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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()}-${a}`}\n              session={session}\n              feature={f}\n              alt={a}\n              view={view}\n              model={model}\n              assembly={assembly}\n            />\n          )) ?? (\n            <Arc\n              key={f.id()}\n              session={session}\n              feature={f}\n              view={view}\n              model={model}\n              assembly={assembly}\n            />\n          )\n        )\n      })}\n    </Wrapper>\n  ) : null\n})\n\nexport default Arcs\n","import React from 'react'\nimport { getContainingView, when } from '@jbrowse/core/util'\n\n// locals\nimport { LinearArcDisplayModel } from './model'\nimport Arcs from './components/Arcs'\nimport { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\nexport async function renderArcSvg(\n  model: LinearArcDisplayModel,\n  _opts: {\n    rasterizeLayers?: boolean\n  },\n) {\n  await when(() => !model.loading)\n\n  const view = getContainingView(model) as LinearGenomeViewModel\n  const width = view.dynamicBlocks.totalWidthPx\n  const height = model.height\n  const clipid = `arc-${model.id}`\n  return (\n    <>\n      <defs>\n        <clipPath id={clipid}>\n          <rect x={0} y={0} width={width} height={height} />\n        </clipPath>\n      </defs>\n      <g clipPath={`url(#${clipid})`}>\n        <Arcs model={model} exportSVG={true} />\n      </g>\n    </>\n  )\n}\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","async","renderArcSvg","_opts","when","loading","clipid","x","y","clipPath","Arcs"],"sourceRoot":""}