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Christopher Fields
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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->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.


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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:


AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org


Allen Day <allenday@ucla.edu>


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
   -internal_node_id : what is stored in the internal node ids, 
                       bootstrap values or ids, coded as 
                       'bootstrap' or 'id'


 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   : 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)


 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)


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