npm - @jbrowse/plugin-variants - Versions diffs - 2.2.2 → 2.3.1 - Mend

@jbrowse/plugin-variants 2.2.2 → 2.3.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (78) hide show

package/dist/ChordVariantDisplay/index.js CHANGED Viewed

@@ -13,6 +13,7 @@ exports.default = (pluginManager) => {
         const stateModel = (0, stateModelFactory_1.default)(configSchema);
         return new DisplayType_1.default({
             name: 'ChordVariantDisplay',
+            displayName: 'Chord variant display',
             configSchema,
             stateModel,
             trackType: 'VariantTrack',

package/dist/ChordVariantDisplay/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChordVariantDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,wEAAyE;AACzE,kGAAyE;AACzE,yEAAiD;AACjD,mFAAoD;AAEpD,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;QACjD,MAAM,UAAU,GAAG,IAAA,2BAAW,EAAC,YAAY,CAAC,CAAA;QAC5C,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,WAAW,EAAE,uBAAuB;YACpC,YAAY;YACZ,UAAU;YACV,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,cAAc;YACxB,cAAc,EAAE,gDAAyB;SAC1C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/ChordVariantDisplay/models/stateModelFactory.d.ts CHANGED Viewed

@@ -76,22 +76,24 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
     filled: boolean;
     reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
     data: undefined;
+    html: string | undefined;
     message: string;
     renderingComponent: import("@jbrowse/core/util").AnyReactComponentType | undefined;
     refNameMap: Record<string, string> | undefined;
 } & {
     onChordClick(feature: import("@jbrowse/core/util").Feature): void;
 } & {
-    readonly blockDefinitions: any;
+    readonly blockDefinitions: import("@jbrowse/plugin-circular-view/src/CircularView/models/slices").Slice[];
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
     isCompatibleWithRenderer(renderer: import("@jbrowse/core/pluggableElementTypes").RendererType): boolean;
     readonly selectedFeatureId: string | undefined;
 } & {
     renderStarted(): void;
-    renderSuccess({ message, data, reactElement, renderingComponent, }: {
+    renderSuccess({ message, data, reactElement, html, renderingComponent, }: {
         message: string;
         data: any;
+        html: string;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
         renderingComponent: import("@jbrowse/core/util").AnyReactComponentType;
     }): void;

package/dist/ChordVariantDisplay/models/stateModelFactory.js CHANGED Viewed

@@ -39,8 +39,7 @@ const stateModelFactory = (configSchema) => {
                 displayModel: self,
                 bezierRadius: view.radiusPx * self.bezierRadiusRatio,
                 radius: view.radiusPx,
-                // @ts-ignore
-                blockDefinitions: this.blockDefinitions,
+                blockDefinitions: self.blockDefinitions,
                 config: self.configuration.renderer,
                 onChordClick: self.onChordClick,
             };

package/dist/ChordVariantDisplay/models/stateModelFactory.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"stateModelFactory.js","sourceRoot":"","sources":["../../../src/ChordVariantDisplay/models/stateModelFactory.ts"],"names":[],"mappings":";;AAAA,wEAAqE;AACrE,+DAGoC;AACpC,qDAAuC;AACvC,6CAAsD;AACtD,sDAAgE;AAEhE;;;GAGG;AACH,MAAM,iBAAiB,GAAG,CAAC,YAAwC,EAAE,EAAE;IACrE,OAAO,uBAAK;SACT,OAAO,CACN,qBAAqB,EACrB,4CAAqB,EACrB,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,qBAAqB,CAAC;QAC1C;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;QAED;;WAEG;QACH,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;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;AACP,CAAC,CAAA;AAED,0EAA0E;AAE1E,wDAAwD;AAExD,2BAA2B;AAC3B,EAAE;AACF,kBAAe,iBAAiB,CAAA"}

package/dist/LinearVariantDisplay/index.js CHANGED Viewed

@@ -12,6 +12,7 @@ exports.default = (pluginManager) => {
         const configSchema = (0, configSchema_1.default)(pluginManager);
         return new DisplayType_1.default({
             name: 'LinearVariantDisplay',
+            displayName: 'Variant display',
             configSchema,
             stateModel: (0, model_1.default)(configSchema),
             trackType: 'VariantTrack',

package/dist/LinearVariantDisplay/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,kFAA+E;AAC/E,kGAAyE;AACzE,oDAAuC;AACvC,kEAA0C;AAE1C,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;QACjD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,sBAAsB;YAC5B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAiB,EAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,kFAA+E;AAC/E,kGAAyE;AACzE,oDAAuC;AACvC,kEAA0C;AAE1C,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAa,EAAC,aAAa,CAAC,CAAA;QACjD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,sBAAsB;YAC5B,WAAW,EAAE,iBAAiB;YAC9B,YAAY;YACZ,UAAU,EAAE,IAAA,eAAiB,EAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/LinearVariantDisplay/model.d.ts CHANGED Viewed

@@ -130,10 +130,10 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
     reload(): void;
 } & {
     currBpPerPx: number;
+    scrollTop: 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;
 } & {

package/dist/StructuralVariantChordRenderer/Chord.d.ts ADDED Viewed

@@ -0,0 +1,32 @@
+/// <reference types="react" />
+import { Feature } from '@jbrowse/core/util';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export interface Region {
+    end: number;
+    start: number;
+    refName: string;
+    elided?: false;
+}
+export interface ElidedRegion {
+    elided: true;
+    regions: Region[];
+}
+export type AnyRegion = Region | ElidedRegion;
+export interface Block {
+    flipped: boolean;
+    bpPerRadian: number;
+    startRadians: number;
+    region: AnyRegion;
+}
+declare const Chord: ({ feature, blocksForRefs, radius, config, 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;
+}) => JSX.Element | null;
+export default Chord;

package/dist/StructuralVariantChordRenderer/Chord.js ADDED Viewed

@@ -0,0 +1,88 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const mobx_react_1 = require("mobx-react");
+const util_1 = require("@jbrowse/core/util");
+const configuration_1 = require("@jbrowse/core/configuration");
+const vcf_1 = require("@gmod/vcf");
+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;
+    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;
+    // 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 && (0, vcf_1.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 = (0, util_1.polarToCartesian)(radius, startRadians);
+        const endXY = (0, util_1.polarToCartesian)(radius, endRadians);
+        const controlXY = (0, util_1.polarToCartesian)(bezierRadius, (endRadians + startRadians) / 2);
+        const strokeColor = selected
+            ? (0, configuration_1.readConfObject)(config, 'strokeColorSelected', { feature })
+            : (0, configuration_1.readConfObject)(config, 'strokeColor', { feature });
+        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 => {
+                if (endBlock && startBlock) {
+                    onClick(feature, startBlock.region, endBlock.region, evt);
+                }
+            }, onMouseOver: evt => {
+                if (!selected) {
+                    evt.currentTarget.style.stroke = hoverStrokeColor;
+                    evt.currentTarget.style.strokeWidth = '3px';
+                }
+            }, onMouseOut: evt => {
+                if (!selected) {
+                    evt.currentTarget.style.stroke = strokeColor;
+                    evt.currentTarget.style.strokeWidth = '1px';
+                }
+            } }));
+    }
+    return null;
+});
+exports.default = Chord;
+//# sourceMappingURL=Chord.js.map

package/dist/StructuralVariantChordRenderer/Chord.js.map ADDED Viewed

@@ -0,0 +1 @@

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package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts CHANGED Viewed

@@ -1,23 +1,7 @@
 /// <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[];
-}
-type AnyRegion = Region | ElidedRegion;
-interface Block {
-    flipped: boolean;
-    bpPerRadian: number;
-    startRadians: number;
-    region: AnyRegion;
-}
+import { Block, AnyRegion } from './Chord';
 declare function StructuralVariantChords(props: {
     features: Map<string, Feature>;
     radius: number;

package/dist/StructuralVariantChordRenderer/ReactComponent.js CHANGED Viewed

@@ -22,112 +22,30 @@ 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 vcf_1 = require("@gmod/vcf");
-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;
-    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;
-    // 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 && (0, vcf_1.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 = (0, util_1.polarToCartesian)(radius, startRadians);
-        const endXY = (0, util_1.polarToCartesian)(radius, endRadians);
-        const controlXY = (0, util_1.polarToCartesian)(bezierRadius, (endRadians + startRadians) / 2);
-        const strokeColor = selected
-            ? (0, configuration_1.readConfObject)(config, 'strokeColorSelected', { feature })
-            : (0, configuration_1.readConfObject)(config, 'strokeColor', { feature });
-        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 => {
-                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;
-                }
-            } }));
-    }
-    return null;
-});
+// locals
+const Chord_1 = __importDefault(require("./Chord"));
 function StructuralVariantChords(props) {
     const { features, config, displayModel, blockDefinitions, radius, bezierRadius, displayModel: { selectedFeatureId }, onChordClick, } = props;
     // make a map of refName -> blockDefinition
     const blocksForRefsMemo = (0, react_1.useMemo)(() => {
         const blocksForRefs = {};
         blockDefinitions.forEach(block => {
-            const regions = block.region.elided
-                ? block.region.regions
-                : [block.region];
-            regions.forEach(region => {
-                blocksForRefs[region.refName] = block;
-            });
+            ;
+            (block.region.elided ? block.region.regions : [block.region]).forEach(r => (blocksForRefs[r.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_1.default.createElement(Chord, { key: id, feature: feature, config: config, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
+    for (const feature of features.values()) {
+        const id = feature.id();
+        const selected = String(selectedFeatureId) === String(id);
+        chords.push(react_1.default.createElement(Chord_1.default, { 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" },

package/dist/StructuralVariantChordRenderer/ReactComponent.js.map CHANGED Viewed

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

@@ -1,3 +1,3 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const ChordRendererConfigF: (pluginManager: PluginManager) => void;
-export default ChordRendererConfigF;
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/StructuralVariantChordRenderer/index.js CHANGED Viewed

@@ -6,13 +6,13 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const CircularChordRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 const ReactComponent_1 = __importDefault(require("./ReactComponent"));
-const ChordRendererConfigF = (pluginManager) => {
+exports.default = (pluginManager) => {
     pluginManager.addRendererType(() => new CircularChordRendererType_1.default({
         name: 'StructuralVariantChordRenderer',
+        displayName: 'SV chord renderer',
         ReactComponent: ReactComponent_1.default,
         configSchema: configSchema_1.default,
         pluginManager,
     }));
 };
-exports.default = ChordRendererConfigF;
 //# sourceMappingURL=index.js.map

package/dist/StructuralVariantChordRenderer/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/VariantFeatureWidget/BreakendOptionDialog.js CHANGED Viewed

@@ -27,15 +27,16 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
-const ui_1 = require("@jbrowse/core/ui");
 const mui_1 = require("tss-react/mui");
 const mobx_state_tree_1 = require("mobx-state-tree");
+// jbrowse
+const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
+const useStyles = (0, mui_1.makeStyles)()({
     block: {
         display: 'block',
     },
-}));
+});
 function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
     const { classes } = useStyles();
     const [copyTracks, setCopyTracks] = (0, react_1.useState)(true);
@@ -50,14 +51,18 @@ function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
                     const session = (0, util_1.getSession)(model);
                     try {
                         const viewSnapshot = viewType.snapshotFromBreakendFeature(feature, view);
+                        function remapIds(arr) {
+                            return arr.map((v) => ({
+                                ...v,
+                                id: v.trackId + '-' + Math.random(),
+                            }));
+                        }
                         viewSnapshot.views[0].offsetPx -= view.width / 2 + 100;
                         viewSnapshot.views[1].offsetPx -= view.width / 2 + 100;
                         viewSnapshot.featureData = feature;
                         const viewTracks = (0, mobx_state_tree_1.getSnapshot)(view.tracks);
-                        viewSnapshot.views[0].tracks = viewTracks;
-                        viewSnapshot.views[1].tracks = mirrorTracks
-                            ? viewTracks.slice().reverse()
-                            : viewTracks;
+                        viewSnapshot.views[0].tracks = remapIds(viewTracks);
+                        viewSnapshot.views[1].tracks = remapIds(mirrorTracks ? viewTracks.slice().reverse() : viewTracks);
                         session.addView('BreakpointSplitView', viewSnapshot);
                     }
                     catch (e) {

package/dist/VariantFeatureWidget/BreakendOptionDialog.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/VariantTrack/index.js CHANGED Viewed

@@ -11,6 +11,7 @@ exports.default = (pm) => {
         const configSchema = (0, configSchema_1.default)(pm);
         return new TrackType_1.default({
             name: 'VariantTrack',
+            displayName: 'Variant track',
             configSchema,
             stateModel: (0, models_1.createBaseTrackModel)(pm, 'VariantTrack', configSchema),
         });

package/dist/VariantTrack/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VariantTrack/index.ts"],"names":[],"mappings":";;;;;AACA,8FAAqE;AACrE,uEAAiF;AACjF,kEAA0C;AAE1C,kBAAe,CAAC,EAAiB,EAAE,EAAE;IACnC,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,IAAA,sBAAa,EAAC,EAAE,CAAC,CAAA;QACtC,OAAO,IAAI,mBAAS,CAAC;YACnB,IAAI,EAAE,cAAc;YACpB,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAAC,EAAE,EAAE,cAAc,EAAE,YAAY,CAAC;SACnE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VariantTrack/index.ts"],"names":[],"mappings":";;;;;AACA,8FAAqE;AACrE,uEAAiF;AACjF,kEAA0C;AAE1C,kBAAe,CAAC,EAAiB,EAAE,EAAE;IACnC,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,IAAA,sBAAa,EAAC,EAAE,CAAC,CAAA;QACtC,OAAO,IAAI,mBAAS,CAAC;YACnB,IAAI,EAAE,cAAc;YACpB,WAAW,EAAE,eAAe;YAC5B,YAAY;YACZ,UAAU,EAAE,IAAA,6BAAoB,EAAC,EAAE,EAAE,cAAc,EAAE,YAAY,CAAC;SACnE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/VcfAdapter/VcfAdapter.js CHANGED Viewed

@@ -9,6 +9,7 @@ const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const vcf_1 = __importDefault(require("@gmod/vcf"));
+// local
 const VcfFeature_1 = __importDefault(require("../VcfTabixAdapter/VcfFeature"));
 const readVcf = (f) => {
     const header = [];

package/dist/VcfAdapter/VcfAdapter.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAE1D,8EAAoD;AACpD,2DAA6C;AAC7C,oDAA2B;AAE3B,QAAQ;AACR,+EAAsD;AAEtD,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC;SAClB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACJ,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAqB,UAAW,SAAQ,oCAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAE1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAEnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;QAEtC,MAAM,YAAY,GAAG,KAAK;aACvB,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,EAAE,EAAE;;YAChB,MAAM,CAAC,OAAO,EAAE,MAAM,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,AAAD,EAAG,AAAD,EAAG,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7D,MAAM,KAAK,GAAG,CAAC,MAAM,GAAG,CAAC,CAAA;YACzB,MAAM,GAAG,GAAG,CAAC,CAAC,CAAA,MAAA,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,0CAAG,CAAC,EAAE,IAAI,EAAE,KAAI,KAAK,GAAG,GAAG,CAAC,MAAM,CAAC,CAAA;YACxE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,CAAA;QAC1C,CAAC,CAAC;aACD,MAAM,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE;YACnB,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAA;YACvB,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gBACb,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,uBAAY,EAAE,CAAA;aAC9B;YACD,GAAG,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;YAC1C,OAAO,GAAG,CAAA;QACZ,CAAC,EAAE,EAAkC,CAAC,CAAA;QAExC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACzC,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAiB,EAAE;QAC1C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC3C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;gBACtC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;gBACnD,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;gBAC1C,MAAA,YAAY,CAAC,OAAO,CAAC,0CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CACtD,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAU,CAAC;oBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;oBACjC,MAAM;oBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,EAAE,EAAE;iBACzB,CAAC,CACH,CACF,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AA1FjC,6BA2FC;AA1Fe,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA"}

package/dist/VcfAdapter/index.js CHANGED Viewed

@@ -31,6 +31,7 @@ const configSchema_1 = __importDefault(require("./configSchema"));
 exports.default = (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'VcfAdapter',
+        displayName: 'VCF adapter',
         configSchema: configSchema_1.default,
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./VcfAdapter'))).then(r => r.default),
     }));

package/dist/VcfAdapter/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,YAAY;QAClB,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,cAAc,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACnE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,YAAY;QAClB,WAAW,EAAE,aAAa;QAC1B,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,cAAc,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACnE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/VcfTabixAdapter/VcfTabixAdapter.js CHANGED Viewed

@@ -9,23 +9,20 @@ const util_1 = require("@jbrowse/core/util");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const tabix_1 = require("@gmod/tabix");
 const vcf_1 = __importDefault(require("@gmod/vcf"));
-const configuration_1 = require("@jbrowse/core/configuration");
+// local
 const VcfFeature_1 = __importDefault(require("./VcfFeature"));
 class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configurePre() {
-        const vcfGzLocation = (0, configuration_1.readConfObject)(this.config, 'vcfGzLocation');
-        const location = (0, configuration_1.readConfObject)(this.config, ['index', 'location']);
-        const indexType = (0, configuration_1.readConfObject)(this.config, ['index', 'indexType']);
-        const filehandle = (0, io_1.openLocation)(vcfGzLocation, this.pluginManager);
+        const pm = this.pluginManager;
+        const vcfGzLocation = this.getConf('vcfGzLocation');
+        const location = this.getConf(['index', 'location']);
+        const indexType = this.getConf(['index', 'indexType']);
+        const filehandle = (0, io_1.openLocation)(vcfGzLocation, pm);
         const isCSI = indexType === 'CSI';
         const vcf = new tabix_1.TabixIndexedFile({
             filehandle,
-            csiFilehandle: isCSI
-                ? (0, io_1.openLocation)(location, this.pluginManager)
-                : undefined,
-            tbiFilehandle: !isCSI
-                ? (0, io_1.openLocation)(location, this.pluginManager)
-                : undefined,
+            csiFilehandle: isCSI ? (0, io_1.openLocation)(location, pm) : undefined,
+            tbiFilehandle: !isCSI ? (0, io_1.openLocation)(location, pm) : undefined,
             chunkCacheSize: 50 * 2 ** 20,
             chunkSizeLimit: 1000000000,
         });

package/dist/VcfTabixAdapter/VcfTabixAdapter.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/VcfTabixAdapter/index.js CHANGED Viewed

@@ -34,6 +34,7 @@ Object.defineProperty(exports, "configSchema", { enumerable: true, get: function
 exports.default = (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'VcfTabixAdapter',
+        displayName: 'VCF tabix adapter',
         configSchema: configSchema_1.default,
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./VcfTabixAdapter'))).then(r => r.default),
     }));

package/dist/VcfTabixAdapter/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAyC;AAEzC,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB;AAEhC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,iBAAiB;QACvB,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,mBAAmB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACxE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AACzE,kEAAyC;AAEzC,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB;AAEhC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,iBAAiB;QACvB,WAAW,EAAE,mBAAmB;QAChC,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,mBAAmB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACxE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/ChordVariantDisplay/index.js CHANGED Viewed

@@ -8,6 +8,7 @@ export default (pluginManager) => {
         const stateModel = stateModelF(configSchema);
         return new DisplayType({
             name: 'ChordVariantDisplay',
+            displayName: 'Chord variant display',
             configSchema,
             stateModel,
             trackType: 'VariantTrack',