@jbrowse/plugin-linear-comparative-view 2.10.3 → 2.11.1

package/dist/SyntenyFeatureDetail/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function SyntenyFeatureWidgetF(pluginManager: PluginManager): void;

package/dist/SyntenyFeatureDetail/index.js

@@ -46,7 +46,7 @@ const stateModel = mobx_state_tree_1.types
         self.featureData = undefined;
     },
 }));
-exports.default = (pluginManager) => {
+function SyntenyFeatureWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => new WidgetType_1.default({
         name: 'SyntenyFeatureWidget',
         heading: 'Synteny feature details',
@@ -54,4 +54,5 @@ exports.default = (pluginManager) => {
         stateModel,
         ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SyntenyFeatureDetail')))),
     }));
-};
+}
+exports.default = SyntenyFeatureWidgetF;

package/dist/index.d.ts

@@ -1,6 +1,6 @@
 import Plugin from '@jbrowse/core/Plugin';
 import PluginManager from '@jbrowse/core/PluginManager';
-export default class extends Plugin {
+export default class LinearComparativeViewPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;
     configure(pluginManager: PluginManager): void;

package/dist/index.js

@@ -15,7 +15,7 @@ const LaunchLinearSyntenyView_1 = __importDefault(require("./LaunchLinearSynteny
 const SyntenyTrack_1 = __importDefault(require("./SyntenyTrack"));
 const SyntenyFeatureDetail_1 = __importDefault(require("./SyntenyFeatureDetail"));
 const LinearReadVsRef_1 = __importDefault(require("./LinearReadVsRef"));
-class default_1 extends Plugin_1.default {
+class LinearComparativeViewPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
         this.name = 'LinearComparativeViewPlugin';
@@ -43,4 +43,4 @@ class default_1 extends Plugin_1.default {
         }
     }
 }
-exports.default = default_1;
+exports.default = LinearComparativeViewPlugin;

package/esm/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js

@@ -33,7 +33,8 @@ export default function LaunchSyntenyViewDialog({ model, feature, handleClose, }
                             });
                         }
                         catch (e) {
-                            getSession(model).notify(`${e}`, 'error');
+                            console.error(e);
+                            getSession(model).notifyError(`${e}`, e);
                         }
                     })();
                     handleClose();

package/esm/LGVSyntenyDisplay/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LGVSyntenyDisplayF(pluginManager: PluginManager): void;

package/esm/LGVSyntenyDisplay/index.js

@@ -2,7 +2,7 @@ import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 import configSchemaF from './configSchemaF';
 import stateModelF from './model';
 import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
-export default (pluginManager) => {
+export default function LGVSyntenyDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaF(pluginManager);
         const stateModel = stateModelF(configSchema);
@@ -15,4 +15,4 @@ export default (pluginManager) => {
             ReactComponent: BaseLinearDisplayComponent,
         });
     });
-};
+}

package/esm/LaunchLinearSyntenyView.js

@@ -38,7 +38,7 @@ export default function LaunchLinearSyntenyView(pluginManager) {
             }
         }
         catch (e) {
-            session.notify(`${e}`, 'error');
+            session.notifyError(`${e}`, e);
             throw e;
         }
     });

package/esm/LinearComparativeDisplay/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearComparativeDisplayF(pluginManager: PluginManager): void;

package/esm/LinearComparativeDisplay/index.js

@@ -1,7 +1,7 @@
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 import configSchemaFactory from './configSchemaF';
 import stateModelFactory from './stateModelFactory';
-export default (pluginManager) => {
+export default function LinearComparativeDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaFactory(pluginManager);
         return new DisplayType({
@@ -15,4 +15,4 @@ export default (pluginManager) => {
             },
         });
     });
-};
+}

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

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

package/esm/LinearComparativeView/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearComparativeViewF(pluginManager: PluginManager): void;

package/esm/LinearComparativeView/index.js

@@ -1,7 +1,7 @@
 import { lazy } from 'react';
 import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
 import modelFactory from './model';
-export default (pluginManager) => {
+export default function LinearComparativeViewF(pluginManager) {
     pluginManager.addViewType(() => {
         return new ViewType({
             name: 'LinearComparativeView',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
             ReactComponent: lazy(() => import('./components/LinearComparativeView')),
         });
     });
-};
+}

package/esm/LinearComparativeView/model.d.ts

@@ -49,7 +49,8 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         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").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
+        colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }, {
         width: number;
     } & {
@@ -105,6 +106,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         rewriteOnClicks(trackType: string, viewMenuActions: MenuItem[]): void;
         readonly trackTypeActions: Map<string, MenuItem[]>;
     } & {
+        setColorByCDS(flag: boolean): void;
         setShowCytobands(flag: boolean): void;
         setWidth(newWidth: number): void;
         setError(error: unknown): void;
@@ -112,7 +114,9 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         setHideHeaderOverview(b: boolean): void;
         setHideNoTracksActive(b: boolean): void;
         setShowGridlines(b: boolean): void;
-        setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
+        addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
+        setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
+        removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
         scrollTo(offsetPx: number): number;
         zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
         setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
@@ -122,6 +126,10 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
         hideTrack(trackId: string): number;
     } & {
+        moveTrackDown(id: string): void;
+        moveTrackUp(id: string): void;
+        moveTrackToTop(id: string): void;
+        moveTrackToBottom(id: string): void;
         moveTrack(movingId: string, targetId: string): void;
         closeView(): void;
         toggleTrack(trackId: string): boolean;
@@ -321,7 +329,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
             index: number;
             offsetPx: number;
         } | undefined;
-        centerAt(coord: number, refName: string, regionNumber: number): void;
+        centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
         pxToBp(px: number): {
             coord: number;
             index: number;
@@ -346,7 +354,37 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         } | 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<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
+        colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    }>>, import("mobx-state-tree")._NotCustomized>>;
     viewTrackConfigs: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
 }, {
     width: number;

package/esm/LinearReadVsRef/index.d.ts

@@ -1,2 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function (pm: PluginManager): void;
+export default function LinearReadVsRefMenuItemF(pm: PluginManager): void;

package/esm/LinearReadVsRef/index.js

@@ -7,7 +7,7 @@ const ReadVsRefDialog = lazy(() => import('./LinearReadVsRef'));
 function isDisplay(elt) {
     return elt.name === 'LinearPileupDisplay';
 }
-export default function (pm) {
+export default function LinearReadVsRefMenuItemF(pm) {
     pm.addToExtensionPoint('Core-extendPluggableElement', (pluggableElement) => {
         if (!isDisplay(pluggableElement)) {
             return pluggableElement;

package/esm/LinearSyntenyDisplay/components/SyntenyContextMenu.js

@@ -37,13 +37,13 @@ export default function SyntenyContextMenu({ model, onClose, anchorEl, }) {
                         .navToLocString(`${refName}:${start}-${end}`)
                         .catch(e => {
                         console.error(e);
-                        getSession(model).notify(`${e}`, 'error');
+                        getSession(model).notifyError(`${e}`, e);
                     });
                     view.views[1]
                         .navToLocString(`${mate.refName}:${mate.start}-${mate.end}`)
                         .catch(e => {
                         console.error(e);
-                        getSession(model).notify(`${e}`, 'error');
+                        getSession(model).notifyError(`${e}`, e);
                     });
                 },
             },

package/esm/LinearSyntenyDisplay/components/SyntenyTooltip.js

@@ -30,6 +30,7 @@ const SyntenyTooltip = observer(function ({ title }) {
     const { classes } = useStyles();
     const { refs, floatingStyles, context } = useFloating({
         placement: 'right',
+        strategy: 'fixed',
     });
     const clientPoint = useClientPoint(context);
     const { getFloatingProps } = useInteractions([clientPoint]);

package/esm/LinearSyntenyDisplay/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearSyntenyDisplayF(pluginManager: PluginManager): void;

package/esm/LinearSyntenyDisplay/index.js

@@ -3,7 +3,7 @@ import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 import configSchemaF from './configSchemaF';
 import stateModelFactory from './model';
 import { lazy } from 'react';
-export default (pluginManager) => {
+export default function LinearSyntenyDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaF(pluginManager);
         return new DisplayType({
@@ -15,4 +15,4 @@ export default (pluginManager) => {
             ReactComponent: lazy(() => import('./components/Component')),
         });
     });
-};
+}

package/esm/LinearSyntenyView/components/ExportSvgDialog.js

@@ -10,6 +10,10 @@ function LoadingMessage() {
 function useSvgLocal(key, val) {
     return useLocalStorage('svg-' + key, val);
 }
+function TextField2({ children, ...rest }) {
+    return (React.createElement("div", null,
+        React.createElement(TextField, { ...rest }, children)));
+}
 export default function ExportSvgDialog({ model, handleClose, }) {
     const session = getSession(model);
     const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
@@ -22,15 +26,14 @@ export default function ExportSvgDialog({ model, handleClose, }) {
     return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
         React.createElement(DialogContent, null,
             error ? (React.createElement(ErrorMessage, { error: error })) : loading ? (React.createElement(LoadingMessage, null)) : null,
-            React.createElement(TextField, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
-            React.createElement("br", null),
-            React.createElement(TextField, { select: true, label: "Track label positioning", variant: "outlined", value: trackLabels, style: { width: 150 }, onChange: event => setTrackLabels(event.target.value) },
+            React.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
+            React.createElement(TextField2, { select: true, label: "Track label positioning", variant: "outlined", value: trackLabels, style: { width: 150 }, onChange: event => setTrackLabels(event.target.value) },
                 React.createElement(MenuItem, { value: "offset" }, "Offset"),
                 React.createElement(MenuItem, { value: "overlay" }, "Overlay"),
                 React.createElement(MenuItem, { value: "left" }, "Left"),
                 React.createElement(MenuItem, { value: "none" }, "None")),
             React.createElement("br", null),
-            session.allThemes ? (React.createElement(TextField, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (React.createElement(MenuItem, { key: key, value: key }, 
+            session.allThemes ? (React.createElement(TextField2, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (React.createElement(MenuItem, { key: key, value: key }, 
             // @ts-expect-error
             val.name || '(Unknown name)'))))) : null,
             offscreenCanvas ? (React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: rasterizeLayers, onChange: () => setRasterizeLayers(val => !val) }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (React.createElement(Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),

package/esm/LinearSyntenyView/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearSyntenyViewF(pluginManager: PluginManager): void;

package/esm/LinearSyntenyView/index.js

@@ -1,7 +1,7 @@
 import { lazy } from 'react';
 import modelFactory from './model';
 import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType';
-export default (pluginManager) => {
+export default function LinearSyntenyViewF(pluginManager) {
     pluginManager.addViewType(() => {
         return new ViewType({
             name: 'LinearSyntenyView',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
             ReactComponent: lazy(() => import('./components/LinearSyntenyView')),
         });
     });
-};
+}

package/esm/LinearSyntenyView/model.d.ts

@@ -68,7 +68,8 @@ export default 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").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
+        colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }, {
         width: number;
     } & {
@@ -124,6 +125,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
         readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
     } & {
+        setColorByCDS(flag: boolean): void;
         setShowCytobands(flag: boolean): void;
         setWidth(newWidth: number): void;
         setError(error: unknown): void;
@@ -131,7 +133,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setHideHeaderOverview(b: boolean): void;
         setHideNoTracksActive(b: boolean): void;
         setShowGridlines(b: boolean): void;
-        setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
+        addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
+        setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
+        removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
         scrollTo(offsetPx: number): number;
         zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
         setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
@@ -141,6 +145,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
         hideTrack(trackId: string): number;
     } & {
+        moveTrackDown(id: string): void;
+        moveTrackUp(id: string): void;
+        moveTrackToTop(id: string): void;
+        moveTrackToBottom(id: string): void;
         moveTrack(movingId: string, targetId: string): void;
         closeView(): void;
         toggleTrack(trackId: string): boolean;
@@ -338,7 +346,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             index: number;
             offsetPx: number;
         } | undefined;
-        centerAt(coord: number, refName: string, regionNumber: number): void;
+        centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
         pxToBp(px: number): {
             coord: number;
             index: number;
@@ -363,7 +371,41 @@ export default 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>; /**
+             * #property/
+             */
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
+             * #action
+             */
+        }, {
+            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<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
+        colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    }>>, import("mobx-state-tree")._NotCustomized>>;
     viewTrackConfigs: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearSyntenyView">;
@@ -421,7 +463,8 @@ export default 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").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
+        colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }>>[]): void;
     removeView(view: {
         id: string;
@@ -466,7 +509,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         showCytobandsSetting: boolean;
         trackLabels: string;
         showGridlines: boolean;
-        highlight: (Required<import("@jbrowse/core/util").ParsedLocString> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>>) | undefined;
+        highlight: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>>;
+        colorByCDS: boolean;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         width: number;
     } & {
@@ -522,6 +566,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
         readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
     } & {
+        setColorByCDS(flag: boolean): void;
         setShowCytobands(flag: boolean): void;
         setWidth(newWidth: number): void;
         setError(error: unknown): void;
@@ -529,7 +574,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setHideHeaderOverview(b: boolean): void;
         setHideNoTracksActive(b: boolean): void;
         setShowGridlines(b: boolean): void;
-        setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
+        addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
+        setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
+        removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
         scrollTo(offsetPx: number): number;
         zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
         setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
@@ -539,6 +586,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
         hideTrack(trackId: string): number;
     } & {
+        moveTrackDown(id: string): void;
+        moveTrackUp(id: string): void;
+        moveTrackToTop(id: string): void;
+        moveTrackToBottom(id: string): void;
         moveTrack(movingId: string, targetId: string): void;
         closeView(): void;
         toggleTrack(trackId: string): boolean;
@@ -736,7 +787,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             index: number;
             offsetPx: number;
         } | undefined;
-        centerAt(coord: number, refName: string, regionNumber: number): void;
+        centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
         pxToBp(px: number): {
             coord: number;
             index: number;
@@ -793,7 +844,8 @@ export default 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").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
+        highlight: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
+        colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     }, {
         width: number;
     } & {
@@ -849,6 +901,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         rewriteOnClicks(trackType: string, viewMenuActions: import("@jbrowse/core/ui").MenuItem[]): void;
         readonly trackTypeActions: Map<string, import("@jbrowse/core/ui").MenuItem[]>;
     } & {
+        setColorByCDS(flag: boolean): void;
         setShowCytobands(flag: boolean): void;
         setWidth(newWidth: number): void;
         setError(error: unknown): void;
@@ -856,7 +909,9 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         setHideHeaderOverview(b: boolean): void;
         setHideNoTracksActive(b: boolean): void;
         setShowGridlines(b: boolean): void;
-        setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
+        addToHighlights(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
+        setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>[] | undefined): void;
+        removeHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString>): void;
         scrollTo(offsetPx: number): number;
         zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
         setOffsets(left?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, right?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): void;
@@ -866,6 +921,10 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
         hideTrack(trackId: string): number;
     } & {
+        moveTrackDown(id: string): void;
+        moveTrackUp(id: string): void;
+        moveTrackToTop(id: string): void;
+        moveTrackToBottom(id: string): void;
         moveTrack(movingId: string, targetId: string): void;
         closeView(): void;
         toggleTrack(trackId: string): boolean;
@@ -1063,7 +1122,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             index: number;
             offsetPx: number;
         } | undefined;
-        centerAt(coord: number, refName: string, regionNumber: number): void;
+        centerAt(coord: number, refName: string, regionNumber?: number | undefined): void;
         pxToBp(px: number): {
             coord: number;
             index: number;
@@ -1088,7 +1147,41 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         } | undefined;
     } & {
         afterCreate(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): 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>>;
+        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>; /**
+             * #property/
+             */
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
+             * #action
+             */
+        }, {
+            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<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>, [undefined]>;
+        colorByCDS: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    }>>, import("mobx-state-tree")._NotCustomized>>): void;
     closeView(): void;
     setMiddleComparativeHeight(n: number): number;
     toggleLinkViews(): void;