@weng-lab/genomebrowser-ui 0.3.6 → 0.4.0-beta.1

package/dist/TrackSelect/Folders/mohd/human.d.ts

@@ -0,0 +1 @@
+export declare const humanMohdFolder: import('..').FolderDefinition<import('..').MohdRowInfo>;

package/dist/TrackSelect/Folders/mohd/shared/MohdGroupingCell.d.ts

@@ -0,0 +1,2 @@
+import { GridRenderCellParams } from '@mui/x-data-grid-premium';
+export declare function MohdGroupingCell(params: GridRenderCellParams): import("react/jsx-runtime").JSX.Element;

package/dist/TrackSelect/Folders/mohd/shared/MohdTreeItem.d.ts

@@ -0,0 +1,3 @@
+import { default as React } from 'react';
+import { CustomTreeItemProps } from '../../../types';
+export declare const MohdTreeItem: React.ForwardRefExoticComponent<CustomTreeItemProps & React.RefAttributes<HTMLLIElement>>;

package/dist/TrackSelect/Folders/mohd/shared/MohdViewSelector.d.ts

@@ -0,0 +1,7 @@
+import { FolderView } from '../../types';
+export interface MohdViewSelectorProps {
+    views: FolderView[];
+    activeViewId: string;
+    onChange: (viewId: string) => void;
+}
+export declare function MohdViewSelector({ views, activeViewId, onChange, }: MohdViewSelectorProps): import("react/jsx-runtime").JSX.Element;

package/dist/TrackSelect/Folders/mohd/shared/columns.d.ts

@@ -0,0 +1,5 @@
+import { GridColDef } from '@mui/x-data-grid-premium';
+import { FolderView } from '../../types';
+import { MohdRowInfo } from './types';
+export declare const mohdColumns: GridColDef<MohdRowInfo>[];
+export declare const mohdViews: FolderView[];

package/dist/TrackSelect/Folders/mohd/shared/config.d.ts

@@ -0,0 +1,42 @@
+export declare const MOHD_BASE_URL = "https://downloads.mohdconsortium.org";
+export declare const MOHD_OME_CONFIG: {
+    readonly atac: {
+        readonly label: "ATAC";
+        readonly color: "#02c7b9";
+        readonly downloadPath: "2_ATAC";
+    };
+    readonly rna: {
+        readonly label: "RNA";
+        readonly color: "#00aa00";
+        readonly downloadPath: "3_RNA";
+    };
+    readonly wgbs: {
+        readonly label: "WGBS";
+        readonly color: "#648bd8";
+        readonly downloadPath: "1_WGBS";
+    };
+};
+export type MohdRawOme = keyof typeof MOHD_OME_CONFIG;
+export type MohdOme = (typeof MOHD_OME_CONFIG)[MohdRawOme]["label"];
+export declare function getMohdOmeConfig(rawOme: string): {
+    readonly label: "ATAC";
+    readonly color: "#02c7b9";
+    readonly downloadPath: "2_ATAC";
+} | {
+    readonly label: "RNA";
+    readonly color: "#00aa00";
+    readonly downloadPath: "3_RNA";
+} | {
+    readonly label: "WGBS";
+    readonly color: "#648bd8";
+    readonly downloadPath: "1_WGBS";
+};
+export declare function createMohdFileUrl({ ome, sampleId, filename, }: {
+    ome: string;
+    sampleId: string;
+    filename: string;
+}): string;
+export declare function isMohdOmeLabel(value: string): boolean;
+export declare function MohdOmeIcon({ type }: {
+    type: string;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/TrackSelect/Folders/mohd/shared/createFolder.d.ts

@@ -0,0 +1,9 @@
+import { FolderDefinition } from '../../types';
+import { MohdDataFile, MohdRowInfo } from './types';
+export interface CreateMohdFolderOptions {
+    id: string;
+    label: string;
+    description?: string;
+    data: MohdDataFile;
+}
+export declare function createMohdFolder(options: CreateMohdFolderOptions): FolderDefinition<MohdRowInfo>;

package/dist/TrackSelect/Folders/mohd/shared/toTrack.d.ts

@@ -0,0 +1,9 @@
+import { Track, ValuedPoint } from '@weng-lab/genomebrowser';
+import { FC } from 'react';
+import { CreateTrackOptions } from '../../types';
+import { MohdRowInfo } from './types';
+export type MohdTrackContext = {
+    mohdSignalTooltip?: FC<ValuedPoint[]>;
+    mohdMethylTooltip?: FC<ValuedPoint[]>;
+};
+export declare function createMohdTrack(row: MohdRowInfo, options: CreateTrackOptions): Track | null;

package/dist/TrackSelect/Folders/mohd/shared/types.d.ts

@@ -0,0 +1,40 @@
+import { MohdOme } from './config';
+export type MohdMethylStrandUrls = {
+    cpg: string;
+    chg: string;
+    chh: string;
+    depth: string;
+};
+export type MohdDataRow = {
+    ome: string;
+    site: string;
+    sample_id: string;
+    file_type: string;
+    filename: string;
+    sex: string;
+    status: string;
+};
+type MohdBaseRowInfo = {
+    id: string;
+    ome: MohdOme;
+    site: string;
+    sampleId: string;
+    sex: string;
+    status: string;
+    description: string;
+    trackCategory: "Signal" | "Annotation" | "Methylation";
+};
+export type MohdFileRowInfo = MohdBaseRowInfo & {
+    kind: "file";
+    filename: string;
+};
+export type MohdWgbsMethylRowInfo = MohdBaseRowInfo & {
+    kind: "wgbs-methyl";
+    filenames: {
+        plusStrand: MohdMethylStrandUrls;
+        minusStrand: MohdMethylStrandUrls;
+    };
+};
+export type MohdRowInfo = MohdFileRowInfo | MohdWgbsMethylRowInfo;
+export type MohdDataFile = MohdDataRow[];
+export {};

package/dist/TrackSelect/Folders/other-tracks/shared/toTrack.d.ts

@@ -0,0 +1,5 @@
+import { Track } from '@weng-lab/genomebrowser';
+import { CreateTrackOptions } from '../../types';
+import { OtherTrackInfo } from './types';
+export type OtherTracksTrackContext = {};
+export declare function createOtherTrack(row: OtherTrackInfo, _options: CreateTrackOptions): Track | null;

package/dist/TrackSelect/Folders/other-tracks/shared/types.d.ts

@@ -1,5 +1,6 @@
 export type OtherTrackInfo = {
     id: string;
+    sourceId?: string;
     name: string;
     description: string;
 };

package/dist/TrackSelect/Folders/types.d.ts

@@ -1,18 +1,19 @@
 import { GridColDef, GridRenderCellParams } from '@mui/x-data-grid-premium';
-import { TreeViewBaseItem } from '@mui/x-tree-view';
-import { ExtendedTreeItemProps, CustomTreeItemProps } from '../types';
+import { Track } from '@weng-lab/genomebrowser';
+import { TrackSelectTrackContext } from '../trackContext';
+import { CustomTreeItemProps } from '../types';
 export type Assembly = "GRCh38" | "mm10";
-/**
- * Runtime configuration that can be modified by ToolbarExtras components.
- * This allows folder-specific UI (like AssayToggle) to dynamically update
- * how the DataGrid and TreeView display data.
- */
-export interface FolderRuntimeConfig {
+export interface FolderView {
+    id: string;
+    label: string;
     columns: GridColDef[];
     groupingModel: string[];
     leafField: string;
-    /** Optional override for the tree builder function */
-    buildTree?: (selectedIds: string[], rowById: Map<string, any>) => TreeViewBaseItem<ExtendedTreeItemProps>[];
+}
+/** Options passed to folder-owned track factories. */
+export interface CreateTrackOptions {
+    assembly: Assembly;
+    trackContext?: TrackSelectTrackContext;
 }
 /**
  * Definition for a folder in TrackSelect.
@@ -24,61 +25,28 @@ export interface FolderRuntimeConfig {
  * @template TRow - The type of row data stored in this folder
  */
 export interface FolderDefinition<TRow = any> {
-    /** Unique identifier for this folder */
     id: string;
-    /** Display label shown in the UI */
     label: string;
-    /** Optional description shown in folder cards */
     description?: string;
-    /**
-     * Single source of truth for all row data.
-     * Maps row ID to the full row object.
-     */
-    rowById: Map<string, TRow>;
-    /**
-     * Function to extract the unique ID from a row object.
-     * Used for selection tracking and lookups.
-     */
-    getRowId: (row: TRow) => string;
-    /** Column definitions for the DataGrid */
+    rows: TRow[];
     columns: GridColDef[];
-    /** Fields to group by in the DataGrid (row grouping) */
     groupingModel: string[];
-    /** The field that represents the leaf level in the grouping hierarchy */
     leafField: string;
     /**
-     * Builds a tree structure from selected row IDs.
-     * Used to display selected items in the TreeView panel.
-     *
-     * @param selectedIds - Array of selected row IDs
-     * @param rowById - Map of row ID to row data (same as this.rowById)
-     * @returns Array of tree items to render in the TreeView
-     */
-    buildTree: (selectedIds: string[], rowById: Map<string, TRow>) => TreeViewBaseItem<ExtendedTreeItemProps>[];
-    /**
-     * Optional component to render folder-specific toolbar controls.
-     * For example, biosamples folder uses this to render an assay toggle
-     * that switches between sample-grouped and assay-grouped views.
+     * Creates a browser track from a folder row.
      *
-     * @param updateConfig - Callback to update the folder's runtime config
-     * @param folderId - The folder's unique identifier
-     * @param label - The folder's display label
-     * @param config - The current runtime config for this folder
+     * This keeps folder-specific track creation logic colocated with the
+     * folder's data and presentation logic instead of requiring consumers to
+     * branch on folder IDs.
      */
-    ToolbarExtras?: React.FC<{
-        updateConfig: (partial: Partial<FolderRuntimeConfig>) => void;
-        folderId: string;
-        label: string;
-        config: FolderRuntimeConfig;
+    createTrack: (row: TRow, options: CreateTrackOptions) => Track | null;
+    views?: FolderView[];
+    ViewSelector?: React.FC<{
+        views: FolderView[];
+        activeViewId: string;
+        onChange: (viewId: string) => void;
     }>;
-    /**
-     * Optional custom component for rendering grouping cells in the DataGrid.
-     * If not provided, a default grouping cell renderer will be used.
-     */
     GroupingCellComponent?: React.FC<GridRenderCellParams>;
-    /**
-     * Optional custom TreeItem component for the TreeView.
-     * If not provided, the default CustomTreeItem will be used.
-     */
     TreeItemComponent?: React.ForwardRefExoticComponent<CustomTreeItemProps & React.RefAttributes<HTMLLIElement>>;
+    LeafTreeItemComponent?: React.ForwardRefExoticComponent<CustomTreeItemProps & React.RefAttributes<HTMLLIElement>>;
 }

package/dist/TrackSelect/TrackSelect.d.ts

@@ -1,15 +1,18 @@
-import { FolderDefinition } from './Folders/types';
+import { TrackStoreInstance } from '@weng-lab/genomebrowser';
+import { Assembly, FolderDefinition } from './Folders/types';
+import { TrackSelectTrackContext } from './trackContext';
+export type InitialSelectedIdsByAssembly = Partial<Record<Assembly, Record<string, string[]>>>;
 export interface TrackSelectProps {
+    assembly: Assembly;
     folders: FolderDefinition[];
-    onSubmit: (selectedByFolder: Map<string, Set<string>>) => void;
+    initialSelectedIds?: InitialSelectedIdsByAssembly;
+    sessionStorageKey?: string;
+    trackStore?: TrackStoreInstance;
     onCancel?: () => void;
-    onClear?: () => void;
     maxTracks?: number;
-    storageKey?: string;
-    /** Initial selection to use when no stored selection exists */
-    initialSelection?: Map<string, Set<string>>;
+    trackContext?: TrackSelectTrackContext;
     open: boolean;
     onClose: () => void;
     title?: string;
 }
-export default function TrackSelect({ folders, onSubmit, onCancel, onClear, maxTracks, storageKey, initialSelection, open, onClose, title, }: TrackSelectProps): import("react/jsx-runtime").JSX.Element;
+export default function TrackSelect({ assembly, folders, initialSelectedIds, sessionStorageKey, trackStore, onCancel, maxTracks, trackContext, open, onClose, title, }: TrackSelectProps): import("react/jsx-runtime").JSX.Element;

package/dist/TrackSelect/TreeView/TreeViewWrapper.d.ts

@@ -1,2 +1,2 @@
 import { TreeViewWrapperProps } from '../types';
-export declare function TreeViewWrapper({ folderTrees, selectedCount, onRemove, }: TreeViewWrapperProps): import("react/jsx-runtime").JSX.Element;
+export declare function TreeViewWrapper({ folders, selectedByFolder, activeViewIdByFolder, selectedCount, onRemove, }: TreeViewWrapperProps): import("react/jsx-runtime").JSX.Element;

package/dist/TrackSelect/buildSelectedTree.d.ts

@@ -0,0 +1,15 @@
+import { TreeViewBaseItem } from '@mui/x-tree-view';
+import { ExtendedTreeItemProps } from './types';
+type TreeRow = {
+    id: string;
+    [key: string]: unknown;
+};
+type BuildSelectedTreeOptions = {
+    folderId: string;
+    rootLabel: string;
+    selectedRows: TreeRow[];
+    groupingModel: string[];
+    leafField: string;
+};
+export declare const buildSelectedTree: ({ folderId, rootLabel, selectedRows, groupingModel, leafField, }: BuildSelectedTreeOptions) => TreeViewBaseItem<ExtendedTreeItemProps>[];
+export {};

package/dist/TrackSelect/managedTracks.d.ts

@@ -0,0 +1,13 @@
+import { Track } from '@weng-lab/genomebrowser';
+import { Assembly, FolderDefinition } from './Folders/types';
+import { TrackSelectTrackContext } from './trackContext';
+export declare const diffManagedTracks: ({ assembly, currentTracks, folders, selectedByFolder, trackContext, }: {
+    assembly: Assembly;
+    currentTracks: Track[];
+    folders: FolderDefinition[];
+    selectedByFolder: Map<string, Set<string>>;
+    trackContext?: TrackSelectTrackContext;
+}) => {
+    idsToRemove: string[];
+    tracksToAdd: Track[];
+};

package/dist/TrackSelect/resolveFolderView.d.ts

@@ -0,0 +1,2 @@
+import { FolderDefinition, FolderView } from './Folders/types';
+export declare const resolveFolderView: (folder: FolderDefinition, activeViewIdByFolder: Map<string, string>) => FolderView;

package/dist/TrackSelect/trackContext.d.ts

@@ -0,0 +1,5 @@
+import { BiosampleTrackContext } from './Folders/biosamples/shared/toTrack';
+import { GeneTrackContext } from './Folders/genes/shared/toTrack';
+import { MohdTrackContext } from './Folders/mohd/shared/toTrack';
+import { OtherTracksTrackContext } from './Folders/other-tracks/shared/toTrack';
+export type TrackSelectTrackContext = GeneTrackContext & BiosampleTrackContext & MohdTrackContext & OtherTracksTrackContext;

package/dist/TrackSelect/types.d.ts

@@ -3,6 +3,7 @@ import { TreeViewBaseItem } from '@mui/x-tree-view';
 import { DataGridPremiumProps, GridColDef, GridRenderCellParams } from '@mui/x-data-grid-premium';
 import { ReactElement, ReactNode } from 'react';
 import { SvgIconOwnProps } from '@mui/material';
+import { FolderDefinition } from './Folders/types';
 /**
  * Custom Tree Props for RichTreeView Panel
  */
@@ -10,60 +11,38 @@ export type ExtendedTreeItemProps = {
     id: string;
     label: string;
     icon: string;
+    kind?: "root" | "group" | "leaf";
+    field?: string;
+    value?: string;
+    rowId?: string;
     folderId?: string;
-    isAssayItem?: boolean;
-    /**
-     * The assay name for leaf nodes (experiment accession items)
-     */
-    assayName?: string;
+    isHighlightedItem?: boolean;
+    highlightName?: string;
     /**
      * list of all the experimentAccession values in the children/grandchildren of the item, or the accession of the item itself
      * this is used in updating the rowSelectionModel when removing items from the Tree View panel
      */
     allExpAccessions?: string[];
 };
-/**
- * Configuration for a single folder's tree in the TreeViewWrapper.
- * Each folder gets its own tree with its own TreeItemComponent.
- */
-export type FolderTreeConfig = {
-    folderId: string;
-    items: TreeViewBaseItem<ExtendedTreeItemProps>[];
-    /** Optional custom TreeItem component for this folder */
-    TreeItemComponent?: React.ForwardRefExoticComponent<CustomTreeItemProps & React.RefAttributes<HTMLLIElement>>;
-};
 export type TreeViewWrapperProps = {
-    /** Array of folder tree configurations, one per folder with selections */
-    folderTrees: FolderTreeConfig[];
+    folders: FolderDefinition[];
+    selectedByFolder: Map<string, Set<string>>;
+    activeViewIdByFolder: Map<string, string>;
     selectedCount: number;
     onRemove: (item: TreeViewBaseItem<ExtendedTreeItemProps>) => void;
 };
 export interface CustomLabelProps {
     id: string;
     children: React.ReactNode;
-    isAssayItem?: boolean;
-    assayName?: string;
+    isHighlightedItem?: boolean;
+    highlightName?: string;
     icon?: React.ElementType | React.ReactElement | ReactNode;
-    /** Optional function to render custom icons for assay items */
     renderIcon?: (name: string) => ReactNode;
 }
 export interface CustomTreeItemProps extends Omit<UseTreeItemParameters, "rootRef">, Omit<React.HTMLAttributes<HTMLLIElement>, "onFocus"> {
     onRemove?: (item: TreeViewBaseItem<ExtendedTreeItemProps>) => void;
-    /** Optional function to render custom icons for assay items */
     renderIcon?: (name: string) => ReactNode;
 }
-/**
- * Types for useSelectionStore to keep track of selected DataGrid rows/tracks
- */
-export type SelectionState = {
-    selectedByFolder: Map<string, Set<string>>;
-    activeFolderId: string;
-};
-export type SelectionAction = {
-    clear: (folderId?: string) => void;
-    setActiveFolder: (folderId: string) => void;
-    setSelection: (folderId: string, ids: Set<string>) => void;
-};
 /**
  * DataGrid Props
  */