[Jalview-discuss] Re: linkUrl and regexp

Tue Sep 9 08:01:40 BST 2008

>>> 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.

I have tried this syntax but it fails with an error in the java console:
Sequence not found: <html><a 
href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSG00000166598'>ensembl</a></html> 
ENPL_HUMAN	-1	-1	-1	DBRef

Feature lines look like this:
<html><a 
href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSG00000166598'>ensembl</a></html> 
ENPL_HUMAN	-1	-1	-1	DBRef
<html><a 
href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSPTRG00000005372'>ensembl</a></html> 
HSP90B1_PANTR	-1	-1	-1	DBRef

And sequence headers look like this:
 >ENPL_HUMAN	 ID=ENST00000299767.4 GENEID=ENSG00000166598
 >HSP90B1_PANTR	 ID=ENSPTRT00000009873.3 GENEID=ENSPTRG00000005372

So, it seems the features cannot be allocated to the proper sequences.
What should be the right sequence name in this case ?

Thanks

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4056
http://bioinfo.unil.ch/