@jbrowse/wiggle-core 5.0.0-beta.13 → 5.0.0-beta.14

package/esm/autoscale.js

@@ -1,7 +1,7 @@
 import { fenceOutliers, quantileExtent, } from '@jbrowse/core/util/quantileExtent';
-/** The wiggle packer's arrays as a span, under a summary mode. */
-export function datasetSpan({ data, visStart, visEnd }, summaryScoreMode) {
-    const { low, high } = boundArrays(summaryScoreMode);
+/** The wiggle packer's arrays as a span, under an aggregate and an extent. */
+export function datasetSpan({ data, visStart, visEnd }, aggregate, extent) {
+    const { low, high } = boundArrays(aggregate, extent);
     return {
         count: data.numFeatures,
         starts: data.featurePositions,
@@ -17,13 +17,13 @@ export function datasetSpan({ data, visStart, visEnd }, summaryScoreMode) {
 }
 /**
  * #api
- * Per-feature scalar score array for a summary mode: the min/max summary array
+ * Per-feature scalar score array for an aggregate: the min/max summary array
  * for `'min'`/`'max'`, otherwise the average score.
  */
-export function getEffectiveScores(data, summaryScoreMode) {
-    return summaryScoreMode === 'min'
+export function getEffectiveScores(data, aggregate) {
+    return aggregate === 'min'
         ? data.featureMinScores
-        : summaryScoreMode === 'max'
+        : aggregate === 'max'
             ? data.featureMaxScores
             : data.featureScores;
 }
@@ -31,19 +31,15 @@ export function getEffectiveScores(data, summaryScoreMode) {
 function overlaps(fStart, fEnd, visStart, visEnd) {
     return fEnd > visStart && fStart < visEnd;
 }
-// Which per-feature array each end of the domain comes from. Whiskers spreads
-// the two ends across the min/max summary arrays; every other mode draws both
-// from a single scalar. One table because the extent and the clipped bound have
-// to read the same arrays, or a domain clips its own data.
-function boundArrays(summaryScoreMode) {
-    const useWhiskers = summaryScoreMode === 'whiskers';
+// Which per-feature array each end of the domain comes from. A min-max extent
+// spreads the two ends across the min/max summary arrays; without one both come
+// from the aggregate's single array. One table because the data's span and the
+// clipped bound have to read the same arrays, or a domain clips its own data.
+function boundArrays(aggregate, extent) {
+    const minMax = extent === 'min-max';
     return {
-        low: (data) => useWhiskers
-            ? data.featureMinScores
-            : getEffectiveScores(data, summaryScoreMode),
-        high: (data) => useWhiskers
-            ? data.featureMaxScores
-            : getEffectiveScores(data, summaryScoreMode),
+        low: (data) => minMax ? data.featureMinScores : getEffectiveScores(data, aggregate),
+        high: (data) => minMax ? data.featureMaxScores : getEffectiveScores(data, aggregate),
     };
 }
 // First index whose instance STARTS at or after `bp`. `starts` is sorted by
@@ -122,8 +118,8 @@ export function computeSpanStats(spans) {
         : undefined;
 }
 /** `computeSpanStats` over the wiggle packer's datasets. */
-export function computeScoreStats(summaryScoreMode, datasets) {
-    return computeSpanStats(datasets.map(d => datasetSpan(d, summaryScoreMode)));
+export function computeScoreStats(aggregate, datasets, extent) {
+    return computeSpanStats(datasets.map(d => datasetSpan(d, aggregate, extent)));
 }
 /**
  * #api
@@ -161,12 +157,12 @@ export function autoscaleDomainFromSpans({ stats, quantile, zero, spans, }) {
     });
 }
 /** `autoscaleDomainFromSpans` over the wiggle packer's datasets. */
-export function autoscaleDomainFromStats({ stats, quantile, zero, summaryScoreMode, visibleEntries, }) {
+export function autoscaleDomainFromStats({ stats, quantile, zero, aggregate, extent, visibleEntries, }) {
     return autoscaleDomainFromSpans({
         stats,
         quantile,
         zero,
-        spans: visibleEntries.map(d => datasetSpan(d, summaryScoreMode)),
+        spans: visibleEntries.map(d => datasetSpan(d, aggregate, extent)),
     });
 }
 /**
@@ -175,8 +171,8 @@ export function autoscaleDomainFromStats({ stats, quantile, zero, summaryScoreMo
  * `scales.y.domainQuantile` says, its outliers fenced for an axis that
  * reaches 0 under `zero`.
  */
-export function computeAutoscaleDomain(quantile, summaryScoreMode, visibleEntries, zero) {
-    const spans = visibleEntries.map(d => datasetSpan(d, summaryScoreMode));
+export function computeAutoscaleDomain(quantile, aggregate, visibleEntries, zero, extent = 'none') {
+    const spans = visibleEntries.map(d => datasetSpan(d, aggregate, extent));
     const stats = computeSpanStats(spans);
     return stats
         ? autoscaleDomainFromSpans({ stats, quantile, zero, spans })

package/esm/chrome.d.ts

@@ -1,4 +1,3 @@
 export { AxisGutter, CrossHatchLines, CrossHatches, ScoreDomainCaption, ScoreRuleLines, ScoreRules, YScaleBar, YScaleBarOverlay, } from '@jbrowse/display-ui';
 export { makeResolutionSubMenuItem } from './ResolutionStepper.tsx';
-export { makePointSizeSubMenu, pointSizeAccess } from './pointSizeMenu.tsx';
-export type { PointSizeAccess } from './pointSizeMenu.tsx';
+export { makeMarkSizeSubMenu } from './pointSizeMenu.tsx';

package/esm/chrome.js

@@ -3,4 +3,4 @@
 // an adapter or an RPC method never does.
 export { AxisGutter, CrossHatchLines, CrossHatches, ScoreDomainCaption, ScoreRuleLines, ScoreRules, YScaleBar, YScaleBarOverlay, } from '@jbrowse/display-ui';
 export { makeResolutionSubMenuItem } from './ResolutionStepper.js';
-export { makePointSizeSubMenu, pointSizeAccess } from './pointSizeMenu.js';
+export { makeMarkSizeSubMenu } from './pointSizeMenu.js';

package/esm/dataTypes.d.ts

@@ -20,4 +20,6 @@ export interface WiggleDataResult {
     zoomRange?: ZoomRange;
     /** The bounds the adapter's values lie in by definition (`getValueDomain`). */
     valueDomain?: [number, number];
+    /** What the adapter's source listing dropped or could not match. */
+    warnings?: string[];
 }

package/esm/index.d.ts

@@ -1,5 +1,5 @@
-export { retiredAxisSpellings, scalesSchema, valueScaleSchema, } from './valueScaleConfigSchema.ts';
-export type { ScalesConfigSchema, ValueScaleConfigSchema, ValueScaleOptions, } from './valueScaleConfigSchema.ts';
+export { retiredAxisSpellings, retiredScaleSpellings, scalesSchema, valueScaleOf, valueScaleSchema, } from './valueScaleConfigSchema.ts';
+export type { ScalesConfigSchema, ValueScaleConfigSchema, ValueScaleOptions, ValueScaleRuleConfig, } from './valueScaleConfigSchema.ts';
 export { getNiceDomain, getNiceScale, getScale } from './scale.ts';
 export type { ScaleOpts } from './scale.ts';
 export { toP } from './formatNumber.ts';
@@ -11,7 +11,6 @@ export { DEFAULT_RULE_COLOR, SCORE_CAPTION_HEIGHT, YSCALEBAR_LABEL_OFFSET, } fro
 export { AXIS_GUTTER_WIDTH_PX, axisPlotBox, clampStrokeInsideAxis, scoreToAxisY, } from '@jbrowse/display-ui/yScaleTicks';
 export type { ValueScale, ValueScaleRule, YAxis, YScaleTicks, } from '@jbrowse/display-ui';
 export { computeYTicks } from './computeYTicks.ts';
-export { rowLabelOffset } from './rowLabelOffset.ts';
 export { resolveRenderState } from './resolveRenderState.ts';
 export { visibleStatsDomain, visibleStatsRange } from './visibleStatsDomain.ts';
 export type { SettledBlocksView, VisibleEntry, VisibleStatsDomainSpec, VisibleStatsRangeSpec, } from './visibleStatsDomain.ts';
@@ -23,10 +22,10 @@ export type { ScoreAxisMenuItemOptions, ScoreRulesModel, ScoreScaleModel, } from
 export { ScoreAxisMixin } from './ScoreAxisMixin.ts';
 export { ScoreScaleMixin } from './ScoreScaleMixin.ts';
 export type { ScoreScaleHost } from './ScoreScaleMixin.ts';
-export { WiggleScoreConfigMixin, wiggleScoreConfigExtraSlots, } from './WiggleScoreConfigMixin.ts';
+export { WiggleScoreConfigMixin } from './WiggleScoreConfigMixin.ts';
 export type { WiggleScoreConfigHost } from './WiggleScoreConfigMixin.ts';
-export { ScoreFieldConfigMixin } from './ScoreFieldConfigMixin.ts';
-export { DEFAULT_SCORE_FIELD, scoreFieldConfigSchemaFields, } from './scoreFieldConfigSchemaFields.ts';
+export { YFieldConfigMixin } from './YFieldConfigMixin.ts';
+export { DEFAULT_SCORE_FIELD, yFieldConfigSchemaFields, } from './yFieldConfigSchemaFields.ts';
 export { MAX_WIGGLE_CUTS, MIN_FILL_WIDTH_PX, NO_PREV_START, RENDERING_TYPE_DENSITY, RENDERING_TYPE_LINE, RENDERING_TYPE_LINE_CENTER, RENDERING_TYPE_SCATTER, RENDERING_TYPE_XYPLOT, } from './renderingBackendTypes.ts';
 export type { SourceRenderData, WiggleGPURenderState, WiggleRenderingBackend, WiggleRenderingType, } from './renderingBackendTypes.ts';
 export type { SourceInfo, WiggleDataResult, WiggleFeatureArrays, WiggleSourceData, } from './dataTypes.ts';

package/esm/index.js

@@ -1,4 +1,4 @@
-export { retiredAxisSpellings, scalesSchema, valueScaleSchema, } from './valueScaleConfigSchema.js';
+export { retiredAxisSpellings, retiredScaleSpellings, scalesSchema, valueScaleOf, valueScaleSchema, } from './valueScaleConfigSchema.js';
 export { getNiceDomain, getNiceScale, getScale } from './scale.js';
 export { toP } from './formatNumber.js';
 export { SCALE_TYPE_LINEAR, SCALE_TYPE_LOG, SCALE_TYPE_SYMLOG, makeScoreNormalizer, resolveSymlogConstant, } from './normalize.js';
@@ -11,7 +11,6 @@ export { axisDrawn } from '@jbrowse/display-ui/axisPlacement';
 export { DEFAULT_RULE_COLOR, SCORE_CAPTION_HEIGHT, YSCALEBAR_LABEL_OFFSET, } from '@jbrowse/display-ui/yAxisConstants';
 export { AXIS_GUTTER_WIDTH_PX, axisPlotBox, clampStrokeInsideAxis, scoreToAxisY, } from '@jbrowse/display-ui/yScaleTicks';
 export { computeYTicks } from './computeYTicks.js';
-export { rowLabelOffset } from './rowLabelOffset.js';
 export { resolveRenderState } from './resolveRenderState.js';
 export { visibleStatsDomain, visibleStatsRange } from './visibleStatsDomain.js';
 export { scoreRuleMarks, widenRangeToRules } from './scoreRuleMarks.js';
@@ -19,9 +18,9 @@ export { DEFAULT_POINT_DIAMETER_PX, SMALL_POINT_MAX_DIAMETER_PX, appendPointMark
 export { COVERAGE_AXIS_LABEL, SCORE_RANGE_LABEL, Y_AXIS_LABEL, makeScoreAxisMenuItem, } from './scoreMenuItems.js';
 export { ScoreAxisMixin } from './ScoreAxisMixin.js';
 export { ScoreScaleMixin } from './ScoreScaleMixin.js';
-export { WiggleScoreConfigMixin, wiggleScoreConfigExtraSlots, } from './WiggleScoreConfigMixin.js';
-export { ScoreFieldConfigMixin } from './ScoreFieldConfigMixin.js';
-export { DEFAULT_SCORE_FIELD, scoreFieldConfigSchemaFields, } from './scoreFieldConfigSchemaFields.js';
+export { WiggleScoreConfigMixin } from './WiggleScoreConfigMixin.js';
+export { YFieldConfigMixin } from './YFieldConfigMixin.js';
+export { DEFAULT_SCORE_FIELD, yFieldConfigSchemaFields, } from './yFieldConfigSchemaFields.js';
 export { MAX_WIGGLE_CUTS, MIN_FILL_WIDTH_PX, NO_PREV_START, RENDERING_TYPE_DENSITY, RENDERING_TYPE_LINE, RENDERING_TYPE_LINE_CENTER, RENDERING_TYPE_SCATTER, RENDERING_TYPE_XYPLOT, } from './renderingBackendTypes.js';
 export {} from './displayModel.js';
 export { collectWiggleTransferables } from './transferables.js';

package/esm/pointSizeMenu.d.ts

@@ -1,32 +1,20 @@
-import type { ConfigModelForFields } from '@jbrowse/core/configuration';
 import type { MenuItem } from '@jbrowse/core/ui';
-/** Where a display keeps its point size: the value shown, its default, and the write. */
-export interface PointSizeAccess {
-    value: () => number;
-    defaultValue: number;
-    set: (n?: number) => void;
-}
-/**
- * The point size a display holding `WiggleScoreConfigMixin`'s `size` slot
- * shows and writes.
- */
-export declare function pointSizeAccess(self: {
-    size: number;
-    setSize: (n?: number) => void;
-    configuration: ConfigModelForFields<{
-        size: {
-            type: 'number';
-            defaultValue: number;
-        };
-    }>;
-}): PointSizeAccess;
+import type { ElementType } from 'react';
 /**
- * A top-level submenu holding the point-size slider, or nothing where the plot
- * draws no points, so every score plot's menu resets and clamps alike.
+ * A top-level submenu holding a mark's size slider, or nothing where the plot
+ * draws no such mark, so every score plot's menu resets and clamps alike.
  * Top-level rather than under Score because the size describes the mark, not
  * the axis.
  */
-export declare function makePointSizeSubMenu({ label, applies, value, defaultValue, set, }: PointSizeAccess & {
+export declare function makeMarkSizeSubMenu({ label, title, icon, applies, value, isDefault, set, min, max, step, }: {
     label: string;
+    title?: string;
+    icon?: ElementType;
     applies: boolean;
+    value: () => number;
+    isDefault: boolean;
+    set: (n?: number) => void;
+    min?: number;
+    max?: number;
+    step?: number;
 }): MenuItem[];

package/esm/pointSizeMenu.js

@@ -1,37 +1,26 @@
-import { getSlotDefinition } from '@jbrowse/core/configuration';
 import { makeSizeMenu } from '@jbrowse/core/ui';
 import ScatterPlotIcon from '@mui/icons-material/ScatterPlot';
 /**
- * The point size a display holding `WiggleScoreConfigMixin`'s `size` slot
- * shows and writes.
- */
-export function pointSizeAccess(self) {
-    return {
-        value: () => self.size,
-        defaultValue: Number(getSlotDefinition(self.configuration, 'size').defaultValue),
-        set: n => {
-            self.setSize(n);
-        },
-    };
-}
-/**
- * A top-level submenu holding the point-size slider, or nothing where the plot
- * draws no points, so every score plot's menu resets and clamps alike.
+ * A top-level submenu holding a mark's size slider, or nothing where the plot
+ * draws no such mark, so every score plot's menu resets and clamps alike.
  * Top-level rather than under Score because the size describes the mark, not
  * the axis.
  */
-export function makePointSizeSubMenu({ label, applies, value, defaultValue, set, }) {
+export function makeMarkSizeSubMenu({ label, title = 'Point size', icon = ScatterPlotIcon, applies, value, isDefault, set, min, max, step, }) {
     return applies
         ? [
             {
                 label,
-                icon: ScatterPlotIcon,
+                icon,
                 subMenu: [
                     makeSizeMenu({
                         label,
-                        title: 'Point size',
+                        title,
+                        min,
+                        max,
+                        step,
                         getValue: value,
-                        isDefault: value() === defaultValue,
+                        isDefault,
                         onChange: set,
                         onReset: () => {
                             set();

package/esm/renderingBackendTypes.d.ts

@@ -41,6 +41,7 @@ export interface SourceRenderData {
     colorsAbgr?: Uint32Array;
     negColor?: [number, number, number];
     gapLimitBp?: number;
+    gapScore?: number;
     band?: {
         minScores: Float32Array;
     };

package/esm/renderingBackendTypes.js

@@ -27,6 +27,6 @@ export const NO_PREV_START = GENERATED_NO_PREV_START;
 // It was a `1.5` in each, kept together by a comment in each pointing at the
 // other.
 export const MIN_FILL_WIDTH_PX = GENERATED_MIN_FILL_WIDTH_PX;
-// The most cuts a threshold colour parts a plot at: the shader's uniform
+// The most cuts a threshold color parts a plot at: the shader's uniform
 // block holds this many.
 export const MAX_WIGGLE_CUTS = GENERATED_MAX_WIGGLE_CUTS;

package/esm/scale.d.ts

@@ -37,10 +37,11 @@ export declare function getScale({ domain, range, scaleType, symlogConstant, nic
 /**
  * #api
  * Rounds a domain to "nice" endpoints. `zero` reaches a linear or symlog
- * domain to 0 (`scales.y.zero`, ADR-182); a log domain has no 0 and floors at
- * 1 instead. 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.
+ * domain to 0 (`scales.y.zero`, ADR-182); a log domain has no 0, so a min at
+ * or below it floors to a positive value and a positive min stays where the
+ * data put it. 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, which the `log-floor` rule reports.
  *
  * The result never descends and never collapses: a bound that would put `min`
  * above `max` widens the other end instead, and one value in view widens

package/esm/scale.js

@@ -65,10 +65,11 @@ export function getScale({ domain, range, scaleType, symlogConstant, nice = true
 /**
  * #api
  * Rounds a domain to "nice" endpoints. `zero` reaches a linear or symlog
- * domain to 0 (`scales.y.zero`, ADR-182); a log domain has no 0 and floors at
- * 1 instead. 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.
+ * domain to 0 (`scales.y.zero`, ADR-182); a log domain has no 0, so a min at
+ * or below it floors to a positive value and a positive min stays where the
+ * data put it. 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, which the `log-floor` rule reports.
  *
  * The result never descends and never collapses: a bound that would put `min`
  * above `max` widens the other end instead, and one value in view widens
@@ -92,11 +93,6 @@ export function getNiceDomain({ scaleType, domain, bounds, zero, }) {
             min = 0;
         }
     }
-    if (scaleType === 'log') {
-        if (min >= 0 && max > 1) {
-            min = 1;
-        }
-    }
     if (minScore !== undefined) {
         min = minScore;
     }

package/esm/valueScaleConfigSchema.d.ts

@@ -41,7 +41,7 @@ export type ValueScaleRuleConfig = Instance<ReturnType<typeof valueScaleRuleSche
  *
  * 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.
  *
@@ -180,6 +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
@@ -56,7 +57,7 @@ function valueScaleRuleSchema() {
  *
  * 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.
  *
@@ -117,8 +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.
@@ -156,7 +157,7 @@ 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.
+         * color and has no axis, spans its values whatever this says.
          * The Y axis panel's "Include 0" toggles it.
          */
         zero: {
@@ -192,15 +193,15 @@ export function valueScaleSchema({ domainQuantile = 1, symlogConstant = 0, } = {
         },
         /**
          * #slot scales.y.domainQuantile
-         * Where an unpinned end's outliers are fenced. An end follows the
+         * 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 colour ramp's `domainQuantile` clips at the
-         * quantile itself, since a saturated colour hides nothing its key does
+         * 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: {
@@ -262,6 +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.13",
+  "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": [
@@ -33,15 +33,15 @@
     "esm"
   ],
   "dependencies": {
-    "@jbrowse/mobx-state-tree": "^6.7.0",
-    "@mui/icons-material": "^9.4.0",
-    "@mui/material": "^9.4.0",
+    "@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.13",
-    "@jbrowse/display-kit": "^5.0.0-beta.13",
-    "@jbrowse/render-core": "^5.0.0-beta.13",
-    "@jbrowse/display-ui": "^5.0.0-beta.13"
+    "@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/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/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;