npm - @jbrowse/plugin-linear-genome-view - Versions diffs - 2.1.0 → 2.1.3 - Mend

@jbrowse/plugin-linear-genome-view 2.1.0 → 2.1.3

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 (139) 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": "2.1.0",
+  "version": "2.1.3",
   "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": "ebd548ceb52adb36cf6ab437082b5b5feac1338e"
 }

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()

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

@@ -9,7 +9,7 @@ import CloseIcon from '@mui/icons-material/Close'
 // locals
 import RefNameAutocomplete from './RefNameAutocomplete'
-import { fetchResults } from './util'
+import { fetchResults, splitLast } from './util'
 import { LinearGenomeViewModel, WIDGET_HEIGHT } from '..'
 const SearchResultsDialog = lazy(() => import('./SearchResultsDialog'))
@@ -34,6 +34,8 @@ const ImportForm = observer(({ model }: { model: LGV }) => {
   const { rankSearchResults, isSearchDialogDisplayed, error } = model
   const [selectedAsm, setSelectedAsm] = useState(assemblyNames[0])
   const [importError, setImportError] = useState(error)
+  const [option, setOption] = useState<BaseResult>()
   const searchScope = model.searchScope(selectedAsm)
   const assembly = assemblyManager.get(selectedAsm)
@@ -45,11 +47,16 @@ const ImportForm = observer(({ model }: { model: LGV }) => {
   const [myVal, setValue] = useState('')
   const value = myVal || regions[0]?.refName
-  // use this instead of useState initializer because the useState initializer
-  // won't update in response to an observable
-  const option = new BaseResult({
-    label: value,
-  })
+  function navToOption(option: BaseResult) {
+    const location = option.getLocation()
+    const trackId = option.getTrackId()
+    if (location) {
+      model.navToLocString(location, selectedAsm)
+      if (trackId) {
+        model.showTrack(trackId)
+      }
+    }
+  }
   // gets a string as input, or use stored option results from previous query,
   // then re-query and
@@ -57,45 +64,34 @@ const ImportForm = observer(({ model }: { model: LGV }) => {
   // 2) if it's a single result navigate to it
   // 3) else assume it's a locstring and navigate to it
   async function handleSelectedRegion(input: string) {
-    if (!option) {
-      return
-    }
-    let trackId = option.getTrackId()
-    let location = input || option.getLocation() || ''
-    const [ref, rest] = location.split(':')
-    const allRefs = assembly?.allRefNames || []
     try {
-      // instead of querying text-index, first:
-      // - check if input matches a refname directly
-      // - or looks like locstring
-      // then just navigate as if it were a locstring
-      if (
-        allRefs.includes(location) ||
-        (allRefs.includes(ref) &&
-          rest !== undefined &&
-          !Number.isNaN(parseInt(rest, 10)))
-      ) {
-        model.navToLocString(location, selectedAsm)
+      if (option?.getDisplayString() === input && option.hasLocation()) {
+        navToOption(option)
       } else {
-        const results = await fetchResults({
-          queryString: input,
-          searchType: 'exact',
-          searchScope,
-          rankSearchResults,
-          textSearchManager,
-          assembly,
-        })
-        if (results.length > 1) {
-          model.setSearchResults(results, input.toLowerCase())
-          return
-        } else if (results.length === 1) {
-          location = results[0].getLocation()
-          trackId = results[0].getTrackId()
-        }
+        const [ref, rest] = splitLast(input, ':')
+        const allRefs = assembly?.allRefNamesWithLowerCase || []
+        if (
+          allRefs.includes(input) ||
+          (allRefs.includes(ref) && !Number.isNaN(parseInt(rest, 10)))
+        ) {
+          model.navToLocString(input, selectedAsm)
+        } else {
+          const results = await fetchResults({
+            queryString: input,
+            searchType: 'exact',
+            searchScope,
+            rankSearchResults,
+            textSearchManager,
+            assembly,
+          })
-        model.navToLocString(location, selectedAsm)
-        if (trackId) {
-          model.showTrack(trackId)
+          if (results.length > 1) {
+            model.setSearchResults(results, input.toLowerCase())
+          } else if (results.length === 1) {
+            navToOption(results[0])
+          } else {
+            model.navToLocString(input, selectedAsm)
+          }
         }
       }
     } catch (e) {
@@ -132,6 +128,7 @@ const ImportForm = observer(({ model }: { model: LGV }) => {
                 onChange={val => {
                   setImportError('')
                   setSelectedAsm(val)
+                  setValue('')
                 }}
                 session={session}
                 selected={selectedAsm}
@@ -159,6 +156,7 @@ const ImportForm = observer(({ model }: { model: LGV }) => {
                     // note: minWidth 270 accomodates full width of helperText
                     minWidth={270}
                     onChange={str => setValue(str)}
+                    onSelect={val => setOption(val)}
                     TextFieldProps={{
                       variant: 'outlined',
                       helperText:

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
@@ -62,9 +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/LinearGenomeViewSvg.tsx CHANGED Viewed

@@ -235,10 +235,10 @@ function SVGTracks({
         const current = offset
         const trackName =
           getConf(track, 'name') ||
-          `Reference sequence (${readConfObject(
-            getParent(track.configuration),
-            'name',
-          )})`
+          `Reference sequence (${
+            readConfObject(getParent(track.configuration), 'displayName') ||
+            readConfObject(getParent(track.configuration), 'name')
+          })`
         const display = track.displays[0]
         offset += display.height + paddingHeight + textHeight
         return (

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)
@@ -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 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/RefNameAutocomplete.tsx CHANGED Viewed

@@ -19,7 +19,6 @@ import HelpIcon from '@mui/icons-material/Help'
 // locals
 import { LinearGenomeViewModel } from '..'
-import { dedupe } from './util'
 // lazy
 const HelpDialog = lazy(() => import('./HelpDialog'))
@@ -74,8 +73,8 @@ function RefNameAutocomplete({
   const [inputValue, setInputValue] = useState('')
   const [searchOptions, setSearchOptions] = useState<Option[]>()
   const debouncedSearch = useDebounce(currentSearch, 300)
-  const { coarseVisibleLocStrings, hasDisplayedRegions } = model
   const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined
+  const { coarseVisibleLocStrings, hasDisplayedRegions } = model
   // eslint-disable-next-line react-hooks/exhaustive-deps
   const regions = assembly?.regions || []
@@ -104,11 +103,31 @@ function RefNameAutocomplete({
         setLoaded(false)
         const results = await fetchResults(debouncedSearch)
         if (active) {
-          setSearchOptions(
-            dedupe(results, r => r.getDisplayString()).map(result => ({
-              result,
-            })),
-          )
+          const m: { [key: string]: BaseResult[] } = {}
+          for (let i = 0; i < results.length; i++) {
+            const r = results[i]
+            const d = r.getDisplayString()
+            if (!m[d]) {
+              m[d] = []
+            }
+            m[d].push(r)
+          }
+          const display = Object.entries(m).map(([displayString, results]) => {
+            if (results.length === 1) {
+              return { result: results[0] }
+            } else {
+              return {
+                result: new BaseResult({
+                  displayString,
+                  results,
+                  label: displayString,
+                }),
+              }
+            }
+          })
+          setSearchOptions(display)
           setLoaded(true)
         }
       } catch (e) {
@@ -150,7 +169,7 @@ function RefNameAutocomplete({
         value={inputBoxVal}
         loading={!loaded}
         inputValue={inputValue}
-        onInputChange={(event, newInputValue) => {
+        onInputChange={(_event, newInputValue) => {
           setInputValue(newInputValue)
           onChange?.(newInputValue)
         }}

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)

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

@@ -2,12 +2,12 @@ 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'
-import { fetchResults } from './util'
+import { fetchResults, splitLast } from './util'
 import { LinearGenomeViewModel, SPACING, WIDGET_HEIGHT } from '..'
 const useStyles = makeStyles()(() => ({
@@ -33,49 +33,52 @@ function SearchBox({
   const assembly = assemblyManager.get(assemblyName)
   const searchScope = model.searchScope(assemblyName)
+  function navToOption(option: BaseResult) {
+    const location = option.getLocation()
+    const trackId = option.getTrackId()
+    if (location) {
+      model.navToLocString(location, assemblyName)
+      if (trackId) {
+        model.showTrack(trackId)
+      }
+    }
+  }
   // gets a string as input, or use stored option results from previous query,
   // then re-query and
   // 1) if it has multiple results: pop a dialog
   // 2) if it's a single result navigate to it
   // 3) else assume it's a locstring and navigate to it
   async function handleSelectedRegion(option: BaseResult) {
-    let trackId = option.getTrackId()
-    let location = option.getLocation()
-    const label = option.getLabel()
-    const [ref, rest] = location.split(':')
-    const allRefs = assembly?.allRefNames || []
     try {
-      // instead of querying text-index, first:
-      // - check if input matches a refName directly
-      // - or looks like locString
-      // then just navigate as if it were a locString
-      if (
-        allRefs.includes(location) ||
-        (allRefs.includes(ref) &&
-          rest !== undefined &&
-          !Number.isNaN(parseInt(rest, 10)))
-      ) {
-        model.navToLocString(location, assemblyName)
+      if (option.hasLocation()) {
+        navToOption(option)
       } else {
-        const results = await fetchResults({
-          queryString: label,
-          searchType: 'exact',
-          searchScope,
-          rankSearchResults,
-          textSearchManager,
-          assembly,
-        })
-        if (results.length > 1) {
-          model.setSearchResults(results, label.toLowerCase())
-          return
-        } else if (results.length === 1) {
-          location = results[0].getLocation()
-          trackId = results[0].getTrackId()
-        }
+        const input = option.getLabel()
+        const [ref, rest] = splitLast(input, ':')
+        const allRefs = assembly?.allRefNamesWithLowerCase || []
+        if (
+          allRefs.includes(input) ||
+          (allRefs.includes(ref) && !Number.isNaN(parseInt(rest, 10)))
+        ) {
+          model.navToLocString(input, assemblyName)
+        } else {
+          const results = await fetchResults({
+            queryString: input,
+            searchType: 'exact',
+            searchScope,
+            rankSearchResults,
+            textSearchManager,
+            assembly,
+          })
-        model.navToLocString(location, assemblyName)
-        if (trackId) {
-          model.showTrack(trackId)
+          if (results.length > 1) {
+            model.setSearchResults(results, input.toLowerCase())
+          } else if (results.length === 1) {
+            navToOption(results[0])
+          } else {
+            model.navToLocString(input, assemblyName)
+          }
         }
       }
     } catch (e) {

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

@@ -150,10 +150,13 @@ export default function SearchResultsDialog({
                       <TableCell align="right">
                         <Button
                           onClick={() => {
-                            handleClick(result.getLocation())
-                            const resultTrackId = result.getTrackId()
-                            if (resultTrackId) {
-                              model.showTrack(resultTrackId)
+                            const location = result.getLocation()
+                            if (location) {
+                              handleClick(location)
+                              const resultTrackId = result.getTrackId()
+                              if (resultTrackId) {
+                                model.showTrack(resultTrackId)
+                              }
                             }
                             handleClose()
                           }}