@jbrowse/plugin-variants 1.7.9 → 2.0.0

package/esm/ChordVariantDisplay/models/ChordVariantDisplay.js

@@ -0,0 +1,40 @@
+import { baseChordDisplayConfig, BaseChordDisplayModel, } from '@jbrowse/plugin-circular-view';
+import { ConfigurationSchema, ConfigurationReference, } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+import { getContainingView } from '@jbrowse/core/util';
+import { getParentRenderProps } from '@jbrowse/core/util/tracks';
+const ChordVariantDisplayF = pluginManager => {
+    const configSchema = ConfigurationSchema('ChordVariantDisplay', {
+        renderer: types.optional(pluginManager.pluggableConfigSchemaType('renderer'), { type: 'StructuralVariantChordRenderer' }),
+    }, { baseConfiguration: baseChordDisplayConfig, explicitlyTyped: true });
+    const stateModel = types
+        .compose('ChordVariantDisplay', BaseChordDisplayModel, types.model({
+        type: types.literal('ChordVariantDisplay'),
+        configuration: ConfigurationReference(configSchema),
+    }))
+        .views(self => ({
+        get rendererTypeName() {
+            return self.configuration.renderer.type;
+        },
+        renderProps() {
+            const view = getContainingView(self);
+            return {
+                ...getParentRenderProps(self),
+                rpcDriverName: self.rpcDriverName,
+                displayModel: self,
+                bezierRadius: view.radiusPx * self.bezierRadiusRatio,
+                radius: view.radiusPx,
+                blockDefinitions: this.blockDefinitions,
+                config: self.configuration.renderer,
+                onChordClick: self.onChordClick,
+            };
+        },
+    }));
+    return { stateModel, configSchema };
+};
+// http://localhost:3000/test_data/hs37d5.HG002-SequelII-CCS.sv.vcf.gz.tbi
+// render request is for 1.5x the current viewing window
+// tracks all have a height
+//
+export default ChordVariantDisplayF;
+//# sourceMappingURL=ChordVariantDisplay.js.map

package/esm/ChordVariantDisplay/models/ChordVariantDisplay.js.map

@@ -0,0 +1 @@
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package/esm/LinearVariantDisplay/configSchema.d.ts

@@ -0,0 +1,5 @@
+import { Instance } from 'mobx-state-tree';
+import PluginManager from '@jbrowse/core/PluginManager';
+export declare function LinearVariantDisplayConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export declare type LinearVariantDisplayConfigModel = ReturnType<typeof LinearVariantDisplayConfigFactory>;
+export declare type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>;

package/esm/LinearVariantDisplay/configSchema.js

@@ -0,0 +1,7 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view';
+export function LinearVariantDisplayConfigFactory(pluginManager) {
+    const configSchema = linearBasicDisplayConfigSchemaFactory(pluginManager);
+    return ConfigurationSchema('LinearVariantDisplay', {}, { baseConfiguration: configSchema, explicitlyTyped: true });
+}
+//# sourceMappingURL=configSchema.js.map

package/esm/LinearVariantDisplay/configSchema.js.map

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

@@ -0,0 +1,2 @@
+export { LinearVariantDisplayConfigFactory as configSchemaFactory } from './configSchema';
+export { default as modelFactory } from './model';

package/esm/LinearVariantDisplay/index.js

@@ -0,0 +1,3 @@
+export { LinearVariantDisplayConfigFactory as configSchemaFactory } from './configSchema';
+export { default as modelFactory } from './model';
+//# sourceMappingURL=index.js.map

package/esm/LinearVariantDisplay/index.js.map

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

@@ -0,0 +1,212 @@
+/// <reference types="react" />
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { LinearVariantDisplayConfigModel } from './configSchema';
+export default function (configSchema: LinearVariantDisplayConfigModel): 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: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        features: Map<string, 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: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            features: Map<string, Feature>;
+            layout: any;
+            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<"LinearBasicDisplay">;
+    trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearVariantDisplay">;
+    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+} & {
+    readonly RenderingComponent: import("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>>;
+        onHorizontalScroll?: Function | undefined;
+        blockState?: Record<string, any> | undefined;
+    }>;
+    readonly DisplayBlurb: import("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: any;
+    readonly DisplayMessageComponent: import("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;
+    message: string;
+    featureIdUnderMouse: string | undefined;
+    contextMenuFeature: Feature | undefined;
+    scrollTop: number;
+    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: import("react").FC<any>;
+    readonly selectedFeatureId: string | undefined;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+} & {
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
+    readonly featureUnderMouse: 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: Feature): void;
+    clearFeatureSelection(): void;
+    setFeatureIdUnderMouse(feature: string | undefined): void;
+    reload(): void;
+    setContextMenuFeature(feature?: 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 | undefined;
+    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: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
+        overrideHeight: number;
+    }): Promise<JSX.Element>;
+} & {
+    readonly rendererTypeName: any;
+    readonly showLabels: any;
+    readonly showDescriptions: any;
+    readonly maxHeight: any;
+    readonly displayMode: any;
+} & {
+    readonly rendererConfig: any;
+} & {
+    toggleShowLabels(): void;
+    toggleShowDescriptions(): void;
+    setDisplayMode(val: string): void;
+    setMaxHeight(val: number): void;
+} & {
+    renderProps(): {
+        config: any;
+    };
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+} & {
+    selectFeature(feature: Feature): Promise<void>;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/LinearVariantDisplay/model.js

@@ -0,0 +1,34 @@
+import { getConf, ConfigurationReference } from '@jbrowse/core/configuration';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { getContainingTrack, getSession, getContainingView, isSessionModelWithWidgets, } from '@jbrowse/core/util';
+import { linearBasicDisplayModelFactory } from '@jbrowse/plugin-linear-genome-view';
+import { types } from 'mobx-state-tree';
+export default function (configSchema) {
+    return types
+        .compose('LinearVariantDisplay', linearBasicDisplayModelFactory(configSchema), types.model({
+        type: types.literal('LinearVariantDisplay'),
+        configuration: ConfigurationReference(configSchema),
+    }))
+        .actions(self => ({
+        async selectFeature(feature) {
+            const session = getSession(self);
+            if (isSessionModelWithWidgets(session)) {
+                const { rpcManager } = session;
+                const sessionId = getRpcSessionId(self);
+                const track = getContainingTrack(self);
+                const adapterConfig = getConf(track, 'adapter');
+                const header = await rpcManager.call(sessionId, 'CoreGetMetadata', {
+                    adapterConfig,
+                });
+                const featureWidget = session.addWidget('VariantFeatureWidget', 'variantFeature', {
+                    featureData: feature.toJSON(),
+                    view: getContainingView(self),
+                    descriptions: header,
+                });
+                session.showWidget(featureWidget);
+            }
+            session.setSelection(feature);
+        },
+    }));
+}
+//# sourceMappingURL=model.js.map

package/esm/LinearVariantDisplay/model.js.map

@@ -0,0 +1 @@
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package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts

@@ -0,0 +1,24 @@
+declare function _default(props: any): JSX.Element;
+declare namespace _default {
+    namespace propTypes {
+        const features: PropTypes.Validator<Map<unknown, unknown>>;
+        const config: PropTypes.Validator<any>;
+        const displayModel: React.Requireable<any>;
+        const blockDefinitions: PropTypes.Validator<any[]>;
+        const radius: PropTypes.Validator<number>;
+        const bezierRadius: PropTypes.Validator<number>;
+        const selectedFeatureId: PropTypes.Requireable<string>;
+        const onChordClick: PropTypes.Requireable<string | ((...args: any[]) => any)>;
+    }
+    namespace defaultProps {
+        const displayModel_1: undefined;
+        export { displayModel_1 as displayModel };
+        const selectedFeatureId_1: string;
+        export { selectedFeatureId_1 as selectedFeatureId };
+        const onChordClick_1: undefined;
+        export { onChordClick_1 as onChordClick };
+    }
+}
+export default _default;
+import PropTypes from "prop-types";
+import React from "react";

package/esm/StructuralVariantChordRenderer/ReactComponent.js

@@ -0,0 +1,133 @@
+import React, { useMemo } from 'react';
+import { observer, PropTypes as MobxPropTypes } from 'mobx-react';
+import { polarToCartesian } from '@jbrowse/core/util';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { PropTypes as CommonPropTypes } from '@jbrowse/core/util/types/mst';
+import { parseBreakend } from '@gmod/vcf';
+import PropTypes from 'prop-types';
+function bpToRadians(block, pos) {
+    const blockStart = block.region.elided ? 0 : block.region.start;
+    const blockEnd = block.region.elided ? 0 : block.region.end;
+    const bpOffset = block.flipped ? blockEnd - pos : pos - blockStart;
+    const radians = bpOffset / block.bpPerRadian + block.startRadians;
+    return radians;
+}
+const Chord = observer(function Chord({ feature, blocksForRefs, radius, config, bezierRadius, selected, onClick, }) {
+    var _a, _b, _c, _d, _e;
+    // find the blocks that our start and end points belong to
+    const startBlock = blocksForRefs[feature.get('refName')];
+    if (!startBlock) {
+        return null;
+    }
+    let svType;
+    if (feature.get('INFO')) {
+        ;
+        [svType] = feature.get('INFO').SVTYPE || [];
+    }
+    else if (feature.get('mate')) {
+        svType = 'mate';
+    }
+    let endPosition;
+    let endBlock;
+    const alt = (_a = feature.get('ALT')) === null || _a === void 0 ? void 0 : _a[0];
+    const bnd = alt && parseBreakend(alt);
+    if (bnd) {
+        // VCF BND
+        const matePosition = bnd.MatePosition.split(':');
+        endPosition = +matePosition[1];
+        endBlock = blocksForRefs[matePosition[0]];
+    }
+    else if (alt === '<TRA>') {
+        // VCF TRA
+        const chr2 = (_c = (_b = feature.get('INFO')) === null || _b === void 0 ? void 0 : _b.CHR2) === null || _c === void 0 ? void 0 : _c[0];
+        const end = (_e = (_d = feature.get('INFO')) === null || _d === void 0 ? void 0 : _d.END) === null || _e === void 0 ? void 0 : _e[0];
+        endPosition = parseInt(end, 10);
+        endBlock = blocksForRefs[chr2];
+    }
+    else if (svType === 'mate') {
+        // generic simplefeatures arcs
+        const mate = feature.get('mate');
+        const chr2 = mate.refName;
+        endPosition = mate.start;
+        endBlock = blocksForRefs[chr2];
+    }
+    if (endBlock) {
+        const startPos = feature.get('start');
+        const startRadians = bpToRadians(startBlock, startPos);
+        const endRadians = bpToRadians(endBlock, endPosition);
+        const startXY = polarToCartesian(radius, startRadians);
+        const endXY = polarToCartesian(radius, endRadians);
+        const controlXY = polarToCartesian(bezierRadius, (endRadians + startRadians) / 2);
+        const strokeColor = selected
+            ? readConfObject(config, 'strokeColorSelected', { feature })
+            : readConfObject(config, 'strokeColor', { feature });
+        const hoverStrokeColor = readConfObject(config, 'strokeColorHover', {
+            feature,
+        });
+        return (React.createElement("path", { "data-testid": `chord-${feature.id()}`, d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), style: { stroke: strokeColor }, onClick: evt => onClick(feature, startBlock.region, endBlock.region, evt), onMouseOver: evt => {
+                if (!selected) {
+                    evt.target.style.stroke = hoverStrokeColor;
+                    evt.target.style.strokeWidth = 3;
+                }
+            }, onMouseOut: evt => {
+                if (!selected) {
+                    evt.target.style.stroke = strokeColor;
+                    evt.target.style.strokeWidth = 1;
+                }
+            } }));
+    }
+    return null;
+});
+function StructuralVariantChords(props) {
+    const { features, config, displayModel, blockDefinitions, radius, bezierRadius, displayModel: { selectedFeatureId }, onChordClick, } = props;
+    // make a map of refName -> blockDefinition
+    const blocksForRefsMemo = useMemo(() => {
+        const blocksForRefs = {};
+        blockDefinitions.forEach(block => {
+            const regions = block.region.elided
+                ? block.region.regions
+                : [block.region];
+            regions.forEach(region => {
+                blocksForRefs[region.refName] = block;
+            });
+        });
+        return blocksForRefs;
+    }, [blockDefinitions]);
+    // console.log(blocksForRefs)
+    const chords = [];
+    for (const [id, feature] of features) {
+        const selected = String(selectedFeatureId) === String(feature.id());
+        chords.push(React.createElement(Chord, { key: id, feature: feature, config: config, displayModel: displayModel, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
+    }
+    const trackStyleId = `chords-${displayModel.id}`;
+    return (React.createElement("g", { id: trackStyleId, "data-testid": "structuralVariantChordRenderer" },
+        React.createElement("style", { 
+            // eslint-disable-next-line react/no-danger
+            dangerouslySetInnerHTML: {
+                __html: `
+          #${trackStyleId} > path {
+            cursor: crosshair;
+            fill: none;
+          }
+`,
+            } }),
+        chords));
+}
+StructuralVariantChords.propTypes = {
+    features: PropTypes.instanceOf(Map).isRequired,
+    config: CommonPropTypes.ConfigSchema.isRequired,
+    displayModel: MobxPropTypes.objectOrObservableObject,
+    blockDefinitions: PropTypes.arrayOf(MobxPropTypes.objectOrObservableObject)
+        .isRequired,
+    radius: PropTypes.number.isRequired,
+    bezierRadius: PropTypes.number.isRequired,
+    selectedFeatureId: PropTypes.string,
+    onChordClick: PropTypes.oneOfType([PropTypes.func, PropTypes.string]),
+};
+StructuralVariantChords.defaultProps = {
+    displayModel: undefined,
+    selectedFeatureId: '',
+    onChordClick: undefined,
+};
+export default observer(StructuralVariantChords);
+//# sourceMappingURL=ReactComponent.js.map

package/esm/StructuralVariantChordRenderer/ReactComponent.js.map

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package/esm/StructuralVariantChordRenderer/index.d.ts

@@ -0,0 +1,3 @@
+export default ChordRendererConfigF;
+declare function ChordRendererConfigF(pluginManager: any): ChordRendererType;
+import ChordRendererType from "@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType";

package/esm/StructuralVariantChordRenderer/index.js

@@ -0,0 +1,33 @@
+import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType';
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import ReactComponent from './ReactComponent';
+const ChordRendererConfigF = pluginManager => {
+    const configSchema = ConfigurationSchema('StructuralVariantChordRenderer', {
+        strokeColor: {
+            type: 'color',
+            description: 'the line color of each arc',
+            defaultValue: 'rgba(255,133,0,0.32)',
+            contextVariable: ['feature'],
+        },
+        strokeColorSelected: {
+            type: 'color',
+            description: 'the line color of an arc that has been selected',
+            defaultValue: 'black',
+            contextVariable: ['feature'],
+        },
+        strokeColorHover: {
+            type: 'color',
+            description: 'the line color of an arc that is being hovered over with the mouse',
+            defaultValue: '#555',
+            contextVariable: ['feature'],
+        },
+    }, { explicitlyTyped: true });
+    return new ChordRendererType({
+        name: 'StructuralVariantChordRenderer',
+        ReactComponent,
+        configSchema,
+        pluginManager,
+    });
+};
+export default ChordRendererConfigF;
+//# sourceMappingURL=index.js.map

package/esm/StructuralVariantChordRenderer/index.js.map

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package/esm/VariantFeatureWidget/BreakendOptionDialog.d.ts

@@ -0,0 +1,10 @@
+/// <reference types="react" />
+import { Feature } from '@jbrowse/core/util';
+declare function BreakendOptionDialog({ model, handleClose, feature, viewType, }: {
+    model: any;
+    handleClose: () => void;
+    feature: Feature;
+    viewType: any;
+}): JSX.Element;
+declare const _default: typeof BreakendOptionDialog;
+export default _default;

package/esm/VariantFeatureWidget/BreakendOptionDialog.js

@@ -0,0 +1,58 @@
+/* eslint-disable @typescript-eslint/no-explicit-any */
+import React, { useState } from 'react';
+import { observer } from 'mobx-react';
+import { Button, Checkbox, Dialog, DialogActions, DialogContent, DialogTitle, Divider, FormControlLabel, IconButton, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import CloseIcon from '@mui/icons-material/Close';
+import { getSnapshot } from 'mobx-state-tree';
+import { getSession } from '@jbrowse/core/util';
+const useStyles = makeStyles()(theme => ({
+    closeButton: {
+        position: 'absolute',
+        right: theme.spacing(1),
+        top: theme.spacing(1),
+        color: theme.palette.grey[500],
+    },
+    block: {
+        display: 'block',
+    },
+}));
+function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
+    const { classes } = useStyles();
+    const [copyTracks, setCopyTracks] = useState(true);
+    const [mirrorTracks, setMirrorTracks] = useState(true);
+    return (React.createElement(Dialog, { open: true, onClose: handleClose },
+        React.createElement(DialogTitle, null,
+            "Breakpoint split view options",
+            handleClose ? (React.createElement(IconButton, { className: classes.closeButton, onClick: () => handleClose() },
+                React.createElement(CloseIcon, null))) : null),
+        React.createElement(Divider, null),
+        React.createElement(DialogContent, null,
+            React.createElement(FormControlLabel, { className: classes.block, control: React.createElement(Checkbox, { checked: copyTracks, onChange: () => setCopyTracks(val => !val) }), label: "Copy tracks into the new view" }),
+            React.createElement(FormControlLabel, { className: classes.block, control: React.createElement(Checkbox, { checked: mirrorTracks, onChange: () => setMirrorTracks(val => !val) }), label: "Mirror tracks vertically in vertically stacked view" })),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { onClick: () => {
+                    const { view } = model;
+                    const session = getSession(model);
+                    try {
+                        const viewSnapshot = viewType.snapshotFromBreakendFeature(feature, view);
+                        viewSnapshot.views[0].offsetPx -= view.width / 2 + 100;
+                        viewSnapshot.views[1].offsetPx -= view.width / 2 + 100;
+                        viewSnapshot.featureData = feature;
+                        const viewTracks = getSnapshot(view.tracks);
+                        viewSnapshot.views[0].tracks = viewTracks;
+                        viewSnapshot.views[1].tracks = mirrorTracks
+                            ? viewTracks.slice().reverse()
+                            : viewTracks;
+                        session.addView('BreakpointSplitView', viewSnapshot);
+                    }
+                    catch (e) {
+                        console.error(e);
+                        session.notify(`${e}`);
+                    }
+                    handleClose();
+                }, variant: "contained", color: "primary", autoFocus: true }, "OK"),
+            React.createElement(Button, { onClick: () => handleClose(), color: "secondary", variant: "contained" }, "Cancel"))));
+}
+export default observer(BreakendOptionDialog);
+//# sourceMappingURL=BreakendOptionDialog.js.map

package/esm/VariantFeatureWidget/BreakendOptionDialog.js.map

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

@@ -0,0 +1,4 @@
+/// <reference types="react" />
+declare function VariantFeatureDetails(props: any): JSX.Element;
+declare const _default: typeof VariantFeatureDetails;
+export default _default;