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

package/src/LinearGenomeView/components/SequenceSearchDialog.tsx

@@ -2,36 +2,24 @@ import React, { useState } from 'react'
 import {
   Button,
   Checkbox,
-  Dialog,
   DialogActions,
   DialogContent,
-  DialogTitle,
-  Divider,
   FormGroup,
   FormControlLabel,
-  IconButton,
   TextField,
   Typography,
 } from '@mui/material'
+import { Dialog } from '@jbrowse/core/ui'
 import { getSnapshot } from 'mobx-state-tree'
 import { makeStyles } from 'tss-react/mui'
 import { observer } from 'mobx-react'
 import { getSession } from '@jbrowse/core/util'
 
-// icons
-import CloseIcon from '@mui/icons-material/Close'
-
-const useStyles = makeStyles()(theme => ({
-  closeButton: {
-    position: 'absolute',
-    right: theme.spacing(1),
-    top: theme.spacing(1),
-    color: theme.palette.grey[500],
-  },
+const useStyles = makeStyles()({
   dialogContent: {
     width: '40em',
   },
-}))
+})
 
 function SequenceDialog({
   model,
@@ -55,21 +43,7 @@ function SequenceDialog({
   }
 
   return (
-    <Dialog maxWidth="xl" open onClose={handleClose}>
-      <DialogTitle>
-        Sequence search
-        {handleClose ? (
-          <IconButton
-            className={classes.closeButton}
-            onClick={() => handleClose()}
-            size="large"
-          >
-            <CloseIcon />
-          </IconButton>
-        ) : null}
-      </DialogTitle>
-      <Divider />
-
+    <Dialog maxWidth="xl" open onClose={handleClose} title="Sequence search">
       <DialogContent className={classes.dialogContent}>
         <Typography>
           Supply a sequence to search for. A track will be created with the

package/src/LinearGenomeView/components/TrackContainer.tsx

@@ -3,9 +3,12 @@ import { Paper } from '@mui/material'
 import { makeStyles } from 'tss-react/mui'
 import { observer } from 'mobx-react'
 import { isAlive } from 'mobx-state-tree'
+import { ErrorBoundary } from 'react-error-boundary'
+
+// jbrowse core
 import { BaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models'
 import { getConf } from '@jbrowse/core/configuration'
-import { ResizeHandle } from '@jbrowse/core/ui'
+import { ResizeHandle, ErrorMessage } from '@jbrowse/core/ui'
 import { useDebouncedCallback } from '@jbrowse/core/util'
 
 // locals
@@ -34,7 +37,7 @@ const useStyles = makeStyles()({
     zIndex: 3,
   },
 
-  // aligns with block bounderies. check for example the breakpoint split view
+  // aligns with block boundaries. check for example the breakpoint split view
   // demo to see if features align if wanting to change things
   renderingComponentContainer: {
     position: 'absolute',
@@ -92,6 +95,7 @@ function TrackContainer({
   const trackId = getConf(track, 'trackId')
   const ref = useRef(null)
   const dimmed = draggingTrackId !== undefined && draggingTrackId !== display.id
+  const minimized = track.minimized
   const debouncedOnDragEnter = useDebouncedCallback(() => {
     if (isAlive(display) && dimmed) {
       moveTrack(draggingTrackId, track.id)
@@ -109,36 +113,45 @@ function TrackContainer({
   return (
     <Paper className={classes.root} variant="outlined">
       <TrackContainerLabel model={track} view={model} />
-      <div
-        className={classes.trackRenderingContainer}
-        style={{ height }}
-        onScroll={event => display.setScrollTop(event.currentTarget.scrollTop)}
-        onDragEnter={debouncedOnDragEnter}
-        data-testid={`trackRenderingContainer-${model.id}-${trackId}`}
+      <ErrorBoundary
+        key={track.id}
+        FallbackComponent={({ error }) => <ErrorMessage error={error} />}
       >
         <div
-          ref={ref}
-          className={classes.renderingComponentContainer}
-          style={{ transform: `scaleX(${model.scaleFactor})` }}
+          className={classes.trackRenderingContainer}
+          style={{ height: minimized ? 20 : height }}
+          onScroll={evt => display.setScrollTop(evt.currentTarget.scrollTop)}
+          onDragEnter={debouncedOnDragEnter}
+          data-testid={`trackRenderingContainer-${model.id}-${trackId}`}
         >
-          <RenderingComponent
-            model={display}
-            onHorizontalScroll={horizontalScroll}
-          />
-        </div>
+          {!minimized ? (
+            <>
+              <div
+                ref={ref}
+                className={classes.renderingComponentContainer}
+                style={{ transform: `scaleX(${model.scaleFactor})` }}
+              >
+                <RenderingComponent
+                  model={display}
+                  onHorizontalScroll={horizontalScroll}
+                />
+              </div>
 
-        {DisplayBlurb ? (
-          <div
-            style={{
-              position: 'absolute',
-              left: 0,
-              top: display.height - 20,
-            }}
-          >
-            <DisplayBlurb model={display} />
-          </div>
-        ) : null}
-      </div>
+              {DisplayBlurb ? (
+                <div
+                  style={{
+                    position: 'absolute',
+                    left: 0,
+                    top: display.height - 20,
+                  }}
+                >
+                  <DisplayBlurb model={display} />
+                </div>
+              ) : null}
+            </>
+          ) : null}
+        </div>
+      </ErrorBoundary>
       <div
         className={classes.overlay}
         style={{

package/src/LinearGenomeView/components/TrackLabel.tsx

@@ -18,6 +18,8 @@ import {
 import MoreVertIcon from '@mui/icons-material/MoreVert'
 import DragIcon from '@mui/icons-material/DragIndicator'
 import CloseIcon from '@mui/icons-material/Close'
+import MinimizeIcon from '@mui/icons-material/Minimize'
+import AddIcon from '@mui/icons-material/Add'
 
 import { LinearGenomeViewModel } from '..'
 
@@ -64,6 +66,7 @@ const TrackLabel = React.forwardRef<HTMLDivElement, Props>(
     const view = getContainingView(track) as LGV
     const session = getSession(track)
     const trackConf = track.configuration
+    const minimized = track.minimized
     const trackId = getConf(track, 'trackId')
     const trackName = getTrackName(trackConf, session)
 
@@ -73,6 +76,11 @@ const TrackLabel = React.forwardRef<HTMLDivElement, Props>(
     })
 
     const items = [
+      {
+        label: minimized ? 'Restore track' : 'Minimize track',
+        icon: minimized ? AddIcon : MinimizeIcon,
+        onClick: () => track.setMinimized(!minimized),
+      },
       ...(session.getTrackActionMenuItems?.(trackConf) || []),
       ...track.trackMenuItems(),
     ].sort((a, b) => (b.priority || 0) - (a.priority || 0))
@@ -103,12 +111,13 @@ const TrackLabel = React.forwardRef<HTMLDivElement, Props>(
         >
           <CloseIcon fontSize="small" />
         </IconButton>
+
         <Typography
           variant="body1"
           component="span"
           className={classes.trackName}
         >
-          {trackName}
+          {trackName + (minimized ? ' (minimized)' : '')}
         </Typography>
         <IconButton
           {...bindTrigger(popupState)}

package/src/LinearGenomeView/components/TracksContainer.tsx

@@ -1,14 +1,19 @@
-import React, { useEffect, useRef, useState } from 'react'
+import React, { useRef } from 'react'
 import { makeStyles } from 'tss-react/mui'
 import { observer } from 'mobx-react'
-import normalizeWheel from 'normalize-wheel'
+import { Menu } from '@jbrowse/core/ui'
 
-// locals
+// local utils
 import { LinearGenomeViewModel, SCALE_BAR_HEIGHT } from '..'
-import RubberBand from './RubberBand'
-import ScaleBar from './ScaleBar'
+import { useSideScroll, useRangeSelect, useWheelScroll } from './hooks'
+
+// local components
+import Rubberband from './Rubberband'
+import Scalebar from './Scalebar'
 import Gridlines from './Gridlines'
 import CenterLine from './CenterLine'
+import VerticalGuide from './VerticalGuide'
+import RubberbandSpan from './RubberbandSpan'
 
 const useStyles = makeStyles()({
   tracksContainer: {
@@ -22,7 +27,6 @@ const useStyles = makeStyles()({
 })
 
 type LGV = LinearGenomeViewModel
-type Timer = ReturnType<typeof setTimeout>
 
 function TracksContainer({
   children,
@@ -32,149 +36,68 @@ function TracksContainer({
   model: LGV
 }) {
   const { classes } = useStyles()
-  // refs are to store these variables to avoid repeated rerenders associated
-  // with useState/setState
-  const delta = useRef(0)
-  const scheduled = useRef(false)
-  const timeout = useRef<Timer>()
+  const { mouseDown: mouseDown1, mouseUp } = useSideScroll(model)
   const ref = useRef<HTMLDivElement>(null)
-  const prevX = useRef<number>(0)
-
-  const [mouseDragging, setMouseDragging] = useState(false)
-
-  useEffect(() => {
-    let cleanup = () => {}
-
-    function globalMouseMove(event: MouseEvent) {
-      event.preventDefault()
-      const currX = event.clientX
-      const distance = currX - prevX.current
-      if (distance) {
-        // use rAF to make it so multiple event handlers aren't fired per-frame
-        // see https://calendar.perfplanet.com/2013/the-runtime-performance-checklist/
-        if (!scheduled.current) {
-          scheduled.current = true
-          window.requestAnimationFrame(() => {
-            model.horizontalScroll(-distance)
-            scheduled.current = false
-            prevX.current = event.clientX
-          })
-        }
-      }
-    }
-
-    function globalMouseUp() {
-      prevX.current = 0
-      if (mouseDragging) {
-        setMouseDragging(false)
-      }
-    }
-
-    if (mouseDragging) {
-      window.addEventListener('mousemove', globalMouseMove, true)
-      window.addEventListener('mouseup', globalMouseUp, true)
-      cleanup = () => {
-        window.removeEventListener('mousemove', globalMouseMove, true)
-        window.removeEventListener('mouseup', globalMouseUp, true)
-      }
-    }
-    return cleanup
-  }, [model, mouseDragging, prevX])
-
-  function mouseDown(event: React.MouseEvent) {
-    // check if clicking a draggable element or a resize handle
-    const target = event.target as HTMLElement
-    if (target.draggable || target.dataset.resizer) {
-      return
-    }
-
-    // otherwise do click and drag scroll
-    if (event.button === 0) {
-      prevX.current = event.clientX
-      setMouseDragging(true)
-    }
-  }
-
-  // this local mouseup is used in addition to the global because sometimes
-  // the global add/remove are not called in time, resulting in issue #533
-  function mouseUp(event: React.MouseEvent) {
-    event.preventDefault()
-    setMouseDragging(false)
-  }
-
-  function mouseLeave(event: React.MouseEvent) {
-    event.preventDefault()
-  }
-
-  useEffect(() => {
-    const curr = ref.current
-    // if ctrl is held down, zoom in with y-scroll
-    // else scroll horizontally with x-scroll
-    function onWheel(origEvent: WheelEvent) {
-      const event = normalizeWheel(origEvent)
-      if (origEvent.ctrlKey === true) {
-        origEvent.preventDefault()
-        delta.current += event.pixelY / 500
-        model.setScaleFactor(
-          delta.current < 0 ? 1 - delta.current : 1 / (1 + delta.current),
-        )
-        if (timeout.current) {
-          clearTimeout(timeout.current)
-        }
-        timeout.current = setTimeout(() => {
-          model.setScaleFactor(1)
-          model.zoomTo(
-            delta.current > 0
-              ? model.bpPerPx * (1 + delta.current)
-              : model.bpPerPx / (1 - delta.current),
-          )
-          delta.current = 0
-        }, 300)
-      } else {
-        // this is needed to stop the event from triggering "back button
-        // action" on MacOSX etc.  but is a heuristic to avoid preventing the
-        // inner-track scroll behavior
-        if (Math.abs(event.pixelX) > Math.abs(2 * event.pixelY)) {
-          origEvent.preventDefault()
-        }
-        delta.current += event.pixelX
-        if (!scheduled.current) {
-          // use rAF to make it so multiple event handlers aren't fired per-frame
-          // see https://calendar.perfplanet.com/2013/the-runtime-performance-checklist/
-          scheduled.current = true
-          window.requestAnimationFrame(() => {
-            model.horizontalScroll(delta.current)
-            delta.current = 0
-            scheduled.current = false
-          })
-        }
-      }
-    }
-    if (curr) {
-      curr.addEventListener('wheel', onWheel)
-      return () => {
-        curr.removeEventListener('wheel', onWheel)
-      }
-    }
-    return () => {}
-  }, [model])
+  const {
+    guideX,
+    rubberbandOn,
+    leftBpOffset,
+    rightBpOffset,
+    numOfBpSelected,
+    width,
+    left,
+    anchorPosition,
+    handleMenuItemClick,
+    open,
+    handleClose,
+    mouseMove,
+    mouseDown: mouseDown2,
+  } = useRangeSelect(ref, model, true)
+  useWheelScroll(ref, model)
 
   return (
     <div
       ref={ref}
       data-testid="trackContainer"
       className={classes.tracksContainer}
-      onMouseDown={mouseDown}
+      onMouseDown={event => {
+        mouseDown1(event)
+        mouseDown2(event)
+      }}
+      onMouseMove={mouseMove}
       onMouseUp={mouseUp}
-      onMouseLeave={mouseLeave}
     >
       {model.showGridlines ? <Gridlines model={model} /> : null}
       {model.showCenterLine ? <CenterLine model={model} /> : null}
-
-      <RubberBand
+      {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}
+
+      <Rubberband
         model={model}
         ControlComponent={
-          <ScaleBar
+          <Scalebar
             model={model}
             style={{ height: SCALE_BAR_HEIGHT, boxSizing: 'border-box' }}
           />

package/src/LinearGenomeView/components/VerticalGuide.tsx

@@ -0,0 +1,37 @@
+import React from 'react'
+import { Tooltip } from '@mui/material'
+import { makeStyles } from 'tss-react/mui'
+import { observer } from 'mobx-react'
+import { stringify } from '@jbrowse/core/util'
+
+// locals
+import { LinearGenomeViewModel } from '..'
+
+type LGV = LinearGenomeViewModel
+
+const useStyles = makeStyles()({
+  guide: {
+    pointerEvents: 'none',
+    height: '100%',
+    width: 1,
+    position: 'absolute',
+    zIndex: 10,
+  },
+})
+
+function VerticalGuide({ model, coordX }: { model: LGV; coordX: number }) {
+  const { classes } = useStyles()
+  return (
+    <Tooltip open placement="top" title={stringify(model.pxToBp(coordX))} arrow>
+      <div
+        className={classes.guide}
+        style={{
+          left: coordX,
+          background: 'red',
+        }}
+      />
+    </Tooltip>
+  )
+}
+
+export default observer(VerticalGuide)