@jbrowse/plugin-wiggle 2.5.0 → 2.6.2

package/src/MultiWiggleRendering.tsx

@@ -1,125 +0,0 @@
-import { observer } from 'mobx-react'
-import React, { useRef } from 'react'
-
-import { Region } from '@jbrowse/core/util/types'
-import { SimpleFeature, Feature } from '@jbrowse/core/util'
-import { PrerenderedCanvas } from '@jbrowse/core/ui'
-import { Source } from './util'
-
-function WiggleRendering(props: {
-  regions: Region[]
-  features: Map<string, Feature>
-  bpPerPx: number
-  width: number
-  height: number
-  onMouseLeave: Function
-  onMouseMove: Function
-  onFeatureClick: Function
-  blockKey: string
-  sources: Source[]
-  displayModel: { isMultiRow: boolean }
-}) {
-  const {
-    regions,
-    features,
-    bpPerPx,
-    width,
-    height,
-    sources,
-    onMouseLeave = () => {},
-    onMouseMove = () => {},
-    onFeatureClick = () => {},
-    displayModel,
-  } = props
-  const [region] = regions
-  const ref = useRef<HTMLDivElement>(null)
-
-  function getFeatureUnderMouse(eventClientX: number, eventClientY: number) {
-    if (!ref.current) {
-      return
-    }
-    const rect = ref.current.getBoundingClientRect()
-    const offsetX = eventClientX - rect.left
-    const offsetY = eventClientY - rect.top
-    const source = sources[Math.floor((offsetY / height) * sources.length)]
-    if (!source) {
-      return
-    }
-    const px = region.reversed ? width - offsetX : offsetX
-    const mouseoverBp = region.start + bpPerPx * px
-    let featureUnderMouse
-    if (displayModel.isMultiRow) {
-      for (const feature of features.values()) {
-        if (feature.get('source') !== source.name) {
-          continue
-        }
-        if (
-          mouseoverBp <= feature.get('end') + bpPerPx &&
-          mouseoverBp >= feature.get('start')
-        ) {
-          featureUnderMouse = feature
-          break
-        }
-      }
-    } else {
-      const featuresUnderMouse = []
-      for (const feature of features.values()) {
-        if (
-          mouseoverBp <= feature.get('end') + bpPerPx &&
-          mouseoverBp >= feature.get('start')
-        ) {
-          featuresUnderMouse.push(feature)
-        }
-      }
-
-      if (featuresUnderMouse.length) {
-        const pos = Math.floor(mouseoverBp)
-        featureUnderMouse = new SimpleFeature({
-          uniqueId: 'mouseoverfeat',
-          sources: Object.fromEntries(
-            featuresUnderMouse
-              .map(f => f.toJSON())
-              .map(f => {
-                const { refName, start, end, source, ...rest } = f
-                return [source, rest]
-              }),
-          ),
-          ...region,
-          start: pos,
-          end: pos + 1,
-        })
-      }
-    }
-    return featureUnderMouse
-  }
-
-  return (
-    <div
-      ref={ref}
-      onMouseMove={event => {
-        const featureUnderMouse = getFeatureUnderMouse(
-          event.clientX,
-          event.clientY,
-        )
-        onMouseMove(event, featureUnderMouse)
-      }}
-      onClick={event => {
-        const featureUnderMouse = getFeatureUnderMouse(
-          event.clientX,
-          event.clientY,
-        )
-        onFeatureClick(event, featureUnderMouse)
-      }}
-      onMouseLeave={event => onMouseLeave(event)}
-      style={{
-        overflow: 'visible',
-        position: 'relative',
-        height,
-      }}
-    >
-      <PrerenderedCanvas {...props} />
-    </div>
-  )
-}
-
-export default observer(WiggleRendering)

package/src/MultiXYPlotRenderer/MultiXYPlotRenderer.ts

@@ -1,32 +0,0 @@
-import { Feature } from '@jbrowse/core/util'
-import { drawXY } from '../drawxy'
-import { groupBy, YSCALEBAR_LABEL_OFFSET } from '../util'
-
-import WiggleBaseRenderer, {
-  MultiRenderArgsDeserialized as MultiArgs,
-} from '../WiggleBaseRenderer'
-
-export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
-  // @ts-expect-error
-  async draw(ctx: CanvasRenderingContext2D, props: MultiArgs) {
-    const { sources, features } = props
-    const groups = groupBy([...features.values()], f => f.get('source'))
-    const Color = await import('color').then(f => f.default)
-    let feats = [] as Feature[]
-    for (const source of sources) {
-      const features = groups[source.name]
-      if (!features) {
-        continue
-      }
-      const { reducedFeatures } = drawXY(ctx, {
-        ...props,
-        features,
-        offset: YSCALEBAR_LABEL_OFFSET,
-        colorCallback: () => source.color || 'blue',
-        Color,
-      })
-      feats = [...feats, ...reducedFeatures]
-    }
-    return { reducedFeatures: feats }
-  }
-}

package/src/MultiXYPlotRenderer/configSchema.ts

@@ -1,54 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { types } from 'mobx-state-tree'
-import baseWiggleRendererConfigSchema from '../configSchema'
-
-/**
- * #config MultiXYPlotRenderer
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const configSchema = ConfigurationSchema(
-  'MultiXYPlotRenderer',
-  {
-    /**
-     * #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: 'avg',
-    },
-    /**
-     * #slot
-     */
-    minSize: {
-      type: 'number',
-      defaultValue: 0,
-    },
-  },
-  {
-    /**
-     * #baseConfiguration
-     */
-    baseConfiguration: baseWiggleRendererConfigSchema,
-    explicitlyTyped: true,
-  },
-)
-export default configSchema

package/src/MultiXYPlotRenderer/index.ts

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

package/src/QuantitativeTrack/configSchema.ts

@@ -1,23 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes/models'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-/**
- * #config QuantitativeTrack
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-function configSchemaFactory(pluginManager: PluginManager) {
-  return ConfigurationSchema(
-    'QuantitativeTrack',
-    {},
-    {
-      /**
-       * #baseConfiguration
-       */
-      baseConfiguration: createBaseTrackConfig(pluginManager),
-    },
-  )
-}
-
-export default configSchemaFactory

package/src/QuantitativeTrack/index.ts

@@ -1,20 +0,0 @@
-import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models'
-import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
-import PluginManager from '@jbrowse/core/PluginManager'
-import configSchemaF from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addTrackType(() => {
-    const configSchema = configSchemaF(pluginManager)
-    return new TrackType({
-      name: 'QuantitativeTrack',
-      displayName: 'Quantitative track',
-      configSchema,
-      stateModel: createBaseTrackModel(
-        pluginManager,
-        'QuantitativeTrack',
-        configSchema,
-      ),
-    })
-  })
-}

package/src/Tooltip.tsx

@@ -1,123 +0,0 @@
-import React, { useMemo, useState } from 'react'
-import { observer } from 'mobx-react'
-import { alpha, Portal } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import { Feature } from '@jbrowse/core/util'
-
-// locals
-import { YSCALEBAR_LABEL_OFFSET, round } from './util'
-import { usePopper } from 'react-popper'
-
-const useStyles = makeStyles()(theme => ({
-  // these styles come from
-  // https://github.com/mui-org/material-ui/blob/master/packages/material-ui/src/Tooltip/Tooltip.js
-  tooltip: {
-    position: 'absolute',
-    pointerEvents: 'none',
-    backgroundColor: alpha(theme.palette.grey[700], 0.9),
-    borderRadius: theme.shape.borderRadius,
-    color: theme.palette.common.white,
-    fontFamily: theme.typography.fontFamily,
-    padding: '4px 8px',
-    fontSize: theme.typography.pxToRem(12),
-    lineHeight: `${round(14 / 10)}em`,
-    maxWidth: 300,
-    wordWrap: 'break-word',
-  },
-
-  hoverVertical: {
-    background: '#333',
-    border: 'none',
-    width: 1,
-    height: '100%',
-    top: YSCALEBAR_LABEL_OFFSET,
-    cursor: 'default',
-    position: 'absolute',
-    pointerEvents: 'none',
-  },
-}))
-
-type Coord = [number, number]
-
-// React.forwardRef component for the tooltip, the ref is used for measuring
-// the size of the tooltip
-export type TooltipContentsComponent = React.ForwardRefExoticComponent<
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  { feature: Feature; model: any } & React.RefAttributes<HTMLDivElement>
->
-
-function Tooltip({
-  model,
-  height,
-  clientMouseCoord,
-  offsetMouseCoord,
-  clientRect,
-  TooltipContents,
-  useClientY,
-}: {
-  model: { featureUnderMouse: Feature }
-  useClientY?: boolean
-  height: number
-  clientMouseCoord: Coord
-  offsetMouseCoord: Coord
-  clientRect?: DOMRect
-  TooltipContents: TooltipContentsComponent
-}) {
-  const { featureUnderMouse } = model
-  const [width, setWidth] = useState(0)
-  const [anchorEl, setAnchorEl] = useState<HTMLDivElement | null>(null)
-  const { classes } = useStyles()
-
-  // must be memoized a la https://github.com/popperjs/react-popper/issues/391
-  const virtElement = useMemo(
-    () => ({
-      getBoundingClientRect: () => {
-        const x = clientMouseCoord[0] + width / 2 + 20
-        const y = useClientY ? clientMouseCoord[1] : clientRect?.top || 0
-        return {
-          top: y,
-          left: x,
-          bottom: y,
-          right: x,
-          width: 0,
-          height: 0,
-          x,
-          y,
-          toJSON() {},
-        }
-      },
-    }),
-    [clientRect?.top, clientMouseCoord, width, useClientY],
-  )
-  const { styles, attributes } = usePopper(virtElement, anchorEl)
-
-  return featureUnderMouse ? (
-    <>
-      <Portal>
-        <div
-          ref={setAnchorEl}
-          className={classes.tooltip}
-          // zIndex needed to go over widget drawer
-          style={{ ...styles.popper, zIndex: 100000 }}
-          {...attributes.popper}
-        >
-          <TooltipContents
-            ref={elt => setWidth(elt?.getBoundingClientRect().width || 0)}
-            model={model}
-            feature={featureUnderMouse}
-          />
-        </div>
-      </Portal>
-
-      <div
-        className={classes.hoverVertical}
-        style={{
-          left: offsetMouseCoord[0],
-          height: height - YSCALEBAR_LABEL_OFFSET * 2,
-        }}
-      />
-    </>
-  ) : null
-}
-
-export default observer(Tooltip)

package/src/WiggleBaseRenderer.tsx

@@ -1,91 +0,0 @@
-import FeatureRendererType, {
-  RenderArgs as FeatureRenderArgs,
-  RenderArgsDeserialized as FeatureRenderArgsDeserialized,
-} from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType'
-import { renderToAbstractCanvas, Feature } from '@jbrowse/core/util'
-import { ThemeOptions } from '@mui/material'
-import { ScaleOpts, Source } from './util'
-
-export interface RenderArgs extends FeatureRenderArgs {
-  scaleOpts: ScaleOpts
-}
-
-export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
-  bpPerPx: number
-  height: number
-  highResolutionScaling: number
-  scaleOpts: ScaleOpts
-  displayCrossHatches: boolean
-  ticks: { values: number[] }
-  themeOptions: ThemeOptions
-}
-
-export interface RenderArgsDeserializedWithFeatures
-  extends RenderArgsDeserialized {
-  features: Map<string, Feature>
-}
-
-export interface MultiRenderArgsDeserialized
-  extends RenderArgsDeserializedWithFeatures {
-  sources: Source[]
-}
-
-export default abstract class WiggleBaseRenderer extends FeatureRendererType {
-  supportsSVG = true
-
-  async render(renderProps: RenderArgsDeserialized) {
-    const features = await this.getFeatures(renderProps)
-    const { height, regions, bpPerPx } = renderProps
-    const [region] = regions
-    const width = (region.end - region.start) / bpPerPx
-
-    // @ts-expect-error
-    const { reducedFeatures, ...rest } = await renderToAbstractCanvas(
-      width,
-      height,
-      renderProps,
-      ctx =>
-        this.draw(ctx, {
-          ...renderProps,
-          features,
-        }),
-    )
-
-    const results = await super.render({
-      ...renderProps,
-      ...rest,
-      features,
-      height,
-      width,
-    })
-
-    return {
-      ...results,
-      ...rest,
-      features: reducedFeatures
-        ? new Map<string, Feature>(
-            reducedFeatures.map((r: Feature) => [r.id(), r]),
-          )
-        : results.features,
-      height,
-      width,
-      containsNoTransferables: true,
-    }
-  }
-
-  /**
-   * draw features to context given props, to be used by derived renderer
-   * classes
-   */
-  abstract draw<T extends RenderArgsDeserializedWithFeatures>(
-    ctx: CanvasRenderingContext2D,
-    props: T,
-  ): Promise<Record<string, unknown> | void>
-}
-
-export {
-  type RenderArgsSerialized,
-  type RenderResults,
-  type ResultsDeserialized,
-  type ResultsSerialized,
-} from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType'

package/src/WiggleRPC/MultiWiggleGetSources.ts

@@ -1,68 +0,0 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
-import { renameRegionsIfNeeded, Region } from '@jbrowse/core/util'
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration'
-
-export class MultiWiggleGetSources extends RpcMethodType {
-  name = 'MultiWiggleGetSources'
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  async deserializeArguments(args: any, rpcDriverClassName: string) {
-    const l = await super.deserializeArguments(args, rpcDriverClassName)
-    return {
-      ...l,
-      filters: args.filters
-        ? new SerializableFilterChain({
-            filters: args.filters,
-          })
-        : undefined,
-    }
-  }
-
-  async serializeArguments(
-    args: RenderArgs & {
-      signal?: AbortSignal
-      statusCallback?: (arg: string) => void
-    },
-    rpcDriverClassName: string,
-  ) {
-    const pm = this.pluginManager
-    const assemblyManager = pm.rootModel?.session?.assemblyManager
-    if (!assemblyManager) {
-      return args
-    }
-
-    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
-      ...args,
-      filters: args.filters?.toJSON().filters,
-    })
-
-    return super.serializeArguments(renamedArgs, rpcDriverClassName)
-  }
-
-  async execute(
-    args: {
-      adapterConfig: AnyConfigurationModel
-      signal?: RemoteAbortSignal
-      sessionId: string
-      headers?: Record<string, string>
-      regions: Region[]
-      bpPerPx: number
-    },
-    rpcDriverClassName: string,
-  ) {
-    const pm = this.pluginManager
-    const deserializedArgs = await this.deserializeArguments(
-      args,
-      rpcDriverClassName,
-    )
-    const { regions, adapterConfig, sessionId } = deserializedArgs
-    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
-
-    // @ts-expect-error
-    return dataAdapter.getSources(regions, deserializedArgs)
-  }
-}

package/src/WiggleRPC/WiggleGetGlobalQuantitativeStats.ts

@@ -1,44 +0,0 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
-import { QuantitativeStats } from '@jbrowse/core/util/stats'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration'
-
-export class WiggleGetGlobalQuantitativeStats extends RpcMethodType {
-  name = 'WiggleGetGlobalQuantitativeStats'
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  async deserializeArguments(args: any, rpcDriverClassName: string) {
-    const l = await super.deserializeArguments(args, rpcDriverClassName)
-    return {
-      ...l,
-      filters: args.filters
-        ? new SerializableFilterChain({
-            filters: args.filters,
-          })
-        : undefined,
-    }
-  }
-
-  async execute(
-    args: {
-      adapterConfig: AnyConfigurationModel
-      signal?: RemoteAbortSignal
-      headers?: Record<string, string>
-      sessionId: string
-    },
-    rpcDriverClassName: string,
-  ): Promise<QuantitativeStats> {
-    const pm = this.pluginManager
-    const deserializedArgs = await this.deserializeArguments(
-      args,
-      rpcDriverClassName,
-    )
-    const { adapterConfig, sessionId } = deserializedArgs
-    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
-
-    // @ts-expect-error
-    return dataAdapter.getGlobalStats(deserializedArgs)
-  }
-}

package/src/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.ts

@@ -1,73 +0,0 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
-import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
-import { Region, renameRegionsIfNeeded } from '@jbrowse/core/util'
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-
-export class WiggleGetMultiRegionQuantitativeStats extends RpcMethodType {
-  name = 'WiggleGetMultiRegionQuantitativeStats'
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  async deserializeArguments(args: any, rpcDriverClassName: string) {
-    const l = await super.deserializeArguments(args, rpcDriverClassName)
-    return {
-      ...l,
-      filters: args.filters
-        ? new SerializableFilterChain({
-            filters: args.filters,
-          })
-        : undefined,
-    }
-  }
-
-  async serializeArguments(
-    args: RenderArgs & {
-      signal?: AbortSignal
-      statusCallback?: (arg: string) => void
-    },
-    rpcDriverClassName: string,
-  ) {
-    const pm = this.pluginManager
-    const assemblyManager = pm.rootModel?.session?.assemblyManager
-    if (!assemblyManager) {
-      return args
-    }
-
-    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
-      ...args,
-      filters: args.filters?.toJSON().filters,
-    })
-
-    return super.serializeArguments(renamedArgs, rpcDriverClassName)
-  }
-
-  async execute(
-    args: {
-      adapterConfig: {}
-      signal?: RemoteAbortSignal
-      sessionId: string
-      headers?: Record<string, string>
-      regions: Region[]
-      bpPerPx: number
-    },
-    rpcDriverClassName: string,
-  ) {
-    const pm = this.pluginManager
-    const deserializedArgs = await this.deserializeArguments(
-      args,
-      rpcDriverClassName,
-    )
-    const { regions, adapterConfig, sessionId } = deserializedArgs
-    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
-
-    if (dataAdapter instanceof BaseFeatureDataAdapter) {
-      return dataAdapter.getMultiRegionQuantitativeStats(
-        regions,
-        deserializedArgs,
-      )
-    }
-    throw new Error('Data adapter not found')
-  }
-}

package/src/WiggleRPC/rpcMethods.ts

@@ -1,3 +0,0 @@
-export * from './MultiWiggleGetSources'
-export * from './WiggleGetMultiRegionQuantitativeStats'
-export * from './WiggleGetGlobalQuantitativeStats'