"""prefilter.py — PeVe v1.1"""
from __future__ import annotations
from dataclasses import dataclass, field
from typing import Optional
from config import VEP_CONSEQUENCE_MAP, L3_SUBSTITUTION_INVALID

@dataclass
class VariantClass:
    raw_consequence: str
    all_consequences: list
    variant_class: str
    l3_substitution_valid: bool
    rna_priority: bool
    protein_priority: bool
    protein_deprioritised: bool
    transcript_conflict: bool
    out_of_scope: bool
    flags: list = field(default_factory=list)

def classify_variant(ref, alt, vep_consequence, all_vep_consequences=None):
    if all_vep_consequences is None:
        all_vep_consequences = [vep_consequence]
    cons     = vep_consequence.lower().strip()
    all_cons = [c.lower().strip() for c in all_vep_consequences]

    # MNV detection
    if len(ref) > 1 and len(alt) > 1 and len(ref) == len(alt):
        return VariantClass(cons, all_cons, "mnv", False, False, False, False, False, True,
                            ["MNV: single-variant assessment may be incomplete"])

    variant_class = VEP_CONSEQUENCE_MAP.get(cons, "unknown")
    if variant_class == "unknown":
        variant_class = _infer(ref, alt)

    mapped = {VEP_CONSEQUENCE_MAP.get(c, "unknown") for c in all_cons}
    tx_conflict = len(mapped) > 1

    l3_valid             = variant_class not in L3_SUBSTITUTION_INVALID
    rna_priority         = variant_class == "canonical_splice"
    protein_priority     = variant_class == "substitution_missense"
    protein_deprio       = variant_class == "substitution_synonymous"
    out_of_scope         = variant_class in {"utr_regulatory", "mnv", "unknown"}

    flags = []
    if variant_class == "utr_regulatory":
        flags.append("UTR/regulatory: no mechanism pathway in PeVe v1.1.")
    if variant_class in {"frameshift", "stop_gained", "start_lost"}:
        flags.append(f"{variant_class}: Layer 3 substitution metrics NOT APPLICABLE.")
    if variant_class == "in_frame_indel":
        flags.append("In-frame indel: substitution biochemistry NOT APPLICABLE.")
    if variant_class == "deep_intronic":
        flags.append("Deep intronic: RNA interpretation down-prioritised.")
    if variant_class == "substitution_synonymous":
        flags.append("Synonymous: context signal alone cannot classify pathogenic.")
    if tx_conflict:
        flags.append("Transcript conflict: consequence differs across transcripts.")
    if variant_class == "unknown":
        flags.append("Variant class unknown — outputs are exploratory only.")

    return VariantClass(cons, all_cons, variant_class, l3_valid,
                        rna_priority, protein_priority, protein_deprio,
                        tx_conflict, out_of_scope, flags)

def _infer(ref, alt):
    if len(ref) == 1 and len(alt) == 1:
        return "substitution_missense"
    diff = len(alt) - len(ref)
    if diff % 3 == 0:
        return "in_frame_indel"
    return "frameshift"