Ellen Schofield
2014-09-08 11:17:11 UTC
Hi All,
We have recently hit an issue in searching in our version of GBrowse
(2.35). According to the online docs, there is the ability to turn
searching off on a specific database using the search:none flag...
http://gmod.org/wiki/GBrowse_2.0_HOWTO#Database_Search_Options
We have done this on some of our larger databases that produce xy
scatter plots as searching isn't needed. However, it would appear that
by loading in gff using the Name attribute, that searching is still
done, even with "none" set on all databases. This is slightly
counter-intuitive to myself. I would expect that using the none, which
is used to " Disable all searching on this database" should do just this?
I have tracked the issue down to a few lines of code in
Bio::Graphics::Browser2::Region (lines 247-251)
https://github.com/GMOD/GBrowse/blob/master/lib/Bio/Graphics/Browser2/Region.pm
Firstly, can I confirm that what I am seeing is the expected behaviours,
ie setting search:none on a db still allows searching on feature names
in that db?
Secondly, if no, can I suggest that this portion of code is removed to
reduce the confusion of "incorrect" results?
I look forward to hearing from you.
Yours,
Ellen.
We have recently hit an issue in searching in our version of GBrowse
(2.35). According to the online docs, there is the ability to turn
searching off on a specific database using the search:none flag...
http://gmod.org/wiki/GBrowse_2.0_HOWTO#Database_Search_Options
We have done this on some of our larger databases that produce xy
scatter plots as searching isn't needed. However, it would appear that
by loading in gff using the Name attribute, that searching is still
done, even with "none" set on all databases. This is slightly
counter-intuitive to myself. I would expect that using the none, which
is used to " Disable all searching on this database" should do just this?
I have tracked the issue down to a few lines of code in
Bio::Graphics::Browser2::Region (lines 247-251)
https://github.com/GMOD/GBrowse/blob/master/lib/Bio/Graphics/Browser2/Region.pm
Firstly, can I confirm that what I am seeing is the expected behaviours,
ie setting search:none on a db still allows searching on feature names
in that db?
Secondly, if no, can I suggest that this portion of code is removed to
reduce the confusion of "incorrect" results?
I look forward to hearing from you.
Yours,
Ellen.
--
***@cimr.cam.ac.uk
JDRF/Wellcome Trust Diabetes and Inflammation Laboratory,
NIHR Cambridge Biomedical Research Centre,
Cambridge Institute for Medical Research,
University of Cambridge,
WT/MRC Bldg, Addenbrooke's Hospital,
Hills Rd., Cambridge CB2 0XY UK
Tel: 01223 763215
***@cimr.cam.ac.uk
JDRF/Wellcome Trust Diabetes and Inflammation Laboratory,
NIHR Cambridge Biomedical Research Centre,
Cambridge Institute for Medical Research,
University of Cambridge,
WT/MRC Bldg, Addenbrooke's Hospital,
Hills Rd., Cambridge CB2 0XY UK
Tel: 01223 763215