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

package/dist/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js

@@ -58,7 +58,8 @@ function LaunchSyntenyViewDialog({ model, feature, handleClose, }) {
                             });
                         }
                         catch (e) {
-                            (0, util_1.getSession)(model).notify(`${e}`, 'error');
+                            console.error(e);
+                            (0, util_1.getSession)(model).notifyError(`${e}`, e);
                         }
                     })();
                     handleClose();

package/dist/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/dist/LGVSyntenyDisplay/index.js

@@ -7,7 +7,7 @@ const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTyp
 const configSchemaF_1 = __importDefault(require("./configSchemaF"));
 const model_1 = __importDefault(require("./model"));
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-exports.default = (pluginManager) => {
+function LGVSyntenyDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchemaF_1.default)(pluginManager);
         const stateModel = (0, model_1.default)(configSchema);
@@ -20,4 +20,5 @@ exports.default = (pluginManager) => {
             ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,
         });
     });
-};
+}
+exports.default = LGVSyntenyDisplayF;

package/dist/LaunchLinearSyntenyView.js

@@ -40,7 +40,7 @@ function LaunchLinearSyntenyView(pluginManager) {
             }
         }
         catch (e) {
-            session.notify(`${e}`, 'error');
+            session.notifyError(`${e}`, e);
             throw e;
         }
     });

package/dist/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/dist/LinearComparativeDisplay/index.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 const configSchemaF_1 = __importDefault(require("./configSchemaF"));
 const stateModelFactory_1 = __importDefault(require("./stateModelFactory"));
-exports.default = (pluginManager) => {
+function LinearComparativeDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchemaF_1.default)(pluginManager);
         return new DisplayType_1.default({
@@ -20,4 +20,5 @@ exports.default = (pluginManager) => {
             },
         });
     });
-};
+}
+exports.default = LinearComparativeDisplayF;

package/dist/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/dist/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/dist/LinearComparativeView/index.js

@@ -29,7 +29,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = require("react");
 const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
 const model_1 = __importDefault(require("./model"));
-exports.default = (pluginManager) => {
+function LinearComparativeViewF(pluginManager) {
     pluginManager.addViewType(() => {
         return new ViewType_1.default({
             name: 'LinearComparativeView',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
             ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/LinearComparativeView')))),
         });
     });
-};
+}
+exports.default = LinearComparativeViewF;

package/dist/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/dist/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/dist/LinearReadVsRef/index.js

@@ -35,7 +35,7 @@ const ReadVsRefDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __i
 function isDisplay(elt) {
     return elt.name === 'LinearPileupDisplay';
 }
-function default_1(pm) {
+function LinearReadVsRefMenuItemF(pm) {
     pm.addToExtensionPoint('Core-extendPluggableElement', (pluggableElement) => {
         if (!isDisplay(pluggableElement)) {
             return pluggableElement;
@@ -75,4 +75,4 @@ function default_1(pm) {
         return pluggableElement;
     });
 }
-exports.default = default_1;
+exports.default = LinearReadVsRefMenuItemF;

package/dist/LinearSyntenyDisplay/components/SyntenyContextMenu.js

@@ -42,13 +42,13 @@ function SyntenyContextMenu({ model, onClose, anchorEl, }) {
                         .navToLocString(`${refName}:${start}-${end}`)
                         .catch(e => {
                         console.error(e);
-                        (0, util_1.getSession)(model).notify(`${e}`, 'error');
+                        (0, util_1.getSession)(model).notifyError(`${e}`, e);
                     });
                     view.views[1]
                         .navToLocString(`${mate.refName}:${mate.start}-${mate.end}`)
                         .catch(e => {
                         console.error(e);
-                        (0, util_1.getSession)(model).notify(`${e}`, 'error');
+                        (0, util_1.getSession)(model).notifyError(`${e}`, e);
                     });
                 },
             },

package/dist/LinearSyntenyDisplay/components/SyntenyTooltip.js

@@ -35,6 +35,7 @@ const SyntenyTooltip = (0, mobx_react_1.observer)(function ({ title }) {
     const { classes } = useStyles();
     const { refs, floatingStyles, context } = (0, react_2.useFloating)({
         placement: 'right',
+        strategy: 'fixed',
     });
     const clientPoint = (0, react_2.useClientPoint)(context);
     const { getFloatingProps } = (0, react_2.useInteractions)([clientPoint]);

package/dist/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/dist/LinearSyntenyDisplay/index.js

@@ -31,7 +31,7 @@ const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTyp
 const configSchemaF_1 = __importDefault(require("./configSchemaF"));
 const model_1 = __importDefault(require("./model"));
 const react_1 = require("react");
-exports.default = (pluginManager) => {
+function LinearSyntenyDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchemaF_1.default)(pluginManager);
         return new DisplayType_1.default({
@@ -43,4 +43,5 @@ exports.default = (pluginManager) => {
             ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/Component')))),
         });
     });
-};
+}
+exports.default = LinearSyntenyDisplayF;

package/dist/LinearSyntenyView/components/ExportSvgDialog.js

@@ -35,6 +35,10 @@ function LoadingMessage() {
 function useSvgLocal(key, val) {
     return (0, util_1.useLocalStorage)('svg-' + key, val);
 }
+function TextField2({ children, ...rest }) {
+    return (react_1.default.createElement("div", null,
+        react_1.default.createElement(material_1.TextField, { ...rest }, children)));
+}
 function ExportSvgDialog({ model, handleClose, }) {
     const session = (0, util_1.getSession)(model);
     const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
@@ -47,15 +51,14 @@ function ExportSvgDialog({ model, handleClose, }) {
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
         react_1.default.createElement(material_1.DialogContent, null,
             error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : loading ? (react_1.default.createElement(LoadingMessage, null)) : null,
-            react_1.default.createElement(material_1.TextField, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
-            react_1.default.createElement("br", null),
-            react_1.default.createElement(material_1.TextField, { select: true, label: "Track label positioning", variant: "outlined", value: trackLabels, style: { width: 150 }, onChange: event => setTrackLabels(event.target.value) },
+            react_1.default.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
+            react_1.default.createElement(TextField2, { select: true, label: "Track label positioning", variant: "outlined", value: trackLabels, style: { width: 150 }, onChange: event => setTrackLabels(event.target.value) },
                 react_1.default.createElement(material_1.MenuItem, { value: "offset" }, "Offset"),
                 react_1.default.createElement(material_1.MenuItem, { value: "overlay" }, "Overlay"),
                 react_1.default.createElement(material_1.MenuItem, { value: "left" }, "Left"),
                 react_1.default.createElement(material_1.MenuItem, { value: "none" }, "None")),
             react_1.default.createElement("br", null),
-            session.allThemes ? (react_1.default.createElement(material_1.TextField, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key }, 
+            session.allThemes ? (react_1.default.createElement(TextField2, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key }, 
             // @ts-expect-error
             val.name || '(Unknown name)'))))) : null,
             offscreenCanvas ? (react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => setRasterizeLayers(val => !val) }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (react_1.default.createElement(material_1.Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),

package/dist/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/dist/LinearSyntenyView/index.js

@@ -29,7 +29,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = require("react");
 const model_1 = __importDefault(require("./model"));
 const ViewType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ViewType"));
-exports.default = (pluginManager) => {
+function LinearSyntenyViewF(pluginManager) {
     pluginManager.addViewType(() => {
         return new ViewType_1.default({
             name: 'LinearSyntenyView',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
             ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/LinearSyntenyView')))),
         });
     });
-};
+}
+exports.default = LinearSyntenyViewF;

package/dist/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;

package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

@@ -19,9 +19,9 @@ const drawSynteny_1 = require("../../LinearSyntenyDisplay/drawSynteny");
 async function renderToSvg(model, opts) {
     var _a;
     await (0, mobx_1.when)(() => model.initialized);
-    const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', Wrapper = ({ children }) => react_1.default.createElement(react_1.default.Fragment, null, children), themeName = 'default', } = opts;
+    const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', Wrapper = ({ children }) => children, themeName = 'default', } = opts;
     const session = (0, util_1.getSession)(model);
-    const theme = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
+    const themeVar = (_a = session.allThemes) === null || _a === void 0 ? void 0 : _a.call(session)[themeName];
     const { width, views, middleComparativeHeight: synH, tracks } = model;
     const shift = 50;
     const offset = headerHeight + rulerHeight;
@@ -34,7 +34,10 @@ async function renderToSvg(model, opts) {
         data: await Promise.all(view.tracks.map(async (track) => {
             const d = track.displays[0];
             await (0, mobx_1.when)(() => (d.ready !== undefined ? d.ready : true));
-            return { track, result: await d.renderSvg({ ...opts, theme }) };
+            return {
+                track,
+                result: await d.renderSvg({ ...opts, theme: themeVar }),
+            };
         })),
     })));
     const renderings = await Promise.all(tracks.map(async (track) => {
@@ -60,15 +63,15 @@ async function renderToSvg(model, opts) {
     const trackLabelMaxLen = (0, util_1.max)(views.flatMap(view => view.tracks.map(t => (0, util_1.measureText)((0, tracks_1.getTrackName)(t.configuration, session), fontSize))), 0) + 40;
     const trackLabelOffset = trackLabels === 'left' ? trackLabelMaxLen : 0;
     const w = width + trackLabelOffset;
-    const t = (0, ui_1.createJBrowseTheme)(theme);
+    const theme = (0, ui_1.createJBrowseTheme)(themeVar);
     // the xlink namespace is used for rendering <image> tag
-    return (0, util_1.renderToStaticMarkup)(react_1.default.createElement(material_1.ThemeProvider, { theme: (0, ui_1.createJBrowseTheme)(theme) },
+    return (0, util_1.renderToStaticMarkup)(react_1.default.createElement(material_1.ThemeProvider, { theme: theme },
         react_1.default.createElement(Wrapper, null,
             react_1.default.createElement("svg", { width: width, height: totalHeightSvg, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, w + shift * 2, totalHeightSvg].toString() },
                 react_1.default.createElement(SVGBackground_1.default, { width: w, height: totalHeightSvg, shift: shift }),
                 react_1.default.createElement("g", { transform: `translate(${shift} ${fontSize})` },
                     react_1.default.createElement("g", { transform: `translate(${trackLabelOffset})` },
-                        react_1.default.createElement("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary }, views[0].assemblyNames.join(', ')),
+                        react_1.default.createElement("text", { x: 0, fontSize: fontSize, ...(0, util_1.getFillProps)(theme.palette.text.primary) }, views[0].assemblyNames.join(', ')),
                         react_1.default.createElement(plugin_linear_genome_view_1.SVGRuler, { model: displayResults[0].view, fontSize: fontSize })),
                     react_1.default.createElement(plugin_linear_genome_view_1.SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[0].view, displayResults: displayResults[0].data, offset: offset, trackLabelOffset: trackLabelOffset })),
                 react_1.default.createElement("defs", null,
@@ -77,7 +80,7 @@ async function renderToSvg(model, opts) {
                 react_1.default.createElement("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize + heights[0]})`, clipPath: `url(#synclip)` }, renderings.map((r, i) => (react_1.default.createElement(util_1.ReactRendering, { key: i, rendering: r })))),
                 react_1.default.createElement("g", { transform: `translate(${shift} ${fontSize + heights[0] + synH})` },
                     react_1.default.createElement("g", { transform: `translate(${trackLabelOffset})` },
-                        react_1.default.createElement("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary }, views[1].assemblyNames.join(', ')),
+                        react_1.default.createElement("text", { x: 0, fontSize: fontSize, ...(0, util_1.getFillProps)(theme.palette.text.primary) }, views[1].assemblyNames.join(', ')),
                         react_1.default.createElement(plugin_linear_genome_view_1.SVGRuler, { model: displayResults[1].view, fontSize: fontSize })),
                     react_1.default.createElement(plugin_linear_genome_view_1.SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, offset: offset, trackLabelOffset: trackLabelOffset }))))), createRootFn);
 }