@jbrowse/plugin-alignments 2.2.1 → 2.3.0

package/esm/LinearReadArcsDisplay/drawFeats.js

@@ -0,0 +1,157 @@
+import { getContainingView, getSession } from '@jbrowse/core/util';
+// locals
+import { getOrientationColor, getInsertSizeColor, getInsertSizeAndOrientationColor, } from '../shared/color';
+import { featurizeSA } from '../MismatchParser';
+export function hasPairedReads(features) {
+    for (const f of features.chains.values()) {
+        if (f[0].flags & 1) {
+            return true;
+        }
+    }
+    return false;
+}
+export default async function drawFeats(self, ctx) {
+    var _a;
+    const { chainData } = self;
+    if (!chainData) {
+        return;
+    }
+    const displayHeight = self.height;
+    const view = getContainingView(self);
+    const { assemblyManager } = getSession(self);
+    self.setLastDrawnOffsetPx(view.offsetPx);
+    ctx.lineWidth = self.lineWidthSetting;
+    const { chains, stats } = chainData;
+    const hasPaired = hasPairedReads(chainData);
+    const assemblyName = view.assemblyNames[0];
+    const asm = assemblyManager.get(assemblyName);
+    const type = ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) || 'insertSizeAndOrientation';
+    function draw(k1, k2, longRange) {
+        const s1 = k1.strand;
+        const s2 = k2.strand;
+        const f1 = s1 === -1;
+        const f2 = s2 === -1;
+        const p1 = f1 ? k1.start : k1.end;
+        const p2 = hasPaired ? (f2 ? k2.start : k2.end) : f2 ? k2.end : k2.start;
+        const r1 = view.bpToPx({ refName: k1.refName, coord: p1 });
+        const r2 = view.bpToPx({ refName: k2.refName, coord: p2 });
+        if (r1 && r2) {
+            const radius = (r2.offsetPx - r1.offsetPx) / 2;
+            const absrad = Math.abs(radius);
+            const p = r1.offsetPx - view.offsetPx;
+            // bezier (used for non-long-range arcs) requires moveTo before beginPath
+            // arc (used for long-range) requires moveTo after beginPath (or else a
+            // unwanted line at y=0 is rendered along with the arc)
+            if (longRange) {
+                ctx.moveTo(p, 0);
+                ctx.beginPath();
+            }
+            else {
+                ctx.beginPath();
+                ctx.moveTo(p, 0);
+            }
+            if (longRange) {
+                ctx.strokeStyle = 'red';
+            }
+            else {
+                if (hasPaired) {
+                    if (type === 'insertSizeAndOrientation') {
+                        ctx.strokeStyle = getInsertSizeAndOrientationColor(k1, k2, stats);
+                    }
+                    else if (type === 'orientation') {
+                        ctx.strokeStyle = getOrientationColor(k1);
+                    }
+                    else if (type === 'insertSize') {
+                        ctx.strokeStyle = getInsertSizeColor(k1, k2, stats) || 'grey';
+                    }
+                    else if (type === 'gradient') {
+                        ctx.strokeStyle = `hsl(${Math.log10(Math.abs(p1 - p2)) * 10},50%,50%)`;
+                    }
+                }
+                else {
+                    if (type === 'orientation' || type === 'insertSizeAndOrientation') {
+                        if (s1 === -1 && s2 === 1) {
+                            ctx.strokeStyle = 'navy';
+                        }
+                        else if (s1 === 1 && s2 === -1) {
+                            ctx.strokeStyle = 'green';
+                        }
+                        else {
+                            ctx.strokeStyle = 'grey';
+                        }
+                    }
+                    else if (type === 'gradient') {
+                        ctx.strokeStyle = `hsl(${Math.log10(Math.abs(p1 - p2)) * 10},50%,50%)`;
+                    }
+                }
+            }
+            const destX = p + radius * 2;
+            const destY = Math.min(displayHeight, absrad);
+            if (longRange) {
+                ctx.arc(p + radius, 0, absrad, 0, Math.PI);
+            }
+            else {
+                ctx.bezierCurveTo(p, destY, destX, destY, destX, 0);
+            }
+            ctx.stroke();
+        }
+        else if (r1 && self.drawInter) {
+            // draws a vertical line off to middle of nowhere if the second end not found
+            const p = r1.offsetPx - view.offsetPx;
+            ctx.strokeStyle = 'purple';
+            ctx.beginPath();
+            ctx.moveTo(p, 0);
+            ctx.lineTo(p, displayHeight);
+            ctx.stroke();
+        }
+    }
+    for (let i = 0; i < chains.length; i++) {
+        let chain = chains[i];
+        if (chain.length === 1 && self.drawLongRange) {
+            // singleton feature
+            const f = chain[0];
+            // special case where we look at RPOS/RNEXT
+            if (hasPaired) {
+                // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+                const refName = (asm === null || asm === void 0 ? void 0 : asm.getCanonicalRefName(f.next_ref)) || f.next_ref;
+                // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+                const coord = f.next_pos;
+                draw(f, {
+                    refName,
+                    start: coord,
+                    end: coord,
+                    strand: f.strand,
+                }, true);
+            }
+            // special case where we look at SA
+            else {
+                const suppAlns = featurizeSA(f.SA, f.id, f.strand, f.name);
+                const features = [f, ...suppAlns].sort((a, b) => a.clipPos - b.clipPos);
+                for (let i = 0; i < features.length - 1; i++) {
+                    const f = features[i];
+                    const v1 = features[i + 1];
+                    draw(f, {
+                        refName: (asm === null || asm === void 0 ? void 0 : asm.getCanonicalRefName(v1.refName)) || v1.refName,
+                        start: v1.start,
+                        end: v1.end,
+                        strand: v1.strand,
+                    }, true);
+                }
+            }
+        }
+        else {
+            if (!hasPaired) {
+                chain.sort((a, b) => a.clipPos - b.clipPos);
+                chain = chain.filter(f => !(f.flags & 256));
+            }
+            else {
+                // ignore split/supplementary reads for hasPaired=true for now
+                chain = chain.filter(f => !(f.flags & 2048));
+            }
+            for (let i = 0; i < chain.length - 1; i++) {
+                draw(chain[i], chain[i + 1], false);
+            }
+        }
+    }
+}
+//# sourceMappingURL=drawFeats.js.map

package/esm/LinearReadArcsDisplay/drawFeats.js.map

@@ -0,0 +1 @@
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package/esm/LinearReadArcsDisplay/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function register(pluginManager: PluginManager): void;

package/esm/LinearReadArcsDisplay/index.js

@@ -0,0 +1,21 @@
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
+// locals
+import ReactComponent from './components/ReactComponent';
+import configSchemaF from './configSchema';
+import stateModelF from './model';
+export default function register(pluginManager) {
+    pluginManager.addDisplayType(() => {
+        const configSchema = configSchemaF(pluginManager);
+        return new DisplayType({
+            name: 'LinearReadArcsDisplay',
+            displayName: 'Arc display',
+            configSchema,
+            stateModel: stateModelF(configSchema),
+            trackType: 'AlignmentsTrack',
+            viewType: 'LinearGenomeView',
+            subDisplay: { type: 'LinearAlignmentsDisplay', lowerPanel: true },
+            ReactComponent,
+        });
+    });
+}
+//# sourceMappingURL=index.js.map

package/esm/LinearReadArcsDisplay/index.js.map

@@ -0,0 +1 @@
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package/esm/LinearReadArcsDisplay/model.d.ts

@@ -0,0 +1,342 @@
+import React from 'react';
+import { Instance } from 'mobx-state-tree';
+import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import { ChainData } from '../shared/fetchChains';
+import { ExportSvgOptions } from '@jbrowse/plugin-linear-genome-view/src/LinearGenomeView';
+interface Filter {
+    flagInclude: number;
+    flagExclude: number;
+    readName?: string;
+    tagFilter?: {
+        tag: string;
+        value: string;
+    };
+}
+/**
+ * #stateModel LinearReadArcsDisplay
+ * extends `BaseLinearDisplay`
+ */
+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>>;
+} & {
+    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+        key: import("mobx-state-tree").ISimpleType<string>;
+        region: 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>;
+        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    }, {
+        renderInProgress: AbortController | undefined;
+        filled: boolean;
+        reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: any;
+        }) => any;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(abortController: AbortController): void;
+        setMessage(messageText: string): void;
+        setRendered(props: {
+            reactElement: React.ReactElement<any, string | React.JSXElementConstructor<any>>;
+            features: Map<string, import("@jbrowse/core/util").Feature>;
+            layout: any; /**
+             * #action
+             */
+            maxHeightReached: boolean;
+            renderProps: any;
+        } | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        beforeDestroy(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearReadArcsDisplay">;
+    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+        flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+        readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            tag: import("mobx-state-tree").ISimpleType<string>;
+            value: import("mobx-state-tree").ISimpleType<string>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    lineWidth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+        type: import("mobx-state-tree").ISimpleType<string>;
+        tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        extra: import("mobx-state-tree").IType<any, any, any>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    drawInter: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawLongRange: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+}, {
+    rendererTypeName: string;
+    error: unknown; /**
+     * #action
+     * thin, bold, extrabold, etc
+     */
+} & {
+    readonly RenderingComponent: React.FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown; /**
+             * #getter
+             */
+        } & 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>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        onHorizontalScroll?: Function | undefined;
+        blockState?: Record<string, any> | undefined;
+    }>;
+    readonly DisplayBlurb: React.FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+        } & 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>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }> | null;
+    readonly adapterConfig: any;
+    readonly parentTrack: any;
+    renderProps(): any;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
+    readonly DisplayMessageComponent: React.FC<any> | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): undefined;
+} & {
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    currBpPerPx: number;
+    scrollTop: number;
+    message: string;
+    featureIdUnderMouse: string | undefined;
+    contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
+    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+} & {
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
+} & {
+    readonly renderDelay: number;
+    readonly TooltipComponent: React.FC<any>;
+    readonly selectedFeatureId: string | undefined;
+    readonly DisplayMessageComponent: React.FC<any> | undefined;
+} & {
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
+    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly estimatedStatsReady: boolean;
+    readonly maxAllowableBytes: number;
+} & {
+    setMessage(message: string): void;
+    afterAttach(): void;
+    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
+        headers?: Record<string, string> | undefined;
+        signal?: AbortSignal | undefined;
+        filters?: string[] | undefined;
+    }): Promise<{}>;
+    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
+    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    clearRegionStats(): void;
+    setHeight(displayHeight: number): number;
+    resizeHeight(distance: number): number;
+    setScrollTop(scrollTop: number): void;
+    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+    addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
+    setCurrBpPerPx(n: number): void;
+    deleteBlock(key: string): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    clearFeatureSelection(): void;
+    setFeatureIdUnderMouse(feature: string | undefined): void;
+    reload(): void;
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
+} & {
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    reload(): Promise<void>;
+    afterAttach(): void;
+} & {
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    contextMenuItems(): {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+    }[];
+    renderProps(): any;
+} & {
+    renderSvg(opts: ExportSvgOptions & {
+        overrideHeight: number;
+    }): Promise<JSX.Element>;
+} & {
+    loading: boolean;
+    drawn: boolean;
+    chainData: ChainData | undefined;
+    ref: HTMLCanvasElement | null;
+    lastDrawnOffsetPx: number;
+} & {
+    /**
+     * #action
+     * internal, a reference to a HTMLCanvas because we use a autorun to draw the canvas
+     */
+    reload(): void;
+    /**
+     * #action
+     * internal, a reference to a HTMLCanvas because we use a autorun to draw the canvas
+     */
+    setRef(ref: HTMLCanvasElement | null): void;
+    /**
+     * #action
+     */
+    setColorScheme(s: {
+        type: string;
+    }): void;
+    /**
+     * #action
+     */
+    setChainData(args: ChainData): void;
+    /**
+     * #action
+     */
+    setDrawInter(f: boolean): void;
+    /**
+     * #action
+     */
+    setDrawLongRange(f: boolean): void;
+    /**
+     * #action
+     */
+    setLoading(f: boolean): void;
+    /**
+     * #action
+     * used during tests to detect when we can complete a snapshot test
+     */
+    setDrawn(f: boolean): void;
+    /**
+     * #action
+     */
+    setFilterBy(filter: Filter): void;
+    /**
+     * #action
+     * allows the drawing to slide around a little bit if it takes a long time to refresh
+     */
+    setLastDrawnOffsetPx(n: number): void;
+    /**
+     * #action
+     * thin, bold, extrabold, etc
+     */
+    setLineWidth(n: number): void;
+} & {
+    /**
+     * #getter
+     */
+    readonly lineWidthSetting: any;
+    /**
+     * #getter
+     */
+    readonly ready: boolean;
+    readonly rendererTypeName: string;
+    renderProps(): any;
+    /**
+     * #method
+     */
+    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 | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+        type?: undefined;
+        checked?: undefined;
+        subMenu?: undefined;
+    } | {
+        label: string;
+        type: string;
+        checked: boolean;
+        onClick: () => void;
+        icon?: undefined;
+        subMenu?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        subMenu: {
+            label: string;
+            onClick: () => void;
+        }[];
+        onClick?: undefined;
+        type?: undefined;
+        checked?: undefined;
+    })[];
+} & {
+    /**
+     * #method
+     */
+    renderSvg(opts: ExportSvgOptions): Promise<JSX.Element | undefined>;
+} & {
+    afterAttach(): void;
+}, import("mobx-state-tree")._NotCustomized, {
+    type: string;
+    height: number;
+    id: string;
+    rpcDriverName: string | undefined;
+    userBpPerPxLimit: number | undefined;
+    userByteSizeLimit: number | undefined;
+} & import("mobx-state-tree")._NotCustomized>;
+export type LinearReadArcsDisplayStateModel = ReturnType<typeof stateModelFactory>;
+export type LinearReadArcsDisplayModel = Instance<LinearReadArcsDisplayStateModel>;
+export default stateModelFactory;