[Jalview-discuss] Re: linkUrl and regexp

Mon Sep 8 13:29:52 BST 2008

Sebastien MORETTI wrote:
>> The easiest way to do generate these links without changing the existing
>> URL link behaviour would be to create a features file with URL links
>> embedded in the description line - these will be shown in the link menu
>> when the user right clicks on the sequence ID.
> 
> I think I will try this.
> Should I use this kind of syntax:
> http://...    seq_ID
> 
> With URL as description, a tab, sequence identifier ?
not quite...

Here's an example from http://www.jalview.org/examples/exampleFeatures.txt :

<html>Fer2 Status: True Positive <a
href="http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00111">Pfam
8_8</a></html>	FER_CAPAA	-1	8	83	Pfam
Ferredoxin_fold Status: True Positive 	FER_CAPAA	-1	3	93	Cath

Specify start and end as -1 in order to add a non-positional feature
Jalview will recognise the anchors embedded in the description and parse
them as  URL links where the link text is used for the menu name.

I see that this process is not described in the features file
documentation (
http://www.jalview.org/help/html/features/featuresFormat.html ) -
that'll have to be fixed !

Jim

ps. With regard to 'magic FeatureTypes' - Jalview does not do anything
intelligent with feature types, currently (with the exception of the
disulphide_bond type), which is a big limitation. It is easy to imagine
that features like 'DBRef' or 'Reference' might be translated into
database accession links and citation lists, and may actually be
implemented in the future.