@jbrowse/plugin-arc 2.13.0 → 2.14.0

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Files changed (23) hide show
  1. package/dist/ArcRenderer/ArcRendering.d.ts +2 -2
  2. package/dist/ArcRenderer/ArcRendering.js +17 -4
  3. package/dist/ArcTooltip.js +1 -1
  4. package/dist/LinearArcDisplay/model.d.ts +2 -4
  5. package/dist/LinearArcDisplay/model.js +6 -2
  6. package/dist/LinearPairedArcDisplay/components/Arcs.js +22 -4
  7. package/dist/LinearPairedArcDisplay/components/BaseDisplayComponent.js +3 -1
  8. package/dist/LinearPairedArcDisplay/components/util.js +1 -1
  9. package/dist/LinearPairedArcDisplay/model.d.ts +1 -1
  10. package/dist/LinearPairedArcDisplay/renderSvg.js +1 -1
  11. package/dist/LinearPairedArcDisplay/util.d.ts +1 -1
  12. package/esm/ArcRenderer/ArcRendering.d.ts +2 -2
  13. package/esm/ArcRenderer/ArcRendering.js +17 -4
  14. package/esm/ArcTooltip.js +1 -1
  15. package/esm/LinearArcDisplay/model.d.ts +2 -4
  16. package/esm/LinearArcDisplay/model.js +6 -2
  17. package/esm/LinearPairedArcDisplay/components/Arcs.js +22 -4
  18. package/esm/LinearPairedArcDisplay/components/BaseDisplayComponent.js +3 -1
  19. package/esm/LinearPairedArcDisplay/components/util.js +1 -1
  20. package/esm/LinearPairedArcDisplay/model.d.ts +1 -1
  21. package/esm/LinearPairedArcDisplay/renderSvg.js +1 -1
  22. package/esm/LinearPairedArcDisplay/util.d.ts +1 -1
  23. package/package.json +3 -3
package/dist/ArcRenderer/ArcRendering.d.ts CHANGED
@@ -1,13 +1,13 @@
1
1
  import React from 'react';
2
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  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
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  import { Feature, Region } from '@jbrowse/core/util';
4
- declare const ArcRendering: ({ features, config, regions, bpPerPx, height, exportSVG, onFeatureClick, displayModel: { selectedFeatureId }, }: {
4
+ declare const ArcRendering: ({ features, config, regions, bpPerPx, height, exportSVG, displayModel, onFeatureClick, }: {
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  features: Map<string, Feature>;
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  config: AnyConfigurationModel;
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  regions: Region[];
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  bpPerPx: number;
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  height: number;
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- displayModel: {
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+ displayModel?: {
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  selectedFeatureId: string;
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  };
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  onFeatureClick: (event: React.MouseEvent, featureId: string) => void;
package/dist/ArcRenderer/ArcRendering.js CHANGED
@@ -51,7 +51,13 @@ function Arc({ selectedFeatureId, region, bpPerPx, config, onFeatureClick, featu
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  const t1 = 1 - t;
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  const textYCoord = 3 * (t1 * t1) * (t * height) + 3 * t1 * (t * t) * height;
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  return (react_1.default.createElement("g", null,
54
- react_1.default.createElement("path", { ref: ref, ...(0, util_1.getStrokeProps)(stroke), d: `M ${left} 0 C ${left} ${height}, ${right} ${height}, ${right} 0`, strokeWidth: strokeWidth, fill: "transparent", onClick: e => onFeatureClick === null || onFeatureClick === void 0 ? void 0 : onFeatureClick(e, featureId), onMouseOver: () => setIsMouseOvered(true), onMouseLeave: () => setIsMouseOvered(false), pointerEvents: "stroke" }),
54
+ react_1.default.createElement("path", { ref: ref, ...(0, util_1.getStrokeProps)(stroke), d: `M ${left} 0 C ${left} ${height}, ${right} ${height}, ${right} 0`, strokeWidth: strokeWidth, fill: "transparent", onClick: e => {
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+ onFeatureClick(e, featureId);
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+ }, onMouseOver: () => {
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+ setIsMouseOvered(true);
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+ }, onMouseLeave: () => {
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+ setIsMouseOvered(false);
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+ }, pointerEvents: "stroke" }),
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  isMouseOvered ? react_1.default.createElement(ArcTooltip_1.default, { contents: caption }) : null,
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  react_1.default.createElement("text", { x: left + (right - left) / 2, y: textYCoord + 3, stroke: "white", strokeWidth: "0.6em" }, label),
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  react_1.default.createElement("text", { x: left + (right - left) / 2, y: textYCoord + 3, stroke: textStroke }, label)));
@@ -96,15 +102,22 @@ function SemiCircles({ selectedFeatureId, region, bpPerPx, config, onFeatureClic
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  const ref = react_1.default.createRef();
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  const textYCoord = (right - left) / 2;
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  return (react_1.default.createElement("g", null,
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- react_1.default.createElement("path", { d: describeArc(left + (right - left) / 2, 0, (right - left) / 2, 90, 270), ...(0, util_1.getStrokeProps)(stroke), strokeWidth: strokeWidth, fill: "transparent", onClick: e => onFeatureClick === null || onFeatureClick === void 0 ? void 0 : onFeatureClick(e, featureId), onMouseOver: () => setIsMouseOvered(true), onMouseLeave: () => setIsMouseOvered(false), ref: ref, pointerEvents: "stroke" }),
105
+ react_1.default.createElement("path", { d: describeArc(left + (right - left) / 2, 0, (right - left) / 2, 90, 270), ...(0, util_1.getStrokeProps)(stroke), strokeWidth: strokeWidth, fill: "transparent", onClick: e => {
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+ onFeatureClick(e, featureId);
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+ }, onMouseOver: () => {
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+ setIsMouseOvered(true);
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+ }, onMouseLeave: () => {
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+ setIsMouseOvered(false);
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+ }, ref: ref, pointerEvents: "stroke" }),
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  isMouseOvered ? react_1.default.createElement(ArcTooltip_1.default, { contents: caption }) : null,
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  react_1.default.createElement("text", { x: left + (right - left) / 2, y: textYCoord + 3, stroke: "white", strokeWidth: "0.6em" }, label),
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  react_1.default.createElement("text", { x: left + (right - left) / 2, y: textYCoord + 3, stroke: textStroke }, label)));
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  }
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- const ArcRendering = (0, mobx_react_1.observer)(function ({ features, config, regions, bpPerPx, height, exportSVG, onFeatureClick, displayModel: { selectedFeatureId }, }) {
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- const [region] = regions;
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+ const ArcRendering = (0, mobx_react_1.observer)(function ({ features, config, regions, bpPerPx, height, exportSVG, displayModel, onFeatureClick, }) {
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+ const region = regions[0];
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  const width = (region.end - region.start) / bpPerPx;
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  const semicircles = (0, configuration_1.readConfObject)(config, 'displayMode') === 'semicircles';
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+ const { selectedFeatureId } = displayModel || {};
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  return (react_1.default.createElement(Wrapper, { exportSVG: exportSVG, width: width, height: height }, [...features.values()].map(f => semicircles ? (react_1.default.createElement(SemiCircles, { key: f.id(), config: config, region: region, bpPerPx: bpPerPx, selectedFeatureId: selectedFeatureId, onFeatureClick: onFeatureClick, feature: f })) : (react_1.default.createElement(Arc, { key: f.id(), config: config, region: region, bpPerPx: bpPerPx, selectedFeatureId: selectedFeatureId, onFeatureClick: onFeatureClick, feature: f })))));
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  });
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  function Wrapper({ exportSVG, width, height, children, }) {
package/dist/ArcTooltip.js CHANGED
@@ -40,7 +40,7 @@ const ArcTooltip = (0, mobx_react_1.observer)(function ({ contents }) {
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  });
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  const clientPoint = (0, react_2.useClientPoint)(context);
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  const { getFloatingProps } = (0, react_2.useInteractions)([clientPoint]);
43
- const popperTheme = (_a = theme === null || theme === void 0 ? void 0 : theme.components) === null || _a === void 0 ? void 0 : _a.MuiPopper;
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+ const popperTheme = (_a = theme.components) === null || _a === void 0 ? void 0 : _a.MuiPopper;
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  return contents ? (react_1.default.createElement(material_1.Portal, { container: (_b = popperTheme === null || popperTheme === void 0 ? void 0 : popperTheme.defaultProps) === null || _b === void 0 ? void 0 : _b.container },
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  react_1.default.createElement("div", { className: classes.tooltip, ref: refs.setFloating, style: {
46
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  ...floatingStyles,
package/dist/LinearArcDisplay/model.d.ts CHANGED
@@ -133,7 +133,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  error: unknown;
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  message: string | undefined;
135
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
136
- onHorizontalScroll?: Function;
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+ onHorizontalScroll?: () => void;
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  blockState?: Record<string, any>;
138
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  }>;
139
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  readonly DisplayBlurb: import("react").FC<{
@@ -146,9 +146,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
146
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  error: unknown;
147
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  message: string | undefined;
148
148
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
149
- id: import("mobx-state-tree" /**
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- * #method
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- */).IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
149
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
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  type: import("mobx-state-tree").ISimpleType<string>;
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  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
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  }, {
package/dist/LinearArcDisplay/model.js CHANGED
@@ -107,13 +107,17 @@ function stateModelFactory(configSchema) {
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  {
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  type: 'radio',
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  label: 'Arcs',
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- onClick: () => self.setDisplayMode('arcs'),
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+ onClick: () => {
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+ self.setDisplayMode('arcs');
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+ },
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  checked: self.displayMode === 'arcs',
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  },
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  {
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  type: 'radio',
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  label: 'Semi-circles',
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- onClick: () => self.setDisplayMode('semicircles'),
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+ onClick: () => {
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+ self.setDisplayMode('semicircles');
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+ },
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  checked: self.displayMode === 'semicircles',
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  },
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  ],
package/dist/LinearPairedArcDisplay/components/Arcs.js CHANGED
@@ -56,9 +56,27 @@ const Arc = (0, mobx_react_1.observer)(function ({ model, feature, alt, assembly
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  const col = mouseOvered ? 'black' : c;
57
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  const sw = 3;
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  return absrad > 1 ? (react_1.default.createElement(react_1.default.Fragment, null,
59
- react_1.default.createElement("path", { d: `M ${left} 0 C ${left} ${destY}, ${right} ${destY}, ${right} 0`, ref: ref, ...(0, util_1.getStrokeProps)(col), strokeWidth: sw, onMouseOut: () => setMouseOvered(false), onMouseOver: () => setMouseOvered(true), onClick: () => model.selectFeature(feature), fill: "none", pointerEvents: "stroke" }),
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- k1.mateDirection !== undefined ? (react_1.default.createElement("line", { ...(0, util_1.getStrokeProps)(col), strokeWidth: sw, onMouseOut: () => setMouseOvered(false), onMouseOver: () => setMouseOvered(true), onClick: () => model.selectFeature(feature), x1: left, x2: left + k1.mateDirection * 20, y1: 1.5, y2: 1.5 })) : null,
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- k2.mateDirection !== undefined ? (react_1.default.createElement("line", { ...(0, util_1.getStrokeProps)(col), strokeWidth: sw, onMouseOut: () => setMouseOvered(false), onMouseOver: () => setMouseOvered(true), onClick: () => model.selectFeature(feature), x1: right, x2: right + k2.mateDirection * 20, y1: 1.5, y2: 1.5 })) : null,
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+ react_1.default.createElement("path", { d: `M ${left} 0 C ${left} ${destY}, ${right} ${destY}, ${right} 0`, ref: ref, ...(0, util_1.getStrokeProps)(col), strokeWidth: sw, onMouseOut: () => {
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+ setMouseOvered(false);
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+ }, onMouseOver: () => {
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+ setMouseOvered(true);
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+ }, onClick: () => {
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+ model.selectFeature(feature);
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+ }, fill: "none", pointerEvents: "stroke" }),
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+ k1.mateDirection ? (react_1.default.createElement("line", { ...(0, util_1.getStrokeProps)(col), strokeWidth: sw, onMouseOut: () => {
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+ setMouseOvered(false);
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+ }, onMouseOver: () => {
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+ setMouseOvered(true);
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+ }, onClick: () => {
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+ model.selectFeature(feature);
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+ }, x1: left, x2: left + k1.mateDirection * 20, y1: 1.5, y2: 1.5 })) : null,
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+ k2.mateDirection ? (react_1.default.createElement("line", { ...(0, util_1.getStrokeProps)(col), strokeWidth: sw, onMouseOut: () => {
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+ setMouseOvered(false);
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+ }, onMouseOver: () => {
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+ setMouseOvered(true);
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+ }, onClick: () => {
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+ model.selectFeature(feature);
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+ }, x1: right, x2: right + k2.mateDirection * 20, y1: 1.5, y2: 1.5 })) : null,
62
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  mouseOvered ? (react_1.default.createElement(ArcTooltip_1.default, { contents: (0, util_2.makeSummary)(feature, alt) })) : null)) : null;
63
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  }
64
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  return null;
@@ -78,7 +96,7 @@ const Arcs = (0, mobx_react_1.observer)(function ({ model, exportSVG, }) {
78
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  return assembly ? (react_1.default.createElement(Wrapper, { model: model, exportSVG: exportSVG }, features === null || features === void 0 ? void 0 : features.map(f => {
79
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  var _a;
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  const alts = f.get('ALT');
81
- return ((_a = alts === null || alts === void 0 ? void 0 : alts.map(a => (react_1.default.createElement(Arc, { key: f.id() + '-' + a, session: session, feature: f, alt: a, view: view, model: model, assembly: assembly })))) !== null && _a !== void 0 ? _a : (react_1.default.createElement(Arc, { key: f.id(), session: session, feature: f, view: view, model: model, assembly: assembly })));
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+ return ((_a = alts === null || alts === void 0 ? void 0 : alts.map(a => (react_1.default.createElement(Arc, { key: `${f.id()}-${a}`, session: session, feature: f, alt: a, view: view, model: model, assembly: assembly })))) !== null && _a !== void 0 ? _a : (react_1.default.createElement(Arc, { key: f.id(), session: session, feature: f, view: view, model: model, assembly: assembly })));
82
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  }))) : null;
83
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  });
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  exports.default = Arcs;
package/dist/LinearPairedArcDisplay/components/BaseDisplayComponent.js CHANGED
@@ -54,7 +54,9 @@ const BaseDisplayComponent = (0, mobx_react_1.observer)(function ({ model, child
54
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  const { error, regionTooLarge } = model;
55
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  return error ? (react_1.default.createElement(plugin_linear_genome_view_1.BlockMsg, { message: `${error}`, severity: "error", action: react_1.default.createElement(react_1.default.Fragment, null,
56
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  react_1.default.createElement(material_1.Tooltip, { title: "Reload" },
57
- react_1.default.createElement(material_1.IconButton, { "data-testid": "reload_button", onClick: () => model.reload() },
57
+ react_1.default.createElement(material_1.IconButton, { "data-testid": "reload_button", onClick: () => {
58
+ model.reload();
59
+ } },
58
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  react_1.default.createElement(Refresh_1.default, null))),
59
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  react_1.default.createElement(material_1.Tooltip, { title: "Show stack trace" },
60
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  react_1.default.createElement(material_1.IconButton, { onClick: () => {
package/dist/LinearPairedArcDisplay/components/util.js CHANGED
@@ -49,7 +49,7 @@ function makeFeaturePair(feature, alt) {
49
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  mateDirection,
50
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  },
51
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  k2: mate !== null && mate !== void 0 ? mate : {
52
- refName: mateRefName,
52
+ refName: mateRefName || 'unknown',
53
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  end: mateEnd,
54
54
  start: mateStart,
55
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  mateDirection: joinDirection,
package/dist/LinearPairedArcDisplay/model.d.ts CHANGED
@@ -65,7 +65,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
65
65
  }, import("mobx-state-tree" /**
66
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  * #action
67
67
  */)._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
68
- onHorizontalScroll?: Function;
68
+ onHorizontalScroll?: () => void;
69
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  blockState?: Record<string, any>;
70
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  }>;
71
71
  readonly DisplayBlurb: React.FC<{
package/dist/LinearPairedArcDisplay/renderSvg.js CHANGED
@@ -12,7 +12,7 @@ async function renderArcSvg(model, _opts) {
12
12
  const view = (0, util_1.getContainingView)(model);
13
13
  const width = view.dynamicBlocks.totalWidthPx;
14
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  const height = model.height;
15
- const clipid = 'arc-' + model.id;
15
+ const clipid = `arc-${model.id}`;
16
16
  return (react_1.default.createElement(react_1.default.Fragment, null,
17
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  react_1.default.createElement("defs", null,
18
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  react_1.default.createElement("clipPath", { id: clipid },
package/dist/LinearPairedArcDisplay/util.d.ts CHANGED
@@ -18,7 +18,7 @@ export declare const pairMap: {
18
18
  export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
19
19
  export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
20
20
  export declare function shouldFetchReferenceSequence(type?: string): type is "methylation";
21
- export declare const modificationColors: Record<string, string | undefined>;
21
+ export declare const modificationColors: Record<string, string>;
22
22
  type DisplayModel = IAnyStateTreeNode & {
23
23
  setError: (arg: unknown) => void;
24
24
  };
package/esm/ArcRenderer/ArcRendering.d.ts CHANGED
@@ -1,13 +1,13 @@
1
1
  import React from 'react';
2
2
  import { AnyConfigurationModel } from '@jbrowse/core/configuration';
3
3
  import { Feature, Region } from '@jbrowse/core/util';
4
- declare const ArcRendering: ({ features, config, regions, bpPerPx, height, exportSVG, onFeatureClick, displayModel: { selectedFeatureId }, }: {
4
+ declare const ArcRendering: ({ features, config, regions, bpPerPx, height, exportSVG, displayModel, onFeatureClick, }: {
5
5
  features: Map<string, Feature>;
6
6
  config: AnyConfigurationModel;
7
7
  regions: Region[];
8
8
  bpPerPx: number;
9
9
  height: number;
10
- displayModel: {
10
+ displayModel?: {
11
11
  selectedFeatureId: string;
12
12
  };
13
13
  onFeatureClick: (event: React.MouseEvent, featureId: string) => void;
package/esm/ArcRenderer/ArcRendering.js CHANGED
@@ -23,7 +23,13 @@ function Arc({ selectedFeatureId, region, bpPerPx, config, onFeatureClick, featu
23
23
  const t1 = 1 - t;
24
24
  const textYCoord = 3 * (t1 * t1) * (t * height) + 3 * t1 * (t * t) * height;
25
25
  return (React.createElement("g", null,
26
- React.createElement("path", { ref: ref, ...getStrokeProps(stroke), d: `M ${left} 0 C ${left} ${height}, ${right} ${height}, ${right} 0`, strokeWidth: strokeWidth, fill: "transparent", onClick: e => onFeatureClick === null || onFeatureClick === void 0 ? void 0 : onFeatureClick(e, featureId), onMouseOver: () => setIsMouseOvered(true), onMouseLeave: () => setIsMouseOvered(false), pointerEvents: "stroke" }),
26
+ React.createElement("path", { ref: ref, ...getStrokeProps(stroke), d: `M ${left} 0 C ${left} ${height}, ${right} ${height}, ${right} 0`, strokeWidth: strokeWidth, fill: "transparent", onClick: e => {
27
+ onFeatureClick(e, featureId);
28
+ }, onMouseOver: () => {
29
+ setIsMouseOvered(true);
30
+ }, onMouseLeave: () => {
31
+ setIsMouseOvered(false);
32
+ }, pointerEvents: "stroke" }),
27
33
  isMouseOvered ? React.createElement(ArcTooltip, { contents: caption }) : null,
28
34
  React.createElement("text", { x: left + (right - left) / 2, y: textYCoord + 3, stroke: "white", strokeWidth: "0.6em" }, label),
29
35
  React.createElement("text", { x: left + (right - left) / 2, y: textYCoord + 3, stroke: textStroke }, label)));
@@ -68,15 +74,22 @@ function SemiCircles({ selectedFeatureId, region, bpPerPx, config, onFeatureClic
68
74
  const ref = React.createRef();
69
75
  const textYCoord = (right - left) / 2;
70
76
  return (React.createElement("g", null,
71
- React.createElement("path", { d: describeArc(left + (right - left) / 2, 0, (right - left) / 2, 90, 270), ...getStrokeProps(stroke), strokeWidth: strokeWidth, fill: "transparent", onClick: e => onFeatureClick === null || onFeatureClick === void 0 ? void 0 : onFeatureClick(e, featureId), onMouseOver: () => setIsMouseOvered(true), onMouseLeave: () => setIsMouseOvered(false), ref: ref, pointerEvents: "stroke" }),
77
+ React.createElement("path", { d: describeArc(left + (right - left) / 2, 0, (right - left) / 2, 90, 270), ...getStrokeProps(stroke), strokeWidth: strokeWidth, fill: "transparent", onClick: e => {
78
+ onFeatureClick(e, featureId);
79
+ }, onMouseOver: () => {
80
+ setIsMouseOvered(true);
81
+ }, onMouseLeave: () => {
82
+ setIsMouseOvered(false);
83
+ }, ref: ref, pointerEvents: "stroke" }),
72
84
  isMouseOvered ? React.createElement(ArcTooltip, { contents: caption }) : null,
73
85
  React.createElement("text", { x: left + (right - left) / 2, y: textYCoord + 3, stroke: "white", strokeWidth: "0.6em" }, label),
74
86
  React.createElement("text", { x: left + (right - left) / 2, y: textYCoord + 3, stroke: textStroke }, label)));
75
87
  }
76
- const ArcRendering = observer(function ({ features, config, regions, bpPerPx, height, exportSVG, onFeatureClick, displayModel: { selectedFeatureId }, }) {
77
- const [region] = regions;
88
+ const ArcRendering = observer(function ({ features, config, regions, bpPerPx, height, exportSVG, displayModel, onFeatureClick, }) {
89
+ const region = regions[0];
78
90
  const width = (region.end - region.start) / bpPerPx;
79
91
  const semicircles = readConfObject(config, 'displayMode') === 'semicircles';
92
+ const { selectedFeatureId } = displayModel || {};
80
93
  return (React.createElement(Wrapper, { exportSVG: exportSVG, width: width, height: height }, [...features.values()].map(f => semicircles ? (React.createElement(SemiCircles, { key: f.id(), config: config, region: region, bpPerPx: bpPerPx, selectedFeatureId: selectedFeatureId, onFeatureClick: onFeatureClick, feature: f })) : (React.createElement(Arc, { key: f.id(), config: config, region: region, bpPerPx: bpPerPx, selectedFeatureId: selectedFeatureId, onFeatureClick: onFeatureClick, feature: f })))));
81
94
  });
82
95
  function Wrapper({ exportSVG, width, height, children, }) {
package/esm/ArcTooltip.js CHANGED
@@ -35,7 +35,7 @@ const ArcTooltip = observer(function ({ contents }) {
35
35
  });
36
36
  const clientPoint = useClientPoint(context);
37
37
  const { getFloatingProps } = useInteractions([clientPoint]);
38
- const popperTheme = (_a = theme === null || theme === void 0 ? void 0 : theme.components) === null || _a === void 0 ? void 0 : _a.MuiPopper;
38
+ const popperTheme = (_a = theme.components) === null || _a === void 0 ? void 0 : _a.MuiPopper;
39
39
  return contents ? (React.createElement(Portal, { container: (_b = popperTheme === null || popperTheme === void 0 ? void 0 : popperTheme.defaultProps) === null || _b === void 0 ? void 0 : _b.container },
40
40
  React.createElement("div", { className: classes.tooltip, ref: refs.setFloating, style: {
41
41
  ...floatingStyles,
package/esm/LinearArcDisplay/model.d.ts CHANGED
@@ -133,7 +133,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
133
133
  error: unknown;
134
134
  message: string | undefined;
135
135
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
136
- onHorizontalScroll?: Function;
136
+ onHorizontalScroll?: () => void;
137
137
  blockState?: Record<string, any>;
138
138
  }>;
139
139
  readonly DisplayBlurb: import("react").FC<{
@@ -146,9 +146,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
146
146
  error: unknown;
147
147
  message: string | undefined;
148
148
  } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
149
- id: import("mobx-state-tree" /**
150
- * #method
151
- */).IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
149
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
152
150
  type: import("mobx-state-tree").ISimpleType<string>;
153
151
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
154
152
  }, {
package/esm/LinearArcDisplay/model.js CHANGED
@@ -104,13 +104,17 @@ export function stateModelFactory(configSchema) {
104
104
  {
105
105
  type: 'radio',
106
106
  label: 'Arcs',
107
- onClick: () => self.setDisplayMode('arcs'),
107
+ onClick: () => {
108
+ self.setDisplayMode('arcs');
109
+ },
108
110
  checked: self.displayMode === 'arcs',
109
111
  },
110
112
  {
111
113
  type: 'radio',
112
114
  label: 'Semi-circles',
113
- onClick: () => self.setDisplayMode('semicircles'),
115
+ onClick: () => {
116
+ self.setDisplayMode('semicircles');
117
+ },
114
118
  checked: self.displayMode === 'semicircles',
115
119
  },
116
120
  ],
package/esm/LinearPairedArcDisplay/components/Arcs.js CHANGED
@@ -28,9 +28,27 @@ const Arc = observer(function ({ model, feature, alt, assembly, view, }) {
28
28
  const col = mouseOvered ? 'black' : c;
29
29
  const sw = 3;
30
30
  return absrad > 1 ? (React.createElement(React.Fragment, null,
31
- React.createElement("path", { d: `M ${left} 0 C ${left} ${destY}, ${right} ${destY}, ${right} 0`, ref: ref, ...getStrokeProps(col), strokeWidth: sw, onMouseOut: () => setMouseOvered(false), onMouseOver: () => setMouseOvered(true), onClick: () => model.selectFeature(feature), fill: "none", pointerEvents: "stroke" }),
32
- k1.mateDirection !== undefined ? (React.createElement("line", { ...getStrokeProps(col), strokeWidth: sw, onMouseOut: () => setMouseOvered(false), onMouseOver: () => setMouseOvered(true), onClick: () => model.selectFeature(feature), x1: left, x2: left + k1.mateDirection * 20, y1: 1.5, y2: 1.5 })) : null,
33
- k2.mateDirection !== undefined ? (React.createElement("line", { ...getStrokeProps(col), strokeWidth: sw, onMouseOut: () => setMouseOvered(false), onMouseOver: () => setMouseOvered(true), onClick: () => model.selectFeature(feature), x1: right, x2: right + k2.mateDirection * 20, y1: 1.5, y2: 1.5 })) : null,
31
+ React.createElement("path", { d: `M ${left} 0 C ${left} ${destY}, ${right} ${destY}, ${right} 0`, ref: ref, ...getStrokeProps(col), strokeWidth: sw, onMouseOut: () => {
32
+ setMouseOvered(false);
33
+ }, onMouseOver: () => {
34
+ setMouseOvered(true);
35
+ }, onClick: () => {
36
+ model.selectFeature(feature);
37
+ }, fill: "none", pointerEvents: "stroke" }),
38
+ k1.mateDirection ? (React.createElement("line", { ...getStrokeProps(col), strokeWidth: sw, onMouseOut: () => {
39
+ setMouseOvered(false);
40
+ }, onMouseOver: () => {
41
+ setMouseOvered(true);
42
+ }, onClick: () => {
43
+ model.selectFeature(feature);
44
+ }, x1: left, x2: left + k1.mateDirection * 20, y1: 1.5, y2: 1.5 })) : null,
45
+ k2.mateDirection ? (React.createElement("line", { ...getStrokeProps(col), strokeWidth: sw, onMouseOut: () => {
46
+ setMouseOvered(false);
47
+ }, onMouseOver: () => {
48
+ setMouseOvered(true);
49
+ }, onClick: () => {
50
+ model.selectFeature(feature);
51
+ }, x1: right, x2: right + k2.mateDirection * 20, y1: 1.5, y2: 1.5 })) : null,
34
52
  mouseOvered ? (React.createElement(ArcTooltip, { contents: makeSummary(feature, alt) })) : null)) : null;
35
53
  }
36
54
  return null;
@@ -50,7 +68,7 @@ const Arcs = observer(function ({ model, exportSVG, }) {
50
68
  return assembly ? (React.createElement(Wrapper, { model: model, exportSVG: exportSVG }, features === null || features === void 0 ? void 0 : features.map(f => {
51
69
  var _a;
52
70
  const alts = f.get('ALT');
53
- return ((_a = alts === null || alts === void 0 ? void 0 : alts.map(a => (React.createElement(Arc, { key: f.id() + '-' + a, session: session, feature: f, alt: a, view: view, model: model, assembly: assembly })))) !== null && _a !== void 0 ? _a : (React.createElement(Arc, { key: f.id(), session: session, feature: f, view: view, model: model, assembly: assembly })));
71
+ return ((_a = alts === null || alts === void 0 ? void 0 : alts.map(a => (React.createElement(Arc, { key: `${f.id()}-${a}`, session: session, feature: f, alt: a, view: view, model: model, assembly: assembly })))) !== null && _a !== void 0 ? _a : (React.createElement(Arc, { key: f.id(), session: session, feature: f, view: view, model: model, assembly: assembly })));
54
72
  }))) : null;
55
73
  });
56
74
  export default Arcs;
package/esm/LinearPairedArcDisplay/components/BaseDisplayComponent.js CHANGED
@@ -26,7 +26,9 @@ const BaseDisplayComponent = observer(function ({ model, children, }) {
26
26
  const { error, regionTooLarge } = model;
27
27
  return error ? (React.createElement(BlockMsg, { message: `${error}`, severity: "error", action: React.createElement(React.Fragment, null,
28
28
  React.createElement(Tooltip, { title: "Reload" },
29
- React.createElement(IconButton, { "data-testid": "reload_button", onClick: () => model.reload() },
29
+ React.createElement(IconButton, { "data-testid": "reload_button", onClick: () => {
30
+ model.reload();
31
+ } },
30
32
  React.createElement(RefreshIcon, null))),
31
33
  React.createElement(Tooltip, { title: "Show stack trace" },
32
34
  React.createElement(IconButton, { onClick: () => {
package/esm/LinearPairedArcDisplay/components/util.js CHANGED
@@ -45,7 +45,7 @@ export function makeFeaturePair(feature, alt) {
45
45
  mateDirection,
46
46
  },
47
47
  k2: mate !== null && mate !== void 0 ? mate : {
48
- refName: mateRefName,
48
+ refName: mateRefName || 'unknown',
49
49
  end: mateEnd,
50
50
  start: mateStart,
51
51
  mateDirection: joinDirection,
package/esm/LinearPairedArcDisplay/model.d.ts CHANGED
@@ -65,7 +65,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
65
65
  }, import("mobx-state-tree" /**
66
66
  * #action
67
67
  */)._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
68
- onHorizontalScroll?: Function;
68
+ onHorizontalScroll?: () => void;
69
69
  blockState?: Record<string, any>;
70
70
  }>;
71
71
  readonly DisplayBlurb: React.FC<{
package/esm/LinearPairedArcDisplay/renderSvg.js CHANGED
@@ -6,7 +6,7 @@ export async function renderArcSvg(model, _opts) {
6
6
  const view = getContainingView(model);
7
7
  const width = view.dynamicBlocks.totalWidthPx;
8
8
  const height = model.height;
9
- const clipid = 'arc-' + model.id;
9
+ const clipid = `arc-${model.id}`;
10
10
  return (React.createElement(React.Fragment, null,
11
11
  React.createElement("defs", null,
12
12
  React.createElement("clipPath", { id: clipid },
package/esm/LinearPairedArcDisplay/util.d.ts CHANGED
@@ -18,7 +18,7 @@ export declare const pairMap: {
18
18
  export declare function getColorWGBS(strand: number, base: string): "#f00" | "#00f" | "#888";
19
19
  export declare function fetchSequence(region: AugmentedRegion, adapter: BaseFeatureDataAdapter): Promise<any>;
20
20
  export declare function shouldFetchReferenceSequence(type?: string): type is "methylation";
21
- export declare const modificationColors: Record<string, string | undefined>;
21
+ export declare const modificationColors: Record<string, string>;
22
22
  type DisplayModel = IAnyStateTreeNode & {
23
23
  setError: (arg: unknown) => void;
24
24
  };
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-arc",
3
- "version": "2.13.0",
3
+ "version": "2.14.0",
4
4
  "description": "JBrowse 2 arc adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -24,7 +24,7 @@
24
24
  ],
25
25
  "scripts": {
26
26
  "build": "npm-run-all build:*",
27
- "test": "cd ../..; jest plugins/arc",
27
+ "test": "cd ../..; jest --passWithNoTests plugins/arc",
28
28
  "prepublishOnly": "yarn test",
29
29
  "prepack": "yarn build && yarn useDist",
30
30
  "postpack": "yarn useSrc",
@@ -53,5 +53,5 @@
53
53
  "publishConfig": {
54
54
  "access": "public"
55
55
  },
56
- "gitHead": "efe02fb9616e20e929cceeed46eb96420c1b6923"
56
+ "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
57
57
  }