Manual Reference Pages - BIO::PHYLO::PARSERS::JSON (3)
Bio::Phylo::Parsers::Json - Parser used by Bio::Phylo::IO, no serviceable parts inside
This module is used to import NeXML data that was re-formatted as JSON, using
the mapping implemented by XML::XML2JSON. This module is experimental in that
complex NeXML-to-JSON mapped strings may fail to yield valid NeXML (and,
consequently, valid Bio::Phylo objects) in the round trip. The reason for this
is that the XML2JSON omits xmlns declarations in its JSON output. We try to work
around this here by re-introducing the default namespaces, but if any additional
ones were present in the original NeXML (e.g. to specify namspaces for metadata
predicates) these cant be reconstructed. In addition, the JSON that XML2JSON
produces doesnt preserve element order. We try to be lenient about this when
parsing the intermediate NeXML, though it is actually invalid.
There is a mailing list at <https://groups.google.com/forum/#!forum/bio-phylo>
for any user or developer questions and discussions.
If you use Bio::Phylo in published research, please cite it:
<B>Rutger A VosB>, <B>Jason CaravasB>, <B>Klaas HartmannB>, <B>Mark A JensenB>
and <B>Chase MillerB>, 2011. Bio::Phylo - phyloinformatic analysis using Perl.
BMC Bioinformatics <B>12B>:63.
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