[EMBOSS] density

[Sebastien Moretti]

> 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

Following Mahmut' tests, it seems to work with your modifications.
Thanks

>> 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 graph seems to have been replaced by ggraph and dgraph.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

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Sébastien Moretti
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