"""Exon-aware annotation — alignment + exon mapping + NMD logic.

NO NETWORK. We never call Ensembl: a GeneStructure is built by hand and
the pure mapping functions are exercised directly.
"""
import random

import pytest

from dee.core.exon import (
    Exon,
    GeneStructure,
    annotate_guides_with_exons,
    _align_input_to_cds,
    _exon_at_cds_position,
)

# A deterministic, NON-repeating 300-nt CDS so 40-mer seeds align
# unambiguously (a repeating sequence would make find() return the
# wrong offset). Seed the RNG ONCE — instantiating Random(42) per
# iteration would re-seed every draw and yield a constant base.
_RNG = random.Random(42)
CDS = "".join(_RNG.choice("ACGT") for _ in range(300))

GENE = GeneStructure(
    organism="human",
    gene_symbol="TESTG",
    transcript_id="ENST00000TEST",
    strand=1,
    cds_sequence=CDS,
    exons=[
        Exon(number=1, chrom_start=1000, chrom_end=1099, cds_start=0, cds_end=100),
        Exon(number=2, chrom_start=2000, chrom_end=2099, cds_start=100, cds_end=200),
        Exon(number=3, chrom_start=3000, chrom_end=3099, cds_start=200, cds_end=300),
    ],
    last_junction_cds_pos=200,
)


def test_align_exact_and_offset():
    assert _align_input_to_cds(CDS, CDS) == 0
    assert _align_input_to_cds(CDS[30:], CDS) == 30


def test_align_returns_none_for_short_or_unmatched():
    assert _align_input_to_cds("ACGT", CDS) is None          # < 30 nt
    assert _align_input_to_cds("", CDS) is None
    assert _align_input_to_cds("Z" * 50, CDS) is None        # nothing valid


def test_exon_at_cds_position():
    assert _exon_at_cds_position(GENE, 50).number == 1
    assert _exon_at_cds_position(GENE, 150).number == 2
    assert _exon_at_cds_position(GENE, 250).number == 3
    assert _exon_at_cds_position(GENE, 350) is None          # past CDS end


def _annotate_single(cut):
    return annotate_guides_with_exons(CDS, [(cut, "+", cut)], GENE)[0]


def test_annotate_maps_cut_to_exon():
    ctx = _annotate_single(50)
    assert ctx.in_cds is True
    assert ctx.exon_number == 1
    assert ctx.distance_to_splice_5p == 50      # 50 - cds_start(0)
    assert ctx.distance_to_splice_3p == 49      # cds_end(100) - 50 - 1
    assert "exon 1 of 3" in ctx.summary


def test_nmd_zone_rule():
    # PTC > 50 nt upstream of the last junction (cds pos 200) → NMD likely.
    assert _annotate_single(50).in_nmd_zone is True     # 50 < 150
    assert _annotate_single(250).in_nmd_zone is False   # last exon, escapes NMD


def test_cut_outside_cds_marked_not_in_cds():
    ctx = _annotate_single(500)                          # beyond CDS length
    assert ctx.in_cds is False
    assert ctx.exon_number == 0


def test_annotation_order_matches_input():
    cuts = [(50, "+", 50), (150, "+", 150), (250, "+", 250)]
    out = annotate_guides_with_exons(CDS, cuts, GENE)
    assert [c.exon_number for c in out] == [1, 2, 3]