IMHO zero should not be used as a way to filter out positional/non-positional
features
'type' can be used to filter out what is not needed, i.e
/das/source/features?segment=P99999 returns all features
/das/source/features?segment=P99999:1,150 returns all features within 1..150
region (i,e the positional features)
/das/source/features?segment=P99999;type=annotation returns all features that
have type annotation ( or non-positional or whatever )
cheers
E
On 30/07/2010 16:00, Andy Jenkinson wrote:
Hi list,
I'd like to canvas for opinion on what is "expected" behaviour concerning how
servers respond to features queries in some circumstances. So, bear with me...
Since protein DAS came along, the format of the segment parameter no longer
requires the start and end position. Personally, my take on this has always
been that this means that these two queries are effectively identical:
/das/source/features?segment=P99999
/das/source/features?segment=P99999:1,150 [i.e. the full length of the
protein]
This interpretation is reflected in the 1.6 spec, with the advantage that it is quite
easy to explain the behaviour (use parts of the spec also use a "if omitted, the
default is XYX" paradigm). If you follow this interpretation, nonpositional features
(those without start/end positions) will always be returned no matter what the start and
end are, or indeed whether they are included (since behaviour in both cases is
identical). For me this is fine because nonpositional features are annotations that apply
to the whole sequence/object, which includes all parts of it.
Leyla came to a different view from me, reasoning that only the former of these
queries should return nonpositional features because they are really outside
the range of the second request. She has suggested that queries like these
could be possible ways to further control whether nonpositional and/or
positional features are returned:
/das/source/features?segment=P99999:0,0 [only nonpositional features]
/das/source/features?segment=P99999:0,150 [all positional and
nonpositional features]
I guess this would be an additional functionality as I do not know of any
clients or servers that use zero as a meaningful query range, but i recognise
the logic so would like to know: what do others think? How do your existing
servers function?
Sorry for the long email (as usual!)
Cheers,
Andy
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