bio::treeio::nexml(3pm) [debian man page]
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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Bio::TreeIO::svggraph(3pm) User Contributed Perl Documentation Bio::TreeIO::svggraph(3pm) NAME
Bio::TreeIO::svggraph - A simple output format that converts a Tree object to an SVG output SYNOPSIS
use Bio::TreeIO; my $in = Bio::TreeIO->new(-file => 'input', -format => 'newick'); my $out = Bio::TreeIO->new(-file => '>output', -format => 'svggraph'); while( my $tree = $in->next_tree ) { my $svg_xml = $out->write_tree($tree); } DESCRIPTION
This outputs a tree as an SVG graphic using the SVG::Graph API 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 - Brian OConnor Email brian.oconnor-at-excite.com CONTRIBUTORS
Allen Day Guillaume Rousse, Guillaume-dot-Rousse-at-inria-dot-fr 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::TreeIO::svggraph->new(); Function: Builds a new Bio::TreeIO::svggraph object Returns : Bio::TreeIO::svggraph Args :-width => image width (default 1600) -height => image height (default 1000) -margin => margin (default 30) -stroke => stroke color (default 'black') -stroke_width=> stroke width (default 2) -font_size=> font size (default '10px') -nomalize => undef or 'log' (default is undef) write_tree Title : write_tree Usage : $treeio->write_tree($tree); Function: Write a tree out to data stream in newick/phylip format Returns : none Args : Bio::Tree::TreeI object decorateRoot Title : _decorateRoot Usage : internal methods Function: Example : Returns : Args : next_tree Title : next_tree Usage : Function: Sorry not possible with this format Returns : none Args : none perl v5.14.2 2012-03-02 Bio::TreeIO::svggraph(3pm)