@jbrowse/plugin-variants 1.7.11 → 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 @@
+{"version":3,"file":"ChordVariantDisplay.js","sourceRoot":"","sources":["../../../src/ChordVariantDisplay/models/ChordVariantDisplay.js"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,EACtB,qBAAqB,GACtB,MAAM,+BAA+B,CAAA;AACtC,OAAO,EACL,mBAAmB,EACnB,sBAAsB,GACvB,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACvC,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,EAAE,oBAAoB,EAAE,MAAM,2BAA2B,CAAA;AAEhE,MAAM,oBAAoB,GAAG,aAAa,CAAC,EAAE;IAC3C,MAAM,YAAY,GAAG,mBAAmB,CACtC,qBAAqB,EACrB;QACE,QAAQ,EAAE,KAAK,CAAC,QAAQ,CACtB,aAAa,CAAC,yBAAyB,CAAC,UAAU,CAAC,EACnD,EAAE,IAAI,EAAE,gCAAgC,EAAE,CAC3C;KACF,EACD,EAAE,iBAAiB,EAAE,sBAAsB,EAAE,eAAe,EAAE,IAAI,EAAE,CACrE,CAAA;IAED,MAAM,UAAU,GAAG,KAAK;SACrB,OAAO,CACN,qBAAqB,EACrB,qBAAqB,EACrB,KAAK,CAAC,KAAK,CAAC;QACV,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,qBAAqB,CAAC;QAC1C,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;QAED,WAAW;YACT,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAA;YACpC,OAAO;gBACL,GAAG,oBAAoB,CAAC,IAAI,CAAC;gBAC7B,aAAa,EAAE,IAAI,CAAC,aAAa;gBACjC,YAAY,EAAE,IAAI;gBAClB,YAAY,EAAE,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,iBAAiB;gBACpD,MAAM,EAAE,IAAI,CAAC,QAAQ;gBACrB,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;gBACvC,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;gBACnC,YAAY,EAAE,IAAI,CAAC,YAAY;aAChC,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;IAEL,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,CAAA;AACrC,CAAC,CAAA;AAED,0EAA0E;AAE1E,wDAAwD;AAExD,2BAA2B;AAC3B,EAAE;AACF,eAAe,oBAAoB,CAAA"}

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 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAGjE,OAAO,EAAE,qCAAqC,EAAE,MAAM,oCAAoC,CAAA;AAE1F,MAAM,UAAU,iCAAiC,CAC/C,aAA4B;IAE5B,MAAM,YAAY,GAAG,qCAAqC,CAAC,aAAa,CAAC,CAAA;IAEzE,OAAO,mBAAmB,CACxB,sBAAsB,EACtB,EAAE,EACF,EAAE,iBAAiB,EAAE,YAAY,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA;AACH,CAAC"}

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 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,iCAAiC,IAAI,mBAAmB,EAAE,MAAM,gBAAgB,CAAA;AACzF,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,SAAS,CAAA"}

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 @@
+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,sBAAsB,EAAE,MAAM,6BAA6B,CAAA;AAC7E,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAC3D,OAAO,EACL,kBAAkB,EAClB,UAAU,EACV,iBAAiB,EACjB,yBAAyB,GAC1B,MAAM,oBAAoB,CAAA;AAG3B,OAAO,EAAE,8BAA8B,EAAE,MAAM,oCAAoC,CAAA;AACnF,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAGvC,MAAM,CAAC,OAAO,WAAW,YAA6C;IACpE,OAAO,KAAK;SACT,OAAO,CACN,sBAAsB,EACtB,8BAA8B,CAAC,YAAY,CAAC,EAC5C,KAAK,CAAC,KAAK,CAAC;QACV,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,KAAK,CAAC,aAAa,CAAC,OAAgB;YAClC,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAChC,IAAI,yBAAyB,CAAC,OAAO,CAAC,EAAE;gBACtC,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;gBAC9B,MAAM,SAAS,GAAG,eAAe,CAAC,IAAI,CAAC,CAAA;gBACvC,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;gBACtC,MAAM,aAAa,GAAG,OAAO,CAAC,KAAK,EAAE,SAAS,CAAC,CAAA;gBAC/C,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,iBAAiB,EAAE;oBACjE,aAAa;iBACd,CAAC,CAAA;gBACF,MAAM,aAAa,GAAG,OAAO,CAAC,SAAS,CACrC,sBAAsB,EACtB,gBAAgB,EAChB;oBACE,WAAW,EAAE,OAAO,CAAC,MAAM,EAAE;oBAC7B,IAAI,EAAE,iBAAiB,CAAC,IAAI,CAAC;oBAC7B,YAAY,EAAE,MAAM;iBACrB,CACF,CAAA;gBACD,OAAO,CAAC,UAAU,CAAC,aAAa,CAAC,CAAA;aAClC;YAED,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;QAC/B,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}

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

@@ -0,0 +1 @@
+{"version":3,"file":"ReactComponent.js","sourceRoot":"","sources":["../../src/StructuralVariantChordRenderer/ReactComponent.js"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,OAAO,CAAA;AACtC,OAAO,EAAE,QAAQ,EAAE,SAAS,IAAI,aAAa,EAAE,MAAM,YAAY,CAAA;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AACrD,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EAAE,SAAS,IAAI,eAAe,EAAE,MAAM,8BAA8B,CAAA;AAC3E,OAAO,EAAE,aAAa,EAAE,MAAM,WAAW,CAAA;AACzC,OAAO,SAAS,MAAM,YAAY,CAAA;AAElC,SAAS,WAAW,CAAC,KAAK,EAAE,GAAG;IAC7B,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAA;IAC/D,MAAM,QAAQ,GAAG,KAAK,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,GAAG,CAAA;IAC3D,MAAM,QAAQ,GAAG,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,QAAQ,GAAG,GAAG,CAAC,CAAC,CAAC,GAAG,GAAG,UAAU,CAAA;IAClE,MAAM,OAAO,GAAG,QAAQ,GAAG,KAAK,CAAC,WAAW,GAAG,KAAK,CAAC,YAAY,CAAA;IACjE,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,KAAK,CAAC,EACpC,OAAO,EACP,aAAa,EACb,MAAM,EACN,MAAM,EACN,YAAY,EACZ,QAAQ,EACR,OAAO,GACR;;IACC,0DAA0D;IAC1D,MAAM,UAAU,GAAG,aAAa,CAAC,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,CAAA;IACxD,IAAI,CAAC,UAAU,EAAE;QACf,OAAO,IAAI,CAAA;KACZ;IACD,IAAI,MAAM,CAAA;IACV,IAAI,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;QACvB,CAAC;QAAA,CAAC,MAAM,CAAC,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,MAAM,IAAI,EAAE,CAAA;KAC7C;SAAM,IAAI,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;QAC9B,MAAM,GAAG,MAAM,CAAA;KAChB;IACD,IAAI,WAAW,CAAA;IACf,IAAI,QAAQ,CAAA;IACZ,MAAM,GAAG,GAAG,MAAA,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,0CAAG,CAAC,CAAC,CAAA;IACnC,MAAM,GAAG,GAAG,GAAG,IAAI,aAAa,CAAC,GAAG,CAAC,CAAA;IACrC,IAAI,GAAG,EAAE;QACP,UAAU;QACV,MAAM,YAAY,GAAG,GAAG,CAAC,YAAY,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAChD,WAAW,GAAG,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,CAAA;KAC1C;SAAM,IAAI,GAAG,KAAK,OAAO,EAAE;QAC1B,UAAU;QACV,MAAM,IAAI,GAAG,MAAA,MAAA,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,0CAAE,IAAI,0CAAG,CAAC,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,MAAA,MAAA,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,0CAAE,GAAG,0CAAG,CAAC,CAAC,CAAA;QACzC,WAAW,GAAG,QAAQ,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;QAC/B,QAAQ,GAAG,aAAa,CAAC,IAAI,CAAC,CAAA;KAC/B;SAAM,IAAI,MAAM,KAAK,MAAM,EAAE;QAC5B,8BAA8B;QAC9B,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;QAChC,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAA;QACzB,WAAW,GAAG,IAAI,CAAC,KAAK,CAAA;QACxB,QAAQ,GAAG,aAAa,CAAC,IAAI,CAAC,CAAA;KAC/B;IAED,IAAI,QAAQ,EAAE;QACZ,MAAM,QAAQ,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QACrC,MAAM,YAAY,GAAG,WAAW,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QACtD,MAAM,UAAU,GAAG,WAAW,CAAC,QAAQ,EAAE,WAAW,CAAC,CAAA;QACrD,MAAM,OAAO,GAAG,gBAAgB,CAAC,MAAM,EAAE,YAAY,CAAC,CAAA;QACtD,MAAM,KAAK,GAAG,gBAAgB,CAAC,MAAM,EAAE,UAAU,CAAC,CAAA;QAClD,MAAM,SAAS,GAAG,gBAAgB,CAChC,YAAY,EACZ,CAAC,UAAU,GAAG,YAAY,CAAC,GAAG,CAAC,CAChC,CAAA;QAED,MAAM,WAAW,GAAG,QAAQ;YAC1B,CAAC,CAAC,cAAc,CAAC,MAAM,EAAE,qBAAqB,EAAE,EAAE,OAAO,EAAE,CAAC;YAC5D,CAAC,CAAC,cAAc,CAAC,MAAM,EAAE,aAAa,EAAE,EAAE,OAAO,EAAE,CAAC,CAAA;QAEtD,MAAM,gBAAgB,GAAG,cAAc,CAAC,MAAM,EAAE,kBAAkB,EAAE;YAClE,OAAO;SACR,CAAC,CAAA;QACF,OAAO,CACL,6CACe,SAAS,OAAO,CAAC,EAAE,EAAE,EAAE,EACpC,CAAC,EAAE,CAAC,GAAG,EAAE,GAAG,OAAO,EAAE,GAAG,EAAE,GAAG,SAAS,EAAE,GAAG,KAAK,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAC3D,KAAK,EAAE,EAAE,MAAM,EAAE,WAAW,EAAE,EAC9B,OAAO,EAAE,GAAG,CAAC,EAAE,CACb,OAAO,CAAC,OAAO,EAAE,UAAU,CAAC,MAAM,EAAE,QAAQ,CAAC,MAAM,EAAE,GAAG,CAAC,EAE3D,WAAW,EAAE,GAAG,CAAC,EAAE;gBACjB,IAAI,CAAC,QAAQ,EAAE;oBACb,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,GAAG,gBAAgB,CAAA;oBAC1C,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,WAAW,GAAG,CAAC,CAAA;iBACjC;YACH,CAAC,EACD,UAAU,EAAE,GAAG,CAAC,EAAE;gBAChB,IAAI,CAAC,QAAQ,EAAE;oBACb,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,GAAG,WAAW,CAAA;oBACrC,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,WAAW,GAAG,CAAC,CAAA;iBACjC;YACH,CAAC,GACD,CACH,CAAA;KACF;IAED,OAAO,IAAI,CAAA;AACb,CAAC,CAAC,CAAA;AAEF,SAAS,uBAAuB,CAAC,KAAK;IACpC,MAAM,EACJ,QAAQ,EACR,MAAM,EACN,YAAY,EACZ,gBAAgB,EAChB,MAAM,EACN,YAAY,EACZ,YAAY,EAAE,EAAE,iBAAiB,EAAE,EAEnC,YAAY,GACb,GAAG,KAAK,CAAA;IACT,2CAA2C;IAC3C,MAAM,iBAAiB,GAAG,OAAO,CAAC,GAAG,EAAE;QACrC,MAAM,aAAa,GAAG,EAAE,CAAA;QACxB,gBAAgB,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;YAC/B,MAAM,OAAO,GAAG,KAAK,CAAC,MAAM,CAAC,MAAM;gBACjC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,OAAO;gBACtB,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;YAClB,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;gBACvB,aAAa,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;YACvC,CAAC,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;QACF,OAAO,aAAa,CAAA;IACtB,CAAC,EAAE,CAAC,gBAAgB,CAAC,CAAC,CAAA;IACtB,6BAA6B;IAC7B,MAAM,MAAM,GAAG,EAAE,CAAA;IACjB,KAAK,MAAM,CAAC,EAAE,EAAE,OAAO,CAAC,IAAI,QAAQ,EAAE;QACpC,MAAM,QAAQ,GAAG,MAAM,CAAC,iBAAiB,CAAC,KAAK,MAAM,CAAC,OAAO,CAAC,EAAE,EAAE,CAAC,CAAA;QACnE,MAAM,CAAC,IAAI,CACT,oBAAC,KAAK,IACJ,GAAG,EAAE,EAAE,EACP,OAAO,EAAE,OAAO,EAChB,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,YAAY,EAC1B,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,YAAY,EAC1B,aAAa,EAAE,iBAAiB,EAChC,QAAQ,EAAE,QAAQ,EAClB,OAAO,EAAE,YAAY,GACrB,CACH,CAAA;KACF;IACD,MAAM,YAAY,GAAG,UAAU,YAAY,CAAC,EAAE,EAAE,CAAA;IAChD,OAAO,CACL,2BAAG,EAAE,EAAE,YAAY,iBAAc,gCAAgC;QAC/D;YACE,2CAA2C;YAC3C,uBAAuB,EAAE;gBACvB,MAAM,EAAE;aACL,YAAY;;;;CAIxB;aACQ,GACD;QACD,MAAM,CACL,CACL,CAAA;AACH,CAAC;AAED,uBAAuB,CAAC,SAAS,GAAG;IAClC,QAAQ,EAAE,SAAS,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,UAAU;IAC9C,MAAM,EAAE,eAAe,CAAC,YAAY,CAAC,UAAU;IAC/C,YAAY,EAAE,aAAa,CAAC,wBAAwB;IACpD,gBAAgB,EAAE,SAAS,CAAC,OAAO,CAAC,aAAa,CAAC,wBAAwB,CAAC;SACxE,UAAU;IACb,MAAM,EAAE,SAAS,CAAC,MAAM,CAAC,UAAU;IACnC,YAAY,EAAE,SAAS,CAAC,MAAM,CAAC,UAAU;IACzC,iBAAiB,EAAE,SAAS,CAAC,MAAM;IACnC,YAAY,EAAE,SAAS,CAAC,SAAS,CAAC,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC;CACtE,CAAA;AAED,uBAAuB,CAAC,YAAY,GAAG;IACrC,YAAY,EAAE,SAAS;IACvB,iBAAiB,EAAE,EAAE;IACrB,YAAY,EAAE,SAAS;CACxB,CAAA;AAED,eAAe,QAAQ,CAAC,uBAAuB,CAAC,CAAA"}

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

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/StructuralVariantChordRenderer/index.js"],"names":[],"mappings":"AAAA,OAAO,iBAAiB,MAAM,yEAAyE,CAAA;AACvG,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAE7C,MAAM,oBAAoB,GAAG,aAAa,CAAC,EAAE;IAC3C,MAAM,YAAY,GAAG,mBAAmB,CACtC,gCAAgC,EAChC;QACE,WAAW,EAAE;YACX,IAAI,EAAE,OAAO;YACb,WAAW,EAAE,4BAA4B;YACzC,YAAY,EAAE,sBAAsB;YACpC,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;QACD,mBAAmB,EAAE;YACnB,IAAI,EAAE,OAAO;YACb,WAAW,EAAE,iDAAiD;YAC9D,YAAY,EAAE,OAAO;YACrB,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;QACD,gBAAgB,EAAE;YAChB,IAAI,EAAE,OAAO;YACb,WAAW,EACT,oEAAoE;YACtE,YAAY,EAAE,MAAM;YACpB,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;KACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;IACD,OAAO,IAAI,iBAAiB,CAAC;QAC3B,IAAI,EAAE,gCAAgC;QACtC,cAAc;QACd,YAAY;QACZ,aAAa;KACd,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,eAAe,oBAAoB,CAAA"}

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 @@
+{"version":3,"file":"BreakendOptionDialog.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendOptionDialog.tsx"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,QAAQ,EACR,MAAM,EACN,aAAa,EACb,aAAa,EACb,WAAW,EACX,OAAO,EACP,gBAAgB,EAChB,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,SAAS,MAAM,2BAA2B,CAAA;AACjD,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,OAAO,EAAE,UAAU,EAAW,MAAM,oBAAoB,CAAA;AAExD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,WAAW,EAAE;QACX,QAAQ,EAAE,UAAU;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACvB,GAAG,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QACrB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;KAC/B;IACD,KAAK,EAAE;QACL,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,oBAAoB,CAAC,EAC5B,KAAK,EACL,WAAW,EACX,OAAO,EACP,QAAQ,GAMT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAClD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAEtD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW;QAC/B,oBAAC,WAAW;;YAET,WAAW,CAAC,CAAC,CAAC,CACb,oBAAC,UAAU,IACT,SAAS,EAAE,OAAO,CAAC,WAAW,EAC9B,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE;gBAE5B,oBAAC,SAAS,OAAG,CACF,CACd,CAAC,CAAC,CAAC,IAAI,CACI;QACd,oBAAC,OAAO,OAAG;QAEX,oBAAC,aAAa;YACZ,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,UAAU,EACnB,QAAQ,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC1C,EAEJ,KAAK,EAAC,+BAA+B,GACrC;YAEF,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,GAAG,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC5C,EAEJ,KAAK,EAAC,qDAAqD,GAC3D,CACY;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBACjC,IAAI;wBACF,MAAM,YAAY,GAAG,QAAQ,CAAC,2BAA2B,CACvD,OAAO,EACP,IAAI,CACL,CAAA;wBACD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,WAAW,GAAG,OAAO,CAAA;wBAClC,MAAM,UAAU,GAAQ,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;wBAChD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,UAAU,CAAA;wBACzC,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,YAAY;4BACzC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,CAAC,OAAO,EAAE;4BAC9B,CAAC,CAAC,UAAU,CAAA;wBAEd,OAAO,CAAC,OAAO,CAAC,qBAAqB,EAAE,YAAY,CAAC,CAAA;qBACrD;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;qBACvB;oBACD,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,eAGF;YACT,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAC5B,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,aAGZ,CACK,CACT,CACV,CAAA;AACH,CAAC;AACD,eAAe,QAAQ,CAAC,oBAAoB,CAAC,CAAA"}

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;