Sebastien MORETTI wrote:
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
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:
I have tried this syntax, but nothing appends.
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.