void GeneOntology::writeTrees(){
populateRecursiveValues();
// compute depths
computeDepths(m_cellularComponentHandle,0);
computeDepths(m_molecularFunctionHandle,0);
computeDepths(m_biologicalProcessHandle,0);
int withoutDepth=0;
for(map<GeneOntologyIdentifier,GeneOntologyDomain>::iterator i=m_termDomains.begin();
i!=m_termDomains.end();i++){
GeneOntologyIdentifier handle=i->first;
if(m_depths.count(handle)==0){
withoutDepth++;
}
}
cout<<"Gene ontology terms without depth information: "<<withoutDepth<<endl;
writeOntologyProfile(GENE_ONTOLOGY_DOMAIN_biological_process);
writeOntologyProfile(GENE_ONTOLOGY_DOMAIN_cellular_component);
writeOntologyProfile(GENE_ONTOLOGY_DOMAIN_molecular_function);
}
void GeneOntology::computeDepths(GeneOntologyIdentifier handle,int depth){
if(m_depths.count(depth)==1){
return;
}
m_depths[handle]=depth;
bool skipDifferentDomain=true;
vector<GeneOntologyIdentifier> children;
getChildren(handle,&children);
for(int i=0;i<(int)children.size();i++){
GeneOntologyIdentifier child=children[i];
if(skipDifferentDomain && getDomain(child)!=getDomain(handle)){
continue;
}
computeDepths(child,depth+1);
}
}
/*public*/
void
BufferSubgraph::computeDepth(int outsideDepth)
{
clearVisitedEdges();
// find an outside edge to assign depth to
DirectedEdge *de=finder.getEdge();
#if GEOS_DEBUG
cerr<<"outside depth: "<<outsideDepth<<endl;
#endif
//Node *n=de->getNode();
//Label *label=de->getLabel();
// right side of line returned by finder is on the outside
de->setEdgeDepths(Position::RIGHT, outsideDepth);
copySymDepths(de);
//computeNodeDepth(n, de);
computeDepths(de);
}
