[Biopython-dev] [Bug 3045] TreeMixin, please define enumerator and other convenience methods

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http://bugzilla.open-bio.org/show_bug.cgi?id=3045





------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2010-04-07 02:44 EST -------
Hi Eric,

(In reply to comment #2)
> > I'm not fond of the name of the existing method get_terminals (which currently
> > returns a list). My feeling is that using just terminals seems nicer (as a
> > property, so no order argument - if you need that use the find method). Is
> > there any advantage to returning a list vs an iterator? Everything is all in
> > memory anyway, right?
> 
> I took the method names from Bio.Nexus.Trees wherever it seemed reasonable --
> one day I'd like Bio.Phylo to be a drop-in replacement for that module (as much
> as possible). Otherwise I'd be fine with a method called terminals().

OK, that is a reasonable argument in favour.

> The tree object doesn't keep a list of terminal nodes under the hood, so to get
> the terminal nodes it does a full search of the tree, with run time linear to
> the number of nodes in the tree. I feel uneasy about properties that don't run
> in O(1) time.

OK, so a property does seem unwise.

> The find* methods return iterators, and the get* methods return lists. I found
> that the results of get* usually needed to be converted to a list immediately,
> for indexing or length-checking, and aren't liable to be unexpectedly large --
> smaller than the whole tree, anyway. Plus, get_terminals() is really just a
> shortcut for list(tree.find_clades(terminal=True)), for those who prefer to
> dive into the module or save some typing.

If there is a good reason, that seems fine.

> > Given a terminals property (be it a read only list or an iterator), one might
> > go further and add a sister property for the internal nodes (non-terminal
> > nodes).
> 
> Apparently there's some demand for it. It would be the same as
> list(tree.find_clades(terminal=False)), and forcing users to learn how find_*
> methods work after they're hooked on get_terminals() has some appeal, but I
> suppose we should just pick a name and add it.

Maybe get_internals() would match, or get_non_terminals() might be clearer.

Peter


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