Provided by: libbio-perl-perl_1.6.901-2_all bug

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, "\n";
             }
         }

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    :