npm - jbrowse-plugin-protein3d - Versions diffs - 0.4.0 → 0.4.1 - Mend

jbrowse-plugin-protein3d 0.4.0 → 0.4.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (58) hide show

package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js CHANGED Viewed

@@ -67,7 +67,7 @@ const AlphaFoldDBSearch = observer(function AlphaFoldDBSearch({ feature, model,
                 state.showSequenceSearchStatus && (React.createElement(SequenceSearchStatus, { isLoading: state.isSequenceSearchLoading, uniprotId: state.uniprotId, url: state.url, hasProteinSequence: !!state.userSelectedProteinSequence, sequenceSearchType: state.sequenceSearchType })),
                 state.showAlphaFoldDBSearchStatus && (React.createElement(AlphaFoldDBSearchStatus, { uniprotId: state.uniprotId, selectedTranscript: state.selectedTranscript, structureSequence: state.structureSequence, isoformSequences: state.isoformSequences, url: state.url }))))),
         React.createElement(DialogActions, null,
-            React.createElement(ProteinViewActions, { handleClose: handleClose, uniprotId: state.uniprotId, userSelectedProteinSequence: state.userSelectedProteinSequence, selectedTranscript: state.selectedTranscript, url: state.url, confidenceUrl: state.confidenceUrl, feature: feature, view: view, session: session, alignmentAlgorithm: alignmentAlgorithm, onAlignmentAlgorithmChange: onAlignmentAlgorithmChange, sequencesMatch: state.sequencesMatch, isLoading: state.isLoading }))));
+            React.createElement(ProteinViewActions, { handleClose: handleClose, uniprotId: state.uniprotId, userSelectedProteinSequence: state.userSelectedProteinSequence, selectedTranscript: state.selectedTranscript, url: state.url, confidenceUrl: state.confidenceUrl, feature: feature, view: view, session: session, alignmentAlgorithm: alignmentAlgorithm, onAlignmentAlgorithmChange: onAlignmentAlgorithmChange, sequencesMatch: state.sequencesMatch, isLoading: state.isLoading, error: state.error }))));
 });
 export default AlphaFoldDBSearch;
 //# sourceMappingURL=AlphaFoldDBSearch.js.map

package/dist/LaunchProteinView/components/AlphaFoldDBSearch.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"AlphaFoldDBSearch.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/AlphaFoldDBSearch.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAChE,OAAO,EAAE,iBAAiB,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAClE,OAAO,EAAE,aAAa,EAAE,aAAa,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AACxE,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAC/D,OAAO,sBAAsB,MAAM,0BAA0B,CAAA;AAC7D,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,oBAAoB,MAAM,wBAAwB,CAAA;AACzD,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AACrD,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AACvD,OAAO,YAAY,MAAM,+BAA+B,CAAA;AACxD,OAAO,oBAAoB,MAAM,+BAA+B,CAAA;AAMhE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;QACb,OAAO,EAAE;YACP,YAAY,EAAE,EAAE;SACjB;QACD,kBAAkB,EAAE;YAClB,YAAY,EAAE,CAAC;SAChB;KACF;IACD,YAAY,EAAE;QACZ,OAAO,EAAE,MAAM;QACf,aAAa,EAAE,KAAK;QACpB,GAAG,EAAE,EAAE;QACP,UAAU,EAAE,YAAY;KACzB;CACF,CAAC,CAAA;AAEF,MAAM,iBAAiB,GAAG,QAAQ,CAAC,SAAS,iBAAiB,CAAC,EAC5D,OAAO,EACP,KAAK,EACL,WAAW,EACX,kBAAkB,EAClB,0BAA0B,GAO3B;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,iBAAiB,CAAC,KAAK,CAA0B,CAAA;IAE9D,MAAM,KAAK,GAAG,oBAAoB,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAErD,OAAO,CACL;QACE,oBAAC,aAAa,IAAC,SAAS,EAAE,OAAO,CAAC,aAAa;YAC5C,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,CAAC,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;YAE1D,oBAAC,cAAc,IACb,UAAU,EAAE,KAAK,CAAC,UAAU,EAC5B,kBAAkB,EAAE,KAAK,CAAC,aAAa,EACvC,eAAe,EAAE,KAAK,CAAC,eAAe,EACtC,uBAAuB,EAAE,KAAK,CAAC,kBAAkB,EACjD,gBAAgB,EAAE,KAAK,CAAC,gBAAgB,EACxC,kBAAkB,EAAE,CAAC,CAAC,KAAK,CAAC,2BAA2B,EAAE,GAAG,EAC5D,kBAAkB,EAAE,KAAK,CAAC,kBAAkB,EAC5C,0BAA0B,EAAE,KAAK,CAAC,qBAAqB,EACvD,UAAU,EACR,KAAK,CAAC,sBAAsB,CAAC,CAAC,CAAC,CAC7B,oBAAC,kBAAkB,IACjB,aAAa,EAAE,KAAK,CAAC,aAAa,EAClC,QAAQ,EAAE,KAAK,CAAC,QAAQ,EACxB,UAAU,EAAE,KAAK,CAAC,eAAe,EACjC,kBAAkB,EAAE,KAAK,CAAC,kBAAkB,GAC5C,CACH,CAAC,CAAC,CAAC,IAAI,GAEV;YAED,KAAK,CAAC,eAAe,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CACnC,oBAAC,eAAe,IAAC,GAAG,EAAE,MAAM,EAAE,OAAO,EAAC,WAAW,EAAC,OAAO,EAAE,MAAM,GAAI,CACtE,CAAC;YAED,KAAK,CAAC,kBAAkB,IAAI,CAC3B;gBACE,oBAAC,UAAU,IAAC,OAAO,EAAC,OAAO,EAAC,KAAK,EAAC,eAAe;;oBAC1B,KAAK,CAAC,iBAAiB,CACjC;gBACb,oBAAC,mBAAmB,IAClB,OAAO,EAAE,KAAK,CAAC,cAAc,EAC7B,iBAAiB,EAAE,KAAK,CAAC,sBAAsB,EAC/C,QAAQ,EAAE,KAAK,CAAC,oBAAoB,GACpC;gBACF,oBAAC,UAAU,IAAC,OAAO,EAAC,OAAO,EAAC,KAAK,EAAC,eAAe;;oBAEpB,GAAG;oBAC9B,oBAAC,YAAY,IAAC,IAAI,EAAC,0BAA0B,cAE9B;oBAAC,GAAG;2DAER,CACZ,CACJ;YAEA,KAAK,CAAC,aAAa,IAAI,CACtB,oBAAC,UAAU,IAAC,OAAO,EAAC,OAAO,EAAC,KAAK,EAAC,eAAe;;gBACjB,KAAK,CAAC,mBAAmB;;gBACjB,GAAG;gBACzC,oBAAC,YAAY,IAAC,IAAI,EAAC,0BAA0B,cAAuB;gBAAC,GAAG;8HAG7D,CACd;YAEA,KAAK,CAAC,sBAAsB,IAAI,CAC/B;gBACE,6BAAK,SAAS,EAAE,OAAO,CAAC,YAAY;oBAClC,oBAAC,kBAAkB,IACjB,GAAG,EAAE,KAAK,CAAC,aAAa,EACxB,MAAM,EAAE,KAAK,CAAC,gBAAgB,EAC9B,iBAAiB,EAAE,KAAK,CAAC,iBAAiB,EAC1C,OAAO,EAAE,OAAO,EAChB,QAAQ,EAAE,KAAK,CAAC,iBAAiB,EACjC,gBAAgB,EAAE,KAAK,CAAC,gBAAiB,GACzC;oBACD,KAAK,CAAC,0BAA0B,IAAI,CACnC,oBAAC,sBAAsB,IACrB,WAAW,EAAE,KAAK,CAAC,WAAY,EAC/B,kBAAkB,EAAE,KAAK,CAAC,kBAAkB,EAC5C,iBAAiB,EAAE,KAAK,CAAC,qBAAqB,GAC9C,CACH,CACG;gBACL,KAAK,CAAC,wBAAwB,IAAI,CACjC,oBAAC,oBAAoB,IACnB,SAAS,EAAE,KAAK,CAAC,uBAAuB,EACxC,SAAS,EAAE,KAAK,CAAC,SAAS,EAC1B,GAAG,EAAE,KAAK,CAAC,GAAG,EACd,kBAAkB,EAAE,CAAC,CAAC,KAAK,CAAC,2BAA2B,EACvD,kBAAkB,EAAE,KAAK,CAAC,kBAAkB,GAC5C,CACH;gBACA,KAAK,CAAC,2BAA2B,IAAI,CACpC,oBAAC,uBAAuB,IACtB,SAAS,EAAE,KAAK,CAAC,SAAS,EAC1B,kBAAkB,EAAE,KAAK,CAAC,kBAAkB,EAC5C,iBAAiB,EAAE,KAAK,CAAC,iBAAiB,EAC1C,gBAAgB,EAAE,KAAK,CAAC,gBAAiB,EACzC,GAAG,EAAE,KAAK,CAAC,GAAG,GACd,CACH,CACA,CACJ,CACa;QAChB,oBAAC,aAAa;YACZ,oBAAC,kBAAkB,IACjB,WAAW,EAAE,WAAW,EACxB,SAAS,EAAE,KAAK,CAAC,SAAS,EAC1B,2BAA2B,EAAE,KAAK,CAAC,2BAA2B,EAC9D,kBAAkB,EAAE,KAAK,CAAC,kBAAkB,EAC5C,GAAG,EAAE,KAAK,CAAC,GAAG,EACd,aAAa,EAAE,KAAK,CAAC,aAAa,EAClC,OAAO,EAAE,OAAO,EAChB,IAAI,EAAE,IAAI,EACV,OAAO,EAAE,OAAO,EAChB,kBAAkB,EAAE,kBAAkB,EACtC,0BAA0B,EAAE,0BAA0B,EACtD,cAAc,EAAE,KAAK,CAAC,cAAc,EACpC,SAAS,EAAE,KAAK,CAAC,SAAS,EAC1B,KAAK,EAAE,KAAK,CAAC,KAAK,GAClB,CACY,CACf,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,iBAAiB,CAAA"}

package/dist/LaunchProteinView/components/FoldseekActionMenu.js CHANGED Viewed

@@ -1,6 +1,7 @@
 import React, { useState } from 'react';
 import { Button, Menu, MenuItem } from '@mui/material';
 import { caCoordsToPdb, hasValidCaCoords } from '../utils/caCoordsToPdb';
+import { safeLaunch } from '../utils/launchHelpers';
 import { getConfidenceUrlFromTarget, getUniprotIdFromAlphaFoldTarget, hasMsaViewPlugin, launch1DProteinView, launch3DProteinView, launchMsaView, } from '../utils/launchViewUtils';
 export default function FoldseekActionMenu({ hit, session, view, feature, selectedTranscript, userProvidedTranscriptSequence, onClose, }) {
     const [anchorEl, setAnchorEl] = useState(null);
@@ -12,53 +13,32 @@ export default function FoldseekActionMenu({ hit, session, view, feature, select
     const handleMenuClose = () => {
         setAnchorEl(null);
     };
-    const handleLaunch3D = () => {
+    const baseParams = { session, view, feature, selectedTranscript, uniprotId };
+    const runLaunch = (fn) => () => {
         handleMenuClose();
+        void safeLaunch(session, fn, onClose);
+    };
+    const handleLaunch3D = runLaunch(() => {
         // Use tCa coordinates to generate PDB data if no URL is available
         const pdbData = !hit.structureUrl && hasValidCaCoords(hit.tCa, hit.tSeq)
             ? caCoordsToPdb(hit.tCa, hit.tSeq, 'A', hit.target)
             : undefined;
         launch3DProteinView({
-            session,
-            view,
-            feature,
-            selectedTranscript,
-            uniprotId,
+            ...baseParams,
             url: hit.structureUrl,
             data: pdbData,
             userProvidedTranscriptSequence,
         });
-        onClose();
-    };
-    const handleLaunch1D = async () => {
-        handleMenuClose();
-        try {
-            await launch1DProteinView({
-                session,
-                view,
-                feature,
-                selectedTranscript,
-                uniprotId,
-                confidenceUrl: getConfidenceUrlFromTarget(hit.target),
-            });
-        }
-        catch (e) {
-            console.error(e);
-            session.notifyError(`${e}`, e);
-        }
-        onClose();
-    };
-    const handleLaunchMSA = () => {
-        handleMenuClose();
-        launchMsaView({
-            session,
-            view,
-            feature,
-            selectedTranscript,
-            uniprotId,
+    });
+    const handleLaunch1D = runLaunch(async () => {
+        await launch1DProteinView({
+            ...baseParams,
+            confidenceUrl: getConfidenceUrlFromTarget(hit.target),
         });
-        onClose();
-    };
+    });
+    const handleLaunchMSA = runLaunch(() => {
+        launchMsaView(baseParams);
+    });
     const canLoad = hit.structureUrl ?? hasValidCaCoords(hit.tCa, hit.tSeq);
     if (!canLoad) {
         return React.createElement("span", null, "-");
@@ -67,9 +47,7 @@ export default function FoldseekActionMenu({ hit, session, view, feature, select
         React.createElement(Button, { size: "small", variant: "outlined", onClick: handleClick }, "Load"),
         React.createElement(Menu, { anchorEl: anchorEl, open: open, onClose: handleMenuClose },
             React.createElement(MenuItem, { onClick: handleLaunch3D }, "Launch 3D protein view"),
-            uniprotId ? (React.createElement(MenuItem, { onClick: () => {
-                    void handleLaunch1D();
-                } }, "Launch 1D protein annotation view")) : null,
+            uniprotId ? (React.createElement(MenuItem, { onClick: handleLaunch1D }, "Launch 1D protein annotation view")) : null,
             uniprotId && hasMsaViewPlugin() ? (React.createElement(MenuItem, { onClick: handleLaunchMSA }, "Launch MSA view (AlphaFoldDB a3m)")) : null)));
 }
 //# sourceMappingURL=FoldseekActionMenu.js.map

package/dist/LaunchProteinView/components/FoldseekActionMenu.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LaunchProteinView/components/LaunchOptionsDialog.d.ts ADDED Viewed

@@ -0,0 +1,13 @@
+import React from 'react';
+interface LaunchOption {
+    key: string;
+    title: string;
+    description: string;
+    onClick: () => void;
+}
+export default function LaunchOptionsDialog({ open, onClose, options, }: {
+    open: boolean;
+    onClose: () => void;
+    options: LaunchOption[];
+}): React.JSX.Element;
+export {};

package/dist/LaunchProteinView/components/LaunchOptionsDialog.js ADDED Viewed

@@ -0,0 +1,12 @@
+import React from 'react';
+import { Dialog, DialogContent, DialogTitle, MenuItem, MenuList, Typography, } from '@mui/material';
+export default function LaunchOptionsDialog({ open, onClose, options, }) {
+    return (React.createElement(Dialog, { open: open, onClose: onClose },
+        React.createElement(DialogTitle, null, "Launch options"),
+        React.createElement(DialogContent, null,
+            React.createElement(MenuList, null, options.map(opt => (React.createElement(MenuItem, { key: opt.key, onClick: opt.onClick },
+                React.createElement("div", null,
+                    React.createElement(Typography, { variant: "body1" }, opt.title),
+                    React.createElement(Typography, { variant: "body2", color: "text.secondary" }, opt.description)))))))));
+}
+//# sourceMappingURL=LaunchOptionsDialog.js.map

package/dist/LaunchProteinView/components/LaunchOptionsDialog.js.map ADDED Viewed

@@ -0,0 +1 @@

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package/dist/LaunchProteinView/components/ProteinViewActions.d.ts CHANGED Viewed

@@ -18,6 +18,12 @@ interface ProteinViewActionsProps {
     onAlignmentAlgorithmChange: (algorithm: AlignmentAlgorithm) => void;
     sequencesMatch?: boolean;
     isLoading?: boolean;
+    /**
+     * Real error from the lookup/data pipeline. When present, "No UniProt ID
+     * found" is suppressed so it doesn't compete with the actual error message
+     * shown above by <ErrorMessage>.
+     */
+    error?: unknown;
 }
-export default function ProteinViewActions({ handleClose, uniprotId, userSelectedProteinSequence, selectedTranscript, url, confidenceUrl, feature, view, session, alignmentAlgorithm, onAlignmentAlgorithmChange, sequencesMatch, isLoading, }: ProteinViewActionsProps): React.JSX.Element;
+export default function ProteinViewActions({ handleClose, uniprotId, userSelectedProteinSequence, selectedTranscript, url, confidenceUrl, feature, view, session, alignmentAlgorithm, onAlignmentAlgorithmChange, sequencesMatch, isLoading, error, }: ProteinViewActionsProps): React.JSX.Element;
 export {};

package/dist/LaunchProteinView/components/ProteinViewActions.js CHANGED Viewed

@@ -1,127 +1,107 @@
 import React, { useState } from 'react';
 import ArrowDropDownIcon from '@mui/icons-material/ArrowDropDown';
-import { Button, ButtonGroup, Dialog, DialogContent, DialogTitle, MenuItem, MenuList, Typography, } from '@mui/material';
-import AlignmentSettingsButton from './AlignmentSettingsButton';
-import { ALIGNMENT_ALGORITHM_LABELS } from '../../ProteinView/types';
+import { Button, ButtonGroup, Typography } from '@mui/material';
+import LaunchOptionsDialog from './LaunchOptionsDialog';
+import SequenceMismatchNotice from './SequenceMismatchNotice';
+import { getLaunchMissingReasons, safeLaunch, } from '../utils/launchHelpers';
 import { hasMsaViewPlugin, launch1DProteinView, launch3DProteinView, launch3DProteinViewWithMsa, launchMsaView, } from '../utils/launchViewUtils';
-export default function ProteinViewActions({ handleClose, uniprotId, userSelectedProteinSequence, selectedTranscript, url, confidenceUrl, feature, view, session, alignmentAlgorithm, onAlignmentAlgorithmChange, sequencesMatch, isLoading, }) {
+export default function ProteinViewActions({ handleClose, uniprotId, userSelectedProteinSequence, selectedTranscript, url, confidenceUrl, feature, view, session, alignmentAlgorithm, onAlignmentAlgorithmChange, sequencesMatch, isLoading, error, }) {
     const [dialogOpen, setDialogOpen] = useState(false);
-    const canLaunch = !!uniprotId && !!userSelectedProteinSequence && !!selectedTranscript;
-    const missingReasons = isLoading
-        ? []
-        : [
-            !uniprotId && 'No UniProt ID found',
-            !userSelectedProteinSequence &&
-                'Could not compute protein sequence (feature may be missing CDS subfeatures)',
-            !selectedTranscript && 'No transcript selected',
-        ].filter(Boolean);
-    const handleLaunch3DView = () => {
+    // Disable launch while loading — SWR's keepPreviousData would otherwise let
+    // a user click Launch on stale results (wrong UniProt ID) during a refetch.
+    const canLaunch = !isLoading &&
+        !!uniprotId &&
+        !!userSelectedProteinSequence &&
+        !!selectedTranscript;
+    const missingReasons = getLaunchMissingReasons({
+        uniprotId,
+        userSelectedProteinSequence,
+        selectedTranscript,
+        isLoading,
+        error,
+    });
+    const closeMenu = () => {
         setDialogOpen(false);
-        if (!selectedTranscript) {
-            return;
-        }
-        launch3DProteinView({
-            session,
-            view,
-            feature,
-            selectedTranscript,
-            uniprotId,
-            url,
-            userProvidedTranscriptSequence: userSelectedProteinSequence?.seq,
-            alignmentAlgorithm,
-        });
-        handleClose();
     };
+    const baseParams = {
+        session,
+        view,
+        feature,
+        selectedTranscript,
+        uniprotId,
+    };
+    const launch3DParams = {
+        ...baseParams,
+        url,
+        userProvidedTranscriptSequence: userSelectedProteinSequence?.seq,
+        alignmentAlgorithm,
+    };
+    const runLaunch = (fn) => () => {
+        closeMenu();
+        void safeLaunch(session, fn, handleClose);
+    };
+    const handleLaunch3DView = runLaunch(() => {
+        if (selectedTranscript) {
+            launch3DProteinView(launch3DParams);
+        }
+    });
+    const handleLaunch1DView = runLaunch(async () => {
+        if (uniprotId && selectedTranscript) {
+            await launch1DProteinView({ ...baseParams, confidenceUrl });
+        }
+    });
+    const handleLaunchMsa = runLaunch(() => {
+        if (selectedTranscript && uniprotId) {
+            launchMsaView(baseParams);
+        }
+    });
+    const handleLaunch3DWithMsa = runLaunch(() => {
+        if (selectedTranscript && uniprotId) {
+            launch3DProteinViewWithMsa(launch3DParams);
+        }
+    });
+    const launchOptions = [
+        {
+            key: '3d',
+            title: 'Launch 3D protein structure view',
+            description: 'View protein structure with genome-to-structure coordinate mapping',
+            onClick: handleLaunch3DView,
+        },
+        {
+            key: '1d',
+            title: 'Launch 1D protein annotation view',
+            description: 'View protein features and annotations as a linear track',
+            onClick: handleLaunch1DView,
+        },
+        ...(hasMsaViewPlugin()
+            ? [
+                {
+                    key: 'msa',
+                    title: 'Launch MSA view',
+                    description: 'View AlphaFold a3m multiple sequence alignment',
+                    onClick: handleLaunchMsa,
+                },
+                {
+                    key: '3d-msa',
+                    title: 'Launch 3D structure + MSA view',
+                    description: 'Launch both views with AlphaFold a3m MSA',
+                    onClick: handleLaunch3DWithMsa,
+                },
+            ]
+            : []),
+    ];
     return (React.createElement(React.Fragment, null,
-        sequencesMatch === false ? (React.createElement(Typography, { variant: "body2", sx: { mr: 2, display: 'flex', alignItems: 'center' } },
-            "Transcript and structure sequences differ, will run",
-            ' ',
-            ALIGNMENT_ALGORITHM_LABELS[alignmentAlgorithm] ?? alignmentAlgorithm,
-            ' ',
-            "alignment",
-            React.createElement(AlignmentSettingsButton, { value: alignmentAlgorithm, onChange: onAlignmentAlgorithmChange }))) : null,
-        React.createElement(Button, { variant: "contained", color: "secondary", size: "small", onClick: handleClose }, "Cancel"),
-        !canLaunch ? (React.createElement(Typography, { variant: "body2", color: "error", sx: { mr: 2 } }, missingReasons.join('. '))) : null,
+        sequencesMatch === false ? (React.createElement(SequenceMismatchNotice, { alignmentAlgorithm: alignmentAlgorithm, onAlignmentAlgorithmChange: onAlignmentAlgorithmChange })) : null,
+        React.createElement(Button, { variant: "contained", color: "secondary", size: "small", onClick: () => {
+                handleClose();
+            } }, "Cancel"),
+        !canLaunch && missingReasons.length > 0 ? (React.createElement(Typography, { variant: "body2", color: "error", sx: { mr: 2 } }, missingReasons.join('. '))) : null,
         React.createElement(ButtonGroup, { variant: "contained", color: "primary", size: "small" },
             React.createElement(Button, { disabled: !canLaunch, onClick: handleLaunch3DView }, "Launch"),
             React.createElement(Button, { disabled: !canLaunch, onClick: () => {
                     setDialogOpen(true);
                 }, "aria-label": "More launch options" },
                 React.createElement(ArrowDropDownIcon, null))),
-        React.createElement(Dialog, { open: dialogOpen, onClose: () => {
-                setDialogOpen(false);
-            } },
-            React.createElement(DialogTitle, null, "Launch options"),
-            React.createElement(DialogContent, null,
-                React.createElement(MenuList, null,
-                    React.createElement(MenuItem, { onClick: handleLaunch3DView },
-                        React.createElement("div", null,
-                            React.createElement(Typography, { variant: "body1" }, "Launch 3D protein structure view"),
-                            React.createElement(Typography, { variant: "body2", color: "text.secondary" }, "View protein structure with genome-to-structure coordinate mapping"))),
-                    React.createElement(MenuItem, { onClick: async () => {
-                            setDialogOpen(false);
-                            if (!uniprotId || !selectedTranscript) {
-                                return;
-                            }
-                            try {
-                                await launch1DProteinView({
-                                    session,
-                                    view,
-                                    feature,
-                                    selectedTranscript,
-                                    uniprotId,
-                                    confidenceUrl,
-                                });
-                            }
-                            catch (e) {
-                                console.error(e);
-                                session.notifyError(`${e}`, e);
-                            }
-                            handleClose();
-                        } },
-                        React.createElement("div", null,
-                            React.createElement(Typography, { variant: "body1" }, "Launch 1D protein annotation view"),
-                            React.createElement(Typography, { variant: "body2", color: "text.secondary" }, "View protein features and annotations as a linear track"))),
-                    hasMsaViewPlugin()
-                        ? [
-                            React.createElement(MenuItem, { key: "msa", onClick: () => {
-                                    setDialogOpen(false);
-                                    if (!selectedTranscript || !uniprotId) {
-                                        return;
-                                    }
-                                    launchMsaView({
-                                        session,
-                                        view,
-                                        feature,
-                                        selectedTranscript,
-                                        uniprotId,
-                                    });
-                                    handleClose();
-                                } },
-                                React.createElement("div", null,
-                                    React.createElement(Typography, { variant: "body1" }, "Launch MSA view"),
-                                    React.createElement(Typography, { variant: "body2", color: "text.secondary" }, "View AlphaFold a3m multiple sequence alignment"))),
-                            React.createElement(MenuItem, { key: "3d-msa", onClick: () => {
-                                    setDialogOpen(false);
-                                    if (!selectedTranscript || !uniprotId) {
-                                        return;
-                                    }
-                                    launch3DProteinViewWithMsa({
-                                        session,
-                                        view,
-                                        feature,
-                                        selectedTranscript,
-                                        uniprotId,
-                                        url,
-                                        userProvidedTranscriptSequence: userSelectedProteinSequence?.seq,
-                                        alignmentAlgorithm,
-                                    });
-                                    handleClose();
-                                } },
-                                React.createElement("div", null,
-                                    React.createElement(Typography, { variant: "body1" }, "Launch 3D structure + MSA view"),
-                                    React.createElement(Typography, { variant: "body2", color: "text.secondary" }, "Launch both views with AlphaFold a3m MSA"))),
-                        ]
-                        : null)))));
+        React.createElement(LaunchOptionsDialog, { open: dialogOpen, onClose: closeMenu, options: launchOptions })));
 }
 //# sourceMappingURL=ProteinViewActions.js.map

package/dist/LaunchProteinView/components/ProteinViewActions.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"ProteinViewActions.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/ProteinViewActions.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,iBAAiB,MAAM,mCAAmC,CAAA;AACjE,OAAO,EAAE,MAAM,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE/D,OAAO,mBAAmB,MAAM,uBAAuB,CAAA;AACvD,OAAO,sBAAsB,MAAM,0BAA0B,CAAA;AAC7D,OAAO,EACL,uBAAuB,EACvB,UAAU,GACX,MAAM,wBAAwB,CAAA;AAC/B,OAAO,EACL,gBAAgB,EAChB,mBAAmB,EACnB,mBAAmB,EACnB,0BAA0B,EAC1B,aAAa,GACd,MAAM,0BAA0B,CAAA;AA4BjC,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,EACzC,WAAW,EACX,SAAS,EACT,2BAA2B,EAC3B,kBAAkB,EAClB,GAAG,EACH,aAAa,EACb,OAAO,EACP,IAAI,EACJ,OAAO,EACP,kBAAkB,EAClB,0BAA0B,EAC1B,cAAc,EACd,SAAS,EACT,KAAK,GACmB;IACxB,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACnD,4EAA4E;IAC5E,4EAA4E;IAC5E,MAAM,SAAS,GACb,CAAC,SAAS;QACV,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,2BAA2B;QAC7B,CAAC,CAAC,kBAAkB,CAAA;IAEtB,MAAM,cAAc,GAAG,uBAAuB,CAAC;QAC7C,SAAS;QACT,2BAA2B;QAC3B,kBAAkB;QAClB,SAAS;QACT,KAAK;KACN,CAAC,CAAA;IAEF,MAAM,SAAS,GAAG,GAAG,EAAE;QACrB,aAAa,CAAC,KAAK,CAAC,CAAA;IACtB,CAAC,CAAA;IAED,MAAM,UAAU,GAAG;QACjB,OAAO;QACP,IAAI;QACJ,OAAO;QACP,kBAAkB;QAClB,SAAS;KACV,CAAA;IACD,MAAM,cAAc,GAAG;QACrB,GAAG,UAAU;QACb,GAAG;QACH,8BAA8B,EAAE,2BAA2B,EAAE,GAAG;QAChE,kBAAkB;KACnB,CAAA;IAED,MAAM,SAAS,GAAG,CAAC,EAA8B,EAAE,EAAE,CAAC,GAAG,EAAE;QACzD,SAAS,EAAE,CAAA;QACX,KAAK,UAAU,CAAC,OAAO,EAAE,EAAE,EAAE,WAAW,CAAC,CAAA;IAC3C,CAAC,CAAA;IAED,MAAM,kBAAkB,GAAG,SAAS,CAAC,GAAG,EAAE;QACxC,IAAI,kBAAkB,EAAE,CAAC;YACvB,mBAAmB,CAAC,cAAc,CAAC,CAAA;QACrC,CAAC;IACH,CAAC,CAAC,CAAA;IAEF,MAAM,kBAAkB,GAAG,SAAS,CAAC,KAAK,IAAI,EAAE;QAC9C,IAAI,SAAS,IAAI,kBAAkB,EAAE,CAAC;YACpC,MAAM,mBAAmB,CAAC,EAAE,GAAG,UAAU,EAAE,aAAa,EAAE,CAAC,CAAA;QAC7D,CAAC;IACH,CAAC,CAAC,CAAA;IAEF,MAAM,eAAe,GAAG,SAAS,CAAC,GAAG,EAAE;QACrC,IAAI,kBAAkB,IAAI,SAAS,EAAE,CAAC;YACpC,aAAa,CAAC,UAAU,CAAC,CAAA;QAC3B,CAAC;IACH,CAAC,CAAC,CAAA;IAEF,MAAM,qBAAqB,GAAG,SAAS,CAAC,GAAG,EAAE;QAC3C,IAAI,kBAAkB,IAAI,SAAS,EAAE,CAAC;YACpC,0BAA0B,CAAC,cAAc,CAAC,CAAA;QAC5C,CAAC;IACH,CAAC,CAAC,CAAA;IAEF,MAAM,aAAa,GAAG;QACpB;YACE,GAAG,EAAE,IAAI;YACT,KAAK,EAAE,kCAAkC;YACzC,WAAW,EACT,oEAAoE;YACtE,OAAO,EAAE,kBAAkB;SAC5B;QACD;YACE,GAAG,EAAE,IAAI;YACT,KAAK,EAAE,mCAAmC;YAC1C,WAAW,EAAE,yDAAyD;YACtE,OAAO,EAAE,kBAAkB;SAC5B;QACD,GAAG,CAAC,gBAAgB,EAAE;YACpB,CAAC,CAAC;gBACE;oBACE,GAAG,EAAE,KAAK;oBACV,KAAK,EAAE,iBAAiB;oBACxB,WAAW,EAAE,gDAAgD;oBAC7D,OAAO,EAAE,eAAe;iBACzB;gBACD;oBACE,GAAG,EAAE,QAAQ;oBACb,KAAK,EAAE,gCAAgC;oBACvC,WAAW,EAAE,0CAA0C;oBACvD,OAAO,EAAE,qBAAqB;iBAC/B;aACF;YACH,CAAC,CAAC,EAAE,CAAC;KACR,CAAA;IAED,OAAO,CACL;QACG,cAAc,KAAK,KAAK,CAAC,CAAC,CAAC,CAC1B,oBAAC,sBAAsB,IACrB,kBAAkB,EAAE,kBAAkB,EACtC,0BAA0B,EAAE,0BAA0B,GACtD,CACH,CAAC,CAAC,CAAC,IAAI;QACR,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,WAAW,EACjB,IAAI,EAAC,OAAO,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,WAAW,EAAE,CAAA;YACf,CAAC,aAGM;QACR,CAAC,SAAS,IAAI,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CACzC,oBAAC,UAAU,IAAC,OAAO,EAAC,OAAO,EAAC,KAAK,EAAC,OAAO,EAAC,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,EAAE,IACpD,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,CACf,CACd,CAAC,CAAC,CAAC,IAAI;QACR,oBAAC,WAAW,IAAC,OAAO,EAAC,WAAW,EAAC,KAAK,EAAC,SAAS,EAAC,IAAI,EAAC,OAAO;YAC3D,oBAAC,MAAM,IAAC,QAAQ,EAAE,CAAC,SAAS,EAAE,OAAO,EAAE,kBAAkB,aAEhD;YACT,oBAAC,MAAM,IACL,QAAQ,EAAE,CAAC,SAAS,EACpB,OAAO,EAAE,GAAG,EAAE;oBACZ,aAAa,CAAC,IAAI,CAAC,CAAA;gBACrB,CAAC,gBACU,qBAAqB;gBAEhC,oBAAC,iBAAiB,OAAG,CACd,CACG;QACd,oBAAC,mBAAmB,IAClB,IAAI,EAAE,UAAU,EAChB,OAAO,EAAE,SAAS,EAClB,OAAO,EAAE,aAAa,GACtB,CACD,CACJ,CAAA;AACH,CAAC"}

package/dist/LaunchProteinView/components/SequenceMismatchNotice.d.ts ADDED Viewed

@@ -0,0 +1,6 @@
+import React from 'react';
+import { type AlignmentAlgorithm } from '../../ProteinView/types';
+export default function SequenceMismatchNotice({ alignmentAlgorithm, onAlignmentAlgorithmChange, }: {
+    alignmentAlgorithm: AlignmentAlgorithm;
+    onAlignmentAlgorithmChange: (algorithm: AlignmentAlgorithm) => void;
+}): React.JSX.Element;

package/dist/LaunchProteinView/components/SequenceMismatchNotice.js ADDED Viewed

@@ -0,0 +1,14 @@
+import React from 'react';
+import { Typography } from '@mui/material';
+import AlignmentSettingsButton from './AlignmentSettingsButton';
+import { ALIGNMENT_ALGORITHM_LABELS, } from '../../ProteinView/types';
+export default function SequenceMismatchNotice({ alignmentAlgorithm, onAlignmentAlgorithmChange, }) {
+    return (React.createElement(Typography, { variant: "body2", sx: { mr: 2, display: 'flex', alignItems: 'center' } },
+        "Transcript and structure sequences differ, will run",
+        ' ',
+        ALIGNMENT_ALGORITHM_LABELS[alignmentAlgorithm] ?? alignmentAlgorithm,
+        ' ',
+        "alignment",
+        React.createElement(AlignmentSettingsButton, { value: alignmentAlgorithm, onChange: onAlignmentAlgorithmChange })));
+}
+//# sourceMappingURL=SequenceMismatchNotice.js.map

package/dist/LaunchProteinView/components/SequenceMismatchNotice.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"SequenceMismatchNotice.js","sourceRoot":"","sources":["../../../src/LaunchProteinView/components/SequenceMismatchNotice.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,OAAO,uBAAuB,MAAM,2BAA2B,CAAA;AAC/D,OAAO,EACL,0BAA0B,GAE3B,MAAM,yBAAyB,CAAA;AAEhC,MAAM,CAAC,OAAO,UAAU,sBAAsB,CAAC,EAC7C,kBAAkB,EAClB,0BAA0B,GAI3B;IACC,OAAO,CACL,oBAAC,UAAU,IACT,OAAO,EAAC,OAAO,EACf,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,EAAE,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE;;QAEA,GAAG;QACtD,0BAA0B,CAAC,kBAAkB,CAAC,IAAI,kBAAkB;QAAE,GAAG;;QAE1E,oBAAC,uBAAuB,IACtB,KAAK,EAAE,kBAAkB,EACzB,QAAQ,EAAE,0BAA0B,GACpC,CACS,CACd,CAAA;AACH,CAAC"}

package/dist/LaunchProteinView/components/UserProvidedStructure.js CHANGED Viewed

@@ -4,17 +4,16 @@ import { getContainingView, getSession } from '@jbrowse/core/util';
 import { Button, DialogActions, DialogContent, FormControl, FormControlLabel, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import AlignmentSettingsButton from './AlignmentSettingsButton';
 import HelpButton from './HelpButton';
 import MSATable from './MSATable';
+import SequenceMismatchNotice from './SequenceMismatchNotice';
 import TranscriptSelector from './TranscriptSelector';
-import { ALIGNMENT_ALGORITHM_LABELS } from '../../ProteinView/types';
 import ExternalLink from '../../components/ExternalLink';
 import useIsoformProteinSequences from '../hooks/useIsoformProteinSequences';
 import useLocalStructureFileSequence from '../hooks/useLocalStructureFileSequence';
 import useRemoteStructureFileSequence from '../hooks/useRemoteStructureFileSequence';
 import useTranscriptSelection from '../hooks/useTranscriptSelection';
-import { launch3DProteinView } from '../utils/launchViewUtils';
+import { getPdbStructureUrl, launch3DProteinView, } from '../utils/launchViewUtils';
 import { getGeneDisplayName, getId, getTranscriptDisplayName, getTranscriptFeatures, stripStopCodon, } from '../utils/util';
 const useStyles = makeStyles()(theme => ({
     dialogContent: {
@@ -60,6 +59,34 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
     const selectedTranscript = options.find(val => getId(val) === userSelection);
     const protein = userSelection ? isoformSequences?.[userSelection] : undefined;
     const error = isoformError ?? submitError ?? localFileError ?? remoteFileError;
+    const canLaunch = !!(structureURL || file) && !!protein && !!selectedTranscript;
+    const sequencesDiffer = !!protein?.seq &&
+        !!structureSequence &&
+        stripStopCodon(protein.seq) !== structureSequence;
+    const handleLaunch = async () => {
+        if (!protein || !selectedTranscript || !(structureURL || file)) {
+            return;
+        }
+        try {
+            const structureData = file ? await file.text() : undefined;
+            launch3DProteinView({
+                session,
+                view,
+                feature,
+                selectedTranscript,
+                url: structureURL || undefined,
+                data: structureData,
+                userProvidedTranscriptSequence: protein.seq,
+                alignmentAlgorithm,
+                displayName: `Protein view ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
+            });
+            handleClose();
+        }
+        catch (e) {
+            console.error(e);
+            setSubmitError(e);
+        }
+    };
     return (React.createElement(React.Fragment, null,
         React.createElement(DialogContent, { className: classes.dialogContent },
             error ? React.createElement(ErrorMessage, { error: error }) : null,
@@ -93,7 +120,7 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
                 choice === 'pdb' ? (React.createElement(TextField, { value: pdbId, onChange: event => {
                         const s = event.target.value;
                         setPdbId(s);
-                        setStructureURL(`https://files.rcsb.org/download/${s}.cif`);
+                        setStructureURL(getPdbStructureUrl(s));
                     }, label: "PDB ID" })) : null),
             React.createElement("div", { style: { margin: 20 } }, isoformSequences ? (structureSequence ? (React.createElement(React.Fragment, null,
                 React.createElement(TranscriptSelector, { val: userSelection, setVal: setUserSelection, structureSequence: structureSequence, isoforms: options, feature: feature, isoformSequences: isoformSequences }),
@@ -105,43 +132,12 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
                         : 'Show all isoform protein sequences'),
                     showAllProteinSequences ? (React.createElement(MSATable, { structureSequence: structureSequence, structureName: structureName, isoformSequences: isoformSequences })) : null))) : null) : (React.createElement(LoadingEllipses, { title: "Loading protein sequences", variant: "h6" })))),
         React.createElement(DialogActions, null,
-            protein?.seq &&
-                structureSequence &&
-                stripStopCodon(protein.seq) !== structureSequence ? (React.createElement(Typography, { variant: "body2", sx: { mr: 2, display: 'flex', alignItems: 'center' } },
-                "Transcript and structure sequences differ, will run",
-                ' ',
-                ALIGNMENT_ALGORITHM_LABELS[alignmentAlgorithm] ??
-                    alignmentAlgorithm,
-                ' ',
-                "alignment",
-                React.createElement(AlignmentSettingsButton, { value: alignmentAlgorithm, onChange: onAlignmentAlgorithmChange }))) : null,
+            sequencesDiffer ? (React.createElement(SequenceMismatchNotice, { alignmentAlgorithm: alignmentAlgorithm, onAlignmentAlgorithmChange: onAlignmentAlgorithmChange })) : null,
             React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
                     handleClose();
                 } }, "Cancel"),
-            React.createElement(Button, { variant: "contained", color: "primary", disabled: !(structureURL || file) || !protein || !selectedTranscript, onClick: () => {
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                    ;
-                    (async () => {
-                        try {
-                            const structureData = file ? await file.text() : undefined;
-                            launch3DProteinView({
-                                session,
-                                view,
-                                feature,
-                                selectedTranscript,
-                                url: structureURL || undefined,
-                                data: structureData,
-                                userProvidedTranscriptSequence: protein?.seq ?? '',
-                                alignmentAlgorithm,
-                                displayName: `Protein view ${getGeneDisplayName(feature)} - ${getTranscriptDisplayName(selectedTranscript)}`,
-                            });
-                            handleClose();
-                        }
-                        catch (e) {
-                            console.error(e);
-                            setSubmitError(e);
-                        }
-                    })();
+            React.createElement(Button, { variant: "contained", color: "primary", disabled: !canLaunch, onClick: () => {
+                    void handleLaunch();
                 } }, "Launch 3-D protein structure view"))));
 });
 export default UserProvidedStructure;

package/dist/LaunchProteinView/components/UserProvidedStructure.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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