{Tiv dZddlmZddlmZddlmZddlmZddlmZddlmZeeeedZ dd lm Z e e d <d Z d Z d ZddZy#e $rYwxYw)zI/O function wrappers for phylogenetic tree formats. This API follows the same semantics as Biopython's ``SeqIO`` and ``AlignIO``. )File)BaseTree)NewickIO)NeXMLIO)NexusIO) PhyloXMLIO)newicknexusphyloxmlnexml)CDAOIOcdaoc+Ktj|5}tt|d|fi|Ed{dddy7 #1swYyxYww)alParse a file iteratively, and yield each of the trees it contains. If a file only contains one tree, this still returns an iterable object that contains one element. Examples -------- >>> import Bio.Phylo >>> trees = Bio.Phylo.parse('PhyloXML/apaf.xml', 'phyloxml') >>> for tree in trees: ... print(tree.rooted) True parseN)r as_handlegetattrsupported_formats)fileformatkwargsfps @/home/agent/.local/lib/python3.12/site-packages/Bio/Phylo/_io.pyrr$sZ  M>7,V4g>rLVLLLMMLMMs+AAAA AAA Ac t||fi|}t|} t|td#t$r tddwxYw#t$r|cYSwxYw)zParse a file in the given format and return a single tree. Raises a ``ValueError`` if there are zero or multiple trees -- if this occurs, use ``parse`` instead to get the complete sequence of trees. z There are no trees in this file.Nz;There are multiple trees in this file; use parse() instead.)rnext StopIteration ValueError)rrrtree_gentrees rreadr7ss Gv00H~X XVWW G;<$FG  s1 A A AAc t|tjtjfr|g}t j |d5}t t|d||fi|}ddd|S#1swYSxYw)z6Write a sequence of trees to file in the given format.zw+writeN) isinstancerTreeCladerrrr)treesrrrrns rr!r!Jsm%(--89 d #Mr 7G%f-w 7r LV LM HM Hs A**A4Nc @|i}t||fi|}t|||fi|S)z&Convert between two tree file formats.)rr!)in_file in_formatout_file out_format parse_argsrr%s rconvertr-Ts2 '9 3 3E * 7 77)N)__doc__Bior Bio.Phylorrrrrrr ImportErrorrrr!r-r.rr4sr       &f M&X& 8i  s AAA