npm - @jbrowse/plugin-alignments - Versions diffs - 3.7.0 → 4.0.0 - Mend

@jbrowse/plugin-alignments 3.7.0 → 4.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (669) hide show

package/esm/LinearPileupDisplay/model.d.ts CHANGED Viewed

@@ -1,29 +1,29 @@
-import type { ModificationType, ModificationTypeWithColor, SortedBy } from '../shared/types';
+import type { SortedBy } from '../shared/types.ts';
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import type { Instance } from 'mobx-state-tree';
-declare function stateModelFactory(configSchema: 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").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
-        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
-        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+import type { Instance } from '@jbrowse/mobx-state-tree';
+declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("@jbrowse/mobx-state-tree").IModelType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+} & {
+    heightPreConfig: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+} & {
+    userBpPerPxLimit: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+} & {
+    blockState: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
+        key: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        region: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
+        reloadFlag: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        stopToken: string | undefined;
+        stopToken: import("@jbrowse/core/util").StopToken | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
-        status: string;
+        blockStatusMessage: string;
         error: unknown;
         message: string | undefined;
         maxHeightReached: boolean;
@@ -31,25 +31,32 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             model: {
                 error?: unknown;
                 reload: () => void;
-                message: React.ReactNode;
-                filled?: boolean;
-                status?: string;
+                message?: React.ReactNode;
+                statusMessage?: string;
                 reactElement?: React.ReactElement;
+                isRenderingPending?: boolean;
             };
-        }) => import("react/jsx-runtime").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element;
         renderProps: any;
+        renderArgs: Record<string, unknown> | undefined;
+        isRenderingPending: boolean;
+        cachedDisplay: import("@jbrowse/core/util").AbstractDisplayModel | undefined;
     } & {
         doReload(): void;
-        afterAttach(): void;
-        setStatus(message: string): void;
-        setLoading(newStopToken: string): void;
+        setStatusMessage(message: string): void;
+        setLoading(newStopToken: import("@jbrowse/core/util").StopToken): void;
         setMessage(messageText: string): void;
-        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
+        setCachedDisplay(display: import("@jbrowse/core/util").AbstractDisplayModel): void;
         beforeDestroy(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    } & {
+        readonly statusMessage: any;
+    } & {
+        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<{
         maxFeatureScreenDensity: {
             type: string;
             description: string;
@@ -76,46 +83,50 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             description: string;
             defaultValue: never[];
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").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>>;
 } & {
     configuration: AnyConfigurationSchemaType;
-    featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    colorBySetting: import("mobx-state-tree").IType<import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined>;
-    filterBySetting: import("mobx-state-tree").IType<import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined>;
-    jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
-    hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
+    featureHeight: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    noSpacing: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    fadeLikelihood: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    trackMaxHeight: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    colorBySetting: import("@jbrowse/mobx-state-tree").IType<import("../shared/types.ts").ColorBy | undefined, import("../shared/types.ts").ColorBy | undefined, import("../shared/types.ts").ColorBy | undefined>;
+    filterBySetting: import("@jbrowse/mobx-state-tree").IType<import("../shared/types.ts").FilterBy | undefined, import("../shared/types.ts").FilterBy | undefined, import("../shared/types.ts").FilterBy | undefined>;
+    jexlFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    hideSmallIndelsSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    hideMismatchesSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    hideLargeIndelsSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+} & {
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
     configuration: AnyConfigurationSchemaType;
-    showSoftClipping: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    mismatchAlpha: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    sortedBy: import("mobx-state-tree").IType<SortedBy | undefined, SortedBy | undefined, SortedBy | undefined>;
+    showSoftClipping: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    mismatchAlpha: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    sortedBy: import("@jbrowse/mobx-state-tree").IType<SortedBy | undefined, SortedBy | undefined, SortedBy | undefined>;
 }, {
     rendererTypeName: string;
     error: unknown;
-    message: string | undefined;
+    statusMessage: string | undefined;
 } & {
     readonly RenderingComponent: React.FC<{
         model: {
             id: string;
             type: string;
             rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import("@jbrowse/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>>;
+            statusMessage: string | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            statusMessage: string | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
         onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
@@ -124,30 +135,142 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             id: string;
             type: string;
             rpcDriverName: string | undefined;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import("@jbrowse/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>>;
+            statusMessage: string | undefined;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+            statusMessage: string | undefined;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
-    readonly parentTrack: any;
+    readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly parentDisplay: any;
+    readonly effectiveRpcDriverName: any;
+} & {
     renderProps(): any;
+    renderingProps(): {
+        displayModel: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & {
+            readonly RenderingComponent: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: () => void;
+                blockState?: Record<string, any>;
+            }>;
+            readonly DisplayBlurb: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly parentDisplay: any;
+            readonly effectiveRpcDriverName: any;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & {
+            readonly RenderingComponent: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: () => void;
+                blockState?: Record<string, any>;
+            }>;
+            readonly DisplayBlurb: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly parentDisplay: any;
+            readonly effectiveRpcDriverName: any;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    };
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: undefined | React.FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
 } & {
-    setMessage(arg?: string): void;
+    setStatusMessage(arg?: string): void;
     setError(error?: unknown): void;
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
@@ -182,12 +305,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
-    readonly statsReadyAndRegionNotTooLarge: boolean;
+    readonly featureDensityStatsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     mouseoverExtraInformation: string | undefined;
     featureIdUnderMouse: undefined | string;
+    subfeatureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
     readonly DisplayMessageComponent: undefined | React.FC<any>;
@@ -196,27 +320,23 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
+    legendItems(_theme?: import("@mui/material").Theme): import("@jbrowse/plugin-linear-genome-view").LegendItem[];
+    svgLegendWidth(theme?: import("@mui/material").Theme): number;
     readonly selectedFeatureId: string | undefined;
-    copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
+    readonly featureWidgetType: {
+        type: string;
+        id: string;
+    };
 } & {
+    readonly showTooltipsEnabled: boolean;
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
-    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
-        label?: string;
-        description?: string;
-        refName: string;
-    }]>;
+    getFeatureById(featureId: string, parentFeatureId?: string): import("@jbrowse/core/util").Feature | undefined;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord>;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
-        label?: string;
-        description?: string;
-        refName: string;
-    }]) | undefined;
-    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
-        label?: string;
-        description?: string;
-        refName: string;
-    }]) | undefined;
+    getFeatureByID(blockKey: string, id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord | undefined;
+    searchFeatureByID(id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord | undefined;
+    readonly floatingLabelData: Map<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/components/util.ts").FeatureLabelData>;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
@@ -224,13 +344,746 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
+    setSubfeatureIdUnderMouse(subfeatureId?: string): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
     setMouseoverExtraInformation(extra?: string): void;
+    setShowLegend(s: boolean): void;
+    setShowTooltips(arg: boolean): void;
 } & {
     reload(): Promise<void>;
+} & {
+    selectFeatureById: (featureId: string, parentFeatureId?: string | undefined, topLevelFeatureId?: string | undefined) => Promise<void>;
+    setContextMenuFeatureById: (featureId: string, parentFeatureId?: string | undefined, topLevelFeatureId?: string | undefined) => Promise<void>;
 } & {
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    renderingProps(): {
+        displayModel: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+            heightPreConfig: number | undefined;
+            userBpPerPxLimit: number | undefined;
+            userByteSizeLimit: number | undefined;
+            blockState: import("@jbrowse/mobx-state-tree").IMSTMap<import("@jbrowse/mobx-state-tree").IModelType<{
+                key: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                region: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
+                reloadFlag: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+                isLeftEndOfDisplayedRegion: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                isRightEndOfDisplayedRegion: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+            }, {
+                stopToken: import("@jbrowse/core/util").StopToken | undefined;
+                filled: boolean;
+                reactElement: React.ReactElement | undefined;
+                features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+                layout: any;
+                blockStatusMessage: string;
+                error: unknown;
+                message: string | undefined;
+                maxHeightReached: boolean;
+                ReactComponent: ({ model, }: {
+                    model: {
+                        error?: unknown;
+                        reload: () => void;
+                        message?: React.ReactNode;
+                        statusMessage?: string;
+                        reactElement?: React.ReactElement;
+                        isRenderingPending?: boolean;
+                    };
+                }) => import("react/jsx-runtime").JSX.Element;
+                renderProps: any;
+                renderArgs: Record<string, unknown> | undefined;
+                isRenderingPending: boolean;
+                cachedDisplay: import("@jbrowse/core/util").AbstractDisplayModel | undefined;
+            } & {
+                doReload(): void;
+                setStatusMessage(message: string): void;
+                setLoading(newStopToken: import("@jbrowse/core/util").StopToken): void;
+                setMessage(messageText: string): void;
+                setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts").RenderedProps | undefined): void;
+                setError(error: unknown): void;
+                reload(): void;
+                setCachedDisplay(display: import("@jbrowse/core/util").AbstractDisplayModel): void;
+                beforeDestroy(): void;
+            } & {
+                readonly statusMessage: any;
+            } & {
+                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<{
+                key: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                region: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
+                reloadFlag: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+                isLeftEndOfDisplayedRegion: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                isRightEndOfDisplayedRegion: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+            }, {
+                stopToken: import("@jbrowse/core/util").StopToken | undefined;
+                filled: boolean;
+                reactElement: React.ReactElement | undefined;
+                features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+                layout: any;
+                blockStatusMessage: string;
+                error: unknown;
+                message: string | undefined;
+                maxHeightReached: boolean;
+                ReactComponent: ({ model, }: {
+                    model: {
+                        error?: unknown;
+                        reload: () => void;
+                        message?: React.ReactNode;
+                        statusMessage?: string;
+                        reactElement?: React.ReactElement;
+                        isRenderingPending?: boolean;
+                    };
+                }) => import("react/jsx-runtime").JSX.Element;
+                renderProps: any;
+                renderArgs: Record<string, unknown> | undefined;
+                isRenderingPending: boolean;
+                cachedDisplay: import("@jbrowse/core/util").AbstractDisplayModel | undefined;
+            } & {
+                doReload(): void;
+                setStatusMessage(message: string): void;
+                setLoading(newStopToken: import("@jbrowse/core/util").StopToken): void;
+                setMessage(messageText: string): void;
+                setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts").RenderedProps | undefined): void;
+                setError(error: unknown): void;
+                reload(): void;
+                setCachedDisplay(display: import("@jbrowse/core/util").AbstractDisplayModel): void;
+                beforeDestroy(): void;
+            } & {
+                readonly statusMessage: any;
+            } & {
+                afterAttach(): void;
+            }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>>;
+            configuration: {
+                [x: string]: any;
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                    [x: string]: any;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    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>);
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+            } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+                maxFeatureScreenDensity: {
+                    type: string;
+                    description: string;
+                    defaultValue: number;
+                };
+                fetchSizeLimit: {
+                    type: string;
+                    defaultValue: number;
+                    description: string;
+                };
+                height: {
+                    type: string;
+                    defaultValue: number;
+                    description: string;
+                };
+                mouseover: {
+                    type: string;
+                    description: string;
+                    defaultValue: string;
+                    contextVariable: string[];
+                };
+                jexlFilters: {
+                    type: string;
+                    description: string;
+                    defaultValue: never[];
+                };
+            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "displayId">>>;
+            showLegend: boolean | undefined;
+            showTooltips: boolean | undefined;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & {
+            readonly RenderingComponent: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: () => void;
+                blockState?: Record<string, any>;
+            }>;
+            readonly DisplayBlurb: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly parentDisplay: any;
+            readonly effectiveRpcDriverName: any;
+        } & {
+            renderProps(): any;
+            renderingProps(): {
+                displayModel: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & {
+                    readonly RenderingComponent: React.FC<{
+                        model: {
+                            id: string;
+                            type: string;
+                            rpcDriverName: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                        }, {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                        onHorizontalScroll?: () => void;
+                        blockState?: Record<string, any>;
+                    }>;
+                    readonly DisplayBlurb: React.FC<{
+                        model: {
+                            id: string;
+                            type: string;
+                            rpcDriverName: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                        }, {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                    }> | null;
+                    readonly adapterConfig: any;
+                    readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly parentDisplay: any;
+                    readonly effectiveRpcDriverName: any;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & {
+                    readonly RenderingComponent: React.FC<{
+                        model: {
+                            id: string;
+                            type: string;
+                            rpcDriverName: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                        }, {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                        onHorizontalScroll?: () => void;
+                        blockState?: Record<string, any>;
+                    }>;
+                    readonly DisplayBlurb: React.FC<{
+                        model: {
+                            id: string;
+                            type: string;
+                            rpcDriverName: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                        }, {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                    }> | null;
+                    readonly adapterConfig: any;
+                    readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly parentDisplay: any;
+                    readonly effectiveRpcDriverName: any;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+            };
+            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+            readonly DisplayMessageComponent: undefined | React.FC<any>;
+            trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+            regionCannotBeRendered(): null;
+        } & {
+            setStatusMessage(arg?: string): 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: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+            featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
+            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): void;
+            getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+            setFeatureDensityStatsP(arg: any): void;
+            setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
+            clearFeatureDensityStats(): void;
+        } & {
+            readonly regionTooLarge: boolean;
+            readonly regionTooLargeReason: string;
+        } & {
+            readonly featureDensityStatsReadyAndRegionNotTooLarge: boolean;
+            regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
+            regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
+        } & {
+            mouseoverExtraInformation: string | undefined;
+            featureIdUnderMouse: undefined | string;
+            subfeatureIdUnderMouse: undefined | string;
+            contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
+        } & {
+            readonly DisplayMessageComponent: undefined | React.FC<any>;
+            readonly blockType: "staticBlocks" | "dynamicBlocks";
+            readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
+        } & {
+            readonly renderDelay: number;
+            readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
+            legendItems(_theme?: import("@mui/material").Theme): import("@jbrowse/plugin-linear-genome-view").LegendItem[];
+            svgLegendWidth(theme?: import("@mui/material").Theme): number;
+            readonly selectedFeatureId: string | undefined;
+            readonly featureWidgetType: {
+                type: string;
+                id: string;
+            };
+        } & {
+            readonly showTooltipsEnabled: boolean;
+            readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
+            readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+            getFeatureById(featureId: string, parentFeatureId?: string): import("@jbrowse/core/util").Feature | undefined;
+            readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord>;
+            getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
+            getFeatureByID(blockKey: string, id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord | undefined;
+            searchFeatureByID(id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord | undefined;
+            readonly floatingLabelData: Map<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/components/util.ts").FeatureLabelData>;
+        } & {
+            addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
+            deleteBlock(key: string): void;
+            selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+            navToFeature(feature: import("@jbrowse/core/util").Feature): void;
+            clearFeatureSelection(): void;
+            setFeatureIdUnderMouse(feature?: string): void;
+            setSubfeatureIdUnderMouse(subfeatureId?: string): void;
+            setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
+            setMouseoverExtraInformation(extra?: string): void;
+            setShowLegend(s: boolean): void;
+            setShowTooltips(arg: boolean): void;
+        } & {
+            reload(): Promise<void>;
+        } & {
+            selectFeatureById: (featureId: string, parentFeatureId?: string | undefined, topLevelFeatureId?: string | undefined) => Promise<void>;
+            setContextMenuFeatureById: (featureId: string, parentFeatureId?: string | undefined, topLevelFeatureId?: string | undefined) => Promise<void>;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        } & {
+            heightPreConfig: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+        } & {
+            userBpPerPxLimit: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+            userByteSizeLimit: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+        } & {
+            blockState: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
+                key: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                region: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
+                reloadFlag: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+                isLeftEndOfDisplayedRegion: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+                isRightEndOfDisplayedRegion: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+            }, {
+                stopToken: import("@jbrowse/core/util").StopToken | undefined;
+                filled: boolean;
+                reactElement: React.ReactElement | undefined;
+                features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+                layout: any;
+                blockStatusMessage: string;
+                error: unknown;
+                message: string | undefined;
+                maxHeightReached: boolean;
+                ReactComponent: ({ model, }: {
+                    model: {
+                        error?: unknown;
+                        reload: () => void;
+                        message?: React.ReactNode;
+                        statusMessage?: string;
+                        reactElement?: React.ReactElement;
+                        isRenderingPending?: boolean;
+                    };
+                }) => import("react/jsx-runtime").JSX.Element;
+                renderProps: any;
+                renderArgs: Record<string, unknown> | undefined;
+                isRenderingPending: boolean;
+                cachedDisplay: import("@jbrowse/core/util").AbstractDisplayModel | undefined;
+            } & {
+                doReload(): void;
+                setStatusMessage(message: string): void;
+                setLoading(newStopToken: import("@jbrowse/core/util").StopToken): void;
+                setMessage(messageText: string): void;
+                setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts").RenderedProps | undefined): void;
+                setError(error: unknown): void;
+                reload(): void;
+                setCachedDisplay(display: import("@jbrowse/core/util").AbstractDisplayModel): void;
+                beforeDestroy(): void;
+            } & {
+                readonly statusMessage: any;
+            } & {
+                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<{
+                maxFeatureScreenDensity: {
+                    type: string;
+                    description: string;
+                    defaultValue: number;
+                };
+                fetchSizeLimit: {
+                    type: string;
+                    defaultValue: number;
+                    description: string;
+                };
+                height: {
+                    type: string;
+                    defaultValue: number;
+                    description: string;
+                };
+                mouseover: {
+                    type: string;
+                    description: string;
+                    defaultValue: string;
+                    contextVariable: string[];
+                };
+                jexlFilters: {
+                    type: string;
+                    description: string;
+                    defaultValue: never[];
+                };
+            }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").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>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & {
+            readonly RenderingComponent: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: () => void;
+                blockState?: Record<string, any>;
+            }>;
+            readonly DisplayBlurb: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly parentDisplay: any;
+            readonly effectiveRpcDriverName: any;
+        } & {
+            renderProps(): any;
+            renderingProps(): {
+                displayModel: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & {
+                    readonly RenderingComponent: React.FC<{
+                        model: {
+                            id: string;
+                            type: string;
+                            rpcDriverName: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                        }, {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                        onHorizontalScroll?: () => void;
+                        blockState?: Record<string, any>;
+                    }>;
+                    readonly DisplayBlurb: React.FC<{
+                        model: {
+                            id: string;
+                            type: string;
+                            rpcDriverName: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                        }, {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                    }> | null;
+                    readonly adapterConfig: any;
+                    readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly parentDisplay: any;
+                    readonly effectiveRpcDriverName: any;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & {
+                    readonly RenderingComponent: React.FC<{
+                        model: {
+                            id: string;
+                            type: string;
+                            rpcDriverName: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                        }, {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                        onHorizontalScroll?: () => void;
+                        blockState?: Record<string, any>;
+                    }>;
+                    readonly DisplayBlurb: React.FC<{
+                        model: {
+                            id: string;
+                            type: string;
+                            rpcDriverName: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                        }, {
+                            rendererTypeName: string;
+                            error: unknown;
+                            statusMessage: string | undefined;
+                        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                    }> | null;
+                    readonly adapterConfig: any;
+                    readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly parentDisplay: any;
+                    readonly effectiveRpcDriverName: any;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+            };
+            readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+            readonly DisplayMessageComponent: undefined | React.FC<any>;
+            trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+            readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+            regionCannotBeRendered(): null;
+        } & {
+            setStatusMessage(arg?: string): 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: undefined | Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+            featureDensityStats: undefined | import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats;
+            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): void;
+            getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
+            setFeatureDensityStatsP(arg: any): void;
+            setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats): void;
+            clearFeatureDensityStats(): void;
+        } & {
+            readonly regionTooLarge: boolean;
+            readonly regionTooLargeReason: string;
+        } & {
+            readonly featureDensityStatsReadyAndRegionNotTooLarge: boolean;
+            regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
+            regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
+        } & {
+            mouseoverExtraInformation: string | undefined;
+            featureIdUnderMouse: undefined | string;
+            subfeatureIdUnderMouse: undefined | string;
+            contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
+        } & {
+            readonly DisplayMessageComponent: undefined | React.FC<any>;
+            readonly blockType: "staticBlocks" | "dynamicBlocks";
+            readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
+        } & {
+            readonly renderDelay: number;
+            readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
+            legendItems(_theme?: import("@mui/material").Theme): import("@jbrowse/plugin-linear-genome-view").LegendItem[];
+            svgLegendWidth(theme?: import("@mui/material").Theme): number;
+            readonly selectedFeatureId: string | undefined;
+            readonly featureWidgetType: {
+                type: string;
+                id: string;
+            };
+        } & {
+            readonly showTooltipsEnabled: boolean;
+            readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
+            readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+            getFeatureById(featureId: string, parentFeatureId?: string): import("@jbrowse/core/util").Feature | undefined;
+            readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord>;
+            getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
+            getFeatureByID(blockKey: string, id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord | undefined;
+            searchFeatureByID(id: string): import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/types.ts").LayoutRecord | undefined;
+            readonly floatingLabelData: Map<string, import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/components/util.ts").FeatureLabelData>;
+        } & {
+            addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
+            deleteBlock(key: string): void;
+            selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+            navToFeature(feature: import("@jbrowse/core/util").Feature): void;
+            clearFeatureSelection(): void;
+            setFeatureIdUnderMouse(feature?: string): void;
+            setSubfeatureIdUnderMouse(subfeatureId?: string): void;
+            setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
+            setMouseoverExtraInformation(extra?: string): void;
+            setShowLegend(s: boolean): void;
+            setShowTooltips(arg: boolean): void;
+        } & {
+            reload(): Promise<void>;
+        } & {
+            selectFeatureById: (featureId: string, parentFeatureId?: string | undefined, topLevelFeatureId?: string | undefined) => Promise<void>;
+            setContextMenuFeatureById: (featureId: string, parentFeatureId?: string | undefined, topLevelFeatureId?: string | undefined) => Promise<void>;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+        onMouseMove(_: unknown, featureId?: string): void;
+        onMouseLeave(_: unknown): void;
+        onContextMenu(_: unknown): void;
+    };
     renderProps(): any;
 } & {
     renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
@@ -245,38 +1098,48 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     readonly autorunReady: boolean;
     readonly hideSmallIndels: boolean | undefined;
+    readonly hideMismatches: boolean | undefined;
+    readonly hideLargeIndels: boolean | undefined;
 } & {
     setTagsReady(flag: boolean): void;
     setMaxHeight(n?: number): void;
     setFeatureHeight(n?: number): void;
     setNoSpacing(flag?: boolean): void;
-    setColorScheme(colorScheme: import("../shared/types").ColorBy): void;
+    setColorScheme(colorScheme: import("../shared/types.ts").ColorBy): void;
     updateColorTagMap(uniqueTag: string[]): void;
     setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     setConfig(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
-    setFilterBy(filter: import("../shared/types").FilterBy): void;
+    setFilterBy(filter: import("../shared/types.ts").FilterBy): void;
     setJexlFilters(filters: string[]): void;
     setHideSmallIndels(arg: boolean): void;
+    setHideMismatches(arg: boolean): void;
+    setHideLargeIndels(arg: boolean): void;
 } & {
-    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
-    readonly rendererConfig: {
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): Promise<void>;
+    readonly rendererConfig: any;
 } & {
     readonly maxHeight: any;
     readonly featureHeightSetting: any;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
     renderReady(): boolean;
     readonly filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
+    legendItems(theme: import("@mui/material").Theme): import("@jbrowse/plugin-linear-genome-view").LegendItem[];
+    showSubMenuItems(): ({
+        label: string;
+        type: "subMenu";
+        subMenu: {
+            label: string;
+            type: "radio";
+            checked: boolean | undefined;
+            onClick: () => void;
+        }[];
+    } | {
+        label: string;
+        type: string;
+        checked: boolean | undefined;
+        onClick: () => void;
+    })[];
 } & {
     readonly rendererTypeName: string;
     contextMenuItems(): {
@@ -291,7 +1154,119 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             sortedBy?: SortedBy;
         };
     }) => import("react/jsx-runtime").JSX.Element | null;
-    renderPropsPre(): any;
+    adapterRenderProps(): any;
+    renderingProps(): {
+        onFeatureClick(_: unknown, featureId?: string): Promise<void>;
+        onClick(): void;
+        onFeatureContextMenu(_: unknown, featureId?: string): Promise<void>;
+        displayModel: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & {
+            readonly RenderingComponent: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: () => void;
+                blockState?: Record<string, any>;
+            }>;
+            readonly DisplayBlurb: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly parentDisplay: any;
+            readonly effectiveRpcDriverName: any;
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+            id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+            statusMessage: string | undefined;
+        } & {
+            readonly RenderingComponent: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+                onHorizontalScroll?: () => void;
+                blockState?: Record<string, any>;
+            }>;
+            readonly DisplayBlurb: React.FC<{
+                model: {
+                    id: string;
+                    type: string;
+                    rpcDriverName: string | undefined;
+                } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
+                    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+                    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+                    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+                }, {
+                    rendererTypeName: string;
+                    error: unknown;
+                    statusMessage: string | undefined;
+                }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+            }> | null;
+            readonly adapterConfig: any;
+            readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly parentDisplay: any;
+            readonly effectiveRpcDriverName: any;
+        }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    };
     colorSchemeSubMenuItems(): {
         label: string;
         onClick: () => void;
@@ -299,10 +1274,43 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
         priority: number;
-        type: string;
-        checked: boolean | undefined;
-        onClick: () => void;
+        subMenu: ({
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        } | {
+            label: string;
+            onClick: () => void;
+            type?: undefined;
+            checked?: undefined;
+        })[];
         icon?: undefined;
+        type?: undefined;
+        onClick?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        priority: number;
+        type: string;
+        subMenu: ({
+            label: string;
+            type: "subMenu";
+            subMenu: {
+                label: string;
+                type: "radio";
+                checked: boolean | undefined;
+                onClick: () => void;
+            }[];
+        } | {
+            label: string;
+            type: string;
+            checked: boolean | undefined;
+            onClick: () => void;
+        })[];
+        onClick?: undefined;
     } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
@@ -310,52 +1318,61 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         };
         onClick: () => void;
         priority?: undefined;
+        subMenu?: undefined;
         type?: undefined;
-        checked?: undefined;
     })[];
 } & {
     renderProps(): any;
 } & {
     afterAttach(): void;
 } & {
-    sortReady: boolean;
-    currSortBpPerPx: number;
-    visibleModifications: import("mobx").ObservableMap<string, ModificationTypeWithColor>;
+    visibleModifications: import("mobx").ObservableMap<string, import("../shared/types.ts").ModificationTypeWithColor>;
     simplexModifications: Set<string>;
     modificationsReady: boolean;
 } & {
-    setCurrSortBpPerPx(n: number): void;
-    updateVisibleModifications(uniqueModifications: ModificationType[]): void;
+    readonly visibleModificationTypes: string[];
+} & {
+    updateVisibleModifications(uniqueModifications: import("../shared/types.ts").ModificationType[]): void;
     setSimplexModifications(simplex: string[]): void;
     setModificationsReady(flag: boolean): void;
+} & {
+    sortReady: boolean;
+    currSortBpPerPx: number;
+} & {
+    setCurrSortBpPerPx(n: number): void;
     setSortReady(flag: boolean): void;
     clearSelected(): void;
     toggleSoftClipping(): void;
     toggleMismatchAlpha(): void;
     setSortedBy(type: string, tag?: string): void;
+    setSortedByAtPosition(type: string, pos: number, refName: string): void;
     setFeatureHeight(n?: number): void;
 } & {
     reload(): void;
 } & {
-    readonly visibleModificationTypes: string[];
     readonly modificationThreshold: any;
-    readonly rendererConfig: {
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
+    readonly rendererConfig: any;
 } & {
     readonly mismatchAlphaSetting: any;
     renderReady(): boolean;
 } & {
-    renderPropsPre(): any;
+    adapterRenderProps(): any;
     renderProps(): any;
+    showSubMenuItems(): ({
+        label: string;
+        type: "subMenu";
+        subMenu: {
+            label: string;
+            type: "radio";
+            checked: boolean | undefined;
+            onClick: () => void;
+        }[];
+    } | {
+        label: string;
+        type: string;
+        checked: any;
+        onClick: () => void;
+    })[];
     trackMenuItems(): readonly [...import("@jbrowse/core/ui").MenuItem[], {
         readonly label: "Sort by...";
         readonly icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
@@ -388,10 +1405,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                 onClick: () => void;
                 type?: undefined;
             } | {
-                type: string;
+                type: "divider";
                 label?: undefined;
                 onClick?: undefined;
-            })[];
+            })[] | {
+                label: string;
+            }[];
         }, {
             readonly label: "Insert size";
             readonly onClick: () => void;
@@ -405,47 +1424,34 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             muiName: string;
         };
         readonly onClick: () => void;
-    }, {
-        readonly label: "Show soft clipping";
-        readonly icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        readonly type: "checkbox";
-        readonly checked: boolean;
-        readonly onClick: () => void;
-    }, {
-        readonly label: "Fade mismatches by quality";
-        readonly type: "checkbox";
-        readonly checked: any;
-        readonly onClick: () => void;
     }];
 } & {
     afterAttach(): void;
 }, {
     type: string;
-} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<string>;
-    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-} & {
-    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-} & {
-    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-} & {
-    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
-        key: import("mobx-state-tree").ISimpleType<string>;
-        region: import("mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
-        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
-        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+} & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+} & {
+    heightPreConfig: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+} & {
+    userBpPerPxLimit: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+} & {
+    blockState: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
+        key: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        region: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
+        reloadFlag: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        stopToken: string | undefined;
+        stopToken: import("@jbrowse/core/util").StopToken | undefined;
         filled: boolean;
         reactElement: React.ReactElement | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
-        status: string;
+        blockStatusMessage: string;
         error: unknown;
         message: string | undefined;
         maxHeightReached: boolean;
@@ -453,25 +1459,129 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             model: {
                 error?: unknown;
                 reload: () => void;
-                message: React.ReactNode;
-                filled?: boolean;
-                status?: string;
+                message?: React.ReactNode;
+                statusMessage?: string;
                 reactElement?: React.ReactElement;
+                isRenderingPending?: boolean;
             };
-        }) => import("react/jsx-runtime").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element;
         renderProps: any;
+        renderArgs: Record<string, unknown> | undefined;
+        isRenderingPending: boolean;
+        cachedDisplay: import("@jbrowse/core/util").AbstractDisplayModel | undefined;
     } & {
         doReload(): void;
+        setStatusMessage(message: string): void;
+        setLoading(newStopToken: import("@jbrowse/core/util").StopToken): void;
+        setMessage(messageText: string): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts").RenderedProps | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        setCachedDisplay(display: import("@jbrowse/core/util").AbstractDisplayModel): void;
+        beforeDestroy(): void;
+    } & {
+        readonly statusMessage: any;
+    } & {
         afterAttach(): void;
-        setStatus(message: string): void;
-        setLoading(newStopToken: string): void;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
+    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
+        maxFeatureScreenDensity: {
+            type: string;
+            description: string;
+            defaultValue: number;
+        };
+        fetchSizeLimit: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        height: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+        mouseover: {
+            type: string;
+            description: string;
+            defaultValue: string;
+            contextVariable: string[];
+        };
+        jexlFilters: {
+            type: string;
+            description: string;
+            defaultValue: never[];
+        };
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").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>>;
+} & {
+    configuration: AnyConfigurationSchemaType;
+    featureHeight: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    noSpacing: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    fadeLikelihood: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    trackMaxHeight: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    colorBySetting: import("@jbrowse/mobx-state-tree").IType<import("../shared/types.ts").ColorBy | undefined, import("../shared/types.ts").ColorBy | undefined, import("../shared/types.ts").ColorBy | undefined>;
+    filterBySetting: import("@jbrowse/mobx-state-tree").IType<import("../shared/types.ts").FilterBy | undefined, import("../shared/types.ts").FilterBy | undefined, import("../shared/types.ts").FilterBy | undefined>;
+    jexlFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    hideSmallIndelsSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    hideMismatchesSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    hideLargeIndelsSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+}>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+} & {
+    heightPreConfig: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+} & {
+    userBpPerPxLimit: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+} & {
+    blockState: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").IModelType<{
+        key: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        region: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region, import("@jbrowse/core/util").Region>;
+        reloadFlag: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    }, {
+        stopToken: import("@jbrowse/core/util").StopToken | undefined;
+        filled: boolean;
+        reactElement: React.ReactElement | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+        layout: any;
+        blockStatusMessage: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message?: React.ReactNode;
+                statusMessage?: string;
+                reactElement?: React.ReactElement;
+                isRenderingPending?: boolean;
+            };
+        }) => import("react/jsx-runtime").JSX.Element;
+        renderProps: any;
+        renderArgs: Record<string, unknown> | undefined;
+        isRenderingPending: boolean;
+        cachedDisplay: import("@jbrowse/core/util").AbstractDisplayModel | undefined;
+    } & {
+        doReload(): void;
+        setStatusMessage(message: string): void;
+        setLoading(newStopToken: import("@jbrowse/core/util").StopToken): void;
         setMessage(messageText: string): void;
-        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock").RenderedProps | undefined): void;
+        setRendered(props: import("@jbrowse/plugin-linear-genome-view/src/BaseLinearDisplay/models/serverSideRenderedBlock.ts").RenderedProps | undefined): void;
         setError(error: unknown): void;
         reload(): void;
+        setCachedDisplay(display: import("@jbrowse/core/util").AbstractDisplayModel): void;
         beforeDestroy(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    } & {
+        readonly statusMessage: any;
+    } & {
+        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<{
         maxFeatureScreenDensity: {
             type: string;
             description: string;
@@ -498,18 +1608,28 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             description: string;
             defaultValue: never[];
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").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>>;
+} & {
+    configuration: AnyConfigurationSchemaType;
+    featureHeight: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    noSpacing: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    fadeLikelihood: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    trackMaxHeight: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    colorBySetting: import("@jbrowse/mobx-state-tree").IType<import("../shared/types.ts").ColorBy | undefined, import("../shared/types.ts").ColorBy | undefined, import("../shared/types.ts").ColorBy | undefined>;
+    filterBySetting: import("@jbrowse/mobx-state-tree").IType<import("../shared/types.ts").FilterBy | undefined, import("../shared/types.ts").FilterBy | undefined, import("../shared/types.ts").FilterBy | undefined>;
+    jexlFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    hideSmallIndelsSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    hideMismatchesSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    hideLargeIndelsSetting: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
 } & {
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
     configuration: AnyConfigurationSchemaType;
-    featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    colorBySetting: import("mobx-state-tree").IType<import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined>;
-    filterBySetting: import("mobx-state-tree").IType<import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined>;
-    jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
-    hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+    showSoftClipping: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    mismatchAlpha: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    sortedBy: import("@jbrowse/mobx-state-tree").IType<SortedBy | undefined, SortedBy | undefined, SortedBy | undefined>;
+}>>;
 export type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>;
 export default stateModelFactory;