@jbrowse/plugin-lollipop 2.6.1 → 2.6.2

package/dist/LinearLollipopDisplay/configSchema.js

@@ -10,4 +10,3 @@ function configSchemaFactory(pluginManager) {
     });
 }
 exports.configSchemaFactory = configSchemaFactory;
-//# sourceMappingURL=configSchema.js.map

package/dist/LinearLollipopDisplay/index.js

@@ -5,4 +5,3 @@ var configSchema_1 = require("./configSchema");
 Object.defineProperty(exports, "configSchemaFactory", { enumerable: true, get: function () { return configSchema_1.configSchemaFactory; } });
 var model_1 = require("./model");
 Object.defineProperty(exports, "stateModelFactory", { enumerable: true, get: function () { return model_1.stateModelFactory; } });
-//# sourceMappingURL=index.js.map

package/dist/LinearLollipopDisplay/model.js

@@ -33,4 +33,3 @@ function stateModelFactory(configSchema) {
     });
 }
 exports.stateModelFactory = stateModelFactory;
-//# sourceMappingURL=model.js.map

package/dist/LollipopRenderer/Layout.js

@@ -113,4 +113,3 @@ class PrecomputedFloatingLayout {
     }
 }
 exports.PrecomputedFloatingLayout = PrecomputedFloatingLayout;
-//# sourceMappingURL=Layout.js.map

package/dist/LollipopRenderer/LollipopRenderer.js

@@ -49,4 +49,3 @@ class default_1 extends BoxRendererType_1.default {
     }
 }
 exports.default = default_1;
-//# sourceMappingURL=LollipopRenderer.js.map

package/dist/LollipopRenderer/components/Lollipop.js

@@ -60,4 +60,3 @@ exports.default = (0, mobx_react_1.observer)(function Lollipop(props) {
         radiusPx - strokeWidth <= 2 ? null : (react_1.default.createElement("circle", { cx: anchorLocation, cy: y + radiusPx, r: radiusPx - strokeWidth, style: styleInner, onMouseDown: onFeatureMouseDown, onMouseEnter: onFeatureMouseEnter, onMouseOut: onFeatureMouseOut, onMouseOver: onFeatureMouseOver, onMouseUp: onFeatureMouseUp, onMouseLeave: onFeatureMouseLeave, onMouseMove: onFeatureMouseMove, onClick: onFeatureClick, onFocus: onFeatureMouseOver, onBlur: onFeatureMouseOut })),
         react_1.default.createElement(ScoreText_1.default, { feature: feature, config: config, layoutRecord: layoutRecord })));
 });
-//# sourceMappingURL=Lollipop.js.map

package/dist/LollipopRenderer/components/LollipopRendering.js

@@ -77,4 +77,3 @@ exports.default = (0, mobx_react_1.observer)(function LollipopRendering(props) {
             react_1.default.createElement(Lollipop_1.default, { ...props, layoutRecord: layoutRecord, feature: feature, key: `body-${feature.id()}`, selectedFeatureId: selectedFeatureId })));
     })));
 });
-//# sourceMappingURL=LollipopRendering.js.map

package/dist/LollipopRenderer/components/ScoreText.js

@@ -17,4 +17,3 @@ function ScoreText({ feature, config, layoutRecord: { y, data: { anchorX, radius
     return (react_1.default.createElement("text", { style: { fontSize: fontHeight, fill: (0, color_1.contrastingTextColor)(innerColor) }, x: anchorX, y: y + radiusPx - fontHeight / 2.4, textAnchor: "middle", dominantBaseline: "hanging" }, scoreString));
 }
 exports.default = ScoreText;
-//# sourceMappingURL=ScoreText.js.map

package/dist/LollipopRenderer/components/Stick.js

@@ -9,4 +9,3 @@ const mobx_react_1 = require("mobx-react");
 exports.default = (0, mobx_react_1.observer)(function Stick({ feature, config, layoutRecord: { anchorLocation, y, data: { radiusPx }, }, }) {
     return (react_1.default.createElement("line", { x1: anchorLocation, y1: 0, x2: anchorLocation, y2: y + 2 * radiusPx, stroke: (0, configuration_1.readConfObject)(config, 'stickColor', { feature }), strokeWidth: (0, configuration_1.readConfObject)(config, 'stickWidth', { feature }) }));
 });
-//# sourceMappingURL=Stick.js.map

package/dist/LollipopRenderer/configSchema.js

@@ -56,4 +56,3 @@ exports.default = (0, configuration_1.ConfigurationSchema)('LollipopRenderer', {
         contextVariable: ['feature'],
     },
 }, { explicitlyTyped: true });
-//# sourceMappingURL=configSchema.js.map

package/dist/LollipopRenderer/index.js

@@ -10,4 +10,3 @@ var configSchema_1 = require("./configSchema");
 Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
 var LollipopRenderer_1 = require("./LollipopRenderer");
 Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(LollipopRenderer_1).default; } });
-//# sourceMappingURL=index.js.map

package/dist/index.js

@@ -57,4 +57,3 @@ class default_1 extends Plugin_1.default {
     }
 }
 exports.default = default_1;
-//# sourceMappingURL=index.js.map

package/esm/LinearLollipopDisplay/configSchema.js

@@ -6,4 +6,3 @@ export function configSchemaFactory(pluginManager) {
         explicitlyTyped: true,
     });
 }
-//# sourceMappingURL=configSchema.js.map

package/esm/LinearLollipopDisplay/index.js

@@ -1,3 +1,2 @@
 export { configSchemaFactory } from './configSchema';
 export { stateModelFactory } from './model';
-//# sourceMappingURL=index.js.map

package/esm/LinearLollipopDisplay/model.js

@@ -29,4 +29,3 @@ export function stateModelFactory(configSchema) {
         };
     });
 }
-//# sourceMappingURL=model.js.map

package/esm/LollipopRenderer/Layout.js

@@ -108,4 +108,3 @@ export class PrecomputedFloatingLayout {
         return new PrecomputedFloatingLayout(json);
     }
 }
-//# sourceMappingURL=Layout.js.map

package/esm/LollipopRenderer/LollipopRenderer.js

@@ -20,4 +20,3 @@ export default class extends BoxRendererType {
         return new PrecomputedFloatingLayout(json);
     }
 }
-//# sourceMappingURL=LollipopRenderer.js.map

package/esm/LollipopRenderer/components/Lollipop.js

@@ -55,4 +55,3 @@ export default observer(function Lollipop(props) {
         radiusPx - strokeWidth <= 2 ? null : (React.createElement("circle", { cx: anchorLocation, cy: y + radiusPx, r: radiusPx - strokeWidth, style: styleInner, onMouseDown: onFeatureMouseDown, onMouseEnter: onFeatureMouseEnter, onMouseOut: onFeatureMouseOut, onMouseOver: onFeatureMouseOver, onMouseUp: onFeatureMouseUp, onMouseLeave: onFeatureMouseLeave, onMouseMove: onFeatureMouseMove, onClick: onFeatureClick, onFocus: onFeatureMouseOver, onBlur: onFeatureMouseOut })),
         React.createElement(ScoreText, { feature: feature, config: config, layoutRecord: layoutRecord })));
 });
-//# sourceMappingURL=Lollipop.js.map

package/esm/LollipopRenderer/components/LollipopRendering.js

@@ -72,4 +72,3 @@ export default observer(function LollipopRendering(props) {
             React.createElement(Lollipop, { ...props, layoutRecord: layoutRecord, feature: feature, key: `body-${feature.id()}`, selectedFeatureId: selectedFeatureId })));
     })));
 });
-//# sourceMappingURL=LollipopRendering.js.map

package/esm/LollipopRenderer/components/ScoreText.js

@@ -11,4 +11,3 @@ export default function ScoreText({ feature, config, layoutRecord: { y, data: {
     }
     return (React.createElement("text", { style: { fontSize: fontHeight, fill: contrastingTextColor(innerColor) }, x: anchorX, y: y + radiusPx - fontHeight / 2.4, textAnchor: "middle", dominantBaseline: "hanging" }, scoreString));
 }
-//# sourceMappingURL=ScoreText.js.map

package/esm/LollipopRenderer/components/Stick.js

@@ -4,4 +4,3 @@ import { observer } from 'mobx-react';
 export default observer(function Stick({ feature, config, layoutRecord: { anchorLocation, y, data: { radiusPx }, }, }) {
     return (React.createElement("line", { x1: anchorLocation, y1: 0, x2: anchorLocation, y2: y + 2 * radiusPx, stroke: readConfObject(config, 'stickColor', { feature }), strokeWidth: readConfObject(config, 'stickWidth', { feature }) }));
 });
-//# sourceMappingURL=Stick.js.map

package/esm/LollipopRenderer/configSchema.js

@@ -54,4 +54,3 @@ export default ConfigurationSchema('LollipopRenderer', {
         contextVariable: ['feature'],
     },
 }, { explicitlyTyped: true });
-//# sourceMappingURL=configSchema.js.map

package/esm/LollipopRenderer/index.js

@@ -1,4 +1,3 @@
 export { default as ReactComponent } from './components/LollipopRendering';
 export { default as configSchema } from './configSchema';
 export { default } from './LollipopRenderer';
-//# sourceMappingURL=index.js.map

package/esm/index.js

@@ -28,4 +28,3 @@ export default class extends Plugin {
         });
     }
 }
-//# sourceMappingURL=index.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-lollipop",
-  "version": "2.6.1",
+  "version": "2.6.2",
   "description": "JBrowse 2 plugin for lollipops",
   "keywords": [
     "jbrowse",
@@ -20,7 +20,6 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src",
     "esm"
   ],
   "scripts": {
@@ -33,7 +32,7 @@
     "useSrc": "node ../../scripts/useSrc.js",
     "prebuild": "npm run clean",
     "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "peerDependencies": {
@@ -52,5 +51,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
 }

package/dist/LinearLollipopDisplay/configSchema.js.map

@@ -1 +0,0 @@
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package/dist/LinearLollipopDisplay/index.js.map

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package/dist/LinearLollipopDisplay/model.js.map

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package/dist/LollipopRenderer/Layout.js.map

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package/dist/LollipopRenderer/LollipopRenderer.js.map

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package/esm/LollipopRenderer/LollipopRenderer.js.map

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package/esm/LollipopRenderer/components/Lollipop.js.map

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package/esm/LollipopRenderer/components/LollipopRendering.js.map

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package/esm/LollipopRenderer/components/ScoreText.js.map

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package/esm/LollipopRenderer/components/Stick.js.map

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package/esm/LollipopRenderer/configSchema.js.map

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package/esm/LollipopRenderer/index.js.map

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package/esm/index.js.map

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package/src/LinearLollipopDisplay/configSchema.ts

@@ -1,14 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'
-
-export function configSchemaFactory(pluginManager: PluginManager) {
-  return ConfigurationSchema(
-    'LinearLollipopDisplay',
-    { renderer: pluginManager.pluggableConfigSchemaType('renderer') },
-    {
-      baseConfiguration: baseLinearDisplayConfigSchema,
-      explicitlyTyped: true,
-    },
-  )
-}

package/src/LinearLollipopDisplay/index.ts

@@ -1,2 +0,0 @@
-export { configSchemaFactory } from './configSchema'
-export { stateModelFactory } from './model'

package/src/LinearLollipopDisplay/model.ts

@@ -1,40 +0,0 @@
-import {
-  AnyConfigurationSchemaType,
-  ConfigurationReference,
-} from '@jbrowse/core/configuration'
-import { types } from 'mobx-state-tree'
-import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view'
-
-export function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
-  return types
-    .compose(
-      'LinearLollipopDisplay',
-      BaseLinearDisplay,
-      types.model({
-        type: types.literal('LinearLollipopDisplay'),
-        configuration: ConfigurationReference(configSchema),
-      }),
-    )
-
-    .views(self => {
-      const { renderProps: superRenderProps } = self
-      return {
-        get blockType() {
-          return 'dynamicBlocks'
-        },
-        get renderDelay() {
-          return 500
-        },
-        renderProps() {
-          return {
-            ...superRenderProps(),
-            rpcDriverName: self.rpcDriverName,
-            config: self.configuration.renderer,
-          }
-        },
-        get rendererTypeName() {
-          return self.configuration.renderer.type
-        },
-      }
-    })
-}

package/src/LollipopRenderer/Layout.ts

@@ -1,172 +0,0 @@
-import { readConfObject } from '@jbrowse/core/configuration'
-import { doesIntersect2 } from '@jbrowse/core/util/range'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration'
-
-interface LayoutItem {
-  uniqueId: string
-  anchorLocation: number
-  width: number
-  height: number
-  data: { score: number }
-}
-
-type LayoutEntry = LayoutItem & { x: number; y: number }
-
-type LayoutMap = Map<string, LayoutEntry>
-
-export class FloatingLayout {
-  width: number
-
-  totalHeight = 0
-
-  constructor({ width }: { width: number }) {
-    if (!width) {
-      throw new Error('width required to make a new FloatingLayout')
-    }
-    this.width = width
-  }
-
-  items: LayoutItem[] = []
-
-  layout: LayoutMap = new Map()
-
-  layoutDirty = false
-
-  add(
-    uniqueId: string,
-    anchorLocation: number,
-    width: number,
-    height: number,
-    data: { score: number },
-  ) {
-    this.items.push({ uniqueId, anchorLocation, width, height, data })
-    this.layoutDirty = true
-  }
-
-  /**
-   * @returns Map of `uniqueId => {x,y,anchorLocation,width,height,data}`
-   */
-  getLayout(configuration?: AnyConfigurationModel) {
-    if (!this.layoutDirty) {
-      return this.layout
-    }
-    if (!configuration) {
-      throw new Error('configuration object required')
-    }
-
-    const minY = readConfObject(configuration, 'minStickLength')
-
-    // sort them by score ascending, so higher scores will always end up
-    // stacked last (toward the bottom)
-    const sorted = this.items.sort((a, b) => a.data.score - b.data.score)
-
-    // bump them
-    let maxBottom = 0
-    const layoutEntries: [string, LayoutEntry][] = new Array(sorted.length)
-    for (let i = 0; i < sorted.length; i += 1) {
-      const currentItem = sorted[i]
-      const { anchorLocation, width, height } = currentItem
-      const start = anchorLocation - width / 2
-      const end = start + width
-      let top = minY
-      let bottom = top + height
-
-      // figure out how far down to put it
-      for (let j = 0; j < i; j += 1) {
-        const [, previouslyLaidOutItem] = layoutEntries[j]
-        const {
-          x: prevStart,
-          y: prevTop,
-          width: prevWidth,
-          height: prevHeight,
-        } = previouslyLaidOutItem
-        const prevEnd = prevStart + prevWidth
-        const prevBottom = prevTop + prevHeight
-        if (
-          doesIntersect2(prevStart, prevEnd, start, end) &&
-          doesIntersect2(prevTop, prevBottom, top, bottom)
-        ) {
-          // bump this one to the bottom of the previous one
-          top = prevBottom
-          bottom = top + height
-          j = -1 // we need to check all of them again after bumping
-        }
-      }
-
-      // record the entry and update the maxBottom
-      layoutEntries[i] = [
-        currentItem.uniqueId,
-        { ...currentItem, x: start, y: top },
-      ]
-      if (bottom > maxBottom) {
-        maxBottom = bottom
-      }
-    }
-
-    // try to tile them left to right all at the same level
-    // if they don't fit, try to alternate them on 2 levels, then 3
-    this.totalHeight = maxBottom
-    this.layout = new Map(layoutEntries)
-    this.layoutDirty = false
-    return this.layout
-  }
-
-  getTotalHeight() {
-    if (this.layoutDirty) {
-      throw new Error('getTotalHeight does not work when the layout is dirty.')
-    }
-    return this.totalHeight
-  }
-
-  serializeRegion() {
-    return this.toJSON()
-  }
-
-  toJSON() {
-    if (this.layoutDirty) {
-      throw new Error('toJSON does not work when the layout is dirty.')
-    }
-    return { pairs: [...this.getLayout()], totalHeight: this.getTotalHeight() }
-  }
-
-  static fromJSON() {
-    throw new Error('not supported')
-  }
-}
-
-export class PrecomputedFloatingLayout {
-  layout: LayoutMap
-
-  totalHeight: number
-
-  constructor({
-    pairs,
-    totalHeight,
-  }: {
-    pairs: [string, LayoutEntry][]
-    totalHeight: number
-  }) {
-    this.layout = new Map(pairs)
-    this.totalHeight = totalHeight
-  }
-
-  add(uniqueId: string) {
-    if (!this.layout.has(uniqueId)) {
-      throw new Error(`layout error, precomputed layout is missing ${uniqueId}`)
-    }
-  }
-
-  getLayout() {
-    return this.layout
-  }
-
-  getTotalHeight() {
-    return this.totalHeight
-  }
-
-  static fromJSON(
-    json: ConstructorParameters<typeof PrecomputedFloatingLayout>[0],
-  ) {
-    return new PrecomputedFloatingLayout(json)
-  }
-}

package/src/LollipopRenderer/LollipopRenderer.js

@@ -1,29 +0,0 @@
-import BoxRendererType, {
-  LayoutSession,
-} from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType'
-import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout'
-import { FloatingLayout, PrecomputedFloatingLayout } from './Layout'
-
-class FloatingLayoutSession extends LayoutSession {
-  makeLayout() {
-    'sequenceAdapter'
-
-    const { end, start } = this.regions[0]
-    const widthPx = (end - start) / this.bpPerPx
-    return new MultiLayout(FloatingLayout, { width: widthPx })
-  }
-
-  layoutIsValid(/* layout */) {
-    return false // layout.left layout.width === this.width
-  }
-}
-
-export default class extends BoxRendererType {
-  createSession(args) {
-    return new FloatingLayoutSession(args)
-  }
-
-  deserializeLayoutInClient(json) {
-    return new PrecomputedFloatingLayout(json)
-  }
-}

package/src/LollipopRenderer/components/Lollipop.tsx

@@ -1,113 +0,0 @@
-import React from 'react'
-import { readConfObject } from '@jbrowse/core/configuration'
-import { observer } from 'mobx-react'
-import ScoreText from './ScoreText'
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-export default observer(function Lollipop(props: Record<string, any>) {
-  const { feature, config, layoutRecord, selectedFeatureId } = props
-  const {
-    anchorLocation,
-    y,
-    data: { radiusPx },
-  } = layoutRecord
-
-  const onFeatureMouseDown = (event: React.MouseEvent) => {
-    const { onFeatureMouseDown: handler, feature } = props
-    return handler?.(event, feature.id())
-  }
-
-  const onFeatureMouseEnter = (event: React.MouseEvent) => {
-    const { onFeatureMouseEnter: handler, feature } = props
-    return handler?.(event, feature.id())
-  }
-
-  const onFeatureMouseOut = (event: React.MouseEvent | React.FocusEvent) => {
-    const { onFeatureMouseOut: handler, feature } = props
-    return handler?.(event, feature.id())
-  }
-
-  const onFeatureMouseOver = (event: React.MouseEvent | React.FocusEvent) => {
-    const { onFeatureMouseOver: handler, feature } = props
-    return handler?.(event, feature.id())
-  }
-
-  const onFeatureMouseUp = (event: React.MouseEvent) => {
-    const { onFeatureMouseUp: handler, feature } = props
-    return handler?.(event, feature.id())
-  }
-
-  const onFeatureMouseLeave = (event: React.MouseEvent) => {
-    const { onFeatureMouseLeave: handler, feature } = props
-    return handler?.(event, feature.id())
-  }
-
-  const onFeatureMouseMove = (event: React.MouseEvent) => {
-    const { onFeatureMouseMove: handler, feature } = props
-    return handler?.(event, feature.id())
-  }
-
-  const onFeatureClick = (event: React.MouseEvent) => {
-    const { onFeatureClick: handler, feature } = props
-    event.stopPropagation()
-    return handler?.(event, feature.id())
-  }
-
-  const styleOuter = {
-    fill: readConfObject(config, 'strokeColor', { feature }),
-  }
-  if (String(selectedFeatureId) === String(feature.id())) {
-    styleOuter.fill = 'red'
-  }
-
-  const styleInner = {
-    fill: readConfObject(config, 'innerColor', { feature }),
-  }
-
-  const strokeWidth = readConfObject(config, 'strokeWidth', { feature })
-
-  return (
-    <g data-testid={feature.id()}>
-      <title>{readConfObject(config, 'caption', { feature })}</title>
-      <circle
-        cx={anchorLocation}
-        cy={y + radiusPx}
-        r={radiusPx}
-        style={styleOuter}
-        onMouseDown={onFeatureMouseDown}
-        onMouseEnter={onFeatureMouseEnter}
-        onMouseOut={onFeatureMouseOut}
-        onMouseOver={onFeatureMouseOver}
-        onMouseUp={onFeatureMouseUp}
-        onMouseLeave={onFeatureMouseLeave}
-        onMouseMove={onFeatureMouseMove}
-        onClick={onFeatureClick}
-        onFocus={onFeatureMouseOver}
-        onBlur={onFeatureMouseOut}
-      />
-      {radiusPx - strokeWidth <= 2 ? null : (
-        <circle
-          cx={anchorLocation}
-          cy={y + radiusPx}
-          r={radiusPx - strokeWidth}
-          style={styleInner}
-          onMouseDown={onFeatureMouseDown}
-          onMouseEnter={onFeatureMouseEnter}
-          onMouseOut={onFeatureMouseOut}
-          onMouseOver={onFeatureMouseOver}
-          onMouseUp={onFeatureMouseUp}
-          onMouseLeave={onFeatureMouseLeave}
-          onMouseMove={onFeatureMouseMove}
-          onClick={onFeatureClick}
-          onFocus={onFeatureMouseOver}
-          onBlur={onFeatureMouseOut}
-        />
-      )}
-      <ScoreText
-        feature={feature}
-        config={config}
-        layoutRecord={layoutRecord}
-      />
-    </g>
-  )
-})

package/src/LollipopRenderer/components/LollipopRendering.test.js

@@ -1,45 +0,0 @@
-import SimpleFeature from '@jbrowse/core/util/simpleFeature'
-import React from 'react'
-import { render } from '@testing-library/react'
-import ConfigSchema from '../configSchema'
-import { FloatingLayout, PrecomputedFloatingLayout } from '../Layout'
-import Rendering from './LollipopRendering'
-
-// these tests do very little, let's try to expand them at some point
-test('no features', () => {
-  const { container } = render(
-    <Rendering
-      width={500}
-      height={500}
-      regions={[{ refName: 'zonk', start: 0, end: 300 }]}
-      layout={new PrecomputedFloatingLayout({ pairs: [], totalHeight: 20 })}
-      config={{}}
-      bpPerPx={3}
-    />,
-  )
-
-  expect(container.firstChild).toMatchSnapshot()
-})
-
-test('one feature', () => {
-  const { container } = render(
-    <Rendering
-      width={500}
-      height={500}
-      regions={[{ refName: 'zonk', start: 0, end: 1000 }]}
-      layout={new FloatingLayout({ width: 100 })}
-      features={
-        new Map([
-          [
-            'one',
-            new SimpleFeature({ uniqueId: 'one', score: 10, start: 1, end: 3 }),
-          ],
-        ])
-      }
-      config={ConfigSchema.create({})}
-      bpPerPx={3}
-    />,
-  )
-
-  expect(container.firstChild).toMatchSnapshot()
-})

package/src/LollipopRenderer/components/LollipopRendering.tsx

@@ -1,140 +0,0 @@
-import React from 'react'
-import {
-  AnyConfigurationModel,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-import { Feature, Region, bpToPx } from '@jbrowse/core/util'
-import { observer } from 'mobx-react'
-
-// locals
-import Lollipop from './Lollipop'
-import Stick from './Stick'
-
-function layoutFeat(args: {
-  feature: Feature
-  bpPerPx: number
-  region: Region
-  layout: { add: (...args: unknown[]) => void }
-  config: AnyConfigurationModel
-}) {
-  const { feature, bpPerPx, config, region, layout } = args
-
-  const centerBp = Math.abs(feature.get('end') + feature.get('start')) / 2
-  const centerPx = bpToPx(centerBp, region, bpPerPx)
-  const radiusPx = readConfObject(config, 'radius', { feature })
-
-  if (!radiusPx) {
-    console.error(
-      new Error(
-        `lollipop radius ${radiusPx} configured for feature ${feature.id()}`,
-      ),
-    )
-  }
-  layout.add(feature.id(), centerPx, radiusPx * 2, radiusPx * 2, {
-    featureId: feature.id(),
-    anchorX: centerPx,
-    radiusPx,
-    score: readConfObject(args.config, 'score', { feature }),
-  })
-}
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-export default observer(function LollipopRendering(props: Record<string, any>) {
-  const onMouseDown = (event: React.MouseEvent) => {
-    const { onMouseDown: handler } = props
-    return handler?.(event)
-  }
-
-  const onMouseUp = (event: React.MouseEvent) => {
-    const { onMouseUp: handler } = props
-    return handler?.(event)
-  }
-
-  const onMouseEnter = (event: React.MouseEvent | React.FocusEvent) => {
-    const { onMouseEnter: handler } = props
-    return handler?.(event)
-  }
-
-  const onMouseLeave = (event: React.MouseEvent | React.FocusEvent) => {
-    const { onMouseLeave: handler } = props
-    return handler?.(event)
-  }
-
-  const onMouseOver = (event: React.MouseEvent) => {
-    const { onMouseOver: handler } = props
-    return handler?.(event)
-  }
-
-  const onMouseOut = (event: React.MouseEvent) => {
-    const { onMouseOut: handler } = props
-    return handler?.(event)
-  }
-
-  const onClick = (event: React.MouseEvent) => {
-    const { onClick: handler } = props
-    return handler?.(event)
-  }
-
-  const {
-    regions,
-    bpPerPx,
-    layout,
-    config,
-    features = new Map(),
-    displayModel = {},
-  } = props
-  const { selectedFeatureId } = displayModel
-  const [region] = regions
-  for (const feature of features.values()) {
-    layoutFeat({
-      feature,
-      bpPerPx,
-      region,
-      config,
-      layout,
-    })
-  }
-
-  const width = (region.end - region.start) / bpPerPx
-  const records = [...layout.getLayout(config).values()]
-  const height = layout.getTotalHeight()
-
-  return (
-    <svg
-      width={width}
-      height={height}
-      style={{ position: 'relative' }}
-      onMouseDown={onMouseDown}
-      onMouseUp={onMouseUp}
-      onMouseEnter={onMouseEnter}
-      onMouseLeave={onMouseLeave}
-      onMouseOver={onMouseOver}
-      onMouseOut={onMouseOut}
-      onFocus={onMouseEnter}
-      onBlur={onMouseLeave}
-      onClick={onClick}
-    >
-      {records.map(layoutRecord => {
-        const feature = features.get(layoutRecord.data.featureId)
-        return (
-          <React.Fragment key={feature.id()}>
-            <Stick
-              {...props}
-              config={config}
-              layoutRecord={layoutRecord}
-              feature={feature}
-              key={`stick-${feature.id()}`}
-            />
-            <Lollipop
-              {...props}
-              layoutRecord={layoutRecord}
-              feature={feature}
-              key={`body-${feature.id()}`}
-              selectedFeatureId={selectedFeatureId}
-            />
-          </React.Fragment>
-        )
-      })}
-    </svg>
-  )
-})

package/src/LollipopRenderer/components/ScoreText.tsx

@@ -1,43 +0,0 @@
-import React from 'react'
-import {
-  AnyConfigurationModel,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-import { contrastingTextColor } from '@jbrowse/core/util/color'
-import { Feature } from '@jbrowse/core/util'
-
-export default function ScoreText({
-  feature,
-  config,
-  layoutRecord: {
-    y,
-    data: { anchorX, radiusPx, score },
-  },
-}: {
-  feature: Feature
-  config: AnyConfigurationModel
-  layoutRecord: {
-    y: number
-    data: { anchorX: number; radiusPx: number; score: number }
-  }
-}) {
-  const innerColor = readConfObject(config, 'innerColor', { feature })
-
-  const scoreString = String(score)
-  const fontWidth = (radiusPx * 2) / scoreString.length
-  const fontHeight = fontWidth * 1.1
-  if (fontHeight < 12) {
-    return null
-  }
-  return (
-    <text
-      style={{ fontSize: fontHeight, fill: contrastingTextColor(innerColor) }}
-      x={anchorX}
-      y={y + radiusPx - fontHeight / 2.4}
-      textAnchor="middle"
-      dominantBaseline="hanging"
-    >
-      {scoreString}
-    </text>
-  )
-}

package/src/LollipopRenderer/components/Stick.tsx

@@ -1,36 +0,0 @@
-import React from 'react'
-import {
-  AnyConfigurationModel,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-import { observer } from 'mobx-react'
-import { Feature } from '@jbrowse/core/util'
-
-export default observer(function Stick({
-  feature,
-  config,
-  layoutRecord: {
-    anchorLocation,
-    y,
-    data: { radiusPx },
-  },
-}: {
-  feature: Feature
-  config: AnyConfigurationModel
-  layoutRecord: {
-    anchorLocation: number
-    y: number
-    data: { radiusPx: number }
-  }
-}) {
-  return (
-    <line
-      x1={anchorLocation}
-      y1={0}
-      x2={anchorLocation}
-      y2={y + 2 * radiusPx}
-      stroke={readConfObject(config, 'stickColor', { feature })}
-      strokeWidth={readConfObject(config, 'stickWidth', { feature })}
-    />
-  )
-})

package/src/LollipopRenderer/components/__snapshots__/LollipopRendering.test.js.snap

@@ -1,37 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`no features 1`] = `
-<svg
-  height="20"
-  style="position: relative;"
-  width="100"
-/>
-`;
-
-exports[`one feature 1`] = `
-<svg
-  height="16.286652959662007"
-  style="position: relative;"
-  width="333.3333333333333"
->
-  <line
-    stroke="black"
-    stroke-width="2"
-    x1="0.7"
-    x2="0.7"
-    y1="0"
-    y2="16.286652959662007"
-  />
-  <g
-    data-testid="one"
-  >
-    <title />
-    <circle
-      cx="0.7"
-      cy="10.643326479831003"
-      r="5.643326479831003"
-      style="fill: green;"
-    />
-  </g>
-</svg>
-`;

package/src/LollipopRenderer/configSchema.ts

@@ -1,63 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-export default ConfigurationSchema(
-  'LollipopRenderer',
-  {
-    strokeColor: {
-      type: 'color',
-      description: 'the outer color of each lollipop',
-      defaultValue: 'green',
-      contextVariable: ['feature'],
-    },
-    innerColor: {
-      type: 'color',
-      description: 'the inner color of each lollipop',
-      defaultValue: '#7fc75f',
-      contextVariable: ['feature'],
-    },
-    strokeWidth: {
-      type: 'number',
-      description: 'width of the stroked border',
-      defaultValue: 4,
-      contextVariable: ['feature'],
-    },
-    radius: {
-      type: 'number',
-      description: 'radius in pixels of each lollipop body',
-      defaultValue: `jexl:sqrt(max(3, (get(feature,'score')*10)/3.14))`,
-      contextVariable: ['feature'],
-    },
-    caption: {
-      type: 'string',
-      description:
-        'the tooltip caption displayed when the mouse hovers over a lollipop',
-      defaultValue: `jexl:get(feature,'name')`,
-      contextVariable: ['feature'],
-    },
-    minStickLength: {
-      type: 'number',
-      description: 'minimum lollipop "stick" length, in pixels',
-      defaultValue: 5,
-    },
-    stickColor: {
-      type: 'color',
-      description: 'color of the lollipop stick',
-      defaultValue: 'black',
-      contextVariable: ['feature'],
-    },
-    stickWidth: {
-      type: 'number',
-      description: 'width in pixels of the lollipop stick',
-      defaultValue: 2,
-      contextVariable: ['feature'],
-    },
-    score: {
-      type: 'number',
-      description:
-        'the "score" of each lollipop, displayed as a number in the center of the circle',
-      defaultValue: `jexl:get(feature,'score')`,
-      contextVariable: ['feature'],
-    },
-  },
-  { explicitlyTyped: true },
-)

package/src/LollipopRenderer/index.ts

@@ -1,3 +0,0 @@
-export { default as ReactComponent } from './components/LollipopRendering'
-export { default as configSchema } from './configSchema'
-export { default } from './LollipopRenderer'

package/src/index.ts

@@ -1,41 +0,0 @@
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'
-import {
-  configSchemaFactory as linearLollipopDisplayConfigSchemaFactory,
-  stateModelFactory as LinearLollipopDisplayStateModelFactory,
-} from './LinearLollipopDisplay'
-import LollipopRenderer, {
-  configSchema as lollipopRendererConfigSchema,
-  ReactComponent as LollipopRendererReactComponent,
-} from './LollipopRenderer'
-
-export default class extends Plugin {
-  name = 'LollipopPlugin'
-
-  install(pluginManager: PluginManager) {
-    pluginManager.addRendererType(
-      () =>
-        new LollipopRenderer({
-          name: 'LollipopRenderer',
-          ReactComponent: LollipopRendererReactComponent,
-          configSchema: lollipopRendererConfigSchema,
-          pluginManager,
-        }),
-    )
-
-    pluginManager.addDisplayType(() => {
-      const configSchema =
-        linearLollipopDisplayConfigSchemaFactory(pluginManager)
-      return new DisplayType({
-        name: 'LinearLollipopDisplay',
-        configSchema,
-        stateModel: LinearLollipopDisplayStateModelFactory(configSchema),
-        trackType: 'LollipopTrack',
-        viewType: 'LinearGenomeView',
-        ReactComponent: BaseLinearDisplayComponent,
-      })
-    })
-  }
-}