Works a bit better.

scripts/geneontology/go-distance/godist.c

@@ -49,6 +49,7 @@ int godist_init() {
     printf(" %d edges\n", link_count);
 
     accumulate_evidence(get_bp());
+    print_term(get_bp());
 }
 
 void godist_exit() {
@@ -83,6 +84,7 @@ int godist_read_term(FILE *fd) {
         struct node *n = (struct node*) malloc(sizeof(struct node));
 	n->parentc = 0;
 	n->childrenc = 0;
+	n->visited = 0;
 	for (i=0; i<12; i++) {
 	    n->evidence[i] = ev[i];
 	    n->acc_evidence[i] = 0;
@@ -91,8 +93,13 @@ int godist_read_term(FILE *fd) {
 
 	/* add to hash table */
 	e.key = n->term;
+	e.data = (void*)n;
 	res = hsearch(e, ENTER);
-
+/*	if (res);
+	    printf("hash-insert: %s", ((struct node*)res->data)->term);
+        else
+            printf("hash-insert: error");
+*/
         term_array[term_array_size++] = n;
     } 
 
@@ -106,6 +113,14 @@ float go_distance(char *term1, char *term2) {
 
 void add_node(char *term, int parentc, struct node **parents) {
     
+
+}
+
+void clear_flags(struct node *n) {
+    int i;
+    for (i=0; i<n->childrenc; i++) 
+	clear_flags(n->children[i]);
+    n->visited = 0;
 }
 
 void add_link(char *parent_id, char *child_id) {
@@ -135,30 +150,43 @@ void add_link(char *parent_id, char *child_id) {
         printf("FIXME: increase child count");
 	return;
     }
-    parent->children[parent->childrenc++] = child;
-    child->parents[child->parentc++] = parent;
+    parent->children[parent->childrenc] = child;
+    parent->childrenc++;
+/*    printf("adding %x as child of %x\n", child, parent);*/
+    child->parents[child->parentc] = parent;
+    child->parentc++;
 }
 
 struct node *get_bp() {
     ENTRY e, *ep;
     e.key = "GO:0008150";
     ep = hsearch(e, FIND);
-    if (ep)
-	return ep;
-    if (ep == ESRCH)
-	printf("ESRCH\n");
-    if (ep == ESRCH)
-	printf("ENOMEM\n");
+ 
+    if (ep) {
+/*	printf("BP is %x and %s\n", (int) ep->data, ep->key);
+	printf("%d\n", ((struct node*)ep->data)->childrenc );
+	printf("%s\n", ((struct node*)ep->data)->term);*/
+	return ep->data;
+    }
     return NULL;
 }
 
 void accumulate_evidence(struct node *n) {
     int i, j;
+    if (n->visited)
+        return;
+
+    for (i=0; i<12; i++)
+        n->acc_evidence[i] = n->evidence[i];
+
     for (i=0; i<(n->childrenc); i++) {
-	accumulate_evidence(n->children[i]);
-	for (j=0; j<12; j++)
-            n->evidence[j] += n->children[i]->evidence[j];
+	if (!n->children[i]->visited) {
+            accumulate_evidence(n->children[i]);
+	    for (j=0; j<12; j++)
+                n->acc_evidence[j] += n->children[i]->acc_evidence[j];
+        }
     }
+/*    printf(".");*/
 }
 
 void print_terms() {
@@ -168,3 +196,18 @@ void print_terms() {
     }
 }
 
+void print_term(struct node *n) {
+    int i;
+    printf("%s\n", n->term);
+    printf("    children: %d\n", n->childrenc);
+    printf("    parents:  %d\n", n->parentc);
+    printf("    evidence: ");
+    for (i=0; i<12; i++)
+        printf("%d ", n->evidence[i]);
+    printf("\n");
+    printf("    accumulated evidence: ");
+    for (i=0; i<12; i++)
+        printf("%d ", n->acc_evidence[i]);
+    printf("\n");
+}
+

scripts/geneontology/go-distance/godist.h

@@ -27,6 +27,9 @@ struct node {
     /* Child count and children */
     int childrenc;
     struct node *children[MAX_CHILDREN];
+
+    /* Flag to ensure that a node is only visited once in DAG operations */
+    char visited;
 };
 
 struct node* term_array[MAX_NODES];