uniprotkb/search?query=${encodeURIComponent(query)}&fields=${UNIPROT_FIELDS}&size=${size}`;
-    const data = (await jsonfetch(url));
+    const data = await jsonfetch(url);
     return data.results.map(mapApiResultToEntry);
 }
 async function searchByXref(id) {

package/dist/LaunchProteinView/utils/calculateProteinSequence.js

@@ -30,20 +30,20 @@ export function dedupe(list) {
     return list.filter((item, pos, ary) => !pos || getItemId(item) !== getItemId(ary[pos - 1]));
 }
 export function getProteinSequence({ feature, seq, }) {
-    // @ts-expect-error
-    const f = feature.toJSON();
-    const subfeatures = f.subfeatures;
+    const featureStart = feature.get('start');
+    const strand = feature.get('strand');
+    const subfeatures = feature.get('subfeatures') ?? [];
     const cds = dedupe(subfeatures
-        .toSorted((a, b) => a.start - b.start)
+        .toSorted((a, b) => a.get('start') - b.get('start'))
         .map(sub => ({
-        ...sub,
-        start: sub.start - f.start,
-        end: sub.end - f.start,
+        start: sub.get('start') - featureStart,
+        end: sub.get('end') - featureStart,
+        type: sub.get('type'),
     }))
         .filter(f => f.type === 'CDS'));
     return calculateProteinSequence({
-        cds: f.strand === -1 ? revlist(cds, seq.length) : cds,
-        sequence: f.strand === -1 ? revcom(seq) : seq,
+        cds: strand === -1 ? revlist(cds, seq.length) : cds,
+        sequence: strand === -1 ? revcom(seq) : seq,
         codonTable: generateCodonTable(defaultCodonTable),
     });
 }

package/dist/ProteinView/applyLociInteractivity.js

@@ -1,9 +1,22 @@
 import loadMolstar from './loadMolstar';
 import { getMolstarStructureSelection } from './util';
-export async function applyLociInteractivityMultiple({ structure, residues, plugin, mode, }) {
-    if (mode === 'clear' || residues.length === 0) {
+function clearLoci(plugin) {
+    plugin.managers.interactivity.lociHighlights.clearHighlights();
+    plugin.managers.interactivity.lociSelects.deselectAll();
+}
+function applyLoci(plugin, loci, mode) {
+    if (mode === 'highlight') {
         plugin.managers.interactivity.lociHighlights.clearHighlights();
+        plugin.managers.interactivity.lociHighlights.highlight({ loci });
+    }
+    else {
         plugin.managers.interactivity.lociSelects.deselectAll();
+        plugin.managers.interactivity.lociSelects.select({ loci });
+    }
+}
+export async function applyLociInteractivityMultiple({ structure, residues, plugin, mode, }) {
+    if (mode === 'clear' || residues.length === 0) {
+        clearLoci(plugin);
         return;
     }
     const { StructureSelection, Script } = await loadMolstar();
@@ -15,18 +28,11 @@ export async function applyLociInteractivityMultiple({ structure, residues, plug
         'group-by': Q.struct.atomProperty.macromolecular.residueKey(),
     }), structure);
     const loci = StructureSelection.toLociWithSourceUnits(sel);
-    if (mode === 'highlight') {
-        plugin.managers.interactivity.lociHighlights.clearHighlights();
-        plugin.managers.interactivity.lociHighlights.highlight({ loci });
-    }
-    else {
-        plugin.managers.interactivity.lociSelects.deselectAll();
-        plugin.managers.interactivity.lociSelects.select({ loci });
-    }
+    applyLoci(plugin, loci, mode);
 }
 export async function applyLociInteractivity({ structure, startResidue, endResidue, plugin, mode, }) {
     if (mode === 'clear') {
-        plugin.managers.interactivity.lociHighlights.clearHighlights();
+        clearLoci(plugin);
         return;
     }
     const { StructureSelection, Script } = await loadMolstar();
@@ -44,18 +50,11 @@ export async function applyLociInteractivity({ structure, startResidue, endResid
         'group-by': Q.struct.atomProperty.macromolecular.residueKey(),
     }), structure);
     const loci = StructureSelection.toLociWithSourceUnits(sel);
-    if (mode === 'highlight') {
-        plugin.managers.interactivity.lociHighlights.clearHighlights();
-        plugin.managers.interactivity.lociHighlights.highlight({ loci });
-    }
-    else {
-        plugin.managers.interactivity.lociSelects.deselectAll();
-        plugin.managers.interactivity.lociSelects.select({ loci });
-    }
+    applyLoci(plugin, loci, mode);
 }
 export async function applyLociInteractivitySingle({ structure, selectedResidue, plugin, mode, }) {
     if (mode === 'clear') {
-        plugin.managers.interactivity.lociHighlights.clearHighlights();
+        clearLoci(plugin);
         return;
     }
     const { StructureSelection } = await loadMolstar();
@@ -64,12 +63,5 @@ export async function applyLociInteractivitySingle({ structure, selectedResidue,
         selectedResidue: selectedResidue + 1,
     });
     const loci = StructureSelection.toLociWithSourceUnits(sel);
-    if (mode === 'highlight') {
-        plugin.managers.interactivity.lociHighlights.clearHighlights();
-        plugin.managers.interactivity.lociHighlights.highlight({ loci });
-    }
-    else {
-        plugin.managers.interactivity.lociSelects.deselectAll();
-        plugin.managers.interactivity.lociSelects.select({ loci });
-    }
+    applyLoci(plugin, loci, mode);
 }

package/dist/fetchUtils.d.ts

@@ -1,3 +1,3 @@
 export declare function myfetch(url: string, args?: RequestInit): Promise<Response>;
-export declare function jsonfetch(url: string, args?: RequestInit): Promise<any>;
+export declare function jsonfetch<T = unknown>(url: string, args?: RequestInit): Promise<T>;
 export declare function timeout(time: number): Promise<unknown>;