npm - @jbrowse/plugin-linear-genome-view - Versions diffs - 2.0.0 → 2.1.2 - Mend

@jbrowse/plugin-linear-genome-view 2.0.0 → 2.1.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (144) hide show

package/esm/LinearGenomeView/index.js.map CHANGED Viewed

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1	- 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "2.0.0",
+  "version": "2.1.2",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -39,7 +39,6 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@babel/runtime": "^7.17.9",
     "@mui/icons-material": "^5.0.1",
     "@popperjs/core": "^2.11.0",
     "clone": "^2.1.2",
@@ -51,7 +50,7 @@
     "react-popper": "^2.0.0"
   },
   "peerDependencies": {
-    "@jbrowse/core": "^1.0.0",
+    "@jbrowse/core": "^2.0.0",
     "@mui/material": "^5.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^7.0.0",
@@ -65,5 +64,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "ecc7f5d47351a5ea04bc00f3a6eb6dfb607342e6"
+  "gitHead": "449b17325c9a4a97181f7ddddf48e80219f03b8d"
 }

package/src/BaseLinearDisplay/components/BaseLinearDisplay.tsx CHANGED Viewed

@@ -104,7 +104,6 @@ const BaseLinearDisplay = observer(
           }
           style={{ zIndex: theme.zIndex.tooltip }}
           menuItems={contextMenuItems()}
-          data-testid="base_linear_display_context_menu"
         />
       </div>
     )

package/src/BaseLinearDisplay/components/ServerSideRenderedBlockContent.tsx CHANGED Viewed

@@ -87,7 +87,8 @@ const LoadingMessage = observer(({ model }: { model: any }) => {
   }, [])
   const { status: blockStatus } = model
-  const { message: displayStatus } = getParent(model, 2)
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  const { message: displayStatus } = getParent<any>(model, 2)
   const status = displayStatus || blockStatus
   return (
     <>

package/src/LinearGenomeView/components/{SequenceDialog.tsx → GetSequenceDialog.tsx} RENAMED Viewed

@@ -15,11 +15,9 @@ import {
 } from '@mui/material'
 import { observer } from 'mobx-react'
 import { saveAs } from 'file-saver'
-import { Region } from '@jbrowse/core/util/types'
 import { getConf } from '@jbrowse/core/configuration'
 import copy from 'copy-to-clipboard'
-import { getSession } from '@jbrowse/core/util'
-import { Feature } from '@jbrowse/core/util/simpleFeature'
+import { getSession, Feature, Region } from '@jbrowse/core/util'
 import { formatSeqFasta } from '@jbrowse/core/util/formatFastaStrings'
 // icons
@@ -31,9 +29,6 @@ import GetAppIcon from '@mui/icons-material/GetApp'
 import { LinearGenomeViewModel } from '..'
 const useStyles = makeStyles()(theme => ({
-  loadingMessage: {
-    padding: theme.spacing(5),
-  },
   closeButton: {
     position: 'absolute',
     right: theme.spacing(1),
@@ -89,7 +84,7 @@ function SequenceDialog({
   model,
   handleClose,
 }: {
-  model: LinearGenomeViewModel
+  model: LGV
   handleClose: () => void
 }) {
   const { classes } = useStyles()
@@ -162,19 +157,11 @@ function SequenceDialog({
   const sequenceTooLarge = sequence ? sequence.length > 1_000_000 : false
   return (
-    <Dialog
-      data-testid="sequence-dialog"
-      maxWidth="xl"
-      open
-      onClose={handleClose}
-      aria-labelledby="alert-dialog-title"
-      aria-describedby="alert-dialog-description"
-    >
-      <DialogTitle id="alert-dialog-title">
+    <Dialog maxWidth="xl" open onClose={handleClose}>
+      <DialogTitle>
         Reference sequence
         {handleClose ? (
           <IconButton
-            data-testid="close-seqDialog"
             className={classes.closeButton}
             onClick={() => {
               handleClose()
@@ -248,7 +235,7 @@ function SequenceDialog({
         >
           Download FASTA
         </Button>
-        <Button onClick={handleClose} color="primary" autoFocus>
+        <Button onClick={handleClose} variant="contained">
           Close
         </Button>
       </DialogActions>

package/src/LinearGenomeView/components/{VerticalGuides.tsx → Gridlines.tsx} RENAMED Viewed

File without changes

package/src/LinearGenomeView/components/ImportForm.tsx CHANGED Viewed

@@ -132,6 +132,7 @@ const ImportForm = observer(({ model }: { model: LGV }) => {
                 onChange={val => {
                   setImportError('')
                   setSelectedAsm(val)
+                  setValue('')
                 }}
                 session={session}
                 selected={selectedAsm}

package/src/LinearGenomeView/components/LinearGenomeView.tsx CHANGED Viewed

@@ -11,7 +11,7 @@ import TrackContainer from './TrackContainer'
 import TracksContainer from './TracksContainer'
 import ImportForm from './ImportForm'
 import MiniControls from './MiniControls'
-import SequenceDialog from './SequenceDialog'
+import GetSequenceDialog from './GetSequenceDialog'
 import SearchResultsDialog from './SearchResultsDialog'
 type LGV = LinearGenomeViewModel
@@ -62,19 +62,15 @@ const LinearGenomeView = observer(({ model }: { model: LGV }) => {
   return (
     <div style={{ position: 'relative' }}>
       {model.seqDialogDisplayed ? (
-        <SequenceDialog
+        <GetSequenceDialog
           model={model}
-          handleClose={() => {
-            model.setSequenceDialogOpen(false)
-          }}
+          handleClose={() => model.setGetSequenceDialogOpen(false)}
         />
       ) : null}
       {model.isSearchDialogDisplayed ? (
         <SearchResultsDialog
           model={model}
-          handleClose={() => {
-            model.setSearchResults(undefined, undefined)
-          }}
+          handleClose={() => model.setSearchResults(undefined, undefined)}
         />
       ) : null}
       {!hideHeader ? (

package/src/LinearGenomeView/components/OverviewRubberBand.tsx CHANGED Viewed

@@ -2,15 +2,13 @@ import React, { useRef, useEffect, useState } from 'react'
 import { Popover, Tooltip, Typography, alpha } from '@mui/material'
 import { makeStyles } from 'tss-react/mui'
 import { getSession, stringify } from '@jbrowse/core/util'
-import { observer, PropTypes as MobxPropTypes } from 'mobx-react'
-import ReactPropTypes from 'prop-types'
+import { observer } from 'mobx-react'
 import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel'
 import { LinearGenomeViewModel, HEADER_OVERVIEW_HEIGHT } from '..'
 type LGV = LinearGenomeViewModel
 const useStyles = makeStyles()(theme => {
-  // @ts-ignore
   const { tertiary, primary } = theme.palette
   const background = tertiary
     ? alpha(tertiary.main, 0.7)
@@ -107,7 +105,7 @@ function OverviewRubberBand({
   const [currentX, setCurrentX] = useState<number>()
   const [guideX, setGuideX] = useState<number>()
   const controlsRef = useRef<HTMLDivElement>(null)
-  const rubberBandRef = useRef(null)
+  const rubberBandRef = useRef<HTMLDivElement>(null)
   const { classes } = useStyles()
   const mouseDragging = startX !== undefined
@@ -121,30 +119,27 @@ function OverviewRubberBand({
     }
     function globalMouseUp() {
-      if (
-        controlsRef.current &&
-        startX !== undefined &&
-        currentX !== undefined
-      ) {
+      // click and drag
+      if (startX !== undefined && currentX !== undefined) {
         if (Math.abs(currentX - startX) > 3) {
-          model.zoomToDisplayedRegions(
-            overview.pxToBp(startX - cytobandOffset),
-            overview.pxToBp(currentX - cytobandOffset),
+          const left = Math.min(startX, currentX)
+          const right = Math.max(startX, currentX)
+          model.moveTo(
+            overview.pxToBp(left - cytobandOffset),
+            overview.pxToBp(right - cytobandOffset),
           )
         }
       }
-      /* handling clicking and centering at a specific Bp */
-      if (
-        controlsRef.current &&
-        startX !== undefined &&
-        currentX === undefined
-      ) {
-        const clickedAt = overview.pxToBp(startX - cytobandOffset)
-        model.centerAt(
-          Math.round(clickedAt.coord),
-          clickedAt.refName,
-          clickedAt.index,
-        )
+      // 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)
@@ -312,14 +307,4 @@ function OverviewRubberBand({
   )
 }
-OverviewRubberBand.propTypes = {
-  model: MobxPropTypes.objectOrObservableObject.isRequired,
-  overview: MobxPropTypes.objectOrObservableObject.isRequired,
-  ControlComponent: ReactPropTypes.node,
-}
-OverviewRubberBand.defaultProps = {
-  ControlComponent: <div />,
-}
 export default observer(OverviewRubberBand)

package/src/LinearGenomeView/components/OverviewScaleBar.tsx CHANGED Viewed

@@ -88,7 +88,6 @@ const Polygon = observer(
       model
     const { contentBlocks, totalWidthPxWithoutBorders } = dynamicBlocks
-    // @ts-ignore
     const { tertiary, primary } = theme.palette
     const polygonColor = tertiary ? tertiary.light : primary.light
@@ -398,7 +397,6 @@ const ScaleBar = observer(
     const visibleRegions = dynamicBlocks.contentBlocks
     const overviewVisibleRegions = overview.dynamicBlocks
-    // @ts-ignore
     const { tertiary, primary } = theme.palette
     const scaleBarColor = tertiary ? tertiary.light : primary.light

package/src/LinearGenomeView/components/RubberBand.tsx CHANGED Viewed

@@ -9,7 +9,6 @@ import { LinearGenomeViewModel } from '..'
 type LGV = LinearGenomeViewModel
 const useStyles = makeStyles()(theme => {
-  // @ts-ignore
   const { primary, tertiary } = theme.palette
   const background = tertiary
     ? alpha(tertiary.main, 0.7)
@@ -103,7 +102,6 @@ function RubberBand({
       }
       let leftPx = startX
       let rightPx = offsetX
-      // handles clicking and draging to the left
       if (rightPx < leftPx) {
         ;[leftPx, rightPx] = [rightPx, leftPx]
       }

package/src/LinearGenomeView/components/SearchBox.tsx CHANGED Viewed

@@ -2,8 +2,8 @@ import React from 'react'
 import { observer } from 'mobx-react'
 import { useTheme, alpha } from '@mui/material'
 import { makeStyles } from 'tss-react/mui'
-import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
 import { getSession } from '@jbrowse/core/util'
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
 // locals
 import RefNameAutocomplete from './RefNameAutocomplete'

package/src/LinearGenomeView/components/SequenceSearchDialog.tsx ADDED Viewed

@@ -0,0 +1,165 @@
+import React, { useState } from 'react'
+import {
+  Button,
+  Checkbox,
+  Dialog,
+  DialogActions,
+  DialogContent,
+  DialogTitle,
+  Divider,
+  FormGroup,
+  FormControlLabel,
+  IconButton,
+  TextField,
+  Typography,
+} from '@mui/material'
+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'
+// locals
+import { LinearGenomeViewModel } from '..'
+const useStyles = makeStyles()(theme => ({
+  closeButton: {
+    position: 'absolute',
+    right: theme.spacing(1),
+    top: theme.spacing(1),
+    color: theme.palette.grey[500],
+  },
+  dialogContent: {
+    width: '40em',
+  },
+}))
+function SequenceDialog({
+  model,
+  handleClose,
+}: {
+  model: LinearGenomeViewModel
+  handleClose: () => void
+}) {
+  const { classes } = useStyles()
+  const [value, setValue] = useState('')
+  const [searchForward, setSearchForward] = useState(true)
+  const [searchReverse, setSearchReverse] = useState(true)
+  const [caseInsensitive, setCaseInsensitive] = useState(true)
+  let error
+  try {
+    new RegExp(value)
+  } catch (e) {
+    error = e
+  }
+  return (
+    <Dialog maxWidth="xl" open onClose={handleClose}>
+      <DialogTitle>
+        Sequence search
+        {handleClose ? (
+          <IconButton
+            className={classes.closeButton}
+            onClick={() => handleClose()}
+            size="large"
+          >
+            <CloseIcon />
+          </IconButton>
+        ) : null}
+      </DialogTitle>
+      <Divider />
+      <DialogContent className={classes.dialogContent}>
+        <Typography>
+          Supply a sequence to search for. A track will be created with the
+          resulting matches once submitted. You can also supply regex style
+          expressions e.g. AACT(C|T).
+        </Typography>
+        <TextField
+          value={value}
+          onChange={e => setValue(e.target.value)}
+          helperText="Sequence search pattern"
+        />
+        <FormGroup>
+          <FormControlLabel
+            control={
+              <Checkbox
+                checked={searchForward}
+                onChange={event => setSearchForward(event.target.checked)}
+              />
+            }
+            label="Search forward strand"
+          />
+          <FormControlLabel
+            control={
+              <Checkbox
+                checked={searchReverse}
+                onChange={event => setSearchReverse(event.target.checked)}
+              />
+            }
+            label="Search reverse strand"
+          />
+          <FormControlLabel
+            control={
+              <Checkbox
+                checked={caseInsensitive}
+                onChange={event => setCaseInsensitive(event.target.checked)}
+              />
+            }
+            label="Case insensitive"
+          />
+        </FormGroup>
+        {error ? <Typography color="error">{`${error}`}</Typography> : null}
+      </DialogContent>
+      <DialogActions>
+        <Button
+          onClick={() => {
+            if (value) {
+              const trackId = `sequence_search_${+Date.now()}`
+              const session = getSession(model)
+              const { assemblyManager } = session
+              const assemblyName = model.assemblyNames[0]
+              session.addTrackConf({
+                trackId,
+                name: `Sequence search ${value}`,
+                assemblyNames: [assemblyName],
+                type: 'FeatureTrack',
+                adapter: {
+                  type: 'SequenceSearchAdapter',
+                  search: value,
+                  searchForward,
+                  searchReverse,
+                  caseInsensitive,
+                  sequenceAdapter: getSnapshot(
+                    assemblyManager.get(assemblyName)?.configuration.sequence
+                      .adapter,
+                  ),
+                },
+              })
+              model.toggleTrack(trackId)
+            }
+            handleClose()
+          }}
+          variant="contained"
+          color="primary"
+        >
+          Submit
+        </Button>
+        <Button
+          onClick={() => handleClose()}
+          variant="contained"
+          color="secondary"
+        >
+          Close
+        </Button>
+      </DialogActions>
+    </Dialog>
+  )
+}
+export default observer(SequenceDialog)