/**
* @param xmlTree
* @param xmlNode
* @param mesNode
* @param mesTree
*/
private void readTree(
Network<?> xmlTree, Node xmlNode, MesquiteTree mesTree, int mesNode, Map otuLookup) {
// store the ID of the OTU, if there is one. We do this
// in a separate hash from whence we later retrieve only
// those OTUs that are actually terminal in the topology.
OTU xmlOTU = xmlNode.getOTU();
if (xmlOTU != null) {
Taxa mesTaxa = mesTree.getTaxa();
int mesTaxon = mesTaxa.findByUniqueID(xmlOTU.getId());
otuLookup.put(mesNode, mesTaxon);
}
// copy the node label and the RDFa annotations
mesTree.setNodeLabel(xmlNode.getLabel(), mesNode);
readAnnotations(mesTree, xmlNode, mesNode, mesTree);
// iterate over children
for (Node xmlChild : xmlTree.getOutNodes(xmlNode)) {
// make child, copy annotations
int mesChild = mesTree.sproutDaughter(mesNode, false);
// copy branch length, if any, and branch annotations
Edge edge = xmlTree.getEdge(xmlNode, xmlChild);
if (edge.getLength() != null) {
mesTree.setBranchLength(mesChild, edge.getLength().doubleValue(), false);
}
readAnnotations(mesTree, edge, mesChild, mesTree);
// traverse deeper
readTree(xmlTree, xmlChild, mesTree, mesChild, otuLookup);
}
}
