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+ saLength\n            const sp = start - extra\n            const ep = end + extra\n            const locString = `${saRef}:${Math.max(1, sp)}-${ep}`\n            const displayStart = start.toLocaleString('en-US')\n            const displayEnd = end.toLocaleString('en-US')\n            const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand}) [${saLength}bp]`\n            return (\n              /* biome-ignore lint/suspicious/noArrayIndexKey: */\n              <li key={`${locString}-${idx}`}>\n                <Link\n                  href=\"#\"\n                  onClick={async event => {\n                    event.preventDefault()\n\n                    // eslint-disable-next-line @typescript-eslint/no-floating-promises\n                    navToLoc(locString, model)\n                  }}\n                >\n                  {displayString}\n                </Link>\n              </li>\n            )\n          })}\n      </ul>\n    </div>\n  )\n}\n","import React, { lazy, useEffect, useState } from 'react'\nimport { Typography, Link } from '@mui/material'\nimport {\n  SimpleFeature,\n  SimpleFeatureSerialized,\n  getSession,\n  toLocale,\n} from '@jbrowse/core/util'\nimport { ErrorMessage } from '@jbrowse/core/ui'\nimport { ViewType } from '@jbrowse/core/pluggableElementTypes'\n\n// locals\nimport { AlignmentFeatureWidgetModel } from './stateModelFactory'\nimport { ReducedFeature, getSAFeatures } from './getSAFeatures'\n\n// lazies\nconst BreakendMultiLevelOptionDialog = lazy(\n  () => import('./BreakendMultiLevelOptionDialog'),\n)\nconst BreakendSingleLevelOptionDialog = lazy(\n  () => import('./BreakendSingleLevelOptionDialog'),\n)\n\nexport default function LaunchBreakpointSplitViewPanel({\n  model,\n  feature,\n  viewType,\n}: {\n  model: AlignmentFeatureWidgetModel\n  feature: SimpleFeatureSerialized\n  viewType: ViewType\n}) {\n  const session = getSession(model)\n  const { view } = model\n  const [res, setRes] = useState<ReducedFeature[]>()\n  const [error, setError] = useState<unknown>()\n  useEffect(() => {\n    // eslint-disable-next-line @typescript-eslint/no-floating-promises\n    ;(async () => {\n      try {\n        const feats = await getSAFeatures({\n          view,\n          feature: new SimpleFeature(feature),\n        })\n        setRes(feats)\n      } catch (e) {\n        setError(e)\n        console.error(e)\n      }\n    })()\n  }, [feature, view])\n\n  const ret = [] as [ReducedFeature, ReducedFeature][]\n  if (res) {\n    for (let i = 0; i < res.length - 1; i++) {\n      ret.push([res[i]!, res[i + 1]!] as const)\n    }\n  }\n  return ret.length ? (\n    <div>\n      <Typography>Launch split view</Typography>\n      {error ? <ErrorMessage error={error} /> : null}\n      <ul>\n        {ret.map((arg, index) => {\n          const [f1, f2] = arg\n          return (\n            <li key={`${JSON.stringify(arg)}-${index}`}>\n              {f1.refName}:{toLocale(f1.strand === 1 ? f1.end : f1.start)} -&gt;{' '}\n              {f2.refName}:{toLocale(f2.strand === 1 ? f2.start : f2.end)}{' '}\n              <Link\n                href=\"#\"\n                onClick={event => {\n                  event.preventDefault()\n                  session.queueDialog(handleClose => [\n                    BreakendMultiLevelOptionDialog,\n                    {\n                      handleClose,\n                      model,\n                      feature: new SimpleFeature({ ...f1, mate: f2 }),\n                      // @ts-expect-error\n                      viewType,\n                      view: model.view,\n                      assemblyName: model.view.displayedRegions[0].assemblyName,\n                    },\n                  ])\n                }}\n              >\n                (top/bottom)\n              </Link>{' '}\n              <Link\n                href=\"#\"\n                onClick={event => {\n                  event.preventDefault()\n                  session.queueDialog(handleClose => [\n                    BreakendSingleLevelOptionDialog,\n                    {\n                      handleClose,\n                      model,\n                      feature: new SimpleFeature({ ...f1, mate: f2 }),\n                      // @ts-expect-error\n                      viewType,\n                      view: model.view,\n                      assemblyName: model.view.displayedRegions[0].assemblyName,\n                    },\n                  ])\n                }}\n              >\n                (single row)\n              </Link>\n            </li>\n          )\n        })}\n      </ul>\n    </div>\n  ) : null\n}\n","import { Feature, getSession } from '@jbrowse/core/util'\n\n// locals\nimport { featurizeSA, getClip, getLengthSansClipping } from '../MismatchParser'\nimport { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\nimport { getTag } from '../util'\n\nexport interface ReducedFeature {\n  refName: string\n  start: number\n  clipPos: number\n  end: number\n  strand: number\n  seqLength: number\n  syntenyId?: number\n  uniqueId: string\n  mate: {\n    refName: string\n    start: number\n    end: number\n    syntenyId?: number\n    uniqueId?: string\n  }\n}\n\nexport async function getSAFeatures({\n  view,\n  feature,\n}: {\n  view: LinearGenomeViewModel\n  feature: Feature\n}) {\n  const { assemblyManager } = getSession(view)\n  const cigar = feature.get('CIGAR') as string\n  const origStrand = feature.get('strand') as number\n  const SA = (getTag(feature, 'SA') as string) || ''\n  const readName = feature.get('name') as string\n  const clipPos = getClip(cigar, 1)\n\n  // get the canonical refname for the read because if the read.get('refName')\n  // is chr1 and the actual fasta refName is 1 then no tracks can be opened on\n  // the top panel of the linear read vs ref\n  const assembly = await assemblyManager.waitForAssembly(view.assemblyNames[0]!)\n  if (!assembly) {\n    throw new Error('assembly not found')\n  }\n\n  const suppAlns = featurizeSA(SA, feature.id(), origStrand, readName, true)\n\n  const feat = feature.toJSON()\n  feat.clipPos = clipPos\n  feat.strand = 1\n\n  feat.mate = {\n    refName: readName,\n    start: clipPos,\n    end: clipPos + getLengthSansClipping(cigar),\n  }\n  const features = [feat, ...suppAlns] as ReducedFeature[]\n\n  features.forEach((f, idx) => {\n    f.refName = assembly.getCanonicalRefName(f.refName) || f.refName\n    f.syntenyId = idx\n    f.mate.syntenyId = idx\n    f.mate.uniqueId = `${f.uniqueId}_mate`\n  })\n  features.sort((a, b) => a.clipPos - b.clipPos)\n  return features\n}\n","import React from 'react'\nimport { BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'\nimport { SimpleFeatureSerialized, getEnv, getSession } from '@jbrowse/core/util'\nimport { ViewType } from '@jbrowse/core/pluggableElementTypes'\n\n// locals\nimport { AlignmentFeatureWidgetModel } from './stateModelFactory'\nimport SupplementaryAlignmentsLocStrings from './SupplementaryAlignmentsLocStrings'\nimport LaunchBreakpointSplitViewPanel from './LaunchSupplementaryAlignmentBreakpointSplitViewPanel'\n\nexport default function SupplementaryAlignments(props: {\n  tag: string\n  model: AlignmentFeatureWidgetModel\n  feature: SimpleFeatureSerialized\n}) {\n  const { model, tag, feature } = props\n  const session = getSession(model)\n  const { pluginManager } = getEnv(session)\n  let viewType: ViewType | undefined\n\n  try {\n    viewType = pluginManager.getViewType('BreakpointSplitView')\n  } catch (e) {\n    // ignore\n  }\n\n  return (\n    <BaseCard {...props} title=\"Supplementary alignments\">\n      <SupplementaryAlignmentsLocStrings model={model} tag={tag} />\n      {viewType ? (\n        <LaunchBreakpointSplitViewPanel\n          viewType={viewType}\n          model={model}\n          feature={feature}\n        />\n      ) : null}\n    </BaseCard>\n  )\n}\n"],"names":["SupplementaryAlignmentsLocStrings","tag","model","React","Typography","split","filter","SA","map","idx","saRef","saStart","saStrand","saCigar","saLength","getLengthOnRef","extra","Math","floor","start","end","sp","ep","locString","max","displayString","toLocaleString","key","Link","href","onClick","async","event","preventDefault","navToLoc","BreakendMultiLevelOptionDialog","lazy","BreakendSingleLevelOptionDialog","LaunchBreakpointSplitViewPanel","feature","viewType","session","getSession","view","res","setRes","useState","error","setError","useEffect","feats","assemblyManager","cigar","get","origStrand","getTag","readName","clipPos","getClip","assembly","waitForAssembly","assemblyNames","Error","suppAlns","featurizeSA","id","feat","toJSON","strand","mate","refName","getLengthSansClipping","features","forEach","f","getCanonicalRefName","syntenyId","uniqueId","sort","a","b","getSAFeatures","SimpleFeature","e","console","ret","i","length","push","ErrorMessage","arg","index","f1","f2","JSON","stringify","toLocale","queueDialog","handleClose","assemblyName","displayedRegions","SupplementaryAlignments","props","pluginManager","getEnv","getViewType","BaseCard","_extends","title"],"sourceRoot":""}
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