Fixed resnik distances.

scripts/geneontology/go-distance/godist.c

@@ -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;
+    int i, j;
-    for (i=0; i<n->childrenc; i++) 
+    for (i=0; i<term_array_size; i++) {
-	clear_flags(n->children[i]);
+	term_array[i]->visited = 0;
-    n->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);
+    while (retval != EOF) {
+	printf(".");
+    	fflush(stdout);
+	terms[(*termc)++] = get_term(term);
 	retval = fscanf(fd, " %10s ", term);
-    if (retval != EOF) {
-	terms[*termc++] = get_term(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 (i=0; i<termc; i++) {
-	for (int j=0; j<termc; j++) {
+	for (j=0; j<termc; j++) {
-
+            printf("%f ", resnik(terms[i], terms[j]));
+	}
+	printf("\n");
+    }
        
 
     fclose(fd);

scripts/geneontology/go-distance/godist.h

@@ -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