@jbrowse/plugin-linear-genome-view 2.10.2 → 2.11.0

package/esm/LinearGenomeView/components/OverviewScalebar.js

@@ -4,7 +4,7 @@ import { makeStyles } from 'tss-react/mui';
 import { observer } from 'mobx-react';
 // core
 import Base1DView from '@jbrowse/core/util/Base1DViewModel';
-import { getSession, getTickDisplayStr } from '@jbrowse/core/util';
+import { getEnv, getSession, getTickDisplayStr } from '@jbrowse/core/util';
 import { ContentBlock } from '@jbrowse/core/util/blockTypes';
 // locals
 import { HEADER_BAR_HEIGHT, HEADER_OVERVIEW_HEIGHT, } from '..';
@@ -13,6 +13,7 @@ import { getCytobands } from './util';
 import OverviewRubberband from './OverviewRubberband';
 import Cytobands from './Cytobands';
 import OverviewScalebarPolygon from './OverviewScalebarPolygon';
+import OverviewHighlight from './OverviewHighlight';
 const wholeSeqSpacer = 2;
 const useStyles = makeStyles()(theme => ({
     scalebar: {
@@ -117,6 +118,7 @@ const Scalebar = observer(function ({ model, scale, overview, }) {
     const { classes } = useStyles();
     const theme = useTheme();
     const { dynamicBlocks, showCytobands, cytobandOffset } = model;
+    const { pluginManager } = getEnv(model);
     const visibleRegions = dynamicBlocks.contentBlocks;
     const overviewVisibleRegions = overview.dynamicBlocks;
     const { tertiary, primary } = theme.palette;
@@ -137,6 +139,7 @@ const Scalebar = observer(function ({ model, scale, overview, }) {
     }) || 0;
     const color = showCytobands ? '#f00' : scalebarColor;
     const transparency = showCytobands ? 0.1 : 0.3;
+    const additional = pluginManager.evaluateExtensionPoint('LinearGenomeView-OverviewScalebarComponent', undefined, { model, overview });
     return (React.createElement("div", { className: classes.scalebar },
         React.createElement("div", { className: classes.scalebarVisibleRegion, style: {
                 width: lastOverviewPx - firstOverviewPx,
@@ -151,7 +154,9 @@ const Scalebar = observer(function ({ model, scale, overview, }) {
                     backgroundColor: '#999',
                     backgroundImage: 'repeating-linear-gradient(90deg, transparent, transparent 1px, rgba(255,255,255,.5) 1px, rgba(255,255,255,.5) 3px)',
                 } })) : (React.createElement(OverviewBox, { scale: scale, block: block, model: model, overview: overview, key: `${JSON.stringify(block)}-${idx}` }));
-        })));
+        }),
+        React.createElement(OverviewHighlight, { model: model, overview: overview }),
+        additional));
 });
 const OverviewScalebar = observer(function ({ model, children, }) {
     const { classes } = useStyles();

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

@@ -4,6 +4,6 @@ import { LinearGenomeViewModel } from '..';
 declare const OverviewScalebarPolygon: ({ model, overview, useOffset, }: {
     model: LinearGenomeViewModel;
     overview: Base1DViewModel;
-    useOffset?: boolean | undefined;
+    useOffset?: boolean;
 }) => React.JSX.Element | null;
 export default OverviewScalebarPolygon;

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

@@ -4,15 +4,15 @@ import { TextFieldProps as TFP } from '@mui/material';
 import { LinearGenomeViewModel } from '../../model';
 declare const RefNameAutocomplete: ({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp, minWidth, maxWidth, TextFieldProps, }: {
     model: LinearGenomeViewModel;
-    onSelect?: ((region: BaseResult) => void) | undefined;
-    onChange?: ((val: string) => void) | undefined;
-    assemblyName?: string | undefined;
-    value?: string | undefined;
+    onSelect?: (region: BaseResult) => void;
+    onChange?: (val: string) => void;
+    assemblyName?: string;
+    value?: string;
     fetchResults: (query: string) => Promise<BaseResult[]>;
-    style?: React.CSSProperties | undefined;
-    minWidth?: number | undefined;
-    maxWidth?: number | undefined;
-    showHelp?: boolean | undefined;
-    TextFieldProps?: TFP | undefined;
+    style?: React.CSSProperties;
+    minWidth?: number;
+    maxWidth?: number;
+    showHelp?: boolean;
+    TextFieldProps?: TFP;
 }) => React.JSX.Element;
 export default RefNameAutocomplete;

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

@@ -17,7 +17,8 @@ const RefNameAutocomplete = observer(function ({ model, onSelect, assemblyName,
     const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined;
     const { coarseVisibleLocStrings, hasDisplayedRegions } = model;
     useEffect(() => {
-        let active = true;
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
         (async () => {
             try {
                 if (debouncedSearch === '' || !assemblyName) {
@@ -25,21 +26,14 @@ const RefNameAutocomplete = observer(function ({ model, onSelect, assemblyName,
                 }
                 setLoaded(false);
                 const results = await fetchResults(debouncedSearch);
-                if (active) {
-                    setLoaded(true);
-                    setSearchOptions(getDeduplicatedResult(results));
-                }
+                setLoaded(true);
+                setSearchOptions(getDeduplicatedResult(results));
             }
             catch (e) {
                 console.error(e);
-                if (active) {
-                    session.notify(`${e}`, 'error');
-                }
+                session.notifyError(`${e}`, e);
             }
         })();
-        return () => {
-            active = false;
-        };
     }, [assemblyName, fetchResults, debouncedSearch, session, model]);
     const inputBoxVal = coarseVisibleLocStrings || value || '';
     // heuristic, text width + 60 accommodates help icon and search icon
@@ -54,29 +48,28 @@ const RefNameAutocomplete = observer(function ({ model, onSelect, assemblyName,
     }))) || [], [regions]);
     // notes on implementation:
     // The selectOnFocus setting helps highlight the field when clicked
-    return (React.createElement(React.Fragment, null,
-        React.createElement(Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: { ...style, width }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (_event, newInputValue) => {
-                setInputValue(newInputValue);
-                onChange === null || onChange === void 0 ? void 0 : onChange(newInputValue);
-            }, loadingText: "loading results", open: open, onOpen: () => setOpen(true), onClose: () => {
-                setOpen(false);
-                setLoaded(true);
-                if (hasDisplayedRegions) {
-                    setCurrentSearch('');
-                    setSearchOptions(undefined);
-                }
-            }, onChange: (_event, selectedOption) => {
-                if (!selectedOption || !assemblyName) {
-                    return;
-                }
-                if (typeof selectedOption === 'string') {
-                    // handles string inputs on keyPress enter
-                    onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResult({ label: selectedOption }));
-                }
-                else {
-                    onSelect === null || onSelect === void 0 ? void 0 : onSelect(selectedOption.result);
-                }
-                setInputValue(inputBoxVal);
-            }, options: (searchOptions === null || searchOptions === void 0 ? void 0 : searchOptions.length) ? searchOptions : regionOptions, getOptionDisabled: option => option.group === 'limitOption', filterOptions: (opts, { inputValue }) => getFiltered(opts, inputValue), renderInput: params => (React.createElement(AutocompleteTextField, { showHelp: showHelp, params: params, inputBoxVal: inputBoxVal, TextFieldProps: TextFieldProps, setCurrentSearch: setCurrentSearch, setInputValue: setInputValue })), getOptionLabel: opt => typeof opt === 'string' ? opt : opt.result.getDisplayString() })));
+    return (React.createElement(Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: { ...style, width }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (_event, newInputValue) => {
+            setInputValue(newInputValue);
+            onChange === null || onChange === void 0 ? void 0 : onChange(newInputValue);
+        }, loadingText: "loading results", open: open, onOpen: () => setOpen(true), onClose: () => {
+            setOpen(false);
+            setLoaded(true);
+            if (hasDisplayedRegions) {
+                setCurrentSearch('');
+                setSearchOptions(undefined);
+            }
+        }, onChange: (_event, selectedOption) => {
+            if (!selectedOption || !assemblyName) {
+                return;
+            }
+            if (typeof selectedOption === 'string') {
+                // handles string inputs on keyPress enter
+                onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResult({ label: selectedOption }));
+            }
+            else {
+                onSelect === null || onSelect === void 0 ? void 0 : onSelect(selectedOption.result);
+            }
+            setInputValue(inputBoxVal);
+        }, options: (searchOptions === null || searchOptions === void 0 ? void 0 : searchOptions.length) ? searchOptions : regionOptions, getOptionDisabled: option => option.group === 'limitOption', filterOptions: (opts, { inputValue }) => getFiltered(opts, inputValue), renderInput: params => (React.createElement(AutocompleteTextField, { showHelp: showHelp, params: params, inputBoxVal: inputBoxVal, TextFieldProps: TextFieldProps, setCurrentSearch: setCurrentSearch, setInputValue: setInputValue })), getOptionLabel: opt => typeof opt === 'string' ? opt : opt.result.getDisplayString() }));
 });
 export default RefNameAutocomplete;

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

@@ -3,6 +3,6 @@ import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare const Rubberband: ({ model, ControlComponent, }: {
     model: LGV;
-    ControlComponent?: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+    ControlComponent?: React.ReactElement;
 }) => React.JSX.Element;
 export default Rubberband;

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

@@ -1,7 +1,7 @@
 import React from 'react';
 import { LinearGenomeViewModel } from '..';
 declare const SearchBox: ({ model, showHelp, }: {
-    showHelp?: boolean | undefined;
+    showHelp?: boolean;
     model: LinearGenomeViewModel;
 }) => React.JSX.Element;
 export default SearchBox;

package/esm/LinearGenomeView/components/SearchResultsTable.js

@@ -69,7 +69,7 @@ export default function SearchResultsTable({ searchResults, assemblyName: optAss
                             }
                             catch (e) {
                                 console.error(e);
-                                session.notify(`${e}`, 'error');
+                                session.notifyError(`${e}`, e);
                             }
                             handleClose();
                         }, color: "primary", variant: "contained" }, "Go")))))))));

package/esm/LinearGenomeView/components/TrackContainer.js

@@ -5,7 +5,6 @@ import { observer } from 'mobx-react';
 import { isAlive } from 'mobx-state-tree';
 import { ErrorBoundary } from 'react-error-boundary';
 import { ResizeHandle, ErrorMessage } from '@jbrowse/core/ui';
-import { useDebouncedCallback } from '@jbrowse/core/util';
 import TrackLabelContainer from './TrackLabelContainer';
 import TrackRenderingContainer from './TrackRenderingContainer';
 const useStyles = makeStyles()({
@@ -18,40 +17,28 @@ const useStyles = makeStyles()({
         position: 'relative',
         zIndex: 2,
     },
-    overlay: {
-        pointerEvents: 'none',
-        position: 'absolute',
-        top: 0,
-        left: 0,
-        width: '100%',
-        zIndex: 3,
-    },
 });
 const TrackContainer = observer(function ({ model, track, }) {
     const { classes } = useStyles();
     const display = track.displays[0];
     const { draggingTrackId } = model;
-    const ref2 = useRef(null);
-    const dimmed = draggingTrackId !== undefined && draggingTrackId !== display.id;
-    const debouncedOnDragEnter = useDebouncedCallback(() => {
-        if (isAlive(display) && dimmed) {
-            model.moveTrack(draggingTrackId, track.id);
-        }
-    }, 100);
-    return (React.createElement(Paper, { ref: ref2, className: classes.root, variant: "outlined", onClick: event => {
+    const ref = useRef(null);
+    return (React.createElement(Paper, { ref: ref, className: classes.root, variant: "outlined", onClick: event => {
             var _a;
             if (event.detail === 2 && !track.displays[0].featureIdUnderMouse) {
-                const left = ((_a = ref2.current) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect().left) || 0;
+                const left = ((_a = ref.current) === null || _a === void 0 ? void 0 : _a.getBoundingClientRect().left) || 0;
                 model.zoomTo(model.bpPerPx / 2, event.clientX - left, true);
             }
         } },
         React.createElement(TrackLabelContainer, { track: track, view: model }),
         React.createElement(ErrorBoundary, { FallbackComponent: e => React.createElement(ErrorMessage, { error: e.error }) },
-            React.createElement(TrackRenderingContainer, { model: model, track: track, onDragEnter: debouncedOnDragEnter })),
-        React.createElement("div", { className: classes.overlay, style: {
-                height: display.height,
-                background: dimmed ? 'rgba(0, 0, 0, 0.4)' : undefined,
-            }, onDragEnter: debouncedOnDragEnter }),
+            React.createElement(TrackRenderingContainer, { model: model, track: track, onDragEnter: () => {
+                    if (isAlive(display) &&
+                        draggingTrackId !== undefined &&
+                        draggingTrackId !== display.id) {
+                        model.moveTrack(draggingTrackId, track.id);
+                    }
+                } })),
         React.createElement(ResizeHandle, { onDrag: display.resizeHeight, className: classes.resizeHandle })));
 });
 export default TrackContainer;

package/esm/LinearGenomeView/components/TrackLabel.js

@@ -12,6 +12,10 @@ import MoreVertIcon from '@mui/icons-material/MoreVert';
 import CloseIcon from '@mui/icons-material/Close';
 import MinimizeIcon from '@mui/icons-material/Minimize';
 import AddIcon from '@mui/icons-material/Add';
+import KeyboardDoubleArrowDownIcon from '@mui/icons-material/KeyboardDoubleArrowDown';
+import KeyboardDoubleArrowUpIcon from '@mui/icons-material/KeyboardDoubleArrowUp';
+import KeyboardArrowDownIcon from '@mui/icons-material/KeyboardArrowDown';
+import KeyboardArrowUpIcon from '@mui/icons-material/KeyboardArrowUp';
 import TrackLabelDragHandle from './TrackLabelDragHandle';
 const useStyles = makeStyles()(theme => ({
     root: {
@@ -19,9 +23,6 @@ const useStyles = makeStyles()(theme => ({
         '&:hover': {
             background: theme.palette.background.paper,
         },
-        transition: theme.transitions.create(['background'], {
-            duration: theme.transitions.duration.shortest,
-        }),
     },
     trackName: {
         margin: '0 auto',
@@ -44,9 +45,35 @@ const TrackLabel = observer(React.forwardRef(function TrackLabel2({ track, class
     const trackName = getTrackName(trackConf, session);
     const items = [
         {
-            label: minimized ? 'Restore track' : 'Minimize track',
-            icon: minimized ? AddIcon : MinimizeIcon,
-            onClick: () => track.setMinimized(!minimized),
+            label: 'Track order',
+            type: 'subMenu',
+            subMenu: [
+                {
+                    label: minimized ? 'Restore track' : 'Minimize track',
+                    icon: minimized ? AddIcon : MinimizeIcon,
+                    onClick: () => track.setMinimized(!minimized),
+                },
+                {
+                    label: 'Move track to top',
+                    icon: KeyboardDoubleArrowUpIcon,
+                    onClick: () => view.moveTrackToTop(track.id),
+                },
+                {
+                    label: 'Move track up',
+                    icon: KeyboardArrowUpIcon,
+                    onClick: () => view.moveTrackUp(track.id),
+                },
+                {
+                    label: 'Move track down',
+                    icon: KeyboardArrowDownIcon,
+                    onClick: () => view.moveTrackDown(track.id),
+                },
+                {
+                    label: 'Move track to bottom',
+                    icon: KeyboardDoubleArrowDownIcon,
+                    onClick: () => view.moveTrackToBottom(track.id),
+                },
+            ],
         },
         ...(((_a = session.getTrackActionMenuItems) === null || _a === void 0 ? void 0 : _a.call(session, trackConf)) || []),
         ...track.trackMenuItems(),

package/esm/LinearGenomeView/components/TracksContainer.js

@@ -13,6 +13,7 @@ import Gridlines from './Gridlines';
 import CenterLine from './CenterLine';
 import VerticalGuide from './VerticalGuide';
 import RubberbandSpan from './RubberbandSpan';
+import HighlightGroup from './Highlight';
 const useStyles = makeStyles()({
     tracksContainer: {
         position: 'relative',
@@ -39,6 +40,7 @@ const TracksContainer = observer(function TracksContainer({ children, model, })
                 top: anchorPosition.clientY,
             }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: model.rubberBandMenuItems() })) : null,
         React.createElement(Rubberband, { model: model, ControlComponent: React.createElement(Scalebar, { model: model, style: { height: SCALE_BAR_HEIGHT, boxSizing: 'border-box' } }) }),
+        React.createElement(HighlightGroup, { model: model }),
         additional,
         children));
 });

package/esm/LinearGenomeView/components/ZoomControls.js

@@ -17,16 +17,16 @@ const useStyles = makeStyles()(theme => ({
 }));
 const ZoomControls = observer(function ({ model, }) {
     const { classes } = useStyles();
-    const { maxBpPerPx, minBpPerPx, bpPerPx, scaleFactor } = model;
+    const { maxBpPerPx, minBpPerPx, bpPerPx } = model;
     const [value, setValue] = useState(-Math.log2(bpPerPx) * 100);
     useEffect(() => {
         setValue(-Math.log2(bpPerPx) * 100);
     }, [setValue, bpPerPx]);
     return (React.createElement("div", { className: classes.container },
-        React.createElement(IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1, size: "large" },
+        React.createElement(IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001, size: "large" },
             React.createElement(ZoomOut, null)),
-        React.createElement(Slider, { size: "small", className: classes.slider, value: value, min: -Math.log2(maxBpPerPx) * 100, max: -Math.log2(minBpPerPx) * 100, onChange: (_, val) => setValue(val), onChangeCommitted: () => model.zoomTo(2 ** (-value / 100)), disabled: scaleFactor !== 1 }),
-        React.createElement(IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(model.bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1, size: "large" },
+        React.createElement(Slider, { size: "small", className: classes.slider, value: value, min: -Math.log2(maxBpPerPx) * 100, max: -Math.log2(minBpPerPx) * 100, onChange: (_, val) => setValue(val), onChangeCommitted: () => model.zoomTo(2 ** (-value / 100)) }),
+        React.createElement(IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(model.bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001, size: "large" },
             React.createElement(ZoomIn, null))));
 });
 export default ZoomControls;

package/esm/LinearGenomeView/model.d.ts

@@ -81,6 +81,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<ParsedLocString>, Required<ParsedLocString>, Required<ParsedLocString>>>, [undefined]>;
+    colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, {
     width: number;
 } & {
@@ -223,6 +225,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     readonly trackTypeActions: Map<string, MenuItem[]>;
 } & {
+    /**
+     * #action
+     */
+    setColorByCDS(flag: boolean): void;
     /**
      * #action
      */
@@ -251,6 +257,18 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     setShowGridlines(b: boolean): void;
+    /**
+     * #action
+     */
+    addToHighlights(highlight: Required<ParsedLocString>): void;
+    /**
+     * #action
+     */
+    setHighlight(highlight: Required<ParsedLocString>[] | undefined): void;
+    /**
+     * #action
+     */
+    removeHighlight(highlight: Required<ParsedLocString>): void;
     /**
      * #action
      */
@@ -287,6 +305,22 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      */
     hideTrack(trackId: string): number;
 } & {
+    /**
+     * #action
+     */
+    moveTrackDown(id: string): void;
+    /**
+     * #action
+     */
+    moveTrackUp(id: string): void;
+    /**
+     * #action
+     */
+    moveTrackToTop(id: string): void;
+    /**
+     * #action
+     */
+    moveTrackToBottom(id: string): void;
     /**
      * #action
      */
@@ -523,20 +557,21 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     bpToPx({ refName, coord, regionNumber, }: {
         refName: string;
         coord: number;
-        regionNumber?: number | undefined;
+        regionNumber?: number;
     }): {
         index: number;
         offsetPx: number;
     } | undefined;
     /**
      * #method
-     * scrolls the view to center on the given bp. if that is not in any
-     * of the displayed regions, does nothing
+     * scrolls the view to center on the given bp. if that is not in any of
+     * the displayed regions, does nothing
+     *
      * @param coord - basepair at which you want to center the view
      * @param refName - refName of the displayedRegion you are centering at
      * @param regionNumber - index of the displayedRegion
      */
-    centerAt(coord: number, refName: string, regionNumber: number): void;
+    centerAt(coord: number, refName: string, regionNumber?: number): void;
     /**
      * #method
      */
@@ -567,7 +602,37 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } | undefined;
 } & {
     afterCreate(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, 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>>;
+    minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+} & {
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").IType<string | undefined, string, string>;
+    offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+    bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+    displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+        refName: import("mobx-state-tree").ISimpleType<string>;
+        start: import("mobx-state-tree").ISimpleType<number>;
+        end: import("mobx-state-tree").ISimpleType<number>;
+        reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    } & {
+        assemblyName: import("mobx-state-tree").ISimpleType<string>;
+    }, {
+        setRefName(newRefName: string): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
+    hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<ParsedLocString>, Required<ParsedLocString>, Required<ParsedLocString>>>, [undefined]>;
+    colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+}>>, import("mobx-state-tree")._NotCustomized>;
 export type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
 export { default as ReactComponent, default as LinearGenomeView, } from './components/LinearGenomeView';