/ 
BioPerl-1.007000
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Nexml::Factory

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

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