// ========================================================================== // SeqAn - The Library for Sequence Analysis // ========================================================================== // Copyright (c) 2006-2010, Knut Reinert, FU Berlin // All rights reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions and the following disclaimer. // * Redistributions in binary form must reproduce the above copyright // notice, this list of conditions and the following disclaimer in the // documentation and/or other materials provided with the distribution. // * Neither the name of Knut Reinert or the FU Berlin nor the names of // its contributors may be used to endorse or promote products derived // from this software without specific prior written permission. // // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER // CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT // LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH // DAMAGE. // // ========================================================================== // Author: Manuel Holtgrewe // ========================================================================== // Tests for the seeds module. // ========================================================================== #include // Includes testing infrastructure. #include // Required to print strings in tests. #include // Include module under test. #include "test_align_chain_banded.h" #include "test_align_dynprog_affine.h" #include "test_align_dynprog_banded_affine.h" #include "test_align_dynprog_banded_linear.h" #include "test_align_dynprog_linear.h" #include "test_basic_iter_indirect.h" #include "test_seeds_combination.h" #include "test_seeds_extension.h" #include "test_seeds_global_chaining.h" #include "test_seeds_seed_base.h" #include "test_seeds_seed_chained.h" #include "test_seeds_seed_diagonal.h" #include "test_seeds_seed_set_base.h" #include "test_seeds_seed_simple.h" SEQAN_BEGIN_TESTSUITE(test_seeds) { // Test indirect iterator. // SEQAN_CALL_TEST(test_seeds_basic_iter_indirect_constructors); // SEQAN_CALL_TEST(test_seeds_basic_iter_indirect_metafunctions); // SEQAN_CALL_TEST(test_seeds_basic_iter_indirect_basic_functions); // Tests for seed diagonals. SEQAN_CALL_TEST(test_seeds_seed_diagonal_constructors); SEQAN_CALL_TEST(test_seeds_seed_diagonal_metafunctions); // Tests for seeds. SEQAN_CALL_TEST(test_seeds_seed_base_constructors_simple); SEQAN_CALL_TEST(test_seeds_seed_base_metafunctions_simple); SEQAN_CALL_TEST(test_seeds_seed_base_getters_setters_simple); SEQAN_CALL_TEST(test_seeds_seed_base_basic_functions_simple); SEQAN_CALL_TEST(test_seeds_seed_base_assign_simple); SEQAN_CALL_TEST(test_seeds_seed_base_constructors_chained); SEQAN_CALL_TEST(test_seeds_seed_base_metafunctions_chained); SEQAN_CALL_TEST(test_seeds_seed_base_getters_setters_chained); SEQAN_CALL_TEST(test_seeds_seed_base_basic_functions_chained); SEQAN_CALL_TEST(test_seeds_seed_base_assign_chained); SEQAN_CALL_TEST(test_seeds_seed_chained_assign); SEQAN_CALL_TEST(test_seeds_seed_chained_metafunctions); SEQAN_CALL_TEST(test_seeds_seed_chained_append_diagonal); SEQAN_CALL_TEST(test_seeds_seed_chained_truncate_diagonals); SEQAN_CALL_TEST(test_seeds_seed_chained_iterators); SEQAN_CALL_TEST(test_seeds_seed_chained_front_back); SEQAN_CALL_TEST(test_seeds_seed_simple_constructors); SEQAN_CALL_TEST(test_seeds_seed_simple_setters); // Tests for the combination of seeds. SEQAN_CALL_TEST(test_seeds_combination_seeds_combineable_merge_chained); SEQAN_CALL_TEST(test_seeds_combination_seeds_combineable_simple_chaining_chained); SEQAN_CALL_TEST(test_seeds_combination_seeds_combineable_simple_chaos_chaining_chained); SEQAN_CALL_TEST(test_seeds_combination_combine_seeds_merge_chained); SEQAN_CALL_TEST(test_seeds_combination_combine_seeds_simple_chaining_chained); SEQAN_CALL_TEST(test_seeds_combination_combine_seeds_simple_chaos_chaining_chained); // Tests for unordered seed sets and simple seeds. SEQAN_CALL_TEST(test_seeds_seed_set_base_container_functions_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_single_threshold_reached_length_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_single_threshold_not_reached_length_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_single_threshold_reached_score_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_single_threshold_not_reached_score_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_merge_left_merging_possible_no_threshold_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_merge_right_merging_possible_no_threshold_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_merge_left_merging_impossible_no_threshold_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_merge_left_merging_possible_threshold_not_reached_length_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_merge_left_merging_possible_threshold_reached_length_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_merge_left_merging_possible_threshold_not_reached_scored_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_merge_left_merging_possible_threshold_reached_scored_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_simple_chain_left_chaining_possible_no_threshold_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_simple_chain_right_chaining_possible_no_threshold_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_simple_chain_left_chaining_impossible_no_threshold_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_simple_chain_left_chaining_possible_threshold_not_reached_length_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_simple_chain_left_chaining_possible_threshold_reached_length_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_simple_chain_left_chaining_possible_threshold_not_reached_scored_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_simple_chain_left_chaining_possible_threshold_reached_scored_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chaos_left_chaining_possible_no_threshold_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chaos_right_chaining_possible_no_threshold_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chaos_left_chaining_impossible_no_threshold_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chaos_left_chaining_possible_threshold_not_reached_length_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chaos_left_chaining_possible_threshold_reached_length_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chaos_left_chaining_possible_threshold_not_reached_scored_simple_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chaos_left_chaining_possible_threshold_reached_scored_simple_unordered); // Tests for unordered seed sets and chained seeds. SEQAN_CALL_TEST(test_seeds_seed_set_base_container_functions_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_single_threshold_reached_length_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_single_threshold_not_reached_length_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_single_threshold_reached_score_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_single_threshold_not_reached_score_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_merge_left_merging_possible_no_threshold_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_merge_right_merging_possible_no_threshold_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_merge_left_merging_impossible_no_threshold_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_merge_left_merging_possible_threshold_not_reached_length_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_merge_left_merging_possible_threshold_reached_length_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_merge_left_merging_possible_threshold_not_reached_scored_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_merge_left_merging_possible_threshold_reached_scored_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chained_chain_left_chaining_possible_no_threshold_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chained_chain_right_chaining_possible_no_threshold_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chained_chain_left_chaining_impossible_no_threshold_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chained_chain_left_chaining_possible_threshold_not_reached_length_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chained_chain_left_chaining_possible_threshold_reached_length_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chained_chain_left_chaining_possible_threshold_not_reached_scored_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chained_chain_left_chaining_possible_threshold_reached_scored_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chaos_left_chaining_possible_no_threshold_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chaos_right_chaining_possible_no_threshold_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chaos_left_chaining_impossible_no_threshold_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chaos_left_chaining_possible_threshold_not_reached_length_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chaos_left_chaining_possible_threshold_reached_length_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chaos_left_chaining_possible_threshold_not_reached_scored_chained_unordered); SEQAN_CALL_TEST(test_seeds_seed_set_base_add_seed_chaos_left_chaining_possible_threshold_reached_scored_chained_unordered); // Tests for seed algorithms SEQAN_CALL_TEST(test_seeds_extension_match_extension_simple); SEQAN_CALL_TEST(test_seeds_extension_ungapped_xdrop_extension_simple); SEQAN_CALL_TEST(test_seeds_extension_gapped_xdrop_extension_simple); SEQAN_CALL_TEST(test_seeds_extension_match_extension_chained); SEQAN_CALL_TEST(test_seeds_extension_ungapped_xdrop_extension_chained); // Disabled the test for now. Extension function contains a // force-failure assertion and instruction show to implement this. // See http://trac.mi.fu-berlin.de/seqan/ticket/344 for details. // // TODO(holtgrew): Implement this. // // SEQAN_CALL_TEST(test_seeds_extension_gapped_xdrop_extension_chained); // Tests for the banded chain alignment algorithms. SEQAN_CALL_TEST(test_align_chain_banded_compute_upper_left_overlap); SEQAN_CALL_TEST(test_align_chain_banded_compute_lower_right_overlap); SEQAN_CALL_TEST(test_align_chain_banded_align_linear); // TODO(holtgrew): Not testing banded chain alignment with affine gap costs for now. // SEQAN_CALL_TEST(test_align_chain_banded_align_affine); // Tests for the classic NW dynamic programming. SEQAN_CALL_TEST(test_align_dynprog_linear_resize_matrix); SEQAN_CALL_TEST(test_align_dynprog_linear_init_gutter_free); SEQAN_CALL_TEST(test_align_dynprog_linear_init_gutter_not_free); SEQAN_CALL_TEST(test_align_dynprog_linear_fill_matrix); SEQAN_CALL_TEST(test_align_dynprog_linear_traceback); // Tests for the banded NW dynamic programming. SEQAN_CALL_TEST(test_align_dynprog_banded_linear_resize_matrix); SEQAN_CALL_TEST(test_align_dynprog_banded_linear_init_gutter_free); SEQAN_CALL_TEST(test_align_dynprog_banded_linear_init_gutter_not_free); SEQAN_CALL_TEST(test_align_dynprog_banded_linear_fill_matrix); SEQAN_CALL_TEST(test_align_dynprog_banded_linear_traceback); // Tests for the classic Gotoh dynamic programming. SEQAN_CALL_TEST(test_align_dynprog_affine_resize_matrix); SEQAN_CALL_TEST(test_align_dynprog_affine_init_gutter_free); SEQAN_CALL_TEST(test_align_dynprog_affine_init_gutter_not_free); SEQAN_CALL_TEST(test_align_dynprog_affine_fill_matrix); SEQAN_CALL_TEST(test_align_dynprog_affine_traceback); // Tests for the banded Gotoh dynamic programming. SEQAN_CALL_TEST(test_align_dynprog_banded_affine_resize_matrix); SEQAN_CALL_TEST(test_align_dynprog_banded_affine_init_gutter_free); SEQAN_CALL_TEST(test_align_dynprog_banded_affine_init_gutter_not_free); SEQAN_CALL_TEST(test_align_dynprog_banded_affine_fill_matrix); SEQAN_CALL_TEST(test_align_dynprog_banded_affine_traceback); // Test global chaining of seeds. SEQAN_CALL_TEST(test_seeds_global_chaining_sparse_length); SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/seeds2/align_chain_banded.h"); SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/seeds2/align_dynprog_affine.h"); SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/seeds2/align_dynprog_banded_affine.h"); SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/seeds2/align_dynprog_banded_linear.h"); SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/seeds2/align_dynprog_linear.h"); // TODO(holtgrew): Write tests for indirect iterator and uncomment this. // SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/seeds2/basic_iter_indirect.h"); SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/seeds2/seeds_combination.h"); SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/seeds2/seeds_extension.h"); SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/seeds2/seeds_global_chaining.h"); SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/seeds2/seeds_seed_base.h"); SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/seeds2/seeds_seed_chained.h"); SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/seeds2/seeds_seed_diagonal.h"); SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/seeds2/seeds_seed_set_base.h"); SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/seeds2/seeds_seed_set_unordered.h"); SEQAN_VERIFY_CHECKPOINTS("core/include/seqan/seeds2/seeds_seed_simple.h"); } SEQAN_END_TESTSUITE