@jbrowse/plugin-linear-genome-view 3.1.0 → 3.2.0

package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -78,14 +78,14 @@ function stateModelFactory() {
             return (_b = (_a = self.blockState.get(blockKey)) === null || _a === void 0 ? void 0 : _a.layout) === null || _b === void 0 ? void 0 : _b.getByID(id);
         },
         searchFeatureByID(id) {
+            var _a;
             let ret;
-            self.blockState.forEach(block => {
-                var _a;
+            for (const block of self.blockState.values()) {
                 const val = (_a = block.layout) === null || _a === void 0 ? void 0 : _a.getByID(id);
                 if (val) {
                     ret = val;
                 }
-            });
+            }
             return ret;
         },
     }))
@@ -138,9 +138,9 @@ function stateModelFactory() {
                 self.setError();
                 self.setCurrStatsBpPerPx(0);
                 self.clearFeatureDensityStats();
-                [...self.blockState.values()].forEach(val => {
+                for (const val of self.blockState.values()) {
                     val.doReload();
-                });
+                }
                 superReload();
             },
         };
@@ -230,17 +230,17 @@ function stateModelFactory() {
                 if (!view.initialized) {
                     return;
                 }
-                self.blockDefinitions.contentBlocks.forEach(block => {
+                for (const block of self.blockDefinitions.contentBlocks) {
                     blocksPresent[block.key] = true;
                     if (!self.blockState.has(block.key)) {
                         self.addBlock(block.key, block);
                     }
-                });
-                self.blockState.forEach((_, key) => {
+                }
+                for (const key of self.blockState.keys()) {
                     if (!blocksPresent[key]) {
                         self.deleteBlock(key);
                     }
-                });
+                }
             }));
         },
     }))

package/esm/LaunchLinearGenomeView/index.js

@@ -20,7 +20,7 @@ export default function LaunchLinearGenomeViewF(pluginManager) {
                 view.setHideHeader(!nav);
             }
             if (highlight !== undefined) {
-                highlight.forEach(async (h) => {
+                for (const h of highlight) {
                     const p = parseLocString(h, refName => assemblyManager.isValidRefName(refName, assembly));
                     const { start, end } = p;
                     if (start !== undefined && end !== undefined) {
@@ -31,13 +31,17 @@ export default function LaunchLinearGenomeViewF(pluginManager) {
                             assemblyName: assembly,
                         });
                     }
-                });
+                }
             }
-            await handleSelectedRegion({ input: loc, model: view, assembly: asm });
+            await handleSelectedRegion({
+                input: loc,
+                model: view,
+                assembly: asm,
+            });
             const idsNotFound = [];
-            tracks.forEach(track => {
+            for (const track of tracks) {
                 tryTrack(view, track, idsNotFound);
-            });
+            }
             if (idsNotFound.length) {
                 throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
             }

package/esm/LinearGenomeView/components/OverviewRubberband.js

@@ -1,9 +1,9 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useEffect, useRef, useState } from 'react';
-import { getSession, stringify } from '@jbrowse/core/util';
-import { Tooltip } from '@mui/material';
+import { getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
+import OverviewRubberbandHoverTooltip from './OverviewRubberbandHoverTooltip';
 import RubberbandSpan from './RubberbandSpan';
 import { getRelativeX } from './util';
 const useStyles = makeStyles()({
@@ -22,18 +22,6 @@ const useStyles = makeStyles()({
         position: 'relative',
     },
 });
-const HoverTooltip = observer(function ({ model, open, guideX, overview, }) {
-    var _a;
-    const { classes } = useStyles();
-    const { cytobandOffset } = model;
-    const { assemblyManager } = getSession(model);
-    const px = overview.pxToBp(guideX - cytobandOffset);
-    const assembly = assemblyManager.get(px.assemblyName);
-    const cytoband = (_a = assembly === null || assembly === void 0 ? void 0 : assembly.cytobands) === null || _a === void 0 ? void 0 : _a.find(f => px.coord > f.get('start') &&
-        px.coord < f.get('end') &&
-        px.refName === assembly.getCanonicalRefName(f.get('refName')));
-    return (_jsx(Tooltip, { open: open, placement: "top", title: [stringify(px), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('name')].join(' '), arrow: true, children: _jsx("div", { className: classes.guide, style: { left: guideX } }) }));
-});
 const OverviewRubberband = observer(function OverviewRubberband({ model, overview, ControlComponent = _jsx("div", {}), }) {
     const { cytobandOffset } = model;
     const [startX, setStartX] = useState();
@@ -103,7 +91,7 @@ const OverviewRubberband = observer(function OverviewRubberband({ model, overvie
         setGuideX(undefined);
     }
     if (startX === undefined) {
-        return (_jsxs("div", { className: classes.rel, children: [guideX !== undefined ? (_jsx(HoverTooltip, { model: model, open: !mouseDragging, overview: overview, guideX: guideX })) : null, _jsx("div", { className: classes.rubberbandControl, ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove, children: ControlComponent })] }));
+        return (_jsxs("div", { className: classes.rel, children: [guideX !== undefined ? (_jsx(OverviewRubberbandHoverTooltip, { model: model, open: !mouseDragging, overview: overview, guideX: guideX })) : null, _jsx("div", { className: classes.rubberbandControl, ref: controlsRef, onMouseDown: mouseDown, onMouseOut: mouseOut, onMouseMove: mouseMove, children: ControlComponent })] }));
     }
     let left = startX || 0;
     let width = 0;

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

@@ -0,0 +1,10 @@
+import type { LinearGenomeViewModel } from '..';
+import type { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
+type LGV = LinearGenomeViewModel;
+declare const OverviewRubberbandHoverTooltip: ({ model, open, guideX, overview, }: {
+    model: LGV;
+    open: boolean;
+    guideX: number;
+    overview: Base1DViewModel;
+}) => import("react/jsx-runtime").JSX.Element;
+export default OverviewRubberbandHoverTooltip;

package/esm/LinearGenomeView/components/OverviewRubberbandHoverTooltip.js

@@ -0,0 +1,34 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { getSession, stringify } from '@jbrowse/core/util';
+import { Tooltip } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()({
+    rubberbandControl: {
+        cursor: 'crosshair',
+        width: '100%',
+        minHeight: 8,
+    },
+    guide: {
+        pointerEvents: 'none',
+        height: '100%',
+        width: 1,
+        position: 'absolute',
+    },
+    rel: {
+        position: 'relative',
+    },
+});
+const OverviewRubberbandHoverTooltip = observer(function ({ model, open, guideX, overview, }) {
+    var _a;
+    const { classes } = useStyles();
+    const { cytobandOffset } = model;
+    const { assemblyManager } = getSession(model);
+    const px = overview.pxToBp(guideX - cytobandOffset);
+    const assembly = assemblyManager.get(px.assemblyName);
+    const cytoband = (_a = assembly === null || assembly === void 0 ? void 0 : assembly.cytobands) === null || _a === void 0 ? void 0 : _a.find(f => px.coord > f.get('start') &&
+        px.coord < f.get('end') &&
+        px.refName === assembly.getCanonicalRefName(f.get('refName')));
+    return (_jsx(Tooltip, { open: open, placement: "top", title: [stringify(px), cytoband === null || cytoband === void 0 ? void 0 : cytoband.get('name')].join(' '), arrow: true, children: _jsx("div", { className: classes.guide, style: { left: guideX } }) }));
+});
+export default OverviewRubberbandHoverTooltip;

package/esm/LinearGenomeView/components/Rubberband.js

@@ -1,14 +1,11 @@
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { useRef } from 'react';
-import { Menu, VIEW_HEADER_HEIGHT } from '@jbrowse/core/ui';
-import { getSession } from '@jbrowse/core/util';
-import { isSessionWithMultipleViews } from '@jbrowse/product-core';
+import { Menu } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import RubberbandSpan from './RubberbandSpan';
 import VerticalGuide from './VerticalGuide';
 import { useRangeSelect } from './useRangeSelect';
-import { HEADER_BAR_HEIGHT, HEADER_OVERVIEW_HEIGHT } from '../consts';
 const useStyles = makeStyles()({
     rubberbandControl: {
         cursor: 'crosshair',
@@ -20,28 +17,13 @@ const useStyles = makeStyles()({
 const Rubberband = observer(function ({ model, ControlComponent = _jsx("div", {}), }) {
     const ref = useRef(null);
     const { classes } = useStyles();
-    const session = getSession(model);
+    const { stickyViewHeaders, rubberbandTop } = model;
     const { guideX, rubberbandOn, leftBpOffset, rightBpOffset, numOfBpSelected, width, left, anchorPosition, open, handleMenuItemClick, handleClose, mouseMove, mouseDown, mouseOut, } = useRangeSelect(ref, model);
-    let stickyViewHeaders = false;
-    if (isSessionWithMultipleViews(session)) {
-        ;
-        ({ stickyViewHeaders } = session);
-    }
-    let rubberbandControlTop = 0;
-    if (stickyViewHeaders) {
-        rubberbandControlTop = VIEW_HEADER_HEIGHT;
-        if (!model.hideHeader) {
-            rubberbandControlTop += HEADER_BAR_HEIGHT;
-            if (!model.hideHeaderOverview) {
-                rubberbandControlTop += HEADER_OVERVIEW_HEIGHT;
-            }
-        }
-    }
-    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: rubberbandControlTop, sticky: stickyViewHeaders })) : null, anchorPosition ? (_jsx(Menu, { anchorReference: "anchorPosition", anchorPosition: {
+    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,
                     top: anchorPosition.clientY,
                 }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: model.rubberBandMenuItems() })) : null, _jsx("div", { "data-testid": "rubberband_controls", className: classes.rubberbandControl, style: {
-                    top: rubberbandControlTop,
+                    top: rubberbandTop,
                     position: stickyViewHeaders ? 'sticky' : undefined,
                 }, ref: ref, onMouseDown: mouseDown, onMouseMove: mouseMove, onMouseOut: mouseOut, children: ControlComponent })] }));
 });

package/esm/LinearGenomeView/components/RubberbandSpan.js

@@ -1,8 +1,9 @@
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { useState } from 'react';
 import { stringify, toLocale } from '@jbrowse/core/util';
-import { Popover, Typography, alpha } from '@mui/material';
+import { Typography, alpha } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
+import RubberbandTooltip from './RubberbandTooltip';
 const useStyles = makeStyles()(theme => {
     const { tertiary } = theme.palette;
     const background = alpha(tertiary.light, 0.7);
@@ -20,32 +21,14 @@ const useStyles = makeStyles()(theme => {
             minHeight: 8,
         },
         rubberbandText: {
-            color: tertiary.contrastText,
-        },
-        popover: {
-            mouseEvents: 'none',
-            cursor: 'crosshair',
-        },
-        paper: {
-            paddingLeft: theme.spacing(1),
-            paddingRight: theme.spacing(1),
+            color: theme.palette.tertiary.contrastText,
         },
     };
 });
-function Tooltip({ 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' ? 'right' : 'left',
-        }, transformOrigin: {
-            vertical: 'bottom',
-            horizontal: side === 'left' ? 'left' : 'right',
-        }, keepMounted: true, disableRestoreFocus: true, children: _jsx(Typography, { children: text }) }));
-}
 export default function RubberbandSpan({ leftBpOffset, rightBpOffset, numOfBpSelected, left, width, top = 0, sticky = false, }) {
     const { classes } = useStyles();
     const [anchorEl, setAnchorEl] = useState(null);
-    return (_jsxs(_Fragment, { children: [anchorEl ? (_jsxs(_Fragment, { children: [_jsx(Tooltip, { side: "left", anchorEl: anchorEl, text: stringify(leftBpOffset) }), _jsx(Tooltip, { side: "right", anchorEl: anchorEl, text: stringify(rightBpOffset) })] })) : null, _jsx("div", { className: classes.rubberband, style: { left, width }, children: numOfBpSelected ? (_jsxs(Typography, { ref: el => {
+    return (_jsxs(_Fragment, { children: [anchorEl ? (_jsxs(_Fragment, { children: [_jsx(RubberbandTooltip, { side: "left", anchorEl: anchorEl, text: stringify(leftBpOffset) }), _jsx(RubberbandTooltip, { side: "right", anchorEl: anchorEl, text: stringify(rightBpOffset) })] })) : null, _jsx("div", { className: classes.rubberband, style: { left, width }, children: numOfBpSelected ? (_jsxs(Typography, { ref: el => {
                         setAnchorEl(el);
                     }, variant: "h6", className: classes.rubberbandText, style: {
                         top,

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

@@ -0,0 +1,5 @@
+export default function RubberbandTooltip({ anchorEl, side, text, }: {
+    anchorEl: HTMLSpanElement;
+    side: string;
+    text: string;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/LinearGenomeView/components/RubberbandTooltip.js

@@ -0,0 +1,25 @@
+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),
+        },
+    };
+});
+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 }) }));
+}

package/esm/LinearGenomeView/components/TracksContainer.js

@@ -24,7 +24,7 @@ const TracksContainer = observer(function TracksContainer({ children, model, })
     const { classes } = useStyles();
     const { pluginManager } = getEnv(model);
     const { mouseDown: mouseDown1, mouseUp } = useSideScroll(model);
-    const { stickyViewHeaders, pinnedTracksTop, showGridlines, showCenterLine } = model;
+    const { stickyViewHeaders, rubberbandTop, showGridlines, showCenterLine } = model;
     const ref = useRef(null);
     const { guideX, rubberbandOn, leftBpOffset, rightBpOffset, numOfBpSelected, width, left, anchorPosition, open, handleMenuItemClick, handleClose, mouseMove, mouseDown: mouseDown2, } = useRangeSelect(ref, model, true);
     useWheelScroll(ref, model);
@@ -32,7 +32,7 @@ const TracksContainer = observer(function TracksContainer({ children, model, })
     return (_jsxs("div", { ref: ref, "data-testid": "tracksContainer", className: classes.tracksContainer, onMouseDown: event => {
             mouseDown1(event);
             mouseDown2(event);
-        }, onMouseMove: mouseMove, onMouseUp: mouseUp, children: [showGridlines ? _jsx(Gridlines, { model: model }) : null, _jsx(Suspense, { fallback: null, children: showCenterLine ? _jsx(CenterLine, { model: model }) : null }), guideX !== undefined ? (_jsx(VerticalGuide, { model: model, coordX: guideX })) : rubberbandOn ? (_jsx(Suspense, { fallback: null, children: _jsx(RubberbandSpan, { leftBpOffset: leftBpOffset, rightBpOffset: rightBpOffset, numOfBpSelected: numOfBpSelected, width: width, left: left, top: pinnedTracksTop, sticky: stickyViewHeaders }) })) : null, anchorPosition ? (_jsx(Menu, { anchorReference: "anchorPosition", anchorPosition: {
+        }, onMouseMove: mouseMove, onMouseUp: mouseUp, children: [showGridlines ? _jsx(Gridlines, { model: model }) : null, _jsx(Suspense, { fallback: null, children: showCenterLine ? _jsx(CenterLine, { model: model }) : null }), guideX !== undefined ? (_jsx(VerticalGuide, { model: model, coordX: guideX })) : rubberbandOn ? (_jsx(Suspense, { fallback: null, children: _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,
                     top: anchorPosition.clientY,
                 }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: model.rubberBandMenuItems() })) : null, _jsx(Rubberband, { model: model, ControlComponent: _jsx(Scalebar, { model: model, style: {

package/esm/LinearGenomeView/components/VerticalGuide.js

@@ -1,11 +1,8 @@
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
-import { VIEW_HEADER_HEIGHT } from '@jbrowse/core/ui';
-import { getSession, stringify } from '@jbrowse/core/util';
-import { isSessionWithMultipleViews } from '@jbrowse/product-core';
+import { stringify } from '@jbrowse/core/util';
 import { Tooltip } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import { HEADER_BAR_HEIGHT, HEADER_OVERVIEW_HEIGHT } from '../consts';
 const useStyles = makeStyles()({
     guide: {
         pointerEvents: 'none',
@@ -13,7 +10,7 @@ const useStyles = makeStyles()({
         width: 1,
         position: 'absolute',
         background: 'red',
-        zIndex: 4,
+        zIndex: 1001,
     },
     tooltipTarget: {
         position: 'sticky',
@@ -22,25 +19,10 @@ const useStyles = makeStyles()({
 });
 const VerticalGuide = observer(function VerticalGuide({ model, coordX, }) {
     const { classes } = useStyles();
-    const session = getSession(model);
-    let stickyViewHeaders = false;
-    if (isSessionWithMultipleViews(session)) {
-        ;
-        ({ stickyViewHeaders } = session);
-    }
-    let tooltipTop = 0;
-    if (stickyViewHeaders) {
-        tooltipTop = VIEW_HEADER_HEIGHT;
-        if (!model.hideHeader) {
-            tooltipTop += HEADER_BAR_HEIGHT;
-            if (!model.hideHeaderOverview) {
-                tooltipTop += HEADER_OVERVIEW_HEIGHT;
-            }
-        }
-    }
+    const { stickyViewHeaders, rubberbandTop } = model;
     return (_jsxs(_Fragment, { children: [_jsx(Tooltip, { open: true, placement: "top", title: stringify(model.pxToBp(coordX)), arrow: true, children: _jsx("div", { className: classes.tooltipTarget, style: {
                         left: coordX + 6,
-                        top: tooltipTop,
+                        top: rubberbandTop,
                         position: stickyViewHeaders ? 'sticky' : undefined,
                     } }) }), _jsx("div", { className: classes.guide, style: { left: coordX } })] }));
 });

package/esm/LinearGenomeView/model.d.ts

@@ -1,5 +1,5 @@
 import type React from 'react';
-import type { BpOffset, ExportSvgOptions, HighlightType, NavLocation } from './types';
+import type { BpOffset, ExportSvgOptions, HighlightType, InitState, NavLocation } from './types';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type BaseResult from '@jbrowse/core/TextSearch/BaseResults';
 import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
@@ -30,6 +30,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<HighlightType, HighlightType, HighlightType>>, [undefined]>;
     colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    init: import("mobx-state-tree").IType<InitState | undefined, InitState | undefined, InitState | undefined>;
 }, {
     width: number;
 } & {
@@ -58,6 +59,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly interRegionPaddingWidth: number;
     readonly assemblyNames: string[];
     readonly stickyViewHeaders: boolean;
+    readonly rubberbandTop: number;
     readonly pinnedTracksTop: number;
 } & {
     scaleBarDisplayPrefix(): string | undefined;
@@ -144,6 +146,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setDraggingTrackId(idx?: string): void;
     setScaleFactor(factor: number): void;
     clearView(): void;
+    setInit(arg?: InitState): void;
     exportSvg(opts?: ExportSvgOptions): Promise<void>;
 } & {
     slide: (viewWidths: number) => void;
@@ -164,7 +167,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly coarseVisibleLocStrings: string;
 } & {
     setCoarseDynamicBlocks(blocks: BlockSet): void;
-    afterAttach(): void;
 } & {
     moveTo(start?: BpOffset, end?: BpOffset): void;
     navToLocString(input: string, optAssemblyName?: string): Promise<void>;
@@ -210,6 +212,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } | undefined;
 } & {
     afterCreate(): void;
+    afterAttach(): void;
 }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -232,7 +235,28 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<HighlightType, HighlightType, HighlightType>>, [undefined]>;
     colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showTrackOutlines: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-}>>, import("mobx-state-tree")._NotCustomized>;
+    init: import("mobx-state-tree").IType<InitState | undefined, InitState | undefined, InitState | undefined>;
+}>>, {
+    type: string;
+    id: string;
+    displayName: string | undefined;
+    tracks: any[];
+    minimized: boolean;
+    displayedRegions: Region[];
+    offsetPx: number;
+    bpPerPx: number;
+    hideHeader: boolean;
+    hideHeaderOverview: boolean;
+    hideNoTracksActive: boolean;
+    trackSelectorType: string;
+    showCenterLine: boolean;
+    showCytobandsSetting: boolean;
+    trackLabels: string;
+    showGridlines: boolean;
+    highlight: HighlightType[];
+    colorByCDS: boolean;
+    showTrackOutlines: boolean;
+}>;
 export type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
 export { default as LinearGenomeView, default as ReactComponent, } from './components/LinearGenomeView';

package/esm/LinearGenomeView/model.js

@@ -53,6 +53,7 @@ export function stateModelFactory(pluginManager) {
         highlight: types.optional(types.array(types.frozen()), []),
         colorByCDS: types.optional(types.boolean, () => localStorageGetBoolean('lgv-colorByCDS', false)),
         showTrackOutlines: types.optional(types.boolean, () => localStorageGetBoolean('lgv-showTrackOutlines', true)),
+        init: types.frozen(),
     }))
         .volatile(() => ({
         volatileWidth: undefined,
@@ -101,10 +102,10 @@ export function stateModelFactory(pluginManager) {
                 ? session.stickyViewHeaders
                 : false;
         },
-        get pinnedTracksTop() {
+        get rubberbandTop() {
             let pinnedTracksTop = 0;
             if (this.stickyViewHeaders) {
-                pinnedTracksTop = VIEW_HEADER_HEIGHT + SCALE_BAR_HEIGHT;
+                pinnedTracksTop = VIEW_HEADER_HEIGHT;
                 if (!self.hideHeader) {
                     pinnedTracksTop += HEADER_BAR_HEIGHT;
                     if (!self.hideHeaderOverview) {
@@ -114,6 +115,9 @@ export function stateModelFactory(pluginManager) {
             }
             return pinnedTracksTop;
         },
+        get pinnedTracksTop() {
+            return this.rubberbandTop + SCALE_BAR_HEIGHT;
+        },
     }))
         .views(self => ({
         scaleBarDisplayPrefix() {
@@ -227,32 +231,32 @@ export function stateModelFactory(pluginManager) {
             return results;
         },
         rewriteOnClicks(trackType, viewMenuActions) {
-            viewMenuActions.forEach(action => {
+            for (const action of viewMenuActions) {
                 if ('subMenu' in action) {
                     this.rewriteOnClicks(trackType, action.subMenu);
                 }
                 if ('onClick' in action) {
                     const holdOnClick = action.onClick;
                     action.onClick = (...args) => {
-                        self.tracks.forEach(track => {
+                        for (const track of self.tracks) {
                             if (track.type === trackType) {
                                 holdOnClick.apply(track, [track, ...args]);
                             }
-                        });
+                        }
                     };
                 }
-            });
+            }
         },
         get trackTypeActions() {
             const allActions = new Map();
-            self.tracks.forEach(track => {
+            for (const track of self.tracks) {
                 const trackInMap = allActions.get(track.type);
                 if (!trackInMap) {
                     const viewMenuActions = structuredClone(track.viewMenuActions);
                     this.rewriteOnClicks(track.type, viewMenuActions);
                     allActions.set(track.type, viewMenuActions);
                 }
-            });
+            }
             return allActions;
         },
     }))
@@ -377,11 +381,13 @@ export function stateModelFactory(pluginManager) {
         hideTrack(trackId) {
             const schema = pluginManager.pluggableConfigSchemaType('track');
             const conf = resolveIdentifier(schema, getRoot(self), trackId);
-            const t = self.tracks.filter(t => t.configuration === conf);
+            const tracks = self.tracks.filter(t => t.configuration === conf);
             transaction(() => {
-                t.forEach(t => self.tracks.remove(t));
+                for (const track of tracks) {
+                    self.tracks.remove(track);
+                }
             });
-            return t.length;
+            return tracks.length;
         },
     }))
         .actions(self => ({
@@ -522,6 +528,9 @@ export function stateModelFactory(pluginManager) {
             self.scrollTo(0);
             self.zoomTo(10);
         },
+        setInit(arg) {
+            self.init = arg;
+        },
         async exportSvg(opts = {}) {
             const { renderToSvg } = await import('./svgcomponents/SVGLinearGenomeView');
             const html = await renderToSvg(self, opts);
@@ -742,7 +751,9 @@ export function stateModelFactory(pluginManager) {
             for (const [key, value] of self.trackTypeActions.entries()) {
                 if (value.length) {
                     menuItems.push({ type: 'divider' }, { type: 'subHeader', label: key });
-                    value.forEach(action => menuItems.push(action));
+                    for (const action of value) {
+                        menuItems.push(action);
+                    }
                 }
             }
             return menuItems;
@@ -784,20 +795,6 @@ export function stateModelFactory(pluginManager) {
             self.coarseDynamicBlocks = blocks.contentBlocks;
             self.coarseTotalBp = blocks.totalBp;
         },
-        afterAttach() {
-            addDisposer(self, autorun(() => {
-                if (self.initialized) {
-                    this.setCoarseDynamicBlocks(self.dynamicBlocks);
-                }
-            }, { delay: 150 }));
-            addDisposer(self, autorun(() => {
-                const s = (s) => JSON.stringify(s);
-                const { showCytobandsSetting, showCenterLine, colorByCDS } = self;
-                localStorageSetItem('lgv-showCytobands', s(showCytobandsSetting));
-                localStorageSetItem('lgv-showCenterLine', s(showCenterLine));
-                localStorageSetItem('lgv-colorByCDS', s(colorByCDS));
-            }));
-        },
     }))
         .actions(self => ({
         moveTo(start, end) {
@@ -964,6 +961,33 @@ export function stateModelFactory(pluginManager) {
                 document.removeEventListener('keydown', handler);
             });
         },
+        afterAttach() {
+            addDisposer(self, autorun(() => {
+                var _a;
+                const { init } = self;
+                if (init) {
+                    self
+                        .navToLocString(init.loc, init.assembly)
+                        .catch((e) => {
+                        getSession(self).notifyError(`${e}`, e);
+                    });
+                    (_a = init.tracks) === null || _a === void 0 ? void 0 : _a.map(t => self.showTrack(t));
+                    self.setInit(undefined);
+                }
+            }));
+            addDisposer(self, autorun(() => {
+                if (self.initialized) {
+                    self.setCoarseDynamicBlocks(self.dynamicBlocks);
+                }
+            }, { delay: 150 }));
+            addDisposer(self, autorun(() => {
+                const s = (s) => JSON.stringify(s);
+                const { showCytobandsSetting, showCenterLine, colorByCDS } = self;
+                localStorageSetItem('lgv-showCytobands', s(showCytobandsSetting));
+                localStorageSetItem('lgv-showCenterLine', s(showCenterLine));
+                localStorageSetItem('lgv-colorByCDS', s(colorByCDS));
+            }));
+        },
     }))
         .preProcessSnapshot(snap => {
         if (!snap) {
@@ -976,6 +1000,15 @@ export function stateModelFactory(pluginManager) {
                 : [highlight],
             ...rest,
         };
+    })
+        .postProcessSnapshot(snap => {
+        if (!snap) {
+            return snap;
+        }
+        else {
+            const { init, ...rest } = snap;
+            return rest;
+        }
     });
 }
 export { default as LinearGenomeView, default as ReactComponent, } from './components/LinearGenomeView';

package/esm/LinearGenomeView/types.d.ts

@@ -36,3 +36,8 @@ export interface NavLocation {
     end?: number;
     assemblyName?: string;
 }
+export interface InitState {
+    loc: string;
+    assembly: string;
+    tracks?: string[];
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "3.1.0",
+  "version": "3.2.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -38,7 +38,7 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@jbrowse/core": "^3.1.0",
+    "@jbrowse/core": "^3.2.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "@types/file-saver": "^2.0.1",
@@ -58,5 +58,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
+  "gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
 }