def enable_ncl():
from dendropy.dataio import nexusreader_ncl
if nexusreader_ncl.DENDROPY_NCL_AVAILABILITY:
_LOG.debug('Enabling Nexus Class Library bindings: using NCL NEXUS parser')
ioclient.register("nexus", nexusreader_ncl.NexusReader, nexuswriter.NexusWriter, nexustreeiter.tree_source_iter)
else:
_LOG.debug('Nexus Class Library bindings are not available: using native Python NEXUS parser')
def disable_ncl():
_LOG.debug(
'Disabling Nexus Class Library bindings: using native Python NEXUS parser'
)
from dendropy.dataio import nexusreader_py
ioclient.register("nexus", nexusreader_py.NexusReader,
nexuswriter.NexusWriter, nexustreeiter.tree_source_iter)
def enable_ncl():
from dendropy.dataio import nexusreader_ncl
if nexusreader_ncl.DENDROPY_NCL_AVAILABILITY:
_LOG.debug(
'Enabling Nexus Class Library bindings: using NCL NEXUS parser')
ioclient.register("nexus", nexusreader_ncl.NexusReader,
nexuswriter.NexusWriter,
nexustreeiter.tree_source_iter)
else:
_LOG.debug(
'Nexus Class Library bindings are not available: using native Python NEXUS parser'
)
def disable_ncl():
_LOG.debug('Disabling Nexus Class Library bindings: using native Python NEXUS parser')
from dendropy.dataio import nexusreader_py
ioclient.register("nexus", nexusreader_py.NexusReader, nexuswriter.NexusWriter, nexustreeiter.tree_source_iter)
from dendropy.dataio import nexuswriter
from dendropy.dataio import fasta
from dendropy.dataio import phylip
from dendropy.dataio import nexml
from dendropy.dataio import beast
from dendropy.dataio.ioclient import get_reader, get_writer, tree_source_iter, multi_tree_source_iter
_LOG = messaging.get_logger(__name__)
###############################################################################
## Data Schema Handlers
##
## Syntax is:
## ioclient.register(<FORMAT NAME>, <READER TYPE>, <WRITER TYPE>, <TREE ITERATOR>)
##
ioclient.register("nexus", nexusreader_py.NexusReader, nexuswriter.NexusWriter, nexustreeiter.tree_source_iter)
ioclient.register("newick", newick.NewickReader, newick.NewickWriter, newick.tree_source_iter)
ioclient.register("nexus/newick", None, None, nexustreeiter.generalized_tree_source_iter)
ioclient.register("fasta", fasta.FastaReader, fasta.FastaWriter, None)
ioclient.register("dnafasta", fasta.DNAFastaReader, fasta.FastaWriter, None)
ioclient.register("rnafasta", fasta.RNAFastaReader, fasta.FastaWriter, None)
ioclient.register("proteinfasta", fasta.ProteinFastaReader, fasta.FastaWriter, None)
ioclient.register("phylip", phylip.PhylipReader, phylip.PhylipWriter, None)
ioclient.register("nexml", nexml.NexmlReader, nexml.NexmlWriter, None)
ioclient.register("beast-summary-tree", beast.BeastSummaryTreeReader, None, beast.summary_tree_source_iter)
###############################################################################
## NEXUS Parser Implementation Selection
##
def disable_ncl():
from dendropy.dataio import nexuswriter
from dendropy.dataio import fasta
from dendropy.dataio import phylip
from dendropy.dataio import nexml
from dendropy.dataio import beast
from dendropy.dataio.ioclient import get_reader, get_writer, tree_source_iter, multi_tree_source_iter
_LOG = messaging.get_logger(__name__)
###############################################################################
## Data Schema Handlers
##
## Syntax is:
## ioclient.register(<FORMAT NAME>, <READER TYPE>, <WRITER TYPE>, <TREE ITERATOR>)
##
ioclient.register("nexus", nexusreader_py.NexusReader, nexuswriter.NexusWriter,
nexustreeiter.tree_source_iter)
ioclient.register("newick", newick.NewickReader, newick.NewickWriter,
newick.tree_source_iter)
ioclient.register("nexus/newick", None, None,
nexustreeiter.generalized_tree_source_iter)
ioclient.register("fasta", fasta.FastaReader, fasta.FastaWriter, None)
ioclient.register("dnafasta", fasta.DNAFastaReader, fasta.FastaWriter, None)
ioclient.register("rnafasta", fasta.RNAFastaReader, fasta.FastaWriter, None)
ioclient.register("proteinfasta", fasta.ProteinFastaReader, fasta.FastaWriter,
None)
ioclient.register("phylip", phylip.PhylipReader, phylip.PhylipWriter, None)
ioclient.register("nexml", nexml.NexmlReader, nexml.NexmlWriter, None)
ioclient.register("beast-summary-tree", beast.BeastSummaryTreeReader, None,
beast.summary_tree_source_iter)
###############################################################################