static p_search_result setup_searcher_16_test( char * query_string, char * db_file, size_t hit_count ) {
set_max_compute_capability( COMPUTE_ON_SSE2 );
mat_init_constant_scoring( 1, -1 );
init_symbol_translation( NUCLEOTIDE, FORWARD_STRAND, 3, 3 );
p_query query = query_read_from_string( query_string );
s_init( NEEDLEMAN_WUNSCH, BIT_WIDTH_16, query );
ssa_db_init( concat( "./tests/testdata/", db_file ) );
gapO = -1;
gapE = -1;
adp_init( hit_count );
p_search_result res = s_search( &hit_count );
minheap_sort( res->heap );
query_free( query );
return res;
}
}END_TEST
START_TEST (test_add_more)
{
p_minheap m = minheap_init( 5 );
ck_assert_int_eq( 0, m->count );
ck_assert_int_eq( 5, m->alloc );
for( int i = 0; i < 20; i++ ) {
elem_t e = new_elem( i, i, i );
minheap_add( m, &e );
}
minheap_sort( m );
ck_assert_int_eq( 5, m->count );
ck_assert_int_eq( 5, m->alloc );
ck_assert_int_eq( 19, m->array[0].score );
ck_assert_int_eq( 19, m->array[0].query_id );
ck_assert_int_eq( 19, m->array[0].db_id );
ck_assert_int_eq( 18, m->array[1].score );
ck_assert_int_eq( 17, m->array[2].score );
ck_assert_int_eq( 16, m->array[3].score );
ck_assert_int_eq( 15, m->array[4].score );
minheap_exit( m );
}END_TEST
}END_TEST
static void test_searcher_overflow_to_64bit( int search_type ) {
init_constant_scores( 127, -1 );
init_symbol_translation( AMINOACID, FORWARD_STRAND, 3, 3 );
p_query query = query_read_from_file( "./tests/testdata/NP_009305.1.fas" );
s_init( search_type, BIT_WIDTH_8, query );
ssa_db_init( "./tests/testdata/NP_009305.1.fas" );
gapO = -1;
gapE = -1;
size_t hit_count = 1;
adp_init( hit_count );
p_search_result res = s_search( &hit_count );
minheap_sort( res->heap );
query_free( query );
ck_assert_int_eq( hit_count, res->heap->count );
ck_assert_int_eq( 1, res->overflow_8_bit_count );
ck_assert_int_eq( 1, res->overflow_16_bit_count );
int result[2] = { 67818, 0 };
test_result( res, result, 2 );
}
}END_TEST
static p_search_result setup_BLOSUM62_test( int bit_width, int search_type, size_t hit_count ) {
init_symbol_translation( AMINOACID, FORWARD_STRAND, 3, 3 );
mat_init_buildin( BLOSUM62 );
p_query query = query_read_from_string(
"HPEVYILIIPGFGIISHVVSTYSKKPVFGEISMVYAMASIGLLGFLVWSHHMYIVGLDADTRAYFTSATMIIAIPTGIKI" );
s_init( search_type, bit_width, query );
ssa_db_init( concat( "./tests/testdata/", "short_AA.fas" ) );
gapO = -1;
gapE = -1;
adp_init( hit_count );
p_search_result res = s_search( &hit_count );
minheap_sort( res->heap );
query_free( query );
ck_assert_int_eq( hit_count, res->heap->count );
return res;
}
}END_TEST
static void test_result( p_search_result res, int * result, int result_len ) {
minheap_sort( res->heap );
ck_assert_int_eq( result_len / 2, res->heap->count );
p_minheap heap = res->heap;
/*
* Result contains tuple of the score and the database ID
*/
for( int i = 0; i < result_len; i += 2 ) { // TODO test query ID as well!!
ck_assert_int_eq( result[i], heap->array[i / 2].score );
ck_assert_int_eq( result[i + 1], heap->array[i / 2].db_id );
}
exit_searcher_test( res );
}
static p_search_result setup_searcher_test( int bit_width, int search_type, char * query_string, char * db_file,
size_t hit_count, int symtype, int strands ) {
init_symbol_translation( symtype, strands, 3, 3 );
mat_init_constant_scoring( 1, -1 );
p_query query = query_read_from_string( query_string );
s_init( search_type, bit_width, query );
ssa_db_init( concat( "./tests/testdata/", db_file ) );
gapO = -1;
gapE = -1;
adp_init( hit_count );
p_search_result res = s_search( &hit_count );
minheap_sort( res->heap );
query_free( query );
return res;
}
int main(void)
{
uint32_t cnt, i, data[] =
{14, 2, 22, 13, 23, 10, 90, 36, 108, 12,
9, 91, 1, 51, 11, 3, 15, 80, 3, 78, 53,
5, 12, 21, 65, 70, 4};
const uint32_t data_len = sizeof(data)/sizeof(uint32_t);
struct heap heap = heap_create(data_len + 5);
printf(COL_BEG "push data...\n" COL_END);
for (i = 0; i < data_len; i++)
if (!heap_full(&heap))
heap_push(&heap, &data[i]);
printf("data len = %u, heap size = %u.\n", data_len,
heap_size(&heap));
printf(COL_BEG "heap tree:\n" COL_END);
heap_print_tr(&heap, &test_print);
printf(COL_BEG "heap array:\n" COL_END);
heap_print_arr(&heap, &test_print);
heap_set_callbk(&heap, &test_less_than);
printf(COL_BEG "after heapify:\n" COL_END);
minheap_heapify(&heap);
heap_print_tr(&heap, &test_print);
cnt = 0;
printf(COL_BEG "ranking emulation...:\n" COL_END);
while (cnt < 100) {
i = (i + 1) % data_len;
if (!heap_full(&heap)) {
printf("insert %d\n", data[i]);
minheap_insert(&heap, &data[i]);
} else {
void *top = heap_top(&heap);
if (test_less_than(top, &data[i])) {
printf("replace with %d\n", data[i]);
minheap_delete(&heap, 0);
minheap_insert(&heap, &data[i]);
}
}
cnt ++;
}
printf(COL_BEG "a heavy heap tree now:\n" COL_END);
heap_print_tr(&heap, &test_print);
minheap_sort(&heap);
printf(COL_BEG "heap array after min-heap sort:\n" COL_END);
heap_print_arr(&heap, &test_print);
heap_destory(&heap);
printf(COL_BEG "a new heap...\n" COL_END);
heap = heap_create(data_len + 5);
heap_set_callbk(&heap, &test_less_than);
for (i = 0; i < data_len; i++)
if (!heap_full(&heap))
heap_push(&heap, &data[i]);
printf(COL_BEG "heap array:\n" COL_END);
heap_print_arr(&heap, &test_print);
heap_sort_desc(&heap);
printf(COL_BEG "heap array after heap sort:\n" COL_END);
heap_print_arr(&heap, &test_print);
heap_print_tr(&heap, &test_print);
heap_destory(&heap);
printf(COL_BEG "sort a heap with one element...\n" COL_END);
heap = heap_create(data_len + 5);
heap_set_callbk(&heap, &test_less_than);
heap_push(&heap, &data[0]);
heap_print_tr(&heap, &test_print);
heap_sort_desc(&heap);
heap_destory(&heap);
return 0;
}