@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/dist/LinearReadCloudDisplay/model.js.map

@@ -1 +1 @@
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+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearReadCloudDisplay/model.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,iCAAmC;AACnC,qDAAuD;AACvD,+EAAiE;AACjE,+DAGoC;AACpC,6CAA+C;AAC/C,kFAG2C;AAE3C,QAAQ;AACR,0EAAqD;AACrD,4EAAyD;AAEzD,SAAS;AACT,sCAAuC;AAGvC,QAAQ;AACR,MAAM,cAAc,GAAG,IAAA,YAAI,EAAC,GAAG,EAAE,mDAAQ,uBAAuB,GAAC,CAAC,CAAA;AASlE;;;GAGG;AACH,SAAS,iBAAiB,CAAC,YAAwC;IACjE,OAAO,uBAAK;SACT,OAAO,CACN,wBAAwB,EACxB,mCAAW,EACX,IAAA,4CAAgB,GAAE,EAClB,IAAA,+CAAmB,GAAE,EACrB,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,wBAAwB,CAAC;QAC7C;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;QAEnD;;WAEG;QACH,QAAQ,EAAE,uBAAK,CAAC,QAAQ,CAAC,oBAAW,EAAE,EAAE,CAAC;QAEzC;;WAEG;QACH,OAAO,EAAE,uBAAK,CAAC,KAAK,CAClB,uBAAK,CAAC,KAAK,CAAC;YACV,IAAI,EAAE,uBAAK,CAAC,MAAM;YAClB,GAAG,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;YAC9B,KAAK,EAAE,uBAAK,CAAC,MAAM,EAAE;SACtB,CAAC,CACH;QAED;;WAEG;QACH,cAAc,EAAE,IAAI;KACrB,CAAC,CACH;SACA,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,OAAO,EAAE,KAAK;QACd,SAAS,EAAE,SAAkC;QAC7C,iBAAiB,EAAE,SAA+B;QAClD,gBAAgB,EAAE,CAAC;QACnB,GAAG,EAAE,IAAgC;KACtC,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,iBAAiB,CAAC,CAAU;YAC1B,IAAI,CAAC,cAAc,GAAG,CAAC,CAAA;QACzB,CAAC;QACD;;WAEG;QACH,oBAAoB,CAAC,CAAS;YAC5B,IAAI,CAAC,iBAAiB,GAAG,CAAC,CAAA;QAC5B,CAAC;QACD;;WAEG;QACH,mBAAmB,CAAC,CAAS;YAC3B,IAAI,CAAC,gBAAgB,GAAG,CAAC,CAAA;QAC3B,CAAC;QAED;;WAEG;QACH,UAAU,CAAC,CAAU;YACnB,IAAI,CAAC,OAAO,GAAG,CAAC,CAAA;QAClB,CAAC;QACD;;WAEG;QACH,MAAM;YACJ,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;QACxB,CAAC;QACD;;;;WAIG;QACH,MAAM,CAAC,GAA6B;YAClC,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;QAED,cAAc,CAAC,CAAmB;YAChC,IAAI,CAAC,OAAO,GAAG,IAAA,sBAAI,EAAC,CAAC,CAAC,CAAA;QACxB,CAAC;QAED;;WAEG;QACH,YAAY,CAAC,IAAe;YAC1B,IAAI,CAAC,SAAS,GAAG,IAAI,CAAA;QACvB,CAAC;QAED;;WAEG;QACH,WAAW,CAAC,MAAc;YACxB,IAAI,CAAC,QAAQ,GAAG,IAAA,sBAAI,EAAC,MAAM,CAAC,CAAA;QAC9B,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd,IAAI,KAAK;YACP,OAAO,IAAI,CAAC,iBAAiB,KAAK,SAAS,CAAA;QAC7C,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,EACJ,cAAc,EAAE,mBAAmB,EACnC,WAAW,EAAE,gBAAgB,GAC9B,GAAG,IAAI,CAAA;QAER,OAAO;YACL,gEAAgE;YAChE,0BAA0B;YAC1B,WAAW;gBACT,OAAO;oBACL,GAAG,gBAAgB,EAAE;oBACrB,QAAQ,EAAE,CAAC,IAAI,CAAC,SAAS;iBAC1B,CAAA;YACH,CAAC;YAED;;eAEG;YACH,cAAc;gBACZ,OAAO;oBACL,GAAG,mBAAmB,EAAE;oBACxB;wBACE,KAAK,EAAE,iBAAiB;wBACxB,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,IAAI,CAAC,cAAc;wBAC5B,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC,IAAI,CAAC,cAAc,CAAC;qBAC5D;oBACD;wBACE,KAAK,EAAE,WAAW;wBAClB,IAAI,EAAE,kBAAc;wBACpB,OAAO,EAAE,GAAG,EAAE;4BACZ,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;gCAC1C,cAAc;gCACd,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE;6BAC7B,CAAC,CAAA;wBACJ,CAAC;qBACF;oBAED;wBACE,KAAK,EAAE,cAAc;wBACrB,IAAI,EAAE,iBAAW;wBACjB,OAAO,EAAE;4BACP;gCACE,KAAK,EAAE,kCAAkC;gCACzC,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,0BAA0B,EAAE,CAAC;6BAC5D;4BACD;gCACE,KAAK,EAAE,kBAAkB;gCACzB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC;6BAC3D;4BACD;gCACE,KAAK,EAAE,aAAa;gCACpB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,aAAa,EAAE,CAAC;6BAC5D;4BACD;gCACE,KAAK,EAAE,sBAAsB;gCAC7B,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,UAAU,EAAE,CAAC;6BACzD;yBACF;qBACF;iBACF,CAAA;YACH,CAAC;YAED;;eAEG;YACH,KAAK,CAAC,SAAS,CAAC,IAEf;gBACC,MAAM,EAAE,SAAS,EAAE,GAAG,wDAAa,qBAAqB,GAAC,CAAA;gBACzD,MAAM,EAAE,SAAS,EAAE,GAAG,wDAAa,aAAa,GAAC,CAAA;gBACjD,OAAO,SAAS,CAAC,IAAmC,EAAE,IAAI,EAAE,SAAS,CAAC,CAAA;YACxE,CAAC;SACF,CAAA;IACH,CAAC,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,WAAW;YACT,mEAAmE;YACnE,CAAC;YAAA,CAAC,KAAK,IAAI,EAAE;gBACX,IAAI;oBACF,MAAM,EAAE,aAAa,EAAE,GAAG,wDAAa,uBAAuB,GAAC,CAAA;oBAC/D,MAAM,EAAE,SAAS,EAAE,GAAG,wDAAa,aAAa,GAAC,CAAA;oBACjD,aAAa,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;iBAC/B;gBAAC,OAAO,CAAC,EAAE;oBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;oBAChB,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;iBACjB;YACH,CAAC,CAAC,EAAE,CAAA;QACN,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AAQD,kBAAe,iBAAiB,CAAA"}

package/dist/LinearReadCloudDisplay/util.d.ts

@@ -0,0 +1,2 @@
+export declare function fillRectCtx(x: number, y: number, width: number, height: number, ctx: CanvasRenderingContext2D, fillColor?: string): void;
+export declare function strokeRectCtx(x: number, y: number, width: number, height: number, ctx: CanvasRenderingContext2D, strokeColor?: string): void;

package/dist/LinearReadCloudDisplay/util.js

@@ -0,0 +1,35 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.strokeRectCtx = exports.fillRectCtx = void 0;
+// avoid drawing negative width features for SVG exports
+function fillRectCtx(x, y, width, height, ctx, fillColor) {
+    if (width < 0) {
+        x += width;
+        width = -width;
+    }
+    if (height < 0) {
+        y += height;
+        height = -height;
+    }
+    if (fillColor) {
+        ctx.fillStyle = fillColor;
+    }
+    ctx.fillRect(x, y, width, height);
+}
+exports.fillRectCtx = fillRectCtx;
+function strokeRectCtx(x, y, width, height, ctx, strokeColor) {
+    if (width < 0) {
+        x += width;
+        width = -width;
+    }
+    if (height < 0) {
+        y += height;
+        height = -height;
+    }
+    if (strokeColor) {
+        ctx.strokeStyle = strokeColor;
+    }
+    ctx.strokeRect(x, y, width, height);
+}
+exports.strokeRectCtx = strokeRectCtx;
+//# sourceMappingURL=util.js.map

package/dist/LinearReadCloudDisplay/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/LinearReadCloudDisplay/util.ts"],"names":[],"mappings":";;;AAAA,wDAAwD;AACxD,SAAgB,WAAW,CACzB,CAAS,EACT,CAAS,EACT,KAAa,EACb,MAAc,EACd,GAA6B,EAC7B,SAAkB;IAElB,IAAI,KAAK,GAAG,CAAC,EAAE;QACb,CAAC,IAAI,KAAK,CAAA;QACV,KAAK,GAAG,CAAC,KAAK,CAAA;KACf;IACD,IAAI,MAAM,GAAG,CAAC,EAAE;QACd,CAAC,IAAI,MAAM,CAAA;QACX,MAAM,GAAG,CAAC,MAAM,CAAA;KACjB;IAED,IAAI,SAAS,EAAE;QACb,GAAG,CAAC,SAAS,GAAG,SAAS,CAAA;KAC1B;IAED,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;AACnC,CAAC;AAtBD,kCAsBC;AAED,SAAgB,aAAa,CAC3B,CAAS,EACT,CAAS,EACT,KAAa,EACb,MAAc,EACd,GAA6B,EAC7B,WAAoB;IAEpB,IAAI,KAAK,GAAG,CAAC,EAAE;QACb,CAAC,IAAI,KAAK,CAAA;QACV,KAAK,GAAG,CAAC,KAAK,CAAA;KACf;IACD,IAAI,MAAM,GAAG,CAAC,EAAE;QACd,CAAC,IAAI,MAAM,CAAA;QACX,MAAM,GAAG,CAAC,MAAM,CAAA;KACjB;IAED,IAAI,WAAW,EAAE;QACf,GAAG,CAAC,WAAW,GAAG,WAAW,CAAA;KAC9B;IACD,GAAG,CAAC,UAAU,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;AACrC,CAAC;AArBD,sCAqBC"}

package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import { Feature } from '@jbrowse/core/util';
 type Coord = [number, number];
 declare const SNPCoverageTooltip: (props: {
@@ -9,5 +9,5 @@ declare const SNPCoverageTooltip: (props: {
     offsetMouseCoord: Coord;
     clientMouseCoord: Coord;
     clientRect?: DOMRect;
-}) => JSX.Element | null;
+}) => React.JSX.Element | null;
 export default SNPCoverageTooltip;

package/dist/LinearSNPCoverageDisplay/models/configSchema.d.ts

@@ -1,2 +1,80 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    autoscale: {
+        type: string;
+        defaultValue: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    minScore: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    maxScore: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    scaleType: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */ inverted: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    multiTicks: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        SNPCoverageRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, 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>>;

package/dist/LinearSNPCoverageDisplay/models/model.d.ts

@@ -11,6 +11,10 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     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<{
@@ -47,7 +51,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>; /**
+             * #getter
+             */
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -57,11 +63,33 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         reload(): void;
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            /**
+             * #getter
+             */
+            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<"LinearWiggleDisplay">;
-    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
     selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
@@ -73,13 +101,14 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
-     * #action
-     */
+    displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     constraints: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         max: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
         min: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    configuration: AnyConfigurationSchemaType;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
 } & {
     /**
      * #property
@@ -119,6 +148,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 }, {
     rendererTypeName: string;
     error: unknown;
+    message: string | undefined;
 } & {
     readonly RenderingComponent: import("react").FC<{
         model: {
@@ -128,6 +158,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         } & 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>;
@@ -135,6 +166,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         }, {
             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;
@@ -143,14 +175,11 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         model: {
             id: string;
             type: string;
-            rpcDriverName: string | undefined; /**
-             * #getter
-             */
+            rpcDriverName: string | undefined;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            rendererTypeName: string; /**
-             * #getter
-             */
+            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>;
@@ -158,6 +187,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         }, {
             rendererTypeName: string;
             error: unknown;
+            message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
@@ -167,21 +197,49 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
-    regionCannotBeRendered(): undefined;
+    regionCannotBeRendered(): null;
 } & {
+    setMessage(arg?: string | undefined): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
-    currBpPerPx: number;
     scrollTop: number;
-    message: string;
+} & {
+    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: import("@jbrowse/core/util").Feature | undefined;
-    estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
-    estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -195,49 +253,22 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     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;
-    readonly currentBytesRequested: number;
-    readonly currentFeatureScreenDensity: number;
-    readonly maxFeatureScreenDensity: any;
-    readonly estimatedStatsReady: boolean;
-    readonly maxAllowableBytes: number;
-} & {
-    setMessage(message: string): void;
 } & {
-    afterAttach(): void;
-    estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
-    setRegionsStatsP(arg: any): void;
-    setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
-    clearRegionsStats(): void;
-    setHeight(displayHeight: number): number;
-    resizeHeight(distance: number): number;
-    setScrollTop(scrollTop: number): void;
-    updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
-    setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
-    setFeatureIdUnderMouse(feature: string | undefined): void;
-    reload(): void;
+    setFeatureIdUnderMouse(feature?: string | undefined): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
-} & {
-    readonly regionTooLarge: boolean;
-    readonly regionTooLargeReason: string;
 } & {
     reload(): Promise<void>;
 } & {
-    afterAttach(): void;
-} & {
-    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
-        overrideHeight: number;
-        theme: import("@mui/material").ThemeOptions;
-    }): Promise<JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    afterAttach(): void;
 } & {
     message: string | undefined;
     stats: {
@@ -246,7 +277,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     } | undefined;
     statsFetchInProgress: AbortController | undefined;
 } & {
-    updateStats(stats: {
+    updateQuantitativeStats(stats: {
         scoreMin: number;
         scoreMax: number;
     }): void;
@@ -267,25 +298,25 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     toggleCrossHatches(): void;
     setCrossHatches(cross: boolean): void;
 } & {
-    readonly TooltipComponent: import("react").FC<{}>;
     readonly adapterTypeName: any;
     readonly rendererTypeNameSimple: any;
-    readonly rendererTypeName: string;
     readonly filters: undefined;
     readonly scaleType: any;
     readonly maxScore: any;
     readonly minScore: any;
 } & {
+    readonly adapterCapabilities: string[];
     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 autoscaleType: any;
 } & {
-    readonly filled: any;
-    readonly summaryScoreModeSetting: any;
     readonly domain: number[] | undefined;
-    readonly needsScalebar: boolean;
+} & {
+    readonly filled: boolean;
+    readonly summaryScoreModeSetting: string;
     readonly scaleOpts: {
         domain: number[] | undefined;
         stats: {
@@ -297,8 +328,36 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         inverted: any;
     };
     readonly canHaveFill: boolean;
-    readonly autoscaleType: any;
-    readonly displayCrossHatchesSetting: any;
+    readonly displayCrossHatchesSetting: boolean;
+    readonly hasResolution: boolean;
+    readonly hasGlobalStats: boolean;
+} & {
+    scoreTrackMenuItems(): ({
+        label: string;
+        subMenu: {
+            label: string;
+            onClick: () => void;
+        }[];
+        onClick?: undefined;
+    } | {
+        label: string;
+        subMenu: {
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        }[];
+        onClick?: undefined;
+    } | {
+        label: string;
+        onClick: () => void;
+        subMenu?: undefined;
+    })[];
+} & {
+    reload(): Promise<void>;
+} & {
+    readonly TooltipComponent: import("react").FC<{}>;
+    readonly rendererTypeName: string;
 } & {
     readonly ticks: {
         range: number[];
@@ -306,14 +365,38 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         format: (d: import("d3-scale").NumberValue) => string;
         position: import("d3-scale").ScaleLinear<number, number, never> | import("d3-scale").ScaleQuantize<number, never>;
     } | undefined;
-    readonly adapterCapabilities: string[];
 } & {
     renderProps(): any;
-    readonly hasResolution: boolean;
-    readonly hasGlobalStats: boolean;
+    readonly needsScalebar: boolean;
     readonly fillSetting: 0 | 1 | 2;
 } & {
     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: ({
+            label: string;
+            subMenu: {
+                label: string;
+                onClick: () => void;
+            }[];
+            onClick?: undefined;
+        } | {
+            label: string;
+            subMenu: {
+                label: string;
+                type: string;
+                checked: boolean;
+                onClick: () => void;
+            }[];
+            onClick?: undefined;
+        } | {
+            label: string;
+            onClick: () => void;
+            subMenu?: undefined;
+        })[];
+        type?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
+    } | {
         label: string;
         subMenu: {
             label: string;
@@ -327,19 +410,16 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     } | {
         type: string;
         label: string;
-        checked: any;
+        checked: boolean;
         onClick: () => void;
         subMenu?: undefined;
     })[];
 } & {
-    reload(): Promise<void>;
     afterAttach(): void;
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
-        overrideHeight: number;
-        theme: import("@mui/material").ThemeOptions;
-    }): Promise<JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
 } & {
-    modificationTagMap: Record<string, string> | undefined;
+    modificationTagMap: import("mobx").ObservableMap<string, string>;
+    modificationsReady: boolean;
 } & {
     /**
      * #action
@@ -392,12 +472,18 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     /**
      * #getter
      */
-    readonly modificationsReady: boolean;
+    readonly autorunReady: boolean;
+    readonly renderReady: boolean;
+    readonly ready: boolean;
     /**
      * #method
      */
     renderProps(): any;
 } & {
+    /**
+     * #action
+     */
+    setModificationsReady(flag: boolean): void;
     /**
      * #action
      */
@@ -410,6 +496,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
      * #action
      */
     toggleDrawArcs(): void;
+} & {
     afterAttach(): void;
 } & {
     /**
@@ -423,7 +510,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
         offsetMouseCoord: [number, number];
         clientMouseCoord: [number, number];
         clientRect?: DOMRect | undefined;
-    }) => JSX.Element | null;
+    }) => import("react").JSX.Element | null;
     /**
      * #getter
      */