@weng-lab/genomebrowser-ui 0.4.1 → 0.4.2

package/dist/genomebrowser-ui.es.js.map

@@ -1 +1 @@
-{"version":3,"file":"genomebrowser-ui.es.js","sources":["../src/muiLicense.ts","../../../node_modules/.pnpm/react@19.2.3/node_modules/react/cjs/react-jsx-runtime.production.js","../../../node_modules/.pnpm/react@19.2.3/node_modules/react/cjs/react-jsx-runtime.development.js","../../../node_modules/.pnpm/react@19.2.3/node_modules/react/jsx-runtime.js","../src/TrackSelect/DataGrid/DefaultGroupingCell.tsx","../src/TrackSelect/DataGrid/DataGridWrapper.tsx","../src/TrackSelect/Dialogs/ClearDialog.tsx","../src/TrackSelect/Dialogs/LimitDialog.tsx","../src/TrackSelect/Dialogs/ResetDialog.tsx","../src/TrackSelect/FolderList/Breadcrumb.tsx","../src/TrackSelect/FolderList/FolderCard.tsx","../src/TrackSelect/FolderList/FolderList.tsx","../src/TrackSelect/managedTracks.ts","../src/TrackSelect/resolveFolderView.ts","../src/TrackSelect/buildSelectedTree.ts","../src/TrackSelect/TreeView/CustomTreeItem.tsx","../src/TrackSelect/TreeView/TreeViewWrapper.tsx","../src/TrackSelect/TrackSelect.tsx","../src/TrackSelect/Folders/biosamples/shared/constants.tsx","../src/TrackSelect/Folders/biosamples/shared/columns.tsx","../src/TrackSelect/Folders/biosamples/shared/BiosampleViewSelector.tsx","../src/TrackSelect/Folders/biosamples/shared/BiosampleGroupingCell.tsx","../src/TrackSelect/Folders/biosamples/shared/BiosampleTreeItem.tsx","../src/TrackSelect/Folders/biosamples/shared/toTrack.ts","../src/TrackSelect/Folders/biosamples/shared/createFolder.ts","../src/TrackSelect/Folders/biosamples/human.ts","../src/TrackSelect/Folders/biosamples/mouse.ts","../src/TrackSelect/Folders/genes/shared/columns.tsx","../src/TrackSelect/Folders/genes/shared/toTrack.ts","../src/TrackSelect/Folders/genes/shared/createFolder.ts","../src/TrackSelect/Folders/genes/human.ts","../src/TrackSelect/Folders/genes/mouse.ts","../src/TrackSelect/Folders/other-tracks/shared/columns.tsx","../../../node_modules/.pnpm/logo-test@0.0.5_react-dom@19.2.3_react@19.2.3__react@19.2.3/node_modules/logo-test/dist/logo-test.es.js","../src/TrackSelect/Custom/TfPeaks.tsx","../src/TrackSelect/Folders/other-tracks/shared/toTrack.ts","../src/TrackSelect/Folders/other-tracks/shared/createFolder.ts","../src/TrackSelect/Folders/other-tracks/human.ts","../src/TrackSelect/Folders/mohd/shared/config.tsx","../src/TrackSelect/Folders/mohd/shared/columns.tsx","../src/TrackSelect/Folders/mohd/shared/MohdGroupingCell.tsx","../src/TrackSelect/Folders/mohd/shared/MohdTreeItem.tsx","../src/TrackSelect/Folders/mohd/shared/bigBedSchemas.ts","../src/TrackSelect/Folders/mohd/shared/MohdBigBedTooltip.tsx","../src/TrackSelect/Folders/mohd/shared/toTrack.ts","../src/TrackSelect/Folders/mohd/shared/MohdViewSelector.tsx","../src/TrackSelect/Folders/mohd/shared/createFolder.ts","../src/TrackSelect/Folders/mohd/human.ts","../src/TrackSelect/Folders/psychscreen/shared/columns.tsx","../src/TrackSelect/Folders/psychscreen/shared/PsychscreenGroupingCell.tsx","../src/TrackSelect/Folders/psychscreen/shared/toTrack.ts","../src/TrackSelect/Folders/psychscreen/shared/createFolder.ts","../src/TrackSelect/Folders/psychscreen/human.ts","../src/TrackSelect/Folders/index.ts"],"sourcesContent":["import { LicenseInfo } from \"@mui/x-license\";\n\nconst muiLicenseKey =\n  import.meta.env.NEXT_PUBLIC_MUI_X_LICENSE_KEY ??\n  import.meta.env.VITE_MUI_X_LICENSE_KEY;\n\nif (muiLicenseKey) {\n  LicenseInfo.setLicenseKey(muiLicenseKey);\n}\n","/**\n * @license React\n * react-jsx-runtime.production.js\n *\n * Copyright (c) Meta Platforms, Inc. and affiliates.\n *\n * This source code is licensed under the MIT license found in the\n * LICENSE file in the root directory of this source tree.\n */\n\n\"use strict\";\nvar REACT_ELEMENT_TYPE = Symbol.for(\"react.transitional.element\"),\n  REACT_FRAGMENT_TYPE = Symbol.for(\"react.fragment\");\nfunction jsxProd(type, config, maybeKey) {\n  var key = null;\n  void 0 !== maybeKey && (key = \"\" + maybeKey);\n  void 0 !== config.key && (key = \"\" + config.key);\n  if (\"key\" in config) {\n    maybeKey = {};\n    for (var propName in config)\n      \"key\" !== propName && (maybeKey[propName] = config[propName]);\n  } else maybeKey = config;\n  config = maybeKey.ref;\n  return {\n    $$typeof: REACT_ELEMENT_TYPE,\n    type: type,\n    key: key,\n    ref: void 0 !== config ? config : null,\n    props: maybeKey\n  };\n}\nexports.Fragment = REACT_FRAGMENT_TYPE;\nexports.jsx = jsxProd;\nexports.jsxs = jsxProd;\n","/**\n * @license React\n * react-jsx-runtime.development.js\n *\n * Copyright (c) Meta Platforms, Inc. and affiliates.\n *\n * This source code is licensed under the MIT license found in the\n * LICENSE file in the root directory of this source tree.\n */\n\n\"use strict\";\n\"production\" !== process.env.NODE_ENV &&\n  (function () {\n    function getComponentNameFromType(type) {\n      if (null == type) return null;\n      if (\"function\" === typeof type)\n        return type.$$typeof === REACT_CLIENT_REFERENCE\n          ? null\n          : type.displayName || type.name || null;\n      if (\"string\" === typeof type) return type;\n      switch (type) {\n        case REACT_FRAGMENT_TYPE:\n          return \"Fragment\";\n        case REACT_PROFILER_TYPE:\n          return \"Profiler\";\n        case REACT_STRICT_MODE_TYPE:\n          return \"StrictMode\";\n        case REACT_SUSPENSE_TYPE:\n          return \"Suspense\";\n        case REACT_SUSPENSE_LIST_TYPE:\n          return \"SuspenseList\";\n        case REACT_ACTIVITY_TYPE:\n          return \"Activity\";\n      }\n      if (\"object\" === typeof type)\n        switch (\n          (\"number\" === typeof type.tag &&\n            console.error(\n              \"Received an unexpected object in getComponentNameFromType(). This is likely a bug in React. Please file an issue.\"\n            ),\n          type.$$typeof)\n        ) {\n          case REACT_PORTAL_TYPE:\n            return \"Portal\";\n          case REACT_CONTEXT_TYPE:\n            return type.displayName || \"Context\";\n          case REACT_CONSUMER_TYPE:\n            return (type._context.displayName || \"Context\") + \".Consumer\";\n          case REACT_FORWARD_REF_TYPE:\n            var innerType = type.render;\n            type = type.displayName;\n            type ||\n              ((type = innerType.displayName || innerType.name || \"\"),\n              (type = \"\" !== type ? \"ForwardRef(\" + type + \")\" : \"ForwardRef\"));\n            return type;\n          case REACT_MEMO_TYPE:\n            return (\n              (innerType = type.displayName || null),\n              null !== innerType\n                ? innerType\n                : getComponentNameFromType(type.type) || \"Memo\"\n            );\n          case REACT_LAZY_TYPE:\n            innerType = type._payload;\n            type = type._init;\n            try {\n              return getComponentNameFromType(type(innerType));\n            } catch (x) {}\n        }\n      return null;\n    }\n    function testStringCoercion(value) {\n      return \"\" + value;\n    }\n    function checkKeyStringCoercion(value) {\n      try {\n        testStringCoercion(value);\n        var JSCompiler_inline_result = !1;\n      } catch (e) {\n        JSCompiler_inline_result = !0;\n      }\n      if (JSCompiler_inline_result) {\n        JSCompiler_inline_result = console;\n        var JSCompiler_temp_const = JSCompiler_inline_result.error;\n        var JSCompiler_inline_result$jscomp$0 =\n          (\"function\" === typeof Symbol &&\n            Symbol.toStringTag &&\n            value[Symbol.toStringTag]) ||\n          value.constructor.name ||\n          \"Object\";\n        JSCompiler_temp_const.call(\n          JSCompiler_inline_result,\n          \"The provided key is an unsupported type %s. This value must be coerced to a string before using it here.\",\n          JSCompiler_inline_result$jscomp$0\n        );\n        return testStringCoercion(value);\n      }\n    }\n    function getTaskName(type) {\n      if (type === REACT_FRAGMENT_TYPE) return \"<>\";\n      if (\n        \"object\" === typeof type &&\n        null !== type &&\n        type.$$typeof === REACT_LAZY_TYPE\n      )\n        return \"<...>\";\n      try {\n        var name = getComponentNameFromType(type);\n        return name ? \"<\" + name + \">\" : \"<...>\";\n      } catch (x) {\n        return \"<...>\";\n      }\n    }\n    function getOwner() {\n      var dispatcher = ReactSharedInternals.A;\n      return null === dispatcher ? null : dispatcher.getOwner();\n    }\n    function UnknownOwner() {\n      return Error(\"react-stack-top-frame\");\n    }\n    function hasValidKey(config) {\n      if (hasOwnProperty.call(config, \"key\")) {\n        var getter = Object.getOwnPropertyDescriptor(config, \"key\").get;\n        if (getter && getter.isReactWarning) return !1;\n      }\n      return void 0 !== config.key;\n    }\n    function defineKeyPropWarningGetter(props, displayName) {\n      function warnAboutAccessingKey() {\n        specialPropKeyWarningShown ||\n          ((specialPropKeyWarningShown = !0),\n          console.error(\n            \"%s: `key` is not a prop. Trying to access it will result in `undefined` being returned. If you need to access the same value within the child component, you should pass it as a different prop. (https://react.dev/link/special-props)\",\n            displayName\n          ));\n      }\n      warnAboutAccessingKey.isReactWarning = !0;\n      Object.defineProperty(props, \"key\", {\n        get: warnAboutAccessingKey,\n        configurable: !0\n      });\n    }\n    function elementRefGetterWithDeprecationWarning() {\n      var componentName = getComponentNameFromType(this.type);\n      didWarnAboutElementRef[componentName] ||\n        ((didWarnAboutElementRef[componentName] = !0),\n        console.error(\n          \"Accessing element.ref was removed in React 19. ref is now a regular prop. It will be removed from the JSX Element type in a future release.\"\n        ));\n      componentName = this.props.ref;\n      return void 0 !== componentName ? componentName : null;\n    }\n    function ReactElement(type, key, props, owner, debugStack, debugTask) {\n      var refProp = props.ref;\n      type = {\n        $$typeof: REACT_ELEMENT_TYPE,\n        type: type,\n        key: key,\n        props: props,\n        _owner: owner\n      };\n      null !== (void 0 !== refProp ? refProp : null)\n        ? Object.defineProperty(type, \"ref\", {\n            enumerable: !1,\n            get: elementRefGetterWithDeprecationWarning\n          })\n        : Object.defineProperty(type, \"ref\", { enumerable: !1, value: null });\n      type._store = {};\n      Object.defineProperty(type._store, \"validated\", {\n        configurable: !1,\n        enumerable: !1,\n        writable: !0,\n        value: 0\n      });\n      Object.defineProperty(type, \"_debugInfo\", {\n        configurable: !1,\n        enumerable: !1,\n        writable: !0,\n        value: null\n      });\n      Object.defineProperty(type, \"_debugStack\", {\n        configurable: !1,\n        enumerable: !1,\n        writable: !0,\n        value: debugStack\n      });\n      Object.defineProperty(type, \"_debugTask\", {\n        configurable: !1,\n        enumerable: !1,\n        writable: !0,\n        value: debugTask\n      });\n      Object.freeze && (Object.freeze(type.props), Object.freeze(type));\n      return type;\n    }\n    function jsxDEVImpl(\n      type,\n      config,\n      maybeKey,\n      isStaticChildren,\n      debugStack,\n      debugTask\n    ) {\n      var children = config.children;\n      if (void 0 !== children)\n        if (isStaticChildren)\n          if (isArrayImpl(children)) {\n            for (\n              isStaticChildren = 0;\n              isStaticChildren < children.length;\n              isStaticChildren++\n            )\n              validateChildKeys(children[isStaticChildren]);\n            Object.freeze && Object.freeze(children);\n          } else\n            console.error(\n              \"React.jsx: Static children should always be an array. You are likely explicitly calling React.jsxs or React.jsxDEV. Use the Babel transform instead.\"\n            );\n        else validateChildKeys(children);\n      if (hasOwnProperty.call(config, \"key\")) {\n        children = getComponentNameFromType(type);\n        var keys = Object.keys(config).filter(function (k) {\n          return \"key\" !== k;\n        });\n        isStaticChildren =\n          0 < keys.length\n            ? \"{key: someKey, \" + keys.join(\": ..., \") + \": ...}\"\n            : \"{key: someKey}\";\n        didWarnAboutKeySpread[children + isStaticChildren] ||\n          ((keys =\n            0 < keys.length ? \"{\" + keys.join(\": ..., \") + \": ...}\" : \"{}\"),\n          console.error(\n            'A props object containing a \"key\" prop is being spread into JSX:\\n  let props = %s;\\n  <%s {...props} />\\nReact keys must be passed directly to JSX without using spread:\\n  let props = %s;\\n  <%s key={someKey} {...props} />',\n            isStaticChildren,\n            children,\n            keys,\n            children\n          ),\n          (didWarnAboutKeySpread[children + isStaticChildren] = !0));\n      }\n      children = null;\n      void 0 !== maybeKey &&\n        (checkKeyStringCoercion(maybeKey), (children = \"\" + maybeKey));\n      hasValidKey(config) &&\n        (checkKeyStringCoercion(config.key), (children = \"\" + config.key));\n      if (\"key\" in config) {\n        maybeKey = {};\n        for (var propName in config)\n          \"key\" !== propName && (maybeKey[propName] = config[propName]);\n      } else maybeKey = config;\n      children &&\n        defineKeyPropWarningGetter(\n          maybeKey,\n          \"function\" === typeof type\n            ? type.displayName || type.name || \"Unknown\"\n            : type\n        );\n      return ReactElement(\n        type,\n        children,\n        maybeKey,\n        getOwner(),\n        debugStack,\n        debugTask\n      );\n    }\n    function validateChildKeys(node) {\n      isValidElement(node)\n        ? node._store && (node._store.validated = 1)\n        : \"object\" === typeof node &&\n          null !== node &&\n          node.$$typeof === REACT_LAZY_TYPE &&\n          (\"fulfilled\" === node._payload.status\n            ? isValidElement(node._payload.value) &&\n              node._payload.value._store &&\n              (node._payload.value._store.validated = 1)\n            : node._store && (node._store.validated = 1));\n    }\n    function isValidElement(object) {\n      return (\n        \"object\" === typeof object &&\n        null !== object &&\n        object.$$typeof === REACT_ELEMENT_TYPE\n      );\n    }\n    var React = require(\"react\"),\n      REACT_ELEMENT_TYPE = Symbol.for(\"react.transitional.element\"),\n      REACT_PORTAL_TYPE = Symbol.for(\"react.portal\"),\n      REACT_FRAGMENT_TYPE = Symbol.for(\"react.fragment\"),\n      REACT_STRICT_MODE_TYPE = Symbol.for(\"react.strict_mode\"),\n      REACT_PROFILER_TYPE = Symbol.for(\"react.profiler\"),\n      REACT_CONSUMER_TYPE = Symbol.for(\"react.consumer\"),\n      REACT_CONTEXT_TYPE = Symbol.for(\"react.context\"),\n      REACT_FORWARD_REF_TYPE = Symbol.for(\"react.forward_ref\"),\n      REACT_SUSPENSE_TYPE = Symbol.for(\"react.suspense\"),\n      REACT_SUSPENSE_LIST_TYPE = Symbol.for(\"react.suspense_list\"),\n      REACT_MEMO_TYPE = Symbol.for(\"react.memo\"),\n      REACT_LAZY_TYPE = Symbol.for(\"react.lazy\"),\n      REACT_ACTIVITY_TYPE = Symbol.for(\"react.activity\"),\n      REACT_CLIENT_REFERENCE = Symbol.for(\"react.client.reference\"),\n      ReactSharedInternals =\n        React.__CLIENT_INTERNALS_DO_NOT_USE_OR_WARN_USERS_THEY_CANNOT_UPGRADE,\n      hasOwnProperty = Object.prototype.hasOwnProperty,\n      isArrayImpl = Array.isArray,\n      createTask = console.createTask\n        ? console.createTask\n        : function () {\n            return null;\n          };\n    React = {\n      react_stack_bottom_frame: function (callStackForError) {\n        return callStackForError();\n      }\n    };\n    var specialPropKeyWarningShown;\n    var didWarnAboutElementRef = {};\n    var unknownOwnerDebugStack = React.react_stack_bottom_frame.bind(\n      React,\n      UnknownOwner\n    )();\n    var unknownOwnerDebugTask = createTask(getTaskName(UnknownOwner));\n    var didWarnAboutKeySpread = {};\n    exports.Fragment = REACT_FRAGMENT_TYPE;\n    exports.jsx = function (type, config, maybeKey) {\n      var trackActualOwner =\n        1e4 > ReactSharedInternals.recentlyCreatedOwnerStacks++;\n      return jsxDEVImpl(\n        type,\n        config,\n        maybeKey,\n        !1,\n        trackActualOwner\n          ? Error(\"react-stack-top-frame\")\n          : unknownOwnerDebugStack,\n        trackActualOwner ? createTask(getTaskName(type)) : unknownOwnerDebugTask\n      );\n    };\n    exports.jsxs = function (type, config, maybeKey) {\n      var trackActualOwner =\n        1e4 > ReactSharedInternals.recentlyCreatedOwnerStacks++;\n      return jsxDEVImpl(\n        type,\n        config,\n        maybeKey,\n        !0,\n        trackActualOwner\n          ? Error(\"react-stack-top-frame\")\n          : unknownOwnerDebugStack,\n        trackActualOwner ? createTask(getTaskName(type)) : unknownOwnerDebugTask\n      );\n    };\n  })();\n","'use strict';\n\nif (process.env.NODE_ENV === 'production') {\n  module.exports = require('./cjs/react-jsx-runtime.production.js');\n} else {\n  module.exports = require('./cjs/react-jsx-runtime.development.js');\n}\n","import { Tooltip, Box, IconButton } from \"@mui/material\";\nimport {\n  GridRenderCellParams,\n  useGridApiContext,\n  GridGroupNode,\n} from \"@mui/x-data-grid-premium\";\nimport ChevronRightIcon from \"@mui/icons-material/ChevronRight\";\nimport ExpandMoreIcon from \"@mui/icons-material/ExpandMore\";\n\n/**\n * Default grouping cell that handles expand/collapse, truncation, and tooltips.\n * This is a generic implementation without any folder-specific logic.\n */\nexport function DefaultGroupingCell(params: GridRenderCellParams) {\n  const apiRef = useGridApiContext();\n  const isGroup = params.rowNode.type === \"group\";\n  const groupNode = params.rowNode as GridGroupNode;\n  const isExpanded = isGroup ? groupNode.childrenExpanded : false;\n  const depth = params.rowNode.depth ?? 0;\n\n  const handleExpandClick = (e: React.MouseEvent) => {\n    e.stopPropagation();\n    apiRef.current.setRowChildrenExpansion(params.id, !isExpanded);\n  };\n\n  const value = String(params.value ?? \"\");\n\n  // Indent based on depth (2 units per level)\n  const indentLevel = depth * 2;\n\n  return (\n    <Box\n      sx={{\n        display: \"flex\",\n        alignItems: \"center\",\n        width: \"100%\",\n        ml: indentLevel,\n      }}\n    >\n      {isGroup && (\n        <IconButton size=\"small\" onClick={handleExpandClick} sx={{ mr: 0.5 }}>\n          {isExpanded ? (\n            <ExpandMoreIcon fontSize=\"small\" />\n          ) : (\n            <ChevronRightIcon fontSize=\"small\" />\n          )}\n        </IconButton>\n      )}\n      <Tooltip title={value} placement=\"top-start\" enterDelay={500}>\n        <Box\n          sx={{\n            overflow: \"hidden\",\n            textOverflow: \"ellipsis\",\n            whiteSpace: \"nowrap\",\n            flex: 1,\n            fontWeight: isGroup ? \"bold\" : undefined,\n          }}\n        >\n          {params.formattedValue}\n        </Box>\n      </Tooltip>\n    </Box>\n  );\n}\n","import { Box, Paper } from \"@mui/material\";\nimport {\n  DataGridPremium,\n  FilterColumnsArgs,\n  GridAutosizeOptions,\n  GridColDef,\n  GridColumnVisibilityModel,\n  GridRenderCellParams,\n  GridRowSelectionModel,\n  useGridApiRef,\n} from \"@mui/x-data-grid-premium\";\nimport { useEffect, useMemo, useState } from \"react\";\nimport { DataGridProps } from \"../types\";\nimport { DefaultGroupingCell } from \"./DefaultGroupingCell\";\n\nconst autosizeOptions: GridAutosizeOptions = {\n  expand: true,\n  includeHeaders: true,\n  outliersFactor: 1.5,\n};\n\nexport function DataGridWrapper(props: DataGridProps) {\n  const {\n    columns,\n    groupingModel,\n    leafField,\n    onSelectionChange,\n    rows,\n    selectedIds,\n    GroupingCellComponent,\n  } = props;\n\n  const GroupingCell = GroupingCellComponent ?? DefaultGroupingCell;\n\n  const apiRef = useGridApiRef();\n\n  useEffect(() => {\n    if (apiRef.current && apiRef.current.autosizeColumns) {\n      apiRef.current.autosizeColumns(autosizeOptions);\n    }\n  }, [columns, groupingModel, leafField]);\n\n  const baseVisibility = useMemo(() => {\n    const visibility: GridColumnVisibilityModel = {\n      id: false,\n    };\n\n    // Only hide leafField if we have grouping (it shows in grouping column)\n    if (groupingModel.length > 0) {\n      visibility[leafField] = false;\n    }\n\n    groupingModel.forEach((field) => {\n      visibility[field] = false;\n    });\n\n    return visibility;\n  }, [groupingModel, leafField]);\n\n  const [columnVisibilityModel, setColumnVisibilityModel] =\n    useState<GridColumnVisibilityModel>(baseVisibility);\n\n  useEffect(() => {\n    setColumnVisibilityModel(baseVisibility);\n  }, [baseVisibility]);\n\n  // functions to customize the column and filter panel in the toolbar\n  const filterColumns = ({ columns }: FilterColumnsArgs) => {\n    return columns\n      .filter((column) => column.type !== \"custom\")\n      .map((column) => column.field);\n  };\n\n  const getTogglableColumns = (columns: GridColDef[]) => {\n    return columns\n      .filter((column) => column.type !== \"custom\")\n      .map((column) => column.field);\n  };\n\n  return (\n    <Paper sx={{ width: \"100%\" }}>\n      <Box\n        sx={{\n          height: 500,\n          width: \"100%\",\n          overflow: \"auto\",\n        }}\n      >\n        <DataGridPremium\n          apiRef={apiRef}\n          rows={rows}\n          columns={columns}\n          getRowId={(row: { id: string }) => row.id}\n          autosizeOptions={autosizeOptions}\n          rowGroupingModel={groupingModel}\n          groupingColDef={{\n            leafField,\n            display: \"flex\",\n            minWidth: 300,\n            maxWidth: 500,\n            flex: 2,\n            renderCell: (params: GridRenderCellParams) => (\n              <GroupingCell {...params} />\n            ),\n          }}\n          columnVisibilityModel={columnVisibilityModel}\n          onColumnVisibilityModelChange={setColumnVisibilityModel}\n          onRowSelectionModelChange={(selection: GridRowSelectionModel) => {\n            const ids = selection.ids ?? new Set<string>();\n            onSelectionChange(new Set([...ids].map(String)));\n          }}\n          rowSelectionPropagation={{ descendants: true, parents: false }}\n          disableRowGrouping={false}\n          rowSelectionModel={{\n            type: \"include\",\n            ids: selectedIds,\n          }}\n          slotProps={{\n            filterPanel: {\n              filterFormProps: {\n                filterColumns,\n              },\n            },\n            columnsManagement: {\n              getTogglableColumns,\n            },\n          }}\n          keepNonExistentRowsSelected\n          showToolbar\n          disableAggregation\n          disableRowSelectionExcludeModel\n          disablePivoting\n          checkboxSelection\n          autosizeOnMount\n          pagination\n          hideFooterSelectedRowCount\n        />\n      </Box>\n    </Paper>\n  );\n}\n","import {\n  Button,\n  Dialog,\n  DialogActions,\n  DialogContent,\n  DialogContentText,\n  DialogTitle,\n} from \"@mui/material\";\n\ninterface ClearDialogProps {\n  open: boolean;\n  onClose: () => void;\n  onConfirm: () => void;\n  folderLabel: string;\n  clearAll: boolean;\n}\n\nexport function ClearDialog({\n  open,\n  onClose,\n  onConfirm,\n  folderLabel,\n  clearAll,\n}: ClearDialogProps) {\n  return (\n    <Dialog open={open} onClose={onClose}>\n      <DialogTitle\n        sx={{\n          bgcolor: \"primary.main\",\n          color: \"primary.contrastText\",\n          fontWeight: \"bold\",\n        }}\n      >\n        {clearAll ? \"Clear All Folders\" : `Clear ${folderLabel}`}\n      </DialogTitle>\n      <DialogContent sx={{ mt: 2 }}>\n        <DialogContentText>\n          {clearAll ? (\n            \"Are you sure you want to clear all selections?\"\n          ) : (\n            <>\n              Are you sure you want to clear the selection for{\" \"}\n              <strong>{folderLabel}</strong>?\n            </>\n          )}\n        </DialogContentText>\n      </DialogContent>\n      <DialogActions sx={{ justifyContent: \"center\", gap: 2, pb: 2 }}>\n        <Button variant=\"contained\" color=\"primary\" onClick={onClose} autoFocus>\n          Cancel\n        </Button>\n        <Button variant=\"outlined\" color=\"secondary\" onClick={onConfirm}>\n          Clear\n        </Button>\n      </DialogActions>\n    </Dialog>\n  );\n}\n","import {\n  Button,\n  Dialog,\n  DialogActions,\n  DialogContent,\n  DialogContentText,\n  DialogTitle,\n} from \"@mui/material\";\n\ninterface LimitDialogProps {\n  open: boolean;\n  onClose: () => void;\n  maxTracks: number;\n}\n\nexport function LimitDialog({ open, onClose, maxTracks }: LimitDialogProps) {\n  return (\n    <Dialog open={open} onClose={onClose}>\n      <DialogTitle>Track Limit Reached</DialogTitle>\n      <DialogContent>\n        <DialogContentText>\n          You can select up to {maxTracks} tracks at a time. Please remove a\n          track before adding another.\n        </DialogContentText>\n      </DialogContent>\n      <DialogActions>\n        <Button onClick={onClose} autoFocus>\n          OK\n        </Button>\n      </DialogActions>\n    </Dialog>\n  );\n}\n","import {\n  Button,\n  Dialog,\n  DialogActions,\n  DialogContent,\n  DialogContentText,\n  DialogTitle,\n} from \"@mui/material\";\n\ninterface ResetDialogProps {\n  open: boolean;\n  onClose: () => void;\n  onConfirm: () => void;\n}\n\nexport function ResetDialog({ open, onClose, onConfirm }: ResetDialogProps) {\n  return (\n    <Dialog open={open} onClose={onClose}>\n      <DialogTitle\n        sx={{\n          bgcolor: \"primary.main\",\n          color: \"primary.contrastText\",\n          fontWeight: \"bold\",\n        }}\n      >\n        Reset to Browser State\n      </DialogTitle>\n      <DialogContent sx={{ mt: 2 }}>\n        <DialogContentText>\n          Are you sure you want to reset all selections to the current browser\n          state?\n        </DialogContentText>\n      </DialogContent>\n      <DialogActions sx={{ justifyContent: \"center\", gap: 2, pb: 2 }}>\n        <Button variant=\"contained\" color=\"primary\" onClick={onClose} autoFocus>\n          Cancel\n        </Button>\n        <Button variant=\"outlined\" color=\"secondary\" onClick={onConfirm}>\n          Reset\n        </Button>\n      </DialogActions>\n    </Dialog>\n  );\n}\n","import { Breadcrumbs, Link, Typography } from \"@mui/material\";\nimport NavigateNextIcon from \"@mui/icons-material/NavigateNext\";\nimport { FolderDefinition } from \"../Folders/types\";\n\nexport interface BreadcrumbProps {\n  currentFolder: FolderDefinition | null;\n  onNavigateToRoot: () => void;\n}\n\nexport function Breadcrumb({\n  currentFolder,\n  onNavigateToRoot,\n}: BreadcrumbProps) {\n  return (\n    <Breadcrumbs separator={<NavigateNextIcon fontSize=\"small\" />}>\n      {currentFolder ? (\n        <Link\n          component=\"button\"\n          variant=\"body1\"\n          onClick={onNavigateToRoot}\n          underline=\"hover\"\n          sx={{ cursor: \"pointer\" }}\n        >\n          All Folders\n        </Link>\n      ) : (\n        <Typography variant=\"body1\" color=\"text.primary\">\n          All Folders\n        </Typography>\n      )}\n      {currentFolder && (\n        <Typography variant=\"body1\" color=\"text.primary\">\n          {currentFolder.label}\n        </Typography>\n      )}\n    </Breadcrumbs>\n  );\n}\n","import { Paper, Typography } from \"@mui/material\";\nimport { FolderDefinition } from \"../Folders/types\";\n\nexport interface FolderCardProps {\n  folder: FolderDefinition;\n  onClick: () => void;\n}\n\nexport function FolderCard({ folder, onClick }: FolderCardProps) {\n  return (\n    <Paper\n      elevation={1}\n      onClick={onClick}\n      onKeyDown={(e) => {\n        if (e.key === \"Enter\" || e.key === \" \") {\n          e.preventDefault();\n          onClick();\n        }\n      }}\n      role=\"button\"\n      tabIndex={0}\n      sx={{\n        p: 3,\n        cursor: \"pointer\",\n        transition: \"all 0.2s ease-in-out\",\n        \"&:hover\": {\n          elevation: 3,\n          boxShadow: 3,\n          bgcolor: \"action.hover\",\n        },\n        \"&:focus\": {\n          outline: \"2px solid\",\n          outlineColor: \"primary.main\",\n          outlineOffset: 2,\n        },\n      }}\n    >\n      <Typography variant=\"h6\" gutterBottom>\n        {folder.label}\n      </Typography>\n      {folder.description && (\n        <Typography variant=\"body2\" color=\"text.secondary\" gutterBottom>\n          {folder.description}\n        </Typography>\n      )}\n      <Typography variant=\"caption\" color=\"text.secondary\">\n        {folder.rows.length.toLocaleString()} tracks available\n      </Typography>\n    </Paper>\n  );\n}\n","import { Paper, Stack, Typography } from \"@mui/material\";\nimport { FolderDefinition } from \"../Folders/types\";\nimport { FolderCard } from \"./FolderCard\";\n\nexport interface FolderListProps {\n  folders: FolderDefinition[];\n  onFolderSelect: (folderId: string) => void;\n}\n\nexport function FolderList({ folders, onFolderSelect }: FolderListProps) {\n  if (folders.length === 0) {\n    return (\n      <Paper\n        variant=\"outlined\"\n        sx={{\n          height: 500,\n          borderWidth: 2,\n        }}\n      >\n        <Typography color=\"text.secondary\" sx={{ p: 3 }}>\n          No folders available\n        </Typography>\n      </Paper>\n    );\n  }\n\n  return (\n    <Paper\n      variant=\"outlined\"\n      sx={{\n        height: 500,\n        overflow: \"auto\",\n        borderWidth: 2,\n      }}\n    >\n      <Stack spacing={2} sx={{ p: 2 }}>\n        {folders.map((folder) => (\n          <FolderCard\n            key={folder.id}\n            folder={folder}\n            onClick={() => onFolderSelect(folder.id)}\n          />\n        ))}\n      </Stack>\n    </Paper>\n  );\n}\n","import { Track } from \"@weng-lab/genomebrowser\";\nimport { Assembly, FolderDefinition } from \"./Folders/types\";\nimport type { TrackSelectTrackContext } from \"./trackContext\";\n\nconst buildManagedTrack = ({\n  assembly,\n  folder,\n  id,\n  trackContext,\n}: {\n  assembly: Assembly;\n  folder: FolderDefinition;\n  id: string;\n  trackContext?: TrackSelectTrackContext;\n}) => {\n  const row = folder.rows.find((candidate) => candidate.id === id);\n  if (!row) {\n    return null;\n  }\n\n  const track = folder.createTrack(row, { assembly, trackContext });\n  if (!track) {\n    return null;\n  }\n\n  return track;\n};\n\nexport const diffManagedTracks = ({\n  assembly,\n  currentTracks,\n  folders,\n  selectedByFolder,\n  trackContext,\n}: {\n  assembly: Assembly;\n  currentTracks: Track[];\n  folders: FolderDefinition[];\n  selectedByFolder: Map<string, Set<string>>;\n  trackContext?: TrackSelectTrackContext;\n}) => {\n  const nextManagedIds = new Set<string>();\n  const currentManagedIds = new Set<string>();\n  const idsToRemove: string[] = [];\n  const tracksToAdd: Track[] = [];\n\n  currentTracks.forEach((track) => {\n    if (folders.some((folder) => track.id.startsWith(`${folder.id}/`))) {\n      currentManagedIds.add(track.id);\n    }\n  });\n\n  folders.forEach((folder) => {\n    const selectedIds = selectedByFolder.get(folder.id) ?? new Set<string>();\n\n    selectedIds.forEach((id) => {\n      nextManagedIds.add(id);\n    });\n  });\n\n  currentManagedIds.forEach((id) => {\n    if (!nextManagedIds.has(id)) {\n      idsToRemove.push(id);\n    }\n  });\n\n  folders.forEach((folder) => {\n    const selectedIds = selectedByFolder.get(folder.id) ?? new Set<string>();\n\n    selectedIds.forEach((id) => {\n      if (currentManagedIds.has(id)) {\n        return;\n      }\n\n      const track = buildManagedTrack({\n        assembly,\n        folder,\n        id,\n        trackContext,\n      });\n\n      if (track) {\n        tracksToAdd.push(track);\n      }\n    });\n  });\n\n  return {\n    idsToRemove,\n    tracksToAdd,\n  };\n};\n","import { FolderDefinition, FolderView } from \"./Folders/types\";\n\nexport const resolveFolderView = (\n  folder: FolderDefinition,\n  activeViewIdByFolder: Map<string, string>,\n): FolderView => {\n  const activeViewId = activeViewIdByFolder.get(folder.id);\n  const activeView = folder.views?.find((view) => view.id === activeViewId);\n\n  return (\n    activeView ??\n    folder.views?.[0] ?? {\n      id: \"default\",\n      label: folder.label,\n      columns: folder.columns,\n      groupingModel: folder.groupingModel,\n      leafField: folder.leafField,\n    }\n  );\n};\n","import { TreeViewBaseItem } from \"@mui/x-tree-view\";\nimport { ExtendedTreeItemProps } from \"./types\";\n\ntype TreeRow = {\n  id: string;\n  [key: string]: unknown;\n};\n\ntype BuildSelectedTreeOptions = {\n  folderId: string;\n  rootLabel: string;\n  selectedRows: TreeRow[];\n  groupingModel: string[];\n  leafField: string;\n};\n\nconst toLabel = (value: unknown, fallback: string) => {\n  if (value === null || value === undefined || value === \"\") {\n    return fallback;\n  }\n\n  return String(value);\n};\n\nconst isHighlightedField = (field: string) => {\n  return field === \"assay\" || field === \"ome\";\n};\n\nconst createRootNode = (\n  folderId: string,\n  rootLabel: string,\n): TreeViewBaseItem<ExtendedTreeItemProps> => ({\n  id: `${folderId}::root`,\n  kind: \"root\",\n  label: rootLabel,\n  icon: \"folder\",\n  children: [],\n  allExpAccessions: [],\n});\n\nconst createLeafNode = (\n  row: TreeRow,\n  leafField: string,\n): TreeViewBaseItem<ExtendedTreeItemProps> => {\n  const value = row[leafField];\n  const label = toLabel(value, row.id);\n\n  return {\n    id: row.id,\n    kind: \"leaf\",\n    field: leafField,\n    value: label,\n    rowId: row.id,\n    label,\n    icon: \"removeable\",\n    highlightName: isHighlightedField(leafField) ? label : undefined,\n    isHighlightedItem: isHighlightedField(leafField),\n    children: [],\n    allExpAccessions: [row.id],\n  };\n};\n\nconst appendGroupedRows = (\n  parent: TreeViewBaseItem<ExtendedTreeItemProps>,\n  rows: TreeRow[],\n  groupingModel: string[],\n  depth: number,\n  folderId: string,\n  leafField: string,\n  path: string[],\n) => {\n  if (depth >= groupingModel.length) {\n    rows.forEach((row) => {\n      const leafNode = createLeafNode(row, leafField);\n      parent.children!.push(leafNode);\n      parent.allExpAccessions!.push(row.id);\n    });\n    return;\n  }\n\n  const field = groupingModel[depth];\n  const groupedRows = new Map<string, TreeRow[]>();\n\n  rows.forEach((row) => {\n    const value = toLabel(row[field], row.id);\n    const groupRows = groupedRows.get(value);\n    if (groupRows) {\n      groupRows.push(row);\n      return;\n    }\n\n    groupedRows.set(value, [row]);\n  });\n\n  groupedRows.forEach((groupRows, value) => {\n    const nodeId = `${folderId}::${[...path, `${field}=${encodeURIComponent(value)}`].join(\"::\")}`;\n    const groupNode: TreeViewBaseItem<ExtendedTreeItemProps> = {\n      id: nodeId,\n      kind: \"group\",\n      field,\n      value,\n      label: value,\n      icon: \"removeable\",\n      highlightName: isHighlightedField(field) ? value : undefined,\n      isHighlightedItem: isHighlightedField(field),\n      children: [],\n      allExpAccessions: [],\n    };\n\n    appendGroupedRows(\n      groupNode,\n      groupRows,\n      groupingModel,\n      depth + 1,\n      folderId,\n      leafField,\n      [...path, `${field}=${encodeURIComponent(value)}`],\n    );\n\n    parent.children!.push(groupNode);\n    parent.allExpAccessions!.push(...groupNode.allExpAccessions!);\n  });\n};\n\nexport const buildSelectedTree = ({\n  folderId,\n  rootLabel,\n  selectedRows,\n  groupingModel,\n  leafField,\n}: BuildSelectedTreeOptions): TreeViewBaseItem<ExtendedTreeItemProps>[] => {\n  const root = createRootNode(folderId, rootLabel);\n\n  appendGroupedRows(\n    root,\n    selectedRows,\n    groupingModel,\n    0,\n    folderId,\n    leafField,\n    [],\n  );\n\n  return [root];\n};\n","import Folder from \"@mui/icons-material/Folder\";\nimport IndeterminateCheckBoxRoundedIcon from \"@mui/icons-material/IndeterminateCheckBoxRounded\";\nimport { Box, Stack, Tooltip, Typography } from \"@mui/material\";\nimport Collapse from \"@mui/material/Collapse\";\nimport { alpha, styled } from \"@mui/material/styles\";\nimport {\n  TreeItemCheckbox,\n  TreeItemIconContainer,\n  TreeItemLabel,\n} from \"@mui/x-tree-view/TreeItem\";\nimport { TreeItemIcon } from \"@mui/x-tree-view/TreeItemIcon\";\nimport { TreeItemProvider } from \"@mui/x-tree-view/TreeItemProvider\";\nimport { useTreeItemModel } from \"@mui/x-tree-view/hooks\";\nimport { useTreeItem } from \"@mui/x-tree-view/useTreeItem\";\nimport React, { ReactNode } from \"react\";\nimport {\n  CustomLabelProps,\n  CustomTreeItemProps,\n  ExtendedTreeItemProps,\n} from \"../types\";\n\nconst TreeItemRoot = styled(\"li\")(({ theme }) => ({\n  listStyle: \"none\",\n  margin: 0,\n  padding: 0,\n  outline: 4,\n  color: theme.palette.grey[400],\n  ...theme.applyStyles(\"light\", {\n    color: theme.palette.grey[600],\n  }),\n}));\n\nconst TreeItemLabelText = styled(Typography)(({ theme }) => ({\n  color: theme.palette.text.primary,\n  fontFamily: \"inherit\",\n  overflow: \"hidden\",\n  textOverflow: \"ellipsis\",\n  whiteSpace: \"nowrap\",\n}));\n\nfunction CustomLabel({\n  icon: Icon,\n  children,\n  isHighlightedItem,\n  highlightName,\n  renderIcon,\n  ...other\n}: CustomLabelProps) {\n  const variant = \"body2\";\n  const fontWeight = 500;\n  const labelText = typeof children === \"string\" ? children : \"\";\n  return (\n    <TreeItemLabel\n      {...other}\n      sx={{\n        display: \"flex\",\n        alignItems: \"center\",\n        minWidth: 0,\n        overflow: \"hidden\",\n        flex: 1,\n      }}\n    >\n      {Icon && React.isValidElement(Icon) ? (\n        <Box className=\"labelIcon\" sx={{ mr: 1, flexShrink: 0 }}>\n          {Icon}\n        </Box>\n      ) : (\n        <Box\n          component={Icon as React.ElementType}\n          className=\"labelIcon\"\n          color=\"inherit\"\n          sx={{ mr: 1, fontSize: \"1.2rem\", flexShrink: 0 }}\n        />\n      )}\n      <Stack\n        direction=\"row\"\n        spacing={1}\n        alignItems=\"center\"\n        sx={{ minWidth: 0, overflow: \"hidden\", flex: 1 }}\n      >\n        {isHighlightedItem && highlightName && renderIcon && (\n          <Box sx={{ flexShrink: 0 }}>{renderIcon(highlightName)}</Box>\n        )}\n        <Tooltip title={labelText} enterDelay={500} placement=\"top\">\n          <TreeItemLabelText fontWeight={fontWeight} variant={variant}>\n            {labelText}\n          </TreeItemLabelText>\n        </Tooltip>\n      </Stack>\n    </TreeItemLabel>\n  );\n}\n\nconst TreeItemContent = styled(\"div\")(({ theme }) => ({\n  padding: theme.spacing(0.5),\n  paddingRight: theme.spacing(2),\n  paddingLeft: `calc(${theme.spacing(1)} + 6px * var(--TreeView-itemDepth))`,\n  width: \"100%\",\n  boxSizing: \"border-box\",\n  position: \"relative\",\n  display: \"flex\",\n  alignItems: \"center\",\n  gap: theme.spacing(1),\n  cursor: \"pointer\",\n  WebkitTapHighlightColor: \"transparent\",\n  flexDirection: \"row-reverse\",\n  borderRadius: theme.spacing(0.7),\n  marginBottom: theme.spacing(0.5),\n  marginTop: theme.spacing(0.5),\n  fontWeight: 500,\n  \"&:hover\": {\n    backgroundColor: alpha(theme.palette.primary.main, 0.1),\n    color: \"white\",\n    ...theme.applyStyles(\"light\", {\n      color: theme.palette.primary.main,\n    }),\n  },\n}));\n\nconst getIconFromTreeItemType = (\n  itemType: string,\n  renderIcon?: (name: string) => ReactNode,\n) => {\n  switch (itemType) {\n    case \"folder\":\n      return Folder;\n    case \"removeable\":\n      return IndeterminateCheckBoxRoundedIcon;\n    default:\n      return renderIcon ? renderIcon(itemType) : Folder;\n  }\n};\n\nexport const CustomTreeItem = React.forwardRef(function CustomTreeItem(\n  props: CustomTreeItemProps,\n  ref: React.Ref<HTMLLIElement>,\n) {\n  const {\n    id,\n    itemId,\n    label,\n    disabled,\n    children,\n    onRemove,\n    renderIcon,\n    ...other\n  } = props;\n\n  const {\n    getContextProviderProps,\n    getRootProps,\n    getContentProps,\n    getIconContainerProps,\n    getCheckboxProps,\n    getLabelProps,\n    getGroupTransitionProps,\n    status,\n  } = useTreeItem({\n    id,\n    itemId,\n    children,\n    label,\n    disabled,\n    rootRef: ref as never,\n  });\n\n  const item = useTreeItemModel<ExtendedTreeItemProps>(itemId)!;\n  const icon = getIconFromTreeItemType(item.icon, renderIcon);\n  const rootProps = getRootProps(other) as React.ComponentPropsWithoutRef<\"li\">;\n\n  const handleRemoveIconClick = (e: React.MouseEvent) => {\n    e.stopPropagation();\n    onRemove?.(item);\n  };\n\n  return (\n    <TreeItemProvider {...getContextProviderProps()}>\n      <TreeItemRoot {...rootProps}>\n        <TreeItemContent {...getContentProps()}>\n          <TreeItemIconContainer {...getIconContainerProps()}>\n            <TreeItemIcon status={status} />\n          </TreeItemIconContainer>\n          <TreeItemCheckbox {...getCheckboxProps()} />\n          <CustomLabel\n            {...getLabelProps({\n              icon:\n                item.icon === \"removeable\" ? (\n                  <Box\n                    onClick={handleRemoveIconClick}\n                    sx={{\n                      width: 20,\n                      height: 20,\n                      display: \"flex\",\n                      alignItems: \"center\",\n                      justifyContent: \"center\",\n                      borderRadius: \"4px\",\n                      cursor: \"pointer\",\n                      mr: 1,\n                      \"&:hover\": {\n                        backgroundColor: \"rgba(0,0,0,0.1)\",\n                      },\n                    }}\n                  >\n                    <IndeterminateCheckBoxRoundedIcon fontSize=\"small\" />\n                  </Box>\n                ) : (\n                  icon\n                ),\n              expandable: (status.expandable && status.expanded).toString(),\n              isHighlightedItem: item.isHighlightedItem,\n              highlightName: item.highlightName,\n              id: item.id,\n              renderIcon,\n            })}\n          />\n        </TreeItemContent>\n        {children && <Collapse {...getGroupTransitionProps()} />}\n      </TreeItemRoot>\n    </TreeItemProvider>\n  );\n});\n","import { Avatar, Box, Paper, Typography } from \"@mui/material\";\nimport { RichTreeView, TreeViewBaseItem } from \"@mui/x-tree-view\";\nimport { useTreeItemModel } from \"@mui/x-tree-view/hooks\";\nimport React, { useEffect, useMemo, useState } from \"react\";\nimport { buildSelectedTree } from \"../buildSelectedTree\";\nimport {\n  CustomTreeItemProps,\n  ExtendedTreeItemProps,\n  TreeViewWrapperProps,\n} from \"../types\";\nimport { resolveFolderView } from \"../resolveFolderView\";\nimport { CustomTreeItem } from \"./CustomTreeItem\";\n\nconst attachFolderId = (\n  items: TreeViewBaseItem<ExtendedTreeItemProps>[],\n  folderId: string,\n): TreeViewBaseItem<ExtendedTreeItemProps>[] => {\n  return items.map((item) => ({\n    ...item,\n    folderId,\n    children: item.children\n      ? attachFolderId(item.children, folderId)\n      : undefined,\n  }));\n};\n\nfunction getAllExpandableItemIds(\n  items: TreeViewBaseItem<ExtendedTreeItemProps>[],\n): string[] {\n  const ids: string[] = [];\n  for (const item of items) {\n    if (item.children && item.children.length > 0) {\n      ids.push(item.id);\n      ids.push(...getAllExpandableItemIds(item.children));\n    }\n  }\n  return ids;\n}\n\nfunction FolderTree({\n  items,\n  LeafTreeItemComponent,\n  TreeItemComponent,\n  onRemove,\n}: {\n  items: TreeViewBaseItem<ExtendedTreeItemProps>[];\n  LeafTreeItemComponent?: React.ForwardRefExoticComponent<\n    CustomTreeItemProps & React.RefAttributes<HTMLLIElement>\n  >;\n  TreeItemComponent?: React.ForwardRefExoticComponent<\n    CustomTreeItemProps & React.RefAttributes<HTMLLIElement>\n  >;\n  onRemove: (item: TreeViewBaseItem<ExtendedTreeItemProps>) => void;\n}) {\n  const allExpandableIds = useMemo(\n    () => getAllExpandableItemIds(items),\n    [items],\n  );\n  const [expandedItems, setExpandedItems] =\n    useState<string[]>(allExpandableIds);\n\n  useEffect(() => {\n    setExpandedItems((prev) => {\n      const newIds = allExpandableIds.filter((id) => !prev.includes(id));\n      if (newIds.length > 0) {\n        return [...prev, ...newIds];\n      }\n      return prev;\n    });\n  }, [allExpandableIds]);\n\n  const handleRemoveTreeItem = (\n    item: TreeViewBaseItem<ExtendedTreeItemProps>,\n  ) => {\n    onRemove(item);\n  };\n\n  const TreeItem = useMemo(\n    () =>\n      TreeItemComponent || LeafTreeItemComponent\n        ? React.forwardRef<HTMLLIElement, CustomTreeItemProps>(\n            function TreeItem(props, ref) {\n              const item = useTreeItemModel<ExtendedTreeItemProps>(\n                props.itemId,\n              );\n              const Component =\n                item?.kind === \"leaf\"\n                  ? (LeafTreeItemComponent ??\n                    TreeItemComponent ??\n                    CustomTreeItem)\n                  : (TreeItemComponent ?? CustomTreeItem);\n\n              return <Component {...props} ref={ref} />;\n            },\n          )\n        : CustomTreeItem,\n    [LeafTreeItemComponent, TreeItemComponent],\n  );\n\n  return (\n    <RichTreeView\n      items={items}\n      expandedItems={expandedItems}\n      onExpandedItemsChange={(\n        _event: React.SyntheticEvent | null,\n        ids: string[],\n      ) => setExpandedItems(ids)}\n      slots={{ item: TreeItem }}\n      slotProps={{\n        item: {\n          onRemove: handleRemoveTreeItem,\n        } as Partial<CustomTreeItemProps>,\n      }}\n      sx={{\n        ml: 1,\n        mr: 1,\n        \"& ul\": {\n          paddingInlineStart: \"12px\",\n        },\n      }}\n      itemChildrenIndentation={0}\n    />\n  );\n}\n\nexport function TreeViewWrapper({\n  folders,\n  selectedByFolder,\n  activeViewIdByFolder,\n  selectedCount,\n  onRemove,\n}: TreeViewWrapperProps) {\n  const folderTrees = useMemo(\n    () =>\n      folders.flatMap((folder) => {\n        const folderSelectedIds = selectedByFolder.get(folder.id);\n        if (!folderSelectedIds || folderSelectedIds.size === 0) {\n          return [];\n        }\n\n        const activeView = resolveFolderView(folder, activeViewIdByFolder);\n        const selectedRows = folder.rows.filter((row) =>\n          folderSelectedIds.has(row.id),\n        );\n\n        return [\n          {\n            folderId: folder.id,\n            items: attachFolderId(\n              buildSelectedTree({\n                folderId: folder.id,\n                rootLabel: folder.label,\n                selectedRows,\n                groupingModel: activeView.groupingModel,\n                leafField: activeView.leafField,\n              }),\n              folder.id,\n            ),\n            TreeItemComponent: folder.TreeItemComponent,\n            LeafTreeItemComponent: folder.LeafTreeItemComponent,\n          },\n        ];\n      }),\n    [activeViewIdByFolder, folders, selectedByFolder],\n  );\n\n  return (\n    <Paper\n      sx={{\n        height: 500,\n        width: \"100%\",\n        border: \"10px solid\",\n        borderColor: \"grey.200\",\n        boxSizing: \"border-box\",\n        borderRadius: 2,\n        display: \"flex\",\n        flexDirection: \"column\",\n      }}\n    >\n      <Box\n        sx={{\n          display: \"flex\",\n          alignItems: \"center\",\n          gap: 1,\n          py: 1,\n          backgroundColor: \"grey.200\",\n          flexShrink: 0,\n        }}\n      >\n        <Avatar\n          sx={{\n            width: 30,\n            height: 30,\n            fontSize: 14,\n            fontWeight: \"bold\",\n            bgcolor: \"white\",\n            color: \"text.primary\",\n          }}\n        >\n          {selectedCount}\n        </Avatar>\n        <Typography fontWeight=\"bold\">Active Tracks</Typography>\n      </Box>\n      <Box\n        sx={{\n          flex: 1,\n          overflow: \"auto\",\n        }}\n      >\n        {folderTrees.map((folderTree) => (\n          <FolderTree\n            key={folderTree.folderId}\n            items={folderTree.items}\n            LeafTreeItemComponent={folderTree.LeafTreeItemComponent}\n            TreeItemComponent={folderTree.TreeItemComponent}\n            onRemove={onRemove}\n          />\n        ))}\n      </Box>\n    </Paper>\n  );\n}\n","import { TreeViewBaseItem } from \"@mui/x-tree-view\";\nimport { TrackStoreInstance } from \"@weng-lab/genomebrowser\";\nimport CloseIcon from \"@mui/icons-material/Close\";\nimport {\n  Box,\n  Button,\n  Dialog,\n  DialogContent,\n  DialogTitle,\n  IconButton,\n  Stack,\n} from \"@mui/material\";\nimport { useEffect, useState } from \"react\";\nimport { Assembly, FolderDefinition } from \"./Folders/types\";\nimport { DataGridWrapper } from \"./DataGrid/DataGridWrapper\";\nimport { ClearDialog } from \"./Dialogs/ClearDialog\";\nimport { LimitDialog } from \"./Dialogs/LimitDialog\";\nimport { ResetDialog } from \"./Dialogs/ResetDialog\";\nimport { Breadcrumb } from \"./FolderList/Breadcrumb\";\nimport { FolderList } from \"./FolderList/FolderList\";\nimport { diffManagedTracks } from \"./managedTracks\";\nimport { resolveFolderView } from \"./resolveFolderView\";\nimport type { TrackSelectTrackContext } from \"./trackContext\";\nimport { ExtendedTreeItemProps } from \"./types\";\nimport { TreeViewWrapper } from \"./TreeView/TreeViewWrapper\";\n\nexport type InitialSelectedIdsByAssembly = Partial<\n  Record<Assembly, Record<string, string[]>>\n>;\n\nexport interface TrackSelectProps {\n  assembly: Assembly;\n  folders: FolderDefinition[];\n  initialSelectedIds?: InitialSelectedIdsByAssembly;\n  sessionStorageKey?: string;\n  trackStore?: TrackStoreInstance;\n  onCancel?: () => void;\n  maxTracks?: number;\n  trackContext?: TrackSelectTrackContext;\n  open: boolean;\n  onClose: () => void;\n  title?: string;\n}\n\nconst DEFAULT_MAX_TRACKS = 30;\n\nconst DEFAULT_TITLE = \"Track Select\";\n\ntype ViewState = \"folder-list\" | \"folder-detail\";\n\nconst createEmptySelectedByFolder = (folders: FolderDefinition[]) => {\n  return new Map(folders.map((folder) => [folder.id, new Set<string>()]));\n};\n\nconst cloneSelectedByFolder = (selectedByFolder: Map<string, Set<string>>) => {\n  return new Map(\n    Array.from(selectedByFolder, ([folderId, ids]) => [folderId, new Set(ids)]),\n  );\n};\n\nconst normalizeSelectedByFolder = ({\n  folders,\n  selectedIdsByFolder,\n}: {\n  folders: FolderDefinition[];\n  selectedIdsByFolder?: Record<string, string[]>;\n}) => {\n  const normalized = createEmptySelectedByFolder(folders);\n\n  if (!selectedIdsByFolder) {\n    return normalized;\n  }\n\n  folders.forEach((folder) => {\n    const ids = selectedIdsByFolder[folder.id];\n    if (!ids) {\n      return;\n    }\n\n    normalized.set(\n      folder.id,\n      new Set(ids.filter((id) => id.startsWith(`${folder.id}/`))),\n    );\n  });\n\n  return normalized;\n};\n\nconst loadSelectedByFolder = ({\n  assembly,\n  folders,\n  initialSelectedIds,\n  sessionStorageKey,\n}: {\n  assembly: Assembly;\n  folders: FolderDefinition[];\n  initialSelectedIds?: InitialSelectedIdsByAssembly;\n  sessionStorageKey?: string;\n}) => {\n  const fallback = normalizeSelectedByFolder({\n    folders,\n    selectedIdsByFolder: initialSelectedIds?.[assembly],\n  });\n\n  if (!sessionStorageKey || typeof window === \"undefined\") {\n    return fallback;\n  }\n\n  const storedValue = window.sessionStorage.getItem(sessionStorageKey);\n  if (!storedValue) {\n    return fallback;\n  }\n\n  try {\n    const parsed = JSON.parse(storedValue) as Record<string, string[]>;\n    return normalizeSelectedByFolder({\n      folders,\n      selectedIdsByFolder: parsed,\n    });\n  } catch {\n    return fallback;\n  }\n};\n\nconst saveSelectedByFolder = ({\n  selectedByFolder,\n  sessionStorageKey,\n}: {\n  selectedByFolder: Map<string, Set<string>>;\n  sessionStorageKey?: string;\n}) => {\n  if (!sessionStorageKey || typeof window === \"undefined\") {\n    return;\n  }\n\n  const serialized = Object.fromEntries(\n    Array.from(selectedByFolder, ([folderId, ids]) => [\n      folderId,\n      Array.from(ids),\n    ]),\n  );\n  window.sessionStorage.setItem(sessionStorageKey, JSON.stringify(serialized));\n};\n\nexport default function TrackSelect({\n  assembly,\n  folders,\n  initialSelectedIds,\n  sessionStorageKey,\n  trackStore,\n  onCancel,\n  maxTracks,\n  trackContext,\n  open,\n  onClose,\n  title = DEFAULT_TITLE,\n}: TrackSelectProps) {\n  const [limitDialogOpen, setLimitDialogOpen] = useState(false);\n  const [clearDialogOpen, setClearDialogOpen] = useState(false);\n  const [resetDialogOpen, setResetDialogOpen] = useState(false);\n  const [currentView, setCurrentView] = useState<ViewState>(() =>\n    folders.length > 1 ? \"folder-list\" : \"folder-detail\",\n  );\n  const [activeFolderId, setActiveFolderId] = useState(\n    () => folders[0]?.id ?? \"\",\n  );\n  const [activeViewIdByFolder, setActiveViewIdByFolder] = useState(\n    () =>\n      new Map(\n        folders.flatMap((folder) =>\n          folder.views?.[0] ? [[folder.id, folder.views[0].id] as const] : [],\n        ),\n      ),\n  );\n  const [committedSelectedByFolder, setCommittedSelectedByFolder] = useState(\n    () =>\n      loadSelectedByFolder({\n        assembly,\n        folders,\n        initialSelectedIds,\n        sessionStorageKey,\n      }),\n  );\n  const [selectedByFolder, setSelectedByFolder] = useState(() =>\n    cloneSelectedByFolder(committedSelectedByFolder),\n  );\n  const maxTracksLimit = maxTracks ?? DEFAULT_MAX_TRACKS;\n\n  useEffect(() => {\n    setActiveFolderId((currentFolderId) => {\n      if (folders.some((folder) => folder.id === currentFolderId)) {\n        return currentFolderId;\n      }\n\n      return folders[0]?.id ?? \"\";\n    });\n\n    if (folders.length <= 1) {\n      setCurrentView(\"folder-detail\");\n    }\n\n    setActiveViewIdByFolder((current) => {\n      return new Map(\n        folders.flatMap((folder) => {\n          if (!folder.views?.length) {\n            return [];\n          }\n\n          const activeViewId = current.get(folder.id);\n          if (\n            activeViewId &&\n            folder.views.some((view) => view.id === activeViewId)\n          ) {\n            return [[folder.id, activeViewId] as const];\n          }\n\n          return [[folder.id, folder.views[0].id] as const];\n        }),\n      );\n    });\n  }, [folders]);\n\n  useEffect(() => {\n    const nextCommittedSelection = loadSelectedByFolder({\n      assembly,\n      folders,\n      initialSelectedIds,\n      sessionStorageKey,\n    });\n    setCommittedSelectedByFolder(nextCommittedSelection);\n    setSelectedByFolder(cloneSelectedByFolder(nextCommittedSelection));\n  }, [assembly, folders, initialSelectedIds, sessionStorageKey]);\n\n  useEffect(() => {\n    if (!open) {\n      return;\n    }\n\n    setSelectedByFolder(cloneSelectedByFolder(committedSelectedByFolder));\n  }, [committedSelectedByFolder, open]);\n\n  useEffect(() => {\n    if (!assembly || !trackStore) {\n      return;\n    }\n\n    const { idsToRemove, tracksToAdd } = diffManagedTracks({\n      assembly,\n      currentTracks: trackStore.getState().tracks,\n      folders,\n      selectedByFolder: committedSelectedByFolder,\n      trackContext,\n    });\n\n    const { insertTrack, removeTrack } = trackStore.getState();\n    idsToRemove.forEach((id) => removeTrack(id));\n    tracksToAdd.forEach((track) => insertTrack(track));\n  }, [assembly, committedSelectedByFolder, folders, trackContext, trackStore]);\n\n  const activeFolder =\n    folders.find((folder) => folder.id === activeFolderId) ?? folders[0];\n  const activeConfig = activeFolder\n    ? resolveFolderView(activeFolder, activeViewIdByFolder)\n    : undefined;\n  const activeViewId = activeConfig?.id ?? \"\";\n  const rows = activeFolder?.rows ?? [];\n  const selectedIds = new Set(\n    selectedByFolder.get(activeFolder?.id ?? \"\") ?? [],\n  );\n  let selectedCount = 0;\n  selectedByFolder.forEach((ids) => {\n    selectedCount += ids.size;\n  });\n\n  const handleFolderSelect = (folderId: string) => {\n    setActiveFolderId(folderId);\n    setCurrentView(\"folder-detail\");\n  };\n\n  const handleNavigateToRoot = () => {\n    setCurrentView(\"folder-list\");\n  };\n\n  const handleCancel = () => {\n    onCancel?.();\n    onClose();\n  };\n\n  const ViewSelector = activeFolder?.ViewSelector;\n\n  const confirmReset = () => {\n    setResetDialogOpen(false);\n    setSelectedByFolder(cloneSelectedByFolder(committedSelectedByFolder));\n  };\n\n  const confirmClear = () => {\n    setClearDialogOpen(false);\n\n    const nextSelectedByFolder = new Map(selectedByFolder);\n\n    if (currentView === \"folder-detail\") {\n      nextSelectedByFolder.set(activeFolderId, new Set<string>());\n    } else {\n      folders.forEach((folder) =>\n        nextSelectedByFolder.set(folder.id, new Set<string>()),\n      );\n    }\n\n    setSelectedByFolder(nextSelectedByFolder);\n  };\n\n  const handleActiveViewChange = (viewId: string) => {\n    if (!activeFolder) {\n      return;\n    }\n\n    setActiveViewIdByFolder((prev) => {\n      const next = new Map(prev);\n      next.set(activeFolder.id, viewId);\n      return next;\n    });\n  };\n\n  const handleSelectionChange = (ids: Set<string>) => {\n    if (!activeFolder) {\n      return;\n    }\n\n    const filteredIds = new Set(\n      Array.from(ids).filter((id) =>\n        activeFolder.rows.some((row) => row.id === id),\n      ),\n    );\n\n    let nextTotal = filteredIds.size;\n    selectedByFolder.forEach((folderIds, folderId) => {\n      if (folderId !== activeFolder.id) {\n        nextTotal += folderIds.size;\n      }\n    });\n\n    if (nextTotal > maxTracksLimit) {\n      setLimitDialogOpen(true);\n      return;\n    }\n\n    const nextSelectedByFolder = new Map(selectedByFolder);\n    nextSelectedByFolder.set(activeFolder.id, filteredIds);\n    setSelectedByFolder(nextSelectedByFolder);\n  };\n\n  const handleRemoveTreeItem = (\n    item: TreeViewBaseItem<ExtendedTreeItemProps>,\n  ) => {\n    const folderId = item.folderId;\n    if (!folderId || !item.allExpAccessions?.length) {\n      return;\n    }\n\n    const nextSelectedByFolder = new Map(selectedByFolder);\n    const nextSet = new Set(\n      nextSelectedByFolder.get(folderId) ?? new Set<string>(),\n    );\n    item.allExpAccessions.forEach((id) => nextSet.delete(id));\n    nextSelectedByFolder.set(folderId, nextSet);\n    setSelectedByFolder(nextSelectedByFolder);\n  };\n\n  const handleSubmit = () => {\n    saveSelectedByFolder({ selectedByFolder, sessionStorageKey });\n    setCommittedSelectedByFolder(cloneSelectedByFolder(selectedByFolder));\n    onClose();\n  };\n\n  return (\n    <Dialog open={open} onClose={handleCancel} maxWidth=\"lg\" fullWidth>\n      <DialogTitle\n        sx={{\n          bgcolor: \"primary.main\",\n          color: \"primary.contrastText\",\n          display: \"flex\",\n          justifyContent: \"space-between\",\n          alignItems: \"center\",\n          fontWeight: \"bold\",\n        }}\n      >\n        {title}\n        <IconButton\n          size=\"large\"\n          onClick={handleCancel}\n          sx={{ color: \"primary.contrastText\", p: 0 }}\n        >\n          <CloseIcon fontSize=\"large\" />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent sx={{ marginTop: \"5px\" }}>\n        {!activeFolder || !activeConfig ? (\n          <Box sx={{ p: 2 }}>No folders available.</Box>\n        ) : (\n          <Box sx={{ flex: 1, pt: 1 }}>\n            <Box\n              display=\"flex\"\n              justifyContent=\"space-between\"\n              alignItems=\"center\"\n              sx={{ mb: 2 }}\n            >\n              {folders.length > 1 ? (\n                <Breadcrumb\n                  currentFolder={\n                    currentView === \"folder-detail\" ? activeFolder : null\n                  }\n                  onNavigateToRoot={handleNavigateToRoot}\n                />\n              ) : (\n                <Box />\n              )}\n              {currentView === \"folder-detail\" &&\n              ViewSelector &&\n              activeFolder.views ? (\n                <ViewSelector\n                  views={activeFolder.views}\n                  activeViewId={activeViewId}\n                  onChange={handleActiveViewChange}\n                />\n              ) : null}\n            </Box>\n            <Stack\n              direction={{ xs: \"column\", md: \"row\" }}\n              spacing={2}\n              sx={{ width: \"100%\" }}\n            >\n              <Box\n                sx={{\n                  flex: { xs: \"none\", md: 3 },\n                  minWidth: 0,\n                  width: { xs: \"100%\", md: \"auto\" },\n                }}\n              >\n                {currentView === \"folder-list\" ? (\n                  <FolderList\n                    folders={folders}\n                    onFolderSelect={handleFolderSelect}\n                  />\n                ) : (\n                  <DataGridWrapper\n                    rows={rows}\n                    columns={activeConfig.columns}\n                    groupingModel={activeConfig.groupingModel}\n                    leafField={activeConfig.leafField}\n                    label={`${rows.length} Available ${activeFolder.label}`}\n                    selectedIds={selectedIds}\n                    onSelectionChange={handleSelectionChange}\n                    GroupingCellComponent={activeFolder.GroupingCellComponent}\n                  />\n                )}\n              </Box>\n              <Box\n                sx={{\n                  flex: { xs: \"none\", md: 2 },\n                  minWidth: 0,\n                  width: { xs: \"100%\", md: \"auto\" },\n                }}\n              >\n                <TreeViewWrapper\n                  folders={folders}\n                  selectedByFolder={selectedByFolder}\n                  activeViewIdByFolder={activeViewIdByFolder}\n                  selectedCount={selectedCount}\n                  onRemove={handleRemoveTreeItem}\n                />\n              </Box>\n            </Stack>\n            <Box\n              sx={{\n                display: \"flex\",\n                justifyContent: \"space-between\",\n                alignItems: \"center\",\n                mt: 2,\n                gap: 1,\n              }}\n            >\n              <Box sx={{ display: \"flex\", gap: 1 }}>\n                <Button\n                  variant=\"outlined\"\n                  color=\"secondary\"\n                  size=\"small\"\n                  onClick={() => setClearDialogOpen(true)}\n                >\n                  Clear\n                </Button>\n                {Boolean(trackStore) ? (\n                  <Button\n                    variant=\"outlined\"\n                    color=\"secondary\"\n                    size=\"small\"\n                    onClick={() => setResetDialogOpen(true)}\n                  >\n                    Reset\n                  </Button>\n                ) : null}\n              </Box>\n              <Box sx={{ display: \"flex\", gap: 1 }}>\n                <Button variant=\"outlined\" size=\"small\" onClick={handleCancel}>\n                  Cancel\n                </Button>\n                <Button\n                  variant=\"contained\"\n                  color=\"primary\"\n                  size=\"small\"\n                  onClick={handleSubmit}\n                >\n                  Submit\n                </Button>\n              </Box>\n            </Box>\n            <LimitDialog\n              open={limitDialogOpen}\n              onClose={() => setLimitDialogOpen(false)}\n              maxTracks={maxTracksLimit}\n            />\n            <ClearDialog\n              open={clearDialogOpen}\n              onClose={() => setClearDialogOpen(false)}\n              onConfirm={confirmClear}\n              folderLabel={activeFolder.label}\n              clearAll={currentView === \"folder-list\"}\n            />\n            <ResetDialog\n              open={resetDialogOpen}\n              onClose={() => setResetDialogOpen(false)}\n              onConfirm={confirmReset}\n            />\n          </Box>\n        )}\n      </DialogContent>\n    </Dialog>\n  );\n}\n","import { Box } from \"@mui/material\";\nimport type { Assembly } from \"../../types\";\n\nexport type { Assembly };\n\nexport const assayTypes = [\n  \"cCRE\",\n  \"DNase\",\n  \"H3K4me3\",\n  \"H3K27ac\",\n  \"ATAC\",\n  \"CTCF\",\n  \"RNA-seq\",\n  \"ChromHMM\",\n  \"WGBS\",\n];\n\nexport const lifeStages = [\"Adult\", \"Embryonic\", \"N/A\"];\n\nexport const ontologyTypes = [\n  \"Aggregate\",\n  \"Adipose\",\n  \"Adrenal gland\",\n  \"Blood\",\n  \"Blood vessel\",\n  \"Bone\",\n  \"Bone marrow\",\n  \"Brain\",\n  \"Breast\",\n  \"Connective tissue\",\n  \"Embryo\",\n  \"Epithelium\",\n  \"Esophagus\",\n  \"Eye\",\n  \"Fallopian Tube\",\n  \"Gallbladder\",\n  \"Heart\",\n  \"Kidney\",\n  \"Large Intestine\",\n  \"Limb\",\n  \"Liver\",\n  \"Lung\",\n  \"Lymphoid Tissue\",\n  \"Muscle\",\n  \"Mouth\",\n  \"Nerve\",\n  \"Nose\",\n  \"Pancreas\",\n  \"Parathyroid Gland\",\n  \"Ovary\",\n  \"Penis\",\n  \"Placenta\",\n  \"Prostate\",\n  \"Skin\",\n  \"Small Intestine\",\n  \"Spinal Cord\",\n  \"Spleen\",\n  \"Stomach\",\n  \"Testis\",\n  \"Thymus\",\n  \"Thyroid\",\n  \"Urinary Bladder\",\n  \"Uterus\",\n  \"Vagina\",\n];\n\n/** Color mapping for assay types */\nexport const assayColorMap: { [key: string]: string } = {\n  DNase: \"#06da93\",\n  ATAC: \"#02c7b9\",\n  H3K4me3: \"#ff2020\",\n  ChromHMM: \"#0097a7\",\n  H3K27ac: \"#fdc401\",\n  CTCF: \"#01a6f1\",\n  cCRE: \"#000000\",\n  \"RNA-seq\": \"#00aa00\",\n  WGBS: \"#648bd8\",\n};\n\n/**\n * Creates the assay icon for DataGrid and RichTreeView\n * @param type - assay type\n * @returns an icon of the assay's respective color\n */\nexport function AssayIcon(type: string) {\n  const color = assayColorMap[type];\n  return (\n    <Box\n      sx={{\n        width: 12,\n        height: 12,\n        borderRadius: \"20%\",\n        bgcolor: color,\n      }}\n    />\n  );\n}\n\n/**\n * Mapping from JSON assay keys to display names.\n * This is the single source of truth for assay name formatting.\n */\nconst assayJsonToDisplay: Record<string, string> = {\n  dnase: \"DNase\",\n  atac: \"ATAC\",\n  h3k4me3: \"H3K4me3\",\n  h3k27ac: \"H3K27ac\",\n  ctcf: \"CTCF\",\n  chromhmm: \"ChromHMM\",\n  ccre: \"cCRE\",\n  rnaseq: \"RNA-seq\",\n  wgbs: \"WGBS\",\n};\n\n/**\n * Convert JSON assay key to display name.\n * Used only during data loading to normalize assay names.\n */\nexport function formatAssayType(jsonKey: string): string {\n  return assayJsonToDisplay[jsonKey.toLowerCase()] ?? jsonKey;\n}\n","import {\n  GridColDef,\n  GridRenderCellParams,\n  GridGroupNode,\n  useGridApiContext,\n} from \"@mui/x-data-grid-premium\";\nimport { Stack, capitalize } from \"@mui/material\";\nimport { AssayIcon, ontologyTypes, assayTypes, lifeStages } from \"./constants\";\nimport { BiosampleRowInfo, CollectionType } from \"./types\";\n\nconst collectionTypes: CollectionType[] = [\"Core\", \"Ancillary\", \"Partial\", \"NA\"];\n\nfunction CollectionCell(params: GridRenderCellParams<BiosampleRowInfo>) {\n  const apiRef = useGridApiContext();\n\n  if (params.rowNode.type !== \"group\") {\n    return params.value ?? null;\n  }\n\n  const groupNode = params.rowNode as GridGroupNode;\n  if (groupNode.groupingField !== \"displayName\") {\n    return null;\n  }\n\n  const childIds = groupNode.children;\n  if (!childIds || childIds.length === 0) {\n    return null;\n  }\n\n  const firstChildRow = apiRef.current.getRow(\n    childIds[0],\n  ) as BiosampleRowInfo | null;\n\n  return firstChildRow?.collection ?? null;\n}\n\nconst displayNameCol: GridColDef<BiosampleRowInfo> = {\n  field: \"displayName\",\n  headerName: \"Name\",\n  valueFormatter: (value) => value && capitalize(value),\n  maxWidth: 300,\n};\n\nconst sortedByAssayOntologyCol: GridColDef<BiosampleRowInfo> = {\n  field: \"ontology\",\n  headerName: \"Ontology\",\n  type: \"singleSelect\",\n  valueOptions: ontologyTypes,\n  renderCell: (params) => {\n    if (params.rowNode.type === \"group\") {\n      if (params.value === undefined) {\n        return null;\n      }\n      const val = params.value;\n      return (\n        <div>\n          <b>{val}</b>\n        </div>\n      );\n    }\n  },\n};\n\nconst sortedByAssayAssayCol: GridColDef<BiosampleRowInfo> = {\n  field: \"assay\",\n  headerName: \"Assay\",\n  valueOptions: assayTypes,\n  renderCell: (params) => {\n    if (params.rowNode.type === \"group\") {\n      if (params.value === undefined) {\n        return null;\n      }\n      const val = params.value;\n      return (\n        <Stack direction=\"row\" spacing={2} alignItems=\"center\">\n          {AssayIcon(val)}\n          <div>\n            <b>{val}</b>\n          </div>\n        </Stack>\n      );\n    }\n  },\n};\n\nconst defaultOntologyCol: GridColDef<BiosampleRowInfo> = {\n  field: \"ontology\",\n  headerName: \"Ontology\",\n  type: \"singleSelect\",\n  valueOptions: ontologyTypes,\n  renderCell: (params) => {\n    if (params.rowNode.type === \"group\") {\n      if (params.value === undefined) {\n        return null;\n      }\n      const val = params.value;\n      return (\n        <div>\n          <b>{val}</b>\n        </div>\n      );\n    }\n  },\n};\n\nconst defaultAssayCol: GridColDef<BiosampleRowInfo> = {\n  field: \"assay\",\n  headerName: \"Assay\",\n  valueOptions: assayTypes,\n  renderCell: (params) => {\n    if (params.value === undefined) {\n      return null;\n    }\n    const val = params.value;\n    return (\n      <Stack direction=\"row\" spacing={2} alignItems=\"center\" sx={{ ml: 6 }}>\n        {AssayIcon(val)}\n        <div>{val}</div>\n      </Stack>\n    );\n  },\n};\n\nconst sampleTypeCol: GridColDef<BiosampleRowInfo> = {\n  field: \"sampleType\",\n  headerName: \"Sample Type\",\n  type: \"singleSelect\",\n  valueOptions: ontologyTypes,\n  valueFormatter: (value) => value && capitalize(value),\n};\n\nconst lifeStageCol: GridColDef<BiosampleRowInfo> = {\n  field: \"lifeStage\",\n  headerName: \"Life Stage\",\n  type: \"singleSelect\",\n  valueOptions: lifeStages,\n  valueFormatter: (value) => value && capitalize(value),\n};\n\nconst collectionCol: GridColDef<BiosampleRowInfo> = {\n  field: \"collection\",\n  headerName: \"Collection\",\n  type: \"singleSelect\",\n  valueOptions: collectionTypes,\n  width: 100,\n  renderCell: (params) => <CollectionCell {...params} />,\n};\n\nconst experimentCol: GridColDef<BiosampleRowInfo> = {\n  field: \"experimentAccession\",\n  headerName: \"Experiment Accession\",\n};\n\nconst fileCol: GridColDef<BiosampleRowInfo> = {\n  field: \"fileAccession\",\n  headerName: \"File Accession\",\n};\n\nconst idCol: GridColDef<BiosampleRowInfo> = {\n  field: \"id\",\n  headerName: \"ID\",\n};\n\n/** Columns for sorted-by-assay view (assay as top-level grouping) */\nexport const sortedByAssayColumns: GridColDef<BiosampleRowInfo>[] = [\n  displayNameCol,\n  sortedByAssayOntologyCol,\n  collectionCol,\n  sampleTypeCol,\n  lifeStageCol,\n  sortedByAssayAssayCol,\n  experimentCol,\n  fileCol,\n  idCol,\n];\n\n/** Default columns (ontology as top-level grouping) */\nexport const defaultColumns: GridColDef<BiosampleRowInfo>[] = [\n  defaultAssayCol,\n  collectionCol,\n  sampleTypeCol,\n  lifeStageCol,\n  defaultOntologyCol,\n  displayNameCol,\n  experimentCol,\n  fileCol,\n  idCol,\n];\n\n/** Grouping model for sorted-by-assay view */\nexport const sortedByAssayGroupingModel = [\"assay\", \"ontology\"];\n\n/** Default grouping model (ontology-based) */\nexport const defaultGroupingModel = [\"ontology\", \"displayName\"];\n\n/** Leaf field for sorted-by-assay view */\nexport const sortedByAssayLeafField = \"displayName\";\n\n/** Default leaf field */\nexport const defaultLeafField = \"assay\";\n","import { ToggleButton, ToggleButtonGroup } from \"@mui/material\";\nimport { FolderView } from \"../../types\";\n\nexport interface BiosampleViewSelectorProps {\n  views: FolderView[];\n  activeViewId: string;\n  onChange: (viewId: string) => void;\n}\n\nexport function BiosampleViewSelector({\n  views,\n  activeViewId,\n  onChange,\n}: BiosampleViewSelectorProps) {\n  return (\n    <ToggleButtonGroup\n      exclusive\n      value={activeViewId}\n      size=\"small\"\n      onChange={(_event, viewId: string | null) => {\n        if (viewId) {\n          onChange(viewId);\n        }\n      }}\n    >\n      {views.map((view) => (\n        <ToggleButton key={view.id} value={view.id}>\n          {view.label}\n        </ToggleButton>\n      ))}\n    </ToggleButtonGroup>\n  );\n}\n","import { Stack, Tooltip, Box, IconButton } from \"@mui/material\";\nimport {\n  GridRenderCellParams,\n  useGridApiContext,\n  GridGroupNode,\n} from \"@mui/x-data-grid-premium\";\nimport { assayTypes, AssayIcon } from \"./constants\";\nimport ChevronRightIcon from \"@mui/icons-material/ChevronRight\";\nimport ExpandMoreIcon from \"@mui/icons-material/ExpandMore\";\n\n/**\n * Biosample-specific grouping cell that renders AssayIcon for assay groups/values.\n * Handles expand/collapse, truncation, and tooltips.\n */\nexport default function BiosampleGroupingCell(params: GridRenderCellParams) {\n  const apiRef = useGridApiContext();\n  const isGroup = params.rowNode.type === \"group\";\n  const groupNode = params.rowNode as GridGroupNode;\n  const isExpanded = isGroup ? groupNode.childrenExpanded : false;\n  const groupingField = isGroup ? groupNode.groupingField : null;\n  const depth = params.rowNode.depth ?? 0;\n\n  const handleExpandClick = (e: React.MouseEvent) => {\n    e.stopPropagation();\n    apiRef.current.setRowChildrenExpansion(params.id, !isExpanded);\n  };\n\n  // Render content based on grouping field\n  const renderContent = () => {\n    const value = String(params.value ?? \"\");\n\n    // For assay groups, show the colored icon\n    if (isGroup && groupingField === \"assay\") {\n      return (\n        <Stack\n          direction=\"row\"\n          spacing={1}\n          alignItems=\"center\"\n          sx={{ flex: 1, overflow: \"hidden\" }}\n        >\n          {AssayIcon(value)}\n          <Tooltip title={value} placement=\"top-start\" enterDelay={500}>\n            <Box\n              sx={{\n                overflow: \"hidden\",\n                textOverflow: \"ellipsis\",\n                whiteSpace: \"nowrap\",\n                fontWeight: \"bold\",\n              }}\n            >\n              {params.formattedValue}\n            </Box>\n          </Tooltip>\n        </Stack>\n      );\n    }\n\n    // For other groups (ontology, displayName), show bold text\n    if (isGroup) {\n      return (\n        <Tooltip title={value} placement=\"top-start\" enterDelay={500}>\n          <Box\n            sx={{\n              overflow: \"hidden\",\n              textOverflow: \"ellipsis\",\n              whiteSpace: \"nowrap\",\n              flex: 1,\n              fontWeight: \"bold\",\n            }}\n          >\n            {params.formattedValue}\n          </Box>\n        </Tooltip>\n      );\n    }\n\n    // For leaf rows - check if it's an assay value\n    const isAssayValue = assayTypes\n      .map((a) => a.toLowerCase())\n      .includes(value.toLowerCase());\n\n    if (isAssayValue) {\n      return (\n        <Stack\n          direction=\"row\"\n          spacing={1}\n          alignItems=\"center\"\n          sx={{ flex: 1, overflow: \"hidden\" }}\n        >\n          {AssayIcon(value)}\n          <Tooltip title={value} placement=\"top-start\" enterDelay={500}>\n            <Box\n              sx={{\n                overflow: \"hidden\",\n                textOverflow: \"ellipsis\",\n                whiteSpace: \"nowrap\",\n              }}\n            >\n              {params.formattedValue}\n            </Box>\n          </Tooltip>\n        </Stack>\n      );\n    }\n\n    return (\n      <Tooltip title={value} placement=\"top-start\" enterDelay={500}>\n        <Box\n          sx={{\n            overflow: \"hidden\",\n            textOverflow: \"ellipsis\",\n            whiteSpace: \"nowrap\",\n            flex: 1,\n          }}\n        >\n          {params.formattedValue}\n        </Box>\n      </Tooltip>\n    );\n  };\n\n  // Indent based on depth (2 units per level)\n  const indentLevel = depth * 2;\n\n  return (\n    <Box\n      sx={{\n        display: \"flex\",\n        alignItems: \"center\",\n        width: \"100%\",\n        ml: indentLevel,\n      }}\n    >\n      {isGroup && (\n        <IconButton size=\"small\" onClick={handleExpandClick} sx={{ mr: 0.5 }}>\n          {isExpanded ? (\n            <ExpandMoreIcon fontSize=\"small\" />\n          ) : (\n            <ChevronRightIcon fontSize=\"small\" />\n          )}\n        </IconButton>\n      )}\n      {renderContent()}\n    </Box>\n  );\n}\n","import React from \"react\";\nimport { CustomTreeItem } from \"../../../TreeView/CustomTreeItem\";\nimport { CustomTreeItemProps } from \"../../../types\";\nimport { AssayIcon } from \"./constants\";\n\n/**\n * Biosample-specific TreeItem that renders AssayIcon for assay items.\n * Wraps the generic CustomTreeItem with the AssayIcon renderer.\n */\nexport const BiosampleTreeItem = React.forwardRef<\n  HTMLLIElement,\n  CustomTreeItemProps\n>(function BiosampleTreeItem(props, ref) {\n  return <CustomTreeItem {...props} ref={ref} renderIcon={AssayIcon} />;\n});\n","import {\n  BigBedConfig,\n  BigWigConfig,\n  DisplayMode,\n  MethylCConfig,\n  Rect,\n  Track,\n  TrackType,\n  ValuedPoint,\n} from \"@weng-lab/genomebrowser\";\nimport type { FC } from \"react\";\nimport { CreateTrackOptions } from \"../../types\";\nimport { BiosampleRowInfo } from \"./types\";\n\nexport type BiosampleTrackContext = {\n  onBiosampleFeatureClick?: (args: {\n    trackId: string;\n    row: BiosampleRowInfo;\n    rect: Rect;\n  }) => void;\n  onBiosampleFeatureHover?: (args: {\n    trackId: string;\n    row: BiosampleRowInfo;\n    rect: Rect;\n  }) => void;\n  biosampleFeatureTooltip?: FC<Rect>;\n  biosampleSignalTooltip?: FC<ValuedPoint[]>;\n  biosampleMethylTooltip?: FC<ValuedPoint[]>;\n};\n\nconst assayColors: Record<string, string> = {\n  dnase: \"#06da93\",\n  h3k4me3: \"#ff0000\",\n  h3k27ac: \"#ffcd00\",\n  ctcf: \"#00b0d0\",\n  atac: \"#02c7b9\",\n  rnaseq: \"#00aa00\",\n  chromhmm: \"#00ff00\",\n  ccre: \"#000000\",\n  wgbs: \"#648bd8\",\n};\n\nconst defaultBigWig: Omit<BigWigConfig, \"id\" | \"title\" | \"url\"> = {\n  trackType: TrackType.BigWig,\n  height: 50,\n  displayMode: DisplayMode.Full,\n  titleSize: 12,\n};\n\nconst defaultBigBed: Omit<BigBedConfig, \"id\" | \"title\" | \"url\"> = {\n  trackType: TrackType.BigBed,\n  height: 20,\n  displayMode: DisplayMode.Dense,\n  titleSize: 12,\n};\n\nconst defaultMethylC: Omit<MethylCConfig, \"id\" | \"title\" | \"urls\"> = {\n  trackType: TrackType.MethylC,\n  height: 100,\n  displayMode: DisplayMode.Split,\n  titleSize: 12,\n  color: \"#648bd8\",\n  colors: {\n    cpg: \"#648bd8\",\n    chg: \"#ff944d\",\n    chh: \"#ff00ff\",\n    depth: \"#525252\",\n  },\n};\n\nexport function createBiosampleTrack(\n  row: BiosampleRowInfo,\n  options: CreateTrackOptions,\n): Track {\n  const assay = row.assay.toLowerCase();\n  const color = assayColors[assay] ?? \"#000000\";\n  const trackContext = options.trackContext;\n\n  switch (assay) {\n    case \"chromhmm\":\n    case \"ccre\":\n      return {\n        ...defaultBigBed,\n        id: row.id,\n        url: row.url ?? \"\",\n        title: row.displayName,\n        color,\n        onClick: trackContext?.onBiosampleFeatureClick\n          ? (rect: Rect) =>\n              trackContext.onBiosampleFeatureClick?.({\n                trackId: row.id,\n                row,\n                rect,\n              })\n          : undefined,\n        onHover: trackContext?.onBiosampleFeatureHover\n          ? (rect: Rect) =>\n              trackContext.onBiosampleFeatureHover?.({\n                trackId: row.id,\n                row,\n                rect,\n              })\n          : undefined,\n        tooltip: trackContext?.biosampleFeatureTooltip,\n      };\n    case \"wgbs\":\n      return {\n        ...defaultMethylC,\n        id: row.id,\n        title: row.displayName,\n        maskCpgByCoverage: true,\n        tooltip: trackContext?.biosampleMethylTooltip,\n        urls: {\n          plusStrand: {\n            cpg: { url: row.cpgPlus ?? \"\" },\n            chg: { url: \"\" },\n            chh: { url: \"\" },\n            depth: { url: row.coverage ?? \"\" },\n          },\n          minusStrand: {\n            cpg: { url: row.cpgMinus ?? \"\" },\n            chg: { url: \"\" },\n            chh: { url: \"\" },\n            depth: { url: row.coverage ?? \"\" },\n          },\n        },\n      };\n    default:\n      return {\n        ...defaultBigWig,\n        id: row.id,\n        url: row.url ?? \"\",\n        title: row.displayName,\n        color,\n        tooltip: trackContext?.biosampleSignalTooltip,\n      };\n  }\n}\n","import { capitalize } from \"@mui/material\";\nimport { FolderDefinition } from \"../../types\";\nimport {\n  BiosampleDataFile,\n  BiosampleRowInfo,\n  BiosampleTrackInfo,\n} from \"./types\";\nimport {\n  defaultColumns,\n  defaultGroupingModel,\n  defaultLeafField,\n  sortedByAssayColumns,\n  sortedByAssayGroupingModel,\n  sortedByAssayLeafField,\n} from \"./columns\";\nimport { formatAssayType } from \"./constants\";\nimport { BiosampleViewSelector } from \"./BiosampleViewSelector\";\nimport BiosampleGroupingCell from \"./BiosampleGroupingCell\";\nimport { BiosampleTreeItem } from \"./BiosampleTreeItem\";\nimport { createBiosampleTrack } from \"./toTrack\";\n\n/** Flatten a biosample track into one row per assay. */\nfunction flattenTrackIntoRows(\n  folderId: string,\n  track: BiosampleTrackInfo,\n): BiosampleRowInfo[] {\n  const { ontology, lifeStage, sampleType, displayName, collection } = track;\n\n  // Keep cCRE rows first so aggregate selections stay prominent in the UI.\n  const sortedAssays = [...track.assays].sort((a, b) => {\n    const aIsCcre = a.assay.toLowerCase() === \"ccre\";\n    const bIsCcre = b.assay.toLowerCase() === \"ccre\";\n    if (aIsCcre && !bIsCcre) return -1;\n    if (!aIsCcre && bIsCcre) return 1;\n    return 0;\n  });\n\n  return sortedAssays.map(\n    ({\n      id,\n      assay,\n      experimentAccession,\n      fileAccession,\n      url,\n      cpgPlus,\n      cpgMinus,\n      coverage,\n    }) => ({\n      id: `${folderId}/${id}`,\n      ontology: capitalize(ontology),\n      lifeStage: capitalize(lifeStage),\n      sampleType: capitalize(sampleType),\n      displayName: capitalize(displayName),\n      assay: formatAssayType(assay),\n      experimentAccession,\n      fileAccession,\n      url,\n      collection,\n      cpgPlus,\n      cpgMinus,\n      coverage,\n    }),\n  );\n}\n\nfunction transformData(\n  folderId: string,\n  data: BiosampleDataFile,\n): BiosampleRowInfo[] {\n  return data.tracks.flatMap((track) => flattenTrackIntoRows(folderId, track));\n}\n\nexport interface CreateBiosampleFolderOptions {\n  id: string;\n  label: string;\n  description?: string;\n  data: BiosampleDataFile;\n}\n\n/**\n * Build a biosample folder with its data, tree builder, and track factory.\n */\nexport function createBiosampleFolder(\n  options: CreateBiosampleFolderOptions,\n): FolderDefinition<BiosampleRowInfo> {\n  const { id, label, description, data } = options;\n  const rows = transformData(id, data);\n  const views = [\n    {\n      id: \"default\",\n      label: \"Tissue\",\n      columns: defaultColumns,\n      groupingModel: defaultGroupingModel,\n      leafField: defaultLeafField,\n    },\n    {\n      id: \"by-assay\",\n      label: \"Assay\",\n      columns: sortedByAssayColumns,\n      groupingModel: sortedByAssayGroupingModel,\n      leafField: sortedByAssayLeafField,\n    },\n  ];\n\n  return {\n    id,\n    label,\n    description,\n    rows,\n    columns: defaultColumns,\n    groupingModel: defaultGroupingModel,\n    leafField: defaultLeafField,\n    createTrack: createBiosampleTrack,\n    views,\n    ViewSelector: BiosampleViewSelector,\n    GroupingCellComponent: BiosampleGroupingCell,\n    TreeItemComponent: BiosampleTreeItem,\n  };\n}\n","import { createBiosampleFolder } from \"./shared/createFolder\";\nimport humanData from \"./data/humans_fixed.json\";\nimport { BiosampleDataFile } from \"./shared/types\";\n\n/**\n * Human biosamples folder configuration for GRCh38 assembly.\n *\n * Contains epigenomic data (DNase, ATAC, H3K4me3, H3K27ac, CTCF, cCRE, RNA-seq, ChromHMM)\n * from human tissue samples, primary cells, cell lines, and organoids.\n */\nexport const humanBiosamplesFolder = createBiosampleFolder({\n  id: \"human-biosamples\",\n  label: \"Human Biosamples\",\n  description:\n    \"Epigenomic data from human tissue samples, primary cells, cell lines, and organoids.\",\n  data: humanData as BiosampleDataFile,\n});\n","import { createBiosampleFolder } from \"./shared/createFolder\";\nimport mouseData from \"./data/mouse.json\";\nimport { BiosampleDataFile } from \"./shared/types\";\n\n/**\n * Mouse biosamples folder configuration for mm10 assembly.\n *\n * Contains epigenomic data (DNase, ATAC, H3K4me3, H3K27ac, CTCF, cCRE, RNA-seq, ChromHMM)\n * from mouse tissue samples, primary cells, cell lines, and organoids.\n */\nexport const mouseBiosamplesFolder = createBiosampleFolder({\n  id: \"mouse-biosamples\",\n  label: \"Mouse Biosamples\",\n  description:\n    \"Epigenomic data from mouse tissue samples, primary cells, cell lines, and organoids.\",\n  data: mouseData as BiosampleDataFile,\n});\n","import { GridColDef } from \"@mui/x-data-grid-premium\";\nimport { GeneRowInfo } from \"./types\";\n\n/**\n * Format versions array as comma-separated string with \"v\" prefix\n * e.g., [29, 40] -> \"v29, v40\"\n */\nfunction formatVersions(versions: number[]): string {\n  return versions.map((v) => `v${v}`).join(\", \");\n}\n\nconst displayNameCol: GridColDef<GeneRowInfo> = {\n  field: \"displayName\",\n  headerName: \"Name\",\n  flex: 1,\n  minWidth: 200,\n};\n\nconst versionsCol: GridColDef<GeneRowInfo> = {\n  field: \"versions\",\n  headerName: \"Versions\",\n  width: 150,\n  valueFormatter: (value: number[]) => value && formatVersions(value),\n};\n\n/**\n * Default columns for genes DataGrid (flat list, no grouping)\n */\nexport const defaultColumns: GridColDef<GeneRowInfo>[] = [\n  displayNameCol,\n  versionsCol,\n];\n\n/**\n * No grouping for genes - flat list\n */\nexport const defaultGroupingModel: string[] = [];\n\n/**\n * Leaf field - the raw track ID (without folder prefix) used as the tree view leaf label\n */\nexport const defaultLeafField = \"trackId\";\n","import {\n  DisplayMode,\n  Track,\n  TrackType,\n  Transcript,\n  TranscriptConfig,\n} from \"@weng-lab/genomebrowser\";\nimport type { FC } from \"react\";\nimport { CreateTrackOptions } from \"../../types\";\nimport { GeneRowInfo } from \"./types\";\n\nexport type GeneTrackContext = {\n  onGeneClick?: (args: {\n    trackId: string;\n    row: GeneRowInfo;\n    transcript: Transcript;\n  }) => void;\n  onGeneHover?: (args: {\n    trackId: string;\n    row: GeneRowInfo;\n    transcript: Transcript;\n  }) => void;\n  geneTooltip?: FC<Transcript>;\n};\n\nconst defaultTranscript: Omit<TranscriptConfig, \"id\" | \"assembly\" | \"version\"> =\n  {\n    title: \"GENCODE Genes\",\n    trackType: TrackType.Transcript,\n    displayMode: DisplayMode.Squish,\n    height: 100,\n    color: \"#0c184a\",\n    canonicalColor: \"#100e98\",\n    highlightColor: \"#3c69e8\",\n    titleSize: 12,\n  };\n\nexport function createGeneTrack(\n  row: GeneRowInfo,\n  options: CreateTrackOptions,\n): Track {\n  const trackContext = options.trackContext;\n\n  return {\n    ...defaultTranscript,\n    id: row.id,\n    assembly: options.assembly,\n    version: row.versions[row.versions.length - 1],\n    onClick: trackContext?.onGeneClick\n      ? (transcript: Transcript) =>\n          trackContext.onGeneClick?.({ trackId: row.id, row, transcript })\n      : undefined,\n    onHover: trackContext?.onGeneHover\n      ? (transcript: Transcript) =>\n          trackContext.onGeneHover?.({ trackId: row.id, row, transcript })\n      : undefined,\n    tooltip: trackContext?.geneTooltip,\n  };\n}\n","import { FolderDefinition } from \"../../types\";\nimport { GeneDataFile, GeneRowInfo, GeneTrackInfo } from \"./types\";\nimport {\n  defaultColumns,\n  defaultGroupingModel,\n  defaultLeafField,\n} from \"./columns\";\nimport { createGeneTrack } from \"./toTrack\";\n\n/** Genes map 1:1 from JSON track entries to table rows. */\nfunction trackToRow(folderId: string, track: GeneTrackInfo): GeneRowInfo {\n  return {\n    id: `${folderId}/${track.id}`,\n    trackId: track.id,\n    displayName: track.displayName,\n    versions: track.versions,\n  };\n}\n\nfunction transformData(folderId: string, data: GeneDataFile): GeneRowInfo[] {\n  return data.map((track) => trackToRow(folderId, track));\n}\n\nexport interface CreateGeneFolderOptions {\n  id: string;\n  label: string;\n  description?: string;\n  data: GeneDataFile;\n}\n\n/** Build a gene folder with its row lookup, tree, and track factory. */\nexport function createGeneFolder(\n  options: CreateGeneFolderOptions,\n): FolderDefinition<GeneRowInfo> {\n  const { id, label, description, data } = options;\n  const rows = transformData(id, data);\n\n  return {\n    id,\n    label,\n    description,\n    rows,\n    columns: defaultColumns,\n    groupingModel: defaultGroupingModel,\n    leafField: defaultLeafField,\n    createTrack: createGeneTrack,\n  };\n}\n","import { createGeneFolder } from \"./shared/createFolder\";\nimport humanData from \"./data/human.json\";\nimport { GeneDataFile } from \"./shared/types\";\n\n/**\n * Gene annotations folder for human (GRCh38 assembly)\n *\n * Contains gene annotation tracks like GENCODE that users can\n * select to display in the genome browser.\n */\nexport const humanGenesFolder = createGeneFolder({\n  id: \"human-genes\",\n  label: \"Genes\",\n  description: \"Gene annotation tracks\",\n  data: humanData as GeneDataFile,\n});\n","import { createGeneFolder } from \"./shared/createFolder\";\nimport mouseData from \"./data/mouse.json\";\nimport { GeneDataFile } from \"./shared/types\";\n\n/**\n * Gene annotations folder for human (GRCh38 assembly)\n *\n * Contains gene annotation tracks like GENCODE that users can\n * select to display in the genome browser.\n */\nexport const mouseGenesFolder = createGeneFolder({\n  id: \"mouse-genes\",\n  label: \"Genes\",\n  description: \"Gene annotation tracks\",\n  data: mouseData as GeneDataFile,\n});\n","import { GridColDef } from \"@mui/x-data-grid-premium\";\nimport { OtherTrackInfo } from \"./types\";\n\nconst nameCol: GridColDef<OtherTrackInfo> = {\n  field: \"name\",\n  headerName: \"Name\",\n  flex: 1,\n  minWidth: 200,\n};\n\nconst descriptionCol: GridColDef<OtherTrackInfo> = {\n  field: \"description\",\n  headerName: \"Description\",\n  flex: 2,\n  minWidth: 300,\n};\n\nexport const defaultColumns: GridColDef<OtherTrackInfo>[] = [\n  nameCol,\n  descriptionCol,\n];\n\nexport const defaultGroupingModel: string[] = [];\n\nexport const defaultLeafField = \"id\";\n","import { jsxs as h, jsx as e } from \"react/jsx-runtime\";\nconst _0 = (o) => /* @__PURE__ */ h(\"g\", { children: [\n  /* @__PURE__ */ e(\n    \"path\",\n    {\n      d: \"M 10 20 C 5 -5 95 -10 100 35 L 100 100 L 80 100 L 80 90 C 90 105 10 105 0 80 C 0 45 40 40 60 45 L 80 50 C 95 30 40 5 10 35\",\n      ...o\n    }\n  ),\n  /* @__PURE__ */ e(\"path\", { fill: \"#ffffff\", d: \"M 77 70 C 70 90 30 90 22 80 C 10 50 80 60 77 70\" })\n] }), A0 = (o) => /* @__PURE__ */ h(\"g\", { children: [\n  /* @__PURE__ */ e(\n    \"path\",\n    {\n      d: \"M 20 0 L 0 0 L 0 100 L 20 100 L 20 80 C 10 110 90 110 100 70 L 100 60 C 90 10 10 10 20 40 L 20 40 L 20 0\",\n      ...o\n    }\n  ),\n  /* @__PURE__ */ e(\"path\", { d: \"M 79 60 C 80 95 20 95 20 65 C 20 30 80 30 79 65\", fill: \"#ffffff\" })\n] }), N0 = (o) => /* @__PURE__ */ h(\"g\", { children: [\n  /* 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RNAAlphabet,\n  Xo as RNALogo,\n  Fo as RawLogo,\n  H as S,\n  W as T,\n  X as U,\n  b as V,\n  j as W,\n  o0 as X,\n  u0 as XAxis,\n  p0 as Y,\n  zo as YAxis,\n  Ro as YAxisFrequency,\n  Bo as YAxisWithNegatives,\n  x0 as YGridlines,\n  Q as Z,\n  _0 as a,\n  A0 as b,\n  N0 as d,\n  w0 as e,\n  E0 as f,\n  S0 as g,\n  v0 as h,\n  O0 as i,\n  T0 as j,\n  z0 as k,\n  R0 as l,\n  B0 as m,\n  F0 as n,\n  G0 as p,\n  I0 as q,\n  Y0 as r,\n  D0 as t,\n  H0 as u,\n  b0 as y\n};\n//# sourceMappingURL=logo-test.es.js.map\n","import {\n  ClipPath,\n  CustomTrackConfig,\n  CustomTrackProps,\n  DisplayMode,\n  fetchBigBedUrl,\n  Rect,\n  renderSquishBigBedData,\n  TrackType,\n  useBrowserStore,\n  useInteraction,\n  useRowHeight,\n  useXTransform,\n  Vibrant,\n  useTrackStore,\n} from \"@weng-lab/genomebrowser\";\nimport { DNALogo } from \"logo-test\";\nimport { useMemo, useState } from \"react\";\nimport motifData from \"./green-motifs.json\";\n\n// --- TF Peak BigBed Parser ---\n\ninterface TfPeakBigBedData {\n  chr: string;\n  start: number;\n  end: number;\n  name?: string;\n  score?: number;\n  color?: string;\n  tfName?: string;\n  expRatio?: string;\n  cCREId?: string;\n  experimentId?: string;\n  expSupport?: Record<string, Record<string, string>>;\n}\n\nfunction parseTfPeakBigBed(\n  chrom: string,\n  startBase: number,\n  endBase: number,\n  rest: string,\n): TfPeakBigBedData {\n  const entry: TfPeakBigBedData = {\n    chr: chrom,\n    start: startBase,\n    end: endBase,\n  };\n  const tokens = rest.split(\"\\t\");\n  if (tokens.length > 0) entry.name = tokens[0];\n  if (tokens.length > 1) entry.score = parseFloat(tokens[1]);\n  // tokens[2] = strand, tokens[3] = thickStart, tokens[4] = thickEnd\n  if (tokens.length > 5 && tokens[5] !== \".\" && tokens[5] !== \"0\") {\n    entry.color = tokens[5].includes(\",\")\n      ? tokens[5].startsWith(\"rgb\")\n        ? tokens[5]\n        : \"rgb(\" + tokens[5] + \")\"\n      : tokens[5];\n  }\n  // tokens[6] = blockCount, tokens[7] = blockSizes, tokens[8] = blockStarts\n  if (tokens.length > 9) entry.tfName = tokens[9];\n  if (tokens.length > 10) entry.expRatio = tokens[10];\n  if (tokens.length > 11) entry.cCREId = tokens[11];\n  if (tokens.length > 12) entry.experimentId = tokens[12];\n  if (tokens.length > 13) {\n    try {\n      entry.expSupport = JSON.parse(tokens[13]);\n    } catch {\n      // leave undefined if JSON is malformed\n    }\n  }\n  return entry;\n}\n\n// --- Types ---\n\ntype OverlayData = {\n  primary: TfPeakBigBedData[];\n  overlay: Rect[];\n};\n\ntype OverlayInteractionRect = Rect & {\n  chr?: string;\n  pwm?: number[][];\n  tfName?: string;\n  expRatio?: string;\n  cCREId?: string;\n  experimentId?: string;\n  expSupport?: Record<string, Record<string, string>>;\n};\n\n// The config type — extra fields go directly on the config\ntype OverlayBigBedConfig = CustomTrackConfig<OverlayInteractionRect> & {\n  primaryUrl: string;\n  overlayUrl: string;\n  baseColor?: string;\n  overlayColor?: string;\n  filter?: string[];\n};\n\n// --- Helpers ---\n\nfunction nameKey(name?: string) {\n  if (!name) return \"\";\n  return name.split(/[-_]/)[0].trim().toLowerCase();\n}\n\nfunction buildOverlayIndex(rects: Rect[]) {\n  return rects.reduce<Record<string, Rect[]>>((acc, rect) => {\n    const key = nameKey(rect.name);\n    if (!key) return acc;\n    (acc[key] ??= []).push(rect);\n    return acc;\n  }, {});\n}\n\nfunction intervalsOverlap(\n  aStart: number,\n  aEnd: number,\n  bStart: number,\n  bEnd: number,\n) {\n  return aStart <= bEnd && bStart <= aEnd;\n}\n\nfunction scoreColor(score?: number) {\n  const t = Math.min(Math.max(score ?? 0, 0), 1000) / 1000;\n  const r = Math.round(0xe3 + (0x00 - 0xe3) * t);\n  const g = Math.round(0xe3 + (0x00 - 0xe3) * t);\n  const b = Math.round(0xe3 + (0x00 - 0xe3) * t);\n  return `#${r.toString(16).padStart(2, \"0\")}${g.toString(16).padStart(2, \"0\")}${b.toString(16).padStart(2, \"0\")}`;\n}\n\n// --- Motif data lookup ---\n\ntype MotifEntry = { trimmed_ppm: number[][] };\nconst motifLookup = motifData as Record<string, MotifEntry>;\n\nfunction lookupPwm(name?: string): number[][] | undefined {\n  const key = nameKey(name)?.toUpperCase();\n  if (!key) return undefined;\n  const entry = motifLookup[key];\n  return entry?.trimmed_ppm;\n}\n\n// --- Tooltip ---\n\nfunction tfDisplayName(name?: string): string {\n  return nameKey(name)?.toUpperCase() || name || \"Unknown\";\n}\n\nfunction TooltipRow({\n  label,\n  value,\n  y,\n}: {\n  label: string;\n  value: string;\n  y: number;\n}) {\n  return (\n    <g transform={`translate(0, ${y})`}>\n      <text x={8} y={0} fontSize={10} fill=\"#888\" dominantBaseline=\"hanging\">\n        {label}\n      </text>\n      <text x={100} y={0} fontSize={10} fill=\"#333\" dominantBaseline=\"hanging\">\n        {value}\n      </text>\n    </g>\n  );\n}\n\nfunction TfPeaksTooltip(rect: OverlayInteractionRect) {\n  const pwm = rect.pwm;\n  const label = tfDisplayName(rect.name);\n  const totalWidth = 340;\n  const pad = 8;\n  const lineH = 14;\n  const titleH = 18;\n\n  // Build metadata rows (single-value rows)\n  const metaRows: { label: string; value: string }[] = [];\n  if (rect.score != null)\n    metaRows.push({ label: \"Score\", value: `${rect.score}` });\n  metaRows.push({\n    label: \"Position\",\n    value: `${rect.chr ? rect.chr + \":\" : \"\"}${rect.start.toLocaleString()}-${rect.end.toLocaleString()}`,\n  });\n\n  // Multi-value rows: split comma-separated cCREs, group 4 per row, cap at 5\n  const allCCREItems = rect.cCREId\n    ? rect.cCREId\n        .split(\",\")\n        .map((s) => s.trim())\n        .filter(Boolean)\n    : [];\n  const maxCCREs = 5;\n  const cCREItems = allCCREItems.slice(0, maxCCREs);\n  const hiddenCCREs = Math.max(0, allCCREItems.length - maxCCREs);\n  const cCRERows: string[][] = [];\n  for (let i = 0; i < cCREItems.length; i += 4) {\n    cCRERows.push(cCREItems.slice(i, i + 4));\n  }\n\n  // Extract unique sorted biosamples from expSupport\n  const allBiosamples: string[] = [];\n  if (rect.expSupport) {\n    const seen = new Set<string>();\n    for (const cellLine of Object.keys(rect.expSupport)) {\n      if (!seen.has(cellLine)) {\n        seen.add(cellLine);\n        allBiosamples.push(cellLine);\n      }\n    }\n    allBiosamples.sort((a, b) => a.localeCompare(b));\n  }\n  const maxBiosamples = 12;\n  const biosampleItems = allBiosamples.slice(0, maxBiosamples);\n  const hiddenBiosamples = Math.max(0, allBiosamples.length - maxBiosamples);\n  const biosampleText = biosampleItems.join(\", \");\n  const biosampleMoreText =\n    hiddenBiosamples > 0 ? ` ...and ${hiddenBiosamples} more` : \"\";\n  const biosampleCharsPerLine = Math.floor((totalWidth - 2 * pad) / 5.2);\n  const biosampleContentLines = Math.max(\n    1,\n    Math.ceil(\n      (biosampleText.length + biosampleMoreText.length) / biosampleCharsPerLine,\n    ),\n  );\n\n  // Layout: compute y offsets upfront\n  const hasLogo = pwm && pwm.length > 0;\n\n  const logoHeight = hasLogo ? 80 : 0;\n  const logoSectionH = hasLogo ? logoHeight + 4 : 0;\n  const metaSectionH = metaRows.length * lineH;\n\n  // cCRE section: label row + one row per group of 4 + optional \"+N more\" row\n  const cCREGap = cCRERows.length > 0 ? 8 : 0;\n  const cCREHeaderH = cCRERows.length > 0 ? lineH : 0;\n  const cCREMoreH = hiddenCCREs > 0 ? lineH : 0;\n  const cCRESectionH = cCRERows.length * lineH + cCREMoreH;\n\n  // Biosamples section\n  const biosampleGap = biosampleContentLines > 0 ? 8 : 0;\n  const biosampleHeaderH = biosampleContentLines > 0 ? lineH : 0;\n  const biosampleSectionH = biosampleContentLines * lineH;\n\n  const titleY = pad;\n  const logoY = titleY + titleH;\n  const metaY = logoY + logoSectionH;\n  const cCREY = metaY + metaSectionH + cCREGap;\n  const cCREDataY = cCREY + cCREHeaderH;\n  const biosampleY = cCREDataY + cCRESectionH + biosampleGap;\n  const biosampleDataY = biosampleY + biosampleHeaderH;\n  const totalHeight = biosampleDataY + biosampleSectionH + pad;\n\n  return (\n    <g>\n      <rect\n        width={totalWidth}\n        height={totalHeight}\n        fill=\"white\"\n        rx={3}\n        style={{ filter: \"drop-shadow(0px 0px 5px rgba(0,0,0,0.3))\" }}\n      />\n\n      {/* Title */}\n      <text x={pad} y={titleY + 12} fontSize={12} fontWeight=\"bold\" fill=\"#333\">\n        {label}\n      </text>\n\n      {/* Logo */}\n      {hasLogo && (\n        <g transform={`translate(${pad}, ${logoY})`}>\n          <DNALogo\n            ppm={pwm!}\n            mode=\"INFORMATION_CONTENT\"\n            width={totalWidth - 2 * pad}\n            height={logoHeight}\n          />\n        </g>\n      )}\n\n      {/* Metadata rows */}\n      {metaRows.map((row, i) => (\n        <TooltipRow\n          key={row.label}\n          label={row.label}\n          value={row.value}\n          y={metaY + i * lineH}\n        />\n      ))}\n\n      {/* Overlapping cCREs */}\n      {cCRERows.length > 0 && (\n        <g>\n          <line\n            x1={pad}\n            x2={totalWidth - pad}\n            y1={cCREY - 4}\n            y2={cCREY - 4}\n            stroke=\"#ddd\"\n          />\n          <text\n            x={pad}\n            y={cCREY + 2}\n            fontSize={9}\n            fontWeight=\"bold\"\n            fill=\"#666\"\n            dominantBaseline=\"hanging\"\n          >\n            Overlapping cCREs\n          </text>\n          {cCRERows.map((group, i) => (\n            <text\n              key={i}\n              x={pad}\n              y={cCREDataY + i * lineH + 2}\n              fontSize={9}\n              fill=\"#333\"\n              dominantBaseline=\"hanging\"\n            >\n              {group.join(\", \")}\n            </text>\n          ))}\n          {hiddenCCREs > 0 && (\n            <text\n              x={pad}\n              y={cCREDataY + cCRERows.length * lineH + 2}\n              fontSize={9}\n              fill=\"#aaa\"\n              dominantBaseline=\"hanging\"\n            >\n              +{hiddenCCREs} more...\n            </text>\n          )}\n        </g>\n      )}\n\n      {/* Biosamples */}\n      {biosampleContentLines > 0 && (\n        <g>\n          <line\n            x1={pad}\n            x2={totalWidth - pad}\n            y1={biosampleY - 4}\n            y2={biosampleY - 4}\n            stroke=\"#ddd\"\n          />\n          <text\n            x={pad}\n            y={biosampleY + 2}\n            fontSize={9}\n            fontWeight=\"bold\"\n            fill=\"#666\"\n            dominantBaseline=\"hanging\"\n          >\n            Biosamples\n          </text>\n          <foreignObject\n            x={pad}\n            y={biosampleDataY}\n            width={totalWidth - 2 * pad}\n            height={biosampleSectionH}\n          >\n            <div\n              style={{\n                color: \"#333\",\n                fontSize: \"9px\",\n                lineHeight: `${lineH}px`,\n                margin: 0,\n                padding: 0,\n                overflow: \"hidden\",\n                whiteSpace: \"normal\",\n                wordBreak: \"break-word\",\n              }}\n            >\n              {biosampleText}\n              {hiddenBiosamples > 0 && (\n                <span style={{ color: \"#aaa\" }}>{biosampleMoreText}</span>\n              )}\n            </div>\n          </foreignObject>\n        </g>\n      )}\n    </g>\n  );\n}\n\n// --- Settings Panel ---\n\nfunction TfPeaksSettings({ id }: { id: string }) {\n  const track = useTrackStore((state) => state.getTrack(id)) as\n    | OverlayBigBedConfig\n    | undefined;\n  const editTrack = useTrackStore((state) => state.editTrack);\n  const [input, setInput] = useState((track?.filter || []).join(\", \"));\n\n  const handleChange = (e: React.ChangeEvent<HTMLInputElement>) => {\n    const value = e.target.value;\n    setInput(value);\n    const names = value\n      .split(\",\")\n      .map((s) => s.trim().toUpperCase())\n      .filter(Boolean);\n    editTrack<OverlayBigBedConfig>(id, {\n      filter: names.length > 0 ? names : undefined,\n    });\n  };\n\n  return (\n    <div\n      style={{\n        display: \"flex\",\n        flexDirection: \"column\",\n        alignItems: \"flex-start\",\n        paddingBlock: \"5px\",\n        paddingInline: \"10px\",\n        gap: \"3px\",\n      }}\n    >\n      <div style={{ fontWeight: \"bold\" }}>Filter TFs</div>\n      <input\n        value={input}\n        onChange={handleChange}\n        placeholder=\"e.g. CTCF, TP53, GATA1\"\n        style={{ width: \"100%\" }}\n      />\n    </div>\n  );\n}\n\n// --- Renderer ---\n\nfunction OverlayBigBedRenderer(\n  props: CustomTrackProps<OverlayData> & OverlayBigBedConfig,\n) {\n  const {\n    data,\n    dimensions,\n    id,\n    height: trackHeight,\n    color: _color,\n    baseColor: _baseColorProp,\n    overlayColor: overlayColorProp,\n    filter,\n    ...rest\n  } = props;\n  const domain = useBrowserStore((state) => state.domain);\n  const { totalWidth, sideWidth } = dimensions;\n  const { x, reverseX } = useXTransform(totalWidth);\n\n  const filterSet = useMemo(\n    () =>\n      filter && filter.length > 0\n        ? new Set(filter.map((f) => f.toUpperCase()))\n        : null,\n    [filter],\n  );\n\n  const visiblePrimary = useMemo(() => {\n    let visible = (data?.primary || []).filter(\n      (r) => r.end >= domain.start && r.start <= domain.end,\n    );\n    if (filterSet) {\n      visible = visible.filter((r) =>\n        filterSet.has(nameKey(r.name)?.toUpperCase()),\n      );\n    }\n    return visible;\n  }, [data, domain.end, domain.start, filterSet]);\n\n  const rows = useMemo(\n    () => renderSquishBigBedData(visiblePrimary, x),\n    [visiblePrimary, x],\n  );\n\n  // Index primary data by \"name:start:end\" for fast TF metadata lookup\n  const primaryIndex = useMemo(() => {\n    const index = new Map<string, TfPeakBigBedData>();\n    for (const item of visiblePrimary) {\n      index.set(`${item.name}:${item.start}:${item.end}`, item);\n    }\n    return index;\n  }, [visiblePrimary]);\n\n  const rowHeight = useRowHeight(rows.length, id);\n  const height = Math.max(trackHeight, rowHeight * Math.max(rows.length, 1));\n  const overlayByName = useMemo(\n    () => buildOverlayIndex(data?.overlay || []),\n    [data],\n  );\n\n  const overlayColor = overlayColorProp || Vibrant[3];\n  const cursor = rest.onClick ? \"pointer\" : \"default\";\n\n  const { handleClick, handleHover, handleLeave } =\n    useInteraction<OverlayInteractionRect>({\n      onClick: rest.onClick,\n      onHover: rest.onHover,\n      onLeave: rest.onLeave,\n      tooltip: rest.tooltip,\n    });\n\n  return (\n    <g\n      width={totalWidth}\n      height={height}\n      clipPath={`url(#${id})`}\n      transform={`translate(-${sideWidth}, 0)`}\n    >\n      <rect width={totalWidth} height={height} fill=\"transparent\" />\n      <defs>\n        <ClipPath id={id} width={totalWidth} height={height} />\n      </defs>\n      {rows.map((row, rowIndex) => {\n        const baseY = rowHeight * 0.2;\n        const baseH = rowHeight * 0.6;\n        return (\n          <g\n            key={`row_${rowIndex}`}\n            transform={`translate(0, ${rowIndex * rowHeight})`}\n          >\n            {row.map((rect, ri) => {\n              const realStart = Math.round(reverseX(rect.start));\n              const realEnd = Math.round(reverseX(rect.end));\n              const baseName = rect.rectname;\n              const attached = (\n                overlayByName[nameKey(rect.rectname)] || []\n              ).filter((a) =>\n                intervalsOverlap(realStart, realEnd, a.start, a.end),\n              );\n              const fill = scoreColor(rect.score);\n              const meta = primaryIndex.get(\n                `${baseName}:${realStart}:${realEnd}`,\n              );\n              const baseRect: OverlayInteractionRect = {\n                start: realStart,\n                end: realEnd,\n                name: baseName,\n                color: fill,\n                score: rect.score,\n                chr: meta?.chr,\n                pwm: attached.length > 0 ? lookupPwm(baseName) : undefined,\n                tfName: meta?.tfName,\n                expRatio: meta?.expRatio,\n                cCREId: meta?.cCREId,\n                experimentId: meta?.experimentId,\n                expSupport: meta?.expSupport,\n              };\n\n              return (\n                <g key={`${id}_${rowIndex}_${ri}`}>\n                  <rect\n                    style={{ cursor }}\n                    x={rect.start}\n                    y={baseY}\n                    width={Math.max(rect.end - rect.start, 1)}\n                    height={baseH}\n                    fill={fill}\n                    opacity={0.9}\n                    onClick={() => handleClick(baseRect)}\n                    onMouseOver={(e) =>\n                      handleHover(baseRect, baseRect.name || \"\", e)\n                    }\n                    onMouseOut={() => handleLeave(baseRect)}\n                  />\n                  {attached.map((a, ai) => {\n                    const left = x(a.start);\n                    const right = x(a.end);\n                    return (\n                      <rect\n                        style={{ cursor }}\n                        key={`${id}_${rowIndex}_${ri}_a_${ai}`}\n                        x={left}\n                        y={baseY}\n                        width={Math.max(right - left, 1)}\n                        height={baseH}\n                        fill={a.color || overlayColor}\n                        opacity={0.9}\n                        onClick={() => handleClick(baseRect)}\n                        onMouseOver={(e) =>\n                          handleHover(baseRect, baseRect.name || \"\", e)\n                        }\n                        onMouseOut={() => handleLeave(baseRect)}\n                      />\n                    );\n                  })}\n                </g>\n              );\n            })}\n          </g>\n        );\n      })}\n    </g>\n  );\n}\n\n// --- Track config ---\n\nexport const PEAKS_BIGBED_URL =\n  \"https://users.wenglab.org/gaomingshi/no_trim.TF_name.rPeaks.bb\";\nexport const DECORATOR_BIGBED_URL =\n  \"https://users.wenglab.org/gaomingshi/no_trim.TF_name.decorator.bb\";\n\nexport const tfPeaksTrack: OverlayBigBedConfig = {\n  id: \"custom-tf-peaks\",\n  title: \"TF Peaks (Overlay)\",\n  shortLabel: \"TF Peaks\",\n  trackType: TrackType.Custom,\n  displayMode: DisplayMode.Full,\n  color: Vibrant[0],\n  height: 80,\n  primaryUrl: PEAKS_BIGBED_URL,\n  overlayUrl: DECORATOR_BIGBED_URL,\n  baseColor: \"#d1d5db\",\n  overlayColor: \"#36dd81\",\n  onClick: (rect) => {\n    console.log(\"Clicked on rect:\", rect);\n  },\n  tooltip: TfPeaksTooltip,\n  settingsPanel: TfPeaksSettings,\n  renderers: {\n    [DisplayMode.Full]: OverlayBigBedRenderer,\n  },\n  fetcher: async (ctx) => {\n    const track = ctx.track as OverlayBigBedConfig;\n    const [primary, overlay] = await Promise.all([\n      fetchBigBedUrl(track.primaryUrl, ctx, parseTfPeakBigBed),\n      fetchBigBedUrl(track.overlayUrl, ctx),\n    ]);\n    const error =\n      [primary.error, overlay.error].filter(Boolean).join(\"\\n\") || null;\n    return {\n      data: { primary: primary.data || [], overlay: overlay.data || [] },\n      error,\n    };\n  },\n};\n","import { Track } from \"@weng-lab/genomebrowser\";\nimport { tfPeaksTrack } from \"../../../Custom/TfPeaks\";\nimport { CreateTrackOptions } from \"../../types\";\nimport { OtherTrackInfo } from \"./types\";\n\nexport type OtherTracksTrackContext = {};\n\nexport function createOtherTrack(\n  row: OtherTrackInfo,\n  _options: CreateTrackOptions,\n): Track | null {\n  if ((row.sourceId ?? row.id) === \"tf-peaks\") {\n    return { ...tfPeaksTrack, id: row.id };\n  }\n\n  return null;\n}\n","import { FolderDefinition } from \"../../types\";\nimport { OtherTrackDataFile, OtherTrackInfo } from \"./types\";\nimport {\n  defaultColumns,\n  defaultGroupingModel,\n  defaultLeafField,\n} from \"./columns\";\nimport { createOtherTrack } from \"./toTrack\";\n\nfunction transformData(\n  folderId: string,\n  data: OtherTrackDataFile,\n): OtherTrackInfo[] {\n  return data.map((row) => ({\n    ...row,\n    sourceId: row.id,\n    id: `${folderId}/${row.id}`,\n  }));\n}\n\nexport interface CreateOtherTracksFolderOptions {\n  id: string;\n  label: string;\n  description?: string;\n  data: OtherTrackDataFile;\n}\n\nexport function createOtherTracksFolder(\n  options: CreateOtherTracksFolderOptions,\n): FolderDefinition<OtherTrackInfo> {\n  const { id, label, description, data } = options;\n  const rows = transformData(id, data);\n\n  return {\n    id,\n    label,\n    description,\n    rows,\n    columns: defaultColumns,\n    groupingModel: defaultGroupingModel,\n    leafField: defaultLeafField,\n    createTrack: createOtherTrack,\n  };\n}\n","import { createOtherTracksFolder } from \"./shared/createFolder\";\nimport humanData from \"./data/human.json\";\nimport { OtherTrackDataFile } from \"./shared/types\";\n\nexport const humanOtherTracksFolder = createOtherTracksFolder({\n  id: \"human-other-tracks\",\n  label: \"Other Tracks\",\n  description: \"Additional tracks\",\n  data: humanData as OtherTrackDataFile,\n});\n","import { Box } from \"@mui/material\";\n\nexport const MOHD_BASE_URL = \"https://downloads.mohdconsortium.org\";\n\nexport const MOHD_OME_CONFIG = {\n  atac: {\n    label: \"ATAC\",\n    color: \"#02c7b9\",\n    downloadPath: \"2_ATAC\",\n  },\n  rna: {\n    label: \"RNA\",\n    color: \"#00aa00\",\n    downloadPath: \"3_RNA\",\n  },\n  wgbs: {\n    label: \"WGBS\",\n    color: \"#648bd8\",\n    downloadPath: \"1_WGBS\",\n  },\n} as const;\n\nexport type MohdRawOme = keyof typeof MOHD_OME_CONFIG;\nexport type MohdOme = (typeof MOHD_OME_CONFIG)[MohdRawOme][\"label\"];\n\nconst MOHD_OME_LABELS = Object.values(MOHD_OME_CONFIG).map(\n  (config) => config.label,\n);\n\nexport function getMohdOmeConfig(rawOme: string) {\n  const config = MOHD_OME_CONFIG[rawOme.toLowerCase() as MohdRawOme];\n\n  if (!config) {\n    throw new Error(`Unknown MOHD ome: ${rawOme}`);\n  }\n\n  return config;\n}\n\nexport function createMohdFileUrl({\n  ome,\n  sampleId,\n  filename,\n}: {\n  ome: string;\n  sampleId: string;\n  filename: string;\n}) {\n  const { downloadPath } = getMohdOmeConfig(ome);\n  return `${MOHD_BASE_URL}/${downloadPath}/${sampleId}/${filename}`;\n}\n\nexport function isMohdOmeLabel(value: string) {\n  return MOHD_OME_LABELS.includes(value as MohdOme);\n}\n\nexport function MohdOmeIcon({ type }: { type: string }) {\n  const { color } = getMohdOmeConfig(type);\n\n  return (\n    <Box\n      data-testid={`mohd-ome-icon-${type.toLowerCase()}`}\n      sx={{\n        width: 12,\n        height: 12,\n        borderRadius: \"20%\",\n        bgcolor: color,\n      }}\n    />\n  );\n}\n","import { GridColDef } from \"@mui/x-data-grid-premium\";\nimport { FolderView } from \"../../types\";\nimport { MohdRowInfo } from \"./types\";\n\nconst descriptionCol: GridColDef<MohdRowInfo> = {\n  field: \"description\",\n  headerName: \"Description\",\n  minWidth: 220,\n  flex: 1.5,\n};\n\nconst sampleIdCol: GridColDef<MohdRowInfo> = {\n  field: \"sampleId\",\n  headerName: \"Sample ID\",\n  minWidth: 180,\n  flex: 1,\n};\n\nconst kitIdCol: GridColDef<MohdRowInfo> = {\n  field: \"kitId\",\n  headerName: \"Kit ID\",\n  minWidth: 140,\n  flex: 1,\n};\n\nconst trackCategoryCol: GridColDef<MohdRowInfo> = {\n  field: \"trackCategory\",\n  headerName: \"Track Type\",\n  minWidth: 140,\n  width: 140,\n};\n\nconst omeCol: GridColDef<MohdRowInfo> = {\n  field: \"ome\",\n  headerName: \"Ome\",\n  minWidth: 120,\n  width: 120,\n};\n\nconst siteCol: GridColDef<MohdRowInfo> = {\n  field: \"site\",\n  headerName: \"Site\",\n  minWidth: 100,\n  width: 100,\n};\n\nconst sexCol: GridColDef<MohdRowInfo> = {\n  field: \"sex\",\n  headerName: \"Sex\",\n  minWidth: 120,\n  width: 120,\n};\n\nconst statusCol: GridColDef<MohdRowInfo> = {\n  field: \"status\",\n  headerName: \"Status\",\n  minWidth: 120,\n  flex: 1,\n};\n\nexport const mohdColumns: GridColDef<MohdRowInfo>[] = [\n  descriptionCol,\n  trackCategoryCol,\n  sampleIdCol,\n  kitIdCol,\n  omeCol,\n  siteCol,\n  sexCol,\n  statusCol,\n];\n\nexport const mohdViews: FolderView[] = [\n  {\n    id: \"ome\",\n    label: \"Ome\",\n    columns: mohdColumns,\n    groupingModel: [\"ome\", \"site\", \"sampleId\"],\n    leafField: \"description\",\n  },\n  {\n    id: \"site\",\n    label: \"Site\",\n    columns: mohdColumns,\n    groupingModel: [\"site\", \"ome\", \"sampleId\"],\n    leafField: \"description\",\n  },\n];\n","import ChevronRightIcon from \"@mui/icons-material/ChevronRight\";\nimport ExpandMoreIcon from \"@mui/icons-material/ExpandMore\";\nimport { Box, IconButton, Stack, Tooltip } from \"@mui/material\";\nimport {\n  GridGroupNode,\n  GridRenderCellParams,\n  useGridApiContext,\n} from \"@mui/x-data-grid-premium\";\nimport { isMohdOmeLabel, MohdOmeIcon } from \"./config\";\n\nexport function MohdGroupingCell(params: GridRenderCellParams) {\n  const apiRef = useGridApiContext();\n  const isGroup = params.rowNode.type === \"group\";\n  const groupNode = params.rowNode as GridGroupNode;\n  const isExpanded = isGroup ? groupNode.childrenExpanded : false;\n  const groupingField = isGroup ? groupNode.groupingField : null;\n  const depth = params.rowNode.depth ?? 0;\n  const value = String(params.value ?? \"\");\n  const showOmeIcon =\n    (isGroup && groupingField === \"ome\") || isMohdOmeLabel(value);\n\n  const handleExpandClick = (e: React.MouseEvent) => {\n    e.stopPropagation();\n    apiRef.current.setRowChildrenExpansion(params.id, !isExpanded);\n  };\n\n  return (\n    <Box\n      sx={{\n        display: \"flex\",\n        alignItems: \"center\",\n        width: \"100%\",\n        ml: depth * 2,\n      }}\n    >\n      {isGroup && (\n        <IconButton size=\"small\" onClick={handleExpandClick} sx={{ mr: 0.5 }}>\n          {isExpanded ? (\n            <ExpandMoreIcon fontSize=\"small\" />\n          ) : (\n            <ChevronRightIcon fontSize=\"small\" />\n          )}\n        </IconButton>\n      )}\n      <Stack\n        direction=\"row\"\n        spacing={1}\n        alignItems=\"center\"\n        sx={{ flex: 1, overflow: \"hidden\" }}\n      >\n        {showOmeIcon && <MohdOmeIcon type={value} />}\n        <Tooltip title={value} placement=\"top-start\" enterDelay={500}>\n          <Box\n            sx={{\n              overflow: \"hidden\",\n              textOverflow: \"ellipsis\",\n              whiteSpace: \"nowrap\",\n              flex: 1,\n              fontWeight: isGroup ? \"bold\" : undefined,\n            }}\n          >\n            {params.formattedValue}\n          </Box>\n        </Tooltip>\n      </Stack>\n    </Box>\n  );\n}\n","import React from \"react\";\nimport { CustomTreeItem } from \"../../../TreeView/CustomTreeItem\";\nimport { CustomTreeItemProps } from \"../../../types\";\nimport { MohdOmeIcon } from \"./config\";\n\nexport const MohdTreeItem = React.forwardRef<\n  HTMLLIElement,\n  CustomTreeItemProps\n>(function MohdTreeItem(props, ref) {\n  return (\n    <CustomTreeItem\n      {...props}\n      ref={ref}\n      renderIcon={(type) => <MohdOmeIcon type={type} />}\n    />\n  );\n});\n","import { defineBigBedSchema } from \"@weng-lab/genomebrowser\";\nimport type { MohdFileRowInfo } from \"./types\";\n\nexport const mohdAtacFdrPeaksSchema = defineBigBedSchema({\n  name: \"string\",\n  score: \"number\",\n  strand: \"string\",\n  signalValue: \"number\",\n  pValue: \"number\",\n  qValue: \"number\",\n  peak: \"number\",\n});\n\nexport const mohdAtacPseudorepPeaksSchema = defineBigBedSchema({\n  name: \"string\",\n  score: \"number\",\n  strand: \"string\",\n  signalValue: \"number\",\n  pValue: \"number\",\n  qValue: \"number\",\n  peak: \"number\",\n});\n\nexport function getMohdBigBedSchema(row: MohdFileRowInfo) {\n  if (row.description === \"FDR 0.05 peaks\") {\n    return mohdAtacFdrPeaksSchema;\n  }\n\n  if (row.description === \"Pseudorep peaks\") {\n    return mohdAtacPseudorepPeaksSchema;\n  }\n\n  return undefined;\n}\n","import { InferBigBedRow } from \"@weng-lab/genomebrowser\";\nimport {\n  mohdAtacFdrPeaksSchema,\n  mohdAtacPseudorepPeaksSchema,\n} from \"./bigBedSchemas\";\n\ntype MohdBigBedRow =\n  | InferBigBedRow<typeof mohdAtacFdrPeaksSchema>\n  | InferBigBedRow<typeof mohdAtacPseudorepPeaksSchema>;\n\nfunction TooltipRow({\n  label,\n  value,\n  y,\n}: {\n  label: string;\n  value: string;\n  y: number;\n}) {\n  return (\n    <g transform={`translate(0, ${y})`}>\n      <text x={8} y={0} fontSize={10} fill=\"#888\" dominantBaseline=\"hanging\">\n        {label}\n      </text>\n      <text x={100} y={0} fontSize={10} fill=\"#333\" dominantBaseline=\"hanging\">\n        {value}\n      </text>\n    </g>\n  );\n}\n\nfunction formatValue(value: string | number | undefined) {\n  if (value === undefined) {\n    return \"-\";\n  }\n\n  return `${value}`;\n}\n\nexport function MohdBigBedTooltip(rect: MohdBigBedRow) {\n  const rows = [\n    {\n      label: \"Position\",\n      value: `${rect.chr}:${rect.start.toLocaleString()}-${rect.end.toLocaleString()}`,\n    },\n    { label: \"Name\", value: formatValue(rect.name) },\n    { label: \"Score\", value: formatValue(rect.score) },\n    { label: \"Strand\", value: formatValue(rect.strand) },\n    { label: \"Signal\", value: formatValue(rect.signalValue) },\n    { label: \"pValue\", value: formatValue(rect.pValue) },\n    { label: \"qValue\", value: formatValue(rect.qValue) },\n    { label: \"Peak\", value: formatValue(rect.peak) },\n  ];\n  const pad = 8;\n  const lineH = 14;\n  const titleH = 18;\n  const width = 280;\n  const height = pad + titleH + rows.length * lineH + pad;\n\n  return (\n    <g>\n      <rect\n        width={width}\n        height={height}\n        fill=\"white\"\n        rx={3}\n        style={{ filter: \"drop-shadow(0px 0px 5px rgba(0,0,0,0.3))\" }}\n      />\n      <text x={pad} y={pad + 12} fontSize={12} fontWeight=\"bold\" fill=\"#333\">\n        {rect.name || \"MOHD peak\"}\n      </text>\n      {rows.map((row, index) => (\n        <TooltipRow\n          key={row.label}\n          label={row.label}\n          value={row.value}\n          y={pad + titleH + index * lineH}\n        />\n      ))}\n    </g>\n  );\n}\n","import {\n  BigBedConfig,\n  BigWigConfig,\n  DisplayMode,\n  InferBigBedRow,\n  MethylCConfig,\n  Track,\n  TrackType,\n  ValuedPoint,\n} from \"@weng-lab/genomebrowser\";\nimport type { FC } from \"react\";\nimport { CreateTrackOptions } from \"../../types\";\nimport {\n  getMohdBigBedSchema,\n  mohdAtacFdrPeaksSchema,\n  mohdAtacPseudorepPeaksSchema,\n} from \"./bigBedSchemas\";\nimport { createMohdFileUrl, getMohdOmeConfig } from \"./config\";\nimport { MohdBigBedTooltip } from \"./MohdBigBedTooltip\";\nimport { MohdRowInfo } from \"./types\";\n\nexport type MohdTrackContext = {\n  mohdSignalTooltip?: FC<ValuedPoint[]>;\n  mohdMethylTooltip?: FC<ValuedPoint[]>;\n};\n\nconst defaultBigWig: Omit<BigWigConfig, \"id\" | \"title\" | \"url\"> = {\n  trackType: TrackType.BigWig,\n  height: 30,\n  displayMode: DisplayMode.Full,\n  titleSize: 12,\n  color: \"#02c7b9\",\n};\n\nconst defaultBigBed: Omit<BigBedConfig, \"id\" | \"title\" | \"url\"> = {\n  trackType: TrackType.BigBed,\n  height: 20,\n  displayMode: DisplayMode.Dense,\n  titleSize: 12,\n};\n\nconst defaultMethylC: Omit<MethylCConfig, \"id\" | \"title\" | \"urls\"> = {\n  trackType: TrackType.MethylC,\n  height: 75,\n  displayMode: DisplayMode.Split,\n  titleSize: 12,\n  color: \"#648bd8\",\n  maskCpgByCoverage: true,\n  colors: {\n    cpg: \"#648bd8\",\n    chg: \"#ff944d\",\n    chh: \"#ff00ff\",\n    depth: \"#525252\",\n  },\n};\n\ntype MohdBigBedRow =\n  | InferBigBedRow<typeof mohdAtacFdrPeaksSchema>\n  | InferBigBedRow<typeof mohdAtacPseudorepPeaksSchema>;\n\nfunction createTrackTitle(row: MohdRowInfo) {\n  return `${row.sampleId} ${row.description}`;\n}\n\nexport function createMohdTrack(\n  row: MohdRowInfo,\n  options: CreateTrackOptions,\n): Track | null {\n  const trackContext = options.trackContext;\n\n  if (row.kind === \"wgbs-methyl\") {\n    return {\n      ...defaultMethylC,\n      id: row.id,\n      title: createTrackTitle(row),\n      tooltip: trackContext?.mohdMethylTooltip,\n      urls: {\n        plusStrand: {\n          cpg: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.plusStrand.cpg,\n            }),\n          },\n          chg: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.plusStrand.chg,\n            }),\n          },\n          chh: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.plusStrand.chh,\n            }),\n          },\n          depth: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.plusStrand.depth,\n            }),\n          },\n        },\n        minusStrand: {\n          cpg: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.minusStrand.cpg,\n            }),\n          },\n          chg: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.minusStrand.chg,\n            }),\n          },\n          chh: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.minusStrand.chh,\n            }),\n          },\n          depth: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.minusStrand.depth,\n            }),\n          },\n        },\n      },\n    };\n  }\n\n  if (row.kind !== \"file\") {\n    return null;\n  }\n\n  const { color } = getMohdOmeConfig(row.ome);\n  const url = createMohdFileUrl({\n    ome: row.ome,\n    sampleId: row.sampleId,\n    filename: row.filename,\n  });\n\n  if (row.filename.endsWith(\".bigWig\")) {\n    return {\n      ...defaultBigWig,\n      id: row.id,\n      title: createTrackTitle(row),\n      url,\n      color,\n      tooltip: trackContext?.mohdSignalTooltip,\n    };\n  }\n\n  if (row.filename.endsWith(\".bigBed\")) {\n    return {\n      ...defaultBigBed,\n      id: row.id,\n      title: createTrackTitle(row),\n      url,\n      color,\n      schema: getMohdBigBedSchema(row),\n      tooltip: MohdBigBedTooltip,\n      onClick: (rect: MohdBigBedRow) => {\n        console.log(rect);\n      },\n    };\n  }\n\n  return null;\n}\n","import { ToggleButton, ToggleButtonGroup } from \"@mui/material\";\nimport { FolderView } from \"../../types\";\n\nexport interface MohdViewSelectorProps {\n  views: FolderView[];\n  activeViewId: string;\n  onChange: (viewId: string) => void;\n}\n\nexport function MohdViewSelector({\n  views,\n  activeViewId,\n  onChange,\n}: MohdViewSelectorProps) {\n  return (\n    <ToggleButtonGroup\n      exclusive\n      value={activeViewId}\n      size=\"small\"\n      onChange={(_event, viewId: string | null) => {\n        if (viewId) {\n          onChange(viewId);\n        }\n      }}\n    >\n      {views.map((view) => (\n        <ToggleButton key={view.id} value={view.id}>\n          {view.label}\n        </ToggleButton>\n      ))}\n    </ToggleButtonGroup>\n  );\n}\n","import { FolderDefinition } from \"../../types\";\nimport { MohdDataFile, MohdRowInfo } from \"./types\";\nimport { getMohdOmeConfig } from \"./config\";\nimport { mohdViews } from \"./columns\";\nimport { MohdGroupingCell } from \"./MohdGroupingCell\";\nimport { MohdTreeItem } from \"./MohdTreeItem\";\nimport { createMohdTrack } from \"./toTrack\";\nimport { MohdViewSelector } from \"./MohdViewSelector\";\n\nconst WGBS_DESCRIPTION = \"DNA Methylation\";\n\nfunction createBaseRow(folderId: string, row: MohdDataFile[number]) {\n  return {\n    id: `${folderId}/${row.sample_id}::${row.filename}`,\n    ome: getMohdOmeConfig(row.ome).label,\n    site: row.site,\n    sampleId: row.sample_id,\n    kitId: row.kit_id,\n    sex: row.sex,\n    status: row.status,\n  };\n}\n\nfunction createFileRow(\n  folderId: string,\n  row: MohdDataFile[number],\n): MohdRowInfo {\n  const trackCategory = row.filename.endsWith(\".bigBed\")\n    ? \"Annotation\"\n    : \"Signal\";\n\n  return {\n    ...createBaseRow(folderId, row),\n    kind: \"file\",\n    description: row.file_type,\n    trackCategory,\n    filename: row.filename,\n  };\n}\n\nfunction getRequiredWgbsFilename(\n  sampleRows: MohdDataFile,\n  includesText: string,\n) {\n  const match = sampleRows.find((row) => row.filename.includes(includesText));\n\n  if (!match) {\n    throw new Error(`Missing WGBS file matching ${includesText}`);\n  }\n\n  return match.filename;\n}\n\nfunction createWgbsMethylRow(\n  folderId: string,\n  sampleRows: MohdDataFile,\n): MohdRowInfo {\n  const sampleId = sampleRows[0]?.sample_id;\n\n  if (!sampleId) {\n    throw new Error(\"Cannot build WGBS row without a sample ID\");\n  }\n\n  const base = createBaseRow(folderId, sampleRows[0]!);\n\n  return {\n    ...base,\n    id: `${folderId}/${sampleId}`,\n    kind: \"wgbs-methyl\",\n    description: WGBS_DESCRIPTION,\n    trackCategory: \"Methylation\",\n    filenames: {\n      plusStrand: {\n        cpg: getRequiredWgbsFilename(sampleRows, \"DNAme-CpG-plus\"),\n        chg: getRequiredWgbsFilename(sampleRows, \"DNAme-CHG-plus\"),\n        chh: getRequiredWgbsFilename(sampleRows, \"DNAme-CHH-plus\"),\n        depth: getRequiredWgbsFilename(sampleRows, \"coverage-plus\"),\n      },\n      minusStrand: {\n        cpg: getRequiredWgbsFilename(sampleRows, \"DNAme-CpG-minus\"),\n        chg: getRequiredWgbsFilename(sampleRows, \"DNAme-CHG-minus\"),\n        chh: getRequiredWgbsFilename(sampleRows, \"DNAme-CHH-minus\"),\n        depth: getRequiredWgbsFilename(sampleRows, \"coverage-minus\"),\n      },\n    },\n  };\n}\n\nfunction transformData(folderId: string, data: MohdDataFile): MohdRowInfo[] {\n  const signalRows = data\n    .filter((row) => row.ome !== \"wgbs\")\n    .map((row) => createFileRow(folderId, row));\n  const wgbsRowsBySampleId = new Map<string, MohdDataFile>();\n\n  data.forEach((row) => {\n    if (row.ome !== \"wgbs\") {\n      return;\n    }\n\n    const sampleRows = wgbsRowsBySampleId.get(row.sample_id);\n\n    if (sampleRows) {\n      sampleRows.push(row);\n      return;\n    }\n\n    wgbsRowsBySampleId.set(row.sample_id, [row]);\n  });\n\n  const methylationRows = Array.from(wgbsRowsBySampleId.values()).map(\n    (sampleRows) => createWgbsMethylRow(folderId, sampleRows),\n  );\n\n  return [...signalRows, ...methylationRows];\n}\n\nexport interface CreateMohdFolderOptions {\n  id: string;\n  label: string;\n  description?: string;\n  data: MohdDataFile;\n}\n\nexport function createMohdFolder(\n  options: CreateMohdFolderOptions,\n): FolderDefinition<MohdRowInfo> {\n  const { id, label, description, data } = options;\n  const rows = transformData(id, data);\n  const defaultView = mohdViews[0]!;\n\n  return {\n    id,\n    label,\n    description,\n    rows,\n    columns: defaultView.columns,\n    groupingModel: defaultView.groupingModel,\n    leafField: defaultView.leafField,\n    createTrack: createMohdTrack,\n    views: mohdViews,\n    ViewSelector: MohdViewSelector,\n    GroupingCellComponent: MohdGroupingCell,\n    TreeItemComponent: MohdTreeItem,\n  };\n}\n","import humanData from \"./data/human.json\";\nimport { createMohdFolder } from \"./shared/createFolder\";\nimport { MohdDataFile } from \"./shared/types\";\n\nexport const humanMohdFolder = createMohdFolder({\n  id: \"human-mohd\",\n  label: \"MOHD\",\n  description: \"Public MOHD signal, methylation, and annotation tracks.\",\n  data: humanData as MohdDataFile,\n});\n","import { GridColDef } from \"@mui/x-data-grid-premium\";\nimport { PsychscreenTrackInfo } from \"./types\";\n\nexport const psychscreenCategoryColors: Record<string, string> = {\n  \"Epigenetic Tracks\": \"#9479bc\",\n  \"Deep Learned Models\": \"#758c7b\",\n  \"Pseudo bulk ATAC\": \"#cd8c66\",\n  \"Evolutionary Conservation\": \"#c0a9e2\",\n  \"ATAC Seq Peaks\": \"#9479bc\",\n};\n\nexport function getPsychscreenCategoryColor(category: string) {\n  return psychscreenCategoryColors[category] ?? \"#000000\";\n}\n\nconst titleCol: GridColDef<PsychscreenTrackInfo> = {\n  field: \"title\",\n  headerName: \"Title\",\n  flex: 1,\n  minWidth: 240,\n};\n\nconst categoryCol: GridColDef<PsychscreenTrackInfo> = {\n  field: \"category\",\n  headerName: \"Category\",\n  flex: 1,\n  minWidth: 180,\n};\n\nconst subcategoryCol: GridColDef<PsychscreenTrackInfo> = {\n  field: \"subcategory\",\n  headerName: \"Subcategory\",\n  flex: 1,\n  minWidth: 240,\n};\n\nconst trackTypeCol: GridColDef<PsychscreenTrackInfo> = {\n  field: \"trackType\",\n  headerName: \"Track Type\",\n  width: 120,\n};\n\nexport const defaultColumns: GridColDef<PsychscreenTrackInfo>[] = [\n  titleCol,\n  categoryCol,\n  subcategoryCol,\n  trackTypeCol,\n];\n\nexport const defaultGroupingModel = [\"category\", \"subcategory\"];\n\nexport const defaultLeafField = \"title\";\n","import ChevronRightIcon from \"@mui/icons-material/ChevronRight\";\nimport ExpandMoreIcon from \"@mui/icons-material/ExpandMore\";\nimport { Box, IconButton, Tooltip } from \"@mui/material\";\nimport { alpha } from \"@mui/material/styles\";\nimport {\n  GridGroupNode,\n  GridRenderCellParams,\n  useGridApiContext,\n} from \"@mui/x-data-grid-premium\";\nimport { getPsychscreenCategoryColor } from \"./columns\";\n\nexport function PsychscreenGroupingCell(params: GridRenderCellParams) {\n  const apiRef = useGridApiContext();\n  const isGroup = params.rowNode.type === \"group\";\n  const groupNode = params.rowNode as GridGroupNode;\n  const isExpanded = isGroup ? groupNode.childrenExpanded : false;\n  const groupingField = isGroup ? groupNode.groupingField : null;\n  const isCategoryGroup = groupingField === \"category\";\n  const color = getPsychscreenCategoryColor(\n    isCategoryGroup ? String(params.value ?? \"\") : params.row.category,\n  );\n  const label = String(params.formattedValue ?? params.value ?? \"\");\n  const depth = params.rowNode.depth ?? 0;\n\n  const handleExpandClick = (e: React.MouseEvent) => {\n    e.stopPropagation();\n    apiRef.current.setRowChildrenExpansion(params.id, !isExpanded);\n  };\n\n  return (\n    <Box\n      sx={{\n        display: \"flex\",\n        alignItems: \"center\",\n        width: \"100%\",\n        gap: 1,\n        ml: depth * 2,\n      }}\n    >\n      {isGroup && (\n        <IconButton size=\"small\" onClick={handleExpandClick} sx={{ mr: 0.25 }}>\n          {isExpanded ? (\n            <ExpandMoreIcon fontSize=\"small\" />\n          ) : (\n            <ChevronRightIcon fontSize=\"small\" />\n          )}\n        </IconButton>\n      )}\n      {isCategoryGroup && (\n        <Box\n          sx={{\n            width: 9,\n            height: 9,\n            borderRadius: \"50%\",\n            bgcolor: alpha(color, 0.65),\n            flexShrink: 0,\n          }}\n        />\n      )}\n      <Tooltip title={label} placement=\"top-start\" enterDelay={500}>\n        <Box\n          sx={{\n            bgcolor: isCategoryGroup ? alpha(color, 0.06) : undefined,\n            borderRadius: isCategoryGroup ? 1 : undefined,\n            px: isCategoryGroup ? 0.75 : 0,\n            overflow: \"hidden\",\n            textOverflow: \"ellipsis\",\n            whiteSpace: \"nowrap\",\n            flex: 1,\n            fontWeight: isGroup ? 700 : undefined,\n          }}\n        >\n          {label}\n        </Box>\n      </Tooltip>\n    </Box>\n  );\n}\n","import {\n  BigBedConfig,\n  BigWigConfig,\n  DisplayMode,\n  Track,\n  TrackType,\n} from \"@weng-lab/genomebrowser\";\nimport { CreateTrackOptions } from \"../../types\";\nimport { PsychscreenTrackInfo } from \"./types\";\n\nexport type PsychscreenTrackContext = {};\n\nconst defaultBigWig: Omit<BigWigConfig, \"id\" | \"title\" | \"url\"> = {\n  trackType: TrackType.BigWig,\n  height: 50,\n  displayMode: DisplayMode.Full,\n  titleSize: 12,\n};\n\nconst defaultBigBed: Omit<BigBedConfig, \"id\" | \"title\" | \"url\"> = {\n  trackType: TrackType.BigBed,\n  height: 30,\n  displayMode: DisplayMode.Dense,\n  titleSize: 12,\n};\n\nexport function createPsychscreenTrack(\n  row: PsychscreenTrackInfo,\n  _options: CreateTrackOptions,\n): Track {\n  if (row.trackType === \"bigbed\") {\n    return {\n      ...defaultBigBed,\n      id: row.id,\n      title: row.title,\n      url: row.url,\n      color: row.color ?? \"#000000\",\n    };\n  }\n\n  return {\n    ...defaultBigWig,\n    id: row.id,\n    title: row.title,\n    url: row.url,\n    color: row.color ?? \"#000000\",\n  };\n}\n","import { FolderDefinition } from \"../../types\";\nimport { PsychscreenDataFile, PsychscreenTrackInfo } from \"./types\";\nimport {\n  defaultColumns,\n  defaultGroupingModel,\n  defaultLeafField,\n} from \"./columns\";\nimport { PsychscreenGroupingCell } from \"./PsychscreenGroupingCell\";\nimport { createPsychscreenTrack } from \"./toTrack\";\n\nfunction transformData(\n  folderId: string,\n  data: PsychscreenDataFile,\n): PsychscreenTrackInfo[] {\n  return data.map((row) => ({\n    ...row,\n    sourceId: row.id,\n    id: `${folderId}/${row.id}`,\n  }));\n}\n\nexport interface CreatePsychscreenFolderOptions {\n  id: string;\n  label: string;\n  description?: string;\n  data: PsychscreenDataFile;\n}\n\nexport function createPsychscreenFolder(\n  options: CreatePsychscreenFolderOptions,\n): FolderDefinition<PsychscreenTrackInfo> {\n  const { id, label, description, data } = options;\n\n  return {\n    id,\n    label,\n    description,\n    rows: transformData(id, data),\n    columns: defaultColumns,\n    groupingModel: defaultGroupingModel,\n    leafField: defaultLeafField,\n    createTrack: createPsychscreenTrack,\n    GroupingCellComponent: PsychscreenGroupingCell,\n  };\n}\n","import { createPsychscreenFolder } from \"./shared/createFolder\";\nimport humanData from \"./data/human.json\";\nimport { PsychscreenDataFile } from \"./shared/types\";\n\nexport const humanPsychscreenFolder = createPsychscreenFolder({\n  id: \"human-psychscreen\",\n  label: \"PsychSCREEN\",\n  description: \"PsychSCREEN browser tracks\",\n  data: humanData as PsychscreenDataFile,\n});\n","import { Assembly, FolderDefinition } from \"./types\";\nimport { humanBiosamplesFolder } from \"./biosamples/human\";\nimport { mouseBiosamplesFolder } from \"./biosamples/mouse\";\nimport { humanGenesFolder } from \"./genes/human\";\nimport { mouseGenesFolder } from \"./genes/mouse\";\nimport { humanOtherTracksFolder } 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This value must be coerced to a string before using it here.\",\n          JSCompiler_inline_result$jscomp$0\n        );\n        return testStringCoercion(value);\n      }\n    }\n    function getTaskName(type) {\n      if (type === REACT_FRAGMENT_TYPE) return \"<>\";\n      if (\n        \"object\" === typeof type &&\n        null !== type &&\n        type.$$typeof === REACT_LAZY_TYPE\n      )\n        return \"<...>\";\n      try {\n        var name = getComponentNameFromType(type);\n        return name ? \"<\" + name + \">\" : \"<...>\";\n      } catch (x) {\n        return \"<...>\";\n      }\n    }\n    function getOwner() {\n      var dispatcher = ReactSharedInternals.A;\n      return null === dispatcher ? null : dispatcher.getOwner();\n    }\n    function UnknownOwner() {\n      return Error(\"react-stack-top-frame\");\n    }\n    function hasValidKey(config) {\n      if (hasOwnProperty.call(config, \"key\")) {\n        var getter = Object.getOwnPropertyDescriptor(config, \"key\").get;\n        if (getter && getter.isReactWarning) return !1;\n      }\n      return void 0 !== config.key;\n    }\n    function defineKeyPropWarningGetter(props, displayName) {\n      function warnAboutAccessingKey() {\n        specialPropKeyWarningShown ||\n          ((specialPropKeyWarningShown = !0),\n          console.error(\n            \"%s: `key` is not a prop. Trying to access it will result in `undefined` being returned. If you need to access the same value within the child component, you should pass it as a different prop. (https://react.dev/link/special-props)\",\n            displayName\n          ));\n      }\n      warnAboutAccessingKey.isReactWarning = !0;\n      Object.defineProperty(props, \"key\", {\n        get: warnAboutAccessingKey,\n        configurable: !0\n      });\n    }\n    function elementRefGetterWithDeprecationWarning() {\n      var componentName = getComponentNameFromType(this.type);\n      didWarnAboutElementRef[componentName] ||\n        ((didWarnAboutElementRef[componentName] = !0),\n        console.error(\n          \"Accessing element.ref was removed in React 19. ref is now a regular prop. It will be removed from the JSX Element type in a future release.\"\n        ));\n      componentName = this.props.ref;\n      return void 0 !== componentName ? componentName : null;\n    }\n    function ReactElement(type, key, props, owner, debugStack, debugTask) {\n      var refProp = props.ref;\n      type = {\n        $$typeof: REACT_ELEMENT_TYPE,\n        type: type,\n        key: key,\n        props: props,\n        _owner: owner\n      };\n      null !== (void 0 !== refProp ? refProp : null)\n        ? Object.defineProperty(type, \"ref\", {\n            enumerable: !1,\n            get: elementRefGetterWithDeprecationWarning\n          })\n        : Object.defineProperty(type, \"ref\", { enumerable: !1, value: null });\n      type._store = {};\n      Object.defineProperty(type._store, \"validated\", {\n        configurable: !1,\n        enumerable: !1,\n        writable: !0,\n        value: 0\n      });\n      Object.defineProperty(type, \"_debugInfo\", {\n        configurable: !1,\n        enumerable: !1,\n        writable: !0,\n        value: null\n      });\n      Object.defineProperty(type, \"_debugStack\", {\n        configurable: !1,\n        enumerable: !1,\n        writable: !0,\n        value: debugStack\n      });\n      Object.defineProperty(type, \"_debugTask\", {\n        configurable: !1,\n        enumerable: !1,\n        writable: !0,\n        value: debugTask\n      });\n      Object.freeze && (Object.freeze(type.props), Object.freeze(type));\n      return type;\n    }\n    function jsxDEVImpl(\n      type,\n      config,\n      maybeKey,\n      isStaticChildren,\n      debugStack,\n      debugTask\n    ) {\n      var children = config.children;\n      if (void 0 !== children)\n        if (isStaticChildren)\n          if (isArrayImpl(children)) {\n            for (\n              isStaticChildren = 0;\n              isStaticChildren < children.length;\n              isStaticChildren++\n            )\n              validateChildKeys(children[isStaticChildren]);\n            Object.freeze && Object.freeze(children);\n          } else\n            console.error(\n              \"React.jsx: Static children should always be an array. You are likely explicitly calling React.jsxs or React.jsxDEV. Use the Babel transform instead.\"\n            );\n        else validateChildKeys(children);\n      if (hasOwnProperty.call(config, \"key\")) {\n        children = getComponentNameFromType(type);\n        var keys = Object.keys(config).filter(function (k) {\n          return \"key\" !== k;\n        });\n        isStaticChildren =\n          0 < keys.length\n            ? \"{key: someKey, \" + keys.join(\": ..., \") + \": ...}\"\n            : \"{key: someKey}\";\n        didWarnAboutKeySpread[children + isStaticChildren] ||\n          ((keys =\n            0 < keys.length ? \"{\" + keys.join(\": ..., \") + \": ...}\" : \"{}\"),\n          console.error(\n            'A props object containing a \"key\" prop is being spread into JSX:\\n  let props = %s;\\n  <%s {...props} />\\nReact keys must be passed directly to JSX without using spread:\\n  let props = %s;\\n  <%s key={someKey} {...props} />',\n            isStaticChildren,\n            children,\n            keys,\n            children\n          ),\n          (didWarnAboutKeySpread[children + isStaticChildren] = !0));\n      }\n      children = null;\n      void 0 !== maybeKey &&\n        (checkKeyStringCoercion(maybeKey), (children = \"\" + maybeKey));\n      hasValidKey(config) &&\n        (checkKeyStringCoercion(config.key), (children = \"\" + config.key));\n      if (\"key\" in config) {\n        maybeKey = {};\n        for (var propName in config)\n          \"key\" !== propName && (maybeKey[propName] = config[propName]);\n      } else maybeKey = config;\n      children &&\n        defineKeyPropWarningGetter(\n          maybeKey,\n          \"function\" === typeof type\n            ? type.displayName || type.name || \"Unknown\"\n            : type\n        );\n      return ReactElement(\n        type,\n        children,\n        maybeKey,\n        getOwner(),\n        debugStack,\n        debugTask\n      );\n    }\n    function validateChildKeys(node) {\n      isValidElement(node)\n        ? node._store && (node._store.validated = 1)\n        : \"object\" === typeof node &&\n          null !== node &&\n          node.$$typeof === REACT_LAZY_TYPE &&\n          (\"fulfilled\" === node._payload.status\n            ? isValidElement(node._payload.value) &&\n              node._payload.value._store &&\n              (node._payload.value._store.validated = 1)\n            : node._store && (node._store.validated = 1));\n    }\n    function isValidElement(object) {\n      return (\n        \"object\" === typeof object &&\n        null !== object &&\n        object.$$typeof === REACT_ELEMENT_TYPE\n      );\n    }\n    var React = require(\"react\"),\n      REACT_ELEMENT_TYPE = Symbol.for(\"react.transitional.element\"),\n      REACT_PORTAL_TYPE = Symbol.for(\"react.portal\"),\n      REACT_FRAGMENT_TYPE = Symbol.for(\"react.fragment\"),\n      REACT_STRICT_MODE_TYPE = Symbol.for(\"react.strict_mode\"),\n      REACT_PROFILER_TYPE = Symbol.for(\"react.profiler\"),\n      REACT_CONSUMER_TYPE = Symbol.for(\"react.consumer\"),\n      REACT_CONTEXT_TYPE = Symbol.for(\"react.context\"),\n      REACT_FORWARD_REF_TYPE = Symbol.for(\"react.forward_ref\"),\n      REACT_SUSPENSE_TYPE = Symbol.for(\"react.suspense\"),\n      REACT_SUSPENSE_LIST_TYPE = Symbol.for(\"react.suspense_list\"),\n      REACT_MEMO_TYPE = Symbol.for(\"react.memo\"),\n      REACT_LAZY_TYPE = Symbol.for(\"react.lazy\"),\n      REACT_ACTIVITY_TYPE = Symbol.for(\"react.activity\"),\n      REACT_CLIENT_REFERENCE = Symbol.for(\"react.client.reference\"),\n      ReactSharedInternals =\n        React.__CLIENT_INTERNALS_DO_NOT_USE_OR_WARN_USERS_THEY_CANNOT_UPGRADE,\n      hasOwnProperty = Object.prototype.hasOwnProperty,\n      isArrayImpl = Array.isArray,\n      createTask = console.createTask\n        ? console.createTask\n        : function () {\n            return null;\n          };\n    React = {\n      react_stack_bottom_frame: function (callStackForError) {\n        return callStackForError();\n      }\n    };\n    var specialPropKeyWarningShown;\n    var didWarnAboutElementRef = {};\n    var unknownOwnerDebugStack = React.react_stack_bottom_frame.bind(\n      React,\n      UnknownOwner\n    )();\n    var unknownOwnerDebugTask = createTask(getTaskName(UnknownOwner));\n    var didWarnAboutKeySpread = {};\n    exports.Fragment = REACT_FRAGMENT_TYPE;\n    exports.jsx = function (type, config, maybeKey) {\n      var trackActualOwner =\n        1e4 > ReactSharedInternals.recentlyCreatedOwnerStacks++;\n      return jsxDEVImpl(\n        type,\n        config,\n        maybeKey,\n        !1,\n        trackActualOwner\n          ? Error(\"react-stack-top-frame\")\n          : unknownOwnerDebugStack,\n        trackActualOwner ? createTask(getTaskName(type)) : unknownOwnerDebugTask\n      );\n    };\n    exports.jsxs = function (type, config, maybeKey) {\n      var trackActualOwner =\n        1e4 > ReactSharedInternals.recentlyCreatedOwnerStacks++;\n      return jsxDEVImpl(\n        type,\n        config,\n        maybeKey,\n        !0,\n        trackActualOwner\n          ? Error(\"react-stack-top-frame\")\n          : unknownOwnerDebugStack,\n        trackActualOwner ? createTask(getTaskName(type)) : unknownOwnerDebugTask\n      );\n    };\n  })();\n","'use strict';\n\nif (process.env.NODE_ENV === 'production') {\n  module.exports = require('./cjs/react-jsx-runtime.production.js');\n} else {\n  module.exports = require('./cjs/react-jsx-runtime.development.js');\n}\n","import { Tooltip, Box, IconButton } from \"@mui/material\";\nimport {\n  GridRenderCellParams,\n  useGridApiContext,\n  GridGroupNode,\n} from \"@mui/x-data-grid-premium\";\nimport ChevronRightIcon from \"@mui/icons-material/ChevronRight\";\nimport ExpandMoreIcon from \"@mui/icons-material/ExpandMore\";\n\n/**\n * Default grouping cell that handles expand/collapse, truncation, and tooltips.\n * This is a generic implementation without any folder-specific logic.\n */\nexport function DefaultGroupingCell(params: GridRenderCellParams) {\n  const apiRef = useGridApiContext();\n  const isGroup = params.rowNode.type === \"group\";\n  const groupNode = params.rowNode as GridGroupNode;\n  const isExpanded = isGroup ? groupNode.childrenExpanded : false;\n  const depth = params.rowNode.depth ?? 0;\n\n  const handleExpandClick = (e: React.MouseEvent) => {\n    e.stopPropagation();\n    apiRef.current.setRowChildrenExpansion(params.id, !isExpanded);\n  };\n\n  const value = String(params.value ?? \"\");\n\n  // Indent based on depth (2 units per level)\n  const indentLevel = depth * 2;\n\n  return (\n    <Box\n      sx={{\n        display: \"flex\",\n        alignItems: \"center\",\n        width: \"100%\",\n        ml: indentLevel,\n      }}\n    >\n      {isGroup && (\n        <IconButton size=\"small\" onClick={handleExpandClick} sx={{ mr: 0.5 }}>\n          {isExpanded ? (\n            <ExpandMoreIcon fontSize=\"small\" />\n          ) : (\n            <ChevronRightIcon fontSize=\"small\" />\n          )}\n        </IconButton>\n      )}\n      <Tooltip title={value} placement=\"top-start\" enterDelay={500}>\n        <Box\n          sx={{\n            overflow: \"hidden\",\n            textOverflow: \"ellipsis\",\n            whiteSpace: \"nowrap\",\n            flex: 1,\n            fontWeight: isGroup ? \"bold\" : undefined,\n          }}\n        >\n          {params.formattedValue}\n        </Box>\n      </Tooltip>\n    </Box>\n  );\n}\n","import { Box, Paper } from \"@mui/material\";\nimport {\n  DataGridPremium,\n  FilterColumnsArgs,\n  GridAutosizeOptions,\n  GridColDef,\n  GridColumnVisibilityModel,\n  GridRenderCellParams,\n  GridRowId,\n  GridRowSelectionModel,\n  useGridApiRef,\n} from \"@mui/x-data-grid-premium\";\nimport { useCallback, useEffect, useMemo, useState } from \"react\";\nimport { DataGridProps } from \"../types\";\nimport { DefaultGroupingCell } from \"./DefaultGroupingCell\";\n\nconst autosizeOptions: GridAutosizeOptions = {\n  expand: true,\n  includeHeaders: true,\n  outliersFactor: 1.5,\n};\n\nconst areSetsEqual = <T,>(a: Set<T>, b: Set<T>) => {\n  if (a.size !== b.size) {\n    return false;\n  }\n\n  for (const value of a) {\n    if (!b.has(value)) {\n      return false;\n    }\n  }\n\n  return true;\n};\n\nconst areSelectionModelsEqual = (\n  a: GridRowSelectionModel,\n  b: GridRowSelectionModel,\n) => a.type === b.type && areSetsEqual(a.ids, b.ids);\n\nexport function DataGridWrapper(props: DataGridProps) {\n  const {\n    columns,\n    groupingModel,\n    leafField,\n    onSelectionChange,\n    rows,\n    selectedIds,\n    GroupingCellComponent,\n  } = props;\n\n  const GroupingCell = GroupingCellComponent ?? DefaultGroupingCell;\n\n  const apiRef = useGridApiRef();\n\n  const rowIdSet = useMemo(\n    () => new Set(rows.map((row: { id: string }) => row.id)),\n    [rows],\n  );\n\n  const filterToLeafIds = useCallback(\n    (ids: Set<GridRowId>) =>\n      new Set([...ids].map(String).filter((id) => rowIdSet.has(id))),\n    [rowIdSet],\n  );\n\n  const getPropagatedSelectionModel = useCallback(\n    (ids: Set<GridRowId>) => {\n      const selectionModel: GridRowSelectionModel = {\n        type: \"include\",\n        ids,\n      };\n\n      return apiRef.current.getPropagatedRowSelectionModel\n        ? apiRef.current.getPropagatedRowSelectionModel(selectionModel)\n        : selectionModel;\n    },\n    [apiRef],\n  );\n\n  const [rowSelectionModel, setRowSelectionModel] =\n    useState<GridRowSelectionModel>(() => ({\n      type: \"include\",\n      ids: new Set(selectedIds),\n    }));\n\n  useEffect(() => {\n    const currentLeafIds = filterToLeafIds(rowSelectionModel.ids);\n    if (areSetsEqual(currentLeafIds, selectedIds)) {\n      return;\n    }\n\n    const nextSelectionModel = getPropagatedSelectionModel(\n      new Set(selectedIds),\n    );\n\n    setRowSelectionModel((currentSelectionModel) =>\n      areSelectionModelsEqual(currentSelectionModel, nextSelectionModel)\n        ? currentSelectionModel\n        : nextSelectionModel,\n    );\n  }, [\n    filterToLeafIds,\n    getPropagatedSelectionModel,\n    groupingModel,\n    rowSelectionModel.ids,\n    selectedIds,\n  ]);\n\n  useEffect(() => {\n    if (apiRef.current && apiRef.current.autosizeColumns) {\n      apiRef.current.autosizeColumns(autosizeOptions);\n    }\n  }, [columns, groupingModel, leafField]);\n\n  const baseVisibility = useMemo(() => {\n    const visibility: GridColumnVisibilityModel = {\n      id: false,\n    };\n\n    // Only hide leafField if we have grouping (it shows in grouping column)\n    if (groupingModel.length > 0) {\n      visibility[leafField] = false;\n    }\n\n    groupingModel.forEach((field) => {\n      visibility[field] = false;\n    });\n\n    return visibility;\n  }, [groupingModel, leafField]);\n\n  const [columnVisibilityModel, setColumnVisibilityModel] =\n    useState<GridColumnVisibilityModel>(baseVisibility);\n\n  useEffect(() => {\n    setColumnVisibilityModel(baseVisibility);\n  }, [baseVisibility]);\n\n  // functions to customize the column and filter panel in the toolbar\n  const filterColumns = ({ columns }: FilterColumnsArgs) => {\n    return columns\n      .filter((column) => column.type !== \"custom\")\n      .map((column) => column.field);\n  };\n\n  const getTogglableColumns = (columns: GridColDef[]) => {\n    return columns\n      .filter((column) => column.type !== \"custom\")\n      .map((column) => column.field);\n  };\n\n  return (\n    <Paper sx={{ width: \"100%\" }}>\n      <Box\n        sx={{\n          height: 500,\n          width: \"100%\",\n          overflow: \"auto\",\n        }}\n      >\n        <DataGridPremium\n          apiRef={apiRef}\n          rows={rows}\n          columns={columns}\n          getRowId={(row: { id: string }) => row.id}\n          autosizeOptions={autosizeOptions}\n          rowGroupingModel={groupingModel}\n          groupingColDef={{\n            leafField,\n            display: \"flex\",\n            minWidth: 300,\n            maxWidth: 500,\n            flex: 2,\n            renderCell: (params: GridRenderCellParams) => (\n              <GroupingCell {...params} />\n            ),\n          }}\n          columnVisibilityModel={columnVisibilityModel}\n          onColumnVisibilityModelChange={setColumnVisibilityModel}\n          onRowSelectionModelChange={(selection: GridRowSelectionModel) => {\n            const nextSelectionModel = getPropagatedSelectionModel(\n              selection.ids,\n            );\n\n            setRowSelectionModel((currentSelectionModel) =>\n              areSelectionModelsEqual(currentSelectionModel, nextSelectionModel)\n                ? currentSelectionModel\n                : nextSelectionModel,\n            );\n\n            const leafIds = filterToLeafIds(nextSelectionModel.ids);\n\n            if (!areSetsEqual(leafIds, selectedIds)) {\n              onSelectionChange(leafIds);\n            }\n          }}\n          rowSelectionPropagation={{ descendants: true, parents: true }}\n          disableRowGrouping={false}\n          rowSelectionModel={rowSelectionModel}\n          slotProps={{\n            filterPanel: {\n              filterFormProps: {\n                filterColumns,\n              },\n            },\n            columnsManagement: {\n              getTogglableColumns,\n            },\n          }}\n          keepNonExistentRowsSelected\n          showToolbar\n          disableAggregation\n          disableRowSelectionExcludeModel\n          disablePivoting\n          checkboxSelection\n          autosizeOnMount\n          pagination\n          hideFooterSelectedRowCount\n        />\n      </Box>\n    </Paper>\n  );\n}\n","import {\n  Button,\n  Dialog,\n  DialogActions,\n  DialogContent,\n  DialogContentText,\n  DialogTitle,\n} from \"@mui/material\";\n\ninterface ClearDialogProps {\n  open: boolean;\n  onClose: () => void;\n  onConfirm: () => void;\n  folderLabel: string;\n  clearAll: boolean;\n}\n\nexport function ClearDialog({\n  open,\n  onClose,\n  onConfirm,\n  folderLabel,\n  clearAll,\n}: ClearDialogProps) {\n  return (\n    <Dialog open={open} onClose={onClose}>\n      <DialogTitle\n        sx={{\n          bgcolor: \"primary.main\",\n          color: \"primary.contrastText\",\n          fontWeight: \"bold\",\n        }}\n      >\n        {clearAll ? \"Clear All Folders\" : `Clear ${folderLabel}`}\n      </DialogTitle>\n      <DialogContent sx={{ mt: 2 }}>\n        <DialogContentText>\n          {clearAll ? (\n            \"Are you sure you want to clear all selections?\"\n          ) : (\n            <>\n              Are you sure you want to clear the selection for{\" \"}\n              <strong>{folderLabel}</strong>?\n            </>\n          )}\n        </DialogContentText>\n      </DialogContent>\n      <DialogActions sx={{ justifyContent: \"center\", gap: 2, pb: 2 }}>\n        <Button variant=\"contained\" color=\"primary\" onClick={onClose} autoFocus>\n          Cancel\n        </Button>\n        <Button variant=\"outlined\" color=\"secondary\" onClick={onConfirm}>\n          Clear\n        </Button>\n      </DialogActions>\n    </Dialog>\n  );\n}\n","import {\n  Button,\n  Dialog,\n  DialogActions,\n  DialogContent,\n  DialogContentText,\n  DialogTitle,\n} from \"@mui/material\";\n\ninterface LimitDialogProps {\n  open: boolean;\n  onClose: () => void;\n  maxTracks: number;\n}\n\nexport function LimitDialog({ open, onClose, maxTracks }: LimitDialogProps) {\n  return (\n    <Dialog open={open} onClose={onClose}>\n      <DialogTitle>Track Limit Reached</DialogTitle>\n      <DialogContent>\n        <DialogContentText>\n          You can select up to {maxTracks} tracks at a time. Please remove a\n          track before adding another.\n        </DialogContentText>\n      </DialogContent>\n      <DialogActions>\n        <Button onClick={onClose} autoFocus>\n          OK\n        </Button>\n      </DialogActions>\n    </Dialog>\n  );\n}\n","import {\n  Button,\n  Dialog,\n  DialogActions,\n  DialogContent,\n  DialogContentText,\n  DialogTitle,\n} from \"@mui/material\";\n\ninterface ResetDialogProps {\n  open: boolean;\n  onClose: () => void;\n  onConfirm: () => void;\n}\n\nexport function ResetDialog({ open, onClose, onConfirm }: ResetDialogProps) {\n  return (\n    <Dialog open={open} onClose={onClose}>\n      <DialogTitle\n        sx={{\n          bgcolor: \"primary.main\",\n          color: \"primary.contrastText\",\n          fontWeight: \"bold\",\n        }}\n      >\n        Reset to Browser State\n      </DialogTitle>\n      <DialogContent sx={{ mt: 2 }}>\n        <DialogContentText>\n          Are you sure you want to reset all selections to the current browser\n          state?\n        </DialogContentText>\n      </DialogContent>\n      <DialogActions sx={{ justifyContent: \"center\", gap: 2, pb: 2 }}>\n        <Button variant=\"contained\" color=\"primary\" onClick={onClose} autoFocus>\n          Cancel\n        </Button>\n        <Button variant=\"outlined\" color=\"secondary\" onClick={onConfirm}>\n          Reset\n        </Button>\n      </DialogActions>\n    </Dialog>\n  );\n}\n","import { Breadcrumbs, Link, Typography } from \"@mui/material\";\nimport NavigateNextIcon from \"@mui/icons-material/NavigateNext\";\nimport { FolderDefinition } from \"../Folders/types\";\n\nexport interface BreadcrumbProps {\n  currentFolder: FolderDefinition | null;\n  onNavigateToRoot: () => void;\n}\n\nexport function Breadcrumb({\n  currentFolder,\n  onNavigateToRoot,\n}: BreadcrumbProps) {\n  return (\n    <Breadcrumbs separator={<NavigateNextIcon fontSize=\"small\" />}>\n      {currentFolder ? (\n        <Link\n          component=\"button\"\n          variant=\"body1\"\n          onClick={onNavigateToRoot}\n          underline=\"hover\"\n          sx={{ cursor: \"pointer\" }}\n        >\n          All Folders\n        </Link>\n      ) : (\n        <Typography variant=\"body1\" color=\"text.primary\">\n          All Folders\n        </Typography>\n      )}\n      {currentFolder && (\n        <Typography variant=\"body1\" color=\"text.primary\">\n          {currentFolder.label}\n        </Typography>\n      )}\n    </Breadcrumbs>\n  );\n}\n","import { Paper, Typography } from \"@mui/material\";\nimport { FolderDefinition } from \"../Folders/types\";\n\nexport interface FolderCardProps {\n  folder: FolderDefinition;\n  onClick: () => void;\n}\n\nexport function FolderCard({ folder, onClick }: FolderCardProps) {\n  return (\n    <Paper\n      elevation={1}\n      onClick={onClick}\n      onKeyDown={(e) => {\n        if (e.key === \"Enter\" || e.key === \" \") {\n          e.preventDefault();\n          onClick();\n        }\n      }}\n      role=\"button\"\n      tabIndex={0}\n      sx={{\n        p: 3,\n        cursor: \"pointer\",\n        transition: \"all 0.2s ease-in-out\",\n        \"&:hover\": {\n          elevation: 3,\n          boxShadow: 3,\n          bgcolor: \"action.hover\",\n        },\n        \"&:focus\": {\n          outline: \"2px solid\",\n          outlineColor: \"primary.main\",\n          outlineOffset: 2,\n        },\n      }}\n    >\n      <Typography variant=\"h6\" gutterBottom>\n        {folder.label}\n      </Typography>\n      {folder.description && (\n        <Typography variant=\"body2\" color=\"text.secondary\" gutterBottom>\n          {folder.description}\n        </Typography>\n      )}\n      <Typography variant=\"caption\" color=\"text.secondary\">\n        {folder.rows.length.toLocaleString()} tracks available\n      </Typography>\n    </Paper>\n  );\n}\n","import { Paper, Stack, Typography } from \"@mui/material\";\nimport { FolderDefinition } from \"../Folders/types\";\nimport { FolderCard } from \"./FolderCard\";\n\nexport interface FolderListProps {\n  folders: FolderDefinition[];\n  onFolderSelect: (folderId: string) => void;\n}\n\nexport function FolderList({ folders, onFolderSelect }: FolderListProps) {\n  if (folders.length === 0) {\n    return (\n      <Paper\n        variant=\"outlined\"\n        sx={{\n          height: 500,\n          borderWidth: 2,\n        }}\n      >\n        <Typography color=\"text.secondary\" sx={{ p: 3 }}>\n          No folders available\n        </Typography>\n      </Paper>\n    );\n  }\n\n  return (\n    <Paper\n      variant=\"outlined\"\n      sx={{\n        height: 500,\n        overflow: \"auto\",\n        borderWidth: 2,\n      }}\n    >\n      <Stack spacing={2} sx={{ p: 2 }}>\n        {folders.map((folder) => (\n          <FolderCard\n            key={folder.id}\n            folder={folder}\n            onClick={() => onFolderSelect(folder.id)}\n          />\n        ))}\n      </Stack>\n    </Paper>\n  );\n}\n","import { Track } from \"@weng-lab/genomebrowser\";\nimport { Assembly, FolderDefinition } from \"./Folders/types\";\nimport type { TrackSelectTrackContext } from \"./trackContext\";\n\nconst buildManagedTrack = ({\n  assembly,\n  folder,\n  id,\n  trackContext,\n}: {\n  assembly: Assembly;\n  folder: FolderDefinition;\n  id: string;\n  trackContext?: TrackSelectTrackContext;\n}) => {\n  const row = folder.rows.find((candidate) => candidate.id === id);\n  if (!row) {\n    return null;\n  }\n\n  const track = folder.createTrack(row, { assembly, trackContext });\n  if (!track) {\n    return null;\n  }\n\n  return track;\n};\n\nexport const diffManagedTracks = ({\n  assembly,\n  currentTracks,\n  folders,\n  selectedByFolder,\n  trackContext,\n}: {\n  assembly: Assembly;\n  currentTracks: Track[];\n  folders: FolderDefinition[];\n  selectedByFolder: Map<string, Set<string>>;\n  trackContext?: TrackSelectTrackContext;\n}) => {\n  const nextManagedIds = new Set<string>();\n  const currentManagedIds = new Set<string>();\n  const idsToRemove: string[] = [];\n  const tracksToAdd: Track[] = [];\n\n  currentTracks.forEach((track) => {\n    if (folders.some((folder) => track.id.startsWith(`${folder.id}/`))) {\n      currentManagedIds.add(track.id);\n    }\n  });\n\n  folders.forEach((folder) => {\n    const selectedIds = selectedByFolder.get(folder.id) ?? new Set<string>();\n\n    selectedIds.forEach((id) => {\n      nextManagedIds.add(id);\n    });\n  });\n\n  currentManagedIds.forEach((id) => {\n    if (!nextManagedIds.has(id)) {\n      idsToRemove.push(id);\n    }\n  });\n\n  folders.forEach((folder) => {\n    const selectedIds = selectedByFolder.get(folder.id) ?? new Set<string>();\n\n    selectedIds.forEach((id) => {\n      if (currentManagedIds.has(id)) {\n        return;\n      }\n\n      const track = buildManagedTrack({\n        assembly,\n        folder,\n        id,\n        trackContext,\n      });\n\n      if (track) {\n        tracksToAdd.push(track);\n      }\n    });\n  });\n\n  return {\n    idsToRemove,\n    tracksToAdd,\n  };\n};\n","import { FolderDefinition, FolderView } from \"./Folders/types\";\n\nexport const resolveFolderView = (\n  folder: FolderDefinition,\n  activeViewIdByFolder: Map<string, string>,\n): FolderView => {\n  const activeViewId = activeViewIdByFolder.get(folder.id);\n  const activeView = folder.views?.find((view) => view.id === activeViewId);\n\n  return (\n    activeView ??\n    folder.views?.[0] ?? {\n      id: \"default\",\n      label: folder.label,\n      columns: folder.columns,\n      groupingModel: folder.groupingModel,\n      leafField: folder.leafField,\n    }\n  );\n};\n","import { TreeViewBaseItem } from \"@mui/x-tree-view\";\nimport { ExtendedTreeItemProps } from \"./types\";\n\ntype TreeRow = {\n  id: string;\n  [key: string]: unknown;\n};\n\ntype BuildSelectedTreeOptions = {\n  folderId: string;\n  rootLabel: string;\n  selectedRows: TreeRow[];\n  groupingModel: string[];\n  leafField: string;\n};\n\nconst toLabel = (value: unknown, fallback: string) => {\n  if (value === null || value === undefined || value === \"\") {\n    return fallback;\n  }\n\n  return String(value);\n};\n\nconst isHighlightedField = (field: string) => {\n  return field === \"assay\" || field === \"ome\";\n};\n\nconst createRootNode = (\n  folderId: string,\n  rootLabel: string,\n): TreeViewBaseItem<ExtendedTreeItemProps> => ({\n  id: `${folderId}::root`,\n  kind: \"root\",\n  label: rootLabel,\n  icon: \"folder\",\n  children: [],\n  allExpAccessions: [],\n});\n\nconst createLeafNode = (\n  row: TreeRow,\n  leafField: string,\n): TreeViewBaseItem<ExtendedTreeItemProps> => {\n  const value = row[leafField];\n  const label = toLabel(value, row.id);\n\n  return {\n    id: row.id,\n    kind: \"leaf\",\n    field: leafField,\n    value: label,\n    rowId: row.id,\n    label,\n    icon: \"removeable\",\n    highlightName: isHighlightedField(leafField) ? label : undefined,\n    isHighlightedItem: isHighlightedField(leafField),\n    children: [],\n    allExpAccessions: [row.id],\n  };\n};\n\nconst appendGroupedRows = (\n  parent: TreeViewBaseItem<ExtendedTreeItemProps>,\n  rows: TreeRow[],\n  groupingModel: string[],\n  depth: number,\n  folderId: string,\n  leafField: string,\n  path: string[],\n) => {\n  if (depth >= groupingModel.length) {\n    rows.forEach((row) => {\n      const leafNode = createLeafNode(row, leafField);\n      parent.children!.push(leafNode);\n      parent.allExpAccessions!.push(row.id);\n    });\n    return;\n  }\n\n  const field = groupingModel[depth];\n  const groupedRows = new Map<string, TreeRow[]>();\n\n  rows.forEach((row) => {\n    const value = toLabel(row[field], row.id);\n    const groupRows = groupedRows.get(value);\n    if (groupRows) {\n      groupRows.push(row);\n      return;\n    }\n\n    groupedRows.set(value, [row]);\n  });\n\n  groupedRows.forEach((groupRows, value) => {\n    const nodeId = `${folderId}::${[...path, `${field}=${encodeURIComponent(value)}`].join(\"::\")}`;\n    const groupNode: TreeViewBaseItem<ExtendedTreeItemProps> = {\n      id: nodeId,\n      kind: \"group\",\n      field,\n      value,\n      label: value,\n      icon: \"removeable\",\n      highlightName: isHighlightedField(field) ? value : undefined,\n      isHighlightedItem: isHighlightedField(field),\n      children: [],\n      allExpAccessions: [],\n    };\n\n    appendGroupedRows(\n      groupNode,\n      groupRows,\n      groupingModel,\n      depth + 1,\n      folderId,\n      leafField,\n      [...path, `${field}=${encodeURIComponent(value)}`],\n    );\n\n    parent.children!.push(groupNode);\n    parent.allExpAccessions!.push(...groupNode.allExpAccessions!);\n  });\n};\n\nexport const buildSelectedTree = ({\n  folderId,\n  rootLabel,\n  selectedRows,\n  groupingModel,\n  leafField,\n}: BuildSelectedTreeOptions): TreeViewBaseItem<ExtendedTreeItemProps>[] => {\n  const root = createRootNode(folderId, rootLabel);\n\n  appendGroupedRows(\n    root,\n    selectedRows,\n    groupingModel,\n    0,\n    folderId,\n    leafField,\n    [],\n  );\n\n  return [root];\n};\n","import Folder from \"@mui/icons-material/Folder\";\nimport IndeterminateCheckBoxRoundedIcon from \"@mui/icons-material/IndeterminateCheckBoxRounded\";\nimport { Box, Stack, Tooltip, Typography } from \"@mui/material\";\nimport Collapse from \"@mui/material/Collapse\";\nimport { alpha, styled } from \"@mui/material/styles\";\nimport {\n  TreeItemCheckbox,\n  TreeItemIconContainer,\n  TreeItemLabel,\n} from \"@mui/x-tree-view/TreeItem\";\nimport { TreeItemIcon } from \"@mui/x-tree-view/TreeItemIcon\";\nimport { TreeItemProvider } from \"@mui/x-tree-view/TreeItemProvider\";\nimport { useTreeItemModel } from \"@mui/x-tree-view/hooks\";\nimport { useTreeItem } from \"@mui/x-tree-view/useTreeItem\";\nimport React, { ReactNode } from \"react\";\nimport {\n  CustomLabelProps,\n  CustomTreeItemProps,\n  ExtendedTreeItemProps,\n} from \"../types\";\n\nconst TreeItemRoot = styled(\"li\")(({ theme }) => ({\n  listStyle: \"none\",\n  margin: 0,\n  padding: 0,\n  outline: 4,\n  color: theme.palette.grey[400],\n  ...theme.applyStyles(\"light\", {\n    color: theme.palette.grey[600],\n  }),\n}));\n\nconst TreeItemLabelText = styled(Typography)(({ theme }) => ({\n  color: theme.palette.text.primary,\n  fontFamily: \"inherit\",\n  overflow: \"hidden\",\n  textOverflow: \"ellipsis\",\n  whiteSpace: \"nowrap\",\n}));\n\nfunction CustomLabel({\n  icon: Icon,\n  children,\n  isHighlightedItem,\n  highlightName,\n  renderIcon,\n  ...other\n}: CustomLabelProps) {\n  const variant = \"body2\";\n  const fontWeight = 500;\n  const labelText = typeof children === \"string\" ? children : \"\";\n  return (\n    <TreeItemLabel\n      {...other}\n      sx={{\n        display: \"flex\",\n        alignItems: \"center\",\n        minWidth: 0,\n        overflow: \"hidden\",\n        flex: 1,\n      }}\n    >\n      {Icon && React.isValidElement(Icon) ? (\n        <Box className=\"labelIcon\" sx={{ mr: 1, flexShrink: 0 }}>\n          {Icon}\n        </Box>\n      ) : (\n        <Box\n          component={Icon as React.ElementType}\n          className=\"labelIcon\"\n          color=\"inherit\"\n          sx={{ mr: 1, fontSize: \"1.2rem\", flexShrink: 0 }}\n        />\n      )}\n      <Stack\n        direction=\"row\"\n        spacing={1}\n        alignItems=\"center\"\n        sx={{ minWidth: 0, overflow: \"hidden\", flex: 1 }}\n      >\n        {isHighlightedItem && highlightName && renderIcon && (\n          <Box sx={{ flexShrink: 0 }}>{renderIcon(highlightName)}</Box>\n        )}\n        <Tooltip title={labelText} enterDelay={500} placement=\"top\">\n          <TreeItemLabelText fontWeight={fontWeight} variant={variant}>\n            {labelText}\n          </TreeItemLabelText>\n        </Tooltip>\n      </Stack>\n    </TreeItemLabel>\n  );\n}\n\nconst TreeItemContent = styled(\"div\")(({ theme }) => ({\n  padding: theme.spacing(0.5),\n  paddingRight: theme.spacing(2),\n  paddingLeft: `calc(${theme.spacing(1)} + 6px * var(--TreeView-itemDepth))`,\n  width: \"100%\",\n  boxSizing: \"border-box\",\n  position: \"relative\",\n  display: \"flex\",\n  alignItems: \"center\",\n  gap: theme.spacing(1),\n  cursor: \"pointer\",\n  WebkitTapHighlightColor: \"transparent\",\n  flexDirection: \"row-reverse\",\n  borderRadius: theme.spacing(0.7),\n  marginBottom: theme.spacing(0.5),\n  marginTop: theme.spacing(0.5),\n  fontWeight: 500,\n  \"&:hover\": {\n    backgroundColor: alpha(theme.palette.primary.main, 0.1),\n    color: \"white\",\n    ...theme.applyStyles(\"light\", {\n      color: theme.palette.primary.main,\n    }),\n  },\n}));\n\nconst getIconFromTreeItemType = (\n  itemType: string,\n  renderIcon?: (name: string) => ReactNode,\n) => {\n  switch (itemType) {\n    case \"folder\":\n      return Folder;\n    case \"removeable\":\n      return IndeterminateCheckBoxRoundedIcon;\n    default:\n      return renderIcon ? renderIcon(itemType) : Folder;\n  }\n};\n\nexport const CustomTreeItem = React.forwardRef(function CustomTreeItem(\n  props: CustomTreeItemProps,\n  ref: React.Ref<HTMLLIElement>,\n) {\n  const {\n    id,\n    itemId,\n    label,\n    disabled,\n    children,\n    onRemove,\n    renderIcon,\n    ...other\n  } = props;\n\n  const {\n    getContextProviderProps,\n    getRootProps,\n    getContentProps,\n    getIconContainerProps,\n    getCheckboxProps,\n    getLabelProps,\n    getGroupTransitionProps,\n    status,\n  } = useTreeItem({\n    id,\n    itemId,\n    children,\n    label,\n    disabled,\n    rootRef: ref as never,\n  });\n\n  const item = useTreeItemModel<ExtendedTreeItemProps>(itemId)!;\n  const icon = getIconFromTreeItemType(item.icon, renderIcon);\n  const rootProps = getRootProps(other) as React.ComponentPropsWithoutRef<\"li\">;\n\n  const handleRemoveIconClick = (e: React.MouseEvent) => {\n    e.stopPropagation();\n    onRemove?.(item);\n  };\n\n  return (\n    <TreeItemProvider {...getContextProviderProps()}>\n      <TreeItemRoot {...rootProps}>\n        <TreeItemContent {...getContentProps()}>\n          <TreeItemIconContainer {...getIconContainerProps()}>\n            <TreeItemIcon status={status} />\n          </TreeItemIconContainer>\n          <TreeItemCheckbox {...getCheckboxProps()} />\n          <CustomLabel\n            {...getLabelProps({\n              icon:\n                item.icon === \"removeable\" ? (\n                  <Box\n                    onClick={handleRemoveIconClick}\n                    sx={{\n                      width: 20,\n                      height: 20,\n                      display: \"flex\",\n                      alignItems: \"center\",\n                      justifyContent: \"center\",\n                      borderRadius: \"4px\",\n                      cursor: \"pointer\",\n                      mr: 1,\n                      \"&:hover\": {\n                        backgroundColor: \"rgba(0,0,0,0.1)\",\n                      },\n                    }}\n                  >\n                    <IndeterminateCheckBoxRoundedIcon fontSize=\"small\" />\n                  </Box>\n                ) : (\n                  icon\n                ),\n              expandable: (status.expandable && status.expanded).toString(),\n              isHighlightedItem: item.isHighlightedItem,\n              highlightName: item.highlightName,\n              id: item.id,\n              renderIcon,\n            })}\n          />\n        </TreeItemContent>\n        {children && <Collapse {...getGroupTransitionProps()} />}\n      </TreeItemRoot>\n    </TreeItemProvider>\n  );\n});\n","import { Avatar, Box, Paper, Typography } from \"@mui/material\";\nimport { RichTreeView, TreeViewBaseItem } from \"@mui/x-tree-view\";\nimport { useTreeItemModel } from \"@mui/x-tree-view/hooks\";\nimport React, { useEffect, useMemo, useState } from \"react\";\nimport { buildSelectedTree } from \"../buildSelectedTree\";\nimport {\n  CustomTreeItemProps,\n  ExtendedTreeItemProps,\n  TreeViewWrapperProps,\n} from \"../types\";\nimport { resolveFolderView } from \"../resolveFolderView\";\nimport { CustomTreeItem } from \"./CustomTreeItem\";\n\nconst attachFolderId = (\n  items: TreeViewBaseItem<ExtendedTreeItemProps>[],\n  folderId: string,\n): TreeViewBaseItem<ExtendedTreeItemProps>[] => {\n  return items.map((item) => ({\n    ...item,\n    folderId,\n    children: item.children\n      ? attachFolderId(item.children, folderId)\n      : undefined,\n  }));\n};\n\nfunction getAllExpandableItemIds(\n  items: TreeViewBaseItem<ExtendedTreeItemProps>[],\n): string[] {\n  const ids: string[] = [];\n  for (const item of items) {\n    if (item.children && item.children.length > 0) {\n      ids.push(item.id);\n      ids.push(...getAllExpandableItemIds(item.children));\n    }\n  }\n  return ids;\n}\n\nfunction FolderTree({\n  items,\n  LeafTreeItemComponent,\n  TreeItemComponent,\n  onRemove,\n}: {\n  items: TreeViewBaseItem<ExtendedTreeItemProps>[];\n  LeafTreeItemComponent?: React.ForwardRefExoticComponent<\n    CustomTreeItemProps & React.RefAttributes<HTMLLIElement>\n  >;\n  TreeItemComponent?: React.ForwardRefExoticComponent<\n    CustomTreeItemProps & React.RefAttributes<HTMLLIElement>\n  >;\n  onRemove: (item: TreeViewBaseItem<ExtendedTreeItemProps>) => void;\n}) {\n  const allExpandableIds = useMemo(\n    () => getAllExpandableItemIds(items),\n    [items],\n  );\n  const [expandedItems, setExpandedItems] =\n    useState<string[]>(allExpandableIds);\n\n  useEffect(() => {\n    setExpandedItems((prev) => {\n      const newIds = allExpandableIds.filter((id) => !prev.includes(id));\n      if (newIds.length > 0) {\n        return [...prev, ...newIds];\n      }\n      return prev;\n    });\n  }, [allExpandableIds]);\n\n  const handleRemoveTreeItem = (\n    item: TreeViewBaseItem<ExtendedTreeItemProps>,\n  ) => {\n    onRemove(item);\n  };\n\n  const TreeItem = useMemo(\n    () =>\n      TreeItemComponent || LeafTreeItemComponent\n        ? React.forwardRef<HTMLLIElement, CustomTreeItemProps>(\n            function TreeItem(props, ref) {\n              const item = useTreeItemModel<ExtendedTreeItemProps>(\n                props.itemId,\n              );\n              const Component =\n                item?.kind === \"leaf\"\n                  ? (LeafTreeItemComponent ??\n                    TreeItemComponent ??\n                    CustomTreeItem)\n                  : (TreeItemComponent ?? CustomTreeItem);\n\n              return <Component {...props} ref={ref} />;\n            },\n          )\n        : CustomTreeItem,\n    [LeafTreeItemComponent, TreeItemComponent],\n  );\n\n  return (\n    <RichTreeView\n      items={items}\n      expandedItems={expandedItems}\n      onExpandedItemsChange={(\n        _event: React.SyntheticEvent | null,\n        ids: string[],\n      ) => setExpandedItems(ids)}\n      slots={{ item: TreeItem }}\n      slotProps={{\n        item: {\n          onRemove: handleRemoveTreeItem,\n        } as Partial<CustomTreeItemProps>,\n      }}\n      sx={{\n        ml: 1,\n        mr: 1,\n        \"& ul\": {\n          paddingInlineStart: \"12px\",\n        },\n      }}\n      itemChildrenIndentation={0}\n    />\n  );\n}\n\nexport function TreeViewWrapper({\n  folders,\n  selectedByFolder,\n  activeViewIdByFolder,\n  selectedCount,\n  onRemove,\n}: TreeViewWrapperProps) {\n  const folderTrees = useMemo(\n    () =>\n      folders.flatMap((folder) => {\n        const folderSelectedIds = selectedByFolder.get(folder.id);\n        if (!folderSelectedIds || folderSelectedIds.size === 0) {\n          return [];\n        }\n\n        const activeView = resolveFolderView(folder, activeViewIdByFolder);\n        const selectedRows = folder.rows.filter((row) =>\n          folderSelectedIds.has(row.id),\n        );\n\n        return [\n          {\n            folderId: folder.id,\n            items: attachFolderId(\n              buildSelectedTree({\n                folderId: folder.id,\n                rootLabel: folder.label,\n                selectedRows,\n                groupingModel: activeView.groupingModel,\n                leafField: activeView.leafField,\n              }),\n              folder.id,\n            ),\n            TreeItemComponent: folder.TreeItemComponent,\n            LeafTreeItemComponent: folder.LeafTreeItemComponent,\n          },\n        ];\n      }),\n    [activeViewIdByFolder, folders, selectedByFolder],\n  );\n\n  return (\n    <Paper\n      sx={{\n        height: 500,\n        width: \"100%\",\n        border: \"10px solid\",\n        borderColor: \"grey.200\",\n        boxSizing: \"border-box\",\n        borderRadius: 2,\n        display: \"flex\",\n        flexDirection: \"column\",\n      }}\n    >\n      <Box\n        sx={{\n          display: \"flex\",\n          alignItems: \"center\",\n          gap: 1,\n          py: 1,\n          backgroundColor: \"grey.200\",\n          flexShrink: 0,\n        }}\n      >\n        <Avatar\n          sx={{\n            width: 30,\n            height: 30,\n            fontSize: 14,\n            fontWeight: \"bold\",\n            bgcolor: \"white\",\n            color: \"text.primary\",\n          }}\n        >\n          {selectedCount}\n        </Avatar>\n        <Typography fontWeight=\"bold\">Active Tracks</Typography>\n      </Box>\n      <Box\n        sx={{\n          flex: 1,\n          overflow: \"auto\",\n        }}\n      >\n        {folderTrees.map((folderTree) => (\n          <FolderTree\n            key={folderTree.folderId}\n            items={folderTree.items}\n            LeafTreeItemComponent={folderTree.LeafTreeItemComponent}\n            TreeItemComponent={folderTree.TreeItemComponent}\n            onRemove={onRemove}\n          />\n        ))}\n      </Box>\n    </Paper>\n  );\n}\n","import { TreeViewBaseItem } from \"@mui/x-tree-view\";\nimport { TrackStoreInstance } from \"@weng-lab/genomebrowser\";\nimport CloseIcon from \"@mui/icons-material/Close\";\nimport {\n  Box,\n  Button,\n  Dialog,\n  DialogContent,\n  DialogTitle,\n  IconButton,\n  Stack,\n} from \"@mui/material\";\nimport { useEffect, useState } from \"react\";\nimport { Assembly, FolderDefinition } from \"./Folders/types\";\nimport { DataGridWrapper } from \"./DataGrid/DataGridWrapper\";\nimport { ClearDialog } from \"./Dialogs/ClearDialog\";\nimport { LimitDialog } from \"./Dialogs/LimitDialog\";\nimport { ResetDialog } from \"./Dialogs/ResetDialog\";\nimport { Breadcrumb } from \"./FolderList/Breadcrumb\";\nimport { FolderList } from \"./FolderList/FolderList\";\nimport { diffManagedTracks } from \"./managedTracks\";\nimport { resolveFolderView } from \"./resolveFolderView\";\nimport type { TrackSelectTrackContext } from \"./trackContext\";\nimport { ExtendedTreeItemProps } from \"./types\";\nimport { TreeViewWrapper } from \"./TreeView/TreeViewWrapper\";\n\nexport type InitialSelectedIdsByAssembly = Partial<\n  Record<Assembly, Record<string, string[]>>\n>;\n\nexport interface TrackSelectProps {\n  assembly: Assembly;\n  folders: FolderDefinition[];\n  initialSelectedIds?: InitialSelectedIdsByAssembly;\n  sessionStorageKey?: string;\n  trackStore?: TrackStoreInstance;\n  onCancel?: () => void;\n  maxTracks?: number;\n  trackContext?: TrackSelectTrackContext;\n  open: boolean;\n  onClose: () => void;\n  title?: string;\n}\n\nconst DEFAULT_MAX_TRACKS = 30;\n\nconst DEFAULT_TITLE = \"Track Select\";\n\ntype ViewState = \"folder-list\" | \"folder-detail\";\n\nconst createEmptySelectedByFolder = (folders: FolderDefinition[]) => {\n  return new Map(folders.map((folder) => [folder.id, new Set<string>()]));\n};\n\nconst cloneSelectedByFolder = (selectedByFolder: Map<string, Set<string>>) => {\n  return new Map(\n    Array.from(selectedByFolder, ([folderId, ids]) => [folderId, new Set(ids)]),\n  );\n};\n\nconst normalizeSelectedByFolder = ({\n  folders,\n  selectedIdsByFolder,\n}: {\n  folders: FolderDefinition[];\n  selectedIdsByFolder?: Record<string, string[]>;\n}) => {\n  const normalized = createEmptySelectedByFolder(folders);\n\n  if (!selectedIdsByFolder) {\n    return normalized;\n  }\n\n  folders.forEach((folder) => {\n    const ids = selectedIdsByFolder[folder.id];\n    if (!ids) {\n      return;\n    }\n\n    normalized.set(\n      folder.id,\n      new Set(ids.filter((id) => id.startsWith(`${folder.id}/`))),\n    );\n  });\n\n  return normalized;\n};\n\nconst loadSelectedByFolder = ({\n  assembly,\n  folders,\n  initialSelectedIds,\n  sessionStorageKey,\n}: {\n  assembly: Assembly;\n  folders: FolderDefinition[];\n  initialSelectedIds?: InitialSelectedIdsByAssembly;\n  sessionStorageKey?: string;\n}) => {\n  const fallback = normalizeSelectedByFolder({\n    folders,\n    selectedIdsByFolder: initialSelectedIds?.[assembly],\n  });\n\n  if (!sessionStorageKey || typeof window === \"undefined\") {\n    return fallback;\n  }\n\n  const storedValue = window.sessionStorage.getItem(sessionStorageKey);\n  if (!storedValue) {\n    return fallback;\n  }\n\n  try {\n    const parsed = JSON.parse(storedValue) as Record<string, string[]>;\n    return normalizeSelectedByFolder({\n      folders,\n      selectedIdsByFolder: parsed,\n    });\n  } catch {\n    return fallback;\n  }\n};\n\nconst saveSelectedByFolder = ({\n  selectedByFolder,\n  sessionStorageKey,\n}: {\n  selectedByFolder: Map<string, Set<string>>;\n  sessionStorageKey?: string;\n}) => {\n  if (!sessionStorageKey || typeof window === \"undefined\") {\n    return;\n  }\n\n  const serialized = Object.fromEntries(\n    Array.from(selectedByFolder, ([folderId, ids]) => [\n      folderId,\n      Array.from(ids),\n    ]),\n  );\n  window.sessionStorage.setItem(sessionStorageKey, JSON.stringify(serialized));\n};\n\nexport default function TrackSelect({\n  assembly,\n  folders,\n  initialSelectedIds,\n  sessionStorageKey,\n  trackStore,\n  onCancel,\n  maxTracks,\n  trackContext,\n  open,\n  onClose,\n  title = DEFAULT_TITLE,\n}: TrackSelectProps) {\n  const [limitDialogOpen, setLimitDialogOpen] = useState(false);\n  const [clearDialogOpen, setClearDialogOpen] = useState(false);\n  const [resetDialogOpen, setResetDialogOpen] = useState(false);\n  const [currentView, setCurrentView] = useState<ViewState>(() =>\n    folders.length > 1 ? \"folder-list\" : \"folder-detail\",\n  );\n  const [activeFolderId, setActiveFolderId] = useState(\n    () => folders[0]?.id ?? \"\",\n  );\n  const [activeViewIdByFolder, setActiveViewIdByFolder] = useState(\n    () =>\n      new Map(\n        folders.flatMap((folder) =>\n          folder.views?.[0] ? [[folder.id, folder.views[0].id] as const] : [],\n        ),\n      ),\n  );\n  const [committedSelectedByFolder, setCommittedSelectedByFolder] = useState(\n    () =>\n      loadSelectedByFolder({\n        assembly,\n        folders,\n        initialSelectedIds,\n        sessionStorageKey,\n      }),\n  );\n  const [selectedByFolder, setSelectedByFolder] = useState(() =>\n    cloneSelectedByFolder(committedSelectedByFolder),\n  );\n  const maxTracksLimit = maxTracks ?? DEFAULT_MAX_TRACKS;\n\n  useEffect(() => {\n    setActiveFolderId((currentFolderId) => {\n      if (folders.some((folder) => folder.id === currentFolderId)) {\n        return currentFolderId;\n      }\n\n      return folders[0]?.id ?? \"\";\n    });\n\n    if (folders.length <= 1) {\n      setCurrentView(\"folder-detail\");\n    }\n\n    setActiveViewIdByFolder((current) => {\n      return new Map(\n        folders.flatMap((folder) => {\n          if (!folder.views?.length) {\n            return [];\n          }\n\n          const activeViewId = current.get(folder.id);\n          if (\n            activeViewId &&\n            folder.views.some((view) => view.id === activeViewId)\n          ) {\n            return [[folder.id, activeViewId] as const];\n          }\n\n          return [[folder.id, folder.views[0].id] as const];\n        }),\n      );\n    });\n  }, [folders]);\n\n  useEffect(() => {\n    const nextCommittedSelection = loadSelectedByFolder({\n      assembly,\n      folders,\n      initialSelectedIds,\n      sessionStorageKey,\n    });\n    setCommittedSelectedByFolder(nextCommittedSelection);\n    setSelectedByFolder(cloneSelectedByFolder(nextCommittedSelection));\n  }, [assembly, folders, initialSelectedIds, sessionStorageKey]);\n\n  useEffect(() => {\n    if (!open) {\n      return;\n    }\n\n    setSelectedByFolder(cloneSelectedByFolder(committedSelectedByFolder));\n  }, [committedSelectedByFolder, open]);\n\n  useEffect(() => {\n    if (!assembly || !trackStore) {\n      return;\n    }\n\n    const { idsToRemove, tracksToAdd } = diffManagedTracks({\n      assembly,\n      currentTracks: trackStore.getState().tracks,\n      folders,\n      selectedByFolder: committedSelectedByFolder,\n      trackContext,\n    });\n\n    const { insertTrack, removeTrack } = trackStore.getState();\n    idsToRemove.forEach((id) => removeTrack(id));\n    tracksToAdd.forEach((track) => insertTrack(track));\n  }, [assembly, committedSelectedByFolder, folders, trackContext, trackStore]);\n\n  const activeFolder =\n    folders.find((folder) => folder.id === activeFolderId) ?? folders[0];\n  const activeConfig = activeFolder\n    ? resolveFolderView(activeFolder, activeViewIdByFolder)\n    : undefined;\n  const activeViewId = activeConfig?.id ?? \"\";\n  const rows = activeFolder?.rows ?? [];\n  const selectedIds = new Set(\n    selectedByFolder.get(activeFolder?.id ?? \"\") ?? [],\n  );\n  let selectedCount = 0;\n  selectedByFolder.forEach((ids) => {\n    selectedCount += ids.size;\n  });\n\n  const handleFolderSelect = (folderId: string) => {\n    setActiveFolderId(folderId);\n    setCurrentView(\"folder-detail\");\n  };\n\n  const handleNavigateToRoot = () => {\n    setCurrentView(\"folder-list\");\n  };\n\n  const handleCancel = () => {\n    onCancel?.();\n    onClose();\n  };\n\n  const ViewSelector = activeFolder?.ViewSelector;\n\n  const confirmReset = () => {\n    setResetDialogOpen(false);\n    setSelectedByFolder(cloneSelectedByFolder(committedSelectedByFolder));\n  };\n\n  const confirmClear = () => {\n    setClearDialogOpen(false);\n\n    const nextSelectedByFolder = new Map(selectedByFolder);\n\n    if (currentView === \"folder-detail\") {\n      nextSelectedByFolder.set(activeFolderId, new Set<string>());\n    } else {\n      folders.forEach((folder) =>\n        nextSelectedByFolder.set(folder.id, new Set<string>()),\n      );\n    }\n\n    setSelectedByFolder(nextSelectedByFolder);\n  };\n\n  const handleActiveViewChange = (viewId: string) => {\n    if (!activeFolder) {\n      return;\n    }\n\n    setActiveViewIdByFolder((prev) => {\n      const next = new Map(prev);\n      next.set(activeFolder.id, viewId);\n      return next;\n    });\n  };\n\n  const handleSelectionChange = (ids: Set<string>) => {\n    if (!activeFolder) {\n      return;\n    }\n\n    const filteredIds = new Set(\n      Array.from(ids).filter((id) =>\n        activeFolder.rows.some((row) => row.id === id),\n      ),\n    );\n\n    let nextTotal = filteredIds.size;\n    selectedByFolder.forEach((folderIds, folderId) => {\n      if (folderId !== activeFolder.id) {\n        nextTotal += folderIds.size;\n      }\n    });\n\n    if (nextTotal > maxTracksLimit) {\n      setLimitDialogOpen(true);\n      return;\n    }\n\n    const nextSelectedByFolder = new Map(selectedByFolder);\n    nextSelectedByFolder.set(activeFolder.id, filteredIds);\n    setSelectedByFolder(nextSelectedByFolder);\n  };\n\n  const handleRemoveTreeItem = (\n    item: TreeViewBaseItem<ExtendedTreeItemProps>,\n  ) => {\n    const folderId = item.folderId;\n    if (!folderId || !item.allExpAccessions?.length) {\n      return;\n    }\n\n    const nextSelectedByFolder = new Map(selectedByFolder);\n    const nextSet = new Set(\n      nextSelectedByFolder.get(folderId) ?? new Set<string>(),\n    );\n    item.allExpAccessions.forEach((id) => nextSet.delete(id));\n    nextSelectedByFolder.set(folderId, nextSet);\n    setSelectedByFolder(nextSelectedByFolder);\n  };\n\n  const handleSubmit = () => {\n    saveSelectedByFolder({ selectedByFolder, sessionStorageKey });\n    setCommittedSelectedByFolder(cloneSelectedByFolder(selectedByFolder));\n    onClose();\n  };\n\n  return (\n    <Dialog open={open} onClose={handleCancel} maxWidth=\"lg\" fullWidth>\n      <DialogTitle\n        sx={{\n          bgcolor: \"primary.main\",\n          color: \"primary.contrastText\",\n          display: \"flex\",\n          justifyContent: \"space-between\",\n          alignItems: \"center\",\n          fontWeight: \"bold\",\n        }}\n      >\n        {title}\n        <IconButton\n          size=\"large\"\n          onClick={handleCancel}\n          sx={{ color: \"primary.contrastText\", p: 0 }}\n        >\n          <CloseIcon fontSize=\"large\" />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent sx={{ marginTop: \"5px\" }}>\n        {!activeFolder || !activeConfig ? (\n          <Box sx={{ p: 2 }}>No folders available.</Box>\n        ) : (\n          <Box sx={{ flex: 1, pt: 1 }}>\n            <Box\n              display=\"flex\"\n              justifyContent=\"space-between\"\n              alignItems=\"center\"\n              sx={{ mb: 2 }}\n            >\n              {folders.length > 1 ? (\n                <Breadcrumb\n                  currentFolder={\n                    currentView === \"folder-detail\" ? activeFolder : null\n                  }\n                  onNavigateToRoot={handleNavigateToRoot}\n                />\n              ) : (\n                <Box />\n              )}\n              {currentView === \"folder-detail\" &&\n              ViewSelector &&\n              activeFolder.views ? (\n                <ViewSelector\n                  views={activeFolder.views}\n                  activeViewId={activeViewId}\n                  onChange={handleActiveViewChange}\n                />\n              ) : null}\n            </Box>\n            <Stack\n              direction={{ xs: \"column\", md: \"row\" }}\n              spacing={2}\n              sx={{ width: \"100%\" }}\n            >\n              <Box\n                sx={{\n                  flex: { xs: \"none\", md: 3 },\n                  minWidth: 0,\n                  width: { xs: \"100%\", md: \"auto\" },\n                }}\n              >\n                {currentView === \"folder-list\" ? (\n                  <FolderList\n                    folders={folders}\n                    onFolderSelect={handleFolderSelect}\n                  />\n                ) : (\n                  <DataGridWrapper\n                    rows={rows}\n                    columns={activeConfig.columns}\n                    groupingModel={activeConfig.groupingModel}\n                    leafField={activeConfig.leafField}\n                    label={`${rows.length} Available ${activeFolder.label}`}\n                    selectedIds={selectedIds}\n                    onSelectionChange={handleSelectionChange}\n                    GroupingCellComponent={activeFolder.GroupingCellComponent}\n                  />\n                )}\n              </Box>\n              <Box\n                sx={{\n                  flex: { xs: \"none\", md: 2 },\n                  minWidth: 0,\n                  width: { xs: \"100%\", md: \"auto\" },\n                }}\n              >\n                <TreeViewWrapper\n                  folders={folders}\n                  selectedByFolder={selectedByFolder}\n                  activeViewIdByFolder={activeViewIdByFolder}\n                  selectedCount={selectedCount}\n                  onRemove={handleRemoveTreeItem}\n                />\n              </Box>\n            </Stack>\n            <Box\n              sx={{\n                display: \"flex\",\n                justifyContent: \"space-between\",\n                alignItems: \"center\",\n                mt: 2,\n                gap: 1,\n              }}\n            >\n              <Box sx={{ display: \"flex\", gap: 1 }}>\n                <Button\n                  variant=\"outlined\"\n                  color=\"secondary\"\n                  size=\"small\"\n                  onClick={() => setClearDialogOpen(true)}\n                >\n                  Clear\n                </Button>\n                {Boolean(trackStore) ? (\n                  <Button\n                    variant=\"outlined\"\n                    color=\"secondary\"\n                    size=\"small\"\n                    onClick={() => setResetDialogOpen(true)}\n                  >\n                    Reset\n                  </Button>\n                ) : null}\n              </Box>\n              <Box sx={{ display: \"flex\", gap: 1 }}>\n                <Button variant=\"outlined\" size=\"small\" onClick={handleCancel}>\n                  Cancel\n                </Button>\n                <Button\n                  variant=\"contained\"\n                  color=\"primary\"\n                  size=\"small\"\n                  onClick={handleSubmit}\n                >\n                  Submit\n                </Button>\n              </Box>\n            </Box>\n            <LimitDialog\n              open={limitDialogOpen}\n              onClose={() => setLimitDialogOpen(false)}\n              maxTracks={maxTracksLimit}\n            />\n            <ClearDialog\n              open={clearDialogOpen}\n              onClose={() => setClearDialogOpen(false)}\n              onConfirm={confirmClear}\n              folderLabel={activeFolder.label}\n              clearAll={currentView === \"folder-list\"}\n            />\n            <ResetDialog\n              open={resetDialogOpen}\n              onClose={() => setResetDialogOpen(false)}\n              onConfirm={confirmReset}\n            />\n          </Box>\n        )}\n      </DialogContent>\n    </Dialog>\n  );\n}\n","import { Box } from \"@mui/material\";\nimport type { Assembly } from \"../../types\";\n\nexport type { Assembly };\n\nexport const assayTypes = [\n  \"cCRE\",\n  \"DNase\",\n  \"H3K4me3\",\n  \"H3K27ac\",\n  \"ATAC\",\n  \"CTCF\",\n  \"RNA-seq\",\n  \"ChromHMM\",\n  \"WGBS\",\n];\n\nexport const lifeStages = [\"Adult\", \"Embryonic\", \"N/A\"];\n\nexport const ontologyTypes = [\n  \"Aggregate\",\n  \"Adipose\",\n  \"Adrenal gland\",\n  \"Blood\",\n  \"Blood vessel\",\n  \"Bone\",\n  \"Bone marrow\",\n  \"Brain\",\n  \"Breast\",\n  \"Connective tissue\",\n  \"Embryo\",\n  \"Epithelium\",\n  \"Esophagus\",\n  \"Eye\",\n  \"Fallopian Tube\",\n  \"Gallbladder\",\n  \"Heart\",\n  \"Kidney\",\n  \"Large Intestine\",\n  \"Limb\",\n  \"Liver\",\n  \"Lung\",\n  \"Lymphoid Tissue\",\n  \"Muscle\",\n  \"Mouth\",\n  \"Nerve\",\n  \"Nose\",\n  \"Pancreas\",\n  \"Parathyroid Gland\",\n  \"Ovary\",\n  \"Penis\",\n  \"Placenta\",\n  \"Prostate\",\n  \"Skin\",\n  \"Small Intestine\",\n  \"Spinal Cord\",\n  \"Spleen\",\n  \"Stomach\",\n  \"Testis\",\n  \"Thymus\",\n  \"Thyroid\",\n  \"Urinary Bladder\",\n  \"Uterus\",\n  \"Vagina\",\n];\n\n/** Color mapping for assay types */\nexport const assayColorMap: { [key: string]: string } = {\n  DNase: \"#06da93\",\n  ATAC: \"#02c7b9\",\n  H3K4me3: \"#ff2020\",\n  ChromHMM: \"#0097a7\",\n  H3K27ac: \"#fdc401\",\n  CTCF: \"#01a6f1\",\n  cCRE: \"#000000\",\n  \"RNA-seq\": \"#00aa00\",\n  WGBS: \"#648bd8\",\n};\n\n/**\n * Creates the assay icon for DataGrid and RichTreeView\n * @param type - assay type\n * @returns an icon of the assay's respective color\n */\nexport function AssayIcon(type: string) {\n  const color = assayColorMap[type];\n  return (\n    <Box\n      sx={{\n        width: 12,\n        height: 12,\n        borderRadius: \"20%\",\n        bgcolor: color,\n      }}\n    />\n  );\n}\n\n/**\n * Mapping from JSON assay keys to display names.\n * This is the single source of truth for assay name formatting.\n */\nconst assayJsonToDisplay: Record<string, string> = {\n  dnase: \"DNase\",\n  atac: \"ATAC\",\n  h3k4me3: \"H3K4me3\",\n  h3k27ac: \"H3K27ac\",\n  ctcf: \"CTCF\",\n  chromhmm: \"ChromHMM\",\n  ccre: \"cCRE\",\n  rnaseq: \"RNA-seq\",\n  wgbs: \"WGBS\",\n};\n\n/**\n * Convert JSON assay key to display name.\n * Used only during data loading to normalize assay names.\n */\nexport function formatAssayType(jsonKey: string): string {\n  return assayJsonToDisplay[jsonKey.toLowerCase()] ?? jsonKey;\n}\n","import {\n  GridColDef,\n  GridRenderCellParams,\n  GridGroupNode,\n  useGridApiContext,\n} from \"@mui/x-data-grid-premium\";\nimport { Stack, capitalize } from \"@mui/material\";\nimport { AssayIcon, ontologyTypes, assayTypes, lifeStages } from \"./constants\";\nimport { BiosampleRowInfo, CollectionType } from \"./types\";\n\nconst collectionTypes: CollectionType[] = [\"Core\", \"Ancillary\", \"Partial\", \"NA\"];\n\nfunction CollectionCell(params: GridRenderCellParams<BiosampleRowInfo>) {\n  const apiRef = useGridApiContext();\n\n  if (params.rowNode.type !== \"group\") {\n    return params.value ?? null;\n  }\n\n  const groupNode = params.rowNode as GridGroupNode;\n  if (groupNode.groupingField !== \"displayName\") {\n    return null;\n  }\n\n  const childIds = groupNode.children;\n  if (!childIds || childIds.length === 0) {\n    return null;\n  }\n\n  const firstChildRow = apiRef.current.getRow(\n    childIds[0],\n  ) as BiosampleRowInfo | null;\n\n  return firstChildRow?.collection ?? null;\n}\n\nconst displayNameCol: GridColDef<BiosampleRowInfo> = {\n  field: \"displayName\",\n  headerName: \"Name\",\n  valueFormatter: (value) => value && capitalize(value),\n  maxWidth: 300,\n};\n\nconst sortedByAssayOntologyCol: GridColDef<BiosampleRowInfo> = {\n  field: \"ontology\",\n  headerName: \"Ontology\",\n  type: \"singleSelect\",\n  valueOptions: ontologyTypes,\n  renderCell: (params) => {\n    if (params.rowNode.type === \"group\") {\n      if (params.value === undefined) {\n        return null;\n      }\n      const val = params.value;\n      return (\n        <div>\n          <b>{val}</b>\n        </div>\n      );\n    }\n  },\n};\n\nconst sortedByAssayAssayCol: GridColDef<BiosampleRowInfo> = {\n  field: \"assay\",\n  headerName: \"Assay\",\n  valueOptions: assayTypes,\n  renderCell: (params) => {\n    if (params.rowNode.type === \"group\") {\n      if (params.value === undefined) {\n        return null;\n      }\n      const val = params.value;\n      return (\n        <Stack direction=\"row\" spacing={2} alignItems=\"center\">\n          {AssayIcon(val)}\n          <div>\n            <b>{val}</b>\n          </div>\n        </Stack>\n      );\n    }\n  },\n};\n\nconst defaultOntologyCol: GridColDef<BiosampleRowInfo> = {\n  field: \"ontology\",\n  headerName: \"Ontology\",\n  type: \"singleSelect\",\n  valueOptions: ontologyTypes,\n  renderCell: (params) => {\n    if (params.rowNode.type === \"group\") {\n      if (params.value === undefined) {\n        return null;\n      }\n      const val = params.value;\n      return (\n        <div>\n          <b>{val}</b>\n        </div>\n      );\n    }\n  },\n};\n\nconst defaultAssayCol: GridColDef<BiosampleRowInfo> = {\n  field: \"assay\",\n  headerName: \"Assay\",\n  valueOptions: assayTypes,\n  renderCell: (params) => {\n    if (params.value === undefined) {\n      return null;\n    }\n    const val = params.value;\n    return (\n      <Stack direction=\"row\" spacing={2} alignItems=\"center\" sx={{ ml: 6 }}>\n        {AssayIcon(val)}\n        <div>{val}</div>\n      </Stack>\n    );\n  },\n};\n\nconst sampleTypeCol: GridColDef<BiosampleRowInfo> = {\n  field: \"sampleType\",\n  headerName: \"Sample Type\",\n  type: \"singleSelect\",\n  valueOptions: ontologyTypes,\n  valueFormatter: (value) => value && capitalize(value),\n};\n\nconst lifeStageCol: GridColDef<BiosampleRowInfo> = {\n  field: \"lifeStage\",\n  headerName: \"Life Stage\",\n  type: \"singleSelect\",\n  valueOptions: lifeStages,\n  valueFormatter: (value) => value && capitalize(value),\n};\n\nconst collectionCol: GridColDef<BiosampleRowInfo> = {\n  field: \"collection\",\n  headerName: \"Collection\",\n  type: \"singleSelect\",\n  valueOptions: collectionTypes,\n  width: 100,\n  renderCell: (params) => <CollectionCell {...params} />,\n};\n\nconst experimentCol: GridColDef<BiosampleRowInfo> = {\n  field: \"experimentAccession\",\n  headerName: \"Experiment Accession\",\n};\n\nconst fileCol: GridColDef<BiosampleRowInfo> = {\n  field: \"fileAccession\",\n  headerName: \"File Accession\",\n};\n\nconst idCol: GridColDef<BiosampleRowInfo> = {\n  field: \"id\",\n  headerName: \"ID\",\n};\n\n/** Columns for sorted-by-assay view (assay as top-level grouping) */\nexport const sortedByAssayColumns: GridColDef<BiosampleRowInfo>[] = [\n  displayNameCol,\n  sortedByAssayOntologyCol,\n  collectionCol,\n  sampleTypeCol,\n  lifeStageCol,\n  sortedByAssayAssayCol,\n  experimentCol,\n  fileCol,\n  idCol,\n];\n\n/** Default columns (ontology as top-level grouping) */\nexport const defaultColumns: GridColDef<BiosampleRowInfo>[] = [\n  defaultAssayCol,\n  collectionCol,\n  sampleTypeCol,\n  lifeStageCol,\n  defaultOntologyCol,\n  displayNameCol,\n  experimentCol,\n  fileCol,\n  idCol,\n];\n\n/** Grouping model for sorted-by-assay view */\nexport const sortedByAssayGroupingModel = [\"assay\", \"ontology\"];\n\n/** Default grouping model (ontology-based) */\nexport const defaultGroupingModel = [\"ontology\", \"displayName\"];\n\n/** Leaf field for sorted-by-assay view */\nexport const sortedByAssayLeafField = \"displayName\";\n\n/** Default leaf field */\nexport const defaultLeafField = \"assay\";\n","import { ToggleButton, ToggleButtonGroup } from \"@mui/material\";\nimport { FolderView } from \"../../types\";\n\nexport interface BiosampleViewSelectorProps {\n  views: FolderView[];\n  activeViewId: string;\n  onChange: (viewId: string) => void;\n}\n\nexport function BiosampleViewSelector({\n  views,\n  activeViewId,\n  onChange,\n}: BiosampleViewSelectorProps) {\n  return (\n    <ToggleButtonGroup\n      exclusive\n      value={activeViewId}\n      size=\"small\"\n      onChange={(_event, viewId: string | null) => {\n        if (viewId) {\n          onChange(viewId);\n        }\n      }}\n    >\n      {views.map((view) => (\n        <ToggleButton key={view.id} value={view.id}>\n          {view.label}\n        </ToggleButton>\n      ))}\n    </ToggleButtonGroup>\n  );\n}\n","import { Stack, Tooltip, Box, IconButton } from \"@mui/material\";\nimport {\n  GridRenderCellParams,\n  useGridApiContext,\n  GridGroupNode,\n} from \"@mui/x-data-grid-premium\";\nimport { assayTypes, AssayIcon } from \"./constants\";\nimport ChevronRightIcon from \"@mui/icons-material/ChevronRight\";\nimport ExpandMoreIcon from \"@mui/icons-material/ExpandMore\";\n\n/**\n * Biosample-specific grouping cell that renders AssayIcon for assay groups/values.\n * Handles expand/collapse, truncation, and tooltips.\n */\nexport default function BiosampleGroupingCell(params: GridRenderCellParams) {\n  const apiRef = useGridApiContext();\n  const isGroup = params.rowNode.type === \"group\";\n  const groupNode = params.rowNode as GridGroupNode;\n  const isExpanded = isGroup ? groupNode.childrenExpanded : false;\n  const groupingField = isGroup ? groupNode.groupingField : null;\n  const depth = params.rowNode.depth ?? 0;\n\n  const handleExpandClick = (e: React.MouseEvent) => {\n    e.stopPropagation();\n    apiRef.current.setRowChildrenExpansion(params.id, !isExpanded);\n  };\n\n  // Render content based on grouping field\n  const renderContent = () => {\n    const value = String(params.value ?? \"\");\n\n    // For assay groups, show the colored icon\n    if (isGroup && groupingField === \"assay\") {\n      return (\n        <Stack\n          direction=\"row\"\n          spacing={1}\n          alignItems=\"center\"\n          sx={{ flex: 1, overflow: \"hidden\" }}\n        >\n          {AssayIcon(value)}\n          <Tooltip title={value} placement=\"top-start\" enterDelay={500}>\n            <Box\n              sx={{\n                overflow: \"hidden\",\n                textOverflow: \"ellipsis\",\n                whiteSpace: \"nowrap\",\n                fontWeight: \"bold\",\n              }}\n            >\n              {params.formattedValue}\n            </Box>\n          </Tooltip>\n        </Stack>\n      );\n    }\n\n    // For other groups (ontology, displayName), show bold text\n    if (isGroup) {\n      return (\n        <Tooltip title={value} placement=\"top-start\" enterDelay={500}>\n          <Box\n            sx={{\n              overflow: \"hidden\",\n              textOverflow: \"ellipsis\",\n              whiteSpace: \"nowrap\",\n              flex: 1,\n              fontWeight: \"bold\",\n            }}\n          >\n            {params.formattedValue}\n          </Box>\n        </Tooltip>\n      );\n    }\n\n    // For leaf rows - check if it's an assay value\n    const isAssayValue = assayTypes\n      .map((a) => a.toLowerCase())\n      .includes(value.toLowerCase());\n\n    if (isAssayValue) {\n      return (\n        <Stack\n          direction=\"row\"\n          spacing={1}\n          alignItems=\"center\"\n          sx={{ flex: 1, overflow: \"hidden\" }}\n        >\n          {AssayIcon(value)}\n          <Tooltip title={value} placement=\"top-start\" enterDelay={500}>\n            <Box\n              sx={{\n                overflow: \"hidden\",\n                textOverflow: \"ellipsis\",\n                whiteSpace: \"nowrap\",\n              }}\n            >\n              {params.formattedValue}\n            </Box>\n          </Tooltip>\n        </Stack>\n      );\n    }\n\n    return (\n      <Tooltip title={value} placement=\"top-start\" enterDelay={500}>\n        <Box\n          sx={{\n            overflow: \"hidden\",\n            textOverflow: \"ellipsis\",\n            whiteSpace: \"nowrap\",\n            flex: 1,\n          }}\n        >\n          {params.formattedValue}\n        </Box>\n      </Tooltip>\n    );\n  };\n\n  // Indent based on depth (2 units per level)\n  const indentLevel = depth * 2;\n\n  return (\n    <Box\n      sx={{\n        display: \"flex\",\n        alignItems: \"center\",\n        width: \"100%\",\n        ml: indentLevel,\n      }}\n    >\n      {isGroup && (\n        <IconButton size=\"small\" onClick={handleExpandClick} sx={{ mr: 0.5 }}>\n          {isExpanded ? (\n            <ExpandMoreIcon fontSize=\"small\" />\n          ) : (\n            <ChevronRightIcon fontSize=\"small\" />\n          )}\n        </IconButton>\n      )}\n      {renderContent()}\n    </Box>\n  );\n}\n","import React from \"react\";\nimport { CustomTreeItem } from \"../../../TreeView/CustomTreeItem\";\nimport { CustomTreeItemProps } from \"../../../types\";\nimport { AssayIcon } from \"./constants\";\n\n/**\n * Biosample-specific TreeItem that renders AssayIcon for assay items.\n * Wraps the generic CustomTreeItem with the AssayIcon renderer.\n */\nexport const BiosampleTreeItem = React.forwardRef<\n  HTMLLIElement,\n  CustomTreeItemProps\n>(function BiosampleTreeItem(props, ref) {\n  return <CustomTreeItem {...props} ref={ref} renderIcon={AssayIcon} />;\n});\n","import {\n  BigBedConfig,\n  BigWigConfig,\n  DisplayMode,\n  MethylCConfig,\n  Rect,\n  Track,\n  TrackType,\n  ValuedPoint,\n} from \"@weng-lab/genomebrowser\";\nimport type { FC } from \"react\";\nimport { CreateTrackOptions } from \"../../types\";\nimport { BiosampleRowInfo } from \"./types\";\n\nexport type BiosampleTrackContext = {\n  onBiosampleFeatureClick?: (args: {\n    trackId: string;\n    row: BiosampleRowInfo;\n    rect: Rect;\n  }) => void;\n  onBiosampleFeatureHover?: (args: {\n    trackId: string;\n    row: BiosampleRowInfo;\n    rect: Rect;\n  }) => void;\n  biosampleFeatureTooltip?: FC<Rect>;\n  biosampleSignalTooltip?: FC<ValuedPoint[]>;\n  biosampleMethylTooltip?: FC<ValuedPoint[]>;\n};\n\nconst assayColors: Record<string, string> = {\n  dnase: \"#06da93\",\n  h3k4me3: \"#ff0000\",\n  h3k27ac: \"#ffcd00\",\n  ctcf: \"#00b0d0\",\n  atac: \"#02c7b9\",\n  rnaseq: \"#00aa00\",\n  chromhmm: \"#00ff00\",\n  ccre: \"#000000\",\n  wgbs: \"#648bd8\",\n};\n\nconst defaultBigWig: Omit<BigWigConfig, \"id\" | \"title\" | \"url\"> = {\n  trackType: TrackType.BigWig,\n  height: 50,\n  displayMode: DisplayMode.Full,\n  titleSize: 12,\n};\n\nconst defaultBigBed: Omit<BigBedConfig, \"id\" | \"title\" | \"url\"> = {\n  trackType: TrackType.BigBed,\n  height: 20,\n  displayMode: DisplayMode.Dense,\n  titleSize: 12,\n};\n\nconst defaultMethylC: Omit<MethylCConfig, \"id\" | \"title\" | \"urls\"> = {\n  trackType: TrackType.MethylC,\n  height: 100,\n  displayMode: DisplayMode.Split,\n  titleSize: 12,\n  color: \"#648bd8\",\n  colors: {\n    cpg: \"#648bd8\",\n    chg: \"#ff944d\",\n    chh: \"#ff00ff\",\n    depth: \"#525252\",\n  },\n};\n\nexport function createBiosampleTrack(\n  row: BiosampleRowInfo,\n  options: CreateTrackOptions,\n): Track {\n  const assay = row.assay.toLowerCase();\n  const color = assayColors[assay] ?? \"#000000\";\n  const trackContext = options.trackContext;\n\n  switch (assay) {\n    case \"chromhmm\":\n    case \"ccre\":\n      return {\n        ...defaultBigBed,\n        id: row.id,\n        url: row.url ?? \"\",\n        title: row.displayName,\n        color,\n        onClick: trackContext?.onBiosampleFeatureClick\n          ? (rect: Rect) =>\n              trackContext.onBiosampleFeatureClick?.({\n                trackId: row.id,\n                row,\n                rect,\n              })\n          : undefined,\n        onHover: trackContext?.onBiosampleFeatureHover\n          ? (rect: Rect) =>\n              trackContext.onBiosampleFeatureHover?.({\n                trackId: row.id,\n                row,\n                rect,\n              })\n          : undefined,\n        tooltip: trackContext?.biosampleFeatureTooltip,\n      };\n    case \"wgbs\":\n      return {\n        ...defaultMethylC,\n        id: row.id,\n        title: row.displayName,\n        maskCpgByCoverage: true,\n        tooltip: trackContext?.biosampleMethylTooltip,\n        urls: {\n          plusStrand: {\n            cpg: { url: row.cpgPlus ?? \"\" },\n            chg: { url: \"\" },\n            chh: { url: \"\" },\n            depth: { url: row.coverage ?? \"\" },\n          },\n          minusStrand: {\n            cpg: { url: row.cpgMinus ?? \"\" },\n            chg: { url: \"\" },\n            chh: { url: \"\" },\n            depth: { url: row.coverage ?? \"\" },\n          },\n        },\n      };\n    default:\n      return {\n        ...defaultBigWig,\n        id: row.id,\n        url: row.url ?? \"\",\n        title: row.displayName,\n        color,\n        tooltip: trackContext?.biosampleSignalTooltip,\n      };\n  }\n}\n","import { capitalize } from \"@mui/material\";\nimport { FolderDefinition } from \"../../types\";\nimport {\n  BiosampleDataFile,\n  BiosampleRowInfo,\n  BiosampleTrackInfo,\n} from \"./types\";\nimport {\n  defaultColumns,\n  defaultGroupingModel,\n  defaultLeafField,\n  sortedByAssayColumns,\n  sortedByAssayGroupingModel,\n  sortedByAssayLeafField,\n} from \"./columns\";\nimport { formatAssayType } from \"./constants\";\nimport { BiosampleViewSelector } from \"./BiosampleViewSelector\";\nimport BiosampleGroupingCell from \"./BiosampleGroupingCell\";\nimport { BiosampleTreeItem } from \"./BiosampleTreeItem\";\nimport { createBiosampleTrack } from \"./toTrack\";\n\n/** Flatten a biosample track into one row per assay. */\nfunction flattenTrackIntoRows(\n  folderId: string,\n  track: BiosampleTrackInfo,\n): BiosampleRowInfo[] {\n  const { ontology, lifeStage, sampleType, displayName, collection } = track;\n\n  // Keep cCRE rows first so aggregate selections stay prominent in the UI.\n  const sortedAssays = [...track.assays].sort((a, b) => {\n    const aIsCcre = a.assay.toLowerCase() === \"ccre\";\n    const bIsCcre = b.assay.toLowerCase() === \"ccre\";\n    if (aIsCcre && !bIsCcre) return -1;\n    if (!aIsCcre && bIsCcre) return 1;\n    return 0;\n  });\n\n  return sortedAssays.map(\n    ({\n      id,\n      assay,\n      experimentAccession,\n      fileAccession,\n      url,\n      cpgPlus,\n      cpgMinus,\n      coverage,\n    }) => ({\n      id: `${folderId}/${id}`,\n      ontology: capitalize(ontology),\n      lifeStage: capitalize(lifeStage),\n      sampleType: capitalize(sampleType),\n      displayName: capitalize(displayName),\n      assay: formatAssayType(assay),\n      experimentAccession,\n      fileAccession,\n      url,\n      collection,\n      cpgPlus,\n      cpgMinus,\n      coverage,\n    }),\n  );\n}\n\nfunction transformData(\n  folderId: string,\n  data: BiosampleDataFile,\n): BiosampleRowInfo[] {\n  return data.tracks.flatMap((track) => flattenTrackIntoRows(folderId, track));\n}\n\nexport interface CreateBiosampleFolderOptions {\n  id: string;\n  label: string;\n  description?: string;\n  data: BiosampleDataFile;\n}\n\n/**\n * Build a biosample folder with its data, tree builder, and track factory.\n */\nexport function createBiosampleFolder(\n  options: CreateBiosampleFolderOptions,\n): FolderDefinition<BiosampleRowInfo> {\n  const { id, label, description, data } = options;\n  const rows = transformData(id, data);\n  const views = [\n    {\n      id: \"default\",\n      label: \"Tissue\",\n      columns: defaultColumns,\n      groupingModel: defaultGroupingModel,\n      leafField: defaultLeafField,\n    },\n    {\n      id: \"by-assay\",\n      label: \"Assay\",\n      columns: sortedByAssayColumns,\n      groupingModel: sortedByAssayGroupingModel,\n      leafField: sortedByAssayLeafField,\n    },\n  ];\n\n  return {\n    id,\n    label,\n    description,\n    rows,\n    columns: defaultColumns,\n    groupingModel: defaultGroupingModel,\n    leafField: defaultLeafField,\n    createTrack: createBiosampleTrack,\n    views,\n    ViewSelector: BiosampleViewSelector,\n    GroupingCellComponent: BiosampleGroupingCell,\n    TreeItemComponent: BiosampleTreeItem,\n  };\n}\n","import { createBiosampleFolder } from \"./shared/createFolder\";\nimport humanData from \"./data/humans_fixed.json\";\nimport { BiosampleDataFile } from \"./shared/types\";\n\n/**\n * Human biosamples folder configuration for GRCh38 assembly.\n *\n * Contains epigenomic data (DNase, ATAC, H3K4me3, H3K27ac, CTCF, cCRE, RNA-seq, ChromHMM)\n * from human tissue samples, primary cells, cell lines, and organoids.\n */\nexport const humanBiosamplesFolder = createBiosampleFolder({\n  id: \"human-biosamples\",\n  label: \"Human Biosamples\",\n  description:\n    \"Epigenomic data from human tissue samples, primary cells, cell lines, and organoids.\",\n  data: humanData as BiosampleDataFile,\n});\n","import { createBiosampleFolder } from \"./shared/createFolder\";\nimport mouseData from \"./data/mouse.json\";\nimport { BiosampleDataFile } from \"./shared/types\";\n\n/**\n * Mouse biosamples folder configuration for mm10 assembly.\n *\n * Contains epigenomic data (DNase, ATAC, H3K4me3, H3K27ac, CTCF, cCRE, RNA-seq, ChromHMM)\n * from mouse tissue samples, primary cells, cell lines, and organoids.\n */\nexport const mouseBiosamplesFolder = createBiosampleFolder({\n  id: \"mouse-biosamples\",\n  label: \"Mouse Biosamples\",\n  description:\n    \"Epigenomic data from mouse tissue samples, primary cells, cell lines, and organoids.\",\n  data: mouseData as BiosampleDataFile,\n});\n","import { GridColDef } from \"@mui/x-data-grid-premium\";\nimport { GeneRowInfo } from \"./types\";\n\n/**\n * Format versions array as comma-separated string with \"v\" prefix\n * e.g., [29, 40] -> \"v29, v40\"\n */\nfunction formatVersions(versions: number[]): string {\n  return versions.map((v) => `v${v}`).join(\", \");\n}\n\nconst displayNameCol: GridColDef<GeneRowInfo> = {\n  field: \"displayName\",\n  headerName: \"Name\",\n  flex: 1,\n  minWidth: 200,\n};\n\nconst versionsCol: GridColDef<GeneRowInfo> = {\n  field: \"versions\",\n  headerName: \"Versions\",\n  width: 150,\n  valueFormatter: (value: number[]) => value && formatVersions(value),\n};\n\n/**\n * Default columns for genes DataGrid (flat list, no grouping)\n */\nexport const defaultColumns: GridColDef<GeneRowInfo>[] = [\n  displayNameCol,\n  versionsCol,\n];\n\n/**\n * No grouping for genes - flat list\n */\nexport const defaultGroupingModel: string[] = [];\n\n/**\n * Leaf field - the raw track ID (without folder prefix) used as the tree view leaf label\n */\nexport const defaultLeafField = \"trackId\";\n","import {\n  DisplayMode,\n  Track,\n  TrackType,\n  Transcript,\n  TranscriptConfig,\n} from \"@weng-lab/genomebrowser\";\nimport type { FC } from \"react\";\nimport { CreateTrackOptions } from \"../../types\";\nimport { GeneRowInfo } from \"./types\";\n\nexport type GeneTrackContext = {\n  onGeneClick?: (args: {\n    trackId: string;\n    row: GeneRowInfo;\n    transcript: Transcript;\n  }) => void;\n  onGeneHover?: (args: {\n    trackId: string;\n    row: GeneRowInfo;\n    transcript: Transcript;\n  }) => void;\n  geneTooltip?: FC<Transcript>;\n};\n\nconst defaultTranscript: Omit<TranscriptConfig, \"id\" | \"assembly\" | \"version\"> =\n  {\n    title: \"GENCODE Genes\",\n    trackType: TrackType.Transcript,\n    displayMode: DisplayMode.Squish,\n    height: 100,\n    color: \"#0c184a\",\n    canonicalColor: \"#100e98\",\n    highlightColor: \"#3c69e8\",\n    titleSize: 12,\n  };\n\nexport function createGeneTrack(\n  row: GeneRowInfo,\n  options: CreateTrackOptions,\n): Track {\n  const trackContext = options.trackContext;\n\n  return {\n    ...defaultTranscript,\n    id: row.id,\n    assembly: options.assembly,\n    version: row.versions[row.versions.length - 1],\n    onClick: trackContext?.onGeneClick\n      ? (transcript: Transcript) =>\n          trackContext.onGeneClick?.({ trackId: row.id, row, transcript })\n      : undefined,\n    onHover: trackContext?.onGeneHover\n      ? (transcript: Transcript) =>\n          trackContext.onGeneHover?.({ trackId: row.id, row, transcript })\n      : undefined,\n    tooltip: trackContext?.geneTooltip,\n  };\n}\n","import { FolderDefinition } from \"../../types\";\nimport { GeneDataFile, GeneRowInfo, GeneTrackInfo } from \"./types\";\nimport {\n  defaultColumns,\n  defaultGroupingModel,\n  defaultLeafField,\n} from \"./columns\";\nimport { createGeneTrack } from \"./toTrack\";\n\n/** Genes map 1:1 from JSON track entries to table rows. */\nfunction trackToRow(folderId: string, track: GeneTrackInfo): GeneRowInfo {\n  return {\n    id: `${folderId}/${track.id}`,\n    trackId: track.id,\n    displayName: track.displayName,\n    versions: track.versions,\n  };\n}\n\nfunction transformData(folderId: string, data: GeneDataFile): GeneRowInfo[] {\n  return data.map((track) => trackToRow(folderId, track));\n}\n\nexport interface CreateGeneFolderOptions {\n  id: string;\n  label: string;\n  description?: string;\n  data: GeneDataFile;\n}\n\n/** Build a gene folder with its row lookup, tree, and track factory. */\nexport function createGeneFolder(\n  options: CreateGeneFolderOptions,\n): FolderDefinition<GeneRowInfo> {\n  const { id, label, description, data } = options;\n  const rows = transformData(id, data);\n\n  return {\n    id,\n    label,\n    description,\n    rows,\n    columns: defaultColumns,\n    groupingModel: defaultGroupingModel,\n    leafField: defaultLeafField,\n    createTrack: createGeneTrack,\n  };\n}\n","import { createGeneFolder } from \"./shared/createFolder\";\nimport humanData from \"./data/human.json\";\nimport { GeneDataFile } from \"./shared/types\";\n\n/**\n * Gene annotations folder for human (GRCh38 assembly)\n *\n * Contains gene annotation tracks like GENCODE that users can\n * select to display in the genome browser.\n */\nexport const humanGenesFolder = createGeneFolder({\n  id: \"human-genes\",\n  label: \"Genes\",\n  description: \"Gene annotation tracks\",\n  data: humanData as GeneDataFile,\n});\n","import { createGeneFolder } from \"./shared/createFolder\";\nimport mouseData from \"./data/mouse.json\";\nimport { GeneDataFile } from \"./shared/types\";\n\n/**\n * Gene annotations folder for human (GRCh38 assembly)\n *\n * Contains gene annotation tracks like GENCODE that users can\n * select to display in the genome browser.\n */\nexport const mouseGenesFolder = createGeneFolder({\n  id: \"mouse-genes\",\n  label: \"Genes\",\n  description: \"Gene annotation tracks\",\n  data: mouseData as GeneDataFile,\n});\n","import { GridColDef } from \"@mui/x-data-grid-premium\";\nimport { OtherTrackInfo } from \"./types\";\n\nconst nameCol: GridColDef<OtherTrackInfo> = {\n  field: \"name\",\n  headerName: \"Name\",\n  flex: 1,\n  minWidth: 200,\n};\n\nconst descriptionCol: GridColDef<OtherTrackInfo> = {\n  field: \"description\",\n  headerName: \"Description\",\n  flex: 2,\n  minWidth: 300,\n};\n\nexport const defaultColumns: GridColDef<OtherTrackInfo>[] = 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RNAAlphabet,\n  Xo as RNALogo,\n  Fo as RawLogo,\n  H as S,\n  W as T,\n  X as U,\n  b as V,\n  j as W,\n  o0 as X,\n  u0 as XAxis,\n  p0 as Y,\n  zo as YAxis,\n  Ro as YAxisFrequency,\n  Bo as YAxisWithNegatives,\n  x0 as YGridlines,\n  Q as Z,\n  _0 as a,\n  A0 as b,\n  N0 as d,\n  w0 as e,\n  E0 as f,\n  S0 as g,\n  v0 as h,\n  O0 as i,\n  T0 as j,\n  z0 as k,\n  R0 as l,\n  B0 as m,\n  F0 as n,\n  G0 as p,\n  I0 as q,\n  Y0 as r,\n  D0 as t,\n  H0 as u,\n  b0 as y\n};\n//# sourceMappingURL=logo-test.es.js.map\n","import {\n  ClipPath,\n  CustomTrackConfig,\n  CustomTrackProps,\n  DisplayMode,\n  fetchBigBedUrl,\n  Rect,\n  renderSquishBigBedData,\n  TrackType,\n  useBrowserStore,\n  useInteraction,\n  useRowHeight,\n  useXTransform,\n  Vibrant,\n  useTrackStore,\n} from \"@weng-lab/genomebrowser\";\nimport { DNALogo } from \"logo-test\";\nimport { useMemo, useState } from \"react\";\nimport motifData from \"./green-motifs.json\";\n\n// --- TF Peak BigBed Parser ---\n\ninterface TfPeakBigBedData {\n  chr: string;\n  start: number;\n  end: number;\n  name?: string;\n  score?: number;\n  color?: string;\n  tfName?: string;\n  expRatio?: string;\n  cCREId?: string;\n  experimentId?: string;\n  expSupport?: Record<string, Record<string, string>>;\n}\n\nfunction parseTfPeakBigBed(\n  chrom: string,\n  startBase: number,\n  endBase: number,\n  rest: string,\n): TfPeakBigBedData {\n  const entry: TfPeakBigBedData = {\n    chr: chrom,\n    start: startBase,\n    end: endBase,\n  };\n  const tokens = rest.split(\"\\t\");\n  if (tokens.length > 0) entry.name = tokens[0];\n  if (tokens.length > 1) entry.score = parseFloat(tokens[1]);\n  // tokens[2] = strand, tokens[3] = thickStart, tokens[4] = thickEnd\n  if (tokens.length > 5 && tokens[5] !== \".\" && tokens[5] !== \"0\") {\n    entry.color = tokens[5].includes(\",\")\n      ? tokens[5].startsWith(\"rgb\")\n        ? tokens[5]\n        : \"rgb(\" + tokens[5] + \")\"\n      : tokens[5];\n  }\n  // tokens[6] = blockCount, tokens[7] = blockSizes, tokens[8] = blockStarts\n  if (tokens.length > 9) entry.tfName = tokens[9];\n  if (tokens.length > 10) entry.expRatio = tokens[10];\n  if (tokens.length > 11) entry.cCREId = tokens[11];\n  if (tokens.length > 12) entry.experimentId = tokens[12];\n  if (tokens.length > 13) {\n    try {\n      entry.expSupport = JSON.parse(tokens[13]);\n    } catch {\n      // leave undefined if JSON is malformed\n    }\n  }\n  return entry;\n}\n\n// --- Types ---\n\ntype OverlayData = {\n  primary: TfPeakBigBedData[];\n  overlay: Rect[];\n};\n\ntype OverlayInteractionRect = Rect & {\n  chr?: string;\n  pwm?: number[][];\n  tfName?: string;\n  expRatio?: string;\n  cCREId?: string;\n  experimentId?: string;\n  expSupport?: Record<string, Record<string, string>>;\n};\n\n// The config type — extra fields go directly on the config\ntype OverlayBigBedConfig = CustomTrackConfig<OverlayInteractionRect> & {\n  primaryUrl: string;\n  overlayUrl: string;\n  baseColor?: string;\n  overlayColor?: string;\n  filter?: string[];\n};\n\n// --- Helpers ---\n\nfunction nameKey(name?: string) {\n  if (!name) return \"\";\n  return name.split(/[-_]/)[0].trim().toLowerCase();\n}\n\nfunction buildOverlayIndex(rects: Rect[]) {\n  return rects.reduce<Record<string, Rect[]>>((acc, rect) => {\n    const key = nameKey(rect.name);\n    if (!key) return acc;\n    (acc[key] ??= []).push(rect);\n    return acc;\n  }, {});\n}\n\nfunction intervalsOverlap(\n  aStart: number,\n  aEnd: number,\n  bStart: number,\n  bEnd: number,\n) {\n  return aStart <= bEnd && bStart <= aEnd;\n}\n\nfunction scoreColor(score?: number) {\n  const t = Math.min(Math.max(score ?? 0, 0), 1000) / 1000;\n  const r = Math.round(0xe3 + (0x00 - 0xe3) * t);\n  const g = Math.round(0xe3 + (0x00 - 0xe3) * t);\n  const b = Math.round(0xe3 + (0x00 - 0xe3) * t);\n  return `#${r.toString(16).padStart(2, \"0\")}${g.toString(16).padStart(2, \"0\")}${b.toString(16).padStart(2, \"0\")}`;\n}\n\n// --- Motif data lookup ---\n\ntype MotifEntry = { trimmed_ppm: number[][] };\nconst motifLookup = motifData as Record<string, MotifEntry>;\n\nfunction lookupPwm(name?: string): number[][] | undefined {\n  const key = nameKey(name)?.toUpperCase();\n  if (!key) return undefined;\n  const entry = motifLookup[key];\n  return entry?.trimmed_ppm;\n}\n\n// --- Tooltip ---\n\nfunction tfDisplayName(name?: string): string {\n  return nameKey(name)?.toUpperCase() || name || \"Unknown\";\n}\n\nfunction TooltipRow({\n  label,\n  value,\n  y,\n}: {\n  label: string;\n  value: string;\n  y: number;\n}) {\n  return (\n    <g transform={`translate(0, ${y})`}>\n      <text x={8} y={0} fontSize={10} fill=\"#888\" dominantBaseline=\"hanging\">\n        {label}\n      </text>\n      <text x={100} y={0} fontSize={10} fill=\"#333\" dominantBaseline=\"hanging\">\n        {value}\n      </text>\n    </g>\n  );\n}\n\nfunction TfPeaksTooltip(rect: OverlayInteractionRect) {\n  const pwm = rect.pwm;\n  const label = tfDisplayName(rect.name);\n  const totalWidth = 340;\n  const pad = 8;\n  const lineH = 14;\n  const titleH = 18;\n\n  // Build metadata rows (single-value rows)\n  const metaRows: { label: string; value: string }[] = [];\n  if (rect.score != null)\n    metaRows.push({ label: \"Score\", value: `${rect.score}` });\n  metaRows.push({\n    label: \"Position\",\n    value: `${rect.chr ? rect.chr + \":\" : \"\"}${rect.start.toLocaleString()}-${rect.end.toLocaleString()}`,\n  });\n\n  // Multi-value rows: split comma-separated cCREs, group 4 per row, cap at 5\n  const allCCREItems = rect.cCREId\n    ? rect.cCREId\n        .split(\",\")\n        .map((s) => s.trim())\n        .filter(Boolean)\n    : [];\n  const maxCCREs = 5;\n  const cCREItems = allCCREItems.slice(0, maxCCREs);\n  const hiddenCCREs = Math.max(0, allCCREItems.length - maxCCREs);\n  const cCRERows: string[][] = [];\n  for (let i = 0; i < cCREItems.length; i += 4) {\n    cCRERows.push(cCREItems.slice(i, i + 4));\n  }\n\n  // Extract unique sorted biosamples from expSupport\n  const allBiosamples: string[] = [];\n  if (rect.expSupport) {\n    const seen = new Set<string>();\n    for (const cellLine of Object.keys(rect.expSupport)) {\n      if (!seen.has(cellLine)) {\n        seen.add(cellLine);\n        allBiosamples.push(cellLine);\n      }\n    }\n    allBiosamples.sort((a, b) => a.localeCompare(b));\n  }\n  const maxBiosamples = 12;\n  const biosampleItems = allBiosamples.slice(0, maxBiosamples);\n  const hiddenBiosamples = Math.max(0, allBiosamples.length - maxBiosamples);\n  const biosampleText = biosampleItems.join(\", \");\n  const biosampleMoreText =\n    hiddenBiosamples > 0 ? ` ...and ${hiddenBiosamples} more` : \"\";\n  const biosampleCharsPerLine = Math.floor((totalWidth - 2 * pad) / 5.2);\n  const biosampleContentLines = Math.max(\n    1,\n    Math.ceil(\n      (biosampleText.length + biosampleMoreText.length) / biosampleCharsPerLine,\n    ),\n  );\n\n  // Layout: compute y offsets upfront\n  const hasLogo = pwm && pwm.length > 0;\n\n  const logoHeight = hasLogo ? 80 : 0;\n  const logoSectionH = hasLogo ? logoHeight + 4 : 0;\n  const metaSectionH = metaRows.length * lineH;\n\n  // cCRE section: label row + one row per group of 4 + optional \"+N more\" row\n  const cCREGap = cCRERows.length > 0 ? 8 : 0;\n  const cCREHeaderH = cCRERows.length > 0 ? lineH : 0;\n  const cCREMoreH = hiddenCCREs > 0 ? lineH : 0;\n  const cCRESectionH = cCRERows.length * lineH + cCREMoreH;\n\n  // Biosamples section\n  const biosampleGap = biosampleContentLines > 0 ? 8 : 0;\n  const biosampleHeaderH = biosampleContentLines > 0 ? lineH : 0;\n  const biosampleSectionH = biosampleContentLines * lineH;\n\n  const titleY = pad;\n  const logoY = titleY + titleH;\n  const metaY = logoY + logoSectionH;\n  const cCREY = metaY + metaSectionH + cCREGap;\n  const cCREDataY = cCREY + cCREHeaderH;\n  const biosampleY = cCREDataY + cCRESectionH + biosampleGap;\n  const biosampleDataY = biosampleY + biosampleHeaderH;\n  const totalHeight = biosampleDataY + biosampleSectionH + pad;\n\n  return (\n    <g>\n      <rect\n        width={totalWidth}\n        height={totalHeight}\n        fill=\"white\"\n        rx={3}\n        style={{ filter: \"drop-shadow(0px 0px 5px rgba(0,0,0,0.3))\" }}\n      />\n\n      {/* Title */}\n      <text x={pad} y={titleY + 12} fontSize={12} fontWeight=\"bold\" fill=\"#333\">\n        {label}\n      </text>\n\n      {/* Logo */}\n      {hasLogo && (\n        <g transform={`translate(${pad}, ${logoY})`}>\n          <DNALogo\n            ppm={pwm!}\n            mode=\"INFORMATION_CONTENT\"\n            width={totalWidth - 2 * pad}\n            height={logoHeight}\n          />\n        </g>\n      )}\n\n      {/* Metadata rows */}\n      {metaRows.map((row, i) => (\n        <TooltipRow\n          key={row.label}\n          label={row.label}\n          value={row.value}\n          y={metaY + i * lineH}\n        />\n      ))}\n\n      {/* Overlapping cCREs */}\n      {cCRERows.length > 0 && (\n        <g>\n          <line\n            x1={pad}\n            x2={totalWidth - pad}\n            y1={cCREY - 4}\n            y2={cCREY - 4}\n            stroke=\"#ddd\"\n          />\n          <text\n            x={pad}\n            y={cCREY + 2}\n            fontSize={9}\n            fontWeight=\"bold\"\n            fill=\"#666\"\n            dominantBaseline=\"hanging\"\n          >\n            Overlapping cCREs\n          </text>\n          {cCRERows.map((group, i) => (\n            <text\n              key={i}\n              x={pad}\n              y={cCREDataY + i * lineH + 2}\n              fontSize={9}\n              fill=\"#333\"\n              dominantBaseline=\"hanging\"\n            >\n              {group.join(\", \")}\n            </text>\n          ))}\n          {hiddenCCREs > 0 && (\n            <text\n              x={pad}\n              y={cCREDataY + cCRERows.length * lineH + 2}\n              fontSize={9}\n              fill=\"#aaa\"\n              dominantBaseline=\"hanging\"\n            >\n              +{hiddenCCREs} more...\n            </text>\n          )}\n        </g>\n      )}\n\n      {/* Biosamples */}\n      {biosampleContentLines > 0 && (\n        <g>\n          <line\n            x1={pad}\n            x2={totalWidth - pad}\n            y1={biosampleY - 4}\n            y2={biosampleY - 4}\n            stroke=\"#ddd\"\n          />\n          <text\n            x={pad}\n            y={biosampleY + 2}\n            fontSize={9}\n            fontWeight=\"bold\"\n            fill=\"#666\"\n            dominantBaseline=\"hanging\"\n          >\n            Biosamples\n          </text>\n          <foreignObject\n            x={pad}\n            y={biosampleDataY}\n            width={totalWidth - 2 * pad}\n            height={biosampleSectionH}\n          >\n            <div\n              style={{\n                color: \"#333\",\n                fontSize: \"9px\",\n                lineHeight: `${lineH}px`,\n                margin: 0,\n                padding: 0,\n                overflow: \"hidden\",\n                whiteSpace: \"normal\",\n                wordBreak: \"break-word\",\n              }}\n            >\n              {biosampleText}\n              {hiddenBiosamples > 0 && (\n                <span style={{ color: \"#aaa\" }}>{biosampleMoreText}</span>\n              )}\n            </div>\n          </foreignObject>\n        </g>\n      )}\n    </g>\n  );\n}\n\n// --- Settings Panel ---\n\nfunction TfPeaksSettings({ id }: { id: string }) {\n  const track = useTrackStore((state) => state.getTrack(id)) as\n    | OverlayBigBedConfig\n    | undefined;\n  const editTrack = useTrackStore((state) => state.editTrack);\n  const [input, setInput] = useState((track?.filter || []).join(\", \"));\n\n  const handleChange = (e: React.ChangeEvent<HTMLInputElement>) => {\n    const value = e.target.value;\n    setInput(value);\n    const names = value\n      .split(\",\")\n      .map((s) => s.trim().toUpperCase())\n      .filter(Boolean);\n    editTrack<OverlayBigBedConfig>(id, {\n      filter: names.length > 0 ? names : undefined,\n    });\n  };\n\n  return (\n    <div\n      style={{\n        display: \"flex\",\n        flexDirection: \"column\",\n        alignItems: \"flex-start\",\n        paddingBlock: \"5px\",\n        paddingInline: \"10px\",\n        gap: \"3px\",\n      }}\n    >\n      <div style={{ fontWeight: \"bold\" }}>Filter TFs</div>\n      <input\n        value={input}\n        onChange={handleChange}\n        placeholder=\"e.g. CTCF, TP53, GATA1\"\n        style={{ width: \"100%\" }}\n      />\n    </div>\n  );\n}\n\n// --- Renderer ---\n\nfunction OverlayBigBedRenderer(\n  props: CustomTrackProps<OverlayData> & OverlayBigBedConfig,\n) {\n  const {\n    data,\n    dimensions,\n    id,\n    height: trackHeight,\n    color: _color,\n    baseColor: _baseColorProp,\n    overlayColor: overlayColorProp,\n    filter,\n    ...rest\n  } = props;\n  const domain = useBrowserStore((state) => state.domain);\n  const { totalWidth, sideWidth } = dimensions;\n  const { x, reverseX } = useXTransform(totalWidth);\n\n  const filterSet = useMemo(\n    () =>\n      filter && filter.length > 0\n        ? new Set(filter.map((f) => f.toUpperCase()))\n        : null,\n    [filter],\n  );\n\n  const visiblePrimary = useMemo(() => {\n    let visible = (data?.primary || []).filter(\n      (r) => r.end >= domain.start && r.start <= domain.end,\n    );\n    if (filterSet) {\n      visible = visible.filter((r) =>\n        filterSet.has(nameKey(r.name)?.toUpperCase()),\n      );\n    }\n    return visible;\n  }, [data, domain.end, domain.start, filterSet]);\n\n  const rows = useMemo(\n    () => renderSquishBigBedData(visiblePrimary, x),\n    [visiblePrimary, x],\n  );\n\n  // Index primary data by \"name:start:end\" for fast TF metadata lookup\n  const primaryIndex = useMemo(() => {\n    const index = new Map<string, TfPeakBigBedData>();\n    for (const item of visiblePrimary) {\n      index.set(`${item.name}:${item.start}:${item.end}`, item);\n    }\n    return index;\n  }, [visiblePrimary]);\n\n  const rowHeight = useRowHeight(rows.length, id);\n  const height = Math.max(trackHeight, rowHeight * Math.max(rows.length, 1));\n  const overlayByName = useMemo(\n    () => buildOverlayIndex(data?.overlay || []),\n    [data],\n  );\n\n  const overlayColor = overlayColorProp || Vibrant[3];\n  const cursor = rest.onClick ? \"pointer\" : \"default\";\n\n  const { handleClick, handleHover, handleLeave } =\n    useInteraction<OverlayInteractionRect>({\n      onClick: rest.onClick,\n      onHover: rest.onHover,\n      onLeave: rest.onLeave,\n      tooltip: rest.tooltip,\n    });\n\n  return (\n    <g\n      width={totalWidth}\n      height={height}\n      clipPath={`url(#${id})`}\n      transform={`translate(-${sideWidth}, 0)`}\n    >\n      <rect width={totalWidth} height={height} fill=\"transparent\" />\n      <defs>\n        <ClipPath id={id} width={totalWidth} height={height} />\n      </defs>\n      {rows.map((row, rowIndex) => {\n        const baseY = rowHeight * 0.2;\n        const baseH = rowHeight * 0.6;\n        return (\n          <g\n            key={`row_${rowIndex}`}\n            transform={`translate(0, ${rowIndex * rowHeight})`}\n          >\n            {row.map((rect, ri) => {\n              const realStart = Math.round(reverseX(rect.start));\n              const realEnd = Math.round(reverseX(rect.end));\n              const baseName = rect.rectname;\n              const attached = (\n                overlayByName[nameKey(rect.rectname)] || []\n              ).filter((a) =>\n                intervalsOverlap(realStart, realEnd, a.start, a.end),\n              );\n              const fill = scoreColor(rect.score);\n              const meta = primaryIndex.get(\n                `${baseName}:${realStart}:${realEnd}`,\n              );\n              const baseRect: OverlayInteractionRect = {\n                start: realStart,\n                end: realEnd,\n                name: baseName,\n                color: fill,\n                score: rect.score,\n                chr: meta?.chr,\n                pwm: attached.length > 0 ? lookupPwm(baseName) : undefined,\n                tfName: meta?.tfName,\n                expRatio: meta?.expRatio,\n                cCREId: meta?.cCREId,\n                experimentId: meta?.experimentId,\n                expSupport: meta?.expSupport,\n              };\n\n              return (\n                <g key={`${id}_${rowIndex}_${ri}`}>\n                  <rect\n                    style={{ cursor }}\n                    x={rect.start}\n                    y={baseY}\n                    width={Math.max(rect.end - rect.start, 1)}\n                    height={baseH}\n                    fill={fill}\n                    opacity={0.9}\n                    onClick={() => handleClick(baseRect)}\n                    onMouseOver={(e) =>\n                      handleHover(baseRect, baseRect.name || \"\", e)\n                    }\n                    onMouseOut={() => handleLeave(baseRect)}\n                  />\n                  {attached.map((a, ai) => {\n                    const left = x(a.start);\n                    const right = x(a.end);\n                    return (\n                      <rect\n                        style={{ cursor }}\n                        key={`${id}_${rowIndex}_${ri}_a_${ai}`}\n                        x={left}\n                        y={baseY}\n                        width={Math.max(right - left, 1)}\n                        height={baseH}\n                        fill={a.color || overlayColor}\n                        opacity={0.9}\n                        onClick={() => handleClick(baseRect)}\n                        onMouseOver={(e) =>\n                          handleHover(baseRect, baseRect.name || \"\", e)\n                        }\n                        onMouseOut={() => handleLeave(baseRect)}\n                      />\n                    );\n                  })}\n                </g>\n              );\n            })}\n          </g>\n        );\n      })}\n    </g>\n  );\n}\n\n// --- Track config ---\n\nexport const PEAKS_BIGBED_URL =\n  \"https://users.wenglab.org/gaomingshi/no_trim.TF_name.rPeaks.bb\";\nexport const DECORATOR_BIGBED_URL =\n  \"https://users.wenglab.org/gaomingshi/no_trim.TF_name.decorator.bb\";\n\nexport const tfPeaksTrack: OverlayBigBedConfig = {\n  id: \"custom-tf-peaks\",\n  title: \"TF Peaks (Overlay)\",\n  shortLabel: \"TF Peaks\",\n  trackType: TrackType.Custom,\n  displayMode: DisplayMode.Full,\n  color: Vibrant[0],\n  height: 80,\n  primaryUrl: PEAKS_BIGBED_URL,\n  overlayUrl: DECORATOR_BIGBED_URL,\n  baseColor: \"#d1d5db\",\n  overlayColor: \"#36dd81\",\n  onClick: (rect) => {\n    console.log(\"Clicked on rect:\", rect);\n  },\n  tooltip: TfPeaksTooltip,\n  settingsPanel: TfPeaksSettings,\n  renderers: {\n    [DisplayMode.Full]: OverlayBigBedRenderer,\n  },\n  fetcher: async (ctx) => {\n    const track = ctx.track as OverlayBigBedConfig;\n    const [primary, overlay] = await Promise.all([\n      fetchBigBedUrl(track.primaryUrl, ctx, parseTfPeakBigBed),\n      fetchBigBedUrl(track.overlayUrl, ctx),\n    ]);\n    const error =\n      [primary.error, overlay.error].filter(Boolean).join(\"\\n\") || null;\n    return {\n      data: { primary: primary.data || [], overlay: overlay.data || [] },\n      error,\n    };\n  },\n};\n","import { Track } from \"@weng-lab/genomebrowser\";\nimport { tfPeaksTrack } from \"../../../Custom/TfPeaks\";\nimport { CreateTrackOptions } from \"../../types\";\nimport { OtherTrackInfo } from \"./types\";\n\nexport type OtherTracksTrackContext = {};\n\nexport function createOtherTrack(\n  row: OtherTrackInfo,\n  _options: CreateTrackOptions,\n): Track | null {\n  if ((row.sourceId ?? row.id) === \"tf-peaks\") {\n    return { ...tfPeaksTrack, id: row.id };\n  }\n\n  return null;\n}\n","import { FolderDefinition } from \"../../types\";\nimport { OtherTrackDataFile, OtherTrackInfo } from \"./types\";\nimport {\n  defaultColumns,\n  defaultGroupingModel,\n  defaultLeafField,\n} from \"./columns\";\nimport { createOtherTrack } from \"./toTrack\";\n\nfunction transformData(\n  folderId: string,\n  data: OtherTrackDataFile,\n): OtherTrackInfo[] {\n  return data.map((row) => ({\n    ...row,\n    sourceId: row.id,\n    id: `${folderId}/${row.id}`,\n  }));\n}\n\nexport interface CreateOtherTracksFolderOptions {\n  id: string;\n  label: string;\n  description?: string;\n  data: OtherTrackDataFile;\n}\n\nexport function createOtherTracksFolder(\n  options: CreateOtherTracksFolderOptions,\n): FolderDefinition<OtherTrackInfo> {\n  const { id, label, description, data } = options;\n  const rows = transformData(id, data);\n\n  return {\n    id,\n    label,\n    description,\n    rows,\n    columns: defaultColumns,\n    groupingModel: defaultGroupingModel,\n    leafField: defaultLeafField,\n    createTrack: createOtherTrack,\n  };\n}\n","import { createOtherTracksFolder } from \"./shared/createFolder\";\nimport humanData from \"./data/human.json\";\nimport { OtherTrackDataFile } from \"./shared/types\";\n\nexport const humanOtherTracksFolder = createOtherTracksFolder({\n  id: \"human-other-tracks\",\n  label: \"Other Tracks\",\n  description: \"Additional tracks\",\n  data: humanData as OtherTrackDataFile,\n});\n","import { Box } from \"@mui/material\";\n\nexport const MOHD_BASE_URL = \"https://downloads.mohdconsortium.org\";\n\nexport const MOHD_OME_CONFIG = {\n  atac: {\n    label: \"ATAC\",\n    color: \"#02c7b9\",\n    downloadPath: \"2_ATAC\",\n  },\n  rna: {\n    label: \"RNA\",\n    color: \"#00aa00\",\n    downloadPath: \"3_RNA\",\n  },\n  wgbs: {\n    label: \"WGBS\",\n    color: \"#648bd8\",\n    downloadPath: \"1_WGBS\",\n  },\n} as const;\n\nexport type MohdRawOme = keyof typeof MOHD_OME_CONFIG;\nexport type MohdOme = (typeof MOHD_OME_CONFIG)[MohdRawOme][\"label\"];\n\nconst MOHD_OME_LABELS = Object.values(MOHD_OME_CONFIG).map(\n  (config) => config.label,\n);\n\nexport function getMohdOmeConfig(rawOme: string) {\n  const config = MOHD_OME_CONFIG[rawOme.toLowerCase() as MohdRawOme];\n\n  if (!config) {\n    throw new Error(`Unknown MOHD ome: ${rawOme}`);\n  }\n\n  return config;\n}\n\nexport function createMohdFileUrl({\n  ome,\n  sampleId,\n  filename,\n}: {\n  ome: string;\n  sampleId: string;\n  filename: string;\n}) {\n  const { downloadPath } = getMohdOmeConfig(ome);\n  return `${MOHD_BASE_URL}/${downloadPath}/${sampleId}/${filename}`;\n}\n\nexport function isMohdOmeLabel(value: string) {\n  return MOHD_OME_LABELS.includes(value as MohdOme);\n}\n\nexport function MohdOmeIcon({ type }: { type: string }) {\n  const { color } = getMohdOmeConfig(type);\n\n  return (\n    <Box\n      data-testid={`mohd-ome-icon-${type.toLowerCase()}`}\n      sx={{\n        width: 12,\n        height: 12,\n        borderRadius: \"20%\",\n        bgcolor: color,\n      }}\n    />\n  );\n}\n","import { GridColDef } from \"@mui/x-data-grid-premium\";\nimport { FolderView } from \"../../types\";\nimport { MohdRowInfo } from \"./types\";\n\nconst descriptionCol: GridColDef<MohdRowInfo> = {\n  field: \"description\",\n  headerName: \"Description\",\n  minWidth: 220,\n  flex: 1.5,\n};\n\nconst sampleIdCol: GridColDef<MohdRowInfo> = {\n  field: \"sampleId\",\n  headerName: \"Sample ID\",\n  minWidth: 180,\n  flex: 1,\n};\n\nconst kitIdCol: GridColDef<MohdRowInfo> = {\n  field: \"kitId\",\n  headerName: \"Kit ID\",\n  minWidth: 140,\n  flex: 1,\n};\n\nconst trackCategoryCol: GridColDef<MohdRowInfo> = {\n  field: \"trackCategory\",\n  headerName: \"Track Type\",\n  minWidth: 140,\n  width: 140,\n};\n\nconst omeCol: GridColDef<MohdRowInfo> = {\n  field: \"ome\",\n  headerName: \"Ome\",\n  minWidth: 120,\n  width: 120,\n};\n\nconst siteCol: GridColDef<MohdRowInfo> = {\n  field: \"site\",\n  headerName: \"Site\",\n  minWidth: 100,\n  width: 100,\n};\n\nconst sexCol: GridColDef<MohdRowInfo> = {\n  field: \"sex\",\n  headerName: \"Sex\",\n  minWidth: 120,\n  width: 120,\n};\n\nconst statusCol: GridColDef<MohdRowInfo> = {\n  field: \"status\",\n  headerName: \"Status\",\n  minWidth: 120,\n  flex: 1,\n};\n\nexport const mohdColumns: GridColDef<MohdRowInfo>[] = [\n  descriptionCol,\n  trackCategoryCol,\n  sampleIdCol,\n  kitIdCol,\n  omeCol,\n  siteCol,\n  sexCol,\n  statusCol,\n];\n\nexport const mohdViews: FolderView[] = [\n  {\n    id: \"ome\",\n    label: \"Ome\",\n    columns: mohdColumns,\n    groupingModel: [\"ome\", \"site\", \"sampleId\"],\n    leafField: \"description\",\n  },\n  {\n    id: \"site\",\n    label: \"Site\",\n    columns: mohdColumns,\n    groupingModel: [\"site\", \"ome\", \"sampleId\"],\n    leafField: \"description\",\n  },\n];\n","import ChevronRightIcon from \"@mui/icons-material/ChevronRight\";\nimport ExpandMoreIcon from \"@mui/icons-material/ExpandMore\";\nimport { Box, IconButton, Stack, Tooltip } from \"@mui/material\";\nimport {\n  GridGroupNode,\n  GridRenderCellParams,\n  useGridApiContext,\n} from \"@mui/x-data-grid-premium\";\nimport { isMohdOmeLabel, MohdOmeIcon } from \"./config\";\n\nexport function MohdGroupingCell(params: GridRenderCellParams) {\n  const apiRef = useGridApiContext();\n  const isGroup = params.rowNode.type === \"group\";\n  const groupNode = params.rowNode as GridGroupNode;\n  const isExpanded = isGroup ? groupNode.childrenExpanded : false;\n  const groupingField = isGroup ? groupNode.groupingField : null;\n  const depth = params.rowNode.depth ?? 0;\n  const value = String(params.value ?? \"\");\n  const showOmeIcon =\n    (isGroup && groupingField === \"ome\") || isMohdOmeLabel(value);\n\n  const handleExpandClick = (e: React.MouseEvent) => {\n    e.stopPropagation();\n    apiRef.current.setRowChildrenExpansion(params.id, !isExpanded);\n  };\n\n  return (\n    <Box\n      sx={{\n        display: \"flex\",\n        alignItems: \"center\",\n        width: \"100%\",\n        ml: depth * 2,\n      }}\n    >\n      {isGroup && (\n        <IconButton size=\"small\" onClick={handleExpandClick} sx={{ mr: 0.5 }}>\n          {isExpanded ? (\n            <ExpandMoreIcon fontSize=\"small\" />\n          ) : (\n            <ChevronRightIcon fontSize=\"small\" />\n          )}\n        </IconButton>\n      )}\n      <Stack\n        direction=\"row\"\n        spacing={1}\n        alignItems=\"center\"\n        sx={{ flex: 1, overflow: \"hidden\" }}\n      >\n        {showOmeIcon && <MohdOmeIcon type={value} />}\n        <Tooltip title={value} placement=\"top-start\" enterDelay={500}>\n          <Box\n            sx={{\n              overflow: \"hidden\",\n              textOverflow: \"ellipsis\",\n              whiteSpace: \"nowrap\",\n              flex: 1,\n              fontWeight: isGroup ? \"bold\" : undefined,\n            }}\n          >\n            {params.formattedValue}\n          </Box>\n        </Tooltip>\n      </Stack>\n    </Box>\n  );\n}\n","import React from \"react\";\nimport { CustomTreeItem } from \"../../../TreeView/CustomTreeItem\";\nimport { CustomTreeItemProps } from \"../../../types\";\nimport { MohdOmeIcon } from \"./config\";\n\nexport const MohdTreeItem = React.forwardRef<\n  HTMLLIElement,\n  CustomTreeItemProps\n>(function MohdTreeItem(props, ref) {\n  return (\n    <CustomTreeItem\n      {...props}\n      ref={ref}\n      renderIcon={(type) => <MohdOmeIcon type={type} />}\n    />\n  );\n});\n","import { defineBigBedSchema } from \"@weng-lab/genomebrowser\";\nimport type { MohdFileRowInfo } from \"./types\";\n\nexport const mohdAtacFdrPeaksSchema = defineBigBedSchema({\n  name: \"string\",\n  score: \"number\",\n  strand: \"string\",\n  signalValue: \"number\",\n  pValue: \"number\",\n  qValue: \"number\",\n  peak: \"number\",\n});\n\nexport const mohdAtacPseudorepPeaksSchema = defineBigBedSchema({\n  name: \"string\",\n  score: \"number\",\n  strand: \"string\",\n  signalValue: \"number\",\n  pValue: \"number\",\n  qValue: \"number\",\n  peak: \"number\",\n});\n\nexport function getMohdBigBedSchema(row: MohdFileRowInfo) {\n  if (row.description === \"FDR 0.05 peaks\") {\n    return mohdAtacFdrPeaksSchema;\n  }\n\n  if (row.description === \"Pseudorep peaks\") {\n    return mohdAtacPseudorepPeaksSchema;\n  }\n\n  return undefined;\n}\n","import { InferBigBedRow } from \"@weng-lab/genomebrowser\";\nimport {\n  mohdAtacFdrPeaksSchema,\n  mohdAtacPseudorepPeaksSchema,\n} from \"./bigBedSchemas\";\n\ntype MohdBigBedRow =\n  | InferBigBedRow<typeof mohdAtacFdrPeaksSchema>\n  | InferBigBedRow<typeof mohdAtacPseudorepPeaksSchema>;\n\nfunction TooltipRow({\n  label,\n  value,\n  y,\n}: {\n  label: string;\n  value: string;\n  y: number;\n}) {\n  return (\n    <g transform={`translate(0, ${y})`}>\n      <text x={8} y={0} fontSize={10} fill=\"#888\" dominantBaseline=\"hanging\">\n        {label}\n      </text>\n      <text x={100} y={0} fontSize={10} fill=\"#333\" dominantBaseline=\"hanging\">\n        {value}\n      </text>\n    </g>\n  );\n}\n\nfunction formatValue(value: string | number | undefined) {\n  if (value === undefined) {\n    return \"-\";\n  }\n\n  return `${value}`;\n}\n\nexport function MohdBigBedTooltip(rect: MohdBigBedRow) {\n  const rows = [\n    {\n      label: \"Position\",\n      value: `${rect.chr}:${rect.start.toLocaleString()}-${rect.end.toLocaleString()}`,\n    },\n    { label: \"Name\", value: formatValue(rect.name) },\n    { label: \"Score\", value: formatValue(rect.score) },\n    { label: \"Strand\", value: formatValue(rect.strand) },\n    { label: \"Signal\", value: formatValue(rect.signalValue) },\n    { label: \"pValue\", value: formatValue(rect.pValue) },\n    { label: \"qValue\", value: formatValue(rect.qValue) },\n    { label: \"Peak\", value: formatValue(rect.peak) },\n  ];\n  const pad = 8;\n  const lineH = 14;\n  const titleH = 18;\n  const width = 280;\n  const height = pad + titleH + rows.length * lineH + pad;\n\n  return (\n    <g>\n      <rect\n        width={width}\n        height={height}\n        fill=\"white\"\n        rx={3}\n        style={{ filter: \"drop-shadow(0px 0px 5px rgba(0,0,0,0.3))\" }}\n      />\n      <text x={pad} y={pad + 12} fontSize={12} fontWeight=\"bold\" fill=\"#333\">\n        {rect.name || \"MOHD peak\"}\n      </text>\n      {rows.map((row, index) => (\n        <TooltipRow\n          key={row.label}\n          label={row.label}\n          value={row.value}\n          y={pad + titleH + index * lineH}\n        />\n      ))}\n    </g>\n  );\n}\n","import {\n  BigBedConfig,\n  BigWigConfig,\n  DisplayMode,\n  InferBigBedRow,\n  MethylCConfig,\n  Track,\n  TrackType,\n  ValuedPoint,\n} from \"@weng-lab/genomebrowser\";\nimport type { FC } from \"react\";\nimport { CreateTrackOptions } from \"../../types\";\nimport {\n  getMohdBigBedSchema,\n  mohdAtacFdrPeaksSchema,\n  mohdAtacPseudorepPeaksSchema,\n} from \"./bigBedSchemas\";\nimport { createMohdFileUrl, getMohdOmeConfig } from \"./config\";\nimport { MohdBigBedTooltip } from \"./MohdBigBedTooltip\";\nimport { MohdRowInfo } from \"./types\";\n\nexport type MohdTrackContext = {\n  mohdSignalTooltip?: FC<ValuedPoint[]>;\n  mohdMethylTooltip?: FC<ValuedPoint[]>;\n};\n\nconst defaultBigWig: Omit<BigWigConfig, \"id\" | \"title\" | \"url\"> = {\n  trackType: TrackType.BigWig,\n  height: 30,\n  displayMode: DisplayMode.Full,\n  titleSize: 12,\n  color: \"#02c7b9\",\n};\n\nconst defaultBigBed: Omit<BigBedConfig, \"id\" | \"title\" | \"url\"> = {\n  trackType: TrackType.BigBed,\n  height: 20,\n  displayMode: DisplayMode.Dense,\n  titleSize: 12,\n};\n\nconst defaultMethylC: Omit<MethylCConfig, \"id\" | \"title\" | \"urls\"> = {\n  trackType: TrackType.MethylC,\n  height: 75,\n  displayMode: DisplayMode.Split,\n  titleSize: 12,\n  color: \"#648bd8\",\n  maskCpgByCoverage: true,\n  colors: {\n    cpg: \"#648bd8\",\n    chg: \"#ff944d\",\n    chh: \"#ff00ff\",\n    depth: \"#525252\",\n  },\n};\n\ntype MohdBigBedRow =\n  | InferBigBedRow<typeof mohdAtacFdrPeaksSchema>\n  | InferBigBedRow<typeof mohdAtacPseudorepPeaksSchema>;\n\nfunction createTrackTitle(row: MohdRowInfo) {\n  return `${row.sampleId} ${row.description}`;\n}\n\nexport function createMohdTrack(\n  row: MohdRowInfo,\n  options: CreateTrackOptions,\n): Track | null {\n  const trackContext = options.trackContext;\n\n  if (row.kind === \"wgbs-methyl\") {\n    return {\n      ...defaultMethylC,\n      id: row.id,\n      title: createTrackTitle(row),\n      tooltip: trackContext?.mohdMethylTooltip,\n      urls: {\n        plusStrand: {\n          cpg: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.plusStrand.cpg,\n            }),\n          },\n          chg: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.plusStrand.chg,\n            }),\n          },\n          chh: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.plusStrand.chh,\n            }),\n          },\n          depth: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.plusStrand.depth,\n            }),\n          },\n        },\n        minusStrand: {\n          cpg: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.minusStrand.cpg,\n            }),\n          },\n          chg: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.minusStrand.chg,\n            }),\n          },\n          chh: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.minusStrand.chh,\n            }),\n          },\n          depth: {\n            url: createMohdFileUrl({\n              ome: row.ome,\n              sampleId: row.sampleId,\n              filename: row.filenames.minusStrand.depth,\n            }),\n          },\n        },\n      },\n    };\n  }\n\n  if (row.kind !== \"file\") {\n    return null;\n  }\n\n  const { color } = getMohdOmeConfig(row.ome);\n  const url = createMohdFileUrl({\n    ome: row.ome,\n    sampleId: row.sampleId,\n    filename: row.filename,\n  });\n\n  if (row.filename.endsWith(\".bigWig\")) {\n    return {\n      ...defaultBigWig,\n      id: row.id,\n      title: createTrackTitle(row),\n      url,\n      color,\n      tooltip: trackContext?.mohdSignalTooltip,\n    };\n  }\n\n  if (row.filename.endsWith(\".bigBed\")) {\n    return {\n      ...defaultBigBed,\n      id: row.id,\n      title: createTrackTitle(row),\n      url,\n      color,\n      schema: getMohdBigBedSchema(row),\n      tooltip: MohdBigBedTooltip,\n      onClick: (rect: MohdBigBedRow) => {\n        console.log(rect);\n      },\n    };\n  }\n\n  return null;\n}\n","import { ToggleButton, ToggleButtonGroup } from \"@mui/material\";\nimport { FolderView } from \"../../types\";\n\nexport interface MohdViewSelectorProps {\n  views: FolderView[];\n  activeViewId: string;\n  onChange: (viewId: string) => void;\n}\n\nexport function MohdViewSelector({\n  views,\n  activeViewId,\n  onChange,\n}: MohdViewSelectorProps) {\n  return (\n    <ToggleButtonGroup\n      exclusive\n      value={activeViewId}\n      size=\"small\"\n      onChange={(_event, viewId: string | null) => {\n        if (viewId) {\n          onChange(viewId);\n        }\n      }}\n    >\n      {views.map((view) => (\n        <ToggleButton key={view.id} value={view.id}>\n          {view.label}\n        </ToggleButton>\n      ))}\n    </ToggleButtonGroup>\n  );\n}\n","import { FolderDefinition } from \"../../types\";\nimport { MohdDataFile, MohdRowInfo } from \"./types\";\nimport { getMohdOmeConfig } from \"./config\";\nimport { mohdViews } from \"./columns\";\nimport { MohdGroupingCell } from \"./MohdGroupingCell\";\nimport { MohdTreeItem } from \"./MohdTreeItem\";\nimport { createMohdTrack } from \"./toTrack\";\nimport { MohdViewSelector } from \"./MohdViewSelector\";\n\nconst WGBS_DESCRIPTION = \"DNA Methylation\";\n\nfunction createBaseRow(folderId: string, row: MohdDataFile[number]) {\n  return {\n    id: `${folderId}/${row.sample_id}::${row.filename}`,\n    ome: getMohdOmeConfig(row.ome).label,\n    site: row.site,\n    sampleId: row.sample_id,\n    kitId: row.kit_id,\n    sex: row.sex,\n    status: row.status,\n  };\n}\n\nfunction createFileRow(\n  folderId: string,\n  row: MohdDataFile[number],\n): MohdRowInfo {\n  const trackCategory = row.filename.endsWith(\".bigBed\")\n    ? \"Annotation\"\n    : \"Signal\";\n\n  return {\n    ...createBaseRow(folderId, row),\n    kind: \"file\",\n    description: row.file_type,\n    trackCategory,\n    filename: row.filename,\n  };\n}\n\nfunction getRequiredWgbsFilename(\n  sampleRows: MohdDataFile,\n  includesText: string,\n) {\n  const match = sampleRows.find((row) => row.filename.includes(includesText));\n\n  if (!match) {\n    throw new Error(`Missing WGBS file matching ${includesText}`);\n  }\n\n  return match.filename;\n}\n\nfunction createWgbsMethylRow(\n  folderId: string,\n  sampleRows: MohdDataFile,\n): MohdRowInfo {\n  const sampleId = sampleRows[0]?.sample_id;\n\n  if (!sampleId) {\n    throw new Error(\"Cannot build WGBS row without a sample ID\");\n  }\n\n  const base = createBaseRow(folderId, sampleRows[0]!);\n\n  return {\n    ...base,\n    id: `${folderId}/${sampleId}`,\n    kind: \"wgbs-methyl\",\n    description: WGBS_DESCRIPTION,\n    trackCategory: \"Methylation\",\n    filenames: {\n      plusStrand: {\n        cpg: getRequiredWgbsFilename(sampleRows, \"DNAme-CpG-plus\"),\n        chg: getRequiredWgbsFilename(sampleRows, \"DNAme-CHG-plus\"),\n        chh: getRequiredWgbsFilename(sampleRows, \"DNAme-CHH-plus\"),\n        depth: getRequiredWgbsFilename(sampleRows, \"coverage-plus\"),\n      },\n      minusStrand: {\n        cpg: getRequiredWgbsFilename(sampleRows, \"DNAme-CpG-minus\"),\n        chg: getRequiredWgbsFilename(sampleRows, \"DNAme-CHG-minus\"),\n        chh: getRequiredWgbsFilename(sampleRows, \"DNAme-CHH-minus\"),\n        depth: getRequiredWgbsFilename(sampleRows, \"coverage-minus\"),\n      },\n    },\n  };\n}\n\nfunction transformData(folderId: string, data: MohdDataFile): MohdRowInfo[] {\n  const signalRows = data\n    .filter((row) => row.ome !== \"wgbs\")\n    .map((row) => createFileRow(folderId, row));\n  const wgbsRowsBySampleId = new Map<string, MohdDataFile>();\n\n  data.forEach((row) => {\n    if (row.ome !== \"wgbs\") {\n      return;\n    }\n\n    const sampleRows = wgbsRowsBySampleId.get(row.sample_id);\n\n    if (sampleRows) {\n      sampleRows.push(row);\n      return;\n    }\n\n    wgbsRowsBySampleId.set(row.sample_id, [row]);\n  });\n\n  const methylationRows = Array.from(wgbsRowsBySampleId.values()).map(\n    (sampleRows) => createWgbsMethylRow(folderId, sampleRows),\n  );\n\n  return [...signalRows, ...methylationRows];\n}\n\nexport interface CreateMohdFolderOptions {\n  id: string;\n  label: string;\n  description?: string;\n  data: MohdDataFile;\n}\n\nexport function createMohdFolder(\n  options: CreateMohdFolderOptions,\n): FolderDefinition<MohdRowInfo> {\n  const { id, label, description, data } = options;\n  const rows = transformData(id, data);\n  const defaultView = mohdViews[0]!;\n\n  return {\n    id,\n    label,\n    description,\n    rows,\n    columns: defaultView.columns,\n    groupingModel: defaultView.groupingModel,\n    leafField: defaultView.leafField,\n    createTrack: createMohdTrack,\n    views: mohdViews,\n    ViewSelector: MohdViewSelector,\n    GroupingCellComponent: MohdGroupingCell,\n    TreeItemComponent: MohdTreeItem,\n  };\n}\n","import humanData from \"./data/human.json\";\nimport { createMohdFolder } from \"./shared/createFolder\";\nimport { MohdDataFile } from \"./shared/types\";\n\nexport const humanMohdFolder = createMohdFolder({\n  id: \"human-mohd\",\n  label: \"MOHD\",\n  description: \"Public MOHD signal, methylation, and annotation tracks.\",\n  data: humanData as MohdDataFile,\n});\n","import { GridColDef } from \"@mui/x-data-grid-premium\";\nimport { PsychscreenTrackInfo } from \"./types\";\n\nexport const psychscreenCategoryColors: Record<string, string> = {\n  \"Epigenetic Tracks\": \"#9479bc\",\n  \"Deep Learned Models\": \"#758c7b\",\n  \"Pseudo bulk ATAC\": \"#cd8c66\",\n  \"Evolutionary Conservation\": \"#c0a9e2\",\n  \"ATAC Seq Peaks\": \"#9479bc\",\n};\n\nexport function getPsychscreenCategoryColor(category: string) {\n  return psychscreenCategoryColors[category] ?? \"#000000\";\n}\n\nconst titleCol: GridColDef<PsychscreenTrackInfo> = {\n  field: \"title\",\n  headerName: \"Title\",\n  flex: 1,\n  minWidth: 240,\n};\n\nconst categoryCol: GridColDef<PsychscreenTrackInfo> = {\n  field: \"category\",\n  headerName: \"Category\",\n  flex: 1,\n  minWidth: 180,\n};\n\nconst subcategoryCol: GridColDef<PsychscreenTrackInfo> = {\n  field: \"subcategory\",\n  headerName: \"Subcategory\",\n  flex: 1,\n  minWidth: 240,\n};\n\nconst trackTypeCol: GridColDef<PsychscreenTrackInfo> = {\n  field: \"trackType\",\n  headerName: \"Track Type\",\n  width: 120,\n};\n\nexport const defaultColumns: GridColDef<PsychscreenTrackInfo>[] = [\n  titleCol,\n  categoryCol,\n  subcategoryCol,\n  trackTypeCol,\n];\n\nexport const defaultGroupingModel = [\"category\", \"subcategory\"];\n\nexport const defaultLeafField = \"title\";\n","import ChevronRightIcon from \"@mui/icons-material/ChevronRight\";\nimport ExpandMoreIcon from \"@mui/icons-material/ExpandMore\";\nimport { Box, IconButton, Tooltip } from \"@mui/material\";\nimport { alpha } from \"@mui/material/styles\";\nimport {\n  GridGroupNode,\n  GridRenderCellParams,\n  useGridApiContext,\n} from \"@mui/x-data-grid-premium\";\nimport { getPsychscreenCategoryColor } from \"./columns\";\n\nexport function PsychscreenGroupingCell(params: GridRenderCellParams) {\n  const apiRef = useGridApiContext();\n  const isGroup = params.rowNode.type === \"group\";\n  const groupNode = params.rowNode as GridGroupNode;\n  const isExpanded = isGroup ? groupNode.childrenExpanded : false;\n  const groupingField = isGroup ? groupNode.groupingField : null;\n  const isCategoryGroup = groupingField === \"category\";\n  const color = getPsychscreenCategoryColor(\n    isCategoryGroup ? String(params.value ?? \"\") : params.row.category,\n  );\n  const label = String(params.formattedValue ?? params.value ?? \"\");\n  const depth = params.rowNode.depth ?? 0;\n\n  const handleExpandClick = (e: React.MouseEvent) => {\n    e.stopPropagation();\n    apiRef.current.setRowChildrenExpansion(params.id, !isExpanded);\n  };\n\n  return (\n    <Box\n      sx={{\n        display: \"flex\",\n        alignItems: \"center\",\n        width: \"100%\",\n        gap: 1,\n        ml: depth * 2,\n      }}\n    >\n      {isGroup && (\n        <IconButton size=\"small\" onClick={handleExpandClick} sx={{ mr: 0.25 }}>\n          {isExpanded ? (\n            <ExpandMoreIcon fontSize=\"small\" />\n          ) : (\n            <ChevronRightIcon fontSize=\"small\" />\n          )}\n        </IconButton>\n      )}\n      {isCategoryGroup && (\n        <Box\n          sx={{\n            width: 9,\n            height: 9,\n            borderRadius: \"50%\",\n            bgcolor: alpha(color, 0.65),\n            flexShrink: 0,\n          }}\n        />\n      )}\n      <Tooltip title={label} placement=\"top-start\" enterDelay={500}>\n        <Box\n          sx={{\n            bgcolor: isCategoryGroup ? alpha(color, 0.06) : undefined,\n            borderRadius: isCategoryGroup ? 1 : undefined,\n            px: isCategoryGroup ? 0.75 : 0,\n            overflow: \"hidden\",\n            textOverflow: \"ellipsis\",\n            whiteSpace: \"nowrap\",\n            flex: 1,\n            fontWeight: isGroup ? 700 : undefined,\n          }}\n        >\n          {label}\n        </Box>\n      </Tooltip>\n    </Box>\n  );\n}\n","import {\n  BigBedConfig,\n  BigWigConfig,\n  DisplayMode,\n  Track,\n  TrackType,\n} from \"@weng-lab/genomebrowser\";\nimport { CreateTrackOptions } from \"../../types\";\nimport { PsychscreenTrackInfo } from \"./types\";\n\nexport type PsychscreenTrackContext = {};\n\nconst defaultBigWig: Omit<BigWigConfig, \"id\" | \"title\" | \"url\"> = {\n  trackType: TrackType.BigWig,\n  height: 50,\n  displayMode: DisplayMode.Full,\n  titleSize: 12,\n};\n\nconst defaultBigBed: Omit<BigBedConfig, \"id\" | \"title\" | \"url\"> = {\n  trackType: TrackType.BigBed,\n  height: 30,\n  displayMode: DisplayMode.Dense,\n  titleSize: 12,\n};\n\nexport function createPsychscreenTrack(\n  row: PsychscreenTrackInfo,\n  _options: CreateTrackOptions,\n): Track {\n  if (row.trackType === \"bigbed\") {\n    return {\n      ...defaultBigBed,\n      id: row.id,\n      title: row.title,\n      url: row.url,\n      color: row.color ?? \"#000000\",\n    };\n  }\n\n  return {\n    ...defaultBigWig,\n    id: row.id,\n    title: row.title,\n    url: row.url,\n    color: row.color ?? \"#000000\",\n  };\n}\n","import { FolderDefinition } from \"../../types\";\nimport { PsychscreenDataFile, PsychscreenTrackInfo } from \"./types\";\nimport {\n  defaultColumns,\n  defaultGroupingModel,\n  defaultLeafField,\n} from \"./columns\";\nimport { PsychscreenGroupingCell } from \"./PsychscreenGroupingCell\";\nimport { createPsychscreenTrack } from \"./toTrack\";\n\nfunction transformData(\n  folderId: string,\n  data: PsychscreenDataFile,\n): PsychscreenTrackInfo[] {\n  return data.map((row) => ({\n    ...row,\n    sourceId: row.id,\n    id: `${folderId}/${row.id}`,\n  }));\n}\n\nexport interface CreatePsychscreenFolderOptions {\n  id: string;\n  label: string;\n  description?: string;\n  data: PsychscreenDataFile;\n}\n\nexport function createPsychscreenFolder(\n  options: CreatePsychscreenFolderOptions,\n): FolderDefinition<PsychscreenTrackInfo> {\n  const { id, label, description, data } = options;\n\n  return {\n    id,\n    label,\n    description,\n    rows: transformData(id, data),\n    columns: defaultColumns,\n    groupingModel: defaultGroupingModel,\n    leafField: defaultLeafField,\n    createTrack: createPsychscreenTrack,\n    GroupingCellComponent: PsychscreenGroupingCell,\n  };\n}\n","import { createPsychscreenFolder } from \"./shared/createFolder\";\nimport humanData from \"./data/human.json\";\nimport { PsychscreenDataFile } from \"./shared/types\";\n\nexport const humanPsychscreenFolder = createPsychscreenFolder({\n  id: \"human-psychscreen\",\n  label: \"PsychSCREEN\",\n  description: \"PsychSCREEN browser tracks\",\n  data: humanData as PsychscreenDataFile,\n});\n","import { Assembly, FolderDefinition } from \"./types\";\nimport { humanBiosamplesFolder } from \"./biosamples/human\";\nimport { mouseBiosamplesFolder } from \"./biosamples/mouse\";\nimport { humanGenesFolder } from \"./genes/human\";\nimport { mouseGenesFolder } from \"./genes/mouse\";\nimport { humanOtherTracksFolder } from \"./other-tracks/human\";\nimport { humanMohdFolder } from \"./mohd/human\";\nimport { humanPsychscreenFolder } from \"./psychscreen/human\";\n\nexport { type Assembly, type FolderDefinition, type FolderView } from \"./types\";\n\nexport type { BiosampleRowInfo } from \"./biosamples/shared/types\";\nexport type { BiosampleTrackContext } from \"./biosamples/shared/toTrack\";\nexport type { GeneRowInfo } from \"./genes/shared/types\";\nexport type { GeneTrackContext } from \"./genes/shared/toTrack\";\nexport type { MohdRowInfo } from \"./mohd/shared/types\";\nexport type { MohdTrackContext } from \"./mohd/shared/toTrack\";\nexport type { PsychscreenTrackInfo } from \"./psychscreen/shared/types\";\nexport type { PsychscreenTrackContext } from \"./psychscreen/shared/toTrack\";\nexport type { OtherTrackInfo } from \"./other-tracks/shared/types\";\nexport type { OtherTracksTrackContext } from \"./other-tracks/shared/toTrack\";\n\n// Registry of folders by assembly\nexport const 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