@jbrowse/plugin-linear-genome-view 4.0.3 → 4.1.1

package/esm/LinearFeatureDisplay/model.d.ts

@@ -95,7 +95,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     trackDisplayMode: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     trackMaxHeight: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
     configuration: AnyConfigurationSchemaType;
-    jexlFilters: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
+    jexlFiltersSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -143,6 +143,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -199,6 +200,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -252,6 +254,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -533,6 +536,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -589,6 +593,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -642,6 +647,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -868,6 +874,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -924,6 +931,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -977,6 +985,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1083,7 +1092,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     featureUnderMouseVolatile: Feature | undefined;
 } & {
-    readonly activeFilters: any;
+    activeFilters(): string[];
     readonly rendererTypeName: any;
     readonly sequenceAdapter: any;
     readonly showLabels: any;
@@ -1171,6 +1180,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1224,11 +1234,16 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     };
+    filterMenuItems(): MenuItem[];
+} & {
     trackMenuItems(): MenuItem[];
+} & {
+    afterAttach(): void;
 }, {
     type: string;
 } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
@@ -1408,7 +1423,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     trackDisplayMode: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     trackMaxHeight: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
     configuration: AnyConfigurationSchemaType;
-    jexlFilters: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
+    jexlFiltersSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
 }>>;
 export type LinearFeatureDisplayStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearFeatureDisplayModel = Instance<LinearFeatureDisplayStateModel>;

package/esm/LinearFeatureDisplay/model.js

@@ -3,8 +3,10 @@ import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import { SimpleFeature, getSession } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-import { cast, getParent, isAlive, types } from '@jbrowse/mobx-state-tree';
+import { addDisposer, cast, getParent, isAlive, types, } from '@jbrowse/mobx-state-tree';
+import ClearAllIcon from '@mui/icons-material/ClearAll';
 import VisibilityIcon from '@mui/icons-material/Visibility';
+import { reaction, toJS } from 'mobx';
 import { BaseLinearDisplay } from "../BaseLinearDisplay/index.js";
 const SetMaxHeightDialog = lazy(() => import("./components/SetMaxHeightDialog.js"));
 const AddFiltersDialog = lazy(() => import("./components/AddFiltersDialog.js"));
@@ -17,14 +19,14 @@ function stateModelFactory(configSchema) {
         trackDisplayMode: types.maybe(types.string),
         trackMaxHeight: types.maybe(types.number),
         configuration: ConfigurationReference(configSchema),
-        jexlFilters: types.maybe(types.array(types.string)),
+        jexlFiltersSetting: types.maybe(types.array(types.string)),
     }))
         .volatile(() => ({
         featureUnderMouseVolatile: undefined,
     }))
         .views(self => ({
-        get activeFilters() {
-            return (self.jexlFilters ??
+        activeFilters() {
+            return (toJS(self.jexlFiltersSetting) ??
                 getConf(self, 'jexlFilters').map((r) => `jexl:${r}`));
         },
         get rendererTypeName() {
@@ -66,7 +68,7 @@ function stateModelFactory(configSchema) {
     }))
         .actions(self => ({
         setJexlFilters(f) {
-            self.jexlFilters = cast(f);
+            self.jexlFiltersSetting = cast(f);
         },
         setFeatureUnderMouse(feat) {
             self.featureUnderMouseVolatile = feat;
@@ -90,7 +92,7 @@ function stateModelFactory(configSchema) {
         },
     }))
         .views(self => {
-        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, renderingProps: superRenderingProps, } = self;
+        const { renderProps: superRenderProps, renderingProps: superRenderingProps, } = self;
         return {
             renderProps() {
                 const superProps = superRenderProps();
@@ -98,7 +100,7 @@ function stateModelFactory(configSchema) {
                     ...superProps,
                     config: self.rendererConfig,
                     filters: new SerializableFilterChain({
-                        filters: self.activeFilters,
+                        filters: self.activeFilters(),
                     }),
                     sequenceAdapter: self.sequenceAdapter,
                 };
@@ -162,6 +164,27 @@ function stateModelFactory(configSchema) {
                     },
                 };
             },
+            filterMenuItems() {
+                return [
+                    {
+                        label: 'Edit filters...',
+                        onClick: () => {
+                            getSession(self).queueDialog(handleClose => [
+                                AddFiltersDialog,
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
+                            ]);
+                        },
+                    },
+                ];
+            },
+        };
+    })
+        .views(self => {
+        const { trackMenuItems: superTrackMenuItems } = self;
+        return {
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -225,31 +248,48 @@ function stateModelFactory(configSchema) {
                         },
                     },
                     {
-                        label: 'Filters',
-                        subMenu: [
-                            {
-                                label: 'Edit filters...',
-                                onClick: () => {
-                                    getSession(self).queueDialog(handleClose => [
-                                        AddFiltersDialog,
-                                        {
-                                            model: self,
-                                            handleClose,
-                                        },
-                                    ]);
-                                },
-                            },
-                        ],
+                        label: 'Filter by...',
+                        icon: ClearAllIcon,
+                        subMenu: self.filterMenuItems(),
                     },
                 ];
             },
         };
     })
+        .actions(self => ({
+        afterAttach() {
+            addDisposer(self, reaction(() => self.featureIdUnderMouse, async (featureId) => {
+                if (!featureId) {
+                    self.setFeatureUnderMouse(undefined);
+                    return;
+                }
+                const session = getSession(self);
+                const { rpcManager } = session;
+                const { parentTrack } = self;
+                try {
+                    const sessionId = getRpcSessionId(self);
+                    const { feature } = (await rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
+                        featureId,
+                        sessionId,
+                        trackInstanceId: parentTrack.id,
+                        rendererType: self.rendererTypeName,
+                    }));
+                    if (isAlive(self) &&
+                        feature &&
+                        self.featureIdUnderMouse === featureId) {
+                        self.setFeatureUnderMouse(new SimpleFeature(feature));
+                    }
+                }
+                catch (e) {
+                }
+            }, { delay: 50, name: 'LinearFeatureDisplayMouseoverReaction' }));
+        },
+    }))
         .postProcessSnapshot(snap => {
         if (!snap) {
             return snap;
         }
-        const { trackShowLabels, trackShowDescriptions, trackDisplayMode, trackMaxHeight, jexlFilters, ...rest } = snap;
+        const { trackShowLabels, trackShowDescriptions, trackDisplayMode, trackMaxHeight, jexlFiltersSetting, ...rest } = snap;
         return {
             ...rest,
             ...(trackShowLabels !== undefined ? { trackShowLabels } : {}),
@@ -258,7 +298,7 @@ function stateModelFactory(configSchema) {
                 : {}),
             ...(trackDisplayMode !== undefined ? { trackDisplayMode } : {}),
             ...(trackMaxHeight !== undefined ? { trackMaxHeight } : {}),
-            ...(jexlFilters?.length ? { jexlFilters } : {}),
+            ...(jexlFiltersSetting?.length ? { jexlFiltersSetting } : {}),
         };
     });
 }

package/esm/LinearGenomeView/afterAttach.js

@@ -34,11 +34,17 @@ export function setupInitAutorun(self) {
                 const idsNotFound = [];
                 for (const t of init.tracks) {
                     try {
-                        self.showTrack(t);
+                        if (typeof t === 'string') {
+                            self.showTrack(t);
+                        }
+                        else {
+                            self.showTrack(t.trackId, t.trackSnapshot ?? {}, t.displaySnapshot ?? {});
+                        }
                     }
                     catch (e) {
+                        const trackId = typeof t === 'string' ? t : t.trackId;
                         if (/Could not resolve identifier/.exec(`${e}`)) {
-                            idsNotFound.push(t);
+                            idsNotFound.push(trackId);
                         }
                         else {
                             throw e;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 type LGV = LinearGenomeViewModel;
 declare const CenterLine: ({ model }: {
     model: LGV;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 type LGV = LinearGenomeViewModel;
 declare const Gridlines: ({ model, offset, }: {
     model: LGV;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 declare const LinearGenomeViewHeader: ({ model, }: {
     model: LinearGenomeViewModel;
 }) => import("react/jsx-runtime").JSX.Element | null;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 type LGV = LinearGenomeViewModel;
 export default function HeaderPanControls({ model }: {
     model: LGV;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 declare const HeaderRegionWidth: ({ model, }: {
     model: LinearGenomeViewModel;
 }) => import("react/jsx-runtime").JSX.Element;

package/esm/LinearGenomeView/components/HeaderRegionWidth.js

@@ -12,7 +12,7 @@ const useStyles = makeStyles()({
 });
 const HeaderRegionWidth = observer(function HeaderRegionWidth({ model, }) {
     const { classes } = useStyles();
-    const { coarseTotalBpDisplayStr } = model;
-    return (_jsx(Typography, { variant: "body2", color: "textSecondary", className: classes.bp, children: coarseTotalBpDisplayStr }));
+    const { effectiveTotalBpDisplayStr } = model;
+    return (_jsx(Typography, { variant: "body2", color: "textSecondary", className: classes.bp, children: effectiveTotalBpDisplayStr }));
 });
 export default HeaderRegionWidth;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 declare const HeaderTrackSelectorButton: ({ model, }: {
     model: LinearGenomeViewModel;
 }) => import("react/jsx-runtime").JSX.Element;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 declare const HeaderZoomControls: ({ model, }: {
     model: LinearGenomeViewModel;
 }) => import("react/jsx-runtime").JSX.Element;

package/esm/LinearGenomeView/components/HeaderZoomControls.js

@@ -26,13 +26,13 @@ function ValueLabelComponent(props) {
 }
 const HeaderZoomControls = observer(function HeaderZoomControls({ model, }) {
     const { classes } = useStyles();
-    const { width, maxBpPerPx, minBpPerPx, bpPerPx } = model;
+    const { width, maxBpPerPx, minBpPerPx, bpPerPx, effectiveBpPerPx } = model;
     const [value, setValue] = useState(-Math.log2(bpPerPx) * 100);
     useEffect(() => {
-        setValue(-Math.log2(bpPerPx) * 100);
-    }, [bpPerPx]);
-    const zoomInDisabled = bpPerPx <= minBpPerPx + 0.0001;
-    const zoomOutDisabled = bpPerPx >= maxBpPerPx - 0.0001;
+        setValue(-Math.log2(effectiveBpPerPx) * 100);
+    }, [effectiveBpPerPx]);
+    const zoomInDisabled = effectiveBpPerPx <= minBpPerPx + 0.0001;
+    const zoomOutDisabled = effectiveBpPerPx >= maxBpPerPx - 0.0001;
     return (_jsxs("div", { className: classes.container, children: [_jsx(Tooltip, { title: "Zoom out 2x", children: _jsx("span", { children: _jsx(IconButton, { "data-testid": "zoom_out", disabled: zoomOutDisabled, onClick: () => {
                             model.zoom(bpPerPx * 2);
                         }, children: _jsx(ZoomOut, {}) }) }) }), _jsx(Slider, { size: "small", className: classes.slider, value: value, min: -Math.log2(maxBpPerPx) * 100, max: -Math.log2(minBpPerPx) * 100, onChangeCommitted: () => model.zoomTo(2 ** (-value / 100)), valueLabelDisplay: "auto", valueLabelFormat: newValue => `Window size: ${getBpDisplayStr(2 ** (-newValue / 100) * width)}`, slots: {

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 type LGV = LinearGenomeViewModel;
 declare const LinearGenomeViewImportForm: ({ model }: {
     model: LGV;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 import type BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 type LGV = LinearGenomeViewModel;
 declare const ImportFormRefNameAutocomplete: ({ model, selectedAsm, value, setValue, setOption, }: {

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 declare const LinearGenomeView: ({ model, }: {
     model: LinearGenomeViewModel;
 }) => import("react/jsx-runtime").JSX.Element;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 declare const LinearGenomeViewContainer: ({ model, }: {
     model: LinearGenomeViewModel;
 }) => import("react/jsx-runtime").JSX.Element;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 declare const MiniControls: ({ model, }: {
     model: LinearGenomeViewModel;
 }) => import("react/jsx-runtime").JSX.Element | null;

package/esm/LinearGenomeView/components/MiniControls.js

@@ -20,12 +20,12 @@ const useStyles = makeStyles()(theme => ({
 }));
 const MiniControls = observer(function MiniControls({ model, }) {
     const { classes } = useStyles();
-    const { id, bpPerPx, maxBpPerPx, minBpPerPx, hideHeader } = model;
+    const { id, bpPerPx, maxBpPerPx, minBpPerPx, hideHeader, effectiveBpPerPx } = model;
     const { focusedViewId } = getSession(model);
     return hideHeader ? (_jsx(Paper, { className: classes.background, children: _jsxs(Paper, { className: focusedViewId === id ? classes.focusedBackground : undefined, children: [_jsx(CascadingMenuButton, { menuItems: () => model.menuItems(), children: _jsx(ArrowDown, { fontSize: "small" }) }), _jsx(IconButton, { "data-testid": "zoom_out", onClick: () => {
                         model.zoom(bpPerPx * 2);
-                    }, disabled: bpPerPx >= maxBpPerPx - 0.0001, children: _jsx(ZoomOut, { fontSize: "small" }) }), _jsx(IconButton, { "data-testid": "zoom_in", onClick: () => {
+                    }, disabled: effectiveBpPerPx >= maxBpPerPx - 0.0001, children: _jsx(ZoomOut, { fontSize: "small" }) }), _jsx(IconButton, { "data-testid": "zoom_in", onClick: () => {
                         model.zoom(bpPerPx / 2);
-                    }, disabled: bpPerPx <= minBpPerPx + 0.0001, children: _jsx(ZoomIn, { fontSize: "small" }) })] }) })) : null;
+                    }, disabled: effectiveBpPerPx <= minBpPerPx + 0.0001, children: _jsx(ZoomIn, { fontSize: "small" }) })] }) })) : null;
 });
 export default MiniControls;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 declare const NoTracksActiveButton: ({ model, }: {
     model: LinearGenomeViewModel;
 }) => import("react/jsx-runtime").JSX.Element;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 import type { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
 type LGV = LinearGenomeViewModel;
 declare const OverviewRubberband: ({ model, overview, ControlComponent, }: {

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 import type { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
 type LGV = LinearGenomeViewModel;
 declare const OverviewRubberbandHoverTooltip: ({ model, open, guideX, overview, }: {

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 type LGV = LinearGenomeViewModel;
 declare const OverviewScalebar: ({ model, children, }: {
     model: LGV;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 import type { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
 declare const OverviewScalebarPolygon: ({ model, overview, useOffset, }: {
     model: LinearGenomeViewModel;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 import type { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
 import type { ContentBlock } from '@jbrowse/core/util/blockTypes';
 declare const OverviewScalebarTickLabels: ({ block, scale, overview, model, }: {

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

@@ -2,11 +2,13 @@ import { jsx as _jsx } from "react/jsx-runtime";
 import { TextField } from '@mui/material';
 export default function AutocompleteTextField({ TextFieldProps, inputBoxVal, params, setInputValue, setCurrentSearch, }) {
     const { helperText, slotProps = {} } = TextFieldProps;
+    const { ref: inputRef, ...restInputProps } = params.InputProps;
+    const { InputProps: _InputProps, ...restParams } = params;
     return (_jsx(TextField, { onBlur: () => {
             setInputValue(inputBoxVal);
-        }, ...params, ...TextFieldProps, size: "small", helperText: helperText, slotProps: {
+        }, ...restParams, ...TextFieldProps, inputRef: inputRef, size: "small", helperText: helperText, slotProps: {
             input: {
-                ...params.InputProps,
+                ...restInputProps,
                 ...slotProps.input,
             },
         }, placeholder: "Search for location", onChange: e => {

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 type LGV = LinearGenomeViewModel;
 declare const Rubberband: ({ model, ControlComponent, }: {
     model: LGV;

package/esm/LinearGenomeView/components/Rubberband.js

@@ -17,10 +17,10 @@ const useStyles = makeStyles()({
 const Rubberband = observer(function Rubberband({ model, ControlComponent = _jsx("div", {}), }) {
     const ref = useRef(null);
     const { classes } = useStyles();
-    const { stickyViewHeaders, rubberbandTop } = model;
+    const { stickyViewHeaders, rubberbandTop, isScalebarRefNameMenuOpen } = model;
     const { guideX, rubberbandOn, leftBpOffset, rightBpOffset, numOfBpSelected, width, left, anchorPosition, open, isClick, clickBpOffset, handleMenuItemClick, handleClose, mouseMove, mouseDown, mouseOut, } = useRangeSelect(ref, model);
-    return (_jsxs(_Fragment, { children: [guideX !== undefined ? (_jsx(VerticalGuide, { model: model, coordX: guideX })) : rubberbandOn ? (_jsx(RubberbandSpan, { leftBpOffset: leftBpOffset, rightBpOffset: rightBpOffset, numOfBpSelected: numOfBpSelected, width: width, left: left, top: rubberbandTop, sticky: stickyViewHeaders })) : null, anchorPosition ? (_jsx(Menu, { anchorReference: "anchorPosition", anchorPosition: {
-                    left: anchorPosition.clientX,
+    return (_jsxs(_Fragment, { children: [guideX !== undefined && !isScalebarRefNameMenuOpen ? (_jsx(VerticalGuide, { model: model, coordX: guideX })) : rubberbandOn ? (_jsx(RubberbandSpan, { leftBpOffset: leftBpOffset, rightBpOffset: rightBpOffset, numOfBpSelected: numOfBpSelected, width: width, left: left, top: rubberbandTop, sticky: stickyViewHeaders })) : null, anchorPosition ? (_jsx(Menu, { anchorReference: "anchorPosition", anchorPosition: {
+                    left: anchorPosition.clientX + 10,
                     top: anchorPosition.clientY,
                 }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: isClick && clickBpOffset
                     ? model.rubberbandClickMenuItems(clickBpOffset)

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

@@ -1,10 +1,10 @@
 import type React from 'react';
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 type LGV = LinearGenomeViewModel;
 interface ScalebarProps {
     model: LGV;
     style?: React.CSSProperties;
     className?: string;
 }
-declare const Scalebar: React.ForwardRefExoticComponent<ScalebarProps & React.RefAttributes<HTMLDivElement>>;
+declare const Scalebar: ({ model, style, className, ...other }: ScalebarProps) => import("react/jsx-runtime").JSX.Element;
 export default Scalebar;

package/esm/LinearGenomeView/components/Scalebar.js

@@ -1,5 +1,4 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { forwardRef } from 'react';
 import { cx, makeStyles } from '@jbrowse/core/util/tss-react';
 import { Paper } from '@mui/material';
 import { observer } from 'mobx-react';
@@ -20,14 +19,14 @@ const useStyles = makeStyles()({
         pointerEvents: 'none',
     },
 });
-const Scalebar = observer(forwardRef(function Scalebar2({ model, style, className, ...other }, ref) {
+const Scalebar = observer(function Scalebar({ model, style, className, ...other }) {
     const { classes } = useStyles();
     const { scaleFactor, staticBlocks, offsetPx } = model;
-    return (_jsxs(Paper, { "data-resizer": "true", className: cx(classes.container, className), variant: "outlined", ref: ref, style: { ...style, '--offset-px': `${offsetPx}px` }, ...other, children: [_jsx(Gridlines, { model: model, offset: 1 }), _jsx("div", { className: classes.zoomContainer, style: {
+    return (_jsxs(Paper, { "data-resizer": "true", className: cx(classes.container, className), variant: "outlined", style: { ...style, '--offset-px': `${offsetPx}px` }, ...other, children: [_jsx(Gridlines, { model: model, offset: 1 }), _jsx("div", { className: classes.zoomContainer, style: {
                     transform: scaleFactor !== 1 ? `scaleX(${scaleFactor})` : undefined,
                 }, children: _jsx("div", { className: classes.scalebar, style: {
                         transform: `translateX(calc(${staticBlocks.offsetPx}px - var(--offset-px) - 1px))`,
                         width: staticBlocks.totalWidthPx,
                     }, children: _jsx(ScalebarCoordinateLabels, { model: model }) }) }), _jsx(ScalebarRefNameLabels, { model: model })] }));
-}));
+});
 export default Scalebar;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 type LGV = LinearGenomeViewModel;
 declare const ScalebarCoordinateLabels: ({ model, }: {
     model: LGV;

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

@@ -1,4 +1,4 @@
-import type { LinearGenomeViewModel } from '..';
+import type { LinearGenomeViewModel } from '../index.ts';
 type LGV = LinearGenomeViewModel;
 declare const ScalebarRefNameLabels: ({ model, }: {
     model: LGV;