def __init__(self, newick=None, format=0):
# ## From ete2.Tree class definition
self._children = []
self._up = None
self._dist = 1.0
self._support = 1.0
self._count = 0 # added
self._gains = 0 # added
self._losses = 0 # added
self._change = 0 # added
self._events = [] # added
self._taxon_set = None # added
self._already_deleted = [] # added
self.features = set([])
# Add basic features
self.add_features(name='NoName')
self.features.update(['dist', 'support'])
# Initialize tree
if newick is not None:
read_newick(newick, root_node=self, format=format)
if TREEVIEW:
self._faces = _FaceAreas()
for node in self.traverse():
node._taxon_set = set(node.get_species())
def __init__(self, newick=None, format=0):
# ## From ete2.Tree class definition
self._children = []
self._up = None
self._dist = 1.0
self._support = 1.0
self._taxon_set = None # added
self._species_subtree = None # added
self._index = None # added
self.features = set([])
# Add basic features
self.add_features(name='NoName')
self.features.update(['dist', 'support'])
# Initialize tree
if newick is not None:
read_newick(newick, root_node=self, format=format)
if TREEVIEW:
self._faces = _FaceAreas()
for node in self.traverse():
node._taxon_set = set(node.get_species())
def nf(name):
return name
self.set_species_naming_function(nf)
def __init__(self, newick=None, format=0):
### From ete2.Tree class definition
self._children = []
self._up = None
self._dist = 1.0
self._support = 1.0
self._count = 0 # added
self._change = 0 # added
self._fitchset = set([]) # added
self._sankoff = [None,None] # added
self._events = [] # added
self._taxon_set = None # added
self.features = set([])
# Add basic features
self.add_features(name="NoName")
self.features.update(["dist", "support"])
# Initialize tree
if newick is not None:
read_newick(newick, root_node = self, format=format)
if TREEVIEW:
self._faces = _FaceAreas()
for node in self.traverse():
node._taxon_set = set(node.get_species())
def __init__(self, newick=None, alignment=None, alg_format="fasta", \
sp_naming_function=_parse_species, format=0):
self.nexml_tree = FloatTree()
self.nexml_tree.set_anyAttributes_({'xsi:type': 'FloatTree'})
self.nexml_node = TreeNode()
self.nexml_edge = TreeFloatEdge()
self.nexml_node.id = "node_%s" % hash(self)
self.nexml_edge.id = "edge_%s" % hash(self)
self.nexml_project = None
self._nexml_support = LiteralMeta(datatype="float",
property="branch_support",
content=1.0)
self.nexml_edge.length = 0.0
self.nexml_edge.add_meta(self._nexml_support)
# Initialize empty PhyloTree
super(NexmlTree, self).__init__()
self._children = Children()
self._children.node = self
if alignment:
self.link_to_alignment(alignment, alg_format)
if newick:
read_newick(newick, root_node=self, format=format)
self.set_species_naming_function(sp_naming_function)
def __init__(self, newick=None, alignment=None, alg_format="fasta", sp_naming_function=_parse_species, format=0):
self.nexml_tree = FloatTree()
self.nexml_tree.set_anyAttributes_({"xsi:type": "FloatTree"})
self.nexml_node = TreeNode()
self.nexml_edge = TreeFloatEdge()
self.nexml_node.id = "node_%s" % hash(self)
self.nexml_edge.id = "edge_%s" % hash(self)
self.nexml_project = None
self._nexml_support = LiteralMeta(datatype="float", property="branch_support", content=1.0)
self.nexml_edge.length = 0.0
self.nexml_edge.add_meta(self._nexml_support)
# Initialize empty PhyloTree
super(NexmlTree, self).__init__()
self._children = Children()
self._children.node = self
if alignment:
self.link_to_alignment(alignment, alg_format)
if newick:
read_newick(newick, root_node=self, format=format)
self.set_species_naming_function(sp_naming_function)
def __init__(self, newick=None, format=0):
# ## From ete2.Tree class definition
self._children = []
self._up = None
self._dist = 1.0
self._support = 1.0
self.features = set([])
self._taxon_set = None # added
self._species_subtree = None # added
self.root = False # added
self.duplication = False # added
self.speciation = False # added
self.ambiguous = False # added
self.leaf = False # added
# Add basic features
self.add_features(name="NoName")
self.features.update(["dist", "support"])
# Initialize tree
if newick is not None:
read_newick(newick, root_node=self, format=format)
if TREEVIEW:
self._faces = _FaceAreas()
for node in self.traverse():
node._taxon_set = set(node.get_species())
def nf(name):
return name
self.set_species_naming_function(nf)