def __init__(self, **kwargs):
self.tree_lineage_names = None
self.config_lineage_names = None
self.is_case_sensitive = kwargs.pop("is_case_sensitive", False)
self.is_fail_on_extra_tree_lineages = kwargs.pop(
"is_fail_on_extra_tree_lineages", True)
self.is_fail_on_extra_configuration_lineages = kwargs.pop(
"is_fail_on_extra_configuration_lineages", True)
self.logger = kwargs.pop("logger")
self.original_to_normalized_lineage_name_map = {}
self.config_name_normalization_report = {}
self.preanalysis_constrained_species_lineages_map = {}
if self.is_case_sensitive:
self.normalized_tree_lineage_names = {}
self.normalized_config_lineage_names = {}
self.species_names = {}
self.preanalysis_constrained_lineage_species_map = {}
else:
self.normalized_tree_lineage_names = OrderedCaselessDict()
self.normalized_config_lineage_names = OrderedCaselessDict()
self.normalized_species_names = OrderedCaselessDict()
self.preanalysis_constrained_lineage_species_map = OrderedCaselessDict(
)
self.extra_tree_lineage_names = []
self.extra_configuration_lineages = []
def read_configuration_table_species(self,
conf_lineage_species_map,
conf_constrained_lineages):
if self.is_case_sensitive:
nccl = {}
else:
nccl = OrderedCaselessDict()
for ln in conf_constrained_lineages:
nccl[ln] = True
for lineage_name in conf_lineage_species_map:
if lineage_name not in nccl:
continue
species_name = conf_lineage_species_map[lineage_name]
if species_name not in self.normalized_species_names:
self.normalized_species_names[species_name] = species_name
else:
species_name = self.normalized_species_names[species_name]
try:
normalized_lineage_name = self.original_to_normalized_lineage_name_map[lineage_name]
except KeyError:
utility.error_exit(
msg="Lineage '{}' not defined (missing on tree?)".format(lineage_name),
logger=self.logger)
if normalized_lineage_name in self.preanalysis_constrained_lineage_species_map:
utility.error_exit(
msg="Duplicate lineage species assignment: '{}'".format(normalized_lineage_name),
logger=self.logger)
self.preanalysis_constrained_lineage_species_map[normalized_lineage_name] = species_name
try:
self.preanalysis_constrained_species_lineages_map[species_name].add(normalized_lineage_name)
except KeyError:
self.preanalysis_constrained_species_lineages_map[species_name] = set([normalized_lineage_name])
self.preanalysis_constrained_species_report()
def __init__(self, citation=None):
"""
Sets up internal dictionary of BibTeX fields, and initializes
if argument is given.
"""
self.bibtype = None
self.citekey = None
if isinstance(citation, BibTexEntry):
self._entry_dict = OrderedCaselessDict(citation._entry_dict)
elif isinstance(citation, dict):
self._entry_dict = OrderedCaselessDict()
for k, v in citation.items():
self._entry_dict[k.lower()] = v
self.bibtype = self._entry_dict.get("bibtype", None)
self.citekey = self._entry_dict.get("citekey", None)
else:
self._entry_dict = OrderedCaselessDict()
self.parse_text(citation)
