react-cheminfo 0.9.0 → 0.11.0

package/lib/scatter3d/ui/scatterCloudProps.d.ts

@@ -0,0 +1,185 @@
+/**
+ * What a caller hands a `ScatterCloud`.
+ *
+ * The types live beside the component rather than inside it because the
+ * component's own file would otherwise be mostly prose, exactly as the flat
+ * scatter's are.
+ */
+import type { ReactNode } from 'react';
+import type { EllipseSize } from '../../scatter/core/confidenceEllipse.ts';
+import type { ScatterSelectionMode } from '../../scatter/core/scatterSelection.ts';
+import type { ScatterGroup, ScatterPointOpen } from '../../scatter/ui/scatterPlotProps.ts';
+import type { SelectionChange } from '../../scatter/ui/useScatterSelection.ts';
+import type { CloudGesture } from '../core/cloudGesture.ts';
+import type { OrbitCamera } from '../core/orbitCamera.ts';
+export type { CloudGesture } from '../core/cloudGesture.ts';
+/** What a `ScatterCloud` needs. */
+export interface ScatterCloudProps {
+    /** Where every sample sits along the axis that runs left to right, in data units. */
+    x: ArrayLike<number>;
+    /** Along the axis that runs bottom to top, in the same order. */
+    y: ArrayLike<number>;
+    /** Along the axis that runs away from the reader. */
+    z: ArrayLike<number>;
+    /** Total width, in pixels, from `useContainerSize`. */
+    width: number;
+    /** Total height. */
+    height: number;
+    /** What the axis running left to right is called, written on the frame. */
+    xLabel: string;
+    /** What the axis running bottom to top is called. */
+    yLabel: string;
+    /** What the axis running away from the reader is called. */
+    zLabel: string;
+    /**
+     * Which group each sample belongs to, as an index into `groups`. A sample
+     * with `-1`, or an index outside the range, is drawn in the muted ink and
+     * left out of every shell.
+     * @default undefined — every sample is one crowd
+     */
+    groupOf?: ArrayLike<number>;
+    /**
+     * The groups, in the order they are coloured and listed.
+     * @default undefined
+     */
+    groups?: readonly ScatterGroup[];
+    /**
+     * Which groups are drawn faint, by id — what a legend entry switches.
+     * @default undefined — every group is drawn in full
+     */
+    mutedGroups?: ReadonlySet<string>;
+    /**
+     * How large the group shells are, or `null` for none. A share is read in
+     * three dimensions here, so the same share gives a wider shell than the same
+     * call gives on the map — which is the point of asking for a share rather
+     * than for a distance.
+     * @default null
+     */
+    ellipsoid?: EllipseSize | null;
+    /**
+     * How many samples a group needs before it is given a shell. Below four a
+     * group has no volume to measure, so anything less is read as four.
+     * @default 4
+     */
+    ellipsoidMinimumPoints?: number;
+    /**
+     * How solid the glass is; `0` draws no shells at all.
+     * @default SHELL_FILL_OPACITY
+     */
+    ellipsoidFillOpacity?: number;
+    /**
+     * Whether each group's name is written once, over the middle of its own
+     * shell. It needs `groups`, since it is their names it writes.
+     * @default false
+     */
+    showGroupLabels?: boolean;
+    /**
+     * What each sample is called, written beside its own dot. A sample whose
+     * entry is `undefined` is left unnamed.
+     * @default undefined — no sample is named
+     */
+    pointLabels?: ReadonlyArray<string | undefined>;
+    /**
+     * Radius of a dot at the middle of the box, in pixels. One at the front is
+     * drawn larger and one at the back smaller, about this.
+     * @default 3.5
+     */
+    pointRadius?: number;
+    /**
+     * The index from which samples are drawn as outlines rather than filled,
+     * which is how one the model was fitted on is told from one placed into it
+     * afterwards.
+     * @default undefined — every sample is filled
+     */
+    outlinedFrom?: number;
+    /**
+     * What a drag does. The cloud never changes it on its own, because the
+     * control belongs in the bar above the figure rather than on top of the
+     * picture, so it is a plain setting rather than a controlled value.
+     * @default 'turn'
+     */
+    gesture?: CloudGesture;
+    /**
+     * Where the reader is standing. Present, the caller owns the camera, which
+     * is how a site puts a viewpoint in a share link.
+     * @default undefined — the cloud keeps its own
+     */
+    camera?: OrbitCamera;
+    /**
+     * Called with the camera every frame of a turn leaves behind.
+     * @default undefined
+     */
+    onCameraChange?: (camera: OrbitCamera) => void;
+    /**
+     * How far in the reader has zoomed; `1` is the resting size. Present, the
+     * caller owns it.
+     * @default undefined — the cloud keeps its own
+     */
+    zoom?: number;
+    /**
+     * Called with the zoom a wheel asks for.
+     * @default undefined
+     */
+    onZoomChange?: (zoom: number) => void;
+    /**
+     * Whether the wheel zooms the box. On, because a cloud that cannot be zoomed
+     * cannot be read where its groups overlap; a figure set in a column of prose
+     * should turn it off so a reader on their way past keeps their scroll.
+     * @default true
+     */
+    wheelZoom?: boolean;
+    /**
+     * The selected rows. Present, the caller owns the selection.
+     * @default undefined — the cloud keeps its own
+     */
+    selected?: readonly number[];
+    /**
+     * The rows selected before the reader touches anything.
+     * @default undefined
+     */
+    defaultSelected?: readonly number[];
+    /**
+     * Called when a lasso is released or a dot is tapped — never while a lasso
+     * is being drawn, and never while the box is being turned.
+     * @default undefined
+     */
+    onSelectionChange?: (change: SelectionChange) => void;
+    /**
+     * What a gesture with no modifier held does to the selection. Shift always
+     * adds and Alt always removes, exactly as on the map.
+     * @default 'replace'
+     */
+    selectMode?: ScatterSelectionMode;
+    /**
+     * Called with the row under the pointer, or `-1`.
+     * @default undefined
+     */
+    onHoverChange?: (index: number) => void;
+    /**
+     * Called when the reader double-clicks a sample, exactly as on the flat map:
+     * the gesture for "tell me more about this one", or "let me change it".
+     *
+     * It fires whichever gesture a drag is set to, because a double click is not
+     * a drag — a reader turning the box must not have to switch to Select to
+     * open a sample. The sample is selected first, since a double click is also
+     * two clicks; the map says why, and the two behave alike on purpose.
+     * @default undefined
+     */
+    onPointDoubleClick?: (point: ScatterPointOpen) => void;
+    /**
+     * What floats over the figure — a bar, a key, a caption, a card.
+     * @default undefined
+     */
+    overlay?: ReactNode;
+    /**
+     * What a screen reader is told the figure shows.
+     * @default a sentence built from the three axis names and the sample count
+     */
+    label?: string;
+    /**
+     * Value of the `data-testid` attribute of the wrapper.
+     * @default undefined
+     */
+    testId?: string;
+}
+//# sourceMappingURL=scatterCloudProps.d.ts.map

package/lib/scatter3d/ui/scatterCloudProps.d.ts.map

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package/lib/scatter3d/ui/scatterCloudProps.js

@@ -0,0 +1,9 @@
+/**
+ * What a caller hands a `ScatterCloud`.
+ *
+ * The types live beside the component rather than inside it because the
+ * component's own file would otherwise be mostly prose, exactly as the flat
+ * scatter's are.
+ */
+export {};
+//# sourceMappingURL=scatterCloudProps.js.map

package/lib/scatter3d/ui/scatterCloudProps.js.map

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package/lib/scatter3d/ui/useOrbitDrag.d.ts

@@ -0,0 +1,60 @@
+import type { ScatterSelectionMode } from '../../scatter/core/scatterSelection.ts';
+import type { ScatterSurfaceProps } from '../../scatter/ui/lassoGesture.ts';
+import type { OrbitCamera } from '../core/orbitCamera.ts';
+/** What {@link useOrbitDrag} needs. */
+export interface OrbitDragOptions {
+    /**
+     * Whether a drag turns the box at all. Off, the surface still reports a tap,
+     * so the reader can pick a sample while the drag belongs to something else.
+     * @default true
+     */
+    enabled?: boolean;
+    /** Called with the camera each frame of a drag leaves behind. */
+    onOrbit: (turn: (camera: OrbitCamera) => OrbitCamera) => void;
+    /**
+     * Called when a press and release happened in one place — a click, however
+     * the reader's hand shook.
+     * @default undefined
+     */
+    onTap?: (x: number, y: number, mode: ScatterSelectionMode) => void;
+    /**
+     * Called with the pointer's position on every frame it moves without
+     * turning, which is what raises the card under it.
+     * @default undefined
+     */
+    onMove?: (x: number, y: number) => void;
+    /**
+     * Called when the pointer leaves the surface without a drag in progress.
+     * @default undefined
+     */
+    onLeave?: () => void;
+    /**
+     * What a tap with no modifier held does to the selection.
+     * @default 'replace'
+     */
+    mode?: ScatterSelectionMode;
+}
+/** A drag that turns the box, and the taps it lets through. */
+export interface OrbitDrag {
+    /** Whether the box is being turned right now. */
+    turning: boolean;
+    /** Spread onto the transparent rectangle over the figure. */
+    surface: ScatterSurfaceProps;
+}
+/**
+ * Turning the box with the pointer.
+ *
+ * It is the lasso's twin and is built the same way — the pointer is captured
+ * on the way down so a drag that wanders off the figure keeps turning it, all
+ * three ways a capture can end lead to one function, and moves are coalesced
+ * to one a frame because a pointer emits many per frame and each one that
+ * reaches the caller repaints every dot and every face.
+ *
+ * A press that goes nowhere is a tap rather than a turn of no degrees, because
+ * nobody presses a mouse button without moving it a pixel or two and a reader
+ * who meant to pick a sample must not have to hold their hand still to do it.
+ * @param options - See {@link OrbitDragOptions}.
+ * @returns The drag. See {@link OrbitDrag}.
+ */
+export declare function useOrbitDrag(options: OrbitDragOptions): OrbitDrag;
+//# sourceMappingURL=useOrbitDrag.d.ts.map

package/lib/scatter3d/ui/useOrbitDrag.d.ts.map

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package/lib/scatter3d/ui/useOrbitDrag.js

@@ -0,0 +1,129 @@
+import { useCallback, useMemo, useRef, useState } from 'react';
+import { capturePointer, dropFrame, modifierMode, scheduleFrame, surfacePosition, } from "../../scatter/ui/lassoGesture.js";
+import { orbitByDrag } from "../core/orbitCamera.js";
+/**
+ * Turning the box with the pointer.
+ *
+ * It is the lasso's twin and is built the same way — the pointer is captured
+ * on the way down so a drag that wanders off the figure keeps turning it, all
+ * three ways a capture can end lead to one function, and moves are coalesced
+ * to one a frame because a pointer emits many per frame and each one that
+ * reaches the caller repaints every dot and every face.
+ *
+ * A press that goes nowhere is a tap rather than a turn of no degrees, because
+ * nobody presses a mouse button without moving it a pixel or two and a reader
+ * who meant to pick a sample must not have to hold their hand still to do it.
+ * @param options - See {@link OrbitDragOptions}.
+ * @returns The drag. See {@link OrbitDrag}.
+ */
+export function useOrbitDrag(options) {
+    const { enabled = true, onOrbit, onTap, onMove, onLeave, mode: restingMode = 'replace', } = options;
+    const pointerRef = useRef(null);
+    const lastRef = useRef({ x: 0, y: 0 });
+    const travelRef = useRef(0);
+    const frameRef = useRef(null);
+    const pendingRef = useRef(null);
+    const [turning, setTurning] = useState(false);
+    const flush = useCallback(() => {
+        frameRef.current = null;
+        const next = pendingRef.current;
+        pendingRef.current = null;
+        if (next === null)
+            return;
+        if (pointerRef.current === null) {
+            onMove?.(next.x, next.y);
+            return;
+        }
+        onOrbit((camera) => orbitByDrag(camera, next.dx, next.dy));
+    }, [onMove, onOrbit]);
+    const end = useCallback((event, commit) => {
+        if (event.pointerId !== pointerRef.current)
+            return;
+        pointerRef.current = null;
+        pendingRef.current = null;
+        dropFrame(frameRef);
+        setTurning(false);
+        if (!commit || travelRef.current > TAP_SLACK)
+            return;
+        const at = surfacePosition(event, 0, 0);
+        onTap?.(at.x, at.y, modifierMode(event, restingMode));
+    }, [onTap, restingMode]);
+    const handleDown = useCallback((event) => {
+        if (pointerRef.current !== null || event.button > 0)
+            return;
+        pointerRef.current = event.pointerId;
+        lastRef.current = { x: event.clientX, y: event.clientY };
+        travelRef.current = 0;
+        setTurning(true);
+        capturePointer(event);
+    }, []);
+    const handleMove = useCallback((event) => {
+        const active = pointerRef.current;
+        if (active === null) {
+            const at = surfacePosition(event, 0, 0);
+            pendingRef.current = { x: at.x, y: at.y, dx: 0, dy: 0 };
+            scheduleFrame(frameRef, flush);
+            return;
+        }
+        if (event.pointerId !== active)
+            return;
+        const last = lastRef.current;
+        const dx = event.clientX - last.x;
+        const dy = event.clientY - last.y;
+        lastRef.current = { x: event.clientX, y: event.clientY };
+        travelRef.current += Math.abs(dx) + Math.abs(dy);
+        if (!enabled)
+            return;
+        const waiting = pendingRef.current;
+        pendingRef.current = {
+            x: 0,
+            y: 0,
+            dx: (waiting?.dx ?? 0) + dx,
+            dy: (waiting?.dy ?? 0) + dy,
+        };
+        scheduleFrame(frameRef, flush);
+    }, [enabled, flush]);
+    const handleUp = useCallback((event) => {
+        end(event, true);
+    }, [end]);
+    const handleAbandon = useCallback((event) => {
+        end(event, false);
+    }, [end]);
+    const handleLeave = useCallback(() => {
+        if (pointerRef.current !== null)
+            return;
+        pendingRef.current = null;
+        onLeave?.();
+    }, [onLeave]);
+    const surface = useMemo(() => ({
+        onPointerDown: handleDown,
+        onPointerMove: handleMove,
+        onPointerUp: handleUp,
+        onPointerCancel: handleAbandon,
+        onLostPointerCapture: handleAbandon,
+        onPointerLeave: handleLeave,
+        style: {
+            cursor: enabled ? (turning ? 'grabbing' : 'grab') : 'default',
+            touchAction: 'none',
+        },
+    }), [
+        enabled,
+        handleAbandon,
+        handleDown,
+        handleLeave,
+        handleMove,
+        handleUp,
+        turning,
+    ]);
+    return { turning, surface };
+}
+/**
+ * How far a press may travel and still be a tap, in pixels of total travel.
+ *
+ * Generous on purpose: a mouse moves a pixel or two under the click of its own
+ * button, and a finger moves rather more, so a stricter number turns "pick
+ * this sample" into "turn the box by nothing at all" for anybody whose hand is
+ * not steady.
+ */
+const TAP_SLACK = 5;
+//# sourceMappingURL=useOrbitDrag.js.map

package/lib/scatter3d/ui/useOrbitDrag.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"useOrbitDrag.js","sourceRoot":"","sources":["../../../src/scatter3d/ui/useOrbitDrag.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAC;AAI/D,OAAO,EACL,cAAc,EACd,SAAS,EACT,YAAY,EACZ,aAAa,EACb,eAAe,GAChB,MAAM,kCAAkC,CAAC;AAE1C,OAAO,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AA4CrD;;;;;;;;;;;;;;GAcG;AACH,MAAM,UAAU,YAAY,CAAC,OAAyB;IACpD,MAAM,EACJ,OAAO,GAAG,IAAI,EACd,OAAO,EACP,KAAK,EACL,MAAM,EACN,OAAO,EACP,IAAI,EAAE,WAAW,GAAG,SAAS,GAC9B,GAAG,OAAO,CAAC;IAEZ,MAAM,UAAU,GAAG,MAAM,CAAgB,IAAI,CAAC,CAAC;IAC/C,MAAM,OAAO,GAAG,MAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;IACvC,MAAM,SAAS,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;IAC5B,MAAM,QAAQ,GAAG,MAAM,CAAgB,IAAI,CAAC,CAAC;IAC7C,MAAM,UAAU,GAAG,MAAM,CAAqB,IAAI,CAAC,CAAC;IACpD,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAC;IAE9C,MAAM,KAAK,GAAG,WAAW,CAAC,GAAG,EAAE;QAC7B,QAAQ,CAAC,OAAO,GAAG,IAAI,CAAC;QACxB,MAAM,IAAI,GAAG,UAAU,CAAC,OAAO,CAAC;QAChC,UAAU,CAAC,OAAO,GAAG,IAAI,CAAC;QAC1B,IAAI,IAAI,KAAK,IAAI;YAAE,OAAO;QAC1B,IAAI,UAAU,CAAC,OAAO,KAAK,IAAI,EAAE,CAAC;YAChC,MAAM,EAAE,CAAC,IAAI,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC;YACzB,OAAO;QACT,CAAC;QACD,OAAO,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC;IAC7D,CAAC,EAAE,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC;IAEtB,MAAM,GAAG,GAAG,WAAW,CACrB,CAAC,KAAiC,EAAE,MAAe,EAAE,EAAE;QACrD,IAAI,KAAK,CAAC,SAAS,KAAK,UAAU,CAAC,OAAO;YAAE,OAAO;QACnD,UAAU,CAAC,OAAO,GAAG,IAAI,CAAC;QAC1B,UAAU,CAAC,OAAO,GAAG,IAAI,CAAC;QAC1B,SAAS,CAAC,QAAQ,CAAC,CAAC;QACpB,UAAU,CAAC,KAAK,CAAC,CAAC;QAClB,IAAI,CAAC,MAAM,IAAI,SAAS,CAAC,OAAO,GAAG,SAAS;YAAE,OAAO;QACrD,MAAM,EAAE,GAAG,eAAe,CAAC,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;QACxC,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,YAAY,CAAC,KAAK,EAAE,WAAW,CAAC,CAAC,CAAC;IACxD,CAAC,EACD,CAAC,KAAK,EAAE,WAAW,CAAC,CACrB,CAAC;IAEF,MAAM,UAAU,GAAG,WAAW,CAAC,CAAC,KAAiC,EAAE,EAAE;QACnE,IAAI,UAAU,CAAC,OAAO,KAAK,IAAI,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC;YAAE,OAAO;QAC5D,UAAU,CAAC,OAAO,GAAG,KAAK,CAAC,SAAS,CAAC;QACrC,OAAO,CAAC,OAAO,GAAG,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC;QACzD,SAAS,CAAC,OAAO,GAAG,CAAC,CAAC;QACtB,UAAU,CAAC,IAAI,CAAC,CAAC;QACjB,cAAc,CAAC,KAAK,CAAC,CAAC;IACxB,CAAC,EAAE,EAAE,CAAC,CAAC;IAEP,MAAM,UAAU,GAAG,WAAW,CAC5B,CAAC,KAAiC,EAAE,EAAE;QACpC,MAAM,MAAM,GAAG,UAAU,CAAC,OAAO,CAAC;QAClC,IAAI,MAAM,KAAK,IAAI,EAAE,CAAC;YACpB,MAAM,EAAE,GAAG,eAAe,CAAC,KAAK,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC;YACxC,UAAU,CAAC,OAAO,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC;YACxD,aAAa,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;YAC/B,OAAO;QACT,CAAC;QACD,IAAI,KAAK,CAAC,SAAS,KAAK,MAAM;YAAE,OAAO;QACvC,MAAM,IAAI,GAAG,OAAO,CAAC,OAAO,CAAC;QAC7B,MAAM,EAAE,GAAG,KAAK,CAAC,OAAO,GAAG,IAAI,CAAC,CAAC,CAAC;QAClC,MAAM,EAAE,GAAG,KAAK,CAAC,OAAO,GAAG,IAAI,CAAC,CAAC,CAAC;QAClC,OAAO,CAAC,OAAO,GAAG,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC;QACzD,SAAS,CAAC,OAAO,IAAI,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QACjD,IAAI,CAAC,OAAO;YAAE,OAAO;QACrB,MAAM,OAAO,GAAG,UAAU,CAAC,OAAO,CAAC;QACnC,UAAU,CAAC,OAAO,GAAG;YACnB,CAAC,EAAE,CAAC;YACJ,CAAC,EAAE,CAAC;YACJ,EAAE,EAAE,CAAC,OAAO,EAAE,EAAE,IAAI,CAAC,CAAC,GAAG,EAAE;YAC3B,EAAE,EAAE,CAAC,OAAO,EAAE,EAAE,IAAI,CAAC,CAAC,GAAG,EAAE;SAC5B,CAAC;QACF,aAAa,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;IACjC,CAAC,EACD,CAAC,OAAO,EAAE,KAAK,CAAC,CACjB,CAAC;IAEF,MAAM,QAAQ,GAAG,WAAW,CAC1B,CAAC,KAAiC,EAAE,EAAE;QACpC,GAAG,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC;IACnB,CAAC,EACD,CAAC,GAAG,CAAC,CACN,CAAC;IAEF,MAAM,aAAa,GAAG,WAAW,CAC/B,CAAC,KAAiC,EAAE,EAAE;QACpC,GAAG,CAAC,KAAK,EAAE,KAAK,CAAC,CAAC;IACpB,CAAC,EACD,CAAC,GAAG,CAAC,CACN,CAAC;IAEF,MAAM,WAAW,GAAG,WAAW,CAAC,GAAG,EAAE;QACnC,IAAI,UAAU,CAAC,OAAO,KAAK,IAAI;YAAE,OAAO;QACxC,UAAU,CAAC,OAAO,GAAG,IAAI,CAAC;QAC1B,OAAO,EAAE,EAAE,CAAC;IACd,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC,CAAC;IAEd,MAAM,OAAO,GAAG,OAAO,CACrB,GAAG,EAAE,CAAC,CAAC;QACL,aAAa,EAAE,UAAU;QACzB,aAAa,EAAE,UAAU;QACzB,WAAW,EAAE,QAAQ;QACrB,eAAe,EAAE,aAAa;QAC9B,oBAAoB,EAAE,aAAa;QACnC,cAAc,EAAE,WAAW;QAC3B,KAAK,EAAE;YACL,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,SAAS;YAC7D,WAAW,EAAE,MAAM;SACpB;KACF,CAAC,EACF;QACE,OAAO;QACP,aAAa;QACb,UAAU;QACV,WAAW;QACX,UAAU;QACV,QAAQ;QACR,OAAO;KACR,CACF,CAAC;IAEF,OAAO,EAAE,OAAO,EAAE,OAAO,EAAE,CAAC;AAC9B,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,SAAS,GAAG,CAAC,CAAC"}

package/lib/share/core/query.d.ts

@@ -12,10 +12,16 @@ export type QueryEntry = readonly [key: string, value: string];
  */
 export declare function parseQuery(search: string): QueryEntry[];
 /**
- * Write pairs back into a query string, keeping the two characters a reader
- * of these links cares about legible: a comma stays a comma rather than
- * `%2C`, and a plus stays a plus rather than `%2B`. Both parse back
- * identically through {@link parseQuery}.
+ * Write pairs back into a query string, keeping the comma legible — `hide=a,b`
+ * rather than `hide=a%2Cb` — because a teacher has to read these links, and a
+ * comma has only one reading.
+ *
+ * A plus is written `%2B`, even though {@link parseQuery} would read a literal
+ * one back. We are liberal in what we accept and strict in what we write: a
+ * bare `+` in a query string is read as a space by `URLSearchParams`,
+ * `query-string` and every server-side parser, so `ionizations=H+` comes back
+ * as `H ` and `smiles=CC[N+](C)(C)C` as a different molecule — silently,
+ * anywhere the link is read by something other than {@link parseQuery}.
  * @param entries - The pairs to write, in the order they should appear.
  * @returns The query string, without its leading `?`.
  */

package/lib/share/core/query.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"query.d.ts","sourceRoot":"","sources":["../../../src/share/core/query.ts"],"names":[],"mappings":"AAAA,+DAA+D;AAC/D,MAAM,MAAM,UAAU,GAAG,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC;AAE/D;;;;;;;;;GASG;AACH,wBAAgB,UAAU,CAAC,MAAM,EAAE,MAAM,GAAG,UAAU,EAAE,CAYvD;AAED;;;;;;;GAOG;AACH,wBAAgB,cAAc,CAAC,OAAO,EAAE,SAAS,UAAU,EAAE,GAAG,MAAM,CAMrE;AAED;;;;;GAKG;AACH,wBAAgB,WAAW,CACzB,OAAO,EAAE,SAAS,UAAU,EAAE,GAC7B,WAAW,CAAC,MAAM,EAAE,MAAM,CAAC,CAM7B"}
+{"version":3,"file":"query.d.ts","sourceRoot":"","sources":["../../../src/share/core/query.ts"],"names":[],"mappings":"AAAA,+DAA+D;AAC/D,MAAM,MAAM,UAAU,GAAG,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC;AAE/D;;;;;;;;;GASG;AACH,wBAAgB,UAAU,CAAC,MAAM,EAAE,MAAM,GAAG,UAAU,EAAE,CAYvD;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,cAAc,CAAC,OAAO,EAAE,SAAS,UAAU,EAAE,GAAG,MAAM,CAMrE;AAED;;;;;GAKG;AACH,wBAAgB,WAAW,CACzB,OAAO,EAAE,SAAS,UAAU,EAAE,GAC7B,WAAW,CAAC,MAAM,EAAE,MAAM,CAAC,CAM7B"}

package/lib/share/core/query.js

@@ -24,10 +24,16 @@ export function parseQuery(search) {
     return entries;
 }
 /**
- * Write pairs back into a query string, keeping the two characters a reader
- * of these links cares about legible: a comma stays a comma rather than
- * `%2C`, and a plus stays a plus rather than `%2B`. Both parse back
- * identically through {@link parseQuery}.
+ * Write pairs back into a query string, keeping the comma legible — `hide=a,b`
+ * rather than `hide=a%2Cb` — because a teacher has to read these links, and a
+ * comma has only one reading.
+ *
+ * A plus is written `%2B`, even though {@link parseQuery} would read a literal
+ * one back. We are liberal in what we accept and strict in what we write: a
+ * bare `+` in a query string is read as a space by `URLSearchParams`,
+ * `query-string` and every server-side parser, so `ionizations=H+` comes back
+ * as `H ` and `smiles=CC[N+](C)(C)C` as a different molecule — silently,
+ * anywhere the link is read by something other than {@link parseQuery}.
  * @param entries - The pairs to write, in the order they should appear.
  * @returns The query string, without its leading `?`.
  */
@@ -61,8 +67,6 @@ function decodeComponent(value) {
     }
 }
 function encodeComponent(value) {
-    return encodeURIComponent(value)
-        .replaceAll('%2C', ',')
-        .replaceAll('%2B', '+');
+    return encodeURIComponent(value).replaceAll('%2C', ',');
 }
 //# sourceMappingURL=query.js.map

package/lib/share/core/query.js.map

@@ -1 +1 @@
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+{"version":3,"file":"query.js","sourceRoot":"","sources":["../../../src/share/core/query.ts"],"names":[],"mappings":"AAGA;;;;;;;;;GASG;AACH,MAAM,UAAU,UAAU,CAAC,MAAc;IACvC,MAAM,IAAI,GAAG,MAAM,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC;IAC/D,MAAM,OAAO,GAAiB,EAAE,CAAC;IACjC,IAAI,IAAI,KAAK,EAAE;QAAE,OAAO,OAAO,CAAC;IAChC,KAAK,MAAM,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;QACpC,IAAI,KAAK,KAAK,EAAE;YAAE,SAAS;QAC3B,MAAM,SAAS,GAAG,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;QACrC,MAAM,GAAG,GAAG,SAAS,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,SAAS,CAAC,CAAC;QACjE,MAAM,KAAK,GAAG,SAAS,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,SAAS,GAAG,CAAC,CAAC,CAAC;QACjE,OAAO,CAAC,IAAI,CAAC,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,eAAe,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;IAC/D,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC;AAED;;;;;;;;;;;;;GAaG;AACH,MAAM,UAAU,cAAc,CAAC,OAA8B;IAC3D,MAAM,MAAM,GAAa,EAAE,CAAC;IAC5B,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,OAAO,EAAE,CAAC;QACnC,MAAM,CAAC,IAAI,CAAC,GAAG,eAAe,CAAC,GAAG,CAAC,IAAI,eAAe,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACnE,CAAC;IACD,OAAO,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;AAC1B,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,WAAW,CACzB,OAA8B;IAE9B,MAAM,MAAM,GAAG,IAAI,GAAG,EAAkB,CAAC;IACzC,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,OAAO,EAAE,CAAC;QACnC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC;YAAE,MAAM,CAAC,GAAG,CAAC,GAAG,EAAE,KAAK,CAAC,CAAC;IAC/C,CAAC;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,SAAS,eAAe,CAAC,KAAa;IACpC,IAAI,CAAC;QACH,OAAO,kBAAkB,CAAC,KAAK,CAAC,CAAC;IACnC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,KAAK,CAAC;IACf,CAAC;AACH,CAAC;AAED,SAAS,eAAe,CAAC,KAAa;IACpC,OAAO,kBAAkB,CAAC,KAAK,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;AAC1D,CAAC"}

package/lib/spectra/core/axisEntries.d.ts

@@ -0,0 +1,50 @@
+export declare const AXIS_ENTRIES: {
+    readonly xFunction: {
+        readonly label: "Apply a formula to x";
+        readonly group: "x-axis";
+        readonly summary: "Rewrites every x through an expression, read the same way as the y one.";
+        readonly fields: readonly [import("./filterFields.ts").FilterField];
+        readonly caution: "Every range below is then read in the new units — including the resampling range, which runs last unless you resample first.";
+    };
+    readonly fromTo: {
+        readonly label: "Crop";
+        readonly group: "x-axis";
+        readonly summary: "Keeps one stretch of the spectrum and drops the rest.";
+        readonly fields: readonly [...import("./filterFields.ts").FilterField[], import("./filterFields.ts").FilterField, import("./filterFields.ts").FilterField];
+        readonly caution: "Give x values or point numbers, not both: a point number silently wins over an x value.";
+    };
+    readonly filterX: {
+        readonly label: "Keep or drop x zones";
+        readonly group: "x-axis";
+        readonly summary: "Keeps the points falling in the zones named, without resampling anything.";
+        readonly fields: readonly import("./filterFields.ts").FilterField[];
+    };
+    readonly equallySpaced: {
+        readonly label: "Resample on a regular grid";
+        readonly group: "x-axis";
+        readonly summary: "Interpolates onto evenly spaced x values.";
+        readonly fields: readonly import("./filterFields.ts").FilterField[];
+        readonly caution: "The settings above already resample once, so this resamples twice; whichever of the two runs last sets the point count.";
+    };
+    readonly calibrateX: {
+        readonly label: "Calibrate x on a peak";
+        readonly group: "x-axis";
+        readonly summary: "Finds the strongest peaks in a stretch and shifts the whole axis so their mean lands on the value asked for.";
+        readonly fields: readonly [...import("./filterFields.ts").FilterField[], import("./filterFields.ts").FilterField, import("./filterFields.ts").FilterField, import("./filterFields.ts").FilterField, import("./filterFields.ts").FilterField, import("./filterFields.ts").FilterField, import("./filterFields.ts").FilterField, import("./filterFields.ts").FilterField, import("./filterFields.ts").FilterField, import("./filterFields.ts").FilterField, import("./filterFields.ts").FilterField];
+        readonly caution: "When fewer peaks are found than asked for, the spectrum is returned untouched and nothing says so.";
+    };
+    readonly ensureGrowing: {
+        readonly label: "Make x strictly increasing";
+        readonly group: "utility";
+        readonly summary: "Drops the points that repeat or go backwards, which resampling and cropping both assume never happens.";
+        readonly fields: readonly [];
+    };
+    readonly reverseIfNeeded: {
+        readonly label: "Reverse a descending x";
+        readonly group: "utility";
+        readonly summary: "Turns a descending axis the right way round.";
+        readonly fields: readonly [];
+        readonly caution: "The chain already does this before every step, so adding it here changes nothing.";
+    };
+};
+//# sourceMappingURL=axisEntries.d.ts.map

package/lib/spectra/core/axisEntries.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"axisEntries.d.ts","sourceRoot":"","sources":["../../../src/spectra/core/axisEntries.ts"],"names":[],"mappings":"AAUA,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAgG8B,CAAC"}

package/lib/spectra/core/axisEntries.js

@@ -0,0 +1,78 @@
+import { RANGE_FIELDS, ZONE_FIELDS } from "./filterEntries.js";
+import { booleanField, enumField, formulaField, integerField, numberField, } from "./filterFields.js";
+export const AXIS_ENTRIES = {
+    xFunction: {
+        label: 'Apply a formula to x',
+        group: 'x-axis',
+        summary: 'Rewrites every x through an expression, read the same way as the y one.',
+        fields: [
+            formulaField('function', 'Expression in x', 'For instance 10000000/x, which reads nanometres as wavenumbers.'),
+        ],
+        caution: 'Every range below is then read in the new units — including the resampling range, which runs last unless you resample first.',
+    },
+    fromTo: {
+        label: 'Crop',
+        group: 'x-axis',
+        summary: 'Keeps one stretch of the spectrum and drops the rest.',
+        fields: [
+            ...RANGE_FIELDS,
+            integerField('fromIndex', 'From (point)', '0'),
+            integerField('toIndex', 'To (point)', 'the last point'),
+        ],
+        caution: 'Give x values or point numbers, not both: a point number silently wins over an x value.',
+    },
+    filterX: {
+        label: 'Keep or drop x zones',
+        group: 'x-axis',
+        summary: 'Keeps the points falling in the zones named, without resampling anything.',
+        fields: [...RANGE_FIELDS, ...ZONE_FIELDS],
+    },
+    equallySpaced: {
+        label: 'Resample on a regular grid',
+        group: 'x-axis',
+        summary: 'Interpolates onto evenly spaced x values.',
+        fields: [
+            ...RANGE_FIELDS,
+            integerField('numberOfPoints', 'Number of points', '100'),
+            ...ZONE_FIELDS,
+        ],
+        caution: 'The settings above already resample once, so this resamples twice; whichever of the two runs last sets the point count.',
+    },
+    calibrateX: {
+        label: 'Calibrate x on a peak',
+        group: 'x-axis',
+        summary: 'Finds the strongest peaks in a stretch and shifts the whole axis so their mean lands on the value asked for.',
+        fields: [
+            ...RANGE_FIELDS,
+            integerField('nbPeaks', 'Peaks to find', '1'),
+            numberField('targetX', 'Move them to', '0'),
+            booleanField('gsd.smoothY', 'Smooth before picking'),
+            booleanField('gsd.maxCriteria', 'Pick maxima', 'Off picks minima instead.'),
+            numberField('gsd.minMaxRatio', 'Smallest peak kept', '0.00025', 'As a fraction of the tallest. A step added here starts at 0.1; empty the box and this far lower default takes over.'),
+            numberField('gsd.noiseLevel', 'Noise level', 'not set'),
+            booleanField('gsd.realTopDetection', 'Refine the summit'),
+            integerField('gsd.sgOptions.windowSize', 'Peak-picking window', '9'),
+            integerField('gsd.sgOptions.polynomial', 'Peak-picking polynomial', '3'),
+            enumField('gsd.peakDetectionAlgorithm', 'Detected on', [
+                { value: 'first', label: 'The first derivative' },
+                { value: 'second', label: 'The second derivative' },
+                { value: 'auto', label: 'Whichever fits' },
+            ]),
+        ],
+        caution: 'When fewer peaks are found than asked for, the spectrum is returned untouched and nothing says so.',
+    },
+    ensureGrowing: {
+        label: 'Make x strictly increasing',
+        group: 'utility',
+        summary: 'Drops the points that repeat or go backwards, which resampling and cropping both assume never happens.',
+        fields: [],
+    },
+    reverseIfNeeded: {
+        label: 'Reverse a descending x',
+        group: 'utility',
+        summary: 'Turns a descending axis the right way round.',
+        fields: [],
+        caution: 'The chain already does this before every step, so adding it here changes nothing.',
+    },
+};
+//# sourceMappingURL=axisEntries.js.map

package/lib/spectra/core/axisEntries.js.map

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package/lib/spectra/core/chainProblems.d.ts

@@ -0,0 +1,14 @@
+import type { SettingsProblem } from './problems.ts';
+import type { SpectrumFilter } from './settings.ts';
+/**
+ * Everything wrong, or probably wrong, with one chain.
+ *
+ * The order of a chain is its meaning — scaling measured before a baseline is
+ * removed measures an offset that is about to change — so the advice below is
+ * as much about where a step sits as about what it is set to.
+ * @param chain - The steps, in the order they run.
+ * @param resampleFirst - Whether the settings resample before the chain runs.
+ * @returns Every problem found, errors and advice together.
+ */
+export declare function chainProblems(chain: readonly SpectrumFilter[], resampleFirst: boolean): SettingsProblem[];
+//# sourceMappingURL=chainProblems.d.ts.map

package/lib/spectra/core/chainProblems.d.ts.map

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