@jbrowse/plugin-wiggle 2.6.1 → 2.6.3

package/src/index.ts

@@ -1,130 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { FileLocation } from '@jbrowse/core/util/types'
-import {
-  AdapterGuesser,
-  TrackTypeGuesser,
-  getFileName,
-} from '@jbrowse/core/util/tracks'
-
-// locals
-import WiggleBaseRenderer from './WiggleBaseRenderer'
-
-import BigWigAdapterF from './BigWigAdapter'
-import QuantitativeTrackF from './QuantitativeTrack'
-import MultiQuantitativeTrackF from './MultiQuantitativeTrack'
-import MultiWiggleAdapterF from './MultiWiggleAdapter'
-import DensityRendererF from './DensityRenderer'
-import XYPlotRendererF from './XYPlotRenderer'
-import LinePlotRendererF from './LinePlotRenderer'
-import LinearWiggleDisplayF from './LinearWiggleDisplay'
-import MultiLinearWiggleDisplayF from './MultiLinearWiggleDisplay'
-import MultiXYPlotRendererF from './MultiXYPlotRenderer'
-import MultiRowXYPlotRendererF from './MultiRowXYPlotRenderer'
-import MultiDensityRendererF from './MultiDensityRenderer'
-import MultiLineRendererF from './MultiLineRenderer'
-import MultiRowLineRendererF from './MultiRowLineRenderer'
-import CreateMultiWiggleExtensionF from './CreateMultiWiggleExtension'
-import MultiWiggleAddTrackWidgetF from './MultiWiggleAddTrackWidget'
-
-import * as utils from './util'
-
-import {
-  WiggleGetGlobalQuantitativeStats,
-  WiggleGetMultiRegionQuantitativeStats,
-  MultiWiggleGetSources,
-} from './WiggleRPC/rpcMethods'
-
-import {
-  ReactComponent as LinearWiggleDisplayReactComponent,
-  modelFactory as linearWiggleDisplayModelFactory,
-} from './LinearWiggleDisplay'
-
-import {
-  ReactComponent as XYPlotRendererReactComponent,
-  configSchema as xyPlotRendererConfigSchema,
-  XYPlotRenderer,
-} from './XYPlotRenderer'
-
-export default class WigglePlugin extends Plugin {
-  name = 'WigglePlugin'
-
-  install(pm: PluginManager) {
-    MultiWiggleAdapterF(pm)
-    BigWigAdapterF(pm)
-    QuantitativeTrackF(pm)
-    MultiQuantitativeTrackF(pm)
-    LinearWiggleDisplayF(pm)
-    MultiLinearWiggleDisplayF(pm)
-    LinePlotRendererF(pm)
-    XYPlotRendererF(pm)
-    DensityRendererF(pm)
-    MultiXYPlotRendererF(pm)
-    MultiRowXYPlotRendererF(pm)
-    MultiDensityRendererF(pm)
-    MultiLineRendererF(pm)
-    MultiRowLineRendererF(pm)
-    MultiWiggleAddTrackWidgetF(pm)
-    CreateMultiWiggleExtensionF(pm)
-
-    pm.addToExtensionPoint(
-      'Core-guessAdapterForLocation',
-      (cb: AdapterGuesser) => {
-        return (file: FileLocation, index?: FileLocation, hint?: string) => {
-          const regexGuess = /\.(bw|bigwig)$/i
-          const adapterName = 'BigWigAdapter'
-          const fileName = getFileName(file)
-          const obj = {
-            type: adapterName,
-            bigWigLocation: file,
-          }
-
-          if (regexGuess.test(fileName) && !hint) {
-            return obj
-          } else if (hint === adapterName) {
-            return obj
-          }
-
-          return cb(file, index, hint)
-        }
-      },
-    )
-    pm.addToExtensionPoint(
-      'Core-guessTrackTypeForLocation',
-      (trackTypeGuesser: TrackTypeGuesser) => {
-        return (adapterName: string) => {
-          if (adapterName === 'BigWigAdapter') {
-            return 'QuantitativeTrack'
-          }
-          return trackTypeGuesser(adapterName)
-        }
-      },
-    )
-
-    pm.addRpcMethod(() => new WiggleGetGlobalQuantitativeStats(pm))
-    pm.addRpcMethod(() => new WiggleGetMultiRegionQuantitativeStats(pm))
-    pm.addRpcMethod(() => new MultiWiggleGetSources(pm))
-  }
-
-  exports = {
-    LinearWiggleDisplayReactComponent,
-    XYPlotRendererReactComponent,
-    XYPlotRenderer,
-    WiggleBaseRenderer,
-    linearWiggleDisplayModelFactory,
-    xyPlotRendererConfigSchema,
-    utils,
-  }
-}
-
-export * from './util'
-
-export { default as WiggleRendering } from './WiggleRendering'
-export {
-  Tooltip,
-  ReactComponent as LinearWiggleDisplayReactComponent,
-  modelFactory as linearWiggleDisplayModelFactory,
-} from './LinearWiggleDisplay'
-export { type TooltipContentsComponent } from './Tooltip'
-
-export { default as WiggleBaseRenderer } from './WiggleBaseRenderer'

package/src/shared/SetMinMaxDialog.tsx

@@ -1,88 +0,0 @@
-import React, { useState } from 'react'
-import {
-  Button,
-  DialogActions,
-  DialogContent,
-  TextField,
-  Typography,
-} from '@mui/material'
-import { Dialog } from '@jbrowse/core/ui'
-
-export default function SetMinMaxDlg(props: {
-  model: {
-    minScore: number
-    maxScore: number
-    scaleType: string
-    setMinScore: Function
-    setMaxScore: Function
-  }
-  handleClose: () => void
-}) {
-  const { model, handleClose } = props
-  const { minScore, maxScore, scaleType } = model
-
-  const [min, setMin] = useState(
-    `${minScore !== Number.MIN_VALUE ? minScore : ''}`,
-  )
-  const [max, setMax] = useState(
-    `${maxScore !== Number.MAX_VALUE ? maxScore : ''}`,
-  )
-
-  const ok =
-    min !== '' && max !== '' && !Number.isNaN(+min) && !Number.isNaN(+max)
-      ? +max > +min
-      : true
-
-  const logOk =
-    scaleType === 'log' && min !== '' && !Number.isNaN(+min) ? +min > 0 : true
-
-  return (
-    <Dialog open onClose={handleClose} title="Set min/max score for track">
-      <DialogContent>
-        <Typography>Enter min/max score: </Typography>
-        {!ok ? (
-          <Typography color="error">
-            Max is greater than or equal to min
-          </Typography>
-        ) : null}
-
-        {!logOk ? (
-          <Typography color="error">
-            Min score should be greater than 0 for log scale
-          </Typography>
-        ) : null}
-
-        <TextField
-          value={min}
-          onChange={event => setMin(event.target.value)}
-          placeholder="Enter min score"
-        />
-        <TextField
-          value={max}
-          onChange={event => setMax(event.target.value)}
-          placeholder="Enter max score"
-        />
-      </DialogContent>
-      <DialogActions>
-        <Button
-          variant="contained"
-          color="primary"
-          type="submit"
-          style={{ marginLeft: 20 }}
-          disabled={!ok}
-          onClick={() => {
-            model.setMinScore(
-              min !== '' && !Number.isNaN(+min) ? +min : undefined,
-            )
-            model.setMaxScore(
-              max !== '' && !Number.isNaN(+max) ? +max : undefined,
-            )
-            handleClose()
-          }}
-        >
-          Submit
-        </Button>
-      </DialogActions>
-    </Dialog>
-  )
-}

package/src/shared/YScaleBar.tsx

@@ -1,27 +0,0 @@
-import React from 'react'
-import { useTheme } from '@mui/material'
-import { observer } from 'mobx-react'
-import { axisPropsFromTickScale, Axis, LEFT, RIGHT } from 'react-d3-axis-mod'
-
-type Ticks = ReturnType<typeof axisPropsFromTickScale>
-
-export default observer(function YScaleBar({
-  model,
-  orientation,
-}: {
-  model: { ticks?: Ticks }
-  orientation?: string
-}) {
-  const { ticks } = model
-  const theme = useTheme()
-  return ticks ? (
-    <Axis
-      {...ticks}
-      shadow={2}
-      format={(n: number) => n}
-      style={{ orient: orientation === 'left' ? LEFT : RIGHT }}
-      bg={theme.palette.background.default}
-      fg={theme.palette.text.primary}
-    />
-  ) : null
-})

package/src/shared/configShared.ts

@@ -1,90 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'
-import { types } from 'mobx-state-tree'
-
-/**
- * #config SharedWiggleDisplay
- */
-export default function sharedWiggleConfigFactory() {
-  return ConfigurationSchema(
-    'MultiLinearWiggleDisplay',
-    {
-      /**
-       * #slot
-       */
-      autoscale: {
-        type: 'stringEnum',
-        defaultValue: 'local',
-        model: types.enumeration('Autoscale type', [
-          'global',
-          'local',
-          'globalsd',
-          'localsd',
-          'zscore',
-        ]),
-        description:
-          'global/local using their min/max values or w/ standard deviations (globalsd/localsd)',
-      },
-
-      /**
-       * #slot
-       */
-      minimalTicks: {
-        type: 'boolean',
-        defaultValue: false,
-        description: 'use the minimal amount of ticks',
-      },
-
-      /**
-       * #slot
-       */
-      minScore: {
-        type: 'number',
-        defaultValue: Number.MIN_VALUE,
-        description: 'minimum value for the y-scale',
-      },
-      /**
-       * #slot
-       */
-      maxScore: {
-        type: 'number',
-        description: 'maximum value for the y-scale',
-        defaultValue: Number.MAX_VALUE,
-      },
-      /**
-       * #slot
-       */
-      numStdDev: {
-        type: 'number',
-        description:
-          'number of standard deviations to use for autoscale types globalsd or localsd',
-        defaultValue: 3,
-      },
-      /**
-       * #slot
-       */
-      scaleType: {
-        type: 'stringEnum',
-        model: types.enumeration('Scale type', ['linear', 'log']), // todo zscale
-        description: 'The type of scale to use',
-        defaultValue: 'linear',
-      },
-
-      /**
-       * #slot
-       */
-      inverted: {
-        type: 'boolean',
-        description: 'draw upside down',
-        defaultValue: false,
-      },
-    },
-    {
-      /**
-       * #baseConfiguration
-       */
-      baseConfiguration: baseLinearDisplayConfigSchema,
-      explicitlyTyped: true,
-    },
-  )
-}