Search options in GBrowse (none)

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Search options in GBrowse (none)

Ellen Schofield
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.
-- 
[hidden email]
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

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Re: Search options in GBrowse (none)

Ellen Schofield
Just wondering if anybody could help or comment on this please?

Thanks,
Ellen.
-- 
[hidden email]
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
On 08/09/14 12:17, Ellen Schofield wrote:
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.
-- 
[hidden email]
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


------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk


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