Bio::TreeIO - Parser for Tree files
{ use Bio::TreeIO; my $treeio = new Bio::TreeIO('-format' => 'newick', '-file' => 'globin.dnd'); while( my $tree = $treeio->next_tree ) { print "Tree is ", $tree->size, "\n"; } }
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.
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/MailList.shtml - About the mailing lists
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 email or the web:
bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/
Email jason@bioperl.org
Describe contact details here
Additional contributors names and emails here
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = new Bio::TreeIO(); Function: Builds a new Bio::TreeIO object Returns : Bio::TreeIO Args :
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
Title : write_tree Usage : $treeio->write_tree($tree); Function: Writes a tree onto the stream Returns : none Args : Bio::Tree::TreeI
Title : attach_EventHandler Usage : $parser->attatch_EventHandler($handler) Function: Adds an event handler to listen for events Returns : none Args : Bio::Event::EventHandlerI
Title : _eventHandler Usage : private Function: Get the EventHandler Returns : Bio::Event::EventHandlerI Args : none
Title : _load_format_module Usage : *INTERNAL TreeIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args :
Title : _guess_format Usage : $obj->_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args :
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.