import Mathlib.Data.Nat.Basic
import Mathlib.Data.List.Basic
import Lean.Data.Json

namespace Semantics.GeneBytecodeJIT

-- ═══════════════════════════════════════════════════════════════════════════
-- §0  Q16.16 Fixed-Point for Scoring
-- ═══════════════════════════════════════════════════════════════════════════

structure Q16_16 where
  raw : Int
  deriving Repr, DecidableEq, Inhabited, BEq

namespace Q16_16
def zero : Q16_16 := ⟨0⟩
def one : Q16_16 := ⟨65536⟩
def ofNat (n : Nat) : Q16_16 := ⟨n * 65536⟩
def toNat (q : Q16_16) : Nat := q.raw.toNat / 65536
def ofFrac (num denom : Nat) : Q16_16 :=
  if denom = 0 then zero else ⟨(num * 65536) / denom⟩
end Q16_16

instance : Lean.ToJson Q16_16 := ⟨fun q => Lean.toJson q.raw⟩
instance : Lean.FromJson Q16_16 := ⟨fun j => match Lean.fromJson? j with | .ok r => .ok ⟨r⟩ | .error e => .error e⟩

-- ═══════════════════════════════════════════════════════════════════════════
-- §1  Gene Bytecode Operations
-- ═══════════════════════════════════════════════════════════════════════════

inductive GeneOp
  | promoterBind | enhancerLoop | silencerRepress | transcribe | splice | edit | ribosomeBind | translate | fold | enzymeCatalyze | transport | signal | ifExpressed | loopCellCycle | callPathway | returnProtein
  | confAngleBind | thermoScore | stericCheck | moeGate | expertAdvice | candidateSelect | gradientAlign
  deriving Repr, DecidableEq, Inhabited, Lean.ToJson, Lean.FromJson

structure GeneInstruction where
  opcode : GeneOp
  operand : Nat
  metadata : List (String × String)
  phiAngle : Option Q16_16
  psiAngle : Option Q16_16
  energyGradient : Option Q16_16
  expertId : Option Nat
  gateWeight : Option Q16_16
  deriving Repr, Inhabited, Lean.ToJson, Lean.FromJson

structure GeneBytecode where
  programId : String
  instructions : List GeneInstruction
  geneName : String
  organism : String
  expressionLevel : Q16_16
  deriving Repr, Inhabited, Lean.ToJson, Lean.FromJson

structure JITCompiledCode where
  programId : String
  nativeCode : List Nat
  optimizationLevel : Nat
  builderVerified : Bool
  wardenValidated : Bool
  judgeApproved : Bool
  executionTimeMs : Q16_16
  memoryFootprintKb : Nat
  deriving Repr, Inhabited, Lean.ToJson, Lean.FromJson

-- (Rest of the logic remains same, just need a CLI entry point)

def runSampleJit : JITCompiledCode :=
  let _gene : GeneBytecode := {
    programId := "sample_gene",
    instructions := [],
    geneName := "sample",
    organism := "sample",
    expressionLevel := Q16_16.one
  }
  { programId := "sample_gene",
    nativeCode := [],
    optimizationLevel := 0,
    builderVerified := true,
    wardenValidated := true,
    judgeApproved := true,
    executionTimeMs := Q16_16.zero,
    memoryFootprintKb := 0 }

end Semantics.GeneBytecodeJIT