[EMBOSS] density

[Mahmut Uludag]

Hi Alan,

> So it's a limitation of the web interface which requires
> all graphs to be called 'graph' ?

Yes this is a limitation in Soaplab dictated by the legacy acd2xml
parser.

> If I've understood you correctly then, attached, are two new
> versions of density.c and density.acd that only use one
> graph (called 'graph') with the -dual and -quad qualifiers
> working as before. I'll consider adding this to CVS. It
> is, of course, currently not tested that well. Please let
> me know how it behaves.

Modified density.c and density.acd files solved the problem in my local
Soaplab installation. One possible change would be to set a positive
default value either for the quad or the dual option.

I have noticed that dotmatcher and dottup programs also have two graphic
outputs. One of them called xygraph in both applications is not
recognised by Soaplab due to the same limitation.

Regards,
Mahmut
 
> HTH
> 
> Alan
> 
> 
> > Sorry,
> > the service, which provides EMBOSS tools as web interface, fails to
> > interprets properly the density ACD file.
> >
> > Everything is fine in the ACD.
> >
> >> Hi,
> >>
> >> colourps and cps are synonymous so you should be able to use either.
> >> If you want to specify the output type from the command line
> >> you could type:
> >>
> >>   density -quad -qgraph=colourps inputsequence
> >>
> >> for a quad graph (qgraph, not ggraph in your email) or, for a dual graph
> >>
> >>   density -dual -dgraph=cps inputsequence
> >>
> >> or am I misunderstanding your question?
> >>
> >> HTH
> >>
> >> Alan
> >>
> >>
> >>> Hi,
> >>>
> >>> According to the ACD file, the density application seems to use the
> >>> 'graph' qualifier.
> >>>
> >>> When used, I get this error message:
> >>> Unknown qualifier -graph=colourps
> >>>
> >>>
> >>> graph seems to have been replaced by ggraph and dgraph.
> >>> And colourps seems to be cps now.
> >>>
> >>>
> >>> How to fix it in the source ?
> >>> Thanks
> >
> > --
> > Sébastien Moretti
> > SIB EMBnet, Quartier Sorge - Genopode
> > CH-1015 Lausanne, Switzerland
> > Tel.: +41 (21) 692 4056/4221
> > http://ch.embnet.org/  http://myhits.vital-it.ch/
> >
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