def __init__(self, prop_dict, taxomachine_wrapper=None, taxonomy=None, taxon=None):
if taxon is None:
taxon = TaxonWrapper(taxomachine_wrapper=taxomachine_wrapper,
taxonomy=taxonomy,
prop_dict=prop_dict)
TaxonHolder.__init__(self, taxon)
self._score = prop_dict.get('score')
self._is_approximate_match = prop_dict.get('is_approximate_match')
def __init__(self, prop_dict, taxomachine_wrapper=None, taxonomy=None, taxon=None):
if taxon is None:
taxon = TaxonWrapper(taxomachine_wrapper=taxomachine_wrapper,
taxonomy=taxonomy,
prop_dict=prop_dict)
TaxonHolder.__init__(self, taxon)
self._score = prop_dict.get('score')
self._is_approximate_match = prop_dict.get('is_approximate_match')
def __init__(self,
prop_dict,
treemachine_wrapper=None,
graph_of_life=None,
taxon=None,
nearest_taxon=None,
node_id=None):
self._treemachine_wrapper = treemachine_wrapper
self._graph_of_life = graph_of_life
if node_id is None:
self._node_id = prop_dict['mrca_node_id']
else:
self._node_id = node_id
if taxon is None:
oi = prop_dict.get('ott_id')
if oi == 'null':
oi = None
if oi is not None:
taxon_dict = {'ot:ottId': oi,
'rank': prop_dict.get('mrca_rank'),
'ot:ottTaxonName': prop_dict.get('mrca_name'),
'unique_name': prop_dict.get('mrca_unique_name'),
'treemachine_node_id': self.node_id
}
#TODO should write wrappers for getting the taxomachine wrapper from treemachine wrapper...
taxon = TaxonWrapper(prop_dict=taxon_dict)
if nearest_taxon is None:
taxon_dict = {'ot:ottId': prop_dict['nearest_taxon_mrca_ott_id'],
'rank': prop_dict.get('nearest_taxon_mrca_rank'),
'ot:ottTaxonName': prop_dict.get('nearest_taxon_mrca_name'),
'unique_name': prop_dict.get('nearest_taxon_mrca_unique_name'),
'treemachine_node_id': prop_dict.get('nearest_taxon_mrca_node_id')
}
assert prop_dict['nearest_taxon_mrca_ott_id'] != 'null'
#TODO should write wrappers for getting the taxomachine wrapper from treemachine wrapper...
self._nearest_taxon = TaxonWrapper(prop_dict=taxon_dict)
else:
self._nearest_taxon = nearest_taxon
TaxonHolder.__init__(self, taxon)
if self._taxon is not None:
assert (nearest_taxon is None) or (nearest_taxon is self._taxon)
self._nearest_taxon = self._taxon
self._subtree_newick = None
self._synth_sources = prop_dict.get('synth_sources')
self._in_synth_tree = prop_dict.get('in_synth_tree')
self._tax_source = prop_dict.get('tax_source')
self._in_graph = prop_dict.get('in_graph')
self._num_tips = prop_dict.get('num_tips')
self._num_synth_children = prop_dict.get('num_synth_children')