[Jalview-discuss] Re: linkUrl and regexp

Tue Sep 9 10:24:35 BST 2008

Sebastien MORETTI a écrit :
>>>> 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

"Sequence not found" message came from a forgotten tab. It is resolved 
now, sorry.

But I do not have links yet.

Now, feature file looks like this:
ensembl	red
<html><a 
href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSG00000166598'>ensembl</a></html> 
ENPL_HUMAN	-1	-1	-1	ensembl
<html><a 
href='http://www.ensembl.org/Homo_sapiens/searchview?species=;idx=;q=ENSPTRG00000005372'>ensembl</a></html> 
HSP90B1_PANTR	-1	-1	-1	ensembl
...

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

I have nothing but SRS link in the links menu.

-- 
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/