@jbrowse/plugin-dotplot-view 2.6.1

package/esm/DotplotView/model.d.ts

@@ -0,0 +1,616 @@
+import React from 'react';
+import { Instance, SnapshotIn } from 'mobx-state-tree';
+import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons';
+type Coord = [number, number];
+export interface ExportSvgOptions {
+    rasterizeLayers?: boolean;
+    filename?: string;
+    Wrapper?: React.FC<any>;
+    themeName?: string;
+}
+/**
+ * #stateModel DotplotView
+ * #category view
+ * extends  `BaseViewModel`
+ */
+export default function stateModelFactory(pm: PluginManager): import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+} & {
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<"DotplotView">;
+    height: import("mobx-state-tree").IType<number | undefined, number, number>;
+    borderSize: import("mobx-state-tree").IType<number | undefined, number, number>;
+    tickSize: import("mobx-state-tree").IType<number | undefined, number, number>;
+    vtextRotation: import("mobx-state-tree").IType<number | undefined, number, number>;
+    htextRotation: import("mobx-state-tree").IType<number | undefined, number, number>;
+    fontSize: import("mobx-state-tree").IType<number | undefined, number, number>;
+    trackSelectorType: import("mobx-state-tree").IType<string | undefined, string, string>;
+    assemblyNames: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
+    drawCigar: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    hview: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+        displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+            refName: import("mobx-state-tree").ISimpleType<string>;
+            start: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+        offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+        interRegionPaddingWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+        minimumBlockWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    }, {
+        features: import("@jbrowse/core/util").Feature[] | undefined;
+        volatileWidth: number;
+    } & {
+        setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
+        setBpPerPx(val: number): void;
+        setVolatileWidth(width: number): void;
+    } & {
+        readonly width: number;
+        readonly assemblyNames: string[];
+        readonly displayedRegionsTotalPx: number;
+        readonly maxOffset: number; /**
+         * #property
+         */
+        readonly minOffset: number;
+        readonly totalBp: number;
+    } & {
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet; /**
+         * #property
+         */
+        readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly currBp: number;
+    } & {
+        pxToBp(px: number): {
+            coord: number;
+            index: number;
+            refName: string;
+            oob: boolean;
+            assemblyName: string;
+            offset: number;
+            start: number;
+            end: number;
+            reversed: boolean;
+        };
+        bpToPx({ refName, coord, regionNumber, }: {
+            refName: string;
+            coord: number;
+            regionNumber?: number | undefined;
+        }): number | undefined;
+    } & {
+        setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
+        showAllRegions(): void;
+        zoomOut(): void;
+        zoomIn(): void;
+        zoomTo(bpPerPx: number, offset?: number | undefined): number;
+        scrollTo(offsetPx: number): number;
+        centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
+        scroll(distance: number): number;
+    } & {
+        moveTo(start?: import("@jbrowse/core/util/Base1DUtils").BpOffset | undefined, end?: import("@jbrowse/core/util/Base1DUtils").BpOffset | undefined): void;
+    } & {
+        setScaleFactor(n: number): void;
+        center(): void;
+    } & {
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly scaleFactor: number;
+        readonly maxBpPerPx: number;
+        readonly minBpPerPx: number;
+        readonly maxOffset: number;
+        readonly minOffset: number;
+    } & {
+        readonly width: any;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    vview: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+        displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+            refName: import("mobx-state-tree").ISimpleType<string>;
+            start: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+        offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+        interRegionPaddingWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+        minimumBlockWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    }, {
+        features: import("@jbrowse/core/util").Feature[] | undefined;
+        volatileWidth: number;
+    } & {
+        setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
+        setBpPerPx(val: number): void;
+        setVolatileWidth(width: number): void;
+    } & {
+        readonly width: number;
+        readonly assemblyNames: string[];
+        readonly displayedRegionsTotalPx: number;
+        readonly maxOffset: number; /**
+         * #property
+         */
+        readonly minOffset: number;
+        readonly totalBp: number;
+    } & {
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet; /**
+         * #property
+         */
+        readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly currBp: number;
+    } & {
+        pxToBp(px: number): {
+            coord: number;
+            index: number;
+            refName: string;
+            oob: boolean;
+            assemblyName: string;
+            offset: number;
+            start: number;
+            end: number;
+            reversed: boolean;
+        };
+        bpToPx({ refName, coord, regionNumber, }: {
+            refName: string;
+            coord: number;
+            regionNumber?: number | undefined;
+        }): number | undefined;
+    } & {
+        setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
+        showAllRegions(): void;
+        zoomOut(): void;
+        zoomIn(): void;
+        zoomTo(bpPerPx: number, offset?: number | undefined): number;
+        scrollTo(offsetPx: number): number;
+        centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
+        scroll(distance: number): number;
+    } & {
+        moveTo(start?: import("@jbrowse/core/util/Base1DUtils").BpOffset | undefined, end?: import("@jbrowse/core/util/Base1DUtils").BpOffset | undefined): void;
+    } & {
+        setScaleFactor(n: number): void;
+        center(): void;
+    } & {
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly scaleFactor: number;
+        readonly maxBpPerPx: number;
+        readonly minBpPerPx: number;
+        readonly maxOffset: number;
+        readonly minOffset: number;
+    } & {
+        readonly width: any;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    tracks: import("mobx-state-tree").IArrayType<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>;
+        configuration: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+        minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
+    }, {
+        readonly rpcSessionId: any;
+        readonly name: any;
+        readonly textSearchAdapter: any;
+        readonly adapterType: import("@jbrowse/core/pluggableElementTypes").AdapterType;
+        readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+        readonly canConfigure: any;
+    } & {
+        setMinimized(flag: boolean): void;
+        activateConfigurationUI(): void;
+        showDisplay(displayId: string, initialSnapshot?: {} | undefined): void;
+        hideDisplay(displayId: string): number;
+        replaceDisplay(oldId: string, newId: string, initialSnapshot?: {} | undefined): void;
+    } & {
+        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 | {
+            type: string; /**
+             * #property
+             */
+            label: string;
+            subMenu: {
+                type: string;
+                label: string; /**
+                 * #property
+                 */
+                checked: boolean;
+                onClick: () => void;
+            }[];
+        })[];
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    viewTrackConfigs: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+}, {
+    width: number;
+} & {
+    menuItems(): import("@jbrowse/core/ui").MenuItem[];
+} & {
+    setDisplayName(name: string): void;
+    setWidth(newWidth: number): void;
+    setMinimized(flag: boolean): void;
+} & {
+    volatileWidth: number | undefined;
+    volatileError: unknown;
+    cursorMode: string;
+    showPanButtons: boolean;
+    wheelMode: string;
+    borderX: number;
+    borderY: number;
+} & {
+    /**
+     * #getter
+     */
+    readonly width: number;
+} & {
+    /**
+     * #getter
+     */
+    readonly assemblyErrors: string;
+    /**
+     * #getter
+     */
+    readonly assembliesInitialized: boolean;
+} & {
+    /**
+     * #getter
+     */
+    readonly initialized: boolean;
+    /**
+     * #getter
+     */
+    readonly hticks: {
+        type: string;
+        base: number;
+        index: number;
+        refName: string;
+    }[];
+    /**
+     * #getter
+     */
+    readonly vticks: {
+        type: string;
+        base: number;
+        index: number;
+        refName: string;
+    }[];
+    /**
+     * #getter
+     */
+    readonly loading: boolean;
+    /**
+     * #getter
+     */
+    readonly viewWidth: number;
+    /**
+     * #getter
+     */
+    readonly viewHeight: number;
+    /**
+     * #getter
+     */
+    readonly views: ({
+        id: string;
+        displayedRegions: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
+            refName: import("mobx-state-tree").ISimpleType<string>;
+            start: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+            refName: import("mobx-state-tree").ISimpleType<string>;
+            start: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
+        bpPerPx: number;
+        offsetPx: number;
+        interRegionPaddingWidth: number;
+        minimumBlockWidth: number;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        features: import("@jbrowse/core/util").Feature[] | undefined;
+        volatileWidth: number;
+    } & {
+        setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
+        setBpPerPx(val: number): void;
+        setVolatileWidth(width: number): void;
+    } & {
+        readonly width: number;
+        readonly assemblyNames: string[];
+        readonly displayedRegionsTotalPx: number;
+        readonly maxOffset: number; /**
+         * #property
+         */
+        readonly minOffset: number;
+        readonly totalBp: number;
+    } & {
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet; /**
+         * #property
+         */
+        readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly currBp: number;
+    } & {
+        pxToBp(px: number): {
+            coord: number;
+            index: number;
+            refName: string;
+            oob: boolean;
+            assemblyName: string;
+            offset: number;
+            start: number;
+            end: number;
+            reversed: boolean;
+        };
+        bpToPx({ refName, coord, regionNumber, }: {
+            refName: string;
+            coord: number;
+            regionNumber?: number | undefined;
+        }): number | undefined;
+    } & {
+        setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
+        showAllRegions(): void;
+        zoomOut(): void;
+        zoomIn(): void;
+        zoomTo(bpPerPx: number, offset?: number | undefined): number;
+        scrollTo(offsetPx: number): number;
+        centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
+        scroll(distance: number): number;
+    } & {
+        moveTo(start?: import("@jbrowse/core/util/Base1DUtils").BpOffset | undefined, end?: import("@jbrowse/core/util/Base1DUtils").BpOffset | undefined): void;
+    } & {
+        setScaleFactor(n: number): void;
+        center(): void;
+    } & {
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly scaleFactor: number;
+        readonly maxBpPerPx: number;
+        readonly minBpPerPx: number;
+        readonly maxOffset: number;
+        readonly minOffset: number;
+    } & {
+        readonly width: any;
+    } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+        displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+            refName: import("mobx-state-tree").ISimpleType<string>;
+            start: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+        offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
+        interRegionPaddingWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+        minimumBlockWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    }, {
+        features: import("@jbrowse/core/util").Feature[] | undefined;
+        volatileWidth: number;
+    } & {
+        setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
+        setBpPerPx(val: number): void;
+        setVolatileWidth(width: number): void;
+    } & {
+        readonly width: number;
+        readonly assemblyNames: string[];
+        readonly displayedRegionsTotalPx: number;
+        readonly maxOffset: number; /**
+         * #property
+         */
+        readonly minOffset: number;
+        readonly totalBp: number;
+    } & {
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet; /**
+         * #property
+         */
+        readonly staticBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly currBp: number;
+    } & {
+        pxToBp(px: number): {
+            coord: number;
+            index: number;
+            refName: string;
+            oob: boolean;
+            assemblyName: string;
+            offset: number;
+            start: number;
+            end: number;
+            reversed: boolean;
+        };
+        bpToPx({ refName, coord, regionNumber, }: {
+            refName: string;
+            coord: number;
+            regionNumber?: number | undefined;
+        }): number | undefined;
+    } & {
+        setFeatures(features: import("@jbrowse/core/util").Feature[]): void;
+        showAllRegions(): void;
+        zoomOut(): void;
+        zoomIn(): void;
+        zoomTo(bpPerPx: number, offset?: number | undefined): number;
+        scrollTo(offsetPx: number): number;
+        centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
+        scroll(distance: number): number;
+    } & {
+        moveTo(start?: import("@jbrowse/core/util/Base1DUtils").BpOffset | undefined, end?: import("@jbrowse/core/util/Base1DUtils").BpOffset | undefined): void;
+    } & {
+        setScaleFactor(n: number): void;
+        center(): void;
+    } & {
+        readonly dynamicBlocks: import("@jbrowse/core/util/blockTypes").BlockSet;
+        readonly scaleFactor: number;
+        readonly maxBpPerPx: number;
+        readonly minBpPerPx: number;
+        readonly maxOffset: number;
+        readonly minOffset: number;
+    } & {
+        readonly width: any;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>>)[];
+    /**
+     * #method
+     */
+    renderProps(): any;
+} & {
+    /**
+     * #action
+     */
+    setShowPanButtons(flag: boolean): void;
+    /**
+     * #action
+     */
+    setWheelMode(str: string): void;
+    /**
+     * #action
+     */
+    setCursorMode(str: string): void;
+    /**
+     * #action
+     */
+    setDrawCigar(flag: boolean): void;
+    /**
+     * #action
+     * returns to the import form
+     */
+    clearView(): void;
+    /**
+     * #action
+     */
+    setBorderX(n: number): void;
+    /**
+     * #action
+     */
+    setBorderY(n: number): void;
+    /**
+     * #action
+     */
+    setWidth(newWidth: number): number;
+    /**
+     * #action
+     */
+    setHeight(newHeight: number): number;
+    /**
+     * #action
+     */
+    setError(e: unknown): void;
+    /**
+     * #action
+     * removes the view itself from the state tree entirely by calling the
+     * parent removeView
+     */
+    closeView(): void;
+    /**
+     * #action
+     */
+    zoomOutButton(): void;
+    /**
+     * #action
+     */
+    zoomInButton(): void;
+    /**
+     * #action
+     */
+    activateTrackSelector(): import("@jbrowse/core/util").Widget;
+    /**
+     * #action
+     */
+    showTrack(trackId: string, initialSnapshot?: {}): void;
+    /**
+     * #action
+     */
+    hideTrack(trackId: string): number;
+    /**
+     * #action
+     */
+    toggleTrack(trackId: string): void;
+    /**
+     * #action
+     */
+    setAssemblyNames(target: string, query: string): void;
+    /**
+     * #action
+     */
+    setViews(arr: SnapshotIn<Base1DViewModel>[]): void;
+    /**
+     * #action
+     */
+    getCoords(mousedown: Coord, mouseup: Coord): {
+        coord: number;
+        index: number;
+        refName: string;
+        oob: boolean;
+        assemblyName: string;
+        offset: number;
+        start: number;
+        end: number;
+        reversed: boolean;
+    }[] | undefined;
+    /**
+     * #action
+     * zooms into clicked and dragged region
+     */
+    zoomIn(mousedown: Coord, mouseup: Coord): void;
+    /**
+     * #action
+     */
+    showAllRegions(): void;
+    /**
+     * #action
+     * creates a linear synteny view from the clicked and dragged region
+     */
+    onDotplotView(mousedown: Coord, mouseup: Coord): void;
+} & {
+    /**
+     * #action
+     * creates an svg export and save using FileSaver
+     */
+    exportSvg(opts?: ExportSvgOptions): Promise<void>;
+    beforeDestroy(): void;
+    afterAttach(): void;
+    /**
+     * #action
+     */
+    squareView(): void;
+    /**
+     * #action
+     */
+    squareViewProportional(): void;
+} & {
+    /**
+     * #method
+     */
+    menuItems(): ({
+        label: string;
+        onClick: () => void;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+    } | {
+        label: string;
+        onClick: () => void;
+        icon?: undefined;
+    } | {
+        label: string;
+        onClick: () => import("@jbrowse/core/util").Widget;
+        icon: typeof TrackSelectorIcon;
+    })[];
+    /**
+     * #getter
+     */
+    readonly error: {};
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export type DotplotViewStateModel = ReturnType<typeof stateModelFactory>;
+export type DotplotViewModel = Instance<DotplotViewStateModel>;
+export { type Dotplot1DViewModel, Dotplot1DView } from './1dview';