// general
template<typename T> inline
void add(size_t N, T *Z, const T *X, const T *Y)
{
add_T(N, Z, X, Y);
}
void rescan_seq( char *seq, size_t seq_len, uint *count_array, size_t cutoff )
{
/* Martin A. Hansen, September 2008 */
/* Run a sliding window over a given sequence. The window */
/* consists of a list where new blocks of 4 nucleotides */
/* are pushed onto one end while at the same time old */
/* blocks are popped from the other end. The number of */
/* in the list is determined by the maximum seperator. */
/* Everytime we have a full window, the window is scanned */
/* for motifs. */
bitblock *block = NULL;
size_t b_count = 0;
ushort n_count = 0;
size_t i = 0;
uchar bin = 0;
bool first_node = TRUE;
node_sl *new_node = NULL;
node_sl *old_node = NULL;
list_sl *list = list_sl_new();
uint *output_array = NULL;
output_array = mem_get_zero( sizeof( uint ) * ( seq_len + 1 ) );
for ( i = 0; seq[ i ]; i++ )
{
bin <<= BITS_IN_NT;
switch( seq[ i ] )
{
case 'A': case 'a': add_A( bin ); break;
case 'T': case 't': add_T( bin ); break;
case 'C': case 'c': add_C( bin ); break;
case 'G': case 'g': add_G( bin ); break;
default: n_count = BLOCK_SIZE_NT; break;
}
if ( i > BLOCK_SIZE_NT - 2 )
{
b_count++;
block = bitblock_new();
block->bin = bin;
if ( n_count > 0 )
{
block->hasN = TRUE;
n_count--;
}
new_node = node_sl_new();
new_node->val = block;
if ( first_node ) {
list_sl_add_beg( &list, &new_node );
} else {
list_sl_add_after( &old_node, &new_node );
}
old_node = new_node;
first_node = FALSE;
if ( b_count > BLOCK_SPACE_MAX + BLOCK_SIZE_NT )
{
// bitblock_list_print( list ); /* DEBUG */
rescan_list( list, count_array, i, cutoff, output_array );
mem_free( &list->first->val );
list_sl_remove_beg( &list );
}
}
}
/* if the list is shorter than BLOCK_SPACE_MAX + BLOCK_SIZE_NT */
if ( b_count <= BLOCK_SPACE_MAX + BLOCK_SIZE_NT )
{
// bitblock_list_print( list ); /* DEBUG */
rescan_list( list, count_array, i, cutoff, output_array );
}
list_sl_destroy( &list );
for ( i = 0; i < seq_len; i++ ) {
printf( "%zu\t%u\n", i, output_array[ i ] );
}
free( output_array );
}
