[Bioperl-l] Need help for implementing a new TreeIO module

[Guillaume Rousse]

Jason Stajich wrote:
> Guillaume -
> 
> Ironic - I was just starting to download a bunch of jpackage stuff and 
> seeing your name everywhere....  Trying to get FOP working so can try 
> and build our docbook HOWTOs on linux.
Funny :)
Actually, I'm not involved anymore in jpackage project, I left Java 
since I discovered perl two years ago. If you need help, you'd better 
ask on the mailing lists, even if they are currently down due to 
migration problems on the boxes hosting the project.

> The thing is you need to build the tree by connecting the nodes, so the 
> order they are created in is very important.  You can't just build the 
> leaves first and then the (internal) nodes later.  You need to build 
> from the top down - if you read a newick format from left to right, that 
> is exactly how we are building the tree up using the EventListener.
> 
> In a way the builder basically assumes you have already have the tree 
> built, just encoded.  So you start with a root node, you add children.  
> For each child you add more children where appropriate until you get to 
> a leaf node and you are done with that recursion.
OK, thanks for the explanations. However, I don't understand how to add 
branch length informations. I guess leave labels are just introduced 
using characters() method, right ?
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