jbrowse-plugin-protein3d 0.11.1 → 0.11.2

package/dist/AddHighlightModel/index.js

@@ -1,9 +1,9 @@
 import React from 'react';
 import HighlightComponents from './HighlightComponents';
 export default function AddHighlightModelF(pluginManager) {
-    pluginManager.addToExtensionPoint('LinearGenomeView-TracksContainerComponent', 
-    // @ts-expect-error
-    (rest, { model }) => {
+    pluginManager.addToExtensionPoint(
+    // @ts-expect-error v4 hosts have no contributeToExtensionPoint
+    'LinearGenomeView-TracksContainerComponent', (rest, { model }) => {
         return [
             ...rest,
             React.createElement(HighlightComponents, { key: "highlight_protein_viewer_protein3d", model: model }),

package/dist/LaunchProteinView/components/FoldseekSearch.js

@@ -66,14 +66,13 @@ const FoldseekSearch = observer(function FoldseekSearch({ feature, session, view
                 React.createElement(TextField, { label: "Protein sequence (amino acids)", multiline: true, rows: 4, value: sequence, onChange: e => {
                         setUserEditedSequence(e.target.value);
                         invalidatePrediction();
-                    }, placeholder: `MKTVRQERLKSIVRILERSKEPVSGAQLAEEL...`, disabled: isBusy, InputProps: {
-                        className: classes.sequenceInput,
+                    }, placeholder: `MKTVRQERLKSIVRILERSKEPVSGAQLAEEL...`, disabled: isBusy, slotProps: {
+                        input: { className: classes.sequenceInput },
                     } }))) : null,
             di3Sequence ? (React.createElement("div", { className: classes.di3Section },
                 React.createElement(Typography, { variant: "subtitle2" }, "3Di structural alphabet (used for searching):"),
-                React.createElement(TextField, { multiline: true, rows: 4, value: di3Sequence, InputProps: {
-                        className: classes.sequenceInput,
-                        readOnly: true,
+                React.createElement(TextField, { multiline: true, rows: 4, value: di3Sequence, slotProps: {
+                        input: { className: classes.sequenceInput, readOnly: true },
                     } }))) : null,
             React.createElement(FoldseekDatabaseSelector, { selected: selectedDatabases, onChange: setSelectedDatabases, disabled: isBusy }),
             statusMessage ? (React.createElement(LoadingEllipses, { variant: "subtitle2", message: statusMessage })) : null,

package/dist/LaunchProteinView/components/launchProteinAnnotationView.js

@@ -13,10 +13,13 @@ export async function launchProteinAnnotationView({ session, feature, selectedTr
     const proteinLinkage = connectedViewId && selectedTranscript
         ? { connectedViewId, feature: selectedTranscript.toJSON(), uniprotId }
         : undefined;
-    const view = session.addView('LinearGenomeView', {
+    // a named object, because proteinLinkage comes from this plugin's own
+    // LinearGenomeView extension, which the launch snapshot type cannot see
+    const snapshot = {
         type: 'LinearGenomeView',
         displayName: formatViewName('Protein annotations', feature, selectedTranscript, uniprotId),
         proteinLinkage,
-    });
+    };
+    const view = session.addView('LinearGenomeView', snapshot);
     await view.navToLocString(uniprotId, uniprotId);
 }

package/dist/LaunchProteinView/components/proteinTrackSetup.js

@@ -92,6 +92,18 @@ function addAlphaFoldConfidenceTrack({ session, uniprotId, confidenceUrl, }) {
                 },
             },
             assemblyNames: [uniprotId],
+            displays: [
+                {
+                    type: 'LinearWiggleDisplay',
+                    displayId: `${uniprotId}-AlphaFold-confidence-LinearWiggleDisplay`,
+                    // pLDDT 50 is AlphaFold's own line between low and very low
+                    // confidence: residues above it in AlphaFold's blue, below in its
+                    // orange
+                    bicolorPivot: 50,
+                    posColor: '#0053d6',
+                    negColor: '#ff7d45',
+                },
+            ],
         });
     }
 }
@@ -115,14 +127,11 @@ function addAlphaMissenseTrack({ session, uniprotId, }) {
                 type: 'MultiLinearWiggleDisplay',
                 displayId: `${uniprotId}-AlphaMissense-scores-MultiLinearWiggleDisplay`,
                 defaultRendering: 'multirowdensity',
-                renderers: {
-                    MultiDensityRenderer: {
-                        type: 'MultiDensityRenderer',
-                        bicolorPivotValue: 0.5,
-                        posColor: 'red',
-                        negColor: 'blue',
-                    },
-                },
+                // AlphaMissense's own reading: likely pathogenic red, likely benign
+                // blue, fading to white at the midpoint of its 0-1 score
+                bicolorPivot: 0.5,
+                posColor: '#d7191c',
+                negColor: '#2c7bb6',
             },
         ],
     });

package/dist/LaunchProteinView/utils/calculateProteinSequence.js

@@ -34,14 +34,14 @@ export function getProteinSequence({ feature, seq, assemblyGeneticCodeId, }) {
     const strand = feature.get('strand');
     const subfeatures = feature.get('subfeatures') ?? [];
     const cds = dedupe(subfeatures
+        .filter(sub => sub.get('type') === 'CDS')
         .toSorted((a, b) => a.get('start') - b.get('start'))
         .map(sub => ({
         start: sub.get('start') - featureStart,
         end: sub.get('end') - featureStart,
-        type: sub.get('type'),
+        type: 'CDS',
         phase: sub.get('phase'),
-    }))
-        .filter(f => f.type === 'CDS'));
+    })));
     // RefSeq declares transl_table=2 on a mitochondrial CDS, usually on the CDS
     // rather than the transcript. GENCODE and UCSC declare nothing, so without
     // the assembly's code all 13 human mitochondrial proteins read TGA as a stop
@@ -68,19 +68,20 @@ export async function fetchProteinSeq({ feature, session, assemblyName, }) {
         throw new Error('assembly not found');
     }
     const sessionId = 'getSequence';
-    const feats = await rpcManager.call(sessionId, 'CoreGetFeatures', {
+    // a named object keeps sessionId, which v4 hosts read from the args
+    const args = {
         adapterConfig: getConf(assembly, ['sequence', 'adapter']),
         sessionId,
         regions: [
             {
                 start,
                 end,
-                refName: assembly.getCanonicalRefName(refName),
-                assemblyName,
+                refName: assembly.getCanonicalRefName(refName) ?? refName,
+                assemblyName: assembly.name,
             },
         ],
-    });
-    const [feat] = feats;
+    };
+    const [feat] = await rpcManager.call(sessionId, 'CoreGetFeatures', args);
     const seq = feat?.get('seq');
     return seq
         ? getProteinSequence({

package/dist/LaunchProteinView/utils/launchViewUtils.js

@@ -1,4 +1,4 @@
-import { isSessionWithAddTracks } from '@jbrowse/core/util';
+import { isSessionWithAddTracks } from './sessionWithAddTracks';
 import { maybeLaunchSideBySide } from './sideBySide';
 import { getGeneDisplayName, getTranscriptDisplayName } from './util';
 import { proteinViewSnapshot } from '../../ProteinView/proteinViewSpec';

package/dist/LaunchProteinView/utils/sessionWithAddTracks.js

@@ -0,0 +1,6 @@
+import { isSessionModel } from '@jbrowse/core/util';
+export function isSessionWithAddTracks(t) {
+    return (isSessionModel(t) &&
+        'addTrackConf' in t &&
+        !('disableAddTracks' in t && t.disableAddTracks));
+}

package/dist/LaunchProteinView/utils/util.js

@@ -54,13 +54,16 @@ export function stripTrailingVersion(s) {
 export function getId(val) {
     return val === undefined ? '' : val.id();
 }
+function firstString(...vals) {
+    return vals.find((v) => typeof v === 'string') ?? '';
+}
 export function getTranscriptDisplayName(val) {
     return val === undefined ? '' : (val.get('name') ?? val.get('id') ?? '');
 }
 export function getGeneDisplayName(val) {
     return val === undefined
         ? ''
-        : (val.get('gene_name') ?? val.get('name') ?? val.get('id') ?? '');
+        : firstString(val.get('gene_name'), val.get('name'), val.get('id'));
 }
 const DB_ID_PATTERNS = [
     { db: 'ensembl', pattern: /^ENS[A-Z]*G\d+/i, label: 'Ensembl gene' },

package/dist/LaunchProteinViewExtensionPoint/index.js

@@ -13,14 +13,6 @@ export default function LaunchProteinViewExtensionPointF(pluginManager) {
     // assumption that the result was ignored; it is not. The handler returns
     // its extendee at each exit now, like jbrowse-components' own
     // LaunchDotplotView does.
-    //
-    // The suppression stays, and is NOT about the return value: this builds
-    // against @jbrowse/core 4.3.0, whose signature is `(extendee: T, props) => T`
-    // with no `| Promise<T>` and no ExtensionPointRegistry, so an async handler
-    // cannot be typed against it at all. jbrowse-components has since widened
-    // that signature; drop the suppression when the core dependency is bumped
-    // past it, not before.
-    // @ts-expect-error
     async (args) => {
         const { session, url, uniprotId, pdbId, transcriptId, userProvidedTranscriptSequence, feature, connectedViewId, connectedView, alignmentAlgorithm, colorScheme, displayName, height, showControls, showHighlight, showAlignment, showProteinTracks, compactTracks, autoScrollAlignment, zoomToBaseLevel, sideBySide, initialSelection, initialResidues, initialTranscriptResidues, } = args;
         const requested = args.structures?.length
@@ -77,6 +69,8 @@ export default function LaunchProteinViewExtensionPointF(pluginManager) {
             (connectedView
                 ? session.addView('LinearGenomeView', {
                     type: 'LinearGenomeView',
+                    // a spec's connectedView is unvalidated json, so a missing
+                    // assembly reaches the view and is reported there, as before
                     init: connectedView,
                 }).id
                 : undefined);

package/dist/LaunchProteinViewExtensionPoint/resolveShortLaunch.js

@@ -72,11 +72,13 @@ export async function resolveShortLaunch({ session, structureUrl, transcriptId,
         if (!trackConf) {
             continue;
         }
-        const feats = (await session.rpcManager.call(sessionId, 'CoreGetFeatures', {
+        // a named object keeps sessionId, which v4 hosts read from the args
+        const args = {
             adapterConfig: readConfObject(trackConf, 'adapter'),
             sessionId,
             regions: [region],
-        }));
+        };
+        const feats = await session.rpcManager.call(sessionId, 'CoreGetFeatures', args);
         for (const feat of feats) {
             transcripts.push(...getTranscriptFeatures(feat));
         }

package/dist/ProteinView/connectedHover.js

@@ -9,9 +9,9 @@ import { genomeHoverToTranscriptPos } from './util';
  * this holds for any alignment whose query row is linked to the transcript,
  * such as a Pfam seed row cut to one domain.
  */
-export function connectedHoverTranscriptPos({ hovered, views, mapping, connectedViewId, genomeViewReady, }) {
+export function connectedHoverTranscriptPos({ hovered, views, mapping, connectedViewId, genomeViewReady, canonical = r => r, }) {
     const fromGenome = genomeViewReady
-        ? genomeHoverToTranscriptPos(hovered, mapping)
+        ? genomeHoverToTranscriptPos(hovered, mapping, canonical)
         : undefined;
     if (fromGenome !== undefined) {
         return { transcriptPos: fromGenome, source: 'genome' };
@@ -19,7 +19,7 @@ export function connectedHoverTranscriptPos({ hovered, views, mapping, connected
     const codon = connectedViewId
         ? views.find(v => v.type === 'MsaView' && v.connectedViewId === connectedViewId)?.connectedHoverHighlights?.[0]
         : undefined;
-    const fromMsa = mapping && codon?.refName === mapping.refName
+    const fromMsa = mapping && codon && canonical(codon.refName) === canonical(mapping.refName)
         ? mapping.g2p[codon.start]
         : undefined;
     return fromMsa === undefined

package/dist/ProteinView/structureModel.js

@@ -990,13 +990,15 @@ const Structure = types
             }
         }));
         addDisposer(self, autorun(() => {
-            const { hovered, views } = getSession(self);
+            const { hovered, views, assemblyManager } = getSession(self);
+            const assembly = assemblyManager.get(self.connectedView?.assemblyNames[0] ?? '');
             const hover = connectedHoverTranscriptPos({
                 hovered,
                 views,
                 mapping: self.genomeToTranscriptSeqMapping,
                 connectedViewId: self.connectedViewId,
                 genomeViewReady: !!self.connectedView?.initialized,
+                canonical: r => assembly?.getCanonicalRefName(r) ?? r,
             });
             if (hover) {
                 self.setConnectedHoveredPosition(self.transcriptSeqToStructureSeqPosition?.[hover.transcriptPos], hover.source);

package/dist/ProteinView/util.js

@@ -19,11 +19,22 @@ export function invertMap(arg) {
  * the transcript's *own* refName, so the refName gate is load-bearing: without
  * it the same numeric coordinate on an unrelated chromosome matches a key and
  * reports a residue for a different locus.
+ *
+ * The two sides name the chromosome independently, so the gate has to compare
+ * canonical names. The view reports the assembly's own (`1` on jbrowse.org's
+ * hg38), while the mapping carries the feature's, straight out of the file
+ * (`chr1` in GENCODE) — equal strings only by luck of which pair of files a
+ * config happens to use. Compared raw, every hover on such a config silently
+ * missed, which is how it shipped: nothing throws, the residue just never
+ * lights up. `canonical` defaults to identity so the pure function stays
+ * testable; the model passes the assembly's resolver.
  */
-export function genomeHoverToTranscriptPos(hovered, mapping) {
+export function genomeHoverToTranscriptPos(hovered, mapping, canonical = r => r) {
     if (!mapping || !checkHovered(hovered)) {
         return undefined;
     }
     const { coord, refName } = hovered.hoverPosition;
-    return refName === mapping.refName ? mapping.g2p[coord - 1] : undefined;
+    return canonical(refName) === canonical(mapping.refName)
+        ? mapping.g2p[coord - 1]
+        : undefined;
 }