[DAS] LDAS link question

[James Freeman]

Hi Tom,

Assuming you have set up the LDAS server:

http://www.biodas.org/servers/LDAS.html

 with the correct information (from above):

{
The [LINKS] section

 [LINKS]
 default    = 
http://stein.cshl.org/cgi-bin/test-cgi.pl?name=$name;class=$class;type=$type
 exon       = 
http://stein.cshl.org/cgi-bin/test-cgi.pl/exon?name=$name;class=$class
 transcript = 
http://stein.cshl.org/cgi-bin/test-cgi.pl/transcript?name=$name;class=$class
 insertion  = 
http://stein.cshl.org/cgi-bin/test-cgi.pl/insertion?name=$name;class=$class
The DAS protocol allows the LDAS server to generate a web link for each 
feature and group of features. The [LINKS] section tells the LDAS server 
how to create these links.

Each option name is a defined annotation type, and can use the short 
format (``exon'') or the extended one (``exon:curated''). The value is a 
URL. When the LDAS server is running, it will scan the URL for the 
keywords $name, $class and $type, and replace them with the name of the 
annotation, its class, and its type.

The default option provides a generic link to use when no more specific 
type is defined.

If you do not want a link to be generated at all, use ``none'' for the 
URL. The following example generates links for all features except those 
whose types are ``alu'' or ``LINE'':

 default    = 
http://stein.cshl.org/cgi-bin/test-cgi.pl?name=$name;class=$class;type=$type
 alu        = none
 LINE       = none
The stein.cshl.org URL given in the examples is a test CGI script that 
merely echoes back its arguments. It is useful for debugging, but you will 
want to replace it with a URL that provides more specific information 
about the selected feature.
}

If you did it correctly you should see the link tag get populated from the 
raw XML from a features call.  Since you have something in contigview 
anyway, it should show up in the popup, and if you are pointing to 
Lincoln's server you should get back the arguments as shown above.

Please, let me know if that doesn't work.

Regards,

Jim
--
James Freeman 
Bioinformatics Consultant at Biogen
Email: james_freeman@biogen.com
Voice: 617-914-5804
Mobile: 617-429-6352





"Tom Fahland" <tfahland@dgt.com>
Sent by: das-admin@biodas.org
02-Aug-2002 06:55 PM

 
        To:     <das@biodas.org>
        cc: 
        Subject:        [DAS] LDAS link question


Hello All. 

I had a question about enabling the links in LDAS. I have a local ldas
server running and populated with internal data and viewable from
contigview on Ensembl. But I am still confused about what is required to
get the links part to work, ie, when at mouseover on the feature in
contig, I want a link present to another url for each feature (the
default is catagory, id,method,type).  I just need to get another line
in there for a link like other external DAS sources. 

Thanks
Tom Fahland
Bioinformatics 
Digital Gene
_______________________________________________
DAS mailing list
DAS@biodas.org
http://biodas.org/mailman/listinfo/das