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

package/README.md

@@ -33,7 +33,7 @@ under `zero`.
 
 ```js
 // type signature
-(quantile: number, summaryScoreMode: string, visibleEntries: { data: FeatureArrays; visStart: number; visEnd: number; }[], zero: boolean) => [number, number] | undefined
+(quantile: number, aggregate: string, visibleEntries: { data: FeatureArrays; visStart: number; visEnd: number; }[], zero: boolean, extent?: string) => [number, number] | undefined
 ```
 
 [Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/autoscale.ts)
@@ -101,12 +101,12 @@ against, so there is nothing to call a hole.
 
 ### getEffectiveScores
 
-Per-feature scalar score array for a summary mode: the min/max summary array for
+Per-feature scalar score array for an aggregate: 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<...>
+(data: { featureScores: Float32Array<ArrayBufferLike>; featureMinScores: Float32Array<ArrayBufferLike>; featureMaxScores: Float32Array<ArrayBufferLike>; }, aggregate: string) => Float32Array<ArrayBufferLike>
 ```
 
 [Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/autoscale.ts)
@@ -114,10 +114,11 @@ Per-feature scalar score array for a summary mode: the min/max summary array for
 ### getNiceDomain
 
 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
+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.
+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 away from
@@ -125,7 +126,7 @@ itself, so no consumer has to guess what a backwards or a flat domain means.
 
 ```js
 // type signature
-({…}: { scaleType: string; domain: readonly [number, number]; bounds: readonly [number | undefined, number | undefined]; zero: boolean; }) => [number, number]
+({ scaleType, domain, bounds, zero, }: { scaleType: string; domain: readonly [number, number]; bounds: readonly [number | undefined, number | undefined]; zero: boolean; }) => [number, number]
 ```
 
 [Source code](https://github.com/GMOD/jbrowse-components/blob/main/packages/wiggle-core/src/scale.ts)
@@ -208,7 +209,7 @@ differently, and the alignments coverage band does.
 
 ```js
 // type signature
-({…}: { rules: readonly ValueScaleRule[]; domain: [number, number] | undefined; box: { yTop: number; yBottom: number; }; normalize: (score: number) => number; }) => ScoreRuleMark[]
+({ rules, domain, box, normalize, }: { rules: readonly ValueScaleRule[]; 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)

package/esm/ResolutionStepper.js

@@ -40,7 +40,7 @@ const ResolutionStepper = observer(function ResolutionStepper({ getState, onFine
 // 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;
-// `trailingItems` follow the stepper (wiggle's summary score mode, which reads
+// `trailingItems` follow the stepper (wiggle's aggregate, which reads
 // the same bins).
 export function makeResolutionSubMenuItem(opts) {
     const { getState, onFiner, onCoarser, onReset, icon, resetTitle, trailingItems = [], } = opts;

package/esm/ScoreAxisWidget/ReferenceLines.d.ts

@@ -1,7 +1,7 @@
 import type { ScoreAxisDisplay } from './types.ts';
 /**
  * `scales.y.rules`, one row per line: its value on the plot's own scale, its
- * label and its colour, an empty colour taking the display's. The lines
+ * label and its color, an empty color taking the display's. The lines
  * redraw as soon as every row reads; a half-typed row waits.
  */
 declare const _default: ({ display, }: {

package/esm/ScoreAxisWidget/ReferenceLines.js

@@ -23,7 +23,7 @@ function ruleOf(row) {
 }
 /**
  * `scales.y.rules`, one row per line: its value on the plot's own scale, its
- * label and its colour, an empty colour taking the display's. The lines
+ * label and its color, an empty color taking the display's. The lines
  * redraw as soon as every row reads; a half-typed row waits.
  */
 export default observer(function ReferenceLines({ display, }) {

package/esm/ScoreAxisWidget/ResetAxisButton.d.ts

@@ -1,6 +1,7 @@
 import type { ScoreAxisDisplay } from './types.ts';
 export declare function resetAxis(display: ScoreAxisDisplay): void;
-export default function ResetAxisButton({ display, onReset, }: {
+declare const ResetAxisButton: ({ display, onReset, }: {
     display: ScoreAxisDisplay;
     onReset: () => void;
-}): import("react").JSX.Element;
+}) => import("react").JSX.Element;
+export default ResetAxisButton;

package/esm/ScoreAxisWidget/ResetAxisButton.js

@@ -2,6 +2,7 @@ import { jsx as _jsx } from "react/jsx-runtime";
 import { setConf } from '@jbrowse/core/configuration';
 import { baseDisplayConfig } from '@jbrowse/core/util/baseDisplayConfig';
 import { Button } from '@mui/material';
+import { observer } from 'mobx-react';
 import { writeThrough } from './writeThrough.js';
 // Back to what the config.json says, or to what a session-owned track was
 // added with, so an admin's declared axis survives a reset; slots the base
@@ -12,9 +13,10 @@ export function resetAxis(display) {
         setConf(display.configuration, ['scales', 'y'], base?.y ?? {});
     });
 }
-export default function ResetAxisButton({ display, onReset, }) {
+const ResetAxisButton = observer(function ResetAxisButton({ display, onReset, }) {
     return (_jsx("div", { children: _jsx(Button, { variant: "outlined", size: "small", onClick: () => {
                 resetAxis(display);
                 onReset();
             }, children: "Reset to defaults" }) }));
-}
+});
+export default ResetAxisButton;

package/esm/ScoreAxisWidget/ScoreAxisWidget.js

@@ -23,7 +23,7 @@ const SCALE_TYPE_LABELS = {
     log: 'Log',
     symlog: 'Symlog',
 };
-// A density plot maps score to colour and rules no band, so it has no 0 to
+// A density plot maps score to color and rules no band, so it has no 0 to
 // include and no lines to draw across it.
 function rulesABand(display) {
     return display.scoreRulesDrawn === true;

package/esm/ScoreAxisWidget/Section.d.ts

@@ -1,5 +1,6 @@
 import type { ReactNode } from 'react';
-export default function Section({ title, children, }: {
+declare const Section: ({ title, children, }: {
     title: string;
     children: ReactNode;
-}): import("react").JSX.Element;
+}) => import("react").JSX.Element;
+export default Section;

package/esm/ScoreAxisWidget/Section.js

@@ -1,13 +1,15 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { Typography } from '@mui/material';
+import { observer } from 'mobx-react';
 const useStyles = makeStyles()(theme => ({
     section: {
         display: 'grid',
         gap: theme.spacing(0.5),
     },
 }));
-export default function Section({ title, children, }) {
+const Section = observer(function Section({ title, children, }) {
     const { classes } = useStyles();
     return (_jsxs("div", { className: classes.section, children: [_jsx(Typography, { variant: "subtitle2", children: title }), children] }));
-}
+});
+export default Section;

package/esm/ScorePlotChrome.d.ts

@@ -9,14 +9,12 @@ interface PlotBox {
     yTop: number;
     plotHeight: number;
 }
-interface ContextMenuView {
+export interface ScorePlotContextMenuHost<ContextHit> {
     contextMenuInfo?: ContextMenuAnchor;
     contextMenuItems: () => MenuItem[];
     closeContextMenu: () => void;
-}
-export interface ScorePlotContextMenuHost<Hit> extends ContextMenuView {
     openContextMenu: (info: ContextMenuAnchor & {
-        hit: Hit;
+        hit: ContextHit;
     }) => void;
     clearHoveredFeature: () => void;
 }
@@ -29,18 +27,20 @@ export type ScorePlotChromeModel<Hit, TRegion, TState extends FrameDimensions> =
 /**
  * The on-screen chrome of a display drawing a mark list on a score axis: the
  * canvas in the axis plot box, hover and click resolved through `findHit`, the
- * pointer-following `tooltip`, and the right-click menu where `contextMenu`
- * names the model that owns it. `findHit` takes y from the plot's own top.
+ * pointer-following `tooltip`, and the right-click menu where the model
+ * composes `ContextMenuMixin`. `findHit` takes y from the plot's own top.
+ * `findContextHit` is for a display whose menu is about something other than
+ * the hovered record (the wiggle's column, which exists where no bin does).
  */
-export declare const ScorePlotChrome: <Hit, TRegion, TState extends FrameDimensions>({ model, marks, testid, plotGeometry, findHit, tooltip, overlay, indicators, contextMenu, }: {
+export declare const ScorePlotChrome: <Hit, TRegion, TState extends FrameDimensions, ContextHit = Hit>({ model, marks, testid, plotGeometry, findHit, findContextHit, tooltip, overlay, indicators, }: {
     model: ScorePlotChromeModel<Hit, TRegion, TState>;
     marks: readonly Mark<TRegion, TState>[];
     testid: string;
     plotGeometry?: PlotBox;
     findHit: (x: number, y: number) => Hit | undefined;
+    findContextHit?: (x: number, y: number) => ContextHit | undefined;
     tooltip: (mouseState: MouseState | undefined) => ReactNode;
     overlay?: (plotGeometry: PlotBox) => ReactNode;
     indicators?: () => ReactNode;
-    contextMenu?: ScorePlotContextMenuHost<Hit>;
 }) => import("react").JSX.Element;
 export {};

package/esm/ScorePlotChrome.js

@@ -3,21 +3,27 @@ import { useMemo } from 'react';
 import { eventPoint } from '@jbrowse/core/util/eventPoint';
 import BottomRightIndicators from '@jbrowse/display-kit/BottomRightIndicators';
 import DisplayChrome from '@jbrowse/display-kit/DisplayChrome';
-import { DisplayContextMenu, openContextMenuFromEvent, } from '@jbrowse/display-kit/DisplayContextMenu';
+import { isContextMenuHost, openContextMenuFromEvent, } from '@jbrowse/display-kit/DisplayContextMenu';
 import { PointerLayer, axisPlotBox } from '@jbrowse/display-ui';
 import { createMarkBackend } from '@jbrowse/render-core/marks/backend';
 import { observer } from 'mobx-react';
+function isScorePlotMenuHost(model) {
+    return isContextMenuHost(model) && 'openContextMenu' in model;
+}
 /**
  * The on-screen chrome of a display drawing a mark list on a score axis: the
  * canvas in the axis plot box, hover and click resolved through `findHit`, the
- * pointer-following `tooltip`, and the right-click menu where `contextMenu`
- * names the model that owns it. `findHit` takes y from the plot's own top.
+ * pointer-following `tooltip`, and the right-click menu where the model
+ * composes `ContextMenuMixin`. `findHit` takes y from the plot's own top.
+ * `findContextHit` is for a display whose menu is about something other than
+ * the hovered record (the wiggle's column, which exists where no bin does).
  */
-export const ScorePlotChrome = observer(function ScorePlotChrome({ model, marks, testid, plotGeometry, findHit, tooltip, overlay, indicators, contextMenu, }) {
+export const ScorePlotChrome = observer(function ScorePlotChrome({ model, marks, testid, plotGeometry, findHit, findContextHit, tooltip, overlay, indicators, }) {
     const { height, canvasWidthPx: width } = model;
     const box = plotGeometry ?? axisPlotBox(height);
     const factory = useMemo(() => (canvas) => createMarkBackend(canvas, marks), [marks]);
     const hitAt = (x, y) => findHit(x, y - box.yTop);
+    const contextMenu = isScorePlotMenuHost(model) ? model : undefined;
     return (_jsx(DisplayChrome, { model: model, factory: factory, testid: testid, style: { width, whiteSpace: 'nowrap', textAlign: 'left' }, onPointerPosition: state => {
             model.setHoveredFeature(state ? hitAt(state.x, state.y) : undefined);
         }, onClick: event => {
@@ -29,19 +35,21 @@ export const ScorePlotChrome = observer(function ScorePlotChrome({ model, marks,
         }, onContextMenu: contextMenu
             ? event => {
                 const { x, y } = eventPoint(event);
-                const hit = hitAt(x, y);
+                const hit = findContextHit
+                    ? findContextHit(x, y - box.yTop)
+                    : hitAt(x, y);
                 openContextMenuFromEvent(contextMenu, event, hit
                     ? { clientX: event.clientX, clientY: event.clientY, hit }
                     : undefined);
             }
-            : undefined, children: ({ canvasRef, mouseTracker }) => (_jsx(ScorePlotBody, { model: model, canvasRef: canvasRef, mouseTracker: mouseTracker, width: width, plotGeometry: box, tooltip: tooltip, overlay: overlay, indicators: indicators, contextMenu: contextMenu })) }));
+            : undefined, children: ({ canvasRef, mouseTracker }) => (_jsx(ScorePlotBody, { model: model, canvasRef: canvasRef, mouseTracker: mouseTracker, width: width, plotGeometry: box, tooltip: tooltip, overlay: overlay, indicators: indicators })) }));
 });
-const ScorePlotBody = observer(function ScorePlotBody({ model, canvasRef, mouseTracker, width, plotGeometry, tooltip, overlay, indicators, contextMenu, }) {
+const ScorePlotBody = observer(function ScorePlotBody({ model, canvasRef, mouseTracker, width, plotGeometry, tooltip, overlay, indicators, }) {
     return (_jsxs(_Fragment, { children: [_jsx("canvas", { ref: canvasRef, style: {
                     width,
                     height: plotGeometry.plotHeight,
                     position: 'absolute',
                     left: 0,
                     top: plotGeometry.yTop,
-                } }), overlay?.(plotGeometry), _jsx(PointerLayer, { mouseTracker: mouseTracker, children: tooltip }), indicators ? (_jsx(BottomRightIndicators, { scrollableHeight: model.scrollableHeight, children: indicators() })) : null, contextMenu ? _jsx(DisplayContextMenu, { model: contextMenu }) : null] }));
+                } }), overlay?.(plotGeometry), _jsx(PointerLayer, { mouseTracker: mouseTracker, children: tooltip }), indicators ? (_jsx(BottomRightIndicators, { scrollableHeight: model.scrollableHeight, children: indicators() })) : null] }));
 });

package/esm/ScoreScaleMixin.d.ts

@@ -89,13 +89,6 @@ export declare function ScoreScaleMixin(): import("@jbrowse/mobx-state-tree").IM
      * The upper bound the config pins, `undefined` where it pins none.
      */
     readonly manualMaxScore: number | undefined;
-    /**
-     * #getter
-     * What `scales.y`'s ends say together that the axis cannot draw as
-     * written, as corner-notice lines, by the rule a colour ramp's ends
-     * answer to. The mark display reports them through its rule list.
-     */
-    readonly valueScaleNotices: string[];
     /**
      * #getter
      * `scales.y.autoscaleGroup`, `undefined` while it names none.
@@ -120,8 +113,8 @@ export declare function ScoreScaleMixin(): import("@jbrowse/mobx-state-tree").IM
      * #getter
      * Whether this display draws `scales.y.rules`, which is whether the
      * Y axis panel offers Include 0 and the reference lines: a scale it places y through
-     * rules a band for them to cross, which a density plot's colour-mapped
-     * rows and a colour ramp do not.
+     * rules a band for them to cross, which a density plot's color-mapped
+     * rows and a color ramp do not.
      */
     readonly scoreRulesDrawn: boolean;
     /**

package/esm/ScoreScaleMixin.js

@@ -1,5 +1,4 @@
 import { getConf, getSlotDefinition, readConfObject, setConf, } from '@jbrowse/core/configuration';
-import { noticeLines, scaleEndProblems } from '@jbrowse/core/util/colorScale';
 import { clipQuantileOf } from '@jbrowse/core/util/quantileExtent';
 import { rulesABand } from '@jbrowse/display-ui/axisPlacement';
 import { ScoreAxisMixin } from './ScoreAxisMixin.js';
@@ -86,19 +85,6 @@ export function ScoreScaleMixin() {
         get manualMaxScore() {
             return getConf(confNode(self), ['scales', 'y', 'domainMax']);
         },
-        /**
-         * #getter
-         * What `scales.y`'s ends say together that the axis cannot draw as
-         * written, as corner-notice lines, by the rule a colour ramp's ends
-         * answer to. The mark display reports them through its rule list.
-         */
-        get valueScaleNotices() {
-            return noticeLines('scales.y', scaleEndProblems({
-                domainMin: this.manualMinScore,
-                domainMax: this.manualMaxScore,
-                domainQuantile: this.domainQuantile,
-            }));
-        },
         /**
          * #getter
          * `scales.y.autoscaleGroup`, `undefined` while it names none.
@@ -132,8 +118,8 @@ export function ScoreScaleMixin() {
          * #getter
          * Whether this display draws `scales.y.rules`, which is whether the
          * Y axis panel offers Include 0 and the reference lines: a scale it places y through
-         * rules a band for them to cross, which a density plot's colour-mapped
-         * rows and a colour ramp do not.
+         * rules a band for them to cross, which a density plot's color-mapped
+         * rows and a color ramp do not.
          */
         get scoreRulesDrawn() {
             return self.valueScales.some(rulesABand);

package/esm/WiggleScoreConfigMixin.d.ts

@@ -1,25 +1,18 @@
 import type { scalesSchema } from './valueScaleConfigSchema.ts';
 import type { ConfigModelForFields } from '@jbrowse/core/configuration';
-/** The slots its composers each declare, with their own defaults. */
-export declare const wiggleScoreConfigExtraSlots: {
-    readonly size: {
-        readonly type: 'number';
-        readonly defaultValue: 2;
-    };
-};
 export interface WiggleScoreConfigHost {
     configuration: ConfigModelForFields<{
         scales: ReturnType<typeof scalesSchema>;
-    } & typeof wiggleScoreConfigExtraSlots>;
+    }>;
 }
 /**
  * #stateModel WiggleScoreConfigMixin
  * #category display
  *
  * The score-plot config every display with a score axis shares: the axis
- * and its guides (`ScoreScaleMixin`) and the scatter point size. A
- * display plotting one configured field composes `ScoreFieldConfigMixin`,
- * which adds `scoreField`.
+ * and its guides (`ScoreScaleMixin`). A display plotting one configured
+ * field composes `YFieldConfigMixin`,
+ * which adds the `y` slot.
  */
 export declare function WiggleScoreConfigMixin(): import("@jbrowse/mobx-state-tree").IModelType<Omit<{}, never>, {
     readonly scaleType: string;
@@ -48,7 +41,6 @@ export declare function WiggleScoreConfigMixin(): import("@jbrowse/mobx-state-tr
     readonly symlogConstant: number;
     readonly manualMinScore: number | undefined;
     readonly manualMaxScore: number | undefined;
-    readonly valueScaleNotices: string[];
     readonly autoscaleGroup: string | undefined;
     readonly scaleTitle: string;
     readonly grid: boolean;
@@ -65,10 +57,6 @@ export declare function WiggleScoreConfigMixin(): import("@jbrowse/mobx-state-tr
     setGrid(grid: boolean): void;
     setScoreRules(rules: (number | import("@jbrowse/display-ui").ValueScaleRule)[]): void;
 } & {
-    /**
-     * #getter
-     */
-    readonly size: number;
     /**
      * #getter
      * Whether score maps to color instead of height; a display overrides it.
@@ -77,13 +65,8 @@ export declare function WiggleScoreConfigMixin(): import("@jbrowse/mobx-state-tr
 } & {
     /**
      * #getter
-     * A density row maps score to colour and has no axis to start at 0, so
+     * A density row maps score to color and has no axis to start at 0, so
      * its domain spans the values whatever `scales.y.zero` says.
      */
     readonly axisReachesZero: boolean;
-} & {
-    /**
-     * #action
-     */
-    setSize(val?: number): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;

package/esm/WiggleScoreConfigMixin.js

@@ -1,30 +1,18 @@
-import { getConf, setConf } from '@jbrowse/core/configuration';
 import { types } from '@jbrowse/mobx-state-tree';
 import { ScoreScaleMixin } from './ScoreScaleMixin.js';
-/** The slots its composers each declare, with their own defaults. */
-export const wiggleScoreConfigExtraSlots = {
-    size: { type: 'number', defaultValue: 2 },
-};
-const confNode = (self) => self;
 /**
  * #stateModel WiggleScoreConfigMixin
  * #category display
  *
  * The score-plot config every display with a score axis shares: the axis
- * and its guides (`ScoreScaleMixin`) and the scatter point size. A
- * display plotting one configured field composes `ScoreFieldConfigMixin`,
- * which adds `scoreField`.
+ * and its guides (`ScoreScaleMixin`). A display plotting one configured
+ * field composes `YFieldConfigMixin`,
+ * which adds the `y` slot.
  */
 export function WiggleScoreConfigMixin() {
     return types
         .compose('WiggleScoreConfigMixin', ScoreScaleMixin(), types.model({}))
-        .views(self => ({
-        /**
-         * #getter
-         */
-        get size() {
-            return getConf(confNode(self), 'size');
-        },
+        .views(() => ({
         /**
          * #getter
          * Whether score maps to color instead of height; a display overrides it.
@@ -36,19 +24,11 @@ export function WiggleScoreConfigMixin() {
         .views(self => ({
         /**
          * #getter
-         * A density row maps score to colour and has no axis to start at 0, so
+         * A density row maps score to color and has no axis to start at 0, so
          * its domain spans the values whatever `scales.y.zero` says.
          */
         get axisReachesZero() {
             return self.scaleZero && !self.isDensityMode;
         },
-    }))
-        .actions(self => ({
-        /**
-         * #action
-         */
-        setSize(val) {
-            setConf(confNode(self), 'size', val);
-        },
     }));
 }

package/esm/{ScoreFieldConfigMixin.d.ts → YFieldConfigMixin.d.ts}

@@ -1,17 +1,17 @@
-import type { ScoreFieldConfigModel } from './scoreFieldConfigSchemaFields.ts';
-export interface ScoreFieldConfigHost {
-    configuration: ScoreFieldConfigModel;
+import type { YFieldConfigModel } from './yFieldConfigSchemaFields.ts';
+export interface YFieldConfigHost {
+    configuration: YFieldConfigModel;
 }
 /**
- * #stateModel ScoreFieldConfigMixin
+ * #stateModel YFieldConfigMixin
  * #category display
  *
- * `WiggleScoreConfigMixin` plus `scoreField`, for a display that plots one
- * configured feature field and so declares `scoreFieldConfigSchemaFields`:
+ * `WiggleScoreConfigMixin` plus the `y` slot, for a display that plots one
+ * configured feature field and so declares `yFieldConfigSchemaFields`:
  * the wiggle display. `LinearMarkDisplay` names a field per mark and composes
  * the base instead.
  */
-export declare function ScoreFieldConfigMixin(): import("@jbrowse/mobx-state-tree").IModelType<Omit<{}, never>, {
+export declare function YFieldConfigMixin(): import("@jbrowse/mobx-state-tree").IModelType<Omit<{}, never>, {
     readonly scaleType: string;
     readonly scaleZero: boolean;
     readonly manualMinScore: number | undefined;
@@ -38,7 +38,6 @@ export declare function ScoreFieldConfigMixin(): import("@jbrowse/mobx-state-tre
     readonly symlogConstant: number;
     readonly manualMinScore: number | undefined;
     readonly manualMaxScore: number | undefined;
-    readonly valueScaleNotices: string[];
     readonly autoscaleGroup: string | undefined;
     readonly scaleTitle: string;
     readonly grid: boolean;
@@ -55,18 +54,15 @@ export declare function ScoreFieldConfigMixin(): import("@jbrowse/mobx-state-tre
     setGrid(grid: boolean): void;
     setScoreRules(rules: (number | import("@jbrowse/display-ui").ValueScaleRule)[]): void;
 } & {
-    readonly size: number;
     readonly isDensityMode: boolean;
 } & {
     readonly axisReachesZero: boolean;
-} & {
-    setSize(val?: number): void;
 } & {
     /**
      * #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.
+     * The feature field the worker plots on the value axis, the `y` slot,
+     * `score` by default. A fetch input: every composing display carries it in
+     * its `rpcProps()`, since the field is read where the features are.
      */
-    readonly scoreField: string;
+    readonly yField: string;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;

package/esm/YFieldConfigMixin.js

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

package/esm/autoscale.d.ts

@@ -48,21 +48,21 @@ export interface ScoreSpan {
     row?: Uint32Array;
     drawnKeys?: Uint8Array;
 }
-/** The wiggle packer's arrays as a span, under a summary mode. */
-export declare function datasetSpan({ data, visStart, visEnd }: Dataset, summaryScoreMode: string): ScoreSpan;
+/** The wiggle packer's arrays as a span, under an aggregate and an extent. */
+export declare function datasetSpan({ data, visStart, visEnd }: Dataset, aggregate: string, extent: string): ScoreSpan;
 /**
  * #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 declare function getEffectiveScores(data: {
     featureScores: Float32Array;
     featureMinScores: Float32Array;
     featureMaxScores: Float32Array;
-}, summaryScoreMode: string): Float32Array<ArrayBufferLike>;
+}, aggregate: string): Float32Array<ArrayBufferLike>;
 export declare function computeSpanStats(spans: ScoreSpan[]): ScoreStats | undefined;
 /** `computeSpanStats` over the wiggle packer's datasets. */
-export declare function computeScoreStats(summaryScoreMode: string, datasets: Dataset[]): ScoreStats | undefined;
+export declare function computeScoreStats(aggregate: string, datasets: Dataset[], extent: string): ScoreStats | undefined;
 /**
  * #api
  * The domain the visible instances autoscale to: at a `quantile` of 1 their
@@ -79,11 +79,12 @@ export declare function autoscaleDomainFromSpans({ stats, quantile, zero, spans,
     spans: ScoreSpan[];
 }): [number, number];
 /** `autoscaleDomainFromSpans` over the wiggle packer's datasets. */
-export declare function autoscaleDomainFromStats({ stats, quantile, zero, summaryScoreMode, visibleEntries, }: {
+export declare function autoscaleDomainFromStats({ stats, quantile, zero, aggregate, extent, visibleEntries, }: {
     stats: ScoreStats;
     quantile: number;
     zero: boolean;
-    summaryScoreMode: string;
+    aggregate: string;
+    extent: string;
     visibleEntries: Dataset[];
 }): [number, number];
 /**
@@ -92,8 +93,8 @@ export declare function autoscaleDomainFromStats({ stats, quantile, zero, summar
  * `scales.y.domainQuantile` says, its outliers fenced for an axis that
  * reaches 0 under `zero`.
  */
-export declare function computeAutoscaleDomain(quantile: number, summaryScoreMode: string, visibleEntries: {
+export declare function computeAutoscaleDomain(quantile: number, aggregate: string, visibleEntries: {
     data: FeatureArrays;
     visStart: number;
     visEnd: number;
-}[], zero: boolean): [number, number] | undefined;
+}[], zero: boolean, extent?: string): [number, number] | undefined;