@jbrowse/plugin-variants 2.1.4 → 2.1.6
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.
- package/dist/ChordVariantDisplay/models/ChordVariantDisplay.d.ts +7 -5
- package/dist/ChordVariantDisplay/models/ChordVariantDisplay.js +2 -1
- package/dist/ChordVariantDisplay/models/ChordVariantDisplay.js.map +1 -1
- package/dist/LinearVariantDisplay/model.d.ts +12 -4
- package/dist/LinearVariantDisplay/model.js +7 -6
- package/dist/LinearVariantDisplay/model.js.map +1 -1
- package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts +32 -22
- package/dist/StructuralVariantChordRenderer/ReactComponent.js +11 -25
- package/dist/StructuralVariantChordRenderer/ReactComponent.js.map +1 -1
- package/dist/StructuralVariantChordRenderer/index.d.ts +3 -2
- package/dist/StructuralVariantChordRenderer/index.js +1 -1
- package/dist/StructuralVariantChordRenderer/index.js.map +1 -1
- package/dist/VariantFeatureWidget/BreakendPanel.js +1 -2
- package/dist/VariantFeatureWidget/BreakendPanel.js.map +1 -1
- package/dist/VariantFeatureWidget/index.d.ts +7 -0
- package/dist/VcfAdapter/VcfAdapter.js +1 -1
- package/dist/VcfAdapter/VcfAdapter.js.map +1 -1
- package/dist/VcfTabixAdapter/VcfTabixAdapter.js.map +1 -1
- package/esm/ChordVariantDisplay/models/ChordVariantDisplay.d.ts +7 -5
- package/esm/ChordVariantDisplay/models/ChordVariantDisplay.js +2 -1
- package/esm/ChordVariantDisplay/models/ChordVariantDisplay.js.map +1 -1
- package/esm/LinearVariantDisplay/model.d.ts +12 -4
- package/esm/LinearVariantDisplay/model.js +7 -6
- package/esm/LinearVariantDisplay/model.js.map +1 -1
- package/esm/StructuralVariantChordRenderer/ReactComponent.d.ts +32 -22
- package/esm/StructuralVariantChordRenderer/ReactComponent.js +13 -24
- package/esm/StructuralVariantChordRenderer/ReactComponent.js.map +1 -1
- package/esm/StructuralVariantChordRenderer/index.d.ts +3 -2
- package/esm/StructuralVariantChordRenderer/index.js +1 -1
- package/esm/StructuralVariantChordRenderer/index.js.map +1 -1
- package/esm/VariantFeatureWidget/BreakendPanel.js +1 -2
- package/esm/VariantFeatureWidget/BreakendPanel.js.map +1 -1
- package/esm/VariantFeatureWidget/index.d.ts +7 -0
- package/esm/VcfAdapter/VcfAdapter.js +1 -1
- package/esm/VcfAdapter/VcfAdapter.js.map +1 -1
- package/esm/VcfTabixAdapter/VcfTabixAdapter.js.map +1 -1
- package/package.json +2 -2
- package/src/ChordVariantDisplay/models/{ChordVariantDisplay.js → ChordVariantDisplay.ts} +5 -2
- package/src/LinearVariantDisplay/model.ts +13 -10
- package/src/StructuralVariantChordRenderer/{ReactComponent.js → ReactComponent.tsx} +67 -34
- package/src/StructuralVariantChordRenderer/{index.js → index.ts} +3 -1
- package/src/VariantFeatureWidget/BreakendPanel.tsx +1 -2
- package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.js.snap +39 -0
- package/src/VcfAdapter/VcfAdapter.ts +1 -1
- package/src/VcfTabixAdapter/VcfTabixAdapter.ts +1 -1
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const bezierRadius: PropTypes.Validator<number>;
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const selectedFeatureId: PropTypes.Requireable<string>;
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const onChordClick: PropTypes.Requireable<NonNullable<string | ((...args: any[]) => any) | null | undefined>>;
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}
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namespace defaultProps {
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const displayModel_1: undefined;
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export { displayModel_1 as displayModel };
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const selectedFeatureId_1: string;
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export { selectedFeatureId_1 as selectedFeatureId };
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const onChordClick_1: undefined;
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export { onChordClick_1 as onChordClick };
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}
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/// <reference types="react" />
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import { Feature } from '@jbrowse/core/util';
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import { AnyConfigurationModel } from '@jbrowse/core/configuration';
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interface Region {
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end: number;
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start: number;
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refName: string;
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elided?: false;
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}
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interface ElidedRegion {
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elided: true;
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regions: Region[];
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}
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declare type AnyRegion = Region | ElidedRegion;
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interface Block {
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flipped: boolean;
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bpPerRadian: number;
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startRadians: number;
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region: AnyRegion;
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}
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declare function StructuralVariantChords(props: {
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features: Map<string, Feature>;
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radius: number;
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config: AnyConfigurationModel;
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displayModel: {
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id: string;
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selectedFeatureId: string;
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};
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blockDefinitions: Block[];
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bezierRadius: number;
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onChordClick: (feature: Feature, reg: AnyRegion, endBlock: AnyRegion, evt: unknown) => void;
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}): JSX.Element;
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declare const _default: typeof StructuralVariantChords;
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export default _default;
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import PropTypes from "prop-types";
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import React from "react";
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import React, { useMemo } from 'react';
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import { observer
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import { observer } from 'mobx-react';
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import { polarToCartesian } from '@jbrowse/core/util';
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import { readConfObject } from '@jbrowse/core/configuration';
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import { PropTypes as CommonPropTypes } from '@jbrowse/core/util/types/mst';
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import { readConfObject, } from '@jbrowse/core/configuration';
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import { parseBreakend } from '@gmod/vcf';
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import PropTypes from 'prop-types';
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function bpToRadians(block, pos) {
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const blockStart = block.region.elided ? 0 : block.region.start;
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const blockEnd = block.region.elided ? 0 : block.region.end;
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const bpOffset = block.flipped ? blockEnd - pos : pos - blockStart;
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return radians;
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return bpOffset / block.bpPerRadian + block.startRadians;
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}
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const Chord = observer(function Chord({ feature, blocksForRefs, radius, config, bezierRadius, selected, onClick, }) {
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var _a, _b, _c, _d, _e;
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@@ -64,14 +61,22 @@ const Chord = observer(function Chord({ feature, blocksForRefs, radius, config,
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const hoverStrokeColor = readConfObject(config, 'strokeColorHover', {
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feature,
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});
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return (React.createElement("path", { "data-testid": `chord-${feature.id()}`, d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), style: { stroke: strokeColor }, onClick: evt =>
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return (React.createElement("path", { "data-testid": `chord-${feature.id()}`, d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), style: { stroke: strokeColor }, onClick: evt => {
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if (endBlock && startBlock) {
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onClick(feature, startBlock.region, endBlock.region, evt);
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}
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}, onMouseOver: evt => {
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if (!selected) {
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// @ts-ignore
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evt.target.style.stroke = hoverStrokeColor;
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// @ts-ignore
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evt.target.style.strokeWidth = 3;
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}
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}, onMouseOut: evt => {
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if (!selected) {
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evt.target.style.stroke = strokeColor;
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evt.target.style.strokeWidth = 1;
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}
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} }));
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const chords = [];
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for (const [id, feature] of features) {
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const selected = String(selectedFeatureId) === String(feature.id());
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chords.push(React.createElement(Chord, { key: id, feature: feature, config: config,
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chords.push(React.createElement(Chord, { key: id, feature: feature, config: config, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }));
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}
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const trackStyleId = `chords-${displayModel.id}`;
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return (React.createElement("g", { id: trackStyleId, "data-testid": "structuralVariantChordRenderer" },
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} }),
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chords));
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}
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StructuralVariantChords.propTypes = {
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features: PropTypes.instanceOf(Map).isRequired,
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config: CommonPropTypes.ConfigSchema.isRequired,
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displayModel: MobxPropTypes.objectOrObservableObject,
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blockDefinitions: PropTypes.arrayOf(MobxPropTypes.objectOrObservableObject)
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.isRequired,
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radius: PropTypes.number.isRequired,
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bezierRadius: PropTypes.number.isRequired,
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selectedFeatureId: PropTypes.string,
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onChordClick: PropTypes.oneOfType([PropTypes.func, PropTypes.string]),
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};
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StructuralVariantChords.defaultProps = {
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displayModel: undefined,
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selectedFeatureId: '',
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onChordClick: undefined,
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};
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export default observer(StructuralVariantChords);
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//# sourceMappingURL=ReactComponent.js.map
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{"version":3,"file":"ReactComponent.js","sourceRoot":"","sources":["../../src/StructuralVariantChordRenderer/ReactComponent.
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{"version":3,"file":"ReactComponent.js","sourceRoot":"","sources":["../../src/StructuralVariantChordRenderer/ReactComponent.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,OAAO,CAAA;AACtC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,gBAAgB,EAAW,MAAM,oBAAoB,CAAA;AAC9D,OAAO,EAEL,cAAc,GACf,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,aAAa,EAAE,MAAM,WAAW,CAAA;AAuBzC,SAAS,WAAW,CAAC,KAAY,EAAE,GAAW;IAC5C,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAA;IAC/D,MAAM,QAAQ,GAAG,KAAK,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,GAAG,CAAA;IAC3D,MAAM,QAAQ,GAAG,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,QAAQ,GAAG,GAAG,CAAC,CAAC,CAAC,GAAG,GAAG,UAAU,CAAA;IAClE,OAAO,QAAQ,GAAG,KAAK,CAAC,WAAW,GAAG,KAAK,CAAC,YAAY,CAAA;AAC1D,CAAC;AAED,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,KAAK,CAAC,EACpC,OAAO,EACP,aAAa,EACb,MAAM,EACN,MAAM,EACN,YAAY,EACZ,QAAQ,EACR,OAAO,GAcR;;IACC,0DAA0D;IAC1D,MAAM,UAAU,GAAG,aAAa,CAAC,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,CAAA;IACxD,IAAI,CAAC,UAAU,EAAE;QACf,OAAO,IAAI,CAAA;KACZ;IACD,IAAI,MAAM,CAAA;IACV,IAAI,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;QACvB,CAAC;QAAA,CAAC,MAAM,CAAC,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,MAAM,IAAI,EAAE,CAAA;KAC7C;SAAM,IAAI,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;QAC9B,MAAM,GAAG,MAAM,CAAA;KAChB;IACD,IAAI,WAAW,CAAA;IACf,IAAI,QAA2B,CAAA;IAC/B,MAAM,GAAG,GAAG,MAAA,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,0CAAG,CAAC,CAAC,CAAA;IACnC,MAAM,GAAG,GAAG,GAAG,IAAI,aAAa,CAAC,GAAG,CAAC,CAAA;IACrC,IAAI,GAAG,EAAE;QACP,UAAU;QACV,MAAM,YAAY,GAAG,GAAG,CAAC,YAAY,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAChD,WAAW,GAAG,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;QAC9B,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,CAAA;KAC1C;SAAM,IAAI,GAAG,KAAK,OAAO,EAAE;QAC1B,UAAU;QACV,MAAM,IAAI,GAAG,MAAA,MAAA,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,0CAAE,IAAI,0CAAG,CAAC,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,MAAA,MAAA,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,0CAAE,GAAG,0CAAG,CAAC,CAAC,CAAA;QACzC,WAAW,GAAG,QAAQ,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;QAC/B,QAAQ,GAAG,aAAa,CAAC,IAAI,CAAC,CAAA;KAC/B;SAAM,IAAI,MAAM,KAAK,MAAM,EAAE;QAC5B,8BAA8B;QAC9B,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;QAChC,MAAM,IAAI,GAAG,IAAI,CAAC,OAAO,CAAA;QACzB,WAAW,GAAG,IAAI,CAAC,KAAK,CAAA;QACxB,QAAQ,GAAG,aAAa,CAAC,IAAI,CAAC,CAAA;KAC/B;IAED,IAAI,QAAQ,EAAE;QACZ,MAAM,QAAQ,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QACrC,MAAM,YAAY,GAAG,WAAW,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QACtD,MAAM,UAAU,GAAG,WAAW,CAAC,QAAQ,EAAE,WAAW,CAAC,CAAA;QACrD,MAAM,OAAO,GAAG,gBAAgB,CAAC,MAAM,EAAE,YAAY,CAAC,CAAA;QACtD,MAAM,KAAK,GAAG,gBAAgB,CAAC,MAAM,EAAE,UAAU,CAAC,CAAA;QAClD,MAAM,SAAS,GAAG,gBAAgB,CAChC,YAAY,EACZ,CAAC,UAAU,GAAG,YAAY,CAAC,GAAG,CAAC,CAChC,CAAA;QAED,MAAM,WAAW,GAAG,QAAQ;YAC1B,CAAC,CAAC,cAAc,CAAC,MAAM,EAAE,qBAAqB,EAAE,EAAE,OAAO,EAAE,CAAC;YAC5D,CAAC,CAAC,cAAc,CAAC,MAAM,EAAE,aAAa,EAAE,EAAE,OAAO,EAAE,CAAC,CAAA;QAEtD,MAAM,gBAAgB,GAAG,cAAc,CAAC,MAAM,EAAE,kBAAkB,EAAE;YAClE,OAAO;SACR,CAAC,CAAA;QACF,OAAO,CACL,6CACe,SAAS,OAAO,CAAC,EAAE,EAAE,EAAE,EACpC,CAAC,EAAE,CAAC,GAAG,EAAE,GAAG,OAAO,EAAE,GAAG,EAAE,GAAG,SAAS,EAAE,GAAG,KAAK,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAC3D,KAAK,EAAE,EAAE,MAAM,EAAE,WAAW,EAAE,EAC9B,OAAO,EAAE,GAAG,CAAC,EAAE;gBACb,IAAI,QAAQ,IAAI,UAAU,EAAE;oBAC1B,OAAO,CAAC,OAAO,EAAE,UAAU,CAAC,MAAM,EAAE,QAAQ,CAAC,MAAM,EAAE,GAAG,CAAC,CAAA;iBAC1D;YACH,CAAC,EACD,WAAW,EAAE,GAAG,CAAC,EAAE;gBACjB,IAAI,CAAC,QAAQ,EAAE;oBACb,aAAa;oBACb,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,GAAG,gBAAgB,CAAA;oBAC1C,aAAa;oBACb,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,WAAW,GAAG,CAAC,CAAA;iBACjC;YACH,CAAC,EACD,UAAU,EAAE,GAAG,CAAC,EAAE;gBAChB,IAAI,CAAC,QAAQ,EAAE;oBACb,aAAa;oBACb,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,GAAG,WAAW,CAAA;oBACrC,aAAa;oBACb,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,WAAW,GAAG,CAAC,CAAA;iBACjC;YACH,CAAC,GACD,CACH,CAAA;KACF;IAED,OAAO,IAAI,CAAA;AACb,CAAC,CAAC,CAAA;AAEF,SAAS,uBAAuB,CAAC,KAahC;IACC,MAAM,EACJ,QAAQ,EACR,MAAM,EACN,YAAY,EACZ,gBAAgB,EAChB,MAAM,EACN,YAAY,EACZ,YAAY,EAAE,EAAE,iBAAiB,EAAE,EACnC,YAAY,GACb,GAAG,KAAK,CAAA;IACT,2CAA2C;IAC3C,MAAM,iBAAiB,GAAG,OAAO,CAAC,GAAG,EAAE;QACrC,MAAM,aAAa,GAAG,EAA8B,CAAA;QACpD,gBAAgB,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;YAC/B,MAAM,OAAO,GAAG,KAAK,CAAC,MAAM,CAAC,MAAM;gBACjC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,OAAO;gBACtB,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;YAClB,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;gBACvB,aAAa,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;YACvC,CAAC,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;QACF,OAAO,aAAa,CAAA;IACtB,CAAC,EAAE,CAAC,gBAAgB,CAAC,CAAC,CAAA;IACtB,6BAA6B;IAC7B,MAAM,MAAM,GAAG,EAAE,CAAA;IACjB,KAAK,MAAM,CAAC,EAAE,EAAE,OAAO,CAAC,IAAI,QAAQ,EAAE;QACpC,MAAM,QAAQ,GAAG,MAAM,CAAC,iBAAiB,CAAC,KAAK,MAAM,CAAC,OAAO,CAAC,EAAE,EAAE,CAAC,CAAA;QACnE,MAAM,CAAC,IAAI,CACT,oBAAC,KAAK,IACJ,GAAG,EAAE,EAAE,EACP,OAAO,EAAE,OAAO,EAChB,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,YAAY,EAC1B,aAAa,EAAE,iBAAiB,EAChC,QAAQ,EAAE,QAAQ,EAClB,OAAO,EAAE,YAAY,GACrB,CACH,CAAA;KACF;IACD,MAAM,YAAY,GAAG,UAAU,YAAY,CAAC,EAAE,EAAE,CAAA;IAChD,OAAO,CACL,2BAAG,EAAE,EAAE,YAAY,iBAAc,gCAAgC;QAC/D;YACE,2CAA2C;YAC3C,uBAAuB,EAAE;gBACvB,MAAM,EAAE;aACL,YAAY;;;;CAIxB;aACQ,GACD;QACD,MAAM,CACL,CACL,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,uBAAuB,CAAC,CAAA"}
|
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@@ -1,3 +1,4 @@
|
|
|
1
|
+
import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType';
|
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2
|
+
import PluginManager from '@jbrowse/core/PluginManager';
|
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3
|
+
declare const ChordRendererConfigF: (pluginManager: PluginManager) => ChordRendererType;
|
|
1
4
|
export default ChordRendererConfigF;
|
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2
|
-
declare function ChordRendererConfigF(pluginManager: any): ChordRendererType;
|
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3
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-
import ChordRendererType from "@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType";
|
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@@ -1,7 +1,7 @@
|
|
|
1
1
|
import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType';
|
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2
2
|
import { ConfigurationSchema } from '@jbrowse/core/configuration';
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3
3
|
import ReactComponent from './ReactComponent';
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4
|
-
const ChordRendererConfigF = pluginManager => {
|
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4
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+
const ChordRendererConfigF = (pluginManager) => {
|
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5
5
|
const configSchema = ConfigurationSchema('StructuralVariantChordRenderer', {
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6
|
strokeColor: {
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7
7
|
type: 'color',
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/StructuralVariantChordRenderer/index.
|
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1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/StructuralVariantChordRenderer/index.ts"],"names":[],"mappings":"AAAA,OAAO,iBAAiB,MAAM,yEAAyE,CAAA;AACvG,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAGjE,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAE7C,MAAM,oBAAoB,GAAG,CAAC,aAA4B,EAAE,EAAE;IAC5D,MAAM,YAAY,GAAG,mBAAmB,CACtC,gCAAgC,EAChC;QACE,WAAW,EAAE;YACX,IAAI,EAAE,OAAO;YACb,WAAW,EAAE,4BAA4B;YACzC,YAAY,EAAE,sBAAsB;YACpC,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;QACD,mBAAmB,EAAE;YACnB,IAAI,EAAE,OAAO;YACb,WAAW,EAAE,iDAAiD;YAC9D,YAAY,EAAE,OAAO;YACrB,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;QACD,gBAAgB,EAAE;YAChB,IAAI,EAAE,OAAO;YACb,WAAW,EACT,oEAAoE;YACtE,YAAY,EAAE,MAAM;YACpB,eAAe,EAAE,CAAC,SAAS,CAAC;SAC7B;KACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;IACD,OAAO,IAAI,iBAAiB,CAAC;QAC3B,IAAI,EAAE,gCAAgC;QACtC,cAAc;QACd,YAAY;QACZ,aAAa;KACd,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,eAAe,oBAAoB,CAAA"}
|
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@@ -2,8 +2,7 @@
|
|
|
2
2
|
import React, { useState } from 'react';
|
|
3
3
|
import { Link, Typography } from '@mui/material';
|
|
4
4
|
import SimpleFeature from '@jbrowse/core/util/simpleFeature';
|
|
5
|
-
import { getSession } from '@jbrowse/core/util';
|
|
6
|
-
import { getEnv } from 'mobx-state-tree';
|
|
5
|
+
import { getEnv, getSession } from '@jbrowse/core/util';
|
|
7
6
|
import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
|
|
8
7
|
import BreakendOptionDialog from './BreakendOptionDialog';
|
|
9
8
|
export default function BreakendPanel(props) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"BreakendPanel.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendPanel.tsx"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAChD,OAAO,aAEN,MAAM,kCAAkC,CAAA;AACzC,OAAO,EAAE,
|
|
1
|
+
{"version":3,"file":"BreakendPanel.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendPanel.tsx"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAChD,OAAO,aAEN,MAAM,kCAAkC,CAAA;AACzC,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AACvD,OAAO,EAAE,QAAQ,EAAE,MAAM,mDAAmD,CAAA;AAC5E,OAAO,oBAAoB,MAAM,wBAAwB,CAAA;AAEzD,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,KAIrC;IACC,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,CAAC,OAAO,CAAC,CAAA;IACzC,MAAM,CAAC,gBAAgB,EAAE,mBAAmB,CAAC,GAAG,QAAQ,CAAC,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,aAAa,CAAC,OAAO,CAAC,CAAA;IAChD,OAAO,CACL,oBAAC,QAAQ,OAAK,KAAK,EAAE,KAAK,EAAC,WAAW;QACpC,oBAAC,UAAU,oDAAuD;QAClE,gCACG,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,CAC3B,4BAAI,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,EAAE;YACrC,oBAAC,IAAI,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,oBAAC,UAAU,6DAEE;YACb,gCACG,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,CAC3B,4BAAI,GAAG,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,EAAE;gBACrC,oBAAC,IAAI,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,oBAAC,oBAAoB,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"}
|
|
@@ -8,6 +8,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
|
|
|
8
8
|
unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
|
|
9
9
|
view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
|
|
10
10
|
track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
|
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11
|
+
trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
12
|
+
trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
11
13
|
} & {
|
|
12
14
|
type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
|
|
13
15
|
descriptions: import("mobx-state-tree").IType<any, any, any>;
|
|
@@ -15,6 +17,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
|
|
|
15
17
|
setFeatureData(featureData: Record<string, unknown>): void;
|
|
16
18
|
clearFeatureData(): void;
|
|
17
19
|
setFormattedData(feat: Record<string, unknown>): void;
|
|
20
|
+
setExtra(type?: string | undefined, trackId?: string | undefined): void;
|
|
18
21
|
} & {
|
|
19
22
|
afterCreate(): void;
|
|
20
23
|
}, {
|
|
@@ -27,11 +30,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
|
|
|
27
30
|
unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
|
|
28
31
|
view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
|
|
29
32
|
track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
|
|
33
|
+
trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
34
|
+
trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
|
|
30
35
|
}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
|
|
31
36
|
id: string;
|
|
32
37
|
type: "BaseFeatureWidget";
|
|
33
38
|
track: import("mobx-state-tree").ReferenceIdentifier | undefined;
|
|
34
39
|
view: import("mobx-state-tree").ReferenceIdentifier | undefined;
|
|
40
|
+
trackId: string | undefined;
|
|
41
|
+
trackType: string | undefined;
|
|
35
42
|
formattedFields: any;
|
|
36
43
|
finalizedFeatureData: any;
|
|
37
44
|
} & import("mobx-state-tree")._NotCustomized>;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
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|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"VcfTabixAdapter.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAMhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAC9C,OAAO,SAAS,MAAM,WAAW,CAAA;AAEjC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,UAAU,MAAM,cAAc,CAAA;AAGrC,MAAM,CAAC,OAAO,MAAO,SAAQ,sBAAsB;IAOzC,KAAK,CAAC,YAAY;QACxB,MAAM,aAAa,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAClE,MAAM,QAAQ,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QACnE,MAAM,SAAS,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAErE,MAAM,UAAU,GAAG,YAAY,CAC7B,aAA6B,EAC7B,IAAI,CAAC,aAAa,CACnB,CAAA;QACD,MAAM,KAAK,GAAG,SAAS,KAAK,KAAK,CAAA;QACjC,MAAM,GAAG,GAAG,IAAI,gBAAgB,CAAC;YAC/B,UAAU;YACV,aAAa,EAAE,KAAK;gBAClB,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACb,aAAa,EAAE,CAAC,KAAK;gBACnB,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACb,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,SAAS,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,gBAAgB,CAAU,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,
|
|
1
|
+
{"version":3,"file":"VcfTabixAdapter.js","sourceRoot":"","sources":["../../src/VcfTabixAdapter/VcfTabixAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAMhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAE1D,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAC9C,OAAO,SAAS,MAAM,WAAW,CAAA;AAEjC,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,UAAU,MAAM,cAAc,CAAA;AAGrC,MAAM,CAAC,OAAO,MAAO,SAAQ,sBAAsB;IAOzC,KAAK,CAAC,YAAY;QACxB,MAAM,aAAa,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAClE,MAAM,QAAQ,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QACnE,MAAM,SAAS,GAAG,cAAc,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAErE,MAAM,UAAU,GAAG,YAAY,CAC7B,aAA6B,EAC7B,IAAI,CAAC,aAAa,CACnB,CAAA;QACD,MAAM,KAAK,GAAG,SAAS,KAAK,KAAK,CAAA;QACjC,MAAM,GAAG,GAAG,IAAI,gBAAgB,CAAC;YAC/B,UAAU;YACV,aAAa,EAAE,KAAK;gBAClB,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACb,aAAa,EAAE,CAAC,KAAK;gBACnB,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACb,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,SAAS,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,gBAAgB,CAAU,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,UAAU,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,gBAAgB,CAAU,KAAK,EAAE,QAA2B,EAAE,EAAE;YACrE,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAEtC,aAAa;YACb,MAAM,KAAK,GAAG,MAAM,eAAe,CAAC,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"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-variants",
|
|
3
|
-
"version": "2.1.
|
|
3
|
+
"version": "2.1.6",
|
|
4
4
|
"description": "JBrowse 2 variant adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -65,5 +65,5 @@
|
|
|
65
65
|
"distModule": "esm/index.js",
|
|
66
66
|
"srcModule": "src/index.ts",
|
|
67
67
|
"module": "esm/index.js",
|
|
68
|
-
"gitHead": "
|
|
68
|
+
"gitHead": "df810d2a4f057adcd8f5345d54972508fba007a7"
|
|
69
69
|
}
|
|
@@ -9,8 +9,9 @@ import {
|
|
|
9
9
|
import { types } from 'mobx-state-tree'
|
|
10
10
|
import { getContainingView } from '@jbrowse/core/util'
|
|
11
11
|
import { getParentRenderProps } from '@jbrowse/core/util/tracks'
|
|
12
|
+
import PluginManager from '@jbrowse/core/PluginManager'
|
|
12
13
|
|
|
13
|
-
const ChordVariantDisplayF = pluginManager => {
|
|
14
|
+
const ChordVariantDisplayF = (pluginManager: PluginManager) => {
|
|
14
15
|
const configSchema = ConfigurationSchema(
|
|
15
16
|
'ChordVariantDisplay',
|
|
16
17
|
{
|
|
@@ -36,7 +37,7 @@ const ChordVariantDisplayF = pluginManager => {
|
|
|
36
37
|
return self.configuration.renderer.type
|
|
37
38
|
},
|
|
38
39
|
|
|
39
|
-
renderProps() {
|
|
40
|
+
renderProps(): Record<string, unknown> {
|
|
40
41
|
const view = getContainingView(self)
|
|
41
42
|
return {
|
|
42
43
|
...getParentRenderProps(self),
|
|
@@ -44,6 +45,8 @@ const ChordVariantDisplayF = pluginManager => {
|
|
|
44
45
|
displayModel: self,
|
|
45
46
|
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onChordClick: self.onChordClick,
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@@ -29,20 +29,23 @@ export default function (configSchema: LinearVariantDisplayConfigModel) {
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const { rpcManager } = session
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const
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'VariantFeatureWidget',
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'variantFeature',
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const descriptions = await rpcManager.call(
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sessionId,
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'CoreGetMetadata',
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{
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adapterConfig,
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},
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)
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session.showWidget(
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session.showWidget(
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session.addWidget('VariantFeatureWidget', 'variantFeature', {
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featureData: feature.toJSON(),
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view,
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track,
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descriptions,
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)
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}
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session.setSelection(feature)
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@@ -1,17 +1,38 @@
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1
1
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import React, { useMemo } from 'react'
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import { observer
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import { polarToCartesian } from '@jbrowse/core/util'
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import {
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import { observer } from 'mobx-react'
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import { polarToCartesian, Feature } from '@jbrowse/core/util'
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import {
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AnyConfigurationModel,
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readConfObject,
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} from '@jbrowse/core/configuration'
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import { parseBreakend } from '@gmod/vcf'
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import PropTypes from 'prop-types'
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interface Region {
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end: number
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start: number
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refName: string
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elided?: false
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}
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interface ElidedRegion {
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elided: true
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regions: Region[]
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}
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type AnyRegion = Region | ElidedRegion
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interface Block {
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flipped: boolean
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bpPerRadian: number
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startRadians: number
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region: AnyRegion
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}
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function bpToRadians(block: Block, pos: number) {
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const blockEnd = block.region.elided ? 0 : block.region.end
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const bpOffset = block.flipped ? blockEnd - pos : pos - blockStart
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-
|
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-
return radians
|
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return bpOffset / block.bpPerRadian + block.startRadians
|
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15
36
|
}
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const Chord = observer(function Chord({
|
|
@@ -22,6 +43,19 @@ const Chord = observer(function Chord({
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22
43
|
bezierRadius,
|
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23
44
|
selected,
|
|
24
45
|
onClick,
|
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+
}: {
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feature: Feature
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+
blocksForRefs: { [key: string]: Block }
|
|
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radius: number
|
|
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config: AnyConfigurationModel
|
|
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|
+
bezierRadius: number
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selected: boolean
|
|
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onClick: (
|
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+
feature: Feature,
|
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+
reg: AnyRegion,
|
|
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|
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endBlock: AnyRegion,
|
|
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|
+
evt: unknown,
|
|
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|
+
) => void
|
|
25
59
|
}) {
|
|
26
60
|
// find the blocks that our start and end points belong to
|
|
27
61
|
const startBlock = blocksForRefs[feature.get('refName')]
|
|
@@ -35,7 +69,7 @@ const Chord = observer(function Chord({
|
|
|
35
69
|
svType = 'mate'
|
|
36
70
|
}
|
|
37
71
|
let endPosition
|
|
38
|
-
let endBlock
|
|
72
|
+
let endBlock: Block | undefined
|
|
39
73
|
const alt = feature.get('ALT')?.[0]
|
|
40
74
|
const bnd = alt && parseBreakend(alt)
|
|
41
75
|
if (bnd) {
|
|
@@ -80,18 +114,24 @@ const Chord = observer(function Chord({
|
|
|
80
114
|
data-testid={`chord-${feature.id()}`}
|
|
81
115
|
d={['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' ')}
|
|
82
116
|
style={{ stroke: strokeColor }}
|
|
83
|
-
onClick={evt =>
|
|
84
|
-
|
|
85
|
-
|
|
117
|
+
onClick={evt => {
|
|
118
|
+
if (endBlock && startBlock) {
|
|
119
|
+
onClick(feature, startBlock.region, endBlock.region, evt)
|
|
120
|
+
}
|
|
121
|
+
}}
|
|
86
122
|
onMouseOver={evt => {
|
|
87
123
|
if (!selected) {
|
|
124
|
+
// @ts-ignore
|
|
88
125
|
evt.target.style.stroke = hoverStrokeColor
|
|
126
|
+
// @ts-ignore
|
|
89
127
|
evt.target.style.strokeWidth = 3
|
|
90
128
|
}
|
|
91
129
|
}}
|
|
92
130
|
onMouseOut={evt => {
|
|
93
131
|
if (!selected) {
|
|
132
|
+
// @ts-ignore
|
|
94
133
|
evt.target.style.stroke = strokeColor
|
|
134
|
+
// @ts-ignore
|
|
95
135
|
evt.target.style.strokeWidth = 1
|
|
96
136
|
}
|
|
97
137
|
}}
|
|
@@ -102,7 +142,20 @@ const Chord = observer(function Chord({
|
|
|
102
142
|
return null
|
|
103
143
|
})
|
|
104
144
|
|
|
105
|
-
function StructuralVariantChords(props
|
|
145
|
+
function StructuralVariantChords(props: {
|
|
146
|
+
features: Map<string, Feature>
|
|
147
|
+
radius: number
|
|
148
|
+
config: AnyConfigurationModel
|
|
149
|
+
displayModel: { id: string; selectedFeatureId: string }
|
|
150
|
+
blockDefinitions: Block[]
|
|
151
|
+
bezierRadius: number
|
|
152
|
+
onChordClick: (
|
|
153
|
+
feature: Feature,
|
|
154
|
+
reg: AnyRegion,
|
|
155
|
+
endBlock: AnyRegion,
|
|
156
|
+
evt: unknown,
|
|
157
|
+
) => void
|
|
158
|
+
}) {
|
|
106
159
|
const {
|
|
107
160
|
features,
|
|
108
161
|
config,
|
|
@@ -111,12 +164,11 @@ function StructuralVariantChords(props) {
|
|
|
111
164
|
radius,
|
|
112
165
|
bezierRadius,
|
|
113
166
|
displayModel: { selectedFeatureId },
|
|
114
|
-
|
|
115
167
|
onChordClick,
|
|
116
168
|
} = props
|
|
117
169
|
// make a map of refName -> blockDefinition
|
|
118
170
|
const blocksForRefsMemo = useMemo(() => {
|
|
119
|
-
const blocksForRefs = {}
|
|
171
|
+
const blocksForRefs = {} as { [key: string]: Block }
|
|
120
172
|
blockDefinitions.forEach(block => {
|
|
121
173
|
const regions = block.region.elided
|
|
122
174
|
? block.region.regions
|
|
@@ -136,7 +188,6 @@ function StructuralVariantChords(props) {
|
|
|
136
188
|
key={id}
|
|
137
189
|
feature={feature}
|
|
138
190
|
config={config}
|
|
139
|
-
displayModel={displayModel}
|
|
140
191
|
radius={radius}
|
|
141
192
|
bezierRadius={bezierRadius}
|
|
142
193
|
blocksForRefs={blocksForRefsMemo}
|
|
@@ -164,22 +215,4 @@ function StructuralVariantChords(props) {
|
|
|
164
215
|
)
|
|
165
216
|
}
|
|
166
217
|
|
|
167
|
-
StructuralVariantChords.propTypes = {
|
|
168
|
-
features: PropTypes.instanceOf(Map).isRequired,
|
|
169
|
-
config: CommonPropTypes.ConfigSchema.isRequired,
|
|
170
|
-
displayModel: MobxPropTypes.objectOrObservableObject,
|
|
171
|
-
blockDefinitions: PropTypes.arrayOf(MobxPropTypes.objectOrObservableObject)
|
|
172
|
-
.isRequired,
|
|
173
|
-
radius: PropTypes.number.isRequired,
|
|
174
|
-
bezierRadius: PropTypes.number.isRequired,
|
|
175
|
-
selectedFeatureId: PropTypes.string,
|
|
176
|
-
onChordClick: PropTypes.oneOfType([PropTypes.func, PropTypes.string]),
|
|
177
|
-
}
|
|
178
|
-
|
|
179
|
-
StructuralVariantChords.defaultProps = {
|
|
180
|
-
displayModel: undefined,
|
|
181
|
-
selectedFeatureId: '',
|
|
182
|
-
onChordClick: undefined,
|
|
183
|
-
}
|
|
184
|
-
|
|
185
218
|
export default observer(StructuralVariantChords)
|
|
@@ -1,8 +1,10 @@
|
|
|
1
1
|
import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType'
|
|
2
2
|
import { ConfigurationSchema } from '@jbrowse/core/configuration'
|
|
3
|
+
import PluginManager from '@jbrowse/core/PluginManager'
|
|
4
|
+
|
|
3
5
|
import ReactComponent from './ReactComponent'
|
|
4
6
|
|
|
5
|
-
const ChordRendererConfigF = pluginManager => {
|
|
7
|
+
const ChordRendererConfigF = (pluginManager: PluginManager) => {
|
|
6
8
|
const configSchema = ConfigurationSchema(
|
|
7
9
|
'StructuralVariantChordRenderer',
|
|
8
10
|
{
|
|
@@ -4,8 +4,7 @@ import { Link, Typography } from '@mui/material'
|
|
|
4
4
|
import SimpleFeature, {
|
|
5
5
|
SimpleFeatureSerialized,
|
|
6
6
|
} from '@jbrowse/core/util/simpleFeature'
|
|
7
|
-
import { getSession } from '@jbrowse/core/util'
|
|
8
|
-
import { getEnv } from 'mobx-state-tree'
|
|
7
|
+
import { getEnv, getSession } from '@jbrowse/core/util'
|
|
9
8
|
import { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
|
|
10
9
|
import BreakendOptionDialog from './BreakendOptionDialog'
|
|
11
10
|
|
|
@@ -189,6 +189,45 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
|
|
|
189
189
|
</div>
|
|
190
190
|
</div>
|
|
191
191
|
</div>
|
|
192
|
+
<div
|
|
193
|
+
class="tss-1upvn7b-container2"
|
|
194
|
+
>
|
|
195
|
+
<button
|
|
196
|
+
class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium css-sghohy-MuiButtonBase-root-MuiButton-root"
|
|
197
|
+
tabindex="0"
|
|
198
|
+
type="button"
|
|
199
|
+
>
|
|
200
|
+
Show feature sequence
|
|
201
|
+
<span
|
|
202
|
+
class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
|
|
203
|
+
/>
|
|
204
|
+
</button>
|
|
205
|
+
<div
|
|
206
|
+
class="MuiFormControl-root tss-1x17dzq-formControl css-1nrlq1o-MuiFormControl-root"
|
|
207
|
+
>
|
|
208
|
+
<button
|
|
209
|
+
class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeMedium css-78trlr-MuiButtonBase-root-MuiIconButton-root"
|
|
210
|
+
tabindex="0"
|
|
211
|
+
type="button"
|
|
212
|
+
>
|
|
213
|
+
<svg
|
|
214
|
+
aria-hidden="true"
|
|
215
|
+
class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
|
|
216
|
+
data-testid="HelpIcon"
|
|
217
|
+
focusable="false"
|
|
218
|
+
viewBox="0 0 24 24"
|
|
219
|
+
>
|
|
220
|
+
<path
|
|
221
|
+
d="M12 2C6.48 2 2 6.48 2 12s4.48 10 10 10 10-4.48 10-10S17.52 2 12 2zm1 17h-2v-2h2v2zm2.07-7.75-.9.92C13.45 12.9 13 13.5 13 15h-2v-.5c0-1.1.45-2.1 1.17-2.83l1.24-1.26c.37-.36.59-.86.59-1.41 0-1.1-.9-2-2-2s-2 .9-2 2H8c0-2.21 1.79-4 4-4s4 1.79 4 4c0 .88-.36 1.68-.93 2.25z"
|
|
222
|
+
/>
|
|
223
|
+
</svg>
|
|
224
|
+
<span
|
|
225
|
+
class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
|
|
226
|
+
/>
|
|
227
|
+
</button>
|
|
228
|
+
</div>
|
|
229
|
+
<br />
|
|
230
|
+
</div>
|
|
192
231
|
</div>
|
|
193
232
|
</div>
|
|
194
233
|
</div>
|
|
@@ -85,7 +85,7 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
85
85
|
const { refName, start, end } = query
|
|
86
86
|
const { vcf, parser } = await this.configure()
|
|
87
87
|
await vcf.getLines(refName, start, end, {
|
|
88
|
-
lineCallback: (line
|
|
88
|
+
lineCallback: (line, fileOffset) => {
|
|
89
89
|
observer.next(
|
|
90
90
|
new VcfFeature({
|
|
91
91
|
variant: parser.parseLine(line),
|