@jbrowse/plugin-linear-genome-view 2.6.1 → 2.6.3

package/src/LinearGenomeView/components/OverviewRubberband.tsx

@@ -1,219 +0,0 @@
-import React, { useRef, useEffect, useState } from 'react'
-import { Tooltip } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import { getSession, stringify } from '@jbrowse/core/util'
-import { observer } from 'mobx-react'
-import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel'
-
-// locals
-import { LinearGenomeViewModel } from '..'
-import RubberbandSpan from './RubberbandSpan'
-import { getRelativeX } from './util'
-
-type LGV = LinearGenomeViewModel
-
-const useStyles = makeStyles()({
-  rubberbandControl: {
-    cursor: 'crosshair',
-    width: '100%',
-    minHeight: 8,
-  },
-  guide: {
-    pointerEvents: 'none',
-    height: '100%',
-    width: 1,
-    position: 'absolute',
-    zIndex: 10,
-  },
-})
-
-const HoverTooltip = observer(function ({
-  model,
-  open,
-  guideX,
-  overview,
-}: {
-  model: LGV
-  open: boolean
-  guideX: number
-  overview: Base1DViewModel
-}) {
-  const { classes } = useStyles()
-  const { cytobandOffset } = model
-  const { assemblyManager } = getSession(model)
-
-  const px = overview.pxToBp(guideX - cytobandOffset)
-  const assembly = assemblyManager.get(px.assemblyName)
-  const cytoband = assembly?.cytobands?.find(
-    f =>
-      px.coord > f.get('start') &&
-      px.coord < f.get('end') &&
-      px.refName === assembly.getCanonicalRefName(f.get('refName')),
-  )
-
-  return (
-    <Tooltip
-      open={open}
-      placement="top"
-      title={[stringify(px), cytoband?.get('name')].join(' ')}
-      arrow
-    >
-      <div className={classes.guide} style={{ left: guideX }} />
-    </Tooltip>
-  )
-})
-
-export default observer(function OverviewRubberband({
-  model,
-  overview,
-  ControlComponent = <div />,
-}: {
-  model: LGV
-  overview: Base1DViewModel
-  ControlComponent?: React.ReactElement
-}) {
-  const { cytobandOffset } = model
-  const [startX, setStartX] = useState<number>()
-  const [currentX, setCurrentX] = useState<number>()
-  const [guideX, setGuideX] = useState<number>()
-  const controlsRef = useRef<HTMLDivElement>(null)
-  const { classes } = useStyles()
-  const mouseDragging = startX !== undefined
-
-  useEffect(() => {
-    function globalMouseMove(event: MouseEvent) {
-      const ref = controlsRef.current
-      if (ref && mouseDragging) {
-        setCurrentX(getRelativeX(event, ref))
-      }
-    }
-
-    function globalMouseUp() {
-      // click and drag
-      if (startX !== undefined && currentX !== undefined) {
-        if (Math.abs(currentX - startX) > 3) {
-          const left = Math.min(startX, currentX)
-          const right = Math.max(startX, currentX)
-          model.moveTo(
-            overview.pxToBp(left - cytobandOffset),
-            overview.pxToBp(right - cytobandOffset),
-          )
-        }
-      }
-
-      // just a click
-      if (startX !== undefined && currentX === undefined) {
-        const click = overview.pxToBp(startX - cytobandOffset)
-        if (!click.refName) {
-          getSession(model).notify('unknown position clicked')
-          console.error('unknown position clicked', click)
-        } else {
-          model.centerAt(Math.round(click.coord), click.refName, click.index)
-        }
-      }
-      setStartX(undefined)
-      setCurrentX(undefined)
-
-      if (startX !== undefined) {
-        setGuideX(undefined)
-      }
-    }
-
-    function globalKeyDown(event: KeyboardEvent) {
-      if (event.key === 'Escape') {
-        setStartX(undefined)
-        setCurrentX(undefined)
-      }
-    }
-
-    if (mouseDragging) {
-      window.addEventListener('mousemove', globalMouseMove, true)
-      window.addEventListener('mouseup', globalMouseUp, true)
-      window.addEventListener('keydown', globalKeyDown, true)
-      return () => {
-        window.removeEventListener('mousemove', globalMouseMove, true)
-        window.removeEventListener('mouseup', globalMouseUp, true)
-        window.removeEventListener('keydown', globalKeyDown, true)
-      }
-    }
-    return () => {}
-  }, [mouseDragging, currentX, startX, model, overview, cytobandOffset])
-
-  function mouseDown(event: React.MouseEvent<HTMLDivElement>) {
-    event.preventDefault()
-    event.stopPropagation()
-    setStartX(getRelativeX(event, controlsRef.current))
-  }
-
-  function mouseMove(event: React.MouseEvent<HTMLDivElement>) {
-    setGuideX(getRelativeX(event, controlsRef.current))
-  }
-
-  function mouseOut() {
-    setGuideX(undefined)
-  }
-
-  if (startX === undefined) {
-    return (
-      <div style={{ position: 'relative' }}>
-        {guideX !== undefined ? (
-          <HoverTooltip
-            model={model}
-            open={!mouseDragging}
-            overview={overview}
-            guideX={guideX}
-          />
-        ) : null}
-        <div
-          className={classes.rubberbandControl}
-          ref={controlsRef}
-          onMouseDown={mouseDown}
-          onMouseOut={mouseOut}
-          onMouseMove={mouseMove}
-        >
-          {ControlComponent}
-        </div>
-      </div>
-    )
-  }
-
-  let left = startX || 0
-  let width = 0
-  if (startX !== undefined && currentX !== undefined) {
-    left = currentX < startX ? currentX : startX
-    width = currentX - startX
-  }
-  // calculate the start and end bp of drag
-  let leftBpOffset
-  let rightBpOffset
-  if (startX) {
-    leftBpOffset = overview.pxToBp(startX - cytobandOffset)
-    rightBpOffset = overview.pxToBp(startX + width - cytobandOffset)
-    if (currentX !== undefined && currentX < startX) {
-      ;[leftBpOffset, rightBpOffset] = [rightBpOffset, leftBpOffset]
-    }
-  }
-
-  return (
-    <div style={{ position: 'relative' }}>
-      {leftBpOffset && rightBpOffset ? (
-        <RubberbandSpan
-          leftBpOffset={leftBpOffset}
-          rightBpOffset={rightBpOffset}
-          width={Math.abs(width)}
-          left={left}
-        />
-      ) : null}
-      <div
-        data-testid="rubberband_controls"
-        className={classes.rubberbandControl}
-        ref={controlsRef}
-        onMouseDown={mouseDown}
-        onMouseOut={mouseOut}
-        onMouseMove={mouseMove}
-      >
-        {ControlComponent}
-      </div>
-    </div>
-  )
-})

package/src/LinearGenomeView/components/OverviewScalebar.tsx

@@ -1,351 +0,0 @@
-import React from 'react'
-import { Typography, useTheme, alpha } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import { observer } from 'mobx-react'
-
-// core
-import Base1DView, { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel'
-import { getSession, getTickDisplayStr } from '@jbrowse/core/util'
-import { ContentBlock } from '@jbrowse/core/util/blockTypes'
-
-// locals
-import {
-  LinearGenomeViewModel,
-  HEADER_BAR_HEIGHT,
-  HEADER_OVERVIEW_HEIGHT,
-} from '..'
-import { chooseGridPitch } from '../util'
-import OverviewRubberband from './OverviewRubberband'
-import Cytobands from './Cytobands'
-import { getCytobands } from './util'
-
-const wholeSeqSpacer = 2
-
-const useStyles = makeStyles()(theme => ({
-  scalebar: {
-    height: HEADER_OVERVIEW_HEIGHT,
-  },
-  scalebarBorder: {
-    border: '1px solid',
-  },
-  scalebarContig: {
-    backgroundColor: theme.palette.background.default,
-    position: 'absolute',
-    top: 0,
-    height: HEADER_OVERVIEW_HEIGHT,
-    overflow: 'hidden',
-  },
-  scalebarContigForward: {
-    backgroundImage: `url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 15 9'%3E%3Cpath d='M-.1 0L6 4.5L-.1 9' fill='none' stroke='${theme.palette.divider}'/%3E%3C/svg%3E")`,
-    backgroundRepeat: 'repeat',
-  },
-  scalebarContigReverse: {
-    backgroundImage: `url("data:image/svg+xml,%3Csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 15 9'%3E%3Cpath d='M6 0L0 4.5L6 9' fill='none' stroke='${theme.palette.divider}'/%3E%3C/svg%3E")`,
-    backgroundRepeat: 'repeat',
-  },
-
-  scalebarRefName: {
-    position: 'absolute',
-    fontWeight: 'bold',
-    pointerEvents: 'none',
-    zIndex: 100,
-  },
-  scalebarLabel: {
-    height: HEADER_OVERVIEW_HEIGHT,
-    position: 'absolute',
-    display: 'flex',
-    justifyContent: 'center',
-    pointerEvents: 'none',
-  },
-  scalebarVisibleRegion: {
-    position: 'absolute',
-    height: HEADER_OVERVIEW_HEIGHT,
-    pointerEvents: 'none',
-    zIndex: 100,
-    border: '1px solid',
-  },
-  overview: {
-    height: HEADER_BAR_HEIGHT,
-    position: 'relative',
-  },
-  overviewSvg: {
-    pointerEvents: 'none',
-    width: '100%',
-    position: 'absolute',
-  },
-}))
-
-const Polygon = observer(function ({
-  model,
-  overview,
-  useOffset = true,
-}: {
-  model: LGV
-  overview: Base1DViewModel
-  useOffset?: boolean
-}) {
-  const theme = useTheme()
-  const multiplier = Number(useOffset)
-  const { interRegionPaddingWidth, offsetPx, dynamicBlocks, cytobandOffset } =
-    model
-  const { contentBlocks, totalWidthPxWithoutBorders } = dynamicBlocks
-
-  const { tertiary, primary } = theme.palette
-  const polygonColor = tertiary ? tertiary.light : primary.light
-
-  // catches possible null from at's below
-  if (!contentBlocks.length) {
-    return null
-  }
-  // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
-  const first = contentBlocks.at(0)!
-  // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
-  const last = contentBlocks.at(-1)!
-  const topLeft =
-    (overview.bpToPx({
-      ...first,
-      coord: first.reversed ? first.end : first.start,
-    }) || 0) +
-    cytobandOffset * multiplier
-  const topRight =
-    (overview.bpToPx({
-      ...last,
-      coord: last.reversed ? last.start : last.end,
-    }) || 0) +
-    cytobandOffset * multiplier
-
-  const startPx = Math.max(0, -offsetPx)
-  const endPx =
-    startPx +
-    totalWidthPxWithoutBorders +
-    (contentBlocks.length * interRegionPaddingWidth) / 2
-
-  const points = [
-    [startPx, HEADER_BAR_HEIGHT],
-    [endPx, HEADER_BAR_HEIGHT],
-    [topRight, 0],
-    [topLeft, 0],
-  ]
-
-  return (
-    <polygon
-      points={points.toString()}
-      fill={alpha(polygonColor, 0.3)}
-      stroke={alpha(polygonColor, 0.8)}
-    />
-  )
-})
-
-type LGV = LinearGenomeViewModel
-
-const OverviewBox = observer(function ({
-  scale,
-  model,
-  block,
-  overview,
-}: {
-  scale: number
-  model: LGV
-  block: ContentBlock
-  overview: Base1DViewModel
-}) {
-  const { classes, cx } = useStyles()
-  const theme = useTheme()
-  const { cytobandOffset, showCytobands } = model
-  const { start, end, reversed, refName, assemblyName } = block
-  const { majorPitch } = chooseGridPitch(scale, 120, 15)
-  const { assemblyManager } = getSession(model)
-  const assembly = assemblyManager.get(assemblyName)
-  const refNameColor = assembly?.getRefNameColor(refName)
-
-  const tickLabels = []
-  for (let i = 0; i < Math.floor((end - start) / majorPitch); i++) {
-    const offsetLabel = (i + 1) * majorPitch
-    tickLabels.push(reversed ? end - offsetLabel : start + offsetLabel)
-  }
-
-  const canDisplayCytobands =
-    showCytobands && getCytobands(assembly, block.refName).length
-
-  return (
-    <div>
-      {/* name of sequence */}
-      <Typography
-        style={{
-          left: block.offsetPx + 3,
-          color: canDisplayCytobands
-            ? theme.palette.text.primary
-            : refNameColor,
-        }}
-        className={classes.scalebarRefName}
-      >
-        {refName}
-      </Typography>
-      <div
-        className={cx(
-          classes.scalebarContig,
-          canDisplayCytobands
-            ? undefined
-            : reversed
-            ? classes.scalebarContigReverse
-            : classes.scalebarContigForward,
-          !canDisplayCytobands ? classes.scalebarBorder : undefined,
-        )}
-        style={{
-          left: block.offsetPx + cytobandOffset,
-          width: block.widthPx,
-          borderColor: refNameColor,
-        }}
-      >
-        {!canDisplayCytobands
-          ? tickLabels.map((tickLabel, labelIdx) => (
-              <Typography
-                key={`${JSON.stringify(block)}-${tickLabel}-${labelIdx}`}
-                className={classes.scalebarLabel}
-                variant="body2"
-                style={{
-                  left: ((labelIdx + 1) * majorPitch) / scale,
-                  pointerEvents: 'none',
-                  color: refNameColor,
-                }}
-              >
-                {getTickDisplayStr(tickLabel, overview.bpPerPx)}
-              </Typography>
-            ))
-          : null}
-
-        {canDisplayCytobands ? (
-          <svg style={{ width: '100%' }}>
-            <Cytobands overview={overview} assembly={assembly} block={block} />
-          </svg>
-        ) : null}
-      </div>
-    </div>
-  )
-})
-
-const Scalebar = observer(function ({
-  model,
-  scale,
-  overview,
-}: {
-  model: LGV
-  overview: Base1DViewModel
-  scale: number
-}) {
-  const { classes } = useStyles()
-  const theme = useTheme()
-  const { dynamicBlocks, showCytobands, cytobandOffset } = model
-  const visibleRegions = dynamicBlocks.contentBlocks
-  const overviewVisibleRegions = overview.dynamicBlocks
-
-  const { tertiary, primary } = theme.palette
-  const scalebarColor = tertiary ? tertiary.light : primary.light
-  // catches possible null from at's below
-  if (!visibleRegions.length) {
-    return null
-  }
-  // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
-  const first = visibleRegions.at(0)!
-  // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
-  const last = visibleRegions.at(-1)!
-
-  const firstOverviewPx =
-    overview.bpToPx({
-      ...first,
-      coord: first.reversed ? first.end : first.start,
-    }) || 0
-
-  const lastOverviewPx =
-    overview.bpToPx({
-      ...last,
-      coord: last.reversed ? last.start : last.end,
-    }) || 0
-
-  const color = showCytobands ? '#f00' : scalebarColor
-  const transparency = showCytobands ? 0.1 : 0.3
-
-  return (
-    <div className={classes.scalebar}>
-      <div
-        className={classes.scalebarVisibleRegion}
-        style={{
-          width: lastOverviewPx - firstOverviewPx,
-          left: firstOverviewPx + cytobandOffset,
-          background: alpha(color, transparency),
-          borderColor: color,
-        }}
-      />
-      {/* this is the entire scale bar */}
-      {overviewVisibleRegions.map((block, idx) => {
-        return !(block instanceof ContentBlock) ? (
-          <div
-            key={`${JSON.stringify(block)}-${idx}`}
-            className={classes.scalebarContig}
-            style={{
-              width: block.widthPx,
-              left: block.offsetPx,
-              backgroundColor: '#999',
-              backgroundImage:
-                'repeating-linear-gradient(90deg, transparent, transparent 1px, rgba(255,255,255,.5) 1px, rgba(255,255,255,.5) 3px)',
-            }}
-          />
-        ) : (
-          <OverviewBox
-            scale={scale}
-            block={block}
-            model={model}
-            overview={overview}
-            key={`${JSON.stringify(block)}-${idx}`}
-          />
-        )
-      })}
-    </div>
-  )
-})
-
-export default observer(function OverviewScalebar({
-  model,
-  children,
-}: {
-  model: LGV
-  children: React.ReactNode
-}) {
-  const { classes } = useStyles()
-  const { totalBp, width, cytobandOffset, displayedRegions } = model
-
-  const overview = Base1DView.create({
-    displayedRegions: JSON.parse(JSON.stringify(displayedRegions)),
-    interRegionPaddingWidth: 0,
-    minimumBlockWidth: model.minimumBlockWidth,
-  })
-
-  const modWidth = width - cytobandOffset
-  overview.setVolatileWidth(modWidth)
-  overview.showAllRegions()
-
-  const scale =
-    totalBp / (modWidth - (displayedRegions.length - 1) * wholeSeqSpacer)
-
-  return (
-    <div>
-      <OverviewRubberband
-        model={model}
-        overview={overview}
-        ControlComponent={
-          <Scalebar model={model} overview={overview} scale={scale} />
-        }
-      />
-      <div className={classes.overview}>
-        <svg height={HEADER_BAR_HEIGHT} className={classes.overviewSvg}>
-          <Polygon model={model} overview={overview} />
-        </svg>
-        {children}
-      </div>
-    </div>
-  )
-})
-
-export { Polygon }
-
-export { default as Cytobands } from './Cytobands'

package/src/LinearGenomeView/components/RefNameAutocomplete/AutocompleteTextField.tsx

@@ -1,53 +0,0 @@
-import React from 'react'
-import {
-  AutocompleteRenderInputParams,
-  TextField,
-  TextFieldProps as TFP,
-} from '@mui/material'
-
-// locals
-import EndAdornment from './EndAdornment'
-
-export default function AutocompleteTextField({
-  TextFieldProps,
-  inputBoxVal,
-  params,
-  showHelp,
-  setInputValue,
-  setCurrentSearch,
-}: {
-  TextFieldProps: TFP
-  inputBoxVal: string
-  showHelp?: boolean
-  params: AutocompleteRenderInputParams
-  setInputValue: (arg: string) => void
-  setCurrentSearch: (arg: string) => void
-}) {
-  const { helperText, InputProps = {} } = TextFieldProps
-  return (
-    <TextField
-      onBlur={() =>
-        // this is used to restore a refName or the non-user-typed input
-        // to the box on blurring
-        setInputValue(inputBoxVal)
-      }
-      {...params}
-      {...TextFieldProps}
-      size="small"
-      helperText={helperText}
-      InputProps={{
-        ...params.InputProps,
-        ...InputProps,
-
-        endAdornment: (
-          <EndAdornment
-            showHelp={showHelp}
-            endAdornment={params.InputProps.endAdornment}
-          />
-        ),
-      }}
-      placeholder="Search for location"
-      onChange={e => setCurrentSearch(e.target.value)}
-    />
-  )
-}

package/src/LinearGenomeView/components/RefNameAutocomplete/EndAdornment.tsx

@@ -1,44 +0,0 @@
-import React, { Suspense, lazy, useState } from 'react'
-
-import { IconButton, InputAdornment } from '@mui/material'
-
-// icons
-import SearchIcon from '@mui/icons-material/Search'
-import HelpIcon from '@mui/icons-material/Help'
-
-// lazy
-const HelpDialog = lazy(() => import('./HelpDialog'))
-
-function HelpAdornment() {
-  const [isHelpDialogDisplayed, setHelpDialogDisplayed] = useState(false)
-  return (
-    <>
-      <IconButton onClick={() => setHelpDialogDisplayed(true)} size="small">
-        <HelpIcon fontSize="small" />
-      </IconButton>
-      {isHelpDialogDisplayed ? (
-        <Suspense fallback={<div />}>
-          <HelpDialog handleClose={() => setHelpDialogDisplayed(false)} />
-        </Suspense>
-      ) : null}
-    </>
-  )
-}
-
-export default function EndAdornment({
-  showHelp,
-  endAdornment,
-}: {
-  showHelp?: boolean
-  endAdornment: React.ReactNode
-}) {
-  return (
-    <>
-      <InputAdornment position="end" style={{ marginRight: 7 }}>
-        <SearchIcon fontSize="small" />
-        {showHelp ? <HelpAdornment /> : null}
-      </InputAdornment>
-      {endAdornment}
-    </>
-  )
-}