react-cheminfo 0.69.0 → 0.71.0

package/lib/mass/core/fromText.js

@@ -0,0 +1,39 @@
+/**
+ * Read two columns of m/z and intensity, through `xy-parser`.
+ *
+ * Whatever separates the columns — a tab, a comma, spaces, a semicolon — and
+ * whatever header lines come before the numbers, `xy-parser` finds the numbers,
+ * so a peak list copied out of an instrument report, a CSV export and a
+ * hand-typed table are all one format here.
+ */
+import { parseXY } from 'xy-parser';
+import { describeSource } from "../../error/core/index.js";
+import { ascendingTrace } from "./ascendingTrace.js";
+/**
+ * Read the one spectrum two columns of numbers make.
+ *
+ * Nothing is said about the acquisition, because two columns say nothing: the
+ * spectrum comes back with no metadata and no name of its own, and is called
+ * after its file.
+ * @param data - The file, as bytes or as text.
+ * @param options - The file's name.
+ * @returns The spectrum, as a list of one, the way every reader answers.
+ * @throws {Error} When no line of it holds two numbers.
+ */
+export function fromText(data, options = {}) {
+    const { fileName } = options;
+    const { x, y } = parseXY(data);
+    if (x.length === 0) {
+        throw new Error(`${describeSource(fileName)} holds no two columns of numbers — a spectrum in text is one line per point, the m/z first and the intensity after it.`);
+    }
+    return [
+        {
+            trace: ascendingTrace(x, y),
+            meta: null,
+            origin: fileName === undefined
+                ? { format: 'text' }
+                : { format: 'text', fileName },
+        },
+    ];
+}
+//# sourceMappingURL=fromText.js.map

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

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

@@ -0,0 +1,70 @@
+/**
+ * What a mass spectrum is, and everything true of one that draws nothing.
+ *
+ * Reading a JCAMP-DX or a two-column text file, picking the peaks of a profile,
+ * deciding whether the spectrum is high resolution, choosing which peaks are
+ * worth a label, writing the spectra back out as JCAMP — none of it needs
+ * React, so a script that reads a directory of spectra loads none.
+ *
+ * Nothing here knows what a glycan, a peptide or a polymer is, and nothing
+ * should: a mass spectrum answers for whatever was put in the source.
+ */
+export type { AnalyseSpectrumOptions, AnalysedSpectrum, } from './analyseSpectrum.ts';
+export { analyseSpectrum } from './analyseSpectrum.ts';
+export { ascendingTrace } from './ascendingTrace.ts';
+export type { MassPeakObject, SelectCentroidPeaksOptions, } from './centroidPeaks.ts';
+export { centroidPeakObjects, selectCentroidPeaks } from './centroidPeaks.ts';
+export type { DetectedMassFormat } from './detectMassFormat.ts';
+export { detectMassFormat } from './detectMassFormat.ts';
+export { downloadMassSpectra, downloadMassSpectrum, } from './downloadSpectra.ts';
+export type { MassJcampReadOptions, MassJcampReadResult } from './fromJcamp.ts';
+export type { MassTextReadOptions } from './fromText.ts';
+export type { JcampBlockHeader } from './jcampTechnique.ts';
+export { otherTechnique } from './jcampTechnique.ts';
+export type { HoveredPeak, StackBox } from './labelStackBox.ts';
+export { labelStackBox } from './labelStackBox.ts';
+export type { LabelledPeak, SelectLabelledPeaksOptions, } from './labelledPeaks.ts';
+export { LABEL_SLOTS, LABEL_THRESHOLD, selectLabelledPeaks, } from './labelledPeaks.ts';
+export type { LoadMassSpectraOptions, LoadMassSpectraResult, } from './loadMassSpectra.ts';
+export { DEFAULT_MAX_SPECTRA, loadMassSpectra } from './loadMassSpectra.ts';
+export type { LoadedMassSpectrum } from './loadedMassSpectrum.ts';
+export type { MassCommand, MassCommandHandlers, MassCommandId, MassGesture, MassShortcut, RunMassCommand, } from './massCommands.ts';
+export { massCommandLabel, massCommands } from './massCommands.ts';
+export type { MzFrameOptions } from './massDomain.ts';
+export { MZ_FRAME_HALF_WIDTH, X_DOMAIN_PADDING, Y_DOMAIN_HEADROOM, basePeakOf, fittedTo, fullDomain, mzFrame, } from './massDomain.ts';
+export type { MassEditorHandle, MassPlotClick, ZoomToMzOptions, } from './massEditorApi.ts';
+export { INTENSITY_DECIMALS, formatIntensity, formatMz, formatMzRange, massFormatLabel, resolutionBasisLabel, resolutionLabel, resolvingPowerLabel, } from './massFormat.ts';
+export type { MassMetaRecord, MassMetaSource } from './massMeta.ts';
+export { buildMassMeta, metaRecord, recordText } from './massMeta.ts';
+export type { MassAction, SpectrumVisibility } from './massReducer.ts';
+export { massReducer } from './massReducer.ts';
+export type { MassResolution, MassResolutionBasis, MassResolutionKind, WidthPeak, } from './massResolution.ts';
+export { HIGH_RESOLVING_POWER, MEASURED_PEAKS, MZ_DECIMALS, measuredResolution, statedResolution, } from './massResolution.ts';
+export type { MassPanelId, MassSidePanelId } from './massSidePanels.ts';
+export { massSidePanels } from './massSidePanels.ts';
+export type { MassDomain, MassFormat, MassMeta, MassMetaField, MassOrigin, MassPeaks, MassSpectrum, MassTrace, } from './massSpectrum.ts';
+export { isSpectrumDrawn } from './massSpectrum.ts';
+export type { CreateMassStateOptions, MassData, MassSettings, MassState, MassTool, MassView, PartialMassState, } from './massState.ts';
+export { DEFAULT_LABEL_LIMIT, DEFAULT_SETTINGS, DEFAULT_SIDE_PANEL, DEFAULT_SIDE_PANELS, MAXIMUM_LABEL_LIMIT, createMassState, isMassWindow, mergeMassSettings, } from './massState.ts';
+export type { SpectrumSubtitleOptions } from './massSummary.ts';
+export { spectrumFileFields, spectrumMetaRows, spectrumResolutionRows, spectrumSubtitle, } from './massSummary.ts';
+export type { MzDecimalsSetting } from './mzDecimalsSetting.ts';
+export { MAXIMUM_MZ_DECIMALS, mzDecimalsFor, readMzDecimalsSetting, } from './mzDecimalsSetting.ts';
+export type { NearestPeak } from './nearestPeak.ts';
+export { PEAK_HIT_RADIUS, nearestPeakMz, peakAtMz, sameNearestPeak, } from './nearestPeak.ts';
+export type { PeakLabelLine, PeakLabelLineKind, PeakLabelLinesOptions, } from './peakLabelLines.ts';
+export { peakKey, peakLabelLines } from './peakLabelLines.ts';
+export type { PeakLabelPlan, PlanPeakLabelsOptions } from './peakLabelPlan.ts';
+export { LABEL_SPACING, planPeakLabels } from './peakLabelPlan.ts';
+export type { PeakTableOptions } from './peakTable.ts';
+export { PEAK_TABLE_LIMIT, PEAK_TABLE_THRESHOLD, peakTableRows, peakTableToTsv, } from './peakTable.ts';
+export type { DecideResolutionOptions } from './resolutionOf.ts';
+export { decideResolution, mzDecimalsOf, resolutionOf, } from './resolutionOf.ts';
+export { parseScanFilter } from './scanFilter.ts';
+export type { MassTraceKind, TraceIconClick, TraceIconState, } from './traceIcon.ts';
+export { nextTraceIconClick, traceIconState } from './traceIcon.ts';
+export { JCAMP_EXTENSION, JCAMP_MIME_TYPE, massSpectraToJcamp, massSpectrumToJcamp, } from './spectrumJcamp.ts';
+export type { ToMassSpectrumOptions } from './toMassSpectrum.ts';
+export { toMassSpectra, toMassSpectrum } from './toMassSpectrum.ts';
+export { MAXIMUM_WRITTEN_DECIMALS, writtenDecimals, writtenResolution, } from './writtenResolution.ts';
+//# sourceMappingURL=index.d.ts.map

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

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package/lib/mass/core/index.js

@@ -0,0 +1,42 @@
+/**
+ * What a mass spectrum is, and everything true of one that draws nothing.
+ *
+ * Reading a JCAMP-DX or a two-column text file, picking the peaks of a profile,
+ * deciding whether the spectrum is high resolution, choosing which peaks are
+ * worth a label, writing the spectra back out as JCAMP — none of it needs
+ * React, so a script that reads a directory of spectra loads none.
+ *
+ * Nothing here knows what a glycan, a peptide or a polymer is, and nothing
+ * should: a mass spectrum answers for whatever was put in the source.
+ */
+export { analyseSpectrum } from "./analyseSpectrum.js";
+export { ascendingTrace } from "./ascendingTrace.js";
+export { centroidPeakObjects, selectCentroidPeaks } from "./centroidPeaks.js";
+export { detectMassFormat } from "./detectMassFormat.js";
+export { downloadMassSpectra, downloadMassSpectrum, } from "./downloadSpectra.js";
+export { otherTechnique } from "./jcampTechnique.js";
+export { labelStackBox } from "./labelStackBox.js";
+export { LABEL_SLOTS, LABEL_THRESHOLD, selectLabelledPeaks, } from "./labelledPeaks.js";
+export { DEFAULT_MAX_SPECTRA, loadMassSpectra } from "./loadMassSpectra.js";
+export { massCommandLabel, massCommands } from "./massCommands.js";
+export { MZ_FRAME_HALF_WIDTH, X_DOMAIN_PADDING, Y_DOMAIN_HEADROOM, basePeakOf, fittedTo, fullDomain, mzFrame, } from "./massDomain.js";
+export { INTENSITY_DECIMALS, formatIntensity, formatMz, formatMzRange, massFormatLabel, resolutionBasisLabel, resolutionLabel, resolvingPowerLabel, } from "./massFormat.js";
+export { buildMassMeta, metaRecord, recordText } from "./massMeta.js";
+export { massReducer } from "./massReducer.js";
+export { HIGH_RESOLVING_POWER, MEASURED_PEAKS, MZ_DECIMALS, measuredResolution, statedResolution, } from "./massResolution.js";
+export { massSidePanels } from "./massSidePanels.js";
+export { isSpectrumDrawn } from "./massSpectrum.js";
+export { DEFAULT_LABEL_LIMIT, DEFAULT_SETTINGS, DEFAULT_SIDE_PANEL, DEFAULT_SIDE_PANELS, MAXIMUM_LABEL_LIMIT, createMassState, isMassWindow, mergeMassSettings, } from "./massState.js";
+export { spectrumFileFields, spectrumMetaRows, spectrumResolutionRows, spectrumSubtitle, } from "./massSummary.js";
+export { MAXIMUM_MZ_DECIMALS, mzDecimalsFor, readMzDecimalsSetting, } from "./mzDecimalsSetting.js";
+export { PEAK_HIT_RADIUS, nearestPeakMz, peakAtMz, sameNearestPeak, } from "./nearestPeak.js";
+export { peakKey, peakLabelLines } from "./peakLabelLines.js";
+export { LABEL_SPACING, planPeakLabels } from "./peakLabelPlan.js";
+export { PEAK_TABLE_LIMIT, PEAK_TABLE_THRESHOLD, peakTableRows, peakTableToTsv, } from "./peakTable.js";
+export { decideResolution, mzDecimalsOf, resolutionOf, } from "./resolutionOf.js";
+export { parseScanFilter } from "./scanFilter.js";
+export { nextTraceIconClick, traceIconState } from "./traceIcon.js";
+export { JCAMP_EXTENSION, JCAMP_MIME_TYPE, massSpectraToJcamp, massSpectrumToJcamp, } from "./spectrumJcamp.js";
+export { toMassSpectra, toMassSpectrum } from "./toMassSpectrum.js";
+export { MAXIMUM_WRITTEN_DECIMALS, writtenDecimals, writtenResolution, } from "./writtenResolution.js";
+//# sourceMappingURL=index.js.map

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

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

@@ -0,0 +1,38 @@
+/**
+ * Which blocks of a JCAMP a mass viewer has any business reading.
+ *
+ * JCAMP-DX is a container for whatever an instrument wanted to export, and the
+ * file says nothing about which viewer opened it: a file of five infrared
+ * spectra, one of UV/VIS ones and a gas-chromatography export writing a whole
+ * chromatogram under `##XUNITS= TIME` are all valid JCAMPs. Read as mass
+ * spectra they draw a wavenumber, a wavelength or a minute on an m/z axis, and
+ * every mass read off them afterwards is a mass of something never measured.
+ *
+ * So the technique the file states is believed, and only a block that states
+ * another one is refused. A block that states none is kept: plenty of
+ * instruments write no `##DATA TYPE` at all, and the file was handed to a mass
+ * viewer, so mass spectrometry is the right assumption where the file is silent.
+ */
+/** What `jcampconverter` says about one block, as far as this is concerned. */
+export interface JcampBlockHeader {
+    /**
+     * The `##DATA TYPE=` record.
+     * @default undefined
+     */
+    dataType?: string;
+    /** The standard records, where `##XUNITS=` is. */
+    info: Record<string, unknown>;
+}
+/**
+ * What a block says it is, when what it says is not mass spectrometry.
+ *
+ * Both halves of the answer are read: the technique names it, and the axis unit
+ * is what a chemist looking at a refusal can check against the file in front of
+ * them — `INFRARED SPECTRUM in 1/CM` is a sentence they can act on where
+ * `unsupported data type` is not.
+ * @param entry - The block, as `jcampconverter` read it.
+ * @returns The phrase naming it, or `null` when the block may be read as a mass
+ * spectrum.
+ */
+export declare function otherTechnique(entry: JcampBlockHeader): string | null;
+//# sourceMappingURL=jcampTechnique.d.ts.map

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

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

@@ -0,0 +1,70 @@
+/**
+ * Which blocks of a JCAMP a mass viewer has any business reading.
+ *
+ * JCAMP-DX is a container for whatever an instrument wanted to export, and the
+ * file says nothing about which viewer opened it: a file of five infrared
+ * spectra, one of UV/VIS ones and a gas-chromatography export writing a whole
+ * chromatogram under `##XUNITS= TIME` are all valid JCAMPs. Read as mass
+ * spectra they draw a wavenumber, a wavelength or a minute on an m/z axis, and
+ * every mass read off them afterwards is a mass of something never measured.
+ *
+ * So the technique the file states is believed, and only a block that states
+ * another one is refused. A block that states none is kept: plenty of
+ * instruments write no `##DATA TYPE` at all, and the file was handed to a mass
+ * viewer, so mass spectrometry is the right assumption where the file is silent.
+ */
+import { recordText } from "./massMeta.js";
+/**
+ * What a block says it is, when what it says is not mass spectrometry.
+ *
+ * Both halves of the answer are read: the technique names it, and the axis unit
+ * is what a chemist looking at a refusal can check against the file in front of
+ * them — `INFRARED SPECTRUM in 1/CM` is a sentence they can act on where
+ * `unsupported data type` is not.
+ * @param entry - The block, as `jcampconverter` read it.
+ * @returns The phrase naming it, or `null` when the block may be read as a mass
+ * spectrum.
+ */
+export function otherTechnique(entry) {
+    const dataType = (entry.dataType ?? '').toUpperCase();
+    const units = recordText(entry.info.XUNITS).toUpperCase();
+    if (MASS_SPECTROMETRY.test(dataType))
+        return null;
+    if (OTHER_TECHNIQUE.test(dataType)) {
+        return units === '' ? dataType : `${dataType} in ${units}`;
+    }
+    // A block naming no technique is still refused when it names an axis no mass
+    // spectrum has: `##XUNITS= 1/CM` is a wavenumber whoever wrote the file was
+    // measuring, whatever the header left out.
+    if (OTHER_AXIS.test(units)) {
+        return dataType === '' ? `an axis in ${units}` : `${dataType} in ${units}`;
+    }
+    return null;
+}
+/**
+ * The techniques that are a mass spectrum however the file spells them.
+ *
+ * Read before the refusals below, so that `GC-MS` and `LC-MS` — both of which
+ * name a separation this reader would otherwise refuse — are kept: what came
+ * off the column is still measured by mass.
+ */
+const MASS_SPECTROMETRY = /\bMASS\b|\bMS\b/;
+/**
+ * The techniques that are certainly not a mass spectrum.
+ *
+ * Named rather than matching `MASS SPECTRUM` positively, so that a file typed
+ * `CONTINUOUS MASS SPECTRUM`, `GC-MS` or nothing at all is read without this
+ * list having to anticipate every spelling an exporter might choose.
+ */
+const OTHER_TECHNIQUE = /\b(?:RAMAN|NMR|INFRARED|FTIR|IR|UV|VIS|VISIBLE|FLUORESCENCE|XRD|EPR|ESR|CHROMATOGRAM|CHROMATOGRAPH)\b/;
+/**
+ * The axis units that are certainly not an m/z.
+ *
+ * A wavenumber, a wavelength, a frequency, a chemical shift and a retention
+ * time each name an axis some other instrument sweeps; `ARBITRARY`, `M/Z`,
+ * `MASS UNITS` and `DALTONS` are all left out, since a mass spectrum is written
+ * with every one of them. The unit is looked for as a word inside the record,
+ * because a file that states no technique spells it as `Wavenumber (1/cm)`.
+ */
+const OTHER_AXIS = /\b(?:1\/CM|CM-1|WAVENUMBERS?|NM|NANOMETERS?|MICROMETERS?|MICRONS?|HZ|PPM|SECONDS?|MINUTES?|TIME)\b/;
+//# sourceMappingURL=jcampTechnique.js.map

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

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

@@ -0,0 +1,49 @@
+/**
+ * The room a stack of labels over a peak takes, and the peak a pointer resting
+ * on it reports.
+ *
+ * The numbers of a stack take no pointer event of their own: the room they
+ * occupy does, as one rectangle per stack, so a stack can be interrogated —
+ * resting on it opens whatever a host shows about that peak — without the
+ * glyphs becoming a control or stopping the crosshair underneath.
+ */
+/** A rectangle in the pixels of the SVG. */
+export interface StackBox {
+    /** Its left edge. */
+    x: number;
+    /** Its top edge. */
+    y: number;
+    /** How wide it is. */
+    width: number;
+    /** How tall. */
+    height: number;
+}
+/** The peak the pointer is resting on, as the labels report it. */
+export interface HoveredPeak {
+    /** `${spectrumId}:${index}`, which is how anything said about it is found. */
+    key: string;
+    /** The m/z measured for it. */
+    mz: number;
+    /** Its intensity, in the units its spectrum was drawn in. */
+    intensity: number;
+    /** The charge established for it, `0` when none was. */
+    charge: number;
+    /** Where a card about it is anchored, in pixels across the SVG. */
+    x: number;
+    /** The edge of the label stack it hangs off, in pixels down the SVG. */
+    y: number;
+}
+/**
+ * The room a stack of labels takes, which is what answers the pointer.
+ *
+ * A baseline is where the glyphs of a line *sit*, so the box starts a line
+ * height above the topmost one and stops just under the lowest. How wide it is
+ * cannot be measured from here — an SVG knows nothing of the host's font until
+ * it is on screen — so it is the width the theme says a label claims, which is
+ * the same number the stacks are spaced by.
+ * @param x - Where the stack is centred, in pixels.
+ * @param baselines - Where each of its lines is written, in any order.
+ * @returns The box, of no size at all when the stack has no lines.
+ */
+export declare function labelStackBox(x: number, baselines: readonly number[] | Float64Array): StackBox;
+//# sourceMappingURL=labelStackBox.d.ts.map

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

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

@@ -0,0 +1,44 @@
+/**
+ * The room a stack of labels over a peak takes, and the peak a pointer resting
+ * on it reports.
+ *
+ * The numbers of a stack take no pointer event of their own: the room they
+ * occupy does, as one rectangle per stack, so a stack can be interrogated —
+ * resting on it opens whatever a host shows about that peak — without the
+ * glyphs becoming a control or stopping the crosshair underneath.
+ */
+import { PEAK_LABEL } from "../../chart/core/chartTheme.js";
+/**
+ * The room a stack of labels takes, which is what answers the pointer.
+ *
+ * A baseline is where the glyphs of a line *sit*, so the box starts a line
+ * height above the topmost one and stops just under the lowest. How wide it is
+ * cannot be measured from here — an SVG knows nothing of the host's font until
+ * it is on screen — so it is the width the theme says a label claims, which is
+ * the same number the stacks are spaced by.
+ * @param x - Where the stack is centred, in pixels.
+ * @param baselines - Where each of its lines is written, in any order.
+ * @returns The box, of no size at all when the stack has no lines.
+ */
+export function labelStackBox(x, baselines) {
+    const { lineHeight, hoverHalfWidth } = PEAK_LABEL;
+    let highest = Number.POSITIVE_INFINITY;
+    let lowest = Number.NEGATIVE_INFINITY;
+    for (const baseline of baselines) {
+        if (baseline < highest)
+            highest = baseline;
+        if (baseline > lowest)
+            lowest = baseline;
+    }
+    if (!Number.isFinite(highest))
+        return { x, y: 0, width: 0, height: 0 };
+    return {
+        x: x - hoverHalfWidth,
+        y: highest - lineHeight,
+        width: hoverHalfWidth * 2,
+        height: lowest - highest + lineHeight + DESCENDER,
+    };
+}
+/** How far a glyph reaches below its baseline, near enough for a hit area. */
+const DESCENDER = 3;
+//# sourceMappingURL=labelStackBox.js.map

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

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

@@ -0,0 +1,79 @@
+/**
+ * Which peaks of a spectrum are worth writing a label beside.
+ *
+ * A centroid holds tens of thousands of peaks and a chart has room for a dozen
+ * labels, so something has to choose — and the choice is `ms-spectrum`'s slot
+ * mechanism rather than anything invented here. The window is cut into ten
+ * slots, the tallest peak of each is taken, and a peak falling in a slot that is
+ * already spoken for comes back marked `close`. **Dropping the marked ones is
+ * the whole of the selection**; what then still collides on a narrow chart is
+ * settled by `planPeakLabels`, which gives the room to the taller peak.
+ *
+ * The slots are cut from the *window* and not from the spectrum, which is what
+ * makes the choice follow the zoom: a survey scan has room to name its base peak
+ * and a handful of others, and the same spectrum zoomed onto one isotopologue
+ * cluster has room to name every line of it.
+ */
+import type { MassPeakObject } from './centroidPeaks.ts';
+import type { MassSpectrum } from './massSpectrum.ts';
+/**
+ * How many slots the window is cut into.
+ *
+ * Ten is `ms-spectrum`'s own default and is kept rather than exposed: it is the
+ * number of labels a chart of any usual width can carry across it without one
+ * sitting on the next.
+ */
+export declare const LABEL_SLOTS = 10;
+/** How faint a peak may be, against the tallest one in the window, and still be labelled. */
+export declare const LABEL_THRESHOLD = 0.01;
+/** One peak that has earned a label, and where it sits in its centroid. */
+export interface LabelledPeak extends MassPeakObject {
+    /** Its index in the centroid, which is how anything else about it is found. */
+    index: number;
+}
+/** The window the labels are chosen for, and how many there is room for. */
+export interface SelectLabelledPeaksOptions {
+    /**
+     * Lowest m/z on screen.
+     * @default the m/z of the first peak
+     */
+    from?: number;
+    /**
+     * Highest m/z on screen.
+     * @default the m/z of the last peak
+     */
+    to?: number;
+    /**
+     * The tallest intensity the window shows. A peak above it has its tip off the
+     * top of the plot, so a label placed there would name a stick whose height
+     * cannot be read anyway — and leaving it out is also what puts the threshold
+     * back on the tallest peak that *is* on screen, which is the whole point of
+     * zooming into a baseline.
+     * @default Number.POSITIVE_INFINITY
+     */
+    maxValue?: number;
+    /**
+     * How many peaks are labelled at most, the most intense first.
+     * @default DEFAULT_LABEL_LIMIT
+     */
+    limit?: number;
+    /**
+     * How faint a peak may be against the tallest one in the window.
+     * @default LABEL_THRESHOLD
+     */
+    threshold?: number;
+}
+/**
+ * The peaks of a window that have earned a label.
+ *
+ * The peak objects are read off the centroid's cache rather than rebuilt, so a
+ * zoom costs the selection alone and not a fresh object per peak of the
+ * spectrum. What comes back is a copy each time — `getBestPeaks` clones what it
+ * keeps, since it writes its `close` verdict onto the peak — so nothing here can
+ * scribble on the cache every other reader shares.
+ * @param spectrum - The spectrum whose peaks are being labelled.
+ * @param options - The window, and how many labels there is room for.
+ * @returns The chosen peaks, in increasing m/z, with the crowded ones dropped.
+ */
+export declare function selectLabelledPeaks(spectrum: MassSpectrum, options?: SelectLabelledPeaksOptions): LabelledPeak[];
+//# sourceMappingURL=labelledPeaks.d.ts.map

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

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

@@ -0,0 +1,74 @@
+/**
+ * Which peaks of a spectrum are worth writing a label beside.
+ *
+ * A centroid holds tens of thousands of peaks and a chart has room for a dozen
+ * labels, so something has to choose — and the choice is `ms-spectrum`'s slot
+ * mechanism rather than anything invented here. The window is cut into ten
+ * slots, the tallest peak of each is taken, and a peak falling in a slot that is
+ * already spoken for comes back marked `close`. **Dropping the marked ones is
+ * the whole of the selection**; what then still collides on a narrow chart is
+ * settled by `planPeakLabels`, which gives the room to the taller peak.
+ *
+ * The slots are cut from the *window* and not from the spectrum, which is what
+ * makes the choice follow the zoom: a survey scan has room to name its base peak
+ * and a handful of others, and the same spectrum zoomed onto one isotopologue
+ * cluster has room to name every line of it.
+ */
+import { xFindClosestIndex } from 'ml-spectra-processing';
+import { getBestPeaks } from 'ms-spectrum';
+import { centroidPeakObjects } from "./centroidPeaks.js";
+import { DEFAULT_LABEL_LIMIT } from "./massState.js";
+/**
+ * How many slots the window is cut into.
+ *
+ * Ten is `ms-spectrum`'s own default and is kept rather than exposed: it is the
+ * number of labels a chart of any usual width can carry across it without one
+ * sitting on the next.
+ */
+export const LABEL_SLOTS = 10;
+/** How faint a peak may be, against the tallest one in the window, and still be labelled. */
+export const LABEL_THRESHOLD = 0.01;
+/**
+ * The peaks of a window that have earned a label.
+ *
+ * The peak objects are read off the centroid's cache rather than rebuilt, so a
+ * zoom costs the selection alone and not a fresh object per peak of the
+ * spectrum. What comes back is a copy each time — `getBestPeaks` clones what it
+ * keeps, since it writes its `close` verdict onto the peak — so nothing here can
+ * scribble on the cache every other reader shares.
+ * @param spectrum - The spectrum whose peaks are being labelled.
+ * @param options - The window, and how many labels there is room for.
+ * @returns The chosen peaks, in increasing m/z, with the crowded ones dropped.
+ */
+export function selectLabelledPeaks(spectrum, options = {}) {
+    const { from, to, maxValue, limit = DEFAULT_LABEL_LIMIT, threshold = LABEL_THRESHOLD, } = options;
+    const { centroid } = spectrum;
+    const peaks = centroidPeakObjects(centroid);
+    // `getBestPeaks` reads the window it was given no bounds for off the first and
+    // last peak, which it cannot do when there are none.
+    if (peaks.length === 0 || limit <= 0)
+        return [];
+    const best = getBestPeaks(peaks, {
+        from,
+        to,
+        maxValue,
+        limit,
+        threshold,
+        numberSlots: LABEL_SLOTS,
+    });
+    const labelled = [];
+    for (const peak of best) {
+        // A peak the slots called close stands within a slot of one already
+        // labelled, so labelling it too writes one label over the other.
+        if (peak.close)
+            continue;
+        labelled.push({
+            x: peak.x,
+            y: peak.y,
+            charge: peak.charge,
+            index: xFindClosestIndex(centroid.x, peak.x),
+        });
+    }
+    return labelled;
+}
+//# sourceMappingURL=labelledPeaks.js.map

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

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

@@ -0,0 +1,57 @@
+/**
+ * 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 type { LoadedMassSpectrum } from './loadedMassSpectrum.ts';
+/**
+ * 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 declare const DEFAULT_MAX_SPECTRA = 100;
+/** How a file is read. */
+export interface LoadMassSpectraOptions {
+    /**
+     * The file's name, which decides the reader when the content is silent and is
+     * carried onto every spectrum read out of it.
+     * @default undefined
+     */
+    fileName?: string;
+    /**
+     * At most how many spectra are read out of the file.
+     * @default DEFAULT_MAX_SPECTRA
+     */
+    maxSpectra?: number;
+}
+/** What a file turned out to hold. */
+export interface LoadMassSpectraResult {
+    /** The spectra it held, in the order the file wrote them. */
+    spectra: LoadedMassSpectrum[];
+    /** What it turned out to be. */
+    format: 'jcamp' | 'text';
+    /**
+     * How many spectra `maxSpectra` left unread, `0` when none. Reported rather
+     * than passed over in silence: a run truncated without a word looks exactly
+     * like a run that only held a hundred scans.
+     */
+    dropped: number;
+}
+/**
+ * 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 declare function loadMassSpectra(data: Uint8Array | ArrayBuffer | string, options?: LoadMassSpectraOptions): Promise<LoadMassSpectraResult>;
+//# sourceMappingURL=loadMassSpectra.d.ts.map

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