@jbrowse/plugin-linear-comparative-view 2.6.1

package/dist/util.d.ts

@@ -0,0 +1,25 @@
+import { Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+export type LayoutRecord = [number, number, number, number];
+export interface ReducedLinearGenomeView {
+    bpPerPx: number;
+    offsetPx: number;
+    staticBlocks: Region[];
+    dynamicBlocks: Region[];
+    displayedRegions: Region[];
+    headerHeight: number;
+    scaleBarHeight: number;
+    height: number;
+    features: Feature[];
+    tracks: {
+        scrollTop: number;
+        height: number;
+        configuration: string;
+        skip: number;
+    }[];
+}
+export declare function cheight(chunk: LayoutRecord): number;
+export declare function getTrackPos(view: ReducedLinearGenomeView, trackConfigId: string): number;
+export declare function getPxFromCoordinate(view: ReducedLinearGenomeView, refName: string, coord: number): number;
+export declare function overlayYPos(trackConfigId: string, level: number, views: ReducedLinearGenomeView[], c: LayoutRecord, cond: boolean): number;
+export declare function interstitialYPos(cond: boolean, height: number): number;

package/dist/util.js

@@ -0,0 +1,77 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.interstitialYPos = exports.overlayYPos = exports.getPxFromCoordinate = exports.getTrackPos = exports.cheight = void 0;
+const util_1 = require("@jbrowse/core/util");
+const [, TOP, , BOTTOM] = [0, 1, 2, 3];
+function cheight(chunk) {
+    return chunk[BOTTOM] - chunk[TOP];
+}
+exports.cheight = cheight;
+function heightFromSpecificLevel(views, trackConfigId, level) {
+    const heightUpUntilThisPoint = views
+        .slice(0, level)
+        .map(v => v.height + 7)
+        .reduce((a, b) => a + b, 0);
+    return (heightUpUntilThisPoint +
+        views[level].headerHeight +
+        views[level].scaleBarHeight +
+        getTrackPos(views[level], trackConfigId) +
+        1);
+}
+function getTrackPos(view, trackConfigId) {
+    const idx = view.tracks.findIndex(t => t.configuration === trackConfigId);
+    let accum = 0;
+    for (let i = 0; i < idx; i += 1) {
+        accum += view.tracks[i].height + 3; // +1px for trackresizehandle
+    }
+    return accum;
+}
+exports.getTrackPos = getTrackPos;
+// Uses bpToPx to get the screen pixel coordinates but ignores some conditions
+// where bpToPx could return undefined
+function getPxFromCoordinate(view, refName, coord) {
+    return (((bpToPx(view, { refName, coord }) || {}).offsetPx || 0) - view.offsetPx);
+}
+exports.getPxFromCoordinate = getPxFromCoordinate;
+// Retrieves the y-position of a layout record in a track
+// If track not found returns 0
+function overlayYPos(trackConfigId, level, views, c, cond) {
+    const track = views[level].tracks.find(t => t.configuration === trackConfigId);
+    const ypos = track
+        ? (0, util_1.clamp)(c[TOP] - (track.scrollTop || 0), 0, track.height) +
+            heightFromSpecificLevel(views, trackConfigId, level) +
+            track.skip
+        : 0;
+    return ypos + (cond ? cheight(c) : 0);
+}
+exports.overlayYPos = overlayYPos;
+// Returns the pixel screen position of a refName:coord input, or undefined if
+// the input could not be located. Uses view.displayedRegions as a representation
+// of what is on the screen
+//
+// Note: does not consider that this refName:coord input could multi-match
+function bpToPx(view, { refName, coord }) {
+    let offsetBp = 0;
+    const index = view.displayedRegions.findIndex(r => {
+        if (refName === r.refName && coord >= r.start && coord <= r.end) {
+            offsetBp += coord - r.start;
+            return true;
+        }
+        offsetBp += r.end - r.start;
+        return false;
+    });
+    const foundRegion = view.displayedRegions[index];
+    if (foundRegion) {
+        return {
+            index,
+            offsetPx: Math.round(offsetBp / view.bpPerPx),
+        };
+    }
+    return undefined;
+}
+// Returns either 0 or height depending on condition
+function interstitialYPos(cond, height) {
+    return cond ? 0 : height;
+}
+exports.interstitialYPos = interstitialYPos;
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;AAAA,6CAA0C;AAwB1C,MAAM,CAAC,EAAE,GAAG,EAAE,AAAD,EAAG,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;AAEtC,SAAgB,OAAO,CAAC,KAAmB;IACzC,OAAO,KAAK,CAAC,MAAM,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;AACnC,CAAC;AAFD,0BAEC;AACD,SAAS,uBAAuB,CAC9B,KAAgC,EAChC,aAAqB,EACrB,KAAa;IAEb,MAAM,sBAAsB,GAAG,KAAK;SACjC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC;SACf,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC;SACtB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAA;IAE7B,OAAO,CACL,sBAAsB;QACtB,KAAK,CAAC,KAAK,CAAC,CAAC,YAAY;QACzB,KAAK,CAAC,KAAK,CAAC,CAAC,cAAc;QAC3B,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,aAAa,CAAC;QACxC,CAAC,CACF,CAAA;AACH,CAAC;AAED,SAAgB,WAAW,CACzB,IAA6B,EAC7B,aAAqB;IAErB,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,KAAK,aAAa,CAAC,CAAA;IACzE,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE;QAC/B,KAAK,IAAI,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA,CAAC,6BAA6B;KACjE;IACD,OAAO,KAAK,CAAA;AACd,CAAC;AAVD,kCAUC;AAED,8EAA8E;AAC9E,sCAAsC;AACtC,SAAgB,mBAAmB,CACjC,IAA6B,EAC7B,OAAe,EACf,KAAa;IAEb,OAAO,CACL,CAAC,CAAC,MAAM,CAAC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,QAAQ,CACzE,CAAA;AACH,CAAC;AARD,kDAQC;AAED,yDAAyD;AACzD,+BAA+B;AAC/B,SAAgB,WAAW,CACzB,aAAqB,EACrB,KAAa,EACb,KAAgC,EAChC,CAAe,EACf,IAAa;IAEb,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,KAAK,aAAa,CAAC,CAAA;IAC9E,MAAM,IAAI,GAAG,KAAK;QAChB,CAAC,CAAC,IAAA,YAAK,EAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,CAAC,MAAM,CAAC;YACvD,uBAAuB,CAAC,KAAK,EAAE,aAAa,EAAE,KAAK,CAAC;YACpD,KAAK,CAAC,IAAI;QACZ,CAAC,CAAC,CAAC,CAAA;IAEL,OAAO,IAAI,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACvC,CAAC;AAfD,kCAeC;AAED,8EAA8E;AAC9E,iFAAiF;AACjF,2BAA2B;AAC3B,EAAE;AACF,0EAA0E;AAC1E,SAAS,MAAM,CACb,IAA6B,EAC7B,EAAE,OAAO,EAAE,KAAK,EAAsC;IAEtD,IAAI,QAAQ,GAAG,CAAC,CAAA;IAEhB,MAAM,KAAK,GAAG,IAAI,CAAC,gBAAgB,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE;QAChD,IAAI,OAAO,KAAK,CAAC,CAAC,OAAO,IAAI,KAAK,IAAI,CAAC,CAAC,KAAK,IAAI,KAAK,IAAI,CAAC,CAAC,GAAG,EAAE;YAC/D,QAAQ,IAAI,KAAK,GAAG,CAAC,CAAC,KAAK,CAAA;YAC3B,OAAO,IAAI,CAAA;SACZ;QACD,QAAQ,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK,CAAA;QAC3B,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;IACF,MAAM,WAAW,GAAG,IAAI,CAAC,gBAAgB,CAAC,KAAK,CAAC,CAAA;IAChD,IAAI,WAAW,EAAE;QACf,OAAO;YACL,KAAK;YACL,QAAQ,EAAE,IAAI,CAAC,KAAK,CAAC,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC;SAC9C,CAAA;KACF;IACD,OAAO,SAAS,CAAA;AAClB,CAAC;AAED,oDAAoD;AACpD,SAAgB,gBAAgB,CAAC,IAAa,EAAE,MAAc;IAC5D,OAAO,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;AAC1B,CAAC;AAFD,4CAEC"}

package/esm/LGVSyntenyDisplay/configSchemaF.d.ts

@@ -0,0 +1,52 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+/**
+ * #config LGVSyntenyDisplay
+ */
+declare function configSchemaF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    defaultRendering: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        defaultValue: string; /**
+         * #baseConfiguration
+         */
+    };
+    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        PileupRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    maxFeatureScreenDensity: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    colorScheme: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    renderer: import("mobx-state-tree").IAnyModelType;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<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[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>, undefined>>, undefined>>;
+export default configSchemaF;

package/esm/LGVSyntenyDisplay/configSchemaF.js

@@ -0,0 +1,16 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { linearPileupDisplayConfigSchemaFactory } from '@jbrowse/plugin-alignments';
+/**
+ * #config LGVSyntenyDisplay
+ */
+function configSchemaF(pluginManager) {
+    return ConfigurationSchema('LGVSyntenyDisplay', {}, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: linearPileupDisplayConfigSchemaFactory(pluginManager),
+        explicitlyTyped: true,
+    });
+}
+export default configSchemaF;
+//# sourceMappingURL=configSchemaF.js.map

package/esm/LGVSyntenyDisplay/configSchemaF.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchemaF.js","sourceRoot":"","sources":["../../src/LGVSyntenyDisplay/configSchemaF.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,OAAO,EAAE,sCAAsC,EAAE,MAAM,4BAA4B,CAAA;AAEnF;;GAEG;AACH,SAAS,aAAa,CAAC,aAA4B;IACjD,OAAO,mBAAmB,CACxB,mBAAmB,EACnB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,sCAAsC,CAAC,aAAa,CAAC;QACxE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAED,eAAe,aAAa,CAAA"}

package/esm/LGVSyntenyDisplay/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/LGVSyntenyDisplay/index.js

@@ -0,0 +1,19 @@
+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) => {
+    pluginManager.addDisplayType(() => {
+        const configSchema = configSchemaF(pluginManager);
+        const stateModel = stateModelF(configSchema);
+        return new DisplayType({
+            name: 'LGVSyntenyDisplay',
+            configSchema,
+            stateModel,
+            trackType: 'SyntenyTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: BaseLinearDisplayComponent,
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/esm/LGVSyntenyDisplay/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LGVSyntenyDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAC3C,OAAO,WAAW,MAAM,SAAS,CAAA;AACjC,OAAO,EAAE,0BAA0B,EAAE,MAAM,oCAAoC,CAAA;AAE/E,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QACjD,MAAM,UAAU,GAAG,WAAW,CAAC,YAAY,CAAC,CAAA;QAC5C,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,mBAAmB;YACzB,YAAY;YACZ,UAAU;YACV,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,0BAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/LGVSyntenyDisplay/model.d.ts

@@ -0,0 +1,380 @@
+/// <reference types="react" />
+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import { Feature } from '@jbrowse/core/util';
+/**
+ * #stateModel LGVSyntenyDisplay
+ * extends `LinearPileupDisplay`, displays location of "synteny" feature in a
+ * plain LGV, allowing linking out to external synteny views
+ */
+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").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").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>;
+        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;
+        filled: boolean;
+        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        features: Map<string, Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: any;
+        }) => any;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(abortController: AbortController): void;
+        setMessage(messageText: string): void;
+        setRendered(props: {
+            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            features: Map<string, Feature>;
+            layout: any;
+            maxHeightReached: boolean;
+            renderProps: any;
+        } | 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[];
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
+    configuration: AnyConfigurationSchemaType;
+    showSoftClipping: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    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>>;
+    mismatchAlpha: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    sortedBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+        type: import("mobx-state-tree").ISimpleType<string>;
+        pos: import("mobx-state-tree").ISimpleType<number>;
+        tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        refName: import("mobx-state-tree").ISimpleType<string>;
+        assemblyName: import("mobx-state-tree").ISimpleType<string>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+        type: import("mobx-state-tree").ISimpleType<string>;
+        tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        extra: import("mobx-state-tree").IType<any, any, any>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+        flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+        readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            tag: import("mobx-state-tree").ISimpleType<string>;
+            value: import("mobx-state-tree").ISimpleType<string>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+} & {
+    /**
+     * #property
+     */
+    type: import("mobx-state-tree").ISimpleType<"LGVSyntenyDisplay">;
+    /**
+     * #property
+     */
+    configuration: AnyConfigurationSchemaType;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+    message: string | undefined;
+} & {
+    readonly RenderingComponent: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        } & import("mobx-state-tree").IStateTreeNode<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").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        onHorizontalScroll?: Function | undefined;
+        blockState?: Record<string, any> | undefined;
+    }>;
+    readonly DisplayBlurb: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        } & import("mobx-state-tree").IStateTreeNode<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").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            message: string | undefined;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }> | null;
+    readonly adapterConfig: any;
+    readonly parentTrack: any;
+    renderProps(): any;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): null;
+} & {
+    setMessage(arg?: string | undefined): void;
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    scrollTop: number;
+} & {
+    readonly height: number;
+} & {
+    setScrollTop(scrollTop: number): void;
+    setHeight(displayHeight: number): number;
+    resizeHeight(distance: number): number;
+} & {
+    featureDensityStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats> | undefined;
+    featureDensityStats: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined;
+    currStatsBpPerPx: number;
+} & {
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly featureDensityStatsReady: boolean;
+    readonly maxAllowableBytes: number;
+} & {
+    afterAttach(): void;
+} & {
+    setCurrStatsBpPerPx(n: number): void;
+    setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+    setFeatureDensityStatsP(arg: any): void;
+    setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
+    clearFeatureDensityStats(): void;
+} & {
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+} & {
+    featureIdUnderMouse: string | undefined;
+    contextMenuFeature: Feature | undefined;
+} & {
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
+    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
+} & {
+    readonly renderDelay: number;
+    readonly TooltipComponent: import("react").FC<any>;
+    readonly selectedFeatureId: string | undefined;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+} & {
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
+    readonly featureUnderMouse: Feature | undefined;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
+    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
+    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+} & {
+    addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
+    deleteBlock(key: string): void;
+    selectFeature(feature: Feature): void;
+    clearFeatureSelection(): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
+    setContextMenuFeature(feature?: Feature | undefined): void;
+} & {
+    reload(): Promise<void>;
+} & {
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    renderProps(): any;
+} & {
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    afterAttach(): void;
+} & {
+    colorTagMap: import("mobx").ObservableMap<string, string>;
+    modificationTagMap: import("mobx").ObservableMap<string, string>;
+    featureUnderMouseVolatile: Feature | undefined;
+    currSortBpPerPx: number;
+    modificationsReady: boolean;
+    sortReady: boolean;
+    tagsReady: boolean;
+} & {
+    readonly autorunReady: boolean;
+} & {
+    setModificationsReady(flag: boolean): void;
+    setTagsReady(flag: boolean): void;
+    setSortReady(flag: boolean): void;
+    setCurrSortBpPerPx(n: number): void;
+    setMaxHeight(n: number): void;
+    setFeatureHeight(n?: number | undefined): void;
+    setNoSpacing(flag?: boolean | undefined): void;
+    setColorScheme(colorScheme: {
+        type: string;
+        tag?: string | undefined;
+    }): void;
+    updateModificationColorMap(uniqueModifications: string[]): void;
+    updateColorTagMap(uniqueTag: string[]): void;
+    setFeatureUnderMouse(feat?: Feature | undefined): void;
+    selectFeature(feature: Feature): void;
+    clearSelected(): void;
+    copyFeatureToClipboard(feature: Feature): void;
+    toggleSoftClipping(): void;
+    toggleMismatchAlpha(): void;
+    setConfig(conf: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>): void;
+    setSortedBy(type: string, tag?: string | undefined): void;
+    setFilterBy(filter: import("@jbrowse/plugin-alignments/src/LinearPileupDisplay/model").Filter): void;
+} & {
+    reload(): void;
+} & {
+    readonly rendererConfig: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+} & {
+    readonly maxHeight: any;
+    readonly featureHeightSetting: any;
+    readonly mismatchAlphaSetting: any;
+    readonly featureUnderMouse: Feature | undefined;
+    readonly renderReady: boolean;
+} & {
+    readonly rendererTypeName: string;
+    contextMenuItems(): ({
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+    } | {
+        label: string;
+        icon: typeof import("@jbrowse/core/ui/Icons").ContentCopy;
+        onClick: () => void;
+    })[];
+    readonly DisplayBlurb: (props: import("@jbrowse/plugin-alignments/src/LinearPileupDisplay/components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => import("react").JSX.Element | null;
+    renderPropsPre(): any;
+    renderProps(): any;
+    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;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        type: string;
+        checked: boolean;
+        onClick: () => void;
+        disabled?: undefined;
+        subMenu?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        disabled: boolean;
+        subMenu: {
+            label: string;
+            onClick: () => void;
+        }[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        subMenu: {
+            label: string;
+            onClick: () => void;
+        }[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
+        disabled?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+        type?: undefined;
+        checked?: undefined;
+        disabled?: undefined;
+        subMenu?: undefined;
+    } | {
+        label: string;
+        type: string;
+        checked: any;
+        onClick: () => void;
+        icon?: undefined;
+        disabled?: undefined;
+        subMenu?: undefined;
+    })[];
+} & {
+    afterAttach(): void;
+} & {
+    contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+} & {
+    afterCreate(): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default stateModelFactory;