react-cheminfo 0.69.0 → 0.71.0

package/lib/mass/core/massMeta.js

@@ -0,0 +1,182 @@
+/**
+ * What the file says about how the spectrum was acquired, made displayable.
+ *
+ * A JCAMP written by a Thermo instrument carries the answer to every question a
+ * chemist asks of a spectrum — which analyser, which polarity, which collision
+ * energy — but carries it in whichever of two record bags the exporting
+ * software felt like using, and leaves half of them blank. A JCAMP of the older
+ * MS dialect states the same facts under standard records of its own,
+ * `##.SPECTROMETER TYPE=` and `##.IONIZATION MODE=`. So each field names the
+ * records it may live in, in the order they are worth trying, and anything
+ * still blank falls back to the instrument's own scan description.
+ *
+ * A field that is absent or empty is left out entirely rather than shown as a
+ * dash, which is what keeps the table short enough to read at a glance: every
+ * line in it is a fact the file actually stated.
+ */
+import { parseScanFilter } from "./scanFilter.js";
+/**
+ * Read the acquisition metadata a file carries.
+ *
+ * Returns `null` rather than an empty table when the file said nothing at all,
+ * so the panel can leave the section out instead of drawing a heading over
+ * nothing — the normal outcome for a pasted peak list.
+ * @param source - The record bags the reader recovered.
+ * @returns The metadata, or `null` when the file carries none.
+ */
+export function buildMassMeta(source) {
+    const bags = { info: source.info ?? {}, meta: source.meta ?? {} };
+    const conditions = recordText(bags.meta.CONDITIONS);
+    const derived = parseScanFilter(conditions);
+    const fields = [];
+    for (const field of FIELDS) {
+        const value = firstValue(bags, field.records) || (derived[field.label] ?? '');
+        if (value)
+            fields.push({ label: field.label, value });
+    }
+    const title = recordText(source.title) || recordText(bags.info.TITLE) || null;
+    const molecularFormula = firstValue(bags, MOLECULAR_FORMULA_RECORDS) || null;
+    if (fields.length === 0 && !title && !conditions && !molecularFormula) {
+        return null;
+    }
+    return { title, molecularFormula, fields, conditions: conditions || null };
+}
+/**
+ * The record a row of the table is written back to.
+ *
+ * The inverse of the table below, and it lives beside it for that reason: a
+ * writer holding a second list of record names is a writer whose `MSLEVEL`
+ * becomes `MS_LEVEL` the day a spelling is added here, and the round trip then
+ * loses the field without anything going wrong loudly. Only the first of each
+ * row's records is offered — the others exist to read what other exporters
+ * wrote, and writing our own file is not the place to imitate them.
+ * @param label - The row's label, as the table displays it.
+ * @returns The record, or `null` when the label is not one of the table's rows.
+ */
+export function metaRecord(label) {
+    for (const field of FIELDS) {
+        if (field.label === label)
+            return field.records[0] ?? null;
+    }
+    return null;
+}
+/**
+ * A standard record.
+ * @param key - Its label without spaces.
+ * @returns The record.
+ */
+function standard(key) {
+    return { key, info: true };
+}
+/**
+ * A `$`-prefixed record.
+ * @param key - Its label without the `$`.
+ * @returns The record.
+ */
+function custom(key) {
+    return { key, info: false };
+}
+/**
+ * Every row the table can show, in the order it shows them.
+ *
+ * The order runs from what the sample was measured on down to who measured it,
+ * because that is the order a chemist reads a method in. The alternatives on
+ * each row are the records real exporters were observed to write: `IONISATION`
+ * and `IONIZATION` are the same field spelled by two vendors.
+ *
+ * `EXPERIMENT` is deliberately not a fallback for the collision energy, however
+ * tempting the name is: on real Orbitrap exports it holds what kind of run this
+ * was — `MS/MS`, `Accurate mass` — while the energy is in `REPORT` or in the
+ * instrument's own scan filter.
+ */
+const FIELDS = [
+    { label: 'Source', records: [standard('ORIGIN')] },
+    {
+        label: 'Instrument',
+        records: [custom('INSTRUMENT'), standard('SPECTROMETER/DATASYSTEM')],
+    },
+    {
+        label: 'Analyser',
+        records: [
+            custom('ANALYZER'),
+            custom('ANALYSER'),
+            standard('.SPECTROMETERTYPE'),
+        ],
+    },
+    {
+        label: 'Instrument parameters',
+        records: [standard('.INSTRUMENTPARAMETERS')],
+    },
+    {
+        label: 'Ionization',
+        records: [
+            custom('IONISATION'),
+            custom('IONIZATION'),
+            standard('.IONIZATIONMODE'),
+        ],
+    },
+    { label: 'Inlet', records: [custom('INJECTION'), standard('.INLET')] },
+    { label: 'Polarity', records: [custom('MODE'), custom('POLARITY')] },
+    { label: 'Experiment', records: [custom('EXPERIMENT')] },
+    { label: 'MS level', records: [custom('MSLEVEL')] },
+    { label: 'Isolation m/z', records: [custom('ISOLATION')] },
+    {
+        label: 'Collision energy',
+        records: [custom('COLLISIONENERGY'), custom('REPORT')],
+    },
+    { label: 'Scan range', records: [custom('SCANRANGE')] },
+    { label: 'Retention time', records: [custom('RETENTIONTIME')] },
+    { label: 'Scans', records: [custom('SCANS')] },
+    { label: 'Averaged scans', records: [custom('AVERAGEDSCANS')] },
+    { label: 'Raw file', records: [custom('RAWFILE')] },
+    {
+        label: 'Operator',
+        records: [custom('USER'), custom('OWNER'), standard('OWNER')],
+    },
+    { label: 'Note', records: [custom('NOTE')] },
+];
+/**
+ * Where the formula the file was measured for may be stated: the standard
+ * record first, then the one an accurate-mass tool writes its answer into.
+ */
+const MOLECULAR_FORMULA_RECORDS = [
+    standard('MOLFORM'),
+    standard('MOLFORMULA'),
+    custom('ACCURATE_MF'),
+];
+/**
+ * The first record that holds anything.
+ * @param bags - The records to look in.
+ * @param records - The records to try, in order.
+ * @returns The value as the file states it, or `''` when none is populated.
+ */
+function firstValue(bags, records) {
+    for (const record of records) {
+        const value = recordText((record.info ? bags.info : bags.meta)[record.key]);
+        if (value)
+            return value;
+    }
+    return '';
+}
+/**
+ * A record's value as a trimmed string, whatever dynamic typing made of it.
+ *
+ * `jcampconverter` reads `##$SCANS=1` as the number `1` and a record written
+ * twice as an array of both values, so a row that is only ever shown has to
+ * accept all three shapes. A repeated record shows its first occurrence, which
+ * is the one the exporter wrote for the acquisition rather than for a later
+ * reprocessing of it.
+ * @param value - The record, as dynamic typing left it.
+ * @returns The value as text, `''` when there is none.
+ */
+export function recordText(value) {
+    if (typeof value === 'string')
+        return value.trim();
+    if (typeof value === 'number' || typeof value === 'boolean') {
+        return String(value);
+    }
+    if (Array.isArray(value))
+        return recordText(value[0]);
+    return '';
+}
+//# sourceMappingURL=massMeta.js.map

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

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

@@ -0,0 +1,82 @@
+/**
+ * Every change the viewer can undergo, as one function over one object.
+ *
+ * A reducer rather than a graph of signals: a published component must not
+ * impose a state library on the page that mounts it, and two viewers on one
+ * page must not share a module-level singleton. The state is a plain object, so
+ * a host can save it, restore it and compare it.
+ *
+ * Every case returns the state **itself** when it has nothing to do, so a render
+ * memoised on the state is not defeated by an action that changed nothing —
+ * selecting the spectrum already selected, closing an error already closed.
+ */
+import type { MassPanelId } from './massSidePanels.ts';
+import type { MassDomain, MassSpectrum } from './massSpectrum.ts';
+import type { MassSettings, MassState, MassTool, PartialMassState } from './massState.ts';
+/**
+ * Which of a spectrum's two traces are drawn. Both are named every time,
+ * because they are an either/or: drawing one is also the gesture that puts the
+ * other away.
+ */
+export interface SpectrumVisibility {
+    /** Whether the continuous trace is drawn. */
+    showProfile: boolean;
+    /** Whether the centroid sticks are drawn. */
+    showCentroid: boolean;
+}
+/** Everything that can be asked of the viewer. */
+export type MassAction = {
+    type: 'addSpectra';
+    spectra: MassSpectrum[];
+} | {
+    type: 'setSpectra';
+    spectra: MassSpectrum[];
+} | {
+    type: 'removeSpectrum';
+    id: string;
+} | {
+    type: 'renameSpectrum';
+    id: string;
+    name: string;
+} | {
+    type: 'setSpectrumColor';
+    id: string;
+    color: string;
+} | {
+    type: 'setSpectrumVisibility';
+    id: string;
+    visibility: SpectrumVisibility;
+} | {
+    type: 'selectSpectrum';
+    id: string | null;
+} | {
+    type: 'setDomain';
+    domain: MassDomain;
+} | {
+    type: 'resetDomain';
+} | {
+    type: 'setTool';
+    tool: MassTool;
+} | {
+    type: 'togglePanel';
+    panelId: MassPanelId;
+} | {
+    type: 'setError';
+    error: string | null;
+} | {
+    type: 'setSettings';
+    settings: Partial<MassSettings>;
+} | {
+    type: 'loadState';
+    state: PartialMassState;
+} | {
+    type: 'clear';
+};
+/**
+ * Fold one action into the state.
+ * @param state - The state in force.
+ * @param action - What is being asked.
+ * @returns The new state, or the old one when nothing changed.
+ */
+export declare function massReducer(state: MassState, action: MassAction): MassState;
+//# sourceMappingURL=massReducer.d.ts.map

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

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

@@ -0,0 +1,163 @@
+/**
+ * Every change the viewer can undergo, as one function over one object.
+ *
+ * A reducer rather than a graph of signals: a published component must not
+ * impose a state library on the page that mounts it, and two viewers on one
+ * page must not share a module-level singleton. The state is a plain object, so
+ * a host can save it, restore it and compare it.
+ *
+ * Every case returns the state **itself** when it has nothing to do, so a render
+ * memoised on the state is not defeated by an action that changed nothing —
+ * selecting the spectrum already selected, closing an error already closed.
+ */
+import { isMassWindow, mergeMassSettings } from "./massState.js";
+import { arriving, mapSpectrum, restoreState, withError, } from "./massStateEdits.js";
+/**
+ * Fold one action into the state.
+ * @param state - The state in force.
+ * @param action - What is being asked.
+ * @returns The new state, or the old one when nothing changed.
+ */
+export function massReducer(state, action) {
+    switch (action.type) {
+        case 'addSpectra': {
+            const added = arriving(state, action.spectra);
+            if (added.length === 0)
+                return state;
+            return {
+                ...state,
+                data: { spectra: [...state.data.spectra, ...added] },
+                view: {
+                    ...state.view,
+                    // Whatever arrived is what somebody wants to look at, so it takes the
+                    // selection — but only when nothing was selected, since a spectrum
+                    // added for comparison must not steal the panels from the one being
+                    // read.
+                    selectedId: state.view.selectedId ?? added[0]?.id ?? null,
+                    error: null,
+                },
+            };
+        }
+        case 'setSpectra': {
+            const spectra = arriving({ ...state, data: { spectra: [] } }, action.spectra);
+            return {
+                ...state,
+                data: { spectra },
+                view: {
+                    ...state.view,
+                    selectedId: spectra[0]?.id ?? null,
+                    // Replacing what is drawn is the one change that throws the window
+                    // away: a window over one spectrum's masses means nothing over
+                    // another's, and the chart refits when it is handed `null`.
+                    domain: null,
+                    error: null,
+                },
+            };
+        }
+        case 'removeSpectrum': {
+            const spectra = state.data.spectra.filter((spectrum) => spectrum.id !== action.id);
+            if (spectra.length === state.data.spectra.length)
+                return state;
+            return {
+                ...state,
+                data: { spectra },
+                view: {
+                    ...state.view,
+                    selectedId: state.view.selectedId === action.id
+                        ? (spectra[0]?.id ?? null)
+                        : state.view.selectedId,
+                },
+            };
+        }
+        case 'renameSpectrum': {
+            const name = action.name.trim();
+            if (name === '') {
+                return withError(state, 'A spectrum needs a name to be called by.');
+            }
+            return mapSpectrum(state, action.id, (spectrum) => spectrum.name === name ? spectrum : { ...spectrum, name });
+        }
+        case 'setSpectrumColor': {
+            return mapSpectrum(state, action.id, (spectrum) => spectrum.color === action.color
+                ? spectrum
+                : { ...spectrum, color: action.color });
+        }
+        case 'setSpectrumVisibility': {
+            return mapSpectrum(state, action.id, (spectrum) => {
+                // A spectrum read from a peak table has no profile to draw, and asking
+                // for one must not leave it drawn as nothing at all.
+                const showProfile = action.visibility.showProfile && spectrum.profile !== null;
+                const { showCentroid } = action.visibility;
+                return spectrum.showProfile === showProfile &&
+                    spectrum.showCentroid === showCentroid
+                    ? spectrum
+                    : { ...spectrum, showProfile, showCentroid };
+            });
+        }
+        case 'selectSpectrum': {
+            if (state.view.selectedId === action.id)
+                return state;
+            return { ...state, view: { ...state.view, selectedId: action.id } };
+        }
+        case 'setDomain': {
+            if (!isMassWindow(action.domain))
+                return state;
+            return { ...state, view: { ...state.view, domain: action.domain } };
+        }
+        case 'resetDomain': {
+            if (state.view.domain === null)
+                return state;
+            return { ...state, view: { ...state.view, domain: null } };
+        }
+        case 'setTool': {
+            if (state.view.tool === action.tool)
+                return state;
+            return { ...state, view: { ...state.view, tool: action.tool } };
+        }
+        case 'togglePanel': {
+            const { openPanelIds } = state.view;
+            const open = openPanelIds.includes(action.panelId);
+            return {
+                ...state,
+                view: {
+                    ...state.view,
+                    openPanelIds: open
+                        ? openPanelIds.filter((id) => id !== action.panelId)
+                        : [...openPanelIds, action.panelId],
+                },
+            };
+        }
+        case 'setError': {
+            if (state.view.error === action.error)
+                return state;
+            return { ...state, view: { ...state.view, error: action.error } };
+        }
+        case 'setSettings': {
+            const settings = mergeMassSettings(state.settings, action.settings);
+            const { showLabels, labelLimit, showCharges, mzDecimals } = state.settings;
+            if (settings.showLabels === showLabels &&
+                settings.labelLimit === labelLimit &&
+                settings.showCharges === showCharges &&
+                settings.mzDecimals === mzDecimals) {
+                return state;
+            }
+            return { ...state, settings };
+        }
+        case 'loadState': {
+            return restoreState(state, action.state);
+        }
+        case 'clear': {
+            if (state.data.spectra.length === 0 && state.view.error === null) {
+                return state;
+            }
+            return {
+                ...state,
+                data: { spectra: [] },
+                view: { ...state.view, selectedId: null, domain: null, error: null },
+            };
+        }
+        /* Every action is handled above, and TypeScript is what keeps that true
+           when one is added — so there is nothing for a fallback to do. */
+        // no default
+    }
+}
+//# sourceMappingURL=massReducer.js.map

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

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

@@ -0,0 +1,92 @@
+/**
+ * Whether a spectrum resolves masses finely enough for their decimals to mean
+ * anything.
+ *
+ * A peak table typed out of a low-resolution instrument report holds whole
+ * numbers — `163`, `325`, `487` — and writing them as `163.0000` claims four
+ * digits of accuracy nobody measured. A high-resolution measurement is the
+ * opposite case: `325.1129` and `325.1503` are different ions, and rounding them
+ * together loses the whole point of having measured them. Nothing about a single
+ * number says which of the two it is, so the answer is read off the spectrum.
+ *
+ * Three kinds of evidence are read, and the strongest one present decides —
+ * `decideResolution` is where they are weighed:
+ *
+ * 1. **The peaks themselves.** A profile carries the width of every peak, and
+ *    the resolving power `m / Δm` at half height is what "high resolution" is
+ *    defined by. This is a measurement, so it is believed over anything a file
+ *    says about itself.
+ * 2. **What the file says the instrument was.** A Thermo scan filter starting
+ *    `FTMS` is an Orbitrap, one starting `ITMS` an ion trap, and a JCAMP of the
+ *    old MS dialect writes `##.INSTRUMENT PARAMETERS= LOW RESOLUTION` outright.
+ * 3. **How many decimals the masses were written with**, which is all a bare
+ *    peak table has to say — `writtenResolution.ts`.
+ */
+import type { MassMeta } from './massSpectrum.ts';
+/** How finely a spectrum resolves masses. */
+export type MassResolutionKind = 'high' | 'low' | 'nominal';
+/** Which evidence the verdict was read from, the strongest first. */
+export type MassResolutionBasis = 'peakWidth' | 'instrument' | 'decimals';
+/** The verdict on one spectrum, and what it rests on. */
+export interface MassResolution {
+    /** Whether the masses are resolved, resolved coarsely, or written whole. */
+    kind: MassResolutionKind;
+    /**
+     * The resolving power `m / Δm` at half height, the median over the tallest
+     * peaks — `null` unless it was measured, which needs a profile.
+     */
+    resolvingPower: number | null;
+    /** What the verdict was read from. */
+    basis: MassResolutionBasis;
+    /** How many decimals an m/z of this spectrum is written with. */
+    decimals: number;
+}
+/** A picked peak with the width the peak picking measured for it. */
+export interface WidthPeak {
+    /** Where it sits, in m/z. */
+    x: number;
+    /** How tall it is. */
+    y: number;
+    /** Its width between inflection points, in m/z, as `ml-gsd` reports it. */
+    width: number;
+}
+/**
+ * The resolving power from which a spectrum counts as high resolution.
+ *
+ * Ten thousand at half height is the conventional threshold, and it falls in
+ * the gap between the two families of instrument rather than inside either:
+ * quadrupoles, ion traps and linear time-of-flights work at a few thousand at
+ * most, while reflectron time-of-flights, Orbitraps and FT-ICRs start above it.
+ */
+export declare const HIGH_RESOLVING_POWER = 10000;
+/** How many of the tallest peaks the resolving power is the median of. */
+export declare const MEASURED_PEAKS = 20;
+/** How many decimals an m/z is written with, for each kind of spectrum. */
+export declare const MZ_DECIMALS: Readonly<Record<MassResolutionKind, number>>;
+/**
+ * The resolving power measured on the peaks of a profile.
+ *
+ * The median over the tallest peaks rather than over all of them, because a
+ * peak a few counts above the noise has a width the noise decided, and rather
+ * than the base peak alone, because one peak sitting on an unresolved shoulder
+ * would decide the whole spectrum. The width `ml-gsd` reports is the distance
+ * between the inflection points, which is converted to the width at half height
+ * as a gaussian's is: what a resolving power is quoted against.
+ * @param peaks - The peaks the profile was picked into, each with its width.
+ * @returns The verdict, `null` when no peak carries a usable width.
+ */
+export declare function measuredResolution(peaks: readonly WidthPeak[]): MassResolution | null;
+/**
+ * The resolution the file says the instrument worked at, when it says so.
+ *
+ * Only the rows that name an instrument are read, and a high verdict is looked
+ * for first: an `LTQ-Orbitrap` names an ion trap and an Orbitrap, and the
+ * spectrum came out of the Orbitrap. A time-of-flight is deliberately left
+ * undecided — a reflectron one is high resolution and a linear one is not, and
+ * the name is the same.
+ * @param meta - What the file said about the acquisition.
+ * @returns The verdict, `null` when the file names no instrument it can be
+ * read off.
+ */
+export declare function statedResolution(meta: MassMeta | null): MassResolution | null;
+//# sourceMappingURL=massResolution.d.ts.map

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

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