def testReroot(self):
tree = NX.DiGraph()
edges = [(1,2), (1,3), (2,4), (2,5), (5,6), (5,7), (5,8)]
for edge in edges:
tree.add_edge(edge[0], edge[1])
nxTree = NXTree(tree)
nxTree.setWeight(1, 2, 3.1)
to = [x for x in nxTree.breadthFirstTraversal()]
testTree = copy.deepcopy(nxTree)
testTree.reroot(1)
t = [x for x in testTree.breadthFirstTraversal()]
assert t == to
testTree = copy.deepcopy(nxTree)
testTree.reroot(2)
t = [x for x in testTree.breadthFirstTraversal()]
assert t[0] == 2
assert sorted(t[1:4]) == [1,4,5]
assert sorted(t[4:]) == [3,6,7,8]
assert testTree.getWeight(2, 1) == 3.1
testTree = copy.deepcopy(nxTree)
testTree.reroot(7)
t = [x for x in testTree.breadthFirstTraversal()]
assert t[0] == 7
assert t[1] == 5
assert sorted(t[2:5]) == [2,6,8]
assert sorted(t[5:7]) == [1,4]
assert t[7] == 3
def parseString(self, newickString, addImpliedRoots=True):
self.nxTree = NXTree()
self.inString = self.__filterWhitespace(newickString)
self.__createBracketTable()
self.nextId = 0
assert self.inString[-1] == ';'
self.__addNode(0, len(self.inString) - 1, None, addImpliedRoots)
self.nxTree.isTree()
return self.nxTree
def testTraversals(self):
for tree in self.trees:
nxTree = NXTree(tree)
dfs = [x for x in nxTree.preOrderTraversal()]
assert len(set(dfs)) == len(nxTree.nxDg.nodes())
dfs = [x for x in nxTree.postOrderTraversal()]
assert len(set(dfs)) == len(nxTree.nxDg.nodes())
bfs = [x for x in nxTree.breadthFirstTraversal()]
assert len(set(bfs)) == len(nxTree.nxDg.nodes())
def starTree(self):
self.tree = NXTree()
label = 0
self.tree.nxDg.add_node(label)
self.tree.rootId = label
for name in self.pathMap.keys():
label += 1
self.tree.nxDg.add_edge(0, label)
self.tree.setName(label, name)
self.tree.setWeight(0, label, SeqFile.branchLen)
def testRoot(self):
for tree in self.trees:
nxTree = NXTree(tree)
rootId = nxTree.getRootId()
assert rootId is not None
assert nxTree.getParent(rootId) is None