Bio::Nexml::Factory(3pm) User Contributed Perl Documentation Bio::Nexml::Factory(3pm)
NAME
Bio::Nexml::Factory - A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents
SYNOPSIS
Do not use this module directly. It shoulde be used through
Bio::NexmlIO, Bio::SeqIO::nexml, Bio::AlignIO::nexml, or
Bio::TreeIO::nexml
DESCRIPTION
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.
FEEDBACK
Mailing Lists
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
Support
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.
Reporting Bugs
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chase Miller
Email chmille4@gmail.com
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
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
create_bperl_aln
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]
create_bperl_tree
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]
create_bperl_seq
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]
create_bphylo_tree
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
create_bphylo_node
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
create_bphylo_aln
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
create_bphylo_seq
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
create_bphylo_taxa
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
create_bphylo_datum
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
CREATOR
bioperl_create
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
perl v5.14.2 2012-03-02 Bio::Nexml::Factory(3pm)