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

package/.env.local

@@ -1 +1 @@
-VITE_MUI_X_LICENSE_KEY=a8a7caa0861db35745fbff677471cad5Tz0xMjMzMTQsRT0xNzk3NTUxOTk5MDAwLFM9cHJlbWl1bSxMTT1zdWJzY3JpcHRpb24sUFY9aW5pdGlhbCxLVj0y
+NEXT_PUBLIC_MUI_X_LICENSE_KEY=a8a7caa0861db35745fbff677471cad5Tz0xMjMzMTQsRT0xNzk3NTUxOTk5MDAwLFM9cHJlbWl1bSxMTT1zdWJzY3JpcHRpb24sUFY9aW5pdGlhbCxLVj0y

package/dist/TrackSelect/Folders/biosamples/shared/BiosampleViewSelector.d.ts

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

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

@@ -1,24 +1,12 @@
 import { FolderDefinition } from '../../types';
 import { BiosampleDataFile, BiosampleRowInfo } from './types';
 export interface CreateBiosampleFolderOptions {
-    /** Unique identifier for this folder */
     id: string;
-    /** Display label shown in the UI */
     label: string;
-    /** Optional description shown in folder cards */
     description?: string;
-    /** Raw biosample data from JSON file */
     data: BiosampleDataFile;
 }
 /**
- * Factory function that creates a FolderDefinition for biosample data.
- *
- * This handles all the common setup for biosample folders:
- * - Transforms JSON data into flattened rows
- * - Creates the rowById lookup map
- * - Configures columns, grouping, and tree building
- *
- * @param options - Configuration options for the folder
- * @returns A complete FolderDefinition for the biosample data
+ * Build a biosample folder with its data, tree builder, and track factory.
  */
 export declare function createBiosampleFolder(options: CreateBiosampleFolderOptions): FolderDefinition<BiosampleRowInfo>;

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

@@ -0,0 +1,20 @@
+import { Rect, Track, ValuedPoint } from '@weng-lab/genomebrowser';
+import { FC } from 'react';
+import { CreateTrackOptions } from '../../types';
+import { BiosampleRowInfo } from './types';
+export type BiosampleTrackContext = {
+    onBiosampleFeatureClick?: (args: {
+        trackId: string;
+        row: BiosampleRowInfo;
+        rect: Rect;
+    }) => void;
+    onBiosampleFeatureHover?: (args: {
+        trackId: string;
+        row: BiosampleRowInfo;
+        rect: Rect;
+    }) => void;
+    biosampleFeatureTooltip?: FC<Rect>;
+    biosampleSignalTooltip?: FC<ValuedPoint[]>;
+    biosampleMethylTooltip?: FC<ValuedPoint[]>;
+};
+export declare function createBiosampleTrack(row: BiosampleRowInfo, options: CreateTrackOptions): Track;

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

@@ -1,10 +1,6 @@
-/**
- * Types for biosample folder data
- */
 export type CollectionType = "Core" | "Ancillary" | "Partial";
 /**
- * Assay information from the JSON data.
- * Standard assays have a single `url`, while WGBS assays have `cpgPlus`, `cpgMinus`, `coverage`.
+ * One assay entry from the source data. WGBS rows carry strand-specific URLs.
  */
 export type BiosampleAssayInfo = {
     id: string;
@@ -16,9 +12,7 @@ export type BiosampleAssayInfo = {
     cpgMinus?: string;
     coverage?: string;
 };
-/**
- * Track information from the JSON data
- */
+/** One biosample entry from the source data. */
 export type BiosampleTrackInfo = {
     name: string;
     ontology: string;
@@ -29,8 +23,7 @@ export type BiosampleTrackInfo = {
     collection: CollectionType;
 };
 /**
- * Row format for DataGrid (flattened from TrackInfo).
- * Standard assays have a single `url`, while WGBS assays have `cpgPlus`, `cpgMinus`, `coverage`.
+ * Flattened table row used by TrackSelect and track creation.
  */
 export type BiosampleRowInfo = {
     id: string;
@@ -47,9 +40,7 @@ export type BiosampleRowInfo = {
     cpgMinus?: string;
     coverage?: string;
 };
-/**
- * Structure of the biosample JSON data files
- */
+/** Root shape for biosample JSON files. */
 export type BiosampleDataFile = {
     tracks: BiosampleTrackInfo[];
 };

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

@@ -9,6 +9,6 @@ export declare const defaultColumns: GridColDef<GeneRowInfo>[];
  */
 export declare const defaultGroupingModel: string[];
 /**
- * Leaf field - the unique identifier
+ * Leaf field - the raw track ID (without folder prefix) used as the tree view leaf label
  */
-export declare const defaultLeafField = "id";
+export declare const defaultLeafField = "trackId";

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

@@ -6,7 +6,5 @@ export interface CreateGeneFolderOptions {
     description?: string;
     data: GeneDataFile;
 }
-/**
- * Factory function that creates a FolderDefinition for genes
- */
+/** Build a gene folder with its row lookup, tree, and track factory. */
 export declare function createGeneFolder(options: CreateGeneFolderOptions): FolderDefinition<GeneRowInfo>;

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

@@ -0,0 +1,18 @@
+import { Track, Transcript } from '@weng-lab/genomebrowser';
+import { FC } from 'react';
+import { CreateTrackOptions } from '../../types';
+import { GeneRowInfo } from './types';
+export type GeneTrackContext = {
+    onGeneClick?: (args: {
+        trackId: string;
+        row: GeneRowInfo;
+        transcript: Transcript;
+    }) => void;
+    onGeneHover?: (args: {
+        trackId: string;
+        row: GeneRowInfo;
+        transcript: Transcript;
+    }) => void;
+    geneTooltip?: FC<Transcript>;
+};
+export declare function createGeneTrack(row: GeneRowInfo, options: CreateTrackOptions): Track;

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

@@ -17,6 +17,8 @@ export type GeneTrackInfo = {
  */
 export type GeneRowInfo = {
     id: string;
+    /** The raw track ID without the folder prefix, used as the tree view leaf label */
+    trackId: string;
     displayName: string;
     versions: number[];
 };

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

@@ -1,17 +1,11 @@
 import { Assembly, FolderDefinition } from './types';
-export { type Assembly, type FolderDefinition, type FolderRuntimeConfig, } from './types';
+export { type Assembly, type FolderDefinition, type FolderView } from './types';
 export type { BiosampleRowInfo } from './biosamples/shared/types';
+export type { BiosampleTrackContext } from './biosamples/shared/toTrack';
 export type { GeneRowInfo } from './genes/shared/types';
+export type { GeneTrackContext } from './genes/shared/toTrack';
+export type { MohdRowInfo } from './mohd/shared/types';
+export type { MohdTrackContext } from './mohd/shared/toTrack';
 export type { OtherTrackInfo } from './other-tracks/shared/types';
-/**
- * Registry of folders available for each assembly.
- *
- * Each assembly can have multiple folders (e.g., biosamples, genes, etc.).
- * TrackSelect receives the folders for the current assembly and renders
- * them as tabs or a folder selector.
- *
- * To add a new folder:
- * 1. Create a folder config file (e.g., folders/genes/human.ts)
- * 2. Import and add it to the appropriate assembly array below
- */
+export type { OtherTracksTrackContext } from './other-tracks/shared/toTrack';
 export declare const foldersByAssembly: Record<Assembly, FolderDefinition[]>;