@jbrowse/plugin-linear-genome-view 1.7.10 → 2.0.1

package/{dist/LinearGenomeView/components/VerticalGuides.d.ts → esm/LinearGenomeView/components/TracksContainer.d.ts}

@@ -1,9 +1,10 @@
-/// <reference types="react" />
+import React from 'react';
 import { Instance } from 'mobx-state-tree';
 import { LinearGenomeViewStateModel } from '..';
 declare type LGV = Instance<LinearGenomeViewStateModel>;
-declare function VerticalGuides({ model }: {
+declare function TracksContainer({ children, model, }: {
+    children: React.ReactNode;
     model: LGV;
 }): JSX.Element;
-declare const _default: typeof VerticalGuides;
+declare const _default: typeof TracksContainer;
 export default _default;

package/esm/LinearGenomeView/components/TracksContainer.js

@@ -0,0 +1,142 @@
+import React, { useEffect, useRef, useState } from 'react';
+import { makeStyles } from 'tss-react/mui';
+import { observer } from 'mobx-react';
+import normalizeWheel from 'normalize-wheel';
+import { SCALE_BAR_HEIGHT } from '..';
+import RubberBand from './RubberBand';
+import ScaleBar from './ScaleBar';
+import Gridlines from './Gridlines';
+import CenterLine from './CenterLine';
+const useStyles = makeStyles()({
+    tracksContainer: {
+        position: 'relative',
+        overflow: 'hidden',
+    },
+    spacer: {
+        position: 'relative',
+        height: 3,
+    },
+});
+function TracksContainer({ children, model, }) {
+    const { classes } = useStyles();
+    // refs are to store these variables to avoid repeated rerenders associated
+    // with useState/setState
+    const delta = useRef(0);
+    const scheduled = useRef(false);
+    const timeout = useRef();
+    const ref = useRef(null);
+    const prevX = useRef(0);
+    const [mouseDragging, setMouseDragging] = useState(false);
+    useEffect(() => {
+        let cleanup = () => { };
+        function globalMouseMove(event) {
+            event.preventDefault();
+            const currX = event.clientX;
+            const distance = currX - prevX.current;
+            if (distance) {
+                // use rAF to make it so multiple event handlers aren't fired per-frame
+                // see https://calendar.perfplanet.com/2013/the-runtime-performance-checklist/
+                if (!scheduled.current) {
+                    scheduled.current = true;
+                    window.requestAnimationFrame(() => {
+                        model.horizontalScroll(-distance);
+                        scheduled.current = false;
+                        prevX.current = event.clientX;
+                    });
+                }
+            }
+        }
+        function globalMouseUp() {
+            prevX.current = 0;
+            if (mouseDragging) {
+                setMouseDragging(false);
+            }
+        }
+        if (mouseDragging) {
+            window.addEventListener('mousemove', globalMouseMove, true);
+            window.addEventListener('mouseup', globalMouseUp, true);
+            cleanup = () => {
+                window.removeEventListener('mousemove', globalMouseMove, true);
+                window.removeEventListener('mouseup', globalMouseUp, true);
+            };
+        }
+        return cleanup;
+    }, [model, mouseDragging, prevX]);
+    function mouseDown(event) {
+        // check if clicking a draggable element or a resize handle
+        const target = event.target;
+        if (target.draggable || target.dataset.resizer) {
+            return;
+        }
+        // otherwise do click and drag scroll
+        if (event.button === 0) {
+            prevX.current = event.clientX;
+            setMouseDragging(true);
+        }
+    }
+    // this local mouseup is used in addition to the global because sometimes
+    // the global add/remove are not called in time, resulting in issue #533
+    function mouseUp(event) {
+        event.preventDefault();
+        setMouseDragging(false);
+    }
+    function mouseLeave(event) {
+        event.preventDefault();
+    }
+    useEffect(() => {
+        const curr = ref.current;
+        // if ctrl is held down, zoom in with y-scroll
+        // else scroll horizontally with x-scroll
+        function onWheel(origEvent) {
+            const event = normalizeWheel(origEvent);
+            if (origEvent.ctrlKey === true) {
+                origEvent.preventDefault();
+                delta.current += event.pixelY / 500;
+                model.setScaleFactor(delta.current < 0 ? 1 - delta.current : 1 / (1 + delta.current));
+                if (timeout.current) {
+                    clearTimeout(timeout.current);
+                }
+                timeout.current = setTimeout(() => {
+                    model.setScaleFactor(1);
+                    model.zoomTo(delta.current > 0
+                        ? model.bpPerPx * (1 + delta.current)
+                        : model.bpPerPx / (1 - delta.current));
+                    delta.current = 0;
+                }, 300);
+            }
+            else {
+                // this is needed to stop the event from triggering "back button
+                // action" on MacOSX etc.  but is a heuristic to avoid preventing the
+                // inner-track scroll behavior
+                if (Math.abs(event.pixelX) > Math.abs(2 * event.pixelY)) {
+                    origEvent.preventDefault();
+                }
+                delta.current += event.pixelX;
+                if (!scheduled.current) {
+                    // use rAF to make it so multiple event handlers aren't fired per-frame
+                    // see https://calendar.perfplanet.com/2013/the-runtime-performance-checklist/
+                    scheduled.current = true;
+                    window.requestAnimationFrame(() => {
+                        model.horizontalScroll(delta.current);
+                        delta.current = 0;
+                        scheduled.current = false;
+                    });
+                }
+            }
+        }
+        if (curr) {
+            curr.addEventListener('wheel', onWheel);
+            return () => {
+                curr.removeEventListener('wheel', onWheel);
+            };
+        }
+        return () => { };
+    }, [model]);
+    return (React.createElement("div", { ref: ref, "data-testid": "trackContainer", className: classes.tracksContainer, onMouseDown: mouseDown, onMouseUp: mouseUp, onMouseLeave: mouseLeave },
+        model.showGridlines ? React.createElement(Gridlines, { model: model }) : null,
+        model.showCenterLine ? React.createElement(CenterLine, { model: model }) : null,
+        React.createElement(RubberBand, { model: model, ControlComponent: React.createElement(ScaleBar, { model: model, style: { height: SCALE_BAR_HEIGHT, boxSizing: 'border-box' } }) }),
+        children));
+}
+export default observer(TracksContainer);
+//# sourceMappingURL=TracksContainer.js.map

package/esm/LinearGenomeView/components/TracksContainer.js.map

@@ -0,0 +1 @@
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package/esm/LinearGenomeView/components/ZoomControls.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { LinearGenomeViewModel } from '..';
+declare function ZoomControls({ model }: {
+    model: LinearGenomeViewModel;
+}): JSX.Element;
+declare const _default: typeof ZoomControls;
+export default _default;

package/esm/LinearGenomeView/components/ZoomControls.js

@@ -0,0 +1,32 @@
+import React, { useState, useEffect } from 'react';
+import { observer } from 'mobx-react';
+import { Slider, IconButton } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import ZoomIn from '@mui/icons-material/ZoomIn';
+import ZoomOut from '@mui/icons-material/ZoomOut';
+const useStyles = makeStyles()({
+    container: {
+        display: 'flex',
+        flexDirection: 'row',
+        alignItems: 'center',
+    },
+    slider: {
+        width: 70,
+    },
+});
+function ZoomControls({ model }) {
+    const { classes } = useStyles();
+    const { maxBpPerPx, minBpPerPx, bpPerPx, scaleFactor } = model;
+    const [value, setValue] = useState(-Math.log2(bpPerPx) * 100);
+    useEffect(() => {
+        setValue(-Math.log2(bpPerPx) * 100);
+    }, [setValue, bpPerPx]);
+    return (React.createElement("div", { className: classes.container },
+        React.createElement(IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1, color: "secondary", size: "large" },
+            React.createElement(ZoomOut, null)),
+        React.createElement(Slider, { size: "small", className: classes.slider, value: value, min: -Math.log2(maxBpPerPx) * 100, max: -Math.log2(minBpPerPx) * 100, onChange: (_, val) => setValue(val), onChangeCommitted: () => model.zoomTo(2 ** (-value / 100)), disabled: scaleFactor !== 1 }),
+        React.createElement(IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(model.bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1, color: "secondary", size: "large" },
+            React.createElement(ZoomIn, null))));
+}
+export default observer(ZoomControls);
+//# sourceMappingURL=ZoomControls.js.map

package/esm/LinearGenomeView/components/ZoomControls.js.map

@@ -0,0 +1 @@
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package/esm/LinearGenomeView/components/util.d.ts

@@ -0,0 +1,14 @@
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import { SearchType } from '@jbrowse/core/data_adapters/BaseAdapter';
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+import { SearchScope } from '@jbrowse/core/TextSearch/TextSearchManager';
+import { TextSearchManager } from '@jbrowse/core/util';
+export declare function dedupe(results: BaseResult[] | undefined, cb: (result: BaseResult) => string): BaseResult[];
+export declare function fetchResults({ queryString, searchType, searchScope, rankSearchResults, textSearchManager, assembly, }: {
+    queryString: string;
+    searchScope: SearchScope;
+    rankSearchResults: (results: BaseResult[]) => BaseResult[];
+    searchType?: SearchType;
+    textSearchManager?: TextSearchManager;
+    assembly?: Assembly;
+}): Promise<BaseResult[]>;

package/esm/LinearGenomeView/components/util.js

@@ -0,0 +1,17 @@
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+export function dedupe(results = [], cb) {
+    return results.filter((elt, idx, self) => idx === self.findIndex(t => cb(t) === cb(elt)));
+}
+export async function fetchResults({ queryString, searchType, searchScope, rankSearchResults, textSearchManager, assembly, }) {
+    var _a;
+    if (!textSearchManager) {
+        console.warn('No text search manager');
+    }
+    const textSearchResults = await (textSearchManager === null || textSearchManager === void 0 ? void 0 : textSearchManager.search({
+        queryString,
+        searchType,
+    }, searchScope, rankSearchResults));
+    const refNameResults = (_a = assembly === null || assembly === void 0 ? void 0 : assembly.allRefNames) === null || _a === void 0 ? void 0 : _a.filter(ref => ref.toLowerCase().startsWith(queryString.toLowerCase())).slice(0, 10).map(r => new BaseResult({ label: r }));
+    return dedupe([...(refNameResults || []), ...(textSearchResults || [])], elt => elt.getId());
+}
+//# sourceMappingURL=util.js.map

package/esm/LinearGenomeView/components/util.js.map

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package/esm/LinearGenomeView/index.d.ts

@@ -0,0 +1,275 @@
+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';
+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;
+}
+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;
+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<"hierarchical">, [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;
+} & {
+    readonly width: number;
+    readonly interRegionPaddingWidth: number;
+    readonly assemblyNames: string[];
+} & {
+    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[]>;
+} & {
+    setShowCytobands(flag: boolean): void;
+    setWidth(newWidth: number): void;
+    setError(error: Error | undefined): void;
+    toggleHeader(): void;
+    toggleHeaderOverview(): void;
+    toggleNoTracksActive(): void;
+    toggleShowGridlines(): void;
+    scrollTo(offsetPx: number): number;
+    zoomTo(bpPerPx: number): number;
+    setOffsets(left: undefined | BpOffset, right: undefined | BpOffset): void;
+    setSearchResults(results: BaseResult[] | undefined, query: string | undefined): void;
+    setSequenceDialogOpen(open: boolean): void;
+    setNewView(bpPerPx: number, offsetPx: number): void;
+    horizontallyFlip(): void;
+    showTrack(trackId: string, initialSnapshot?: {}, displayInitialSnapshot?: {}): any;
+    hideTrack(trackId: string): number;
+} & {
+    moveTrack(movingId: string, targetId: string): void;
+    closeView(): void;
+    toggleTrack(trackId: string): void;
+    setTrackLabels(setting: 'overlapping' | 'offset' | 'hidden'): void;
+    toggleCenterLine(): void;
+    setDisplayedRegions(regions: Region[]): void;
+    activateTrackSelector(): import("@jbrowse/core/util").Widget;
+    /**
+     * 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;
+    }[];
+    afterDisplayedRegionsSet(cb: Function): void;
+    horizontalScroll(distance: number): number;
+    center(): void;
+    showAllRegions(): void;
+    showAllRegionsInAssembly(assemblyName?: string): void;
+    setDraggingTrackId(idx?: string): void;
+    setScaleFactor(factor: number): void;
+} & {
+    slide: (viewWidths: number) => void;
+} & {
+    zoom: (targetBpPerPx: number) => void;
+} & {
+    readonly canShowCytobands: boolean;
+    readonly showCytobands: boolean;
+    readonly anyCytobandsExist: boolean;
+    readonly cytobandOffset: number;
+} & {
+    menuItems(): MenuItem[];
+} & {
+    readonly staticBlocks: BlockSet;
+    readonly dynamicBlocks: BlockSet;
+    readonly roundedDynamicBlocks: {
+        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;
+    }[];
+    readonly visibleLocStrings: string;
+    readonly coarseVisibleLocStrings: string;
+} & {
+    clearView(): void;
+    setCoarseDynamicBlocks(blocks: BlockSet): void;
+    afterAttach(): void;
+} & {
+    exportSvg(opts?: ExportSvgOptions): Promise<void>;
+    /**
+     * 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;
+    navToLocString(locString: string, optAssemblyName?: string): void;
+    /**
+     * 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 location - a proposed location to navigate to
+     */
+    navTo(query: NavLocation): void;
+    navToMultiple(locations: NavLocation[]): void;
+} & {
+    rubberBandMenuItems(): MenuItem[];
+    bpToPx({ refName, coord, regionNumber, }: {
+        refName: string;
+        coord: number;
+        regionNumber?: number | undefined;
+    }): {
+        index: number;
+        offsetPx: number;
+    } | undefined;
+    /**
+     * 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;
+    pxToBp(px: number): {
+        coord: number;
+        index: number;
+        refName: string;
+        oob: boolean;
+        assemblyName: string;
+        offset: number;
+        start: number;
+        end: number;
+        reversed: boolean;
+    };
+    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 };
+export declare type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
+export declare type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
+export { default as ReactComponent } from './components/LinearGenomeView';