react-cheminfo 0.47.0 → 0.48.0

package/lib/taxonomy/core/organismName.js

@@ -0,0 +1,188 @@
+/**
+ * Which parts of an organism's name nomenclature sets in italics.
+ *
+ * The genus, the species epithet and an infraspecific epithet are italic; the
+ * authority, a strain, `sp.`, a cultivar and the words announcing a rank
+ * (`subsp.`, `var.`, `f.`) are upright. Names arrive the way their source wrote
+ * them — "Catharanthus roseus (L.) G. Don", "Streptomyces sp. CHQ-64",
+ * "Isodon Shikokiana Var. Occidentalis" — so this reads them by their shape,
+ * and a name it cannot place is left upright rather than guessed at.
+ */
+import { BEFORE_EPITHET, CANDIDATUS, HYBRID, NOT_EPITHET, NOT_GENUS, RANK_MARKERS, UNNAMED, } from "./organismWords.js";
+const CONSORTIUM = /(?<plus>\s+\+\s+)/;
+const VIRUS = /\b(?:virus|viruses|phage|bacteriophage|viroid|satellite)\b/i;
+const SEPARATOR = /^[\s_]+$/;
+const TRAILING_MARK = /^(?<word>.+?)(?<mark>[,;]+)$/;
+const GENUS = /^[A-Z][a-z]+$/;
+const ABBREVIATED_GENUS = /^[A-Z]\.$/;
+// A family, a subfamily or a tribe written where a genus would stand:
+// -aceae, -oideae and -eae in botany, -idae in zoology. No genus ends so.
+const FAMILY = /(?:eae|idae)$/;
+const BRACKETED_GENUS = /^\[(?<genus>[A-Z][a-z]+)\]$/;
+const JOINED_MARKER = /^(?<marker>subsp\.|ssp\.|var\.|f\.|pv\.)(?<epithet>[a-z][a-z-]+)$/i;
+const EPITHET = /^[a-zß-öø-ÿ][a-zß-öø-ÿ-]+$/;
+const CAPITALISED_EPITHET = /^[A-Z][a-zß-öø-ÿ-]+$/;
+const STARTS_WITH_LETTER = /^\p{L}/u;
+const STARTS_UPPERCASE = /^\p{Lu}/u;
+/**
+ * The runs of an organism's name, each set upright or in italics.
+ *
+ * Joined together, the runs give back the name exactly. A consortium written
+ * `A + B` is read as two names; a virus, and anything that does not open with
+ * a genus, is one upright run.
+ * @param name - The name, as its source writes it.
+ * @returns The runs, consecutive runs never set the same way.
+ */
+export function splitOrganismName(name) {
+    if (name === '')
+        return [];
+    if (VIRUS.test(name))
+        return [{ text: name, italic: false }];
+    const pieces = [];
+    for (const segment of name.split(CONSORTIUM)) {
+        if (CONSORTIUM.test(segment)) {
+            pieces.push({ text: segment, word: false, italic: false });
+        }
+        else {
+            pieces.push(...styledPieces(segment));
+        }
+    }
+    return mergedRuns(pieces);
+}
+function styledPieces(text) {
+    const pieces = tokenize(text);
+    const words = pieces.filter((piece) => piece.word);
+    styleWords(words);
+    for (let index = 0; index < pieces.length; index++) {
+        const piece = pieces[index];
+        if (piece.word)
+            continue;
+        piece.italic =
+            pieces[index - 1]?.italic === true && pieces[index + 1]?.italic === true;
+    }
+    return pieces;
+}
+function tokenize(text) {
+    const pieces = [];
+    for (const chunk of text.split(/(?<gap>[\s_]+)/)) {
+        if (chunk === '')
+            continue;
+        if (SEPARATOR.test(chunk)) {
+            pieces.push({ text: chunk, word: false, italic: false });
+            continue;
+        }
+        // A comma or a semicolon closing a word is punctuation, not part of it.
+        const { word: bare = chunk, mark } = TRAILING_MARK.exec(chunk)?.groups ?? {};
+        const joined = JOINED_MARKER.exec(bare)?.groups;
+        const bracketed = BRACKETED_GENUS.exec(bare)?.groups;
+        const words = joined !== undefined
+            ? [joined.marker, joined.epithet]
+            : bracketed !== undefined
+                ? ['[', bracketed.genus, ']']
+                : [bare];
+        for (const word of words) {
+            pieces.push({ text: word ?? '', word: true, italic: false });
+        }
+        if (mark !== undefined) {
+            pieces.push({ text: mark, word: false, italic: false });
+        }
+    }
+    return pieces;
+}
+function styleWords(words) {
+    let index = words[0]?.text === '×' ? 1 : 0;
+    const first = words[index];
+    if (first === undefined)
+        return;
+    if (CANDIDATUS.has(first.text)) {
+        first.italic = true;
+        return;
+    }
+    let genus;
+    if (first.text === '[' && words[index + 2]?.text === ']') {
+        genus = words[index + 1];
+        index += 3;
+    }
+    else if (GENUS.test(first.text) || ABBREVIATED_GENUS.test(first.text)) {
+        genus = first;
+        index += 1;
+    }
+    if (genus === undefined ||
+        NOT_GENUS.has(genus.text.toLowerCase()) ||
+        FAMILY.test(genus.text)) {
+        return;
+    }
+    genus.italic = true;
+    const titleCase = isTitleCase(words);
+    const next = words[index]?.text;
+    if (next === undefined || UNNAMED.has(next.toLowerCase()))
+        return;
+    let announced = false;
+    if (HYBRID.has(next) || BEFORE_EPITHET.has(next.toLowerCase())) {
+        index += 1;
+        announced = true;
+    }
+    if (isEpithet(words[index], titleCase || announced)) {
+        words[index].italic = true;
+        index += 1;
+        // A zoological trinomial names its subspecies with no word announcing it.
+        if (isEpithet(words[index], false)) {
+            words[index].italic = true;
+            index += 1;
+        }
+    }
+    for (; index < words.length; index++) {
+        const word = words[index].text;
+        const marks = RANK_MARKERS.has(word.toLowerCase()) || HYBRID.has(word);
+        if (marks && isEpithet(words[index + 1], true)) {
+            words[index + 1].italic = true;
+            index += 1;
+        }
+    }
+}
+function isEpithet(word, capitalised) {
+    if (word === undefined)
+        return false;
+    const lower = word.text.toLowerCase();
+    if (NOT_EPITHET.has(lower) ||
+        UNNAMED.has(lower) ||
+        RANK_MARKERS.has(lower) ||
+        HYBRID.has(word.text)) {
+        return false;
+    }
+    return (EPITHET.test(word.text) ||
+        (capitalised && CAPITALISED_EPITHET.test(word.text)));
+}
+// A source that capitalises every word ("Agave Americana") still means a
+// binomial; the words announcing a rank are left out of the count.
+function isTitleCase(words) {
+    let lettered = 0;
+    for (const { text } of words) {
+        const lower = text.toLowerCase();
+        if (RANK_MARKERS.has(lower) || UNNAMED.has(lower) || HYBRID.has(text)) {
+            continue;
+        }
+        if (!STARTS_WITH_LETTER.test(text))
+            continue;
+        if (!STARTS_UPPERCASE.test(text))
+            return false;
+        lettered += 1;
+    }
+    return lettered >= 2;
+}
+function mergedRuns(pieces) {
+    const runs = [];
+    for (const piece of pieces) {
+        if (piece.text === '')
+            continue;
+        const last = runs.at(-1);
+        if (last?.italic === piece.italic) {
+            last.text += piece.text;
+        }
+        else {
+            runs.push({ text: piece.text, italic: piece.italic });
+        }
+    }
+    return runs;
+}
+//# sourceMappingURL=organismName.js.map

package/lib/taxonomy/core/organismName.js.map

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package/lib/taxonomy/core/organismWords.d.ts

@@ -0,0 +1,20 @@
+/**
+ * The words an organism's name is read by: the signs and abbreviations that
+ * announce a rank or qualify a name, and the ordinary words a source writes
+ * where a genus or an epithet would stand.
+ */
+/** The hybrid sign, and the letters written for it. */
+export declare const HYBRID: Set<string>;
+/** The word that opens a provisional bacterial name; it alone is italic. */
+export declare const CANDIDATUS: Set<string>;
+/** Qualifiers set before the epithet they qualify, in lower case. */
+export declare const BEFORE_EPITHET: Set<string>;
+/** An unnamed species of the genus, in lower case. */
+export declare const UNNAMED: Set<string>;
+/** The abbreviations announcing a lower-rank epithet, in lower case. */
+export declare const RANK_MARKERS: Set<string>;
+/** Words that open a description rather than a binomial, in lower case. */
+export declare const NOT_GENUS: Set<string>;
+/** Lower-case words that follow a binomial without being an epithet. */
+export declare const NOT_EPITHET: Set<string>;
+//# sourceMappingURL=organismWords.d.ts.map

package/lib/taxonomy/core/organismWords.d.ts.map

@@ -0,0 +1 @@
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package/lib/taxonomy/core/organismWords.js

@@ -0,0 +1,86 @@
+/**
+ * The words an organism's name is read by: the signs and abbreviations that
+ * announce a rank or qualify a name, and the ordinary words a source writes
+ * where a genus or an epithet would stand.
+ */
+/** The hybrid sign, and the letters written for it. */
+export const HYBRID = new Set(['×', 'x', 'X']);
+/** The word that opens a provisional bacterial name; it alone is italic. */
+export const CANDIDATUS = new Set(['Candidatus', 'Ca.']);
+/** Qualifiers set before the epithet they qualify, in lower case. */
+export const BEFORE_EPITHET = new Set(['cf.', 'cf', 'aff.', 'aff', 'nr.']);
+/** An unnamed species of the genus, in lower case. */
+export const UNNAMED = new Set(['sp.', 'sp', 'spp.', 'spp']);
+/** The abbreviations announcing a lower-rank epithet, in lower case. */
+export const RANK_MARKERS = new Set([
+    'subsp.',
+    'ssp.',
+    'nothosubsp.',
+    'var.',
+    'nothovar.',
+    'subvar.',
+    'f.',
+    'fo.',
+    'forma',
+    'subf.',
+    'pv.',
+    'subgen.',
+    'sect.',
+    'subsect.',
+    'ser.',
+    'subser.',
+]);
+/** Words that open a description rather than a binomial, in lower case. */
+export const NOT_GENUS = new Set([
+    'unknown',
+    'unidentified',
+    'uncultured',
+    'unclassified',
+    'environmental',
+    'fungal',
+    'bacterial',
+    'marine',
+    'endophytic',
+    'mixed',
+    'fungus',
+    'bacterium',
+    'endophyte',
+    'strain',
+    'isolate',
+    'plant',
+    'soil',
+    'sponge',
+]);
+/** Lower-case words that follow a binomial without being an epithet. */
+export const NOT_EPITHET = new Set([
+    'strain',
+    'isolate',
+    'symbiont',
+    'endophyte',
+    'clone',
+    'group',
+    'complex',
+    'culture',
+    'cultivar',
+    'serovar',
+    'biovar',
+    'pathovar',
+    'species',
+    'incertae',
+    'sedis',
+    'and',
+    'et',
+    'ex',
+    'in',
+    'non',
+    'sensu',
+    'auct',
+    'de',
+    'du',
+    'la',
+    'le',
+    'van',
+    'von',
+    'der',
+]);
+//# sourceMappingURL=organismWords.js.map

package/lib/taxonomy/core/organismWords.js.map

@@ -0,0 +1 @@
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package/lib/taxonomy/core/ranks.d.ts

@@ -0,0 +1,51 @@
+/**
+ * The ranks of the NCBI Taxonomy, from the top of the tree down.
+ *
+ * NCBI also files taxa under ranks that are not steps of a hierarchy — `no
+ * rank`, `clade`, the two roots — and those are deliberately absent here: a
+ * clade can sit anywhere, so it has no place in an order.
+ */
+/**
+ * Every rank NCBI places in its hierarchy, from the top down.
+ *
+ * `realm` heads the viruses and `domain` the cellular organisms, the name NCBI
+ * gave in 2025 to what it called `superkingdom` before; all three stand at the
+ * top, so a lineage read from an older dump sorts the same way.
+ */
+export declare const TAXON_RANKS: readonly ["realm", "domain", "superkingdom", "kingdom", "subkingdom", "superphylum", "phylum", "subphylum", "superclass", "class", "subclass", "infraclass", "cohort", "subcohort", "superorder", "order", "suborder", "infraorder", "parvorder", "superfamily", "family", "subfamily", "tribe", "subtribe", "genus", "subgenus", "section", "subsection", "series", "subseries", "species group", "species subgroup", "species", "forma specialis", "subspecies", "varietas", "subvariety", "forma", "pathogroup", "serogroup", "serotype", "biotype", "genotype", "morph", "strain", "isolate"];
+/** A rank of the NCBI hierarchy. */
+export type TaxonRank = (typeof TAXON_RANKS)[number];
+/**
+ * The ranks a lineage is summarised by: the eight a textbook names, with the
+ * three names the top of the tree goes by.
+ */
+export declare const PRINCIPAL_RANKS: readonly ["realm", "domain", "superkingdom", "kingdom", "phylum", "class", "order", "family", "genus", "species"];
+/**
+ * Where a rank stands in the hierarchy.
+ * @param rank - The rank, as NCBI writes it.
+ * @returns Its position from the top, 0 for `realm`, or `undefined` for a
+ * rank that is not a step of the hierarchy (`no rank`, `clade`).
+ */
+export declare function rankOrder(rank: string): number | undefined;
+/**
+ * Whether a rank is one a lineage is summarised by.
+ * @param rank - The rank, as NCBI writes it.
+ * @returns Whether it is one of {@link PRINCIPAL_RANKS}.
+ */
+export declare function isPrincipalRank(rank: string): boolean;
+/**
+ * Whether a rank is the genus or one under it — the ranks whose names
+ * nomenclature sets in italics.
+ * @param rank - The rank, as NCBI writes it.
+ * @returns `false` for a rank above the genus and for one with no place in the
+ * hierarchy.
+ */
+export declare function isGenusOrBelow(rank: string): boolean;
+/**
+ * Whether a rank stands above the genus, so its name is set upright.
+ * @param rank - The rank, as NCBI writes it.
+ * @returns `false` for the genus and below, and for a rank with no place in
+ * the hierarchy.
+ */
+export declare function isAboveGenus(rank: string): boolean;
+//# sourceMappingURL=ranks.d.ts.map

package/lib/taxonomy/core/ranks.d.ts.map

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package/lib/taxonomy/core/ranks.js

@@ -0,0 +1,123 @@
+/**
+ * The ranks of the NCBI Taxonomy, from the top of the tree down.
+ *
+ * NCBI also files taxa under ranks that are not steps of a hierarchy — `no
+ * rank`, `clade`, the two roots — and those are deliberately absent here: a
+ * clade can sit anywhere, so it has no place in an order.
+ */
+/**
+ * Every rank NCBI places in its hierarchy, from the top down.
+ *
+ * `realm` heads the viruses and `domain` the cellular organisms, the name NCBI
+ * gave in 2025 to what it called `superkingdom` before; all three stand at the
+ * top, so a lineage read from an older dump sorts the same way.
+ */
+export const TAXON_RANKS = [
+    'realm',
+    'domain',
+    'superkingdom',
+    'kingdom',
+    'subkingdom',
+    'superphylum',
+    'phylum',
+    'subphylum',
+    'superclass',
+    'class',
+    'subclass',
+    'infraclass',
+    'cohort',
+    'subcohort',
+    'superorder',
+    'order',
+    'suborder',
+    'infraorder',
+    'parvorder',
+    'superfamily',
+    'family',
+    'subfamily',
+    'tribe',
+    'subtribe',
+    'genus',
+    'subgenus',
+    'section',
+    'subsection',
+    'series',
+    'subseries',
+    'species group',
+    'species subgroup',
+    'species',
+    'forma specialis',
+    'subspecies',
+    'varietas',
+    'subvariety',
+    'forma',
+    'pathogroup',
+    'serogroup',
+    'serotype',
+    'biotype',
+    'genotype',
+    'morph',
+    'strain',
+    'isolate',
+];
+/**
+ * The ranks a lineage is summarised by: the eight a textbook names, with the
+ * three names the top of the tree goes by.
+ */
+export const PRINCIPAL_RANKS = [
+    'realm',
+    'domain',
+    'superkingdom',
+    'kingdom',
+    'phylum',
+    'class',
+    'order',
+    'family',
+    'genus',
+    'species',
+];
+const ORDER = new Map();
+for (let index = 0; index < TAXON_RANKS.length; index++) {
+    ORDER.set(TAXON_RANKS[index], index);
+}
+const PRINCIPAL = new Set(PRINCIPAL_RANKS);
+const GENUS = ORDER.get('genus') ?? 0;
+/**
+ * Where a rank stands in the hierarchy.
+ * @param rank - The rank, as NCBI writes it.
+ * @returns Its position from the top, 0 for `realm`, or `undefined` for a
+ * rank that is not a step of the hierarchy (`no rank`, `clade`).
+ */
+export function rankOrder(rank) {
+    return ORDER.get(rank);
+}
+/**
+ * Whether a rank is one a lineage is summarised by.
+ * @param rank - The rank, as NCBI writes it.
+ * @returns Whether it is one of {@link PRINCIPAL_RANKS}.
+ */
+export function isPrincipalRank(rank) {
+    return PRINCIPAL.has(rank);
+}
+/**
+ * Whether a rank is the genus or one under it — the ranks whose names
+ * nomenclature sets in italics.
+ * @param rank - The rank, as NCBI writes it.
+ * @returns `false` for a rank above the genus and for one with no place in the
+ * hierarchy.
+ */
+export function isGenusOrBelow(rank) {
+    const order = ORDER.get(rank);
+    return order !== undefined && order >= GENUS;
+}
+/**
+ * Whether a rank stands above the genus, so its name is set upright.
+ * @param rank - The rank, as NCBI writes it.
+ * @returns `false` for the genus and below, and for a rank with no place in
+ * the hierarchy.
+ */
+export function isAboveGenus(rank) {
+    const order = ORDER.get(rank);
+    return order !== undefined && order < GENUS;
+}
+//# sourceMappingURL=ranks.js.map

package/lib/taxonomy/core/ranks.js.map

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package/lib/taxonomy/ui/OrganismName.d.ts

@@ -0,0 +1,28 @@
+import type { ReactElement } from 'react';
+/** What an {@link OrganismName} needs. */
+export interface OrganismNameProps {
+    /** The name, as its source writes it. */
+    name: string;
+    /**
+     * The rank of the taxon the name belongs to. A name ranked above the genus
+     * (a family, an order) is set upright whatever its shape.
+     * @default undefined — the name is read by its shape alone
+     */
+    rank?: string;
+    /**
+     * Class names added to the root element.
+     * @default undefined
+     */
+    className?: string;
+}
+/**
+ * An organism's name, with the genus and the epithets in italics and the
+ * authority, the strain and `sp.` upright, as nomenclature sets them.
+ *
+ * The italics are `<i>`, the element HTML names for a taxonomic designation,
+ * and the name keeps every character its source gave it.
+ * @param props - See {@link OrganismNameProps}.
+ * @returns The name.
+ */
+export declare function OrganismName(props: OrganismNameProps): ReactElement;
+//# sourceMappingURL=OrganismName.d.ts.map

package/lib/taxonomy/ui/OrganismName.d.ts.map

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package/lib/taxonomy/ui/OrganismName.js

@@ -0,0 +1,28 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { Fragment } from 'react';
+import { joinClassNames } from "../../shared/ui/joinClassNames.js";
+import { splitOrganismName } from "../core/organismName.js";
+import { isAboveGenus } from "../core/ranks.js";
+/**
+ * An organism's name, with the genus and the epithets in italics and the
+ * authority, the strain and `sp.` upright, as nomenclature sets them.
+ *
+ * The italics are `<i>`, the element HTML names for a taxonomic designation,
+ * and the name keeps every character its source gave it.
+ * @param props - See {@link OrganismNameProps}.
+ * @returns The name.
+ */
+export function OrganismName(props) {
+    const { name, rank, className } = props;
+    const parts = rank !== undefined && isAboveGenus(rank)
+        ? [{ text: name, italic: false }]
+        : splitOrganismName(name);
+    const children = [];
+    let offset = 0;
+    for (const part of parts) {
+        children.push(part.italic ? (_jsx("i", { children: part.text }, offset)) : (_jsx(Fragment, { children: part.text }, offset)));
+        offset += part.text.length;
+    }
+    return (_jsx("span", { className: joinClassNames('organism-name', className), children: children }));
+}
+//# sourceMappingURL=OrganismName.js.map

package/lib/taxonomy/ui/OrganismName.js.map

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package/lib/taxonomy/ui/TaxonLineage.d.ts

@@ -0,0 +1,67 @@
+import type { ReactElement } from 'react';
+import type { Taxon, TaxonLineage as Lineage } from '../core/lineage.ts';
+/** What a {@link TaxonLineage} needs. */
+export interface TaxonLineageProps {
+    /** The lineage, from the top of the tree down to the taxon it leads to. */
+    lineage: Lineage;
+    /**
+     * Whether only the principal ranks are shown — domain, kingdom, phylum,
+     * class, order, family, genus, species — with the last taxon kept whatever
+     * its rank. Off, every taxon is shown, the clades included.
+     * @default true
+     */
+    principal?: boolean;
+    /**
+     * The address of a taxon's page on the site. A taxon it answers `undefined`
+     * for is written as plain text, and so is every taxon without it.
+     * @default undefined
+     */
+    taxonHref?: (taxon: Taxon) => string | undefined;
+    /**
+     * What the site does when a taxon's link is followed with a plain click —
+     * move to its page without a reload. A modified click is left to the
+     * browser, so a taxon still opens in a tab of its own.
+     * @default undefined
+     */
+    onTaxonSelect?: (taxon: Taxon) => void;
+    /**
+     * Whether each taxon carries its rank as a small label over its name.
+     * Without it the rank is the taxon's tooltip, and is read to a screen reader
+     * after the name.
+     * @default false
+     */
+    showRanks?: boolean;
+    /**
+     * Whether a link to the last taxon's page in the NCBI Taxonomy Browser
+     * follows the lineage, when that taxon has an id.
+     * @default false
+     */
+    ncbiLink?: boolean;
+    /**
+     * Whether the last taxon is the page being read: it is then marked as the
+     * current page and is never a link.
+     * @default false
+     */
+    current?: boolean;
+    /**
+     * What names the breadcrumb to a screen reader.
+     * @default the catalog's "Lineage"
+     */
+    label?: string;
+    /**
+     * Class names added to the root element.
+     * @default undefined
+     */
+    className?: string;
+}
+/**
+ * A lineage as a breadcrumb: the taxa from the top of the tree down, each
+ * named with its rank, the last one emphasised.
+ *
+ * The names under a genus are set in italics as nomenclature sets them, by
+ * {@link OrganismName}; the ranks are the chrome's words, translated with it.
+ * @param props - See {@link TaxonLineageProps}.
+ * @returns The breadcrumb, or nothing for an empty lineage.
+ */
+export declare function TaxonLineage(props: TaxonLineageProps): ReactElement | null;
+//# sourceMappingURL=TaxonLineage.d.ts.map

package/lib/taxonomy/ui/TaxonLineage.d.ts.map

@@ -0,0 +1 @@
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