def __init__(self):
super(Phyloxml_Parser, self).__init__()
self.phyloTree = PhyloTree()
self.tagsOfInterest = {
"clade": "",
"name": "name",
"branch_length": "length",
"confidence": "bootstrap",
"events": "events"
}
def _parseNewickToJson(self, newickString, treeName=None, nameMap=None):
"""parses a newick representation of a tree into a PhyloTree data structure,
which can be easily converted to json"""
self.phyloTree = PhyloTree()
newickString = self.cleanNewickString(newickString)
if nameMap:
newickString = self._mapName(newickString, nameMap)
self.phyloTree.root = self.parseNode(newickString, 0)
if nameMap:
self.phyloTree.addAttributesToRoot({"treeName": treeName})
return self.phyloTree.generateJsonableDict()
