GEN-3a: Uw=G alias, second spotting locus Sls (SlSl lethal), Sp×Sls Superschecke, flag/metadata token tolerance (dea/WFNZ/DP/RV/GV)

gerbil-manager-web/src/genetics/genotype.ts

@@ -64,18 +64,28 @@ export function makeGenotype(input: Record<LocusKey, AllelePair>): Genotype {
 export function wildType(): Genotype {
   const out = {} as Record<LocusKey, AllelePair>
   for (const locus of LOCUS_ORDER) {
-    // Wild-type is homozygous for the most dominant allele, EXCEPT the
-    // marker loci Sp/Re whose wild form is the recessive (unmarked) allele.
+    // Wild-type is homozygous for the most dominant allele, EXCEPT the marker
+    // loci Sp/Re/Sls whose wild form is the recessive (unmarked) allele.
     const alleles = LOCI[locus].alleles
-    const a = locus === 'Sp' || locus === 'Re' ? alleles[alleles.length - 1] : alleles[0]
+    const marker = locus === 'Sp' || locus === 'Re' || locus === 'Sls'
+    const a = marker ? alleles[alleles.length - 1] : alleles[0]
     out[locus] = [a, a]
   }
   return out
 }
 
-/** Compact display string, e.g. "Aa CC Dd EE GG Pp spsp rere". */
+/**
+ * Compact display string, e.g. "Aa CC Dd EE GG Pp spsp rere".
+ * The Sls locus is OMITTED when wild-type (sl/sl) so legacy 8-locus strings and
+ * the colour catalog stay byte-identical; it only appears for WP/Sls carriers
+ * (e.g. "… spsp rere Slsl"). Round-trips: a missing Sls re-parses to sl/sl.
+ */
 export function toDisplayString(g: Genotype): string {
-  return LOCUS_ORDER.map((locus) => g[locus][0] + g[locus][1]).join(' ')
+  return LOCUS_ORDER.filter(
+    (locus) => locus !== 'Sls' || !(g.Sls[0] === 'sl' && g.Sls[1] === 'sl'),
+  )
+    .map((locus) => g[locus][0] + g[locus][1])
+    .join(' ')
 }
 
 /** Stable JSON-storable object (already the in-memory shape; returned as a copy). */
@@ -114,14 +124,72 @@ function splitToken(token: string): [string, string] {
 }
 
 /**
- * Parse a display string ("Aa CC Dd EE GG Pp Spsp rere") back into a Genotype.
- * Tokens may be given in any order; each token must belong to a distinct locus.
+ * GEN-3a: tokens that are NOT genotype loci — health/provenance metadata that may
+ * appear in a herd-book genotype string. Stripped on parse (see extractGenotypeFlags).
+ *  - dea/Dea/taub = deafness flag (after spsp); DP/DarkPatch = non-Mendelian patch flag
+ *  - WFNZ/RV/GV = provenance/breeding-method annotations
+ */
+const FLAG_TOKENS = new Set(['DP', 'DarkPatch', 'dea', 'Dea', 'taub', 'WFNZ', 'RV', 'GV'])
+
+/**
+ * Normalize one whitespace-token to canonical allele symbols, or null if it is a
+ * non-genotype flag/metadata token (to be stripped):
+ *  - Uw/uw  -> G/g          (international Underwhite == German Grey locus)
+ *  - S(l)/s(l) -> Sl/sl     (second spotting locus notation)
+ *  - WP     -> Slsl         (WP is the visible S(l)s(l) heterozygote)
+ */
+function normalizeToken(tok: string): string | null {
+  if (FLAG_TOKENS.has(tok)) return null
+  let t = tok
+  if (t === 'WP') t = 'Slsl'
+  t = t.replace(/S\(l\)/g, 'Sl').replace(/s\(l\)/g, 'sl')
+  t = t.replace(/Uw/g, 'G').replace(/uw/g, 'g')
+  return t
+}
+
+/**
+ * Canonical normalized genotype string (flags/metadata removed, Uw/S(l)/WP
+ * resolved). Exported so the import pipeline (GEN-3b) can mirror this exactly.
+ */
+export function normalizeGenotypeString(input: string): string {
+  return input
+    .trim()
+    .split(/\s+/)
+    .filter(Boolean)
+    .map(normalizeToken)
+    .filter((t): t is string => t !== null)
+    .join(' ')
+}
+
+/**
+ * Extract non-Punkett flags from a raw genotype string: deafness (dea/taub =
+ * deaf, Dea = hearing) and provenance/pattern tags (WFNZ/RV/GV/DP).
+ */
+export function extractGenotypeFlags(input: string): { deaf?: boolean; tags: string[] } {
+  const tokens = input.trim().split(/\s+/).filter(Boolean)
+  let deaf: boolean | undefined
+  const tags: string[] = []
+  for (const tok of tokens) {
+    if (tok === 'dea' || tok === 'taub') deaf = true
+    else if (tok === 'Dea') deaf = false
+    else if (tok === 'DP' || tok === 'DarkPatch' || tok === 'WFNZ' || tok === 'RV' || tok === 'GV')
+      tags.push(tok)
+  }
+  return { deaf, tags }
+}
+
+/**
+ * Parse a display string ("Aa CC Dd EE GG Pp Spsp rere [Slsl]") back into a
+ * Genotype. Tokens may be in any order; each must belong to a distinct locus.
+ * Uw/S(l)/WP are normalized and flag/metadata tokens (dea, WFNZ, …) are stripped.
  * Missing loci default to wild-type.
  */
 export function fromDisplayString(input: string): Genotype {
   const tokens = input.trim().split(/\s+/).filter(Boolean)
   const acc = {} as Record<LocusKey, AllelePair>
-  for (const token of tokens) {
+  for (const raw of tokens) {
+    const token = normalizeToken(raw)
+    if (token === null) continue // flag/metadata token — not a locus
     const [a, b] = splitToken(token)
     const refAllele = a === WILDCARD ? b : a
     if (refAllele === WILDCARD) {

gerbil-manager-web/src/genetics/lethality.ts

@@ -25,6 +25,7 @@ interface LethalRule {
 
 const LETHAL_RULES: readonly LethalRule[] = [
   { locus: 'Sp', allele: 'Sp', kind: 'lethal', warning: GeneticsWarningCode.ScheckeLethal },
+  { locus: 'Sls', allele: 'Sl', kind: 'lethal', warning: GeneticsWarningCode.SlsLethal },
   { locus: 'Re', allele: 'Re', kind: 'semi', warning: GeneticsWarningCode.RexSemiLethal },
 ]
 
@@ -67,14 +68,23 @@ export function applyLethality(dist: DistEntry<Genotype>[]): LethalityResult {
       ? survivors
       : survivors.map((e) => ({ value: e.value, probability: divide(e.probability, survivingMass) }))
 
-  if (lethalMass.num > 0) {
-    warnings.push({
-      code: GeneticsWarningCode.ScheckeLethal,
-      detail: {
-        youngLostFraction: toString(lethalMass),
-        youngLostPercent: Number(((lethalMass.num / lethalMass.den) * 100).toFixed(2)),
-      },
-    })
+  // One lethal warning PER lethal rule that actually removed young (so SpSp ->
+  // ScheckeLethal and S(l)S(l) -> SlsLethal are reported distinctly).
+  for (const rule of LETHAL_RULES) {
+    if (rule.kind !== 'lethal') continue
+    const mass = dist.reduce<Fraction>(
+      (acc, e) => (isHomozygous(e.value, rule.locus, rule.allele) ? add(acc, e.probability) : acc),
+      ZERO,
+    )
+    if (mass.num > 0) {
+      warnings.push({
+        code: rule.warning,
+        detail: {
+          youngLostFraction: toString(mass),
+          youngLostPercent: Number(((mass.num / mass.den) * 100).toFixed(2)),
+        },
+      })
+    }
   }
 
   // Semi-lethal: warn if any surviving genotype is homozygous for a semi-lethal allele.
@@ -95,5 +105,22 @@ export function applyLethality(dist: DistEntry<Genotype>[]): LethalityResult {
     }
   }
 
+  // Superschecke: surviving young carrying BOTH spotting markers (Sp present and
+  // S(l) present) are very-high-white and deafness-prone — info warning.
+  const superMass = distribution.reduce<Fraction>((acc, e) => {
+    const hasSp = e.value.Sp.includes('Sp')
+    const hasSl = e.value.Sls.includes('Sl')
+    return hasSp && hasSl ? add(acc, e.probability) : acc
+  }, ZERO)
+  if (superMass.num > 0) {
+    warnings.push({
+      code: GeneticsWarningCode.SuperscheckeDeaf,
+      detail: {
+        affectedFraction: toString(superMass),
+        affectedPercent: Number(((superMass.num / superMass.den) * 100).toFixed(2)),
+      },
+    })
+  }
+
   return { distribution, warnings }
 }

gerbil-manager-web/src/genetics/loci.ts

@@ -12,8 +12,12 @@
  *  - de.wikibooks.org/wiki/Die_Rennmaus/_Farbvarianten_und_Farbgenetik
  */
 
-/** Canonical locus keys, in conventional display order. */
-export const LOCUS_ORDER = ['A', 'C', 'D', 'E', 'G', 'P', 'Sp', 'Re'] as const
+/**
+ * Canonical locus keys, in conventional display order. Sls (second spotting
+ * locus) is appended LAST so legacy 8-locus genotype strings still parse — a
+ * missing Sls token defaults to wild-type sl/sl.
+ */
+export const LOCUS_ORDER = ['A', 'C', 'D', 'E', 'G', 'P', 'Sp', 'Re', 'Sls'] as const
 export type LocusKey = (typeof LOCUS_ORDER)[number]
 
 export interface LocusDef {
@@ -33,9 +37,12 @@ export interface LocusDef {
  *   E  = full extension
  *   ef = Schimmel/roan (progressive whitening)
  *   e  = Fox (suppresses eumelanin)
- * Sp/Re are dominant markers, lethal/semi-lethal when homozygous (see lethality.ts):
- *   Sp = Schecke (checkered); checkered animals are always Spsp, SpSp dies in utero.
- *   Re = Rex (curly coat); rex animals are Re-, ReRe is semi-lethal.
+ * Sp/Re/Sls are dominant markers, lethal/semi-lethal when homozygous (see lethality.ts):
+ *   Sp  = Schecke (checkered); checkered animals are always Spsp, SpSp dies in utero.
+ *   Re  = Rex (curly coat); rex animals are Re-, ReRe is semi-lethal.
+ *   Sls = second spotting locus (S(l), WP/Minimalschecke). S(l)s(l) het = the WP
+ *         phenotype; S(l)S(l) homozygous = lethal (Rumpback/megacolon). Sp + Sls
+ *         together => Superschecke (very high white, deafness-prone).
  */
 export const LOCI: Readonly<Record<LocusKey, LocusDef>> = {
   A: { key: 'A', nameDe: 'Agouti', alleles: ['A', 'a'] },
@@ -46,6 +53,7 @@ export const LOCI: Readonly<Record<LocusKey, LocusDef>> = {
   P: { key: 'P', nameDe: 'Rotaugenaufhellung (Pink-Eye)', alleles: ['P', 'p'] },
   Sp: { key: 'Sp', nameDe: 'Schecke', alleles: ['Sp', 'sp'] },
   Re: { key: 'Re', nameDe: 'Rex', alleles: ['Re', 're'] },
+  Sls: { key: 'Sls', nameDe: 'Zweite Scheckung (WP)', alleles: ['Sl', 'sl'] },
 }
 
 /** Set of all valid allele symbols, longest-first (for maximal-munch parsing). */

gerbil-manager-web/src/genetics/warnings.ts

@@ -10,6 +10,10 @@ export const GeneticsWarningCode = {
   ScheckeLethal: 'SCHECKE_LETHAL',
   /** Rex × Rex: ReRe is semi-lethal; reduced viability of homozygous young. */
   RexSemiLethal: 'REX_SEMI_LETHAL',
+  /** WP × WP: S(l)S(l) is prenatal-lethal (Rumpback/megacolon); fewer live young. */
+  SlsLethal: 'SLS_LETHAL',
+  /** Sp + Sls together -> Superschecke: very high white, deafness-prone (info). */
+  SuperscheckeDeaf: 'SUPERSCHECKE_DEAF',
 } as const
 
 export type GeneticsWarningCode =