@jbrowse/plugin-linear-genome-view 3.5.0 → 3.6.0

package/dist/BaseLinearDisplay/components/BaseLinearDisplay.js

@@ -8,7 +8,6 @@ const jsx_runtime_1 = require("react/jsx-runtime");
 const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
 const LinearBlocks_1 = __importDefault(require("./LinearBlocks"));
@@ -23,7 +22,6 @@ const useStyles = (0, mui_1.makeStyles)()({
 });
 const BaseLinearDisplay = (0, mobx_react_1.observer)(function (props) {
     const { classes } = useStyles();
-    const theme = (0, material_1.useTheme)();
     const ref = (0, react_1.useRef)(null);
     const [clientRect, setClientRect] = (0, react_1.useState)();
     const [offsetMouseCoord, setOffsetMouseCoord] = (0, react_1.useState)([0, 0]);
@@ -32,6 +30,7 @@ const BaseLinearDisplay = (0, mobx_react_1.observer)(function (props) {
     const { model, children } = props;
     const { TooltipComponent, DisplayMessageComponent, height } = model;
     const items = model.contextMenuItems();
+    const open = Boolean(contextCoord) && items.length > 0;
     return ((0, jsx_runtime_1.jsxs)("div", { ref: ref, "data-testid": `display-${(0, configuration_1.getConf)(model, 'displayId')}`, className: classes.display, onContextMenu: event => {
             event.preventDefault();
             if (contextCoord) {
@@ -49,7 +48,7 @@ const BaseLinearDisplay = (0, mobx_react_1.observer)(function (props) {
             setOffsetMouseCoord([event.clientX - left, event.clientY - top]);
             setClientMouseCoord([event.clientX, event.clientY]);
             setClientRect(rect);
-        }, children: [DisplayMessageComponent ? ((0, jsx_runtime_1.jsx)(DisplayMessageComponent, { model: model })) : ((0, jsx_runtime_1.jsx)(LinearBlocks_1.default, { ...props })), children, (0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: null, children: (0, jsx_runtime_1.jsx)(TooltipComponent, { model: model, height: height, offsetMouseCoord: offsetMouseCoord, clientMouseCoord: clientMouseCoord, clientRect: clientRect, mouseCoord: offsetMouseCoord }) }), (0, jsx_runtime_1.jsx)(ui_1.Menu, { open: Boolean(contextCoord) && items.length > 0, onMenuItemClick: (_, callback) => {
+        }, children: [DisplayMessageComponent ? ((0, jsx_runtime_1.jsx)(DisplayMessageComponent, { model: model })) : ((0, jsx_runtime_1.jsx)(LinearBlocks_1.default, { ...props })), children, (0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: null, children: (0, jsx_runtime_1.jsx)(TooltipComponent, { model: model, height: height, offsetMouseCoord: offsetMouseCoord, clientMouseCoord: clientMouseCoord, clientRect: clientRect, mouseCoord: offsetMouseCoord }) }), open ? ((0, jsx_runtime_1.jsx)(ui_1.Menu, { open: true, onMenuItemClick: (_, callback) => {
                     callback();
                     setContextCoord(undefined);
                 }, onClose: () => {
@@ -64,9 +63,7 @@ const BaseLinearDisplay = (0, mobx_react_1.observer)(function (props) {
                     },
                 }, anchorReference: "anchorPosition", anchorPosition: contextCoord
                     ? { top: contextCoord[1], left: contextCoord[0] }
-                    : undefined, style: {
-                    zIndex: theme.zIndex.tooltip,
-                }, menuItems: items })] }));
+                    : undefined, menuItems: items })) : null] }));
 });
 exports.default = BaseLinearDisplay;
 var Tooltip_1 = require("./Tooltip");

package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -197,6 +197,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     readonly renderDelay: number;
     readonly TooltipComponent: AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: Feature): void;
 } & {
     readonly features: CompositeMap<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;

package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -44,7 +44,9 @@ const util_1 = require("@jbrowse/core/util");
 const compositeMap_1 = __importDefault(require("@jbrowse/core/util/compositeMap"));
 const tracks_1 = require("@jbrowse/core/util/tracks");
 const CenterFocusStrong_1 = __importDefault(require("@mui/icons-material/CenterFocusStrong"));
+const ContentCopy_1 = __importDefault(require("@mui/icons-material/ContentCopy"));
 const MenuOpen_1 = __importDefault(require("@mui/icons-material/MenuOpen"));
+const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 const mobx_1 = require("mobx");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const FeatureDensityMixin_1 = __importDefault(require("./FeatureDensityMixin"));
@@ -93,6 +95,12 @@ function stateModelFactory() {
             }
             return undefined;
         },
+        copyInfoToClipboard(feature) {
+            const { uniqueId, ...rest } = feature.toJSON();
+            const session = (0, util_1.getSession)(self);
+            (0, copy_to_clipboard_1.default)(JSON.stringify(rest, null, 4));
+            session.notify('Copied to clipboard', 'success');
+        },
     }))
         .views(self => ({
         get features() {
@@ -205,30 +213,32 @@ function stateModelFactory() {
             return [];
         },
         contextMenuItems() {
-            return [
-                ...(self.contextMenuFeature
-                    ? [
-                        {
-                            label: 'Open feature details',
-                            icon: MenuOpen_1.default,
-                            onClick: () => {
-                                if (self.contextMenuFeature) {
-                                    self.selectFeature(self.contextMenuFeature);
-                                }
-                            },
+            const feat = self.contextMenuFeature;
+            return feat
+                ? [
+                    {
+                        label: 'Open feature details',
+                        icon: MenuOpen_1.default,
+                        onClick: () => {
+                            self.selectFeature(feat);
+                        },
+                    },
+                    {
+                        label: 'Zoom to feature',
+                        icon: CenterFocusStrong_1.default,
+                        onClick: () => {
+                            self.navToFeature(feat);
                         },
-                        {
-                            label: 'Zoom to feature',
-                            icon: CenterFocusStrong_1.default,
-                            onClick: () => {
-                                if (self.contextMenuFeature) {
-                                    self.navToFeature(self.contextMenuFeature);
-                                }
-                            },
+                    },
+                    {
+                        label: 'Copy info to clipboard',
+                        icon: ContentCopy_1.default,
+                        onClick: () => {
+                            self.copyInfoToClipboard(feat);
                         },
-                    ]
-                    : []),
-            ];
+                    },
+                ]
+                : [];
         },
         renderProps() {
             return {

package/dist/LinearBareDisplay/model.d.ts

@@ -181,6 +181,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;

package/dist/LinearBasicDisplay/model.d.ts

@@ -189,6 +189,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;

package/dist/LinearGenomeView/components/GetSequenceDialog.d.ts

@@ -1,7 +1,6 @@
 import type { LinearGenomeViewModel } from '..';
-type LGV = LinearGenomeViewModel;
 declare const GetSequenceDialog: ({ model, handleClose, }: {
-    model: LGV;
+    model: LinearGenomeViewModel;
     handleClose: () => void;
 }) => import("react/jsx-runtime").JSX.Element;
 export default GetSequenceDialog;

package/dist/LinearGenomeView/components/GetSequenceDialog.js

@@ -5,17 +5,17 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const jsx_runtime_1 = require("react/jsx-runtime");
 const react_1 = require("react");
-const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
-const Icons_1 = require("@jbrowse/core/ui/Icons");
 const util_1 = require("@jbrowse/core/util");
 const formatFastaStrings_1 = require("@jbrowse/core/util/formatFastaStrings");
+const ContentCopy_1 = __importDefault(require("@mui/icons-material/ContentCopy"));
 const GetApp_1 = __importDefault(require("@mui/icons-material/GetApp"));
 const material_1 = require("@mui/material");
 const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 const file_saver_1 = require("file-saver");
 const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
+const fetchSequence_1 = require("./fetchSequence");
 const useStyles = (0, mui_1.makeStyles)()({
     dialogContent: {
         width: '80em',
@@ -27,30 +27,6 @@ const useStyles = (0, mui_1.makeStyles)()({
         marginLeft: 10,
     },
 });
-async function fetchSequence(model, regions) {
-    const session = (0, util_1.getSession)(model);
-    const { leftOffset, rightOffset } = model;
-    if (!leftOffset || !rightOffset) {
-        throw new Error('no offsets on model to use for range');
-    }
-    const assemblyNames = new Set(regions.map(r => r.assemblyName));
-    if (assemblyNames.size > 1) {
-        throw new Error('not able to fetch sequences from multiple assemblies currently');
-    }
-    const { rpcManager, assemblyManager } = session;
-    const assemblyName = leftOffset.assemblyName || rightOffset.assemblyName || '';
-    const assembly = assemblyManager.get(assemblyName);
-    if (!assembly) {
-        throw new Error(`assembly ${assemblyName} not found`);
-    }
-    const adapterConfig = (0, configuration_1.getConf)(assembly, ['sequence', 'adapter']);
-    const sessionId = 'getSequence';
-    return rpcManager.call(sessionId, 'CoreGetFeatures', {
-        adapterConfig,
-        regions,
-        sessionId,
-    });
-}
 const GetSequenceDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
     const { classes } = useStyles();
     const [error, setError] = (0, react_1.useState)();
@@ -59,7 +35,7 @@ const GetSequenceDialog = (0, mobx_react_1.observer)(function ({ model, handleCl
     const [copied, setCopied] = (0, react_1.useState)(false);
     const [comp, setComplement] = (0, react_1.useState)(false);
     const { leftOffset, rightOffset } = model;
-    const loading = Boolean(sequenceChunks === undefined);
+    const loading = sequenceChunks === undefined;
     (0, react_1.useEffect)(() => {
         const controller = new AbortController();
         (async () => {
@@ -68,8 +44,7 @@ const GetSequenceDialog = (0, mobx_react_1.observer)(function ({ model, handleCl
                 if (selection.length === 0) {
                     throw new Error('Selected region is out of bounds');
                 }
-                const chunks = await fetchSequence(model, selection);
-                setSequenceChunks(chunks);
+                setSequenceChunks(await (0, fetchSequence_1.fetchSequence)(model, selection));
             }
             catch (e) {
                 console.error(e);
@@ -106,7 +81,7 @@ const GetSequenceDialog = (0, mobx_react_1.observer)(function ({ model, handleCl
     return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: () => {
             handleClose();
             model.setOffsets();
-        }, title: "Reference sequence", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [error ? ((0, jsx_runtime_1.jsx)(material_1.Typography, { color: "error", children: `${error}` })) : loading ? ((0, jsx_runtime_1.jsxs)(material_1.Container, { children: ["Retrieving reference sequence...", (0, jsx_runtime_1.jsx)(material_1.CircularProgress, { className: classes.ml, size: 20, disableShrink: true })] })) : null, (0, jsx_runtime_1.jsx)(material_1.TextField, { "data-testid": "rubberband-sequence", variant: "outlined", multiline: true, minRows: 5, maxRows: 10, disabled: sequenceTooLarge, className: classes.dialogContent, fullWidth: true, value: sequenceTooLarge
+        }, title: "Reference sequence", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : loading ? ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { message: "Retrieving sequences" })) : null, (0, jsx_runtime_1.jsx)(material_1.TextField, { "data-testid": "rubberband-sequence", variant: "outlined", multiline: true, minRows: 5, maxRows: 10, disabled: sequenceTooLarge, className: classes.dialogContent, fullWidth: true, value: sequenceTooLarge
                             ? 'Reference sequence too large to display, use the download FASTA button'
                             : sequence, slotProps: {
                             input: {
@@ -125,7 +100,7 @@ const GetSequenceDialog = (0, mobx_react_1.observer)(function ({ model, handleCl
                             setTimeout(() => {
                                 setCopied(false);
                             }, 500);
-                        }, disabled: loading || !!error || sequenceTooLarge, color: "primary", startIcon: (0, jsx_runtime_1.jsx)(Icons_1.ContentCopy, {}), children: copied ? 'Copied' : 'Copy to clipboard' }), (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
+                        }, disabled: loading || !!error || sequenceTooLarge, color: "primary", startIcon: (0, jsx_runtime_1.jsx)(ContentCopy_1.default, {}), children: copied ? 'Copied' : 'Copy to clipboard' }), (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
                             (0, file_saver_1.saveAs)(new Blob([sequence || ''], {
                                 type: 'text/x-fasta;charset=utf-8',
                             }), 'jbrowse_ref_seq.fa');

package/dist/LinearGenomeView/components/RefNameAutocomplete/index.js

@@ -52,38 +52,48 @@ const RefNameAutocomplete = (0, mobx_react_1.observer)(function ({ model, onSele
     const [currentSearch, setCurrentSearch] = (0, react_1.useState)('');
     const [inputValue, setInputValue] = (0, react_1.useState)('');
     const [searchOptions, setSearchOptions] = (0, react_1.useState)();
-    const debouncedSearch = (0, util_1.useDebounce)(currentSearch, 300);
+    const debouncedSearch = (0, util_1.useDebounce)(currentSearch, 50);
     const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined;
     const { coarseVisibleLocStrings, hasDisplayedRegions } = model;
     (0, react_1.useEffect)(() => {
-        ;
+        const isCurrent = { cancelled: false };
         (async () => {
             try {
                 if (debouncedSearch === '' || !assemblyName) {
                     return;
                 }
                 setLoaded(false);
-                setSearchOptions((0, util_2.getDeduplicatedResult)(await fetchResults(debouncedSearch)));
+                const results = await fetchResults(debouncedSearch);
+                if (!isCurrent.cancelled) {
+                    setSearchOptions((0, util_2.getDeduplicatedResult)(results));
+                }
             }
             catch (e) {
                 console.error(e);
-                session.notifyError(`${e}`, e);
+                if (!isCurrent.cancelled) {
+                    session.notifyError(`${e}`, e);
+                }
             }
             finally {
-                setLoaded(true);
+                if (!isCurrent.cancelled) {
+                    setLoaded(true);
+                }
             }
         })();
+        return () => {
+            isCurrent.cancelled = true;
+        };
     }, [assemblyName, fetchResults, debouncedSearch, session]);
     const inputBoxVal = coarseVisibleLocStrings || value || '';
     const regions = assembly === null || assembly === void 0 ? void 0 : assembly.regions;
-    const regionOptions = (regions === null || regions === void 0 ? void 0 : regions.map(region => ({
+    const regionOptions = (0, react_1.useMemo)(() => (regions === null || regions === void 0 ? void 0 : regions.map(region => ({
         result: new BaseResults_1.RefSequenceResult({
             refName: region.refName,
             label: region.refName,
             displayString: region.refName,
             matchedAttribute: 'refName',
         }),
-    }))) || [];
+    }))) || [], [regions]);
     return ((0, jsx_runtime_1.jsx)(material_1.Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: {
             ...style,
             width: Math.min(Math.max((0, util_1.measureText)(inputBoxVal, 14) + 100, minWidth), maxWidth),

package/dist/LinearGenomeView/components/RubberbandTooltip.d.ts

@@ -1,5 +1,5 @@
 export default function RubberbandTooltip({ anchorEl, side, text, }: {
     anchorEl: HTMLSpanElement;
     side: string;
-    text: string;
+    text: React.ReactNode;
 }): import("react/jsx-runtime").JSX.Element;

package/dist/LinearGenomeView/components/RubberbandTooltip.js

@@ -3,26 +3,18 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = RubberbandTooltip;
 const jsx_runtime_1 = require("react/jsx-runtime");
 const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(theme => {
-    return {
-        popover: {
-            mouseEvents: 'none',
-            cursor: 'crosshair',
-        },
-        paper: {
-            paddingLeft: theme.spacing(1),
-            paddingRight: theme.spacing(1),
-        },
-    };
-});
 function RubberbandTooltip({ anchorEl, side, text, }) {
-    const { classes } = useStyles();
-    return ((0, jsx_runtime_1.jsx)(material_1.Popover, { className: classes.popover, classes: { paper: classes.paper }, open: true, anchorEl: anchorEl, anchorOrigin: {
-            vertical: 'top',
-            horizontal: side === 'left' ? 'left' : 'right',
-        }, transformOrigin: {
-            vertical: 'bottom',
-            horizontal: side === 'left' ? 'right' : 'left',
-        }, keepMounted: true, disableRestoreFocus: true, children: (0, jsx_runtime_1.jsx)(material_1.Typography, { children: text }) }));
+    return ((0, jsx_runtime_1.jsx)(material_1.Tooltip, { title: text, open: true, placement: side === 'left' ? 'left-start' : 'right-start', slotProps: {
+            popper: {
+                anchorEl,
+                modifiers: [
+                    {
+                        name: 'offset',
+                        options: {
+                            offset: [-30, -10],
+                        },
+                    },
+                ],
+            },
+        }, children: (0, jsx_runtime_1.jsx)("span", {}) }));
 }

package/dist/LinearGenomeView/components/SearchResultsTable.js

@@ -43,18 +43,34 @@ function SearchResultsTable({ searchResults, assemblyName: optAssemblyName, mode
             session.notify(`${e}`, 'warning');
         }
     }
-    return ((0, jsx_runtime_1.jsx)(material_1.TableContainer, { component: material_1.Paper, children: (0, jsx_runtime_1.jsxs)(material_1.Table, { children: [(0, jsx_runtime_1.jsx)(material_1.TableHead, { children: (0, jsx_runtime_1.jsxs)(material_1.TableRow, { children: [(0, jsx_runtime_1.jsx)(material_1.TableCell, { children: "Name" }), (0, jsx_runtime_1.jsx)(material_1.TableCell, { align: "right", children: "Location" }), (0, jsx_runtime_1.jsx)(material_1.TableCell, { align: "right", children: "Track" }), (0, jsx_runtime_1.jsx)(material_1.TableCell, { align: "right" })] }) }), (0, jsx_runtime_1.jsx)(material_1.TableBody, { children: searchResults.map(result => ((0, jsx_runtime_1.jsxs)(material_1.TableRow, { children: [(0, jsx_runtime_1.jsx)(material_1.TableCell, { component: "th", scope: "row", children: result.getLabel() }), (0, jsx_runtime_1.jsx)(material_1.TableCell, { align: "right", children: result.getLocation() }), (0, jsx_runtime_1.jsx)(material_1.TableCell, { align: "right", children: getTrackName(result.getTrackId()) || 'N/A' }), (0, jsx_runtime_1.jsx)(material_1.TableCell, { align: "right", children: (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: async () => {
-                                        try {
-                                            await handleClick(result.getLocation() || result.getLabel());
-                                            const resultTrackId = result.getTrackId();
-                                            if (resultTrackId) {
-                                                model.showTrack(resultTrackId);
+    return ((0, jsx_runtime_1.jsx)(material_1.TableContainer, { component: material_1.Paper, children: (0, jsx_runtime_1.jsxs)(material_1.Table, { children: [(0, jsx_runtime_1.jsx)(material_1.TableHead, { children: (0, jsx_runtime_1.jsxs)(material_1.TableRow, { children: [(0, jsx_runtime_1.jsx)(material_1.TableCell, { children: "Name" }), (0, jsx_runtime_1.jsx)(material_1.TableCell, { align: "right", children: "Location" }), (0, jsx_runtime_1.jsx)(material_1.TableCell, { align: "right", children: "Track" }), (0, jsx_runtime_1.jsx)(material_1.TableCell, { align: "right" })] }) }), (0, jsx_runtime_1.jsx)(material_1.TableBody, { children: searchResults.map(result => {
+                        const locString = result.getLocation();
+                        let loc;
+                        try {
+                            loc = locString
+                                ? (0, util_1.parseLocString)(locString, refName => assembly.isValidRefName(refName))
+                                : undefined;
+                        }
+                        catch (e) { }
+                        return ((0, jsx_runtime_1.jsxs)(material_1.TableRow, { children: [(0, jsx_runtime_1.jsx)(material_1.TableCell, { component: "th", scope: "row", children: result.getLabel() }), (0, jsx_runtime_1.jsx)(material_1.TableCell, { align: "right", children: loc
+                                        ? (0, util_1.assembleLocString)({
+                                            ...loc,
+                                            refName: assembly.getCanonicalRefName(loc.refName) ||
+                                                loc.refName,
+                                        })
+                                        : locString }), (0, jsx_runtime_1.jsx)(material_1.TableCell, { align: "right", children: getTrackName(result.getTrackId()) || 'N/A' }), (0, jsx_runtime_1.jsx)(material_1.TableCell, { align: "right", children: (0, jsx_runtime_1.jsx)(material_1.Button, { onClick: async () => {
+                                            try {
+                                                await handleClick(result.getLocation() || result.getLabel());
+                                                const resultTrackId = result.getTrackId();
+                                                if (resultTrackId) {
+                                                    model.showTrack(resultTrackId);
+                                                }
                                             }
-                                        }
-                                        catch (e) {
-                                            console.error(e);
-                                            session.notifyError(`${e}`, e);
-                                        }
-                                        handleClose();
-                                    }, color: "primary", variant: "contained", children: "Go" }) })] }, result.getId()))) })] }) }));
+                                            catch (e) {
+                                                console.error(e);
+                                                session.notifyError(`${e}`, e);
+                                            }
+                                            handleClose();
+                                        }, color: "primary", variant: "contained", children: "Go" }) })] }, result.getId()));
+                    }) })] }) }));
 }

package/dist/LinearGenomeView/components/fetchSequence.d.ts

@@ -0,0 +1,4 @@
+import type { LinearGenomeViewModel } from '../model';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
+export declare function fetchSequence(model: LinearGenomeViewModel, regions: Region[]): Promise<Feature[]>;

package/dist/LinearGenomeView/components/fetchSequence.js

@@ -0,0 +1,29 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.fetchSequence = fetchSequence;
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+async function fetchSequence(model, regions) {
+    const session = (0, util_1.getSession)(model);
+    const { leftOffset, rightOffset } = model;
+    if (!leftOffset || !rightOffset) {
+        throw new Error('no offsets on model to use for range');
+    }
+    const assemblyNames = new Set(regions.map(r => r.assemblyName));
+    if (assemblyNames.size > 1) {
+        throw new Error('not able to fetch sequences from multiple assemblies currently');
+    }
+    const { rpcManager, assemblyManager } = session;
+    const assemblyName = leftOffset.assemblyName || rightOffset.assemblyName || '';
+    const assembly = assemblyManager.get(assemblyName);
+    if (!assembly) {
+        throw new Error(`assembly ${assemblyName} not found`);
+    }
+    const adapterConfig = (0, configuration_1.getConf)(assembly, ['sequence', 'adapter']);
+    const sessionId = 'getSequence';
+    return rpcManager.call(sessionId, 'CoreGetFeatures', {
+        adapterConfig,
+        regions,
+        sessionId,
+    });
+}

package/dist/LinearGenomeView/model.d.ts

@@ -58,6 +58,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly width: number;
     readonly interRegionPaddingWidth: number;
     readonly assemblyNames: string[];
+    readonly assemblyDisplayNames: string[];
     readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
     readonly stickyViewHeaders: boolean | undefined;
     readonly rubberbandTop: number;

package/dist/LinearGenomeView/model.js

@@ -136,6 +136,14 @@ function stateModelFactory(pluginManager) {
                 ...new Set(self.displayedRegions.map(region => region.assemblyName)),
             ];
         },
+        get assemblyDisplayNames() {
+            const { assemblyManager } = (0, util_1.getSession)(self);
+            return this.assemblyNames.map(assemblyName => {
+                var _a;
+                const assembly = assemblyManager.get(assemblyName);
+                return (_a = assembly === null || assembly === void 0 ? void 0 : assembly.displayName) !== null && _a !== void 0 ? _a : assemblyName;
+            });
+        },
         get isTopLevelView() {
             const session = (0, util_1.getSession)(self);
             return session.views.find(r => r.id === self.id);
@@ -166,7 +174,7 @@ function stateModelFactory(pluginManager) {
         .views(self => ({
         scaleBarDisplayPrefix() {
             return (0, mobx_state_tree_1.getParent)(self, 2).type === 'LinearSyntenyView'
-                ? self.assemblyNames[0]
+                ? self.assemblyDisplayNames[0]
                 : '';
         },
         MiniControlsComponent() {

package/dist/index.d.ts

@@ -186,6 +186,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             readonly renderDelay: number;
             readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
             readonly selectedFeatureId: string | undefined;
+            copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
         } & {
             readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
             readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;

package/esm/BaseLinearDisplay/components/BaseLinearDisplay.js

@@ -2,7 +2,6 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { Suspense, useRef, useState } from 'react';
 import { getConf } from '@jbrowse/core/configuration';
 import { Menu } from '@jbrowse/core/ui';
-import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import LinearBlocks from './LinearBlocks';
@@ -17,7 +16,6 @@ const useStyles = makeStyles()({
 });
 const BaseLinearDisplay = observer(function (props) {
     const { classes } = useStyles();
-    const theme = useTheme();
     const ref = useRef(null);
     const [clientRect, setClientRect] = useState();
     const [offsetMouseCoord, setOffsetMouseCoord] = useState([0, 0]);
@@ -26,6 +24,7 @@ const BaseLinearDisplay = observer(function (props) {
     const { model, children } = props;
     const { TooltipComponent, DisplayMessageComponent, height } = model;
     const items = model.contextMenuItems();
+    const open = Boolean(contextCoord) && items.length > 0;
     return (_jsxs("div", { ref: ref, "data-testid": `display-${getConf(model, 'displayId')}`, className: classes.display, onContextMenu: event => {
             event.preventDefault();
             if (contextCoord) {
@@ -43,7 +42,7 @@ const BaseLinearDisplay = observer(function (props) {
             setOffsetMouseCoord([event.clientX - left, event.clientY - top]);
             setClientMouseCoord([event.clientX, event.clientY]);
             setClientRect(rect);
-        }, children: [DisplayMessageComponent ? (_jsx(DisplayMessageComponent, { model: model })) : (_jsx(LinearBlocks, { ...props })), children, _jsx(Suspense, { fallback: null, children: _jsx(TooltipComponent, { model: model, height: height, offsetMouseCoord: offsetMouseCoord, clientMouseCoord: clientMouseCoord, clientRect: clientRect, mouseCoord: offsetMouseCoord }) }), _jsx(Menu, { open: Boolean(contextCoord) && items.length > 0, onMenuItemClick: (_, callback) => {
+        }, children: [DisplayMessageComponent ? (_jsx(DisplayMessageComponent, { model: model })) : (_jsx(LinearBlocks, { ...props })), children, _jsx(Suspense, { fallback: null, children: _jsx(TooltipComponent, { model: model, height: height, offsetMouseCoord: offsetMouseCoord, clientMouseCoord: clientMouseCoord, clientRect: clientRect, mouseCoord: offsetMouseCoord }) }), open ? (_jsx(Menu, { open: true, onMenuItemClick: (_, callback) => {
                     callback();
                     setContextCoord(undefined);
                 }, onClose: () => {
@@ -58,9 +57,7 @@ const BaseLinearDisplay = observer(function (props) {
                     },
                 }, anchorReference: "anchorPosition", anchorPosition: contextCoord
                     ? { top: contextCoord[1], left: contextCoord[0] }
-                    : undefined, style: {
-                    zIndex: theme.zIndex.tooltip,
-                }, menuItems: items })] }));
+                    : undefined, menuItems: items })) : null] }));
 });
 export default BaseLinearDisplay;
 export { default as Tooltip } from './Tooltip';

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -197,6 +197,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
     readonly renderDelay: number;
     readonly TooltipComponent: AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: Feature): void;
 } & {
     readonly features: CompositeMap<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -5,7 +5,9 @@ import { getContainingTrack, getContainingView, getSession, isFeature, isSelecti
 import CompositeMap from '@jbrowse/core/util/compositeMap';
 import { getParentRenderProps, getRpcSessionId, } from '@jbrowse/core/util/tracks';
 import CenterFocusStrongIcon from '@mui/icons-material/CenterFocusStrong';
+import ContentCopyIcon from '@mui/icons-material/ContentCopy';
 import MenuOpenIcon from '@mui/icons-material/MenuOpen';
+import copy from 'copy-to-clipboard';
 import { autorun } from 'mobx';
 import { addDisposer, isAlive, types } from 'mobx-state-tree';
 import FeatureDensityMixin from './FeatureDensityMixin';
@@ -54,6 +56,12 @@ function stateModelFactory() {
             }
             return undefined;
         },
+        copyInfoToClipboard(feature) {
+            const { uniqueId, ...rest } = feature.toJSON();
+            const session = getSession(self);
+            copy(JSON.stringify(rest, null, 4));
+            session.notify('Copied to clipboard', 'success');
+        },
     }))
         .views(self => ({
         get features() {
@@ -166,30 +174,32 @@ function stateModelFactory() {
             return [];
         },
         contextMenuItems() {
-            return [
-                ...(self.contextMenuFeature
-                    ? [
-                        {
-                            label: 'Open feature details',
-                            icon: MenuOpenIcon,
-                            onClick: () => {
-                                if (self.contextMenuFeature) {
-                                    self.selectFeature(self.contextMenuFeature);
-                                }
-                            },
+            const feat = self.contextMenuFeature;
+            return feat
+                ? [
+                    {
+                        label: 'Open feature details',
+                        icon: MenuOpenIcon,
+                        onClick: () => {
+                            self.selectFeature(feat);
+                        },
+                    },
+                    {
+                        label: 'Zoom to feature',
+                        icon: CenterFocusStrongIcon,
+                        onClick: () => {
+                            self.navToFeature(feat);
                         },
-                        {
-                            label: 'Zoom to feature',
-                            icon: CenterFocusStrongIcon,
-                            onClick: () => {
-                                if (self.contextMenuFeature) {
-                                    self.navToFeature(self.contextMenuFeature);
-                                }
-                            },
+                    },
+                    {
+                        label: 'Copy info to clipboard',
+                        icon: ContentCopyIcon,
+                        onClick: () => {
+                            self.copyInfoToClipboard(feat);
                         },
-                    ]
-                    : []),
-            ];
+                    },
+                ]
+                : [];
         },
         renderProps() {
             return {

package/esm/LinearBareDisplay/model.d.ts

@@ -181,6 +181,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;

package/esm/LinearBasicDisplay/model.d.ts

@@ -189,6 +189,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;

package/esm/LinearGenomeView/components/GetSequenceDialog.d.ts

@@ -1,7 +1,6 @@
 import type { LinearGenomeViewModel } from '..';
-type LGV = LinearGenomeViewModel;
 declare const GetSequenceDialog: ({ model, handleClose, }: {
-    model: LGV;
+    model: LinearGenomeViewModel;
     handleClose: () => void;
 }) => import("react/jsx-runtime").JSX.Element;
 export default GetSequenceDialog;

package/esm/LinearGenomeView/components/GetSequenceDialog.js

@@ -1,16 +1,16 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useEffect, useState } from 'react';
-import { getConf } from '@jbrowse/core/configuration';
-import { Dialog } from '@jbrowse/core/ui';
-import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
-import { complement, getSession, reverse } from '@jbrowse/core/util';
+import { Dialog, ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
+import { complement, reverse } from '@jbrowse/core/util';
 import { formatSeqFasta } from '@jbrowse/core/util/formatFastaStrings';
+import ContentCopyIcon from '@mui/icons-material/ContentCopy';
 import GetAppIcon from '@mui/icons-material/GetApp';
-import { Button, Checkbox, CircularProgress, Container, DialogActions, DialogContent, FormControlLabel, FormGroup, TextField, Typography, } from '@mui/material';
+import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, FormGroup, TextField, Typography, } from '@mui/material';
 import copy from 'copy-to-clipboard';
 import { saveAs } from 'file-saver';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
+import { fetchSequence } from './fetchSequence';
 const useStyles = makeStyles()({
     dialogContent: {
         width: '80em',
@@ -22,30 +22,6 @@ const useStyles = makeStyles()({
         marginLeft: 10,
     },
 });
-async function fetchSequence(model, regions) {
-    const session = getSession(model);
-    const { leftOffset, rightOffset } = model;
-    if (!leftOffset || !rightOffset) {
-        throw new Error('no offsets on model to use for range');
-    }
-    const assemblyNames = new Set(regions.map(r => r.assemblyName));
-    if (assemblyNames.size > 1) {
-        throw new Error('not able to fetch sequences from multiple assemblies currently');
-    }
-    const { rpcManager, assemblyManager } = session;
-    const assemblyName = leftOffset.assemblyName || rightOffset.assemblyName || '';
-    const assembly = assemblyManager.get(assemblyName);
-    if (!assembly) {
-        throw new Error(`assembly ${assemblyName} not found`);
-    }
-    const adapterConfig = getConf(assembly, ['sequence', 'adapter']);
-    const sessionId = 'getSequence';
-    return rpcManager.call(sessionId, 'CoreGetFeatures', {
-        adapterConfig,
-        regions,
-        sessionId,
-    });
-}
 const GetSequenceDialog = observer(function ({ model, handleClose, }) {
     const { classes } = useStyles();
     const [error, setError] = useState();
@@ -54,7 +30,7 @@ const GetSequenceDialog = observer(function ({ model, handleClose, }) {
     const [copied, setCopied] = useState(false);
     const [comp, setComplement] = useState(false);
     const { leftOffset, rightOffset } = model;
-    const loading = Boolean(sequenceChunks === undefined);
+    const loading = sequenceChunks === undefined;
     useEffect(() => {
         const controller = new AbortController();
         (async () => {
@@ -63,8 +39,7 @@ const GetSequenceDialog = observer(function ({ model, handleClose, }) {
                 if (selection.length === 0) {
                     throw new Error('Selected region is out of bounds');
                 }
-                const chunks = await fetchSequence(model, selection);
-                setSequenceChunks(chunks);
+                setSequenceChunks(await fetchSequence(model, selection));
             }
             catch (e) {
                 console.error(e);
@@ -101,7 +76,7 @@ const GetSequenceDialog = observer(function ({ model, handleClose, }) {
     return (_jsxs(Dialog, { maxWidth: "xl", open: true, onClose: () => {
             handleClose();
             model.setOffsets();
-        }, title: "Reference sequence", children: [_jsxs(DialogContent, { children: [error ? (_jsx(Typography, { color: "error", children: `${error}` })) : loading ? (_jsxs(Container, { children: ["Retrieving reference sequence...", _jsx(CircularProgress, { className: classes.ml, size: 20, disableShrink: true })] })) : null, _jsx(TextField, { "data-testid": "rubberband-sequence", variant: "outlined", multiline: true, minRows: 5, maxRows: 10, disabled: sequenceTooLarge, className: classes.dialogContent, fullWidth: true, value: sequenceTooLarge
+        }, title: "Reference sequence", children: [_jsxs(DialogContent, { children: [error ? (_jsx(ErrorMessage, { error: error })) : loading ? (_jsx(LoadingEllipses, { message: "Retrieving sequences" })) : null, _jsx(TextField, { "data-testid": "rubberband-sequence", variant: "outlined", multiline: true, minRows: 5, maxRows: 10, disabled: sequenceTooLarge, className: classes.dialogContent, fullWidth: true, value: sequenceTooLarge
                             ? 'Reference sequence too large to display, use the download FASTA button'
                             : sequence, slotProps: {
                             input: {

package/esm/LinearGenomeView/components/RefNameAutocomplete/index.js

@@ -1,5 +1,5 @@
 import { jsx as _jsx } from "react/jsx-runtime";
-import { useEffect, useState } from 'react';
+import { useEffect, useMemo, useState } from 'react';
 import BaseResult, { RefSequenceResult, } from '@jbrowse/core/TextSearch/BaseResults';
 import { getSession, measureText, useDebounce } from '@jbrowse/core/util';
 import { Autocomplete } from '@mui/material';
@@ -14,38 +14,48 @@ const RefNameAutocomplete = observer(function ({ model, onSelect, assemblyName,
     const [currentSearch, setCurrentSearch] = useState('');
     const [inputValue, setInputValue] = useState('');
     const [searchOptions, setSearchOptions] = useState();
-    const debouncedSearch = useDebounce(currentSearch, 300);
+    const debouncedSearch = useDebounce(currentSearch, 50);
     const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined;
     const { coarseVisibleLocStrings, hasDisplayedRegions } = model;
     useEffect(() => {
-        ;
+        const isCurrent = { cancelled: false };
         (async () => {
             try {
                 if (debouncedSearch === '' || !assemblyName) {
                     return;
                 }
                 setLoaded(false);
-                setSearchOptions(getDeduplicatedResult(await fetchResults(debouncedSearch)));
+                const results = await fetchResults(debouncedSearch);
+                if (!isCurrent.cancelled) {
+                    setSearchOptions(getDeduplicatedResult(results));
+                }
             }
             catch (e) {
                 console.error(e);
-                session.notifyError(`${e}`, e);
+                if (!isCurrent.cancelled) {
+                    session.notifyError(`${e}`, e);
+                }
             }
             finally {
-                setLoaded(true);
+                if (!isCurrent.cancelled) {
+                    setLoaded(true);
+                }
             }
         })();
+        return () => {
+            isCurrent.cancelled = true;
+        };
     }, [assemblyName, fetchResults, debouncedSearch, session]);
     const inputBoxVal = coarseVisibleLocStrings || value || '';
     const regions = assembly === null || assembly === void 0 ? void 0 : assembly.regions;
-    const regionOptions = (regions === null || regions === void 0 ? void 0 : regions.map(region => ({
+    const regionOptions = useMemo(() => (regions === null || regions === void 0 ? void 0 : regions.map(region => ({
         result: new RefSequenceResult({
             refName: region.refName,
             label: region.refName,
             displayString: region.refName,
             matchedAttribute: 'refName',
         }),
-    }))) || [];
+    }))) || [], [regions]);
     return (_jsx(Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: {
             ...style,
             width: Math.min(Math.max(measureText(inputBoxVal, 14) + 100, minWidth), maxWidth),

package/esm/LinearGenomeView/components/RubberbandTooltip.d.ts

@@ -1,5 +1,5 @@
 export default function RubberbandTooltip({ anchorEl, side, text, }: {
     anchorEl: HTMLSpanElement;
     side: string;
-    text: string;
+    text: React.ReactNode;
 }): import("react/jsx-runtime").JSX.Element;

package/esm/LinearGenomeView/components/RubberbandTooltip.js

@@ -1,25 +1,17 @@
 import { jsx as _jsx } from "react/jsx-runtime";
-import { Popover, Typography } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-const useStyles = makeStyles()(theme => {
-    return {
-        popover: {
-            mouseEvents: 'none',
-            cursor: 'crosshair',
-        },
-        paper: {
-            paddingLeft: theme.spacing(1),
-            paddingRight: theme.spacing(1),
-        },
-    };
-});
+import { Tooltip } from '@mui/material';
 export default function RubberbandTooltip({ anchorEl, side, text, }) {
-    const { classes } = useStyles();
-    return (_jsx(Popover, { className: classes.popover, classes: { paper: classes.paper }, open: true, anchorEl: anchorEl, anchorOrigin: {
-            vertical: 'top',
-            horizontal: side === 'left' ? 'left' : 'right',
-        }, transformOrigin: {
-            vertical: 'bottom',
-            horizontal: side === 'left' ? 'right' : 'left',
-        }, keepMounted: true, disableRestoreFocus: true, children: _jsx(Typography, { children: text }) }));
+    return (_jsx(Tooltip, { title: text, open: true, placement: side === 'left' ? 'left-start' : 'right-start', slotProps: {
+            popper: {
+                anchorEl,
+                modifiers: [
+                    {
+                        name: 'offset',
+                        options: {
+                            offset: [-30, -10],
+                        },
+                    },
+                ],
+            },
+        }, children: _jsx("span", {}) }));
 }

package/esm/LinearGenomeView/components/SearchResultsTable.js

@@ -1,5 +1,5 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { getEnv, getSession } from '@jbrowse/core/util';
+import { assembleLocString, getEnv, getSession, parseLocString, } from '@jbrowse/core/util';
 import { Button, Paper, Table, TableBody, TableCell, TableContainer, TableHead, TableRow, } from '@mui/material';
 import { getRoot, resolveIdentifier } from 'mobx-state-tree';
 export default function SearchResultsTable({ searchResults, assemblyName: optAssemblyName, model, handleClose, }) {
@@ -40,18 +40,34 @@ export default function SearchResultsTable({ searchResults, assemblyName: optAss
             session.notify(`${e}`, 'warning');
         }
     }
-    return (_jsx(TableContainer, { component: Paper, children: _jsxs(Table, { children: [_jsx(TableHead, { children: _jsxs(TableRow, { children: [_jsx(TableCell, { children: "Name" }), _jsx(TableCell, { align: "right", children: "Location" }), _jsx(TableCell, { align: "right", children: "Track" }), _jsx(TableCell, { align: "right" })] }) }), _jsx(TableBody, { children: searchResults.map(result => (_jsxs(TableRow, { children: [_jsx(TableCell, { component: "th", scope: "row", children: result.getLabel() }), _jsx(TableCell, { align: "right", children: result.getLocation() }), _jsx(TableCell, { align: "right", children: getTrackName(result.getTrackId()) || 'N/A' }), _jsx(TableCell, { align: "right", children: _jsx(Button, { onClick: async () => {
-                                        try {
-                                            await handleClick(result.getLocation() || result.getLabel());
-                                            const resultTrackId = result.getTrackId();
-                                            if (resultTrackId) {
-                                                model.showTrack(resultTrackId);
+    return (_jsx(TableContainer, { component: Paper, children: _jsxs(Table, { children: [_jsx(TableHead, { children: _jsxs(TableRow, { children: [_jsx(TableCell, { children: "Name" }), _jsx(TableCell, { align: "right", children: "Location" }), _jsx(TableCell, { align: "right", children: "Track" }), _jsx(TableCell, { align: "right" })] }) }), _jsx(TableBody, { children: searchResults.map(result => {
+                        const locString = result.getLocation();
+                        let loc;
+                        try {
+                            loc = locString
+                                ? parseLocString(locString, refName => assembly.isValidRefName(refName))
+                                : undefined;
+                        }
+                        catch (e) { }
+                        return (_jsxs(TableRow, { children: [_jsx(TableCell, { component: "th", scope: "row", children: result.getLabel() }), _jsx(TableCell, { align: "right", children: loc
+                                        ? assembleLocString({
+                                            ...loc,
+                                            refName: assembly.getCanonicalRefName(loc.refName) ||
+                                                loc.refName,
+                                        })
+                                        : locString }), _jsx(TableCell, { align: "right", children: getTrackName(result.getTrackId()) || 'N/A' }), _jsx(TableCell, { align: "right", children: _jsx(Button, { onClick: async () => {
+                                            try {
+                                                await handleClick(result.getLocation() || result.getLabel());
+                                                const resultTrackId = result.getTrackId();
+                                                if (resultTrackId) {
+                                                    model.showTrack(resultTrackId);
+                                                }
                                             }
-                                        }
-                                        catch (e) {
-                                            console.error(e);
-                                            session.notifyError(`${e}`, e);
-                                        }
-                                        handleClose();
-                                    }, color: "primary", variant: "contained", children: "Go" }) })] }, result.getId()))) })] }) }));
+                                            catch (e) {
+                                                console.error(e);
+                                                session.notifyError(`${e}`, e);
+                                            }
+                                            handleClose();
+                                        }, color: "primary", variant: "contained", children: "Go" }) })] }, result.getId()));
+                    }) })] }) }));
 }

package/esm/LinearGenomeView/components/fetchSequence.d.ts

@@ -0,0 +1,4 @@
+import type { LinearGenomeViewModel } from '../model';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
+export declare function fetchSequence(model: LinearGenomeViewModel, regions: Region[]): Promise<Feature[]>;

package/esm/LinearGenomeView/components/fetchSequence.js

@@ -0,0 +1,26 @@
+import { getConf } from '@jbrowse/core/configuration';
+import { getSession } from '@jbrowse/core/util';
+export async function fetchSequence(model, regions) {
+    const session = getSession(model);
+    const { leftOffset, rightOffset } = model;
+    if (!leftOffset || !rightOffset) {
+        throw new Error('no offsets on model to use for range');
+    }
+    const assemblyNames = new Set(regions.map(r => r.assemblyName));
+    if (assemblyNames.size > 1) {
+        throw new Error('not able to fetch sequences from multiple assemblies currently');
+    }
+    const { rpcManager, assemblyManager } = session;
+    const assemblyName = leftOffset.assemblyName || rightOffset.assemblyName || '';
+    const assembly = assemblyManager.get(assemblyName);
+    if (!assembly) {
+        throw new Error(`assembly ${assemblyName} not found`);
+    }
+    const adapterConfig = getConf(assembly, ['sequence', 'adapter']);
+    const sessionId = 'getSequence';
+    return rpcManager.call(sessionId, 'CoreGetFeatures', {
+        adapterConfig,
+        regions,
+        sessionId,
+    });
+}

package/esm/LinearGenomeView/model.d.ts

@@ -58,6 +58,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly width: number;
     readonly interRegionPaddingWidth: number;
     readonly assemblyNames: string[];
+    readonly assemblyDisplayNames: string[];
     readonly isTopLevelView: import("@jbrowse/core/util").AbstractViewModel | undefined;
     readonly stickyViewHeaders: boolean | undefined;
     readonly rubberbandTop: number;

package/esm/LinearGenomeView/model.js

@@ -96,6 +96,14 @@ export function stateModelFactory(pluginManager) {
                 ...new Set(self.displayedRegions.map(region => region.assemblyName)),
             ];
         },
+        get assemblyDisplayNames() {
+            const { assemblyManager } = getSession(self);
+            return this.assemblyNames.map(assemblyName => {
+                var _a;
+                const assembly = assemblyManager.get(assemblyName);
+                return (_a = assembly === null || assembly === void 0 ? void 0 : assembly.displayName) !== null && _a !== void 0 ? _a : assemblyName;
+            });
+        },
         get isTopLevelView() {
             const session = getSession(self);
             return session.views.find(r => r.id === self.id);
@@ -126,7 +134,7 @@ export function stateModelFactory(pluginManager) {
         .views(self => ({
         scaleBarDisplayPrefix() {
             return getParent(self, 2).type === 'LinearSyntenyView'
-                ? self.assemblyNames[0]
+                ? self.assemblyDisplayNames[0]
                 : '';
         },
         MiniControlsComponent() {

package/esm/index.d.ts

@@ -186,6 +186,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             readonly renderDelay: number;
             readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
             readonly selectedFeatureId: string | undefined;
+            copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
         } & {
             readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
             readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "3.5.0",
+  "version": "3.6.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -38,13 +38,12 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@jbrowse/core": "^3.5.0",
+    "@jbrowse/core": "^3.6.0",
     "@mui/icons-material": "^7.0.0",
     "@mui/material": "^7.0.0",
     "@types/file-saver": "^2.0.1",
     "copy-to-clipboard": "^3.3.1",
     "file-saver": "^2.0.0",
-    "material-ui-popup-state": "^5.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -58,5 +57,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "8a8aa0aab2229dece106a5715a767e649e2fe92b"
+  "gitHead": "133a68815ab348d156c18d83cffc997356c3cfbb"
 }