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from __future__ import absolute_import
from __future__ import print_function
# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ETE is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
# License for more details.
#
# You should have received a copy of the GNU General Public License
# along with ETE. If not, see <http://www.gnu.org/licenses/>.
#
#
# ABOUT THE ETE PACKAGE
# =====================
#
# ETE is distributed under the GPL copyleft license (2008-2015).
#
# If you make use of ETE in published work, please cite:
#
# Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabaldon.
# ETE: a python Environment for Tree Exploration. Jaime BMC
# Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24
#
# Note that extra references to the specific methods implemented in
# the toolkit may be available in the documentation.
#
# More info at http://etetoolkit.org. Contact: huerta@embl.de
#
#
# #END_LICENSE#############################################################
import sys
from ._nexml import MixedContainer, FloatTree, TreeFloatEdge, TreeNode, LiteralMeta
from .. import PhyloTree
from ..phylo.phylotree import _parse_species
from ..parser.newick import read_newick
class Children(list):
def append(self, item):
list.append(self, item)
item.nexml_edge.source = self.node.nexml_node.id
item.nexml_edge.target = item.nexml_node.id
class NexmlTree(PhyloTree):
"""
Special PhyloTree object with nexml support
"""
def __repr__(self):
return "NexML ETE tree <%s>" %hex(hash(self))
def _get_dist(self):
return self.nexml_edge.get_length()
def _set_dist(self, value):
try:
self.nexml_edge.set_length(value)
except ValueError:
raise
def _get_support(self):
return self._nexml_support.content
def _set_support(self, value):
try:
self._nexml_support.content = float(value)
except ValueError:
raise
def _get_name(self):
return self.nexml_node.get_label()
def _set_name(self, value):
try:
self.nexml_node.set_label(value)
except ValueError:
raise
def _get_children(self):
return self._children
def _set_children(self, value):
if isinstance(value, Children) and \
len(set([type(n)==type(self) for n in value]))<2:
self._children = value
else:
raise ValueError("children:wrong type")
dist = property(fget=_get_dist, fset=_set_dist)
support = property(fget=_get_support, fset=_set_support)
children = property(fget=_get_children, fset=_set_children)
name = property(fget=_get_name, fset=_set_name)
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 set_nexml_project(self, nexml_obj):
self.nexml_project = nexml_obj
def build(self, node):
self.nexml_tree = FloatTree()
tree = self.nexml_tree
tree.build(node)
# This detects the outgroup of the tree even if the root tag
# is not set in any node
rootid = set([e.source for e in tree.edge]) - set([e.target for e in tree.edge])
nodeid2node = {rootid.pop(): self}
for xmledge in tree.edge:
child = nodeid2node.setdefault(xmledge.target, self.__class__() )
parent = nodeid2node.setdefault(xmledge.source, self.__class__() )
child.name = xmledge.target
child.nexml_node.id = xmledge.target
parent.name = xmledge.source
parent.nexml_node.id = xmledge.source
child.nexml_edge = xmledge
if xmledge.length is not None:
child.dist = float(xmledge.length)
parent.add_child(child)
for xmlnode in tree.node:
# just a warning. I don't know if this can occur
if xmlnode.id not in nodeid2node:
print("Unused node", xmlnode.id, file=sys.stderr)
continue
ete_node = nodeid2node[xmlnode.id]
ete_node.nexml_node = xmlnode
if xmlnode.label:
ete_node.name = xmlnode.label
elif xmlnode.id is not None:
ete_node.name = xmlnode.id
def export(self, outfile=sys.stdout, level=0, namespace_='', name_='FloatTree', namespacedef_=''):
if self.nexml_tree:
info = [(n.nexml_edge, n.nexml_node) for n in self.traverse()]
self.nexml_node.set_root(True)
self.nexml_tree.set_edge([i[0] for i in info])
self.nexml_tree.set_node([i[1] for i in info])
self.nexml_tree.export(outfile=outfile, level=level, name_=name_, namespacedef_=namespacedef_)
def exportChildren(self, outfile, level, namespace_='', name_='FloatTree'):
sorted_nodes = []
sorted_edges = []
for n in self.traverse():
# process node
node_obj = self.mixedclass_(MixedContainer.CategoryComplex,
MixedContainer.TypeNone, 'node', n.nexml_node)
sorted_nodes.append(node_obj)
# process edge
if n.nexml_edge:
edge_obj = self.mixedclass_(MixedContainer.CategoryComplex,
MixedContainer.TypeNone, 'edge', n.nexml_edge)
sorted_edges.append(edge_obj)
# process the nodes and edges
self.tree.content_ = sorted_nodes + sorted_edges
for item_ in self.tree.content_:
item_.export(outfile, level, item_.name, namespace_)
# end class AbstractTreeSub
NexmlNode = NexmlTree
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