@jbrowse/plugin-linear-genome-view 2.2.0 → 2.2.2

package/src/LinearGenomeView/components/{OverviewScaleBar.tsx → OverviewScalebar.tsx}

@@ -3,6 +3,7 @@ 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'
@@ -15,46 +16,46 @@ import {
   HEADER_OVERVIEW_HEIGHT,
 } from '..'
 import { chooseGridPitch } from '../util'
-import OverviewRubberBand from './OverviewRubberBand'
+import OverviewRubberband from './OverviewRubberband'
 
 const wholeSeqSpacer = 2
 
 const useStyles = makeStyles()(theme => ({
-  scaleBar: {
+  scalebar: {
     height: HEADER_OVERVIEW_HEIGHT,
   },
-  scaleBarBorder: {
+  scalebarBorder: {
     border: '1px solid',
   },
-  scaleBarContig: {
+  scalebarContig: {
     backgroundColor: theme.palette.background.default,
     position: 'absolute',
     top: 0,
     height: HEADER_OVERVIEW_HEIGHT,
   },
-  scaleBarContigForward: {
+  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='%23ddd'/%3E%3C/svg%3E")`,
     backgroundRepeat: 'repeat',
   },
-  scaleBarContigReverse: {
+  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='%23ddd'/%3E%3C/svg%3E")`,
     backgroundRepeat: 'repeat',
   },
 
-  scaleBarRefName: {
+  scalebarRefName: {
     position: 'absolute',
     fontWeight: 'bold',
     pointerEvents: 'none',
     zIndex: 100,
   },
-  scaleBarLabel: {
+  scalebarLabel: {
     height: HEADER_OVERVIEW_HEIGHT,
     position: 'absolute',
     display: 'flex',
     justifyContent: 'center',
     pointerEvents: 'none',
   },
-  scaleBarVisibleRegion: {
+  scalebarVisibleRegion: {
     position: 'absolute',
     height: HEADER_OVERVIEW_HEIGHT,
     pointerEvents: 'none',
@@ -328,19 +329,19 @@ const OverviewBox = observer(
             left: block.offsetPx + 3,
             color: canDisplayCytobands ? 'black' : refNameColor,
           }}
-          className={classes.scaleBarRefName}
+          className={classes.scalebarRefName}
         >
           {refName}
         </Typography>
         <div
           className={cx(
-            classes.scaleBarContig,
+            classes.scalebarContig,
             canDisplayCytobands
               ? undefined
               : reversed
-              ? classes.scaleBarContigReverse
-              : classes.scaleBarContigForward,
-            !canDisplayCytobands ? classes.scaleBarBorder : undefined,
+              ? classes.scalebarContigReverse
+              : classes.scalebarContigForward,
+            !canDisplayCytobands ? classes.scalebarBorder : undefined,
           )}
           style={{
             left: block.offsetPx + cytobandOffset,
@@ -352,7 +353,7 @@ const OverviewBox = observer(
             ? tickLabels.map((tickLabel, labelIdx) => (
                 <Typography
                   key={`${JSON.stringify(block)}-${tickLabel}-${labelIdx}`}
-                  className={classes.scaleBarLabel}
+                  className={classes.scalebarLabel}
                   variant="body2"
                   style={{
                     left: ((labelIdx + 1) * majorPitch) / scale,
@@ -380,7 +381,7 @@ const OverviewBox = observer(
   },
 )
 
-const ScaleBar = observer(
+const Scalebar = observer(
   ({
     model,
     scale,
@@ -397,7 +398,7 @@ const ScaleBar = observer(
     const overviewVisibleRegions = overview.dynamicBlocks
 
     const { tertiary, primary } = theme.palette
-    const scaleBarColor = tertiary ? tertiary.light : primary.light
+    const scalebarColor = tertiary ? tertiary.light : primary.light
 
     if (!visibleRegions.length) {
       return null
@@ -416,13 +417,13 @@ const ScaleBar = observer(
         coord: last.reversed ? last.start : last.end,
       }) || 0
 
-    const color = showCytobands ? '#f00' : scaleBarColor
+    const color = showCytobands ? '#f00' : scalebarColor
     const transparency = showCytobands ? 0.1 : 0.3
 
     return (
-      <div className={classes.scaleBar}>
+      <div className={classes.scalebar}>
         <div
-          className={classes.scaleBarVisibleRegion}
+          className={classes.scalebarVisibleRegion}
           style={{
             width: lastOverviewPx - firstOverviewPx,
             left: firstOverviewPx + cytobandOffset,
@@ -435,7 +436,7 @@ const ScaleBar = observer(
           return !(block instanceof ContentBlock) ? (
             <div
               key={`${JSON.stringify(block)}-${idx}`}
-              className={classes.scaleBarContig}
+              className={classes.scalebarContig}
               style={{
                 width: block.widthPx,
                 left: block.offsetPx,
@@ -459,7 +460,7 @@ const ScaleBar = observer(
   },
 )
 
-function OverviewScaleBar({
+function OverviewScalebar({
   model,
   children,
 }: {
@@ -484,11 +485,11 @@ function OverviewScaleBar({
 
   return (
     <div>
-      <OverviewRubberBand
+      <OverviewRubberband
         model={model}
         overview={overview}
         ControlComponent={
-          <ScaleBar model={model} overview={overview} scale={scale} />
+          <Scalebar model={model} overview={overview} scale={scale} />
         }
       />
       <div className={classes.overview}>
@@ -501,6 +502,6 @@ function OverviewScaleBar({
   )
 }
 
-export default observer(OverviewScaleBar)
+export default observer(OverviewScalebar)
 
 export { Cytobands, Polygon }

package/src/LinearGenomeView/components/RefNameAutocomplete.tsx

@@ -94,6 +94,7 @@ function RefNameAutocomplete({
   useEffect(() => {
     let active = true
 
+    // eslint-disable-next-line @typescript-eslint/no-floating-promises
     ;(async () => {
       try {
         if (debouncedSearch === '' || !assemblyName) {
@@ -146,7 +147,7 @@ function RefNameAutocomplete({
   const inputBoxVal = coarseVisibleLocStrings || value || ''
 
   // heuristic, text width + icon width
-  // + 45 accomodates help icon and search icon
+  // + 45 accommodates help icon and search icon
   const width = Math.min(
     Math.max(measureText(inputBoxVal, 16) + 45, minWidth),
     550,

package/src/LinearGenomeView/components/Rubberband.tsx

@@ -0,0 +1,89 @@
+import React, { useRef } from 'react'
+import { observer } from 'mobx-react'
+import { makeStyles } from 'tss-react/mui'
+import { Menu } from '@jbrowse/core/ui'
+
+// locals
+import VerticalGuide from './VerticalGuide'
+import RubberbandSpan from './RubberbandSpan'
+import { useRangeSelect } from './hooks'
+import { LinearGenomeViewModel } from '..'
+
+type LGV = LinearGenomeViewModel
+
+const useStyles = makeStyles()({
+  rubberbandControl: {
+    cursor: 'crosshair',
+    width: '100%',
+    minHeight: 8,
+  },
+})
+
+function Rubberband({
+  model,
+  ControlComponent = <div />,
+}: {
+  model: LGV
+  ControlComponent?: React.ReactElement
+}) {
+  const ref = useRef<HTMLDivElement>(null)
+  const { classes } = useStyles()
+
+  const {
+    guideX,
+    rubberbandOn,
+    leftBpOffset,
+    rightBpOffset,
+    numOfBpSelected,
+    width,
+    left,
+    anchorPosition,
+    handleMenuItemClick,
+    open,
+    handleClose,
+    mouseMove,
+    mouseDown,
+    mouseOut,
+  } = useRangeSelect(ref, model)
+
+  return (
+    <>
+      {guideX !== undefined ? (
+        <VerticalGuide model={model} coordX={guideX} />
+      ) : rubberbandOn ? (
+        <RubberbandSpan
+          leftBpOffset={leftBpOffset}
+          rightBpOffset={rightBpOffset}
+          numOfBpSelected={numOfBpSelected}
+          width={width}
+          left={left}
+        />
+      ) : null}
+      {anchorPosition ? (
+        <Menu
+          anchorReference="anchorPosition"
+          anchorPosition={{
+            left: anchorPosition.clientX,
+            top: anchorPosition.clientY,
+          }}
+          onMenuItemClick={handleMenuItemClick}
+          open={open}
+          onClose={handleClose}
+          menuItems={model.rubberBandMenuItems()}
+        />
+      ) : null}
+      <div
+        data-testid="rubberband_controls"
+        className={classes.rubberbandControl}
+        ref={ref}
+        onMouseDown={mouseDown}
+        onMouseMove={mouseMove}
+        onMouseOut={mouseOut}
+      >
+        {ControlComponent}
+      </div>
+    </>
+  )
+}
+
+export default observer(Rubberband)

package/src/LinearGenomeView/components/RubberbandSpan.tsx

@@ -0,0 +1,116 @@
+import React, { useRef } from 'react'
+import { makeStyles } from 'tss-react/mui'
+
+import { Popover, Typography, alpha } from '@mui/material'
+import { stringify, toLocale } from '@jbrowse/core/util'
+
+const useStyles = makeStyles()(theme => {
+  const { primary, tertiary } = theme.palette
+  const background = tertiary
+    ? alpha(tertiary.main, 0.7)
+    : alpha(primary.main, 0.7)
+  return {
+    rubberband: {
+      height: '100%',
+      background,
+      position: 'absolute',
+      zIndex: 10,
+      textAlign: 'center',
+      overflow: 'hidden',
+    },
+    rubberbandControl: {
+      cursor: 'crosshair',
+      width: '100%',
+      minHeight: 8,
+    },
+    rubberbandText: {
+      color: tertiary ? tertiary.contrastText : primary.contrastText,
+    },
+    popover: {
+      mouseEvents: 'none',
+      cursor: 'crosshair',
+    },
+    paper: {
+      paddingLeft: theme.spacing(1),
+      paddingRight: theme.spacing(1),
+    },
+  }
+})
+
+interface Offset {
+  coord: number
+  refName?: string
+  oob?: boolean
+}
+
+function RubberbandSpan({
+  leftBpOffset,
+  rightBpOffset,
+  numOfBpSelected,
+  left,
+  width,
+}: {
+  leftBpOffset: Offset
+  rightBpOffset: Offset
+  numOfBpSelected?: number
+  left: number
+  width: number
+}) {
+  const ref = useRef(null)
+  const { classes } = useStyles()
+  return (
+    <>
+      {ref.current ? (
+        <>
+          <Popover
+            className={classes.popover}
+            classes={{ paper: classes.paper }}
+            open
+            anchorEl={ref.current}
+            anchorOrigin={{
+              vertical: 'top',
+              horizontal: 'left',
+            }}
+            transformOrigin={{
+              vertical: 'bottom',
+              horizontal: 'right',
+            }}
+            keepMounted
+            disableRestoreFocus
+          >
+            <Typography>{stringify(leftBpOffset)}</Typography>
+          </Popover>
+          <Popover
+            className={classes.popover}
+            classes={{
+              paper: classes.paper,
+            }}
+            open
+            anchorEl={ref.current}
+            anchorOrigin={{
+              vertical: 'top',
+              horizontal: 'right',
+            }}
+            transformOrigin={{
+              vertical: 'bottom',
+              horizontal: 'left',
+            }}
+            keepMounted
+            disableRestoreFocus
+          >
+            <Typography>{stringify(rightBpOffset)}</Typography>
+          </Popover>
+        </>
+      ) : null}
+      <div ref={ref} className={classes.rubberband} style={{ left, width }}>
+        {numOfBpSelected ? (
+          <Typography variant="h6" className={classes.rubberbandText}>
+            {toLocale(numOfBpSelected)} bp
+          </Typography>
+        ) : null}
+      </div>
+    </>
+  )
+}
+
+export default RubberbandSpan

package/src/LinearGenomeView/components/{ScaleBar.test.tsx → Scalebar.test.tsx}

@@ -2,10 +2,10 @@
 import React from 'react'
 import { render } from '@testing-library/react'
 import { createTestSession } from '@jbrowse/web/src/rootModel'
-import ScaleBar from './ScaleBar'
+import Scalebar from './Scalebar'
 jest.mock('@jbrowse/web/src/makeWorkerInstance', () => () => {})
 
-describe('ScaleBar genome view component', () => {
+describe('Scalebar genome view component', () => {
   it('renders two regions', () => {
     const session = createTestSession({
       views: [
@@ -47,7 +47,7 @@ describe('ScaleBar genome view component', () => {
       },
     })
     const model = session.views[0]
-    const { getByTestId } = render(<ScaleBar model={model} />)
+    const { getByTestId } = render(<Scalebar model={model} />)
     const ret1 = getByTestId('refLabel-ctgA')
     const ret2 = getByTestId('refLabel-ctgB')
     expect(ret1.style.left).toBe('-1px')
@@ -89,7 +89,7 @@ describe('ScaleBar genome view component', () => {
       },
     })
     const model = session.views[0]
-    const { getByTestId } = render(<ScaleBar model={model} />)
+    const { getByTestId } = render(<Scalebar model={model} />)
     const ret1 = getByTestId('refLabel-ctgA')
     const ret2 = getByTestId('refLabel-ctgB')
     expect(ret1.style.left).toBe('99px')
@@ -134,7 +134,7 @@ describe('ScaleBar genome view component', () => {
       },
     })
     const model = session.views[0]
-    const { queryByTestId } = render(<ScaleBar model={model} />)
+    const { queryByTestId } = render(<Scalebar model={model} />)
     const ret2 = queryByTestId('refLabel-ctgB')
     const ret3 = queryByTestId('refLabel-ctgC')
     const ret4 = queryByTestId('refLabel-ctgD')

package/src/LinearGenomeView/components/{ScaleBar.tsx → Scalebar.tsx}

@@ -19,15 +19,15 @@ import { getTickDisplayStr } from '@jbrowse/core/util'
 type LGV = LinearGenomeViewModel
 
 const useStyles = makeStyles()(theme => ({
-  scaleBarContainer: {
+  scalebarContainer: {
     overflow: 'hidden',
     position: 'relative',
   },
-  scaleBarZoomContainer: {
+  scalebarZoomContainer: {
     position: 'relative',
     zIndex: 1,
   },
-  scaleBar: {
+  scalebar: {
     position: 'absolute',
     display: 'flex',
     pointerEvents: 'none',
@@ -94,7 +94,7 @@ const RenderedRefNameLabels = observer(({ model }: { model: LGV }) => {
   )
 })
 
-const RenderedScaleBarLabels = observer(({ model }: { model: LGV }) => {
+const RenderedScalebarLabels = observer(({ model }: { model: LGV }) => {
   const { classes } = useStyles()
   const { bpPerPx, staticBlocks } = model
 
@@ -150,13 +150,13 @@ const RenderedScaleBarLabels = observer(({ model }: { model: LGV }) => {
   )
 })
 
-interface ScaleBarProps {
+interface ScalebarProps {
   model: LGV
   style?: React.CSSProperties
   className?: string
 }
 
-const ScaleBar = React.forwardRef<HTMLDivElement, ScaleBarProps>(
+const Scalebar = React.forwardRef<HTMLDivElement, ScalebarProps>(
   ({ model, style, className, ...other }, ref) => {
     const { classes, cx } = useStyles()
 
@@ -164,14 +164,14 @@ const ScaleBar = React.forwardRef<HTMLDivElement, ScaleBarProps>(
     return (
       <Paper
         data-resizer="true" // used to avoid click-and-drag scrolls on trackscontainer
-        className={cx(classes.scaleBarContainer, className)}
+        className={cx(classes.scalebarContainer, className)}
         variant="outlined"
         ref={ref}
         style={style}
         {...other}
       >
         <div
-          className={classes.scaleBarZoomContainer}
+          className={classes.scalebarZoomContainer}
           style={{
             transform:
               model.scaleFactor !== 1
@@ -180,14 +180,14 @@ const ScaleBar = React.forwardRef<HTMLDivElement, ScaleBarProps>(
           }}
         >
           <div
-            className={classes.scaleBar}
+            className={classes.scalebar}
             style={{
               left: offsetLeft - 1,
               width: model.staticBlocks.totalWidthPx,
               ...style,
             }}
           >
-            <RenderedScaleBarLabels model={model} />
+            <RenderedScalebarLabels model={model} />
           </div>
         </div>
         <RenderedRefNameLabels model={model} />
@@ -196,4 +196,4 @@ const ScaleBar = React.forwardRef<HTMLDivElement, ScaleBarProps>(
   },
 )
 
-export default observer(ScaleBar)
+export default observer(Scalebar)

package/src/LinearGenomeView/components/SearchBox.tsx

@@ -33,11 +33,11 @@ function SearchBox({
   const assembly = assemblyManager.get(assemblyName)
   const searchScope = model.searchScope(assemblyName)
 
-  function navToOption(option: BaseResult) {
+  async function navToOption(option: BaseResult) {
     const location = option.getLocation()
     const trackId = option.getTrackId()
     if (location) {
-      model.navToLocString(location, assemblyName)
+      await model.navToLocString(location, assemblyName)
       if (trackId) {
         model.showTrack(trackId)
       }
@@ -52,7 +52,7 @@ function SearchBox({
   async function handleSelectedRegion(option: BaseResult) {
     try {
       if (option.hasLocation()) {
-        navToOption(option)
+        await navToOption(option)
       } else {
         const input = option.getLabel()
         const [ref, rest] = splitLast(input, ':')
@@ -61,7 +61,7 @@ function SearchBox({
           allRefs.includes(input) ||
           (allRefs.includes(ref) && !Number.isNaN(parseInt(rest, 10)))
         ) {
-          model.navToLocString(input, assemblyName)
+          await model.navToLocString(input, assemblyName)
         } else {
           const results = await fetchResults({
             queryString: input,
@@ -75,9 +75,9 @@ function SearchBox({
           if (results.length > 1) {
             model.setSearchResults(results, input.toLowerCase())
           } else if (results.length === 1) {
-            navToOption(results[0])
+            await navToOption(results[0])
           } else {
-            model.navToLocString(input, assemblyName)
+            await model.navToLocString(input, assemblyName)
           }
         }
       }

package/src/LinearGenomeView/components/SearchResultsDialog.tsx

@@ -1,15 +1,12 @@
 import React from 'react'
-import { makeStyles } from 'tss-react/mui'
 import { resolveIdentifier, getRoot } from 'mobx-state-tree'
 import { getSession, getEnv } from '@jbrowse/core/util'
+import { Dialog } from '@jbrowse/core/ui'
 import {
   Button,
-  Dialog,
   DialogActions,
   DialogContent,
-  DialogTitle,
   Divider,
-  IconButton,
   Paper,
   Table,
   TableBody,
@@ -19,20 +16,8 @@ import {
   TableRow,
   Typography,
 } from '@mui/material'
-import CloseIcon from '@mui/icons-material/Close'
-import { LinearGenomeViewModel } from '../..'
 
-const useStyles = makeStyles()(theme => ({
-  dialogContent: {
-    width: '80em',
-  },
-  closeButton: {
-    position: 'absolute',
-    right: theme.spacing(1),
-    top: theme.spacing(1),
-    color: theme.palette.grey[500],
-  },
-}))
+import { LinearGenomeViewModel } from '../..'
 
 export default function SearchResultsDialog({
   model,
@@ -43,7 +28,6 @@ export default function SearchResultsDialog({
   optAssemblyName?: string
   handleClose: () => void
 }) {
-  const { classes } = useStyles()
   const session = getSession(model)
   const { pluginManager } = getEnv(session)
   const { assemblyManager } = session
@@ -63,7 +47,7 @@ export default function SearchResultsDialog({
   }
   const assemblyRegions = assembly.regions
 
-  function handleClick(location: string) {
+  async function handleClick(location: string) {
     try {
       const newRegion = assemblyRegions.find(
         region => location === region.refName,
@@ -74,7 +58,7 @@ export default function SearchResultsDialog({
         // region visible, xref #1703
         model.showAllRegions()
       } else {
-        model.navToLocString(location, assemblyName)
+        await model.navToLocString(location, assemblyName)
       }
     } catch (e) {
       console.warn(e)
@@ -92,23 +76,7 @@ export default function SearchResultsDialog({
   }
 
   return (
-    <Dialog open maxWidth="xl" onClose={handleClose}>
-      <DialogTitle>
-        Search results
-        {handleClose ? (
-          <IconButton
-            data-testid="close-resultsDialog"
-            className={classes.closeButton}
-            onClick={() => {
-              handleClose()
-            }}
-            size="large"
-          >
-            <CloseIcon />
-          </IconButton>
-        ) : null}
-      </DialogTitle>
-      <Divider />
+    <Dialog open maxWidth="xl" onClose={handleClose} title="Search results">
       <DialogContent>
         {!model.searchResults?.length ? (
           <Typography>
@@ -143,14 +111,19 @@ export default function SearchResultsDialog({
                       </TableCell>
                       <TableCell align="right">
                         <Button
-                          onClick={() => {
-                            const location = result.getLocation()
-                            if (location) {
-                              handleClick(location)
-                              const resultTrackId = result.getTrackId()
-                              if (resultTrackId) {
-                                model.showTrack(resultTrackId)
+                          onClick={async () => {
+                            try {
+                              const location = result.getLocation()
+                              if (location) {
+                                await handleClick(location)
+                                const resultTrackId = result.getTrackId()
+                                if (resultTrackId) {
+                                  model.showTrack(resultTrackId)
+                                }
                               }
+                            } catch (e) {
+                              console.error(e)
+                              session.notify(`${e}`, 'error')
                             }
                             handleClose()
                           }}