@weng-lab/genomebrowser-ui 0.1.9 → 0.1.11

package/src/lib.ts

@@ -7,8 +7,5 @@ import {
 } from "./TrackSelect/store.ts";
 export { createSelectionStore, SelectionStoreInstance };
 
-import { rowById } from "./TrackSelect/consts.ts";
-export { rowById };
-
 import type { RowInfo } from "./TrackSelect/types.ts";
 export { RowInfo };

package/test/main.tsx

@@ -1,9 +1,84 @@
-import { useEffect, useMemo } from "react";
-import { createSelectionStore } from "../src/TrackSelect/store";
-import TrackSelect from "../src/TrackSelect/TrackSelect";
+// react
+import { useCallback, useEffect, useMemo, useState } from "react";
 import { createRoot } from "react-dom/client";
 
-function getLocalStorage(assembly: string): Set<string> | null {
+// mui
+import EditIcon from "@mui/icons-material/Edit";
+import CloseIcon from "@mui/icons-material/Close";
+import {
+  Box,
+  Button,
+  Dialog,
+  DialogContent,
+  DialogTitle,
+  IconButton,
+  Typography,
+} from "@mui/material";
+
+// weng lab
+import {
+  BigBedConfig,
+  BigWigConfig,
+  Browser,
+  createBrowserStoreMemo,
+  createTrackStoreMemo,
+  DisplayMode,
+  Domain,
+  GQLWrapper,
+  Rect,
+  Track,
+  TrackType,
+  TranscriptConfig,
+} from "@weng-lab/genomebrowser";
+
+// local
+import { createSelectionStore, TrackSelect, RowInfo } from "../src/lib";
+import { Exon } from "@weng-lab/genomebrowser/dist/components/tracks/transcript/types";
+
+interface Transcript {
+  id: string;
+  name: string;
+  coordinates: Domain;
+  strand: string;
+  exons?: Exon[];
+  color?: string;
+}
+
+const enum Assembly {
+  human = "GRCh38",
+  mouse = "mm10",
+}
+
+// Callback types for track interactions (using any to avoid type conflicts with library types)
+interface TrackCallbacks {
+  onHover: (item: any) => void;
+  onLeave: () => void;
+  onCCREClick: (item: any) => void;
+  onGeneClick: (item: any) => void;
+}
+
+// Helper to inject callbacks based on track type
+function injectCallbacks(track: Track, callbacks: TrackCallbacks): Track {
+  if (track.trackType === TrackType.Transcript) {
+    return {
+      ...track,
+      onHover: callbacks.onHover,
+      onLeave: callbacks.onLeave,
+      onClick: callbacks.onGeneClick,
+    };
+  }
+  if (track.trackType === TrackType.BigBed) {
+    return {
+      ...track,
+      onHover: callbacks.onHover,
+      onLeave: callbacks.onLeave,
+      onClick: callbacks.onCCREClick,
+    };
+  }
+  return track;
+}
+
+function getLocalStorage(assembly: Assembly): Set<string> | null {
   if (typeof window === "undefined" || !window.sessionStorage) return null;
 
   const selectedIds = sessionStorage.getItem(assembly + "-selected-tracks");
@@ -12,32 +87,339 @@ function getLocalStorage(assembly: string): Set<string> | null {
   return new Set(idsArray);
 }
 
-function setLocalStorage(trackIds: Set<string>, assembly: string) {
+function setLocalStorage(trackIds: Set<string>, assembly: Assembly) {
   sessionStorage.setItem(
     assembly + "-selected-tracks",
     JSON.stringify([...trackIds]),
   );
 }
 
-const assembly = "grch38";
 function Main() {
+  const [open, setOpen] = useState(false);
+  const currentAssembly = Assembly.mouse;
+
+  const browserStore = createBrowserStoreMemo({
+    // chr12:53,380,176-53,416,446
+    domain: { chromosome: "chr12", start: 53380176, end: 53416446 },
+    marginWidth: 100,
+    trackWidth: 1400,
+    multiplier: 3,
+  });
+
+  const addHighlight = browserStore((s) => s.addHighlight);
+  const removeHighlight = browserStore((s) => s.removeHighlight);
+  const onHover = useCallback(
+    (item: Rect | Transcript) => {
+      const domain =
+        "start" in item
+          ? { start: item.start, end: item.end }
+          : { start: item.coordinates.start, end: item.coordinates.end };
+
+      addHighlight({
+        id: "hover-highlight",
+        domain,
+        color: item.color || "blue",
+      });
+    },
+    [addHighlight],
+  );
+  const onLeave = useCallback(() => {
+    removeHighlight("hover-highlight");
+  }, [removeHighlight]);
+
+  const onCCREClick = useCallback((item: Rect) => {
+    console.log(item);
+  }, []);
+  const onGeneClick = useCallback((item: Transcript) => {
+    console.log(item);
+  }, []);
+
+  // Bundle callbacks for track injection
+  const callbacks = useMemo<TrackCallbacks>(
+    () => ({
+      onHover,
+      onLeave,
+      onCCREClick,
+      onGeneClick,
+    }),
+    [onHover, onLeave, onCCREClick, onGeneClick],
+  );
+
+  const trackStore = useLocalTracks(currentAssembly, callbacks);
+
+  const tracks = trackStore((s) => s.tracks);
+  const insertTrack = trackStore((s) => s.insertTrack);
+  const removeTrack = trackStore((s) => s.removeTrack);
+
   const selectionStore = useMemo(() => {
-    const localIds = getLocalStorage(assembly);
+    const localIds = getLocalStorage(currentAssembly);
     const ids = localIds != null ? localIds : new Set<string>();
-    return createSelectionStore(ids);
-  }, [assembly]);
+    return createSelectionStore(currentAssembly, ids);
+  }, [currentAssembly]);
 
-  const selectedIds = selectionStore((s) => s.selectedIds);
-  const getTrackIds = selectionStore((s) => s.getTrackIds);
+  const rowById = selectionStore((s) => s.rowById);
 
-  // Get only real track IDs (no auto-generated group IDs)
-  const trackIds = useMemo(() => getTrackIds(), [selectedIds, getTrackIds]);
+  // Handle submit: sync tracks to browser and save to localStorage
+  const handleSubmit = useCallback(
+    (newTrackIds: Set<string>) => {
+      const currentIds = new Set(tracks.map((t) => t.id));
 
-  useEffect(() => {
-    setLocalStorage(trackIds, assembly);
-  }, [assembly, trackIds]);
+      // Build tracks to add from newTrackIds + rowById lookup
+      const tracksToAdd = Array.from(newTrackIds)
+        .filter((id) => !currentIds.has(id)) // not in current track list
+        .map((id) => rowById.get(id)) // get RowInfo object
+        .filter((track): track is RowInfo => track !== undefined); // filter out undefined
+
+      const tracksToRemove = tracks.filter((t) => {
+        return !t.id.includes("ignore") && !newTrackIds.has(t.id);
+      });
+
+      console.log("removing", tracksToRemove);
+      for (const t of tracksToRemove) {
+        removeTrack(t.id);
+      }
+
+      for (const s of tracksToAdd) {
+        const track = generateTrack(s, callbacks);
+        if (track === null) continue;
+        insertTrack(track);
+      }
+
+      // Save the track IDs (not the auto-generated group IDs)
+      setLocalStorage(newTrackIds, currentAssembly);
+      // Close the dialog
+      setOpen(false);
+    },
+    [tracks, removeTrack, insertTrack, callbacks],
+  );
+
+  const handleCancel = () => {
+    setOpen(false);
+  };
+
+  // Handle reset: clear selections and remove non-default tracks
+  const handleReset = () => {
+    // Clear the selection store
+    selectionStore.getState().clear();
 
-  return <TrackSelect store={selectionStore} />;
+    // Remove all non-default tracks from the browser
+    const tracksToRemove = tracks.filter((t) => !t.id.includes("ignore"));
+    for (const t of tracksToRemove) {
+      removeTrack(t.id);
+    }
+
+    // Clear localStorage for selected tracks
+    setLocalStorage(new Set(), currentAssembly);
+  };
+
+  return (
+    <>
+      <Button
+        variant="contained"
+        startIcon={<EditIcon />}
+        size="small"
+        onClick={() => setOpen(true)}
+      >
+        Select Tracks
+      </Button>
+      <Dialog
+        open={open}
+        onClose={() => setOpen(false)}
+        maxWidth="lg"
+        fullWidth
+      >
+        <DialogTitle
+          bgcolor="#0c184a"
+          color="white"
+          display={"flex"}
+          justifyContent={"space-between"}
+          alignItems={"center"}
+          fontWeight={"bold"}
+        >
+          Biosample Tracks
+          <IconButton
+            size="large"
+            onClick={() => setOpen(false)}
+            sx={{ color: "white", padding: 0 }}
+          >
+            <CloseIcon fontSize="large" />
+          </IconButton>
+        </DialogTitle>
+        <DialogContent sx={{ marginTop: "5px" }}>
+          <TrackSelect
+            store={selectionStore}
+            onSubmit={handleSubmit}
+            onCancel={handleCancel}
+            onReset={handleReset}
+          />
+        </DialogContent>
+      </Dialog>
+      <GQLWrapper>
+        <Browser browserStore={browserStore} trackStore={trackStore} />
+      </GQLWrapper>
+    </>
+  );
 }
 
 createRoot(document.getElementById("root")!).render(<Main />);
+
+const ASSAY_COLORS: Record<string, string> = {
+  dnase: "#06da93",
+  h3k4me3: "#ff0000",
+  h3k27ac: "#ffcd00",
+  ctcf: "#00b0d0",
+  atac: "#02c7b9",
+  rnaseq: "#00aa00",
+  chromhmm: "#00ff00",
+  ccre: "#0c184a",
+};
+
+function generateTrack(sel: RowInfo, callbacks?: TrackCallbacks): Track {
+  const color = ASSAY_COLORS[sel.assay.toLowerCase()] || "#000000";
+  let track: Track;
+
+  switch (sel.assay.toLowerCase()) {
+    case "chromhmm":
+      track = {
+        ...defaultBigBed,
+        id: sel.id,
+        url: sel.url,
+        title: sel.displayname,
+        color,
+      };
+      break;
+    case "ccre":
+      track = {
+        ...defaultBigBed,
+        id: sel.id,
+        url: sel.url,
+        title: sel.displayname,
+        color,
+      };
+      break;
+    default:
+      track = {
+        ...defaultBigWig,
+        id: sel.id,
+        url: sel.url,
+        title: sel.displayname,
+        color,
+      };
+  }
+
+  return callbacks ? injectCallbacks(track, callbacks) : track;
+}
+
+export const defaultBigWig: Omit<BigWigConfig, "id" | "title" | "url"> = {
+  trackType: TrackType.BigWig,
+  height: 50,
+  displayMode: DisplayMode.Full,
+  titleSize: 12,
+};
+
+export const defaultBigBed: Omit<BigBedConfig, "id" | "title" | "url"> = {
+  trackType: TrackType.BigBed,
+  height: 20,
+  displayMode: DisplayMode.Dense,
+  titleSize: 12,
+};
+
+export const defaultTranscript: Omit<
+  TranscriptConfig,
+  "id" | "assembly" | "version"
+> = {
+  title: "GENCODE Genes",
+  trackType: TrackType.Transcript,
+  displayMode: DisplayMode.Squish,
+  height: 100,
+  color: "#0c184a", // screen theme default
+  canonicalColor: "#100e98", // screen theme light
+  highlightColor: "#3c69e8", // bright blue
+  titleSize: 12,
+};
+
+export function useLocalTracks(assembly: string, callbacks?: TrackCallbacks) {
+  const localTracks = getLocalTracks(assembly);
+
+  const defaultTracks =
+    assembly === "GRCh38" ? defaultHumanTracks : defaultMouseTracks;
+
+  // Get base tracks (from storage or defaults)
+  let initialTracks = localTracks || defaultTracks;
+
+  // Inject callbacks if provided (callbacks are lost on JSON serialization)
+  if (callbacks) {
+    initialTracks = initialTracks.map((t) => injectCallbacks(t, callbacks));
+  }
+
+  const trackStore = createTrackStoreMemo(initialTracks, []);
+  const tracks = trackStore((state) => state.tracks);
+
+  // any time the track list changes, update local storage
+  useEffect(() => {
+    setLocalTracks(tracks, assembly);
+  }, [tracks, assembly]);
+
+  return trackStore;
+}
+
+export function getLocalTracks(assembly: string): Track[] | null {
+  if (typeof window === "undefined" || !window.sessionStorage) return null;
+
+  const localTracks = sessionStorage.getItem(assembly + "-" + "tracks");
+  if (!localTracks) return null;
+  const localTracksJson = JSON.parse(localTracks) as Track[];
+  return localTracksJson;
+}
+
+export function setLocalTracks(tracks: Track[], assembly: string) {
+  sessionStorage.setItem(assembly + "-tracks", JSON.stringify(tracks));
+}
+
+const defaultHumanTracks = [
+  {
+    ...defaultTranscript,
+    color: ASSAY_COLORS.ccre,
+    id: "human-genes-ignore",
+    assembly: "GRCh38",
+    version: 40,
+  },
+  {
+    ...defaultBigBed,
+    color: ASSAY_COLORS.ccre,
+    id: "human-ccre-ignore",
+    title: "All cCREs colored by group",
+    url: "https://downloads.wenglab.org/GRCh38-cCREs.DCC.bigBed",
+  },
+  {
+    ...defaultBigWig,
+    color: ASSAY_COLORS.dnase,
+    id: "human-dnase-aggregate-ignore",
+    title: "Aggregated DNase signal, all ENCODE biosamples",
+    url: "https://downloads.wenglab.org/DNAse_All_ENCODE_MAR20_2024_merged.bw",
+  },
+];
+
+const defaultMouseTracks = [
+  {
+    ...defaultTranscript,
+    color: ASSAY_COLORS.ccre,
+    id: "mouse-genes-ignore",
+    assembly: "mm10",
+    version: 21,
+  },
+  {
+    ...defaultBigBed,
+    color: ASSAY_COLORS.ccre,
+    id: "mouse-ccre-ignore",
+    title: "All cCREs colored by group",
+    url: "https://downloads.wenglab.org/mm10-cCREs.DCC.bigBed",
+  },
+  {
+    ...defaultBigWig,
+    color: ASSAY_COLORS.dnase,
+    id: "mouse-dnase-aggregate-ignore",
+    title: "Aggregated DNase signal, all ENCODE biosamples",
+    url: "https://downloads.wenglab.org/DNase_MM10_ENCODE_DEC2024_merged_nanrm.bigWig",
+  },
+];

package/dist/TrackSelect/treeViewHelpers.d.ts

@@ -1 +0,0 @@
-export {};

package/src/TrackSelect/.claude/settings.local.json

@@ -1,7 +0,0 @@
-{
-  "permissions": {
-    "allow": [
-      "mcp__Ref__ref_read_url"
-    ]
-  }
-}