[DAS] Re: "detailed view" das view problem

[Matthew Pocock]

Hi.

Is there a rationalle for only guaranteeing to return features entirely 
contained by a region, rather than returning all features overlapping 
the range? In principle you could have features that have one end in 
your viewer region and another end at one/other end of the chromsome 
being viewed. This should realy be pulled down but in the 'must be 
contained' case is only pulled down when you fetch the whole chromosome. 
Assuming feature a and b have a start and end property, the overlaps 
query is quite easy to express:

a overlaps b iff not (
   a.end < b.start || a.start > b.end
)

Matthew

Tony Cox wrote:
> On 13 May 2002, Frank R Visser wrote:
> 
> Hi Frank,
> 
> This is a tricky one. Most of the contig code will do selects on features that
> fall entrirely within the bounds of the region you are looking at. There are
> areas of the code that have been optimised so that partial or overlapping
> features are returned. One often gets into horrible situations where one has to
> "walk" outwards from the viewable region to try and catch incomplete features,
> but then you run into the problems of how far do you walk to find a feature that
> may or may not be there? Yuck.
> 
> I'm not sure what the DAS spec says on this point...ah here it is:
> 
> "Annotation servers are only required to return annotations which are completely
> contained within the indicated segment. Servers may also return annotations
> which overlap the segment, but are not completely contained within
> them."
> 
> ...which I guess means you can do what you like to be OK with the spec and is
> therefore both a feature and a bug ;-)
> 
> You should however be able to get features that completely overlap the viewable
> region. Do you noe see these? I think we need to look at how the features are
> selected and see if we can catch these things.
> 
> 
> Tony
> 
> 
> 
> +>Hello,
> +>
> +>I have a problem with the "Detailed View" viewer. If I zoom in on a feature,
> +>and
> +>the begin point of the feature falls out of the window, the feature disappears.
> +>As an example, switching on the DAS NCBI GenomeScan feature, this URL shows the
> +>a feature:
> +>
> +>http://www.ensembl.org/Homo_sapiens/contigview?chr=2&vc_start=39675358
> +>
> +>but this URL, which should show a small part of the feature, does not:
> +>
> +>http://www.ensembl.org/Homo_sapiens/contigview?highlight=&chr=2&vc_start=3963535
> +>9&vc_end=39670000&x=31&y=15
> +>
> +>It even explicitly states that there are no such features in the
> +>region which is wrong. This is causing problems for me because I am
> +>being asked to publish, using DAS, several large areas, which are (a
> +>lot) bigger than 1MB and therefore are almost always invisible.
> +>
> +>Is this done by design or is this a bug? If this is not a bug, what is
> +>the reason for it?
> +>
> +>Txh for any feedback,
> +>
> +>Frank
> +>
> +>
> 
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> Sanger Institute		WWW:www.sanger.ac.uk
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