[BioRuby] BioRuby: newick parser

[Naohisa GOTO]

Hi Pjotr,

The design of Bio::Tree that a nod has no tree information and
only tree object have node information was what I intended.
This makes easy to split a tree into subtrees, to build a tree
from scratch, to concatenate trees, to replace nodes and edges, etc.
However, as you described, for traversing a static tree,
indirect operations are needed which are sometimes annoying.

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org


On Mon, 12 Mar 2012 17:24:38 +0100
Pjotr Prins <pjotr.public14 at thebird.nl> wrote:

> On Mon, Mar 12, 2012 at 03:18:48PM +0900, Naohisa GOTO wrote:
> > When writing HOWTO based on BioPerl HOWTO:Trees,
> > (http://bioruby.open-bio.org/wiki/HOWTO:Trees but still incomplete)
> > I'm thinking to add/modify some API about speficying nodes/edges.
> 
> After some trying I agree. The Bio::Tree::Node object should know
> 'more' about its state. I would like to do something like:
> 
>   root.leaf?.should == false
>   node = root.childeren.first
>   node.leaf?.should == false
>   node2 == node.childeren.first
>   node.leaf?.should == true
>   node2.edge(node).distance.should == 1.34
> 
> now I need to do something like 
> 
>   tree = @tree
>   node = tree.get_node_by_name('node')
>   tree.get_edge(node, tree.parent(node)).distance.should == 1.34
> 
> which uses the tree state to get a node edge, and does not feel that
> intuitive.
> 
> I'll try to extend Bio::Tree for bio-alignment, see what works.
> 
> Pj.