def __init__(self, newick = None, text_array = None, \
fdist=clustvalidation.default_dist):
# Default dist is spearman_dist when scipy module is loaded
# otherwise, it is set to euclidean_dist.
# Initialize basic tree features and loads the newick (if any)
TreeNode.__init__(self, newick)
self._fdist = None
self._silhouette = None
self._intercluster_dist = None
self._intracluster_dist = None
self._profile = None
self._std_profile = None
# Cluster especific features
self.features.add("intercluster_dist")
self.features.add("intracluster_dist")
self.features.add("silhouette")
self.features.add("profile")
self.features.add("deviation")
# Initialize tree with array data
if text_array:
self.link_to_arraytable(text_array)
if newick:
self.set_distance_function(fdist)
def __init__(self, newick=None, alignment=None, alg_format="fasta", \
sp_naming_function=_parse_species, format=0):
# _update names?
self._name = "NoName"
self._species = "Unknown"
self._speciesFunction = None
# Caution! native __init__ has to be called after setting
# _speciesFunction to None!!
TreeNode.__init__(self, newick=newick, format=format)
# This will be only executed after reading the whole tree,
# because the argument 'alignment' is not passed to the
# PhyloNode constructor during parsing
if alignment:
self.link_to_alignment(alignment, alg_format)
if newick:
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, **kargs):
# _update names?
self._name = "NoName"
self._species = "Unknown"
self._speciesFunction = None
# Caution! native __init__ has to be called after setting
# _speciesFunction to None!!
TreeNode.__init__(self, newick=newick, format=format, **kargs)
# This will be only executed after reading the whole tree,
# because the argument 'alignment' is not passed to the
# PhyloNode constructor during parsing
if alignment:
self.link_to_alignment(alignment, alg_format)
if newick:
self.set_species_naming_function(sp_naming_function)
