@jbrowse/wiggle-core 4.3.0

package/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [2020] [Evolutionary Software Foundation]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

package/README.md

@@ -0,0 +1,292 @@
+# @jbrowse/wiggle-core
+
+Shared scale and autoscale utilities for wiggle and coverage displays
+
+<!-- API_DOCS_START -->
+
+## API
+
+Auto-generated from `#api` JSDoc tags in this package. Do not edit by hand.
+
+### computeAutoscaleDomain
+
+Computes a score domain from the visible feature arrays for the `local` /
+`localsd` / `localpercentile` autoscale types.
+
+```js
+// type signature
+(autoscaleType: string, summaryScoreMode: string, numStdDev: number, visibleEntries: {…}[], numQuantile?: number) => [...] | undefined
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/autoscale.ts)
+
+### DEFAULT_GAP_BREAK_MULTIPLE
+
+Default `multiple` for the wiggle interpolated line — the `maxGapMultiple`
+config slot's default. 0 means the line never breaks: one connected polyline
+across every hole, which is how the interpolated line behaved before gap
+breaking existed.
+
+OFF BY DEFAULT, deliberately and after having been on. It shipped at 20 and the
+calibration behind that number still holds — a hole worth breaking on runs
+orders of magnitude past the mean, and bbi's reduced zoom levels emit
+fixed-width bins so the series tiles (measured on volvox_microarray.bw at three
+zooms: 500 bins, every gap exactly 1.0x the mean, no break at any threshold).
+What changed is the call about whether a reader wants the break at all: "we
+added this feature awhile back but i dont think i like it now. might consider
+going back to not skipping". A broken line reads as missing data whether or not
+data is missing there, and the chord across a hole is at least continuous with
+what the neighbouring points say.
+
+The mechanism stays, whole, because it is the only way to get the other behavior
+back: set `maxGapMultiple` on the track, 20 being the calibrated value. Nothing
+about `gapBreakLimit` itself changes — a caller passing a positive multiple gets
+exactly what it always got.
+
+```js
+// type signature
+0
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/gapBreak.ts)
+
+### domainFromStats
+
+Converts score stats into a `[min, max]` domain, applying std-dev expansion for
+the `localsd` autoscale type.
+
+```js
+// type signature
+(stats: ScoreStats, autoscaleType: string, numStdDev: number) => [number, number]
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/autoscale.ts)
+
+### gapBreakLimit
+
+How far apart two consecutive points of an interpolated (point-to-point) line
+may be before the span between them counts as a hole rather than a segment to
+draw. Returns `Infinity` when there is nothing to decide, so a caller can always
+compare against it unguarded.
+
+The limit is a multiple of the series' own _mean_ spacing rather than an
+absolute distance, which is what makes one number work across zoom levels and
+data types: reduced BigWig bins get wider as you zoom out, so any fixed bp
+threshold would be either useless at one end or destructive at the other. It
+also lets the same rule serve a bp axis (wiggle's linecenter) and a px one — the
+caller picks the space, this only cares that the units are consistent.
+
+Mean, not median: it is O(1) from the endpoints, and it errs the safe way. A
+series' holes inflate their own mean, which raises the limit and so breaks
+_less_ — a line that stays connected is the status quo, whereas a spuriously
+broken one destroys data the user can see nowhere else. Sorting for a true
+median would cost O(n log n) per source per region on the encode path, for a
+threshold this coarse.
+
+`count < 3` returns Infinity: two points have no "typical" spacing to be unusual
+against, so there is nothing to call a hole.
+
+```js
+// type signature
+({ first, last, count, multiple, }: { first: number; last: number; count: number; multiple: number; }) => number
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/gapBreak.ts)
+
+### getEffectiveScores
+
+Per-feature scalar score array for a summary mode: the min/max summary array for
+`'min'`/`'max'`, otherwise the average score.
+
+```js
+// type signature
+(data: { featureScores: Float32Array<…>; featureMinScores: Float32Array<ArrayBufferLike>; featureMaxScores: Float32Array<...>; }, summaryScoreMode: string) => Float32Array<...>
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/autoscale.ts)
+
+### getNiceDomain
+
+Rounds a domain to "nice" endpoints, clamped to the origin. An end given an
+explicit `bounds` value keeps that value exactly — only an autoscaled end is
+rounded. A log scale's floor still outranks a bound it cannot hold.
+
+The result never descends: a bound that would put `min` above `max` widens the
+other end instead, so no consumer has to guess what a backwards domain means.
+
+```js
+// type signature
+({ scaleType, domain, bounds, }: { scaleType: string; domain: readonly [number, number]; bounds: readonly [number | undefined, number | undefined]; }) => [number, number]
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/scale.ts)
+
+### getNiceScale
+
+Returns a niced `{min, max}` domain for a maximum score value. Uses log base-2
+when `useLogScale` is true (domain is clamped to [1, max]).
+
+```js
+// type signature
+(maxScore: number, useLogScale?: boolean | undefined) => { min: number; max: number; }
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/scale.ts)
+
+### getScale
+
+Builds a d3 scale (linear/log/symlog) from a `ScaleOpts`, nicing the domain
+unless `nice: false` says it is already the one being drawn with.
+
+```js
+// type signature
+({ domain, range, scaleType, symlogConstant, nice, }: ScaleOpts) => Scale
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/scale.ts)
+
+### makeScoreNormalizer
+
+Returns a loop-hoistable function normalizing a score to [0,1].
+
+`symlogConstant` is only read for `SCALE_TYPE_SYMLOG`, and is expected to be
+already resolved by resolveSymlogConstant — the shader gets the same resolved
+number as a uniform, so the "auto" rule lives on this side only and the two
+backends compare like for like.
+
+A range that is zero **or negative** normalizes everything to 0, which is the
+rule `scoreScale.slang` spells as `range <= 0.0`. Testing `range === 0` here
+instead let a descending domain through to a negative `1 / range`, so every
+score saturated to 1 on this side while the shader flattened them all to 0 — one
+view, opposite plots. `normalizeScoreParity.test.ts` sweeps the two.
+
+```js
+// type signature
+(min: number, max: number, scaleType: WiggleScaleType, symlogConstant?: number) => (score: number) => number
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/normalize.ts)
+
+### parseScoreRules
+
+Normalizes whatever a `scoreRules` config slot holds into `ScoreRule`s, dropping
+entries that are not usable. Config is user-authored JSON, so a bare number, a
+missing value or a non-numeric one all have to survive being read.
+
+```js
+// type signature
+(value: unknown) => ScoreRule[]
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/scoreRuleMarks.ts)
+
+### resolveSymlogConstant
+
+The symlog constant actually used for a domain. `0` (the config default) means
+"pick one from the domain": a thousandth of its largest magnitude, so the
+log-ish part of the curve covers the top three decades of whatever the track
+holds and the linear knee sits below the data rather than through it.
+
+The alternative — d3's default of 1 — is `log(x + 1)`, which is fine for read
+depth and useless for anything living below 1, because the entire domain then
+falls in the linear part of the curve. A p-value track configured that way is
+just a linear track wearing a log label, which is the reason this is resolved
+rather than hard-coded.
+
+```js
+// type signature
+(min: number, max: number, configured: number) => number
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/normalize.ts)
+
+### scaleTypeFromString
+
+Maps the `'log'`/`'symlog'`/`'linear'` string to the numeric `WiggleScaleType`.
+
+```js
+// type signature
+(scaleType: string) => WiggleScaleType
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/normalize.ts)
+
+### ScoreRule
+
+One horizontal rule across a score plot, at a score the user chose.
+
+`label` is free text and carries no meaning this package assigns. That is
+deliberate: the obvious use is reading a coverage or CNV track against copy
+number, and there is no ploidy JBrowse could assume on the user's behalf. A
+whole-genome triplication is not diploid, plenty of genomes are not diploid to
+begin with, and a cancer sample can be neither — so "2 copies" is a claim only
+the person looking at the track can make.
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/scoreRuleMarks.ts)
+
+### scoreRuleMarks
+
+Screen y for each rule that falls inside the plotted domain, dropping the rest.
+
+Out-of-domain is a real case rather than a guard: the domain is whatever
+autoscale resolved for the visible data, so panning to a quiet stretch can put a
+rule above everything on screen, and a rule pinned to the top edge there reads
+as "the whole view is over the line".
+
+`normalize` is the display's OWN score normalizer — the same one the renderer
+draws with. It is a parameter rather than a linear interpolation of the domain
+because the axis need not be linear: on a log or symlog track, placing a rule at
+`(value - min) / (max - min)` puts the line somewhere the data it is meant to be
+read against is not.
+
+`box` is likewise the caller's own — hand it the same `{yTop, yBottom}` the
+display's ticks were built with (a `YScaleTicks` satisfies it). Recomputing a
+box here would silently disagree with any band that lays its axis out
+differently, and the alignments coverage band does.
+
+```js
+// type signature
+({…}: { rules: readonly ScoreRule[]; domain: [number, number] | undefined; box: { yTop: number; yBottom: number; }; normalize: (score: number) => number; }) => ScoreRuleMark[]
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/scoreRuleMarks.ts)
+
+### visibleStatsDomain
+
+The visible score domain four displays derive identically: walk the settled
+blocks, accumulate the stats of what each one shows, and nice-round the
+autoscaled range inside the configured bounds. `undefined` while there is
+nothing to scale against — no data, a hidden band, or a view that has not
+initialized — which every caller distinguishes from a domain.
+
+```js
+// type signature
+<Payload, Item, Stats>({ active, view, payloadFor, itemsFor, accumulate, range, bounds, scaleType, }: VisibleStatsDomainSpec<Payload, Item, Stats>) => [number, number] | undefined
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/visibleStatsDomain.ts)
+
+### widenRangeToRules
+
+Widens an autoscaled range so every configured rule stays on the axis.
+
+Without this a rule silently disappears in exactly the window that makes it
+worth having. Autoscale follows the visible data, so over a homozygous deletion
+a coverage domain collapses to about `[0, 1]` and a rule at the diploid depth
+falls outside it — and "2 copies would be up there" is the most informative
+thing that view can say. The reader has no menu to check either: `scoreRules` is
+set by whoever wrote the config, so a rule that vanishes leaves nothing behind
+to notice.
+
+Applied to the raw range, before `getNiceDomain` takes the `minScore` /
+`maxScore` bounds. Those still win: a rule outside an explicitly bounded axis is
+one the config asked not to be shown, and it drops as before.
+
+```js
+// type signature
+(range: [number, number], ruleValues: readonly number[]) => [number, number]
+```
+
+[Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/scoreRuleMarks.ts)
+
+<!-- API_DOCS_END -->

package/esm/CrossHatches.d.ts

@@ -0,0 +1,11 @@
+import type { YScaleTicks } from './yScaleTicks.ts';
+export declare function CrossHatchLines({ ticks, width, offsetY, }: {
+    ticks: YScaleTicks;
+    width: number;
+    offsetY?: number;
+}): import("react").JSX.Element;
+export default function CrossHatches({ ticks, width, height, }: {
+    ticks: YScaleTicks;
+    width: number;
+    height: number;
+}): import("react").JSX.Element;

package/esm/CrossHatches.js

@@ -0,0 +1,32 @@
+import { Fragment as _Fragment, jsx as _jsx } from "react/jsx-runtime";
+import { clampStrokeInsideAxis } from './yScaleTicks.js';
+// Bare <line> set for the Y-scale tick guide lines, no wrapping <svg>. Shared by
+// the absolutely-positioned on-screen CrossHatches overlay and the flat SVG
+// export (single- and multi-wiggle), so the three can't drift. `offsetY` shifts
+// every line down for per-row rendering in multi-wiggle.
+export function CrossHatchLines({ ticks, width, offsetY = 0, }) {
+    return (_jsx(_Fragment, { children: ticks.items.map(({ value, y }) => {
+            // Same clamp the axis ticks take, so a guide line and the tick it
+            // belongs to can't disagree at the bottom edge — where, in multi-wiggle,
+            // "one pixel lower" is the next sample's row. Only that edge moves; the
+            // guide lines don't crispen to a half pixel the way the axis does.
+            const lineY = offsetY + clampStrokeInsideAxis(y, ticks.yBottom);
+            return (_jsx("line", { x1: 0, x2: width, y1: lineY, y2: lineY, stroke: "rgb(200,200,200)", 
+                // a separate stroke-opacity attribute (not baked into an rgba()
+                // string) survives the SVG export, whose renderToStaticMarkup strips
+                // rgba() alpha
+                strokeOpacity: 0.8, strokeWidth: 1 }, `${value}-${y}`));
+        }) }));
+}
+// Horizontal guide lines at each Y-scale tick. Pointer-events disabled so
+// the underlying canvas still receives mouse events.
+export default function CrossHatches({ ticks, width, height, }) {
+    return (_jsx("svg", { style: {
+            position: 'absolute',
+            top: 0,
+            left: 0,
+            pointerEvents: 'none',
+            height,
+            width,
+        }, children: _jsx(CrossHatchLines, { ticks: ticks, width: width }) }));
+}

package/esm/ResolutionStepper.d.ts

@@ -0,0 +1,17 @@
+import type { MenuItem } from '@jbrowse/core/ui';
+import type React from 'react';
+interface ResolutionStepperState {
+    label: string;
+    finerDisabled: boolean;
+    coarserDisabled: boolean;
+    resetDisabled: boolean;
+}
+export declare function makeResolutionSubMenuItem(opts: {
+    getState: () => ResolutionStepperState;
+    onFiner: () => void;
+    onCoarser: () => void;
+    onReset: () => void;
+    icon?: React.ElementType;
+    resetTitle?: string;
+}): MenuItem;
+export {};

package/esm/ResolutionStepper.js

@@ -0,0 +1,56 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { INLINE_MENU_ROW_WIDTH, ResetToDefaultButton } from '@jbrowse/core/ui';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
+import { Button, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+const useStyles = makeStyles()(theme => ({
+    row: {
+        display: 'flex',
+        alignItems: 'center',
+        gap: theme.spacing(0.5),
+        width: INLINE_MENU_ROW_WIDTH,
+    },
+    // subtle text buttons: no uppercase, minimal padding, inherit text color so
+    // "Coarser"/"Finer" read as quiet affordances rather than prominent CTAs
+    step: {
+        textTransform: 'none',
+        minWidth: 0,
+        padding: '0 4px',
+    },
+    value: {
+        flex: 1,
+        textAlign: 'center',
+    },
+}));
+// Subtle inline stepper: [−] label [+] [reset]. The −/+ icon buttons let the
+// user step finer/coarser repeatedly without reopening the menu. Shared by the
+// wiggle binning multiplier and the Hi-C matrix binsize, which differ only in
+// how they format the label and bound the steps.
+const ResolutionStepper = observer(function ResolutionStepper({ getState, onFiner, onCoarser, onReset, resetTitle, }) {
+    const { classes } = useStyles();
+    const { label, finerDisabled, coarserDisabled, resetDisabled } = getState();
+    return (_jsxs("div", { className: classes.row, children: [_jsx(Button, { className: classes.step, size: "small", color: "inherit", disabled: coarserDisabled, onClick: () => {
+                    onCoarser();
+                }, children: "Coarser" }), _jsx(Typography, { variant: "caption", color: "textSecondary", className: classes.value, children: label }), _jsx(Button, { className: classes.step, size: "small", color: "inherit", disabled: finerDisabled, onClick: () => {
+                    onFiner();
+                }, children: "Finer" }), _jsx(ResetToDefaultButton, { title: resetTitle, disabled: resetDisabled, onClick: () => {
+                    onReset();
+                } })] }));
+});
+// A "Resolution" submenu whose single row is the inline stepper, so it sits
+// alongside the other track-menu submenus but keeps the menu open while
+// stepping. Callers own the label formatting, step bounds, and step actions.
+export function makeResolutionSubMenuItem(opts) {
+    const { getState, onFiner, onCoarser, onReset, icon, resetTitle } = opts;
+    return {
+        label: 'Resolution',
+        icon,
+        subMenu: [
+            {
+                label: 'Resolution stepper',
+                type: 'custom',
+                render: () => (_jsx(ResolutionStepper, { getState: getState, onFiner: onFiner, onCoarser: onCoarser, onReset: onReset, resetTitle: resetTitle })),
+            },
+        ],
+    };
+}

package/esm/ScoreRules.d.ts

@@ -0,0 +1,11 @@
+import type { ScoreRuleMark } from './scoreRuleMarks.ts';
+export declare function ScoreRuleLines({ marks, width, offsetY, }: {
+    marks: ScoreRuleMark[];
+    width: number;
+    offsetY?: number;
+}): import("react").JSX.Element;
+export default function ScoreRules({ marks, width, height, }: {
+    marks: ScoreRuleMark[];
+    width: number;
+    height: number;
+}): import("react").JSX.Element;

package/esm/ScoreRules.js

@@ -0,0 +1,37 @@
+import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { usePalette } from '@jbrowse/core/ui/PaletteContext';
+const DEFAULT_RULE_COLOR = 'rgb(120,120,120)';
+// Bare marks, no wrapping <svg>, so the on-screen overlay and the SVG export
+// draw the same elements from the same y. Same split as CrossHatchLines.
+export function ScoreRuleLines({ marks, width, offsetY = 0, }) {
+    // A caption sits over the plot, not beside it, so it needs the halo the tick
+    // labels next to it already draw (YScaleBar) — without one a rule crossing
+    // filled bars captions itself in grey on the fill and cannot be read. From
+    // the palette rather than a hardcoded white, which inverts into a glare in
+    // dark mode.
+    const haloColor = usePalette().background.default;
+    return (_jsx(_Fragment, { children: marks.map(({ value, label, color, y }) => {
+            const lineY = offsetY + y;
+            const stroke = color ?? DEFAULT_RULE_COLOR;
+            return (_jsxs("g", { children: [_jsx("line", { x1: 0, x2: width, y1: lineY, y2: lineY, stroke: stroke, 
+                        // separate attribute rather than an rgba() string: the SVG
+                        // export's renderToStaticMarkup strips rgba() alpha
+                        strokeOpacity: 0.9, strokeWidth: 1, strokeDasharray: "4 3" }), label ? (_jsx("text", { x: width - 4, y: lineY - 2, textAnchor: "end", fontSize: 10, 
+                        // full alpha, unlike the line: 0.9 is there to let the rule
+                        // recede into the plot, and a caption that has to be read wants
+                        // the opposite
+                        fill: stroke, stroke: haloColor, strokeWidth: 2.5, paintOrder: "stroke", children: label })) : null] }, `${value}-${y}`));
+        }) }));
+}
+// Pointer-events disabled so the canvas underneath still gets mouse events,
+// matching CrossHatches.
+export default function ScoreRules({ marks, width, height, }) {
+    return (_jsx("svg", { style: {
+            position: 'absolute',
+            top: 0,
+            left: 0,
+            pointerEvents: 'none',
+            height,
+            width,
+        }, children: _jsx(ScoreRuleLines, { marks: marks, width: width }) }));
+}