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