Linux and UNIX Man Pages

Linux & Unix Commands - Search Man Pages

bio::nexml::factory(3pm) [debian man page]

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)
Man Page

Featured Tech Videos