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React, { lazy } from 'react'\nimport { observer } from 'mobx-react'\nimport { Link } from '@mui/material'\nimport { makeStyles } from 'tss-react/mui'\nimport { DataGrid, GRID_CHECKBOX_SELECTION_COL_DEF } from '@mui/x-data-grid'\nimport {\n  getSession,\n  assembleLocString,\n  measureGridWidth,\n  measureText,\n} from '@jbrowse/core/util'\nimport ColorPicker from '@jbrowse/core/ui/ColorPicker'\n\n// locals\nimport { navToBookmark } from '../utils'\nimport { GridBookmarkModel } from '../model'\n\nconst EditBookmarkLabelDialog = lazy(\n  () => import('./dialogs/EditBookmarkLabelDialog'),\n)\n\nconst useStyles = makeStyles()(() => ({\n  cell: {\n    whiteSpace: 'nowrap',\n    overflow: 'hidden',\n    textOverflow: 'ellipsis',\n  },\n}))\n\nconst BookmarkGrid = observer(function ({\n  model,\n}: {\n  model: GridBookmarkModel\n}) {\n  const { classes } = useStyles()\n  const {\n    bookmarks,\n    bookmarksWithValidAssemblies,\n    selectedAssemblies,\n    selectedBookmarks,\n  } = model\n\n  const session = getSession(model)\n  const selectedSet = new Set(selectedAssemblies)\n  const rows = bookmarks\n    .filter(r => selectedSet.has(r.assemblyName))\n    .map((region, index) => {\n      const { assemblyName, ...rest } = region\n      return {\n        ...region,\n        id: index,\n        assemblyName,\n        locString: assembleLocString(rest),\n        correspondingObj: region,\n      }\n    })\n\n  const widths = [\n    50,\n    Math.max(\n      measureText('Bookmark link', 12) + 30,\n      measureGridWidth(rows.map(row => row.locString)),\n    ),\n    Math.max(\n      measureText('Label', 12) + 30,\n      measureGridWidth(rows.map(row => row.label)),\n    ),\n    Math.max(\n      measureText('Assembly', 12) + 30,\n      measureGridWidth(rows.map(row => row.assemblyName)),\n    ),\n    100,\n  ]\n\n  return (\n    <DataGrid\n      autoHeight\n      density=\"compact\"\n      rows={rows}\n      columns={[\n        {\n          ...GRID_CHECKBOX_SELECTION_COL_DEF,\n          width: widths[0],\n        },\n        {\n          field: 'locString',\n          headerName: 'Bookmark link',\n          width: widths[1],\n          renderCell: ({ value, row }) => (\n            <Link\n              className={classes.cell}\n              href=\"#\"\n              onClick={async event => {\n                event.preventDefault()\n                const { views } = session\n                await navToBookmark(value, row.assemblyName, views, model)\n              }}\n            >\n              {value}\n            </Link>\n          ),\n        },\n        {\n          field: 'label',\n          headerName: 'Label',\n          width: widths[2],\n          editable: true,\n        },\n        {\n          field: 'assemblyName',\n          headerName: 'Assembly',\n          width: widths[3],\n        },\n        {\n          field: 'highlight',\n          headerName: 'Highlight',\n          width: widths[4],\n          renderCell: ({ value, row }) => (\n            <ColorPicker\n              color={value || 'black'}\n              onChange={event => {\n                model.updateBookmarkHighlight(row, event)\n              }}\n            />\n          ),\n        },\n      ]}\n      onCellDoubleClick={({ row }) => {\n        getSession(model).queueDialog(onClose => [\n          EditBookmarkLabelDialog,\n          { onClose, model, dialogRow: row },\n        ])\n      }}\n      processRowUpdate={row => {\n        const target = rows[row.id]!\n        model.updateBookmarkLabel(target, row.label)\n        return row\n      }}\n      onProcessRowUpdateError={e => {\n        session.notifyError(`${e}`, e)\n      }}\n      checkboxSelection\n      onRowSelectionModelChange={newRowSelectionModel => {\n        if (bookmarksWithValidAssemblies.length > 0) {\n          model.setSelectedBookmarks(\n            newRowSelectionModel.map(value => ({\n              ...rows[value as number]!,\n            })),\n          )\n        }\n      }}\n      rowSelectionModel={selectedBookmarks.map(r => r.id)}\n      disableRowSelectionOnClick\n    />\n  )\n})\n\nexport default BookmarkGrid\n","import React from 'react'\nimport { observer } from 'mobx-react'\n\nimport {\n  Checkbox,\n  FormControl,\n  InputLabel,\n  ListItemText,\n  MenuItem,\n  OutlinedInput,\n  Select,\n} from '@mui/material'\n\n// locals\nimport { GridBookmarkModel } from '../model'\n\nconst AssemblySelector = observer(function ({\n  model,\n}: {\n  model: GridBookmarkModel\n}) {\n  const { validAssemblies, selectedAssemblies } = model\n  const noAssemblies = validAssemblies.size === 0\n  const label = 'Select assemblies'\n  const id = 'select-assemblies-label'\n  const selectedSet = new Set(selectedAssemblies)\n  const isAllSelected = [...validAssemblies].every(e => selectedSet.has(e))\n\n  return (\n    <FormControl disabled={noAssemblies} fullWidth>\n      <InputLabel id={id}>{label}</InputLabel>\n      <Select\n        labelId={id}\n        multiple\n        value={selectedAssemblies}\n        onChange={event => {\n          model.setSelectedAssemblies([...event.target.value])\n        }}\n        input={<OutlinedInput label={label} />}\n        renderValue={selected => selected.join(', ')}\n      >\n        <MenuItem\n          onClickCapture={event => {\n            // onClickCapture allows us to avoid the parent Select onChange from triggering\n            if (isAllSelected) {\n              model.setSelectedAssemblies([])\n            } else {\n              model.setSelectedAssemblies(undefined)\n            }\n            event.preventDefault()\n          }}\n        >\n          <Checkbox\n            checked={isAllSelected}\n            indeterminate={!isAllSelected && selectedAssemblies.length > 0}\n          />\n          <ListItemText primary=\"Select all\" />\n        </MenuItem>\n        {[...validAssemblies].map(name => (\n          <MenuItem key={name} value={name}>\n            <Checkbox checked={selectedAssemblies.includes(name)} />\n            <ListItemText primary={name} />\n          </MenuItem>\n        ))}\n      </Select>\n    </FormControl>\n  )\n})\n\nexport default AssemblySelector\n","import React, { lazy } from 'react'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\nimport { getSession } from '@jbrowse/core/util'\nimport { Alert } from '@mui/material'\nimport CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton'\n\n// locals\nimport BookmarkGrid from './BookmarkGrid'\nimport AssemblySelector from './AssemblySelector'\nimport { GridBookmarkModel } from '../model'\n\n// icons\nimport Menu from '@mui/icons-material/Menu'\nimport GetApp from '@mui/icons-material/GetApp'\nimport Publish from '@mui/icons-material/Publish'\nimport Settings from '@mui/icons-material/Settings'\nimport Palette from '@mui/icons-material/Palette'\nimport Share from '@mui/icons-material/Share'\nimport Delete from '@mui/icons-material/Delete'\n\n// lazies\nconst ExportBookmarksDialog = lazy(\n  () => import('./dialogs/ExportBookmarksDialog'),\n)\nconst ImportBookmarksDialog = lazy(\n  () => import('./dialogs/ImportBookmarksDialog'),\n)\nconst ShareBookmarksDialog = lazy(\n  () => import('./dialogs/ShareBookmarksDialog'),\n)\nconst HighlightSettingsDialog = lazy(\n  () => import('./dialogs/HighlightSettingsDialog'),\n)\nconst EditHighlightColorDialog = lazy(\n  () => import('./dialogs/EditHighlightColorDialog'),\n)\nconst DeleteBookmarksDialog = lazy(\n  () => import('./dialogs/DeleteBookmarksDialog'),\n)\n\nconst useStyles = makeStyles()({\n  flex: {\n    display: 'flex',\n  },\n})\n\nconst GridBookmarkWidget = observer(function GridBookmarkWidget({\n  model,\n}: {\n  model: GridBookmarkModel\n}) {\n  const { classes } = useStyles()\n  return (\n    <div>\n      <Alert severity=\"info\">\n        Click and type within the <strong>label</strong> field to annotate your\n        bookmark. Double click the <strong>label</strong> field to do so within\n        a dialog.\n      </Alert>\n      <div className={classes.flex}>\n        <CascadingMenuButton\n          data-testid=\"grid_bookmark_menu\"\n          menuItems={[\n            {\n              label: 'Export',\n              icon: GetApp,\n              onClick: () => {\n                getSession(model).queueDialog(onClose => [\n                  ExportBookmarksDialog,\n                  { onClose, model },\n                ])\n              },\n            },\n            {\n              label: 'Import',\n              icon: Publish,\n              onClick: () => {\n                getSession(model).queueDialog(onClose => [\n                  ImportBookmarksDialog,\n                  { model, onClose },\n                ])\n              },\n            },\n            {\n              label: 'Delete',\n              icon: Delete,\n              onClick: () => {\n                getSession(model).queueDialog(onClose => [\n                  DeleteBookmarksDialog,\n                  { model, onClose },\n                ])\n              },\n            },\n            {\n              label: 'Share',\n              icon: Share,\n              onClick: () => {\n                getSession(model).queueDialog(onClose => [\n                  ShareBookmarksDialog,\n                  { model, onClose },\n                ])\n              },\n            },\n            {\n              label: 'Edit colors',\n              icon: Palette,\n              onClick: () => {\n                getSession(model).queueDialog(onClose => [\n                  EditHighlightColorDialog,\n                  { model, onClose },\n                ])\n              },\n            },\n            {\n              label: 'Settings',\n              icon: Settings,\n              onClick: () => {\n                getSession(model).queueDialog(onClose => [\n                  HighlightSettingsDialog,\n                  { model, onClose },\n                ])\n              },\n            },\n          ]}\n        >\n          <Menu />\n        </CascadingMenuButton>\n\n        <AssemblySelector model={model} />\n      </div>\n      <BookmarkGrid model={model} />\n    </div>\n  )\n})\n\nexport default GridBookmarkWidget\n","import { saveAs } from 'file-saver'\nimport { getSession, assembleLocString } from '@jbrowse/core/util'\nimport { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\nimport { AbstractViewModel } from '@jbrowse/core/util/types'\n\n// locals\nimport { GridBookmarkModel } from './model'\n\ntype LGV = LinearGenomeViewModel\n\ntype MaybeLGV = LGV | undefined\n\nexport async function navToBookmark(\n  locString: string,\n  assembly: string,\n  views: AbstractViewModel[],\n  model: GridBookmarkModel,\n) {\n  const session = getSession(model)\n  try {\n    // get the focused view\n    let view = views.find(view => view.id === session.focusedViewId) as MaybeLGV\n\n    // check if the focused view is the appropriate assembly, if not proceed\n    if (view?.assemblyNames[0] !== assembly) {\n      view = views.find(\n        elt =>\n          // @ts-expect-error\n          elt.type === 'LinearGenomeView' && elt.assemblyNames[0] === assembly,\n      ) as MaybeLGV\n    }\n\n    // if no view is opened of the selectedAssembly, open a new\n    // view with that assembly\n    if (!view) {\n      const newViewId = `${model.id}_${assembly}`\n      view = session.addView('LinearGenomeView', {\n        id: newViewId,\n      }) as LGV\n    }\n    await view.navToLocString(locString, assembly)\n  } catch (e) {\n    console.error(e)\n    session.notifyError(`${e}`, e)\n  }\n}\n\nexport function downloadBookmarkFile(\n  fileFormat: string,\n  model: GridBookmarkModel,\n) {\n  const { selectedBookmarks, bookmarksWithValidAssemblies } = model\n  const bookmarksToDownload =\n    selectedBookmarks.length === 0\n      ? bookmarksWithValidAssemblies\n      : selectedBookmarks\n\n  if (fileFormat === 'BED') {\n    const fileHeader = ''\n    const fileContents: Record<string, string[]> = {}\n    bookmarksToDownload.forEach(bookmark => {\n      const { label } = bookmark\n      const labelVal = label === '' ? '.' : label\n      const line = `${bookmark.refName}\\t${bookmark.start}\\t${bookmark.end}\\t${labelVal}\\n`\n\n      if (fileContents[bookmark.assemblyName]) {\n        fileContents[bookmark.assemblyName]!.push(line)\n      } else {\n        fileContents[bookmark.assemblyName] = [line]\n      }\n    })\n\n    for (const assembly in fileContents) {\n      const fileContent = fileContents[assembly]!.reduce(\n        (a, b) => a + b,\n        fileHeader,\n      )\n      const blob = new Blob([fileContent || ''], {\n        type: 'text/x-bed;charset=utf-8',\n      })\n      const fileName = `jbrowse_bookmarks_${assembly}.bed`\n      saveAs(blob, fileName)\n    }\n  } else {\n    // TSV\n    const fileHeader = 'chrom\\tstart\\tend\\tlabel\\tassembly_name\\tcoord_range\\n'\n\n    const fileContents = bookmarksToDownload\n      .map(bookmark => {\n        const { label } = bookmark\n        const labelVal = label === '' ? '.' : label\n        const locString = assembleLocString(bookmark)\n        return `${bookmark.refName}\\t${bookmark.start + 1}\\t${\n          bookmark.end\n        }\\t${labelVal}\\t${bookmark.assemblyName}\\t${locString}\\n`\n      })\n      .reduce((a, b) => a + b, fileHeader)\n\n    const blob = new Blob([fileContents || ''], {\n      type: 'text/tab-separated-values;charset=utf-8',\n    })\n    const fileName = 'jbrowse_bookmarks.tsv'\n    saveAs(blob, fileName)\n  }\n}\n\n/**\n * Pad the end of a base64 string with \"=\" to make it valid\n * @param b64 - unpadded b64 string\n */\nexport function b64PadSuffix(b64: string): string {\n  let num = 0\n  const mo = b64.length % 4\n  switch (mo) {\n    case 3:\n      num = 1\n      break\n    case 2:\n      num = 2\n      break\n    case 0:\n      num = 0\n      break\n    default:\n      throw new Error('base64 not a valid length')\n  }\n  return b64 + '='.repeat(num)\n}\n\n/**\n * Decode and inflate a url-safe base64 to a string\n * See {@link https://en.wikipedia.org/wiki/Base64#URL_applications}\n * @param b64 - a base64 string to decode and inflate\n */\nexport async function fromUrlSafeB64(b64: string) {\n  const originalB64 = b64PadSuffix(\n    b64.replaceAll('-', '+').replaceAll('_', '/'),\n  )\n  const { toByteArray } = await import('base64-js')\n  const { inflate } = await import('pako')\n  const bytes = toByteArray(originalB64)\n  const inflated = inflate(bytes)\n  return new TextDecoder().decode(inflated)\n}\n\n/**\n * Compress and encode a string as url-safe base64\n * See {@link https://en.wikipedia.org/wiki/Base64#URL_applications}\n * @param str-  a string to compress and encode\n */\nexport async function toUrlSafeB64(str: string) {\n  const bytes = new TextEncoder().encode(str)\n  const { deflate } = await import('pako')\n  const { fromByteArray } = await import('base64-js')\n  const deflated = deflate(bytes)\n  const encoded = fromByteArray(deflated)\n  const pos = encoded.indexOf('=')\n  return pos > 0\n    ? encoded.slice(0, pos).replaceAll('+', '-').replaceAll('/', '_')\n    : encoded.replaceAll('+', '-').replaceAll('/', '_')\n}\n"],"names":["EditBookmarkLabelDialog","lazy","useStyles","makeStyles","cell","whiteSpace","overflow","textOverflow","observer","model","classes","bookmarks","bookmarksWithValidAssemblies","selectedAssemblies","selectedBookmarks","session","getSession","selectedSet","Set","rows","filter","r","has","assemblyName","map","region","index","rest","id","locString","assembleLocString","correspondingObj","widths","Math","max","measureText","measureGridWidth","row","label","React","DataGrid","autoHeight","density","columns","GRID_CHECKBOX_SELECTION_COL_DEF","width","field","headerName","renderCell","value","Link","className","href","onClick","async","event","preventDefault","views","navToBookmark","editable","ColorPicker","color","onChange","updateBookmarkHighlight","onCellDoubleClick","queueDialog","onClose","dialogRow","processRowUpdate","target","updateBookmarkLabel","onProcessRowUpdateError","e","notifyError","checkboxSelection","onRowSelectionModelChange","newRowSelectionModel","length","setSelectedBookmarks","rowSelectionModel","disableRowSelectionOnClick","validAssemblies","noAssemblies","size","isAllSelected","every","FormControl","disabled","fullWidth","InputLabel","Select","labelId","multiple","setSelectedAssemblies","input","OutlinedInput","renderValue","selected","join","MenuItem","onClickCapture","undefined","Checkbox","checked","indeterminate","ListItemText","primary","name","key","includes","ExportBookmarksDialog","ImportBookmarksDialog","ShareBookmarksDialog","HighlightSettingsDialog","EditHighlightColorDialog","DeleteBookmarksDialog","flex","display","Alert","severity","CascadingMenuButton","menuItems","icon","GetApp","Publish","Delete","Share","Palette","Settings","Menu","AssemblySelector","BookmarkGrid","assembly","view","find","focusedViewId","assemblyNames","elt","type","newViewId","addView","navToLocString","console","error","downloadBookmarkFile","fileFormat","bookmarksToDownload","fileHeader","fileContents","forEach","bookmark","labelVal","line","refName","start","end","push","fileContent","reduce","a","b","blob","Blob","fileName","saveAs","fromUrlSafeB64","b64","originalB64","num","Error","repeat","b64PadSuffix","replaceAll","toByteArray","inflate","inflated","TextDecoder","decode","toUrlSafeB64","str","bytes","TextEncoder","encode","deflate","fromByteArray","encoded","pos","indexOf","slice"],"sourceRoot":""}