@jbrowse/plugin-variants 2.1.4 → 2.1.6

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>;
@@ -53,7 +54,7 @@ declare function ChordVariantDisplayF(pluginManager: any): {
         readonly adapterConfig: any;
         readonly parentTrack: any;
         renderProps(): any;
-        readonly rendererType: any;
+        readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
         readonly DisplayMessageComponent: import("react").FC<any> | undefined;
         trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
         readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -74,7 +75,7 @@ declare function ChordVariantDisplayF(pluginManager: any): {
     } & {
         readonly blockDefinitions: any;
         renderProps(): any;
-        readonly rendererType: any;
+        readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
         isCompatibleWithRenderer(renderer: import("@jbrowse/core/pluggableElementTypes").RendererType): boolean;
         readonly selectedFeatureId: string | undefined;
     } & {
@@ -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

@@ -108,7 +108,7 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
-    readonly rendererType: any;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -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;
@@ -196,7 +196,11 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     readonly maxHeight: any;
     readonly displayMode: any;
 } & {
-    readonly rendererConfig: any;
+    readonly rendererConfig: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
 } & {
     toggleShowLabels(): void;
     toggleShowDescriptions(): void;
@@ -204,7 +208,11 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     setMaxHeight(val: number): void;
 } & {
     renderProps(): {
-        config: any;
+        config: {
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: unknown): any;
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
     };
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
 } & {

package/dist/LinearVariantDisplay/model.js

@@ -18,16 +18,17 @@ function default_1(configSchema) {
                 const { rpcManager } = session;
                 const sessionId = (0, tracks_1.getRpcSessionId)(self);
                 const track = (0, util_1.getContainingTrack)(self);
+                const view = (0, util_1.getContainingView)(self);
                 const adapterConfig = (0, configuration_1.getConf)(track, 'adapter');
-                const header = await rpcManager.call(sessionId, 'CoreGetMetadata', {
+                const descriptions = await rpcManager.call(sessionId, 'CoreGetMetadata', {
                     adapterConfig,
                 });
-                const featureWidget = session.addWidget('VariantFeatureWidget', 'variantFeature', {
+                session.showWidget(session.addWidget('VariantFeatureWidget', 'variantFeature', {
                     featureData: feature.toJSON(),
-                    view: (0, util_1.getContainingView)(self),
-                    descriptions: header,
-                });
-                session.showWidget(featureWidget);
+                    view,
+                    track,
+                    descriptions,
+                }));
             }
             session.setSelection(feature);
         },

package/dist/LinearVariantDisplay/model.js.map

@@ -1 +1 @@
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+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/model.ts"],"names":[],"mappings":";;AAAA,+DAA6E;AAC7E,sDAA2D;AAC3D,6CAK2B;AAG3B,kFAAmF;AACnF,qDAAuC;AAGvC,mBAAyB,YAA6C;IACpE,OAAO,uBAAK;SACT,OAAO,CACN,sBAAsB,EACtB,IAAA,0DAA8B,EAAC,YAAY,CAAC,EAC5C,uBAAK,CAAC,KAAK,CAAC;QACV,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,KAAK,CAAC,aAAa,CAAC,OAAgB;YAClC,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAI,IAAA,gCAAyB,EAAC,OAAO,CAAC,EAAE;gBACtC,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;gBAC9B,MAAM,SAAS,GAAG,IAAA,wBAAe,EAAC,IAAI,CAAC,CAAA;gBACvC,MAAM,KAAK,GAAG,IAAA,yBAAkB,EAAC,IAAI,CAAC,CAAA;gBACtC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;gBACpC,MAAM,aAAa,GAAG,IAAA,uBAAO,EAAC,KAAK,EAAE,SAAS,CAAC,CAAA;gBAC/C,MAAM,YAAY,GAAG,MAAM,UAAU,CAAC,IAAI,CACxC,SAAS,EACT,iBAAiB,EACjB;oBACE,aAAa;iBACd,CACF,CAAA;gBACD,OAAO,CAAC,UAAU,CAChB,OAAO,CAAC,SAAS,CAAC,sBAAsB,EAAE,gBAAgB,EAAE;oBAC1D,WAAW,EAAE,OAAO,CAAC,MAAM,EAAE;oBAC7B,IAAI;oBACJ,KAAK;oBACL,YAAY;iBACb,CAAC,CACH,CAAA;aACF;YAED,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;QAC/B,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AAvCD,4BAuCC"}

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

@@ -1 +1 @@
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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/dist/VariantFeatureWidget/BreakendPanel.js

@@ -31,13 +31,12 @@ const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const util_1 = require("@jbrowse/core/util");
-const mobx_state_tree_1 = require("mobx-state-tree");
 const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
 const BreakendOptionDialog_1 = __importDefault(require("./BreakendOptionDialog"));
 function BreakendPanel(props) {
     const { model, locStrings, feature } = props;
     const session = (0, util_1.getSession)(model);
-    const { pluginManager } = (0, mobx_state_tree_1.getEnv)(session);
+    const { pluginManager } = (0, util_1.getEnv)(session);
     const [breakpointDialog, setBreakpointDialog] = (0, react_1.useState)(false);
     let viewType;
     try {

package/dist/VariantFeatureWidget/BreakendPanel.js.map

@@ -1 +1 @@
-{"version":3,"file":"BreakendPanel.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendPanel.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uDAAuD;AACvD,+CAAuC;AACvC,4CAAgD;AAChD,qFAEyC;AACzC,6CAA+C;AAC/C,qDAAwC;AACxC,yFAA4E;AAC5E,kFAAyD;AAEzD,SAAwB,aAAa,CAAC,KAIrC;IACC,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAA,wBAAM,EAAC,OAAO,CAAC,CAAA;IACzC,MAAM,CAAC,gBAAgB,EAAE,mBAAmB,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IAC/D,IAAI,QAAQ,CAAA;IAEZ,IAAI;QACF,QAAQ,GAAG,aAAa,CAAC,WAAW,CAAC,qBAAqB,CAAC,CAAA;KAC5D;IAAC,OAAO,CAAC,EAAE;QACV,SAAS;KACV;IAED,MAAM,aAAa,GAAG,IAAI,uBAAa,CAAC,OAAO,CAAC,CAAA;IAChD,OAAO,CACL,8BAAC,4BAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,WAAW;QACpC,8BAAC,qBAAU,oDAAuD;QAClE,0CACG,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,CAC3B,sCAAI,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,EAAE;YACrC,8BAAC,eAAI,IACH,IAAI,EAAC,GAAG,EACR,OAAO,EAAE,KAAK,CAAC,EAAE;;oBACf,KAAK,CAAC,cAAc,EAAE,CAAA;oBACtB,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,IAAI;wBACF,IAAI,IAAI,EAAE;4BACR,MAAA,IAAI,CAAC,cAAc,qDAAG,SAAS,CAAC,CAAA;yBACjC;6BAAM;4BACL,MAAM,IAAI,KAAK,CACb,2DAA2D,CAC5D,CAAA;yBACF;qBACF;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;qBACvB;gBACH,CAAC,IAEA,SAAS,SAAS,EAAE,CAChB,CACJ,CACN,CAAC,CACC;QACJ,QAAQ,CAAC,CAAC,CAAC,CACV;YACE,8BAAC,qBAAU,6DAEE;YACb,0CACG,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,CAC3B,sCAAI,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,EAAE;gBACrC,8BAAC,eAAI,IACH,IAAI,EAAC,GAAG,EACR,OAAO,EAAE,KAAK,CAAC,EAAE;wBACf,KAAK,CAAC,cAAc,EAAE,CAAA;wBACtB,mBAAmB,CAAC,IAAI,CAAC,CAAA;oBAC3B,CAAC,IAEA,GAAG,OAAO,CAAC,OAAO,IAAI,OAAO,CAAC,KAAK,OAAO,SAAS,eAAe,CAC9D,CACJ,CACN,CAAC,CACC;YACJ,gBAAgB,CAAC,CAAC,CAAC,CAClB,8BAAC,8BAAoB,IACnB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,aAAa,EACtB,QAAQ,EAAE,QAAQ,EAClB,WAAW,EAAE,GAAG,EAAE;oBAChB,mBAAmB,CAAC,KAAK,CAAC,CAAA;gBAC5B,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAC,CAAC,CAAC,IAAI,CACC,CACZ,CAAA;AACH,CAAC;AAlFD,gCAkFC"}
+{"version":3,"file":"BreakendPanel.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendPanel.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uDAAuD;AACvD,+CAAuC;AACvC,4CAAgD;AAChD,qFAEyC;AACzC,6CAAuD;AACvD,yFAA4E;AAC5E,kFAAyD;AAEzD,SAAwB,aAAa,CAAC,KAIrC;IACC,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,aAAa,EAAE,GAAG,IAAA,aAAM,EAAC,OAAO,CAAC,CAAA;IACzC,MAAM,CAAC,gBAAgB,EAAE,mBAAmB,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IAC/D,IAAI,QAAQ,CAAA;IAEZ,IAAI;QACF,QAAQ,GAAG,aAAa,CAAC,WAAW,CAAC,qBAAqB,CAAC,CAAA;KAC5D;IAAC,OAAO,CAAC,EAAE;QACV,SAAS;KACV;IAED,MAAM,aAAa,GAAG,IAAI,uBAAa,CAAC,OAAO,CAAC,CAAA;IAChD,OAAO,CACL,8BAAC,4BAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,WAAW;QACpC,8BAAC,qBAAU,oDAAuD;QAClE,0CACG,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,CAC3B,sCAAI,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,EAAE;YACrC,8BAAC,eAAI,IACH,IAAI,EAAC,GAAG,EACR,OAAO,EAAE,KAAK,CAAC,EAAE;;oBACf,KAAK,CAAC,cAAc,EAAE,CAAA;oBACtB,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,IAAI;wBACF,IAAI,IAAI,EAAE;4BACR,MAAA,IAAI,CAAC,cAAc,qDAAG,SAAS,CAAC,CAAA;yBACjC;6BAAM;4BACL,MAAM,IAAI,KAAK,CACb,2DAA2D,CAC5D,CAAA;yBACF;qBACF;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;qBACvB;gBACH,CAAC,IAEA,SAAS,SAAS,EAAE,CAChB,CACJ,CACN,CAAC,CACC;QACJ,QAAQ,CAAC,CAAC,CAAC,CACV;YACE,8BAAC,qBAAU,6DAEE;YACb,0CACG,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,CAC3B,sCAAI,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,EAAE;gBACrC,8BAAC,eAAI,IACH,IAAI,EAAC,GAAG,EACR,OAAO,EAAE,KAAK,CAAC,EAAE;wBACf,KAAK,CAAC,cAAc,EAAE,CAAA;wBACtB,mBAAmB,CAAC,IAAI,CAAC,CAAA;oBAC3B,CAAC,IAEA,GAAG,OAAO,CAAC,OAAO,IAAI,OAAO,CAAC,KAAK,OAAO,SAAS,eAAe,CAC9D,CACJ,CACN,CAAC,CACC;YACJ,gBAAgB,CAAC,CAAC,CAAC,CAClB,8BAAC,8BAAoB,IACnB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,aAAa,EACtB,QAAQ,EAAE,QAAQ,EAClB,WAAW,EAAE,GAAG,EAAE;oBAChB,mBAAmB,CAAC,KAAK,CAAC,CAAA;gBAC5B,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAC,CAAC,CAAC,IAAI,CACC,CACZ,CAAA;AACH,CAAC;AAlFD,gCAkFC"}

package/dist/VariantFeatureWidget/index.d.ts

@@ -8,6 +8,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
     descriptions: import("mobx-state-tree").IType<any, any, any>;
@@ -15,6 +17,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
     setFormattedData(feat: Record<string, unknown>): void;
+    setExtra(type?: string | undefined, trackId?: string | undefined): void;
 } & {
     afterCreate(): void;
 }, {
@@ -27,11 +30,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     id: string;
     type: "BaseFeatureWidget";
     track: import("mobx-state-tree").ReferenceIdentifier | undefined;
     view: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    trackId: string | undefined;
+    trackType: string | undefined;
     formattedFields: any;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;

package/dist/VcfAdapter/VcfAdapter.js

@@ -13,7 +13,7 @@ const VcfFeature_1 = __importDefault(require("../VcfTabixAdapter/VcfFeature"));
 const readVcf = (f) => {
     const header = [];
     const rest = [];
-    f.split('\n')
+    f.split(/\n|\r\n|\r/)
         .map(f => f.trim())
         .filter(f => !!f)
         .forEach(line => {

package/dist/VcfAdapter/VcfAdapter.js.map

@@ -1 +1 @@
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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>;
@@ -53,7 +54,7 @@ declare function ChordVariantDisplayF(pluginManager: any): {
         readonly adapterConfig: any;
         readonly parentTrack: any;
         renderProps(): any;
-        readonly rendererType: any;
+        readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
         readonly DisplayMessageComponent: import("react").FC<any> | undefined;
         trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
         readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -74,7 +75,7 @@ declare function ChordVariantDisplayF(pluginManager: any): {
     } & {
         readonly blockDefinitions: any;
         renderProps(): any;
-        readonly rendererType: any;
+        readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
         isCompatibleWithRenderer(renderer: import("@jbrowse/core/pluggableElementTypes").RendererType): boolean;
         readonly selectedFeatureId: string | undefined;
     } & {
@@ -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

@@ -1 +1 @@
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+{"version":3,"file":"ChordVariantDisplay.js","sourceRoot":"","sources":["../../../src/ChordVariantDisplay/models/ChordVariantDisplay.ts"],"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;AAGhE,MAAM,oBAAoB,GAAG,CAAC,aAA4B,EAAE,EAAE;IAC5D,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;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,eAAe,oBAAoB,CAAA"}

package/esm/LinearVariantDisplay/model.d.ts

@@ -108,7 +108,7 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
-    readonly rendererType: any;
+    readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -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;
@@ -196,7 +196,11 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     readonly maxHeight: any;
     readonly displayMode: any;
 } & {
-    readonly rendererConfig: any;
+    readonly rendererConfig: {
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
 } & {
     toggleShowLabels(): void;
     toggleShowDescriptions(): void;
@@ -204,7 +208,11 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     setMaxHeight(val: number): void;
 } & {
     renderProps(): {
-        config: any;
+        config: {
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: unknown): any;
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
     };
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
 } & {

package/esm/LinearVariantDisplay/model.js

@@ -16,16 +16,17 @@ export default function (configSchema) {
                 const { rpcManager } = session;
                 const sessionId = getRpcSessionId(self);
                 const track = getContainingTrack(self);
+                const view = getContainingView(self);
                 const adapterConfig = getConf(track, 'adapter');
-                const header = await rpcManager.call(sessionId, 'CoreGetMetadata', {
+                const descriptions = await rpcManager.call(sessionId, 'CoreGetMetadata', {
                     adapterConfig,
                 });
-                const featureWidget = session.addWidget('VariantFeatureWidget', 'variantFeature', {
+                session.showWidget(session.addWidget('VariantFeatureWidget', 'variantFeature', {
                     featureData: feature.toJSON(),
-                    view: getContainingView(self),
-                    descriptions: header,
-                });
-                session.showWidget(featureWidget);
+                    view,
+                    track,
+                    descriptions,
+                }));
             }
             session.setSelection(feature);
         },

package/esm/LinearVariantDisplay/model.js.map

@@ -1 +1 @@
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