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)