@jbrowse/plugin-linear-genome-view 2.1.0 → 2.1.2

package/esm/LinearGenomeView/index.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "2.1.0",
+  "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",
@@ -65,5 +64,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "0db0462fa1f9f15ab4869da085bcab032b9483c3"
+  "gitHead": "449b17325c9a4a97181f7ddddf48e80219f03b8d"
 }

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

@@ -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()

package/src/LinearGenomeView/components/ImportForm.tsx

@@ -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

@@ -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
@@ -62,9 +62,9 @@ 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 ? (

package/src/LinearGenomeView/components/OverviewRubberBand.tsx

@@ -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)
@@ -124,9 +122,11 @@ function OverviewRubberBand({
       // 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(startX - cytobandOffset),
-            overview.pxToBp(currentX - cytobandOffset),
+            overview.pxToBp(left - cytobandOffset),
+            overview.pxToBp(right - cytobandOffset),
           )
         }
       }
@@ -307,14 +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

@@ -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

@@ -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)

package/src/LinearGenomeView/components/SearchBox.tsx

@@ -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

@@ -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)

package/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.js.snap

@@ -90,7 +90,7 @@ exports[`<LinearGenomeView /> renders one track, one region 1`] = `
         class="tss-ig8oez-headerBar"
       >
         <button
-          class="MuiButton-root MuiButton-text MuiButton-textSecondary MuiButton-sizeMedium MuiButton-textSizeMedium MuiButtonBase-root tss-19jxj46-toggleButton css-1d3f8j8-MuiButtonBase-root-MuiButton-root"
+          class="MuiButtonBase-root MuiButton-root MuiButton-text MuiButton-textSecondary MuiButton-sizeMedium MuiButton-textSizeMedium tss-19jxj46-toggleButton css-1d3f8j8-MuiButtonBase-root-MuiButton-root"
           tabindex="0"
           title="Open track selector"
           type="button"
@@ -117,7 +117,7 @@ exports[`<LinearGenomeView /> renders one track, one region 1`] = `
           class="MuiFormGroup-root MuiFormGroup-row tss-4gub8h-headerForm css-qfz70r-MuiFormGroup-root"
         >
           <button
-            class="MuiButton-root MuiButton-outlined MuiButton-outlinedPrimary MuiButton-sizeMedium MuiButton-outlinedSizeMedium MuiButtonBase-root tss-7ktir1-panButton css-1rwt2y5-MuiButtonBase-root-MuiButton-root"
+            class="MuiButtonBase-root MuiButton-root MuiButton-outlined MuiButton-outlinedPrimary MuiButton-sizeMedium MuiButton-outlinedSizeMedium tss-7ktir1-panButton css-1rwt2y5-MuiButtonBase-root-MuiButton-root"
             tabindex="0"
             type="button"
           >
@@ -137,7 +137,7 @@ exports[`<LinearGenomeView /> renders one track, one region 1`] = `
             />
           </button>
           <button
-            class="MuiButton-root MuiButton-outlined MuiButton-outlinedPrimary MuiButton-sizeMedium MuiButton-outlinedSizeMedium MuiButtonBase-root tss-7ktir1-panButton css-1rwt2y5-MuiButtonBase-root-MuiButton-root"
+            class="MuiButtonBase-root MuiButton-root MuiButton-outlined MuiButton-outlinedPrimary MuiButton-sizeMedium MuiButton-outlinedSizeMedium tss-7ktir1-panButton css-1rwt2y5-MuiButtonBase-root-MuiButton-root"
             tabindex="0"
             type="button"
           >
@@ -166,7 +166,7 @@ exports[`<LinearGenomeView /> renders one track, one region 1`] = `
               style="margin: 7px; min-width: 175px;"
             >
               <div
-                class="MuiOutlinedInput-root MuiInputBase-root MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-adornedEnd MuiAutocomplete-inputRoot css-154xyx0-MuiInputBase-root-MuiOutlinedInput-root"
+                class="MuiInputBase-root MuiOutlinedInput-root MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-adornedEnd MuiAutocomplete-inputRoot css-154xyx0-MuiInputBase-root-MuiOutlinedInput-root"
                 style="padding: 0px; height: 32px; background: rgba(255, 255, 255, 0.8);"
               >
                 <input
@@ -175,7 +175,7 @@ exports[`<LinearGenomeView /> renders one track, one region 1`] = `
                   aria-invalid="false"
                   autocapitalize="none"
                   autocomplete="off"
-                  class="MuiOutlinedInput-input MuiInputBase-input MuiInputBase-inputAdornedEnd MuiAutocomplete-input MuiAutocomplete-inputFocused css-nxo287-MuiInputBase-input-MuiOutlinedInput-input"
+                  class="MuiInputBase-input MuiOutlinedInput-input MuiInputBase-inputAdornedEnd MuiAutocomplete-input MuiAutocomplete-inputFocused css-nxo287-MuiInputBase-input-MuiOutlinedInput-input"
                   id="refNameAutocomplete-lgv"
                   placeholder="Search for location"
                   role="combobox"
@@ -265,7 +265,7 @@ exports[`<LinearGenomeView /> renders one track, one region 1`] = `
             </svg>
           </button>
           <span
-            class="MuiSlider-colorPrimary MuiSlider-sizeSmall MuiSlider-root tss-1c03ro5-slider css-53tbrc-MuiSlider-root"
+            class="MuiSlider-root MuiSlider-colorPrimary MuiSlider-sizeSmall tss-1c03ro5-slider css-53tbrc-MuiSlider-root"
           >
             <span
               class="MuiSlider-rail css-14pt78w-MuiSlider-rail"
@@ -275,7 +275,7 @@ exports[`<LinearGenomeView /> renders one track, one region 1`] = `
               style="left: 0%; width: 0%;"
             />
             <span
-              class="MuiSlider-thumbColorPrimary MuiSlider-thumbSizeSmall MuiSlider-thumb css-14gf62f-MuiSlider-thumb"
+              class="MuiSlider-thumb MuiSlider-thumbColorPrimary MuiSlider-thumbSizeSmall css-14gf62f-MuiSlider-thumb"
               data-focusvisible="false"
               data-index="0"
               style="left: 0%;"
@@ -655,7 +655,7 @@ exports[`<LinearGenomeView /> renders two tracks, two regions 1`] = `
         class="tss-ig8oez-headerBar"
       >
         <button
-          class="MuiButton-root MuiButton-text MuiButton-textSecondary MuiButton-sizeMedium MuiButton-textSizeMedium MuiButtonBase-root tss-19jxj46-toggleButton css-1d3f8j8-MuiButtonBase-root-MuiButton-root"
+          class="MuiButtonBase-root MuiButton-root MuiButton-text MuiButton-textSecondary MuiButton-sizeMedium MuiButton-textSizeMedium tss-19jxj46-toggleButton css-1d3f8j8-MuiButtonBase-root-MuiButton-root"
           tabindex="0"
           title="Open track selector"
           type="button"
@@ -682,7 +682,7 @@ exports[`<LinearGenomeView /> renders two tracks, two regions 1`] = `
           class="MuiFormGroup-root MuiFormGroup-row tss-4gub8h-headerForm css-qfz70r-MuiFormGroup-root"
         >
           <button
-            class="MuiButton-root MuiButton-outlined MuiButton-outlinedPrimary MuiButton-sizeMedium MuiButton-outlinedSizeMedium MuiButtonBase-root tss-7ktir1-panButton css-1rwt2y5-MuiButtonBase-root-MuiButton-root"
+            class="MuiButtonBase-root MuiButton-root MuiButton-outlined MuiButton-outlinedPrimary MuiButton-sizeMedium MuiButton-outlinedSizeMedium tss-7ktir1-panButton css-1rwt2y5-MuiButtonBase-root-MuiButton-root"
             tabindex="0"
             type="button"
           >
@@ -702,7 +702,7 @@ exports[`<LinearGenomeView /> renders two tracks, two regions 1`] = `
             />
           </button>
           <button
-            class="MuiButton-root MuiButton-outlined MuiButton-outlinedPrimary MuiButton-sizeMedium MuiButton-outlinedSizeMedium MuiButtonBase-root tss-7ktir1-panButton css-1rwt2y5-MuiButtonBase-root-MuiButton-root"
+            class="MuiButtonBase-root MuiButton-root MuiButton-outlined MuiButton-outlinedPrimary MuiButton-sizeMedium MuiButton-outlinedSizeMedium tss-7ktir1-panButton css-1rwt2y5-MuiButtonBase-root-MuiButton-root"
             tabindex="0"
             type="button"
           >
@@ -731,7 +731,7 @@ exports[`<LinearGenomeView /> renders two tracks, two regions 1`] = `
               style="margin: 7px; min-width: 175px;"
             >
               <div
-                class="MuiOutlinedInput-root MuiInputBase-root MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-adornedEnd MuiAutocomplete-inputRoot css-154xyx0-MuiInputBase-root-MuiOutlinedInput-root"
+                class="MuiInputBase-root MuiOutlinedInput-root MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl MuiInputBase-adornedEnd MuiAutocomplete-inputRoot css-154xyx0-MuiInputBase-root-MuiOutlinedInput-root"
                 style="padding: 0px; height: 32px; background: rgba(255, 255, 255, 0.8);"
               >
                 <input
@@ -740,7 +740,7 @@ exports[`<LinearGenomeView /> renders two tracks, two regions 1`] = `
                   aria-invalid="false"
                   autocapitalize="none"
                   autocomplete="off"
-                  class="MuiOutlinedInput-input MuiInputBase-input MuiInputBase-inputAdornedEnd MuiAutocomplete-input MuiAutocomplete-inputFocused css-nxo287-MuiInputBase-input-MuiOutlinedInput-input"
+                  class="MuiInputBase-input MuiOutlinedInput-input MuiInputBase-inputAdornedEnd MuiAutocomplete-input MuiAutocomplete-inputFocused css-nxo287-MuiInputBase-input-MuiOutlinedInput-input"
                   id="refNameAutocomplete-lgv"
                   placeholder="Search for location"
                   role="combobox"
@@ -832,7 +832,7 @@ exports[`<LinearGenomeView /> renders two tracks, two regions 1`] = `
             />
           </button>
           <span
-            class="MuiSlider-colorPrimary MuiSlider-sizeSmall MuiSlider-root tss-1c03ro5-slider css-53tbrc-MuiSlider-root"
+            class="MuiSlider-root MuiSlider-colorPrimary MuiSlider-sizeSmall tss-1c03ro5-slider css-53tbrc-MuiSlider-root"
           >
             <span
               class="MuiSlider-rail css-14pt78w-MuiSlider-rail"
@@ -842,7 +842,7 @@ exports[`<LinearGenomeView /> renders two tracks, two regions 1`] = `
               style="left: 0%; width: 9.774680693120512%;"
             />
             <span
-              class="MuiSlider-thumbColorPrimary MuiSlider-thumbSizeSmall MuiSlider-thumb css-14gf62f-MuiSlider-thumb"
+              class="MuiSlider-thumb MuiSlider-thumbColorPrimary MuiSlider-thumbSizeSmall css-14gf62f-MuiSlider-thumb"
               data-focusvisible="false"
               data-index="0"
               style="left: 9.774680693120512%;"