react-cheminfo 0.69.0 → 0.71.0

package/lib/mass/ui/useMassEditor.js

@@ -0,0 +1,93 @@
+/**
+ * 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 { useEffect, useMemo, useReducer, useRef } from 'react';
+import { massReducer } from "../core/massReducer.js";
+import { isSpectrumDrawn } from "../core/massSpectrum.js";
+import { createMassState } from "../core/massState.js";
+import { mzDecimalsFor } from "../core/mzDecimalsSetting.js";
+import { mzDecimalsOf } from "../core/resolutionOf.js";
+import { createMassActions } from "./massActions.js";
+/**
+ * Hold one viewer's state.
+ * @param options - What it opens on.
+ * @returns The state, what follows from it, and everything to do.
+ */
+export function useMassEditor(options = {}) {
+    const { onChange, ...initial } = options;
+    const [state, dispatch] = useReducer(massReducer, initial, createMassState);
+    const actions = useMemo(() => createMassActions(dispatch), [dispatch]);
+    const { spectra } = state.data;
+    const { selectedId } = state.view;
+    const visibleSpectra = useMemo(() => {
+        const visible = [];
+        for (const spectrum of spectra) {
+            if (isSpectrumDrawn(spectrum))
+                visible.push(spectrum);
+        }
+        return visible;
+    }, [spectra]);
+    const selectedSpectrum = useMemo(() => {
+        if (selectedId === null)
+            return null;
+        for (const spectrum of spectra) {
+            if (spectrum.id === selectedId)
+                return spectrum;
+        }
+        return null;
+    }, [spectra, selectedId]);
+    const decimalsSetting = state.settings.mzDecimals;
+    const shownSpectra = useMemo(() => (selectedSpectrum === null ? visibleSpectra : [selectedSpectrum]), [visibleSpectra, selectedSpectrum]);
+    const autoMzDecimals = useMemo(() => mzDecimalsOf(shownSpectra), [shownSpectra]);
+    const mzDecimals = useMemo(() => mzDecimalsFor(decimalsSetting, shownSpectra), [decimalsSetting, shownSpectra]);
+    // What was reported last, so a host passing a fresh callback on every render
+    // is not told about spectra that did not change. The identities are compared
+    // rather than the array: a rename or a colour builds a new spectrum around
+    // the same peaks, and that is not a change of what is loaded.
+    const reported = useRef(spectra);
+    useEffect(() => {
+        if (sameSpectra(reported.current, spectra))
+            return;
+        reported.current = spectra;
+        onChange?.(spectra);
+    }, [spectra, onChange]);
+    return useMemo(() => ({
+        state,
+        visibleSpectra,
+        selectedSpectrum,
+        mzDecimals,
+        autoMzDecimals,
+        actions,
+    }), [
+        state,
+        visibleSpectra,
+        selectedSpectrum,
+        mzDecimals,
+        autoMzDecimals,
+        actions,
+    ]);
+}
+/**
+ * Whether two lists hold the same spectra, in order.
+ * @param current - What was reported last.
+ * @param next - What is open now.
+ * @returns Whether the report can be skipped.
+ */
+function sameSpectra(current, next) {
+    if (current === next)
+        return true;
+    if (current.length !== next.length)
+        return false;
+    for (let index = 0; index < current.length; index++) {
+        if (current[index].id !== next[index].id) {
+            return false;
+        }
+    }
+    return true;
+}
+//# sourceMappingURL=useMassEditor.js.map

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

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

@@ -0,0 +1,22 @@
+/**
+ * Reading the files a chemist drops on the chart or picks from a dialog.
+ *
+ * Every file is read on its own, and one that cannot be read is said rather
+ * than stopping the others: a drop of eleven files with one infrared JCAMP among
+ * them draws the ten mass spectra and names the eleventh in the status bar.
+ */
+/** How files reach the viewer. */
+export interface MassFiles {
+    /**
+     * Read these files and add what they hold.
+     * @param files - What was dropped or chosen.
+     * @returns Once every file has been read.
+     */
+    readFiles: (files: readonly File[]) => Promise<void>;
+}
+/**
+ * Read files into the viewer this is called inside.
+ * @returns How to read them.
+ */
+export declare function useMassFiles(): MassFiles;
+//# sourceMappingURL=useMassFiles.d.ts.map

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

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

@@ -0,0 +1,71 @@
+/**
+ * Reading the files a chemist drops on the chart or picks from a dialog.
+ *
+ * Every file is read on its own, and one that cannot be read is said rather
+ * than stopping the others: a drop of eleven files with one infrared JCAMP among
+ * them draws the ten mass spectra and names the eleventh in the status bar.
+ */
+import { useCallback, useMemo } from 'react';
+import { errorMessage } from "../../error/core/index.js";
+import { loadMassSpectra } from "../core/loadMassSpectra.js";
+import { toMassSpectra } from "../core/toMassSpectrum.js";
+import { useMassActions, useMassEditorState } from "./massStateContext.js";
+/**
+ * Read files into the viewer this is called inside.
+ * @returns How to read them.
+ */
+export function useMassFiles() {
+    const { state } = useMassEditorState();
+    const actions = useMassActions();
+    const { spectra: open } = state.data;
+    const readFiles = useCallback(async (files) => {
+        // Read together, since each read is the browser's work rather than ours,
+        // and then dressed in the order the files were given, so the colours are
+        // handed out in that order too.
+        const results = await Promise.all(files.map(readFile));
+        const colors = open.map((spectrum) => spectrum.color);
+        const read = [];
+        const problems = [];
+        for (const [index, result] of results.entries()) {
+            const name = files[index]?.name ?? 'A file';
+            if (typeof result === 'string') {
+                problems.push(result);
+                continue;
+            }
+            try {
+                const spectra = toMassSpectra(result.spectra, { taken: colors });
+                for (const spectrum of spectra)
+                    colors.push(spectrum.color);
+                read.push(...spectra);
+            }
+            catch (error) {
+                problems.push(`${name} could not be peak picked — ${errorMessage(error)}`);
+                continue;
+            }
+            if (result.dropped > 0) {
+                problems.push(`${name} holds ${result.spectra.length + result.dropped} spectra and only the first ${result.spectra.length} were read.`);
+            }
+        }
+        if (read.length > 0)
+            actions.addSpectra(read);
+        // After the spectra, which clear any error standing from before.
+        if (problems.length > 0)
+            actions.setError(problems.join(' '));
+    }, [actions, open]);
+    return useMemo(() => ({ readFiles }), [readFiles]);
+}
+/**
+ * Read one file, saying why when it cannot be.
+ * @param file - The file.
+ * @returns What it held, or the sentence its refusal came with.
+ */
+async function readFile(file) {
+    try {
+        const bytes = new Uint8Array(await file.arrayBuffer());
+        return await loadMassSpectra(bytes, { fileName: file.name });
+    }
+    catch (error) {
+        return errorMessage(error);
+    }
+}
+//# sourceMappingURL=useMassFiles.js.map

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

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

@@ -0,0 +1,15 @@
+/**
+ * The handle a host drives the viewer through, filled in from its state.
+ *
+ * A hook of its own beside the shell, because every gesture on the handle reads
+ * the state the shell already reads — and the shell is long enough without it.
+ */
+import type { Ref } from 'react';
+import type { MassEditorHandle } from '../core/massEditorApi.ts';
+/**
+ * Fill in a host's handle on the viewer this is called inside.
+ * @param handle - The handle to fill in, if the host asked for one.
+ * @param readFiles - How a file is read into the viewer, as a drop reads it.
+ */
+export declare function useMassHandle(handle: Ref<MassEditorHandle> | undefined, readFiles: (files: readonly File[]) => Promise<void>): void;
+//# sourceMappingURL=useMassHandle.d.ts.map

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

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

@@ -0,0 +1,35 @@
+/**
+ * The handle a host drives the viewer through, filled in from its state.
+ *
+ * A hook of its own beside the shell, because every gesture on the handle reads
+ * the state the shell already reads — and the shell is long enough without it.
+ */
+import { useImperativeHandle } from 'react';
+import { mzFrame } from "../core/massDomain.js";
+import { useMassActions, useMassEditorState } from "./massStateContext.js";
+/**
+ * Fill in a host's handle on the viewer this is called inside.
+ * @param handle - The handle to fill in, if the host asked for one.
+ * @param readFiles - How a file is read into the viewer, as a drop reads it.
+ */
+export function useMassHandle(handle, readFiles) {
+    const { state, visibleSpectra } = useMassEditorState();
+    const actions = useMassActions();
+    const { domain } = state.view;
+    useImperativeHandle(handle, () => ({
+        getSpectra: () => state.data.spectra,
+        setSpectra: (spectra) => actions.setSpectra(spectra),
+        addSpectra: (spectra) => actions.addSpectra(spectra),
+        openFiles: (files) => readFiles(files),
+        clear: () => actions.clear(),
+        setDomain: (next) => actions.setDomain(next),
+        resetDomain: () => actions.resetDomain(),
+        zoomToMz: (mz, options = {}) => {
+            actions.setDomain(mzFrame(mz, visibleSpectra, domain, options.halfWidth === undefined
+                ? {}
+                : { halfWidth: options.halfWidth }));
+        },
+        selectSpectrum: (id) => actions.selectSpectrum(id),
+    }), [state.data.spectra, actions, readFiles, domain, visibleSpectra]);
+}
+//# sourceMappingURL=useMassHandle.js.map

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

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

@@ -0,0 +1,70 @@
+/**
+ * What a mass chart reads under the pointer, and which peak it is asking about.
+ *
+ * Following the pointer at all is `useChartPointer` in the shared chart:
+ * placing it in user units, refusing the margins, and reporting only when the
+ * answer changed. What it *reads* there is the part that is about mass, and is
+ * the whole of this file — the m/z, the intensity, and the peak within reach.
+ */
+import type { RefObject } from 'react';
+import type { PlotRect } from '../../chart/core/chartGeometry.ts';
+import type { ChartScale } from '../../chart/core/chartScale.ts';
+import type { ChartPointer } from '../../chart/ui/useChartPointer.ts';
+import type { MassSpectrum } from '../core/massSpectrum.ts';
+import type { NearestPeak } from '../core/nearestPeak.ts';
+/** What the axes say under the pointer, which is what a readout prints. */
+export interface MassReadout {
+    /** What the m/z axis reads there. */
+    mz: number;
+    /** What the intensity axis reads there. */
+    intensity: number;
+    /** The peak within reach of the pointer, `null` when none is. */
+    peak: NearestPeak | null;
+}
+export interface MassPointerOptions {
+    /** The SVG the chart is drawn on, as it was handed to its `ref`. */
+    svgRef: RefObject<SVGSVGElement | null>;
+    /** Where the plot sits inside that SVG. */
+    plot: PlotRect;
+    /** The m/z axis as it is currently zoomed. */
+    xScale: ChartScale;
+    /** The intensity axis as it is currently zoomed. */
+    yScale: ChartScale;
+    /** What the chart draws, for the peak under the pointer to be found. */
+    spectra: readonly MassSpectrum[];
+    /**
+     * Told which peak the pointer has come to rest on, and told `null` when it
+     * leaves one — called only when the answer changes, so it is safe to hang a
+     * highlight that redraws half the page on it.
+     * @default undefined
+     */
+    onPeak?: (peak: NearestPeak | null) => void;
+    /**
+     * Told when the pointer leaves the plot, and only then.
+     *
+     * `onPeak` says `null` for the gap between two sticks as well, so it cannot
+     * be read as the reading being over — which is the one thing a host drawing a
+     * picture of whatever is crossed has to know.
+     * @default undefined
+     */
+    onAway?: () => void;
+}
+/**
+ * Follow the pointer over a mass chart.
+ * @param options - The chart, its axes and what it holds.
+ * @returns Where the pointer is and what it reads, both `null` while it is
+ * anywhere but over the plot.
+ */
+export declare function useMassPointer(options: MassPointerOptions): ChartPointer<MassReadout>;
+/**
+ * Whether two readings are about the same peak.
+ *
+ * The peak alone, and never the m/z under the crosshair: that fractional value
+ * changes on every pixel the pointer moves, and comparing it would report a new
+ * answer for every tremor of a hand resting on one stick.
+ * @param current - What was last read.
+ * @param next - What has just been read.
+ * @returns Whether both are about the same peak.
+ */
+export declare function sameMassReadout(current: MassReadout, next: MassReadout): boolean;
+//# sourceMappingURL=useMassPointer.d.ts.map

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

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

@@ -0,0 +1,57 @@
+/**
+ * What a mass chart reads under the pointer, and which peak it is asking about.
+ *
+ * Following the pointer at all is `useChartPointer` in the shared chart:
+ * placing it in user units, refusing the margins, and reporting only when the
+ * answer changed. What it *reads* there is the part that is about mass, and is
+ * the whole of this file — the m/z, the intensity, and the peak within reach.
+ */
+import { useCallback, useMemo } from 'react';
+import { chartValue } from "../../chart/core/chartScale.js";
+import { useChartPointer } from "../../chart/ui/useChartPointer.js";
+import { nearestPeakMz, sameNearestPeak } from "../core/nearestPeak.js";
+/**
+ * Follow the pointer over a mass chart.
+ * @param options - The chart, its axes and what it holds.
+ * @returns Where the pointer is and what it reads, both `null` while it is
+ * anywhere but over the plot.
+ */
+export function useMassPointer(options) {
+    const { svgRef, plot, xScale, yScale, spectra, onPeak, onAway } = options;
+    const read = useCallback((point) => ({
+        mz: chartValue(xScale, point.x),
+        intensity: chartValue(yScale, point.y),
+        peak: nearestPeakMz(spectra, xScale, point.x),
+    }), [xScale, yScale, spectra]);
+    const onReadout = useMemo(() => onPeak === undefined && onAway === undefined
+        ? undefined
+        : (readout) => {
+            onPeak?.(readout?.peak ?? null);
+            // Only the whole reading is absent off the plot: inside it there is
+            // always an m/z and an intensity, whether or not a stick is within
+            // reach. So this is the leave, and the `null` peak above is not.
+            if (readout === null)
+                onAway?.();
+        }, [onPeak, onAway]);
+    return useChartPointer({
+        svgRef,
+        plot,
+        read,
+        sameReadout: sameMassReadout,
+        onReadout,
+    });
+}
+/**
+ * Whether two readings are about the same peak.
+ *
+ * The peak alone, and never the m/z under the crosshair: that fractional value
+ * changes on every pixel the pointer moves, and comparing it would report a new
+ * answer for every tremor of a hand resting on one stick.
+ * @param current - What was last read.
+ * @param next - What has just been read.
+ * @returns Whether both are about the same peak.
+ */
+export function sameMassReadout(current, next) {
+    return sameNearestPeak(current.peak, next.peak);
+}
+//# sourceMappingURL=useMassPointer.js.map

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

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

@@ -0,0 +1,21 @@
+/**
+ * The keys, heard on the viewer's own root rather than on the document.
+ *
+ * Two viewers on one page must not both answer `f`, and a page that holds this
+ * beside an infrared viewer must not have its own keys eaten. So the viewer
+ * hears a key only while it holds the caret — the root carries `tabIndex={-1}`
+ * so a click anywhere in it does — and a key it acted on goes no further.
+ */
+import type { MassCommandHandlers } from '../core/massCommands.ts';
+/**
+ * Fire the viewer's commands from the keyboard.
+ *
+ * The handlers are read live through a ref rather than closed over, so the
+ * listener is attached once for the life of the viewer instead of being torn
+ * down and rebuilt on every render — and the chart re-renders on every move of
+ * the pointer across it.
+ * @param root - The viewer's root, `null` until it is mounted.
+ * @param handlers - What each command does.
+ */
+export declare function useMassShortcuts(root: HTMLElement | null, handlers: MassCommandHandlers): void;
+//# sourceMappingURL=useMassShortcuts.d.ts.map

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

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

@@ -0,0 +1,66 @@
+/**
+ * The keys, heard on the viewer's own root rather than on the document.
+ *
+ * Two viewers on one page must not both answer `f`, and a page that holds this
+ * beside an infrared viewer must not have its own keys eaten. So the viewer
+ * hears a key only while it holds the caret — the root carries `tabIndex={-1}`
+ * so a click anywhere in it does — and a key it acted on goes no further.
+ */
+import { useEffect, useLayoutEffect, useRef } from 'react';
+import { isEditingField } from "../../panel/core/isEditingField.js";
+import { massCommands } from "../core/massCommands.js";
+/**
+ * Fire the viewer's commands from the keyboard.
+ *
+ * The handlers are read live through a ref rather than closed over, so the
+ * listener is attached once for the life of the viewer instead of being torn
+ * down and rebuilt on every render — and the chart re-renders on every move of
+ * the pointer across it.
+ * @param root - The viewer's root, `null` until it is mounted.
+ * @param handlers - What each command does.
+ */
+export function useMassShortcuts(root, handlers) {
+    const latest = useRef(handlers);
+    useLayoutEffect(() => {
+        latest.current = handlers;
+    });
+    useEffect(() => {
+        if (root === null)
+            return;
+        /**
+         * Run the command a key names, if it names one.
+         * @param event - The key that arrived.
+         */
+        function onKeyDown(event) {
+            // A key pressed with a modifier belongs to the browser or to the page:
+            // Ctrl+F is a search, and a viewer that swallowed it to fit its chart
+            // would be a viewer people stop typing in.
+            if (event.ctrlKey || event.metaKey || event.altKey)
+                return;
+            // Never while a name is being typed into the spectra panel.
+            if (isEditingField(event.target))
+                return;
+            const id = KEYS.get(event.key.toLowerCase());
+            if (id === undefined)
+                return;
+            const handler = latest.current[id];
+            if (handler === undefined)
+                return;
+            event.preventDefault();
+            // So the same key does not also reach a viewer mounted beside this one.
+            event.stopPropagation();
+            handler();
+        }
+        root.addEventListener('keydown', onKeyDown);
+        return () => {
+            root.removeEventListener('keydown', onKeyDown);
+        };
+    }, [root]);
+}
+/**
+ * Every key the viewer answers to, against the command it runs — built once
+ * from the command table, lower-cased so a capital arriving from a held shift
+ * still reaches the command a lowercase key names.
+ */
+const KEYS = new Map(Object.entries(massCommands).flatMap(([id, command]) => (command.shortcut?.keys ?? []).map((key) => [key.toLowerCase(), id])));
+//# sourceMappingURL=useMassShortcuts.js.map

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

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

@@ -0,0 +1,27 @@
+/**
+ * The side of the viewer: the panels it offers, whether any of them is open,
+ * and what dragging the splitter shut and back open does to them.
+ *
+ * A hook of its own beside the shell, because the shell lays the side out and
+ * this decides what is on it.
+ */
+import type { MassHostPanel, MassStackPanel } from './massHostPanels.ts';
+/** The side, as the shell lays it out. */
+export interface MassSide {
+    /** Every panel on offer, in the order their icons are stacked. */
+    panels: readonly MassStackPanel[];
+    /** Whether a panel on offer is open, which is whether the side is. */
+    isOpen: boolean;
+    /**
+     * Open or close the side, as the splitter is dragged shut and back open.
+     * @param open - Whether the side is now open.
+     */
+    setOpen: (open: boolean) => void;
+}
+/**
+ * The side of the viewer this is called inside.
+ * @param hostPanels - The panels the host adds to the viewer's own.
+ * @returns The panels on offer, whether the side is open, and how to open it.
+ */
+export declare function useMassSide(hostPanels: readonly MassHostPanel[]): MassSide;
+//# sourceMappingURL=useMassSide.d.ts.map

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

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

@@ -0,0 +1,45 @@
+/**
+ * The side of the viewer: the panels it offers, whether any of them is open,
+ * and what dragging the splitter shut and back open does to them.
+ *
+ * A hook of its own beside the shell, because the shell lays the side out and
+ * this decides what is on it.
+ */
+import { useMemo } from 'react';
+import { DEFAULT_SIDE_PANEL } from "../core/massState.js";
+import { massStackPanels } from "./massHostPanels.js";
+import { useMassActions, useMassEditorState } from "./massStateContext.js";
+/**
+ * The side of the viewer this is called inside.
+ * @param hostPanels - The panels the host adds to the viewer's own.
+ * @returns The panels on offer, whether the side is open, and how to open it.
+ */
+export function useMassSide(hostPanels) {
+    const { state } = useMassEditorState();
+    const actions = useMassActions();
+    const { openPanelIds } = state.view;
+    const panels = useMemo(() => massStackPanels(hostPanels), [hostPanels]);
+    // Read off the panels on offer rather than off the ids: an id no panel
+    // answers to opens nothing, and a side open on it alone is an empty column.
+    const isOpen = useMemo(() => {
+        const open = new Set(openPanelIds);
+        return panels.some((panel) => open.has(panel.id));
+    }, [panels, openPanelIds]);
+    /**
+     * Open or close the side.
+     * @param open - Whether the side is now open.
+     */
+    function setOpen(open) {
+        if (!open) {
+            for (const panelId of openPanelIds)
+                actions.togglePanel(panelId);
+            return;
+        }
+        // Dragging the splitter back open must land on something, or it opens on an
+        // empty column and reads as broken.
+        if (!isOpen)
+            actions.togglePanel(DEFAULT_SIDE_PANEL);
+    }
+    return { panels, isOpen, setOpen };
+}
+//# sourceMappingURL=useMassSide.js.map

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

@@ -0,0 +1 @@
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