@jbrowse/plugin-linear-genome-view 2.2.0 → 2.2.2

package/dist/LinearGenomeView/index.d.ts

@@ -1,454 +1,4 @@
-import React from 'react';
-import { Region } from '@jbrowse/core/util/types';
-import { MenuItem } from '@jbrowse/core/ui';
-import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
-import { BlockSet, BaseBlock } from '@jbrowse/core/util/blockTypes';
-import { Instance } from 'mobx-state-tree';
 import PluginManager from '@jbrowse/core/PluginManager';
-import { renderToSvg } from './components/LinearGenomeViewSvg';
-import RefNameAutocomplete from './components/RefNameAutocomplete';
-import SearchBox from './components/SearchBox';
-import ZoomControls from './components/ZoomControls';
-import LinearGenomeView from './components/LinearGenomeView';
-export interface BpOffset {
-    refName?: string;
-    index: number;
-    offset: number;
-    start?: number;
-    end?: number;
-    coord?: number;
-    reversed?: boolean;
-    assemblyName?: string;
-    oob?: boolean;
-}
-export interface ExportSvgOptions {
-    rasterizeLayers?: boolean;
-    filename?: string;
-    Wrapper?: React.FC<any>;
-}
-export interface NavLocation {
-    refName: string;
-    start?: number;
-    end?: number;
-    assemblyName?: string;
-}
-export declare const HEADER_BAR_HEIGHT = 48;
-export declare const HEADER_OVERVIEW_HEIGHT = 20;
-export declare const SCALE_BAR_HEIGHT = 17;
-export declare const RESIZE_HANDLE_HEIGHT = 3;
-export declare const INTER_REGION_PADDING_WIDTH = 2;
-export declare const SPACING = 7;
-export declare const WIDGET_HEIGHT = 32;
-/**
- * #stateModel LinearGenomeView
- */
-export declare function stateModelFactory(pluginManager: 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>>;
-} & {
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"LinearGenomeView">;
-    offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-    bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-    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>>;
-    tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
-    hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    hideNoTracksActive: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    trackSelectorType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    showCenterLine: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-}, {
-    width: number;
-} & {
-    menuItems(): MenuItem[];
-} & {
-    setDisplayName(name: string): void;
-    setWidth(newWidth: number): void;
-} & {
-    volatileWidth: number | undefined;
-    minimumBlockWidth: number;
-    draggingTrackId: string | undefined;
-    volatileError: Error | undefined;
-    afterDisplayedRegionsSetCallbacks: Function[];
-    scaleFactor: number;
-    trackRefs: {
-        [key: string]: any;
-    };
-    coarseDynamicBlocks: BaseBlock[];
-    coarseTotalBp: number;
-    leftOffset: BpOffset | undefined;
-    rightOffset: BpOffset | undefined;
-    searchResults: BaseResult[] | undefined;
-    searchQuery: string | undefined;
-    seqDialogDisplayed: boolean;
-} & {
-    /**
-     * #getter
-     */
-    readonly width: number;
-    /**
-     * #getter
-     */
-    readonly interRegionPaddingWidth: number;
-    /**
-     * #getter
-     */
-    readonly assemblyNames: string[];
-} & {
-    MiniControlsComponent(): React.FC<any>;
-    HeaderComponent(): React.FC<any>;
-    readonly assemblyErrors: string;
-    readonly assembliesInitialized: boolean;
-    readonly initialized: boolean;
-    readonly hasDisplayedRegions: boolean;
-    readonly isSearchDialogDisplayed: boolean;
-    readonly scaleBarHeight: number;
-    readonly headerHeight: number;
-    readonly trackHeights: any;
-    readonly trackHeightsWithResizeHandles: any;
-    readonly height: any;
-    readonly totalBp: number;
-    readonly maxBpPerPx: number;
-    readonly minBpPerPx: number;
-    readonly error: string | Error;
-    readonly maxOffset: number;
-    readonly minOffset: number;
-    readonly displayedRegionsTotalPx: number;
-    renderProps(): any;
-    searchScope(assemblyName: string): {
-        assemblyName: string;
-        includeAggregateIndexes: boolean;
-        tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
-    };
-    getTrack(id: string): any;
-    rankSearchResults(results: BaseResult[]): BaseResult[];
-    rewriteOnClicks(trackType: string, viewMenuActions: MenuItem[]): void;
-    readonly trackTypeActions: Map<string, MenuItem[]>;
-} & {
-    /**
-     * #action
-     */
-    setShowCytobands(flag: boolean): void;
-    /**
-     * #action
-     */
-    setWidth(newWidth: number): void;
-    /**
-     * #action
-     */
-    setError(error: Error | undefined): void;
-    /**
-     * #action
-     */
-    toggleHeader(): void;
-    /**
-     * #action
-     */
-    toggleHeaderOverview(): void;
-    /**
-     * #action
-     */
-    toggleNoTracksActive(): void;
-    /**
-     * #action
-     */
-    toggleShowGridlines(): void;
-    /**
-     * #action
-     */
-    scrollTo(offsetPx: number): number;
-    /**
-     * #action
-     */
-    zoomTo(bpPerPx: number): number;
-    /**
-     * #action
-     * sets offsets used in the get sequence dialog
-     */
-    setOffsets(left?: BpOffset, right?: BpOffset): void;
-    /**
-     * #action
-     */
-    setSearchResults(results?: BaseResult[], query?: string): void;
-    /**
-     * #action
-     */
-    setGetSequenceDialogOpen(open: boolean): void;
-    /**
-     * #action
-     */
-    setNewView(bpPerPx: number, offsetPx: number): void;
-    /**
-     * #action
-     */
-    horizontallyFlip(): void;
-    /**
-     * #action
-     */
-    showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
-    hideTrack(trackId: string): number;
-} & {
-    /**
-     * #action
-     */
-    moveTrack(movingId: string, targetId: string): void;
-    /**
-     * #action
-     */
-    closeView(): void;
-    /**
-     * #action
-     */
-    toggleTrack(trackId: string): void;
-    /**
-     * #action
-     */
-    setTrackLabels(setting: 'overlapping' | 'offset' | 'hidden'): void;
-    /**
-     * #action
-     */
-    toggleCenterLine(): void;
-    /**
-     * #action
-     */
-    setDisplayedRegions(regions: Region[]): void;
-    /**
-     * #action
-     */
-    activateTrackSelector(): import("@jbrowse/core/util").Widget;
-    /**
-     * #method
-     * Helper method for the fetchSequence.
-     * Retrieves the corresponding regions that were selected by the rubberband
-     *
-     * @param leftOffset - `object as {start, end, index, offset}`, offset = start of user drag
-     * @param rightOffset - `object as {start, end, index, offset}`, offset = end of user drag
-     * @returns array of Region[]
-     */
-    getSelectedRegions(leftOffset?: BpOffset, rightOffset?: BpOffset): {
-        start: number;
-        end: number;
-        regionNumber?: number | undefined;
-        reversed?: boolean | undefined;
-        refName: string;
-        assemblyName: string;
-        key: string;
-        offsetPx: number;
-        widthPx: number;
-        variant?: string | undefined;
-        isLeftEndOfDisplayedRegion?: boolean | undefined;
-    }[];
-    /**
-     * #action
-     * schedule something to be run after the next time displayedRegions is set
-     */
-    afterDisplayedRegionsSet(cb: Function): void;
-    /**
-     * #action
-     */
-    horizontalScroll(distance: number): number;
-    /**
-     * #action
-     */
-    center(): void;
-    /**
-     * #action
-     */
-    showAllRegions(): void;
-    /**
-     * #action
-     */
-    showAllRegionsInAssembly(assemblyName?: string): void;
-    /**
-     * #action
-     */
-    setDraggingTrackId(idx?: string): void;
-    /**
-     * #action
-     */
-    setScaleFactor(factor: number): void;
-    /**
-     * #action
-     * this "clears the view" and makes the view return to the import form
-     */
-    clearView(): void;
-    /**
-     * #action
-     * creates an svg export and save using FileSaver
-     */
-    exportSvg(opts?: ExportSvgOptions): Promise<void>;
-} & {
-    slide: (viewWidths: number) => void;
-} & {
-    zoom: (targetBpPerPx: number) => void;
-} & {
-    /**
-     * #getter
-     */
-    readonly canShowCytobands: boolean;
-    /**
-     * #getter
-     */
-    readonly showCytobands: boolean;
-    /**
-     * #getter
-     */
-    readonly anyCytobandsExist: boolean;
-    /**
-     * #getter
-     * the cytoband is displayed to the right of the chromosome name,
-     * and that offset is calculated manually with this method
-     */
-    readonly cytobandOffset: number;
-} & {
-    /**
-     * #method
-     * return the view menu items
-     */
-    menuItems(): MenuItem[];
-} & {
-    /**
-     * #getter
-     * static blocks are an important concept jbrowse uses to avoid
-     * re-rendering when you scroll to the side. when you horizontally
-     * scroll to the right, old blocks to the left may be removed, and
-     * new blocks may be instantiated on the right. tracks may use the
-     * static blocks to render their data for the region represented by
-     * the block
-     */
-    readonly staticBlocks: BlockSet;
-    /**
-     * #getter
-     * dynamic blocks represent the exact coordinates of the currently
-     * visible genome regions on the screen. they are similar to static
-     * blocks, but statcic blocks can go offscreen while dynamic blocks
-     * represent exactly what is on screen
-     */
-    readonly dynamicBlocks: BlockSet;
-    /**
-     * #getter
-     * rounded dynamic blocks are dynamic blocks without fractions of bp
-     */
-    readonly roundedDynamicBlocks: BaseBlock[];
-    /**
-     * #getter
-     * a single "combo-locstring" representing all the regions visible
-     * on the screen
-     */
-    readonly visibleLocStrings: string;
-    /**
-     * #getter
-     * same as visibleLocStrings, but only updated every 300ms
-     */
-    readonly coarseVisibleLocStrings: string;
-} & {
-    /**
-     * #action
-     */
-    setCoarseDynamicBlocks(blocks: BlockSet): void;
-    afterAttach(): void;
-} & {
-    /**
-     * #action
-     * offset is the base-pair-offset in the displayed region, index is the index of the
-     * displayed region in the linear genome view
-     *
-     * @param start - object as `{start, end, offset, index}`
-     * @param end - object as `{start, end, offset, index}`
-     */
-    moveTo(start?: BpOffset, end?: BpOffset): void;
-    /**
-     * #action
-     * navigate to the given locstring
-     *
-     * @param locString - e.g. "chr1:1-100"
-     * @param optAssemblyName - (optional) the assembly name to use when navigating to the locstring
-     */
-    navToLocString(locString: string, optAssemblyName?: string): Promise<void>;
-    /**
-     * #action
-     * Navigate to a location based on its refName and optionally start, end,
-     * and assemblyName. Can handle if there are multiple displayedRegions
-     * from same refName. Only navigates to a location if it is entirely
-     * within a displayedRegion. Navigates to the first matching location
-     * encountered.
-     *
-     * Throws an error if navigation was unsuccessful
-     *
-     * @param query - a proposed location to navigate to
-     */
-    navTo(query: NavLocation): void;
-    /**
-     * #action
-     */
-    navToMultiple(locations: NavLocation[]): void;
-} & {
-    /**
-     * #method
-     */
-    rubberBandMenuItems(): MenuItem[];
-    /**
-     * #method
-     */
-    bpToPx({ refName, coord, regionNumber, }: {
-        refName: string;
-        coord: number;
-        regionNumber?: number | undefined;
-    }): {
-        index: number;
-        offsetPx: number;
-    } | undefined;
-    /**
-     * #method
-     * scrolls the view to center on the given bp. if that is not in any
-     * of the displayed regions, does nothing
-     * @param coord - basepair at which you want to center the view
-     * @param refName - refName of the displayedRegion you are centering at
-     * @param regionNumber - index of the displayedRegion
-     */
-    centerAt(coord: number, refName: string, regionNumber: number): void;
-    /**
-     * #method
-     */
-    pxToBp(px: number): {
-        coord: number;
-        index: number;
-        refName: string;
-        oob: boolean;
-        assemblyName: string;
-        offset: number;
-        start: number;
-        end: number;
-        reversed: boolean;
-    };
-    /**
-     * #getter
-     */
-    readonly centerLineInfo: {
-        coord: number;
-        index: number;
-        refName: string;
-        oob: boolean;
-        assemblyName: string;
-        offset: number;
-        start: number;
-        end: number;
-        reversed: boolean;
-    } | undefined;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export { renderToSvg, RefNameAutocomplete, SearchBox, ZoomControls, LinearGenomeView, };
-export declare type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
-export declare type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
-export { default as ReactComponent } from './components/LinearGenomeView';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;
+export * from './model';