@jbrowse/plugin-variants 2.1.3 → 2.1.5

package/dist/ChordVariantDisplay/models/ChordVariantDisplay.d.ts

@@ -1,5 +1,6 @@
-export default ChordVariantDisplayF;
-declare function ChordVariantDisplayF(pluginManager: any): {
+/// <reference types="react" />
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const ChordVariantDisplayF: (pluginManager: PluginManager) => {
     stateModel: 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>;
@@ -91,7 +92,8 @@ declare function ChordVariantDisplayF(pluginManager: any): {
         afterAttach(): void;
     } & {
         readonly rendererTypeName: any;
-        renderProps(): any;
+        renderProps(): Record<string, unknown>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
     configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
 };
+export default ChordVariantDisplayF;

package/dist/ChordVariantDisplay/models/ChordVariantDisplay.js

@@ -5,7 +5,7 @@ const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
-const ChordVariantDisplayF = pluginManager => {
+const ChordVariantDisplayF = (pluginManager) => {
     const configSchema = (0, configuration_1.ConfigurationSchema)('ChordVariantDisplay', {
         renderer: mobx_state_tree_1.types.optional(pluginManager.pluggableConfigSchemaType('renderer'), { type: 'StructuralVariantChordRenderer' }),
     }, { baseConfiguration: plugin_circular_view_1.baseChordDisplayConfig, explicitlyTyped: true });
@@ -26,6 +26,7 @@ const ChordVariantDisplayF = pluginManager => {
                 displayModel: self,
                 bezierRadius: view.radiusPx * self.bezierRadiusRatio,
                 radius: view.radiusPx,
+                // @ts-ignore
                 blockDefinitions: this.blockDefinitions,
                 config: self.configuration.renderer,
                 onChordClick: self.onChordClick,

package/dist/ChordVariantDisplay/models/ChordVariantDisplay.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ChordVariantDisplay.js","sourceRoot":"","sources":["../../../src/ChordVariantDisplay/models/ChordVariantDisplay.ts"],"names":[],"mappings":";;AAAA,wEAGsC;AACtC,+DAGoC;AACpC,qDAAuC;AACvC,6CAAsD;AACtD,sDAAgE;AAGhE,MAAM,oBAAoB,GAAG,CAAC,aAA4B,EAAE,EAAE;IAC5D,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,qBAAqB,EACrB;QACE,QAAQ,EAAE,uBAAK,CAAC,QAAQ,CACtB,aAAa,CAAC,yBAAyB,CAAC,UAAU,CAAC,EACnD,EAAE,IAAI,EAAE,gCAAgC,EAAE,CAC3C;KACF,EACD,EAAE,iBAAiB,EAAE,6CAAsB,EAAE,eAAe,EAAE,IAAI,EAAE,CACrE,CAAA;IAED,MAAM,UAAU,GAAG,uBAAK;SACrB,OAAO,CACN,qBAAqB,EACrB,4CAAqB,EACrB,uBAAK,CAAC,KAAK,CAAC;QACV,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,qBAAqB,CAAC;QAC1C,aAAa,EAAE,IAAA,sCAAsB,EAAC,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,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;YACpC,OAAO;gBACL,GAAG,IAAA,6BAAoB,EAAC,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;gBAErB,aAAa;gBACb,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,kBAAe,oBAAoB,CAAA"}

package/dist/LinearVariantDisplay/model.d.ts

@@ -175,7 +175,7 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     afterAttach(): void;
 } & {
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): {
         label: string;

package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts

@@ -1,24 +1,34 @@
-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<NonNullable<string | ((...args: any[]) => any) | null | undefined>>;
-    }
-    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 };
-    }
+/// <reference types="react" />
+import { Feature } from '@jbrowse/core/util';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+interface Region {
+    end: number;
+    start: number;
+    refName: string;
+    elided?: false;
 }
+interface ElidedRegion {
+    elided: true;
+    regions: Region[];
+}
+declare type AnyRegion = Region | ElidedRegion;
+interface Block {
+    flipped: boolean;
+    bpPerRadian: number;
+    startRadians: number;
+    region: AnyRegion;
+}
+declare function StructuralVariantChords(props: {
+    features: Map<string, Feature>;
+    radius: number;
+    config: AnyConfigurationModel;
+    displayModel: {
+        id: string;
+        selectedFeatureId: string;
+    };
+    blockDefinitions: Block[];
+    bezierRadius: number;
+    onChordClick: (feature: Feature, reg: AnyRegion, endBlock: AnyRegion, evt: unknown) => void;
+}): JSX.Element;
+declare const _default: typeof StructuralVariantChords;
 export default _default;
-import PropTypes from "prop-types";
-import React from "react";

package/dist/StructuralVariantChordRenderer/ReactComponent.js

@@ -22,23 +22,17 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
 const util_1 = require("@jbrowse/core/util");
 const configuration_1 = require("@jbrowse/core/configuration");
-const mst_1 = require("@jbrowse/core/util/types/mst");
 const vcf_1 = require("@gmod/vcf");
-const prop_types_1 = __importDefault(require("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;
+    return bpOffset / block.bpPerRadian + block.startRadians;
 }
 const Chord = (0, mobx_react_1.observer)(function Chord({ feature, blocksForRefs, radius, config, bezierRadius, selected, onClick, }) {
     var _a, _b, _c, _d, _e;
@@ -92,14 +86,22 @@ const Chord = (0, mobx_react_1.observer)(function Chord({ feature, blocksForRefs
         const hoverStrokeColor = (0, configuration_1.readConfObject)(config, 'strokeColorHover', {
             feature,
         });
-        return (react_1.default.createElement("path", { "data-testid": `chord-${feature.id()}`, d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), style: { stroke: strokeColor }, onClick: evt => onClick(feature, startBlock.region, endBlock.region, evt), onMouseOver: evt => {
+        return (react_1.default.createElement("path", { "data-testid": `chord-${feature.id()}`, d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), style: { stroke: strokeColor }, onClick: evt => {
+                if (endBlock && startBlock) {
+                    onClick(feature, startBlock.region, endBlock.region, evt);
+                }
+            }, onMouseOver: evt => {
                 if (!selected) {
+                    // @ts-ignore
                     evt.target.style.stroke = hoverStrokeColor;
+                    // @ts-ignore
                     evt.target.style.strokeWidth = 3;
                 }
             }, onMouseOut: evt => {
                 if (!selected) {
+                    // @ts-ignore
                     evt.target.style.stroke = strokeColor;
+                    // @ts-ignore
                     evt.target.style.strokeWidth = 1;
                 }
             } }));
@@ -125,7 +127,7 @@ function StructuralVariantChords(props) {
     const chords = [];
     for (const [id, feature] of features) {
         const selected = String(selectedFeatureId) === String(feature.id());
-        chords.push(react_1.default.createElement(Chord, { key: id, feature: feature, config: config, displayModel: displayModel, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
+        chords.push(react_1.default.createElement(Chord, { key: id, feature: feature, config: config, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
     }
     const trackStyleId = `chords-${displayModel.id}`;
     return (react_1.default.createElement("g", { id: trackStyleId, "data-testid": "structuralVariantChordRenderer" },
@@ -141,21 +143,5 @@ function StructuralVariantChords(props) {
             } }),
         chords));
 }
-StructuralVariantChords.propTypes = {
-    features: prop_types_1.default.instanceOf(Map).isRequired,
-    config: mst_1.PropTypes.ConfigSchema.isRequired,
-    displayModel: mobx_react_1.PropTypes.objectOrObservableObject,
-    blockDefinitions: prop_types_1.default.arrayOf(mobx_react_1.PropTypes.objectOrObservableObject)
-        .isRequired,
-    radius: prop_types_1.default.number.isRequired,
-    bezierRadius: prop_types_1.default.number.isRequired,
-    selectedFeatureId: prop_types_1.default.string,
-    onChordClick: prop_types_1.default.oneOfType([prop_types_1.default.func, prop_types_1.default.string]),
-};
-StructuralVariantChords.defaultProps = {
-    displayModel: undefined,
-    selectedFeatureId: '',
-    onChordClick: undefined,
-};
 exports.default = (0, mobx_react_1.observer)(StructuralVariantChords);
 //# sourceMappingURL=ReactComponent.js.map

package/dist/StructuralVariantChordRenderer/ReactComponent.js.map

@@ -1 +1 @@
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package/dist/StructuralVariantChordRenderer/index.d.ts

@@ -1,3 +1,4 @@
+import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const ChordRendererConfigF: (pluginManager: PluginManager) => ChordRendererType;
 export default ChordRendererConfigF;
-declare function ChordRendererConfigF(pluginManager: any): ChordRendererType;
-import ChordRendererType from "@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType";

package/dist/StructuralVariantChordRenderer/index.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const CircularChordRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType"));
 const configuration_1 = require("@jbrowse/core/configuration");
 const ReactComponent_1 = __importDefault(require("./ReactComponent"));
-const ChordRendererConfigF = pluginManager => {
+const ChordRendererConfigF = (pluginManager) => {
     const configSchema = (0, configuration_1.ConfigurationSchema)('StructuralVariantChordRenderer', {
         strokeColor: {
             type: 'color',

package/dist/StructuralVariantChordRenderer/index.js.map

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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/StructuralVariantChordRenderer/index.ts"],"names":[],"mappings":";;;;;AAAA,wIAAuG;AACvG,+DAAiE;AAGjE,sEAA6C;AAE7C,MAAM,oBAAoB,GAAG,CAAC,aAA4B,EAAE,EAAE;IAC5D,MAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,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,mCAAiB,CAAC;QAC3B,IAAI,EAAE,gCAAgC;QACtC,cAAc,EAAd,wBAAc;QACd,YAAY;QACZ,aAAa;KACd,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,kBAAe,oBAAoB,CAAA"}

package/esm/ChordVariantDisplay/models/ChordVariantDisplay.d.ts

@@ -1,5 +1,6 @@
-export default ChordVariantDisplayF;
-declare function ChordVariantDisplayF(pluginManager: any): {
+/// <reference types="react" />
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const ChordVariantDisplayF: (pluginManager: PluginManager) => {
     stateModel: 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>;
@@ -91,7 +92,8 @@ declare function ChordVariantDisplayF(pluginManager: any): {
         afterAttach(): void;
     } & {
         readonly rendererTypeName: any;
-        renderProps(): any;
+        renderProps(): Record<string, unknown>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
     configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
 };
+export default ChordVariantDisplayF;

package/esm/ChordVariantDisplay/models/ChordVariantDisplay.js

@@ -3,7 +3,7 @@ import { ConfigurationSchema, ConfigurationReference, } from '@jbrowse/core/conf
 import { types } from 'mobx-state-tree';
 import { getContainingView } from '@jbrowse/core/util';
 import { getParentRenderProps } from '@jbrowse/core/util/tracks';
-const ChordVariantDisplayF = pluginManager => {
+const ChordVariantDisplayF = (pluginManager) => {
     const configSchema = ConfigurationSchema('ChordVariantDisplay', {
         renderer: types.optional(pluginManager.pluggableConfigSchemaType('renderer'), { type: 'StructuralVariantChordRenderer' }),
     }, { baseConfiguration: baseChordDisplayConfig, explicitlyTyped: true });
@@ -24,6 +24,7 @@ const ChordVariantDisplayF = pluginManager => {
                 displayModel: self,
                 bezierRadius: view.radiusPx * self.bezierRadiusRatio,
                 radius: view.radiusPx,
+                // @ts-ignore
                 blockDefinitions: this.blockDefinitions,
                 config: self.configuration.renderer,
                 onChordClick: self.onChordClick,

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

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package/esm/LinearVariantDisplay/model.d.ts

@@ -175,7 +175,7 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     afterAttach(): void;
 } & {
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): {
         label: string;

package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts

@@ -1,24 +1,34 @@
-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<NonNullable<string | ((...args: any[]) => any) | null | undefined>>;
-    }
-    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 };
-    }
+/// <reference types="react" />
+import { Feature } from '@jbrowse/core/util';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+interface Region {
+    end: number;
+    start: number;
+    refName: string;
+    elided?: false;
 }
+interface ElidedRegion {
+    elided: true;
+    regions: Region[];
+}
+declare type AnyRegion = Region | ElidedRegion;
+interface Block {
+    flipped: boolean;
+    bpPerRadian: number;
+    startRadians: number;
+    region: AnyRegion;
+}
+declare function StructuralVariantChords(props: {
+    features: Map<string, Feature>;
+    radius: number;
+    config: AnyConfigurationModel;
+    displayModel: {
+        id: string;
+        selectedFeatureId: string;
+    };
+    blockDefinitions: Block[];
+    bezierRadius: number;
+    onChordClick: (feature: Feature, reg: AnyRegion, endBlock: AnyRegion, evt: unknown) => void;
+}): JSX.Element;
+declare const _default: typeof StructuralVariantChords;
 export default _default;
-import PropTypes from "prop-types";
-import React from "react";

package/esm/StructuralVariantChordRenderer/ReactComponent.js

@@ -1,16 +1,13 @@
 import React, { useMemo } from 'react';
-import { observer, PropTypes as MobxPropTypes } from 'mobx-react';
+import { observer } 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 { readConfObject, } from '@jbrowse/core/configuration';
 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;
+    return bpOffset / block.bpPerRadian + block.startRadians;
 }
 const Chord = observer(function Chord({ feature, blocksForRefs, radius, config, bezierRadius, selected, onClick, }) {
     var _a, _b, _c, _d, _e;
@@ -64,14 +61,22 @@ const Chord = observer(function Chord({ feature, blocksForRefs, radius, config,
         const hoverStrokeColor = readConfObject(config, 'strokeColorHover', {
             feature,
         });
-        return (React.createElement("path", { "data-testid": `chord-${feature.id()}`, d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), style: { stroke: strokeColor }, onClick: evt => onClick(feature, startBlock.region, endBlock.region, evt), onMouseOver: evt => {
+        return (React.createElement("path", { "data-testid": `chord-${feature.id()}`, d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), style: { stroke: strokeColor }, onClick: evt => {
+                if (endBlock && startBlock) {
+                    onClick(feature, startBlock.region, endBlock.region, evt);
+                }
+            }, onMouseOver: evt => {
                 if (!selected) {
+                    // @ts-ignore
                     evt.target.style.stroke = hoverStrokeColor;
+                    // @ts-ignore
                     evt.target.style.strokeWidth = 3;
                 }
             }, onMouseOut: evt => {
                 if (!selected) {
+                    // @ts-ignore
                     evt.target.style.stroke = strokeColor;
+                    // @ts-ignore
                     evt.target.style.strokeWidth = 1;
                 }
             } }));
@@ -97,7 +102,7 @@ function StructuralVariantChords(props) {
     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 }));
+        chords.push(React.createElement(Chord, { key: id, feature: feature, config: config, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
     }
     const trackStyleId = `chords-${displayModel.id}`;
     return (React.createElement("g", { id: trackStyleId, "data-testid": "structuralVariantChordRenderer" },
@@ -113,21 +118,5 @@ function StructuralVariantChords(props) {
             } }),
         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

@@ -1 +1 @@
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}

package/esm/StructuralVariantChordRenderer/index.d.ts

@@ -1,3 +1,4 @@
+import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const ChordRendererConfigF: (pluginManager: PluginManager) => ChordRendererType;
 export default ChordRendererConfigF;
-declare function ChordRendererConfigF(pluginManager: any): ChordRendererType;
-import ChordRendererType from "@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType";

package/esm/StructuralVariantChordRenderer/index.js

@@ -1,7 +1,7 @@
 import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import ReactComponent from './ReactComponent';
-const ChordRendererConfigF = pluginManager => {
+const ChordRendererConfigF = (pluginManager) => {
     const configSchema = ConfigurationSchema('StructuralVariantChordRenderer', {
         strokeColor: {
             type: 'color',

package/esm/StructuralVariantChordRenderer/index.js.map

@@ -1 +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"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/StructuralVariantChordRenderer/index.ts"],"names":[],"mappings":"AAAA,OAAO,iBAAiB,MAAM,yEAAyE,CAAA;AACvG,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAGjE,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAE7C,MAAM,oBAAoB,GAAG,CAAC,aAA4B,EAAE,EAAE;IAC5D,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/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "2.1.3",
+  "version": "2.1.5",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -65,5 +65,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "ebd548ceb52adb36cf6ab437082b5b5feac1338e"
+  "gitHead": "bc5253ecdddeceeb999fffebf6dc6cf5f444e1c9"
 }

package/src/ChordVariantDisplay/models/{ChordVariantDisplay.js → ChordVariantDisplay.ts}

@@ -9,8 +9,9 @@ import {
 import { types } from 'mobx-state-tree'
 import { getContainingView } from '@jbrowse/core/util'
 import { getParentRenderProps } from '@jbrowse/core/util/tracks'
+import PluginManager from '@jbrowse/core/PluginManager'
 
-const ChordVariantDisplayF = pluginManager => {
+const ChordVariantDisplayF = (pluginManager: PluginManager) => {
   const configSchema = ConfigurationSchema(
     'ChordVariantDisplay',
     {
@@ -36,7 +37,7 @@ const ChordVariantDisplayF = pluginManager => {
         return self.configuration.renderer.type
       },
 
-      renderProps() {
+      renderProps(): Record<string, unknown> {
         const view = getContainingView(self)
         return {
           ...getParentRenderProps(self),
@@ -44,6 +45,8 @@ const ChordVariantDisplayF = pluginManager => {
           displayModel: self,
           bezierRadius: view.radiusPx * self.bezierRadiusRatio,
           radius: view.radiusPx,
+
+          // @ts-ignore
           blockDefinitions: this.blockDefinitions,
           config: self.configuration.renderer,
           onChordClick: self.onChordClick,

package/src/StructuralVariantChordRenderer/{ReactComponent.js → ReactComponent.tsx}

@@ -1,17 +1,38 @@
 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 { observer } from 'mobx-react'
+import { polarToCartesian, Feature } from '@jbrowse/core/util'
+import {
+  AnyConfigurationModel,
+  readConfObject,
+} from '@jbrowse/core/configuration'
 import { parseBreakend } from '@gmod/vcf'
-import PropTypes from 'prop-types'
 
-function bpToRadians(block, pos) {
+interface Region {
+  end: number
+  start: number
+  refName: string
+  elided?: false
+}
+
+interface ElidedRegion {
+  elided: true
+  regions: Region[]
+}
+
+type AnyRegion = Region | ElidedRegion
+
+interface Block {
+  flipped: boolean
+  bpPerRadian: number
+  startRadians: number
+  region: AnyRegion
+}
+
+function bpToRadians(block: Block, pos: number) {
   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
+  return bpOffset / block.bpPerRadian + block.startRadians
 }
 
 const Chord = observer(function Chord({
@@ -22,6 +43,19 @@ const Chord = observer(function Chord({
   bezierRadius,
   selected,
   onClick,
+}: {
+  feature: Feature
+  blocksForRefs: { [key: string]: Block }
+  radius: number
+  config: AnyConfigurationModel
+  bezierRadius: number
+  selected: boolean
+  onClick: (
+    feature: Feature,
+    reg: AnyRegion,
+    endBlock: AnyRegion,
+    evt: unknown,
+  ) => void
 }) {
   // find the blocks that our start and end points belong to
   const startBlock = blocksForRefs[feature.get('refName')]
@@ -35,7 +69,7 @@ const Chord = observer(function Chord({
     svType = 'mate'
   }
   let endPosition
-  let endBlock
+  let endBlock: Block | undefined
   const alt = feature.get('ALT')?.[0]
   const bnd = alt && parseBreakend(alt)
   if (bnd) {
@@ -80,18 +114,24 @@ const Chord = observer(function Chord({
         data-testid={`chord-${feature.id()}`}
         d={['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' ')}
         style={{ stroke: strokeColor }}
-        onClick={evt =>
-          onClick(feature, startBlock.region, endBlock.region, evt)
-        }
+        onClick={evt => {
+          if (endBlock && startBlock) {
+            onClick(feature, startBlock.region, endBlock.region, evt)
+          }
+        }}
         onMouseOver={evt => {
           if (!selected) {
+            // @ts-ignore
             evt.target.style.stroke = hoverStrokeColor
+            // @ts-ignore
             evt.target.style.strokeWidth = 3
           }
         }}
         onMouseOut={evt => {
           if (!selected) {
+            // @ts-ignore
             evt.target.style.stroke = strokeColor
+            // @ts-ignore
             evt.target.style.strokeWidth = 1
           }
         }}
@@ -102,7 +142,20 @@ const Chord = observer(function Chord({
   return null
 })
 
-function StructuralVariantChords(props) {
+function StructuralVariantChords(props: {
+  features: Map<string, Feature>
+  radius: number
+  config: AnyConfigurationModel
+  displayModel: { id: string; selectedFeatureId: string }
+  blockDefinitions: Block[]
+  bezierRadius: number
+  onChordClick: (
+    feature: Feature,
+    reg: AnyRegion,
+    endBlock: AnyRegion,
+    evt: unknown,
+  ) => void
+}) {
   const {
     features,
     config,
@@ -111,12 +164,11 @@ function StructuralVariantChords(props) {
     radius,
     bezierRadius,
     displayModel: { selectedFeatureId },
-
     onChordClick,
   } = props
   // make a map of refName -> blockDefinition
   const blocksForRefsMemo = useMemo(() => {
-    const blocksForRefs = {}
+    const blocksForRefs = {} as { [key: string]: Block }
     blockDefinitions.forEach(block => {
       const regions = block.region.elided
         ? block.region.regions
@@ -136,7 +188,6 @@ function StructuralVariantChords(props) {
         key={id}
         feature={feature}
         config={config}
-        displayModel={displayModel}
         radius={radius}
         bezierRadius={bezierRadius}
         blocksForRefs={blocksForRefsMemo}
@@ -164,22 +215,4 @@ function StructuralVariantChords(props) {
   )
 }
 
-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)

package/src/StructuralVariantChordRenderer/{index.js → index.ts}

@@ -1,8 +1,10 @@
 import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import PluginManager from '@jbrowse/core/PluginManager'
+
 import ReactComponent from './ReactComponent'
 
-const ChordRendererConfigF = pluginManager => {
+const ChordRendererConfigF = (pluginManager: PluginManager) => {
   const configSchema = ConfigurationSchema(
     'StructuralVariantChordRenderer',
     {