jbrowse-plugin-protein3d 0.8.1 → 0.8.3

package/dist/LaunchProteinView/components/AlignmentSettingsButton.js

@@ -42,7 +42,7 @@ export default function AlignmentSettingsButton({ value, onChange, onManualAlign
         React.createElement(IconButton, { onClick: handleOpen, size: "small", title: "Alignment settings" },
             React.createElement(SettingsIcon, null)),
         React.createElement(Dialog, { open: open, onClose: handleCancel, maxWidth: "sm", fullWidth: true },
-            React.createElement(DialogTitle, null, "Alignment Settings"),
+            React.createElement(DialogTitle, null, "Alignment settings"),
             React.createElement(DialogContent, null,
                 React.createElement(Tabs, { value: tabValue, onChange: (_, val) => {
                         setTabValue(val);
@@ -71,5 +71,5 @@ b  MKAAYLSMFGKEDHKPFGD`, value: manualAlignment, onChange: e => {
                     parseError ? (React.createElement(Typography, { color: "error", variant: "body2", sx: { mt: 1 } }, parseError)) : null))),
             React.createElement(DialogActions, null,
                 React.createElement(Button, { onClick: handleCancel }, "Cancel"),
-                React.createElement(Button, { onClick: handleSave, variant: "contained", color: "primary", disabled: tabValue === 1 && !manualAlignment.trim() }, tabValue === 0 ? 'Save' : 'Apply Alignment')))));
+                React.createElement(Button, { onClick: handleSave, variant: "contained", color: "primary", disabled: tabValue === 1 && !manualAlignment.trim() }, tabValue === 0 ? 'Save' : 'Apply alignment')))));
 }

package/dist/LaunchProteinView/components/FoldseekActionMenu.js

@@ -3,7 +3,7 @@ import { ErrorMessage } from '@jbrowse/core/ui';
 import { Button, Menu, MenuItem } from '@mui/material';
 import { useSafeLaunch } from '../hooks/useSafeLaunch';
 import { caCoordsToPdb, hasValidCaCoords } from '../utils/caCoordsToPdb';
-import { getConditionalProteinLaunches, launch3DProteinView, } from '../utils/launchViewUtils';
+import { PROTEIN_LAUNCH_LABELS, getConditionalProteinLaunches, launch3DProteinView, } from '../utils/launchViewUtils';
 import { getConfidenceUrlFromTarget, getUniprotIdFromAlphaFoldTarget, } from '../utils/structureUrls';
 export default function FoldseekActionMenu({ hit, session, view, feature, selectedTranscript, userProvidedTranscriptSequence, onClose, }) {
     const [anchorEl, setAnchorEl] = useState(null);
@@ -41,7 +41,7 @@ export default function FoldseekActionMenu({ hit, session, view, feature, select
         launchError ? React.createElement(ErrorMessage, { error: launchError }) : null,
         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"),
-            launch1D ? (React.createElement(MenuItem, { onClick: runLaunch(launch1D) }, "Launch 1D protein annotation view")) : null,
-            launchMsa ? (React.createElement(MenuItem, { onClick: runLaunch(launchMsa) }, "Launch MSA view (AlphaFoldDB a3m)")) : null)));
+            React.createElement(MenuItem, { "data-testid": "protein-launch-option-3d", onClick: handleLaunch3D }, PROTEIN_LAUNCH_LABELS['3d']),
+            launch1D ? (React.createElement(MenuItem, { "data-testid": "protein-launch-option-1d", onClick: runLaunch(launch1D) }, PROTEIN_LAUNCH_LABELS['1d'])) : null,
+            launchMsa ? (React.createElement(MenuItem, { "data-testid": "protein-launch-option-msa", onClick: runLaunch(launchMsa) }, PROTEIN_LAUNCH_LABELS.msa)) : null)));
 }

package/dist/LaunchProteinView/components/LaunchOptionsDialog.js

@@ -1,10 +1,10 @@
 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 },
+    return (React.createElement(Dialog, { open: open, onClose: onClose, "data-testid": "protein-launch-options-dialog" },
         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(MenuList, null, options.map(opt => (React.createElement(MenuItem, { key: opt.key, "data-testid": `protein-launch-option-${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)))))))));

package/dist/LaunchProteinView/components/LaunchProteinViewDialog.js

@@ -14,7 +14,7 @@ export default function LaunchProteinViewDialog({ handleClose, feature, model, }
     const [alignmentAlgorithm, setAlignmentAlgorithm] = useLocalStorage('jbrowse-protein3d-alignment-algorithm', DEFAULT_ALIGNMENT_ALGORITHM);
     const session = getSession(model);
     const view = getContainingView(model);
-    return (React.createElement(Dialog, { maxWidth: "xl", title: "Launch protein view", titleNode: React.createElement(React.Fragment, null,
+    return (React.createElement(Dialog, { "data-testid": "launch-protein-view-dialog", maxWidth: "xl", title: "Launch protein view", titleNode: React.createElement(React.Fragment, null,
             "Launch protein view ",
             React.createElement(HelpButton, null)), open: true, onClose: handleClose },
         React.createElement(Tabs, { value: choice, onChange: (_, val) => {

package/dist/LaunchProteinView/components/ProteinViewActions.js

@@ -8,7 +8,7 @@ import LaunchSettingsDialog from './LaunchSettingsDialog';
 import SequenceMismatchNotice from './SequenceMismatchNotice';
 import { useSafeLaunch } from '../hooks/useSafeLaunch';
 import { getLaunchMissingReasons } from '../utils/launchHelpers';
-import { getConditionalProteinLaunches, launch3DProteinView, launch3DProteinViewWithMsa, } from '../utils/launchViewUtils';
+import { PROTEIN_LAUNCH_LABELS, getConditionalProteinLaunches, launch3DProteinView, launch3DProteinViewWithMsa, } from '../utils/launchViewUtils';
 export default function ProteinViewActions({ handleClose, uniprotId, userSelectedProteinSequence, selectedTranscript, url, confidenceUrl, feature, view, session, alignmentAlgorithm, onAlignmentAlgorithmChange, sequencesMatch, isLoading, error, }) {
     const [dialogOpen, setDialogOpen] = useState(false);
     const [settingsOpen, setSettingsOpen] = useState(false);
@@ -51,7 +51,7 @@ export default function ProteinViewActions({ handleClose, uniprotId, userSelecte
     const launchOptions = [
         {
             key: '3d',
-            title: 'Launch 3D protein structure view',
+            title: PROTEIN_LAUNCH_LABELS['3d'],
             description: 'View protein structure with genome-to-structure coordinate mapping',
             onClick: handleLaunch3DView,
         },
@@ -59,7 +59,7 @@ export default function ProteinViewActions({ handleClose, uniprotId, userSelecte
             ? [
                 {
                     key: '1d',
-                    title: 'Launch 1D protein annotation view',
+                    title: PROTEIN_LAUNCH_LABELS['1d'],
                     description: 'View protein features and annotations as a linear track',
                     onClick: runLaunch(launch1D),
                 },
@@ -69,13 +69,13 @@ export default function ProteinViewActions({ handleClose, uniprotId, userSelecte
             ? [
                 {
                     key: 'msa',
-                    title: 'Launch MSA view',
+                    title: PROTEIN_LAUNCH_LABELS.msa,
                     description: 'View AlphaFold a3m multiple sequence alignment',
                     onClick: runLaunch(launchMsa),
                 },
                 {
                     key: '3d-msa',
-                    title: 'Launch 3D structure + MSA view',
+                    title: PROTEIN_LAUNCH_LABELS['3d-msa'],
                     description: 'Launch both views with AlphaFold a3m MSA',
                     onClick: runLaunch(() => launch3DProteinViewWithMsa(launch3DParams)),
                 },
@@ -95,8 +95,8 @@ export default function ProteinViewActions({ handleClose, uniprotId, userSelecte
             } }, "Cancel"),
         showMissingReasons ? (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: () => {
+            React.createElement(Button, { "data-testid": "protein-launch-button", disabled: !canLaunch, onClick: handleLaunch3DView }, "Launch"),
+            React.createElement(Button, { "data-testid": "protein-launch-options-button", disabled: !canLaunch, onClick: () => {
                     setDialogOpen(true);
                 }, "aria-label": "More launch options" },
                 React.createElement(ArrowDropDownIcon, null))),

package/dist/LaunchProteinView/components/StructureSourcePicker.js

@@ -22,7 +22,7 @@ export default function StructureSourcePicker({ choice, setChoice, structureURL,
         choice === 'file' ? (React.createElement("div", { style: { paddingTop: 20 } },
             React.createElement(Typography, null, "Open a PDB/mmCIF/etc. file from your local drive"),
             React.createElement(Button, { variant: "outlined", component: "label" },
-                "Choose File",
+                "Choose file",
                 React.createElement("input", { type: "file", hidden: true, onChange: ({ target }) => {
                         const f = target.files?.[0];
                         if (f) {

package/dist/LaunchProteinView/components/UserProvidedStructure.js

@@ -79,6 +79,6 @@ const UserProvidedStructure = observer(function UserProvidedStructure({ feature,
                 } }, "Cancel"),
             React.createElement(Button, { variant: "contained", color: "primary", disabled: !canLaunch, onClick: () => {
                     handleLaunch();
-                } }, "Launch 3-D protein structure view"))));
+                } }, "Launch 3D protein structure view"))));
 });
 export default UserProvidedStructure;

package/dist/LaunchProteinView/index.js

@@ -61,12 +61,16 @@ function launchProteinView(self, target) {
 }
 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(),
+                    ...superContextMenuItems.call(self),
                     ...(target && PROTEIN_FEATURE_TYPES.includes(target.type)
                         ? [
                             {

package/dist/LaunchProteinView/utils/launchViewUtils.d.ts

@@ -25,6 +25,12 @@ export declare function launch3DProteinView({ session, view, feature, selectedTr
     connectedMsaViewId?: string;
     sideBySide?: boolean;
 }): import("@jbrowse/core/util").AbstractViewModel;
+export declare const PROTEIN_LAUNCH_LABELS: {
+    readonly '3d': "Launch 3D protein structure view";
+    readonly '1d': "Launch 1D protein annotation view";
+    readonly msa: "Launch MSA view (AlphaFold a3m)";
+    readonly '3d-msa': "Launch 3D structure + MSA view";
+};
 export declare function getConditionalProteinLaunches({ session, view, feature, selectedTranscript, uniprotId, confidenceUrl, }: LaunchViewParams & {
     confidenceUrl?: string;
 }): {

package/dist/LaunchProteinView/utils/launchViewUtils.js

@@ -77,6 +77,23 @@ function launchMsaView({ session, view, feature, selectedTranscript, uniprotId,
 function hasMsaViewPlugin() {
     return window.JBrowsePluginMsaView !== undefined;
 }
+// What the launches below are CALLED, shared for the same reason their
+// availability is: the AlphaFold and Foldseek menus offer the same three
+// actions, and had drifted to different names for two of them ("Launch 3D
+// protein structure view" vs "Launch 3D protein view", and an MSA item that
+// named its source on one menu and not the other). Two names for one action
+// reads as two actions.
+//
+// The MSA item says "(AlphaFold a3m)" rather than a bare "Launch MSA view"
+// because msaview contributes a gene right-click item by that exact name, and
+// the two build different things: msaview's is one row per species from NCBI's
+// orthologs, this one is the deep unlabelled alignment AlphaFold folded from.
+export const PROTEIN_LAUNCH_LABELS = {
+    '3d': 'Launch 3D protein structure view',
+    '1d': 'Launch 1D protein annotation view',
+    msa: 'Launch MSA view (AlphaFold a3m)',
+    '3d-msa': 'Launch 3D structure + MSA view',
+};
 // The 1D-annotation and MSA launches share identical availability rules across
 // the AlphaFold and Foldseek launch menus: the 1D view needs an add-tracks
 // session and a uniprotId, the MSA view needs the msaview plugin and a

package/dist/ProteinView/components/AddStructureDialog.js

@@ -50,7 +50,7 @@ const AddStructureDialog = observer(function AddStructureDialog({ model, }) {
         (choice === 'pdb' && pdbId !== '') ||
         (choice === 'uniprot' && uniprotId !== '');
     return (React.createElement(Dialog, { open: true, onClose: handleClose, maxWidth: "sm", fullWidth: true },
-        React.createElement(DialogTitle, null, "Add Structure"),
+        React.createElement(DialogTitle, null, "Add structure"),
         React.createElement(DialogContent, null,
             error ? React.createElement(ErrorMessage, { error: error }) : null,
             React.createElement(Typography, { variant: "body2", color: "text.secondary", sx: { mb: 2 } }, "Add another structure to superpose on the existing structure(s)."),
@@ -73,7 +73,7 @@ const AddStructureDialog = observer(function AddStructureDialog({ model, }) {
                 }, placeholder: "https://files.rcsb.org/download/1CRN.cif", sx: { mb: 2 } })) : null,
             choice === 'file' ? (React.createElement("div", { style: { marginBottom: 16 } },
                 React.createElement(Button, { variant: "outlined", component: "label" },
-                    file ? file.name : 'Choose File',
+                    file ? file.name : 'Choose file',
                     React.createElement("input", { type: "file", hidden: true, accept: ".pdb,.cif,.mmcif,.ent", onChange: ({ target }) => {
                             const f = target.files?.[0];
                             if (f) {
@@ -90,6 +90,6 @@ const AddStructureDialog = observer(function AddStructureDialog({ model, }) {
                 } }, "Cancel"),
             React.createElement(Button, { onClick: () => {
                     void handleAdd();
-                }, variant: "contained", color: "primary", disabled: !canAdd }, "Add Structure"))));
+                }, variant: "contained", color: "primary", disabled: !canAdd }, "Add structure"))));
 });
 export default AddStructureDialog;

package/dist/ProteinView/components/ManualAlignmentDialog.js

@@ -42,7 +42,7 @@ const ManualAlignmentDialog = observer(function ManualAlignmentDialog({ model, }
         return null;
     }
     return (React.createElement(Dialog, { open: true, onClose: handleClose, maxWidth: "md", fullWidth: true },
-        React.createElement(DialogTitle, null, "Import Manual Alignment"),
+        React.createElement(DialogTitle, null, "Import manual alignment"),
         React.createElement(DialogContent, null,
             React.createElement(Typography, { variant: "body2", color: "text.secondary", sx: { mb: 2 } }, "Paste a pre-computed alignment in Clustal format. The first sequence should be the transcript and the second should be the structure."),
             React.createElement(TextField, { multiline: true, rows: 12, fullWidth: true, placeholder: `Example:
@@ -61,6 +61,6 @@ structure   MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAG`, value: alignment, onChange:
                 } }, "Cancel"),
             React.createElement(Button, { onClick: () => {
                     handleApply();
-                }, variant: "contained", color: "primary", disabled: !alignment.trim() }, "Apply Alignment"))));
+                }, variant: "contained", color: "primary", disabled: !alignment.trim() }, "Apply alignment"))));
 });
 export default ManualAlignmentDialog;

package/dist/ProteinView/components/ProteinAlignment.js

@@ -10,7 +10,7 @@ import ResidueValueTrack from './ResidueValueTrack';
 import SplitString, { AlignmentHighlights } from './SplitString';
 import { uniprotEntryUrl } from '../../LaunchProteinView/utils/structureUrls';
 import ExternalLink from '../../components/ExternalLink';
-import { structureAlignedSeq, transcriptAlignedSeq, } from '../../mappings';
+import { structureAlignedSeq, transcriptAlignedSeq } from '../../mappings';
 import { largeJumpScrollTarget, offScreenCenterTarget } from '../autoScroll';
 import { CHAR_WIDTH, LABEL_WIDTH, ROW_HEIGHT } from '../constants';
 import useProteinFeatureTrackData from '../hooks/useProteinFeatureTrackData';

package/dist/ProteinView/components/ProteinView.js

@@ -29,7 +29,7 @@ const ProteinViewContainer = observer(function ProteinViewContainer({ model, par
     return (React.createElement("div", { style: { background: '#ccc' }, "data-testid": ready ? 'protein-view-ready' : 'protein-view-loading' },
         error ? React.createElement(ErrorMessage, { error: error }) : null,
         loading ? (React.createElement(LoadingEllipses, { message: "Loading protein viewer" })) : (React.createElement(ProteinViewHeader, { model: model })),
-        React.createElement("div", { ref: parentRef, style: {
+        React.createElement("div", { ref: parentRef, "data-testid": "protein-view-molstar", style: {
                 position: 'relative',
                 width,
                 height,

package/dist/ProteinView/model.d.ts

@@ -38,7 +38,9 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
             end: number;
         } | undefined;
         hoverPosition: {
-            structureSeqPos?: number;
+            structureSeqPos? /**
+             * #action
+             */: number;
             code?: string;
             chain?: string;
             source: "structure" | "genome";
@@ -780,7 +782,9 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
             end: number;
         } | undefined;
         hoverPosition: {
-            structureSeqPos?: number;
+            structureSeqPos? /**
+             * #action
+             */: number;
             code?: string;
             chain?: string;
             source: "structure" | "genome";
@@ -1414,7 +1418,9 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
             end: number;
         } | undefined;
         hoverPosition: {
-            structureSeqPos?: number;
+            structureSeqPos? /**
+             * #action
+             */: number;
             code?: string;
             chain?: string;
             source: "structure" | "genome";

package/dist/ProteinView/structureFormat.js

@@ -31,9 +31,7 @@ export function structureFileExtension(nameOrUrl) {
  * hand out `.cif`).
  */
 export function structureFormatFromName(nameOrUrl) {
-    return PDB_EXTENSIONS.has(structureFileExtension(nameOrUrl))
-        ? 'pdb'
-        : 'mmcif';
+    return PDB_EXTENSIONS.has(structureFileExtension(nameOrUrl)) ? 'pdb' : 'mmcif';
 }
 /** Whether a URL points at a binary-encoded structure, which molstar must be
  * told to download as bytes rather than text. */

package/dist/ProteinView/structureModel.js

@@ -13,7 +13,7 @@ import subscribeMolstarInteraction from './subscribeMolstarInteraction';
 import { genomeHoverToTranscriptPos } from './util';
 import { getUniprotIdFromAlphaFoldTarget, resolveStructureUrl, } from '../LaunchProteinView/utils/structureUrls';
 import { stripStopCodon } from '../LaunchProteinView/utils/util';
-import { alignmentLength, genomeToTranscriptSeqMapping, } from '../mappings';
+import { alignmentLength, genomeToTranscriptSeqMapping } from '../mappings';
 import { makeLabelSeqIdIndex, rangeToLabelSeqIds, toLabelSeqIds, } from './extractStructureSequences';
 const Structure = types
     .model({