npm - @jbrowse/plugin-variants - Versions diffs - 2.2.1 → 2.3.0 - Mend

@jbrowse/plugin-variants 2.2.1 → 2.3.0

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 (79) hide show

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"VcfTabixAdapter.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfTabixAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAMhD,8CAAoD;AACpD,6CAAoD;AACpD,kDAA0D;AAE1D,uCAA8C;AAC9C,oDAAiC;AAIjC,QAAQ;AACR,8DAAqC;AAErC,eAAqB,SAAQ,oCAAsB;IAOzC,KAAK,CAAC,YAAY;QACxB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAC,CAAA;QACnD,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QACpD,MAAM,SAAS,GAAG,IAAI,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAEtD,MAAM,UAAU,GAAG,IAAA,iBAAY,EAAC,aAA6B,EAAE,EAAE,CAAC,CAAA;QAClE,MAAM,KAAK,GAAG,SAAS,KAAK,KAAK,CAAA;QACjC,MAAM,GAAG,GAAG,IAAI,wBAAgB,CAAC;YAC/B,UAAU;YACV,aAAa,EAAE,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC7D,aAAa,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,IAAA,iBAAY,EAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS;YAC9D,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;YAC5B,cAAc,EAAE,UAAU;SAC3B,CAAC,CAAA;QAEF,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,SAAS,EAAE,CAAA;QACpC,OAAO;YACL,UAAU;YACV,GAAG;YACH,MAAM,EAAE,IAAI,aAAS,CAAC,EAAE,MAAM,EAAE,CAAC;SAClC,CAAA;IACH,CAAC;IAES,KAAK,CAAC,SAAS;QACvB,IAAI,CAAC,IAAI,CAAC,UAAU,EAAE;YACpB,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAC9C,IAAI,CAAC,UAAU,GAAG,SAAS,CAAA;gBAC3B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,UAAU,CAAA;IACxB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IAC5C,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACtC,OAAO,GAAG,CAAC,SAAS,EAAE,CAAA;IACxB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QACzC,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAEM,WAAW,CAAC,KAAuB,EAAE,OAAoB,EAAE;QAChE,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,KAAK,CAAA;YACrC,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC9C,MAAM,GAAG,CAAC,QAAQ,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE;gBACtC,YAAY,EAAE,CAAC,IAAI,EAAE,UAAU,EAAE,EAAE;oBACjC,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAU,CAAC;wBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC;wBAC/B,MAAM;wBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,QAAQ,UAAU,EAAE;qBACnC,CAAC,CACH,CAAA;gBACH,CAAC;gBACD,GAAG,IAAI;aACR,CAAC,CAAA;YACF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED;;;;;;;;;;;;;OAaG;IACI,4BAA4B,CACjC,OAAiB,EACjB,OAAoB,EAAE;QAEtB,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAE,QAA2B,EAAE,EAAE;YACrE,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAEtC,aAAa;YACb,MAAM,KAAK,GAAG,MAAM,IAAA,sBAAe,EAAC,OAAO,EAAE,GAAG,CAAC,KAAK,CAAC,CAAA;YACvD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,IAAI,GAAG,MAAM,UAAU,CAAC,IAAI,EAAE,CAAA;YACpC,IAAI,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,GAAG,CAAC,CAAA;YAC/C,IAAI,GAAG,GAAG,GAAG,EAAE;gBACb,yDAAyD;gBACzD,GAAG,GAAG,GAAG,CAAA;aACV;YACD,IAAI,GAAG,GAAG,EAAE,EAAE;gBACZ,OAAO,CAAC,IAAI,CACV,yCAAyC,GAAG,6DAA6D,CAC1G,CAAA;aACF;YACD,KAAK,CAAC,4BAA4B,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;QACvE,CAAC,CAAC,CAAA;IACJ,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD;AApHD,4BAoHC"}

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',

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

	@@ -1 +1 @@
1	- {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChordVariantDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,yBAAyB,EAAE,MAAM,+BAA+B,CAAA;AACzE,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,aAAa,MAAM,uBAAuB,CAAA;AACjD,OAAO,WAAW,MAAM,4BAA4B,CAAA;AAEpD,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QACjD,MAAM,UAAU,GAAG,WAAW,CAAC,YAAY,CAAC,CAAA;QAC5C,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,YAAY;YACZ,UAAU;YACV,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,cAAc;YACxB,cAAc,EAAE,yBAAyB;SAC1C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChordVariantDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,yBAAyB,EAAE,MAAM,+BAA+B,CAAA;AACzE,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,aAAa,MAAM,uBAAuB,CAAA;AACjD,OAAO,WAAW,MAAM,4BAA4B,CAAA;AAEpD,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QACjD,MAAM,UAAU,GAAG,WAAW,CAAC,YAAY,CAAC,CAAA;QAC5C,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,qBAAqB;YAC3B,WAAW,EAAE,uBAAuB;YACpC,YAAY;YACZ,UAAU;YACV,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,cAAc;YACxB,cAAc,EAAE,yBAAyB;SAC1C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

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

@@ -37,8 +37,7 @@ 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/esm/ChordVariantDisplay/models/stateModelFactory.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/LinearVariantDisplay/index.js CHANGED Viewed

@@ -7,6 +7,7 @@ export default (pluginManager) => {
         const configSchema = configSchemaF(pluginManager);
         return new DisplayType({
             name: 'LinearVariantDisplay',
+            displayName: 'Variant display',
             configSchema,
             stateModel: stateModelFactory(configSchema),
             trackType: 'VariantTrack',

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,0BAA0B,EAAE,MAAM,oCAAoC,CAAA;AAC/E,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,iBAAiB,MAAM,SAAS,CAAA;AACvC,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,aAAa,CAAC,aAAa,CAAC,CAAA;QACjD,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,sBAAsB;YAC5B,WAAW,EAAE,iBAAiB;YAC9B,YAAY;YACZ,UAAU,EAAE,iBAAiB,CAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,0BAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

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

@@ -61,12 +61,8 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">; /**
-     * #property
-     */
-    trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
-     * #property
-     */
+    type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
+    trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
@@ -134,10 +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/esm/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/esm/StructuralVariantChordRenderer/Chord.js ADDED Viewed

@@ -0,0 +1,83 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import { polarToCartesian } from '@jbrowse/core/util';
+import { readConfObject, } from '@jbrowse/core/configuration';
+import { parseBreakend } from '@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 = observer(function Chord({ feature, blocksForRefs, radius, config, bezierRadius, selected, onClick, }) {
+    var _a, _b, _c, _d, _e;
+    // find the blocks that our start and end points belong to
+    const startBlock = blocksForRefs[feature.get('refName')];
+    if (!startBlock) {
+        return null;
+    }
+    let svType;
+    if (feature.get('INFO')) {
+        ;
+        [svType] = feature.get('INFO').SVTYPE || [];
+    }
+    else if (feature.get('mate')) {
+        svType = 'mate';
+    }
+    let endPosition;
+    let endBlock;
+    const alt = (_a = feature.get('ALT')) === null || _a === void 0 ? void 0 : _a[0];
+    const bnd = alt && parseBreakend(alt);
+    if (bnd) {
+        // VCF BND
+        const matePosition = bnd.MatePosition.split(':');
+        endPosition = +matePosition[1];
+        endBlock = blocksForRefs[matePosition[0]];
+    }
+    else if (alt === '<TRA>') {
+        // VCF TRA
+        const chr2 = (_c = (_b = feature.get('INFO')) === null || _b === void 0 ? void 0 : _b.CHR2) === null || _c === void 0 ? void 0 : _c[0];
+        const end = (_e = (_d = feature.get('INFO')) === null || _d === void 0 ? void 0 : _d.END) === null || _e === void 0 ? void 0 : _e[0];
+        endPosition = parseInt(end, 10);
+        endBlock = blocksForRefs[chr2];
+    }
+    else if (svType === 'mate') {
+        // generic simplefeatures arcs
+        const mate = feature.get('mate');
+        const chr2 = mate.refName;
+        endPosition = mate.start;
+        endBlock = blocksForRefs[chr2];
+    }
+    if (endBlock) {
+        const startPos = feature.get('start');
+        const startRadians = bpToRadians(startBlock, startPos);
+        const endRadians = bpToRadians(endBlock, endPosition);
+        const startXY = polarToCartesian(radius, startRadians);
+        const endXY = polarToCartesian(radius, endRadians);
+        const controlXY = polarToCartesian(bezierRadius, (endRadians + startRadians) / 2);
+        const strokeColor = selected
+            ? readConfObject(config, 'strokeColorSelected', { feature })
+            : readConfObject(config, 'strokeColor', { feature });
+        const hoverStrokeColor = readConfObject(config, 'strokeColorHover', {
+            feature,
+        });
+        return (React.createElement("path", { "data-testid": `chord-${feature.id()}`, d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), style: { stroke: strokeColor }, onClick: evt => {
+                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;
+});
+export default Chord;
+//# sourceMappingURL=Chord.js.map

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

@@ -0,0 +1 @@

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package/esm/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/esm/StructuralVariantChordRenderer/ReactComponent.js CHANGED Viewed

@@ -1,107 +1,22 @@
 import React, { useMemo } from 'react';
 import { observer } from 'mobx-react';
-import { polarToCartesian } from '@jbrowse/core/util';
-import { readConfObject, } from '@jbrowse/core/configuration';
-import { parseBreakend } from '@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 = observer(function Chord({ feature, blocksForRefs, radius, config, bezierRadius, selected, onClick, }) {
-    var _a, _b, _c, _d, _e;
-    // find the blocks that our start and end points belong to
-    const startBlock = blocksForRefs[feature.get('refName')];
-    if (!startBlock) {
-        return null;
-    }
-    let svType;
-    if (feature.get('INFO')) {
-        ;
-        [svType] = feature.get('INFO').SVTYPE || [];
-    }
-    else if (feature.get('mate')) {
-        svType = 'mate';
-    }
-    let endPosition;
-    let endBlock;
-    const alt = (_a = feature.get('ALT')) === null || _a === void 0 ? void 0 : _a[0];
-    const bnd = alt && parseBreakend(alt);
-    if (bnd) {
-        // VCF BND
-        const matePosition = bnd.MatePosition.split(':');
-        endPosition = +matePosition[1];
-        endBlock = blocksForRefs[matePosition[0]];
-    }
-    else if (alt === '<TRA>') {
-        // VCF TRA
-        const chr2 = (_c = (_b = feature.get('INFO')) === null || _b === void 0 ? void 0 : _b.CHR2) === null || _c === void 0 ? void 0 : _c[0];
-        const end = (_e = (_d = feature.get('INFO')) === null || _d === void 0 ? void 0 : _d.END) === null || _e === void 0 ? void 0 : _e[0];
-        endPosition = parseInt(end, 10);
-        endBlock = blocksForRefs[chr2];
-    }
-    else if (svType === 'mate') {
-        // generic simplefeatures arcs
-        const mate = feature.get('mate');
-        const chr2 = mate.refName;
-        endPosition = mate.start;
-        endBlock = blocksForRefs[chr2];
-    }
-    if (endBlock) {
-        const startPos = feature.get('start');
-        const startRadians = bpToRadians(startBlock, startPos);
-        const endRadians = bpToRadians(endBlock, endPosition);
-        const startXY = polarToCartesian(radius, startRadians);
-        const endXY = polarToCartesian(radius, endRadians);
-        const controlXY = polarToCartesian(bezierRadius, (endRadians + startRadians) / 2);
-        const strokeColor = selected
-            ? readConfObject(config, 'strokeColorSelected', { feature })
-            : readConfObject(config, 'strokeColor', { feature });
-        const hoverStrokeColor = readConfObject(config, 'strokeColorHover', {
-            feature,
-        });
-        return (React.createElement("path", { "data-testid": `chord-${feature.id()}`, d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), style: { stroke: strokeColor }, onClick: evt => {
-                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
+import Chord from './Chord';
 function StructuralVariantChords(props) {
     const { features, config, displayModel, blockDefinitions, radius, bezierRadius, displayModel: { selectedFeatureId }, onChordClick, } = props;
     // make a map of refName -> blockDefinition
     const blocksForRefsMemo = useMemo(() => {
         const blocksForRefs = {};
         blockDefinitions.forEach(block => {
-            const regions = block.region.elided
-                ? block.region.regions
-                : [block.region];
-            regions.forEach(region => {
-                blocksForRefs[region.refName] = block;
-            });
+            ;
+            (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());
+    for (const feature of features.values()) {
+        const id = feature.id();
+        const selected = String(selectedFeatureId) === String(id);
         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}`;

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	@@ -1 +1 @@
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package/esm/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/esm/StructuralVariantChordRenderer/index.js CHANGED Viewed

@@ -1,13 +1,13 @@
 import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType';
 import configSchema from './configSchema';
 import ReactComponent from './ReactComponent';
-const ChordRendererConfigF = (pluginManager) => {
+export default (pluginManager) => {
     pluginManager.addRendererType(() => new ChordRendererType({
         name: 'StructuralVariantChordRenderer',
+        displayName: 'SV chord renderer',
         ReactComponent,
         configSchema,
         pluginManager,
     }));
 };
-export default ChordRendererConfigF;
 //# sourceMappingURL=index.js.map

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

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

@@ -1,32 +1,22 @@
 /* eslint-disable @typescript-eslint/no-explicit-any */
 import React, { useState } from 'react';
 import { observer } from 'mobx-react';
-import { Button, Checkbox, Dialog, DialogActions, DialogContent, DialogTitle, Divider, FormControlLabel, IconButton, } from '@mui/material';
+import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
-import CloseIcon from '@mui/icons-material/Close';
 import { getSnapshot } from 'mobx-state-tree';
+// jbrowse
+import { Dialog } from '@jbrowse/core/ui';
 import { getSession } from '@jbrowse/core/util';
-const useStyles = makeStyles()(theme => ({
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
+const useStyles = makeStyles()({
     block: {
         display: 'block',
     },
-}));
+});
 function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
     const { classes } = useStyles();
     const [copyTracks, setCopyTracks] = useState(true);
     const [mirrorTracks, setMirrorTracks] = useState(true);
-    return (React.createElement(Dialog, { open: true, onClose: handleClose },
-        React.createElement(DialogTitle, null,
-            "Breakpoint split view options",
-            handleClose ? (React.createElement(IconButton, { className: classes.closeButton, onClick: () => handleClose() },
-                React.createElement(CloseIcon, null))) : null),
-        React.createElement(Divider, null),
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Breakpoint split view options" },
         React.createElement(DialogContent, null,
             React.createElement(FormControlLabel, { className: classes.block, control: React.createElement(Checkbox, { checked: copyTracks, onChange: () => setCopyTracks(val => !val) }), label: "Copy tracks into the new view" }),
             React.createElement(FormControlLabel, { className: classes.block, control: React.createElement(Checkbox, { checked: mirrorTracks, onChange: () => setMirrorTracks(val => !val) }), label: "Mirror tracks vertically in vertically stacked view" })),
@@ -36,14 +26,18 @@ function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
                     const session = 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 = 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/esm/VariantFeatureWidget/BreakendOptionDialog.js.map CHANGED Viewed

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

@@ -6,6 +6,7 @@ export default (pm) => {
         const configSchema = configSchemaF(pm);
         return new TrackType({
             name: 'VariantTrack',
+            displayName: 'Variant track',
             configSchema,
             stateModel: createBaseTrackModel(pm, 'VariantTrack', configSchema),
         });

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/VariantTrack/index.ts"],"names":[],"mappings":"AACA,OAAO,SAAS,MAAM,+CAA+C,CAAA;AACrE,OAAO,EAAE,oBAAoB,EAAE,MAAM,4CAA4C,CAAA;AACjF,OAAO,aAAa,MAAM,gBAAgB,CAAA;AAE1C,eAAe,CAAC,EAAiB,EAAE,EAAE;IACnC,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,aAAa,CAAC,EAAE,CAAC,CAAA;QACtC,OAAO,IAAI,SAAS,CAAC;YACnB,IAAI,EAAE,cAAc;YACpB,WAAW,EAAE,eAAe;YAC5B,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAAC,EAAE,EAAE,cAAc,EAAE,YAAY,CAAC;SACnE,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/esm/VcfAdapter/VcfAdapter.js CHANGED Viewed

@@ -4,6 +4,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import IntervalTree from '@flatten-js/interval-tree';
 import { unzip } from '@gmod/bgzf-filehandle';
 import VCF from '@gmod/vcf';
+// local
 import VcfFeature from '../VcfTabixAdapter/VcfFeature';
 const readVcf = (f) => {
     const header = [];

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

	@@ -1 +1 @@
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package/esm/VcfAdapter/index.js CHANGED Viewed

@@ -3,6 +3,7 @@ import configSchema from './configSchema';
 export default (pluginManager) => {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'VcfAdapter',
+        displayName: 'VCF adapter',
         configSchema,
         getAdapterClass: () => import('./VcfAdapter').then(r => r.default),
     }));

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

	@@ -1 +1 @@
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