[Jalview-discuss] Re: linkUrl and regexp

[Sebastien MORETTI]

> G'day Sebastien.

Hi Jim,

>> With JalView 2.4, we try to extract an identifier from gene description
>> to make an external link.
>>
>> Does it work with sequence description ?
> no it doesn't, I'm afraid. When I put the regex feature in, I tried to
> keep the behaviour similar to 2.3 to avoid 'unexpected' additional URLs
> being generated.
> 
> If the URL generation is extended so it operates on the description line
> then static URL links result in the whole description line being
> substituted for $SEQUENCE_ID$ - so a sequence header like
> 
>> FER1_SPIOL/1-147 Ferredoxin-1, chloroplast precursor
> 
> generates two SRS links - one for FER1_SPIOL and the other for
> "Ferredoxin-1, chloroplast precursor".
> 
> I didn't want to clutter the existing URL link menu too much, so I
> didn't include this additional URL generation step, but the
> implementation is trivial (and I'll leave it in the development code,
> but commented out).  Does anyone else have an opinion on whether this
> behaviour should be included by default ?
> 
>> If it does, how to extract this kind of pattern:
>> GENEID=ENSPTRG00000030533 TAXID=9598
>>
>> I have tried this syntax, but nothing appends.
>> $SEQUENCE_ID=/GENEID=(\w+) /=$
> 
> 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 ?

Or is there a featureType keyword to change URL description to link to add ?


Thanks

> Jim
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Sébastien

-- 
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/