static int
Sort_Array(netsnmp_container *c)
{
binary_array_table *t = (binary_array_table*)c->container_data;
netsnmp_assert(t!=NULL);
netsnmp_assert(c->compare!=NULL);
if (c->flags & CONTAINER_KEY_UNSORTED)
return 0;
if (t->dirty) {
/*
* Sort the table
*/
if (t->count > 1)
array_qsort(t->data, 0, t->count - 1, c->compare);
t->dirty = 0;
/*
* no way to know if it actually changed... just assume so.
*/
++c->sync;
}
return 1;
}
static void
array_qsort(void **data, int first, int last, netsnmp_container_compare *f)
{
int i, j;
void *mid, *tmp;
i = first;
j = last;
mid = data[(first+last)/2];
do {
while (i < last && (*f)(data[i], mid) < 0)
++i;
while (j > first && (*f)(mid, data[j]) < 0)
--j;
if(i < j) {
tmp = data[i];
data[i] = data[j];
data[j] = tmp;
++i;
--j;
}
else if (i == j) {
++i;
--j;
break;
}
} while(i <= j);
if (j > first)
array_qsort(data, first, j, f);
if (i < last)
array_qsort(data, i, last, f);
}
int align_backbone (Descr *descr1, Protein * protein1, Representation *rep1,
Descr *descr2, Protein * protein2, Representation *rep2,
List_of_maps *list){
if ( list->best_array_used == 0) return 1;
int best_ctr, map_ctr, retval;
int * new_best;
double *bb_score_array;
Map *current_map;
if ( !(bb_score_array = emalloc(list->best_array_used*sizeof(double)))) return 1;
if ( !(new_best = emalloc(list->best_array_used*sizeof(int)))) return 1;
for (best_ctr=0; best_ctr<list->best_array_used; best_ctr++) {
map_ctr = list->map_best[best_ctr];
if ( map_ctr >= list->best_array_allocated) {
printf ("%s:%d error assigning array size.\n", __FILE__, __LINE__ );
exit (1);
}
current_map = list->map+map_ctr;
retval = single_map_align_backbone (descr1, protein1, rep1, descr2, protein2, rep2, current_map);
if (retval) {
printf (" error doing bb alignment db:%s query:%s \n",
descr1->name, descr2->name);
exit (retval);
}
new_best[best_ctr] = map_ctr;
/* the array_qsort sorts in the increasing order, so use negative aln score: */
bb_score_array[best_ctr] = -current_map->aln_score;
}
array_qsort ( new_best, bb_score_array, list->best_array_used);
memcpy (list->map_best, new_best, list->best_array_used*sizeof(int));
free (bb_score_array);
free (new_best);
return 0;
}
static int dealias_ipid32_bo(scamper_dealias_probe_t **probes, int probec)
{
scamper_dealias_probe_t **s = NULL;
uint32_t a, b, c = 1, max_bs = 0, max_nobs = 0, u32;
int i, rc = 2;
if((s = memdup(probes, sizeof(scamper_dealias_probe_t *) * probec)) == NULL)
return -1;
array_qsort((void **)s, probec, (array_cmp_t)dealias_probe_def_cmp);
for(i=0; i<probec-1; i++)
{
if(s[i]->def != s[i+1]->def)
{
if(c >= 3)
{
if(max_nobs < max_bs)
rc = 0;
else if(max_nobs > max_bs)
rc = 1;
if(rc == 0)
goto done;
}
c = 1; max_nobs = 0; max_bs = 0;
}
else
{
a = s[i]->replies[0]->ipid32; b = s[i+1]->replies[0]->ipid32;
u32 = dealias_ipid32_diff(a, b);
if(u32 > max_nobs || max_nobs == 0)
max_nobs = u32;
u32 = dealias_ipid32_diff(byteswap32(a), byteswap32(b));
if(u32 > max_bs || max_bs == 0)
max_bs = u32;
c++;
}
}
done:
if(s != NULL) free(s);
return rc;
}
void scamper_dealias_probes_sort_def(scamper_dealias_t *dealias)
{
array_qsort((void **)dealias->probes, dealias->probec,
(array_cmp_t)dealias_probe_def_cmp);
return;
}
int coverage ( Alignment * alignment, double * score, double * res_fract_rank, int gap_treatment) {
int *sorted_res;
int pos, ctr, ctr2;
int first, cvg_ctr;
int almt_pos, gaps;
int new_length = alignment->length;
int usable_position, ref_s = 0, g;
int *int_cvg;
double *protein_score, prev_score; /* "score" refers to alignment positions */
Group *group, *ref_group;
if (gap_treatment > 0) {
group = alignment->group+gap_treatment-1;
}
sorted_res = (int *) emalloc ( alignment->length*sizeof (int) );
if (!sorted_res) return 1;
if ( ! (int_cvg = emalloc(alignment->length*sizeof(int) ) ) ) return 1;
if ( gap_treatment <= -100 ) {
g = -(gap_treatment+100);
ref_group = alignment->group+ g;
ref_s = ref_group->group_member[0];
gaps = 0;
for (almt_pos=0; almt_pos < alignment->length; almt_pos ++ ) {
if ( score[almt_pos] == ALL_GAPS
|| alignment->sequence[ref_s][almt_pos] == '.') gaps++;
}
new_length = alignment->length - gaps;
} else if ( gap_treatment == -2 ) {
new_length = alignment->length;
} else if ( gap_treatment == -1 ) {
new_length = alignment->length - alignment->number_of_sunk_positions;
} else if ( gap_treatment == 0 ) {
gaps = 0;
for (almt_pos=0; almt_pos < alignment->length; almt_pos ++ ) {
if ( score[almt_pos] == ALL_GAPS ) gaps++;
}
new_length = alignment->length - gaps;
} else {
ref_group = alignment->group+ gap_treatment-1;
ref_s = ref_group->group_member[0];
gaps = 0;
for (almt_pos=0; almt_pos < alignment->length; almt_pos ++ ) {
if (alignment->sequence[ref_s][almt_pos] == '.') gaps++;
}
new_length = alignment->length - gaps;
}
/*allocate */
protein_score = (double *) emalloc ( new_length*sizeof (double) );
if (!protein_score ) return 1;
/* remove gapped positions from the score array */
pos = 0;
for (almt_pos=0; almt_pos < alignment->length; almt_pos ++ ) {
usable_position = 1;
if (gap_treatment <= -100) {
if ( score[almt_pos] == ALL_GAPS ||
alignment->sequence[ref_s][almt_pos] == '.')
usable_position = 0;
} else if ( gap_treatment == -1 ) {
if ( alignment->sunk[almt_pos] ) usable_position = 0;
} else if (gap_treatment == 0) {
if ( score[almt_pos] == ALL_GAPS) usable_position = 0;
} else if (gap_treatment > 0) {
if (alignment->sequence[ref_s][almt_pos] == '.') usable_position = 0;
}
if ( ! usable_position) continue;
if ( pos >= new_length ) {
fprintf (stderr, "Error: pos ctr (%d) >= allocated length (%d) \n", pos, new_length);
exit (1);
}
protein_score[pos] = score[almt_pos];
pos ++;
}
/* sort protein residues according to the new array */
for (pos=0; pos < new_length; pos++) sorted_res[pos] = pos;
array_qsort ( sorted_res, protein_score, new_length);
/* turn the sorted array to coverage info */
/* the lowest score in the game */
prev_score = protein_score[ sorted_res[0] ];
first = 0;
cvg_ctr = 0;
int_cvg[cvg_ctr] = 0;
for (ctr=0; ctr < alignment->length; ctr++) {
res_fract_rank[ctr] = 1.0;
}
for (ctr=0; ctr < new_length; ctr++) {
if ( protein_score[ sorted_res[ctr] ] <= prev_score ) {
int_cvg[cvg_ctr] ++;
} else {
prev_score = protein_score[ sorted_res[ctr] ];
for (ctr2=first; ctr2 <ctr; ctr2++ ) {
res_fract_rank[ sorted_res[ctr2] ] = (double) int_cvg[cvg_ctr]/new_length;
}
first = ctr;
cvg_ctr ++;
if ( cvg_ctr < alignment->length) {
int_cvg[cvg_ctr] = int_cvg[cvg_ctr-1] + 1;
}
}
}
for (ctr2=first; ctr2 <ctr; ctr2++ ) {
res_fract_rank[ sorted_res[ctr2] ] = (double) int_cvg[cvg_ctr]/new_length;
}
/* free */
free (protein_score);
free (sorted_res);
free (int_cvg);
return 0;
}
