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bio::tree::nodenhx(3pm) [debian man page]

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::TreeIO::nexml(3pm) 				User Contributed Perl Documentation				   Bio::TreeIO::nexml(3pm)

NAME
Bio::TreeIO::nexml - A TreeIO driver module for parsing NeXML tree files SYNOPSIS
use Bio::TreeIO; my $in = Bio::TreeIO->new(-file => 'data.nexml' -format => 'Nexml'); while( my $tree = $in->next_tree ) { } DESCRIPTION
This is a driver module for parsing tree data in a NeXML format. For more information on NeXML, visit <http://www.nexml.org>. 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 _ next_tree Title : next_tree Usage : my $tree = $treeio->next_tree Function: Gets the next tree in the stream Returns : L<Bio::Tree::TreeI> Args : none doc Title : doc Usage : $treeio->doc Function: Returns the biophylo nexml document object Returns : Bio::Phylo::Project Args : none or Bio::Phylo::Project object rewind Title : rewind Usage : $treeio->rewind Function: Resets the stream Returns : none Args : none write_tree Title : write_tree Usage : $treeio->write_tree($tree); Function: Writes a tree onto the stream Returns : none Args : L<Bio::Tree::TreeI> perl v5.14.2 2012-03-02 Bio::TreeIO::nexml(3pm)
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