[Gmod-ajax] Modify 'details'

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[Gmod-ajax] Modify 'details'

Gwendoline Andres
Hello,

I want to modify informations that are displayed in the details window
('View details').

First of all, I notice that exons (and UTR) are displayed in an aleatory
order. I think it would be better if they were ordered by position...
How can I configure that?

Secondary, my users think that polypeptide is a mix between exon
information and protein sequence, it bothers them. So I am thinking
about removing polypeptide from this display but maybe it's not the best
solution...

Last, is it possible to put links in this display?
For example I have some InterPro numbers and I would like to link them
with the corresponding web page (for example :
http://www.ebi.ac.uk/interpro/entry/IPR003395)

Regards,

--
Gwendoline Andres
Service Informatique et Bio-informatique (SIB)
Embrc-France JDA3
Station Biologique de Roscoff
CNRS - UPMC
Place Georges Teissier
CS 90074
29688 ROSCOFF CEDEX
FRANCE
Tel : (+33) 2 98 29 56 46


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Re: Modify 'details'

Robert Buels-2
Hi Gwendoline,

JBrowse 1.11.3 has some new configuration variables that can be used to
customize the display of certain fields, see
http://gmod.org/wiki/JBrowse_Configuration_Guide#Customizing_parts_of_the_.27View_details.27_Pop-ups_with_callbacks.

To change the displayed order of exons and UTRs, my only idea is that
you could try changing their order in the data you are loading.  I'm not
sure if it would work, but it's worth a try.

Also, if you want to remove polypeptide features, you probably would
need to remove those from the data you are loading from, as well.  I
seem to remember that you use Bio::DB::Das::Chado, though.  I don't
think there is currently a way to filter out certain type of subfeatures
with that.  If you know Perl, you might consider working on a patch for
JBrowse to make that possible, however!

Hope this helps!

Rob


On 01/22/2014 05:42 AM, Gwendoline Andres wrote:

> Hello,
>
> I want to modify informations that are displayed in the details window
> ('View details').
>
> First of all, I notice that exons (and UTR) are displayed in an aleatory
> order. I think it would be better if they were ordered by position...
> How can I configure that?
>
> Secondary, my users think that polypeptide is a mix between exon
> information and protein sequence, it bothers them. So I am thinking
> about removing polypeptide from this display but maybe it's not the best
> solution...
>
> Last, is it possible to put links in this display?
> For example I have some InterPro numbers and I would like to link them
> with the corresponding web page (for example :
> http://www.ebi.ac.uk/interpro/entry/IPR003395)
>
> Regards,
>

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Re: Modify 'details'

Gwendoline Andres
Hi,

Thank you very much for your answer!

I will try JBrowse 1.11.3 and your other suggestions

Thank you for your great job,

Gwendoline

Le 09/03/2014 17:17, Robert Buels a écrit :

> Hi Gwendoline,
>
> JBrowse 1.11.3 has some new configuration variables that can be used
> to customize the display of certain fields, see
> http://gmod.org/wiki/JBrowse_Configuration_Guide#Customizing_parts_of_the_.27View_details.27_Pop-ups_with_callbacks.
>
> To change the displayed order of exons and UTRs, my only idea is that
> you could try changing their order in the data you are loading.  I'm
> not sure if it would work, but it's worth a try.
>
> Also, if you want to remove polypeptide features, you probably would
> need to remove those from the data you are loading from, as well.  I
> seem to remember that you use Bio::DB::Das::Chado, though.  I don't
> think there is currently a way to filter out certain type of
> subfeatures with that.  If you know Perl, you might consider working
> on a patch for JBrowse to make that possible, however!
>
> Hope this helps!
>
> Rob
>
>
> On 01/22/2014 05:42 AM, Gwendoline Andres wrote:
>> Hello,
>>
>> I want to modify informations that are displayed in the details window
>> ('View details').
>>
>> First of all, I notice that exons (and UTR) are displayed in an aleatory
>> order. I think it would be better if they were ordered by position...
>> How can I configure that?
>>
>> Secondary, my users think that polypeptide is a mix between exon
>> information and protein sequence, it bothers them. So I am thinking
>> about removing polypeptide from this display but maybe it's not the best
>> solution...
>>
>> Last, is it possible to put links in this display?
>> For example I have some InterPro numbers and I would like to link them
>> with the corresponding web page (for example :
>> http://www.ebi.ac.uk/interpro/entry/IPR003395)
>>
>> Regards,
>>

--
Gwendoline Andres
Service Informatique et Bio-informatique (SIB)
Embrc-France JDA3
Station Biologique de Roscoff
CNRS - UPMC
Place Georges Teissier
CS 90074
29688 ROSCOFF CEDEX
FRANCE
Tel : (+33) 2 98 29 56 46


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