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"""Tests for the unified mode interface (default/fast/precise)."""
import os
import tempfile
import pytest
import kalign
TEST_SEQUENCES = ["ATCGATCGATCG", "ATCGTCGATCG", "ATCGATCATCG"]
PROTEIN_SEQUENCES = [
"MKFLILLFNILCLFPVLAADNHGVSLHCTTATAIP",
"MKFLILLFNILCLFPVLAADNHGVSLHCTTATAIP",
"MKFLILLFNILCLFPVLAADNHGVSLHCTTATAIP",
]
TEST_FILE = os.path.join(os.path.dirname(__file__), "..", "data", "BB11001.tfa")
class TestModeConstants:
"""Test mode constant exports."""
def test_mode_constants_exist(self):
assert kalign.MODE_DEFAULT == "default"
assert kalign.MODE_FAST == "fast"
assert kalign.MODE_PRECISE == "precise"
class TestAlignModes:
"""Test mode parameter on align()."""
def test_default_mode_no_kwarg(self):
"""Default mode (no mode kwarg) produces alignment."""
result = kalign.align(TEST_SEQUENCES)
assert isinstance(result, list)
assert len(result) == len(TEST_SEQUENCES)
assert all(len(s) == len(result[0]) for s in result)
def test_default_mode_explicit(self):
"""mode='default' produces alignment."""
result = kalign.align(TEST_SEQUENCES, mode="default")
assert isinstance(result, list)
assert len(result) == len(TEST_SEQUENCES)
def test_fast_mode(self):
"""mode='fast' produces alignment."""
result = kalign.align(TEST_SEQUENCES, mode="fast")
assert isinstance(result, list)
assert len(result) == len(TEST_SEQUENCES)
assert all(len(s) == len(result[0]) for s in result)
def test_precise_mode(self):
"""mode='precise' produces alignment (ensemble)."""
result = kalign.align(TEST_SEQUENCES, mode="precise")
# precise uses ensemble, which returns (seqs, confidence) tuple
if isinstance(result, tuple):
seqs = result[0]
else:
seqs = result
assert len(seqs) == len(TEST_SEQUENCES)
assert all(len(s) == len(seqs[0]) for s in seqs)
def test_invalid_mode(self):
"""Invalid mode raises ValueError."""
with pytest.raises(ValueError, match="Invalid mode"):
kalign.align(TEST_SEQUENCES, mode="turbo")
def test_explicit_param_overrides_mode(self):
"""Explicit consistency=10 overrides fast mode default (consistency=0)."""
# This should not crash — fast base + explicit consistency
result = kalign.align(TEST_SEQUENCES, mode="fast", consistency=10)
assert isinstance(result, list)
assert len(result) == len(TEST_SEQUENCES)
def test_mode_case_insensitive(self):
"""Mode names are case-insensitive."""
result = kalign.align(TEST_SEQUENCES, mode="FAST")
assert isinstance(result, list)
assert len(result) == len(TEST_SEQUENCES)
@pytest.mark.skipif(not os.path.exists(TEST_FILE), reason="Test data not found")
class TestAlignFromFileModes:
"""Test mode parameter on align_from_file()."""
def test_default_mode(self):
result = kalign.align_from_file(TEST_FILE)
names, sequences = result
assert len(names) > 0
assert len(sequences) == len(names)
def test_fast_mode(self):
result = kalign.align_from_file(TEST_FILE, mode="fast")
names, sequences = result
assert len(names) > 0
def test_precise_mode(self):
result = kalign.align_from_file(TEST_FILE, mode="precise")
names, sequences = result
assert len(names) > 0
@pytest.mark.skipif(not os.path.exists(TEST_FILE), reason="Test data not found")
class TestAlignFileToFileModes:
"""Test mode parameter on align_file_to_file()."""
def test_default_mode(self):
with tempfile.NamedTemporaryFile(suffix=".fa", delete=False) as f:
out = f.name
try:
kalign.align_file_to_file(TEST_FILE, out)
assert os.path.getsize(out) > 0
finally:
os.unlink(out)
def test_fast_mode(self):
with tempfile.NamedTemporaryFile(suffix=".fa", delete=False) as f:
out = f.name
try:
kalign.align_file_to_file(TEST_FILE, out, mode="fast")
assert os.path.getsize(out) > 0
finally:
os.unlink(out)
def test_precise_mode(self):
with tempfile.NamedTemporaryFile(suffix=".fa", delete=False) as f:
out = f.name
try:
kalign.align_file_to_file(TEST_FILE, out, mode="precise")
assert os.path.getsize(out) > 0
finally:
os.unlink(out)
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