# ############################################################################
# # Copyright (c) 2022-2026 University of Helsinki
# # Copyright (c) 2019-2022 Saint Petersburg State University
# # # All Rights Reserved
# # See file LICENSE for details.
# ############################################################################
#
# import unittest
# from unittest.mock import Mock
# from src.intron_graph import *
# from src.gene_info import GeneInfo
# from src.isoform_assignment import ReadAssignment, ReadAssignmentType, IsoformMatch, PolyAInfo
# from src.common import junctions_from_blocks
#
#
# class MockParams:
#     """Mock parameters object for testing"""
#     def __init__(self):
#         self.delta = 6
#         self.graph_clustering_distance = 10
#         self.min_novel_intron_count = 2
#         self.min_novel_isolated_intron_abs = 3
#         self.min_novel_isolated_intron_rel = 0.02
#         self.terminal_position_abs = 1
#         self.terminal_position_rel = 0.05
#         self.singleton_adjacent_cov = 100
#
#
# def create_mock_gene_info(exons_list, chr_id="chr1"):
#     """
#     Create a mock GeneInfo object with given exons.
#     exons_list: list of tuples representing exon coordinates
#     """
#     gene_info = Mock(spec=GeneInfo)
#     gene_info.chr_id = chr_id
#     gene_info.start = min(e[0] for e in exons_list)
#     gene_info.end = max(e[1] for e in exons_list)
#     gene_info.all_isoforms_introns = {}
#     gene_info.all_isoforms_exons = {"transcript1": exons_list}
#
#     # Create intron profiles
#     introns = junctions_from_blocks(exons_list)
#     gene_info.intron_profiles = Mock()
#     gene_info.intron_profiles.features = introns
#
#     return gene_info
#
#
# def create_read_assignment(read_id, exon_blocks, chr_id="chr1", strand="+",
#                           assignment_type=ReadAssignmentType.unique, polyA_found=False):
#     """
#     Create a ReadAssignment object for testing.
#     """
#     match = IsoformMatch(None, None, None)
#     match.assigned_gene = "gene1"
#     match.assigned_transcript = "transcript1"
#
#     read_assignment = ReadAssignment(read_id, assignment_type, match)
#     read_assignment.chr_id = chr_id
#     read_assignment.strand = strand
#     read_assignment.mapped_strand = strand
#     read_assignment.exons = exon_blocks
#     read_assignment.corrected_exons = exon_blocks
#     read_assignment.corrected_introns = junctions_from_blocks(exon_blocks)
#     read_assignment.genomic_region = (exon_blocks[0][0], exon_blocks[-1][1])
#     read_assignment.polyA_found = polyA_found
#     read_assignment.polya_info = PolyAInfo(-1, -1, -1, -1)
#     read_assignment.read_group = "test_group"
#     read_assignment.mapping_quality = 60
#
#     return read_assignment
#
#
# class TestIntronCollector(unittest.TestCase):
#     """Test the IntronCollector class"""
#
#     def setUp(self):
#         self.exons = [(100, 200), (300, 400), (500, 600)]
#         self.gene_info = create_mock_gene_info(self.exons)
#         self.params = MockParams()
#
#     def test_collector(self):
#         """Test IntronCollector initialization"""
#         collector = IntronCollector(self.gene_info, self.params)
#         self.assertEqual(collector.gene_info, self.gene_info)
#         self.assertEqual(collector.delta, self.params.delta)
#         self.assertIsNotNone(collector.known_introns)
#
#     def test_collect_introns_simple(self):
#         """Test collecting introns from reads matching known structure"""
#         collector = IntronCollector(self.gene_info, self.params)
#
#         # Create reads matching the gene structure
#         read1 = create_read_assignment("read1", self.exons)
#         read2 = create_read_assignment("read2", self.exons)
#
#         read_assignments = [read1, read2]
#         all_introns = collector.collect_introns(read_assignments)
#
#         # Should have collected the known introns
#         expected_introns = junctions_from_blocks(self.exons)
#         for intron in expected_introns:
#             self.assertIn(intron, all_introns)
#
#     def test_collect_novel_introns(self):
#         """Test collecting novel introns"""
#         collector = IntronCollector(self.gene_info, self.params)
#
#         # Create read with novel intron
#         novel_exons = [(100, 200), (350, 400), (500, 600)]  # Different middle exon
#         read1 = create_read_assignment("read1", novel_exons)
#         read2 = create_read_assignment("read2", novel_exons)
#         read3 = create_read_assignment("read3", novel_exons)
#
#         read_assignments = [read1, read2, read3]
#         all_introns = collector.collect_introns(read_assignments)
#
#         # Should have collected the novel intron
#         novel_introns = junctions_from_blocks(novel_exons)
#         for intron in novel_introns:
#             self.assertIn(intron, all_introns)
#
#
# class TestIntronGraph(unittest.TestCase):
#     """Test the IntronGraph class"""
#
#     def setUp(self):
#         self.exons = [(100, 200), (300, 400), (500, 600)]
#         self.gene_info = create_mock_gene_info(self.exons)
#         self.params = MockParams()
#
#     def test_initialization(self):
#         """Test IntronGraph initialization"""
#         read_assignments = []
#         graph = IntronGraph(read_assignments, self.gene_info, self.params)
#
#         self.assertEqual(graph.gene_info, self.gene_info)
#         self.assertEqual(graph.params, self.params)
#         self.assertIsNotNone(graph.intron_collector)
#
#     def test_simple_linear_graph(self):
#         """Test graph construction for simple linear transcript"""
#         # Create reads matching the gene structure
#         reads = [
#             create_read_assignment("read1", self.exons),
#             create_read_assignment("read2", self.exons),
#             create_read_assignment("read3", self.exons),
#         ]
#
#         graph = IntronGraph(reads, self.gene_info, self.params)
#         graph.construct()
#
#         # Graph should have vertices for each intron boundary
#         introns = junctions_from_blocks(self.exons)
#         self.assertGreater(len(graph.outgoing_edges), 0)
#
#     def test_graph_with_alternative_splicing(self):
#         """Test graph construction with alternative splicing"""
#         # Create reads with different exon structures
#         variant1_exons = [(100, 200), (300, 400), (500, 600)]
#         variant2_exons = [(100, 200), (350, 450), (500, 600)]  # Alternative middle exon
#
#         reads = [
#             create_read_assignment("read1", variant1_exons),
#             create_read_assignment("read2", variant1_exons),
#             create_read_assignment("read3", variant2_exons),
#             create_read_assignment("read4", variant2_exons),
#         ]
#
#         graph = IntronGraph(reads, self.gene_info, self.params)
#         graph.construct()
#
#         # Graph should have branches for alternative splicing
#         self.assertGreater(len(graph.outgoing_edges), 0)
#
#     def test_monoexonic_transcript(self):
#         """Test graph with monoexonic (single exon) transcript"""
#         mono_exons = [(100, 500)]
#         mono_gene_info = create_mock_gene_info(mono_exons)
#
#         reads = [
#             create_read_assignment("read1", mono_exons),
#             create_read_assignment("read2", mono_exons),
#         ]
#
#         graph = IntronGraph(reads, mono_gene_info, self.params)
#         graph.construct()
#
#         # Monoexonic should have minimal graph structure
#         # No introns, so graph should be simple or empty
#         self.assertIsNotNone(graph.outgoing_edges)
#
#     def test_add_edge(self):
#         """Test adding edges to the graph"""
#         reads = [create_read_assignment("read1", self.exons)]
#         graph = IntronGraph(reads, self.gene_info, self.params)
#
#         # Add an edge
#         v1 = (200, 'R')  # Right end of first exon
#         v2 = (300, 'L')  # Left end of second exon
#         graph.add_edge(v1, v2)
#
#         self.assertIn(v1, graph.outgoing_edges)
#         self.assertIn(v2, graph.outgoing_edges[v1])
#         self.assertEqual(graph.edge_weights[(v1, v2)], 1)
#
#     def test_get_outgoing_edges(self):
#         """Test retrieving outgoing edges"""
#         reads = [
#             create_read_assignment("read1", self.exons),
#             create_read_assignment("read2", self.exons),
#         ]
#
#         graph = IntronGraph(reads, self.gene_info, self.params)
#         graph.construct()
#
#         # Find a vertex with outgoing edges
#         if graph.outgoing_edges:
#             vertex = list(graph.outgoing_edges.keys())[0]
#             outgoing = graph.get_outgoing(vertex)
#             self.assertIsInstance(outgoing, list)
#
#     def test_is_isolated(self):
#         """Test checking if a vertex is isolated"""
#         reads = [create_read_assignment("read1", self.exons)]
#         graph = IntronGraph(reads, self.gene_info, self.params)
#         graph.construct()
#
#         # Create an isolated vertex
#         isolated_vertex = (9999, 'L')
#         result = graph.is_isolated(isolated_vertex)
#         # An isolated vertex has no connections
#         self.assertTrue(result or isolated_vertex not in graph.outgoing_edges)
#
#
# class TestTerminalVertexFunctions(unittest.TestCase):
#     """Test terminal vertex helper functions"""
#
#     def test_is_terminal_vertex(self):
#         """Test identifying terminal vertices"""
#         self.assertTrue(is_terminal_vertex(VERTEX_polya))
#         self.assertTrue(is_terminal_vertex(VERTEX_read_end))
#         self.assertFalse(is_terminal_vertex((100, 'L')))
#
#     def test_is_starting_vertex(self):
#         """Test identifying starting vertices"""
#         self.assertTrue(is_starting_vertex(VERTEX_polyt))
#         self.assertTrue(is_starting_vertex(VERTEX_read_start))
#         self.assertFalse(is_starting_vertex((100, 'R')))
#
#
# class TestComplexGraphScenarios(unittest.TestCase):
#     """Test complex graph construction scenarios"""
#
#     def setUp(self):
#         self.params = MockParams()
#
#     def test_multiple_isoforms(self):
#         """Test graph with multiple isoforms from same gene"""
#         # Create gene with two isoforms
#         isoform1_exons = [(100, 200), (300, 400), (500, 600), (700, 800)]
#         isoform2_exons = [(100, 200), (300, 400), (700, 800)]  # Skips middle exon
#
#         gene_info = create_mock_gene_info(isoform1_exons)
#
#         reads = [
#             create_read_assignment("read1", isoform1_exons),
#             create_read_assignment("read2", isoform1_exons),
#             create_read_assignment("read3", isoform2_exons),
#             create_read_assignment("read4", isoform2_exons),
#         ]
#
#         graph = IntronGraph(reads, gene_info, self.params)
#         graph.construct()
#
#         # Should have vertices for both isoforms
#         self.assertGreater(len(graph.outgoing_edges), 0)
#
#     def test_reads_with_polya(self):
#         """Test graph construction with polyA-containing reads"""
#         exons = [(100, 200), (300, 400), (500, 600)]
#         gene_info = create_mock_gene_info(exons)
#
#         reads = [
#             create_read_assignment("read1", exons, polyA_found=True),
#             create_read_assignment("read2", exons, polyA_found=True),
#             create_read_assignment("read3", exons, polyA_found=False),
#         ]
#
#         graph = IntronGraph(reads, gene_info, self.params)
#         graph.construct()
#
#         # PolyA reads should influence terminal positions
#         self.assertIsNotNone(graph.terminal_known_positions)
#
#     def test_partial_read_coverage(self):
#         """Test reads that don't cover full transcript"""
#         full_exons = [(100, 200), (300, 400), (500, 600), (700, 800)]
#         gene_info = create_mock_gene_info(full_exons)
#
#         # Reads covering different parts
#         reads = [
#             create_read_assignment("read1", [(100, 200), (300, 400)]),  # First half
#             create_read_assignment("read2", [(500, 600), (700, 800)]),  # Second half
#             create_read_assignment("read3", full_exons),  # Full length
#         ]
#
#         graph = IntronGraph(reads, gene_info, self.params)
#         graph.construct()
#
#         # Should handle partial coverage
#         self.assertIsNotNone(graph.outgoing_edges)
#
#     def test_noisy_introns(self):
#         """Test graph with low-coverage (noisy) introns"""
#         main_exons = [(100, 200), (300, 400), (500, 600)]
#         gene_info = create_mock_gene_info(main_exons)
#
#         # Most reads follow main pattern
#         reads = [create_read_assignment(f"read{i}", main_exons) for i in range(10)]
#
#         # One read has a noisy intron
#         noisy_exons = [(100, 200), (320, 380), (500, 600)]
#         reads.append(create_read_assignment("noisy_read", noisy_exons))
#
#         graph = IntronGraph(reads, gene_info, self.params)
#         graph.construct()
#
#         # Noisy intron should be filtered or have low weight
#         self.assertIsNotNone(graph.edge_weights)
#
#
# class TestGraphSimplification(unittest.TestCase):
#     """Test graph simplification methods"""
#
#     def setUp(self):
#         self.params = MockParams()
#         self.exons = [(100, 200), (300, 400), (500, 600)]
#         self.gene_info = create_mock_gene_info(self.exons)
#
#     def test_simplify_graph(self):
#         """Test graph simplification"""
#         reads = [create_read_assignment(f"read{i}", self.exons) for i in range(5)]
#
#         graph = IntronGraph(reads, self.gene_info, self.params)
#         graph.construct()
#         graph.simplify()
#
#         # After simplification, graph should still be valid
#         self.assertIsNotNone(graph.outgoing_edges)
#
#     def test_remove_low_coverage_edges(self):
#         """Test removal of low-coverage edges"""
#         main_exons = [(100, 200), (300, 400), (500, 600)]
#
#         # High coverage for main path
#         reads = [create_read_assignment(f"read{i}", main_exons) for i in range(20)]
#
#         # Low coverage alternative
#         alt_exons = [(100, 200), (350, 450), (500, 600)]
#         reads.append(create_read_assignment("alt_read", alt_exons))
#
#         graph = IntronGraph(reads, self.gene_info, self.params)
#         graph.construct()
#
#         # Low coverage edges may be removed during simplification
#         initial_edge_count = len(graph.edge_weights)
#         graph.simplify()
#         # Simplification may reduce edges
#         self.assertLessEqual(len(graph.edge_weights), initial_edge_count + 10)
#
#
# if __name__ == '__main__':
#     unittest.main()
