jbrowse-plugin-protein3d 0.16.0 → 1.0.1

package/dist/AddHighlightModel/Highlight.js

@@ -1,9 +1,9 @@
 import React from 'react';
 import { observer } from 'mobx-react';
-import { getHighlightCoords, useStyles } from './util';
+import { useStyles } from './util';
 const Highlight = observer(function Highlight({ region, model, }) {
     const { cx, classes } = useStyles();
-    const coords = getHighlightCoords(model, region);
+    const coords = model.getHighlightCoords(region);
     return coords ? (React.createElement("div", { className: cx(classes.highlight, coords.width <= 3 ? classes.thinborder : undefined), style: { left: coords.left, width: coords.width } })) : null;
 });
 export default Highlight;

package/dist/AddHighlightModel/index.js

@@ -1,14 +1,5 @@
-import React from 'react';
+import { addExtensionElement } from '@jbrowse/core/ui';
 import HighlightComponents from './HighlightComponents';
 export default function AddHighlightModelF(pluginManager) {
-    pluginManager.addToExtensionPoint(
-    // @ts-expect-error v4 hosts have no contributeToExtensionPoint
-    'LinearGenomeView-TracksContainerComponent', 
-    // v4 hosts seed this point with undefined rather than []
-    (rest, { model }) => {
-        return [
-            ...(rest ?? []),
-            React.createElement(HighlightComponents, { key: "highlight_protein_viewer_protein3d", model: model }),
-        ];
-    });
+    addExtensionElement(pluginManager, 'LinearGenomeView-TracksContainerComponent', HighlightComponents);
 }

package/dist/AddHighlightModel/util.js

@@ -1,24 +1,4 @@
-import { getSession } from '@jbrowse/core/util';
 import { makeStyles } from 'tss-react/mui';
-// Local mirror of core's getLayoutHighlightCoords / model.getHighlightCoords,
-// added to jbrowse after 4.3.0. Kept here so the plugin still builds against
-// 4.3.0; once the minimum jbrowse version ships the model method, replace the
-// body with `model.getHighlightCoords(region)`.
-export function getHighlightCoords(model, region) {
-    const { assemblyManager } = getSession(model);
-    const assembly = region.assemblyName
-        ? assemblyManager.get(region.assemblyName)
-        : undefined;
-    const refName = assembly?.getCanonicalRefName(region.refName) ?? region.refName;
-    const s = model.bpToPx({ refName, coord: region.start });
-    const e = model.bpToPx({ refName, coord: region.end });
-    return s && e
-        ? {
-            width: Math.max(Math.abs(e.offsetPx - s.offsetPx), 3),
-            left: Math.min(s.offsetPx, e.offsetPx) - model.offsetPx,
-        }
-        : undefined;
-}
 export const useStyles = makeStyles()({
     highlight: {
         height: '100%',

package/dist/LaunchProteinView/codingFeature.js

@@ -1,9 +1,4 @@
-// Copied from @jbrowse/core's featureTypes: the barrel export reads undefined
-// on a v4 host, and the deep path is not in core's exports map.
-const GENE_LIKE_TYPE = /gene(_segment)?$|rna$|transcript/;
-export function isGeneLikeType(type) {
-    return type !== undefined && GENE_LIKE_TYPE.test(type.toLowerCase());
-}
+import { isGeneLikeType } from '@jbrowse/core/util';
 function isCDS(feature) {
     return feature.get('type')?.toLowerCase() === 'cds';
 }
@@ -22,12 +17,3 @@ export function codingTranscripts(feature) {
 export function isCodingFeature(feature) {
     return codingTranscripts(feature).length > 0;
 }
-// The outermost gene-like ancestor, so a click on an isoform opens the dialog
-// on the gene with every transcript to choose from, as the canvas host does.
-export function geneLikeRoot(feature) {
-    let root = feature;
-    for (let parent = root.parent?.(); parent && isGeneLikeType(parent.get('type')); parent = parent.parent?.()) {
-        root = parent;
-    }
-    return root;
-}

package/dist/LaunchProteinView/components/PdbSearch.js

@@ -70,16 +70,30 @@ const PdbSearch = observer(function PdbSearch({ feature, preferredTranscriptId,
         preferredTranscriptId,
         resetKey: uniprotId,
     });
-    const loadingStatuses = [
-        isLookupLoading && 'Looking up UniProt ID',
+    const isoformStatuses = [
         isIsoformLoading && 'Loading protein sequences from transcript isoforms',
         isRanking && 'Aligning isoforms to the structure',
+    ];
+    const lookupStatuses = [
+        isLookupLoading && 'Looking up UniProt ID',
         isPdbLoading && 'Listing PDB entries from PDBe',
-    ].filter((s) => !!s);
+    ];
+    const loadingStatuses = [...lookupStatuses, ...isoformStatuses].filter((s) => !!s);
     const isLoading = loadingStatuses.length > 0;
     const error = isLoading
         ? undefined
         : (isoformError ?? lookup.lookupError ?? pdbError);
+    // A typed PDB ID exists to get around a lookup that is slow, failing or
+    // wrong, so only the isoforms it is ranked against hold its launch back
+    const typedIdOverrides = isPdbId(debouncedTypedPdbId);
+    const launchWaiting = typedIdOverrides
+        ? isoformStatuses.some(Boolean)
+        : isLoading;
+    const launchError = typedIdOverrides
+        ? launchWaiting
+            ? undefined
+            : isoformError
+        : error;
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
             error ? React.createElement(ErrorMessage, { error: error }) : null,
@@ -113,6 +127,6 @@ const PdbSearch = observer(function PdbSearch({ feature, preferredTranscriptId,
                 ". The AlphaFoldDB tab has a predicted one."))) : null,
             ranking && selectedTranscript ? (React.createElement(TranscriptSelector, { val: selectedTranscriptId, setVal: setSelectedTranscriptId, structureSequence: structureSequence, feature: feature, isoforms: transcripts, ranking: ranking })) : null),
         React.createElement(DialogActions, null,
-            React.createElement(ProteinViewActions, { handleClose: handleClose, uniprotId: uniprotId, userSelectedProteinSequence: selectedIsoform, selectedTranscript: selectedTranscript, url: structureUrl, pdbId: selectedPdbId, feature: feature, view: view, session: session, sideBySide: sideBySide, onSideBySideChange: onSideBySideChange, isLoading: isLoading, error: error }))));
+            React.createElement(ProteinViewActions, { handleClose: handleClose, uniprotId: uniprotId, userSelectedProteinSequence: selectedIsoform, selectedTranscript: selectedTranscript, url: structureUrl, pdbId: selectedPdbId, feature: feature, view: view, session: session, sideBySide: sideBySide, onSideBySideChange: onSideBySideChange, isLoading: launchWaiting, error: launchError }))));
 });
 export default PdbSearch;

package/dist/LaunchProteinView/components/proteinTrackSetup.js

@@ -1,6 +1,5 @@
-import { getEnv } from '@jbrowse/mobx-state-tree';
 import { myfetch, uniprotGffUrl } from 'p2s_mapper';
-import { jexlBandColor, thresholdBandColor } from './wiggleBandColors';
+import { thresholdBandColor } from './wiggleBandColors';
 import { PLDDT_BANDS } from '../../ProteinView/residueTracks';
 /**
  * Fetches UniProt GFF data and extracts unique feature types
@@ -23,7 +22,7 @@ async function fetchUniProtFeatureTypes(uniprotId) {
 function addUniProtFeatureTracks({ session, uniprotId, featureTypes, }) {
     featureTypes.forEach(type => {
         const trackId = `${uniprotId}-${type}`;
-        session.addTrackConf({
+        session.addSessionTrackConf({
             type: 'FeatureTrack',
             trackId,
             name: type,
@@ -48,7 +47,7 @@ function addUniProtFeatureTracks({ session, uniprotId, featureTypes, }) {
  * Adds antigen annotation track from EBI
  */
 function addAntigenTrack({ session, uniprotId, }) {
-    session.addTrackConf({
+    session.addSessionTrackConf({
         type: 'FeatureTrack',
         trackId: `${uniprotId}-Antigen`,
         name: 'Antigen',
@@ -65,7 +64,7 @@ function addAntigenTrack({ session, uniprotId, }) {
  * Adds variation track from EBI
  */
 function addVariationTrack({ session, uniprotId, }) {
-    session.addTrackConf({
+    session.addSessionTrackConf({
         type: 'FeatureTrack',
         trackId: `${uniprotId}-Variation`,
         name: 'Variation',
@@ -83,7 +82,7 @@ function addVariationTrack({ session, uniprotId, }) {
  */
 function addAlphaFoldConfidenceTrack({ session, uniprotId, confidenceUrl, }) {
     if (confidenceUrl) {
-        session.addTrackConf({
+        session.addSessionTrackConf({
             type: 'QuantitativeTrack',
             trackId: `${uniprotId}-AlphaFold-confidence`,
             name: 'AlphaFold confidence',
@@ -98,12 +97,6 @@ function addAlphaFoldConfidenceTrack({ session, uniprotId, confidenceUrl, }) {
                 {
                     type: 'LinearWiggleDisplay',
                     displayId: `${uniprotId}-AlphaFold-confidence-LinearWiggleDisplay`,
-                    // Each host drops the key it does not declare: v4 reads the
-                    // renderers, v5 the display's `color`.
-                    renderers: {
-                        XYPlotRenderer: { color: jexlBandColor('score', PLDDT_BANDS) },
-                        DensityRenderer: { color: jexlBandColor('score', PLDDT_BANDS) },
-                    },
                     color: thresholdBandColor('score', PLDDT_BANDS),
                 },
             ],
@@ -113,8 +106,8 @@ function addAlphaFoldConfidenceTrack({ session, uniprotId, confidenceUrl, }) {
 /**
  * Adds AlphaMissense pathogenicity scores track
  */
-function addAlphaMissenseTrack({ session, uniprotId, hasMultiWiggleDisplay, }) {
-    session.addTrackConf({
+function addAlphaMissenseTrack({ session, uniprotId, }) {
+    session.addSessionTrackConf({
         type: 'MultiQuantitativeTrack',
         trackId: `${uniprotId}-AlphaMissense-scores`,
         name: 'AlphaMissense scores',
@@ -125,28 +118,18 @@ function addAlphaMissenseTrack({ session, uniprotId, hasMultiWiggleDisplay, }) {
                 uri: `https://alphafold.ebi.ac.uk/files/AF-${uniprotId}-F1-aa-substitutions.csv`,
             },
         },
-        // v5 folded MultiLinearWiggleDisplay into LinearWiggleDisplay and warns on
-        // a config naming the old type. v4's density renderer ramps from white to
-        // posColor, so pathogenic reads red; v5 diverges at AlphaMissense's 0.5.
         displays: [
-            hasMultiWiggleDisplay
-                ? {
-                    type: 'MultiLinearWiggleDisplay',
-                    displayId: `${uniprotId}-AlphaMissense-scores-MultiLinearWiggleDisplay`,
-                    defaultRendering: 'multirowdensity',
-                    renderers: { MultiDensityRenderer: { posColor: '#d7191c' } },
-                }
-                : {
-                    type: 'LinearWiggleDisplay',
-                    displayId: `${uniprotId}-AlphaMissense-scores-LinearWiggleDisplay`,
-                    defaultRendering: 'density',
-                    color: {
-                        field: 'score',
-                        scale: 'linear',
-                        range: ['#2c7bb6', '#ffffff', '#d7191c'],
-                        domainMid: 0.5,
-                    },
+            {
+                type: 'LinearWiggleDisplay',
+                displayId: `${uniprotId}-AlphaMissense-scores-LinearWiggleDisplay`,
+                defaultRendering: 'density',
+                color: {
+                    field: 'score',
+                    scale: 'linear',
+                    range: ['#2c7bb6', '#ffffff', '#d7191c'],
+                    domainMid: 0.5,
                 },
+            },
         ],
     });
 }
@@ -178,9 +161,6 @@ export async function addAllProteinTracks({ session, uniprotId, confidenceUrl, }
         addAlphaMissenseTrack({
             session,
             uniprotId,
-            hasMultiWiggleDisplay: getEnv(session)
-                .pluginManager.getDisplayElements()
-                .some(d => d.name === 'MultiLinearWiggleDisplay'),
         });
     }
 }

package/dist/LaunchProteinView/components/wiggleBandColors.js

@@ -1,21 +1,7 @@
 /**
- * A v4 wiggle renderer's `color` callback painting `field` by band. v4 hosts
- * read colour only from the renderer, and only a callback can place a cut
- * anywhere but 0 on v4.3.0, which drops a configured pivot on its way to the
- * worker. v4 also evaluates it once with no feature, and a throw there leaves
- * the track an error message, hence the guard.
- */
-export function jexlBandColor(field, bands) {
-    const value = `get(feature,'${field}')`;
-    const body = bands.reduceRight((rest, band) => band.upTo === Infinity
-        ? `'${band.color}'`
-        : `(${value}<=${band.upTo}?'${band.color}':${rest})`, "'#cccccc'");
-    return `jexl:feature?${body}:'#cccccc'`;
-}
-/**
- * The same bands as the display-level threshold scale v5 hosts read. That
- * scale puts a value equal to a cut in the upper band, so each cut moves just
- * past its bound to keep the bound in its own band, as `bandColor` does.
+ * The display-level threshold scale puts a value equal to a cut in the upper
+ * band, so each cut moves just past its bound to keep the bound in its own
+ * band, as `bandColor` does.
  */
 export function thresholdBandColor(field, bands) {
     return {

package/dist/LaunchProteinView/hooks/useAlphaFoldData.js

@@ -7,8 +7,11 @@ import useIsoformProteinSequences from './useIsoformProteinSequences';
 export default function useAlphaFoldData({ uniprotId, feature, view, }) {
     const { data, isLoading, isValidating, error } = useSWR(uniprotId ? ['alphafold-models', uniprotId] : null, ([, id]) => fetchAlphaFoldModels(id), { ...STATIC_SWR_OPTIONS, keepPreviousData: true });
     const { isoformSequences } = useIsoformProteinSequences({ feature, view });
-    // with an error, data is the previous accession's (keepPreviousData)
-    const model = useMemo(() => data && !error ? pickAlphaFoldModel(data, isoformSequences) : undefined, [data, error, isoformSequences]);
+    // keepPreviousData hands back the last accession's models after an error
+    // and after the accession is cleared, when the key is null
+    const model = useMemo(() => uniprotId && data && !error
+        ? pickAlphaFoldModel(data, isoformSequences)
+        : undefined, [uniprotId, data, error, isoformSequences]);
     return {
         isLoading,
         isValidating,

package/dist/LaunchProteinView/hooks/useUniProtIdLookup.js

@@ -17,10 +17,16 @@ export function describeOrganism(taxonId, source) {
  * to every tab, so all of them run one search and agree on what the gene is.
  */
 export default function useUniProtIdLookup({ feature, view, }) {
-    const [lookupMode, setLookupMode] = useState('auto');
+    const geneIds = extractFeatureIdentifiers(feature);
+    const featureUniprotId = geneIds.uniprotId;
+    const hasSearchableIdentifier = geneIds.recognizedIds.length > 0 || !!geneIds.geneName;
+    // Nothing to search and no accession on the feature: the auto mode has no
+    // query to run, so the dialog opens on the manual field instead of reporting
+    // an empty result for an empty query. Only the opening mode is chosen here;
+    // deciding it on every render snapped the user's pick back.
+    const [lookupMode, setLookupMode] = useState(() => featureUniprotId ? 'feature' : hasSearchableIdentifier ? 'auto' : 'manual');
     const [manualUniprotId, setManualUniprotId] = useState('');
     const [taxonIdInput, setTaxonIdInput] = useState('');
-    const geneIds = extractFeatureIdentifiers(feature);
     // The gene-name UniProt search is ambiguous across species, so scope it to
     // the assembly's organism where the assembly says what that is. jb2hubs
     // assemblies carry the NCBI taxon in the reference-sequence track metadata
@@ -46,17 +52,7 @@ export default function useUniProtIdLookup({ feature, view, }) {
     const taxonIdError = typedTaxon !== '' && !hasOverride;
     const [selectedQueryId, setSelectedQueryId] = useState('auto');
     const [selectedUniprotId, setSelectedUniprotId] = useState();
-    const featureUniprotId = geneIds.uniprotId;
-    const hasSearchableIdentifier = geneIds.recognizedIds.length > 0 || !!geneIds.geneName;
-    // Nothing to search and no accession on the feature: the auto mode has no
-    // query to run, so the dialog opens on the manual field instead of reporting
-    // an empty result for an empty query.
-    const effectiveLookupMode = lookupMode === 'auto' && featureUniprotId
-        ? 'feature'
-        : lookupMode === 'auto' && !hasSearchableIdentifier
-            ? 'manual'
-            : lookupMode;
-    const isAutoMode = effectiveLookupMode === 'auto';
+    const isAutoMode = lookupMode === 'auto';
     const { entries: uniprotEntries, isLoading: isLookupLoading, error: lookupError, partialFailure: lookupPartialFailure, } = useUniProtSearch({
         recognizedIds: geneIds.recognizedIds,
         geneId: geneIds.geneId,
@@ -74,13 +70,13 @@ export default function useUniProtIdLookup({ feature, view, }) {
         ? selectedUniprotId
         : undefined;
     const autoUniprotId = uniprotEntries[0]?.accession;
-    const uniprotId = effectiveLookupMode === 'feature'
+    const uniprotId = lookupMode === 'feature'
         ? featureUniprotId
         : isAutoMode
             ? (pickedUniprotId ?? autoUniprotId)
             : debouncedManualUniprotId;
     return {
-        lookupMode: effectiveLookupMode,
+        lookupMode,
         setLookupMode,
         manualUniprotId,
         setManualUniprotId,

package/dist/LaunchProteinView/index.js

@@ -1,12 +1,15 @@
-import { getContainingTrack, getSession } from '@jbrowse/core/util';
+import { getContainingTrack, getSession, isGeneLikeType, } from '@jbrowse/core/util';
 import AddIcon from '@mui/icons-material/Add';
-import { extendPluggableStateModel } from '../extendStateModel';
-import { geneLikeRoot, isCodingFeature, isGeneLikeType } from './codingFeature';
+import { isCodingFeature } from './codingFeature';
 import LaunchProteinViewDialog from './components/LaunchProteinViewDialog';
 function isDisplay(elt) {
     return elt.name === 'LinearBasicDisplay';
 }
-function canvasTarget(info, fetchFullFeature) {
+export function resolveTarget(self) {
+    const info = self.contextMenuInfo;
+    if (!info) {
+        return undefined;
+    }
     const { item, subfeature, displayedRegionIndex } = info;
     const type = subfeature ? subfeature.type : item.type;
     // The parent gene, not the clicked isoform: the dialog picks the transcript
@@ -16,32 +19,10 @@ function canvasTarget(info, fetchFullFeature) {
         ? undefined
         : {
             type,
-            fetchFeature: () => fetchFullFeature(parentId, displayedRegionIndex),
+            fetchFeature: () => self.fetchFullFeature(parentId, displayedRegionIndex),
             preferredTranscriptId: subfeature?.featureId,
         };
 }
-// The hit test only carries a type, so a canvas host learns whether the gene
-// codes for anything after the fetch; a legacy host has the whole feature and
-// can decline up front.
-function legacyTarget(feature) {
-    const root = geneLikeRoot(feature);
-    const type = root.get('type');
-    return type === undefined || !isCodingFeature(root)
-        ? undefined
-        : {
-            type,
-            feature: root,
-            preferredTranscriptId: root === feature ? undefined : feature.id(),
-        };
-}
-export function resolveTarget(self) {
-    const { contextMenuFeature, contextMenuInfo, fetchFullFeature } = self;
-    return contextMenuInfo && fetchFullFeature
-        ? canvasTarget(contextMenuInfo, fetchFullFeature)
-        : contextMenuFeature
-            ? legacyTarget(contextMenuFeature)
-            : undefined;
-}
 function launchProteinView(self, target) {
     const track = getContainingTrack(self);
     const session = getSession(track);
@@ -52,41 +33,32 @@ function launchProteinView(self, target) {
             { model: track, handleClose, feature, preferredTranscriptId },
         ]);
     };
-    if ('feature' in target) {
-        openDialog(target.feature);
-    }
-    else {
-        target
-            .fetchFeature()
-            .then(feature => {
-            if (!feature) {
-                session.notify('Could not load feature for protein view', 'warning');
-            }
-            else if (!isCodingFeature(feature)) {
-                session.notify(`${feature.get('name') ?? feature.get('id') ?? 'This feature'} has no coding sequence, so there is no protein to show`, 'info');
-            }
-            else {
-                openDialog(feature);
-            }
-        })
-            .catch((e) => {
-            console.error(e);
-            session.notifyError(`${e}`, e);
-        });
-    }
+    target
+        .fetchFeature()
+        .then(feature => {
+        if (!feature) {
+            session.notify('Could not load feature for protein view', 'warning');
+        }
+        else if (!isCodingFeature(feature)) {
+            session.notify(`${feature.get('name') ?? feature.get('id') ?? 'This feature'} has no coding sequence, so there is no protein to show`, 'info');
+        }
+        else {
+            openDialog(feature);
+        }
+    })
+        .catch((e) => {
+        console.error(e);
+        session.notifyError(`${e}`, e);
+    });
 }
 function extendStateModel(stateModel) {
     return stateModel.views((self) => {
-        // .call(self), not a bare call: the canvas display's own contextMenuItems
-        // reads `this.isGeneLike`, so invoking it detached throws on undefined and
-        // the ErrorBoundary around the menu swallows it -- the user right-clicks a
-        // feature and gets no menu at all, not merely no protein item.
         const superContextMenuItems = self.contextMenuItems;
         return {
             contextMenuItems() {
                 const target = resolveTarget(self);
                 return [
-                    ...superContextMenuItems.call(self),
+                    ...superContextMenuItems(),
                     ...(target && isGeneLikeType(target.type)
                         ? [
                             {
@@ -106,7 +78,7 @@ function extendStateModel(stateModel) {
 export default function LaunchProteinViewF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-extendPluggableElement', (elt) => {
         if (isDisplay(elt)) {
-            extendPluggableStateModel(elt, extendStateModel);
+            elt.extendStateModel(extendStateModel);
         }
         return elt;
     });

package/dist/LaunchProteinView/services/foldseekApi.js

@@ -69,11 +69,35 @@ export async function submitFoldseekSearch({ aaSequence, di3Sequence, databases,
     if (!response.ok) {
         throw await httpError(response, url);
     }
-    // Read the body as text rather than response.json() so a non-JSON error page
-    // (a gateway 500's HTML) surfaces as itself instead of an opaque
-    // SyntaxError.
+    // The server answers a refusal (RATELIMIT, MAINTENANCE) with a 200 and no
+    // id, which used to be polled as ticket "undefined" for three minutes
     const text = await response.text();
-    return JSON.parse(text);
+    const ticket = parseTicket(text);
+    if (!ticket) {
+        throw new Error(`Foldseek did not accept the search: ${text.slice(0, 200)}`);
+    }
+    return ticket;
+}
+function parseTicket(text) {
+    let body;
+    try {
+        body = JSON.parse(text);
+    }
+    catch {
+        return undefined;
+    }
+    if (typeof body !== 'object' || body === null) {
+        return undefined;
+    }
+    const id = Reflect.get(body, 'id');
+    const status = Reflect.get(body, 'status');
+    return typeof id === 'string' &&
+        (status === 'PENDING' ||
+            status === 'RUNNING' ||
+            status === 'COMPLETE' ||
+            status === 'ERROR')
+        ? { id, status }
+        : undefined;
 }
 async function pollFoldseekStatus({ ticketId, signal, }) {
     // Use the /tickets endpoint (plural) with POST
@@ -114,10 +138,6 @@ export async function waitForFoldseekResults({ ticketId, onStatusChange, signal,
             throw abortError(signal);
         }
         const status = await pollFoldseekStatus({ ticketId, signal });
-        if (status.status === 'ERROR') {
-            console.error('[Foldseek] Search error:', status);
-            throw new Error(`Foldseek search failed: ${status.error ?? 'Unknown error'}`);
-        }
         if (status.status === 'COMPLETE') {
             onStatusChange?.('Fetching results...');
             const apiResponse = await getFoldseekResults({ ticketId, signal });
@@ -131,6 +151,11 @@ export async function waitForFoldseekResults({ ticketId, onStatusChange, signal,
             };
             return results;
         }
+        // the server also answers RATELIMIT, MAINTENANCE and UNKNOWN, none of
+        // which a wait resolves
+        if (status.status !== 'PENDING' && status.status !== 'RUNNING') {
+            throw new Error(`Foldseek search failed: ${status.error ?? status.status}`);
+        }
         onStatusChange?.(`Search ${status.status.toLowerCase()}... (${elapsedSeconds()}s)`);
         await timeout(1000, signal);
     }

package/dist/LaunchProteinView/utils/launchHelpers.js

@@ -22,9 +22,9 @@ export async function safeLaunch(fn, onSuccess, onError) {
  * A launch that names its own structure needs no accession. Bypassing a lookup
  * that failed or resolved the wrong gene is the whole point of typing a PDB id,
  * and the view resolves SIFTS from the entry itself; the accession only feeds
- * the feature tracks and the view's name, both of which do without it. The
- * AlphaFold tab keeps the requirement for free — its structure url is derived
- * from the accession, so no accession means no structure either.
+ * the feature tracks and the view's name, both of which do without it. On the
+ * AlphaFold tab the url is derived from the accession, so no accession means
+ * no url either; `useAlphaFoldData` makes sure of it.
  */
 export function getLaunchMissingReasons({ uniprotId, userSelectedProteinSequence, selectedTranscript, url, pdbId, }) {
     const namesOwnStructure = !!url || !!pdbId;

package/dist/LaunchProteinView/utils/launchViewUtils.js

@@ -1,4 +1,4 @@
-import { isSessionWithAddTracks } from './sessionWithAddTracks';
+import { isSessionWithAddSessionTrack } from '@jbrowse/core/util';
 import { maybeLaunchSideBySide } from './sideBySide';
 import { getGeneDisplayName, getTranscriptDisplayName } from './util';
 import { proteinViewSnapshot } from '../../ProteinView/proteinViewSpec';
@@ -35,7 +35,7 @@ export function launch3DProteinView({ session, view, feature, selectedTranscript
     return proteinView;
 }
 // The 1D annotation view adds temporary tracks/assemblies, so it requires a
-// SessionWithAddTracks and a known uniprotId. Demanding both in the signature
+// SessionWithAddSessionTrack and a known uniprotId. Demanding both in the signature
 // forces callers to narrow up front — there's no silent no-op when a wide
 // session or missing id slips through.
 async function launch1DProteinView({ session, view, feature, selectedTranscript, uniprotId, confidenceUrl, }) {
@@ -63,7 +63,9 @@ export const PROTEIN_LAUNCH_LABELS = {
 // single source of truth — an unavailable action is unrepresentable rather than
 // a menu item that silently no-ops.
 export function getConditionalProteinLaunches({ session, view, feature, selectedTranscript, uniprotId, confidenceUrl, }) {
-    const addTracksSession = isSessionWithAddTracks(session) ? session : undefined;
+    const addTracksSession = isSessionWithAddSessionTrack(session)
+        ? session
+        : undefined;
     return {
         launch1D: addTracksSession && uniprotId
             ? () => launch1DProteinView({

package/dist/LaunchProteinView/utils/sideBySide.js

@@ -21,39 +21,16 @@ let warnedPartial = false;
 function isSessionWithWorkspaces(session) {
     const canEnable = hasAction(session, 'setUseWorkspaces');
     const canPlace = hasAction(session, 'setPendingMove');
-    // Missing BOTH is an embedded session: it has no workspaces, there is nothing
-    // to ask for, and silence is the right answer.
-    //
-    // Missing ONE is a host that has workspaces but places views some other way —
-    // and silence there is how this broke before. jbrowse-web folded
-    // `setPendingMove` into its layout `init`, this guard went false, and the
-    // plugin simply stopped asking for the split: no error, no missing feature,
-    // just two views quietly stacking. Nobody noticed for weeks. Feature
-    // detection cannot ask the host to announce a change, but it can tell "not
-    // supported here" from "supported, and gone".
-    //
-    // Two very different hosts produce this one shape, and nothing on the session
-    // tells them apart, so the message carries both rather than the guess:
-    //
-    // - Releases through v4.3.0, where placement is `setPendingMoveToSplitRight`,
-    //   a module function in @jbrowse/app-core's DockviewContext, not a session
-    //   action. Nothing is wrong and nothing needs fixing; this plugin targets v5+
-    //   and does not reach for v4's door. Measured 2026-08-17: v4.3.0 and latest
-    //   stack, main splits.
-    // - A newer host that moved the action out from under us, which is the
-    //   regression this warning exists to catch.
-    //
-    // Do not quiet the first case by sniffing the version. The alarm is only worth
-    // having if it fires on a shape it cannot explain, and these two shapes are
-    // identical.
+    // Missing BOTH is an embedded session, with no workspaces to ask for. Missing
+    // ONE means the host moved the action out from under us: jbrowse-web once
+    // folded `setPendingMove` into its layout `init`, and the views quietly
+    // stacked for weeks, so that shape warns.
     if (canEnable !== canPlace && !warnedPartial) {
         warnedPartial = true;
         console.warn(`jbrowse-plugin-protein3d: this session supports workspaces but not ` +
             `${canPlace ? 'setUseWorkspaces' : 'setPendingMove'}, so the ` +
-            `side-by-side launch was skipped and the views will stack. Expected on ` +
-            `releases through v4.3.0, which place views through @jbrowse/app-core ` +
-            `instead; on a newer host it means the session API moved and the plugin ` +
-            `needs updating to match.`);
+            `side-by-side launch was skipped and the views will stack. The session ` +
+            `API moved and the plugin needs updating to match.`);
     }
     return canEnable && canPlace;
 }

package/dist/LaunchProteinView/utils/translateTranscripts.js

@@ -16,11 +16,8 @@ export async function fetchRegionSequence({ session, assemblyName, refName, star
     if (!assembly) {
         throw new Error('assembly not found');
     }
-    const sessionId = 'getSequence';
-    // a named object keeps sessionId, which v4 hosts read from the args
-    const args = {
+    const [feat] = await rpcManager.call('getSequence', 'CoreGetFeatures', {
         adapterConfig: getConf(assembly, ['sequence', 'adapter']),
-        sessionId,
         regions: [
             {
                 start,
@@ -29,10 +26,9 @@ export async function fetchRegionSequence({ session, assemblyName, refName, star
                 assemblyName: assembly.name,
             },
         ],
-    };
-    const [feat] = await rpcManager.call(sessionId, 'CoreGetFeatures', args);
+    });
     const seq = feat?.get('seq');
-    return { seq, assemblyGeneticCodeId: assemblyGeneticCode(assembly, refName) };
+    return { seq, assemblyGeneticCodeId: assembly.getGeneticCodeId(refName) };
 }
 export async function fetchProteinSeq({ feature, session, assemblyName, }) {
     const { seq, assemblyGeneticCodeId } = await fetchRegionSequence({
@@ -85,8 +81,3 @@ export async function fetchTranscriptProteinSeqs({ transcripts, session, assembl
         fetchSpan: span => fetchRegionSequence({ session, assemblyName, ...span }),
     });
 }
-// v5 hosts only; a v4 assembly has neither the method nor the config slot
-function assemblyGeneticCode(assembly, refName) {
-    const { getGeneticCodeId } = assembly;
-    return getGeneticCodeId?.call(assembly, refName);
-}