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

package/esm/LinearGenomeView/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearGenomeView/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAE5B,OAAO,EAAE,QAAQ,EAAE,MAAM,qCAAqC,CAAA;AAC9D,OAAO,EAAE,iBAAiB,EAAE,MAAM,SAAS,CAAA;AAE3C,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,WAAW,CACvB,GAAG,EAAE,CACH,IAAI,QAAQ,CAAC;QACX,IAAI,EAAE,kBAAkB;QACxB,UAAU,EAAE,iBAAiB,CAAC,aAAa,CAAC;QAC5C,cAAc,EAAE,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,+BAA+B,CAAC,CAAC;KACpE,CAAC,CACL,CAAA;AACH,CAAC,CAAA;AAED,cAAc,SAAS,CAAA"}

package/esm/LinearGenomeView/model.d.ts

@@ -0,0 +1,535 @@
+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>>;
+    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").IType<string | undefined, string, string>;
+    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;
+    setMinimized(flag: boolean): 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[];
+} & {
+    /**
+     * #method
+     */
+    MiniControlsComponent(): React.FC<any>;
+    /**
+     * #method
+     */
+    HeaderComponent(): React.FC<any>;
+    /**
+     * #getter
+     */
+    readonly assemblyErrors: string;
+    /**
+     * #getter
+     */
+    readonly assembliesInitialized: boolean;
+    /**
+     * #getter
+     */
+    readonly initialized: boolean;
+    /**
+     * #getter
+     */
+    readonly hasDisplayedRegions: boolean;
+    /**
+     * #getter
+     */
+    readonly isSearchDialogDisplayed: boolean;
+    /**
+     * #getter
+     */
+    readonly scaleBarHeight: number;
+    /**
+     * #getter
+     */
+    readonly headerHeight: number;
+    /**
+     * #getter
+     */
+    readonly trackHeights: any;
+    /**
+     * #getter
+     */
+    readonly trackHeightsWithResizeHandles: any;
+    /**
+     * #getter
+     */
+    readonly height: any;
+    /**
+     * #getter
+     */
+    readonly totalBp: number;
+    /**
+     * #getter
+     */
+    readonly maxBpPerPx: number;
+    /**
+     * #getter
+     */
+    readonly minBpPerPx: number;
+    /**
+     * #getter
+     */
+    readonly error: string | Error;
+    /**
+     * #getter
+     */
+    readonly maxOffset: number;
+    /**
+     * #getter
+     */
+    readonly minOffset: number;
+    /**
+     * #getter
+     */
+    readonly displayedRegionsTotalPx: number;
+    /**
+     * #method
+     */
+    renderProps(): any;
+    /**
+     * #method
+     */
+    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>>;
+    };
+    /**
+     * #method
+     */
+    getTrack(id: string): any;
+    /**
+     * #method
+     */
+    rankSearchResults(results: BaseResult[]): BaseResult[];
+    /**
+     * #method
+     * modifies view menu action onClick to apply to all tracks of same type
+     */
+    rewriteOnClicks(trackType: string, viewMenuActions: MenuItem[]): void;
+    /**
+     * #getter
+     */
+    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;
+    /**
+     * #action
+     */
+    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 type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
+export type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
+export { default as ReactComponent } from './components/LinearGenomeView';