@jbrowse/plugin-linear-genome-view 5.0.0-beta.15 → 5.0.0-beta.16

package/esm/LinearGenomeView/model.d.ts

@@ -612,8 +612,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
     /**
      * #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.
      */
     readonly loading: import("@jbrowse/core/util/viewStatus").ViewLoading | undefined;
     /**
@@ -655,12 +655,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * `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
@@ -710,7 +710,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly headerHeight: number;
     /**
      * #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
@@ -789,8 +789,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
      */
     readonly sharedFitBpPerPx: number;
@@ -1033,7 +1033,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #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
@@ -1080,15 +1080,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #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
      */
     readonly canShowCytobands: boolean;
     /**
      * #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
      */
     readonly effectiveShowCytobands: boolean;
@@ -1141,9 +1141,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #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
      */
     readonly dynamicBlocks: BlockSet;
     /**
@@ -1175,12 +1174,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
@@ -1192,13 +1189,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
      */
@@ -1241,11 +1237,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
@@ -1257,7 +1253,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      *   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.
      *
@@ -1277,7 +1273,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
      */
     readonly scalebarRefNameLabels: {
         labels: import("./util.ts").ScalebarRefNameLabel[];
@@ -1289,7 +1285,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
@@ -1304,11 +1300,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      *   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.
      *
@@ -1397,7 +1393,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
      */
@@ -1483,17 +1479,16 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
      */
@@ -1519,8 +1514,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     moveTo(start?: BpOffset, end?: BpOffset): void;
     /**
      * #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.
@@ -1529,7 +1524,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #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.
@@ -1551,8 +1546,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setWindowFrame(windowWidthBp: number, windowStartBp: number): void;
     /**
      * #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: Region[]): void;
@@ -1787,7 +1782,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #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: HighlightType): MenuItem[];
 } & {
@@ -2345,8 +2340,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>) | undefined;
     /**
      * #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.
      */
     readonly loading: import("@jbrowse/core/util/viewStatus").ViewLoading | undefined;
     /**
@@ -2388,12 +2383,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * `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
@@ -2443,7 +2438,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly headerHeight: number;
     /**
      * #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
@@ -2522,8 +2517,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
      */
     readonly sharedFitBpPerPx: number;
@@ -2766,7 +2761,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #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
@@ -2813,15 +2808,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #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
      */
     readonly canShowCytobands: boolean;
     /**
      * #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
      */
     readonly effectiveShowCytobands: boolean;
@@ -2874,9 +2869,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #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
      */
     readonly dynamicBlocks: BlockSet;
     /**
@@ -2908,12 +2902,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
@@ -2925,13 +2917,12 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
      */
@@ -2974,11 +2965,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
@@ -2990,7 +2981,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      *   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.
      *
@@ -3010,7 +3001,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
      */
     readonly scalebarRefNameLabels: {
         labels: import("./util.ts").ScalebarRefNameLabel[];
@@ -3022,7 +3013,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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
@@ -3037,11 +3028,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      *   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.
      *
@@ -3130,7 +3121,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
      */
@@ -3216,17 +3207,16 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * 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.
      */
@@ -3252,8 +3242,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     moveTo(start?: BpOffset, end?: BpOffset): void;
     /**
      * #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.
@@ -3262,7 +3252,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #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.
@@ -3284,8 +3274,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     setWindowFrame(windowWidthBp: number, windowStartBp: number): void;
     /**
      * #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: Region[]): void;
@@ -3520,7 +3510,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #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: HighlightType): MenuItem[];
 } & {

package/esm/LinearGenomeView/model.js

@@ -192,17 +192,16 @@ 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 +214,15 @@ 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 +231,8 @@ 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(), []),
         /**
@@ -283,11 +282,11 @@ 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') ?? ''),
         /**
@@ -659,8 +658,8 @@ 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 +713,12 @@ 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 +795,7 @@ 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 +925,8 @@ 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() {
@@ -1454,7 +1453,7 @@ 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 +1583,8 @@ 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 +1612,8 @@ 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 +1625,7 @@ 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 +1749,8 @@ 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 +1792,10 @@ 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 +1807,12 @@ 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 +1865,11 @@ 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 +1881,7 @@ 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 +1901,7 @@ 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 +1916,7 @@ 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 +1931,11 @@ 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 +2037,7 @@ 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 +2176,16 @@ 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 +2246,8 @@ 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 +2260,7 @@ 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 +2290,8 @@ 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 +2750,7 @@ 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 [];

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/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.16",
   "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.16",
+    "@jbrowse/display-kit": "^5.0.0-beta.16",
+    "@jbrowse/display-ui": "^5.0.0-beta.16",
+    "@jbrowse/render-core": "^5.0.0-beta.16"
   },
   "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.16"
   },
   "scripts": {
     "prebuild": "pnpm clean",