[Bioperl-l] question about a Bio::Tree::Tree method

Jason Stajich jason at bioperl.org
Thu Nov 26 12:16:17 EST 2009

Emilio - please ask your questions on the list - many people there can  
help answer questions.

get_nodes returns all the nodes in the tree, the options specify the  
order they are returned in.  Depending on your question the order  
probably won't matter so you can just call it without any arguments  
like in the examples and the HOWTO.

The documentation for the method says:
  Title   : get_nodes
         Usage   : my @nodes = $tree‐>get_nodes()
         Function: Return list of Bio::Tree::NodeI objects
         Returns : array of Bio::Tree::NodeI objects
         Args    : (named values) hash with one value
                   order => ’b⎪breadth’ first order or  
’d⎪depth’ first order

So you can provide no arguments and get the default (breadth-first I  
believe) or you can specify
-order => 'd'
-order => 'depth'

to get the nodes in depth-first order.

On Nov 26, 2009, at 7:19 AM, miglio83 at libero.it wrote:

> Hi Jason,
> I'm Emilio Siena, a PhD student of the University of Perugia.
> I have
> a question about the method "get_nodes" of the  "Bio::Tree::Tree"  
> class.
> In
> particular I didn't understand which type of arguments it accepts  
> and in which
> format an argument should be given.
> Thank you in advance!
> Emilio

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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