@jbrowse/plugin-arc 2.6.1 → 2.6.3

package/dist/ArcRenderer/ArcRenderer.js

@@ -7,4 +7,3 @@ const FeatureRendererType_1 = __importDefault(require("@jbrowse/core/pluggableEl
 class default_1 extends FeatureRendererType_1.default {
 }
 exports.default = default_1;
-//# sourceMappingURL=ArcRenderer.js.map

package/dist/ArcRenderer/ArcRendering.js

@@ -59,4 +59,3 @@ function ArcRendering(props) {
         } }, arcsRendered));
 }
 exports.default = (0, mobx_react_1.observer)(ArcRendering);
-//# sourceMappingURL=ArcRendering.js.map

package/dist/ArcRenderer/configSchema.js

@@ -53,4 +53,3 @@ const ArcRenderer = (0, configuration_1.ConfigurationSchema)('ArcRenderer', {
     },
 }, { explicitlyTyped: true });
 exports.default = ArcRenderer;
-//# sourceMappingURL=configSchema.js.map

package/dist/ArcRenderer/index.js

@@ -14,4 +14,3 @@ exports.default = (pluginManager) => {
         pluginManager,
     }));
 };
-//# sourceMappingURL=index.js.map

package/dist/LinearArcDisplay/configSchema.js

@@ -22,4 +22,3 @@ function configSchemaFactory(pluginManager) {
     });
 }
 exports.configSchemaFactory = configSchemaFactory;
-//# sourceMappingURL=configSchema.js.map

package/dist/LinearArcDisplay/index.js

@@ -18,4 +18,3 @@ exports.default = (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/LinearArcDisplay/model.js

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

package/dist/index.js

@@ -20,4 +20,3 @@ class ArcPlugin extends Plugin_1.default {
     }
 }
 exports.default = ArcPlugin;
-//# sourceMappingURL=index.js.map

package/esm/ArcRenderer/ArcRenderer.js

@@ -1,4 +1,3 @@
 import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
 export default class extends FeatureRendererType {
 }
-//# sourceMappingURL=ArcRenderer.js.map

package/esm/ArcRenderer/ArcRendering.js

@@ -54,4 +54,3 @@ function ArcRendering(props) {
         } }, arcsRendered));
 }
 export default observer(ArcRendering);
-//# sourceMappingURL=ArcRendering.js.map

package/esm/ArcRenderer/configSchema.js

@@ -51,4 +51,3 @@ const ArcRenderer = ConfigurationSchema('ArcRenderer', {
     },
 }, { explicitlyTyped: true });
 export default ArcRenderer;
-//# sourceMappingURL=configSchema.js.map

package/esm/ArcRenderer/index.js

@@ -9,4 +9,3 @@ export default (pluginManager) => {
         pluginManager,
     }));
 };
-//# sourceMappingURL=index.js.map

package/esm/LinearArcDisplay/configSchema.js

@@ -18,4 +18,3 @@ export function configSchemaFactory(pluginManager) {
         explicitlyTyped: true,
     });
 }
-//# sourceMappingURL=configSchema.js.map

package/esm/LinearArcDisplay/index.js

@@ -16,4 +16,3 @@ export default (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/esm/LinearArcDisplay/model.js

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

package/esm/index.js

@@ -14,4 +14,3 @@ export default class ArcPlugin extends Plugin {
         });
     }
 }
-//# sourceMappingURL=index.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-arc",
-  "version": "2.6.1",
+  "version": "2.6.3",
   "description": "JBrowse 2 arc adapters, tracks, etc.",
   "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"
   },
   "dependencies": {
@@ -57,5 +56,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+  "gitHead": "ed402c87efb0904858d602c363bd1757d5742129"
 }

package/dist/ArcRenderer/ArcRenderer.js.map

@@ -1 +0,0 @@
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package/dist/ArcRenderer/ArcRendering.js.map

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package/dist/ArcRenderer/configSchema.js.map

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package/dist/ArcRenderer/index.js.map

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package/dist/LinearArcDisplay/configSchema.js.map

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package/dist/LinearArcDisplay/index.js.map

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package/dist/LinearArcDisplay/model.js.map

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package/dist/index.js.map

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package/esm/ArcRenderer/ArcRenderer.js.map

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package/esm/ArcRenderer/ArcRendering.js.map

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package/esm/ArcRenderer/configSchema.js.map

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package/esm/ArcRenderer/index.js.map

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package/esm/LinearArcDisplay/configSchema.js.map

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package/esm/LinearArcDisplay/index.js.map

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package/esm/LinearArcDisplay/model.js.map

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package/esm/index.js.map

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package/src/ArcRenderer/ArcRenderer.ts

@@ -1,3 +0,0 @@
-import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType'
-
-export default class extends FeatureRendererType {}

package/src/ArcRenderer/ArcRendering.test.tsx

@@ -1,45 +0,0 @@
-import SimpleFeature from '@jbrowse/core/util/simpleFeature'
-import React from 'react'
-import { render } from '@testing-library/react'
-import Rendering from './ArcRendering'
-
-test('no features', () => {
-  const { container } = render(
-    <Rendering
-      width={500}
-      height={500}
-      regions={[{ refName: 'zonk', start: 0, end: 300 }]}
-      blockKey={1}
-      config={{}}
-      bpPerPx={3}
-      displayModel={{}}
-      features={new Map()}
-    />,
-  )
-
-  expect(container.firstChild).toMatchSnapshot()
-})
-
-test('one feature', () => {
-  const { container } = render(
-    <Rendering
-      width={500}
-      height={500}
-      regions={[{ refName: 'zonk', start: 0, end: 1000 }]}
-      blockKey={1}
-      features={
-        new Map([
-          [
-            'one',
-            new SimpleFeature({ uniqueId: 'one', score: 10, start: 1, end: 3 }),
-          ],
-        ])
-      }
-      config={{ type: 'DummyRenderer' }}
-      bpPerPx={3}
-      displayModel={{}}
-    />,
-  )
-
-  expect(container.firstChild).toMatchSnapshot()
-})

package/src/ArcRenderer/ArcRendering.tsx

@@ -1,131 +0,0 @@
-import React from 'react'
-import { readConfObject } from '@jbrowse/core/configuration'
-import { bpSpanPx, measureText } from '@jbrowse/core/util'
-import { observer } from 'mobx-react'
-import { Tooltip } from 'react-svg-tooltip'
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-function ArcRendering(props: any) {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  const onClick = (event: any, id: any) => {
-    const { onFeatureClick: handler } = props
-    if (!handler) {
-      return undefined
-    }
-    return handler(event, id)
-  }
-
-  const {
-    features,
-    config,
-    regions,
-    blockKey,
-    bpPerPx,
-    displayModel: { selectedFeatureId },
-  } = props
-  const [region] = regions
-  const arcsRendered = []
-
-  for (const feature of features.values()) {
-    const [left, right] = bpSpanPx(
-      feature.get('start'),
-      feature.get('end'),
-      region,
-      bpPerPx,
-    )
-
-    const featureId = feature.id()
-    const id = blockKey + '-' + featureId
-    let stroke = readConfObject(config, 'color', { feature })
-    let textStroke = 'black'
-    if (
-      selectedFeatureId &&
-      String(selectedFeatureId) === String(feature.id())
-    ) {
-      stroke = textStroke = 'red'
-    }
-    const label = readConfObject(config, 'label', { feature })
-    const caption = readConfObject(config, 'caption', { feature })
-    const strokeWidth = readConfObject(config, 'thickness', { feature }) || 1
-    const height = readConfObject(config, 'height', { feature }) || 100
-    const ref = React.createRef<SVGPathElement>()
-    const tooltipWidth = 20 + measureText(caption?.toString())
-
-    const t = 0.5
-    // formula: https://en.wikipedia.org/wiki/B%C3%A9zier_curve#Cubic_B%C3%A9zier_curves
-    const textYCoord =
-      (1 - t) * (1 - t) * (1 - t) * 0 +
-      3 * ((1 - t) * (1 - t)) * (t * height) +
-      3 * (1 - t) * (t * t) * height +
-      t * t * t * 0
-
-    arcsRendered.push(
-      <g key={id} onClick={e => onClick(e, featureId)}>
-        <path
-          id={id}
-          d={`M ${left} 0 C ${left} ${height}, ${right} ${height}, ${right} 0`}
-          stroke={stroke}
-          strokeWidth={strokeWidth}
-          fill="transparent"
-          onClick={e => onClick(e, featureId)}
-          ref={ref}
-          pointerEvents="stroke"
-        />
-        <Tooltip triggerRef={ref}>
-          <rect
-            x={12}
-            y={0}
-            width={tooltipWidth}
-            height={20}
-            rx={5}
-            ry={5}
-            fill="black"
-            fillOpacity="50%"
-          />
-          <text
-            x={22}
-            y={14}
-            fontSize={10}
-            fill="white"
-            textLength={tooltipWidth - 20}
-          >
-            {caption}
-          </text>
-        </Tooltip>
-        <text
-          x={left + (right - left) / 2}
-          y={textYCoord + 3}
-          style={{ stroke: 'white', strokeWidth: '0.6em' }}
-        >
-          {label}
-        </text>
-        <text
-          x={left + (right - left) / 2}
-          y={textYCoord + 3}
-          style={{ stroke: textStroke }}
-        >
-          {label}
-        </text>
-      </g>,
-    )
-  }
-
-  const width = (region.end - region.start) / bpPerPx
-  const height = 500
-
-  return (
-    <svg
-      className="ArcRendering"
-      width={width}
-      height={height}
-      style={{
-        outline: 'none',
-        position: 'relative',
-      }}
-    >
-      {arcsRendered}
-    </svg>
-  )
-}
-
-export default observer(ArcRendering)

package/src/ArcRenderer/__snapshots__/ArcRendering.test.tsx.snap

@@ -1,40 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`no features 1`] = `
-<svg
-  class="ArcRendering"
-  height="500"
-  style="outline: none; position: relative;"
-  width="100"
-/>
-`;
-
-exports[`one feature 1`] = `
-<svg
-  class="ArcRendering"
-  height="500"
-  style="outline: none; position: relative;"
-  width="333.3333333333333"
->
-  <g>
-    <path
-      d="M 0.3 0 C 0.3 100, 1 100, 1 0"
-      fill="transparent"
-      id="1-one"
-      pointer-events="stroke"
-      stroke-width="1"
-    />
-    <g />
-    <text
-      style="stroke: white; stroke-width: 0.6em;"
-      x="0.6499999999999999"
-      y="78"
-    />
-    <text
-      style="stroke: black;"
-      x="0.6499999999999999"
-      y="78"
-    />
-  </g>
-</svg>
-`;

package/src/ArcRenderer/configSchema.ts

@@ -1,60 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config ArcRenderer
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const ArcRenderer = ConfigurationSchema(
-  'ArcRenderer',
-  {
-    /**
-     * #slot
-     */
-    color: {
-      type: 'color',
-      description: 'the color of the arcs',
-      defaultValue: 'darkblue',
-      contextVariable: ['feature'],
-    },
-    /**
-     * #slot
-     */
-    thickness: {
-      type: 'number',
-      description: 'the thickness of the arcs',
-      defaultValue: `jexl:logThickness(feature,'score')`,
-      contextVariable: ['feature'],
-    },
-    /**
-     * #slot
-     */
-    label: {
-      type: 'string',
-      description: 'the label to appear at the apex of the arcs',
-      defaultValue: `jexl:get(feature,'score')`,
-      contextVariable: ['feature'],
-    },
-    /**
-     * #slot
-     */
-    height: {
-      type: 'number',
-      description: 'the height of the arcs',
-      defaultValue: `jexl:log10(get(feature,'end')-get(feature,'start'))*50`,
-      contextVariable: ['feature'],
-    },
-    /**
-     * #slot
-     */
-    caption: {
-      type: 'string',
-      description:
-        'the caption to appear when hovering over any point on the arcs',
-      defaultValue: `jexl:get(feature,'name')`,
-      contextVariable: ['feature'],
-    },
-  },
-  { explicitlyTyped: true },
-)
-export default ArcRenderer

package/src/ArcRenderer/index.ts

@@ -1,17 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-
-import ReactComponent from './ArcRendering'
-import configSchema from './configSchema'
-import ArcRenderer from './ArcRenderer'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addRendererType(
-    () =>
-      new ArcRenderer({
-        name: 'ArcRenderer',
-        ReactComponent,
-        configSchema,
-        pluginManager,
-      }),
-  )
-}

package/src/LinearArcDisplay/configSchema.ts

@@ -1,29 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { types } from 'mobx-state-tree'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'
-
-/**
- * #config LinearArcDisplay
- */
-export function configSchemaFactory(pluginManager: PluginManager) {
-  return ConfigurationSchema(
-    'LinearArcDisplay',
-    {
-      /**
-       * #slot
-       */
-      renderer: types.optional(
-        pluginManager.pluggableConfigSchemaType('renderer'),
-        { type: 'ArcRenderer' },
-      ),
-    },
-    {
-      /**
-       * #baseConfiguration
-       */
-      baseConfiguration: baseLinearDisplayConfigSchema,
-      explicitlyTyped: true,
-    },
-  )
-}

package/src/LinearArcDisplay/index.ts

@@ -1,21 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { DisplayType } from '@jbrowse/core/pluggableElementTypes'
-import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'
-
-import { configSchemaFactory } from './configSchema'
-import { stateModelFactory } from './model'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addDisplayType(() => {
-    const configSchema = configSchemaFactory(pluginManager)
-    return new DisplayType({
-      name: 'LinearArcDisplay',
-      displayName: 'Arc display',
-      configSchema,
-      stateModel: stateModelFactory(configSchema),
-      trackType: 'FeatureTrack',
-      viewType: 'LinearGenomeView',
-      ReactComponent: BaseLinearDisplayComponent,
-    })
-  })
-}

package/src/LinearArcDisplay/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(
-      'LinearArcDisplay',
-      BaseLinearDisplay,
-      types.model({
-        type: types.literal('LinearArcDisplay'),
-        configuration: ConfigurationReference(configSchema),
-      }),
-    )
-
-    .views(self => {
-      const { renderProps: superRenderProps } = self
-      return {
-        get blockType() {
-          return 'staticBlocks'
-        },
-        get renderDelay() {
-          return 500
-        },
-        renderProps() {
-          return {
-            ...superRenderProps(),
-            rpcDriverName: self.rpcDriverName,
-            config: self.configuration.renderer,
-          }
-        },
-        get rendererTypeName() {
-          return self.configuration.renderer.type
-        },
-      }
-    })
-}

package/src/declare.d.ts

@@ -1 +0,0 @@
-declare module '*.json'

package/src/index.ts

@@ -1,20 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import LinearArcDisplayF from './LinearArcDisplay'
-import ArcRendererF from './ArcRenderer'
-import { Feature } from '@jbrowse/core/util'
-
-export default class ArcPlugin extends Plugin {
-  name = 'ArcRenderer'
-  install(pluginManager: PluginManager) {
-    ArcRendererF(pluginManager)
-    LinearArcDisplayF(pluginManager)
-
-    pluginManager.jexl.addFunction(
-      'logThickness',
-      (feature: Feature, attributeName: string) => {
-        return Math.log(feature.get(attributeName) + 1)
-      },
-    )
-  }
-}