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Fixed resnik distances.

This commit is contained in:
Einar Ryeng 2007-05-15 18:16:07 +00:00
parent 335efe231a
commit c7bfefe358
2 changed files with 43 additions and 14 deletions
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49
scripts/geneontology/go-distance/godist.c
View File

@ -71,6 +71,9 @@ int godist_init() {
total_ann += n->acc_evidence[i];
printf("Using %d annotations.\n", total_ann);
print_term(get_term("GO:0006006"));
print_term(get_term("GO:0019318"));
print_term(get_term("GO:0005996"));
print_term(get_bp());
/*
print_term(get_term("GO:0040007"));
@ -155,10 +158,12 @@ float go_distance(char *term1, char *term2) {
}
void clear_flags(struct node *n) {
int i;
for (i=0; i<n->childrenc; i++)
clear_flags(n->children[i]);
n->visited = 0;
int i, j;
for (i=0; i<term_array_size; i++) {
term_array[i]->visited = 0;
for (j=0; j<12; j++)
term_array[i]->temp_acc[j] = 0;
}
}
void add_link(char *parent_id, char *child_id) {
@ -210,19 +215,27 @@ struct node *get_term(char *term) {
}
void accumulate_evidence(struct node *n) {
int i;
acc_ev(n);
for (i=0; i<12; i++) {
n->acc_evidence[i] = n->temp_acc[i];
}
}
void acc_ev(struct node *n) {
int i, j;
if (n->visited)
return;
n->visited = 1;
for (i=0; i<12; i++)
n->acc_evidence[i] = n->evidence[i];
n->temp_acc[i] = n->evidence[i];
for (i=0; i<(n->childrenc); i++) {
if (!n->children[i]->visited) {
accumulate_evidence(n->children[i]);
acc_ev(n->children[i]);
for (j=0; j<12; j++)
n->acc_evidence[j] += n->children[i]->acc_evidence[j];
n->temp_acc[j] += n->children[i]->temp_acc[j];
}
}
}
@ -270,7 +283,7 @@ void calc_ic(struct node *n, unsigned int evidence) {
if (evidence & 1<<i)
ann += (float) n->acc_evidence[i];
n->ic = -log(ann/total_ann);
printf("%f\n", n->ic);
/* printf("%f\n", n->ic);*/
}
struct node *common_subsumer(struct node *n1, struct node *n2) {
@ -288,7 +301,7 @@ struct node *common_subsumer(struct node *n1, struct node *n2) {
if ((!retval) || (anc1[i]->ic > retval->ic))
retval = anc1[i];
if (retval)
printf("Retval: %s\n", retval->term);
;// printf("Retval: %s\n", retval->term);
else
printf("No value to return");
return retval;
@ -313,9 +326,13 @@ float resnik(struct node *n1, struct node *n2) {
int read_terms(FILE *fd, struct node *terms[], int *termc) {
char term[11];
int retval;
printf("read_terms\n");
retval = fscanf(fd, " %10s ", term);
if (retval != EOF) {
terms[*termc++] = get_term(term);
while (retval != EOF) {
printf(".");
fflush(stdout);
terms[(*termc)++] = get_term(term);
retval = fscanf(fd, " %10s ", term);
}
return retval;
}
@ -326,11 +343,15 @@ void build_dataset() {
int i, j;
FILE *fd = fopen("dimension", "r");
read_terms(fd, terms, &termc);
for (int i=0; i<termc; i++) {
for (int j=0; j<termc; j++) {
for (i=0; i<termc; i++) {
for (j=0; j<termc; j++) {
printf("%f ", resnik(terms[i], terms[j]));
}
printf("\n");
}
fclose(fd);

8
scripts/geneontology/go-distance/godist.h
View File

@ -33,6 +33,9 @@ struct node {
/* Accumulated evidence codes */
int acc_evidence[12];
/* Working memory */
int temp_acc[12];
/* Parent count and parents */
int parentc;
struct node *parents[MAX_PARENTS];
@ -65,5 +68,10 @@ void calc_ic(struct node *n, unsigned int evidence);
void clear_flags(struct node *n);
void print_term(struct node *n);
void add_ancestors(int *ancc, struct node *anc[], struct node *n);
void calculate_ics(unsigned int);
void acc_ev(struct node*);
#endif