react-cheminfo 0.69.0 → 0.71.0

package/lib/mass/core/loadMassSpectra.js

@@ -0,0 +1,45 @@
+/**
+ * One entry point for whatever was dropped, opened or pasted.
+ *
+ * The format is decided from the bytes and the right reader is called, so a
+ * caller hands over a file and gets spectra back without knowing what it turned
+ * out to be. Each reader is imported only once the bytes turn out to need it, so
+ * a page that never opens a JCAMP never downloads its converter.
+ */
+import { describeSource } from "../../error/core/index.js";
+import { detectMassFormat } from "./detectMassFormat.js";
+/**
+ * How many spectra one file is read for at most.
+ *
+ * A JCAMP of a GC/MS run writes a page per scan, thousands of them, and a list
+ * of thousands of rows is a list nobody can find anything in. A hundred keeps
+ * every file somebody exported deliberately and stops a whole run at its start,
+ * where saying so is better than hanging the page.
+ */
+export const DEFAULT_MAX_SPECTRA = 100;
+/**
+ * Read every mass spectrum a file holds.
+ * @param data - The file, as bytes, or the pasted text.
+ * @param options - The file's name, and how many spectra to read at most.
+ * @returns The spectra, the format they were read from and how many were left
+ * unread.
+ * @throws {Error} When nothing in the file names a format this can read, or when
+ * the reader for that format gave up on it — always with a sentence naming the
+ * file.
+ */
+export async function loadMassSpectra(data, options = {}) {
+    const { fileName, maxSpectra = DEFAULT_MAX_SPECTRA } = options;
+    const content = data instanceof ArrayBuffer ? new Uint8Array(data) : data;
+    const format = detectMassFormat(content, fileName);
+    const named = fileName === undefined ? {} : { fileName };
+    if (format === 'jcamp') {
+        const { fromJcamp } = await import("./fromJcamp.js");
+        return { ...fromJcamp(content, { ...named, maxSpectra }), format };
+    }
+    if (format === 'text') {
+        const { fromText } = await import("./fromText.js");
+        return { spectra: fromText(content, named), format, dropped: 0 };
+    }
+    throw new Error(`${describeSource(fileName)} is not a spectrum this viewer can read — JCAMP-DX files (.jdx, .dx) and two columns of m/z and intensity (.txt, .csv, .xy) are understood.`);
+}
+//# sourceMappingURL=loadMassSpectra.js.map

package/lib/mass/core/loadMassSpectra.js.map

@@ -0,0 +1 @@
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package/lib/mass/core/loadedMassSpectrum.d.ts

@@ -0,0 +1,42 @@
+/**
+ * What a reader hands back, before the peaks are picked.
+ *
+ * A JCAMP holds a title and twenty instrument records, a pasted peak table two
+ * columns and nothing else — and both end up here, so `toMassSpectrum` has one
+ * shape to turn into a `MassSpectrum`. A reader does not pick peaks, choose a
+ * colour or mint an identity, because those are decisions about the session
+ * rather than about the file.
+ *
+ * One spectrum is one acquisition. A file holding twelve gives twelve and never
+ * a merged one — an averaged spectrum is something the chemist asks for, not
+ * something a reader quietly does on the way in.
+ */
+import type { MassMeta, MassOrigin, MassTrace } from './massSpectrum.ts';
+/** One acquisition, as the file gave it up. */
+export interface LoadedMassSpectrum {
+    /**
+     * The points, m/z ascending, the intensities as the file wrote them — counts
+     * on one instrument and relative abundance on the next. They are put on one
+     * scale when the peaks are picked.
+     */
+    trace: MassTrace;
+    /** What the file said about the acquisition, `null` when it said nothing. */
+    meta: MassMeta | null;
+    /** Where it came from. */
+    origin: MassOrigin;
+    /**
+     * What the file calls it, absent when the file names nothing, so the caller
+     * can fall back to the file name without having to recognise a placeholder
+     * it invented itself.
+     * @default undefined
+     */
+    name?: string;
+    /**
+     * Whether the file said outright that this is a continuous profile rather
+     * than a peak table, absent when it did not — which is what the spacing of
+     * the points is then asked.
+     * @default undefined
+     */
+    continuous?: boolean;
+}
+//# sourceMappingURL=loadedMassSpectrum.d.ts.map

package/lib/mass/core/loadedMassSpectrum.d.ts.map

@@ -0,0 +1 @@
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package/lib/mass/core/loadedMassSpectrum.js

@@ -0,0 +1,15 @@
+/**
+ * What a reader hands back, before the peaks are picked.
+ *
+ * A JCAMP holds a title and twenty instrument records, a pasted peak table two
+ * columns and nothing else — and both end up here, so `toMassSpectrum` has one
+ * shape to turn into a `MassSpectrum`. A reader does not pick peaks, choose a
+ * colour or mint an identity, because those are decisions about the session
+ * rather than about the file.
+ *
+ * One spectrum is one acquisition. A file holding twelve gives twelve and never
+ * a merged one — an averaged spectrum is something the chemist asks for, not
+ * something a reader quietly does on the way in.
+ */
+export {};
+//# sourceMappingURL=loadedMassSpectrum.js.map

package/lib/mass/core/loadedMassSpectrum.js.map

@@ -0,0 +1 @@
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package/lib/mass/core/massCommands.d.ts

@@ -0,0 +1,170 @@
+/**
+ * Everything the viewer offers, what each is called, and the key it answers to.
+ *
+ * One table, read by three things that must agree: the toolbar draws it, the
+ * tooltip explains it, and the key handler fires it. Written apart from all
+ * three so a command cannot be added to the toolbar without a name, or bound to
+ * a key nothing tells the reader about.
+ *
+ * The keys are the infrared viewer's wherever the two viewers share a command,
+ * so a chemist who has learned one has learned the other.
+ */
+/** The key a command answers to. */
+export interface MassShortcut {
+    /** The `event.key` values it fires on, the first being the one shown. */
+    keys: readonly string[];
+    /**
+     * How to write the key in a tooltip, where the raw value would read badly.
+     * @default the first of `keys`
+     */
+    label?: readonly string[];
+}
+/** A gesture that does the same thing, listed under the tooltip's title. */
+export interface MassGesture {
+    /** Where the gesture is made, or what it is made with. */
+    title: string;
+    /** The buttons, keys or wheel that make it. */
+    shortcuts: readonly string[];
+}
+/** One thing the viewer can be asked to do. */
+export interface MassCommand {
+    /** What it is called, which is what the tooltip is titled. */
+    title: string;
+    /**
+     * The key it answers to, absent for a command with none.
+     * @default undefined
+     */
+    shortcut?: MassShortcut;
+    /**
+     * What it does, in a sentence, under the title in the tooltip.
+     * @default undefined
+     */
+    description?: string;
+    /**
+     * The gestures that do the same thing, for the ones a key cannot describe.
+     * @default undefined
+     */
+    gestures?: readonly MassGesture[];
+}
+/** Everything the viewer offers, in the order it is reached for. */
+export declare const massCommands: {
+    readonly about: {
+        readonly title: "About the mass spectrum viewer";
+        readonly description: "What it reads, what it is built on, and what it credits.";
+    };
+    readonly documentation: {
+        readonly title: "Documentation";
+        readonly shortcut: {
+            readonly keys: readonly ["h"];
+        };
+        readonly description: "How to open a spectrum, what the panels hold, and every gesture.";
+    };
+    readonly fullScreen: {
+        readonly title: "Full screen";
+        readonly description: "The viewer takes the whole screen rather than its corner of the page. Esc gives it back.";
+    };
+    readonly openFiles: {
+        readonly title: "Open spectra…";
+        readonly shortcut: {
+            readonly keys: readonly ["o"];
+        };
+        readonly description: "Reads JCAMP-DX files and two-column text files of m/z and intensity, and adds what they hold to the chart.";
+        readonly gestures: readonly [{
+            readonly title: "Over the chart";
+            readonly shortcuts: readonly ["Drop files"];
+        }];
+    };
+    readonly readTool: {
+        readonly title: "Read";
+        readonly shortcut: {
+            readonly keys: readonly ["r"];
+        };
+        readonly description: "A drag narrows the m/z axis, which is the question a spectrum is nearly always asked. Released below the baseline, it takes the intensity axis with it.";
+        readonly gestures: readonly [{
+            readonly title: "Over the chart";
+            readonly shortcuts: readonly ["Drag"];
+        }];
+    };
+    readonly boxTool: {
+        readonly title: "Square zoom";
+        readonly shortcut: {
+            readonly keys: readonly ["b"];
+        };
+        readonly description: "A drag zooms to exactly the rectangle it sweeps out, both axes at once — for looking into the baseline under a cluster rather than across the spectrum.";
+        readonly gestures: readonly [{
+            readonly title: "Over the chart";
+            readonly shortcuts: readonly ["Drag a rectangle"];
+        }];
+    };
+    readonly zoomIn: {
+        readonly title: "Zoom in";
+        readonly shortcut: {
+            readonly keys: readonly ["+", "="];
+        };
+        readonly description: "Brings the small peaks up, scaling the intensity about zero.";
+        readonly gestures: readonly [{
+            readonly title: "Over the chart";
+            readonly shortcuts: readonly ["Scroll wheel"];
+        }];
+    };
+    readonly zoomOut: {
+        readonly title: "Zoom out";
+        readonly shortcut: {
+            readonly keys: readonly ["-"];
+        };
+        readonly description: "Puts the intensity axis back out again.";
+        readonly gestures: readonly [{
+            readonly title: "Over the chart";
+            readonly shortcuts: readonly ["Scroll wheel"];
+        }];
+    };
+    readonly resetZoom: {
+        readonly title: "Zoom to fit";
+        readonly shortcut: {
+            readonly keys: readonly ["f"];
+        };
+        readonly description: "Shows every spectrum that is drawn, whole.";
+        readonly gestures: readonly [{
+            readonly title: "Over the chart";
+            readonly shortcuts: readonly ["Double click"];
+        }];
+    };
+    readonly toggleLabels: {
+        readonly title: "Label the peaks";
+        readonly shortcut: {
+            readonly keys: readonly ["l"];
+        };
+        readonly description: "Writes the m/z and the intensity over the tallest peaks of the selected spectrum. Which peaks follows the zoom: zoom onto a cluster and every line of it is labelled.";
+    };
+    readonly toggleCharges: {
+        readonly title: "Write the charges";
+        readonly shortcut: {
+            readonly keys: readonly ["z"];
+        };
+        readonly description: "Adds the charge to the label of every peak whose isotopologue spacing, or charge ladder, established one.";
+    };
+    readonly exportImage: {
+        readonly title: "Save figure…";
+        readonly shortcut: {
+            readonly keys: readonly ["x"];
+        };
+        readonly description: "The chart as it stands, saved as a PNG or an SVG at a chosen resolution, or copied as a PNG.";
+    };
+    readonly clear: {
+        readonly title: "Close every spectrum";
+        readonly description: "Empties the chart and starts again.";
+    };
+};
+/** Identity of one of the commands the viewer offers. */
+export type MassCommandId = keyof typeof massCommands;
+/** What to do when each command is run, as the shell wires them. */
+export type MassCommandHandlers = Partial<Record<MassCommandId, (() => void) | undefined>>;
+/** How a component runs a command. */
+export type RunMassCommand = (id: MassCommandId) => void;
+/**
+ * What a command is called, with its key, for a label and an `aria-label`.
+ * @param id - Which command.
+ * @returns The title, and the key in parentheses when it has one.
+ */
+export declare function massCommandLabel(id: MassCommandId): string;
+//# sourceMappingURL=massCommands.d.ts.map

package/lib/mass/core/massCommands.d.ts.map

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package/lib/mass/core/massCommands.js

@@ -0,0 +1,95 @@
+/**
+ * Everything the viewer offers, what each is called, and the key it answers to.
+ *
+ * One table, read by three things that must agree: the toolbar draws it, the
+ * tooltip explains it, and the key handler fires it. Written apart from all
+ * three so a command cannot be added to the toolbar without a name, or bound to
+ * a key nothing tells the reader about.
+ *
+ * The keys are the infrared viewer's wherever the two viewers share a command,
+ * so a chemist who has learned one has learned the other.
+ */
+/** Where the chart is, for a gesture made anywhere on it. */
+const OVER_THE_CHART = 'Over the chart';
+/** Everything the viewer offers, in the order it is reached for. */
+export const massCommands = {
+    about: {
+        title: 'About the mass spectrum viewer',
+        description: 'What it reads, what it is built on, and what it credits.',
+    },
+    documentation: {
+        title: 'Documentation',
+        shortcut: { keys: ['h'] },
+        description: 'How to open a spectrum, what the panels hold, and every gesture.',
+    },
+    fullScreen: {
+        title: 'Full screen',
+        description: 'The viewer takes the whole screen rather than its corner of the page. Esc gives it back.',
+    },
+    openFiles: {
+        title: 'Open spectra…',
+        shortcut: { keys: ['o'] },
+        description: 'Reads JCAMP-DX files and two-column text files of m/z and intensity, and adds what they hold to the chart.',
+        gestures: [{ title: OVER_THE_CHART, shortcuts: ['Drop files'] }],
+    },
+    readTool: {
+        title: 'Read',
+        shortcut: { keys: ['r'] },
+        description: 'A drag narrows the m/z axis, which is the question a spectrum is nearly always asked. Released below the baseline, it takes the intensity axis with it.',
+        gestures: [{ title: OVER_THE_CHART, shortcuts: ['Drag'] }],
+    },
+    boxTool: {
+        title: 'Square zoom',
+        shortcut: { keys: ['b'] },
+        description: 'A drag zooms to exactly the rectangle it sweeps out, both axes at once — for looking into the baseline under a cluster rather than across the spectrum.',
+        gestures: [{ title: OVER_THE_CHART, shortcuts: ['Drag a rectangle'] }],
+    },
+    zoomIn: {
+        title: 'Zoom in',
+        shortcut: { keys: ['+', '='] },
+        description: 'Brings the small peaks up, scaling the intensity about zero.',
+        gestures: [{ title: OVER_THE_CHART, shortcuts: ['Scroll wheel'] }],
+    },
+    zoomOut: {
+        title: 'Zoom out',
+        shortcut: { keys: ['-'] },
+        description: 'Puts the intensity axis back out again.',
+        gestures: [{ title: OVER_THE_CHART, shortcuts: ['Scroll wheel'] }],
+    },
+    resetZoom: {
+        title: 'Zoom to fit',
+        shortcut: { keys: ['f'] },
+        description: 'Shows every spectrum that is drawn, whole.',
+        gestures: [{ title: OVER_THE_CHART, shortcuts: ['Double click'] }],
+    },
+    toggleLabels: {
+        title: 'Label the peaks',
+        shortcut: { keys: ['l'] },
+        description: 'Writes the m/z and the intensity over the tallest peaks of the selected spectrum. Which peaks follows the zoom: zoom onto a cluster and every line of it is labelled.',
+    },
+    toggleCharges: {
+        title: 'Write the charges',
+        shortcut: { keys: ['z'] },
+        description: 'Adds the charge to the label of every peak whose isotopologue spacing, or charge ladder, established one.',
+    },
+    exportImage: {
+        title: 'Save figure…',
+        shortcut: { keys: ['x'] },
+        description: 'The chart as it stands, saved as a PNG or an SVG at a chosen resolution, or copied as a PNG.',
+    },
+    clear: {
+        title: 'Close every spectrum',
+        description: 'Empties the chart and starts again.',
+    },
+};
+/**
+ * What a command is called, with its key, for a label and an `aria-label`.
+ * @param id - Which command.
+ * @returns The title, and the key in parentheses when it has one.
+ */
+export function massCommandLabel(id) {
+    const entry = massCommands[id];
+    const key = entry.shortcut?.label?.[0] ?? entry.shortcut?.keys[0];
+    return key === undefined ? entry.title : `${entry.title} (${key})`;
+}
+//# sourceMappingURL=massCommands.js.map

package/lib/mass/core/massCommands.js.map

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package/lib/mass/core/massDomain.d.ts

@@ -0,0 +1,121 @@
+/**
+ * The window a chart opens on, worked out from the spectra it was handed.
+ *
+ * This is what "zoom to fit" and the first render both call, so it has to be
+ * right for a peak table of four rows and for a profile scan of half a million
+ * points alike, and it has to answer something usable when it is handed nothing
+ * at all — a chart with no data is still mounted, still measured, and still
+ * builds its scales.
+ */
+import type { MassDomain, MassSpectrum } from './massSpectrum.ts';
+/**
+ * How much air is left either side of the outermost peak, as a fraction.
+ *
+ * A stick drawn exactly on the axis reads as a spectrum that was cut off there;
+ * two percent is enough to show that it was not.
+ */
+export declare const X_DOMAIN_PADDING = 0.02;
+/**
+ * How far above the tallest peak the intensity axis runs.
+ *
+ * The base peak carries the label nobody wants to lose — its m/z and its
+ * intensity, on two lines — and it is drawn above the stick. Twenty percent is
+ * the room those lines take at the top of a chart of any usual height.
+ */
+export declare const Y_DOMAIN_HEADROOM = 1.2;
+/**
+ * The window that shows everything currently drawn.
+ *
+ * A spectrum marked `excludeFromDomain` is left out of the extents, because it
+ * is a preview rather than data: a predicted pattern that appears and
+ * disappears with the pointer would throw away the zoom the user set every
+ * time it moved the axes. The exclusion is dropped when it would leave nothing
+ * at all — previewing into an empty chart has to show the preview, not an empty
+ * axis from 0 to 1.
+ *
+ * In mirror mode the negative half is the reflection of the positive one rather
+ * than its own extent. Two spectra compared head-to-head are only comparable if
+ * a peak of the same height means the same intensity in both halves; giving each
+ * half its own scale makes the weaker spectrum look as intense as the stronger,
+ * which is precisely the comparison the view exists to make.
+ * @param spectra - What the chart draws.
+ * @param mirror - Whether the chart reflects its spectra about zero. Defaults
+ * to `false`.
+ * @returns The window, in m/z and in intensity.
+ */
+export declare function fullDomain(spectra: readonly MassSpectrum[], mirror?: boolean): MassDomain;
+/**
+ * What a fitted window was fitted *to*, as one string two renders can compare.
+ *
+ * The chart puts its window back to `fullDomain` when it is handed different
+ * data, and must not when the same data is merely drawn differently — so
+ * something has to tell the two apart. It is the identities that are compared
+ * and never the extents: a spectrum switched from its profile to its sticks
+ * moves the fitted window by a hair, and refitting on a hair throws away the
+ * zoom somebody set, which is the whole reason this exists. Loading a spectrum,
+ * closing one and reflecting the chart about zero are the changes that have to
+ * be shown, and every one of them shows up here.
+ *
+ * A spectrum kept out of the automatic domain is kept out of this too, for the
+ * reason it is kept out of the extents: a predicted pattern previewed under the
+ * pointer comes and goes with the pointer, and refitting on it would throw the
+ * zoom away every time a search result is read. The identities are joined by a
+ * character no identity holds, so `a b` and `a` then `b` are two fits.
+ * @param spectra - What the chart draws.
+ * @param mirror - Whether the chart reflects its spectra about zero. Defaults
+ * to `false`.
+ * @returns A string equal to itself exactly when a fit would be made to the
+ * same thing.
+ */
+export declare function fittedTo(spectra: readonly MassSpectrum[], mirror?: boolean): string;
+/**
+ * The tallest intensity among the traces a set of spectra currently draws.
+ *
+ * What "how tall is this chart" comes to, in the units the spectra are in, with
+ * the headroom `fullDomain` adds left off — so it answers a question about the
+ * measurement rather than about the plot. A preview kept out of the extents is
+ * kept out of this too, and a chart holding nothing but a preview is measured
+ * by it rather than answering zero.
+ * @param spectra - The spectra to measure, drawn or not.
+ * @returns The tallest intensity drawn, or `0` when nothing is.
+ */
+export declare function basePeakOf(spectra: readonly MassSpectrum[]): number;
+/**
+ * How much of the axis framing a peak shows, either side of its mass.
+ *
+ * Wide enough to hold the isotopologue cluster of a singly charged ion, because
+ * a peak is read in its cluster and not alone: the M+1 says how much carbon it
+ * holds and the spacing says what charge it carries.
+ */
+export declare const MZ_FRAME_HALF_WIDTH = 2.5;
+/** How a mass is framed. */
+export interface MzFrameOptions {
+    /**
+     * How much of the axis to show either side of the mass.
+     * @default MZ_FRAME_HALF_WIDTH
+     */
+    halfWidth?: number;
+    /**
+     * Whether the chart reflects its spectra about zero, which decides the height
+     * it opens on when it has no window of its own.
+     * @default false
+     */
+    mirror?: boolean;
+}
+/**
+ * The window that frames one mass, keeping the intensity axis where it was.
+ *
+ * The vertical extent is deliberately not recomputed from what falls inside the
+ * new window: a click is a request to look somewhere else along the m/z axis,
+ * and rescaling the height at the same time makes whatever was just clicked fill
+ * the plot, so every peak looks like the base peak and the one number the eye
+ * reads off a spectrum stops meaning anything. It is only worked out from the
+ * spectra when the chart has no window of its own to keep.
+ * @param mz - The mass to frame.
+ * @param spectra - What the chart is drawing, for the height it opens on.
+ * @param domain - The window the chart is showing, `null` when it is fitting.
+ * @param options - How wide a window, and whether the chart is mirrored.
+ * @returns The window to show.
+ */
+export declare function mzFrame(mz: number, spectra: readonly MassSpectrum[], domain: MassDomain | null, options?: MzFrameOptions): MassDomain;
+//# sourceMappingURL=massDomain.d.ts.map

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