@jbrowse/plugin-linear-genome-view 5.0.0-beta.19 → 5.0.0-beta.20

package/esm/LinearGenomeView/rExport/rScript.js

@@ -1,36 +1,43 @@
 import { expandAssemblySequence, expandSidecarShorthand, refNameAliasAdapterType, } from '@jbrowse/core/assemblyManager/expandAssemblyConfigShorthand';
 import { resolveUri } from '@jbrowse/core/util';
+const VCF_ADAPTERS = {
+    VcfTabixAdapter: { slot: 'vcfGzLocation', ext: /\.vcf\.gz$/, index: '.tbi' },
+    VcfAdapter: { slot: 'vcfLocation', ext: /\.vcf$/ },
+};
 /**
  * Each display ggjbrowse reads, by the reader that reads it, and the adapters
- * it opens (the slot holding the file and the extension the reader knows it
- * by).
+ * it opens: the slot holding the file, the extension the reader knows it by,
+ * and the suffix of the index the reader looks for beside it.
  */
 export const READERS = {
     LinearBasicDisplay: {
         call: 'jbrowse_features',
         adapters: {
-            Gff3TabixAdapter: { slot: 'gffGzLocation', ext: /\.gff3?\.gz$/ },
+            Gff3TabixAdapter: {
+                slot: 'gffGzLocation',
+                ext: /\.gff3?\.gz$/,
+                index: '.tbi',
+            },
             Gff3Adapter: { slot: 'gffLocation', ext: /\.gff3?$/ },
-            GtfTabixAdapter: { slot: 'gtfGzLocation', ext: /\.gtf\.gz$/ },
+            GtfTabixAdapter: {
+                slot: 'gtfGzLocation',
+                ext: /\.gtf\.gz$/,
+                index: '.tbi',
+            },
             GtfAdapter: { slot: 'gtfLocation', ext: /\.gtf$/ },
-            BedTabixAdapter: { slot: 'bedGzLocation', ext: /\.bed\.gz$/ },
+            BedTabixAdapter: {
+                slot: 'bedGzLocation',
+                ext: /\.bed\.gz$/,
+                index: '.tbi',
+            },
             BedAdapter: { slot: 'bedLocation', ext: /\.bed$/ },
             BigBedAdapter: { slot: 'bigBedLocation', ext: /\.(bb|bigbed)$/ },
         },
     },
     LinearVariantDisplay: {
-        call: 'jbrowse_features',
-        adapters: {
-            VcfTabixAdapter: { slot: 'vcfGzLocation', ext: /\.vcf\.gz$/ },
-            VcfAdapter: { slot: 'vcfLocation', ext: /\.vcf$/ },
-        },
-    },
-    LinearMultiSampleVariantDisplay: {
         call: 'jbrowse_variants',
-        adapters: {
-            VcfTabixAdapter: { slot: 'vcfGzLocation', ext: /\.vcf\.gz$/ },
-            VcfAdapter: { slot: 'vcfLocation', ext: /\.vcf$/ },
-        },
+        recordsOnlyCall: 'jbrowse_features',
+        adapters: VCF_ADAPTERS,
     },
     LinearWiggleDisplay: {
         call: 'jbrowse_wiggle',
@@ -42,14 +49,17 @@ export const READERS = {
     LinearAlignmentsDisplay: {
         call: 'jbrowse_alignments',
         adapters: {
-            BamAdapter: { slot: 'bamLocation', ext: /(?<!\.cram)$/ },
-            CramAdapter: { slot: 'cramLocation', ext: /\.cram$/ },
+            BamAdapter: { slot: 'bamLocation', ext: /(?<!\.cram)$/, index: '.bai' },
+            CramAdapter: { slot: 'cramLocation', ext: /\.cram$/, index: '.crai' },
         },
     },
 };
-/** The ggjbrowse release whose readers and `jbrowse_stack` the script calls. */
-export const GGJBROWSE_VERSION = '0.10.0';
-const INSTALL = 'remotes::install_github("GMOD/ggjbrowse")';
+/**
+ * The ggjbrowse release the script is tested against: its floor, and the tag
+ * its install line pins. The R export workflow installs this tag on a push.
+ */
+export const GGJBROWSE_VERSION = '0.11.0';
+const INSTALL = `remotes::install_github("GMOD/ggjbrowse@v${GGJBROWSE_VERSION}")`;
 function isSet(value) {
     return !(value === undefined ||
         value === null ||
@@ -189,20 +199,10 @@ function fileArgument(adapters, adapter) {
             skipped: 'it reads a file opened in the browser, which R cannot reach',
         };
     }
-    const file = known.slot
-        ? (locationPath(adapter[known.slot]) ??
-            (typeof adapter.uri === 'string' ? adapter.uri : undefined))
-        : undefined;
+    const file = known.slot ? locationPath(adapter[known.slot]) : undefined;
     const index = adapter.index;
     const indexPath = locationPath(index?.location) ?? locationPath(adapter.craiLocation);
-    const besideSuffix = type === 'CramAdapter' ? '.crai' : type === 'BamAdapter' ? '.bai' : '.tbi';
-    const plainSlots = new Set([
-        'type',
-        'uri',
-        'index',
-        'craiLocation',
-        known.slot,
-    ]);
+    const plainSlots = new Set(['type', 'index', 'craiLocation', known.slot]);
     const plain = file !== undefined &&
         known.ext?.test(file.replace(/\?.*$/, '').toLowerCase()) &&
         Object.keys(located).every(k => plainSlots.has(k)) &&
@@ -211,7 +211,7 @@ function fileArgument(adapters, adapter) {
     return plain
         ? {
             file: rStr(file),
-            index: indexPath && indexPath !== `${file}${besideSuffix}`
+            index: indexPath && indexPath !== `${file}${known.index}`
                 ? indexPath
                 : undefined,
             uris,
@@ -345,6 +345,44 @@ function stackArgument(title, name) {
         : `${isIdentifier(title) ? title : rStr(title)} = ${name}`;
 }
 /** What the figure cannot show of a track whose settings ggjbrowse reads. */
+// The variant display's record settings, under `records`, as the feature
+// track's top-level spelling `jbrowse_features` reads; the genotype rows'
+// settings stay behind.
+const RECORD_SETTINGS = [
+    'displayMode',
+    'mark',
+    'labels',
+    'facet',
+    'maxFeatureScreenDensity',
+];
+const SHARED_SETTINGS = [
+    'filter',
+    'encoding',
+    'legend',
+    'heightMode',
+    'growMaxHeight',
+];
+function isRecord(x) {
+    return typeof x === 'object' && x !== null && !Array.isArray(x);
+}
+function setEntries(source, keys) {
+    return keys.flatMap(k => {
+        const entry = [k, source[k]];
+        return entry[1] === undefined ? [] : [entry];
+    });
+}
+function recordsAsFeatureDisplay(display) {
+    const records = isRecord(display.records) ? display.records : {};
+    const tooltip = {
+        ...(isRecord(display.tooltip) ? display.tooltip : {}),
+        ...(isRecord(records.tooltip) ? records.tooltip : {}),
+    };
+    return Object.fromEntries([
+        ...setEntries(display, SHARED_SETTINGS),
+        ...setEntries(records, RECORD_SETTINGS),
+        ...setEntries({ tooltip }, Object.keys(tooltip).length > 0 ? ['tooltip'] : []),
+    ]);
+}
 function settingNotes(track) {
     const { color } = track.display.encoding ?? {};
     return [
@@ -371,46 +409,50 @@ export function exportTracksToR({ tracks, regions, assembly: assemblySnapshot, b
     const assemblyValue = assembly && 'value' in assembly ? assembly.value : undefined;
     const loci = regions.map(r => locusOf(r.refName, r.start, r.end));
     const totalBp = regions.reduce((sum, r) => sum + r.end - r.start, 0);
-    const viewPx = bpPerPx ? Math.round(totalBp / bpPerPx) : undefined;
-    const widthReaders = [];
+    const viewPx = Math.round(totalBp / bpPerPx);
     const names = trackNames(tracks);
     const reads = [];
     const drawn = [];
     const bands = [];
     let alignments;
     tracks.forEach((track, i) => {
-        const reader = READERS[track.displayType];
-        if (!reader) {
+        const known = READERS[track.displayType];
+        if (!known) {
             notes.push(`${track.trackName}: ${track.displayType} has no R reader in ggjbrowse yet`);
             return;
         }
+        const recordsCall = track.recordsOnly ? known.recordsOnlyCall : undefined;
+        const asRecords = recordsCall !== undefined;
+        const reader = {
+            adapters: known.adapters,
+            call: recordsCall ?? known.call,
+        };
         const source = fileArgument(reader.adapters, track.adapter);
         if ('skipped' in source) {
             notes.push(`${track.trackName}: ${source.skipped}`);
             return;
         }
         const { heightMode, height } = track;
+        const written = asRecords
+            ? recordsAsFeatureDisplay(track.display)
+            : track.display;
         const display = reader.call === 'jbrowse_features'
             ? {
-                ...track.display,
+                ...written,
                 ...(heightMode === undefined ? {} : { heightMode }),
                 ...(height === undefined ? {} : { height }),
             }
-            : track.display;
-        const width = viewPx !== undefined;
+            : written;
         const geneTrack = track.displayType === 'LinearBasicDisplay';
         const args = [
             ...(Object.keys(display).length ? [`display = ${rValue(display)}`] : []),
-            ...(width ? ['width = width'] : []),
+            'width = width',
             ...(assemblyValue ? ['assembly = assembly'] : []),
             ...(geneTrack && colorByFrame ? ['color_by_cds = TRUE'] : []),
             ...(geneTrack && !showAminoAcids ? ['amino_acids = FALSE'] : []),
             ...(source.index ? [`index = ${rStr(source.index)}`] : []),
         ];
         const name = names[i];
-        if (width) {
-            widthReaders.push(name);
-        }
         reads.push([
             `# ${track.trackName}`,
             `${name} <- ${reader.call}(${source.file},`,
@@ -466,14 +508,10 @@ export function exportTracksToR({ tracks, regions, assembly: assemblySnapshot, b
                 `assembly <- ${assemblyValue}`,
             ]
             : []),
-        ...(widthReaders.length
-            ? [
-                "# The view's pixels across its regions. A smaller number lays the tracks",
-                '# out as a narrower browser window would, for a narrower figure with',
-                '# fewer labels at the same size.',
-                `width <- ${viewPx}`,
-            ]
-            : []),
+        "# The view's pixels across its regions. A smaller number lays the tracks",
+        '# out as a narrower browser window would, for a narrower figure with',
+        '# fewer labels at the same size.',
+        `width <- ${viewPx}`,
         '',
         reads.join('\n\n'),
         '',

package/esm/LinearGenomeView/showRegionsWithUndo.js

@@ -42,9 +42,11 @@ export function showRegionsWithUndo({ view, regions, message, alsoUndo, }) {
     getNotificationSink(view).notify(message, 'info', {
         name: 'Undo',
         onClick: () => {
-            view.setDisplayedRegions(previous.displayedRegions);
-            view.setWindow(previous.windowWidthBp, previous.windowStartBp);
-            alsoUndo?.();
+            transaction(() => {
+                view.setDisplayedRegions(previous.displayedRegions);
+                view.setWindow(previous.windowWidthBp, previous.windowStartBp);
+                alsoUndo?.();
+            });
         },
     });
 }

package/esm/LinearGenomeView/svgcomponents/SVGHighlights.d.ts

@@ -1,5 +1,7 @@
+import type { BandGap } from '../components/SVGHighlightBand.tsx';
 import type { LinearGenomeViewModel } from '../index.ts';
-export default function SVGHighlights({ model, height, }: {
+export default function SVGHighlights({ model, height, gaps, }: {
     model: LinearGenomeViewModel;
     height: number;
+    gaps: BandGap[];
 }): (import("react").JSX.Element | null)[] | null;

package/esm/LinearGenomeView/svgcomponents/SVGHighlights.js

@@ -14,13 +14,13 @@ import { getHighlightColor, highlightKey } from '../components/util.js';
 // bands across track bodies that were still drawn where the snapshot left them.
 // The file export renders the whole document in one synchronous pass, so it
 // never needed the subscription either.
-export default function SVGHighlights({ model, height, }) {
+export default function SVGHighlights({ model, height, gaps, }) {
     const theme = useStyleTheme();
     const session = getSession(model);
     return session.highlightsVisible
         ? model.highlights.map((h, idx) => {
             const coords = model.getHighlightCoords(h);
-            return coords ? (_jsx(SVGHighlightBand, { coords: coords, height: height, color: getHighlightColor(h, theme).toRgbString(), label: session.highlightLabelsVisible ? h.label : undefined, labelColor: theme.palette.text.primary }, highlightKey(h, idx))) : null;
+            return coords ? (_jsx(SVGHighlightBand, { coords: coords, height: height, gaps: gaps, color: getHighlightColor(h, theme).toRgbString(), label: session.highlightLabelsVisible ? h.label : undefined, labelColor: theme.palette.text.primary }, highlightKey(h, idx))) : null;
         })
         : null;
 }

package/esm/LinearGenomeView/svgcomponents/SVGHighlightsOverlay.d.ts

@@ -1,5 +1,7 @@
+import type { BandGap } from '../components/SVGHighlightBand.tsx';
 import type { LinearGenomeViewModel } from '../index.ts';
-export default function SVGHighlightsOverlay({ model, tracksHeight, }: {
+export default function SVGHighlightsOverlay({ model, tracksHeight, gaps, }: {
     model: LinearGenomeViewModel;
     tracksHeight: number;
+    gaps: BandGap[];
 }): import("react").JSX.Element;

package/esm/LinearGenomeView/svgcomponents/SVGHighlightsOverlay.js

@@ -7,7 +7,7 @@ import SVGHighlights from './SVGHighlights.js';
 // The highlight layer over one view's tracks area: the view's highlights plus
 // whatever plugins contribute, clipped to the view width. Callers translate
 // this to the top-left of the tracks area.
-export default function SVGHighlightsOverlay({ model, tracksHeight, }) {
+export default function SVGHighlightsOverlay({ model, tracksHeight, gaps, }) {
     const { pluginManager } = getEnv(model);
-    return (_jsxs(SvgClipRect, { id: `highlight-clip-${svgNodeId(model)}`, width: model.width, height: tracksHeight, children: [_jsx(SVGHighlights, { model: model, height: tracksHeight }), _jsx(PluggableElements, { pluginManager: pluginManager, name: "LinearGenomeView-HighlightSVGComponent", props: { model, height: tracksHeight } })] }));
+    return (_jsxs(SvgClipRect, { id: `highlight-clip-${svgNodeId(model)}`, width: model.width, height: tracksHeight, children: [_jsx(SVGHighlights, { model: model, height: tracksHeight, gaps: gaps }), _jsx(PluggableElements, { pluginManager: pluginManager, name: "LinearGenomeView-HighlightSVGComponent", props: { model, height: tracksHeight } })] }));
 }

package/esm/LinearGenomeView/svgcomponents/SVGView.js

@@ -2,6 +2,7 @@ import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-run
 import SVGGridlines from './SVGGridlines.js';
 import SVGHighlightsOverlay from './SVGHighlightsOverlay.js';
 import SVGTracks from './SVGTracks.js';
+import { labelOffset, trackBoxOffsets } from './util.js';
 // One LGV's worth of exported SVG: a caller-supplied header on top, then
 // optional gridlines, the track bodies, and the highlight layer over them.
 // Shared by all three exports that stack an LGV — the standalone one, and the
@@ -9,5 +10,18 @@ import SVGTracks from './SVGTracks.js';
 // drift. It did drift while the standalone export kept its own copy of these
 // four groups.
 export default function SVGView({ view, displayResults, header, fontSize, textHeight, trackLabels, trackLabelOffset, contentTop, tracksHeight, showGridlines, leftBuffer, }) {
-    return (_jsxs(_Fragment, { children: [_jsx("g", { transform: `translate(${trackLabelOffset})`, children: header }), showGridlines ? (_jsx("g", { transform: `translate(${trackLabelOffset} ${contentTop})`, children: _jsx(SVGGridlines, { model: view, height: tracksHeight }) })) : null, _jsx("g", { transform: `translate(0 ${contentTop})`, children: _jsx(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: view, displayResults: displayResults, trackLabelOffset: trackLabelOffset, leftBuffer: leftBuffer }) }), _jsx("g", { transform: `translate(${trackLabelOffset} ${contentTop})`, children: _jsx(SVGHighlightsOverlay, { model: view, tracksHeight: tracksHeight }) })] }));
+    const tracks = displayResults.map(r => r.track);
+    const offsets = trackBoxOffsets(tracks, trackLabels, textHeight);
+    const nonGenomicBands = tracks.flatMap((track, i) => {
+        const display = track.displays[0];
+        return display.drawsGenomicCoordinates === false
+            ? [
+                {
+                    top: offsets[i] + labelOffset(track, trackLabels, textHeight),
+                    height: display.height,
+                },
+            ]
+            : [];
+    });
+    return (_jsxs(_Fragment, { children: [_jsx("g", { transform: `translate(${trackLabelOffset})`, children: header }), showGridlines ? (_jsx("g", { transform: `translate(${trackLabelOffset} ${contentTop})`, children: _jsx(SVGGridlines, { model: view, height: tracksHeight }) })) : null, _jsx("g", { transform: `translate(0 ${contentTop})`, children: _jsx(SVGTracks, { textHeight: textHeight, trackLabels: trackLabels, fontSize: fontSize, model: view, displayResults: displayResults, trackLabelOffset: trackLabelOffset, leftBuffer: leftBuffer }) }), _jsx("g", { transform: `translate(${trackLabelOffset} ${contentTop})`, children: _jsx(SVGHighlightsOverlay, { model: view, tracksHeight: tracksHeight, gaps: nonGenomicBands }) })] }));
 }

package/esm/LinearGenomeView/svgcomponents/util.d.ts

@@ -17,6 +17,7 @@ export interface SvgDisplayResult {
         displays: ({
             height: number;
             regionTooLarge?: boolean;
+            drawsGenomicCoordinates?: boolean;
         } & SidebarDisplay)[];
     };
     result: ReactNode;

package/esm/LinearGenomeView/types.d.ts

@@ -39,3 +39,9 @@ export interface InitState {
     highlight?: (string | HighlightInput)[];
 }
 export type LinearGenomeViewLaunchProps = Partial<Omit<SnapshotIn<LinearGenomeViewStateModel>, keyof InitState | 'id' | 'type' | 'launch'>>;
+/**
+ * One LinearGenomeView panel inside another view (a breakpoint split view's
+ * stack, a synteny view's rows): the LGV's launch keys and props, less `nav`
+ * and `tracklist`, the header and the track selector a panel does not show.
+ */
+export type LinearGenomeViewPanelInit = Omit<InitState, 'nav' | 'tracklist'> & LinearGenomeViewLaunchProps;

package/esm/LinearGenomeView/types.js

@@ -1,2 +1 @@
 export {};
-// #endregion

package/esm/LinearGenomeView/util.js

@@ -1,4 +1,4 @@
-import { UnknownRefNameError, assembleLocStrings, getTickDisplayStr, measureText, parseBpString, parseLocString, } from '@jbrowse/core/util';
+import { UnknownRefNameError, assembleLocString, assembleLocStrings, getTickDisplayStr, measureText, parseBpString, parseLocString, } from '@jbrowse/core/util';
 import { bpOffsetInRegion } from '@jbrowse/core/util/Base1DUtils';
 import { chooseGridPitch } from '@jbrowse/core/util/chooseGridPitch';
 import { tickLabelsWorthDrawing } from '@jbrowse/core/util/tickLabels';
@@ -558,6 +558,10 @@ export function makeBlockTicks({ start, end, reversed = false, }, bpPerPx, inclu
  * navigating to a feature
  */
 export async function generateLocations({ regions, assemblyManager, assemblyName, grow, }) {
+    const backwards = regions.find(({ start, end }) => start !== undefined && end !== undefined && start > end);
+    if (backwards) {
+        throw new Error(`found start greater than end in ${assembleLocString(backwards)}`);
+    }
     return Promise.all(regions.map(async (region) => {
         const asmName = region.assemblyName || assemblyName;
         if (!asmName) {
@@ -609,14 +613,12 @@ export async function generateLocations({ regions, assemblyManager, assemblyName
  * Used by navToLocString
  */
 export function parseLocStrings(input, assemblyName, isValidRefName) {
-    const inputs = input
-        .split(/(\s+)/)
-        .map(f => f.trim())
-        .filter(f => !!f);
+    const inputs = input.split(/\s+/).filter(Boolean);
+    const isRef = (ref, asm) => isValidRefName(ref, asm ?? assemblyName);
     // first try interpreting as a whitespace-separated sequence of
     // multiple locstrings
     try {
-        return inputs.map(loc => parseLocString(loc, ref => isValidRefName(ref, assemblyName)));
+        return inputs.map(loc => parseLocString(loc, isRef));
     }
     catch (e) {
         // if this fails, try interpreting as a whitespace-separated refname,
@@ -629,9 +631,7 @@ export function parseLocStrings(input, assemblyName, isValidRefName) {
             inputs.length === 3 &&
             parseBpString(start) !== undefined &&
             parseBpString(end) !== undefined) {
-            return [
-                parseLocString(`${refName}:${start}..${end}`, ref => isValidRefName(ref, assemblyName)),
-            ];
+            return [parseLocString(`${refName}:${start}..${end}`, isRef)];
         }
         throw e;
     }

package/esm/MultiLevelRubberband/useRangeSelect.js

@@ -57,18 +57,20 @@ export function useRangeSelect(ref, model) {
         onCancel: handleClose,
     });
     function mouseDown(event) {
-        event.preventDefault();
-        event.stopPropagation();
-        // clear any leftover menu/selection so a fresh drag isn't blocked by a
-        // stale anchorPosition keeping mouseDragging false
-        setAnchorPosition(undefined);
-        // the guide is what the pointer was showing up to now, and mouseMove won't
-        // touch it during the drag — leaving it set keeps the selection span from
-        // ever rendering, since the guide wins that either/or
-        setGuideX(undefined);
-        const relativeX = getRelativeX(event, ref.current);
-        setStartX(relativeX);
-        setCurrentX(relativeX);
+        if (event.button === 0) {
+            event.preventDefault();
+            event.stopPropagation();
+            // clear any leftover menu/selection so a fresh drag isn't blocked by a
+            // stale anchorPosition keeping mouseDragging false
+            setAnchorPosition(undefined);
+            // the guide is what the pointer was showing up to now, and mouseMove
+            // won't touch it during the drag — leaving it set keeps the selection
+            // span from ever rendering, since the guide wins that either/or
+            setGuideX(undefined);
+            const relativeX = getRelativeX(event, ref.current);
+            setStartX(relativeX);
+            setCurrentX(relativeX);
+        }
     }
     function mouseMove(event) {
         // Don't update guideX while a menu is open — the guide is what the click

package/esm/TrackModifiers/index.d.ts

@@ -74,7 +74,10 @@ export declare function launchTrackInit(view: ModifierView & IAnyStateTreeNode,
  * after every other modifier, so a member write keeps the rest of the setting
  * whatever order the command line gives them in. A display replaces a color
  * or facet object whole, which is why these cannot ride in on the launch
- * snapshot.
+ * snapshot. A keyed object (`rows`, ADR-257) seeds only its field and the
+ * objects written whole that the writes reach, such as `rows.color`: seeded
+ * whole it would restate the arrangement a field write must drop, and
+ * unseeded a spec holding the patch would lose the field and the channel.
  */
 export declare function writeMembers(view: Pick<ModifierView, 'tracks' | 'showTrack'>, trackId: string, members: string[]): Record<string, unknown>;
 export {};

package/esm/TrackModifiers/index.js

@@ -1,4 +1,4 @@
-import { mergeConfSettings } from '@jbrowse/core/configuration';
+import { keyedWritesAt, mergeConfSettings, writesWholeAt, } from '@jbrowse/core/configuration';
 import { getEnv, getSession } from '@jbrowse/core/util';
 import { basePaintedAt } from '@jbrowse/core/util/Base1DUtils';
 import { predicatesOf, testsSomething, withFields, } from '@jbrowse/core/util/fieldPredicate';
@@ -181,12 +181,24 @@ export async function launchTrackInit(view, t) {
         session.notify(notes.join('; '), 'warning');
     }
 }
+// the named members of a keyed object as configured, undefined when it
+// states none of them
+function keyedSeed(member, names) {
+    const configured = isStateTreeNode(member)
+        ? getSnapshot(member)
+        : {};
+    const seed = Object.fromEntries(names.flatMap(name => configured[name] === undefined ? [] : [[name, configured[name]]]));
+    return Object.keys(seed).length > 0 ? seed : undefined;
+}
 /**
  * Write a track's `memberWrites` onto what its display in `view` already has,
  * after every other modifier, so a member write keeps the rest of the setting
  * whatever order the command line gives them in. A display replaces a color
  * or facet object whole, which is why these cannot ride in on the launch
- * snapshot.
+ * snapshot. A keyed object (`rows`, ADR-257) seeds only its field and the
+ * objects written whole that the writes reach, such as `rows.color`: seeded
+ * whole it would restate the arrangement a field write must drop, and
+ * unseeded a spec holding the patch would lose the field and the channel.
  */
 export function writeMembers(view, trackId, members) {
     if (members.length === 0) {
@@ -198,14 +210,21 @@ export function writeMembers(view, trackId, members) {
     }
     const { configuration } = track.activeDisplay;
     const configured = getSnapshot(configuration);
-    const patch = memberPatch(members, root => {
+    const type = getType(configuration);
+    const patch = memberPatch(members, (root, reached) => {
         // a list at a default the snapshot strips, Manhattan's marks, still seeds
         // the write, so `marks.0.mark=bar` edits the mark drawn
         const member = configuration[root];
-        return (configured[root] ??
-            (isStateTreeNode(member) && isArrayType(getType(member))
-                ? getSnapshot(member)
-                : undefined));
+        const keyed = keyedWritesAt(type, [root]);
+        return keyed
+            ? keyedSeed(member, [
+                keyed.keyedBy,
+                ...reached.filter(m => writesWholeAt(type, [root, m])),
+            ])
+            : (configured[root] ??
+                (isStateTreeNode(member) && isArrayType(getType(member))
+                    ? getSnapshot(member)
+                    : undefined));
     });
     view.showTrack(trackId, {}, patch);
     return patch;

package/esm/displayKitTests/perRegionTestEnv.d.ts

@@ -537,6 +537,7 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             notifyError(message: string): void;
             queueDialog(cb: (handleClose: () => void) => import("@jbrowse/display-test-utils").QueuedDialog): void;
             setSelection(thing: unknown): void;
+            clearSelection(): void;
             addWidget(type: string, id: string, initialState?: Record<string, unknown>): {
                 type: string;
                 id: string;
@@ -578,6 +579,7 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             notifyError(message: string): void;
             queueDialog(cb: (handleClose: () => void) => import("@jbrowse/display-test-utils").QueuedDialog): void;
             setSelection(thing: unknown): void;
+            clearSelection(): void;
             addWidget(type: string, id: string, initialState?: Record<string, unknown>): {
                 type: string;
                 id: string;

package/esm/index.d.ts

@@ -28,13 +28,13 @@ export { default as HeaderSearchBoxRow } from './LinearGenomeView/components/Hea
 export { searchBoxMenuItems, useSearchBoxPrefs, } from './LinearGenomeView/components/useSearchBoxPrefs.ts';
 export type { SearchBoxPrefs } from './LinearGenomeView/components/useSearchBoxPrefs.ts';
 export { normalizeTrackInit } from '@jbrowse/core/util/tracks';
-export { applyInitHighlights } from './LinearGenomeView/afterAttach.ts';
+export { applyInitHighlights, navToInitLoc, showInitTracks, } from './LinearGenomeView/afterAttach.ts';
 export { launchTrackInit, launchTrackWithModifiers, openedDisplayType, writeFilter, writeMembers, writeReadFilter, } from './TrackModifiers/index.ts';
 export type { ModifierView } from './TrackModifiers/index.ts';
 export { MultiLevelRubberband, multiLevelRowClickMenuItems, multiLevelRowMenuItems, rowLabels, } from './MultiLevelRubberband/index.ts';
 export { fetchResults, SearchResultsNotFoundError } from './searchUtils.ts';
 export type { LaunchLinearGenomeViewArgs } from './LaunchLinearGenomeView/index.ts';
-export type { BpOffset, ExportSvgOptions, HighlightInput, HighlightType, InitState, LinearGenomeViewLaunchProps, NavLocation, TrackLabelMode, ViewTrackLabelMode, VolatileGuide, } from './LinearGenomeView/types.ts';
+export type { BpOffset, ExportSvgOptions, HighlightInput, HighlightType, InitState, LinearGenomeViewLaunchProps, LinearGenomeViewPanelInit, NavLocation, TrackLabelMode, ViewTrackLabelMode, VolatileGuide, } from './LinearGenomeView/types.ts';
 export type { ScalebarRefNameLabel } from './LinearGenomeView/util.ts';
 export type { HighlightRegion, SearchHits, SearchPickerRow, SearchPickerState, } from './LinearGenomeView/model.ts';
 export type { RegionsOrientation } from './LinearGenomeView/util.ts';

package/esm/index.js

@@ -68,7 +68,7 @@ export { default as SearchBox } from './LinearGenomeView/components/SearchBox.js
 export { default as HeaderSearchBoxRow } from './LinearGenomeView/components/HeaderSearchBoxRow.js';
 export { searchBoxMenuItems, useSearchBoxPrefs, } from './LinearGenomeView/components/useSearchBoxPrefs.js';
 export { normalizeTrackInit } from '@jbrowse/core/util/tracks';
-export { applyInitHighlights } from './LinearGenomeView/afterAttach.js';
+export { applyInitHighlights, navToInitLoc, showInitTracks, } from './LinearGenomeView/afterAttach.js';
 export { launchTrackInit, launchTrackWithModifiers, openedDisplayType, writeFilter, writeMembers, writeReadFilter, } from './TrackModifiers/index.js';
 export { MultiLevelRubberband, multiLevelRowClickMenuItems, multiLevelRowMenuItems, rowLabels, } from './MultiLevelRubberband/index.js';
 export { fetchResults, SearchResultsNotFoundError } from './searchUtils.js';

package/esm/searchUtils.d.ts

@@ -23,7 +23,7 @@ export declare function navigateToSelectedOption({ option, model, assemblyName,
     option: BaseResult;
     model: LinearGenomeViewModel;
     assemblyName: string;
-}): Promise<void>;
+}): Promise<boolean>;
 export declare function isOpenInView(result: BaseResult, model: LinearGenomeViewModel): boolean;
 export declare function distinctDestinations({ results, model, session, assembly, }: {
     results: BaseResult[];
@@ -58,7 +58,6 @@ export declare function handleSelectedRegion({ input, model, assemblyName, grow,
     grow?: number;
     showHitTrack?: boolean;
 }): Promise<boolean>;
-export declare function checkRef(str: string, isRef: (name: string) => boolean): boolean;
 interface SearchArgs {
     queryString: string;
     assemblyName: string;
@@ -84,5 +83,4 @@ export declare function nameNotFound(input: string, assemblyName: string, { inde
     indexCount: number;
     failures: unknown[];
 }): Error;
-export declare function splitLast(str: string, split: string): [string, string];
 export {};