@jbrowse/plugin-wiggle 4.1.3 → 4.1.4

package/esm/MultiLinearWiggleDisplay/model.d.ts

@@ -1,4 +1,5 @@
 import type { Source } from '../util.ts';
+import type { HoveredTreeNode } from './components/treeTypes.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import type { AnyReactComponentType, Feature } from '@jbrowse/core/util';
@@ -39,6 +40,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                 statusMessage?: string;
                 reactElement?: React.ReactElement;
                 isRenderingPending?: boolean;
+                displayHeight?: number;
             };
         }) => import("react/jsx-runtime").JSX.Element;
         renderProps: any;
@@ -57,10 +59,11 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
         beforeDestroy(): void;
     } & {
         readonly statusMessage: any;
+        readonly displayHeight: number | undefined;
     } & {
         afterAttach(): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
             description: string;
@@ -87,7 +90,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
             description: string;
             defaultValue: never[];
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
     showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
 } & {
@@ -112,6 +115,10 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
     type: import("@jbrowse/mobx-state-tree").ISimpleType<"MultiLinearWiggleDisplay">;
     layout: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<Source[], Source[], Source[]>, [undefined]>;
     showSidebar: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    clusterTree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    showTreeSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    subtreeFilter: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -400,6 +407,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -418,6 +426,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -444,6 +453,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -462,6 +472,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
@@ -475,7 +486,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                         [x: string]: any;
                     } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 maxFeatureScreenDensity: {
                     type: string;
                     description: string;
@@ -502,7 +513,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                     description: string;
                     defaultValue: never[];
                 };
-            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>>;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>>;
             showLegend: boolean | undefined;
             showTooltips: boolean | undefined;
         } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -792,6 +803,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -810,10 +822,11 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-            configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+            configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 maxFeatureScreenDensity: {
                     type: string;
                     description: string;
@@ -840,7 +853,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                     description: string;
                     defaultValue: never[];
                 };
-            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
             showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
             showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
         }, {
@@ -1111,6 +1124,8 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
         currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
+        scoreMeanMin?: number;
+        scoreMeanMax?: number;
         statsRegion?: string;
     } | undefined;
     statsFetchInProgress: undefined | StopToken;
@@ -1119,6 +1134,8 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
         currStatsBpPerPx: number;
         scoreMin: number;
         scoreMax: number;
+        scoreMeanMin?: number;
+        scoreMeanMax?: number;
     }, statsRegion?: string): void;
     setColor(color?: string): void;
     setPosColor(color?: string): void;
@@ -1167,6 +1184,8 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
             currStatsBpPerPx: number;
             scoreMin: number;
             scoreMax: number;
+            scoreMeanMin?: number;
+            scoreMeanMax?: number;
             statsRegion?: string;
         } | undefined;
         autoscaleType: string;
@@ -1205,11 +1224,21 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
     sourcesLoadingStopToken: StopToken | undefined;
     featureUnderMouseVolatile: Feature | undefined;
     sourcesVolatile: Source[] | undefined;
+    hoveredTreeNode: HoveredTreeNode | undefined;
+    treeCanvas: HTMLCanvasElement | undefined;
+    mouseoverCanvas: HTMLCanvasElement | undefined;
 } & {
     setShowSidebar(arg: boolean): void;
     setSourcesLoading(str: StopToken): void;
-    setLayout(layout: Source[]): void;
+    setLayout(layout: Source[], clearTree?: boolean): void;
     clearLayout(): void;
+    setClusterTree(tree?: string): void;
+    setTreeAreaWidth(width: number): void;
+    setShowTree(arg: boolean): void;
+    setSubtreeFilter(names?: string[]): void;
+    setHoveredTreeNode(node?: HoveredTreeNode): void;
+    setTreeCanvasRef(ref: HTMLCanvasElement | null): void;
+    setMouseoverCanvasRef(ref: HTMLCanvasElement | null): void;
     setSources(sources: Source[]): void;
     setFeatureUnderMouse(f?: Feature): void;
 } & {
@@ -1240,9 +1269,14 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
     }[] | undefined;
     readonly quantitativeStatsReady: boolean;
 } & {
+    readonly showTree: boolean;
     readonly rowHeight: number;
     readonly rowHeightTooSmallForScalebar: boolean;
     readonly useMinimalTicks: boolean;
+    readonly root: any;
+} & {
+    readonly totalHeight: number;
+    readonly hierarchy: any;
 } & {
     adapterProps(): any;
     readonly ticks: {
@@ -1290,6 +1324,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -1308,6 +1343,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1334,6 +1370,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -1352,6 +1389,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
@@ -1365,7 +1403,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                         [x: string]: any;
                     } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 maxFeatureScreenDensity: {
                     type: string;
                     description: string;
@@ -1392,7 +1430,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                     description: string;
                     defaultValue: never[];
                 };
-            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">> & AnyConfigurationSchemaType> & {
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">> & AnyConfigurationSchemaType> & {
                 setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
                     [x: string]: any;
                 } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
@@ -1420,6 +1458,10 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
             }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>>;
             layout: Source[] & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<Source[], Source[], Source[]>, [undefined]>>;
             showSidebar: boolean;
+            clusterTree: string | undefined;
+            treeAreaWidth: number;
+            showTreeSetting: boolean | undefined;
+            subtreeFilter: (import("@jbrowse/mobx-state-tree").IMSTArray<import("@jbrowse/mobx-state-tree").ISimpleType<string>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>>) | undefined;
         } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
@@ -1708,6 +1750,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                                 statusMessage?: string;
                                 reactElement?: React.ReactElement;
                                 isRenderingPending?: boolean;
+                                displayHeight?: number;
                             };
                         }) => import("react/jsx-runtime").JSX.Element;
                         renderProps: any;
@@ -1726,6 +1769,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                         beforeDestroy(): void;
                     } & {
                         readonly statusMessage: any;
+                        readonly displayHeight: number | undefined;
                     } & {
                         afterAttach(): void;
                     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1752,6 +1796,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                                 statusMessage?: string;
                                 reactElement?: React.ReactElement;
                                 isRenderingPending?: boolean;
+                                displayHeight?: number;
                             };
                         }) => import("react/jsx-runtime").JSX.Element;
                         renderProps: any;
@@ -1770,6 +1815,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                         beforeDestroy(): void;
                     } & {
                         readonly statusMessage: any;
+                        readonly displayHeight: number | undefined;
                     } & {
                         afterAttach(): void;
                     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
@@ -1783,7 +1829,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                                 [x: string]: any;
                             } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
                         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-                    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+                    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                         maxFeatureScreenDensity: {
                             type: string;
                             description: string;
@@ -1810,7 +1856,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                             description: string;
                             defaultValue: never[];
                         };
-                    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>>;
+                    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>>;
                     showLegend: boolean | undefined;
                     showTooltips: boolean | undefined;
                 } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -2100,6 +2146,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                                 statusMessage?: string;
                                 reactElement?: React.ReactElement;
                                 isRenderingPending?: boolean;
+                                displayHeight?: number;
                             };
                         }) => import("react/jsx-runtime").JSX.Element;
                         renderProps: any;
@@ -2118,10 +2165,11 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                         beforeDestroy(): void;
                     } & {
                         readonly statusMessage: any;
+                        readonly displayHeight: number | undefined;
                     } & {
                         afterAttach(): void;
                     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-                    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+                    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                         maxFeatureScreenDensity: {
                             type: string;
                             description: string;
@@ -2148,7 +2196,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                             description: string;
                             defaultValue: never[];
                         };
-                    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+                    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
                     showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
                     showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
                 }, {
@@ -2419,6 +2467,8 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                 currStatsBpPerPx: number;
                 scoreMin: number;
                 scoreMax: number;
+                scoreMeanMin?: number;
+                scoreMeanMax?: number;
                 statsRegion?: string;
             } | undefined;
             statsFetchInProgress: undefined | StopToken;
@@ -2427,6 +2477,8 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                 currStatsBpPerPx: number;
                 scoreMin: number;
                 scoreMax: number;
+                scoreMeanMin?: number;
+                scoreMeanMax?: number;
             }, statsRegion?: string): void;
             setColor(color?: string): void;
             setPosColor(color?: string): void;
@@ -2475,6 +2527,8 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                     currStatsBpPerPx: number;
                     scoreMin: number;
                     scoreMax: number;
+                    scoreMeanMin?: number;
+                    scoreMeanMax?: number;
                     statsRegion?: string;
                 } | undefined;
                 autoscaleType: string;
@@ -2513,11 +2567,21 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
             sourcesLoadingStopToken: StopToken | undefined;
             featureUnderMouseVolatile: Feature | undefined;
             sourcesVolatile: Source[] | undefined;
+            hoveredTreeNode: HoveredTreeNode | undefined;
+            treeCanvas: HTMLCanvasElement | undefined;
+            mouseoverCanvas: HTMLCanvasElement | undefined;
         } & {
             setShowSidebar(arg: boolean): void;
             setSourcesLoading(str: StopToken): void;
-            setLayout(layout: Source[]): void;
+            setLayout(layout: Source[], clearTree?: boolean): void;
             clearLayout(): void;
+            setClusterTree(tree?: string): void;
+            setTreeAreaWidth(width: number): void;
+            setShowTree(arg: boolean): void;
+            setSubtreeFilter(names?: string[]): void;
+            setHoveredTreeNode(node?: HoveredTreeNode): void;
+            setTreeCanvasRef(ref: HTMLCanvasElement | null): void;
+            setMouseoverCanvasRef(ref: HTMLCanvasElement | null): void;
             setSources(sources: Source[]): void;
             setFeatureUnderMouse(f?: Feature): void;
         } & {
@@ -2548,9 +2612,14 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
             }[] | undefined;
             readonly quantitativeStatsReady: boolean;
         } & {
+            readonly showTree: boolean;
             readonly rowHeight: number;
             readonly rowHeightTooSmallForScalebar: boolean;
             readonly useMinimalTicks: boolean;
+            readonly root: any;
+        } & {
+            readonly totalHeight: number;
+            readonly hierarchy: any;
         } & {
             adapterProps(): any;
             readonly ticks: {
@@ -2595,6 +2664,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                         statusMessage?: string;
                         reactElement?: React.ReactElement;
                         isRenderingPending?: boolean;
+                        displayHeight?: number;
                     };
                 }) => import("react/jsx-runtime").JSX.Element;
                 renderProps: any;
@@ -2613,10 +2683,11 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                 beforeDestroy(): void;
             } & {
                 readonly statusMessage: any;
+                readonly displayHeight: number | undefined;
             } & {
                 afterAttach(): void;
             }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-            configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+            configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                 maxFeatureScreenDensity: {
                     type: string;
                     description: string;
@@ -2643,7 +2714,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                     description: string;
                     defaultValue: never[];
                 };
-            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+            }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
             showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
             showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
         } & {
@@ -2668,6 +2739,10 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
             type: import("@jbrowse/mobx-state-tree").ISimpleType<"MultiLinearWiggleDisplay">;
             layout: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<Source[], Source[], Source[]>, [undefined]>;
             showSidebar: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+            clusterTree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+            treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+            showTreeSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+            subtreeFilter: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
         }, {
             rendererTypeName: string;
             error: unknown;
@@ -2956,6 +3031,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                                 statusMessage?: string;
                                 reactElement?: React.ReactElement;
                                 isRenderingPending?: boolean;
+                                displayHeight?: number;
                             };
                         }) => import("react/jsx-runtime").JSX.Element;
                         renderProps: any;
@@ -2974,6 +3050,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                         beforeDestroy(): void;
                     } & {
                         readonly statusMessage: any;
+                        readonly displayHeight: number | undefined;
                     } & {
                         afterAttach(): void;
                     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>> & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -3000,6 +3077,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                                 statusMessage?: string;
                                 reactElement?: React.ReactElement;
                                 isRenderingPending?: boolean;
+                                displayHeight?: number;
                             };
                         }) => import("react/jsx-runtime").JSX.Element;
                         renderProps: any;
@@ -3018,6 +3096,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                         beforeDestroy(): void;
                     } & {
                         readonly statusMessage: any;
+                        readonly displayHeight: number | undefined;
                     } & {
                         afterAttach(): void;
                     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
@@ -3031,7 +3110,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                                 [x: string]: any;
                             } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
                         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-                    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+                    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                         maxFeatureScreenDensity: {
                             type: string;
                             description: string;
@@ -3058,7 +3137,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                             description: string;
                             defaultValue: never[];
                         };
-                    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>>;
+                    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>>;
                     showLegend: boolean | undefined;
                     showTooltips: boolean | undefined;
                 } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -3348,6 +3427,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                                 statusMessage?: string;
                                 reactElement?: React.ReactElement;
                                 isRenderingPending?: boolean;
+                                displayHeight?: number;
                             };
                         }) => import("react/jsx-runtime").JSX.Element;
                         renderProps: any;
@@ -3366,10 +3446,11 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                         beforeDestroy(): void;
                     } & {
                         readonly statusMessage: any;
+                        readonly displayHeight: number | undefined;
                     } & {
                         afterAttach(): void;
                     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-                    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+                    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
                         maxFeatureScreenDensity: {
                             type: string;
                             description: string;
@@ -3396,7 +3477,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                             description: string;
                             defaultValue: never[];
                         };
-                    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+                    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
                     showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
                     showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
                 }, {
@@ -3667,6 +3748,8 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                 currStatsBpPerPx: number;
                 scoreMin: number;
                 scoreMax: number;
+                scoreMeanMin?: number;
+                scoreMeanMax?: number;
                 statsRegion?: string;
             } | undefined;
             statsFetchInProgress: undefined | StopToken;
@@ -3675,6 +3758,8 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                 currStatsBpPerPx: number;
                 scoreMin: number;
                 scoreMax: number;
+                scoreMeanMin?: number;
+                scoreMeanMax?: number;
             }, statsRegion?: string): void;
             setColor(color?: string): void;
             setPosColor(color?: string): void;
@@ -3723,6 +3808,8 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                     currStatsBpPerPx: number;
                     scoreMin: number;
                     scoreMax: number;
+                    scoreMeanMin?: number;
+                    scoreMeanMax?: number;
                     statsRegion?: string;
                 } | undefined;
                 autoscaleType: string;
@@ -3761,11 +3848,21 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
             sourcesLoadingStopToken: StopToken | undefined;
             featureUnderMouseVolatile: Feature | undefined;
             sourcesVolatile: Source[] | undefined;
+            hoveredTreeNode: HoveredTreeNode | undefined;
+            treeCanvas: HTMLCanvasElement | undefined;
+            mouseoverCanvas: HTMLCanvasElement | undefined;
         } & {
             setShowSidebar(arg: boolean): void;
             setSourcesLoading(str: StopToken): void;
-            setLayout(layout: Source[]): void;
+            setLayout(layout: Source[], clearTree?: boolean): void;
             clearLayout(): void;
+            setClusterTree(tree?: string): void;
+            setTreeAreaWidth(width: number): void;
+            setShowTree(arg: boolean): void;
+            setSubtreeFilter(names?: string[]): void;
+            setHoveredTreeNode(node?: HoveredTreeNode): void;
+            setTreeCanvasRef(ref: HTMLCanvasElement | null): void;
+            setMouseoverCanvasRef(ref: HTMLCanvasElement | null): void;
             setSources(sources: Source[]): void;
             setFeatureUnderMouse(f?: Feature): void;
         } & {
@@ -3796,9 +3893,14 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
             }[] | undefined;
             readonly quantitativeStatsReady: boolean;
         } & {
+            readonly showTree: boolean;
             readonly rowHeight: number;
             readonly rowHeightTooSmallForScalebar: boolean;
             readonly useMinimalTicks: boolean;
+            readonly root: any;
+        } & {
+            readonly totalHeight: number;
+            readonly hierarchy: any;
         } & {
             adapterProps(): any;
             readonly ticks: {
@@ -3853,12 +3955,25 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
-        subMenu: {
+        subMenu: ({
+            label: string;
+            type: string;
+            checked: boolean;
+            disabled: boolean;
+            onClick: () => void;
+        } | {
+            label: string;
+            onClick: () => void;
+            type?: undefined;
+            checked?: undefined;
+            disabled?: undefined;
+        } | {
             type: string;
             label: string;
             checked: any;
             onClick: () => void;
-        }[];
+            disabled?: undefined;
+        })[];
     } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
@@ -3932,6 +4047,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
                 statusMessage?: string;
                 reactElement?: React.ReactElement;
                 isRenderingPending?: boolean;
+                displayHeight?: number;
             };
         }) => import("react/jsx-runtime").JSX.Element;
         renderProps: any;
@@ -3950,10 +4066,11 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
         beforeDestroy(): void;
     } & {
         readonly statusMessage: any;
+        readonly displayHeight: number | undefined;
     } & {
         afterAttach(): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
-    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         maxFeatureScreenDensity: {
             type: string;
             description: string;
@@ -3980,7 +4097,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
             description: string;
             defaultValue: never[];
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
     showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     showTooltips: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
 } & {
@@ -4005,6 +4122,10 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
     type: import("@jbrowse/mobx-state-tree").ISimpleType<"MultiLinearWiggleDisplay">;
     layout: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IType<Source[], Source[], Source[]>, [undefined]>;
     showSidebar: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    clusterTree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    showTreeSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    subtreeFilter: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>>;
 }>>;
 export type WiggleDisplayStateModel = ReturnType<typeof stateModelFactory>;
 export type WiggleDisplayModel = Instance<WiggleDisplayStateModel>;