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.

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/MailList.shtml - About the mailing lists

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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email jason@bioperl.org Allen Day <allenday@ucla.edu> The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::TreeIO(); 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 :