bio::treeio::newickparser(3pm) [debian man page]
Bio::TreeIO::NewickParser(3pm) User Contributed Perl Documentation Bio::TreeIO::NewickParser(3pm) NAME
Module which implements a newick string parser as a finite state machine which enables it to parse the full Newick specification. Taken largely from the Ensembl Compara file with the same name (Bio::EnsEMBL::Compara::Graph::NewickParser), this module adapts the parser to work with BioPerl's event handler-based parsing scheme. This module is used by nhx.pm and newick.pm, and is NOT called directly. Instead, both of those parsing modules extend this module in order to gain access to the main parsing method. SYNOPSIS
# From newick.pm use base qw(Bio::TreeIO Bio::TreeIO::NewickParser); # in the next_tree method... $self->parse_newick($_); DESCRIPTION
This module correctly parses the Newick and NHX formats, sending calls to the BioPerl TreeEventHandler when appropriate in order to build and populate the node 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 - Jessica Severin (EnsEMBL implementation), Greg Jordan (BioPerl adaptation) perl v5.14.2 2012-03-02 Bio::TreeIO::NewickParser(3pm)
Check Out this Related Man Page
Bio::TreeIO(3pm) User Contributed Perl Documentation Bio::TreeIO(3pm) NAME
Bio::TreeIO - Parser for Tree files SYNOPSIS
{ use Bio::TreeIO; my $treeio = Bio::TreeIO->new('-format' => 'newick', '-file' => 'globin.dnd'); while( my $tree = $treeio->next_tree ) { print "Tree is ", $tree->number_nodes, " "; } } DESCRIPTION
This is the driver module for Tree reading from data streams and flatfiles. This is intended to be able to create Bio::Tree::TreeI 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 - Jason Stajich Email jason-at-bioperl-dot-org CONTRIBUTORS
Allen Day <allenday@ucla.edu> 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->new(); Function: Builds a new Bio::TreeIO object Returns : Bio::TreeIO Args : a hash. useful keys: -format : Specify the format of the file. Supported formats: newick Newick tree format nexus Nexus tree format nhx NHX tree format svggraph SVG graphical representation of tree tabtree ASCII text representation of tree lintree lintree output format next_tree Title : next_tree Usage : my $tree = $treeio->next_tree; Function: Gets the next tree off the stream Returns : Bio::Tree::TreeI or undef if no more trees Args : none write_tree Title : write_tree Usage : $treeio->write_tree($tree); Function: Writes a tree onto the stream Returns : none Args : Bio::Tree::TreeI attach_EventHandler Title : attach_EventHandler Usage : $parser->attatch_EventHandler($handler) Function: Adds an event handler to listen for events Returns : none Args : Bio::Event::EventHandlerI _eventHandler Title : _eventHandler Usage : private Function: Get the EventHandler Returns : Bio::Event::EventHandlerI Args : none _load_format_module Title : _load_format_module Usage : *INTERNAL TreeIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args : _guess_format Title : _guess_format Usage : $obj->_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args : perl v5.14.2 2012-03-02 Bio::TreeIO(3pm)