static
void
cleanup(void)
{
recursive_cleanup(".", 0);
chdir("..");
cleanup_rmdir(TESTDIR);
}
int recursive_cleanup (Node *node, int * related, double * probability) {
if ( node->number_of_leaves < MIN_NO_LEAVES || node->type == LEAF ) {
return 0;
}
recursive_cleanup (node->left, related, probability);
recursive_cleanup (node->right, related, probability);
if ( ! related [node->left->id] && ! related [node->right->id] ) {
return 0;
}
/* if both related */
if ( related [node->left->id] && related [node->right->id] ) {
int distr_overlap ( int * pool_population, int * node_population, int no_bins, double * ovlp );
double ovlp;
distr_overlap ( node->left->population, node->right->population, ASCII, & ovlp );
if ( ovlp > 0.8) { /* if the distributions overlap, keep the parent */
related [node->right->id] = 0;
related [node->left->id] = 0;
related [node->id] = 1;
} else { /* keep the children and drop the parent */
related [node->id] = 0;
}
} else {
//return 0;
int child_id;
/* if one related, compare with parent, and keep the one with the smaller p*/
child_id = related [node->left->id] ? related [node->left->id] : related [node->right->id];
related [node->id] = 0;
related [child_id] = 1;
/* if ( probability[node->id] > probability [child_id] ) { */
/* related [node->id] = 0; */
/* related [child_id] = 1; */
/* } else { */
/* related [node->id] = 1; */
/* related [child_id] = 0; */
/* } */
}
return 0;
}
static
void
recursive_cleanup(const char *sofar, int depth)
{
char buf[NAMESIZE*2];
int i;
for (i=0; i<NNAMES; i++) {
snprintf(buf, sizeof(buf), "%s/%s", sofar, names[i]);
if (rmdir(buf)<0) {
if (errno==ENOTEMPTY) {
recursive_cleanup(buf, depth+1);
cleanup_rmdir(buf);
}
else if (errno!=ENOENT) {
say("cleanup: rmdir %s: %s\n", getpid(),
buf, strerror(errno));
}
}
}
}
int output_specs_score ( Options *options, Protein * protein, Alignment * alignment,
int *almt2prot, Node * leaf,
double ** score, double ** complement_score, double ** p_value,
double **probability, double **overlap,
double cutoff, int ** is_precedent) {
# if 0
char *base_filename = options ->outname;
int node_id, pos, no_seqs = alignment->number_of_seqs;
int node_id_2;
int node_ctr,* print, first;
int ** related;
int int_max_gaps = MAX_GAPS*no_seqs;
Node *root;
int refseq_number, refseq_2_number = -1;
char filename[BUFFLEN];
char in_qry2;
FILE * fptr;
int print_leaves (FILE * fptr, Node * node);
int recursive_cleanup (Node *node, int * related, double * probability);
if ( ! ( related = intmatrix (alignment->length+1, no_seqs ) ) ) exit (1);
if ( ! ( print = emalloc (no_seqs*sizeof(int) ) ) ) exit (1);
printf ("in output\n");
#if 1
sprintf (filename, "%s.specs", base_filename);
fptr = efopen (filename, "w");
if ( !fptr) return 1;
# else
fptr = stdout;
# endif
if ( ! options->refseq ) {
fprintf ( stderr, "Please define refseq.\n");
exit (0);
}
/* locate the refseq */
refseq_number = find_refseq (alignment, options->refseq);
if ( options->qry2[0]) refseq_2_number = find_refseq (alignment, options->qry2);
/* associate nodes and positions */
for ( node_id = 2; node_id < no_seqs; node_id++ ) {
node_ctr = 2*no_seqs -1 - node_id;
if ( (leaf+node_ctr)-> number_of_leaves < MIN_NO_LEAVES) continue;
for ( pos=0; pos < alignment->length; pos++) {
if ( alignment->column_gaps[pos] > int_max_gaps) continue;
if ( overlap[pos][node_id] < MAX_OVERLAP && probability[pos][node_id] <= MAX_PROB) {
related[pos][node_id] = 1;
}
}
}
/* recursive cleanup (so parents and children do not appear for the same reason */
for ( pos=0; pos < alignment->length; pos++) {
if ( alignment->column_gaps[pos] > int_max_gaps ) continue;
recursive_cleanup ( root = leaf+2*no_seqs-1 - 1, related[pos], probability[pos] ) ;
}
/* which nodes should be printed? */
for ( node_id = 2; node_id < no_seqs; node_id++ ) {
for ( pos=0; pos < alignment->length; pos++) {
if ( alignment->column_gaps[pos] > int_max_gaps ) continue;
if ( related[pos][node_id] ) {
print[node_id] = 1;
break;
}
}
}
for ( node_id = 2; node_id < no_seqs; node_id++ ) {
node_ctr = 2*no_seqs-1 - node_id;
if ( ! print[node_id] ) continue;
fprintf ( fptr, "\n\nnode %d\n=============\n", node_id);
fprintf ( fptr, " %4s %4s %4s %4s %5s %5s %5s %5s other nodes\n",
"pos", "pdbid", "qry1", "qry2", "entr", "c_entr", "prob", "ovlp");
for ( pos=0; pos < alignment->length; pos++) {
if ( ! related[pos][node_id] ) continue;
in_qry2 = (options->qry2[0]) ? alignment->sequence[refseq_2_number][pos]: '-';
fprintf ( fptr, " %4d %4s %1c %1c %5.1lf %5.1lf %5.1le %5.2lf ",
pos+1, protein->sequence[ almt2prot[pos]].pdb_id,
alignment->sequence[refseq_number][pos],
in_qry2,
score[pos][node_id], complement_score[pos][node_id],
probability[pos][node_id], overlap[pos][node_id] );
/* other nodes which have this same pos as discriminant */
first = 1;
for ( node_id_2 = 2; node_id_2 < no_seqs; node_id_2 ++ ) {
if ( node_id_2 == node_id ) continue;
if ( related[pos][node_id_2] ) {
if ( ! first ) {
fprintf ( fptr, ",");
}
fprintf ( fptr, "%d",node_id_2);
first = 0;
}
}
fprintf ( fptr, "\n");
}
}
fclose (fptr);
/* print out leaves */
sprintf (filename, "%s.leaves", base_filename);
fptr = efopen (filename, "w");
if ( !fptr) return 1;
for ( node_id = 2; node_id < no_seqs; node_id++ ) {
if ( ! print[node_id] ) continue;
node_ctr = 2*no_seqs -1 - node_id;
fprintf ( fptr, "\n\nnode %d\n=============\n", node_id);
print_leaves ( fptr, leaf+node_ctr);
fprintf (fptr, "\n");
}
fclose (fptr);
# endif
return 0;
}