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

package/esm/valueScaleConfigSchema.d.ts

@@ -1,7 +1,7 @@
 import type { Instance } from '@jbrowse/mobx-state-tree';
 export declare const VALUE_SCALE_TYPES: readonly ['linear', 'log', 'symlog'];
 export interface ValueScaleOptions {
-    /** `domainQuantile`'s default: 1 follows the extremes, 0.99 clips the outermost 1% */
+    /** `domainQuantile`'s default: 1 follows the extremes, 0.99 fences a spike */
     domainQuantile?: number;
     /** `symlogConstant`'s default */
     symlogConstant?: number;
@@ -35,14 +35,13 @@ export type ValueScaleRuleConfig = Instance<ReturnType<typeof valueScaleRuleSche
  * autoscaled linear or symlog axis reaches 0 whatever those regions hold.
  *
  * Two defaults come from the display rather than from the scale.
- * `domainQuantile` starts at `0.99` on the wiggle plot, clipping the outermost
- * 1% of each sign, and at `1`, the extremes, on the coverage band and the mark
- * display. `symlogConstant` starts at `0` on the wiggle family and the mark
+ * `domainQuantile` starts at `0.99` on the wiggle plot, fencing a spike, and
+ * at `1`, the extremes, on the coverage band and the mark display. `symlogConstant` starts at `0` on the wiggle family and the mark
  * display and at `1` on the coverage band.
  *
  * Every scale carries the same guides: `rules`, reference lines at chosen
  * values, `grid`, a line at every tick, `minimalTicks`, and `title`, the
- * caption beside the axis. A rule naming no `color` draws in the one colour
+ * caption beside the axis. A rule naming no `color` draws in the one color
  * the chrome rules every plot in, so a red line is a claim its author makes
  * rather than a meaning a display assigns.
  *
@@ -65,7 +64,7 @@ export type ValueScaleRuleConfig = Instance<ReturnType<typeof valueScaleRuleSche
  * ```
  *
  * #example
- * The whole visible range, rather than the 99th percentile the wiggle
+ * The whole visible range, spikes included, rather than the fence the wiggle
  * displays start on:
  * ```js
  * {
@@ -181,6 +180,81 @@ export declare const retiredAxisSpellings: {
         };
     };
 };
+/**
+ * v4's display-level scale settings as the `scales.y` members they became.
+ * `localpercentile` is a clip; `local`, `localsd`, `global` and `globalsd`
+ * all follow the extremes closely enough to become one.
+ */
+export declare function valueScaleOf({ scale, autoscale, constraints, }: Record<string, unknown>): {
+    scales: {
+        y: {
+            type?: string | undefined;
+            domainQuantile?: number | undefined;
+            domainMin?: number | undefined;
+            domainMax?: number | undefined;
+        };
+    };
+} | {
+    scales?: undefined;
+};
+/**
+ * The scale slots v4 declared on a display, as `retired` declares them on
+ * each display whose `scales.y` took them over. `minScore` and `maxScore`
+ * were unset at v4's own sentinels; `numStdDev` and `inverted` have no
+ * successor and are let go.
+ */
+export declare const retiredScaleSpellings: {
+    scaleType: (scale: unknown) => {
+        scales: {
+            y: {
+                type?: string | undefined;
+                domainQuantile?: number | undefined;
+                domainMin?: number | undefined;
+                domainMax?: number | undefined;
+            };
+        };
+    } | {
+        scales?: undefined;
+    };
+    autoscale: (autoscale: unknown) => {
+        scales: {
+            y: {
+                type?: string | undefined;
+                domainQuantile?: number | undefined;
+                domainMin?: number | undefined;
+                domainMax?: number | undefined;
+            };
+        };
+    } | {
+        scales?: undefined;
+    };
+    minScore: (min: unknown) => {
+        scales: {
+            y: {
+                type?: string | undefined;
+                domainQuantile?: number | undefined;
+                domainMin?: number | undefined;
+                domainMax?: number | undefined;
+            };
+        };
+    } | {
+        scales?: undefined;
+    };
+    maxScore: (max: unknown) => {
+        scales: {
+            y: {
+                type?: string | undefined;
+                domainQuantile?: number | undefined;
+                domainMin?: number | undefined;
+                domainMax?: number | undefined;
+            };
+        };
+    } | {
+        scales?: undefined;
+    };
+    numStdDev: () => {};
+    inverted: () => {};
+};
 /**
  * The `scales` object a display declares, one member per aesthetic the
  * grammar gives a scale. `y` is the only one so far, and every mark, bar or

package/esm/valueScaleConfigSchema.js

@@ -1,11 +1,12 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { DEFAULT_CLIP_QUANTILE } from '@jbrowse/core/util/quantileExtent';
 import { types } from '@jbrowse/mobx-state-tree';
 export const VALUE_SCALE_TYPES = ['linear', 'log', 'symlog'];
 function valueScaleRuleSchema() {
     return ConfigurationSchema('ValueScaleRule', {
         /**
          * #slot scales.y.rules.value
-         * Where the rule sits on the axis, in the units the axis plots: a
+         * The rule's position on the axis, in the units the axis plots: a
          * `-log10(p)` over a Manhattan plot, a depth over coverage.
          */
         value: {
@@ -15,14 +16,14 @@ function valueScaleRuleSchema() {
         },
         /**
          * #slot scales.y.rules.color
-         * The line's colour, and its label's. Unset draws every rule in the one
-         * colour the chrome rules plots in, so a threshold that means something
+         * The line's color, and its label's. Unset draws every rule in the one
+         * color the chrome rules plots in, so a threshold that means something
          * particular — genome-wide significance, a diploid depth — is one an
          * author paints, on the plot where it means it.
          */
         color: {
             type: 'maybeColor',
-            description: 'line and label colour; unset is the chrome’s own',
+            description: 'line and label color; unset is the chrome’s own',
         },
         /**
          * #slot scales.y.rules.label
@@ -50,14 +51,13 @@ function valueScaleRuleSchema() {
  * autoscaled linear or symlog axis reaches 0 whatever those regions hold.
  *
  * Two defaults come from the display rather than from the scale.
- * `domainQuantile` starts at `0.99` on the wiggle plot, clipping the outermost
- * 1% of each sign, and at `1`, the extremes, on the coverage band and the mark
- * display. `symlogConstant` starts at `0` on the wiggle family and the mark
+ * `domainQuantile` starts at `0.99` on the wiggle plot, fencing a spike, and
+ * at `1`, the extremes, on the coverage band and the mark display. `symlogConstant` starts at `0` on the wiggle family and the mark
  * display and at `1` on the coverage band.
  *
  * Every scale carries the same guides: `rules`, reference lines at chosen
  * values, `grid`, a line at every tick, `minimalTicks`, and `title`, the
- * caption beside the axis. A rule naming no `color` draws in the one colour
+ * caption beside the axis. A rule naming no `color` draws in the one color
  * the chrome rules every plot in, so a red line is a claim its author makes
  * rather than a meaning a display assigns.
  *
@@ -80,7 +80,7 @@ function valueScaleRuleSchema() {
  * ```
  *
  * #example
- * The whole visible range, rather than the 99th percentile the wiggle
+ * The whole visible range, spikes included, rather than the fence the wiggle
  * displays start on:
  * ```js
  * {
@@ -118,8 +118,8 @@ export function valueScaleSchema({ domainQuantile = 1, symlogConstant = 0, } = {
     return ConfigurationSchema('ValueScale', {
         /**
          * #slot scales.y.type
-         * How the axis reads its domain — the ticks, the cross-hatches and the
-         * renderer's placement all come from it. `log` cannot represent 0 or
+         * The axis's scale type, which sets the ticks, the cross-hatches and the
+         * renderer's placement. `log` cannot represent 0 or
          * negative values and floors the domain above them; `symlog` is log-like
          * away from zero and linear through it, so a track whose values touch or
          * cross 0 keeps them.
@@ -135,8 +135,8 @@ export function valueScaleSchema({ domainQuantile = 1, symlogConstant = 0, } = {
         /**
          * #slot scales.y.domainMin
          * The bottom of the axis, pinning what would otherwise autoscale to the
-         * loaded regions. Unset autoscales that end. The score menu's "Set
-         * min/max" writes here.
+         * loaded regions. Unset autoscales that end. The Y axis panel's Min
+         * field writes here.
          */
         domainMin: {
             type: 'maybeNumber',
@@ -157,8 +157,8 @@ export function valueScaleSchema({ domainQuantile = 1, symlogConstant = 0, } = {
          * 30 and 60 draws 0 to 60, and a bar always shows its whole height.
          * Off, the axis spans the values alone. A pinned end is unmoved either
          * way, a log axis has no 0, and a density plot, which maps score to
-         * colour and has no axis, spans its values whatever this says.
-         * The score menu's "Start axis at 0" toggles it.
+         * color and has no axis, spans its values whatever this says.
+         * The Y axis panel's "Include 0" toggles it.
          */
         zero: {
             type: 'boolean',
@@ -170,8 +170,8 @@ export function valueScaleSchema({ domainQuantile = 1, symlogConstant = 0, } = {
          * A name shared by the tracks whose axes autoscale together: each
          * unpinned end spans the data of every track in the view naming the
          * same group, so three coverage lanes stay comparable as the view
-         * moves. A pinned end stays this track's own. The score menu's
-         * "Autoscale with other tracks" writes it.
+         * moves. A pinned end stays this track's own. The Y axis panel's
+         * "Share axis with" writes it.
          */
         autoscaleGroup: {
             type: 'maybeString',
@@ -193,24 +193,27 @@ export function valueScaleSchema({ domainQuantile = 1, symlogConstant = 0, } = {
         },
         /**
          * #slot scales.y.domainQuantile
-         * What an unpinned end follows over the loaded values: `1` their
-         * extremes, and below it that quantile of the values on its side of 0,
-         * so `0.99` drops the outermost 1% at each end and one spike no longer
-         * flattens the rest. Where both signs appear each end is measured on its
-         * own sign, so a sparse minority tail stays visible; whether the axis
-         * then reaches 0 is `zero`'s. The score menu's "Clip outliers" toggles
-         * it.
+         * The fence for an unpinned end's outliers. An end follows the
+         * loaded values' extreme; below `1`, an extreme that would stretch the
+         * axis past twice the span this quantile of the values draws stops at
+         * that fence, and the bars past it wear the red clip strip. So `0.99`
+         * leaves a plot with no spike whole and keeps one spike from flattening
+         * the rest. Each end's quantile is measured among the values on its side
+         * of 0, so a sparse minority tail stays visible, and the span includes 0
+         * where `zero` reaches it. A color ramp's `domainQuantile` clips at the
+         * quantile itself, since a saturated color hides nothing its key does
+         * not say. The Y axis panel's "Clip extreme outliers" toggles it.
          */
         domainQuantile: {
             type: 'number',
             defaultValue: domainQuantile,
-            description: 'the quantile an unpinned end follows: 1 the extremes, 0.99 drops the outermost 1% at each end, each sign measured on its own',
+            description: 'fences outliers: 1 follows the extremes; below it an extreme past twice the span this quantile draws is cut there',
         },
         /**
          * #slot scales.y.grid
          * Rule the plot across at every tick, ggplot2's panel grid and
-         * Vega-Lite's `axis.grid`. The score menu's "Show cross hatches"
-         * toggles it.
+         * Vega-Lite's `axis.grid`. The Y axis panel's "Grid lines" toggles
+         * it.
          */
         grid: {
             type: 'boolean',
@@ -260,6 +263,43 @@ export const retiredAxisSpellings = {
         scales: { y: { minimalTicks } },
     }),
 };
+const isRecord = (v) => !!v && typeof v === 'object' && !Array.isArray(v);
+/**
+ * v4's display-level scale settings as the `scales.y` members they became.
+ * `localpercentile` is a clip; `local`, `localsd`, `global` and `globalsd`
+ * all follow the extremes closely enough to become one.
+ */
+export function valueScaleOf({ scale, autoscale, constraints, }) {
+    const y = {
+        ...(typeof scale === 'string' ? { type: scale } : {}),
+        ...(typeof autoscale === 'string'
+            ? {
+                domainQuantile: autoscale === 'localpercentile' ? DEFAULT_CLIP_QUANTILE : 1,
+            }
+            : {}),
+        ...(isRecord(constraints) && typeof constraints.min === 'number'
+            ? { domainMin: constraints.min }
+            : {}),
+        ...(isRecord(constraints) && typeof constraints.max === 'number'
+            ? { domainMax: constraints.max }
+            : {}),
+    };
+    return Object.keys(y).length > 0 ? { scales: { y } } : {};
+}
+/**
+ * The scale slots v4 declared on a display, as `retired` declares them on
+ * each display whose `scales.y` took them over. `minScore` and `maxScore`
+ * were unset at v4's own sentinels; `numStdDev` and `inverted` have no
+ * successor and are let go.
+ */
+export const retiredScaleSpellings = {
+    scaleType: (scale) => valueScaleOf({ scale }),
+    autoscale: (autoscale) => valueScaleOf({ autoscale }),
+    minScore: (min) => min === Number.MIN_VALUE ? {} : valueScaleOf({ constraints: { min } }),
+    maxScore: (max) => max === Number.MAX_VALUE ? {} : valueScaleOf({ constraints: { max } }),
+    numStdDev: () => ({}),
+    inverted: () => ({}),
+};
 /**
  * The `scales` object a display declares, one member per aesthetic the
  * grammar gives a scale. `y` is the only one so far, and every mark, bar or

package/esm/yFieldConfigSchemaFields.d.ts

@@ -0,0 +1,10 @@
+import type { ConfigModelForFields } from '@jbrowse/core/configuration';
+export declare const DEFAULT_SCORE_FIELD = "score";
+export declare const yFieldConfigSchemaFields: {
+    readonly y: {
+        readonly type: 'featureField';
+        readonly defaultValue: "score";
+        readonly description: "the feature field plotted on the value axis, as a mark's encoding.y names one: a name, a dotted path or a `jexl:` expression. The default `score` is the field every adapter serves, including the value a BED adapter's `scoreColumn` rewrote it to; an explicit name reaches a raw column the adapter left alone (a BED extra column, a GFF attribute). A feature with no finite value in the field plots at 0";
+    };
+};
+export type YFieldConfigModel = ConfigModelForFields<typeof yFieldConfigSchemaFields>;

package/esm/yFieldConfigSchemaFields.js

@@ -0,0 +1,8 @@
+export const DEFAULT_SCORE_FIELD = 'score';
+export const yFieldConfigSchemaFields = {
+    y: {
+        type: 'featureField',
+        defaultValue: DEFAULT_SCORE_FIELD,
+        description: "the feature field plotted on the value axis, as a mark's encoding.y names one: a name, a dotted path or a `jexl:` expression. The default `score` is the field every adapter serves, including the value a BED adapter's `scoreColumn` rewrote it to; an explicit name reaches a raw column the adapter left alone (a BED extra column, a GFF attribute). A feature with no finite value in the field plots at 0",
+    },
+};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/wiggle-core",
-  "version": "5.0.0-beta.11",
+  "version": "5.0.0-beta.14",
   "type": "module",
   "description": "Score-axis scale, autoscale, config mixins and plot chrome shared by wiggle, Manhattan, mark and coverage displays",
   "keywords": [
@@ -26,21 +26,22 @@
     "./chrome": "./esm/chrome.js",
     "./constants": "./esm/constants.js",
     "./normalize": "./esm/normalize.js",
-    "./renderingBackendTypes": "./esm/renderingBackendTypes.js"
+    "./renderingBackendTypes": "./esm/renderingBackendTypes.js",
+    "./scoreAxisWidget": "./esm/ScoreAxisWidget/index.js"
   },
   "files": [
     "esm"
   ],
   "dependencies": {
-    "@jbrowse/mobx-state-tree": "^6.7.0",
-    "@mui/icons-material": "^9.4.0",
-    "@mui/material": "^9.4.0",
-    "mobx": "^7.0.5",
+    "@jbrowse/mobx-state-tree": "^6.9.0",
+    "@mui/icons-material": "^9.5.0",
+    "@mui/material": "^9.5.0",
+    "mobx": "^7.0.6",
     "mobx-react": "^10.0.2",
-    "@jbrowse/core": "^5.0.0-beta.11",
-    "@jbrowse/display-ui": "^5.0.0-beta.11",
-    "@jbrowse/display-kit": "^5.0.0-beta.11",
-    "@jbrowse/render-core": "^5.0.0-beta.11"
+    "@jbrowse/display-ui": "^5.0.0-beta.14",
+    "@jbrowse/render-core": "^5.0.0-beta.14",
+    "@jbrowse/display-kit": "^5.0.0-beta.14",
+    "@jbrowse/core": "^5.0.0-beta.14"
   },
   "peerDependencies": {
     "react": ">=19.0.0",

package/esm/AutoscaleGroupDialog.d.ts

@@ -1,7 +0,0 @@
-import type { AutoscalePeer } from './autoscaleGroup.ts';
-import type { IStateTreeNode } from '@jbrowse/mobx-state-tree';
-declare const _default: ({ model, handleClose, }: {
-    model: AutoscalePeer & IStateTreeNode;
-    handleClose: () => void;
-}) => import("react").JSX.Element;
-export default _default;

package/esm/AutoscaleGroupDialog.js

@@ -1,26 +0,0 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { useState } from 'react';
-import { LabeledCheckbox, SubmitDialog } from '@jbrowse/core/ui';
-import { Typography } from '@mui/material';
-import { observer } from 'mobx-react';
-import { autoscalePeers, autoscaleWith } from './autoscaleGroup.js';
-export default observer(function AutoscaleGroupDialog({ model, handleClose, }) {
-    const peers = autoscalePeers(model);
-    const group = model.autoscaleGroup;
-    const [chosen, setChosen] = useState(() => new Set(group === undefined
-        ? []
-        : peers.map(p => p.display).filter(d => d.autoscaleGroup === group)));
-    return (_jsxs(SubmitDialog, { open: true, title: "Autoscale with other tracks", submitText: "Apply", onCancel: handleClose, onSubmit: () => {
-            autoscaleWith(model, peers.map(p => p.display), chosen);
-            handleClose();
-        }, children: [_jsx(Typography, { color: "text.secondary", children: "The tracks ticked here share this track's axis: each end nobody pinned spans all of their data, and follows it as the view moves." }), peers.map(({ display, key, name }) => (_jsx("div", { children: _jsx(LabeledCheckbox, { checked: chosen.has(display), label: name, onChange: checked => {
-                        const next = new Set(chosen);
-                        if (checked) {
-                            next.add(display);
-                        }
-                        else {
-                            next.delete(display);
-                        }
-                        setChosen(next);
-                    } }) }, key)))] }));
-});

package/esm/ScoreFieldConfigMixin.js

@@ -1,25 +0,0 @@
-import { getConf } from '@jbrowse/core/configuration';
-import { WiggleScoreConfigMixin } from './WiggleScoreConfigMixin.js';
-const confNode = (self) => self;
-/**
- * #stateModel ScoreFieldConfigMixin
- * #category display
- *
- * `WiggleScoreConfigMixin` plus `scoreField`, for a display that plots one
- * configured feature field and so declares `scoreFieldConfigSchemaFields`:
- * the wiggle display. `LinearMarkDisplay` names a field per mark and composes
- * the base instead.
- */
-export function ScoreFieldConfigMixin() {
-    return WiggleScoreConfigMixin().views(self => ({
-        /**
-         * #getter
-         * The feature field the worker plots on the score axis, `score` by
-         * default. A fetch input: every composing display carries it in its
-         * `rpcProps()`, since the field is read where the features are.
-         */
-        get scoreField() {
-            return getConf(confNode(self), 'scoreField');
-        },
-    }));
-}

package/esm/SetMinMaxDialog.d.ts

@@ -1,12 +0,0 @@
-declare const _default: (props: {
-    model: {
-        manualMinScore: number | undefined;
-        manualMaxScore: number | undefined;
-        scaleType: string;
-        setMinScore: (arg?: number) => void;
-        setMaxScore: (arg?: number) => void;
-    };
-    domain?: [number, number];
-    handleClose: () => void;
-}) => import("react").JSX.Element;
-export default _default;

package/esm/SetMinMaxDialog.js

@@ -1,32 +0,0 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { useState } from 'react';
-import { NumberTextField, SubmitDialog } from '@jbrowse/core/ui';
-import { Button, Typography } from '@mui/material';
-import { observer } from 'mobx-react';
-// The two fields open on what the config really pins, which is the mixin's
-// `manual*` pair rather than the raw slots — the sentinel comparison is one
-// answer per end and lives there. Submitting `undefined` writes the sentinel
-// back, so an emptied field is how autoscale resumes.
-export default observer(function SetMinMaxDialog(props) {
-    const { model, domain, handleClose } = props;
-    const { manualMinScore, manualMaxScore, scaleType } = model;
-    const [min, setMin] = useState(manualMinScore);
-    const [max, setMax] = useState(manualMaxScore);
-    // The fields own their text, so filling them from the button remounts them.
-    const [fill, setFill] = useState(0);
-    const rangeOk = min === undefined || max === undefined || max > min;
-    const logOk = !(scaleType === 'log' && min !== undefined && min <= 0);
-    return (_jsxs(SubmitDialog, { open: true, title: "Set min/max score for track", submitDisabled: !rangeOk || !logOk, onCancel: handleClose, onSubmit: () => {
-            model.setMinScore(min);
-            model.setMaxScore(max);
-            handleClose();
-        }, children: [_jsx(Typography, { children: "Enter min/max score, or leave a field empty to autoscale that end" }), !rangeOk ? (_jsx(Typography, { color: "error", children: "Max must be greater than min" })) : null, !logOk ? (_jsx(Typography, { color: "error", children: "Min score should be greater than 0 for log scale" })) : null, _jsx(NumberTextField, { defaultValue: min, onValueChange: setMin, placeholder: "Enter min score" }, `min-${fill}`), _jsx(NumberTextField, { defaultValue: max, onValueChange: setMax, placeholder: "Enter max score" }, `max-${fill}`), _jsxs("div", { children: [domain ? (_jsx(Button, { onClick: () => {
-                            setMin(domain[0]);
-                            setMax(domain[1]);
-                            setFill(n => n + 1);
-                        }, children: "Use current range" })) : null, _jsx(Button, { disabled: min === undefined && max === undefined, onClick: () => {
-                            setMin(undefined);
-                            setMax(undefined);
-                            setFill(n => n + 1);
-                        }, children: "Clear" })] })] }));
-});

package/esm/SetScoreRulesDialog.d.ts

@@ -1,14 +0,0 @@
-import type { ValueScaleRule } from '@jbrowse/display-ui';
-/**
- * The score menu's editor for `scales.y.rules`: one row per reference line,
- * its value on the plot's own scale, its label and its colour. An empty colour
- * is the display's default, and removing every row removes every line.
- */
-declare const _default: ({ model, handleClose, }: {
-    model: {
-        scoreRules: ValueScaleRule[];
-        setScoreRules: (rules: ValueScaleRule[]) => void;
-    };
-    handleClose: () => void;
-}) => import("react").JSX.Element;
-export default _default;

package/esm/SetScoreRulesDialog.js

@@ -1,45 +0,0 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { useState } from 'react';
-import { SubmitDialog } from '@jbrowse/core/ui';
-import { isCssColor } from '@jbrowse/core/util/colorBits';
-import DeleteIcon from '@mui/icons-material/Delete';
-import { Button, IconButton, TextField, Typography } from '@mui/material';
-import { observer } from 'mobx-react';
-function rowOf({ value, label = '', color = '' }) {
-    return { value: String(value), label, color };
-}
-function valueOk({ value }) {
-    return value.trim() !== '' && Number.isFinite(Number(value));
-}
-function colorOk({ color }) {
-    return color.trim() === '' || isCssColor(color);
-}
-/**
- * The score menu's editor for `scales.y.rules`: one row per reference line,
- * its value on the plot's own scale, its label and its colour. An empty colour
- * is the display's default, and removing every row removes every line.
- */
-export default observer(function SetScoreRulesDialog({ model, handleClose, }) {
-    const [rows, setRows] = useState(() => model.scoreRules.map(rowOf));
-    const setRow = (index, patch) => {
-        setRows(rows.map((row, i) => (i === index ? { ...row, ...patch } : row)));
-    };
-    return (_jsxs(SubmitDialog, { open: true, title: "Reference lines", submitDisabled: !rows.every(row => valueOk(row) && colorOk(row)), onCancel: handleClose, onSubmit: () => {
-            model.setScoreRules(rows.map(row => ({
-                value: Number(row.value),
-                ...(row.label ? { label: row.label } : {}),
-                ...(row.color.trim() ? { color: row.color.trim() } : {}),
-            })));
-            handleClose();
-        }, children: [_jsx(Typography, { children: "A horizontal line at each value, on the same scale as the plot" }), rows.map((row, index) => (_jsxs("div", { style: { display: 'flex', gap: 8, marginTop: 8 }, children: [_jsx(TextField, { label: "Value", value: row.value, error: !valueOk(row), onChange: event => {
-                            setRow(index, { value: event.target.value });
-                        } }), _jsx(TextField, { label: "Label", value: row.label, onChange: event => {
-                            setRow(index, { label: event.target.value });
-                        } }), _jsx(TextField, { label: "Color", value: row.color, error: !colorOk(row), onChange: event => {
-                            setRow(index, { color: event.target.value });
-                        } }), _jsx(IconButton, { "aria-label": "remove line", onClick: () => {
-                            setRows(rows.filter((_, i) => i !== index));
-                        }, children: _jsx(DeleteIcon, {}) })] }, index))), _jsx(Button, { onClick: () => {
-                    setRows([...rows, { value: '', label: '', color: '' }]);
-                }, children: "Add line" })] }));
-});

package/esm/rowLabelOffset.d.ts

@@ -1,8 +0,0 @@
-import type { YAxis } from '@jbrowse/display-ui';
-/**
- * Where row labels start: `offset`, past the dendrogram, or past the axis each
- * row repeats where one draws, since a label grows rightward over the plot.
- * `exportContentLeft` is the export shell's, which moves an axis nothing
- * pushes right into the margin, so the labels follow it there.
- */
-export declare function rowLabelOffset(axes: readonly YAxis[], offset: number, exportContentLeft?: number): number;

package/esm/rowLabelOffset.js

@@ -1,16 +0,0 @@
-import { axisDrawn, axisGutterLeft, axisGutterWidth, } from '@jbrowse/display-ui/axisPlacement';
-const AXIS_TO_LABEL_GAP_PX = 4;
-/**
- * Where row labels start: `offset`, past the dendrogram, or past the axis each
- * row repeats where one draws, since a label grows rightward over the plot.
- * `exportContentLeft` is the export shell's, which moves an axis nothing
- * pushes right into the margin, so the labels follow it there.
- */
-export function rowLabelOffset(axes, offset, exportContentLeft) {
-    const axis = axes.find(axisDrawn);
-    return axis
-        ? Math.max(offset, axisGutterLeft(axis, 0, 0, exportContentLeft) +
-            axisGutterWidth(axis) +
-            AXIS_TO_LABEL_GAP_PX)
-        : offset;
-}

package/esm/scoreFieldConfigSchemaFields.d.ts

@@ -1,10 +0,0 @@
-import type { ConfigModelForFields } from '@jbrowse/core/configuration';
-export declare const DEFAULT_SCORE_FIELD = "score";
-export declare const scoreFieldConfigSchemaFields: {
-    readonly scoreField: {
-        readonly type: 'string';
-        readonly defaultValue: "score";
-        readonly description: "Feature field plotted on the score axis, read natively off each feature. The default `score` is the field every adapter serves — including the value a BED adapter's `scoreColumn` rewrote it to — so an explicit name here reaches a raw column the adapter left alone (a BED extra column, a GFF attribute) and takes precedence over that adapter-tier rewrite. The Manhattan plot skips a feature with no finite value in the field; the wiggle renderings plot it at 0";
-    };
-};
-export type ScoreFieldConfigModel = ConfigModelForFields<typeof scoreFieldConfigSchemaFields>;

package/esm/scoreFieldConfigSchemaFields.js

@@ -1,8 +0,0 @@
-export const DEFAULT_SCORE_FIELD = 'score';
-export const scoreFieldConfigSchemaFields = {
-    scoreField: {
-        type: 'string',
-        defaultValue: DEFAULT_SCORE_FIELD,
-        description: "Feature field plotted on the score axis, read natively off each feature. The default `score` is the field every adapter serves — including the value a BED adapter's `scoreColumn` rewrote it to — so an explicit name here reaches a raw column the adapter left alone (a BED extra column, a GFF attribute) and takes precedence over that adapter-tier rewrite. The Manhattan plot skips a feature with no finite value in the field; the wiggle renderings plot it at 0",
-    },
-};