| Bio::Nexml::Factory(3pm) | User Contributed Perl Documentation | Bio::Nexml::Factory(3pm) |
Bio::Nexml::Factory - A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents
Do not use this module directly. It shoulde be used through Bio::NexmlIO, Bio::SeqIO::nexml, Bio::AlignIO::nexml, or Bio::TreeIO::nexml
This is a factory/utility module in the Nexml namespace. It contains methods that are needed by multiple modules.
This module handles the creation of BioPerl objects from Bio::Phylo objects and vice versa, which is used to read and write nexml documents to and from BioPerl objects.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
Email chmille4@gmail.com
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = Bio::Nexml::Factory->new(); Function: Builds a new L<Bio::Nexml::Factory> object Returns : L<Bio::Nexml::Factory> object Args : none
Title : create_bperl_aln Usage : my @alns = $factory->create_bperl_aln($objIO); Function: Converts Bio::Phylo::Matrices::Matrix objects into L<Bio::SimpleAlign> objects Returns : an array of L<Bio::SimpleAlign> objects Args : Bio::NexmlIO, Bio::SeqIO, Bio::AlignIO, or Bio::TreeIO
see [http://search.cpan.org/~rvosa/Bio-Phylo/lib/Bio/Phylo/Project.pm Bio::Phylo::Project]
Title : create_bperl_tree Usage : my @trees = $factory->create_bperl_seq($objIO); Function: Converts Bio::Phylo::Forest::Tree objects into L<Bio::Tree::Tree> objects Returns : an array of L<Bio::Tree::Tree> objects Args : Bio::NexmlIO, Bio::SeqIO, Bio::AlignIO, or Bio::TreeIO
see [http://search.cpan.org/~rvosa/Bio-Phylo/lib/Bio/Phylo/Project.pm Bio::Phylo::Project]
Title : create_bperl_seq Usage : my @seqs = $factory->create_bperl_seq($objIO); Function: Converts Bio::Phylo::Matrices::Datum objects into L<Bio::Seq> objects Returns : an array of L<Bio::Seq> objects Args : Bio::NexmlIO, Bio::SeqIO, Bio::AlignIO, or Bio::TreeIO
see [http://search.cpan.org/~rvosa/Bio-Phylo/lib/Bio/Phylo/Project.pm Bio::Phylo::Project]
Title : create_bphylo_tree Usage : my $bphylo_tree = $factory->create_bphylo_tree($bperl_tree); Function: Converts a L<Bio::Tree::Tree> object into Bio::Phylo::Forest::Tree object Returns : a Bio::Phylo::Forest::Tree object Args : Bio::Tree::Tree object
Title : create_bphylo_node Usage : my $bphylo_node = $factory->create_bphylo_node($bperl_node); Function: Converts a L<Bio::Tree::Node> object into Bio::Phylo::Forest::Node object Returns : a Bio::Phylo::Forest::Node object Args : L<Bio::Tree::Node> object
Title : create_bphylo_aln Usage : my $bphylo_aln = $factory->create_bphylo_aln($bperl_aln); Function: Converts a L<Bio::SimpleAlign> object into Bio::Phylo::Matrices::Matrix object Returns : a Bio::Phylo::Matrices::Matrix object Args : Bio::SimpleAlign object
Title : create_bphylo_seq Usage : my $bphylo_seq = $factory->create_bphylo_seq($bperl_seq); Function: Converts a L<Bio::Seq> object into Bio::Phylo::Matrices::Matrix object Returns : a Bio::Phylo::Matrices::Matrix object Args : Bio::Seq object
Title : create_bphylo_seq Usage : my $taxa = $factory->create_bphylo_taxa($bperl_obj); Function: creates a taxa object from the data attached to a bioperl object Returns : a Bio::Phylo::Taxa object Args : L<Bio::Seq> object, or L<Bio::SimpleAlign> object, or L<Bio::Tree::Tree> object
Title : create_bphylo_datum
Usage : my $bphylo_datum = $factory->create_bphylo_datum($bperl_datum);
Function: Converts a L<Bio::Seq> object into Bio::Phylo::Matrices::datum object
Returns : a Bio::Phylo::Matrices::datum object
Args : Bio::Seq object, Bio::Phylo::Taxa object,
[optional] arrayref to SeqFeatures,
[optional] key => value pairs to pass to Bio::Phylo constructor
Title : bioperl_create
Usage : $bioperl_obj = $fac->bioperl_create($obj_type, $biophylo_proj);
Function: Create a specified bioperl object using a Bio::Phylo project
Args : scalar string ('aln', 'tree', 'seq') type designator
Bio::Phylo::Project object
Returns : Appropriate BioPerl object
| 2018-10-27 | perl v5.26.2 |