Reference

Bio::Nexml::Factory(3pm)

A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Chase Miller

Email [email protected]

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

History