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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566
author fubar
date Sat, 05 Oct 2024 23:58:05 +0000
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rev   line source
125
49f3d3878413 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566
fubar
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1 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React from 'react'\nimport { makeStyles } from 'tss-react/mui'\nimport { observer } from 'mobx-react'\nimport { getSnapshot } from 'mobx-state-tree'\nimport {\n getFillProps,\n getStrokeProps,\n getTickDisplayStr,\n} from '@jbrowse/core/util'\nimport { bpToPx } from '@jbrowse/core/util/Base1DUtils'\nimport { useTheme } from '@mui/material'\n\n// locals\nimport { getBlockLabelKeysToHide } from './util'\nimport { DotplotViewModel } from '../model'\n\nconst useStyles = makeStyles()(() => ({\n vtext: {\n gridColumn: '1/2',\n gridRow: '1/2',\n pointerEvents: 'none',\n userSelect: 'none',\n },\n htext: {\n gridColumn: '2/2',\n gridRow: '2/2',\n pointerEvents: 'none',\n userSelect: 'none',\n },\n}))\nexport const HorizontalAxis = observer(function ({\n model,\n}: {\n model: DotplotViewModel\n}) {\n const { viewWidth, borderY } = model\n const { classes } = useStyles()\n return (\n <svg width={viewWidth} height={borderY} className={classes.htext}>\n <HorizontalAxisRaw model={model} />\n </svg>\n )\n})\n\nexport const HorizontalAxisRaw = observer(function ({\n model,\n}: {\n model: DotplotViewModel\n}) {\n const { viewWidth, borderX, borderY, hview, htextRotation, hticks } = model\n const { offsetPx, width, dynamicBlocks, bpPerPx } = hview\n const dblocks = dynamicBlocks.contentBlocks\n const hide = getBlockLabelKeysToHide(dblocks, viewWidth, offsetPx)\n const theme = useTheme()\n const hviewSnap = {\n ...getSnapshot(hview),\n width,\n staticBlocks: hview.staticBlocks,\n }\n\n const ticks = hticks\n .map(\n tick =>\n [\n tick,\n bpToPx({\n refName: tick.refName,\n coord: tick.base,\n self: hviewSnap,\n })?.offsetPx,\n ] as const,\n )\n .filter(f => f[1] !== undefined)\n .map(f => [f[0], f[1]! - offsetPx] as const)\n\n return (\n <>\n {dblocks\n .filter(region => !hide.has(region.key))\n .map(region => {\n const x = region.offsetPx\n const y = 0\n const xoff = Math.floor(x - hview.offsetPx)\n\n return (\n <text\n transform={`rotate(${htextRotation},${xoff},${y})`}\n key={JSON.stringify(region)}\n x={xoff}\n y={y + 1}\n fontSize={11}\n dominantBaseline=\"hanging\"\n textAnchor=\"end\"\n {...getFillProps(theme.palette.text.primary)}\n >\n {region.refName}\n </text>\n )\n })}\n {ticks.map(([tick, x]) =>\n x > 0 && x < width ? (\n <line\n key={`line-${JSON.stringify(tick)}`}\n x1={x}\n x2={x}\n y1={0}\n y2={tick.type === 'major' ? 6 : 4}\n strokeWidth={1}\n {...getFillProps(theme.palette.text.primary)}\n />\n ) : null,\n )}\n {ticks\n .filter(t => t[0].type === 'major')\n .map(([tick, x]) =>\n x > 10 && x < width ? (\n <text\n x={x - 7}\n y={0}\n transform={`rotate(${htextRotation},${x},0)`}\n key={`text-${JSON.stringify(tick)}`}\n fontSize={11}\n dominantBaseline=\"middle\"\n textAnchor=\"end\"\n {...getFillProps(theme.palette.text.primary)}\n >\n {getTickDisplayStr(tick.base + 1, bpPerPx)}\n </text>\n ) : null,\n )}\n <text\n y={borderY - 12}\n x={(viewWidth - borderX) / 2}\n textAnchor=\"middle\"\n fontSize={11}\n dominantBaseline=\"hanging\"\n {...getFillProps(theme.palette.text.primary)}\n >\n {hview.assemblyNames.join(',')}\n </text>\n </>\n )\n})\nexport const VerticalAxis = observer(function ({\n model,\n}: {\n model: DotplotViewModel\n}) {\n const { borderX, viewHeight } = model\n const { classes } = useStyles()\n return (\n <svg className={classes.vtext} width={borderX} height={viewHeight}>\n <VerticalAxisRaw model={model} />\n </svg>\n )\n})\n\nexport const VerticalAxisRaw = observer(function ({\n model,\n}: {\n model: DotplotViewModel\n}) {\n const { viewHeight, borderX, borderY, vview, vtextRotation, vticks } = model\n const { offsetPx, width, dynamicBlocks, bpPerPx } = vview\n const dblocks = dynamicBlocks.contentBlocks\n const hide = getBlockLabelKeysToHide(dblocks, viewHeight, offsetPx)\n const theme = useTheme()\n const vviewSnap = {\n ...getSnapshot(vview),\n width,\n staticBlocks: vview.staticBlocks,\n }\n const ticks = vticks\n .map(\n tick =>\n [\n tick,\n bpToPx({\n refName: tick.refName,\n coord: tick.base,\n self: vviewSnap,\n })?.offsetPx,\n ] as const,\n )\n .filter(f => f[1] !== undefined)\n .map(f => [f[0], f[1]! - offsetPx] as const)\n\n return (\n <>\n {dblocks\n .filter(region => !hide.has(region.key))\n .map(region => {\n const y = region.offsetPx\n const x = borderX\n const yoff = Math.floor(viewHeight - y + offsetPx)\n\n return (\n <text\n transform={`rotate(${vtextRotation},${x},${y})`}\n key={JSON.stringify(region)}\n x={x}\n y={yoff}\n fontSize={11}\n textAnchor=\"end\"\n {...getFillProps(theme.palette.text.primary)}\n >\n {region.refName}\n </text>\n )\n })}\n {ticks.map(([tick, y]) =>\n y > 0 ? (\n <line\n key={`line-${JSON.stringify(tick)}`}\n y1={viewHeight - y}\n y2={viewHeight - y}\n x1={borderX}\n x2={borderX - (tick.type === 'major' ? 6 : 4)}\n strokeWidth={1}\n {...getStrokeProps(theme.palette.grey[400])}\n />\n ) : null,\n )}\n {ticks\n .filter(t => t[0].type === 'major')\n .map(([tick, y]) =>\n y > 10 && y < viewHeight ? (\n <text\n y={viewHeight - y - 3}\n x={borderX - 7}\n key={`text-${JSON.stringify(tick)}`}\n textAnchor=\"end\"\n dominantBaseline=\"hanging\"\n fontSize={11}\n {...getFillProps(theme.palette.text.primary)}\n >\n {getTickDisplayStr(tick.base + 1, bpPerPx)}\n </text>\n ) : null,\n )}\n <text\n y={(viewHeight - borderY) / 2}\n x={12}\n transform={`rotate(-90,12,${(viewHeight - borderY) / 2})`}\n textAnchor=\"middle\"\n fontSize={11}\n {...getFillProps(theme.palette.text.primary)}\n >\n {vview.assemblyNames.join(',')}\n </text>\n </>\n )\n})\n","import React, { useState, useEffect } from 'react'\nimport { SnapshotIn } from 'mobx-state-tree'\nimport {\n FormControlLabel,\n Grid,\n Paper,\n Radio,\n RadioGroup,\n Typography,\n} from '@mui/material'\nimport { ErrorMessage, FileSelector } from '@jbrowse/core/ui'\nimport { FileLocation } from '@jbrowse/core/util/types'\nimport { observer } from 'mobx-react'\nimport { AnyConfigurationModel } from '@jbrowse/core/configuration'\nimport { basename, extName, getName, stripGz } from './util'\n\nfunction getAdapter({\n radioOption,\n assembly1,\n assembly2,\n fileLocation,\n indexFileLocation,\n bed1Location,\n bed2Location,\n}: {\n radioOption: string\n assembly1: string\n assembly2: string\n fileLocation?: FileLocation\n indexFileLocation?: FileLocation\n bed1Location?: FileLocation\n bed2Location?: FileLocation\n}) {\n if (radioOption === '.paf') {\n return {\n type: 'PAFAdapter',\n pafLocation: fileLocation,\n queryAssembly: assembly1,\n targetAssembly: assembly2,\n }\n } else if (radioOption === '.out') {\n return {\n type: 'MashMapAdapter',\n outLocation: fileLocation,\n queryAssembly: assembly1,\n targetAssembly: assembly2,\n }\n } else if (radioOption === '.delta') {\n return {\n type: 'DeltaAdapter',\n deltaLocation: fileLocation,\n queryAssembly: assembly1,\n targetAssembly: assembly2,\n }\n } else if (radioOption === '.chain') {\n return {\n type: 'ChainAdapter',\n chainLocation: fileLocation,\n queryAssembly: assembly1,\n targetAssembly: assembly2,\n }\n } else if (radioOption === '.anchors') {\n return {\n type: 'MCScanAnchorsAdapter',\n mcscanAnchorsLocation: fileLocation,\n bed1Location,\n bed2Location,\n assemblyNames: [assembly1, assembly2],\n }\n } else if (radioOption === '.anchors.simple') {\n return {\n type: 'MCScanSimpleAnchorsAdapter',\n mcscanSimpleAnchorsLocation: fileLocation,\n bed1Location,\n bed2Location,\n assemblyNames: [assembly1, assembly2],\n }\n } else if (radioOption === '.pif.gz') {\n return {\n type: 'PairwiseIndexedPAFAdapter',\n pifGzLocation: fileLocation,\n index: { location: indexFileLocation },\n assemblyNames: [assembly1, assembly2],\n }\n } else {\n throw new Error(\n `Unknown to detect type ${radioOption} from filename (select radio button to clarify)`,\n )\n }\n}\n\ntype Conf = SnapshotIn<AnyConfigurationModel>\n\nconst ImportCustomTrack = observer(function ({\n assembly1,\n assembly2,\n setSessionTrackData,\n}: {\n sessionTrackData: Conf\n assembly1: string\n assembly2: string\n setSessionTrackData: (arg: Conf) => void\n}) {\n const [bed2Location, setBed2Location] = useState<FileLocation>()\n const [bed1Location, setBed1Location] = useState<FileLocation>()\n const [fileLocation, setFileLocation] = useState<FileLocation>()\n const [indexFileLocation, setIndexFileLocation] = useState<FileLocation>()\n const [value, setValue] = useState('')\n const [error, setError] = useState<unknown>()\n const fileName = getName(fileLocation)\n\n const radioOption = value || (fileName ? extName(stripGz(fileName)) : '')\n\n useEffect(() => {\n try {\n if (fileLocation) {\n const fn = fileName ? basename(fileName) : 'MyTrack'\n const trackId = `${fn}-${Date.now()}`\n setError(undefined)\n\n setSessionTrackData({\n trackId,\n name: fn,\n assemblyNames: [assembly2, assembly1],\n type: 'SyntenyTrack',\n adapter: getAdapter({\n radioOption,\n assembly1,\n assembly2,\n fileLocation,\n indexFileLocation,\n bed1Location,\n bed2Location,\n }),\n })\n }\n } catch (e) {\n console.error(e)\n setError(e)\n }\n }, [\n fileName,\n assembly1,\n assembly2,\n bed1Location,\n bed2Location,\n fileLocation,\n indexFileLocation,\n radioOption,\n setSessionTrackData,\n ])\n return (\n <Paper style={{ padding: 12 }}>\n {error ? <ErrorMessage error={error} /> : null}\n <Typography style={{ textAlign: 'center' }}>\n Add a .paf, .out (MashMap), .delta (Mummer), .chain, .anchors or\n .anchors.simple (MCScan) file to view. These file types can also be\n gzipped. The first assembly should be the query sequence (e.g. left\n column of the PAF) and the second assembly should be the target sequence\n (e.g. right column of the PAF)\n </Typography>\n <RadioGroup\n value={radioOption}\n onChange={event => {\n setValue(event.target.value)\n }}\n >\n <Grid container justifyContent=\"center\">\n <Grid item>\n <FormControlLabel value=\".paf\" control={<Radio />} label=\".paf\" />\n </Grid>\n <Grid item>\n <FormControlLabel value=\".out\" control={<Radio />} label=\".out\" />\n </Grid>\n\n <Grid item>\n <FormControlLabel\n value=\".delta\"\n control={<Radio />}\n label=\".delta\"\n />\n </Grid>\n <Grid item>\n <FormControlLabel\n value=\".chain\"\n control={<Radio />}\n label=\".chain\"\n />\n </Grid>\n <Grid item>\n <FormControlLabel\n value=\".anchors\"\n control={<Radio />}\n label=\".anchors\"\n />\n </Grid>\n <Grid item>\n <FormControlLabel\n value=\".anchors.simple\"\n control={<Radio />}\n label=\".anchors.simple\"\n />\n </Grid>\n <Grid item>\n <FormControlLabel\n value=\".pif.gz\"\n control={<Radio />}\n label=\".pif.gz\"\n />\n </Grid>\n </Grid>\n </RadioGroup>\n <Grid container justifyContent=\"center\">\n <Grid item>\n {value === '.anchors' || value === '.anchors.simple' ? (\n <div>\n <div style={{ margin: 20 }}>\n Open the {value} and .bed files for both genome assemblies from\n the MCScan (Python version) pipeline{' '}\n <a href=\"https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)\">\n (more info)\n </a>\n </div>\n <div style={{ display: 'flex' }}>\n <div>\n <FileSelector\n name=\".anchors file\"\n description=\"\"\n location={fileLocation}\n setLocation={loc => {\n setFileLocation(loc)\n }}\n />\n </div>\n <div>\n <FileSelector\n name=\"genome 1 .bed (left column of anchors file)\"\n description=\"\"\n location={bed1Location}\n setLocation={loc => {\n setBed1Location(loc)\n }}\n />\n </div>\n <div>\n <FileSelector\n name=\"genome 2 .bed (right column of anchors file)\"\n description=\"\"\n location={bed2Location}\n setLocation={loc => {\n setBed2Location(loc)\n }}\n />\n </div>\n </div>\n </div>\n ) : value === '.pif.gz' ? (\n <div style={{ display: 'flex' }}>\n <div>\n <FileSelector\n name={`${value} location`}\n description=\"\"\n location={fileLocation}\n setLocation={loc => {\n setFileLocation(loc)\n }}\n />\n </div>\n <div>\n <FileSelector\n name={`${value} index location`}\n description=\"\"\n location={indexFileLocation}\n setLocation={loc => {\n setIndexFileLocation(loc)\n }}\n />\n </div>\n </div>\n ) : (\n <FileSelector\n name={value ? `${value} location` : ''}\n description=\"\"\n location={fileLocation}\n setLocation={loc => {\n setFileLocation(loc)\n }}\n />\n )}\n </Grid>\n </Grid>\n </Paper>\n )\n})\n\nexport default ImportCustomTrack\n","export function getName(\n sessionTrackData?: { uri: string } | { localPath: string } | { name: string },\n) {\n return sessionTrackData\n ? // @ts-expect-error\n sessionTrackData.uri ||\n // @ts-expect-error\n sessionTrackData.localPath ||\n // @ts-expect-error\n sessionTrackData.name\n : undefined\n}\n\nexport function stripGz(fileName: string) {\n return fileName.endsWith('.gz') ? fileName.slice(0, -3) : fileName\n}\n\nexport function basename(str: string) {\n return str.split('#')[0]!.split('?')[0]!.split('/').pop()\n}\nexport function extName(str: string) {\n const r = str.split('.').pop()\n return r ? `.${r}` : ''\n}\n","import React, { useState, useEffect } from 'react'\nimport { Select, MenuItem, Paper, Typography } from '@mui/material'\nimport { getTrackName } from '@jbrowse/core/util/tracks'\nimport { getSession } from '@jbrowse/core/util'\nimport { ErrorMessage } from '@jbrowse/core/ui'\nimport {\n AnyConfigurationModel,\n readConfObject,\n} from '@jbrowse/core/configuration'\nimport { observer } from 'mobx-react'\n\n// icons\nimport { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons'\n\n// locals\nimport { DotplotViewModel } from '../../model'\n\nfunction f(track: AnyConfigurationModel, assembly1: string, assembly2: string) {\n const assemblyNames = readConfObject(track, 'assemblyNames')\n return (\n assemblyNames.includes(assembly1) &&\n assemblyNames.includes(assembly2) &&\n track.type.includes('Synteny')\n )\n}\n\nconst Selector = observer(\n ({\n model,\n assembly1,\n assembly2,\n setShowTrackId,\n }: {\n model: DotplotViewModel\n assembly1: string\n assembly2: string\n setShowTrackId: (arg: string) => void\n }) => {\n const session = getSession(model)\n const { tracks, sessionTracks } = session\n const allTracks = [\n ...tracks,\n ...(sessionTracks || []),\n ] as AnyConfigurationModel[]\n const filteredTracks = allTracks.filter(t => f(t, assembly2, assembly1))\n const resetTrack = filteredTracks[0]?.trackId || ''\n const [value, setValue] = useState(resetTrack)\n useEffect(() => {\n // if assembly1/assembly2 changes, then we will want to use this effect to change\n // the state of the useState because it otherwise gets locked to a stale value\n setValue(resetTrack)\n }, [resetTrack])\n\n useEffect(() => {\n // sets track data in a useEffect because the initial load is needed as well as\n // onChange's to the select box\n setShowTrackId(value)\n }, [value, setShowTrackId])\n\n return (\n <Paper style={{ padding: 12 }}>\n <Typography paragraph>\n Select a track from the select box below, the track will be shown when\n you hit \"Launch\".\n </Typography>\n\n <Typography paragraph>\n Note: there is a track selector <i>inside</i> the DotplotView, which\n can turn on one or more SyntenyTracks (more than one can be displayed\n at once). Look for the track selector icon <TrackSelectorIcon />\n </Typography>\n {filteredTracks.length ? (\n <Select\n value={value}\n onChange={event => {\n setValue(event.target.value)\n }}\n >\n {filteredTracks.map(track => (\n <MenuItem key={track.trackId} value={track.trackId}>\n {getTrackName(track, session)}\n </MenuItem>\n ))}\n </Select>\n ) : (\n <ErrorMessage\n error={`No synteny tracks found for ${assembly1},${assembly2}`}\n />\n )}\n </Paper>\n )\n },\n)\n\nexport default Selector\n","import React, { useState, useEffect } from 'react'\nimport {\n Button,\n Container,\n FormControl,\n FormLabel,\n FormControlLabel,\n Grid,\n Paper,\n Radio,\n RadioGroup,\n Typography,\n} from '@mui/material'\nimport { makeStyles } from 'tss-react/mui'\nimport { observer } from 'mobx-react'\nimport { transaction } from 'mobx'\nimport { SnapshotIn } from 'mobx-state-tree'\nimport { AnyConfigurationModel } from '@jbrowse/core/configuration'\nimport { getSession, isSessionWithAddTracks } from '@jbrowse/core/util'\nimport { ErrorMessage, AssemblySelector } from '@jbrowse/core/ui'\n\n// locals\nimport { DotplotViewModel } from '../../model'\nimport ImportCustomTrack from './ImportCustomTrack'\nimport ImportSyntenyTrackSelector from './ImportSyntenyTrackSelector'\n\nconst useStyles = makeStyles()(theme => ({\n importFormContainer: {\n padding: theme.spacing(4),\n margin: '0 auto',\n },\n assemblySelector: {\n width: '75%',\n margin: '0 auto',\n },\n}))\n\ntype Conf = SnapshotIn<AnyConfigurationModel>\n\nfunction TrackSelector({\n setSessionTrackData,\n setShowTrackId,\n sessionTrackData,\n assembly1,\n assembly2,\n model,\n}: {\n sessionTrackData: Conf\n setSessionTrackData: (arg: Conf) => void\n setShowTrackId: (arg?: string) => void\n model: DotplotViewModel\n assembly1: string\n assembly2: string\n}) {\n const [choice, setChoice] = useState('tracklist')\n\n useEffect(() => {\n if (choice === 'none') {\n setSessionTrackData(undefined)\n setShowTrackId(undefined)\n }\n }, [choice, setSessionTrackData, setShowTrackId])\n return (\n <>\n <FormControl>\n <FormLabel id=\"group-label\">\n (Optional) Select or add a synteny track\n </FormLabel>\n <RadioGroup\n row\n value={choice}\n onChange={event => {\n setChoice(event.target.value)\n }}\n aria-labelledby=\"group-label\"\n >\n <FormControlLabel value=\"none\" control={<Radio />} label=\"None\" />\n <FormControlLabel\n value=\"tracklist\"\n control={<Radio />}\n label=\"Existing track\"\n />\n <FormControlLabel\n value=\"custom\"\n control={<Radio />}\n label=\"New track\"\n />\n </RadioGroup>\n </FormControl>\n {choice === 'custom' ? (\n <ImportCustomTrack\n setSessionTrackData={setSessionTrackData}\n sessionTrackData={sessionTrackData}\n assembly2={assembly2}\n assembly1={assembly1}\n />\n ) : null}\n {choice === 'tracklist' ? (\n <ImportSyntenyTrackSelector\n model={model}\n assembly1={assembly1}\n assembly2={assembly2}\n setShowTrackId={setShowTrackId}\n />\n ) : null}\n </>\n )\n}\n\nconst DotplotImportForm = observer(({ model }: { model: DotplotViewModel }) => {\n const { classes } = useStyles()\n const session = getSession(model)\n const { assemblyNames } = session\n const [assembly2, setAssembly2] = useState(assemblyNames[0] || '')\n const [assembly1, setAssembly1] = useState(assemblyNames[0] || '')\n const [error, setError] = useState<unknown>()\n const [sessionTrackData, setSessionTrackData] = useState<Conf>()\n const [showTrackId, setShowTrackId] = useState<string>()\n\n function onOpenClick() {\n try {\n if (!isSessionWithAddTracks(session)) {\n return\n }\n setError(undefined)\n model.setError(undefined)\n transaction(() => {\n if (sessionTrackData) {\n session.addTrackConf(sessionTrackData)\n model.toggleTrack(sessionTrackData.trackId)\n } else if (showTrackId) {\n model.showTrack(showTrackId)\n }\n\n model.setViews([\n { bpPerPx: 0.1, offsetPx: 0 },\n { bpPerPx: 0.1, offsetPx: 0 },\n ])\n model.setAssemblyNames(assembly2, assembly1)\n })\n } catch (e) {\n console.error(e)\n setError(e)\n }\n }\n\n // this is a combination of any displayed error message we have\n const displayError = error || model.error\n return (\n <Container className={classes.importFormContainer}>\n {displayError ? <ErrorMessage error={displayError} /> : null}\n <Grid\n container\n spacing={1}\n justifyContent=\"center\"\n alignItems=\"center\"\n className={classes.assemblySelector}\n >\n <Grid item>\n <Paper style={{ padding: 12 }}>\n <Typography style={{ textAlign: 'center' }}>\n Select assemblies for dotplot view\n </Typography>\n <Grid\n container\n spacing={1}\n justifyContent=\"center\"\n alignItems=\"center\"\n >\n <Grid item>\n <AssemblySelector\n selected={assembly1}\n onChange={val => {\n setAssembly1(val)\n }}\n session={session}\n />\n </Grid>\n <Grid item>\n <AssemblySelector\n selected={assembly2}\n onChange={val => {\n setAssembly2(val)\n }}\n session={session}\n />\n </Grid>\n <Grid item>\n <FormControl>\n <Button\n onClick={onOpenClick}\n variant=\"contained\"\n color=\"primary\"\n >\n Launch\n </Button>\n </FormControl>\n </Grid>\n </Grid>\n </Paper>\n <TrackSelector\n setShowTrackId={setShowTrackId}\n assembly2={assembly2}\n assembly1={assembly1}\n setSessionTrackData={setSessionTrackData}\n sessionTrackData={sessionTrackData}\n model={model}\n />\n </Grid>\n </Grid>\n </Container>\n )\n})\n\nexport default DotplotImportForm\n","import React, { lazy, useState } from 'react'\nimport { Alert, Button } from '@mui/material'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { DotplotViewModel } from '../model'\n// lazy components\nconst WarningDialog = lazy(() => import('./WarningDialog'))\n\nconst DotplotWarnings = observer(function ({\n model,\n}: {\n model: DotplotViewModel\n}) {\n const trackWarnings = model.tracks.filter(t => t.displays[0].warnings?.length)\n const [shown, setShown] = useState(false)\n const [hide, setHide] = useState(false)\n return trackWarnings.length && !hide ? (\n <Alert severity=\"warning\">\n Warnings during render{' '}\n <Button\n onClick={() => {\n setShown(true)\n }}\n >\n More info\n </Button>\n {shown ? (\n <WarningDialog\n trackWarnings={trackWarnings}\n handleClose={() => {\n setShown(false)\n }}\n />\n ) : null}\n <Button\n variant=\"contained\"\n onClick={() => {\n setHide(true)\n }}\n >\n Dismiss\n </Button>\n </Alert>\n ) : null\n})\n\nexport default DotplotWarnings\n","import React from 'react'\nimport { IconButton, Paper } from '@mui/material'\nimport { makeStyles } from 'tss-react/mui'\nimport { observer } from 'mobx-react'\n\n// icons\nimport ArrowDropDown from '@mui/icons-material/ArrowDropDown'\nimport ArrowDropUp from '@mui/icons-material/ArrowDropUp'\nimport ArrowLeft from '@mui/icons-material/ArrowLeft'\nimport ArrowRight from '@mui/icons-material/ArrowRight'\nimport ZoomIn from '@mui/icons-material/ZoomIn'\nimport ZoomOut from '@mui/icons-material/ZoomOut'\n\n// locals\nimport { DotplotViewModel } from '../model'\n\nconst useStyles = makeStyles()({\n dpad: {\n display: 'grid',\n gridTemplateColumns: 'repeat(3, 1fr)',\n margin: 0,\n position: 'absolute',\n right: 50,\n zIndex: 1000,\n top: 50,\n },\n icon: {\n padding: 0,\n margin: 0,\n },\n})\n\nconst PanButtons = observer(function PanButtons({\n model,\n}: {\n model: DotplotViewModel\n}) {\n const { classes } = useStyles()\n return (\n <Paper className={classes.dpad} elevation={6}>\n <div />\n <IconButton\n className={classes.icon}\n onClick={() => model.vview.scroll(100)}\n >\n <ArrowDropUp />\n </IconButton>\n <div />\n\n <IconButton\n className={classes.icon}\n onClick={() => model.hview.scroll(-100)}\n >\n <ArrowLeft />\n </IconButton>\n <div />\n <IconButton\n className={classes.icon}\n onClick={() => model.hview.scroll(100)}\n >\n <ArrowRight />\n </IconButton>\n\n <div />\n <IconButton\n className={classes.icon}\n onClick={() => model.vview.scroll(-100)}\n >\n <ArrowDropDown />\n </IconButton>\n <div />\n <IconButton\n className={classes.icon}\n onClick={() => {\n model.hview.zoomIn()\n model.vview.zoomIn()\n }}\n >\n <ZoomIn />\n </IconButton>\n <div />\n <IconButton\n className={classes.icon}\n onClick={() => {\n model.hview.zoomOut()\n model.vview.zoomOut()\n }}\n >\n <ZoomOut />\n </IconButton>\n </Paper>\n )\n})\n\nexport default PanButtons\n","import SvgIcon, { SvgIconProps } from '@mui/material/SvgIcon'\nimport React from 'react'\n\nexport function CursorMove(props: SvgIconProps) {\n return (\n <SvgIcon {...props}>\n <path\n fill=\"currentColor\"\n d=\"M13,6V11H18V7.75L22.25,12L18,16.25V13H13V18H16.25L12,22.25L7.75,18H11V13H6V16.25L1.75,12L6,7.75V11H11V6H7.75L12,1.75L16.25,6H13Z\"\n />\n </SvgIcon>\n )\n}\n\nexport function CursorMouse(props: SvgIconProps) {\n return (\n <SvgIcon {...props}>\n <path\n fill=\"currentColor\"\n d=\"M10.07,14.27C10.57,14.03 11.16,14.25 11.4,14.75L13.7,19.74L15.5,18.89L13.19,13.91C12.95,13.41 13.17,12.81 13.67,12.58L13.95,12.5L16.25,12.05L8,5.12V15.9L9.82,14.43L10.07,14.27M13.64,21.97C13.14,22.21 12.54,22 12.31,21.5L10.13,16.76L7.62,18.78C7.45,18.92 7.24,19 7,19A1,1 0 0,1 6,18V3A1,1 0 0,1 7,2C7.24,2 7.47,2.09 7.64,2.23L7.65,2.22L19.14,11.86C19.57,12.22 19.62,12.85 19.27,13.27C19.12,13.45 18.91,13.57 18.7,13.61L15.54,14.23L17.74,18.96C18,19.46 17.76,20.05 17.26,20.28L13.64,21.97Z\"\n />\n </SvgIcon>\n )\n}\n","import React from 'react'\nimport { IconButton } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton'\n\n// icons\nimport ZoomOut from '@mui/icons-material/ZoomOut'\nimport ZoomIn from '@mui/icons-material/ZoomIn'\nimport MoreVert from '@mui/icons-material/MoreVert'\nimport { CursorMouse, CursorMove } from './CursorIcon'\nimport { TrackSelector as TrackSelectorIcon } from '@jbrowse/core/ui/Icons'\n\n// locals\nimport { DotplotViewModel } from '../model'\n\nconst DotplotControls = observer(function ({\n model,\n}: {\n model: DotplotViewModel\n}) {\n return (\n <div>\n <IconButton onClick={model.zoomOutButton}>\n <ZoomOut />\n </IconButton>\n\n <IconButton onClick={model.zoomInButton}>\n <ZoomIn />\n </IconButton>\n\n <IconButton\n onClick={() => model.activateTrackSelector()}\n title=\"Open track selector\"\n >\n <TrackSelectorIcon />\n </IconButton>\n\n <CascadingMenuButton\n menuItems={[\n {\n onClick: () => {\n model.squareView()\n },\n label: 'Square view - same base pairs per pixel',\n },\n {\n onClick: () => {\n model.squareViewProportional()\n },\n label: 'Rectanglularize view - same total bp',\n },\n {\n onClick: () => {\n model.showAllRegions()\n },\n label: 'Show all regions',\n },\n {\n onClick: () => {\n model.setDrawCigar(!model.drawCigar)\n },\n type: 'checkbox',\n label: 'Draw CIGAR',\n checked: model.drawCigar,\n },\n {\n onClick: () => {\n model.setShowPanButtons(!model.showPanButtons)\n },\n label: 'Show pan buttons',\n type: 'checkbox',\n checked: model.showPanButtons,\n },\n {\n label: 'Click and drag mode',\n subMenu: [\n {\n onClick: () => {\n model.setCursorMode('move')\n },\n label:\n 'Pan by default, select region when ctrl/cmd key is held',\n icon: CursorMove,\n type: 'radio',\n checked: model.cursorMode === 'move',\n },\n {\n onClick: () => {\n model.setCursorMode('crosshair')\n },\n label:\n 'Select region by default, pan when ctrl/cmd key is held',\n icon: CursorMouse,\n type: 'radio',\n checked: model.cursorMode === 'crosshair',\n },\n ],\n },\n {\n label: 'Wheel scroll mode',\n subMenu: [\n {\n onClick: () => {\n model.setWheelMode('pan')\n },\n label: 'Pans view',\n type: 'radio',\n checked: model.wheelMode === 'pan',\n },\n {\n onClick: () => {\n model.setWheelMode('zoom')\n },\n label: 'Zooms view',\n type: 'radio',\n checked: model.wheelMode === 'zoom',\n },\n {\n onClick: () => {\n model.setWheelMode('none')\n },\n label: 'Disable',\n type: 'radio',\n checked: model.wheelMode === 'none',\n },\n ],\n },\n ]}\n >\n <MoreVert />\n </CascadingMenuButton>\n </div>\n )\n})\n\nexport default DotplotControls\n","import React from 'react'\nimport { Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\nimport { getBpDisplayStr } from '@jbrowse/core/util'\n\n// locals\nimport { DotplotViewModel } from '../model'\nimport DotplotWarnings from './DotplotWarnings'\nimport PanButtons from './PanButtons'\nimport DotplotControls from './DotplotControls'\n\nconst useStyles = makeStyles()({\n bp: {\n display: 'flex',\n alignItems: 'center',\n marginLeft: 10,\n },\n spacer: {\n flexGrow: 1,\n },\n headerBar: {\n display: 'flex',\n position: 'relative',\n },\n})\n\nconst DotplotHeader = observer(function ({\n model,\n selection,\n}: {\n model: DotplotViewModel\n selection?: { width: number; height: number }\n}) {\n const { classes } = useStyles()\n const { hview, vview, showPanButtons } = model\n return (\n <div className={classes.headerBar}>\n <DotplotControls model={model} />\n <Typography className={classes.bp} variant=\"body2\" color=\"textSecondary\">\n x: {hview.assemblyNames.join(',')} {getBpDisplayStr(hview.currBp)}\n <br />\n y: {vview.assemblyNames.join(',')} {getBpDisplayStr(vview.currBp)}\n </Typography>\n {selection ? (\n <Typography\n className={classes.bp}\n variant=\"body2\"\n color=\"textSecondary\"\n >\n {`width:${getBpDisplayStr(hview.bpPerPx * selection.width)}`} <br />\n {`height:${getBpDisplayStr(vview.bpPerPx * selection.height)}`}\n </Typography>\n ) : null}\n <div className={classes.spacer} />\n <DotplotWarnings model={model} />\n {showPanButtons ? <PanButtons model={model} /> : null}\n </div>\n )\n})\n\nexport default DotplotHeader\n","import React, { useState, useEffect, useRef, lazy, Suspense } from 'react'\nimport { LoadingEllipses, Menu, ResizeHandle } from '@jbrowse/core/ui'\nimport { observer } from 'mobx-react'\nimport { transaction } from 'mobx'\nimport { makeStyles } from 'tss-react/mui'\n\n// locals\nimport { DotplotViewModel } from '../model'\nimport ImportForm from './ImportForm'\nimport Header from './Header'\nimport Grid from './Grid'\nimport { VerticalAxis, HorizontalAxis } from './Axes'\n\nconst TooltipWhereClicked = lazy(() => import('./DotplotTooltipClick'))\nconst TooltipWhereMouseovered = lazy(() => import('./DotplotTooltipMouseover'))\n\nconst blank = { left: 0, top: 0, width: 0, height: 0 }\n\nconst useStyles = makeStyles()(theme => ({\n spacer: {\n gridColumn: '1/2',\n gridRow: '2/2',\n },\n root: {\n position: 'relative',\n marginBottom: theme.spacing(1),\n overflow: 'hidden',\n },\n\n container: {\n display: 'grid',\n padding: 5,\n position: 'relative',\n },\n overlay: {\n pointerEvents: 'none',\n overflow: 'hidden',\n display: 'flex',\n width: '100%',\n gridRow: '1/2',\n gridColumn: '2/2',\n zIndex: 100, // needs to be below controls\n '& path': {\n cursor: 'crosshair',\n fill: 'none',\n },\n },\n\n content: {\n position: 'relative',\n gridColumn: '2/2',\n gridRow: '1/2',\n },\n\n resizeHandle: {\n height: 4,\n background: '#ccc',\n boxSizing: 'border-box',\n borderTop: '1px solid #fafafa',\n },\n}))\n\ntype Coord = [number, number] | undefined\ninterface Rect {\n left: number\n top: number\n}\n\n// produces offsetX/offsetY coordinates from a clientX and an element's\n// getBoundingClientRect\nfunction getOffset(coord: Coord, rect: Rect) {\n return coord && ([coord[0] - rect.left, coord[1] - rect.top] as Coord)\n}\n\nconst RenderedComponent = observer(({ model }: { model: DotplotViewModel }) => {\n const { classes } = useStyles()\n return (\n <div className={classes.overlay}>\n {model.tracks.map(track => {\n const [display] = track.displays\n const { RenderingComponent } = display\n return RenderingComponent ? (\n <RenderingComponent\n key={track.configuration.trackId}\n model={display}\n />\n ) : null\n })}\n </div>\n )\n})\n\nconst DotplotViewInternal = observer(function ({\n model,\n}: {\n model: DotplotViewModel\n}) {\n const { classes } = useStyles()\n const [mousecurrClient, setMouseCurrClient] = useState<Coord>()\n const [mousedownClient, setMouseDownClient] = useState<Coord>()\n const [mouseOvered, setMouseOvered] = useState(false)\n const [mouseupClient, setMouseUpClient] = useState<Coord>()\n const ref = useRef<HTMLDivElement>(null)\n const root = useRef<HTMLDivElement>(null)\n const distanceX = useRef(0)\n const distanceY = useRef(0)\n const scheduled = useRef(false)\n const [ctrlKeyWasUsed, setCtrlKeyWasUsed] = useState(false)\n const [ctrlKeyDown, setCtrlKeyDown] = useState(false)\n const svg = ref.current?.getBoundingClientRect() || blank\n const rootRect = ref.current?.getBoundingClientRect() || blank\n const mousedown = getOffset(mousedownClient, svg)\n const mousecurr = getOffset(mousecurrClient, svg)\n const mouseup = getOffset(mouseupClient, svg)\n const mouserect = mouseup || mousecurr\n const mouserectClient = mouseupClient || mousecurrClient\n const xdistance = mousedown && mouserect ? mouserect[0] - mousedown[0] : 0\n const ydistance = mousedown && mouserect ? mouserect[1] - mousedown[1] : 0\n const { hview, vview, wheelMode, cursorMode } = model\n\n const validPan =\n (cursorMode === 'move' && !ctrlKeyWasUsed) ||\n (cursorMode === 'crosshair' && ctrlKeyWasUsed)\n\n const validSelect =\n (cursorMode === 'move' && ctrlKeyWasUsed) ||\n (cursorMode === 'crosshair' && !ctrlKeyWasUsed)\n\n // use non-React wheel handler to properly prevent body scrolling\n useEffect(() => {\n function onWheel(event: WheelEvent) {\n event.preventDefault()\n\n distanceX.current += event.deltaX\n distanceY.current -= event.deltaY\n if (!scheduled.current) {\n scheduled.current = true\n\n window.requestAnimationFrame(() => {\n transaction(() => {\n if (wheelMode === 'pan') {\n hview.scroll(distanceX.current / 3)\n vview.scroll(distanceY.current / 10)\n } else if (wheelMode === 'zoom') {\n if (\n Math.abs(distanceY.current) > Math.abs(distanceX.current) * 2 &&\n mousecurr\n ) {\n const val = distanceY.current < 0 ? 1.1 : 0.9\n hview.zoomTo(hview.bpPerPx * val, mousecurr[0])\n vview.zoomTo(\n vview.bpPerPx * val,\n rootRect.height - mousecurr[1],\n )\n }\n }\n })\n scheduled.current = false\n distanceX.current = 0\n distanceY.current = 0\n })\n }\n }\n if (ref.current) {\n const curr = ref.current\n curr.addEventListener('wheel', onWheel)\n return () => {\n curr.removeEventListener('wheel', onWheel)\n }\n }\n return () => {}\n }, [hview, vview, wheelMode, mousecurr, rootRect.height])\n\n useEffect(() => {\n function globalMouseMove(event: MouseEvent) {\n setMouseCurrClient([event.clientX, event.clientY])\n\n if (mousecurrClient && mousedownClient && validPan && !mouseupClient) {\n hview.scroll(-event.clientX + mousecurrClient[0])\n vview.scroll(event.clientY - mousecurrClient[1])\n }\n }\n\n window.addEventListener('mousemove', globalMouseMove)\n return () => {\n window.removeEventListener('mousemove', globalMouseMove)\n }\n }, [validPan, mousecurrClient, mousedownClient, mouseupClient, hview, vview])\n\n useEffect(() => {\n function globalCtrlKeyDown(event: KeyboardEvent) {\n if (event.metaKey || event.ctrlKey) {\n setCtrlKeyDown(true)\n }\n }\n function globalCtrlKeyUp(event: KeyboardEvent) {\n if (!event.metaKey && !event.ctrlKey) {\n setCtrlKeyDown(false)\n }\n }\n window.addEventListener('keydown', globalCtrlKeyDown)\n window.addEventListener('keyup', globalCtrlKeyUp)\n return () => {\n window.removeEventListener('keydown', globalCtrlKeyDown)\n window.addEventListener('keyup', globalCtrlKeyUp)\n }\n }, [])\n\n // detect a mouseup after a mousedown was submitted, autoremoves mouseup once\n // that single mouseup is set\n useEffect(() => {\n function globalMouseUp(event: MouseEvent) {\n if (Math.abs(xdistance) > 3 && Math.abs(ydistance) > 3 && validSelect) {\n setMouseUpClient([event.clientX, event.clientY])\n } else {\n setMouseDownClient(undefined)\n }\n }\n if (mousedown && !mouseup) {\n window.addEventListener('mouseup', globalMouseUp, true)\n return () => {\n window.removeEventListener('mouseup', globalMouseUp, true)\n }\n }\n return () => {}\n }, [validSelect, mousedown, mouseup, xdistance, ydistance])\n\n return (\n <div>\n <Header\n model={model}\n selection={\n !validSelect || !(mousedown && mouserect)\n ? undefined\n : {\n width: Math.abs(xdistance),\n height: Math.abs(ydistance),\n }\n }\n />\n <div\n ref={root}\n className={classes.root}\n onMouseLeave={() => {\n setMouseOvered(false)\n }}\n onMouseEnter={() => {\n setMouseOvered(true)\n }}\n >\n <div className={classes.container}>\n <VerticalAxis model={model} />\n <HorizontalAxis model={model} />\n <div ref={ref} className={classes.content}>\n {mouseOvered && validSelect ? (\n <Suspense fallback={null}>\n <TooltipWhereMouseovered\n model={model}\n mouserect={mouserect}\n mouserectClient={mouserectClient}\n xdistance={xdistance}\n />\n </Suspense>\n ) : null}\n {validSelect ? (\n <Suspense fallback={null}>\n <TooltipWhereClicked\n model={model}\n mousedown={mousedown}\n mousedownClient={mousedownClient}\n xdistance={xdistance}\n ydistance={ydistance}\n />\n </Suspense>\n ) : null}\n <div\n style={{ cursor: ctrlKeyDown ? 'pointer' : cursorMode }}\n onMouseDown={event => {\n if (event.button === 0) {\n const { clientX, clientY } = event\n setMouseDownClient([clientX, clientY])\n setMouseCurrClient([clientX, clientY])\n setCtrlKeyWasUsed(ctrlKeyDown)\n }\n }}\n >\n <Grid model={model}>\n {validSelect && mousedown && mouserect ? (\n <rect\n fill=\"rgba(255,0,0,0.3)\"\n x={Math.min(mouserect[0], mousedown[0])}\n y={Math.min(mouserect[1], mousedown[1])}\n width={Math.abs(xdistance)}\n height={Math.abs(ydistance)}\n />\n ) : null}\n </Grid>\n </div>\n <div className={classes.spacer} />\n </div>\n <RenderedComponent model={model} />\n <Menu\n open={Boolean(mouseup)}\n onMenuItemClick={(_, callback) => {\n callback()\n setMouseUpClient(undefined)\n setMouseDownClient(undefined)\n }}\n onClose={() => {\n setMouseUpClient(undefined)\n setMouseDownClient(undefined)\n }}\n anchorReference=\"anchorPosition\"\n anchorPosition={\n mouseupClient\n ? {\n top: mouseupClient[1] + 50,\n left: mouseupClient[0] + 50,\n }\n : undefined\n }\n style={{ zIndex: 10000 }}\n menuItems={[\n {\n label: 'Zoom in',\n onClick: () => {\n if (mousedown && mouseup) {\n model.zoomIn(mousedown, mouseup)\n }\n // below line is needed to prevent tooltip from sticking\n setMouseOvered(false)\n },\n },\n {\n label: 'Open linear synteny view',\n onClick: () => {\n if (mousedown && mouseup) {\n model.onDotplotView(mousedown, mouseup)\n }\n // below line is needed to prevent tooltip from sticking\n setMouseOvered(false)\n },\n },\n ]}\n />\n </div>\n <ResizeHandle\n onDrag={n => model.setHeight(model.height + n)}\n className={classes.resizeHandle}\n />\n </div>\n </div>\n )\n})\nconst DotplotView = observer(function ({ model }: { model: DotplotViewModel }) {\n const { initialized, loading, error } = model\n\n if ((!initialized && !loading) || error) {\n return <ImportForm model={model} />\n }\n\n if (loading) {\n return <LoadingEllipses variant=\"h6\" />\n }\n\n return <DotplotViewInternal model={model} />\n})\n\nexport default DotplotView\n","import React from 'react'\nimport { observer } from 'mobx-react'\nimport { useTheme } from '@mui/material'\n\n// locals\nimport { DotplotViewModel } from '../model'\nimport { getFillProps, getStrokeProps } from '@jbrowse/core/util'\n\nexport const GridRaw = observer(function ({\n model,\n children,\n}: {\n model: DotplotViewModel\n children?: React.ReactNode\n}) {\n const { viewWidth, viewHeight, hview, vview } = model\n const hblocks = hview.dynamicBlocks.contentBlocks\n const vblocks = vview.dynamicBlocks.contentBlocks\n if (!hblocks.length || !vblocks.length) {\n return null\n }\n const htop = hview.displayedRegionsTotalPx - hview.offsetPx\n const vtop = vview.displayedRegionsTotalPx - vview.offsetPx\n const hbottom = hblocks[0]!.offsetPx - hview.offsetPx\n const vbottom = vblocks[0]!.offsetPx - vview.offsetPx\n const theme = useTheme()\n const stroke = theme.palette.divider\n\n // Uses math.max/min avoid making very large SVG rect offscreen element,\n // which can sometimes fail to draw\n const rx = Math.max(hbottom, 0)\n const ry = Math.max(viewHeight - vtop, 0)\n const w = Math.min(htop - hbottom, viewWidth)\n const h = Math.min(viewHeight - vbottom - ry, viewHeight)\n\n let lastx = Number.POSITIVE_INFINITY\n let lasty = Number.POSITIVE_INFINITY\n return (\n <>\n <rect\n x={rx}\n y={ry}\n width={w}\n height={h}\n {...getFillProps(theme.palette.background.default)}\n />\n <g>\n {hblocks.map(region => {\n const x = region.offsetPx - hview.offsetPx\n const render = Math.floor(x) !== Math.floor(lastx)\n if (render) {\n lastx = x\n }\n return render ? (\n <line\n key={JSON.stringify(region)}\n x1={x}\n y1={0}\n x2={x}\n y2={viewHeight}\n {...getStrokeProps(stroke)}\n />\n ) : null\n })}\n {vblocks.map(region => {\n const y = viewHeight - (region.offsetPx - vview.offsetPx)\n const render = Math.floor(y) !== Math.floor(lasty)\n if (render) {\n lasty = y\n }\n return render ? (\n <line\n key={JSON.stringify(region)}\n x1={0}\n y1={y}\n x2={viewWidth}\n y2={y}\n {...getStrokeProps(stroke)}\n />\n ) : null\n })}\n <line\n x1={htop}\n y1={0}\n x2={htop}\n y2={viewHeight}\n {...getStrokeProps(stroke)}\n />\n <line\n x1={0}\n y1={viewHeight - vtop}\n x2={viewWidth}\n y2={viewHeight - vtop}\n {...getStrokeProps(stroke)}\n />\n </g>\n {children}\n </>\n )\n})\n\nexport default function Grid({\n model,\n children,\n}: {\n model: DotplotViewModel\n children?: React.ReactNode\n}) {\n const { viewWidth, viewHeight } = model\n return (\n <svg\n width={viewWidth}\n height={viewHeight}\n style={{ background: 'rgba(0,0,0,0.12)' }}\n >\n <GridRaw model={model}>{children}</GridRaw>\n </svg>\n )\n}\n"],"names":["useStyles","makeStyles","vtext","gridColumn","gridRow","pointerEvents","userSelect","htext","HorizontalAxis","observer","model","viewWidth","borderY","classes","React","width","height","className","HorizontalAxisRaw","borderX","hview","htextRotation","hticks","offsetPx","dynamicBlocks","bpPerPx","dblocks","contentBlocks","hide","getBlockLabelKeysToHide","theme","useTheme","hviewSnap","getSnapshot","staticBlocks","ticks","map","tick","bpToPx","refName","coord","base","self","filter","f","undefined","region","has","key","x","xoff","Math","floor","_extends","transform","JSON","stringify","y","fontSize","dominantBaseline","textAnchor","getFillProps","palette","text","primary","x1","x2","y1","y2","type","strokeWidth","t","getTickDisplayStr","assemblyNames","join","VerticalAxis","viewHeight","VerticalAxisRaw","vview","vtextRotation","vticks","vviewSnap","yoff","getStrokeProps","grey","getAdapter","radioOption","assembly1","assembly2","fileLocation","indexFileLocation","bed1Location","bed2Location","pafLocation","queryAssembly","targetAssembly","outLocation","deltaLocation","chainLocation","mcscanAnchorsLocation","mcscanSimpleAnchorsLocation","pifGzLocation","index","location","Error","setSessionTrackData","setBed2Location","useState","setBed1Location","setFileLocation","setIndexFileLocation","value","setValue","error","setError","fileName","sessionTrackData","uri","localPath","name","str","r","split","pop","extName","endsWith","slice","stripGz","useEffect","fn","trackId","Date","now","adapter","e","console","Paper","style","padding","ErrorMessage","Typography","textAlign","RadioGroup","onChange","event","target","Grid","container","justifyContent","item","FormControlLabel","control","Radio","label","margin","href","display","FileSelector","description","setLocation","loc","setShowTrackId","session","getSession","tracks","sessionTracks","filteredTracks","track","readConfObject","includes","resetTrack","paragraph","TrackSelectorIcon","length","Select","MenuItem","getTrackName","importFormContainer","spacing","assemblySelector","TrackSelector","choice","setChoice","FormControl","FormLabel","id","row","ImportCustomTrack","ImportSyntenyTrackSelector","setAssembly2","setAssembly1","showTrackId","displayError","Container","alignItems","AssemblySelector","selected","val","Button","onClick","isSessionWithAddTracks","transaction","addTrackConf","toggleTrack","showTrack","setViews","setAssemblyNames","variant","color","WarningDialog","lazy","trackWarnings","displays","warnings","shown","setShown","setHide","Alert","severity","handleClose","dpad","gridTemplateColumns","position","right","zIndex","top","icon","elevation","IconButton","scroll","ArrowDropUp","ArrowLeft","ArrowRight","ArrowDropDown","zoomIn","ZoomIn","zoomOut","ZoomOut","CursorMove","props","SvgIcon","fill","d","CursorMouse","zoomOutButton","zoomInButton","activateTrackSelector","title","CascadingMenuButton","menuItems","squareView","squareViewProportional","showAllRegions","setDrawCigar","drawCigar","checked","setShowPanButtons","showPanButtons","subMenu","setCursorMode","cursorMode","setWheelMode","wheelMode","MoreVert","bp","marginLeft","spacer","flexGrow","headerBar","selection","DotplotControls","getBpDisplayStr","currBp","DotplotWarnings","PanButtons","TooltipWhereClicked","TooltipWhereMouseovered","blank","left","root","marginBottom","overflow","overlay","cursor","content","resizeHandle","background","boxSizing","borderTop","getOffset","rect","RenderedComponent","RenderingComponent","configuration","DotplotViewInternal","mousecurrClient","setMouseCurrClient","mousedownClient","setMouseDownClient","mouseOvered","setMouseOvered","mouseupClient","setMouseUpClient","ref","useRef","distanceX","distanceY","scheduled","ctrlKeyWasUsed","setCtrlKeyWasUsed","ctrlKeyDown","setCtrlKeyDown","svg","current","getBoundingClientRect","rootRect","mousedown","mousecurr","mouseup","mouserect","mouserectClient","xdistance","ydistance","validPan","validSelect","onWheel","preventDefault","deltaX","deltaY","window","requestAnimationFrame","abs","zoomTo","curr","addEventListener","removeEventListener","globalMouseMove","clientX","clientY","globalCtrlKeyDown","metaKey","ctrlKey","globalCtrlKeyUp","globalMouseUp","Header","onMouseLeave","onMouseEnter","Suspense","fallback","onMouseDown","button","min","Menu","open","Boolean","onMenuItemClick","_","callback","onClose","anchorReference","anchorPosition","onDotplotView","ResizeHandle","onDrag","n","setHeight","initialized","loading","ImportForm","LoadingEllipses","GridRaw","children","hblocks","vblocks","htop","displayedRegionsTotalPx","vtop","hbottom","vbottom","stroke","divider","rx","max","ry","w","h","lastx","Number","POSITIVE_INFINITY","lasty","default","render"],"sourceRoot":""}