jbrowse-plugin-protein3d 0.4.4 → 0.4.5

package/dist/AddHighlightModel/ProteinToGenomeHighlightInner.js

@@ -12,6 +12,6 @@ const ProteinToGenomeHighlightInner = observer(function ProteinToGenomeHighlight
     const assembly = assemblyName
         ? assemblyManager.get(assemblyName)
         : undefined;
-    return assembly && assemblyName ? (React.createElement(React.Fragment, null, proteinView?.structures.map((structure, idx) => structure[field].map((r, idx2) => (React.createElement(Highlight, { key: `${r.refName}-${r.start}-${r.end}-${idx}-${idx2}`, start: r.start, end: r.end, refName: r.refName, assemblyName: assemblyName, model: model })))))) : null;
+    return assembly && assemblyName ? (React.createElement(React.Fragment, null, proteinView?.structures.flatMap((structure, idx) => structure[field].map((r, idx2) => (React.createElement(Highlight, { key: `${r.refName}-${r.start}-${r.end}-${idx}-${idx2}`, start: r.start, end: r.end, refName: r.refName, assemblyName: assemblyName, model: model })))))) : null;
 });
 export default ProteinToGenomeHighlightInner;

package/dist/LaunchProteinView/components/AlphaFoldDBSearchStatus.js

@@ -10,15 +10,13 @@ function NotFound({ uniprotId }) {
         React.createElement(ExternalLink, { href: `https://alphafold.ebi.ac.uk/search/text/${uniprotId}` }, "(search for results)")));
 }
 export default function AlphaFoldDBSearchStatus({ uniprotId, selectedTranscript, structureSequence, isoformSequences, url, }) {
-    const url2 = uniprotId
-        ? `https://www.uniprot.org/uniprotkb/${uniprotId}/entry`
-        : undefined;
     const [showAllProteinSequences, setShowAllProteinSequences] = useState(false);
     return uniprotId ? (React.createElement(React.Fragment, null,
         React.createElement("div", null,
             React.createElement(Typography, null,
-                "UniProt link: ",
-                React.createElement(ExternalLink, { href: url2 }, uniprotId)),
+                "UniProt link:",
+                ' ',
+                React.createElement(ExternalLink, { href: `https://www.uniprot.org/uniprotkb/${uniprotId}/entry` }, uniprotId)),
             React.createElement(Typography, null,
                 "AlphaFoldDB link: ",
                 React.createElement(ExternalLink, { href: url }, url))),

package/dist/LaunchProteinView/components/FoldseekResultsTable.js

@@ -22,27 +22,11 @@ const useStyles = makeStyles()({
     },
 });
 function flattenResults(results) {
-    const hits = [];
-    for (const dbResult of results.results) {
-        if (!dbResult.alignments) {
-            continue;
-        }
-        for (const alignmentGroup of dbResult.alignments) {
-            if (!alignmentGroup) {
-                continue;
-            }
-            for (const alignment of alignmentGroup) {
-                if (!alignment) {
-                    continue;
-                }
-                hits.push({
-                    ...alignment,
-                    db: dbResult.db,
-                    structureUrl: getStructureUrlFromTarget(alignment.target, dbResult.db),
-                });
-            }
-        }
-    }
+    const hits = results.results.flatMap(dbResult => (dbResult.alignments ?? []).flat().map(alignment => ({
+        ...alignment,
+        db: dbResult.db,
+        structureUrl: getStructureUrlFromTarget(alignment.target, dbResult.db),
+    })));
     hits.sort((a, b) => (a.eval ?? Infinity) - (b.eval ?? Infinity));
     return hits.slice(0, 100);
 }

package/dist/LaunchProteinView/components/MSATable.js

@@ -18,7 +18,7 @@ export default function MSATable({ structureName, structureSequence, isoformSequ
         { ...val, seq: stripStopCodon(val.seq) },
     ]));
     const exactMatchIsoformAndStructureSeq = Object.entries(removedStars).find(([_, val]) => structureSequence === val.seq);
-    const sname = `${structureName || ''} (structure residues)`;
+    const sname = `${structureName} (structure residues)`;
     const maxKeyLen = max([
         sname.length,
         ...Object.entries(removedStars).map(([_, val]) => getTranscriptDisplayName(val.feature).length),
@@ -38,8 +38,8 @@ export default function MSATable({ structureName, structureSequence, isoformSequ
                         ? `${getTranscriptDisplayName(exactMatchIsoformAndStructureSeq[1].feature).padEnd(maxKeyLen)}* ${exactMatchIsoformAndStructureSeq[1].seq}`
                         : undefined,
                     ...Object.entries(removedStars)
-                        .map(([_, val]) => `${getTranscriptDisplayName(val.feature).padEnd(maxKeyLen)}  ${val.seq}`)
-                        .filter(([k]) => k !== exactMatchIsoformAndStructureSeq?.[0]),
+                        .filter(([k]) => k !== exactMatchIsoformAndStructureSeq?.[0])
+                        .map(([_, val]) => `${getTranscriptDisplayName(val.feature).padEnd(maxKeyLen)}  ${val.seq}`),
                 ]
                     .filter(f => !!f)
                     .join('\n'), slotProps: {

package/dist/LaunchProteinView/components/UserProvidedStructure.js

@@ -64,17 +64,21 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
         !!structureSequence &&
         stripStopCodon(protein.seq) !== structureSequence;
     const handleLaunch = async () => {
-        if (!protein || !selectedTranscript || !(structureURL || file)) {
+        if (!protein || !selectedTranscript) {
             return;
         }
         try {
             const structureData = file ? await file.text() : undefined;
+            const url = structureURL ? structureURL : undefined;
+            if (!url && !structureData) {
+                return;
+            }
             launch3DProteinView({
                 session,
                 view,
                 feature,
                 selectedTranscript,
-                url: structureURL || undefined,
+                url,
                 data: structureData,
                 userProvidedTranscriptSequence: protein.seq,
                 alignmentAlgorithm,

package/dist/LaunchProteinView/components/launchProteinAnnotationView.js

@@ -23,7 +23,9 @@ export async function launchProteinAnnotationView({ session, feature, selectedTr
             uniprotId,
             getGeneDisplayName(feature),
             getTranscriptDisplayName(selectedTranscript),
-        ].join(' - '),
+        ]
+            .filter(s => !!s)
+            .join(' - '),
     });
     // Register the 1D view for linked highlighting
     if (connectedViewId && selectedTranscript) {

package/dist/LaunchProteinView/hooks/useTranscriptSelection.js

@@ -2,18 +2,9 @@ import { useMemo, useState } from 'react';
 import { selectBestTranscript } from '../utils/util';
 export default function useTranscriptSelection({ options, isoformSequences, structureSequence, }) {
     const [userSelection, setUserSelection] = useState();
-    // SYNC: src/LaunchProteinView/hooks/useAlphaFoldDBSearch.ts (same pattern)
-    // Auto-select synchronously to avoid render gap
-    const autoSelection = useMemo(() => {
-        if (isoformSequences !== undefined && userSelection === undefined) {
-            return selectBestTranscript({
-                options,
-                isoformSequences,
-                structureSequence,
-            })?.id();
-        }
-        return undefined;
-    }, [options, structureSequence, isoformSequences, userSelection]);
+    const autoSelection = useMemo(() => isoformSequences !== undefined
+        ? selectBestTranscript({ options, isoformSequences, structureSequence })?.id()
+        : undefined, [options, structureSequence, isoformSequences]);
     const effectiveSelection = userSelection ?? autoSelection;
     return { userSelection: effectiveSelection, setUserSelection };
 }

package/dist/LaunchProteinView/services/foldseekApi.d.ts

@@ -55,7 +55,7 @@ export interface FoldseekAlignment {
 }
 export interface FoldseekDatabaseResult {
     db: string;
-    alignments?: ((FoldseekAlignment | undefined)[] | undefined)[];
+    alignments?: FoldseekAlignment[][];
 }
 export interface FoldseekResult {
     query: {

package/dist/LaunchProteinView/utils/launchViewUtils.js

@@ -54,12 +54,13 @@ function formatViewName(prefix, feature, selectedTranscript, uniprotId) {
             getGeneDisplayName(feature),
             getTranscriptDisplayName(selectedTranscript),
         ]),
-    ].join(' - ');
+    ]
+        .filter(s => !!s)
+        .join(' - ');
 }
 export function launch3DProteinView({ session, view, feature, selectedTranscript, uniprotId, url, data, userProvidedTranscriptSequence, alignmentAlgorithm, displayName, connectedMsaViewId, }) {
-    return session.addView('ProteinView', {
+    const snap = {
         type: 'ProteinView',
-        isFloating: true,
         alignmentAlgorithm,
         connectedMsaViewId,
         structures: [
@@ -73,7 +74,17 @@ export function launch3DProteinView({ session, view, feature, selectedTranscript
         ],
         displayName: displayName ??
             formatViewName('Protein view', feature, selectedTranscript, uniprotId),
-    });
+    };
+    // eslint-disable-next-line no-console
+    console.log('[protein3d debug] addView ProteinView snapshot:', JSON.stringify(snap, (_k, v) => (typeof v === 'function' ? '<fn>' : v), 2));
+    try {
+        return session.addView('ProteinView', snap);
+    }
+    catch (e) {
+        // eslint-disable-next-line no-console
+        console.log('[protein3d debug] addView threw:', e.message);
+        throw e;
+    }
 }
 export async function launch1DProteinView({ session, view, feature, selectedTranscript, uniprotId, confidenceUrl, }) {
     if (!uniprotId || !isSessionWithAddTracks(session)) {

package/dist/LaunchProteinView/utils/util.js

@@ -64,13 +64,9 @@ export function isRecognizedDatabaseId(id) {
  * Get the database type for a recognized ID (used for UniProt xref queries)
  */
 export function getDatabaseTypeForId(id) {
-    if (ensemblGenePattern.test(id)) {
-        return 'ensembl';
-    }
-    if (ensemblTranscriptPattern.test(id)) {
-        return 'ensembl';
-    }
-    if (ensemblProteinPattern.test(id)) {
+    if (ensemblGenePattern.test(id) ||
+        ensemblTranscriptPattern.test(id) ||
+        ensemblProteinPattern.test(id)) {
         return 'ensembl';
     }
     if (refSeqTranscriptPattern.test(id) || refSeqProteinPattern.test(id)) {

package/dist/ProteinView/components/AddStructureDialog.js

@@ -21,19 +21,22 @@ const AddStructureDialog = observer(function AddStructureDialog({ model, }) {
     };
     const handleAdd = async () => {
         try {
-            let url = structureURL;
+            let url;
             let data;
             if (choice === 'pdb' && pdbId) {
                 url = getPdbStructureUrl(pdbId);
             }
-            if (choice === 'uniprot' && uniprotId) {
+            else if (choice === 'uniprot' && uniprotId) {
                 url = getAlphaFoldStructureUrl(uniprotId.toUpperCase());
             }
-            if (choice === 'file' && file) {
+            else if (choice === 'url' && structureURL) {
+                url = structureURL;
+            }
+            else if (choice === 'file' && file) {
                 data = await file.text();
             }
-            if (url || data) {
-                await model.addStructureAndSuperpose({ url: url || undefined, data });
+            if (url !== undefined || data !== undefined) {
+                await model.addStructureAndSuperpose({ url, data });
                 handleClose();
             }
         }

package/dist/ProteinView/components/HeaderStructureInfo.js

@@ -4,7 +4,7 @@ const HeaderStructureInfo = observer(function HeaderStructureInfo({ model, }) {
     const { structures } = model;
     return structures.map((structure, idx) => {
         const { hoverString } = structure;
-        return (React.createElement("span", { key: `${hoverString}-${idx}` },
+        return (React.createElement("span", { key: idx },
             hoverString ? `Hover: ${hoverString}` : '',
             "\u00A0"));
     });

package/dist/ProteinView/components/ProteinFeatureTrack.js

@@ -5,6 +5,13 @@ import { CHAR_WIDTH, HIDE_BUTTON_COLOR, HOVERED_BORDER, HOVER_MARKER_COLOR, SELE
 import { selectResidueRange } from '../highlightResidueRange';
 import { getFeatureColor } from '../hooks/useUniProtFeatures';
 import { clickProteinToGenome } from '../proteinToGenomeMapping';
+function getFeatureAlignmentRange(feature, structurePositionToAlignmentMap) {
+    const startAlignmentPos = structurePositionToAlignmentMap?.[feature.start - 1];
+    const endAlignmentPos = structurePositionToAlignmentMap?.[feature.end - 1];
+    return startAlignmentPos !== undefined && endAlignmentPos !== undefined
+        ? { start: startAlignmentPos, end: endAlignmentPos }
+        : undefined;
+}
 function getVisibleTypes(featureTypes, hiddenFeatureTypes) {
     return featureTypes.filter(type => !hiddenFeatureTypes.has(type));
 }
@@ -31,20 +38,9 @@ const FeatureBar = observer(function FeatureBar({ feature, model, }) {
     const [isHovered, setIsHovered] = useState(false);
     const { molstarPluginContext, selectedFeatureId, structurePositionToAlignmentMap, } = model;
     const isSelected = selectedFeatureId === feature.uniqueId;
-    const getAlignmentRange = () => {
-        if (!structurePositionToAlignmentMap) {
-            return undefined;
-        }
-        const startAlignmentPos = structurePositionToAlignmentMap[feature.start - 1];
-        const endAlignmentPos = structurePositionToAlignmentMap[feature.end - 1];
-        if (startAlignmentPos !== undefined && endAlignmentPos !== undefined) {
-            return { start: startAlignmentPos, end: endAlignmentPos };
-        }
-        return undefined;
-    };
     const handleMouseEnter = () => {
         setIsHovered(true);
-        const range = getAlignmentRange();
+        const range = getFeatureAlignmentRange(feature, structurePositionToAlignmentMap);
         if (range) {
             model.setAlignmentHoverRange(range);
         }

package/dist/ProteinView/components/ProteinViewHeader.js

@@ -31,10 +31,7 @@ const ProteinViewHeader = observer(function ProteinViewHeader({ model, }) {
                         model.setAutoScrollAlignment(!autoScrollAlignment);
                     } }))),
         showAlignment
-            ? structures.map((structure, idx) => {
-                const { pairwiseAlignment } = structure;
-                return (React.createElement("div", { key: idx }, pairwiseAlignment ? (React.createElement(ProteinAlignment, { key: idx, model: structure })) : (React.createElement(LoadingEllipses, { message: "Loading pairwise alignment" }))));
-            })
+            ? structures.map((structure, idx) => (React.createElement("div", { key: idx }, structure.pairwiseAlignment ? (React.createElement(ProteinAlignment, { model: structure })) : (React.createElement(LoadingEllipses, { message: "Loading pairwise alignment" })))))
             : null,
         React.createElement(AddStructureDialog, { model: model })));
 });