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