npm - @jbrowse/plugin-alignments - Versions diffs - 3.7.0 → 4.0.1 - Mend

@jbrowse/plugin-alignments 3.7.0 → 4.0.1

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Files changed (669) hide show

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

@@ -1,53 +1,60 @@
 import type React from 'react';
-import type { ReducedFeature } from '../shared/fetchChains';
+import type { ReducedFeature } 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>>;
+import type { Instance } from '@jbrowse/mobx-state-tree';
+import type { ExportSvgDisplayOptions, LegendItem } from '@jbrowse/plugin-linear-genome-view';
+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("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    heightPreConfig: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/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>>;
+    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>>;
 } & {
-    filterBySetting: import("mobx-state-tree").IType<import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined, import("../shared/types").FilterBy | undefined>;
-    colorBySetting: import("mobx-state-tree").IType<import("../shared/types").ColorBy | undefined, import("../shared/types").ColorBy | undefined, import("../shared/types").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>;
+    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>;
 } & {
-    drawSingletons: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    drawProperPairs: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    flipStrandLongReadChains: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    drawSingletons: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawProperPairs: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    flipStrandLongReadChains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    featureHeight: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"LinearReadCloudDisplay">;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"LinearReadCloudDisplay">;
     configuration: AnyConfigurationSchemaType;
-    drawCloud: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    drawCloud: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    noSpacing: 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>>;
+    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>>;
+    showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    showYScalebar: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showOutline: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [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>;
     }>;
@@ -56,30 +63,142 @@ 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;
@@ -114,53 +233,101 @@ 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;
 } & {
     loading: boolean;
-    chainData: import("../shared/fetchChains").ChainData | undefined;
     lastDrawnOffsetPx: number | undefined;
-    lastDrawnBpPerPx: number;
     ref: HTMLCanvasElement | null;
+    renderingImageData: ImageBitmap | undefined;
+    renderingStopToken: import("@jbrowse/core/util").StopToken | undefined;
+    statusMessage: string | undefined;
+} & {
+    readonly drawn: boolean;
 } & {
     setLastDrawnOffsetPx(n: number): void;
-    setLastDrawnBpPerPx(n: number): void;
     setLoading(f: boolean): void;
     setRef(ref: HTMLCanvasElement | null): void;
+    setRenderingImageData(imageData: ImageBitmap | undefined): void;
+    setRenderingStopToken(token?: import("@jbrowse/core/util").StopToken): void;
+    setStatusMessage(msg?: string): void;
+} & {
+    beforeDestroy(): void;
+} & {
+    chainData: import("../shared/types.ts").ChainData | undefined;
+    lastDrawnBpPerPx: number;
+} & {
+    setLastDrawnBpPerPx(n: number): void;
     setColorScheme(colorBy: {
         type: string;
     }): void;
-    setChainData(args: import("../shared/fetchChains").ChainData): void;
-    setFilterBy(filter: import("../shared/types").FilterBy): void;
-} & {
-    readonly drawn: boolean;
+    setChainData(args: import("../shared/types.ts").ChainData): void;
+    setFilterBy(filter: import("../shared/types.ts").FilterBy): void;
 } & {
     featureLayout: import("@jbrowse/core/util/flatbush").default | undefined;
     mouseoverRef: HTMLCanvasElement | null;
-    featuresForFlatbush: import("../shared/flatbushType").FlatbushEntry[];
+    featuresForFlatbush: import("../shared/flatbushType.ts").FlatbushEntry[];
+    mismatchLayout: import("@jbrowse/core/util/flatbush").default | undefined;
+    mismatchItems: import("../PileupRenderer/types.ts").FlatbushItem[];
 } & {
     setFeatureLayout(layout: import("@jbrowse/core/util/flatbush").default): void;
     setMouseoverRef(ref: HTMLCanvasElement | null): void;
-    setFeaturesForFlatbush(features: import("../shared/flatbushType").FlatbushEntry[]): void;
+    setFeaturesForFlatbush(features: import("../shared/flatbushType.ts").FlatbushEntry[]): void;
+    setMismatchLayout(layout: import("@jbrowse/core/util/flatbush").default): void;
+    setMismatchItems(items: import("../PileupRenderer/types.ts").FlatbushItem[]): void;
 } & {
     setDrawSingletons(f: boolean): void;
     setDrawProperPairs(f: boolean): void;
     setFlipStrandLongReadChains(f: boolean): void;
     setFeatureHeight(n?: number): void;
+} & {
+    visibleModifications: import("mobx").ObservableMap<string, import("../shared/types.ts").ModificationTypeWithColor>;
+    simplexModifications: Set<string>;
+    modificationsReady: boolean;
+} & {
+    readonly visibleModificationTypes: string[];
+} & {
+    updateVisibleModifications(uniqueModifications: import("../shared/types.ts").ModificationType[]): void;
+    setSimplexModifications(simplex: string[]): void;
+    setModificationsReady(flag: boolean): void;
 } & {
     layoutHeight: number;
+    selectedFeatureId: string | undefined;
+    cloudMaxDistance: number | undefined;
 } & {
     readonly colorBy: any;
     readonly filterBy: any;
-    readonly featureHeightSetting: any;
 } & {
     reload(): void;
+} & {
+    readonly dataTestId: "cloud-canvas" | "stack-canvas";
+    readonly featureHeightSetting: any;
+    readonly hideSmallIndels: any;
+    readonly hideMismatches: any;
+    readonly hideLargeIndels: any;
+} & {
+    readonly modificationThreshold: any;
+    readonly cloudDomain: [number, number] | undefined;
+} & {
+    readonly cloudTicks: import("../RenderLinearReadCloudDisplayRPC/drawFeatsCloud.ts").CloudTicks | undefined;
+} & {
     setNoSpacing(flag?: boolean): void;
     setMaxHeight(n?: number): void;
     setLayoutHeight(n: number): void;
+    setCloudMaxDistance(maxDistance: number): void;
+    setShowYScalebar(show: boolean): void;
+    setShowOutline(show: boolean): void;
     selectFeature(chain: ReducedFeature[]): void;
     setDrawCloud(b: boolean): void;
+    setSelectedFeatureId(id: string | undefined): void;
+    setHideSmallIndels(arg: boolean): void;
+    setHideMismatches(arg: boolean): void;
+    setHideLargeIndels(arg: boolean): void;
+    setShowLegend(s: boolean): void;
+} & {
+    legendItems(): LegendItem[];
+    svgLegendWidth(): number;
 } & {
     renderProps(): any;
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
@@ -168,28 +335,123 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
-        subMenu: {
+        subMenu: ({
+            label: string;
+            type: "subMenu";
+            subMenu: ({
+                label: string;
+                onClick: () => void;
+                type?: undefined;
+            } | {
+                type: "divider";
+                label?: undefined;
+                onClick?: undefined;
+            })[] | {
+                label: string;
+            }[];
+        } | {
             label: string;
             onClick: () => void;
-        }[];
+        })[];
     } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
-        onClick: () => void;
+        type: "subMenu";
+        subMenu: ({
+            label: string;
+            type: "checkbox";
+            checked: boolean;
+            onClick: () => void;
+        } | {
+            type: "divider";
+            label?: undefined;
+            checked?: undefined;
+            onClick?: undefined;
+        } | {
+            label: string;
+            onClick: () => void;
+            type?: undefined;
+            checked?: undefined;
+        })[];
     } | {
         label: string;
+        subMenu: ({
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        } | {
+            label: string;
+            onClick: () => void;
+            type?: undefined;
+            checked?: undefined;
+        })[];
+        icon?: undefined;
+        type?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         type: string;
-        checked: boolean;
-        onClick: () => void;
+        subMenu: ({
+            label: string;
+            type: "subMenu";
+            subMenu: {
+                label: string;
+                type: "radio";
+                checked: boolean | undefined;
+                onClick: () => void;
+            }[];
+        } | {
+            label: string;
+            type: string;
+            checked: boolean | undefined;
+            onClick: () => void;
+            helpText?: undefined;
+        } | {
+            label: string;
+            type: string;
+            helpText: string;
+            checked: boolean;
+            onClick: () => void;
+        })[];
     })[];
-    renderSvg(opts: {
-        rasterizeLayers?: boolean;
-    }): Promise<React.ReactNode>;
+    renderSvg(opts: ExportSvgDisplayOptions): Promise<React.ReactNode>;
 } & {
     afterAttach(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, 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>>;
+} & {
+    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>;
+    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>;
+} & {
+    drawSingletons: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawProperPairs: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    flipStrandLongReadChains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    featureHeight: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+} & {
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"LinearReadCloudDisplay">;
+    configuration: AnyConfigurationSchemaType;
+    drawCloud: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    noSpacing: 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>>;
+    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>>;
+    showLegend: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
+    showYScalebar: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    showOutline: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+}>>;
 export type LinearReadCloudDisplayStateModel = ReturnType<typeof stateModelFactory>;
 export type LinearReadCloudDisplayModel = Instance<LinearReadCloudDisplayStateModel>;
 export default stateModelFactory;