382 lines
15 KiB
TypeScript
382 lines
15 KiB
TypeScript
import { describe, expect, it } from 'vitest'
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import {
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add,
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divide,
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frac,
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multiply,
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toNumber,
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toString,
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equals,
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} from '../fraction'
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import {
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fromDisplayString,
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makeGenotype,
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toDisplayString,
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toJSON,
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fromJSON,
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wildType,
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extractGenotypeFlags,
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} from '../genotype'
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import { combineLocus } from '../punnett'
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import { LOCI, type LocusKey } from '../loci'
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import {
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farbschlagFor,
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genotypeToFarbschlag,
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representativeGenotype,
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BASE_COLORS,
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CATALOG,
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CATALOG_SIZE,
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} from '../catalog'
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/** The first 18 entries are the frozen contract names (must round-trip exactly). */
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const FROZEN_COUNT = 17
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import { breed } from '../breed'
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import { GeneticsWarningCode } from '../warnings'
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describe('Fraction', () => {
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it('reduces and does exact arithmetic', () => {
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expect(toString(frac(2, 4))).toBe('1/2')
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expect(toString(add(frac(1, 4), frac(1, 4)))).toBe('1/2')
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expect(toString(multiply(frac(1, 2), frac(1, 2)))).toBe('1/4')
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expect(toString(divide(frac(1, 4), frac(3, 4)))).toBe('1/3')
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expect(equals(frac(3, 6), frac(1, 2))).toBe(true)
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})
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})
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describe('Genotype serialization', () => {
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it('round-trips display string <-> structured form', () => {
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const g = fromDisplayString('Aa CC Dd EE GG Pp Spsp rere')
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expect(toDisplayString(g)).toBe('Aa CC Dd EE GG Pp Spsp rere')
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expect(toDisplayString(fromJSON(toJSON(g)))).toBe('Aa CC Dd EE GG Pp Spsp rere')
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})
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it('parses multi-char C-series alleles via maximal munch', () => {
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const g = fromDisplayString('aa cchmch DD EE GG PP spsp rere')
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expect(g.C).toEqual(['cchm', 'ch'])
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})
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it('orders allele pairs most-dominant-first', () => {
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const g = makeGenotype({
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A: ['a', 'A'],
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C: ['ch', 'C'],
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D: ['D', 'D'],
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E: ['E', 'E'],
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G: ['G', 'G'],
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P: ['p', 'P'],
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Sp: ['sp', 'sp'],
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Re: ['re', 're'],
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Sls: ['sl', 'sl'],
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})
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expect(g.A).toEqual(['A', 'a'])
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expect(g.C).toEqual(['C', 'ch'])
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expect(g.P).toEqual(['P', 'p'])
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})
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it('wild type is AA CC DD EE GG PP spsp rere', () => {
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expect(toDisplayString(wildType())).toBe('AA CC DD EE GG PP spsp rere')
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})
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})
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describe('Punnett single locus', () => {
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it('Aa x Aa -> 1/4 AA, 1/2 Aa, 1/4 aa', () => {
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const dist = combineLocus('A', ['A', 'a'], ['A', 'a'])
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expect(toString(dist.get('AA')!.probability)).toBe('1/4')
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expect(toString(dist.get('Aa')!.probability)).toBe('1/2')
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expect(toString(dist.get('aa')!.probability)).toBe('1/4')
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})
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it('AA x aa -> all Aa', () => {
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const dist = combineLocus('A', ['A', 'A'], ['a', 'a'])
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expect(dist.size).toBe(1)
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expect(toString(dist.get('Aa')!.probability)).toBe('1')
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})
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})
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describe('Worked example from research report', () => {
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// Agouti AA CC DD EE GG PP x Platin aa CC DD EE GG pp -> all Aa Cc Dd Ee Gg Pp
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// (every locus where parents differ becomes heterozygous with prob 1)
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it('Agouti x Platin yields a single uniform heterozygous genotype', () => {
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const father = fromDisplayString('AA CC DD EE GG PP spsp rere')
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const mother = fromDisplayString('aa CC DD EE GG pp spsp rere')
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const result = breed(father, mother)
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expect(result.offspring).toHaveLength(1)
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const only = result.offspring[0]
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expect(only.genotype).toBe('Aa CC DD EE GG Pp spsp rere')
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expect(only.probability.text).toBe('1')
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expect(result.warnings).toHaveLength(0)
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})
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})
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describe('Schecke × Schecke lethality (SpSp)', () => {
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it('removes SpSp, renormalises, and warns ~25% fewer young', () => {
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// Spsp x Spsp at the Sp locus -> 1/4 SpSp (lethal), 1/2 Spsp, 1/4 spsp.
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// After removing SpSp the survivors renormalise to 2/3 Spsp : 1/3 spsp.
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const father = fromDisplayString('AA CC DD EE GG PP Spsp rere')
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const mother = fromDisplayString('AA CC DD EE GG PP Spsp rere')
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const result = breed(father, mother)
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// No surviving genotype is SpSp.
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expect(result.offspring.every((o) => !o.genotype.includes('SpSp'))).toBe(true)
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// Probabilities renormalise to sum to exactly 1.
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const sum = result.offspring.reduce((acc, o) => acc + o.probability.value, 0)
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expect(sum).toBeCloseTo(1, 10)
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// Survivors: 2/3 checkered (Spsp), 1/3 non-checkered (spsp).
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const spsp = result.offspring.find((o) => o.genotype.includes('Spsp'))!
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const homRec = result.offspring.find((o) => o.genotype.includes('spsp'))!
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expect(spsp.probability.text).toBe('2/3')
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expect(homRec.probability.text).toBe('1/3')
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// Warning emitted, carrying the 1/4 young-lost stat.
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const warn = result.warnings.find((w) => w.code === GeneticsWarningCode.ScheckeLethal)
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expect(warn).toBeDefined()
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expect(warn!.detail?.youngLostFraction).toBe('1/4')
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})
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})
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describe('Rex × Rex semi-lethality (ReRe)', () => {
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it('keeps ReRe but emits a semi-lethal warning', () => {
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const father = fromDisplayString('AA CC DD EE GG PP spsp Rere')
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const mother = fromDisplayString('AA CC DD EE GG PP spsp Rere')
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const result = breed(father, mother)
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// ReRe survives (semi-lethal, not removed).
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expect(result.offspring.some((o) => o.genotype.includes('ReRe'))).toBe(true)
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const sum = result.offspring.reduce((acc, o) => acc + o.probability.value, 0)
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expect(sum).toBeCloseTo(1, 10)
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const warn = result.warnings.find((w) => w.code === GeneticsWarningCode.RexSemiLethal)
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expect(warn).toBeDefined()
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})
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})
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describe('Farbschlag catalog', () => {
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it('names the wild type Agouti', () => {
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expect(farbschlagFor(wildType()).name).toBe('Agouti')
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})
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it('names Platin (aa CC DD EE GG pp)', () => {
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expect(farbschlagFor(fromDisplayString('aa CC DD EE GG pp spsp rere')).name).toBe('Platin')
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})
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it('names Schwarz (aa CC DD EE GG PP)', () => {
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expect(farbschlagFor(fromDisplayString('aa CC DD EE GG PP spsp rere')).name).toBe('Schwarz')
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})
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it('appends Schecke and Rex modifiers', () => {
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expect(farbschlagFor(fromDisplayString('AA CC DD EE GG PP Spsp rere')).name).toBe('Agouti Schecke')
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expect(farbschlagFor(fromDisplayString('AA CC DD EE GG PP Spsp Rere')).name).toBe(
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'Agouti Schecke Rex',
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)
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})
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it('falls back to Unbekannter Farbschlag for uncatalogued genotypes', () => {
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// E-dominant (no Fuchs/Schimmel family) + an uncatalogued cchm/dd/gg/pp combo.
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const match = farbschlagFor(fromDisplayString('aa cchmcchm dd EE gg pp spsp rere'))
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expect(match.unknown).toBe(true)
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expect(match.name).toBe('Unbekannter Farbschlag')
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})
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it('has the expected catalogue coverage (GEN-2: frozen 18 + 55 portal varieties)', () => {
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expect(CATALOG_SIZE).toBe(73)
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})
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it('frozen contract names round-trip to themselves (DB-key guard)', () => {
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// The first 18 are the frozen ColorVariety keys — their representative
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// genotype MUST resolve back to their own name, never a later variety.
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for (const entry of BASE_COLORS.slice(0, FROZEN_COUNT)) {
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expect(genotypeToFarbschlag(representativeGenotype(entry))).toBe(entry.name)
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}
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})
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it('every entry resolves to a named variety (no self-Unbekannt)', () => {
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// Each catalogued variety's representative genotype must resolve to SOME
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// named variety — never "Unbekannt". Genotype-identical synonyms (e.g.
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// "-hell") or entries that omit a locus may resolve to an earlier primary;
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// that's expected first-match behaviour, not an error.
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for (const entry of BASE_COLORS) {
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expect(farbschlagFor(representativeGenotype(entry)).unknown).toBe(false)
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}
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})
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it('has no duplicate variety names and only valid allele tokens', () => {
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const names = BASE_COLORS.map((e) => e.name)
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expect(new Set(names).size).toBe(names.length)
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for (const entry of BASE_COLORS) {
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for (const [locus, value] of Object.entries(entry.tokens)) {
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expect(LOCI[locus as LocusKey].alleles).toContain(value)
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}
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}
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})
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it('CATALOG seed view mirrors the ColorVariety table shape', () => {
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expect(CATALOG).toHaveLength(CATALOG_SIZE)
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expect(CATALOG[0]).toMatchObject({ name: 'Pink Eyed White (PEW)', sortOrder: 0 })
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// Every row has a non-empty canonical genotype display string and unique name.
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expect(new Set(CATALOG.map((c) => c.name)).size).toBe(CATALOG.length)
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expect(CATALOG.every((c) => /^[A-Za-z?]+( [A-Za-z?]+){7}$/.test(c.canonicalGenotype))).toBe(true)
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})
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it('genotypeToFarbschlag (DATA-1 denormalization contract) returns the plain name', () => {
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expect(genotypeToFarbschlag(wildType())).toBe('Agouti')
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expect(genotypeToFarbschlag(fromDisplayString('aa CC DD EE GG pp spsp rere'))).toBe('Platin')
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expect(genotypeToFarbschlag(fromDisplayString('aa cchmcchm dd EE gg pp spsp rere'))).toBe(
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'Unbekannter Farbschlag',
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)
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})
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})
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describe('Partially-unknown parents (wildcards)', () => {
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it('handles an A? parent (phenotype agouti, genotype unknown)', () => {
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// A? x aa at the A locus -> father gamete: 1/2 A, 1/4 (each of A,a) from "?"
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// = effectively 3/4 A, 1/4 a ; mother always a.
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// Offspring: 3/4 Aa, 1/4 aa.
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const father = makeGenotype({
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A: ['A', '?'],
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C: ['C', 'C'],
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D: ['D', 'D'],
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E: ['E', 'E'],
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G: ['G', 'G'],
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P: ['P', 'P'],
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Sp: ['sp', 'sp'],
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Re: ['re', 're'],
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Sls: ['sl', 'sl'],
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})
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const mother = fromDisplayString('aa CC DD EE GG PP spsp rere')
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const result = breed(father, mother)
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const agouti = result.byFarbschlag.find((f) => f.farbschlag === 'Agouti')!
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const schwarz = result.byFarbschlag.find((f) => f.farbschlag === 'Schwarz')!
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expect(agouti.probability.text).toBe('3/4')
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expect(schwarz.probability.text).toBe('1/4')
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})
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})
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describe('Probabilities are exact fractions summing to 1', () => {
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it('Aa Cc x Aa Cc -> 9 genotypes summing to 1', () => {
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const father = fromDisplayString('Aa Cch DD EE GG PP spsp rere')
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const mother = fromDisplayString('Aa Cch DD EE GG PP spsp rere')
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const result = breed(father, mother)
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const sum = result.offspring.reduce(
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(acc, o) => add(acc, o.probability.fraction),
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frac(0, 1),
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)
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expect(toNumber(sum)).toBeCloseTo(1, 10)
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})
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})
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describe('GEN-3a: Uw=G alias', () => {
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it('Uwuw parses as Gg, UwUw as GG', () => {
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expect(fromDisplayString('AA CC DD EE Uwuw PP spsp rere').G).toEqual(['G', 'g'])
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expect(fromDisplayString('AA CC DD EE UwUw PP spsp rere').G).toEqual(['G', 'G'])
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expect(fromDisplayString('AA CC DD EE uwuw PP spsp rere').G).toEqual(['g', 'g'])
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})
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it('always RENDERS G, never Uw (breeder preference)', () => {
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// Uw/uw is an input/import alias only; output must echo G/g.
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expect(toDisplayString(fromDisplayString('AA CC DD EE Uwuw PP spsp rere'))).toBe(
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'AA CC DD EE Gg PP spsp rere',
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)
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expect(toDisplayString(fromDisplayString('AA CC DD EE uwuw PP spsp rere'))).not.toContain('uw')
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})
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})
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describe('GEN-3a: second spotting locus Sls (WP)', () => {
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it('S(l)s(l) and WP both parse to the Sls heterozygote Slsl', () => {
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expect(fromDisplayString('AA CC DD EE GG PP spsp rere S(l)s(l)').Sls).toEqual(['Sl', 'sl'])
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expect(fromDisplayString('AA CC DD EE GG PP spsp rere WP').Sls).toEqual(['Sl', 'sl'])
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})
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it('toDisplayString omits wild-type Sls but shows Slsl', () => {
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expect(toDisplayString(wildType())).toBe('AA CC DD EE GG PP spsp rere')
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expect(toDisplayString(fromDisplayString('AA CC DD EE GG PP spsp rere WP'))).toBe(
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'AA CC DD EE GG PP spsp rere Slsl',
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)
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})
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it('WP × WP: S(l)S(l) is lethal — removed, renormalized, SLS_LETHAL warning', () => {
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const parent = fromDisplayString('AA CC DD EE GG PP spsp rere Slsl')
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const result = breed(parent, parent)
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expect(result.offspring.every((o) => !o.genotype.includes('SlSl'))).toBe(true)
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const sum = result.offspring.reduce((acc, o) => acc + o.probability.value, 0)
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expect(sum).toBeCloseTo(1, 10)
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// survivors 2/3 Slsl : 1/3 slsl
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const wp = result.offspring.find((o) => o.genotype.includes('Slsl'))!
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expect(wp.probability.text).toBe('2/3')
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const warn = result.warnings.find((w) => w.code === GeneticsWarningCode.SlsLethal)
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expect(warn?.detail?.youngLostFraction).toBe('1/4')
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})
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it('Sp × Sls → Superschecke deafness warning', () => {
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const father = fromDisplayString('AA CC DD EE GG PP Spsp rere')
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const mother = fromDisplayString('AA CC DD EE GG PP spsp rere Slsl')
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const result = breed(father, mother)
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expect(
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result.warnings.some((w) => w.code === GeneticsWarningCode.SuperscheckeDeaf),
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).toBe(true)
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})
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})
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describe('GEN-3a: flag/metadata tokens tolerated', () => {
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it('dea/taub/Dea/DP/WFNZ/RV/GV do not break parsing (stripped)', () => {
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const g = fromDisplayString('AA CC DD EE GG PP spsp rere dea WFNZ DP RV GV')
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expect(toDisplayString(g)).toBe('AA CC DD EE GG PP spsp rere')
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})
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it('extractGenotypeFlags reads deafness + tags', () => {
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expect(extractGenotypeFlags('AA CC DD EE GG PP spsp rere dea WFNZ').deaf).toBe(true)
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expect(extractGenotypeFlags('AA CC DD EE GG PP spsp rere Dea').deaf).toBe(false)
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expect(extractGenotypeFlags('AA CC DD EE GG PP spsp rere WFNZ RV').tags).toEqual(['WFNZ', 'RV'])
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})
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})
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describe('GEN-3a: Schimmel catalog fix (breeder C5)', () => {
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it('efef base -> Orangeschimmel (not Schwarzschimmel)', () => {
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expect(genotypeToFarbschlag(fromDisplayString('AA CC DD efef GG PP spsp rere'))).toBe(
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'Orangeschimmel',
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)
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})
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it('efef pp -> Rotaugenschimmel, efef gg -> Silberschimmel', () => {
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expect(genotypeToFarbschlag(fromDisplayString('AA CC DD efef GG pp spsp rere'))).toBe(
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'Rotaugenschimmel',
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)
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expect(genotypeToFarbschlag(fromDisplayString('AA CC DD efef gg PP spsp rere'))).toBe(
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'Silberschimmel',
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)
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})
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it('no Schwarzschimmel anywhere in the catalog', () => {
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expect(BASE_COLORS.some((e) => e.name === 'Schwarzschimmel')).toBe(false)
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})
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})
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describe("GEN-3c: unknown allele displays as '-' (stored as '?')", () => {
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it("accepts '-' input, stores '?', displays '-'", () => {
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const g = fromDisplayString('Aa C- DD EE GG Pp spsp rere')
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expect(g.C).toEqual(['C', '?']) // stored internal contract stays '?'
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expect(toDisplayString(g)).toBe('Aa C- DD EE GG Pp spsp rere') // displayed as '-'
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})
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it("'?' and '-' inputs are equivalent", () => {
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expect(toDisplayString(fromDisplayString('Aa C? DD EE GG Pp spsp rere'))).toBe(
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'Aa C- DD EE GG Pp spsp rere',
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)
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})
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})
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describe('GEN-3c: no Unbekannt when the E locus is known (family fallback)', () => {
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it('eef with unknown other loci -> Fuchsschimmel (the reported bug case)', () => {
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expect(genotypeToFarbschlag(fromDisplayString('aa C- D- eef Gg Pp spsp --'))).toBe(
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'Fuchsschimmel',
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)
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})
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it('ee -> Fuchs family, efef -> a Schimmel (never Unbekannt) even with unknowns', () => {
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expect(farbschlagFor(fromDisplayString('a- C- D- ee G- P-')).unknown).toBe(false)
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expect(farbschlagFor(fromDisplayString('A- C- D- efef G- P-')).unknown).toBe(false)
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})
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it('unknown allele no longer blocks a match (wildcard, never Unbekannt)', () => {
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// C unknown must not force Unbekannt — it resolves to SOME named variety.
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expect(farbschlagFor(fromDisplayString('aa C- DD EE GG PP spsp rere')).unknown).toBe(false)
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})
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})
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