react-cheminfo 0.28.0 → 0.29.0

package/README.md

@@ -41,6 +41,7 @@ only when it drags a heavy dependency behind it.
 | `react-cheminfo/conformers`        | conformer generation, ranking and refinement      | OCL                                              |
 | `react-cheminfo/slides`            | the deck format and the slideshow player          | React, react-markdown                            |
 | `react-cheminfo/spectra`           | the spectra processing settings editors           | React; types only from spectra-processor, ml-pca |
+| `react-cheminfo/ir`                | the infrared chart, band table and editor         | React, ir-spectrum, convert-to-jcamp             |
 | `react-cheminfo/xtb`               | GFN2-xTB as a geometry relaxer                    | nothing on import; xtb-wasm on the first call    |
 | `react-cheminfo/styles/chrome.css` | the shared tokens and site-header stylesheet      | nothing                                          |
 | `react-cheminfo/styles/slides.css` | the deck stylesheet, themed on the site's colours | nothing                                          |
@@ -56,6 +57,16 @@ site that never imports `react-cheminfo/slides` bundles none of it. The same hol
 for `openchemlib`, which every function of `react-cheminfo/conformers` runs at
 module scope: a site that never imports that door bundles none of it.
 
+`react-cheminfo/ir` is a viewer rather than a helper, and it is a door for the
+usual reason: reading a spectrum drags the formats one may arrive in —
+`ir-spectrum` for the band correlations and the absorbance/transmittance pair,
+`convert-to-jcamp` for writing them back out, and a JCAMP or SPC reader fetched
+only once the bytes turn out to need it. The chart it is drawn with is **not**
+behind that door: scales, ticks, plot geometry, the zoom gestures, the label
+placement and the panel chrome are in `core` and `ui`, because a spectrum of any
+kind is drawn with them and the next viewer built on them should find them
+already there rather than reach through an infrared package for them.
+
 `react-cheminfo/xtb` is the door a page opens only when a visitor asks for a
 better number. `refineConformers` in
 `react-cheminfo/conformers` orchestrates a refinement against the
@@ -74,31 +85,33 @@ through a wildcard subpath exactly as `react-science` serves its own.
 
 ## What is in it
 
-| Area                       | `…/core`                                                                                                                                                                                                                                                                   | `…/ui`                                                                                                                                                                                  |
-| -------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| **Site identity**          | `siteById`, `findSiteByHost`, `siteTokensCss`                                                                                                                                                                                                                              | `SiteMark`, `Wordmark`, `SiteTheme`, `SiteTile`, `EcosystemButton`, `EcosystemLinks`                                                                                                    |
-| **Chrome**                 | —                                                                                                                                                                                                                                                                          | `SiteHeader`, `SiteFooter`, `NavLink`, `NavMenuButton`, `MenuButton`, `useCompactHeader`                                                                                                |
-| **Languages**              | `LANGUAGES`, `DEFAULT_LANGUAGE`, `LANGUAGE_LABELS`, `isLanguage`, `MessageCatalog`, `CHROME_CATALOG`, `setMessageSession`, `loadCatalogs`, `LANGUAGE_PARAM`, `withLanguageParam`                                                                                           | `useT`, `useChromeT`, `useLanguage`, `LanguageSelect`, `SiteLanguage`                                                                                                                   |
-| **Citation**               | `formatCitation`, `formatCitations`, `citationSegments`, `downloadCitation`, `citedReferences`, `doiUrl`                                                                                                                                                                   | `CiteButton`, `CitationMenu`, `CitationPreview`                                                                                                                                         |
-| **Share & embed**          | `parseShareConfig`, `applyShareConfig`, `buildShareUrl`, `buildEmbedCode`, `isHidden`, `visibleShareParts`, `applySharePreset`, `findSharePreset`, the param codecs, `syncPreferencesWithUrl`, `applyPreferencesFromSearch`, `writePreferencesToSearch`                    | `ShareDialog`, `ShareButton`, `HiddenPartsProvider`, `PagePart`, `useIsHidden`                                                                                                          |
-| **Routing & head**         | `createTabRouter`, `readRoute`, `writeRoute`, `subscribeToRoute`, `adoptLegacyHashAddress`, `writeDocumentMeta`                                                                                                                                                            | `useTabRoute`                                                                                                                                                                           |
-| **Indexing**               | `injectPageMeta`, `pageHeadTags`, `pageDocumentMeta`, `fill`, `PAGE_HEAD_MARKER`, `PAGE_BODY_MARKER`, `robotsTxt`, `sitemapXml`, `noscriptIndex`, `structuredDataScript`, `assertRoutes`, `routeFor`, `homeRoute`                                                          | `cheminfoPrerender`, `ogCardHtml`, `OG_WIDTH`, `OG_HEIGHT` (all `/vite`)                                                                                                                |
-| **Pedagogy**               | `parseGlossaryMarkers`, `localStorageProgressStore`, `progressSummary`, `finishValidation`                                                                                                                                                                                 | `GlossaryText`, `SyntaxTooltip`, `HintLadder`, `ExerciseActions`, `ExerciseProgressHeader`, `TutorialStepStrip`, `ReferenceGrid`, `TestCaseList`                                        |
-| **Clipboard & files**      | `writeToClipboard`, `downloadBlob`, `downloadText`, `sanitizeFileName`, `toDelimited`, `readDelimited`, `downloadFigure`, `figureSvg`, `figurePng`, `figureSize`                                                                                                           | `ClickToCopy`, `CopyButton`, `CopyableValue`, `CodeBlock`, `DelimitedTextDialog`, `FigureDownload`                                                                                      |
-| **Formatting & colour**    | `formatInteger`, `formatDecimal`, `formatBytes`, `pluralize`, `readableInk`, `contrastRatio`, `COLOR_SCALES`, `resolveColorScale`, `formatColorScale`, `colorAt`, `swatchAt`, `sampleScale`, `colorScaleGradient`, `rgbToHsv`                                              | `ColorScaleLegend`, `ColorScaleSelect`, `ColorScaleEditor`, `ColorScaleBar`                                                                                                             |
-| **Widgets**                | `CREDITS`, `credits`                                                                                                                                                                                                                                                       | `ErrorBoundary`, `CollapsibleSection`, `CapsuleFilter`, `HelpTooltip`, `CreditsList`                                                                                                    |
-| **Hooks & state**          | `createWorkerChannel`, `persistBucket`, `persistSignalBucket`                                                                                                                                                                                                              | `useDebouncedValue`, `useContainerSize`, `useListKeyboardNavigation`, `useDisclosure`                                                                                                   |
-| **Chemistry**              | `atomicOrbitalsOf`, `configurationOf`, `classifyMolfile`, `readStructure`, `toMolfileExport`                                                                                                                                                                               | `AtomicOrbitalViewer` (`/orbital`), `StructureEditor`, `Structure` (`/structure`)                                                                                                       |
-| **Conformers**             | `generateConformers`, `continueConformers`, `refineConformers`, `conformerShape`, `isSameMinimum`, `rankByEnergy`, `minimiseConformer`, `DEFAULT_CONFORMER_OPTIONS`, `CONFORMER_STRATEGIES` (all `/conformers`); `GeometryRelaxer`, `readRelaxableGeometry`, `centredRmsd` | —                                                                                                                                                                                       |
-| **Spectra**                | `FILTER_CATALOG`, `filterMenu`, `settingsProblems`, `normalizationFilters`, `addFilter`, `moveFilter`, `setFilterOption`, `principalComponentChoices`, `clampPrincipalComponents`, `EMPTY_SETTINGS` (all `/spectra`)                                                       | `SpectraSettingsEditor`, `FilterChainEditor`, `PrincipalComponentSelect` (all `/spectra`)                                                                                               |
-| **About**                  | `resolveAbout`, `aboutProblems`                                                                                                                                                                                                                                            | `AboutPage`                                                                                                                                                                             |
-| **Which build is running** | `formatBuiltAt`, `shortCommit`, `BuildInfo`                                                                                                                                                                                                                                | `AboutBuild`, `cheminfoBuildInfo` (`/vite`)                                                                                                                                             |
-| **Slideshows**             | `parseTalk`, `splitDemoLinks`, `slideActionForKey`, `parseTalkOrigin`, `buildTalkManifest` (all `/slides`)                                                                                                                                                                 | `Slideshow`, `SlideView`, `TalkList`, `BackToSlides` (all `/slides`), `cheminfoTalks` (`/vite`)                                                                                         |
-| **Token guard**            | `findTokenViolations`                                                                                                                                                                                                                                                      | `cheminfo-check-tokens`, `cheminfo-check-messages`, `cheminfo-check-deploy` (the bins)                                                                                                  |
-| **Figures**                | `chartScale`, `chartAxisScale`, `chartAxisTitle`, `chartShare`, `chartColumnExtent`, `chartBinCounts`, `chartSeriesColor`, `rowMatrix`, `stackedMatrix`, `emptiestCorner`, `placeOverlayCard`, `overlayMetrics`                                                            | `ChartFrame`, `ChartAxis`, `TrackedLineChart`, `OverlayBar`, `OverlaySelect`, `OverlaySegmented`, `OverlayToggle`, `OverlayNumber`, `OverlayLegend`, `OverlayCaption`, `OverlayReadout` |
-| **Projections**            | `pcaResult`, `embeddingResult`, `projectionTabs`, `loadingProfiles`, `explainedShares`, `confidenceEllipse`, `projectEllipse`, `pointsInPolygon`, `resolveProjectionGroups`, `resolveProjectionShapes`, `PROJECTION_COPY`                                                  | `PcaViewer`, `ProjectionViewer`, `ScatterPlot`, `ScatterMatrix`                                                                                                                         |
-| **Parallel coordinates**   | `parallelAxisOf`, `parallelAxisLayouts`, `parallelIncludedMask`, `parallelKeptCount`, `parallelNearestRow`, `parallelSegmentAt`, `parallelBandAt`, `parallelRangeOf`, `parallelPalette`, `parallelColorSteps`, `paintParallelLines`                                        | `ParallelCoordinates`                                                                                                                                                                   |
-| **Periodic table**         | `PERIODIC_ELEMENTS`, `elementBySymbol`, `elementByAtomicNumber`, `cellOf`, `placedElements`, `elementByArrowKey`, `categorySwatch`, `CATEGORY_LABELS`                                                                                                                      | `PeriodicTable`, `ElementCell`, `CategoryLegend`                                                                                                                                        |
+| Area                       | `…/core`                                                                                                                                                                                                                                                                                                         | `…/ui`                                                                                                                                                                                                                                                                                             |
+| -------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **Site identity**          | `siteById`, `findSiteByHost`, `siteTokensCss`                                                                                                                                                                                                                                                                    | `SiteMark`, `Wordmark`, `SiteTheme`, `SiteTile`, `EcosystemButton`, `EcosystemLinks`                                                                                                                                                                                                               |
+| **Chrome**                 | —                                                                                                                                                                                                                                                                                                                | `SiteHeader`, `SiteFooter`, `NavLink`, `NavMenuButton`, `MenuButton`, `useCompactHeader`                                                                                                                                                                                                           |
+| **Languages**              | `LANGUAGES`, `DEFAULT_LANGUAGE`, `LANGUAGE_LABELS`, `isLanguage`, `MessageCatalog`, `CHROME_CATALOG`, `setMessageSession`, `loadCatalogs`, `LANGUAGE_PARAM`, `withLanguageParam`                                                                                                                                 | `useT`, `useChromeT`, `useLanguage`, `LanguageSelect`, `SiteLanguage`                                                                                                                                                                                                                              |
+| **Citation**               | `formatCitation`, `formatCitations`, `citationSegments`, `downloadCitation`, `citedReferences`, `doiUrl`                                                                                                                                                                                                         | `CiteButton`, `CitationMenu`, `CitationPreview`                                                                                                                                                                                                                                                    |
+| **Share & embed**          | `parseShareConfig`, `applyShareConfig`, `buildShareUrl`, `buildEmbedCode`, `isHidden`, `visibleShareParts`, `applySharePreset`, `findSharePreset`, the param codecs, `syncPreferencesWithUrl`, `applyPreferencesFromSearch`, `writePreferencesToSearch`                                                          | `ShareDialog`, `ShareButton`, `HiddenPartsProvider`, `PagePart`, `useIsHidden`                                                                                                                                                                                                                     |
+| **Routing & head**         | `createTabRouter`, `readRoute`, `writeRoute`, `subscribeToRoute`, `adoptLegacyHashAddress`, `writeDocumentMeta`                                                                                                                                                                                                  | `useTabRoute`                                                                                                                                                                                                                                                                                      |
+| **Indexing**               | `injectPageMeta`, `pageHeadTags`, `pageDocumentMeta`, `fill`, `PAGE_HEAD_MARKER`, `PAGE_BODY_MARKER`, `robotsTxt`, `sitemapXml`, `noscriptIndex`, `structuredDataScript`, `assertRoutes`, `routeFor`, `homeRoute`                                                                                                | `cheminfoPrerender`, `ogCardHtml`, `OG_WIDTH`, `OG_HEIGHT` (all `/vite`)                                                                                                                                                                                                                           |
+| **Pedagogy**               | `parseGlossaryMarkers`, `localStorageProgressStore`, `progressSummary`, `finishValidation`                                                                                                                                                                                                                       | `GlossaryText`, `SyntaxTooltip`, `HintLadder`, `ExerciseActions`, `ExerciseProgressHeader`, `TutorialStepStrip`, `ReferenceGrid`, `TestCaseList`                                                                                                                                                   |
+| **Clipboard & files**      | `writeToClipboard`, `downloadBlob`, `downloadText`, `sanitizeFileName`, `toDelimited`, `readDelimited`, `downloadFigure`, `figureSvg`, `figurePng`, `figureSize`                                                                                                                                                 | `ClickToCopy`, `CopyButton`, `CopyableValue`, `CodeBlock`, `DelimitedTextDialog`, `FigureDownload`                                                                                                                                                                                                 |
+| **Formatting & colour**    | `formatInteger`, `formatDecimal`, `formatBytes`, `pluralize`, `readableInk`, `contrastRatio`, `COLOR_SCALES`, `resolveColorScale`, `formatColorScale`, `colorAt`, `swatchAt`, `sampleScale`, `colorScaleGradient`, `rgbToHsv`                                                                                    | `ColorScaleLegend`, `ColorScaleSelect`, `ColorScaleEditor`, `ColorScaleBar`                                                                                                                                                                                                                        |
+| **Widgets**                | `CREDITS`, `credits`                                                                                                                                                                                                                                                                                             | `ErrorBoundary`, `CollapsibleSection`, `CapsuleFilter`, `HelpTooltip`, `CreditsList`                                                                                                                                                                                                               |
+| **Hooks & state**          | `createWorkerChannel`, `persistBucket`, `persistSignalBucket`                                                                                                                                                                                                                                                    | `useDebouncedValue`, `useContainerSize`, `useListKeyboardNavigation`, `useDisclosure`                                                                                                                                                                                                              |
+| **Chemistry**              | `atomicOrbitalsOf`, `configurationOf`, `classifyMolfile`, `readStructure`, `toMolfileExport`                                                                                                                                                                                                                     | `AtomicOrbitalViewer` (`/orbital`), `StructureEditor`, `Structure` (`/structure`)                                                                                                                                                                                                                  |
+| **Conformers**             | `generateConformers`, `continueConformers`, `refineConformers`, `conformerShape`, `isSameMinimum`, `rankByEnergy`, `minimiseConformer`, `DEFAULT_CONFORMER_OPTIONS`, `CONFORMER_STRATEGIES` (all `/conformers`); `GeometryRelaxer`, `readRelaxableGeometry`, `centredRmsd`                                       | —                                                                                                                                                                                                                                                                                                  |
+| **Spectrum charts**        | `chartScale`, `chartAxisScale`, `plotRect`, `zoomDomain`, `zoomSelection`, `labelStackBaselines`, `layoutAnnotationBoxes`, `profilePath`, `stickPath`, `guidePlacement`, `readoutPlacement`, `stackCapacity`, `nextSpectrumColor`, `panelStyles`, `statusBar`, `pictureSize`, `savePngPicture`, `saveSvgPicture` | `Axes`, `AxisGuide`, `ChartTracker`, `ChartStack`, `SelectionRect`, `TraceLegend`, `PlotCaption`, `useChartZoom`, `useChartPointer`, `useChartSize`, `SidePanelStack`, `PanelRail`, `Section`, `FilterInput`, `AboutDialogFrame`, `DocumentationDialogFrame`, `ExportImageDialog`, `useDrawingBox` |
+| **Infrared**               | `loadIrSpectra`, `toIrSpectrum`, `pickBands`, `assignBands`, `BAND_ASSIGNMENTS`, `irSpectrumToJcamp`, `IR_MODE_RULES`, `nearestBandAt`, `planBandLabels`, `irReducer` (all `/ir`)                                                                                                                                | `IrEditor`, `IrChart`, `BandsPanel`, `SpectraPanel`, `MetadataPanel`, `useIrEditor` (all `/ir`)                                                                                                                                                                                                    |
+| **Spectra**                | `FILTER_CATALOG`, `filterMenu`, `settingsProblems`, `normalizationFilters`, `addFilter`, `moveFilter`, `setFilterOption`, `principalComponentChoices`, `clampPrincipalComponents`, `EMPTY_SETTINGS` (all `/spectra`)                                                                                             | `SpectraSettingsEditor`, `FilterChainEditor`, `PrincipalComponentSelect` (all `/spectra`)                                                                                                                                                                                                          |
+| **About**                  | `resolveAbout`, `aboutProblems`                                                                                                                                                                                                                                                                                  | `AboutPage`                                                                                                                                                                                                                                                                                        |
+| **Which build is running** | `formatBuiltAt`, `shortCommit`, `BuildInfo`                                                                                                                                                                                                                                                                      | `AboutBuild`, `cheminfoBuildInfo` (`/vite`)                                                                                                                                                                                                                                                        |
+| **Slideshows**             | `parseTalk`, `splitDemoLinks`, `slideActionForKey`, `parseTalkOrigin`, `buildTalkManifest` (all `/slides`)                                                                                                                                                                                                       | `Slideshow`, `SlideView`, `TalkList`, `BackToSlides` (all `/slides`), `cheminfoTalks` (`/vite`)                                                                                                                                                                                                    |
+| **Token guard**            | `findTokenViolations`                                                                                                                                                                                                                                                                                            | `cheminfo-check-tokens`, `cheminfo-check-messages`, `cheminfo-check-deploy` (the bins)                                                                                                                                                                                                             |
+| **Figures**                | `chartScale`, `chartAxisScale`, `chartAxisTitle`, `chartShare`, `chartColumnExtent`, `chartBinCounts`, `chartSeriesColor`, `rowMatrix`, `stackedMatrix`, `emptiestCorner`, `placeOverlayCard`, `overlayMetrics`                                                                                                  | `ChartFrame`, `ChartAxis`, `TrackedLineChart`, `OverlayBar`, `OverlaySelect`, `OverlaySegmented`, `OverlayToggle`, `OverlayNumber`, `OverlayLegend`, `OverlayCaption`, `OverlayReadout`                                                                                                            |
+| **Projections**            | `pcaResult`, `embeddingResult`, `projectionTabs`, `loadingProfiles`, `explainedShares`, `confidenceEllipse`, `projectEllipse`, `pointsInPolygon`, `resolveProjectionGroups`, `resolveProjectionShapes`, `PROJECTION_COPY`                                                                                        | `PcaViewer`, `ProjectionViewer`, `ScatterPlot`, `ScatterMatrix`                                                                                                                                                                                                                                    |
+| **Parallel coordinates**   | `parallelAxisOf`, `parallelAxisLayouts`, `parallelIncludedMask`, `parallelKeptCount`, `parallelNearestRow`, `parallelSegmentAt`, `parallelBandAt`, `parallelRangeOf`, `parallelPalette`, `parallelColorSteps`, `paintParallelLines`                                                                              | `ParallelCoordinates`                                                                                                                                                                                                                                                                              |
+| **Periodic table**         | `PERIODIC_ELEMENTS`, `elementBySymbol`, `elementByAtomicNumber`, `cellOf`, `placedElements`, `elementByArrowKey`, `categorySwatch`, `CATEGORY_LABELS`                                                                                                                                                            | `PeriodicTable`, `ElementCell`, `CategoryLegend`                                                                                                                                                                                                                                                   |
 
 Everything in that table is exported from `./core`, `./ui`, `./slides`,
 `./vite` or `./structure` and nothing else is: the sub-components a component is built

package/lib/chart/core/axisLabels.d.ts

@@ -0,0 +1,82 @@
+/**
+ * How a number is written wherever a chart writes one.
+ *
+ * The axis decides, not the number: the precision comes from the tick step, and
+ * the notation from the largest tick, so every label on one axis is written the
+ * same way and a reader can run an eye down a column of them. `chartAxisScale`
+ * works both out; this is where they turn into text.
+ *
+ * It is a second way of writing the labels `chartAxisScale` already carries,
+ * and it exists because the two answer different questions. A figure lifts a
+ * common power of ten into its axis title and writes short labels under it — a
+ * chart whose axis title is fixed by the measurement cannot, so a spectrum
+ * writes the magnitude into each label instead.
+ */
+import type { ChartAxisScale } from './chartAxisScale.ts';
+/**
+ * Write a number the way an axis label or a readout wants it.
+ *
+ * The decimals come from the axis, so every label on it is written to the same
+ * precision — but a tick that happens to land on a round number then reads
+ * `500.0000` where `500` was meant, and half its width is zeros carrying
+ * nothing. They are trimmed off the end only, never out of the middle, so
+ * `500.0002` keeps every digit it needs.
+ *
+ * `toFixed` also writes `-0` for anything that rounds to zero from below, which
+ * is never what an axis means and is jarring on the one tick a chemist looks at
+ * most.
+ * @param value - The number to write.
+ * @param decimals - How many decimals to write it to, as `niceTicks` derived.
+ * @returns The label.
+ */
+export declare function formatNumber(value: number, decimals: number): string;
+/**
+ * The magnitude above which a number is quicker read as a power of ten.
+ *
+ * An ion count is quoted in whatever the instrument counted in, so an intensity
+ * axis written out in full reads `200000000` — nine digits a reader has to group
+ * into threes before knowing which power of ten they are looking at, and wide
+ * enough to run into the axis title printed beside them. Above this the same
+ * tick is written `2e+8`, which says the magnitude first and in four characters.
+ *
+ * A hundred thousand rather than a million because that is where a number stops
+ * being read at a glance, and because it is the threshold every intensity in the
+ * mass side is already written against — a colourbar and an axis that disagreed
+ * about how one count is spelled would read as two measurements.
+ */
+export declare const SCIENTIFIC_ABOVE = 100000;
+/**
+ * The magnitude below which the digits that mean anything are all behind zeros.
+ *
+ * The mirror of `SCIENTIFIC_ABOVE`: `0.00002` is four characters of nothing
+ * followed by the one digit that was measured.
+ */
+export declare const SCIENTIFIC_BELOW = 0.0001;
+/**
+ * Write a number as a mantissa and a power of ten.
+ *
+ * With no precision asked for, the mantissa keeps only the digits it needs — a
+ * tick at a hundred and fifty million is `1.5e+8` and the one above it `2e+8`,
+ * rather than both being padded to the same width with zeros that say nothing.
+ * The value is rounded to a few significant digits first, because a tick is
+ * reached by multiplying a step by an index and `3 * 0.1` is `0.30000000000000004`
+ * — which the shortest form would write out in full, every digit of it noise.
+ * @param value - The number to write.
+ * @param digits - How many decimals the mantissa carries. Left out, it carries
+ * as few as tell this number from its neighbours.
+ * @returns The number in scientific notation, or `0` for zero, which has no
+ * exponent and is written the same way on any axis.
+ */
+export declare function formatScientific(value: number, digits?: number): string;
+/**
+ * How one axis writes every one of its labels.
+ *
+ * The notation is chosen once, from the largest tick on the axis, and then used
+ * for all of them — including the small ones and the zero. An axis is read by
+ * running an eye along it, and one whose labels changed notation partway would
+ * have to be read a label at a time instead.
+ * @param axis - The axis, as `chartAxisScale` divided it.
+ * @returns A writer for every label on that axis.
+ */
+export declare function axisLabeller(axis: ChartAxisScale): (value: number) => string;
+//# sourceMappingURL=axisLabels.d.ts.map

package/lib/chart/core/axisLabels.d.ts.map

@@ -0,0 +1 @@
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package/lib/chart/core/axisLabels.js

@@ -0,0 +1,111 @@
+/**
+ * How a number is written wherever a chart writes one.
+ *
+ * The axis decides, not the number: the precision comes from the tick step, and
+ * the notation from the largest tick, so every label on one axis is written the
+ * same way and a reader can run an eye down a column of them. `chartAxisScale`
+ * works both out; this is where they turn into text.
+ *
+ * It is a second way of writing the labels `chartAxisScale` already carries,
+ * and it exists because the two answer different questions. A figure lifts a
+ * common power of ten into its axis title and writes short labels under it — a
+ * chart whose axis title is fixed by the measurement cannot, so a spectrum
+ * writes the magnitude into each label instead.
+ */
+/**
+ * Write a number the way an axis label or a readout wants it.
+ *
+ * The decimals come from the axis, so every label on it is written to the same
+ * precision — but a tick that happens to land on a round number then reads
+ * `500.0000` where `500` was meant, and half its width is zeros carrying
+ * nothing. They are trimmed off the end only, never out of the middle, so
+ * `500.0002` keeps every digit it needs.
+ *
+ * `toFixed` also writes `-0` for anything that rounds to zero from below, which
+ * is never what an axis means and is jarring on the one tick a chemist looks at
+ * most.
+ * @param value - The number to write.
+ * @param decimals - How many decimals to write it to, as `niceTicks` derived.
+ * @returns The label.
+ */
+export function formatNumber(value, decimals) {
+    const text = value.toFixed(Math.min(20, Math.max(0, Math.floor(decimals))));
+    const trimmed = text.includes('.') ? text.replace(/\.?0+$/, '') : text;
+    return trimmed === '-0' ? '0' : trimmed;
+}
+/**
+ * The magnitude above which a number is quicker read as a power of ten.
+ *
+ * An ion count is quoted in whatever the instrument counted in, so an intensity
+ * axis written out in full reads `200000000` — nine digits a reader has to group
+ * into threes before knowing which power of ten they are looking at, and wide
+ * enough to run into the axis title printed beside them. Above this the same
+ * tick is written `2e+8`, which says the magnitude first and in four characters.
+ *
+ * A hundred thousand rather than a million because that is where a number stops
+ * being read at a glance, and because it is the threshold every intensity in the
+ * mass side is already written against — a colourbar and an axis that disagreed
+ * about how one count is spelled would read as two measurements.
+ */
+export const SCIENTIFIC_ABOVE = 1e5;
+/**
+ * The magnitude below which the digits that mean anything are all behind zeros.
+ *
+ * The mirror of `SCIENTIFIC_ABOVE`: `0.00002` is four characters of nothing
+ * followed by the one digit that was measured.
+ */
+export const SCIENTIFIC_BELOW = 1e-4;
+/**
+ * Write a number as a mantissa and a power of ten.
+ *
+ * With no precision asked for, the mantissa keeps only the digits it needs — a
+ * tick at a hundred and fifty million is `1.5e+8` and the one above it `2e+8`,
+ * rather than both being padded to the same width with zeros that say nothing.
+ * The value is rounded to a few significant digits first, because a tick is
+ * reached by multiplying a step by an index and `3 * 0.1` is `0.30000000000000004`
+ * — which the shortest form would write out in full, every digit of it noise.
+ * @param value - The number to write.
+ * @param digits - How many decimals the mantissa carries. Left out, it carries
+ * as few as tell this number from its neighbours.
+ * @returns The number in scientific notation, or `0` for zero, which has no
+ * exponent and is written the same way on any axis.
+ */
+export function formatScientific(value, digits) {
+    if (value === 0)
+        return '0';
+    if (digits === undefined) {
+        return Number(value.toPrecision(SCIENTIFIC_DIGITS)).toExponential();
+    }
+    return value.toExponential(Math.min(100, Math.max(0, Math.floor(digits))));
+}
+/**
+ * How one axis writes every one of its labels.
+ *
+ * The notation is chosen once, from the largest tick on the axis, and then used
+ * for all of them — including the small ones and the zero. An axis is read by
+ * running an eye along it, and one whose labels changed notation partway would
+ * have to be read a label at a time instead.
+ * @param axis - The axis, as `chartAxisScale` divided it.
+ * @returns A writer for every label on that axis.
+ */
+export function axisLabeller(axis) {
+    const { values, decimals } = axis;
+    let largest = 0;
+    for (const tick of values) {
+        const magnitude = Math.abs(tick);
+        if (magnitude > largest)
+            largest = magnitude;
+    }
+    const scientific = largest >= SCIENTIFIC_ABOVE || (largest > 0 && largest < SCIENTIFIC_BELOW);
+    return scientific
+        ? (value) => formatScientific(value)
+        : (value) => formatNumber(value, decimals);
+}
+/**
+ * How many significant digits survive the rounding that sheds floating noise.
+ *
+ * A tick is 1, 2 or 5 times a power of ten times an index, so two digits carry
+ * every one of them and six is room to spare for a readout written this way.
+ */
+const SCIENTIFIC_DIGITS = 6;
+//# sourceMappingURL=axisLabels.js.map

package/lib/chart/core/axisLabels.js.map

@@ -0,0 +1 @@
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package/lib/chart/core/boxLayout.d.ts

@@ -0,0 +1,53 @@
+/**
+ * Keeping the labels above the peaks apart from one another.
+ *
+ * An annotated spectrum wants a box over every peak it explains, and an
+ * isotopologue cluster puts four of them within a few pixels. Sliding them
+ * apart is most of the job, and the leader line back to the stick is what says
+ * which peak a box belongs to — so a box a little out of place is still
+ * readable.
+ *
+ * A box slid *far* out of place is not. Spacing a crowd out marches the last of
+ * them across the whole plot, where it comes to rest over peaks it says nothing
+ * about, with a leader long enough to be read as pointing at one of them. Those
+ * are dropped, and only those: a mark still sits on every annotated peak, so
+ * the fragment is not one the chemist concludes the spectrum lacks — it is one
+ * whose picture is a zoom away.
+ */
+import type { NumberArray } from 'cheminfo-types';
+/**
+ * Slide overlapping boxes apart, keeping every one of them inside the plot.
+ *
+ * Two sweeps, and the order of the clamps is the whole behaviour. The first
+ * sweep runs left to right and pushes each box far enough past its neighbour to
+ * clear it, which piles the crowding up against the right edge; the second runs
+ * back the other way, pulling that pile inside the right bound and spacing it
+ * out leftwards again.
+ *
+ * The left bound is then applied last, after the spacing, and so beats it. A
+ * cluster too wide for the room it is in therefore ends with its leftmost boxes
+ * overlapping rather than with one of them hanging off the plot — an overlap is
+ * two labels a reader can still pick apart with the leader lines, while a box
+ * outside the plot is clipped away and reads as an annotation that was never
+ * made.
+ * @param centres - Where each box would like to be centred, in pixels; any
+ * order, and the result comes back in that same order.
+ * @param bounds - `[from, to]` in pixels that no box may extend beyond.
+ * @param width - How wide every box is.
+ * @param gap - The clear space wanted between two neighbouring boxes.
+ * @param maximumDrift - How far a box may be slid from where it wanted to be
+ * before it is dropped instead, in pixels. Defaults to two whole box steps.
+ * @returns The centre each box was actually given, `NaN` for one that was slid
+ * too far and dropped.
+ */
+export declare function layoutAnnotationBoxes(centres: NumberArray, bounds: readonly [number, number], width: number, gap: number, maximumDrift?: number): Float64Array;
+/**
+ * How far a picture may be slid from its peak, counted in whole box steps.
+ *
+ * Two: a box may be pushed past two neighbours and still be read as belonging
+ * to the peak under it, which is what a cluster of three peaks needs. Past that
+ * the leader is longer than the box is wide and reaches across other peaks, so
+ * the picture reads as answering for one of them instead.
+ */
+export declare const MAXIMUM_DRIFT_STEPS = 2;
+//# sourceMappingURL=boxLayout.d.ts.map

package/lib/chart/core/boxLayout.d.ts.map

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package/lib/chart/core/boxLayout.js

@@ -0,0 +1,112 @@
+/**
+ * Keeping the labels above the peaks apart from one another.
+ *
+ * An annotated spectrum wants a box over every peak it explains, and an
+ * isotopologue cluster puts four of them within a few pixels. Sliding them
+ * apart is most of the job, and the leader line back to the stick is what says
+ * which peak a box belongs to — so a box a little out of place is still
+ * readable.
+ *
+ * A box slid *far* out of place is not. Spacing a crowd out marches the last of
+ * them across the whole plot, where it comes to rest over peaks it says nothing
+ * about, with a leader long enough to be read as pointing at one of them. Those
+ * are dropped, and only those: a mark still sits on every annotated peak, so
+ * the fragment is not one the chemist concludes the spectrum lacks — it is one
+ * whose picture is a zoom away.
+ */
+/**
+ * Slide overlapping boxes apart, keeping every one of them inside the plot.
+ *
+ * Two sweeps, and the order of the clamps is the whole behaviour. The first
+ * sweep runs left to right and pushes each box far enough past its neighbour to
+ * clear it, which piles the crowding up against the right edge; the second runs
+ * back the other way, pulling that pile inside the right bound and spacing it
+ * out leftwards again.
+ *
+ * The left bound is then applied last, after the spacing, and so beats it. A
+ * cluster too wide for the room it is in therefore ends with its leftmost boxes
+ * overlapping rather than with one of them hanging off the plot — an overlap is
+ * two labels a reader can still pick apart with the leader lines, while a box
+ * outside the plot is clipped away and reads as an annotation that was never
+ * made.
+ * @param centres - Where each box would like to be centred, in pixels; any
+ * order, and the result comes back in that same order.
+ * @param bounds - `[from, to]` in pixels that no box may extend beyond.
+ * @param width - How wide every box is.
+ * @param gap - The clear space wanted between two neighbouring boxes.
+ * @param maximumDrift - How far a box may be slid from where it wanted to be
+ * before it is dropped instead, in pixels. Defaults to two whole box steps.
+ * @returns The centre each box was actually given, `NaN` for one that was slid
+ * too far and dropped.
+ */
+export function layoutAnnotationBoxes(centres, bounds, width, gap, maximumDrift = (width + gap) * MAXIMUM_DRIFT_STEPS) {
+    const count = centres.length;
+    const placed = new Float64Array(count);
+    if (count === 0)
+        return placed;
+    const half = width / 2;
+    const minimumCentre = bounds[0] + half;
+    const maximumCentre = bounds[1] - half;
+    const step = width + gap;
+    const order = ascendingOrder(centres);
+    let previous = Number.NEGATIVE_INFINITY;
+    for (let position = 0; position < count; position++) {
+        const index = order[position];
+        let centre = Math.min(Math.max(centres[index], minimumCentre), maximumCentre);
+        if (centre < previous + step)
+            centre = previous + step;
+        placed[index] = centre;
+        previous = centre;
+    }
+    let next = Number.POSITIVE_INFINITY;
+    for (let position = count - 1; position >= 0; position--) {
+        const index = order[position];
+        let centre = placed[index];
+        if (centre > maximumCentre)
+            centre = maximumCentre;
+        if (centre > next - step)
+            centre = next - step;
+        if (centre < minimumCentre)
+            centre = minimumCentre;
+        placed[index] = centre;
+        next = centre;
+    }
+    // A picture that has been slid too far from the peak it explains is worse
+    // than no picture: it hangs over a peak it says nothing about, and the leader
+    // back to its own is long enough to be read as pointing at something else.
+    // Those are dropped rather than drawn, and the mark on the peak still says
+    // the annotation is there.
+    for (let index = 0; index < count; index++) {
+        const wanted = centres[index];
+        if (Math.abs(placed[index] - wanted) > maximumDrift) {
+            placed[index] = Number.NaN;
+        }
+    }
+    return placed;
+}
+/**
+ * How far a picture may be slid from its peak, counted in whole box steps.
+ *
+ * Two: a box may be pushed past two neighbours and still be read as belonging
+ * to the peak under it, which is what a cluster of three peaks needs. Past that
+ * the leader is longer than the box is wide and reaches across other peaks, so
+ * the picture reads as answering for one of them instead.
+ */
+export const MAXIMUM_DRIFT_STEPS = 2;
+/**
+ * The indices of the boxes, ordered by where they want to be.
+ *
+ * The sweeps only make sense left to right, and the caller's order is whatever
+ * the annotations came in — usually by mass, but a second producer's marks are
+ * appended rather than merged.
+ * @param centres - Where each box would like to be centred.
+ * @returns The indices, ascending by centre.
+ */
+function ascendingOrder(centres) {
+    const order = new Uint32Array(centres.length);
+    for (let index = 0; index < centres.length; index++) {
+        order[index] = index;
+    }
+    return order.toSorted((first, second) => centres[first] - centres[second]);
+}
+//# sourceMappingURL=boxLayout.js.map

package/lib/chart/core/boxLayout.js.map

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package/lib/chart/core/chartAxisScale.d.ts

@@ -13,6 +13,21 @@ export interface ChartAxisScale {
     /** One label per value, already written out. */
     readonly labels: readonly string[];
 }
+/**
+ * How the step is chosen when an even division lands between two nice ones.
+ *
+ * - `nearest` — take whichever of 1, 2 or 5 the division is closest to, which
+ *   puts the tick count near what was asked for from either side.
+ * - `atMost` — always take the larger, so the count asked for is a budget the
+ *   axis never exceeds.
+ *
+ * The difference is not cosmetic. A figure asking for about five ticks wants
+ * them spaced as evenly as the numbers allow, and one either way costs it
+ * nothing. An axis in a two-hundred-pixel panel has worked its count out from
+ * the room it has and the width of a label, so one tick more than it asked for
+ * is two labels touching.
+ */
+export type ChartAxisStep = 'nearest' | 'atMost';
 /** How an axis is divided. */
 export interface ChartAxisScaleOptions {
     /**
@@ -23,10 +38,15 @@ export interface ChartAxisScaleOptions {
     /**
      * Whether to widen the domain outward to whole steps, so the axis ends on a
      * labelled tick. Turn it off when the domain is already exact — a share that
-     * must end at 100%.
+     * must end at 100%, or a window a reader dragged out for themselves.
      * @default true
      */
     nice?: boolean;
+    /**
+     * How the step is chosen. See {@link ChartAxisStep}.
+     * @default 'nearest'
+     */
+    step?: ChartAxisStep;
 }
 /**
  * The ticks an axis over `min`..`max` should carry.
@@ -55,9 +75,10 @@ export declare function chartAxisScale(min: number, max: number, options?: Chart
  * @param min - One end, in either order.
  * @param max - The other end.
  * @param count - Roughly how many ticks the domain will carry. Defaults to `5`.
+ * @param rounding - How the step is chosen. See {@link ChartAxisStep}.
  * @returns The widened domain, ascending.
  */
-export declare function chartNiceDomain(min: number, max: number, count?: number): [number, number];
+export declare function chartNiceDomain(min: number, max: number, count?: number, rounding?: ChartAxisStep): [number, number];
 /**
  * How many decimals a label needs so that every tick on one axis is written
  * the same width.

package/lib/chart/core/chartAxisScale.d.ts.map

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