@jbrowse/core 5.0.0-beta.10 → 5.0.0-beta.11

package/esm/util/springAnimate.js

@@ -61,7 +61,7 @@ export function springAnimate({ from, to, write, read, onFinish = () => { }, pre
             animationFrameId = requestAnimationFrame(() => {
                 update({
                     lastPosition: position,
-                    lastTime: time,
+                    lastTime: lastTime + numSteps,
                     lastVelocity: velocity,
                 });
             });

package/esm/util/stepTables.d.ts

@@ -1,3 +1,4 @@
+import { DerivedTable } from './featureTable.ts';
 import type { Column, FeatureTable, MadeRows } from './featureTable.ts';
 import type { AggregateOp, AggregateStep, BinStep } from './markEncodingTypes.ts';
 import type { Feature, SimpleFeatureSerialized } from './simpleFeature.ts';
@@ -15,6 +16,19 @@ export interface Staged {
     table: FeatureTable;
     bounds: Bounds;
 }
+export declare function boundsThrough(bounds: Bounds, parentRow: Uint32Array): Bounds;
+/**
+ * The entries a `flatten` fanned out, one row each over the container row it
+ * came from. A container kept with nothing to fan out is a row of its own
+ * that reads everything off itself.
+ */
+export declare abstract class FannedTable extends DerivedTable {
+    get madeFrom(): boolean;
+    /** A container kept with nothing to fan out: the row is the container. */
+    abstract isKept(i: number): boolean;
+    abstract get hasKept(): boolean;
+    row(i: number): Feature;
+}
 export declare function stepReader(table: FeatureTable, ref: string, step: string): (i: number) => unknown;
 export declare function stepNumberReader(table: FeatureTable, ref: string, step: string): (i: number) => number;
 export declare function groupKey(value: unknown): unknown;

package/esm/util/stepTables.js

@@ -1,14 +1,48 @@
-// The pieces of the transform steps that the fused bin-and-aggregate kernel
-// shares with the steps themselves. Imported by relative path only, so none
-// of it is a package subpath or part of the plugin ABI.
+// The pieces of the transform steps that the fused kernels share with the
+// steps themselves. Imported by relative path only, so none of it is a
+// package subpath or part of the plugin ABI.
 import { aggregateFieldName } from './aggregateFieldName.js';
-import { NO_COLUMN, TableRow, numberReaderOf, readerOf, valueAt, } from './featureTable.js';
+import { DerivedTable, NO_COLUMN, TableRow, numberReaderOf, readerOf, valueAt, } from './featureTable.js';
 import { fieldReader, isPlainFieldRef } from './fieldReader.js';
 import { isJexl } from './jexlStrings.js';
 import { numericValue } from './numericValue.js';
 export const DEFAULT_BIN_AS = ['start', 'end'];
 /** What a `bin` over `fields` writes on each piece: the bases of its interval inside its bin. */
 export const BIN_OVERLAP_FIELD = 'overlap';
+// Section starts through a step whose rows came from its input's in order:
+// each section starts at the first row whose parent row is in it.
+export function boundsThrough(bounds, parentRow) {
+    const out = new Uint32Array(bounds.length);
+    let lo = 0;
+    for (let s = 0; s < bounds.length; s++) {
+        const edge = bounds[s];
+        let hi = parentRow.length;
+        while (lo < hi) {
+            const mid = (lo + hi) >>> 1;
+            if (parentRow[mid] < edge) {
+                lo = mid + 1;
+            }
+            else {
+                hi = mid;
+            }
+        }
+        out[s] = lo;
+    }
+    return out;
+}
+/**
+ * The entries a `flatten` fanned out, one row each over the container row it
+ * came from. A container kept with nothing to fan out is a row of its own
+ * that reads everything off itself.
+ */
+export class FannedTable extends DerivedTable {
+    get madeFrom() {
+        return true;
+    }
+    row(i) {
+        return this.isKept(i) ? this.parent.row(this.parentOf(i)) : super.row(i);
+    }
+}
 // A step reads a name or a dotted path. A plain name reads the table's column;
 // a path walks each row, chosen once per step. A computed field is a `formula`
 // step's to make.

package/esm/util/tabix.d.ts

@@ -90,7 +90,9 @@ export declare function readTabixLinesRedispatched(file: TabixLineSource, query:
  * structural for the same reason as {@link TabixLineSource}.
  */
 interface TabixHeaderSource {
-    getHeaderLines(): Promise<string[]>;
+    getHeaderLines(opts?: {
+        signal?: AbortSignal;
+    }): Promise<string[]>;
 }
 /**
  * The header lines of a tabix-indexed file, however that file kept them.
@@ -121,5 +123,7 @@ interface TabixHeaderSource {
  * commented block and then the counted rows used to fetch and decompress the
  * same bytes twice, which every bare-header file did on every call.
  */
-export declare function readTabixHeaderLines(file: TabixHeaderSource): Promise<string[]>;
+export declare function readTabixHeaderLines(file: TabixHeaderSource, opts?: {
+    signal?: AbortSignal;
+}): Promise<string[]>;
 export {};

package/esm/util/tabix.js

@@ -143,6 +143,6 @@ function mergeTabixLines(...groups) {
  * commented block and then the counted rows used to fetch and decompress the
  * same bytes twice, which every bare-header file did on every call.
  */
-export function readTabixHeaderLines(file) {
-    return file.getHeaderLines();
+export function readTabixHeaderLines(file, opts) {
+    return file.getHeaderLines(opts);
 }

package/esm/util/tracks.d.ts

@@ -1,5 +1,8 @@
 export { getFileName } from './getFileName.ts';
 export { getRpcSessionId } from './parentWalk.ts';
+export { makeIndex } from './formatGuessers.ts';
+export { isLooseTrackConfig, type LooseTrackInput, } from '@jbrowse/add-track-core';
+import { type LooseTrackInput } from '@jbrowse/add-track-core';
 import type PluginManager from '../PluginManager.ts';
 import type { AnyConfigurationModel } from '../configuration/index.ts';
 import type { BlobLocation, FileHandleLocation, FileLocation, PreFileLocation } from './types/data.ts';
@@ -132,23 +135,6 @@ export declare function restoreFileHandlesFromSnapshot(sessionSnapshot: unknown,
     success: false;
     error: unknown;
 })[]>;
-/**
- * creates a new location from the provided location including the appropriate
- * suffix and location type
- *
- * @param location - the FileLocation
- * @param suffix - the file suffix (e.g. .bam)
- * @returns the constructed location object from the provided parameters
- */
-export declare function makeIndex(location: FileLocation, suffix: string): BlobLocation | FileHandleLocation | {
-    uri: string;
-    locationType: string;
-    baseUri?: string | undefined;
-    localPath?: undefined;
-} | {
-    localPath: string;
-    locationType: string;
-};
 /**
  * constructs a potential index file (with suffix) from the provided file name
  *
@@ -227,12 +213,6 @@ export declare function addTrackTypeGuesser(pluginManager: PluginManager, guess:
 export declare function stripFileExtension(name: string): string;
 export declare function guessAdapter(file: FileLocation, index: FileLocation | undefined, adapterHint?: string, model?: IAnyStateTreeNode): AdapterConfig;
 export declare function guessTrackType(adapterType: string, model?: IAnyStateTreeNode, file?: FileLocation): string;
-export interface LooseTrackInput {
-    uri: string;
-    index?: string;
-    baseUri?: string;
-    [key: string]: unknown;
-}
 /**
  * Expand a loose track description — a bare data-file URI, or an object with
  * `uri` (and optional `index`) plus any extra config keys — into a full track
@@ -268,13 +248,6 @@ export declare function guessTrackConfForLocation(file: FileLocation, index: Fil
     assemblyNames: string[];
     adapter: AdapterConfig;
 };
-/**
- * Whether a track snapshot is the loose `{ uri, ... }` form — a data file with
- * no `adapter` — that {@link expandLooseTrackConfig} expands.
- */
-export declare function isLooseTrackConfig(snap: unknown): snap is LooseTrackInput & {
-    trackId?: string;
-};
 /**
  * Expand a loose track config into a full one and leave any other snapshot
  * untouched, so it can sit on every path a track snapshot enters the tree by:

package/esm/util/tracks.js

@@ -8,12 +8,16 @@ export { getFileName } from './getFileName.js';
 // it. `fetchContext.ts` takes it from mstUtils instead, which is what keeps the
 // configuration schemas this file pulls in out of the fetch harness's graph.
 export { getRpcSessionId } from './parentWalk.js';
+export { makeIndex } from './formatGuessers.js';
+export { isLooseTrackConfig, } from '@jbrowse/add-track-core';
+import { isLooseTrackConfig, } from '@jbrowse/add-track-core';
 import { asModelType, getParent, getSnapshot, getType, hasParent, isAlive, isStateTreeNode, } from '@jbrowse/mobx-state-tree';
 import { observable, runInAction, untracked } from 'mobx';
 import { readConfObject } from '../configuration/index.js';
 import { adapterConfigCacheKey } from '../data_adapters/dataAdapterCache.js';
 import { displayCandidates, displayTypesFedBy, } from '../pluggableElementTypes/models/baseTrackConfig.js';
 import { getFileHandle, storeFileHandle, verifyPermission, } from './fileHandleStore.js';
+import { makeIndex } from './formatGuessers.js';
 import { getFileName } from './getFileName.js';
 import { getContainingView, getEnv, getSession, objectHash, } from './mstUtils.js';
 import { isViewModel } from './types/index.js';
@@ -279,34 +283,6 @@ export function findFileHandleIds(obj) {
 export async function restoreFileHandlesFromSnapshot(sessionSnapshot, requestPermission = false) {
     return restoreFileHandles([...findFileHandleIds(sessionSnapshot)], requestPermission);
 }
-/**
- * creates a new location from the provided location including the appropriate
- * suffix and location type
- *
- * @param location - the FileLocation
- * @param suffix - the file suffix (e.g. .bam)
- * @returns the constructed location object from the provided parameters
- */
-export function makeIndex(location, suffix) {
-    if ('uri' in location) {
-        return {
-            uri: location.uri + suffix,
-            locationType: 'UriLocation',
-            // carry the parent's baseUri so a derived sibling index resolves against
-            // the same config location as the file it indexes
-            ...(location.baseUri ? { baseUri: location.baseUri } : {}),
-        };
-    }
-    else if ('localPath' in location) {
-        return {
-            localPath: location.localPath + suffix,
-            locationType: 'LocalPathLocation',
-        };
-    }
-    else {
-        return location;
-    }
-}
 /**
  * constructs a potential index file (with suffix) from the provided file name
  *
@@ -450,17 +426,6 @@ export function guessTrackConfForLocation(file, index, pluginManager, assemblyNa
         adapter,
     };
 }
-/**
- * Whether a track snapshot is the loose `{ uri, ... }` form — a data file with
- * no `adapter` — that {@link expandLooseTrackConfig} expands.
- */
-export function isLooseTrackConfig(snap) {
-    return (typeof snap === 'object' &&
-        snap !== null &&
-        !Array.isArray(snap) &&
-        typeof snap.uri === 'string' &&
-        !('adapter' in snap));
-}
 /**
  * Expand a loose track config into a full one and leave any other snapshot
  * untouched, so it can sit on every path a track snapshot enters the tree by:

package/esm/util/unknownSnapshotKeys.d.ts

@@ -25,7 +25,9 @@ export declare function displaySetterName(key: string): string;
 export declare function setterOnlyMessage(label: string, keys: string[]): string;
 /**
  * Name the keys a view was handed and could not place, from the partition
- * `withLaunchInput` runs on the snapshot.
+ * `withLaunchInput` runs on the snapshot. The console alone, like
+ * `reportLegacyInit`: the view opened without them, and the keys are usually a
+ * v4 session's retired state that a visitor holding the link cannot act on.
  */
 export declare function reportUnknownKeys(self: IStateTreeNode, keys: string[]): void;
 /**

package/esm/util/unknownSnapshotKeys.js

@@ -28,19 +28,13 @@ export function setterOnlyMessage(label, keys) {
 }
 /**
  * Name the keys a view was handed and could not place, from the partition
- * `withLaunchInput` runs on the snapshot.
+ * `withLaunchInput` runs on the snapshot. The console alone, like
+ * `reportLegacyInit`: the view opened without them, and the keys are usually a
+ * v4 session's retired state that a visitor holding the link cannot act on.
  */
 export function reportUnknownKeys(self, keys) {
-    if (!keys.length) {
-        return;
-    }
-    const message = unknownKeysMessage(viewLabel(self), keys);
-    console.warn(message);
-    try {
-        getNotificationSink(self).notify(message, 'warning');
-    }
-    catch {
-        // a view built outside a session has nowhere to put it
+    if (keys.length) {
+        console.warn(unknownKeysMessage(viewLabel(self), keys));
     }
 }
 /**

package/esm/util/usePanZoom.js

@@ -113,6 +113,9 @@ export function usePanZoom(ref, view, { touchAction = 'none', } = {}) {
         };
     }, [ref, touchAction]);
     function endDrag(event) {
+        if (dragRef.current?.pointerId !== event.pointerId) {
+            return;
+        }
         dragRef.current = undefined;
         // release only what the move handler took — a press that stayed under the
         // threshold never captured anything
@@ -131,7 +134,7 @@ export function usePanZoom(ref, view, { touchAction = 'none', } = {}) {
                 // lands on an icon inside the control. Shift is left alone too: it is
                 // what a range-select of the host's own would want, and it is what
                 // JBrowse's own view uses it for.
-                if (event.button !== 0 || event.shiftKey) {
+                if (!event.isPrimary || event.button !== 0 || event.shiftKey) {
                     return;
                 }
                 if (event.target instanceof Element &&
@@ -139,11 +142,15 @@ export function usePanZoom(ref, view, { touchAction = 'none', } = {}) {
                     return;
                 }
                 // Note what this does *not* do: capture the pointer. See onPointerMove.
-                dragRef.current = { x: event.clientX, panning: false };
+                dragRef.current = {
+                    x: event.clientX,
+                    panning: false,
+                    pointerId: event.pointerId,
+                };
             },
             onPointerMove(event) {
                 const drag = dragRef.current;
-                if (!drag) {
+                if (!drag || drag.pointerId !== event.pointerId) {
                     return;
                 }
                 if (!drag.panning) {

package/esm/util/useRafCommit.js

@@ -18,6 +18,7 @@ export function useRafCommit(commit) {
         const pending = pendingRef.current;
         if (pending) {
             cancelAnimationFrame(pending.id);
+            pendingRef.current = undefined;
         }
     }, []);
     const schedule = useCallback((value) => {

package/esm/util/withFeatureDetails.js

@@ -1,4 +1,5 @@
 import { isAlive } from '@jbrowse/mobx-state-tree';
+import { isAbortException } from './aborting.js';
 import { notifyFeatureDetailsMiss } from './openFeatureWidget.js';
 import { getNotificationSink } from './sessionServices.js';
 /**
@@ -48,6 +49,9 @@ export async function withFeatureDetails(self, fetch, onFeat, onMiss = () => {
         }
     }
     catch (e) {
+        if (isAbortException(e)) {
+            return;
+        }
         // Logged whatever happened, and only toasted while the display is still
         // there: `getSession` throws on a detached node, and a message naming a
         // track the user has already closed is noise they cannot act on.

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "5.0.0-beta.10",
+  "version": "5.0.0-beta.11",
   "type": "module",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
@@ -166,6 +166,7 @@
     "./util/assemblyConfigUtils": "./esm/util/assemblyConfigUtils.js",
     "./util/bandHeight": "./esm/util/bandHeight.js",
     "./util/bandLayout": "./esm/util/bandLayout.js",
+    "./util/baseDisplayConfig": "./esm/util/baseDisplayConfig.js",
     "./util/bgzfWorkerPool": "./esm/util/bgzfWorkerPool.js",
     "./util/blockTypes": "./esm/util/blockTypes.js",
     "./util/cacheBudgets": "./esm/util/cacheBudgets.js",
@@ -297,12 +298,12 @@
     "@emotion/utils": "^1.4.2",
     "@floating-ui/react": "^0.27.20",
     "@gmod/bgzf-filehandle": "^6.7.0",
-    "@gmod/range-cache-filehandle": "^1.4.0",
+    "@gmod/range-cache-filehandle": "^1.5.0",
     "@gmod/shared-read-cache": "^1.7.2",
     "@gmod/vcf": "^7.2.0",
     "@jbrowse/jexl": "^6.0.0",
-    "@jbrowse/mobx-state-tree": "^6.6.1",
-    "@jbrowse/quick-lru": "^7.3.5",
+    "@jbrowse/mobx-state-tree": "^6.7.0",
+    "@jbrowse/quick-lru": "^8.0.0",
     "@leeoniya/ufuzzy": "^1.0.19",
     "@mui/icons-material": "^9.4.0",
     "@mui/material": "^9.4.0",
@@ -311,14 +312,14 @@
     "canvas-sequencer-ts": "^3.1.3",
     "compare-versions": "^6.1.1",
     "dompurify": "^3.4.16",
-    "generic-filehandle2": "^2.4.0",
+    "generic-filehandle2": "^2.5.0",
     "idb": "^8.0.3",
     "mobx": "^7.0.5",
     "mobx-react": "^10.0.2",
     "rxjs": "^7.8.2",
-    "source-map-js": "^1.2.1",
-    "@jbrowse/add-track-core": "^5.0.0-beta.10",
-    "@jbrowse/render-core": "^5.0.0-beta.10"
+    "source-map-js": "^1.2.2",
+    "@jbrowse/add-track-core": "^5.0.0-beta.11",
+    "@jbrowse/render-core": "^5.0.0-beta.11"
   },
   "peerDependencies": {
     "react": ">=19.0.0",