@jbrowse/plugin-wiggle 2.5.0 → 2.6.2

package/src/WiggleRendering.test.js

@@ -1,21 +0,0 @@
-import React from 'react'
-import { render, fireEvent } from '@testing-library/react'
-import WiggleRendering from './WiggleRendering'
-
-// these tests do very little, let's try to expand them at some point
-test('one', async () => {
-  const { container, getByTestId } = render(
-    <WiggleRendering
-      width={500}
-      height={500}
-      features={new Map()}
-      highResolutionScaling={1}
-      regions={[{ refName: 'chr1', start: 1, end: 3 }]}
-      bpPerPx={3}
-      config={{ type: 'DummyRenderer' }}
-    />,
-  )
-  const test = getByTestId('wiggle-rendering-test')
-  expect(fireEvent.click(test)).toBeTruthy()
-  expect(container.firstChild).toMatchSnapshot()
-})

package/src/WiggleRendering.tsx

@@ -1,76 +0,0 @@
-import { observer } from 'mobx-react'
-import React, { useRef } from 'react'
-
-import { Region } from '@jbrowse/core/util/types'
-import { Feature } from '@jbrowse/core/util'
-import { PrerenderedCanvas } from '@jbrowse/core/ui'
-
-function WiggleRendering(props: {
-  regions: Region[]
-  features: Map<string, Feature>
-  bpPerPx: number
-  width: number
-  height: number
-  onMouseLeave: Function
-  onMouseMove: Function
-  onFeatureClick: Function
-  blockKey: string
-}) {
-  const {
-    regions,
-    features,
-    bpPerPx,
-    width,
-    height,
-    onMouseLeave = () => {},
-    onMouseMove = () => {},
-    onFeatureClick = () => {},
-  } = props
-  const [region] = regions
-  const ref = useRef<HTMLDivElement>(null)
-
-  function getFeatureUnderMouse(eventClientX: number) {
-    // calculates feature under mouse
-    let offset = 0
-    if (ref.current) {
-      offset = ref.current.getBoundingClientRect().left
-    }
-    const offsetX = eventClientX - offset
-    const px = region.reversed ? width - offsetX : offsetX
-    const clientBp = region.start + bpPerPx * px
-    let featureUnderMouse
-    for (const feature of features.values()) {
-      // bpPerPx added to the end to accommodate "reduced features" (one feature per px)
-      if (
-        clientBp <= feature.get('end') + bpPerPx &&
-        clientBp >= feature.get('start')
-      ) {
-        featureUnderMouse = feature
-        break
-      }
-    }
-    return featureUnderMouse
-  }
-  return (
-    <div
-      ref={ref}
-      data-testid="wiggle-rendering-test"
-      onMouseMove={event =>
-        onMouseMove(event, getFeatureUnderMouse(event.clientX)?.id())
-      }
-      onClick={event =>
-        onFeatureClick(event, getFeatureUnderMouse(event.clientX)?.id())
-      }
-      onMouseLeave={event => onMouseLeave(event)}
-      style={{
-        overflow: 'visible',
-        position: 'relative',
-        height,
-      }}
-    >
-      <PrerenderedCanvas {...props} />
-    </div>
-  )
-}
-
-export default observer(WiggleRendering)

package/src/XYPlotRenderer/XYPlotRenderer.test.ts

@@ -1,52 +0,0 @@
-import { SimpleFeature, renderToAbstractCanvas } from '@jbrowse/core/util'
-import { Image, createCanvas } from 'canvas'
-
-// locals
-import configSchema from './configSchema'
-import XYPlotRenderer from './XYPlotRenderer'
-import ReactComponent from '../WiggleRendering'
-
-// @ts-expect-error
-global.nodeImage = Image
-// @ts-expect-error
-global.nodeCreateCanvas = createCanvas
-
-test('several features', async () => {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  const pluginManager = {} as any
-  const renderer = new XYPlotRenderer({
-    name: 'XYPlotRenderer',
-    ReactComponent,
-    configSchema,
-    pluginManager,
-  })
-  const renderProps = {
-    features: [
-      new SimpleFeature({ id: 't1', data: { start: 1, end: 100, score: 1 } }),
-      new SimpleFeature({ id: 't2', data: { start: 101, end: 200, score: 2 } }),
-    ],
-    regions: [
-      {
-        end: 100,
-        start: 1,
-      },
-    ],
-    scaleOpts: {
-      domain: [0, 100],
-      scaleType: 'linear',
-    },
-    config: {},
-    bpPerPx: 3,
-    highResolutionScaling: 1,
-    height: 100,
-    ticks: { values: [0, 100] },
-  }
-
-  const res = await renderToAbstractCanvas(1000, 200, renderProps, ctx =>
-    // @ts-expect-error
-    renderer.draw(ctx, renderProps),
-  )
-  expect(res).toMatchSnapshot({
-    imageData: expect.any(Object),
-  })
-})

package/src/XYPlotRenderer/XYPlotRenderer.ts

@@ -1,37 +0,0 @@
-import { readConfObject } from '@jbrowse/core/configuration'
-import { Feature } from '@jbrowse/core/util'
-import { drawXY } from '../drawxy'
-import WiggleBaseRenderer, {
-  RenderArgsDeserializedWithFeatures,
-} from '../WiggleBaseRenderer'
-import { YSCALEBAR_LABEL_OFFSET } from '../util'
-
-export default class XYPlotRenderer extends WiggleBaseRenderer {
-  async draw(
-    ctx: CanvasRenderingContext2D,
-    props: RenderArgsDeserializedWithFeatures,
-  ) {
-    const { features, config } = props
-
-    // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
-    // wiggle display, and makes the height of the actual drawn area add
-    // "padding" to the top and bottom of the display
-    const pivotValue = readConfObject(config, 'bicolorPivotValue')
-    const negColor = readConfObject(config, 'negColor')
-    const posColor = readConfObject(config, 'posColor')
-    const Color = await import('color').then(f => f.default)
-
-    return drawXY(ctx, {
-      ...props,
-      colorCallback:
-        readConfObject(config, 'color') === '#f0f'
-          ? (_: Feature, score: number) =>
-              score < pivotValue ? negColor : posColor
-          : (feature: Feature, _score: number) =>
-              readConfObject(config, 'color', { feature }),
-      offset: YSCALEBAR_LABEL_OFFSET,
-      features: [...features.values()],
-      Color,
-    })
-  }
-}

package/src/XYPlotRenderer/__snapshots__/XYPlotRenderer.test.ts.snap

@@ -1,21 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`several features 1`] = `
-{
-  "imageData": Any<Object>,
-  "reducedFeatures": [
-    {
-      "end": 100,
-      "score": 1,
-      "start": 1,
-      "uniqueId": "t1",
-    },
-    {
-      "end": 200,
-      "score": 2,
-      "start": 101,
-      "uniqueId": "t2",
-    },
-  ],
-}
-`;

package/src/XYPlotRenderer/configSchema.ts

@@ -1,55 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import baseWiggleRendererConfigSchema from '../configSchema'
-import { types } from 'mobx-state-tree'
-
-/**
- * #config XYPlotRenderer
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const configSchema = ConfigurationSchema(
-  'XYPlotRenderer',
-  {
-    /**
-     * #slot
-     */
-    filled: {
-      type: 'boolean',
-      defaultValue: true,
-    },
-    /**
-     * #slot
-     */
-    displayCrossHatches: {
-      type: 'boolean',
-      description: 'choose to draw cross hatches (sideways lines)',
-      defaultValue: false,
-    },
-    /**
-     * #slot
-     */
-    summaryScoreMode: {
-      type: 'stringEnum',
-      model: types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
-      description:
-        'choose whether to use max/min/average or whiskers which combines all three into the same rendering',
-      defaultValue: 'whiskers',
-    },
-    /**
-     * #slot
-     */
-    minSize: {
-      type: 'number',
-      defaultValue: 0,
-    },
-  },
-  {
-    /**
-     * #baseConfiguration
-     */
-    baseConfiguration: baseWiggleRendererConfigSchema,
-    explicitlyTyped: true,
-  },
-)
-
-export default configSchema

package/src/XYPlotRenderer/index.ts

@@ -1,20 +0,0 @@
-import ReactComponent from '../WiggleRendering'
-import PluginManager from '@jbrowse/core/PluginManager'
-import XYPlotRenderer from './XYPlotRenderer'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addRendererType(
-    () =>
-      new XYPlotRenderer({
-        name: 'XYPlotRenderer',
-        ReactComponent,
-        configSchema,
-        pluginManager,
-      }),
-  )
-}
-
-export { default as XYPlotRenderer } from './XYPlotRenderer'
-export { default as ReactComponent } from '../WiggleRendering'
-export { default as configSchema } from './configSchema'

package/src/__snapshots__/WiggleRendering.test.js.snap

@@ -1,15 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`one 1`] = `
-<div
-  data-testid="wiggle-rendering-test"
-  style="overflow: visible; position: relative; height: 500px;"
->
-  <canvas
-    data-testid="prerendered_canvas"
-    height="500"
-    style="width: 500px; height: 500px;"
-    width="500"
-  />
-</div>
-`;

package/src/__snapshots__/index.test.ts.snap

@@ -1,3 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`plugin in a stock JBrowse 1`] = `{}`;

package/src/configSchema.ts

@@ -1,70 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { types } from 'mobx-state-tree'
-
-/**
- * #config WiggleRenderer
- * this is the "base wiggle renderer config schema"
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const WiggleRenderer = ConfigurationSchema(
-  'WiggleRenderer',
-  {
-    /**
-     * #slot
-     */
-    color: {
-      type: 'color',
-      description: 'the color of track, overrides posColor and negColor',
-      defaultValue: '#f0f',
-    },
-    /**
-     * #slot
-     */
-    posColor: {
-      type: 'color',
-      description: 'the color to use when the score is positive',
-      defaultValue: 'blue',
-    },
-    /**
-     * #slot
-     */
-    negColor: {
-      type: 'color',
-      description: 'the color to use when the score is negative',
-      defaultValue: 'red',
-    },
-    /**
-     * #slot
-     */
-    clipColor: {
-      type: 'color',
-      description: 'the color of the clipping marker',
-      defaultValue: 'red',
-    },
-    /**
-     * #slot
-     */
-    bicolorPivot: {
-      type: 'stringEnum',
-      model: types.enumeration('Scale type', [
-        'numeric',
-        'mean',
-        'z_score',
-        'none',
-      ]),
-      description: 'type of bicolor pivot',
-      defaultValue: 'numeric',
-    },
-    /**
-     * #slot
-     */
-    bicolorPivotValue: {
-      type: 'number',
-      defaultValue: 0,
-      description: 'value to use for bicolor pivot',
-    },
-  },
-  { explicitlyTyped: true },
-)
-export default WiggleRenderer