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Bio::Tree::NodeNHX(3pm) 				User Contributed Perl Documentation				   Bio::Tree::NodeNHX(3pm)

NAME
Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags SYNOPSIS
use Bio::Tree::NodeNHX; my $nodeA = Bio::Tree::NodeNHX->new(); my $nodeL = Bio::Tree::NodeNHX->new(); my $nodeR = Bio::Tree::NodeNHX->new(); my $node = Bio::Tree::NodeNHX->new(); $node->add_Descendents($nodeL); $node->add_Descendents($nodeR); print "node is not a leaf " if( $node->is_leaf); DESCRIPTION
Makes a Tree Node with NHX tags, suitable for building a Tree. See Bio::Tree::Node for a full list of functionality. 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 - Aaron Mackey Email amackey@virginia.edu CONTRIBUTORS
The NHX (New Hampshire eXtended) format was created by Chris Zmasek, and is described at: http://sourceforge.net/projects/forester-atv/ 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::Tree::NodeNHX->new(); Function: Builds a new Bio::Tree::NodeNHX object Returns : Bio::Tree::NodeNHX Args : -left => pointer to Left descendent (optional) -right => pointer to Right descenent (optional) -branch_length => branch length [integer] (optional) -bootstrap => bootstrap value (string) -description => description of node -id => unique id for node -nhx => hashref of NHX tags and values nhx_tag Title : nhx_tag Usage : my $tag = $nodenhx->nhx_tag(%tags); Function: Set tag-value pairs for NHX nodes Returns : none Args : hashref to update the tags/value pairs OR with a scalar value update the bootstrap value by default perl v5.14.2 2012-03-02 Bio::Tree::NodeNHX(3pm)

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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)
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