@jbrowse/core 5.0.0-beta.11 → 5.0.0-beta.14

package/esm/util/windowStep.js

@@ -0,0 +1,153 @@
+// The `window` step, Vega-Lite's window transform over a group's rows in
+// start order. Imported by relative path only.
+import { aggregateFieldName } from './aggregateFieldName.js';
+import { numberReaderOf, readerOf, withColumns } from './featureTable.js';
+import { isPlainFieldRef } from './fieldReader.js';
+import { groupRows, isWeighted, sortByStart, stepNumberReader, stepReader, } from './stepTables.js';
+export const DEFAULT_WINDOW_FRAME = [-10, 10];
+// The rows grouped, groups in the order first met and so sections outermost,
+// each group's rows in start order, an unreadable start sorting last; and
+// where each group's rows begin.
+function windowOrder(table, groupOf, groups) {
+    const n = table.length;
+    const groupStart = new Uint32Array(groups + 1);
+    for (let i = 0; i < n; i++) {
+        groupStart[groupOf[i] + 1]++;
+    }
+    for (let g = 0; g < groups; g++) {
+        groupStart[g + 1] += groupStart[g];
+    }
+    const order = new Uint32Array(n);
+    const next = groupStart.slice(0, groups);
+    for (let i = 0; i < n; i++) {
+        order[next[groupOf[i]]++] = i;
+    }
+    const readStart = numberReaderOf(table.column('start'));
+    const starts = new Float64Array(n);
+    for (let i = 0; i < n; i++) {
+        const s = readStart(i);
+        starts[i] = Number.isNaN(s) ? Infinity : s;
+    }
+    for (let g = 0; g < groups; g++) {
+        const rows = order.subarray(groupStart[g], groupStart[g + 1]);
+        let sorted = true;
+        for (let k = 1; k < rows.length && sorted; k++) {
+            sorted = starts[rows[k]] >= starts[rows[k - 1]];
+        }
+        if (!sorted) {
+            sortByStart(rows, starts);
+        }
+    }
+    return { order, groupStart };
+}
+// The rows `[first, last]` of a group of `m` around its row `j`, empty where
+// `first` passes `last`.
+function frameAt([before, after], j, m) {
+    return [
+        before === null ? 0 : Math.max(0, j + before),
+        after === null ? m - 1 : Math.min(m - 1, j + after),
+    ];
+}
+// A sum, count or mean over each frame from running totals, which answer an
+// empty frame exactly 0, since the totals hold one value across it.
+function totalsOver(op, values, weights, frame, lo, hi, out) {
+    const m = hi - lo;
+    const weightTotal = new Float64Array(m + 1);
+    const sumTotal = new Float64Array(m + 1);
+    for (let j = 0; j < m; j++) {
+        const v = values[lo + j];
+        const w = weights[lo + j];
+        const counted = Number.isFinite(v) && Number.isFinite(w);
+        weightTotal[j + 1] = weightTotal[j] + (counted ? w : 0);
+        sumTotal[j + 1] = sumTotal[j] + (counted ? v * w : 0);
+    }
+    for (let j = 0; j < m; j++) {
+        const [a, b] = frameAt(frame, j, m);
+        const weight = a > b ? 0 : weightTotal[b + 1] - weightTotal[a];
+        const sum = a > b ? 0 : sumTotal[b + 1] - sumTotal[a];
+        out[lo + j] =
+            op === 'count'
+                ? weight
+                : op === 'sum'
+                    ? sum
+                    : weight === 0
+                        ? Number.NaN
+                        : sum / weight;
+    }
+}
+// A min or max over each frame through a monotonic queue of row positions,
+// which holds because neither end of a frame ever moves back.
+function extremeOver(op, values, frame, lo, hi, out) {
+    const m = hi - lo;
+    const queue = new Uint32Array(m);
+    let head = 0;
+    let tail = 0;
+    let added = 0;
+    for (let j = 0; j < m; j++) {
+        const [a, b] = frameAt(frame, j, m);
+        for (; added <= b; added++) {
+            const v = values[lo + added];
+            if (!Number.isFinite(v)) {
+                continue;
+            }
+            while (tail > head &&
+                (op === 'min'
+                    ? values[lo + queue[tail - 1]] >= v
+                    : values[lo + queue[tail - 1]] <= v)) {
+                tail--;
+            }
+            queue[tail++] = added;
+        }
+        while (head < tail && queue[head] < a) {
+            head++;
+        }
+        out[lo + j] = head < tail ? values[lo + queue[head]] : Number.NaN;
+    }
+}
+function windowColumn(table, agg, order, groupStart, frame) {
+    const { op, field, weight } = agg;
+    if (op !== 'count' && field === undefined) {
+        throw new Error(`a window ${op} needs a field`);
+    }
+    const n = order.length;
+    const readValue = field === undefined || op === 'count'
+        ? () => 0
+        : stepNumberReader(table, field, 'a window');
+    const readWeight = weight !== undefined && isWeighted(agg)
+        ? stepNumberReader(table, weight, 'a window')
+        : () => 1;
+    const values = new Float64Array(n);
+    const weights = new Float64Array(n);
+    for (let k = 0; k < n; k++) {
+        values[k] = readValue(order[k]);
+        weights[k] = readWeight(order[k]);
+    }
+    const out = new Float64Array(n);
+    for (let g = 0; g + 1 < groupStart.length; g++) {
+        const lo = groupStart[g];
+        const hi = groupStart[g + 1];
+        if (op === 'min' || op === 'max') {
+            extremeOver(op, values, frame, lo, hi, out);
+        }
+        else {
+            totalsOver(op, values, weights, frame, lo, hi, out);
+        }
+    }
+    return op === 'count' || op === 'sum'
+        ? { kind: 'number', values: out, at: undefined }
+        : { kind: 'number', values: out, at: undefined, nanIsAbsent: true };
+}
+export function windowStep({ table, bounds }, step) {
+    const { groupby = [], ops, frame = DEFAULT_WINDOW_FRAME } = step;
+    const keyed = groupby.some(field => !isPlainFieldRef(field));
+    const reads = groupby.map(field => keyed
+        ? stepReader(table, field, 'a window')
+        : readerOf(table.column(field)));
+    const { groupOf, firstRow } = groupRows(table.length, bounds, reads, !keyed);
+    const { order, groupStart } = windowOrder(table, groupOf, firstRow.length);
+    const written = new Map(ops.map(agg => [
+        aggregateFieldName(agg),
+        windowColumn(table, agg, order, groupStart, frame),
+    ]));
+    return { table: withColumns(table, written, order), bounds };
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "5.0.0-beta.11",
+  "version": "5.0.0-beta.14",
   "type": "module",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
@@ -33,6 +33,7 @@
     "./PluginManager": "./esm/PluginManager.js",
     "./ReExports/list": "./esm/ReExports/list.js",
     "./ReExports/modules": "./esm/ReExports/modules.js",
+    "./ReExports/names": "./esm/ReExports/names.js",
     "./ReExports/registry": "./esm/ReExports/registry.js",
     "./ReExports/uiStub": "./esm/ReExports/uiStub.js",
     "./ReExports/workerModules": "./esm/ReExports/workerModules.js",
@@ -42,6 +43,8 @@
     "./assemblyManager": "./esm/assemblyManager/index.js",
     "./assemblyManager/assembly": "./esm/assemblyManager/assembly.js",
     "./assemblyManager/assemblyConfigSchema": "./esm/assemblyManager/assemblyConfigSchema.js",
+    "./assemblyManager/expandAssemblyConfigShorthand": "./esm/assemblyManager/expandAssemblyConfigShorthand.js",
+    "./assemblyManager/refNameMaps": "./esm/assemblyManager/refNameMaps.js",
     "./checkPlugins": "./esm/checkPlugins.js",
     "./configuration": "./esm/configuration/index.js",
     "./configuration/configurationSchema": "./esm/configuration/configurationSchema.js",
@@ -97,6 +100,7 @@
     "./ui/CascadingMenuButton": "./esm/ui/CascadingMenuButton.js",
     "./ui/ColorPicker": "./esm/ui/ColorPicker.js",
     "./ui/ConfirmDialog": "./esm/ui/ConfirmDialog.js",
+    "./ui/ContextMenu": "./esm/ui/ContextMenu.js",
     "./ui/DataGridFlexContainer": "./esm/ui/DataGridFlexContainer.js",
     "./ui/Dialog": "./esm/ui/Dialog.js",
     "./ui/DraggableDialog": "./esm/ui/DraggableDialog.js",
@@ -130,6 +134,7 @@
     "./ui/Snackbar": "./esm/ui/Snackbar.js",
     "./ui/SnackbarModel": "./esm/ui/SnackbarModel.js",
     "./ui/StackTraceButton": "./esm/ui/StackTraceButton.js",
+    "./ui/SubmitDialog": "./esm/ui/SubmitDialog.js",
     "./ui/SvgColorLegend": "./esm/ui/SvgColorLegend.js",
     "./ui/VerticalScrollbar": "./esm/ui/VerticalScrollbar.js",
     "./ui/buildExtraTrackMenuItems": "./esm/ui/buildExtraTrackMenuItems.js",
@@ -144,6 +149,7 @@
     "./ui/multiTrackMenuItems": "./esm/ui/multiTrackMenuItems.js",
     "./ui/palette": "./esm/ui/palette.js",
     "./ui/persistentScrollbarStyle": "./esm/ui/persistentScrollbarStyle.js",
+    "./ui/rampKey": "./esm/ui/rampKey.js",
     "./ui/scrollZoomLabels": "./esm/ui/scrollZoomLabels.js",
     "./ui/showSubMenu": "./esm/ui/showSubMenu.js",
     "./ui/styleTheme": "./esm/ui/styleTheme.js",
@@ -161,6 +167,7 @@
     "./util/adapterMetadata": "./esm/util/adapterMetadata.js",
     "./util/addRelativeUris": "./esm/util/addRelativeUris.js",
     "./util/aggregateFieldName": "./esm/util/aggregateFieldName.js",
+    "./util/alignedBytes": "./esm/util/alignedBytes.js",
     "./util/analytics": "./esm/util/analytics.js",
     "./util/animationAllowed": "./esm/util/animationAllowed.js",
     "./util/assemblyConfigUtils": "./esm/util/assemblyConfigUtils.js",
@@ -217,6 +224,7 @@
     "./util/io/RemoteFileWithRangeCache": "./esm/util/io/RemoteFileWithRangeCache.js",
     "./util/isDataCurrent": "./esm/util/isDataCurrent.js",
     "./util/isTextEntryFocused": "./esm/util/isTextEntryFocused.js",
+    "./util/isoformRank": "./esm/util/isoformRank.js",
     "./util/jexl": "./esm/util/jexl.js",
     "./util/jexlFilters": "./esm/util/jexlFilters.js",
     "./util/jexlStrings": "./esm/util/jexlStrings.js",
@@ -238,9 +246,11 @@
     "./util/numericUtils": "./esm/util/numericUtils.js",
     "./util/offscreenCanvasPonyfill": "./esm/util/offscreenCanvasPonyfill.js",
     "./util/openViews": "./esm/util/openViews.js",
+    "./util/originCut": "./esm/util/originCut.js",
     "./util/paintLayer": "./esm/util/paintLayer.js",
     "./util/parseLineByLine": "./esm/util/parseLineByLine.js",
     "./util/preloadComponent": "./esm/util/preloadComponent.js",
+    "./util/pressOwner": "./esm/util/pressOwner.js",
     "./util/progress": "./esm/util/progress.js",
     "./util/quantileExtent": "./esm/util/quantileExtent.js",
     "./util/range": "./esm/util/range.js",
@@ -257,6 +267,7 @@
     "./util/simpleFeature": "./esm/util/simpleFeature.js",
     "./util/starFusion": "./esm/util/starFusion.js",
     "./util/stats": "./esm/util/stats.js",
+    "./util/stepOutputs": "./esm/util/stepOutputs.js",
     "./util/svAlt": "./esm/util/svAlt.js",
     "./util/svgColorProps": "./esm/util/svgColorProps.js",
     "./util/systemColorScheme": "./esm/util/systemColorScheme.js",
@@ -297,29 +308,29 @@
     "@emotion/serialize": "^1.3.3",
     "@emotion/utils": "^1.4.2",
     "@floating-ui/react": "^0.27.20",
-    "@gmod/bgzf-filehandle": "^6.7.0",
-    "@gmod/range-cache-filehandle": "^1.5.0",
-    "@gmod/shared-read-cache": "^1.7.2",
-    "@gmod/vcf": "^7.2.0",
+    "@gmod/bgzf-filehandle": "^6.8.0",
+    "@gmod/range-cache-filehandle": "^1.5.2",
+    "@gmod/shared-read-cache": "^2.1.0",
+    "@gmod/vcf": "^7.4.0",
     "@jbrowse/jexl": "^6.0.0",
-    "@jbrowse/mobx-state-tree": "^6.7.0",
+    "@jbrowse/mobx-state-tree": "^6.9.0",
     "@jbrowse/quick-lru": "^8.0.0",
     "@leeoniya/ufuzzy": "^1.0.19",
-    "@mui/icons-material": "^9.4.0",
-    "@mui/material": "^9.4.0",
-    "@mui/system": "^9.4.0",
-    "@mui/x-data-grid": "^9.14.0",
+    "@mui/icons-material": "^9.5.0",
+    "@mui/material": "^9.5.0",
+    "@mui/system": "^9.5.0",
+    "@mui/x-data-grid": "^9.15.0",
     "canvas-sequencer-ts": "^3.1.3",
     "compare-versions": "^6.1.1",
-    "dompurify": "^3.4.16",
-    "generic-filehandle2": "^2.5.0",
-    "idb": "^8.0.3",
-    "mobx": "^7.0.5",
+    "dompurify": "^3.4.17",
+    "generic-filehandle2": "^2.5.1",
+    "idb": "^8.0.4",
+    "mobx": "^7.0.6",
     "mobx-react": "^10.0.2",
     "rxjs": "^7.8.2",
     "source-map-js": "^1.2.2",
-    "@jbrowse/add-track-core": "^5.0.0-beta.11",
-    "@jbrowse/render-core": "^5.0.0-beta.11"
+    "@jbrowse/add-track-core": "^5.0.0-beta.14",
+    "@jbrowse/render-core": "^5.0.0-beta.14"
   },
   "peerDependencies": {
     "react": ">=19.0.0",

package/esm/data_adapters/BaseAdapter/featureDensity.d.ts

@@ -1,40 +0,0 @@
-/**
- * A density source's intervals over one region, the payload of the density
- * tier that stands in for the features a gated fetch refused: features per bin
- * for a `make-density` sidecar, whatever the bigWig measures otherwise, each
- * value a level over its span so a zoomed read means the same thing. Absolute
- * genomic coordinates.
- */
-export interface FeatureDensity {
-    starts: Uint32Array;
-    ends: Uint32Array;
-    scores: Float32Array;
-}
-/**
- * The slot a feature adapter spreads to take a density sidecar — a
- * quantitative sub-adapter (typically a BigWig of feature starts per bin) the
- * display reads at the view's bp/px in place of features the region-too-large
- * gate refused. Mirrors MAF's `summaryAdapter`: on the adapter, so the tier
- * names the file it summarizes.
- */
-export declare const densityAdapterConfigSchemaFields: {
-    /**
-     * #slot
-     */
-    readonly densityAdapter: {
-        readonly type: 'maybeFrozen';
-        readonly description: 'optional quantitative sub-adapter (e.g. a BigWigAdapter over a features-per-bin bigWig) drawn as a density band where the region is too large to fetch features; leave it unset to disable';
-    };
-};
-/**
- * Whether the `densityAdapter` slot holds something a sub-adapter can be built
- * from. Beside the slot because both ends of the tier ask it and they have to
- * agree: the display, deciding the band stands in, and `getFeatureDensity`,
- * resolving the sidecar. They disagreed — the display took any object, the
- * adapter wanted a type — so the shorthand every location slot accepts
- * (`{ uri }`) turned the band on for a read that answered `undefined`, which
- * commits nothing, and the phase then waited on bins no read would ever bring.
- */
-export declare function isSubAdapterConfig(value: unknown): value is Record<string, unknown> & {
-    type: string;
-};

package/esm/data_adapters/BaseAdapter/featureDensity.js

@@ -1,31 +0,0 @@
-/**
- * The slot a feature adapter spreads to take a density sidecar — a
- * quantitative sub-adapter (typically a BigWig of feature starts per bin) the
- * display reads at the view's bp/px in place of features the region-too-large
- * gate refused. Mirrors MAF's `summaryAdapter`: on the adapter, so the tier
- * names the file it summarizes.
- */
-export const densityAdapterConfigSchemaFields = {
-    /**
-     * #slot
-     */
-    densityAdapter: {
-        type: 'maybeFrozen',
-        description: 'optional quantitative sub-adapter (e.g. a BigWigAdapter over a features-per-bin bigWig) drawn as a density band where the region is too large to fetch features; leave it unset to disable',
-    },
-};
-/**
- * Whether the `densityAdapter` slot holds something a sub-adapter can be built
- * from. Beside the slot because both ends of the tier ask it and they have to
- * agree: the display, deciding the band stands in, and `getFeatureDensity`,
- * resolving the sidecar. They disagreed — the display took any object, the
- * adapter wanted a type — so the shorthand every location slot accepts
- * (`{ uri }`) turned the band on for a read that answered `undefined`, which
- * commits nothing, and the phase then waited on bins no read would ever bring.
- */
-export function isSubAdapterConfig(value) {
-    return (typeof value === 'object' &&
-        value !== null &&
-        'type' in value &&
-        typeof value.type === 'string');
-}

package/esm/rpc/methods/CoreGetFeatureDensity.d.ts

@@ -1,11 +0,0 @@
-import RpcMethodTypeWithRenameRegions from '../../pluggableElementTypes/RpcMethodTypeWithRenameRegions.ts';
-import type { RpcExecuteArgs } from '../RpcRegistry.ts';
-/**
- * The density tier's read: features per bin at the view's bp/px for regions the
- * region-too-large gate refused. Answers `undefined` for an adapter with no
- * density source, and the display keeps the banner.
- */
-export default class CoreGetFeatureDensity extends RpcMethodTypeWithRenameRegions<'CoreGetFeatureDensity'> {
-    name: 'CoreGetFeatureDensity';
-    execute(args: RpcExecuteArgs<'CoreGetFeatureDensity'>): Promise<import("../../data_adapters/BaseAdapter/featureDensity.ts").FeatureDensity[] | undefined>;
-}

package/esm/rpc/methods/CoreGetFeatureDensity.js

@@ -1,22 +0,0 @@
-import { isFeatureAdapter } from '../../data_adapters/BaseAdapter/index.js';
-import { getAdapter } from '../../data_adapters/dataAdapterCache.js';
-import RpcMethodTypeWithRenameRegions from '../../pluggableElementTypes/RpcMethodTypeWithRenameRegions.js';
-/**
- * The density tier's read: features per bin at the view's bp/px for regions the
- * region-too-large gate refused. Answers `undefined` for an adapter with no
- * density source, and the display keeps the banner.
- */
-export default class CoreGetFeatureDensity extends RpcMethodTypeWithRenameRegions {
-    name = 'CoreGetFeatureDensity';
-    async execute(args) {
-        const { adapterConfig, sessionId, regions, bpPerPx, signal } = args;
-        const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, adapterConfig, args.sequenceAdapter);
-        return isFeatureAdapter(dataAdapter)
-            ? dataAdapter.getFeatureDensity(regions, {
-                bpPerPx,
-                signal,
-                statusCallback: args.statusCallback,
-            })
-            : undefined;
-    }
-}

package/esm/rpc/methods/CoreLoadAdapterCode.d.ts

@@ -1,13 +0,0 @@
-import RpcMethodType from '../../pluggableElementTypes/RpcMethodType.ts';
-import type { RpcExecuteArgs } from '../RpcRegistry.ts';
-/**
- * Load these adapter types' code in the worker a track is about to use. An
- * adapter's class arrives by dynamic import on the track's first request
- * otherwise, and that download waits for the view to lay out and the assembly
- * to load.
- */
-export default class CoreLoadAdapterCode extends RpcMethodType<'CoreLoadAdapterCode'> {
-    name: 'CoreLoadAdapterCode';
-    execute({ adapterTypes }: RpcExecuteArgs<'CoreLoadAdapterCode'>): Promise<void>;
-    serializeArguments(args: Record<string, unknown>): Promise<Record<string, unknown>>;
-}

package/esm/rpc/methods/CoreLoadAdapterCode.js

@@ -1,16 +0,0 @@
-import RpcMethodType from '../../pluggableElementTypes/RpcMethodType.js';
-/**
- * Load these adapter types' code in the worker a track is about to use. An
- * adapter's class arrives by dynamic import on the track's first request
- * otherwise, and that download waits for the view to lay out and the assembly
- * to load.
- */
-export default class CoreLoadAdapterCode extends RpcMethodType {
-    name = 'CoreLoadAdapterCode';
-    async execute({ adapterTypes }) {
-        await Promise.all(adapterTypes.map(type => this.pluginManager.getAdapterType(type).getAdapterClass()));
-    }
-    async serializeArguments(args) {
-        return args;
-    }
-}