view x/static/js/7126.b4b7d70b.chunk.js.map @ 125:49f3d3878413 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

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{ parseBreakend } from '@gmod/vcf'\nimport { Feature, assembleLocString } from '@jbrowse/core/util'\n\nexport function makeFeaturePair(feature: Feature, alt?: string) {\n  const bnd = alt ? parseBreakend(alt) : undefined\n  const start = feature.get('start')\n  let end = feature.get('end')\n  const strand = feature.get('strand')\n  const mate = feature.get('mate') as\n    | {\n        refName: string\n        start: number\n        end: number\n        mateDirection?: number\n      }\n    | undefined\n  const refName = feature.get('refName')\n\n  let mateRefName: string | undefined\n  let mateEnd = 0\n  let mateStart = 0\n  let joinDirection = 0\n  let mateDirection = 0\n\n  // one sided bracket used, because there could be <INS:ME> and we just check\n  // startswith below\n  const symbolicAlleles = ['<TRA', '<DEL', '<INV', '<INS', '<DUP', '<CNV']\n  if (symbolicAlleles.some(a => alt?.startsWith(a))) {\n    // END is defined to be a single value, not an array. CHR2 not defined in\n    // VCF spec, but should be similar\n    const info = feature.get('INFO')\n    const e = info?.END?.[0] ?? end\n    mateRefName = info?.CHR2?.[0] ?? refName\n    mateEnd = e\n    mateStart = e - 1\n    // re-adjust the arc to be from start to end of feature by re-assigning end\n    // to the 'mate'\n    end = start + 1\n  } else if (bnd?.MatePosition) {\n    const matePosition = bnd.MatePosition.split(':')\n    mateDirection = bnd.MateDirection === 'left' ? 1 : -1\n    joinDirection = bnd.Join === 'left' ? -1 : 1\n    mateEnd = +matePosition[1]!\n    mateStart = +matePosition[1]! - 1\n    mateRefName = matePosition[0]\n  }\n\n  return {\n    k1: {\n      refName,\n      start,\n      end,\n      strand,\n      mateDirection,\n    },\n    k2: mate ?? {\n      refName: mateRefName || 'unknown',\n      end: mateEnd,\n      start: mateStart,\n      mateDirection: joinDirection,\n    },\n  }\n}\n\nexport function makeSummary(feature: Feature, alt?: string) {\n  const { k1, k2 } = makeFeaturePair(feature, alt)\n  return [\n    feature.get('name'),\n    feature.get('id'),\n    assembleLocString(k1),\n    assembleLocString(k2),\n    feature.get('INFO')?.SVTYPE,\n    alt,\n  ]\n    .filter(f => !!f)\n    .join(' - ')\n}\n","import React, { lazy, Suspense, useRef, useState } from 'react'\nimport { observer } from 'mobx-react'\nimport {\n  AbstractSessionModel,\n  Feature,\n  getContainingView,\n  getSession,\n  getStrokeProps,\n} from '@jbrowse/core/util'\nimport { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\nimport { Assembly } from '@jbrowse/core/assemblyManager/assembly'\nimport { getConf } from '@jbrowse/core/configuration'\n\n// local\nimport { LinearArcDisplayModel } from '../model'\nimport { makeFeaturePair, makeSummary } from './util'\n\nconst ArcTooltip = lazy(() => import('../../ArcTooltip'))\n\ntype LGV = LinearGenomeViewModel\n\nconst Arc = observer(function ({\n  model,\n  feature,\n  alt,\n  assembly,\n  view,\n}: {\n  feature: Feature\n  alt?: string\n  model: LinearArcDisplayModel\n  assembly: Assembly\n  session: AbstractSessionModel\n  view: LinearGenomeViewModel\n}) {\n  const [mouseOvered, setMouseOvered] = useState(false)\n  const { height } = model\n  const { k1, k2 } = makeFeaturePair(feature, alt)\n  const ref = useRef<SVGPathElement>(null)\n  const c = getConf(model, 'color', { feature, alt })\n  const ra1 = assembly.getCanonicalRefName(k1.refName) || k1.refName\n  const ra2 = assembly.getCanonicalRefName(k2.refName) || k2.refName\n  const p1 = k1.start\n  const p2 = k2.start\n  const r1 = view.bpToPx({ refName: ra1, coord: p1 })?.offsetPx\n  const r2 = view.bpToPx({ refName: ra2, coord: p2 })?.offsetPx\n\n  if (r1 !== undefined && r2 !== undefined) {\n    const radius = (r2 - r1) / 2\n    const absrad = Math.abs(radius)\n    const destY = Math.min(height, absrad)\n    const p1 = r1 - view.offsetPx\n    const p2 = r2 - view.offsetPx\n    const left = p1\n    const right = p2\n    const col = mouseOvered ? 'black' : c\n    const sw = 3\n\n    return absrad > 1 ? (\n      <>\n        <path\n          d={`M ${left} 0 C ${left} ${destY}, ${right} ${destY}, ${right} 0`}\n          ref={ref}\n          {...getStrokeProps(col)}\n          strokeWidth={sw}\n          onMouseOut={() => {\n            setMouseOvered(false)\n          }}\n          onMouseOver={() => {\n            setMouseOvered(true)\n          }}\n          onClick={() => {\n            model.selectFeature(feature)\n          }}\n          fill=\"none\"\n          pointerEvents=\"stroke\"\n        />\n        {k1.mateDirection ? (\n          <line\n            {...getStrokeProps(col)}\n            strokeWidth={sw}\n            onMouseOut={() => {\n              setMouseOvered(false)\n            }}\n            onMouseOver={() => {\n              setMouseOvered(true)\n            }}\n            onClick={() => {\n              model.selectFeature(feature)\n            }}\n            x1={left}\n            x2={left + k1.mateDirection * 20}\n            y1={1.5}\n            y2={1.5}\n          />\n        ) : null}\n        {k2.mateDirection ? (\n          <line\n            {...getStrokeProps(col)}\n            strokeWidth={sw}\n            onMouseOut={() => {\n              setMouseOvered(false)\n            }}\n            onMouseOver={() => {\n              setMouseOvered(true)\n            }}\n            onClick={() => {\n              model.selectFeature(feature)\n            }}\n            x1={right}\n            x2={right + k2.mateDirection * 20}\n            y1={1.5}\n            y2={1.5}\n          />\n        ) : null}\n        {mouseOvered ? (\n          <Suspense fallback={null}>\n            <ArcTooltip contents={makeSummary(feature, alt)} />\n          </Suspense>\n        ) : null}\n      </>\n    ) : null\n  }\n  return null\n})\n\nconst Wrapper = observer(function ({\n  model,\n  exportSVG,\n  children,\n}: {\n  model: LinearArcDisplayModel\n  exportSVG?: boolean\n  children: React.ReactNode\n}) {\n  const { height } = model\n  const view = getContainingView(model) as LGV\n  const width = Math.round(view.dynamicBlocks.totalWidthPx)\n  return exportSVG ? (\n    children\n  ) : (\n    <svg width={width} height={height}>\n      {children}\n    </svg>\n  )\n})\n\nconst Arcs = observer(function ({\n  model,\n  exportSVG,\n}: {\n  model: LinearArcDisplayModel\n  exportSVG?: boolean\n}) {\n  const view = getContainingView(model) as LGV\n  const session = getSession(model)\n  const { assemblyManager } = session\n  const { features } = model\n  const assembly = assemblyManager.get(view.assemblyNames[0]!)\n\n  return assembly ? (\n    <Wrapper model={model} exportSVG={exportSVG}>\n      {features?.map(f => {\n        const alts = f.get('ALT') as string[] | undefined\n        return (\n          alts?.map(a => (\n            <Arc\n              key={`${f.id()}-${a}`}\n              session={session}\n              feature={f}\n              alt={a}\n              view={view}\n              model={model}\n              assembly={assembly}\n            />\n          )) ?? (\n            <Arc\n              key={f.id()}\n              session={session}\n              feature={f}\n              view={view}\n              model={model}\n              assembly={assembly}\n            />\n          )\n        )\n      })}\n    </Wrapper>\n  ) : null\n})\n\nexport default Arcs\n","import React, { lazy } from 'react'\nimport { IconButton, Tooltip } from '@mui/material'\nimport { LoadingEllipses } from '@jbrowse/core/ui'\nimport { BlockMsg } from '@jbrowse/plugin-linear-genome-view'\nimport { makeStyles } from 'tss-react/mui'\nimport { observer } from 'mobx-react'\n\n// local\nimport { LinearArcDisplayModel } from '../model'\n\n// icons\nimport RefreshIcon from '@mui/icons-material/Refresh'\nimport ReportIcon from '@mui/icons-material/Report'\n\nimport { getSession } from '@jbrowse/core/util'\n\nconst ErrorMessageStackTraceDialog = lazy(\n  () => import('@jbrowse/core/ui/ErrorMessageStackTraceDialog'),\n)\n\nconst useStyles = makeStyles()(theme => ({\n  loading: {\n    backgroundColor: theme.palette.background.default,\n    backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${theme.palette.action.disabledBackground} 5px, ${theme.palette.action.disabledBackground} 10px)`,\n    position: 'absolute',\n    bottom: 0,\n    height: 50,\n    width: 300,\n    right: 0,\n    pointerEvents: 'none',\n    textAlign: 'center',\n  },\n}))\n\nconst BaseDisplayComponent = observer(function ({\n  model,\n  children,\n}: {\n  model: LinearArcDisplayModel\n  children?: React.ReactNode\n}) {\n  const { error, regionTooLarge } = model\n  return error ? (\n    <BlockMsg\n      message={`${error}`}\n      severity=\"error\"\n      action={\n        <>\n          <Tooltip title=\"Reload\">\n            <IconButton\n              data-testid=\"reload_button\"\n              onClick={() => {\n                model.reload()\n              }}\n            >\n              <RefreshIcon />\n            </IconButton>\n          </Tooltip>\n          <Tooltip title=\"Show stack trace\">\n            <IconButton\n              onClick={() => {\n                getSession(model).queueDialog(onClose => [\n                  ErrorMessageStackTraceDialog,\n                  { onClose, error: model.error as Error },\n                ])\n              }}\n            >\n              <ReportIcon />\n            </IconButton>\n          </Tooltip>\n        </>\n      }\n    />\n  ) : regionTooLarge ? (\n    model.regionCannotBeRendered()\n  ) : (\n    <DataDisplay model={model}>{children}</DataDisplay>\n  )\n})\n\nconst DataDisplay = observer(function ({\n  model,\n  children,\n}: {\n  model: LinearArcDisplayModel\n  children?: React.ReactNode\n}) {\n  const { loading } = model\n  return (\n    <div>\n      {children}\n      {loading ? <LoadingBar model={model} /> : null}\n    </div>\n  )\n})\n\nconst LoadingBar = observer(function ({\n  model,\n}: {\n  model: LinearArcDisplayModel\n}) {\n  const { classes } = useStyles()\n  const { message } = model\n  return (\n    <div className={classes.loading}>\n      <LoadingEllipses message={message} />\n    </div>\n  )\n})\n\nexport default BaseDisplayComponent\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\n// local\nimport { LinearArcDisplayModel } from '../model'\nimport BaseDisplayComponent from './BaseDisplayComponent'\nimport Arcs from './Arcs'\n\nconst LinearArcReactComponent = observer(function ({\n  model,\n  exportSVG,\n}: {\n  model: LinearArcDisplayModel\n  exportSVG?: boolean\n}) {\n  return (\n    <BaseDisplayComponent model={model}>\n      <Arcs model={model} exportSVG={exportSVG} />\n    </BaseDisplayComponent>\n  )\n})\n\nexport default LinearArcReactComponent\n"],"names":["makeFeaturePair","feature","alt","bnd","parseBreakend","undefined","start","get","end","strand","mate","refName","mateRefName","mateEnd","mateStart","joinDirection","mateDirection","some","a","startsWith","info","e","END","CHR2","MatePosition","matePosition","split","MateDirection","Join","k1","k2","makeSummary","assembleLocString","SVTYPE","filter","f","join","ArcTooltip","lazy","Arc","observer","model","assembly","view","mouseOvered","setMouseOvered","useState","height","ref","useRef","c","getConf","ra1","getCanonicalRefName","ra2","p1","p2","r1","bpToPx","coord","offsetPx","r2","radius","absrad","Math","abs","destY","min","left","right","col","sw","React","_extends","d","getStrokeProps","strokeWidth","onMouseOut","onMouseOver","onClick","selectFeature","fill","pointerEvents","x1","x2","y1","y2","Suspense","fallback","contents","Wrapper","exportSVG","children","getContainingView","width","round","dynamicBlocks","totalWidthPx","session","getSession","assemblyManager","features","assemblyNames","map","alts","key","id","ErrorMessageStackTraceDialog","useStyles","makeStyles","theme","loading","backgroundColor","palette","background","default","backgroundImage","action","disabledBackground","position","bottom","textAlign","BaseDisplayComponent","error","regionTooLarge","BlockMsg","message","severity","Tooltip","title","IconButton","reload","RefreshIcon","queueDialog","onClose","ReportIcon","regionCannotBeRendered","DataDisplay","LoadingBar","classes","className","LoadingEllipses","Arcs"],"sourceRoot":""}