Bio::TreeIO(3)        User Contributed Perl Documentation       Bio::TreeIO(3)



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-lATbioperl.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-lATbioperl.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:

         http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich
       Email jason-at-bioperl-dot-org

CONTRIBUTORS
       Allen Day <allendayATucla.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
          -internal_node_id : what is stored in the internal node ids,
                              bootstrap values or ids, coded as
                              'bootstrap' or 'id'

   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    :

   newline_each_node
        Title   : newline_each_node
        Usage   : $obj->newline_each_node($newval)
        Function: Get/set newline each node flag which is only applicable
                  for writing tree formats for nhx and newick, will
                  print a newline after each node or paren
        Returns : value of newline_each_node (boolean)
        Args    : on set, new value (a boolean or undef, optional)

   internal_node_id
        Title   : internal_node_id
        Usage   : $obj->internal_node_id($newval)
        Function: Internal Node Id type, coded as 'bootstrap' or 'id'
                  Default is 'id'
        Returns : value of internal_node_id (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   _guess_format
        Title   : _guess_format
        Usage   : $obj->_guess_format($filename)
        Function:
        Example :
        Returns : guessed format of filename (lower case)
        Args    :



perl v5.12.2                                                 February 24, 2011