website/src/data/mockData.ts

// Mock "compute" for the HydroPD UI (Milestone 1). Model metadata is REAL
// (see data/models.ts + generated JSON); the per-peptide scores and training
// runs here are deterministic stand-ins pending Milestone 2 (backend inference).

import { parseSequences, type ParsedSequence } from '../lib/parseSequences'
import type { RealModel } from './models'

export const CONTACT_EMAIL = 'rsaqe@uwaterloo.ca'

// ---------------------------------------------------------------------------
// Sample sequences (for "load example" buttons)
// ---------------------------------------------------------------------------
export const SAMPLE_PEPTIDES = `VLPVPQK
IPP
NALKPDNR
FEEPQQPQQR
GQEIYIQQGK
VPP
SYTNGPQEIYIQQGK
AGVALSR
LLPHH
CTLNR
IYIVQGR
FESSSQQFQG
PLVHLLAQNIR
AQQLQQLVLANLAAYSQEQQ
EPQQPQQRG
FAQPQQLFPE
AADSFKHK`

// Example protein for the allergen-origin screen: Tri a 39.0101, a recognized wheat
// allergen (Triticum aestivum; WHO/IUIS, AllergenOnline). Matches the allergen index exactly.
export const SAMPLE_PROTEIN = `>Tri_a_39.0101 wheat allergen (Triticum aestivum)
MSPVVKKPEGRNTDTSDHHNQKTEWPELVGKSVEEAKKVILQDKSEAQIVVLPVGTIVTMEYRIDRVRLFVDSLDKIAQVPRVG`

// ---------------------------------------------------------------------------
// Deterministic pseudo-randomness (stable across renders)
// ---------------------------------------------------------------------------
function hashString(s: string): number {
  let h = 2166136261
  for (let i = 0; i < s.length; i++) {
    h ^= s.charCodeAt(i)
    h = Math.imul(h, 16777619)
  }
  return (h >>> 0) / 4294967295 // -> [0, 1)
}

// ---------------------------------------------------------------------------
// Mock detectability prediction (illustrative, Milestone 2 will run the .joblib)
// ---------------------------------------------------------------------------
export interface DetectabilityRow {
  peptide: string
  length: number
  score: number
  prediction: 'Detectable' | 'Not detectable'
  model: string
  // Was this peptide in the selected model's training set? Flag so a memorised
  // high-confidence call isn't mistaken for generalisation. null = held out / unknown.
  inTraining?: 'positive' | 'negative' | null
  // Known bioactivity classes for this peptide (';'-joined), merged from the
  // bioactivity screen so the prediction output carries function too. '' = none found.
  bioactivities?: string
}

const DETECT_THRESHOLD = 0.5

export function runDetectability(
  input: string,
  model: RealModel,
): DetectabilityRow[] {
  const peptides = parseSequences(input)
  return peptides.map((p: ParsedSequence) => {
    const base = hashString(p.seq + '|' + model.code)
    const lengthBias = p.seq.length >= 7 && p.seq.length <= 20 ? 0.12 : -0.08
    const hydrophobic = (p.seq.match(/[FLIVWY]/g)?.length ?? 0) / p.seq.length
    const score = Math.min(
      0.99,
      Math.max(0.01, base * 0.7 + lengthBias + hydrophobic * 0.25),
    )
    return {
      peptide: p.seq,
      length: p.seq.length,
      score: Number(score.toFixed(3)),
      prediction: score >= DETECT_THRESHOLD ? 'Detectable' : 'Not detectable',
      model: `${model.code} · ${model.species}`,
    }
  })
}

// ---------------------------------------------------------------------------
// Bioactivity / allergen screening (exact-DB match, no offline compute possible)
// ---------------------------------------------------------------------------
export interface BioactivityRow {
  peptide: string
  bioactivities: string // ';'-joined canonical activity classes ('' = no hit)
  sources: string // ';'-joined DBs the hit came from
  igeEpitope: boolean // retains a documented linear IgE epitope (Q2)
}

export interface AllergenRow {
  protein: string
  isAllergen: boolean // recognized-allergen protein match (Q1)
  allergenName: string
  organism: string
  source: string
}

// Screening is an exact match against a static database, it cannot be faked offline.
// The mocks parse the input and return empty hits; the page's offline badge makes clear
// these are not real screening calls (no fabricated bioactivity/allergen claims).
export function runBioactivityPeptides(input: string): BioactivityRow[] {
  return parseSequences(input).map((p: ParsedSequence) => ({
    peptide: p.seq,
    bioactivities: '',
    sources: '',
    igeEpitope: false,
  }))
}

export function runAllergenOrigin(input: string): AllergenRow[] {
  return parseSequences(input).map((p: ParsedSequence) => ({
    protein: p.seq.length > 60 ? p.seq.slice(0, 57) + '…' : p.seq,
    isAllergen: false,
    allergenName: '',
    organism: '',
    source: '',
  }))
}

// ---------------------------------------------------------------------------
// Mock training result (illustrative)
// ---------------------------------------------------------------------------
export interface FoldResult {
  fold: number
  rocAuc: number
  prAuc: number
  nTrain: number
  nTest: number
}

export interface TrainingResult {
  rocAuc: number
  prAuc: number
  folds: FoldResult[]
  nPositives: number
  nNegatives: number
}

export function runTraining(input: string, seed: string): TrainingResult {
  const peptides = parseSequences(input)
  const nPos = peptides.length
  const nNeg = Math.round(nPos * 1.0)
  const base = 0.72 + hashString(seed + nPos) * 0.18 // 0.72 - 0.90
  const folds: FoldResult[] = Array.from({ length: 5 }, (_, i) => {
    const jitter = (hashString(seed + 'fold' + i) - 0.5) * 0.06
    const roc = Math.min(0.97, Math.max(0.55, base + jitter))
    return {
      fold: i + 1,
      rocAuc: Number(roc.toFixed(3)),
      prAuc: Number((roc - 0.06).toFixed(3)),
      nTrain: Math.round((nPos + nNeg) * 0.8),
      nTest: Math.round((nPos + nNeg) * 0.2),
    }
  })
  const mean = folds.reduce((s, f) => s + f.rocAuc, 0) / folds.length
  return {
    rocAuc: Number(mean.toFixed(3)),
    prAuc: Number((mean - 0.06).toFixed(3)),
    folds,
    nPositives: nPos,
    nNegatives: nNeg,
  }
}

// ---------------------------------------------------------------------------
// Training-spec option sets, REAL vocabulary from the Step-4 pipeline
// ---------------------------------------------------------------------------
export const FEATURE_SET_OPTIONS = [
  { id: 'phys', label: 'Physicochemical (14 descriptors)', desc: 'PeptideRanker descriptors' },
  { id: 'pepbert', label: 'PepBERT', desc: 'PepBERT-large-UniParc embeddings' },
  { id: 'esm2', label: 'ESM2-t12-35M', desc: 'ESM2 protein language model' },
  { id: 'pep_phys', label: 'PepBERT ⊕ physicochemical', desc: 'Embedding + descriptors' },
  { id: 'esm2_phys', label: 'ESM2 ⊕ physicochemical', desc: 'Top-ranked feature set (default)' },
  { id: 'pfly', label: 'Pfly (sequence-only)', desc: 'dlomix DetectabilityModel, reads the sequence directly' },
]

export const CLASSIFIER_OPTIONS = [
  { id: 'xgb', label: 'XGBoost', desc: 'Gradient-boosted trees (most consistent winner)' },
  { id: 'rf', label: 'Random forest', desc: 'Bagged trees, balanced' },
  { id: 'mlp', label: 'Neural net (MLP)', desc: 'MLP over features, standardized' },
  { id: 'pfly', label: 'Pfly (fine-tuned)', desc: 'dlomix BiGRU, sequence-only (feature set ignored)' },
]

export const SPLIT_OPTIONS = [
  { id: 'protein', label: 'Group by protein', desc: 'Production default, avoids peptide leakage' },
  { id: 'cluster90', label: 'Cluster (90% id)', desc: 'MMseqs2 sequence-identity clusters' },
  { id: 'cluster50', label: 'Cluster (50% id)', desc: 'Stricter homology grouping' },
  { id: 'peptide', label: 'By peptide', desc: 'Leakage baseline (inflates AUROC)' },
]

export interface TrainingConfig {
  featureSet: string
  classifier: string
  split: string
  folds: number
  balance: string
}

export const DEFAULT_TRAINING_CONFIG: TrainingConfig = {
  featureSet: 'esm2_phys',
  classifier: 'xgb',
  split: 'protein',
  folds: 5,
  balance: '1:1',
}