def _getStructure(self,prsd=None,reroot=False):
''' PRIVATE: Acquires a newick string without any
defined branch lengths. '''
if prsd: p = prsd
else: p = newick.newickParser(self.newick).parse()
if reroot:
topo = rearrangement.topology(p)
p = topo.getRoot()
newick.removeBranchLengths(p)
return str(p) + ';'
def findTreeTopology(self, newick):
''' Find a tree by topology, not taking into account branch lengths.
:param newick: a Newick string
:type newick: a string
:return: a tree name (usually an integer index) or None if not found
'''
s = newickParser(newick).parse()
removeBranchLengths(s)
s = str(s) + ';'
return self.findTreeTopologyByStructure(s)
def findTreeTopology(self,newick):
''' Find a tree by topology, not taking into account branch lengths.
:param newick: a Newick string
:type newick: a string
:return: a tree name (usually an integer index) or None if not found
'''
s = newickParser(newick).parse()
removeBranchLengths(s)
s = str(s) + ';'
return self.findTreeTopologyByStructure(s)
def getSimpleNewick(self):
''' Return a Newick string with all taxa name replaced with
successive integers.
:return: a string
'''
o = newick.newickParser(self.newick).parse()
t = base.treeStructure(o)
n = t.getAllLeaves()
for _ in xrange(1,len(n)+1): n[_-1].label = str(_)
return str(o) + ';'
def reinterpretNewick(self, tr):
''' Revert the replacing of taxa names with shortened names by changing
them back to their original form.
:param tr: a Newick string
:type tr: a string
:return: a Newick string with all replaced names
'''
p = newickParser(tr).parse()
nodes = base.treeStructure(p).getAllNodes()
for node in nodes:
l = node.label
if l in self.namedict: node.label = self.namedict[l]
return str(p) + ';'
def reinterpretNewick(self,tr):
''' Revert the replacing of taxa names with shortened names by changing
them back to their original form.
:param tr: a Newick string
:type tr: a string
:return: a Newick string with all replaced names
'''
p = newickParser(tr).parse()
nodes = base.treeStructure(p).getAllNodes()
for node in nodes:
l = node.label
if l in self.namedict: node.label = self.namedict[l]
return str(p) + ';'
def parse(self, newickstr):
''' Parse a newick string and assign the tree to this object. Cannot
already be initialized with a tree.
:return: None
'''
if self.root != None:
raise RearrangementError('Structure already initialized.')
p = newick.newickParser(newickstr)
self.root = p.parse()
self.orig = newickstr
if self.rerootFlag: self.rerootToLeaf(self.rerootLoc)
self._getAllBranches()
self._getForbiddenStates()
self._clearInteriorNodeNames()
if self.rerootFlag: self._lockLeafBranch()
def convertOriginalNewick(self, tr):
''' Return a Newick string with (original) taxa names that are replaced
with the shortened forms as they are defined in this object.
:param tr: a Newick string
:type tr: a string
:return: a Newick string with all replaced names
'''
p = newickParser(tr).parse()
nodes = base.treeStructure(p).getAllNodes()
for node in nodes:
l = node.label
if l in self.namedict.values():
for n in self.namedict:
if self.namedict[n] == l:
node.label = n
break
return str(p) + ';'
def convertOriginalNewick(self,tr):
''' Return a Newick string with (original) taxa names that are replaced
with the shortened forms as they are defined in this object.
:param tr: a Newick string
:type tr: a string
:return: a Newick string with all replaced names
'''
p = newickParser(tr).parse()
nodes = base.treeStructure(p).getAllNodes()
for node in nodes:
l = node.label
if l in self.namedict.values():
for n in self.namedict:
if self.namedict[n] == l:
node.label = n
break
return str(p) + ';'