def getBipartitionFoundInTreeByIndex(self,tr,brind,topol=None):
''' Given a tree node and a branch index, return the associated
bipartition.
:param tr: a tree name
:param brind: a branch index in that tree, a la post-order traversal
:return: a :class:`.tree.bipartition` object
'''
# Check for presence of tree.
if (not topol) and (not tr in self.graph.node): return None
# Acquire metadata for tree.
if not topol:
tr = self.graph.node[tr]['tree']
topl = tr.toTopology()
# Get bipartition for branch.
nodes = postOrderTraversal(topl.getRoot())
if not brind in xrange(len(nodes)): return None
bnode = nodes[brind]
bipa = tree.bipartition(topl,bnode.parent)
# Return the bipartition.
return bipa
def getBipartitionFoundInTreeByIndex(self, tr, brind, topol=None):
''' Given a tree node and a branch index, return the associated
bipartition.
:param tr: a tree name
:param brind: a branch index in that tree, a la post-order traversal
:return: a :class:`.tree.bipartition` object
'''
# Check for presence of tree.
if (not topol) and (not tr in self.graph.node): return None
# Acquire metadata for tree.
if not topol:
tr = self.graph.node[tr]['tree']
topl = tr.toTopology()
# Get bipartition for branch.
nodes = postOrderTraversal(topl.getRoot())
if not brind in xrange(len(nodes)): return None
bnode = nodes[brind]
bipa = tree.bipartition(topl, bnode.parent)
# Return the bipartition.
return bipa
def lockBranchFoundInTree(self,tr,br):
''' Given a tree node and a branch object, add a given
bipartition to the bipartition lock list. Returns
bipartition if locked.
:param tr: a tree name
:param br: a branch in that tree
:type br: a :class:`.base.treeBranch` object
:return: a :class:`.tree.bipartition` object that has been locked or None
'''
# Check for presence of tree.
g = self.graph.node
if (not tr in g): return None
# Acquire metadata for tree.
tr = self.getTree(tr)
topl = tr.toTopology()
# Get bipartition for branch.
bipa = tree.bipartition(topl,br)
# Toggle the lock.
self.toggleLock(bipa)
return bipa
def lockBranchFoundInTree(self, tr, br):
''' Given a tree node and a branch object, add a given
bipartition to the bipartition lock list. Returns
bipartition if locked.
:param tr: a tree name
:param br: a branch in that tree
:type br: a :class:`.base.treeBranch` object
:return: a :class:`.tree.bipartition` object that has been locked or None
'''
# Check for presence of tree.
g = self.graph.node
if (not tr in g): return None
# Acquire metadata for tree.
tr = self.getTree(tr)
topl = tr.toTopology()
# Get bipartition for branch.
bipa = tree.bipartition(topl, br)
# Toggle the lock.
self.toggleLock(bipa)
return bipa
def getNeighborsOfBranch(self, br):
''' Get corresponding neighbors of a branch in this vertex's tree. '''
tr = self.getTree()
topl = tr.toTopology()
bipa = tree.bipartition(topl, br)
return self.getNeighborsOfBipartition(bipa)
def getNeighborsOfBranch(self, br):
''' Get corresponding neighbors of a branch in this vertex's tree. '''
tr = self.getTree()
topl = tr.toTopology()
bipa = tree.bipartition(topl,br)
return self.getNeighborsOfBipartition(bipa)
def dup(topo, where=None):
if where: new = topology(toLeaf=where)
else: new = topology()
new.fromNewick(topo.toNewick())
if where:
fake = tree.bipartition(topo, new.fakebranch)
# Retain locks.
for lock in new.locked:
if lock != fake: new.locked.append(lock)
return new
def getBipartitions(self):
''' Get all bipartitions.
:return: a list of :class:`.tree.bipartition` objects
'''
bili = []
br = self.branches
for b in br:
bi = tree.bipartition(self, b)
if not bi in bili: bili.append(bi)
return bili
def iterBipartitions(self):
''' Return a generator to iterate over all bipartitions for this vertex.
'''
# Get tree object.
tr = self.getTree()
# Get corresponding topology.
topo = tr.toTopology()
nodes = postOrderTraversal(topo.getRoot())
# Get branches + bipartitions of the topology.
bp = []
br = [x.parent for x in nodes]
for b in br:
if b:
bi = tree.bipartition(topo,b)
yield bi
else: yield None
def iterBipartitions(self):
''' Return a generator to iterate over all bipartitions for this vertex.
'''
# Get tree object.
tr = self.getTree()
# Get corresponding topology.
topo = tr.toTopology()
nodes = postOrderTraversal(topo.getRoot())
# Get branches + bipartitions of the topology.
bp = []
br = [x.parent for x in nodes]
for b in br:
if b:
bi = tree.bipartition(topo, b)
yield bi
else:
yield None
def lockBranch(self, branch):
''' Given a branch, lock it such that no transitions can ever occur
across it.
:param branch: a branch
:type branch: a :class:`.newick.branch` object
:return: a boolean (True if success)
'''
# Transform to bipartition object.
bipart = tree.bipartition(self, branch)
# Has already been locked?
if bipart in self.locked: return True
# Is it even in this topology?
isintopol = (branch in self.branches)
if (not isintopol): return False
self.locked.append(bipart)
return True
def _flipOperation(self, opname, br):
''' PRIVATE: Try a particular rearrangement operation on a flipped
version of the tree. '''
# Check what bipartition is represented.
bipart = tree.bipartition(self, br)
# Get a leaf that can be rerooted to.
newleaf = None
leaves = base.treeStructure.leaves(br.child)
curleaf = sorted(self.getAllLeaves(), key=lambda d: d.label)[0]
for leaf in leaves:
if leaf != curleaf:
newleaf = leaf
break
if (newleaf == None): return []
# Make flipped tree structure.
n = dup(self, newleaf)
# Get corresponding branch.
b = n.getBranchFromBipartition(bipart)
# Do possible moves from the other way.
op = getattr(n, opname)
return op(b, flip=False)