Provided by: libbio-perl-perl_1.7.6-3_all bug


       Bio::TreeIO - Parser for Tree files


             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";


       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.


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AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-org


       Allen Day <>


       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        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

        Title   : format
        Usage   : $format = $obj->format()
        Function: Get the tree format
        Returns : tree format
        Args    : none

        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)
        Example :
        Returns : guessed format of filename (lower case)
        Args    :