SYMBOL INDEX (8100 symbols across 109 files) FILE: c/examples/api_structure.c function main (line 11) | int FILE: c/examples/cpp_sorting_example.cpp function handle_tskit_return_code (line 10) | static void type edge_plus_time (line 20) | struct edge_plus_time { function sort_edges (line 26) | int function main (line 72) | int FILE: c/examples/error_handling.c function main (line 5) | int FILE: c/examples/haploid_wright_fisher.c function simulate (line 13) | void function main (line 78) | int FILE: c/examples/json_struct_metadata.c function load_u64_le (line 14) | static uint64_t function set_u64_le (line 29) | static void function json_struct_codec_get_components (line 45) | void function json_struct_codec_create_buffer (line 96) | void function main (line 128) | int FILE: c/examples/multichrom_wright_fisher.c function init_tables (line 15) | static void function free_tables (line 29) | static void function join_tables (line 43) | static void type chunk_work (line 65) | struct chunk_work { type chunk_work (line 76) | struct chunk_work type chunk_work (line 76) | struct chunk_work function sort_and_simplify_all (line 91) | void function simplify_tables (line 122) | void function simulate (line 178) | void function main (line 247) | int FILE: c/examples/multichrom_wright_fisher_singlethreaded.c function simulate (line 14) | void function main (line 93) | int FILE: c/examples/streaming.c function main (line 11) | int FILE: c/examples/take_ownership.c function main (line 11) | int FILE: c/examples/tree_iteration.c function main (line 12) | int FILE: c/examples/tree_traversal.c function traverse_standard (line 12) | static void function _traverse (line 37) | static void function traverse_recursive (line 52) | static void function traverse_stack (line 58) | static void function traverse_upwards (line 83) | static void function main (line 100) | int FILE: c/subprojects/kastore/kastore.c function kas_version_t (line 80) | kas_version_t function type_size (line 91) | static size_t function compare_items (line 100) | static int function kastore_get_read_io_error (line 117) | static int KAS_WARN_UNUSED function kastore_write_header (line 128) | static int KAS_WARN_UNUSED function kastore_read_header (line 153) | static int KAS_WARN_UNUSED function kastore_pack_items (line 199) | static void function kastore_write_descriptors (line 222) | static int KAS_WARN_UNUSED function kastore_read_descriptors (line 254) | static int KAS_WARN_UNUSED function kastore_write_data (line 339) | static int KAS_WARN_UNUSED function kastore_read_file (line 381) | static int KAS_WARN_UNUSED function kastore_read_item (line 434) | static int KAS_WARN_UNUSED function kastore_write_file (line 463) | static int KAS_WARN_UNUSED function kastore_read (line 486) | static int KAS_WARN_UNUSED function kastore_insert_all (line 527) | static int KAS_WARN_UNUSED function kastore_open (line 546) | int KAS_WARN_UNUSED function kastore_openf (line 609) | int KAS_WARN_UNUSED function kastore_close (line 642) | int KAS_WARN_UNUSED function kastore_find_item (line 686) | static int function kastore_contains (line 714) | int KAS_WARN_UNUSED function kastore_containss (line 727) | int KAS_WARN_UNUSED function kastore_get (line 733) | int KAS_WARN_UNUSED function kastore_gets (line 759) | int KAS_WARN_UNUSED function kastore_gets_type (line 766) | static int KAS_WARN_UNUSED function kastore_gets_int8 (line 785) | int KAS_WARN_UNUSED function kastore_gets_uint8 (line 791) | int KAS_WARN_UNUSED function kastore_gets_int16 (line 797) | int KAS_WARN_UNUSED function kastore_gets_uint16 (line 803) | int KAS_WARN_UNUSED function kastore_gets_int32 (line 810) | int KAS_WARN_UNUSED function kastore_gets_uint32 (line 816) | int KAS_WARN_UNUSED function kastore_gets_int64 (line 823) | int KAS_WARN_UNUSED function kastore_gets_uint64 (line 829) | int KAS_WARN_UNUSED function kastore_gets_float32 (line 836) | int KAS_WARN_UNUSED function kastore_gets_float64 (line 842) | int KAS_WARN_UNUSED function kastore_put_item (line 848) | static int KAS_WARN_UNUSED function kastore_bput (line 910) | static int KAS_WARN_UNUSED function kastore_put (line 932) | int KAS_WARN_UNUSED function kastore_oput (line 970) | int KAS_WARN_UNUSED function kastore_puts (line 992) | int KAS_WARN_UNUSED function kastore_puts_int8 (line 999) | int KAS_WARN_UNUSED function kastore_puts_uint8 (line 1006) | int KAS_WARN_UNUSED function kastore_puts_int16 (line 1013) | int KAS_WARN_UNUSED function kastore_puts_uint16 (line 1020) | int KAS_WARN_UNUSED function kastore_puts_int32 (line 1027) | int KAS_WARN_UNUSED function kastore_puts_uint32 (line 1034) | int KAS_WARN_UNUSED function kastore_puts_int64 (line 1041) | int KAS_WARN_UNUSED function kastore_puts_uint64 (line 1048) | int KAS_WARN_UNUSED function kastore_puts_float32 (line 1055) | int KAS_WARN_UNUSED function kastore_puts_float64 (line 1062) | int KAS_WARN_UNUSED function kastore_oputs (line 1069) | int KAS_WARN_UNUSED function kastore_oputs_int8 (line 1076) | int KAS_WARN_UNUSED function kastore_oputs_uint8 (line 1083) | int KAS_WARN_UNUSED function kastore_oputs_int16 (line 1090) | int KAS_WARN_UNUSED function kastore_oputs_uint16 (line 1097) | int KAS_WARN_UNUSED function kastore_oputs_int32 (line 1104) | int KAS_WARN_UNUSED function kastore_oputs_uint32 (line 1111) | int KAS_WARN_UNUSED function kastore_oputs_int64 (line 1118) | int KAS_WARN_UNUSED function kastore_oputs_uint64 (line 1125) | int KAS_WARN_UNUSED function kastore_oputs_float32 (line 1132) | int KAS_WARN_UNUSED function kastore_oputs_float64 (line 1139) | int KAS_WARN_UNUSED function kastore_print_state (line 1146) | void FILE: c/subprojects/kastore/kastore.h type kaitem_t (line 191) | typedef struct { type kastore_t (line 206) | typedef struct { type kas_version_t (line 221) | typedef struct { FILE: c/tests/meson-subproject/example.c function test_kas_strerror (line 33) | void function test_strerror (line 41) | void function test_load_error (line 49) | void function test_table_basics (line 59) | void function main (line 76) | int FILE: c/tests/test_convert.c function test_single_tree_newick (line 31) | static void function test_single_tree_newick_errors (line 77) | static void function main (line 118) | int FILE: c/tests/test_core.c function test_strerror (line 32) | static void function test_strerror_kastore (line 48) | static void function test_generate_uuid (line 64) | static void function test_double_round (line 86) | static void function test_blkalloc (line 287) | static void function test_unknown_time (line 340) | static void function test_malloc_zero (line 351) | static void function test_malloc_overflow (line 364) | static void function test_debug_stream (line 377) | static void function validate_avl_node (line 392) | static int function test_avl_empty (line 420) | static void function validate_avl (line 440) | static void function test_avl_sequential (line 488) | static void function test_avl_interleaved (line 498) | static void function test_avl_random (line 516) | static void function test_bit_arrays (line 530) | static void function test_meson_version (line 638) | static void function main (line 649) | int FILE: c/tests/test_file_format.c type write_table_col_t (line 28) | typedef struct { function write_table_cols (line 35) | static void function copy_store_drop_columns (line 48) | static void function test_format_data_load_errors (line 101) | static void function test_missing_optional_column_pairs (line 271) | static void function test_missing_required_column_pairs (line 312) | static void function verify_bad_offset_columns (line 356) | static void function test_bad_offset_columns (line 444) | static void function test_force_offset_64 (line 474) | static void function test_missing_indexes (line 521) | static void function test_malformed_indexes (line 558) | static void function test_missing_reference_sequence (line 639) | static void function test_bad_column_types (line 680) | static void function test_missing_required_columns (line 760) | static void function test_metadata_schemas_optional (line 806) | static void function test_load_bad_file_formats (line 848) | static void function test_load_errors (line 884) | static void function test_load_eof (line 936) | static void function test_dump_errors (line 995) | static void function test_load_node_table_errors (line 1039) | static void function test_example_round_trip (line 1127) | static void function test_multiple_round_trip (line 1186) | static void function test_copy_store_drop_columns (line 1251) | static void function test_skip_tables (line 1272) | static void function test_skip_reference_sequence (line 1342) | static void function main (line 1403) | int FILE: c/tests/test_genotypes.c function test_simplest_missing_data (line 32) | static void function test_simplest_missing_data_user_alleles (line 74) | static void function test_simplest_missing_data_mutations (line 129) | static void function test_simplest_missing_data_mutations_all_samples (line 187) | static void function test_single_tree_user_alleles (line 247) | static void function test_single_tree_char_alphabet (line 354) | static void function test_single_tree_binary_alphabet (line 446) | static void function test_single_tree_non_samples (line 504) | static void function test_isolated_internal_node (line 598) | static void function test_single_tree_errors (line 652) | static void function test_single_tree_user_alleles_errors (line 684) | static void function test_single_tree_subsample (line 732) | static void function test_single_tree_many_alleles (line 821) | static void function test_single_tree_silent_mutations (line 877) | static void function test_multiple_variant_decode (line 966) | static void function test_variant_decode_errors (line 1025) | static void function assert_variants_equal (line 1053) | static void function test_variant_copy (line 1082) | static void function test_variant_copy_long_alleles (line 1120) | static void function test_variant_copy_memory_management (line 1163) | static void function build_balanced_three_example_align (line 1202) | static void function test_alignments_basic_default (line 1219) | static void function test_alignments_reference_sequence (line 1247) | static void function test_alignments_partial_isolation (line 1274) | static void function test_alignments_return_code_truncated_interval (line 1300) | static void function test_alignments_invalid_allele_length (line 1329) | static void function test_alignments_bad_reference_length (line 1347) | static void function test_alignments_non_integer_bounds (line 1364) | static void function test_alignments_discrete_genome_required (line 1381) | static void function test_alignments_null_reference (line 1399) | static void function test_alignments_null_nodes_or_buf (line 1417) | static void function test_alignments_node_out_of_bounds (line 1440) | static void function test_alignments_isolated_as_not_missing (line 1457) | static void function test_alignments_internal_node_non_sample (line 1484) | static void function test_alignments_missing_char_collision (line 1500) | static void function test_alignments_zero_nodes_ok (line 1519) | static void function test_alignments_bad_bounds_cases (line 1531) | static void function test_alignments_order_preserved (line 1549) | static void function test_alignments_missing_char_custom (line 1571) | static void function test_alignments_embedded_null_reference (line 1592) | static void function test_alignments_growing_allele_buffer (line 1620) | static void function main (line 1662) | int FILE: c/tests/test_haplotype_matching.c function test_single_tree_missing_alleles (line 31) | static void function test_single_tree_exact_match (line 60) | static void function test_single_tree_missing_haplotype_data (line 119) | static void function test_single_tree_match_impossible (line 162) | static void function test_single_tree_errors (line 206) | static void function test_single_tree_compressed_matrix (line 270) | static void function test_single_tree_viterbi_matrix (line 340) | static void function test_multi_tree_exact_match (line 412) | static void function test_multi_tree_errors (line 479) | static void function test_caterpillar_tree_many_values (line 506) | static void function main (line 558) | int FILE: c/tests/test_minimal_cpp.cpp function test_kas_strerror (line 38) | void function test_strerror (line 47) | void function test_load_error (line 56) | void function test_table_basics (line 66) | void function cpp_sort_edges (line 87) | int function test_edge_sorting (line 146) | void function sort_edges_raises_exception (line 193) | int function sort_edges_raises_non_exception (line 200) | int function safe_sort_edges (line 207) | int function test_edge_sorting_errors (line 227) | void function main (line 265) | int FILE: c/tests/test_stats.c function multi_mutations_exist (line 33) | static bool function verify_ld (line 50) | static void function verify_genealogical_nearest_neighbours (line 191) | static void function verify_mean_descendants (line 230) | static void function verify_divergence_matrix (line 269) | static void function verify_pair_coalescence_counts (line 309) | static void function verify_pair_coalescence_quantiles (line 413) | static void function verify_pair_coalescence_rates (line 518) | static void type general_stat_error_params_t (line 635) | typedef struct { function general_stat_error (line 641) | static int function verify_window_errors (line 656) | static void function verify_summary_func_errors (line 708) | static void function verify_branch_general_stat_errors (line 755) | static void function verify_site_general_stat_errors (line 762) | static void function verify_node_general_stat_errors (line 769) | static void function verify_one_way_weighted_func_errors (line 776) | static void function verify_one_way_weighted_covariate_func_errors (line 799) | static void function verify_one_way_stat_func_errors (line 824) | static void function verify_one_way_stat_func_errors_tw (line 880) | static void function verify_two_way_stat_func_errors (line 950) | static void function verify_two_way_weighted_stat_func_errors (line 979) | static void function verify_three_way_stat_func_errors (line 1005) | static void function verify_four_way_stat_func_errors (line 1033) | static void function general_stat_identity (line 1061) | static int function verify_branch_general_stat_identity (line 1075) | static void function general_stat_sum (line 1126) | static int function verify_general_stat_dims (line 1144) | static void function verify_general_stat_windows (line 1169) | static void function verify_default_general_stat (line 1204) | static void function verify_general_stat (line 1232) | static void function verify_afs (line 1256) | static void function test_general_stat_input_errors (line 1298) | static void function test_empty_ts_ld (line 1332) | static void function test_empty_ts_mean_descendants (line 1344) | static void function test_empty_ts_genealogical_nearest_neighbours (line 1355) | static void function test_empty_ts_general_stat (line 1366) | static void function test_empty_ts_afs (line 1381) | static void function test_single_tree_ld (line 1392) | static void function test_single_tree_mean_descendants (line 1403) | static void function test_single_tree_genealogical_nearest_neighbours (line 1414) | static void function test_single_tree_general_stat (line 1425) | static void function test_single_tree_general_stat_errors (line 1440) | static void function test_single_tree_divergence_matrix (line 1453) | static void function test_single_tree_divergence_matrix_internal_samples (line 1504) | static void function test_single_tree_divergence_matrix_multi_root (line 1576) | static void function test_paper_ex_ld (line 1625) | static void function test_paper_ex_mean_descendants (line 1656) | static void function test_paper_ex_genealogical_nearest_neighbours (line 1667) | static void function test_paper_ex_general_stat (line 1678) | static void function test_paper_ex_general_stat_errors (line 1693) | static void function test_paper_ex_diversity_errors (line 1706) | static void function test_paper_ex_diversity (line 1717) | static void function test_paper_ex_trait_covariance_errors (line 1744) | static void function test_paper_ex_trait_covariance (line 1755) | static void function test_paper_ex_trait_correlation_errors (line 1786) | static void function test_paper_ex_trait_correlation (line 1797) | static void function test_paper_ex_trait_linear_model_errors (line 1820) | static void function test_paper_ex_trait_linear_model (line 1831) | static void function test_paper_ex_segregating_sites_errors (line 1861) | static void function test_paper_ex_segregating_sites (line 1872) | static void function test_paper_ex_Y1_errors (line 1899) | static void function test_paper_ex_Y1 (line 1910) | static void function test_paper_ex_divergence_errors (line 1934) | static void function test_paper_ex_divergence (line 1945) | static void function test_paper_ex_genetic_relatedness (line 1973) | static void function test_paper_ex_genetic_relatedness_errors (line 1997) | static void function test_paper_ex_genetic_relatedness_weighted (line 2012) | static void function test_paper_ex_genetic_relatedness_weighted_errors (line 2049) | static void function test_empty_genetic_relatedness_vector (line 2065) | static void function verify_genetic_relatedness_vector (line 2116) | static void function test_paper_ex_genetic_relatedness_vector (line 2170) | static void function test_paper_ex_genetic_relatedness_vector_errors (line 2190) | static void function test_paper_ex_genetic_relatedness_vector_node_errors (line 2259) | static void function test_paper_ex_Y2_errors (line 2304) | static void function test_paper_ex_Y2 (line 2315) | static void function test_paper_ex_f2_errors (line 2342) | static void function test_paper_ex_f2 (line 2353) | static void function test_paper_ex_Y3_errors (line 2388) | static void function test_paper_ex_Y3 (line 2399) | static void function test_paper_ex_f3_errors (line 2419) | static void function test_paper_ex_f3 (line 2430) | static void function test_paper_ex_f4_errors (line 2457) | static void function test_paper_ex_f4 (line 2468) | static void function test_paper_ex_afs_errors (line 2487) | static void function test_paper_ex_afs (line 2517) | static void function test_paper_ex_divergence_matrix (line 2550) | static void function test_unary_ex_afs (line 2566) | static void function test_nonbinary_ex_ld (line 2599) | static void function test_nonbinary_ex_mean_descendants (line 2610) | static void function test_nonbinary_ex_genealogical_nearest_neighbours (line 2621) | static void function test_nonbinary_ex_general_stat (line 2632) | static void function test_nonbinary_ex_general_stat_errors (line 2647) | static void function test_caterpillar_tree_ld (line 2660) | static void function test_ld_multi_mutations (line 2688) | static void function test_ld_silent_mutations (line 2705) | static void function test_paper_ex_two_site (line 2733) | static void function test_paper_ex_two_branch (line 2848) | static void function test_two_site_correlated_multiallelic (line 3005) | static void function test_two_site_uncorrelated_multiallelic (line 3192) | static void function test_two_site_backmutation (line 3385) | static void function test_two_locus_branch_all_stats (line 3454) | static void function test_paper_ex_two_site_subset (line 3593) | static void function test_two_locus_stat_input_errors (line 3648) | static void function test_simplest_divergence_matrix (line 3819) | static void function test_simplest_divergence_matrix_windows (line 3907) | static void function test_simplest_divergence_matrix_internal_sample (line 3966) | static void function test_multiroot_divergence_matrix (line 3995) | static void function test_pair_coalescence_counts (line 4011) | static void function test_pair_coalescence_counts_missing (line 4025) | static void function test_pair_coalescence_quantiles (line 4036) | static void function test_pair_coalescence_rates (line 4046) | static void function main (line 4056) | int FILE: c/tests/test_tables.c function reverse_migrations (line 33) | static void function reverse_edges (line 62) | static void function reverse_mutations (line 90) | static void function insert_edge_metadata (line 119) | static void function test_table_collection_equals_options (line 144) | static void function test_table_collection_simplify_errors (line 341) | static void function test_reference_sequence_state_machine (line 406) | static void function test_reference_sequence_take (line 470) | static void function test_reference_sequence (line 526) | static void function test_table_collection_reference_sequence (line 632) | static void function test_table_collection_has_reference_sequence (line 752) | static void function test_table_collection_metadata (line 775) | static void function test_table_collection_time_units (line 878) | static void function test_node_table (line 945) | static void function test_node_table_takeset (line 1299) | static void function test_node_table_update_row (line 1412) | static void function test_node_table_keep_rows (line 1494) | static void function test_edge_table_with_options (line 1594) | static void function test_edge_table (line 2002) | static void function test_edge_table_update_row (line 2009) | static void function test_edge_table_update_row_no_metadata (line 2091) | static void function test_edge_table_keep_rows (line 2137) | static void function test_edge_table_keep_rows_no_metadata (line 2237) | static void function test_edge_table_takeset_with_options (line 2334) | static void function test_edge_table_takeset (line 2452) | static void function test_edge_table_copy_semantics (line 2459) | static void function test_edge_table_squash (line 2510) | static void function test_edge_table_squash_multiple_parents (line 2548) | static void function test_edge_table_squash_empty (line 2592) | static void function test_edge_table_squash_single_edge (line 2619) | static void function test_edge_table_squash_bad_intervals (line 2644) | static void function test_edge_table_squash_metadata (line 2671) | static void function test_site_table (line 2701) | static void function test_site_table_takeset (line 3034) | static void function test_site_table_update_row (line 3155) | static void function test_site_table_keep_rows (line 3258) | static void function test_mutation_table (line 3359) | static void function test_mutation_table_takeset (line 3764) | static void function test_mutation_table_update_row (line 3914) | static void function test_mutation_table_keep_rows (line 4044) | static void function test_mutation_table_keep_rows_parent_references (line 4151) | static void function test_migration_table (line 4237) | static void function test_migration_table_takeset (line 4606) | static void function test_migration_table_update_row (line 4745) | static void function test_migration_table_keep_rows (line 4838) | static void function test_individual_table (line 4940) | static void function test_individual_table_takeset (line 5402) | static void function test_individual_table_update_row (line 5539) | static void function test_individual_table_keep_rows (line 5665) | static void function test_individual_table_keep_rows_parent_references (line 5773) | static void function test_population_table (line 5860) | static void function test_population_table_takeset (line 6105) | static void function test_population_table_update_row (line 6176) | static void function test_population_table_keep_rows (line 6237) | static void function test_provenance_table (line 6333) | static void function test_provenance_table_takeset (line 6590) | static void function test_provenance_table_update_row (line 6687) | static void function test_provenance_table_keep_rows (line 6772) | static void function test_table_size_increments (line 6872) | static void function test_table_expansion (line 6982) | static void function test_ragged_expansion (line 7499) | static void function test_link_ancestors_input_errors (line 7573) | static void function test_link_ancestors_single_tree (line 7649) | static void function test_link_ancestors_no_edges (line 7689) | static void function test_link_ancestors_samples_and_ancestors_overlap (line 7715) | static void function test_link_ancestors_paper (line 7757) | static void function test_link_ancestors_multiple_to_single_tree (line 7798) | static void function verify_ibd_segment_list (line 7836) | static void function verify_ibd_result (line 7859) | static void function test_ibd_segments_debug (line 7918) | static void function test_ibd_segments_caterpillar_tree (line 7956) | static void function test_ibd_segments_single_tree (line 7972) | static void function test_ibd_segments_single_tree_options (line 8090) | static void function test_ibd_segments_single_tree_between (line 8192) | static void function test_ibd_segments_multiple_trees (line 8258) | static void function test_ibd_segments_empty_result (line 8311) | static void function test_ibd_segments_min_span_max_time (line 8340) | static void function test_ibd_segments_errors (line 8378) | static void function test_ibd_segments_samples_are_descendants (line 8462) | static void function test_ibd_segments_multiple_ibd_paths (line 8501) | static void function test_ibd_segments_odd_topologies (line 8543) | static void function test_simplify_tables_drops_indexes (line 8576) | static void function test_simplify_empty_tables (line 8598) | static void function test_simplify_metadata (line 8616) | static void function test_edge_update_invalidates_index (line 8632) | static void function test_copy_table_collection (line 8670) | static void function test_sort_tables_offsets (line 8705) | static void function test_sort_tables_drops_indexes_with_options (line 8811) | static void function test_sort_tables_drops_indexes (line 8832) | static void function test_sort_tables_edge_metadata (line 8839) | static void function test_sort_tables_no_edge_metadata (line 8865) | static void function test_sort_tables_errors (line 8904) | static void function test_sort_tables_mutation_times (line 9002) | static void function test_sort_tables_mutations (line 9062) | static void function test_sort_tables_canonical_errors (line 9176) | static void function test_sort_tables_canonical (line 9269) | static void function test_sort_tables_migrations (line 9398) | static void function test_sort_tables_individuals (line 9443) | static void function test_sorter_interface (line 9509) | static void function test_dump_unindexed_with_options (line 9577) | static void function test_dump_unindexed (line 9606) | static void function test_dump_load_empty_with_options (line 9613) | static void function test_dump_load_empty (line 9632) | static void function test_dump_load_unsorted_with_options (line 9639) | static void function test_dump_load_unsorted (line 9692) | static void function test_dump_load_metadata_schema (line 9699) | static void function test_dump_fail_no_file (line 9734) | static void function test_load_reindex (line 9783) | static void function test_table_overflow (line 9821) | static void function test_column_overflow (line 9877) | static void function test_table_collection_check_integrity_with_options (line 10036) | static void function test_table_collection_check_integrity_no_populations (line 10519) | static void function test_table_collection_check_integrity (line 10570) | static void function test_table_collection_check_integrity_bad_indexes_example (line 10577) | static void function test_table_collection_check_integrity_bad_indexes (line 10628) | static void function test_check_integrity_bad_mutation_parent_topology (line 10720) | static void function test_table_collection_compute_mutation_parents_tolerates_invalid_input (line 10778) | static void function test_table_collection_compute_mutation_parents_restores_on_error (line 10814) | static void function test_table_collection_subset_with_options (line 10857) | static void function test_table_collection_subset (line 11027) | static void function test_table_collection_subset_unsorted (line 11034) | static void function test_table_collection_subset_errors (line 11099) | static void function test_table_collection_union (line 11177) | static void function test_table_collection_disjoint_union (line 11322) | static void function test_table_collection_union_middle_merge (line 11425) | static void function test_table_collection_union_errors (line 11583) | static void function test_table_collection_clear_with_options (line 11669) | static void function test_table_collection_clear (line 11771) | static void function test_table_collection_takeset_indexes (line 11789) | static void function test_table_collection_delete_older (line 11836) | static void function main (line 11889) | int FILE: c/tests/test_trees.c function check_trees_equal (line 38) | static void function check_trees_identical (line 55) | static void function verify_compute_mutation_parents (line 106) | static void function verify_compute_mutation_times (line 132) | static void function verify_individual_nodes (line 158) | static void function verify_tree_pos (line 178) | static void function verify_trees (line 326) | static void function tsk_tree_t (line 405) | static tsk_tree_t * function verify_tree_next_prev (line 432) | static void function verify_edge_array_single_tree (line 554) | static void function verify_edge_array_trees (line 582) | static void function verify_simplify_genotypes (line 615) | static void function verify_simplify_properties (line 670) | static void function verify_simplify (line 782) | static void type sample_count_test_t (line 824) | typedef struct { function verify_sample_counts (line 830) | static void function verify_sample_sets_for_tree (line 949) | static void function verify_sample_sets (line 1014) | static void function verify_empty_tree_sequence (line 1050) | static void function test_simplest_discrete_genome (line 1066) | static void function test_simplest_discrete_time (line 1164) | static void function test_simplest_min_time (line 1239) | static void function test_simplest_max_time (line 1290) | static void function test_simplest_records (line 1341) | static void function test_simplest_nonbinary_records (line 1385) | static void function test_simplest_unary_records (line 1433) | static void function test_simplest_unary_with_individuals (line 1495) | static void function test_simplest_non_sample_leaf_records (line 1563) | static void function test_simplest_degenerate_multiple_root_records (line 1639) | static void function test_simplest_multiple_root_records (line 1691) | static void function test_simplest_zero_root_tree (line 1734) | static void function test_simplest_multi_root_tree (line 1773) | static void function test_simplest_tree_mrca (line 1833) | static void function test_simplest_root_mutations (line 1866) | static void function test_simplest_back_mutations (line 1901) | static void function test_simplest_general_samples (line 1945) | static void function test_simplest_holey_tree_sequence (line 1987) | static void function test_simplest_holey_tsk_treeseq_mutation_parents (line 2030) | static void function test_simplest_initial_gap_tree_sequence (line 2072) | static void function test_simplest_initial_gap_zero_roots (line 2123) | static void function test_simplest_holey_tsk_treeseq_zero_roots (line 2171) | static void function test_simplest_initial_gap_tsk_treeseq_mutation_parents (line 2235) | static void function test_simplest_final_gap_tree_sequence (line 2274) | static void function test_simplest_final_gap_tsk_treeseq_mutation_parents (line 2311) | static void function test_simplest_individuals (line 2350) | static void function test_simplest_bad_individuals (line 2448) | static void function test_simplest_bad_edges (line 2542) | static void function test_simplest_bad_indexes (line 2731) | static void function test_simplest_bad_migrations (line 2792) | static void function test_simplest_migration_simplify (line 2907) | static void function test_simplest_overlapping_parents (line 2941) | static void function test_simplest_contradictory_children (line 2989) | static void function test_simplest_overlapping_edges_simplify (line 3018) | static void function test_simplest_overlapping_unary_edges_simplify (line 3068) | static void function test_simplest_overlapping_unary_edges_internal_samples_simplify (line 3111) | static void function test_simplest_reduce_site_topology (line 3153) | static void function test_simplest_simplify_defragment (line 3200) | static void function test_simplest_population_filter (line 3263) | static void function test_simplest_individual_filter (line 3301) | static void function test_simplest_no_node_filter (line 3339) | static void function test_simplest_no_update_flags (line 3405) | static void function test_simplest_map_mutations (line 3435) | static void function test_simplest_nonbinary_map_mutations (line 3515) | static void function test_simplest_unary_map_mutations (line 3559) | static void function test_simplest_non_sample_leaf_map_mutations (line 3605) | static void function test_simplest_internal_sample_map_mutations (line 3649) | static void function test_simplest_multiple_root_map_mutations (line 3702) | static void function test_simplest_chained_map_mutations (line 3759) | static void function test_simplest_mutation_edges (line 3808) | static void function test_single_tree_good_records (line 3869) | static void function test_single_nonbinary_tree_good_records (line 3885) | static void function test_single_tree_bad_records (line 3913) | static void function test_single_tree_good_mutations (line 3963) | static void function test_single_tree_bad_mutations (line 4030) | static void function test_single_tree_iter (line 4210) | static void function test_single_nonbinary_tree_iter (line 4272) | static void function test_single_tree_general_samples_iter (line 4367) | static void function test_single_tree_iter_times (line 4433) | static void function test_single_tree_iter_depths (line 4479) | static void function test_single_tree_simplify (line 4525) | static void function test_single_tree_simplify_debug (line 4582) | static void function test_single_tree_simplify_keep_input_roots (line 4605) | static void function test_single_tree_simplify_no_sample_nodes (line 4631) | static void function test_single_tree_simplify_null_samples (line 4660) | static void function test_single_tree_compute_mutation_parents (line 4683) | static void function test_single_tree_compute_mutation_times (line 4792) | static void function test_single_tree_mutation_edges (line 4910) | static void function test_single_tree_is_descendant (line 4948) | static void function test_single_tree_total_branch_length (line 4988) | static void function test_single_tree_num_lineages (line 5026) | static void function test_single_tree_map_mutations (line 5065) | static void function test_single_tree_map_mutations_internal_samples (line 5193) | static void function test_single_tree_tracked_samples (line 5239) | static void function test_single_tree_tree_pos (line 5322) | static void function test_simple_multi_tree (line 5424) | static void function test_multi_tree_direction_switching_tree_pos (line 5444) | static void function test_unary_multi_tree (line 5548) | static void function test_internal_sample_multi_tree (line 5568) | static void function test_internal_sample_simplified_multi_tree (line 5588) | static void function test_nonbinary_multi_tree (line 5620) | static void function test_simplify_keep_input_roots_multi_tree (line 5641) | static void function test_left_to_right_multi_tree (line 5696) | static void function test_gappy_multi_tree (line 5740) | static void function test_tsk_treeseq_bad_records (line 5786) | static void function test_convenience_arrays_multi_tree (line 5832) | static void function test_multiroot_mrca (line 5857) | static void function test_simple_sample_sets (line 5890) | static void function test_nonbinary_sample_sets (line 5910) | static void function test_internal_sample_sample_sets (line 5930) | static void function test_non_sample_leaf_sample_lists (line 5951) | static void function test_virtual_root_properties (line 5989) | static void function test_no_sample_count_semantics (line 6049) | static void function verify_node_lists (line 6088) | static void function test_single_tree_traversal (line 6099) | static void function test_multiroot_tree_traversal (line 6214) | static void function verify_seek_multi_tree (line 6318) | static void function test_seek_multi_tree (line 6391) | static void function test_seek_errors (line 6398) | static void function test_isolated_node_kc (line 6429) | static void function test_single_tree_kc (line 6469) | static void function test_two_trees_kc (line 6510) | static void function test_empty_tree_kc (line 6563) | static void function test_nonbinary_tree_kc (line 6617) | static void function test_nonzero_samples_kc (line 6646) | static void function test_internal_samples_kc (line 6676) | static void function test_non_sample_leaf_kc (line 6705) | static void function test_unequal_sample_size_kc (line 6735) | static void function test_unequal_samples_kc (line 6779) | static void function test_unary_nodes_kc (line 6828) | static void function test_no_sample_lists_kc (line 6854) | static void function test_unequal_sequence_lengths_kc (line 6876) | static void function test_different_number_trees_kc (line 6902) | static void function test_offset_trees_with_errors_kc (line 6953) | static void function test_genealogical_nearest_neighbours_errors (line 6990) | static void function test_single_tree_balance (line 7082) | static void function test_multiroot_balance (line 7117) | static void function test_nonbinary_balance (line 7156) | static void function test_empty_tree_balance (line 7191) | static void function test_b2_bad_base (line 7225) | static void function test_tree_errors (line 7258) | static void function test_treeseq_row_access_errors (line 7340) | static void function test_treeseq_get_individuals_population_errors (line 7374) | static void function test_treeseq_get_individuals_population (line 7409) | static void function test_treeseq_get_individuals_time_errors (line 7457) | static void function test_treeseq_get_individuals_time (line 7492) | static void function test_tree_copy_flags (line 7540) | static void function test_deduplicate_sites (line 7603) | static void function test_deduplicate_sites_errors (line 7687) | static void function test_deduplicate_sites_zero_rows (line 7761) | static void function test_deduplicate_sites_multichar (line 7779) | static void function test_empty_tree_sequence (line 7817) | static void function test_zero_edges (line 7864) | static void function test_tree_sequence_metadata (line 7939) | static void function dummy_stat (line 7991) | static int function test_time_uncalibrated (line 8004) | static void function test_reference_sequence (line 8084) | static void function test_split_edges_no_populations (line 8110) | static void function test_split_edges_populations (line 8175) | static void function test_split_edges_errors (line 8221) | static void function test_extend_haplotypes_simple (line 8275) | static void function test_extend_haplotypes_errors (line 8299) | static void function assert_equal_except_edges_and_mutation_nodes (line 8339) | static void function test_extend_haplotypes (line 8364) | static void function test_extend_haplotypes_conflicting_times (line 8448) | static void function test_extend_haplotypes_new_edge (line 8487) | static void function test_init_take_ownership_no_edge_metadata (line 8556) | static void function test_init_compute_mutation_parents (line 8577) | static void function test_init_compute_mutation_parents_errors (line 8638) | static void function main (line 8683) | int FILE: c/tests/testlib.c function parse_nodes (line 410) | void function parse_edges (line 464) | void function parse_migrations (line 527) | void function parse_sites (line 584) | void function parse_mutations (line 622) | void function parse_individuals (line 675) | void function tsk_treeseq_from_text (line 766) | void function tsk_treeseq_t (line 844) | tsk_treeseq_t * function unsort_edges (line 967) | void function tskit_suite_init (line 992) | static int function tskit_suite_cleanup (line 1018) | static int function handle_cunit_error (line 1031) | static void function test_main (line 1038) | int FILE: c/tskit/convert.c type tsk_newick_converter_t (line 44) | typedef struct { function tsk_newick_converter_run (line 52) | static int function tsk_newick_converter_init (line 154) | static int function tsk_newick_converter_free (line 174) | static int function tsk_convert_newick (line 181) | int FILE: c/tskit/core.c function get_random_bytes (line 42) | static int TSK_WARN_UNUSED function get_random_bytes (line 74) | static int TSK_WARN_UNUSED function tsk_generate_uuid (line 102) | int function tsk_set_kas_error (line 712) | int function tsk_is_kas_error (line 725) | bool function tsk_get_kas_error (line 731) | int function __tsk_safe_free (line 747) | void function tsk_blkalloc_print_state (line 762) | void function tsk_blkalloc_reset (line 773) | int TSK_WARN_UNUSED function tsk_blkalloc_init (line 784) | int TSK_WARN_UNUSED function tsk_blkalloc_free (line 850) | void function tsk_size_t (line 867) | tsk_size_t function tsk_round (line 898) | double function tsk_is_unknown_time (line 918) | bool function tsk_isnan (line 941) | bool function tsk_isfinite (line 951) | bool function tsk_memcmp (line 1022) | int function tsk_set_debug_stream (line 1035) | void function FILE (line 1041) | FILE * function tsk_avl_tree_int_print_node (line 1055) | static void function tsk_avl_tree_int_print_state (line 1070) | void function tsk_avl_tree_int_init (line 1077) | int function tsk_avl_tree_int_free (line 1084) | int function tsk_avl_node_int_t (line 1090) | tsk_avl_node_int_t * function tsk_avl_node_int_t (line 1096) | tsk_avl_node_int_t * function tsk_avl_tree_int_insert_empty (line 1113) | static int function tsk_avl_tree_int_insert_non_empty (line 1135) | static int function tsk_avl_tree_int_insert (line 1233) | int function ordered_nodes_traverse (line 1253) | static int function tsk_avl_tree_int_ordered_nodes (line 1264) | int function tsk_bitset_init (line 1274) | int function tsk_bitset_intersect (line 1292) | void function tsk_bitset_subtract (line 1304) | void function tsk_bitset_union (line 1315) | void function tsk_bitset_set_bit (line 1326) | void function tsk_bitset_contains (line 1334) | bool function popcount (line 1342) | static inline uint32_t function tsk_size_t (line 1364) | tsk_size_t function tsk_bitset_get_items (line 1377) | void function tsk_bitset_free (line 1407) | void FILE: c/tskit/core.h type tsk_id_t (line 95) | typedef int64_t tsk_id_t; type tsk_id_t (line 99) | typedef int32_t tsk_id_t; type tsk_size_t (line 111) | typedef uint64_t tsk_size_t; type tsk_flags_t (line 123) | typedef uint32_t tsk_flags_t; type tsk_bool_t (line 133) | typedef uint8_t tsk_bool_t; function __tsk_nan_f (line 165) | static inline double function _tsk_trace_error (line 982) | static inline int type tsk_blkalloc_t (line 1044) | typedef struct { type tsk_avl_node_int_t (line 1060) | typedef struct _tsk_avl_node_int_t { type tsk_avl_tree_int_t (line 1071) | typedef struct { type tsk_bitset_val_t (line 1134) | typedef uint32_t tsk_bitset_val_t; type tsk_bitset_t (line 1136) | typedef struct { FILE: c/tskit/genotypes.c function tsk_variant_print_state (line 38) | void function tsk_vargen_print_state (line 53) | void function tsk_variant_copy_alleles (line 61) | static int function variant_init_samples_and_index_map (line 91) | static int function tsk_variant_init (line 128) | int function tsk_vargen_init (line 237) | int function tsk_variant_free (line 258) | int function tsk_vargen_free (line 275) | int function tsk_variant_expand_alleles (line 282) | static int function tsk_variant_update_genotypes_sample_list (line 317) | static int TSK_WARN_UNUSED function tsk_variant_traverse (line 355) | static int TSK_WARN_UNUSED function tsk_variant_visit (line 391) | static int function tsk_variant_update_genotypes_traversal (line 406) | static int TSK_WARN_UNUSED function tsk_size_t (line 413) | static tsk_size_t function tsk_size_t (line 438) | static tsk_size_t function tsk_id_t (line 457) | static tsk_id_t function tsk_variant_decode (line 473) | int function tsk_variant_restricted_copy (line 596) | int function tsk_vargen_next (line 649) | int function tsk_treeseq_decode_alignments_overlay_missing (line 667) | static int function tsk_treeseq_decode_alignments_overlay_sites (line 720) | static int function tsk_treeseq_decode_alignments (line 804) | int FILE: c/tskit/genotypes.h type tsk_variant_t (line 45) | typedef struct { type tsk_vargen_t (line 83) | typedef struct { FILE: c/tskit/haplotype_matching.c function cmp_double (line 39) | static int function cmp_argsort (line 47) | static int function tsk_ls_hmm_check_state (line 60) | static void function tsk_ls_hmm_print_state (line 84) | void function tsk_ls_hmm_init (line 121) | int TSK_WARN_UNUSED function tsk_ls_hmm_set_precision (line 201) | int function tsk_ls_hmm_free (line 208) | int function tsk_ls_hmm_reset (line 231) | static int function tsk_ls_hmm_remove_dead_roots (line 262) | static int function tsk_ls_hmm_update_tree (line 294) | static int function tsk_ls_hmm_get_allele_index (line 363) | static int function tsk_ls_hmm_update_probabilities (line 387) | static int function tsk_ls_hmm_discretise_values (line 467) | static int function tsk_id_t (line 512) | static inline tsk_id_t function set_bit (line 530) | static inline uint64_t function bit_is_set (line 536) | static inline bool function tsk_id_t (line 542) | static inline tsk_id_t function all_zero (line 559) | static inline bool function element_in (line 571) | static inline bool function set_optimal_value (line 579) | static inline void function compute_optimal_value_1 (line 595) | static void function compute_optimal_value_general (line 631) | static void function compute_optimal_value (line 689) | static void function tsk_ls_hmm_setup_optimal_value_sets (line 702) | static int function tsk_ls_hmm_build_optimal_value_sets (line 733) | static int function tsk_ls_hmm_redistribute_transitions (line 791) | static int function tsk_ls_hmm_compress (line 889) | static int function tsk_ls_hmm_process_site_forward (line 914) | static int function tsk_ls_hmm_run_forward (line 954) | static int function tsk_ls_hmm_compute_normalisation_factor_forward (line 1001) | static double function tsk_ls_hmm_next_probability_forward (line 1031) | static int function tsk_ls_hmm_forward (line 1050) | int function tsk_ls_hmm_next_probability_backward (line 1085) | static int function tsk_ls_hmm_process_site_backward (line 1101) | static int function tsk_ls_hmm_run_backward (line 1152) | static int function tsk_ls_hmm_backward (line 1208) | int function tsk_ls_hmm_compute_normalisation_factor_viterbi (line 1243) | static double function tsk_ls_hmm_next_probability_viterbi (line 1263) | static int function tsk_ls_hmm_viterbi (line 1291) | int function tsk_compressed_matrix_init (line 1326) | int function tsk_compressed_matrix_free (line 1358) | int function tsk_compressed_matrix_clear (line 1369) | int function tsk_compressed_matrix_print_state (line 1380) | void function tsk_compressed_matrix_store_site (line 1405) | int function tsk_compressed_matrix_decode_site (line 1439) | static int function tsk_compressed_matrix_decode (line 1478) | int function tsk_viterbi_matrix_expand_recomb_records (line 1527) | static int function tsk_viterbi_matrix_init (line 1543) | int function tsk_viterbi_matrix_free (line 1572) | int function tsk_viterbi_matrix_clear (line 1580) | int function tsk_viterbi_matrix_print_state (line 1588) | void function TSK_WARN_UNUSED (line 1611) | TSK_WARN_UNUSED int function tsk_id_t (line 1634) | static tsk_id_t function tsk_viterbi_matrix_traceback (line 1684) | int FILE: c/tskit/haplotype_matching.h type tsk_value_transition_t (line 38) | typedef struct { type tsk_argsort_t (line 44) | typedef struct { type tsk_transition_stack_t (line 49) | typedef struct { type tsk_site_probability_t (line 56) | typedef struct { type tsk_compressed_matrix_t (line 63) | typedef struct { type tsk_recomb_required_record (line 75) | typedef struct { type tsk_viterbi_matrix_t (line 81) | typedef struct { type tsk_ls_hmm_t (line 88) | typedef struct _tsk_ls_hmm_t { FILE: c/tskit/stats.c function tsk_ld_calc_print_state (line 33) | void function tsk_ld_calc_init (line 41) | int TSK_WARN_UNUSED function tsk_ld_calc_free (line 63) | int function tsk_ld_calc_check_site (line 71) | static int function tsk_ld_calc_set_focal_samples (line 93) | static int function tsk_ld_calc_initialise (line 108) | static int function tsk_ld_calc_compute_r2 (line 133) | static int function tsk_ld_calc_compute_and_append (line 155) | static int function tsk_ld_calc_run_forward (line 178) | static int function tsk_ld_calc_run_reverse (line 215) | static int function tsk_ld_calc_get_r2 (line 252) | int function tsk_ld_calc_get_r2_array (line 278) | int FILE: c/tskit/stats.h type tsk_ld_calc_t (line 35) | typedef struct { FILE: c/tskit/tables.c type read_table_col_t (line 41) | typedef struct { type read_table_ragged_col_t (line 48) | typedef struct { type read_table_property_t (line 57) | typedef struct { type write_table_col_t (line 65) | typedef struct { type write_table_ragged_col_t (line 72) | typedef struct { function check_table_overflow (line 85) | static bool function check_offset_overflow (line 95) | static bool function read_table_cols (line 106) | static int function cast_offset_array (line 148) | static int function read_table_ragged_cols (line 168) | static int function read_table_properties (line 268) | static int function read_table (line 302) | static int function free_read_table_mem (line 336) | static void function write_offset_col (line 362) | static int function write_table_ragged_cols (line 407) | static int function write_table_cols (line 430) | static int function write_table (line 449) | static int function check_offsets (line 467) | static int function calculate_max_rows (line 493) | static int function calculate_max_length (line 535) | static int function expand_column (line 582) | static int function expand_ragged_column (line 598) | static int function replace_string (line 624) | static int function takeset_string (line 644) | static int function alloc_empty_ragged_column (line 653) | static int function check_ragged_column (line 668) | static int function takeset_ragged_column (line 686) | static int function takeset_optional_id_column (line 705) | static int function write_metadata_schema_header (line 728) | static int function tsk_size_t (line 740) | static tsk_size_t function keep_mask_to_id_map (line 754) | static void function tsk_size_t (line 770) | static tsk_size_t function tsk_size_t (line 796) | static tsk_size_t function tsk_size_t (line 812) | static tsk_size_t function tsk_size_t (line 828) | static tsk_size_t function tsk_size_t (line 844) | static tsk_size_t function tsk_size_t (line 868) | static tsk_size_t function tsk_size_t (line 892) | static tsk_size_t function tsk_reference_sequence_init (line 924) | int function tsk_reference_sequence_free (line 932) | int function tsk_reference_sequence_is_null (line 942) | bool function tsk_reference_sequence_equals (line 949) | bool function tsk_reference_sequence_copy (line 972) | int function tsk_reference_sequence_set_data (line 1012) | int function tsk_reference_sequence_set_url (line 1019) | int function tsk_reference_sequence_set_metadata (line 1026) | int function tsk_reference_sequence_set_metadata_schema (line 1034) | int function tsk_reference_sequence_takeset_data (line 1042) | int function tsk_reference_sequence_takeset_metadata (line 1049) | int function tsk_individual_table_free_columns (line 1061) | static void function tsk_individual_table_free (line 1073) | int function tsk_individual_table_expand_main_columns (line 1081) | static int function tsk_individual_table_expand_location (line 1119) | static int function tsk_individual_table_expand_parents (line 1128) | static int function tsk_individual_table_expand_metadata (line 1137) | static int function tsk_individual_table_set_max_rows_increment (line 1146) | int function tsk_individual_table_set_max_metadata_length_increment (line 1154) | int function tsk_individual_table_set_max_location_length_increment (line 1162) | int function tsk_individual_table_set_max_parents_length_increment (line 1170) | int function tsk_individual_table_init (line 1178) | int function tsk_individual_table_copy (line 1218) | int TSK_WARN_UNUSED function tsk_individual_table_set_columns (line 1242) | int TSK_WARN_UNUSED function tsk_individual_table_takeset_columns (line 1260) | int TSK_WARN_UNUSED function tsk_individual_table_append_columns (line 1316) | int function tsk_id_t (line 1423) | static tsk_id_t function tsk_id_t (line 1449) | tsk_id_t function tsk_individual_table_update_row_rewrite (line 1478) | static int function tsk_individual_table_update_row (line 1523) | int function tsk_individual_table_clear (line 1559) | int function tsk_individual_table_truncate (line 1565) | int function tsk_individual_table_extend (line 1582) | int function tsk_individual_table_print_state (line 1621) | void function tsk_individual_table_get_row_unsafe (line 1668) | static inline void function tsk_individual_table_get_row (line 1688) | int function tsk_individual_table_set_metadata_schema (line 1703) | int function tsk_individual_table_dump_text (line 1711) | int function tsk_individual_table_equals (line 1773) | bool function tsk_individual_table_keep_rows (line 1810) | int function tsk_individual_table_dump (line 1875) | static int function tsk_individual_table_load (line 1899) | static int function tsk_node_table_free_columns (line 1966) | static void function tsk_node_table_free (line 1977) | int function tsk_node_table_expand_main_columns (line 1985) | static int function tsk_node_table_expand_metadata (line 2025) | static int function tsk_node_table_set_max_rows_increment (line 2033) | int function tsk_node_table_set_max_metadata_length_increment (line 2041) | int function tsk_node_table_init (line 2049) | int function tsk_node_table_copy (line 2075) | int TSK_WARN_UNUSED function tsk_node_table_set_columns (line 2098) | int TSK_WARN_UNUSED function tsk_node_table_takeset_columns (line 2115) | int TSK_WARN_UNUSED function tsk_node_table_append_columns (line 2156) | int function tsk_id_t (line 2220) | static tsk_id_t function tsk_id_t (line 2238) | tsk_id_t function tsk_node_table_update_row_rewrite (line 2259) | static int function tsk_node_table_update_row (line 2303) | int function tsk_node_table_clear (line 2335) | int TSK_WARN_UNUSED function tsk_node_table_truncate (line 2341) | int function tsk_node_table_extend (line 2356) | int function tsk_node_table_print_state (line 2393) | void function tsk_node_table_set_metadata_schema (line 2425) | int function tsk_node_table_dump_text (line 2433) | int function tsk_node_table_equals (line 2465) | bool function tsk_node_table_get_row_unsafe (line 2496) | static inline void function tsk_node_table_get_row (line 2510) | int function tsk_node_table_keep_rows (line 2524) | int function tsk_node_table_dump (line 2547) | static int function tsk_node_table_load (line 2570) | static int function tsk_edge_table_free_columns (line 2631) | static void function tsk_edge_table_free (line 2642) | int function tsk_edge_table_has_metadata (line 2650) | static int function tsk_edge_table_expand_main_columns (line 2656) | static int function tsk_edge_table_expand_metadata (line 2697) | static int function tsk_edge_table_set_max_rows_increment (line 2705) | int function tsk_edge_table_set_max_metadata_length_increment (line 2713) | int function tsk_edge_table_init (line 2721) | int function tsk_id_t (line 2751) | tsk_id_t function tsk_edge_table_update_row_rewrite (line 2791) | static int function tsk_edge_table_update_row (line 2835) | int function tsk_edge_table_copy (line 2869) | int TSK_WARN_UNUSED function tsk_edge_table_set_columns (line 2906) | int function tsk_edge_table_takeset_columns (line 2923) | int TSK_WARN_UNUSED function tsk_edge_table_append_columns (line 2961) | int function tsk_edge_table_clear (line 3022) | int function tsk_edge_table_truncate (line 3028) | int function tsk_edge_table_extend (line 3045) | int function tsk_edge_table_get_row_unsafe (line 3082) | static inline void function tsk_edge_table_get_row (line 3101) | int function tsk_edge_table_print_state (line 3115) | void function tsk_edge_table_set_metadata_schema (line 3134) | int function tsk_edge_table_dump_text (line 3142) | int function tsk_edge_table_equals (line 3173) | bool function tsk_edge_table_keep_rows (line 3216) | int function tsk_edge_table_dump (line 3239) | static int function tsk_edge_table_load (line 3275) | static int function tsk_edge_table_squash (line 3333) | int function tsk_site_table_free_columns (line 3382) | static void function tsk_site_table_free (line 3392) | int function tsk_site_table_expand_main_columns (line 3400) | static int function tsk_site_table_expand_ancestral_state (line 3432) | static int function tsk_site_table_expand_metadata (line 3441) | static int function tsk_site_table_set_max_rows_increment (line 3449) | int function tsk_site_table_set_max_metadata_length_increment (line 3457) | int function tsk_site_table_set_max_ancestral_state_length_increment (line 3465) | int function tsk_site_table_init (line 3473) | int function tsk_id_t (line 3507) | tsk_id_t function tsk_site_table_update_row_rewrite (line 3549) | static int function tsk_site_table_update_row (line 3593) | int function tsk_site_table_append_columns (line 3625) | int function tsk_site_table_copy (line 3699) | int TSK_WARN_UNUSED function tsk_site_table_set_columns (line 3723) | int function tsk_site_table_takeset_columns (line 3741) | int function tsk_site_table_equals (line 3782) | bool function tsk_site_table_clear (line 3813) | int function tsk_site_table_truncate (line 3819) | int function tsk_site_table_extend (line 3835) | int function tsk_site_table_print_state (line 3872) | void function tsk_site_table_get_row_unsafe (line 3900) | static inline void function tsk_site_table_get_row (line 3918) | int function tsk_site_table_set_metadata_schema (line 3932) | int function tsk_site_table_dump_text (line 3940) | int function tsk_site_table_keep_rows (line 3974) | int function tsk_site_table_dump (line 3996) | static int function tsk_site_table_load (line 4017) | static int function tsk_mutation_table_free_columns (line 4077) | static void function tsk_mutation_table_free (line 4090) | int function tsk_mutation_table_expand_main_columns (line 4098) | static int function tsk_mutation_table_expand_derived_state (line 4143) | static int function tsk_mutation_table_expand_metadata (line 4152) | static int function tsk_mutation_table_set_max_rows_increment (line 4161) | int function tsk_mutation_table_set_max_metadata_length_increment (line 4169) | int function tsk_mutation_table_set_max_derived_state_length_increment (line 4177) | int function tsk_mutation_table_init (line 4185) | int function tsk_id_t (line 4219) | tsk_id_t function tsk_mutation_table_update_row_rewrite (line 4263) | static int function tsk_mutation_table_update_row (line 4308) | int function tsk_mutation_table_append_columns (line 4343) | int function tsk_mutation_table_takeset_columns (line 4434) | int TSK_WARN_UNUSED function tsk_mutation_table_copy (line 4497) | int TSK_WARN_UNUSED function tsk_mutation_table_set_columns (line 4521) | int function tsk_mutation_table_equals (line 4540) | bool function tsk_mutation_table_clear (line 4577) | int function tsk_mutation_table_truncate (line 4583) | int function tsk_mutation_table_extend (line 4599) | int function tsk_mutation_table_print_state (line 4637) | void function tsk_mutation_table_get_row_unsafe (line 4664) | static inline void function tsk_mutation_table_get_row (line 4682) | int function tsk_mutation_table_set_metadata_schema (line 4697) | int function tsk_mutation_table_dump_text (line 4705) | int function tsk_mutation_table_keep_rows (line 4739) | int function tsk_mutation_table_dump (line 4798) | static int function tsk_mutation_table_load (line 4824) | static int function tsk_migration_table_free_columns (line 4893) | static void function tsk_migration_table_free (line 4906) | int function tsk_migration_table_expand_main_columns (line 4914) | static int function tsk_migration_table_expand_metadata (line 4963) | static int function tsk_migration_table_set_max_rows_increment (line 4972) | int function tsk_migration_table_set_max_metadata_length_increment (line 4980) | int function tsk_migration_table_init (line 4988) | int function tsk_migration_table_append_columns (line 5015) | int function tsk_migration_table_takeset_columns (line 5073) | int TSK_WARN_UNUSED function tsk_migration_table_copy (line 5111) | int TSK_WARN_UNUSED function tsk_migration_table_set_columns (line 5135) | int function tsk_id_t (line 5153) | tsk_id_t function tsk_migration_table_update_row_rewrite (line 5187) | static int function tsk_migration_table_update_row (line 5231) | int function tsk_migration_table_clear (line 5265) | int function tsk_migration_table_truncate (line 5271) | int function tsk_migration_table_extend (line 5286) | int function tsk_migration_table_print_state (line 5325) | void function tsk_migration_table_get_row_unsafe (line 5343) | static inline void function tsk_migration_table_get_row (line 5359) | int function tsk_migration_table_set_metadata_schema (line 5374) | int function tsk_migration_table_dump_text (line 5382) | int function tsk_migration_table_equals (line 5414) | bool function tsk_migration_table_keep_rows (line 5443) | int function tsk_migration_table_dump (line 5468) | static int function tsk_migration_table_load (line 5493) | static int function tsk_population_table_free_columns (line 5562) | static void function tsk_population_table_free (line 5569) | int function tsk_population_table_expand_main_columns (line 5577) | static int function tsk_population_table_expand_metadata (line 5601) | static int function tsk_population_table_set_max_rows_increment (line 5610) | int function tsk_population_table_set_max_metadata_length_increment (line 5618) | int function tsk_population_table_init (line 5626) | int function tsk_population_table_copy (line 5652) | int TSK_WARN_UNUSED function tsk_population_table_set_columns (line 5675) | int function tsk_population_table_append_columns (line 5690) | int function tsk_population_table_takeset_columns (line 5729) | int function tsk_id_t (line 5758) | static tsk_id_t function tsk_id_t (line 5774) | tsk_id_t function tsk_population_table_update_row_rewrite (line 5793) | static int function tsk_population_table_update_row (line 5835) | int function tsk_population_table_clear (line 5862) | int function tsk_population_table_truncate (line 5868) | int function tsk_population_table_extend (line 5883) | int function tsk_population_table_print_state (line 5921) | void function tsk_population_table_get_row_unsafe (line 5950) | static inline void function tsk_population_table_get_row (line 5960) | int function tsk_population_table_set_metadata_schema (line 5975) | int function tsk_population_table_dump_text (line 5983) | int function tsk_population_table_equals (line 6013) | bool function tsk_population_table_keep_rows (line 6037) | int function tsk_population_table_dump (line 6055) | static int function tsk_population_table_load (line 6073) | static int function tsk_provenance_table_free_columns (line 6121) | static void function tsk_provenance_table_free (line 6130) | int function tsk_provenance_table_expand_main_columns (line 6137) | static int function tsk_provenance_table_expand_timestamp (line 6166) | static int function tsk_provenance_table_expand_record (line 6175) | static int function tsk_provenance_table_set_max_rows_increment (line 6184) | int function tsk_provenance_table_set_max_timestamp_length_increment (line 6192) | int function tsk_provenance_table_set_max_record_length_increment (line 6200) | int function tsk_provenance_table_init (line 6208) | int function tsk_provenance_table_copy (line 6240) | int TSK_WARN_UNUSED function tsk_provenance_table_set_columns (line 6258) | int function tsk_provenance_table_append_columns (line 6275) | int function tsk_provenance_table_takeset_columns (line 6332) | int function tsk_id_t (line 6372) | static tsk_id_t function tsk_id_t (line 6395) | tsk_id_t function tsk_provenance_table_update_row_rewrite (line 6419) | static int function tsk_provenance_table_update_row (line 6463) | int function tsk_provenance_table_clear (line 6494) | int function tsk_provenance_table_truncate (line 6500) | int function tsk_provenance_table_extend (line 6516) | int function tsk_provenance_table_print_state (line 6554) | void function tsk_provenance_table_get_row_unsafe (line 6590) | static inline void function tsk_provenance_table_get_row (line 6602) | int function tsk_provenance_table_dump_text (line 6617) | int function tsk_provenance_table_equals (line 6643) | bool function tsk_provenance_table_keep_rows (line 6667) | int function tsk_provenance_table_dump (line 6685) | static int function tsk_provenance_table_load (line 6700) | static int type edge_sort_t (line 6741) | typedef struct { type mutation_sort_t (line 6756) | typedef struct { type individual_canonical_sort_t (line 6762) | typedef struct { type migration_sort_t (line 6768) | typedef struct { function cmp_site (line 6779) | static int function cmp_mutation (line 6798) | static int function cmp_individual_canonical (line 6831) | static int function cmp_edge (line 6847) | static int function cmp_migration (line 6869) | static int function tsk_table_sorter_sort_edges (line 6895) | static int function tsk_table_sorter_sort_migrations (line 6950) | static int function tsk_table_sorter_sort_sites (line 7002) | static int function tsk_table_sorter_sort_mutations (line 7049) | static int function tsk_individual_table_topological_sort (line 7131) | static int function tsk_table_collection_individual_topological_sort (line 7209) | int function tsk_table_sorter_sort_individuals_canonical (line 7284) | static int function tsk_table_sorter_run (line 7383) | int function tsk_table_sorter_init (line 7454) | int function tsk_table_sorter_free (line 7486) | int type interval_list_t (line 7497) | typedef struct _interval_list_t { type mutation_id_list_t (line 7503) | typedef struct _mutation_id_list_t { type tsk_segment_t (line 7508) | typedef struct _tsk_segment_t { type segment_overlapper_t (line 7516) | typedef struct { type simplifier_t (line 7530) | typedef struct { function cmp_segment (line 7567) | static int function segment_overlapper_alloc (line 7580) | static int TSK_WARN_UNUSED function segment_overlapper_free (line 7596) | static int function segment_overlapper_start (line 7606) | static int TSK_WARN_UNUSED function segment_overlapper_next (line 7642) | static int TSK_WARN_UNUSED function cmp_node_id (line 7703) | static int type ancestor_mapper_t (line 7720) | typedef struct { function tsk_segment_t (line 7745) | static tsk_segment_t *TSK_WARN_UNUSED function interval_list_t (line 7763) | static interval_list_t *TSK_WARN_UNUSED function ancestor_mapper_flush_edges (line 7779) | static int function ancestor_mapper_record_edge (line 7813) | static int function ancestor_mapper_add_ancestry (line 7849) | static int TSK_WARN_UNUSED function ancestor_mapper_find_oldest_node (line 7883) | static void function ancestor_mapper_init_samples (line 7900) | static int function ancestor_mapper_init_ancestors (line 7927) | static int function ancestor_mapper_init (line 7949) | static int function ancestor_mapper_free (line 8023) | static int function ancestor_mapper_enqueue_segment (line 8040) | static int TSK_WARN_UNUSED function ancestor_mapper_merge_ancestors (line 8070) | static int TSK_WARN_UNUSED function ancestor_mapper_process_parent_edges (line 8147) | static int TSK_WARN_UNUSED function ancestor_mapper_run (line 8186) | static int TSK_WARN_UNUSED function pair_to_integer (line 8243) | static inline int64_t function integer_to_pair (line 8255) | static inline void function tsk_identity_segments_get_key (line 8262) | static int64_t function tsk_identity_segment_t (line 8282) | static tsk_identity_segment_t *TSK_WARN_UNUSED function tsk_avl_node_int_t (line 8301) | static tsk_avl_node_int_t * function tsk_identity_segments_init (line 8318) | static int function tsk_identity_segments_print_state (line 8350) | void function tsk_size_t (line 8390) | tsk_size_t function tsk_identity_segments_get_total_span (line 8396) | double function tsk_size_t (line 8402) | tsk_size_t function get_keys_traverse (line 8412) | static int function tsk_identity_segments_get_keys (line 8427) | int function get_items_traverse (line 8438) | static int function tsk_identity_segments_get_items (line 8455) | int function tsk_identity_segments_free (line 8467) | int function tsk_identity_segments_update_pair (line 8475) | static int TSK_WARN_UNUSED function tsk_identity_segments_add_segment (line 8516) | static int TSK_WARN_UNUSED function tsk_identity_segments_get (line 8534) | int TSK_WARN_UNUSED type tsk_ibd_finder_t (line 8563) | typedef struct { function tsk_segment_t (line 8581) | static tsk_segment_t *TSK_WARN_UNUSED function tsk_ibd_finder_add_ancestry (line 8599) | static int TSK_WARN_UNUSED function tsk_ibd_finder_init_samples_from_set (line 8624) | static int function tsk_ibd_finder_init_samples_from_nodes (line 8649) | static void function tsk_ibd_finder_add_sample_ancestry (line 8663) | static int function tsk_ibd_finder_init (line 8684) | static int TSK_WARN_UNUSED function tsk_ibd_finder_enqueue_segment (line 8730) | static int TSK_WARN_UNUSED function tsk_ibd_finder_passes_filters (line 8761) | static bool function tsk_ibd_finder_record_ibd (line 8778) | static int TSK_WARN_UNUSED function tsk_ibd_finder_add_queued_ancestry (line 8805) | static int TSK_WARN_UNUSED function tsk_ibd_finder_print_state (line 8824) | static void function tsk_ibd_finder_init_within (line 8857) | static int TSK_WARN_UNUSED function tsk_ibd_finder_init_between (line 8877) | static int TSK_WARN_UNUSED function tsk_ibd_finder_run (line 8907) | static int TSK_WARN_UNUSED function tsk_ibd_finder_free (line 8949) | static int function simplifier_check_state (line 8964) | static void function print_segment_chain (line 9044) | static void function simplifier_print_state (line 9054) | static void function tsk_segment_t (line 9141) | static tsk_segment_t *TSK_WARN_UNUSED function interval_list_t (line 9158) | static interval_list_t *TSK_WARN_UNUSED function tsk_id_t (line 9176) | static tsk_id_t TSK_WARN_UNUSED function simplifier_rewind_node (line 9196) | static int function simplifier_flush_edges (line 9203) | static int function simplifier_init_position_lookup (line 9239) | static int function simplifier_map_reduced_coordinates (line 9263) | static bool function simplifier_record_edge (line 9287) | static int function simplifier_init_sites (line 9332) | static int function simplifier_map_mutations (line 9373) | static void function simplifier_add_ancestry (line 9392) | static int TSK_WARN_UNUSED function simplifier_init_tables (line 9429) | static int function simplifier_init_nodes (line 9474) | static int function simplifier_init (line 9525) | static int function simplifier_free (line 9624) | static int function simplifier_enqueue_segment (line 9647) | static int TSK_WARN_UNUSED function simplifier_merge_ancestors (line 9676) | static int TSK_WARN_UNUSED function simplifier_extract_ancestry (line 9790) | static int TSK_WARN_UNUSED function simplifier_process_parent_edges (line 9853) | static int TSK_WARN_UNUSED function simplifier_finalise_site_references (line 9884) | static int TSK_WARN_UNUSED function simplifier_finalise_population_references (line 9920) | static int TSK_WARN_UNUSED function simplifier_finalise_individual_references (line 9977) | static int TSK_WARN_UNUSED function simplifier_output_sites (line 10049) | static int TSK_WARN_UNUSED function simplifier_flush_output (line 10109) | static int TSK_WARN_UNUSED function simplifier_set_edge_sort_offset (line 10150) | static void function simplifier_sort_edges (line 10165) | static int TSK_WARN_UNUSED function simplifier_insert_input_roots (line 10179) | static int TSK_WARN_UNUSED function simplifier_run (line 10226) | static int TSK_WARN_UNUSED type index_sort_t (line 10284) | typedef struct { function cmp_index_sort (line 10293) | static int function tsk_table_collection_check_offsets (line 10311) | static int function tsk_table_collection_check_node_integrity (line 10361) | static int function tsk_table_collection_check_edge_integrity (line 10396) | static int function tsk_table_collection_check_site_integrity (line 10509) | static int TSK_WARN_UNUSED function tsk_table_collection_check_mutation_integrity (line 10547) | static int TSK_WARN_UNUSED function tsk_table_collection_check_migration_integrity (line 10662) | static int TSK_WARN_UNUSED function tsk_table_collection_check_individual_integrity (line 10727) | static int TSK_WARN_UNUSED function tsk_id_t (line 10764) | static tsk_id_t TSK_WARN_UNUSED function tsk_table_collection_check_index_integrity (line 10893) | static int TSK_WARN_UNUSED function tsk_table_collection_compute_mutation_parents_to_array (line 10920) | static int TSK_WARN_UNUSED function tsk_table_collection_check_mutation_parents (line 11027) | static int TSK_WARN_UNUSED function tsk_id_t (line 11062) | tsk_id_t TSK_WARN_UNUSED function tsk_table_collection_print_state (line 11138) | void function tsk_table_collection_init (line 11162) | int TSK_WARN_UNUSED function tsk_table_collection_free (line 11220) | int function tsk_table_collection_equals (line 11241) | bool function tsk_table_collection_set_time_units (line 11293) | int function tsk_table_collection_set_metadata (line 11301) | int function tsk_table_collection_takeset_metadata (line 11309) | int function tsk_table_collection_set_metadata_schema (line 11317) | int function tsk_table_collection_set_indexes (line 11325) | int function tsk_table_collection_takeset_indexes (line 11347) | int function tsk_table_collection_has_index (line 11365) | bool function tsk_table_collection_has_reference_sequence (line 11374) | bool function tsk_table_collection_drop_index (line 11380) | int function tsk_table_collection_build_index (line 11392) | int TSK_WARN_UNUSED function tsk_table_collection_set_file_uuid (line 11460) | static int TSK_WARN_UNUSED function tsk_table_collection_copy (line 11482) | int TSK_WARN_UNUSED function tsk_table_collection_read_format_data (line 11571) | static int TSK_WARN_UNUSED function tsk_table_collection_dump_indexes (line 11721) | static int TSK_WARN_UNUSED function tsk_table_collection_load_indexes (line 11742) | static int TSK_WARN_UNUSED function tsk_table_collection_load_reference_sequence (line 11787) | static int function tsk_table_collection_loadf_inited (line 11850) | static int TSK_WARN_UNUSED function tsk_table_collection_loadf (line 11942) | int TSK_WARN_UNUSED function tsk_table_collection_load (line 11961) | int TSK_WARN_UNUSED function tsk_table_collection_dump_reference_sequence (line 11997) | static int TSK_WARN_UNUSED function tsk_table_collection_dump (line 12018) | int TSK_WARN_UNUSED function tsk_table_collection_dumpf (line 12049) | int TSK_WARN_UNUSED function tsk_table_collection_simplify (line 12147) | int TSK_WARN_UNUSED function tsk_table_collection_link_ancestors (line 12207) | int TSK_WARN_UNUSED function tsk_table_collection_ibd_within (line 12236) | int TSK_WARN_UNUSED function tsk_table_collection_ibd_between (line 12268) | int TSK_WARN_UNUSED function tsk_table_collection_sort (line 12302) | int TSK_WARN_UNUSED function tsk_table_collection_canonicalise (line 12322) | int TSK_WARN_UNUSED function tsk_table_collection_deduplicate_sites (line 12364) | int TSK_WARN_UNUSED function tsk_table_collection_compute_mutation_parents (line 12434) | int TSK_WARN_UNUSED function tsk_table_collection_compute_mutation_times (line 12482) | int TSK_WARN_UNUSED function tsk_table_collection_delete_older (line 12612) | int TSK_WARN_UNUSED function tsk_table_collection_record_num_rows (line 12722) | int function tsk_table_collection_truncate (line 12737) | int TSK_WARN_UNUSED function tsk_table_collection_clear (line 12782) | int TSK_WARN_UNUSED function tsk_table_collection_add_and_remap_node (line 12843) | static int function tsk_table_collection_subset (line 12911) | int TSK_WARN_UNUSED function tsk_check_subset_equality (line 13142) | static int function tsk_table_collection_union (line 13211) | int TSK_WARN_UNUSED function cmp_edge_cl (line 13420) | static int function tsk_squash_edges (line 13439) | int TSK_WARN_UNUSED FILE: c/tskit/tables.h type tsk_individual_t (line 57) | typedef struct { type tsk_node_t (line 89) | typedef struct { type tsk_edge_t (line 114) | typedef struct { type tsk_mutation_t (line 139) | typedef struct { type tsk_site_t (line 175) | typedef struct { type tsk_migration_t (line 202) | typedef struct { type tsk_population_t (line 232) | typedef struct { type tsk_provenance_t (line 250) | typedef struct { type tsk_individual_table_t (line 275) | typedef struct { type tsk_node_table_t (line 319) | typedef struct { type tsk_edge_table_t (line 353) | typedef struct { type tsk_migration_table_t (line 389) | typedef struct { type tsk_site_table_t (line 427) | typedef struct { type tsk_mutation_table_t (line 462) | typedef struct { type tsk_population_table_t (line 503) | typedef struct { type tsk_provenance_table_t (line 529) | typedef struct { type tsk_reference_sequence_t (line 552) | typedef struct { type tsk_table_collection_t (line 566) | typedef struct { type tsk_bookmark_t (line 606) | typedef struct { type tsk_table_sorter_t (line 628) | typedef struct _tsk_table_sorter_t { type tsk_identity_segment_t (line 653) | typedef struct _tsk_identity_segment_t { type tsk_identity_segment_list_t (line 660) | typedef struct { type tsk_identity_segments_t (line 667) | typedef struct { type tsk_edge_list_node_t (line 678) | typedef struct _tsk_edge_list_node_t { type tsk_edge_list_t (line 684) | typedef struct { type _tsk_table_sorter_t (line 4722) | struct _tsk_table_sorter_t type _tsk_table_sorter_t (line 4756) | struct _tsk_table_sorter_t type _tsk_table_sorter_t (line 4764) | struct _tsk_table_sorter_t FILE: c/tskit/trees.c function is_discrete (line 36) | static inline bool function tsk_treeseq_check_state (line 46) | static void function tsk_treeseq_print_state (line 66) | void function tsk_treeseq_free (line 106) | int function tsk_treeseq_init_sites (line 128) | static int function tsk_treeseq_init_individuals (line 181) | static int function tsk_treeseq_init_trees (line 243) | static int function tsk_treeseq_init_migrations (line 361) | static void function tsk_treeseq_init_mutations (line 382) | static void function tsk_treeseq_init_nodes (line 404) | static int function tsk_treeseq_init (line 455) | int TSK_WARN_UNUSED function tsk_treeseq_copy_tables (line 547) | int TSK_WARN_UNUSED function tsk_treeseq_load (line 554) | int TSK_WARN_UNUSED function tsk_treeseq_loadf (line 584) | int TSK_WARN_UNUSED function tsk_treeseq_dump (line 614) | int TSK_WARN_UNUSED function tsk_treeseq_dumpf (line 620) | int TSK_WARN_UNUSED function tsk_size_t (line 634) | tsk_size_t function tsk_size_t (line 646) | tsk_size_t function tsk_size_t (line 658) | tsk_size_t function tsk_treeseq_get_sequence_length (line 664) | double function tsk_size_t (line 676) | tsk_size_t function tsk_size_t (line 682) | tsk_size_t function tsk_size_t (line 688) | tsk_size_t function tsk_size_t (line 694) | tsk_size_t function tsk_size_t (line 700) | tsk_size_t function tsk_size_t (line 706) | tsk_size_t function tsk_size_t (line 712) | tsk_size_t function tsk_size_t (line 718) | tsk_size_t function tsk_size_t (line 724) | tsk_size_t function tsk_size_t (line 730) | tsk_size_t function tsk_id_t (line 742) | const tsk_id_t * function tsk_id_t (line 748) | const tsk_id_t * function tsk_treeseq_is_sample (line 754) | bool function tsk_treeseq_get_discrete_genome (line 765) | bool function tsk_treeseq_get_discrete_time (line 771) | bool function tsk_treeseq_get_min_time (line 777) | double function tsk_treeseq_get_max_time (line 783) | double function tsk_treeseq_has_reference_sequence (line 789) | bool function tsk_treeseq_get_individuals_population (line 795) | int function tsk_treeseq_get_individuals_time (line 827) | int function increment_nd_array_value (line 872) | static inline void function tsk_treeseq_genealogical_nearest_neighbours (line 890) | int TSK_WARN_UNUSED function tsk_treeseq_mean_descendants (line 1075) | int TSK_WARN_UNUSED function tsk_treeseq_check_windows (line 1244) | static int function tsk_treeseq_check_time_windows (line 1288) | static int function update_state (line 1317) | static inline void function update_node_summary (line 1329) | static inline int function update_running_sum (line 1339) | static inline void function tsk_treeseq_branch_general_stat (line 1352) | static int function get_allele_weights (line 1525) | static int function compute_general_stat_site_result (line 1614) | static int function tsk_treeseq_site_general_stat (line 1654) | static int function increment_row (line 1778) | static inline void function tsk_treeseq_node_general_stat (line 1788) | static int function span_normalise (line 1920) | static void type unpolarised_summary_func_args (line 1936) | typedef struct { function unpolarised_summary_func (line 1944) | static int function tsk_polarisable_func_general_stat (line 1979) | static int function tsk_treeseq_general_stat (line 2035) | int function check_set_indexes (line 2097) | static int function tsk_treeseq_check_sample_sets (line 2114) | static int type weight_stat_params_t (line 2151) | typedef struct { type covariates_stat_params_t (line 2155) | typedef struct { type sample_count_stat_params_t (line 2161) | typedef struct { type indexed_weight_stat_params_t (line 2168) | typedef struct { function tsk_treeseq_sample_count_stat (line 2174) | static int function get_allele_samples (line 2226) | static int function norm_hap_weighted (line 2300) | static int function norm_hap_weighted_ij (line 2317) | static int function norm_total_weighted (line 2343) | static int function get_all_samples_bits (line 2356) | static void type two_locus_work_t (line 2371) | typedef struct { function two_locus_work_init (line 2378) | static int function two_locus_work_free (line 2401) | static void function compute_general_normed_two_site_stat_result (line 2410) | static int function compute_general_two_site_stat_result (line 2463) | static int function get_site_row_col_indices (line 2494) | static void function get_mutation_samples (line 2539) | static int function get_mutation_sample_sets (line 2628) | static void function tsk_treeseq_two_site_count_stat (line 2652) | static int function sample_sets_to_bitset (line 2764) | static int function check_sites (line 2796) | static int function check_positions (line 2829) | static int function positions_to_tree_indexes (line 2863) | static int function get_index_counts (line 2891) | static int type iter_state (line 2922) | typedef struct { function iter_state_init (line 2933) | static int function get_node_samples (line 2965) | static int function iter_state_clear (line 2994) | static void function iter_state_free (line 3009) | static void function advance_collect_edges (line 3021) | static int function compute_two_tree_branch_state_update (line 3089) | static int function compute_two_tree_branch_stat (line 3142) | static int function tsk_treeseq_two_branch_count_stat (line 3242) | static int function check_sample_set_dups (line 3353) | static int function tsk_treeseq_two_locus_count_stat (line 3387) | int function fold (line 3469) | static inline void function tsk_treeseq_update_site_afs (line 3498) | static int function tsk_treeseq_site_allele_frequency_spectrum (line 3547) | static int function tsk_treeseq_update_branch_afs (line 3650) | static void function tsk_treeseq_branch_allele_frequency_spectrum (line 3696) | static int function tsk_treeseq_allele_frequency_spectrum (line 3815) | int function diversity_summary_func (line 3934) | static int function tsk_treeseq_diversity (line 3950) | int function trait_covariance_summary_func (line 3960) | static int function tsk_treeseq_trait_covariance (line 3975) | int function trait_correlation_summary_func (line 4025) | static int function tsk_treeseq_trait_correlation (line 4046) | int function trait_linear_model_summary_func (line 4107) | static int function tsk_treeseq_trait_linear_model (line 4153) | int function segregating_sites_summary_func (line 4221) | static int function tsk_treeseq_segregating_sites (line 4238) | int function Y1_summary_func (line 4248) | static int function tsk_treeseq_Y1 (line 4266) | int function D_summary_func (line 4276) | static int function tsk_treeseq_D (line 4300) | int function D2_summary_func (line 4314) | static int function tsk_treeseq_D2 (line 4339) | int function r2_summary_func (line 4352) | static int function tsk_treeseq_r2 (line 4379) | int function D_prime_summary_func (line 4391) | static int function tsk_treeseq_D_prime (line 4421) | int function r_summary_func (line 4435) | static int function tsk_treeseq_r (line 4462) | int function Dz_summary_func (line 4476) | static int function tsk_treeseq_Dz (line 4502) | int function pi2_summary_func (line 4515) | static int function tsk_treeseq_pi2 (line 4538) | int function D2_unbiased_summary_func (line 4551) | static int function tsk_treeseq_D2_unbiased (line 4575) | int function Dz_unbiased_summary_func (line 4588) | static int function tsk_treeseq_Dz_unbiased (line 4613) | int function pi2_unbiased_summary_func (line 4626) | static int function tsk_treeseq_pi2_unbiased (line 4650) | int function check_sample_stat_inputs (line 4667) | static int function divergence_summary_func (line 4690) | static int function tsk_treeseq_divergence (line 4711) | int function genetic_relatedness_summary_func (line 4729) | static int function genetic_relatedness_noncentred_summary_func (line 4755) | static int function tsk_treeseq_genetic_relatedness (line 4775) | int function genetic_relatedness_weighted_summary_func (line 4800) | static int function genetic_relatedness_weighted_noncentred_summary_func (line 4821) | static int function tsk_treeseq_genetic_relatedness_weighted (line 4838) | int function Y2_summary_func (line 4899) | static int function tsk_treeseq_Y2 (line 4920) | int function f2_summary_func (line 4938) | static int function tsk_treeseq_f2 (line 4961) | int function D2_ij_summary_func (line 4979) | static int function tsk_treeseq_D2_ij (line 5018) | int function D2_ij_unbiased_summary_func (line 5039) | static int function tsk_treeseq_D2_ij_unbiased (line 5092) | int function r2_ij_summary_func (line 5113) | static int function tsk_treeseq_r2_ij (line 5152) | int function Y3_summary_func (line 5177) | static int function tsk_treeseq_Y3 (line 5201) | int function f3_summary_func (line 5219) | static int function tsk_treeseq_f3 (line 5244) | int function f4_summary_func (line 5266) | static int function tsk_treeseq_f4 (line 5293) | int function tsk_treeseq_get_node (line 5313) | int TSK_WARN_UNUSED function tsk_treeseq_get_edge (line 5319) | int TSK_WARN_UNUSED function tsk_treeseq_get_migration (line 5325) | int TSK_WARN_UNUSED function tsk_treeseq_get_mutation (line 5332) | int TSK_WARN_UNUSED function tsk_treeseq_get_site (line 5350) | int TSK_WARN_UNUSED function tsk_treeseq_get_individual (line 5365) | int TSK_WARN_UNUSED function tsk_treeseq_get_population (line 5381) | int TSK_WARN_UNUSED function tsk_treeseq_get_provenance (line 5388) | int TSK_WARN_UNUSED function tsk_treeseq_simplify (line 5395) | int TSK_WARN_UNUSED function tsk_treeseq_split_edges (line 5427) | int TSK_WARN_UNUSED function tsk_tree_position_set_null (line 5546) | static void function tsk_tree_position_init (line 5554) | int function tsk_tree_position_free (line 5564) | int function tsk_tree_position_print_state (line 5570) | int function tsk_tree_position_next (line 5583) | bool function tsk_tree_position_prev (line 5641) | bool function tsk_tree_position_seek_forward (line 5701) | int TSK_WARN_UNUSED function tsk_tree_position_seek_backward (line 5765) | int TSK_WARN_UNUSED function tsk_id_t (line 5838) | static tsk_id_t function tsk_tree_init (line 5849) | int TSK_WARN_UNUSED function tsk_tree_set_root_threshold (line 5912) | int function tsk_size_t (line 5934) | tsk_size_t function tsk_tree_free (line 5940) | int function tsk_tree_has_sample_lists (line 5959) | bool function tsk_tree_has_sample_counts (line 5965) | bool function tsk_tree_reset_tracked_samples (line 5971) | static int TSK_WARN_UNUSED function tsk_tree_set_tracked_samples (line 5986) | int TSK_WARN_UNUSED function tsk_tree_track_descendant_samples (line 6028) | int TSK_WARN_UNUSED function tsk_tree_copy (line 6073) | int TSK_WARN_UNUSED function tsk_tree_equals (line 6132) | bool TSK_WARN_UNUSED function tsk_tree_check_node (line 6143) | static int function tsk_tree_is_descendant (line 6153) | bool function tsk_tree_get_mrca (line 6169) | int TSK_WARN_UNUSED function tsk_tree_get_num_samples_by_traversal (line 6215) | static int function tsk_tree_get_num_samples (line 6246) | int TSK_WARN_UNUSED function tsk_tree_get_num_tracked_samples (line 6265) | int TSK_WARN_UNUSED function tsk_tree_is_sample (line 6284) | bool function tsk_id_t (line 6290) | tsk_id_t function tsk_id_t (line 6296) | tsk_id_t function tsk_size_t (line 6302) | tsk_size_t function tsk_tree_get_parent (line 6308) | int TSK_WARN_UNUSED function tsk_tree_get_time (line 6322) | int TSK_WARN_UNUSED function tsk_tree_get_branch_length_unsafe (line 6341) | static inline double function tsk_tree_get_branch_length (line 6350) | int TSK_WARN_UNUSED function tsk_tree_get_total_branch_length (line 6364) | int function tsk_tree_get_sites (line 6398) | int TSK_WARN_UNUSED function tsk_tree_get_depth_unsafe (line 6408) | static int function tsk_tree_get_depth (line 6424) | int TSK_WARN_UNUSED function tsk_id_t (line 6439) | static tsk_id_t function tsk_tree_check_state (line 6450) | static void function tsk_tree_print_state (line 6529) | void function tsk_tree_update_sample_lists (line 6577) | static inline void function tsk_tree_remove_branch (line 6612) | static inline void function tsk_tree_insert_branch (line 6640) | static inline void function tsk_tree_insert_root (line 6666) | static inline void function tsk_tree_remove_root (line 6673) | static inline void function tsk_tree_remove_edge (line 6679) | static void function tsk_tree_insert_edge (line 6721) | static void function tsk_tree_first (line 6762) | int TSK_WARN_UNUSED function tsk_tree_last (line 6776) | int TSK_WARN_UNUSED function tsk_tree_update_index_and_interval (line 6790) | static void function tsk_tree_next (line 6805) | int TSK_WARN_UNUSED function tsk_tree_prev (line 6837) | int TSK_WARN_UNUSED function tsk_tree_position_in_interval (line 6869) | static inline bool function tsk_tree_seek_from_null (line 6875) | static int function tsk_tree_seek_forward (line 6929) | static int TSK_WARN_UNUSED function tsk_tree_seek_backward (line 6971) | static int TSK_WARN_UNUSED function tsk_tree_seek_index (line 7013) | int TSK_WARN_UNUSED function tsk_tree_seek_linear (line 7029) | static int TSK_WARN_UNUSED function tsk_tree_seek_skip (line 7069) | static int TSK_WARN_UNUSED function tsk_tree_seek (line 7092) | int TSK_WARN_UNUSED function tsk_tree_clear (line 7117) | int TSK_WARN_UNUSED function tsk_size_t (line 7186) | tsk_size_t function tsk_id_t (line 7213) | static tsk_id_t * function tsk_tree_preorder (line 7219) | int function tsk_tree_preorder_from (line 7225) | int function tsk_tree_preorder_samples_from (line 7282) | int function tsk_tree_postorder (line 7341) | int function tsk_tree_postorder_from (line 7346) | int function tsk_tree_sackin_index (line 7413) | int function tsk_tree_colless_index (line 7468) | int function tsk_tree_b1_index (line 7519) | int function general_log (line 7559) | static double function tsk_tree_b2_index (line 7565) | int function tsk_tree_num_lineages (line 7621) | int function set_bit (line 7672) | static inline uint64_t function bit_is_set (line 7678) | static inline bool function get_smallest_set_bit (line 7684) | static inline int8_t function tsk_tree_map_mutations (line 7714) | int TSK_WARN_UNUSED type kc_vectors (line 7870) | typedef struct { function kc_vectors_alloc (line 7877) | static int function kc_vectors_free (line 7895) | static void function update_kc_vectors_single_sample (line 7902) | static inline void function update_kc_vectors_all_pairs (line 7913) | static inline void type kc_stack_elmt (line 7954) | struct kc_stack_elmt { function fill_kc_vectors (line 7959) | static int function norm_kc_vectors (line 8014) | static double function check_kc_distance_tree_inputs (line 8030) | static int function check_kc_distance_samples_inputs (line 8057) | static int function tsk_tree_kc_distance (line 8082) | int function check_kc_distance_tree_sequence_inputs (line 8126) | static int function update_kc_pair_with_sample (line 8146) | static void function update_kc_subtree_state (line 8168) | static int function update_kc_incremental (line 8206) | static int function tsk_treeseq_kc_distance (line 8256) | int type sv_tables_t (line 8363) | typedef struct { function sv_tables_init (line 8378) | static int function sv_tables_free (line 8401) | static int function sv_tables_reset (line 8414) | static void function sv_tables_convert_tree (line 8428) | static void function sv_tables_build_index (line 8450) | static void function sv_tables_build (line 8526) | static void function tsk_id_t (line 8534) | static tsk_id_t function tsk_id_t (line 8572) | static tsk_id_t function tsk_treeseq_divergence_matrix_branch (line 8579) | static int function update_site_divergence (line 8684) | static void function group_alleles (line 8717) | static void function remap_to_sample_sets (line 8739) | static void function tsk_treeseq_divergence_matrix_site (line 8753) | static int function get_sample_set_index_map (line 8832) | static int function fill_lower_triangle_count_normalise (line 8876) | static void function tsk_treeseq_divergence_matrix (line 8901) | int type edge_list_t (line 9007) | typedef struct _edge_list_t { function edge_list_print (line 9015) | static void function edge_list_append_entry (line 9036) | static void function remove_unextended (line 9052) | static void function edge_list_set_extended (line 9078) | static void function tsk_treeseq_slide_mutation_nodes_up (line 9094) | static int type haplotype_extender_t (line 9142) | typedef struct { function haplotype_extender_init (line 9156) | static int function haplotype_extender_print_state (line 9220) | static void function haplotype_extender_free (line 9264) | static int function haplotype_extender_next_tree (line 9278) | static int function haplotype_extender_add_or_extend_edge (line 9360) | static int function haplotype_extender_mergeable (line 9430) | static float function haplotype_extender_merge_paths (line 9482) | static int function haplotype_extender_extend_paths (line 9531) | static int function extend_haplotypes_iter (line 9617) | static int function tsk_treeseq_extend_haplotypes (line 9643) | int TSK_WARN_UNUSED function check_node_bin_map (line 9749) | static int function TRANSPOSE_2D (line 9776) | static inline void function pair_coalescence_count (line 9787) | static inline void function tsk_treeseq_pair_coalescence_stat (line 9807) | int function pair_coalescence_weights (line 10132) | static int function tsk_treeseq_pair_coalescence_counts (line 10142) | int function pair_coalescence_quantiles (line 10154) | static int function check_quantiles (line 10184) | static int function check_sorted_node_bin_map (line 10201) | static int function tsk_treeseq_pair_coalescence_quantiles (line 10250) | int function pair_coalescence_rates (line 10280) | static int function check_coalescence_rate_time_windows (line 10313) | static int function tsk_treeseq_pair_coalescence_rates (line 10372) | int type tsk_matvec_calculator_t (line 10402) | typedef struct { function tsk_matvec_calculator_print_state (line 10421) | static void function tsk_matvec_calculator_init (line 10445) | static int function tsk_matvec_calculator_free (line 10539) | static int function tsk_matvec_calculator_add_z (line 10553) | static inline void function tsk_matvec_calculator_adjust_path_up (line 10575) | static void function tsk_matvec_calculator_remove_edge (line 10609) | static void function tsk_matvec_calculator_insert_edge (line 10626) | static void function tsk_matvec_calculator_write_output (line 10636) | static int function tsk_matvec_calculator_run (line 10702) | static int function tsk_treeseq_genetic_relatedness_vector (line 10782) | int FILE: c/tskit/trees.h type tsk_treeseq_t (line 86) | typedef struct { type tsk_tree_position_t (line 121) | typedef struct { type tsk_tree_t (line 169) | typedef struct { type tsk_state_transition_t (line 1971) | typedef struct { FILE: python/_tskitmodule.c type TableCollection (line 80) | typedef struct _TableCollection { type IndividualTable (line 90) | typedef struct { type NodeTable (line 97) | typedef struct { type EdgeTable (line 104) | typedef struct { type SiteTable (line 111) | typedef struct { type MutationTable (line 118) | typedef struct { type MigrationTable (line 125) | typedef struct { type PopulationTable (line 132) | typedef struct { type ProvenanceTable (line 139) | typedef struct { type TreeSequence (line 146) | typedef struct { type Tree (line 151) | typedef struct { type Variant (line 157) | typedef struct { type LdCalculator (line 163) | typedef struct { type LsHmm (line 169) | typedef struct { type CompressedMatrix (line 175) | typedef struct { type ViterbiMatrix (line 181) | typedef struct { type ReferenceSequence (line 187) | typedef struct { type IdentitySegments (line 194) | typedef struct { type IdentitySegmentList (line 199) | typedef struct { function handle_library_error (line 230) | static void function PyObject (line 306) | static PyObject * function PyObject (line 331) | static PyObject * function PyObject (line 338) | static PyObject * function PyObject (line 356) | static PyObject * function PyObject (line 375) | static PyObject * function PyObject (line 400) | static PyObject * function PyObject (line 415) | static PyObject * function PyObject (line 426) | static PyObject * function PyObject (line 455) | static PyObject * function PyObject (line 487) | static PyObject * function PyObject (line 502) | static PyObject * function PyObject (line 523) | static PyObject * function PyObject (line 540) | static PyObject * function PyObject (line 557) | static PyObject * function PyObject (line 582) | static PyObject * function PyObject (line 615) | static PyObject * function PyObject (line 635) | static PyObject * function PyObject (line 660) | static PyObject * function PyObject (line 687) | static PyObject * function PyObject (line 721) | static PyObject * function parse_sample_sets (line 798) | static int function PyObject (line 850) | static PyObject * function PyObject (line 868) | static PyObject * function FILE (line 886) | static FILE * function uint32_converter (line 913) | static int function tsk_id_converter (line 938) | static int function array_converter (line 963) | static int function int32_array_converter (line 981) | static int function bool_array_converter (line 987) | static int function PyObject (line 1001) | static PyObject * function DEFINE_TABLE_METADATA_SCHEMA_SETTER (line 1415) | DEFINE_TABLE_METADATA_SCHEMA_GETTER(Individual) function PyObject (line 1493) | static PyObject * function DEFINE_TABLE_METADATA_SCHEMA_SETTER (line 1669) | DEFINE_TABLE_METADATA_SCHEMA_GETTER(Node) function PyObject (line 1717) | static PyObject * function DEFINE_TABLE_METADATA_SCHEMA_SETTER (line 1857) | DEFINE_TABLE_METADATA_SCHEMA_GETTER(Edge) function PyObject (line 1901) | static PyObject * function PyObject (line 1939) | static PyObject * function DEFINE_TABLE_METADATA_SCHEMA_SETTER (line 2058) | DEFINE_TABLE_METADATA_SCHEMA_GETTER(Migration) function PyObject (line 2106) | static PyObject * function DEFINE_TABLE_METADATA_SCHEMA_SETTER (line 2245) | DEFINE_TABLE_METADATA_SCHEMA_GETTER(Site) function PyObject (line 2289) | static PyObject * function DEFINE_TABLE_METADATA_SCHEMA_SETTER (line 2428) | DEFINE_TABLE_METADATA_SCHEMA_GETTER(Mutation) function PyObject (line 2480) | static PyObject * function DEFINE_TABLE_METADATA_SCHEMA_SETTER (line 2625) | DEFINE_TABLE_METADATA_SCHEMA_GETTER(Population) function PyObject (line 2663) | static PyObject * function PyObject (line 2794) | static PyObject * function PyObject (line 2822) | static PyObject * function PyObject (line 2851) | static PyObject * function IdentitySegmentList_check_state (line 2972) | static int function IdentitySegmentList_check_segments_stored (line 2985) | static int function IdentitySegmentList_dealloc (line 2999) | static void function IdentitySegmentList_init (line 3008) | static int function PyObject (line 3019) | static PyObject * function PyObject (line 3033) | static PyObject * function PyObject (line 3047) | static PyObject * function PyObject (line 3080) | static PyObject * function PyObject (line 3113) | static PyObject * function IdentitySegments_check_state (line 3189) | static int function IdentitySegments_dealloc (line 3202) | static void function IdentitySegments_init (line 3213) | static int function PyObject (line 3229) | static PyObject * function PyObject (line 3272) | static PyObject * function PyObject (line 3302) | static PyObject * function PyObject (line 3328) | static PyObject * function PyObject (line 3342) | static PyObject * function PyObject (line 3356) | static PyObject * function ReferenceSequence_check_read (line 3423) | static int function ReferenceSequence_check_write (line 3436) | static int function ReferenceSequence_dealloc (line 3456) | static void function ReferenceSequence_init (line 3464) | static int function PyObject (line 3473) | static PyObject * function ReferenceSequence_set_string_attr (line 3492) | static int function ReferenceSequence_set_data (line 3527) | static int function PyObject (line 3534) | static PyObject * function ReferenceSequence_set_url (line 3548) | static int function PyObject (line 3555) | static PyObject * function ReferenceSequence_set_metadata_schema (line 3569) | static int function PyObject (line 3577) | static PyObject * function ReferenceSequence_set_metadata (line 3592) | static int function PyObject (line 3623) | static PyObject * function PyObject (line 3680) | static PyObject * function TableCollection_check_state (line 3711) | static int function TableCollection_alloc (line 3722) | static int function TableCollection_dealloc (line 3742) | static void function TableCollection_init (line 3753) | static int function PyObject (line 3790) | static PyObject * function PyObject (line 3810) | static PyObject * function PyObject (line 3830) | static PyObject * function PyObject (line 3850) | static PyObject * function PyObject (line 3870) | static PyObject * function PyObject (line 3890) | static PyObject * function PyObject (line 3910) | static PyObject * function PyObject (line 3930) | static PyObject * function PyObject (line 3950) | static PyObject * function TableCollection_set_sequence_length (line 3963) | static int function PyObject (line 3986) | static PyObject * function PyObject (line 3999) | static PyObject * function TableCollection_set_time_units (line 4013) | static int function PyObject (line 4039) | static PyObject * function TableCollection_set_metadata (line 4053) | static int function PyObject (line 4083) | static PyObject * function TableCollection_set_metadata_schema (line 4097) | static int function PyObject (line 4123) | static PyObject * function PyObject (line 4137) | static PyObject * function PyObject (line 4226) | static PyObject * function PyObject (line 4288) | static PyObject * function PyObject (line 4339) | static PyObject * function PyObject (line 4400) | static PyObject * function PyObject (line 4464) | static PyObject * function PyObject (line 4525) | static PyObject * function PyObject (line 4557) | static PyObject * function PyObject (line 4577) | static PyObject * function PyObject (line 4606) | static PyObject * function PyObject (line 4629) | static PyObject * function PyObject (line 4648) | static PyObject * function PyObject (line 4667) | static PyObject * function PyObject (line 4686) | static PyObject * function PyObject (line 4705) | static PyObject * function PyObject (line 4724) | static PyObject * function TableCollection_set_indexes (line 4770) | static int function PyObject (line 4789) | static PyObject * function PyObject (line 4803) | static PyObject * function PyObject (line 4817) | static PyObject * function PyObject (line 4869) | static PyObject * function PyObject (line 4908) | static PyObject * function PyObject (line 4942) | static PyObject * function PyObject (line 4994) | static PyObject * function PyObject (line 5013) | static PyObject * function TreeSequence_check_state (line 5208) | static int function TreeSequence_dealloc (line 5219) | static void function TreeSequence_alloc (line 5230) | static int function TreeSequence_init (line 5250) | static int function PyObject (line 5257) | static PyObject * function PyObject (line 5291) | static PyObject * function PyObject (line 5322) | static PyObject * function PyObject (line 5347) | static PyObject * function PyObject (line 5410) | static PyObject * function PyObject (line 5462) | static PyObject * function PyObject (line 5491) | static PyObject * function PyObject (line 5520) | static PyObject * function PyObject (line 5550) | static PyObject * function PyObject (line 5579) | static PyObject * function PyObject (line 5593) | static PyObject * function PyObject (line 5608) | static PyObject * function PyObject (line 5622) | static PyObject * function PyObject (line 5670) | static PyObject * function PyObject (line 5700) | static PyObject * function PyObject (line 5730) | static PyObject * function PyObject (line 5760) | static PyObject * function PyObject (line 5790) | static PyObject * function PyObject (line 5805) | static PyObject * function PyObject (line 5820) | static PyObject * function PyObject (line 5835) | static PyObject * function PyObject (line 5850) | static PyObject * function PyObject (line 5865) | static PyObject * function PyObject (line 5878) | static PyObject * function PyObject (line 5891) | static PyObject * function PyObject (line 5904) | static PyObject * function PyObject (line 5917) | static PyObject * function PyObject (line 5930) | static PyObject * function PyObject (line 5955) | static PyObject * function PyObject (line 5968) | static PyObject * function PyObject (line 5983) | static PyObject * function PyObject (line 5998) | static PyObject * function PyObject (line 6027) | static PyObject * function PyObject (line 6059) | static PyObject * function PyObject (line 6090) | static PyObject * function PyObject (line 6145) | static PyObject * function PyObject (line 6237) | static PyObject * function PyObject (line 6265) | static PyObject * function PyObject (line 6369) | static PyObject * function PyObject (line 6397) | static PyObject * function PyObject (line 6485) | static PyObject * function general_stat_func (line 6532) | static int function parse_stats_mode (line 6588) | static int function parse_windows (line 6609) | static int function PyArrayObject (line 6638) | static PyArrayObject * function PyObject (line 6665) | static PyObject * function PyObject (line 6747) | static PyObject * function PyObject (line 6820) | static PyObject * function PyObject (line 6909) | static PyObject * function PyObject (line 6977) | static PyObject * function PyObject (line 7064) | static PyObject * function PyObject (line 7070) | static PyObject * function PyObject (line 7077) | static PyObject * function PyObject (line 7084) | static PyObject * function PyObject (line 7091) | static PyObject * function PyObject (line 7098) | static PyObject * function PyObject (line 7104) | static PyObject * function PyObject (line 7196) | static PyObject * function PyObject (line 7284) | static PyObject * function PyObject (line 7376) | static PyObject * function PyObject (line 7382) | static PyObject * function PyObject (line 7389) | static PyObject * function PyObject (line 7397) | static PyObject * function PyObject (line 7405) | static PyObject * function PyObject (line 7411) | static PyObject * function PyObject (line 7417) | static PyObject * function PyObject (line 7423) | static PyObject * function PyObject (line 7429) | static PyObject * function PyObject (line 7435) | static PyObject * function parse_node_bin_map (line 7511) | static int function parse_set_indexes (line 7554) | static int function PyObject (line 7582) | static PyObject * function parse_quantiles (line 7670) | static int function PyObject (line 7697) | static PyObject * function parse_time_windows (line 7786) | static int function PyObject (line 7813) | static PyObject * function PyArrayObject (line 7901) | static PyArrayObject * function PyArrayObject (line 7926) | static PyArrayObject * function PyObject (line 7949) | static PyObject * function PyObject (line 8052) | static PyObject * function PyObject (line 8058) | static PyObject * function PyObject (line 8064) | static PyObject * function PyObject (line 8070) | static PyObject * function PyObject (line 8076) | static PyObject * function PyObject (line 8082) | static PyObject * function PyObject (line 8088) | static PyObject * function PyObject (line 8094) | static PyObject * function PyObject (line 8100) | static PyObject * function PyObject (line 8106) | static PyObject * function PyObject (line 8112) | static PyObject * function PyObject (line 8233) | static PyObject * function PyObject (line 8239) | static PyObject * function PyObject (line 8245) | static PyObject * function PyObject (line 8251) | static PyObject * function PyObject (line 8266) | static PyObject * function PyObject (line 8281) | static PyObject * function PyObject (line 8296) | static PyObject * function PyObject (line 8344) | static PyObject * function PyObject (line 8358) | static PyObject * function PyObject (line 8373) | static PyObject * function PyObject (line 8399) | static PyObject * function PyObject (line 8406) | PyObject * function PyObject (line 8483) | static PyObject * function PyObject (line 8625) | static PyObject * function PyObject (line 8641) | static PyObject * function Tree_check_state (line 9173) | static int function Tree_check_bounds (line 9184) | static int function Tree_dealloc (line 9195) | static void function Tree_init (line 9207) | static int function PyObject (line 9283) | static PyObject * function PyObject (line 9302) | static PyObject * function PyObject (line 9321) | static PyObject * function PyObject (line 9340) | static PyObject * function PyObject (line 9359) | static PyObject * function PyObject (line 9387) | static PyObject * function PyObject (line 9415) | static PyObject * function PyObject (line 9434) | static PyObject * function PyObject (line 9447) | static PyObject * function PyObject (line 9460) | static PyObject * function PyObject (line 9473) | static PyObject * function PyObject (line 9486) | static PyObject * function PyObject (line 9506) | static PyObject * function PyObject (line 9519) | static PyObject * function PyObject (line 9532) | static PyObject * function PyObject (line 9545) | static PyObject * function Tree_get_node_argument (line 9558) | static int function PyObject (line 9576) | static PyObject * function PyObject (line 9590) | static PyObject * function PyObject (line 9614) | static PyObject * function PyObject (line 9630) | static PyObject * function PyObject (line 9650) | static PyObject * function PyObject (line 9670) | static PyObject * function PyObject (line 9686) | static PyObject * function PyObject (line 9702) | static PyObject * function PyObject (line 9718) | static PyObject * function PyObject (line 9734) | static PyObject * function PyObject (line 9750) | static PyObject * function PyObject (line 9784) | static PyObject * function Tree_check_sample_list (line 9804) | static bool function PyObject (line 9815) | static PyObject * function PyObject (line 9834) | static PyObject * function PyObject (line 9853) | static PyObject * function PyObject (line 9880) | static PyObject * function PyObject (line 9910) | static PyObject * function PyObject (line 9926) | static PyObject * function PyObject (line 9946) | static PyObject * function PyObject (line 9967) | static PyObject * function PyObject (line 9980) | static PyObject * function PyObject (line 9993) | static PyObject * function PyObject (line 10045) | static PyObject * function PyObject (line 10114) | static PyObject * function PyObject (line 10134) | static PyObject * function PyObject (line 10166) | static PyObject * function PyObject (line 10193) | static PyObject * function PyObject (line 10214) | static PyObject * function PyObject (line 10235) | static PyObject * function PyObject (line 10256) | static PyObject * function PyObject (line 10280) | static PyObject * function PyObject (line 10304) | static PyObject * function PyObject (line 10317) | static PyObject * function PyObject (line 10344) | static PyObject * function PyObject (line 10393) | static PyObject * function PyObject (line 10399) | static PyObject * function PyObject (line 10411) | static PyObject * function PyObject (line 10417) | static PyObject * function PyObject (line 10430) | static PyObject * function PyObject (line 10443) | static PyObject * function PyObject (line 10456) | static PyObject * function PyObject (line 10469) | static PyObject * function PyObject (line 10482) | static PyObject * function PyObject (line 10495) | static PyObject * function Variant_check_state (line 10765) | static int function Variant_dealloc (line 10776) | static void function Variant_init (line 10788) | static int function PyObject (line 10857) | static PyObject * function PyObject (line 10881) | static PyObject * function PyObject (line 10915) | static PyObject * function PyObject (line 10927) | static PyObject * function PyObject (line 10940) | static PyObject * function PyObject (line 10953) | static PyObject * function PyObject (line 10968) | static PyObject * function LdCalculator_check_state (line 11050) | static int function LdCalculator_dealloc (line 11061) | static void function LdCalculator_init (line 11073) | static int function PyObject (line 11108) | static PyObject * function PyObject (line 11132) | static PyObject * function CompressedMatrix_check_state (line 11236) | static int function CompressedMatrix_dealloc (line 11249) | static void function CompressedMatrix_init (line 11261) | static int function PyObject (line 11299) | static PyObject * function PyObject (line 11312) | static PyObject * function PyObject (line 11336) | static PyObject * function PyObject (line 11360) | static PyObject * function PyObject (line 11377) | static PyObject * function ViterbiMatrix_check_state (line 11434) | static int function ViterbiMatrix_dealloc (line 11447) | static void function ViterbiMatrix_init (line 11459) | static int function PyObject (line 11497) | static PyObject * function PyObject (line 11526) | static PyObject * function PyObject (line 11547) | static PyObject * function PyObject (line 11571) | static PyObject * function PyObject (line 11596) | static PyObject * function PyObject (line 11613) | static PyObject * function LsHmm_check_state (line 11674) | static int function LsHmm_dealloc (line 11687) | static void function LsHmm_init (line 11699) | static int function PyObject (line 11777) | static PyObject * function PyObject (line 11818) | static PyObject * function PyObject (line 11876) | static PyObject * function PyObject (line 11952) | static PyObject * function PyObject (line 11958) | static PyObject * type PyModuleDef (line 11976) | struct PyModuleDef function PyObject (line 11984) | PyObject * FILE: python/benchmark/run-for-all-releases.py function versions (line 9) | def versions(package_name): function sh (line 15) | def sh(command): FILE: python/benchmark/run.py function system_info (line 25) | def system_info(): function make_file (line 44) | def make_file(): function autotime (line 77) | def autotime(setup, code): function run_benchmarks (line 88) | def run_benchmarks(keyword_filter): function generate_report (line 135) | def generate_report(all_versions_results): function print_result (line 196) | def print_result(results): function run_benchmark_and_save (line 212) | def run_benchmark_and_save(keyword_filter, print_results): FILE: python/lwt_interface/cython_example/_lwtc.c type PyModuleDef (line 45) | struct PyModuleDef function PyMODINIT_FUNC (line 52) | PyMODINIT_FUNC FILE: python/lwt_interface/dict_encoding_testlib.py function full_ts (line 46) | def full_ts(): function tables (line 103) | def tables(full_ts): function test_check_ts_full (line 107) | def test_check_ts_full(tmp_path, full_ts): class TestEncodingVersion (line 117) | class TestEncodingVersion: method test_version (line 118) | def test_version(self): class TestRoundTrip (line 123) | class TestRoundTrip: method verify (line 128) | def verify(self, tables): method test_simple (line 134) | def test_simple(self): method test_empty (line 138) | def test_empty(self): method test_individuals (line 142) | def test_individuals(self): method test_sequence_length (line 152) | def test_sequence_length(self): method test_migration (line 158) | def test_migration(self): method test_example (line 170) | def test_example(self, tables): class TestMissingData (line 194) | class TestMissingData: method test_missing_sequence_length (line 199) | def test_missing_sequence_length(self, tables): method test_missing_time_units (line 206) | def test_missing_time_units(self, tables): method test_missing_metadata (line 215) | def test_missing_metadata(self, tables): method test_missing_metadata_schema (line 225) | def test_missing_metadata_schema(self, tables): method test_missing_tables (line 234) | def test_missing_tables(self, tables): class TestBadTypes (line 253) | class TestBadTypes: method verify_columns (line 258) | def verify_columns(self, value, tables): method test_2d_array (line 280) | def test_2d_array(self, tables): method test_str (line 283) | def test_str(self, tables): method test_bad_top_level_types (line 286) | def test_bad_top_level_types(self, tables): class TestBadLengths (line 297) | class TestBadLengths: method verify (line 302) | def verify(self, num_rows, tables): method test_two_rows (line 324) | def test_two_rows(self, tables): method test_zero_rows (line 327) | def test_zero_rows(self, tables): method test_bad_index_length (line 330) | def test_bad_index_length(self, tables): class TestParsingUtilities (line 354) | class TestParsingUtilities: method test_missing_required (line 355) | def test_missing_required(self, tables): method test_string_bad_type (line 362) | def test_string_bad_type(self, tables): method test_bytes_bad_type (line 369) | def test_bytes_bad_type(self, tables): method test_dict_bad_type (line 376) | def test_dict_bad_type(self, tables): method test_bad_strings (line 383) | def test_bad_strings(self, tables): class TestRequiredAndOptionalColumns (line 412) | class TestRequiredAndOptionalColumns: method verify_required_columns (line 418) | def verify_required_columns(self, tables, table_name, required_cols): method verify_optional_column (line 450) | def verify_optional_column(self, tables, table_len, table_name, col_na... method verify_offset_pair (line 461) | def verify_offset_pair( method verify_metadata_schema (line 531) | def verify_metadata_schema(self, tables, table_name): method test_individuals (line 541) | def test_individuals(self, tables): method test_nodes (line 562) | def test_nodes(self, tables): method test_edges (line 569) | def test_edges(self, tables): method test_migrations (line 576) | def test_migrations(self, tables): method test_sites (line 584) | def test_sites(self, tables): method test_mutations (line 591) | def test_mutations(self, tables): method test_populations (line 607) | def test_populations(self, tables): method test_provenances (line 614) | def test_provenances(self, tables): method test_index (line 621) | def test_index(self, tables): method test_index_bad_type (line 655) | def test_index_bad_type(self, tables): method test_reference_sequence (line 662) | def test_reference_sequence(self, tables): method test_top_level_time_units (line 684) | def test_top_level_time_units(self, tables): method test_top_level_metadata (line 700) | def test_top_level_metadata(self, tables): method test_top_level_metadata_schema (line 712) | def test_top_level_metadata_schema(self, tables): class TestLifecycle (line 725) | class TestLifecycle: method test_unassigned_empty (line 726) | def test_unassigned_empty(self): method test_del_empty (line 730) | def test_del_empty(self): method test_del_full (line 736) | def test_del_full(self, tables): method test_del_lwt_and_tables (line 743) | def test_del_lwt_and_tables(self, tables): class TestForceOffset64 (line 753) | class TestForceOffset64: method get_offset_columns (line 754) | def get_offset_columns(self, dict_encoding): method test_bad_args (line 761) | def test_bad_args(self, tables): method test_off_by_default (line 768) | def test_off_by_default(self, tables): method test_types_64 (line 775) | def test_types_64(self, tables): method test_types_32 (line 782) | def test_types_32(self, tables): method test_values_equal (line 789) | def test_values_equal(self, tables): function test_fromdict_bad_type (line 803) | def test_fromdict_bad_type(bad_type): FILE: python/lwt_interface/example_c_module.c function PyObject (line 41) | static PyObject * function PyObject (line 90) | static PyObject * example_modifying(PyObject *self, PyObject *args) { type PyModuleDef (line 134) | struct PyModuleDef function PyMODINIT_FUNC (line 141) | PyMODINIT_FUNC FILE: python/lwt_interface/setup.py class local_build_ext (line 12) | class local_build_ext(build_ext): # noqa N801 method finalize_options (line 13) | def finalize_options(self): FILE: python/lwt_interface/test_example_c_module.py function test_example_receiving (line 27) | def test_example_receiving(): function test_example_modifying (line 48) | def test_example_modifying(): FILE: python/lwt_interface/tskit_lwt_interface.h type LightweightTableCollection (line 33) | typedef struct { function handle_tskit_error (line 40) | static void function PyObject (line 46) | static PyObject * function PyObject (line 68) | static PyObject * function PyObject (line 86) | static PyObject * function PyObject (line 104) | static PyObject * function PyObject (line 122) | static PyObject * function PyArrayObject (line 140) | static PyArrayObject * function PyArrayObject (line 168) | static PyArrayObject * function parse_individual_table_dict (line 226) | static int function parse_node_table_dict (line 394) | static int function parse_edge_table_dict (line 533) | static int function parse_migration_table_dict (line 663) | static int function parse_site_table_dict (line 817) | static int function parse_mutation_table_dict (line 942) | static int function parse_population_table_dict (line 1113) | static int function parse_provenance_table_dict (line 1187) | static int function parse_indexes_dict (line 1265) | static int function parse_reference_sequence_dict (line 1328) | static int function parse_table_collection_dict (line 1411) | static int type tsklwt_table_col_t (line 1582) | typedef struct _tsklwt_table_col_t { type tsklwt_ragged_col_t (line 1589) | typedef struct _tsklwt_ragged_col_t { type tsklwt_table_desc_t (line 1598) | typedef struct _tsklwt_table_desc_t { function write_table_col (line 1606) | static int function write_ragged_col (line 1626) | static int function write_string_to_dict (line 1675) | static int function write_bytes_to_dict (line 1693) | static int function PyObject (line 1712) | static PyObject * function write_table_arrays (line 1753) | static int function write_top_level_data (line 1942) | static int function PyObject (line 1996) | static PyObject * function PyObject (line 2035) | static PyObject * function LightweightTableCollection_check_state (line 2081) | static int function LightweightTableCollection_dealloc (line 2092) | static void function LightweightTableCollection_init (line 2103) | static int function PyObject (line 2132) | static PyObject * function PyObject (line 2151) | static PyObject * function register_lwt_class (line 2199) | static int FILE: python/stress_lowlevel.py function main (line 18) | def main(stdscr): FILE: python/tests/__init__.py class PythonTree (line 32) | class PythonTree: method __init__ (line 39) | def __init__(self, num_nodes): method from_tree (line 56) | def from_tree(cls, tree): method roots (line 75) | def roots(self): method children (line 83) | def children(self, u): method get_interval (line 91) | def get_interval(self): method get_parent (line 94) | def get_parent(self, node): method get_children (line 97) | def get_children(self, node): method get_index (line 100) | def get_index(self): method get_parent_dict (line 103) | def get_parent_dict(self): method sites (line 111) | def sites(self): method __eq__ (line 114) | def __eq__(self, other): method __ne__ (line 123) | def __ne__(self, other): class PythonTreeSequence (line 127) | class PythonTreeSequence: method __init__ (line 136) | def __init__(self, tree_sequence, breakpoints=None): method trees (line 186) | def trees(self): class MRCACalculator (line 209) | class MRCACalculator: method __init__ (line 225) | def __init__(self, oriented_forest): method __preprocess (line 231) | def __preprocess(self, oriented_forest): method get_mrca (line 302) | def get_mrca(self, x, y): method _sv_mrca (line 314) | def _sv_mrca(self, x, y): function base64_encode (line 339) | def base64_encode(metadata): function cached_example (line 347) | def cached_example(ts_func): FILE: python/tests/conftest.py function pytest_addoption (line 48) | def pytest_addoption(parser): function pytest_configure (line 75) | def pytest_configure(config): function pytest_collection_modifyitems (line 83) | def pytest_collection_modifyitems(config, items): function overwrite_viz (line 97) | def overwrite_viz(request): function draw_plotbox (line 102) | def draw_plotbox(request): function simple_degree1_ts_fixture (line 107) | def simple_degree1_ts_fixture(): function simple_degree2_ts_fixture (line 112) | def simple_degree2_ts_fixture(): function ts_fixture (line 119) | def ts_fixture(): function ts_fixture_for_simplify (line 127) | def ts_fixture_for_simplify(): function replicate_ts_fixture (line 135) | def replicate_ts_fixture(): FILE: python/tests/ibd.py class Segment (line 34) | class Segment: method __init__ (line 43) | def __init__(self, left=None, right=None, node=None, next_seg=None): method __str__ (line 49) | def __str__(self): method __repr__ (line 55) | def __repr__(self): method __eq__ (line 58) | def __eq__(self, other): method __lt__ (line 66) | def __lt__(self, other): class SegmentList (line 74) | class SegmentList: method __init__ (line 82) | def __init__(self, head=None, tail=None): method __str__ (line 86) | def __str__(self): method __repr__ (line 89) | def __repr__(self): method extend (line 97) | def extend(self, seglist): method append (line 110) | def append(self, segment): class IbdResult (line 123) | class IbdResult: method __init__ (line 129) | def __init__(self): method __repr__ (line 132) | def __repr__(self): method __str__ (line 135) | def __str__(self): method add_segment_deprecated (line 138) | def add_segment_deprecated(self, a, b, seg): method add_segment (line 143) | def add_segment(self, a, b, seg): class IbdFinder (line 203) | class IbdFinder: method __init__ (line 208) | def __init__(self, ts, *, within=None, between=None, min_span=0, max_t... method print_state (line 232) | def print_state(self): method run (line 241) | def run(self, squash=False): method record_ibd (line 265) | def record_ibd(self, current_parent, child_segs, squash): method filter_by_min_span (line 299) | def filter_by_min_span(self): method passes_filters (line 316) | def passes_filters(self, a, b, left, right): FILE: python/tests/simplify.py function overlapping_segments (line 35) | def overlapping_segments(segments): class Segment (line 70) | class Segment: method __init__ (line 79) | def __init__(self, left=None, right=None, node=None, next_segment=None): method __str__ (line 85) | def __str__(self): method __repr__ (line 91) | def __repr__(self): method __lt__ (line 94) | def __lt__(self, other): class Simplifier (line 98) | class Simplifier: method __init__ (line 104) | def __init__( method record_node (line 179) | def record_node(self, input_id): method rewind_node (line 195) | def rewind_node(self, input_id, output_id): method flush_edges (line 205) | def flush_edges(self): method record_edge (line 218) | def record_edge(self, left, right, parent, child): method print_state (line 247) | def print_state(self): method map_mutations (line 273) | def map_mutations(self, left, right, input_id, output_id): method add_ancestry (line 285) | def add_ancestry(self, input_id, left, right, node): method merge_labeled_ancestors (line 301) | def merge_labeled_ancestors(self, S, input_id): method extract_ancestry (line 353) | def extract_ancestry(self, edge): method process_parent_edges (line 398) | def process_parent_edges(self, edges): method finalise_sites (line 410) | def finalise_sites(self): method finalise_references (line 446) | def finalise_references(self): method insert_input_roots (line 508) | def insert_input_roots(self): method simplify (line 540) | def simplify(self): method check_state (line 559) | def check_state(self): class AncestorMap (line 594) | class AncestorMap: method __init__ (line 600) | def __init__(self, ts, sample, ancestors): method link_ancestors (line 617) | def link_ancestors(self): method process_parent_edges (line 631) | def process_parent_edges(self, edges): method merge_labeled_ancestors (line 648) | def merge_labeled_ancestors(self, S, input_id): method record_edge (line 687) | def record_edge(self, left, right, parent, child): method add_ancestry (line 700) | def add_ancestry(self, left, right, node, current_node): method flush_edges (line 714) | def flush_edges(self): method check_state (line 727) | def check_state(self): method print_state (line 750) | def print_state(self): FILE: python/tests/test_avl_tree.py class Node (line 53) | class Node: method __str__ (line 59) | def __str__(self): function get_link (line 71) | def get_link(a, P): function set_link (line 78) | def set_link(a, P, val): class AvlTree (line 85) | class AvlTree: method __init__ (line 86) | def __init__(self): method root (line 92) | def root(self): method __str__ (line 95) | def __str__(self): method ordered_keys (line 106) | def ordered_keys(self): method search (line 120) | def search(self, key): method __insert_empty (line 131) | def __insert_empty(self, key): method __insert (line 138) | def __insert(self, K): method insert (line 253) | def insert(self, key): class TestAvlTree (line 259) | class TestAvlTree: method verify_tree (line 260) | def verify_tree(self, tree): method verify (line 308) | def verify(self, keys): method test_sequential (line 346) | def test_sequential(self, n): method test_sequential_reversed (line 350) | def test_sequential_reversed(self, n): method test_random_integers (line 354) | def test_random_integers(self, n): method test_random_floats (line 360) | def test_random_floats(self, n): FILE: python/tests/test_balance_metrics.py function sackin_index_definition (line 39) | def sackin_index_definition(tree): function colless_index_definition (line 43) | def colless_index_definition(tree): function b1_index_definition (line 62) | def b1_index_definition(tree): function b2_index_definition (line 70) | def b2_index_definition(tree, base=10): class TestDefinitions (line 80) | class TestDefinitions: method test_sackin (line 82) | def test_sackin(self, ts): method test_colless (line 87) | def test_colless(self, ts): method test_b1 (line 101) | def test_b1(self, ts): method test_b2 (line 106) | def test_b2(self, ts): method test_b2_base (line 118) | def test_b2_base(self, ts, base): class TestBalancedBinaryOdd (line 131) | class TestBalancedBinaryOdd: method tree (line 139) | def tree(self): method test_sackin (line 142) | def test_sackin(self): method test_colless (line 145) | def test_colless(self): method test_b1 (line 148) | def test_b1(self): method test_b2 (line 151) | def test_b2(self): class TestBalancedBinaryEven (line 155) | class TestBalancedBinaryEven: method tree (line 163) | def tree(self): method test_sackin (line 166) | def test_sackin(self): method test_colless (line 169) | def test_colless(self): method test_b1 (line 172) | def test_b1(self): method test_b2 (line 175) | def test_b2(self): method test_b2_base (line 191) | def test_b2_base(self, base, expected): method test_b2_bad_base (line 195) | def test_b2_bad_base(self, base): method test_b2_base1 (line 199) | def test_b2_base1(self): class TestBalancedTernary (line 204) | class TestBalancedTernary: method tree (line 212) | def tree(self): method test_sackin (line 215) | def test_sackin(self): method test_colless (line 218) | def test_colless(self): method test_b1 (line 222) | def test_b1(self): method test_b2 (line 225) | def test_b2(self): class TestStarN10 (line 229) | class TestStarN10: method tree (line 235) | def tree(self): method test_sackin (line 238) | def test_sackin(self): method test_colless (line 241) | def test_colless(self): method test_b1 (line 245) | def test_b1(self): method test_b2 (line 248) | def test_b2(self): class TestCombN5 (line 252) | class TestCombN5: method tree (line 264) | def tree(self): method test_sackin (line 267) | def test_sackin(self): method test_colless (line 270) | def test_colless(self): method test_b1 (line 273) | def test_b1(self): method test_b2 (line 276) | def test_b2(self): class TestMultiRootBinary (line 280) | class TestMultiRootBinary: method tree (line 290) | def tree(self): method test_sackin (line 299) | def test_sackin(self): method test_colless (line 302) | def test_colless(self): method test_b1 (line 306) | def test_b1(self): method test_b2 (line 309) | def test_b2(self): class TestEmpty (line 314) | class TestEmpty: method tree (line 316) | def tree(self): method test_sackin (line 320) | def test_sackin(self): method test_colless (line 323) | def test_colless(self): method test_b1 (line 327) | def test_b1(self): method test_b2 (line 330) | def test_b2(self): class TestTreeInNullState (line 335) | class TestTreeInNullState: method tree (line 337) | def tree(self): method test_sackin (line 342) | def test_sackin(self): method test_colless (line 345) | def test_colless(self): method test_b1 (line 349) | def test_b1(self): method test_b2 (line 352) | def test_b2(self): class TestAllRootsN5 (line 357) | class TestAllRootsN5: method tree (line 359) | def tree(self): method test_sackin (line 365) | def test_sackin(self): method test_colless (line 368) | def test_colless(self): method test_b1 (line 372) | def test_b1(self): method test_b2 (line 375) | def test_b2(self): FILE: python/tests/test_cli.py class TestException (line 43) | class TestException(Exception): function capture_output (line 50) | def capture_output(func, *args, **kwargs): class TestCli (line 76) | class TestCli(unittest.TestCase): method setUp (line 81) | def setUp(self): method tearDown (line 85) | def tearDown(self): class TestTskitArgumentParser (line 89) | class TestTskitArgumentParser: method test_individuals_default_values (line 94) | def test_individuals_default_values(self): method test_individuals_short_args (line 102) | def test_individuals_short_args(self): method test_individuals_long_args (line 110) | def test_individuals_long_args(self): method test_nodes_default_values (line 118) | def test_nodes_default_values(self): method test_nodes_short_args (line 126) | def test_nodes_short_args(self): method test_nodes_long_args (line 134) | def test_nodes_long_args(self): method test_edges_default_values (line 142) | def test_edges_default_values(self): method test_edges_short_args (line 150) | def test_edges_short_args(self): method test_edges_long_args (line 158) | def test_edges_long_args(self): method test_sites_default_values (line 166) | def test_sites_default_values(self): method test_sites_short_args (line 174) | def test_sites_short_args(self): method test_sites_long_args (line 182) | def test_sites_long_args(self): method test_mutations_default_values (line 190) | def test_mutations_default_values(self): method test_mutations_short_args (line 198) | def test_mutations_short_args(self): method test_mutations_long_args (line 206) | def test_mutations_long_args(self): method test_provenances_default_values (line 214) | def test_provenances_default_values(self): method test_provenances_short_args (line 222) | def test_provenances_short_args(self): method test_provenances_long_args (line 230) | def test_provenances_long_args(self): method test_fasta_default_values (line 239) | def test_fasta_default_values(self): method test_fasta_short_args (line 248) | def test_fasta_short_args(self): method test_fasta_long_args (line 257) | def test_fasta_long_args(self): method test_vcf_ploidy (line 273) | def test_vcf_ploidy(self, flags, expected): method test_vcf_contig_id (line 289) | def test_vcf_contig_id(self, flags, expected): method test_vcf_allow_position_zero (line 305) | def test_vcf_allow_position_zero(self, flags, expected): method test_info_default_values (line 313) | def test_info_default_values(self): method test_populations_default_values (line 320) | def test_populations_default_values(self): method test_migrations_default_values (line 327) | def test_migrations_default_values(self): method test_migrations_short_args (line 334) | def test_migrations_short_args(self): method test_migrations_long_args (line 342) | def test_migrations_long_args(self): method test_trees_default_values (line 350) | def test_trees_default_values(self): method test_trees_short_args (line 359) | def test_trees_short_args(self): method test_trees_long_args (line 368) | def test_trees_long_args(self): class TestTskitConversionOutput (line 378) | class TestTskitConversionOutput(unittest.TestCase): method setUpClass (line 384) | def setUpClass(cls): method tearDownClass (line 405) | def tearDownClass(cls): method verify_individuals (line 408) | def verify_individuals(self, output_individuals, precision): method test_individuals (line 415) | def test_individuals(self): method verify_nodes (line 425) | def verify_nodes(self, output_nodes, precision): method test_nodes (line 432) | def test_nodes(self): method verify_edges (line 442) | def verify_edges(self, output_edges, precision): method test_edges (line 449) | def test_edges(self): method verify_sites (line 459) | def verify_sites(self, output_sites, precision): method test_sites (line 466) | def test_sites(self): method verify_mutations (line 476) | def verify_mutations(self, output_mutations, precision): method test_mutations (line 483) | def test_mutations(self): method verify_migrations (line 493) | def verify_migrations(self, output_migrations, precision): method test_migrations (line 500) | def test_migrations(self): method verify_provenances (line 510) | def verify_provenances(self, output_provenances): method test_provenances (line 517) | def test_provenances(self): method test_provenances_human (line 524) | def test_provenances_human(self): method verify_fasta (line 534) | def verify_fasta(self, output_fasta): method test_fasta (line 542) | def test_fasta(self): method verify_vcf (line 548) | def verify_vcf(self, output_vcf): method test_vcf (line 555) | def test_vcf(self): method verify_info (line 563) | def verify_info(self, ts, output_info): method test_info (line 566) | def test_info(self): method test_trees_no_draw (line 573) | def test_trees_no_draw(self): method test_trees_draw (line 580) | def test_trees_draw(self): class TestVCFZeroPosition (line 590) | class TestVCFZeroPosition: method test_zero_position (line 595) | def test_zero_position(self, tmp_path): class TestBadFile (line 606) | class TestBadFile: method verify (line 611) | def verify(self, command): method test_info (line 619) | def test_info(self): method test_fasta (line 622) | def test_fasta(self): method test_vcf (line 625) | def test_vcf(self): method test_nodes (line 628) | def test_nodes(self): method test_edges (line 631) | def test_edges(self): method test_sites (line 634) | def test_sites(self): method test_mutations (line 637) | def test_mutations(self): method test_migrations (line 640) | def test_migrations(self): method test_provenances (line 643) | def test_provenances(self): FILE: python/tests/test_coalrate.py function _single_tree_example (line 37) | def _single_tree_example(L, T): function _nonmissing_window_span (line 63) | def _nonmissing_window_span(ts, windows): function _pair_coalescence_weights (line 93) | def _pair_coalescence_weights( function _pair_coalescence_rates (line 100) | def _pair_coalescence_rates( function _pair_coalescence_quantiles (line 136) | def _pair_coalescence_quantiles( function _pair_coalescence_stat (line 169) | def _pair_coalescence_stat( function proto_pair_coalescence_counts (line 382) | def proto_pair_coalescence_counts( function proto_pair_coalescence_rates (line 457) | def proto_pair_coalescence_rates( function proto_pair_coalescence_quantiles (line 540) | def proto_pair_coalescence_quantiles( function naive_pair_coalescence_counts (line 608) | def naive_pair_coalescence_counts(ts, sample_set_0, sample_set_1): function _numpy_weighted_quantile (line 633) | def _numpy_weighted_quantile(values, weights, quantiles): function _numpy_hazard_rate (line 648) | def _numpy_hazard_rate(values, weights, breaks): function convert_to_nonsuccinct (line 677) | def convert_to_nonsuccinct(ts): class TestCoalescingPairsOneTree (line 717) | class TestCoalescingPairsOneTree: method example_ts (line 722) | def example_ts(self): method test_total_pairs (line 757) | def test_total_pairs(self): method test_population_pairs (line 779) | def test_population_pairs(self): method test_internal_samples (line 809) | def test_internal_samples(self): method test_windows (line 838) | def test_windows(self): method test_time_windows (line 853) | def test_time_windows(self): method test_pair_normalise (line 880) | def test_pair_normalise(self): method test_multiple_roots (line 906) | def test_multiple_roots(self): class TestCoalescingPairsTwoTree (line 918) | class TestCoalescingPairsTwoTree: method example_ts (line 923) | def example_ts(self, S, L): method test_total_pairs (line 950) | def test_total_pairs(self): method test_population_pairs (line 972) | def test_population_pairs(self): method test_internal_samples (line 1003) | def test_internal_samples(self): method test_windows (line 1030) | def test_windows(self): method test_time_windows (line 1056) | def test_time_windows(self): method test_pair_normalise (line 1092) | def test_pair_normalise(self): method test_multiple_roots (line 1119) | def test_multiple_roots(self): class TestCoalescingPairsSimulated (line 1134) | class TestCoalescingPairsSimulated: method example_ts (line 1140) | def example_ts(self): method _check_total_pairs (line 1162) | def _check_total_pairs(ts, windows): method _check_subset_pairs (line 1176) | def _check_subset_pairs(ts, windows): method test_sequence (line 1201) | def test_sequence(self): method test_missing_interval (line 1207) | def test_missing_interval(self): method test_missing_leaves (line 1218) | def test_missing_leaves(self): method test_multiple_roots (line 1238) | def test_multiple_roots(self): method test_windows (line 1248) | def test_windows(self): method test_windows_are_trees (line 1254) | def test_windows_are_trees(self): method test_windows_inside_trees (line 1263) | def test_windows_inside_trees(self): method test_nonsuccinct_sequence (line 1273) | def test_nonsuccinct_sequence(self): method test_span_normalise (line 1282) | def test_span_normalise(self): method test_span_normalise_with_missing_flanks (line 1296) | def test_span_normalise_with_missing_flanks(self): method test_span_normalise_with_missing_interior (line 1315) | def test_span_normalise_with_missing_interior(self): method test_empty_windows (line 1339) | def test_empty_windows(self): method test_pair_normalise (line 1354) | def test_pair_normalise(self): method test_internal_nodes_are_samples (line 1371) | def test_internal_nodes_are_samples(self): method test_time_windows (line 1387) | def test_time_windows(self): method test_time_windows_truncated (line 1411) | def test_time_windows_truncated(self): method test_time_windows_unique (line 1440) | def test_time_windows_unique(self): method test_diversity (line 1464) | def test_diversity(self): method test_divergence (line 1479) | def test_divergence(self): class TestCoalescingPairsUsage (line 1499) | class TestCoalescingPairsUsage: method example_ts (line 1505) | def example_ts(self): method test_bad_windows (line 1514) | def test_bad_windows(self): method test_bad_sample_sets (line 1527) | def test_bad_sample_sets(self): method test_bad_indexes (line 1532) | def test_bad_indexes(self): method test_no_indexes (line 1539) | def test_no_indexes(self): method test_oob_samples (line 1545) | def test_oob_samples(self): method test_uncalibrated_time (line 1551) | def test_uncalibrated_time(self): method test_bad_time_windows (line 1559) | def test_bad_time_windows(self, time_windows): method test_unsorted_time_windows (line 1564) | def test_unsorted_time_windows(self): method test_empty_time_windows (line 1570) | def test_empty_time_windows(self): method test_output_dim (line 1577) | def test_output_dim(self): method test_extra_time_windows (line 1596) | def test_extra_time_windows(self): class TestPairCoalescenceQuantiles (line 1616) | class TestPairCoalescenceQuantiles: method example_ts (line 1622) | def example_ts(self): method test_quantiles (line 1641) | def test_quantiles(self): method test_windows (line 1652) | def test_windows(self): method test_sample_sets (line 1663) | def test_sample_sets(self): method test_observations_are_quantiles (line 1680) | def test_observations_are_quantiles(self): method test_errors (line 1691) | def test_errors(self): method test_long_sequence (line 1702) | def test_long_sequence(self): method test_empty_windows (line 1725) | def test_empty_windows(self): class TestPairCoalescenceRates (line 1739) | class TestPairCoalescenceRates: method example_ts (line 1745) | def example_ts(self): method test_simulated (line 1762) | def test_simulated(self): method test_windowed (line 1772) | def test_windowed(self): method test_truncated (line 1786) | def test_truncated(self): method test_empty (line 1795) | def test_empty(self): method test_single (line 1810) | def test_single(self): method test_indexes (line 1819) | def test_indexes(self): method test_errors (line 1830) | def test_errors(self): method test_long_sequence (line 1843) | def test_long_sequence(self): method test_extra_time_windows (line 1867) | def test_extra_time_windows(self): method test_missing_sequence (line 1886) | def test_missing_sequence(self): method test_empty_windows (line 1902) | def test_empty_windows(self): FILE: python/tests/test_combinatorics.py class TestCombination (line 45) | class TestCombination: method test_combination_with_replacement_rank_unrank (line 46) | def test_combination_with_replacement_rank_unrank(self): method test_combination_rank_unrank (line 58) | def test_combination_rank_unrank(self): method test_combination_unrank_errors (line 67) | def test_combination_unrank_errors(self): method verify_unrank_errors (line 71) | def verify_unrank_errors(self, rank, n, k): class TestPartition (line 76) | class TestPartition: method test_rule_asc (line 77) | def test_rule_asc(self): method verify_rule_asc (line 103) | def verify_rule_asc(self, n, partitions): method test_partitions (line 106) | def test_partitions(self): method test_group_partition (line 111) | def test_group_partition(self): class TestRankTree (line 118) | class TestRankTree: method test_num_shapes (line 120) | def test_num_shapes(self, n): method test_num_labellings (line 125) | def test_num_labellings(self, n): method test_num_labelled_trees (line 132) | def test_num_labelled_trees(self): method test_all_labelled_trees_3 (line 139) | def test_all_labelled_trees_3(self): method test_all_labelled_trees_4 (line 144) | def test_all_labelled_trees_4(self): method test_generate_trees_roundtrip (line 182) | def test_generate_trees_roundtrip(self): method test_generate_treeseq_roundtrip (line 189) | def test_generate_treeseq_roundtrip(self): method test_all_shapes_roundtrip (line 199) | def test_all_shapes_roundtrip(self): method test_all_labellings_roundtrip (line 206) | def test_all_labellings_roundtrip(self): method test_unrank_labelled (line 216) | def test_unrank_labelled(self, n): method test_unrank_unlabelled (line 223) | def test_unrank_unlabelled(self, n): method test_unrank_errors (line 233) | def test_unrank_errors(self): method verify_unrank_errors (line 253) | def verify_unrank_errors(self, rank, n): method test_shape_rank (line 260) | def test_shape_rank(self, n): method test_shape_unrank (line 265) | def test_shape_unrank(self, n): method test_shape_unrank_tsk_tree (line 271) | def test_shape_unrank_tsk_tree(self, n): method test_label_rank (line 279) | def test_label_rank(self, n): method test_label_unrank (line 285) | def test_label_unrank(self, n): method test_rank_names (line 293) | def test_rank_names(self): method test_unrank_rank_round_trip (line 303) | def test_unrank_rank_round_trip(self, n): method test_is_canonical (line 315) | def test_is_canonical(self): method test_unranking_is_canonical (line 362) | def test_unranking_is_canonical(self, n): method test_to_from_tsk_tree (line 373) | def test_to_from_tsk_tree(self, n): method test_to_tsk_tree_internal_nodes (line 382) | def test_to_tsk_tree_internal_nodes(self, n): method test_from_unary_tree (line 397) | def test_from_unary_tree(self): method test_to_tsk_tree_errors (line 407) | def test_to_tsk_tree_errors(self): method test_rank_errors_multiple_roots (line 415) | def test_rank_errors_multiple_roots(self): method test_span (line 430) | def test_span(self): method test_big_trees (line 440) | def test_big_trees(self): method test_symmetrical_trees (line 455) | def test_symmetrical_trees(self): method test_equal (line 461) | def test_equal(self): method test_is_symmetrical (line 482) | def test_is_symmetrical(self): class TestPartialTopologyCounter (line 496) | class TestPartialTopologyCounter: method test_add_sibling_topologies_simple (line 497) | def test_add_sibling_topologies_simple(self): method test_add_sibling_topologies_polytomy (line 521) | def test_add_sibling_topologies_polytomy(self): method test_join_topologies (line 587) | def test_join_topologies(self): method verify_join_topologies (line 607) | def verify_join_topologies(self, topologies, expected_topology): class TestCountTopologies (line 612) | class TestCountTopologies: method verify_topologies (line 613) | def verify_topologies(self, ts, sample_sets=None, expected=None): method test_no_iterate (line 638) | def test_no_iterate(self): method subsample_topologies (line 643) | def subsample_topologies(self, ts, sample_sets, sample_set_indexes): method test_single_population (line 655) | def test_single_population(self): method test_three_populations (line 662) | def test_three_populations(self): method test_multiple_roots (line 708) | def test_multiple_roots(self): method test_no_sample_subtrees (line 724) | def test_no_sample_subtrees(self): method test_no_full_topology (line 740) | def test_no_full_topology(self): method test_polytomies (line 759) | def test_polytomies(self): method test_custom_key (line 777) | def test_custom_key(self): method test_ignores_non_sample_leaves (line 825) | def test_ignores_non_sample_leaves(self): method test_internal_samples_errors (line 873) | def test_internal_samples_errors(self): method test_non_sample_nodes_errors (line 885) | def test_non_sample_nodes_errors(self): method verify_value_error (line 901) | def verify_value_error(self, ts, sample_sets=None): method verify_node_out_of_bounds_error (line 907) | def verify_node_out_of_bounds_error(self, ts, sample_sets=None): method test_standard_msprime_migrations (line 913) | def test_standard_msprime_migrations(self): method simulate_multiple_populations (line 919) | def simulate_multiple_populations(self, sample_sizes): method test_msprime_dtwf (line 937) | def test_msprime_dtwf(self): method test_forward_time_wright_fisher_unsimplified_all_sample_sets (line 971) | def test_forward_time_wright_fisher_unsimplified_all_sample_sets(self): method test_forward_time_wright_fisher_unsimplified (line 985) | def test_forward_time_wright_fisher_unsimplified(self): method test_forward_time_wright_fisher_simplified (line 999) | def test_forward_time_wright_fisher_simplified(self): class TestTreeNode (line 1014) | class TestTreeNode: method verify_tree (line 1019) | def verify_tree(self, root, labels): method test_random_binary_tree (line 1039) | def test_random_binary_tree(self, n): method test_balanced_binary (line 1046) | def test_balanced_binary(self, n): method test_balanced_arity (line 1051) | def test_balanced_arity(self, arity): function num_leaf_labelled_binary_trees (line 1057) | def num_leaf_labelled_binary_trees(n): class TestPolytomySplitting (line 1069) | class TestPolytomySplitting: method ts_polytomy_44344 (line 1104) | def ts_polytomy_44344(self): method verify_trees (line 1111) | def verify_trees(self, source_tree, split_tree, epsilon=None): method test_resolve_star (line 1133) | def test_resolve_star(self, n): method test_large_epsilon (line 1137) | def test_large_epsilon(self): method test_small_epsilon (line 1143) | def test_small_epsilon(self): method test_nextafter_near_zero (line 1149) | def test_nextafter_near_zero(self): method test_nextafter_large_tree (line 1154) | def test_nextafter_large_tree(self): method test_epsilon_near_one (line 1166) | def test_epsilon_near_one(self): method verify_tree_sequence_splits (line 1171) | def verify_tree_sequence_splits(self, ts): method test_complex_examples (line 1204) | def test_complex_examples(self): method test_nonbinary_simulation (line 1207) | def test_nonbinary_simulation(self): method test_seeds (line 1220) | def test_seeds(self): method test_internal_polytomy (line 1232) | def test_internal_polytomy(self): method test_binary_tree (line 1248) | def test_binary_tree(self): method test_bad_method (line 1254) | def test_bad_method(self): method test_epsilon_too_large (line 1260) | def test_epsilon_too_large(self, epsilon): method test_epsilon_too_small (line 1274) | def test_epsilon_too_small(self): method test_unsplittable_branch (line 1289) | def test_unsplittable_branch(self): method test_epsilon_for_mutations (line 1305) | def test_epsilon_for_mutations(self): method test_mutation_within_eps_parent (line 1319) | def test_mutation_within_eps_parent(self): method test_provenance (line 1336) | def test_provenance(self): method test_kwargs (line 1347) | def test_kwargs(self): method test_all_topologies (line 1354) | def test_all_topologies(self, n): class TreeGeneratorTestBase (line 1366) | class TreeGeneratorTestBase: method method (line 1373) | def method(self, n, **kwargs): method test_leaves (line 1377) | def test_leaves(self, n): method test_bad_n (line 1381) | def test_bad_n(self): method test_bad_span (line 1389) | def test_bad_span(self): method test_bad_branch_length (line 1393) | def test_bad_branch_length(self): method test_span (line 1398) | def test_span(self, span): method test_branch_length (line 1403) | def test_branch_length(self, branch_length): method test_provenance (line 1409) | def test_provenance(self): method test_rank_unrank_round_trip (line 1418) | def test_rank_unrank_round_trip(self, n): method test_kwargs (line 1426) | def test_kwargs(self): class TestGenerateStar (line 1431) | class TestGenerateStar(TreeGeneratorTestBase): method test_unrank_equal (line 1435) | def test_unrank_equal(self, n): method test_branch_length_semantics (line 1441) | def test_branch_length_semantics(self): class TestGenerateBalanced (line 1450) | class TestGenerateBalanced(TreeGeneratorTestBase): method test_arity_leaves (line 1454) | def test_arity_leaves(self, arity): method test_binary_unrank_equal (line 1460) | def test_binary_unrank_equal(self, n): method test_rank_unrank_round_trip_arity (line 1470) | def test_rank_unrank_round_trip_arity(self, n, arity): method test_bad_arity (line 1478) | def test_bad_arity(self): method test_branch_length_semantics (line 1483) | def test_branch_length_semantics(self): class TestGenerateRandomBinary (line 1492) | class TestGenerateRandomBinary(TreeGeneratorTestBase): method method (line 1495) | def method(self, n, **kwargs): method test_all_topologies (line 1500) | def test_all_topologies(self, n): method test_leaves (line 1511) | def test_leaves(self, n): method test_rank_unrank_round_trip_seeds (line 1517) | def test_rank_unrank_round_trip_seeds(self, seed): class TestGenerateComb (line 1527) | class TestGenerateComb(TreeGeneratorTestBase): method test_unrank_equal (line 1532) | def test_unrank_equal(self, n, rank): method test_branch_length_semantics (line 1538) | def test_branch_length_semantics(self): class TestEqualChunks (line 1544) | class TestEqualChunks: method test_evenly_divisible (line 1546) | def test_evenly_divisible(self, n, k): method test_one_chunk (line 1555) | def test_one_chunk(self, n): method test_empty_chunks (line 1561) | def test_empty_chunks(self, n, k): method test_trailing_chunk (line 1570) | def test_trailing_chunk(self, n, k): method test_empty_list (line 1576) | def test_empty_list(self): method test_bad_num_chunks (line 1580) | def test_bad_num_chunks(self): FILE: python/tests/test_dict_encoding.py function test_pickled_examples (line 40) | def test_pickled_examples(): FILE: python/tests/test_distance_metrics.py function c_kc_distance (line 43) | def c_kc_distance(tree1, tree2, lambda_=0): function naive_kc_distance (line 69) | def naive_kc_distance(tree1, tree2, lambda_=0): class KCVectors (line 110) | class KCVectors: method __init__ (line 121) | def __init__(self, n): function fill_kc_vectors (line 128) | def fill_kc_vectors(tree, kc_vecs): function update_kc_vectors_single_leaf (line 152) | def update_kc_vectors_single_leaf(kc_vecs, u, time, sample_index_map): function update_kc_vectors_all_pairs (line 158) | def update_kc_vectors_all_pairs(tree, kc_vecs, c1, c2, depth, time): function update_kc_vectors_pair (line 172) | def update_kc_vectors_pair(kc_vecs, n1, n2, depth, time): function norm_kc_vectors (line 181) | def norm_kc_vectors(kc_vecs1, kc_vecs2, lambda_): class TestKCMetric (line 193) | class TestKCMetric(unittest.TestCase): method test_same_tree_zero_distance (line 198) | def test_same_tree_zero_distance(self): method test_sample_2_zero_distance (line 212) | def test_sample_2_zero_distance(self): method test_different_samples_error (line 223) | def test_different_samples_error(self): method validate_trees (line 258) | def validate_trees(self, n): method test_sample_3 (line 273) | def test_sample_3(self): method test_sample_4 (line 276) | def test_sample_4(self): method test_sample_10 (line 279) | def test_sample_10(self): method test_sample_20 (line 282) | def test_sample_20(self): method validate_nonbinary_trees (line 285) | def validate_nonbinary_trees(self, n): method test_non_binary_sample_10 (line 315) | def test_non_binary_sample_10(self): method test_non_binary_sample_20 (line 318) | def test_non_binary_sample_20(self): method test_non_binary_sample_30 (line 321) | def test_non_binary_sample_30(self): method verify_result (line 324) | def verify_result(self, tree1, tree2, lambda_, result, places=None): method test_known_kc_sample_3 (line 339) | def test_known_kc_sample_3(self): method test_10_samples (line 369) | def test_10_samples(self): method test_15_samples (line 476) | def test_15_samples(self): method test_nobinary_trees (line 625) | def test_nobinary_trees(self): method test_multiple_roots (line 740) | def test_multiple_roots(self): method do_kc_distance (line 760) | def do_kc_distance(self, t1, t2, lambda_=0): method test_non_initial_samples (line 773) | def test_non_initial_samples(self): method test_internal_samples (line 781) | def test_internal_samples(self): method test_root_sample (line 791) | def test_root_sample(self): method test_non_sample_leaf (line 798) | def test_non_sample_leaf(self): method test_ignores_subtrees_with_no_samples (line 822) | def test_ignores_subtrees_with_no_samples(self): function ts_kc_distance (line 887) | def ts_kc_distance(ts1, ts2, lambda_=0): function ts_kc_distance_incremental (line 908) | def ts_kc_distance_incremental(ts1, ts2, lambda_=0): function update_kc_incremental (line 946) | def update_kc_incremental(tree, kc, edge_diffs, sample_index_map, depths): function update_kc_subtree_state (line 977) | def update_kc_subtree_state(tree, kc, u, sample_index_map, depths): function update_kc_pairs_with_leaf (line 1000) | def update_kc_pairs_with_leaf(tree, kc, leaf, sample_index_map, depths): function check_kc_tree_sequence_inputs (line 1017) | def check_kc_tree_sequence_inputs(ts1, ts2): function check_kc_tree_inputs (line 1032) | def check_kc_tree_inputs(tree1, tree2): class TestKCSequenceMetric (line 1041) | class TestKCSequenceMetric(unittest.TestCase): method test_0_distance_from_self (line 1046) | def test_0_distance_from_self(self): method verify_errors (line 1050) | def verify_errors(self, ts1, ts2): method test_errors_diff_seq_length (line 1058) | def test_errors_diff_seq_length(self): method test_errors_diff_num_samples (line 1063) | def test_errors_diff_num_samples(self): method test_errors_different_sample_lists (line 1068) | def test_errors_different_sample_lists(self): method test_errors_unary_nodes (line 1104) | def test_errors_unary_nodes(self): method test_errors_different_samples (line 1123) | def test_errors_different_samples(self): method verify_result (line 1128) | def verify_result(self, ts1, ts2, lambda_, result, places=None): method verify_same_kc (line 1143) | def verify_same_kc(self, ts1, ts2, lambda_=0): method validate_trees (line 1156) | def validate_trees(self, n): method test_sample_5 (line 1164) | def test_sample_5(self): method test_sample_10 (line 1167) | def test_sample_10(self): method test_sample_20 (line 1170) | def test_sample_20(self): method validate_nonbinary_trees (line 1173) | def validate_nonbinary_trees(self, n): method test_non_binary_sample_10 (line 1206) | def test_non_binary_sample_10(self): method test_non_binary_sample_20 (line 1209) | def test_non_binary_sample_20(self): method test_permit_internal_samples (line 1212) | def test_permit_internal_samples(self): method test_known_kc_sample_trees_different_shapes (line 1223) | def test_known_kc_sample_trees_different_shapes(self): method test_known_kc_sample_trees_same_shape_different_times (line 1258) | def test_known_kc_sample_trees_same_shape_different_times(self): method test_known_kc_same_tree_twice_same_metric (line 1288) | def test_known_kc_same_tree_twice_same_metric(self): method test_remove_root (line 1317) | def test_remove_root(self): method test_ignores_subtrees_with_no_samples (line 1357) | def test_ignores_subtrees_with_no_samples(self): class TestTreeSameSamples (line 1428) | class TestTreeSameSamples: method tree (line 1448) | def tree(self): method tree_other (line 1452) | def tree_other(self): method test_rf_distance (line 1455) | def test_rf_distance(self): class TestTreeDifferentSamples (line 1459) | class TestTreeDifferentSamples: method tree (line 1481) | def tree(self): method tree_other (line 1485) | def tree_other(self): method test_rf_distance (line 1488) | def test_rf_distance(self): class TestTreeMultiRoots (line 1492) | class TestTreeMultiRoots: method tree (line 1516) | def tree(self): method tree_other (line 1520) | def tree_other(self): method test_rf_distance (line 1529) | def test_rf_distance(self): class TestEmpty (line 1534) | class TestEmpty: method tree (line 1536) | def tree(self): method tree_other (line 1541) | def tree_other(self): method test_rf_distance (line 1545) | def test_rf_distance(self): class TestTreeInNullState (line 1550) | class TestTreeInNullState: method tsk_tree1 (line 1552) | def tsk_tree1(self): method tree_other (line 1558) | def tree_other(self): method test_rf_distance (line 1563) | def test_rf_distance(self): class TestAllRootsN5 (line 1568) | class TestAllRootsN5: method tree (line 1570) | def tree(self): method test_rf_distance (line 1576) | def test_rf_distance(self): class TestWithPackages (line 1581) | class TestWithPackages: method to_dendropy (line 1582) | def to_dendropy(self, newick_data, tns): method dendropy_rf_distance (line 1590) | def dendropy_rf_distance(self, tree1, tree2, weighted=False): method test_rf_distance_against_dendropy (line 1602) | def test_rf_distance_against_dendropy(self, n): class TestDistanceBetween (line 1612) | class TestDistanceBetween: method test_distance_between_sample (line 1617) | def test_distance_between_sample(self, u, v): method test_distance_between_same_node (line 1626) | def test_distance_between_same_node(self): method test_distance_between_nodes (line 1633) | def test_distance_between_nodes(self): method test_distance_between_invalid_nodes (line 1648) | def test_distance_between_invalid_nodes(self): FILE: python/tests/test_divmat.py function sv_tables_init (line 50) | def sv_tables_init(parent_array): function _sv_mrca (line 126) | def _sv_mrca(x, y, lambd, pi, tau, beta, alpha): function sv_mrca (line 151) | def sv_mrca(x, y, lambd, pi, tau, beta, alpha): function local_root (line 156) | def local_root(tree, u): function span_normalise_windows (line 162) | def span_normalise_windows(D, windows): function sample_set_normalisation (line 169) | def sample_set_normalisation(sample_sets): function branch_divergence_matrix (line 183) | def branch_divergence_matrix(ts, sample_sets=None, windows=None, span_no... function divergence_matrix (line 238) | def divergence_matrix( function stats_api_divergence_matrix (line 261) | def stats_api_divergence_matrix(ts, *args, **kwargs): function stats_api_genetic_relatedness_matrix (line 265) | def stats_api_genetic_relatedness_matrix(ts, *args, **kwargs): function stats_api_matrix_method (line 270) | def stats_api_matrix_method( function group_alleles (line 331) | def group_alleles(genotypes, num_alleles): function site_divergence_matrix (line 346) | def site_divergence_matrix(ts, sample_sets, *, windows=None, span_normal... function check_divmat (line 395) | def check_divmat( class TestExamplesWithAnswer (line 456) | class TestExamplesWithAnswer: method test_single_tree_zero_samples (line 458) | def test_single_tree_zero_samples(self, mode): method test_single_tree_zero_samples_windows (line 465) | def test_single_tree_zero_samples_windows(self, num_windows, mode): method test_single_tree_sites_per_branch (line 472) | def test_single_tree_sites_per_branch(self, m): method test_single_tree_mutations_per_branch (line 493) | def test_single_tree_mutations_per_branch(self, m): method test_single_tree_unique_sample_alleles (line 517) | def test_single_tree_unique_sample_alleles(self, n): method test_single_tree_sequence_length (line 529) | def test_single_tree_sequence_length(self, L): method test_single_tree_sequence_length_span_normalise (line 549) | def test_single_tree_sequence_length_span_normalise(self, L): method test_single_tree_diploid_individuals (line 569) | def test_single_tree_diploid_individuals(self, mode): method test_single_tree_gap_at_end (line 589) | def test_single_tree_gap_at_end(self, num_windows, mode): method test_single_tree_subset_permuted_samples (line 615) | def test_single_tree_subset_permuted_samples(self, mode): method test_single_tree_mixed_non_sample_samples (line 635) | def test_single_tree_mixed_non_sample_samples(self, mode): method test_single_tree_duplicate_samples (line 648) | def test_single_tree_duplicate_samples(self, mode): method test_single_tree_multiroot (line 661) | def test_single_tree_multiroot(self, mode): method test_single_tree_interval (line 683) | def test_single_tree_interval(self, left, right): method test_single_tree_equal_windows (line 703) | def test_single_tree_equal_windows(self, num_windows): method test_single_tree_no_sites (line 728) | def test_single_tree_no_sites(self, n): class TestExamples (line 734) | class TestExamples: method test_all_trees_interval (line 740) | def test_all_trees_interval(self, interval, mode, span_normalise): method test_all_trees_windows (line 759) | def test_all_trees_windows(self, windows, mode, span_normalise): method test_all_trees_windows_gap_at_end (line 769) | def test_all_trees_windows_gap_at_end(self, num_windows, mode, span_no... method test_small_sims (line 781) | def test_small_sims(self, n, seed, mode): method test_sims_windows (line 797) | def test_sims_windows(self, n, num_windows, mode): method test_single_balanced_tree (line 819) | def test_single_balanced_tree(self, n, mode): method test_internal_sample (line 826) | def test_internal_sample(self, mode): method test_one_internal_sample_sims (line 838) | def test_one_internal_sample_sims(self, seed, mode): method test_missing_flanks (line 858) | def test_missing_flanks(self, mode): method test_dangling_on_samples (line 875) | def test_dangling_on_samples(self, n, mode): method test_dangling_on_all (line 893) | def test_dangling_on_all(self, n, mode): method test_disconnected_non_sample_topology (line 910) | def test_disconnected_non_sample_topology(self, mode): class TestSuiteExamples (line 928) | class TestSuiteExamples: method check (line 935) | def check( method test_defaults (line 979) | def test_defaults(self, ts, mode): method test_subset_samples (line 984) | def test_subset_samples(self, ts, mode): method test_ploidy_sample_sets (line 991) | def test_ploidy_sample_sets(self, ts, mode, ploidy): method test_windows (line 1000) | def test_windows(self, ts, mode, span_normalise): method test_threads_no_windows (line 1006) | def test_threads_no_windows(self, ts, mode): method test_threads_windows (line 1011) | def test_threads_windows(self, ts, mode): class TestThreadsNoWindows (line 1016) | class TestThreadsNoWindows: method check (line 1017) | def check(self, ts, num_threads, samples=None, mode=None, span_normali... method test_all_trees (line 1032) | def test_all_trees(self, num_threads, mode, span_normalise): method test_all_trees_samples (line 1039) | def test_all_trees_samples(self, samples, mode): method test_simple_sims (line 1047) | def test_simple_sims(self, n, num_threads, mode): class TestThreadsWindows (line 1060) | class TestThreadsWindows: method check (line 1061) | def check(self, ts, num_threads, *, windows, samples=None, mode=None): method test_all_trees (line 1083) | def test_all_trees(self, num_threads, windows, mode): method test_all_trees_samples (line 1099) | def test_all_trees_samples(self, samples, windows, mode): method test_simple_sims (line 1117) | def test_simple_sims(self, num_threads, windows, mode): class TestChunkByTree (line 1136) | class TestChunkByTree: method test_all_trees_ts_26 (line 1149) | def test_all_trees_ts_26(self, num_chunks, expected): method test_all_trees_ts_4 (line 1165) | def test_all_trees_ts_4(self, num_chunks, expected): method test_all_trees_ts_4_trees_span (line 1183) | def test_all_trees_ts_4_trees_span(self, span, num_chunks, expected): method test_empty_ts (line 1194) | def test_empty_ts(self, num_chunks): method test_single_tree (line 1201) | def test_single_tree(self, num_chunks): method test_bad_chunks (line 1208) | def test_bad_chunks(self, num_chunks): class TestChunkWindows (line 1214) | class TestChunkWindows: method test_examples (line 1227) | def test_examples(self, windows, num_chunks, expected): method test_bad_chunks (line 1232) | def test_bad_chunks(self, num_chunks): class TestGroupAlleles (line 1237) | class TestGroupAlleles: method test_examples (line 1250) | def test_examples(self, G, num_alleles, A, offsets): method test_simple_simulation (line 1255) | def test_simple_simulation(self): class TestSampleSetParsing (line 1281) | class TestSampleSetParsing: method test_good_args (line 1299) | def test_good_args(self, arg, flattened, sizes): method test_nested_bad_types (line 1318) | def test_nested_bad_types(self, arg): method test_nested_arrays (line 1330) | def test_nested_arrays(self, arg): method test_string_args (line 1335) | def test_string_args(self, arg): method test_dict_args (line 1347) | def test_dict_args(self, arg): method test_bad_arg_types (line 1361) | def test_bad_arg_types(self, arg): class TestGeneticRelatednessMatrix (line 1366) | class TestGeneticRelatednessMatrix: method check (line 1367) | def check(self, ts, mode, *, sample_sets=None, windows=None, span_norm... method test_single_tree (line 1394) | def test_single_tree(self, mode): method test_single_tree_mutations_per_branch (line 1406) | def test_single_tree_mutations_per_branch(self, m): method test_single_tree_sample_sets (line 1430) | def test_single_tree_sample_sets(self, mode): method test_single_tree_single_samples (line 1442) | def test_single_tree_single_samples(self, mode): method test_single_tree_windows (line 1456) | def test_single_tree_windows(self, mode): method test_suite_defaults (line 1469) | def test_suite_defaults(self, ts, mode): method test_suite_span_normalise (line 1475) | def test_suite_span_normalise(self, ts, mode, span_normalise): method test_suite_sample_sets (line 1481) | def test_suite_sample_sets(self, ts, mode, num_sets): FILE: python/tests/test_drawing.py class TestTreeDraw (line 50) | class TestTreeDraw: method get_binary_tree (line 56) | def get_binary_tree(self): method get_nonbinary_ts (line 60) | def get_nonbinary_ts(self): method get_nonbinary_tree (line 73) | def get_nonbinary_tree(self): method get_zero_edge_tree (line 80) | def get_zero_edge_tree(self): method get_zero_roots_tree (line 90) | def get_zero_roots_tree(self): method get_multiroot_tree (line 102) | def get_multiroot_tree(self): method get_mutations_over_roots_tree (line 120) | def get_mutations_over_roots_tree(self): method get_unary_node_tree (line 135) | def get_unary_node_tree(self): method get_empty_tree (line 154) | def get_empty_tree(self): method get_simple_ts (line 159) | def get_simple_ts(self, use_mutation_times=False): method get_ts_varying_min_times (line 227) | def get_ts_varying_min_times(self, *args, **kwargs): method fail (line 249) | def fail(self, *args, **kwargs): function closest_left_node (line 256) | def closest_left_node(tree, u): function get_left_neighbour (line 267) | def get_left_neighbour(tree, traversal_order): class TestClosestLeftNode (line 292) | class TestClosestLeftNode(TestTreeDraw): method verify (line 297) | def verify(self, tree): method test_2_binary (line 308) | def test_2_binary(self): method test_5_binary (line 312) | def test_5_binary(self): method test_10_binary (line 316) | def test_10_binary(self): method test_20_binary (line 320) | def test_20_binary(self): method test_nonbinary (line 324) | def test_nonbinary(self): method test_zero_edge (line 327) | def test_zero_edge(self): method test_zero_roots (line 330) | def test_zero_roots(self): method test_multiroot (line 333) | def test_multiroot(self): method test_left_child (line 336) | def test_left_child(self): method test_null_node_left_child (line 343) | def test_null_node_left_child(self): method test_leaf_node_left_child (line 349) | def test_leaf_node_left_child(self): class TestOrder (line 357) | class TestOrder(TestTreeDraw): method test_bad_order (line 362) | def test_bad_order(self): method test_default_order (line 367) | def test_default_order(self): method test_order_mapping (line 371) | def test_order_mapping(self): method test_tree_svg_variants (line 375) | def test_tree_svg_variants(self): method test_tree_text_variants (line 389) | def test_tree_text_variants(self): method test_tree_sequence_text_variants (line 403) | def test_tree_sequence_text_variants(self): method test_tree_sequence_svg_variants (line 414) | def test_tree_sequence_svg_variants(self): class TestFormats (line 426) | class TestFormats(TestTreeDraw): method test_svg_variants (line 431) | def test_svg_variants(self): method test_default (line 438) | def test_default(self): method test_ascii_variants (line 448) | def test_ascii_variants(self): method test_unicode_variants (line 457) | def test_unicode_variants(self): method test_bad_formats (line 466) | def test_bad_formats(self): class TestDrawText (line 473) | class TestDrawText(TestTreeDraw): method verify_basic_text (line 481) | def verify_basic_text(self, text): method test_draw_defaults (line 485) | def test_draw_defaults(self): method test_draw_nonbinary (line 490) | def test_draw_nonbinary(self): method test_draw_multiroot (line 495) | def test_draw_multiroot(self): method test_draw_mutations_over_roots (line 500) | def test_draw_mutations_over_roots(self): method test_draw_unary (line 505) | def test_draw_unary(self): method test_draw_empty_tree (line 510) | def test_draw_empty_tree(self): method test_draw_zero_roots_tree (line 515) | def test_draw_zero_roots_tree(self): method test_draw_zero_edge_tree (line 520) | def test_draw_zero_edge_tree(self): method test_even_num_children_tree (line 525) | def test_even_num_children_tree(self): method test_odd_num_children_tree (line 554) | def test_odd_num_children_tree(self): method test_node_labels (line 581) | def test_node_labels(self): method test_long_internal_labels (line 591) | def test_long_internal_labels(self): method test_no_node_labels (line 597) | def test_no_node_labels(self): method test_unused_args (line 605) | def test_unused_args(self): class TestDrawUnicode (line 633) | class TestDrawUnicode(TestDrawText): class TestDrawTextErrors (line 642) | class TestDrawTextErrors: method test_bad_orientation (line 647) | def test_bad_orientation(self): class TestDrawTextExamples (line 654) | class TestDrawTextExamples(TestTreeDraw): method verify_text_rendering (line 659) | def verify_text_rendering(self, drawn, drawn_tree, debug=False): method test_simple_tree (line 672) | def test_simple_tree(self): method test_simple_tree_long_label (line 731) | def test_simple_tree_long_label(self): method test_four_leaves (line 795) | def test_four_leaves(self): method test_trident_tree (line 936) | def test_trident_tree(self): method test_pitchfork_tree (line 991) | def test_pitchfork_tree(self): method test_stick_tree (line 1076) | def test_stick_tree(self): method test_draw_forky_tree (line 1127) | def test_draw_forky_tree(self): method test_draw_multiroot_forky_tree (line 1219) | def test_draw_multiroot_forky_tree(self): method test_simple_tree_sequence (line 1290) | def test_simple_tree_sequence(self): method test_tree_sequence_non_minlex (line 1366) | def test_tree_sequence_non_minlex(self): method test_max_time (line 1435) | def test_max_time(self): method test_no_repr_svg (line 1472) | def test_no_repr_svg(self): class TestDrawSvgBase (line 1479) | class TestDrawSvgBase(TestTreeDraw, xmlunittest.XmlTestMixin): method verify_basic_svg (line 1484) | def verify_basic_svg(self, svg, width=200, height=200, num_trees=1, ha... class TestDrawSvg (line 1527) | class TestDrawSvg(TestDrawSvgBase): method test_repr_svg (line 1532) | def test_repr_svg(self): method test_draw_to_file (line 1541) | def test_draw_to_file(self, tmp_path): method test_nonimplemented_base_class (line 1569) | def test_nonimplemented_base_class(self): method test_bad_tick_spacing (line 1578) | def test_bad_tick_spacing(self): method test_no_mixed_yscales (line 1587) | def test_no_mixed_yscales(self): method test_draw_defaults (line 1592) | def test_draw_defaults(self): method test_draw_svg_y_axis_parameter_combos (line 1610) | def test_draw_svg_y_axis_parameter_combos( method test_draw_multiroot (line 1632) | def test_draw_multiroot(self): method test_draw_mutations_over_roots (line 1639) | def test_draw_mutations_over_roots(self): method test_draw_unary (line 1648) | def test_draw_unary(self): method test_draw_empty (line 1655) | def test_draw_empty(self): method test_draw_zero_roots (line 1662) | def test_draw_zero_roots(self): method test_draw_zero_edge (line 1669) | def test_draw_zero_edge(self): method test_mutations_present (line 1676) | def test_mutations_present(self): method test_sites_omitted (line 1690) | def test_sites_omitted(self): method test_width_height (line 1704) | def test_width_height(self): method test_node_labels (line 1713) | def test_node_labels(self): method test_one_node_label (line 1723) | def test_one_node_label(self): method test_no_node_labels (line 1733) | def test_no_node_labels(self): method test_one_node_colour (line 1740) | def test_one_node_colour(self): method test_all_nodes_colour (line 1751) | def test_all_nodes_colour(self): method test_unplotted_node (line 1765) | def test_unplotted_node(self): method test_one_edge_colour (line 1773) | def test_one_edge_colour(self): method test_one_mutation_label_colour (line 1784) | def test_one_mutation_label_colour(self): method test_bad_y_axis (line 1791) | def test_bad_y_axis(self): method test_bad_time_scale (line 1797) | def test_bad_time_scale(self): method test_bad_max_time (line 1806) | def test_bad_max_time(self): method test_bad_min_time (line 1815) | def test_bad_min_time(self): method test_bad_neg_log_time (line 1824) | def test_bad_neg_log_time(self): method test_time_scale_time_and_max_time (line 1831) | def test_time_scale_time_and_max_time(self): method test_time_scale_rank_and_max_time (line 1849) | def test_time_scale_rank_and_max_time(self): method test_min_tree_time (line 1865) | def test_min_tree_time(self): method test_min_ts_time (line 1878) | def test_min_ts_time(self): method test_numeric_max_time_with_mutations_over_roots (line 1889) | def test_numeric_max_time_with_mutations_over_roots(self): method test_all_edges_colour (line 1919) | def test_all_edges_colour(self): method test_unplotted_edge (line 1927) | def test_unplotted_edge(self): method test_mutations_unknown_time (line 1936) | def test_mutations_unknown_time(self): method test_mutation_labels (line 1946) | def test_mutation_labels(self): method test_one_mutation_label (line 1953) | def test_one_mutation_label(self): method test_no_mutation_labels (line 1960) | def test_no_mutation_labels(self): method test_one_mutation_colour (line 1967) | def test_one_mutation_colour(self): method test_all_mutations_colour (line 1975) | def test_all_mutations_colour(self): method test_unplotted_mutation (line 1983) | def test_unplotted_mutation(self): method test_extra_mutations (line 1994) | def test_extra_mutations(self, all_muts, x_axis): method test_max_time (line 2019) | def test_max_time(self): method test_min_time (line 2070) | def test_min_time(self): method test_draw_sized_tree (line 2106) | def test_draw_sized_tree(self): method test_canvas_size_tree (line 2111) | def test_canvas_size_tree(self): method test_draw_bad_sized_treebox (line 2123) | def test_draw_bad_sized_treebox(self): method test_draw_bad_sized_tree (line 2129) | def test_draw_bad_sized_tree(self): method test_draw_simple_ts (line 2135) | def test_draw_simple_ts(self): method test_draw_integer_breaks_ts (line 2140) | def test_draw_integer_breaks_ts(self): method test_draw_integer_times_ts (line 2152) | def test_draw_integer_times_ts(self): method test_draw_integer_times_tree (line 2163) | def test_draw_integer_times_tree(self): method test_draw_even_height_ts (line 2174) | def test_draw_even_height_ts(self): method test_draw_sized_ts (line 2182) | def test_draw_sized_ts(self): method test_canvas_size_ts (line 2187) | def test_canvas_size_ts(self): method test_time_scale (line 2199) | def test_time_scale(self): method test_x_scale (line 2219) | def test_x_scale(self): method test_bad_x_scale (line 2226) | def test_bad_x_scale(self): method test_x_axis (line 2232) | def test_x_axis(self): method test_y_axis (line 2241) | def test_y_axis(self): method test_y_axis_noticks (line 2268) | def test_y_axis_noticks(self): method test_y_axis_tick_warning (line 2277) | def test_y_axis_tick_warning(self, caplog): method test_symbol_size (line 2296) | def test_symbol_size(self): method test_no_edges_invalid (line 2310) | def test_no_edges_invalid(self): method test_no_edges_show_empty (line 2322) | def test_no_edges_show_empty(self): method test_no_edges_with_muts (line 2339) | def test_no_edges_with_muts(self): method test_empty_flanks (line 2355) | def test_empty_flanks(self): method test_bad_xlim (line 2370) | def test_bad_xlim(self): method test_xlim_on_empty (line 2385) | def test_xlim_on_empty(self): method test_xlim_edge_cases (line 2394) | def test_xlim_edge_cases(self): method test_xlim_maintains_tree_ids (line 2417) | def test_xlim_maintains_tree_ids(self): method test_xlim_maintains_site_and_mutation_ids (line 2427) | def test_xlim_maintains_site_and_mutation_ids(self): method test_xlim_with_ranks (line 2455) | def test_xlim_with_ranks(self): method test_half_truncated (line 2463) | def test_half_truncated(self): method test_tree_root_branch (line 2471) | def test_tree_root_branch(self): method test_debug_box (line 2496) | def test_debug_box(self): method test_bad_max_num_trees (line 2508) | def test_bad_max_num_trees(self, max_trees): method test_max_num_trees (line 2514) | def test_max_num_trees(self, max_trees): method test_edge_ids (line 2538) | def test_edge_ids(self): method test_draw_tree_symbol_titles (line 2548) | def test_draw_tree_symbol_titles(self): method test_nodraw_x_axis (line 2561) | def test_nodraw_x_axis(self): method test_x_regions_ts (line 2568) | def test_x_regions_ts(self): method test_x_regions_tree (line 2586) | def test_x_regions_tree(self): method test_unsupported_x_regions (line 2595) | def test_unsupported_x_regions(self): method test_bad_x_regions (line 2603) | def test_bad_x_regions(self): method test_title (line 2614) | def test_title(self): method test_bad_ts_order (line 2621) | def test_bad_ts_order(self): method test_good_tree_order (line 2626) | def test_good_tree_order(self): method test_nonpostorder_tree_order (line 2630) | def test_nonpostorder_tree_order(self): method test_only_subset_nodes_in_rank (line 2635) | def test_only_subset_nodes_in_rank(self, caplog): method test_polytomy_collapsing (line 2656) | def test_polytomy_collapsing(self): method test_preamble (line 2671) | def test_preamble(self, tree_or_ts): method test_non_svg_preamble (line 2686) | def test_non_svg_preamble(self, tree_or_ts): class TestDrawKnownSvg (line 2694) | class TestDrawKnownSvg(TestDrawSvgBase): method verify_known_svg (line 2699) | def verify_known_svg(self, svg, filename, save=False, **kwargs): method test_known_svg_tree_no_mut (line 2712) | def test_known_svg_tree_no_mut(self, overwrite_viz, draw_plotbox): method test_known_svg_tree_x_axis (line 2725) | def test_known_svg_tree_x_axis(self, overwrite_viz, draw_plotbox): method test_known_svg_tree_y_axis_rank (line 2740) | def test_known_svg_tree_y_axis_rank(self, overwrite_viz, draw_plotbox): method test_known_svg_tree_both_axes (line 2761) | def test_known_svg_tree_both_axes(self, overwrite_viz, draw_plotbox): method test_known_svg_tree_root_mut (line 2771) | def test_known_svg_tree_root_mut(self, overwrite_viz, draw_plotbox): method test_known_svg_tree_mut_all_edge (line 2776) | def test_known_svg_tree_mut_all_edge(self, overwrite_viz, draw_plotbox): method test_known_svg_tree_timed_root_mut (line 2790) | def test_known_svg_tree_timed_root_mut(self, overwrite_viz, draw_plotb... method test_known_svg_ts (line 2796) | def test_known_svg_ts(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_title (line 2807) | def test_known_svg_ts_title(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_no_axes (line 2814) | def test_known_svg_ts_no_axes(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_internal_sample (line 2827) | def test_known_svg_ts_internal_sample(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_highlighted_mut (line 2838) | def test_known_svg_ts_highlighted_mut(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_rank (line 2852) | def test_known_svg_ts_rank(self, overwrite_viz, draw_plotbox): method test_known_svg_nonbinary_ts (line 2865) | def test_known_svg_nonbinary_ts(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_plain (line 2874) | def test_known_svg_ts_plain(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_plain_no_xlab (line 2886) | def test_known_svg_ts_plain_no_xlab(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_plain_y (line 2897) | def test_known_svg_ts_plain_y(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_with_xlabel (line 2915) | def test_known_svg_ts_with_xlabel(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_y_axis (line 2927) | def test_known_svg_ts_y_axis(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_y_axis_regular (line 2936) | def test_known_svg_ts_y_axis_regular(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_y_axis_log (line 2948) | def test_known_svg_ts_y_axis_log(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_mutation_times (line 2960) | def test_known_svg_ts_mutation_times(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_titles (line 2970) | def test_known_svg_ts_titles(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_mutation_times_logscale (line 2988) | def test_known_svg_ts_mutation_times_logscale(self, overwrite_viz, dra... method test_known_svg_ts_mut_no_edges (line 2997) | def test_known_svg_ts_mut_no_edges(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_timed_mut_no_edges (line 3013) | def test_known_svg_ts_timed_mut_no_edges(self, overwrite_viz, draw_plo... method test_known_svg_ts_multiroot (line 3032) | def test_known_svg_ts_multiroot(self, overwrite_viz, draw_plotbox): method test_known_svg_ts_xlim (line 3054) | def test_known_svg_ts_xlim(self, overwrite_viz, draw_plotbox): method test_known_max_num_trees (line 3061) | def test_known_max_num_trees(self, overwrite_viz, draw_plotbox): method test_known_max_num_trees_treewise (line 3082) | def test_known_max_num_trees_treewise(self, overwrite_viz, draw_plotbox): method test_known_svg_tree_collapsed (line 3101) | def test_known_svg_tree_collapsed(self, overwrite_viz, draw_plotbox): method test_known_svg_tree_subtree (line 3121) | def test_known_svg_tree_subtree(self, overwrite_viz, draw_plotbox): method test_known_svg_tree_subtrees_with_collapsed (line 3133) | def test_known_svg_tree_subtrees_with_collapsed(self, overwrite_viz, d... method test_known_svg_tree_polytomy (line 3156) | def test_known_svg_tree_polytomy(self, overwrite_viz, draw_plotbox): method test_known_svg_tree_polytomy_tracked (line 3167) | def test_known_svg_tree_polytomy_tracked(self, overwrite_viz, draw_plo... method test_known_svg_tree_polytomy_tracked_collapse (line 3182) | def test_known_svg_tree_polytomy_tracked_collapse(self, overwrite_viz,... class TestRounding (line 3200) | class TestRounding: method test_rnd (line 3201) | def test_rnd(self): class TestDrawingTraversals (line 3212) | class TestDrawingTraversals: FILE: python/tests/test_extend_haplotypes.py function _slide_mutation_nodes_up (line 15) | def _slide_mutation_nodes_up(ts, mutations): function print_edge_list (line 51) | def print_edge_list(head, edges, left, right): class HaplotypeExtender (line 65) | class HaplotypeExtender: method __init__ (line 66) | def __init__(self, ts, forwards): method print_state (line 138) | def print_state(self): method next_tree (line 175) | def next_tree(self, tree_pos): method check_state_at (line 239) | def check_state_at(self, pos, before, degree, nodes_edge): method check_parent (line 260) | def check_parent(self, parent, edge_ids): method check_state (line 268) | def check_state(self, here): method add_or_extend_edge (line 280) | def add_or_extend_edge(self, new_parent, child, left, right): method add_edge (line 326) | def add_edge(self, parent, child, left, right): method mergeable (line 337) | def mergeable(self, c): method merge_paths (line 382) | def merge_paths(self, c, left, right): method extend_haplotypes (line 416) | def extend_haplotypes(self): function extend_haplotypes (line 474) | def extend_haplotypes(ts, max_iter=10): function _path_pairs (line 500) | def _path_pairs(tree): function _path_up (line 508) | def _path_up(c, p, tree, include_parent=False): function _path_up_pairs (line 519) | def _path_up_pairs(c, p, tree, others): function _path_overlaps (line 539) | def _path_overlaps(c, p, tree1, tree2): function _paths_mergeable (line 546) | def _paths_mergeable(c, p, tree1, tree2): function _extend_nodes (line 567) | def _extend_nodes(ts, interval, extendable): function _naive_pass (line 614) | def _naive_pass(ts, direction): function naive_extend_haplotypes (line 643) | def naive_extend_haplotypes(ts, max_iter=20): class TestExtendThings (line 653) | class TestExtendThings: method verify_simplify_equality (line 658) | def verify_simplify_equality(self, ts, ets): method naive_verify (line 666) | def naive_verify(self, ts): class TestExtendHaplotypes (line 671) | class TestExtendHaplotypes(TestExtendThings): method get_example1 (line 676) | def get_example1(self): method get_example2 (line 766) | def get_example2(self): method get_example3 (line 897) | def get_example3(self): method get_example4 (line 942) | def get_example4(self): method get_example5 (line 1006) | def get_example5(self): method get_example (line 1072) | def get_example(self, j): method verify_extend_haplotypes (line 1087) | def verify_extend_haplotypes(self, ts, max_iter=10): method test_runs (line 1093) | def test_runs(self): method test_example (line 1099) | def test_example(self, j): method test_redundant_breakpoitns (line 1107) | def test_redundant_breakpoitns(self, j): method test_migrations_disallowed (line 1115) | def test_migrations_disallowed(self): method test_unknown_times (line 1127) | def test_unknown_times(self): method test_max_iter (line 1139) | def test_max_iter(self): method test_very_simple (line 1150) | def test_very_simple(self): method test_internal_samples (line 1182) | def test_internal_samples(self): method test_wf (line 1238) | def test_wf(self, seed): class TestExamples (line 1246) | class TestExamples(TestExtendThings): method check (line 1251) | def check(self, ts): method test_suite_examples_defaults (line 1266) | def test_suite_examples_defaults(self, ts): method test_all_trees_ts (line 1277) | def test_all_trees_ts(self, n): FILE: python/tests/test_file_format.py function single_locus_no_mutation_example (line 48) | def single_locus_no_mutation_example(): function single_locus_with_mutation_example (line 52) | def single_locus_with_mutation_example(): function multi_locus_with_mutation_example (line 56) | def multi_locus_with_mutation_example(): function recurrent_mutation_example (line 62) | def recurrent_mutation_example(): function general_mutation_example (line 67) | def general_mutation_example(): function multichar_mutation_example (line 77) | def multichar_mutation_example(): function migration_example (line 82) | def migration_example(): function bottleneck_example (line 107) | def bottleneck_example(): function historical_sample_example (line 119) | def historical_sample_example(): function no_provenance_example (line 128) | def no_provenance_example(): function provenance_timestamp_only_example (line 135) | def provenance_timestamp_only_example(): function node_metadata_example (line 143) | def node_metadata_example(): function site_metadata_example (line 159) | def site_metadata_example(): function mutation_metadata_example (line 167) | def mutation_metadata_example(): function migration_metadata_example (line 176) | def migration_metadata_example(): function edge_metadata_example (line 194) | def edge_metadata_example(): class TestFileFormat (line 212) | class TestFileFormat(unittest.TestCase): method setUp (line 217) | def setUp(self): method tearDown (line 221) | def tearDown(self): class TestLoadLegacyExamples (line 225) | class TestLoadLegacyExamples(TestFileFormat): method verify_tree_sequence (line 230) | def verify_tree_sequence(self, ts): method verify_0_3_3 (line 245) | def verify_0_3_3(self, ts): method test_format_too_old_raised_for_hdf5 (line 254) | def test_format_too_old_raised_for_hdf5(self): method test_tskit_v_0_3_3 (line 274) | def test_tskit_v_0_3_3(self): class TestErrors (line 280) | class TestErrors(TestFileFormat): method test_tszip_file (line 285) | def test_tszip_file(self): class TestDumpFormat (line 294) | class TestDumpFormat(TestFileFormat): method verify_keys (line 299) | def verify_keys(self, ts): method verify_uuid (line 368) | def verify_uuid(self, ts, uuid): method verify_dump_format (line 375) | def verify_dump_format(self, ts): method test_single_locus_no_mutation (line 535) | def test_single_locus_no_mutation(self): method test_single_locus_with_mutation (line 538) | def test_single_locus_with_mutation(self): method test_multi_locus_with_mutation (line 541) | def test_multi_locus_with_mutation(self): method test_migration_example (line 544) | def test_migration_example(self): method test_bottleneck_example (line 547) | def test_bottleneck_example(self): method test_historical_sample_example (line 550) | def test_historical_sample_example(self): method test_node_metadata_example (line 553) | def test_node_metadata_example(self): method test_edge_metadata_example (line 556) | def test_edge_metadata_example(self): method test_site_metadata_example (line 559) | def test_site_metadata_example(self): method test_mutation_metadata_example (line 562) | def test_mutation_metadata_example(self): method test_migration_metadata_example (line 565) | def test_migration_metadata_example(self): method test_general_mutation_example (line 568) | def test_general_mutation_example(self): method test_multichar_mutation_example (line 571) | def test_multichar_mutation_example(self): class TestUuid (line 575) | class TestUuid(TestFileFormat): method test_different_files_same_ts (line 580) | def test_different_files_same_ts(self): class TestOptionalColumns (line 590) | class TestOptionalColumns(TestFileFormat): method test_empty_edge_metadata (line 595) | def test_empty_edge_metadata(self): method test_empty_migration_metadata (line 610) | def test_empty_migration_metadata(self): method test_empty_mutation_time (line 625) | def test_empty_mutation_time(self): method test_empty_individual_parents (line 641) | def test_empty_individual_parents(self): class TestReferenceSequence (line 663) | class TestReferenceSequence: method test_fixture_has_reference_sequence (line 664) | def test_fixture_has_reference_sequence(self, ts_fixture): method test_round_trip (line 667) | def test_round_trip(self, ts_fixture, tmp_path): method test_no_reference_sequence (line 674) | def test_no_reference_sequence(self, ts_fixture, tmp_path): method test_missing_attr (line 694) | def test_missing_attr(self, ts_fixture, tmp_path, attr): method test_missing_metadata (line 706) | def test_missing_metadata(self, ts_fixture, tmp_path): method test_missing_metadata_schema (line 718) | def test_missing_metadata_schema(self, ts_fixture, tmp_path): class TestFileFormatErrors (line 731) | class TestFileFormatErrors(TestFileFormat): method verify_missing_fields (line 736) | def verify_missing_fields(self, ts): method test_missing_fields (line 755) | def test_missing_fields(self): method verify_equal_length_columns (line 758) | def verify_equal_length_columns(self, ts, table): method test_equal_length_columns (line 782) | def test_equal_length_columns(self): method verify_offset_columns (line 787) | def verify_offset_columns(self, ts): method test_offset_columns (line 816) | def test_offset_columns(self): method test_index_columns (line 820) | def test_index_columns(self): method test_load_empty_kastore (line 860) | def test_load_empty_kastore(self): method test_old_version_load_error (line 865) | def test_old_version_load_error(self): method test_new_version_load_error (line 876) | def test_new_version_load_error(self): method test_format_name_error (line 887) | def test_format_name_error(self): method test_load_bad_formats (line 898) | def test_load_bad_formats(self): method test_load_bad_formats_fileobj (line 914) | def test_load_bad_formats_fileobj(self): function assert_tables_empty (line 927) | def assert_tables_empty(tables): class TestSkipTables (line 932) | class TestSkipTables: method test_ts_read_path_interface (line 937) | def test_ts_read_path_interface(self, tmp_path, ts_fixture): method test_ts_read_one_stream (line 948) | def test_ts_read_one_stream(self, tmp_path, ts_fixture): method test_ts_twofile_stream_noskip (line 957) | def test_ts_twofile_stream_noskip(self, tmp_path, ts_fixture): method test_ts_twofile_stream_fails (line 968) | def test_ts_twofile_stream_fails(self, tmp_path, ts_fixture): method test_table_collection_load_path (line 979) | def test_table_collection_load_path(self, tmp_path, ts_fixture): method test_table_collection_load_stream (line 988) | def test_table_collection_load_stream(self, tmp_path, ts_fixture): class TestSkipReferenceSequence (line 999) | class TestSkipReferenceSequence: method test_ts_load_path (line 1005) | def test_ts_load_path(self, tmp_path, ts_fixture): method test_ts_load_stream (line 1014) | def test_ts_load_stream(self, tmp_path, ts_fixture): method test_ts_twofile_stream_fails (line 1023) | def test_ts_twofile_stream_fails(self, tmp_path, ts_fixture): method test_table_collection_load_path (line 1034) | def test_table_collection_load_path(self, tmp_path, ts_fixture): method test_table_collection_load_stream (line 1045) | def test_table_collection_load_stream(self, tmp_path, ts_fixture): FILE: python/tests/test_fileobj.py class TestPath (line 47) | class TestPath: method tempfile_name (line 49) | def tempfile_name(self): method test_pathlib (line 53) | def test_pathlib(self, ts_fixture, tempfile_name): class TestPathLib (line 59) | class TestPathLib: method pathlib_tempfile (line 61) | def pathlib_tempfile(self): method test_pathlib (line 68) | def test_pathlib(self, ts_fixture, pathlib_tempfile): class TestFileObj (line 74) | class TestFileObj: method fileobj (line 76) | def fileobj(self): method test_fileobj (line 81) | def test_fileobj(self, ts_fixture, fileobj): method test_fileobj_multi (line 87) | def test_fileobj_multi(self, replicate_ts_fixture, fileobj): class TestFileObjRW (line 101) | class TestFileObjRW: method fileobj (line 103) | def fileobj(self): method test_fileobj (line 109) | def test_fileobj(self, ts_fixture, fileobj): method test_fileobj_multi (line 115) | def test_fileobj_multi(self, replicate_ts_fixture, fileobj): class TestFD (line 128) | class TestFD: method fd (line 130) | def fd(self): method test_fd (line 136) | def test_fd(self, ts_fixture, fd): method test_fd_multi (line 142) | def test_fd_multi(self, replicate_ts_fixture, fd): class TestUnsupportedObjects (line 151) | class TestUnsupportedObjects: method test_string_io (line 152) | def test_string_io(self, ts_fixture): function dump_to_stream (line 163) | def dump_to_stream(q_err, q_in, file_out): function load_from_stream (line 180) | def load_from_stream(q_err, q_out, file_in): function stream (line 198) | def stream(fifo, ts_list): class TestFIFO (line 247) | class TestFIFO: method fifo (line 249) | def fifo(self): method test_single_stream (line 256) | def test_single_stream(self, fifo, ts_fixture): method test_multi_stream (line 259) | def test_multi_stream(self, fifo, replicate_ts_fixture): class Server (line 266) | class Server(socketserver.ThreadingTCPServer): class StoreEchoHandler (line 270) | class StoreEchoHandler(socketserver.BaseRequestHandler): method handle (line 271) | def handle(self): function server_process (line 281) | def server_process(q): class TestSocket (line 291) | class TestSocket: method client_fd (line 293) | def client_fd(self): method verify_stream (line 304) | def verify_stream(self, ts_list, client_fd): method test_single_then_multi (line 310) | def test_single_then_multi(self, ts_fixture, replicate_ts_fixture, cli... function write_to_fifo (line 315) | def write_to_fifo(path, file_path): function read_from_fifo (line 321) | def read_from_fifo(path, expected_exception, error_text, read_func): function write_and_read_from_fifo (line 327) | def write_and_read_from_fifo(fifo_path, file_path, expected_exception, e... class TestBadStream (line 345) | class TestBadStream: method test_bad_stream (line 346) | def test_bad_stream(self, tmp_path): method test_legacy_stream (line 354) | def test_legacy_stream(self, tmp_path): method test_tszip_stream (line 363) | def test_tszip_stream(self, tmp_path, ts_fixture): FILE: python/tests/test_genotype_matching.py function mirror_coordinates (line 20) | def mirror_coordinates(ts): class ValueTransition (line 37) | class ValueTransition: method __init__ (line 40) | def __init__(self, tree_node=-1, inner_summation=-1, value_list=-1, va... method copy (line 46) | def copy(self): method __repr__ (line 54) | def __repr__(self): method __str__ (line 57) | def __str__(self): class InternalValueTransition (line 61) | class InternalValueTransition: method __init__ (line 64) | def __init__(self, tree_node=-1, value=-1, inner_summation=-1): method __repr__ (line 69) | def __repr__(self): method __str__ (line 72) | def __str__(self): class LsHmmAlgorithm (line 76) | class LsHmmAlgorithm: method __init__ (line 81) | def __init__(self, ts, rho, mu, precision=30): method decode_site_dict (line 100) | def decode_site_dict(self): method check_integrity (line 121) | def check_integrity(self): method stupid_compress_dict (line 131) | def stupid_compress_dict(self): method update_tree (line 251) | def update_tree(self): method update_probabilities (line 358) | def update_probabilities(self, site, genotype_state): method process_site (line 475) | def process_site( method run_forward (line 539) | def run_forward(self, g): method run_backward (line 557) | def run_backward(self, g): method compute_normalisation_factor_dict (line 573) | def compute_normalisation_factor_dict(self): method compute_next_probability_dict (line 576) | def compute_next_probability_dict( class CompressedMatrix (line 591) | class CompressedMatrix: method __init__ (line 600) | def __init__(self, ts, normalisation_factor=None): method store_site (line 611) | def store_site(self, site, normalisation_factor, value_transitions): method num_transitions (line 618) | def num_transitions(self): method get_site (line 622) | def get_site(self, site): method decode_site_dict (line 625) | def decode_site_dict(self, tree, site_id): method decode (line 643) | def decode(self): class ForwardMatrix (line 655) | class ForwardMatrix(CompressedMatrix): class BackwardMatrix (line 659) | class BackwardMatrix(CompressedMatrix): class ViterbiMatrix (line 663) | class ViterbiMatrix(CompressedMatrix): method __init__ (line 668) | def __init__(self, ts): method add_single_recombination_required (line 675) | def add_single_recombination_required(self, site, node_s1, node_s2, re... method add_double_recombination_required (line 678) | def add_double_recombination_required(self, site, node_s1, node_s2, re... method choose_sample_double (line 681) | def choose_sample_double(self, site_id, tree): method choose_sample_single (line 717) | def choose_sample_single(self, site_id, tree, current_nodes): method traceback (line 789) | def traceback(self): class ForwardAlgorithm (line 895) | class ForwardAlgorithm(LsHmmAlgorithm): method __init__ (line 898) | def __init__(self, ts, rho, mu, precision=30): method inner_summation_evaluation (line 902) | def inner_summation_evaluation( method compute_normalisation_factor_dict (line 910) | def compute_normalisation_factor_dict(self): method compute_normalisation_factor_inner_dict (line 918) | def compute_normalisation_factor_inner_dict(self, node): method compute_next_probability_dict (line 927) | def compute_next_probability_dict( class BackwardAlgorithm (line 976) | class BackwardAlgorithm(LsHmmAlgorithm): method __init__ (line 979) | def __init__(self, ts, rho, mu, normalisation_factor, precision=10): method inner_summation_evaluation (line 983) | def inner_summation_evaluation( method compute_normalisation_factor_dict (line 991) | def compute_normalisation_factor_dict(self): method compute_normalisation_factor_inner_dict (line 999) | def compute_normalisation_factor_inner_dict(self, node): method compute_next_probability_dict (line 1008) | def compute_next_probability_dict( class ViterbiAlgorithm (line 1049) | class ViterbiAlgorithm(LsHmmAlgorithm): method __init__ (line 1054) | def __init__(self, ts, rho, mu, precision=10): method inner_summation_evaluation (line 1058) | def inner_summation_evaluation( method compute_normalisation_factor_dict (line 1066) | def compute_normalisation_factor_dict(self): method compute_normalisation_factor_inner_dict (line 1079) | def compute_normalisation_factor_inner_dict(self, node): method compute_next_probability_dict (line 1091) | def compute_next_probability_dict( function ls_forward_tree (line 1163) | def ls_forward_tree(g, ts, rho, mu, precision=30): function ls_backward_tree (line 1169) | def ls_backward_tree(g, ts_mirror, rho, mu, normalisation_factor, precis... function ls_viterbi_tree (line 1175) | def ls_viterbi_tree(g, ts, rho, mu, precision=30): class LSBase (line 1183) | class LSBase: method genotype_emission (line 1186) | def genotype_emission(self, mu, m): method example_genotypes (line 1197) | def example_genotypes(self, ts): method example_parameters_genotypes (line 1226) | def example_parameters_genotypes(self, ts, seed=42): method assertAllClose (line 1252) | def assertAllClose(self, A, B): method test_simple_n_10_no_recombination (line 1259) | def test_simple_n_10_no_recombination(self): method test_simple_n_6 (line 1267) | def test_simple_n_6(self): method test_simple_n_8_high_recombination (line 1273) | def test_simple_n_8_high_recombination(self): method verify (line 1307) | def verify(self, ts): class FBAlgorithmBase (line 1311) | class FBAlgorithmBase(LSBase): class VitAlgorithmBase (line 1315) | class VitAlgorithmBase(LSBase): class TestMirroringDipdict (line 1319) | class TestMirroringDipdict(FBAlgorithmBase): method verify (line 1323) | def verify(self, ts): class TestForwardDipTree (line 1363) | class TestForwardDipTree(FBAlgorithmBase): method verify (line 1367) | def verify(self, ts): class TestForwardBackwardTree (line 1393) | class TestForwardBackwardTree(FBAlgorithmBase): method verify (line 1397) | def verify(self, ts): class TestTreeViterbiDip (line 1450) | class TestTreeViterbiDip(VitAlgorithmBase): method verify (line 1456) | def verify(self, ts): FILE: python/tests/test_genotypes.py function get_example_discrete_genome_tree_sequences (line 53) | def get_example_discrete_genome_tree_sequences(): function naive_get_ancestral_haplotypes (line 65) | def naive_get_ancestral_haplotypes(ts): class TestGetAncestralHaplotypes (line 88) | class TestGetAncestralHaplotypes: method verify (line 93) | def verify(self, ts): method test_single_tree (line 106) | def test_single_tree(self): method test_many_trees (line 110) | def test_many_trees(self): method test_single_tree_jukes_cantor (line 118) | def test_single_tree_jukes_cantor(self): method test_single_tree_multichar_mutations (line 123) | def test_single_tree_multichar_mutations(self): method test_many_trees_infinite_sites (line 128) | def test_many_trees_infinite_sites(self): method test_wright_fisher_initial_generation (line 134) | def test_wright_fisher_initial_generation(self): method test_wright_fisher_simplified (line 144) | def test_wright_fisher_simplified(self): method test_empty_ts (line 159) | def test_empty_ts(self): function isolated_samples_genotype_matrix (line 167) | def isolated_samples_genotype_matrix(ts): class TestVariantGenerator (line 187) | class TestVariantGenerator: method get_tree_sequence (line 192) | def get_tree_sequence(self): method test_dtype (line 199) | def test_dtype(self): method test_dtype_conversion (line 204) | def test_dtype_conversion(self): method test_multichar_alleles (line 219) | def test_multichar_alleles(self): method test_many_alleles (line 228) | def test_many_alleles(self): method test_many_alleles_missing_data (line 254) | def test_many_alleles_missing_data(self): method test_site_information (line 286) | def test_site_information(self): method test_no_mutations (line 292) | def test_no_mutations(self): method test_genotype_matrix (line 299) | def test_genotype_matrix(self, samples): method test_recurrent_mutations_over_samples (line 312) | def test_recurrent_mutations_over_samples(self): method test_silent_mutations (line 334) | def test_silent_mutations(self): method test_zero_samples (line 350) | def test_zero_samples(self): method test_samples (line 357) | def test_samples(self): method test_samples_64bit (line 379) | def test_samples_64bit(self): method test_samples_missing_data (line 386) | def test_samples_missing_data(self): method test_non_sample_samples (line 411) | def test_non_sample_samples(self): method verify_jukes_cantor (line 438) | def verify_jukes_cantor(self, ts): method test_jukes_cantor_n5 (line 454) | def test_jukes_cantor_n5(self): method test_jukes_cantor_n20 (line 459) | def test_jukes_cantor_n20(self): method test_zero_edge_missing_data (line 464) | def test_zero_edge_missing_data(self): method test_empty_ts_missing_data (line 504) | def test_empty_ts_missing_data(self): method test_empty_ts_incomplete_samples (line 517) | def test_empty_ts_incomplete_samples(self): method test_missing_data_samples (line 529) | def test_missing_data_samples(self): method test_mutation_over_isolated_sample_not_missing (line 559) | def test_mutation_over_isolated_sample_not_missing(self): method test_multiple_mutations_over_isolated_sample (line 573) | def test_multiple_mutations_over_isolated_sample(self): method test_snipped_tree_sequence_missing_data (line 589) | def test_snipped_tree_sequence_missing_data(self): method test_snipped_tree_sequence_mutations_over_isolated (line 623) | def test_snipped_tree_sequence_mutations_over_isolated(self): method get_missing_data_ts (line 660) | def get_missing_data_ts(self): method test_states (line 672) | def test_states(self): method test_states_haplotypes_equiv (line 695) | def test_states_haplotypes_equiv(self, missing): method test_bad_states (line 708) | def test_bad_states(self, s): class TestLimitInterval (line 718) | class TestLimitInterval: method test_simple_case (line 719) | def test_simple_case(self, ts_fixture): method test_left (line 743) | def test_left(self, left, expected): method test_right (line 763) | def test_right(self, right, expected): method test_bad_left (line 772) | def test_bad_left(self, bad_left): method test_bad_right (line 778) | def test_bad_right(self, bad_right): method test_bad_left_right (line 783) | def test_bad_left_right(self): class TestHaplotypeGenerator (line 789) | class TestHaplotypeGenerator: method verify_haplotypes (line 794) | def verify_haplotypes(self, n, haplotypes): method verify_tree_sequence (line 814) | def verify_tree_sequence(self, tree_sequence): method verify_simulation (line 828) | def verify_simulation(self, n, m, r, theta): method test_random_parameters (line 838) | def test_random_parameters(self): method test_nonbinary_trees (line 847) | def test_nonbinary_trees(self): method test_acgt_mutations (line 862) | def test_acgt_mutations(self): method test_fails_multiletter_mutations (line 883) | def test_fails_multiletter_mutations(self): method test_fails_deletion_mutations (line 891) | def test_fails_deletion_mutations(self): method test_nonascii_mutations (line 899) | def test_nonascii_mutations(self): method test_recurrent_mutations_over_samples (line 907) | def test_recurrent_mutations_over_samples(self): method test_silent_mutations (line 922) | def test_silent_mutations(self): method test_back_mutations (line 936) | def test_back_mutations(self): method test_missing_data (line 942) | def test_missing_data(self): method test_restrict_samples (line 979) | def test_restrict_samples(self): method test_restrict_positions (line 991) | def test_restrict_positions(self): class TestUserAlleles (line 1003) | class TestUserAlleles: method test_simple_01 (line 1008) | def test_simple_01(self): method test_simple_01_trailing_alleles (line 1021) | def test_simple_01_trailing_alleles(self): method test_simple_01_leading_alleles (line 1033) | def test_simple_01_leading_alleles(self): method test_simple_01_duplicate_alleles (line 1045) | def test_simple_01_duplicate_alleles(self): method test_simple_acgt (line 1062) | def test_simple_acgt(self): method test_missing_alleles (line 1078) | def test_missing_alleles(self): method test_too_many_alleles (line 1097) | def test_too_many_alleles(self): method test_zero_allele (line 1106) | def test_zero_allele(self): method test_missing_data (line 1113) | def test_missing_data(self): class TestUserAllelesRoundTrip (line 1137) | class TestUserAllelesRoundTrip: method verify (line 1143) | def verify(self, ts, alleles): method test_simple_01 (line 1149) | def test_simple_01(self): method test_simple_acgt (line 1162) | def test_simple_acgt(self): method test_jukes_cantor (line 1176) | def test_jukes_cantor(self): method test_multichar_mutations (line 1187) | def test_multichar_mutations(self): method test_simple_01_missing_data (line 1198) | def test_simple_01_missing_data(self): class TestBinaryTreeExample (line 1216) | class TestBinaryTreeExample: method ts (line 1227) | def ts(self): method test_haplotypes (line 1236) | def test_haplotypes(self): method test_haplotypes_empty_interval (line 1242) | def test_haplotypes_empty_interval(self): method test_genotypes (line 1247) | def test_genotypes(self): method test_alignments_default (line 1252) | def test_alignments_default(self): method test_alignments_restricted (line 1258) | def test_alignments_restricted(self): method test_empty_samples (line 1266) | def test_empty_samples(self): method test_non_sample_samples (line 1271) | def test_non_sample_samples(self): method test_alignments_samples_order_preserved (line 1276) | def test_alignments_samples_order_preserved(self): method test_variants_internal_nodes (line 1286) | def test_variants_internal_nodes(self): method test_genotype_matrix_internal_nodes (line 1306) | def test_genotype_matrix_internal_nodes(self): method test_haplotypes_internal_nodes (line 1325) | def test_haplotypes_internal_nodes(self): method test_alignments_missing_data_char (line 1332) | def test_alignments_missing_data_char(self): method test_alignments_reference_sequence (line 1338) | def test_alignments_reference_sequence(self): method test_alignments_reference_sequence_embedded_null (line 1345) | def test_alignments_reference_sequence_embedded_null(self): method test_fasta_default (line 1354) | def test_fasta_default(self): method test_fasta_missing_Q (line 1367) | def test_fasta_missing_Q(self): method test_fasta_reference_sequence (line 1380) | def test_fasta_reference_sequence(self): method test_nexus_default (line 1394) | def test_nexus_default(self): method test_nexus_missing_N (line 1418) | def test_nexus_missing_N(self): method test_nexus_reference_sequence (line 1442) | def test_nexus_reference_sequence(self): class TestBinaryTreeWithReferenceExample (line 1468) | class TestBinaryTreeWithReferenceExample: method ts (line 1479) | def ts(self): method test_alignments_default (line 1489) | def test_alignments_default(self): method test_alignments_missing_data_char (line 1495) | def test_alignments_missing_data_char(self): method test_alignments_restricted_embedded_reference (line 1501) | def test_alignments_restricted_embedded_reference(self): method test_alignments_reference_sequence (line 1510) | def test_alignments_reference_sequence(self): method test_fasta_default (line 1517) | def test_fasta_default(self): method test_fasta_reference_sequence (line 1530) | def test_fasta_reference_sequence(self): method test_nexus_default (line 1544) | def test_nexus_default(self): method test_nexus_reference_sequence (line 1568) | def test_nexus_reference_sequence(self): class TestMissingDataExample (line 1594) | class TestMissingDataExample: method ts (line 1605) | def ts(self): method test_haplotypes (line 1615) | def test_haplotypes(self): method test_haplotypes_missing_data_char (line 1622) | def test_haplotypes_missing_data_char(self): method test_genotypes (line 1629) | def test_genotypes(self): method test_alignments_default (line 1634) | def test_alignments_default(self): method test_alignments_impute_missing (line 1641) | def test_alignments_impute_missing(self): method test_alignments_missing_char (line 1649) | def test_alignments_missing_char(self): method test_alignments_missing_char_ref (line 1656) | def test_alignments_missing_char_ref(self): method test_alignments_reference_sequence (line 1663) | def test_alignments_reference_sequence(self): method test_alignments_reference_sequence_missing_data_char (line 1671) | def test_alignments_reference_sequence_missing_data_char(self): method test_alignments_left_right_subinterval (line 1681) | def test_alignments_left_right_subinterval(self): method test_fasta_reference_sequence (line 1688) | def test_fasta_reference_sequence(self): method test_fasta_reference_sequence_missing_data_char (line 1704) | def test_fasta_reference_sequence_missing_data_char(self): method test_fasta_impute_missing (line 1722) | def test_fasta_impute_missing(self): method test_nexus_reference_sequence (line 1743) | def test_nexus_reference_sequence(self): method test_nexus_reference_sequence_missing_data_char (line 1768) | def test_nexus_reference_sequence_missing_data_char(self): method test_nexus_impute_missing (line 1795) | def test_nexus_impute_missing(self): class TestAlignmentsPartialIsolation (line 1823) | class TestAlignmentsPartialIsolation: method build_ts (line 1824) | def build_ts(self): method test_whole_window_missing_at_ends (line 1836) | def test_whole_window_missing_at_ends(self): method test_subwindow (line 1844) | def test_subwindow(self): class TestMultiRootExample (line 1852) | class TestMultiRootExample: method ts (line 1861) | def ts(self): method test_haplotypes (line 1875) | def test_haplotypes(self): method test_genotypes (line 1882) | def test_genotypes(self): method test_alignments_default (line 1887) | def test_alignments_default(self): method test_alignments_N_ref (line 1894) | def test_alignments_N_ref(self): method test_alignments_multichar_allele_raises (line 1901) | def test_alignments_multichar_allele_raises(self): method test_fasta_reference_sequence (line 1911) | def test_fasta_reference_sequence(self): class TestInternalNodeMissingness (line 1928) | class TestInternalNodeMissingness: method ts_missing (line 1930) | def ts_missing(self): method test_variants_internal_isolated (line 1944) | def test_variants_internal_isolated(self): method test_genotype_matrix_internal_isolated (line 1957) | def test_genotype_matrix_internal_isolated(self): method test_haplotypes_internal_isolated (line 1968) | def test_haplotypes_internal_isolated(self): class TestVariantTopologyCombos (line 1980) | class TestVariantTopologyCombos: method test_all_parent_child_combinations (line 1981) | def test_all_parent_child_combinations(self): class TestInternalNode (line 2020) | class TestInternalNode: method ts_single_tree (line 2022) | def ts_single_tree(self): method ts_isolated_internal (line 2026) | def ts_isolated_internal(self): method test_isolated_internal_node_all_missing (line 2035) | def test_isolated_internal_node_all_missing(self): method ts_dead_branch (line 2051) | def ts_dead_branch(self): method test_dead_branch_internal_and_leaf (line 2077) | def test_dead_branch_internal_and_leaf(self): method ts_presence_switch (line 2092) | def ts_presence_switch(self): method test_internal_presence_switch (line 2121) | def test_internal_presence_switch(self): method test_isolated_sample_mark_missing_any (line 2139) | def test_isolated_sample_mark_missing_any(self): method ts_mutation_overrides_missing (line 2151) | def ts_mutation_overrides_missing(self): method test_mutation_overrides_missing (line 2165) | def test_mutation_overrides_missing(self): method test_mixed_samples_ordering (line 2173) | def test_mixed_samples_ordering(self): method test_variants_copy_false_internal (line 2193) | def test_variants_copy_false_internal(self): class TestAlignmentsErrors (line 2205) | class TestAlignmentsErrors: method simplest_ts (line 2207) | def simplest_ts(self): method test_non_discrete_genome (line 2212) | def test_non_discrete_genome(self): method test_reference_length_mismatch (line 2219) | def test_reference_length_mismatch(self, ref_length): method test_reference_sequence_length_mismatch (line 2229) | def test_reference_sequence_length_mismatch(self, ref): method test_non_ascii_references (line 2237) | def test_non_ascii_references(self, ref): method test_non_ascii_embedded_references (line 2243) | def test_non_ascii_embedded_references(self, ref): method test_non_ascii_missing_data_char (line 2252) | def test_non_ascii_missing_data_char(self, missing_data_char): method test_multichar_missing_data_char (line 2257) | def test_multichar_missing_data_char(self): method test_missing_char_clashes_with_allele (line 2263) | def test_missing_char_clashes_with_allele(self): method test_invalid_negative_node (line 2273) | def test_invalid_negative_node(self): method test_invalid_out_of_bounds_node (line 2278) | def test_invalid_out_of_bounds_node(self): method test_bad_left (line 2283) | def test_bad_left(self): method test_bad_right (line 2288) | def test_bad_right(self): method test_bad_restricted (line 2293) | def test_bad_restricted(self): method test_no_samples_default (line 2302) | def test_no_samples_default(self): method test_boundary_sites_left_and_right (line 2311) | def test_boundary_sites_left_and_right(self): method test_reference_sequence_too_short_with_interval (line 2329) | def test_reference_sequence_too_short_with_interval(self): method test_reference_sequence_length_must_match_sequence (line 2339) | def test_reference_sequence_length_must_match_sequence(self): class TestAlignmentExamples (line 2350) | class TestAlignmentExamples: method test_defaults (line 2352) | def test_defaults(self, ts): method test_reference_sequence (line 2365) | def test_reference_sequence(self, ts): function _reference_alignments (line 2381) | def _reference_alignments( class TestAlignmentsReferenceImpl (line 2438) | class TestAlignmentsReferenceImpl: method test_against_python_reference (line 2448) | def test_against_python_reference(self, ts, case): function test_allele_remap (line 2559) | def test_allele_remap(alleles_from, alleles_to, allele_map): class TestVariant (line 2563) | class TestVariant: method test_variant_init (line 2566) | def test_variant_init(self, ts_fixture): method test_not_decoded (line 2579) | def test_not_decoded(self, ts_fixture): method test_variant_decode (line 2593) | def test_variant_decode(self, ts_fixture): method test_variant_num_missing (line 2602) | def test_variant_num_missing(self, ts_fixture): method test_variant_counts (line 2607) | def test_variant_counts(self, ts_fixture): method test_variant_counts_empty (line 2620) | def test_variant_counts_empty(self): method test_variant_simple_frequencies (line 2628) | def test_variant_simple_frequencies(self): method test_variant_frequencies (line 2650) | def test_variant_frequencies(self, ts_fixture): method test_variant_frequencies_limit_samples (line 2671) | def test_variant_frequencies_limit_samples(self, ts_fixture): method test_variant_nonsample_freqs (line 2681) | def test_variant_nonsample_freqs(self): method test_variant_frequencies_no_samples (line 2698) | def test_variant_frequencies_no_samples(self, ts_fixture, caplog): method test_variant_str (line 2709) | def test_variant_str(self): method test_variant_str_no_samples (line 2765) | def test_variant_str_no_samples(self): method test_variant_str_no_site (line 2781) | def test_variant_str_no_site(self): method test_variant_html_repr (line 2793) | def test_variant_html_repr(self, ts_fixture): method test_variant_html_repr_no_site (line 2800) | def test_variant_html_repr_no_site(self): method test_variant_repr (line 2808) | def test_variant_repr(self, ts_fixture): FILE: python/tests/test_haplotype_matching.py function check_alleles (line 41) | def check_alleles(alleles, m): function mirror_coordinates (line 58) | def mirror_coordinates(ts): class ValueTransition (line 75) | class ValueTransition: method __init__ (line 78) | def __init__(self, tree_node=-1, value=-1, value_index=-1): method copy (line 83) | def copy(self): method __repr__ (line 90) | def __repr__(self): method __str__ (line 93) | def __str__(self): class LsHmmAlgorithm (line 97) | class LsHmmAlgorithm: method __init__ (line 102) | def __init__( method check_integrity (line 127) | def check_integrity(self): method compress (line 137) | def compress(self): method update_tree (line 235) | def update_tree(self, direction=tskit.FORWARD): method update_probabilities (line 306) | def update_probabilities(self, site, haplotype_state): method process_site (line 347) | def process_site(self, site, haplotype_state): method compute_emission_proba (line 358) | def compute_emission_proba(self, site_id, is_match): method initialise (line 388) | def initialise(self, value): method run (line 395) | def run(self, h): method compute_normalisation_factor (line 404) | def compute_normalisation_factor(self): method compute_next_probability (line 407) | def compute_next_probability( class ForwardAlgorithm (line 413) | class ForwardAlgorithm(LsHmmAlgorithm): method __init__ (line 418) | def __init__( method compute_normalisation_factor (line 432) | def compute_normalisation_factor(self): method compute_next_probability (line 440) | def compute_next_probability( class BackwardAlgorithm (line 453) | class BackwardAlgorithm(ForwardAlgorithm): method compute_next_probability (line 458) | def compute_next_probability( method process_site (line 467) | def process_site(self, site, haplotype_state, s): method run (line 490) | def run(self, h, normalisation_factor): class ViterbiAlgorithm (line 499) | class ViterbiAlgorithm(LsHmmAlgorithm): method __init__ (line 504) | def __init__( method compute_normalisation_factor (line 518) | def compute_normalisation_factor(self): method compute_next_probability (line 530) | def compute_next_probability( function assert_compressed_matrices_equal (line 554) | def assert_compressed_matrices_equal(cm1, cm2): class CompressedMatrix (line 570) | class CompressedMatrix: method __init__ (line 579) | def __init__(self, ts): method store_site (line 586) | def store_site(self, site, normalisation_factor, value_transitions): method num_transitions (line 594) | def num_transitions(self): method get_site (line 598) | def get_site(self, site): method decode (line 601) | def decode(self): class ViterbiMatrix (line 618) | class ViterbiMatrix(CompressedMatrix): method __init__ (line 623) | def __init__(self, ts): method add_recombination_required (line 629) | def add_recombination_required(self, site, node, required): method choose_sample (line 632) | def choose_sample(self, site_id, tree): method traceback (line 651) | def traceback(self): function get_site_alleles (line 698) | def get_site_alleles(ts, h, alleles): function ls_forward_tree (line 721) | def ls_forward_tree( function ls_backward_tree (line 737) | def ls_backward_tree(h, ts, rho, mu, normalisation_factor, precision=30,... function ls_viterbi_tree (line 750) | def ls_viterbi_tree( class LSBase (line 766) | class LSBase: method example_haplotypes (line 769) | def example_haplotypes(self, ts): method example_parameters_haplotypes (line 790) | def example_parameters_haplotypes(self, ts, seed=42): method assertAllClose (line 818) | def assertAllClose(self, A, B): method test_simple_n_10_no_recombination (line 824) | def test_simple_n_10_no_recombination(self): method test_simple_n_10_no_recombination_high_mut (line 831) | def test_simple_n_10_no_recombination_high_mut(self): method test_simple_n_10_no_recombination_higher_mut (line 836) | def test_simple_n_10_no_recombination_higher_mut(self): method test_simple_n_6 (line 841) | def test_simple_n_6(self): method test_simple_n_8 (line 846) | def test_simple_n_8(self): method test_simple_n_8_high_recombination (line 851) | def test_simple_n_8_high_recombination(self): method test_simple_n_16 (line 857) | def test_simple_n_16(self): method verify (line 913) | def verify(self, ts): class FBAlgorithmBase (line 917) | class FBAlgorithmBase(LSBase): class VitAlgorithmBase (line 921) | class VitAlgorithmBase(LSBase): class TestMirroringHap (line 925) | class TestMirroringHap(FBAlgorithmBase): method verify (line 929) | def verify(self, ts): class TestForwardHapTree (line 961) | class TestForwardHapTree(FBAlgorithmBase): method verify (line 965) | def verify(self, ts): class TestForwardBackwardTree (line 996) | class TestForwardBackwardTree(FBAlgorithmBase): method verify (line 1000) | def verify(self, ts): class TestTreeViterbiHap (line 1042) | class TestTreeViterbiHap(VitAlgorithmBase): method verify (line 1046) | def verify(self, ts): function check_viterbi (line 1077) | def check_viterbi(ts, h, recombination=None, mutation=None): function check_forward_matrix (line 1134) | def check_forward_matrix(ts, h, recombination=None, mutation=None): function check_backward_matrix (line 1182) | def check_backward_matrix(ts, h, forward_cm, recombination=None, mutatio... function add_unique_sample_mutations (line 1230) | def add_unique_sample_mutations(ts, start=0): class TestSingleBalancedTreeExample (line 1247) | class TestSingleBalancedTreeExample: method ts (line 1256) | def ts(): method test_match_sample (line 1263) | def test_match_sample(self, j): method test_match_sample_missing_flanks (line 1273) | def test_match_sample_missing_flanks(self, j): method test_switch_each_sample (line 1284) | def test_switch_each_sample(self): method test_switch_each_sample_missing_flanks (line 1292) | def test_switch_each_sample_missing_flanks(self): method test_switch_each_sample_missing_middle (line 1302) | def test_switch_each_sample_missing_middle(self): class TestSimulationExamples (line 1313) | class TestSimulationExamples: method test_continuous_genome (line 1317) | def test_continuous_genome(self, n, L): FILE: python/tests/test_highlevel.py function traversal_preorder (line 64) | def traversal_preorder(tree, root=None): function traversal_postorder (line 72) | def traversal_postorder(tree, root=None): function traversal_inorder (line 80) | def traversal_inorder(tree, root=None): function traversal_levelorder (line 92) | def traversal_levelorder(tree, root=None): function _traversal_minlex_postorder (line 96) | def _traversal_minlex_postorder(tree, u): function traversal_minlex_postorder (line 118) | def traversal_minlex_postorder(tree, root=None): function traversal_timeasc (line 125) | def traversal_timeasc(tree, root=None): function traversal_timedesc (line 129) | def traversal_timedesc(tree, root=None): function simple_get_pairwise_diversity (line 145) | def simple_get_pairwise_diversity(haplotypes): function simplify_tree_sequence (line 159) | def simplify_tree_sequence(ts, samples, filter_sites=True): class TestLinkAncestorsExamples (line 168) | class TestLinkAncestorsExamples: method test_link_ancestors_runs_and_is_sane (line 169) | def test_link_ancestors_runs_and_is_sane(self, ts): function oriented_forests (line 208) | def oriented_forests(n): function get_mrca (line 238) | def get_mrca(pi, x, y): function get_samples (line 262) | def get_samples(ts, time=None, population=None): class TestTreeTraversals (line 279) | class TestTreeTraversals: method test_bad_traversal_order (line 280) | def test_bad_traversal_order(self, simple_degree2_ts_fixture): method test_returned_types (line 287) | def test_returned_types(self, order): method test_traversals_virtual_root (line 299) | def test_traversals_virtual_root(self, ts, order): method test_traversals (line 308) | def test_traversals(self, ts, order): method test_binary_example (line 315) | def test_binary_example(self): method test_ternary_example (line 356) | def test_ternary_example(self): method test_multiroot_example (line 395) | def test_multiroot_example(self): method test_multiroot_non_lexical_example (line 434) | def test_multiroot_non_lexical_example(self): method test_ts_example (line 540) | def test_ts_example(self, order, expected): method test_polytomy_inorder (line 584) | def test_polytomy_inorder(self): method test_minlex_postorder_multiple_roots (line 639) | def test_minlex_postorder_multiple_roots(self): class TestMRCA (line 679) | class TestMRCA: method test_two_or_more_args (line 692) | def test_two_or_more_args(self, args, expected): method test_less_than_two_args (line 696) | def test_less_than_two_args(self): method test_no_args (line 702) | def test_no_args(self): method test_same_args (line 708) | def test_same_args(self): method test_different_tree_levels (line 712) | def test_different_tree_levels(self): method test_out_of_bounds_args (line 716) | def test_out_of_bounds_args(self): method test_virtual_root_arg (line 722) | def test_virtual_root_arg(self): method test_multiple_roots (line 726) | def test_multiple_roots(self): class TestPathLength (line 736) | class TestPathLength: method test_tmrca_leaf (line 748) | def test_tmrca_leaf(self): method test_equal_depth (line 753) | def test_equal_depth(self): method test_two_leaves (line 756) | def test_two_leaves(self): method test_two_leaves_depth (line 759) | def test_two_leaves_depth(self): method test_bad_num_args (line 763) | def test_bad_num_args(self, args): method test_bad_arg_type (line 768) | def test_bad_arg_type(self, bad_arg): method test_same_args (line 774) | def test_same_args(self): method test_different_tree_levels (line 777) | def test_different_tree_levels(self): method test_out_of_bounds_args (line 780) | def test_out_of_bounds_args(self): method test_virtual_root_arg (line 785) | def test_virtual_root_arg(self, u): method test_both_args_virtual_root (line 789) | def test_both_args_virtual_root(self): method test_no_mrca (line 792) | def test_no_mrca(self): class TestMRCACalculator (line 798) | class TestMRCACalculator: method test_all_oriented_forests (line 806) | def test_all_oriented_forests(self): class HighLevelTestCase (line 818) | class HighLevelTestCase: method verify_tree_mrcas (line 823) | def verify_tree_mrcas(self, st): method verify_tree_branch_lengths (line 835) | def verify_tree_branch_lengths(self, tree): method verify_tree_structure (line 845) | def verify_tree_structure(self, st): method verify_tree_depths (line 895) | def verify_tree_depths(self, st): method verify_tree (line 904) | def verify_tree(self, st): method verify_trees (line 910) | def verify_trees(self, ts): class TestNumpySamples (line 955) | class TestNumpySamples: method get_tree_sequence (line 961) | def get_tree_sequence(self, num_demes=4, times=None, n=40): method test_samples (line 980) | def test_samples(self): method test_bad_samples (line 997) | def test_bad_samples(self, pop): method test_good_samples (line 1003) | def test_good_samples(self, pop): method test_samples_time (line 1008) | def test_samples_time(self, time): method test_samples_time_interval (line 1027) | def test_samples_time_interval(self, time_interval): method test_samples_example (line 1041) | def test_samples_example(self): method test_samples_time_errors (line 1136) | def test_samples_time_errors(self): method test_samples_args (line 1151) | def test_samples_args(self, ts_fixture): method test_genotype_matrix_indexing (line 1156) | def test_genotype_matrix_indexing(self): method test_genotype_indexing (line 1168) | def test_genotype_indexing(self): method test_pairwise_diversity (line 1182) | def test_pairwise_diversity(self): method test_simplify (line 1194) | def test_simplify(self): class TestTreeSequence (line 1205) | class TestTreeSequence(HighLevelTestCase): method test_row_getter (line 1211) | def test_row_getter(self, ts): method test_bad_row_getter (line 1225) | def test_bad_row_getter(self, index, simple_degree2_ts_fixture): method test_discrete_genome (line 1238) | def test_discrete_genome(self, ts): method test_discrete_time (line 1254) | def test_discrete_time(self, ts): method test_trees (line 1267) | def test_trees(self, ts): method test_mutations (line 1271) | def test_mutations(self, ts): method test_mutation_inherited_state_property (line 1276) | def test_mutation_inherited_state_property(self, ts): method verify_pairwise_diversity (line 1289) | def verify_pairwise_diversity(self, ts): method test_pairwise_diversity (line 1311) | def test_pairwise_diversity(self, ts): method test_bad_node_iteration_order (line 1315) | def test_bad_node_iteration_order(self, order): method test_node_iteration_order (line 1321) | def test_node_iteration_order(self, ts): method verify_edgesets (line 1335) | def verify_edgesets(self, ts): method test_edge_ids (line 1373) | def test_edge_ids(self, ts): method test_edge_span_property (line 1378) | def test_edge_span_property(self, ts): method test_edge_interval_property (line 1383) | def test_edge_interval_property(self, ts): method test_edgesets (line 1390) | def test_edgesets(self): method test_breakpoints (line 1401) | def test_breakpoints(self, ts): method verify_coalescence_records (line 1412) | def verify_coalescence_records(self, ts): method test_coalescence_records (line 1429) | def test_coalescence_records(self, ts): method test_compute_mutation_parent (line 1433) | def test_compute_mutation_parent(self, ts): method test_compute_mutation_time (line 1441) | def test_compute_mutation_time(self, ts): method test_tracked_samples (line 1450) | def test_tracked_samples(self, ts): method test_tracked_samples_is_first_arg (line 1470) | def test_tracked_samples_is_first_arg(self): method test_deprecated_sample_aliases (line 1477) | def test_deprecated_sample_aliases(self, ts): method verify_samples (line 1501) | def verify_samples(self, ts): method test_samples (line 1513) | def test_samples(self, ts): method test_first_last (line 1529) | def test_first_last(self, ts): method test_trees_interface (line 1551) | def test_trees_interface(self): method test_get_pairwise_diversity (line 1571) | def test_get_pairwise_diversity(self, ts): method test_populations (line 1586) | def test_populations(self): method test_individuals (line 1599) | def test_individuals(self): method test_get_population (line 1626) | def test_get_population(self, ts): method test_get_time (line 1639) | def test_get_time(self, ts): method test_max_root_time (line 1652) | def test_max_root_time(self, ts): method test_max_root_time_corner_cases (line 1664) | def test_max_root_time_corner_cases(self): method test_subset_reverse_all_nodes (line 1676) | def test_subset_reverse_all_nodes(self): method test_subset_reverse_internal_nodes (line 1687) | def test_subset_reverse_internal_nodes(self): method test_deprecated_apis (line 1697) | def test_deprecated_apis(self): method test_sites (line 1711) | def test_sites(self): method verify_mutations (line 1757) | def verify_mutations(self, ts): method test_sites_mutations (line 1769) | def test_sites_mutations(self, ts): method test_removed_methods (line 1773) | def test_removed_methods(self): method test_dump_pathlib (line 1784) | def test_dump_pathlib(self, ts_fixture, tmp_path): method test_dump_load_errors (line 1793) | def test_dump_load_errors(self): method test_zlib_compression_warning (line 1817) | def test_zlib_compression_warning(self, ts_fixture, tmp_path): method test_tables_sequence_length_round_trip (line 1827) | def test_tables_sequence_length_round_trip(self): method test_migrations (line 1836) | def test_migrations(self): method test_len_trees (line 1858) | def test_len_trees(self, ts): method test_list (line 1863) | def test_list(self, ts): method test_reversed_trees (line 1881) | def test_reversed_trees(self, ts): method test_at_index (line 1892) | def test_at_index(self, ts): method test_at (line 1907) | def test_at(self, ts): method test_sequence_iteration (line 1930) | def test_sequence_iteration(self, ts): method test_load_tables (line 1964) | def test_load_tables(self, ts): method test_html_repr (line 1988) | def test_html_repr(self, ts): method test_bad_provenance (line 2003) | def test_bad_provenance(self, ts_fixture): method test_provenance_summary_html (line 2009) | def test_provenance_summary_html(self, ts_fixture): method test_html_repr_limit (line 2016) | def test_html_repr_limit(self, ts_fixture): method test_str (line 2026) | def test_str(self, ts): method test_nbytes (line 2035) | def test_nbytes(self, tmp_path, ts_fixture): method test_equals (line 2049) | def test_equals(self): method test_equals_options (line 2086) | def test_equals_options(self, ts_fixture): method test_tree_node_edges (line 2161) | def test_tree_node_edges(self, ts): method verify_individual_vectors (line 2183) | def verify_individual_vectors(self, ts): method test_individuals_population_errors (line 2209) | def test_individuals_population_errors(self): method test_individuals_time_errors (line 2239) | def test_individuals_time_errors(self): method test_individual_vectors (line 2251) | def test_individual_vectors(self, n): method test_individuals_location_errors (line 2263) | def test_individuals_location_errors(self): method test_individuals_location (line 2282) | def test_individuals_location(self, nlocs, num_indivs): method verify_individual_properties (line 2299) | def verify_individual_properties(self, ts): method test_individual_getter_population (line 2324) | def test_individual_getter_population(self): method test_individual_getter_time (line 2349) | def test_individual_getter_time(self): method test_individual_properties (line 2373) | def test_individual_properties(self, n): method test_array_attr_properties (line 2417) | def test_array_attr_properties(self, ts_fixture, array): method test_arrays_equal_to_tables (line 2428) | def test_arrays_equal_to_tables(self, ts_fixture): method test_impute_unknown_mutations_time (line 2466) | def test_impute_unknown_mutations_time(self, ts): method test_mutation_parent_errors (line 2565) | def test_mutation_parent_errors(self, mutations, error): method test_union (line 2592) | def test_union(self, ts_fixture): class TestSimplify (line 2615) | class TestSimplify: method verify_simplify_provenance (line 2620) | def verify_simplify_provenance(self, ts): method verify_simplify_topology (line 2633) | def verify_simplify_topology(self, ts, sample): method verify_simplify_equality (line 2688) | def verify_simplify_equality(self, ts, sample): method verify_simplify_variants (line 2707) | def verify_simplify_variants(self, ts, sample): method verify_tables_api_equality (line 2723) | def verify_tables_api_equality(self, ts): method test_simplify_tables_equality (line 2733) | def test_simplify_tables_equality(self, ts): method test_simplify_provenance (line 2739) | def test_simplify_provenance(self, ts): method test_simplify (line 2749) | def test_simplify(self, ts): method test_simplify_bugs (line 2764) | def test_simplify_bugs(self): method test_simplify_migrations_fails (line 2792) | def test_simplify_migrations_fails(self): method test_no_update_sample_flags_no_filter_nodes (line 2808) | def test_no_update_sample_flags_no_filter_nodes(self, ts): class TestMinMaxTime (line 2821) | class TestMinMaxTime: method get_example_tree_sequence (line 2822) | def get_example_tree_sequence(self, use_unknown_time): method get_empty_tree_sequence (line 2852) | def get_empty_tree_sequence(self): method test_example (line 2861) | def test_example(self): method test_example_unknown_mutation_times (line 2868) | def test_example_unknown_mutation_times(self): method test_empty (line 2875) | def test_empty(self): class TestSiteAlleles (line 2881) | class TestSiteAlleles: method test_no_mutations (line 2882) | def test_no_mutations(self): method test_k_mutations (line 2889) | def test_k_mutations(self, k): class TestEdgeDiffs (line 2906) | class TestEdgeDiffs: method test_correct_trees_forward (line 2908) | def test_correct_trees_forward(self, ts): method test_correct_trees_reverse (line 2919) | def test_correct_trees_reverse(self, ts): method test_elements_are_like_named_tuple (line 2932) | def test_elements_are_like_named_tuple(self, simple_degree2_ts_fixture): method test_bad_direction (line 2940) | def test_bad_direction(self, direction, simple_degree2_ts_fixture): method test_edge_properties (line 2946) | def test_edge_properties(self, direction, simple_degree2_ts_fixture): method test_include_terminal (line 2960) | def test_include_terminal(self, ts, direction): class TestTreeSequenceMethodSignatures (line 2985) | class TestTreeSequenceMethodSignatures: method test_kwargs_only (line 2988) | def test_kwargs_only(self): method test_trees_params (line 3006) | def test_trees_params(self): class TestTreeSequenceMetadata (line 3021) | class TestTreeSequenceMetadata: method test_tree_sequence_metadata_schema (line 3046) | def test_tree_sequence_metadata_schema(self): method test_tree_sequence_metadata (line 3058) | def test_tree_sequence_metadata(self): method test_tree_sequence_time_units (line 3076) | def test_tree_sequence_time_units(self): method test_table_metadata_schemas (line 3090) | def test_table_metadata_schemas(self): method test_table_metadata_round_trip_via_row_getters (line 3121) | def test_table_metadata_round_trip_via_row_getters(self): function test_pickle_round_trip (line 3169) | def test_pickle_round_trip(ts_fixture): class TestFileUuid (line 3177) | class TestFileUuid(HighLevelTestCase): method validate (line 3182) | def validate(self, ts): method test_simple_simulation (line 3222) | def test_simple_simulation(self): method test_empty_tables (line 3226) | def test_empty_tables(self): class TestTreeSequenceTextIO (line 3231) | class TestTreeSequenceTextIO(HighLevelTestCase): method verify_nodes_format (line 3236) | def verify_nodes_format(self, ts, nodes_file, precision, base64_metada... method verify_edges_format (line 3266) | def verify_edges_format(self, ts, edges_file, precision, base64_metada... method verify_sites_format (line 3294) | def verify_sites_format(self, ts, sites_file, precision, base64_metada... method verify_mutations_format (line 3318) | def verify_mutations_format(self, ts, mutations_file, precision, base6... method verify_individuals_format (line 3351) | def verify_individuals_format( method verify_populations_format (line 3381) | def verify_populations_format( method verify_migrations_format (line 3405) | def verify_migrations_format(self, ts, migrations_file, precision, bas... method test_output_format (line 3439) | def test_output_format(self, precision, base64_metadata, ts): method verify_approximate_equality (line 3475) | def verify_approximate_equality(self, ts1, ts2): method test_text_record_round_trip (line 3547) | def test_text_record_round_trip(self, ts1): method test_empty_files (line 3592) | def test_empty_files(self): method test_empty_files_sequence_length (line 3609) | def test_empty_files_sequence_length(self): method test_load_text_no_populations (line 3633) | def test_load_text_no_populations(self): method test_load_text_populations (line 3640) | def test_load_text_populations(self): class TestTree (line 3656) | class TestTree(HighLevelTestCase): method get_tree (line 3661) | def get_tree(self, sample_lists=False): method verify_mutations (line 3665) | def verify_mutations(self, tree): method test_simple_mutations (line 3677) | def test_simple_mutations(self): method test_complex_mutations (line 3681) | def test_complex_mutations(self): method test_str (line 3685) | def test_str(self, ts_fixture): method test_html_repr (line 3712) | def test_html_repr(self, ts_fixture): method test_samples (line 3719) | def test_samples(self): method test_num_children (line 3747) | def test_num_children(self): method test_ancestors (line 3752) | def test_ancestors(self): method test_ancestors_empty (line 3763) | def test_ancestors_empty(self): method test_virtual_root_semantics (line 3770) | def test_virtual_root_semantics(self, ts): method test_root_properties (line 3779) | def test_root_properties(self): method test_as_dict_of_dicts (line 3799) | def test_as_dict_of_dicts(self): method verify_nx_graph_topology (line 3810) | def verify_nx_graph_topology(self, tree, g): method verify_nx_algorithm_equivalence (line 3821) | def verify_nx_algorithm_equivalence(self, tree, g): method verify_nx_for_tutorial_algorithms (line 3846) | def verify_nx_for_tutorial_algorithms(self, tree, g): method verify_nx_nearest_neighbor_search (line 3885) | def verify_nx_nearest_neighbor_search(self): method test_total_branch_length (line 3915) | def test_total_branch_length(self): method test_branch_length_empty_tree (line 3926) | def test_branch_length_empty_tree(self): method test_bad_val_root_threshold (line 3938) | def test_bad_val_root_threshold(self, r_threshold): method test_bad_type_root_threshold (line 3943) | def test_bad_type_root_threshold(self, r_threshold): method test_simple_root_threshold (line 3947) | def test_simple_root_threshold(self): method test_is_root (line 3954) | def test_is_root(self, root_threshold): method test_is_descendant (line 3968) | def test_is_descendant(self): method test_apis (line 3990) | def test_apis(self): method test_deprecated_apis (line 4020) | def test_deprecated_apis(self): method test_deprecated_api_warnings (line 4026) | def test_deprecated_api_warnings(self): method test_seek_index (line 4033) | def test_seek_index(self, skip): method test_seek_index_errors (line 4056) | def test_seek_index_errors(self): method test_first_last (line 4068) | def test_first_last(self): method test_eq_different_tree_sequence (line 4084) | def test_eq_different_tree_sequence(self): method test_next_prev (line 4090) | def test_next_prev(self): method test_interval (line 4116) | def test_interval(self): method verify_tree_arrays (line 4134) | def verify_tree_arrays(self, tree): method verify_tree_arrays_python_ts (line 4153) | def verify_tree_arrays_python_ts(self, ts): method test_tree_arrays (line 4166) | def test_tree_arrays(self): method test_tree_array_properties (line 4185) | def test_tree_array_properties(self, array): method verify_empty_tree (line 4197) | def verify_empty_tree(self, tree): method test_empty_tree (line 4220) | def test_empty_tree(self): method test_clear (line 4232) | def test_clear(self): method verify_trees_identical (line 4246) | def verify_trees_identical(self, t1, t2): method test_copy_seek (line 4257) | def test_copy_seek(self): method test_copy_tracked_samples (line 4294) | def test_copy_tracked_samples(self): method test_copy_multiple_roots (line 4307) | def test_copy_multiple_roots(self): method test_map_mutations (line 4323) | def test_map_mutations(self): method test_sample_count_deprecated (line 4343) | def test_sample_count_deprecated(self): method test_node_edges (line 4355) | def test_node_edges(self): class TestSiblings (line 4381) | class TestSiblings: method test_balanced_binary_tree (line 4382) | def test_balanced_binary_tree(self): method test_star (line 4401) | def test_star(self): method test_multiroot_tree (line 4417) | def test_multiroot_tree(self): method test_isolated_node (line 4436) | def test_isolated_node(self, flag, expected): class TestNodeOrdering (line 4444) | class TestNodeOrdering(HighLevelTestCase): method verify_tree_sequences_equal (line 4452) | def verify_tree_sequences_equal(self, ts1, ts2, approximate=False): method verify_random_permutation (line 4479) | def verify_random_permutation(self, ts): method test_single_locus (line 4538) | def test_single_locus(self): method test_multi_locus (line 4543) | def test_multi_locus(self): method test_nonbinary (line 4548) | def test_nonbinary(self): function assert_trees_identical (line 4570) | def assert_trees_identical(t1, t2): function assert_trees_equivalent (line 4580) | def assert_trees_equivalent(t1, t2): function assert_same_tree_different_order (line 4590) | def assert_same_tree_different_order(t1, t2): function seek (line 4597) | def seek(tree, x): class TestSeekDirection (line 4622) | class TestSeekDirection: method ts (line 4634) | def ts(self): method get_tree_pair (line 4637) | def get_tree_pair(self): method test_index_from_different_directions (line 4648) | def test_index_from_different_directions(self, index): method test_seek_from_null (line 4659) | def test_seek_from_null(self, position): method test_skip_from_null (line 4668) | def test_skip_from_null(self, position): method test_seek_next_tree (line 4678) | def test_seek_next_tree(self, index, skip): method test_seek_prev_tree (line 4689) | def test_seek_prev_tree(self, index, skip): method test_seek_1_from_0 (line 4699) | def test_seek_1_from_0(self, skip): method test_seek_1_5_from_0 (line 4708) | def test_seek_1_5_from_0(self, skip): method test_seek_1_5_from_1 (line 4717) | def test_seek_1_5_from_1(self, skip): method test_seek_3_from_null (line 4726) | def test_seek_3_from_null(self, skip): method test_seek_3_from_null_prev (line 4733) | def test_seek_3_from_null_prev(self, skip): method test_seek_3_from_0 (line 4741) | def test_seek_3_from_0(self): method test_skip_3_from_0 (line 4748) | def test_skip_3_from_0(self): method test_skip_0_from_3 (line 4755) | def test_skip_0_from_3(self): method test_seek_0_from_3 (line 4763) | def test_seek_0_from_3(self): method test_seek_mid_null_and_middle (line 4772) | def test_seek_mid_null_and_middle(self, ts): method test_seek_skip_middle (line 4790) | def test_seek_skip_middle(self, ts): method test_seek_last_then_prev (line 4801) | def test_seek_last_then_prev(self, ts): class TestSeek (line 4813) | class TestSeek: method test_new_seek_breakpoints (line 4815) | def test_new_seek_breakpoints(self, ts): method test_new_seek_mid (line 4823) | def test_new_seek_mid(self, ts): method test_same_seek_breakpoints (line 4832) | def test_same_seek_breakpoints(self, ts): method test_new_seek_breakpoints_reversed (line 4840) | def test_new_seek_breakpoints_reversed(self, ts): method test_same_seek_breakpoints_reversed (line 4848) | def test_same_seek_breakpoints_reversed(self, ts): method test_example (line 4855) | def test_example(self): method test_errors (line 4875) | def test_errors(self, ts_fixture): class SimpleContainersMixin (line 4883) | class SimpleContainersMixin: method test_equality (line 4888) | def test_equality(self): method test_repr (line 4898) | def test_repr(self): class SimpleContainersWithMetadataMixin (line 4903) | class SimpleContainersWithMetadataMixin: method test_metadata (line 4908) | def test_metadata(self): method test_decoder_run_once (line 4921) | def test_decoder_run_once(self): class TestIndividualContainer (line 4941) | class TestIndividualContainer(SimpleContainersMixin, SimpleContainersWit... method get_instances (line 4942) | def get_instances(self, n): class TestNodeContainer (line 4957) | class TestNodeContainer(SimpleContainersMixin, SimpleContainersWithMetad... method get_instances (line 4958) | def get_instances(self, n): class TestEdgeContainer (line 4973) | class TestEdgeContainer(SimpleContainersMixin, SimpleContainersWithMetad... method get_instances (line 4974) | def get_instances(self, n): class TestSiteContainer (line 4989) | class TestSiteContainer(SimpleContainersMixin, SimpleContainersWithMetad... method get_instances (line 4990) | def get_instances(self, n): class TestMutationContainer (line 5004) | class TestMutationContainer(SimpleContainersMixin, SimpleContainersWithM... method get_instances (line 5005) | def get_instances(self, n): method test_nan_equality (line 5020) | def test_nan_equality(self): class TestMigrationContainer (line 5061) | class TestMigrationContainer(SimpleContainersMixin, SimpleContainersWith... method get_instances (line 5062) | def get_instances(self, n): class TestPopulationContainer (line 5079) | class TestPopulationContainer(SimpleContainersMixin, SimpleContainersWit... method get_instances (line 5080) | def get_instances(self, n): class TestProvenanceContainer (line 5091) | class TestProvenanceContainer(SimpleContainersMixin): method get_instances (line 5092) | def get_instances(self, n): class TestEdgesetContainer (line 5098) | class TestEdgesetContainer(SimpleContainersMixin): method get_instances (line 5099) | def get_instances(self, n): class TestContainersAppend (line 5103) | class TestContainersAppend: method test_containers_append (line 5104) | def test_containers_append(self, ts_fixture): class TestTskitConversionOutput (line 5117) | class TestTskitConversionOutput(unittest.TestCase): method setUpClass (line 5123) | def setUpClass(cls): method test_macs (line 5138) | def test_macs(self): method test_macs_error (line 5158) | def test_macs_error(self): class TestTreeSequenceGetSite (line 5170) | class TestTreeSequenceGetSite: method get_example_ts_discrete_coordinates (line 5176) | def get_example_ts_discrete_coordinates(self): method get_example_ts_continuous_coordinates (line 5183) | def get_example_ts_continuous_coordinates(self): method get_example_ts_without_sites (line 5190) | def get_example_ts_without_sites(self): method test_site_id (line 5195) | def test_site_id(self, id_): method test_position_discrete_coordinates (line 5201) | def test_position_discrete_coordinates(self, position): method test_position_continuous_coordinates (line 5207) | def test_position_continuous_coordinates(self, position): method test_position_not_found (line 5213) | def test_position_not_found(self, position): method test_position_good_type (line 5226) | def test_position_good_type(self, position): method test_position_not_scalar (line 5230) | def test_position_not_scalar(self): method test_position_out_of_bounds (line 5238) | def test_position_out_of_bounds(self, position): method test_query_position_siteless_ts (line 5246) | def test_query_position_siteless_ts(self): method test_site_id_and_position_are_none (line 5251) | def test_site_id_and_position_are_none(self): method test_site_id_and_position_are_specified (line 5256) | def test_site_id_and_position_are_specified(self): function num_lineages_definition (line 5264) | def num_lineages_definition(tree, t): class TestNumLineages (line 5274) | class TestNumLineages: method test_tree_midpoint_definition (line 5276) | def test_tree_midpoint_definition(self, ts): method test_nonfinite_time (line 5284) | def test_nonfinite_time(self, t): method test_number_types (line 5290) | def test_number_types(self, t): method test_balanced_ternary (line 5313) | def test_balanced_ternary(self, t, expected): method test_multiroot_different_times (line 5340) | def test_multiroot_different_times(self, t, expected): method test_comb_different_leaf_times (line 5372) | def test_comb_different_leaf_times(self, t, expected): method test_missing_data_different_times (line 5393) | def test_missing_data_different_times(self, t, expected): function struct_metadata_ts (line 5403) | def struct_metadata_ts(ts_fixture): class TestStructuredNumpyMetadata (line 5431) | class TestStructuredNumpyMetadata: method test_not_implemented_json (line 5443) | def test_not_implemented_json(self, table_name, ts_fixture): method test_array_attr_properties (line 5448) | def test_array_attr_properties(self, struct_metadata_ts, table_name): method test_array_contents (line 5461) | def test_array_contents(self, struct_metadata_ts, table_name): method test_error_if_no_schema (line 5473) | def test_error_if_no_schema(self, table_name): class TestIndividualsNodes (line 5479) | class TestIndividualsNodes: method test_basic_individuals_nodes (line 5480) | def test_basic_individuals_nodes(self, tmp_path): method test_variable_ploidy (line 5495) | def test_variable_ploidy(self, tmp_path): method test_no_individuals (line 5524) | def test_no_individuals(self): method test_no_nodes_with_individuals (line 5534) | def test_no_nodes_with_individuals(self): method test_individual_with_no_nodes (line 5546) | def test_individual_with_no_nodes(self): method test_mixed_sample_status (line 5559) | def test_mixed_sample_status(self): class TestRaggedArrays (line 5572) | class TestRaggedArrays: method test_site_ancestral_state (line 5576) | def test_site_ancestral_state(self, num_rows, column): method test_equality_sites_ancestral_state (line 5621) | def test_equality_sites_ancestral_state(self, ts): method test_equality_mutations_derived_state (line 5628) | def test_equality_mutations_derived_state(self, ts): method test_equality_mutations_inherited_state (line 5636) | def test_equality_mutations_inherited_state(self, ts): method test_mutations_inherited_state (line 5644) | def test_mutations_inherited_state(self, ts): method test_ragged_array_not_supported (line 5671) | def test_ragged_array_not_supported(self, column): method test_tables_emits_warning (line 5682) | def test_tables_emits_warning(self): class TestSampleNodesByPloidy (line 5697) | class TestSampleNodesByPloidy: method test_various_ploidy_scenarios (line 5707) | def test_various_ploidy_scenarios(self, n_samples, ploidy, expected): method test_mixed_sample_status (line 5718) | def test_mixed_sample_status(self): method test_no_sample_nodes (line 5733) | def test_no_sample_nodes(self): method test_not_multiple_of_ploidy (line 5742) | def test_not_multiple_of_ploidy(self): method test_with_existing_individuals (line 5751) | def test_with_existing_individuals(self): method test_different_node_flags (line 5768) | def test_different_node_flags(self): class TestMapToVcfModel (line 5781) | class TestMapToVcfModel: method test_no_individuals_default_ploidy (line 5782) | def test_no_individuals_default_ploidy(self): method test_no_individuals_custom_ploidy (line 5802) | def test_no_individuals_custom_ploidy(self): method test_no_individuals_uneven_ploidy (line 5817) | def test_no_individuals_uneven_ploidy(self): method test_with_individuals (line 5826) | def test_with_individuals(self): method test_with_individuals_and_ploidy_error (line 5842) | def test_with_individuals_and_ploidy_error(self): method test_specific_individuals (line 5851) | def test_specific_individuals(self): method test_individual_with_no_nodes (line 5872) | def test_individual_with_no_nodes(self): method test_individual_with_no_nodes_only (line 5885) | def test_individual_with_no_nodes_only(self): method test_invalid_individual_id (line 5898) | def test_invalid_individual_id(self): method test_mixed_sample_non_sample_ordering (line 5910) | def test_mixed_sample_non_sample_ordering(self): method test_samples_without_individuals_warning (line 5936) | def test_samples_without_individuals_warning(self): method test_metadata_key_for_names (line 5952) | def test_metadata_key_for_names(self): method test_custom_individual_names (line 5976) | def test_custom_individual_names(self): method test_name_conflict_error (line 5990) | def test_name_conflict_error(self): method test_name_count_mismatch_error (line 6001) | def test_name_count_mismatch_error(self): method test_all_individuals_no_nodes (line 6014) | def test_all_individuals_no_nodes(self): method test_position_transform_default_and_custom (line 6022) | def test_position_transform_default_and_custom(self): method test_legacy_position_transform (line 6041) | def test_legacy_position_transform(self): method test_position_transform_no_sites (line 6056) | def test_position_transform_no_sites(self): method test_invalid_position_transform_return_shape (line 6065) | def test_invalid_position_transform_return_shape(self): method test_contig_id (line 6081) | def test_contig_id(self): method test_isolated_as_missing (line 6093) | def test_isolated_as_missing(self): function test_mutations_edge (line 6107) | def test_mutations_edge(ts): FILE: python/tests/test_ibd.py function example_ts (line 28) | def example_ts(): function ibd_segments (line 32) | def ibd_segments( function naive_ibd (line 71) | def naive_ibd(ts, a, b): function naive_ibd_all_pairs (line 93) | def naive_ibd_all_pairs(ts, samples=None): class TestIbdDefinition (line 102) | class TestIbdDefinition: method test_all_pairs (line 106) | def test_all_pairs(self, ts): method test_all_pairs_python_only (line 118) | def test_all_pairs_python_only(self, ts): method test_wright_fisher_examples (line 127) | def test_wright_fisher_examples(self, N, T): class TestIbdImplementations (line 139) | class TestIbdImplementations: method test_all_pairs (line 143) | def test_all_pairs(self, ts): function assert_ibd_equal (line 150) | def assert_ibd_equal(dict1, dict2): class TestIbdSingleBinaryTree (line 165) | class TestIbdSingleBinaryTree: method ts (line 167) | def ts(self): method test_defaults (line 195) | def test_defaults(self): method test_within (line 204) | def test_within(self): method test_between_0_1 (line 211) | def test_between_0_1(self): method test_between_0_2 (line 218) | def test_between_0_2(self): method test_between_0_1_2 (line 225) | def test_between_0_1_2(self): method test_between_0_12 (line 234) | def test_between_0_12(self): method test_time (line 242) | def test_time(self): method test_length (line 251) | def test_length(self): class TestIbdInterface (line 256) | class TestIbdInterface: method test_input_errors_within (line 258) | def test_input_errors_within(self, ts): method test_input_errors_between (line 265) | def test_input_errors_between(self, ts): method test_within_between_mutually_exclusive (line 272) | def test_within_between_mutually_exclusive(self, ts): method test_tables_interface (line 277) | def test_tables_interface(self, ts): method test_empty_within (line 283) | def test_empty_within(self, ts): method test_empty_between (line 288) | def test_empty_between(self, ts): method test_empty_in_between (line 293) | def test_empty_in_between(self, ts): class TestIbdTwoSamplesTwoTrees (line 298) | class TestIbdTwoSamplesTwoTrees: method ts (line 308) | def ts(self): method test_basic (line 328) | def test_basic(self): method test_time (line 339) | def test_time(self): method test_length (line 345) | def test_length(self): class TestIbdUnrelatedSamples (line 351) | class TestIbdUnrelatedSamples: method ts (line 358) | def ts(self): method test_basic (line 378) | def test_basic(self): method test_time (line 382) | def test_time(self): method test_length (line 386) | def test_length(self): class TestIbdNoSamples (line 391) | class TestIbdNoSamples: method ts (line 400) | def ts(self): method test_defaults (line 418) | def test_defaults(self): method test_specified_samples (line 422) | def test_specified_samples(self): class TestIbdSamplesAreDescendants (line 432) | class TestIbdSamplesAreDescendants: method ts (line 441) | def ts(self): method test_basic (line 464) | def test_basic(self): method test_input_within (line 473) | def test_input_within(self): method test_all_samples (line 481) | def test_all_samples(self): class TestIbdSimpleInternalSampleChain (line 495) | class TestIbdSimpleInternalSampleChain: method ts (line 504) | def ts(self): method test_basic (line 522) | def test_basic(self): class TestIbdDifferentPaths (line 534) | class TestIbdDifferentPaths: method ts (line 546) | def ts(self): method test_defaults (line 572) | def test_defaults(self): method test_time (line 581) | def test_time(self): method test_length (line 585) | def test_length(self): class TestIbdDifferentPaths2 (line 591) | class TestIbdDifferentPaths2: method ts (line 605) | def ts(self): method test_defaults (line 631) | def test_defaults(self): method test_length (line 640) | def test_length(self): class TestIbdDifferentPaths3 (line 652) | class TestIbdDifferentPaths3: method ts (line 660) | def ts(self): method test_defaults (line 675) | def test_defaults(self): method test_length (line 682) | def test_length(self): class TestIbdPolytomies (line 690) | class TestIbdPolytomies: method ts (line 704) | def ts(self): method test_defaults (line 730) | def test_defaults(self): method test_time (line 756) | def test_time(self): method test_length (line 767) | def test_length(self): method test_input_within (line 779) | def test_input_within(self): class TestIbdInternalSamples (line 795) | class TestIbdInternalSamples: method ts (line 805) | def ts(self): method test_defaults (line 825) | def test_defaults(self): class TestIbdLengthThreshold (line 833) | class TestIbdLengthThreshold: method ts (line 847) | def ts(self): method test_length_exceeds_segment (line 866) | def test_length_exceeds_segment(self): method test_length_is_negative (line 870) | def test_length_is_negative(self): method test_equal_to_length (line 874) | def test_equal_to_length(self): class TestIbdProperties (line 880) | class TestIbdProperties: method test_default_within_all_samples (line 882) | def test_default_within_all_samples(self, ts): method test_within_subset (line 889) | def test_within_subset(self, ts): method test_between_two_subsets (line 898) | def test_between_two_subsets(self, ts): method test_between_same_segments_as_filtered_within_pair (line 909) | def test_between_same_segments_as_filtered_within_pair(self, ts): method test_between_same_segments_as_filtered_within_triple (line 922) | def test_between_same_segments_as_filtered_within_triple(self, ts): class TestIdentitySegments (line 940) | class TestIdentitySegments: method verify_segments (line 945) | def verify_segments(self, ts, ibd_segments): method test_str (line 976) | def test_str(self, store_segments, store_pairs): method test_repr_store_segments (line 984) | def test_repr_store_segments(self): method test_repr_without_store_segments (line 993) | def test_repr_without_store_segments(self): method test_store_segs_implies_store_pairs (line 1002) | def test_store_segs_implies_store_pairs(self): method test_operations_available_by_default (line 1009) | def test_operations_available_by_default(self): method test_operations_available_store_pairs (line 1029) | def test_operations_available_store_pairs(self): method test_pairs_all_samples (line 1052) | def test_pairs_all_samples(self, n): method test_pairs_subset (line 1060) | def test_pairs_subset(self, n): method test_max_time (line 1068) | def test_max_time(self, max_time): method test_max_time_default (line 1074) | def test_max_time_default(self): method test_min_span (line 1081) | def test_min_span(self, min_span): method test_min_span_longer_than_seq_length (line 1088) | def test_min_span_longer_than_seq_length(self, min_span): method test_recombination_discrete (line 1097) | def test_recombination_discrete(self): method test_recombination_continuous (line 1105) | def test_recombination_continuous(self): method test_dict_interface (line 1117) | def test_dict_interface(self): class TestIdentitySegmentsList (line 1130) | class TestIdentitySegmentsList: method test_list_semantics (line 1139) | def test_list_semantics(self): method test_str (line 1147) | def test_str(self): method test_repr (line 1152) | def test_repr(self): method test_eq_semantics (line 1157) | def test_eq_semantics(self): method test_eq_fails_without_store_segments (line 1171) | def test_eq_fails_without_store_segments(self): method test_list_contents (line 1180) | def test_list_contents(self): FILE: python/tests/test_immutable_table_collection.py function get_mutable_and_immutable (line 17) | def get_mutable_and_immutable(ts): class TestCollectionParity (line 25) | class TestCollectionParity: method test_basic_properties_match (line 26) | def test_basic_properties_match(self, ts): method test_asdict_equals (line 37) | def test_asdict_equals(self, ts): method test_equals_bidirectional (line 54) | def test_equals_bidirectional(self, ts): method test_equals_ignore_flags (line 66) | def test_equals_ignore_flags(self, ts): method test_nbytes_parity (line 83) | def test_nbytes_parity(self, ts): method test_reference_sequence_and_index_flags (line 87) | def test_reference_sequence_and_index_flags(self, ts): method test_copy_dump_tree_sequence_roundtrip (line 106) | def test_copy_dump_tree_sequence_roundtrip(self, tmp_path, ts): method test_str_contains_identifier (line 125) | def test_str_contains_identifier(self, ts): method test_link_ancestors_parity (line 130) | def test_link_ancestors_parity(self, ts): class TestTablesParity (line 153) | class TestTablesParity: method test_table_name_map_and_lengths (line 154) | def test_table_name_map_and_lengths(self, ts): method test_columns_and_rows_equal (line 163) | def test_columns_and_rows_equal(self, ts): method test_slicing_and_boolean_index (line 193) | def test_slicing_and_boolean_index(self, ts): method test_mask_then_slice (line 211) | def test_mask_then_slice(self, ts): method test_slice_then_mask (line 235) | def test_slice_then_mask(self, ts): method test_slice_view_indexing (line 258) | def test_slice_view_indexing(self, ts): method test_slice_view_iteration (line 301) | def test_slice_view_iteration(self, ts): method test_slice_view_ragged_column_access (line 320) | def test_slice_view_ragged_column_access(self, ts): method test_nested_slicing (line 351) | def test_nested_slicing(self, ts): method test_random_access_on_slice (line 382) | def test_random_access_on_slice(self, ts): method test_table_equals_bidirectional (line 408) | def test_table_equals_bidirectional(self, ts): class TestImmutableErrors (line 425) | class TestImmutableErrors: method test_collection_mutators_raise (line 426) | def test_collection_mutators_raise(self, ts): method test_collection_property_setters_raise (line 432) | def test_collection_property_setters_raise(self, ts): method test_table_mutators_raise (line 441) | def test_table_mutators_raise(self, ts): method test_table_metadata_schema_setter_raises (line 448) | def test_table_metadata_schema_setter_raises(self, ts): method test_table_attribute_assignment_raises (line 455) | def test_table_attribute_assignment_raises(self, ts): method test_collection_attribute_assignment_raises (line 471) | def test_collection_attribute_assignment_raises(self, ts): class TestMethodParity (line 487) | class TestMethodParity: method test_immutable_has_method_or_mutator (line 488) | def test_immutable_has_method_or_mutator(self, ts_fixture): method test_immutable_tables_have_method_or_mutator (line 522) | def test_immutable_tables_have_method_or_mutator(self, ts_fixture): class TestImmutableTimestampHandling (line 556) | class TestImmutableTimestampHandling: method test_assert_equals_ignore_timestamps_roundtrip (line 557) | def test_assert_equals_ignore_timestamps_roundtrip(self): method test_assert_equals_ignore_timestamps_guard (line 575) | def test_assert_equals_ignore_timestamps_guard(self, ts_fixture, monke... method test_assert_equals_ignore_timestamps_other_difference (line 581) | def test_assert_equals_ignore_timestamps_other_difference(self): class TestImmutableIndexViews (line 603) | class TestImmutableIndexViews: method test_index_view_ragged_columns (line 604) | def test_index_view_ragged_columns(self, ts_fixture): method test_index_view_offset_columns (line 642) | def test_index_view_offset_columns(self): method test_index_view_empty_selection (line 659) | def test_index_view_empty_selection(self): method test_index_out_of_bounds (line 674) | def test_index_out_of_bounds(self, ts_fixture): method test_boolean_index_length_mismatch (line 681) | def test_boolean_index_length_mismatch(self, ts_fixture): function test_immutable_table_metadata_schema_difference (line 690) | def test_immutable_table_metadata_schema_difference(): FILE: python/tests/test_intervals.py class TestRateMapErrors (line 44) | class TestRateMapErrors: method test_bad_input (line 56) | def test_bad_input(self, position, rate): method test_zero_length_interval (line 60) | def test_zero_length_interval(self): method test_bad_length (line 64) | def test_bad_length(self): method test_bad_first_pos (line 70) | def test_bad_first_pos(self): method test_bad_rate (line 76) | def test_bad_rate(self): method test_bad_rate_with_missing (line 82) | def test_bad_rate_with_missing(self): method test_read_only (line 88) | def test_read_only(self): class TestGetRateAllKnown (line 116) | class TestGetRateAllKnown: method test_get_rate_mid (line 127) | def test_get_rate_mid(self, rate_map): method test_get_rate_left (line 134) | def test_get_rate_left(self, rate_map): method test_get_rate_right (line 141) | def test_get_rate_right(self, rate_map): class TestOperations (line 148) | class TestOperations: method test_num_intervals (line 163) | def test_num_intervals(self, rate_map): method test_mask_arrays (line 169) | def test_mask_arrays(self, rate_map): method test_missing_intervals (line 174) | def test_missing_intervals(self, rate_map): method test_mean_rate (line 185) | def test_mean_rate(self, rate_map): method test_total_mass (line 195) | def test_total_mass(self, rate_map): method test_get_cumulative_mass (line 199) | def test_get_cumulative_mass(self, rate_map): method test_get_rate (line 209) | def test_get_rate(self, rate_map): method test_map_semantics (line 217) | def test_map_semantics(self, rate_map): method test_asdict (line 225) | def test_asdict(self): class TestFindIndex (line 232) | class TestFindIndex: method test_one_interval (line 233) | def test_one_interval(self): method test_two_intervals (line 240) | def test_two_intervals(self): method test_three_intervals (line 250) | def test_three_intervals(self): method test_out_of_bounds (line 264) | def test_out_of_bounds(self): method test_input_types (line 270) | def test_input_types(self): class TestSimpleExamples (line 277) | class TestSimpleExamples: method test_all_missing_one_interval (line 278) | def test_all_missing_one_interval(self): method test_all_missing_two_intervals (line 282) | def test_all_missing_two_intervals(self): method test_count (line 286) | def test_count(self): method test_missing_arrays (line 292) | def test_missing_arrays(self): method test_missing_at_start_mean_rate (line 297) | def test_missing_at_start_mean_rate(self): method test_missing_at_end_mean_rate (line 303) | def test_missing_at_end_mean_rate(self): method test_interval_properties_all_known (line 309) | def test_interval_properties_all_known(self): method test_pickle_non_missing (line 317) | def test_pickle_non_missing(self): method test_pickle_missing (line 322) | def test_pickle_missing(self): method test_get_cumulative_mass_all_known (line 327) | def test_get_cumulative_mass_all_known(self): method test_cumulative_mass_missing (line 332) | def test_cumulative_mass_missing(self): class TestDisplay (line 337) | class TestDisplay: method test_str (line 338) | def test_str(self): method test_str_scinot (line 349) | def test_str_scinot(self): method test_repr (line 360) | def test_repr(self): method test_repr_html (line 365) | def test_repr_html(self): method test_long_table (line 374) | def test_long_table(self): method test_short_table (line 384) | def test_short_table(self): class TestRateMapIsMapping (line 395) | class TestRateMapIsMapping: method test_items (line 396) | def test_items(self): method test_keys (line 403) | def test_keys(self): method test_values (line 407) | def test_values(self): method test_in_points (line 411) | def test_in_points(self): method test_in_slices (line 420) | def test_in_slices(self): method test_other_types_not_in (line 432) | def test_other_types_not_in(self): method test_len (line 437) | def test_len(self): method test_immutable (line 445) | def test_immutable(self): method test_eq (line 452) | def test_eq(self): method test_getitem_value (line 466) | def test_getitem_value(self): method test_getitem_slice (line 481) | def test_getitem_slice(self): method test_getitem_slice_step (line 490) | def test_getitem_slice_step(self): class TestMappingMissingData (line 497) | class TestMappingMissingData: method test_get_missing (line 498) | def test_get_missing(self): method test_in_missing (line 505) | def test_in_missing(self): method test_keys_missing (line 511) | def test_keys_missing(self): class TestGetIntermediates (line 516) | class TestGetIntermediates: method test_get_rate (line 517) | def test_get_rate(self): method test_get_rate_out_of_bounds (line 523) | def test_get_rate_out_of_bounds(self): method test_get_cumulative_mass (line 532) | def test_get_cumulative_mass(self): method test_get_bad_cumulative_mass (line 539) | def test_get_bad_cumulative_mass(self): class TestSlice (line 549) | class TestSlice: method test_slice_no_params (line 550) | def test_slice_no_params(self): method test_slice_left_examples (line 559) | def test_slice_left_examples(self): method test_slice_right_examples (line 576) | def test_slice_right_examples(self): method test_slice_left_right_examples (line 588) | def test_slice_left_right_examples(self): method test_slice_right_missing (line 610) | def test_slice_right_missing(self): method test_slice_left_missing (line 624) | def test_slice_left_missing(self): method test_slice_with_floats (line 636) | def test_slice_with_floats(self): method test_slice_trim_left (line 646) | def test_slice_trim_left(self): method test_slice_trim_right (line 653) | def test_slice_trim_right(self): method test_slice_error (line 660) | def test_slice_error(self): class TestReadHapmap (line 674) | class TestReadHapmap: method test_read_hapmap_simple (line 675) | def test_read_hapmap_simple(self): method test_read_hapmap_from_filename (line 687) | def test_read_hapmap_from_filename(self, tmp_path): method test_read_hapmap_empty (line 701) | def test_read_hapmap_empty(self): method test_read_hapmap_col_pos (line 709) | def test_read_hapmap_col_pos(self): method test_read_hapmap_map_and_rate (line 721) | def test_read_hapmap_map_and_rate(self): method test_read_hapmap_duplicate_pos (line 732) | def test_read_hapmap_duplicate_pos(self): method test_read_hapmap_nonzero_rate_start (line 743) | def test_read_hapmap_nonzero_rate_start(self): method test_read_hapmap_nonzero_rate_end (line 754) | def test_read_hapmap_nonzero_rate_end(self): method test_read_hapmap_gzipped (line 764) | def test_read_hapmap_gzipped(self, tmp_path): method test_read_hapmap_nonzero_map_start (line 775) | def test_read_hapmap_nonzero_map_start(self): method test_read_hapmap_bad_nonzero_map_start (line 787) | def test_read_hapmap_bad_nonzero_map_start(self): method test_sequence_length (line 798) | def test_sequence_length(self): method test_bad_sequence_length (line 816) | def test_bad_sequence_length(self): method test_no_header (line 827) | def test_no_header(self): method test_hapmap_fragment (line 841) | def test_hapmap_fragment(self): FILE: python/tests/test_jit.py function test_numba_import_error (line 15) | def test_numba_import_error(): function _verify_tree_index_state (line 35) | def _verify_tree_index_state(tree_index, edge_diff, tree, reverse=False): function test_correct_trees_forward (line 68) | def test_correct_trees_forward(ts): function test_correct_trees_backwards (line 81) | def test_correct_trees_backwards(ts): function test_correct_trees_backwards_and_forwards (line 94) | def test_correct_trees_backwards_and_forwards(ts): function test_child_index_correctness (line 121) | def test_child_index_correctness(ts): function test_parent_index_correctness (line 143) | def test_parent_index_correctness(ts): function test_parent_index_tree_reconstruction (line 167) | def test_parent_index_tree_reconstruction(ts): function test_child_parent_index_from_jit_function (line 192) | def test_child_parent_index_from_jit_function(): function test_using_tree_index_from_jit_function (line 239) | def test_using_tree_index_from_jit_function(): function test_jit_diversity (line 284) | def test_jit_diversity(ts): function test_jitwrap_properties (line 380) | def test_jitwrap_properties(ts): function test_numba_edge_range (line 439) | def test_numba_edge_range(): function test_numba_tree_index_set_null (line 449) | def test_numba_tree_index_set_null(ts_fixture): function test_numba_tree_index_constants (line 466) | def test_numba_tree_index_constants(ts_fixture): function test_numba_tree_index_edge_cases (line 492) | def test_numba_tree_index_edge_cases(): function test_jit_descendant_span (line 520) | def test_jit_descendant_span(ts): function test_jit_descendant_edges (line 567) | def test_jit_descendant_edges(ts): function test_jit_ancestral_edges (line 620) | def test_jit_ancestral_edges(ts): FILE: python/tests/test_ld_matrix.py function suppress_overflow_div0_warning (line 44) | def suppress_overflow_div0_warning(): class BitSet (line 49) | class BitSet: method __init__ (line 61) | def __init__(self: "BitSet", num_bits: int, length: int) -> None: method intersect (line 67) | def intersect( method difference (line 87) | def difference( method union (line 104) | def union(self: "BitSet", self_row: int, other: "BitSet", other_row: i... method add (line 119) | def add(self: "BitSet", row: int, bit: int) -> None: method get_items (line 129) | def get_items(self: "BitSet", row: int) -> Generator[int, None, None]: method contains (line 154) | def contains(self: "BitSet", row: int, bit: int) -> bool: method count (line 167) | def count(self: "BitSet", row: int) -> int: method count_naive (line 193) | def count_naive(self: "BitSet", row: int) -> int: function norm_hap_weighted (line 215) | def norm_hap_weighted( function norm_hap_weighted_ij (line 241) | def norm_hap_weighted_ij( function norm_total_weighted (line 277) | def norm_total_weighted( function check_order_bounds_dups (line 301) | def check_order_bounds_dups(values, max_value): function get_site_row_col_indices (line 327) | def get_site_row_col_indices( function get_all_samples_bits (line 382) | def get_all_samples_bits(num_samples: int) -> BitSet: function get_allele_samples (line 395) | def get_allele_samples( function get_mutation_samples (line 444) | def get_mutation_samples( function compute_general_two_site_stat_result (line 508) | def compute_general_two_site_stat_result( function two_site_count_stat (line 589) | def two_site_count_stat( function get_index_repeats (line 668) | def get_index_repeats(indices): function two_branch_count_stat (line 691) | def two_branch_count_stat( function sample_sets_to_bit_array (line 773) | def sample_sets_to_bit_array( function positions_to_tree_indices (line 813) | def positions_to_tree_indices(bp, positions): function two_locus_count_stat (line 834) | def two_locus_count_stat( function r2_summary_func (line 984) | def r2_summary_func( function r2_ij_summary_func (line 1018) | def r2_ij_summary_func( function D_summary_func (line 1052) | def D_summary_func( function D2_summary_func (line 1072) | def D2_summary_func( function D_prime_summary_func (line 1093) | def D_prime_summary_func( function r_summary_func (line 1118) | def r_summary_func( function Dz_summary_func (line 1142) | def Dz_summary_func( function pi2_summary_func (line 1164) | def pi2_summary_func( function pi2_unbiased_summary_func (line 1195) | def pi2_unbiased_summary_func( function Dz_unbiased_summary_func (line 1217) | def Dz_unbiased_summary_func( function D2_unbiased_summary_func (line 1243) | def D2_unbiased_summary_func( function D2_ij_summary_func (line 1265) | def D2_ij_summary_func( function D2_ij_unbiased_summary_func (line 1297) | def D2_ij_unbiased_summary_func( function check_set_indexes (line 1405) | def check_set_indexes( function check_sample_stat_inputs (line 1414) | def check_sample_stat_inputs( function ld_matrix (line 1430) | def ld_matrix( function get_paper_ex_ts (line 1456) | def get_paper_ex_ts(): function get_matrix_partitions (line 1534) | def get_matrix_partitions(n): function test_subset_sites (line 1562) | def test_subset_sites(partition): function test_subset_positions (line 1583) | def test_subset_positions(partition): function test_positions_to_tree_indices (line 1616) | def test_positions_to_tree_indices(positions, truth): function test_bad_positions (line 1621) | def test_bad_positions(): function test_subset_sites_one_list (line 1628) | def test_subset_sites_one_list(sites): function test_subset_positions_one_list (line 1637) | def test_subset_positions_one_list(tree_index): function test_repeated_position_elements (line 1669) | def test_repeated_position_elements(tree_index): function test_sample_sets (line 1705) | def test_sample_sets(partition): function test_compare_to_ld_calculator (line 1717) | def test_compare_to_ld_calculator(): function test_multiallelic_with_back_mutation (line 1730) | def test_multiallelic_with_back_mutation(stat): function test_ld_matrix (line 1754) | def test_ld_matrix(ts, stat): function test_ld_empty_examples (line 1764) | def test_ld_empty_examples(ts): function test_input_validation (line 1771) | def test_input_validation(): class TreeState (line 1809) | class TreeState: method __init__ (line 1829) | def __init__(self, ts, sample_sets, num_sample_sets, sample_index_map): method advance (line 1844) | def advance(self, index): function compute_branch_stat_update (line 1890) | def compute_branch_stat_update( function compute_branch_stat (line 1945) | def compute_branch_stat( function test_branch_ld_matrix (line 2102) | def test_branch_ld_matrix(ts, stat): function get_test_branch_sample_set_test_cases (line 2108) | def get_test_branch_sample_set_test_cases(): function test_branch_ld_matrix_sample_sets (line 2132) | def test_branch_ld_matrix_sample_sets(ts, sample_set, stat): function get_test_branch_2pop_test_cases (line 2139) | def get_test_branch_2pop_test_cases(): function test_branch_ld_matrix_2pop_sample_sets (line 2172) | def test_branch_ld_matrix_2pop_sample_sets(ts, sample_set, stat): function test_branch_ld_matrix_2pop_sample_sets_unbiased (line 2186) | def test_branch_ld_matrix_2pop_sample_sets_unbiased(ts, sample_set, stat): function gen_dims_test_cases (line 2196) | def gen_dims_test_cases(ts, mode): function get_test_dims_test_cases (line 2239) | def get_test_dims_test_cases(): function test_dims (line 2259) | def test_dims(ts, params, shape): function test_two_way_branch_ld_matrix (line 2265) | def test_two_way_branch_ld_matrix(ts, sample_sets, stat): function test_two_way_site_ld_matrix (line 2285) | def test_two_way_site_ld_matrix(ts, stat): function test_multipopulation_r2_varying_unequal_set_sizes (line 2385) | def test_multipopulation_r2_varying_unequal_set_sizes(genotypes, sample_... FILE: python/tests/test_metadata.py class TestMetadataRoundTrip (line 48) | class TestMetadataRoundTrip(unittest.TestCase): method setUp (line 53) | def setUp(self): method tearDown (line 57) | def tearDown(self): method test_json (line 60) | def test_json(self): method test_pickle (line 86) | def test_pickle(self): class ExampleMetadata (line 113) | class ExampleMetadata: method __init__ (line 118) | def __init__(self, one=None, two=None): class TestMetadataPickleDecoding (line 123) | class TestMetadataPickleDecoding: method test_nodes (line 128) | def test_nodes(self): method test_sites (line 141) | def test_sites(self): method test_mutations (line 155) | def test_mutations(self): class TestLoadTextMetadata (line 173) | class TestLoadTextMetadata: method test_individuals (line 178) | def test_individuals(self): method test_nodes (line 205) | def test_nodes(self): method test_edges_metadata (line 225) | def test_edges_metadata(self, base64_metadata, metadata_text, expected): method test_edges_without_metadata_column (line 239) | def test_edges_without_metadata_column(self): method test_sites (line 250) | def test_sites(self): method test_mutations (line 266) | def test_mutations(self): method test_populations (line 281) | def test_populations(self): method test_migrations (line 299) | def test_migrations(self, base64_metadata, expected): class TestMetadataModule (line 314) | class TestMetadataModule: method test_metadata_schema (line 319) | def test_metadata_schema(self): method test_schema_str (line 345) | def test_schema_str(self): method test_register_codec (line 359) | def test_register_codec(self): method test_parse (line 366) | def test_parse(self): method test_canonical_string (line 385) | def test_canonical_string(self): method test_equality (line 411) | def test_equality(self): method test_bad_top_level_type (line 451) | def test_bad_top_level_type(self): method test_null_union_top_level (line 461) | def test_null_union_top_level(self, codec): method test_null_codec (line 479) | def test_null_codec(self): method test_json_codec (line 490) | def test_json_codec(self): method test_msgpack_codec (line 517) | def test_msgpack_codec(self): class TestJSONCodec (line 547) | class TestJSONCodec: method test_simple_default (line 548) | def test_simple_default(self): method test_nested_default_error (line 561) | def test_nested_default_error(self): method test_bad_type_error (line 588) | def test_bad_type_error(self): method test_skip_validation (line 596) | def test_skip_validation(self): method test_dont_skip_validation (line 603) | def test_dont_skip_validation(self): method test_dont_skip_validation_other_codecs (line 610) | def test_dont_skip_validation_other_codecs(self): method test_zero_length (line 625) | def test_zero_length(self): class TestJSONStructCodec (line 630) | class TestJSONStructCodec: method test_requires_subschemas (line 631) | def test_requires_subschemas(self): method test_disallow_duplicate_keys (line 638) | def test_disallow_duplicate_keys(self): method test_round_trip_with_struct_and_json (line 652) | def test_round_trip_with_struct_and_json(self): method schema_with_binary (line 692) | def schema_with_binary(self, num_binary_ints): method test_byte_alignment (line 719) | def test_byte_alignment(self, k): method test_json_defaults_applied (line 754) | def test_json_defaults_applied(self): method test_nested_default_error (line 767) | def test_nested_default_error(self): method test_decode_without_magic_errors (line 797) | def test_decode_without_magic_errors(self): method test_decode_version_mismatch (line 808) | def test_decode_version_mismatch(self): method test_decode_truncated_lengths (line 828) | def test_decode_truncated_lengths(self): method test_missing_struct_property_fails_validation (line 847) | def test_missing_struct_property_fails_validation(self): class TestStructCodec (line 861) | class TestStructCodec: method encode_decode (line 862) | def encode_decode(self, method_name, sub_schema, obj, buffer): method test_order_schema (line 874) | def test_order_schema(self): method test_make_encode_and_decode (line 1054) | def test_make_encode_and_decode(self): method test_make_array_encode_and_decode (line 1097) | def test_make_array_encode_and_decode(self): method test_make_array_no_length_encoding_exhaust_buffer (line 1140) | def test_make_array_no_length_encoding_exhaust_buffer(self): method test_make_object_encode_and_decode (line 1199) | def test_make_object_encode_and_decode(self): method test_make_string_encode_and_decode (line 1235) | def test_make_string_encode_and_decode(self): method test_make_null_encode_and_decode (line 1312) | def test_make_null_encode_and_decode(self): method test_make_numeric_encode_and_decode (line 1321) | def test_make_numeric_encode_and_decode(self): method test_null_union_top_level (line 1332) | def test_null_union_top_level(self): method test_default_values (line 1352) | def test_default_values(self): method test_defaults_object_or_null (line 1369) | def test_defaults_object_or_null(self): method test_add_property_to_schema (line 1388) | def test_add_property_to_schema(self): class TestStructCodecRoundTrip (line 1408) | class TestStructCodecRoundTrip: method round_trip (line 1409) | def round_trip(self, schema, row_data): method test_simple_types (line 1413) | def test_simple_types(self): method test_flat_object (line 1436) | def test_flat_object(self): method test_nested_object (line 1452) | def test_nested_object(self): method test_flat_array (line 1484) | def test_flat_array(self): method test_nested_array (line 1513) | def test_nested_array(self): method test_array_of_objects (line 1553) | def test_array_of_objects(self): method test_object_with_array (line 1610) | def test_object_with_array(self): method test_array_length_format (line 1627) | def test_array_length_format(self): method test_string_encoding (line 1643) | def test_string_encoding(self): method test_ordering_of_fields (line 1657) | def test_ordering_of_fields(self): method test_fixed_length_array (line 1697) | def test_fixed_length_array(self): method test_mixed_fixed_and_variable_arrays (line 1751) | def test_mixed_fixed_and_variable_arrays(self): method test_edge_case_zero_length_array (line 1808) | def test_edge_case_zero_length_array(self): class TestStructCodecErrors (line 1846) | class TestStructCodecErrors: method encode (line 1847) | def encode(self, schema, row_data): method test_missing_and_extra_property (line 1851) | def test_missing_and_extra_property(self): method test_bad_schema_union_type (line 1872) | def test_bad_schema_union_type(self): method test_bad_schema_hetrogeneous_array (line 1888) | def test_bad_schema_hetrogeneous_array(self): method test_bad_binary_format (line 1904) | def test_bad_binary_format(self): method test_bad_array_length_format (line 1935) | def test_bad_array_length_format(self): method test_missing_binary_format (line 1946) | def test_missing_binary_format(self): method test_bad_string_encoding (line 1958) | def test_bad_string_encoding(self): method test_bad_null_terminated (line 1975) | def test_bad_null_terminated(self): method test_bad_no_length_encoding_exhaust_buffer (line 1992) | def test_bad_no_length_encoding_exhaust_buffer(self): method test_too_long_array (line 2009) | def test_too_long_array(self): method test_additional_properties (line 2031) | def test_additional_properties(self): method test_unrequired_property_needs_default (line 2043) | def test_unrequired_property_needs_default(self): method test_no_default_implies_required (line 2059) | def test_no_default_implies_required(self): method test_fixed_length_array_wrong_length (line 2074) | def test_fixed_length_array_wrong_length(self): method test_fixed_length_array_conflicts (line 2098) | def test_fixed_length_array_conflicts(self): method test_fixed_length_with_length_format (line 2118) | def test_fixed_length_with_length_format(self): method test_negative_fixed_length (line 2137) | def test_negative_fixed_length(self): class TestSLiMDecoding (line 2154) | class TestSLiMDecoding: method test_node (line 2159) | def test_node(self): method test_individual (line 2181) | def test_individual(self): method test_mutation (line 2224) | def test_mutation(self): method test_population (line 2343) | def test_population(self): class TestTableCollectionEquality (line 2401) | class TestTableCollectionEquality: method test_equality (line 2402) | def test_equality(self): method test_fixing_uncanonical (line 2435) | def test_fixing_uncanonical(self): class TestStructuredArrays (line 2455) | class TestStructuredArrays: method test_not_implemented_json (line 2460) | def test_not_implemented_json(self): method test_types (line 2488) | def test_types(self, type_name, format_code, numpy_type): method test_object_with_multiple_fields (line 2529) | def test_object_with_multiple_fields(self): method test_nested_objects (line 2563) | def test_nested_objects(self): method test_fixed_length_arrays (line 2600) | def test_fixed_length_arrays(self): method test_complex_nested_structure (line 2647) | def test_complex_nested_structure(self): method test_unsupported_formats (line 2723) | def test_unsupported_formats(self): method test_variable_length_arrays_not_supported (line 2734) | def test_variable_length_arrays_not_supported(self): method test_null_union_top_level_not_supported (line 2749) | def test_null_union_top_level_not_supported(self): method test_explicit_ordering (line 2764) | def test_explicit_ordering(self): FILE: python/tests/test_ms.py function get_ms_file_quantity (line 45) | def get_ms_file_quantity(ms_file, quantity): class TestNumReplicates (line 86) | class TestNumReplicates(unittest.TestCase): method verify_num_replicates (line 92) | def verify_num_replicates(self, tree_seq, num_replicates): method test_num_replicates (line 113) | def test_num_replicates(self): method test_num_replicates_multiple (line 119) | def test_num_replicates_multiple(self): class TestNumHaplotypes (line 130) | class TestNumHaplotypes(unittest.TestCase): method verify_num_haplotypes (line 136) | def verify_num_haplotypes(self, tree_seq, tree_seq2, num_replicates): method test_num_haplotypes (line 161) | def test_num_haplotypes(self): method test_num_haplotypes_replicates (line 167) | def test_num_haplotypes_replicates(self): class TestNumSites (line 179) | class TestNumSites(unittest.TestCase): method verify_num_sites (line 185) | def verify_num_sites(self, tree_seq, tree_seq2, num_replicates): method test_num_sites (line 216) | def test_num_sites(self): method test_num_sites_replicates (line 222) | def test_num_sites_replicates(self): class TestGenotypes (line 234) | class TestGenotypes(unittest.TestCase): method get_genotypes (line 239) | def get_genotypes(self, tree_seq): method verify_genotypes (line 247) | def verify_genotypes(self, tree_seq, tree_seq2, num_replicates): method test_genotypes (line 272) | def test_genotypes(self): method test_genotypes_replicates (line 278) | def test_genotypes_replicates(self): class TestPositions (line 290) | class TestPositions(unittest.TestCase): method get_positions (line 296) | def get_positions(self, tree_seq): method verify_positions (line 305) | def verify_positions(self, tree_seq, tree_seq2, num_replicates): method test_positions (line 330) | def test_positions(self): method test_positions_replicates (line 336) | def test_positions_replicates(self): FILE: python/tests/test_parsimony.py function bp_sankoff_score (line 41) | def bp_sankoff_score(tree, genotypes, cost_matrix): function bp_fitch_score (line 62) | def bp_fitch_score(tree, genotypes): function sankoff_score (line 77) | def sankoff_score(tree, genotypes, cost_matrix): function fitch_score (line 96) | def fitch_score(tree, genotypes): function fitch_map_mutations (line 114) | def fitch_map_mutations(tree, genotypes, alleles): function hartigan_map_mutations (line 184) | def hartigan_map_mutations(tree, genotypes, alleles, ancestral_state=None): function reconstruct_states (line 260) | def reconstruct_states(tree, genotypes, S, cost_matrix): function sankoff_map_mutations (line 286) | def sankoff_map_mutations(tree, genotypes, cost_matrix=None): function felsenstein_tables (line 304) | def felsenstein_tables(): function felsenstein_example (line 336) | def felsenstein_example(): class TestSankoff (line 344) | class TestSankoff: method test_felsenstein_example_score (line 349) | def test_felsenstein_example_score(self): method test_felsenstein_example_reconstruct (line 369) | def test_felsenstein_example_reconstruct(self): method verify_infinite_sites (line 382) | def verify_infinite_sites(self, ts): method test_infinite_sites_binary_n2 (line 392) | def test_infinite_sites_binary_n2(self): method test_infinite_sites_binary_n50 (line 396) | def test_infinite_sites_binary_n50(self): method test_infinite_sites_acgt_n2 (line 400) | def test_infinite_sites_acgt_n2(self): method test_infinite_sites_acgt_n15 (line 407) | def test_infinite_sites_acgt_n15(self): method verify_jukes_cantor (line 414) | def verify_jukes_cantor(self, ts, cost_matrix): method test_jukes_cantor_n2_simple_matrix (line 424) | def test_jukes_cantor_n2_simple_matrix(self): method test_jukes_cantor_n20_simple_matrix (line 431) | def test_jukes_cantor_n20_simple_matrix(self): method test_jukes_cantor_n2_felsenstein_matrix (line 438) | def test_jukes_cantor_n2_felsenstein_matrix(self): method test_jukes_cantor_n20_felsenstein_matrix (line 446) | def test_jukes_cantor_n20_felsenstein_matrix(self): class TestFitchParsimonyDistance (line 455) | class TestFitchParsimonyDistance: method verify (line 460) | def verify(self, ts): method test_infinite_sites_binary_n2 (line 486) | def test_infinite_sites_binary_n2(self): method test_infinite_sites_binary_n50 (line 490) | def test_infinite_sites_binary_n50(self): method test_infinite_sites_acgt_n2 (line 494) | def test_infinite_sites_acgt_n2(self): method test_jukes_cantor_n2 (line 501) | def test_jukes_cantor_n2(self): method test_jukes_cantor_n5 (line 506) | def test_jukes_cantor_n5(self): method test_jukes_cantor_n20 (line 511) | def test_jukes_cantor_n20(self): method test_jukes_cantor_n50 (line 516) | def test_jukes_cantor_n50(self): class TestParsimonyBase (line 522) | class TestParsimonyBase: method do_map_mutations (line 527) | def do_map_mutations( class TestParsimonyBadAlleles (line 548) | class TestParsimonyBadAlleles(TestParsimonyBase): method test_too_many_alleles (line 551) | def test_too_many_alleles(self): method test_ancestral_state_too_big (line 558) | def test_ancestral_state_too_big(self): class TestParsimonyRoundTrip (line 568) | class TestParsimonyRoundTrip(TestParsimonyBase): method verify (line 574) | def verify(self, ts): method test_infinite_sites_n3 (line 619) | def test_infinite_sites_n3(self): method test_infinite_sites_n20 (line 623) | def test_infinite_sites_n20(self): method test_infinite_sites_n20_recombination (line 627) | def test_infinite_sites_n20_recombination(self): method test_infinite_sites_n5_internal_samples (line 632) | def test_infinite_sites_n5_internal_samples(self): method test_infinite_sites_n20_internal_samples (line 636) | def test_infinite_sites_n20_internal_samples(self): method test_jukes_cantor_n5 (line 640) | def test_jukes_cantor_n5(self): method test_jukes_cantor_n20 (line 645) | def test_jukes_cantor_n20(self): method test_jukes_cantor_n50 (line 650) | def test_jukes_cantor_n50(self): method test_jukes_cantor_n5_internal_samples (line 655) | def test_jukes_cantor_n5_internal_samples(self): method test_jukes_cantor_n20_internal_samples (line 661) | def test_jukes_cantor_n20_internal_samples(self): method test_jukes_cantor_n50_internal_samples (line 666) | def test_jukes_cantor_n50_internal_samples(self): method test_jukes_cantor_balanced_ternary_internal_samples (line 671) | def test_jukes_cantor_balanced_ternary_internal_samples(self): method test_infinite_sites_n20_multiroot (line 677) | def test_infinite_sites_n20_multiroot(self): method test_jukes_cantor_n15_multiroot (line 681) | def test_jukes_cantor_n15_multiroot(self): method test_jukes_cantor_balanced_ternary_multiroot (line 687) | def test_jukes_cantor_balanced_ternary_multiroot(self): method test_jukes_cantor_n50_multiroot (line 695) | def test_jukes_cantor_n50_multiroot(self): method test_jukes_cantor_root_polytomy_n5 (line 701) | def test_jukes_cantor_root_polytomy_n5(self): method test_jukes_cantor_leaf_polytomy_n5 (line 707) | def test_jukes_cantor_leaf_polytomy_n5(self): method test_many_states_binary (line 717) | def test_many_states_binary(self, tree_builder, n): method test_many_states_arity (line 729) | def test_many_states_arity(self, n, arity): class TestParsimonyRoundTripMissingData (line 740) | class TestParsimonyRoundTripMissingData(TestParsimonyRoundTrip): method verify (line 746) | def verify(self, ts): class TestParsimonyMissingData (line 776) | class TestParsimonyMissingData(TestParsimonyBase): method test_all_missing (line 782) | def test_all_missing(self, n): method test_one_non_missing (line 795) | def test_one_non_missing(self, n): method test_one_non_missing_balanced (line 808) | def test_one_non_missing_balanced(self, arity): method test_many_states_half_missing (line 821) | def test_many_states_half_missing(self, n): method test_one_missing (line 832) | def test_one_missing(self, n): method test_one_missing_balanced (line 846) | def test_one_missing_balanced(self, arity): method test_one_missing_derived_state (line 859) | def test_one_missing_derived_state(self): class TestParsimonyExamples (line 876) | class TestParsimonyExamples(TestParsimonyBase): method test_mutation_over_0 (line 916) | def test_mutation_over_0(self): method test_mutation_over_5 (line 923) | def test_mutation_over_5(self): method test_mutation_over_7 (line 930) | def test_mutation_over_7(self): method test_mutation_over_7_0 (line 937) | def test_mutation_over_7_0(self): method test_mutation_over_7_0_alleles (line 945) | def test_mutation_over_7_0_alleles(self): method test_mutation_over_7_missing_data_0 (line 956) | def test_mutation_over_7_missing_data_0(self): method test_mutation_over_leaf_sibling_missing (line 963) | def test_mutation_over_leaf_sibling_missing(self): method test_mutation_over_6_missing_data_0 (line 982) | def test_mutation_over_6_missing_data_0(self): method test_mutation_over_0_missing_data_4 (line 989) | def test_mutation_over_0_missing_data_4(self): method test_multi_mutation_missing_data (line 996) | def test_multi_mutation_missing_data(self): class TestParsimonyExamplesPolytomy (line 1005) | class TestParsimonyExamplesPolytomy(TestParsimonyBase): method test_all_zeros (line 1049) | def test_all_zeros(self): method test_mutation_over_8 (line 1055) | def test_mutation_over_8(self): method test_mutation_over_6 (line 1062) | def test_mutation_over_6(self): method test_mutation_over_0_5 (line 1069) | def test_mutation_over_0_5(self): method test_mutation_over_7_back_mutation_4 (line 1078) | def test_mutation_over_7_back_mutation_4(self): class TestParsimonyExamplesStar (line 1087) | class TestParsimonyExamplesStar(TestParsimonyBase): method test_two_states_freq_n_minus_1 (line 1093) | def test_two_states_freq_n_minus_1(self, n): method test_two_states_freq_n_minus_2 (line 1110) | def test_two_states_freq_n_minus_2(self, n): method test_three_states_freq_n_minus_2 (line 1129) | def test_three_states_freq_n_minus_2(self, n): method test_n_states (line 1141) | def test_n_states(self, n): method test_missing_data (line 1149) | def test_missing_data(self, n): class TestParsimonyExamplesBalancedTernary (line 1160) | class TestParsimonyExamplesBalancedTernary(TestParsimonyBase): method test_mutation_over_27_29 (line 1174) | def test_mutation_over_27_29(self): method test_three_clades (line 1185) | def test_three_clades(self): method test_nonzero_ancestral_state (line 1195) | def test_nonzero_ancestral_state(self): method test_many_states (line 1205) | def test_many_states(self): method test_least_parsimonious (line 1211) | def test_least_parsimonious(self): class TestParsimonyExamplesUnary (line 1218) | class TestParsimonyExamplesUnary(TestParsimonyBase): method test_all_zeros (line 1268) | def test_all_zeros(self): method test_mutation_over_6 (line 1274) | def test_mutation_over_6(self): method test_mutation_over_7 (line 1281) | def test_mutation_over_7(self): method test_reversed_mutation_over_7 (line 1288) | def test_reversed_mutation_over_7(self): class TestParsimonyExamplesAncestralState (line 1296) | class TestParsimonyExamplesAncestralState(TestParsimonyBase): method test_mutation_over_0 (line 1315) | def test_mutation_over_0(self): method test_mutation_over_3 (line 1331) | def test_mutation_over_3(self): method test_novel_ancestral_state (line 1354) | def test_novel_ancestral_state(self): method test_mutations_over_root (line 1364) | def test_mutations_over_root(self): method test_all_isolated_different_from_ancestral (line 1388) | def test_all_isolated_different_from_ancestral(self): method test_ancestral_as_string (line 1404) | def test_ancestral_as_string(self): method test_bad_ancestral_state (line 1413) | def test_bad_ancestral_state(self): class TestReconstructAllTuples (line 1429) | class TestReconstructAllTuples: method verify (line 1435) | def verify(self, ts, k): method test_simple_n3_k2 (line 1468) | def test_simple_n3_k2(self): method test_simple_n3_k4 (line 1472) | def test_simple_n3_k4(self): method test_simple_n4_k2 (line 1476) | def test_simple_n4_k2(self): method test_simple_n4_k4 (line 1480) | def test_simple_n4_k4(self): method test_simple_n4_k5 (line 1484) | def test_simple_n4_k5(self): method test_simple_n5_k4 (line 1488) | def test_simple_n5_k4(self): method test_simple_n6_k3 (line 1492) | def test_simple_n6_k3(self): method test_root_polytomy_n5_k4 (line 1496) | def test_root_polytomy_n5_k4(self): method test_leaf_polytomy_n5_k4 (line 1500) | def test_leaf_polytomy_n5_k4(self): method test_leaf_polytomy_n5_k5 (line 1504) | def test_leaf_polytomy_n5_k5(self): FILE: python/tests/test_phylo_formats.py function alignment_example (line 51) | def alignment_example(sequence_length, include_reference=True): function missing_data_example (line 67) | def missing_data_example(): function alignment_map (line 87) | def alignment_map(ts, **kwargs): function assert_fully_labelled_trees_equal (line 92) | def assert_fully_labelled_trees_equal(tree, root, node_labels, dpy_tree): function assert_sample_labelled_trees_equal (line 114) | def assert_sample_labelled_trees_equal(tree, dpy_tree): function assert_dpy_tree_list_equal (line 135) | def assert_dpy_tree_list_equal(ts, tree_list): class TestBackendsGiveIdenticalOutput (line 151) | class TestBackendsGiveIdenticalOutput: method test_default_precision (line 157) | def test_default_precision(self, ts): class TestNewickRoundTrip (line 165) | class TestNewickRoundTrip: method test_leaf_labels_newick_lib (line 172) | def test_leaf_labels_newick_lib(self, ts): method test_all_node_labels_dendropy (line 197) | def test_all_node_labels_dendropy(self, ts): class TestNexusTreeRoundTrip (line 213) | class TestNexusTreeRoundTrip: method test_dendropy_defaults (line 220) | def test_dendropy_defaults(self, ts): class TestNexusIncludeSections (line 235) | class TestNexusIncludeSections: method ts (line 241) | def ts(self): method test_nexus_default (line 259) | def test_nexus_default(self): method test_nexus_no_trees (line 284) | def test_nexus_no_trees(self): method test_nexus_no_alignments (line 308) | def test_nexus_no_alignments(self): method test_nexus_no_trees_or_alignments (line 323) | def test_nexus_no_trees_or_alignments(self): class TestNexusNodeLabels (line 338) | class TestNexusNodeLabels: method balanced_tree (line 340) | def balanced_tree(self): method test_as_nexus_labels_basic (line 348) | def test_as_nexus_labels_basic(self): method test_as_nexus_labels_partial (line 366) | def test_as_nexus_labels_partial(self): method test_as_nexus_labels_none (line 384) | def test_as_nexus_labels_none(self): method test_parseable (line 401) | def test_parseable(self, ts): class TestNewickCodePaths (line 429) | class TestNewickCodePaths: method test_default_newick (line 439) | def test_default_newick(self, ts): method test_default_as_newick (line 448) | def test_default_as_newick(self, ts): class TestBalancedBinaryExample (line 457) | class TestBalancedBinaryExample: method tree (line 464) | def tree(self): method test_newick_default (line 467) | def test_newick_default(self): method test_as_newick_default (line 474) | def test_as_newick_default(self): method test_newick_zero_precision (line 478) | def test_newick_zero_precision(self): method test_as_newick_zero_precision (line 482) | def test_as_newick_zero_precision(self): method test_as_newick_precision_1 (line 486) | def test_as_newick_precision_1(self): method test_as_newick_precision_1_explicit_labels (line 490) | def test_as_newick_precision_1_explicit_labels(self): method test_newick_no_branch_lengths (line 496) | def test_newick_no_branch_lengths(self): method test_as_newick_no_branch_lengths (line 500) | def test_as_newick_no_branch_lengths(self): method test_newick_all_node_labels (line 504) | def test_newick_all_node_labels(self): method test_as_newick_all_node_labels (line 510) | def test_as_newick_all_node_labels(self): method test_as_newick_variable_length_node_labels (line 516) | def test_as_newick_variable_length_node_labels(self): method test_as_newick_empty_node_labels (line 522) | def test_as_newick_empty_node_labels(self): method test_newick_partial_node_labels (line 527) | def test_newick_partial_node_labels(self): method test_newick_root (line 533) | def test_newick_root(self): method test_as_nexus_default (line 537) | def test_as_nexus_default(self): method test_as_nexus_precision_1 (line 553) | def test_as_nexus_precision_1(self): class TestFractionalBranchLengths (line 570) | class TestFractionalBranchLengths: method tree (line 578) | def tree(self): method test_newick_default (line 581) | def test_newick_default(self): method test_as_newick_default (line 588) | def test_as_newick_default(self): method test_c_and_py_output_equal (line 595) | def test_c_and_py_output_equal(self): method test_as_newick_precision_3 (line 601) | def test_as_newick_precision_3(self): method test_newick_precision_3 (line 605) | def test_newick_precision_3(self): method test_as_newick_precision_3_labels (line 609) | def test_as_newick_precision_3_labels(self): class TestLargeBranchLengths (line 615) | class TestLargeBranchLengths: method tree (line 623) | def tree(self): method test_newick_default (line 626) | def test_newick_default(self): method test_as_newick_default (line 633) | def test_as_newick_default(self): method test_newick_precision_3 (line 637) | def test_newick_precision_3(self): method test_as_newick_precision_3 (line 641) | def test_as_newick_precision_3(self): class TestInternalSampleExample (line 646) | class TestInternalSampleExample: method tree (line 654) | def tree(self): method test_newick_default (line 661) | def test_newick_default(self): method test_as_newick_default (line 669) | def test_as_newick_default(self): method test_dendropy_parsing (line 674) | def test_dendropy_parsing(self): class TestAncientSampleExample (line 690) | class TestAncientSampleExample: method tree (line 699) | def tree(self): method test_as_newick (line 709) | def test_as_newick(self): method test_newick (line 713) | def test_newick(self): class TestNonSampleLeafExample (line 718) | class TestNonSampleLeafExample: method tree (line 726) | def tree(self): method test_newick (line 733) | def test_newick(self): method test_as_newick_default (line 738) | def test_as_newick_default(self): method test_dendropy_parsing (line 743) | def test_dendropy_parsing(self): method test_newick_lib_parsing (line 763) | def test_newick_lib_parsing(self): class TestNonBinaryExample (line 772) | class TestNonBinaryExample: method tree (line 780) | def tree(self): method test_as_newick (line 783) | def test_as_newick(self): method test_newick (line 787) | def test_newick(self): class TestMultiRootExample (line 792) | class TestMultiRootExample: method tree (line 799) | def tree(self): method test_as_newick_fails (line 808) | def test_as_newick_fails(self): method test_newick_fails (line 812) | def test_newick_fails(self): method test_as_newick_per_root (line 816) | def test_as_newick_per_root(self): method test_newick_per_root (line 822) | def test_newick_per_root(self): class TestLineTree (line 829) | class TestLineTree: method tree (line 840) | def tree(self): method test_newick (line 849) | def test_newick(self): method test_as_newick (line 853) | def test_as_newick(self): method test_dendropy_parsing (line 857) | def test_dendropy_parsing(self): class TestEmptyTree (line 868) | class TestEmptyTree: method tree (line 874) | def tree(self): method test_newick (line 878) | def test_newick(self): method test_as_newick (line 882) | def test_as_newick(self): method test_as_nexus (line 886) | def test_as_nexus(self): class TestSingleNodeTree (line 891) | class TestSingleNodeTree: method tree (line 892) | def tree(self): method test_newick (line 897) | def test_newick(self): method test_as_newick (line 900) | def test_as_newick(self): method test_as_newick_labels (line 903) | def test_as_newick_labels(self): class TestIntegerTreeSequence (line 907) | class TestIntegerTreeSequence: method ts (line 917) | def ts(self): method test_nexus_defaults (line 943) | def test_nexus_defaults(self): method test_nexus_precision_2 (line 960) | def test_nexus_precision_2(self): method test_file_version_identical (line 978) | def test_file_version_identical(self, precision): class TestFloatTimeTreeSequence (line 985) | class TestFloatTimeTreeSequence: method ts (line 995) | def ts(self): method test_nexus_defaults (line 1021) | def test_nexus_defaults(self): method test_nexus_precision_2 (line 1038) | def test_nexus_precision_2(self): class TestFloatPositionTreeSequence (line 1056) | class TestFloatPositionTreeSequence: method ts (line 1066) | def ts(self): method test_nexus_defaults (line 1092) | def test_nexus_defaults(self): method test_nexus_precision_2 (line 1109) | def test_nexus_precision_2(self): function test_newick_buffer_too_small_bug (line 1127) | def test_newick_buffer_too_small_bug(): class TestWrapText (line 1160) | class TestWrapText: method test_even_split (line 1161) | def test_even_split(self): method test_non_even_split (line 1166) | def test_non_even_split(self): method test_width_one (line 1171) | def test_width_one(self): method test_width_full_length (line 1176) | def test_width_full_length(self): method test_width_more_than_length (line 1181) | def test_width_more_than_length(self): method test_width_0 (line 1186) | def test_width_0(self): method test_width_negative (line 1192) | def test_width_negative(self, width): class TestFastaLineLength (line 1200) | class TestFastaLineLength: method verify_line_length (line 1206) | def verify_line_length(self, length, wrap_width=60): method test_wrap_length_default_easy (line 1251) | def test_wrap_length_default_easy(self): method test_wrap_length_default_harder (line 1255) | def test_wrap_length_default_harder(self): method test_wrap_length_custom_easy (line 1259) | def test_wrap_length_custom_easy(self): method test_wrap_length_custom_harder (line 1263) | def test_wrap_length_custom_harder(self): method test_wrap_length_no_wrap (line 1267) | def test_wrap_length_no_wrap(self): method test_negative_wrap (line 1271) | def test_negative_wrap(self): method test_floating_wrap (line 1276) | def test_floating_wrap(self): method test_numpy_wrap (line 1281) | def test_numpy_wrap(self): class TestFileTextOutputEqual (line 1288) | class TestFileTextOutputEqual: method ts (line 1290) | def ts(self): method test_fasta_defaults (line 1293) | def test_fasta_defaults(self): method test_fasta_wrap_width (line 1299) | def test_fasta_wrap_width(self): method test_nexus_defaults (line 1305) | def test_nexus_defaults(self): method test_nexus_precision (line 1311) | def test_nexus_precision(self): class TestFlexibleFileArgFasta (line 1318) | class TestFlexibleFileArgFasta: method ts (line 1320) | def ts(self): method test_pathlib (line 1323) | def test_pathlib(self, tmp_path): method test_path_str (line 1330) | def test_path_str(self, tmp_path): method test_fileobj (line 1337) | def test_fileobj(self, tmp_path): class TestFlexibleFileArgNexus (line 1346) | class TestFlexibleFileArgNexus: method ts (line 1348) | def ts(self): method test_pathlib (line 1351) | def test_pathlib(self, tmp_path): method test_path_str (line 1358) | def test_path_str(self, tmp_path): method test_fileobj (line 1365) | def test_fileobj(self, tmp_path): function get_alignment_map (line 1374) | def get_alignment_map(ts, reference_sequence=None): class TestFastaBioPythonRoundTrip (line 1379) | class TestFastaBioPythonRoundTrip: method verify (line 1385) | def verify(self, ts, wrap_width=60, reference_sequence=None): method test_equal_lines (line 1393) | def test_equal_lines(self): method test_unequal_lines (line 1398) | def test_unequal_lines(self): method test_unwrapped (line 1403) | def test_unwrapped(self): method test_A_reference (line 1408) | def test_A_reference(self): method test_missing_data (line 1412) | def test_missing_data(self): class TestFastaDendropyRoundTrip (line 1416) | class TestFastaDendropyRoundTrip: method parse (line 1417) | def parse(self, fasta): method test_wrapped (line 1421) | def test_wrapped(self): method test_unwrapped (line 1427) | def test_unwrapped(self): method test_no_reference (line 1433) | def test_no_reference(self): method test_missing_data (line 1439) | def test_missing_data(self): class TestDendropyMissingReference (line 1446) | class TestDendropyMissingReference: method ts (line 1457) | def ts(self): method assert_missing_data_encoded (line 1466) | def assert_missing_data_encoded(self, d): method test_fasta (line 1486) | def test_fasta(self): method test_fasta_missing_question (line 1493) | def test_fasta_missing_question(self): method test_nexus (line 1500) | def test_nexus(self): method test_nexus_missing_N (line 1507) | def test_nexus_missing_N(self): class TestDendropyMissingData (line 1515) | class TestDendropyMissingData: method ts (line 1531) | def ts(self): method assert_missing_data_encoded_A_ref (line 1541) | def assert_missing_data_encoded_A_ref(self, d): method test_fasta_defaults_A_ref (line 1560) | def test_fasta_defaults_A_ref(self): method test_nexus_defaults_A_ref (line 1567) | def test_nexus_defaults_A_ref(self): FILE: python/tests/test_provenance.py function get_provenance (line 47) | def get_provenance( class TestSchema (line 66) | class TestSchema: method test_empty (line 71) | def test_empty(self): method test_missing_keys (line 75) | def test_missing_keys(self): method test_software_types (line 92) | def test_software_types(self): method test_schema_version_empth (line 101) | def test_schema_version_empth(self): method test_software_empty_strings (line 106) | def test_software_empty_strings(self): method test_minimal (line 114) | def test_minimal(self): method test_extra_stuff (line 123) | def test_extra_stuff(self): method test_resources (line 133) | def test_resources(self): method test_resources_error (line 148) | def test_resources_error(self): class TestOutputProvenance (line 165) | class TestOutputProvenance: method test_simplify (line 170) | def test_simplify(self): class TestEnvironment (line 180) | class TestEnvironment: method test_os (line 185) | def test_os(self): method test_python (line 196) | def test_python(self): method test_libraries (line 204) | def test_libraries(self): class TestGetResources (line 221) | class TestGetResources: method test_get_resources_keys (line 222) | def test_get_resources_keys(self): method test_get_resources_values (line 230) | def test_get_resources_values(self): method test_get_resources_platform (line 244) | def test_get_resources_platform(self): class TestGetSchema (line 250) | class TestGetSchema: method test_file_equal (line 255) | def test_file_equal(self): method test_caching (line 262) | def test_caching(self): method test_form (line 271) | def test_form(self): class TestTreeSeqEditMethods (line 277) | class TestTreeSeqEditMethods: method test_keep_delete_different (line 282) | def test_keep_delete_different(self): FILE: python/tests/test_python_c.py function get_tracked_sample_counts (line 45) | def get_tracked_sample_counts(ts, st, tracked_samples): function get_sample_counts (line 61) | def get_sample_counts(tree_sequence, st): class LowLevelTestCase (line 74) | class LowLevelTestCase: method verify_tree_dict (line 79) | def verify_tree_dict(self, n, pi): method get_example_tree_sequence (line 111) | def get_example_tree_sequence( method get_example_tree_sequences (line 123) | def get_example_tree_sequences(self): method get_example_migration_tree_sequence (line 129) | def get_example_migration_tree_sequence(self): method verify_iterator (line 141) | def verify_iterator(self, iterator): class MetadataTestMixin (line 153) | class MetadataTestMixin: class TestTableCollection (line 165) | class TestTableCollection(LowLevelTestCase): method test_skip_tables (line 170) | def test_skip_tables(self, tmp_path): method test_skip_reference_sequence (line 189) | def test_skip_reference_sequence(self, tmp_path): method test_file_errors (line 209) | def test_file_errors(self): method test_file_format_eof_error (line 224) | def test_file_format_eof_error(self, tmp_path): method test_file_format_kas_error (line 232) | def test_file_format_kas_error(self, tmp_path): method test_dump_equality (line 243) | def test_dump_equality(self, tmp_path): method test_reference_deletion (line 254) | def test_reference_deletion(self): method test_set_sequence_length_errors (line 273) | def test_set_sequence_length_errors(self): method test_set_sequence_length (line 281) | def test_set_sequence_length(self): method test_set_time_units_errors (line 288) | def test_set_time_units_errors(self): method test_set_time_units (line 296) | def test_set_time_units(self): method test_set_metadata_errors (line 303) | def test_set_metadata_errors(self): method test_set_metadata (line 311) | def test_set_metadata(self): method test_set_metadata_schema_errors (line 319) | def test_set_metadata_schema_errors(self): method test_set_metadata_schema (line 327) | def test_set_metadata_schema(self): method test_simplify_bad_args (line 335) | def test_simplify_bad_args(self): method test_simplify_flags (line 372) | def test_simplify_flags(self, flag, value): method test_link_ancestors_bad_args (line 376) | def test_link_ancestors_bad_args(self): method test_link_ancestors (line 392) | def test_link_ancestors(self): method test_subset_bad_args (line 400) | def test_subset_bad_args(self): method test_union_bad_args (line 412) | def test_union_bad_args(self): method test_union_options (line 446) | def test_union_options(self, flag, value): method test_equals_bad_args (line 455) | def test_equals_bad_args(self): method test_asdict (line 479) | def test_asdict(self): method test_fromdict (line 488) | def test_fromdict(self): method test_asdict_bad_args (line 497) | def test_asdict_bad_args(self): method test_fromdict_bad_args (line 504) | def test_fromdict_bad_args(self): method test_sort_individuals (line 510) | def test_sort_individuals(self): method test_delete_older_bad_args (line 514) | def test_delete_older_bad_args(self): class TestIbd (line 523) | class TestIbd: method test_uninitialised (line 524) | def test_uninitialised(self): method test_get_keys (line 537) | def test_get_keys(self): method test_store_pairs (line 544) | def test_store_pairs(self): method test_within_all_pairs (line 571) | def test_within_all_pairs(self): method test_between_all_pairs (line 580) | def test_between_all_pairs(self): method test_within_bad_args (line 588) | def test_within_bad_args(self): method test_between_bad_args (line 607) | def test_between_bad_args(self): method test_get_output (line 635) | def test_get_output(self): method test_get_bad_args (line 654) | def test_get_bad_args(self): method test_print_state (line 671) | def test_print_state(self): method test_direct_instantiation (line 685) | def test_direct_instantiation(self): class TestIdentitySegmentList (line 698) | class TestIdentitySegmentList: method test_direct_instantiation (line 699) | def test_direct_instantiation(self): method test_memory_management_within (line 707) | def test_memory_management_within(self): method test_memory_management_between (line 722) | def test_memory_management_between(self): class TestTableMethods (line 738) | class TestTableMethods: method test_table_extend (line 744) | def test_table_extend(self, table_name, ts_fixture): method test_table_extend_types (line 772) | def test_table_extend_types( method test_table_keep_rows_errors (line 786) | def test_table_keep_rows_errors(self, table_name, ts_fixture): method test_table_keep_rows_all (line 798) | def test_table_keep_rows_all(self, table_name, ts_fixture): method test_table_keep_rows_none (line 809) | def test_table_keep_rows_none(self, table_name, ts_fixture): method test_mutation_table_keep_rows_ref_error (line 819) | def test_mutation_table_keep_rows_ref_error(self): method test_individual_table_keep_rows_ref_error (line 825) | def test_individual_table_keep_rows_ref_error(self): method test_table_update (line 842) | def test_table_update(self, ts_fixture, table_name, column_name): method test_update_defaults (line 871) | def test_update_defaults(self): method test_update_bad_data (line 920) | def test_update_bad_data(self): class TestTableMethodsErrors (line 1001) | class TestTableMethodsErrors: method yield_tables (line 1006) | def yield_tables(self, ts): method test_table_extend_bad_args (line 1014) | def test_table_extend_bad_args(self, ts_fixture, table_name): method test_update_bad_row_index (line 1047) | def test_update_bad_row_index(self, ts_fixture, table_name): method test_equals_bad_args (line 1064) | def test_equals_bad_args(self, ts_fixture): method test_get_row_bad_args (line 1075) | def test_get_row_bad_args(self, ts_fixture): method test_flag_underflow_overflow (line 1082) | def test_flag_underflow_overflow(self, table): method test_index (line 1098) | def test_index(self): method test_no_indexes (line 1129) | def test_no_indexes(self): method test_bad_indexes (line 1134) | def test_bad_indexes(self): class TestTreeSequence (line 1193) | class TestTreeSequence(LowLevelTestCase, MetadataTestMixin): method setUp (line 1249) | def setUp(self): method tearDown (line 1253) | def tearDown(self): method test_skip_tables (line 1256) | def test_skip_tables(self, tmp_path): method test_skip_reference_sequence (line 1278) | def test_skip_reference_sequence(self, tmp_path): method test_file_errors (line 1302) | def test_file_errors(self): method test_initial_state (line 1316) | def test_initial_state(self): method test_num_nodes (line 1336) | def test_num_nodes(self): method test_dump_equality (line 1346) | def test_dump_equality(self, tmp_path): method test_get_mutation_interface (line 1364) | def test_get_mutation_interface(self): method test_get_edge_interface (line 1389) | def test_get_edge_interface(self): method test_get_node_interface (line 1402) | def test_get_node_interface(self): method test_get_migration_interface (line 1415) | def test_get_migration_interface(self): method test_get_samples (line 1428) | def test_get_samples(self): method test_genealogical_nearest_neighbours (line 1437) | def test_genealogical_nearest_neighbours(self): method test_mean_descendants (line 1475) | def test_mean_descendants(self): method test_link_ancestors_bad_args (line 1496) | def test_link_ancestors_bad_args(self): method test_link_ancestors (line 1511) | def test_link_ancestors(self): method test_metadata_schemas (line 1537) | def test_metadata_schemas(self): method test_metadata (line 1559) | def test_metadata(self): method test_metadata_schema (line 1571) | def test_metadata_schema(self): method test_time_units (line 1583) | def test_time_units(self): method test_extend_haplotypes (line 1595) | def test_extend_haplotypes(self): method test_extend_haplotypes_bad_args (line 1602) | def test_extend_haplotypes_bad_args(self): method test_ld_matrix (line 1633) | def test_ld_matrix(self, stat_method_name): method test_ld_matrix_multipop (line 1798) | def test_ld_matrix_multipop(self, stat_method_name): method test_kc_distance_errors (line 1990) | def test_kc_distance_errors(self): method verify_kc_library_error (line 2011) | def verify_kc_library_error(self, ts1, ts2): method test_kc_distance (line 2015) | def test_kc_distance(self): method test_divergence_matrix (line 2023) | def test_divergence_matrix(self): method test_load_tables_build_indexes (line 2063) | def test_load_tables_build_indexes(self): method test_clear_table (line 2091) | def test_clear_table(self, ts_fixture): method test_discrete_genome (line 2124) | def test_discrete_genome(self): method test_discrete_time (line 2131) | def test_discrete_time(self): method test_min_time (line 2138) | def test_min_time(self): method test_max_time (line 2142) | def test_max_time(self): method test_split_edges_return_type (line 2146) | def test_split_edges_return_type(self): method test_split_edges_bad_types (line 2151) | def test_split_edges_bad_types(self): method test_split_edges_bad_population (line 2169) | def test_split_edges_bad_population(self): method test_array_read_only (line 2180) | def test_array_read_only(self, name, ts_fixture): method test_array_properties (line 2196) | def test_array_properties(self, name, ts_fixture): method test_array_lifetime (line 2212) | def test_array_lifetime(self, name, ts_fixture): method test_generated_columns (line 2227) | def test_generated_columns(self, ts_fixture, name): method test_string_arrays (line 2268) | def test_string_arrays(self, ts_fixture, str_lengths, string_array): class StatsInterfaceMixin (line 2412) | class StatsInterfaceMixin: method test_mode_errors (line 2417) | def test_mode_errors(self): method test_window_errors (line 2427) | def test_window_errors(self): method test_time_window_errors (line 2451) | def test_time_window_errors(self): method test_polarisation (line 2474) | def test_polarisation(self): method test_windows_output (line 2483) | def test_windows_output(self): class WeightMixin (line 2493) | class WeightMixin(StatsInterfaceMixin): method get_example (line 2494) | def get_example(self): method test_bad_weights (line 2502) | def test_bad_weights(self): method test_output_dims (line 2514) | def test_output_dims(self): class WeightCovariateMixin (line 2537) | class WeightCovariateMixin(StatsInterfaceMixin): method get_example (line 2538) | def get_example(self): method test_output_dims (line 2549) | def test_output_dims(self): class SampleSetMixin (line 2572) | class SampleSetMixin(StatsInterfaceMixin): method test_bad_sample_sets (line 2573) | def test_bad_sample_sets(self): class OneWaySampleStatsMixin (line 2597) | class OneWaySampleStatsMixin(SampleSetMixin): method get_example (line 2602) | def get_example(self): method test_basic_example (line 2611) | def test_basic_example(self): method test_output_dims (line 2629) | def test_output_dims(self): method test_polarised (line 2655) | def test_polarised(self): class TestDiversity (line 2663) | class TestDiversity(LowLevelTestCase, OneWaySampleStatsMixin): method get_method (line 2668) | def get_method(self): class TestTraitCovariance (line 2673) | class TestTraitCovariance(LowLevelTestCase, WeightMixin): method get_method (line 2678) | def get_method(self): class TestTraitCorrelation (line 2683) | class TestTraitCorrelation(LowLevelTestCase, WeightMixin): method get_method (line 2688) | def get_method(self): class TestTraitLinearModel (line 2693) | class TestTraitLinearModel(LowLevelTestCase, WeightCovariateMixin): method get_method (line 2698) | def get_method(self): class TestSegregatingSites (line 2703) | class TestSegregatingSites(LowLevelTestCase, OneWaySampleStatsMixin): method get_method (line 2708) | def get_method(self): class TestY1 (line 2713) | class TestY1(LowLevelTestCase, OneWaySampleStatsMixin): method get_method (line 2718) | def get_method(self): class TestAlleleFrequencySpectrum (line 2723) | class TestAlleleFrequencySpectrum(LowLevelTestCase, OneWaySampleStatsMix... method get_method (line 2728) | def get_method(self): method get_example (line 2732) | def get_example(self): method test_basic_example (line 2744) | def test_basic_example(self, mode): method test_output_dims (line 2766) | def test_output_dims(self, mode): method test_node_mode_not_supported (line 2800) | def test_node_mode_not_supported(self): class TwoWaySampleStatsMixin (line 2812) | class TwoWaySampleStatsMixin(SampleSetMixin): method get_example (line 2817) | def get_example(self): method test_basic_example (line 2827) | def test_basic_example(self): method test_output_dims (line 2837) | def test_output_dims(self): method test_set_index_errors (line 2863) | def test_set_index_errors(self): class TwoWayWeightedStatsMixin (line 2880) | class TwoWayWeightedStatsMixin(StatsInterfaceMixin): method get_example (line 2885) | def get_example(self): method test_basic_example (line 2894) | def test_basic_example(self): method test_bad_weights (line 2903) | def test_bad_weights(self): method test_output_dims (line 2916) | def test_output_dims(self): method test_set_index_errors (line 2937) | def test_set_index_errors(self): class ThreeWaySampleStatsMixin (line 2952) | class ThreeWaySampleStatsMixin(SampleSetMixin): method get_example (line 2957) | def get_example(self): method test_basic_example (line 2967) | def test_basic_example(self): method test_output_dims (line 2977) | def test_output_dims(self): method test_set_index_errors (line 3015) | def test_set_index_errors(self): class FourWaySampleStatsMixin (line 3032) | class FourWaySampleStatsMixin(SampleSetMixin): method get_example (line 3037) | def get_example(self): method test_basic_example (line 3047) | def test_basic_example(self): method test_output_dims (line 3057) | def test_output_dims(self): method test_set_index_errors (line 3103) | def test_set_index_errors(self): class TestDivergence (line 3120) | class TestDivergence(LowLevelTestCase, TwoWaySampleStatsMixin): method get_method (line 3121) | def get_method(self): class TestY2 (line 3126) | class TestY2(LowLevelTestCase, TwoWaySampleStatsMixin): method get_method (line 3127) | def get_method(self): class Testf2 (line 3132) | class Testf2(LowLevelTestCase, TwoWaySampleStatsMixin): method get_method (line 3133) | def get_method(self): class TestGeneticRelatedness (line 3138) | class TestGeneticRelatedness(LowLevelTestCase, TwoWaySampleStatsMixin): method get_method (line 3139) | def get_method(self): method test_options (line 3143) | def test_options(self): class TestY3 (line 3162) | class TestY3(LowLevelTestCase, ThreeWaySampleStatsMixin): method get_method (line 3163) | def get_method(self): class Testf3 (line 3168) | class Testf3(LowLevelTestCase, ThreeWaySampleStatsMixin): method get_method (line 3169) | def get_method(self): class Testf4 (line 3174) | class Testf4(LowLevelTestCase, FourWaySampleStatsMixin): method get_method (line 3175) | def get_method(self): class TestWeightedGeneticRelatedness (line 3180) | class TestWeightedGeneticRelatedness(LowLevelTestCase, TwoWayWeightedSta... method get_method (line 3181) | def get_method(self): method test_options (line 3185) | def test_options(self): class TestGeneticRelatednessVector (line 3207) | class TestGeneticRelatednessVector(LowLevelTestCase): method get_example (line 3208) | def get_example(self, num_weights=2): method test_basic_example (line 3222) | def test_basic_example(self, mode, num_weights): method test_good_nodes (line 3233) | def test_good_nodes(self, mode): method test_bad_nodes (line 3246) | def test_bad_nodes(self): method test_bad_args (line 3258) | def test_bad_args(self): method test_modes_not_supported (line 3280) | def test_modes_not_supported(self, mode): method test_bad_weights (line 3287) | def test_bad_weights(self, mode): method test_window_errors (line 3302) | def test_window_errors(self): class TestDecodeAlignmentsLowLevel (line 3329) | class TestDecodeAlignmentsLowLevel(LowLevelTestCase): method get_simple_example (line 3330) | def get_simple_example(self): method test_basic_bytes_roundtrip (line 3340) | def test_basic_bytes_roundtrip(self): method test_nodes_type_and_bounds (line 3357) | def test_nodes_type_and_bounds(self): method test_missing_char_validation (line 3368) | def test_missing_char_validation(self): method test_argument_parsing_error (line 3376) | def test_argument_parsing_error(self): method test_reference_sequence_type_validation (line 3386) | def test_reference_sequence_type_validation(self): method test_missing_char_type_validation (line 3393) | def test_missing_char_type_validation(self): method test_missing_char_unicode_error (line 3400) | def test_missing_char_unicode_error(self): method test_isolated_as_missing_flag_false (line 3414) | def test_isolated_as_missing_flag_false(self): method test_length_and_interval_validation (line 3431) | def test_length_and_interval_validation(self): class TestGeneralStatsInterface (line 3451) | class TestGeneralStatsInterface(LowLevelTestCase, StatsInterfaceMixin): method get_example (line 3456) | def get_example(self): method test_basic_example (line 3467) | def test_basic_example(self): method test_non_numpy_return (line 3475) | def test_non_numpy_return(self): method test_complicated_numpy_function (line 3487) | def test_complicated_numpy_function(self): method test_input_dims (line 3498) | def test_input_dims(self): method test_W_errors (line 3511) | def test_W_errors(self): method test_summary_func_errors (line 3523) | def test_summary_func_errors(self): class TestVariant (line 3568) | class TestVariant(LowLevelTestCase): method test_uninitialised_tree_sequence (line 3573) | def test_uninitialised_tree_sequence(self): method test_constructor (line 3578) | def test_constructor(self): method test_bad_decode (line 3593) | def test_bad_decode(self): method test_alleles (line 3605) | def test_alleles(self): method test_samples (line 3617) | def test_samples(self): method test_isolated_as_missing (line 3630) | def test_isolated_as_missing(self): method test_undecoded (line 3639) | def test_undecoded(self): method test_properties_unwritable (line 3651) | def test_properties_unwritable(self): method test_missing_data (line 3665) | def test_missing_data(self): method test_variants_lifecycle (line 3679) | def test_variants_lifecycle(self): method test_copy (line 3697) | def test_copy(self, isolated_as_missing, samples, alleles): class TestLdCalculator (line 3758) | class TestLdCalculator(LowLevelTestCase): method test_uninitialised_tree_sequence (line 3763) | def test_uninitialised_tree_sequence(self): method test_constructor (line 3768) | def test_constructor(self): method test_get_r2 (line 3774) | def test_get_r2(self): method test_get_r2_array (line 3784) | def test_get_r2_array(self): method test_r2_array_properties (line 3803) | def test_r2_array_properties(self): method test_r2_array_lifetime (line 3815) | def test_r2_array_lifetime(self): class TestLsHmm (line 3836) | class TestLsHmm(LowLevelTestCase): method test_uninitialised_tree_sequence (line 3841) | def test_uninitialised_tree_sequence(self): method test_constructor (line 3846) | def test_constructor(self): method test_bad_rate_arrays (line 3859) | def test_bad_rate_arrays(self): method test_haplotype_input (line 3871) | def test_haplotype_input(self): method test_norm_input (line 3894) | def test_norm_input(self): method test_output_type_errors (line 3909) | def test_output_type_errors(self): method test_empty_forward_matrix (line 3933) | def test_empty_forward_matrix(self): method test_empty_viterbi_matrix (line 3946) | def test_empty_viterbi_matrix(self): method verify_compressed_matrix (line 3960) | def verify_compressed_matrix(self, ts, output): method test_forward_matrix (line 3982) | def test_forward_matrix(self): method test_backward_matrix (line 3991) | def test_backward_matrix(self): method test_viterbi_matrix (line 4002) | def test_viterbi_matrix(self): class TestTree (line 4014) | class TestTree(LowLevelTestCase): method test_options (line 4029) | def test_options(self): method test_site_errors (line 4063) | def test_site_errors(self): method test_mutation_errors (line 4069) | def test_mutation_errors(self): method test_individual_errors (line 4075) | def test_individual_errors(self): method test_population_errors (line 4081) | def test_population_errors(self): method test_provenance_errors (line 4087) | def test_provenance_errors(self): method test_sites (line 4093) | def test_sites(self): method test_root_threshold_errors (line 4135) | def test_root_threshold_errors(self): method test_seek_errors (line 4150) | def test_seek_errors(self): method seek_skip_errors (line 4160) | def seek_skip_errors(self): method test_seek_index_errors (line 4169) | def test_seek_index_errors(self): method test_seek_zero (line 4180) | def test_seek_zero(self, skip): method test_root_threshold (line 4189) | def test_root_threshold(self): method test_constructor (line 4201) | def test_constructor(self): method test_bad_tracked_samples (line 4227) | def test_bad_tracked_samples(self): method test_while_loop_semantics (line 4255) | def test_while_loop_semantics(self): method test_count_all_samples (line 4277) | def test_count_all_samples(self): method test_count_tracked_samples (line 4294) | def test_count_tracked_samples(self): method test_bounds_checking (line 4329) | def test_bounds_checking(self): method test_mrca_interface (line 4355) | def test_mrca_interface(self): method test_newick_precision (line 4370) | def test_newick_precision(self): method test_newick_legacy_ms (line 4381) | def test_newick_legacy_ms(self): method test_cleared_tree (line 4391) | def test_cleared_tree(self): method test_newick_interface (line 4416) | def test_newick_interface(self): method test_newick_buffer_size (line 4429) | def test_newick_buffer_size(self): method test_index (line 4445) | def test_index(self): method test_bad_mutations (line 4453) | def test_bad_mutations(self): method test_sample_list (line 4508) | def test_sample_list(self): method test_equality (line 4541) | def test_equality(self): method test_b2_errors (line 4564) | def test_b2_errors(self): method test_b2 (line 4573) | def test_b2(self): method test_num_lineages_errors (line 4579) | def test_num_lineages_errors(self): method test_num_lineages (line 4590) | def test_num_lineages(self): method test_kc_distance_errors (line 4596) | def test_kc_distance_errors(self): method verify_kc_library_error (line 4643) | def verify_kc_library_error(self, t1, t2): method test_kc_distance (line 4647) | def test_kc_distance(self): method test_copy (line 4659) | def test_copy(self): method test_map_mutations_null (line 4669) | def test_map_mutations_null(self): method test_map_mutations (line 4688) | def test_map_mutations(self): method test_map_mutations_fixed_ancestral_state (line 4698) | def test_map_mutations_fixed_ancestral_state(self): method test_map_mutations_errors (line 4708) | def test_map_mutations_errors(self): method test_array_read_only (line 4740) | def test_array_read_only(self, array): method test_array_properties (line 4759) | def test_array_properties(self, array): method test_array_lifetime (line 4789) | def test_array_lifetime(self, array): method test_traversal_arrays (line 4808) | def test_traversal_arrays(self, ordering): class TestTableMetadataSchema (line 4827) | class TestTableMetadataSchema(MetadataTestMixin): method test_metadata_schema_attribute (line 4828) | def test_metadata_schema_attribute(self): class TestMetadataSchemaNamedTuple (line 4850) | class TestMetadataSchemaNamedTuple(MetadataTestMixin): method test_named_tuple_init (line 4851) | def test_named_tuple_init(self): class TestReferenceSequenceInputErrors (line 4886) | class TestReferenceSequenceInputErrors: method test_string_bad_type (line 4889) | def test_string_bad_type(self, attr, bad_type): method test_metadata_bad_type (line 4895) | def test_metadata_bad_type(self, bad_type): method test_unicode_error (line 4901) | def test_unicode_error(self, attr): method test_del_attr (line 4907) | def test_del_attr(self, attr): class TestReferenceSequenceUpdates (line 4913) | class TestReferenceSequenceUpdates: method test_set_string (line 4916) | def test_set_string(self, attr, value): method test_set_string_null_none (line 4924) | def test_set_string_null_none(self, attr): method test_set_metadata (line 4933) | def test_set_metadata(self, value): class TestReferenceSequenceTableCollection (line 4942) | class TestReferenceSequenceTableCollection: method test_references (line 4943) | def test_references(self): method test_state (line 4948) | def test_state(self): method test_data (line 4959) | def test_data(self, ref_data): method test_url (line 4968) | def test_url(self, url): method test_metadata_default_none (line 4976) | def test_metadata_default_none(self): method test_metadata_schema (line 4983) | def test_metadata_schema(self, schema): method test_metadata (line 4990) | def test_metadata(self, metadata): class TestReferenceSequenceTreeSequence (line 4997) | class TestReferenceSequenceTreeSequence: method test_references (line 4998) | def test_references(self): method test_state (line 5007) | def test_state(self): method test_write (line 5014) | def test_write(self): method test_data (line 5030) | def test_data(self, ref_data): method test_url (line 5039) | def test_url(self, url): method test_metadata_schema (line 5049) | def test_metadata_schema(self, schema): method test_metadata (line 5059) | def test_metadata(self, metadata): class TestModuleFunctions (line 5069) | class TestModuleFunctions: method test_kastore_version (line 5074) | def test_kastore_version(self): method test_tskit_version (line 5078) | def test_tskit_version(self): method test_tskit_version_file (line 5082) | def test_tskit_version_file(self): function test_uninitialised (line 5088) | def test_uninitialised(): function test_constants (line 5121) | def test_constants(): class TestPairCoalescenceCountsErrors (line 5126) | class TestPairCoalescenceCountsErrors: method example_ts (line 5127) | def example_ts(self, sample_size=10): method pair_coalescence_counts (line 5138) | def pair_coalescence_counts( method test_output_dims (line 5173) | def test_output_dims(self): method test_node_shuffle (line 5183) | def test_node_shuffle(self): method test_c_tsk_err_node_out_of_bounds (line 5193) | def test_c_tsk_err_node_out_of_bounds(self, bad_node): method test_c_tsk_err_bad_windows (line 5201) | def test_c_tsk_err_bad_windows(self): method test_c_tsk_err_bad_node_bin_map (line 5207) | def test_c_tsk_err_bad_node_bin_map(self): method test_c_tsk_err_bad_sample_set_index (line 5215) | def test_c_tsk_err_bad_sample_set_index(self, bad_index): method test_cpy_bad_sample_sets (line 5221) | def test_cpy_bad_sample_sets(self, bad_ss_size): method test_cpy_bad_parse_inputs (line 5231) | def test_cpy_bad_parse_inputs(self): method test_cpy_bad_windows (line 5236) | def test_cpy_bad_windows(self): method test_cpy_bad_indexes (line 5242) | def test_cpy_bad_indexes(self, indexes): method test_cpy_bad_node_bin_map (line 5249) | def test_cpy_bad_node_bin_map(self): class TestPairCoalescenceQuantilesErrors (line 5261) | class TestPairCoalescenceQuantilesErrors: method example_ts (line 5262) | def example_ts(self, sample_size=10): method pair_coalescence_quantiles (line 5273) | def pair_coalescence_quantiles( method test_output_dims (line 5308) | def test_output_dims(self): method test_c_tsk_err_bad_quantiles (line 5315) | def test_c_tsk_err_bad_quantiles(self, quantiles): method test_c_tsk_err_unsorted_times (line 5320) | def test_c_tsk_err_unsorted_times(self): method test_c_tsk_err_bad_windows (line 5328) | def test_c_tsk_err_bad_windows(self): method test_cpy_bad_sample_sets (line 5334) | def test_cpy_bad_sample_sets(self, bad_ss_size): method test_cpy_bad_windows (line 5344) | def test_cpy_bad_windows(self): method test_cpy_bad_indexes (line 5350) | def test_cpy_bad_indexes(self, indexes): method test_cpy_bad_node_bin_map (line 5357) | def test_cpy_bad_node_bin_map(self): method test_cpy_bad_inputs (line 5368) | def test_cpy_bad_inputs(self): method test_cpy_bad_quantiles (line 5381) | def test_cpy_bad_quantiles(self): class TestPairCoalescenceRatesErrors (line 5391) | class TestPairCoalescenceRatesErrors: method example_ts (line 5392) | def example_ts(self, sample_size=10): method pair_coalescence_rates (line 5403) | def pair_coalescence_rates( method test_output_dims (line 5439) | def test_output_dims(self): method test_c_tsk_err_bad_time_windows (line 5445) | def test_c_tsk_err_bad_time_windows(self): method test_c_tsk_err_bad_node_time_window (line 5452) | def test_c_tsk_err_bad_node_time_window(self): method test_c_tsk_err_bad_sample_pair_times (line 5458) | def test_c_tsk_err_bad_sample_pair_times(self): method test_c_tsk_err_bad_windows (line 5463) | def test_c_tsk_err_bad_windows(self): method test_cpy_bad_sample_sets (line 5469) | def test_cpy_bad_sample_sets(self, bad_ss_size): method test_cpy_bad_indexes (line 5480) | def test_cpy_bad_indexes(self, indexes): method test_cpy_bad_node_bin_map (line 5487) | def test_cpy_bad_node_bin_map(self): method test_cpy_bad_time_windows (line 5498) | def test_cpy_bad_time_windows(self): method test_cpy_bad_inputs (line 5512) | def test_cpy_bad_inputs(self): FILE: python/tests/test_reference_sequence.py class TestTablesProperties (line 31) | class TestTablesProperties: method test_initially_not_set (line 32) | def test_initially_not_set(self): method test_does_not_have_reference_sequence_if_empty (line 39) | def test_does_not_have_reference_sequence_if_empty(self): method test_same_object (line 45) | def test_same_object(self): method test_clear (line 54) | def test_clear(self, ts_fixture): method test_write_object_fails_bad_type (line 59) | def test_write_object_fails_bad_type(self): method test_write_object (line 64) | def test_write_object(self, ts_fixture): method test_asdict_no_reference (line 69) | def test_asdict_no_reference(self): method test_asdict_reference_no_metadata (line 74) | def test_asdict_reference_no_metadata(self): method test_asdict_reference_metadata (line 83) | def test_asdict_reference_metadata(self): method test_fromdict_reference_data (line 95) | def test_fromdict_reference_data(self): method test_fromdict_reference_url (line 105) | def test_fromdict_reference_url(self): method test_fromdict_reference_metadata (line 115) | def test_fromdict_reference_metadata(self): method test_fromdict_no_reference (line 130) | def test_fromdict_no_reference(self): method test_fromdict_all_values_empty (line 135) | def test_fromdict_all_values_empty(self): class TestSummaries (line 142) | class TestSummaries: method test_repr (line 143) | def test_repr(self): class TestEquals (line 150) | class TestEquals: method test_equal_self (line 151) | def test_equal_self(self, ts_fixture): method test_equal_empty (line 157) | def test_equal_empty(self): method test_unequal_attr_missing (line 164) | def test_unequal_attr_missing(self, ts_fixture, attr): method test_different_not_equal (line 187) | def test_different_not_equal(self, ts_fixture, attr, val): method test_different_but_ignore (line 208) | def test_different_but_ignore(self, ts_fixture, attr, val): class TestTreeSequenceProperties (line 226) | class TestTreeSequenceProperties: method test_data_inherited_from_tables (line 228) | def test_data_inherited_from_tables(self, data): method test_url_inherited_from_tables (line 236) | def test_url_inherited_from_tables(self, url): method test_no_reference_sequence (line 243) | def test_no_reference_sequence(self): method test_write_data_fails (line 249) | def test_write_data_fails(self): method test_write_url_fails (line 256) | def test_write_url_fails(self): method test_write_metadata_fails (line 263) | def test_write_metadata_fails(self): method test_write_metadata_schema_fails (line 272) | def test_write_metadata_schema_fails(self): method test_write_object_fails (line 281) | def test_write_object_fails(self, ts_fixture): FILE: python/tests/test_relatedness_vector.py class RelatednessVector (line 43) | class RelatednessVector: method __init__ (line 44) | def __init__( method print_state (line 96) | def print_state(self, msg=""): method remove_edge (line 150) | def remove_edge(self, p, c): method insert_edge (line 159) | def insert_edge(self, p, c): method adjust_path_up (line 168) | def adjust_path_up(self, p, c, sign): method get_z (line 177) | def get_z(self, u): method mrca (line 185) | def mrca(self, a, b): method write_output (line 195) | def write_output(self): method current_state (line 212) | def current_state(self): method run (line 232) | def run(self): function relatedness_vector (line 300) | def relatedness_vector(ts, sample_weights, windows=None, nodes=None, **k... function relatedness_matrix (line 338) | def relatedness_matrix(ts, windows, centre, nodes=None, span_normalise=T... function verify_relatedness_vector (line 386) | def verify_relatedness_vector( function check_relatedness_vector (line 444) | def check_relatedness_vector( class TestRelatednessVector (line 490) | class TestRelatednessVector: method test_bad_weights (line 491) | def test_bad_weights(self): method test_bad_windows (line 503) | def test_bad_windows(self): method test_nodes_centred_error (line 517) | def test_nodes_centred_error(self): method test_bad_nodes (line 529) | def test_bad_nodes(self): method test_good_nodes (line 554) | def test_good_nodes(self): method test_small_internal_checks (line 599) | def test_small_internal_checks(self, n, seed, centre, span_normalise, ... method test_simple_sims (line 621) | def test_simple_sims(self, n, seed, centre, span_normalise, num_windows): method test_simple_sims_windows (line 639) | def test_simple_sims_windows(self): method test_simple_span_normalise (line 667) | def test_simple_span_normalise(self, mode): method test_single_balanced_tree (line 690) | def test_single_balanced_tree(self, n, centre): method test_internal_sample (line 695) | def test_internal_sample(self, centre): method test_one_internal_sample_sims (line 707) | def test_one_internal_sample_sims(self, seed, centre, num_windows): method test_missing_flanks (line 727) | def test_missing_flanks(self, centre, num_windows): method test_suite_examples_centre (line 743) | def test_suite_examples_centre(self, ts, centre): method test_suite_examples_span_normalise (line 749) | def test_suite_examples_span_normalise(self, ts, span_normalise): method test_dangling_on_samples (line 754) | def test_dangling_on_samples(self, n): method test_dangling_on_all (line 771) | def test_dangling_on_all(self, n, centre): method test_disconnected_non_sample_topology (line 789) | def test_disconnected_non_sample_topology(self, centre): function pca (line 808) | def pca(ts, windows, centre, samples=None, individuals=None, time_window... function allclose_up_to_sign (line 854) | def allclose_up_to_sign(x, y, **kwargs): function assert_pcs_equal (line 868) | def assert_pcs_equal(U, D, U_full, D_full, rtol=1e-5, atol=1e-8): function assert_errors_bound (line 887) | def assert_errors_bound(pca_res, D, U, w=None): class TestPCA (line 939) | class TestPCA: method verify_error_est (line 940) | def verify_error_est( method verify_pca (line 1010) | def verify_pca( method test_bad_windows (line 1086) | def test_bad_windows(self): method test_bad_params (line 1099) | def test_bad_params(self): method test_bad_range_sketch (line 1129) | def test_bad_range_sketch(self): method test_indivs_and_samples (line 1165) | def test_indivs_and_samples(self): method test_modes (line 1175) | def test_modes(self): method test_simple_sims (line 1191) | def test_simple_sims(self, n, centre, num_windows, num_components): method test_range_sketch (line 1211) | def test_range_sketch(self): method test_num_iterations (line 1246) | def test_num_iterations(self): method test_seed (line 1272) | def test_seed(self): method test_samples (line 1288) | def test_samples(self, centre, num_windows): method test_err_samples (line 1311) | def test_err_samples(self, centre, num_windows): method test_individuals_matches_samples (line 1333) | def test_individuals_matches_samples(self, centre): method test_individuals (line 1385) | def test_individuals(self, centre, num_windows, ploidy): method test_err_individuals (line 1408) | def test_err_individuals(self, centre, num_windows, ploidy): FILE: python/tests/test_stats.py function suppress_division_by_zero_warning (line 42) | def suppress_division_by_zero_warning(): function get_r2_matrix (line 47) | def get_r2_matrix(ts): function _compute_r2 (line 70) | def _compute_r2(tree, n, f_a, site_b): function ts_r2 (line 82) | def ts_r2(ts, a, b): class LdArrayCalculator (line 99) | class LdArrayCalculator: method __init__ (line 105) | def __init__(self, ts, focal_site_id, direction, max_sites, max_distan... method _check_site (line 114) | def _check_site(self, site): method _compute_and_append (line 118) | def _compute_and_append(self, target_site): method _compute_forward (line 130) | def _compute_forward(self): method _compute_backward (line 143) | def _compute_backward(self): method run (line 156) | def run(self): function ts_r2_array (line 172) | def ts_r2_array(ts, a, *, direction=1, max_sites=None, max_distance=None): class TestLdSingleTree (line 179) | class TestLdSingleTree: method ts (line 190) | def ts(self): method test_r2 (line 202) | def test_r2(self, a, b, expected): method test_r2_array (line 215) | def test_r2_array(self, a, direction): class TestLdFixedSites (line 223) | class TestLdFixedSites: method ts (line 234) | def ts(self): method test_r2_fixed_fixed (line 246) | def test_r2_fixed_fixed(self): method test_r2_fixed_non_fixed (line 254) | def test_r2_fixed_non_fixed(self): method test_r2_non_fixed_fixed (line 262) | def test_r2_non_fixed_fixed(self): class BaseTestLd (line 271) | class BaseTestLd: method test_r2_all_pairs (line 279) | def test_r2_all_pairs(self): method test_r2_array_first_site_forward (line 288) | def test_r2_array_first_site_forward(self): method test_r2_array_mid_forward (line 296) | def test_r2_array_mid_forward(self): method test_r2_array_first_site_forward_max_sites (line 305) | def test_r2_array_first_site_forward_max_sites(self): method test_r2_array_first_site_forward_max_distance (line 313) | def test_r2_array_first_site_forward_max_distance(self): method test_r2_array_last_site_backward (line 320) | def test_r2_array_last_site_backward(self): method test_r2_array_mid_backward (line 329) | def test_r2_array_mid_backward(self): method test_r2_array_last_site_backward_max_sites (line 338) | def test_r2_array_last_site_backward_max_sites(self): method test_r2_array_last_site_backward_max_distance (line 347) | def test_r2_array_last_site_backward_max_distance(self): method test_r2_array_forward_max_sites_zero (line 356) | def test_r2_array_forward_max_sites_zero(self, max_sites): method test_r2_array_backward_max_sites_zero (line 366) | def test_r2_array_backward_max_sites_zero(self, max_sites): class TestLdOneSitePerTree (line 376) | class TestLdOneSitePerTree(BaseTestLd): method ts (line 378) | def ts(self): class TestLdAllSitesOneTree (line 395) | class TestLdAllSitesOneTree(BaseTestLd): method ts (line 397) | def ts(self): class TestLdSitesEveryOtherTree (line 413) | class TestLdSitesEveryOtherTree(BaseTestLd): method ts (line 415) | def ts(self): class TestLdErrors (line 432) | class TestLdErrors: method test_multi_mutations (line 433) | def test_multi_mutations(self): method test_silent_mutations (line 449) | def test_silent_mutations(self, state): class TestLdCalculator (line 464) | class TestLdCalculator: method verify_matrix (line 471) | def verify_matrix(self, ts): method verify_max_distance (line 498) | def verify_max_distance(self, ts): method verify_max_mutations (line 530) | def verify_max_mutations(self, ts): method test_single_tree_simulated_mutations (line 546) | def test_single_tree_simulated_mutations(self): method test_deprecated_get_aliases (line 552) | def test_deprecated_get_aliases(self): method test_deprecated_max_mutations_alias (line 564) | def test_deprecated_max_mutations_alias(self): method test_single_tree_regular_mutations (line 570) | def test_single_tree_regular_mutations(self): method test_tree_sequence_regular_mutations (line 579) | def test_tree_sequence_regular_mutations(self): method test_tree_sequence_simulated_mutations (line 595) | def test_tree_sequence_simulated_mutations(self): function set_partitions (line 604) | def set_partitions(collection): function naive_mean_descendants (line 620) | def naive_mean_descendants(ts, reference_sets): class TestMeanDescendants (line 644) | class TestMeanDescendants: method verify (line 649) | def verify(self, ts, reference_sets): method test_two_populations_high_migration (line 658) | def test_two_populations_high_migration(self): method test_single_tree (line 671) | def test_single_tree(self): method test_single_tree_partial_samples (line 680) | def test_single_tree_partial_samples(self): method test_single_tree_all_sample_sets (line 689) | def test_single_tree_all_sample_sets(self): method test_many_trees_all_sample_sets (line 698) | def test_many_trees_all_sample_sets(self): method test_wright_fisher_unsimplified_all_sample_sets (line 704) | def test_wright_fisher_unsimplified_all_sample_sets(self): method test_wright_fisher_unsimplified (line 718) | def test_wright_fisher_unsimplified(self): method test_wright_fisher_simplified (line 732) | def test_wright_fisher_simplified(self): function naive_genealogical_nearest_neighbours (line 747) | def naive_genealogical_nearest_neighbours(ts, focal, reference_sets): function parse_time_windows (line 795) | def parse_time_windows(ts, time_windows): function windowed_genealogical_nearest_neighbours (line 801) | def windowed_genealogical_nearest_neighbours( class TestGenealogicalNearestNeighbours (line 911) | class TestGenealogicalNearestNeighbours: method verify (line 946) | def verify(self, ts, reference_sets, focal=None): method test_simple_example_all_samples (line 971) | def test_simple_example_all_samples(self): method test_simple_example_missing_samples (line 988) | def test_simple_example_missing_samples(self): method test_simple_example_internal_focal_node (line 999) | def test_simple_example_internal_focal_node(self): method test_two_populations_high_migration (line 1021) | def test_two_populations_high_migration(self): method test_single_tree (line 1034) | def test_single_tree(self): method test_single_tree_internal_reference_sets (line 1039) | def test_single_tree_internal_reference_sets(self): method test_single_tree_all_nodes (line 1045) | def test_single_tree_all_nodes(self): method test_single_tree_partial_samples (line 1050) | def test_single_tree_partial_samples(self): method test_single_tree_all_sample_sets (line 1055) | def test_single_tree_all_sample_sets(self): method test_many_trees_all_sample_sets (line 1060) | def test_many_trees_all_sample_sets(self): method test_many_trees_sequence_length (line 1066) | def test_many_trees_sequence_length(self): method test_many_trees_all_nodes (line 1071) | def test_many_trees_all_nodes(self): method test_wright_fisher_unsimplified_all_sample_sets (line 1076) | def test_wright_fisher_unsimplified_all_sample_sets(self): method test_wright_fisher_unsimplified (line 1090) | def test_wright_fisher_unsimplified(self): method test_wright_fisher_initial_generation (line 1104) | def test_wright_fisher_initial_generation(self): method test_wright_fisher_initial_generation_no_deep_history (line 1121) | def test_wright_fisher_initial_generation_no_deep_history(self): method test_wright_fisher_unsimplified_multiple_roots (line 1138) | def test_wright_fisher_unsimplified_multiple_roots(self): method test_wright_fisher_simplified (line 1152) | def test_wright_fisher_simplified(self): method test_wright_fisher_simplified_multiple_roots (line 1166) | def test_wright_fisher_simplified_multiple_roots(self): method test_empty_ts (line 1180) | def test_empty_ts(self): class TestWindowedGenealogicalNearestNeighbours (line 1188) | class TestWindowedGenealogicalNearestNeighbours(TestGenealogicalNearestN... method get_two_tree_ts (line 1219) | def get_two_tree_ts(self): method verify (line 1227) | def verify(self, ts, reference_sets, focal=None, windows=None, time_wi... method test_one_tree_windows (line 1255) | def test_one_tree_windows(self): method test_two_tree_windows (line 1268) | def test_two_tree_windows(self): method test_one_tree_time_windows (line 1277) | def test_one_tree_time_windows(self): method test_two_tree_time_windows (line 1290) | def test_two_tree_time_windows(self): method test_one_tree_windows_time_windows (line 1301) | def test_one_tree_windows_time_windows(self): method test_two_tree_windows_time_windows (line 1335) | def test_two_tree_windows_time_windows(self): method test_span_normalise (line 1358) | def test_span_normalise(self): method test_time_normalise (line 1393) | def test_time_normalise(self): function exact_genealogical_nearest_neighbours (line 1467) | def exact_genealogical_nearest_neighbours(ts, focal, reference_sets): function local_gnn (line 1512) | def local_gnn(ts, focal, reference_sets): class TestExactGenealogicalNearestNeighbours (line 1566) | class TestExactGenealogicalNearestNeighbours(TestGenealogicalNearestNeig... method verify (line 1570) | def verify(self, ts, reference_sets, focal=None): FILE: python/tests/test_table_transforms.py function delete_older_definition (line 43) | def delete_older_definition(tables, time): class TestDeleteOlderExamples (line 78) | class TestDeleteOlderExamples: method test_definition (line 80) | def test_definition(self, ts): method test_mutation_parents (line 89) | def test_mutation_parents(self, ts): class TestDeleteOlderSimpleTree (line 99) | class TestDeleteOlderSimpleTree: method tables (line 106) | def tables(self): method test_before_first_internal_node (line 112) | def test_before_first_internal_node(self, time): method test_t1_to_2 (line 125) | def test_t1_to_2(self, time): method test_t2 (line 145) | def test_t2(self, time): class TestDeleteOlderSimpleTreeMutationExamples (line 152) | class TestDeleteOlderSimpleTreeMutationExamples: method test_single_mutation_no_time (line 153) | def test_single_mutation_no_time(self): method test_single_mutation_before_time (line 179) | def test_single_mutation_before_time(self): method test_single_mutation_at_time (line 202) | def test_single_mutation_at_time(self): method test_multi_mutation_no_time (line 226) | def test_multi_mutation_no_time(self): method test_multi_mutation_out_of_order (line 250) | def test_multi_mutation_out_of_order(self): method test_mutation_not_on_branch (line 276) | def test_mutation_not_on_branch(self): class TestDeleteOlderSimpleTreeMigrationExamples (line 286) | class TestDeleteOlderSimpleTreeMigrationExamples: method ts (line 288) | def ts(self): method test_t099 (line 306) | def test_t099(self): method test_t1 (line 312) | def test_t1(self): method test_older (line 319) | def test_older(self, time): function split_edges_definition (line 326) | def split_edges_definition(ts, time, *, flags=0, population=None, metada... class TestSplitEdgesSimpleTree (line 359) | class TestSplitEdgesSimpleTree: method ts (line 367) | def ts(self): method test_lowest_branches (line 371) | def test_lowest_branches(self, time): method test_same_time_as_node (line 389) | def test_same_time_as_node(self): method test_top_branches (line 406) | def test_top_branches(self, time): method test_at_leaf_or_root_time (line 426) | def test_at_leaf_or_root_time(self, time): method test_outside_time_scales (line 431) | def test_outside_time_scales(self, time): class TestSplitEdgesSimpleTreeMutationExamples (line 436) | class TestSplitEdgesSimpleTreeMutationExamples: method test_single_mutation_no_time (line 437) | def test_single_mutation_no_time(self): method test_single_mutation_split_before_time (line 464) | def test_single_mutation_split_before_time(self): method test_single_mutation_split_at_time (line 493) | def test_single_mutation_split_at_time(self): method test_multi_mutation_no_time (line 521) | def test_multi_mutation_no_time(self): method test_multi_mutation_over_sample_time (line 545) | def test_multi_mutation_over_sample_time(self): method test_mutation_not_on_branch (line 577) | def test_mutation_not_on_branch(self): class TestSplitEdgesExamples (line 586) | class TestSplitEdgesExamples: method test_genotypes_round_trip (line 588) | def test_genotypes_round_trip(self, ts): method test_definition (line 599) | def test_definition(self, ts, population): class TestSplitEdgesInterface (line 612) | class TestSplitEdgesInterface: method test_migrations_fail (line 613) | def test_migrations_fail(self, ts_fixture): method test_population_out_of_bounds (line 618) | def test_population_out_of_bounds(self): method test_bad_flags (line 624) | def test_bad_flags(self): method test_bad_metadata_no_schema (line 629) | def test_bad_metadata_no_schema(self): method test_bad_metadata_json_schema (line 634) | def test_bad_metadata_json_schema(self): method test_nonfinite_time (line 642) | def test_nonfinite_time(self, time): class TestSplitEdgesNodeValues (line 649) | class TestSplitEdgesNodeValues: method ts (line 651) | def ts(self): method ts_with_schema (line 661) | def ts_with_schema(self): method test_default_population (line 671) | def test_default_population(self): method test_specify_population (line 676) | def test_specify_population(self, population): method test_default_flags (line 680) | def test_default_flags(self): method test_specify_flags (line 685) | def test_specify_flags(self, flags): method test_default_metadata_no_schema (line 689) | def test_default_metadata_no_schema(self): method test_specify_metadata_no_schema (line 694) | def test_specify_metadata_no_schema(self, metadata): method test_default_metadata_with_schema (line 698) | def test_default_metadata_with_schema(self): method test_specify_metadata_with_schema (line 703) | def test_specify_metadata_with_schema(self, metadata): function decapitate_definition (line 708) | def decapitate_definition(ts, time, *, flags=0, population=None, metadat... class TestDecapitateExamples (line 745) | class TestDecapitateExamples: method test_defaults (line 747) | def test_defaults(self, ts): method test_no_population (line 755) | def test_no_population(self, ts): class TestDecapitateSimpleTree (line 763) | class TestDecapitateSimpleTree: method ts (line 771) | def ts(self): method test_t0_or_before (line 776) | def test_t0_or_before(self, time): method test_t0_to_1 (line 787) | def test_t0_to_1(self, time): method test_t1 (line 806) | def test_t1(self): method test_t1_to_2 (line 824) | def test_t1_to_2(self, time): method test_t2 (line 844) | def test_t2(self, time): class TestDecapitateSimpleTreeMutationExamples (line 850) | class TestDecapitateSimpleTreeMutationExamples: method test_single_mutation_over_sample (line 851) | def test_single_mutation_over_sample(self): method test_single_mutation_at_decap_time (line 874) | def test_single_mutation_at_decap_time(self): method test_multi_mutation_over_sample (line 900) | def test_multi_mutation_over_sample(self): method test_multi_mutation_over_sample_time (line 924) | def test_multi_mutation_over_sample_time(self): method test_multi_mutation_over_root (line 949) | def test_multi_mutation_over_root(self): class TestDecapitateSimpleTsExample (line 977) | class TestDecapitateSimpleTsExample: method ts (line 994) | def ts(self): method test_at_time_of_5 (line 1055) | def test_at_time_of_5(self): method test_at_time6 (line 1080) | def test_at_time6(self): class TestDecapitateNodeValues (line 1109) | class TestDecapitateNodeValues: method ts (line 1111) | def ts(self): method ts_with_schema (line 1121) | def ts_with_schema(self): method test_default_population (line 1131) | def test_default_population(self): method test_specify_population (line 1136) | def test_specify_population(self, population): method test_default_flags (line 1140) | def test_default_flags(self): method test_specify_flags (line 1145) | def test_specify_flags(self, flags): method test_default_metadata_no_schema (line 1149) | def test_default_metadata_no_schema(self): method test_specify_metadata_no_schema (line 1154) | def test_specify_metadata_no_schema(self, metadata): method test_default_metadata_with_schema (line 1158) | def test_default_metadata_with_schema(self): method test_specify_metadata_with_schema (line 1163) | def test_specify_metadata_with_schema(self, metadata): class TestDecapitateInterface (line 1168) | class TestDecapitateInterface: method ts (line 1170) | def ts(self): method test_bad_types (line 1175) | def test_bad_types(self, bad_type): method test_number_types (line 1182) | def test_number_types(self, time): method test_migrations_not_supported (line 1187) | def test_migrations_not_supported(self, ts_fixture): method test_population_out_of_bounds (line 1191) | def test_population_out_of_bounds(self): method test_bad_flags (line 1197) | def test_bad_flags(self): method test_bad_metadata_no_schema (line 1202) | def test_bad_metadata_no_schema(self): method test_bad_metadata_json_schema (line 1207) | def test_bad_metadata_json_schema(self): method test_nonfinite_time (line 1215) | def test_nonfinite_time(self, time): FILE: python/tests/test_tables.py class Column (line 56) | class Column: method __init__ (line 57) | def __init__(self, name): class Int32Column (line 61) | class Int32Column(Column): method get_input (line 62) | def get_input(self, n): class UInt8Column (line 66) | class UInt8Column(Column): method get_input (line 67) | def get_input(self, n): class UInt32Column (line 71) | class UInt32Column(Column): method get_input (line 72) | def get_input(self, n): class CharColumn (line 76) | class CharColumn(Column): method get_input (line 77) | def get_input(self, n): class DoubleColumn (line 82) | class DoubleColumn(Column): method get_input (line 83) | def get_input(self, n): class CommonTestsMixin (line 87) | class CommonTestsMixin: method make_input_data (line 93) | def make_input_data(self, num_rows): method make_transposed_input_data (line 103) | def make_transposed_input_data(self, num_rows): method test_rows (line 127) | def test_rows(self, scope="session"): method table (line 138) | def table(self, test_rows): method table_5row (line 145) | def table_5row(self, test_rows): method test_asdict (line 151) | def test_asdict(self, table, test_rows): method test_max_rows_increment (line 159) | def test_max_rows_increment(self): method test_low_level_get_row (line 174) | def test_low_level_get_row(self): method test_low_level_equals (line 184) | def test_low_level_equals(self): method test_low_level_set_columns (line 192) | def test_low_level_set_columns(self): method test_input_parameters_errors (line 199) | def test_input_parameters_errors(self): method test_input_parameter_values (line 209) | def test_input_parameter_values(self): method test_set_columns_string_errors (line 216) | def test_set_columns_string_errors(self): method test_set_columns_interface (line 235) | def test_set_columns_interface(self): method test_set_columns_from_dict (line 258) | def test_set_columns_from_dict(self): method test_set_columns_dimension (line 267) | def test_set_columns_dimension(self): method test_set_columns_input_sizes (line 294) | def test_set_columns_input_sizes(self): method test_set_read_only_attributes (line 313) | def test_set_read_only_attributes(self): method test_set_column_attributes_empty (line 325) | def test_set_column_attributes_empty(self): method test_set_column_attributes_data (line 332) | def test_set_column_attributes_data(self): method test_set_column_attributes_errors (line 368) | def test_set_column_attributes_errors(self): method test_defaults (line 395) | def test_defaults(self): method test_add_row_data (line 405) | def test_add_row_data(self): method test_add_row_round_trip (line 419) | def test_add_row_round_trip(self): method test_append_row (line 433) | def test_append_row(self): method test_append_duck_type (line 447) | def test_append_duck_type(self): method test_append_error (line 462) | def test_append_error(self): method test_setitem (line 469) | def test_setitem(self): method test_setitem_duck_type (line 487) | def test_setitem_duck_type(self): method test_setitem_error (line 506) | def test_setitem_error(self): method test_set_columns_data (line 527) | def test_set_columns_data(self): method test_truncate (line 552) | def test_truncate(self): method test_truncate_errors (line 585) | def test_truncate_errors(self): method test_append_columns_data (line 601) | def test_append_columns_data(self): method test_append_columns_max_rows (line 626) | def test_append_columns_max_rows(self): method test_keep_rows_data (line 642) | def test_keep_rows_data(self): method test_str (line 654) | def test_str(self): method test_str_pos_time_integer (line 674) | def test_str_pos_time_integer(self): method test_repr_html (line 701) | def test_repr_html(self): method test_copy (line 720) | def test_copy(self): method test_pickle (line 732) | def test_pickle(self): method test_equality (line 745) | def test_equality(self): method test_nbytes (line 805) | def test_nbytes(self): method test_bad_offsets (line 814) | def test_bad_offsets(self): method test_replace_with_wrong_class (line 858) | def test_replace_with_wrong_class(self): class MetadataTestsMixin (line 864) | class MetadataTestsMixin: method metadata_example_data (line 885) | def metadata_example_data(self): method input_data_for_add_row (line 897) | def input_data_for_add_row(self): method test_random_metadata (line 906) | def test_random_metadata(self): method test_drop_metadata (line 920) | def test_drop_metadata(self): method test_optional_metadata (line 939) | def test_optional_metadata(self): method test_packset_metadata (line 956) | def test_packset_metadata(self): method test_set_metadata_schema (line 967) | def test_set_metadata_schema(self): method test_drop_metadata_with_schema (line 1002) | def test_drop_metadata_with_schema(self): method test_drop_metadata_keep_schema (line 1013) | def test_drop_metadata_keep_schema(self): method test_default_metadata_schema (line 1024) | def test_default_metadata_schema(self): method test_default_metadata_add_row (line 1039) | def test_default_metadata_add_row(self): method test_row_round_trip_metadata_schema (line 1054) | def test_row_round_trip_metadata_schema(self): method test_bad_row_metadata_schema (line 1061) | def test_bad_row_metadata_schema(self): method test_absent_metadata_with_required_schema (line 1070) | def test_absent_metadata_with_required_schema(self): method test_unsupported_type (line 1078) | def test_unsupported_type(self): method test_round_trip_set_columns (line 1093) | def test_round_trip_set_columns(self): method test_set_null_metadata (line 1121) | def test_set_null_metadata(self, codec): method test_set_empty_metadata_json (line 1148) | def test_set_empty_metadata_json(self): method test_set_with_optional_properties (line 1178) | def test_set_with_optional_properties(self, codec): method test_copy_metadata_schema (line 1210) | def test_copy_metadata_schema(self): method test_set_columns_metadata_schema (line 1222) | def test_set_columns_metadata_schema(self): method verify_metadata_vector (line 1230) | def verify_metadata_vector(self, table, key, dtype, default_value=9999): method test_metadata_vector_errors (line 1254) | def test_metadata_vector_errors(self): method test_metadata_vector_nodefault (line 1295) | def test_metadata_vector_nodefault(self): method test_metadata_vector (line 1324) | def test_metadata_vector(self): class AssertEqualsMixin (line 1373) | class AssertEqualsMixin: method test_equal (line 1374) | def test_equal(self, table_5row, test_rows): method test_type (line 1380) | def test_type(self, table_5row): method test_metadata_schema (line 1387) | def test_metadata_schema(self, table_5row): method test_degenerate_metadata_schema (line 1399) | def test_degenerate_metadata_schema(self, table_5row): method test_row_changes (line 1414) | def test_row_changes(self, table_5row, test_rows): method test_num_rows (line 1471) | def test_num_rows(self, table_5row, test_rows): method test_metadata (line 1481) | def test_metadata(self, table_5row, test_rows): method test_timestamp (line 1502) | def test_timestamp(self, table_5row, test_rows): class FancyIndexingMixin (line 1524) | class FancyIndexingMixin: method test_slice (line 1542) | def test_slice(self, table, test_rows, slic): method test_boolean_array (line 1559) | def test_boolean_array(self, table_5row, test_rows, mask): method test_index_array (line 1583) | def test_index_array(self, table_5row, index_array): method test_index_range (line 1592) | def test_index_range(self, table_5row): method test_bad_dtypes (line 1608) | def test_bad_dtypes(self, table, dtype): method test_bad_casts (line 1620) | def test_bad_casts(self, table, dtype): method test_extrema (line 1624) | def test_extrema(self, table): method test_bad_shapes (line 1644) | def test_bad_shapes(self, table, bad_shape): method test_bad_bool_length (line 1648) | def test_bad_bool_length(self, table): method test_bad_indexes (line 1658) | def test_bad_indexes(self, table): class TestIndividualTable (line 1687) | class TestIndividualTable(*common_tests): method test_simple_example (line 1700) | def test_simple_example(self): method test_add_row_defaults (line 1718) | def test_add_row_defaults(self): method test_add_row_bad_data (line 1729) | def test_add_row_bad_data(self): method test_packset_location (line 1740) | def test_packset_location(self): method test_packset_parents (line 1751) | def test_packset_parents(self): method test_missing_time_equal_to_self (line 1762) | def test_missing_time_equal_to_self(self): method test_various_not_equals (line 1768) | def test_various_not_equals(self): method test_keep_rows_data (line 1813) | def test_keep_rows_data(self): class TestNodeTable (line 1829) | class TestNodeTable(*common_tests): method test_simple_example (line 1843) | def test_simple_example(self): method test_add_row_defaults (line 1862) | def test_add_row_defaults(self): method test_optional_population (line 1872) | def test_optional_population(self): method test_add_row_bad_data (line 1895) | def test_add_row_bad_data(self): class TestEdgeTable (line 1909) | class TestEdgeTable(*common_tests): method test_simple_example (line 1923) | def test_simple_example(self): method test_add_row_defaults (line 1940) | def test_add_row_defaults(self): method test_add_row_bad_data (line 1946) | def test_add_row_bad_data(self): class TestSiteTable (line 1956) | class TestSiteTable(*common_tests): method test_simple_example (line 1968) | def test_simple_example(self): method test_add_row_bad_data (line 1987) | def test_add_row_bad_data(self): method test_packset_ancestral_state (line 1997) | def test_packset_ancestral_state(self): class TestMutationTable (line 2011) | class TestMutationTable(*common_tests): method test_simple_example (line 2028) | def test_simple_example(self): method test_add_row_defaults (line 2057) | def test_add_row_defaults(self): method test_add_row_bad_data (line 2064) | def test_add_row_bad_data(self): method test_packset_derived_state (line 2078) | def test_packset_derived_state(self): method test_keep_rows_data (line 2089) | def test_keep_rows_data(self): class TestMigrationTable (line 2105) | class TestMigrationTable(*common_tests): method test_simple_example (line 2121) | def test_simple_example(self): method test_add_row_defaults (line 2140) | def test_add_row_defaults(self): method test_add_row_bad_data (line 2146) | def test_add_row_bad_data(self): class TestProvenanceTable (line 2156) | class TestProvenanceTable(CommonTestsMixin, AssertEqualsMixin): method test_simple_example (line 2168) | def test_simple_example(self): method test_add_row_bad_data (line 2182) | def test_add_row_bad_data(self): method test_packset_timestamp (line 2190) | def test_packset_timestamp(self): method test_packset_record (line 2198) | def test_packset_record(self): method test_assert_equals_ignore_timestamps_with_other_difference (line 2206) | def test_assert_equals_ignore_timestamps_with_other_difference(self): class TestPopulationTable (line 2227) | class TestPopulationTable(*common_tests): method test_simple_example (line 2237) | def test_simple_example(self): method test_add_row_defaults (line 2250) | def test_add_row_defaults(self): method test_add_row_bad_data (line 2256) | def test_add_row_bad_data(self): class TestTableCollectionIndexes (line 2263) | class TestTableCollectionIndexes: method test_index (line 2264) | def test_index(self): class TestSortTables (line 2282) | class TestSortTables: method verify_sort_equality (line 2289) | def verify_sort_equality(self, tables, seed): method verify_canonical_equality (line 2307) | def verify_canonical_equality(self, tables, seed): method verify_sort_mutation_consistency (line 2322) | def verify_sort_mutation_consistency(self, orig_tables, seed): method verify_randomise_tables (line 2338) | def verify_randomise_tables(self, orig_tables, seed): method verify_sort (line 2376) | def verify_sort(self, tables, seed): method verify_sort_offset (line 2382) | def verify_sort_offset(self, ts): method get_wf_example (line 2431) | def get_wf_example(self, seed): method test_wf_example (line 2444) | def test_wf_example(self): method test_single_tree_no_mutations (line 2456) | def test_single_tree_no_mutations(self): method test_single_tree_no_mutations_metadata (line 2461) | def test_single_tree_no_mutations_metadata(self): method test_many_trees_no_mutations (line 2466) | def test_many_trees_no_mutations(self): method test_single_tree_mutations (line 2472) | def test_single_tree_mutations(self): method test_single_tree_mutations_metadata (line 2478) | def test_single_tree_mutations_metadata(self): method test_single_tree_multichar_mutations (line 2484) | def test_single_tree_multichar_mutations(self): method test_single_tree_multichar_mutations_metadata (line 2489) | def test_single_tree_multichar_mutations_metadata(self): method test_many_trees_mutations (line 2495) | def test_many_trees_mutations(self): method test_many_trees_multichar_mutations (line 2504) | def test_many_trees_multichar_mutations(self): method test_many_trees_multichar_mutations_metadata (line 2510) | def test_many_trees_multichar_mutations_metadata(self): method get_nonbinary_example (line 2517) | def get_nonbinary_example(self, mutation_rate): method test_nonbinary_trees (line 2537) | def test_nonbinary_trees(self): method test_nonbinary_trees_mutations (line 2542) | def test_nonbinary_trees_mutations(self): method test_unknown_times (line 2549) | def test_unknown_times(self): method test_stable_individual_order (line 2555) | def test_stable_individual_order(self): method test_discrete_times (line 2564) | def test_discrete_times(self): method test_incompatible_edges (line 2569) | def test_incompatible_edges(self): method test_incompatible_sites (line 2581) | def test_incompatible_sites(self): method test_incompatible_mutation_nodes (line 2594) | def test_incompatible_mutation_nodes(self): method test_empty_tables (line 2608) | def test_empty_tables(self): class TestSortMigrations (line 2618) | class TestSortMigrations: method test_msprime_output_unmodified (line 2623) | def test_msprime_output_unmodified(self): method test_full_sort_order (line 2638) | def test_full_sort_order(self): class TestSortMutations (line 2661) | class TestSortMutations: method test_sort_mutations_stability (line 2666) | def test_sort_mutations_stability(self): method test_sort_mutations_remap_parent_id (line 2713) | def test_sort_mutations_remap_parent_id(self): method test_sort_mutations_bad_parent_id (line 2762) | def test_sort_mutations_bad_parent_id(self): method test_sort_mutations_time (line 2796) | def test_sort_mutations_time(self): method test_add_mutations_to_nodes (line 2857) | def test_add_mutations_to_nodes(self): class TestTablesToTreeSequence (line 2889) | class TestTablesToTreeSequence: method test_round_trip (line 2894) | def test_round_trip(self): method test_nonfinite_sequence_length (line 2901) | def test_nonfinite_sequence_length(self, sequence_length): class TestMutationTimeErrors (line 2907) | class TestMutationTimeErrors: method test_younger_than_node_below (line 2908) | def test_younger_than_node_below(self): method test_older_than_node_above (line 2919) | def test_older_than_node_above(self): method test_older_than_parent_node (line 2932) | def test_older_than_parent_node(self): method test_older_than_parent_mutation (line 2954) | def test_older_than_parent_mutation(self): method test_unsorted_times (line 2971) | def test_unsorted_times(self): method test_mixed_known_and_unknown (line 3017) | def test_mixed_known_and_unknown(self): class TestNanDoubleValues (line 3043) | class TestNanDoubleValues: method test_edge_coords (line 3048) | def test_edge_coords(self): method test_migrations (line 3063) | def test_migrations(self): method test_site_positions (line 3084) | def test_site_positions(self): method test_node_times (line 3093) | def test_node_times(self): method test_mutation_times (line 3106) | def test_mutation_times(self): method test_individual (line 3120) | def test_individual(self): class TestSimplifyTables (line 3131) | class TestSimplifyTables: method test_deprecated_zero_mutation_sites (line 3138) | def test_deprecated_zero_mutation_sites(self): method test_zero_mutation_sites (line 3147) | def test_zero_mutation_sites(self): method test_full_samples (line 3159) | def test_full_samples(self): method test_bad_samples (line 3177) | def test_bad_samples(self): method test_bad_edge_ordering (line 3185) | def test_bad_edge_ordering(self): method test_bad_edges (line 3199) | def test_bad_edges(self): method test_bad_mutation_nodes (line 3253) | def test_bad_mutation_nodes(self): method test_bad_mutation_sites (line 3270) | def test_bad_mutation_sites(self): method test_bad_site_positions (line 3287) | def test_bad_site_positions(self): method test_duplicate_positions (line 3305) | def test_duplicate_positions(self): method test_samples_interface (line 3312) | def test_samples_interface(self): method wf_sim_with_individual_metadata (line 3330) | def wf_sim_with_individual_metadata(self): method test_individual_parent_mapping (line 3357) | def test_individual_parent_mapping(self, wf_sim_with_individual_metada... method verify_complete_genetic_pedigree (line 3371) | def verify_complete_genetic_pedigree(self, tables): method test_no_complete_genetic_pedigree (line 3379) | def test_no_complete_genetic_pedigree(self, wf_sim_with_individual_met... method test_complete_genetic_pedigree (line 3385) | def test_complete_genetic_pedigree(self, wf_sim_with_individual_metada... method test_shuffled_individual_parent_mapping (line 3391) | def test_shuffled_individual_parent_mapping(self, wf_sim_with_individu... method test_individual_mapping (line 3424) | def test_individual_mapping(self): method test_bad_individuals (line 3449) | def test_bad_individuals(self, simple_degree1_ts_fixture): method test_unsorted_individuals_ok (line 3462) | def test_unsorted_individuals_ok(self, simple_degree1_ts_fixture): method test_filter_none (line 3471) | def test_filter_none(self, simple_degree1_ts_fixture): class TestTableCollection (line 3498) | class TestTableCollection: method tc (line 3504) | def tc(self, request, ts_fixture): method test_table_references (line 3510) | def test_table_references(self): method test_compute_mutation_parents_ignores_existing_values (line 3539) | def test_compute_mutation_parents_ignores_existing_values(self): method test_compute_mutation_parents_restores_on_index_error (line 3551) | def test_compute_mutation_parents_restores_on_index_error(self): method test_compute_mutation_parents_tolerates_various_invalid_values (line 3567) | def test_compute_mutation_parents_tolerates_various_invalid_values(self): method test_compute_mutation_parents_tolerates_cross_site_and_loops (line 3589) | def test_compute_mutation_parents_tolerates_cross_site_and_loops(self): method test_str (line 3618) | def test_str(self): method test_nbytes_empty_tables (line 3624) | def test_nbytes_empty_tables(self): method test_nbytes (line 3628) | def test_nbytes(self, tmp_path, tc): method test_asdict (line 3642) | def test_asdict(self, tc): method test_asdict_force_offset_64 (line 3669) | def test_asdict_force_offset_64(self, tc, force_offset_64): method test_asdict_force_offset_64_default (line 3679) | def test_asdict_force_offset_64_default(self, tc): method test_asdict_lifecycle (line 3686) | def test_asdict_lifecycle(self, tc, ts_fixture): method test_from_dict (line 3693) | def test_from_dict(self, tc): method test_roundtrip_dict (line 3715) | def test_roundtrip_dict(self, tc): method test_table_name_map (line 3720) | def test_table_name_map(self, tc): method test_equals_empty (line 3744) | def test_equals_empty(self): method test_equals_sequence_length (line 3747) | def test_equals_sequence_length(self): method test_copy (line 3752) | def test_copy(self, ts_fixture): method test_clear_table (line 3760) | def test_clear_table(self, ts_fixture): method test_equals (line 3788) | def test_equals(self): method test_equals_options (line 3848) | def test_equals_options(self, ts_fixture): method test_equals_cross_type (line 3908) | def test_equals_cross_type(self, tc): method test_sequence_length (line 3972) | def test_sequence_length(self): method test_uuid_simulation (line 3977) | def test_uuid_simulation(self, tc): method test_uuid_empty (line 3980) | def test_uuid_empty(self): method test_empty_indexes (line 3984) | def test_empty_indexes(self): method test_index_unsorted (line 3992) | def test_index_unsorted(self): method test_index_from_ts (line 4014) | def test_index_from_ts(self, tc): method test_set_sequence_length_errors (line 4027) | def test_set_sequence_length_errors(self): method test_set_sequence_length (line 4035) | def test_set_sequence_length(self): method test_bad_sequence_length (line 4041) | def test_bad_sequence_length(self, ts_fixture): method test_sequence_length_longer_than_edges (line 4058) | def test_sequence_length_longer_than_edges(self, ts_fixture): method test_indexes (line 4071) | def test_indexes(self, simple_degree1_ts_fixture): method test_indexes_roundtrip (line 4103) | def test_indexes_roundtrip(self, simple_degree1_ts_fixture): method test_asdict_lwt_concordance (line 4113) | def test_asdict_lwt_concordance(self, tc): method test_dump_pathlib (line 4150) | def test_dump_pathlib(self, tc, tmp_path): method test_dump_load_errors (line 4159) | def test_dump_load_errors(self, tc): method test_set_table (line 4182) | def test_set_table(self): class TestEqualityOptions (line 4189) | class TestEqualityOptions: method test_equals_provenance (line 4190) | def test_equals_provenance(self): method test_equals_node_metadata (line 4201) | def test_equals_node_metadata(self, ts_fixture): method test_equals_edge_metadata (line 4211) | def test_equals_edge_metadata(self, ts_fixture): method test_equals_migration_metadata (line 4224) | def test_equals_migration_metadata(self, ts_fixture): method test_equals_site_metadata (line 4239) | def test_equals_site_metadata(self, ts_fixture): method test_equals_mutation_metadata (line 4250) | def test_equals_mutation_metadata(self, ts_fixture): method test_equals_population_metadata (line 4261) | def test_equals_population_metadata(self, ts_fixture): class TestTableCollectionAssertEquals (line 4272) | class TestTableCollectionAssertEquals: method t1 (line 4274) | def t1(self, ts_fixture): method t2 (line 4278) | def t2(self, ts_fixture): method test_equal (line 4281) | def test_equal(self, t1, t2): method test_type (line 4285) | def test_type(self, t1): method test_sequence_length (line 4295) | def test_sequence_length(self, t1, t2): method test_metadata_schema (line 4302) | def test_metadata_schema(self, t1, t2): method test_metadata (line 4312) | def test_metadata(self, t1, t2): method test_time_units (line 4322) | def test_time_units(self, t1, t2): method test_tables (line 4333) | def test_tables(self, t1, t2, table_name): method test_ignore_metadata (line 4344) | def test_ignore_metadata(self, t1, t2, table_name): method test_ignore_provenance (line 4355) | def test_ignore_provenance(self, t1, t2): method test_ignore_timestamps (line 4370) | def test_ignore_timestamps(self, t1, t2): method test_ignore_tables (line 4389) | def test_ignore_tables(self, t1, t2): method test_ignore_reference_sequence (line 4404) | def test_ignore_reference_sequence(self, t1, t2): method test_degenerate_metadata_schema (line 4413) | def test_degenerate_metadata_schema(self, t1, t2): class TestTableCollectionMethodSignatures (line 4425) | class TestTableCollectionMethodSignatures: method test_kwargs_only (line 4428) | def test_kwargs_only(self): class TestTableCollectionMetadata (line 4433) | class TestTableCollectionMetadata: method metadata_example_data (line 4450) | def metadata_example_data(self, val=0): method test_set_metadata_schema (line 4458) | def test_set_metadata_schema(self): method test_set_metadata (line 4482) | def test_set_metadata(self): method test_set_time_units (line 4511) | def test_set_time_units(self): method test_default_metadata_schema (line 4530) | def test_default_metadata_schema(self): method test_round_trip_metadata (line 4539) | def test_round_trip_metadata(self): method test_bad_metadata (line 4547) | def test_bad_metadata(self): function add_tc_metadata (line 4557) | def add_tc_metadata(tc): class TestTableCollectionPickle (line 4579) | class TestTableCollectionPickle: method verify (line 4584) | def verify(self, tables): method test_simple_simulation (line 4589) | def test_simple_simulation(self): method test_simulation_populations (line 4593) | def test_simulation_populations(self): method test_simulation_sites (line 4605) | def test_simulation_sites(self): method test_simulation_individuals (line 4610) | def test_simulation_individuals(self): method test_empty_tables (line 4616) | def test_empty_tables(self): class TestDeduplicateSites (line 4620) | class TestDeduplicateSites: method test_empty (line 4625) | def test_empty(self): method test_unsorted (line 4630) | def test_unsorted(self): method test_bad_position (line 4644) | def test_bad_position(self): method test_no_effect (line 4651) | def test_no_effect(self): method test_same_sites (line 4658) | def test_same_sites(self): method test_order_maintained (line 4672) | def test_order_maintained(self): method test_multichar_ancestral_state (line 4680) | def test_multichar_ancestral_state(self): method test_multichar_metadata (line 4701) | def test_multichar_metadata(self): class TestMutableBaseTable (line 4726) | class TestMutableBaseTable: method test_set_columns_not_implemented (line 4731) | def test_set_columns_not_implemented(self): method test_replace_with (line 4736) | def test_replace_with(self, ts_fixture): class TestSubsetTables (line 4751) | class TestSubsetTables: method get_msprime_example (line 4756) | def get_msprime_example(self, sample_size=10, seed=1234): method get_wf_example (line 4776) | def get_wf_example(self, N=5, ngens=2, seed=1249): method get_examples (line 4785) | def get_examples(self, seed): method verify_subset_equality (line 4789) | def verify_subset_equality(self, tables, nodes): method verify_subset (line 4809) | def verify_subset(self, tables, nodes): method test_ts_subset (line 4899) | def test_ts_subset(self): method test_subset_all (line 4907) | def test_subset_all(self): method test_shuffled_tables (line 4924) | def test_shuffled_tables(self): method test_doesnt_reorder_individuals (line 4950) | def test_doesnt_reorder_individuals(self): method test_random_subsets (line 4957) | def test_random_subsets(self): method test_empty_nodes (line 4964) | def test_empty_nodes(self): method test_no_remove_unreferenced (line 4977) | def test_no_remove_unreferenced(self): method test_subset_reverse_all_nodes (line 5000) | def test_subset_reverse_all_nodes(self): method test_subset_reverse_internal_nodes (line 5015) | def test_subset_reverse_internal_nodes(self): class TestUnionTables (line 5030) | class TestUnionTables(unittest.TestCase): method get_msprime_example (line 5035) | def get_msprime_example(self, sample_size, T, seed): method get_wf_example (line 5060) | def get_wf_example(self, N, T, seed): method split_example (line 5070) | def split_example(self, ts, T): method verify_union (line 5089) | def verify_union(self, tables, other, node_mapping, add_populations=Tr... method verify_union_equality (line 5095) | def verify_union_equality(self, tables, other, node_mapping, add_popul... method verify_union_consistency (line 5119) | def verify_union_consistency(self, tables, other, node_mapping): method test_union_empty (line 5250) | def test_union_empty(self): method test_contradictory_children (line 5260) | def test_contradictory_children(self): method test_noshared_example (line 5267) | def test_noshared_example(self): method test_all_shared_example (line 5278) | def test_all_shared_example(self): method test_no_add_pop (line 5287) | def test_no_add_pop(self): method test_provenance (line 5297) | def test_provenance(self): method test_examples (line 5315) | def test_examples(self): method test_split_and_rejoin (line 5333) | def test_split_and_rejoin(self): method test_both_empty (line 5351) | def test_both_empty(self): method test_one_empty (line 5358) | def test_one_empty(self): method test_reciprocal_empty (line 5381) | def test_reciprocal_empty(self): class TestTableSetitemMetadata (line 5410) | class TestTableSetitemMetadata: method test_setitem_metadata (line 5412) | def test_setitem_metadata(self, ts_fixture, table_name): function keep_rows_definition (line 5421) | def keep_rows_definition(table, keep): class KeepRowsBaseTest (line 5432) | class KeepRowsBaseTest: method test_keep_all (line 5435) | def test_keep_all(self, ts_fixture): method test_keep_none (line 5441) | def test_keep_none(self, ts_fixture): method check_keep_rows (line 5446) | def check_keep_rows(self, table, keep): method test_keep_even (line 5453) | def test_keep_even(self, ts_fixture): method test_keep_odd (line 5459) | def test_keep_odd(self, ts_fixture): method test_keep_first (line 5465) | def test_keep_first(self, ts_fixture): method test_keep_last (line 5472) | def test_keep_last(self, ts_fixture): method test_bad_array_dtype (line 5480) | def test_bad_array_dtype(self, ts_fixture, dtype): method test_python_falsey_input (line 5487) | def test_python_falsey_input(self, ts_fixture, truthy): method test_python_truey_input (line 5494) | def test_python_truey_input(self, ts_fixture, truthy): method test_bad_length (line 5502) | def test_bad_length(self, ts_fixture, offset): method test_non_list_input (line 5510) | def test_non_list_input(self, ts_fixture, bad_type): class TestNodeTableKeepRows (line 5516) | class TestNodeTableKeepRows(KeepRowsBaseTest): method get_table (line 5517) | def get_table(self, ts): class TestEdgeTableKeepRows (line 5521) | class TestEdgeTableKeepRows(KeepRowsBaseTest): method get_table (line 5522) | def get_table(self, ts): class TestSiteTableKeepRows (line 5526) | class TestSiteTableKeepRows(KeepRowsBaseTest): method get_table (line 5527) | def get_table(self, ts): class TestMigrationTableKeepRows (line 5531) | class TestMigrationTableKeepRows(KeepRowsBaseTest): method get_table (line 5532) | def get_table(self, ts): class TestPopulationTableKeepRows (line 5536) | class TestPopulationTableKeepRows(KeepRowsBaseTest): method get_table (line 5537) | def get_table(self, ts): class TestProvenanceTableKeepRows (line 5541) | class TestProvenanceTableKeepRows(KeepRowsBaseTest): method get_table (line 5542) | def get_table(self, ts): class TestIndividualTableKeepRows (line 5550) | class TestIndividualTableKeepRows(KeepRowsBaseTest): method get_table (line 5551) | def get_table(self, ts): method check_keep_rows (line 5556) | def check_keep_rows(self, table, keep): method test_delete_unreferenced (line 5566) | def test_delete_unreferenced(self, ts_fixture): class TestMutationTableKeepRows (line 5575) | class TestMutationTableKeepRows(KeepRowsBaseTest): method get_table (line 5576) | def get_table(self, ts): method check_keep_rows (line 5581) | def check_keep_rows(self, table, keep): method test_delete_unreferenced (line 5591) | def test_delete_unreferenced(self, ts_fixture): method test_error_on_bad_ids (line 5598) | def test_error_on_bad_ids(self, ts_fixture): class TestKeepRowsExamples (line 5607) | class TestKeepRowsExamples: method test_detach_subtree (line 5616) | def test_detach_subtree(self): method test_delete_older_edges (line 5637) | def test_delete_older_edges(self): method test_delete_unreferenced_nodes (line 5658) | def test_delete_unreferenced_nodes(self): method test_mutation_ids_auto_remapped (line 5689) | def test_mutation_ids_auto_remapped(self): method test_individual_ids_auto_remapped (line 5733) | def test_individual_ids_auto_remapped(self): function test_ragged_selection_indices_with_lengths (line 5780) | def test_ragged_selection_indices_with_lengths(): function test_ragged_selection_indices_with_zeros (line 5788) | def test_ragged_selection_indices_with_zeros(): function test_ragged_selection_indices_non_monotonic (line 5796) | def test_ragged_selection_indices_non_monotonic(): class TestMutationParentValidation (line 5804) | class TestMutationParentValidation: method _two_leaf_tree (line 5805) | def _two_leaf_tree(self): method _chain_tree (line 5814) | def _chain_tree(self): method test_tree_sequence_bad_mutation_parent_topology (line 5823) | def test_tree_sequence_bad_mutation_parent_topology(self): method test_tree_sequence_mutation_parent_after_child (line 5835) | def test_tree_sequence_mutation_parent_after_child(self): method test_tree_sequence_mutation_parent_different_site (line 5849) | def test_tree_sequence_mutation_parent_different_site(self): method test_tree_sequence_mutation_parent_equal (line 5863) | def test_tree_sequence_mutation_parent_equal(self): method test_tree_sequence_mutation_parent_out_of_bounds (line 5873) | def test_tree_sequence_mutation_parent_out_of_bounds(self): FILE: python/tests/test_text_formats.py class FamEntry (line 37) | class FamEntry: method get_row (line 45) | def get_row(self, delimiter="\t"): class TestParseFam (line 49) | class TestParseFam: method get_parsed_fam (line 54) | def get_parsed_fam(self, entries, delimiter="\t"): method test_empty_file (line 61) | def test_empty_file(self): method test_single_line (line 68) | def test_single_line(self, iid): method test_multiple_line_file (line 78) | def test_multiple_line_file(self, iids): method test_insufficient_cols (line 91) | def test_insufficient_cols(self, n_cols): method test_unrelated_duplicate_iids (line 101) | def test_unrelated_duplicate_iids(self): method test_duplicate_rows (line 111) | def test_duplicate_rows(self): method test_space_delimited (line 116) | def test_space_delimited(self): method test_missing_phen_col (line 124) | def test_missing_phen_col(self): method test_bad_sex_value (line 134) | def test_bad_sex_value(self, sex): method test_empty_sex_value (line 139) | def test_empty_sex_value(self): method test_single_family_map_parent_ids (line 146) | def test_single_family_map_parent_ids(self): method test_missing_parent_id (line 166) | def test_missing_parent_id(self): method test_multiple_family_map_parent_ids (line 188) | def test_multiple_family_map_parent_ids(self): method test_grandparents (line 217) | def test_grandparents(self): method test_children_before_parents (line 232) | def test_children_before_parents(self, tmp_path): FILE: python/tests/test_threads.py function run_threads (line 41) | def run_threads(worker, num_threads): class TestLdCalculatorReplicates (line 53) | class TestLdCalculatorReplicates: method get_tree_sequence (line 61) | def get_tree_sequence(self): method test_get_r2_multiple_instances (line 65) | def test_get_r2_multiple_instances(self): method test_get_r2_single_instance (line 85) | def test_get_r2_single_instance(self): method test_get_r2_array_multiple_instances (line 104) | def test_get_r2_array_multiple_instances(self): method test_get_r2_array_single_instance (line 121) | def test_get_r2_array_single_instance(self): class TestTables (line 145) | class TestTables: method get_tables (line 151) | def get_tables(self): method run_multiple_writers (line 158) | def run_multiple_writers(self, writer, num_writers=32): method run_failing_reader (line 178) | def run_failing_reader(self, writer, reader, num_readers=32): method test_many_simplify_all_tables (line 210) | def test_many_simplify_all_tables(self): method test_many_sort (line 218) | def test_many_sort(self): method run_simplify_access_table (line 226) | def run_simplify_access_table(self, table_name, col_name): method run_sort_access_table (line 241) | def run_sort_access_table(self, table_name, col_name): method test_simplify_access_nodes (line 256) | def test_simplify_access_nodes(self): method test_simplify_access_edges (line 259) | def test_simplify_access_edges(self): method test_simplify_access_sites (line 262) | def test_simplify_access_sites(self): method test_simplify_access_mutations (line 265) | def test_simplify_access_mutations(self): method test_sort_access_nodes (line 268) | def test_sort_access_nodes(self): method test_sort_access_edges (line 271) | def test_sort_access_edges(self): method test_sort_access_sites (line 274) | def test_sort_access_sites(self): method test_sort_access_mutations (line 277) | def test_sort_access_mutations(self): FILE: python/tests/test_topology.py function simple_keep_intervals (line 47) | def simple_keep_intervals(tables, intervals, simplify=True, record_prove... function generate_segments (line 88) | def generate_segments(n, sequence_length=100, seed=None): class ExampleTopologyMixin (line 99) | class ExampleTopologyMixin: method test_single_coalescent_tree (line 104) | def test_single_coalescent_tree(self): method test_coalescent_trees (line 108) | def test_coalescent_trees(self): method test_coalescent_trees_internal_samples (line 113) | def test_coalescent_trees_internal_samples(self): method test_coalescent_trees_all_samples (line 118) | def test_coalescent_trees_all_samples(self): method test_wright_fisher_trees_unsimplified (line 126) | def test_wright_fisher_trees_unsimplified(self): method test_wright_fisher_trees_simplified (line 132) | def test_wright_fisher_trees_simplified(self): method test_wright_fisher_trees_simplified_one_gen (line 139) | def test_wright_fisher_trees_simplified_one_gen(self): method test_nonbinary_trees (line 146) | def test_nonbinary_trees(self): method test_many_multiroot_trees (line 164) | def test_many_multiroot_trees(self): method test_multiroot_tree (line 170) | def test_multiroot_tree(self): method test_all_missing_data (line 175) | def test_all_missing_data(self): class TestOverlappingSegments (line 182) | class TestOverlappingSegments: method test_random (line 188) | def test_random(self): method test_empty (line 194) | def test_empty(self): method test_single_interval (line 198) | def test_single_interval(self): method test_stairs_down (line 208) | def test_stairs_down(self): method test_stairs_up (line 228) | def test_stairs_up(self): method test_pyramid (line 248) | def test_pyramid(self): method test_gap (line 278) | def test_gap(self): class TopologyTestCase (line 294) | class TopologyTestCase: method assert_haplotypes_equal (line 301) | def assert_haplotypes_equal(self, ts1, ts2): method assert_variants_equal (line 306) | def assert_variants_equal(self, ts1, ts2): method check_num_samples (line 314) | def check_num_samples(self, ts, x): method check_num_tracked_samples (line 328) | def check_num_tracked_samples(self, ts, tracked_samples, x): method check_sample_iterator (line 338) | def check_sample_iterator(self, ts, x): class TestZeroRoots (line 354) | class TestZeroRoots: method remove_samples (line 360) | def remove_samples(self, ts): method verify (line 365) | def verify(self, ts, no_root_ts): method test_single_tree (line 373) | def test_single_tree(self): method test_multiple_trees (line 379) | def test_multiple_trees(self): class TestEmptyTreeSequences (line 386) | class TestEmptyTreeSequences(TopologyTestCase): method test_zero_nodes (line 391) | def test_zero_nodes(self): method test_one_node_zero_samples (line 427) | def test_one_node_zero_samples(self): method test_one_node_zero_samples_sites (line 465) | def test_one_node_zero_samples_sites(self): method test_one_node_one_sample (line 493) | def test_one_node_one_sample(self): method test_one_node_one_sample_sites (line 531) | def test_one_node_one_sample_sites(self): class TestHoleyTreeSequences (line 575) | class TestHoleyTreeSequences(TopologyTestCase): method verify_trees (line 581) | def verify_trees(self, ts, expected): method verify_zero_roots (line 593) | def verify_zero_roots(self, ts): method test_simple_hole (line 599) | def test_simple_hole(self): method test_simple_hole_zero_roots (line 621) | def test_simple_hole_zero_roots(self): method test_initial_gap (line 644) | def test_initial_gap(self): method test_initial_gap_zero_roots (line 663) | def test_initial_gap_zero_roots(self): method test_final_gap (line 683) | def test_final_gap(self): method test_final_gap_zero_roots (line 702) | def test_final_gap_zero_roots(self): method test_initial_and_final_gap (line 722) | def test_initial_and_final_gap(self): method test_initial_and_final_gap_zero_roots (line 741) | def test_initial_and_final_gap_zero_roots(self): class TestTsinferExamples (line 762) | class TestTsinferExamples(TopologyTestCase): method test_no_last_tree (line 767) | def test_no_last_tree(self): class TestRecordSquashing (line 843) | class TestRecordSquashing(TopologyTestCase): method test_single_record (line 848) | def test_single_record(self): method test_single_tree (line 873) | def test_single_tree(self): method test_many_trees (line 880) | def test_many_trees(self): class TestRedundantBreakpoints (line 889) | class TestRedundantBreakpoints(TopologyTestCase): method test_single_tree (line 895) | def test_single_tree(self): method test_many_trees (line 906) | def test_many_trees(self): class TestUnaryNodes (line 928) | class TestUnaryNodes(TopologyTestCase): method test_simple_case (line 933) | def test_simple_case(self): method test_ladder_tree (line 986) | def test_ladder_tree(self): method verify_unary_tree_sequence (line 1023) | def verify_unary_tree_sequence(self, ts): method test_binary_tree_sequence_unary_nodes (line 1075) | def test_binary_tree_sequence_unary_nodes(self): method test_nonbinary_tree_sequence_unary_nodes (line 1081) | def test_nonbinary_tree_sequence_unary_nodes(self): class TestGeneralSamples (line 1100) | class TestGeneralSamples(TopologyTestCase): method test_simple_case (line 1106) | def test_simple_case(self): method verify_permuted_nodes (line 1180) | def verify_permuted_nodes(self, ts): method test_single_tree_permuted_nodes (line 1225) | def test_single_tree_permuted_nodes(self): method test_binary_tree_sequence_permuted_nodes (line 1229) | def test_binary_tree_sequence_permuted_nodes(self): method test_nonbinary_tree_sequence_permuted_nodes (line 1235) | def test_nonbinary_tree_sequence_permuted_nodes(self): class TestSimplifyExamples (line 1254) | class TestSimplifyExamples(TopologyTestCase): method verify_simplify (line 1260) | def verify_simplify( method test_unsorted_edges (line 1322) | def test_unsorted_edges(self): method test_single_binary_tree (line 1349) | def test_single_binary_tree(self): method test_single_binary_tree_no_sample_nodes (line 1388) | def test_single_binary_tree_no_sample_nodes(self): method test_single_binary_tree_keep_input_root (line 1427) | def test_single_binary_tree_keep_input_root(self): method test_single_binary_tree_internal_sample (line 1468) | def test_single_binary_tree_internal_sample(self): method test_single_binary_tree_internal_sample_meet_at_root (line 1506) | def test_single_binary_tree_internal_sample_meet_at_root(self): method test_single_binary_tree_simple_mutations (line 1551) | def test_single_binary_tree_simple_mutations(self): method test_single_binary_tree_keep_roots_mutations (line 1634) | def test_single_binary_tree_keep_roots_mutations(self): method test_place_mutations_with_and_without_roots (line 1703) | def test_place_mutations_with_and_without_roots(self): method test_overlapping_edges (line 1780) | def test_overlapping_edges(self): method test_overlapping_edges_internal_samples (line 1806) | def test_overlapping_edges_internal_samples(self): method test_unary_edges_no_overlap (line 1826) | def test_unary_edges_no_overlap(self): method test_unary_edges_no_overlap_internal_sample (line 1856) | def test_unary_edges_no_overlap_internal_sample(self): method test_keep_nodes (line 1876) | def test_keep_nodes(self): class TestNonSampleExternalNodes (line 1909) | class TestNonSampleExternalNodes(TopologyTestCase): method test_simple_case (line 1914) | def test_simple_case(self): method test_unary_non_sample_external_nodes (line 1971) | def test_unary_non_sample_external_nodes(self): class TestMultipleRoots (line 2001) | class TestMultipleRoots(TopologyTestCase): method test_simplest_degenerate_case (line 2006) | def test_simplest_degenerate_case(self): method test_simplest_non_degenerate_case (line 2060) | def test_simplest_non_degenerate_case(self): method test_two_reducible_trees (line 2128) | def test_two_reducible_trees(self): method test_one_reducible_tree (line 2209) | def test_one_reducible_tree(self): method test_mutations_over_roots (line 2253) | def test_mutations_over_roots(self): method test_break_single_tree (line 2318) | def test_break_single_tree(self): class TestWithVisuals (line 2346) | class TestWithVisuals(TopologyTestCase): method verify_simplify_topology (line 2351) | def verify_simplify_topology(self, ts, sample, haplotypes=False): method test_partial_non_sample_external_nodes (line 2378) | def test_partial_non_sample_external_nodes(self): method test_partial_non_sample_external_nodes_2 (line 2441) | def test_partial_non_sample_external_nodes_2(self): method test_single_offspring_records (line 2502) | def test_single_offspring_records(self): method test_many_single_offspring (line 2562) | def test_many_single_offspring(self): method test_tricky_switches (line 2702) | def test_tricky_switches(self): method test_tricky_simplify (line 2824) | def test_tricky_simplify(self): method test_ancestral_samples (line 2943) | def test_ancestral_samples(self): method test_all_ancestral_samples (line 3042) | def test_all_ancestral_samples(self): method test_internal_sampled_node (line 3108) | def test_internal_sampled_node(self): class TestBadTrees (line 3233) | class TestBadTrees: method test_simplest_contradictory_children (line 3239) | def test_simplest_contradictory_children(self): method test_partial_overlap_contradictory_children (line 3259) | def test_partial_overlap_contradictory_children(self): class TestCoiteration (line 3280) | class TestCoiteration: method test_identical_ts (line 3285) | def test_identical_ts(self): method test_intervals (line 3294) | def test_intervals(self): method test_simple_ts (line 3313) | def test_simple_ts(self): method test_nonequal_lengths (line 3355) | def test_nonequal_lengths(self): method test_kwargs (line 3361) | def test_kwargs(self): function do_simplify (line 3369) | def do_simplify( class SimplifyTestBase (line 3468) | class SimplifyTestBase: class TestSimplify (line 3474) | class TestSimplify(SimplifyTestBase): method verify_no_samples (line 3510) | def verify_no_samples(self, ts, keep_unary=False): method verify_single_childified (line 3523) | def verify_single_childified(self, ts, keep_unary=False): method verify_multiroot_internal_samples (line 3553) | def verify_multiroot_internal_samples(self, ts, keep_unary=False): method test_single_tree (line 3575) | def test_single_tree(self): method test_single_tree_mutations (line 3585) | def test_single_tree_mutations(self): method test_many_trees_mutations (line 3594) | def test_many_trees_mutations(self): method test_many_trees (line 3607) | def test_many_trees(self): method test_small_tree_internal_samples (line 3618) | def test_small_tree_internal_samples(self): method test_small_tree_linear_samples (line 3649) | def test_small_tree_linear_samples(self): method test_small_tree_internal_and_external_samples (line 3680) | def test_small_tree_internal_and_external_samples(self): method test_small_tree_mutations (line 3715) | def test_small_tree_mutations(self): method test_small_tree_filter_zero_mutations (line 3740) | def test_small_tree_filter_zero_mutations(self): method test_small_tree_fixed_sites (line 3757) | def test_small_tree_fixed_sites(self): method test_small_tree_mutations_over_root (line 3780) | def test_small_tree_mutations_over_root(self): method test_small_tree_recurrent_mutations (line 3799) | def test_small_tree_recurrent_mutations(self): method test_small_tree_back_mutations (line 3820) | def test_small_tree_back_mutations(self): method test_overlapping_unary_edges (line 3861) | def test_overlapping_unary_edges(self): method test_overlapping_unary_edges_internal_samples (line 3888) | def test_overlapping_unary_edges_internal_samples(self): method test_isolated_samples (line 3913) | def test_isolated_samples(self): method test_internal_samples (line 3937) | def test_internal_samples(self): method test_many_mutations_over_single_sample_ancestral_state (line 3998) | def test_many_mutations_over_single_sample_ancestral_state(self): method test_many_mutations_over_single_sample_derived_state (line 4038) | def test_many_mutations_over_single_sample_derived_state(self): method test_many_trees_filter_zero_mutations (line 4079) | def test_many_trees_filter_zero_mutations(self): method test_many_trees_filter_zero_multichar_mutations (line 4093) | def test_many_trees_filter_zero_multichar_mutations(self): method test_simple_population_filter (line 4107) | def test_simple_population_filter(self): method test_interleaved_populations_filter (line 4122) | def test_interleaved_populations_filter(self): method test_removed_node_population_filter (line 4151) | def test_removed_node_population_filter(self): method test_simple_individual_filter (line 4177) | def test_simple_individual_filter(self): method test_interleaved_individual_filter (line 4194) | def test_interleaved_individual_filter(self): method test_removed_node_individual_filter (line 4215) | def test_removed_node_individual_filter(self): method verify_simplify_haplotypes (line 4241) | def verify_simplify_haplotypes(self, ts, samples, keep_unary=False): method test_single_tree_recurrent_mutations (line 4256) | def test_single_tree_recurrent_mutations(self): method test_many_trees_recurrent_mutations (line 4265) | def test_many_trees_recurrent_mutations(self): method test_single_multiroot_tree_recurrent_mutations (line 4275) | def test_single_multiroot_tree_recurrent_mutations(self): method test_many_multiroot_trees_recurrent_mutations (line 4286) | def test_many_multiroot_trees_recurrent_mutations(self): method test_single_tree_recurrent_mutations_internal_samples (line 4297) | def test_single_tree_recurrent_mutations_internal_samples(self): method test_many_trees_recurrent_mutations_internal_samples (line 4307) | def test_many_trees_recurrent_mutations_internal_samples(self): class TestSimplifyUnreferencedPopulations (line 4319) | class TestSimplifyUnreferencedPopulations: method example (line 4320) | def example(self): method test_no_filter_populations (line 4335) | def test_no_filter_populations(self): method test_no_filter_populations_nodes (line 4342) | def test_no_filter_populations_nodes(self): method test_filter_populations_no_filter_nodes (line 4349) | def test_filter_populations_no_filter_nodes(self): method test_remapped_default (line 4356) | def test_remapped_default(self): class TestSimplifyUnreferencedIndividuals (line 4364) | class TestSimplifyUnreferencedIndividuals: method example (line 4365) | def example(self): method test_no_filter_individuals (line 4380) | def test_no_filter_individuals(self): method test_no_filter_individuals_nodes (line 4387) | def test_no_filter_individuals_nodes(self): method test_filter_individuals_no_filter_nodes (line 4394) | def test_filter_individuals_no_filter_nodes(self): method test_remapped_default (line 4401) | def test_remapped_default(self): class TestSimplifyKeepInputRoots (line 4409) | class TestSimplifyKeepInputRoots(SimplifyTestBase, ExampleTopologyMixin): method verify (line 4414) | def verify(self, ts): method verify_keep_input_roots (line 4422) | def verify_keep_input_roots(self, ts, samples): method test_many_trees (line 4508) | def test_many_trees(self): method test_many_trees_internal_samples (line 4515) | def test_many_trees_internal_samples(self): method test_many_multiroot_trees (line 4523) | def test_many_multiroot_trees(self): method test_wright_fisher_unsimplified (line 4531) | def test_wright_fisher_unsimplified(self): method test_single_tree_recurrent_mutations (line 4545) | def test_single_tree_recurrent_mutations(self): method test_many_trees_recurrent_mutations (line 4553) | def test_many_trees_recurrent_mutations(self): class TestSimplifyFilterNodes (line 4563) | class TestSimplifyFilterNodes: method reverse_node_indexes (line 4568) | def reverse_node_indexes(self, ts): method verify_nodes_unchanged (line 4580) | def verify_nodes_unchanged(self, ts_in, resample_size=None, **kwargs): method test_empty (line 4613) | def test_empty(self): method test_all_samples (line 4617) | def test_all_samples(self): method test_no_topology (line 4628) | def test_no_topology(self, resample_size): method test_stick_tree (line 4635) | def test_stick_tree(self, resample_size): method test_internal_samples (line 4650) | def test_internal_samples(self, resample_size): method test_blank_flanks (line 4661) | def test_blank_flanks(self, resample_size): method test_multiroot (line 4667) | def test_multiroot(self, resample_size): method test_with_metadata (line 4673) | def test_with_metadata(self, ts_fixture_for_simplify, resample_size): method test_complex_ts_with_unary (line 4678) | def test_complex_ts_with_unary(self, resample_size): method test_keeping_unary (line 4695) | def test_keeping_unary(self): method test_find_unreferenced_nodes (line 4708) | def test_find_unreferenced_nodes(self): method test_mutations_on_removed_branches (line 4729) | def test_mutations_on_removed_branches(self): class TestSimplifyNoUpdateSampleFlags (line 4749) | class TestSimplifyNoUpdateSampleFlags: method test_simple_case_filter_nodes (line 4754) | def test_simple_case_filter_nodes(self): method test_simple_case_no_filter_nodes (line 4781) | def test_simple_case_no_filter_nodes(self): class TestMapToAncestors (line 4807) | class TestMapToAncestors: method do_map (line 4888) | def do_map(self, ts, ancestors, samples=None, compare_lib=True): method test_deprecated_name (line 4905) | def test_deprecated_name(self): method test_single_tree_one_ancestor (line 4925) | def test_single_tree_one_ancestor(self): method test_single_tree_unordered_nodes (line 4935) | def test_single_tree_unordered_nodes(self): method test_single_tree_two_ancestors (line 4945) | def test_single_tree_two_ancestors(self): method test_single_tree_no_ancestors (line 4955) | def test_single_tree_no_ancestors(self): method test_single_tree_samples_or_ancestors_not_in_tree (line 4962) | def test_single_tree_samples_or_ancestors_not_in_tree(self): method test_single_tree_ancestors_descend_from_other_ancestors (line 4971) | def test_single_tree_ancestors_descend_from_other_ancestors(self): method test_single_tree_internal_samples (line 4981) | def test_single_tree_internal_samples(self): method test_single_tree_samples_and_ancestors_overlap (line 4991) | def test_single_tree_samples_and_ancestors_overlap(self): method test_single_tree_unary_ancestor (line 5001) | def test_single_tree_unary_ancestor(self): method test_single_tree_ancestors_descend_from_samples (line 5011) | def test_single_tree_ancestors_descend_from_samples(self): method test_single_tree_samples_descend_from_samples (line 5021) | def test_single_tree_samples_descend_from_samples(self): method test_multiple_trees_to_single_tree (line 5031) | def test_multiple_trees_to_single_tree(self): method test_multiple_trees_one_ancestor (line 5041) | def test_multiple_trees_one_ancestor(self): method verify (line 5051) | def verify(self, ts, sample_nodes, ancestral_nodes): method test_sim_single_coalescent_tree (line 5088) | def test_sim_single_coalescent_tree(self): method test_sim_coalescent_trees (line 5095) | def test_sim_coalescent_trees(self): method test_sim_coalescent_trees_internal_samples (line 5102) | def test_sim_coalescent_trees_internal_samples(self): method test_sim_many_multiroot_trees (line 5110) | def test_sim_many_multiroot_trees(self): method test_sim_wright_fisher_generations (line 5119) | def test_sim_wright_fisher_generations(self): class TestMutationParent (line 5137) | class TestMutationParent: method verify_parents (line 5145) | def verify_parents(self, ts): method test_example (line 5154) | def test_example(self): method test_single_muts (line 5206) | def test_single_muts(self): method test_with_jukes_cantor (line 5212) | def test_with_jukes_cantor(self): method test_with_jukes_cantor_multiple_per_node (line 5222) | def test_with_jukes_cantor_multiple_per_node(self): method verify_branch_mutations (line 5232) | def verify_branch_mutations(self, ts, mutations_per_branch): method test_single_tree_one_mutation_per_branch (line 5237) | def test_single_tree_one_mutation_per_branch(self): method test_single_tree_two_mutations_per_branch (line 5241) | def test_single_tree_two_mutations_per_branch(self): method test_single_tree_three_mutations_per_branch (line 5245) | def test_single_tree_three_mutations_per_branch(self): method test_single_multiroot_tree_recurrent_mutations (line 5249) | def test_single_multiroot_tree_recurrent_mutations(self): method test_many_multiroot_trees_recurrent_mutations (line 5255) | def test_many_multiroot_trees_recurrent_mutations(self): class TestMutationEdge (line 5263) | class TestMutationEdge: method verify_mutation_edge (line 5264) | def verify_mutation_edge(self, ts): method verify_branch_mutations (line 5288) | def verify_branch_mutations(self, ts, mutations_per_branch): method test_single_tree_one_mutation_per_branch (line 5293) | def test_single_tree_one_mutation_per_branch(self): method test_single_tree_two_mutations_per_branch (line 5297) | def test_single_tree_two_mutations_per_branch(self): method test_single_tree_three_mutations_per_branch (line 5301) | def test_single_tree_three_mutations_per_branch(self): method test_single_multiroot_tree_recurrent_mutations (line 5305) | def test_single_multiroot_tree_recurrent_mutations(self): method test_many_multiroot_trees_recurrent_mutations (line 5311) | def test_many_multiroot_trees_recurrent_mutations(self): method test_balanced_binary_tree (line 5320) | def test_balanced_binary_tree(self, n, mutations_per_branch): class TestMutationTime (line 5331) | class TestMutationTime: method verify_times (line 5339) | def verify_times(self, ts): method test_example (line 5351) | def test_example(self): method test_single_muts (line 5413) | def test_single_muts(self): method test_with_jukes_cantor (line 5419) | def test_with_jukes_cantor(self): method test_with_jukes_cantor_multiple_per_node (line 5429) | def test_with_jukes_cantor_multiple_per_node(self): method verify_branch_mutations (line 5439) | def verify_branch_mutations(self, ts, mutations_per_branch): method test_single_tree_one_mutation_per_branch (line 5444) | def test_single_tree_one_mutation_per_branch(self): method test_single_tree_two_mutations_per_branch (line 5448) | def test_single_tree_two_mutations_per_branch(self): method test_single_tree_three_mutations_per_branch (line 5452) | def test_single_tree_three_mutations_per_branch(self): method test_single_multiroot_tree_recurrent_mutations (line 5456) | def test_single_multiroot_tree_recurrent_mutations(self): method test_many_multiroot_trees_recurrent_mutations (line 5462) | def test_many_multiroot_trees_recurrent_mutations(self): class TestSimpleTreeAlgorithm (line 5470) | class TestSimpleTreeAlgorithm: method test_zero_nodes (line 5477) | def test_zero_nodes(self): method test_one_node (line 5490) | def test_one_node(self): method test_single_coalescent_tree (line 5504) | def test_single_coalescent_tree(self): method test_coalescent_trees (line 5512) | def test_coalescent_trees(self): class TestVirtualRootAPIs (line 5525) | class TestVirtualRootAPIs(ExampleTopologyMixin): method verify (line 5530) | def verify(self, ts): class TestSampleLists (line 5602) | class TestSampleLists(ExampleTopologyMixin): method verify (line 5607) | def verify(self, ts): class TestOneSampleRoot (line 5651) | class TestOneSampleRoot(ExampleTopologyMixin): method verify (line 5657) | def verify(self, ts): class RootThreshold (line 5684) | class RootThreshold(ExampleTopologyMixin): method verify (line 5689) | def verify(self, ts): class TestRootThreshold1 (line 5753) | class TestRootThreshold1(RootThreshold): class TestRootThreshold2 (line 5757) | class TestRootThreshold2(RootThreshold): class TestRootThreshold3 (line 5761) | class TestRootThreshold3(RootThreshold): class TestRootThreshold4 (line 5765) | class TestRootThreshold4(RootThreshold): class TestRootThreshold10 (line 5769) | class TestRootThreshold10(RootThreshold): class TestSquashEdges (line 5773) | class TestSquashEdges: method do_squash (line 5778) | def do_squash(self, ts, compare_lib=True): method test_simple_case (line 5790) | def test_simple_case(self): method test_simple_case_unordered_intervals (line 5818) | def test_simple_case_unordered_intervals(self): method test_simple_case_unordered_children (line 5843) | def test_simple_case_unordered_children(self): method test_simple_case_unordered_children_and_intervals (line 5871) | def test_simple_case_unordered_children_and_intervals(self): method test_squash_multiple_parents_and_children (line 5899) | def test_squash_multiple_parents_and_children(self): method test_squash_overlapping_intervals (line 5934) | def test_squash_overlapping_intervals(self): method verify_slice_and_squash (line 5953) | def verify_slice_and_squash(self, ts): method test_sim_single_coalescent_tree (line 5995) | def test_sim_single_coalescent_tree(self): method test_sim_big_coalescent_trees (line 6000) | def test_sim_big_coalescent_trees(self): function squash_edges (line 6006) | def squash_edges(ts): function reduce_topology (line 6032) | def reduce_topology(ts): class TestReduceTopology (line 6089) | class TestReduceTopology: method verify (line 6095) | def verify(self, ts): method test_no_recombination_one_site (line 6166) | def test_no_recombination_one_site(self): method test_simple_recombination_one_site (line 6173) | def test_simple_recombination_one_site(self): method test_simple_recombination_fixed_sites (line 6180) | def test_simple_recombination_fixed_sites(self): method get_integer_edge_ts (line 6187) | def get_integer_edge_ts(self, n, m): method test_integer_edges_one_site (line 6196) | def test_integer_edges_one_site(self): method test_integer_edges_all_sites (line 6203) | def test_integer_edges_all_sites(self): method test_simple_recombination_site_at_zero (line 6211) | def test_simple_recombination_site_at_zero(self): method test_simple_recombination (line 6218) | def test_simple_recombination(self): method test_large_recombination (line 6222) | def test_large_recombination(self): method test_no_recombination (line 6226) | def test_no_recombination(self): method test_no_mutation (line 6230) | def test_no_mutation(self): method test_zero_sites (line 6234) | def test_zero_sites(self): method test_branch_sites (line 6241) | def test_branch_sites(self): method test_jiggled_samples (line 6246) | def test_jiggled_samples(self): function search_sorted (line 6252) | def search_sorted(a, v): class TestSearchSorted (line 6274) | class TestSearchSorted: method verify (line 6279) | def verify(self, a): method test_range (line 6293) | def test_range(self): method test_negative_range (line 6297) | def test_negative_range(self): method test_random_unit_interval (line 6301) | def test_random_unit_interval(self): method test_random_interval (line 6308) | def test_random_interval(self): method test_random_negative (line 6317) | def test_random_negative(self): method test_edge_cases (line 6326) | def test_edge_cases(self): class TestDeleteSites (line 6332) | class TestDeleteSites: method ts_with_4_sites (line 6337) | def ts_with_4_sites(self): method test_remove_by_index (line 6346) | def test_remove_by_index(self): method test_remove_all (line 6357) | def test_remove_all(self): method test_remove_repeated_sites (line 6364) | def test_remove_repeated_sites(self): method test_remove_different_orders (line 6372) | def test_remove_different_orders(self): method test_remove_bad (line 6380) | def test_remove_bad(self): method verify_removal (line 6389) | def verify_removal(self, ts, remove_sites): method test_simple_random_metadata (line 6419) | def test_simple_random_metadata(self): method test_simple_mixed_length_states (line 6425) | def test_simple_mixed_length_states(self): method test_jukes_cantor_random_metadata (line 6434) | def test_jukes_cantor_random_metadata(self): method test_jukes_cantor_many_mutations (line 6443) | def test_jukes_cantor_many_mutations(self): method test_jukes_cantor_one_site (line 6451) | def test_jukes_cantor_one_site(self): class TestKeepSingleInterval (line 6459) | class TestKeepSingleInterval(unittest.TestCase): method test_slice_unchanged (line 6464) | def test_slice_unchanged(self): method test_slice_by_tree_positions (line 6472) | def test_slice_by_tree_positions(self): method test_slice_by_position (line 6506) | def test_slice_by_position(self): method test_slice_unsimplified (line 6512) | def test_slice_unsimplified(self): method test_slice_coordinates (line 6521) | def test_slice_coordinates(self): method test_slice_migrations (line 6536) | def test_slice_migrations(self): class TestKeepIntervals (line 6568) | class TestKeepIntervals(TopologyTestCase): method example_intervals (line 6574) | def example_intervals(self, tables): method do_keep_intervals (line 6584) | def do_keep_intervals( method test_migration_error (line 6594) | def test_migration_error(self): method test_bad_intervals (line 6608) | def test_bad_intervals(self): method test_one_interval (line 6617) | def test_one_interval(self): method test_two_intervals (line 6627) | def test_two_intervals(self): method test_ten_intervals (line 6637) | def test_ten_intervals(self): method test_hundred_intervals (line 6647) | def test_hundred_intervals(self): method test_regular_intervals (line 6657) | def test_regular_intervals(self): method test_no_edges_sites (line 6666) | def test_no_edges_sites(self): method verify (line 6677) | def verify(self, tables): method test_empty_tables (line 6682) | def test_empty_tables(self): method test_single_tree_jukes_cantor (line 6686) | def test_single_tree_jukes_cantor(self): method test_single_tree_multichar_mutations (line 6691) | def test_single_tree_multichar_mutations(self): method test_many_trees_infinite_sites (line 6696) | def test_many_trees_infinite_sites(self): method test_many_trees_sequence_length_infinite_sites (line 6702) | def test_many_trees_sequence_length_infinite_sites(self): method test_wright_fisher_unsimplified (line 6709) | def test_wright_fisher_unsimplified(self): method test_wright_fisher_initial_generation (line 6723) | def test_wright_fisher_initial_generation(self): method test_wright_fisher_initial_generation_no_deep_history (line 6733) | def test_wright_fisher_initial_generation_no_deep_history(self): method test_wright_fisher_unsimplified_multiple_roots (line 6748) | def test_wright_fisher_unsimplified_multiple_roots(self): method test_wright_fisher_simplified (line 6762) | def test_wright_fisher_simplified(self): class TestKeepDeleteIntervalsExamples (line 6778) | class TestKeepDeleteIntervalsExamples: method test_tables_single_tree_keep_middle (line 6783) | def test_tables_single_tree_keep_middle(self): method test_tables_single_tree_delete_middle (line 6791) | def test_tables_single_tree_delete_middle(self): method test_ts_single_tree_keep_middle (line 6799) | def test_ts_single_tree_keep_middle(self): method test_ts_single_tree_delete_middle (line 6805) | def test_ts_single_tree_delete_middle(self): method test_ts_migrations (line 6811) | def test_ts_migrations(self): class TestTrim (line 6830) | class TestTrim(unittest.TestCase): method add_mutations (line 6835) | def add_mutations(self, ts, position, ancestral_state, derived_states,... method verify_sites (line 6849) | def verify_sites(self, source_tree, trimmed_tree, position_offset): method verify_ltrim (line 6875) | def verify_ltrim(self, source_ts, trimmed_ts): method verify_rtrim (line 6891) | def verify_rtrim(self, source_ts, trimmed_ts): method clear_left_mutate (line 6904) | def clear_left_mutate(self, ts, left, num_sites): method clear_right_mutate (line 6914) | def clear_right_mutate(self, ts, right, num_sites): method clear_left_right_234 (line 6926) | def clear_left_right_234(self, left, right): method migration_sim (line 6952) | def migration_sim(self): method test_ltrim_single_tree (line 6964) | def test_ltrim_single_tree(self): method test_ltrim_single_tree_no_mutations (line 6969) | def test_ltrim_single_tree_no_mutations(self): method test_ltrim_single_tree_tiny_left (line 6974) | def test_ltrim_single_tree_tiny_left(self): method test_ltrim_many_trees (line 6979) | def test_ltrim_many_trees(self): method test_ltrim_many_trees_left_min (line 6984) | def test_ltrim_many_trees_left_min(self): method test_ltrim_many_trees_left_epsilon (line 6989) | def test_ltrim_many_trees_left_epsilon(self): method test_ltrim_empty (line 6994) | def test_ltrim_empty(self): method test_ltrim_multiple_mutations (line 7000) | def test_ltrim_multiple_mutations(self): method test_ltrim_migrations (line 7009) | def test_ltrim_migrations(self): method test_rtrim_single_tree (line 7020) | def test_rtrim_single_tree(self): method test_rtrim_single_tree_no_mutations (line 7025) | def test_rtrim_single_tree_no_mutations(self): method test_rtrim_single_tree_tiny_left (line 7030) | def test_rtrim_single_tree_tiny_left(self): method test_rtrim_many_trees (line 7035) | def test_rtrim_many_trees(self): method test_rtrim_many_trees_left_min (line 7040) | def test_rtrim_many_trees_left_min(self): method test_rtrim_many_trees_left_epsilon (line 7045) | def test_rtrim_many_trees_left_epsilon(self): method test_rtrim_empty (line 7050) | def test_rtrim_empty(self): method test_rtrim_multiple_mutations (line 7056) | def test_rtrim_multiple_mutations(self): method test_rtrim_migrations (line 7065) | def test_rtrim_migrations(self): method test_trim_multiple_mutations (line 7072) | def test_trim_multiple_mutations(self): method test_trims_no_effect (line 7081) | def test_trims_no_effect(self): method test_failure_with_migrations (line 7092) | def test_failure_with_migrations(self): method test_reference_sequence (line 7107) | def test_reference_sequence(self): class TestShift (line 7120) | class TestShift: method test_shift (line 7126) | def test_shift(self, shift): method test_sequence_length (line 7139) | def test_sequence_length(self): method test_empty (line 7146) | def test_empty(self): method test_migrations (line 7154) | def test_migrations(self): method test_provenance (line 7162) | def test_provenance(self): method test_too_negative (line 7173) | def test_too_negative(self): method test_bad_seq_len (line 7178) | def test_bad_seq_len(self): method test_reference_sequence (line 7183) | def test_reference_sequence(self): class TestConcatenate (line 7192) | class TestConcatenate: method test_simple (line 7193) | def test_simple(self): method test_metadata (line 7212) | def test_metadata(self, ts_fixture): method test_multiple (line 7244) | def test_multiple(self): method test_empty (line 7264) | def test_empty(self): method test_samples_at_end (line 7270) | def test_samples_at_end(self): method test_internal_samples (line 7281) | def test_internal_samples(self): method test_some_shared_samples (line 7293) | def test_some_shared_samples(self): method test_wf_sim (line 7308) | def test_wf_sim(self, simplify): method test_provenance (line 7336) | def test_provenance(self): method test_unequal_samples (line 7346) | def test_unequal_samples(self): method test_duplicate_ts (line 7352) | def test_duplicate_ts(self): method test_node_mappings_bad_len (line 7360) | def test_node_mappings_bad_len(self): class TestMissingData (line 7367) | class TestMissingData: method ts_missing_middle (line 7374) | def ts_missing_middle(self): method test_is_isolated (line 7394) | def test_is_isolated(self): method test_is_isolated_bad (line 7411) | def test_is_isolated_bad(self): FILE: python/tests/test_tree_positioning.py class StatefulTree (line 37) | class StatefulTree: method __init__ (line 43) | def __init__(self, ts): method __str__ (line 48) | def __str__(self): method assert_equal (line 54) | def assert_equal(self, other): method next (line 59) | def next(self): # NOQA: A003 method prev (line 73) | def prev(self): method iter_forward (line 91) | def iter_forward(self, index): method seek_forward (line 95) | def seek_forward(self, index): method seek_backward (line 123) | def seek_backward(self, index): method iter_backward (line 151) | def iter_backward(self, index): function check_iters_forward (line 156) | def check_iters_forward(ts): function check_iters_back (line 202) | def check_iters_back(ts): function check_forward_back_sweep (line 253) | def check_forward_back_sweep(ts): function check_seek_forward_out_range_is_empty (line 279) | def check_seek_forward_out_range_is_empty(ts, index): function check_seek_backward_out_range_is_empty (line 288) | def check_seek_backward_out_range_is_empty(ts, index): function check_seek_forward_from_null (line 297) | def check_seek_forward_from_null(ts, index): function check_seek_backward_from_null (line 305) | def check_seek_backward_from_null(ts, index): function check_seek_forward_from_first (line 313) | def check_seek_forward_from_first(ts, index): function check_seek_backward_from_last (line 322) | def check_seek_backward_from_last(ts, index): class TestDirectionSwitching (line 330) | class TestDirectionSwitching: method ts (line 338) | def ts(self): method test_iter_backward_matches_iter_forward (line 342) | def test_iter_backward_matches_iter_forward(self, index): method test_prev_from_seek_forward (line 351) | def test_prev_from_seek_forward(self, index): method test_seek_forward_from_prev (line 360) | def test_seek_forward_from_prev(self, index): method test_seek_forward_from_null (line 370) | def test_seek_forward_from_null(self, index): method test_seek_forward_next_null (line 374) | def test_seek_forward_next_null(self): method test_next_from_seek_backward (line 382) | def test_next_from_seek_backward(self, index): method test_seek_backward_from_next (line 391) | def test_seek_backward_from_next(self, index): method test_seek_backward_from_null (line 401) | def test_seek_backward_from_null(self, index): method test_seek_backward_prev_null (line 405) | def test_seek_backward_prev_null(self): method test_seek_forward_out_range_is_empty (line 413) | def test_seek_forward_out_range_is_empty(self, index): method test_seek_backward_out_range_is_empty (line 418) | def test_seek_backward_out_range_is_empty(self, index): class TestTreeIndexesStep (line 423) | class TestTreeIndexesStep: method ts (line 424) | def ts(self): method test_tree_position_step_forward (line 428) | def test_tree_position_step_forward(self, index): method test_tree_position_step_backward (line 438) | def test_tree_position_step_backward(self, index): method test_tree_position_step_invalid_direction (line 447) | def test_tree_position_step_invalid_direction(self): class TestSeeking (line 454) | class TestSeeking: method ts (line 456) | def ts(self): method test_seek_forward_from_null (line 462) | def test_seek_forward_from_null(self, index): method test_seek_forward_from_first (line 467) | def test_seek_forward_from_first(self, index): method test_seek_last_from_index (line 472) | def test_seek_last_from_index(self, index): method test_seek_backward_from_null (line 482) | def test_seek_backward_from_null(self, index): method test_seek_backward_from_last (line 487) | def test_seek_backward_from_last(self, index): method test_seek_first_from_index (line 492) | def test_seek_first_from_index(self, index): method test_seek_forward_out_range_is_empty (line 502) | def test_seek_forward_out_range_is_empty(self, index): method test_seek_backward_out_range_is_empty (line 507) | def test_seek_backward_out_range_is_empty(self, index): class TestAllTreesTs (line 512) | class TestAllTreesTs: method test_forward_full (line 514) | def test_forward_full(self, n): method test_back_full (line 519) | def test_back_full(self, n): method test_forward_back (line 524) | def test_forward_back(self, n): class TestManyTreesSimulationExample (line 529) | class TestManyTreesSimulationExample: method ts (line 531) | def ts(self): method test_seek_forward_from_null (line 539) | def test_seek_forward_from_null(self, index): method test_seek_forward_from_mid (line 544) | def test_seek_forward_from_mid(self, num_trees): method test_seek_backward_from_null (line 556) | def test_seek_backward_from_null(self, index): method test_seek_backward_from_mid (line 561) | def test_seek_backward_from_mid(self, num_trees): method test_seek_forward_out_range_is_empty (line 572) | def test_seek_forward_out_range_is_empty(self, index): method test_seek_backward_out_range_is_empty (line 577) | def test_seek_backward_out_range_is_empty(self, index): method test_forward_full (line 581) | def test_forward_full(self): method test_back_full (line 584) | def test_back_full(self): class TestSuiteExamples (line 588) | class TestSuiteExamples: method test_forward_full (line 590) | def test_forward_full(self, ts): method test_back_full (line 594) | def test_back_full(self, ts): method test_seek_forward_from_null (line 598) | def test_seek_forward_from_null(self, ts): method test_seek_forward_from_first (line 603) | def test_seek_forward_from_first(self, ts): method test_seek_backward_from_null (line 608) | def test_seek_backward_from_null(self, ts): method test_seek_backward_from_last (line 613) | def test_seek_backward_from_last(self, ts): method test_seek_forward_out_range_is_empty (line 618) | def test_seek_forward_out_range_is_empty(self, ts): method test_seek_backward_out_range_is_empty (line 623) | def test_seek_backward_out_range_is_empty(self, ts): FILE: python/tests/test_tree_stats.py function cached_np (line 70) | def cached_np(func): function subset_combos (line 89) | def subset_combos(*args, p=0.5, min_tests=3): function path_length (line 114) | def path_length(tr, x, y): function suppress_division_by_zero_warning (line 128) | def suppress_division_by_zero_warning(): function windowed_tree_stat (line 138) | def windowed_tree_stat(ts, stat, windows, span_normalise=True): function naive_branch_general_stat (line 171) | def naive_branch_general_stat( function branch_general_stat (line 207) | def branch_general_stat( function windowed_sitewise_stat (line 300) | def windowed_sitewise_stat(ts, sigma, windows, span_normalise=True): function naive_site_general_stat (line 316) | def naive_site_general_stat( function site_general_stat (line 347) | def site_general_stat( function naive_node_general_stat (line 427) | def naive_node_general_stat( function node_general_stat (line 450) | def node_general_stat( function general_stat (line 519) | def general_stat( function upper_tri_to_matrix (line 547) | def upper_tri_to_matrix(x): class StatsTestCase (line 568) | class StatsTestCase: method assertListAlmostEqual (line 573) | def assertListAlmostEqual(self, x, y): method assertArrayEqual (line 578) | def assertArrayEqual(self, x, y): method assertArrayAlmostEqual (line 581) | def assertArrayAlmostEqual(self, x, y, atol=1e-6, rtol=1e-7): method identity_f (line 584) | def identity_f(self, ts): method cumsum_f (line 587) | def cumsum_f(self, ts): method sum_f (line 590) | def sum_f(self, ts, k=1): class TopologyExamplesMixin (line 594) | class TopologyExamplesMixin: method test_single_tree_sequence_length (line 601) | def test_single_tree_sequence_length(self): method test_single_tree_multiple_roots (line 605) | def test_single_tree_multiple_roots(self): method test_many_trees (line 610) | def test_many_trees(self, ts_4_recomb_fixture): method test_short_sequence_length (line 616) | def test_short_sequence_length(self): method test_wright_fisher_slow (line 622) | def test_wright_fisher_slow(self, wf_fixture_slow): method test_wright_fisher (line 626) | def test_wright_fisher(self, wf_fixture): method test_empty_ts (line 630) | def test_empty_ts(self): method test_non_sample_ancestry (line 639) | def test_non_sample_ancestry(self): function ts_6_fixture (line 665) | def ts_6_fixture(): function ts_10_recomb_fixture (line 671) | def ts_10_recomb_fixture(): function ts_10_mut_fixture (line 677) | def ts_10_mut_fixture(): function ts_10_mut_recomb_fixture (line 685) | def ts_10_mut_recomb_fixture(): function ts_4_recomb_fixture (line 691) | def ts_4_recomb_fixture(): function ts_12_highrecomb_fixture (line 697) | def ts_12_highrecomb_fixture(): function ts_44_recomb_fixture (line 703) | def ts_44_recomb_fixture(): function ts_ancestry_10_fixture (line 709) | def ts_ancestry_10_fixture(): function ts_6_length_factory_fixture (line 715) | def ts_6_length_factory_fixture(): function wf_fixture_sims (line 728) | def wf_fixture_sims(): function wf_fixture (line 784) | def wf_fixture(wf_fixture_sims, request): function wf_fixture_slow (line 796) | def wf_fixture_slow(wf_fixture_sims, request): function four_taxa_test_case (line 808) | def four_taxa_test_case(): function four_taxa_test_case_afs (line 863) | def four_taxa_test_case_afs(four_taxa_test_case): class MutatedTopologyExamplesMixin (line 947) | class MutatedTopologyExamplesMixin: method test_single_tree_no_sites (line 954) | def test_single_tree_no_sites(self, ts_6_fixture): method test_ghost_allele (line 959) | def test_ghost_allele(self): method test_ghost_allele_all_ancestral (line 976) | def test_ghost_allele_all_ancestral(self): method test_non_sample_ancestry (line 993) | def test_non_sample_ancestry(self): method test_single_tree_infinite_sites (line 1022) | def test_single_tree_infinite_sites(self, ts_10_mut_fixture): method test_single_tree_sites_no_mutations (line 1027) | def test_single_tree_sites_no_mutations(self, ts_6_fixture): method test_single_tree_jukes_cantor (line 1035) | def test_single_tree_jukes_cantor(self, ts_10_mut_fixture): method test_single_tree_single_site_many_silent (line 1040) | def test_single_tree_single_site_many_silent(self, ts_6_fixture): method test_single_tree_multichar_mutations (line 1045) | def test_single_tree_multichar_mutations(self, ts_10_mut_fixture): method test_many_trees_infinite_sites (line 1050) | def test_many_trees_infinite_sites(self, ts_10_mut_recomb_fixture): method test_many_trees_sequence_length_infinite_sites (line 1057) | def test_many_trees_sequence_length_infinite_sites( method test_wright_fisher (line 1064) | def test_wright_fisher(self, wf_fixture): method test_wright_fisher_slow (line 1069) | def test_wright_fisher_slow(self, wf_fixture_slow): method test_empty_ts (line 1074) | def test_empty_ts(self): function example_sample_sets (line 1082) | def example_sample_sets(ts, min_size=1): function example_sample_set_index_pairs (line 1104) | def example_sample_set_index_pairs(sample_sets): function example_sample_set_index_triples (line 1112) | def example_sample_set_index_triples(sample_sets): function example_sample_set_index_quads (line 1120) | def example_sample_set_index_quads(sample_sets): function example_windows (line 1127) | def example_windows(ts): class WeightStatsMixin (line 1139) | class WeightStatsMixin: method example_weights (line 1145) | def example_weights(self, ts, min_size=1): method transform_weights (line 1179) | def transform_weights(self, W): method verify (line 1186) | def verify(self, ts): method verify_definition (line 1192) | def verify_definition(self, ts, W, windows, summary_func, ts_method, d... class SampleSetStatsMixin (line 1222) | class SampleSetStatsMixin: method verify (line 1228) | def verify(self, ts): method verify_definition (line 1236) | def verify_definition( class KWaySampleSetStatsMixin (line 1269) | class KWaySampleSetStatsMixin(SampleSetStatsMixin): method verify_definition (line 1275) | def verify_definition( class TwoWaySampleSetStatsMixin (line 1300) | class TwoWaySampleSetStatsMixin(KWaySampleSetStatsMixin): method verify (line 1306) | def verify(self, ts): class ThreeWaySampleSetStatsMixin (line 1316) | class ThreeWaySampleSetStatsMixin(KWaySampleSetStatsMixin): method verify (line 1322) | def verify(self, ts): class FourWaySampleSetStatsMixin (line 1332) | class FourWaySampleSetStatsMixin(KWaySampleSetStatsMixin): method verify (line 1338) | def verify(self, ts): function site_diversity (line 1353) | def site_diversity(ts, sample_sets, windows=None, span_normalise=True): function branch_diversity (line 1384) | def branch_diversity(ts, sample_sets, windows=None, span_normalise=True): function node_diversity (line 1414) | def node_diversity(ts, sample_sets, windows=None, span_normalise=True): function diversity (line 1444) | def diversity(ts, sample_sets, windows=None, mode="site", span_normalise... class TestDiversity (line 1459) | class TestDiversity(StatsTestCase, SampleSetStatsMixin): method verify_sample_sets (line 1463) | def verify_sample_sets(self, ts, sample_sets, windows): class TestBranchDiversity (line 1473) | class TestBranchDiversity(TestDiversity, TopologyExamplesMixin): class TestNodeDiversity (line 1477) | class TestNodeDiversity(TestDiversity, TopologyExamplesMixin): class TestSiteDiversity (line 1481) | class TestSiteDiversity(TestDiversity, MutatedTopologyExamplesMixin): function site_segregating_sites (line 1490) | def site_segregating_sites(ts, sample_sets, windows=None, span_normalise... function branch_segregating_sites (line 1511) | def branch_segregating_sites(ts, sample_sets, windows=None, span_normali... function node_segregating_sites (line 1537) | def node_segregating_sites(ts, sample_sets, windows=None, span_normalise... function segregating_sites (line 1564) | def segregating_sites(ts, sample_sets, windows=None, mode="site", span_n... class TestSegregatingSites (line 1578) | class TestSegregatingSites(StatsTestCase, SampleSetStatsMixin): method verify_sample_sets (line 1582) | def verify_sample_sets(self, ts, sample_sets, windows): class TestBranchSegregatingSites (line 1594) | class TestBranchSegregatingSites(TestSegregatingSites, TopologyExamplesM... class TestNodeSegregatingSites (line 1598) | class TestNodeSegregatingSites(TestSegregatingSites, TopologyExamplesMix... class TestSiteSegregatingSites (line 1602) | class TestSiteSegregatingSites(TestSegregatingSites, MutatedTopologyExam... class TestBranchSegregatingSitesProperties (line 1606) | class TestBranchSegregatingSitesProperties(StatsTestCase, TopologyExampl... method verify (line 1607) | def verify(self, ts): function site_tajimas_d (line 1635) | def site_tajimas_d(ts, sample_sets, windows=None): function tajimas_d (line 1674) | def tajimas_d(ts, sample_sets, windows=None, mode="site", span_normalise... class TestTajimasD (line 1681) | class TestTajimasD(StatsTestCase, SampleSetStatsMixin): method verify (line 1685) | def verify(self, ts): method get_windows (line 1690) | def get_windows(self, ts): method verify_persite_tajimas_d (line 1695) | def verify_persite_tajimas_d(self, ts, sample_sets): class TestSiteTajimasD (line 1709) | class TestSiteTajimasD(TestTajimasD, MutatedTopologyExamplesMixin): function branch_Y1 (line 1718) | def branch_Y1(ts, sample_sets, windows=None, span_normalise=True): function site_Y1 (line 1765) | def site_Y1(ts, sample_sets, windows=None, span_normalise=True): function node_Y1 (line 1802) | def node_Y1(ts, sample_sets, windows=None, span_normalise=True): function Y1 (line 1832) | def Y1(ts, sample_sets, windows=None, mode="site", span_normalise=True): class TestY1 (line 1840) | class TestY1(StatsTestCase, SampleSetStatsMixin): method verify_sample_sets (line 1844) | def verify_sample_sets(self, ts, sample_sets, windows): class TestBranchY1 (line 1855) | class TestBranchY1(TestY1, TopologyExamplesMixin): class TestNodeY1 (line 1859) | class TestNodeY1(TestY1, TopologyExamplesMixin): class TestSiteY1 (line 1863) | class TestSiteY1(TestY1, MutatedTopologyExamplesMixin): function site_divergence (line 1872) | def site_divergence(ts, sample_sets, indexes, windows=None, span_normali... function branch_divergence (line 1904) | def branch_divergence(ts, sample_sets, indexes, windows=None, span_norma... function node_divergence (line 1935) | def node_divergence(ts, sample_sets, indexes, windows=None, span_normali... function divergence (line 1966) | def divergence( class TestDivergence (line 1986) | class TestDivergence(StatsTestCase, TwoWaySampleSetStatsMixin): method verify_sample_sets_indexes (line 1990) | def verify_sample_sets_indexes(self, ts, sample_sets, indexes, windows): class TestBranchDivergence (line 2004) | class TestBranchDivergence(TestDivergence, TopologyExamplesMixin): class TestNodeDivergence (line 2008) | class TestNodeDivergence(TestDivergence, TopologyExamplesMixin): class TestSiteDivergence (line 2012) | class TestSiteDivergence(TestDivergence, MutatedTopologyExamplesMixin): function site_genetic_relatedness (line 2021) | def site_genetic_relatedness( function branch_genetic_relatedness (line 2073) | def branch_genetic_relatedness( function node_genetic_relatedness (line 2135) | def node_genetic_relatedness( function genetic_relatedness (line 2197) | def genetic_relatedness( class TestGeneticRelatedness (line 2232) | class TestGeneticRelatedness(StatsTestCase, TwoWaySampleSetStatsMixin): method verify_definition (line 2236) | def verify_definition( method verify_sample_sets_indexes (line 2300) | def verify_sample_sets_indexes(self, ts, sample_sets, indexes, windows): method test_shapes (line 2345) | def test_shapes(self, proportion): method test_single_sample_set_self_comparison (line 2436) | def test_single_sample_set_self_comparison(self, ts_12_highrecomb_fixt... method test_single_sample_set_invalid_indexes (line 2455) | def test_single_sample_set_invalid_indexes(self, ts_12_highrecomb_fixt... class TestBranchGeneticRelatedness (line 2477) | class TestBranchGeneticRelatedness(TestGeneticRelatedness, TopologyExamp... method test_simple_tree_noncentred (line 2481) | def test_simple_tree_noncentred(self, polarised): class TestNodeGeneticRelatedness (line 2531) | class TestNodeGeneticRelatedness(TestGeneticRelatedness, TopologyExample... class TestSiteGeneticRelatedness (line 2535) | class TestSiteGeneticRelatedness(TestGeneticRelatedness, MutatedTopology... method test_match_K_c0 (line 2538) | def test_match_K_c0(self): function genetic_relatedness_matrix (line 2575) | def genetic_relatedness_matrix( function genetic_relatedness_weighted (line 2644) | def genetic_relatedness_weighted( function example_index_pairs (line 2690) | def example_index_pairs(weights): class TestGeneticRelatednessWeighted (line 2698) | class TestGeneticRelatednessWeighted(StatsTestCase, WeightStatsMixin): method verify_definition (line 2702) | def verify_definition( method verify (line 2761) | def verify(self, ts): method verify_weighted_stat (line 2768) | def verify_weighted_stat(self, ts, W, indexes, windows): class TestBranchGeneticRelatednessWeighted (line 2803) | class TestBranchGeneticRelatednessWeighted( class TestNodeGeneticRelatednessWeighted (line 2809) | class TestNodeGeneticRelatednessWeighted( class TestSiteGeneticRelatednessWeighted (line 2815) | class TestSiteGeneticRelatednessWeighted( class TestGeneticRelatednessWeightedSimpleExamples (line 2825) | class TestGeneticRelatednessWeightedSimpleExamples: method fixture (line 2830) | def fixture(self): method test_no_arguments_site (line 2838) | def test_no_arguments_site(self): method test_windows_site (line 2844) | def test_windows_site(self): method test_no_arguments_branch (line 2851) | def test_no_arguments_branch(self): method test_windows_branch (line 2857) | def test_windows_branch(self): method test_indexes_1D (line 2863) | def test_indexes_1D(self): method test_indexes_2D (line 2870) | def test_indexes_2D(self): method test_indexes_2D_windows (line 2877) | def test_indexes_2D_windows(self): class TestGeneticRelatednessWeightedErrors (line 2887) | class TestGeneticRelatednessWeightedErrors: method ts (line 2888) | def ts(self): method test_bad_weight_size (line 2892) | def test_bad_weight_size(self, W): method test_no_indexes_with_non_2_cols (line 2897) | def test_no_indexes_with_non_2_cols(self, cols): method test_bad_index_shapes (line 2904) | def test_bad_index_shapes(self, indexes): function single_site_Fst (line 2916) | def single_site_Fst(ts, sample_sets, indexes): class TestFst (line 2952) | class TestFst(StatsTestCase, TwoWaySampleSetStatsMixin): method verify (line 2956) | def verify(self, ts): method verify_persite_Fst (line 2962) | def verify_persite_Fst(self, ts, sample_sets, indexes): class FstInterfaceMixin (line 2975) | class FstInterfaceMixin: method test_interface (line 2976) | def test_interface(self): class TestSiteFst (line 2990) | class TestSiteFst(TestFst, MutatedTopologyExamplesMixin, FstInterfaceMix... class TestNodeFst (line 2998) | class TestNodeFst(StatsTestCase, FstInterfaceMixin): class TestBranchFst (line 3002) | class TestBranchFst(StatsTestCase, FstInterfaceMixin): function branch_Y2 (line 3011) | def branch_Y2(ts, sample_sets, indexes, windows=None, span_normalise=True): function site_Y2 (line 3060) | def site_Y2(ts, sample_sets, indexes, windows=None, span_normalise=True): function node_Y2 (line 3099) | def node_Y2(ts, sample_sets, indexes, windows=None, span_normalise=True): function Y2 (line 3130) | def Y2(ts, sample_sets, indexes=None, windows=None, mode="site", span_no... class TestY2 (line 3140) | class TestY2(StatsTestCase, TwoWaySampleSetStatsMixin): method verify_sample_sets_indexes (line 3144) | def verify_sample_sets_indexes(self, ts, sample_sets, indexes, windows): class TestBranchY2 (line 3158) | class TestBranchY2(TestY2, TopologyExamplesMixin): class TestNodeY2 (line 3162) | class TestNodeY2(TestY2, TopologyExamplesMixin): class TestSiteY2 (line 3166) | class TestSiteY2(TestY2, MutatedTopologyExamplesMixin): function branch_Y3 (line 3175) | def branch_Y3(ts, sample_sets, indexes, windows=None, span_normalise=True): function site_Y3 (line 3225) | def site_Y3(ts, sample_sets, indexes, windows=None, span_normalise=True): function node_Y3 (line 3264) | def node_Y3(ts, sample_sets, indexes, windows=None, span_normalise=True): function Y3 (line 3302) | def Y3(ts, sample_sets, indexes=None, windows=None, mode="site", span_no... class TestY3 (line 3312) | class TestY3(StatsTestCase, ThreeWaySampleSetStatsMixin): method verify_sample_sets_indexes (line 3316) | def verify_sample_sets_indexes(self, ts, sample_sets, indexes, windows): class TestBranchY3 (line 3329) | class TestBranchY3(TestY3, TopologyExamplesMixin): class TestNodeY3 (line 3333) | class TestNodeY3(TestY3, TopologyExamplesMixin): class TestSiteY3 (line 3337) | class TestSiteY3(TestY3, MutatedTopologyExamplesMixin): function branch_f2 (line 3346) | def branch_f2(ts, sample_sets, indexes, windows=None, span_normalise=True): function site_f2 (line 3384) | def site_f2(ts, sample_sets, indexes, windows=None, span_normalise=True): function node_f2 (line 3432) | def node_f2(ts, sample_sets, indexes, windows=None, span_normalise=True): function f2 (line 3467) | def f2(ts, sample_sets, indexes=None, windows=None, mode="site", span_no... class Testf2 (line 3480) | class Testf2(StatsTestCase, TwoWaySampleSetStatsMixin): method verify_sample_sets_indexes (line 3484) | def verify_sample_sets_indexes(self, ts, sample_sets, indexes, windows): class TestBranchf2 (line 3502) | class TestBranchf2(Testf2, TopologyExamplesMixin): class TestNodef2 (line 3506) | class TestNodef2(Testf2, TopologyExamplesMixin): class TestSitef2 (line 3510) | class TestSitef2(Testf2, MutatedTopologyExamplesMixin): function branch_f3 (line 3519) | def branch_f3(ts, sample_sets, indexes, windows=None, span_normalise=True): function site_f3 (line 3557) | def site_f3(ts, sample_sets, indexes, windows=None, span_normalise=True): function node_f3 (line 3606) | def node_f3(ts, sample_sets, indexes, windows=None, span_normalise=True): function f3 (line 3651) | def f3(ts, sample_sets, indexes=None, windows=None, mode="site", span_no... class Testf3 (line 3664) | class Testf3(StatsTestCase, ThreeWaySampleSetStatsMixin): method verify_sample_sets_indexes (line 3668) | def verify_sample_sets_indexes(self, ts, sample_sets, indexes, windows): class TestBranchf3 (line 3685) | class TestBranchf3(Testf3, TopologyExamplesMixin): class TestNodef3 (line 3689) | class TestNodef3(Testf3, TopologyExamplesMixin): class TestSitef3 (line 3693) | class TestSitef3(Testf3, MutatedTopologyExamplesMixin): function branch_f4 (line 3702) | def branch_f4(ts, sample_sets, indexes, windows=None, span_normalise=True): function site_f4 (line 3741) | def site_f4(ts, sample_sets, indexes, windows=None, span_normalise=True): function node_f4 (line 3791) | def node_f4(ts, sample_sets, indexes, windows=None, span_normalise=True): function f4 (line 3840) | def f4(ts, sample_sets, indexes=None, windows=None, mode="site", span_no... class Testf4 (line 3852) | class Testf4(StatsTestCase, FourWaySampleSetStatsMixin): method verify_sample_sets_indexes (line 3856) | def verify_sample_sets_indexes(self, ts, sample_sets, indexes, windows): class TestBranchf4 (line 3873) | class TestBranchf4(Testf4, TopologyExamplesMixin): class TestNodef4 (line 3877) | class TestNodef4(Testf4, TopologyExamplesMixin): class TestSitef4 (line 3881) | class TestSitef4(Testf4, MutatedTopologyExamplesMixin): function fold (line 3890) | def fold(x, dims): function foldit (line 3910) | def foldit(A): function fold_windowed (line 3920) | def fold_windowed(X): class TestFold (line 3927) | class TestFold: method test_examples (line 3932) | def test_examples(self): method test_branch_folded (line 3962) | def test_branch_folded(self, ts_ancestry_10_fixture): method test_site_folded (line 3972) | def test_site_folded(self, ts_ancestry_10_fixture): function naive_site_allele_frequency_spectrum (line 3986) | def naive_site_allele_frequency_spectrum( function naive_branch_allele_frequency_spectrum (line 4046) | def naive_branch_allele_frequency_spectrum( function naive_allele_frequency_spectrum (line 4115) | def naive_allele_frequency_spectrum( function branch_allele_frequency_spectrum (line 4141) | def branch_allele_frequency_spectrum( function site_allele_frequency_spectrum (line 4251) | def site_allele_frequency_spectrum( function allele_frequency_spectrum (line 4345) | def allele_frequency_spectrum( class TestAlleleFrequencySpectrum (line 4371) | class TestAlleleFrequencySpectrum(StatsTestCase, SampleSetStatsMixin): method verify_unwrapped_sample_set (line 4375) | def verify_unwrapped_sample_set(self, ts, sample_set): method verify_single_sample_set (line 4383) | def verify_single_sample_set(self, ts): method verify_sample_sets (line 4409) | def verify_sample_sets(self, ts, sample_sets, windows, time_windows=No... class TestBranchAlleleFrequencySpectrum (line 4467) | class TestBranchAlleleFrequencySpectrum( method generate_params (line 4472) | def generate_params(self, ts): method verify (line 4483) | def verify(self, ts): method test_simple_example (line 4487) | def test_simple_example(self): class TestSiteAlleleFrequencySpectrum (line 4499) | class TestSiteAlleleFrequencySpectrum( method test_simple_example (line 4504) | def test_simple_example(self): class TestBranchAlleleFrequencySpectrumProperties (line 4514) | class TestBranchAlleleFrequencySpectrumProperties(StatsTestCase, Topolog... method verify (line 4515) | def verify(self, ts): class TestWindowedTreeStat (line 4556) | class TestWindowedTreeStat(StatsTestCase): method get_tree_sequence (line 4563) | def get_tree_sequence(self): method test_all_trees (line 4568) | def test_all_trees(self): method test_single_interval (line 4581) | def test_single_interval(self): class TestSampleSets (line 4590) | class TestSampleSets(StatsTestCase): method get_example_ts (line 4595) | def get_example_ts(self, ts): method test_duplicate_samples (line 4599) | def test_duplicate_samples(self, ts_10_mut_recomb_fixture): method test_empty_sample_set (line 4609) | def test_empty_sample_set(self, ts_10_mut_recomb_fixture): method test_non_samples (line 4621) | def test_non_samples(self, ts_10_mut_recomb_fixture): method test_span_normalise (line 4632) | def test_span_normalise(self, ts_10_mut_recomb_fixture): class TestSampleSetIndexes (line 4664) | class TestSampleSetIndexes(StatsTestCase): method get_example_ts (line 4670) | def get_example_ts(self, ts_10_mut_fixture): method test_2_way_default (line 4675) | def test_2_way_default(self, ts_10_mut_fixture): method test_3_way_default (line 4690) | def test_3_way_default(self, ts_10_mut_fixture): method test_4_way_default (line 4703) | def test_4_way_default(self, ts_10_mut_fixture): method test_2_way_combinations (line 4716) | def test_2_way_combinations(self, ts_10_mut_fixture): method test_3_way_combinations (line 4727) | def test_3_way_combinations(self, ts_10_mut_fixture): method test_4_way_combinations (line 4738) | def test_4_way_combinations(self, ts_10_mut_fixture): method test_errors (line 4749) | def test_errors(self, ts_10_mut_fixture): class TestGeneralStatInterface (line 4760) | class TestGeneralStatInterface(StatsTestCase): method get_tree_sequence (line 4765) | def get_tree_sequence(self): method test_function_cannot_update_state (line 4769) | def test_function_cannot_update_state(self): method test_default_mode (line 4798) | def test_default_mode(self, ts_10_recomb_fixture): method test_bad_mode (line 4805) | def test_bad_mode(self, ts_10_recomb_fixture): method test_bad_window_strings (line 4812) | def test_bad_window_strings(self): method test_bad_summary_function (line 4821) | def test_bad_summary_function(self): method test_nonnumpy_summary_function (line 4829) | def test_nonnumpy_summary_function(self): class TestGeneralBranchStats (line 4837) | class TestGeneralBranchStats(StatsTestCase): method compare_general_stat (line 4842) | def compare_general_stat(self, ts, W, f, windows=None, polarised=False): method test_simple_identity_f_w_zeros (line 4854) | def test_simple_identity_f_w_zeros(self, ts_12_highrecomb_fixture): method test_simple_identity_f_w_ones (line 4864) | def test_simple_identity_f_w_ones(self, ts_10_recomb_fixture): method test_simple_cumsum_f_w_ones (line 4877) | def test_simple_cumsum_f_w_ones(self): method test_simple_cumsum_f_w_ones_many_windows (line 4886) | def test_simple_cumsum_f_w_ones_many_windows(self): method test_windows_equal_to_ts_breakpoints (line 4894) | def test_windows_equal_to_ts_breakpoints(self): method test_single_tree_windows (line 4912) | def test_single_tree_windows(self): method test_simple_identity_f_w_zeros_windows (line 4922) | def test_simple_identity_f_w_zeros_windows(self, ts_12_highrecomb_fixt... method test_nonstrict_nonancestral_material (line 4932) | def test_nonstrict_nonancestral_material(self): class TestGeneralSiteStats (line 4991) | class TestGeneralSiteStats(StatsTestCase): method compare_general_stat (line 4996) | def compare_general_stat(self, ts, W, f, windows=None, polarised=False): method test_identity_f_W_0_multiple_alleles (line 5008) | def test_identity_f_W_0_multiple_alleles(self): method test_identity_f_W_0_multiple_alleles_windows (line 5019) | def test_identity_f_W_0_multiple_alleles_windows(self): method test_cumsum_f_W_1_multiple_alleles (line 5031) | def test_cumsum_f_W_1_multiple_alleles(self): method test_cumsum_f_W_1_two_alleles (line 5041) | def test_cumsum_f_W_1_two_alleles(self): class TestGeneralNodeStats (line 5051) | class TestGeneralNodeStats(StatsTestCase): method compare_general_stat (line 5056) | def compare_general_stat(self, ts, W, f, windows=None, polarised=False): method test_simple_sum_f_w_zeros (line 5068) | def test_simple_sum_f_w_zeros(self, ts_12_highrecomb_fixture): method test_simple_sum_f_w_ones (line 5078) | def test_simple_sum_f_w_ones(self, ts_44_recomb_fixture): method test_simple_sum_f_w_ones_notstrict (line 5097) | def test_simple_sum_f_w_ones_notstrict(self, ts_44_recomb_fixture): method test_small_tree_windows_polarised (line 5118) | def test_small_tree_windows_polarised(self): method test_one_window_polarised (line 5131) | def test_one_window_polarised(self, ts_4_recomb_fixture): method test_one_window_unpolarised (line 5139) | def test_one_window_unpolarised(self, ts_4_recomb_fixture): method test_many_windows (line 5147) | def test_many_windows(self): method test_one_tree (line 5158) | def test_one_tree(self): function covsq (line 5183) | def covsq(x, y): function corsq (line 5189) | def corsq(x, y): function site_trait_covariance (line 5196) | def site_trait_covariance(ts, W, windows=None, span_normalise=True): function branch_trait_covariance (line 5228) | def branch_trait_covariance(ts, W, windows=None, span_normalise=True): function node_trait_covariance (line 5267) | def node_trait_covariance(ts, W, windows=None, span_normalise=True): function trait_covariance (line 5301) | def trait_covariance(ts, W, windows=None, mode="site", span_normalise=Tr... class TestTraitCovariance (line 5310) | class TestTraitCovariance(StatsTestCase, WeightStatsMixin): method get_example_ts (line 5314) | def get_example_ts(self, ts_10_mut_recomb_fixture): method transform_weights (line 5319) | def transform_weights(self, W): method verify_weighted_stat (line 5326) | def verify_weighted_stat(self, ts, W, windows): method verify_interface (line 5334) | def verify_interface(self, ts, ts_method): method verify_centering (line 5343) | def verify_centering(self, ts, method, ts_method): class TraitCovarianceMixin (line 5362) | class TraitCovarianceMixin: method test_interface (line 5363) | def test_interface(self, ts_10_mut_recomb_fixture): method test_normalisation (line 5367) | def test_normalisation(self, ts_10_mut_recomb_fixture): method test_errors (line 5371) | def test_errors(self, ts_10_mut_recomb_fixture): class TestBranchTraitCovariance (line 5380) | class TestBranchTraitCovariance( class TestNodeTraitCovariance (line 5387) | class TestNodeTraitCovariance( class TestSiteTraitCovariance (line 5393) | class TestSiteTraitCovariance( function site_trait_correlation (line 5404) | def site_trait_correlation(ts, W, windows=None, span_normalise=True): function branch_trait_correlation (line 5440) | def branch_trait_correlation(ts, W, windows=None, span_normalise=True): function node_trait_correlation (line 5485) | def node_trait_correlation(ts, W, windows=None, span_normalise=True): function trait_correlation (line 5525) | def trait_correlation(ts, W, windows=None, mode="site", span_normalise=T... class TestTraitCorrelation (line 5534) | class TestTraitCorrelation(TestTraitCovariance): method transform_weights (line 5538) | def transform_weights(self, W): method verify_weighted_stat (line 5549) | def verify_weighted_stat(self, ts, W, windows): method test_errors (line 5563) | def test_errors(self, ts_10_mut_recomb_fixture): method verify_standardising (line 5573) | def verify_standardising(self, ts, method, ts_method): class TraitCorrelationMixin (line 5592) | class TraitCorrelationMixin: method test_interface (line 5593) | def test_interface(self, ts_10_mut_recomb_fixture): method test_normalisation (line 5597) | def test_normalisation(self, ts_10_mut_recomb_fixture): class TestBranchTraitCorrelation (line 5604) | class TestBranchTraitCorrelation( class TestNodeTraitCorrelation (line 5611) | class TestNodeTraitCorrelation( class TestSiteTraitCorrelation (line 5617) | class TestSiteTraitCorrelation( function linear_model (line 5638) | def linear_model(y, x, z): function _linear_model (line 5645) | def _linear_model(y, x, z): function site_trait_linear_model (line 5672) | def site_trait_linear_model(ts, W, Z, windows=None, span_normalise=True): function branch_trait_linear_model (line 5707) | def branch_trait_linear_model(ts, W, Z, windows=None, span_normalise=True): function node_trait_linear_model (line 5746) | def node_trait_linear_model(ts, W, Z, windows=None, span_normalise=True): function trait_linear_model (line 5780) | def trait_linear_model(ts, W, Z, windows=None, mode="site", span_normali... class TestTraitLinearModel (line 5789) | class TestTraitLinearModel(StatsTestCase, WeightStatsMixin): method get_example_ts (line 5793) | def get_example_ts(self, ts_10_mut_recomb_fixture): method example_covariates (line 5798) | def example_covariates(self, ts, k_values=None): method transform_weights (line 5820) | def transform_weights(self, W, Z): method transform_covariates (line 5824) | def transform_covariates(self, Z): method verify (line 5833) | def verify(self, ts): method verify_trait_linear_model (line 5842) | def verify_trait_linear_model(self, ts, W, Z, windows): class TraitLinearModelMixin (line 5902) | class TraitLinearModelMixin: method test_interface (line 5903) | def test_interface(self, ts_10_mut_recomb_fixture): method test_errors (line 5923) | def test_errors(self, ts_10_mut_recomb_fixture): method test_deprecation (line 5941) | def test_deprecation(self, ts_10_mut_recomb_fixture): class TestBranchTraitLinearModel (line 5950) | class TestBranchTraitLinearModel( class TestNodeTraitLinearModel (line 5957) | class TestNodeTraitLinearModel( class TestSiteTraitLinearModel (line 5963) | class TestSiteTraitLinearModel( class SampleSetStatTestCase (line 5975) | class SampleSetStatTestCase(StatsTestCase): method compare_sfs (line 5986) | def compare_sfs(self, ts, tree_fn, sample_sets, tsc_fn): method check_sfs_interface (line 6003) | def check_sfs_interface(self, ts): method check_sfs (line 6046) | def check_sfs(self, ts): class BranchSampleSetStatsTestCase (line 6063) | class BranchSampleSetStatsTestCase(SampleSetStatTestCase): method setUp (line 6069) | def setUp(self): method get_ts (line 6073) | def get_ts(self): method test_sfs_interface (line 6080) | def test_sfs_interface(self): method test_branch_sfs (line 6106) | def test_branch_sfs(self): class SpecificTreesTestCase (line 6111) | class SpecificTreesTestCase(StatsTestCase): method test_case_1 (line 6118) | def test_case_1(self): method test_case_odds_and_ends (line 6441) | def test_case_odds_and_ends(self): method test_case_four_taxa (line 6486) | def test_case_four_taxa(self, four_taxa_test_case): method test_case_recurrent_muts (line 6562) | def test_case_recurrent_muts(self): method test_case_2 (line 6633) | def test_case_2(self): class TestOutputDimensions (line 6794) | class TestOutputDimensions(StatsTestCase): method test_one_way_no_window_scalar_stat (line 6799) | def test_one_way_no_window_scalar_stat(self, ts_10_mut_fixture): method test_one_way_one_list_scalar_stat (line 6804) | def test_one_way_one_list_scalar_stat(self, ts_10_mut_fixture): method test_one_way_nested_list_not_scalar_stat (line 6809) | def test_one_way_nested_list_not_scalar_stat(self, ts_10_mut_fixture): method test_one_way_one_window_scalar_stat (line 6814) | def test_one_way_one_window_scalar_stat(self, ts_10_mut_fixture): method test_multi_way_no_window_scalar_stat (line 6822) | def test_multi_way_no_window_scalar_stat(self, ts_10_mut_fixture): method test_multi_way_one_window_not_scalar_stat (line 6833) | def test_multi_way_one_window_not_scalar_stat(self, ts_10_mut_fixture): method test_multi_way_no_indexes_scalar_stat (line 6845) | def test_multi_way_no_indexes_scalar_stat(self, ts_10_mut_fixture): method test_multi_way_indexes_not_scalar_stat (line 6856) | def test_multi_way_indexes_not_scalar_stat(self, ts_10_mut_fixture): method test_afs_default_windows (line 6868) | def test_afs_default_windows(self, ts_10_mut_fixture): method test_afs_windows (line 6883) | def test_afs_windows(self, ts_10_mut_fixture): method test_one_way_stat_default_windows (line 6903) | def test_one_way_stat_default_windows(self, ts_10_mut_fixture): method verify_one_way_stat_windows (line 6923) | def verify_one_way_stat_windows(self, ts, method): method test_diversity_windows (line 6972) | def test_diversity_windows(self, ts_10_mut_fixture): method test_Tajimas_D_windows (line 6976) | def test_Tajimas_D_windows(self, ts_10_mut_fixture): method test_segregating_sites_windows (line 6980) | def test_segregating_sites_windows(self, ts_10_mut_fixture): method test_two_way_stat_default_windows (line 6984) | def test_two_way_stat_default_windows(self, ts_10_mut_fixture): method verify_two_way_stat_windows (line 7008) | def verify_two_way_stat_windows(self, ts, method): method test_divergence_windows (line 7055) | def test_divergence_windows(self, ts_10_mut_fixture): method test_Fst_windows (line 7059) | def test_Fst_windows(self, ts_10_mut_fixture): method test_f2_windows (line 7063) | def test_f2_windows(self, ts_10_mut_fixture): method verify_three_way_stat_windows (line 7067) | def verify_three_way_stat_windows(self, ts, method): method test_Y3_windows (line 7117) | def test_Y3_windows(self, ts_10_mut_fixture): method test_f3_windows (line 7121) | def test_f3_windows(self, ts_10_mut_fixture): class TestTimeUncalibratedErrors (line 7126) | class TestTimeUncalibratedErrors: method test_uncalibrated_time_allele_frequency_spectrum (line 7127) | def test_uncalibrated_time_allele_frequency_spectrum(self, ts_fixture): method test_uncalibrated_time_general_stat (line 7140) | def test_uncalibrated_time_general_stat(self, ts_fixture): class TestGeneralStatCallbackErrors (line 7164) | class TestGeneralStatCallbackErrors: method test_zero_d (line 7165) | def test_zero_d(self, ts_fixture): method test_two_d (line 7175) | def test_two_d(self, ts_fixture): method test_wrong_length (line 7185) | def test_wrong_length(self, ts_fixture): class TestTimeWindows (line 7199) | class TestTimeWindows: method test_bad_time_windows (line 7200) | def test_bad_time_windows(self, four_taxa_test_case): method test_drop_dimension (line 7221) | def test_drop_dimension(self, four_taxa_test_case, mode): method test_four_taxon_example (line 7269) | def test_four_taxon_example(self, four_taxa_test_case_afs): FILE: python/tests/test_util.py class TestCanonicalJSON (line 42) | class TestCanonicalJSON: method test_canonical_json (line 43) | def test_canonical_json(self): class TestUnknownTime (line 70) | class TestUnknownTime: method test_unknown_time_bad_types (line 71) | def test_unknown_time_bad_types(self): method test_unknown_time_scalar (line 79) | def test_unknown_time_scalar(self): method test_unknown_time_array (line 90) | def test_unknown_time_array(self): class TestNumpyArrayCasting (line 111) | class TestNumpyArrayCasting: method test_basic_arrays (line 118) | def test_basic_arrays(self): method test_copy (line 132) | def test_copy(self): method test_empty_arrays (line 147) | def test_empty_arrays(self): method test_bad_types (line 157) | def test_bad_types(self): method test_overflow (line 170) | def test_overflow(self): method test_nonrectangular_input (line 186) | def test_nonrectangular_input(self): class TestIntervalOps (line 203) | class TestIntervalOps: method test_bad_intervals (line 208) | def test_bad_intervals(self): method test_empty_interval_list (line 236) | def test_empty_interval_list(self): method test_negate_intervals (line 240) | def test_negate_intervals(self): class TestStringPacking (line 253) | class TestStringPacking: method test_simple_string_case (line 258) | def test_simple_string_case(self): method verify_packing (line 266) | def verify_packing(self, strings): method test_regular_cases (line 274) | def test_regular_cases(self): method test_random_cases (line 279) | def test_random_cases(self): method test_unicode (line 284) | def test_unicode(self): class TestBytePacking (line 288) | class TestBytePacking: method test_simple_string_case (line 293) | def test_simple_string_case(self): method verify_packing (line 301) | def verify_packing(self, data): method test_random_cases (line 310) | def test_random_cases(self): method test_pickle_packing (line 315) | def test_pickle_packing(self): class TestArrayPacking (line 324) | class TestArrayPacking: method test_simple_case (line 329) | def test_simple_case(self): method verify_packing (line 338) | def verify_packing(self, data): method test_regular_cases (line 348) | def test_regular_cases(self): function test_naturalsize (line 367) | def test_naturalsize(value, expected): function test_format_number (line 375) | def test_format_number(): function test_obj_to_collapsed_html (line 434) | def test_obj_to_collapsed_html(obj, expected): function test_truncate_string_end (line 441) | def test_truncate_string_end(): function test_render_metadata (line 447) | def test_render_metadata(): function test_unicode_table (line 455) | def test_unicode_table(): function test_unicode_table_column_alignments (line 521) | def test_unicode_table_column_alignments(): function test_set_printoptions (line 542) | def test_set_printoptions(): class TestRandomNuceotides (line 552) | class TestRandomNuceotides: method test_length (line 554) | def test_length(self, length): method test_default_alphabet (line 559) | def test_default_alphabet(self): method test_length_keyword (line 563) | def test_length_keyword(self): method test_length_required (line 568) | def test_length_required(self): method test_seed_keyword_only (line 572) | def test_seed_keyword_only(self): method test_seed_equality (line 577) | def test_seed_equality(self, seed): method test_different_seed_not_equal (line 582) | def test_different_seed_not_equal(self): method test_no_seed_different_values (line 587) | def test_no_seed_different_values(self): method test_length_bad_value (line 593) | def test_length_bad_value(self, length): method test_length_bad_type (line 598) | def test_length_bad_type(self, length): FILE: python/tests/test_utilities.py class TestJukesCantor (line 34) | class TestJukesCantor: method verify (line 39) | def verify(self, ts): method test_n10_multiroot (line 46) | def test_n10_multiroot(self): method test_n50_multiroot (line 52) | def test_n50_multiroot(self): method test_silent_mutations (line 58) | def test_silent_mutations(self): class TestCaterpillarTree (line 68) | class TestCaterpillarTree: method verify (line 73) | def verify(self, ts, n): method test_n_2 (line 82) | def test_n_2(self): method test_n_3 (line 86) | def test_n_3(self): method test_n_50 (line 90) | def test_n_50(self): method test_n_5_sites (line 94) | def test_n_5_sites(self): method test_n_5_mutations (line 106) | def test_n_5_mutations(self): method test_n_many_mutations (line 114) | def test_n_many_mutations(self): class TestInsertIndividuals (line 126) | class TestInsertIndividuals: method test_ploidy_1 (line 131) | def test_ploidy_1(self): method test_ploidy_2 (line 139) | def test_ploidy_2(self): method test_ploidy_2_reversed (line 147) | def test_ploidy_2_reversed(self): class TestSortIndividuals (line 157) | class TestSortIndividuals: method test_sort_individuals (line 158) | def test_sort_individuals(self): class TestQuintuplyLinkedTrees (line 183) | class TestQuintuplyLinkedTrees: method test_branch_operations_num_children (line 184) | def test_branch_operations_num_children(self): method test_edge_operations (line 194) | def test_edge_operations(self): method verify_tree_edges (line 202) | def verify_tree_edges(self, quintuply_linked_tree, tts): FILE: python/tests/test_vcf.py function ts_to_pysam (line 55) | def ts_to_pysam(ts, *args, **kwargs): function example_individuals (line 66) | def example_individuals(ts, ploidy=1): function legacy_write_vcf (line 78) | def legacy_write_vcf(tree_sequence, output, ploidy, contig_id): class TestLegacyOutput (line 145) | class TestLegacyOutput: method verify (line 151) | def verify(self, ts, ploidy=1, contig_id="1"): method test_msprime_length_1 (line 170) | def test_msprime_length_1(self): method test_msprime_length_10 (line 176) | def test_msprime_length_10(self): method test_contig_id (line 181) | def test_contig_id(self): class ExamplesMixin (line 187) | class ExamplesMixin: method test_simple_infinite_sites_random_ploidy (line 192) | def test_simple_infinite_sites_random_ploidy(self): method test_simple_infinite_sites_ploidy_2 (line 198) | def test_simple_infinite_sites_ploidy_2(self): method test_simple_infinite_sites_ploidy_2_reversed_samples (line 204) | def test_simple_infinite_sites_ploidy_2_reversed_samples(self): method test_simple_jukes_cantor_random_ploidy (line 211) | def test_simple_jukes_cantor_random_ploidy(self): method test_single_tree_multichar_mutations (line 217) | def test_single_tree_multichar_mutations(self): method test_many_trees_infinite_sites (line 223) | def test_many_trees_infinite_sites(self): method test_many_trees_sequence_length_infinite_sites (line 230) | def test_many_trees_sequence_length_infinite_sites(self): method test_wright_fisher_unsimplified (line 239) | def test_wright_fisher_unsimplified(self): method test_wright_fisher_initial_generation (line 254) | def test_wright_fisher_initial_generation(self): method test_wright_fisher_unsimplified_multiple_roots (line 265) | def test_wright_fisher_unsimplified_multiple_roots(self): method test_wright_fisher_simplified (line 280) | def test_wright_fisher_simplified(self): class TestParseHeaderPysam (line 298) | class TestParseHeaderPysam(ExamplesMixin): method verify (line 303) | def verify(self, ts): class TestInterface (line 328) | class TestInterface: method test_bad_ploidy (line 333) | def test_bad_ploidy(self): method test_individuals_no_nodes_default_args (line 346) | def test_individuals_no_nodes_default_args(self): method test_individuals_no_nodes_as_argument (line 362) | def test_individuals_no_nodes_as_argument(self): method test_ploidy_with_sample_individuals (line 375) | def test_ploidy_with_sample_individuals(self): method test_ploidy_with_no_node_individuals (line 381) | def test_ploidy_with_no_node_individuals(self): method test_empty_individuals (line 389) | def test_empty_individuals(self): method test_duplicate_individuals (line 395) | def test_duplicate_individuals(self): method test_samples_with_and_without_individuals (line 401) | def test_samples_with_and_without_individuals(self): method test_bad_individuals (line 418) | def test_bad_individuals(self): method test_ploidy_positional (line 426) | def test_ploidy_positional(self): method test_only_ploidy_positional (line 432) | def test_only_ploidy_positional(self): class TestLimitations (line 438) | class TestLimitations: method test_many_alleles (line 443) | def test_many_alleles(self): class TestPositionTransformErrors (line 461) | class TestPositionTransformErrors: method get_example_ts (line 466) | def get_example_ts(self): method test_wrong_output_dimensions (line 471) | def test_wrong_output_dimensions(self): method test_bad_func (line 477) | def test_bad_func(self): class TestZeroPositionErrors (line 484) | class TestZeroPositionErrors: method test_zero_position_error (line 489) | def test_zero_position_error(self): method test_no_position_zero_ok (line 504) | def test_no_position_zero_ok(self): class TestIndividualNames (line 513) | class TestIndividualNames: method test_bad_length_individuals (line 518) | def test_bad_length_individuals(self): method test_bad_length_ploidy (line 551) | def test_bad_length_ploidy(self): method test_bad_type (line 567) | def test_bad_type(self): function drop_header (line 583) | def drop_header(s): class TestMasking (line 587) | class TestMasking: method ts (line 589) | def ts(self): method test_site_mask_wrong_size (line 595) | def test_site_mask_wrong_size(self, mask): method test_site_mask_bad_type (line 600) | def test_site_mask_bad_type(self, mask): method test_sample_mask_bad_type (line 606) | def test_sample_mask_bad_type(self, mask): method test_no_masks (line 611) | def test_no_masks(self): method test_no_masks_triploid (line 621) | def test_no_masks_triploid(self): method test_site_0_masked (line 633) | def test_site_0_masked(self): method test_site_0_masked_triploid (line 645) | def test_site_0_masked_triploid(self): method test_site_1_masked (line 657) | def test_site_1_masked(self): method test_all_sites_masked (line 669) | def test_all_sites_masked(self): method test_all_sites_not_masked (line 678) | def test_all_sites_not_masked(self): method test_all_samples_not_masked (line 695) | def test_all_samples_not_masked(self, mask): method test_sample_0_masked (line 709) | def test_sample_0_masked(self, mask): method test_sample_1_masked (line 723) | def test_sample_1_masked(self, mask): method test_all_samples_masked (line 737) | def test_all_samples_masked(self, mask): method test_all_functional_sample_mask (line 748) | def test_all_functional_sample_mask(self): method test_mask_ok_with_pysam (line 766) | def test_mask_ok_with_pysam(self): class TestMissingData (line 784) | class TestMissingData: method ts (line 786) | def ts(self): method test_defaults (line 792) | def test_defaults(self): method test_isolated_as_missing_true (line 800) | def test_isolated_as_missing_true(self): method test_isolated_as_missing_false (line 813) | def test_isolated_as_missing_false(self): method test_ok_with_pysam (line 827) | def test_ok_with_pysam(self): function drop_individuals (line 839) | def drop_individuals(ts): class TestSampleOptions (line 848) | class TestSampleOptions: method ts (line 850) | def ts(self): method test_no_individuals_defaults (line 864) | def test_no_individuals_defaults(self): method test_no_individuals_ploidy_3 (line 875) | def test_no_individuals_ploidy_3(self): method test_no_individuals_ploidy_3_names (line 886) | def test_no_individuals_ploidy_3_names(self): method test_defaults (line 902) | def test_defaults(self): method test_individual_0 (line 913) | def test_individual_0(self): method test_individual_1 (line 926) | def test_individual_1(self): method test_reversed (line 939) | def test_reversed(self): method test_reversed_names (line 953) | def test_reversed_names(self): class TestVcfMapping (line 974) | class TestVcfMapping: method test_mix_sample_non_sample (line 975) | def test_mix_sample_non_sample(self): FILE: python/tests/test_version.py class TestPythonVersion (line 31) | class TestPythonVersion: method test_version (line 36) | def test_version(self): FILE: python/tests/test_wright_fisher.py class WrightFisherSimulator (line 40) | class WrightFisherSimulator: method __init__ (line 54) | def __init__( method random_breakpoint (line 81) | def random_breakpoint(self): method run (line 87) | def run(self, ngens): function wf_sim (line 207) | def wf_sim( class TestSimulation (line 237) | class TestSimulation: method test_one_gen_multipop_mig_no_deep (line 244) | def test_one_gen_multipop_mig_no_deep(self): method test_multipop_mig_deep (line 260) | def test_multipop_mig_deep(self): method test_multipop_mig_no_deep (line 289) | def test_multipop_mig_no_deep(self): method test_non_overlapping_generations (line 319) | def test_non_overlapping_generations(self): method test_overlapping_generations (line 340) | def test_overlapping_generations(self): method test_one_generation_no_deep_history (line 354) | def test_one_generation_no_deep_history(self): method test_many_generations_no_deep_history (line 377) | def test_many_generations_no_deep_history(self): method test_with_mutations (line 397) | def test_with_mutations(self): method test_with_recurrent_mutations (line 423) | def test_with_recurrent_mutations(self): method test_record_individuals_initial_state (line 449) | def test_record_individuals_initial_state(self): method test_record_individuals (line 460) | def test_record_individuals(self): function get_wf_sims (line 477) | def get_wf_sims(seed): class TestSimplify (line 495) | class TestSimplify: method verify_simplify (line 500) | def verify_simplify(self, ts, new_ts, samples, node_map): method verify_haplotypes (line 539) | def verify_haplotypes(self, ts, samples): method test_python_simplify_all_samples (line 557) | def test_python_simplify_all_samples(self, ts): method test_python_simplify_sample_subset (line 566) | def test_python_simplify_sample_subset(self, ts, nsamples): method test_simplify_tables (line 577) | def test_simplify_tables(self, ts, nsamples): method test_simplify_keep_unary (line 588) | def test_simplify_keep_unary(self, ts, nsamples): FILE: python/tests/tsutil.py function random_bytes (line 43) | def random_bytes(max_length): function random_strings (line 51) | def random_strings(max_length): function add_provenance (line 59) | def add_provenance(provenance_table, method_name): function subsample_sites (line 64) | def subsample_sites(ts, num_sites): function insert_branch_mutations (line 82) | def insert_branch_mutations(ts, mutations_per_branch=1, num_states=2): function remove_mutation_times (line 119) | def remove_mutation_times(ts): function insert_discrete_time_mutations (line 125) | def insert_discrete_time_mutations(ts, num_times=4, num_sites=10): function insert_branch_sites (line 154) | def insert_branch_sites(ts, m=1): function insert_multichar_mutations (line 178) | def insert_multichar_mutations(ts, seed=1, max_len=10): function insert_random_ploidy_individuals (line 204) | def insert_random_ploidy_individuals( function insert_random_consistent_individuals (line 237) | def insert_random_consistent_individuals( function insert_individuals (line 276) | def insert_individuals(ts, nodes=None, ploidy=1): function mark_metadata (line 304) | def mark_metadata(ts, table_name, prefix="orig_id:"): function permute_nodes (line 314) | def permute_nodes(ts, node_map): function insert_redundant_breakpoints (line 345) | def insert_redundant_breakpoints(ts): function single_childify (line 361) | def single_childify(ts): function add_random_metadata (line 397) | def add_random_metadata(ts, seed=1, max_length=10): function jiggle_samples (line 472) | def jiggle_samples(ts): function generate_site_mutations (line 490) | def generate_site_mutations( function jukes_cantor (line 527) | def jukes_cantor(ts, num_sites, mu, multiple_per_node=True, seed=None): function caterpillar_tree (line 557) | def caterpillar_tree(n, num_sites=0, num_mutations=1): function compute_mutation_parent (line 590) | def compute_mutation_parent(ts): function py_subset (line 630) | def py_subset( function py_union (line 723) | def py_union(tables, other, nodes, record_provenance=True, add_populatio... function compute_mutation_times (line 803) | def compute_mutation_times(ts): function shuffle_tables (line 846) | def shuffle_tables( function cmp_site (line 950) | def cmp_site(i, j, tables): function cmp_mutation (line 957) | def cmp_mutation(i, j, tables, site_order, num_descendants=None): function cmp_edge (line 984) | def cmp_edge(i, j, tables): function cmp_migration (line 998) | def cmp_migration(i, j, tables): function cmp_individual_canonical (line 1011) | def cmp_individual_canonical(i, j, tables, num_descendants): function compute_mutation_num_descendants (line 1027) | def compute_mutation_num_descendants(tables): function compute_individual_num_descendants (line 1037) | def compute_individual_num_descendants(tables): function py_canonicalise (line 1082) | def py_canonicalise(tables, remove_unreferenced=True): function py_sort (line 1091) | def py_sort(tables, canonical=False): function algorithm_T (line 1157) | def algorithm_T(ts): class QuintuplyLinkedTree (line 1196) | class QuintuplyLinkedTree: method __init__ (line 1197) | def __init__(self, n, root_threshold=1): method __str__ (line 1209) | def __str__(self): method roots (line 1222) | def roots(self): method remove_branch (line 1230) | def remove_branch(self, p, c): method insert_branch (line 1246) | def insert_branch(self, p, c): method is_potential_root (line 1261) | def is_potential_root(self, u): method insert_root (line 1266) | def insert_root(self, root): method remove_root (line 1269) | def remove_root(self, root): method remove_edge (line 1272) | def remove_edge(self, edge): method insert_edge (line 1289) | def insert_edge(self, edge): function algorithm_R (line 1307) | def algorithm_R(ts, root_threshold=1): class SampleListTree (line 1344) | class SampleListTree: method __init__ (line 1353) | def __init__(self, tree_sequence, tracked_samples=None): method __str__ (line 1377) | def __str__(self): method remove_edge (line 1405) | def remove_edge(self, edge): method insert_edge (line 1422) | def insert_edge(self, edge): method update_sample_list (line 1438) | def update_sample_list(self, parent): method sample_lists (line 1473) | def sample_lists(self): class LegacyRootThresholdTree (line 1510) | class LegacyRootThresholdTree: method __init__ (line 1521) | def __init__(self, tree_sequence, root_threshold=1): method __str__ (line 1538) | def __str__(self): method is_root (line 1555) | def is_root(self, u): method roots (line 1558) | def roots(self): method add_root (line 1566) | def add_root(self, root): method remove_root (line 1576) | def remove_root(self, root): method remove_edge (line 1589) | def remove_edge(self, edge): method insert_edge (line 1617) | def insert_edge(self, edge): method iterate (line 1667) | def iterate(self): class Interval (line 1708) | class Interval: method __iter__ (line 1712) | def __iter__(self): class EdgeRange (line 1718) | class EdgeRange: class TreeIndexes (line 1724) | class TreeIndexes: method __init__ (line 1725) | def __init__(self, ts): method __str__ (line 1733) | def __str__(self): method assert_equal (line 1740) | def assert_equal(self, other): method set_null (line 1745) | def set_null(self): method next (line 1750) | def next(self): # NOQA: A003 method prev (line 1796) | def prev(self): method seek_forward (line 1843) | def seek_forward(self, index): method seek_backward (line 1901) | def seek_backward(self, index): method step (line 1963) | def step(self, direction): function mean_descendants (line 1972) | def mean_descendants(ts, reference_sets): function genealogical_nearest_neighbours (line 2037) | def genealogical_nearest_neighbours(ts, focal, reference_sets): function sort_individual_table (line 2093) | def sort_individual_table(tables): function insert_unique_metadata (line 2140) | def insert_unique_metadata(tables, table=None, offset=0): function metadata_map (line 2154) | def metadata_map(tables): function all_trees_ts (line 2168) | def all_trees_ts(n): function all_fields_ts (line 2195) | def all_fields_ts(edge_metadata=True, migrations=True): function insert_uniform_mutations (line 2278) | def insert_uniform_mutations(tables, num_mutations, nodes): function get_table_collection_copy (line 2296) | def get_table_collection_copy(tables, sequence_length): function insert_gap (line 2306) | def insert_gap(ts, position, length): function get_decapitated_examples (line 2344) | def get_decapitated_examples(custom_max=None): function get_gap_examples (line 2362) | def get_gap_examples(custom_max=None): function get_internal_samples_examples (line 2399) | def get_internal_samples_examples(): function get_bottleneck_examples (line 2430) | def get_bottleneck_examples(custom_max=None): function get_back_mutation_examples (line 2455) | def get_back_mutation_examples(): function make_example_tree_sequences (line 2466) | def make_example_tree_sequences(custom_max=None): function get_example_tree_sequences (line 2537) | def get_example_tree_sequences(pytest_params=True, custom_max=None): FILE: python/tskit/cli.py function set_sigpipe_handler (line 37) | def set_sigpipe_handler(): function sys_exit (line 43) | def sys_exit(message): function load_tree_sequence (line 47) | def load_tree_sequence(path): function run_info (line 54) | def run_info(args): function run_trees (line 58) | def run_trees(args): function run_individuals (line 72) | def run_individuals(args): function run_nodes (line 77) | def run_nodes(args): function run_edges (line 82) | def run_edges(args): function run_sites (line 87) | def run_sites(args): function run_mutations (line 92) | def run_mutations(args): function run_populations (line 97) | def run_populations(args): function run_migrations (line 102) | def run_migrations(args): function run_provenances (line 107) | def run_provenances(args): function run_fasta (line 121) | def run_fasta(args): function run_vcf (line 126) | def run_vcf(args): function add_tree_sequence_argument (line 136) | def add_tree_sequence_argument(parser): function add_precision_argument (line 140) | def add_precision_argument(parser): function get_tskit_parser (line 150) | def get_tskit_parser(): function tskit_main (line 270) | def tskit_main(arg_list=None): FILE: python/tskit/combinatorics.py class Rank (line 42) | class Rank(NamedTuple): function equal_chunks (line 59) | def equal_chunks(lst, k): class TreeNode (line 84) | class TreeNode: method as_tables (line 93) | def as_tables(self, *, num_leaves, span, branch_length): method random_binary_tree (line 121) | def random_binary_tree(leaf_labels, rng): method balanced_tree (line 174) | def balanced_tree(cls, leaf_labels, arity): function generate_star (line 194) | def generate_star(num_leaves, *, span, branch_length, record_provenance,... function generate_comb (line 225) | def generate_comb(num_leaves, *, span, branch_length, record_provenance,... function generate_balanced (line 258) | def generate_balanced( function generate_random_binary (line 288) | def generate_random_binary( function split_polytomies (line 317) | def split_polytomies( function treeseq_count_topologies (line 434) | def treeseq_count_topologies(ts, sample_sets): function tree_count_topologies (line 481) | def tree_count_topologies(tree, sample_sets): function combine_child_topologies (line 508) | def combine_child_topologies(topology_counters): class TopologyCounter (line 524) | class TopologyCounter: method __init__ (line 534) | def __init__(self): method __getitem__ (line 537) | def __getitem__(self, sample_set_indexes): method __setitem__ (line 541) | def __setitem__(self, sample_set_indexes, counter): method __iter__ (line 545) | def __iter__(self): method _to_key (line 551) | def _to_key(sample_set_indexes): method __eq__ (line 556) | def __eq__(self, other): method merge (line 560) | def merge(topology_counters): method from_sample (line 572) | def from_sample(sample_set_index): class PartialTopologyCounter (line 584) | class PartialTopologyCounter: method __init__ (line 599) | def __init__(self): method add_sibling_topologies (line 602) | def add_sibling_topologies(self, topology_counter): method join_all_combinations (line 630) | def join_all_combinations(self): method join_topologies (line 650) | def join_topologies(child_topologies): function all_trees (line 660) | def all_trees(num_leaves, span=1): function all_tree_shapes (line 676) | def all_tree_shapes(num_leaves, span=1): function all_tree_labellings (line 689) | def all_tree_labellings(tree, span=1): class RankTree (line 705) | class RankTree: method __init__ (line 712) | def __init__(self, children, label=None): method compute_shape_rank (line 725) | def compute_shape_rank(self): method compute_label_rank (line 766) | def compute_label_rank(self): method num_labellings (line 818) | def num_labellings(self): method rank (line 822) | def rank(self): method shape_rank (line 825) | def shape_rank(self): method label_rank (line 830) | def label_rank(self): method unrank (line 837) | def unrank(num_leaves, rank, labels=None): method shape_unrank (line 850) | def shape_unrank(n, shape_rank): method label_unrank (line 864) | def label_unrank(self, label_rank, labels=None): method canonical_order (line 894) | def canonical_order(c): method from_tsk_tree_node (line 901) | def from_tsk_tree_node(tree, u): method from_tsk_tree (line 917) | def from_tsk_tree(tree): method to_tsk_tree (line 923) | def to_tsk_tree(self, span=1, branch_length=1): method all_labelled_trees (line 964) | def all_labelled_trees(n): method all_unlabelled_trees (line 972) | def all_unlabelled_trees(n): method all_subtree_pairings (line 987) | def all_subtree_pairings(grouped_part): method all_labellings (line 1003) | def all_labellings(tree, labels=None): method label_all_groups (line 1021) | def label_all_groups(groups, labels): method label_tree_group (line 1035) | def label_tree_group(trees, labels): method _newick (line 1050) | def _newick(self): method newick (line 1055) | def newick(self): method label (line 1059) | def label(self): method labelled (line 1062) | def labelled(self): method min_label (line 1065) | def min_label(self): method is_leaf (line 1068) | def is_leaf(self): method leaf_partition (line 1071) | def leaf_partition(self): method group_children_by_num_leaves (line 1074) | def group_children_by_num_leaves(self): method group_children_by_shape (line 1080) | def group_children_by_shape(self): method __eq__ (line 1086) | def __eq__(self, other): method __ne__ (line 1098) | def __ne__(self, other): method shape_equal (line 1101) | def shape_equal(self, other): method is_canonical (line 1110) | def is_canonical(self): method is_symmetrical (line 1120) | def is_symmetrical(self): function num_shapes (line 1136) | def num_shapes(n): function num_tree_pairings (line 1146) | def num_tree_pairings(part): function num_labellings (line 1163) | def num_labellings(n, shape_rk): function children_shape_ranks (line 1167) | def children_shape_ranks(rank, n): function children_label_ranks (line 1205) | def children_label_ranks(child_groups, rank, labels): function group_rank (line 1238) | def group_rank(g): function num_list_of_group_labellings (line 1269) | def num_list_of_group_labellings(groups): function num_group_labellings (line 1287) | def num_group_labellings(g): function num_assignments_in_group (line 1299) | def num_assignments_in_group(g): function group_label_ranks (line 1315) | def group_label_ranks(rank, child_group, labels): class Combination (line 1349) | class Combination: method comb (line 1351) | def comb(n, k): method comb_with_replacement (line 1368) | def comb_with_replacement(n, k): method rank (line 1376) | def rank(combination, elements): method from_range_rank (line 1385) | def from_range_rank(combination, n): method unrank (line 1404) | def unrank(rank, elements, k): method with_replacement_rank (line 1418) | def with_replacement_rank(combination, n): method with_replacement_unrank (line 1440) | def with_replacement_unrank(rank, n, k): function set_minus (line 1459) | def set_minus(arr, subset): function partitions (line 1467) | def partitions(n): function rule_asc (line 1478) | def rule_asc(n): function group_by (line 1498) | def group_by(values, equal): function group_partition (line 1513) | def group_partition(part): function merge_tuple (line 1517) | def merge_tuple(tup1, tup2): function isdisjoint (line 1521) | def isdisjoint(iterable1, iterable2): FILE: python/tskit/drawing.py class Element (line 61) | class Element: method __init__ (line 62) | def __init__(self, tag, **kwargs): method __getitem__ (line 76) | def __getitem__(self, key): method __setitem__ (line 79) | def __setitem__(self, key, value): method add (line 82) | def add(self, child): method set_desc (line 86) | def set_desc(self, **kwargs): method _attr_str (line 93) | def _attr_str(self): method tostring (line 107) | def tostring(self): class Drawing (line 134) | class Drawing: method __init__ (line 135) | def __init__(self, size=None, **kwargs): method add (line 153) | def add(self, element): method g (line 156) | def g(self, **kwargs): method rect (line 159) | def rect(self, insert=None, size=None, **kwargs): method circle (line 168) | def circle(self, center=None, r=None, **kwargs): method line (line 176) | def line(self, start=None, end=None, **kwargs): method polyline (line 191) | def polyline(self, points=None, **kwargs): method polygon (line 196) | def polygon(self, points=None, **kwargs): method path (line 201) | def path(self, d=None, **kwargs): method text (line 222) | def text(self, text=None, **kwargs): method style (line 228) | def style(self, content): method tostring (line 235) | def tostring(self, pretty=False): method saveas (line 240) | def saveas(self, path, pretty=False): class Offsets (line 246) | class Offsets: class Timescaling (line 255) | class Timescaling: method __post_init__ (line 264) | def __post_init__(self): method log_transform (line 274) | def log_transform(self, y): method linear_transform (line 282) | def linear_transform(self, y): method with_offset (line 286) | def with_offset(self, y_offset): class SVGString (line 296) | class SVGString(str): method _repr_svg_ (line 299) | def _repr_svg_(self): function check_orientation (line 306) | def check_orientation(orientation): function check_max_time (line 317) | def check_max_time(max_time, allow_numeric=True): function check_min_time (line 328) | def check_min_time(min_time, allow_numeric=True): function check_time_scale (line 341) | def check_time_scale(time_scale): function check_format (line 349) | def check_format(format): # noqa A002 function check_order (line 363) | def check_order(order): function check_x_scale (line 386) | def check_x_scale(x_scale): function check_x_lim (line 400) | def check_x_lim(x_lim, max_x): function check_y_axis (line 420) | def check_y_axis(y_axis): function create_tick_labels (line 433) | def create_tick_labels(tick_values, decimal_places=2): function clip_ts (line 446) | def clip_ts(ts, x_min, x_max, max_num_trees=None): function check_y_ticks (line 546) | def check_y_ticks(ticks: list | Mapping | None) -> Mapping: function rnd (line 558) | def rnd(x): function bold_integer (line 572) | def bold_integer(number): function edge_and_sample_nodes (line 578) | def edge_and_sample_nodes(ts, omit_regions=None): function _postorder_tracked_node_traversal (line 599) | def _postorder_tracked_node_traversal(tree, root, collapse_tracked, key_... function _postorder_tracked_minlex_traversal (line 643) | def _postorder_tracked_minlex_traversal(tree, root=None, *, collapse_tra... function draw_tree (line 674) | def draw_tree( function add_class (line 782) | def add_class(attrs_dict, classes_str): class Plotbox (line 791) | class Plotbox: method set_padding (line 798) | def set_padding(self, top, left, bottom, right): method max_x (line 806) | def max_x(self): method max_y (line 810) | def max_y(self): method top (line 814) | def top(self): # Alias for consistency with top & bottom method left (line 818) | def left(self): # Alias for consistency with top & bottom method bottom (line 822) | def bottom(self): method right (line 826) | def right(self): method width (line 830) | def width(self): method height (line 834) | def height(self): method __post_init__ (line 837) | def __post_init__(self): method _check (line 840) | def _check(self): method draw (line 844) | def draw(self, dwg, add_to, colour="grey"): class SvgPlot (line 870) | class SvgPlot: method __init__ (line 880) | def __init__( method draw (line 910) | def draw(self, path=None): method get_plotbox (line 919) | def get_plotbox(self): method add_text_in_group (line 928) | def add_text_in_group(self, text, add_to, pos, group_class=None, **kwa... class SvgSkippedPlot (line 942) | class SvgSkippedPlot(SvgPlot): method __init__ (line 943) | def __init__( class SvgAxisPlot (line 966) | class SvgAxisPlot(SvgPlot): method __init__ (line 1004) | def __init__( method set_spacing (line 1055) | def set_spacing(self, top=0, left=0, bottom=0, right=0): method get_axes (line 1078) | def get_axes(self): method draw_x_axis (line 1083) | def draw_x_axis( method draw_y_axis (line 1206) | def draw_y_axis( method shade_background (line 1275) | def shade_background( method x_transform (line 1325) | def x_transform(self, x): class SvgTreeSequence (line 1331) | class SvgTreeSequence(SvgAxisPlot): method __init__ (line 1338) | def __init__( method find_used_trees (line 1534) | def find_used_trees(self): method draw_x_axis (line 1554) | def draw_x_axis( class SvgTree (line 1644) | class SvgTree(SvgAxisPlot): method __init__ (line 1659) | def __init__( method process_mutations_over_node (line 1913) | def process_mutations_over_node(self, u, low_bound, high_bound, ignore... method assign_y_coordinates (line 1934) | def assign_y_coordinates( method assign_x_coordinates (line 2054) | def assign_x_coordinates(self): method info_classes (line 2121) | def info_classes(self, focal_node_id): method text_transform (line 2158) | def text_transform(self, position, dy=0): method draw_tree (line 2171) | def draw_tree(self): class TextTreeSequence (line 2362) | class TextTreeSequence: method __init__ (line 2367) | def __init__( method __str__ (line 2437) | def __str__(self): function to_np_unicode (line 2441) | def to_np_unicode(string): function get_left_neighbour (line 2456) | def get_left_neighbour(tree, traversal_order): function get_left_child (line 2484) | def get_left_child(tree, postorder_nodes): function node_time_depth (line 2498) | def node_time_depth(tree, min_branch_length=None, max_time="tree"): class TextTree (line 2545) | class TextTree: method __init__ (line 2551) | def __init__( method __str__ (line 2604) | def __str__(self): class VerticalTextTree (line 2608) | class VerticalTextTree(TextTree): method default_node_label (line 2615) | def default_node_label(self): method _assign_time_positions (line 2618) | def _assign_time_positions(self): method _assign_traversal_positions (line 2626) | def _assign_traversal_positions(self): method _draw (line 2655) | def _draw(self): class HorizontalTextTree (line 2712) | class HorizontalTextTree(TextTree): method default_node_label (line 2719) | def default_node_label(self): method _assign_time_positions (line 2722) | def _assign_time_positions(self): method _assign_traversal_positions (line 2731) | def _assign_traversal_positions(self): method _draw (line 2750) | def _draw(self): FILE: python/tskit/exceptions.py class DuplicatePositionsError (line 36) | class DuplicatePositionsError(TskitException): class ProvenanceValidationError (line 42) | class ProvenanceValidationError(TskitException): class MetadataValidationError (line 48) | class MetadataValidationError(TskitException): class MetadataSchemaValidationError (line 54) | class MetadataSchemaValidationError(TskitException): class MetadataEncodingError (line 60) | class MetadataEncodingError(TskitException): class ImmutableTableError (line 66) | class ImmutableTableError(ValueError): FILE: python/tskit/genotypes.py class Variant (line 38) | class Variant: method __init__ (line 116) | def __init__( method _check_decoded (line 131) | def _check_decoded(self): method site (line 139) | def site(self) -> trees.Site: method alleles (line 147) | def alleles(self) -> tuple[str | None, ...]: method samples (line 157) | def samples(self) -> np.ndarray: method genotypes (line 165) | def genotypes(self) -> np.ndarray: method isolated_as_missing (line 174) | def isolated_as_missing(self) -> bool: method has_missing_data (line 182) | def has_missing_data(self) -> bool: method num_missing (line 191) | def num_missing(self) -> int: method num_alleles (line 198) | def num_alleles(self) -> int: method position (line 211) | def position(self) -> float: method index (line 216) | def index(self) -> int: method __eq__ (line 220) | def __eq__(self, other) -> bool: method decode (line 230) | def decode(self, site_id) -> None: method copy (line 239) | def copy(self) -> Variant: method states (line 251) | def states(self, missing_data_string=None) -> np.ndarray: method counts (line 280) | def counts(self) -> typing.Counter[str | None]: method frequencies (line 302) | def frequencies(self, remove_missing=None) -> dict[str, float]: method __str__ (line 333) | def __str__(self) -> str: method _repr_html_ (line 369) | def _repr_html_(self) -> str: method __repr__ (line 376) | def __repr__(self): function allele_remap (line 391) | def allele_remap(alleles_from, alleles_to): FILE: python/tskit/intervals.py class RateMap (line 39) | class RateMap(collections.abc.Mapping): method __init__ (line 53) | def __init__( method left (line 104) | def left(self): method right (line 111) | def right(self): method mid (line 118) | def mid(self): method span (line 127) | def span(self): method position (line 136) | def position(self): method rate (line 145) | def rate(self): method mass (line 153) | def mass(self): method missing (line 162) | def missing(self): method non_missing (line 170) | def non_missing(self): method num_intervals (line 182) | def num_intervals(self) -> int: method num_missing_intervals (line 191) | def num_missing_intervals(self) -> int: method num_non_missing_intervals (line 199) | def num_non_missing_intervals(self) -> int: method sequence_length (line 207) | def sequence_length(self): method total_mass (line 214) | def total_mass(self): method mean_rate (line 221) | def mean_rate(self): method get_rate (line 229) | def get_rate(self, x): method get_cumulative_mass (line 245) | def get_cumulative_mass(self, x): method find_index (line 261) | def find_index(self, x: float) -> int: method missing_intervals (line 279) | def missing_intervals(self): method asdict (line 296) | def asdict(self): method __iter__ (line 305) | def __iter__(self): method __len__ (line 318) | def __len__(self): method __getitem__ (line 321) | def __getitem__(self, key): method _text_header_and_rows (line 338) | def _text_header_and_rows(self, limit=None): method __str__ (line 358) | def __str__(self): method _repr_html_ (line 369) | def _repr_html_(self): method __repr__ (line 375) | def __repr__(self): method copy (line 382) | def copy(self) -> RateMap: method slice (line 390) | def slice(self, left=None, right=None, *, trim=False) -> RateMap: # n... method uniform (line 440) | def uniform(sequence_length, rate) -> RateMap: method read_hapmap (line 447) | def read_hapmap( FILE: python/tskit/jit/numba.py class EdgeRange (line 38) | class EdgeRange: method __init__ (line 58) | def __init__(self, start, stop, order): class ParentIndex (line 65) | class ParentIndex: method __init__ (line 83) | def __init__(self, edge_index, index_range): class TreeIndex (line 88) | class TreeIndex: method __init__ (line 132) | def __init__(self, ts): method set_null (line 142) | def set_null(self): method next (line 151) | def next(self): # noqa: A003 method prev (line 231) | def prev(self): class NumbaTreeSequence (line 314) | class NumbaTreeSequence: method __init__ (line 378) | def __init__( method tree_index (line 442) | def tree_index(self): method child_index (line 454) | def child_index(self): method parent_index (line 484) | def parent_index(self): function _jitwrap (line 533) | def _jitwrap(max_ancestral_length, max_derived_length, max_inherited_len... function jitwrap (line 612) | def jitwrap(ts): FILE: python/tskit/metadata.py function replace_root_refs (line 51) | def replace_root_refs(obj): class AbstractMetadataCodec (line 84) | class AbstractMetadataCodec(metaclass=abc.ABCMeta): method __init__ (line 89) | def __init__(self, schema: Mapping[str, Any]) -> None: method modify_schema (line 93) | def modify_schema(cls, schema: Mapping) -> Mapping: method is_schema_trivial (line 97) | def is_schema_trivial(cls, schema: Mapping) -> bool: method encode (line 101) | def encode(self, obj: Any) -> bytes: method decode (line 105) | def decode(self, encoded: bytes) -> Any: method numpy_dtype (line 108) | def numpy_dtype(self, schema) -> Any: function register_metadata_codec (line 115) | def register_metadata_codec( class JSONCodec (line 129) | class JSONCodec(AbstractMetadataCodec): method default_validator (line 131) | def default_validator(validator, types, instance, schema): method is_schema_trivial (line 147) | def is_schema_trivial(cls, schema: Mapping) -> bool: method __init__ (line 150) | def __init__(self, schema: Mapping[str, Any]) -> None: method encode (line 163) | def encode(self, obj: Any) -> bytes: method decode (line 171) | def decode(self, encoded: bytes) -> Any: class NOOPCodec (line 187) | class NOOPCodec(AbstractMetadataCodec): method __init__ (line 188) | def __init__(self, schema: Mapping[str, Any]) -> None: method encode (line 191) | def encode(self, data: bytes) -> bytes: method decode (line 194) | def decode(self, data: bytes) -> bytes: class JSONStructCodec (line 198) | class JSONStructCodec(AbstractMetadataCodec): method is_schema_trivial (line 217) | def is_schema_trivial(cls, schema: Mapping) -> bool: method __init__ (line 220) | def __init__(self, schema: Mapping[str, Any]) -> None: method validate_row (line 276) | def validate_row(self, row: Any) -> None: method encode (line 289) | def encode(self, obj: Any) -> bytes: method decode (line 306) | def decode(self, encoded: bytes) -> Any: function binary_format_validator (line 341) | def binary_format_validator(validator, types, instance, schema): function array_length_validator (line 377) | def array_length_validator(validator, types, instance, schema): function required_validator (line 411) | def required_validator(validator, required, instance, schema): class StructCodec (line 497) | class StructCodec(AbstractMetadataCodec): method order_by_index (line 505) | def order_by_index(cls, obj, do_sort=False): method make_decode (line 527) | def make_decode(cls, sub_schema): method make_array_decode (line 545) | def make_array_decode(cls, sub_schema): method make_object_decode (line 581) | def make_object_decode(cls, sub_schema): method make_object_or_null_decode (line 591) | def make_object_or_null_decode(cls, sub_schema): method make_string_decode (line 612) | def make_string_decode(cls, sub_schema): method make_null_decode (line 633) | def make_null_decode(cls, sub_schema): method make_numeric_decode (line 646) | def make_numeric_decode(cls, sub_schema): method make_encode (line 652) | def make_encode(cls, sub_schema): method make_array_encode (line 670) | def make_array_encode(cls, sub_schema): method make_object_encode (line 705) | def make_object_encode(cls, sub_schema): method make_object_or_null_encode (line 728) | def make_object_or_null_encode(cls, sub_schema): method make_string_encode (line 752) | def make_string_encode(cls, sub_schema): method make_null_encode (line 759) | def make_null_encode(cls, sub_schema): method make_numeric_encode (line 763) | def make_numeric_encode(cls, sub_schema): method modify_schema (line 767) | def modify_schema(cls, schema: Mapping) -> Mapping: method __init__ (line 800) | def __init__(self, schema: Mapping[str, Any]) -> None: method encode (line 810) | def encode(self, obj: Any) -> bytes: method decode (line 814) | def decode(self, encoded: bytes) -> Any: method numpy_dtype (line 818) | def numpy_dtype(self, schema): function validate_bytes (line 908) | def validate_bytes(data: bytes | None) -> None: class MetadataSchema (line 915) | class MetadataSchema: method __init__ (line 922) | def __init__(self, schema: Mapping[str, Any] | None) -> None: method __repr__ (line 967) | def __repr__(self) -> str: method __str__ (line 970) | def __str__(self) -> str: method __eq__ (line 980) | def __eq__(self, other) -> bool: method schema (line 984) | def schema(self) -> Mapping[str, Any] | None: method asdict (line 988) | def asdict(self) -> Mapping[str, Any] | None: method validate_and_encode_row (line 996) | def validate_and_encode_row(self, row: Any) -> bytes: method decode_row (line 1009) | def decode_row(self, row: bytes) -> Any: method encode_row (line 1018) | def encode_row(self, row: Any) -> bytes: method numpy_dtype (line 1028) | def numpy_dtype(self) -> Any: method structured_array_from_buffer (line 1031) | def structured_array_from_buffer(self, buffer: Any) -> Any: method permissive_json (line 1039) | def permissive_json(): method null (line 1047) | def null(): function parse_metadata_schema (line 1057) | def parse_metadata_schema(encoded_schema: str) -> MetadataSchema: class _CachedMetadata (line 1077) | class _CachedMetadata: method __get__ (line 1082) | def __get__(self, row, owner): method __set__ (line 1092) | def __set__(self, row, value): function lazy_decode (line 1096) | def lazy_decode(own_init=False): class MetadataProvider (line 1136) | class MetadataProvider: method __init__ (line 1141) | def __init__(self, ll_object): method metadata_schema (line 1145) | def metadata_schema(self) -> MetadataSchema: method metadata_schema (line 1152) | def metadata_schema(self, schema: MetadataSchema) -> None: method metadata (line 1159) | def metadata(self) -> Any: method metadata (line 1166) | def metadata(self, metadata: bytes | dict | None) -> None: method metadata_bytes (line 1171) | def metadata_bytes(self) -> Any: method nbytes (line 1178) | def nbytes(self) -> int: method assert_equals (line 1181) | def assert_equals(self, other: MetadataProvider): class TableMetadataReader (line 1196) | class TableMetadataReader: method metadata_schema (line 1200) | def metadata_schema(self) -> MetadataSchema: method metadata_vector (line 1210) | def metadata_vector(self, key, *, dtype=None, default_value=NOTSET): method _make_row (line 1251) | def _make_row(self, *args): class TableMetadataWriter (line 1255) | class TableMetadataWriter(TableMetadataReader): method metadata_schema (line 1259) | def metadata_schema(self, schema: MetadataSchema) -> None: method packset_metadata (line 1267) | def packset_metadata(self, metadatas): method drop_metadata (line 1281) | def drop_metadata(self, *, keep_schema=False): FILE: python/tskit/provenance.py function get_environment (line 54) | def get_environment(extra_libs=None, include_tskit=True): function get_resources (line 84) | def get_resources(start_time): function get_provenance_dict (line 101) | def get_provenance_dict(parameters=None): function get_schema (line 119) | def get_schema(): function validate_provenance (line 137) | def validate_provenance(provenance): FILE: python/tskit/stats.py class LdCalculator (line 34) | class LdCalculator: method __init__ (line 54) | def __init__(self, tree_sequence): method get_r2 (line 63) | def get_r2(self, a, b): method r2 (line 67) | def r2(self, a, b): method get_r2_array (line 83) | def get_r2_array(self, a, direction=1, max_mutations=None, max_distanc... method r2_array (line 92) | def r2_array( method get_r2_matrix (line 146) | def get_r2_matrix(self): method r2_matrix (line 150) | def r2_matrix(self): FILE: python/tskit/tables.py function _ragged_selection_indices (line 50) | def _ragged_selection_indices(indexed_offsets, lengths64): class IndividualTableRow (line 67) | class IndividualTableRow(util.Dataclass): method __eq__ (line 91) | def __eq__(self, other): class NodeTableRow (line 103) | class NodeTableRow(util.Dataclass): class EdgeTableRow (line 133) | class EdgeTableRow(util.Dataclass): class MigrationTableRow (line 163) | class MigrationTableRow(util.Dataclass): class SiteTableRow (line 201) | class SiteTableRow(util.Dataclass): class MutationTableRow (line 223) | class MutationTableRow(util.Dataclass): method __eq__ (line 255) | def __eq__(self, other): class PopulationTableRow (line 272) | class PopulationTableRow(util.Dataclass): class ProvenanceTableRow (line 285) | class ProvenanceTableRow(util.Dataclass): class TableCollectionIndexes (line 302) | class TableCollectionIndexes(util.Dataclass): method asdict (line 310) | def asdict(self): method nbytes (line 314) | def nbytes(self) -> int: function keep_with_offset (line 326) | def keep_with_offset(keep, data, offset): class BaseTable (line 343) | class BaseTable: method _check_required_args (line 351) | def _check_required_args(self, **kwargs): method nbytes (line 357) | def nbytes(self) -> int: method _equals_internal (line 378) | def _equals_internal(self, other, ignore_metadata=False, *, ignore_tim... method equals (line 395) | def equals(self, other, ignore_metadata=False): method _assert_equals_internal (line 411) | def _assert_equals_internal( method assert_equals (line 428) | def assert_equals(self, other, *, ignore_metadata=False): method _assert_equals (line 441) | def _assert_equals(self, other, *, ignore_metadata=False, ignore_times... method __eq__ (line 503) | def __eq__(self, other): method __len__ (line 506) | def __len__(self): method asdict (line 509) | def asdict(self): method __str__ (line 522) | def __str__(self): method _repr_html_ (line 528) | def _repr_html_(self): method _columns_all_integer (line 537) | def _columns_all_integer(self, *colnames): method _text_header_and_rows (line 544) | def _text_header_and_rows(self, limit=None): function _assert_table_collections_equal (line 590) | def _assert_table_collections_equal( class MutableBaseTable (line 669) | class MutableBaseTable(BaseTable): method __init__ (line 674) | def __init__(self, ll_table, row_class): method _fast_equals (line 678) | def _fast_equals(self, other, **kwargs): method num_rows (line 684) | def num_rows(self) -> int: method max_rows (line 688) | def max_rows(self) -> int: method max_rows_increment (line 692) | def max_rows_increment(self) -> int: method __getattr__ (line 695) | def __getattr__(self, name): method __setattr__ (line 703) | def __setattr__(self, name, value): method _make_row (line 711) | def _make_row(self, *args): method __getitem__ (line 719) | def __getitem__(self, index): method __setitem__ (line 763) | def __setitem__(self, index, new_row): method append (line 800) | def append(self, row): method replace_with (line 821) | def replace_with(self, other): method clear (line 825) | def clear(self): method reset (line 831) | def reset(self): method truncate (line 835) | def truncate(self, num_rows): method keep_rows (line 843) | def keep_rows(self, keep): method __getstate__ (line 868) | def __getstate__(self): method __setstate__ (line 872) | def __setstate__(self, state): method copy (line 876) | def copy(self): method set_columns (line 884) | def set_columns(self, **kwargs): class ImmutableBaseTable (line 892) | class ImmutableBaseTable(BaseTable): method __init__ (line 921) | def __init__(self, ll_tree_sequence, row_indices=None, row_slice=None): method copy (line 942) | def copy(self): method __len__ (line 954) | def __len__(self): method __iter__ (line 957) | def __iter__(self): method _fast_equals (line 972) | def _fast_equals(self, other, *, ignore_metadata=False, ignore_timesta... method __getattr__ (line 997) | def __getattr__(self, name): method _slice_column (line 1036) | def _slice_column(self, full_array, name, is_offset, is_ragged): method _select_column (line 1048) | def _select_column(self, full_array, name, is_offset, is_ragged): method _select_column_offset (line 1061) | def _select_column_offset(self, offset_array, indices): method _select_column_ragged (line 1069) | def _select_column_ragged(self, full_array, name, indices): method __getitem__ (line 1080) | def __getitem__(self, index): method _current_ll_indices (line 1096) | def _current_ll_indices(self): method _resolve_single_index (line 1107) | def _resolve_single_index(self, row_index): method _resolve_selector (line 1113) | def _resolve_selector(self, selector): method _create_row_object (line 1137) | def _create_row_object(self, ll_index): method __setattr__ (line 1151) | def __setattr__(self, name, value): class MutableMetadataTable (line 1166) | class MutableMetadataTable(MutableBaseTable, metadata.TableMetadataWriter): class ImmutableMetadataTable (line 1170) | class ImmutableMetadataTable(ImmutableBaseTable, metadata.TableMetadataR... method metadata_schema (line 1172) | def metadata_schema(self): class IndividualTable (line 1190) | class IndividualTable(MutableMetadataTable): method __init__ (line 1235) | def __init__(self, max_rows_increment=0, ll_table=None): method add_row (line 1240) | def add_row(self, flags=0, location=None, parents=None, metadata=None): method set_columns (line 1266) | def set_columns( method append_columns (line 1333) | def append_columns( method packset_location (line 1391) | def packset_location(self, locations): method packset_parents (line 1406) | def packset_parents(self, parents): method keep_rows (line 1421) | def keep_rows(self, keep): class NodeTable (line 1449) | class NodeTable(MutableMetadataTable): method __init__ (line 1487) | def __init__(self, max_rows_increment=0, ll_table=None): method add_row (line 1492) | def add_row(self, flags=0, time=0, population=-1, individual=-1, metad... method set_columns (line 1516) | def set_columns( method append_columns (line 1571) | def append_columns( class EdgeTable (line 1621) | class EdgeTable(MutableMetadataTable): method __init__ (line 1659) | def __init__(self, max_rows_increment=0, ll_table=None): method add_row (line 1664) | def add_row(self, left, right, parent, child, metadata=None): method set_columns (line 1686) | def set_columns( method append_columns (line 1741) | def append_columns( method squash (line 1783) | def squash(self): class MigrationTable (line 1807) | class MigrationTable(MutableMetadataTable): method __init__ (line 1852) | def __init__(self, max_rows_increment=0, ll_table=None): method add_row (line 1857) | def add_row(self, left, right, node, source, dest, time, metadata=None): method set_columns (line 1881) | def set_columns( method append_columns (line 1945) | def append_columns( class SiteTable (line 2001) | class SiteTable(MutableMetadataTable): method __init__ (line 2039) | def __init__(self, max_rows_increment=0, ll_table=None): method add_row (line 2044) | def add_row(self, position, ancestral_state, metadata=None): method set_columns (line 2064) | def set_columns( method append_columns (line 2123) | def append_columns( method packset_ancestral_state (line 2172) | def packset_ancestral_state(self, ancestral_states): class MutationTable (line 2188) | class MutationTable(MutableMetadataTable): method __init__ (line 2235) | def __init__(self, max_rows_increment=0, ll_table=None): method add_row (line 2240) | def add_row(self, site, node, derived_state, parent=-1, metadata=None,... method set_columns (line 2272) | def set_columns( method append_columns (line 2345) | def append_columns( method packset_derived_state (line 2407) | def packset_derived_state(self, derived_states): method keep_rows (line 2422) | def keep_rows(self, keep): class PopulationTable (line 2450) | class PopulationTable(MutableMetadataTable): method __init__ (line 2474) | def __init__(self, max_rows_increment=0, ll_table=None): method add_row (line 2479) | def add_row(self, metadata=None): method set_columns (line 2497) | def set_columns(self, metadata=None, metadata_offset=None, metadata_sc... method append_columns (line 2528) | def append_columns(self, metadata=None, metadata_offset=None): class ProvenanceTable (line 2551) | class ProvenanceTable(MutableBaseTable): method __init__ (line 2579) | def __init__(self, max_rows_increment=0, ll_table=None): method add_row (line 2584) | def add_row(self, record, timestamp=None): method set_columns (line 2602) | def set_columns( method append_columns (line 2638) | def append_columns( method packset_record (line 2673) | def packset_record(self, records): method packset_timestamp (line 2688) | def packset_timestamp(self, timestamps): method equals (line 2703) | def equals(self, other, ignore_timestamps=False): method assert_equals (line 2716) | def assert_equals(self, other, *, ignore_timestamps=False): class IdentitySegment (line 2730) | class IdentitySegment: method span (line 2744) | def span(self) -> float: class IdentitySegmentList (line 2751) | class IdentitySegmentList(collections.abc.Iterable, collections.abc.Sized): method __init__ (line 2773) | def __init__(self, ll_segment_list): method __iter__ (line 2776) | def __iter__(self): method __len__ (line 2780) | def __len__(self): method __str__ (line 2783) | def __str__(self): method __repr__ (line 2789) | def __repr__(self): method __eq__ (line 2792) | def __eq__(self, other): method total_span (line 2798) | def total_span(self): method left (line 2806) | def left(self): method right (line 2813) | def right(self): method node (line 2820) | def node(self): class IdentitySegments (line 2827) | class IdentitySegments(collections.abc.Mapping): method __init__ (line 2850) | def __init__(self, ll_result, *, max_time, min_span, store_segments, s... method num_segments (line 2858) | def num_segments(self): method num_pairs (line 2865) | def num_pairs(self): method total_span (line 2874) | def total_span(self): method pairs (line 2882) | def pairs(self): method __repr__ (line 2893) | def __repr__(self): method __str__ (line 2898) | def __str__(self): method __getitem__ (line 2917) | def __getitem__(self, key): method __iter__ (line 2921) | def __iter__(self): method __len__ (line 2924) | def __len__(self): class ReferenceSequence (line 2929) | class ReferenceSequence(metadata.MetadataProvider): method __init__ (line 2945) | def __init__(self, ll_reference_sequence): method is_null (line 2949) | def is_null(self) -> bool: method clear (line 2956) | def clear(self): method __repr__ (line 2967) | def __repr__(self): method data (line 2971) | def data(self) -> str: method data (line 2981) | def data(self, value): method url (line 2985) | def url(self) -> str: method url (line 2989) | def url(self, value): method asdict (line 2992) | def asdict(self) -> dict: method __eq__ (line 3000) | def __eq__(self, other): method equals (line 3003) | def equals(self, other, ignore_metadata=False): method assert_equals (line 3010) | def assert_equals(self, other, ignore_metadata=False): method nbytes (line 3024) | def nbytes(self): class TableCollection (line 3030) | class TableCollection(metadata.MetadataProvider): method __init__ (line 3048) | def __init__(self, sequence_length=0, *, ll_tables=None): method individuals (line 3063) | def individuals(self) -> IndividualTable: method individuals (line 3070) | def individuals(self, value): method nodes (line 3074) | def nodes(self) -> NodeTable: method nodes (line 3081) | def nodes(self, value): method edges (line 3085) | def edges(self) -> EdgeTable: method edges (line 3092) | def edges(self, value): method migrations (line 3096) | def migrations(self) -> MigrationTable: method migrations (line 3103) | def migrations(self, value): method sites (line 3107) | def sites(self) -> SiteTable: method sites (line 3114) | def sites(self, value): method mutations (line 3118) | def mutations(self) -> MutationTable: method mutations (line 3125) | def mutations(self, value): method populations (line 3129) | def populations(self) -> PopulationTable: method populations (line 3136) | def populations(self, value): method provenances (line 3140) | def provenances(self) -> ProvenanceTable: method provenances (line 3147) | def provenances(self, value): method indexes (line 3151) | def indexes(self) -> TableCollectionIndexes: method indexes (line 3159) | def indexes(self, indexes): method sequence_length (line 3163) | def sequence_length(self) -> float: method sequence_length (line 3170) | def sequence_length(self, sequence_length): method file_uuid (line 3174) | def file_uuid(self) -> str: method time_units (line 3182) | def time_units(self) -> str: method time_units (line 3189) | def time_units(self, time_units: str) -> None: method has_reference_sequence (line 3192) | def has_reference_sequence(self): method reference_sequence (line 3200) | def reference_sequence(self): method reference_sequence (line 3217) | def reference_sequence(self, value: ReferenceSequence): method asdict (line 3223) | def asdict(self, force_offset_64=False): method table_name_map (line 3241) | def table_name_map(self) -> dict: method name_map (line 3259) | def name_map(self) -> dict: method nbytes (line 3269) | def nbytes(self) -> int: method __str__ (line 3286) | def __str__(self): method equals (line 3317) | def equals( method assert_equals (line 3390) | def assert_equals( method __eq__ (line 3450) | def __eq__(self, other): method __getstate__ (line 3453) | def __getstate__(self): method load (line 3457) | def load(cls, file_or_path, *, skip_tables=False, skip_reference_seque... method dump (line 3491) | def dump(self, file_or_path): method __setstate__ (line 3506) | def __setstate__(self, state): method fromdict (line 3511) | def fromdict(tables_dict): method copy (line 3516) | def copy(self): method tree_sequence (line 3525) | def tree_sequence(self): method simplify (line 3543) | def simplify( method link_ancestors (line 3698) | def link_ancestors(self, samples, ancestors): method map_ancestors (line 3756) | def map_ancestors(self, *args, **kwargs): method sort (line 3760) | def sort(self, edge_start=0, *, site_start=0, mutation_start=0): method sort_individuals (line 3819) | def sort_individuals(self): method canonicalise (line 3829) | def canonicalise(self, remove_unreferenced=None): method compute_mutation_parents (line 3866) | def compute_mutation_parents(self): method compute_mutation_times (line 3883) | def compute_mutation_times(self): method deduplicate_sites (line 3903) | def deduplicate_sites(self): method delete_sites (line 3916) | def delete_sites(self, site_ids, record_provenance=True): method delete_intervals (line 3978) | def delete_intervals(self, intervals, simplify=True, record_provenance... method keep_intervals (line 4005) | def keep_intervals(self, intervals, simplify=True, record_provenance=T... method _check_trim_conditions (line 4075) | def _check_trim_conditions(self): method ltrim (line 4095) | def ltrim(self, record_provenance=True): method rtrim (line 4141) | def rtrim(self, record_provenance=True): method trim (line 4165) | def trim(self, record_provenance=True): method shift (line 4185) | def shift(self, value, *, sequence_length=None, record_provenance=True): method delete_older (line 4224) | def delete_older(self, time): method clear (line 4255) | def clear( method has_index (line 4278) | def has_index(self): method build_index (line 4285) | def build_index(self): method drop_index (line 4292) | def drop_index(self): method subset (line 4300) | def subset( method union (line 4347) | def union( method ibd_segments (line 4404) | def ibd_segments( class ImmutableNodeTable (line 4487) | class ImmutableNodeTable(ImmutableMetadataTable): class ImmutableIndividualTable (line 4501) | class ImmutableIndividualTable(ImmutableMetadataTable): class ImmutableEdgeTable (line 4518) | class ImmutableEdgeTable(ImmutableMetadataTable): class ImmutableMigrationTable (line 4532) | class ImmutableMigrationTable(ImmutableMetadataTable): class ImmutableSiteTable (line 4548) | class ImmutableSiteTable(ImmutableMetadataTable): class ImmutableMutationTable (line 4563) | class ImmutableMutationTable(ImmutableMetadataTable): class ImmutablePopulationTable (line 4581) | class ImmutablePopulationTable(ImmutableMetadataTable): class ImmutableProvenanceTable (line 4588) | class ImmutableProvenanceTable(ImmutableBaseTable): method equals (line 4599) | def equals(self, other, ignore_timestamps=False): method assert_equals (line 4602) | def assert_equals(self, other, *, ignore_timestamps=False): class ImmutableTableCollection (line 4608) | class ImmutableTableCollection(metadata.MetadataProvider): method __init__ (line 4629) | def __init__(self, ll_tree_sequence): method sequence_length (line 4646) | def sequence_length(self): method file_uuid (line 4650) | def file_uuid(self): method time_units (line 4654) | def time_units(self): method reference_sequence (line 4658) | def reference_sequence(self): method metadata_schema (line 4662) | def metadata_schema(self): method metadata (line 4666) | def metadata(self): method metadata_bytes (line 4670) | def metadata_bytes(self): method table_name_map (line 4674) | def table_name_map(self): method indexes (line 4687) | def indexes(self) -> TableCollectionIndexes: method has_index (line 4695) | def has_index(self): method asdict (line 4701) | def asdict(self, force_offset_64=False): method equals (line 4705) | def equals( method assert_equals (line 4732) | def assert_equals( method nbytes (line 4755) | def nbytes(self): method __eq__ (line 4767) | def __eq__(self, other): method __str__ (line 4770) | def __str__(self): method link_ancestors (line 4797) | def link_ancestors(self, samples, ancestors): method map_ancestors (line 4806) | def map_ancestors(self, *args, **kwargs): method copy (line 4837) | def copy(self): method dump (line 4842) | def dump(self, file_or_path): method tree_sequence (line 4845) | def tree_sequence(self): method has_reference_sequence (line 4848) | def has_reference_sequence(self): method __getattr__ (line 4851) | def __getattr__(self, name): method __setattr__ (line 4861) | def __setattr__(self, name, value): FILE: python/tskit/text_formats.py function parse_fam (line 34) | def parse_fam(fam_file): function flexible_file_output (line 96) | def flexible_file_output(ts_export_func): function write_nexus (line 114) | def write_nexus( function wrap_text (line 190) | def wrap_text(text, width): function write_fasta (line 207) | def write_fasta( function _build_newick (line 235) | def _build_newick(tree, *, node, precision, node_labels, include_branch_... function build_newick (line 257) | def build_newick(tree, *, root, precision, node_labels, include_branch_l... function dump_text (line 272) | def dump_text( function text_metadata (line 448) | def text_metadata(base64_metadata, encoding, node): FILE: python/tskit/trees.py class VcfModelMapping (line 61) | class VcfModelMapping: class CoalescenceRecord (line 70) | class CoalescenceRecord(NamedTuple): class Interval (line 79) | class Interval(NamedTuple): method span (line 96) | def span(self) -> float | int: method mid (line 103) | def mid(self) -> float | int: class EdgeDiff (line 110) | class EdgeDiff(NamedTuple): function store_tree_sequence (line 116) | def store_tree_sequence(cls): class Individual (line 131) | class Individual(util.Dataclass): method population (line 182) | def population(self) -> int: method time (line 191) | def time(self) -> int: method __eq__ (line 200) | def __eq__(self, other): class Node (line 213) | class Node(util.Dataclass): method is_sample (line 251) | def is_sample(self): class Edge (line 263) | class Edge(util.Dataclass): method __init__ (line 304) | def __init__( method span (line 323) | def span(self): method interval (line 333) | def interval(self): class Site (line 345) | class Site(util.Dataclass): method __eq__ (line 384) | def __eq__(self, other): method alleles (line 395) | def alleles(self) -> set[str]: class Mutation (line 413) | class Mutation(util.Dataclass): method __init__ (line 488) | def __init__( method __eq__ (line 511) | def __eq__(self, other): class Migration (line 530) | class Migration(util.Dataclass): class Population (line 581) | class Population(util.Dataclass): class Edgeset (line 603) | class Edgeset(util.Dataclass): method __eq__ (line 611) | def __eq__(self, other): class Provenance (line 622) | class Provenance(util.Dataclass): class Tree (line 641) | class Tree: method __init__ (line 687) | def __init__( method copy (line 717) | def copy(self): method _has_isolated_samples (line 734) | def _has_isolated_samples(self): method _make_arrays (line 742) | def _make_arrays(self): method tree_sequence (line 755) | def tree_sequence(self): method root_threshold (line 765) | def root_threshold(self): method __eq__ (line 776) | def __eq__(self, other): method __ne__ (line 782) | def __ne__(self, other): method first (line 785) | def first(self): method last (line 792) | def last(self): method next (line 799) | def next(self): # noqa A002 method prev (line 822) | def prev(self): method clear (line 845) | def clear(self): method seek_index (line 852) | def seek_index(self, index, skip=None): method seek (line 872) | def seek(self, position, skip=None): method rank (line 892) | def rank(self) -> tskit.Rank: method unrank (line 903) | def unrank(num_leaves, rank, *, span=1, branch_length=1) -> Tree: method count_topologies (line 928) | def count_topologies(self, sample_sets=None) -> tskit.TopologyCounter: method get_branch_length (line 978) | def get_branch_length(self, u): method branch_length (line 982) | def branch_length(self, u): method get_total_branch_length (line 1005) | def get_total_branch_length(self): method total_branch_length (line 1010) | def total_branch_length(self): method get_mrca (line 1032) | def get_mrca(self, u, v): method mrca (line 1036) | def mrca(self, *args): method get_tmrca (line 1055) | def get_tmrca(self, u, v): method tmrca (line 1059) | def tmrca(self, *args): method get_parent (line 1086) | def get_parent(self, u): method parent (line 1090) | def parent(self, u): method parent_array (line 1103) | def parent_array(self): method ancestors (line 1118) | def ancestors(self, u): method left_child (line 1130) | def left_child(self, u): method left_child_array (line 1150) | def left_child_array(self): method right_child (line 1165) | def right_child(self, u): method right_child_array (line 1185) | def right_child_array(self): method left_sib (line 1200) | def left_sib(self, u): method left_sib_array (line 1216) | def left_sib_array(self): method right_sib (line 1231) | def right_sib(self, u): method right_sib_array (line 1247) | def right_sib_array(self): method siblings (line 1262) | def siblings(self, u): method num_children_array (line 1290) | def num_children_array(self): method edge (line 1306) | def edge(self, u): method edge_array (line 1319) | def edge_array(self): method left_sample (line 1337) | def left_sample(self, u): method right_sample (line 1340) | def right_sample(self, u): method next_sample (line 1343) | def next_sample(self, u): method virtual_root (line 1347) | def virtual_root(self): method num_edges (line 1358) | def num_edges(self): method left_root (line 1371) | def left_root(self): method right_root (line 1405) | def right_root(self): method get_children (line 1408) | def get_children(self, u): method children (line 1412) | def children(self, u): method get_time (line 1426) | def get_time(self, u): method time (line 1430) | def time(self, u): method depth (line 1443) | def depth(self, u): method get_population (line 1458) | def get_population(self, u): method population (line 1462) | def population(self, u): method is_internal (line 1473) | def is_internal(self, u): method is_leaf (line 1484) | def is_leaf(self, u): method is_isolated (line 1505) | def is_isolated(self, u): method is_sample (line 1519) | def is_sample(self, u): method is_descendant (line 1530) | def is_descendant(self, u, v): method num_nodes (line 1547) | def num_nodes(self): method num_roots (line 1572) | def num_roots(self): method has_single_root (line 1584) | def has_single_root(self): method has_multiple_roots (line 1597) | def has_multiple_roots(self): method roots (line 1610) | def roots(self): method get_root (line 1647) | def get_root(self): method root (line 1652) | def root(self): method is_root (line 1665) | def is_root(self, u) -> bool: method get_index (line 1682) | def get_index(self): method index (line 1687) | def index(self): method get_interval (line 1697) | def get_interval(self): method interval (line 1702) | def interval(self): method get_length (line 1719) | def get_length(self): method length (line 1724) | def length(self): method span (line 1729) | def span(self): method mid (line 1741) | def mid(self): method get_sample_size (line 1753) | def get_sample_size(self): method sample_size (line 1758) | def sample_size(self): method draw_text (line 1763) | def draw_text( method draw_svg (line 1829) | def draw_svg( method draw (line 2015) | def draw( method get_num_mutations (line 2168) | def get_num_mutations(self): method num_mutations (line 2172) | def num_mutations(self): method num_sites (line 2182) | def num_sites(self): method sites (line 2191) | def sites(self): method mutations (line 2205) | def mutations(self): method get_leaves (line 2229) | def get_leaves(self, u): method leaves (line 2236) | def leaves(self, u=None): method _sample_generator (line 2262) | def _sample_generator(self, u): method samples (line 2280) | def samples(self, u=None): method num_children (line 2309) | def num_children(self, u): method get_num_leaves (line 2320) | def get_num_leaves(self, u): method get_num_samples (line 2333) | def get_num_samples(self, u=None): method num_samples (line 2337) | def num_samples(self, u=None): method get_num_tracked_leaves (line 2352) | def get_num_tracked_leaves(self, u): method get_num_tracked_samples (line 2358) | def get_num_tracked_samples(self, u=None): method num_tracked_samples (line 2362) | def num_tracked_samples(self, u=None): method preorder (line 2379) | def preorder(self, u=NULL): method postorder (line 2395) | def postorder(self, u=NULL): method timeasc (line 2411) | def timeasc(self, u=NULL): method timedesc (line 2436) | def timedesc(self, u=NULL): method _preorder_traversal (line 2451) | def _preorder_traversal(self, root): method _postorder_traversal (line 2455) | def _postorder_traversal(self, root): method _inorder_traversal (line 2459) | def _inorder_traversal(self, root): method _levelorder_traversal (line 2475) | def _levelorder_traversal(self, root): method _timeasc_traversal (line 2489) | def _timeasc_traversal(self, root): method _timedesc_traversal (line 2495) | def _timedesc_traversal(self, root): method _minlex_postorder_traversal (line 2501) | def _minlex_postorder_traversal(self, root): method nodes (line 2542) | def nodes(self, root=None, order="preorder"): method _as_newick_fast (line 2624) | def _as_newick_fast(self, *, root, precision, legacy_ms_labels): method as_newick (line 2641) | def as_newick( method newick (line 2752) | def newick( method as_dict_of_dicts (line 2796) | def as_dict_of_dicts(self): method parent_dict (line 2822) | def parent_dict(self): method get_parent_dict (line 2825) | def get_parent_dict(self): method __str__ (line 2833) | def __str__(self): method _repr_html_ (line 2856) | def _repr_html_(self): method map_mutations (line 2863) | def map_mutations(self, genotypes, alleles, ancestral_state=None): method kc_distance (line 2975) | def kc_distance(self, other, lambda_=0.0): method _get_sample_sets (line 2997) | def _get_sample_sets(self): method rf_distance (line 3008) | def rf_distance(self, other): method path_length (line 3043) | def path_length(self, u, v): method distance_between (line 3067) | def distance_between(self, u, v): method b1_index (line 3080) | def b1_index(self): method b2_index (line 3095) | def b2_index(self, base=10): method colless_index (line 3116) | def colless_index(self): method sackin_index (line 3134) | def sackin_index(self): method num_lineages (line 3150) | def num_lineages(self, t): method split_polytomies (line 3168) | def split_polytomies( method generate_star (line 3240) | def generate_star( method generate_balanced (line 3276) | def generate_balanced( method generate_comb (line 3328) | def generate_comb( method generate_random_binary (line 3368) | def generate_random_binary( function load (line 3422) | def load(file, *, skip_tables=False, skip_reference_sequence=False): function parse_individuals (line 3450) | def parse_individuals( function parse_nodes (line 3522) | def parse_nodes(source, strict=True, encoding="utf8", base64_metadata=Tr... function parse_edges (line 3596) | def parse_edges(source, strict=True, table=None, encoding="utf8", base64... function parse_sites (line 3655) | def parse_sites(source, strict=True, encoding="utf8", base64_metadata=Tr... function parse_mutations (line 3705) | def parse_mutations( function parse_populations (line 3781) | def parse_populations( function parse_migrations (line 3823) | def parse_migrations( function load_text (line 3892) | def load_text( class TreeIterator (line 4042) | class TreeIterator: method __init__ (line 4047) | def __init__(self, tree): method __iter__ (line 4052) | def __iter__(self): method __reversed__ (line 4055) | def __reversed__(self): method __next__ (line 4059) | def __next__(self): method __len__ (line 4068) | def __len__(self): class SimpleContainerSequence (line 4072) | class SimpleContainerSequence: method __init__ (line 4082) | def __init__(self, getter, length, order=None): method __len__ (line 4089) | def __len__(self): method __getitem__ (line 4092) | def __getitem__(self, index): class TableMetadataSchemas (line 4097) | class TableMetadataSchemas: class TreeSequence (line 4138) | class TreeSequence: method __init__ (line 4157) | def __init__(self, ll_tree_sequence): method __getstate__ (line 4212) | def __getstate__(self): method __setstate__ (line 4215) | def __setstate__(self, tc): method __eq__ (line 4218) | def __eq__(self, other): method equals (line 4221) | def equals( method ll_tree_sequence (line 4247) | def ll_tree_sequence(self): method get_ll_tree_sequence (line 4250) | def get_ll_tree_sequence(self): method aslist (line 4253) | def aslist(self, **kwargs): method load (line 4271) | def load(cls, file_or_path, *, skip_tables=False, skip_reference_seque... method load_tables (line 4288) | def load_tables(cls, tables, *, build_indexes=False): method dump (line 4293) | def dump(self, file_or_path, zlib_compression=False): method reference_sequence (line 4316) | def reference_sequence(self): method has_reference_sequence (line 4326) | def has_reference_sequence(self): method tables_dict (line 4334) | def tables_dict(self): method tables (line 4343) | def tables(self): method nbytes (line 4370) | def nbytes(self): method dump_tables (line 4378) | def dump_tables(self): method link_ancestors (line 4391) | def link_ancestors(self, samples, ancestors): method dump_text (line 4407) | def dump_text( method __str__ (line 4463) | def __str__(self): method _repr_html_ (line 4493) | def _repr_html_(self): method num_samples (line 4503) | def num_samples(self): method table_metadata_schemas (line 4514) | def table_metadata_schemas(self) -> TableMetadataSchemas: method sample_size (line 4521) | def sample_size(self): method get_sample_size (line 4525) | def get_sample_size(self): method file_uuid (line 4530) | def file_uuid(self): method discrete_genome (line 4534) | def discrete_genome(self): method discrete_time (line 4550) | def discrete_time(self): method min_time (line 4567) | def min_time(self): method max_time (line 4581) | def max_time(self): method sequence_length (line 4595) | def sequence_length(self): method get_sequence_length (line 4609) | def get_sequence_length(self): method metadata (line 4613) | def metadata(self) -> Any: method metadata_schema (line 4620) | def metadata_schema(self) -> metadata_module.MetadataSchema: method time_units (line 4629) | def time_units(self) -> str: method num_edges (line 4636) | def num_edges(self): method get_num_trees (line 4646) | def get_num_trees(self): method num_trees (line 4651) | def num_trees(self): method get_num_sites (line 4662) | def get_num_sites(self): method num_sites (line 4667) | def num_sites(self): method get_num_mutations (line 4677) | def get_num_mutations(self): method num_mutations (line 4682) | def num_mutations(self): method get_num_nodes (line 4692) | def get_num_nodes(self): method num_individuals (line 4697) | def num_individuals(self): method num_nodes (line 4708) | def num_nodes(self): method num_provenances (line 4719) | def num_provenances(self): method num_populations (line 4730) | def num_populations(self): method num_migrations (line 4741) | def num_migrations(self): method max_root_time (line 4752) | def max_root_time(self): method migrations (line 4779) | def migrations(self): method individuals (line 4791) | def individuals(self): method nodes (line 4801) | def nodes(self, *, order=None): method edges (line 4828) | def edges(self): method edgesets (line 4843) | def edgesets(self): method _edge_diffs_forward (line 4874) | def _edge_diffs_forward(self, include_terminal=False): method _edge_diffs_reverse (line 4927) | def _edge_diffs_reverse(self, include_terminal=False): method edge_diffs (line 4980) | def edge_diffs(self, include_terminal=False, *, direction=tskit.FORWARD): method sites (line 5025) | def sites(self): method mutations (line 5037) | def mutations(self): method populations (line 5058) | def populations(self): method provenances (line 5068) | def provenances(self): method breakpoints (line 5078) | def breakpoints(self, as_array=False): method at (line 5102) | def at(self, position, **kwargs): method at_index (line 5122) | def at_index(self, index, **kwargs): method first (line 5139) | def first(self, **kwargs): method last (line 5154) | def last(self, **kwargs): method trees (line 5169) | def trees( method coiterate (line 5230) | def coiterate(self, other, **kwargs): method _check_genomic_range (line 5267) | def _check_genomic_range(self, left, right, ensure_integer=False): method _haplotypes_array (line 5288) | def _haplotypes_array( method haplotypes (line 5344) | def haplotypes( method variants (line 5444) | def variants( method genotype_matrix (line 5563) | def genotype_matrix( method alignments (line 5647) | def alignments( method individuals_population (line 5818) | def individuals_population(self): method individual_populations (line 5832) | def individual_populations(self): method individuals_time (line 5838) | def individuals_time(self): method individual_times (line 5850) | def individual_times(self): method individuals_location (line 5856) | def individuals_location(self): method individual_locations (line 5877) | def individual_locations(self): method individuals_flags (line 5883) | def individuals_flags(self): method individuals_metadata (line 5893) | def individuals_metadata(self): method individuals_nodes (line 5906) | def individuals_nodes(self): method nodes_metadata (line 5920) | def nodes_metadata(self): method nodes_time (line 5933) | def nodes_time(self): method nodes_flags (line 5943) | def nodes_flags(self): method nodes_population (line 5953) | def nodes_population(self): method nodes_individual (line 5963) | def nodes_individual(self): method edges_left (line 5973) | def edges_left(self): method edges_right (line 5983) | def edges_right(self): method edges_parent (line 5993) | def edges_parent(self): method edges_child (line 6003) | def edges_child(self): method edges_metadata (line 6013) | def edges_metadata(self): method sites_position (line 6026) | def sites_position(self): method sites_ancestral_state (line 6036) | def sites_ancestral_state(self): method sites_metadata (line 6052) | def sites_metadata(self): method mutations_site (line 6065) | def mutations_site(self): method mutations_node (line 6079) | def mutations_node(self): method mutations_parent (line 6089) | def mutations_parent(self): method mutations_time (line 6099) | def mutations_time(self): method mutations_derived_state (line 6109) | def mutations_derived_state(self): method mutations_metadata (line 6125) | def mutations_metadata(self): method mutations_edge (line 6138) | def mutations_edge(self): method mutations_inherited_state (line 6150) | def mutations_inherited_state(self): method migrations_left (line 6173) | def migrations_left(self): method migrations_right (line 6183) | def migrations_right(self): method migrations_node (line 6193) | def migrations_node(self): method migrations_source (line 6203) | def migrations_source(self): method migrations_dest (line 6213) | def migrations_dest(self): method migrations_time (line 6223) | def migrations_time(self): method migrations_metadata (line 6233) | def migrations_metadata(self): method populations_metadata (line 6246) | def populations_metadata(self): method indexes_edge_insertion_order (line 6259) | def indexes_edge_insertion_order(self): method indexes_edge_removal_order (line 6270) | def indexes_edge_removal_order(self): method individual (line 6280) | def individual(self, id_): method node (line 6308) | def node(self, id_): method check_index (line 6335) | def check_index(index, length): method edge (line 6346) | def edge(self, id_): method migration (line 6366) | def migration(self, id_): method mutation (line 6396) | def mutation(self, id_): method site (line 6428) | def site(self, id_=None, *, position=None): method population (line 6470) | def population(self, id_): method provenance (line 6486) | def provenance(self, id_): method get_samples (line 6496) | def get_samples(self, population_id=None): method samples (line 6500) | def samples(self, population=None, *, population_id=None, time=None): method as_vcf (line 6551) | def as_vcf(self, *args, **kwargs): method write_vcf (line 6563) | def write_vcf( method write_fasta (line 6727) | def write_fasta( method as_fasta (line 6778) | def as_fasta(self, **kwargs): method write_nexus (line 6790) | def write_nexus( method as_nexus (line 6919) | def as_nexus(self, **kwargs): method to_macs (line 6934) | def to_macs(self): method simplify (line 6958) | def simplify( method delete_sites (line 7105) | def delete_sites(self, site_ids, record_provenance=True): method delete_intervals (line 7125) | def delete_intervals(self, intervals, simplify=True, record_provenance... method keep_intervals (line 7156) | def keep_intervals(self, intervals, simplify=True, record_provenance=T... method ltrim (line 7188) | def ltrim(self, record_provenance=True): method rtrim (line 7204) | def rtrim(self, record_provenance=True): method trim (line 7218) | def trim(self, record_provenance=True): method shift (line 7233) | def shift(self, value, sequence_length=None, record_provenance=True): method concatenate (line 7259) | def concatenate( method split_edges (line 7344) | def split_edges(self, time, *, flags=None, population=None, metadata=N... method decapitate (line 7396) | def decapitate(self, time, *, flags=None, population=None, metadata=No... method extend_haplotypes (line 7442) | def extend_haplotypes(self, max_iter=10): method subset (line 7495) | def subset( method union (line 7557) | def union( method draw_svg (line 7669) | def draw_svg( method draw_text (line 7859) | def draw_text( method general_stat (line 7917) | def general_stat( method sample_count_stat (line 8006) | def sample_count_stat( method parse_windows (line 8108) | def parse_windows(self, windows): method parse_time_windows (line 8133) | def parse_time_windows(self, time_windows): method __run_windowed_stat (line 8138) | def __run_windowed_stat(self, windows, method, *args, **kwargs): method __run_windowed_stat_tw (line 8147) | def __run_windowed_stat_tw(self, windows, time_windows, method, *args,... method __one_way_sample_set_stat (line 8161) | def __one_way_sample_set_stat( method parse_sites (line 8223) | def parse_sites(self, sites): method parse_positions (line 8238) | def parse_positions(self, positions): method __two_locus_sample_set_stat (line 8258) | def __two_locus_sample_set_stat( method __k_way_two_locus_sample_set_stat (line 8312) | def __k_way_two_locus_sample_set_stat( method __k_way_sample_set_stat (line 8359) | def __k_way_sample_set_stat( method __k_way_weighted_stat (line 8414) | def __k_way_weighted_stat( method __weighted_vector_stat (line 8459) | def __weighted_vector_stat( method diversity (line 8496) | def diversity( method divergence (line 8558) | def divergence( method _chunk_sequence_by_tree (line 8633) | def _chunk_sequence_by_tree(self, num_chunks): method _chunk_windows (line 8651) | def _chunk_windows(windows, num_chunks): method _parallelise_divmat_by_tree (line 8671) | def _parallelise_divmat_by_tree(self, num_threads, span_normalise, **k... method _parallelise_divmat_by_window (line 8689) | def _parallelise_divmat_by_window(self, windows, num_threads, **kwargs): method _parse_stat_matrix_sample_sets (line 8708) | def _parse_stat_matrix_sample_sets(ids): method divergence_matrix (line 8739) | def divergence_matrix( method genetic_relatedness (line 8830) | def genetic_relatedness( method genetic_relatedness_matrix (line 8978) | def genetic_relatedness_matrix( method genetic_relatedness_weighted (line 9104) | def genetic_relatedness_weighted( method genetic_relatedness_vector (line 9157) | def genetic_relatedness_vector( method _expand_indices (line 9220) | def _expand_indices(self, x: np.ndarray, indices: np.ndarray) -> np.nd... method _genetic_relatedness_vector_node (line 9226) | def _genetic_relatedness_vector_node( method _genetic_relatedness_vector_individual (line 9248) | def _genetic_relatedness_vector_individual( method pca (line 9284) | def pca( method trait_covariance (line 9559) | def trait_covariance(self, W, windows=None, mode="site", span_normalis... method trait_correlation (line 9621) | def trait_correlation(self, W, windows=None, mode="site", span_normali... method trait_regression (line 9690) | def trait_regression(self, *args, **kwargs): method trait_linear_model (line 9702) | def trait_linear_model( method segregating_sites (line 9790) | def segregating_sites( method allele_frequency_spectrum (line 9844) | def allele_frequency_spectrum( method Tajimas_D (line 9967) | def Tajimas_D(self, sample_sets=None, windows=None, mode="site"): method Fst (line 10024) | def Fst( method Y3 (line 10138) | def Y3( method Y2 (line 10191) | def Y2( method Y1 (line 10235) | def Y1(self, sample_sets, windows=None, mode="site", span_normalise=Tr... method f4 (line 10272) | def f4( method f3 (line 10330) | def f3( method f2 (line 10384) | def f2( method mean_descendants (line 10430) | def mean_descendants(self, sample_sets): method genealogical_nearest_neighbours (line 10452) | def genealogical_nearest_neighbours(self, focal, sample_sets, num_thre... method kc_distance (line 10514) | def kc_distance(self, other, lambda_=0.0): method count_topologies (line 10528) | def count_topologies(self, sample_sets=None): method ibd_segments (line 10549) | def ibd_segments( method pair_coalescence_counts (line 10622) | def pair_coalescence_counts( method pair_coalescence_quantiles (line 10722) | def pair_coalescence_quantiles( method pair_coalescence_rates (line 10803) | def pair_coalescence_rates( method impute_unknown_mutations_time (line 10906) | def impute_unknown_mutations_time( method ld_matrix (line 10936) | def ld_matrix( method sample_nodes_by_ploidy (line 11079) | def sample_nodes_by_ploidy(self, ploidy): method map_to_vcf_model (line 11106) | def map_to_vcf_model( method get_pairwise_diversity (line 11308) | def get_pairwise_diversity(self, samples=None): method pairwise_diversity (line 11312) | def pairwise_diversity(self, samples=None): method get_time (line 11339) | def get_time(self, u): method get_population (line 11346) | def get_population(self, u): method records (line 11353) | def records(self): method get_num_records (line 11364) | def get_num_records(self): method diffs (line 11374) | def diffs(self): method newick_trees (line 11380) | def newick_trees(self, precision=3, breakpoints=None, Ne=1): method to_nexus (line 11386) | def to_nexus(self, precision=14): function write_ms (line 11394) | def write_ms( class PCAResult (line 11500) | class PCAResult: FILE: python/tskit/util.py class Dataclass (line 43) | class Dataclass: method replace (line 44) | def replace(self, **kwargs): method asdict (line 53) | def asdict(self, **kwargs): function canonical_json (line 61) | def canonical_json(obj): function is_unknown_time (line 73) | def is_unknown_time(time): function safe_np_int_cast (line 98) | def safe_np_int_cast(int_array, dtype, copy=False): function pack_bytes (line 139) | def pack_bytes(data): function unpack_bytes (line 160) | def unpack_bytes(packed, offset): function pack_strings (line 179) | def pack_strings(strings, encoding="utf8"): function unpack_strings (line 197) | def unpack_strings(packed, offset, encoding="utf8"): function pack_arrays (line 215) | def pack_arrays(list_of_lists, dtype=np.float64): function unpack_arrays (line 239) | def unpack_arrays(packed, offset): function intervals_to_np_array (line 262) | def intervals_to_np_array(intervals, start, end): function negate_intervals (line 288) | def negate_intervals(intervals, start, end): function naturalsize (line 305) | def naturalsize(value): function obj_to_collapsed_html (line 329) | def obj_to_collapsed_html(d, name=None, open_depth=0, max_items=30, max_... function truncate_string_end (line 391) | def truncate_string_end(string, length): function render_metadata (line 401) | def render_metadata(md, length=40): function unicode_table (line 407) | def unicode_table( function format_number (line 483) | def format_number(number, sig_digits=8, sep="\u2009"): function html_table (line 503) | def html_table(rows, *, header): function tree_sequence_html (line 537) | def tree_sequence_html(ts): function tree_html (line 673) | def tree_html(tree): function variant_html (line 713) | def variant_html(variant): function convert_file_like_to_open_file (line 804) | def convert_file_like_to_open_file(file_like, mode): function set_print_options (line 834) | def set_print_options(*, max_lines=40): function truncate_rows (line 844) | def truncate_rows(num_rows, limit=None): function random_nucleotides (line 858) | def random_nucleotides(length: numbers.Number, *, seed: int | None = Non... function raise_known_file_format_errors (line 876) | def raise_known_file_format_errors(open_file, existing_exception): FILE: python/tskit/vcf.py class VcfWriter (line 32) | class VcfWriter: method __init__ (line 38) | def __init__( method __write_header (line 125) | def __write_header(self, output): method write (line 152) | def write(self, output):