def get_data( self, tree_index=0 ):
"""
Returns trees.
Trees are actually an array of JsonDicts. It's usually one tree, except in the case of Nexus
"""
file_ext = self.original_dataset.datatype.file_ext
file_name = self.original_dataset.file_name
parseMsg = None
jsonDicts = []
rval = { 'dataset_type': self.dataset_type }
if file_ext == "nhx": # parses newick files
newickParser = Newick_Parser()
jsonDicts, parseMsg = newickParser.parseFile( file_name )
elif file_ext == "phyloxml": # parses phyloXML files
phyloxmlParser = Phyloxml_Parser()
jsonDicts, parseMsg = phyloxmlParser.parseFile( file_name )
elif file_ext == "nex": # parses nexus files
nexusParser = Nexus_Parser()
jsonDicts, parseMsg = nexusParser.parseFile( file_name )
jsonDicts = jsonDicts[ int( tree_index ) ]
rval["trees"] = parseMsg
rval[ "data" ] = jsonDicts
rval[ "msg"] = parseMsg
return rval
def get_data(self, tree_index=0):
"""
Returns trees.
Trees are actually an array of JsonDicts. It's usually one tree, except in the case of Nexus
"""
file_ext = self.original_dataset.datatype.file_ext
file_name = self.original_dataset.file_name
parseMsg = None
jsonDicts = []
rval = {'dataset_type': self.dataset_type}
if file_ext in ["newick", "nhx"]: # parses newick files
newickParser = Newick_Parser()
jsonDicts, parseMsg = newickParser.parseFile(file_name)
elif file_ext == "phyloxml": # parses phyloXML files
phyloxmlParser = Phyloxml_Parser()
jsonDicts, parseMsg = phyloxmlParser.parseFile(file_name)
elif file_ext == "nex": # parses nexus files
nexusParser = Nexus_Parser()
jsonDicts, parseMsg = nexusParser.parseFile(file_name)
jsonDicts = jsonDicts[int(tree_index)]
rval["trees"] = parseMsg
rval["data"] = jsonDicts
rval["msg"] = parseMsg
return rval