@jbrowse/plugin-linear-comparative-view 2.11.0 → 2.11.2

package/dist/LGVSyntenyDisplay/configSchemaF.d.ts

@@ -48,5 +48,10 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>, undefined>>;
 export default configSchemaF;

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/LGVSyntenyDisplay/model.d.ts

@@ -85,9 +85,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         height: {
             type: string;
             defaultValue: number;
-            description: string; /**
-             * #method
-             */
+            description: string;
         };
         mouseover: {
             type: string;
@@ -95,6 +93,11 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     configuration: AnyConfigurationSchemaType;
@@ -240,6 +243,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;

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/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

@@ -140,6 +140,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
             start: number;
             end: number;
+            type: string;
             regionNumber?: number | undefined;
             reversed?: boolean | undefined;
             refName: string;

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/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/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

@@ -159,6 +159,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
             start: number;
             end: number;
+            type: string;
             regionNumber?: number | undefined;
             reversed?: boolean | undefined;
             refName: string;
@@ -600,6 +601,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
             start: number;
             end: number;
+            type: string;
             regionNumber?: number | undefined;
             reversed?: boolean | undefined;
             refName: string;
@@ -935,6 +937,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
             start: number;
             end: number;
+            type: string;
             regionNumber?: number | undefined;
             reversed?: boolean | undefined;
             refName: string;

package/dist/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

@@ -21,7 +21,7 @@ async function renderToSvg(model, opts) {
     await (0, mobx_1.when)(() => model.initialized);
     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);
 }

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/configSchemaF.d.ts

@@ -48,5 +48,10 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
         defaultValue: string;
         contextVariable: string[];
     };
+    jexlFilters: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>, undefined>>;
 export default configSchemaF;

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/LGVSyntenyDisplay/model.d.ts

@@ -85,9 +85,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         height: {
             type: string;
             defaultValue: number;
-            description: string; /**
-             * #method
-             */
+            description: string;
         };
         mouseover: {
             type: string;
@@ -95,6 +93,11 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
             defaultValue: string;
             contextVariable: string[];
         };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
     configuration: AnyConfigurationSchemaType;
@@ -240,6 +243,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;

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/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

@@ -140,6 +140,7 @@ declare function stateModelFactory(pluginManager: PluginManager): import("mobx-s
         getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
             start: number;
             end: number;
+            type: string;
             regionNumber?: number | undefined;
             reversed?: boolean | undefined;
             refName: string;

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/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/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

@@ -159,6 +159,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
             start: number;
             end: number;
+            type: string;
             regionNumber?: number | undefined;
             reversed?: boolean | undefined;
             refName: string;
@@ -600,6 +601,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
             start: number;
             end: number;
+            type: string;
             regionNumber?: number | undefined;
             reversed?: boolean | undefined;
             refName: string;
@@ -935,6 +937,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
             start: number;
             end: number;
+            type: string;
             regionNumber?: number | undefined;
             reversed?: boolean | undefined;
             refName: string;

package/esm/LinearSyntenyView/svgcomponents/SVGLinearSyntenyView.js

@@ -2,7 +2,7 @@ import React from 'react';
 import { ThemeProvider } from '@mui/material';
 import { getRoot } from 'mobx-state-tree';
 import { when } from 'mobx';
-import { getSession, getSerializedSvg, max, measureText, ReactRendering, renderToAbstractCanvas, renderToStaticMarkup, sum, } from '@jbrowse/core/util';
+import { getSession, getSerializedSvg, max, measureText, ReactRendering, renderToAbstractCanvas, renderToStaticMarkup, sum, getFillProps, } from '@jbrowse/core/util';
 import { getTrackName } from '@jbrowse/core/util/tracks';
 import { createJBrowseTheme } from '@jbrowse/core/ui';
 import { SVGTracks, SVGRuler, totalHeight, } from '@jbrowse/plugin-linear-genome-view';
@@ -15,7 +15,7 @@ export async function renderToSvg(model, opts) {
     await when(() => model.initialized);
     const { textHeight = 18, headerHeight = 30, rulerHeight = 30, fontSize = 13, trackLabels = 'offset', Wrapper = ({ children }) => children, themeName = 'default', } = opts;
     const session = 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;
@@ -28,7 +28,10 @@ export async function renderToSvg(model, opts) {
         data: await Promise.all(view.tracks.map(async (track) => {
             const d = track.displays[0];
             await 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) => {
@@ -54,15 +57,15 @@ export async function renderToSvg(model, opts) {
     const trackLabelMaxLen = max(views.flatMap(view => view.tracks.map(t => measureText(getTrackName(t.configuration, session), fontSize))), 0) + 40;
     const trackLabelOffset = trackLabels === 'left' ? trackLabelMaxLen : 0;
     const w = width + trackLabelOffset;
-    const t = createJBrowseTheme(theme);
+    const theme = createJBrowseTheme(themeVar);
     // the xlink namespace is used for rendering <image> tag
-    return renderToStaticMarkup(React.createElement(ThemeProvider, { theme: createJBrowseTheme(theme) },
+    return renderToStaticMarkup(React.createElement(ThemeProvider, { theme: theme },
         React.createElement(Wrapper, null,
             React.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.createElement(SVGBackground, { width: w, height: totalHeightSvg, shift: shift }),
                 React.createElement("g", { transform: `translate(${shift} ${fontSize})` },
                     React.createElement("g", { transform: `translate(${trackLabelOffset})` },
-                        React.createElement("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary }, views[0].assemblyNames.join(', ')),
+                        React.createElement("text", { x: 0, fontSize: fontSize, ...getFillProps(theme.palette.text.primary) }, views[0].assemblyNames.join(', ')),
                         React.createElement(SVGRuler, { model: displayResults[0].view, fontSize: fontSize })),
                     React.createElement(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[0].view, displayResults: displayResults[0].data, offset: offset, trackLabelOffset: trackLabelOffset })),
                 React.createElement("defs", null,
@@ -71,7 +74,7 @@ export async function renderToSvg(model, opts) {
                 React.createElement("g", { transform: `translate(${shift + trackLabelOffset} ${fontSize + heights[0]})`, clipPath: `url(#synclip)` }, renderings.map((r, i) => (React.createElement(ReactRendering, { key: i, rendering: r })))),
                 React.createElement("g", { transform: `translate(${shift} ${fontSize + heights[0] + synH})` },
                     React.createElement("g", { transform: `translate(${trackLabelOffset})` },
-                        React.createElement("text", { x: 0, fontSize: fontSize, fill: t.palette.text.primary }, views[1].assemblyNames.join(', ')),
+                        React.createElement("text", { x: 0, fontSize: fontSize, ...getFillProps(theme.palette.text.primary) }, views[1].assemblyNames.join(', ')),
                         React.createElement(SVGRuler, { model: displayResults[1].view, fontSize: fontSize })),
                     React.createElement(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: displayResults[1].view, displayResults: displayResults[1].data, offset: offset, trackLabelOffset: trackLabelOffset }))))), createRootFn);
 }

package/esm/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/esm/SyntenyFeatureDetail/index.js

@@ -18,7 +18,7 @@ const stateModel = types
         self.featureData = undefined;
     },
 }));
-export default (pluginManager) => {
+export default function SyntenyFeatureWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => new WidgetType({
         name: 'SyntenyFeatureWidget',
         heading: 'Synteny feature details',
@@ -26,4 +26,4 @@ export default (pluginManager) => {
         stateModel,
         ReactComponent: lazy(() => import('./SyntenyFeatureDetail')),
     }));
-};
+}

package/esm/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/esm/index.js

@@ -9,8 +9,8 @@ import LinearSyntenyViewF from './LinearSyntenyView';
 import LaunchLinearSyntenyViewF from './LaunchLinearSyntenyView';
 import SyntenyTrackF from './SyntenyTrack';
 import SyntenyFeatureWidgetF from './SyntenyFeatureDetail';
-import LinearReadVsRefMenuItem from './LinearReadVsRef';
-export default class extends Plugin {
+import LinearReadVsRefMenuItemF from './LinearReadVsRef';
+export default class LinearComparativeViewPlugin extends Plugin {
     constructor() {
         super(...arguments);
         this.name = 'LinearComparativeViewPlugin';
@@ -24,7 +24,7 @@ export default class extends Plugin {
         LaunchLinearSyntenyViewF(pluginManager);
         SyntenyTrackF(pluginManager);
         SyntenyFeatureWidgetF(pluginManager);
-        LinearReadVsRefMenuItem(pluginManager);
+        LinearReadVsRefMenuItemF(pluginManager);
     }
     configure(pluginManager) {
         if (isAbstractMenuManager(pluginManager.rootModel)) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-comparative-view",
-  "version": "2.11.0",
+  "version": "2.11.2",
   "description": "JBrowse 2 linear comparative view",
   "keywords": [
     "jbrowse",
@@ -61,5 +61,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
+  "gitHead": "511048cb6965f0bf624c96de244e7fd47fce17d6"
 }