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

[Tony Cox]

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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Tony Cox			Email:avc@sanger.ac.uk
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