@jbrowse/plugin-linear-genome-view 5.0.0-beta.15 → 5.0.0-beta.17

package/esm/LinearGenomeView/model.js

@@ -1,5 +1,5 @@
 import { canonicalLocString } from '@jbrowse/core/TextSearch/places';
-import { getConf } from '@jbrowse/core/configuration';
+import { getConf, readConfObject } from '@jbrowse/core/configuration';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { exportViewSvg } from '@jbrowse/core/svg/exportViewSvg';
 import { assembleLocString, clamp, getBpDisplayStr, getNotificationSink, getSession, isSessionModelWithWidgets, localStorageGetBoolean, localStorageGetItem, localStorageSetBoolean, localStorageSetItem, springAnimate, sum, } from '@jbrowse/core/util';
@@ -15,10 +15,11 @@ import { assemblyErrorMessage, computeViewStatus, viewLoading, } from '@jbrowse/
 import { pendingLaunch, withLaunchInput, } from '@jbrowse/core/util/withLaunchInput';
 import { MIN_DISPLAY_HEIGHT } from '@jbrowse/display-kit/const';
 import { contentRightEdgePx } from '@jbrowse/display-kit/regionHost';
-import { cast, getParent, hasParent, isAlive, types, } from '@jbrowse/mobx-state-tree';
+import { cast, getParent, getSnapshot, hasParent, isAlive, types, } from '@jbrowse/mobx-state-tree';
 import { observable, when } from 'mobx';
 import { handleSelectedRegion, isOpenInView, navToOption, } from '../searchUtils.js';
 import { doAfterAttach } from './afterAttach.js';
+import { linearGenomeViewAxisConfigSchema } from './axisConfigSchema.js';
 import { getCytobands, shouldSwapTracks } from './components/util.js';
 import { HEADER_BAR_HEIGHT, HEADER_OVERVIEW_HEIGHT, MIN_BP_PER_PX, MINIMIZED_TRACK_HEIGHT, MINIMUM_BLOCK_WIDTH, RESIZE_ALL_HANDLE_HEIGHT, RESIZE_HANDLE_HEIGHT, SCALE_BAR_HEIGHT, SHOW_ALL_REGIONS_FILL, TRACK_OUTLINE_BORDER, TRACK_TOP_GAP, } from './consts.js';
 import { planFlight } from './flyTo.js';
@@ -154,7 +155,7 @@ function isTrackSelectorVisible(self) {
  *   views: [
  *     {
  *       type: 'LinearGenomeView',
- *       colorByCDS: true,
+ *       colorByFrame: true,
  *       assembly: 'hg38',
  *       loc: 'chr1:1,000,000-1,100,000',
  *       tracks: ['genes', 'alignments'],
@@ -164,7 +165,7 @@ function isTrackSelectorVisible(self) {
  * ```
  * `assembly`, `loc`, `tracks`, `tracklist`, `nav` and `highlight` need
  * on-attach resolution and are captured into the `launch` property below;
- * `colorByCDS`, `showAminoAcids`, `showCenterLine` and `trackLabels` are plain
+ * `colorByFrame`, `showAminoAcids`, `showCenterLine` and `trackLabels` are plain
  * view props MST restores natively. Both are written the same way.
  * At runtime the same model is driven imperatively — every property and action
  * below is reachable on `viewState.session.views[0]`:
@@ -192,17 +193,16 @@ export function stateModelFactory(pluginManager) {
         /**
          * #property
          * Left edge of the viewport, in linearized bp — the concatenated
-         * `displayedRegions` space that `offsetPx` indexes, which carries no
+         * `displayedRegions` space that `offsetPx` indexes, which has no
          * inter-region padding, so the two differ only by `bpPerPx`. May be
-         * negative, which is the view scrolled past the left end.
+         * negative when the view is scrolled past the left end.
          *
-         * The viewport is stored as the genomic WINDOW it frames rather than as
-         * the pixels that framed it, because pixels mean nothing without the
-         * width they were measured at and a snapshot does not carry one. Storing
-         * them anyway is why a session authored in a 1000px window used to open
-         * at 500px showing half the region its author was looking at, while the
-         * same location as a `&loc=` opened correctly — the two ways to share a
-         * view disagreed, and only the one that stores intent was right.
+         * The view stores the genomic window it frames rather than the pixels
+         * that framed it, because pixels mean nothing without the width they
+         * were measured at and a snapshot does not include one. A session
+         * authored in a 1000px window therefore shows the same region when
+         * opened at 500px, as the same location given as a `&loc=` does: both
+         * ways to share a view store intent.
          */
         windowStartBp: types.stripDefault(types.number, 0),
         /**
@@ -215,14 +215,15 @@ export function stateModelFactory(pluginManager) {
         windowWidthBp: types.stripDefault(types.number, 0),
         /**
          * #property
-         * MIGRATION ONLY, and permanent: share links written before the window
-         * was stored carry `bpPerPx`/`offsetPx`, and there are many of them.
+         * Used for migration only, and permanent: share links written before the
+         * window was stored contain `bpPerPx`/`offsetPx`, and there are many of
+         * them.
          *
-         * A snapshot written before the window was stored carries `offsetPx` and
+         * A snapshot written before the window was stored has `offsetPx` and
          * `bpPerPx` but not the width they were measured at, so the window they
          * framed cannot be recovered. `windowStartBp` can (it is
          * `offsetPx * bpPerPx`, no width needed); the width in bp cannot. This
-         * carries the old `bpPerPx` to the first measure, which adopts it at
+         * property holds the old `bpPerPx` until the first measure, which adopts it at
          * whatever width arrives — exactly what the old code did — and clears
          * this. So an old link keeps its old behavior rather than being
          * reinterpreted, and everything authored since restores its window.
@@ -231,9 +232,8 @@ export function stateModelFactory(pluginManager) {
         /**
          * #property
          * currently displayed regions, can be a single chromosome, arbitrary
-         * subsections, or the entire  set of chromosomes in the genome, but it not
-         * advised to use the entire set of chromosomes if your assembly is very
-         * fragmented
+         * subsections, or the entire set of chromosomes in the genome. The entire
+         * set is not advised if your assembly is very fragmented
          */
         displayedRegions: types.stripDefault(types.frozen(), []),
         /**
@@ -268,7 +268,7 @@ export function stateModelFactory(pluginManager) {
         /**
          * #property
          * show the "center line". A personal preference: never in a session
-         * snapshot. It, showCytobands, trackLabels, colorByCDS, showAminoAcids
+         * snapshot. It, showCytobands, trackLabels, colorByFrame, showAminoAcids
          * and showTrackOutlines start from this browser's last choice, which
          * their setters record.
          */
@@ -283,29 +283,30 @@ export function stateModelFactory(pluginManager) {
         /**
          * #property
          * how to display the track labels, can be "overlapping", "offset", or
-         * "hidden", or empty string "" (which results in the
-         * LinearGenomeViewPlugin config default being used). the resolved value
-         * is the `effectiveTrackLabels` getter. see LinearGenomeViewPlugin
-         * https://jbrowse.org/jb2/docs/config/lineargenomeviewconfigschema/ docs for
-         * how conf is used
+         * "hidden", or empty string "" (which uses the LinearGenomeViewPlugin
+         * config default). The resolved value is the `effectiveTrackLabels`
+         * getter. See the LinearGenomeViewPlugin docs at
+         * https://jbrowse.org/jb2/docs/config/lineargenomeviewconfigschema/ for
+         * how the config is used
          */
         trackLabels: types.optional(types.string, () => localStorageGetItem('lgv-trackLabels') ?? ''),
         /**
          * #property
-         * show the "gridlines" in the track area
+         * The ruler's guide, a [](/docs/config/lineargenomeviewaxis) object:
+         * `{ grid: false }` stops its ticks running down through the tracks.
          */
-        showGridlines: types.stripDefault(types.boolean, true),
+        axis: types.stripDefault(linearGenomeViewAxisConfigSchema, {}),
         /**
          * #property
          * color CDS segments by reading frame
          */
-        colorByCDS: types.optional(types.boolean, () => localStorageGetBoolean('lgv-colorByCDS', false)),
+        colorByFrame: types.optional(types.boolean, () => localStorageGetBoolean('lgv-colorByFrame', false)),
         /**
          * #property
          * draw translated codons on coding features once zoomed in far enough:
          * an alternating per-codon shading, and the amino acid letters on top of
-         * it at base-level zoom. Independent of `colorByCDS`, which only recolors
-         * the segments by frame.
+         * it at base-level zoom. Independent of `colorByFrame`, which only
+         * recolors the segments by frame.
          */
         showAminoAcids: types.optional(types.boolean, () => localStorageGetBoolean('lgv-showAminoAcids', true)),
         /**
@@ -407,6 +408,13 @@ export function stateModelFactory(pluginManager) {
         };
     })
         .views(self => ({
+        /**
+         * #getter
+         * `axis.grid`: whether the ruler's ticks run down through the tracks.
+         */
+        get axisGrid() {
+            return readConfObject(self.axis, 'grid');
+        },
         // The viewport in pixels, derived from the window it frames — declared
         // ahead of every other getter so that the ~300 reads of `self.bpPerPx` /
         // `self.offsetPx` across the codebase go on resolving by name. Only the
@@ -659,8 +667,8 @@ export function stateModelFactory(pluginManager) {
         },
         /**
          * #getter
-         * What the loading screen says while `showLoading`, read off the
-         * assembly whose load is the wait; undefined otherwise.
+         * The loading screen's text while `showLoading`, taken from the
+         * assembly being waited on; undefined otherwise.
          */
         get loading() {
             return viewLoading(this.showLoading, () => this.loadingAssembly);
@@ -714,12 +722,12 @@ export function stateModelFactory(pluginManager) {
          * `width`/`staticBlocks` throw by design before the view has been
          * measured and navigated.
          *
-         * **Not `initialized`**, which is the trap this getter exists to close.
+         * Use this getter rather than `initialized`.
          * That one answers "have the assembly's regions loaded", which is only
          * the first of two async steps: navigating then populates
          * `displayedRegions`, and in the window between the two `initialized` is
          * already true while there is still nothing on screen. `showLoading`
-         * folds in `awaitingInitNavigation`, the getter that exists for exactly
+         * folds in `awaitingInitNavigation`, the getter for exactly
          * that gap.
          *
          * `error` is the third outcome and is why this is not a bare
@@ -796,7 +804,7 @@ export function stateModelFactory(pluginManager) {
         },
         /**
          * #method
-         * rendered height of a single track, collapsing to a fixed height when
+         * rendered height of a single track, using a fixed height when
          * minimized. Shared by trackHeights and getTrackYOffset so the two can't
          * disagree. Reads `activeDisplay` — the display TrackContainer actually
          * mounts — rather than re-picking `displays[0]`, so the view's height math
@@ -926,8 +934,8 @@ export function stateModelFactory(pluginManager) {
          * or 0 for a standalone view, a mode that is off, and a stack that cannot
          * answer yet.
          *
-         * Pulled rather than pushed down into a volatile: the number is a
-         * function of every row's fit, all of which move on a resize, and a
+         * A getter rather than a volatile the container writes: the number is a
+         * function of every row's fit, all of which change on a resize, and a
          * stored copy would be stale by the next layout.
          */
         get sharedFitBpPerPx() {
@@ -1054,9 +1062,9 @@ export function stateModelFactory(pluginManager) {
         /**
          * #action
          */
-        setColorByCDS(flag) {
-            self.colorByCDS = flag;
-            localStorageSetBoolean('lgv-colorByCDS', flag);
+        setColorByFrame(flag) {
+            self.colorByFrame = flag;
+            localStorageSetBoolean('lgv-colorByFrame', flag);
         },
         /**
          * #action
@@ -1172,8 +1180,8 @@ export function stateModelFactory(pluginManager) {
         /**
          * #action
          */
-        setShowGridlines(b) {
-            self.showGridlines = b;
+        setAxisGrid(grid) {
+            self.axis = cast({ ...getSnapshot(self.axis), grid });
         },
         /**
          * #action
@@ -1454,7 +1462,7 @@ export function stateModelFactory(pluginManager) {
         /**
          * #method
          * Helper method for the fetchSequence.
-         * Retrieves the corresponding regions that were selected by the
+         * Returns the regions the user selected with the
          * rubberband
          *
          * @param leftOffset - `object as {start, end, index, offset}`, offset = start
@@ -1584,8 +1592,8 @@ export function stateModelFactory(pluginManager) {
         }
         /**
          * #action
-         * cancel an in-flight animated zoom. The animation already yields to any
-         * other zoom on its own, so this is for stopping it *without* changing the
+         * cancel an in-flight animated zoom. Any other zoom already stops the
+         * animation, so this is for stopping it *without* changing the
          * zoom — the slider grabbing the thumb, before it has a value to commit.
          */
         function cancelZoomAnimation() {
@@ -1613,8 +1621,8 @@ export function stateModelFactory(pluginManager) {
          * #getter
          * an ideogram only reads correctly against an entire chromosome: on a
          * sub-region it is a meaningless slice of bands, and the centromere shows
-         * up as a lone half-triangle. The chromosome needs bands of its own too:
-         * a cytoband file often lists only the main chromosomes, not chrM or the
+         * up as a lone half-triangle. The chromosome also needs bands: a cytoband
+         * file often lists only the main chromosomes, not chrM or the
          * unplaced scaffolds
          */
         get canShowCytobands() {
@@ -1626,7 +1634,7 @@ export function stateModelFactory(pluginManager) {
         /**
          * #getter
          * the `showCytobands` setting gated by whether cytobands can be shown at
-         * all (whole chromosome with bands of its own) and by the header
+         * all (whole chromosome with bands in the cytoband file) and by the header
          * overview they draw in being on, which the SVG export follows too
          */
         get effectiveShowCytobands() {
@@ -1750,9 +1758,8 @@ export function stateModelFactory(pluginManager) {
             /**
              * #getter
              * dynamic blocks represent the exact coordinates of the currently
-             * visible genome regions on the screen. they are similar to static
-             * blocks, but static blocks can go offscreen while dynamic blocks
-             * represent exactly what is on screen
+             * visible genome regions on the screen. Static blocks can go
+             * offscreen, while dynamic blocks represent exactly what is on screen
              */
             get dynamicBlocks() {
                 return calculateDynamicBlocks(self);
@@ -1794,12 +1801,10 @@ export function stateModelFactory(pluginManager) {
              * The frame exists because those three are laid out across every
              * displayed region rather than across the viewport — it overhangs on
              * both sides — so their `x` values are stable under a scroll and only
-             * this number moves. `scalebarRefNameLabels` is the exception and says
-             * so: its `transform` is already a screen x, because a sticky label's
+             * this number moves. `scalebarRefNameLabels` is the exception: its `transform` is already a screen x, because a sticky label's
              * position is a function of the scroll rather than of block geometry.
              *
-             * **The subtraction must happen here, in float64, and that is the
-             * load-bearing part.** `offsetPx` is a whole-genome pixel coordinate —
+             * **The subtraction must happen here, in float64.** `offsetPx` is a whole-genome pixel coordinate —
              * hg38 chr1 at base resolution is already past 1e10 — and a length that
              * size does not survive the trip through CSS: the transform matrix is
              * float32 by the time it reaches the compositor, where consecutive
@@ -1811,13 +1816,12 @@ export function stateModelFactory(pluginManager) {
              * assemblies at high zoom, which is not where anyone tests. Both
              * operands here are large and their difference is bounded by the
              * overhang (a block or two), so what reaches CSS is small and exact.
-             * Same rule as the GPU side, one layer up —
+             * This applies the GPU side's rule one layer up; see
              * `agent-docs/reference/BP_PRECISION.md`.
              *
              * Published because it is the one piece of coordinate arithmetic a host
              * drawing its own chrome would otherwise have to know, and because
-             * having it written out at each call site is how the two in-tree copies
-             * came to disagree about rounding. Round it where the content is text
+             * copies written out at each call site disagree about rounding. Round it where the content is text
              * (a fractional offset blurs a label); leave it alone for paths and
              * boxes.
              */
@@ -1870,11 +1874,11 @@ export function stateModelFactory(pluginManager) {
              * sticky, transform, maxWidth, paddingLeft, text}` each. One per run of
              * same-refName regions, plus a "sticky" one pinned to the viewport's
              * left edge naming the refName under it, so panning into a chromosome
-             * does not scroll its own name off the screen.
+             * does not scroll the chromosome's name off the screen.
              *
-             * Three rules live in here that a host drawing region names will
-             * otherwise rediscover the hard way, and two of them are invisible until
-             * the data is awkward:
+             * This getter applies three rules that a host drawing region names would
+             * otherwise have to rediscover, and two of them are invisible until the
+             * data is awkward:
              *
              * - the sticky label rides the rightmost run that has scrolled off the
              *   left, not the region's first block — that one is gone from
@@ -1886,7 +1890,7 @@ export function stateModelFactory(pluginManager) {
              *   is fitted to the whole run, and `displayedRegionIndex` /
              *   `lastDisplayedRegionIndex` bracket what it stands for.
              * - a name is drawn whole or not at all, measured against the space its
-             *   run leaves. Clipped to its own width, `chr16` reads as `chr1` —
+             *   run leaves. Clipped to that space, `chr16` reads as `chr1` —
              *   a different chromosome rather than a shortened name, which is why
              *   this is a fit test rather than an ellipsis.
              *
@@ -1906,7 +1910,7 @@ export function stateModelFactory(pluginManager) {
              * pins to its right edge rather than the viewport's, and the coordinate
              * numbers stay out from under it. The SVG export deliberately
              * calls `getScalebarRefNameLabels` itself with no prefix rather than
-             * reading this, since it draws its own assembly name above the ruler.
+             * reading this, since it draws the assembly name itself above the ruler.
              */
             get scalebarRefNameLabels() {
                 return getScalebarRefNameLabels({
@@ -1921,7 +1925,7 @@ export function stateModelFactory(pluginManager) {
              * Every span along the row that is not track data, as plain geometry in
              * the staticBlocks frame — the same frame as gridlineTicks and
              * scalebarLabels, so one `translateX(staticBlocksTranslateX)` places all
-             * three. A host drawing its own chrome needs all three kinds:
+             * three. A host that draws the row's chrome itself needs all three kinds:
              *
              * - `seam`: the 3px bar at a region's right edge. Displayed regions are
              *   laid out **contiguously** (calculateStaticBlocks emits boundary
@@ -1936,11 +1940,11 @@ export function stateModelFactory(pluginManager) {
              *   but the 24 chromosomes are under a pixel wide), so a host that
              *   skips them leaves that part of the row empty.
              * - `boundary`: past the start of the first region or the end of the
-             *   last. Greying it shows the last region's seam as the edge of a
+             *   last. Greying it makes the last region's seam read as the edge of a
              *   filled area, where it would otherwise look like a line in the
              *   middle of the track.
              *
-             * Elided blocks get no seam even though they carry the flag: at the
+             * Elided blocks get no seam even though they have the flag: at the
              * zoom where regions elide, one bar per region would fill the row solid
              * grey.
              *
@@ -2042,7 +2046,7 @@ export function stateModelFactory(pluginManager) {
              * array of fresh objects on every pan and zoom frame, so a component
              * that derived this number itself re-rendered on every frame of every
              * gesture — to produce, whenever content fills the track, the unchanged
-             * `trackWidthPx`. Reading the scalar lets MobX's `===` stop the chain at
+             * `trackWidthPx`. A component that reads the scalar lets MobX's `===` stop the chain at
              * this computed instead. Measured over 20 zoom frames: the wiggle
              * family's three body instances fell from 66 renders to 7.
              */
@@ -2181,17 +2185,16 @@ export function stateModelFactory(pluginManager) {
          * as a navigation that didn't happen, and wiggle's autoscale domain is
          * computed over the window the user just left — measured at `[0,200]`
          * against a correct `[0,300]` when a 40bp coarse window survived a jump to
-         * 4040bp on screen. Only the per-region fetch moving to the leading edge
-         * made that reachable: at 600ms the data never landed inside the hole.
+         * 4040bp on screen.
          *
-         * **The continuous paths deliberately do not come through here.** The
+         * **The continuous paths do not call this.** The
          * spring zoom writes through `zoomTo` per frame and a drag through
          * `scrollTo`, so this adds no per-frame work; the settle is idempotent
          * (`setCoarseDynamicBlocks` compares block keys), so the debounced
-         * autorun's own follow-up run costs nothing.
+         * autorun's follow-up run costs nothing.
          *
-         * Every placer calls it, and `placersSettleCoarseBlocks.test.ts` is what
-         * makes that true of the next one — it scans this file for the writes and
+         * Every placer calls it, and `placersSettleCoarseBlocks.test.ts` enforces
+         * that for the next one: it scans this file for the writes and
          * fails on a placer that reaches neither the settle nor its named list of
          * continuous paths. Two passes by hand missed four.
          */
@@ -2252,8 +2255,8 @@ export function stateModelFactory(pluginManager) {
         },
         /**
          * #action
-         * Place the viewport by the pair of PIXEL quantities it used to be stored
-         * as. Prefer `setWindow`: pixels mean nothing without the width they were
+         * Place the viewport by `bpPerPx` and `offsetPx`, the pixel pair the view
+         * stored before it stored the window. Prefer `setWindow`: pixels mean nothing without the width they were
          * measured at, so a round trip through here is only exact while the width
          * holds still. Kept for callers that genuinely have pixels — a wheel
          * gesture, a rubberband.
@@ -2266,7 +2269,7 @@ export function stateModelFactory(pluginManager) {
         /**
          * #action
          * Place the viewport by the pair it is actually STORED as: the window's
-         * width and left edge, both in bp. `setNewView`'s bp-space twin, and the
+         * width and left edge, both in bp. The bp-space counterpart of `setNewView`, and the
          * right one for anything that captures a viewport and puts it back later
          * (an Undo, a saved location) — those two moments can be a window resize
          * apart, and this pair survives one where a pixel pair does not.
@@ -2296,8 +2299,8 @@ export function stateModelFactory(pluginManager) {
         },
         /**
          * #action
-         * The worst jump of them to leave unsettled: the coarse blocks are keyed
-         * by `displayedRegionIndex`, so a set that outlives the region list has a
+         * Settles the coarse blocks, since this is the worst jump to leave
+         * unsettled: they are keyed by `displayedRegionIndex`, so a set that outlives the region list has a
          * consumer reading one contig's data against another's blocks.
          */
         setDisplayedRegions(regions) {
@@ -2756,7 +2759,7 @@ export function stateModelFactory(pluginManager) {
         /**
          * #method
          * returns menu items for a highlight context menu. plugins can extend
-         * this via Core-extendPluggableElement to add their own items
+         * this via Core-extendPluggableElement to add items
          */
         highlightMenuItems(_highlight) {
             return [];
@@ -2897,12 +2900,14 @@ export function stateModelFactory(pluginManager) {
             return snap;
         }
         // v4's `showCytobandsSetting` persists as the bare `showCytobands` prop
-        // (the capability-gated getter is `effectiveShowCytobands`).
-        const { showCytobandsSetting, offsetPx, bpPerPx, ...rest } = snap;
+        // (the capability-gated getter is `effectiveShowCytobands`), and v4's
+        // `colorByCDS` as `colorByFrame`.
+        const { showCytobandsSetting, colorByCDS, offsetPx, bpPerPx, ...rest } = snap;
         return {
             ...(showCytobandsSetting !== undefined
                 ? { showCytobands: showCytobandsSetting }
                 : {}),
+            ...(colorByCDS !== undefined ? { colorByFrame: colorByCDS } : {}),
             // The viewport used to persist as pixels. Half of that converts
             // exactly and needs no width — the left edge in bp is offsetPx *
             // bpPerPx — and half of it cannot convert at all, because the width

package/esm/LinearGenomeView/rExport/rScript.js

@@ -11,6 +11,7 @@ const READERS = {
         adapters: {
             Gff3TabixAdapter: { slot: 'gffGzLocation', ext: /\.gff3?\.gz$/ },
             Gff3Adapter: { slot: 'gffLocation', ext: /\.gff3?$/ },
+            GtfTabixAdapter: { slot: 'gtfGzLocation', ext: /\.gtf\.gz$/ },
             GtfAdapter: { slot: 'gtfLocation', ext: /\.gtf$/ },
             BedTabixAdapter: { slot: 'bedGzLocation', ext: /\.bed\.gz$/ },
             BedAdapter: { slot: 'bedLocation', ext: /\.bed$/ },

package/esm/LinearGenomeView/svgcomponents/useViewSvgFigure.js

@@ -126,7 +126,7 @@ const FrozenSvgFigure = memo(function FrozenSvgFigure({ view, snapshot, }) {
  * (hidden sections, collapses, height overrides: `groupStateKey`), which are
  * volatile and in no snapshot; **the reload counter**, since a Retry or a Force
  * load leaves every snapshot as it was while the figure has an error or a
- * too-large note to replace; **the view's coloring toggles** (`colorByCDS`,
+ * too-large note to replace; **the view's coloring toggles** (`colorByFrame`,
  * `showAminoAcids`), named one by one because the view's own snapshot moves
  * every pan frame; **the width**, since a resize can widen the canvas without
  * moving the locus; **the theme**, since each display bakes colors into its own
@@ -172,7 +172,7 @@ function figureKey(view, themeName) {
                 display?.reloadCounter,
             ];
         }),
-        view.colorByCDS,
+        view.colorByFrame,
         view.showAminoAcids,
         session.getActiveThemeOptions?.(themeName),
         session.highlightsVisible ? view.highlights : false,

package/esm/index.js

@@ -19,7 +19,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
     configurationSchema = ConfigurationSchema('LinearGenomeViewConfigSchema', {
         /**
          * #slot configuration.LinearGenomeViewPlugin.trackLabels
-         * The placement of a track's name: `offset` gives it its own line above the
+         * The placement of a track's name: `offset` puts it on a line above the
          * data, `overlapping` floats it over the top of the data to save vertical
          * space, `hidden` omits it. The view menu's "Track labels" submenu sets the
          * same thing per session

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "5.0.0-beta.15",
+  "version": "5.0.0-beta.17",
   "type": "module",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
@@ -26,10 +26,10 @@
     "@mui/material": "^9.5.0",
     "mobx": "^7.0.6",
     "mobx-react": "^10.0.2",
-    "@jbrowse/display-kit": "^5.0.0-beta.15",
-    "@jbrowse/display-ui": "^5.0.0-beta.15",
-    "@jbrowse/core": "^5.0.0-beta.15",
-    "@jbrowse/render-core": "^5.0.0-beta.15"
+    "@jbrowse/core": "^5.0.0-beta.17",
+    "@jbrowse/display-ui": "^5.0.0-beta.17",
+    "@jbrowse/render-core": "^5.0.0-beta.17",
+    "@jbrowse/display-kit": "^5.0.0-beta.17"
   },
   "peerDependencies": {
     "react": ">=19.0.0",
@@ -40,7 +40,7 @@
   },
   "sideEffects": false,
   "devDependencies": {
-    "@jbrowse/display-test-utils": "^5.0.0-beta.15"
+    "@jbrowse/display-test-utils": "^5.0.0-beta.17"
   },
   "scripts": {
     "prebuild": "pnpm clean",