react-cheminfo 0.69.0 → 0.71.0

package/lib/mass/ui/massActions.js

@@ -0,0 +1,62 @@
+/**
+ * Everything the viewer can be asked to do, as functions rather than actions.
+ *
+ * A component that dispatched action objects would have the shape of the reducer
+ * spread across every panel; one that calls `actions.selectSpectrum(id)` does
+ * not, and the reducer stays free to change how it holds things.
+ */
+/**
+ * Bind every action to a dispatch.
+ * @param dispatch - The reducer's dispatch.
+ * @returns The actions, stable for as long as the dispatch is.
+ */
+export function createMassActions(dispatch) {
+    return {
+        addSpectra(spectra) {
+            dispatch({ type: 'addSpectra', spectra });
+        },
+        setSpectra(spectra) {
+            dispatch({ type: 'setSpectra', spectra });
+        },
+        removeSpectrum(id) {
+            dispatch({ type: 'removeSpectrum', id });
+        },
+        renameSpectrum(id, name) {
+            dispatch({ type: 'renameSpectrum', id, name });
+        },
+        setSpectrumColor(id, color) {
+            dispatch({ type: 'setSpectrumColor', id, color });
+        },
+        setSpectrumVisibility(id, visibility) {
+            dispatch({ type: 'setSpectrumVisibility', id, visibility });
+        },
+        selectSpectrum(id) {
+            dispatch({ type: 'selectSpectrum', id });
+        },
+        setDomain(domain) {
+            dispatch({ type: 'setDomain', domain });
+        },
+        resetDomain() {
+            dispatch({ type: 'resetDomain' });
+        },
+        setTool(tool) {
+            dispatch({ type: 'setTool', tool });
+        },
+        togglePanel(panelId) {
+            dispatch({ type: 'togglePanel', panelId });
+        },
+        setError(error) {
+            dispatch({ type: 'setError', error });
+        },
+        setSettings(settings) {
+            dispatch({ type: 'setSettings', settings });
+        },
+        loadState(state) {
+            dispatch({ type: 'loadState', state });
+        },
+        clear() {
+            dispatch({ type: 'clear' });
+        },
+    };
+}
+//# sourceMappingURL=massActions.js.map

package/lib/mass/ui/massActions.js.map

@@ -0,0 +1 @@
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package/lib/mass/ui/massChartProps.d.ts

@@ -0,0 +1,128 @@
+/**
+ * What a consumer hands the chart, and what the chart tells it back.
+ *
+ * Held apart from the component because it is the whole of the chart's public
+ * API — every spectrum drawn, every peak labelled on it and every gesture that
+ * comes back out is one of these — while the component behind it is an assembly
+ * of half a dozen layers nobody needs to read in order to mount one.
+ *
+ * Everything arrives as a prop and nothing is reached for: the chart reads no
+ * store and no context, so the same component serves an editor, a report page
+ * that only ever draws one spectrum, and a test.
+ */
+import type { ReactNode } from 'react';
+import type { ZoomDragMode } from '../../chart/core/chartDomain.ts';
+import type { MassDomain, MassSpectrum } from '../core/massSpectrum.ts';
+import type { NearestPeak } from '../core/nearestPeak.ts';
+export interface MassChartProps {
+    /** The spectra to draw, each saying in itself which of its traces is drawn. */
+    spectra: readonly MassSpectrum[];
+    /**
+     * Identity of the spectrum whose peaks are labelled, `null` for none. One
+     * spectrum and never all of them: two stacks over every shared peak are the
+     * same m/z written twice, a pixel apart, in two colours.
+     * @default the first spectrum drawn
+     */
+    labelledId?: string | null;
+    /**
+     * Whether that spectrum's peaks are labelled at all.
+     * @default true
+     */
+    showLabels?: boolean;
+    /**
+     * At most how many peaks are labelled; every labelled one is still marked.
+     * @default DEFAULT_LABEL_LIMIT
+     */
+    labelLimit?: number;
+    /**
+     * Whether a label writes the charge of a peak whose charge was established.
+     * @default false
+     */
+    showCharges?: boolean;
+    /**
+     * How many decimals every mass is written with, overriding what the spectra
+     * resolve — where the labels follow the labelled spectrum's own resolution,
+     * and the crosshair what the drawn spectra resolve together.
+     * @default what the spectra resolve, as `mzDecimalsOf` decides
+     */
+    mzDecimals?: number;
+    /**
+     * What explains a peak, keyed as `peakKey` keys it — the name written on top
+     * of its label. This is how a host annotates peaks without the chart having
+     * to know where the names came from.
+     * @default undefined
+     */
+    annotationLabels?: ReadonlyMap<string, string>;
+    /**
+     * The m/z a guide is drawn at, `null` for none — the peak a row of a table
+     * beside the chart is resting on.
+     * @default null
+     */
+    highlightMz?: number | null;
+    /**
+     * Told which picked peak the pointer has come to rest on, and told `null` when
+     * it leaves one — called only when the answer changes.
+     * @default undefined
+     */
+    onPeakHover?: (peak: NearestPeak | null) => void;
+    /**
+     * The window to show, `null` to let the chart show what fits.
+     *
+     * The chart holds a window of its own, so this is an override rather than the
+     * chart's state: every window a gesture arrives at is reported through
+     * `onDomainChange`, and a host that keeps one is expected to hand back what it
+     * is told. Handing back `null` where a window was is how a host asks for the
+     * fit again.
+     * @default null
+     */
+    domain?: MassDomain | null;
+    /**
+     * Told the window the chart has come to show, whenever it changes — a drag, a
+     * turn of the wheel, the double click that fits everything again, or a refit
+     * after what is drawn changed.
+     * @default undefined
+     */
+    onDomainChange?: (domain: MassDomain) => void;
+    /**
+     * Told where a click on the plot landed, in m/z, and the picked peak within
+     * reach of it — `null` when it landed on none. The end of a drag is never a
+     * click.
+     * @default undefined
+     */
+    onPlotClick?: (mz: number, peak: NearestPeak | null) => void;
+    /**
+     * What a drag across the plot asks for: the m/z axis alone, or exactly the
+     * rectangle it sweeps out.
+     * @default 'xAxis'
+     */
+    drag?: ZoomDragMode;
+    /**
+     * Whether the chart answers `f` with the fit itself. A viewer around it that
+     * runs its keys through a command table turns this off.
+     * @default true
+     */
+    answersKeys?: boolean;
+    /**
+     * Identity of the spectrum drawn thicker than the rest, `null` for none.
+     * @default null
+     */
+    emphasisedId?: string | null;
+    /**
+     * How wide the chart is drawn, in pixels.
+     * @default the width of its container
+     */
+    width?: number;
+    /**
+     * How tall it is drawn, in pixels.
+     * @default the height of its container
+     */
+    height?: number;
+    /**
+     * Anything else to draw over the spectra, in the same pixels and under the
+     * same clip. Rendered last inside the plot, so a host adds to the chart
+     * instead of forking it.
+     * @default undefined
+     */
+    children?: ReactNode;
+}
+//# sourceMappingURL=massChartProps.d.ts.map

package/lib/mass/ui/massChartProps.d.ts.map

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package/lib/mass/ui/massChartProps.js

@@ -0,0 +1,14 @@
+/**
+ * What a consumer hands the chart, and what the chart tells it back.
+ *
+ * Held apart from the component because it is the whole of the chart's public
+ * API — every spectrum drawn, every peak labelled on it and every gesture that
+ * comes back out is one of these — while the component behind it is an assembly
+ * of half a dozen layers nobody needs to read in order to mount one.
+ *
+ * Everything arrives as a prop and nothing is reached for: the chart reads no
+ * store and no context, so the same component serves an editor, a report page
+ * that only ever draws one spectrum, and a test.
+ */
+export {};
+//# sourceMappingURL=massChartProps.js.map

package/lib/mass/ui/massChartProps.js.map

@@ -0,0 +1 @@
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package/lib/mass/ui/massCommandContext.d.ts

@@ -0,0 +1,36 @@
+/**
+ * How a component reaches the commands, and what a toolbar item needs to be one.
+ *
+ * The hooks and the context object, with no component of its own: a module that
+ * exports a component and a constant together cannot be hot reloaded, which is
+ * why the provider and the tooltip are files of their own beside this one.
+ */
+import type { MassCommandHandlers, MassCommandId, RunMassCommand } from '../core/massCommands.ts';
+/** What the provider holds. */
+export interface MassCommandContextValue {
+    /** What each command does. */
+    handlers: MassCommandHandlers;
+    /** Run one. */
+    run: RunMassCommand;
+}
+/** Where the provider puts it. */
+export declare const massCommandContext: import("react").Context<MassCommandContextValue | null>;
+/**
+ * Run a command from anywhere inside the viewer.
+ * @returns The runner; a command nothing handles does nothing.
+ */
+export declare function useMassCommand(): RunMassCommand;
+/**
+ * Everything a toolbar item needs to be one command, in one spread.
+ *
+ * The tooltip, the label a screen reader is given and the click handler all come
+ * from the same table entry, so a button cannot end up titled one thing and
+ * doing another.
+ * @returns A function from a command's identity to the props for its button.
+ */
+export declare function useMassCommandProps(): (id: MassCommandId) => {
+    tooltip: import("react").JSX.Element;
+    'aria-label': string;
+    onClick: () => void;
+};
+//# sourceMappingURL=massCommandContext.d.ts.map

package/lib/mass/ui/massCommandContext.d.ts.map

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package/lib/mass/ui/massCommandContext.js

@@ -0,0 +1,45 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+/**
+ * How a component reaches the commands, and what a toolbar item needs to be one.
+ *
+ * The hooks and the context object, with no component of its own: a module that
+ * exports a component and a constant together cannot be hot reloaded, which is
+ * why the provider and the tooltip are files of their own beside this one.
+ */
+import { createContext, useContext } from 'react';
+import { massCommandLabel } from "../core/massCommands.js";
+import { MassCommandTooltip } from "./MassCommandTooltip.js";
+/** Where the provider puts it. */
+export const massCommandContext = createContext(null);
+/**
+ * Run a command from anywhere inside the viewer.
+ * @returns The runner; a command nothing handles does nothing.
+ */
+export function useMassCommand() {
+    const value = useContext(massCommandContext);
+    return value?.run ?? noRun;
+}
+/**
+ * Everything a toolbar item needs to be one command, in one spread.
+ *
+ * The tooltip, the label a screen reader is given and the click handler all come
+ * from the same table entry, so a button cannot end up titled one thing and
+ * doing another.
+ * @returns A function from a command's identity to the props for its button.
+ */
+export function useMassCommandProps() {
+    const run = useMassCommand();
+    return function command(id) {
+        return {
+            tooltip: _jsx(MassCommandTooltip, { id: id }),
+            'aria-label': massCommandLabel(id),
+            onClick: () => run(id),
+        };
+    };
+}
+/** What running a command comes to outside a provider: nothing at all. */
+function noRun() {
+    // Deliberately empty: a chart mounted without the shell has no commands, and
+    // a missing provider is not a reason to throw at a button press.
+}
+//# sourceMappingURL=massCommandContext.js.map

package/lib/mass/ui/massCommandContext.js.map

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package/lib/mass/ui/massHostPanels.d.ts

@@ -0,0 +1,48 @@
+/**
+ * The panels a host adds to the viewer's own, and the one list both make.
+ *
+ * A host panel is a panel like any other once it is in the list: the activity
+ * bar and the stack read the same list, so it toggles, folds and closes exactly
+ * as the spectra or the peaks do. The host brings the body and nothing else —
+ * the header, its close button and the place in the column are the viewer's,
+ * which is what keeps every header reading the same.
+ */
+import type { IconName } from '@blueprintjs/core';
+import type { ReactNode } from 'react';
+import { massSidePanels } from '../core/massSidePanels.ts';
+/** A panel the host adds to the editor's own stack. */
+export interface MassHostPanel {
+    /**
+     * Its identity in the activity bar and in `defaultPanelIds`; never a built-in
+     * id. One that is, or that an earlier host panel already took, is left out:
+     * one icon cannot open two panels.
+     */
+    id: string;
+    /** What its header and its activity-bar item say. */
+    title: string;
+    /** Its glyph in the activity bar (a Blueprint IconName). */
+    icon: IconName;
+    /**
+     * Its body. It brings its own toolbar as first row: the header carries the
+     * close button only. It is rendered inside the viewer, so a component in it
+     * reaches the viewer it stands in through `useMassEditorState` and
+     * `useMassActions` — to overlay a predicted isotopic pattern, say.
+     */
+    content: ReactNode;
+}
+/** One panel of the side: one of the viewer's own, or one a host added. */
+export type MassStackPanel = (typeof massSidePanels)[number] | MassHostPanel;
+/**
+ * Every panel the side offers, in the order the activity bar stacks them: the
+ * host's first, in the order given, then the viewer's own.
+ * @param hostPanels - What the host adds.
+ * @returns The panels; the viewer's own list itself when the host adds none.
+ */
+export declare function massStackPanels(hostPanels: readonly MassHostPanel[]): readonly MassStackPanel[];
+/**
+ * Whether a panel of the side is one a host added, whose body it brings.
+ * @param panel - The panel.
+ * @returns True for a host's panel.
+ */
+export declare function isMassHostPanel(panel: MassStackPanel): panel is MassHostPanel;
+//# sourceMappingURL=massHostPanels.d.ts.map

package/lib/mass/ui/massHostPanels.d.ts.map

@@ -0,0 +1 @@
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package/lib/mass/ui/massHostPanels.js

@@ -0,0 +1,41 @@
+/**
+ * The panels a host adds to the viewer's own, and the one list both make.
+ *
+ * A host panel is a panel like any other once it is in the list: the activity
+ * bar and the stack read the same list, so it toggles, folds and closes exactly
+ * as the spectra or the peaks do. The host brings the body and nothing else —
+ * the header, its close button and the place in the column are the viewer's,
+ * which is what keeps every header reading the same.
+ */
+import { massSidePanels } from "../core/massSidePanels.js";
+/**
+ * Every panel the side offers, in the order the activity bar stacks them: the
+ * host's first, in the order given, then the viewer's own.
+ * @param hostPanels - What the host adds.
+ * @returns The panels; the viewer's own list itself when the host adds none.
+ */
+export function massStackPanels(hostPanels) {
+    if (hostPanels.length === 0)
+        return massSidePanels;
+    const taken = new Set(BUILT_IN_IDS);
+    const panels = [];
+    for (const panel of hostPanels) {
+        if (taken.has(panel.id))
+            continue;
+        taken.add(panel.id);
+        panels.push(panel);
+    }
+    panels.push(...massSidePanels);
+    return panels;
+}
+/**
+ * Whether a panel of the side is one a host added, whose body it brings.
+ * @param panel - The panel.
+ * @returns True for a host's panel.
+ */
+export function isMassHostPanel(panel) {
+    return 'content' in panel;
+}
+/** The ids no host panel may take. */
+const BUILT_IN_IDS = massSidePanels.map((panel) => panel.id);
+//# sourceMappingURL=massHostPanels.js.map

package/lib/mass/ui/massHostPanels.js.map

@@ -0,0 +1 @@
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package/lib/mass/ui/massStateContext.d.ts

@@ -0,0 +1,26 @@
+/**
+ * How a panel reaches the viewer it is inside.
+ *
+ * Two contexts rather than one, because the actions never change while the state
+ * changes on every drag of the chart: a panel that only ever acts — a toolbar
+ * button — reads the second and is not re-rendered by the first.
+ */
+import type { MassEditorActions } from './massActions.ts';
+import type { MassEditorApi } from './useMassEditor.ts';
+/** Everything one viewer knows, as the provider holds it. */
+export declare const massStateContext: import("react").Context<MassEditorApi | null>;
+/** Everything that changes it, as the provider holds it. */
+export declare const massActionsContext: import("react").Context<MassEditorActions | null>;
+/**
+ * Everything the viewer knows, from inside it.
+ * @returns The state and what follows from it.
+ * @throws {Error} When read outside a `MassStateProvider`.
+ */
+export declare function useMassEditorState(): MassEditorApi;
+/**
+ * Everything to do, from inside the viewer.
+ * @returns The actions.
+ * @throws {Error} When read outside a `MassStateProvider`.
+ */
+export declare function useMassActions(): MassEditorActions;
+//# sourceMappingURL=massStateContext.d.ts.map

package/lib/mass/ui/massStateContext.d.ts.map

@@ -0,0 +1 @@
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package/lib/mass/ui/massStateContext.js

@@ -0,0 +1,37 @@
+/**
+ * How a panel reaches the viewer it is inside.
+ *
+ * Two contexts rather than one, because the actions never change while the state
+ * changes on every drag of the chart: a panel that only ever acts — a toolbar
+ * button — reads the second and is not re-rendered by the first.
+ */
+import { createContext, useContext } from 'react';
+/** Everything one viewer knows, as the provider holds it. */
+export const massStateContext = createContext(null);
+/** Everything that changes it, as the provider holds it. */
+export const massActionsContext = createContext(null);
+/**
+ * Everything the viewer knows, from inside it.
+ * @returns The state and what follows from it.
+ * @throws {Error} When read outside a `MassStateProvider`.
+ */
+export function useMassEditorState() {
+    const editor = useContext(massStateContext);
+    if (editor === null) {
+        throw new Error('The mass spectrum viewer state was read outside a MassStateProvider');
+    }
+    return editor;
+}
+/**
+ * Everything to do, from inside the viewer.
+ * @returns The actions.
+ * @throws {Error} When read outside a `MassStateProvider`.
+ */
+export function useMassActions() {
+    const actions = useContext(massActionsContext);
+    if (actions === null) {
+        throw new Error('The mass spectrum viewer actions were read outside a MassStateProvider');
+    }
+    return actions;
+}
+//# sourceMappingURL=massStateContext.js.map

package/lib/mass/ui/massStateContext.js.map

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package/lib/mass/ui/useIntensityZoom.d.ts

@@ -0,0 +1,20 @@
+/**
+ * The zoom in and zoom out commands, which scale the intensity axis alone.
+ *
+ * They scale it about zero, the baseline every stick stands on, so a small peak
+ * comes up out of the baseline rather than the whole spectrum drifting off the
+ * plot — what a turn of the wheel does, at the speed of a key press.
+ */
+/** The two commands, ready to hand to a button or a key. */
+export interface IntensityZoom {
+    /** Bring the peaks up by one step. */
+    zoomIn: () => void;
+    /** Put the axis back out by one step. */
+    zoomOut: () => void;
+}
+/**
+ * Zoom the intensity axis of the viewer this is called inside.
+ * @returns The two commands.
+ */
+export declare function useIntensityZoom(): IntensityZoom;
+//# sourceMappingURL=useIntensityZoom.d.ts.map

package/lib/mass/ui/useIntensityZoom.d.ts.map

@@ -0,0 +1 @@
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package/lib/mass/ui/useIntensityZoom.js

@@ -0,0 +1,42 @@
+/**
+ * The zoom in and zoom out commands, which scale the intensity axis alone.
+ *
+ * They scale it about zero, the baseline every stick stands on, so a small peak
+ * comes up out of the baseline rather than the whole spectrum drifting off the
+ * plot — what a turn of the wheel does, at the speed of a key press.
+ */
+import { useMemo } from 'react';
+import { fullDomain } from "../core/massDomain.js";
+import { useMassActions, useMassEditorState } from "./massStateContext.js";
+/**
+ * Zoom the intensity axis of the viewer this is called inside.
+ * @returns The two commands.
+ */
+export function useIntensityZoom() {
+    const { state, visibleSpectra } = useMassEditorState();
+    const actions = useMassActions();
+    const { domain } = state.view;
+    return useMemo(() => {
+        /**
+         * Scale the intensity axis by a factor, about zero.
+         * @param factor - Above one to zoom out.
+         */
+        function scale(factor) {
+            const shown = domain ?? fullDomain(visibleSpectra);
+            actions.setDomain({
+                x: shown.x,
+                y: [shown.y[0] * factor, shown.y[1] * factor],
+            });
+        }
+        return {
+            zoomIn: () => scale(1 / ZOOM_STEP),
+            zoomOut: () => scale(ZOOM_STEP),
+        };
+    }, [actions, domain, visibleSpectra]);
+}
+/**
+ * What one press of zoom in or out is worth: about what one notch of a mouse
+ * wheel does, so the button and the wheel feel like one gesture at two speeds.
+ */
+const ZOOM_STEP = 1.2;
+//# sourceMappingURL=useIntensityZoom.js.map

package/lib/mass/ui/useIntensityZoom.js.map

@@ -0,0 +1 @@
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package/lib/mass/ui/useMassEditor.d.ts

@@ -0,0 +1,52 @@
+/**
+ * One viewer's state, and everything derived from it.
+ *
+ * What is derived here is what three panels and the chart read alike — which
+ * spectra are drawn, which one is selected, and how many decimals every mass on
+ * screen is written with — so it is worked out once per change rather than once
+ * per reader.
+ */
+import type { MassSpectrum } from '../core/massSpectrum.ts';
+import type { CreateMassStateOptions, MassState } from '../core/massState.ts';
+import type { MassEditorActions } from './massActions.ts';
+/** What a viewer opens on, and who to tell when the spectra change. */
+export interface UseMassEditorOptions extends CreateMassStateOptions {
+    /**
+     * Called whenever the spectra open change — one loaded, one closed, the chart
+     * cleared — with the spectra now open.
+     * @default undefined
+     */
+    onChange?: (spectra: MassSpectrum[]) => void;
+}
+/** What a component drives the viewer through. */
+export interface MassEditorApi {
+    /** Everything the viewer knows, in its three buckets. */
+    state: MassState;
+    /** The spectra currently drawn, by either trace, in the order they were loaded. */
+    visibleSpectra: MassSpectrum[];
+    /** The spectrum the panels act on, `null` while none is selected. */
+    selectedSpectrum: MassSpectrum | null;
+    /**
+     * How many decimals the masses the panels write are written with: the number
+     * chosen in the settings, or else the selected spectrum's own, since the peak
+     * table, the acquisition table and the labels are all about it alone — a
+     * nominal-mass table is written in whole numbers even beside an Orbitrap
+     * scan. With nothing selected, what the drawn spectra resolve together — see
+     * `mzDecimalsOf`.
+     */
+    mzDecimals: number;
+    /**
+     * What `mzDecimals` comes to when nothing is chosen, for a control that says
+     * what choosing nothing would mean.
+     */
+    autoMzDecimals: number;
+    /** Everything to do. */
+    actions: MassEditorActions;
+}
+/**
+ * Hold one viewer's state.
+ * @param options - What it opens on.
+ * @returns The state, what follows from it, and everything to do.
+ */
+export declare function useMassEditor(options?: UseMassEditorOptions): MassEditorApi;
+//# sourceMappingURL=useMassEditor.d.ts.map

package/lib/mass/ui/useMassEditor.d.ts.map

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