[gt-users] New feature announcement

[Brent Pedersen]

On Sat, Jan 24, 2009 at 3:40 AM, Sascha Steinbiss
<steinbiss at zbh.uni-hamburg.de> wrote:
> Brent Pedersen wrote:
>> thanks! is the z_index going into the main repo soon?
>
> Yes, this may happen quite soon.
>
>> also, a couple stylistic questions.
>> 1) would you accept a patch that switches the use of e.g.
>> Feature.create() and Feature.__init__() i think it's more idiomatic to
>> be able to do
>>>>> f = FeatureNode(seqid, "gene", 100, 900, "+")
>> and then
>>>>> f = FeatureNode.create(ptr)
>> than vice-versa and it could rename to FeatureNode.create_from_ptr()
>
> I agree. What does Gordon think of this? This is an interface change, so
> I would rather not decide this alone.
>
>> 2) would you accept a patch that implements python descriptors so one can use:
>>>>> fnode.strand
>> '+'
>>>>> fnode.strand = '-'
>> instead of fnode.get/set_strand() ?
>
> I think it would be best if both methods were available so the interface
> is not too divergent from the C "get/set" method names. Otherwise, this
> sounds more Python-like, of course.
>

the changes i made do keep the original methods.

>> if either both of those seem reasonable, i'll upload a patch to the tracker.
>
> Thanks! I have already pulles your changes from github and keep them in
> a separate branch, ready to merge if everything is ok. I did some minor
> cleanup though (the old FeatureNode constructor was also called in the
> RecMap, FeatureIndex and Block classes,so I adapted them).
>

oops. i guess did the search and replace in the wrong order.
and next time, i'll create a branch. i just did that locally then
merged into my master.

>> -brent
>
> Have a nice weekend,
> Sascha
>
> --
> Sascha Steinbiss
> Center for Bioinformatics
> University of Hamburg
> Bundesstr. 43
> 20146 Hamburg
> Germany
>
> Email:  steinbiss at zbh.uni-hamburg.de
> URL:    http://www.zbh.uni-hamburg.de/steinbiss
> Phone:  +49 (40) 42838 7322
> FAX:    +49 (40) 42838 7312
>
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