static int do_test_one_area(struct mem_test_resource *r, int bus_only,
unsigned cache_flag)
{
int ret;
printf("Testing memory space: "
"0x%08x -> 0x%08x:\n",
r->r->start, r->r->end);
remap_range((void *)r->r->start, r->r->end -
r->r->start + 1, cache_flag);
ret = mem_test_bus_integrity(r->r->start, r->r->end);
if (ret < 0)
return ret;
if (bus_only)
return 0;
ret = mem_test_moving_inversions(r->r->start, r->r->end);
if (ret < 0)
return ret;
printf("done.\n\n");
return 0;
}
unsigned long * compress_site_patterns_diploid(char ** sequence,
const unsigned int * map,
int count,
int * length,
unsigned int ** wptr,
int attrib)
{
int i,j;
char * memptr;
char ** column;
unsigned int * weight;
unsigned long * mapping;
unsigned char ** jc69_invmaps = NULL;
unsigned char charmap[ASCII_SIZE];
unsigned char inv_charmap[ASCII_SIZE];
/* check that at least one sequence is given */
if (!count) return NULL;
/* a map must be given */
if (!map) return NULL;
/* a zero can never be used as a state */
if (map[0]) return NULL;
/* if map states are out of the BYTE range, remap */
if (findmax(map) >= ASCII_SIZE)
{
remap_range(map,charmap);
/* for now only DNA with pll_map_nt */
assert(0);
}
else
{
for (i = 0; i < ASCII_SIZE; ++i)
charmap[i] = (unsigned char)(map[i]);
}
/* create inverse charmap to decode states back to characters when
compression is finished */
for (i = 0; i < ASCII_SIZE; ++i)
if (map[i])
inv_charmap[charmap[i]] = (unsigned char)i;
/* encode sequences using charmap */
encode(sequence,charmap,count,*length);
/* allocate memory for columns */
column = (char **)xmalloc((size_t)(*length)*sizeof(char *));
/* allocate memory for the alignment */
memptr = column[0] = (char *)xmalloc((size_t)(*length) *
(size_t)(count+1) *
sizeof(char));
/* map memory to each column */
for (i = 1; i < *length; ++i)
column[i] = column[i-1] + (count+1);
/* allocate space for weight vector */
weight = (unsigned int *)xmalloc((size_t)(*length)*sizeof(unsigned int));
/* allocate space for mapping vector */
mapping = (unsigned long *)xmalloc((size_t)(*length)*sizeof(unsigned long));
/* split alignment into columns instead of rows */
for (i = 0; i < (*length); ++i)
{
for (j = 0; j < count; ++j)
column[i][j] = sequence[j][i];
column[i][j] = 0;
}
/* allocate space for storing original indices (before sorting sites) */
int * oi = (int *)xmalloc(*length * sizeof(int));
for (i = 0; i < *length; ++i)
oi[i] = i;
/* do the jc69 now */
if (attrib == COMPRESS_JC69)
jc69_invmaps = encode_jc69(column,*length,count);
/* sort the columns and keep original indices */
ssort1(column, *length, 0, oi);
/*first site in uncompressed alignment maps to first site in compressed */
int compressed_length = 1;
size_t ref = 0;
mapping[0] = 0;
weight[ref] = 1;
/* find all unique columns and set their mappings A2->A3 */
int * compressed_oi = (int *)xmalloc(*length * sizeof(int));
compressed_oi[0] = oi[0];
for (i = 1; i < *length; ++i)
{
if (strcmp(column[i],column[i-1]))
{
column[ref+1] = column[i];
compressed_oi[ref+1] = oi[i];
++ref;
++compressed_length;
weight[ref] = 1;
}
else
weight[ref]++;
/* map original index i in uncompressed alignment to index in compressed */
mapping[oi[i]] = ref;
}
/* decode the jc69 encoding */
if (attrib == COMPRESS_JC69)
{
for (i=0; i < compressed_length; ++i)
{
unsigned char * sitemap = jc69_invmaps[compressed_oi[i]];
if (sitemap)
for (j=0; j < count; ++j)
column[i][j] = sitemap[(unsigned int)column[i][j]];
}
for (i = 0; i < *length; ++i)
if (jc69_invmaps[i])
free(jc69_invmaps[i]);
free(jc69_invmaps);
}
/* copy the unique columns over the original sequences */
for (i = 0; i < compressed_length; ++i)
for (j = 0; j < count; ++j)
sequence[j][i] = column[i][j];
/* add terminating zero */
for (j = 0; j < count; ++j)
sequence[j][compressed_length] = 0;
/* deallocate memory */
free(memptr);
free(column);
/* adjust weight vector size to compressed length */
unsigned int * mem = (unsigned int *)xmalloc((size_t)compressed_length *
sizeof(unsigned int));
if (mem)
{
/* copy weights */
for (i = 0; i < compressed_length; ++i)
mem[i] = weight[i];
/* free and re-point */
free(weight);
weight = mem;
}
*wptr = weight;
/* update length */
*length = compressed_length;
/* decode sequences using inv_charmap */
encode(sequence,inv_charmap,count,compressed_length);
free(oi);
free(compressed_oi);
return mapping;
}
