@jbrowse/plugin-wiggle 2.6.1 → 2.6.3

package/src/MultiRowLineRenderer/configSchema.ts

@@ -1,42 +0,0 @@
-import { types } from 'mobx-state-tree'
-
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import baseWiggleRendererConfigSchema from '../configSchema'
-
-/**
- * #config MultiRowLineRenderer
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const configSchema = ConfigurationSchema(
-  'MultiRowLineRenderer',
-  {
-    /**
-     * #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',
-    },
-  },
-  {
-    /**
-     * #baseConfiguration
-     */
-    baseConfiguration: baseWiggleRendererConfigSchema,
-    explicitlyTyped: true,
-  },
-)
-
-export default configSchema

package/src/MultiRowLineRenderer/index.ts

@@ -1,16 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import ReactComponent from '../MultiWiggleRendering'
-import MultiRowLineRenderer from './MultiRowLineRenderer'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addRendererType(
-    () =>
-      new MultiRowLineRenderer({
-        name: 'MultiRowLineRenderer',
-        ReactComponent,
-        configSchema,
-        pluginManager,
-      }),
-  )
-}

package/src/MultiRowXYPlotRenderer/MultiRowXYPlotRenderer.ts

@@ -1,42 +0,0 @@
-import { groupBy, Feature } from '@jbrowse/core/util'
-import { drawXY } from '../drawxy'
-
-import WiggleBaseRenderer, {
-  MultiRenderArgsDeserialized as MultiArgs,
-} from '../WiggleBaseRenderer'
-
-export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
-  // @ts-expect-error
-  async draw(ctx: CanvasRenderingContext2D, props: MultiArgs) {
-    const { bpPerPx, sources, regions, features } = props
-    const [region] = regions
-    const groups = groupBy([...features.values()], f => f.get('source'))
-    const height = props.height / Object.keys(groups).length
-    const width = (region.end - region.start) / bpPerPx
-    const Color = await import('color').then(f => f.default)
-    let feats = [] as Feature[]
-    ctx.save()
-    sources.forEach(source => {
-      const features = groups[source.name]
-      if (!features) {
-        return
-      }
-      const { reducedFeatures } = drawXY(ctx, {
-        ...props,
-        features,
-        height,
-        colorCallback: () => source.color || 'blue',
-        Color,
-      })
-      ctx.strokeStyle = 'rgba(200,200,200,0.8)'
-      ctx.beginPath()
-      ctx.moveTo(0, height)
-      ctx.lineTo(width, height)
-      ctx.stroke()
-      ctx.translate(0, height)
-      feats = [...feats, ...reducedFeatures]
-    })
-    ctx.restore()
-    return { reducedFeatures: feats }
-  }
-}

package/src/MultiRowXYPlotRenderer/configSchema.ts

@@ -1,56 +0,0 @@
-import { types } from 'mobx-state-tree'
-
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import baseWiggleRendererConfigSchema from '../configSchema'
-
-/**
- * #config MultiRowXYPlotRenderer
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const configSchema = ConfigurationSchema(
-  'MultiRowXYPlotRenderer',
-  {
-    /**
-     * #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/MultiRowXYPlotRenderer/index.ts

@@ -1,16 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import ReactComponent from '../MultiWiggleRendering'
-import MultiRowXYPlotRenderer from './MultiRowXYPlotRenderer'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addRendererType(
-    () =>
-      new MultiRowXYPlotRenderer({
-        name: 'MultiRowXYPlotRenderer',
-        ReactComponent,
-        configSchema,
-        pluginManager,
-      }),
-  )
-}

package/src/MultiWiggleAdapter/MultiWiggleAdapter.ts

@@ -1,125 +0,0 @@
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { AugmentedRegion as Region } from '@jbrowse/core/util/types'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { SimpleFeature, Feature, min, max } from '@jbrowse/core/util'
-import { merge } from 'rxjs'
-import { map } from 'rxjs/operators'
-
-interface WiggleOptions extends BaseOptions {
-  resolution?: number
-}
-
-function getFilename(uri: string) {
-  const filename = uri.slice(uri.lastIndexOf('/') + 1)
-  return filename.slice(0, filename.lastIndexOf('.'))
-}
-
-interface AdapterEntry {
-  dataAdapter: BaseFeatureDataAdapter
-  source: string
-  [key: string]: unknown
-}
-
-export default class MultiWiggleAdapter extends BaseFeatureDataAdapter {
-  public static capabilities = [
-    'hasResolution',
-    'hasLocalStats',
-    'hasGlobalStats',
-  ]
-
-  public async getAdapters(): Promise<AdapterEntry[]> {
-    const getSubAdapter = this.getSubAdapter
-    if (!getSubAdapter) {
-      throw new Error('no getSubAdapter available')
-    }
-    let subConfs = this.getConf('subadapters')
-    if (!subConfs?.length) {
-      const entries = this.getConf('bigWigs') as string[]
-      subConfs = entries.map(entry => ({
-        type: 'BigWigAdapter',
-        source: getFilename(entry),
-        bigWigLocation: {
-          uri: entry,
-        },
-      }))
-    }
-
-    return Promise.all(
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      subConfs.map(async (conf: any) => {
-        const dataAdapter = (await getSubAdapter(conf))
-          .dataAdapter as BaseFeatureDataAdapter
-        return {
-          source: conf.name || dataAdapter.id,
-          ...conf,
-          dataAdapter,
-        }
-      }),
-    )
-  }
-
-  // note: can't really have dis-agreeing refNames
-  public async getRefNames(opts?: BaseOptions) {
-    const adapters = await this.getAdapters()
-    const allNames = await Promise.all(
-      adapters.map(a => a.dataAdapter.getRefNames(opts)),
-    )
-    return [...new Set(allNames.flat())]
-  }
-
-  public async getGlobalStats(opts?: BaseOptions) {
-    const adapters = await this.getAdapters()
-    const stats = (
-      await Promise.all(
-        // @ts-expect-error
-        adapters.map(adp => adp.dataAdapter.getGlobalStats?.(opts)),
-      )
-    ).filter(f => !!f)
-    const scoreMin = min(stats.map(s => s.scoreMin))
-    const scoreMax = max(stats.map(s => s.scoreMax))
-    return { scoreMin, scoreMax }
-  }
-
-  public getFeatures(region: Region, opts: WiggleOptions = {}) {
-    return ObservableCreate<Feature>(async observer => {
-      const adapters = await this.getAdapters()
-      merge(
-        ...adapters.map(adp =>
-          adp.dataAdapter.getFeatures(region, opts).pipe(
-            map(p =>
-              // add source field if it does not exist
-              p.get('source')
-                ? p
-                : new SimpleFeature({
-                    ...p.toJSON(),
-                    uniqueId: `${adp.source}-${p.id()}`,
-                    source: adp.source,
-                  }),
-            ),
-          ),
-        ),
-      ).subscribe(observer)
-    }, opts.signal)
-  }
-
-  // always render bigwig instead of calculating a feature density for it
-  async getMultiRegionFeatureDensityStats(_regions: Region[]) {
-    return { featureDensity: 0 }
-  }
-
-  // in another adapter type, this could be dynamic depending on region or
-  // something, but it is static for this particular multi-wiggle adapter type
-  async getSources() {
-    const adapters = await this.getAdapters()
-    return adapters.map(({ dataAdapter, source, name, ...rest }) => ({
-      name: source,
-      __name: name,
-      ...rest,
-    }))
-  }
-
-  public freeResources(): void {}
-}

package/src/MultiWiggleAdapter/configSchema.ts

@@ -1,32 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config MultiWiggleAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const MultiWiggleAdapter = ConfigurationSchema(
-  'MultiWiggleAdapter',
-  {
-    /**
-     * #slot
-     */
-    subadapters: {
-      type: 'frozen',
-      defaultValue: [],
-      description: 'array of subadapter JSON objects',
-    },
-    /**
-     * #slot
-     */
-    bigWigs: {
-      type: 'frozen',
-      description:
-        'array of bigwig filenames, alternative to the subadapters slot',
-      defaultValue: [],
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default MultiWiggleAdapter

package/src/MultiWiggleAdapter/index.ts

@@ -1,24 +0,0 @@
-import configSchema from './configSchema'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'MultiWiggleAdapter',
-        displayName: 'Multi-wiggle adapter',
-        configSchema,
-        adapterCapabilities: [
-          'hasResolution',
-          'hasLocalStats',
-          'hasGlobalStats',
-        ],
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-        getAdapterClass: () =>
-          import('./MultiWiggleAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/MultiWiggleAddTrackWidget/AddTrackWorkflow.tsx

@@ -1,130 +0,0 @@
-import React, { useState } from 'react'
-import { Button, Paper, TextField } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import { getSession, isElectron } from '@jbrowse/core/util'
-import { storeBlobLocation } from '@jbrowse/core/util/tracks'
-import { AddTrackModel } from '@jbrowse/plugin-data-management'
-
-const useStyles = makeStyles()(theme => ({
-  textbox: {
-    width: '100%',
-  },
-  paper: {
-    margin: theme.spacing(),
-    padding: theme.spacing(),
-  },
-  submit: {
-    marginTop: 25,
-    marginBottom: 100,
-    display: 'block',
-  },
-}))
-
-export default function MultiWiggleWidget({ model }: { model: AddTrackModel }) {
-  const { classes } = useStyles()
-  const [val, setVal] = useState('')
-  const [trackName, setTrackName] = useState(`MultiWiggle${+Date.now()}`)
-  return (
-    <Paper className={classes.paper}>
-      <ul>
-        <li>Enter list of URLs for bigwig files in the textbox</li>
-        <li>
-          Or, use the button below the text box to select files from your
-          computer
-        </li>
-      </ul>
-
-      <TextField
-        multiline
-        rows={10}
-        value={val}
-        onChange={event => setVal(event.target.value)}
-        placeholder={'Paste list of URLs here, or use file selector below'}
-        variant="outlined"
-        className={classes.textbox}
-      />
-
-      <Button variant="outlined" component="label">
-        Choose Files from your computer
-        <input
-          type="file"
-          hidden
-          multiple
-          onChange={({ target }) => {
-            const res = [...(target?.files || [])].map(file => ({
-              type: 'BigWigAdapter',
-              bigWigLocation: isElectron
-                ? {
-                    localPath: (file as File & { path: string }).path,
-                    locationType: 'LocalPathLocation',
-                  }
-                : storeBlobLocation({ blob: file }),
-              source: file.name,
-            }))
-            setVal(JSON.stringify(res, null, 2))
-          }}
-        />
-      </Button>
-      <TextField
-        value={trackName}
-        onChange={event => setTrackName(event.target.value)}
-        helperText="Track name"
-      />
-      <Button
-        variant="contained"
-        className={classes.submit}
-        onClick={() => {
-          const session = getSession(model)
-
-          const trackId = [
-            `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
-            `${session.adminMode ? '' : '-sessionTrack'}`,
-          ].join('')
-
-          // allow list of bigwigs in JSON format or line-by-line
-          let bigWigs
-          try {
-            bigWigs = JSON.parse(val)
-          } catch (e) {
-            bigWigs = val.split(/\n|\r\n|\r/)
-          }
-          const obj =
-            typeof bigWigs[0] === 'string'
-              ? { bigWigs }
-              : { subadapters: bigWigs }
-
-          session.addTrackConf({
-            trackId,
-            type: 'MultiQuantitativeTrack',
-            name: trackName,
-            assemblyNames: [model.assembly],
-            adapter: {
-              type: 'MultiWiggleAdapter',
-              ...obj,
-            },
-          })
-          model.view?.showTrack(trackId)
-
-          model.clearData()
-          session.hideWidget(model)
-        }}
-      >
-        Submit
-      </Button>
-
-      <p>Additional notes: </p>
-      <ul>
-        <li>
-          The list of bigwig files in the text box can be a list of URLs, or a
-          list of elements like{' '}
-          <code>{`[{"type":"BigWigAdapter","bigWigLocation":{"uri":"http://host/file.bw"}, "color":"green","source":"name for subtrack"}]`}</code>{' '}
-          to apply e.g. the color attribute to the view
-        </li>
-        <li>
-          Adding local files will update the textbox with JSON contents that are
-          ready to submit with the "Submit" button
-        </li>
-      </ul>
-    </Paper>
-  )
-}

package/src/MultiWiggleAddTrackWidget/index.ts

@@ -1,17 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { AddTrackWorkflowType } from '@jbrowse/core/pluggableElementTypes'
-import { types } from 'mobx-state-tree'
-
-// locals
-import MultiWiggleWidget from './AddTrackWorkflow'
-
-export default (pm: PluginManager) => {
-  pm.addAddTrackWorkflowType(
-    () =>
-      new AddTrackWorkflowType({
-        name: 'Multi-wiggle track',
-        ReactComponent: MultiWiggleWidget,
-        stateModel: types.model({}),
-      }),
-  )
-}

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 { groupBy, Feature } from '@jbrowse/core/util'
-import { drawXY } from '../drawxy'
-import { 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 }
-  }
-}