[Bioperl-l] tree building, analysis interfaces (long)

[Elia Stupka]

> cool. One thing about iterators,and this is an aside, in terms of the
> pipeline, I think I mentioned to u before that fetching of objects
> are done through datahandlers which are essentially method calls.
> We don't really support "while" loops in the pipeline and it really
> doesn't make sense to do so. Thus is it worth having a get_all_xxx
> method as an alternative for the xxxIO modules? Elia what do u think?

I think rather than forcing all external modules to provide it we can have
one InputCreate that does a get_all by doing a while loop if you know what
I mean.

> Very. I will find time to look at this if and when things settle down
> here. We aren't using these modules that much right now but I expect so
> once we start doing the ortholog pipelines. Feel free to modify as u
> please :)

Read: my crazy boss Elia keeps shifting my priorities around and has
recently decided that before we move onto interesting stuff we need to get
the boring stuff, Ciona annotation, sorted out ;)

Elia

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