struct dgNodeRef *dgConstrainedPriorityOrder(struct diGraph *dg)
/* Return traversal of graph in priority order subject to
* constraint that all parents must be output before
* their children regardless of node priority.
* Graph must be cycle free. */
{
struct dlList *sortedList = newDlList();
struct dgNode *graphNode;
struct dlNode *listNode;
struct dgNodeRef *refList = NULL, *ref;
if (dgHasCycles(dg))
errAbort("Call to dgConstrainedPriorityOrder on graph with cycles.");
/* Make up list sorted by priority. */
for (graphNode = dg->nodeList; graphNode != NULL; graphNode = graphNode->next)
{
dlAddValTail(sortedList, graphNode);
graphNode->visited = FALSE;
}
dlSort(sortedList, cmpPriority);
/* Loop taking first member of list with no untraversed parents. */
while (!dlEmpty(sortedList))
{
for (listNode = sortedList->head; listNode->next != NULL; listNode = listNode->next)
{
graphNode = listNode->val;
if (dgParentsAllVisited(graphNode))
{
dlRemove(listNode);
freeMem(listNode);
AllocVar(ref);
ref->node = graphNode;
slAddHead(&refList, ref);
graphNode->visited = TRUE;
break;
}
}
}
freeDlList(&sortedList);
slReverse(&refList);
return refList;
}
void separateEntities(struct dlList *easyList, struct dlList *hardList)
/* Separate out hard (overlapping) entities onto hard list. */
{
struct dlNode *node, *next, *listNode;
int sepCount = 0;
dlSort(easyList, cmpEntities);
for (node = easyList->head; node->next != NULL; node = next)
{
struct entity *ent = node->val;
int eStart = ent->start, eEnd = ent->end;
next = node->next;
for (listNode = easyList->head; listNode->next != NULL; listNode = listNode->next)
{
struct entity *listEnt = listNode->val;
int lStart = listEnt->start, lEnd = listEnt->end;
int start = max(eStart, lStart);
int end = min(eEnd, lEnd);
int overlap = end - start;
if (listEnt != ent && overlap > 0)
{
int eRefCount = slCount(ent->cdaRefList);
int lRefCount = slCount(listEnt->cdaRefList);
/* Move the one with less cDNA to the hard list. */
if (eRefCount > lRefCount)
{
dlRemove(listNode);
dlAddTail(hardList, listNode);
if (listNode == next)
next = node;
}
else
{
dlRemove(node);
dlAddTail(hardList, node);
}
++sepCount;
break;
}
}
}
}