def __init__(self, conv_cfg): NexsonConverter.__init__(self, conv_cfg) self._from_phylografter = conv_cfg.get('_from_phylografter', True) if self._from_phylografter: self._workaround_phylografter_rel_bug = True # pg uses "property" instead of "rel" self._add_tree_xsi_type = True self._coercing_literals = True # phylografter uses "true" for isLeaf else: self._workaround_phylografter_rel_bug = False self._add_tree_xsi_type = False
def __init__(self, conv_cfg): NexsonConverter.__init__(self, conv_cfg) self.input_format = conv_cfg.input_format self.use_default_root_atts = conv_cfg.get('use_default_root_atts', True) self.otu_label = conv_cfg.get('otu_label', 'ot:originalLabel') if self.otu_label.startswith('^'): self.otu_label = self.otu_label[1:] self._migrating_from_bf = _is_badgerfish_version(self.input_format) # TreeBase and phylografter trees often lack the tree xsi:type self._adding_tree_xsi_type = True # we have started using ot:ottTaxonName, ot:originalLabel or ot:ottId self._creating_otu_label = True
def __init__(self, conv_cfg): NexsonConverter.__init__(self, conv_cfg) self.suppress_label_if_ott_taxon = getattr( conv_cfg, 'suppress_label_if_ott_taxon', True)
def __init__(self, conv_cfg): NexsonConverter.__init__(self, conv_cfg) self.suppress_label_if_ott_taxon = getattr(conv_cfg, 'suppress_label_if_ott_taxon', True)
def __init__(self, conv_cfg): NexsonConverter.__init__(self, conv_cfg)
def __init__(self, conv_cfg): NexsonConverter.__init__(self, conv_cfg) self.output_format = conv_cfg.output_format self._badgerfish_style_conversion = _is_badgerfish_version( conv_cfg.output_format)
def __init__(self, conv_cfg): NexsonConverter.__init__(self, conv_cfg) self.output_format = conv_cfg.output_format self._badgerfish_style_conversion = _is_badgerfish_version(conv_cfg.output_format)
def __init__(self, conv_cfg): NexsonConverter.__init__(self, conv_cfg) self.remove_old_structs = getattr(conv_cfg, 'remove_old_structs', True)