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@@ -0,0 +1,1 @@
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React from 'react'\nimport { Checkbox, FormControlLabel } from '@mui/material'\nimport { makeStyles } from 'tss-react/mui'\n\nconst useStyles = makeStyles()({\n  block: {\n    display: 'block',\n  },\n})\n\nexport default function Checkbox2({\n  checked,\n  disabled,\n  label,\n  onChange,\n}: {\n  checked: boolean\n  disabled?: boolean\n  label: string\n  onChange: (event: React.ChangeEvent<HTMLInputElement>) => void\n}) {\n  const { classes } = useStyles()\n  return (\n    <FormControlLabel\n      disabled={disabled}\n      className={classes.block}\n      control={<Checkbox checked={checked} onChange={onChange} />}\n      label={label}\n    />\n  )\n}\n","import React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport { Button, DialogActions, DialogContent } from '@mui/material'\nimport { getSnapshot } from 'mobx-state-tree'\nimport { Dialog } from '@jbrowse/core/ui'\nimport { when } from 'mobx'\nimport { getSession, Feature } from '@jbrowse/core/util'\nimport type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\nimport type { Assembly } from '@jbrowse/core/assemblyManager/assembly'\n\n// locals\nimport Checkbox2 from './Checkbox2'\n\ninterface Display {\n  id: string\n  [key: string]: unknown\n}\ninterface Track {\n  id: string\n  displays: Display[]\n  [key: string]: unknown\n}\n\nfunction stripIds(arr: Track[]) {\n  return arr.map(({ id, displays, ...rest }) => ({\n    ...rest,\n    displays: displays.map(({ id, ...rest }) => rest),\n  }))\n}\n\nconst BreakendMultiLevelOptionDialog = observer(function ({\n  model,\n  handleClose,\n  feature,\n  assemblyName,\n  viewType,\n  view,\n}: {\n  model: unknown\n  handleClose: () => void\n  feature: Feature\n  view: LinearGenomeViewModel\n  assemblyName: string\n  viewType: {\n    getBreakendCoveringRegions: (arg: {\n      feature: Feature\n      assembly: Assembly\n    }) => {\n      pos: number\n      refName: string\n      mateRefName: string\n      matePos: number\n    }\n  }\n}) {\n  const [copyTracks, setCopyTracks] = useState(true)\n  const [mirror, setMirror] = useState(true)\n\n  return (\n    <Dialog\n      open\n      onClose={handleClose}\n      title=\"Multi-level breakpoint split view options\"\n    >\n      <DialogContent>\n        <Checkbox2\n          checked={copyTracks}\n          label=\"Copy tracks into the new view\"\n          onChange={event => {\n            setCopyTracks(event.target.checked)\n          }}\n        />\n\n        {copyTracks ? (\n          <Checkbox2\n            checked={mirror}\n            disabled={!copyTracks}\n            label=\"Mirror the copied tracks (only available if copying tracks and using two level)\"\n            onChange={event => {\n              setMirror(event.target.checked)\n            }}\n          />\n        ) : null}\n      </DialogContent>\n      <DialogActions>\n        <Button\n          onClick={() => {\n            // eslint-disable-next-line @typescript-eslint/no-floating-promises\n            ;(async () => {\n              const session = getSession(model)\n              try {\n                const asm =\n                  await session.assemblyManager.waitForAssembly(assemblyName)\n                if (!asm) {\n                  throw new Error(`assembly ${assemblyName} not found`)\n                }\n\n                const { refName, pos, mateRefName, matePos } =\n                  viewType.getBreakendCoveringRegions({\n                    feature,\n                    assembly: asm,\n                  })\n\n                const viewTracks = getSnapshot(view.tracks) as Track[]\n                const breakpointSplitView = session.addView(\n                  'BreakpointSplitView',\n                  {\n                    type: 'BreakpointSplitView',\n                    displayName: `${\n                      feature.get('name') || feature.get('id') || 'breakend'\n                    } split detail`,\n\n                    views: [\n                      {\n                        type: 'LinearGenomeView',\n                        hideHeader: true,\n                        tracks: stripIds(getSnapshot(view.tracks)),\n                      },\n                      {\n                        type: 'LinearGenomeView',\n                        hideHeader: true,\n                        tracks: stripIds(\n                          mirror ? [...viewTracks].reverse() : viewTracks,\n                        ),\n                      },\n                    ],\n                  },\n                ) as unknown as { views: LinearGenomeViewModel[] }\n                const r1 = asm.regions!.find(r => r.refName === refName)\n                const r2 = asm.regions!.find(r => r.refName === mateRefName)\n                if (!r1 || !r2) {\n                  throw new Error(\"can't find regions\")\n                }\n                await Promise.all([\n                  breakpointSplitView.views[0]!.navToLocations([\n                    {\n                      refName,\n                      start: r1.start,\n                      end: pos,\n                      assemblyName,\n                    },\n                    {\n                      refName,\n                      start: pos + 1,\n                      end: r1.end,\n                      assemblyName,\n                    },\n                  ]),\n                  breakpointSplitView.views[1]!.navToLocations([\n                    {\n                      refName: mateRefName,\n                      start: r2.start,\n                      end: matePos,\n                      assemblyName,\n                    },\n                    {\n                      refName: mateRefName,\n                      start: matePos + 1,\n                      end: r2.end,\n                      assemblyName,\n                    },\n                  ]),\n                ])\n                await when(\n                  () =>\n                    breakpointSplitView.views[1]!.initialized &&\n                    breakpointSplitView.views[0]!.initialized,\n                )\n                breakpointSplitView.views[1]!.zoomTo(10)\n                breakpointSplitView.views[0]!.zoomTo(10)\n                breakpointSplitView.views[1]!.centerAt(matePos, mateRefName)\n                breakpointSplitView.views[0]!.centerAt(pos, refName)\n              } catch (e) {\n                console.error(e)\n                session.notify(`${e}`)\n              }\n            })()\n            handleClose()\n          }}\n          variant=\"contained\"\n          color=\"primary\"\n          autoFocus\n        >\n          OK\n        </Button>\n        <Button\n          color=\"secondary\"\n          variant=\"contained\"\n          onClick={() => {\n            handleClose()\n          }}\n        >\n          Cancel\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default BreakendMultiLevelOptionDialog\n","import React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport { Button, DialogActions, DialogContent, TextField } from '@mui/material'\nimport { getSnapshot } from 'mobx-state-tree'\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  getSession,\n  Feature,\n  gatherOverlaps,\n  useLocalStorage,\n} from '@jbrowse/core/util'\nimport type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\nimport type { Assembly } from '@jbrowse/core/assemblyManager/assembly'\n\n// locals\nimport Checkbox2 from './Checkbox2'\n\ninterface Display {\n  id: string\n  [key: string]: unknown\n}\ninterface Track {\n  id: string\n  displays: Display[]\n  [key: string]: unknown\n}\n\nfunction stripIds(arr: Track[]) {\n  return arr.map(({ id, displays, ...rest }) => ({\n    ...rest,\n    displays: displays.map(({ id, ...rest }) => rest),\n  }))\n}\n\nconst BreakendSingleLevelOptionDialog = observer(function ({\n  model,\n  handleClose,\n  feature,\n  assemblyName,\n  viewType,\n  view,\n}: {\n  model: unknown\n  handleClose: () => void\n  feature: Feature\n  view: LinearGenomeViewModel\n  assemblyName: string\n  viewType: {\n    getBreakendCoveringRegions: (arg: {\n      feature: Feature\n      assembly: Assembly\n    }) => {\n      pos: number\n      refName: string\n      mateRefName: string\n      matePos: number\n    }\n  }\n}) {\n  const [copyTracks, setCopyTracks] = useState(true)\n  const [windowSize, setWindowSize] = useLocalStorage(\n    'breakpointWindowSize',\n    '5000',\n  )\n\n  return (\n    <Dialog\n      open\n      onClose={handleClose}\n      title=\"Single-level breakpoint split view options\"\n    >\n      <DialogContent>\n        <Checkbox2\n          checked={copyTracks}\n          label=\"Copy tracks into the new view\"\n          onChange={event => {\n            setCopyTracks(event.target.checked)\n          }}\n        />\n\n        <TextField\n          label=\"Window size (bp)\"\n          value={windowSize}\n          onChange={event => {\n            setWindowSize(event.target.value)\n          }}\n        />\n      </DialogContent>\n      <DialogActions>\n        <Button\n          onClick={() => {\n            const session = getSession(model)\n            // eslint-disable-next-line @typescript-eslint/no-floating-promises\n            ;(async () => {\n              try {\n                const assembly = session.assemblyManager.get(assemblyName)\n                const w = +windowSize\n                if (Number.isNaN(w)) {\n                  throw new Error('windowSize not a number')\n                }\n                const { refName, pos, mateRefName, matePos } =\n                  // @ts-expect-error\n                  viewType.getBreakendCoveringRegions({ feature, assembly })\n\n                const breakpointSplitView = session.addView(\n                  'BreakpointSplitView',\n                  {\n                    type: 'BreakpointSplitView',\n                    displayName: `${\n                      feature.get('name') || feature.get('id') || 'breakend'\n                    } split detail`,\n                    views: [\n                      {\n                        type: 'LinearGenomeView',\n                        tracks: stripIds(getSnapshot(view.tracks)),\n                      },\n                    ],\n                  },\n                ) as unknown as { views: LinearGenomeViewModel[] }\n\n                await breakpointSplitView.views[0]!.navToLocations(\n                  gatherOverlaps(\n                    [\n                      {\n                        refName,\n                        start: Math.max(0, pos - w),\n                        end: pos + w,\n                        assemblyName,\n                      },\n                      {\n                        refName: mateRefName,\n                        start: Math.max(0, matePos - w),\n                        end: matePos + w,\n                        assemblyName,\n                      },\n                    ],\n                    w,\n                  ),\n                )\n              } catch (e) {\n                console.error(e)\n                session.notify(`${e}`)\n              }\n            })()\n            handleClose()\n          }}\n          variant=\"contained\"\n          color=\"primary\"\n          autoFocus\n        >\n          OK\n        </Button>\n        <Button\n          color=\"secondary\"\n          variant=\"contained\"\n          onClick={() => {\n            handleClose()\n          }}\n        >\n          Cancel\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default BreakendSingleLevelOptionDialog\n"],"names":["useStyles","makeStyles","block","display","Checkbox2","checked","disabled","label","onChange","classes","React","FormControlLabel","className","control","Checkbox","stripIds","arr","map","id","displays","rest","observer","model","handleClose","feature","assemblyName","viewType","view","copyTracks","setCopyTracks","useState","mirror","setMirror","Dialog","open","onClose","title","DialogContent","event","target","DialogActions","Button","onClick","session","getSession","asm","assemblyManager","waitForAssembly","Error","refName","pos","mateRefName","matePos","getBreakendCoveringRegions","assembly","viewTracks","getSnapshot","tracks","breakpointSplitView","addView","type","displayName","get","views","hideHeader","reverse","r1","regions","find","r","r2","Promise","all","navToLocations","start","end","when","initialized","zoomTo","centerAt","e","console","error","notify","variant","color","autoFocus","windowSize","setWindowSize","useLocalStorage","TextField","value","w","Number","isNaN","gatherOverlaps","Math","max"],"sourceRoot":""}
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