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
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_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 );
}
/**
* \brief Initiate example.
*
*/
static void adp_example_init(void)
{
adp_init();
/* Extension board ioport initial */
adp_example_ioport_init();
adp_example_adc_init();
while (adp_wait_for_handshake() != ADP_HANDSHAKE_ACCEPTED) {
}
adp_window_init();
adp_example_tc_init();
}
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;
}
