[Bioperl-l] Bio::Tree::AnnotatableNode

Han, Mira mirhan at indiana.edu
Thu Jun 19 17:23:40 EDT 2008

My current position is that
I will override the internal_id method to store the id_source ids instead of
the creation_id.
And I will use Annotation::SimpleValue instead of the _tags hash in the
I guess in that case I'll have to implement the add_tag_value etc to use
Annotation::SimpleValue internally?

Another quick questions..
Which is the general style, to use hyphenated tags or just normal words for
keys like this?


On 6/19/08 5:07 PM, "Mira Han" <mirhan at indiana.edu> wrote:

> Hi,
> I have a few questions regarding the design of the AnnotatableNode.
> 1. add_tag_value or Annotation::SimpleValue?
> I have property tags for nodes that can be defined by the user, that contains
> generally simple scalar values,
> I'm currently using the Annotation::SimpleValue to contain them in the node.
> What I'm wondering is..
> should I use the tag/value implementation already in NodeI for these instead?
> 2. I have to also maintain a unique identifier for each node called id_source.
> First I was looking to use the internal_id to store the unique ids.
> But now I realized that we cannot set the internal_id to arbitrary ids,
> We can only get the values already determined.
> So now I'm wondering again should I set this id as a tag/value? Or a
> SimpleAnnotation?
> Or can I modify the code so that we can set the internal_id?
> Mira

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