def __init__(self, phyloxml_clade=None, phyloxml_phylogeny=None, **kargs):
if not phyloxml_phylogeny:
self.phyloxml_phylogeny = Phylogeny()
else:
self.phyloxml_phylogeny = phyloxml_phylogeny
if not phyloxml_clade:
self.phyloxml_clade = Clade()
self.phyloxml_clade.set_branch_length(0.0)
self.phyloxml_clade.set_name("NoName")
#self.__support = Confidence(valueOf_=1.0, type_="branch_support")
#self.phyloxml_clade.add_confidence(self.__support)
else:
self.phyloxml_clade = phyloxml_clade
super(PhyloxmlTree, self).__init__(**kargs)
def __init__(self, phyloxml_clade=None, phyloxml_phylogeny=None, **kargs):
if not phyloxml_phylogeny:
self.phyloxml_phylogeny = Phylogeny()
else:
self.phyloxml_phylogeny = phyloxml_phylogeny
if not phyloxml_clade:
self.phyloxml_clade = Clade()
self.phyloxml_clade.set_branch_length(0.0)
self.phyloxml_clade.set_name("NoName")
self.__support = Confidence(valueOf_=1.0, type_="branch_support")
self.phyloxml_clade.add_confidence(self.__support)
else:
self.phyloxml_clade = phyloxml_clade
super(PhyloxmlTree, self).__init__(**kargs)
class PhyloxmlTree(PhyloTree):
''' PhyloTree object supporting phyloXML format. '''
def __repr__(self):
return "PhyloXML ETE tree <%s>" % hex(hash(self))
def _get_dist(self):
v = self.phyloxml_clade.get_branch_length_attr()
if v is None:
v = self.phyloxml_clade.get_branch_length()
if v is None:
self._set_dist(self._dist)
v = self.phyloxml_clade.get_branch_length_attr()
return float(v)
def _set_dist(self, value):
try:
self.phyloxml_clade.set_branch_length(float(value))
self.phyloxml_clade.set_branch_length_attr(float(value))
except ValueError:
raise
def _get_support(self):
if len(self.phyloxml_clade.confidence) == 0:
_c = Confidence(valueOf_=1.0, type_="branch_support")
self.phyloxml_clade.add_confidence(_c)
return float(self.phyloxml_clade.confidence[0].valueOf_)
def _set_support(self, value):
self._get_support()
self.phyloxml_clade.confidence[0].valueOf_ = float(value)
def _get_name(self):
return self.phyloxml_clade.get_name()
def _set_name(self, value):
try:
self.phyloxml_clade.set_name(value)
except ValueError:
raise
def _get_children(self):
return self.phyloxml_clade.clade
dist = property(fget=_get_dist, fset=_set_dist)
support = property(fget=_get_support, fset=_set_support)
children = property(fget=_get_children)
name = property(fget=_get_name, fset=_set_name)
def __init__(self, phyloxml_clade=None, phyloxml_phylogeny=None, **kargs):
if not phyloxml_phylogeny:
self.phyloxml_phylogeny = Phylogeny()
else:
self.phyloxml_phylogeny = phyloxml_phylogeny
if not phyloxml_clade:
self.phyloxml_clade = Clade()
self.phyloxml_clade.set_branch_length(0.0)
self.phyloxml_clade.set_name("NoName")
#self.__support = Confidence(valueOf_=1.0, type_="branch_support")
#self.phyloxml_clade.add_confidence(self.__support)
else:
self.phyloxml_clade = phyloxml_clade
super(PhyloxmlTree, self).__init__(**kargs)
def build(self, node):
nodetype = Tag_pattern_.match(node.tag).groups()[-1]
if nodetype == 'phylogeny':
self.phyloxml_phylogeny.buildAttributes(node, node.attrib, [])
elif nodetype == 'clade':
if "branch_length" in node.attrib:
node.attrib["branch_length_attr"] = node.attrib[
"branch_length"]
self.phyloxml_clade.buildAttributes(node, node.attrib, [])
for child in node:
nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
self.buildChildren(child, node, nodeName_, nodetype=nodetype)
def buildChildren(self,
child_,
node,
nodeName_,
fromsubclass=False,
nodetype=None):
if nodetype == 'phylogeny':
baseclass = self.phyloxml_phylogeny
if nodeName_ == 'clade':
self.build(child_)
else:
baseclass.buildChildren(child_, node, nodeName_)
elif nodetype == 'clade':
baseclass = self.phyloxml_clade
if nodeName_ == 'clade':
new_node = self.add_child()
new_node.build(child_)
else:
baseclass.buildChildren(child_, node, nodeName_)
def export(self,
outfile=sys.stdout,
level=0,
namespace_='phy:',
name_='Phylogeny',
namespacedef_=''):
if not self.up:
self.phyloxml_phylogeny.clade = self.phyloxml_clade
self.phyloxml_clade.clade = self.children
self.phyloxml_phylogeny.export(outfile=outfile,
level=level,
name_=name_,
namespacedef_=namespacedef_)
else:
self.phyloxml_clade.clade = self.children
self.phyloxml_clade.export(outfile=outfile,
level=level,
name_=name_,
namespacedef_=namespacedef_)
class PhyloxmlTree(PhyloTree):
''' PhyloTree object supporting phyloXML format. '''
def __repr__(self):
return "PhyloXML ETE tree <%s>" %hex(hash(self))
def _get_dist(self):
return self.phyloxml_clade.get_branch_length()
def _set_dist(self, value):
try:
self.phyloxml_clade.set_branch_length(float(value))
except ValueError:
raise
def _get_support(self):
return self.__support.get_valueOf_()
def _set_support(self, value):
try:
self.__support.set_valueOf_(float(value))
except ValueError:
raise
def _get_name(self):
return self.phyloxml_clade.get_name()
def _set_name(self, value):
try:
self.phyloxml_clade.set_name(value)
except ValueError:
raise
def _get_children(self):
return self.phyloxml_clade.clade
dist = property(fget=_get_dist, fset=_set_dist)
support = property(fget=_get_support, fset=_set_support)
children = property(fget=_get_children)
name = property(fget=_get_name, fset=_set_name)
def __init__(self, phyloxml_clade=None, phyloxml_phylogeny=None, **kargs):
if not phyloxml_phylogeny:
self.phyloxml_phylogeny = Phylogeny()
else:
self.phyloxml_phylogeny = phyloxml_phylogeny
if not phyloxml_clade:
self.phyloxml_clade = Clade()
self.phyloxml_clade.set_branch_length(0.0)
self.phyloxml_clade.set_name("NoName")
self.__support = Confidence(valueOf_=1.0, type_="branch_support")
self.phyloxml_clade.add_confidence(self.__support)
else:
self.phyloxml_clade = phyloxml_clade
super(PhyloxmlTree, self).__init__(**kargs)
def build(self, node):
nodetype = Tag_pattern_.match(node.tag).groups()[-1]
if nodetype == 'phylogeny':
self.phyloxml_phylogeny.buildAttributes(node, node.attrib, [])
elif nodetype == 'clade':
self.phyloxml_clade.buildAttributes(node, node.attrib, [])
for child in node:
nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
self.buildChildren(child, node, nodeName_, nodetype=nodetype)
def buildChildren(self, child_, node, nodeName_, fromsubclass=False, nodetype=None):
if nodetype == 'phylogeny':
baseclass = self.phyloxml_phylogeny
if nodeName_ == 'clade':
self.build(child_)
else:
baseclass.buildChildren(child_, node, nodeName_)
elif nodetype == 'clade':
baseclass = self.phyloxml_clade
if nodeName_ == 'clade':
new_node = self.add_child()
new_node.build(child_)
else:
baseclass.buildChildren(child_, node, nodeName_)
def export(self, outfile=sys.stdout, level=0, namespace_='phy:', name_='Phylogeny', namespacedef_=''):
if not self.up:
self.phyloxml_phylogeny.clade = self.phyloxml_clade
self.phyloxml_clade.clade = self.children
self.phyloxml_phylogeny.export(outfile=outfile, level=level, name_=name_, namespacedef_=namespacedef_)
else:
self.phyloxml_clade.clade = self.children
self.phyloxml_clade.export(outfile=outfile, level=level, name_=name_, namespacedef_=namespacedef_)