@jbrowse/plugin-linear-comparative-view 2.17.0 → 3.0.0

package/dist/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.d.ts

@@ -1,8 +1,9 @@
-import React from 'react';
-import { Feature } from '@jbrowse/core/util';
-export default function LaunchSyntenyViewDialog({ model, feature, trackId, handleClose, }: {
-    model: unknown;
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+export default function LaunchSyntenyViewDialog({ session, view, feature, trackId, handleClose, }: {
+    session: AbstractSessionModel;
+    view?: LinearGenomeViewModel;
     feature: Feature;
     trackId: string;
     handleClose: () => void;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/LGVSyntenyDisplay/components/LaunchSyntenyViewDialog.js

@@ -1,77 +1,53 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = LaunchSyntenyViewDialog;
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
-// locals
-const util_2 = require("./util");
+const util_1 = require("./util");
 const useStyles = (0, mui_1.makeStyles)()({
     padding: {
         margin: 10,
         border: '1px solid #ccc',
     },
 });
-function LaunchSyntenyViewDialog({ model, feature, trackId, handleClose, }) {
+function LaunchSyntenyViewDialog({ session, view, feature, trackId, handleClose, }) {
     const { classes } = useStyles();
     const inverted = feature.get('strand') === -1;
+    const hasCIGAR = !!feature.get('CIGAR');
     const [horizontallyFlip, setHorizontallyFlip] = (0, react_1.useState)(inverted);
     const [windowSize, setWindowSize] = (0, react_1.useState)('1000');
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, title: "Launch synteny view", onClose: handleClose },
-        react_1.default.createElement(material_1.DialogContent, null,
-            inverted ? (react_1.default.createElement(material_1.FormControlLabel, { className: classes.padding, control: react_1.default.createElement(material_1.Checkbox, { checked: horizontallyFlip, onChange: event => {
-                        setHorizontallyFlip(event.target.checked);
-                    } }), label: "Note: The feature is inverted in orientation on the target\n            sequence. This will result in the lower panel having genomic\n            coordinates decreasing left to right. Horizontally flip?" })) : null,
-            react_1.default.createElement(material_1.TextField, { label: "Add window size in bp", value: windowSize, onChange: event => {
-                    setWindowSize(event.target.value);
-                } })),
-        react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                    ;
-                    (async () => {
-                        try {
-                            await (0, util_2.navToSynteny)({
-                                feature,
-                                windowSize: +windowSize,
-                                horizontallyFlip,
-                                trackId,
-                                model,
-                            });
-                        }
-                        catch (e) {
-                            console.error(e);
-                            (0, util_1.getSession)(model).notifyError(`${e}`, e);
-                        }
-                    })();
-                    handleClose();
-                } }, "Submit"),
-            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
+    const [useRegionOfInterest, setUseRegionOfInterest] = (0, react_1.useState)(true);
+    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, title: "Launch synteny view", onClose: handleClose, children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [view && hasCIGAR ? ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { className: classes.padding, control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: useRegionOfInterest, onChange: event => {
+                                setUseRegionOfInterest(event.target.checked);
+                            } }), label: "Use CIGAR string to navigate the current visible to the target" })) : null, inverted ? ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { className: classes.padding, control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: horizontallyFlip, onChange: event => {
+                                setHorizontallyFlip(event.target.checked);
+                            } }), label: "Note: The feature is inverted in orientation on the target\n            sequence. This will result in the lower panel having genomic\n            coordinates decreasing left to right. Horizontally flip?" })) : null, (0, jsx_runtime_1.jsx)(material_1.TextField, { label: "Add window size in bp", value: windowSize, onChange: event => {
+                            setWindowSize(event.target.value);
+                        } })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
+                            ;
+                            (async () => {
+                                try {
+                                    await (0, util_1.navToSynteny)({
+                                        feature,
+                                        windowSize: +windowSize,
+                                        horizontallyFlip,
+                                        trackId,
+                                        session,
+                                        region: useRegionOfInterest
+                                            ? view === null || view === void 0 ? void 0 : view.dynamicBlocks.contentBlocks[0]
+                                            : undefined,
+                                    });
+                                }
+                                catch (e) {
+                                    console.error(e);
+                                    session.notifyError(`${e}`, e);
+                                }
+                            })();
+                            handleClose();
+                        }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                            handleClose();
+                        }, children: "Cancel" })] })] }));
 }

package/dist/LGVSyntenyDisplay/components/util.d.ts

@@ -1,11 +1,14 @@
-import { Feature } from '@jbrowse/core/util';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function navToSynteny({ feature, windowSize: ws, model, trackId, view, horizontallyFlip, }: {
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+export interface SimpleRegion {
+    refName: string;
+    start: number;
+    end: number;
+}
+export declare function navToSynteny({ feature, windowSize: ws, session, trackId, region, horizontallyFlip, }: {
     windowSize: number;
     trackId: string;
     horizontallyFlip: boolean;
     feature: Feature;
-    view?: LinearGenomeViewModel;
-    model: IAnyStateTreeNode;
+    session: AbstractSessionModel;
+    region?: SimpleRegion;
 }): Promise<void>;

package/dist/LGVSyntenyDisplay/components/util.js

@@ -1,12 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.navToSynteny = navToSynteny;
-const util_1 = require("@jbrowse/core/util");
 const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
 const { parseCigar } = plugin_alignments_1.MismatchParser;
-function f(n) {
-    return Math.floor(n);
-}
 function findPosInCigar(cigar, startX) {
     let featX = 0;
     let mateX = 0;
@@ -30,9 +26,7 @@ function findPosInCigar(cigar, startX) {
     }
     return [featX, mateX];
 }
-async function navToSynteny({ feature, windowSize: ws, model, trackId, view, horizontallyFlip, }) {
-    const session = (0, util_1.getSession)(model);
-    const reg = view === null || view === void 0 ? void 0 : view.dynamicBlocks.contentBlocks[0];
+async function navToSynteny({ feature, windowSize: ws, session, trackId, region, horizontallyFlip, }) {
     const cigar = feature.get('CIGAR');
     const strand = feature.get('strand');
     const featRef = feature.get('refName');
@@ -48,13 +42,12 @@ async function navToSynteny({ feature, windowSize: ws, model, trackId, view, hor
     let rMateEnd;
     let rFeatStart;
     let rFeatEnd;
-    if (reg && cigar) {
-        const regStart = reg.start;
-        const regEnd = reg.end;
+    if (region && cigar) {
+        const regStart = region.start;
+        const regEnd = region.end;
         const p = parseCigar(cigar);
         const [fStartX, mStartX] = findPosInCigar(p, regStart - featStart);
         const [fEndX, mEndX] = findPosInCigar(p, regEnd - featStart);
-        // avoid multiply by 0 with strand undefined
         const flipper = strand === -1 ? -1 : 1;
         rFeatStart = featStart + fStartX;
         rFeatEnd = featStart + fEndX;
@@ -92,10 +85,10 @@ async function navToSynteny({ feature, windowSize: ws, model, trackId, view, hor
             },
         ],
     });
-    const l1 = `${featRef}:${f(rFeatStart - ws)}-${f(rFeatEnd + ws)}`;
+    const l1 = `${featRef}:${Math.floor(rFeatStart - ws)}-${Math.floor(rFeatEnd + ws)}`;
     const m1 = Math.min(rMateStart, rMateEnd);
     const m2 = Math.max(rMateStart, rMateEnd);
-    const l2 = `${mateRef}:${f(m1 - ws)}-${f(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
+    const l2 = `${mateRef}:${Math.floor(m1 - ws)}-${Math.floor(m2 + ws)}${horizontallyFlip ? '[rev]' : ''}`;
     await Promise.all([
         view2.views[0].navToLocString(l1, featAsm),
         view2.views[1].navToLocString(l2, mateAsm),

package/dist/LGVSyntenyDisplay/configSchemaF.d.ts

@@ -1,10 +1,10 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #config LGVSyntenyDisplay
- * extends config
- * - [LinearPileupDisplay](../linearpileupdisplay)
- */
-declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+import type PluginManager from '@jbrowse/core/PluginManager';
+declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    mouseover: {
+        type: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     defaultRendering: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
@@ -18,11 +18,20 @@ declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/c
         description: string;
         defaultValue: number;
     };
-    colorScheme: {
+    colorBy: {
         type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
-        defaultValue: string;
+        defaultValue: {
+            type: string;
+        };
+    };
+    filterBy: {
+        type: string;
+        description: string;
+        defaultValue: {
+            flagInclude: number;
+            flagExclude: number;
+        };
     };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     renderer: import("mobx-state-tree").IAnyModelType;

package/dist/LGVSyntenyDisplay/configSchemaF.js

@@ -2,16 +2,19 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_alignments_1 = require("@jbrowse/plugin-alignments");
-/**
- * #config LGVSyntenyDisplay
- * extends config
- * - [LinearPileupDisplay](../linearpileupdisplay)
- */
 function configSchemaF(pluginManager) {
-    return (0, configuration_1.ConfigurationSchema)('LGVSyntenyDisplay', {}, {
-        /**
-         * #baseConfiguration
-         */
+    pluginManager.jexl.addFunction('lgvSyntenyTooltip', (f) => {
+        const m = f.get('mate');
+        return [f.get('name') || f.get('id'), (m === null || m === void 0 ? void 0 : m.name) || (m === null || m === void 0 ? void 0 : m.id)]
+            .filter(f => !!f)
+            .join('<br/>');
+    });
+    return (0, configuration_1.ConfigurationSchema)('LGVSyntenyDisplay', {
+        mouseover: {
+            type: 'string',
+            defaultValue: 'jexl:lgvSyntenyTooltip(feature)',
+        },
+    }, {
         baseConfiguration: (0, plugin_alignments_1.linearPileupDisplayConfigSchemaFactory)(pluginManager),
         explicitlyTyped: true,
     });

package/dist/LGVSyntenyDisplay/index.d.ts

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

package/dist/LGVSyntenyDisplay/index.js

@@ -5,9 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = LGVSyntenyDisplayF;
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const configSchemaF_1 = __importDefault(require("./configSchemaF"));
 const model_1 = __importDefault(require("./model"));
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 function LGVSyntenyDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchemaF_1.default)(pluginManager);

package/dist/LGVSyntenyDisplay/model.d.ts

@@ -1,24 +1,9 @@
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import { Feature } from '@jbrowse/core/util';
-/**
- * #stateModel LGVSyntenyDisplay
- * displays location of "synteny" feature in a plain LGV, allowing linking out
- * to external synteny views
- *
- * extends
- * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
- */
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
-    rpcDriverName: import("mobx-state-tree" /**
-     * #stateModel LGVSyntenyDisplay
-     * displays location of "synteny" feature in a plain LGV, allowing linking out
-     * to external synteny views
-     *
-     * extends
-     * - [SharedLinearPileupDisplayMixin](../sharedlinearpileupdisplaymixin)
-     */).IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
     heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
@@ -27,23 +12,12 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
 } & {
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
-        region: 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" /**
-             * #property
-             */).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>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
         reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined;
+        stopToken: string | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, Feature> | undefined;
@@ -61,21 +35,15 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void;
+        setLoading(newStopToken: string): void;
         setMessage(messageText: string): void;
-        setRendered(props: {
-            reactElement: React.ReactElement;
-            features: Map<string, Feature>;
-            layout: any;
-            maxHeightReached: boolean;
-            renderProps: any;
-        } | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
@@ -114,17 +82,12 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    colorBy: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined>;
-    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").FilterBy, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy>, [undefined]>;
+    colorBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined>;
+    filterBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined>;
     jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
 } & {
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"LGVSyntenyDisplay">;
-    /**
-     * #property
-     */
     configuration: AnyConfigurationSchemaType;
 }, {
     rendererTypeName: string;
@@ -215,14 +178,15 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -249,14 +213,18 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
     featureUnderMouseVolatile: undefined | Feature;
     tagsReady: boolean;
+} & {
+    readonly colorBy: any;
+    readonly filterBy: any;
 } & {
     readonly autorunReady: boolean;
+    readonly hideSmallIndels: boolean | undefined;
 } & {
     setTagsReady(flag: boolean): void;
     setMaxHeight(n?: number): void;
@@ -270,6 +238,7 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     setConfig(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
     setFilterBy(filter: import("@jbrowse/plugin-alignments/src/shared/types").FilterBy): void;
     setJexlFilters(filters: string[]): void;
+    setHideSmallIndels(arg: boolean): void;
 } & {
     readonly rendererConfig: {
         [x: string]: any;
@@ -303,39 +272,38 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     })[];
     readonly DisplayBlurb: ({ model, }: {
         model: {
-            sortedBy?: {
-                pos: number;
-                refName: number;
-                type: string;
-                tag?: string;
-            };
+            sortedBy?: import("@jbrowse/plugin-alignments/src/shared/types").SortedBy;
         };
-    }) => import("react").JSX.Element | null;
+    }) => import("react/jsx-runtime").JSX.Element | null;
     renderPropsPre(): any;
     colorSchemeSubMenuItems(): {
         label: string;
         onClick: () => void;
     }[];
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+        label: string;
+        priority: number;
+        type: string;
+        checked: boolean | undefined;
+        onClick: () => void;
+        icon?: undefined;
+    } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
+        priority?: undefined;
+        type?: undefined;
+        checked?: undefined;
     })[];
 } & {
     renderProps(): any;
 } & {
     afterAttach(): void;
 } & {
-    /**
-     * #method
-     */
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
 } & {
-    /**
-     * #method
-     */
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
         subMenu: {
@@ -344,10 +312,95 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         }[];
     })[];
 } & {
-    /**
-     * #action
-     */
     selectFeature(feature: Feature): void;
     afterCreate(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, {
+    type: string;
+} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+} & {
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+        key: import("mobx-state-tree").ISimpleType<string>;
+        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
+        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    }, {
+        stopToken: string | undefined;
+        filled: boolean;
+        reactElement: React.ReactElement | undefined;
+        features: Map<string, Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: React.ReactNode;
+                filled?: boolean;
+                status?: string;
+                reactElement?: React.ReactElement;
+            };
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(newStopToken: string): void;
+        setMessage(messageText: string): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        beforeDestroy(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
+} & {
+    configuration: AnyConfigurationSchemaType;
+    featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    colorBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").ColorBy | undefined>;
+    filterBySetting: import("mobx-state-tree").IType<import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined, import("@jbrowse/plugin-alignments/src/shared/types").FilterBy | undefined>;
+    jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default stateModelFactory;